Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007902.1 Hibiscus syriacus cultivar Beakdansim tig00110293_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 611524
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:4000 original size:27 final size:27
Alignment explanation
Indices: 3970--4049 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
3960 TTAGATATTA
3970 TATTAATATTAAATATATAAATAATAT
1 TATTAATATTAAATATATAAATAATAT
* *
3997 TATTCATTATT-AATA-ATTTAATAATAT
1 TATT-AATATTAAATATA-TAAATAATAT
** *
4024 TATTTCTATGAAAT-TATAAATAATAT
1 TATTAATATTAAATATATAAATAATAT
4050 AAATTTTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
26 13 0.30
27 25 0.58
28 5 0.12
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (27 bp):
TATTAATATTAAATATATAAATAATAT
Found at i:4063 original size:18 final size:18
Alignment explanation
Indices: 4037--4088 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 18
4027 TTCTATGAAA
*
4037 TTATAAATAATATAAATT
1 TTATTAATAATATAAATT
* *
4055 TTATTAATAATTTATATT
1 TTATTAATAATATAAATT
* * *
4073 ATATTATTAAAATAAA
1 TTATTAATAATATAAA
4089 AATATAATAT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTATTAATAATATAAATT
Found at i:4095 original size:53 final size:52
Alignment explanation
Indices: 3970--4095 Score: 128
Period size: 53 Copynumber: 2.4 Consensus size: 52
3960 TTAGATATTA
* * *
3970 TATTAATATTAAATATATAAATAATATTATTCATTATTAATAATTTAATAATAT
1 TATTAA-AATAAAAATATAAATAATATAATT-ATTATTAATAATTTAATAATAT
*** * * *
4024 TATTTCTATGAAATTATAAATAATATAAATT-TTATTAATAATTTATATTATAT
1 TATTAAAATAAAAATATAAATAATAT-AATTATTATTAATAATTTA-ATAATAT
4077 TATTAAAATAAAAATATAA
1 TATTAAAATAAAAATATAA
4096 TATCTATATT
Statistics
Matches: 56, Mismatches: 14, Indels: 5
0.75 0.19 0.07
Matches are distributed among these distances:
52 14 0.25
53 35 0.62
54 7 0.12
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.47
Consensus pattern (52 bp):
TATTAAAATAAAAATATAAATAATATAATTATTATTAATAATTTAATAATAT
Found at i:4137 original size:29 final size:30
Alignment explanation
Indices: 4105--4166 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
4095 ATATCTATAT
*
4105 TATAATATAATTGATTA-TAATATTAAAA-A
1 TATAATATAATT-ATTAGAAATATTAAAATA
*
4134 TATAATATTATTATTAGAAATATTAAAATA
1 TATAATATAATTATTAGAAATATTAAAATA
4164 TAT
1 TAT
4167 TTAAATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 4 0.14
29 21 0.72
30 4 0.14
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (30 bp):
TATAATATAATTATTAGAAATATTAAAATA
Found at i:4187 original size:47 final size:47
Alignment explanation
Indices: 4123--4217 Score: 115
Period size: 47 Copynumber: 2.0 Consensus size: 47
4113 AATTGATTAT
*
4123 AATATTAAAAATATAATATTATT-ATTAGAA-ATATTAAAATATATTTA
1 AATATTAAAAATATAATATT-TTGATTAAAAGATATTAAAATAT-TTTA
*
4170 AATATTTAATAAT-TAATATTTTGATTAAAATGATATTAAAATATTTTA
1 AATA-TTAAAAATATAATATTTTGATTAAAA-GATATTAAAATATTTTA
4218 TTAATTAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
46 2 0.05
47 17 0.40
48 11 0.26
49 12 0.29
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (47 bp):
AATATTAAAAATATAATATTTTGATTAAAAGATATTAAAATATTTTA
Found at i:9916 original size:16 final size:17
Alignment explanation
Indices: 9897--9929 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
9887 ATTTAAATAT
9897 AAAT-AAAAAATTTTAA
1 AAATGAAAAAATTTTAA
*
9913 AAATGAAAGAATTTTAA
1 AAATGAAAAAATTTTAA
9930 GCCATAGTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (17 bp):
AAATGAAAAAATTTTAA
Found at i:22870 original size:3 final size:3
Alignment explanation
Indices: 22862--23016 Score: 249
Period size: 3 Copynumber: 51.7 Consensus size: 3
22852 TTAATATATT
*
22862 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
22909 TAA TAA TAA TAA TGA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
22957 TAA TAA TAA TGA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
23003 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
23017 TAAAAAATTA
Statistics
Matches: 140, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
2 2 0.01
3 135 0.96
4 3 0.02
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:23570 original size:113 final size:113
Alignment explanation
Indices: 23331--23965 Score: 1159
Period size: 113 Copynumber: 5.6 Consensus size: 113
23321 GAATTATGCC
* * * *
23331 AAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTTTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
23395 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
23442 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
23507 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
*
23555 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTCCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
23620 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
23668 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
23733 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
23781 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
23846 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
23894 AAAAGGTTGAACAAATTCTTCTCATTATG-ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
23958 TATGAACT
66 TATGAACT
23966 CTACCTGGCA
Statistics
Matches: 512, Mismatches: 10, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
111 4 0.01
112 106 0.21
113 402 0.79
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
Found at i:24768 original size:82 final size:82
Alignment explanation
Indices: 24558--24943 Score: 603
Period size: 82 Copynumber: 4.7 Consensus size: 82
24548 ACTTCCTCAA
* * * *
24558 ATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGC
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGA
*
24623 TTGGTTCTGTTAAACCAG
66 TT-GTTCTGTCAAACCAG
* * *
24641 GTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTCTAAATTCAATGA
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGA
24706 TTGTTCTG-CTAAACCAG
66 TTGTTCTGTC-AAACCAG
24723 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGA
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGA
*
24788 TTGTTCTGTCCAACCAG
66 TTGTTCTGTCAAACCAG
* *
24805 ATCAGATAACTCAAAGAACACTTCCGGAAGATGCTATTGACAAATTCATCTTCTAAACTCAATGA
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGA
*
24870 TTGTTCTGTCCAACCAG
66 TTGTTCTGTCAAACCAG
* *
24887 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCTATTTTCTA
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTC-ATCTTCTA
24944 GTTAATGTTT
Statistics
Matches: 283, Mismatches: 16, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
82 207 0.73
83 69 0.24
84 7 0.02
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (82 bp):
ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGA
TTGTTCTGTCAAACCAG
Found at i:25727 original size:16 final size:17
Alignment explanation
Indices: 25689--25733 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
25679 AATATAAAAG
*
25689 AATAAATTGAATTTCAAA
1 AATAAATTGAATCTC-AA
25707 AATAAATTGAATCTC-A
1 AATAAATTGAATCTCAA
25723 AATAAATTGAA
1 AATAAATTGAA
25734 CTTGAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 12 0.46
18 14 0.54
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.31
Consensus pattern (17 bp):
AATAAATTGAATCTCAA
Found at i:26081 original size:16 final size:16
Alignment explanation
Indices: 26060--26094 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
26050 CCTTGACCCC
26060 TTTCTTTCTTTTTCTT
1 TTTCTTTCTTTTTCTT
*
26076 TTTCTTTTTTTTTCTT
1 TTTCTTTCTTTTTCTT
26092 TTT
1 TTT
26095 TTTTATTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTCTTTCTTTTTCTT
Found at i:26098 original size:10 final size:10
Alignment explanation
Indices: 26064--26098 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
26054 GACCCCTTTC
26064 TTTCTTTTTCTT
1 TTTC-TTTT-TT
26076 TTTCTTTTTT
1 TTTCTTTTTT
26086 TTTCTTTTTT
1 TTTCTTTTTT
26096 TTT
1 TTT
26099 ATTCTCTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 15 0.65
11 4 0.17
12 4 0.17
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:38872 original size:3 final size:3
Alignment explanation
Indices: 38857--39006 Score: 237
Period size: 3 Copynumber: 49.7 Consensus size: 3
38847 TTAATATATT
*
38857 TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
* *
38903 TAA TGA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
38951 TAA TGA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
38999 TAA TAA TA
1 TAA TAA TA
39007 TGGATAAAAA
Statistics
Matches: 134, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
3 131 0.98
4 3 0.02
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:54131 original size:21 final size:21
Alignment explanation
Indices: 54096--54136 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
54086 GTTAATGTAT
54096 TTTTAAAATATCAAAGGTTAAC
1 TTTTAAAATATCAAA-GTTAAC
*
54118 TTTTAAGA-ATCAAAGTTAA
1 TTTTAAAATATCAAAGTTAA
54137 ATTATAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (21 bp):
TTTTAAAATATCAAAGTTAAC
Found at i:55520 original size:43 final size:42
Alignment explanation
Indices: 55456--55618 Score: 168
Period size: 43 Copynumber: 3.8 Consensus size: 42
55446 AACACCCTAA
** * * *
55456 ATTTTTTCAATATCA-TATTTTATCATTAAAATTGAGGCCCCTT
1 ATTTTTTCAATCCCACT-TTTTACCATTATAATTGAGGCCTC-T
* * *
55499 ATTTTTTCAATCTCACTTTTTACCTTTATAATTGAGACCTCT
1 ATTTTTTCAATCCCACTTTTTACCATTATAATTGAGGCCTCT
* * * *
55541 AATTTTTCAATCCCACTTTTTACCTTTATAATTGAGGTCTCAA
1 ATTTTTTCAATCCCACTTTTTACCATTATAATTGAGGCCTC-T
55584 ATTTTTTCAATCCCACTTTTTA-CATTTATAATTGA
1 ATTTTTTCAATCCCACTTTTTACCA-TTATAATTGA
55619 AACTCATAAT
Statistics
Matches: 104, Mismatches: 13, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
42 39 0.38
43 64 0.62
44 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.48
Consensus pattern (42 bp):
ATTTTTTCAATCCCACTTTTTACCATTATAATTGAGGCCTCT
Found at i:55593 original size:85 final size:85
Alignment explanation
Indices: 55329--55637 Score: 299
Period size: 85 Copynumber: 3.6 Consensus size: 85
55319 GGGTCCTAAT
* * *
55329 TTTTTTCAATCAT-ACTTTTTACTTTTATAATTGATA-TTCTAATTTTTGT-AATCCCACGTTTT
1 TTTTTTCAATC-TCACTTTTTACCTTTATAATTGA-ACCTCTAATTTTT-TCAATCCCACTTTTT
* *
55391 ATCTTTATAATTTA--ACTCATAT
63 ATCTTTATAATTGAGGACTCA-AA
* * * **
55413 TTTTTTCAATATCACTTTTCACCTTTATAATTGAACACCCTAAATTTTTTCAATATCA-TATTTT
1 TTTTTTCAATCTCACTTTTTACCTTTATAATTGAAC-CTCT-AATTTTTTCAATCCCACT-TTTT
* * * * **
55477 ATCATTAAAATTGAGGCCCCTTA
63 ATCTTTATAATTGAGGACTCAAA
*
55500 TTTTTTCAATCTCACTTTTTACCTTTATAATTGAGACCTCTAA-TTTTTCAATCCCACTTTTTAC
1 TTTTTTCAATCTCACTTTTTACCTTTATAATTGA-ACCTCTAATTTTTTCAATCCCACTTTTTAT
*
55564 CTTTATAATTGAGGTCTCAAA
65 CTTTATAATTGAGGACTCAAA
* * *
55585 TTTTTTCAATCCCACTTTTTACATTTATAATTGAAACTCATAATTTTTTCAAT
1 TTTTTTCAATCTCACTTTTTACCTTTATAATTGAACCTC-TAATTTTTTCAAT
55638 ACCGTAAAAT
Statistics
Matches: 182, Mismatches: 31, Indels: 22
0.77 0.13 0.09
Matches are distributed among these distances:
83 2 0.01
84 33 0.18
85 69 0.38
86 39 0.21
87 35 0.19
88 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.04, T:0.49
Consensus pattern (85 bp):
TTTTTTCAATCTCACTTTTTACCTTTATAATTGAACCTCTAATTTTTTCAATCCCACTTTTTATC
TTTATAATTGAGGACTCAAA
Found at i:55630 original size:43 final size:43
Alignment explanation
Indices: 55329--55637 Score: 256
Period size: 42 Copynumber: 7.2 Consensus size: 43
55319 GGGTCCTAAT
** * * *
55329 TTTTTTCAATCATACTTTTTACTTTTATAATTGATATTC-TAA
1 TTTTTTCAATCCCACTTTTTACCTTTATAATTGAAACTCATAA
* * * *
55371 TTTTTGT-AATCCCACGTTTTATCTTTATAATT-TAACTCATAT
1 TTTTT-TCAATCCCACTTTTTACCTTTATAATTGAAACTCATAA
** * *
55413 TTTTTTCAATATCACTTTTCACCTTTATAATTGAACAC-CCTAAA
1 TTTTTTCAATCCCACTTTTTACCTTTATAATTGAA-ACTCAT-AA
** * * * ** * * *
55457 TTTTTTCAATATCA-TATTTTATCATTAAAATTGAGGCCCCTTA
1 TTTTTTCAATCCCACT-TTTTACCTTTATAATTGAAACTCATAA
* *
55500 TTTTTTCAATCTCACTTTTTACCTTTATAATTGAGACCTC-TAA
1 TTTTTTCAATCCCACTTTTTACCTTTATAATTGA-AACTCATAA
**
55543 -TTTTTCAATCCCACTTTTTACCTTTATAATTGAGGTCTCA-AA
1 TTTTTTCAATCCCACTTTTTACCTTTATAATTGA-AACTCATAA
*
55585 TTTTTTCAATCCCACTTTTTACATTTATAATTGAAACTCATAA
1 TTTTTTCAATCCCACTTTTTACCTTTATAATTGAAACTCATAA
55628 TTTTTTCAAT
1 TTTTTTCAAT
55638 ACCGTAAAAT
Statistics
Matches: 216, Mismatches: 38, Indels: 25
0.77 0.14 0.09
Matches are distributed among these distances:
41 4 0.02
42 94 0.44
43 81 0.38
44 37 0.17
ACGTcount: A:0.28, C:0.18, G:0.04, T:0.49
Consensus pattern (43 bp):
TTTTTTCAATCCCACTTTTTACCTTTATAATTGAAACTCATAA
Found at i:63745 original size:16 final size:16
Alignment explanation
Indices: 63712--63759 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
63702 GTTGAATGAC
*
63712 TAATAAAATAATTTAAT
1 TAATAAAA-AATTAAAT
**
63729 TAATACTAAATTAAAT
1 TAATAAAAAATTAAAT
63745 TAATAAAAAATTAAA
1 TAATAAAAAATTAAA
63760 CTGGTAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 20 0.77
17 6 0.23
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATAAAAAATTAAAT
Found at i:66743 original size:60 final size:61
Alignment explanation
Indices: 66658--66775 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 61
66648 ACACAAATGG
*
66658 TCCCTCAACTATAGGATAATACTTTGTTGAGT-CTCCTAAATATCAAAAGTTA-AAAATTGA
1 TCCCTCAACTATAGGATAATACTTTGTTAAGTCCTCC-AAATATCAAAAGTTACAAAATTGA
** * * *
66718 TCCCTCAACTATAGGATGTTGCTTTGTTAAGTCCTCCAACTATTAAAAGTTACAAAAT
1 TCCCTCAACTATAGGATAATACTTTGTTAAGTCCTCCAAATATCAAAAGTTACAAAAT
66776 GGTCATCTGA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
60 41 0.82
61 9 0.18
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.34
Consensus pattern (61 bp):
TCCCTCAACTATAGGATAATACTTTGTTAAGTCCTCCAAATATCAAAAGTTACAAAATTGA
Found at i:68917 original size:28 final size:28
Alignment explanation
Indices: 68867--68920 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
68857 ATTAGTGCCG
*
68867 CCGTAGATTAATAAAAACCAAAAAAAAT
1 CCGTAGATTAATAAAAACAAAAAAAAAT
* *
68895 CCGTAGATTAATAAAGATAAAAAAAA
1 CCGTAGATTAATAAAAACAAAAAAAA
68921 TGAACAACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.61, C:0.11, G:0.09, T:0.19
Consensus pattern (28 bp):
CCGTAGATTAATAAAAACAAAAAAAAAT
Found at i:77593 original size:18 final size:18
Alignment explanation
Indices: 77570--77606 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
77560 ATTTTAACCG
77570 GTGATGCTTACTTGTTAT
1 GTGATGCTTACTTGTTAT
77588 GTGATGCTTACTTGTTAT
1 GTGATGCTTACTTGTTAT
77606 G
1 G
77607 CAATGCTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.11, G:0.24, T:0.49
Consensus pattern (18 bp):
GTGATGCTTACTTGTTAT
Found at i:77612 original size:18 final size:18
Alignment explanation
Indices: 77573--77613 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
77563 TTAACCGGTG
**
77573 ATGCTTACTTGTTATGTG
1 ATGCTTACTTGTTATGCA
77591 ATGCTTACTTGTTATGCA
1 ATGCTTACTTGTTATGCA
77609 ATGCT
1 ATGCT
77614 CACACAAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.46
Consensus pattern (18 bp):
ATGCTTACTTGTTATGCA
Found at i:81917 original size:29 final size:30
Alignment explanation
Indices: 81885--81943 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
81875 ATTTAGGTCT
*
81885 CTCAACTTTTAAAAC-TTGCAATATAATCA
1 CTCAACATTTAAAACGTTGCAATATAATCA
**
81914 CTCAACATTTAGTACGTTTGCAATATAATC
1 CTCAACATTTAAAACG-TTGCAATATAATC
81944 CCCGACGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 12 0.48
31 13 0.52
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (30 bp):
CTCAACATTTAAAACGTTGCAATATAATCA
Found at i:84712 original size:31 final size:31
Alignment explanation
Indices: 84674--84739 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
84664 AGTTACGTAG
84674 GGGACCATATTGCAAACGGACTAAATGTTGA
1 GGGACCATATTGCAAACGGACTAAATGTTGA
* *
84705 GGGACCATATTGCAAATGGACTAAATGTTGG
1 GGGACCATATTGCAAACGGACTAAATGTTGA
84736 GGGA
1 GGGA
84740 TTGTATTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Consensus pattern (31 bp):
GGGACCATATTGCAAACGGACTAAATGTTGA
Found at i:89787 original size:30 final size:29
Alignment explanation
Indices: 89732--89789 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
89722 AGGCGGAGTT
*
89732 AGAAAATTTATTTTGAGTATTAAATTTAG
1 AGAAAATTTATTTTGAGTATCAAATTTAG
* *
89761 AGAAAATTTATTTTTGGGTGTCAAATTTA
1 AGAAAATTTA-TTTTGAGTATCAAATTTA
89790 TAAATCGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.38, C:0.02, G:0.16, T:0.45
Consensus pattern (29 bp):
AGAAAATTTATTTTGAGTATCAAATTTAG
Found at i:93998 original size:36 final size:36
Alignment explanation
Indices: 93951--94023 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
93941 GTCAACCAAA
* *
93951 ATGTCACGGCTTATATCATAAACTAATATTTGTGGT
1 ATGTCACGGCTTATATCATAAACTAATAGTTGCGGT
* *
93987 ATGTCATGGCTTATATCATAAGCTAATAGTTGCGGT
1 ATGTCACGGCTTATATCATAAACTAATAGTTGCGGT
94023 A
1 A
94024 CATTGACTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (36 bp):
ATGTCACGGCTTATATCATAAACTAATAGTTGCGGT
Found at i:101337 original size:12 final size:11
Alignment explanation
Indices: 101322--101377 Score: 53
Period size: 12 Copynumber: 4.9 Consensus size: 11
101312 AACCATCTAA
101322 AACAATGACAAT
1 AACAAT-ACAAT
101334 AACAATACAAT
1 AACAATACAAT
*
101345 AAACCAT-CGAA-
1 -AACAATAC-AAT
101356 AACAATGACAAT
1 AACAAT-ACAAT
101368 AACAATACAA
1 AACAATACAA
101378 AAGTATCCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
10 5 0.14
11 12 0.32
12 20 0.54
ACGTcount: A:0.61, C:0.20, G:0.05, T:0.14
Consensus pattern (11 bp):
AACAATACAAT
Found at i:101348 original size:34 final size:34
Alignment explanation
Indices: 101308--101377 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
101298 ACCCATTTCT
*
101308 AATAAACCATCTAAAACAATGACAATAACAATAC
1 AATAAACCATCGAAAACAATGACAATAACAATAC
101342 AATAAACCATCGAAAACAATGACAATAACAATAC
1 AATAAACCATCGAAAACAATGACAATAACAATAC
101376 AA
1 AA
101378 AAGTATCCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.60, C:0.20, G:0.04, T:0.16
Consensus pattern (34 bp):
AATAAACCATCGAAAACAATGACAATAACAATAC
Found at i:101377 original size:17 final size:17
Alignment explanation
Indices: 101323--101377 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
101313 ACCATCTAAA
101323 ACAATGACAATAACAAT
1 ACAATGACAATAACAAT
* * *
101340 ACAAT-A-AACCATCGAAA
1 ACAATGACAA-TAAC-AAT
101357 ACAATGACAATAACAAT
1 ACAATGACAATAACAAT
101374 ACAA
1 ACAA
101378 AAGTATCCTT
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
15 2 0.07
16 3 0.11
17 18 0.64
18 3 0.11
19 2 0.07
ACGTcount: A:0.60, C:0.20, G:0.05, T:0.15
Consensus pattern (17 bp):
ACAATGACAATAACAAT
Found at i:102182 original size:9 final size:9
Alignment explanation
Indices: 102168--102197 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
102158 CGTTATAATT
102168 AAAAAAATC
1 AAAAAAATC
102177 AAAAAAATC
1 AAAAAAATC
102186 AAAAAAAATC
1 -AAAAAAATC
102196 AA
1 AA
102198 TGATATATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAATC
Found at i:102183 original size:10 final size:10
Alignment explanation
Indices: 102168--102197 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
102158 CGTTATAATT
102168 AAAAAAATC-
1 AAAAAAATCA
102177 AAAAAAATCA
1 AAAAAAATCA
102187 AAAAAAATCA
1 AAAAAAATCA
102197 A
1 A
102198 TGATATATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.80, C:0.10, G:0.00, T:0.10
Consensus pattern (10 bp):
AAAAAAATCA
Found at i:108384 original size:2 final size:2
Alignment explanation
Indices: 108377--108408 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
108367 ATAAGAGCAT
108377 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
108409 GAGGCAAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:109566 original size:20 final size:20
Alignment explanation
Indices: 109541--109592 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
109531 TAGTTGAAAA
109541 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
109561 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
109581 TTGCGTTGCGAT
1 TCGCGTTGCGAT
109593 AGTCTACAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.44
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:109638 original size:19 final size:21
Alignment explanation
Indices: 109584--109698 Score: 103
Period size: 22 Copynumber: 5.6 Consensus size: 21
109574 TTCCATTTTG
109584 CGTTGCGATAGTCTACAATGT
1 CGTTGCGATAGTCTACAATGT
**
109605 CGTTGCGATTTTCTA-AAT-T
1 CGTTGCGATAGTCTACAATGT
*
109624 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACA-ATGT
* * *
109646 TGTTGCGAAAGTCTACAGTTGT
1 CGTTGCGATAGTCTACA-ATGT
** *
109668 CGTTGCGATTTTCCA-AAT-T
1 CGTTGCGATAGTCTACAATGT
109687 CGTTGCGATAGT
1 CGTTGCGATAGT
109699 TTAAAAAAAT
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
19 25 0.33
20 5 0.07
21 15 0.20
22 31 0.41
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAATGT
Found at i:109653 original size:22 final size:22
Alignment explanation
Indices: 109584--109676 Score: 104
Period size: 22 Copynumber: 4.4 Consensus size: 22
109574 TTCCATTTTG
*
109584 CGTTGCGATAGTCTACA-ATGT
1 CGTTGCGATAGTCTACAGTTGT
** *
109605 CGTTGCGATTTTCTA-A-AT-T
1 CGTTGCGATAGTCTACAGTTGT
109624 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* *
109646 TGTTGCGAAAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
109668 CGTTGCGAT
1 CGTTGCGAT
109677 TTTCCAAATT
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
19 14 0.23
20 4 0.07
21 14 0.23
22 28 0.47
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:109653 original size:41 final size:41
Alignment explanation
Indices: 109564--109640 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 41
109554 TTCCATTTCG
**
109564 CGTTGCGATTTTCCATTTTGCGTTGCGATAGTCTACAATGT
1 CGTTGCGATTTTCCAAATTGCGTTGCGATAGTCTACAATGT
*
109605 CGTTGCGATTTTCTAAATT-CGTTGCGATAGTCTACA
1 CGTTGCGATTTTCCAAATTGCGTTGCGATAGTCTACA
109641 GTTGTTGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 17 0.52
41 16 0.48
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTGCGTTGCGATAGTCTACAATGT
Found at i:109784 original size:6 final size:6
Alignment explanation
Indices: 109773--109851 Score: 158
Period size: 6 Copynumber: 13.2 Consensus size: 6
109763 GACACGTATT
109773 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
109821 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
109852 GACGGACGGC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 73 1.00
ACGTcount: A:0.34, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:110353 original size:5 final size:5
Alignment explanation
Indices: 110341--110387 Score: 51
Period size: 5 Copynumber: 9.0 Consensus size: 5
110331 GTCTCGTCTC
*
110341 GGTC- GGTCG GGTCG TGGTCG GGTCG GGTCG TGGTCG TGTCG TGGTCG
1 GGTCG GGTCG GGTCG -GGTCG GGTCG GGTCG -GGTCG GGTCG -GGTCG
110388 TACGTGTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
4 4 0.11
5 19 0.51
6 14 0.38
ACGTcount: A:0.00, C:0.19, G:0.53, T:0.28
Consensus pattern (5 bp):
GGTCG
Found at i:110361 original size:11 final size:12
Alignment explanation
Indices: 110345--110388 Score: 60
Period size: 11 Copynumber: 4.0 Consensus size: 12
110335 CGTCTCGGTC
110345 GGTCG-GGTCGT
1 GGTCGTGGTCGT
110356 GGTCG-GGTCG-
1 GGTCGTGGTCGT
110366 GGTCGTGGTCGT
1 GGTCGTGGTCGT
110378 -GTCGTGGTCGT
1 GGTCGTGGTCGT
110389 ACGTGTCTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 5 0.16
11 26 0.84
ACGTcount: A:0.00, C:0.18, G:0.52, T:0.30
Consensus pattern (12 bp):
GGTCGTGGTCGT
Found at i:110366 original size:16 final size:16
Alignment explanation
Indices: 110341--110388 Score: 71
Period size: 16 Copynumber: 3.0 Consensus size: 16
110331 GTCTCGTCTC
110341 GGTC-GGTCGGGTCGT
1 GGTCGGGTCGGGTCGT
110356 GGTCGGGTCGGGTCGT
1 GGTCGGGTCGGGTCGT
*
110372 GGTCGTGTCGTGGTCGT
1 GGTCGGGTCG-GGTCGT
110389 ACGTGTCTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 4 0.13
16 20 0.67
17 6 0.20
ACGTcount: A:0.00, C:0.19, G:0.52, T:0.29
Consensus pattern (16 bp):
GGTCGGGTCGGGTCGT
Found at i:110559 original size:16 final size:16
Alignment explanation
Indices: 110538--110581 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
110528 GAATTGGAAA
110538 ATCGCAACGCGAAACT
1 ATCGCAACGCGAAACT
110554 ATCGCAACGCG-AACT
1 ATCGCAACGCGAAACT
*
110569 -GCGCAACGCGAAA
1 ATCGCAACGCGAAA
110582 TGGAAAATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 9 0.35
15 6 0.23
16 11 0.42
ACGTcount: A:0.36, C:0.32, G:0.23, T:0.09
Consensus pattern (16 bp):
ATCGCAACGCGAAACT
Found at i:110575 original size:14 final size:15
Alignment explanation
Indices: 110540--110580 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
110530 ATTGGAAAAT
*
110540 CGCAACGCGAAACTAT
1 CGCAACGCG-AACTAG
110556 CGCAACGCGAACT-G
1 CGCAACGCGAACTAG
110570 CGCAACGCGAA
1 CGCAACGCGAA
110581 ATGGAAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 11 0.46
15 4 0.17
16 9 0.38
ACGTcount: A:0.34, C:0.34, G:0.24, T:0.07
Consensus pattern (15 bp):
CGCAACGCGAACTAG
Found at i:110614 original size:21 final size:21
Alignment explanation
Indices: 110588--110641 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
110578 GAAATGGAAA
110588 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
110609 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
110630 ATCGCAACGCGA
1 ATCGCAACGCGA
110642 AATGCAACGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:113310 original size:92 final size:92
Alignment explanation
Indices: 113171--113348 Score: 313
Period size: 92 Copynumber: 1.9 Consensus size: 92
113161 TTCGCAACTC
*
113171 GAACATGAAATTTTCGCAACGCTAATGACTGATATAGGTAAACACAACTATTCGCAACGCGAATT
1 GAACATGAAATTTTCGCAACGCTAATGACCGATATAGGTAAACACAACTATTCGCAACGCGAATT
113236 TGAATTCGCAACTCGAACATGCAATTA
66 TGAATTCGCAACTCGAACATGCAATTA
*
113263 GAACATGGAAA-TTTCGCAACGCTAATTACCGATATAGGTAAACACAACTATTCGCAACGCGAAT
1 GAACAT-GAAATTTTCGCAACGCTAATGACCGATATAGGTAAACACAACTATTCGCAACGCGAAT
*
113327 TTGAATTCGCAATTCGAACATG
65 TTGAATTCGCAACTCGAACATG
113349 AAAATTTTCG
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
92 78 0.95
93 4 0.05
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (92 bp):
GAACATGAAATTTTCGCAACGCTAATGACCGATATAGGTAAACACAACTATTCGCAACGCGAATT
TGAATTCGCAACTCGAACATGCAATTA
Found at i:123255 original size:23 final size:24
Alignment explanation
Indices: 123210--123255 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
123200 AAATTTATGT
*
123210 TTTTTTAATATATATATAATTTTA
1 TTTTTTAATATATACATAATTTTA
* *
123234 TTTTTTAAT-TTTACATATTTTT
1 TTTTTTAATATATACATAATTTT
123256 TAAATTATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTTTTAATATATACATAATTTTA
Found at i:123267 original size:17 final size:17
Alignment explanation
Indices: 123232--123269 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
123222 TATATAATTT
*
123232 TATTTTTTAATTTTACA
1 TATTTTTTAATTATACA
123249 TATTTTTTAAATTAT-CA
1 TATTTTTT-AATTATACA
123266 TATT
1 TATT
123270 ATGACACGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTTTTTAATTATACA
Found at i:124535 original size:23 final size:22
Alignment explanation
Indices: 124496--124573 Score: 57
Period size: 23 Copynumber: 3.4 Consensus size: 22
124486 TAAACTGTTA
* * *
124496 AATTATAAAGTACTAAACATAT
1 AATTATAAATTATTAAAAATAT
*
124518 AATTATAAATTAGTTAAAAATTT
1 AATTATAAATTA-TTAAAAATAT
* * *
124541 AAATATAATTTAATTAAATATAGT
1 AATTATAAATT-ATTAAAAATA-T
*
124565 ATTTATAAA
1 AATTATAAA
124574 ACATTAGTTT
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
22 11 0.26
23 23 0.55
24 8 0.19
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.40
Consensus pattern (22 bp):
AATTATAAATTATTAAAAATAT
Found at i:124868 original size:16 final size:16
Alignment explanation
Indices: 124847--124884 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
124837 ATAAAAACTA
124847 ATATTTT-ATAAATATT
1 ATATTTTAATAAA-ATT
*
124863 ATATTTTAATTAAATT
1 ATATTTTAATAAAATT
124879 ATATTT
1 ATATTT
124885 AAATTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATTTTAATAAAATT
Found at i:124889 original size:16 final size:18
Alignment explanation
Indices: 124860--124899 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
124850 TTTTATAAAT
*
124860 ATTATATTTTAA-TTA-A
1 ATTATATTTAAATTTATA
124876 ATTATATTTAAATTTATA
1 ATTATATTTAAATTTATA
124894 ATTATA
1 ATTATA
124900 CATTGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.52
17 3 0.14
18 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTATATTTAAATTTATA
Found at i:125304 original size:19 final size:17
Alignment explanation
Indices: 125280--125330 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 17
125270 AACGTTTTTT
125280 AATAAATTTTTTTTCGTAA
1 AATAAATTTTTTTT--TAA
125299 AATAAATTATATTTTTTAA
1 AATAAATT-T-TTTTTTAA
125318 AATAATATTTTTT
1 AATAA-ATTTTTT
125331 AGAAAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.10
19 17 0.59
20 4 0.14
21 5 0.17
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
AATAAATTTTTTTTTAA
Found at i:125336 original size:17 final size:15
Alignment explanation
Indices: 125302--125342 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
125292 TTCGTAAAAT
*
125302 AAATTATATTTTTTA
1 AAATAATATTTTTTA
125317 AAATAATATTTTTTA
1 AAATAATATTTTTTA
*
125332 GAA-AATATTTT
1 AAATAATATTTT
125343 ACGATGTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
AAATAATATTTTTTA
Found at i:125450 original size:28 final size:26
Alignment explanation
Indices: 125419--125493 Score: 61
Period size: 25 Copynumber: 3.0 Consensus size: 26
125409 TTACAAATAT
125419 TAAATATAATAAATAATATTATTTATCA
1 TAAATAT-ATAAATAATATTATTTAT-A
* * *
125447 TAAA-AT-TTAATATTATTATTT-TT
1 TAAATATATAAATAATATTATTTATA
125470 TAAATAT-TAAAATAAT-TTATTTAT
1 TAAATATAT-AAATAATATTATTTAT
125494 TATTAAAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
23 4 0.10
24 10 0.26
25 19 0.49
27 2 0.05
28 4 0.10
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (26 bp):
TAAATATATAAATAATATTATTTATA
Found at i:125461 original size:50 final size:50
Alignment explanation
Indices: 125407--125504 Score: 110
Period size: 50 Copynumber: 2.0 Consensus size: 50
125397 AAAAATTATT
125407 TATTA-CAAATATTAAATATAATAAATAATATTATTTATCA-TAAAATTTAA
1 TATTATCAAATATTAAATATAA-AAATAAT-TTATTTATCATTAAAATTTAA
* ** * * *
125457 TATTATTATTTTTTAAATATTAAAATAATTTATTTATTATTAAAATTT
1 TATTATCAAATATTAAATATAAAAATAATTTATTTATCATTAAAATTT
125505 TATTTTTATA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
49 9 0.22
50 20 0.50
51 11 0.28
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (50 bp):
TATTATCAAATATTAAATATAAAAATAATTTATTTATCATTAAAATTTAA
Found at i:125497 original size:20 final size:17
Alignment explanation
Indices: 125474--125513 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 17
125464 ATTTTTTAAA
125474 TATTAAAATAATTTATTTAT
1 TATTAAAAT--TTTATTT-T
125494 TATTAAAATTTTATTTT
1 TATTAAAATTTTATTTT
125511 TAT
1 TAT
125514 AATTTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 7 0.35
20 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTAAAATTTTATTTT
Found at i:125508 original size:14 final size:14
Alignment explanation
Indices: 125489--125529 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
125479 AAATAATTTA
125489 TTTATTATTAAAAT
1 TTTATTATTAAAAT
* *
125503 TTTATTTTTATAAT
1 TTTATTATTAAAAT
*
125517 TTTATTAATAAAA
1 TTTATTATTAAAA
125530 ATATTAATAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTATTATTAAAAT
Found at i:125531 original size:49 final size:48
Alignment explanation
Indices: 125424--125532 Score: 114
Period size: 51 Copynumber: 2.2 Consensus size: 48
125414 AATATTAAAT
*
125424 ATAATAAATAATATTATTTATCATAAAATTTAATATTATTATTTTTTAA
1 ATAA-AAATAATATTATTTATCATAAAATTTAATATTATAATTTTTTAA
* * *
125473 ATATTAAAATAAT-TTATTTATTATTAAAATTTTATTTTTATAATTTTATT-A
1 ATA--AAAATAATATTATTTATCA-TAAAA-TTTAATATTATAATTTT-TTAA
125524 ATAAAAATA
1 ATAAAAATA
125533 TTAATATTGT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
49 18 0.35
50 12 0.24
51 19 0.37
52 2 0.04
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (48 bp):
ATAAAAATAATATTATTTATCATAAAATTTAATATTATAATTTTTTAA
Found at i:125657 original size:23 final size:22
Alignment explanation
Indices: 125609--125676 Score: 55
Period size: 23 Copynumber: 3.0 Consensus size: 22
125599 GTGTTATATT
**
125609 ATATTTTAAAATATTAATTAGT
1 ATATTTTAAAATATTAATTAAA
* *
125631 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAA-ATATTAATTAAA
* *
125654 ATATTATTAGATTATTATATTAA
1 ATATT-TTAAAATATTA-ATTAA
125677 TATAAATATA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
22 10 0.29
23 16 0.46
24 9 0.26
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (22 bp):
ATATTTTAAAATATTAATTAAA
Found at i:125801 original size:23 final size:23
Alignment explanation
Indices: 125771--125821 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
125761 TTAAAATAAA
125771 AATATAATAT-CTTATATTATTAT
1 AATATAAT-TGCTTATATTATTAT
* *
125794 AATATAATTGGTTATTTTATTAT
1 AATATAATTGCTTATATTATTAT
125817 AATAT
1 AATAT
125822 TAAAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (23 bp):
AATATAATTGCTTATATTATTAT
Found at i:125839 original size:22 final size:23
Alignment explanation
Indices: 125811--125857 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
125801 TTGGTTATTT
125811 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
125833 TATTATACTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
125856 TA
1 TA
125858 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:140007 original size:36 final size:36
Alignment explanation
Indices: 139960--140030 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
139950 ATAAACGAGA
139960 TGAGATAGATTTGCGAGTTATTCGAGTTTAATTCAG
1 TGAGATAGATTTGCGAGTTATTCGAGTTTAATTCAG
* *
139996 TGAGATAGATTTGTGAGTTATTTGAGTTTAATTCA
1 TGAGATAGATTTGCGAGTTATTCGAGTTTAATTCA
140031 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.06, G:0.24, T:0.42
Consensus pattern (36 bp):
TGAGATAGATTTGCGAGTTATTCGAGTTTAATTCAG
Found at i:146803 original size:16 final size:16
Alignment explanation
Indices: 146782--146837 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
146772 TCAGAGTCAC
*
146782 TAAATCATTCAACATT
1 TAAATCATTCAGCATT
146798 TAAATCATTCAGCATT
1 TAAATCATTCAGCATT
*
146814 TGAATCATTCAGCATT
1 TAAATCATTCAGCATT
146830 T-AATCATT
1 TAAATCATT
146838 TTGAAGTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
15 7 0.18
16 31 0.82
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.39
Consensus pattern (16 bp):
TAAATCATTCAGCATT
Found at i:151223 original size:5 final size:5
Alignment explanation
Indices: 151204--151242 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
151194 GTCCGTCCGT
* * *
151204 CTCGT CTCGT CTCGG CTCGG CACGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
151243 TGGTCGTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.03, C:0.41, G:0.33, T:0.23
Consensus pattern (5 bp):
CTCGG
Found at i:151251 original size:6 final size:6
Alignment explanation
Indices: 151240--151330 Score: 155
Period size: 6 Copynumber: 15.2 Consensus size: 6
151230 TCGGCTCGGC
* * *
151240 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
151288 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
151331 AATACGTGTC
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 83 1.00
ACGTcount: A:0.03, C:0.16, G:0.49, T:0.31
Consensus pattern (6 bp):
TCGTGG
Found at i:151633 original size:22 final size:22
Alignment explanation
Indices: 151608--151662 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
151598 TCAGGAGTTA
* *
151608 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
151630 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
151652 CGGGAGTTATA
1 CAGGAGTTATA
151663 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:157234 original size:6 final size:6
Alignment explanation
Indices: 157223--157325 Score: 188
Period size: 6 Copynumber: 17.2 Consensus size: 6
157213 TCGACTCGAC
* *
157223 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
157271 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
157319 TCGTGG T
1 TCGTGG T
157326 AATACGTGTC
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 95 1.00
ACGTcount: A:0.02, C:0.17, G:0.50, T:0.32
Consensus pattern (6 bp):
TCGTGG
Found at i:157628 original size:22 final size:22
Alignment explanation
Indices: 157603--157657 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
157593 TCAGGAGTTA
* *
157603 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
157625 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
157647 CGGGAGTTATA
1 CAGGAGTTATA
157658 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:162871 original size:31 final size:30
Alignment explanation
Indices: 162836--162943 Score: 82
Period size: 31 Copynumber: 3.6 Consensus size: 30
162826 AATTTTATTA
162836 ATAATTTATTATTTATTATTAAAATAAAAAT
1 ATAATTTA-TATTTATTATTAAAATAAAAAT
* * * *
162867 ATAATATATCTTATATTATTATAAT-ATAAT
1 ATAATTTATATT-TATTATTAAAATAAAAAT
* *
162897 -TGA-TTAT-TTTATTA-TAATATTAAAAAT
1 ATAATTTATATTTATTATTAA-AATAAAAAT
*
162924 ATAATATTATATTTAATATT
1 ATAAT-TTATATTTATTATT
162944 TTAATAATTA
Statistics
Matches: 58, Mismatches: 11, Indels: 15
0.69 0.13 0.18
Matches are distributed among these distances:
25 2 0.03
26 7 0.12
27 6 0.10
28 5 0.09
29 2 0.03
30 11 0.19
31 24 0.41
32 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (30 bp):
ATAATTTATATTTATTATTAAAATAAAAAT
Found at i:162949 original size:57 final size:56
Alignment explanation
Indices: 162822--162949 Score: 145
Period size: 57 Copynumber: 2.3 Consensus size: 56
162812 TAATAAACAA
* * *
162822 TATAA-ATTTTATTAATAATTTATTATTTATTATTAAAATAAAAATATAATATATCT
1 TATAATATTTTAAT-ATAATTGATTATTTATTATTAAAATAAAAATATAATATATAT
* * *
162878 TATATTATTATAATATAATTGATTATTTTATTA-TAATATTAAAAATATAATATTATAT
1 TATAATATTTTAATATAATTGATTA-TTTATTATTAA-AATAAAAATATAATA-TATAT
162936 T-TAATATTTTAATA
1 TATAATATTTTAATA
162950 ATTAATATTT
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
56 17 0.28
57 38 0.63
58 5 0.08
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.52
Consensus pattern (56 bp):
TATAATATTTTAATATAATTGATTATTTATTATTAAAATAAAAATATAATATATAT
Found at i:163397 original size:16 final size:16
Alignment explanation
Indices: 163373--163404 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
163363 ATCAAACTAA
163373 TTAAAATATTACATAT
1 TTAAAATATTACATAT
*
163389 TTAATATATTACATAT
1 TTAAAATATTACATAT
163405 ATATTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAATATTACATAT
Found at i:163576 original size:16 final size:15
Alignment explanation
Indices: 163546--163581 Score: 63
Period size: 15 Copynumber: 2.3 Consensus size: 15
163536 TAATTAAAAA
163546 ATTACAATAAATTTTT
1 ATTA-AATAAATTTTT
163562 ATTAAATAAATTTTT
1 ATTAAATAAATTTTT
163577 ATTAA
1 ATTAA
163582 TTTGAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTAAATAAATTTTT
Found at i:169531 original size:18 final size:18
Alignment explanation
Indices: 169508--169559 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
169498 GCGCATAATT
*
169508 TGTCCCGTAGGACCACTG
1 TGTCCCGAAGGACCACTG
*
169526 TGTCCCGAAAGACCACTG
1 TGTCCCGAAGGACCACTG
169544 TGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
169560 GTAGACCCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.23, C:0.35, G:0.25, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTG
Found at i:172275 original size:22 final size:21
Alignment explanation
Indices: 172220--172276 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
172210 TTTGTGTTTT
*
172220 CTTTTTTAAAAA-ATATATAA
1 CTTTTTTAAAAATATAAATAA
*
172240 CTTTTTTTAAAAATTTTAAATAA
1 C-TTTTTTAAAAA-TATAAATAA
172263 CTTTTTTAAAAATA
1 CTTTTTTAAAAATA
172277 CCAGATTGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 1 0.03
21 12 0.39
22 11 0.35
23 7 0.23
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (21 bp):
CTTTTTTAAAAATATAAATAA
Found at i:175370 original size:27 final size:28
Alignment explanation
Indices: 175332--175386 Score: 103
Period size: 27 Copynumber: 2.0 Consensus size: 28
175322 GAAATCCGAA
175332 AAGAATGGAACTTT-AATCACTATATAT
1 AAGAATGGAACTTTAAATCACTATATAT
175359 AAGAATGGAACTTTAAATCACTATATAT
1 AAGAATGGAACTTTAAATCACTATATAT
175387 CGATATTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (28 bp):
AAGAATGGAACTTTAAATCACTATATAT
Found at i:189058 original size:39 final size:39
Alignment explanation
Indices: 189004--189120 Score: 234
Period size: 39 Copynumber: 3.0 Consensus size: 39
188994 TTCCCTTAAA
189004 CCAAATCATATGATGACAGAGACAAGTGACAGACATAAC
1 CCAAATCATATGATGACAGAGACAAGTGACAGACATAAC
189043 CCAAATCATATGATGACAGAGACAAGTGACAGACATAAC
1 CCAAATCATATGATGACAGAGACAAGTGACAGACATAAC
189082 CCAAATCATATGATGACAGAGACAAGTGACAGACATAAC
1 CCAAATCATATGATGACAGAGACAAGTGACAGACATAAC
189121 TCTAGGTTCC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.46, C:0.21, G:0.18, T:0.15
Consensus pattern (39 bp):
CCAAATCATATGATGACAGAGACAAGTGACAGACATAAC
Found at i:190402 original size:30 final size:30
Alignment explanation
Indices: 190368--190428 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
190358 CTCTCTGAAT
*
190368 GTTAAGTGAACGATTTGAAGCATTGAACAA
1 GTTAAGTGAACAATTTGAAGCATTGAACAA
190398 GTTAAGTGAACAATTTGAAGCATTGAACAA
1 GTTAAGTGAACAATTTGAAGCATTGAACAA
190428 G
1 G
190429 AATGAGTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (30 bp):
GTTAAGTGAACAATTTGAAGCATTGAACAA
Found at i:190426 original size:17 final size:17
Alignment explanation
Indices: 190374--190427 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
190364 GAATGTTAAG
*
190374 TGAACGATTTGAAGCAT
1 TGAACAATTTGAAGCAT
*
190391 TGAACAAGTT-AAG---
1 TGAACAATTTGAAGCAT
190404 TGAACAATTTGAAGCAT
1 TGAACAATTTGAAGCAT
190421 TGAACAA
1 TGAACAA
190428 GAATGAGTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
13 9 0.30
14 3 0.10
16 3 0.10
17 15 0.50
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (17 bp):
TGAACAATTTGAAGCAT
Found at i:193994 original size:58 final size:60
Alignment explanation
Indices: 193897--194084 Score: 156
Period size: 67 Copynumber: 3.0 Consensus size: 60
193887 ATGAATTTGT
* **
193897 GGATGAAATTGGAATATTCAAAAGTTTAGGGACATATTTAGAAAT-A-A-TCATAGTTTAG
1 GGATGAAATTAGAATATTCAAAAGTTTAAAGACATATTTA-AAATGAGAGTCATAGTTTAG
* *
193955 GGATGAAATTATAATGTTCAAAAGTTTAAAGAC-TAATTTAAAATGAGAGTCATAGTTTGAGGTT
1 GGATGAAATTAGAATATTCAAAAGTTTAAAGACAT-ATTTAAAATGAGAGTCATAGTTT-A----
194019 TG
60 -G
* *
194021 AGGATGAAATT-GAACTATTCAAAAGTTT-AGGA-ATCAATTTAAAATGAGAGTCATAGTTTGG
1 -GGATGAAATTAGAA-TATTCAAAAGTTTAAAGACAT--ATTTAAAATGAGAGTCATAGTTTAG
194082 GGA
1 GGA
194085 CATATACTGT
Statistics
Matches: 107, Mismatches: 9, Indels: 26
0.75 0.06 0.18
Matches are distributed among these distances:
57 5 0.05
58 34 0.32
59 1 0.01
60 12 0.11
61 2 0.02
66 7 0.07
67 46 0.43
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.32
Consensus pattern (60 bp):
GGATGAAATTAGAATATTCAAAAGTTTAAAGACATATTTAAAATGAGAGTCATAGTTTAG
Found at i:201236 original size:16 final size:16
Alignment explanation
Indices: 201203--201234 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
201193 TTTAATTAAA
201203 TATTAGTTATATTTTT
1 TATTAGTTATATTTTT
201219 TATTAG-TATATTTTT
1 TATTAGTTATATTTTT
201234 T
1 T
201235 TAAAAGAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (16 bp):
TATTAGTTATATTTTT
Found at i:202666 original size:22 final size:23
Alignment explanation
Indices: 202628--202675 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
202618 TTTTTATTGG
202628 ATTTTTCATTCTCAATA-CCTAA
1 ATTTTTCATTCTCAATATCCTAA
* *
202650 ATTTCTTCA-TCTTAATATTCTAA
1 ATTT-TTCATTCTCAATATCCTAA
202673 ATT
1 ATT
202676 CTTAAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTTTTCATTCTCAATATCCTAA
Found at i:210410 original size:2 final size:2
Alignment explanation
Indices: 210403--210443 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
210393 CTACCAAATG
210403 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
210444 GTTAAAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:212071 original size:16 final size:16
Alignment explanation
Indices: 212052--212090 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
212042 ATTAATTCCA
212052 ATAATTATTTAATAGC
1 ATAATTATTTAATAGC
212068 ATAATTATTTAATAGC
1 ATAATTATTTAATAGC
212084 AT-ATTAT
1 ATAATTAT
212091 ATATAGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 5 0.22
16 18 0.78
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (16 bp):
ATAATTATTTAATAGC
Found at i:219018 original size:20 final size:20
Alignment explanation
Indices: 218992--219060 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
218982 CACGGAATGT
218992 AAGATTACTAGTGAGAATAA
1 AAGATTACTAGTGAGAATAA
* * *
219012 AATATTACCAATGAGAATAA
1 AAGATTACTAGTGAGAATAA
219032 AAGATTACTAG-G-GAAT--
1 AAGATTACTAGTGAGAATAA
219048 AAGATTACT-GTGA
1 AAGATTACTAGTGA
219061 ATGTTGTATT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
15 1 0.02
16 10 0.24
18 4 0.10
19 1 0.02
20 25 0.61
ACGTcount: A:0.48, C:0.07, G:0.19, T:0.26
Consensus pattern (20 bp):
AAGATTACTAGTGAGAATAA
Found at i:220795 original size:12 final size:12
Alignment explanation
Indices: 220778--220803 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
220768 CTTAAATGTG
220778 TATATTATTATA
1 TATATTATTATA
220790 TATATTATTATA
1 TATATTATTATA
220802 TA
1 TA
220804 ATCTATAATA
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TATATTATTATA
Found at i:221969 original size:19 final size:18
Alignment explanation
Indices: 221947--221997 Score: 70
Period size: 16 Copynumber: 2.9 Consensus size: 18
221937 TTTAGGGTTT
*
221947 TTTTTTAAATAATATATTA
1 TTTTTTAAA-AATATATAA
221966 TTTTTTAAAAA-ATA-AA
1 TTTTTTAAAAATATATAA
221982 TTTTTTAAAAATATAT
1 TTTTTTAAAAATATAT
221998 GGTAGTGACA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 12 0.41
17 6 0.21
18 2 0.07
19 9 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTTTAAAAATATATAA
Found at i:223959 original size:4 final size:4
Alignment explanation
Indices: 223318--224982 Score: 873
Period size: 4 Copynumber: 416.2 Consensus size: 4
223308 ACATATACAT
* * * * * * * *
223318 ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
223366 ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * *
223414 ACAC ATAC ACAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
223462 ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
223510 ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * *
223558 ACAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
223606 ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
223654 ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
223702 ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
223750 ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * * *
223798 ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ATAC ACAT
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
223846 ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * * *
223894 ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ATAC ACAT
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * *
223942 ACAC AGAC ACAT ACAT ACAC ACAC ATAC ACAC ACAC ACAC ATAC ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * *
223990 ACAC ACAT ACAC ACAC ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
224038 ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
224086 ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
224134 ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
224182 ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
224230 ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
224278 ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
224326 ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
224374 ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
224422 ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ATAC ACAT ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
224470 ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
224518 ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
224566 ATAC ACAT ACAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
224614 ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
224662 ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
224710 ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * *
224758 ACAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
224806 ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
224854 ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
224902 ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC ATAC ACAT ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * *
224950 ATAT ATAC ACAT ACAC ATAC ATAC ACAT ACAC A
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC A
224983 TACGTACACA
Statistics
Matches: 1127, Mismatches: 534, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
4 1127 1.00
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (4 bp):
ACAC
Found at i:225011 original size:6 final size:6
Alignment explanation
Indices: 223301--225000 Score: 3103
Period size: 6 Copynumber: 285.0 Consensus size: 6
223291 GTATTTTACG
*
223301 CACATA CACATA TACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
223349 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
223397 CACATA CACATA CACATA CACATA CAC--A CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
223443 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
223491 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
223539 CACATA CACATA CACATA CAC--A CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
223585 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
223633 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
223681 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
223729 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
223777 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
223825 CACATA CACAT- -ACATA CACAT- -ACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
223869 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
* *
223917 CACATA CACATA CACATATA CACATA CACAGA CACATA CATACACA CACATA
1 CACATA CACATA CAC--ATA CACATA CACATA CACATA C--ACATA CACATA
* * * * * *
223969 CACACA CACACA CATACA CACACA CACATACA CACACA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACAT--A CACATA CACATA CACATA
224019 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
224067 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
224115 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
224163 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
224211 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
224259 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
224307 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
224355 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
224403 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
224451 CACAT- -ACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
224497 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
224545 CACATA CACATA CACATA CACATA CACATACA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACAT--A CACATA CACATA CACATA
224595 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
224643 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
224691 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
224739 CACATA CACATA CACATA CAC--A CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
224785 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
224833 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
224881 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
*
224929 CACATA CACATA CACATA CACAT- -ATATA CACATA CACAT- -ACATA
1 CACATA CACATA CACATA CACATA CACATA CACATA CACATA CACATA
*
224973 CACATA CACAT- -ACGTA CACATA CACATA
1 CACATA CACATA CACATA CACATA CACATA
225001 TATACACATA
Statistics
Matches: 1652, Mismatches: 16, Indels: 52
0.96 0.01 0.03
Matches are distributed among these distances:
4 34 0.02
6 1596 0.97
8 22 0.01
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.16
Consensus pattern (6 bp):
CACATA
Found at i:225017 original size:6 final size:6
Alignment explanation
Indices: 225008--225113 Score: 131
Period size: 6 Copynumber: 17.7 Consensus size: 6
224998 ATATATACAC
** * *
225008 ATACGT ATACGT ATACGT ATACAC ATACGT ATACAT ATACGT ATATGT
1 ATACGT ATACGT ATACGT ATACGT ATACGT ATACGT ATACGT ATACGT
** * **
225056 ATACAC ATACGT ATACGT ATACGT ATATGT ATACAC ATACGT ATACGT
1 ATACGT ATACGT ATACGT ATACGT ATACGT ATACGT ATACGT ATACGT
225104 ATACGT ATAC
1 ATACGT ATAC
225114 ACCTTATCAC
Statistics
Matches: 82, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 82 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (6 bp):
ATACGT
Found at i:225049 original size:30 final size:30
Alignment explanation
Indices: 225008--225113 Score: 185
Period size: 30 Copynumber: 3.5 Consensus size: 30
224998 ATATATACAC
225008 ATACGTATACGTATACGTATACACATACGT
1 ATACGTATACGTATACGTATACACATACGT
* *
225038 ATACATATACGTATATGTATACACATACGT
1 ATACGTATACGTATACGTATACACATACGT
*
225068 ATACGTATACGTATATGTATACACATACGT
1 ATACGTATACGTATACGTATACACATACGT
225098 ATACGTATACGTATAC
1 ATACGTATACGTATAC
225114 ACCTTATCAC
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 72 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (30 bp):
ATACGTATACGTATACGTATACACATACGT
Found at i:226726 original size:29 final size:31
Alignment explanation
Indices: 226694--226779 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
226684 TATTCAATTA
*
226694 TTTTGAAAGGTTAGGCCCTTA-TTGAAC-CC
1 TTTTGAAAGGTTAGGCCCTTACTTGAACAAC
* ** *
226723 TTTTGAAAGCTTAATCCCTTATTTGAACAAC
1 TTTTGAAAGGTTAGGCCCTTACTTGAACAAC
* * *
226754 TTCTAAAAGGTTAGGCTCTTACTTGA
1 TTTTGAAAGGTTAGGCCCTTACTTGA
226780 GTATTTAACC
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
29 18 0.41
30 6 0.14
31 20 0.45
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (31 bp):
TTTTGAAAGGTTAGGCCCTTACTTGAACAAC
Found at i:227768 original size:31 final size:31
Alignment explanation
Indices: 227733--227796 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
227723 AGAATTGGTT
227733 TTAACTTCTTAATAGAAATTTTAACAATCTG
1 TTAACTTCTTAATAGAAATTTTAACAATCTG
227764 TTAACTTCTTAATAGAAATTTTAACAATCTG
1 TTAACTTCTTAATAGAAATTTTAACAATCTG
227795 TT
1 TT
227797 TCTTTTTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (31 bp):
TTAACTTCTTAATAGAAATTTTAACAATCTG
Found at i:229341 original size:27 final size:25
Alignment explanation
Indices: 229304--229360 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 25
229294 GAACGACCGG
* **
229304 TTTTTTTACCGGATTAAAAATTGGT
1 TTTTTTTACCGGATAAAAAATCAGT
229329 TTTTTTTAAACCGGATAAAAAATCAGT
1 TTTTTTT--ACCGGATAAAAAATCAGT
229356 TTTTT
1 TTTTT
229361 ATCCGAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 7 0.26
27 20 0.74
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (25 bp):
TTTTTTTACCGGATAAAAAATCAGT
Found at i:229426 original size:51 final size:49
Alignment explanation
Indices: 229326--229433 Score: 162
Period size: 49 Copynumber: 2.2 Consensus size: 49
229316 ATTAAAAATT
* * *
229326 GGTTTTTTTTAAACCGGATAAAAAATCAGTTTTTTATCCGAAAAAATCC
1 GGTTTTTTTCAAACCGGATAAAAAACCAGTTTTTTATACGAAAAAATCC
*
229375 GGTTTTTTTCAAACCGGATAAAAAACCGGTTTTTTATACGAAAAAAAATCC
1 GGTTTTTTTCAAACCGGATAAAAAACCAGTTTTTTATACG--AAAAAATCC
229426 GGTTTTTT
1 GGTTTTTT
229434 AAAAAAACTG
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
49 36 0.68
51 17 0.32
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (49 bp):
GGTTTTTTTCAAACCGGATAAAAAACCAGTTTTTTATACGAAAAAATCC
Found at i:229460 original size:39 final size:41
Alignment explanation
Indices: 229394--229491 Score: 137
Period size: 41 Copynumber: 2.4 Consensus size: 41
229384 CAAACCGGAT
*
229394 AAAAAACCGGTTTTTTATACGAAAAAAAATCCGG-TTTTTTA
1 AAAAAACTGGTTTTTTATACG-AAAAAAATCCGGTTTTTTTA
* *
229435 AAAAAACTGGATTTTTATTCG-AAAAAATCCGGTTTTTTTTA
1 AAAAAACTGGTTTTTTATACGAAAAAAATCCGG-TTTTTTTA
229476 AAAAAACTGGTTTTTT
1 AAAAAACTGGTTTTTT
229492 TGCAAACCGA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
39 11 0.22
41 40 0.78
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (41 bp):
AAAAAACTGGTTTTTTATACGAAAAAAATCCGGTTTTTTTA
Found at i:230210 original size:38 final size:38
Alignment explanation
Indices: 230150--230226 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
230140 TGAGCTTCAC
* *
230150 AAATTTTATTATTTGAAAATAATTTTTTAGGTATTTTA
1 AAATTTTATTATTTGAAAATAATTTTTTAAGTAATTTA
* * *
230188 AAATTTTATTGTTTTAATATAATTTTTTAAGTAATTTA
1 AAATTTTATTATTTGAAAATAATTTTTTAAGTAATTTA
230226 A
1 A
230227 TATAATTATA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (38 bp):
AAATTTTATTATTTGAAAATAATTTTTTAAGTAATTTA
Found at i:230572 original size:63 final size:62
Alignment explanation
Indices: 230456--230583 Score: 213
Period size: 62 Copynumber: 2.0 Consensus size: 62
230446 TCTACGGGCT
230456 AAGATATAATAAGTTCATTTTTTCTCATTTTTCATTAAAAATTTGATGACAAATTAAGTTGA
1 AAGATATAATAAGTTCATTTTTTCTCATTTTTCATTAAAAATTTGATGACAAATTAAGTTGA
**
230518 AAGATATAATAAGTTCATTTTTTCTCATTTTTTGTTAAAAAAATTT-ATGACAAATTAAGTTGA
1 AAGATATAATAAGTTCATTTTTTCTCATTTTTCATT--AAAAATTTGATGACAAATTAAGTTGA
230581 AAG
1 AAG
230584 TTAACCTATT
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
62 34 0.55
63 20 0.32
64 8 0.13
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (62 bp):
AAGATATAATAAGTTCATTTTTTCTCATTTTTCATTAAAAATTTGATGACAAATTAAGTTGA
Found at i:231812 original size:34 final size:34
Alignment explanation
Indices: 231766--231837 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
231756 ACAAGGACAA
* *
231766 GGACAGAACTAAGATGAATGATATGTGTGAGCAG
1 GGACAGAACTAAGATCAATGATATGAGTGAGCAG
*
231800 GGACA-AAGCTAAGATCAATGATATGAGTGAGCAT
1 GGACAGAA-CTAAGATCAATGATATGAGTGAGCAG
231834 GGAC
1 GGAC
231838 GGAGGGATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 2 0.06
34 32 0.94
ACGTcount: A:0.39, C:0.11, G:0.31, T:0.19
Consensus pattern (34 bp):
GGACAGAACTAAGATCAATGATATGAGTGAGCAG
Found at i:232052 original size:34 final size:34
Alignment explanation
Indices: 232014--232155 Score: 126
Period size: 34 Copynumber: 4.1 Consensus size: 34
232004 AACTAAGACG
*
232014 AATGATACGTGTGAG-ATGGGACGAAGTTAGGATC
1 AATGATACGTGTGAGCAT-GGACGAAGCTAGGATC
* *
232048 AATGATATGTGTGAGCATGGACGGAGCTAGGATCAATC
1 AATGATACGTGTGAGCATGGACGAAGCTAGG----ATC
* * * *
232086 AATGATATGTGCGAGCATCGACGGAGCTAGGATC
1 AATGATACGTGTGAGCATGGACGAAGCTAGGATC
* * *
232120 AATGATATGCGTGAGCATCGAC-AGAGCTAGGATC
1 AATGATACGTGTGAGCATGGACGA-AGCTAGGATC
232154 AA
1 AA
232156 ATATTAGGAG
Statistics
Matches: 94, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
34 60 0.64
35 2 0.02
38 32 0.34
ACGTcount: A:0.32, C:0.14, G:0.32, T:0.22
Consensus pattern (34 bp):
AATGATACGTGTGAGCATGGACGAAGCTAGGATC
Found at i:232096 original size:38 final size:38
Alignment explanation
Indices: 232045--232155 Score: 158
Period size: 38 Copynumber: 3.0 Consensus size: 38
232035 CGAAGTTAGG
*
232045 ATCAATGATATGTGTGAGCATGGACGGAGCTAGGATCA
1 ATCAATGATATGTGTGAGCATCGACGGAGCTAGGATCA
*
232083 ATCAATGATATGTGCGAGCATCGACGGAGCTAGG----
1 ATCAATGATATGTGTGAGCATCGACGGAGCTAGGATCA
* *
232117 ATCAATGATATGCGTGAGCATCGACAGAGCTAGGATCA
1 ATCAATGATATGTGTGAGCATCGACGGAGCTAGGATCA
232155 A
1 A
232156 ATATTAGGAG
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
34 31 0.48
38 33 0.52
ACGTcount: A:0.32, C:0.16, G:0.30, T:0.22
Consensus pattern (38 bp):
ATCAATGATATGTGTGAGCATCGACGGAGCTAGGATCA
Found at i:234220 original size:60 final size:60
Alignment explanation
Indices: 234146--234320 Score: 162
Period size: 60 Copynumber: 3.0 Consensus size: 60
234136 ATATGTTTTC
* * * * *
234146 AAACTATAATTCTCATTTTAAATTGGTCTTTAAACTTTTGAATATTCTAATTCCATCCTC-
1 AAACTATGACTCTCATTTT-AATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCCTCT
* * * *
234206 AAATTATGACTCTCATTCTAATTAGTCCTTAAAC--TTAAACATTCTAATTTCAT-CTCT
1 AAACTATGACTCTCATTTTAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCCTCT
* * ** *
234263 AAACTATGACACT-ATTTCTTAATTTGTCCCCAAACTTTTGAATATTTTAATTTCATCC
1 AAACTATGACTCTCA-TT-TTAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCC
234321 CAATTTAGAT
Statistics
Matches: 91, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
56 4 0.04
57 29 0.32
58 13 0.14
59 13 0.14
60 31 0.34
61 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (60 bp):
AAACTATGACTCTCATTTTAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCCTCT
Found at i:239614 original size:62 final size:61
Alignment explanation
Indices: 239540--239692 Score: 156
Period size: 60 Copynumber: 2.5 Consensus size: 61
239530 TATCATGTCC
* * *
239540 CCAAACTATGACTTTCATTTTAAATTGA-TCTTTAAATTTTTTTTG-ATATTCCAA-TTCCATCA
1 CCAAACTATGAC--TCATTTTAAATTGAGTCCTTAAA-ATTTTTTGAACATTCCAACTT-CATC-
239602 T
61 T
*
239603 -CAAACTATGACTCATTCTAAATT-AGTCCTTAAAATTTTTTGAACATTCCAACTTCATCT
1 CCAAACTATGACTCATTTTAAATTGAGTCCTTAAAATTTTTTGAACATTCCAACTTCATCT
*
239662 CCAAACTATAACCCTCATTTTAAATTG-GTCC
1 CCAAACTATGA--CTCATTTTAAATTGAGTCC
239693 CCAAACTTTT
Statistics
Matches: 77, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
59 9 0.12
60 39 0.51
61 2 0.03
62 27 0.35
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (61 bp):
CCAAACTATGACTCATTTTAAATTGAGTCCTTAAAATTTTTTGAACATTCCAACTTCATCT
Found at i:239940 original size:60 final size:60
Alignment explanation
Indices: 239847--239962 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
239837 AGTATATACA
* **
239847 CATAGTTTGAGATTAAATTGAAATGTTTAAAAAGTTTGGGGACTAATTTAGAATGAAGGT
1 CATAGTTTGAGATGAAATTGAAATGTTTAAAAAGTTTAAGGACTAATTTAGAATGAAGGT
* * *
239907 CATAGTTTGGTGATGAAATTGAAATG-TTCAAAAGTTTAAGGACTAATTTATAATGA
1 CATAGTTT-GAGATGAAATTGAAATGTTTAAAAAGTTTAAGGACTAATTTAGAATGA
239963 GGTACAATGC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
60 34 0.69
61 15 0.31
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (60 bp):
CATAGTTTGAGATGAAATTGAAATGTTTAAAAAGTTTAAGGACTAATTTAGAATGAAGGT
Found at i:241747 original size:2 final size:2
Alignment explanation
Indices: 241742--241778 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
241732 TCTCTCTCTT
*
241742 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
241779 CATCTTCTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:243714 original size:33 final size:33
Alignment explanation
Indices: 243664--243741 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 33
243654 CATATTAAAT
* *
243664 ATTTCCGAATG-AACATATCAATATTATCAAGA
1 ATTTCCAAATGCAACATATCAATATAATCAAGA
* *
243696 ATTTCCAAATGCAACATATCAATATAATTAAGT
1 ATTTCCAAATGCAACATATCAATATAATCAAGA
243729 ATTTCCAAATGCA
1 ATTTCCAAATGCA
243742 CATCATACTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 10 0.24
33 31 0.76
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.32
Consensus pattern (33 bp):
ATTTCCAAATGCAACATATCAATATAATCAAGA
Found at i:246016 original size:36 final size:36
Alignment explanation
Indices: 245969--246212 Score: 382
Period size: 36 Copynumber: 6.8 Consensus size: 36
245959 ATCAAAAGTT
* * *
245969 CACTTCTGATTCAAGTAGAACGGAAGAAAGCATCGG
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
246005 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
*
246041 CACTTCCGATTCAAGTCGAACGGAGGGAAGCATCGG
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
*
246077 CACTTCCGATTCAAGTCGAACGGAGGGAAGCATCGG
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
* * *
246113 CACTTCTGATTCAAGTCGAACGGAAAGAAGCATCGA
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
**
246149 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCAA
1 CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
246185 CACTTCCGATTCATA-TCGAACGGAAGGA
1 CACTTCCGATTCA-AGTCGAACGGAAGGA
246213 TGTGTCTTAC
Statistics
Matches: 196, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
36 195 0.99
37 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (36 bp):
CACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGG
Found at i:248426 original size:20 final size:20
Alignment explanation
Indices: 248388--248427 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
248378 TGTATACAAT
*
248388 AGTAATAAACATTGATTAAG
1 AGTAATAAACATAGATTAAG
*
248408 AGTAATAAACATAGTTTAAG
1 AGTAATAAACATAGATTAAG
248428 TAGATCTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.15, T:0.30
Consensus pattern (20 bp):
AGTAATAAACATAGATTAAG
Found at i:252325 original size:36 final size:36
Alignment explanation
Indices: 252270--252340 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
252260 GATTATAGGT
* *
252270 TTTATTCTTGTGAAGTAAGAAACTAAAATTAAGGAC
1 TTTATTCTTGTAAAATAAGAAACTAAAATTAAGGAC
** *
252306 TTTATTCTTGTAAAATAAGATGCTGAAATTAAGGA
1 TTTATTCTTGTAAAATAAGAAACTAAAATTAAGGA
252341 TTTTTAATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (36 bp):
TTTATTCTTGTAAAATAAGAAACTAAAATTAAGGAC
Found at i:260465 original size:21 final size:19
Alignment explanation
Indices: 260441--260492 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 19
260431 CTCAGAGGGA
260441 ACCGATTCCCCCCAAGGGGGT
1 ACCGATTCCCCCC-A-GGGGT
*
260462 ACCGATTCCCCTCAGGGGT
1 ACCGATTCCCCCCAGGGGT
260481 ACCGATTCCCCC
1 ACCGATTCCCCC
260493 TTGTATAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 16 0.55
20 1 0.03
21 12 0.41
ACGTcount: A:0.17, C:0.42, G:0.23, T:0.17
Consensus pattern (19 bp):
ACCGATTCCCCCCAGGGGT
Found at i:266776 original size:23 final size:20
Alignment explanation
Indices: 266720--266780 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 20
266710 TTTTGGTGCA
266720 GAGGGAATCGA-TCACCCCTT
1 GAGGGAATCGATTC-CCCCTT
* *
266740 GAGGGAACCAATTCCCCCTTT
1 GAGGGAATCGATTCCCCC-TT
266761 GAAGGGGAATCGATTCCCCC
1 G-A-GGGAATCGATTCCCCC
266781 CACAGGGGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 13 0.39
21 5 0.15
22 1 0.03
23 14 0.42
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.20
Consensus pattern (20 bp):
GAGGGAATCGATTCCCCCTT
Found at i:268466 original size:22 final size:24
Alignment explanation
Indices: 268440--268483 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
268430 TTTTGGAATG
268440 TTGAA-TT-TTTGGATTGATGACT
1 TTGAATTTGTTTGGATTGATGACT
*
268462 TTGAATTTGTTTGGATTTATGA
1 TTGAATTTGTTTGGATTGATGA
268484 ATGGTTTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 2 0.11
24 12 0.63
ACGTcount: A:0.23, C:0.02, G:0.23, T:0.52
Consensus pattern (24 bp):
TTGAATTTGTTTGGATTGATGACT
Found at i:273323 original size:20 final size:20
Alignment explanation
Indices: 273298--273336 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
273288 AGTATGTCCA
273298 GGGGGTATCGATTCCCCCTG
1 GGGGGTATCGATTCCCCCTG
273318 GGGGGTATCGATTCCCCCT
1 GGGGGTATCGATTCCCCCT
273337 AAAGGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.31, G:0.33, T:0.26
Consensus pattern (20 bp):
GGGGGTATCGATTCCCCCTG
Found at i:277479 original size:30 final size:30
Alignment explanation
Indices: 277439--277541 Score: 102
Period size: 30 Copynumber: 3.4 Consensus size: 30
277429 ACATACAAAT
277439 TGTATTTATGTTTGTTTGTTTATTTTTAAA
1 TGTATTTATGTTTGTTTGTTTATTTTTAAA
* * * *
277469 GGTGTTTATGTTCGTTCGTGTTCA--TTTAAA
1 TGTATTTATGTTTGTT--TGTTTATTTTTAAA
* * *
277499 TTGTATTTATGTTTTTTTGTTTGTTTTTTAA
1 -TGTATTTATGTTTGTTTGTTTATTTTTAAA
277530 TGTATTTATGTT
1 TGTATTTATGTT
277542 CGTTCGTGTT
Statistics
Matches: 57, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
29 4 0.07
30 31 0.54
31 17 0.30
32 5 0.09
ACGTcount: A:0.17, C:0.03, G:0.17, T:0.64
Consensus pattern (30 bp):
TGTATTTATGTTTGTTTGTTTATTTTTAAA
Found at i:277510 original size:61 final size:62
Alignment explanation
Indices: 277435--277597 Score: 213
Period size: 61 Copynumber: 2.6 Consensus size: 62
277425 ATTGACATAC
277435 AAATTGTATTTATGTTTGTTTGTTTATTTTTAAAGGTGTTTATGTTCGTTCGTGTTCATTT-
1 AAATTGTATTTATGTTTGTTTGTTTATTTTTAAAGGTGTTTATGTTCGTTCGTGTTCATTTA
* * * * *
277496 AAATTGTATTTATGTTTTTTTGTTTGTTTTTTAATGTATTTATGTTCGTTCGTGTTCATTTA
1 AAATTGTATTTATGTTTGTTTGTTTATTTTTAAAGGTGTTTATGTTCGTTCGTGTTCATTTA
** *
277558 AAATT-TCAATATCGTGTTTGTTTGTTTATTTTTGAAGGTG
1 AAATTGT--AT-TTATGTTTGTTTGTTTATTTTTAAAGGTG
277598 CTCGTGTTCA
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
61 57 0.66
62 5 0.06
63 2 0.02
64 22 0.26
ACGTcount: A:0.19, C:0.05, G:0.17, T:0.59
Consensus pattern (62 bp):
AAATTGTATTTATGTTTGTTTGTTTATTTTTAAAGGTGTTTATGTTCGTTCGTGTTCATTTA
Found at i:277901 original size:24 final size:24
Alignment explanation
Indices: 277874--277927 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
277864 AACCTTGTTT
*
277874 GCTTATAAACAAGTCGATAAACGA
1 GCTTATAAACAAGTCAATAAACGA
277898 GCTTATAAACAAGTCAATAAACGA
1 GCTTATAAACAAGTCAATAAACGA
*
277922 GTTTAT
1 GCTTAT
277928 TTGTGAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (24 bp):
GCTTATAAACAAGTCAATAAACGA
Found at i:279143 original size:41 final size:41
Alignment explanation
Indices: 279098--279179 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
279088 TTTACCGGTT
*
279098 AAAAGAAAGCAGGTGTTCAAGCTACTATAAAGATGATGATA
1 AAAAGAAAGCAGGTGTTCAAGCTACTATAAAGACGATGATA
*
279139 AAAAGAAAGCAGGTGTTGAAGCTACTATAAAGACGATGATA
1 AAAAGAAAGCAGGTGTTCAAGCTACTATAAAGACGATGATA
279180 GTAAGTGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.46, C:0.10, G:0.23, T:0.21
Consensus pattern (41 bp):
AAAAGAAAGCAGGTGTTCAAGCTACTATAAAGACGATGATA
Found at i:284769 original size:13 final size:12
Alignment explanation
Indices: 284745--284799 Score: 62
Period size: 13 Copynumber: 4.6 Consensus size: 12
284735 CCTTAAAAGA
284745 TTAAATATCCTACT
1 TTAAA-ATCCTA-T
284759 TTAAAATCCTAT
1 TTAAAATCCTAT
284771 TT---ATCCTACT
1 TTAAAATCCTA-T
284781 TTAAAATCCTAT
1 TTAAAATCCTAT
284793 TTAAAAT
1 TTAAAAT
284800 TTTAATACTA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
9 6 0.16
10 3 0.08
12 11 0.30
13 12 0.32
14 5 0.14
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.44
Consensus pattern (12 bp):
TTAAAATCCTAT
Found at i:284775 original size:22 final size:22
Alignment explanation
Indices: 284750--284795 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
284740 AAAGATTAAA
284750 TATCCTACTTTAAAATCCTATT
1 TATCCTACTTTAAAATCCTATT
284772 TATCCTACTTTAAAATCCTATT
1 TATCCTACTTTAAAATCCTATT
284794 TA
1 TA
284796 AAATTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.46
Consensus pattern (22 bp):
TATCCTACTTTAAAATCCTATT
Found at i:285791 original size:140 final size:140
Alignment explanation
Indices: 285539--285810 Score: 418
Period size: 140 Copynumber: 1.9 Consensus size: 140
285529 TATATAATAG
* * * * *
285539 AAAAGTCTGATAGATAAAATTTAGGTTAGTGCTGTTGTATTACAGTTTAACTTAGGGTTAATTTA
1 AAAAGTCTGACAGATAAAATTTAGGTTAGTACTGTTGTATCACAGTTTAACTTAAGGTTAACTTA
* *
285604 CGATAGATTTCAATTAAAGATGTTATATATTTTATAATAGTTTTAGTTATAACTAAAAATTTACA
66 CGATAGATTTCAACTAAAGATGTTATACATTTTATAATAGTTTTAGTTATAACTAAAAATTTACA
285669 CAGATAGTAA
131 CAGATAGTAA
**
285679 AAAAGTCTGACAGATAAAATTTAGGTTAGTACTGTTGTATCGTAGTTTAACTTAAGGTTAACTTA
1 AAAAGTCTGACAGATAAAATTTAGGTTAGTACTGTTGTATCACAGTTTAACTTAAGGTTAACTTA
* * * **
285744 CTATAGATTTTAACTAAAGATGTTATACATTTTATTATAGTTTTAGTTATAACTACGAATTTACA
66 CGATAGATTTCAACTAAAGATGTTATACATTTTATAATAGTTTTAGTTATAACTAAAAATTTACA
285809 CA
131 CA
285811 ATGACGGATT
Statistics
Matches: 118, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
140 118 1.00
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (140 bp):
AAAAGTCTGACAGATAAAATTTAGGTTAGTACTGTTGTATCACAGTTTAACTTAAGGTTAACTTA
CGATAGATTTCAACTAAAGATGTTATACATTTTATAATAGTTTTAGTTATAACTAAAAATTTACA
CAGATAGTAA
Found at i:289141 original size:21 final size:20
Alignment explanation
Indices: 289117--289221 Score: 63
Period size: 21 Copynumber: 5.2 Consensus size: 20
289107 GATGATTATC
*
289117 GATACTCTTAGGCTTGATATT
1 GATACTCTTAGG-TGGATATT
* * *
289138 GATACTCATATGAGGATATT
1 GATACTCTTAGGTGGATATT
* * *
289158 GATAC-C--ATGTGGACAGTG
1 GATACTCTTAGGTGGATA-TT
*
289176 GATACTCTTAGGCTTGATATT
1 GATACTCTTAGG-TGGATATT
* * *
289197 GATACTCATATGAGGATATT
1 GATACTCTTAGGTGGATATT
289217 GATAC
1 GATAC
289222 CATGTGGTAT
Statistics
Matches: 64, Mismatches: 15, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
17 7 0.11
18 6 0.09
19 2 0.03
20 22 0.34
21 23 0.36
22 4 0.06
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (20 bp):
GATACTCTTAGGTGGATATT
Found at i:289157 original size:20 final size:20
Alignment explanation
Indices: 289132--289221 Score: 78
Period size: 20 Copynumber: 4.5 Consensus size: 20
289122 TCTTAGGCTT
289132 GATATTGATACTCATATGAG
1 GATATTGATACTCATATGAG
*
289152 GATATTGATAC-C--ATGTG
1 GATATTGATACTCATATGAG
* * * * **
289169 GACAGTGGATACTCTTAGGCTT
1 GATA-TTGATACTCATATG-AG
289191 GATATTGATACTCATATGAG
1 GATATTGATACTCATATGAG
289211 GATATTGATAC
1 GATATTGATAC
289222 CATGTGGTAT
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
17 7 0.13
18 6 0.11
19 2 0.04
20 22 0.41
21 13 0.24
22 4 0.07
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.34
Consensus pattern (20 bp):
GATATTGATACTCATATGAG
Found at i:289186 original size:59 final size:59
Alignment explanation
Indices: 289117--289228 Score: 224
Period size: 59 Copynumber: 1.9 Consensus size: 59
289107 GATGATTATC
289117 GATACTCTTAGGCTTGATATTGATACTCATATGAGGATATTGATACCATGTGGACAGTG
1 GATACTCTTAGGCTTGATATTGATACTCATATGAGGATATTGATACCATGTGGACAGTG
289176 GATACTCTTAGGCTTGATATTGATACTCATATGAGGATATTGATACCATGTGG
1 GATACTCTTAGGCTTGATATTGATACTCATATGAGGATATTGATACCATGTGG
289229 TATTAGTTTC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (59 bp):
GATACTCTTAGGCTTGATATTGATACTCATATGAGGATATTGATACCATGTGGACAGTG
Done.