Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001999.1 Hibiscus syriacus cultivar Beakdansim tig00004090_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: 232417
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 1 of 2
Found at i:3321 original size:27 final size:27
Alignment explanation
Indices: 3291--3354 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
3281 TGAAATCAGG
*
3291 TTCAGTTCAGGTTCGGATCGATTTAAT
1 TTCAGTTCAGGTTCGGATCGAGTTAAT
3318 TTCAGTTCAGGTTCGGATCGAGTTAAT
1 TTCAGTTCAGGTTCGGATCGAGTTAAT
3345 TTCAGTTCAG
1 TTCAGTTCAG
3355 ATCGATGTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.39
Consensus pattern (27 bp):
TTCAGTTCAGGTTCGGATCGAGTTAAT
Found at i:3357 original size:21 final size:23
Alignment explanation
Indices: 3323--3364 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
3313 TTAATTTCAG
*
3323 TTCAGGTTCGGATCGA-GTTAAT
1 TTCAGGTTCAGATCGATGTTAAT
3345 TTCA-GTTCAGATCGATGTTA
1 TTCAGGTTCAGATCGATGTTA
3365 GTTCATGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (23 bp):
TTCAGGTTCAGATCGATGTTAAT
Found at i:3364 original size:22 final size:22
Alignment explanation
Indices: 3296--3364 Score: 59
Period size: 27 Copynumber: 2.9 Consensus size: 22
3286 TCAGGTTCAG
*
3296 TTCAGGTTCGGATCGAT-TTAAT
1 TTCA-GTTCAGATCGATGTTAAT
*
3318 TTCAGTTCAGGTTCGGATCGAGTTAAT
1 TTCAGTTCA-GATC-GAT---GTTAAT
3345 TTCAGTTCAGATCGATGTTA
1 TTCAGTTCAGATCGATGTTA
3365 GTTCATGTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
21 4 0.11
22 11 0.29
23 3 0.08
25 3 0.08
26 3 0.08
27 14 0.37
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.39
Consensus pattern (22 bp):
TTCAGTTCAGATCGATGTTAAT
Found at i:3369 original size:21 final size:22
Alignment explanation
Indices: 3321--3369 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
3311 ATTTAATTTC
*
3321 AGTTCAGGTTCGGATCGAGTTA
1 AGTTCAGGTTCAGATCGAGTTA
*
3343 ATTTCA-GTTCAGATCGATGTT-
1 AGTTCAGGTTCAGATCGA-GTTA
3364 AGTTCA
1 AGTTCA
3370 TGTCAAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.37
Consensus pattern (22 bp):
AGTTCAGGTTCAGATCGAGTTA
Found at i:4397 original size:2 final size:2
Alignment explanation
Indices: 4390--4637 Score: 153
Period size: 2 Copynumber: 126.0 Consensus size: 2
4380 GGATACATAA
* * * *
4390 AT AT AT AT TT AT AT A- AGT AT AT AT AT AT AT AC GT AT A- AC AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* *
4431 AT AT GT AT AT AT AT AT A- AGT AT AT AT AT AT -T AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* * * *
4472 AGT -T AGT AC AT AC AT AC AT AT AT ACT A- AT GT AT AT -T AT AT
1 A-T AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
4512 AT AT AT AT AT AT AT AT AT AT AT AT A- AGT AT -T AT AT AGT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT
* * *
4554 AT AT A- AT AT AT A- AT AT AA AT AT AT GT AT AT A- AGT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * * * **
4594 GT AT GAT GT AT GT AT AC GC AT AT AT AT AT AT AT AT -T 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
4636 AT
1 AT
4638 CTAAGTGACT
Statistics
Matches: 189, Mismatches: 35, Indels: 44
0.71 0.13 0.16
Matches are distributed among these distances:
1 13 0.07
2 163 0.86
3 13 0.07
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4447 original size:27 final size:25
Alignment explanation
Indices: 4409--4576 Score: 109
Period size: 25 Copynumber: 6.7 Consensus size: 25
4399 TATATAAGTA
*
4409 TATATATATATACGTATAACATATAT
1 TATATATATATAAGTAT-ACATATAT
*
4435 GTATATATATATAAGTATATATATAT
1 -TATATATATATAAGTATACATATAT
* *
4461 TATTTATATAT-AGTTAGTACATACA-
1 TATATATATATAAG-TA-TACATATAT
* *
4486 TACATATATACTAATGTATA-TTATA-
1 TATATATATA-TAA-GTATACATATAT
*
4511 TATATATATATATA-TATATATATAT
1 TATATATATATA-AGTATACATATAT
* * *
4536 AAGTAT-TATAT-AGTATATATATAA
1 TA-TATATATATAAGTATACATATAT
*
4560 TATATA-ATATAAATATA
1 TATATATATATAAGTATA
4577 TGTATATAAG
Statistics
Matches: 114, Mismatches: 15, Indels: 27
0.73 0.10 0.17
Matches are distributed among these distances:
23 12 0.11
24 24 0.21
25 39 0.34
26 19 0.17
27 19 0.17
28 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.45
Consensus pattern (25 bp):
TATATATATATAAGTATACATATAT
Found at i:4570 original size:77 final size:73
Alignment explanation
Indices: 4436--4583 Score: 158
Period size: 73 Copynumber: 2.0 Consensus size: 73
4426 AACATATATG
** * *
4436 TATATATATATAAGTATATATATATTATTTATATATAGTTAGTACATACATACATATATACTA-A
1 TATATATATATAAGTATATATATATTAAGTATATATAGTTAGTACATACATAAATATA-AATATA
4500 TGTATATTA
65 TGTATATTA
* *
4509 TATATATATATATA-TATATATATATATAAGTATTATATAGTATA-TATATAATATATAATATAA
1 TATATATATATA-AGTATATATATAT-TAAGTA-TATATAGT-TAGTACAT-ACATA-AATATAA
4572 ATATATGTATAT
60 ATATATGTATAT
4584 AAGTAAATAT
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
73 23 0.37
74 5 0.08
75 12 0.19
76 9 0.15
77 13 0.21
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.46
Consensus pattern (73 bp):
TATATATATATAAGTATATATATATTAAGTATATATAGTTAGTACATACATAAATATAAATATAT
GTATATTA
Found at i:5194 original size:18 final size:19
Alignment explanation
Indices: 5169--5211 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
5159 ATATATTTTA
5169 AAAT-TTTAAATTAT-ATT
1 AAATATTTAAATTATAATT
5186 AAATATTTAAATTATAATT
1 AAATATTTAAATTATAATT
*
5205 AATTATT
1 AAATATT
5212 ACATAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.17
18 10 0.43
19 9 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATATTTAAATTATAATT
Found at i:6737 original size:21 final size:21
Alignment explanation
Indices: 6696--6737 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
6686 AAAATATTAG
* *
6696 GTTCGGATCGAGTTAATTTCA
1 GTTCAGATCGAGTTAAGTTCA
6717 GTTCAGATCGACGTT-AGTTCA
1 GTTCAGATCGA-GTTAAGTTCA
6738 TGTCAAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (21 bp):
GTTCAGATCGAGTTAAGTTCA
Found at i:7793 original size:14 final size:13
Alignment explanation
Indices: 7760--7841 Score: 51
Period size: 13 Copynumber: 6.1 Consensus size: 13
7750 TTATGCATAC
7760 AATATAAATATAT
1 AATATAAATATAT
*
7773 ATTTATAAATTATAT
1 A-ATATAAA-TATAT
*
7788 AATATAAGTATAT
1 AATATAAATATAT
*
7801 -GTATAACATATAT
1 AATATAA-ATATAT
*
7814 GTATATATAATATA-
1 -AATATA-AATATAT
* *
7828 AGTATATATATAT
1 AATATAAATATAT
7841 A
1 A
7842 CTTTTATATA
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
12 10 0.19
13 16 0.30
14 11 0.21
15 15 0.28
16 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.43
Consensus pattern (13 bp):
AATATAAATATAT
Found at i:7805 original size:17 final size:16
Alignment explanation
Indices: 7785--7839 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 16
7775 TTATAAATTA
7785 TATAATATAAGTATAT
1 TATAATATAAGTATAT
*
7801 GTATAACATATATGTATA-
1 -TAT-A-ATATAAGTATAT
7819 TATAATATAAGTATAT
1 TATAATATAAGTATAT
7835 ATATA
1 -TATA
7840 TACTTTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 10 0.31
16 1 0.03
17 10 0.31
18 1 0.03
19 10 0.31
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (16 bp):
TATAATATAAGTATAT
Found at i:7811 original size:19 final size:17
Alignment explanation
Indices: 7781--7839 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 17
7771 ATATTTATAA
7781 ATTATATAATATAAGTAT
1 ATTATA-AATATAAGTAT
*
7799 ATGTATAACATATATGTAT
1 AT-TATAA-ATATAAGTAT
7818 A-TAT-AATATAAGTAT
1 ATTATAAATATAAGTAT
7833 ATATATA
1 AT-TATA
7840 TACTTTTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
15 10 0.29
16 1 0.03
17 6 0.18
18 3 0.09
19 14 0.41
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (17 bp):
ATTATAAATATAAGTAT
Found at i:7893 original size:15 final size:14
Alignment explanation
Indices: 7875--7955 Score: 57
Period size: 13 Copynumber: 5.9 Consensus size: 14
7865 TACATCATAC
7875 ATATATACTAAGTAT
1 ATATATA-TAAGTAT
7890 ATAT-TAT-A-TAT
1 ATATATATAAGTAT
7901 ATATATAT-A-TAT
1 ATATATATAAGTAT
*
7913 ATAAAAGTATAAAGTAT
1 AT-ATA-TAT-AAGTAT
*
7930 ATATATAT-AGCAT
1 ATATATATAAGTAT
*
7943 ATGTATATAAGTA
1 ATATATATAAGTA
7956 AATGTGTATG
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
11 7 0.13
12 10 0.19
13 14 0.26
14 8 0.15
15 7 0.13
16 3 0.06
17 5 0.09
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.41
Consensus pattern (14 bp):
ATATATATAAGTAT
Found at i:7904 original size:26 final size:25
Alignment explanation
Indices: 7767--7909 Score: 73
Period size: 23 Copynumber: 5.6 Consensus size: 25
7757 TACAATATAA
* * *
7767 ATATATATTTATA-AATTATATAAT
1 ATATATATATATATAAGTATATATT
* *
7791 ATA-AGTATATGTATAA-CATATA-T
1 ATATA-TATATATATAAGTATATATT
*
7814 GTATATATA-ATATAAGTATATA-T
1 ATATATATATATATAAGTATATATT
* * *
7837 ATATACTTTTATATATATAGTTAGTACATAC
1 ATATA--TATATATATA-AG-TA-TATAT-T
*
7868 ATCATACATATATACTAAGTATATATT
1 AT-ATATATATATA-TAAGTATATATT
7895 ATATATATATATATA
1 ATATATATATATATA
7910 TATATAAAAG
Statistics
Matches: 90, Mismatches: 15, Indels: 27
0.68 0.11 0.20
Matches are distributed among these distances:
22 5 0.06
23 18 0.20
24 15 0.17
25 7 0.08
26 15 0.17
27 4 0.04
28 6 0.07
29 5 0.06
30 8 0.09
31 4 0.04
32 3 0.03
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (25 bp):
ATATATATATATATAAGTATATATT
Found at i:7951 original size:2 final size:2
Alignment explanation
Indices: 7761--7938 Score: 81
Period size: 2 Copynumber: 89.5 Consensus size: 2
7751 TATGCATACA
* * *
7761 AT AT AA AT AT AT AT TT AT AA AT -T AT AT A- AT AT A- AGT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * *
7801 GT AT A- AC AT AT AT GT AT AT AT A- AT AT A- AGT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* * * *
7841 ACT -T TT AT AT AT AT AGT -T AGT AC AT AC AT CAT AC AT AT AT ACT
1 A-T AT AT AT AT AT AT A-T AT A-T AT AT AT AT -AT AT AT AT AT A-T
* *
7884 A- AGT AT AT AT -T AT AT AT AT AT AT AT AT AT AT A- AA AGT AT AA
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
7925 AGT AT AT AT AT AT A
1 A-T AT AT AT AT AT A
7939 GCATATGTAT
Statistics
Matches: 134, Mismatches: 21, Indels: 42
0.68 0.11 0.21
Matches are distributed among these distances:
1 11 0.08
2 110 0.82
3 13 0.10
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (2 bp):
AT
Found at i:7993 original size:2 final size:2
Alignment explanation
Indices: 7983--8016 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
7973 TACACACGCC
7983 AT AT A- AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8017 GTGACTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:8005 original size:17 final size:17
Alignment explanation
Indices: 7983--8016 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
7973 TACACACGCC
7983 ATATAATATATATATAT
1 ATATAATATATATATAT
8000 ATATAATATATATATAT
1 ATATAATATATATATAT
8017 GTGACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATAATATATATATAT
Found at i:8292 original size:21 final size:21
Alignment explanation
Indices: 8263--8317 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
8253 ATTTTGACTA
8263 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
8284 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
8305 TCGCAATGCGATT
1 TCGCATTGCGATT
8318 ACGTAAATCG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:8330 original size:20 final size:20
Alignment explanation
Indices: 8305--8448 Score: 186
Period size: 20 Copynumber: 7.3 Consensus size: 20
8295 TTTTCCTAAT
8305 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
* * ** *
8325 TCGCAACGCAATTTGGAAAA
1 TCGCAATGCGATTACGTAAA
8345 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
8365 TCGCAATGCGA-TACGTAAA
1 TCGCAATGCGATTACGTAAA
*
8384 TCGCAATGC-AATACGTAAA
1 TCGCAATGCGATTACGTAAA
*
8403 TCGCAATGCAATTACGTAAA
1 TCGCAATGCGATTACGTAAA
*
8423 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGATTAC-GTAAA
8443 TCGCAA
1 TCGCAA
8449 CGAGATTCTG
Statistics
Matches: 108, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
18 1 0.01
19 35 0.32
20 72 0.67
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGATTACGTAAA
Found at i:9331 original size:24 final size:23
Alignment explanation
Indices: 9303--9356 Score: 90
Period size: 24 Copynumber: 2.3 Consensus size: 23
9293 AGTATTCGAA
9303 ATTTGATCTTGGTCAATACCCGG
1 ATTTGATCTTGGTCAATACCCGG
*
9326 ACTTTGATCTTGGTCAATACTCGG
1 A-TTTGATCTTGGTCAATACCCGG
9350 ATTTGAT
1 ATTTGAT
9357 GATTTTTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 7 0.24
24 22 0.76
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (23 bp):
ATTTGATCTTGGTCAATACCCGG
Found at i:11794 original size:20 final size:20
Alignment explanation
Indices: 11769--11862 Score: 127
Period size: 20 Copynumber: 4.7 Consensus size: 20
11759 GACATTCATT
*
11769 TGACTATCGCAATGC-GAATA
1 TGACTATCGCAACGCGGAA-A
*
11789 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* * *
11809 TGACTATCGTAATGCGGAAT
1 TGACTATCGCAACGCGGAAA
11829 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
11849 TGACTATCGCAACG
1 TGACTATCGCAACG
11863 AGAGAATCGC
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 61 0.95
21 3 0.05
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.21
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:11824 original size:40 final size:40
Alignment explanation
Indices: 11769--11860 Score: 150
Period size: 40 Copynumber: 2.3 Consensus size: 40
11759 GACATTCATT
11769 TGACTATCGCAATGC-GAATATGACTATCGCAACACGGAAA
1 TGACTATCGCAATGCGGAAT-TGACTATCGCAACACGGAAA
* *
11809 TGACTATCGTAATGCGGAATTGACTATCGCAACGCGGAAA
1 TGACTATCGCAATGCGGAATTGACTATCGCAACACGGAAA
11849 TGACTATCGCAA
1 TGACTATCGCAA
11861 CGAGAGAATC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
40 44 0.92
41 4 0.08
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (40 bp):
TGACTATCGCAATGCGGAATTGACTATCGCAACACGGAAA
Found at i:11891 original size:19 final size:19
Alignment explanation
Indices: 11867--11946 Score: 80
Period size: 19 Copynumber: 4.4 Consensus size: 19
11857 GCAACGAGAG
*
11867 AATCGCAATGCGAAATGAA
1 AATCGCAATGCAAAATGAA
*
11886 AATCGCAATCCAAAATGAA
1 AATCGCAATGCAAAATGAA
*
11905 AATCGCAATG---AGTG--
1 AATCGCAATGCAAAATGAA
*
11919 AATCGCAATACAAAAATGAA
1 AATCGCAATGC-AAAATGAA
11939 AATCGCAA
1 AATCGCAA
11947 CGCGAAATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
14 9 0.18
16 3 0.06
18 3 0.06
19 26 0.53
20 8 0.16
ACGTcount: A:0.50, C:0.17, G:0.16, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCAAAATGAA
Found at i:12059 original size:20 final size:20
Alignment explanation
Indices: 12008--12048 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
11998 GTTGCCATTT
12008 TCATTT-CGCATTGCGATAG
1 TCATTTCCGCATTGCGATAG
12027 TCATTTCCGCATTGCGATAG
1 TCATTTCCGCATTGCGATAG
12047 TC
1 TC
12049 TGTTTTGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.37
Consensus pattern (20 bp):
TCATTTCCGCATTGCGATAG
Found at i:12117 original size:31 final size:31
Alignment explanation
Indices: 12082--12154 Score: 73
Period size: 31 Copynumber: 2.4 Consensus size: 31
12072 GATTGAAATC
*
12082 AACAAATCAACTATTACAT-TTCA-ATCAATTA
1 AACAAATCAACTATT--ATGTACACATCAATTA
12113 AACAAGCA-CAA-TATTATGTACACATCAATTA
1 AACAA--ATCAACTATTATGTACACATCAATTA
12144 AACAAATCAAC
1 AACAAATCAAC
12155 ATTTACAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
29 3 0.09
30 6 0.17
31 22 0.63
32 3 0.09
33 1 0.03
ACGTcount: A:0.51, C:0.21, G:0.03, T:0.26
Consensus pattern (31 bp):
AACAAATCAACTATTATGTACACATCAATTA
Found at i:12172 original size:13 final size:14
Alignment explanation
Indices: 12145--12180 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
12135 CATCAATTAA
12145 ACAAATCAACATTT
1 ACAAATCAACATTT
*
12159 ACAAATCATC-TTT
1 ACAAATCAACATTT
12172 ACAAATCAA
1 ACAAATCAA
12181 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:13597 original size:42 final size:42
Alignment explanation
Indices: 13533--13643 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 42
13523 CTAGAATGTT
* * *
13533 GGGAGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGGT-G
1 GGGA-GGA-CTCTTGAACGATGACAGGGGCCTCTTGAACGATAG
** * *
13576 GGAGAGGACTCTTGAGGGATGATAGGGGCCTCTTGAATGATAG
1 GG-GAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATAG
13619 GGGAGGACTCTTGAACGATGACAGG
1 GGGAGGACTCTTGAACGATGACAGG
13644 TGAGTCAGGC
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
42 46 0.82
43 8 0.14
44 2 0.04
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (42 bp):
GGGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATAG
Found at i:14160 original size:20 final size:21
Alignment explanation
Indices: 14123--14172 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
14113 GAAACTTAAA
14123 ATCGCAACGCAAAAAATGACT
1 ATCGCAACGCAAAAAATGACT
*
14144 ATCGCAACGC-GAAAATGACT
1 ATCGCAACGCAAAAAATGACT
14164 ATCGCAACG
1 ATCGCAACG
14173 AGAGAATCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.42, C:0.26, G:0.18, T:0.14
Consensus pattern (21 bp):
ATCGCAACGCAAAAAATGACT
Found at i:14194 original size:33 final size:34
Alignment explanation
Indices: 14148--14237 Score: 101
Period size: 33 Copynumber: 2.7 Consensus size: 34
14138 ATGACTATCG
* * *
14148 CAACGCGAAAATGACTATCGCAACGAGAGAATCA
1 CAACGCGAAAATGACTATCGCAACAACAAAATCA
* ** *
14182 CAATGCG-AAATGAAAATCGCAACAACAAAATCG
1 CAACGCGAAAATGACTATCGCAACAACAAAATCA
*
14215 CAACGCGAAAATAACTATCGCAA
1 CAACGCGAAAATGACTATCGCAA
14238 TGCGAATTTG
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
33 26 0.59
34 18 0.41
ACGTcount: A:0.48, C:0.23, G:0.17, T:0.12
Consensus pattern (34 bp):
CAACGCGAAAATGACTATCGCAACAACAAAATCA
Found at i:14236 original size:20 final size:20
Alignment explanation
Indices: 14211--14259 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
14201 CAACAACAAA
14211 ATCGCAACGCGAAAATAACT
1 ATCGCAACGCGAAAATAACT
* ** *
14231 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATAACT
14251 ATCGCAACG
1 ATCGCAACG
14260 AGAGAATCGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATAACT
Found at i:14294 original size:19 final size:19
Alignment explanation
Indices: 14266--14418 Score: 145
Period size: 20 Copynumber: 7.8 Consensus size: 19
14256 AACGAGAGAA
* **
14266 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATAGTCATT
14285 TCGCATTGCGAT--TC-TT
1 TCGCATTGCGATAGTCATT
14301 TCG--TTGCGATAGTCATTT
1 TCGCATTGCGATAGTCA-TT
14319 TCGCATTGCGATAGTCATT
1 TCGCATTGCGATAGTCATT
14338 TCGCATTGCGATAGTCATTTT
1 TCGCATTGCGATAGTCA--TT
*
14359 TGCGCTCTCGTTGCGATAGTCATTT
1 T-CG----CATTGCGATAGTCA-TT
14384 TCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCA-TT
14404 TCGCATTGCGATAGT
1 TCGCATTGCGATAGT
14419 AAACTATTCT
Statistics
Matches: 118, Mismatches: 3, Indels: 25
0.81 0.02 0.17
Matches are distributed among these distances:
14 7 0.06
16 7 0.06
17 2 0.02
18 5 0.04
19 30 0.25
20 43 0.36
21 3 0.03
22 2 0.02
24 2 0.02
25 4 0.03
26 13 0.11
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGCATTGCGATAGTCATT
Found at i:14329 original size:20 final size:20
Alignment explanation
Indices: 14304--14418 Score: 160
Period size: 20 Copynumber: 5.5 Consensus size: 20
14294 GATTCTTTCG
14304 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
14324 TTGCGATAGTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
14343 TTGCGATAGTCATTTTTGCGCTCTCG
1 TTGCGATAGTCA-TTTT-CG----CA
14369 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
14389 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
14409 TTGCGATAGT
1 TTGCGATAGT
14419 AAACTATTCT
Statistics
Matches: 86, Mismatches: 2, Indels: 14
0.84 0.02 0.14
Matches are distributed among these distances:
19 19 0.22
20 43 0.50
21 3 0.03
22 2 0.02
24 2 0.02
25 4 0.05
26 13 0.15
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:16317 original size:20 final size:20
Alignment explanation
Indices: 16294--16348 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
16284 TTGAAACTTT
16294 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
*
16314 AAATTGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** *
16334 CTATCGCAACGCGAA
1 AAATCGCAACACGAA
16349 TTTGACTATC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.49, C:0.22, G:0.16, T:0.13
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:16414 original size:20 final size:20
Alignment explanation
Indices: 16389--16440 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
16379 CGAAATAAAA
16389 TCGCATTGCGATAGTCAAAT
1 TCGCATTGCGATAGTCAAAT
**
16409 TCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCAAAT
*
16429 TCGCGTTGCGAT
1 TCGCATTGCGAT
16441 TCACTCGTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (20 bp):
TCGCATTGCGATAGTCAAAT
Found at i:16828 original size:21 final size:21
Alignment explanation
Indices: 16769--16834 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 21
16759 TGACCGTGAA
* *
16769 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTC-GAGATGGGGAC
16791 TG-TTATCGTC--G-TGGGGAC
1 TGATT-TCGTCGAGATGGGGAC
16809 TGATTTCGTCGAGATGGGGAC
1 TGATTTCGTCGAGATGGGGAC
*
16830 GGATT
1 TGATT
16835 CGCCTTAGAG
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
18 13 0.36
19 3 0.08
20 1 0.03
21 13 0.36
22 6 0.17
ACGTcount: A:0.18, C:0.15, G:0.38, T:0.29
Consensus pattern (21 bp):
TGATTTCGTCGAGATGGGGAC
Found at i:17048 original size:38 final size:39
Alignment explanation
Indices: 17005--17089 Score: 106
Period size: 38 Copynumber: 2.2 Consensus size: 39
16995 GCGATATGTA
17005 AATCGCATTGCGA-TA-GTCAGATTCGCATTGCGATTTAC-T
1 AATCGCATTGCGATTACGT-A-A-TCGCATTGCGATTTACGT
17044 -ATCGCATTGCGATTTACGTAATCGCATTGCGATTTACGT
1 AATCGCATTGCGA-TTACGTAATCGCATTGCGATTTACGT
17083 AATCGCA
1 AATCGCA
17090 ACGCGAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
38 28 0.68
39 2 0.05
40 9 0.22
41 2 0.05
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (39 bp):
AATCGCATTGCGATTACGTAATCGCATTGCGATTTACGT
Found at i:17095 original size:20 final size:20
Alignment explanation
Indices: 17027--17089 Score: 112
Period size: 20 Copynumber: 3.2 Consensus size: 20
17017 ATAGTCAGAT
17027 TCGCATTGCGATTTAC-T-A
1 TCGCATTGCGATTTACGTAA
17045 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAA
17065 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAA
17085 TCGCA
1 TCGCA
17090 ACGCGAATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
18 16 0.37
19 1 0.02
20 26 0.60
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAA
Found at i:17777 original size:11 final size:11
Alignment explanation
Indices: 17749--17780 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
17739 TATTTTAAAA
17749 ATTTAAATTAT
1 ATTTAAATTAT
17760 A-TTAAATTAT
1 ATTTAAATTAT
17770 ATTTAAATTAT
1 ATTTAAATTAT
17781 TAATTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
ATTTAAATTAT
Found at i:18068 original size:19 final size:19
Alignment explanation
Indices: 18028--18069 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
18018 TATTATAAAT
*
18028 TCAAAATCTAACAATTTAA
1 TCAAAATCTAACAATCTAA
*
18047 TCAAAATCTTACAA-CTACA
1 TCAAAATCTAACAATCTA-A
18066 TCAA
1 TCAA
18070 TTGTAACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (19 bp):
TCAAAATCTAACAATCTAA
Found at i:23013 original size:22 final size:22
Alignment explanation
Indices: 22962--23035 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
22952 TTCAATATTC
*
22962 GTCCCGAAGGACCAC--TATA-
1 GTCCCGTAGGACCACTGTATAT
*
22981 -TCCCGAAGGACCACTGTATAT
1 GTCCCGTAGGACCACTGTATAT
*
23002 GTCCTGTAGGACCACTGTATAT
1 GTCCCGTAGGACCACTGTATAT
23024 GTCCCGTAGGAC
1 GTCCCGTAGGAC
23036 TACTCCTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.29
20 4 0.08
22 30 0.62
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (22 bp):
GTCCCGTAGGACCACTGTATAT
Found at i:29496 original size:64 final size:64
Alignment explanation
Indices: 29391--29513 Score: 169
Period size: 64 Copynumber: 1.9 Consensus size: 64
29381 CAATGAAGGT
* * *
29391 ATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTGT-ATTATTACTGGG
1 ATGCATCGATGCACGACTTATGCATCGATGCATAAAATGCATTCGATGTT-TCATTATTACTGGG
* *
29455 ATGCATCGATGCACGCCTTATGCATCGATGCACT-AATTGCATTCGATGTTTCATTATTA
1 ATGCATCGATGCACGACTTATGCATCGATGCA-TAAAATGCATTCGATGTTTCATTATTA
29514 AGAAGTGCAT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.02
64 50 0.96
65 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACGACTTATGCATCGATGCATAAAATGCATTCGATGTTTCATTATTACTGGG
Found at i:32802 original size:22 final size:22
Alignment explanation
Indices: 32767--32825 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
32757 GAATGACCAC
* * *
32767 TATGTCCCGAAGGACCATTGTA
1 TATGTCTCGTAGGACCACTGTA
32789 TATGTCTCGTAGGACCACTGTA
1 TATGTCTCGTAGGACCACTGTA
32811 TATGTCTCGTAGGAC
1 TATGTCTCGTAGGAC
32826 TACTCCTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (22 bp):
TATGTCTCGTAGGACCACTGTA
Found at i:35844 original size:15 final size:15
Alignment explanation
Indices: 35813--35846 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
35803 GGATCCACTC
*
35813 ATGACTTATAACTAA
1 ATGACTTATAACAAA
*
35828 ATGACTTATAGCAAA
1 ATGACTTATAACAAA
35843 ATGA
1 ATGA
35847 ATTGTGTCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (15 bp):
ATGACTTATAACAAA
Found at i:40955 original size:336 final size:336
Alignment explanation
Indices: 40334--41016 Score: 1287
Period size: 336 Copynumber: 2.0 Consensus size: 336
40324 ACTAGTATGC
*
40334 AACT-AACAGTAAAAGGTTTAGGTCCCCAAAATGTAGTAATATCCCTATTTAAATGACTAACAAT
1 AACTGAACCGTAAAAGGTTTAGGTCCCCAAAATGTAGTAATATCCCTATTTAAATGACTAACAAT
*
40398 TTGGCAAGAAACATGTAATTCAAATATAGAAAGTACACTAAAACCTATCACATAAAAAATAAATT
66 TTGGCAAGAAACATGTAATTCAAATATAGAAAGTACACTAAAACCTACCACATAAAAAATAAATT
40463 AAAAAATAATAAAATGGAATTTGAAACAACAGAGCATGTCAAACCTGATATTTGGACAACTAAAA
131 AAAAAATAATAAAATGGAATTTGAAACAACAGAGCATGTCAAACCTGATATTTGGACAACTAAAA
*
40528 AAACTGCACTTTCCAGGGCAATATATCAAGACAAAAGAACAACACATAAACTAAGTTTCATAATT
196 AAACTACACTTTCCAGGGCAATATATCAAGACAAAAGAACAACACATAAACTAAGTTTCATAATT
40593 GAAGATGACTATGACCATCCAGGTAATAGAATTGGAACATAGAAACCATTGAATTCATATAGAAT
261 GAAGATGACTATGACCATCCAGGTAATAGAATTGGAACATAGAAACCATTGAATTCATATAGAAT
40658 TTCATACCTGA
326 TTCATACCTGA
40669 AACTGAACCGTAAAAGGTTTAGGTCCCCAAAATGTAGTAATATCCCTATTTAAATGACTAACAAT
1 AACTGAACCGTAAAAGGTTTAGGTCCCCAAAATGTAGTAATATCCCTATTTAAATGACTAACAAT
40734 TTGGCAAGAAACATGTAATTCAAATATAGAAAGTACACTAAAACCTACCACATAAAAAATAAATT
66 TTGGCAAGAAACATGTAATTCAAATATAGAAAGTACACTAAAACCTACCACATAAAAAATAAATT
*
40799 AAAAAATAATAAAATGGAATTTGAAACAACAGAGTATGTCAAACCTGATATTTGGACAACTAAAA
131 AAAAAATAATAAAATGGAATTTGAAACAACAGAGCATGTCAAACCTGATATTTGGACAACTAAAA
* *
40864 ACATTACACTTTCCAGGGCAATATATCAAGACAAAAGAACAACACATAAACTAAGTTTCATAATT
196 AAACTACACTTTCCAGGGCAATATATCAAGACAAAAGAACAACACATAAACTAAGTTTCATAATT
* *
40929 GTAGATGACTATGACCATCCAGGTAATAGAATTGGACCATAGAAACCATTGAATTCATATAGAAT
261 GAAGATGACTATGACCATCCAGGTAATAGAATTGGAACATAGAAACCATTGAATTCATATAGAAT
40994 TTCATACCTGA
326 TTCATACCTGA
41005 AACTGAACCGTA
1 AACTGAACCGTA
41017 GGGATCGAAT
Statistics
Matches: 339, Mismatches: 8, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
335 4 0.01
336 335 0.99
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (336 bp):
AACTGAACCGTAAAAGGTTTAGGTCCCCAAAATGTAGTAATATCCCTATTTAAATGACTAACAAT
TTGGCAAGAAACATGTAATTCAAATATAGAAAGTACACTAAAACCTACCACATAAAAAATAAATT
AAAAAATAATAAAATGGAATTTGAAACAACAGAGCATGTCAAACCTGATATTTGGACAACTAAAA
AAACTACACTTTCCAGGGCAATATATCAAGACAAAAGAACAACACATAAACTAAGTTTCATAATT
GAAGATGACTATGACCATCCAGGTAATAGAATTGGAACATAGAAACCATTGAATTCATATAGAAT
TTCATACCTGA
Found at i:44042 original size:3 final size:3
Alignment explanation
Indices: 44034--44143 Score: 50
Period size: 3 Copynumber: 37.0 Consensus size: 3
44024 TTTTACCTTT
* * * *
44034 TTA TTA TTA TTA TTA TTA -TA TTA -TA TTT TTA TTA TTC TGTT TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
* * * * * * *
44078 TCTA CTA TTA TTA ATA TT- TT- TTCC CTA ATA TT- TGA TTA TTTA GTA
1 T-TA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA -TTA TTA
44123 TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
44144 AATATATTTA
Statistics
Matches: 82, Mismatches: 17, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
2 9 0.11
3 66 0.80
4 7 0.09
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:44431 original size:19 final size:21
Alignment explanation
Indices: 44407--44445 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
44397 ATACGCTATA
44407 ATTATTATT-TA-ATTTTTCT
1 ATTATTATTATATATTTTTCT
44426 ATTATTATTATATATTTTTC
1 ATTATTATTATATATTTTTC
44446 CCTCTCTCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 2 0.11
21 7 0.39
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTATTATTATATATTTTTCT
Found at i:44432 original size:22 final size:21
Alignment explanation
Indices: 44402--44445 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
44392 ACTTTATACG
*
44402 CTATAATTATTATTTAATTTTT
1 CTATAATTATTATAT-ATTTTT
*
44424 CTATTATTATTATATATTTTT
1 CTATAATTATTATATATTTTT
44445 C
1 C
44446 CCTCTCTCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.64
Consensus pattern (21 bp):
CTATAATTATTATATATTTTT
Found at i:44692 original size:17 final size:17
Alignment explanation
Indices: 44656--44708 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
44646 TATTTGCACA
*
44656 TATTTGATTATAGTTATT
1 TATTT-ATTTTAGTTATT
*
44674 TATTTATTTTAGTTTTT
1 TATTTATTTTAGTTATT
* *
44691 TAGTTTTTTTTATTTATT
1 TA-TTTATTTTAGTTATT
44709 ACTATTATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
17 12 0.41
18 17 0.59
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (17 bp):
TATTTATTTTAGTTATT
Found at i:45734 original size:27 final size:26
Alignment explanation
Indices: 45704--45755 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
45694 TTTTTCCTAA
* *
45704 CCATTTGTTTTTTCTTATGTTTTATTG
1 CCATTTATTTCTTCTTAT-TTTTATTG
*
45731 CCATTTATTTCTTGTTATTTTTATT
1 CCATTTATTTCTTCTTATTTTTATT
45756 TATTTCCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.13, C:0.12, G:0.08, T:0.67
Consensus pattern (26 bp):
CCATTTATTTCTTCTTATTTTTATTG
Found at i:55225 original size:47 final size:48
Alignment explanation
Indices: 55156--55247 Score: 159
Period size: 47 Copynumber: 1.9 Consensus size: 48
55146 AATACTTCGC
*
55156 TTAGGATGAAAACCCGAAAGGGCGTCCTAAGTTGAAAAAA-AAAACGT
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAGTTGAAAAAAGAAAACGT
*
55203 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAGTTGAAAAAAGAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAGTTGAAAAAAGAAAA
55248 AGAGGAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
47 38 0.90
48 4 0.10
ACGTcount: A:0.45, C:0.15, G:0.25, T:0.15
Consensus pattern (48 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAGTTGAAAAAAGAAAACGT
Found at i:56200 original size:105 final size:105
Alignment explanation
Indices: 56018--56681 Score: 1114
Period size: 105 Copynumber: 6.3 Consensus size: 105
56008 AGGTTTTACC
56018 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
*
56083 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
56123 CAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
* *
56188 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATGT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
56228 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
56293 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
56333 TAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCATG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
56398 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
56438 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
*
56503 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * * * * * *
56543 TAGAGCCAATTTTAACTTCACACCGAAGGATGTTGGACTCGAGACAACGCAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
*
56608 ACGAAGGGGCCGCTGGTTGTCAACAAACACTTTC-CAAGTTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACA-TTTCTCAA-TTT
* * * *
56649 CAAAGTCAATTTCAACTTCACACCGAATGATAT
1 CAGAGCCAATTTCAACTTCACAACGAAGGATAT
56682 CGGTCTTGAA
Statistics
Matches: 530, Mismatches: 27, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
105 496 0.94
106 34 0.06
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:58763 original size:19 final size:21
Alignment explanation
Indices: 58739--58777 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
58729 ATACGCTATA
58739 ATTATTATT-TA-ATTTTTCT
1 ATTATTATTATATATTTTTCT
58758 ATTATTATTATATATTTTTC
1 ATTATTATTATATATTTTTC
58778 CCTCTCTCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 2 0.11
21 7 0.39
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTATTATTATATATTTTTCT
Found at i:58764 original size:22 final size:21
Alignment explanation
Indices: 58734--58777 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
58724 ACTTTATACG
*
58734 CTATAATTATTATTTAATTTTT
1 CTATAATTATTATAT-ATTTTT
*
58756 CTATTATTATTATATATTTTT
1 CTATAATTATTATATATTTTT
58777 C
1 C
58778 CCTCTCTCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.64
Consensus pattern (21 bp):
CTATAATTATTATATATTTTT
Found at i:63476 original size:20 final size:20
Alignment explanation
Indices: 63382--63750 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
63372 GATTTTCCAT
* ** *
63382 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
63402 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
63422 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
63442 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
63462 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
63482 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
63502 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
63522 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
63542 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
63562 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
63582 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
63602 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
63622 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
63642 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
63662 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
63682 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
63702 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
63722 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
63742 AATCACAAC
1 AATCGCAAC
63751 ACTTAAATTT
Statistics
Matches: 305, Mismatches: 34, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
19 4 0.01
20 297 0.97
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:64471 original size:24 final size:24
Alignment explanation
Indices: 64432--64478 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
64422 AAATTTGGTC
64432 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
64456 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
64479 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:64669 original size:12 final size:12
Alignment explanation
Indices: 64652--64676 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
64642 ATATAATCCT
64652 GAAGAAGAAAAA
1 GAAGAAGAAAAA
64664 GAAGAAGAAAAA
1 GAAGAAGAAAAA
64676 G
1 G
64677 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:66977 original size:19 final size:19
Alignment explanation
Indices: 66955--67247 Score: 374
Period size: 19 Copynumber: 16.4 Consensus size: 19
66945 CGGAAAATAC
*
66955 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
66974 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
66988 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
67008 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
67022 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
67041 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
67060 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
67074 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
67093 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
67112 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
67131 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
67150 AATCGCAATGCGAAATGAC
1 AATCGCAATGCGAAATGAA
67169 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
67188 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
67202 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
67221 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
67240 AATCGCAA
1 AATCGCAA
67248 CGAGATAATC
Statistics
Matches: 243, Mismatches: 10, Indels: 42
0.82 0.03 0.14
Matches are distributed among these distances:
14 38 0.16
15 1 0.00
16 14 0.06
17 12 0.05
18 2 0.01
19 163 0.67
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:67070 original size:52 final size:55
Alignment explanation
Indices: 66983--67269 Score: 338
Period size: 52 Copynumber: 5.4 Consensus size: 55
66973 AAATCCCAAC
*
66983 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CG-A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
67036 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGACA-G--AATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGA-ATGAAAATCGCAATGCGAA
* *
67088 ATTAAAATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
*
67145 ATGAAAATCGCAATGCGAAATGACAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
67200 A-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAA
*
67250 A-GATAATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAAT
67270 TATAAACGCA
Statistics
Matches: 218, Mismatches: 6, Indels: 21
0.89 0.02 0.09
Matches are distributed among these distances:
50 2 0.01
52 125 0.57
53 16 0.07
54 6 0.03
55 7 0.03
57 62 0.28
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (55 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAA
Found at i:67165 original size:128 final size:128
Alignment explanation
Indices: 66955--67269 Score: 444
Period size: 128 Copynumber: 2.6 Consensus size: 128
66945 CGGAAAATAC
* *
66955 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
* *
67015 A--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAG
65 ATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
* *
67074 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
*
67139 TGCGAAATGAAAATCGCAATGCGAAATGACAATCGCAATGCGAAATGAAAATCGCAACGAAAG
66 TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
*
67202 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GATAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
67262 TGCGAAAT
66 TGCGAAAT
67270 TATAAACGCA
Statistics
Matches: 176, Mismatches: 10, Indels: 16
0.87 0.05 0.08
Matches are distributed among these distances:
119 24 0.14
121 1 0.01
123 34 0.19
124 16 0.09
125 2 0.01
126 2 0.01
127 1 0.01
128 96 0.55
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.15
Consensus pattern (128 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
Found at i:67385 original size:19 final size:19
Alignment explanation
Indices: 67276--67377 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
67266 AAATTATAAA
67276 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
67295 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
67315 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
67331 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
67348 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
67367 CGCATTGCGAT
1 CGCATTGCGAT
67378 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:67503 original size:14 final size:14
Alignment explanation
Indices: 67484--67520 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
67474 CATCAATTAC
67484 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
67498 ACAAATCATCTTTT
1 ACAAATCAACTTTT
67512 ACAAATCAA
1 ACAAATCAA
67521 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:69496 original size:14 final size:14
Alignment explanation
Indices: 69477--69533 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
69467 GCGAAATGAA
*
69477 AATCGCAACGACAG
1 AATCGCAACGAAAG
69491 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
69508 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
69524 AATCGCAACG
1 AATCGCAACG
69534 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:69504 original size:33 final size:33
Alignment explanation
Indices: 69458--69550 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
69448 GCGAAACCAA
*
69458 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
69491 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
69524 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
69551 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:69515 original size:19 final size:19
Alignment explanation
Indices: 69421--69555 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
69411 TAGTTTACTT
* *
69421 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
69441 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
69460 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
69479 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
69493 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
69512 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
69526 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
69545 TCGCAATGCGA
1 TCGCAACGCGA
69556 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:69573 original size:19 final size:19
Alignment explanation
Indices: 69551--69679 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
69541 AAAATCGCAA
69551 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
69570 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
69584 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
69603 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
69617 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
69636 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
69655 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
69675 TGCGA
1 TGCGA
69680 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:69593 original size:33 final size:33
Alignment explanation
Indices: 69551--69642 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
69541 AAAATCGCAA
69551 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
69584 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
69617 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
69643 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:70014 original size:93 final size:93
Alignment explanation
Indices: 69723--70194 Score: 912
Period size: 93 Copynumber: 5.1 Consensus size: 93
69713 TTGAATGGAT
69723 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
69788 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
69816 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
69880 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
69908 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
69973 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
70001 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
70065 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
70093 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
70158 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
70186 AAATTTACT
1 AAATTTACT
70195 AAGCAATCTA
Statistics
Matches: 374, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
92 183 0.49
93 191 0.51
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:70035 original size:185 final size:185
Alignment explanation
Indices: 69723--70194 Score: 926
Period size: 185 Copynumber: 2.6 Consensus size: 185
69713 TTGAATGGAT
69723 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
69788 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
69853 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
69908 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
69973 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
70038 TATATTTCACAGTGTTAAAGAATATACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
70093 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
70158 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
70195 AAGCAATCTA
Statistics
Matches: 285, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 285 1.00
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:71918 original size:14 final size:14
Alignment explanation
Indices: 71899--71955 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
71889 TTGAAATGAA
71899 AATCGCAACGAGAG
1 AATCGCAACGAGAG
71913 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
71930 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
71946 AATCGCAACG
1 AATCGCAACG
71956 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 18 0.47
16 6 0.16
17 6 0.16
19 8 0.21
ACGTcount: A:0.40, C:0.25, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:71936 original size:33 final size:33
Alignment explanation
Indices: 71891--71972 Score: 146
Period size: 33 Copynumber: 2.5 Consensus size: 33
71881 TCTTTTGGTT
71891 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
71924 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
71957 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
71973 TGCGATTTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:71937 original size:19 final size:18
Alignment explanation
Indices: 71898--71977 Score: 68
Period size: 19 Copynumber: 4.8 Consensus size: 18
71888 GTTGAAATGA
71898 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
71913 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
71930 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
71946 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
71963 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
71978 TTTTGGTTTC
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
14 16 0.30
16 10 0.19
17 7 0.13
19 20 0.38
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:72008 original size:14 final size:14
Alignment explanation
Indices: 71989--72043 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
71979 TTTGGTTTCG
71989 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
72003 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
72022 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
72036 CGTTGCGA
1 CGTTGCGA
72044 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:72021 original size:33 final size:33
Alignment explanation
Indices: 71973--72043 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
71963 AAAATCGCAA
**
71973 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
72006 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
72039 TGCGA
1 TGCGA
72044 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:72051 original size:33 final size:33
Alignment explanation
Indices: 71984--72065 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
71974 GCGATTTTGG
***
71984 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
72017 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
72050 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
72066 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:72070 original size:20 final size:20
Alignment explanation
Indices: 71996--72084 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
71986 TCGCGTTGCG
71996 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
72016 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
72029 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
72049 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
72069 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
72085 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:72206 original size:33 final size:33
Alignment explanation
Indices: 72164--72234 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
72154 AATACTAACT
*
72164 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
72197 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
72230 TGAAA
1 TGAAA
72235 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:72467 original size:22 final size:22
Alignment explanation
Indices: 72415--72469 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
72405 TGGTTGTGAG
**
72415 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
72437 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
72459 GGATTTCTTCG
1 GGATTTCTTCG
72470 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:72639 original size:20 final size:20
Alignment explanation
Indices: 72614--72806 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
72604 CTTTAAATAT
72614 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
72634 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
72656 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
72675 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
72695 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
72715 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
72735 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
72755 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
72775 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
72795 CGCGTTGCGATT
1 CGCGTTGCGATT
72807 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:72801 original size:60 final size:60
Alignment explanation
Indices: 72614--72806 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
72604 CTTTAAATAT
**
72614 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
72675 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
72735 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
72795 CGCGTTGCGATT
1 CGCGTTGCGATT
72807 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:72887 original size:20 final size:20
Alignment explanation
Indices: 72862--72913 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
72852 AAGAATCGCG
*
72862 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
72882 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
72902 TTGCGATTCTGG
1 TTGCGATTCTGG
72914 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:73785 original size:25 final size:26
Alignment explanation
Indices: 73759--73820 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 26
73749 TAATACTTAA
*
73759 TTTTATCATTTTA-ACTTCGATTAAAT
1 TTTTA-CATTTTAGAATTCGATTAAAT
*
73785 TTTTACATTTTATGAATTTGATTAAAT
1 TTTTACATTTTA-GAATTCGATTAAAT
73812 TTTTACATT
1 TTTTACATT
73821 GATAATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 7 0.22
26 5 0.16
27 20 0.62
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.56
Consensus pattern (26 bp):
TTTTACATTTTAGAATTCGATTAAAT
Found at i:73835 original size:27 final size:27
Alignment explanation
Indices: 73777--73828 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
73767 TTTTAACTTC
*
73777 GATTAAATTTTTACATTTTATGAATTT
1 GATTAAATTTTTACATTTGATGAATTT
73804 GATTAAATTTTTACA-TTGAT-AATTT
1 GATTAAATTTTTACATTTGATGAATTT
73829 TTTATTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 5 0.21
26 4 0.17
27 15 0.62
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (27 bp):
GATTAAATTTTTACATTTGATGAATTT
Found at i:75728 original size:29 final size:29
Alignment explanation
Indices: 75691--75758 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
75681 AGAAACAAAC
75691 ACGCTGAATGTTGAACGGTTCAACATTCA
1 ACGCTGAATGTTGAACGGTTCAACATTCA
* *
75720 GCGTTGAATGTTGAACGGTTCAACATTCA
1 ACGCTGAATGTTGAACGGTTCAACATTCA
75749 ACGCTGAATG
1 ACGCTGAATG
75759 GTTCCATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (29 bp):
ACGCTGAATGTTGAACGGTTCAACATTCA
Found at i:77935 original size:27 final size:28
Alignment explanation
Indices: 77881--77940 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 28
77871 ATATTCTTAT
*
77881 AATATTTTATGATTTATAATTTAAATATA
1 AATATTTTATGATTTATAAATT-AATATA
77910 AATATTATTAT-ATTTATAAATT-ATATA
1 AATATT-TTATGATTTATAAATTAATATA
77937 AATA
1 AATA
77941 AATAAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 9 0.31
29 16 0.55
30 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (28 bp):
AATATTTTATGATTTATAAATTAATATA
Found at i:80252 original size:17 final size:18
Alignment explanation
Indices: 80219--80252 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
80209 TCTTCCTTGT
80219 AGAAACTATTAGTGGCTA
1 AGAAACTATTAGTGGCTA
*
80237 AGAAATTATT-GTGGCT
1 AGAAACTATTAGTGGCT
80253 TCTCACAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.32
Consensus pattern (18 bp):
AGAAACTATTAGTGGCTA
Found at i:81484 original size:18 final size:18
Alignment explanation
Indices: 81461--81496 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
81451 ACGTTACTTG
81461 ATTCAAAATAATA-TATTT
1 ATTCAAAA-AATATTATTT
81479 ATTCAAAAAATATTATTT
1 ATTCAAAAAATATTATTT
81497 TTATTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTCAAAAAATATTATTT
Found at i:81490 original size:20 final size:20
Alignment explanation
Indices: 81465--81537 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
81455 TACTTGATTC
81465 AAAATAATATATTTATTCAA
1 AAAATAATATATTTATTCAA
* *
81485 AAAATATTATTTTTATTCAA
1 AAAATAATATATTTATTCAA
* * *** *
81505 TAAATTAGGGATTTAATTAAA
1 AAAATAATATATTT-ATTCAA
81526 AAAATAATATAT
1 AAAATAATATAT
81538 AGAGTGGTAT
Statistics
Matches: 37, Mismatches: 15, Indels: 1
0.70 0.28 0.02
Matches are distributed among these distances:
20 25 0.68
21 12 0.32
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (20 bp):
AAAATAATATATTTATTCAA
Found at i:86827 original size:45 final size:45
Alignment explanation
Indices: 86763--86851 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
86753 CCACCCACAA
86763 GAAAACTTAATCACAGTTCTTACCGGTAGGTGTGTGTTAGTAGTT
1 GAAAACTTAATCACAGTTCTTACCGGTAGGTGTGTGTTAGTAGTT
*
86808 GAAAACTTGATCACAGTTCTTACCGGTAGGTGTGTGTTAGTAGT
1 GAAAACTTAATCACAGTTCTTACCGGTAGGTGTGTGTTAGTAGT
86852 AGTGCAAGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (45 bp):
GAAAACTTAATCACAGTTCTTACCGGTAGGTGTGTGTTAGTAGTT
Found at i:90240 original size:2 final size:2
Alignment explanation
Indices: 90233--90262 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
90223 GTAATCTATT
90233 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
90263 ACAAATAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:93880 original size:20 final size:20
Alignment explanation
Indices: 93833--93909 Score: 109
Period size: 20 Copynumber: 3.7 Consensus size: 20
93823 GCTATGAATT
*
93833 TGTCCCGAAGGACCACTATGAAA
1 TGTCCCGAAGGACCA-T-TG-TA
*
93856 TGTCCTGAAGGACCATTGTA
1 TGTCCCGAAGGACCATTGTA
93876 TGTCCCGAAGGACCATTGTA
1 TGTCCCGAAGGACCATTGTA
93896 TGTCCCGAAGGACC
1 TGTCCCGAAGGACC
93910 TATGAACCCT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
20 34 0.67
21 2 0.04
22 1 0.02
23 14 0.27
ACGTcount: A:0.27, C:0.26, G:0.25, T:0.22
Consensus pattern (20 bp):
TGTCCCGAAGGACCATTGTA
Found at i:94232 original size:16 final size:16
Alignment explanation
Indices: 94194--94224 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
94184 CTCTTATGTC
94194 TTCTCATATACATATA
1 TTCTCATATACATATA
94210 TTCTCATATACATAT
1 TTCTCATATACATAT
94225 CATTTCATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.45
Consensus pattern (16 bp):
TTCTCATATACATATA
Found at i:94768 original size:64 final size:64
Alignment explanation
Indices: 94659--94819 Score: 148
Period size: 64 Copynumber: 2.5 Consensus size: 64
94649 TCTTTAACAT
* * * * *
94659 GTGCATCGATGCACTACC-CATGCATTGATACACAAATAACCTTCGATATTT-TCATT-TTAAGG
1 GTGCATCGATGCACT-CCTTATGCATCGATACACAAATAACATTCGATGTTTCT-ATTATTAAGA
*
94721 G
64 A
* * **
94722 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTATTATTAAGAA
1 G-TGCATCGATGCACTCCTTATGCATCGATACACAAATAACATTCGATGTTTCTATTATTAAGAA
* * * *
94787 GTACATCGATGCACTACTTGTGCATCGGTACAC
1 GTGCATCGATGCACTCCTTATGCATCGATACAC
94820 CTTCAACAAT
Statistics
Matches: 79, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
63 3 0.04
64 69 0.87
65 7 0.09
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCACTCCTTATGCATCGATACACAAATAACATTCGATGTTTCTATTATTAAGAA
Found at i:99938 original size:10 final size:10
Alignment explanation
Indices: 99923--99968 Score: 67
Period size: 10 Copynumber: 4.6 Consensus size: 10
99913 AACGCTTGAA
99923 ACCGGTTTTG
1 ACCGGTTTTG
*
99933 ACCGG-TTTA
1 ACCGGTTTTG
99942 ACCGGTTTTG
1 ACCGGTTTTG
99952 AACCGGTTTTG
1 -ACCGGTTTTG
99963 ACCGGT
1 ACCGGT
99969 CACGACCCGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 8 0.25
10 14 0.44
11 10 0.31
ACGTcount: A:0.15, C:0.22, G:0.28, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:99946 original size:19 final size:20
Alignment explanation
Indices: 99922--99960 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
99912 GAACGCTTGA
99922 AACCGGTTTTG-ACCGGTTT
1 AACCGGTTTTGAACCGGTTT
99941 AACCGGTTTTGAACCGGTTT
1 AACCGGTTTTGAACCGGTTT
99961 TGACCGGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.36
Consensus pattern (20 bp):
AACCGGTTTTGAACCGGTTT
Found at i:99983 original size:18 final size:18
Alignment explanation
Indices: 99960--100002 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
99950 TGAACCGGTT
*
99960 TTGACCGGTCACGACCCG
1 TTGACCGGACACGACCCG
* *
99978 TTGACCCGACCCGACCCG
1 TTGACCGGACACGACCCG
99996 TTGACCG
1 TTGACCG
100003 TTGACCGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.16, C:0.42, G:0.26, T:0.16
Consensus pattern (18 bp):
TTGACCGGACACGACCCG
Found at i:100073 original size:29 final size:29
Alignment explanation
Indices: 100009--100084 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
99999 ACCGTTGACC
* *** *
100009 GGTGCTATTCTGGGAATTAATTTGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
*
100038 GGCGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* *
100067 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGGGAATT
100085 TTTTTAAAAG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.21, C:0.09, G:0.28, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:107127 original size:10 final size:10
Alignment explanation
Indices: 107112--107164 Score: 65
Period size: 9 Copynumber: 5.4 Consensus size: 10
107102 CGCTGGAAAT
107112 CGGTTTTGAC
1 CGGTTTTGAC
*
107122 CGG-TTTAAC
1 CGGTTTTGAC
*
107131 CGGTTTTGAAT
1 CGGTTTTG-AC
107142 CGGTTTTGAC
1 CGGTTTTGAC
107152 CGG-TTTGAC
1 CGGTTTTGAC
107161 CGGT
1 CGGT
107165 CACGACCCGT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 17 0.47
10 10 0.28
11 9 0.25
ACGTcount: A:0.13, C:0.19, G:0.30, T:0.38
Consensus pattern (10 bp):
CGGTTTTGAC
Found at i:107147 original size:11 final size:11
Alignment explanation
Indices: 107112--107157 Score: 55
Period size: 10 Copynumber: 4.5 Consensus size: 11
107102 CGCTGGAAAT
107112 CGGTTTTG-AC
1 CGGTTTTGAAC
107122 CGG-TTT-AAC
1 CGGTTTTGAAC
*
107131 CGGTTTTGAAT
1 CGGTTTTGAAC
107142 CGGTTTTG-AC
1 CGGTTTTGAAC
107152 CGGTTT
1 CGGTTT
107158 GACCGGTCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
9 8 0.26
10 13 0.42
11 10 0.32
ACGTcount: A:0.13, C:0.17, G:0.28, T:0.41
Consensus pattern (11 bp):
CGGTTTTGAAC
Found at i:107192 original size:31 final size:31
Alignment explanation
Indices: 107156--107217 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
107146 TTTGACCGGT
* * *
107156 TTGACCGGTCACGACCCGTTTACCCGACCCG
1 TTGACCCGACACGACCCGTTGACCCGACCCG
*
107187 TTGACCCGACCCGACCCGTTGACCCGACCCG
1 TTGACCCGACACGACCCGTTGACCCGACCCG
107218 ACCCGTTGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.16, C:0.45, G:0.23, T:0.16
Consensus pattern (31 bp):
TTGACCCGACACGACCCGTTGACCCGACCCG
Found at i:107200 original size:18 final size:18
Alignment explanation
Indices: 107177--107228 Score: 104
Period size: 18 Copynumber: 2.9 Consensus size: 18
107167 CGACCCGTTT
107177 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
107195 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
107213 ACCCGACCCGTTGACC
1 ACCCGACCCGTTGACC
107229 GGTGCTATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.17, C:0.50, G:0.21, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:107228 original size:13 final size:13
Alignment explanation
Indices: 107167--107199 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
107157 TGACCGGTCA
*
107167 CGACCCGTTTACC
1 CGACCCGTTGACC
107180 CGACCCGTTGACC
1 CGACCCGTTGACC
107193 CGACCCG
1 CGACCCG
107200 ACCCGTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.48, G:0.21, T:0.15
Consensus pattern (13 bp):
CGACCCGTTGACC
Found at i:107290 original size:29 final size:29
Alignment explanation
Indices: 107229--107304 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
107219 CCCGTTGACC
* *** *
107229 GGTGCTATTCTGTGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
*
107258 GGTGTTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* *
107287 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGGGAATT
107305 TTTTTAAAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.21, C:0.08, G:0.26, T:0.45
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:117124 original size:16 final size:16
Alignment explanation
Indices: 117103--117133 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
117093 CTTTTATGTC
117103 TTCTCATATACATATA
1 TTCTCATATACATATA
117119 TTCTCATATACATAT
1 TTCTCATATACATAT
117134 CATTTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.45
Consensus pattern (16 bp):
TTCTCATATACATATA
Found at i:117566 original size:24 final size:20
Alignment explanation
Indices: 117518--117575 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
117508 TTTCCCTTGA
*
117518 AGTGCATTGATGCATTCAAC
1 AGTGCATCGATGCATTCAAC
117538 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC---AAC
117561 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
117576 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
23 4 0.12
24 13 0.39
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCAAC
Found at i:118917 original size:22 final size:22
Alignment explanation
Indices: 118890--118931 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
118880 AAACCATTCA
118890 GGGGGGAATCGGTACCCTCTTG
1 GGGGGGAATCGGTACCCTCTTG
*
118912 GGGGGGAATCGGTTCCCTCT
1 GGGGGGAATCGGTACCCTCT
118932 GAGCAATCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.24, G:0.40, T:0.24
Consensus pattern (22 bp):
GGGGGGAATCGGTACCCTCTTG
Found at i:121594 original size:20 final size:20
Alignment explanation
Indices: 121572--121608 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
121562 TCCCCTGTGG
*
121572 GGGGA-ATCGGTTCCCTCAT
1 GGGGAGATCGATTCCCTCAT
121591 GGGGAGATCGATTCCCTC
1 GGGGAGATCGATTCCCTC
121609 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.16, C:0.27, G:0.32, T:0.24
Consensus pattern (20 bp):
GGGGAGATCGATTCCCTCAT
Found at i:126968 original size:18 final size:19
Alignment explanation
Indices: 126932--126968 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
126922 TGGAGCGTGG
126932 GGGGAATCGGTACTCCCTAT
1 GGGGAATCGGTA-TCCCTAT
126952 GGGGAATCGGT-TCCCTA
1 GGGGAATCGGTATCCCTA
126969 AGTGTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.19, C:0.24, G:0.32, T:0.24
Consensus pattern (19 bp):
GGGGAATCGGTATCCCTAT
Found at i:128452 original size:2 final size:2
Alignment explanation
Indices: 128445--128470 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
128435 AAATTTGATA
128445 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
128471 CTAACACGAA
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:134384 original size:21 final size:19
Alignment explanation
Indices: 134342--134384 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
134332 TAAGATGTTT
*
134342 ATATTTCACAATAACGAAC
1 ATATTTCACAATAAAGAAC
*
134361 ATATTTCTACAGATAAAGATC
1 ATATTTC-ACA-ATAAAGAAC
134382 ATA
1 ATA
134385 CCTCCAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 3 0.15
21 10 0.50
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (19 bp):
ATATTTCACAATAAAGAAC
Found at i:136533 original size:34 final size:34
Alignment explanation
Indices: 136495--136574 Score: 80
Period size: 34 Copynumber: 2.4 Consensus size: 34
136485 AAAAATATTA
136495 ATATAATAATATTAATAAAAATGAAAAAAAAAAT
1 ATATAATAATATTAATAAAAATGAAAAAAAAAAT
* * *
136529 ATAT-AT-ATATATATATAACAATGTAAAAAGAAAT
1 ATATAATAATAT-TA-ATAAAAATGAAAAAAAAAAT
136563 A-A-AA-AATATTAA
1 ATATAATAATATTAA
136575 AATTAGGAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
31 1 0.03
32 6 0.15
33 10 0.26
34 22 0.56
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (34 bp):
ATATAATAATATTAATAAAAATGAAAAAAAAAAT
Found at i:136937 original size:34 final size:34
Alignment explanation
Indices: 136899--136974 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 34
136889 AGTCCTACTT
*
136899 GGACTCAAAATGCATCGGTTTTAGTGTTTCAATA
1 GGACTCAAAATACATCGGTTTTAGTGTTTCAATA
* *
136933 GGACTC-AAATACGTTGGTTTTAGTGTTTCAATA
1 GGACTCAAAATACATCGGTTTTAGTGTTTCAATA
*
136966 GAACTCAAA
1 GGACTCAAA
136975 TACGTTGGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
33 29 0.78
34 8 0.22
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (34 bp):
GGACTCAAAATACATCGGTTTTAGTGTTTCAATA
Found at i:136956 original size:33 final size:33
Alignment explanation
Indices: 136915--136985 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
136905 AAAATGCATC
*
136915 GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
1 GGTTTTAGTGTTTCAATAGAACTCAAATACGTT
136948 GGTTTTAGTGTTTCAATAGAACTCAAATACGTT
1 GGTTTTAGTGTTTCAATAGAACTCAAATACGTT
136981 GGTTT
1 GGTTT
136986 ATTTTCTGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (33 bp):
GGTTTTAGTGTTTCAATAGAACTCAAATACGTT
Found at i:137043 original size:3 final size:3
Alignment explanation
Indices: 137035--137094 Score: 79
Period size: 3 Copynumber: 19.7 Consensus size: 3
137025 GGCCTGTAAA
137035 AAT AAT AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT
137081 ATAT AAT -AT AAT AA
1 A-AT AAT AAT AAT AA
137095 AATGTTTTTA
Statistics
Matches: 53, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.08
3 39 0.74
4 10 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:137071 original size:26 final size:27
Alignment explanation
Indices: 137035--137094 Score: 90
Period size: 26 Copynumber: 2.3 Consensus size: 27
137025 GGCCTGTAAA
137035 AATAATAATAATAAA-ATAATA-ATAAT
1 AATAATAATAATAAATA-AATATATAAT
137061 AATAATAATAATAAATAAATATATAAT
1 AATAATAATAATAAATAAATATATAAT
137088 -ATAATAA
1 AATAATAA
137095 AATGTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
26 26 0.81
27 6 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (27 bp):
AATAATAATAATAAATAAATATATAAT
Found at i:137581 original size:84 final size:82
Alignment explanation
Indices: 137441--138569 Score: 1031
Period size: 84 Copynumber: 13.7 Consensus size: 82
137431 CTGAATGGAA
* * * * *
137441 TCGAACTCGAAGGTCTTTG--GCAGATAGCCCTTCTTGCCTTGAGCTATACTGCAAATGATAGTG
1 TCGAACTCGAAGGTCTTTGTTGCAGATAACCCTTCTAGACTTGAGTTATGCTGCAAATGAT-GTG
* * *
137504 CCTTTGAGCTAAGTGGAG
65 CCTTGGAGCTGAGTGTAG
** *
137522 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGACTTGAGTTATGCTATAAATGTTGGT
1 TCGAACTCGAAGGTCTTTGTTG-CAGATAACCCTTCTAGACTTGAGTTATGCTGCAAATGAT-GT
* *
137587 GCCTTTGAGCTGAGTGTAA
64 GCCTTGGAGCTGAGTGTAG
* * * * *
137606 TCGAACTCGTAGGTCTTTG--GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
1 TCGAACTCGAAGGTCTTTGTTGCAGATAACCCTTCTAGACTTGAGTTATGCTGCAAATGATGTGC
*
137669 CTTGGAGCTGAGCGTAG
66 CTTGGAGCTGAGTGTAG
* * * * *
137686 TCGAACTCGAAGATCTTTGGTTGGCAGAT-ACCCTTCTCGACTTAAGTTATGCTGTAAATGATAT
1 TCGAACTCGAAGGTCTTT-GTT-GCAGATAACCCTTCTAGACTTGAGTTATGCTGCAAATGATGT
*
137750 GCCTTGGAGCTGAGCGTAG
64 GCCTTGGAGCTGAGTGTAG
* * * * * *
137769 TCGAACTCGAAAGTATTTGGTTGGCAGATAACCTTTCTCGACTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTT-GTT-GCAGATAACCCTTCTAGACTTGAGTTATGCTGCAAATGATGT
* *
137834 GCCTTGGAGCTGAGCGTAA
64 GCCTTGGAGCTGAGTGTAG
* ** * * * * * *
137853 TCGAACTCAAAGGTCTTTTGGTCACATATAACACTTATAGCCTTGTGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTT-GTTGCAGATAACCCTTCTAGACTTGAGTTATGCTGCAAATGATGT
* * * *
137918 AACCTCGAAGCTGAGTGTAA
64 -GCCTTGGAGCTGAGTGTAG
* * * * * *
137938 TCAAACTCGAGGGTCTTTG--GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
1 TCGAACTCGAAGGTCTTTGTTGCAGATAACCCTTCTAGACTTGAGTTATGCTGCAAATGATGTGC
*
138001 CTTGGAGCTGAGCGTAG
66 CTTGGAGCTGAGTGTAG
* ** * *
138018 TCAAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTT-GTTGCAGATAACCCTTCTAGACTTGAGTTATGCTGCAAATGATGT
* * * *
138083 GTCCTCGAAGCTGAATGTAA
64 G-CCTTGGAGCTGAGTGTAG
* * * * * * * *
138103 TAGAACTCGAGGGTCTTTG--GCAGATACCCCTTCTCGACTTAAGTTATGTTGTAAATTATGTGC
1 TCGAACTCGAAGGTCTTTGTTGCAGATAACCCTTCTAGACTTGAGTTATGCTGCAAATGATGTGC
138166 CTTGGAGCTGAGTGTAG
66 CTTGGAGCTGAGTGTAG
** * * *
138183 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTT-GTTGCAGATAACCCTTCTAGACTTGAGTTATGCTGCAAATGATGT
* * * *
138248 GTCCTCGAAGCTGAGTGAAA
64 G-CCTTGGAGCTGAGTGTAG
** * * * * * *
138268 TTAAACTCGAAGGTC--T-TTGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATATGC
1 TCGAACTCGAAGGTCTTTGTTGCAGATAACCCTTCTAGACTTGAGTTATGCTGCAAATGATGTGC
*
138330 CTTGGAGCTGAGCGTAG
66 CTTGGAGCTGAGTGTAG
* * * * * *
138347 TCAAACTCGAAGGTATTGGTTGGCAGATAACCCTTCTAGCCTTGATTTATGCTGCAAATGATATG
1 TCGAACTCGAAGGTCTTTGTT-GCAGATAACCCTTCTAGACTTGAGTTATGCTGCAAATGATGTG
* *
138412 CCTTAGAGCTGAGAGTAG
65 CCTTGGAGCTGAGTGTAG
* * * * * * *
138430 TCAAACTCGAAGGTCTTTTGTTGGCAAATATCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGT
1 TCGAACTCGAAGGTC-TTTGTT-GCAGATAACCCTTCTAGACTTGAGTTATGCTGCAAATGATGT
*
138495 GCCTTGGAGCTGAGCGTAG
64 GCCTTGGAGCTGAGTGTAG
* *
138514 TCGAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTAGCCTTGAGTTATGCTGC
1 TCGAACTCGAAGGTCTTT-GTT-GCAGATAACCCTTCTAGACTTGAGTTATGCTGC
138570 CAATAGTTTC
Statistics
Matches: 862, Mismatches: 160, Indels: 49
0.80 0.15 0.05
Matches are distributed among these distances:
79 26 0.03
80 123 0.14
81 125 0.15
82 6 0.01
83 148 0.17
84 349 0.40
85 85 0.10
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (82 bp):
TCGAACTCGAAGGTCTTTGTTGCAGATAACCCTTCTAGACTTGAGTTATGCTGCAAATGATGTGC
CTTGGAGCTGAGTGTAG
Found at i:138004 original size:165 final size:164
Alignment explanation
Indices: 137424--138568 Score: 1344
Period size: 165 Copynumber: 6.9 Consensus size: 164
137414 GTTGATACAC
* * * * * *
137424 CCTCG-AGCTGAATGGAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTAT
1 CCTCGAAGCTGAGTGTAATCAAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
* * * * * * *
137488 ACTGCAAATGATAGTGCCTTTGAGCTAAGTGGAGTCGAACTCGAAGGTC-TTTGTTGACAGATAA
66 GCTGCAAATGAT-GTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAA
* * *
137552 CCCTTCTAGACTTGAGTTATGCTATAAATGTTGGTG
130 CCCTTCTAGCCTTGAGTTATGCTGTAAATGAT-GTG
* * *
137588 CCTTTG-AGCTGAGTGTAATCGAACTCGTAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
1 CC-TCGAAGCTGAGTGTAATCAAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
* **
137652 TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGATC-TTTGGTTGGCAGAT-
65 TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TCACAGATA
* * * *
137715 ACCCTTCTCGACTTAAGTTATGCTGTAAATGATATG
129 ACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
* * * * * * * * *
137751 CCTTGGAGCTGAGCGTAGTCGAACTCGAAAGTATTTGGTTGGCAGATAACCTTTCTCGACTTAAG
1 CCTCGAAGCTGAGTGTAATCAAACTCG-AAG-GTCT--TTGGCAGATAGCCCTTCTCGACTTAAG
* * * * *
137816 TTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAATCGAACTCAAAGGTCTTTTGGTCACATA
62 CTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGA
* * * *
137881 TAACACTTATAGCCTTGTGTTATGCTGTAAATGATGTAA
127 TAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT-G
*
137920 CCTCGAAGCTGAGTGTAATCAAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
1 CCTCGAAGCTGAGTGTAATCAAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
*
137985 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTCACAGATAAC
66 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAAC
138050 CCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
131 CCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
* * * *
138084 TCCTCGAAGCTGAATGTAAT-AGAACTCGAGGGTCTTTGGCAGATACCCCTTCTCGACTTAAGTT
1 -CCTCGAAGCTGAGTGTAATCA-AACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
* * * *
138148 ATGTTGTAAATTATGTGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATA
64 ATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATA
*
138213 ACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTG
129 ACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
* *
138249 TCCTCGAAGCTGAGTGAAATTAAACTCGAAGGTCTTT-GCAGATAGCCCTTCTCGACTTAAGCTA
1 -CCTCGAAGCTGAGTGTAATCAAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
* * * *
138313 TGCTACAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTATTGGTTGG---CAGAT
65 TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT--TTGGTCACAGAT
* * *
138375 AACCCTTCTAGCCTTGATTTATGCTGCAAATGATATG
128 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
* * * * * * * *
138412 CCT-TAGAGCTGAGAGTAGTCAAACTCGAAGGTCTTTTGTTGGCAAATATCCCTTCTTGCCTTGA
1 CCTCGA-AGCTGAGTGTAATCAAACTCGAAGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAA
* *
138476 GCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGA-
61 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-T-CAC
138539 AGATAACCCTTCTAGCCTTGAGTTATGCTG
124 AGATAACCCTTCTAGCCTTGAGTTATGCTG
138569 CCAATAGTTT
Statistics
Matches: 850, Mismatches: 105, Indels: 48
0.85 0.10 0.05
Matches are distributed among these distances:
161 1 0.00
162 29 0.03
163 61 0.07
164 141 0.17
165 379 0.45
166 8 0.01
167 145 0.17
168 64 0.08
169 22 0.03
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (164 bp):
CCTCGAAGCTGAGTGTAATCAAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAAC
CCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
Found at i:139778 original size:31 final size:31
Alignment explanation
Indices: 139740--139991 Score: 185
Period size: 32 Copynumber: 8.0 Consensus size: 31
139730 CCTCGGCAAC
* *
139740 TGTCCATAGGTCCCATAGAACCTAGGTAAAT
1 TGTCCATATGTCCCATAGAACATAGGTAAAT
* *
139771 TGTCCATATGTTCCTTAGAACATAGGTATAA-
1 TGTCCATATGTCCCATAGAACATAGGTA-AAT
* *
139802 TGTCCATATGTCCCGAAAG-ACATAGGTAATT
1 TGTCCATATGTCCC-ATAGAACATAGGTAAAT
*
139833 CTGTCCATATGTCCCGA-A-ATACATAGGTAATT
1 -TGTCCATATGTCCC-ATAGA-ACATAGGTAAAT
* * *
139865 CTGTCCATATGTCCTGAAAG-ACATAGGTAATT
1 -TGTCCATATGTCC-CATAGAACATAGGTAAAT
* * *
139897 CTATCCATATGTCCCGAAAG-ACATAGGTAATT
1 -TGTCCATATGTCCC-ATAGAACATAGGTAAAT
* *
139929 ATGTCCATATGTCCCGAAAG-ACATAGGTAATT
1 -TGTCCATATGTCCC-ATAGAACATAGGTAAAT
* * *
139961 CTGTCCATATATTCCGTAGAACATAGGTAAA
1 -TGTCCATATGTCCCATAGAACATAGGTAAA
139992 CCCTCGACTC
Statistics
Matches: 191, Mismatches: 19, Indels: 21
0.83 0.08 0.09
Matches are distributed among these distances:
30 1 0.01
31 49 0.26
32 140 0.73
33 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (31 bp):
TGTCCATATGTCCCATAGAACATAGGTAAAT
Found at i:139990 original size:32 final size:32
Alignment explanation
Indices: 139802--139970 Score: 302
Period size: 32 Copynumber: 5.3 Consensus size: 32
139792 ATAGGTATAA
139802 TGTCCATATGTCCCGAAAGACATAGGTAATTC
1 TGTCCATATGTCCCGAAAGACATAGGTAATTC
*
139834 TGTCCATATGTCCCGAAATACATAGGTAATTC
1 TGTCCATATGTCCCGAAAGACATAGGTAATTC
*
139866 TGTCCATATGTCCTGAAAGACATAGGTAATTC
1 TGTCCATATGTCCCGAAAGACATAGGTAATTC
* *
139898 TATCCATATGTCCCGAAAGACATAGGTAATTA
1 TGTCCATATGTCCCGAAAGACATAGGTAATTC
139930 TGTCCATATGTCCCGAAAGACATAGGTAATTC
1 TGTCCATATGTCCCGAAAGACATAGGTAATTC
139962 TGTCCATAT
1 TGTCCATAT
139971 ATTCCGTAGA
Statistics
Matches: 129, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 129 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (32 bp):
TGTCCATATGTCCCGAAAGACATAGGTAATTC
Found at i:139990 original size:96 final size:94
Alignment explanation
Indices: 139740--139990 Score: 319
Period size: 96 Copynumber: 2.6 Consensus size: 94
139730 CCTCGGCAAC
* * * *
139740 TGTCCATAGGTCCC-ATAGAACCTAGGTAAAT-TGTCCATATGTTCCTTAGAACATAGGT-ATAA
1 TGTCCATATGTCCCGAAAG-ACATAGGTAATTCTGTCCATAT-TTCC-TAGAACATAGGTAATAA
* *
139802 TGTCCATATGTCCCGAAAGACATAGGTAATTC
63 TATCCATATGTCCCGAAAGACATAGGTAATTA
* * * **
139834 TGTCCATATGTCCCGAAATACATAGGTAATTCTGTCCATATGTCCTGAAAGACATAGGTAATTCT
1 TGTCCATATGTCCCGAAAGACATAGGTAATTCTGTCCATATTTCCT-AGA-ACATAGGTAATAAT
139899 ATCCATATGTCCCGAAAGACATAGGTAATTA
64 ATCCATATGTCCCGAAAGACATAGGTAATTA
139930 TGTCCATATGTCCCGAAAGACATAGGTAATTCTGTCCATATATTCCGTAGAACATAGGTAA
1 TGTCCATATGTCCCGAAAGACATAGGTAATTCTGTCCATAT-TTCC-TAGAACATAGGTAA
139991 ACCCTCGACT
Statistics
Matches: 136, Mismatches: 14, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
93 1 0.01
94 28 0.21
95 19 0.14
96 82 0.60
97 5 0.04
98 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (94 bp):
TGTCCATATGTCCCGAAAGACATAGGTAATTCTGTCCATATTTCCTAGAACATAGGTAATAATAT
CCATATGTCCCGAAAGACATAGGTAATTA
Found at i:140845 original size:35 final size:35
Alignment explanation
Indices: 140772--140846 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
140762 CGTCACTAAC
**
140772 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
140807 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
140842 AGTAA
1 AGTAA
140847 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Done.