Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007956.1 Hibiscus syriacus cultivar Beakdansim tig00110383_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3102597
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 14
Found at i:2652788 original size:21 final size:22
Alignment explanation
Indices: 2652762--2652815 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
2652752 AAGTTCCCCG
2652762 GGTATCGATACC-CT-CCATAT
1 GGTATCGATACCTCTACCATAT
2652782 AGGTATCGATACCTCTACCATAT
1 -GGTATCGATACCTCTACCATAT
2652805 GGTATCGATAC
1 GGTATCGATAC
2652816 TATTTATAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 12 0.39
22 13 0.42
23 6 0.19
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.30
Consensus pattern (22 bp):
GGTATCGATACCTCTACCATAT
Found at i:2653269 original size:21 final size:21
Alignment explanation
Indices: 2653243--2653289 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
2653233 ACTTAATGAT
2653243 TTAAGCTTATATAAG-TTTTCC
1 TTAAGCTTATATAAGCTTTT-C
2653264 TTAAGCTTATATAAGCTTTTC
1 TTAAGCTTATATAAGCTTTTC
2653285 TTAAG
1 TTAAG
2653290 TTTTCCTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.47
Consensus pattern (21 bp):
TTAAGCTTATATAAGCTTTTC
Found at i:2653292 original size:32 final size:32
Alignment explanation
Indices: 2653254--2653321 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
2653244 TAAGCTTATA
2653254 TAAGTTTTCCTTAAGCTTATATAAGCTTTTCT
1 TAAGTTTTCCTTAAGCTTATATAAGCTTTTCT
2653286 TAAGTTTTCCTTAAGCTTATATAAGCTTTTCT
1 TAAGTTTTCCTTAAGCTTATATAAGCTTTTCT
2653318 TAAG
1 TAAG
2653322 CTTATATAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (32 bp):
TAAGTTTTCCTTAAGCTTATATAAGCTTTTCT
Found at i:2653298 original size:11 final size:11
Alignment explanation
Indices: 2653254--2653345 Score: 77
Period size: 11 Copynumber: 8.6 Consensus size: 11
2653244 TAAGCTTATA
2653254 TAAG-TTTTCCT
1 TAAGCTTTT-CT
* *
2653265 TAAGCTTAT-A
1 TAAGCTTTTCT
2653275 TAAGCTTTTCT
1 TAAGCTTTTCT
2653286 TAAG-TTTTCCT
1 TAAGCTTTT-CT
* *
2653297 TAAGCTTAT-A
1 TAAGCTTTTCT
2653307 TAAGCTTTTCT
1 TAAGCTTTTCT
* *
2653318 TAAGCTTAT-A
1 TAAGCTTTTCT
2653328 TAAGCTTTTCT
1 TAAGCTTTTCT
2653339 TAAGCTT
1 TAAGCTT
2653346 ATATAACACC
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
10 28 0.44
11 29 0.46
12 6 0.10
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (11 bp):
TAAGCTTTTCT
Found at i:2653319 original size:21 final size:21
Alignment explanation
Indices: 2653286--2653351 Score: 116
Period size: 21 Copynumber: 3.1 Consensus size: 21
2653276 AAGCTTTTCT
2653286 TAAG-TTTTCCTTAAGCTTATA
1 TAAGCTTTT-CTTAAGCTTATA
2653307 TAAGCTTTTCTTAAGCTTATA
1 TAAGCTTTTCTTAAGCTTATA
2653328 TAAGCTTTTCTTAAGCTTATA
1 TAAGCTTTTCTTAAGCTTATA
2653349 TAA
1 TAA
2653352 CACCCAAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
21 40 0.91
22 4 0.09
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.47
Consensus pattern (21 bp):
TAAGCTTTTCTTAAGCTTATA
Found at i:2658615 original size:18 final size:19
Alignment explanation
Indices: 2658578--2658615 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2658568 CATTCATCGG
*
2658578 GTATCGATACCTGGAGGGTA
1 GTATCGATACC-GAAGGGTA
2658598 GTATCGATACC-AAGGGTA
1 GTATCGATACCGAAGGGTA
2658616 CCGATACCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.29, C:0.16, G:0.32, T:0.24
Consensus pattern (19 bp):
GTATCGATACCGAAGGGTA
Found at i:2660079 original size:2 final size:2
Alignment explanation
Indices: 2660072--2660184 Score: 171
Period size: 2 Copynumber: 58.5 Consensus size: 2
2660062 TCTTTGTATG
2660072 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
2660113 AT AT AT AT AT AT AT CT AT AT AT AT AT AT AT -T AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2660154 AT AT AT AT -T AT AT AT AT AT AT A- AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2660185 ATAAATTATA
Statistics
Matches: 101, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
1 4 0.04
2 97 0.96
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2662656 original size:12 final size:12
Alignment explanation
Indices: 2662641--2662671 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
2662631 CCACTTTCAG
2662641 GCGCACTATCAT
1 GCGCACTATCAT
2662653 GCGCACTATCAT
1 GCGCACTATCAT
2662665 GCGCACT
1 GCGCACT
2662672 TTCAACAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.23
Consensus pattern (12 bp):
GCGCACTATCAT
Found at i:2669157 original size:3 final size:3
Alignment explanation
Indices: 2669144--2669215 Score: 137
Period size: 3 Copynumber: 24.3 Consensus size: 3
2669134 TACACAAATT
2669144 AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
2669191 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
2669216 GAGCAAGATA
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 66 0.97
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2671990 original size:14 final size:14
Alignment explanation
Indices: 2671973--2671999 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2671963 TTCAAGAGAG
2671973 AGGGTTCAGAAAAT
1 AGGGTTCAGAAAAT
2671987 AGGGTTCAGAAAA
1 AGGGTTCAGAAAA
2672000 CCATGTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.30, T:0.19
Consensus pattern (14 bp):
AGGGTTCAGAAAAT
Found at i:2678746 original size:12 final size:13
Alignment explanation
Indices: 2678729--2678757 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2678719 TACATCTATT
2678729 TTTTTAAA-AATA
1 TTTTTAAATAATA
2678741 TTTTTAAATAATA
1 TTTTTAAATAATA
2678754 TTTT
1 TTTT
2678758 ATTAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTTTAAATAATA
Found at i:2678905 original size:3 final size:3
Alignment explanation
Indices: 2678899--2678985 Score: 90
Period size: 3 Copynumber: 28.7 Consensus size: 3
2678889 TAAATAATAA
* * *
2678899 TAT TAT TA- TAT TAT TAT TAA TAT TAT T-T TAT TTT TAC TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2678944 TAT TAT TAT TATT TAT TAT TAT TAT TAAT TAAGT TAT TAT TA
1 TAT TAT TAT TA-T TAT TAT TAT TAT T-AT T-A-T TAT TAT TA
2678986 CAGACCCAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
2 6 0.08
3 55 0.76
4 9 0.12
5 2 0.03
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2678911 original size:23 final size:22
Alignment explanation
Indices: 2678879--2678929 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
2678869 TATATACATT
*
2678879 TTTTTTATTATAAATAATAATA
1 TTTTATATTATAAATAATAATA
* * *
2678901 TTATTATATTATTATTAATATTA
1 TT-TTATATTATAAATAATAATA
2678924 TTTTAT
1 TTTTAT
2678930 TTTTACTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTTTATATTATAAATAATAATA
Found at i:2678981 original size:31 final size:28
Alignment explanation
Indices: 2678901--2678985 Score: 88
Period size: 28 Copynumber: 3.0 Consensus size: 28
2678891 AATAATAATA
2678901 TTATTATATTATTATTAA-TATTATTTTAT
1 TTATTATATTATTATTAATTATTA--TTAT
2678930 TT-TTACTATTA-TATT-ATTATTATTAT
1 TTATTA-TATTATTATTAATTATTATTAT
2678956 TTATTATTATTATTAATTAAGTTATTATTA
1 TTATTA-TATTATT-ATTAA-TTATTATTA
2678986 CAGACCCAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 12
0.79 0.02 0.20
Matches are distributed among these distances:
26 6 0.12
27 9 0.19
28 13 0.27
29 10 0.21
30 1 0.02
31 9 0.19
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (28 bp):
TTATTATATTATTATTAATTATTATTAT
Found at i:2678981 original size:34 final size:36
Alignment explanation
Indices: 2678907--2678985 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 36
2678897 AATATTATTA
*
2678907 TATTATTATTAATATTATTTTATTTTTACTATTATAT
1 TATTATTATTAATATTATTTTATTATTAC-ATTATAT
2678944 TATTATTATT-AT-TTATTATTATTATTA-ATTA-AGT
1 TATTATTATTAATATTATT-TTATTATTACATTATA-T
2678978 TATTATTA
1 TATTATTA
2678986 CAGACCCAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
33 1 0.03
34 13 0.33
35 5 0.13
36 10 0.26
37 10 0.26
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (36 bp):
TATTATTATTAATATTATTTTATTATTACATTATAT
Found at i:2680305 original size:27 final size:27
Alignment explanation
Indices: 2680275--2680337 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
2680265 TATTTAGTTA
*
2680275 TATTTTAATTTTAATTTAAATATTAAT
1 TATTTTAATTTTAATTTAAATATAAAT
* *
2680302 TATTATT-ATTTTATTTTTAATATAAAT
1 TATT-TTAATTTTAATTTAAATATAAAT
2680329 TATTTTAAT
1 TATTTTAAT
2680338 CATGTTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 2 0.06
27 27 0.87
28 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
TATTTTAATTTTAATTTAAATATAAAT
Found at i:2680594 original size:17 final size:17
Alignment explanation
Indices: 2680572--2680609 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2680562 ATATTTTTTT
2680572 TATATTTTATATATAAA
1 TATATTTTATATATAAA
* *
2680589 TATATTTTTTATATAAT
1 TATATTTTATATATAAA
2680606 TATA
1 TATA
2680610 ACTTTGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATTTTATATATAAA
Found at i:2681113 original size:25 final size:23
Alignment explanation
Indices: 2681075--2681121 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
2681065 AATTCTTTTC
*
2681075 TTTCAAAATTTTTATTACTTATTAT
1 TTTCAAAATATTTA-TA-TTATTAT
*
2681100 TTTCATAATATTTATATTATTA
1 TTTCAAAATATTTATATTATTA
2681122 ATGCTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 2 0.10
25 12 0.60
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTCAAAATATTTATATTATTAT
Found at i:2688258 original size:8 final size:9
Alignment explanation
Indices: 2688231--2688261 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
2688221 AAATGGCAAT
2688231 CATTCTTTA
1 CATTCTTTA
2688240 CATTCTTTA
1 CATTCTTTA
2688249 CATT-TTTA
1 CATTCTTTA
2688257 CATTC
1 CATTC
2688262 ATTATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.55
Consensus pattern (9 bp):
CATTCTTTA
Found at i:2691823 original size:22 final size:22
Alignment explanation
Indices: 2691785--2691848 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
2691775 TATTATGCTT
*
2691785 GAAGAAAAAA-AAGGAAAAAAA
1 GAAGAAAAAAGAAAGAAAAAAA
2691806 GAAGAAAAAAGAAAGAAAAAAA
1 GAAGAAAAAAGAAAGAAAAAAA
*
2691828 AAAGAAAAAAGAAAGAAAAAA
1 GAAGAAAAAAGAAAGAAAAAA
2691849 TGTTAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 10 0.25
22 30 0.75
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (22 bp):
GAAGAAAAAAGAAAGAAAAAAA
Found at i:2691868 original size:11 final size:11
Alignment explanation
Indices: 2691786--2691848 Score: 85
Period size: 11 Copynumber: 5.8 Consensus size: 11
2691776 ATTATGCTTG
2691786 AAGAAAAAA-A
1 AAGAAAAAAGA
*
2691796 AGGAAAAAA-A
1 AAGAAAAAAGA
2691806 GAAGAAAAAAGA
1 -AAGAAAAAAGA
*
2691818 AAGAAAAAAAA
1 AAGAAAAAAGA
2691829 AAGAAAAAAGA
1 AAGAAAAAAGA
2691840 AAGAAAAAA
1 AAGAAAAAA
2691849 TGTTAAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
10 9 0.19
11 37 0.79
12 1 0.02
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAGA
Found at i:2692239 original size:18 final size:18
Alignment explanation
Indices: 2692216--2692250 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2692206 CAAGTTTATC
2692216 TTTTTGAAATTCAATTTA
1 TTTTTGAAATTCAATTTA
2692234 TTTTTGAAATTCAATTT
1 TTTTTGAAATTCAATTT
2692251 GTTTCATATA
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:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (18 bp):
TTTTTGAAATTCAATTTA
Found at i:2693720 original size:110 final size:115
Alignment explanation
Indices: 2693405--2693930 Score: 544
Period size: 121 Copynumber: 4.4 Consensus size: 115
2693395 TGGATCAAAT
* * *
2693405 TTTCCAGAAAGTTCATAATGAGAATAACTCATCTGAAGATGAAGAAGAAGTTCATAATGAGAAGA
1 TTTCCAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGA
* * *
2693470 ATTTGTTCAACCTTTTGCTCGATTCTATCACAGAAGGAGATAGATCAACATCAACA
66 ACTTGTTCAACTTTTTGCTCGATTCTATCACACAAGGAG--AGAT----ATCAACA
** *
2693526 TTTCCAGAAGGAGTTCATAATGAGAAGAACCCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAA--AGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGA
* ** *
2693591 AGAGCTTGTTCAACTTTTTGCTCGAATTC-ATCATTCTA-G-G-G-T-TCAACA
63 AGAACTTGTTCAACTTTTTGCTCG-ATTCTATCACACAAGGAGAGATATCAACA
*
2693639 TTTCCAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAATA
1 TTTCCAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGA
* * * *
2693704 ATTTGTTCAACCTTTTGCTCGATTCTATCACAGAAGGAGATAGATTAGCATCAATA
66 ACTTGTTCAACTTTTTGCTCGATTCTATCACACAAGGAG--AGA-T---ATCAACA
** *
2693760 TTTTTAGAAGGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGA
1 TTTCCAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGA
* *
2693825 ACTTGTTCAACTTTTTG-TATGATTCTATCACAGAAGGAGATAGATCAGCTCATCAACA
66 ACTTGTTCAACTTTTTGCT-CGATTCTATCACACAAGGAG--AG---A--T-ATCAACA
*
2693883 TTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAA
1 TTTCCAG-A-AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAA
2693931 CTTGTTCAAC
Statistics
Matches: 347, Mismatches: 35, Indels: 42
0.82 0.08 0.10
Matches are distributed among these distances:
109 4 0.01
110 48 0.14
111 28 0.08
112 1 0.00
113 15 0.04
115 1 0.00
117 1 0.00
118 1 0.00
119 1 0.00
120 1 0.00
121 113 0.33
122 1 0.00
123 40 0.12
124 51 0.15
125 41 0.12
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (115 bp):
TTTCCAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGA
ACTTGTTCAACTTTTTGCTCGATTCTATCACACAAGGAGAGATATCAACA
Found at i:2693807 original size:234 final size:232
Alignment explanation
Indices: 2693405--2693841 Score: 725
Period size: 234 Copynumber: 1.9 Consensus size: 232
2693395 TGGATCAAAT
* *
2693405 TTTCCAGAAAGTTCATAATGAGAATAACTCATCTGAAGATGAAGAAGAAGTTCATAATGAGAAGA
1 TTTCCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGA
2693470 ATTTGTTCAACCTTTTGCTCGATTCTATCACAGAAGGAGATAGATCAACATCAACATTTCCAGAA
66 ATTTGTTCAACCTTTTGCTCGATTCTATCACAGAAGGAGATAGATCAACATCAACATTTCCAGAA
*
2693535 GGAGTTCATAATGAGAAGAACCCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGT
131 GGAGTTCATAATGAGAAGAACCCATCTGAAG--AGAAGAAGAAGTTCATAATGAGAAGAACTTGT
2693600 TCAACTTTTTGCTCGAATTCATCATTCTAGGGTTCAACA
194 TCAACTTTTTGCTCGAATTCATCATTCTAGGGTTCAACA
* *
2693639 TTTCCAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAATA
1 TTTCCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGA
* * * **
2693704 ATTTGTTCAACCTTTTGCTCGATTCTATCACAGAAGGAGATAGATTAGCATCAATATTTTTAGAA
66 ATTTGTTCAACCTTTTGCTCGATTCTATCACAGAAGGAGATAGATCAACATCAACATTTCCAGAA
**
2693769 -G-GTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
131 GGAGTTCATAATGAGAAGAACCCATCTGAAGA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTT
2693832 CAACTTTTTG
195 CAACTTTTTG
2693842 TATGATTCTA
Statistics
Matches: 190, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
230 1 0.01
231 41 0.22
232 26 0.14
233 1 0.01
234 121 0.64
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (232 bp):
TTTCCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGA
ATTTGTTCAACCTTTTGCTCGATTCTATCACAGAAGGAGATAGATCAACATCAACATTTCCAGAA
GGAGTTCATAATGAGAAGAACCCATCTGAAGAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACTTTTTGCTCGAATTCATCATTCTAGGGTTCAACA
Found at i:2693832 original size:20 final size:20
Alignment explanation
Indices: 2693770--2693833 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
2693760 TTTTTAGAAG
2693770 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
2693790 -ATC-TGAA-GAGGAAGAAGAA
1 GTTCAT-AATGA-GAAGAACTT
2693809 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
2693829 GTTCA
1 GTTCA
2693834 ACTTTTTGTA
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 15 0.48
21 3 0.10
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:2694448 original size:3 final size:3
Alignment explanation
Indices: 2694442--2694512 Score: 67
Period size: 3 Copynumber: 23.7 Consensus size: 3
2694432 TAAATAATAA
* * *
2694442 TAT TAT TA- TAT TAT TAT TAA TAT TAT T-T TAT TTT TAC TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2694487 TAT TAT TAT TAAT TAAGT TAT TAT TA
1 TAT TAT TAT T-AT T-A-T TAT TAT TA
2694513 CATACCCAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
2 6 0.11
3 43 0.75
4 6 0.11
5 2 0.04
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2694454 original size:23 final size:22
Alignment explanation
Indices: 2694423--2694472 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
2694413 TATACATTTG
2694423 TTTT-TATTATAAATAATAATA
1 TTTTATATTATAAATAATAATA
* * *
2694444 TTATTATATTATTATTAATATTA
1 TT-TTATATTATAAATAATAATA
2694467 TTTTAT
1 TTTTAT
2694473 TTTTACTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 6 0.25
23 16 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTATATTATAAATAATAATA
Found at i:2694467 original size:17 final size:17
Alignment explanation
Indices: 2694445--2694512 Score: 75
Period size: 17 Copynumber: 3.9 Consensus size: 17
2694435 ATAATAATAT
2694445 TATTATATTATTATTAA
1 TATTATATTATTATTAA
* * *
2694462 TATTATTTTATTTTTAC
1 TATTATATTATTATTAA
*
2694479 TATTATATTATTATTAT
1 TATTATATTATTATTAA
2694496 TAATTA-AGTTATTATTA
1 T-ATTATA-TTATTATTA
2694513 CATACCCAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
17 30 0.70
18 13 0.30
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (17 bp):
TATTATATTATTATTAA
Found at i:2695776 original size:27 final size:26
Alignment explanation
Indices: 2695738--2695821 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 26
2695728 AAATTATAGT
* *
2695738 TTATT-TTA-TTTATTTTAGTCATTAT
1 TTATTATTATTTTATTTTAAT-ATTAA
*
2695763 TTAGTTA-TATTTTAATTTAAATATTAA
1 TTA-TTATTATTTT-ATTTTAATATTAA
*
2695790 TTATTATTATTTTATTTTTAATATAAA
1 TTATTATTATTTTA-TTTTAATATTAA
2695817 TTATT
1 TTATT
2695822 TTAATCATGT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
25 3 0.06
26 8 0.17
27 31 0.65
28 6 0.12
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.63
Consensus pattern (26 bp):
TTATTATTATTTTATTTTAATATTAA
Found at i:2696062 original size:27 final size:27
Alignment explanation
Indices: 2696030--2696087 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
2696020 TCCTTTTCTG
2696030 ATATTTCTA-A-ATAAATAAATATTTTTT
1 ATATTTCTATATATAAAT--ATATTTTTT
*
2696057 ATATTTTTATATATAAATATATTTTTT
1 ATATTTCTATATATAAATATATTTTTT
2696084 ATAT
1 ATAT
2696088 AATTATAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 21 0.75
28 1 0.04
29 6 0.21
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (27 bp):
ATATTTCTATATATAAATATATTTTTT
Found at i:2696081 original size:17 final size:18
Alignment explanation
Indices: 2696056--2696094 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
2696046 AAATATTTTT
2696056 TATATTTTTATATATAAA
1 TATATTTTTATATATAAA
*
2696074 TATATTTTT-TATATAAT
1 TATATTTTTATATATAAA
2696091 TATA
1 TATA
2696095 ACTTTGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATATTTTTATATATAAA
Found at i:2702971 original size:3 final size:3
Alignment explanation
Indices: 2702963--2703020 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
2702953 TTACTATCAC
2702963 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2703011 TAT TAT TAT T
1 TAT TAT TAT T
2703021 TTCATCCTAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2706923 original size:29 final size:30
Alignment explanation
Indices: 2706803--2706924 Score: 99
Period size: 31 Copynumber: 4.0 Consensus size: 30
2706793 CAAAATACAT
* * *
2706803 AACTTTTATAAATTACACTTTTAGTCCCTA
1 AACTTTTAAAAATTACACTTTTGGTCACTA
*
2706833 AACTTTTGAAAAATTACATTTTTGGTTC-CTA
1 AACTTTT-AAAAATTACACTTTTGG-TCACTA
* * *
2706864 AACTCTTACAAACTTTATAC-TTTGG-CTACTA
1 AACTTTTA-AAA-ATTACACTTTTGGTC-ACTA
*
2706895 AACTTTTAAAAATTATA-TTTTGGTCACTA
1 AACTTTTAAAAATTACACTTTTGGTCACTA
2706924 A
1 A
2706925 TAAATATTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
29 16 0.21
30 12 0.16
31 41 0.55
32 6 0.08
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (30 bp):
AACTTTTAAAAATTACACTTTTGGTCACTA
Found at i:2712279 original size:24 final size:24
Alignment explanation
Indices: 2712247--2712302 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
2712237 CTTGAGAGAG
2712247 GCTGATCACCAAGACAGGCGCGAT
1 GCTGATCACCAAGACAGGCGCGAT
*
2712271 GCTGATCACCAAGATAGGCGCGAT
1 GCTGATCACCAAGACAGGCGCGAT
2712295 GCTGATCA
1 GCTGATCA
2712303 GAATCGTCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.29, C:0.27, G:0.29, T:0.16
Consensus pattern (24 bp):
GCTGATCACCAAGACAGGCGCGAT
Found at i:2729903 original size:21 final size:21
Alignment explanation
Indices: 2729872--2729920 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
2729862 CTGGAAGCGG
*
2729872 GCTCTACTGAGAGCTCTACAT
1 GCTCCACTGAGAGCTCTACAT
* *
2729893 TCTCCACTGAGAGCTTTACAT
1 GCTCCACTGAGAGCTCTACAT
2729914 GCTCCAC
1 GCTCCAC
2729921 GATGAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.29
Consensus pattern (21 bp):
GCTCCACTGAGAGCTCTACAT
Found at i:2736368 original size:21 final size:21
Alignment explanation
Indices: 2736343--2736396 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
2736333 TAGGAGCGTG
2736343 GGGTATCGGTACACCTTCAAT
1 GGGTATCGGTACACCTTCAAT
**
2736364 GGGTATCAATACACCTTCAAT
1 GGGTATCGGTACACCTTCAAT
2736385 GGGTATCGGTAC
1 GGGTATCGGTAC
2736397 CTGCAGTGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (21 bp):
GGGTATCGGTACACCTTCAAT
Found at i:2736621 original size:76 final size:74
Alignment explanation
Indices: 2736440--2736621 Score: 249
Period size: 74 Copynumber: 2.4 Consensus size: 74
2736430 AATAACTAGG
* * *
2736440 GGTATCGGTACCACTAAG-GGGGTATCAGTACCCATTGGGCATTCTGTTTTTCTCGGAGCCAAAA
1 GGTATCGGTACC-CTATGAGGGGTATCGGTACCCATTGGGCATTCTATTTTTCTCGGAGCCAAAA
* *
2736504 TTGGCATAGG
65 TTGACATAGA
* * *
2736514 GGTATCGGTACCCTATGAGGGGTATCGGTACCCATTTGGCATTCTATTTTTTTTGGAGCCAAAAT
1 GGTATCGGTACCCTATGAGGGGTATCGGTACCCATTGGGCATTCTATTTTTCTCGGAGCCAAAAT
2736579 TGACATAGA
66 TGACATAGA
*
2736588 GGTATCGGTACACCCTGTGAGGGGTATCGGTACC
1 GGTATCGGT--ACCCTATGAGGGGTATCGGTACC
2736622 TCCCTATTTA
Statistics
Matches: 96, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
73 4 0.04
74 70 0.73
76 22 0.23
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.30
Consensus pattern (74 bp):
GGTATCGGTACCCTATGAGGGGTATCGGTACCCATTGGGCATTCTATTTTTCTCGGAGCCAAAAT
TGACATAGA
Found at i:2737237 original size:18 final size:19
Alignment explanation
Indices: 2737206--2737258 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
2737196 TCAAATAACT
* * *
2737206 AATAATCATTCAAACCAA-
1 AATAAACATCCAAACAAAC
2737224 AATAAACATCCAAACAAAC
1 AATAAACATCCAAACAAAC
2737243 AATTCAAACATCCAAA
1 AA-T-AAACATCCAAA
2737259 TTAAAACACA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 15 0.52
19 2 0.07
20 1 0.03
21 11 0.38
ACGTcount: A:0.58, C:0.25, G:0.00, T:0.17
Consensus pattern (19 bp):
AATAAACATCCAAACAAAC
Found at i:2739223 original size:21 final size:22
Alignment explanation
Indices: 2739173--2739229 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 22
2739163 TACCCTTATT
*
2739173 GGGGTATTGATACACATTCAAA
1 GGGGTATCGATACACATTCAAA
* *
2739195 GAGGGTATCGATACACGTT-GAA
1 G-GGGTATCGATACACATTCAAA
2739217 GGGGTATCGATAC
1 GGGGTATCGATAC
2739230 CCGGTGCACA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 12 0.39
22 4 0.13
23 15 0.48
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.25
Consensus pattern (22 bp):
GGGGTATCGATACACATTCAAA
Found at i:2741190 original size:20 final size:21
Alignment explanation
Indices: 2741152--2741191 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2741142 CAAATGAGAA
*
2741152 TGATGTGGCAAAATGGAATGTC
1 TGATGTGG-AAAATAGAATGTC
2741174 TGATGTGG-AAATAGAATG
1 TGATGTGGAAAATAGAATG
2741192 GTGGTAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.35, C:0.05, G:0.33, T:0.28
Consensus pattern (21 bp):
TGATGTGGAAAATAGAATGTC
Found at i:2742652 original size:20 final size:20
Alignment explanation
Indices: 2742623--2742662 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2742613 ATTCCACCAC
2742623 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* * *
2742643 ATGCATCTATGTGGTCCTAA
1 ATGCAACTATATGCTCCTAA
2742663 TTGAGCTCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:2748476 original size:20 final size:20
Alignment explanation
Indices: 2748447--2748493 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2748437 ATTCCACCAC
2748447 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* * *
2748467 ATGCATCTATGTGGTCCTAA
1 ATGCAACTATATGCTCCTAA
2748487 ATG-AACT
1 ATGCAACT
2748494 CTTAGACATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:2750979 original size:19 final size:19
Alignment explanation
Indices: 2750955--2750999 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
2750945 TGCATTGGGC
2750955 TATGAATTTGAAAATAAGT
1 TATGAATTTGAAAATAAGT
*
2750974 TATGAATTTGGAAATAAGT
1 TATGAATTTGAAAATAAGT
*
2750993 TCTGAAT
1 TATGAAT
2751000 CGAGAATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.42, C:0.02, G:0.18, T:0.38
Consensus pattern (19 bp):
TATGAATTTGAAAATAAGT
Found at i:2751054 original size:13 final size:13
Alignment explanation
Indices: 2751036--2751097 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 13
2751026 TATTGGTTAC
*
2751036 GAAAATGAGATGT
1 GAAAATGAAATGT
2751049 GAAAAT-AAATGT
1 GAAAATGAAATGT
*
2751061 GAAAGTGAAA-GAT
1 GAAAATGAAATG-T
*
2751074 GAAAATGAAATAT
1 GAAAATGAAATGT
2751087 GAAATATGAAA
1 GAAA-ATGAAA
2751098 GTTTGGAGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
12 11 0.27
13 24 0.59
14 6 0.15
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (13 bp):
GAAAATGAAATGT
Found at i:2751633 original size:25 final size:24
Alignment explanation
Indices: 2751600--2751653 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
2751590 GTTTTATGTT
*
2751600 TTAG-ATAAAAATATATATTTTTAA
1 TTAGAATAAAAATATAT-TTTTAAA
*
2751624 TTAGAATAAAGATATATTTTTAAA
1 TTAGAATAAAAATATATTTTTAAA
2751648 TTAGAA
1 TTAGAA
2751654 AGTTTTTAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 16 0.59
25 11 0.41
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (24 bp):
TTAGAATAAAAATATATTTTTAAA
Found at i:2751655 original size:21 final size:21
Alignment explanation
Indices: 2751607--2751654 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 21
2751597 GTTTTAGATA
*
2751607 AAAATATATATTTTTAATTAG
1 AAAAGATATATTTTTAATTAG
2751628 AATAAAGATATATTTTTAAATTAG
1 -A-AAAGATATATTTTT-AATTAG
2751652 AAA
1 AAA
2751655 GTTTTTAGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 3 0.13
23 14 0.61
24 6 0.26
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (21 bp):
AAAAGATATATTTTTAATTAG
Found at i:2752474 original size:16 final size:17
Alignment explanation
Indices: 2752453--2752496 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
2752443 GAGTTTCACC
2752453 AATTAAAATTTAAA-AA
1 AATTAAAATTTAAAGAA
*
2752469 AATTAAAATTAAAAGAA
1 AATTAAAATTTAAAGAA
2752486 AATT-AAATTTA
1 AATTAAAATTTA
2752497 TTATATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 19 0.76
17 6 0.24
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (17 bp):
AATTAAAATTTAAAGAA
Found at i:2756507 original size:24 final size:23
Alignment explanation
Indices: 2756479--2756531 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
2756469 AAGATTTTGA
* *
2756479 AATTTT-ATTTTTTTTATATTTAT
1 AATTTTAATATTTTTAAT-TTTAT
2756502 ACATTTTAATATTTTTAATTTTAT
1 A-ATTTTAATATTTTTAATTTTAT
2756526 AATTTT
1 AATTTT
2756532 CACTTTTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 6 0.23
24 11 0.42
25 9 0.35
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (23 bp):
AATTTTAATATTTTTAATTTTAT
Found at i:2756968 original size:32 final size:32
Alignment explanation
Indices: 2756908--2756970 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
2756898 CATGTGTCAT
* * * *
2756908 ATCATCACTTTGGATGATGTGACGTATGACAG
1 ATCATCACTTTAGAAGAGGTGACATATGACAG
*
2756940 ATCATCACTTTAGAAGAGGTGATATATGACA
1 ATCATCACTTTAGAAGAGGTGACATATGACA
2756971 CACAATCATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.30
Consensus pattern (32 bp):
ATCATCACTTTAGAAGAGGTGACATATGACAG
Found at i:2765191 original size:29 final size:29
Alignment explanation
Indices: 2765136--2765200 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
2765126 CTCAGGGTAC
* * *
2765136 CAATTTTTATATTTATAATTGGGGCCCTT
1 CAATTTTTATATTTATAATTAGAGCCCAT
2765165 CAATTTTTATATTTATAATTAGAGCCCAT
1 CAATTTTTATATTTATAATTAGAGCCCAT
2765194 -AATTTTT
1 CAATTTTT
2765201 CTAAATTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 7 0.21
29 26 0.79
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.49
Consensus pattern (29 bp):
CAATTTTTATATTTATAATTAGAGCCCAT
Found at i:2765368 original size:2 final size:2
Alignment explanation
Indices: 2765361--2765386 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2765351 ACAAGTGATG
2765361 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2765387 GATTACAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2768734 original size:30 final size:31
Alignment explanation
Indices: 2768668--2768730 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
2768658 GTAAGTTTTG
* *
2768668 AAAGTTTAATGGACAAAGTATATACTTTGTA
1 AAAGTTTAATGGACAAAGAATATAATTTGTA
2768699 AAAGTTTAA-GGACCAAA-AATATAATTT-TA
1 AAAGTTTAATGGA-CAAAGAATATAATTTGTA
2768728 AAA
1 AAA
2768731 AGTTATGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 5 0.17
30 11 0.38
31 13 0.45
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.32
Consensus pattern (31 bp):
AAAGTTTAATGGACAAAGAATATAATTTGTA
Found at i:2781292 original size:18 final size:19
Alignment explanation
Indices: 2781269--2781310 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2781259 AAAAGATATG
2781269 AAAAAAATG-GAAAACA-AA
1 AAAAAAATGTGAAAA-AGAA
2781287 AAAAAAATGTGAAAAAGAA
1 AAAAAAATGTGAAAAAGAA
2781306 AAAAA
1 AAAAA
2781311 TCAAATGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (19 bp):
AAAAAAATGTGAAAAAGAA
Found at i:2781293 original size:19 final size:19
Alignment explanation
Indices: 2781269--2781310 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
2781259 AAAAGATATG
*
2781269 AAAAAAATG-GAAAACAAA
1 AAAAAAATGTGAAAAGAAA
2781287 AAAAAAATGTGAAAAAGAAA
1 AAAAAAATGTG-AAAAGAAA
2781307 AAAA
1 AAAA
2781311 TCAAATGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 1 0.05
20 11 0.52
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (19 bp):
AAAAAAATGTGAAAAGAAA
Found at i:2786863 original size:11 final size:10
Alignment explanation
Indices: 2786847--2786871 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2786837 TTATAGGCAT
2786847 AAAAAAAAAC
1 AAAAAAAAAC
2786857 AAAAAAAAAC
1 AAAAAAAAAC
2786867 AAAAA
1 AAAAA
2786872 TATTATATTG
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:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:2790786 original size:131 final size:133
Alignment explanation
Indices: 2790626--2790886 Score: 327
Period size: 131 Copynumber: 2.0 Consensus size: 133
2790616 TTGTGCAACG
* * *
2790626 ATTATCGATCGATTTTTCTTAATGTATAACAGTGCATTATC-ACCATAAAAGGTGCCACTAGTGA
1 ATTATCGATCGATTTATCTTAATGCATAACAGTGCATTATCGA-CATAAAAGGTGCCACTAATGA
*
2790690 AA-ATTATCT-ATC-ATTTTGATT-AATGCACAACGGTACAATATCGACATAAAAGGTACCACTA
65 AAGATTAT-TGATCGATTTTG-TTAAATGCACAACGGTACAATATCGACATAAAAGGTACCACCA
2790751 ATGAAA
128 ATGAAA
* * *
2790757 ATTATCGATCGATTTCAT-TTAATGCATAACGGTTCATTATCGACATCAAAGGTGCCACTAATGA
1 ATTATCGATCGATTT-ATCTTAATGCATAACAGTGCATTATCGACATAAAAGGTGCCACTAATGA
* * * * * *
2790821 AAGATTATTGATCGATTTTGTTAAATGCATAACGGTGCATTATTGGCATAAAAGGTGCCACCAAT
65 AAGATTATTGATCGATTTTGTTAAATGCACAACGGTACAATATCGACATAAAAGGTACCACCAAT
2790886 G
130 G
2790887 GTATTCATAA
Statistics
Matches: 111, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
131 57 0.51
132 12 0.11
133 42 0.38
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (133 bp):
ATTATCGATCGATTTATCTTAATGCATAACAGTGCATTATCGACATAAAAGGTGCCACTAATGAA
AGATTATTGATCGATTTTGTTAAATGCACAACGGTACAATATCGACATAAAAGGTACCACCAATG
AAA
Found at i:2790808 original size:66 final size:65
Alignment explanation
Indices: 2790626--2790886 Score: 287
Period size: 66 Copynumber: 4.0 Consensus size: 65
2790616 TTGTGCAACG
* * * *
2790626 ATTATCGATCGATTTTTCTTAATGTATAACAGTGCATTATC-ACCATAAAAGGTGCCACTAGTGA
1 ATTATCGATCGATTTAT-TTAATGCATAACGGTGCATTATCGA-CATAAAAGGTGCCACTAATGA
2790690 AA
64 AA
* * * * *
2790692 ATTATCTATC-ATTT-TGATTAATGCACAACGGTACAATATCGACATAAAAGGTACCACTAATGA
1 ATTATCGATCGATTTAT--TTAATGCATAACGGTGCATTATCGACATAAAAGGTGCCACTAATGA
2790755 AA
64 AA
* *
2790757 ATTATCGATCGATTTCATTTAATGCATAACGGTTCATTATCGACATCAAAGGTGCCACTAATGAA
1 ATTATCGATCGATTT-ATTTAATGCATAACGGTGCATTATCGACATAAAAGGTGCCACTAATGAA
2790822 A
65 A
* * * *
2790823 GATTATTGATCGATTT-TGTTAAATGCATAACGGTGCATTATTGGCATAAAAGGTGCCACCAATG
1 -ATTATCGATCGATTTAT-TT-AATGCATAACGGTGCATTATCGACATAAAAGGTGCCACTAATG
2790887 GTATTCATAA
Statistics
Matches: 166, Mismatches: 21, Indels: 15
0.82 0.10 0.07
Matches are distributed among these distances:
64 1 0.01
65 53 0.32
66 59 0.36
67 52 0.31
68 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (65 bp):
ATTATCGATCGATTTATTTAATGCATAACGGTGCATTATCGACATAAAAGGTGCCACTAATGAAA
Found at i:2794065 original size:133 final size:133
Alignment explanation
Indices: 2793894--2794151 Score: 412
Period size: 133 Copynumber: 1.9 Consensus size: 133
2793884 TTGTGCAATG
2793894 ATTATCGATCGATTTTGATTAATGCATAACAGTGCATTATCGGCATAAAAGGTACCAATAATGAA
1 ATTATCGATCGATTTTGATTAATGCATAACAGTGCATTATCGGCATAAAAGGTACCAATAATGAA
2793959 A-ATTATCGAATCAATTTTGATT-AATGCATAACGGTGCATCATTGACATAAAAGGTGCCACAAA
66 AGATTATCG-ATCAATTTTG-TTAAATGCATAACGGTGCATCATTGACATAAAAGGTGCCACAAA
2794022 TAAAA
129 TAAAA
* * * * *
2794027 ATTATCGATTGATTTTGATTAATGCATAACGGTGCATTATCGGCATAAGAGGTGCCACTAATGAA
1 ATTATCGATCGATTTTGATTAATGCATAACAGTGCATTATCGGCATAAAAGGTACCAATAATGAA
* * *
2794092 AGATTATCGATCGATTTTGTTAAATGCATAACGGTGCATTATTGGCATAAAAGGTGCCAC
66 AGATTATCGATCAATTTTGTTAAATGCATAACGGTGCATCATTGACATAAAAGGTGCCAC
2794152 TCATGGTATT
Statistics
Matches: 115, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
132 2 0.02
133 106 0.92
134 7 0.06
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (133 bp):
ATTATCGATCGATTTTGATTAATGCATAACAGTGCATTATCGGCATAAAAGGTACCAATAATGAA
AGATTATCGATCAATTTTGTTAAATGCATAACGGTGCATCATTGACATAAAAGGTGCCACAAATA
AAA
Found at i:2794151 original size:67 final size:67
Alignment explanation
Indices: 2793893--2794152 Score: 373
Period size: 67 Copynumber: 3.9 Consensus size: 67
2793883 GTTGTGCAAT
* * *
2793893 GATTATCGATCGATTTTGATTAATGCATAACAGTGCATTATCGGCATAAAAGGTACCAATAATGA
1 GATTATCGATCGATTTTGATTAATGCATAACGGTGCATTATCGGCATAAAAGGTGCCACTAATGA
2793958 AA
66 AA
* * * * *
2793960 -ATTATCGAATCAATTTTGATTAATGCATAACGGTGCATCATTGACATAAAAGGTGCCACAAAT-
1 GATTATCG-ATCGATTTTGATTAATGCATAACGGTGCATTATCGGCATAAAAGGTGCCACTAATG
2794023 AAA
65 AAA
* * *
2794026 AATTATCGATTGATTTTGATTAATGCATAACGGTGCATTATCGGCATAAGAGGTGCCACTAATGA
1 GATTATCGATCGATTTTGATTAATGCATAACGGTGCATTATCGGCATAAAAGGTGCCACTAATGA
2794091 AA
66 AA
*
2794093 GATTATCGATCGATTTTG-TTAAATGCATAACGGTGCATTATTGGCATAAAAGGTGCCACT
1 GATTATCGATCGATTTTGATT-AATGCATAACGGTGCATTATCGGCATAAAAGGTGCCACT
2794153 CATGGTATTC
Statistics
Matches: 170, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
66 60 0.35
67 110 0.65
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (67 bp):
GATTATCGATCGATTTTGATTAATGCATAACGGTGCATTATCGGCATAAAAGGTGCCACTAATGA
AA
Found at i:2797326 original size:132 final size:133
Alignment explanation
Indices: 2797154--2797411 Score: 351
Period size: 132 Copynumber: 1.9 Consensus size: 133
2797144 TTGTGCAATG
* *
2797154 ATTATCGATCGATTTTGATTAATGCATAATAGTGCGTTATCAGCAAAAAAGGTGCCACTAAT-AA
1 ATTATCGATCGATTTTGATTAATGCATAATAGTGCATTATCAACAAAAAAGGTGCCACTAATGAA
* * * * * *
2797218 AAATTATCGATCGATTTT-TATTAATGCATAATGGTGCATTATCGGCATAAATGGTGCCACTAAT
66 AAATTATCGATCAATTTTGT-TCAATGCATAACGATGCATTATCGGCATAAAAGGTGACACTAAT
2797282 GAAA
130 GAAA
* * *
2797286 ATTATCGATCGATTTTGATTAATGCATAAT-GATGCATTATCAATATAAGAGGTGCCACTAATGA
1 ATTATCGATCGATTTTGATTAATGCATAATAG-TGCATTATCAACAAAAAAGGTGCCACTAATGA
* * *
2797350 AATATTATCGATTAATTTTGTTCAATGCATAACGATGCATTATTGGCATAAAAGGTGACACT
65 AAAATTATCGATCAATTTTGTTCAATGCATAACGATGCATTATCGGCATAAAAGGTGACACT
2797412 CATGGTATTT
Statistics
Matches: 109, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
131 1 0.01
132 55 0.50
133 52 0.48
134 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (133 bp):
ATTATCGATCGATTTTGATTAATGCATAATAGTGCATTATCAACAAAAAAGGTGCCACTAATGAA
AAATTATCGATCAATTTTGTTCAATGCATAACGATGCATTATCGGCATAAAAGGTGACACTAATG
AAA
Found at i:2797406 original size:67 final size:65
Alignment explanation
Indices: 2797154--2797411 Score: 311
Period size: 66 Copynumber: 3.9 Consensus size: 65
2797144 TTGTGCAATG
* * * *
2797154 ATTATCGATCGATTTTGATTAATGCATAAT-AGTGCGTTATCAGCAAAAAAGGTGCCACTAATAA
1 ATTATCGATCGATTTTG-TTAATGCATAATGA-TGCATTATCGGCATAAAAGGTGCCACTAATGA
2797218 AA
64 AA
* * *
2797220 ATTATCGATCGATTTTTATTAATGCATAATGGTGCATTATCGGCATAAATGGTGCCACTAATGAA
1 ATTATCGATCGA-TTTTGTTAATGCATAATGATGCATTATCGGCATAAAAGGTGCCACTAATGAA
2797285 A
65 A
*** *
2797286 ATTATCGATCGATTTTGATTAATGCATAATGATGCATTATCAATATAAGAGGTGCCACTAATGAA
1 ATTATCGATCGATTTTG-TTAATGCATAATGATGCATTATCGGCATAAAAGGTGCCACTAATGAA
2797351 A
65 A
** * * *
2797352 TATTATCGATTAATTTTGTTCAATGCATAACGATGCATTATTGGCATAAAAGGTGACACT
1 -ATTATCGATCGATTTTGTT-AATGCATAATGATGCATTATCGGCATAAAAGGTGCCACT
2797412 CATGGTATTT
Statistics
Matches: 164, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
65 4 0.02
66 109 0.66
67 51 0.31
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (65 bp):
ATTATCGATCGATTTTGTTAATGCATAATGATGCATTATCGGCATAAAAGGTGCCACTAATGAAA
Found at i:2799036 original size:27 final size:27
Alignment explanation
Indices: 2798983--2799059 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
2798973 AGGATAAAGA
*
2798983 TAAAAGAAATTTATT---TCTTTT-TT
1 TAAAAGAGATTTATTACCTCTTTTATT
2799006 TAAAAGAGATTTATTACCTCTTTTATT
1 TAAAAGAGATTTATTACCTCTTTTATT
2799033 TAAAAGAGATTTATTAGCC-CTTTTATT
1 TAAAAGAGATTTATTA-CCTCTTTTATT
2799060 GGAATTAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
23 14 0.29
26 6 0.12
27 26 0.54
28 2 0.04
ACGTcount: A:0.34, C:0.09, G:0.08, T:0.49
Consensus pattern (27 bp):
TAAAAGAGATTTATTACCTCTTTTATT
Found at i:2800064 original size:12 final size:11
Alignment explanation
Indices: 2800038--2800073 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
2800028 ATTAGTATGA
*
2800038 TTTTTCTTATT
1 TTTTTCTTTTT
2800049 TTTTTCTTTTT
1 TTTTTCTTTTT
2800060 GTTTTTCTTTTT
1 -TTTTTCTTTTT
2800072 TT
1 TT
2800074 CAAATTCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.03, C:0.08, G:0.03, T:0.86
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:2803594 original size:48 final size:48
Alignment explanation
Indices: 2803515--2803630 Score: 108
Period size: 48 Copynumber: 2.4 Consensus size: 48
2803505 AAAAAATACA
*** *
2803515 TTGCTAGAGGTGCTTGAAACCGACTAAAGTTGTGATACATTAAA-GAAT
1 TTGCTAGAGGTGCCCAAAACCGACTAAAGTTGTGACACATTAAATG-AT
* ** * *
2803563 TTGCTAGAGGTGCCCAAAACCGTCTCTAGTTGTTACATATTAAATGAT
1 TTGCTAGAGGTGCCCAAAACCGACTAAAGTTGTGACACATTAAATGAT
** *
2803611 TCCCTAGAGATGCCCAAAAC
1 TTGCTAGAGGTGCCCAAAAC
2803631 TGGTTATAGT
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
48 54 0.98
49 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (48 bp):
TTGCTAGAGGTGCCCAAAACCGACTAAAGTTGTGACACATTAAATGAT
Found at i:2804280 original size:27 final size:27
Alignment explanation
Indices: 2804242--2804295 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
2804232 AGGATAAAGA
*
2804242 TAAAAGAGATTTATTACCAATTTTATT
1 TAAAAGAGATTTAATACCAATTTTATT
**
2804269 TAAAAGAGATTTAATACCTCTTTTATT
1 TAAAAGAGATTTAATACCAATTTTATT
2804296 GGAATTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.44
Consensus pattern (27 bp):
TAAAAGAGATTTAATACCAATTTTATT
Found at i:2804430 original size:17 final size:17
Alignment explanation
Indices: 2804408--2804443 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
2804398 AGGGAGCACA
2804408 TTCTTATTT-TTCTTTAT
1 TTCTTATTTATT-TTTAT
2804425 TTCTTATTTATTTTTAT
1 TTCTTATTTATTTTTAT
2804442 TT
1 TT
2804444 TCATGGGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (17 bp):
TTCTTATTTATTTTTAT
Found at i:2806492 original size:46 final size:47
Alignment explanation
Indices: 2806440--2806533 Score: 172
Period size: 46 Copynumber: 2.0 Consensus size: 47
2806430 CAATTTATCA
*
2806440 AATATTCTTTAATTTTTAGTTTTCTTCAATTATTGGTAAAA-AATAC
1 AATATTCTTTAATTTTTAGTTTTCTTCAATTAGTGGTAAAATAATAC
2806486 AATATTCTTTAATTTTTAGTTTTCTTCAATTAGTGGTAAAATAATAC
1 AATATTCTTTAATTTTTAGTTTTCTTCAATTAGTGGTAAAATAATAC
2806533 A
1 A
2806534 GTAAAATCAA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 40 0.87
47 6 0.13
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (47 bp):
AATATTCTTTAATTTTTAGTTTTCTTCAATTAGTGGTAAAATAATAC
Found at i:2808312 original size:23 final size:24
Alignment explanation
Indices: 2808253--2808314 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
2808243 CAAAAGATGT
*
2808253 AATAAATCGCTTTTAATAAAAGAA
1 AATAAATCCCTTTTAATAAAAGAA
* * *
2808277 AAAAAATCTCTTTTAATTAAAG-A
1 AATAAATCCCTTTTAATAAAAGAA
2808300 AATAAATCCCTTTTA
1 AATAAATCCCTTTTA
2808315 TCTTTATCCT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
23 14 0.42
24 19 0.58
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (24 bp):
AATAAATCCCTTTTAATAAAAGAA
Found at i:2809942 original size:19 final size:19
Alignment explanation
Indices: 2809920--2809977 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
2809910 ACTTAAAAAT
2809920 AAAAATACAAATAAATAAG
1 AAAAATACAAATAAATAAG
*
2809939 AAAAGA-ACAAATCCAA-AAG
1 AAAA-ATACAAAT-AAATAAG
* *
2809958 -AAAATAAAAATAACTAAG
1 AAAAATACAAATAAATAAG
2809976 AA
1 AA
2809978 GAGTAAATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
17 2 0.07
18 11 0.37
19 14 0.47
20 3 0.10
ACGTcount: A:0.72, C:0.09, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAAATACAAATAAATAAG
Found at i:2816028 original size:27 final size:27
Alignment explanation
Indices: 2815984--2816045 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
2815974 TTTTAATTCT
* *
2815984 AATAAAAGAGATATTAAATTTCTTTTA
1 AATAAAAGAGATAATAAATCTCTTTTA
*
2816011 AATAAAAGAGGTAATAAATCTCTTTTA
1 AATAAAAGAGATAATAAATCTCTTTTA
2816038 AA-AAAAGA
1 AATAAAAGA
2816046 AACAAATCCC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 6 0.19
27 26 0.81
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.32
Consensus pattern (27 bp):
AATAAAAGAGATAATAAATCTCTTTTA
Found at i:2816052 original size:23 final size:25
Alignment explanation
Indices: 2815984--2816060 Score: 68
Period size: 27 Copynumber: 3.0 Consensus size: 25
2815974 TTTTAATTCT
* *
2815984 AATAAAAGAGATATTAAATTTCTTTTA
1 AATAAAAGAGA-A-CAAATCTCTTTTA
*
2816011 AATAAAAGAGGTAATAAATCTCTTTTA
1 AATAAAAGA-G-AACAAATCTCTTTTA
*
2816038 AA-AAAAGA-AACAAATCCCTTTTA
1 AATAAAAGAGAACAAATCTCTTTTA
2816061 TCTTTATCCT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
23 13 0.29
26 6 0.13
27 23 0.51
28 2 0.04
29 1 0.02
ACGTcount: A:0.51, C:0.09, G:0.08, T:0.32
Consensus pattern (25 bp):
AATAAAAGAGAACAAATCTCTTTTA
Found at i:2821362 original size:138 final size:136
Alignment explanation
Indices: 2821113--2821462 Score: 382
Period size: 138 Copynumber: 2.5 Consensus size: 136
2821103 AAATTATTGA
* * * * * *
2821113 ATCGAACAATTAAAATGGAACCTCGGACATAAAGCGATGACCAAATTAAAAATTCACCTAAATTA
1 ATCGAATAATTAAAATGGAACCTCGGATA-AAAGCAAGGATCAAATTAAAAATTCTCCTAAATTA
* * * * **
2821178 AAGGGCTAAAGTGTAATTAATCTATAATAAAGGCTCTAATAATAATCCTAACCAATTTTAGCCAT
65 AAGGACTAAAGTGAAATTAATATAAAATAAAGGCTCTAATAATAATCCTAACCAATTTTAGAAAT
2821243 TTACCGG
130 TTACCGG
2821250 ATCGAATAATTAAAATGGAACCTCGTGTATAAAAGCAAGGATCAAATTAAAAATTCTCCTAAATT
1 ATCGAATAATTAAAATGGAACCTCG-G-ATAAAAGCAAGGATCAAATTAAAAATTCTCCTAAATT
* * *
2821315 AAAGGACTATAA-TGAAATTAATATAAAATGAAGGCTTTAATATTAATCCTAACCAATTTTAGAA
64 AAAGGACTA-AAGTGAAATTAATATAAAATAAAGGCTCTAATAATAATCCTAACCAATTTTAGAA
**
2821379 ATTTATTGG
128 ATTTACCGG
* * * * * * * **
2821388 ACCAAATAATTAAAATGAAATCTGGGGCATAAAAGCAAGG-TCCAATTAAAAGTT-TACGAAAAT
1 ATCGAATAATTAAAATGGAACCT-CGG-ATAAAAGCAAGGATCAAATTAAAAATTCT-CCTAAAT
2821451 TAAAGGACTAAA
63 TAAAGGACTAAA
2821463 TTAAGAGAAA
Statistics
Matches: 181, Mismatches: 27, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
136 3 0.02
137 51 0.28
138 122 0.67
139 5 0.03
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (136 bp):
ATCGAATAATTAAAATGGAACCTCGGATAAAAGCAAGGATCAAATTAAAAATTCTCCTAAATTAA
AGGACTAAAGTGAAATTAATATAAAATAAAGGCTCTAATAATAATCCTAACCAATTTTAGAAATT
TACCGG
Found at i:2826467 original size:25 final size:25
Alignment explanation
Indices: 2826439--2826486 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
2826429 TATGAACAAA
2826439 CCTTGGTTTGAATGATTAAATCAGC
1 CCTTGGTTTGAATGATTAAATCAGC
*
2826464 CCTTGGTTTGGATGATTAAATCA
1 CCTTGGTTTGAATGATTAAATCA
2826487 ACTTGAATGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.38
Consensus pattern (25 bp):
CCTTGGTTTGAATGATTAAATCAGC
Found at i:2826894 original size:17 final size:17
Alignment explanation
Indices: 2826872--2826943 Score: 76
Period size: 17 Copynumber: 4.2 Consensus size: 17
2826862 AATTAAGAGT
2826872 TAGTTT-ATTAAATGAAC
1 TAGTTTAATT-AATGAAC
* *
2826889 TAGTTTGATTAGTGAAC
1 TAGTTTAATTAATGAAC
2826906 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
*
2826923 TAACTTT-ATTCAATGAAC
1 T-AGTTTAATT-AATGAAC
2826941 TAG
1 TAG
2826944 ATGCATGAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
17 32 0.68
18 15 0.32
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:2827503 original size:241 final size:241
Alignment explanation
Indices: 2827080--2827561 Score: 964
Period size: 241 Copynumber: 2.0 Consensus size: 241
2827070 TGTCATGCAA
2827080 CTAATAAAATTCATGCAATGAATGATATCATATGATAAGCATATCCTAAGAGGTAAATACAAACA
1 CTAATAAAATTCATGCAATGAATGATATCATATGATAAGCATATCCTAAGAGGTAAATACAAACA
2827145 TATGATAAAATATAATCCATAAATGAGTAGGTATATGATGAAGTAAGGTAGAACTCCCTTTGAAT
66 TATGATAAAATATAATCCATAAATGAGTAGGTATATGATGAAGTAAGGTAGAACTCCCTTTGAAT
2827210 CAGCCTTGGTGAACTTCAATGATTTAATCAGATAAAGACAAAAGTTAGGGCTGATTGGGATAACA
131 CAGCCTTGGTGAACTTCAATGATTTAATCAGATAAAGACAAAAGTTAGGGCTGATTGGGATAACA
2827275 TCATTCCCCCTCTTTAATGCGATTTGTCCCCAAATCGATGCTTACT
196 TCATTCCCCCTCTTTAATGCGATTTGTCCCCAAATCGATGCTTACT
2827321 CTAATAAAATTCATGCAATGAATGATATCATATGATAAGCATATCCTAAGAGGTAAATACAAACA
1 CTAATAAAATTCATGCAATGAATGATATCATATGATAAGCATATCCTAAGAGGTAAATACAAACA
2827386 TATGATAAAATATAATCCATAAATGAGTAGGTATATGATGAAGTAAGGTAGAACTCCCTTTGAAT
66 TATGATAAAATATAATCCATAAATGAGTAGGTATATGATGAAGTAAGGTAGAACTCCCTTTGAAT
2827451 CAGCCTTGGTGAACTTCAATGATTTAATCAGATAAAGACAAAAGTTAGGGCTGATTGGGATAACA
131 CAGCCTTGGTGAACTTCAATGATTTAATCAGATAAAGACAAAAGTTAGGGCTGATTGGGATAACA
2827516 TCATTCCCCCTCTTTAATGCGATTTGTCCCCAAATCGATGCTTACT
196 TCATTCCCCCTCTTTAATGCGATTTGTCCCCAAATCGATGCTTACT
2827562 ACAAAAGGAA
Statistics
Matches: 241, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
241 241 1.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (241 bp):
CTAATAAAATTCATGCAATGAATGATATCATATGATAAGCATATCCTAAGAGGTAAATACAAACA
TATGATAAAATATAATCCATAAATGAGTAGGTATATGATGAAGTAAGGTAGAACTCCCTTTGAAT
CAGCCTTGGTGAACTTCAATGATTTAATCAGATAAAGACAAAAGTTAGGGCTGATTGGGATAACA
TCATTCCCCCTCTTTAATGCGATTTGTCCCCAAATCGATGCTTACT
Found at i:2828396 original size:19 final size:19
Alignment explanation
Indices: 2828345--2828396 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 19
2828335 AATGTGTTCA
2828345 TTTTC-ACTCTCAATTACC
1 TTTTCAACTCTCAATTACC
*
2828363 TTTTCAATGCTCTCAATGT-CT
1 TTTTCAA--CTCTCAAT-TACC
2828384 TTTTCAACTCTCA
1 TTTTCAACTCTCA
2828397 TTTCTTCTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.17
19 7 0.24
21 16 0.55
22 1 0.03
ACGTcount: A:0.21, C:0.29, G:0.04, T:0.46
Consensus pattern (19 bp):
TTTTCAACTCTCAATTACC
Found at i:2829278 original size:15 final size:14
Alignment explanation
Indices: 2829260--2829289 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2829250 TTTTTATCTA
2829260 TTTTTACTTTATTTT
1 TTTTTACTTT-TTTT
2829275 TTTTTACTTTTTTT
1 TTTTTACTTTTTTT
2829289 T
1 T
2829290 CAATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTACTTTTTTT
Found at i:2830410 original size:25 final size:25
Alignment explanation
Indices: 2830382--2830436 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
2830372 AGAATATGAA
2830382 CAGCCCTTGGTTTGAATGATTAAAT
1 CAGCCCTTGGTTTGAATGATTAAAT
*
2830407 CAGCCCTTGGTTTGGATGATTAAAT
1 CAGCCCTTGGTTTGAATGATTAAAT
2830432 CAGCC
1 CAGCC
2830437 TTGAATGGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (25 bp):
CAGCCCTTGGTTTGAATGATTAAAT
Found at i:2830841 original size:17 final size:17
Alignment explanation
Indices: 2830819--2830890 Score: 67
Period size: 17 Copynumber: 4.2 Consensus size: 17
2830809 ACTTAAGAGT
2830819 TAGTTT-ATTAAATGAAC
1 TAGTTTAATT-AATGAAC
* * *
2830836 TAGTTTGATGAGTGAAC
1 TAGTTTAATTAATGAAC
2830853 TAGTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
*
2830870 TAACTTT-ATTCAATGAAC
1 T-AGTTTAATT-AATGAAC
2830888 TAG
1 TAG
2830891 ATGCATGAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
17 31 0.69
18 14 0.31
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:2830919 original size:52 final size:52
Alignment explanation
Indices: 2830822--2830924 Score: 118
Period size: 52 Copynumber: 2.0 Consensus size: 52
2830812 TAAGAGTTAG
* * * *
2830822 TTTATTAAATGAACTAGTTTGATGAGTGAACTAGTTTAATTAATGAACTAAC
1 TTTATTAAATGAACTAGTATGATGAATGAACTAGCTTAATAAATGAACTAAC
* * * *
2830874 TTTATTCAATGAACTAG-ATGCATGAATGAAGTAGCTTACTAAATGATCTAA
1 TTTATTAAATGAACTAGTATG-ATGAATGAACTAGCTTAATAAATGAACTAA
2830925 ATATGCATAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
51 2 0.05
52 40 0.95
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.36
Consensus pattern (52 bp):
TTTATTAAATGAACTAGTATGATGAATGAACTAGCTTAATAAATGAACTAAC
Found at i:2838893 original size:16 final size:16
Alignment explanation
Indices: 2838874--2838942 Score: 51
Period size: 15 Copynumber: 4.7 Consensus size: 16
2838864 AAAAAGTGTA
2838874 GAAAATTAAATTGTTG
1 GAAAATTAAATTGTTG
**
2838890 GAAAA-TAAATACTT-
1 GAAAATTAAATTGTTG
* * *
2838904 -AAATTTATA-TG-TA
1 GAAAATTAAATTGTTG
2838917 GAAAATTAAATTGTTG
1 GAAAATTAAATTGTTG
2838933 GAAAA-TAAAT
1 GAAAATTAAAT
2838943 ACTTAAATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 11
0.66 0.15 0.19
Matches are distributed among these distances:
12 1 0.03
13 3 0.08
14 10 0.26
15 14 0.36
16 11 0.28
ACGTcount: A:0.51, C:0.01, G:0.13, T:0.35
Consensus pattern (16 bp):
GAAAATTAAATTGTTG
Found at i:2838918 original size:43 final size:43
Alignment explanation
Indices: 2838870--2838969 Score: 191
Period size: 43 Copynumber: 2.3 Consensus size: 43
2838860 AAAGAAAAAG
2838870 TGTAGAAAATTAAATTGTTGGAAAATAAATACTTAAATTTATA
1 TGTAGAAAATTAAATTGTTGGAAAATAAATACTTAAATTTATA
2838913 TGTAGAAAATTAAATTGTTGGAAAATAAATACTTAAATTTATA
1 TGTAGAAAATTAAATTGTTGGAAAATAAATACTTAAATTTATA
*
2838956 GGTAGAAAATTAAA
1 TGTAGAAAATTAAA
2838970 GATAAAATTA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.50, C:0.02, G:0.13, T:0.35
Consensus pattern (43 bp):
TGTAGAAAATTAAATTGTTGGAAAATAAATACTTAAATTTATA
Found at i:2838965 original size:23 final size:23
Alignment explanation
Indices: 2838896--2838965 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
2838886 GTTGGAAAAT
*
2838896 AAATACTTAAATTTATATGTAG-
1 AAATACTTAAATTTATAGGTAGA
* *
2838918 AAA-A-TTAAATTGT-T-GGAAAA
1 AAATACTTAAATT-TATAGGTAGA
2838938 TAAATACTTAAATTTATAGGTAGA
1 -AAATACTTAAATTTATAGGTAGA
2838962 AAAT
1 AAAT
2838966 TAAAGATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 13
0.67 0.09 0.24
Matches are distributed among these distances:
19 2 0.06
20 8 0.22
21 5 0.14
22 5 0.14
23 12 0.33
24 4 0.11
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.36
Consensus pattern (23 bp):
AAATACTTAAATTTATAGGTAGA
Found at i:2840195 original size:38 final size:38
Alignment explanation
Indices: 2840153--2840259 Score: 187
Period size: 38 Copynumber: 2.8 Consensus size: 38
2840143 AAGCTGCAAC
*
2840153 TTTCAACAATTTTCACTTGCACATTTGGTGCACCACAA
1 TTTCAACAATTTTCACTTGCATATTTGGTGCACCACAA
2840191 TTTCAACAATTTTCACTTGCATATTTGGTGCACCACAA
1 TTTCAACAATTTTCACTTGCATATTTGGTGCACCACAA
* *
2840229 TTTCAACAATTTCCACTTGCATATTCGGTGC
1 TTTCAACAATTTTCACTTGCATATTTGGTGC
2840260 CTACCTTGTT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 66 1.00
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.36
Consensus pattern (38 bp):
TTTCAACAATTTTCACTTGCATATTTGGTGCACCACAA
Found at i:2851867 original size:56 final size:52
Alignment explanation
Indices: 2851807--2851917 Score: 136
Period size: 53 Copynumber: 2.0 Consensus size: 52
2851797 ACGGATTTAA
2851807 ACTTTTAATATATTTT-CTTTAATTCTAAGGTTTTAATAAAGAATG-TTTTAATTTGG
1 ACTTTTAATATATTTTACTTT--TT-T-A-GTTTTAATAAAGAA-GATTTTAATTTGG
*
2851863 ACTTTTAATATATTTTAAGTTTTTTAGTTTTAATAAAGAAGATTTTAATTTGG
1 ACTTTTAATATATTTT-ACTTTTTTAGTTTTAATAAAGAAGATTTTAATTTGG
2851916 AC
1 AC
2851918 ATTATATTCT
Statistics
Matches: 51, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
52 1 0.02
53 27 0.53
54 1 0.02
55 1 0.02
56 18 0.35
58 3 0.06
ACGTcount: A:0.33, C:0.05, G:0.11, T:0.51
Consensus pattern (52 bp):
ACTTTTAATATATTTTACTTTTTTAGTTTTAATAAAGAAGATTTTAATTTGG
Found at i:2858633 original size:2 final size:2
Alignment explanation
Indices: 2858626--2858650 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2858616 ACTGGATTTA
2858626 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2858651 GGACTTTAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2879920 original size:59 final size:59
Alignment explanation
Indices: 2879838--2880077 Score: 264
Period size: 59 Copynumber: 4.1 Consensus size: 59
2879828 TATGCACCAA
* * * * *
2879838 AGTGATAACCTGAATATGACACATAAGTTCGTTCCCACCATCTGCACTAGGTATCCTTT
1 AGTGCTAACATGAATATGACACATAAGGTCGTACCCACCATCTGCACTAAGTATCCTTT
* * *
2879897 AGTGCTAACATGAATATGACACATAAGGTCGTGCCCACCATCTACACTAAATATCCTTT
1 AGTGCTAACATGAATATGACACATAAGGTCGTACCCACCATCTGCACTAAGTATCCTTT
* * * ** * * *
2879956 AGTTCTAACATTAATATGACACAAAACATCGAACCCACCATTTGTACTAAGTATCCTTT
1 AGTGCTAACATGAATATGACACATAAGGTCGTACCCACCATCTGCACTAAGTATCCTTT
* * *** * * *
2880015 TGTGCGAACCCAAATATAACACATAAGGTCATACCCACCATCTGCATTAAGTATCCTTT
1 AGTGCTAACATGAATATGACACATAAGGTCGTACCCACCATCTGCACTAAGTATCCTTT
2880074 AGTG
1 AGTG
2880078 TTGACCCGAA
Statistics
Matches: 147, Mismatches: 34, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
59 147 1.00
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.29
Consensus pattern (59 bp):
AGTGCTAACATGAATATGACACATAAGGTCGTACCCACCATCTGCACTAAGTATCCTTT
Found at i:2880741 original size:40 final size:40
Alignment explanation
Indices: 2880681--2880826 Score: 211
Period size: 40 Copynumber: 3.6 Consensus size: 40
2880671 ATTATAGTTC
* *
2880681 TACACATAAAGTCGTTCCCACCATATAAACCAAAGTGCAT
1 TACACATAAAGTCGTGCCCACCATATACACCAAAGTGCAT
* *
2880721 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGCAT
1 TACACATAAAGTCGTGCCCACCATATACACCAAAGTGCAT
* *
2880761 TACACATAAGGTCGTGCCCACCATATACACTAAAGTGCAT
1 TACACATAAAGTCGTGCCCACCATATACACCAAAGTGCAT
* * *
2880801 TACACAAAAATTTGTGCCCACCATAT
1 TACACATAAAGTCGTGCCCACCATAT
2880827 GCTCTTAGTG
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 96 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (40 bp):
TACACATAAAGTCGTGCCCACCATATACACCAAAGTGCAT
Found at i:2881180 original size:23 final size:24
Alignment explanation
Indices: 2881148--2881195 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
2881138 AGTCTTCATG
*
2881148 ATGATGTAT-AAACATCTATGTAC
1 ATGATATATAAAACATCTATGTAC
2881171 ATGATATATAAAACATCTATGTAC
1 ATGATATATAAAACATCTATGTAC
2881195 A
1 A
2881196 ATGTCATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.33
Consensus pattern (24 bp):
ATGATATATAAAACATCTATGTAC
Found at i:2881786 original size:30 final size:31
Alignment explanation
Indices: 2881728--2881798 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
2881718 ACAGCCATTT
* * * *
2881728 ATAACTTTACCAAAATTATCAAATTGGTCCC
1 ATAACTTTTCAAAAATTATAAAAATGGTCCC
*
2881759 TTAACTTTTCAAAAATTA-AAAAATGGTCCC
1 ATAACTTTTCAAAAATTATAAAAATGGTCCC
*
2881789 AAAACTTTTC
1 ATAACTTTTC
2881799 TAAGGCTTGT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
30 18 0.55
31 15 0.45
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.34
Consensus pattern (31 bp):
ATAACTTTTCAAAAATTATAAAAATGGTCCC
Found at i:2885772 original size:20 final size:20
Alignment explanation
Indices: 2885749--2885787 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2885739 TTATATGCTG
*
2885749 GAAATT-AATGTTTGGATGTT
1 GAAATTGAA-GTTAGGATGTT
2885769 GAAATTGAAGTTAGGATGT
1 GAAATTGAAGTTAGGATGT
2885788 AAAATTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.38
Consensus pattern (20 bp):
GAAATTGAAGTTAGGATGTT
Found at i:2889117 original size:2 final size:2
Alignment explanation
Indices: 2889110--2889154 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
2889100 AGGATGTTAC
2889110 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2889151 AT AT
1 AT AT
2889155 CGAATTGTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2889798 original size:60 final size:60
Alignment explanation
Indices: 2889721--2889867 Score: 170
Period size: 60 Copynumber: 2.5 Consensus size: 60
2889711 GAAAAGTTAT
* * * * * * *
2889721 AAAAGTTTATAGACTAATTTATAATTATTGTCATAATTTGAGGATGAAAATGAAATATTC
1 AAAAGTTTAGAGACTAATTTAGAATGATAGTCATAATTTAAAGATGAAAATGAAACATTC
* * * *
2889781 AAAAGTTT-GAAGACTAATTTAGAATGATAGTCATAGTTTAAAGATGAAATTGGAACATTT
1 AAAAGTTTAG-AGACTAATTTAGAATGATAGTCATAATTTAAAGATGAAAATGAAACATTC
*
2889841 AAAAATTTAGAGACTAATTTAGAATGA
1 AAAAGTTTAGAGACTAATTTAGAATGA
2889868 GTGACATATT
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
60 72 0.99
61 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.35
Consensus pattern (60 bp):
AAAAGTTTAGAGACTAATTTAGAATGATAGTCATAATTTAAAGATGAAAATGAAACATTC
Found at i:2891917 original size:39 final size:39
Alignment explanation
Indices: 2891874--2892021 Score: 156
Period size: 39 Copynumber: 3.8 Consensus size: 39
2891864 GGCTCCTCGG
* * *
2891874 CTTTGTGCTCAAGGTAAGTCCATACCACAGGCTCTTATA
1 CTTTGTGCACATGGTAAGTCCTTACCACAGGCTCTTATA
** *
2891913 CTTTGTGCACATGGTAAGTCCTTACTGCAGGCTCCTT-GA
1 CTTTGTGCACATGGTAAGTCCTTACCACAGGCT-CTTATA
* * * *
2891952 CTTTGTGCTCAGGGTAAGTCCTTA-CAGCAGGCTCATATG
1 CTTTGTGCACATGGTAAGTCCTTACCA-CAGGCTCTTATA
* *
2891991 CTTTGTTCACATGGTAAGTCCTTACCGCAGG
1 CTTTGTGCACATGGTAAGTCCTTACCACAGG
2892022 TCCTTATGTT
Statistics
Matches: 88, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
38 2 0.02
39 82 0.93
40 4 0.05
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (39 bp):
CTTTGTGCACATGGTAAGTCCTTACCACAGGCTCTTATA
Found at i:2891995 original size:78 final size:78
Alignment explanation
Indices: 2891857--2892026 Score: 236
Period size: 78 Copynumber: 2.2 Consensus size: 78
2891847 CTCGACTTTG
* * * *
2891857 TACCGTAGGCTCCTCGGCTTTGTGCTCAAGGTAAGTCCATACCACAGGCTCTTATACTTTGTGCA
1 TACCGCAGGCTCCTTGACTTTGTGCTCAAGGTAAGTCCATACCACAGGCTCATATACTTTGTGCA
2891922 CATGGTAAGTCCT
66 CATGGTAAGTCCT
* * * * *
2891935 TACTGCAGGCTCCTTGACTTTGTGCTCAGGGTAAGTCCTTA-CAGCAGGCTCATATGCTTTGTTC
1 TACCGCAGGCTCCTTGACTTTGTGCTCAAGGTAAGTCCATACCA-CAGGCTCATATACTTTGTGC
2891999 ACATGGTAAGTCCT
65 ACATGGTAAGTCCT
2892013 TACCGCAGG-TCCTT
1 TACCGCAGGCTCCTT
2892027 ATGTTGTGTG
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
77 7 0.09
78 74 0.91
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.32
Consensus pattern (78 bp):
TACCGCAGGCTCCTTGACTTTGTGCTCAAGGTAAGTCCATACCACAGGCTCATATACTTTGTGCA
CATGGTAAGTCCT
Found at i:2893829 original size:16 final size:16
Alignment explanation
Indices: 2893810--2893891 Score: 58
Period size: 16 Copynumber: 5.1 Consensus size: 16
2893800 GCATCCATGC
2893810 ATGTATATATATATGT
1 ATGTATATATATATGT
* *
2893826 ATGTGTGTATATATGT
1 ATGTATATATATATGT
* * * *
2893842 ATGCATGTATGA-AAGC
1 ATGTATATAT-ATATGT
* * *
2893858 ATGTATATATGTAAGC
1 ATGTATATATATATGT
*
2893874 ATGTATATATGTATGT
1 ATGTATATATATATGT
2893890 AT
1 AT
2893892 AAAAATATAC
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
16 52 0.98
17 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.20, T:0.43
Consensus pattern (16 bp):
ATGTATATATATATGT
Found at i:2893836 original size:20 final size:20
Alignment explanation
Indices: 2893811--2893849 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2893801 CATCCATGCA
*
2893811 TGTATATATATATGTATGTG
1 TGTATATATATATGCATGTG
*
2893831 TGTATATATGTATGCATGT
1 TGTATATATATATGCATGT
2893850 ATGAAAGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.49
Consensus pattern (20 bp):
TGTATATATATATGCATGTG
Found at i:2893852 original size:28 final size:28
Alignment explanation
Indices: 2893821--2893892 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
2893811 TGTATATATA
* *
2893821 TATGTATGTGTGTATATATGTATGCATG
1 TATGTATGTATGTATATATGTAAGCATG
* * *
2893849 TATGAAAGCATGTATATATGTAAGCATG
1 TATGTATGTATGTATATATGTAAGCATG
*
2893877 TATATATGTATGTATA
1 TATGTATGTATGTATA
2893893 AAAATATACT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (28 bp):
TATGTATGTATGTATATATGTAAGCATG
Found at i:2894110 original size:4 final size:4
Alignment explanation
Indices: 2894101--2894186 Score: 52
Period size: 4 Copynumber: 21.5 Consensus size: 4
2894091 TCGAACAAAT
* * * *
2894101 ATAC ATAC ATAC ATAAC ATAC ATAC AT-G ATAC ATGC ATTA- ATAA AT-T
1 ATAC ATAC ATAC AT-AC ATAC ATAC ATAC ATAC ATAC A-TAC ATAC ATAC
** * *
2894148 ATAC ATTT ATAC ATGC ATATC ATAC ATAC ATAG ATAC AT
1 ATAC ATAC ATAC ATAC ATA-C ATAC ATAC ATAC ATAC AT
2894187 TATACATCAT
Statistics
Matches: 62, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
3 6 0.10
4 47 0.76
5 9 0.15
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.31
Consensus pattern (4 bp):
ATAC
Found at i:2894121 original size:13 final size:13
Alignment explanation
Indices: 2894103--2894127 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2894093 GAACAAATAT
2894103 ACATACATACATA
1 ACATACATACATA
2894116 ACATACATACAT
1 ACATACATACAT
2894128 GATACATGCA
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:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (13 bp):
ACATACATACATA
Found at i:2898735 original size:20 final size:20
Alignment explanation
Indices: 2898712--2898761 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2898702 TTAGGAAAAT
2898712 TTTCGAAACTCTCG-AGATAG
1 TTTCGAAACTCTCGTAGA-AG
*
2898732 TTTCGAAACTCTTGTAGAAG
1 TTTCGAAACTCTCGTAGAAG
*
2898752 TTTCAAAACT
1 TTTCGAAACT
2898762 TCTGGTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 24 0.89
21 3 0.11
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (20 bp):
TTTCGAAACTCTCGTAGAAG
Found at i:2899544 original size:22 final size:22
Alignment explanation
Indices: 2899515--2899558 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2899505 AAAAATATTG
*
2899515 AGTGTTTTAAAATTAAT-TTTA
1 AGTGTTTTAAAATAAATGTTTA
*
2899536 AGTGCTTTTTAAATAAATGTTTA
1 AGTG-TTTTAAAATAAATGTTTA
2899559 TATTCCTGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 11 0.58
23 4 0.21
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.50
Consensus pattern (22 bp):
AGTGTTTTAAAATAAATGTTTA
Found at i:2899872 original size:16 final size:16
Alignment explanation
Indices: 2899851--2899900 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
2899841 TATATAATCT
2899851 AATTTATAATTTAATA
1 AATTTATAATTTAATA
*
2899867 AATTTAATAA-TCAATA
1 AATTT-ATAATTTAATA
* *
2899883 AATTAATCATTTAATA
1 AATTTATAATTTAATA
2899899 AA
1 AA
2899901 ATTAATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 3 0.11
16 21 0.75
17 4 0.14
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTTATAATTTAATA
Found at i:2901135 original size:81 final size:81
Alignment explanation
Indices: 2900993--2901145 Score: 243
Period size: 81 Copynumber: 1.9 Consensus size: 81
2900983 ATGAAAAACA
* * *
2900993 CATCAGATGCATGACGTTGCAGCTTTCAGGTTGGCCAAGGTTATAGATATTGACTTAAAGTTTAT
1 CATCAGATGAATGACGTTGCAGCTTTCAGGTTGACCAAGGTTATAGATATTGACCTAAAGTTTAT
2901058 AATAATTTCTTATATG
66 AATAATTTCTTATATG
* * * *
2901074 CATCAGATGAATGACTTTGCAGCTTTTAGGTTGACCAAGGTTATAGGTATTGACCTCAAGTTTAT
1 CATCAGATGAATGACGTTGCAGCTTTCAGGTTGACCAAGGTTATAGATATTGACCTAAAGTTTAT
2901139 AATAATT
66 AATAATT
2901146 ATATATATAT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 65 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.37
Consensus pattern (81 bp):
CATCAGATGAATGACGTTGCAGCTTTCAGGTTGACCAAGGTTATAGATATTGACCTAAAGTTTAT
AATAATTTCTTATATG
Found at i:2902202 original size:15 final size:15
Alignment explanation
Indices: 2902182--2902211 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2902172 CCCCCGATAA
2902182 AAATATCACATATAT
1 AAATATCACATATAT
2902197 AAATATCACATATAT
1 AAATATCACATATAT
2902212 GTAATATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATATCACATATAT
Found at i:2903655 original size:30 final size:27
Alignment explanation
Indices: 2903601--2903655 Score: 65
Period size: 30 Copynumber: 1.9 Consensus size: 27
2903591 AAACTAATAT
**
2903601 TATTTTATATATTTAATATTAATATAC
1 TATTTTATATATTTAATAAAAATATAC
2903628 TATTTTAGTATCATTTTAATAAAAATAT
1 TATTTTA-TAT-A-TTTAATAAAAATAT
2903656 TCATTAGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 7 0.30
28 3 0.13
29 1 0.04
30 12 0.52
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (27 bp):
TATTTTATATATTTAATAAAAATATAC
Found at i:2910311 original size:42 final size:42
Alignment explanation
Indices: 2910215--2910510 Score: 385
Period size: 42 Copynumber: 7.0 Consensus size: 42
2910205 CTGTACATCG
* * * * *
2910215 GTAAGGCTTAACCTGTGCACAAAGCAGAGGAGCCTAGGAAAACT
1 GTAAGGCTTACCCT-TGCACACAGCAAAGGAACCT-GGGAAACT
* * *
2910259 GTAAGTCTTACCCTTGCACATAGCAAAGGAACCTGGGAAATT
1 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAACT
*
2910301 GTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGAAACT
1 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAACT
* *
2910343 ATAAGGCTTACCCTTGCACACAGCAAAGGAAACTGGGAAACT
1 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAACT
* * *
2910385 GTAAGGCTTACCCTTGCACACATCAAAGGAACCTGAGAAAAT
1 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAACT
* * *
2910427 TTAAGGCTTACCCTTGCACGCAGCAAAGGAACCTGGGACACT
1 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAACT
* * * *
2910469 GTAAGGCTTATCCTTGGACACAGTAAAGAAACCTGGGAAACT
1 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAACT
2910511 TCCTCCAATC
Statistics
Matches: 220, Mismatches: 32, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
42 191 0.87
43 17 0.08
44 12 0.05
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (42 bp):
GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAACT
Found at i:2922502 original size:23 final size:24
Alignment explanation
Indices: 2922472--2922517 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
2922462 GTTGAGGATT
*
2922472 CTATGTGGTCTTTCGGGA-AAATC
1 CTATGTGGTCCTTCGGGACAAATC
2922495 CTATGTGGTCCTTCGGGACAAAT
1 CTATGTGGTCCTTCGGGACAAAT
2922518 ATGTGGCACT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (24 bp):
CTATGTGGTCCTTCGGGACAAATC
Found at i:2922522 original size:21 final size:21
Alignment explanation
Indices: 2922472--2922523 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
2922462 GTTGAGGATT
*
2922472 CTATGTGGTCTTTCGGGAAAA
1 CTATGTGGTCCTTCGGGAAAA
2922493 TCCTATGTGGTCCTTCGGGACAAA
1 --CTATGTGGTCCTTCGGGA-AAA
2922517 -TATGTGG
1 CTATGTGG
2922524 CACTTCAGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 7 0.26
23 17 0.63
24 3 0.11
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.33
Consensus pattern (21 bp):
CTATGTGGTCCTTCGGGAAAA
Found at i:2929670 original size:60 final size:61
Alignment explanation
Indices: 2929584--2929750 Score: 207
Period size: 60 Copynumber: 2.8 Consensus size: 61
2929574 ATATAGTTTG
* ** *
2929584 GGATG-AATTTGAAAAGTTCTAAAAGTTTTTAGACTAATTTAGAATGAAT-GTCATAATTTGA
1 GGATGAAATTAGAAAA-TTC-AAAAGTTTAAAGACTAATTTAGAATGAATAGTCATAATTTAA
* *
2929645 GGATGAAAATTA-AATATTCAAAAGTTTAAAGACTAATTTAGAAT-AATAGTCATAGTTTAA
1 GGATG-AAATTAGAAAATTCAAAAGTTTAAAGACTAATTTAGAATGAATAGTCATAATTTAA
* *
2929705 GGATGAAATTAGAAAATTTAAAAGTTTAGAGACTAATTTAGAATGA
1 GGATGAAATTAGAAAATTCAAAAGTTTAAAGACTAATTTAGAATGA
2929751 GTAATTTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
59 9 0.10
60 67 0.73
61 9 0.10
62 3 0.03
63 4 0.04
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.34
Consensus pattern (61 bp):
GGATGAAATTAGAAAATTCAAAAGTTTAAAGACTAATTTAGAATGAATAGTCATAATTTAA
Found at i:2929702 original size:31 final size:30
Alignment explanation
Indices: 2929664--2929748 Score: 84
Period size: 29 Copynumber: 2.8 Consensus size: 30
2929654 TTAAATATTC
2929664 AAAAGTTTAAAGACTAATTTAGAATAATAGT
1 AAAAGTTTAAAGACTAATTTAGAATAAT-GT
* * * * *
2929695 CATAGTTTAAGGA-TGAAATTAGAA-AATTT
1 AAAAGTTTAAAGACT-AATTTAGAATAATGT
*
2929724 AAAAGTTTAGAGACTAATTTAGAAT
1 AAAAGTTTAAAGACTAATTTAGAAT
2929749 GAGTAATTTC
Statistics
Matches: 41, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
29 18 0.44
30 5 0.12
31 18 0.44
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.33
Consensus pattern (30 bp):
AAAAGTTTAAAGACTAATTTAGAATAATGT
Found at i:2930746 original size:28 final size:28
Alignment explanation
Indices: 2930714--2930768 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
2930704 AAGATATTCA
*
2930714 CTCGAAAGTGCCTCGTAGATAAATTGCT
1 CTCGAAAGTGCCTCATAGATAAATTGCT
* *
2930742 CTCGATAGTGCCTCATAGATAATTTGC
1 CTCGAAAGTGCCTCATAGATAAATTGC
2930769 ACCATAGGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (28 bp):
CTCGAAAGTGCCTCATAGATAAATTGCT
Found at i:2931039 original size:61 final size:61
Alignment explanation
Indices: 2930974--2931123 Score: 160
Period size: 62 Copynumber: 2.4 Consensus size: 61
2930964 ATAAAGGTAC
*
2930974 ATTGGGCAGTTCAAACCTAAAATCATCCGT-AACCATGTAATAAA-GTATCATATAAAAATGA
1 ATTGGGCAGTTCAAACC-AAAATCATCCATAAACCATGTAATAAATG-ATCATATAAAAATGA
* * * * * *
2931035 ATTGGGCAATTCGTAAGCAAAATCATCCATAAACCATTTAATAAATGATTATATAAAAATGT
1 ATTGGGCAGTTC-AAACCAAAATCATCCATAAACCATGTAATAAATGATCATATAAAAATGA
** *
2931097 ATTGGATAGTTCATACCCAAAATCATC
1 ATTGGGCAGTTCA-AACCAAAATCATC
2931124 TTAATACCAT
Statistics
Matches: 72, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
61 22 0.31
62 49 0.68
63 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (61 bp):
ATTGGGCAGTTCAAACCAAAATCATCCATAAACCATGTAATAAATGATCATATAAAAATGA
Found at i:2933298 original size:4 final size:4
Alignment explanation
Indices: 2933289--2933377 Score: 51
Period size: 4 Copynumber: 23.2 Consensus size: 4
2933279 GCAAGCATCC
* * *
2933289 ATGT ATGT A--T ATAT ATGT ATG- -TGT GTGT ATGT GTGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * * * *
2933333 ATGC ATGT GTGT ACGT GTGT ACGT GTGT ATGT GTGT ACGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
2933378 CGTGTGTACG
Statistics
Matches: 61, Mismatches: 20, Indels: 8
0.69 0.22 0.09
Matches are distributed among these distances:
2 4 0.07
4 57 0.93
ACGTcount: A:0.20, C:0.04, G:0.30, T:0.45
Consensus pattern (4 bp):
ATGT
Found at i:2933335 original size:16 final size:16
Alignment explanation
Indices: 2933310--2933425 Score: 106
Period size: 16 Copynumber: 6.9 Consensus size: 16
2933300 TATATGTATG
*
2933310 TGTGTGTATGTGTGTA
1 TGTGTGTACGTGTGTA
*
2933326 TGTATGTATGCATGTGTGTA
1 TGTGTGTA--C--GTGTGTA
*
2933346 CGTGTGTACGTGTGTA
1 TGTGTGTACGTGTGTA
*
2933362 TGTGTGTACGTATGTA
1 TGTGTGTACGTGTGTA
*
2933378 CGTGTGTACGTGTGTA
1 TGTGTGTACGTGTGTA
* * *
2933394 CGTGTGAATGTGTGTA
1 TGTGTGTACGTGTGTA
2933410 CGTGTGTGTACGTGTG
1 --TGTGTGTACGTGTG
2933426 CATAAAAATA
Statistics
Matches: 81, Mismatches: 13, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
16 56 0.69
18 12 0.15
20 13 0.16
ACGTcount: A:0.15, C:0.08, G:0.36, T:0.41
Consensus pattern (16 bp):
TGTGTGTACGTGTGTA
Found at i:2933364 original size:24 final size:24
Alignment explanation
Indices: 2933337--2933425 Score: 124
Period size: 24 Copynumber: 3.6 Consensus size: 24
2933327 GTATGTATGC
2933337 ATGTGTGTACGTGTGTACGTGTGT
1 ATGTGTGTACGTGTGTACGTGTGT
*
2933361 ATGTGTGTACGTATGTACGTGTGT
1 ATGTGTGTACGTGTGTACGTGTGT
* * *
2933385 ACGTGTGTACGTGTGAATGTGTGT
1 ATGTGTGTACGTGTGTACGTGTGT
2933409 ACGTGTGTGTACGTGTG
1 A--TGTGTGTACGTGTG
2933426 CATAAAAATA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
24 44 0.77
26 13 0.23
ACGTcount: A:0.15, C:0.09, G:0.37, T:0.39
Consensus pattern (24 bp):
ATGTGTGTACGTGTGTACGTGTGT
Found at i:2933425 original size:8 final size:8
Alignment explanation
Indices: 2933339--2933416 Score: 120
Period size: 8 Copynumber: 9.8 Consensus size: 8
2933329 ATGTATGCAT
2933339 GTGTGTAC
1 GTGTGTAC
2933347 GTGTGTAC
1 GTGTGTAC
*
2933355 GTGTGTAT
1 GTGTGTAC
2933363 GTGTGTAC
1 GTGTGTAC
*
2933371 GTATGTAC
1 GTGTGTAC
2933379 GTGTGTAC
1 GTGTGTAC
2933387 GTGTGTAC
1 GTGTGTAC
* *
2933395 GTGTGAAT
1 GTGTGTAC
2933403 GTGTGTAC
1 GTGTGTAC
2933411 GTGTGT
1 GTGTGT
2933417 GTACGTGTGC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 62 1.00
ACGTcount: A:0.14, C:0.09, G:0.37, T:0.40
Consensus pattern (8 bp):
GTGTGTAC
Found at i:2941527 original size:49 final size:49
Alignment explanation
Indices: 2941434--2941527 Score: 116
Period size: 49 Copynumber: 1.9 Consensus size: 49
2941424 CTTCGAGACA
* * * * * *
2941434 CAAATCATTTTGAGATTTCGCTATCTAAGACTCTGTCATCTTTCACGTT
1 CAAATAATTCTGAGATTTCGCCACCTAAAACTCTATCATCTTTCACGTT
* *
2941483 CAAATAATTCTGAGATTTCGCCACCTAAAATTCTATCATGTTTCA
1 CAAATAATTCTGAGATTTCGCCACCTAAAACTCTATCATCTTTCA
2941528 TCTTCACCCA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
49 37 1.00
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (49 bp):
CAAATAATTCTGAGATTTCGCCACCTAAAACTCTATCATCTTTCACGTT
Found at i:2941845 original size:81 final size:81
Alignment explanation
Indices: 2941733--2941893 Score: 250
Period size: 81 Copynumber: 2.0 Consensus size: 81
2941723 ATGAAAAACA
* ** *
2941733 CATCAGATGCATGACGTTGCAGCTTTCAGGTTGGTCAAGGTTATAGATATTGACCTAAAGTTTAT
1 CATCAGATGAATGACGTTGCAGCTTTCAGGTTGACCAAGGTTATAGATATTGACCTAAAGGTTAT
2941798 AATAATTTCATATATG
66 AATAATTTCATATATG
* * * *
2941814 CATCAGATGAATGACTTTGCAGCTTTTAGGTTGACCAAGGTTATAGGTATTGACCTCAAGGTTAT
1 CATCAGATGAATGACGTTGCAGCTTTCAGGTTGACCAAGGTTATAGATATTGACCTAAAGGTTAT
2941879 AATAATTTCATATAT
66 AATAATTTCATATAT
2941894 ATATATATAT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 72 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (81 bp):
CATCAGATGAATGACGTTGCAGCTTTCAGGTTGACCAAGGTTATAGATATTGACCTAAAGGTTAT
AATAATTTCATATATG
Found at i:2944357 original size:12 final size:12
Alignment explanation
Indices: 2944317--2944400 Score: 54
Period size: 12 Copynumber: 7.2 Consensus size: 12
2944307 CCTCGAGAAA
*
2944317 AATAAAA-ATAA
1 AATAAAATATAT
2944328 AATAAAAT-TAATT
1 AATAAAATAT-A-T
2944341 AATAAAATATAT
1 AATAAAATATAT
*
2944353 AATAAAGAAATA-
1 AATAAA-ATATAT
2944365 AAT-AAATA-AT
1 AATAAAATATAT
2944375 AATAATAATA-AT
1 AATAA-AATATAT
* *
2944387 AATAGATTATAT
1 AATAAAATATAT
2944399 AA
1 AA
2944401 AAATATTTTC
Statistics
Matches: 59, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
9 1 0.02
10 5 0.08
11 14 0.24
12 25 0.42
13 13 0.22
14 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (12 bp):
AATAAAATATAT
Done.