Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 164 of 279
Found at i:54183691 original size:21 final size:21
Alignment explanation
Indices: 54183667--54183706 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
54183657 TTTTTATATT
54183667 AATTTTT-AGTTTTGATTTTTG
1 AATTTTTGAGTTTTG-TTTTTG
54183688 AATTTTTGAGTTTTGTTTT
1 AATTTTTGAGTTTTGTTTT
54183707 ATGTCCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.68
Consensus pattern (21 bp):
AATTTTTGAGTTTTGTTTTTG
Found at i:54187564 original size:14 final size:12
Alignment explanation
Indices: 54187552--54187597 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
54187542 CACGTATATG
54187552 TATATAAAAATA
1 TATATAAAAATA
54187564 TATATAAAAATTA
1 TATATAAAAA-TA
*
54187577 TAAAATATAAAATA
1 T-ATATA-AAAATA
54187591 TATATAA
1 TATATAA
54187598 GTATGTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 11 0.38
13 7 0.24
14 7 0.24
15 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TATATAAAAATA
Found at i:54187611 original size:27 final size:26
Alignment explanation
Indices: 54187552--54187614 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
54187542 CACGTATATG
54187552 TATATA-AAAATATATATAAAAATTA
1 TATATATAAAATATATATAAAAATTA
* **
54187577 TAAAATATAAAATATATATAAGTATGTA
1 T-ATATATAAAATATATATAAAAAT-TA
54187605 TATATATAAA
1 TATATATAAA
54187615 TGAGGAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 1 0.03
26 4 0.13
27 23 0.74
28 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (26 bp):
TATATATAAAATATATATAAAAATTA
Found at i:54188831 original size:12 final size:12
Alignment explanation
Indices: 54188814--54188839 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54188804 GGAAATAATT
54188814 TATTTTAAAAAA
1 TATTTTAAAAAA
54188826 TATTTTAAAAAA
1 TATTTTAAAAAA
54188838 TA
1 TA
54188840 AAATTAACTT
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TATTTTAAAAAA
Found at i:54212199 original size:61 final size:60
Alignment explanation
Indices: 54212136--54212250 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 60
54212126 ATATATTTTA
* * * *
54212136 TATATTTTATAT-TAAAAGGTAAAAATA-TCTTCAAAATAATGTTTATTACTTTGTTATTC
1 TATATTTAATATAAAAAAGATAAAAATATTC-TCAAAATAATATTTATTACTTTGTTATTC
54212195 TATATTTAATATAAAAAAGATAAAAATATTCTCAAAATAATATTTATTACTTTGTT
1 TATATTTAATATAAAAAAGATAAAAATATTCTCAAAATAATATTTATTACTTTGTT
54212251 GAAATTTGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 11 0.22
60 37 0.74
61 2 0.04
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.45
Consensus pattern (60 bp):
TATATTTAATATAAAAAAGATAAAAATATTCTCAAAATAATATTTATTACTTTGTTATTC
Found at i:54216745 original size:31 final size:31
Alignment explanation
Indices: 54216710--54216770 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
54216700 ACCTAATCAT
54216710 TTAAATAAAAACTTTTAAATAATTCAATAAC
1 TTAAATAAAAACTTTTAAATAATTCAATAAC
* *
54216741 TTAAATAAAAACTTTTGAATAATTTAATAA
1 TTAAATAAAAACTTTTAAATAATTCAATAA
54216771 TAAAATTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.38
Consensus pattern (31 bp):
TTAAATAAAAACTTTTAAATAATTCAATAAC
Found at i:54228073 original size:10 final size:11
Alignment explanation
Indices: 54228032--54228072 Score: 82
Period size: 11 Copynumber: 3.7 Consensus size: 11
54228022 CTCTCTCTAG
54228032 ATTTTTTTTCA
1 ATTTTTTTTCA
54228043 ATTTTTTTTCA
1 ATTTTTTTTCA
54228054 ATTTTTTTTCA
1 ATTTTTTTTCA
54228065 ATTTTTTT
1 ATTTTTTT
54228073 CTCTCTCTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (11 bp):
ATTTTTTTTCA
Found at i:54228630 original size:32 final size:32
Alignment explanation
Indices: 54228587--54228647 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
54228577 GGGTAGAAAT
* *
54228587 TCAAATCTTACAATGTACTTAAATTTTTTAAA
1 TCAAATATTACAATATACTTAAATTTTTTAAA
*
54228619 TCAAATATTACAATATATTTAAATTTTTT
1 TCAAATATTACAATATACTTAAATTTTTT
54228648 GTACTTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.48
Consensus pattern (32 bp):
TCAAATATTACAATATACTTAAATTTTTTAAA
Found at i:54234805 original size:46 final size:44
Alignment explanation
Indices: 54234746--54234860 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
54234736 ACAGGACAGA
* *
54234746 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
54234792 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
54234836 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
54234861 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:54234841 original size:44 final size:45
Alignment explanation
Indices: 54234746--54234879 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
54234736 ACAGGACAGA
* *
54234746 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
54234792 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
54234836 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
54234880 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:54237236 original size:28 final size:30
Alignment explanation
Indices: 54237189--54237247 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 30
54237179 ATAAATAATT
*
54237189 AATATTATTTACTTAGAAATATTTAA-AATA
1 AATATTATATACTTAGAAATA-TTAACAATA
54237219 AATATTATATA-TTA-AAATATTAACAATA
1 AATATTATATACTTAGAAATATTAACAATA
54237247 A
1 A
54237248 GTTATAATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 4 0.15
28 10 0.37
29 3 0.11
30 10 0.37
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (30 bp):
AATATTATATACTTAGAAATATTAACAATA
Found at i:54253474 original size:21 final size:21
Alignment explanation
Indices: 54253448--54253488 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54253438 AGACGAGCAA
* *
54253448 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
54253469 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
54253489 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:54257904 original size:33 final size:35
Alignment explanation
Indices: 54257862--54257935 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
54257852 TGTCTATCTA
*
54257862 TAATAACATATAT-T-AAT-TGCCTTTTTTTTACGT
1 TAATAACATATATATCAATGTG-ATTTTTTTTACGT
54257895 TAATAACATATATATCAATGTGATTTTTTTTACGT
1 TAATAACATATATATCAATGTGATTTTTTTTACGT
54257930 TAATAA
1 TAATAA
54257936 AAATAATTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
33 13 0.35
34 1 0.03
35 21 0.57
36 2 0.05
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (35 bp):
TAATAACATATATATCAATGTGATTTTTTTTACGT
Found at i:54258026 original size:14 final size:14
Alignment explanation
Indices: 54258007--54258036 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
54257997 AAGAATTTTA
54258007 ATTTCATTAAAAAT
1 ATTTCATTAAAAAT
*
54258021 ATTTCATTAAACAT
1 ATTTCATTAAAAAT
54258035 AT
1 AT
54258037 AATAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTTCATTAAAAAT
Found at i:54277266 original size:12 final size:13
Alignment explanation
Indices: 54277245--54277273 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
54277235 AAACTAAAAC
54277245 AAAAGTGAAAAGG
1 AAAAGTGAAAAGG
54277258 AAAAG-GAAAAGG
1 AAAAGTGAAAAGG
54277270 AAAA
1 AAAA
54277274 ATGGCTACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (13 bp):
AAAAGTGAAAAGG
Found at i:54282404 original size:21 final size:21
Alignment explanation
Indices: 54282379--54282420 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
54282369 AAACATGTTG
54282379 CTTAAGAAAAGCCAAACCAGA
1 CTTAAGAAAAGCCAAACCAGA
54282400 CTTAAGAAAAGCCAAACCAGA
1 CTTAAGAAAAGCCAAACCAGA
54282421 TTACCAGTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.14, T:0.10
Consensus pattern (21 bp):
CTTAAGAAAAGCCAAACCAGA
Found at i:54292771 original size:20 final size:21
Alignment explanation
Indices: 54292735--54292787 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
54292725 ATTTTTTAAA
54292735 AAAATG-TTAAAAA-ATATAT
1 AAAATGATTAAAAATATATAT
*
54292754 -AAATGATTAAAAATATATTT
1 AAAATGATTAAAAATATATAT
54292774 AAAAT-ATTAAAAAT
1 AAAATGATTAAAAAT
54292788 TATGGTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 5 0.17
19 7 0.23
20 14 0.47
21 4 0.13
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (21 bp):
AAAATGATTAAAAATATATAT
Found at i:54292796 original size:20 final size:20
Alignment explanation
Indices: 54292735--54292799 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
54292725 ATTTTTTAAA
* *
54292735 AAAATGTTAAAAA-ATATAT
1 AAAATATTAAAAATATATGT
*
54292754 -AAATGATTAAAAATATATTT
1 AAAAT-ATTAAAAATATATGT
54292774 AAAATATTAAAAAT-TATGGT
1 AAAATATTAAAAATATAT-GT
54292794 AAAATA
1 AAAATA
54292800 AAATCAAGCT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 4 0.10
19 10 0.26
20 21 0.54
21 4 0.10
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (20 bp):
AAAATATTAAAAATATATGT
Found at i:54311042 original size:22 final size:22
Alignment explanation
Indices: 54311017--54311060 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
54311007 CTTTATGTGT
*
54311017 TTACTATTAGAGACTTATTATA
1 TTACTATTAAAGACTTATTATA
*
54311039 TTACTATTAAAGATTTATTATA
1 TTACTATTAAAGACTTATTATA
54311061 ATTTATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (22 bp):
TTACTATTAAAGACTTATTATA
Found at i:54315877 original size:19 final size:20
Alignment explanation
Indices: 54315855--54315909 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 20
54315845 TAATATAATT
54315855 TTATTTT-TTTTAAATATTA
1 TTATTTTATTTTAAATATTA
54315874 TTATTTTAAATTTTAAATATTA
1 TTATTTT--ATTTTAAATATTA
*
54315896 TTATTATATTTTAA
1 TTATTTTATTTTAA
54315910 TAATTTTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
19 7 0.22
20 7 0.22
22 18 0.56
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATTTTATTTTAAATATTA
Found at i:54315887 original size:24 final size:24
Alignment explanation
Indices: 54315835--54315900 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
54315825 GGCGCGACCC
* * * *
54315835 ATTTTTTTAATAATATAATTTTAT
1 ATTTTTTAAATATTATTATTTTAA
*
54315859 TTTTTTTAAATATTATTATTTTAA
1 ATTTTTTAAATATTATTATTTTAA
54315883 A--TTTTAAATATTATTATT
1 ATTTTTTAAATATTATTATT
54315901 ATATTTTAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
22 17 0.47
24 19 0.53
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
ATTTTTTAAATATTATTATTTTAA
Found at i:54324337 original size:24 final size:23
Alignment explanation
Indices: 54324299--54324357 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
54324289 ATTTAAAAAT
*
54324299 TATTAAAATATAATAAAATAATAA
1 TATTAAAA-AAAATAAAATAATAA
* *
54324323 TATTTAAAAAAAATAAAATTATAT
1 TA-TTAAAAAAAATAAAATAATAA
54324347 TATTAAAAAAA
1 TATTAAAAAAA
54324358 TGGGTCGCGC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.29
24 16 0.52
25 6 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
TATTAAAAAAAATAAAATAATAA
Found at i:54326273 original size:25 final size:26
Alignment explanation
Indices: 54326215--54326291 Score: 72
Period size: 25 Copynumber: 3.0 Consensus size: 26
54326205 TTAAGATAAA
* *
54326215 AATTTAAAATAAATAATATATAGAAAG
1 AATTTAAAACAAATAACATATA-AAAG
*
54326242 --TTCAAAACAAATAACA-ATAAAAG
1 AATTTAAAACAAATAACATATAAAAG
*
54326265 AATTTAAAATC-ATTAACATATAAAAG
1 AATTTAAAA-CAAATAACATATAAAAG
54326291 A
1 A
54326292 TATATACAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
23 4 0.10
24 3 0.07
25 25 0.61
26 9 0.22
ACGTcount: A:0.62, C:0.06, G:0.05, T:0.26
Consensus pattern (26 bp):
AATTTAAAACAAATAACATATAAAAG
Found at i:54326714 original size:17 final size:16
Alignment explanation
Indices: 54326684--54326722 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
54326674 AAGAATTAAC
* *
54326684 ATAAATATATAAACGA
1 ATAAATATACAAACAA
54326700 ATAACATATACAAACAA
1 ATAA-ATATACAAACAA
54326717 ATAAAT
1 ATAAAT
54326723 GAATGAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.64, C:0.10, G:0.03, T:0.23
Consensus pattern (16 bp):
ATAAATATACAAACAA
Found at i:54326753 original size:5 final size:5
Alignment explanation
Indices: 54326743--54326767 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
54326733 ACCAATGAAT
54326743 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
54326768 GGCTAATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:54327658 original size:25 final size:25
Alignment explanation
Indices: 54327606--54327658 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
54327596 TTCTGTTCTT
* * * *
54327606 TTTTCTCTAATCTTGAATCTTAATG
1 TTTTCTCTAATCTTCAAACTCAAAG
*
54327631 TTTTCTTTAATCTTCAAACTCAAAG
1 TTTTCTCTAATCTTCAAACTCAAAG
54327656 TTT
1 TTT
54327659 CGGAACACTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (25 bp):
TTTTCTCTAATCTTCAAACTCAAAG
Found at i:54334639 original size:19 final size:19
Alignment explanation
Indices: 54334615--54334651 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
54334605 GTATTTATTA
**
54334615 ATTTTTTTTGTTTAATATC
1 ATTTTTTTAATTTAATATC
54334634 ATTTTTTTAATTTAATAT
1 ATTTTTTTAATTTAATAT
54334652 TTTTATTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.68
Consensus pattern (19 bp):
ATTTTTTTAATTTAATATC
Found at i:54338425 original size:13 final size:13
Alignment explanation
Indices: 54338407--54338432 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54338397 TTTCAAGCTT
54338407 TTTTTAATTAATA
1 TTTTTAATTAATA
54338420 TTTTTAATTAATA
1 TTTTTAATTAATA
54338433 ACTATTTTAT
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTAATTAATA
Found at i:54338989 original size:49 final size:47
Alignment explanation
Indices: 54338890--54338989 Score: 114
Period size: 49 Copynumber: 2.1 Consensus size: 47
54338880 TAATTTTTTT
* **
54338890 AAATAAAATTTATTAATTAAAAAGATGAATTAAAAATAAAAACTTGA
1 AAATAAAATTTATTAAATAAAAAGATGAATTAAAAATAAAAACTAAA
*
54338937 AAATAATATATTTATTAAAT-AAAAGTATTAATTTAAAAATAAAAA-TAAA
1 AAATAA-A-ATTTATTAAATAAAAAG-ATGAA-TTAAAAATAAAAACTAAA
54338986 AAAT
1 AAAT
54338990 TTAAACAACA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
47 6 0.13
48 6 0.13
49 20 0.44
50 13 0.29
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (47 bp):
AAATAAAATTTATTAAATAAAAAGATGAATTAAAAATAAAAACTAAA
Found at i:54341365 original size:14 final size:14
Alignment explanation
Indices: 54341341--54341373 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
54341331 AAGAATTAAG
54341341 GAAACAAAGAAACA
1 GAAACAAAGAAACA
54341355 -AAACAAAAGAAACA
1 GAAAC-AAAGAAACA
54341369 GAAAC
1 GAAAC
54341374 GAAGCAGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.24
14 9 0.53
15 4 0.24
ACGTcount: A:0.73, C:0.15, G:0.12, T:0.00
Consensus pattern (14 bp):
GAAACAAAGAAACA
Found at i:54345212 original size:13 final size:13
Alignment explanation
Indices: 54345196--54345221 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54345186 GTTTTTAAAC
54345196 TTTTGGTTTATTT
1 TTTTGGTTTATTT
54345209 TTTTGGTTTATTT
1 TTTTGGTTTATTT
54345222 GTAGATTAGG
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:0.08, C:0.00, G:0.15, T:0.77
Consensus pattern (13 bp):
TTTTGGTTTATTT
Found at i:54345254 original size:6 final size:6
Alignment explanation
Indices: 54345243--54345271 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
54345233 TTGTCCCTTT
54345243 TTAAAA TTAAAA TTAAAA TTAAAA TTAAA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAA
54345272 TAACCCTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
TTAAAA
Found at i:54346025 original size:29 final size:31
Alignment explanation
Indices: 54345993--54346052 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
54345983 TTAATGTTAG
*
54345993 ATAAAAATA-ATTAT-TTATA-TATATAATAT
1 ATAAAAATATATAATGTTATATTA-ATAATAT
*
54346022 ATAAACATATATAATGTTATATTAATAATAT
1 ATAAAAATATATAATGTTATATTAATAATAT
54346053 TGTTATTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 8 0.31
30 4 0.15
31 12 0.46
32 2 0.08
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (31 bp):
ATAAAAATATATAATGTTATATTAATAATAT
Found at i:54348180 original size:19 final size:19
Alignment explanation
Indices: 54348138--54348180 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
54348128 TAATTATTCA
54348138 TTAAACTTAATTAGAATAT
1 TTAAACTTAATTAGAATAT
* *
54348157 ATAAACTATATTTA-AATAT
1 TTAAACT-TAATTAGAATAT
54348176 TTAAA
1 TTAAA
54348181 TATTATCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (19 bp):
TTAAACTTAATTAGAATAT
Found at i:54348588 original size:29 final size:30
Alignment explanation
Indices: 54348543--54348600 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
54348533 AATACATGTA
* *
54348543 TGTATTTGATTATTATTAAGTAAATATTAG
1 TGTATTTGATTACTATTAAATAAATATTAG
*
54348573 TGTATTT-ATTACTATTAAATTAATATTA
1 TGTATTTGATTACTATTAAATAAATATTA
54348601 TATGATAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.52
Consensus pattern (30 bp):
TGTATTTGATTACTATTAAATAAATATTAG
Found at i:54348756 original size:20 final size:20
Alignment explanation
Indices: 54348703--54348742 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
54348693 ATTTAAGTAT
54348703 TAAAATATATTTATTAATTA
1 TAAAATATATTTATTAATTA
54348723 TAAAATATATTTATTAATTA
1 TAAAATATATTTATTAATTA
54348743 AATAATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAAAATATATTTATTAATTA
Found at i:54352157 original size:46 final size:46
Alignment explanation
Indices: 54352090--54352181 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
54352080 AGTGTGCCCT
*
54352090 TTGATATGAAATGTGTAAGACCATTGTTGAAAGATACCATGGCAAC
1 TTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
54352136 TTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 TTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
54352182 NNNNNNNNNN
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (46 bp):
TTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:54354473 original size:38 final size:38
Alignment explanation
Indices: 54354424--54354832 Score: 512
Period size: 38 Copynumber: 9.9 Consensus size: 38
54354414 TGATATGAAA
54354424 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
54354462 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
54354500 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
54354538 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
54354576 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
54354614 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACC-----TG
54354657 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
1 ---TGTGTAAGACCATGGTTGAAAGATACCATGGCAACC-----TG
54354703 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAG
1 ---TGTGTAAGACCATGGTTGAAAGATACCATGGCAACC-----T--G
*
54354751 ATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTG
1 -TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
*
54354790 ACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 ---TG---TG--TAAGACCATGGTTGAAAGATACCATGGCAAC
54354833 ATGACAGAAA
Statistics
Matches: 352, Mismatches: 2, Indels: 26
0.93 0.01 0.07
Matches are distributed among these distances:
38 188 0.53
39 1 0.00
41 4 0.01
43 2 0.01
44 1 0.00
46 155 0.44
48 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (38 bp):
TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
Found at i:54354681 original size:46 final size:46
Alignment explanation
Indices: 54354614--54354876 Score: 402
Period size: 46 Copynumber: 5.7 Consensus size: 46
54354604 TGGCAACCTG
54354614 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
54354660 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
*
54354706 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAGA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
* *
54354752 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
* ** * *
54354798 AGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG-AAA
* * * *
54354844 TGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCA
54354877 TCACGTCAAA
Statistics
Matches: 203, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 1 0.00
46 202 1.00
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
Found at i:54354796 original size:138 final size:129
Alignment explanation
Indices: 54354538--54354876 Score: 433
Period size: 138 Copynumber: 2.6 Consensus size: 129
54354528 TGGCAACCTG
54354538 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACC----TG---TGTGTAAGACCATGGTTGAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAATGAAATGTGTAAGACCATGGTTGAA
*
54354596 AGATACCATGGCAACCTGTGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
66 AGATACCATGGCAACCTGTGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
54354660 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA-ATGAAATGTGTAAGACCATGGTTGA
*
54354725 AAGATACCATGGCAACCTGATATGAGATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTG
65 AAGATACCATGGCAACC-----T--G-TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG
54354790 ACATGAAA
122 ACATGAAA
* ** * * *
54354798 AGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAGTAAGACCATAGTTG
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA-ATG-AAATGTGTAAGACCATGGTTG
* *
54354862 AAAGACACTATGGCA
64 AAAGATACCATGGCA
54354877 TCACGTCAAA
Statistics
Matches: 189, Mismatches: 11, Indels: 18
0.87 0.05 0.08
Matches are distributed among these distances:
122 36 0.19
127 2 0.01
130 36 0.19
135 1 0.01
137 2 0.01
138 112 0.59
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (129 bp):
TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAATGAAATGTGTAAGACCATGGTTGAA
AGATACCATGGCAACCTGTGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
Found at i:54356609 original size:12 final size:12
Alignment explanation
Indices: 54356576--54356614 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
54356566 ATTGTTTAAT
54356576 TCACCGTCATCA
1 TCACCGTCATCA
*
54356588 TCACCATCATCA
1 TCACCGTCATCA
**
54356600 TCGTCGTCATCA
1 TCACCGTCATCA
54356612 TCA
1 TCA
54356615 TTATCACTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.26, C:0.38, G:0.08, T:0.28
Consensus pattern (12 bp):
TCACCGTCATCA
Found at i:54357246 original size:27 final size:26
Alignment explanation
Indices: 54357216--54357291 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 26
54357206 TGTATTTGCC
* *
54357216 TATTTT-TAATTTTTATAATGTTTAAAA
1 TATTTTATATTTTTTAAAAT-TTT-AAA
54357243 TATTTTATATTTTTTTAAAATTTTAAA
1 TATTTTATA-TTTTTTAAAATTTTAAA
54357270 TATTTTATATTTTTTTAAAATT
1 TATTTTATA-TTTTTTAAAATT
54357292 CGATATATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
27 31 0.69
28 5 0.11
29 9 0.20
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (26 bp):
TATTTTATATTTTTTAAAATTTTAAA
Found at i:54357272 original size:20 final size:20
Alignment explanation
Indices: 54357236--54357275 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
54357226 TTTTATAATG
*
54357236 TTTAAAATATTTTATATTTT
1 TTTAAAATATTTAATATTTT
54357256 TTTAAAAT-TTTAAATATTTT
1 TTTAAAATATTT-AATATTTT
54357276 ATATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTAAAATATTTAATATTTT
Found at i:54357299 original size:27 final size:27
Alignment explanation
Indices: 54357240--54357300 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
54357230 ATAATGTTTA
**
54357240 AAATATTTTATATTTTTTTAAAATTTT
1 AAATATTTTATATTTTTTTAAAATTCG
54357267 AAATATTTTATATTTTTTTAAAATTCG
1 AAATATTTTATATTTTTTTAAAATTCG
*
54357294 ATATATT
1 AAATATT
54357301 AATAAGGATG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (27 bp):
AAATATTTTATATTTTTTTAAAATTCG
Found at i:54358462 original size:20 final size:21
Alignment explanation
Indices: 54358423--54358462 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
54358413 AAGAATTTTC
*
54358423 AAAAAAAAAGCGAAATAGAAG
1 AAAAAAAAAACGAAATAGAAG
*
54358444 AAAAAAAAAATGAAA-AGAA
1 AAAAAAAAAACGAAATAGAA
54358463 AACCATTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.78, C:0.03, G:0.15, T:0.05
Consensus pattern (21 bp):
AAAAAAAAAACGAAATAGAAG
Found at i:54372682 original size:15 final size:16
Alignment explanation
Indices: 54372659--54372699 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
54372649 ATTTACATAT
*
54372659 ATTTTTAATAATTA-A
1 ATTTATAATAATTAGA
54372674 ATTTATAATAATTATGA
1 ATTTATAATAATTA-GA
54372691 ATTTATAAT
1 ATTTATAAT
54372700 TTAGGTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.57
17 10 0.43
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATTTATAATAATTAGA
Found at i:54390630 original size:7 final size:7
Alignment explanation
Indices: 54390620--54390660 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
54390610 ATTTTTATCT
54390620 TTTAAAA
1 TTTAAAA
54390627 TTT-AAA
1 TTTAAAA
54390633 TTT-AAA
1 TTTAAAA
* *
54390639 TTCAAAT
1 TTTAAAA
54390646 TTTAAAA
1 TTTAAAA
54390653 TTTAAAA
1 TTTAAAA
54390660 T
1 T
54390661 AAAATTACCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 11 0.38
7 18 0.62
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (7 bp):
TTTAAAA
Found at i:54391688 original size:13 final size:11
Alignment explanation
Indices: 54391660--54391702 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
54391650 AGTTAAATAT
54391660 TATTTTATTAA
1 TATTTTATTAA
54391671 TATTTTACTTAGA
1 TATTTTA-TTA-A
*
54391684 TA-TTTATTAT
1 TATTTTATTAA
54391694 TATTTTATT
1 TATTTTATT
54391703 TAAAGATGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:54398653 original size:20 final size:20
Alignment explanation
Indices: 54398628--54398665 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54398618 TGGAATCAAT
*
54398628 ATTTTTGTTATATTTATTGA
1 ATTTTTGTTATATATATTGA
*
54398648 ATTTTTTTTATATATATT
1 ATTTTTGTTATATATATT
54398666 TAATGATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (20 bp):
ATTTTTGTTATATATATTGA
Found at i:54407303 original size:24 final size:24
Alignment explanation
Indices: 54407274--54407321 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
54407264 AGGAGTGAGA
54407274 ATAAATAGAACCAAAAGGGAAATC
1 ATAAATAGAACCAAAAGGGAAATC
54407298 ATAAATAGAACCAAAAGGGAAATC
1 ATAAATAGAACCAAAAGGGAAATC
54407322 TCTATATCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.58, C:0.12, G:0.17, T:0.12
Consensus pattern (24 bp):
ATAAATAGAACCAAAAGGGAAATC
Found at i:54407610 original size:25 final size:25
Alignment explanation
Indices: 54407577--54407624 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
54407567 AATATGAAGG
*
54407577 TTGTTGTGATAGTAATC-TGACATGA
1 TTGTAGTGATAG-AATCATGACATGA
54407602 TTGTAGTGATAGAATCATGACAT
1 TTGTAGTGATAGAATCATGACAT
54407625 AATTATGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (25 bp):
TTGTAGTGATAGAATCATGACATGA
Found at i:54421538 original size:33 final size:33
Alignment explanation
Indices: 54421496--54421561 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
54421486 ATTTTCCCCA
54421496 ATCCTATGTAAAATCAAGAGATGACTATTAAAG
1 ATCCTATGTAAAATCAAGAGATGACTATTAAAG
54421529 ATCCTATGTAAAATCAAGAGATGACTATTAAAG
1 ATCCTATGTAAAATCAAGAGATGACTATTAAAG
54421562 GTCCAAGGAG
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:0.45, C:0.12, G:0.15, T:0.27
Consensus pattern (33 bp):
ATCCTATGTAAAATCAAGAGATGACTATTAAAG
Found at i:54437097 original size:37 final size:38
Alignment explanation
Indices: 54437008--54437097 Score: 93
Period size: 33 Copynumber: 2.5 Consensus size: 38
54436998 AACCTTTATT
* * *
54437008 TATAATTTAATGTATTTTATATAATATTTATATTGAATA
1 TATAAATT-ATGTATTTTATATAAAATTTATATTAAATA
54437047 TA-AAATTA--T-TTTTAT-TAAAATTTAT-TTCAAATA
1 TATAAATTATGTATTTTATATAAAATTTATATT-AAATA
54437080 TATAAATTATGTATTTTA
1 TATAAATTATGTATTTTA
54437098 ATTTGTAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
32 2 0.05
33 15 0.35
34 12 0.28
35 1 0.02
36 1 0.02
37 6 0.14
38 4 0.09
39 2 0.05
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (38 bp):
TATAAATTATGTATTTTATATAAAATTTATATTAAATA
Found at i:54440367 original size:22 final size:21
Alignment explanation
Indices: 54440314--54440376 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 21
54440304 TACACGACAT
*
54440314 AAAAATAATATAA-AAAATAA
1 AAAAATAATATAACATAATAA
*
54440334 AAAAA-AATTATAACATGATAA
1 AAAAATAA-TATAACATAATAA
54440355 GAAAAATAATATAGACATAATA
1 -AAAAATAATATA-ACATAATA
54440377 CAAATCCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
19 2 0.06
20 10 0.29
21 5 0.14
22 9 0.26
23 9 0.26
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (21 bp):
AAAAATAATATAACATAATAA
Found at i:54441249 original size:22 final size:22
Alignment explanation
Indices: 54441224--54441318 Score: 69
Period size: 21 Copynumber: 4.5 Consensus size: 22
54441214 TCAGTTAAAT
54441224 TTAAAAATAATTGTCAAATCGA
1 TTAAAAATAATTGTCAAATCGA
*
54441246 TT-AAAATAATAG---AAT-GAA
1 TTAAAAATAATTGTCAAATCG-A
* * **
54441264 TTAAAAA-AATTAATCAATTAAA
1 TTAAAAATAATT-GTCAAATCGA
54441286 TTTAAAAATAATTGTCAAATCGA
1 -TTAAAAATAATTGTCAAATCGA
54441309 TT-AAAATAAT
1 TTAAAAATAAT
54441319 AGAATGAATT
Statistics
Matches: 55, Mismatches: 9, Indels: 19
0.66 0.11 0.23
Matches are distributed among these distances:
17 1 0.02
18 9 0.16
19 4 0.07
21 17 0.31
22 7 0.13
23 13 0.24
24 4 0.07
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.33
Consensus pattern (22 bp):
TTAAAAATAATTGTCAAATCGA
Found at i:54441288 original size:63 final size:64
Alignment explanation
Indices: 54441209--54441337 Score: 233
Period size: 63 Copynumber: 2.0 Consensus size: 64
54441199 ATGTTAATTG
*
54441209 ATTAATCAGTTAAATTTAAAAATAATTGTCAAATCGATTAAAATAATAGAATGAA-TTAAAAAA
1 ATTAATCAATTAAATTTAAAAATAATTGTCAAATCGATTAAAATAATAGAATGAATTTAAAAAA
54441272 ATTAATCAATTAAATTTAAAAATAATTGTCAAATCGATTAAAATAATAGAATGAATTTTAAAAAA
1 ATTAATCAATTAAATTTAAAAATAATTGTCAAATCGATTAAAATAATAGAATGAA-TTTAAAAAA
54441337 A
1 A
54441338 CTCTGATTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
63 54 0.86
65 9 0.14
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (64 bp):
ATTAATCAATTAAATTTAAAAATAATTGTCAAATCGATTAAAATAATAGAATGAATTTAAAAAA
Found at i:54450626 original size:25 final size:25
Alignment explanation
Indices: 54450592--54450642 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
54450582 CATATTTTCC
*
54450592 ATTTTTTATAATCCTAGAGTATCGT
1 ATTTTTTATAATCCAAGAGTATCGT
54450617 ATTTTTTATAATCCAAGAGTATCGT
1 ATTTTTTATAATCCAAGAGTATCGT
54450642 A
1 A
54450643 CCTATAAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (25 bp):
ATTTTTTATAATCCAAGAGTATCGT
Found at i:54451187 original size:12 final size:11
Alignment explanation
Indices: 54451155--54451185 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
54451145 TTTAATTAAT
*
54451155 TTTTTAAAATA
1 TTTTAAAAATA
54451166 TTTTAAAAATA
1 TTTTAAAAATA
54451177 TTTTAAAAA
1 TTTTAAAAA
54451186 ATCAAATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TTTTAAAAATA
Found at i:54451376 original size:18 final size:18
Alignment explanation
Indices: 54451349--54451383 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54451339 AATTGATAGG
*
54451349 AAAAAAAACATTATGTTT
1 AAAAAAAACAATATGTTT
*
54451367 AAAAATAACAATATGTT
1 AAAAAAAACAATATGTT
54451384 GTGGAAACCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (18 bp):
AAAAAAAACAATATGTTT
Found at i:54457103 original size:52 final size:48
Alignment explanation
Indices: 54457041--54457215 Score: 194
Period size: 47 Copynumber: 3.6 Consensus size: 48
54457031 GAAATGTGAT
* * *
54457041 TTCCGTATAAGACCATAGCTGGGCTATGGCTTCGGAGAAATGTGATTTGTGC
1 TTCCGTATAAGACCATAGCTGGGATATGGCATC-GAG---TGTGATATGTGC
* *
54457093 TTCCGTATAAGACCATATCCGGGATATGGCATCG-GTGTGATATGTGC
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
* *
54457140 TACCGTATAAGACCATATCTGGGATATGGCATC-AGTGTGATATGTG-
1 TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
* * * *
54457186 ATCCGTGTAAGACCATGGCTGGGCTATGGC
1 TTCCGTATAAGACCATAGCTGGGATATGGC
54457216 CTCGGTATGT
Statistics
Matches: 109, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
46 24 0.22
47 54 0.50
50 1 0.01
51 1 0.01
52 29 0.27
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (48 bp):
TTCCGTATAAGACCATAGCTGGGATATGGCATCGAGTGTGATATGTGC
Found at i:54464405 original size:3 final size:3
Alignment explanation
Indices: 54464397--54464424 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
54464387 AGAACAAAAG
54464397 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
54464425 AAGAGAAGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:54476564 original size:15 final size:15
Alignment explanation
Indices: 54476541--54476580 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
54476531 TCAAATTGAA
* *
54476541 TATTTTTTATATTATT
1 TATTTTTAATA-TAAT
54476557 TATTTTTAATATAAT
1 TATTTTTAATATAAT
54476572 TATTTTTAA
1 TATTTTTAA
54476581 ATTTATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTTTAATATAAT
Found at i:54476948 original size:12 final size:11
Alignment explanation
Indices: 54476928--54476953 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
54476918 AATACTACTC
54476928 AAAATAAAAAA
1 AAAATAAAAAA
54476939 AAAATAAAAAA
1 AAAATAAAAAA
54476950 AAAA
1 AAAA
54476954 CTGTAAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAATAAAAAA
Found at i:54482445 original size:14 final size:14
Alignment explanation
Indices: 54482401--54482453 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
54482391 GAGTTATAAA
* *
54482401 TTTAATATTTATAT
1 TTTAATTTTTATTT
54482415 TTTAATTTGATTA-TT
1 TTTAATTT--TTATTT
54482430 TTTAATTTTTATTT
1 TTTAATTTTTATTT
54482444 TTTGAATTTT
1 TTT-AATTTT
54482454 AAAACCTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
13 3 0.09
14 12 0.36
15 15 0.45
16 3 0.09
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (14 bp):
TTTAATTTTTATTT
Found at i:54487412 original size:2 final size:2
Alignment explanation
Indices: 54487405--54487522 Score: 236
Period size: 2 Copynumber: 59.0 Consensus size: 2
54487395 CAACAGGCTC
54487405 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
54487447 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
54487489 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
54487523 ATCAAAGAAT
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 116 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:54498744 original size:23 final size:23
Alignment explanation
Indices: 54498714--54498772 Score: 118
Period size: 23 Copynumber: 2.6 Consensus size: 23
54498704 CTAATAAACA
54498714 TATGTTCATAACACGAGAGTGTT
1 TATGTTCATAACACGAGAGTGTT
54498737 TATGTTCATAACACGAGAGTGTT
1 TATGTTCATAACACGAGAGTGTT
54498760 TATGTTCATAACA
1 TATGTTCATAACA
54498773 AGTAAATTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.36
Consensus pattern (23 bp):
TATGTTCATAACACGAGAGTGTT
Found at i:54506820 original size:12 final size:12
Alignment explanation
Indices: 54506805--54506830 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54506795 AGAAGAAGAA
54506805 GATGATGATGAC
1 GATGATGATGAC
54506817 GATGATGATGAC
1 GATGATGATGAC
54506829 GA
1 GA
54506831 CGACGACGAC
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:0.35, C:0.08, G:0.35, T:0.23
Consensus pattern (12 bp):
GATGATGATGAC
Found at i:54508233 original size:15 final size:16
Alignment explanation
Indices: 54508201--54508245 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
54508191 CAAAAACATA
54508201 TTATTTAATAATACTT
1 TTATTTAATAATACTT
54508217 TTATTTAA-AATA-TT
1 TTATTTAATAATACTT
*
54508231 TT-TTAAAATAATACT
1 TTATT-TAATAATACT
54508246 AAATTGACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
13 2 0.08
14 6 0.24
15 8 0.32
16 9 0.36
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATTTAATAATACTT
Found at i:54510722 original size:21 final size:21
Alignment explanation
Indices: 54510688--54510744 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
54510678 TGAGTGATAC
*
54510688 TTTAA-TTT-ATTTATTCAAA
1 TTTAATTTTCATTTATGCAAA
54510707 TTTAATTTTCATTTATGCAAA
1 TTTAATTTTCATTTATGCAAA
*
54510728 TTTAATTTTCAGTTATG
1 TTTAATTTTCATTTATG
54510745 ATGTTTGCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.15
20 3 0.09
21 26 0.76
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (21 bp):
TTTAATTTTCATTTATGCAAA
Found at i:54513664 original size:30 final size:30
Alignment explanation
Indices: 54513580--54513667 Score: 117
Period size: 30 Copynumber: 2.9 Consensus size: 30
54513570 ACGACGACGC
* *
54513580 AGGCCTATCAACAGCGCCCACACAATCAGA
1 AGGCCCATCAACAGCGCCCATACAATCAGA
54513610 AGGCCCATCAACAGCGCCCATACAATCAGCA
1 AGGCCCATCAACAGCGCCCATACAATCAG-A
*
54513641 A-GCTCATCAACAGCGCCGC-TACAATCA
1 AGGCCCATCAACAGCGCC-CATACAATCA
54513668 CCGGGCCCAA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
30 50 0.94
31 3 0.06
ACGTcount: A:0.35, C:0.38, G:0.16, T:0.11
Consensus pattern (30 bp):
AGGCCCATCAACAGCGCCCATACAATCAGA
Found at i:54513754 original size:18 final size:18
Alignment explanation
Indices: 54513733--54513775 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
54513723 TGCCAGGTAC
*
54513733 GTATCCTATCCCTTATAT
1 GTATCCTAACCCTTATAT
*
54513751 GTATCCTAACCCTTTTAT
1 GTATCCTAACCCTTATAT
*
54513769 GTTTCCT
1 GTATCCT
54513776 TTTCTTAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.07, T:0.47
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:54517061 original size:19 final size:19
Alignment explanation
Indices: 54517039--54517077 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
54517029 TTTTAAATAG
*
54517039 ATACACATGTATTAATAAT
1 ATACACATGTATAAATAAT
54517058 ATACACATGTATAAATAAT
1 ATACACATGTATAAATAAT
54517077 A
1 A
54517078 AATAAGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.33
Consensus pattern (19 bp):
ATACACATGTATAAATAAT
Found at i:54517971 original size:15 final size:15
Alignment explanation
Indices: 54517923--54517972 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
54517913 TTTATCAAAT
54517923 TTATATTGATTGAAA
1 TTATATTGATTGAAA
* * *
54517938 TCATTTTGATTGAAT
1 TTATATTGATTGAAA
54517953 TTATATTGATTGAAA
1 TTATATTGATTGAAA
54517968 TTATA
1 TTATA
54517973 ATATATATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (15 bp):
TTATATTGATTGAAA
Found at i:54518632 original size:18 final size:19
Alignment explanation
Indices: 54518609--54518649 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
54518599 AATGAAATGA
54518609 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
54518627 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
54518646 GAAA
1 GAAA
54518650 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:54518647 original size:13 final size:13
Alignment explanation
Indices: 54518597--54518636 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
54518587 TTGAGCTATT
54518597 AGAA-TGAAA-TG
1 AGAATTGAAATTG
54518608 AGAAATTG-AATTG
1 AG-AATTGAAATTG
54518621 AGAATTGAAATTG
1 AGAATTGAAATTG
54518634 AGA
1 AGA
54518637 TATGAGATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.08
12 9 0.36
13 14 0.56
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (13 bp):
AGAATTGAAATTG
Found at i:54521170 original size:126 final size:126
Alignment explanation
Indices: 54521020--54521391 Score: 681
Period size: 126 Copynumber: 3.0 Consensus size: 126
54521010 ATAGCCTCAG
* *
54521020 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCATGTGGGAGCTTTTTTCTGAAATTTTGCTGA
1 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
*
54521085 CAGTGCATCCTGCTTAAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
66 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
*
54521146 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTTCACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
1 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
*
54521211 TAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
66 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
* *
54521272 TTTTTCTACGAACTATTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCAAAATTTTGCTGA
1 TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
54521337 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCA
66 CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCA
54521392 ATTAACCTAA
Statistics
Matches: 237, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
126 237 1.00
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.35
Consensus pattern (126 bp):
TTTTTCTACGAACTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTTTTTCCGAAATTTTGCTGA
CAGTGCATCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTACTCAGAATTA
Found at i:54521537 original size:19 final size:19
Alignment explanation
Indices: 54521513--54521585 Score: 58
Period size: 19 Copynumber: 3.8 Consensus size: 19
54521503 ACCATTATGT
54521513 ATCAATTAACCCTAAATTA
1 ATCAATTAACCCTAAATTA
* * * *
54521532 ATCAATTGACGCTCATTTA
1 ATCAATTAACCCTAAATTA
*
54521551 ATCGAA-TAACCCTAATTTA
1 ATC-AATTAACCCTAAATTA
* * *
54521570 ATTAACTAACCATAAA
1 ATCAATTAACCCTAAA
54521586 CCCTAAACTC
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
18 2 0.05
19 38 0.90
20 2 0.05
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.32
Consensus pattern (19 bp):
ATCAATTAACCCTAAATTA
Found at i:54521693 original size:21 final size:21
Alignment explanation
Indices: 54521649--54521700 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
54521639 ATTAACCCTA
*
54521649 AAATCCTAAACCACTAACTAT
1 AAATCCTAAACCACTAACCAT
*
54521670 AAATCCTAAACCACTAACCGT
1 AAATCCTAAACCACTAACCAT
*
54521691 AAACCCTAAA
1 AAATCCTAAA
54521701 ATAACTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.48, C:0.31, G:0.02, T:0.19
Consensus pattern (21 bp):
AAATCCTAAACCACTAACCAT
Found at i:54522446 original size:6 final size:6
Alignment explanation
Indices: 54522429--54522458 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
54522419 CAAATATAAC
*
54522429 ATGAAT AAGAAT ATGAAT ATGAAT ATGAAT
1 ATGAAT ATGAAT ATGAAT ATGAAT ATGAAT
54522459 GCATTAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (6 bp):
ATGAAT
Found at i:54523510 original size:6 final size:6
Alignment explanation
Indices: 54523501--54523532 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
54523491 TTTTTCTTTT
*
54523501 TCTGTT TCTGTC TCTGTC TCTGTC TCTGTC TC
1 TCTGTC TCTGTC TCTGTC TCTGTC TCTGTC TC
54523533 AACATGTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.31, G:0.16, T:0.53
Consensus pattern (6 bp):
TCTGTC
Found at i:54523962 original size:14 final size:14
Alignment explanation
Indices: 54523943--54523970 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
54523933 TTTTATATAT
54523943 TCTACAATTATTAA
1 TCTACAATTATTAA
54523957 TCTACAATTATTAA
1 TCTACAATTATTAA
54523971 ATAAATAATG
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:0.00, T:0.43
Consensus pattern (14 bp):
TCTACAATTATTAA
Found at i:54524915 original size:21 final size:21
Alignment explanation
Indices: 54524886--54524926 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54524876 AAAAAAAAAT
*
54524886 TCTAAAACTGAAGACTTATTA
1 TCTAAAACTAAAGACTTATTA
*
54524907 TCTATAACTAAAGACTTATT
1 TCTAAAACTAAAGACTTATT
54524927 GAACAATGGA
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:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (21 bp):
TCTAAAACTAAAGACTTATTA
Found at i:54535008 original size:4 final size:4
Alignment explanation
Indices: 54534999--54535034 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
54534989 TTCATTATTT
*
54534999 TTAA TTAA TTAA TTAA TTAA TTAA TTAG TTAA TTAA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA
54535035 ATTGAACATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:54535195 original size:28 final size:28
Alignment explanation
Indices: 54535164--54535228 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
54535154 CGTTTGACAA
54535164 GTACCAAATCAAACAAAAAAAAGATTAG
1 GTACCAAATCAAACAAAAAAAAGATTAG
*** *
54535192 GTACCAAATTGGACAAAAAAAAGTTTAG
1 GTACCAAATCAAACAAAAAAAAGATTAG
54535220 GTACCAAAT
1 GTACCAAAT
54535229 TAGGAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.54, C:0.14, G:0.14, T:0.18
Consensus pattern (28 bp):
GTACCAAATCAAACAAAAAAAAGATTAG
Found at i:54535229 original size:28 final size:29
Alignment explanation
Indices: 54535176--54535296 Score: 137
Period size: 28 Copynumber: 4.2 Consensus size: 29
54535166 ACCAAATCAA
*
54535176 ACAAAAAAAAGATTAGGTACCAAATT-GG
1 ACAAAAAAAAGTTTAGGTACCAAATTAGG
54535204 ACAAAAAAAAGTTTAGGTACCAAATTAGG
1 ACAAAAAAAAGTTTAGGTACCAAATTAGG
*
54535233 A-AAAAAGTGTCAAGTTT-GGATACCAAATT-GG
1 ACAAAAA----AAAGTTTAGG-TACCAAATTAGG
54535264 AC-AAAAAAAGTTTAGGTACCAAATTAGG
1 ACAAAAAAAAGTTTAGGTACCAAATTAGG
54535292 A-AAAA
1 ACAAAA
54535297 GTGTCAAGTT
Statistics
Matches: 80, Mismatches: 3, Indels: 20
0.78 0.03 0.19
Matches are distributed among these distances:
27 15 0.19
28 38 0.47
29 3 0.04
31 9 0.11
32 15 0.19
ACGTcount: A:0.51, C:0.10, G:0.18, T:0.21
Consensus pattern (29 bp):
ACAAAAAAAAGTTTAGGTACCAAATTAGG
Found at i:54535257 original size:32 final size:32
Alignment explanation
Indices: 54535212--54535306 Score: 116
Period size: 32 Copynumber: 3.2 Consensus size: 32
54535202 GGACAAAAAA
54535212 AAGTTTAGGTACCAAATTAGGAAAAAAGTGTC
1 AAGTTTAGGTACCAAATTAGGAAAAAAGTGTC
54535244 AAGTTT-GGATACCAAATT-GGACAAAAA-----
1 AAGTTTAGG-TACCAAATTAGGA-AAAAAGTGTC
54535271 AAGTTTAGGTACCAAATTAGG-AAAAAGTGTC
1 AAGTTTAGGTACCAAATTAGGAAAAAAGTGTC
54535302 AAGTT
1 AAGTT
54535307 CAAGTATCAA
Statistics
Matches: 54, Mismatches: 0, Indels: 19
0.74 0.00 0.26
Matches are distributed among these distances:
26 5 0.09
27 15 0.28
28 4 0.07
31 10 0.19
32 20 0.37
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.25
Consensus pattern (32 bp):
AAGTTTAGGTACCAAATTAGGAAAAAAGTGTC
Found at i:54535303 original size:58 final size:60
Alignment explanation
Indices: 54535193--54535306 Score: 214
Period size: 59 Copynumber: 1.9 Consensus size: 60
54535183 AAAGATTAGG
54535193 TACCAAATTGGACAAAAAAAAGTTTAGGTACCAAATTAGGAAAAAAGTGTCAAGTTTGGA
1 TACCAAATTGGACAAAAAAAAGTTTAGGTACCAAATTAGGAAAAAAGTGTCAAGTTTGGA
54535253 TACCAAATTGGAC-AAAAAAAGTTTAGGTACCAAATTAGG-AAAAAGTGTCAAGTT
1 TACCAAATTGGACAAAAAAAAGTTTAGGTACCAAATTAGGAAAAAAGTGTCAAGTT
54535307 CAAGTATCAA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
58 15 0.28
59 26 0.48
60 13 0.24
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.24
Consensus pattern (60 bp):
TACCAAATTGGACAAAAAAAAGTTTAGGTACCAAATTAGGAAAAAAGTGTCAAGTTTGGA
Found at i:54535710 original size:19 final size:20
Alignment explanation
Indices: 54535706--54535770 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 20
54535696 ACCCAAAAGA
54535706 AAAAAGAAAAAAACCTAACCC
1 AAAAA-AAAAAAACCTAACCC
54535727 -AAAAAAAAAAACCTAACCCCCCC
1 AAAAAAAAAAAACCTAA----CCC
54535750 AAAAAAAGAAAAACCTAACCC
1 AAAAAAA-AAAAACCTAACCC
54535771 TCCAAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
19 12 0.32
20 4 0.11
21 3 0.08
23 3 0.08
24 6 0.16
25 10 0.26
ACGTcount: A:0.63, C:0.29, G:0.03, T:0.05
Consensus pattern (20 bp):
AAAAAAAAAAAACCTAACCC
Found at i:54535716 original size:27 final size:27
Alignment explanation
Indices: 54535685--54535737 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
54535675 AGCCCTCCCA
*
54535685 AAAAAAACCTAACCCAAAAGAAAAAAG
1 AAAAAAACCTAACCCAAAAAAAAAAAG
54535712 AAAAAAACCTAACCCAAAAAAAAAAA
1 AAAAAAACCTAACCCAAAAAAAAAAA
54535738 CCTAACCCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.74, C:0.19, G:0.04, T:0.04
Consensus pattern (27 bp):
AAAAAAACCTAACCCAAAAAAAAAAAG
Found at i:54535755 original size:25 final size:24
Alignment explanation
Indices: 54535705--54535780 Score: 81
Period size: 25 Copynumber: 3.3 Consensus size: 24
54535695 AACCCAAAAG
54535705 AAAAAAGAAAAAAACCTAA---CCC
1 AAAAAA-AAAAAAACCTAACCCCCC
54535727 --AAAAAAAAAAACCTAACCCCCCC
1 AAAAAAAAAAAAACCTAA-CCCCCC
* *
54535750 AAAAAAAGAAAAACCTAACCCTCC
1 AAAAAAAAAAAAACCTAACCCCCC
54535774 AAAAAAA
1 AAAAAAA
54535781 TCAAGAAACC
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
19 12 0.26
20 4 0.09
23 3 0.07
24 12 0.26
25 15 0.33
ACGTcount: A:0.64, C:0.28, G:0.03, T:0.05
Consensus pattern (24 bp):
AAAAAAAAAAAAACCTAACCCCCC
Found at i:54535775 original size:24 final size:24
Alignment explanation
Indices: 54535727--54535780 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
54535717 AACCTAACCC
54535727 AAAAAAAAAAACCTAACCCCCCCA
1 AAAAAAAAAAACCTAACCCCCCCA
*
54535751 AAAAAAGAAAAACCTAA-CCCTCCA
1 AAAAAA-AAAAACCTAACCCCCCCA
54535775 AAAAAA
1 AAAAAA
54535781 TCAAGAAACC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 18 0.64
25 10 0.36
ACGTcount: A:0.63, C:0.30, G:0.02, T:0.06
Consensus pattern (24 bp):
AAAAAAAAAAACCTAACCCCCCCA
Found at i:54535778 original size:44 final size:45
Alignment explanation
Indices: 54535677--54535780 Score: 113
Period size: 44 Copynumber: 2.3 Consensus size: 45
54535667 GCCCATTAAG
54535677 CCCTCCCAAAAAAAACCTAACCCAAAAGAAAAAAGAAAAAAACCTAA
1 CCCT-CCAAAAAAAACCTAACCCAAAAGAAAAAAG-AAAAAACCTAA
*** ***
54535724 CCCAAAAAAAAAAACCTAACCCCCCCA-AAAAAAG-AAAAACCTAA
1 CCCTCCAAAAAAAACCTAA-CCCAAAAGAAAAAAGAAAAAACCTAA
54535768 CCCTCCAAAAAAA
1 CCCTCCAAAAAAA
54535781 TCAAGAAACC
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
44 20 0.43
46 20 0.43
47 7 0.15
ACGTcount: A:0.61, C:0.31, G:0.03, T:0.06
Consensus pattern (45 bp):
CCCTCCAAAAAAAACCTAACCCAAAAGAAAAAAGAAAAAACCTAA
Found at i:54536230 original size:22 final size:22
Alignment explanation
Indices: 54536200--54536249 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
54536190 TCCTTTTCCC
*
54536200 CCCTCCCTTCTCTCTTCTTTCT
1 CCCTTCCTTCTCTCTTCTTTCT
* * *
54536222 CCCTTCCTTTTTTTTTCTTTCT
1 CCCTTCCTTCTCTCTTCTTTCT
*
54536244 CTCTTC
1 CCCTTC
54536250 AAAATGATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (22 bp):
CCCTTCCTTCTCTCTTCTTTCT
Found at i:54538673 original size:25 final size:25
Alignment explanation
Indices: 54538636--54538743 Score: 164
Period size: 25 Copynumber: 4.3 Consensus size: 25
54538626 CCTCAGCGTT
54538636 CTCTCT-AATTATTAGCACGCCAATG
1 CTCTCTGAA-TATTAGCACGCCAATG
*
54538661 CTCTCTGAATATTAGCACGCCAGTG
1 CTCTCTGAATATTAGCACGCCAATG
*
54538686 CTCTCTGAATATTAGCAAGCCAATG
1 CTCTCTGAATATTAGCACGCCAATG
* *
54538711 CTCTCTGATTATTAGCATGCCAATG
1 CTCTCTGAATATTAGCACGCCAATG
54538736 CTCTCTGA
1 CTCTCTGA
54538744 CTAGCACATT
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
25 75 0.97
26 2 0.03
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (25 bp):
CTCTCTGAATATTAGCACGCCAATG
Found at i:54538770 original size:22 final size:24
Alignment explanation
Indices: 54538736--54538785 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
54538726 CATGCCAATG
*
54538736 CTCTCTGACTAGCACATT-TGTGCT
1 CTCTCTGACTAGCAC-TTCAGTGCT
54538760 CTCTCT-A-TAGCACTTCAGTGCT
1 CTCTCTGACTAGCACTTCAGTGCT
54538782 CTCT
1 CTCT
54538786 GTTCATTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 2 0.08
22 15 0.62
23 1 0.04
24 6 0.25
ACGTcount: A:0.16, C:0.32, G:0.14, T:0.38
Consensus pattern (24 bp):
CTCTCTGACTAGCACTTCAGTGCT
Found at i:54539619 original size:23 final size:24
Alignment explanation
Indices: 54539579--54539630 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
54539569 GGTACATTTG
**
54539579 TAATTTAAATATTTAAATA-CTTA
1 TAATTTAAATATAAAAATATCTTA
* *
54539602 TAATTTAAGTATAAAAATATTTTA
1 TAATTTAAATATAAAAATATCTTA
54539626 TAATT
1 TAATT
54539631 ATTAATTGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
TAATTTAAATATAAAAATATCTTA
Found at i:54539786 original size:16 final size:16
Alignment explanation
Indices: 54539765--54539795 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54539755 GATATTTTAA
54539765 TATATTATATTAATAT
1 TATATTATATTAATAT
*
54539781 TATATTATGTTAATA
1 TATATTATATTAATA
54539796 AAATAATAAA
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:0.03, T:0.55
Consensus pattern (16 bp):
TATATTATATTAATAT
Found at i:54545115 original size:13 final size:13
Alignment explanation
Indices: 54545097--54545123 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
54545087 CTGTTTTGGG
54545097 TAGCAGCAGTAGT
1 TAGCAGCAGTAGT
54545110 TAGCAGCAGTAGT
1 TAGCAGCAGTAGT
54545123 T
1 T
54545124 TAACTTTGAA
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:0.30, C:0.15, G:0.30, T:0.26
Consensus pattern (13 bp):
TAGCAGCAGTAGT
Found at i:54545528 original size:26 final size:26
Alignment explanation
Indices: 54545499--54545552 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
54545489 TTTAAAGAAT
54545499 AAACTGTACTTATTGGGTAAACCAAA
1 AAACTGTACTTATTGGGTAAACCAAA
54545525 AAACTGTACTTATTGGGTAAACCAAA
1 AAACTGTACTTATTGGGTAAACCAAA
54545551 AA
1 AA
54545553 TTCTGAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (26 bp):
AAACTGTACTTATTGGGTAAACCAAA
Found at i:54546394 original size:292 final size:292
Alignment explanation
Indices: 54545870--54546399 Score: 1060
Period size: 292 Copynumber: 1.8 Consensus size: 292
54545860 AATGTCAAAG
54545870 ATGACTAAATTGAAGGGAATGAATTGTTTTATTATCTAAATTAATAAATTGAATGAAATTATCAA
1 ATGACTAAATTGAAGGGAATGAATTGTTTTATTATCTAAATTAATAAATTGAATGAAATTATCAA
54545935 TTTAAGATTGGGTGAAATTTGGGAAAATAGTAAATTACCAATATGCCCCTAAATCTTGGTATTTC
66 TTTAAGATTGGGTGAAATTTGGGAAAATAGTAAATTACCAATATGCCCCTAAATCTTGGTATTTC
54546000 TGCAGTTTGGTCAGGTAGGTTCGTATATCTTGAATGAGCATGTAAGTATGACAATTTAAATATTG
131 TGCAGTTTGGTCAGGTAGGTTCGTATATCTTGAATGAGCATGTAAGTATGACAATTTAAATATTG
54546065 TATTGTATTTTATATGATGTTTGAATTGAATATTTGAAAAGGAATACCAAGATTAATAAATTGAA
196 TATTGTATTTTATATGATGTTTGAATTGAATATTTGAAAAGGAATACCAAGATTAATAAATTGAA
54546130 TTGTATTGTATTGTATTGTATTTAAATTTTAT
261 TTGTATTGTATTGTATTGTATTTAAATTTTAT
54546162 ATGACTAAATTGAAGGGAATGAATTGTTTTATTATCTAAATTAATAAATTGAATGAAATTATCAA
1 ATGACTAAATTGAAGGGAATGAATTGTTTTATTATCTAAATTAATAAATTGAATGAAATTATCAA
54546227 TTTAAGATTGGGTGAAATTTGGGAAAATAGTAAATTACCAATATGCCCCTAAATCTTGGTATTTC
66 TTTAAGATTGGGTGAAATTTGGGAAAATAGTAAATTACCAATATGCCCCTAAATCTTGGTATTTC
54546292 TGCAGTTTGGTCAGGTAGGTTCGTATATCTTGAATGAGCATGTAAGTATGACAATTTAAATATTG
131 TGCAGTTTGGTCAGGTAGGTTCGTATATCTTGAATGAGCATGTAAGTATGACAATTTAAATATTG
54546357 TATTGTATTTTATATGATGTTTGAATTGAATATTTGAAAAGGA
196 TATTGTATTTTATATGATGTTTGAATTGAATATTTGAAAAGGA
54546400 TGTTACATGA
Statistics
Matches: 238, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
292 238 1.00
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (292 bp):
ATGACTAAATTGAAGGGAATGAATTGTTTTATTATCTAAATTAATAAATTGAATGAAATTATCAA
TTTAAGATTGGGTGAAATTTGGGAAAATAGTAAATTACCAATATGCCCCTAAATCTTGGTATTTC
TGCAGTTTGGTCAGGTAGGTTCGTATATCTTGAATGAGCATGTAAGTATGACAATTTAAATATTG
TATTGTATTTTATATGATGTTTGAATTGAATATTTGAAAAGGAATACCAAGATTAATAAATTGAA
TTGTATTGTATTGTATTGTATTTAAATTTTAT
Found at i:54549705 original size:15 final size:14
Alignment explanation
Indices: 54549685--54549727 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
54549675 ATGTCTTATT
54549685 TAATTATAAAAATTA
1 TAATTA-AAAAATTA
*
54549700 TAATTAAACAATTATA
1 TAATTAAA-AAAT-TA
54549716 TAATTAAAAAAT
1 TAATTAAAAAAT
54549728 AAATTAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 2 0.08
15 12 0.50
16 10 0.42
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (14 bp):
TAATTAAAAAATTA
Found at i:54556820 original size:21 final size:21
Alignment explanation
Indices: 54556796--54556845 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
54556786 CATTGTTTCT
* *
54556796 AATCTCACTGCTACAATATCC
1 AATCTCACCGCTACAATAACC
*
54556817 AATCTCACCGCTACAATAACT
1 AATCTCACCGCTACAATAACC
54556838 AATCTCAC
1 AATCTCAC
54556846 AGCCACCGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.36, C:0.34, G:0.04, T:0.26
Consensus pattern (21 bp):
AATCTCACCGCTACAATAACC
Found at i:54557159 original size:11 final size:11
Alignment explanation
Indices: 54557143--54557174 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
54557133 GAATAAATAA
54557143 ATTAAAAAATT
1 ATTAAAAAATT
54557154 ATTAAAAAA--
1 ATTAAAAAATT
54557163 ATTAAAAAATT
1 ATTAAAAAATT
54557174 A
1 A
54557175 AAAATACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.47
11 10 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
ATTAAAAAATT
Found at i:54557164 original size:20 final size:20
Alignment explanation
Indices: 54557136--54557174 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
54557126 CTTATTAGAA
*
54557136 TAAATAAATTAAAAAATTAT
1 TAAAAAAATTAAAAAATTAT
54557156 TAAAAAAATTAAAAAATTA
1 TAAAAAAATTAAAAAATTA
54557175 AAAATACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAAAAAATTAAAAAATTAT
Found at i:54557166 original size:9 final size:9
Alignment explanation
Indices: 54557136--54557178 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
54557126 CTTATTAGAA
*
54557136 TAAATAAAT
1 TAAAAAAAT
54557145 TAAAAAATTAT
1 TAAAAAA--AT
54557156 TAAAAAAAT
1 TAAAAAAAT
54557165 T-AAAAAAT
1 TAAAAAAAT
54557173 TAAAAA
1 TAAAAA
54557179 TACATAATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
8 8 0.27
9 13 0.43
11 9 0.30
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
TAAAAAAAT
Found at i:54562390 original size:16 final size:14
Alignment explanation
Indices: 54562359--54562393 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
54562349 ATGTACTGAA
54562359 TTTATTATATTAAT
1 TTTATTATATTAAT
54562373 TTTATGTATATATAAT
1 TTTAT-TATAT-TAAT
54562389 TTTAT
1 TTTAT
54562394 ATTAGAGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
15 5 0.26
16 9 0.47
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (14 bp):
TTTATTATATTAAT
Found at i:54575329 original size:22 final size:20
Alignment explanation
Indices: 54575281--54575321 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
54575271 TTTTTTTTCT
*
54575281 TTTTTTAAATTGTTTTTATTTA
1 TTTTTT-AATT-TTTTAATTTA
54575303 TTTTTTAATTTTTTAATTT
1 TTTTTTAATTTTTTAATTT
54575322 CCATTTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 4 0.22
22 6 0.33
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTTTTAATTTTTTAATTTA
Found at i:54575447 original size:27 final size:27
Alignment explanation
Indices: 54575417--54575471 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
54575407 TTTTAATTGT
54575417 TGGTTTCAGTTTTTCTTTTATTTTTAA
1 TGGTTTCAGTTTTTCTTTTATTTTTAA
* *
54575444 TGGTTTCATTTTTTCTTTTCTTTTTAA
1 TGGTTTCAGTTTTTCTTTTATTTTTAA
54575471 T
1 T
54575472 TTTTCCCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.13, C:0.09, G:0.09, T:0.69
Consensus pattern (27 bp):
TGGTTTCAGTTTTTCTTTTATTTTTAA
Found at i:54584881 original size:18 final size:18
Alignment explanation
Indices: 54584854--54584946 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
54584844 TACGACCGTT
54584854 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
54584872 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
54584890 TACAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
54584908 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
54584926 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
54584944 TAC
1 TAC
54584947 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:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:54590228 original size:25 final size:25
Alignment explanation
Indices: 54590194--54590243 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
54590184 TTTTCGGATT
54590194 TTCTTTATTCAATTTGTATAAATTA
1 TTCTTTATTCAATTTGTATAAATTA
54590219 TTCTTTATTCAATTTGTATAAATTA
1 TTCTTTATTCAATTTGTATAAATTA
54590244 CTATGTGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (25 bp):
TTCTTTATTCAATTTGTATAAATTA
Found at i:54593173 original size:2 final size:2
Alignment explanation
Indices: 54593166--54593197 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
54593156 TGGTGGAAGG
*
54593166 GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
54593198 TGGAAGTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:54594656 original size:21 final size:21
Alignment explanation
Indices: 54594632--54594684 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
54594622 CATTGTTTCT
* *
54594632 AATCTCACCGCTACAGTACCC
1 AATCTCACCGCTACAGGAACC
*
54594653 AATCTCACCGCTACAGGAACT
1 AATCTCACCGCTACAGGAACC
54594674 AATCTCACCGC
1 AATCTCACCGC
54594685 CACCACTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.40, G:0.11, T:0.19
Consensus pattern (21 bp):
AATCTCACCGCTACAGGAACC
Found at i:54610300 original size:19 final size:19
Alignment explanation
Indices: 54610276--54610319 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
54610266 TTAATTTTAT
*
54610276 TATTAATTAAG-TAATAATA
1 TATTAA-TAAGATAATAAAA
54610295 TATTAATAAGATAATAAAA
1 TATTAATAAGATAATAAAA
54610314 TATTAA
1 TATTAA
54610320 AATATTTAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (19 bp):
TATTAATAAGATAATAAAA
Found at i:54627605 original size:135 final size:134
Alignment explanation
Indices: 54627363--54627635 Score: 492
Period size: 135 Copynumber: 2.0 Consensus size: 134
54627353 GAAGACGTAC
54627363 CTCTGTTCTTTGTTTCCGTTCATGATTAACAAAAGCAAGGGTTGTATCAAAATCTTGCTGAAGAA
1 CTCTGTTCTTTGTTTCCGTTCATGATTAACAAAAGCAAGGGTTGTATCAAAATCTTGCTGAAGAA
*
54627428 ATCTCCTACAAAAATATACACATTTTAAGCACAAGGAAAAGAACTCAATAATAAAATTATTGAGT
66 ACCTCCTACAAAAATATACACATTTTAAGCACAAGGAAAAGAACTC-ATAATAAAATTATTGAGT
54627493 TTCAA
130 TTCAA
*
54627498 CTCTGTTCTTTGTTTCCTTTCATGATTAACAAAAGCAAGGGTTGTATCAAAATCTTGCTGAAGAA
1 CTCTGTTCTTTGTTTCCGTTCATGATTAACAAAAGCAAGGGTTGTATCAAAATCTTGCTGAAGAA
* * *
54627563 ACCTCCTACAGAAATATACACATTTTAAGCACAAGGAAAAGAACTCATACTAAGATTATTGAGTT
66 ACCTCCTACAAAAATATACACATTTTAAGCACAAGGAAAAGAACTCATAATAAAATTATTGAGTT
54627628 TCAA
131 TCAA
54627632 CTCT
1 CTCT
54627636 TCAGCAGACA
Statistics
Matches: 133, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
134 25 0.19
135 108 0.81
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.32
Consensus pattern (134 bp):
CTCTGTTCTTTGTTTCCGTTCATGATTAACAAAAGCAAGGGTTGTATCAAAATCTTGCTGAAGAA
ACCTCCTACAAAAATATACACATTTTAAGCACAAGGAAAAGAACTCATAATAAAATTATTGAGTT
TCAA
Found at i:54636244 original size:21 final size:21
Alignment explanation
Indices: 54636218--54636260 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
54636208 AGCAATAAGC
54636218 ATTTGTTTCAATTAACTCATG
1 ATTTGTTTCAATTAACTCATG
54636239 ATTTGTTTCAATTAACTCATG
1 ATTTGTTTCAATTAACTCATG
54636260 A
1 A
54636261 AAGCAAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.47
Consensus pattern (21 bp):
ATTTGTTTCAATTAACTCATG
Found at i:54639714 original size:19 final size:19
Alignment explanation
Indices: 54639687--54639768 Score: 69
Period size: 19 Copynumber: 4.3 Consensus size: 19
54639677 AAAAAATATA
* *
54639687 TATATAAATTGTAAAATTT
1 TATAAAAATTATAAAATTT
* **
54639706 TATAAAAATCATAAAAAAT
1 TATAAAAATTATAAAATTT
*
54639725 TAT-AAAATATATAGAAA-TA
1 TATAAAAAT-TATA-AAATTT
*
54639744 TAAAAAAATTATAAAATTT
1 TATAAAAATTATAAAATTT
54639763 TATAAA
1 TATAAA
54639769 GTTGTAAGAA
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
18 8 0.17
19 32 0.67
20 8 0.17
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.35
Consensus pattern (19 bp):
TATAAAAATTATAAAATTT
Found at i:54639759 original size:57 final size:58
Alignment explanation
Indices: 54639692--54639806 Score: 153
Period size: 57 Copynumber: 2.0 Consensus size: 58
54639682 ATATATATAT
* *
54639692 AAATTGTAAAATTTTATAAAAATCATAA-AAAATTAT-AAAATATATAGAAATATAAAA
1 AAATTATAAAATTTTAT-AAAATCATAAGAAAATTATAAAAATATAAAGAAATATAAAA
* **
54639749 AAATTATAAAATTTTATAAAGTTGTAAGAAAATTATACAAAATATAAAGAAATATAAA
1 AAATTATAAAATTTTATAAAATCATAAGAAAATTATA-AAAATATAAAGAAATATAAA
54639807 TTTTGTAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
56 7 0.14
57 24 0.48
59 19 0.38
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (58 bp):
AAATTATAAAATTTTATAAAATCATAAGAAAATTATAAAAATATAAAGAAATATAAAA
Found at i:54639816 original size:57 final size:52
Alignment explanation
Indices: 54639688--54639826 Score: 125
Period size: 57 Copynumber: 2.5 Consensus size: 52
54639678 AAAAATATAT
*
54639688 ATATAAATTGTAAAATTTTATAAAAATCATAAAAAATTATAAAATATATAGAA
1 ATATAAATTGTAAAATTTTAT-AAAATCATAAAAAATTATAAAATATAAAGAA
* * **
54639741 ATATAAAAAAATTATAAAATTTTATAAAGTTGTAAGAAAATTATACAAAATATAAAGAA
1 ATAT----AAATTGTAAAATTTTATAAAATCATAA-AAAATTAT--AAAATATAAAGAA
**
54639800 ATATAAATTTTGTAAAAAATTATAAAA
1 ATATAAA--TTGTAAAATTTTATAAAA
54639827 AAATATCGTA
Statistics
Matches: 68, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
53 4 0.06
55 3 0.04
56 7 0.10
57 38 0.56
59 16 0.24
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.33
Consensus pattern (52 bp):
ATATAAATTGTAAAATTTTATAAAATCATAAAAAATTATAAAATATAAAGAA
Found at i:54639825 original size:10 final size:10
Alignment explanation
Indices: 54639677--54639828 Score: 61
Period size: 10 Copynumber: 15.6 Consensus size: 10
54639667 ATTCAAATAG
54639677 AAAAAATATAT
1 AAAAAAT-TAT
* *
54639688 ATATAAATTGT
1 A-AAAAATTAT
**
54639699 AAAATTTTAT
1 AAAAAATTAT
*
54639709 -AAAAATCAT
1 AAAAAATTAT
54639718 AAAAAATTAT
1 AAAAAATTAT
*
54639728 AAAATA-TAT
1 AAAAAATTAT
*
54639737 -AGAAA-TAT
1 AAAAAATTAT
54639745 AAAAAAATTAT
1 -AAAAAATTAT
*
54639756 --AAAATTTT
1 AAAAAATTAT
* * *
54639764 ATAAAGTTGT
1 AAAAAATTAT
54639774 AAGAAAATTAT
1 AA-AAAATTAT
*
54639785 ACAAAA-TAT
1 AAAAAATTAT
54639794 AAAGAAA-TAT
1 AAA-AAATTAT
** *
54639804 -AAATTTTGT
1 AAAAAATTAT
54639813 AAAAAATTAT
1 AAAAAATTAT
54639823 AAAAAA
1 AAAAAA
54639829 ATATCGTACA
Statistics
Matches: 102, Mismatches: 28, Indels: 23
0.67 0.18 0.15
Matches are distributed among these distances:
8 14 0.14
9 18 0.18
10 51 0.50
11 14 0.14
12 5 0.05
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:54640420 original size:19 final size:21
Alignment explanation
Indices: 54640389--54640433 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
54640379 CGGGATGAGT
54640389 AAAAT-TTTAATTTCAA-AAA
1 AAAATATTTAATTTCAAGAAA
*
54640408 AAAATATTT-ATTTCAAGATA
1 AAAATATTTAATTTCAAGAAA
54640428 AAAATA
1 AAAATA
54640434 ATTAGAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (21 bp):
AAAATATTTAATTTCAAGAAA
Done.