Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015093.1 Kokia drynarioides strain JFW-HI SEQ_130137, 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: 636787
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 555 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:625 original size:20 final size:21
Alignment explanation
Indices: 600--646 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
590 TATTAATCCG
*
600 TAAAATCTCAAATTCAGGA-T
1 TAAAATCTAAAATTCAGGATT
* *
620 TAAAATTTAAAATTTAGGATT
1 TAAAATCTAAAATTCAGGATT
641 TAAAAT
1 TAAAAT
647 TTAGGGAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (21 bp):
TAAAATCTAAAATTCAGGATT
Found at i:643 original size:14 final size:14
Alignment explanation
Indices: 624--651 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
614 CAGGATTAAA
624 ATTTAAAATTTAGG
1 ATTTAAAATTTAGG
638 ATTTAAAATTTAGG
1 ATTTAAAATTTAGG
652 GAACATGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (14 bp):
ATTTAAAATTTAGG
Found at i:878 original size:6 final size:6
Alignment explanation
Indices: 867--898 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
857 TATGTCCATT
867 TCACAG TCACAG TCACAG TCACAG TCACAG TC
1 TCACAG TCACAG TCACAG TCACAG TCACAG TC
899 CCTCTACCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.34, G:0.16, T:0.19
Consensus pattern (6 bp):
TCACAG
Found at i:20183 original size:20 final size:21
Alignment explanation
Indices: 20150--20189 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
20140 ATATTTCCTA
20150 AATTAAATGTAATA-ATTAAT
1 AATTAAATGTAATATATTAAT
20170 AATTAAAT-TAAATATATTAA
1 AATTAAATGT-AATATATTAA
20190 ATTTTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.06
20 12 0.67
21 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
AATTAAATGTAATATATTAAT
Found at i:20915 original size:31 final size:29
Alignment explanation
Indices: 20858--20942 Score: 75
Period size: 30 Copynumber: 2.8 Consensus size: 29
20848 ATTTAAACGT
* * *
20858 GTATGATTGAACCAAAAT-AAAATTTCAT-
1 GTATAATTGCACC-AAATCAAAGTTTCATC
*
20886 GTATACATTTGGACCACAATCAAAGTTTCATGC
1 GTATA-A-TTGCACCA-AATCAAAGTTTCAT-C
20919 GTATAATTGCACCAAATCAAAGTT
1 GTATAATTGCACCAAATCAAAGTT
20943 ATGTATCAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
28 4 0.09
29 2 0.04
30 19 0.40
31 16 0.34
32 1 0.02
33 5 0.11
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (29 bp):
GTATAATTGCACCAAATCAAAGTTTCATC
Found at i:23515 original size:30 final size:30
Alignment explanation
Indices: 23480--23542 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
23470 TTTTTATATA
23480 ATATTTTTAATTTGTTTTCACTAATTTAAT
1 ATATTTTTAATTTGTTTTCACTAATTTAAT
23510 ATATTTTTAATTTGTTTTCACTAATTTAAT
1 ATATTTTTAATTTGTTTTCACTAATTTAAT
23540 ATA
1 ATA
23543 CAAATAGTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (30 bp):
ATATTTTTAATTTGTTTTCACTAATTTAAT
Found at i:25004 original size:3 final size:3
Alignment explanation
Indices: 24996--25027 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
24986 CCGGTACTCG
24996 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
25028 GCTATTATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:35598 original size:16 final size:17
Alignment explanation
Indices: 35574--35607 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
35564 ATTTTGGACC
35574 ATATATAAAAAAA-GTA
1 ATATATAAAAAAATGTA
*
35590 ATATGTAAAAAAATGTA
1 ATATATAAAAAAATGTA
35607 A
1 A
35608 ACTGTGTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (17 bp):
ATATATAAAAAAATGTA
Found at i:35874 original size:20 final size:20
Alignment explanation
Indices: 35849--35889 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
35839 AAATTACAGA
35849 TTTAACAGATTTCAATAAGG
1 TTTAACAGATTTCAATAAGG
35869 TTTAACAGATTTCAATAAGG
1 TTTAACAGATTTCAATAAGG
35889 T
1 T
35890 GAAAAATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (20 bp):
TTTAACAGATTTCAATAAGG
Found at i:36004 original size:8 final size:8
Alignment explanation
Indices: 35993--36048 Score: 67
Period size: 8 Copynumber: 6.9 Consensus size: 8
35983 AAAATTTGAA
35993 AATTTAAC
1 AATTTAAC
36001 AATTTAAC
1 AATTTAAC
36009 AATTTAAC
1 AATTTAAC
* *
36017 AGTGTAAC
1 AATTTAAC
*
36025 AATGTAAC
1 AATTTAAC
*
36033 AATGTAAC
1 AATTTAAC
36041 AATGTTAA
1 AAT-TTAA
36049 AATGTATATT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
8 40 0.93
9 3 0.07
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (8 bp):
AATTTAAC
Found at i:36012 original size:16 final size:16
Alignment explanation
Indices: 35993--36054 Score: 81
Period size: 16 Copynumber: 3.9 Consensus size: 16
35983 AAAATTTGAA
*
35993 AATTTAACAATTTAAC
1 AATTTAACAATGTAAC
*
36009 AATTTAACAGTGTAAC
1 AATTTAACAATGTAAC
*
36025 AATGTAACAATGTAAC
1 AATTTAACAATGTAAC
36041 AATGTTAA-AATGTA
1 AAT-TTAACAATGTA
36055 TATTGTGTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
16 37 0.93
17 3 0.08
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.32
Consensus pattern (16 bp):
AATTTAACAATGTAAC
Found at i:36267 original size:11 final size:11
Alignment explanation
Indices: 36250--36283 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
36240 AAAAAACAGT
36250 TTAAAAAATTG
1 TTAAAAAATTG
36261 TATAAAAAATTG
1 T-TAAAAAATTG
36273 TTAAAGAAATT
1 TTAAA-AAATT
36284 AACAAATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (11 bp):
TTAAAAAATTG
Found at i:36771 original size:237 final size:236
Alignment explanation
Indices: 36315--36787 Score: 858
Period size: 238 Copynumber: 2.0 Consensus size: 236
36305 AATTTAAATA
* * *
36315 TTCTTTTAATGTGGTTGAATGAATTGTAGATTATGTTTTGATTTTTTTGACTACTGTACGTACAG
1 TTCTTTTAATGTGGTTGAATGAATTGTAGATTATGTTCTGATTTTTTTGACTAATATACGTACAG
36380 TTAACAATATCCTTCACTAAACTCCCCATTCATGTGCATTTAGGTGGCATCCTCGTAAAAAATCC
66 TTAACAATATCCTTCACTAAACTCCCCATTCATGTGCATTTAGGTGGCATCCTCGTAAAAAATCC
36445 AAAATTATAGTATATAGGGGGTGAAGTTATGATTTGGTATATAGATCTTGACTTTGTTTCTCTTG
131 AAAATTATAGTATATAGGGGGTGAAGTTATGATTTGGTATATAGATCTTGACTTTGTTTCTCTTG
36510 TTGTTATAAATGAAATGGTAGTTGAAGCAGGGCATAATAGT
196 TTGTTATAAATGAAATGGTAGTTGAAGCAGGGCATAATAGT
* *
36551 TTCTTTTAATGTGGTTGAATGAATTGTAGATTGTGTTCTGATTTTTTTTTTACTAATATACGTAC
1 TTCTTTTAATGTGGTTGAATGAATTGTAGATTATGTTCTGA--TTTTTTTGACTAATATACGTAC
*
36616 AGTTAACAATATCCTTCACTAAACTCCCCATTCATGTGCATTTAGGTGGCATCCTCTTAAAAAAT
64 AGTTAACAATATCCTTCACTAAACTCCCCATTCATGTGCATTTAGGTGGCATCCTCGTAAAAAAT
*
36681 CCAAAATTATAGTATATA-GGTGTGAAGTTATGATTTGGTATATAGATCTTGACTTTGTTTCTCT
129 CCAAAATTATAGTATATAGGGGGTGAAGTTATGATTTGGTATATAGATCTTGACTTTGTTTCTCT
36745 TGTTGTTATAAATGAAATGGTAGTTGAAGCAGGGCATAATAGT
194 TGTTGTTATAAATGAAATGGTAGTTGAAGCAGGGCATAATAGT
36788 GTCAGTAGGG
Statistics
Matches: 228, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
236 39 0.17
237 88 0.39
238 101 0.44
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (236 bp):
TTCTTTTAATGTGGTTGAATGAATTGTAGATTATGTTCTGATTTTTTTGACTAATATACGTACAG
TTAACAATATCCTTCACTAAACTCCCCATTCATGTGCATTTAGGTGGCATCCTCGTAAAAAATCC
AAAATTATAGTATATAGGGGGTGAAGTTATGATTTGGTATATAGATCTTGACTTTGTTTCTCTTG
TTGTTATAAATGAAATGGTAGTTGAAGCAGGGCATAATAGT
Found at i:37186 original size:27 final size:27
Alignment explanation
Indices: 37143--37203 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
37133 GAAGCTTTTT
*
37143 GAGAGAGA-GGGGAGGAAGTTGTTT-CA
1 GAGAGAGACAGGGAGGAA-TTGTTTCCA
* *
37169 GAGGGAGACAGGGAGGAATTTTTTCCA
1 GAGAGAGACAGGGAGGAATTGTTTCCA
37196 GAGAGAGA
1 GAGAGAGA
37204 TAGTGATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 12 0.41
27 17 0.59
ACGTcount: A:0.33, C:0.07, G:0.43, T:0.18
Consensus pattern (27 bp):
GAGAGAGACAGGGAGGAATTGTTTCCA
Found at i:38752 original size:22 final size:22
Alignment explanation
Indices: 38694--38767 Score: 94
Period size: 22 Copynumber: 3.2 Consensus size: 22
38684 GTGGTGGGGA
38694 AACAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
*
38716 AGTAGCAGAAACACACACAGTGCTG
1 A--A-CAGAAGCACACACAGTGCTG
* *
38741 AACAGAAGCACACACATTGCTA
1 AACAGAAGCACACACAGTGCTG
38763 AACAG
1 AACAG
38768 TAAGTGCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
22 23 0.51
23 1 0.02
24 1 0.02
25 20 0.44
ACGTcount: A:0.43, C:0.26, G:0.20, T:0.11
Consensus pattern (22 bp):
AACAGAAGCACACACAGTGCTG
Found at i:44697 original size:23 final size:23
Alignment explanation
Indices: 44663--44718 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
44653 TTTTTGTGCA
44663 TTTTT-ATATTGTTT-TGTTATCG
1 TTTTTAATATTGTTTAT-TTATCG
* *
44685 TTTTTAATGTTGTTTATTTGTCG
1 TTTTTAATATTGTTTATTTATCG
44708 TTTTTAATATT
1 TTTTTAATATT
44719 ATTTGGATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.17
23 23 0.79
24 1 0.03
ACGTcount: A:0.16, C:0.04, G:0.12, T:0.68
Consensus pattern (23 bp):
TTTTTAATATTGTTTATTTATCG
Found at i:45440 original size:125 final size:124
Alignment explanation
Indices: 45211--45459 Score: 464
Period size: 125 Copynumber: 2.0 Consensus size: 124
45201 ATAATTGAAA
45211 AATATTCATTCTATAAATTCGACCTTTGCCAATTGACGCTCACTCTTTCCCCTCTTTTTTTTGTT
1 AATATTCATTCTATAAATTCGACCTTTGCCAATTGACGCTCACTCTTTCCCCTCTTTTTTTTGTT
*
45276 AATCTTCATCGTCATCTGTTTAATTTCCAAAACAAAAGCAACGTCTCAGGTACAAATTC
66 AATCTTCATCGTCATCTGTTTAATTTCCAAAACAAAAGCAACGTCTCAGGTAAAAATTC
45335 AATATTCATTCTATAAATTCGACCTTTGCCAATTGACGCTCACTCTTCTCCCC-CTTTTTTTTTG
1 AATATTCATTCTATAAATTCGACCTTTGCCAATTGACGCTCACTCTT-TCCCCTC-TTTTTTTTG
45399 TTAATCTTCATCGTCATCTGTTTAATTTCCAAAACAAAAGCAACGTCTCAGGTAAAAATTC
64 TTAATCTTCATCGTCATCTGTTTAATTTCCAAAACAAAAGCAACGTCTCAGGTAAAAATTC
45460 TCTTTTCTCG
Statistics
Matches: 122, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
124 48 0.39
125 74 0.61
ACGTcount: A:0.28, C:0.25, G:0.09, T:0.39
Consensus pattern (124 bp):
AATATTCATTCTATAAATTCGACCTTTGCCAATTGACGCTCACTCTTTCCCCTCTTTTTTTTGTT
AATCTTCATCGTCATCTGTTTAATTTCCAAAACAAAAGCAACGTCTCAGGTAAAAATTC
Found at i:47660 original size:161 final size:161
Alignment explanation
Indices: 47386--47874 Score: 818
Period size: 161 Copynumber: 3.0 Consensus size: 161
47376 GATTAAGTCG
*
47386 AAACTTGAG-CACAAAGCTCGGTCTAGTTTCACTTTTAAAGTTCGAATTCAAGTCGAAATAATAA
1 AAACTTGAGACACAAAGCTCGGTCTAGTTTCACTTTTAAAGTTCGAATTCAACTCGAAATAATAA
* *
47450 CCTATCTCACTTGATTAAACCTTTCTTATCAACACATATTTCGAGCTAATTAGGGGTGTTATCAA
66 TCTATCTCACTTGATTAAACCTTTCTTATCAACACATATTTCAAGCTAATTAGGGGTGTTATCAA
*
47515 GCGGAGCTCGAGTTGAAAGTCTCAAAAGTTT
131 GCCGAGCTCGAGTTGAAAGTCTCAAAAGTTT
* * *
47546 AAACTTGAGACACAAAGCTCAGTCTAGTTTCACTTTTAAAGTTCGAATTCAACTTGAGATAATAA
1 AAACTTGAGACACAAAGCTCGGTCTAGTTTCACTTTTAAAGTTCGAATTCAACTCGAAATAATAA
* * *
47611 TCTATCTCACTTGATTAACCCTGTCTTATCAACACATATTTCAAGCTAATTAGGGATGTTATCAA
66 TCTATCTCACTTGATTAAACCTTTCTTATCAACACATATTTCAAGCTAATTAGGGGTGTTATCAA
** *
47676 GCCGAGCTTAAGTTGAAAGTCTCAAGAGTTT
131 GCCGAGCTCGAGTTGAAAGTCTCAAAAGTTT
*
47707 AAACTTGAGACACAAAGCTCGGTCTAGTTTCACTTTTAAAGTTAGAATTCAACTCGAAATAATAA
1 AAACTTGAGACACAAAGCTCGGTCTAGTTTCACTTTTAAAGTTCGAATTCAACTCGAAATAATAA
*
47772 TCTATCTCACTTGATTAAAACTTTCTTATCAACACATATTTCAAGCTAATTAGGGGTGTTATCAA
66 TCTATCTCACTTGATTAAACCTTTCTTATCAACACATATTTCAAGCTAATTAGGGGTGTTATCAA
*
47837 GCCTAGCTCGAGTTGAAAGTCTCAAAAGTTT
131 GCCGAGCTCGAGTTGAAAGTCTCAAAAGTTT
*
47868 AAGCTTG
1 AAACTTG
47875 TTTCACTTTT
Statistics
Matches: 302, Mismatches: 26, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
160 9 0.03
161 293 0.97
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (161 bp):
AAACTTGAGACACAAAGCTCGGTCTAGTTTCACTTTTAAAGTTCGAATTCAACTCGAAATAATAA
TCTATCTCACTTGATTAAACCTTTCTTATCAACACATATTTCAAGCTAATTAGGGGTGTTATCAA
GCCGAGCTCGAGTTGAAAGTCTCAAAAGTTT
Found at i:49199 original size:30 final size:30
Alignment explanation
Indices: 49165--49224 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
49155 GATTTAATGT
49165 ACCTCATTAATAACGAAGAAAAGCAGAAAA
1 ACCTCATTAATAACGAAGAAAAGCAGAAAA
49195 ACCTCATTAATAACGAAGAAAAGCAGAAAA
1 ACCTCATTAATAACGAAGAAAAGCAGAAAA
49225 GTTTTTACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.17, G:0.13, T:0.13
Consensus pattern (30 bp):
ACCTCATTAATAACGAAGAAAAGCAGAAAA
Found at i:59748 original size:11 final size:9
Alignment explanation
Indices: 59719--59757 Score: 51
Period size: 9 Copynumber: 4.0 Consensus size: 9
59709 TTTCATGTTG
59719 TTTTTAATT
1 TTTTTAATT
59728 TTTTTAAATT
1 TTTTT-AATT
59738 TTTAATTAATT
1 TTT--TTAATT
59749 TTTTTAATT
1 TTTTTAATT
59758 AATAAATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 11 0.41
10 7 0.26
11 7 0.26
12 2 0.07
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTTAATT
Found at i:59754 original size:13 final size:13
Alignment explanation
Indices: 59736--59760 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59726 TTTTTTTAAA
59736 TTTTTAATTAATT
1 TTTTTAATTAATT
59749 TTTTTAATTAAT
1 TTTTTAATTAAT
59761 AAATATGTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTAATTAATT
Found at i:67951 original size:20 final size:18
Alignment explanation
Indices: 67918--67959 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 18
67908 TTGATTAAAA
67918 TTTATATAATATATATTTAT
1 TTTATATAATATAT-TTT-T
67938 TTTATTATAA-ATATTTTT
1 TTTA-TATAATATATTTTT
67956 TTTA
1 TTTA
67960 AAAAATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 5 0.24
19 3 0.14
20 8 0.38
21 5 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTATATAATATATTTTT
Found at i:69781 original size:24 final size:24
Alignment explanation
Indices: 69754--69806 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
69744 TGACATCACC
* *
69754 AGCATCTCTCTATACTTATTTTTA
1 AGCATCTCTATATACTTATATTTA
69778 AGCATCTCTATATACTTATATTTA
1 AGCATCTCTATATACTTATATTTA
69802 AGCAT
1 AGCAT
69807 TTTACTGACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.45
Consensus pattern (24 bp):
AGCATCTCTATATACTTATATTTA
Found at i:69899 original size:3 final size:3
Alignment explanation
Indices: 69893--69921 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
69883 AATAATTAAC
69893 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
69922 ATTTTTGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:74158 original size:24 final size:24
Alignment explanation
Indices: 74105--74155 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
74095 TTTGTAAGTC
* * *
74105 AAATAAATTATGTTAATAAATGTA
1 AAATATATTATATTAATAAATCTA
74129 AAATATATTATATTAATAAATACTA
1 AAATATATTATATTAATAAAT-CTA
74154 AA
1 AA
74156 TATTCTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATATTAATAAATCTA
Found at i:80212 original size:32 final size:34
Alignment explanation
Indices: 80162--80230 Score: 79
Period size: 32 Copynumber: 2.1 Consensus size: 34
80152 TTAAAAATAC
* *
80162 TATATATCTTTTTCGGAGG-T-ACTAAAACATTA
1 TATATATCCTTTTCGGAGGATGAATAAAACATTA
* * *
80194 TATATTTCCTTTTGGGAGGATGAATAAAATATTA
1 TATATATCCTTTTCGGAGGATGAATAAAACATTA
80228 TAT
1 TAT
80231 TTTTTCATGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 16 0.53
33 1 0.03
34 13 0.43
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (34 bp):
TATATATCCTTTTCGGAGGATGAATAAAACATTA
Found at i:84213 original size:40 final size:41
Alignment explanation
Indices: 84169--84247 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 41
84159 TGTCAGGTTA
84169 GTAACTCCTAAATTGTTGTTTCAATGTCAATA-TCCCTGTG
1 GTAACTCCTAAATTGTTGTTTCAATGTCAATATTCCCTGTG
*
84209 GTAACTCGTAAATTGTTGTTTCAATGTCAATATTCCCTG
1 GTAACTCCTAAATTGTTGTTTCAATGTCAATATTCCCTG
84248 GCCTAGTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 31 0.84
41 6 0.16
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (41 bp):
GTAACTCCTAAATTGTTGTTTCAATGTCAATATTCCCTGTG
Found at i:89653 original size:3 final size:3
Alignment explanation
Indices: 89647--89673 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
89637 CCATCGGTGG
89647 TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA
89674 ATCACCTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:96233 original size:42 final size:42
Alignment explanation
Indices: 96185--96276 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
96175 TTCGTGAACA
*
96185 TAAACGAATAGAACGCACCTCTATTCGTGTTCGTTCGTTTAT
1 TAAACGAATAGAACACACCTCTATTCGTGTTCGTTCGTTTAT
* * *
96227 TAAACGAATTGAACACACCTTTGTTCGTGTTCGTTCGTTTAT
1 TAAACGAATAGAACACACCTCTATTCGTGTTCGTTCGTTTAT
96269 TAAACGAA
1 TAAACGAA
96277 CATAAAAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (42 bp):
TAAACGAATAGAACACACCTCTATTCGTGTTCGTTCGTTTAT
Found at i:96698 original size:19 final size:18
Alignment explanation
Indices: 96677--96711 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
96667 ATGGCACATA
96677 AAAAAATTTGACAATGTC
1 AAAAAATTTGACAATGTC
96695 AAAAAATTTGACAATGT
1 AAAAAATTTGACAATGT
96712 GATATGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.29
Consensus pattern (18 bp):
AAAAAATTTGACAATGTC
Found at i:105095 original size:7 final size:7
Alignment explanation
Indices: 105079--105111 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
105069 GCGAGGGTAG
105079 GCAT-AT
1 GCATGAT
105085 GCATGAT
1 GCATGAT
105092 GCATGAT
1 GCATGAT
105099 GCATGAT
1 GCATGAT
105106 GCATGA
1 GCATGA
105112 ATGTGATAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.15
7 22 0.85
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.27
Consensus pattern (7 bp):
GCATGAT
Found at i:108044 original size:32 final size:32
Alignment explanation
Indices: 108008--108143 Score: 245
Period size: 32 Copynumber: 4.2 Consensus size: 32
107998 ATATATATGT
108008 ATGGTAATTGCTTTTTATTAATTTTAATATAC
1 ATGGTAATTGCTTTTTATTAATTTTAATATAC
108040 ATGGTAATTGCTTTTTATTAATTTTAATATAC
1 ATGGTAATTGCTTTTTATTAATTTTAATATAC
* *
108072 ATGGTAATTGCATTTTATTAATTTTAATATAT
1 ATGGTAATTGCTTTTTATTAATTTTAATATAC
*
108104 ATGGTAATTGCTTTTTATTAATTTTAATATAT
1 ATGGTAATTGCTTTTTATTAATTTTAATATAC
108136 ATGGTAAT
1 ATGGTAAT
108144 AATGTTTTGG
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 101 1.00
ACGTcount: A:0.32, C:0.04, G:0.10, T:0.53
Consensus pattern (32 bp):
ATGGTAATTGCTTTTTATTAATTTTAATATAC
Found at i:108229 original size:47 final size:46
Alignment explanation
Indices: 108096--108263 Score: 191
Period size: 47 Copynumber: 3.6 Consensus size: 46
108086 TTATTAATTT
* **
108096 TAATATATATGGTAATTGCTTTTTATTAATTTTAATATATATGGTAA
1 TAATAT-TATGGTAATTTCTTTTTATTACCTTTAATATATATGGTAA
* * *
108143 TAATGTTTTGGTAATTACTCTTTTTATTACC--T--TATATATGGCAA
1 TAATATTATGGTAATT--TCTTTTTATTACCTTTAATATATATGGTAA
*
108187 TAATATTATGGTAATGTTCTTTTTATTGCCTTTAATATATATGGTAA
1 TAATATTATGGTAAT-TTCTTTTTATTACCTTTAATATATATGGTAA
*
108234 TAATATTATGGTAATTGCTCTTTTATTACC
1 TAATATTATGGTAATTTCT-TTTTATTACC
108264 ATATAAAATT
Statistics
Matches: 101, Mismatches: 12, Indels: 16
0.78 0.09 0.12
Matches are distributed among these distances:
43 12 0.12
44 24 0.24
45 2 0.02
46 13 0.13
47 40 0.40
48 10 0.10
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.51
Consensus pattern (46 bp):
TAATATTATGGTAATTTCTTTTTATTACCTTTAATATATATGGTAA
Found at i:108230 original size:91 final size:90
Alignment explanation
Indices: 108096--108268 Score: 249
Period size: 91 Copynumber: 1.9 Consensus size: 90
108086 TTATTAATTT
* * *
108096 TAATATATATGGTAATTGCTTTTTATTAATTTTAATATATATGGTAATAATGTTTTGGTAATTAC
1 TAATATATATGGTAATTGCTTTTTATTAACTTTAATATATATGGTAATAATATTATGGTAATTAC
*
108161 TCTTTTTATTACCTTATATATGGCAA
66 TC-TTTTATTACCATATATATGGCAA
* ** *
108187 TAATAT-TATGGTAATGTTCTTTTTATTGCCTTTAATATATATGGTAATAATATTATGGTAATTG
1 TAATATATATGGTAAT-TGCTTTTTATTAACTTTAATATATATGGTAATAATATTATGGTAATTA
108251 CTCTTTTATTACCATATA
65 CTCTTTTATTACCATATA
108269 AAATTAATTG
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
90 23 0.32
91 50 0.68
ACGTcount: A:0.31, C:0.08, G:0.11, T:0.50
Consensus pattern (90 bp):
TAATATATATGGTAATTGCTTTTTATTAACTTTAATATATATGGTAATAATATTATGGTAATTAC
TCTTTTATTACCATATATATGGCAA
Found at i:108245 original size:14 final size:15
Alignment explanation
Indices: 108219--108248 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
108209 TTATTGCCTT
108219 TAATATATATGGTAA
1 TAATATATATGGTAA
108234 TAATAT-TATGGTAA
1 TAATATATATGGTAA
108248 T
1 T
108249 TGCTCTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (15 bp):
TAATATATATGGTAA
Found at i:114625 original size:22 final size:22
Alignment explanation
Indices: 114599--114643 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
114589 TCGACTTCCT
114599 TATTTTCTATTT-GTTTTAATTA
1 TATTTTCT-TTTAGTTTTAATTA
*
114621 TATTTTCTTTTATTTTTAATTA
1 TATTTTCTTTTAGTTTTAATTA
114643 T
1 T
114644 GTTTCTTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.71
Consensus pattern (22 bp):
TATTTTCTTTTAGTTTTAATTA
Found at i:114648 original size:21 final size:22
Alignment explanation
Indices: 114612--114658 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
114602 TTTCTATTTG
* *
114612 TTTTAATTATATTTTCTTTTAT
1 TTTTAATTATAGTTTCTTCTAT
114634 TTTTAATTAT-GTTTCTTCTAT
1 TTTTAATTATAGTTTCTTCTAT
114655 TTTT
1 TTTT
114659 CCTCAGATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTTAATTATAGTTTCTTCTAT
Found at i:114658 original size:22 final size:23
Alignment explanation
Indices: 114603--114658 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 23
114593 CTTCCTTATT
*
114603 TTCTATTTGTTTTAATTATATTTTC
1 TTCTA-TT-TTTTAATTATAGTTTC
*
114628 TTTTA-TTTTTAATTAT-GTTTC
1 TTCTATTTTTTAATTATAGTTTC
114649 TTCTATTTTT
1 TTCTATTTTT
114659 CCTCAGATCG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 8 0.30
22 14 0.52
23 1 0.04
25 4 0.15
ACGTcount: A:0.18, C:0.07, G:0.04, T:0.71
Consensus pattern (23 bp):
TTCTATTTTTTAATTATAGTTTC
Found at i:115864 original size:16 final size:16
Alignment explanation
Indices: 115845--115877 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
115835 TCTGAAGTCG
115845 ATAAGTCTTGAACACC
1 ATAAGTCTTGAACACC
115861 ATAAGTCTTGAACACC
1 ATAAGTCTTGAACACC
115877 A
1 A
115878 AAAGAACATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (16 bp):
ATAAGTCTTGAACACC
Found at i:119103 original size:28 final size:28
Alignment explanation
Indices: 119026--119103 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 28
119016 ATTTTTTTTT
* *
119026 TAATTTGGTACTTAAATTTTTTTGGATC
1 TAATTTGGTACCTAAATTTTTTTAGATC
*
119054 TAATTTGGTACCTAAGTTTTTTTTTAGAT-
1 TAATTTGGTACCTAA--ATTTTTTTAGATC
*
119083 TCAATTTCGTACCTAAATTTT
1 T-AATTTGGTACCTAAATTTT
119104 ATTAAATATT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
28 18 0.43
29 1 0.02
30 23 0.55
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.53
Consensus pattern (28 bp):
TAATTTGGTACCTAAATTTTTTTAGATC
Found at i:120987 original size:31 final size:31
Alignment explanation
Indices: 120950--121008 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
120940 ATTTTGATTA
*
120950 TTTTTAAAA-GATTGATGGTAAAATTTAATTC
1 TTTTTAAAACG-TTGAGGGTAAAATTTAATTC
*
120981 TTTTTAAAACGTTGAGGGTCAAATTTAA
1 TTTTTAAAACGTTGAGGGTAAAATTTAA
121009 CTAAAAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.42
Consensus pattern (31 bp):
TTTTTAAAACGTTGAGGGTAAAATTTAATTC
Found at i:123592 original size:25 final size:25
Alignment explanation
Indices: 123559--123611 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
123549 CTAATATATA
* *
123559 TATATATATAGTTTTTATAT-TTTTT
1 TATAAATATA-TTTTTATATAATTTT
123584 TATAAATATATTTTTATATAATTTT
1 TATAAATATATTTTTATATAATTTT
123609 TAT
1 TAT
123612 CACATTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (25 bp):
TATAAATATATTTTTATATAATTTT
Found at i:123595 original size:16 final size:16
Alignment explanation
Indices: 123574--123604 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
123564 ATATAGTTTT
*
123574 TATATTTTTTTATAAA
1 TATATTTTTATATAAA
123590 TATATTTTTATATAA
1 TATATTTTTATATAA
123605 TTTTTATCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATATTTTTATATAAA
Found at i:135329 original size:22 final size:22
Alignment explanation
Indices: 135285--135330 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
135275 CTTAGCTTTT
* **
135285 TTTTTTTTTTTAATAATCCAAA
1 TTTTTTTATTTAATAATAAAAA
*
135307 TTTTTTTATTTAATTATAAAAA
1 TTTTTTTATTTAATAATAAAAA
135329 TT
1 TT
135331 ATAAAATTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTTTTTATTTAATAATAAAAA
Found at i:142002 original size:15 final size:14
Alignment explanation
Indices: 141971--142009 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
141961 TTGTTTCATT
*
141971 AAAAATAATTTCTG
1 AAAAATGATTTCTG
*
141985 AAAAATGATTTTTG
1 AAAAATGATTTCTG
*
141999 GAAAATGATTT
1 AAAAATGATTT
142010 ACTTTTTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.46, C:0.03, G:0.13, T:0.38
Consensus pattern (14 bp):
AAAAATGATTTCTG
Found at i:153147 original size:18 final size:18
Alignment explanation
Indices: 153124--153160 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
153114 TTTATTCTGG
153124 TCTTAATTTTGATACTGC
1 TCTTAATTTTGATACTGC
153142 TCTTAATTTTGATACTGC
1 TCTTAATTTTGATACTGC
153160 T
1 T
153161 ACACATGCAA
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:0.22, C:0.16, G:0.11, T:0.51
Consensus pattern (18 bp):
TCTTAATTTTGATACTGC
Found at i:156564 original size:28 final size:29
Alignment explanation
Indices: 156523--156577 Score: 103
Period size: 28 Copynumber: 1.9 Consensus size: 29
156513 AACCTACTTA
156523 ACACCATAATTTTAAGCATTTAAATTTGT
1 ACACCATAATTTTAAGCATTTAAATTTGT
156552 ACACCA-AATTTTAAGCATTTAAATTT
1 ACACCATAATTTTAAGCATTTAAATTT
156578 TATATTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (29 bp):
ACACCATAATTTTAAGCATTTAAATTTGT
Found at i:156577 original size:15 final size:15
Alignment explanation
Indices: 156530--156579 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
156520 TTAACACCAT
156530 AATTTTAAGCATTTA
1 AATTTTAAGCATTTA
**
156545 AATTTGT-A-CA-CCA
1 AATTT-TAAGCATTTA
156558 AATTTTAAGCATTTA
1 AATTTTAAGCATTTA
156573 AATTTTA
1 AATTTTA
156580 TATTTTTACG
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
12 1 0.04
13 7 0.26
14 4 0.15
15 14 0.52
16 1 0.04
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (15 bp):
AATTTTAAGCATTTA
Found at i:157342 original size:17 final size:18
Alignment explanation
Indices: 157309--157352 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
157299 ACATATTATA
157309 ATATAAATATTAAAAAATT
1 ATATAAATATT-AAAAATT
*
157328 ATATAAATATTAAAATTT
1 ATATAAATATTAAAAATT
*
157346 AAATAAA
1 ATATAAA
157353 ATATCATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATATAAATATTAAAAATT
Found at i:157354 original size:19 final size:20
Alignment explanation
Indices: 157303--157356 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 20
157293 TCATCCACAT
157303 ATTATAATATAAATATTAAAAA
1 ATTA-AATA-AAATATTAAAAA
*
157325 ATTATAT-AAATATT-AAAA
1 ATTAAATAAAATATTAAAAA
*
157343 TTTAAATAAAATAT
1 ATTAAATAAAATAT
157357 CATATAAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 9 0.32
19 13 0.46
21 2 0.07
22 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTAAATAAAATATTAAAAA
Found at i:159644 original size:28 final size:29
Alignment explanation
Indices: 159599--159668 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 29
159589 GTGATCTACG
*
159599 TGTATTTAGCACTTTGTGTGCTCTCTGTT-
1 TGTAATTAGCACTTTGTGTGCTCT-TGTTC
159628 T-TAATTAGCACTTTGTGTGCTCTTGTTC
1 TGTAATTAGCACTTTGTGTGCTCTTGTTC
159656 TGTAA-TAGCACTT
1 TGTAATTAGCACTT
159669 CGGTGCTTCG
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
27 4 0.11
28 30 0.79
29 4 0.11
ACGTcount: A:0.16, C:0.17, G:0.19, T:0.49
Consensus pattern (29 bp):
TGTAATTAGCACTTTGTGTGCTCTTGTTC
Found at i:160612 original size:8 final size:8
Alignment explanation
Indices: 160599--160624 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
160589 GATTCTTTCG
160599 AAATTTTA
1 AAATTTTA
160607 AAATTTTA
1 AAATTTTA
160615 AAATTTTA
1 AAATTTTA
160623 AA
1 AA
160625 TTAATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AAATTTTA
Found at i:167460 original size:27 final size:27
Alignment explanation
Indices: 167410--167499 Score: 82
Period size: 27 Copynumber: 3.4 Consensus size: 27
167400 TTAAAATGAC
* *
167410 TATATAAAAAT-TTCAATAAATAAAAAA
1 TATATAAAAATATTAAAT-ATTAAAAAA
167437 TATATAAAAATATTAAATATTAAAATAA
1 TATATAAAAATATTAAATATTAAAA-AA
*
167465 TATA-ATATAATA-TAAATATTTAAAAAA
1 TATATA-AAAATATTAAATA-TTAAAAAA
167492 -AT-TAAAAA
1 TATATAAAAA
167500 ATAATATGGA
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
25 3 0.06
26 3 0.06
27 26 0.48
28 22 0.41
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (27 bp):
TATATAAAAATATTAAATATTAAAAAA
Found at i:167466 original size:28 final size:27
Alignment explanation
Indices: 167395--167502 Score: 80
Period size: 27 Copynumber: 3.9 Consensus size: 27
167385 AACATTTAAA
* *
167395 AAATGTTAAAATGACTATATAAAAAT-TT
1 AAATATTAAAAT-AATATA-AAAAATATT
* *
167423 CAATAAATAAAA-AATATATAAAAATATT
1 AAAT-ATTAAAATAATATA-AAAAATATT
*
167451 AAATATTAAAATAATATAATATAATA-T
1 AAATATTAAAATAATATAA-AAAATATT
*
167478 AAATATTTAAAAAAAT-TAAAAAATA
1 AAATA-TTAAAATAATATAAAAAATA
167503 ATATGGACAG
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
26 5 0.08
27 28 0.42
28 28 0.42
29 5 0.08
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (27 bp):
AAATATTAAAATAATATAAAAAATATT
Found at i:180943 original size:62 final size:63
Alignment explanation
Indices: 180836--181010 Score: 194
Period size: 63 Copynumber: 2.8 Consensus size: 63
180826 GTTCTAACCT
* * * ** * * * *
180836 GTTT-TTTTTCACAAGCATCACAACATGCATAATCATTCCCCGCATCAATATCTTTAGC-TCG
1 GTTTATTTTACACAAGCACCACAACATGCACAATCATTCCATGCATCAACATATTCAACATCG
180897 GTTTATTTTACACAAGCACCACAACATGCACAATCATTCCATGCATCAACATATTCAACATCG
1 GTTTATTTTACACAAGCACCACAACATGCACAATCATTCCATGCATCAACATATTCAACATCG
* * * * *
180960 ATTTATTTTATACAAGCACCACAACA-CCGACAATCATTCCTTCCATCAACA
1 GTTTATTTTACACAAGCACCACAACATGC-ACAATCATTCCATGCATCAACA
181011 CCTTCTCTAG
Statistics
Matches: 97, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
61 4 0.04
62 46 0.47
63 47 0.48
ACGTcount: A:0.34, C:0.29, G:0.07, T:0.30
Consensus pattern (63 bp):
GTTTATTTTACACAAGCACCACAACATGCACAATCATTCCATGCATCAACATATTCAACATCG
Found at i:183222 original size:31 final size:31
Alignment explanation
Indices: 183187--183252 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
183177 AAAAAAAATT
*
183187 AATAGCTCAGTGACTTAAATAAAAACTTTTG
1 AATAGCTCAGTGACTTAAATAAAAACTTTCG
* *
183218 AATAGTTTAGTGACTTAAATAAAAACTTTCG
1 AATAGCTCAGTGACTTAAATAAAAACTTTCG
183249 AATA
1 AATA
183253 ATTCAACAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (31 bp):
AATAGCTCAGTGACTTAAATAAAAACTTTCG
Found at i:194162 original size:26 final size:26
Alignment explanation
Indices: 194132--194186 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
194122 AATGTAATAT
* *
194132 GTATGATAGATGTCCGTATGAACTTA
1 GTATGATAGATGCCCATATGAACTTA
194158 GTATGATAGATGCCCATATGAACTTA
1 GTATGATAGATGCCCATATGAACTTA
194184 GTA
1 GTA
194187 ATAGGTTAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.33
Consensus pattern (26 bp):
GTATGATAGATGCCCATATGAACTTA
Found at i:196712 original size:22 final size:22
Alignment explanation
Indices: 196686--196728 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
196676 ATAAATTTAA
*
196686 TTTTTATTGTTTATATTTATTG
1 TTTTTATTGTTTAAATTTATTG
*
196708 TTTTTATTTTTTAAATTTATT
1 TTTTTATTGTTTAAATTTATT
196729 TGATTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (22 bp):
TTTTTATTGTTTAAATTTATTG
Found at i:200044 original size:16 final size:17
Alignment explanation
Indices: 200015--200047 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
200005 GAGTTTAAAA
*
200015 TATTTATTTTTTAATAT
1 TATTTATTTATTAATAT
200032 TATTT-TTTATTAATAT
1 TATTTATTTATTAATAT
200048 CAAAATTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTTATTTATTAATAT
Found at i:206205 original size:29 final size:30
Alignment explanation
Indices: 206136--206215 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
206126 ATATTAAAAC
*
206136 TATACATGAACTATGATTTAATGTGCAATTA
1 TATACATGAACTTTGATTT-ATGTGCAATTA
* *
206167 TGTACATGAACTTTGATTT-TGTGCAATTT
1 TATACATGAACTTTGATTTATGTGCAATTA
* *
206196 TATACGTGAAATTTTGATTT
1 TATACATG-AACTTTGATTT
206216 GATCCAATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 15 0.36
30 10 0.24
31 17 0.40
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (30 bp):
TATACATGAACTTTGATTTATGTGCAATTA
Found at i:208004 original size:22 final size:23
Alignment explanation
Indices: 207957--208007 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
207947 TTTATTTGAA
*
207957 AAATAAATTTTAAAAATGTTTAT
1 AAATATATTTTAAAAATGTTTAT
207980 AAATATATTTT-AAAAT-TTTACT
1 AAATATATTTTAAAAATGTTTA-T
208002 AAATAT
1 AAATAT
208008 TGTAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 4 0.15
22 12 0.46
23 10 0.38
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
AAATATATTTTAAAAATGTTTAT
Found at i:208251 original size:7 final size:7
Alignment explanation
Indices: 208239--208287 Score: 91
Period size: 7 Copynumber: 7.1 Consensus size: 7
208229 TTATTTTATT
208239 ATAATAA
1 ATAATAA
208246 ATAATAA
1 ATAATAA
208253 ATAATAA
1 ATAATAA
208260 ATAATAA
1 ATAATAA
208267 ATAATAA
1 ATAATAA
208274 ATAATAA
1 ATAATAA
208281 AT-ATAA
1 ATAATAA
208287 A
1 A
208288 ATATAAATCA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 5 0.12
7 37 0.88
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
ATAATAA
Found at i:208264 original size:21 final size:21
Alignment explanation
Indices: 208239--208295 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
208229 TTATTTTATT
208239 ATAATAAATAATAAATAATAA
1 ATAATAAATAATAAATAATAA
208260 ATAATAAATAATAAATAATAA
1 ATAATAAATAATAAATAATAA
208281 AT-ATAAA-ATATAAAT
1 ATAATAAATA-ATAAAT
208296 CAAAAGGCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 1 0.03
20 11 0.31
21 23 0.66
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAATAAATAATAAATAATAA
Found at i:210772 original size:23 final size:23
Alignment explanation
Indices: 210746--210791 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
210736 TGATACCAAA
*
210746 GCACTTTGAAGTCTACCTATAAT
1 GCACTTTGAAGTCTAACTATAAT
*
210769 GCACTTTGAAGTTTAACTATAAT
1 GCACTTTGAAGTCTAACTATAAT
210792 TGCATGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (23 bp):
GCACTTTGAAGTCTAACTATAAT
Found at i:216182 original size:378 final size:376
Alignment explanation
Indices: 215399--216533 Score: 1406
Period size: 378 Copynumber: 3.0 Consensus size: 376
215389 GAATCATATT
* * * * * *
215399 TTATTATTGGATTAATGTCCTTTTTATTTAGGT-TGCTCTTGTTTGTTATTTGTTATTCTCGACT
1 TTATTATTGGATTGATGTCCTTTTTATCTA-GTCTGCTCTTGTATGTTATTTGTTACTCTTG-CC
* * * *
215463 CTT-AATCCTTAGCTGGTTTACTACAA-TGACACGAGATGTAAAATTAAATATGTTGCCAAACAT
64 CTTCAATCCTTAACTGGTTTACTACAATTGGCACAAGATGTAAAATTAAATATGTTGCAAAACAT
* * * *
215526 TTATATGTTTAACATTTGATAAATTCAATTTCAAGTAAAGTTTTTTTTTTATTTGTTAAAAAAAT
129 TTATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAA-ATTTATTTTTATTTGTT-AAAAAAT
* * * * * *
215591 TAATTTTGAAGAATTGACAGTTATAGTGTCACTGATCACGTAACGACTGAGAGAGATATTGAATC
192 TAATTTTGGAGAACTGACGGTTATAATGTCACTGATCACGTAACGACTGAGAGAGAGATTGAGTC
* * * * * * *
215656 ACAAACTGTCAAGTGTAAAAAGACCATAATCGCTCTAACGAAAAGGGCTATATTACATCCCTTTC
257 AAAAACAGTCAAGAGTAAAAA-ACCATAATCACCCT-ACGAAAAGGGCCACATTACATCCCTTTC
* *
215721 TTATACGGTCAACAATTGCAAATAAGCGATGCTACATGT--TTAGAAAGTTGTTGGC
320 TTAAACGGTCAACAATTGCAAATAAGCGATGCTACATGTCATTAGAAAGTTGTTGAC
* *
215776 TTATTATTGGATTGATGTCCTTTTTATCTAGTCTGCTTTTGTATGTCATTTGTTACTCTTGCCCT
1 TTATTATTGGATTGATGTCCTTTTTATCTAGTCTGCTCTTGTATGTTATTTGTTACTCTTGCCCT
* *
215841 TCAATCCTTAACTTGTTTACTACAATTGGCACAAGATGTAAAATTAAATATGTTGCAAAACGTTT
66 TCAATCCTTAACTGGTTTACTACAATTGGCACAAGATGTAAAATTAAATATGTTGCAAAACATTT
* *
215906 ATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAATTTCTTTTTATTTGTTAAAATATTAAT
131 ATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAATTTATTTTTATTTGTTAAAAAATTAAT
* * ** *
215971 TTTGGAGACCTAACGGTTATAATGTCACTGATTGCGTAACGACTGAGAGAGAGATTGAGTTAAAA
196 TTTGGAGAACTGACGGTTATAATGTCACTGATCACGTAACGACTGAGAGAGAGATTGAGTCAAAA
*
216036 ACAGTCAAGAGTAAAAAACCCATAATTACCCTAGCGAAAAGGGCCACATTACATCCCTTTCTTAA
261 ACAGTCAAGAGTAAAAAA-CCATAATCACCCTA-CGAAAAGGGCCACATTACATCCCTTTCTTAA
*
216101 ACGGTCAACAATTGCAAATAAGTGATGCTACATGTCATTAGAAAGTTGTTGAC
324 ACGGTCAACAATTGCAAATAAGCGATGCTACATGTCATTAGAAAGTTGTTGAC
*
216154 TTATTATTGGATTGGTGTCCTTTTTATCTAAG-CTGCTCTTGTATGTTATTTGTTACTCTTG-CC
1 TTATTATTGGATTGATGTCCTTTTTATCT-AGTCTGCTCTTGTATGTTATTTGTTACTCTTGCCC
* * * * *
216217 TCTCAATCCTT-AGTCGGTTTACTACAATTGGTATAAGATGTAAAATTAAATATTTTGCGAAACA
65 T-TCAATCCTTAACT-GGTTTACTACAATTGGCACAAGATGTAAAATTAAATATGTTGCAAAACA
* * *** * *
216281 TTTATATGTTTCACATTTGGTAAATCCAATTTCGAGTAAAAAAAAATTTTATTTGCTAAAAAATT
128 TTTATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAATTTATTTTTATTTGTTAAAAAATT
* ** *
216346 AATTTTGGAGAACTGACGGTTATAATATCACTGATCACGTATTGACTGAGAGAGAGACTG-GATC
193 AATTTTGGAGAACTGACGGTTATAATGTCACTGATCACGTAACGACTGAGAGAGAGATTGAG-TC
* * * * * * * * ** ** * *
216410 ATAGACAATCGAGAATAAAATGATCAAAATCACCCTAAAAAAAAAGTCACATTATATCCCTTTCT
257 AAAAACAGTCAAGAGTAAAA-AACCATAATCACCCTACGAAAAGGGCCACATTACATCCCTTTCT
* * *
216475 TAAACTGTCAACAATTGCAAATAAACGATGCTACATGTCATTAGAAAATTGTTGAC
321 TAAACGGTCAACAATTGCAAATAAGCGATGCTACATGTCATTAGAAAGTTGTTGAC
216531 TTA
1 TTA
216534 GCTATCCATT
Statistics
Matches: 658, Mismatches: 88, Indels: 24
0.85 0.11 0.03
Matches are distributed among these distances:
375 2 0.00
376 156 0.24
377 170 0.26
378 327 0.50
379 3 0.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (376 bp):
TTATTATTGGATTGATGTCCTTTTTATCTAGTCTGCTCTTGTATGTTATTTGTTACTCTTGCCCT
TCAATCCTTAACTGGTTTACTACAATTGGCACAAGATGTAAAATTAAATATGTTGCAAAACATTT
ATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAATTTATTTTTATTTGTTAAAAAATTAAT
TTTGGAGAACTGACGGTTATAATGTCACTGATCACGTAACGACTGAGAGAGAGATTGAGTCAAAA
ACAGTCAAGAGTAAAAAACCATAATCACCCTACGAAAAGGGCCACATTACATCCCTTTCTTAAAC
GGTCAACAATTGCAAATAAGCGATGCTACATGTCATTAGAAAGTTGTTGAC
Found at i:216861 original size:68 final size:68
Alignment explanation
Indices: 216728--216866 Score: 188
Period size: 68 Copynumber: 2.0 Consensus size: 68
216718 AGAACTCAAT
* **
216728 AAGTGGTTTCAGTAAAAAAAAAGATGTTGTTAATCTTAAGGGTCTCGGGTTCGAGTGCTTATGTG
1 AAGTGGTTCCAGTAAAAAAAAAGATGTTGTTAATCTTAAGGGTCTCGGGTTCGAACGCTTATGTG
*
216793 TGC
66 TAC
** * * * *
216796 AAGTGGTTCCAGTTGAAAAAAGGATGTTGTTCATCTTAAGGGTCTTGGGTTCGAACGCTTGTGTG
1 AAGTGGTTCCAGTAAAAAAAAAGATGTTGTTAATCTTAAGGGTCTCGGGTTCGAACGCTTATGTG
216861 TAC
66 TAC
216864 AAG
1 AAG
216867 ATGTATATGT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.33
Consensus pattern (68 bp):
AAGTGGTTCCAGTAAAAAAAAAGATGTTGTTAATCTTAAGGGTCTCGGGTTCGAACGCTTATGTG
TAC
Found at i:217587 original size:28 final size:29
Alignment explanation
Indices: 217538--217592 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 29
217528 TTTTAAAAGG
* * *
217538 TTTTAGAATTTTTTTTTTTTTTATAAATA
1 TTTTAGAATTTTGTTGTATTTTATAAATA
*
217567 TTTT-GAATTTTGTTGTATTTTTTAAA
1 TTTTAGAATTTTGTTGTATTTTATAAA
217593 GAGATCAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 18 0.82
29 4 0.18
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.67
Consensus pattern (29 bp):
TTTTAGAATTTTGTTGTATTTTATAAATA
Found at i:219335 original size:324 final size:319
Alignment explanation
Indices: 218112--220611 Score: 2426
Period size: 324 Copynumber: 7.9 Consensus size: 319
218102 AAATATATAT
** * *
218112 ATATTTCCTTAAACATTTATATAATTCACATTTGGTAAATTCAATTTCAAGTCATGTTTGTTTTA
1 ATATTTCC-TAAACATTTATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAGTTT-TTTTA
* * * * * *
218177 TTCGCTAAAATAA-TAATTTTGTAGAATTGACAGTTATAGTGTCACCGATCACGTGACGACTAAG
64 TTTGCTAAAA-AATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATCACGTAACAACTGAG
* * * * **
218241 AGAAAGATTGA-ACCACAAACAATCGAGAGTAAAAAGATCATAATCGCCCTAGTGAAAAGGGATA
128 AGAGAGATTGAGACCACAGACAA-CGAGAGTAAAAAAACCATAATCGCCC-AGTGAAAAGGGCCA
* * * **
218305 CATTACAGCCCTTTCTTAGACTGTCAACAATTGCAAATAAGCGATGTTACATGTCAATAGAAAAA
191 CATTACATCCCTTTCTTAGACTGTCAACAATTGCAAATAAGCGATGCTACATGTCATTAGAAAGT
*
218370 TGTTGGCTTAACTACCCATTGTGTAGCAA-TATATATATATA-AT-GTGTGTGGTATGTGGCCAA
256 TGTTGGCTTAACTACCCATTGTGTAGCAATTATATATATATATATATTGTGT-GTATGTGGCCAA
* * *
218432 ATATTTCCCTAAACATTTATATGTTTCGCATTTGGTAAATTTAATTTCAAGAAAAGTTTCTTTTT
1 ATATTT-CCTAAACATTTATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAG-TT-TTTTT
* * * * * * * * ** *
218497 GTTTGTTAAAAAATTAATTTTAGAAAATTGACGGTTTTAATGTCACTGATCATGTAATGATTGAG
63 ATTTGCTAAAAAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATCACGTAACAACTGAG
* * * * * * *
218562 AGAGA-A-CGAG-TCACAGATAGACGATAGTAAAAAGACCATAATAGCCCAAGTGAAAAGGGCCG
128 AGAGAGATTGAGACCACAGACA-ACGAGAGTAAAAAAACCATAATCGCCC-AGTGAAAAGGGCCA
* * * * * *
218624 CATTACATCCTTTTCTTAGACTGTCAACAATTGCAGATAAACAATGCTACATTTCATTAGAAAAT
191 CATTACATCCCTTTCTTAGACTGTCAACAATTGCAAATAAGCGATGCTACATGTCATTAGAAAGT
* * * *
218689 TGTTAGATTAGCTACCCATTGTGTAGTAA-T-TATATATATATATA-------T-TGT---CAA
256 TGTTGGCTTAACTACCCATTGTGTAGCAATTATATATATATATATATTGTGTGTATGTGGCCAA
* * *
218740 ATATTTCTTAAAATATTTATATGTTTCACATTTGGTAAATTCAATTTCAAGTAATGTTTGTTTTA
1 ATATTTCCT-AAACATTTATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAGTTT-TTTTA
* * * * **
218805 TTTGCTAAATAATTAATTTTGGAGAATTAACAATTATAGTGTCACGGATCACGTAATGACTGAGA
64 TTTGCTAAAAAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATCACGTAACAACTGAGA
* * *
218870 GAGAGATTGA-ACCACAGACAGTCGAGAG-AAAAAAGACCATAATCACCCTAGTGAAAAGGACCA
129 GAGAGATTGAGACCACAGACA-ACGAGAGTAAAAAA-ACCATAATCGCCC-AGTGAAAAGGGCCA
* * * *
218933 CATTACATCTCTTTCTTAGACCGTCAACAATTGCAAATAAACGATGCTACATGTCATTAGAAAGC
191 CATTACATCCCTTTCTTAGACTGTCAACAATTGCAAATAAGCGATGCTACATGTCATTAGAAAGT
* * * * *
218998 TATTGGCTTAACTACACATCGTGTAGCAATATTATATATATATATAATATGTGTTTGTTTGTGGC
256 TGTTGGCTTAACTACCCATTGTGTAGC-A-ATTATATATATATAT-ATAT-TGTGTGTATGTGGC
219063 CAA
317 CAA
**
219066 ATATTTTCCTAAACATTTATATGTTTCACATTTAATAAATTCAATTTCAAGTAAAG-TTTTTTAT
1 ATA-TTTCCTAAACATTTATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAGTTTTTTTAT
* * * * * *
219130 TTGCTAAAAAATTATTTTTAGAGAATTGACAGTTATAGTGTCACTAATTACGTAACGACTGAGAC
65 TTGCTAAAAAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATCACGTAACAACTGAGAG
*
219195 AGAGATTGAGA-CACAGACAATCGAGAGTAAAAAAACCATTATCGCTCCAGTGAAAAGGGCCACA
130 AGAGATTGAGACCACAGACAA-CGAGAGTAAAAAAACCATAATCGC-CCAGTGAAAAGGGCCACA
* * ****
219259 TTACATCCCTTTCTTAGACTGTCAACAATTACAAATAAGCGATGATGTGCGTCATTAGAAAGTTG
193 TTACATCCCTTTCTTAGACTGTCAACAATTGCAAATAAGCGATGCTACATGTCATTAGAAAGTTG
* * * * * * *
219324 TTGGATTAACTACCCATTGCGTAGTAATTATATATATATATATATATATATGTGTGTTGCCAA
258 TTGGCTTAACTACCCATTGTGTAGCAATTATATATATATATATAT-TGTGTGTATGTGGCCAA
* * * * *
219387 GTATTTCTTTAAACATTTATATGTTTCACAATTGGTAAATTTAATTTCAAGTAAAATTTATTTTT
1 ATATTTC-CTAAACATTTATATGTTTCACATTTGGTAAATTCAATTTCAAGT-AAAGTT-TTTTT
* * * ** * * * * *
219452 ATTTGCAAAAAAATTAATTTTGAAAAATTGATGGTTACAATATCATTGATCACGTAATAA-TGGA
63 ATTTGCTAAAAAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATCACGTAACAACT-GA
* * * * * * * *
219516 AAGATAGATT-AGACCTCAGACAGACGAGAGTAAAAAGATCATAATCGGCCTAGTAAAAAGGGCT
127 GAGAGAGATTGAGACCACAGACA-ACGAGAGTAAAAAAACCATAATC-GCCCAGTGAAAAGGGCC
* * * * * * * * * *
219580 ACATAACGTCCCTTACTTAGACTATCAACCATTACAAATAAGCGATGCTACATATCAATAAAAAA
190 ACATTACATCCCTTTCTTAGACTGTCAACAATTGCAAATAAGCGATGCTACATGTCATTAGAAAG
*
219645 TTGTTGGCTTAGCTACCCATTGTGTAGC--------A-AT-TATATA-------TAT-T-GCCAA
255 TTGTTGGCTTAACTACCCATTGTGTAGCAATTATATATATATATATATTGTGTGTATGTGGCCAA
* *
219691 ATATTTCCTTAAACATTTATATGTTTCACATTTGGTAAATTCAATTTCAATTAATGTTTGTTTTA
1 ATATTTCC-TAAACATTTATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAGTTT-TTTTA
* * *
219756 TTTGCTAAAAAATTAATTTTGAAGAATTGACAGTTATAATGTCACTGATCATGTAACAACTGAGA
64 TTTGCTAAAAAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATCACGTAACAACTGAGA
* * * * * * * *
219821 GATAGATTG-GATCATAGACAGCAGAGAGTAAAAAGACCATAATTGCCCTAATGAAAAGGACCAC
129 GAGAGATTGAGACCACAGACAAC-GAGAGTAAAAAAACCATAATCGCCC-AGTGAAAAGGGCCAC
* *
219885 ATTACATCCCTTTCTTAGAGTGTCAACAATTGCAAATAACCGATGCTACATGTCATTAGAAAGTT
192 ATTACATCCCTTTCTTAGACTGTCAACAATTGCAAATAAGCGATGCTACATGTCATTAGAAAGTT
219950 GTTGGCTTAACTACCCATTGTGTAGCAATTATATATATATA-AT-TTGTGTGTATGTGGCCAA
257 GTTGGCTTAACTACCCATTGTGTAGCAATTATATATATATATATATTGTGTGTATGTGGCCAA
*
220011 ATATTTCCTTAAACATTTATATGTTTCACATTTGCTAAATTCAATTTCAAGTAAAGTTTTTTTTA
1 ATATTTCC-TAAACATTTATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAG-TTTTTTTA
* * *
220076 TTTGCTAAAAAATTAATTTTGGAGAATTGACAATTATAGTGTTACTGATCACGTAACAATTGAGA
64 TTTGCTAAAAAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATCACGTAACAACTGAGA
* * * ** *
220141 GAGAAATTG-GACCACA-AGCAACTGAGAGT-AAAAAACCATAATCACCTAGCAAAAATGGCCAC
129 GAGAGATTGAGACCACAGA-CAAC-GAGAGTAAAAAAACCATAATCGCCCAGTGAAAAGGGCCAC
* * *
220203 ATTACATCACTGTCTTAGATTGTCAACAATTGCAAATAAGCGATGCT-CTATGTCATTAGAAAGT
192 ATTACATCCCTTTCTTAGACTGTCAACAATTGCAAATAAGCGATGCTAC-ATGTCATTAGAAAGT
* *
220267 TGTTGGCTTAACTACCCATTGTGTAACAATTATAT-T-T-T-TATATCTGTGTATATGTGGCCAA
256 TGTTGGCTTAACTACCCATTGTGTAGCAATTATATATATATATATAT-TGTGTGTATGTGGCCAA
* *
220328 ATATTTTCTTAAACATTTATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAATGTTTTTTA
1 ATA-TTTCCTAAACATTTATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAGT-TTTTTTA
* * * * * * *
220393 TTTGCAAAAAAAATAATTTTGGAGAATTGACA---AT-TTGTCATTGATTACGTAACGATTGCGA
64 TTTGCTAAAAAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATCACGTAACAACT--GA
* * ** * * * * * * **
220454 AAGAAAGGCTGA-ACTACAGATAATAGAGAGTAAAAAGATCATAATCACCCTAACGAAAAGGGCC
127 GAGAGAGATTGAGACCACAGACAA-CGAGAGTAAAAAAACCATAATCGCCC-AGTGAAAAGGGCC
* * * * * *
220518 ACATTACATCCCTTTTTTTATTAGAGTGTCAACAATTGCAAATAAACGATGTTCCATGTCGTTAG
190 ACATTACATCCC----TTTCTTAGACTGTCAACAATTGCAAATAAGCGATGCTACATGTCATTAG
220583 AAAGTTGTTGGCTTAAC-ACCCATTGTGTA
251 AAAGTTGTTGGCTTAACTACCCATTGTGTA
220612 ACAAGTGCTT
Statistics
Matches: 1806, Mismatches: 285, Indels: 178
0.80 0.13 0.08
Matches are distributed among these distances:
302 5 0.00
303 186 0.10
304 52 0.03
305 1 0.00
306 3 0.00
307 65 0.04
308 56 0.03
309 115 0.06
310 1 0.00
311 5 0.00
312 6 0.00
313 31 0.02
314 11 0.01
315 26 0.01
316 20 0.01
317 124 0.07
318 119 0.07
319 142 0.08
320 209 0.12
321 178 0.10
322 21 0.01
323 9 0.00
324 354 0.20
325 14 0.01
326 48 0.03
327 5 0.00
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.34
Consensus pattern (319 bp):
ATATTTCCTAAACATTTATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAGTTTTTTTATT
TGCTAAAAAATTAATTTTGGAGAATTGACAGTTATAGTGTCACTGATCACGTAACAACTGAGAGA
GAGATTGAGACCACAGACAACGAGAGTAAAAAAACCATAATCGCCCAGTGAAAAGGGCCACATTA
CATCCCTTTCTTAGACTGTCAACAATTGCAAATAAGCGATGCTACATGTCATTAGAAAGTTGTTG
GCTTAACTACCCATTGTGTAGCAATTATATATATATATATATTGTGTGTATGTGGCCAA
Found at i:219888 original size:627 final size:624
Alignment explanation
Indices: 218112--220607 Score: 2380
Period size: 628 Copynumber: 3.9 Consensus size: 624
218102 AAATATATAT
* ** * * *
218112 ATATTTCCTTAAACATTTATATAATTCACATTTGGTAAATTCAATTTCAAGTCATGTTTGTTTTA
1 ATATTTCTTTAAACATTTATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAGTTTTTTTTA
* * * * ** * *
218177 TTCGCTAAAATAA-TAATTTTGTAGAATTGACAGTTATAGTGTCACCGATCACGTGACGACTAAG
66 TTTGCTAAAA-AATTAATTTTGGAGAATTGACAATTATAGTGTCACTGATCACGT-AATAATGAG
* * * * **
218241 AGAAAGATTGAACCACAAACA-ATCGAGAGTAAAAAGATCATAATCGCCCTAGTGAAAAGGGATA
129 AGAGAGATTG-ACCACAGACAGA-CGAGAGTAAAAAGACCATAATCGCCCTAGTAAAAAGGGCCA
* *
218305 CATTACAGCCCTTTCTTAGACTGTCAACAATTGCAAATAAGCGATGTTACATGTCAATAGAAAAA
192 CATTACATCCCTTTCTTAGACTGTCAACAATTGCAAATAAGCGATGCTACATGTCAATA-AAAAA
218370 -TGTTGGCTTAACTACCCATTGTGTAGCAATATATATATATAATGTGTGTGGTATGTGGCCAAAT
256 TTGTTGGCTTAACTACCCATTGTGTAGC-A-ATATATATATAA---------TATGTGGCCAAAT
* * * *
218434 ATTTCCCTAAACATTTATATGTTTCGCATTTGGTAAATTTAATTTCAAGAAAAGTTTCTTTTTGT
310 ATTTCCTTAAACATTTATATGTTTCACATTTGGTAAATTCAATTTCAAGAAAAG--T-TTTTTAT
* * * * *
218499 TTGTTAAAAAATTAATTTTAGAA-AATTGACGGTTTTAATGTCACTGATCATGTAATGATTGAGA
372 TTGCTAAAAAATTAATTTT-GAAGAATTGACAGTTATAATGTCACTGATCATGTAACGACTGAGA
** * * *
218563 G-AGA-ACGAGTCACAGATAG-ACGATAGTAAAAAGACCATAATAGCCCAAGTGAAAAGGGCCGC
436 GAAGATTGGA-TCACAGACAGCA-GAGAGTAAAAAGACCATAATAGCCCAA-TGAAAAGGGCCAC
* * * * *
218625 ATTACATCCTTTTCTTAGACTGTCAACAATTGCAGATAAACAATGCTACATTTCATTAGAAAATT
498 ATTACATCCCTTTCTTAGACTGTCAACAATTGCAAATAAACGATGCTACATGTCATTAGAAAGTT
* * *
218690 GTTAGATTAGCTACCCATT-GT-GT-A--GTA-AT-TATATATATATATA--TTG-T--CAA
563 GTTGGATTAACTACCCATTGGTAGTAATTATATATATATATATATATATATGTTGTTGCCAA
* * * *
218740 ATATTTCTTAAAATATTTATATGTTTCACATTTGGTAAATTCAATTTCAAGTAATGTTTGTTTTA
1 ATATTTCTTTAAACATTTATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAGTTTTTTTTA
* * * *
218805 TTTGCTAAATAATTAATTTTGGAGAATTAACAATTATAGTGTCACGGATCACGTAATGACTGAGA
66 TTTGCTAAAAAATTAATTTTGGAGAATTGACAATTATAGTGTCACTGATCACGTAAT-AATGAGA
* * * * *
218870 GAGAGATTGAACCACAGACAGTCGAGAGAAAAAAGACCATAATCACCCTAGTGAAAAGGACCACA
130 GAGAGATTG-ACCACAGACAGACGAGAGTAAAAAGACCATAATCGCCCTAGTAAAAAGGGCCACA
* * * * * ** *
218935 TTACATCTCTTTCTTAGACCGTCAACAATTGCAAATAAACGATGCTACATGTCATTAGAAAGCTA
194 TTACATCCCTTTCTTAGACTGTCAACAATTGCAAATAAGCGATGCTACATGTCAATAAAAAATTG
* *
219000 TTGGCTTAACTACACATCGTGTAGCAATATTATATATATATATAATATGTGTTTGTTTGTGGCCA
259 TTGGCTTAACTACCCATTGTGTAGC------A-ATATATATATAATA----------TGTGGCCA
** *
219065 AATATTTTCC-TAAACATTTATATGTTTCACATTTAATAAATTCAATTTCAAGTAAAGTTTTTTA
307 AATA-TTTCCTTAAACATTTATATGTTTCACATTTGGTAAATTCAATTTCAAGAAAAGTTTTTTA
* * * * *
219129 TTTGCTAAAAAATT-ATTTTTAGAGAATTGACAGTTATAGTGTCACTAATTACGTAACGACTGAG
371 TTTGCTAAAAAATTAATTTTGA-AGAATTGACAGTTATAATGTCACTGATCATGTAACGACTGAG
* * * * * *
219193 ACAGAGATTGAGA-CACAGACAATC-GAGAGTAAAAAAACCATTATCGCTCCAGTGAAAAGGGCC
435 AGA-AGATTG-GATCACAGAC-AGCAGAGAGTAAAAAGACCATAATAGC-CCAATGAAAAGGGCC
* * * ****
219256 ACATTACATCCCTTTCTTAGACTGTCAACAATTACAAATAAGCGATGATGTGCGTCATTAGAAAG
496 ACATTACATCCCTTTCTTAGACTGTCAACAATTGCAAATAAACGATGCTACATGTCATTAGAAAG
219321 TTGTTGGATTAACTACCCATTGCGTAGTAATTATATATATATATATATATATATGTGTGTTGCCA
561 TTGTTGGATTAACTACCCATTG-GTAGTAATTATATATATATATATATATATATGT-TGTTGCCA
219386 A
624 A
* * * *
219387 GTATTTCTTTAAACATTTATATGTTTCACAATTGGTAAATTTAATTTCAAGTAAAATTTATTTTT
1 ATATTTCTTTAAACATTTATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAGTTT-TTTTT
* * * *** * * * * *
219452 ATTTGCAAAAAAATTAATTTTGAAAAATTGATGGTTACAATATCATTGATCACGTAATAATGGAA
65 ATTTGCTAAAAAATTAATTTTGGAGAATTGACAATTATAGTGTCACTGATCACGTAATAAT-GAG
* * * * *
219517 AGATAGATTAGACCTCAGACAGACGAGAGTAAAAAGATCATAATCGGCCTAGTAAAAAGGGCTAC
129 AGAGAGATT-GACCACAGACAGACGAGAGTAAAAAGACCATAATCGCCCTAGTAAAAAGGGCCAC
* * * * * * *
219582 ATAACGTCCCTTACTTAGACTATCAACCATTACAAATAAGCGATGCTACATATCAATAAAAAATT
193 ATTACATCCCTTTCTTAGACTGTCAACAATTGCAAATAAGCGATGCTACATGTCAATAAAAAATT
*
219647 GTTGGCTTAGCTACCCATTGTGTAGC-A-AT-TATAT-ATAT-T-GCCAAATATTTCCTTAAACA
258 GTTGGCTTAACTACCCATTGTGTAGCAATATATATATAATATGTGGCCAAATATTTCCTTAAACA
** *
219706 TTTATATGTTTCACATTTGGTAAATTCAATTTCAATTAATGTTTGTTTTATTTGCTAAAAAATTA
323 TTTATATGTTTCACATTTGGTAAATTCAATTTCAAGAAAAG-TT-TTTTATTTGCTAAAAAATTA
* *
219771 ATTTTGAAGAATTGACAGTTATAATGTCACTGATCATGTAACAACTGAGAGATAGATTGGATCAT
386 ATTTTGAAGAATTGACAGTTATAATGTCACTGATCATGTAACGACTGAGAGA-AGATTGGATCAC
* *
219836 AGACAGCAGAGAGTAAAAAGACCATAATTGCCCTAATGAAAAGGACCACATTACATCCCTTTCTT
450 AGACAGCAGAGAGTAAAAAGACCATAATAGCCC-AATGAAAAGGGCCACATTACATCCCTTTCTT
* * *
219901 AGAGTGTCAACAATTGCAAATAACCGATGCTACATGTCATTAGAAAGTTGTTGGCTTAACTACCC
514 AGACTGTCAACAATTGCAAATAAACGATGCTACATGTCATTAGAAAGTTGTTGGATTAACTACCC
* * * *
219966 ATTGTGTAGCAATTATATATATATA-AT-T-TGTGTGTATGTGGCCAA
579 ATTG-GTAGTAATTATATATATATATATATATATATGT-TGTTGCCAA
* *
220011 ATATTTCCTTAAACATTTATATGTTTCACATTTGCTAAATTCAATTTCAAGTAAAGTTTTTTTTA
1 ATATTTCTTTAAACATTTATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAGTTTTTTTTA
* *
220076 TTTGCTAAAAAATTAATTTTGGAGAATTGACAATTATAGTGTTACTGATCACGTAACAATTGAGA
66 TTTGCTAAAAAATTAATTTTGGAGAATTGACAATTATAGTGTCACTGATCACGTAATAA-TGAGA
* * * *
220141 GAGAAATTGGACCACA-AGCA-ACTGAGAGTAAAAA-ACCATAATC-ACCTAGCAAAAATGGCCA
130 GAGAGATT-GACCACAGA-CAGAC-GAGAGTAAAAAGACCATAATCGCCCTAGTAAAAAGGGCCA
* * * * * *
220202 CATTACATCACTGTCTTAGATTGTCAACAATTGCAAATAAGCGATGCT-CTATGTCATTAGAAAG
192 CATTACATCCCTTTCTTAGACTGTCAACAATTGCAAATAAGCGATGCTAC-ATGTCAATAAAAAA
* *
220266 TTGTTGGCTTAACTACCCATTGTGTAACAATTATATTTTTATATCTGTGTATATGTGGCCAAATA
256 TTGTTGGCTTAACTACCCATTGTGTAGCAA-TATA----TATA----T-AATATGTGGCCAAATA
*
220331 TTTTCTTAAACATTTATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAATGTTTTTTATTT
311 TTTCCTTAAACATTTATATGTTTCACATTTGGTAAATTCAATTTCAAG-AAAA-GTTTTTTATTT
* * * * * * * * *
220396 GCAAAAAAAATAATTTTGGAGAATTGACA---AT-TTGTCATTGATTACGTAACGATTGCGA-AA
374 GCTAAAAAATTAATTTTGAAGAATTGACAGTTATAATGTCACTGATCATGTAACGACTGAGAGAA
** * * ** * *
220456 GAAAGGCTGAACTACAGATAATAGAGAGTAAAAAGATCATAATCA-CCCTAACGAAAAGGGCCAC
439 G-ATTG--GATC-ACAGACAGCAGAGAGTAAAAAGACCATAAT-AGCCC-AATGAAAAGGGCCAC
* * * * *
220520 ATTACATCCCTTTTTTTATTAGAGTGTCAACAATTGCAAATAAACGATGTTCCATGTCGTTAGAA
498 ATTACATCCC----TTTCTTAGACTGTCAACAATTGCAAATAAACGATGCTACATGTCATTAGAA
*
220585 AGTTGTTGGCTTAAC-ACCCATTG
559 AGTTGTTGGATTAACTACCCATTG
220608 TGTAACAAGT
Statistics
Matches: 1548, Mismatches: 236, Indels: 158
0.80 0.12 0.08
Matches are distributed among these distances:
620 1 0.00
621 89 0.06
622 12 0.01
623 81 0.05
624 76 0.05
625 52 0.03
626 11 0.01
627 205 0.13
628 246 0.16
629 5 0.00
630 6 0.00
631 53 0.03
632 4 0.00
633 145 0.09
634 63 0.04
635 65 0.04
636 3 0.00
637 92 0.06
638 17 0.01
639 66 0.04
640 3 0.00
641 14 0.01
643 1 0.00
644 2 0.00
645 1 0.00
647 57 0.04
648 177 0.11
649 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (624 bp):
ATATTTCTTTAAACATTTATATGTTTCACATTTGGTAAATTCAATTTCAAGTAAAGTTTTTTTTA
TTTGCTAAAAAATTAATTTTGGAGAATTGACAATTATAGTGTCACTGATCACGTAATAATGAGAG
AGAGATTGACCACAGACAGACGAGAGTAAAAAGACCATAATCGCCCTAGTAAAAAGGGCCACATT
ACATCCCTTTCTTAGACTGTCAACAATTGCAAATAAGCGATGCTACATGTCAATAAAAAATTGTT
GGCTTAACTACCCATTGTGTAGCAATATATATATAATATGTGGCCAAATATTTCCTTAAACATTT
ATATGTTTCACATTTGGTAAATTCAATTTCAAGAAAAGTTTTTTATTTGCTAAAAAATTAATTTT
GAAGAATTGACAGTTATAATGTCACTGATCATGTAACGACTGAGAGAAGATTGGATCACAGACAG
CAGAGAGTAAAAAGACCATAATAGCCCAATGAAAAGGGCCACATTACATCCCTTTCTTAGACTGT
CAACAATTGCAAATAAACGATGCTACATGTCATTAGAAAGTTGTTGGATTAACTACCCATTGGTA
GTAATTATATATATATATATATATATATGTTGTTGCCAA
Found at i:219931 original size:303 final size:304
Alignment explanation
Indices: 219363--220611 Score: 1162
Period size: 303 Copynumber: 4.0 Consensus size: 304
219353 ATATATATAT
* * * *
219363 ATATATATATATGTGTGTTGCCAAGTATTTCTTTAAACATTTATATGTTTCACAATTGGTAAATT
1 ATAT-TATATATATGTG--GCCAAATATTTCCTTAAACATTTATATGTTTCACATTTGGTAAATT
* * * ** *
219428 TAATTTCAAGTAAAATTTATTTTTATTTGCAAAAAAATTAATTTTGAAAAATTGATGGTTACAAT
63 CAATTTCAAGTAAAGTTT-TTTTTATTTGCAAAAAAATTAATTTTGAAGAATTGACAGTTATAAT
* * * * * * *
219493 ATCATTGATCACGTAATAATGGAAAGATAGATTAGACCTCAGACAG-ACGAGAGTAAAAAGATCA
127 GTCACTGATCACGTAACAAT-GAGAGATAGATTGGACAT-AGACAGCA-GAGAGTAAAAAGACCA
* * * * * * * * *
219557 TAATCGGCCTAGTAAAAAGGGCTACATAACGTCCCTTACTTAGACTATCAACCATTACAAATAAG
189 TAATTGCCCTAGTAAAAA-GGCCACATTACATCCCTTTCTTAGACTGTCAACAATTGCAAATAAG
* * * * *
219622 CGATGCTACATATCAATAAAAAATTGTTGGCTTAGCTACCCATTGTGTAGC-
253 CGATGCTACATGTCATTAGAAAGTTGTTGGCTTAACTACCCATTGTGTAGCA
219673 A-ATTATATATAT-T-GCCAAATATTTCCTTAAACATTTATATGTTTCACATTTGGTAAATTCAA
1 ATATTATATATATGTGGCCAAATATTTCCTTAAACATTTATATGTTTCACATTTGGTAAATTCAA
* * * *
219735 TTTCAATTAATGTTTGTTTTATTTGCTAAAAAATTAATTTTGAAGAATTGACAGTTATAATGTCA
66 TTTCAAGTAAAGTTTTTTTTATTTGCAAAAAAATTAATTTTGAAGAATTGACAGTTATAATGTCA
*
219800 CTGATCATGTAACAACTGAGAGATAGATTGGATCATAGACAGCAGAGAGTAAAAAGACCATAATT
131 CTGATCACGTAACAA-TGAGAGATAGATTGGA-CATAGACAGCAGAGAGTAAAAAGACCATAATT
* * * *
219865 GCCCTAATGAAAAGGACCACATTACATCCCTTTCTTAGAGTGTCAACAATTGCAAATAACCGATG
194 GCCCTAGTAAAAAGG-CCACATTACATCCCTTTCTTAGACTGTCAACAATTGCAAATAAGCGATG
219930 CTACATGTCATTAGAAAGTTGTTGGCTTAACTACCCATTGTGTAGCAA
258 CTACATGTCATTAGAAAGTTGTTGGCTTAACTACCCATTGTGTAGC-A
219978 TTATATATATATAATTTGTGTGTATGTGGCCAAATATTTCCTTAAACATTTATATGTTTCACATT
1 --ATAT-TATAT-A--------TATGTGGCCAAATATTTCCTTAAACATTTATATGTTTCACATT
* * *
220043 TGCTAAATTCAATTTCAAGTAAAGTTTTTTTTATTTGCTAAAAAATTAATTTTGGAGAATTGACA
54 TGGTAAATTCAATTTCAAGTAAAGTTTTTTTTATTTGCAAAAAAATTAATTTTGAAGAATTGACA
* * * * * * * *
220108 ATTATAGTGTTACTGATCACGTAACAATTGAGAGAGAAATTGGACCACA-AGCAACTGAGAGTAA
119 GTTATAATGTCACTGATCACGTAACAA-TGAGAGATAGATTGGA-CATAGA-CAGCAGAGAGTAA
* * * *
220172 AAA-ACCATAA-T-CACCTAGCAAAAATGGCCACATTACATCACTGTCTTAGATTGTCAACAATT
181 AAAGACCATAATTGC-CCTAGTAAAAA-GGCCACATTACATCCCTTTCTTAGACTGTCAACAATT
*
220234 GCAAATAAGCGATGCT-CTATGTCATTAGAAAGTTGTTGGCTTAACTACCCATTGTGTAACAA
244 GCAAATAAGCGATGCTAC-ATGTCATTAGAAAGTTGTTGGCTTAACTACCCATTGTGTAGC-A
*
220296 TTATATTTTTATATCTGTGTATATGTGGCCAAATATTTTCTTAAACATTTATATGTTTCACATTT
1 --ATA---TTATA------TATATGTGGCCAAATATTTCCTTAAACATTTATATGTTTCACATTT
* * * *
220361 GGTAAATTCAATTTCAAGTAAAATGTTTTTTATTTGCAAAAAAAATAATTTTGGAGAATTGACA-
55 GGTAAATTCAATTTCAAGTAAAGTTTTTTTTATTTGCAAAAAAATTAATTTTGAAGAATTGACAG
* * * * * * ** * * * **
220425 --AT-TTGTCATTGATTACGTAACGATTGCGAAAGAAAGGCTGAACTACAGATAATAGAGAGTAA
120 TTATAATGTCACTGATCACGTAAC-AAT--GAGAGATAGATTGGAC-ATAGACAGCAGAGAGTAA
* ** * * *
220487 AAAGATCATAATCACCCTAACG-AAAAGGGCCACATTACATCCCTTTTTTTATTAGAGTGTCAAC
181 AAAGACCATAATTGCCCT-A-GTAAAAAGGCCACATTACATCCC----TTTCTTAGACTGTCAAC
* * * *
220551 AATTGCAAATAAACGATGTTCCATGTCGTTAGAAAGTTGTTGGCTTAAC-ACCCATTGTGTA
240 AATTGCAAATAAGCGATGCTACATGTCATTAGAAAGTTGTTGGCTTAACTACCCATTGTGTA
220612 ACAAGTGCTT
Statistics
Matches: 796, Mismatches: 94, Indels: 88
0.81 0.10 0.09
Matches are distributed among these distances:
302 2 0.00
303 184 0.23
304 61 0.08
307 2 0.00
308 10 0.01
309 7 0.01
310 2 0.00
313 16 0.02
314 4 0.01
315 25 0.03
316 7 0.01
317 122 0.15
318 113 0.14
319 12 0.02
320 167 0.21
321 59 0.07
322 1 0.00
325 1 0.00
326 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (304 bp):
ATATTATATATATGTGGCCAAATATTTCCTTAAACATTTATATGTTTCACATTTGGTAAATTCAA
TTTCAAGTAAAGTTTTTTTTATTTGCAAAAAAATTAATTTTGAAGAATTGACAGTTATAATGTCA
CTGATCACGTAACAATGAGAGATAGATTGGACATAGACAGCAGAGAGTAAAAAGACCATAATTGC
CCTAGTAAAAAGGCCACATTACATCCCTTTCTTAGACTGTCAACAATTGCAAATAAGCGATGCTA
CATGTCATTAGAAAGTTGTTGGCTTAACTACCCATTGTGTAGCA
Found at i:224199 original size:22 final size:23
Alignment explanation
Indices: 224169--224211 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
224159 AAATTAAGTA
224169 TTTGAACTGTCAAAATAAAATCT
1 TTTGAACTGTCAAAATAAAATCT
* *
224192 TTTG-ACTGTTAAAATTAAAT
1 TTTGAACTGTCAAAATAAAAT
224212 GTCTTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (23 bp):
TTTGAACTGTCAAAATAAAATCT
Found at i:224334 original size:17 final size:17
Alignment explanation
Indices: 224312--224356 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
224302 TTATAAAAGT
**
224312 AATTAAAATTTAATAAA
1 AATTAAAAAATAATAAA
*
224329 AATTAAAAAATATTAAA
1 AATTAAAAAATAATAAA
224346 AATTAGAAAAA
1 AATTA-AAAAA
224357 AAATGTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (17 bp):
AATTAAAAAATAATAAA
Found at i:224547 original size:17 final size:18
Alignment explanation
Indices: 224525--224575 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 18
224515 GTGCCATGTG
224525 ATAAAAAATAATAAAAA-
1 ATAAAAAATAATAAAAAT
224542 AT-AAAAATCAATAAAAATT
1 ATAAAAAAT-AATAAAAA-T
*
224561 ATAAAAAATTATAAA
1 ATAAAAAATAATAAA
224576 TGTTTCTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
16 6 0.21
17 10 0.34
19 7 0.24
20 6 0.21
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (18 bp):
ATAAAAAATAATAAAAAT
Found at i:224606 original size:9 final size:9
Alignment explanation
Indices: 224592--224717 Score: 69
Period size: 9 Copynumber: 13.4 Consensus size: 9
224582 TTTTAGTACG
224592 ATAATTTTT
1 ATAATTTTT
224601 ATAATTTTTTT
1 ATAA--TTTTT
224612 ATGAA-TTTT
1 AT-AATTTTT
*
224621 ATATTTTTT
1 ATAATTTTT
* *
224630 ACATTTTTT
1 ATAATTTTT
224639 ATAATATTCTT
1 ATAAT-TT-TT
** *
224650 ACGA-CTTT
1 ATAATTTTT
224658 ATAATATTTT
1 ATAAT-TTTT
224668 ATAATTTTT
1 ATAATTTTT
* *
224677 TTATATTTCT
1 ATA-ATTTTT
224687 AT-ATGTTTT
1 ATAAT-TTTT
224696 ATAATTTTT
1 ATAATTTTT
**
224705 ACGATTTTT
1 ATAATTTTT
224714 ATAA
1 ATAA
224718 AATTCTAAAT
Statistics
Matches: 88, Mismatches: 18, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
8 7 0.08
9 50 0.57
10 18 0.20
11 11 0.12
12 2 0.02
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (9 bp):
ATAATTTTT
Found at i:224639 original size:38 final size:37
Alignment explanation
Indices: 224596--224717 Score: 99
Period size: 38 Copynumber: 3.2 Consensus size: 37
224586 AGTACGATAA
224596 TTTTTATAATTTTTTTATGAATTTTATATTTTTTACAT
1 TTTTTATAATTTTTTTATG-ATTTTATATTTTTTACAT
* * * *
224634 TTTTTATAATATTCTTACGACTTTATAATATTTTATA-AT
1 TTTTTATAATTTTTTTATGA-TTT-T-ATATTTTTTACAT
* * *
224673 TTTTT-TATATTTCTATATG-TTTTATAATTTTTACGA-
1 TTTTTATA-ATTTTTTTATGATTTTATATTTTTTAC-AT
224709 TTTTTATAA
1 TTTTTATAA
224718 AATTCTAAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
35 8 0.12
36 7 0.11
37 7 0.11
38 21 0.32
39 14 0.21
40 9 0.14
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (37 bp):
TTTTTATAATTTTTTTATGATTTTATATTTTTTACAT
Found at i:224680 original size:11 final size:10
Alignment explanation
Indices: 224592--224763 Score: 59
Period size: 9 Copynumber: 18.2 Consensus size: 10
224582 TTTTAGTACG
224592 ATAAT-TTTT
1 ATAATATTTT
*
224601 ATAATTTTTTT
1 ATAA-TATTTT
*
224612 ATGA-ATTTT
1 ATAATATTTT
224621 AT-AT-TTTT
1 ATAATATTTT
*
224629 -TACATTTTTT
1 ATA-ATATTTT
*
224639 ATAATATTCT
1 ATAATATTTT
** *
224649 -TACGACTTT
1 ATAATATTTT
224658 ATAATATTTT
1 ATAATATTTT
224668 ATAAT-TTTT
1 ATAATATTTT
*
224677 -TTATATTTCT
1 ATAATATTT-T
*
224687 AT-ATGTTTT
1 ATAATATTTT
224696 ATAAT-TTTT
1 ATAATATTTT
**
224705 ACGAT-TTTT
1 ATAATATTTT
* *
224714 ATAAAATTCT
1 ATAATATTTT
224724 A-AATATTTTT
1 ATAATA-TTTT
*
224734 ATTAA-ATTTA
1 A-TAATATTTT
*
224744 ATAA-ATTTA
1 ATAATATTTT
224753 AT-ATATTTT
1 ATAATATTTT
224762 AT
1 AT
224764 TGATTTTTAT
Statistics
Matches: 123, Mismatches: 23, Indels: 34
0.68 0.13 0.19
Matches are distributed among these distances:
7 1 0.01
8 9 0.07
9 59 0.48
10 41 0.33
11 11 0.09
12 2 0.02
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (10 bp):
ATAATATTTT
Found at i:224724 original size:37 final size:37
Alignment explanation
Indices: 224616--224724 Score: 96
Period size: 37 Copynumber: 2.9 Consensus size: 37
224606 TTTTTTATGA
* *
224616 ATTTTATATTTTTTACATTTTTTATAATATTCT-TACG
1 ATTTTATAATTTTTACA-TTTTTATAAAATTCTATACG
* * * * * *
224653 ACTTTATAATATTTTATAATTTTTTTATATTTCTATATG
1 ATTTTATAAT-TTTTA-CATTTTTATAAAATTCTATACG
224692 -TTTTATAATTTTTACGATTTTTATAAAATTCTA
1 ATTTTATAATTTTTAC-ATTTTTATAAAATTCTA
224725 AATATTTTTA
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
37 27 0.49
38 24 0.44
39 4 0.07
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.61
Consensus pattern (37 bp):
ATTTTATAATTTTTACATTTTTATAAAATTCTATACG
Found at i:224751 original size:20 final size:20
Alignment explanation
Indices: 224708--224751 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
224698 AATTTTTACG
*
224708 ATTTTTATAAAATTCTAAAT
1 ATTTTTATAAAATTCTAAAA
*
224728 ATTTTTATTAAATT-TAATAA
1 ATTTTTATAAAATTCTAA-AA
224748 ATTT
1 ATTT
224752 AATATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTTTATAAAATTCTAAAA
Found at i:224772 original size:29 final size:31
Alignment explanation
Indices: 224699--224772 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 31
224689 ATGTTTTATA
*
224699 ATTTTTA-CGATTTTT-ATAAAATTCTAAAT
1 ATTTTTATTGATTTTTAATAAAATTCTAAAT
**
224728 ATTTTTATT-AAATTTAAT-AAATT-T-AAT
1 ATTTTTATTGATTTTTAATAAAATTCTAAAT
224755 ATATTTTATTGATTTTTA
1 AT-TTTTATTGATTTTTA
224773 TTTTTTTATC
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
27 5 0.14
28 8 0.22
29 21 0.58
30 2 0.06
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (31 bp):
ATTTTTATTGATTTTTAATAAAATTCTAAAT
Found at i:233608 original size:53 final size:53
Alignment explanation
Indices: 233528--233684 Score: 260
Period size: 53 Copynumber: 3.0 Consensus size: 53
233518 AGTCAATTTC
* *
233528 TCACACAATTTTATCTCAAGTAATTGAGTGAATCTACGTGTTTTCTTATCATA
1 TCACACAATTTTATCTTAAGTAATTGAGTGAATTTACGTGTTTTCTTATCATA
*
233581 TCACACAATTTTATCTTAAGTAATTGAGTGAATTTATGTGTTTTCTTATCATA
1 TCACACAATTTTATCTTAAGTAATTGAGTGAATTTACGTGTTTTCTTATCATA
* * *
233634 TCACACAATTTTATCTTAAATAATAGAGTGAATTTACATGTTTTCTTATCA
1 TCACACAATTTTATCTTAAGTAATTGAGTGAATTTACGTGTTTTCTTATCA
233685 GAATCAAGTC
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 97 1.00
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (53 bp):
TCACACAATTTTATCTTAAGTAATTGAGTGAATTTACGTGTTTTCTTATCATA
Found at i:236736 original size:22 final size:22
Alignment explanation
Indices: 236711--236758 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
236701 TCAATGTCAT
236711 GACACTCATTTTTCAGTGTCGC
1 GACACTCATTTTTCAGTGTCGC
236733 GACACTCATTTTTCAGTGTCGC
1 GACACTCATTTTTCAGTGTCGC
236755 GACA
1 GACA
236759 TTGACGCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (22 bp):
GACACTCATTTTTCAGTGTCGC
Found at i:238524 original size:19 final size:19
Alignment explanation
Indices: 238502--238541 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
238492 AAAATATTAG
*
238502 AAAATTAAAATATTATCTT
1 AAAATTAAAATATTACCTT
238521 AAAATTAAAATATTACCTT
1 AAAATTAAAATATTACCTT
238540 AA
1 AA
238542 TAAAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATTAAAATATTACCTT
Found at i:238549 original size:17 final size:18
Alignment explanation
Indices: 238503--238549 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
238493 AAATATTAGA
* *
238503 AAATTAAAATATTATCTT
1 AAATAAAAATATTACCTT
*
238521 AAAATTAAAATATTACCTT
1 -AAATAAAAATATTACCTT
238540 -AATAAAAATA
1 AAATAAAAATA
238550 AAACTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 9 0.35
19 17 0.65
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATAAAAATATTACCTT
Found at i:249725 original size:21 final size:21
Alignment explanation
Indices: 249694--249757 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 21
249684 GCAAAAAATA
249694 TATAAA-A-TTTGAATTTTTT
1 TATAAATATTTTGAATTTTTT
249713 TATAAATATTTTGAA-TTTTT
1 TATAAATATTTTGAATTTTTT
* *
249733 GA-AAATTATTTTG-ATTATTT
1 TATAAA-TATTTTGAATTTTTT
249753 TATAA
1 TATAA
249758 TTTTTGTGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
19 10 0.27
20 19 0.51
21 8 0.22
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (21 bp):
TATAAATATTTTGAATTTTTT
Found at i:251617 original size:9 final size:9
Alignment explanation
Indices: 251603--251628 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
251593 TTTCTAAATA
251603 ATAATAATG
1 ATAATAATG
251612 ATAATAATG
1 ATAATAATG
251621 ATAATAAT
1 ATAATAAT
251629 AATCTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (9 bp):
ATAATAATG
Found at i:254395 original size:13 final size:13
Alignment explanation
Indices: 254377--254405 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
254367 CCATGAAAGT
254377 TGACAAAAAACAA
1 TGACAAAAAACAA
254390 TGACAAAAAACAA
1 TGACAAAAAACAA
254403 TGA
1 TGA
254406 GGAAGAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.66, C:0.14, G:0.10, T:0.10
Consensus pattern (13 bp):
TGACAAAAAACAA
Found at i:271492 original size:20 final size:20
Alignment explanation
Indices: 271467--271505 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
271457 CCATTGAGAT
271467 TCATCTTCATATGATTATAA
1 TCATCTTCATATGATTATAA
*
271487 TCATCTTCGTATGATTATA
1 TCATCTTCATATGATTATA
271506 GATTATTCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (20 bp):
TCATCTTCATATGATTATAA
Found at i:278652 original size:7 final size:7
Alignment explanation
Indices: 278637--278675 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
278627 TAGCTAGCCA
*
278637 TGGCCAT
1 TGGCAAT
278644 TGGCAAT
1 TGGCAAT
278651 TGGCAAT
1 TGGCAAT
278658 TGGCAAT
1 TGGCAAT
*
278665 TGGCAAA
1 TGGCAAT
278672 TGGC
1 TGGC
278676 CTGTTGACCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.26
Consensus pattern (7 bp):
TGGCAAT
Found at i:285124 original size:2 final size:2
Alignment explanation
Indices: 285117--285145 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
285107 TGTATTGAGT
285117 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
285146 GTGAAACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:286019 original size:22 final size:22
Alignment explanation
Indices: 285981--286029 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 22
285971 AAATTCAAAA
285981 AAAAATTATAAAAATTA-CTTT
1 AAAAATTATAAAAATTATCTTT
*
286002 AAAAATTA-AAAATCATTATTTTT
1 AAAAATTATAAAA--ATTATCTTT
286025 AAAAA
1 AAAAA
286030 AAAAATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 4 0.17
21 8 0.33
22 4 0.17
23 8 0.33
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAAATTATAAAAATTATCTTT
Found at i:299358 original size:14 final size:14
Alignment explanation
Indices: 299339--299371 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
299329 AGTTCCAAAC
299339 TTTGTCTTGTAATA
1 TTTGTCTTGTAATA
299353 TTTGTCTTGTAATA
1 TTTGTCTTGTAATA
299367 TTTGT
1 TTTGT
299372 TTCTTACCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.06, G:0.15, T:0.61
Consensus pattern (14 bp):
TTTGTCTTGTAATA
Found at i:304081 original size:13 final size:13
Alignment explanation
Indices: 304063--304111 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
304053 TTAGCAAACT
304063 ACACTTTTTTACA
1 ACACTTTTTTACA
**
304076 ACACTTTCCTACA
1 ACACTTTTTTACA
** *
304089 ACACTTTTAAAAA
1 ACACTTTTTTACA
304102 ACACTTTTTT
1 ACACTTTTTT
304112 TCTAACTGAA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (13 bp):
ACACTTTTTTACA
Found at i:309827 original size:34 final size:34
Alignment explanation
Indices: 309755--309827 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
309745 TATAAATAAT
* * * * *
309755 CGATTCAAAAGAAGTAGTATTCCACCCTAACAAT
1 CGATTCAAAAAAAGTAGAATTCCAACATAACAAA
*
309789 CGATTCAAAAAAAGTAGAATTCCAACATGACAAA
1 CGATTCAAAAAAAGTAGAATTCCAACATAACAAA
309823 CGATT
1 CGATT
309828 TAAACATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.22
Consensus pattern (34 bp):
CGATTCAAAAAAAGTAGAATTCCAACATAACAAA
Found at i:315165 original size:22 final size:22
Alignment explanation
Indices: 315131--315189 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
315121 GGAGGGTTTC
* *
315131 TAAAAATAG-AAAATTTTTTAT
1 TAAAAAAAGTAAAATTTTATAT
*
315152 TAAAAAAATTAAAATTTTATAT
1 TAAAAAAAGTAAAATTTTATAT
*
315174 TAATAAAAGTAAAATT
1 TAAAAAAAGTAAAATT
315190 ATTCTTTGGC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 7 0.22
22 25 0.78
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (22 bp):
TAAAAAAAGTAAAATTTTATAT
Found at i:320102 original size:20 final size:19
Alignment explanation
Indices: 320077--320114 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
320067 CTTGTTTAAA
*
320077 ATTTTAAAATATGTTAGAAT
1 ATTTTAAAAAATG-TAGAAT
320097 ATTTTAAAAAATGTAGAA
1 ATTTTAAAAAATGTAGAA
320115 AAATTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (19 bp):
ATTTTAAAAAATGTAGAAT
Found at i:320151 original size:18 final size:18
Alignment explanation
Indices: 320101--320151 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
320091 TAGAATATTT
320101 TAAAAA-ATGTAGAAA-AA
1 TAAAAATAT-TAGAAATAA
* * *
320118 TTAAAATATCAAAAATAA
1 TAAAAATATTAGAAATAA
320136 TAAAAATATTAGAAAT
1 TAAAAATATTAGAAAT
320152 GGTAAAATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (18 bp):
TAAAAATATTAGAAATAA
Found at i:320350 original size:18 final size:16
Alignment explanation
Indices: 320327--320361 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
320317 AATTTAATTT
320327 TAATTAAATTATTTAAAA
1 TAATT-AATT-TTTAAAA
320345 TAATTAATTTTTAAAA
1 TAATTAATTTTTAAAA
320361 T
1 T
320362 TATAAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 4 0.24
18 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATTAATTTTTAAAA
Found at i:321514 original size:12 final size:12
Alignment explanation
Indices: 321482--321522 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
321472 TGTAATACCT
*
321482 GCAAAAAAAGA-
1 GCAAAAACAGAG
321493 GCAAAGAACAGAG
1 GCAAA-AACAGAG
321506 GCAAAAACAGAG
1 GCAAAAACAGAG
321518 GCAAA
1 GCAAA
321523 GAAACAGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 5 0.19
12 17 0.63
13 5 0.19
ACGTcount: A:0.61, C:0.15, G:0.24, T:0.00
Consensus pattern (12 bp):
GCAAAAACAGAG
Found at i:321517 original size:24 final size:26
Alignment explanation
Indices: 321482--321531 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
321472 TGTAATACCT
321482 GCAAAAAAAGA-GCAAAG-AACAGAG
1 GCAAAAAAAGAGGCAAAGAAACAGAG
*
321506 GCAAAAACAGAGGCAAAGAAACAGAG
1 GCAAAAAAAGAGGCAAAGAAACAGAG
321532 TTTTGATGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.43
25 6 0.26
26 7 0.30
ACGTcount: A:0.60, C:0.14, G:0.26, T:0.00
Consensus pattern (26 bp):
GCAAAAAAAGAGGCAAAGAAACAGAG
Found at i:321628 original size:10 final size:11
Alignment explanation
Indices: 321606--321643 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
321596 TTTACCCACG
321606 AAAAATACAAA
1 AAAAATACAAA
321617 AAAAATACAAA
1 AAAAATACAAA
321628 ATCAAAATA-AAA
1 A--AAAATACAAA
321640 AAAA
1 AAAA
321644 GGAGCATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 3 0.12
11 12 0.48
12 4 0.16
13 6 0.24
ACGTcount: A:0.82, C:0.08, G:0.00, T:0.11
Consensus pattern (11 bp):
AAAAATACAAA
Found at i:321815 original size:11 final size:10
Alignment explanation
Indices: 321794--321818 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
321784 ATACATATAC
321794 TTTTATTTTT
1 TTTTATTTTT
321804 TTTTATTTTT
1 TTTTATTTTT
321814 TTTTA
1 TTTTA
321819 GTTCGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTATTTTT
Found at i:323059 original size:30 final size:30
Alignment explanation
Indices: 322683--323072 Score: 445
Period size: 30 Copynumber: 13.1 Consensus size: 30
322673 CTCAAGAGGT
* * * *
322683 CCCC-AAACTTTTCCAAATTTACAATTTAA
1 CCCCTAAACTTTTCCAAAATCATATTTTAA
* *
322712 -CCCTTAACTTTTCTAAAATCATATTTTAA
1 CCCCTAAACTTTTCCAAAATCATATTTTAA
* * *
322741 CCCCTAAAACTTTTCCAAAATTACATTTTGA
1 CCCCT-AAACTTTTCCAAAATCATATTTTAA
*
322772 -CCCTAAACTTTTCCAAAATCATATTATAA
1 CCCCTAAACTTTTCCAAAATCATATTTTAA
* * * *
322801 CACTTAAAATTTTCCAAAATTATATTTTAA
1 CCCCTAAACTTTTCCAAAATCATATTTTAA
*
322831 CCCCTAAACTTTTCCAAAATTGA-ATTTTTAA
1 CCCCTAAACTTTTCCAAAA-TCATA-TTTTAA
322862 CCCC-AAACTTTTCCAAAATCATATTTTAA
1 CCCCTAAACTTTTCCAAAATCATATTTTAA
* *
322891 CACCC-AAACTTTTCCAAAATTACATTTTAA
1 C-CCCTAAACTTTTCCAAAATCATATTTTAA
322921 -CCCTAAACTTTTCCAAAATCATATTTTAA
1 CCCCTAAACTTTTCCAAAATCATATTTTAA
* * *
322950 CCACTAAACTTTTCCAAAATTACA-TTTAA
1 CCCCTAAACTTTTCCAAAATCATATTTTAA
* *
322979 ACCCTAAACTTTTCCAAAATTATATTTTAA
1 CCCCTAAACTTTTCCAAAATCATATTTTAA
* *
323009 CCCCCAAAATTTTCCAAAATCATATTTTAA
1 CCCCTAAACTTTTCCAAAATCATATTTTAA
* * *
323039 CCCCTAAACTTTTCAAAAATCACATTTTGA
1 CCCCTAAACTTTTCCAAAATCATATTTTAA
323069 CCCC
1 CCCC
323073 ATAACTTCTC
Statistics
Matches: 306, Mismatches: 44, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
28 6 0.02
29 98 0.32
30 170 0.56
31 32 0.10
ACGTcount: A:0.38, C:0.25, G:0.01, T:0.36
Consensus pattern (30 bp):
CCCCTAAACTTTTCCAAAATCATATTTTAA
Found at i:324336 original size:28 final size:28
Alignment explanation
Indices: 324304--324367 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
324294 ACAGAAAAAT
*
324304 AACAAAGCACTGGAGAAAGAAAGCTGGA
1 AACAAAACACTGGAGAAAGAAAGCTGGA
* ** *
324332 AACAAAACTCTTTATAAAGAAAGCTGGA
1 AACAAAACACTGGAGAAAGAAAGCTGGA
324360 AACAAAAC
1 AACAAAAC
324368 TCTTTATCTC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.53, C:0.16, G:0.19, T:0.12
Consensus pattern (28 bp):
AACAAAACACTGGAGAAAGAAAGCTGGA
Found at i:324368 original size:28 final size:28
Alignment explanation
Indices: 324319--324374 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
324309 AGCACTGGAG
324319 AAAGAAAGCTGGAAACAAAACTCTTTAT
1 AAAGAAAGCTGGAAACAAAACTCTTTAT
324347 AAAGAAAGCTGGAAACAAAACTCTTTAT
1 AAAGAAAGCTGGAAACAAAACTCTTTAT
324375 CTCTATCCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (28 bp):
AAAGAAAGCTGGAAACAAAACTCTTTAT
Found at i:324774 original size:122 final size:122
Alignment explanation
Indices: 324621--324845 Score: 319
Period size: 122 Copynumber: 1.8 Consensus size: 122
324611 GCCACGAGAC
* * * * * * *
324621 AGAGGAAAAGTATGCCACAATGACAAATAAAAATTAGAAGAAAATCAAAATATAAAAGTAAATAA
1 AGAGGAAAAATATGCCACAAAGACAAATAAAAACTAAAAAAAAACCAAAATATAAAAGAAAATAA
*
324686 GAACT-GAATATAAAAAATTAAGGGGAAAA-AATATCGACGATCGACGTGCCACAAGGT
66 GAA-TAGAATATAAAAAATTAA-GGGAAAAGAATACCGACGATCGACGTGCCACAAGGT
** *
324743 AGAGGAAAAATATGCCACAAAGGTAGATAAAAACTAAAAAAAAACCAAAATATAAAAGAAAATAA
1 AGAGGAAAAATATGCCACAAAGACAAATAAAAACTAAAAAAAAACCAAAATATAAAAGAAAATAA
324808 GAATAGAATATAAAAAATTAAGGGAAAAGAATACCGAC
66 GAATAGAATATAAAAAATTAAGGGAAAAGAATACCGAC
324846 TATCAACGAC
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
121 8 0.09
122 82 0.91
ACGTcount: A:0.58, C:0.10, G:0.16, T:0.16
Consensus pattern (122 bp):
AGAGGAAAAATATGCCACAAAGACAAATAAAAACTAAAAAAAAACCAAAATATAAAAGAAAATAA
GAATAGAATATAAAAAATTAAGGGAAAAGAATACCGACGATCGACGTGCCACAAGGT
Found at i:333734 original size:29 final size:29
Alignment explanation
Indices: 333700--333763 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
333690 AAATGAGACT
*
333700 TTTTGGA-TACTCGGGGGGCAAAATGGTAA
1 TTTTGGACT-CTCGAGGGGCAAAATGGTAA
*
333729 TTTTGGACTCTCGATGGGCAAAATGGTAA
1 TTTTGGACTCTCGAGGGGCAAAATGGTAA
333758 TTTTGG
1 TTTTGG
333764 GAAAATTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 31 0.97
30 1 0.03
ACGTcount: A:0.25, C:0.11, G:0.31, T:0.33
Consensus pattern (29 bp):
TTTTGGACTCTCGAGGGGCAAAATGGTAA
Found at i:333815 original size:58 final size:57
Alignment explanation
Indices: 333748--334022 Score: 227
Period size: 58 Copynumber: 4.8 Consensus size: 57
333738 CTCGATGGGC
* *
333748 AAAATGGTAATTTTGGGAAAATTT-GGGGTTAAAAATGAAATTTTAGATATTCGGGGGT
1 AAAATGGTAATTTT--GAAAATTTCGGGGTAAAAAATGAAATTTTGGATATTCGGGGGT
* * * * *
333806 AAAACGGTAATTTTTAGAAAA--TAGGGATAAAAAACTGAATTTTTGGATAATCGGGGGT
1 AAAATGGTAA-TTTT-GAAAATTTCGGGGTAAAAAA-TGAAATTTTGGATATTCGGGGGT
* ** * *
333864 AAAATGGTAAGTTTTGAAAGTTTCGGGGTAAAAAATGGAGCTTTTGGACATCCGGGGGT
1 AAAATGGTAA-TTTTGAAAATTTCGGGGTAAAAAAT-GAAATTTTGGATATTCGGGGGT
* * * * * *
333923 -AAATGGTAATTTTTGAAAGTTTCGGTGTCAAAAATGGAATTTTGGA-AGTCGAGGGT
1 AAAATGGTAA-TTTTGAAAATTTCGGGGTAAAAAATGAAATTTTGGATATTCGGGGGT
* ** * *
333979 AAAATGGTAATTTTCAAAAGTTTTAGGGTCAAAAATGGAATTTT
1 AAAATGGTAATTTTGAAAA-TTTCGGGGTAAAAAATGAAATTTT
334023 TGGAAGTTCA
Statistics
Matches: 178, Mismatches: 31, Indels: 17
0.79 0.14 0.08
Matches are distributed among these distances:
56 15 0.08
57 51 0.29
58 80 0.45
59 32 0.18
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (57 bp):
AAAATGGTAATTTTGAAAATTTCGGGGTAAAAAATGAAATTTTGGATATTCGGGGGT
Found at i:333867 original size:29 final size:29
Alignment explanation
Indices: 333772--333867 Score: 81
Period size: 29 Copynumber: 3.3 Consensus size: 29
333762 GGGAAAATTT
* * *
333772 GGGGTTAAAAA-TGAAATTTTAGATATTC
1 GGGGGTAAAAACTGAATTTTTAGATAATC
* *
333800 GGGGGT-AAAACGGTAATTTTTAGAAAAT-
1 GGGGGTAAAAACTG-AATTTTTAGATAATC
* * *
333828 AGGGATAAAAAACTGAATTTTTGGATAATC
1 GGGGGT-AAAAACTGAATTTTTAGATAATC
333858 GGGGGTAAAA
1 GGGGGTAAAA
333868 TGGTAAGTTT
Statistics
Matches: 51, Mismatches: 12, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
27 4 0.08
28 10 0.20
29 27 0.53
30 10 0.20
ACGTcount: A:0.41, C:0.04, G:0.26, T:0.29
Consensus pattern (29 bp):
GGGGGTAAAAACTGAATTTTTAGATAATC
Found at i:333999 original size:57 final size:55
Alignment explanation
Indices: 333846--334255 Score: 231
Period size: 58 Copynumber: 7.1 Consensus size: 55
333836 AAAACTGAAT
* * * * *
333846 TTTTGGATAATCGGGGGTAAAATGGTAAGTTTT-GAAAGTTTCGGGGTAAAAAATGGAGC
1 TTTTGGA-AGTCGAGGGTAAAAT-GTAA-TTTTCGAAAGTTT-AGGGTCAAAAATGGA-A
* * *
333905 TTTTGGACA-TCCGGGGGT-AAATGGTAATTTTTGAAAGTTTCGGTGTCAAAAATGGAA
1 TTTTGGA-AGT-CGAGGGTAAAAT-GTAATTTTCGAAAGTTTAGG-GTCAAAAATGGAA
*
333962 TTTTGGAAGTCGAGGGTAAAATGGTAATTTTCAAAAGTTTTAGGGTCAAAAATGGAA
1 TTTTGGAAGTCGAGGGTAAAAT-GTAATTTTCGAAAG-TTTAGGGTCAAAAATGGAA
* * * *
334019 TTTTTGGAAGTTC-AAGGTAAAAATGTAATTTTTGAAAGTTTTGAGGTC-AAAATGTAA
1 -TTTTGGAAG-TCGAGGGT-AAAATGTAATTTTCGAAAGTTTAG-GGTCAAAAATGGAA
*** ** * * *
334076 TTCTCAAAAGTTTAGGGGTAAAATGTAATTCTCAAAAGTTTTAGGGTTAAAAATGGAA
1 TT-TTGGAAGTCGA-GGGTAAAATGTAATTTTCGAAAG-TTTAGGGTCAAAAATGGAA
* * * * * *
334134 TTTTTGGAAGTTTG-GGGTAAAAATGTAATTTTTGGAAGTTTTGAGGTCAAAATTGAAA
1 -TTTTGGAAG-TCGAGGGT-AAAATGTAATTTTCGAAAGTTTAG-GGTCAAAAATGGAA
* * * * *
334192 TTTTTAGAAGTTTTG-GTGGTAAAATTGTAATTTTTGAAAGTTTCGAGGTCCAAAATGGAA
1 -TTTTGGAAG--TCGAG-GGTAAAA-TGTAATTTTCGAAAGTTTAG-GGTCAAAAATGGAA
334252 TTTT
1 TTTT
334256 TAGATAGTTT
Statistics
Matches: 287, Mismatches: 42, Indels: 44
0.77 0.11 0.12
Matches are distributed among these distances:
56 10 0.03
57 88 0.31
58 117 0.41
59 39 0.14
60 33 0.11
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (55 bp):
TTTTGGAAGTCGAGGGTAAAATGTAATTTTCGAAAGTTTAGGGTCAAAAATGGAA
Found at i:334013 original size:115 final size:113
Alignment explanation
Indices: 333846--334195 Score: 314
Period size: 115 Copynumber: 3.0 Consensus size: 113
333836 AAAACTGAAT
* * * ** **
333846 TTTTGGATAATCGGGGGTAAAATGGTAAGTTTT-GAAAGTTTCGGGGTAAAAAATGGAGCTTTTG
1 TTTTGGA-AGTCGAGGGTAAAATGGTAA-TTTTCAAAAGTTTTAGGGTAAAAAATGGAATTTTTG
**
333910 GACA-TCCGGGGGT-AAATGGTAATTTTTGAAAGTTTCG-GTGTCAAAAATGGAA
64 GA-AGTCC-AAGGTAAAAT-GTAATTTTTGAAAGTTTCGAG-GTC-AAAATGGAA
*
333962 TTTTGGAAGTCGAGGGTAAAATGGTAATTTTCAAAAGTTTTAGGGTCAAAAATGGAATTTTTGGA
1 TTTTGGAAGTCGAGGGTAAAATGGTAATTTTCAAAAGTTTTAGGGTAAAAAATGGAATTTTTGGA
* * *
334027 AGTTCAAGGTAAAAATGTAATTTTTGAAAGTTTTGAGGTCAAAATGTAA
66 AGTCCAAGGT-AAAATGTAATTTTTGAAAGTTTCGAGGTCAAAATGGAA
*** ** * *
334076 TTCTCAAAAGTTTAGGGGTAAAAT-GTAATTCTCAAAAGTTTTAGGGTTAAAAATGGAATTTTTG
1 TT-TTGGAAGTCGA-GGGTAAAATGGTAATTTTCAAAAGTTTTAGGGTAAAAAATGGAATTTTTG
**** * * *
334140 GAAGTTTGGGGTAAAAATGTAATTTTTGGAAGTTTTGAGGTCAAAATTGAAA
64 GAAGTCCAAGGT-AAAATGTAATTTTTGAAAGTTTCGAGGTCAAAA-TGGAA
334192 TTTT
1 TTTT
334196 TAGAAGTTTT
Statistics
Matches: 200, Mismatches: 26, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
114 18 0.09
115 155 0.77
116 27 0.14
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.35
Consensus pattern (113 bp):
TTTTGGAAGTCGAGGGTAAAATGGTAATTTTCAAAAGTTTTAGGGTAAAAAATGGAATTTTTGGA
AGTCCAAGGTAAAATGTAATTTTTGAAAGTTTCGAGGTCAAAATGGAA
Found at i:334048 original size:28 final size:28
Alignment explanation
Indices: 333923--334269 Score: 216
Period size: 30 Copynumber: 11.9 Consensus size: 28
333913 ATCCGGGGGT
*
333923 AAATGGTAATTTTTGAAAGTTTCGGTGTCAA
1 AAAT-GTAATTTTTGAAAGTTTAGG-GT-AA
* * **
333954 AAATGGAA-TTTTGGAAGTCGAGGGT-A
1 AAATGTAATTTTTGAAAGTTTAGGGTAA
**
333980 AAATGGTAATTTTCAAAAGTTTTAGGGTCAA
1 AAAT-GTAATTTTTGAAAG-TTTAGGGT-AA
* * * *
334011 AAATGGAATTTTTGGAAGTTCAAGGTAA
1 AAATGTAATTTTTGAAAGTTTAGGGTAA
* *
334039 AAATGTAATTTTTGAAAGTTTTGAGGTCA
1 AAATGTAATTTTTGAAAGTTTAG-GGTAA
* **
334068 AAATGTAATTCTCAAAAGTTTAGGGGT-A
1 AAATGTAATTTTTGAAAGTTTA-GGGTAA
* **
334096 AAATGTAATTCTCAAAAGTTTTAGGGTTAA
1 AAATGTAATTTTTGAAAG-TTTAGGG-TAA
* * *
334126 AAATGGAATTTTTGGAAGTTTGGGGTAA
1 AAATGTAATTTTTGAAAGTTTAGGGTAA
* *
334154 AAATGTAATTTTTGGAAGTTTTGAGGTCAA
1 AAATGTAATTTTTGAAAGTTTAG-GGT-AA
* * *
334184 AATTGAAATTTTT-AGAAGTTTTGGTGGTAA
1 AAATGTAATTTTTGA-AAG-TTTAG-GGTAA
* * *
334214 AATTGTAATTTTTGAAAGTTTCGAGGTCCA
1 AAATGTAATTTTTGAAAGTTTAG-GGT-AA
* *
334244 AAATGGAATTTTTAGATAGTTTAGGG
1 AAATGTAATTTTT-GAAAGTTTAGGG
334270 ACCTCTAGGG
Statistics
Matches: 251, Mismatches: 48, Indels: 35
0.75 0.14 0.10
Matches are distributed among these distances:
26 5 0.02
27 3 0.01
28 74 0.29
29 69 0.27
30 75 0.30
31 25 0.10
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (28 bp):
AAATGTAATTTTTGAAAGTTTAGGGTAA
Found at i:334049 original size:58 final size:58
Alignment explanation
Indices: 333923--334256 Score: 306
Period size: 58 Copynumber: 5.7 Consensus size: 58
333913 ATCCGGGGGT
*
333923 AAATGGTAATTTTTGAAAGTTTCG-GTGTCAAAAATGGAA-TTTTGGAAG-TCGAGGGT-A
1 AAAT-GTAATTTTTGAAAGTTTTGAG-GTCAAAAATGGAATTTTTGGAAGTTC-AGGGTAA
** *
333980 AAATGGTAATTTTCAAAAGTTTT-AGGGTCAAAAATGGAATTTTTGGAAGTTCAAGGTAA
1 AAAT-GTAATTTTTGAAAGTTTTGA-GGTCAAAAATGGAATTTTTGGAAGTTCAGGGTAA
* * *** *
334039 AAATGTAATTTTTGAAAGTTTTGAGGTC-AAAATGTAATTCTCAAAAGTTTAGGGGT-A
1 AAATGTAATTTTTGAAAGTTTTGAGGTCAAAAATGGAATTTTTGGAAGTTCA-GGGTAA
* ** * **
334096 AAATGTAATTCTCAAAAGTTTT-AGGGTTAAAAATGGAATTTTTGGAAGTTTGGGGTAA
1 AAATGTAATTTTTGAAAGTTTTGA-GGTCAAAAATGGAATTTTTGGAAGTTCAGGGTAA
* * * * **
334154 AAATGTAATTTTTGGAAGTTTTGAGGTCAAAATTGAAATTTTTAGAAGTTTTGGTGGTAA
1 AAATGTAATTTTTGAAAGTTTTGAGGTCAAAAATGGAATTTTTGGAAG-TTCAG-GGTAA
* * *
334214 AATTGTAATTTTTGAAAGTTTCGAGGTCCAAAATGGAATTTTT
1 AAATGTAATTTTTGAAAGTTTTGAGGTCAAAAATGGAATTTTT
334257 AGATAGTTTA
Statistics
Matches: 227, Mismatches: 37, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
56 1 0.00
57 77 0.34
58 93 0.41
59 14 0.06
60 42 0.19
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.37
Consensus pattern (58 bp):
AAATGTAATTTTTGAAAGTTTTGAGGTCAAAAATGGAATTTTTGGAAGTTCAGGGTAA
Found at i:347395 original size:2 final size:2
Alignment explanation
Indices: 347388--347421 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
347378 ACATGCAATC
*
347388 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
347422 TCAGGAGGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:350779 original size:26 final size:26
Alignment explanation
Indices: 350736--350785 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
350726 TCTACAACCA
** *
350736 TAAATTTATTTTTTAAAACAAAACTG
1 TAAATTTATTTTAGAAAAAAAAACTG
350762 TAAATTTATTTTAGAAAAAAAAAC
1 TAAATTTATTTTAGAAAAAAAAAC
350786 ATTTGACTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (26 bp):
TAAATTTATTTTAGAAAAAAAAACTG
Found at i:352014 original size:3 final size:3
Alignment explanation
Indices: 352006--352033 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
351996 CCTTTTTGAT
352006 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
352034 AACTATCATA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:361394 original size:70 final size:70
Alignment explanation
Indices: 361278--361408 Score: 244
Period size: 70 Copynumber: 1.9 Consensus size: 70
361268 TCTAATCTCG
361278 ATCAGAAATTTTATTTCCTGAAACTTGTGAGTTTTCTACCAGTTTGCCCTTATTATGCATGTGCA
1 ATCAGAAATTTTATTTCCTGAAACTTGTGAGTTTTCTACCAGTTTGCCCTTATTATGCATGTGCA
361343 TCATA
66 TCATA
* *
361348 ATCAGAAATTTTATTTCCTGCAACTTGTGAGTTTTCTACCATTTTGCCCTTATTATGCATG
1 ATCAGAAATTTTATTTCCTGAAACTTGTGAGTTTTCTACCAGTTTGCCCTTATTATGCATG
361409 CATGTGCATC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 59 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (70 bp):
ATCAGAAATTTTATTTCCTGAAACTTGTGAGTTTTCTACCAGTTTGCCCTTATTATGCATGTGCA
TCATA
Found at i:366960 original size:22 final size:23
Alignment explanation
Indices: 366930--366974 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
366920 TAAAACAGTG
*
366930 AAAAGCAATAGGAAAATAACAAC
1 AAAAGCAATAGAAAAATAACAAC
366953 AAAA-CAATAGAAAAATAACAAC
1 AAAAGCAATAGAAAAATAACAAC
366975 TTTTTTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.69, C:0.13, G:0.09, T:0.09
Consensus pattern (23 bp):
AAAAGCAATAGAAAAATAACAAC
Found at i:367494 original size:2 final size:2
Alignment explanation
Indices: 367487--367520 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
367477 TTAAAAACAA
367487 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
367521 GAGAAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:367553 original size:15 final size:15
Alignment explanation
Indices: 367528--367561 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
367518 CACGAGAAAT
367528 AAAATTACTTTACAAA
1 AAAATTACTTTA-AAA
367544 AAAATT-CTTTAAAA
1 AAAATTACTTTAAAA
367558 AAAA
1 AAAA
367562 AGGAGAACCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 5 0.28
16 6 0.33
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATTACTTTAAAA
Found at i:367562 original size:16 final size:16
Alignment explanation
Indices: 367528--367562 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
367518 CACGAGAAAT
*
367528 AAAATTACTTTACAAA
1 AAAATTACTTTAAAAA
367544 AAAATT-CTTTAAAAA
1 AAAATTACTTTAAAAA
367559 AAAA
1 AAAA
367563 GGAGAACCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATTACTTTAAAAA
Done.