Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397265.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_146.0, 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: 8065533
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 116430 characters in sequence are not A, C, G, or T
File 7 of 18
Found at i:2839569 original size:22 final size:23
Alignment explanation
Indices: 2839494--2839668 Score: 128
Period size: 22 Copynumber: 7.8 Consensus size: 23
2839484 GTCAGTCATG
* *
2839494 TTGTTACATGCCATTTTTCAAAAA
1 TTGTTACACGCCA-TGTTCAAAAA
* *
2839518 -TGTTACATGCCATGTTTAAAAA
1 TTGTTACACGCCATGTTCAAAAA
* * *
2839540 GTGATACACGCCATGTGCAAAAA
1 TTGTTACACGCCATGTTCAAAAA
* * *
2839563 -TGTTACAC-ACAAGTTTAAAAA
1 TTGTTACACGCCATGTTCAAAAA
* * *
2839584 TTGTTACACACCTTATTCAAAAA
1 TTGTTACACGCCATGTTCAAAAA
* *
2839607 -TGTTACATG-CAAGTTCAAAAA
1 TTGTTACACGCCATGTTCAAAAA
* *
2839628 TTGTTACAC-ACAAGTTCAAAAA
1 TTGTTACACGCCATGTTCAAAAA
* *
2839650 TTGTCACACGTCATGTTCA
1 TTGTTACACGCCATGTTCA
2839669 CACCATGTTA
Statistics
Matches: 120, Mismatches: 25, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
21 18 0.15
22 57 0.47
23 45 0.38
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.31
Consensus pattern (23 bp):
TTGTTACACGCCATGTTCAAAAA
Found at i:2839592 original size:44 final size:43
Alignment explanation
Indices: 2839494--2839636 Score: 142
Period size: 44 Copynumber: 3.2 Consensus size: 43
2839484 GTCAGTCATG
* * *
2839494 TTGTTACATGCCATTTTTCAAAAATGTTACATGCCATGTTTAAAAA
1 TTGTTACACGCCA-TATTCAAAAATGTTACA--CCAAGTTTAAAAA
* * * *
2839540 GTGATACACGCCATGTGCAAAAATGTTACACACAAGTTTAAAAA
1 TTGTTACACGCCATATTCAAAAATGTTACAC-CAAGTTTAAAAA
* * * *
2839584 TTGTTACACACCTTATTCAAAAATGTTACATGCAAGTTCAAAAA
1 TTGTTACACGCCATATTCAAAAATGTTACA-CCAAGTTTAAAAA
2839628 TTGTTACAC
1 TTGTTACAC
2839637 ACAAGTTCAA
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
43 1 0.01
44 55 0.68
45 15 0.19
46 10 0.12
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (43 bp):
TTGTTACACGCCATATTCAAAAATGTTACACCAAGTTTAAAAA
Found at i:2839637 original size:44 final size:44
Alignment explanation
Indices: 2839510--2839650 Score: 160
Period size: 44 Copynumber: 3.2 Consensus size: 44
2839500 CATGCCATTT
* * * * *
2839510 TTCAAAAATGTTACATGCCATGTTTAAAAAGTGATACACGCCATG
1 TTCAAAAATGTTACATG-CAAGTTTAAAAATTGTTACACACCATA
* ** *
2839555 TGCAAAAATGTTACACACAAGTTTAAAAATTGTTACACACCTTA
1 TTCAAAAATGTTACATGCAAGTTTAAAAATTGTTACACACCATA
*
2839599 TTCAAAAATGTTACATGCAAGTTCAAAAATTGTTACACA-CA-A
1 TTCAAAAATGTTACATGCAAGTTTAAAAATTGTTACACACCATA
2839641 GTTCAAAAAT
1 -TTCAAAAAT
2839651 TGTCACACGT
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
42 1 0.01
43 10 0.12
44 56 0.69
45 14 0.17
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (44 bp):
TTCAAAAATGTTACATGCAAGTTTAAAAATTGTTACACACCATA
Found at i:2841206 original size:17 final size:17
Alignment explanation
Indices: 2841184--2841218 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2841174 AATTGGATCA
*
2841184 AGGAATAGCTATATTTT
1 AGGAATAACTATATTTT
*
2841201 AGGAATAACTATTTTTT
1 AGGAATAACTATATTTT
2841218 A
1 A
2841219 AAATTAGTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (17 bp):
AGGAATAACTATATTTT
Found at i:2841485 original size:20 final size:20
Alignment explanation
Indices: 2841443--2841486 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2841433 ATAGATTATT
* *
2841443 AATATTTTAAATAAATTATA
1 AATATTTTAAAAAAAATATA
2841463 AATATTTTGAAAAAAAATA-A
1 AATATTTT-AAAAAAAATATA
2841483 AATA
1 AATA
2841487 AAAATAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
AATATTTTAAAAAAAATATA
Found at i:2842096 original size:27 final size:28
Alignment explanation
Indices: 2842063--2842121 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 28
2842053 TATTAATATT
*
2842063 TAAATGACAAATTATTAATA-TTATAAA
1 TAAATGACAAATTATTAATATTTAAAAA
*
2842090 TAAATGATAAATTATTAATATTTAAAAA
1 TAAATGACAAATTATTAATATTTAAAAA
2842118 TAAA
1 TAAA
2842122 ATAGCATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 19 0.66
28 10 0.34
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (28 bp):
TAAATGACAAATTATTAATATTTAAAAA
Found at i:2842207 original size:42 final size:42
Alignment explanation
Indices: 2842158--2842257 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
2842148 ATATTTAAAT
* *
2842158 TAAATAAATTATTAATATTTTACAAT-ATTAATGATTAA-ATTA
1 TAAATAAATTATCAATA-TTTA-AATAATCAATGATTAATATTA
* * *
2842200 TAAATAAAATATCAATATTTAAATAATCAATTATTAATATTT
1 TAAATAAATTATCAATATTTAAATAATCAATGATTAATATTA
*
2842242 TAAGTAAATTATCAAT
1 TAAATAAATTATCAAT
2842258 GATTAATATT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
40 3 0.06
41 14 0.29
42 32 0.65
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (42 bp):
TAAATAAATTATCAATATTTAAATAATCAATGATTAATATTA
Found at i:2842250 original size:27 final size:26
Alignment explanation
Indices: 2842219--2842289 Score: 80
Period size: 27 Copynumber: 2.9 Consensus size: 26
2842209 TATCAATATT
2842219 TAAATAATCAATTATTAATATTTTAA
1 TAAATAATCAATTATTAATATTTTAA
* *
2842245 GTAAATTATCAATGATTAATA-TTTAA
1 -TAAATAATCAATTATTAATATTTTAA
2842271 -AAATAA--AA-TATTAATATTT
1 TAAATAATCAATTATTAATATTT
2842290 AAATTTTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 7 0.18
22 4 0.10
24 5 0.13
26 5 0.13
27 18 0.46
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (26 bp):
TAAATAATCAATTATTAATATTTTAA
Found at i:2842302 original size:70 final size:64
Alignment explanation
Indices: 2842146--2842310 Score: 186
Period size: 70 Copynumber: 2.5 Consensus size: 64
2842136 TTTATCATAA
* * *
2842146 TAATATTTAAATTAAATAAATTATTAATATTTTACAATATTAATGATTAAATTATAAATAAAATA
1 TAATATTTAAATT--ATAAATTATTAATATTTTAAAATATCAATGATTAAATTAAAAATAAAATA
2842211 T
64 T
* * *
2842212 CAATATTTAAATAATCAATTATTAATATTTTAAGTAAATTATCAATGATTAATATTTAAAAATAA
1 TAATATTTAAATTATAAATTATTAATATTTT-A--AAA-TATCAATGATTAA-A-TTAAAAATAA
2842277 AATAT
60 AATAT
* *
2842282 TAATATTTAAATTTTTAATTATTAATATT
1 TAATATTTAAATTATAAATTATTAATATT
2842311 CAAAAATAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
64 17 0.20
65 1 0.01
66 11 0.13
67 2 0.02
68 12 0.14
69 1 0.01
70 39 0.47
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (64 bp):
TAATATTTAAATTATAAATTATTAATATTTTAAAATATCAATGATTAAATTAAAAATAAAATAT
Found at i:2848874 original size:4 final size:4
Alignment explanation
Indices: 2848865--2848892 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2848855 CATTAATCTC
2848865 TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT
2848893 CCAGTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:2853379 original size:29 final size:29
Alignment explanation
Indices: 2853343--2853399 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
2853333 GGATATTCAA
2853343 TATATCTTACTTAGCTACTGTGAATATTG
1 TATATCTTACTTAGCTACTGTGAATATTG
** *
2853372 TATATCTTGTTTAGCTACTGTGGATATT
1 TATATCTTACTTAGCTACTGTGAATATT
2853400 ATAAAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.47
Consensus pattern (29 bp):
TATATCTTACTTAGCTACTGTGAATATTG
Found at i:2855321 original size:2 final size:2
Alignment explanation
Indices: 2855316--2855344 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2855306 ATATATAGCT
2855316 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2855345 TCAAAACCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2856159 original size:8 final size:8
Alignment explanation
Indices: 2856137--2856207 Score: 94
Period size: 8 Copynumber: 9.1 Consensus size: 8
2856127 CTCCTTCTCT
2856137 TTTCTT-C
1 TTTCTTCC
2856144 TTTC-TCC
1 TTTCTTCC
*
2856151 TCTCTTCC
1 TTTCTTCC
2856159 TTTCTTCC
1 TTTCTTCC
2856167 TTTCTTCC
1 TTTCTTCC
2856175 TTTCTT-C
1 TTTCTTCC
*
2856182 TTTCTTTC
1 TTTCTTCC
2856190 TTTCTTCC
1 TTTCTTCC
2856198 TTTGCTTCC
1 TTT-CTTCC
2856207 T
1 T
2856208 AACAAAATCT
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
6 1 0.02
7 15 0.26
8 35 0.61
9 6 0.11
ACGTcount: A:0.00, C:0.35, G:0.01, T:0.63
Consensus pattern (8 bp):
TTTCTTCC
Found at i:2856188 original size:4 final size:4
Alignment explanation
Indices: 2856153--2856200 Score: 53
Period size: 4 Copynumber: 12.2 Consensus size: 4
2856143 CTTTCTCCTC
* * * *
2856153 TCTT CCTT TCTT CCTT TCTT CCTT TC-T TCTT TCTT TCTT TCTT CCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
2856200 T
1 T
2856201 GCTTCCTAAC
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
3 3 0.09
4 32 0.91
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (4 bp):
TCTT
Found at i:2863075 original size:20 final size:20
Alignment explanation
Indices: 2863045--2863089 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2863035 AATAAATAAT
* *
2863045 GAATGCTTGATAATGATTGA
1 GAATACTTGATAATAATTGA
* *
2863065 TAATACTTGATGATAATTGA
1 GAATACTTGATAATAATTGA
2863085 GAATA
1 GAATA
2863090 ACACTTGAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.04, G:0.20, T:0.36
Consensus pattern (20 bp):
GAATACTTGATAATAATTGA
Found at i:2870331 original size:18 final size:18
Alignment explanation
Indices: 2870308--2870343 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2870298 GGGATACTTG
2870308 AGGATAACATATAGGTGC
1 AGGATAACATATAGGTGC
*
2870326 AGGATAACATGTAGGTGC
1 AGGATAACATATAGGTGC
2870344 TTGTTAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.11, G:0.31, T:0.22
Consensus pattern (18 bp):
AGGATAACATATAGGTGC
Found at i:2873749 original size:45 final size:45
Alignment explanation
Indices: 2873656--2873751 Score: 124
Period size: 45 Copynumber: 2.1 Consensus size: 45
2873646 TAGAACCCTA
* * * *
2873656 AACCCTCACCCTAAATCCCCGATTCTTAATCAAAAACTTAACTAT
1 AACCTTCACCCTAAATCCCCAAATCCTAATCAAAAACTTAACTAT
2873701 AACCTTCACCCTAAATCCCCAAATCCTAAT-AAAAACTCTAACCT-T
1 AACCTTCACCCTAAATCCCCAAATCCTAATCAAAAACT-TAA-CTAT
2873746 AACCTT
1 AACCTT
2873752 TATCACAACA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
44 7 0.16
45 36 0.80
46 2 0.04
ACGTcount: A:0.39, C:0.34, G:0.01, T:0.26
Consensus pattern (45 bp):
AACCTTCACCCTAAATCCCCAAATCCTAATCAAAAACTTAACTAT
Found at i:2873942 original size:19 final size:19
Alignment explanation
Indices: 2873918--2873954 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2873908 GTTATAGGAT
*
2873918 GAAGCTTTAAATTGAAAGG
1 GAAGCTTTAAATGGAAAGG
*
2873937 GAAGCTTTTAATGGAAAG
1 GAAGCTTTAAATGGAAAG
2873955 CAAATTTAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.05, G:0.27, T:0.27
Consensus pattern (19 bp):
GAAGCTTTAAATGGAAAGG
Found at i:2881400 original size:32 final size:32
Alignment explanation
Indices: 2881359--2881422 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
2881349 AATATATATG
2881359 TTCTGTTCATTCACTGGTGCTAACAATTTCAA
1 TTCTGTTCATTCACTGGTGCTAACAATTTCAA
2881391 TTCTGTTCATTCACTGGTGCTAACAATTTCAA
1 TTCTGTTCATTCACTGGTGCTAACAATTTCAA
2881423 AACTTTTGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (32 bp):
TTCTGTTCATTCACTGGTGCTAACAATTTCAA
Found at i:2890288 original size:13 final size:14
Alignment explanation
Indices: 2890265--2890298 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
2890255 GTACAACACA
2890265 CTTTATTTCTTT-TT
1 CTTT-TTTCTTTCTT
2890279 CTTTTTTCTTTCTT
1 CTTTTTTCTTTCTT
2890293 CTTTTT
1 CTTTTT
2890299 ACACCCCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (14 bp):
CTTTTTTCTTTCTT
Found at i:2890946 original size:14 final size:14
Alignment explanation
Indices: 2890924--2890955 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2890914 AACATGCAAA
*
2890924 ATAATCAAATAAAG
1 ATAACCAAATAAAG
2890938 ATAACCAAATAAAG
1 ATAACCAAATAAAG
2890952 ATAA
1 ATAA
2890956 ATAAAGACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.66, C:0.09, G:0.06, T:0.19
Consensus pattern (14 bp):
ATAACCAAATAAAG
Found at i:2890981 original size:25 final size:25
Alignment explanation
Indices: 2890947--2891006 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
2890937 GATAACCAAA
*
2890947 TAAAGATAAAT-AAAG-ACCAACAACT
1 TAAAAATAAATAAAAGCACC-A-AACT
2890972 TAAAAATAAATAAAAGCACCAAACT
1 TAAAAATAAATAAAAGCACCAAACT
*
2890997 TAAAACTAAA
1 TAAAAATAAA
2891007 CATTGTCCCC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 23 0.74
26 5 0.16
27 3 0.10
ACGTcount: A:0.63, C:0.15, G:0.05, T:0.17
Consensus pattern (25 bp):
TAAAAATAAATAAAAGCACCAAACT
Found at i:2902513 original size:17 final size:16
Alignment explanation
Indices: 2902484--2902516 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
2902474 CTCTTTCTCT
2902484 AGTAGCTAAGTAGCTG
1 AGTAGCTAAGTAGCTG
2902500 AGTAGCTGAAGTAGCTG
1 AGTAGCT-AAGTAGCTG
2902517 TTATGTGGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.12, G:0.33, T:0.24
Consensus pattern (16 bp):
AGTAGCTAAGTAGCTG
Found at i:2914659 original size:34 final size:35
Alignment explanation
Indices: 2914612--2914770 Score: 112
Period size: 34 Copynumber: 4.4 Consensus size: 35
2914602 TTCAGCACAA
** *
2914612 GATCAAGTGCAACCTTTAA-AAATGCCTTTTCAAG
1 GATCAAGCACAACCTTGAACAAATGCCTTTTCAAG
* **
2914646 GATCAAGCACAACC-TGAACAAAAGTCACTTGCTTTTTAG
1 GATCAAGCACAACCTTGAACAAATG-C-C-T--TTTCAAG
*
2914685 GATCAAGCACAACCTTGACCAAATGCC-TTTCAAG
1 GATCAAGCACAACCTTGAACAAATGCCTTTTCAAG
* * *
2914719 GATTAATCACAA-CTTGTACAACTAAATG-ATTTTCAAG
1 GATCAAGCACAACCTTG---AAC-AAATGCCTTTTCAAG
2914756 GATCAAGCACAACCT
1 GATCAAGCACAACCT
2914771 CTCTACCTTT
Statistics
Matches: 96, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
33 7 0.07
34 31 0.32
35 1 0.01
36 3 0.03
37 23 0.24
38 3 0.03
39 20 0.21
40 8 0.08
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (35 bp):
GATCAAGCACAACCTTGAACAAATGCCTTTTCAAG
Found at i:2918838 original size:54 final size:54
Alignment explanation
Indices: 2918772--2918879 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
2918762 TGTTAAAATA
2918772 TTTAGTTCCATTGATAGTGCATTTTATATATACATATATTTGTCAACTATATAT
1 TTTAGTTCCATTGATAGTGCATTTTATATATACATATATTTGTCAACTATATAT
2918826 TTTAGTTCCATTGATAGTGCATTTTATATATACATATATTTGTCAACTATATAT
1 TTTAGTTCCATTGATAGTGCATTTTATATATACATATATTTGTCAACTATATAT
2918880 GTCTAATTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.48
Consensus pattern (54 bp):
TTTAGTTCCATTGATAGTGCATTTTATATATACATATATTTGTCAACTATATAT
Found at i:2948893 original size:2 final size:2
Alignment explanation
Indices: 2948886--2948916 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2948876 TGTGTAGCTT
2948886 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2948917 GACATAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2949219 original size:2 final size:2
Alignment explanation
Indices: 2949214--2949245 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2949204 GAGGAAGTGA
2949214 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2949246 TCTCTTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2949564 original size:2 final size:2
Alignment explanation
Indices: 2949557--2949612 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
2949547 ACTATTAACC
2949557 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2949599 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
2949613 GCTCTAGAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2950843 original size:2 final size:2
Alignment explanation
Indices: 2950838--2950873 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2950828 TATATGCATG
*
2950838 CT CT CT CT CT CT CT GT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2950874 ATAAATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2961631 original size:17 final size:17
Alignment explanation
Indices: 2961609--2961642 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2961599 GTTCTTGATA
2961609 AAATAA-AACTCCTTATT
1 AAATAATAACT-CTTATT
2961626 AAATAATAACTCTTATT
1 AAATAATAACTCTTATT
2961643 TTATTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATAATAACTCTTATT
Found at i:2961888 original size:29 final size:30
Alignment explanation
Indices: 2961765--2961918 Score: 122
Period size: 30 Copynumber: 5.2 Consensus size: 30
2961755 CTTATCTGTG
* * *
2961765 ATTAAGA-CAAAAATATTTGATCTTGTTTAA
1 ATTAAGACCAAACATATTT-TTCTTGTCTAA
* * *
2961795 ATTGAGA-C-AA-ATATGTTTTCTTATCTAG
1 ATTAAGACCAAACATAT-TTTTCTTGTCTAA
* * * *
2961823 ATTATGACAAAAAATATTTTTCTTGTTTTAA
1 ATTAAGACCAAACATATTTTTCTTG-TCTAA
*
2961854 ATTAAGA-CAAACATATTTTTTTTGTCTAA
1 ATTAAGACCAAACATATTTTTCTTGTCTAA
* *
2961883 ACTAAGACCAAACAT-GTTTTCTTGTCTAA
1 ATTAAGACCAAACATATTTTTCTTGTCTAA
2961912 ATTAAGA
1 ATTAAGA
2961919 NNNNNNNNNN
Statistics
Matches: 98, Mismatches: 20, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
28 16 0.16
29 32 0.33
30 37 0.38
31 13 0.13
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (30 bp):
ATTAAGACCAAACATATTTTTCTTGTCTAA
Found at i:2965815 original size:44 final size:43
Alignment explanation
Indices: 2965754--2965889 Score: 173
Period size: 45 Copynumber: 3.1 Consensus size: 43
2965744 AAAAATATAC
* * *
2965754 AAAGGAAAAGGCACCAACCATAGAAGAAAATGAGAAAGAAAGAGG
1 AAAGGAAAA-GAACCAACCATAGAAGAAAATAAGGAAGAAAGA-G
2965799 AAAGGAAAAGAACCAACCATAGAAGAAAATAAGGAAGAAAGAG
1 AAAGGAAAAGAACCAACCATAGAAGAAAATAAGGAAGAAAGAG
* * * *
2965842 AAATGGAGAAAGAACCTACCACAGAAGAGAATAAGGAAGAAAAAG
1 AAA-GGA-AAAGAACCAACCATAGAAGAAAATAAGGAAGAAAGAG
2965887 AAA
1 AAA
2965890 TAAAGAAAGA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
43 4 0.05
44 33 0.40
45 45 0.55
ACGTcount: A:0.60, C:0.10, G:0.24, T:0.05
Consensus pattern (43 bp):
AAAGGAAAAGAACCAACCATAGAAGAAAATAAGGAAGAAAGAG
Found at i:2965869 original size:45 final size:45
Alignment explanation
Indices: 2965770--2965904 Score: 175
Period size: 45 Copynumber: 3.0 Consensus size: 45
2965760 AAAGGCACCA
* * *
2965770 ACCATAGAAGAAAATGAGAAAGAAAGAGGAAA-GGA-AAAGAACCA
1 ACCATAGAAGAAAATAAGGAAGAAAGA-GAAATGGAGAAAGAACCT
2965814 ACCATAGAAGAAAATAAGGAAGAAAGAGAAATGGAGAAAGAACCT
1 ACCATAGAAGAAAATAAGGAAGAAAGAGAAATGGAGAAAGAACCT
* * * **
2965859 ACCACAGAAGAGAATAAGGAAGAAAAAGAAATAAAGAAAGAACCT
1 ACCATAGAAGAAAATAAGGAAGAAAGAGAAATGGAGAAAGAACCT
2965904 A
1 A
2965905 AGTGGAAAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
43 4 0.05
44 28 0.35
45 49 0.60
ACGTcount: A:0.61, C:0.10, G:0.23, T:0.07
Consensus pattern (45 bp):
ACCATAGAAGAAAATAAGGAAGAAAGAGAAATGGAGAAAGAACCT
Found at i:2967664 original size:17 final size:17
Alignment explanation
Indices: 2967639--2967686 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
2967629 GAAGATTGGA
2967639 TGAGAGAAAAGCCATTT
1 TGAGAGAAAAGCCATTT
*
2967656 TGAGTGAAAAGCCATTT
1 TGAGAGAAAAGCCATTT
2967673 TGAGCA-AAAAGCCA
1 TGAG-AGAAAAGCCA
2967687 AACGTCCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.21
Consensus pattern (17 bp):
TGAGAGAAAAGCCATTT
Found at i:2974399 original size:68 final size:68
Alignment explanation
Indices: 2974289--2974534 Score: 167
Period size: 68 Copynumber: 3.6 Consensus size: 68
2974279 CATAAGGTAA
* * * * * * * * *
2974289 ATGGAAAATACATCATATACGTAATTTCATGGAATTCATCATGCTTTCTCAATCATCTTATGTAC
1 ATGGAATATTCATCATATACATAATCTCATGGAATTCATCATGCATACTCAATCACCTCATATAC
2974354 TAT
66 TAT
* * ** * **
2974357 ATGGAATATTCATCATATACATTATCTCATGGCATTTGTCATGCATACTTAATCACCTCATATGG
1 ATGGAATATTCATCATATACATAATCTCATGGAATTCATCATGCATACTCAATCACCTCATATAC
2974422 TAT
66 TAT
* * * * * ** * * *
2974425 ATGGAAT-TTACATCATATACACAATCTTATAGTATACATTGTGCATACTTAATCA--TCTTACA
1 ATGGAATATT-CATCATATACATAATCTCATGGAATTCATCATGCATACTCAATCACCTCATATA
2974487 CCGTAT
65 -C-TAT
* * *
2974493 ATGGAAT-TTACATCATAGACATAATCTTATGGCATTCATCAT
1 ATGGAATATT-CATCATATACATAATCTCATGGAATTCATCAT
2974535 ATCAAACAGG
Statistics
Matches: 138, Mismatches: 37, Indels: 6
0.76 0.20 0.03
Matches are distributed among these distances:
66 4 0.03
67 2 0.01
68 132 0.96
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (68 bp):
ATGGAATATTCATCATATACATAATCTCATGGAATTCATCATGCATACTCAATCACCTCATATAC
TAT
Found at i:2976240 original size:79 final size:79
Alignment explanation
Indices: 2976153--2976300 Score: 233
Period size: 79 Copynumber: 1.9 Consensus size: 79
2976143 TGTAGTCTTG
** * *
2976153 ATACTTCATTCATTCATTGAATGAAGTCTTAATAACTATGAGGAAGGTATTGATACTTTTATTCG
1 ATACTTCATTCATTCATTGAATGAAGTCTTAATAACTATGAGGAAGGTATCAATACTTTCATTCA
2976218 TACAGCTAGTCTCA
66 TACAGCTAGTCTCA
* * *
2976232 ATACTTCATTCATTCATTGAATGAAGTCTTGATACCTATGAGGAGGGTATCAATACTTTCATTCA
1 ATACTTCATTCATTCATTGAATGAAGTCTTAATAACTATGAGGAAGGTATCAATACTTTCATTCA
2976297 TACA
66 TACA
2976301 TCTCTAAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 62 1.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (79 bp):
ATACTTCATTCATTCATTGAATGAAGTCTTAATAACTATGAGGAAGGTATCAATACTTTCATTCA
TACAGCTAGTCTCA
Found at i:2981554 original size:19 final size:18
Alignment explanation
Indices: 2981530--2981569 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
2981520 TATTTACATT
*
2981530 AAATATCTTAGGTAAATAG
1 AAATATCTTAAGTAAAT-G
2981549 AAATATCTTAAGTAAATG
1 AAATATCTTAAGTAAATG
2981567 AAA
1 AAA
2981570 AGTAAAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.53, C:0.05, G:0.12, T:0.30
Consensus pattern (18 bp):
AAATATCTTAAGTAAATG
Found at i:2984790 original size:65 final size:66
Alignment explanation
Indices: 2984621--2984797 Score: 173
Period size: 65 Copynumber: 2.7 Consensus size: 66
2984611 TATAGGATGG
* * * *
2984621 TGTATATGATGTAAA-TCCTATAAACCGTATGAGTTGATTAAGTATGTATGATTAATGCCATGAG
1 TGTATATGATGTAAATTCC-ATAAACC-TATGAGATGATTAAGCAAGCATGA-TAATGCCATGAG
2984685 AATA
63 AATA
* * * *
2984689 TGTATATGATGTATATTCCATATA-CTACGTAGGATGATTAAGCAAGCAT-A-AATGCCATGTGA
1 TGTATATGATGTAAATTCCATAAACCTATG-A-GATGATTAAGCAAGCATGATAATGCCATGAGA
*
2984751 TTA
64 ATA
* *
2984754 TGTATATGATGTAAATTCCATACACCTTATGAGATGAGTAAGCA
1 TGTATATGATGTAAATTCCATAAACC-TATGAGATGATTAAGCA
2984798 TGTATGTGAA
Statistics
Matches: 91, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
65 46 0.51
66 5 0.05
67 6 0.07
68 31 0.34
69 3 0.03
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (66 bp):
TGTATATGATGTAAATTCCATAAACCTATGAGATGATTAAGCAAGCATGATAATGCCATGAGAAT
A
Found at i:2992910 original size:17 final size:17
Alignment explanation
Indices: 2992890--2992924 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2992880 TGGTTGGCCT
2992890 TCTGATGCTTGATGGAA
1 TCTGATGCTTGATGGAA
2992907 TCTGATGCTTGATGGAA
1 TCTGATGCTTGATGGAA
2992924 T
1 T
2992925 ACATTATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.11, G:0.29, T:0.37
Consensus pattern (17 bp):
TCTGATGCTTGATGGAA
Found at i:3002780 original size:35 final size:34
Alignment explanation
Indices: 3002753--3003007 Score: 273
Period size: 35 Copynumber: 7.3 Consensus size: 34
3002743 TTAATTGTTT
3002753 AATTTAATCAATTAGGCACAATAACTTAATTAAAC
1 AATTTAATCAATTAGGC-CAATAACTTAATTAAAC
* *
3002788 AATTTAATTAATTAGGCCCAATAACTTGATTAAAC
1 AATTTAATCAATTAGG-CCAATAACTTAATTAAAC
****
3002823 AAATTTAATCAATTAGGCTCAATAACTTAATTGTTT
1 -AATTTAATCAATTAGGC-CAATAACTTAATTAAAC
* * *
3002859 AATTTAATGAATGAGGCCTAATAATTTAATTAAAC
1 AATTTAATCAATTAGGCC-AATAACTTAATTAAAC
* * * *
3002894 AGTTTGATCAATTAAGCCCAATAACTTGATTAAAC
1 AATTTAATCAATT-AGGCCAATAACTTAATTAAAC
3002929 AAATTTAATCAATTAGGTCCAATAACTTAATT-AAC
1 -AATTTAATCAATTAGG-CCAATAACTTAATTAAAC
* *
3002964 AATTTAATGAATTAGG-C-ACAACTTAATTAAAC
1 AATTTAATCAATTAGGCCAATAACTTAATTAAAC
3002996 AATTTTAATCAA
1 AA-TTTAATCAA
3003008 GTGCTTGAGA
Statistics
Matches: 182, Mismatches: 29, Indels: 20
0.79 0.13 0.09
Matches are distributed among these distances:
31 10 0.05
32 6 0.03
33 8 0.04
34 16 0.09
35 86 0.47
36 56 0.31
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (34 bp):
AATTTAATCAATTAGGCCAATAACTTAATTAAAC
Found at i:3002831 original size:71 final size:70
Alignment explanation
Indices: 3002753--3003007 Score: 293
Period size: 71 Copynumber: 3.7 Consensus size: 70
3002743 TTAATTGTTT
* *
3002753 AATTTAATCAATTAGGCACAATAACTTAATTAAACAATTTAATTAATTAGGCCCAATAACTTGAT
1 AATTTAATCAATTAGGCACAATAACTTAATTAAACAATTTAATCAATTAGGCCCAATAACTTAAT
3002818 TAAAC
66 TAAAC
* **** * * * *
3002823 AAATTTAATCAATTAGGCTCAATAACTTAATTGTTTAATTTAATGAATGAGGCCTAATAATTTAA
1 -AATTTAATCAATTAGGCACAATAACTTAATTAAACAATTTAATCAATTAGGCCCAATAACTTAA
3002888 TTAAAC
65 TTAAAC
* * * * * *
3002894 AGTTTGATCAATTAAGCCCAATAACTTGATTAAACAAATTTAATCAATTAGGTCCAATAACTTAA
1 AATTTAATCAATTAGGCACAATAACTTAATTAAAC-AATTTAATCAATTAGGCCCAATAACTTAA
3002959 TT-AAC
65 TTAAAC
*
3002964 AATTTAATGAATTAGGCAC---AACTTAATTAAACAATTTTAATCAA
1 AATTTAATCAATTAGGCACAATAACTTAATTAAACAA-TTTAATCAA
3003008 GTGCTTGAGA
Statistics
Matches: 152, Mismatches: 30, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
66 2 0.01
67 21 0.14
70 43 0.28
71 86 0.57
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (70 bp):
AATTTAATCAATTAGGCACAATAACTTAATTAAACAATTTAATCAATTAGGCCCAATAACTTAAT
TAAAC
Found at i:3002853 original size:106 final size:106
Alignment explanation
Indices: 3002739--3003007 Score: 379
Period size: 106 Copynumber: 2.6 Consensus size: 106
3002729 GAAGCCTAAT
* * *
3002739 TAACTTAATTGTTTAATTTAATCAATTAGGCACAATAACTTAATTAAACAATTTAATTAATTAGG
1 TAACTTAATTGTTTAATTTAATGAATTAGGCACAATAACTTAATTAAACAATTTAATCAATTAAG
3002804 CCCAATAACTTGATTAAACAAATTTAATCAATTAGG-CTCAA
66 CCCAATAACTTGATTAAACAAATTTAATCAATTAGGTC-CAA
* * * *
3002845 TAACTTAATTGTTTAATTTAATGAATGAGGC-CTAATAATTTAATTAAACAGTTTGATCAATTAA
1 TAACTTAATTGTTTAATTTAATGAATTAGGCAC-AATAACTTAATTAAACAATTTAATCAATTAA
3002909 GCCCAATAACTTGATTAAACAAATTTAATCAATTAGGTCCAA
65 GCCCAATAACTTGATTAAACAAATTTAATCAATTAGGTCCAA
***
3002951 TAACTTAATT-AACAATTTAATGAATTAGGCAC---AACTTAATTAAACAATTTTAATCAA
1 TAACTTAATTGTTTAATTTAATGAATTAGGCACAATAACTTAATTAAACAA-TTTAATCAA
3003008 GTGCTTGAGA
Statistics
Matches: 145, Mismatches: 14, Indels: 11
0.85 0.08 0.06
Matches are distributed among these distances:
102 13 0.09
103 8 0.06
105 17 0.12
106 106 0.73
107 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (106 bp):
TAACTTAATTGTTTAATTTAATGAATTAGGCACAATAACTTAATTAAACAATTTAATCAATTAAG
CCCAATAACTTGATTAAACAAATTTAATCAATTAGGTCCAA
Found at i:3004721 original size:29 final size:29
Alignment explanation
Indices: 3004667--3004722 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
3004657 CTACACAAAG
* * *
3004667 AAAATAAATAAAGATAATGTAGAGAAATA
1 AAAATAAATAAAAATAATGAAAAGAAATA
3004696 AAAAT-AATAAAAATAACTGAAAAGAAA
1 AAAATAAATAAAAATAA-TGAAAAGAAA
3004723 AGAGGGGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.70, C:0.02, G:0.11, T:0.18
Consensus pattern (29 bp):
AAAATAAATAAAAATAATGAAAAGAAATA
Found at i:3008136 original size:21 final size:22
Alignment explanation
Indices: 3008112--3008155 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
3008102 TGTAAACAAT
* *
3008112 TAAAATTAA-AATTAGAACTAA
1 TAAAACTAATAATTAAAACTAA
3008133 T-AAACTAATAATTAAAACTAA
1 TAAAACTAATAATTAAAACTAA
3008154 TA
1 TA
3008156 TAAAATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (22 bp):
TAAAACTAATAATTAAAACTAA
Found at i:3012621 original size:58 final size:57
Alignment explanation
Indices: 3012531--3012650 Score: 186
Period size: 58 Copynumber: 2.1 Consensus size: 57
3012521 CATAATCATC
* * *
3012531 CAAAGTAGTTTGCATGTGATAGATTTATTTTATGTAATTTAATAAATGTTATGCAATG
1 CAAAGTAGTGTGCATGTGATAGATTTATTTTATGCAATTTAATAAATGCTATGC-ATG
* *
3012589 CAAAGTAGTGTGCGTGTGATAGATTTATTTTATGCGATTTAATAAATGCTATGCATG
1 CAAAGTAGTGTGCATGTGATAGATTTATTTTATGCAATTTAATAAATGCTATGCATG
3012646 CAAAG
1 CAAAG
3012651 ATGAGACCTT
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 8 0.14
58 49 0.86
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.39
Consensus pattern (57 bp):
CAAAGTAGTGTGCATGTGATAGATTTATTTTATGCAATTTAATAAATGCTATGCATG
Found at i:3015016 original size:25 final size:25
Alignment explanation
Indices: 3014988--3015036 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
3014978 TCACAAACAT
* *
3014988 GTATATCAACTTGTGGCCTAGCCAC
1 GTATAACAACTCGTGGCCTAGCCAC
*
3015013 GTATAACAACTCGTGGCCTTGCCA
1 GTATAACAACTCGTGGCCTAGCCA
3015037 AGAATAACCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (25 bp):
GTATAACAACTCGTGGCCTAGCCAC
Found at i:3015043 original size:25 final size:25
Alignment explanation
Indices: 3014994--3015044 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3014984 ACATGTATAT
* * *
3014994 CAACTTGTGGCCTAGCCACGTATAA
1 CAACTCGTGGCCTAGCCAAGAATAA
*
3015019 CAACTCGTGGCCTTGCCAAGAATAA
1 CAACTCGTGGCCTAGCCAAGAATAA
3015044 C
1 C
3015045 CACAAACCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (25 bp):
CAACTCGTGGCCTAGCCAAGAATAA
Found at i:3016914 original size:4 final size:4
Alignment explanation
Indices: 3016905--3016937 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
3016895 CCCTTCCCCA
3016905 CTTT CTTT CTTT CTTT CTTT CTTT CTTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT C-TTT CTTT
3016938 TCTCCTCGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
CTTT
Found at i:3020099 original size:21 final size:21
Alignment explanation
Indices: 3020070--3020117 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
3020060 TTTTGTACAT
*
3020070 GTAAGTATACGTATTGAACAA
1 GTAATTATACGTATTGAACAA
*
3020091 GTAATTATATGTATTGAACAA
1 GTAATTATACGTATTGAACAA
3020112 GTAATT
1 GTAATT
3020118 TAGACAGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (21 bp):
GTAATTATACGTATTGAACAA
Found at i:3021743 original size:35 final size:35
Alignment explanation
Indices: 3021677--3021743 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
3021667 ATTTAGGAAG
*
3021677 ATCAAGCAATAACCCTTACAATGACTATTTATAGC
1 ATCAAGCAATAACCCTTACAACGACTATTTATAGC
* * * *
3021712 ATCAAGCGATAACTCTTACAACGGCTCTTTAT
1 ATCAAGCAATAACCCTTACAACGACTATTTAT
3021744 CAAATTAAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.30
Consensus pattern (35 bp):
ATCAAGCAATAACCCTTACAACGACTATTTATAGC
Found at i:3036589 original size:8 final size:8
Alignment explanation
Indices: 3036576--3036614 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
3036566 TGAAATAAAA
3036576 AATAATAT
1 AATAATAT
3036584 AATAATAT
1 AATAATAT
3036592 AATAATATT
1 AATAATA-T
* *
3036601 ATTAAAAT
1 AATAATAT
3036609 AATAAT
1 AATAAT
3036615 GCAAGGTGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
8 20 0.77
9 6 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
AATAATAT
Found at i:3039173 original size:61 final size:60
Alignment explanation
Indices: 3039071--3039207 Score: 159
Period size: 61 Copynumber: 2.3 Consensus size: 60
3039061 CTAATCTCTC
** * *
3039071 GACTCATATTTGGTGGCATAGGGAGTTCCCGCAAGTAGGTAAAAGGAGACTTGAAGCCCCA
1 GACTCATATTTGGTGGCATACAGAGTTCCCACAAGTAGGTAAAAGGAGACCTGAAG-CCCA
** * *
3039132 -ACTCATATTTGGTGGCAATACAGAGTTCCCATGAGTAGGTAAATGGGGACCTGAAGCCCA
1 GACTCATATTTGGTGGC-ATACAGAGTTCCCACAAGTAGGTAAAAGGAGACCTGAAGCCCA
* *
3039192 GACTTATATTTAGTGG
1 GACTCATATTTGGTGG
3039208 TGTGAGAAGT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
60 20 0.31
61 44 0.69
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (60 bp):
GACTCATATTTGGTGGCATACAGAGTTCCCACAAGTAGGTAAAAGGAGACCTGAAGCCCA
Found at i:3046743 original size:62 final size:62
Alignment explanation
Indices: 3046644--3047024 Score: 165
Period size: 62 Copynumber: 6.2 Consensus size: 62
3046634 CACAAAAGAA
* * * ***
3046644 TTTAAGCCCAATTAAACTAGCATCCAAGATGTATAAGTCTAGTTGTGTTGGCACGAAATGAT
1 TTTAAGCCCAATTAAACTAGAATCCAAGATATATAAGTCCAGTTACATTGGCACGAAATGAT
* * * * *
3046706 TTTAAGTCCAATTTAACTAGAATCCAAGATATTTAAGTCCATTTACATTGGCATGAAATGAT
1 TTTAAGCCCAATTAAACTAGAATCCAAGATATATAAGTCCAGTTACATTGGCACGAAATGAT
* * * * * ** * * ** * * *
3046768 TTTAAACCTAATCAAACTGGCATTGAAGATGT-TCAAGTCTAGTTATGTTGGCAAGAAAAGAG
1 TTTAAGCCCAATTAAACTAGAATCCAAGATATAT-AAGTCCAGTTACATTGGCACGAAATGAT
* ** ** * * ** * * *
3046830 TTTAAGCCCAATCAAAC-ATGTGTCTGAGATGTATAAGTCTAGTTATGTTGGCACAAAAAGAG
1 TTTAAGCCCAATTAAACTA-GAATCCAAGATATATAAGTCCAGTTACATTGGCACGAAATGAT
* * * * * * ** * * * ** *
3046892 TTTATGCCCAATCAAACTGGCATCTAAGATGTATAAGTCTTGTCACGTTAGCA-GAAAAAAG
1 TTTAAGCCCAATTAAACTAGAATCCAAGATATATAAGTCCAGTTACATTGGCACGAAATGAT
* * * * * * * * * **
3046953 TTTAAGCCCAATCAAACTAGAATCCGATATGTTTAAGCCCAGTTATATTGGTAGGAAACAAT
1 TTTAAGCCCAATTAAACTAGAATCCAAGATATATAAGTCCAGTTACATTGGCACGAAATGAT
3047015 TTTAAGCCCA
1 TTTAAGCCCA
3047025 GTTATCTTGG
Statistics
Matches: 248, Mismatches: 66, Indels: 10
0.77 0.20 0.03
Matches are distributed among these distances:
61 45 0.18
62 202 0.81
63 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (62 bp):
TTTAAGCCCAATTAAACTAGAATCCAAGATATATAAGTCCAGTTACATTGGCACGAAATGAT
Found at i:3046772 original size:31 final size:31
Alignment explanation
Indices: 3046691--3046772 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 31
3046681 TCTAGTTGTG
*
3046691 TTGGCACGAAATGATTTTAAGTCCAATTTAA
1 TTGGCATGAAATGATTTTAAGTCCAATTTAA
* * * **
3046722 CTAGAATCCAA-GATATTTAAGTCC-ATTTACA
1 TTGGCATGAAATGAT-TTTAAGTCCAATTTA-A
3046753 TTGGCATGAAATGATTTTAA
1 TTGGCATGAAATGATTTTAA
3046773 ACCTAATCAA
Statistics
Matches: 37, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
30 8 0.22
31 26 0.70
32 3 0.08
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (31 bp):
TTGGCATGAAATGATTTTAAGTCCAATTTAA
Found at i:3046970 original size:61 final size:61
Alignment explanation
Indices: 3046644--3046970 Score: 266
Period size: 62 Copynumber: 5.3 Consensus size: 61
3046634 CACAAAAGAA
* * * * ** *
3046644 TTTAAGCCCAATTAAACTAGCATCCAAGATGTATAAGTCTAGTTGTGTTGGCACGAAATGAT
1 TTTAAGCCCAATCAAACTGGCATCTAAGATGTATAAGTCTAGTTATGTTGGCA-GAAAAAAG
* ** * * * * * * * ** ** *
3046706 TTTAAGTCCAATTTAACTAGAATCCAAGATATTTAAGTCCATTTACATTGGCATGAAATGAT
1 TTTAAGCCCAATCAAACTGGCATCTAAGATGTATAAGTCTAGTTATGTTGGCA-GAAAAAAG
* * *
3046768 TTTAAACCTAATCAAACTGGCAT-TGAAGATGT-TCAAGTCTAGTTATGTTGGCAAGAAAAGAG
1 TTTAAGCCCAATCAAACTGGCATCT-AAGATGTAT-AAGTCTAGTTATGTTGGC-AGAAAAAAG
* *
3046830 TTTAAGCCCAATCAAACATGTG--TCTGAGATGTATAAGTCTAGTTATGTTGGCACAAAAAGAG
1 TTTAAGCCCAATCAAAC-TG-GCATCTAAGATGTATAAGTCTAGTTATGTTGGCAGAAAAA-AG
* * * * *
3046892 TTTATGCCCAATCAAACTGGCATCTAAGATGTATAAGTCTTGTCACGTTAGCAGAAAAAAG
1 TTTAAGCCCAATCAAACTGGCATCTAAGATGTATAAGTCTAGTTATGTTGGCAGAAAAAAG
3046953 TTTAAGCCCAATCAAACT
1 TTTAAGCCCAATCAAACT
3046971 AGAATCCGAT
Statistics
Matches: 216, Mismatches: 39, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
60 1 0.00
61 27 0.12
62 182 0.84
63 5 0.02
64 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (61 bp):
TTTAAGCCCAATCAAACTGGCATCTAAGATGTATAAGTCTAGTTATGTTGGCAGAAAAAAG
Found at i:3048672 original size:16 final size:17
Alignment explanation
Indices: 3048653--3048688 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
3048643 ATATTTAGGT
*
3048653 ATAGA-AAAAAAATTAA
1 ATAGATAAAAAAATAAA
3048669 ATAGATAAAAAAATAAA
1 ATAGATAAAAAAATAAA
3048686 ATA
1 ATA
3048689 TATACATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (17 bp):
ATAGATAAAAAAATAAA
Found at i:3054479 original size:21 final size:21
Alignment explanation
Indices: 3054455--3054495 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3054445 CCTCCTAGCT
3054455 TTTCTTATTT-CTTCCTTCTCC
1 TTTCTT-TTTACTTCCTTCTCC
*
3054476 TTTCTTTTTACTTCTTTCTC
1 TTTCTTTTTACTTCCTTCTC
3054496 NNNNNNNNNN
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.05, C:0.29, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTCTTTTTACTTCCTTCTCC
Found at i:3061901 original size:19 final size:20
Alignment explanation
Indices: 3061854--3061902 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
3061844 CATTTCTTAC
3061854 TAACGTGGCATTGACAATGT
1 TAACGTGGCATTGACAATGT
* *
3061874 TAACATGGCA-TGA-ACATTT
1 TAACGTGGCATTGACA-ATGT
3061893 TAACGTGGCA
1 TAACGTGGCA
3061903 AAAATACTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 1 0.04
19 15 0.60
20 9 0.36
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (20 bp):
TAACGTGGCATTGACAATGT
Found at i:3062418 original size:20 final size:20
Alignment explanation
Indices: 3062393--3062436 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
3062383 GGCCTCAACA
*
3062393 ACTGGTCTTATTCACTAAAT
1 ACTGGTCTTATTCACCAAAT
3062413 ACTGGTCTTATTCACCAAAT
1 ACTGGTCTTATTCACCAAAT
3062433 ACTG
1 ACTG
3062437 AGGTATTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (20 bp):
ACTGGTCTTATTCACCAAAT
Found at i:3072236 original size:14 final size:15
Alignment explanation
Indices: 3072204--3072237 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
3072194 AAGGCTTTGA
3072204 TATTTCTTTGCTATT
1 TATTTCTTTGCTATT
*
3072219 TATTTCTTT-CTCTT
1 TATTTCTTTGCTATT
3072233 TATTT
1 TATTT
3072238 TGTTGTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.12, C:0.15, G:0.03, T:0.71
Consensus pattern (15 bp):
TATTTCTTTGCTATT
Found at i:3073625 original size:35 final size:35
Alignment explanation
Indices: 3073559--3073625 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 35
3073549 ACTTTTGAAC
* * *
3073559 AAGATCAAACATAACTTTTACAACTTGCCTTTTGT
1 AAGATCAAACATAACCTTCACAACTTACCTTTTGT
* * *
3073594 AAGATCAAGCATAACCTTCATAGCTTACCTTT
1 AAGATCAAACATAACCTTCACAACTTACCTTT
3073626 GCAAGACCAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 26 1.00
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.34
Consensus pattern (35 bp):
AAGATCAAACATAACCTTCACAACTTACCTTTTGT
Found at i:3074484 original size:19 final size:19
Alignment explanation
Indices: 3074460--3074499 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3074450 TAGAATTGAT
*
3074460 TCTTTCTTCCTTGCT-TTTC
1 TCTTTCTGCCTT-CTATTTC
3074479 TCTTTCTGCCTTCTATTTC
1 TCTTTCTGCCTTCTATTTC
3074498 TC
1 TC
3074500 CAAAATTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.03, C:0.33, G:0.05, T:0.60
Consensus pattern (19 bp):
TCTTTCTGCCTTCTATTTC
Found at i:3075405 original size:13 final size:14
Alignment explanation
Indices: 3075387--3075417 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3075377 CATGAGATAA
3075387 TTGATTT-TTTGTT
1 TTGATTTATTTGTT
3075400 TTGATTTATTTGTT
1 TTGATTTATTTGTT
3075414 TTGA
1 TTGA
3075418 GGGTTGCTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.13, C:0.00, G:0.16, T:0.71
Consensus pattern (14 bp):
TTGATTTATTTGTT
Found at i:3076829 original size:73 final size:72
Alignment explanation
Indices: 3076718--3076860 Score: 223
Period size: 73 Copynumber: 2.0 Consensus size: 72
3076708 AAACATGAAA
* * * *
3076718 TGTAGTAAAATCATTAGAACATTGCCTACAGCTATTACACACCATGCATGTAACATCTCTAATGC
1 TGTAGCAAAATCATTAGAACATTGCCCAAAGCTATTACACACCATGCATGCAA-ATCTCTAATGC
3076783 ACATGGCG
65 ACATGGCG
* *
3076791 TGTAGCAAAATCATTAGAACATTGCCCAAAGTTATTACACGCCATGCATGCAAATCTCTAATGCA
1 TGTAGCAAAATCATTAGAACATTGCCCAAAGCTATTACACACCATGCATGCAAATCTCTAATGCA
3076856 CATGG
66 CATGG
3076861 TGTATAAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
72 17 0.27
73 47 0.73
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (72 bp):
TGTAGCAAAATCATTAGAACATTGCCCAAAGCTATTACACACCATGCATGCAAATCTCTAATGCA
CATGGCG
Found at i:3076997 original size:26 final size:26
Alignment explanation
Indices: 3076968--3077047 Score: 70
Period size: 31 Copynumber: 2.9 Consensus size: 26
3076958 AGTTTTTCTG
3076968 AACAAGGCATGTAACAAAATTTTTTC
1 AACAAGGCATGTAACAAAATTTTTTC
* *
3076994 AACAAAGCGTGTCATGTAACAACATGTTTTC
1 AAC-AA--G-G-CATGTAACAAAATTTTTTC
* * *
3077025 GACAAGGCGTGTAGCAAAATTTT
1 AACAAGGCATGTAACAAAATTTT
3077048 AGAACATGGC
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
26 15 0.36
27 3 0.07
28 1 0.02
29 1 0.02
30 3 0.07
31 19 0.45
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (26 bp):
AACAAGGCATGTAACAAAATTTTTTC
Found at i:3077011 original size:31 final size:31
Alignment explanation
Indices: 3076975--3077036 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
3076965 CTGAACAAGG
*
3076975 CATGTAACAAAATTTTTTCAACAAAGCGTGT
1 CATGTAACAAAATGTTTTCAACAAAGCGTGT
* * *
3077006 CATGTAACAACATGTTTTCGACAAGGCGTGT
1 CATGTAACAAAATGTTTTCAACAAAGCGTGT
3077037 AGCAAAATTT
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:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (31 bp):
CATGTAACAAAATGTTTTCAACAAAGCGTGT
Found at i:3080149 original size:13 final size:13
Alignment explanation
Indices: 3080131--3080161 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3080121 ATTTAAACAT
3080131 CTTGTTATTCTAG
1 CTTGTTATTCTAG
3080144 CTTGTTATTCTAG
1 CTTGTTATTCTAG
*
3080157 TTTGT
1 CTTGT
3080162 ACTCAAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.13, G:0.16, T:0.58
Consensus pattern (13 bp):
CTTGTTATTCTAG
Found at i:3080851 original size:76 final size:75
Alignment explanation
Indices: 3080755--3081371 Score: 530
Period size: 76 Copynumber: 8.2 Consensus size: 75
3080745 TCTTAAATGT
* * * * *
3080755 TGTTTACATCTTGTGATGACACGCCTTTTCATTGACGTATTATATTGTTACACACCATACTCGAA
1 TGTTTACATCTTGTGGTGACACGCCATGTCATTGACGTATTATATTGTTACATACCACACTCGAA
3080820 TTGTTAGATG
66 TTGTTAGATG
* ** * * **
3080830 CTGTTTATATCTTGTGGTGACACGTTATGTCGTTGACGTATTATATTGTTACACACCATGCTCGA
1 -TGTTTACATCTTGTGGTGACACGCCATGTCATTGACGTATTATATTGTTACATACCACACTCGA
3080895 ATTGTTAGATG
65 ATTGTTAGATG
* * * * * ** *
3080906 TCGCTTACATTTTGTCGTGACATGCCATGTCATTGAAGTATTATAGGGTTACATGCCACA--C--
1 T-GTTTACATCTTGTGGTGACACGCCATGTCATTGACGTATTATATTGTTACATACCACACTCGA
*
3080967 -TTGTTAAATG
65 ATTGTTAGATG
* * * * * * * *
3080977 TTGTTTCCATATTGTTGTGACATGCCATGTCGTTGACATATTATATTGTTACATGCGACACTCGA
1 -TGTTTACATCTTGTGGTGACACGCCATGTCATTGACGTATTATATTGTTACATACCACACTCGA
3081042 ATT-TTAAGATG
65 ATTGTT-AGATG
* * * * * * *
3081053 TCATTTACATCTTATGGTGACACGCCATGTCATTG-CAATATTATATGGTTACATGCCACGCTTG
1 T-GTTTACATCTTGTGGTGACACGCCATGTCATTGAC-GTATTATATTGTTACATACCACACTCG
*
3081117 AATTGTTCGATG
64 AATTGTTAGATG
* * * ** **
3081129 TCGTTTATATCTTGTGGTGACACACCATGTCGTTGACGTATTATAGGGTTACATGTCACACTCGA
1 T-GTTTACATCTTGTGGTGACACGCCATGTCATTGACGTATTATATTGTTACATACCACACTCGA
3081194 ATTGTTAGATG
65 ATTGTTAGATG
* * * * * * * **
3081205 TTGTTTACATCATGTGGTAACAAGCCACGTCAGTGACGTAGTATATTGTTACACACCATGCTCGA
1 -TGTTTACATCTTGTGGTGACACGCCATGTCATTGACGTATTATATTGTTACATACCACACTCGA
3081270 ATTGTTAGATG
65 ATTGTTAGATG
* * * * * *
3081281 TTGTTTACATCTTGTGGTGACACACCATGTCATTGCAC-TTTTATATAGTTACATACCGCGCTCC
1 -TGTTTACATCTTGTGGTGACACGCCATGTCATTG-ACGTATTATATTGTTACATACCACACTCG
3081345 AATTGTTAGATG
64 AATTGTTAGATG
* *
3081357 TCATTTACGTCTTGT
1 T-GTTTACATCTTGT
3081372 CATGACATGC
Statistics
Matches: 437, Mismatches: 89, Indels: 30
0.79 0.16 0.05
Matches are distributed among these distances:
71 57 0.13
72 1 0.00
73 1 0.00
74 1 0.00
75 6 0.01
76 365 0.84
77 6 0.01
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.38
Consensus pattern (75 bp):
TGTTTACATCTTGTGGTGACACGCCATGTCATTGACGTATTATATTGTTACATACCACACTCGAA
TTGTTAGATG
Found at i:3081003 original size:71 final size:71
Alignment explanation
Indices: 3080896--3081116 Score: 212
Period size: 71 Copynumber: 3.0 Consensus size: 71
3080886 CATGCTCGAA
** * *
3080896 TTGTT-AGATGTCGCTTACATTTTGTCGTGACATGCCATGTCATTGAAGTATTATAGGGTTACAT
1 TTGTTAAGATGTCATTTACATATTGTCGTGACATGCCATGTCATTGAA-TATTATATGGTTACAT
3080960 GCCACAC
65 GCCACAC
** * * * *
3080967 TTGTTAA-ATGTTGTTTCCATATTGTTGTGACATGCCATGTCGTTGACATATTATATTGTTACAT
1 TTGTTAAGATGTCATTTACATATTGTCGTGACATGCCATGTCATTGA-ATATTATATGGTTACAT
*
3081031 GCGACAC
65 GCCACAC
* * * * *
3081038 TCGAATTTTAAGATGTCATTTACATCTTATGGTGACACGCCATGTCATTGCAATATTATATGGTT
1 T----TGTTAAGATGTCATTTACATATTGTCGTGACATGCCATGTCATTG-AATATTATATGGTT
*
3081103 ACATGCCACGC
61 ACATGCCACAC
3081114 TTG
1 TTG
3081117 AATTGTTCGA
Statistics
Matches: 120, Mismatches: 22, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
71 59 0.49
72 3 0.03
75 5 0.04
76 52 0.43
77 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (71 bp):
TTGTTAAGATGTCATTTACATATTGTCGTGACATGCCATGTCATTGAATATTATATGGTTACATG
CCACAC
Found at i:3081073 original size:223 final size:222
Alignment explanation
Indices: 3080673--3081401 Score: 696
Period size: 223 Copynumber: 3.2 Consensus size: 222
3080663 CATGCTCCAC
* * ** * * * ** **
3080673 TTGTTAGATGTCATTGACATGGTGTCATGAGATGTCATGTTGTTGAAGTATTATAGGGTTACACA
1 TTGTTAGATGTCGTTTACATCTTGTCGTGACATGCCATGTCATTGAAGTATTATAGGGTTACATG
* ** * * * * * *
3080738 CTATGCTTCTTAAATGTTGTTTACATCTTG-TGATGACACGCCTTTTCATTGACGTATTATATTG
66 CCACACTTGTTAAATGTTGTTTACATATTGTTG-TGACAAGCCATGTCGTTGACGTATTATATTG
* ** *
3080802 TTACACACCATACTCGAATTGTTAGATG-CTGTTTATATCTTGTGGTGACACGTTATGTCGTTGA
130 TTACACACCATACTCGAATTGTTAGATGTC-GTTTACATCTTGTGGTGACACGCCATGTCATTGA
* * *
3080866 CGTATTATATTGTTACACACCATGCTCGAA
194 C-TATTATATAGTTACATACCACGCTCGAA
* *
3080896 TTGTTAGATGTCGCTTACATTTTGTCGTGACATGCCATGTCATTGAAGTATTATAGGGTTACATG
1 TTGTTAGATGTCGTTTACATCTTGTCGTGACATGCCATGTCATTGAAGTATTATAGGGTTACATG
* * *
3080961 CCACACTTGTTAAATGTTGTTTCCATATTGTTGTGACATGCCATGTCGTTGACATATTATATTGT
66 CCACACTTGTTAAATGTTGTTTACATATTGTTGTGACAAGCCATGTCGTTGACGTATTATATTGT
** * * * *
3081026 TACATGCGACACTCGAATT-TTAAGATGTCATTTACATCTTATGGTGACACGCCATGTCATTGCA
131 TACACACCATACTCGAATTGTT-AGATGTCGTTTACATCTTGTGGTGACACGCCATGTCATTG-A
* * * *
3081090 ATATTATATGGTTACATGCCACGCTTGAA
194 CTATTATATAGTTACATACCACGCTCGAA
* * * ** * *
3081119 TTGTTCGATGTCGTTTATATCTTGTGGTGACACACCATGTCGTTGACGTATTATAGGGTTACATG
1 TTGTTAGATGTCGTTTACATCTTGTCGTGACATGCCATGTCATTGAAGTATTATAGGGTTACATG
* * * * * *
3081184 TCACACTCGAATTGTTAGATGTTGTTTACATCA-TGTGGTAACAAGCCACGTCAG-TGACGTAGT
66 -C-CA--C-ACTTGTTAAATGTTGTTTACAT-ATTGTTGTGACAAGCCATGTC-GTTGACGTATT
* * *
3081247 ATATTGTTACACACCATGCTCGAATTGTTAGATGTTGTTTACATCTTGTGGTGACACACCATGTC
124 ATATTGTTACACACCATACTCGAATTGTTAGATGTCGTTTACATCTTGTGGTGACACGCCATGTC
* * *
3081312 ATTGCACTTTTATATAGTTACATACCGCGCTCCAA
189 ATTG-ACTATTATATAGTTACATACCACGCTCGAA
* * * * *
3081347 TTGTTAGATGTCATTTACGTCTTGTCATGACATGCTGA-GTCATTGCAGTATTATA
1 TTGTTAGATGTCGTTTACATCTTGTCGTGACATGC-CATGTCATTGAAGTATTATA
3081402 AAGTGGCACA
Statistics
Matches: 408, Mismatches: 85, Indels: 21
0.79 0.17 0.04
Matches are distributed among these distances:
222 2 0.00
223 230 0.56
224 5 0.01
225 2 0.00
227 1 0.00
228 163 0.40
229 5 0.01
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (222 bp):
TTGTTAGATGTCGTTTACATCTTGTCGTGACATGCCATGTCATTGAAGTATTATAGGGTTACATG
CCACACTTGTTAAATGTTGTTTACATATTGTTGTGACAAGCCATGTCGTTGACGTATTATATTGT
TACACACCATACTCGAATTGTTAGATGTCGTTTACATCTTGTGGTGACACGCCATGTCATTGACT
ATTATATAGTTACATACCACGCTCGAA
Found at i:3081412 original size:152 final size:152
Alignment explanation
Indices: 3080757--3081442 Score: 549
Period size: 152 Copynumber: 4.6 Consensus size: 152
3080747 TTAAATGTTG
* * * * * *
3080757 TTTACATCTTGT-GATGACACGCCTTTTCATTG-ACGTATTATATTGTTACACACCATACTCGAA
1 TTTACATCTTGTCG-TGACATGCCATGTCATTGCA-GTATTATATAGTGACACACCATGCTCGAA
* * *** *
3080820 TTGTTAGATGCTGTTTATATCTTGTGGTGACACGTTATGTCGTTGACGTATTATATTGTTACACA
64 TTGTTAGATGTTGTTTACATCTTGTGGTGACACACCATGTCGTTGACGTATTATATTGTTACATA
** *
3080885 CCATGCTCGAATTGTTAGATGTCG
129 CCACACTCGAATTGTTAGATGTCA
* * * ** * ** *
3080909 CTTACATTTTGTCGTGACATGCCATGTCATTGAAGTATTATAGGGTTACATGCCA----C-ACTT
1 TTTACATCTTGTCGTGACATGCCATGTCATTGCAGTATTATATAGTGACACACCATGCTCGAATT
* * * * ** * * *
3080969 GTTAAATGTTGTTTCCATATTGTTGTGACATGCCATGTCGTTGACATATTATATTGTTACATGCG
66 GTTAGATGTTGTTTACATCTTGTGGTGACACACCATGTCGTTGACGTATTATATTGTTACATACC
3081034 ACACTCGAATT-TTAAGATGTCA
131 ACACTCGAATTGTT-AGATGTCA
* * * * * * ** * *
3081056 TTTACATCTTATGGTGACACGCCATGTCATTGCAATATTATATGGTTACATGCCACGCTTGAATT
1 TTTACATCTTGTCGTGACATGCCATGTCATTGCAGTATTATATAGTGACACACCATGCTCGAATT
* * * ** **
3081121 GTTCGATGTCGTTTATATCTTGTGGTGACACACCATGTCGTTGACGTATTATAGGGTTACATGTC
66 GTTAGATGTTGTTTACATCTTGTGGTGACACACCATGTCGTTGACGTATTATATTGTTACATACC
**
3081186 ACACTCGAATTGTTAGATGTTG
131 ACACTCGAATTGTTAGATGTCA
* * * * * * * * *
3081208 TTTACATCATGTGGTAACAAGCCACGTCAGTG-ACGTAGTATATTGTTACACACCATGCTCGAAT
1 TTTACATCTTGTCGTGACATGCCATGTCATTGCA-GTATTATATAGTGACACACCATGCTCGAAT
* * *
3081272 TGTTAGATGTTGTTTACATCTTGTGGTGACACACCATGTCATTGCAC-TTTTATATAGTTACATA
65 TGTTAGATGTTGTTTACATCTTGTGGTGACACACCATGTCGTTG-ACGTATTATATTGTTACATA
* * *
3081336 CCGCGCTCCAATTGTTAGATGTCA
129 CCACACTCGAATTGTTAGATGTCA
* * * * *
3081360 TTTACGTCTTGTCATGACATGCTGA-GTCATTGCAGTATTATAAAGTGGCACACCATG--C---T
1 TTTACATCTTGTCGTGACATGC-CATGTCATTGCAGTATTATATAGTGACACACCATGCTCGAAT
*
3081419 TGTTAGATGTCGTTTACATCTTGT
65 TGTTAGATGTTGTTTACATCTTGT
3081443 TAAGACAATC
Statistics
Matches: 428, Mismatches: 93, Indels: 31
0.78 0.17 0.06
Matches are distributed among these distances:
146 2 0.00
147 142 0.33
148 1 0.00
150 1 0.00
151 1 0.00
152 273 0.64
153 8 0.02
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (152 bp):
TTTACATCTTGTCGTGACATGCCATGTCATTGCAGTATTATATAGTGACACACCATGCTCGAATT
GTTAGATGTTGTTTACATCTTGTGGTGACACACCATGTCGTTGACGTATTATATTGTTACATACC
ACACTCGAATTGTTAGATGTCA
Found at i:3085780 original size:21 final size:21
Alignment explanation
Indices: 3085754--3085797 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3085744 TGTCGTCTCA
* *
3085754 CATATTCTTACCCTATTGTGT
1 CATATTCTCACCCTATCGTGT
*
3085775 CATATTCTCATCCTATCGTGT
1 CATATTCTCACCCTATCGTGT
3085796 CA
1 CA
3085798 CCATGTCATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.27, G:0.09, T:0.43
Consensus pattern (21 bp):
CATATTCTCACCCTATCGTGT
Found at i:3085822 original size:23 final size:23
Alignment explanation
Indices: 3085795--3086320 Score: 202
Period size: 23 Copynumber: 22.8 Consensus size: 23
3085785 TCCTATCGTG
* *
3085795 TCACCATGTCATCTCACATACTC
1 TCACCATGCCATGTCACATACTC
* *
3085818 TCACCATGCCATGTCACATATTT
1 TCACCATGCCATGTCACATACTC
* * *
3085841 TTACCATGTCATGTCACATATTC
1 TCACCATGCCATGTCACATACTC
* *
3085864 TCACAATGCCATGTCATATACTC
1 TCACCATGCCATGTCACATACTC
* * * **
3085887 CCTCCTTGCTGTGTCACATACTC
1 TCACCATGCCATGTCACATACTC
* *
3085910 TCACCATGCCGTGTCACATATTC
1 TCACCATGCCATGTCACATACTC
****
3085933 TCACTC-TTTTGTGTCACATACTC
1 TCAC-CATGCCATGTCACATACTC
* * *
3085956 TCACCTTACCATGTCACATATTC
1 TCACCATGCCATGTCACATACTC
* * *
3085979 TCACCCTAG-CATGTCACACATTC
1 TCACCAT-GCCATGTCACATACTC
*
3086002 TCACTCTATTG---TGTCACATATTC
1 TCAC-C-A-TGCCATGTCACATACTC
* * * *
3086025 TTAGCTTGCCGTGTCACAT-CTCC
1 TCACCATGCCATGTCACATACT-C
*** * * *
3086048 TCGTTAAGTCATGTCACATATTC
1 TCACCATGCCATGTCACATACTC
* * ** *
3086071 TTACCCTGCTGTGTCACATATTC
1 TCACCATGCCATGTCACATACTC
* * * *
3086094 TTACTATACCATGTCACATATTC
1 TCACCATGCCATGTCACATACTC
* ** *
3086117 TCACCCTGCTGTGTCACATATTC
1 TCACCATGCCATGTCACATACTC
* * * *
3086140 TTACTATACCATGTCACATATTC
1 TCACCATGCCATGTCACATACTC
*** * * *
3086163 TCACCATGGTGTGTCATAAACCC
1 TCACCATGCCATGTCACATACTC
* * * *
3086186 TAAACCCTACCATGTCACATATTC
1 T-CACCATGCCATGTCACATACTC
* * *
3086210 TCACCATGTCATCTCACATATTC
1 TCACCATGCCATGTCACATACTC
** *
3086233 TTTCCATAG-CATGTCACATATTC
1 TCACCAT-GCCATGTCACATACTC
* **
3086256 TCACCCTGCCATGTCACATTTTC
1 TCACCATGCCATGTCACATACTC
* * * **
3086279 TCATCATGGCGTGTCACATTTTC
1 TCACCATGCCATGTCACATACTC
* **
3086302 TCAACATGCTGTGTCACAT
1 TCACCATGCCATGTCACAT
3086321 TTTCCTTTCA
Statistics
Matches: 373, Mismatches: 116, Indels: 28
0.72 0.22 0.05
Matches are distributed among these distances:
20 2 0.01
22 4 0.01
23 348 0.93
24 17 0.05
25 1 0.00
26 1 0.00
ACGTcount: A:0.24, C:0.31, G:0.10, T:0.35
Consensus pattern (23 bp):
TCACCATGCCATGTCACATACTC
Found at i:3085866 original size:46 final size:46
Alignment explanation
Indices: 3085795--3086368 Score: 317
Period size: 46 Copynumber: 12.5 Consensus size: 46
3085785 TCCTATCGTG
* * * *
3085795 TCACCATGTCATCTCACATACTCTCACCATGCCATGTCACATATTT
1 TCACCATGTCGTGTCACATATTCTCACCATGCCATGTCACATATTC
* * * * *
3085841 TTACCATGTCATGTCACATATTCTCACAATGCCATGTCATATACTC
1 TCACCATGTCGTGTCACATATTCTCACCATGCCATGTCACATATTC
* * * * *
3085887 CCTCCTTG-CTGTGTCACATACTCTCACCATGCCGTGTCACATATTC
1 TCACCATGTC-GTGTCACATATTCTCACCATGCCATGTCACATATTC
* * * * *
3085933 TCACTC-TTTTGTGTCACATACTCTCACCTTACCATGTCACATATTC
1 TCAC-CATGTCGTGTCACATATTCTCACCATGCCATGTCACATATTC
* * *
3085979 TCACCCTAG-CATGTCACACATTCTCACTCTATTG---TGTCACATATTC
1 TCACCAT-GTCGTGTCACATATTCTCAC-C-A-TGCCATGTCACATATTC
* * * * * * *** * *
3086025 TTAGCTTGCCGTGTCACATCTCCTCGTTAAGTCATGTCACATATTC
1 TCACCATGTCGTGTCACATATTCTCACCATGCCATGTCACATATTC
* * * * *
3086071 TTACCCTG-CTGTGTCACATATTCTTACTATACCATGTCACATATTC
1 TCACCATGTC-GTGTCACATATTCTCACCATGCCATGTCACATATTC
* * * *
3086117 TCACCCTG-CTGTGTCACATATTCTTACTATACCATGTCACATATTC
1 TCACCATGTC-GTGTCACATATTCTCACCATGCCATGTCACATATTC
* * ** * * *
3086163 TCACCATGGT-GTGTCATAAACCCTAAACCCTACCATGTCACATATTC
1 TCACCAT-GTCGTGTCACATATTCT-CACCATGCCATGTCACATATTC
* * **
3086210 TCACCATGTCATCTCACATATTCTTTCCATAG-CATGTCACATATTC
1 TCACCATGTCGTGTCACATATTCTCACCAT-GCCATGTCACATATTC
* * * * * * * *
3086256 TCACCCTGCCATGTCACATTTTCTCATCATGGCGTGTCACATTTTC
1 TCACCATGTCGTGTCACATATTCTCACCATGCCATGTCACATATTC
* * ** * * *
3086302 TCAACATG-CTGTGTCACATTTTC-CTTTCATGTCATCTCACATAATC
1 TCACCATGTC-GTGTCACATATTCTC-ACCATGCCATGTCACATATTC
* *
3086348 TCACCATGTCGTATCAAATAT
1 TCACCATGTCGTGTCACATAT
3086369 AGTTCTTACC
Statistics
Matches: 413, Mismatches: 93, Indels: 44
0.75 0.17 0.08
Matches are distributed among these distances:
43 1 0.00
44 1 0.00
45 7 0.02
46 365 0.88
47 38 0.09
49 1 0.00
ACGTcount: A:0.24, C:0.31, G:0.10, T:0.36
Consensus pattern (46 bp):
TCACCATGTCGTGTCACATATTCTCACCATGCCATGTCACATATTC
Found at i:3086040 original size:69 final size:68
Alignment explanation
Indices: 3085898--3086281 Score: 240
Period size: 69 Copynumber: 5.6 Consensus size: 68
3085888 CTCCTTGCTG
* * ** * *
3085898 TGTCACATACTCTCACCATGCCGTGTCACATATTCTCACTCTTTTGTGTCACATACTCTCACCTT
1 TGTCACATACTCTCACCCTGCCATGTCACATATTCTCACTCTACTGTGTCACATATTCTTA-CTT
3085963 ACCA
65 ACCA
* * *
3085967 TGTCACATATTCTCACCCTAG-CATGTCACACATTCTCACTCTATTGTGTCACATATTCTTAGCT
1 TGTCACATACTCTCACCCT-GCCATGTCACATATTCTCACTCTACTGTGTCACATATTCTTA-CT
* *
3086031 TGCCG
64 TACCA
* ** * * * *
3086036 TGTCACAT-CTC-CTCGTTAAGTCATGTCACATATTCTTACCCTGCTGTGTCACATATTCTTACT
1 TGTCACATACTCTCACCCT--GCCATGTCACATATTCTCACTCTACTGTGTCACATATTCTTACT
3086099 ATACCA
64 -TACCA
* ** * * ** * *
3086105 TGTCACATATTCTCACCCTGCTGTGTCACATATTCTTACTATACCATGTCACATATTCTCACCAT
1 TGTCACATACTCTCACCCTGCCATGTCACATATTCTCACTCTACTGTGTCACATATTCTTA-CTT
****
3086170 GGTG
65 ACCA
* * * * * *
3086174 TGTCATAAACCCTAAACCCTACCATGTCACATATTCTCAC-C-A-TGTCATCTCACATATTCTTT
1 TGTCACATACTCT-CACCCTGCCATGTCACATATTCTCACTCTACTG---TGTCACATATTC-TT
* * *
3086236 CCATAGCA
61 ACTTACCA
* *
3086244 TGTCACATATTCTCACCCTGCCATGTCACATTTTCTCA
1 TGTCACATACTCTCACCCTGCCATGTCACATATTCTCA
3086282 TCATGGCGTG
Statistics
Matches: 239, Mismatches: 64, Indels: 24
0.73 0.20 0.07
Matches are distributed among these distances:
67 3 0.01
68 7 0.03
69 176 0.74
70 49 0.21
71 4 0.02
ACGTcount: A:0.24, C:0.32, G:0.09, T:0.35
Consensus pattern (68 bp):
TGTCACATACTCTCACCCTGCCATGTCACATATTCTCACTCTACTGTGTCACATATTCTTACTTA
CCA
Found at i:3086271 original size:93 final size:93
Alignment explanation
Indices: 3086100--3086271 Score: 238
Period size: 93 Copynumber: 1.8 Consensus size: 93
3086090 ATTCTTACTA
* * * *
3086100 TACCATGTCACATATTCTCACCCTGCTGTGTCACATATTCTTACTATACCATGTCACATATTCTC
1 TACCATGTCACATATTCTCACCATGCTATCTCACATATTCTTACCATACCATGTCACATATTCTC
***
3086165 ACCATGGTGTGTCATAAACCCTAAACCC
66 ACCATGCCATGTCATAAACCCTAAACCC
* *
3086193 TACCATGTCACATATTCTCACCATG-TCATCTCACATATTCTTTCCATAGCATGTCACATATTCT
1 TACCATGTCACATATTCTCACCATGCT-ATCTCACATATTCTTACCATACCATGTCACATATTCT
*
3086257 CACCCTGCCATGTCA
65 CACCATGCCATGTCA
3086272 CATTTTCTCA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
92 1 0.01
93 67 0.99
ACGTcount: A:0.26, C:0.32, G:0.09, T:0.33
Consensus pattern (93 bp):
TACCATGTCACATATTCTCACCATGCTATCTCACATATTCTTACCATACCATGTCACATATTCTC
ACCATGCCATGTCATAAACCCTAAACCC
Found at i:3086315 original size:139 final size:139
Alignment explanation
Indices: 3085795--3086317 Score: 364
Period size: 138 Copynumber: 3.8 Consensus size: 139
3085785 TCCTATCGTG
* * * * * * *
3085795 TCACCATG-TCATCTCACATACTCTCACCATGCCATGTCACATATTTTTACCATGTCATGTCACA
1 TCACCATGCT-ATCTCACATATTCTTACCATACCATGTCACATATTCTCACCCTGCCATGTCACA
* * * * * ** * * * * * * * *
3085859 TATTCTCACAATGCCATGTCATATACTCCCTCCTTGCTGTGTCACATACTCT-CACCATGCCGTG
65 TATTCTCACTATACCATGTCACATATTCTCAACATGCTGTGTCATAAACCCTAAACCCTACCATG
3085923 TCACATATTC
130 TCACATATTC
** * * * * *
3085933 TCACTC-TTTTGTGTCACATACTCTCACCTTACCATGTCACATATTCTCACCCTAG-CATGTCAC
1 TCAC-CATGCTATCTCACATATTCTTACCATACCATGTCACATATTCTCACCCT-GCCATGTCAC
* * *** * * * * * * ** *
3085996 ACATTCTCACTCTATTGTGTCACATATTCTTAGCTTGCCGTGTCA-CATCTCCT---CGTTAAGT
64 ATATTCTCACTATACCATGTCACATATTCTCAACATGCTGTGTCATAAAC-CCTAAACCCT-A-C
3086057 CATGTCACATATTC
126 CATGTCACATATTC
* * * * * **
3086071 TTACCCTGCTGTGTCACATATTCTTACTATACCATGTCACATATTCTCACCCTGCTGTGTCACAT
1 TCACCATGCTATCTCACATATTCTTACCATACCATGTCACATATTCTCACCCTGCCATGTCACAT
* * *
3086136 ATTCTTACTATACCATGTCACATATTCTCACCATGGTGTGTCATAAACCCTAAACCCTACCATGT
66 ATTCTCACTATACCATGTCACATATTCTCAACATGCTGTGTCATAAACCCTAAACCCTACCATGT
3086201 CACATATTC
131 CACATATTC
* *
3086210 TCACCATG-TCATCTCACATATTCTTTCCATAGCATGTCACATATTCTCACCCTGCCATGTCACA
1 TCACCATGCT-ATCTCACATATTCTTACCATACCATGTCACATATTCTCACCCTGCCATGTCACA
* ** * *
3086274 TTTTCTCA-TCATGGCGTGTCACATTTTCTCAACATGCTGTGTCA
65 TATTCTCACT-ATACCATGTCACATATTCTCAACATGCTGTGTCA
3086318 CATTTTCCTT
Statistics
Matches: 298, Mismatches: 73, Indels: 27
0.75 0.18 0.07
Matches are distributed among these distances:
136 2 0.01
137 3 0.01
138 184 0.62
139 106 0.36
140 1 0.00
141 2 0.01
ACGTcount: A:0.24, C:0.31, G:0.10, T:0.35
Consensus pattern (139 bp):
TCACCATGCTATCTCACATATTCTTACCATACCATGTCACATATTCTCACCCTGCCATGTCACAT
ATTCTCACTATACCATGTCACATATTCTCAACATGCTGTGTCATAAACCCTAAACCCTACCATGT
CACATATTC
Found at i:3089443 original size:27 final size:27
Alignment explanation
Indices: 3089392--3089444 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
3089382 TCTAACAATA
* *
3089392 AGAACACTTTTAACCCATTAGAAGTGG
1 AGAACACTTTTAACCCACTAAAAGTGG
* *
3089419 AGAATACTTTTAATCCACTAAAAGTG
1 AGAACACTTTTAACCCACTAAAAGTG
3089445 TTAAAACGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (27 bp):
AGAACACTTTTAACCCACTAAAAGTGG
Found at i:3097333 original size:37 final size:38
Alignment explanation
Indices: 3097292--3097399 Score: 125
Period size: 38 Copynumber: 2.9 Consensus size: 38
3097282 ACGTTTATGG
*
3097292 CCAAATGCCTTTTAAGGATTAA-CTAC-AA-CTTCTACAA
1 CCAAATGCCTTTTAAGGATCAAGC-ACAAACCTT-TACAA
** *
3097329 CCAAATGTTTTTTAAGGATCAAGCACAAACCTTTGCAA
1 CCAAATGCCTTTTAAGGATCAAGCACAAACCTTTACAA
*
3097367 CCAAATGCCTTTTAAGGATCAAGCA-TAACCTTT
1 CCAAATGCCTTTTAAGGATCAAGCACAAACCTTT
3097400 CTACCTTTTG
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
37 28 0.46
38 30 0.49
39 3 0.05
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (38 bp):
CCAAATGCCTTTTAAGGATCAAGCACAAACCTTTACAA
Found at i:3098316 original size:15 final size:15
Alignment explanation
Indices: 3098298--3098338 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
3098288 GGTGTTTTTC
3098298 TAATTTAAGTTTGAT
1 TAATTTAAGTTTGAT
3098313 TAATTGTTAAG--TGAT
1 TAA-T-TTAAGTTTGAT
3098328 TAATTTAAGTT
1 TAATTTAAGTT
3098339 ATTTTTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 8
0.73 0.00 0.27
Matches are distributed among these distances:
13 5 0.23
14 1 0.05
15 10 0.45
16 1 0.05
17 5 0.23
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (15 bp):
TAATTTAAGTTTGAT
Found at i:3105784 original size:36 final size:35
Alignment explanation
Indices: 3105713--3105835 Score: 129
Period size: 35 Copynumber: 3.5 Consensus size: 35
3105703 CTAAAATTGT
* * * *
3105713 TTAAGTTGTTGGGCTTAATTACTTAAATTGTTTAA
1 TTAAGTTATTGAGCCTAATTAATTAAATTGTTTAA
* *
3105748 TTAAGTTATTGAGCCTAATTGATTAAAATTTTTTAA
1 TTAAGTTATTGAGCCTAATTAATT-AAATTGTTTAA
** * * *
3105784 TTAAGTTGCTGTGCTTAATTAATTATATTGTTTAA
1 TTAAGTTATTGAGCCTAATTAATTAAATTGTTTAA
*
3105819 TTAAGTTATTGGGCCTA
1 TTAAGTTATTGAGCCTA
3105836 NNNNNNNNNN
Statistics
Matches: 70, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
35 41 0.59
36 29 0.41
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (35 bp):
TTAAGTTATTGAGCCTAATTAATTAAATTGTTTAA
Found at i:3107856 original size:29 final size:29
Alignment explanation
Indices: 3107801--3107873 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
3107791 ATAAAATATT
*
3107801 TATAATATCCATAGTAGCTAAATAAGATA
1 TATAATATCCATAGTAGCTAAACAAGATA
* * * *
3107830 TATAATATCTATAGTAGCTGAGCAAGATT
1 TATAATATCCATAGTAGCTAAACAAGATA
3107859 TACTAAATATCCATA
1 TA-T-AATATCCATA
3107874 ATAACTAGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 26 0.72
30 1 0.03
31 9 0.25
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (29 bp):
TATAATATCCATAGTAGCTAAACAAGATA
Found at i:3119303 original size:14 final size:14
Alignment explanation
Indices: 3119284--3119310 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3119274 GTGTGCCAAT
3119284 TCACTTCAACTTCA
1 TCACTTCAACTTCA
3119298 TCACTTCAACTTC
1 TCACTTCAACTTC
3119311 TGCAACATTT
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:0.26, C:0.37, G:0.00, T:0.37
Consensus pattern (14 bp):
TCACTTCAACTTCA
Found at i:3133770 original size:13 final size:13
Alignment explanation
Indices: 3133754--3133780 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3133744 AAATTAGTTG
3133754 CACTAATTTGCAT
1 CACTAATTTGCAT
3133767 CACTAATTTGCAT
1 CACTAATTTGCAT
3133780 C
1 C
3133781 CAAATAGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.37
Consensus pattern (13 bp):
CACTAATTTGCAT
Found at i:3150025 original size:35 final size:35
Alignment explanation
Indices: 3149973--3150054 Score: 119
Period size: 35 Copynumber: 2.3 Consensus size: 35
3149963 AATGTGTAGG
* * *
3149973 TAAAGGTTATGCTTGATCTTGGAAAAGGCAAGTTA
1 TAAAGGTTATGCCTGATCCTGCAAAAGGCAAGTTA
* *
3150008 TAGAGGTTATGCCTGATCCTGCAAAAGGCATGTTA
1 TAAAGGTTATGCCTGATCCTGCAAAAGGCAAGTTA
3150043 TAAAGGTTATGC
1 TAAAGGTTATGC
3150055 TTGGCCATGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (35 bp):
TAAAGGTTATGCCTGATCCTGCAAAAGGCAAGTTA
Found at i:3154167 original size:8 final size:8
Alignment explanation
Indices: 3154147--3154225 Score: 74
Period size: 8 Copynumber: 10.1 Consensus size: 8
3154137 AGATTCGGCT
3154147 AGGAAGCAA
1 AGGAAG-AA
3154156 AGGAAGAA
1 AGGAAGAA
3154164 AGGAAGAA
1 AGGAAGAA
* *
3154172 AGAAATAA
1 AGGAAGAA
3154180 AGG-AGAA
1 AGGAAGAA
3154187 AGGAAGAA
1 AGGAAGAA
*
3154195 ATGAAGAA
1 AGGAAGAA
* * *
3154203 GGGGAGAG
1 AGGAAGAA
3154211 AGG-AGAA
1 AGGAAGAA
3154218 A-GAAGAA
1 AGGAAGAA
3154225 A
1 A
3154226 AGCGAAAGTG
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
6 1 0.02
7 15 0.26
8 35 0.61
9 6 0.11
ACGTcount: A:0.59, C:0.01, G:0.37, T:0.03
Consensus pattern (8 bp):
AGGAAGAA
Found at i:3159444 original size:21 final size:21
Alignment explanation
Indices: 3159418--3159467 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
3159408 ATAAAAAGGC
3159418 TTGAATGATCTTTGAACTTGT
1 TTGAATGATCTTTGAACTTGT
* * *
3159439 TTGAATGATTTTTTAAGTTGT
1 TTGAATGATCTTTGAACTTGT
*
3159460 TTAAATGA
1 TTGAATGA
3159468 GTTTTTAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.18, T:0.50
Consensus pattern (21 bp):
TTGAATGATCTTTGAACTTGT
Found at i:3159472 original size:21 final size:21
Alignment explanation
Indices: 3159435--3159475 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3159425 ATCTTTGAAC
* *
3159435 TTGTTTGAATGATTTTTTAAG
1 TTGTTTAAATGAGTTTTTAAG
3159456 TTGTTTAAATGAGTTTTTAA
1 TTGTTTAAATGAGTTTTTAA
3159476 TTTTAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.56
Consensus pattern (21 bp):
TTGTTTAAATGAGTTTTTAAG
Found at i:3162187 original size:12 final size:12
Alignment explanation
Indices: 3162170--3162196 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3162160 ACATCTTCTA
3162170 TAGCCGTGACTT
1 TAGCCGTGACTT
3162182 TAGCCGTGACTT
1 TAGCCGTGACTT
3162194 TAG
1 TAG
3162197 GTCTCCAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.33
Consensus pattern (12 bp):
TAGCCGTGACTT
Found at i:3162290 original size:18 final size:18
Alignment explanation
Indices: 3162263--3162300 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
3162253 AAGTCTTTCC
3162263 CCAAAGTGTT-TAAACCT
1 CCAAAGTGTTATAAACCT
3162280 CCAATAGTGTTAGTAAACCT
1 CCAA-AGTGTTA-TAAACCT
3162300 C
1 C
3162301 TAAAACATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 6 0.33
20 8 0.44
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (18 bp):
CCAAAGTGTTATAAACCT
Found at i:3166268 original size:2 final size:2
Alignment explanation
Indices: 3166256--3166293 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
3166246 AAATATCCAA
* *
3166256 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3166294 CTCAAAAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3171295 original size:72 final size:73
Alignment explanation
Indices: 3171219--3171353 Score: 200
Period size: 73 Copynumber: 1.9 Consensus size: 73
3171209 TAAGAGACAA
* *
3171219 TGTTAGTCGATTAA-AGCTTACTGCCAAAAACTGAGCTTAGAGACAAAAACGACTTAATCGACTA
1 TGTTAGTCCACTAAGAGCTTACTGCCAAAAACTGAGCTTAGAGACAAAAACGACTTAATCGACTA
3171283 AGAAGTTT
66 AGAAGTTT
* * * * *
3171291 TGTTAGTCCACTAAGAGCTTACTGTCAAAAATTGGGTTTAGAGACAAAGACGACTTAATCGAC
1 TGTTAGTCCACTAAGAGCTTACTGCCAAAAACTGAGCTTAGAGACAAAAACGACTTAATCGAC
3171354 NNNNNNNNNN
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
72 12 0.22
73 43 0.78
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (73 bp):
TGTTAGTCCACTAAGAGCTTACTGCCAAAAACTGAGCTTAGAGACAAAAACGACTTAATCGACTA
AGAAGTTT
Found at i:3180207 original size:73 final size:73
Alignment explanation
Indices: 3180075--3180241 Score: 176
Period size: 73 Copynumber: 2.3 Consensus size: 73
3180065 GACCAAGAGA
* * * *
3180075 CAATGTTAGTAGACTAAGAGCTTATTCCCAAAAATTGAGTTCAAAGATAGAAACAACTTAAT-TG
1 CAATGTTAGTAGACTAAGAGCTTACTACCAAAAATAGAGTTCAAAGACAGAAACAACTTAATCT-
3180139 ACTAAGAAG
65 ACTAAGAAG
*** * * * **
3180148 TTTTGTTAGTTGACTAAGAGCTTACTACCAAAAACTAGA-TTCAGAGACAGAGATGACTTAATCT
1 CAATGTTAGTAGACTAAGAGCTTACTACCAAAAA-TAGAGTTCAAAGACAGAAACAACTTAATCT
*
3180212 ACTAAGTAG
65 ACTAAGAAG
*
3180221 CAATGTTAGTCGACTAAGAGC
1 CAATGTTAGTAGACTAAGAGC
3180242 ATTCTGTCTA
Statistics
Matches: 75, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
73 71 0.95
74 4 0.05
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.28
Consensus pattern (73 bp):
CAATGTTAGTAGACTAAGAGCTTACTACCAAAAATAGAGTTCAAAGACAGAAACAACTTAATCTA
CTAAGAAG
Found at i:3194674 original size:76 final size:76
Alignment explanation
Indices: 3194583--3194745 Score: 220
Period size: 76 Copynumber: 2.1 Consensus size: 76
3194573 TCAATTTTCC
* * * **
3194583 AAATTAAAATACTATCTTTAATTTTAAGAATTTCTTTTAAAGTAGGAAATAATTTTTTATTTTTA
1 AAATTAAAATACTATCCTTAATTTTAAGAATTGCTTTTAAAGTAGGAAACAATTTCCTATTTTTA
**
3194648 TG-AGTCGTCCA
66 TGCA-TCACCCA
* * *
3194659 AAATTAAAATTCTATCCTTAATTTTAGGAATTGCTTTTGAAGTAGGAAACAATTTCCTATTTTTA
1 AAATTAAAATACTATCCTTAATTTTAAGAATTGCTTTTAAAGTAGGAAACAATTTCCTATTTTTA
3194724 TGCATCACCCA
66 TGCATCACCCA
3194735 AAATTAAAATA
1 AAATTAAAATA
3194746 AATGGTATTT
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
76 74 0.99
77 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (76 bp):
AAATTAAAATACTATCCTTAATTTTAAGAATTGCTTTTAAAGTAGGAAACAATTTCCTATTTTTA
TGCATCACCCA
Found at i:3224974 original size:18 final size:18
Alignment explanation
Indices: 3224953--3224990 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3224943 GATATATGGA
3224953 AACA-AAGAAAAGACAATG
1 AACACAAGAAAA-ACAATG
*
3224971 AACACAAGAAGAACAATG
1 AACACAAGAAAAACAATG
3224989 AA
1 AA
3224991 AATGCATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.66, C:0.13, G:0.16, T:0.05
Consensus pattern (18 bp):
AACACAAGAAAAACAATG
Found at i:3227614 original size:21 final size:21
Alignment explanation
Indices: 3227577--3227616 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3227567 TAAAGCAATA
3227577 CCATGTTCAAAATTCCAAAAT
1 CCATGTTCAAAATTCCAAAAT
3227598 CCATGGTTCAAAA-TCCAAA
1 CCAT-GTTCAAAATTCCAAA
3227617 TTTCAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.25
Consensus pattern (21 bp):
CCATGTTCAAAATTCCAAAAT
Found at i:3227876 original size:18 final size:19
Alignment explanation
Indices: 3227839--3227878 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
3227829 ACGAGCCTAA
*
3227839 CAAGCAAGCTCATGAAACT
1 CAAGCAAGCTCATAAAACT
*
3227858 CAAGCAAGC-CTTAAAACT
1 CAAGCAAGCTCATAAAACT
3227876 CAA
1 CAA
3227879 AATCACATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.45, C:0.28, G:0.12, T:0.15
Consensus pattern (19 bp):
CAAGCAAGCTCATAAAACT
Found at i:3237186 original size:71 final size:69
Alignment explanation
Indices: 3237101--3237326 Score: 247
Period size: 71 Copynumber: 3.2 Consensus size: 69
3237091 TAGTTGTGCC
* *
3237101 TAATTGATTAAATTGTTTAATTATGTTATTGGGCCTAATTATTTAAATTTGTTTAATCAAGTTAT
1 TAATTGATCAAATTGTTTAATTAAGTTATTGGGCCTAATTA-TTAAATTTGTTTAATCAAGTTAT
3237166 TGGGCT
65 TGGG-T
* ***
3237172 TAATTGATCAAATTGTTTGATTAAGTTATTGGGCCTAATTGATTAAATTTGTTTAATCAAGNNNN
1 TAATTGATCAAATTGTTTAATTAAGTTATTGGGCCTAATT-ATTAAATTTGTTTAATCAAG-TTA
******
3237237 NNNNNN
64 TTGGGT
* *
3237243 TAATTGATCAAATTGTTTAATTAAGTTATTGGGCCTAATTAATTAAA-TTATTTAATTAAGTTAT
1 TAATTGATCAAATTGTTTAATTAAGTTATTGGGCCTAATT-ATTAAATTTGTTTAATCAAGTTAT
*
3237307 TTGGT
65 TGGGT
*
3237312 CTAATTGATTAAATT
1 -TAATTGATCAAATT
3237327 AAACAATTAA
Statistics
Matches: 126, Mismatches: 26, Indels: 7
0.79 0.16 0.04
Matches are distributed among these distances:
70 24 0.19
71 101 0.80
72 1 0.01
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.45
Consensus pattern (69 bp):
TAATTGATCAAATTGTTTAATTAAGTTATTGGGCCTAATTATTAAATTTGTTTAATCAAGTTATT
GGGT
Found at i:3237327 original size:35 final size:35
Alignment explanation
Indices: 3237071--3237326 Score: 241
Period size: 35 Copynumber: 7.3 Consensus size: 35
3237061 ACTCAAGTAT
* *
3237071 TTGATTAAAATTGTTTAATTTAG---TTGTGCCTAA
1 TTGATT-AAATTGTTTAATTAAGTTATTGGGCCTAA
*
3237104 TTGATTAAATTGTTTAATTATGTTATTGGGCCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
* *
3237139 TT-ATTTAAATTTGTTTAATCAAGTTATTGGGCTTAA
1 TTGA-TTAAA-TTGTTTAATTAAGTTATTGGGCCTAA
* *
3237175 TTGATCAAATTGTTTGATTAAGTTATTGGGCCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
* **********
3237210 TTGATTAAATTTGTTTAATCAAGNNNNNNNNNNTAA
1 TTGATTAAA-TTGTTTAATTAAGTTATTGGGCCTAA
*
3237246 TTGATCAAATTGTTTAATTAAGTTATTGGGCCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
* * * *
3237281 TTAATTAAATTATTTAATTAAGTTATTTGGTCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
3237316 TTGATTAAATT
1 TTGATTAAATT
3237327 AAACAATTAA
Statistics
Matches: 175, Mismatches: 41, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
32 14 0.08
33 6 0.03
34 1 0.01
35 102 0.58
36 51 0.29
37 1 0.01
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.46
Consensus pattern (35 bp):
TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
Found at i:3237335 original size:35 final size:35
Alignment explanation
Indices: 3237261--3237345 Score: 107
Period size: 35 Copynumber: 2.4 Consensus size: 35
3237251 CAAATTGTTT
* ***
3237261 AATTAAGTTATTGGGCCTAATTAATTAAATTATTT
1 AATTAAGTTATTTGGCCTAATTAATTAAATTAAAC
* *
3237296 AATTAAGTTATTTGGTCTAATTGATTAAATTAAAC
1 AATTAAGTTATTTGGCCTAATTAATTAAATTAAAC
*
3237331 AATTAAGTTAATTGG
1 AATTAAGTTATTTGG
3237346 GCTTCTTAAG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.44
Consensus pattern (35 bp):
AATTAAGTTATTTGGCCTAATTAATTAAATTAAAC
Found at i:3252514 original size:15 final size:16
Alignment explanation
Indices: 3252496--3252528 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
3252486 ACCTCCCTAA
3252496 ATTAAAAGCAAA-TGC
1 ATTAAAAGCAAACTGC
3252511 ATTAAAAGCAAACTGC
1 ATTAAAAGCAAACTGC
3252527 AT
1 AT
3252529 CATCCATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.52, C:0.15, G:0.12, T:0.21
Consensus pattern (16 bp):
ATTAAAAGCAAACTGC
Found at i:3261072 original size:72 final size:72
Alignment explanation
Indices: 3260940--3261076 Score: 166
Period size: 72 Copynumber: 1.9 Consensus size: 72
3260930 AGTTAGTGTG
*** * * * * **
3260940 AGGGTTATCACTTGATCTTGTTAAAAAGCGAATGAAAGGGTTATCGCTTGTTCCTGTGAAAAAGT
1 AGGGTTATCACTTGATCCCATGAAAAAGCCAATGAAAGGGTTATCACTTGATCCCATGAAAAAGT
3261005 TGTTATA
66 TGTTATA
* * *
3261012 AGGGTTATCACTTGATCCCATGAAAAAGCCATTGTAAGGGTTATCATTTGATCCCATGAAAAAGT
1 AGGGTTATCACTTGATCCCATGAAAAAGCCAATGAAAGGGTTATCACTTGATCCCATGAAAAAGT
3261077 CGATTGTGAG
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
72 53 1.00
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (72 bp):
AGGGTTATCACTTGATCCCATGAAAAAGCCAATGAAAGGGTTATCACTTGATCCCATGAAAAAGT
TGTTATA
Found at i:3261092 original size:37 final size:36
Alignment explanation
Indices: 3260940--3261092 Score: 135
Period size: 36 Copynumber: 4.2 Consensus size: 36
3260930 AGTTAGTGTG
*** * * * *
3260940 AGGGTTATCACTTGATCTTGTTAAAAAGCGAATGAA
1 AGGGTTATCACTTGATCCCATGAAAAAGCCATTGTA
* * ** *** *
3260976 AGGGTTATCGCTTGTTCCTGTGAAAAAGTTGTTATA
1 AGGGTTATCACTTGATCCCATGAAAAAGCCATTGTA
3261012 AGGGTTATCACTTGATCCCATGAAAAAGCCATTGTA
1 AGGGTTATCACTTGATCCCATGAAAAAGCCATTGTA
* * *
3261048 AGGGTTATCATTTGATCCCATGAAAAAGTCGATTGTG
1 AGGGTTATCACTTGATCCCATGAAAAAG-CCATTGTA
3261085 AGGGTTAT
1 AGGGTTAT
3261093 ATCTAAATCC
Statistics
Matches: 95, Mismatches: 21, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
36 81 0.85
37 14 0.15
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.33
Consensus pattern (36 bp):
AGGGTTATCACTTGATCCCATGAAAAAGCCATTGTA
Found at i:3261103 original size:37 final size:36
Alignment explanation
Indices: 3261010--3261113 Score: 113
Period size: 36 Copynumber: 2.9 Consensus size: 36
3261000 AAAGTTGTTA
*
3261010 TAAGGGTTATCACTT-GATCCCATGAAAAAGCCATTG
1 TAAGGGTTATCA-TTAAATCCCATGAAAAAGCCATTG
** *
3261046 TAAGGGTTATCATTTGATCCCATGAAAAAGTCGATTG
1 TAAGGGTTATCATTAAATCCCATGAAAAAG-CCATTG
* *
3261083 TGAGGGTTAT-ATCTAAATCCCATTAAAAAGC
1 TAAGGGTTATCAT-TAAATCCCATGAAAAAGC
3261114 AAGATTTCTT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
35 2 0.03
36 30 0.50
37 28 0.47
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (36 bp):
TAAGGGTTATCATTAAATCCCATGAAAAAGCCATTG
Found at i:3262328 original size:21 final size:19
Alignment explanation
Indices: 3262302--3262341 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
3262292 CCCTCATCTG
3262302 GATTTTAAAGCTTGGAGAAGT
1 GATTTT-AAGCTTGG-GAAGT
*
3262323 GATTTTGAGCTTGGGAAGT
1 GATTTTAAGCTTGGGAAGT
3262342 AGTTATAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 7 0.39
21 6 0.33
ACGTcount: A:0.28, C:0.05, G:0.33, T:0.35
Consensus pattern (19 bp):
GATTTTAAGCTTGGGAAGT
Found at i:3262799 original size:21 final size:21
Alignment explanation
Indices: 3262775--3262833 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
3262765 AGTGCATTAG
*
3262775 TACATGTTCATGATGTATCAA
1 TACATGTTCATAATGTATCAA
** * *
3262796 TACATG-TGGTCATGTATCGA
1 TACATGTTCATAATGTATCAA
3262816 TACATGTTCATAATGTAT
1 TACATGTTCATAATGTAT
3262834 TGATACAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.39
Consensus pattern (21 bp):
TACATGTTCATAATGTATCAA
Found at i:3262838 original size:21 final size:21
Alignment explanation
Indices: 3262775--3262840 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
3262765 AGTGCATTAG
* *
3262775 TACATGTTCATGATGTATCAA
1 TACATGTTCATAATGTATCGA
** *
3262796 TACATG-TGGTCATGTATCGA
1 TACATGTTCATAATGTATCGA
*
3262816 TACATGTTCATAATGTATTGA
1 TACATGTTCATAATGTATCGA
3262837 TACA
1 TACA
3262841 ATTATTCTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
20 16 0.44
21 20 0.56
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.38
Consensus pattern (21 bp):
TACATGTTCATAATGTATCGA
Found at i:3263927 original size:68 final size:68
Alignment explanation
Indices: 3263812--3264071 Score: 279
Period size: 68 Copynumber: 3.8 Consensus size: 68
3263802 CATGTTTGGT
* *
3263812 ATGATGAATGTCATAAGATTATGTATATGATGTAAATTTCACATACCATATGAGATTATTAAGTA
1 ATGATAAATGCCATAAGATTATGTATATGATGTAAATTTCACATACCATATGAGATTATTAAGTA
3263877 TGC
66 TGC
* * * ** * * *
3263880 ATGATAAATACTATAAGATTGTGTATATGATGTAAATTTCATTTACCATATGAGGTGATTTAGTA
1 ATGATAAATGCCATAAGATTATGTATATGATGTAAATTTCACATACCATATGAGATTATTAAGTA
3263945 TGC
66 TGC
** * * * * ** *
3263948 ATGATAAATGCCACGAGATTATGTACATGATGTATATTCCACATACTATATGAGATTATTGGGAA
1 ATGATAAATGCCATAAGATTATGTATATGATGTAAATTTCACATACCATATGAGATTATTAAGTA
*
3264013 AGC
66 TGC
* * * * *
3264016 ATGATGAATGCCATCAGATTATGTATATGATGT-ATTTTCTATATACCTTATGAGAT
1 ATGATAAATGCCATAAGATTATGTATATGATGTAAATTTC-ACATACCATATGAGAT
3264072 GAGTATGCAT
Statistics
Matches: 154, Mismatches: 37, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
67 3 0.02
68 151 0.98
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (68 bp):
ATGATAAATGCCATAAGATTATGTATATGATGTAAATTTCACATACCATATGAGATTATTAAGTA
TGC
Found at i:3264301 original size:24 final size:24
Alignment explanation
Indices: 3264256--3264301 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3264246 CAAACCATCA
*
3264256 CATTTTAATGTTAATTGAATGAGG
1 CATTTTAATGTTAATGGAATGAGG
*
3264280 CATTTTAATGTTAATGGGATGA
1 CATTTTAATGTTAATGGAATGA
3264302 TTATAGTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.04, G:0.22, T:0.41
Consensus pattern (24 bp):
CATTTTAATGTTAATGGAATGAGG
Found at i:3265171 original size:21 final size:22
Alignment explanation
Indices: 3265142--3265185 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
3265132 AAGTGATTAA
3265142 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
3265163 TTTAGGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
3265185 T
1 T
3265186 ACTTAAGAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:3268361 original size:16 final size:16
Alignment explanation
Indices: 3268327--3268360 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3268317 AAAATTAAAA
*
3268327 TTTATATTTTGATTCT
1 TTTAGATTTTGATTCT
3268343 TTTAGATTTTGATT-T
1 TTTAGATTTTGATTCT
3268358 TTT
1 TTT
3268361 TTCATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.18, C:0.03, G:0.09, T:0.71
Consensus pattern (16 bp):
TTTAGATTTTGATTCT
Found at i:3268532 original size:21 final size:20
Alignment explanation
Indices: 3268504--3268546 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
3268494 TAGAAACTAC
*
3268504 ATTCTGTTTCA-AATGTATCG
1 ATTCTGTTT-ATAATATATCG
3268524 ATTCATGTTTATAATATATCG
1 ATTC-TGTTTATAATATATCG
3268545 AT
1 AT
3268547 ACATATGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
ATTCTGTTTATAATATATCG
Found at i:3270500 original size:45 final size:44
Alignment explanation
Indices: 3270437--3270633 Score: 175
Period size: 45 Copynumber: 4.4 Consensus size: 44
3270427 AAAAGCCAAG
* * * *
3270437 TCATCATCTAGGGTAATCTCTCGACAGATGGAGTCATCAACATAA
1 TCATCATCCAGAGTAATCTC-CAACAGATGGTGTCATCAACATAA
* * * *
3270482 TCATCATCCGGTGTAATCTCCAAACGGATGGTGTCATCAACGTAA
1 TCATCATCCAGAGTAATCTCC-AACAGATGGTGTCATCAACATAA
* *
3270527 TCATCATTCAGAGTAATCTCCTAAC-GACTTGTGTCATCAACATAA
1 TCATCATCCAGAGTAATCTCC-AACAGA-TGGTGTCATCAACATAA
* * * *
3270572 TCATCATTC-GAAGTAATCTCCCAA-TGAATGGTATCATCAACCTAA
1 TCATCATCCAG-AGTAATCT-CCAACAG-ATGGTGTCATCAACATAA
*
3270617 TCATTATCCAGAGTAAT
1 TCATCATCCAGAGTAAT
3270634 ATTCCAATGG
Statistics
Matches: 127, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
44 4 0.03
45 119 0.94
46 4 0.03
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (44 bp):
TCATCATCCAGAGTAATCTCCAACAGATGGTGTCATCAACATAA
Found at i:3270589 original size:90 final size:90
Alignment explanation
Indices: 3270469--3270633 Score: 240
Period size: 90 Copynumber: 1.8 Consensus size: 90
3270459 GACAGATGGA
** * * *
3270469 GTCATCAACATAATCATCATCCGGTGTAATCTCCAAACGGATGGTGTCATCAACGTAATCATCAT
1 GTCATCAACATAATCATCATCCGAAGTAATCTCCAAACGAATGGTATCATCAACCTAATCATCAT
*
3270534 TCAGAGTAATCTCCTAACGACTTGT
66 CCAGAGTAATCTCCTAACGACTTGT
* * * *
3270559 GTCATCAACATAATCATCATTCGAAGTAATCTCCCAATGAATGGTATCATCAACCTAATCATTAT
1 GTCATCAACATAATCATCATCCGAAGTAATCTCCAAACGAATGGTATCATCAACCTAATCATCAT
3270624 CCAGAGTAAT
66 CCAGAGTAAT
3270634 ATTCCAATGG
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
90 65 1.00
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (90 bp):
GTCATCAACATAATCATCATCCGAAGTAATCTCCAAACGAATGGTATCATCAACCTAATCATCAT
CCAGAGTAATCTCCTAACGACTTGT
Found at i:3270747 original size:45 final size:44
Alignment explanation
Indices: 3270470--3270747 Score: 203
Period size: 45 Copynumber: 6.3 Consensus size: 44
3270460 ACAGATGGAG
** *
3270470 TCATCAACATAATCATCATCCGGTGTAATCTCCAAACGGATGGTG
1 TCATCAACATAATCATCATCCGAAGTAATCTCC-AACGGATGGTA
* * * *
3270515 TCATCAACGTAATCATCATTC-AGAGTAATCTCCTAAC-GACTTGTG
1 TCATCAACATAATCATCATCCGA-AGTAATCTCC-AACGGA-TGGTA
* * *
3270560 TCATCAACATAATCATCATTCGAAGTAATCTCCCAATGAATGGTA
1 TCATCAACATAATCATCATCCGAAGTAATCT-CCAACGGATGGTA
* * * * *
3270605 TCATCAACCTAATCATTATCC-AGAGTAATATTCCAATGGATGTTA
1 TCATCAACATAATCATCATCCGA-AGTAAT-CTCCAACGGATGGTA
* ** * * * * *
3270650 TCAT-AGGCATGCTCATC-TCCTAA-TAGTCT-CAATGGGTGGCA
1 TCATCA-ACATAATCATCATCCGAAGTAATCTCCAACGGATGGTA
*
3270691 TCA-CAATATAATCATCATCCGAAGTAATCTCCTAACGGATGGTA
1 TCATCAACATAATCATCATCCGAAGTAATCTCC-AACGGATGGTA
3270735 TCATCAACATAAT
1 TCATCAACATAAT
3270748 TATAGGGGGA
Statistics
Matches: 181, Mismatches: 37, Indels: 30
0.73 0.15 0.12
Matches are distributed among these distances:
40 7 0.04
41 18 0.10
42 6 0.03
43 4 0.02
44 19 0.10
45 122 0.67
46 5 0.03
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.29
Consensus pattern (44 bp):
TCATCAACATAATCATCATCCGAAGTAATCTCCAACGGATGGTA
Found at i:3276746 original size:1 final size:1
Alignment explanation
Indices: 3276742--3276778 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
3276732 GTTTTTCGTG
3276742 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3276779 GTGTCTGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3280960 original size:82 final size:82
Alignment explanation
Indices: 3280823--3280984 Score: 254
Period size: 82 Copynumber: 2.0 Consensus size: 82
3280813 AGAATTCTTC
* * * *
3280823 TTAGCATTGTAATGACACTAATACAAAGTCTATAATAACAATTGAATTACATAATTAGTTTGCAT
1 TTAGCATTCTAATGACACTAATACAAAATCTATAATAACAAGTGAAATACATAATTAGTTTGCAT
*
3280888 GTACATCACTATTTTTT
66 GCACATCACTATTTTTT
*
3280905 TTAGCATTCTAATGACACT-ATCACAAAATCTATAATAACAAGTGAAATATATAATTAGTTTGCA
1 TTAGCATTCTAATGACACTAAT-ACAAAATCTATAATAACAAGTGAAATACATAATTAGTTTGCA
3280969 TGCACATCACTATTTT
65 TGCACATCACTATTTT
3280985 CAAAACCAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
81 2 0.03
82 71 0.97
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (82 bp):
TTAGCATTCTAATGACACTAATACAAAATCTATAATAACAAGTGAAATACATAATTAGTTTGCAT
GCACATCACTATTTTTT
Found at i:3283571 original size:82 final size:82
Alignment explanation
Indices: 3283431--3283590 Score: 257
Period size: 82 Copynumber: 2.0 Consensus size: 82
3283421 TTAAGCAATA
*
3283431 CATCGAGCTCAAGCTTTCATTAGGCATAAAATTTGGAAATTAAGTTTAAGTTCCTATTGAGTTTG
1 CATCGAGCTCAAGCTTTCATTAAGCATAAAATTTGGAAATTAAGTTTAAGTTCCTATTGAGTTTG
3283496 AGCTCAATTTGTTAATT
66 AGCTCAATTTGTTAATT
* * * * * *
3283513 CATCGAGCTCAAGCTTTTATTAAGCCTAAAATTTGTAAATTGAGTTTAGGTTCTTATTGAGTTTG
1 CATCGAGCTCAAGCTTTCATTAAGCATAAAATTTGGAAATTAAGTTTAAGTTCCTATTGAGTTTG
3283578 AGCTCAATTTGTT
66 AGCTCAATTTGTT
3283591 TAAACAAATA
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 71 1.00
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (82 bp):
CATCGAGCTCAAGCTTTCATTAAGCATAAAATTTGGAAATTAAGTTTAAGTTCCTATTGAGTTTG
AGCTCAATTTGTTAATT
Found at i:3291175 original size:2 final size:2
Alignment explanation
Indices: 3291168--3291192 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3291158 AGTTCATAAA
3291168 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
3291193 AAATAAATCC
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:3292032 original size:3 final size:3
Alignment explanation
Indices: 3292026--3292054 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3292016 ATAAAATAAA
3292026 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3292055 GACGTTTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Done.