Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007889.1 Hibiscus syriacus cultivar Beakdansim tig00110271_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: 1663484
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:132848 original size:18 final size:18
Alignment explanation
Indices: 132806--132839 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
132796 ATTATATAAG
132806 TAAAATA-TTAAATAAAT
1 TAAAATACTTAAATAAAT
132823 TAAAATACTTAAATAAA
1 TAAAATACTTAAATAAA
132840 ATTTAATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAATACTTAAATAAAT
Found at i:132907 original size:10 final size:10
Alignment explanation
Indices: 132901--132934 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
132891 ATAAGAGTAT
132901 TTGAGAGAAA
1 TTGAGAGAAA
*
132911 TTGAGATAAA
1 TTGAGAGAAA
*
132921 TTGAGAGAAT
1 TTGAGAGAAA
132931 TTGA
1 TTGA
132935 TATGATGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.29
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:139113 original size:23 final size:25
Alignment explanation
Indices: 139086--139135 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
139076 ATCTTTAATG
*
139086 CCTCCGTTT-CCCTCC-AATACCTT
1 CCTCCGTTTACCCCCCAAATACCTT
*
139109 CCTCCGTTTACCCCCCAAATCCCTT
1 CCTCCGTTTACCCCCCAAATACCTT
139134 CC
1 CC
139136 CTTTTCTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 9 0.39
24 5 0.22
25 9 0.39
ACGTcount: A:0.14, C:0.52, G:0.04, T:0.30
Consensus pattern (25 bp):
CCTCCGTTTACCCCCCAAATACCTT
Found at i:141740 original size:87 final size:87
Alignment explanation
Indices: 141589--141770 Score: 222
Period size: 87 Copynumber: 2.1 Consensus size: 87
141579 ATTCTTGAAG
* * *
141589 ATCAAAACTATGGTCCATGCCTCCACGGGTACTTTAAAAAGACCAAAACTATGCATGCAAAACTA
1 ATCAACACTATGGTCCATGCCTCCACGGGAACTTGAAAAAGACCAAAACTATGCATGCAAAACTA
* *
141654 CATTTAAAAGGGTAAGTTCCAT
66 CATCTAAAAGGGTAAGTTCCAA
* * * * * * *
141676 ATCAACACTATGGTCCATGCTTGCAGGGGAACTTGAAAAAGATCAAAACTCTAG-TTGCAGAACT
1 ATCAACACTATGGTCCATGCCTCCACGGGAACTTGAAAAAGACCAAAACTAT-GCATGCAAAACT
* *
141740 ATATCTAAATGGGTAAGTTCCAA
65 ACATCTAAAAGGGTAAGTTCCAA
141763 ATCAACAC
1 ATCAACAC
141771 CATAGATCCT
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
87 79 0.99
88 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.24
Consensus pattern (87 bp):
ATCAACACTATGGTCCATGCCTCCACGGGAACTTGAAAAAGACCAAAACTATGCATGCAAAACTA
CATCTAAAAGGGTAAGTTCCAA
Found at i:147000 original size:17 final size:17
Alignment explanation
Indices: 146959--147002 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
146949 TAATGGAGTA
146959 AAAAAAATAAAAAAGGT
1 AAAAAAATAAAAAAGGT
* *
146976 AAAGAAATTAAAAAGG-
1 AAAAAAATAAAAAAGGT
146992 AATAAAAATAA
1 AA-AAAAATAA
147003 TGTGTACATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 2 0.09
17 20 0.91
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (17 bp):
AAAAAAATAAAAAAGGT
Found at i:147312 original size:14 final size:14
Alignment explanation
Indices: 147282--147321 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 14
147272 ATATATAATG
147282 ATATAAGATATATATA
1 ATATAA-ATA-ATATA
147298 ATATAAATAATATA
1 ATATAAATAATATA
147312 ATATAAATAA
1 ATATAAATAA
147322 AAAAAGGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 15 0.62
15 3 0.12
16 6 0.25
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (14 bp):
ATATAAATAATATA
Found at i:147315 original size:21 final size:21
Alignment explanation
Indices: 147266--147374 Score: 62
Period size: 19 Copynumber: 5.6 Consensus size: 21
147256 ACATTTATGC
147266 ATATATATATATAATGAT--ATA
1 ATATA-ATATATAAT-ATAAATA
*
147287 AGAT-ATATATAATATAAATA
1 ATATAATATATAATATAAATA
147307 ATATAATATA-AATA-AAA-A
1 ATATAATATATAATATAAATA
*
147325 A-AGGAATATAGTAA-ATAAATA
1 ATA-TAATATA-TAATATAAATA
* *
147346 A-A-AAAATATAAT-TAAAAA
1 ATATAATATATAATATAAATA
147364 ATAT-ATATATA
1 ATATAATATATA
147375 GGGGACGAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 24
0.70 0.06 0.24
Matches are distributed among these distances:
17 1 0.01
18 19 0.27
19 25 0.35
20 15 0.21
21 11 0.15
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (21 bp):
ATATAATATATAATATAAATA
Found at i:147805 original size:17 final size:17
Alignment explanation
Indices: 147768--147810 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
147758 TAACTATTTT
*
147768 TAGAATCCTATTAACAA
1 TAGAATCCTAATAACAA
147785 TAGAATCCTAAT-ACAA
1 TAGAATCCTAATAACAA
*
147801 CTAGACTCCT
1 -TAGAATCCT
147811 TGCTCGGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (17 bp):
TAGAATCCTAATAACAA
Found at i:148915 original size:110 final size:105
Alignment explanation
Indices: 148684--148952 Score: 310
Period size: 110 Copynumber: 2.5 Consensus size: 105
148674 GTGGGTAGTA
* * * *
148684 TTGTTTCGAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTT
1 TTGTCTCGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAACTGGAAAATTGTTT
* * *
148748 GTTGATAGCAGCCGCCCCTTCGCTGTGAAGTTGAGTTTGTG
65 GTTGAAAGCAGCCGCCCATTCGCTGTGAAGTTGAGCTTGTG
* *
148789 TTGTCTCGAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATAAAACT-GAAAAGTT
1 TTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTG----AAACTGGAAAA-TT
* * *
148853 GTTTGTTGACAATCAGTCGCCCATTCGTTGTGAAGTTGAGCTTGTG
61 GTTTGTTGA-AAGCAGCCGCCCATTCGCTGTGAAGTTGAGCTTGTG
* * *
148899 TTGTCTTGAGTCCAATATCAC-TCACTGTGAAGTTGAAATTGGCTCTAAAACTGG
1 TTGTCTCGAGTCCAATATC-CTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGG
148953 GAAGCCCCTT
Statistics
Matches: 138, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
105 41 0.30
106 6 0.04
107 1 0.01
108 4 0.03
109 15 0.11
110 70 0.51
111 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (105 bp):
TTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGAAAATTGTTTG
TTGAAAGCAGCCGCCCATTCGCTGTGAAGTTGAGCTTGTG
Found at i:149830 original size:65 final size:67
Alignment explanation
Indices: 149649--149844 Score: 213
Period size: 65 Copynumber: 2.9 Consensus size: 67
149639 GAAAACGATC
* * * *
149649 TCAAAGATATCTGTTGTTTCATGA-AAACGGTCTCAAG-GAAAACAAAATTTTGTTTTAAGGGAA
1 TCAAAGAT-TTTG-TGTTTCAAGAGAAACTGTCTCAAGAG-AGACAAAA-TTTGTTTTAAGGGAA
149712 ATAAAT
62 ATAAAT
** *
149718 TTGAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATTTGTTTT-AGGAGAAATA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGG-GAAATA
149782 AAT
65 AAT
* * * *
149785 TCAAAGA-TTT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTGTTTCATGGGAAA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAA
149845 CTATCTCAAG
Statistics
Matches: 110, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
65 42 0.38
66 8 0.07
67 31 0.28
68 22 0.20
69 7 0.06
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (67 bp):
TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAA
AT
Found at i:149872 original size:35 final size:36
Alignment explanation
Indices: 149797--149879 Score: 114
Period size: 36 Copynumber: 2.3 Consensus size: 36
149787 AAAGATTTTG
* * **
149797 TTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTG
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
*
149833 TTTCATGGGAAACTATCTCAAGAGAGA-AAAATTCA
1 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
149868 TTTCAAGGGAAA
1 TTTCAAGGGAAA
149880 TGTTTTCAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
35 16 0.39
36 25 0.61
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.25
Consensus pattern (36 bp):
TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
Found at i:151397 original size:69 final size:69
Alignment explanation
Indices: 151286--151419 Score: 241
Period size: 69 Copynumber: 1.9 Consensus size: 69
151276 TCTCTCTTGA
*
151286 TGCTCTATGATCTTCGAGTGGAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATAAATCTCAT
1 TGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATAAATCTCAT
151351 TTGT
66 TTGT
* *
151355 TGCTCTATGATCTTCGAGTGAAGTGGTTCAGTGATTCAGAAATGATTGTGCTTGATCAATCTCAT
1 TGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATAAATCTCAT
151420 AGTTTGAATC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (69 bp):
TGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATAAATCTCAT
TTGT
Found at i:151520 original size:13 final size:13
Alignment explanation
Indices: 151491--151528 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
151481 TTATTCTTCA
151491 ATTTTC-CTTTGTT
1 ATTTTCTCTTT-TT
151504 -TTTTCTCTTTTT
1 ATTTTCTCTTTTT
151516 ATTTTCTCTTTTT
1 ATTTTCTCTTTTT
151529 TTCTCTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.05, C:0.16, G:0.03, T:0.76
Consensus pattern (13 bp):
ATTTTCTCTTTTT
Found at i:154752 original size:18 final size:17
Alignment explanation
Indices: 154720--154766 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
154710 TATTAATGGA
154720 GTAAAAAAATAAAAAAG
1 GTAAAAAAATAAAAAAG
*
154737 GTAAAAGAAATTAAAAAG
1 GTAAAA-AAATAAAAAAG
154755 G-AATAAAAATAA
1 GTAA-AAAAATAA
154767 TGTGTACATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (17 bp):
GTAAAAAAATAAAAAAG
Found at i:154897 original size:11 final size:10
Alignment explanation
Indices: 154862--154939 Score: 65
Period size: 10 Copynumber: 7.6 Consensus size: 10
154852 TACATGATAT
154862 TAAA-AAAAA
1 TAAATAAAAA
154871 T-AAT-AAAA
1 TAAATAAAAA
154879 TAAATAAAAA
1 TAAATAAAAA
154889 TAAAGTAAAAA
1 TAAA-TAAAAA
*
154900 TATAATATATATA
1 TA-AATA-A-AAA
154913 TAAATAAATAA
1 TAAATAAA-AA
154924 -AAATAAAAA
1 TAAATAAAAA
154933 TAGAATA
1 TA-AATA
154940 TTAAGAAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 18
0.74 0.03 0.23
Matches are distributed among these distances:
8 7 0.12
9 6 0.11
10 17 0.30
11 16 0.28
12 7 0.12
13 4 0.07
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (10 bp):
TAAATAAAAA
Found at i:154898 original size:28 final size:27
Alignment explanation
Indices: 154792--154939 Score: 90
Period size: 27 Copynumber: 5.4 Consensus size: 27
154782 TAGTATTTAC
* *
154792 TAAAACAAATAAAAAT-AATAAATATA
1 TAAAATAAATAAAAATAAATAAAAATA
* * *
154818 TAATACTAAGT-AAAACAAATAAAAACTA
1 TAA-AATAAATAAAAATAAATAAAAA-TA
* * * *
154846 -AAGATATACATGATATTAAA-AAAAATAA
1 TAA-A-ATAAATAAAAATAAATAAAAAT-A
154874 TAAAATAAATAAAAATAAAGTAAAAATA
1 TAAAATAAATAAAAATAAA-TAAAAATA
* * *
154902 TAATATATATATAAATAAATAAAAATA
1 TAAAATAAATAAAAATAAATAAAAATA
154929 -AAAATAGAATA
1 TAAAATA-AATA
154940 TTAAGAAAAA
Statistics
Matches: 91, Mismatches: 21, Indels: 19
0.69 0.16 0.15
Matches are distributed among these distances:
26 12 0.13
27 37 0.41
28 29 0.32
29 13 0.14
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.24
Consensus pattern (27 bp):
TAAAATAAATAAAAATAAATAAAAATA
Found at i:154955 original size:46 final size:39
Alignment explanation
Indices: 154922--154997 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
154912 ATAAATAAAT
154922 AAAAATA-AAAATAGAATATTAAGAAAAAATATATATAA
1 AAAAATATAAAATAGAATATTAAGAAAAAATATATATAA
** *
154960 AAACGTATAAAATATAATATTAAGAAAAAATATATATA
1 AAAAATATAAAATAGAATATTAAGAAAAAATATATATA
154998 CATAGTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 5 0.15
39 29 0.85
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.26
Consensus pattern (39 bp):
AAAAATATAAAATAGAATATTAAGAAAAAATATATATAA
Found at i:154957 original size:17 final size:17
Alignment explanation
Indices: 154937--154996 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 17
154927 TAAAAATAGA
154937 ATATTAAGAAAAAATAT
1 ATATTAAGAAAAAATAT
* *
154954 ATATAAAAACGTATAAAATAT
1 ATAT--TAA-G-AAAAAATAT
154975 AATATTAAGAAAAAATAT
1 -ATATTAAGAAAAAATAT
154993 ATAT
1 ATAT
154997 ACATAGTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 8 0.24
18 8 0.24
19 3 0.09
20 3 0.09
21 8 0.24
22 4 0.12
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (17 bp):
ATATTAAGAAAAAATAT
Found at i:155076 original size:25 final size:23
Alignment explanation
Indices: 155032--155078 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
155022 ACATCTATAC
* *
155032 ATATATATATATAATGATATAAG
1 ATATATATATAAAATAATATAAG
155055 ATATATATAATAAAAATAATATAA
1 ATATATAT-AT-AAAATAATATAA
155079 TATAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (23 bp):
ATATATATATAAAATAATATAAG
Found at i:155183 original size:13 final size:12
Alignment explanation
Indices: 155164--155196 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
155154 TATAAAAGTA
155164 AAATTAAAGGGT
1 AAATTAAAGGGT
155176 AAATTTAAA-GGT
1 AAA-TTAAAGGGT
155188 AAATTAAAG
1 AAATTAAAG
155197 ATTAAGATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 5 0.26
12 9 0.47
13 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (12 bp):
AAATTAAAGGGT
Found at i:161621 original size:19 final size:21
Alignment explanation
Indices: 161589--161631 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
161579 GTGATATGGC
*
161589 ACACAAATCTATGCAAGT-AT
1 ACACAAATCGATGCAAGTAAT
161609 ACAC-AATCGATGCAAGTAAT
1 ACACAAATCGATGCAAGTAAT
161629 ACA
1 ACA
161632 GTAGTGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.47, C:0.21, G:0.12, T:0.21
Consensus pattern (21 bp):
ACACAAATCGATGCAAGTAAT
Found at i:166589 original size:26 final size:27
Alignment explanation
Indices: 166538--166590 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
166528 TTAATTTTGA
* * *
166538 AGGGTTTAATTTATGTTTTTTTAAATT
1 AGGGTTTAACTAATGTTTTTTGAAATT
166565 AGGGTTTAACTAAT-TTTTTTGAAATT
1 AGGGTTTAACTAATGTTTTTTGAAATT
166591 TTGAGAGGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.28, C:0.02, G:0.15, T:0.55
Consensus pattern (27 bp):
AGGGTTTAACTAATGTTTTTTGAAATT
Found at i:169544 original size:23 final size:25
Alignment explanation
Indices: 169496--169544 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
169486 GAGTTAGGAA
*
169496 GCAACAGGGGCGTAGTTGGGTTGATG
1 GCAACAGCGGCGTAGTT-GGTTGATG
169522 GCAACAGCGGC-TAGTT-GTTGATG
1 GCAACAGCGGCGTAGTTGGTTGATG
169545 CCCTGTTCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
25 5 0.23
26 10 0.45
ACGTcount: A:0.20, C:0.14, G:0.41, T:0.24
Consensus pattern (25 bp):
GCAACAGCGGCGTAGTTGGTTGATG
Found at i:170822 original size:29 final size:31
Alignment explanation
Indices: 170763--170826 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
170753 CTTTTTTTTA
*
170763 AAATAGATAAAATTAAGGAAATTTAAGGATT
1 AAATAGATAAAATTAAGGAAATTCAAGGATT
*
170794 AAATAGA-AAAA-TATGGAAAATTCAA-GATT
1 AAATAGATAAAATTAAGG-AAATTCAAGGATT
170823 AAAT
1 AAAT
170827 TGAGCTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 12 0.40
30 11 0.37
31 7 0.23
ACGTcount: A:0.58, C:0.02, G:0.14, T:0.27
Consensus pattern (31 bp):
AAATAGATAAAATTAAGGAAATTCAAGGATT
Found at i:183868 original size:25 final size:25
Alignment explanation
Indices: 183834--183883 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
183824 ATACTAGTGA
183834 TATTTGTCTCACTAAAAATCTCATC
1 TATTTGTCTCACTAAAAATCTCATC
183859 TATTTGTCTCACTAAAAATCTCATC
1 TATTTGTCTCACTAAAAATCTCATC
183884 CAACACTCTA
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:0.24, G:0.04, T:0.40
Consensus pattern (25 bp):
TATTTGTCTCACTAAAAATCTCATC
Found at i:184359 original size:20 final size:21
Alignment explanation
Indices: 184334--184409 Score: 73
Period size: 23 Copynumber: 3.6 Consensus size: 21
184324 TATTTGGTAG
184334 AGGGAATCGATACCCCC-ATA
1 AGGGAATCGATACCCCCTATA
* * *
184354 AGGGAACCGATTCCCCCTTTGA
1 AGGGAATCGATACCCCCTAT-A
* *
184376 ATGGGAATTGATTCCCCCTATA
1 A-GGGAATCGATACCCCCTATA
*
184398 GGGGAATCGATA
1 AGGGAATCGATA
184410 TCTCCCTGGG
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
20 15 0.34
21 10 0.23
22 3 0.07
23 16 0.36
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.22
Consensus pattern (21 bp):
AGGGAATCGATACCCCCTATA
Found at i:190054 original size:3 final size:3
Alignment explanation
Indices: 190046--190073 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
190036 AGCATTCTCT
190046 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
190074 AAGCTACTAG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:193054 original size:14 final size:14
Alignment explanation
Indices: 193035--193104 Score: 131
Period size: 14 Copynumber: 5.0 Consensus size: 14
193025 CGTTCGTGAA
*
193035 CGTTCGGTTATGTT
1 CGTTCGTTTATGTT
193049 CGTTCGTTTATGTT
1 CGTTCGTTTATGTT
193063 CGTTCGTTTATGTT
1 CGTTCGTTTATGTT
193077 CGTTCGTTTATGTT
1 CGTTCGTTTATGTT
193091 CGTTCGTTTATGTT
1 CGTTCGTTTATGTT
193105 TAACCCAATC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
14 55 1.00
ACGTcount: A:0.07, C:0.14, G:0.23, T:0.56
Consensus pattern (14 bp):
CGTTCGTTTATGTT
Found at i:193389 original size:6 final size:6
Alignment explanation
Indices: 193380--193422 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
193370 GGGATGATAA
*
193380 ACGGGG ACGGGG ACGGGG ACGGGG ATGGGG ACGGGG ACGGGG A
1 ACGGGG ACGGGG ACGGGG ACGGGG ACGGGG ACGGGG ACGGGG A
193423 AAACTCATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.19, C:0.14, G:0.65, T:0.02
Consensus pattern (6 bp):
ACGGGG
Found at i:193571 original size:24 final size:26
Alignment explanation
Indices: 193544--193606 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 26
193534 ATATATATAT
*
193544 ATAATATTAATA-A-ATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
193568 ATAA-A-AAATATATATTTAATTTAA
1 ATAATATAAATATATATTTAATTTAA
*
193592 AT-ATATATATATATA
1 ATAATATAAATATATA
193607 CCCGGCCCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 3 0.09
24 18 0.55
25 8 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATAATATAAATATATATTTAATTTAA
Found at i:193586 original size:19 final size:19
Alignment explanation
Indices: 193562--193601 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
193552 AATAAATTTA
193562 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
193581 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
193600 AT
1 AT
193602 ATATACCCGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:193648 original size:12 final size:12
Alignment explanation
Indices: 193624--193669 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
193614 CGATTCCCAG
193624 CCCAATA-CCGA
1 CCCAATACCCGA
193635 CCCAATACCCGA
1 CCCAATACCCGA
* * *
193647 CCCAATATCTGG
1 CCCAATACCCGA
193659 CCCAATACCCG
1 CCCAATACCCG
193670 TTTAAATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 7 0.24
12 22 0.76
ACGTcount: A:0.30, C:0.46, G:0.11, T:0.13
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:194678 original size:16 final size:16
Alignment explanation
Indices: 194657--194687 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
194647 AAAAAAATTA
194657 TTCGTTTATGTTCGTG
1 TTCGTTTATGTTCGTG
194673 TTCGTTTATGTTCGT
1 TTCGTTTATGTTCGT
194688 TTATTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TTCGTTTATGTTCGTG
Found at i:197660 original size:35 final size:37
Alignment explanation
Indices: 197589--197661 Score: 89
Period size: 35 Copynumber: 2.0 Consensus size: 37
197579 GTTGAAAAAT
*
197589 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
* *
197626 ATTTATAT-TTTT-TTTTACAAAATTGAAAAT-ATAAA
1 ATTTATATATTTTCTTTAAAAAAATT-AAAATCATAAA
197661 A
1 A
197662 AGGTTTAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 16 0.50
36 8 0.25
37 8 0.25
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:199547 original size:73 final size:73
Alignment explanation
Indices: 199428--199574 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
199418 CTACCAAGAT
199428 GCTTTGGGTCCTTGTTGAGAATTGTTAGGCATAGTTGGGCCTAAAAGAGTGTATTTTTGAAGTGG
1 GCTTTGGGTCCTTGTTGAGAATTGTTAGGCATAGTTGGGCCTAAAAGAGTGTATTTTTGAAGTGG
199493 ATTTAAAA
66 ATTTAAAA
199501 GCTTTGGGTCCTTGTTGAGAATTGTTAGGCATAGTTGGGCCTAAAAGAGTGTATTTTTGAAGTGG
1 GCTTTGGGTCCTTGTTGAGAATTGTTAGGCATAGTTGGGCCTAAAAGAGTGTATTTTTGAAGTGG
199566 ATTTAAAA
66 ATTTAAAA
199574 G
1 G
199575 ATAGAGAATT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.26, C:0.08, G:0.29, T:0.37
Consensus pattern (73 bp):
GCTTTGGGTCCTTGTTGAGAATTGTTAGGCATAGTTGGGCCTAAAAGAGTGTATTTTTGAAGTGG
ATTTAAAA
Found at i:203710 original size:15 final size:15
Alignment explanation
Indices: 203659--203711 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
203649 TCTGATTAAG
*
203659 TTTTAATTGGTTAATTT
1 TTTTAATT--TTAAATT
* *
203676 TTTTATTTTTAGATT
1 TTTTAATTTTAAATT
*
203691 CTTTAATTTTAAATT
1 TTTTAATTTTAAATT
203706 TTTTAA
1 TTTTAA
203712 ATATAATTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
15 22 0.76
17 7 0.24
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (15 bp):
TTTTAATTTTAAATT
Found at i:205606 original size:22 final size:22
Alignment explanation
Indices: 205581--205643 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
205571 GTTTGACAAA
*
205581 ATATATAAGTTTTAAAAATTAT
1 ATATATAAGTTTTAAAAACTAT
**
205603 ATATATGCGTTTTAAAAACTAT
1 ATATATAAGTTTTAAAAACTAT
* *
205625 ATGTTATAA-TTTCAAAAAC
1 AT-ATATAAGTTTTAAAAAC
205644 CATTATAATT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
22 30 0.91
23 3 0.09
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.41
Consensus pattern (22 bp):
ATATATAAGTTTTAAAAACTAT
Found at i:205743 original size:23 final size:25
Alignment explanation
Indices: 205689--205754 Score: 82
Period size: 23 Copynumber: 2.7 Consensus size: 25
205679 TTTTTTTTTA
* *
205689 TCAAAATTATATATTATATATACGTT
1 TCAAAACTATATA-TATATATACATT
*
205715 TTAAAACTATATATAT-TATA-ATT
1 TCAAAACTATATATATATATACATT
205738 TCAAAACTATATATATA
1 TCAAAACTATATATATA
205755 AAGTATAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
23 17 0.49
24 4 0.11
25 3 0.09
26 11 0.31
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.44
Consensus pattern (25 bp):
TCAAAACTATATATATATATACATT
Found at i:205775 original size:25 final size:27
Alignment explanation
Indices: 205722--205778 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
205712 GTTTTAAAAC
* *
205722 TATATATATTATAATTTCAAAACTATA
1 TATATAAAGTATAATTTCAAAACTATA
**
205749 TATATAAAGTATAATTTCAAATGTATA
1 TATATAAAGTATAATTTCAAAACTATA
205776 TAT
1 TAT
205779 TTTAAAAACC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (27 bp):
TATATAAAGTATAATTTCAAAACTATA
Found at i:206943 original size:28 final size:28
Alignment explanation
Indices: 206912--206968 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
206902 CGTCGGTAGT
206912 GGCGTTTACCAAAATTGTCGCCTTATAA
1 GGCGTTTACCAAAATTGTCGCCTTATAA
206940 GGCGTTTACCAAAATTGTCGCCTTATAA
1 GGCGTTTACCAAAATTGTCGCCTTATAA
206968 G
1 G
206969 AGTCAATAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (28 bp):
GGCGTTTACCAAAATTGTCGCCTTATAA
Found at i:210014 original size:54 final size:54
Alignment explanation
Indices: 209950--210058 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
209940 ATTTCATACT
209950 AAAGTTGATTTGCTTGAGGATAAGAAAATATTTGAATGTGGGGGTGGGGGTGGG
1 AAAGTTGATTTGCTTGAGGATAAGAAAATATTTGAATGTGGGGGTGGGGGTGGG
210004 AAAGTTGATTTGCTTGAGGATAAGAAAATATTTGAATGTGGGGGTGGGGGTGGG
1 AAAGTTGATTTGCTTGAGGATAAGAAAATATTTGAATGTGGGGGTGGGGGTGGG
210058 A
1 A
210059 CAGGCGAATA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.28, C:0.02, G:0.40, T:0.29
Consensus pattern (54 bp):
AAAGTTGATTTGCTTGAGGATAAGAAAATATTTGAATGTGGGGGTGGGGGTGGG
Found at i:214288 original size:34 final size:34
Alignment explanation
Indices: 214250--214330 Score: 162
Period size: 34 Copynumber: 2.4 Consensus size: 34
214240 AGCAGCATTA
214250 ATCAATATTTTTTGAGCACTTATTAAAGGTCGTC
1 ATCAATATTTTTTGAGCACTTATTAAAGGTCGTC
214284 ATCAATATTTTTTGAGCACTTATTAAAGGTCGTC
1 ATCAATATTTTTTGAGCACTTATTAAAGGTCGTC
214318 ATCAATATTTTTT
1 ATCAATATTTTTT
214331 CTATCTTCAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (34 bp):
ATCAATATTTTTTGAGCACTTATTAAAGGTCGTC
Found at i:216130 original size:20 final size:19
Alignment explanation
Indices: 216086--216138 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
216076 TAAGTGAACT
*
216086 CAGTATCGATACCACCCTG
1 CAGTATCGATACCACCCTA
*
216105 CGAGTATCGATACCTCACCTA
1 C-AGTATCGATACCAC-CCTA
*
216126 CAGTATCAATACC
1 CAGTATCGATACC
216139 CATTGAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 24 0.83
21 4 0.14
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (19 bp):
CAGTATCGATACCACCCTA
Found at i:221839 original size:44 final size:45
Alignment explanation
Indices: 221752--221848 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 45
221742 ACATGAAAAT
* * * *
221752 TGAAAATTGCAAATGGGAATGGAAATGGAAATTGGGTTTCATTCA
1 TGAAATTTGCAAATGGAAATGAAAATGGAAAATGGGTTTCATTCA
*
221797 TGAAATTTGGAAATGGAAATGAAAAT-GAAAATGGAG-TTCATTCA
1 TGAAATTTGCAAATGGAAATGAAAATGGAAAATGG-GTTTCATTCA
221841 TGAAATTT
1 TGAAATTT
221849 AGCTATGTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
44 23 0.50
45 23 0.50
ACGTcount: A:0.41, C:0.05, G:0.24, T:0.30
Consensus pattern (45 bp):
TGAAATTTGCAAATGGAAATGAAAATGGAAAATGGGTTTCATTCA
Found at i:222017 original size:37 final size:37
Alignment explanation
Indices: 221952--222026 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
221942 AATCATAATC
* *
221952 AAAGATTAGAAGATAACCTTTTAGGCATGGAGAATGG
1 AAAGATTAGAAGATAACCTTTCAAGCATGGAGAATGG
* * *
221989 AAAGATTAGAAGGTGACGTTTCAAGCATGGAGAATGG
1 AAAGATTAGAAGATAACCTTTCAAGCATGGAGAATGG
222026 A
1 A
222027 GATTGATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.40, C:0.08, G:0.29, T:0.23
Consensus pattern (37 bp):
AAAGATTAGAAGATAACCTTTCAAGCATGGAGAATGG
Found at i:229231 original size:23 final size:23
Alignment explanation
Indices: 229201--229252 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
229191 GAGAAATGTT
229201 CTTCCTAGAATATCCCCTAACTA
1 CTTCCTAGAATATCCCCTAACTA
229224 CTTCCTAGAATATCCCCTAACTA
1 CTTCCTAGAATATCCCCTAACTA
229247 CTTCCT
1 CTTCCT
229253 GAGCCAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.27, C:0.37, G:0.04, T:0.33
Consensus pattern (23 bp):
CTTCCTAGAATATCCCCTAACTA
Found at i:231183 original size:6 final size:6
Alignment explanation
Indices: 231172--231198 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
231162 CTCTCTTTCC
231172 CACCAG CACCAG CACCAG CACCAG CAC
1 CACCAG CACCAG CACCAG CACCAG CAC
231199 TATTTTTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
CACCAG
Found at i:235695 original size:2 final size:2
Alignment explanation
Indices: 235688--235755 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
235678 AGCCTTAATA
235688 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
235730 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
235756 TAATTAGTTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:244482 original size:30 final size:28
Alignment explanation
Indices: 244416--244508 Score: 78
Period size: 30 Copynumber: 3.2 Consensus size: 28
244406 ATGGTATCTA
* * *
244416 TACTTTTAGAATATTTCATGTGATACCTG
1 TACTTTTAAAAAATTT-ATGTGATACTTG
* *
244445 CATTTTTACAAAAATTTAATGTGATACTTG
1 TACTTTTA-AAAAATTT-ATGTGATACTTG
** * *
244475 TACTTTTAAAAGGTTTATGTGGTGCTTG
1 TACTTTTAAAAAATTTATGTGATACTTG
244503 TACTTT
1 TACTTT
244509 AATTAAATAT
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
28 16 0.31
29 12 0.24
30 23 0.45
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (28 bp):
TACTTTTAAAAAATTTATGTGATACTTG
Found at i:244914 original size:54 final size:54
Alignment explanation
Indices: 244832--244941 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
244822 TGTCTCAAAA
244832 TACGAGCTAAAGATGTCACATCAATTTTACAAATATTCACTGATCATAAATGGT
1 TACGAGCTAAAGATGTCACATCAATTTTACAAATATTCACTGATCATAAATGGT
244886 TACGAGCTAAAGATGTCACATCAATTTTACAAATATTCACTGATCATAAATGGT
1 TACGAGCTAAAGATGTCACATCAATTTTACAAATATTCACTGATCATAAATGGT
244940 TA
1 TA
244942 AAATTTTGTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (54 bp):
TACGAGCTAAAGATGTCACATCAATTTTACAAATATTCACTGATCATAAATGGT
Found at i:245680 original size:19 final size:19
Alignment explanation
Indices: 245656--245740 Score: 107
Period size: 19 Copynumber: 4.5 Consensus size: 19
245646 TTATTTGTAT
*
245656 ATTCATAACTTATTTTCAG
1 ATTCATAGCTTATTTTCAG
* * *
245675 ACTCATAGCTTACTGTCAG
1 ATTCATAGCTTATTTTCAG
*
245694 ATTCATAGCTTATTTTCAA
1 ATTCATAGCTTATTTTCAG
* *
245713 AGTCATAGCTTATTTTCAA
1 ATTCATAGCTTATTTTCAG
245732 ATTCATAGC
1 ATTCATAGC
245741 CTAATGCATA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 56 1.00
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.41
Consensus pattern (19 bp):
ATTCATAGCTTATTTTCAG
Found at i:250770 original size:24 final size:24
Alignment explanation
Indices: 250738--250793 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
250728 ATCTTTTGTC
* **
250738 TTGAAATGAAATGTTTTAGTAAAA
1 TTGAAATGAAACGTTTTACCAAAA
250762 TTGAAATGAAACGTTTTACCAAAA
1 TTGAAATGAAACGTTTTACCAAAA
*
250786 TTAAAATG
1 TTGAAATG
250794 TTTGAGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.46, C:0.05, G:0.14, T:0.34
Consensus pattern (24 bp):
TTGAAATGAAACGTTTTACCAAAA
Found at i:252084 original size:23 final size:23
Alignment explanation
Indices: 252058--252108 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
252048 CTAGAAACAA
252058 TAACAACTAGGATGACATAAAAG
1 TAACAACTAGGATGACATAAAAG
252081 TAACAACTAGGATGACATAAAAG
1 TAACAACTAGGATGACATAAAAG
252104 TAACA
1 TAACA
252109 TTGTCTGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.53, C:0.14, G:0.16, T:0.18
Consensus pattern (23 bp):
TAACAACTAGGATGACATAAAAG
Found at i:258855 original size:30 final size:30
Alignment explanation
Indices: 258819--258886 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
258809 TGGGATGGTT
258819 TTGAAGCTAAATGAGCTAGGGCATTTATAG
1 TTGAAGCTAAATGAGCTAGGGCATTTATAG
* *
258849 TTGAAGCTAAATGAGTTAGGGTATTTATAG
1 TTGAAGCTAAATGAGCTAGGGCATTTATAG
258879 TTGAAGCT
1 TTGAAGCT
258887 TAAGGACTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.32, C:0.07, G:0.26, T:0.34
Consensus pattern (30 bp):
TTGAAGCTAAATGAGCTAGGGCATTTATAG
Found at i:266138 original size:42 final size:42
Alignment explanation
Indices: 266079--266165 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
266069 GATAGAGATG
266079 TCATTTATCATTCATGTTTTACGTTTTAGTTTCTTAAAGAAC
1 TCATTTATCATTCATGTTTTACGTTTTAGTTTCTTAAAGAAC
266121 TCATTTATCATTCATGTTTTACGTTTTAGTTTCTTAAAGAAC
1 TCATTTATCATTCATGTTTTACGTTTTAGTTTCTTAAAGAAC
266163 TCA
1 TCA
266166 AACGACAAGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.49
Consensus pattern (42 bp):
TCATTTATCATTCATGTTTTACGTTTTAGTTTCTTAAAGAAC
Found at i:267036 original size:20 final size:20
Alignment explanation
Indices: 267011--267050 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
267001 TAGTGAACCG
267011 ATGTTGCTCAAACTCTTCAT
1 ATGTTGCTCAAACTCTTCAT
**
267031 ATGTTGCTCGGACTCTTCAT
1 ATGTTGCTCAAACTCTTCAT
267051 TCTTCTTGAA
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:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (20 bp):
ATGTTGCTCAAACTCTTCAT
Found at i:277466 original size:13 final size:14
Alignment explanation
Indices: 277445--277477 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
277435 GAAGAATAAA
*
277445 TATTAAAAT-AATT
1 TATTTAAATAAATT
277458 TATTTAAATAAATT
1 TATTTAAATAAATT
277472 TATTTA
1 TATTTA
277478 TTATATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TATTTAAATAAATT
Found at i:278884 original size:3 final size:3
Alignment explanation
Indices: 278878--278951 Score: 98
Period size: 3 Copynumber: 25.3 Consensus size: 3
278868 TTTAATAATT
* * *
278878 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TTA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
278926 T-A TAA TAA TTA TAA TAA T-A TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
278952 CAATTAATAT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
2 4 0.06
3 59 0.94
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:279485 original size:110 final size:111
Alignment explanation
Indices: 279358--279783 Score: 647
Period size: 112 Copynumber: 3.9 Consensus size: 111
279348 AAATCAAGCA
* *
279358 AAAGATTGAAC-AGTTCTTCTCATTATGAAC-TCTTCTTCCTTCTTCAGATGAGTT-TCTTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTC-TCATT
279420 ATGAACTTTCTCTGGAAAAGATAATCCATCAATTTGATGATTCAGGT
65 ATGAACTTTCTCTGGAAAAGATAATCCATCAATTTGATGATTCAGGT
279467 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC-TCTCATT
* *
279532 ATGAACCTTCTCTGGAAAAGCTAATCCATCAATTTGATGAATTCAGGT
65 ATGAACTTTCTCTGGAAAAGATAATCCATCAATTTGATG-ATTCAGGT
279580 AAAGGTTGAACAAATTCTT-TCATTATGAACTTCTTCTTCCTTCTTCAGAT-AGTTCTCTCATTA
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTCTCATTA
* * *
279643 TGAACTTTCTCTGGAAATGATGATCCATCAA-ATGATGGATTCAGGT
66 TGAACTTTCTCTGGAAAAGATAATCCATCAATTTGAT-GATTCAGGT
*
279689 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCT-TCATT
1 -AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTCTCATT
*
279753 A-GAAC-TTCTCTGG-AAATATCAATCCATCAAT
65 ATGAACTTTCTCTGGAAAAGAT-AATCCATCAAT
279784 GATAGATTTG
Statistics
Matches: 293, Mismatches: 13, Indels: 21
0.90 0.04 0.06
Matches are distributed among these distances:
108 4 0.01
109 39 0.13
110 77 0.26
111 65 0.22
112 79 0.27
113 29 0.10
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (111 bp):
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTCTCATTA
TGAACTTTCTCTGGAAAAGATAATCCATCAATTTGATGATTCAGGT
Found at i:279686 original size:222 final size:224
Alignment explanation
Indices: 279282--279783 Score: 679
Period size: 222 Copynumber: 2.3 Consensus size: 224
279272 TGAACAAGTT
* * * * *
279282 CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAA-ATA
1 CTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-CTTCTCTGGAAAAGCTAATCCATCAATATA
*
279345 ATGAAATCAAGCAAAAGATTGAACAGTTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAG
62 ATGAAATCAAGCAAAAGATTGAACAATTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAG
*
279410 TTTCTTCATTATGAACTTTCTCTGGAAAAGATAATCCATCAATTTGATGATTCAGGT-AAAGGTT
127 TTTCTTCATTATGAACTTTCTCTGGAAAAGATAATCCATCAATATGATGATTCAGGTAAAAGGTT
*
279474 GAACAAATTCTTCTCATTATGAACTTCTTCTTC
192 GAACAAATTCTTCTCATTATGAACTTATTCTTC
* *
279507 CTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTAATCCATCAATTTGATGA
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTAATCCATCAATATAATGA
* ** *
279572 ATTC-AGGTAAAGGTTGAACAAATTCTT-TCATTATGAACTTCTTCTTCCTTCTTCAGAT-AG-T
66 AATCAAGCAAAAGATTGAAC-AATTCTTCTCATTATGAAC-TCTTCTTCCTTCTTCAGATGAGTT
* *
279633 TCTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAA-ATGATGGATTCAGGTAAAAGGTT
129 TCT-TCATTATGAACTTTCTCTGGAAAAGATAATCCATCAATATGAT-GATTCAGGTAAAAGGTT
279697 GAACAAATTCTTCTCATTATGAACTTATTCTTC
192 GAACAAATTCTTCTCATTATGAACTTATTCTTC
*
279730 CTTCTTCAGATGAGTTC-T-TCATTA-GAA-CTTCTCTGGAAATATC-AATCCATCAAT
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAA-AGCTAATCCATCAAT
279784 GATAGATTTG
Statistics
Matches: 252, Mismatches: 17, Indels: 22
0.87 0.06 0.08
Matches are distributed among these distances:
219 23 0.09
220 5 0.02
221 17 0.07
222 107 0.42
223 89 0.35
225 11 0.04
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.37
Consensus pattern (224 bp):
CTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGCTAATCCATCAATATAATGA
AATCAAGCAAAAGATTGAACAATTCTTCTCATTATGAACTCTTCTTCCTTCTTCAGATGAGTTTC
TTCATTATGAACTTTCTCTGGAAAAGATAATCCATCAATATGATGATTCAGGTAAAAGGTTGAAC
AAATTCTTCTCATTATGAACTTATTCTTC
Found at i:280697 original size:81 final size:82
Alignment explanation
Indices: 280564--280900 Score: 498
Period size: 81 Copynumber: 4.2 Consensus size: 82
280554 TTTCTACTAC
*
280564 GAGCAAATTCAT-TTCCAATTCAATGATTGG-TCTGTCAAACCAGATCAGATAACTCAAAG-A-A
1 GAGCAAATTCATCTTCCAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACA
280625 CTTCCAGAAGATGCTAT
66 CTTCCAGAAGATGCTAT
*
280642 TAGCAAATTCATCTTCCAAATTC-ATGATTGGTTCTGTCCAAACCAGATCAGATAACTCAAAG-A
1 GAGCAAATTCATCTTCC-AATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAA
280705 -ACTTCCAGAAG--GCTAT
64 CACTTCCAGAAGATGCTAT
* *
280721 GAGCACATTCATCTTCCCATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACA
1 GAGCAAATTCATCTTCCAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACA
*
280786 CTTCCAGAAGATGTTAT
66 CTTCCAGAAGATGCTAT
* *
280803 GAGCACATTCATC-TCCCATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACA
1 GAGCAAATTCATCTTCCAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACA
*
280867 CTTCCCGAAGATGCTAT
66 CTTCCAGAAGATGCTAT
*
280884 -TGCAAATTCATCTTCCA
1 GAGCAAATTCATCTTCCA
280901 GTTAATGTTT
Statistics
Matches: 238, Mismatches: 11, Indels: 17
0.89 0.04 0.06
Matches are distributed among these distances:
78 40 0.17
79 46 0.19
80 30 0.13
81 105 0.44
82 17 0.07
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (82 bp):
GAGCAAATTCATCTTCCAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACA
CTTCCAGAAGATGCTAT
Found at i:281691 original size:16 final size:18
Alignment explanation
Indices: 281653--281697 Score: 67
Period size: 16 Copynumber: 2.6 Consensus size: 18
281643 CATATAAAAG
*
281653 AATAAATTGAATTTTCAA
1 AATAAATTGAATTCTCAA
281671 AATAAATTGAA-TCTC-A
1 AATAAATTGAATTCTCAA
281687 AATAAATTGAA
1 AATAAATTGAA
281698 CTTGAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 12 0.46
17 3 0.12
18 11 0.42
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (18 bp):
AATAAATTGAATTCTCAA
Found at i:282058 original size:10 final size:10
Alignment explanation
Indices: 282026--282060 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
282016 CTTGACCCCC
282026 TTTTTC-TTT
1 TTTTTCTTTT
*
282035 TTTCTCTTTT
1 TTTTTCTTTT
282045 TTTTTCTTTT
1 TTTTTCTTTT
282055 TTTTTC
1 TTTTTC
282061 AAGCATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 5 0.22
10 18 0.78
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:292543 original size:12 final size:14
Alignment explanation
Indices: 292526--292558 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
292516 TACCTTGACA
292526 AAATAAATAA-TG-
1 AAATAAATAATTGC
292538 AAATAAATAATTGC
1 AAATAAATAATTGC
292552 AAATAAA
1 AAATAAA
292559 ATAAAACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
13 2 0.11
14 7 0.37
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.24
Consensus pattern (14 bp):
AAATAAATAATTGC
Found at i:293667 original size:196 final size:197
Alignment explanation
Indices: 293460--293865 Score: 587
Period size: 196 Copynumber: 2.1 Consensus size: 197
293450 TTATTTAATA
*
293460 ATTTAGTGACTAAAATAAAATTATCTAAAATTCGGATATTA-TATAAAATAAATTAAAAATATAA
1 ATTTAGTGACTAAAATAAAATTATCTAAAATTCGGATATTAGAATAAAATAAATTAAAAATATAA
293524 AATAGGGATT-AAATATTATTTATTAAAATTAAGGGATCAA-AT-CT-GTTATCCT-AA-ATATT
66 AATAGGGATTAAAATATTATTTATTAAAATTAAGGGATCAATATGCTAGTTATCCTAAATATATT
*
293583 ATTTTAATATAAAGGACTAAAATGAATAAAATTGAAAATTCGAAGA-CTAAATTAAAAATATTAT
131 ATTTTAATATAAAGGACT-AAA--AATAAAATT-AAAATT-AAAGATCTAAATTAAAAATATTAT
293647 AATTTATTT-
191 AA---ATTTG
293656 ATTTAGTGACTAAAATAAAATTATCTAAAATTCGGATATTAGAATAAAATAAATTAAAAATATAA
1 ATTTAGTGACTAAAATAAAATTATCTAAAATTCGGATATTAGAATAAAATAAATTAAAAATATAA
* * * *
293721 ACTAGGGATTAAAATATTATTTATTAAAATTAAGGGATTAATTATGTTATTTATCCTAAATATAT
66 AATAGGGATTAAAATATTATTTATTAAAATTAAGGGATCAA-TATGCTAGTTATCCTAAATATAT
* * *
293786 TATTTTAATATAAAGGACTAAAAATGAAATTAAAATTAAAGATCTGAATTAAAAGTATTATAAAT
130 TATTTTAATATAAAGGACTAAAAATAAAATTAAAATTAAAGATCTAAATTAAAAATATTATAAAT
293851 TTG
195 TTG
293854 ATTTAGTGACTA
1 ATTTAGTGACTA
293866 GAATGTAAAG
Statistics
Matches: 191, Mismatches: 9, Indels: 18
0.88 0.04 0.08
Matches are distributed among these distances:
196 41 0.21
197 35 0.18
198 41 0.21
199 4 0.02
200 26 0.14
201 9 0.05
202 7 0.04
203 5 0.03
204 23 0.12
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (197 bp):
ATTTAGTGACTAAAATAAAATTATCTAAAATTCGGATATTAGAATAAAATAAATTAAAAATATAA
AATAGGGATTAAAATATTATTTATTAAAATTAAGGGATCAATATGCTAGTTATCCTAAATATATT
ATTTTAATATAAAGGACTAAAAATAAAATTAAAATTAAAGATCTAAATTAAAAATATTATAAATT
TG
Found at i:294558 original size:55 final size:55
Alignment explanation
Indices: 294492--294602 Score: 206
Period size: 55 Copynumber: 2.0 Consensus size: 55
294482 ATAGCCATCA
294492 CGGTGCTCATCTCGGACCGGTCCGAAGAATAGAGTTCGGTGAGTC-ACCGGACTCC
1 CGGTGCTCATCTCGGACCGGTCCGAAGAATAGAGTTC-GTGAGTCAACCGGACTCC
294547 CGGTGCTCATCTCGGACCGGTCCGAAGAATAGAGTTCGTGAGTCAACCGGACTCC
1 CGGTGCTCATCTCGGACCGGTCCGAAGAATAGAGTTCGTGAGTCAACCGGACTCC
294602 C
1 C
294603 AGTGGTGACT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
54 7 0.13
55 48 0.87
ACGTcount: A:0.21, C:0.30, G:0.30, T:0.20
Consensus pattern (55 bp):
CGGTGCTCATCTCGGACCGGTCCGAAGAATAGAGTTCGTGAGTCAACCGGACTCC
Found at i:294739 original size:16 final size:16
Alignment explanation
Indices: 294714--294752 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
294704 CCGTTGGCTT
294714 AGGC-GCTGGAGGCAG
1 AGGCGGCTGGAGGCAG
294729 AGGCGGCTGGAGGCAG
1 AGGCGGCTGGAGGCAG
294745 AGGCGGCT
1 AGGCGGCT
294753 AGGGTTAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.18, C:0.21, G:0.54, T:0.08
Consensus pattern (16 bp):
AGGCGGCTGGAGGCAG
Found at i:294868 original size:3 final size:3
Alignment explanation
Indices: 294860--294946 Score: 95
Period size: 3 Copynumber: 29.0 Consensus size: 3
294850 TATATATATT
* * * *
294860 TAA TAA TAA TAA TAA TAT TTA T-A TAA TAA TAA TAA TAT TTA TATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
* * *
294905 TAA TAG TAT TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
294947 ATAAATCAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
2 2 0.03
3 65 0.93
4 3 0.04
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:299234 original size:21 final size:21
Alignment explanation
Indices: 299210--299251 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
299200 AGTTTATTTT
299210 TAAACTTTGTTTCAATTATCG
1 TAAACTTTGTTTCAATTATCG
299231 TAAACTTTGTTTCAATTATCG
1 TAAACTTTGTTTCAATTATCG
299252 AACTTGGAAG
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:0.29, C:0.14, G:0.10, T:0.48
Consensus pattern (21 bp):
TAAACTTTGTTTCAATTATCG
Found at i:299291 original size:33 final size:32
Alignment explanation
Indices: 299240--299316 Score: 118
Period size: 33 Copynumber: 2.4 Consensus size: 32
299230 GTAAACTTTG
*
299240 TTTCAATTATCGAACTTGGAAGTTTTTAAGTA
1 TTTCAATTATCGAACTTGGAAGTATTTAAGTA
* *
299272 TTTGAATTTATCGAGCTTGGAAGTATTTAAGTA
1 TTTCAA-TTATCGAACTTGGAAGTATTTAAGTA
299305 TTTCAATTATCG
1 TTTCAATTATCG
299317 TAAACTTTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 11 0.28
33 29 0.73
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.44
Consensus pattern (32 bp):
TTTCAATTATCGAACTTGGAAGTATTTAAGTA
Found at i:299971 original size:26 final size:26
Alignment explanation
Indices: 299906--299971 Score: 62
Period size: 26 Copynumber: 2.5 Consensus size: 26
299896 AATAATACAT
* * * * *
299906 TATTTATATATATATATATATTTAAT
1 TATTTAAATATAAATATAAAGTTAAA
*
299932 TAATTT-AATTTAAATATAAAGTTAAA
1 T-ATTTAAATATAAATATAAAGTTAAA
299958 TATTTAAATATAAA
1 TATTTAAATATAAA
299972 ATACCTCAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
25 4 0.13
26 23 0.74
27 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
TATTTAAATATAAATATAAAGTTAAA
Found at i:316790 original size:2 final size:2
Alignment explanation
Indices: 316783--316813 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
316773 AAGTTGTTCA
316783 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
316814 TTCTTTTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:320784 original size:28 final size:28
Alignment explanation
Indices: 320749--320817 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
320739 TAAAGTAAAG
320749 ACTAAATTGAAATAAAATAAAAACAGGA
1 ACTAAATTGAAATAAAATAAAAACAGGA
* * ** *
320777 ACTAAATT-ATAATAAATTAGAATTAGGG
1 ACTAAATTGA-AATAAAATAAAAACAGGA
320805 ACTAAATTGAAAT
1 ACTAAATTGAAAT
320818 TAATAGGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
27 1 0.03
28 32 0.94
29 1 0.03
ACGTcount: A:0.57, C:0.06, G:0.12, T:0.26
Consensus pattern (28 bp):
ACTAAATTGAAATAAAATAAAAACAGGA
Found at i:322287 original size:23 final size:23
Alignment explanation
Indices: 322254--322300 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
322244 TTAGTTTGTA
* *
322254 AATAATAATAATATTTATAATAT
1 AATAATAATAATAGTAATAATAT
*
322277 AATAATGATAATAGTAATAATAT
1 AATAATAATAATAGTAATAATAT
322300 A
1 A
322301 GGGGTAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (23 bp):
AATAATAATAATAGTAATAATAT
Found at i:322956 original size:59 final size:59
Alignment explanation
Indices: 322849--323003 Score: 256
Period size: 59 Copynumber: 2.6 Consensus size: 59
322839 GGACTTTTGT
* **
322849 TGATTCGAAATGCAGTGAATCAAGCAATAGGAAATGTTAATCCCTCAAGTGGGGCATTGC
1 TGATTCGAAGTGTTGTGAATCAAGCAA-AGGAAATGTTAATCCCTCAAGTGGGGCATTGC
* *
322909 TGATTCGAAGTGTTGTGAATCGAGCAAAGGAAATGTTAATCCCTCAAGTGGGGCGTTGC
1 TGATTCGAAGTGTTGTGAATCAAGCAAAGGAAATGTTAATCCCTCAAGTGGGGCATTGC
322968 TGATTCGAAGTGTTGTGAATCAAGCAAAGGAAATGT
1 TGATTCGAAGTGTTGTGAATCAAGCAAAGGAAATGT
323004 GAAAATATCC
Statistics
Matches: 89, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
59 66 0.74
60 23 0.26
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.26
Consensus pattern (59 bp):
TGATTCGAAGTGTTGTGAATCAAGCAAAGGAAATGTTAATCCCTCAAGTGGGGCATTGC
Found at i:323164 original size:286 final size:285
Alignment explanation
Indices: 322652--323405 Score: 1028
Period size: 286 Copynumber: 2.6 Consensus size: 285
322642 CTTTCCACTA
* * * * * * * * ** * *
322652 GAAATGTTTATCCCTCGATTGAGGCTTTACTGATTTGAAATGTCATGAATCGAGCAAAGGAAATA
1 GAAATGTTAATCCCTCAAGTGGGGCGTTGCTGATTCGAAGTGTTGTGAATCAAGCAAAGGAAATG
* ** ** * * *
322717 TGAAAACATCATATCTGATGGTCTTATGGATGGCTCGAATAACTTATCATCTTGATCGAAAA-AC
66 TGAAAACATCCTGCCCAAAGGTCTTATGGATGGC-CGAATGACTTATCATCTTGCTC-AAAAGAC
322781 TTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTT
129 TTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTT
* * *
322846 TGTTGATTCGAAATGCAGTGAATCAAGCAATAGGAAATGTTAATCCCTCAAGTGGGGCATTGCTG
194 TGTTAATTCGAAATGCAGTGAATCAAGCAATAGAAAATGTTAATCCCTCAAGTAGGGCATTGCTG
322911 ATTCGAAGTGTTGTGAATCGAGCAAAG
259 ATTCGAAGTGTTGTGAATCGAGCAAAG
322938 GAAATGTTAATCCCTCAAGTGGGGCGTTGCTGATTCGAAGTGTTGTGAATCAAGCAAAGGAAATG
1 GAAATGTTAATCCCTCAAGTGGGGCGTTGCTGATTCGAAGTGTTGTGAATCAAGCAAAGGAAATG
*
323003 TGAAAATATCCTGCCCAAAGGTCTTATGGATGGTCCGAATGACTTATCATCTTGCTCAAAAGACT
66 TGAAAACATCCTGCCCAAAGGTCTTATGGATGG-CCGAATGACTTATCATCTTGCTCAAAAGACT
* * * *
323068 TATAGATGACCCGAAGGATTAAAGAATCATGCTCGAAAGACTTACTGATTGCCCGAATGACTTTT
130 TATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTTT
** * *
323133 -TCTAATTTTAAATGTC-GTGAATCGAGCAATAGAAAATGTTAATCCCTCAAGTAGGGCGTTGCT
195 GT-TAATTCGAAATG-CAGTGAATCAAGCAATAGAAAATGTTAATCCCTCAAGTAGGGCATTGCT
*
323196 GATTCGAAGTGTTGTGAATCGAGGAAAG
258 GATTCGAAGTGTTGTGAATCGAGCAAAG
* * * * *
323224 GAAATGTTAATCCCTTAAGTGGGGTGTTTCTGATTCGAAGTGTTGTGAATCGAGTAAAGGAAATG
1 GAAATGTTAATCCCTCAAGTGGGGCGTTGCTGATTCGAAGTGTTGTGAATCAAGCAAAGGAAATG
* * * * * *
323289 TTAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAAGACTTATCATCTTGCTCGATAGATT
66 TGAAAACATCCTGCCCAAAGGTCTTATGGATGG-CCGAATGACTTATCATCTTGCTCAAAAGACT
*
323354 TATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGC
130 TATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGC
323406 TTGAGGACTT
Statistics
Matches: 414, Mismatches: 50, Indels: 8
0.88 0.11 0.02
Matches are distributed among these distances:
285 5 0.01
286 407 0.98
287 2 0.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (285 bp):
GAAATGTTAATCCCTCAAGTGGGGCGTTGCTGATTCGAAGTGTTGTGAATCAAGCAAAGGAAATG
TGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCGAATGACTTATCATCTTGCTCAAAAGACTT
ATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTTTG
TTAATTCGAAATGCAGTGAATCAAGCAATAGAAAATGTTAATCCCTCAAGTAGGGCATTGCTGAT
TCGAAGTGTTGTGAATCGAGCAAAG
Found at i:323257 original size:59 final size:59
Alignment explanation
Indices: 323149--323292 Score: 216
Period size: 59 Copynumber: 2.4 Consensus size: 59
323139 TTTAAATGTC
*
323149 GTGAATCGAGCAATAGAAAATGTTAATCCCTCAAGTAGGGCGTTGCTGATTCGAAGTGTT
1 GTGAATCGAGCAA-AGGAAATGTTAATCCCTCAAGTAGGGCGTTGCTGATTCGAAGTGTT
* * * * *
323209 GTGAATCGAGGAAAGGAAATGTTAATCCCTTAAGTGGGGTGTTTCTGATTCGAAGTGTT
1 GTGAATCGAGCAAAGGAAATGTTAATCCCTCAAGTAGGGCGTTGCTGATTCGAAGTGTT
*
323268 GTGAATCGAGTAAAGGAAATGTTAA
1 GTGAATCGAGCAAAGGAAATGTTAA
323293 AACATCCTGC
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
59 65 0.84
60 12 0.16
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.29
Consensus pattern (59 bp):
GTGAATCGAGCAAAGGAAATGTTAATCCCTCAAGTAGGGCGTTGCTGATTCGAAGTGTT
Found at i:323640 original size:53 final size:53
Alignment explanation
Indices: 323477--323697 Score: 198
Period size: 53 Copynumber: 4.1 Consensus size: 53
323467 TTACAGTTAT
* * * *
323477 CATCAAGAAACCCCTATAAATTAGGCTTAGGTTCTTTAAAAATTCTTTGGAAATAA
1 CATCAAGAAACCCTTAAAAATCAGGCTTA-GTTCTTTAAAAATTCTTT-TAAA-AA
* * * * *
323533 TCATCAACAAACCCTTGAAAATCATGCTTAGTT-TCTAAAAACTAT-TTTTGAAAA
1 -CATCAAGAAACCCTTAAAAATCAGGCTTAGTTCTTTAAAAA-T-TCTTTTAAAAA
* * * *
323587 CATCAAGAAA-CCTTAAAAATTAAGCTTAGTTTATTTCAAAATTCTTTTAAAAA
1 CATCAAGAAACCCTTAAAAATCAGGCTTAG-TTCTTTAAAAATTCTTTTAAAAA
* * *
323640 CATCAAGAAACCCTTGAAAATCAGGCTTAGCTTCTTT-CAAATTCATTTAAAAA
1 CATCAAGAAACCCTTAAAAATCAGGCTTAG-TTCTTTAAAAATTCTTTTAAAAA
323693 CATCA
1 CATCA
323698 TATTAAGAAA
Statistics
Matches: 135, Mismatches: 23, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
52 17 0.13
53 49 0.36
54 29 0.21
55 9 0.07
56 7 0.05
57 24 0.18
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.33
Consensus pattern (53 bp):
CATCAAGAAACCCTTAAAAATCAGGCTTAGTTCTTTAAAAATTCTTTTAAAAA
Found at i:323668 original size:106 final size:110
Alignment explanation
Indices: 323477--323674 Score: 278
Period size: 106 Copynumber: 1.8 Consensus size: 110
323467 TTACAGTTAT
* * *
323477 CATCAAGAAACCCCTATAAATTAGGCTTAGGTTCTTTAAAAATTCTTTGGAAATAATCATCAACA
1 CATCAAGAAACCCCTAAAAATTAAGCTTAGGTTATTTAAAAATTCTTTGGAAATAATCATCAACA
* *
323542 AACCCTTGAAAATCATGCTTAGTTTCTAAAAACTATTTTTGAAAA
66 AACCCTTGAAAATCAGGCTTAGCTTCTAAAAACTATTTTTGAAAA
* * * * *
323587 CATCAAGAAA-CCTTAAAAATTAAGCTTAGTTTATTTCAAAATTCTTT-TAAA-AA-CATCAAGA
1 CATCAAGAAACCCCTAAAAATTAAGCTTAGGTTATTTAAAAATTCTTTGGAAATAATCATCAACA
323648 AACCCTTGAAAATCAGGCTTAGCTTCT
66 AACCCTTGAAAATCAGGCTTAGCTTCT
323675 TTCAAATTCA
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
106 32 0.41
107 2 0.03
108 3 0.04
109 31 0.40
110 10 0.13
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (110 bp):
CATCAAGAAACCCCTAAAAATTAAGCTTAGGTTATTTAAAAATTCTTTGGAAATAATCATCAACA
AACCCTTGAAAATCAGGCTTAGCTTCTAAAAACTATTTTTGAAAA
Found at i:323733 original size:58 final size:53
Alignment explanation
Indices: 323583--323743 Score: 164
Period size: 58 Copynumber: 2.9 Consensus size: 53
323573 ACTATTTTTG
* * * *
323583 AAAACATCAAGAAACCT-TAAAAATTAAGCTTAGTTTATTTCAAAATTCTTTTA
1 AAAACATCAAGAAACCTCTGAAAATCAAGCTTAGTTTCTTTC-AAATTCATTTA
* *
323636 AAAACATCAAGAAACC-CTTGAAAATCAGGCTTAGCTTCTTTCAAATTCATTTA
1 AAAACATCAAGAAACCTC-TGAAAATCAAGCTTAGTTTCTTTCAAATTCATTTA
* * *
323689 AAAACATCATATTAAGAAACCTCTGAAAATCAAACCTAGTTTCTTTAAAATTCAT
1 AAAACATC-----AAGAAACCTCTGAAAATCAAGCTTAGTTTCTTTCAAATTCAT
323744 CGATTGGGTA
Statistics
Matches: 89, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
53 34 0.38
54 19 0.21
58 35 0.39
59 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.32
Consensus pattern (53 bp):
AAAACATCAAGAAACCTCTGAAAATCAAGCTTAGTTTCTTTCAAATTCATTTA
Found at i:334378 original size:22 final size:22
Alignment explanation
Indices: 334350--334420 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
334340 ACTATACGGT
*
334350 ATGAACAATACCGTGAACAGTA
1 ATGAACAATACCATGAACAGTA
* * *
334372 ATGAACATTGCCATGAACAGTG
1 ATGAACAATACCATGAACAGTA
* * *
334394 ATGAACAGTACTATGAATAGTA
1 ATGAACAATACCATGAACAGTA
*
334416 CTGAA
1 ATGAA
334421 TGCTAAAATT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.23
Consensus pattern (22 bp):
ATGAACAATACCATGAACAGTA
Found at i:335292 original size:32 final size:32
Alignment explanation
Indices: 335184--335502 Score: 472
Period size: 32 Copynumber: 10.1 Consensus size: 32
335174 GCTAGTATAA
*
335184 TAAT-CTGTCCATATGTCCTG-AAGAACATAGG
1 TAATACTGTCCATATGTCCCGAAAG-ACATAGG
*
335215 TAAT-TTGTCCATATGTCCCG-AAGAACATAGG
1 TAATACTGTCCATATGTCCCGAAAG-ACATAGG
335246 TAA-ACTGTCCATATGTCCCGAAAGACATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
* *
335277 TAATACTGTCTATATGTCCCGAAAGACATATG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
335309 TAATACTGTCCATATGTCCCGAAAGACATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
* *
335341 TAATATTGTCCATATGTCCCGAAAGATAT-GG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
335372 TAATACTGTCCATATGTCCCGAAAGACATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
* *
335404 TAATACTGTCCATATGTCCTGAAAGAAATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
* *
335436 TAATACTGTCCATATATCCCGCAAGACATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
335468 TAATACTGT-CATTATGTCCCGAAAGACATAGG
1 TAATACTGTCCA-TATGTCCCGAAAGACATAGG
335500 TAA
1 TAA
335503 CCCTCGACTC
Statistics
Matches: 264, Mismatches: 19, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
31 88 0.33
32 176 0.67
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (32 bp):
TAATACTGTCCATATGTCCCGAAAGACATAGG
Found at i:335374 original size:95 final size:96
Alignment explanation
Indices: 335184--335502 Score: 472
Period size: 95 Copynumber: 3.4 Consensus size: 96
335174 GCTAGTATAA
* *
335184 TAAT-CTGTCCATATGTCCTG-AAGAACATAGGTAAT-TTGTCCATATGTCCCG-AAGAACATAG
1 TAATACTGTCCATATGTCCCGAAAG-ACATAGGTAATACTGTCCATATGTCCCGAAAG-ACATAG
335245 GTAA-ACTGTCCATATGTCCCGAAAGACATAGG
64 GTAATACTGTCCATATGTCCCGAAAGACATAGG
* *
335277 TAATACTGTCTATATGTCCCGAAAGACATATGTAATACTGTCCATATGTCCCGAAAGACATAGGT
1 TAATACTGTCCATATGTCCCGAAAGACATAGGTAATACTGTCCATATGTCCCGAAAGACATAGGT
* *
335342 AATATTGTCCATATGTCCCGAAAGATAT-GG
66 AATACTGTCCATATGTCCCGAAAGACATAGG
* *
335372 TAATACTGTCCATATGTCCCGAAAGACATAGGTAATACTGTCCATATGTCCTGAAAGAAATAGGT
1 TAATACTGTCCATATGTCCCGAAAGACATAGGTAATACTGTCCATATGTCCCGAAAGACATAGGT
* *
335437 AATACTGTCCATATATCCCGCAAGACATAGG
66 AATACTGTCCATATGTCCCGAAAGACATAGG
335468 TAATACTGT-CATTATGTCCCGAAAGACATAGGTAA
1 TAATACTGTCCA-TATGTCCCGAAAGACATAGGTAA
335503 CCCTCGACTC
Statistics
Matches: 205, Mismatches: 14, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
93 4 0.02
94 24 0.12
95 117 0.57
96 60 0.29
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (96 bp):
TAATACTGTCCATATGTCCCGAAAGACATAGGTAATACTGTCCATATGTCCCGAAAGACATAGGT
AATACTGTCCATATGTCCCGAAAGACATAGG
Found at i:335382 original size:127 final size:126
Alignment explanation
Indices: 335184--335502 Score: 477
Period size: 127 Copynumber: 2.5 Consensus size: 126
335174 GCTAGTATAA
*
335184 TAAT-CTGTCCATATGTCCTGAAGAACATAGGTAAT-TTGTCCATATGTCCCG-AAGAACATAGG
1 TAATACTGTCCATATGTCCCGAAG-ACATAGGTAATATTGTCCATATGTCCCGAAAG-ACATAGG
* * *
335246 TAAACTGTCCATATGTCCCGAAAGACATAGGTAATACTGTCTATATGTCCCGAAAGACATATG
64 TAAACTGTCCATATGTCCCGAAAGACATAGGTAATACTGTCCATATGTCCCGAAAGAAATAGG
*
335309 TAATACTGTCCATATGTCCCGAAAGACATAGGTAATATTGTCCATATGTCCCGAAAGATAT-GGT
1 TAATACTGTCCATATGTCCCG-AAGACATAGGTAATATTGTCCATATGTCCCGAAAGACATAGGT
*
335373 AATACTGTCCATATGTCCCGAAAGACATAGGTAATACTGTCCATATGTCCTGAAAGAAATAGG
65 AA-ACTGTCCATATGTCCCGAAAGACATAGGTAATACTGTCCATATGTCCCGAAAGAAATAGG
* *
335436 TAATACTGTCCATATATCCCGCAAGACATAGGTAATACTGT-CATTATGTCCCGAAAGACATAGG
1 TAATACTGTCCATATGTCCCG-AAGACATAGGTAATATTGTCCA-TATGTCCCGAAAGACATAGG
335500 TAA
64 TAA
335503 CCCTCGACTC
Statistics
Matches: 177, Mismatches: 10, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
125 4 0.02
126 33 0.19
127 132 0.75
128 8 0.05
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (126 bp):
TAATACTGTCCATATGTCCCGAAGACATAGGTAATATTGTCCATATGTCCCGAAAGACATAGGTA
AACTGTCCATATGTCCCGAAAGACATAGGTAATACTGTCCATATGTCCCGAAAGAAATAGG
Found at i:336598 original size:23 final size:22
Alignment explanation
Indices: 336551--336616 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 22
336541 TGTTTAATGT
*
336551 AGGTATCGATACCCTCT-A-T-
1 AGGTATCGATACCCCCTAACTG
336570 AGGGTATCGATACACCCCTAACTG
1 A-GGTATCGATAC-CCCCTAACTG
* *
336594 AGGTATCGGTACCCGCTAACTG
1 AGGTATCGATACCCCCTAACTG
336616 A
1 A
336617 CCACTAACTG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
19 1 0.03
20 11 0.28
21 4 0.10
22 11 0.28
23 11 0.28
24 1 0.03
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (22 bp):
AGGTATCGATACCCCCTAACTG
Found at i:336615 original size:22 final size:23
Alignment explanation
Indices: 336572--336616 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
336562 CCCTCTATAG
336572 GGTATCGATACACCCCTAACTGA
1 GGTATCGATACACCCCTAACTGA
* *
336595 GGTATCGGTAC-CCGCTAACTGA
1 GGTATCGATACACCCCTAACTGA
336617 CCACTAACTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (23 bp):
GGTATCGATACACCCCTAACTGA
Found at i:336624 original size:33 final size:33
Alignment explanation
Indices: 336587--336649 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
336577 CGATACACCC
* *
336587 CTAACTGAGGTATCGGTACCCGCTAACTGACCA
1 CTAACTGAGGTATCGATACCCCCTAACTGACCA
336620 CTAACTGAGGTATCGATACCCCCTAACTGA
1 CTAACTGAGGTATCGATACCCCCTAACTGA
336650 GGTATCGGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (33 bp):
CTAACTGAGGTATCGATACCCCCTAACTGACCA
Found at i:336648 original size:22 final size:22
Alignment explanation
Indices: 336620--336662 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
336610 TAACTGACCA
336620 CTAACTGAGGTATCGATACCCC
1 CTAACTGAGGTATCGATACCCC
*
336642 CTAACTGAGGTATCGGTACCC
1 CTAACTGAGGTATCGATACCC
336663 TGCCTAGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (22 bp):
CTAACTGAGGTATCGATACCCC
Found at i:339988 original size:5 final size:5
Alignment explanation
Indices: 339973--340018 Score: 58
Period size: 5 Copynumber: 9.2 Consensus size: 5
339963 GTTTGATCCA
* *
339973 TTTTC -TTTC TTTTC TTTTC TTTTC TCTCTC TTTTG TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC T-TTTC TTTTC TTTTC TTTTC T
340019 CTCCTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
4 4 0.11
5 27 0.77
6 4 0.11
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:340027 original size:21 final size:21
Alignment explanation
Indices: 339973--340026 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
339963 GTTTGATCCA
339973 TTTTCT-T-TCTTTTCTTTTC
1 TTTTCTCTCTCTTTTCTTTTC
*
339992 TTTTCTCTCTCTTTTGTTTTC
1 TTTTCTCTCTCTTTTCTTTTC
340013 TTTTCTCTC-CTTTT
1 TTTTCTCTCTCTTTT
340027 TTATGCTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 6 0.19
20 6 0.19
21 20 0.62
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTTCTCTCTCTTTTCTTTTC
Found at i:345191 original size:43 final size:42
Alignment explanation
Indices: 345138--345219 Score: 101
Period size: 43 Copynumber: 1.9 Consensus size: 42
345128 TAATTAGAGG
* ** *
345138 TGTTTAATAAACAAGCACTGCTATAAAGCTTGACATTTAGCGA
1 TGTTTAATAAACAAACACCACTATAAA-ATTGACATTTAGCGA
* *
345181 TGTTTCATAAATAAACACCACTATAAAATTGACATTTAG
1 TGTTTAATAAACAAACACCACTATAAAATTGACATTTAG
345220 TGTTTACAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
42 11 0.33
43 22 0.67
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (42 bp):
TGTTTAATAAACAAACACCACTATAAAATTGACATTTAGCGA
Found at i:348058 original size:12 final size:12
Alignment explanation
Indices: 348040--348073 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
348030 TTTAATACAT
348040 AAAATAAATAAA
1 AAAATAAATAAA
*
348052 TAAATAAATAAA
1 AAAATAAATAAA
348064 AAAATTAAAT
1 AAAA-TAAAT
348074 GCATAACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATAAATAAA
Found at i:348079 original size:21 final size:21
Alignment explanation
Indices: 348033--348073 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
348023 TTAATCTTTT
*
348033 AATACATAAAATAAATAAATA
1 AATAAATAAAATAAATAAATA
348054 AATAAATAAAA-AAATTAAAT
1 AATAAATAAAATAAA-TAAAT
348074 GCATAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (21 bp):
AATAAATAAAATAAATAAATA
Found at i:348275 original size:28 final size:28
Alignment explanation
Indices: 348250--348346 Score: 140
Period size: 28 Copynumber: 3.5 Consensus size: 28
348240 TTCAAGAAAC
348250 AGTTTTGAAATTTACCTCTTCCAGAATT
1 AGTTTTGAAATTTACCTCTTCCAGAATT
* *
348278 AGTTTGGAAATTTACCACTTCCAGAATT
1 AGTTTTGAAATTTACCTCTTCCAGAATT
* *
348306 AATTTTGAAATTTACCTGTTCCAGAATT
1 AGTTTTGAAATTTACCTCTTCCAGAATT
* *
348334 AATTTTAAAATTT
1 AGTTTTGAAATTT
348347 TCCTTTTCAA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 62 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.42
Consensus pattern (28 bp):
AGTTTTGAAATTTACCTCTTCCAGAATT
Found at i:348345 original size:56 final size:56
Alignment explanation
Indices: 348252--348381 Score: 154
Period size: 56 Copynumber: 2.3 Consensus size: 56
348242 CAAGAAACAG
* * * *
348252 TTTTGAAATTTACCTCTTCCAGAATTAGTTTGGAAATTTACCACTTCCAGAATTAA
1 TTTTGAAATTTACCTGTTCCAGAATTAATTTGAAAATTTACCACTTCAAGAATTAA
* * ** *
348308 TTTTGAAATTTACCTGTTCCAGAATTAATTTTAAAATTTTCCTTTTCAAGAGTTAA
1 TTTTGAAATTTACCTGTTCCAGAATTAATTTGAAAATTTACCACTTCAAGAATTAA
*
348364 -TTTGAAAATTTTCCTGTT
1 TTTTG-AAATTTACCTGTT
348382 ATATATTTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
55 4 0.06
56 59 0.94
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.45
Consensus pattern (56 bp):
TTTTGAAATTTACCTGTTCCAGAATTAATTTGAAAATTTACCACTTCAAGAATTAA
Found at i:348363 original size:28 final size:28
Alignment explanation
Indices: 348252--348374 Score: 138
Period size: 28 Copynumber: 4.4 Consensus size: 28
348242 CAAGAAACAG
* *
348252 TTTTGAAATTTACCTCTTCCAGAATTAG
1 TTTTAAAATTTACCTCTTCCAGAATTAA
** *
348280 TTTGGAAATTTACCACTTCCAGAATTAA
1 TTTTAAAATTTACCTCTTCCAGAATTAA
* *
348308 TTTTGAAATTTACCTGTTCCAGAATTAA
1 TTTTAAAATTTACCTCTTCCAGAATTAA
* * * *
348336 TTTTAAAATTTTCCTTTTCAAGAGTTAA
1 TTTTAAAATTTACCTCTTCCAGAATTAA
*
348364 TTTGAAAATTT
1 TTTTAAAATTT
348375 TCCTGTTATA
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 83 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.44
Consensus pattern (28 bp):
TTTTAAAATTTACCTCTTCCAGAATTAA
Found at i:356367 original size:12 final size:12
Alignment explanation
Indices: 356346--356374 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
356336 AACAGTACAC
356346 ATGT-ATGAACA
1 ATGTCATGAACA
356357 ATGTCATGAACA
1 ATGTCATGAACA
356369 ATGTCA
1 ATGTCA
356375 AATAGTGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (12 bp):
ATGTCATGAACA
Found at i:356425 original size:20 final size:20
Alignment explanation
Indices: 356400--356446 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
356390 TTATTTTTAT
*
356400 ATTTTAACAGCTTTAAACAA
1 ATTTTAACAACTTTAAACAA
* *
356420 ATTTTAAGAACTTTAAACAT
1 ATTTTAACAACTTTAAACAA
356440 ATTTTAA
1 ATTTTAA
356447 TTAACTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (20 bp):
ATTTTAACAACTTTAAACAA
Found at i:359777 original size:20 final size:20
Alignment explanation
Indices: 359754--359791 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
359744 ATTTTAAAAG
*
359754 CTTTAAATACATTTTAATCA
1 CTTTAAACACATTTTAATCA
*
359774 CTTTAAACATATTTTAAT
1 CTTTAAACACATTTTAAT
359792 TAACTAAAAA
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:0.39, C:0.13, G:0.00, T:0.47
Consensus pattern (20 bp):
CTTTAAACACATTTTAATCA
Found at i:367587 original size:18 final size:19
Alignment explanation
Indices: 367559--367594 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
367549 CAATTTGAAA
*
367559 AAAAGAAAAAAAGGAGAGC
1 AAAAGAAAAAAACGAGAGC
367578 AAAA-AAAAAAACGAGAG
1 AAAAGAAAAAAACGAGAG
367595 TTTGAGAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.72, C:0.06, G:0.22, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAAAACGAGAGC
Found at i:368148 original size:13 final size:13
Alignment explanation
Indices: 368132--368183 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
368122 GTTATGAATC
368132 TATGACGCGCATT
1 TATGACGCGCATT
* *
368145 TATGACTCTCATT
1 TATGACGCGCATT
*
368158 TATGACACGCATT
1 TATGACGCGCATT
*
368171 TATGACGCTCATT
1 TATGACGCGCATT
368184 GAGCATCATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:368161 original size:26 final size:26
Alignment explanation
Indices: 368132--368183 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
368122 GTTATGAATC
* *
368132 TATGACGCGCATTTATGACTCTCATT
1 TATGACACGCATTTATGACGCTCATT
368158 TATGACACGCATTTATGACGCTCATT
1 TATGACACGCATTTATGACGCTCATT
368184 GAGCATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (26 bp):
TATGACACGCATTTATGACGCTCATT
Found at i:368278 original size:85 final size:85
Alignment explanation
Indices: 368155--368368 Score: 290
Period size: 85 Copynumber: 2.5 Consensus size: 85
368145 TATGACTCTC
* * * *
368155 ATTTATGACACGCATTTATGACGCT-CATTGAGCATCATTGAAGCCCTCGTTATAAAT-TAAG-A
1 ATTTATGACACGCATGTATGAC-TTACATTGAGCGTCATTGAAGCCCCCGTTATAAATCT--GCA
368217 TGACACACATTTCTGTGTCATAA
63 TGACACACATTTCTGTGTCATAA
*
368240 ATTTATGACACGCATGTATGACTTACATTGAGCGTCATTGAAGCCCCCGTTATAAATCTGCTTGA
1 ATTTATGACACGCATGTATGACTTACATTGAGCGTCATTGAAGCCCCCGTTATAAATCTGCATGA
* *
368305 CATACATTTGTGTGTCATAA
66 CACACATTTCTGTGTCATAA
* * *
368325 ATTTATGATACGCATGTATGACTTACATTGCGTGTCATTGAAGC
1 ATTTATGACACGCATGTATGACTTACATTGAGCGTCATTGAAGC
368369 ACACGTCATT
Statistics
Matches: 116, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
84 2 0.02
85 113 0.97
86 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACTTACATTGAGCGTCATTGAAGCCCCCGTTATAAATCTGCATGA
CACACATTTCTGTGTCATAA
Found at i:368403 original size:85 final size:84
Alignment explanation
Indices: 368155--368405 Score: 247
Period size: 85 Copynumber: 3.0 Consensus size: 84
368145 TATGACTCTC
* * * * * * * *
368155 ATTTATGACACGCATTTATGACGCT-CATTGAGCATCATTGAAGCCCTCGTTATAAATTAAGATG
1 ATTTATGACACGCATGTATGAC-TTACATTGAGCGTCATTGAAGCACACGTCATAAA-AAAGACG
368219 ACACACATTTC-TGTGTCATAA
64 ACACACA-TTCGTGTGTCATAA
* * * ***
368240 ATTTATGACACGCATGTATGACTTACATTGAGCGTCATTGAAGCCCCCGTTATAAATCTG-CTTG
1 ATTTATGACACGCATGTATGACTTACATTGAGCGTCATTGAAGCACACGTCATAAAAAAGAC--G
* *
368304 ACATACATTTGTGTGTCATAA
64 ACACACATTCGTGTGTCATAA
* * *
368325 ATTTATGATACGCATGTATGACTTACATTGCGTGTCATTGAAGCACACGTCATTAAAAAAGACGA
1 ATTTATGACACGCATGTATGACTTACATTGAGCGTCATTGAAGCACACGTCA-TAAAAAAGACGA
*
368390 CACACGTTCGTGTGTC
65 CACACATTCGTGTGTC
368406 GTGATTGTAT
Statistics
Matches: 139, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
84 5 0.04
85 128 0.92
86 5 0.04
87 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (84 bp):
ATTTATGACACGCATGTATGACTTACATTGAGCGTCATTGAAGCACACGTCATAAAAAAGACGAC
ACACATTCGTGTGTCATAA
Found at i:370038 original size:12 final size:12
Alignment explanation
Indices: 370008--370032 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
369998 ATATATTGAT
370008 AATCAAATGAAA
1 AATCAAATGAAA
370020 AATCAAATGAAA
1 AATCAAATGAAA
370032 A
1 A
370033 GACAAACCCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (12 bp):
AATCAAATGAAA
Found at i:373466 original size:18 final size:18
Alignment explanation
Indices: 373443--373494 Score: 104
Period size: 18 Copynumber: 2.9 Consensus size: 18
373433 TGCCTAAATA
373443 ATATTAGAAGTTAGAATC
1 ATATTAGAAGTTAGAATC
373461 ATATTAGAAGTTAGAATC
1 ATATTAGAAGTTAGAATC
373479 ATATTAGAAGTTAGAA
1 ATATTAGAAGTTAGAA
373495 AAAGTTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (18 bp):
ATATTAGAAGTTAGAATC
Found at i:374533 original size:15 final size:15
Alignment explanation
Indices: 374508--374563 Score: 85
Period size: 15 Copynumber: 3.7 Consensus size: 15
374498 GATGCTTTCT
374508 TTTTACTTCTTTGACG
1 TTTT-CTTCTTTGACG
374524 TTTTCTTCTTTGACG
1 TTTTCTTCTTTGACG
*
374539 TTTTCTTCTTAGACG
1 TTTTCTTCTTTGACG
*
374554 TTGTCTTCTT
1 TTTTCTTCTT
374564 ACCCCATGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.09, C:0.20, G:0.12, T:0.59
Consensus pattern (15 bp):
TTTTCTTCTTTGACG
Found at i:377125 original size:20 final size:21
Alignment explanation
Indices: 377095--377139 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 21
377085 CCCTTATAAA
377095 ATTTCCTTAACTTATTATTAT
1 ATTTCCTTAACTTATTATTAT
377116 ATTT-CTTAACTTATTATTAT
1 ATTTCCTTAACTTATTATTAT
377136 ATTT
1 ATTT
377140 TTATCAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTCCTTAACTTATTATTAT
Found at i:379242 original size:18 final size:18
Alignment explanation
Indices: 379221--379256 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
379211 AAATGTGTTG
*
379221 TTTTAATTAAAATTAAAA
1 TTTTAATTAAAATGAAAA
*
379239 TTTTTATTAAAATGAAAA
1 TTTTAATTAAAATGAAAA
379257 ATACGTTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
TTTTAATTAAAATGAAAA
Found at i:387228 original size:41 final size:42
Alignment explanation
Indices: 387136--387257 Score: 106
Period size: 41 Copynumber: 3.0 Consensus size: 42
387126 CCAAAATTGG
* * * * *
387136 TAAGTCTTTCGGGCCATCAATGAGTCTTTCGAGCATGATGCT
1 TAAGTCCTTCGGGCCATCAATAAATCTTTCGAGCAAGATGCA
* **
387178 TAA-TGCTTCGGGCCATCTGTAAATCTTTCGAGCAAGATG-A
1 TAAGTCCTTCGGGCCATCAATAAATCTTTCGAGCAAGATGCA
* * * *
387218 TAAGTCCTTCGGACCATCCATAAGA-CCTTCGGGCAAGATG
1 TAAGTCCTTCGGGCCATCAATAA-ATCTTTCGAGCAAGATG
387258 TTTTCACATG
Statistics
Matches: 64, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
40 3 0.05
41 57 0.89
42 4 0.06
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (42 bp):
TAAGTCCTTCGGGCCATCAATAAATCTTTCGAGCAAGATGCA
Found at i:387281 original size:230 final size:231
Alignment explanation
Indices: 386673--387494 Score: 1018
Period size: 230 Copynumber: 3.6 Consensus size: 231
386663 TTCTTATTTA
* * * * * *
386673 GTAAGTCCTTCAGGCCATCAGTAAGTCTTTCAAGCCTGGTGTTTAAATCTTTCGGGTCATCTGTA
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGTA
*
386738 AATCTTTCGAGCAAGATGATAAGTCCTTTGGA-CCATCCATAAGACCTTCGGGCAGGATGTTTTC
66 AATCTTTCGAGCAAGATGATAAGTCCTTCGGAGCCATCCATAAGACCTTCGGGCAGGATGTTTTC
* * *
386802 ACATGTCTCTCAAAAAATGAGAAAAAATTCTCATTTAAATC-GAAAATTGAAATTGTTGAAAAGT
131 ACATGACTCTC-AAAAATGAG-AAAATTTCTCATTTAAATCTGAAAATTG-AATTTTTGAAAAGT
* * **
386866 AAGGAAAGTTTCTTACCTAGTAAACTATTTGCAAAATCA
193 AAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
* * * *
386905 GTAAGTCCCTT-GGGCCATCAGTAAGTCTTTCGAGAATGATGCTTAAATCCTTTGGGTCATATGT
1 GTAAGT-CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGT
* * * * * * *
386969 AAGTCTTTCGAGCAAGATGATAAGTCATT-TGAGCTATCCACAAGGCCTTTGGGCAGGATGTTTT
65 AAATCTTTCGAGCAAGATGATAAGTCCTTCGGAGCCATCCATAAGACCTTCGGGCAGGATGTTTT
* * **
387033 CACAT-ATTTCTCAAAAATGAGAAATATTTCTCATTTAAATCTAAAAATTG-ATTTTTTTAAAGT
130 CACATGA-CTCTCAAAAATGAGAAA-ATTTCTCATTTAAATCTGAAAATTGAATTTTTGAAAAGT
387096 AAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
193 AAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
* * * *
387135 GTAAGTCTTTCGGGCCATCAATGAGTCTTTCGAGCATGATGCTT-AATGC-TTCGGGCCATCTGT
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAAT-CATTCGGGTCATCTGT
*
387198 AAATCTTTCGAGCAAGATGATAAGTCCTTCGGA-CCATCCATAAGACCTTCGGGCAAGATGTTTT
65 AAATCTTTCGAGCAAGATGATAAGTCCTTCGGAGCCATCCATAAGACCTTCGGGCAGGATGTTTT
* * * * *
387262 CACATGACTCTCGAAAAATGA-AAAGTTCCTCGTTTAAATATGAAAATTGAAAATTTTGAAAAGT
130 CACATGACTCTC-AAAAATGAGAAAATTTCTCATTTAAATCTGAAAATTG-AATTTTTGAAAAGT
*
387326 AAGAAAAGTTTCTTACCTATTAAACTATTTCCAAAATTG
193 AAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
* ** ** *
387365 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGAGTAAATCATTCGCATCATCTATA
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGTA
** * * * *
387430 AGCCTTTCAAGCAAGATGATAAGTTCTTC-GAGCCATCCATAAGACATTCGAGCAGGATGTTTTC
66 AATCTTTCGAGCAAGATGATAAGTCCTTCGGAGCCATCCATAAGACCTTCGGGCAGGATGTTTTC
387494 A
131 A
387495 AAGTTTATCA
Statistics
Matches: 506, Mismatches: 69, Indels: 31
0.83 0.11 0.05
Matches are distributed among these distances:
228 20 0.04
229 82 0.16
230 185 0.37
231 95 0.19
232 120 0.24
233 4 0.01
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (231 bp):
GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGTA
AATCTTTCGAGCAAGATGATAAGTCCTTCGGAGCCATCCATAAGACCTTCGGGCAGGATGTTTTC
ACATGACTCTCAAAAATGAGAAAATTTCTCATTTAAATCTGAAAATTGAATTTTTGAAAAGTAAG
AAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
Found at i:388039 original size:3 final size:3
Alignment explanation
Indices: 388031--388063 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
388021 TTTTCGTCCA
388031 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
388064 TTCATTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:391053 original size:18 final size:17
Alignment explanation
Indices: 390993--391140 Score: 84
Period size: 17 Copynumber: 8.5 Consensus size: 17
390983 GATGAATTCT
* *
390993 AAATGTTTACAATTATC
1 AAATATTTACAGTTATC
* *
391010 AAACATTTCACCGTTAT-
1 AAATATTT-ACAGTTATC
*
391027 AAGATATTTACAATTATC
1 AA-ATATTTACAGTTATC
* *
391045 ATATGATTTTCAGTTATC
1 AAAT-ATTTACAGTTATC
* * *
391063 AGATATTTATAGTTAAC
1 AAATATTTACAGTTATC
* *
391080 AAATGATTTTCAGTTATA
1 AAAT-ATTTACAGTTATC
** *
391098 AAATATTTACAAATATT
1 AAATATTTACAGTTATC
*
391115 AGATGA-TTACAGTTATC
1 AAAT-ATTTACAGTTATC
*
391132 ATATATTTA
1 AAATATTTA
391141 AATATATCAG
Statistics
Matches: 96, Mismatches: 28, Indels: 14
0.70 0.20 0.10
Matches are distributed among these distances:
16 1 0.01
17 55 0.57
18 40 0.42
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (17 bp):
AAATATTTACAGTTATC
Found at i:391061 original size:35 final size:35
Alignment explanation
Indices: 390998--391149 Score: 132
Period size: 35 Copynumber: 4.4 Consensus size: 35
390988 ATTCTAAATG
*
390998 TTTACAATTATCAAA-CA-TTTCACCGTTATAAGATA
1 TTTACAATTATCAAATGATTTTCA--GTTATAAGATA
* *
391033 TTTACAATTATCATATGATTTTCAGTTATCAGATA
1 TTTACAATTATCAAATGATTTTCAGTTATAAGATA
* * * *
391068 TTTATAGTTAACAAATGATTTTCAGTTATAAAATA
1 TTTACAATTATCAAATGATTTTCAGTTATAAGATA
* * * * * *
391103 TTTACAAATATTAGATGA-TTACAGTTATCATATA
1 TTTACAATTATCAAATGATTTTCAGTTATAAGATA
391137 TTTA-AATATATCA
1 TTTACAAT-TATCA
391150 GACGTTTTAC
Statistics
Matches: 94, Mismatches: 20, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
33 2 0.02
34 21 0.22
35 65 0.69
36 1 0.01
37 5 0.05
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (35 bp):
TTTACAATTATCAAATGATTTTCAGTTATAAGATA
Found at i:391138 original size:34 final size:35
Alignment explanation
Indices: 391090--391167 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 35
391080 AAATGATTTT
* * *
391090 CAGTTATAAAATATTTACAA-ATATTAGATG-ATTA
1 CAGTTATCAAATATTTA-AATATATCAGACGTATTA
* *
391124 CAGTTATCATATATTTAAATATATCAGACGTTTTA
1 CAGTTATCAAATATTTAAATATATCAGACGTATTA
391159 CAGTTATCA
1 CAGTTATCA
391168 GACACATATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
33 2 0.05
34 23 0.62
35 12 0.32
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (35 bp):
CAGTTATCAAATATTTAAATATATCAGACGTATTA
Found at i:395851 original size:27 final size:28
Alignment explanation
Indices: 395803--395857 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
395793 ATTACGATGG
395803 AAGTACGATTTAGTTTTATATT-AATTT
1 AAGTACGATTTAGTTTTATATTGAATTT
395830 AAGTATCGATTTTA-TTTT-TATTGAATTT
1 AAGTA-CGA-TTTAGTTTTATATTGAATTT
395858 TATATTTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 9 0.36
28 12 0.48
29 4 0.16
ACGTcount: A:0.31, C:0.04, G:0.11, T:0.55
Consensus pattern (28 bp):
AAGTACGATTTAGTTTTATATTGAATTT
Found at i:396966 original size:36 final size:36
Alignment explanation
Indices: 396901--397014 Score: 105
Period size: 36 Copynumber: 3.2 Consensus size: 36
396891 ACATTTCACC
* * *
396901 GTTATTAGATATTTACGAT-TTTCAGATGATTTTTAA
1 GTTATCAGATATTTAC-ATATATCAAATGATTTTTAA
*
396937 GTTATCAGATATTTACATATATCAAATGA-TTAT-A
1 GTTATCAGATATTTACATATATCAAATGATTTTTAA
* *
396971 GTTATCATATGTTTACATATAT--AA-GATGTTTTACA
1 GTTATCAGATATTTACATATATCAAATGAT-TTTTA-A
397006 GTTATCAGA
1 GTTATCAGA
397015 CACATATTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
31 2 0.03
32 2 0.03
33 3 0.05
34 21 0.32
35 14 0.22
36 23 0.35
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.45
Consensus pattern (36 bp):
GTTATCAGATATTTACATATATCAAATGATTTTTAA
Found at i:402872 original size:60 final size:60
Alignment explanation
Indices: 402764--403249 Score: 785
Period size: 60 Copynumber: 8.1 Consensus size: 60
402754 TTGCTCTAAA
*
402764 ATGAAAAGTTAAATGCCTAACGATGCATTTTGGTAGAAAGGTGCCACTATTGCAAGTTAG
1 ATGAAAAGTTAAATGCCTAACGATGCATTTTGGCAGAAAGGTGCCACTATTGCAAGTTAG
* * * *
402824 ATGAAAAATTAAATGCCTAACGATGCATTTTGGCAAAAATGTGGCACTATTGCAAGTTAG
1 ATGAAAAGTTAAATGCCTAACGATGCATTTTGGCAGAAAGGTGCCACTATTGCAAGTTAG
* *
402884 ATGAAAAGTT-AATGCCTAACGATGCATTTTGGCAGAAAGGTGACACTATTGCAAGTTAT
1 ATGAAAAGTTAAATGCCTAACGATGCATTTTGGCAGAAAGGTGCCACTATTGCAAGTTAG
* *
402943 ATGAAAATTTAAATGACTAACGATGCATTTTGGCAGAAAGGTGCCACTATTGCAAGTTAG
1 ATGAAAAGTTAAATGCCTAACGATGCATTTTGGCAGAAAGGTGCCACTATTGCAAGTTAG
403003 ATGAAAAGTTAAATGCCTAACGATGCATTTTGGCAGAAAGGTGCCACTATTGCAAGTTAG
1 ATGAAAAGTTAAATGCCTAACGATGCATTTTGGCAGAAAGGTGCCACTATTGCAAGTTAG
* * * *
403063 ATGAAAACTTAAATGCCTAACGATGTATTTTGGCAGAAAGGTACCACTAATGCAAGTTAG
1 ATGAAAAGTTAAATGCCTAACGATGCATTTTGGCAGAAAGGTGCCACTATTGCAAGTTAG
* * * *
403123 ATGAAAAGTGAAATGCCTAACTATGCATTTTGGCAGAAATGTGCCACTAATGCAAGTTAG
1 ATGAAAAGTTAAATGCCTAACGATGCATTTTGGCAGAAAGGTGCCACTATTGCAAGTTAG
* * *
403183 ATGAAAAGTTAAATGCCTAACGGTGCATTTTGGCACAAAGGTGCCACTAGTGCAAGTTAG
1 ATGAAAAGTTAAATGCCTAACGATGCATTTTGGCAGAAAGGTGCCACTATTGCAAGTTAG
403243 ATGAAAA
1 ATGAAAA
403250 ACAATGCATT
Statistics
Matches: 393, Mismatches: 32, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
59 54 0.14
60 339 0.86
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (60 bp):
ATGAAAAGTTAAATGCCTAACGATGCATTTTGGCAGAAAGGTGCCACTATTGCAAGTTAG
Found at i:409807 original size:32 final size:31
Alignment explanation
Indices: 409733--409812 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
409723 CTAATGTGAC
* * *
409733 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
** **
409764 TCTCGGGTAGGCCCTACGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTACGGCCCTAAGAT-CAT
409796 TCTTAGGTAGGCCCTAC
1 TCTTAGGTAGGCCCTAC
409813 ATCCCCAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 23 0.59
32 16 0.41
ACGTcount: A:0.16, C:0.28, G:0.29, T:0.28
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
Found at i:412237 original size:21 final size:21
Alignment explanation
Indices: 412211--412278 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
412201 TTTTCACTGA
412211 TTTATCACCCGATTCGATCCG
1 TTTATCACCCGATTCGATCCG
*** * *
412232 TTTAT--CGTAATTAAGCTCCG
1 TTTATCACCCGATT-CGATCCG
*
412252 TTTTTCACCCGATTCGATCCG
1 TTTATCACCCGATTCGATCCG
412273 TTTATC
1 TTTATC
412279 GTAATTAAGC
Statistics
Matches: 32, Mismatches: 12, Indels: 6
0.64 0.24 0.12
Matches are distributed among these distances:
19 4 0.12
20 9 0.28
21 15 0.47
22 4 0.12
ACGTcount: A:0.19, C:0.28, G:0.13, T:0.40
Consensus pattern (21 bp):
TTTATCACCCGATTCGATCCG
Done.