Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 176 of 185
Found at i:53252103 original size:20 final size:20
Alignment explanation
Indices: 53252078--53252120 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
53252068 AATCATTTAA
53252078 AAATTA-ATTTAGTAATATTT
1 AAATTATATTTA-TAATATTT
*
53252098 AAATTATATTTATAATTTTT
1 AAATTATATTTATAATATTT
53252118 AAA
1 AAA
53252121 AAATAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
AAATTATATTTATAATATTT
Found at i:53252130 original size:20 final size:20
Alignment explanation
Indices: 53252072--53252131 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
53252062 TTATGAAATC
*
53252072 ATTTAAAAATTAATTTAGTAAT
1 ATTTAAAAAATAA-TTA-TAAT
** *
53252094 ATTTAAATTATATTTATAAT
1 ATTTAAAAAATAATTATAAT
*
53252114 TTTTAAAAAATAATTATA
1 ATTTAAAAAATAATTATA
53252132 TAGATTTAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 18 0.60
21 3 0.10
22 9 0.30
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
ATTTAAAAAATAATTATAAT
Found at i:53261596 original size:15 final size:14
Alignment explanation
Indices: 53261575--53261610 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
53261565 ATAATCATTA
*
53261575 ATAATTATCTTAAT
1 ATAATTATCCTAAT
53261589 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
53261604 ATAATTA
1 ATAATTA
53261611 AAACAGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:53265144 original size:13 final size:13
Alignment explanation
Indices: 53265128--53265154 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53265118 CCATATTAGT
53265128 TTTTTATATATAA
1 TTTTTATATATAA
53265141 TTTTTATATATAA
1 TTTTTATATATAA
53265154 T
1 T
53265155 ACATCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTTATATATAA
Found at i:53268572 original size:29 final size:29
Alignment explanation
Indices: 53268537--53268595 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
53268527 TCTATTATTC
53268537 TCTCAATTTCCT-TCCAAATTT-CTCTCAAA
1 TCTCAATTTCCTCT-C-AATTTCCTCTCAAA
*
53268566 TCTCAATTTGCTCTCAATTTCCTCTCAAA
1 TCTCAATTTCCTCTCAATTTCCTCTCAAA
53268595 T
1 T
53268596 TTCTCTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 5 0.19
29 21 0.78
30 1 0.04
ACGTcount: A:0.25, C:0.31, G:0.02, T:0.42
Consensus pattern (29 bp):
TCTCAATTTCCTCTCAATTTCCTCTCAAA
Found at i:53269315 original size:230 final size:229
Alignment explanation
Indices: 53268882--53269439 Score: 924
Period size: 230 Copynumber: 2.4 Consensus size: 229
53268872 AAAAACACCA
* * * *
53268882 AAACCCAAATTTAATTCATATTTTCTTAAAAAATAATAAACACGAAAACTAATCCAATTTTAAAA
1 AAACCCTAATTTAATTGATTTTTTCTTAAAAAATAATAAACACGAAAACTAATCCAATTTTGAAA
*
53268947 AATTTATAAATAATTTAATTGACAAACCCTAAACTCTAAACCCTAACTTGTTTGATTTTTCCTTA
66 AATTTTTAAATAATTTAATTGACAAACCCTAAACTCTAAACCCTAACTTGTTTGATTTTTCCTTA
* *
53269012 AAAACCCTTAACTTAAAAACACCAAAACCCTAACAAAAACCCTAACCCTAACCCTAATCTAATTT
131 AAAACCCTTAACCTAAAAACACCAAAACACTAACAAAAACCCTAACCCTAACCCTAATCTAATTT
*
53269077 TTAAATTTTTTAAATTAAATTACTCAAGTAACCCT
196 TAAAATTTTTT-AATTAAATTACTCAAGTAACCCT
* *
53269112 AAACCCTAATTTAATTGATTTTTTCTTAAAAAATAATAAACACCAAAACTTATCCAATTTTGAAA
1 AAACCCTAATTTAATTGATTTTTTCTTAAAAAATAATAAACACGAAAACTAATCCAATTTTGAAA
**
53269177 TTTTTTTAAATAATTTAATTGACAAACCCTAAACTCTAAACCCTAACTTGTTTG-TTTTTCCTTA
66 AATTTTTAAATAATTTAATTGACAAACCCTAAACTCTAAACCCTAACTTGTTTGATTTTTCCTTA
* *
53269241 AAAACCTTTAACCT-AAAACACCAAAACACTTACAAAAACCCTAACCCTAACCCTAATCTAACTT
131 AAAACCCTTAACCTAAAAACACCAAAACACTAACAAAAACCCTAACCCTAACCCTAATCTAA-TT
53269305 TTAAAAATTTTTTAATTAAATTACTCAAGTAACCCT
195 TT-AAAATTTTTTAATTAAATTACTCAAGTAACCCT
* *
53269341 AAACCCTAATTTAATTGCTTTTTTCTT-AAAAATAATAAACATGAAAACTAATCCAATTTTGAAA
1 AAACCCTAATTTAATTGATTTTTTCTTAAAAAATAATAAACACGAAAACTAATCCAATTTTGAAA
53269405 AATTTTTAAATAATTTAATTGACAAACCCTAAACT
66 AATTTTTAAATAATTTAATTGACAAACCCTAAACT
53269440 AGAGGTGTTC
Statistics
Matches: 306, Mismatches: 20, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
228 112 0.37
229 75 0.25
230 119 0.39
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.34
Consensus pattern (229 bp):
AAACCCTAATTTAATTGATTTTTTCTTAAAAAATAATAAACACGAAAACTAATCCAATTTTGAAA
AATTTTTAAATAATTTAATTGACAAACCCTAAACTCTAAACCCTAACTTGTTTGATTTTTCCTTA
AAAACCCTTAACCTAAAAACACCAAAACACTAACAAAAACCCTAACCCTAACCCTAATCTAATTT
TAAAATTTTTTAATTAAATTACTCAAGTAACCCT
Found at i:53269923 original size:14 final size:14
Alignment explanation
Indices: 53269904--53269943 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
53269894 ATTTAATTTT
53269904 AACCCTAAACCCCA
1 AACCCTAAACCCCA
*
53269918 AACCCTAAACACCA
1 AACCCTAAACCCCA
* *
53269932 AATCTTAAACCC
1 AACCCTAAACCC
53269944 TAAAATCCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.45, C:0.42, G:0.00, T:0.12
Consensus pattern (14 bp):
AACCCTAAACCCCA
Found at i:53271656 original size:6 final size:6
Alignment explanation
Indices: 53271640--53271671 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
53271630 ACATTAGTGA
53271640 ATAATAT ATAAAT ATAAAT ATAAAT ATAAAT A
1 ATAA-AT ATAAAT ATAAAT ATAAAT ATAAAT A
53271672 ATTATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.84
7 4 0.16
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATAAAT
Found at i:53271719 original size:29 final size:29
Alignment explanation
Indices: 53271686--53271744 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
53271676 TATTTAAATT
53271686 ATTAGATATGAAAAACCAATAAGATTATG
1 ATTAGATATGAAAAACCAATAAGATTATG
*
53271715 ATTAGATATGAAAAACTAATAAGATTATG
1 ATTAGATATGAAAAACCAATAAGATTATG
53271744 A
1 A
53271745 AAACCAGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.29
Consensus pattern (29 bp):
ATTAGATATGAAAAACCAATAAGATTATG
Found at i:53277059 original size:21 final size:21
Alignment explanation
Indices: 53277034--53277074 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
53277024 AAACCAATCG
53277034 TTTAATCAC-TTTAAAACACGA
1 TTTAAT-ACTTTTAAAACACGA
53277055 TTTAATACTTTTAAAACACG
1 TTTAATACTTTTAAAACACG
53277075 TCAAAACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (21 bp):
TTTAATACTTTTAAAACACGA
Found at i:53281608 original size:26 final size:25
Alignment explanation
Indices: 53281564--53281631 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 25
53281554 AAACCCTAAT
*
53281564 TTTTCCTTTCTTTCTTC-CCCTTTTTC
1 TTTT-CTTTCTTT-TTCTCCCTGTTTC
53281590 TTTTCTTTCTTTTTCTCCCTGTTTC
1 TTTTCTTTCTTTTTCTCCCTGTTTC
* *
53281615 GTTTCTATTCTGTTTCT
1 TTTTCT-TTCTTTTTCT
53281632 TTTATTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 3 0.08
25 21 0.57
26 13 0.35
ACGTcount: A:0.01, C:0.28, G:0.04, T:0.66
Consensus pattern (25 bp):
TTTTCTTTCTTTTTCTCCCTGTTTC
Found at i:53281707 original size:8 final size:8
Alignment explanation
Indices: 53281691--53281722 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
53281681 ATAATTAAGA
53281691 TATAATAT
1 TATAATAT
*
53281699 TAAAATAT
1 TATAATAT
53281707 TATAATAT
1 TATAATAT
53281715 TATAATAT
1 TATAATAT
53281723 ATATTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
TATAATAT
Found at i:53281712 original size:16 final size:16
Alignment explanation
Indices: 53281651--53281722 Score: 56
Period size: 16 Copynumber: 4.2 Consensus size: 16
53281641 TATATTTACT
53281651 TATTATAATATATAAAA
1 TATTATAATAT-TAAAA
*
53281668 TAATAT-ATACTTAATAA
1 TATTATAATA-TTAA-AA
*
53281685 TTAAGATATAATATTAAAA
1 -T-A-TTATAATATTAAAA
*
53281704 TATTATAATATTATAA
1 TATTATAATATTAAAA
53281720 TAT
1 TAT
53281723 ATATTTTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
16 21 0.46
17 9 0.20
18 2 0.04
19 3 0.07
20 8 0.17
21 3 0.07
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (16 bp):
TATTATAATATTAAAA
Found at i:53283886 original size:17 final size:17
Alignment explanation
Indices: 53283864--53283896 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
53283854 TTTTCAGAAA
53283864 ATTTTAATATTTTTTAT
1 ATTTTAATATTTTTTAT
53283881 ATTTTAATATTTTTTA
1 ATTTTAATATTTTTTA
53283897 AAAAATTATT
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:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTAATATTTTTTAT
Found at i:53284455 original size:15 final size:15
Alignment explanation
Indices: 53284435--53284490 Score: 54
Period size: 14 Copynumber: 4.2 Consensus size: 15
53284425 TACATGAATT
53284435 TTTAAAATAATATAA
1 TTTAAAATAATATAA
53284450 TTTAAAAT-ATAT-A
1 TTTAAAATAATATAA
*
53284463 -TT--ATTAATA-AA
1 TTTAAAATAATATAA
53284474 TTTAAAATAAT-TAA
1 TTTAAAATAATATAA
53284488 TTT
1 TTT
53284491 TATTATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 13
0.69 0.04 0.27
Matches are distributed among these distances:
10 2 0.06
11 4 0.12
12 4 0.12
13 1 0.03
14 14 0.42
15 8 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TTTAAAATAATATAA
Found at i:53284572 original size:25 final size:26
Alignment explanation
Indices: 53284543--53284593 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
53284533 AAACTTATTA
*
53284543 TTTAAGTATAA-AATTAAAACCAAAT
1 TTTAAATATAATAATTAAAACCAAAT
*
53284568 TTTAAATATAATAATTAAAATCAAAT
1 TTTAAATATAATAATTAAAACCAAAT
53284594 CTTATTTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (26 bp):
TTTAAATATAATAATTAAAACCAAAT
Found at i:53293436 original size:9 final size:9
Alignment explanation
Indices: 53293422--53293482 Score: 104
Period size: 9 Copynumber: 6.8 Consensus size: 9
53293412 ACCATGATAT
53293422 AATTACCCG
1 AATTACCCG
53293431 AATTACCCG
1 AATTACCCG
53293440 AATTACCCG
1 AATTACCCG
53293449 AATTACCCG
1 AATTACCCG
*
53293458 AATTAACCG
1 AATTACCCG
*
53293467 AATTAACCG
1 AATTACCCG
53293476 AATTACC
1 AATTACC
53293483 GAAAAATACC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.38, C:0.30, G:0.10, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:53298807 original size:46 final size:46
Alignment explanation
Indices: 53298743--53298836 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
53298733 CTTCACTCAT
53298743 CACACACAACAACCTTGATGCTCCTAAGAGGGACCCAGATTATTCA
1 CACACACAACAACCTTGATGCTCCTAAGAGGGACCCAGATTATTCA
*
53298789 CACACACAACAACCTTGATGCTGCTAAGAGGGACCCAGATTATTCA
1 CACACACAACAACCTTGATGCTCCTAAGAGGGACCCAGATTATTCA
53298835 CA
1 CA
53298837 TTCTTTTGAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.35, C:0.30, G:0.16, T:0.19
Consensus pattern (46 bp):
CACACACAACAACCTTGATGCTCCTAAGAGGGACCCAGATTATTCA
Found at i:53302216 original size:12 final size:12
Alignment explanation
Indices: 53302169--53302216 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
53302159 AAGCTGCTCA
53302169 TATTAGTTGTTT
1 TATTAGTTGTTT
* *
53302181 TATTACTTATTCT
1 TATTAGTTGTT-T
* *
53302194 TGTTAGCTGTTT
1 TATTAGTTGTTT
53302206 TATTAGTTGTT
1 TATTAGTTGTT
53302217 AATGATGTAT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
12 19 0.70
13 8 0.30
ACGTcount: A:0.17, C:0.06, G:0.15, T:0.62
Consensus pattern (12 bp):
TATTAGTTGTTT
Found at i:53308156 original size:6 final size:6
Alignment explanation
Indices: 53308145--53308169 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
53308135 AAGGTTGATC
53308145 GTTGAA GTTGAA GTTGAA GTTGAA G
1 GTTGAA GTTGAA GTTGAA GTTGAA G
53308170 AAGGAGAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (6 bp):
GTTGAA
Found at i:53310702 original size:13 final size:13
Alignment explanation
Indices: 53310684--53310708 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53310674 TTAAAAGAAC
53310684 TTATATATAATAT
1 TTATATATAATAT
53310697 TTATATATAATA
1 TTATATATAATA
53310709 AAATTTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTATATATAATAT
Found at i:53321815 original size:30 final size:30
Alignment explanation
Indices: 53321780--53321839 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
53321770 GATGAGTCCC
53321780 TTCAGCATGGTTGACCAATTTGAGGTTTAA
1 TTCAGCATGGTTGACCAATTTGAGGTTTAA
53321810 TTCAGCATGGTTGACCAATTTGAGGTTTAA
1 TTCAGCATGGTTGACCAATTTGAGGTTTAA
53321840 CTCGTTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (30 bp):
TTCAGCATGGTTGACCAATTTGAGGTTTAA
Found at i:53325911 original size:15 final size:15
Alignment explanation
Indices: 53325889--53325922 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
53325879 CAAATTAGGT
53325889 TTAT-AATTATTATA
1 TTATAAATTATTATA
*
53325903 TTATAAATTTTTATA
1 TTATAAATTATTATA
53325918 TTATA
1 TTATA
53325923 TTTTATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATAAATTATTATA
Found at i:53334832 original size:18 final size:18
Alignment explanation
Indices: 53334809--53334846 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
53334799 TACCACTAAA
53334809 TTAATAATTT-ATTTTAAT
1 TTAAT-ATTTAATTTTAAT
53334827 TTAATATTTACATTTTAAT
1 TTAATATTTA-ATTTTAAT
53334846 T
1 T
53334847 GTATTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 5 0.28
19 9 0.50
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
TTAATATTTAATTTTAAT
Found at i:53352474 original size:20 final size:19
Alignment explanation
Indices: 53352416--53352480 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
53352406 TTTATTGTAA
53352416 TTTAAAATAA-TTTAAT-T
1 TTTAAAATAATTTTAATAT
**
53352433 TTTTTAATAATTCTTAATTAT
1 TTTAAAATAATT-TTAA-TAT
53352454 TTTAAAATAATTTTATATAT
1 TTTAAAATAATTTTA-ATAT
53352474 TTTAAAA
1 TTTAAAA
53352481 ATTTAATAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 8 0.21
18 1 0.03
19 4 0.10
20 14 0.36
21 12 0.31
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAAAATAATTTTAATAT
Found at i:53352494 original size:20 final size:20
Alignment explanation
Indices: 53352447--53352503 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
53352437 TAATAATTCT
*
53352447 TAATTATTTTAAAATAATTTTA
1 TAATTATTTT-AAA-AATTTAA
53352469 T-A-TATTTTAAAAATTTAA
1 TAATTATTTTAAAAATTTAA
*
53352487 TAATTATTTGAAAAATT
1 TAATTATTTTAAAAATT
53352504 GCATCCAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 7 0.23
19 4 0.13
20 18 0.58
21 1 0.03
22 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TAATTATTTTAAAAATTTAA
Found at i:53364931 original size:47 final size:47
Alignment explanation
Indices: 53364875--53364977 Score: 145
Period size: 47 Copynumber: 2.2 Consensus size: 47
53364865 GTCGATGAGA
* *
53364875 CACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTCCGATGAAG
1 CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTCCAATGAAG
* * *
53364922 TACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTCCAATGAAG
1 CACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTCCAATGAAG
53364969 CACTATGTG
1 CACTATGTG
53364978 CTTATCCCGG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
47 46 0.96
48 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (47 bp):
CACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTCCAATGAAG
Found at i:53366772 original size:30 final size:30
Alignment explanation
Indices: 53366725--53366784 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
53366715 TTCCCGAGCC
*
53366725 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGAAAAAGTGTAATTATGCAAAAGTT
* *
53366755 TAGGGGAAAAA-TGGTAATTTTGCCAAAGTT
1 TAGGGGAAAAAGT-GTAATTATGCAAAAGTT
53366785 CGTATTAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.28
Consensus pattern (30 bp):
TAGGGGAAAAAGTGTAATTATGCAAAAGTT
Found at i:53372217 original size:39 final size:38
Alignment explanation
Indices: 53372174--53372308 Score: 105
Period size: 39 Copynumber: 3.4 Consensus size: 38
53372164 ACCAATATGG
*
53372174 CACCCAGTGCCTCATCGGA-TAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGACTAG-CCGAAGTAA-AGTTGA
* *
53372213 CACCCAGTGTCTCATC-GACCTAGCCGAAGTAAAGTTGG
1 CACCCAGTGCCTCATCGGA-CTAGCCGAAGTAAAGTTGA
* * * * *
53372251 TACCCAGTACCTCATCGAATCTATCCGAAG-AAATATAGTGA
1 CACCCAGTGCCTCATCGGA-CTAGCCGAAGTAAA-GT--TGA
*
53372292 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
53372309 ACTCGAGGTC
Statistics
Matches: 76, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
38 23 0.30
39 34 0.45
40 3 0.04
41 16 0.21
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGACTAGCCGAAGTAAAGTTGA
Found at i:53372306 original size:41 final size:43
Alignment explanation
Indices: 53372200--53372309 Score: 108
Period size: 38 Copynumber: 2.7 Consensus size: 43
53372190 GGATAGTTCG
53372200 AAGTAATAGTTGACACCCAGTGTCTCATCG-ACCTAGCCGAAGTA
1 AAGT-ATAG-TGACACCCAGTGTCTCATCGAACCTAGCCGAAGTA
* ** * *
53372244 AAGT-T-G-G-TACCCAGTACCTCATCGAATCTATCCGAAG-A
1 AAGTATAGTGACACCCAGTGTCTCATCGAACCTAGCCGAAGTA
53372282 AA-TATAGTGACACCCAGTGTCTCATCGA
1 AAGTATAGTGACACCCAGTGTCTCATCGA
53372310 CTCGAGGTCG
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
37 1 0.02
38 18 0.34
39 12 0.23
40 1 0.02
41 16 0.30
42 1 0.02
44 4 0.08
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (43 bp):
AAGTATAGTGACACCCAGTGTCTCATCGAACCTAGCCGAAGTA
Found at i:53373880 original size:5 final size:5
Alignment explanation
Indices: 53373870--53373899 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
53373860 TGTTTCTTTT
53373870 ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA
53373900 CTTAATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:53379810 original size:20 final size:18
Alignment explanation
Indices: 53379787--53379830 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
53379777 AGAAAAAAAT
53379787 ATAAAATAAAATAAGATAAG
1 ATAAAA-AAAATAAG-TAAG
*
53379807 ATAAAACAAATAAGTAAG
1 ATAAAAAAAATAAGTAAG
*
53379825 AGAAAA
1 ATAAAA
53379831 CAAAGAGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 9 0.41
19 7 0.32
20 6 0.27
ACGTcount: A:0.70, C:0.02, G:0.11, T:0.16
Consensus pattern (18 bp):
ATAAAAAAAATAAGTAAG
Found at i:53379830 original size:18 final size:19
Alignment explanation
Indices: 53379795--53379834 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
53379785 ATATAAAATA
*
53379795 AAATAAGATAAGATAAAAC
1 AAATAAGATAAGAGAAAAC
53379814 AAATAAG-TAAGAGAAAAC
1 AAATAAGATAAGAGAAAAC
53379832 AAA
1 AAA
53379835 GAGGAAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.70, C:0.05, G:0.12, T:0.12
Consensus pattern (19 bp):
AAATAAGATAAGAGAAAAC
Found at i:53381491 original size:4 final size:4
Alignment explanation
Indices: 53381484--53381558 Score: 53
Period size: 4 Copynumber: 18.2 Consensus size: 4
53381474 TTTTTATTTA
* ** * * *
53381484 TTTC TTTC TTTC CTTC TTTC TTTC TCAC GTTTGC TCTC TGTTA GT-C TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTT-C TTTC T-TTC TTTC TTTC
*
53381534 TATC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC T
53381559 CACGTTTGCT
Statistics
Matches: 53, Mismatches: 14, Indels: 8
0.71 0.19 0.11
Matches are distributed among these distances:
3 1 0.02
4 47 0.89
5 4 0.08
6 1 0.02
ACGTcount: A:0.04, C:0.27, G:0.05, T:0.64
Consensus pattern (4 bp):
TTTC
Found at i:53381590 original size:50 final size:51
Alignment explanation
Indices: 53381485--53381590 Score: 171
Period size: 50 Copynumber: 2.1 Consensus size: 51
53381475 TTTTATTTAT
* *
53381485 TTCTTTCTTTCCTTCTTTCTTTCTCACGTTTGCTCTCTGTTAGTCTTTCTA
1 TTCTTTCTTTCCTTCTTTCTTTCTCACGTTTGCTCTCTGTAACTCTTTCTA
*
53381536 -TCTTTCTTTCTTTCTTTCTTTCTCACGTTTGCTCTCTGTAACT-TTTCTA
1 TTCTTTCTTTCCTTCTTTCTTTCTCACGTTTGCTCTCTGTAACTCTTTCTA
53381585 TTCTTT
1 TTCTTT
53381591 ACTCATTATT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
49 6 0.12
50 45 0.88
ACGTcount: A:0.07, C:0.26, G:0.07, T:0.60
Consensus pattern (51 bp):
TTCTTTCTTTCCTTCTTTCTTTCTCACGTTTGCTCTCTGTAACTCTTTCTA
Found at i:53381602 original size:14 final size:14
Alignment explanation
Indices: 53381583--53381613 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
53381573 GTAACTTTTC
53381583 TATTCTTTACTCAT
1 TATTCTTTACTCAT
*
53381597 TATTCTTTATTCAT
1 TATTCTTTACTCAT
53381611 TAT
1 TAT
53381614 ACTATATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTCTTTACTCAT
Found at i:53382802 original size:46 final size:46
Alignment explanation
Indices: 53382750--53383016 Score: 399
Period size: 46 Copynumber: 5.8 Consensus size: 46
53382740 AGTGTGCTCT
*
53382750 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
53382796 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
53382842 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
53382888 GTGATATGAAATGAATAAGACCATGATTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
53382934 CTGACATGAAATGAGTAAGATCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * ** * * *
53382980 ATGACAAAAAACGAGTAAAACCATAGTTGAAAGATAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATAC
53383017 TATGACATCA
Statistics
Matches: 205, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 205 1.00
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:53384172 original size:116 final size:116
Alignment explanation
Indices: 53383823--53384383 Score: 1016
Period size: 116 Copynumber: 4.8 Consensus size: 116
53383813 GGGGTGTTAC
53383823 ATAAAGTAATTGTAATTTACTTTTATATTTTTTAATAAAATGGAAATTATTTTAAATAAGGCAAC
1 ATAAAGTAATTGTAATTTACTTTTATA-TTTTTAATAAAATGGAAATTATTTTAAATAAGGCAAC
53383888 ATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAA
65 ATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAA
53383940 ATAAAGTAATTGTAATTTACTTTTATATTTTTTAATAAAATGGAAATTATTTTAAATAAGGCAAC
1 ATAAAGTAATTGTAATTTACTTTTATA-TTTTTAATAAAATGGAAATTATTTTAAATAAGGCAAC
53384005 ATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAA
65 ATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAA
53384057 ATAAAGTAATTGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGCAACA
1 ATAAAGTAATTGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGCAACA
* *
53384122 TTTTAAATATTTTTAAATTATTTCATGTAATTAGATAAAAGGTTGTTTTAA
66 TTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAA
53384173 ATAAAGTAATTGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAAT-AGGCAACA
1 ATAAAGTAATTGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGCAACA
* * *
53384237 TTTTGAATATTTTTATATTATTTCATGTGATAATATAAAAGGTTGTTTTAA
66 TTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAA
* * * *
53384288 ATAAAGTAATTATAATTTACTTTTATATTTTTAATAAAATGAAAATTATTTTAAATAAAGCAATA
1 ATAAAGTAATTGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGCAACA
53384353 TTTTGAATATTTTTATATTATTTCATGTAAT
66 TTTTGAATATTTTTATATTATTTCATGTAAT
53384384 AAAATACAAA
Statistics
Matches: 431, Mismatches: 12, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
115 108 0.25
116 179 0.42
117 144 0.33
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.47
Consensus pattern (116 bp):
ATAAAGTAATTGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGCAACA
TTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAA
Found at i:53384251 original size:54 final size:54
Alignment explanation
Indices: 53383843--53384371 Score: 274
Period size: 61 Copynumber: 9.2 Consensus size: 54
53383833 TGTAATTTAC
* *
53383843 TTTTATATTTTTTAATAAAATGGAAATTATTTTAAATAAGGCAACATTTTGAATAT
1 TTTTATA-TTTTTAATAAAATGAAAATTATTTTAAATAAAGCAA-ATTTTGAATAT
* * * * *
53383899 TTTTATATTATTTCATGTAATTAGAT-AAAAGGTTGTTTTAAATAAAG-TAATTGT-AATTTAC
1 TTTTATATT-TTT-A-ATAA--A-ATGAAAA--TTATTTTAAATAAAGCAAATTTTGAA--TAT
* *
53383960 TTTTATATTTTTTAATAAAATGGAAATTATTTTAAATAAGGCAACATTTTGAATAT
1 TTTTATA-TTTTTAATAAAATGAAAATTATTTTAAATAAAGCAA-ATTTTGAATAT
* * * * *
53384016 TTTTATATTATTTCATGTAATTAGAT-AAAAGGTTGTTTTAAATAAAG-TAATTGT-AATTTAC
1 TTTTATATT-TTT-A-ATAA--A-ATGAAAA--TTATTTTAAATAAAGCAAATTTTGAA--TAT
* * *
53384077 TTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGCAACATTTTAAATAT
1 TTTTATATTTTTAATAAAATGAAAATTATTTTAAATAAAGCAA-ATTTTGAATAT
* * * * * *
53384132 TTTTAAATTATTTCATGTAATTAGAT-AAAAGGTTGTTTTAAATAAAG-TAATTGT-AATTTAC
1 TTTT--A-TATTT--T-TAATAAAATGAAAA--TTATTTTAAATAAAGCAAATTTTGAA--TAT
* *
53384193 TTTTATATTTTTAATAAAATGGAAATTATTTTAAAT-AGGCAACATTTTGAATAT
1 TTTTATATTTTTAATAAAATGAAAATTATTTTAAATAAAGCAA-ATTTTGAATAT
* * * * *
53384247 TTTTATATTATTTCATGTGATAATAT-AAAAGGTTGTTTTAAATAAAG-TAATTAT-AATTTAC
1 TTTTATATT-TTT-A----ATAAAATGAAAA--TTATTTTAAATAAAGCAAATTTTGAA--TAT
53384308 TTTTATATTTTTAATAAAATGAAAATTATTTTAAATAAAGCAATATTTTGAATAT
1 TTTTATATTTTTAATAAAATGAAAATTATTTTAAATAAAGCAA-ATTTTGAATAT
53384363 TTTTATATT
1 TTTTATATT
53384372 ATTTCATGTA
Statistics
Matches: 359, Mismatches: 56, Indels: 117
0.67 0.11 0.22
Matches are distributed among these distances:
53 2 0.01
54 49 0.14
55 58 0.16
56 48 0.13
57 15 0.04
58 21 0.06
59 17 0.05
60 41 0.11
61 65 0.18
62 43 0.12
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.47
Consensus pattern (54 bp):
TTTTATATTTTTAATAAAATGAAAATTATTTTAAATAAAGCAAATTTTGAATAT
Found at i:53384364 original size:231 final size:233
Alignment explanation
Indices: 53383823--53384383 Score: 1018
Period size: 231 Copynumber: 2.4 Consensus size: 233
53383813 GGGGTGTTAC
53383823 ATAAAGTAATTGTAATTTACTTTTATATTTTTTAATAAAATGGAAATTATTTTAAATAAGGCAAC
1 ATAAAGTAATTGTAATTTACTTTTATA-TTTTTAATAAAATGGAAATTATTTTAAATAAGGCAAC
53383888 ATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAATTGT
65 ATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAATTGT
53383953 AATTTACTTTTATATTTTTTAATAAAATGGAAATTATTTTAAATAAGGCAACATTTTGAATATTT
130 AATTTACTTTTATATTTTTTAATAAAATGGAAATTATTTTAAATAAGGCAACATTTTGAATATTT
*
53384018 TTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAA
195 TTATATTATTTCATGTAATAAGATAAAAGGTTGTTTTAA
53384057 ATAAAGTAATTGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGCAACA
1 ATAAAGTAATTGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGCAACA
* *
53384122 TTTTAAATATTTTTAAATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAATTGTA
66 TTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAATTGTA
53384187 ATTTACTTTTATA-TTTTTAATAAAATGGAAATTATTTTAAAT-AGGCAACATTTTGAATATTTT
131 ATTTACTTTTATATTTTTTAATAAAATGGAAATTATTTTAAATAAGGCAACATTTTGAATATTTT
* *
53384250 TATATTATTTCATGTGATAATATAAAAGGTTGTTTTAA
196 TATATTATTTCATGTAATAAGATAAAAGGTTGTTTTAA
* * * *
53384288 ATAAAGTAATTATAATTTACTTTTATATTTTTAATAAAATGAAAATTATTTTAAATAAAGCAATA
1 ATAAAGTAATTGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGCAACA
53384353 TTTTGAATATTTTTATATTATTTCATGTAAT
66 TTTTGAATATTTTTATATTATTTCATGTAAT
53384384 AAAATACAAA
Statistics
Matches: 316, Mismatches: 11, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
231 146 0.46
232 29 0.09
233 114 0.36
234 27 0.09
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.47
Consensus pattern (233 bp):
ATAAAGTAATTGTAATTTACTTTTATATTTTTAATAAAATGGAAATTATTTTAAATAAGGCAACA
TTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAATTGTA
ATTTACTTTTATATTTTTTAATAAAATGGAAATTATTTTAAATAAGGCAACATTTTGAATATTTT
TATATTATTTCATGTAATAAGATAAAAGGTTGTTTTAA
Found at i:53387312 original size:52 final size:52
Alignment explanation
Indices: 53387233--53388079 Score: 1640
Period size: 52 Copynumber: 16.2 Consensus size: 52
53387223 TACTTCTGAT
* *
53387233 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGA
1 CAAGTGA-AAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
53387286 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
1 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
53387338 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
1 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
53387390 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
1 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
53387442 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
1 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
53387494 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
1 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
53387546 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
1 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
53387598 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
1 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
53387650 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
1 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
53387702 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
1 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
53387754 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
1 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
53387806 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
1 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
53387858 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
1 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
53387910 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
1 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
53387962 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
1 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
*
53388014 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGA
1 CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
*
53388066 CAAAGTGATAAGTG
1 C-AAGTGAAAAGTG
53388080 GCTACACTTA
Statistics
Matches: 789, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
52 771 0.98
53 18 0.02
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.27
Consensus pattern (52 bp):
CAAGTGAAAAGTGAAAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGA
Found at i:53388088 original size:37 final size:37
Alignment explanation
Indices: 53388043--53388151 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
53388033 GATAGCTTTA
53388043 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
53388080 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
53388117 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
53388152 ATCATACGTA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
35 11 0.16
36 4 0.06
37 52 0.78
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:53389598 original size:23 final size:25
Alignment explanation
Indices: 53389572--53389618 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
53389562 TATCATTCAT
*
53389572 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
53389595 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
53389619 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:53389779 original size:13 final size:13
Alignment explanation
Indices: 53389761--53389790 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
53389751 TTCTTGTAAA
53389761 CATTTCATACAAC
1 CATTTCATACAAC
*
53389774 CATTTCATATAAC
1 CATTTCATACAAC
53389787 CATT
1 CATT
53389791 CGTCATCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (13 bp):
CATTTCATACAAC
Found at i:53389939 original size:46 final size:46
Alignment explanation
Indices: 53389879--53390220 Score: 374
Period size: 46 Copynumber: 8.0 Consensus size: 46
53389869 TTTGACGTGA
* * * * * * *
53389879 TGCCATAGTGTCTTTCAACTATTGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
* ** * * *
53389925 TGCCATGGTATCTTTCAACCATGGTCTCATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
53389971 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
53390017 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
53390063 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
53390101 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--AT-AGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
53390139 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--AT-AGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
53390177 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
53390221 AGAGCATACT
Statistics
Matches: 270, Mismatches: 16, Indels: 20
0.88 0.05 0.07
Matches are distributed among these distances:
38 108 0.40
39 1 0.00
40 3 0.01
41 1 0.00
43 1 0.00
44 3 0.01
45 6 0.02
46 147 0.54
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:53390210 original size:38 final size:38
Alignment explanation
Indices: 53390059--53390210 Score: 295
Period size: 38 Copynumber: 4.0 Consensus size: 38
53390049 ATTTCATATC
*
53390059 AGGTTGCCATGGTATCTTTCAACCATGGTCTTACACAC
1 AGGTTGCCATGGTATCTTTCAACCATGGTCTTACACAT
53390097 AGGTTGCCATGGTATCTTTCAACCATGGTCTTACACAT
1 AGGTTGCCATGGTATCTTTCAACCATGGTCTTACACAT
53390135 AGGTTGCCATGGTATCTTTCAACCATGGTCTTACACAT
1 AGGTTGCCATGGTATCTTTCAACCATGGTCTTACACAT
53390173 AGGTTGCCATGGTATCTTTCAACCATGGTCTTACACAT
1 AGGTTGCCATGGTATCTTTCAACCATGGTCTTACACAT
53390211 TTCATATCAG
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
38 113 1.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (38 bp):
AGGTTGCCATGGTATCTTTCAACCATGGTCTTACACAT
Found at i:53395051 original size:125 final size:126
Alignment explanation
Indices: 53394613--53395149 Score: 855
Period size: 126 Copynumber: 4.3 Consensus size: 126
53394603 GCCCAAGTTA
* *
53394613 TTTCAGAAAC-ACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGTTGAAAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
**
53394677 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTATACAGACACGTCTTCTCAAAATTATTT
66 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCACAGACACGTCTTCTCAAAATTATTT
* * * *
53394738 TTTCAGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
*
53394803 TGCATCCTGCTTGAAGCGTTTTT-ACCACTATTTGCATAGACACGTCTTCTCAAAATTATTT
66 TGCATCCTGCTTGAAGCGTTTTTGA-CACTATTTGCACAGACACGTCTTCTCAAAATTATTT
* *
53394864 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTTCTTTCAGTACTTTTGCTGACAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
* *
53394929 TGCATCCTGTTTGAAGCGTTTTTTACACTATTTGCACAGACACGTCTTCTCAAAATTA-TT
66 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCACAGACACGTCTTCTCAAAATTATTT
* * *
53394989 TTTCAGATACTACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
* * *
53395054 TGCATCCTGCTTGAACCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAATTTATTT
66 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCACAGACACGTCTTCTCAAAATTATTT
* *
53395115 TTTCAGATACTATTGTAGCAAAAGAGCGTCCACGT
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGT
53395150 AGAAGCTTTT
Statistics
Matches: 382, Mismatches: 26, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
125 127 0.33
126 254 0.66
127 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.34
Consensus pattern (126 bp):
TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCACAGACACGTCTTCTCAAAATTATTT
Found at i:53395068 original size:251 final size:252
Alignment explanation
Indices: 53394613--53395157 Score: 880
Period size: 251 Copynumber: 2.2 Consensus size: 252
53394603 GCCCAAGTTA
* *
53394613 TTTCAGAAAC-ACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGTTGAAAA
1 TTTCAGAAACTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTTCTTTCAGTACTTTTGCTGAAAA
*
53394677 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTATACAGACACGTCTTCTCAAAATTATTTTTTC
66 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTACACAGACACGTCTTCTCAAAATTATTTTTTC
53394742 AGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAATGCA
131 AGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAATGCA
* *
53394807 TCCTGCTTGAAGCGTTTTT-ACCACTATTTGCATAGACACGTCTTCTCAAAATTATTT
196 TCCTGCTTGAACCGTTTTTGA-CACTATTTGCACAGACACGTCTTCTCAAAATTATTT
* *
53394864 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTTCTTTCAGTACTTTTGCTGACAA
1 TTTCAGAAACTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTTCTTTCAGTACTTTTGCTGAAAA
* * *
53394929 TGCATCCTGTTTGAAGCGTTTTTTACACTATTTGCACAGACACGTCTTCTCAAAATTA-TTTTTC
66 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTACACAGACACGTCTTCTCAAAATTATTTTTTC
* * * * *
53394993 AGATACTACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCA
131 AGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAATGCA
* *
53395058 TCCTGCTTGAACCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAATTTATTT
196 TCCTGCTTGAACCGTTTTTGACACTATTTGCACAGACACGTCTTCTCAAAATTATTT
* * *
53395115 TTTCAGATACTATTGTAGCAAAAGAGCGTCCACGTAGAAGCTT
1 TTTCAGAAACTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTT
53395158 TTTTAGATTA
Statistics
Matches: 272, Mismatches: 20, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
251 166 0.61
252 106 0.39
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (252 bp):
TTTCAGAAACTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTTCTTTCAGTACTTTTGCTGAAAA
TGCATCCTGCTTGAAGCGTTTTTGACACTATTTACACAGACACGTCTTCTCAAAATTATTTTTTC
AGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAATGCA
TCCTGCTTGAACCGTTTTTGACACTATTTGCACAGACACGTCTTCTCAAAATTATTT
Found at i:53395253 original size:15 final size:15
Alignment explanation
Indices: 53395233--53395262 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53395223 TTTCTTAAAT
53395233 ATCCTAAAACCCTAA
1 ATCCTAAAACCCTAA
*
53395248 ATCCTAAAATCCTAA
1 ATCCTAAAACCCTAA
53395263 TCTAATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (15 bp):
ATCCTAAAACCCTAA
Found at i:53395386 original size:96 final size:97
Alignment explanation
Indices: 53395260--53395436 Score: 241
Period size: 96 Copynumber: 1.8 Consensus size: 97
53395250 CCTAAAATCC
* * ** * *
53395260 TAATCTAATTTTTTTTAAATTTATAATTAATTTACTAAAGTAACCCTAAACCCTAATTTATTTGA
1 TAATCTAA-TTTTTTTAAAATTATAATTAATTTAATAAACAAACACTAAACCCTAATTTATTTAA
53395325 -TTTTTTCCTTAAAAACCATAAACACTAAACCA
65 TTTTTTTCCTTAAAAACCATAAACACTAAACCA
* *
53395357 TAATCTAA-TTTTTTAAAATTAGTAATTAATTTAATTAACAAACACTAAACCTTAATTTATTTAA
1 TAATCTAATTTTTTTAAAATTA-TAATTAATTTAATAAACAAACACTAAACCCTAATTTATTTAA
53395421 TTTTTTTTCCTTAAAA
65 -TTTTTTTCCTTAAAA
53395437 CCCTAGAATT
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
95 12 0.17
96 35 0.51
97 8 0.12
98 14 0.20
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.44
Consensus pattern (97 bp):
TAATCTAATTTTTTTAAAATTATAATTAATTTAATAAACAAACACTAAACCCTAATTTATTTAAT
TTTTTTCCTTAAAAACCATAAACACTAAACCA
Found at i:53395454 original size:16 final size:17
Alignment explanation
Indices: 53395433--53395474 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
53395423 TTTTTTCCTT
*
53395433 AAAACCCTAGAATT-TA
1 AAAACCCTAAAATTCTA
*
53395449 AAAACCC-AAAATTCTC
1 AAAACCCTAAAATTCTA
53395465 AAAACCCTAA
1 AAAACCCTAA
53395475 TCCTAATTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 5 0.23
16 15 0.68
17 2 0.09
ACGTcount: A:0.52, C:0.26, G:0.02, T:0.19
Consensus pattern (17 bp):
AAAACCCTAAAATTCTA
Found at i:53401652 original size:35 final size:34
Alignment explanation
Indices: 53401612--53401681 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 34
53401602 TTGAACAAGG
53401612 GAAAGAGAGGACAAAACCACTGGTTAATGAACCA
1 GAAAGAGAGGACAAAACCACTGGTTAATGAACCA
* *
53401646 GNAAAGAGGGGATAAAACCACTGGTTAATGAACCA
1 G-AAAGAGAGGACAAAACCACTGGTTAATGAACCA
53401681 G
1 G
53401682 TAACTAAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
34 1 0.03
35 32 0.97
ACGTcount: A:0.44, C:0.16, G:0.26, T:0.13
Consensus pattern (34 bp):
GAAAGAGAGGACAAAACCACTGGTTAATGAACCA
Found at i:53413686 original size:17 final size:17
Alignment explanation
Indices: 53413666--53413699 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
53413656 AGATTTAGGT
53413666 TTAAAAATTTTAATTAA
1 TTAAAAATTTTAATTAA
*
53413683 TTAAAATTTTTAATTAA
1 TTAAAAATTTTAATTAA
53413700 AAATCTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAAAATTTTAATTAA
Found at i:53418494 original size:16 final size:16
Alignment explanation
Indices: 53418473--53418512 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
53418463 AAAAATGTAA
53418473 AAAAAATTATAATTTT
1 AAAAAATTATAATTTT
* *
53418489 AAAAAATAATATTTTT
1 AAAAAATTATAATTTT
*
53418505 ATAAAATT
1 AAAAAATT
53418513 CTAAAATATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAAAATTATAATTTT
Found at i:53423676 original size:16 final size:16
Alignment explanation
Indices: 53423655--53423694 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
53423645 AAAAATGTAA
53423655 AAAAAATTATAATTTT
1 AAAAAATTATAATTTT
* *
53423671 AAAAAATAATATTTTT
1 AAAAAATTATAATTTT
*
53423687 ATAAAATT
1 AAAAAATT
53423695 CTAAAATATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAAAATTATAATTTT
Found at i:53430054 original size:13 final size:13
Alignment explanation
Indices: 53430038--53430062 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53430028 ACAATTTTTA
53430038 AAAAAAAAATTTG
1 AAAAAAAAATTTG
53430051 AAAAAAAAATTT
1 AAAAAAAAATTT
53430063 TTAAACTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
AAAAAAAAATTTG
Found at i:53433573 original size:22 final size:22
Alignment explanation
Indices: 53433548--53433591 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
53433538 ACTTTGAAGA
53433548 TTCATTCAGGAAAAAGAAAGGG
1 TTCATTCAGGAAAAAGAAAGGG
53433570 TTCATTCAGGAAAAAGAAAGGG
1 TTCATTCAGGAAAAAGAAAGGG
53433592 GCTTCAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.09, G:0.27, T:0.18
Consensus pattern (22 bp):
TTCATTCAGGAAAAAGAAAGGG
Found at i:53434254 original size:22 final size:21
Alignment explanation
Indices: 53434219--53434269 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
53434209 ATAGTGAAAA
*
53434219 CAATTACTCTCAATT-TGAAATT
1 CAATTAGT-TCAATTCTG-AATT
53434241 CAAATTAGTTCAATTCTGAATT
1 C-AATTAGTTCAATTCTGAATT
53434263 CAATTAG
1 CAATTAG
53434270 ATCTCAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 6 0.23
22 12 0.46
23 8 0.31
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (21 bp):
CAATTAGTTCAATTCTGAATT
Found at i:53435411 original size:23 final size:24
Alignment explanation
Indices: 53435363--53435411 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
53435353 AAAATCAGAT
*
53435363 AATTACTTAATTTTTTATTAATTA
1 AATTACTTAATTTTTTATTAAATA
*
53435387 AATTA-TTTATTTTTT-TCTAAATA
1 AATTACTTAATTTTTTAT-TAAATA
53435410 AA
1 AA
53435412 GTAAAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 1 0.05
23 16 0.73
24 5 0.23
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (24 bp):
AATTACTTAATTTTTTATTAAATA
Found at i:53451210 original size:8 final size:8
Alignment explanation
Indices: 53451197--53451221 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
53451187 GGTGTTCGGC
53451197 GCAAGTGG
1 GCAAGTGG
53451205 GCAAGTGG
1 GCAAGTGG
53451213 GCAAGTGG
1 GCAAGTGG
53451221 G
1 G
53451222 GGGTAGGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.52, T:0.12
Consensus pattern (8 bp):
GCAAGTGG
Found at i:53455949 original size:20 final size:20
Alignment explanation
Indices: 53455919--53455957 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
53455909 TAAAAAAATT
53455919 ATAATTTTTATACTTATTTTA
1 ATAATTTTTATACTT-TTTTA
53455940 ATAA-TTTTATACTTTTTT
1 ATAATTTTTATACTTTTTT
53455958 GATGTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
ATAATTTTTATACTTTTTTA
Found at i:53467797 original size:6 final size:6
Alignment explanation
Indices: 53467786--53467816 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
53467776 TTTCCTTTCT
*
53467786 TCACCC TCACCC TCACCC TCACCC TCTCCC T
1 TCACCC TCACCC TCACCC TCACCC TCACCC T
53467817 TCATTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.13, C:0.65, G:0.00, T:0.23
Consensus pattern (6 bp):
TCACCC
Found at i:53470444 original size:14 final size:14
Alignment explanation
Indices: 53470425--53470452 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53470415 CATTTGTCTC
53470425 TTTTGACACAAAAT
1 TTTTGACACAAAAT
53470439 TTTTGACACAAAAT
1 TTTTGACACAAAAT
53470453 CAGATATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
TTTTGACACAAAAT
Found at i:53473411 original size:47 final size:47
Alignment explanation
Indices: 53473302--53473412 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
53473292 CCGGGATAAG
*
53473302 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
* * * *
53473349 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTA-TAGTA
53473396 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
53473413 ACTCAATGTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.02
47 52 0.95
48 2 0.04
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
Found at i:53478721 original size:18 final size:18
Alignment explanation
Indices: 53478694--53478786 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
53478684 TACGACCGTT
53478694 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
53478712 TACGGCACTATTTACGTA
1 TACGGTACTATTCACGTA
53478730 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
53478748 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
53478766 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
53478784 TAC
1 TAC
53478787 AGTAGTTGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:53478741 original size:36 final size:36
Alignment explanation
Indices: 53478694--53478786 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
53478684 TACGACCGTT
*
53478694 TACGGTACTATTCACGTATACGGCACTATTTACGTA
1 TACGGTACTATTCACGTATACGGCACTATTCACGTA
53478730 TACGGTACTATTCACGTATACGGCACTATTCACGTA
1 TACGGTACTATTCACGTATACGGCACTATTCACGTA
*
53478766 TACGGTACTGTTCACGTATAC
1 TACGGTACTATTCACGTATAC
53478787 AGTAGTTGGG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (36 bp):
TACGGTACTATTCACGTATACGGCACTATTCACGTA
Found at i:53496168 original size:20 final size:20
Alignment explanation
Indices: 53496143--53496185 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
53496133 AATGGTTTAA
53496143 AAATTA-ATTTAGTAATATTT
1 AAATTATATTTA-TAATATTT
*
53496163 AAATTATATTTATAATTTTT
1 AAATTATATTTATAATATTT
53496183 AAA
1 AAA
53496186 AAATGATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
AAATTATATTTATAATATTT
Found at i:53499134 original size:17 final size:18
Alignment explanation
Indices: 53499099--53499136 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
53499089 TTTTTTTAGA
**
53499099 TTTACTTTTTTTTTGTTC
1 TTTACTTTTTGATTGTTC
53499117 TTTACTTTTTGATT-TTC
1 TTTACTTTTTGATTGTTC
53499134 TTT
1 TTT
53499137 TTATTTGCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.08, C:0.11, G:0.05, T:0.76
Consensus pattern (18 bp):
TTTACTTTTTGATTGTTC
Found at i:53500002 original size:15 final size:16
Alignment explanation
Indices: 53499973--53500004 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
53499963 TGTGATTTTT
53499973 TAATGTAATTTTTATA
1 TAATGTAATTTTTATA
53499989 TAATGTAA-TTTTATA
1 TAATGTAATTTTTATA
53500004 T
1 T
53500005 TATTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TAATGTAATTTTTATA
Found at i:53502102 original size:33 final size:32
Alignment explanation
Indices: 53502065--53502142 Score: 79
Period size: 33 Copynumber: 2.4 Consensus size: 32
53502055 CAGTACTCTG
*
53502065 CTCCTTCCGGCTCGTATCCACC-CATGTACTCAA
1 CTCCTTCCGGC-CGTATCCACCGC-CGTACTCAA
*
53502098 CTCC-TCCAGAGCCGTATCCACCGCCGTACTCTA
1 CTCCTTCC-G-GCCGTATCCACCGCCGTACTCAA
*
53502131 CTCCTCCCGGCC
1 CTCCTTCCGGCC
53502143 CATTTCCACC
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
32 6 0.16
33 27 0.71
34 5 0.13
ACGTcount: A:0.15, C:0.47, G:0.14, T:0.23
Consensus pattern (32 bp):
CTCCTTCCGGCCGTATCCACCGCCGTACTCAA
Found at i:53515595 original size:45 final size:41
Alignment explanation
Indices: 53515497--53515604 Score: 112
Period size: 41 Copynumber: 2.6 Consensus size: 41
53515487 TTATGCTTAA
*
53515497 GATGAAAACCCGAAAAGGGCATCTTAAAAAAAAAGGATTAG
1 GATGAAAACCCGAAAAGGGCGTCTTAAAAAAAAAGGATTAG
** *
53515538 GGCGAAAACCCGAAAAGGGCGTCTTGATTAGTACAAAAA-GATTAG
1 GATGAAAACCCGAAAAGGGCGTCTT-A--A--AAAAAAAGGATTAG
*
53515583 GATGAAAACCCG-AGAGGGCGTC
1 GATGAAAACCCGAAAAGGGCGTC
53515605 CTAATGAAAC
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
41 22 0.40
42 1 0.02
44 10 0.18
45 16 0.29
46 6 0.11
ACGTcount: A:0.43, C:0.16, G:0.27, T:0.15
Consensus pattern (41 bp):
GATGAAAACCCGAAAAGGGCGTCTTAAAAAAAAAGGATTAG
Found at i:53516553 original size:69 final size:69
Alignment explanation
Indices: 53516379--53516553 Score: 217
Period size: 70 Copynumber: 2.5 Consensus size: 69
53516369 CTTTCCAAGG
* ** *
53516379 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTTG
53516444 TTTT
66 TTTT
* ** * *
53516448 CAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
1 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTT-
53516513 TGTTTT
64 TGTTTT
** *
53516519 -AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
53516554 TTTAATTTTT
Statistics
Matches: 91, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
69 31 0.34
70 55 0.60
71 5 0.05
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.34
Consensus pattern (69 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTTG
TTTT
Found at i:53517004 original size:76 final size:75
Alignment explanation
Indices: 53516571--53516984 Score: 525
Period size: 76 Copynumber: 5.5 Consensus size: 75
53516561 TTTGTTTTTC
* ** *
53516571 AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
53516636 GTTGTTAAAAA
66 GTT-TTAAAAA
* *
53516647 AAAATTAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGG-AGGTTTCAATTTC
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTA-TTTTCAATTTC
53516711 TGTTGTTAAAAA
65 TGTT-TTAAAAA
* *
53516723 AAAATTAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
*
53516788 GTTTT---CA
66 GTTTTAAAAA
* * * *
53516795 AAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
*
53516860 GTTTTCAAAA
66 GTTTTAAAAA
* ** * *
53516870 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAAAT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGG---ACACGCTGAGGTATTTTCAATT
*
53516934 TCTGTTTT-TAAA
63 TCTGTTTTAAAAA
** *
53516946 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAG
53516985 ATTACACACT
Statistics
Matches: 305, Mismatches: 24, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
72 65 0.21
74 1 0.00
75 38 0.12
76 172 0.56
77 29 0.10
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (75 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCT
GTTTTAAAAA
Found at i:53517408 original size:88 final size:88
Alignment explanation
Indices: 53517206--53517540 Score: 442
Period size: 88 Copynumber: 3.8 Consensus size: 88
53517196 TGTTTTAATT
* * *
53517206 TCAACTCATATTGCGAGAGGTAAGTTGAGCCTCAGGACACACGCCGAGGTATTTT-CAATTAAGC
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACA--CCGAGGTATTTTCCATTTATG-
* * * *
53517270 CTTTTGA-T-TTCTGTTTTTAAAAAAAAA
63 -TTTTCATTATTATGTTTTT--GAAAGAA
*
53517297 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACCGAGGTATTTTCCATTTATGTTT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACCGAGGTATTTTCCATTTATGTTT
53517362 TCATTATTATGTTTTTGAAAGAA
66 TCATTATTATGTTTTTGAAAGAA
*
53517385 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACCGAGGTATTTTCCATTTATGTTT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACCGAGGTATTTTCCATTTATGTTT
53517450 TCATTATTATGTTTTTGAAAGAA
66 TCATTATTATGTTTTTGAAAGAA
** * ** * * *
53517473 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTTTGTTT
1 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACCGAGGTATTTTCCATTTATGTTT
53517538 TCA
66 TCA
53517541 AAATTCAACT
Statistics
Matches: 224, Mismatches: 17, Indels: 9
0.90 0.07 0.04
Matches are distributed among these distances:
88 157 0.70
89 13 0.06
90 15 0.07
91 39 0.17
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (88 bp):
TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACCGAGGTATTTTCCATTTATGTTT
TCATTATTATGTTTTTGAAAGAA
Found at i:53518382 original size:73 final size:73
Alignment explanation
Indices: 53517473--53518381 Score: 1698
Period size: 73 Copynumber: 12.5 Consensus size: 73
53517463 TTTGAAAGAA
* * *
53517473 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTTTG-TT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
53517537 TTCAAAAT
66 TTCAAAAT
53517545 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
53517610 TTCAAAAT
66 TTCAAAAT
53517618 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
53517683 TTCAAAAT
66 TTCAAAAT
53517691 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
53517756 TTCAAAAT
66 TTCAAAAT
53517764 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
53517829 TTCAAAAT
66 TTCAAAAT
53517837 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
53517902 TTCAAAAT
66 TTCAAAAT
53517910 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
53517975 TTCAAAAT
66 TTCAAAAT
53517983 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
53518048 TTCAAAAT
66 TTCAAAAT
53518056 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
53518121 TTCAAAAT
66 TTCAAAAT
53518129 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
53518194 TTCAAAAT
66 TTCAAAAT
53518202 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
53518267 TTCAAAAT
66 TTCAAAAT
* * *
53518275 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG-TT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
* *
53518339 GTCAAAAAA
66 TTC-AAAAT
*
53518348 TCAACTCATATTACGA-AAAGTGAGTTGAGCCTCA
1 TCAACTCATATTGCGAGAAA-TGAGTTGAGCCTCA
53518382 GTTCACATGT
Statistics
Matches: 825, Mismatches: 9, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
72 66 0.08
73 759 0.92
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (73 bp):
TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
TTCAAAAT
Found at i:53525360 original size:21 final size:21
Alignment explanation
Indices: 53525335--53525375 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
53525325 AGGGAAAAGA
* *
53525335 AAAAAAAAACAAAATCAAAATC
1 AAAATAAAA-AAAATAAAAATC
53525357 AAAATAAAAAAAATAAAAA
1 AAAATAAAAAAAATAAAAA
53525376 AGAAAAAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.83, C:0.07, G:0.00, T:0.10
Consensus pattern (21 bp):
AAAATAAAAAAAATAAAAATC
Found at i:53525382 original size:28 final size:28
Alignment explanation
Indices: 53525329--53525382 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
53525319 AAAACAAGGG
**
53525329 AAAAGAAAAAAAAAACAAAATCAAAATC
1 AAAAGAAAAAAAAAACAAAAGAAAAATC
*
53525357 AAAATAAAAAAAATAA-AAAAGAAAAA
1 AAAAGAAAAAAAA-AACAAAAGAAAAA
53525383 GAGAAATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 20 0.91
29 2 0.09
ACGTcount: A:0.83, C:0.06, G:0.04, T:0.07
Consensus pattern (28 bp):
AAAAGAAAAAAAAAACAAAAGAAAAATC
Found at i:53527161 original size:43 final size:42
Alignment explanation
Indices: 53527113--53527253 Score: 115
Period size: 43 Copynumber: 3.2 Consensus size: 42
53527103 GAAGCAGGTC
*
53527113 GAAGACATAAACCTTACCTCTTTCGGTTGTGATAGAGCTGGTT
1 GAAGACAAAAACCTT-CCTCTTTCGGTTGTGATAGAGCTGGTT
* * ** * * * *
53527156 GAAGACAAAAGATCTTGC-CTTTCTGCAT-TGACAGCGAAGCAGATC
1 GAAGACAAAA-ACCTTCCTCTTTC-GGTTGTGATA--G-AGCTGGTT
*
53527201 GAAGACACAAACCTTGCCTCTTTCGGTTGTGATAGAGCTGGTT
1 GAAGACAAAAACCTT-CCTCTTTCGGTTGTGATAGAGCTGGTT
53527244 GAAGACAAAA
1 GAAGACAAAA
53527254 GATCTTGCCT
Statistics
Matches: 71, Mismatches: 19, Indels: 16
0.67 0.18 0.15
Matches are distributed among these distances:
42 9 0.13
43 26 0.37
44 10 0.14
45 17 0.24
46 9 0.13
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.26
Consensus pattern (42 bp):
GAAGACAAAAACCTTCCTCTTTCGGTTGTGATAGAGCTGGTT
Found at i:53527224 original size:88 final size:88
Alignment explanation
Indices: 53527075--53527686 Score: 824
Period size: 88 Copynumber: 7.0 Consensus size: 88
53527065 CAATGAAGTT
* * * * * *
53527075 AAAGATCTTGCCTTCCTGCATTGATAGTGAAGCAGGTCGAAGACATAAACCTTACCTCTTTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGT
53527140 TGTGATAGAGCTGGTTGAAGACA
66 TGTGATAGAGCTGGTTGAAGACA
* *
53527163 AAAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGT
53527228 TGTGATAGAGCTGGTTGAAGACA
66 TGTGATAGAGCTGGTTGAAGACA
* * *
53527251 AAAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAGACACAAACGTTGCCTCTCTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGT
* *
53527316 TGTGATGGAGCTGGTTGAAGAAA
66 TGTGATAGAGCTGGTTGAAGACA
* * * *
53527339 AAAGATCTTGCTTTCCTGCATTGACAGCGAAGCAGGTCGAAAAGACAAACCTTGCCTCTCTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGT
53527404 TGTGATAGAGCTGGTTGAAGACA
66 TGTGATAGAGCTGGTTGAAGACA
* *
53527427 AAAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGT
* *
53527492 TGTGATGGAGCTGGTTGAAGAAAA
66 TGTGATAGAGCTGGTTGAAG-ACA
* *
53527516 AAAGATCTTGCTTTCCTGCATTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCCTCTCTCGA
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAA-CCTTGCCTCTCTCG-
*
53527579 G-TGTAGA-AGAGTTGGTTGAAGACA
64 GTTGT-GATAGAGCTGGTTGAAGACA
** * ** * * * *
53527603 ACTGATTTTATCTTCCTGCGTTGACAGTGAAGCAGGTCGAAG--ACAAACCTTACCTCTCTCGGT
1 AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGT
*
53527666 TGT-AGTGGAGCTGGTTGAAGA
66 TGTGA-TAGAGCTGGTTGAAGA
53527687 ATTGCAGATC
Statistics
Matches: 468, Mismatches: 48, Indels: 18
0.88 0.09 0.03
Matches are distributed among these distances:
84 1 0.00
85 1 0.00
86 29 0.06
87 43 0.09
88 350 0.75
89 44 0.09
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (88 bp):
AAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGT
TGTGATAGAGCTGGTTGAAGACA
Found at i:53529553 original size:3 final size:3
Alignment explanation
Indices: 53529545--53529586 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
53529535 TAAAGTTGAC
* *
53529545 ATT ATT ATT ACT ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
53529587 GCTTTTATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:53534071 original size:76 final size:75
Alignment explanation
Indices: 53533935--53534082 Score: 269
Period size: 76 Copynumber: 2.0 Consensus size: 75
53533925 TTTGGGGAAT
53533935 ATATAGGGAAAAATTAAGCATGTGGGCCCCACCAGTTGCGCCTACCAAAAAGGCACAACTAGTCG
1 ATATAGGGAAAAATTAAGCATGTGGGCCCCACCAGTTGCGCCTACCAAAAAGGCACAACTAGTCG
53534000 TGCCTGTAAA
66 TGCCTGTAAA
* *
53534010 ATATAGGAGAAAAATTATGCATGTGGGCCCCACCAGTTGCGCCTACCAAAAAGGCAGAACTAGTC
1 ATATAGG-GAAAAATTAAGCATGTGGGCCCCACCAGTTGCGCCTACCAAAAAGGCACAACTAGTC
53534075 GTGCCTGT
65 GTGCCTGT
53534083 CAGATAGGCT
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
75 7 0.10
76 63 0.90
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (75 bp):
ATATAGGGAAAAATTAAGCATGTGGGCCCCACCAGTTGCGCCTACCAAAAAGGCACAACTAGTCG
TGCCTGTAAA
Found at i:53534091 original size:27 final size:27
Alignment explanation
Indices: 53534061--53534123 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
53534051 CCTACCAAAA
* *
53534061 AGGCAGAACTAGTCGTGCCTGTCAGAT
1 AGGCACAACTAGTCGCGCCTGTCAGAT
* *
53534088 AGGCTCAACTAGTTGCGCCTGTCAGAT
1 AGGCACAACTAGTCGCGCCTGTCAGAT
*
53534115 AGGCGCAAC
1 AGGCACAAC
53534124 ATGTATGTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.21
Consensus pattern (27 bp):
AGGCACAACTAGTCGCGCCTGTCAGAT
Found at i:53541958 original size:21 final size:21
Alignment explanation
Indices: 53541932--53541972 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53541922 AGACGAGCAA
* *
53541932 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
53541953 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
53541973 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:53543911 original size:16 final size:16
Alignment explanation
Indices: 53543878--53543911 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
53543868 GGAAATTGTT
* *
53543878 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
53543894 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
53543910 AA
1 AA
53543912 TACAAAGTGG
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:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:53546739 original size:21 final size:21
Alignment explanation
Indices: 53546713--53546753 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53546703 AGACGAGCAA
* *
53546713 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
53546734 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
53546754 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:53548692 original size:16 final size:16
Alignment explanation
Indices: 53548659--53548692 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
53548649 GGAGACTGTT
* *
53548659 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
53548675 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
53548691 AA
1 AA
53548693 TACAAAGTGG
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:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:53555352 original size:10 final size:10
Alignment explanation
Indices: 53555337--53555373 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
53555327 CTCTCATTTC
53555337 TTTTTTCAAT
1 TTTTTTCAAT
53555347 TTTTTTCAAT
1 TTTTTTCAAT
*
53555357 TTTTTTCATT
1 TTTTTTCAAT
53555367 TTTTTTC
1 TTTTTTC
53555374 CTTATCACCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTTCAAT
Found at i:53556387 original size:27 final size:28
Alignment explanation
Indices: 53556353--53556413 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
53556343 GATTTCACTT
* *
53556353 AATTAAATTA-ACTTTTAAT-TTTGTAA
1 AATTAAAATATACTTTTAATATTTATAA
* *
53556379 TATTAAAATATAGTTTTAATATTTATAA
1 AATTAAAATATACTTTTAATATTTATAA
53556407 AATTAAA
1 AATTAAA
53556414 TTTATATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 8 0.29
27 8 0.29
28 12 0.43
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (28 bp):
AATTAAAATATACTTTTAATATTTATAA
Found at i:53559607 original size:22 final size:22
Alignment explanation
Indices: 53559581--53559630 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
53559571 TAGTAAACAA
*
53559581 ATATATAAATATAAATAAATATTT
1 ATATA-AAATA-AAATAAAAATTT
53559605 ATATAAAATAAAATAAAAATTT
1 ATATAAAATAAAATAAAAATTT
53559627 ATAT
1 ATAT
53559631 TTAAATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 15 0.60
23 5 0.20
24 5 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
ATATAAAATAAAATAAAAATTT
Found at i:53559619 original size:18 final size:18
Alignment explanation
Indices: 53559574--53559616 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
53559564 AACATGTTAG
*
53559574 TAAACAAATATATAAATA
1 TAAATAAATATATAAATA
* *
53559592 TAAATAAATATTTATATA
1 TAAATAAATATATAAATA
53559610 -AAATAAA
1 TAAATAAA
53559617 ATAAAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAATAAATATATAAATA
Found at i:53559681 original size:24 final size:23
Alignment explanation
Indices: 53559638--53559688 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
53559628 TATTTAAATT
* *
53559638 ATTAGATATGAAAAACTAATATG
1 ATTAGATACGAAAAACTAATAAG
*
53559661 ATTAGATACGAAAAAATTAATAAG
1 ATTAGATACG-AAAAACTAATAAG
53559685 ATTA
1 ATTA
53559689 TGAAAACTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.55, C:0.04, G:0.12, T:0.29
Consensus pattern (23 bp):
ATTAGATACGAAAAACTAATAAG
Found at i:53560308 original size:33 final size:33
Alignment explanation
Indices: 53560271--53560337 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
53560261 TTGAACTTGC
53560271 ATCCCCCTACAAGCAAGGTAAGATTTCAAGCTT
1 ATCCCCCTACAAGCAAGGTAAGATTTCAAGCTT
*
53560304 ATCCCCCTACACGCAAGGTAAGATTTCAAGCTT
1 ATCCCCCTACAAGCAAGGTAAGATTTCAAGCTT
53560337 A
1 A
53560338 GTATCACTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (33 bp):
ATCCCCCTACAAGCAAGGTAAGATTTCAAGCTT
Found at i:53560650 original size:22 final size:22
Alignment explanation
Indices: 53560622--53560666 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
53560612 AGGATATTGA
53560622 ATTTCTTATTATTTTACTCAAC
1 ATTTCTTATTATTTTACTCAAC
53560644 ATTTCTTATTATTTTACTCAAC
1 ATTTCTTATTATTTTACTCAAC
53560666 A
1 A
53560667 AAAGTAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTTCTTATTATTTTACTCAAC
Found at i:53565726 original size:22 final size:21
Alignment explanation
Indices: 53565683--53565726 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
53565673 TCTTGATATA
*
53565683 ATTTTTAAAAATTTTATATTT
1 ATTTTTAAAAATTTCATATTT
*
53565704 ATTTTTATAAAATTTCATTTTT
1 ATTTTTA-AAAATTTCATATTT
53565726 A
1 A
53565727 AGTTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTTTAAAAATTTCATATTT
Found at i:53570074 original size:22 final size:23
Alignment explanation
Indices: 53570046--53570099 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
53570036 ACAAACGAAT
*
53570046 AGAGAGCACTA-AAGTGCTATAC
1 AGAGAGCACTAGAAGTGCTAAAC
* *
53570068 AGAGAGCAC-AGATGTGTTAAAC
1 AGAGAGCACTAGAAGTGCTAAAC
53570090 AGAGAGCACT
1 AGAGAGCACT
53570100 TAACATGCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.41, C:0.17, G:0.26, T:0.17
Consensus pattern (23 bp):
AGAGAGCACTAGAAGTGCTAAAC
Found at i:53570836 original size:7 final size:7
Alignment explanation
Indices: 53570826--53570920 Score: 58
Period size: 7 Copynumber: 14.1 Consensus size: 7
53570816 ACTTTATGTT
53570826 TTATATA
1 TTATATA
53570833 -T-TATA
1 TTATATA
53570838 TTATATA
1 TTATATA
*
53570845 TAATATA
1 TTATATA
*
53570852 ATA-ATA
1 TTATATA
*
53570858 TAATATA
1 TTATATA
53570865 TTATATA
1 TTATATA
53570872 TTA-ATA
1 TTATATA
*
53570878 CTTAAATA
1 -TTATATA
53570886 TTA-AGT-
1 TTATA-TA
*
53570892 TAATATA
1 TTATATA
*
53570899 ATATATA
1 TTATATA
*
53570906 ATATATA
1 TTATATA
*
53570913 TTTTATA
1 TTATATA
53570920 T
1 T
53570921 AAAAAATATC
Statistics
Matches: 69, Mismatches: 11, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
5 4 0.06
6 13 0.19
7 49 0.71
8 3 0.04
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (7 bp):
TTATATA
Found at i:53572724 original size:55 final size:54
Alignment explanation
Indices: 53572637--53572891 Score: 278
Period size: 55 Copynumber: 4.8 Consensus size: 54
53572627 ATTAGGGTTT
*
53572637 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAA-GTTTCTAAGGC
* * * * *
53572692 AAGGAAATCATGTAAGACCATGTCAAGACATGGC-ATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTT--TCTAAGGC
* * *
53572747 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGC-ATTGGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTC-TAAGGC
*
53572800 AAGGATACCATGTAAGACCATGTCAAGACATGGCAA-TGGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGGC
* * *
53572849 AAGGATACCACGTAAGACCATGACAAGTCATGGCAA-TGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAG
53572892 GTACCCGTGT
Statistics
Matches: 172, Mismatches: 21, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
49 40 0.23
52 7 0.04
53 41 0.24
54 12 0.07
55 68 0.40
56 4 0.02
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGGC
Found at i:53572843 original size:108 final size:110
Alignment explanation
Indices: 53572644--53572844 Score: 327
Period size: 108 Copynumber: 1.8 Consensus size: 110
53572634 TTTAAGGATA
*
53572644 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
*
53572709 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
* *
53572754 CCATGTAAGACCATGCCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAG
*
53572816 ACCATGTCAAGACATGGCAATGGTAAGTT
65 ACCATGTCAAGACATGGCAATGATAAGTT
53572845 TCAAAAGGAT
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
107 3 0.04
108 48 0.56
109 7 0.08
110 27 0.32
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.22
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:53573104 original size:16 final size:16
Alignment explanation
Indices: 53573083--53573113 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53573073 ATAAATTTGA
53573083 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
53573099 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
53573114 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:53575617 original size:46 final size:46
Alignment explanation
Indices: 53575433--53575616 Score: 305
Period size: 46 Copynumber: 4.0 Consensus size: 46
53575423 AGTGTGCTCT
* * *
53575433 CTGATATGATATGTGTAAGACCATGGTTGAAAGATATCATGGCGAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
53575479 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATAACATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
53575525 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* **
53575571 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
53575617 GAACGAAATA
Statistics
Matches: 131, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 131 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:53575735 original size:16 final size:17
Alignment explanation
Indices: 53575716--53575748 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
53575706 ATGATGGAGC
53575716 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
53575732 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
53575749 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:53586698 original size:20 final size:19
Alignment explanation
Indices: 53586666--53586703 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
53586656 TGGTAATTAC
53586666 TTAAGTTGTAATTCGATTTT
1 TTAAGTTGTAATTC-ATTTT
53586686 TTAAGTT-TAAATTCATTT
1 TTAAGTTGT-AATTCATTT
53586704 ATAAAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (19 bp):
TTAAGTTGTAATTCATTTT
Found at i:53592120 original size:12 final size:12
Alignment explanation
Indices: 53592103--53592150 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
53592093 AAGCTGCTCA
53592103 TATTAGTTGTTT
1 TATTAGTTGTTT
*
53592115 TATTAGTTATTCT
1 TATTAGTTGTT-T
* *
53592128 TGTTAGCTGTTT
1 TATTAGTTGTTT
53592140 TATTAGTTGTT
1 TATTAGTTGTT
53592151 AATGATGTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
12 20 0.69
13 9 0.31
ACGTcount: A:0.17, C:0.04, G:0.17, T:0.62
Consensus pattern (12 bp):
TATTAGTTGTTT
Found at i:53604986 original size:18 final size:18
Alignment explanation
Indices: 53604963--53605019 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
53604953 CCCAACTACT
* *
53604963 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTGCC
53604981 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTGCC
53604999 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTGCC
53605017 GTA
1 GTA
53605020 AACGGTCGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (18 bp):
GTATACGTGAATAGTGCC
Found at i:53605949 original size:23 final size:26
Alignment explanation
Indices: 53605910--53605965 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
53605900 ACAATTTGGC
*
53605910 CTTTAA-ACTCT-ATTTTTT-TTTCA
1 CTTTAATACTCTAATTTTTTGTCTCA
53605933 CTTTAATACT-TAATTTTTTGTCTCA
1 CTTTAATACTCTAATTTTTTGTCTCA
*
53605958 TTTTAATA
1 CTTTAATA
53605966 TTTGAATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 7 0.25
24 10 0.36
25 11 0.39
ACGTcount: A:0.25, C:0.14, G:0.02, T:0.59
Consensus pattern (26 bp):
CTTTAATACTCTAATTTTTTGTCTCA
Found at i:53606139 original size:20 final size:20
Alignment explanation
Indices: 53606106--53606144 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
53606096 CTAAAATGAG
53606106 AAAAAAAAAGTATT-AAAGT
1 AAAAAAAAAGTATTCAAAGT
*
53606125 AAAAAAATAGATATTCAAAG
1 AAAAAAAAAG-TATTCAAAG
53606145 ATCAAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 4 0.24
21 4 0.24
ACGTcount: A:0.67, C:0.03, G:0.10, T:0.21
Consensus pattern (20 bp):
AAAAAAAAAGTATTCAAAGT
Found at i:53607133 original size:7 final size:7
Alignment explanation
Indices: 53607115--53607147 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
53607105 TTACATATAA
53607115 TAAAATT
1 TAAAATT
53607122 T-AAATT
1 TAAAATT
53607128 TAAAATAT
1 TAAAAT-T
53607136 TAAAATT
1 TAAAATT
53607143 TAAAA
1 TAAAA
53607148 ATATTAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.25
7 11 0.46
8 7 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
TAAAATT
Found at i:53607150 original size:16 final size:15
Alignment explanation
Indices: 53607115--53607155 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
53607105 TTACATATAA
53607115 TAAAAT-TT-AAATT
1 TAAAATATTAAAATT
53607128 TAAAATATTAAAATT
1 TAAAATATTAAAATT
53607143 TAAAAATATTAAA
1 T-AAAATATTAAA
53607156 CTTACCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.24
14 2 0.08
15 6 0.24
16 11 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAAATATTAAAATT
Found at i:53607654 original size:14 final size:14
Alignment explanation
Indices: 53607635--53607664 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
53607625 GATGCATCAT
53607635 CACTTTCCACCATG
1 CACTTTCCACCATG
53607649 CACTTTCCACCATG
1 CACTTTCCACCATG
53607663 CA
1 CA
53607665 AAAATAATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.43, G:0.07, T:0.27
Consensus pattern (14 bp):
CACTTTCCACCATG
Found at i:53609688 original size:15 final size:16
Alignment explanation
Indices: 53609657--53609700 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
53609647 TGGTTCATGT
*
53609657 ATTTTAA-TTTAATTA
1 ATTTTAATTTTTATTA
53609672 ATTTTAATTTTTA-TA
1 ATTTTAATTTTTATTA
53609687 ATATTTAATTTTTA
1 AT-TTTAATTTTTA
53609701 AATCCTCACT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTTAATTTTTATTA
Found at i:53612122 original size:21 final size:20
Alignment explanation
Indices: 53612086--53612131 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
53612076 TAATAATTGC
**
53612086 TTTAATATTATTTTTATTTT
1 TTTAATATTATTTTTAAGTT
*
53612106 TTTAATATTTGTTTTTAAGTT
1 TTTAATA-TTATTTTTAAGTT
53612127 TTTAA
1 TTTAA
53612132 ATATATTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (20 bp):
TTTAATATTATTTTTAAGTT
Found at i:53612128 original size:22 final size:21
Alignment explanation
Indices: 53612086--53612135 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
53612076 TAATAATTGC
*
53612086 TTTAATA-TTATTTTTATTTT
1 TTTAATATTTATTTTTAGTTT
*
53612106 TTTAATATTTGTTTTTAAGTTT
1 TTTAATATTTATTTTT-AGTTT
*
53612128 TTAAATAT
1 TTTAATAT
53612136 ATTTGATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.28
21 7 0.28
22 11 0.44
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (21 bp):
TTTAATATTTATTTTTAGTTT
Found at i:53612137 original size:24 final size:26
Alignment explanation
Indices: 53612110--53612158 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
53612100 TATTTTTTTA
53612110 ATATTTG-TTT-TTA-AGTTTTTAAAT
1 ATATTTGATTTATTATA-TTTTTAAAT
53612134 ATATTTGATTTATTATATTTTTAAA
1 ATATTTGATTTATTATATTTTTAAA
53612159 ATTTTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 11 0.50
27 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (26 bp):
ATATTTGATTTATTATATTTTTAAAT
Found at i:53618541 original size:27 final size:27
Alignment explanation
Indices: 53618496--53618548 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
53618486 AAGATAAATT
* *
53618496 AAATTAATAATTTTGAAAATTTTATAA
1 AAATTAATAATTTTAAAAAATTTATAA
53618523 AAATTAA-AATTTTTAAAAAATTTATA
1 AAATTAATAA-TTTTAAAAAATTTATA
53618549 TTTAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (27 bp):
AAATTAATAATTTTAAAAAATTTATAA
Found at i:53618551 original size:17 final size:18
Alignment explanation
Indices: 53618511--53618544 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
53618501 AATAATTTTG
53618511 AAAA-TTTTATAAAAATT
1 AAAATTTTTATAAAAATT
53618528 AAAATTTTTA-AAAAATT
1 AAAATTTTTATAAAAATT
53618545 TATATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATTTTTATAAAAATT
Found at i:53630445 original size:61 final size:64
Alignment explanation
Indices: 53630306--53630455 Score: 189
Period size: 61 Copynumber: 2.3 Consensus size: 64
53630296 TTGAAAACGA
* *
53630306 CTTTTTATTGTTTTGGCAATTTTAGTTAATGTGAAAACCATAACCATAATAATGATGAGTATCTT
1 CTTTTTATTGTTTTGGTAATTTTAGTTAATGTG--AA-CATAACCATAATAATGATGAATATCTT
53630371 CT
63 CT
* * *
53630373 CTTCTAATTGTTTTGGTAATTTTAGTTAATGTG-A-AT-ACCATAATAATGGTGAATATCTTCT
1 CTTTTTATTGTTTTGGTAATTTTAGTTAATGTGAACATAACCATAATAATGATGAATATCTTCT
* *
53630434 CTTTTTCTTGTTTTGGTCATTT
1 CTTTTTATTGTTTTGGTAATTT
53630456 CTTAAGTTAG
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
61 41 0.55
62 2 0.03
64 1 0.01
67 30 0.41
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (64 bp):
CTTTTTATTGTTTTGGTAATTTTAGTTAATGTGAACATAACCATAATAATGATGAATATCTTCT
Found at i:53646469 original size:11 final size:11
Alignment explanation
Indices: 53646453--53646504 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
53646443 ATCCATATTC
53646453 TTATTATTGTA
1 TTATTATTGTA
*
53646464 TTATTATT-AA
1 TTATTATTGTA
* *
53646474 ATATTATAAGTA
1 TTATTAT-TGTA
53646486 TTATTATTGTA
1 TTATTATTGTA
*
53646497 TGATTATT
1 TTATTATT
53646505 AAATATTATT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
10 7 0.22
11 18 0.56
12 7 0.22
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (11 bp):
TTATTATTGTA
Found at i:53646959 original size:11 final size:11
Alignment explanation
Indices: 53646943--53646994 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
53646933 AATAATATTT
*
53646943 AATAATCATAC
1 AATAATAATAC
53646954 AATAATAATAC
1 AATAATAATAC
* **
53646965 TTATAAT-ATTT
1 -AATAATAATAC
53646976 AATAATAATAC
1 AATAATAATAC
53646987 AATAATAA
1 AATAATAA
53646995 AAATATATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
10 5 0.16
11 22 0.69
12 5 0.16
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (11 bp):
AATAATAATAC
Found at i:53654910 original size:33 final size:35
Alignment explanation
Indices: 53654849--53654914 Score: 100
Period size: 33 Copynumber: 1.9 Consensus size: 35
53654839 TAACAGTCTG
*
53654849 TGATTCTCAAAAAGAAAATCACTAACAAATTTCGA
1 TGATTCTCAAAAAGAAAATCACGAACAAATTTCGA
*
53654884 TGATTCTC-AAAAG-AAATCACGGACAAATTTC
1 TGATTCTCAAAAAGAAAATCACGAACAAATTTC
53654915 AGCCACTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 16 0.55
34 5 0.17
35 8 0.28
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.26
Consensus pattern (35 bp):
TGATTCTCAAAAAGAAAATCACGAACAAATTTCGA
Found at i:53657326 original size:11 final size:11
Alignment explanation
Indices: 53657310--53657383 Score: 51
Period size: 12 Copynumber: 6.1 Consensus size: 11
53657300 AATAAAAGTG
53657310 ATATTTTTTTA
1 ATATTTTTTTA
53657321 ATATTTTTTCTCA
1 ATATTTTTT-T-A
*
53657334 AT-TTTTTTAA
1 ATATTTTTTTA
*
53657344 ATATTAATTATATA
1 ATATT--TT-TTTA
53657358 TATACTTTTTTTA
1 -ATA-TTTTTTTA
53657371 ATATTATTTTTA
1 ATATT-TTTTTA
53657383 A
1 A
53657384 AAGTATTTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
10 3 0.06
11 13 0.26
12 17 0.34
13 8 0.16
14 4 0.08
15 3 0.06
16 2 0.04
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (11 bp):
ATATTTTTTTA
Done.