Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007819.1 Hibiscus syriacus cultivar Beakdansim tig00110156_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: 3855360
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2745 characters in sequence are not A, C, G, or T
File 12 of 17
Found at i:2435960 original size:24 final size:23
Alignment explanation
Indices: 2435931--2436004 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 23
2435921 TATCGAACAC
2435931 AATTATTAATTTTATCAAATTAAT
1 AATTATTAATTTTATCAAA-TAAT
* * * *
2435955 AATTATTAATTGGTATCGAA-CAC
1 AATTATTAATT-TTATCAAATAAT
*
2435978 AATTATTAATTTTATAAAACTAAT
1 AATTATTAATTTTATCAAA-TAAT
2436002 AAT
1 AAT
2436005 AATTTGGTAT
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
22 5 0.13
23 12 0.32
24 15 0.39
25 6 0.16
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (23 bp):
AATTATTAATTTTATCAAATAAT
Found at i:2435982 original size:47 final size:47
Alignment explanation
Indices: 2435913--2436004 Score: 166
Period size: 47 Copynumber: 2.0 Consensus size: 47
2435903 TGCATGTACT
* *
2435913 TTAATTGGTATCGAACACAATTATTAATTTTATCAAATTAATAATTA
1 TTAATTGGTATCGAACACAATTATTAATTTTATAAAACTAATAATTA
2435960 TTAATTGGTATCGAACACAATTATTAATTTTATAAAACTAATAAT
1 TTAATTGGTATCGAACACAATTATTAATTTTATAAAACTAATAAT
2436005 AATTTGGTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (47 bp):
TTAATTGGTATCGAACACAATTATTAATTTTATAAAACTAATAATTA
Found at i:2435985 original size:23 final size:23
Alignment explanation
Indices: 2435913--2435988 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
2435903 TGCATGTACT
2435913 TTAATTGGTATCGAACACAATTA
1 TTAATTGGTATCGAACACAATTA
* * * *
2435936 TTAATT-TTATCAAATTAATAATTA
1 TTAATTGGTATCGAA--CACAATTA
2435960 TTAATTGGTATCGAACACAATTA
1 TTAATTGGTATCGAACACAATTA
2435983 TTAATT
1 TTAATT
2435989 TTATAAAACT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
22 6 0.14
23 18 0.43
24 12 0.29
25 6 0.14
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (23 bp):
TTAATTGGTATCGAACACAATTA
Found at i:2436185 original size:33 final size:34
Alignment explanation
Indices: 2436105--2436191 Score: 106
Period size: 33 Copynumber: 2.6 Consensus size: 34
2436095 AATGGTAATA
* *
2436105 AACAAAATTATCAAAATAAATTGAGAAAAAATCC
1 AACAAAATTAACAAAATAAATTGAAAAAAAATCC
* * *
2436139 AACAAAATAAACAACATAAATT-AAAAAAAATCT
1 AACAAAATTAACAAAATAAATTGAAAAAAAATCC
2436172 AATC-AAATTAACAAAATAAA
1 AA-CAAAATTAACAAAATAAA
2436192 GTAAGTATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
33 25 0.56
34 20 0.44
ACGTcount: A:0.67, C:0.11, G:0.02, T:0.20
Consensus pattern (34 bp):
AACAAAATTAACAAAATAAATTGAAAAAAAATCC
Found at i:2440957 original size:33 final size:33
Alignment explanation
Indices: 2440915--2440981 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2440905 GAAAATAAAC
2440915 CAACATATTTAAGTCCTATTAAAACACTAAAAT
1 CAACATATTTAAGTCCTATTAAAACACTAAAAT
* * * *
2440948 CAACGTATTTGATTCTTATTAAAACACTAAAAT
1 CAACATATTTAAGTCCTATTAAAACACTAAAAT
2440981 C
1 C
2440982 GAAGCATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.33
Consensus pattern (33 bp):
CAACATATTTAAGTCCTATTAAAACACTAAAAT
Found at i:2441265 original size:12 final size:11
Alignment explanation
Indices: 2441248--2441419 Score: 54
Period size: 12 Copynumber: 15.5 Consensus size: 11
2441238 AACTTTTGAC
2441248 TTTTTTATTTCA
1 TTTTTTATTT-A
2441260 TTTTTTATTTA
1 TTTTTTATTTA
*
2441271 TTTACTTTATATA
1 TTT--TTTATTTA
* *
2441284 TATATTT-TTCA
1 T-TTTTTATTTA
* ** *
2441295 TTTTCTCCTAA
1 TTTTTTATTTA
*
2441306 TTTTAT-TTTA
1 TTTTTTATTTA
2441316 -TTTTTATTT-
1 TTTTTTATTTA
* *
2441325 CTTTTTATATTG
1 TTTTTTAT-TTA
* *
2441337 TTTTATATATA
1 TTTTTTATTTA
* *
2441348 TATATATATTTA
1 T-TTTTTATTTA
2441360 TTTATTTATTTA
1 TTT-TTTATTTA
*
2441372 TTTTATTA-ATA
1 TTTT-TTATTTA
2441383 TTTTTTA-TTA
1 TTTTTTATTTA
*
2441393 TTTTTT-TTCA
1 TTTTTTATTTA
2441403 TGTTTATT-TTTA
1 T-TTT-TTATTTA
2441415 TTTTT
1 TTTTT
2441420 AAAATCCAAC
Statistics
Matches: 122, Mismatches: 24, Indels: 30
0.69 0.14 0.17
Matches are distributed among these distances:
9 4 0.03
10 30 0.25
11 32 0.26
12 47 0.39
13 8 0.07
14 1 0.01
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.72
Consensus pattern (11 bp):
TTTTTTATTTA
Found at i:2441375 original size:66 final size:68
Alignment explanation
Indices: 2441249--2441387 Score: 153
Period size: 66 Copynumber: 2.1 Consensus size: 68
2441239 ACTTTTGACT
* * *
2441249 TTTTTATTTCATTTTTTATTTATTTACTTTATATATATATTTTTCATTTTCTCCTAATTTTATT-
1 TTTTTATTTCATTTTTTATTTATTTACTATATATATATATATTTCATTTTCTACTAATTTTATTA
*
2441313 TTA
66 ATA
* * *
2441316 TTTTTATTTC-TTTTTATATTGT-TTTA-TATATATATATATATTT-ATTTATTTATTTATTTTA
1 TTTTTATTTCATTTTT-TATT-TATTTACTATATATATATATATTTCATTT-TCTACTAATTTTA
2441377 TTAATA
63 TTAATA
2441383 TTTTT
1 TTTTT
2441388 TATTATTTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
65 4 0.07
66 31 0.51
67 25 0.41
68 1 0.02
ACGTcount: A:0.24, C:0.05, G:0.01, T:0.70
Consensus pattern (68 bp):
TTTTTATTTCATTTTTTATTTATTTACTATATATATATATATTTCATTTTCTACTAATTTTATTA
ATA
Found at i:2441397 original size:22 final size:23
Alignment explanation
Indices: 2441358--2441420 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
2441348 TATATATATT
2441358 TATTTATTTATT-TATTTTATTAA
1 TATTTATTTATTAT-TTTTATTAA
* *
2441381 TATTT-TTTATTATTTTTTTTCA
1 TATTTATTTATTATTTTTATTAA
*
2441403 TGTTTATTT-TTATTTTTA
1 TATTTATTTATTATTTTTA
2441421 AAATCCAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
22 25 0.74
23 9 0.26
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (23 bp):
TATTTATTTATTATTTTTATTAA
Found at i:2448600 original size:60 final size:60
Alignment explanation
Indices: 2448501--2448619 Score: 141
Period size: 60 Copynumber: 2.0 Consensus size: 60
2448491 GATGAATTTG
* * * *
2448501 GGGATGAAATTAAAATATTCAAAAGTTTAGGGACTAATTTAGAACGAGAGCCACAGTTTT
1 GGGATGAAATTAAAATATTCAAAAGTCTAGAGACCAATTTAAAACGAGAGCCACAGTTTT
* * * * *
2448561 GGGATTAAATTAAAATA-TCTAGAAGTCTAGAGACCAATTTAAAATGAGAGTCATAGTTT
1 GGGATGAAATTAAAATATTC-AAAAGTCTAGAGACCAATTTAAAACGAGAGCCACAGTTT
2448620 GAATACATAT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 2 0.04
60 47 0.96
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.29
Consensus pattern (60 bp):
GGGATGAAATTAAAATATTCAAAAGTCTAGAGACCAATTTAAAACGAGAGCCACAGTTTT
Found at i:2448929 original size:18 final size:18
Alignment explanation
Indices: 2448908--2448946 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2448898 AAAAGAAGGG
*
2448908 GAAGGAG-ACAAGAGAGTA
1 GAAGGAGAAC-AGAGAGAA
2448926 GAAGGAGAACAGAGAGAA
1 GAAGGAGAACAGAGAGAA
2448944 GAA
1 GAA
2448947 ACGAACTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.54, C:0.05, G:0.38, T:0.03
Consensus pattern (18 bp):
GAAGGAGAACAGAGAGAA
Found at i:2449463 original size:13 final size:13
Alignment explanation
Indices: 2449445--2449477 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2449435 ATTAATCAAT
*
2449445 TATATTTATTTAA
1 TATATTCATTTAA
2449458 TATATTCATTTAA
1 TATATTCATTTAA
2449471 TATATTC
1 TATATTC
2449478 GATTATTATG
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:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (13 bp):
TATATTCATTTAA
Found at i:2450530 original size:13 final size:13
Alignment explanation
Indices: 2450512--2450536 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2450502 ACAGAAATTA
2450512 ATCGTAAAATTTG
1 ATCGTAAAATTTG
2450525 ATCGTAAAATTT
1 ATCGTAAAATTT
2450537 ATGGAAACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (13 bp):
ATCGTAAAATTTG
Found at i:2453779 original size:19 final size:19
Alignment explanation
Indices: 2453751--2453790 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
2453741 GTTGGTACTC
2453751 GGTAGAATTAATAGGGTTA
1 GGTAGAATTAATAGGGTTA
*
2453770 GGTAGTATTAATAGGGTTA
1 GGTAGAATTAATAGGGTTA
2453789 GG
1 GG
2453791 GGATGGCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.33
Consensus pattern (19 bp):
GGTAGAATTAATAGGGTTA
Found at i:2454866 original size:21 final size:21
Alignment explanation
Indices: 2454840--2454917 Score: 138
Period size: 21 Copynumber: 3.7 Consensus size: 21
2454830 TGAACAATAT
*
2454840 TACAGTGCACTGATGCATTGC
1 TACAGTGCACCGATGCATTGC
2454861 TACAGTGCACCGATGCATTGC
1 TACAGTGCACCGATGCATTGC
*
2454882 TACAGTGCACCGATGCATTAC
1 TACAGTGCACCGATGCATTGC
2454903 TACAGTGCACCGATG
1 TACAGTGCACCGATG
2454918 TACTAAAATT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (21 bp):
TACAGTGCACCGATGCATTGC
Found at i:2455861 original size:20 final size:20
Alignment explanation
Indices: 2455786--2455862 Score: 67
Period size: 20 Copynumber: 4.0 Consensus size: 20
2455776 AAACCATGTA
2455786 GGGGGAATCTGTACCCCCTAG
1 GGGGGAATCTGTACCCCCT-G
** *
2455807 GGGAAAATCTGT---TCCT-
1 GGGGGAATCTGTACCCCCTG
2455823 -GGGGAATC-GATACCCCCTG
1 GGGGGAATCTG-TACCCCCTG
2455842 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
2455862 G
1 G
2455863 ACAATCTGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 15
0.67 0.09 0.23
Matches are distributed among these distances:
14 1 0.02
15 7 0.16
18 6 0.14
20 18 0.42
21 11 0.26
ACGTcount: A:0.19, C:0.27, G:0.32, T:0.21
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCTG
Found at i:2461167 original size:3 final size:3
Alignment explanation
Indices: 2461152--2461190 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
2461142 TATAAACACT
* *
2461152 TAA TAA TAC TAA TAA TAA TAC TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2461191 CCCTGACAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2461169 original size:12 final size:12
Alignment explanation
Indices: 2461152--2461190 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
2461142 TATAAACACT
2461152 TAATAATACTAA
1 TAATAATACTAA
2461164 TAATAATACTAA
1 TAATAATACTAA
*
2461176 TAATAATAATAA
1 TAATAATACTAA
2461188 TAA
1 TAA
2461191 CCCTGACAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (12 bp):
TAATAATACTAA
Found at i:2461477 original size:16 final size:16
Alignment explanation
Indices: 2461423--2461478 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
2461413 AGGAACAAGT
2461423 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
* *
2461439 T-TTCTCCTTTATGATGAGT
1 TCTTCT-CATTATGA--A-C
2461458 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
2461474 TCTTC
1 TCTTC
2461479 ATGGAAATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
15 4 0.13
16 13 0.42
17 1 0.03
18 1 0.03
19 8 0.26
20 4 0.13
ACGTcount: A:0.20, C:0.23, G:0.09, T:0.48
Consensus pattern (16 bp):
TCTTCTCATTATGAAC
Found at i:2461965 original size:92 final size:91
Alignment explanation
Indices: 2461861--2462035 Score: 262
Period size: 91 Copynumber: 1.9 Consensus size: 91
2461851 GTGATAGGTC
*
2461861 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTC-TTTCGGACGAGTTCTTCTCATTATGAGC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTT--GACGAGTTCTTCTCATTATGAAC
*
2461925 TCTCCATTGAAAATGTTGATGCGAAGTT
64 TCTCCACTGAAAATGTTGATGCGAAGTT
* * *
2461953 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTTGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTTGACGAGTTCTTCTCATTATGAACTC
* *
2462018 TTCACTGGAAATGTTGAT
66 TCCACTGAAAATGTTGAT
2462036 CCCTCAAGCG
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
91 38 0.51
92 34 0.45
93 3 0.04
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.39
Consensus pattern (91 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTTGACGAGTTCTTCTCATTATGAACTC
TCCACTGAAAATGTTGATGCGAAGTT
Found at i:2463079 original size:34 final size:34
Alignment explanation
Indices: 2463033--2463130 Score: 121
Period size: 33 Copynumber: 2.9 Consensus size: 34
2463023 CAAACCCTCC
2463033 TTTTTC-TCTTTTTATTTTTTCATTTCTTTTTTCA
1 TTTTTCATCTTTTTATTTTTTCATTT-TTTTTTCA
* *
2463067 TTTTTCATTTTTTTCTTTTTTTCA-TTTTTTTTCA
1 TTTTTCATCTTTTT-ATTTTTTCATTTTTTTTTCA
* *
2463101 -TTTTCATCTTTTTATTTGTTCCTTTTTTTT
1 TTTTTCATCTTTTTATTTTTTCATTTTTTTT
2463131 CTTCAAGCAT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
32 6 0.11
33 19 0.35
34 14 0.25
35 8 0.15
36 8 0.15
ACGTcount: A:0.08, C:0.13, G:0.01, T:0.78
Consensus pattern (34 bp):
TTTTTCATCTTTTTATTTTTTCATTTTTTTTTCA
Found at i:2463080 original size:16 final size:16
Alignment explanation
Indices: 2463059--2463129 Score: 74
Period size: 16 Copynumber: 4.4 Consensus size: 16
2463049 TTTTCATTTC
2463059 TTTTTTCATTTTTCAT
1 TTTTTTCATTTTTCAT
*
2463075 TTTTTTCTTTTTTTCATT
1 TTTTTTC-ATTTTTCA-T
2463093 TTTTTTCA-TTTTCAT
1 TTTTTTCATTTTTCAT
* *
2463108 CTTTTT-ATTTGTTCCT
1 TTTTTTCATTT-TTCAT
2463124 TTTTTT
1 TTTTTT
2463130 TCTTCAAGCA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
14 1 0.02
15 8 0.17
16 22 0.48
17 7 0.15
18 8 0.17
ACGTcount: A:0.08, C:0.13, G:0.01, T:0.77
Consensus pattern (16 bp):
TTTTTTCATTTTTCAT
Found at i:2463112 original size:24 final size:23
Alignment explanation
Indices: 2463047--2463105 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
2463037 TCTCTTTTTA
2463047 TTTTTTCA-TTTCTTTTTTCATT
1 TTTTTTCATTTTCTTTTTTCATT
2463069 TTTCATTT--TTTTCTTTTTTTCATT
1 TTT--TTTCATTTTC-TTTTTTCATT
2463093 TTTTTTCATTTTC
1 TTTTTTCATTTTC
2463106 ATCTTTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
22 6 0.19
23 4 0.13
24 21 0.68
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTTTCATTTTCTTTTTTCATT
Found at i:2463113 original size:19 final size:18
Alignment explanation
Indices: 2463049--2463113 Score: 66
Period size: 19 Copynumber: 3.7 Consensus size: 18
2463039 TCTTTTTATT
*
2463049 TTTTCATTTCTTTTTTCA
1 TTTTCATTTTTTTTTTCA
2463067 TTTTTCATTTTTTTCTTT--
1 -TTTTCATTTTTTT-TTTCA
2463085 TTTTCA--TTTTTTTTCA
1 TTTTCATTTTTTTTTTCA
*
2463101 TTTTCATCTTTTT
1 TTTTCATTTTTTT
2463114 ATTTGTTCCT
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
14 3 0.08
15 5 0.12
16 6 0.15
17 6 0.15
18 5 0.12
19 12 0.30
20 3 0.08
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTCATTTTTTTTTTCA
Found at i:2476973 original size:3 final size:3
Alignment explanation
Indices: 2476958--2477000 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
2476948 TAAACACACT
* *
2476958 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2477001 TTTTTTAACC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.03
3 34 0.97
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:2478908 original size:21 final size:21
Alignment explanation
Indices: 2478882--2478974 Score: 91
Period size: 21 Copynumber: 4.3 Consensus size: 21
2478872 GTCGAGGGTT
2478882 TTATGTGGTCATTCGGGATAA
1 TTATGTGGTCATTCGGGATAA
* *
2478903 TTATGTGGTCTTTCAGGATAA
1 TTATGTGGTCATTCGGGATAA
*
2478924 ATATGTGGT-ACTTCGGAGCA-AA
1 TTATGTGGTCA-TTCGG-G-ATAA
* *
2478946 CCTATGTGGTCATTCGGGACAA
1 -TTATGTGGTCATTCGGGATAA
2478968 TTATGTG
1 TTATGTG
2478975 TCACTTCAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
21 38 0.64
22 6 0.10
23 14 0.24
24 1 0.02
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.35
Consensus pattern (21 bp):
TTATGTGGTCATTCGGGATAA
Found at i:2478989 original size:44 final size:44
Alignment explanation
Indices: 2478904--2478989 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 44
2478894 TCGGGATAAT
* * *
2478904 TATGTGGTCTTTCAGGATAAATATGTGGTACTTCGGAGCAAACC
1 TATGTGGTCATTCAGGACAAATATGTGGTACTTCAGAGCAAACC
* * *
2478948 TATGTGGTCATTCGGGACAATTATGT-GTCACTTCAGTGCAAA
1 TATGTGGTCATTCAGGACAAATATGTGGT-ACTTCAGAGCAAA
2478990 TTACGAGCTG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
43 2 0.06
44 33 0.94
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (44 bp):
TATGTGGTCATTCAGGACAAATATGTGGTACTTCAGAGCAAACC
Found at i:2479653 original size:22 final size:22
Alignment explanation
Indices: 2479628--2479686 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
2479618 ATCAAATATA
*
2479628 TAAACGAACGATACACAAACAC
1 TAAACGAACGATAAACAAACAC
*
2479650 TAAAAC-AACGTTAAACAAACAC
1 T-AAACGAACGATAAACAAACAC
* *
2479672 TAAATGAACGTTAAA
1 TAAACGAACGATAAA
2479687 TGAACATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 3 0.09
22 25 0.78
23 4 0.12
ACGTcount: A:0.56, C:0.20, G:0.08, T:0.15
Consensus pattern (22 bp):
TAAACGAACGATAAACAAACAC
Found at i:2479692 original size:22 final size:22
Alignment explanation
Indices: 2479642--2479686 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2479632 CGAACGATAC
2479642 ACAAACACTAAAACAACGTTAA
1 ACAAACACTAAAACAACGTTAA
**
2479664 ACAAACACTAAATGAACGTTAA
1 ACAAACACTAAAACAACGTTAA
2479686 A
1 A
2479687 TGAACATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.58, C:0.20, G:0.07, T:0.16
Consensus pattern (22 bp):
ACAAACACTAAAACAACGTTAA
Found at i:2479826 original size:24 final size:24
Alignment explanation
Indices: 2479807--2479864 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
2479797 ATAAATGAAC
*
2479807 ATGAACACAATATTGAAAATTTAA
1 ATGAACACAATATTAAAAATTTAA
*
2479831 ATGAACACGATATTAAAAATTTAA
1 ATGAACACAATATTAAAAATTTAA
2479855 ATGAACACAA
1 ATGAACACAA
2479865 ACCCGAATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.55, C:0.10, G:0.09, T:0.26
Consensus pattern (24 bp):
ATGAACACAATATTAAAAATTTAA
Found at i:2488453 original size:121 final size:122
Alignment explanation
Indices: 2488252--2488503 Score: 344
Period size: 121 Copynumber: 2.1 Consensus size: 122
2488242 TTGAAAGTTT
* * * *
2488252 AACTGATAATTTAGTTACTAAACGCTTTAAGTTTTTAACGGCGAGGTACTAAAATGAAATGAAAA
1 AACTGATAATTTAATTACTAAACACGTTAAGTTTTTAACGGCGAGGTACTAAAATGAAACGAAAA
* * * * * *
2488317 CTAAACATTAGATATGGGTTTGAAAAAATTGAAAGTTTATGTATTAAAACGGATCAA
66 CTAAACATTAAATATGAGTTTGAAAAAATTAAAAATTTAGGTACTAAAACGGATCAA
* * *
2488374 AACTGATAGTTTAATTACTAAGCACGTTAAGTTTTTAATGGCG-GGTACTAAAATGAAACGAAAA
1 AACTGATAATTTAATTACTAAACACGTTAAGTTTTTAACGGCGAGGTACTAAAATGAAACGAAAA
* * * *
2488438 CTAAACGTTAAATATGATTTTGAAAAAATTAAAAATTTCGGTACTAAAATGGATCAA
66 CTAAACATTAAATATGAGTTTGAAAAAATTAAAAATTTAGGTACTAAAACGGATCAA
2488495 AACTGATAA
1 AACTGATAA
2488504 CTTATGTAGT
Statistics
Matches: 112, Mismatches: 18, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
121 75 0.67
122 37 0.33
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.31
Consensus pattern (122 bp):
AACTGATAATTTAATTACTAAACACGTTAAGTTTTTAACGGCGAGGTACTAAAATGAAACGAAAA
CTAAACATTAAATATGAGTTTGAAAAAATTAAAAATTTAGGTACTAAAACGGATCAA
Found at i:2494682 original size:19 final size:20
Alignment explanation
Indices: 2494650--2494690 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
2494640 TGTAAGTTGT
* *
2494650 AAAACAAACTAAAATAAAAC
1 AAAACAAACAAAAAAAAAAC
2494670 AAAA-AAACAAAAAAAAAAC
1 AAAACAAACAAAAAAAAAAC
2494689 AA
1 AA
2494691 TTATGTCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.83, C:0.12, G:0.00, T:0.05
Consensus pattern (20 bp):
AAAACAAACAAAAAAAAAAC
Found at i:2494830 original size:17 final size:18
Alignment explanation
Indices: 2494805--2494850 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
2494795 TATGGAATTG
* *
2494805 GATTTCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
2494822 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
2494840 GATTCCAATTC
1 GATTCCAATTC
2494851 ACTCAGAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:2496321 original size:38 final size:38
Alignment explanation
Indices: 2496279--2496355 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
2496269 CCCAGACAGC
2496279 ATTGCGAGATAACTTGTAATCTCCCATGATCCCTGCTG
1 ATTGCGAGATAACTTGTAATCTCCCATGATCCCTGCTG
2496317 ATTGCGAGATAACTTGTAATCTCCCATGATCCCTGCTG
1 ATTGCGAGATAACTTGTAATCTCCCATGATCCCTGCTG
2496355 A
1 A
2496356 CCTTTTAGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (38 bp):
ATTGCGAGATAACTTGTAATCTCCCATGATCCCTGCTG
Found at i:2502839 original size:23 final size:22
Alignment explanation
Indices: 2502813--2502863 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 22
2502803 TTATTAATAC
* *
2502813 TACATATTATATTATATTTTGTT
1 TACATAATATAATATATTTT-TT
2502836 TACATTAATATAATATATTTTTT
1 TACA-TAATATAATATATTTTTT
2502859 TACAT
1 TACAT
2502864 GATTCAGGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 1 0.04
23 10 0.40
24 14 0.56
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (22 bp):
TACATAATATAATATATTTTTT
Found at i:2503774 original size:39 final size:39
Alignment explanation
Indices: 2503730--2503806 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
2503720 CCCTCCATCC
*
2503730 AGCAGCCCCTCCACACATCATTTCCAGCAGCTTCCAGCG
1 AGCAGCCCCTCCACACATCAGTTCCAGCAGCTTCCAGCG
* *
2503769 AGCAGCCCCTCCACGCATCAGTTGCAGCAGCTTCCAGC
1 AGCAGCCCCTCCACACATCAGTTCCAGCAGCTTCCAGC
2503807 ACTGCCAGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.22, C:0.43, G:0.18, T:0.17
Consensus pattern (39 bp):
AGCAGCCCCTCCACACATCAGTTCCAGCAGCTTCCAGCG
Found at i:2504150 original size:17 final size:17
Alignment explanation
Indices: 2504112--2504143 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2504102 CCAACAACAC
2504112 AAAAACCAGAAGAAAAA
1 AAAAACCAGAAGAAAAA
2504129 AAAAA-CAGAAGAAAA
1 AAAAACCAGAAGAAAA
2504144 GGAAAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.78, C:0.09, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAAACCAGAAGAAAAA
Found at i:2505259 original size:12 final size:11
Alignment explanation
Indices: 2505244--2505320 Score: 75
Period size: 12 Copynumber: 6.7 Consensus size: 11
2505234 ATTTCATTAT
2505244 TTATTTGTAATA
1 TTATTT-TAATA
*
2505256 TTATTTTATTA
1 TTATTTTAATA
2505267 TTACTTTTAAT-
1 TTA-TTTTAATA
*
2505278 GTATTTTAATTA
1 TTATTTTAA-TA
*
2505290 TTACTTTAATTA
1 TTATTTTAA-TA
*
2505302 TTATTTTATTA
1 TTATTTTAATA
2505313 TTATTTTA
1 TTATTTTA
2505321 GTCTTATAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
10 6 0.11
11 20 0.36
12 29 0.53
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:2505283 original size:34 final size:34
Alignment explanation
Indices: 2505245--2505309 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
2505235 TTTCATTATT
*
2505245 TATTTGTAA-TATTA-TTTTATTATTACTTTTAATG
1 TATTT-TAATTATTACTTTAATTATTA-TTTTAATG
2505279 TATTTTAATTATTACTTTAATTATTATTTTA
1 TATTTTAATTATTACTTTAATTATTATTTTA
2505310 TTATTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 3 0.11
34 15 0.54
35 10 0.36
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (34 bp):
TATTTTAATTATTACTTTAATTATTATTTTAATG
Found at i:2505289 original size:23 final size:21
Alignment explanation
Indices: 2505255--2505320 Score: 80
Period size: 23 Copynumber: 3.0 Consensus size: 21
2505245 TATTTGTAAT
2505255 ATTATTTTATTATTACTTTTA
1 ATTATTTTATTATTACTTTTA
*
2505276 ATGTATTTTAATTATTACTTTAATT
1 AT-TATTTT-ATTATTACTTT--TA
2505301 ATTATTTTATTATTA-TTTTA
1 ATTATTTTATTATTACTTTTA
2505321 GTCTTATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
20 1 0.03
21 2 0.05
22 9 0.23
23 18 0.46
24 6 0.15
25 3 0.08
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (21 bp):
ATTATTTTATTATTACTTTTA
Found at i:2505337 original size:2 final size:2
Alignment explanation
Indices: 2505325--2505367 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
2505315 ATTTTAGTCT
* *
2505325 TA TA AA TA TA TA TA TA TG 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
2505367 T
1 T
2505368 TTGTTTAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2505481 original size:21 final size:19
Alignment explanation
Indices: 2505457--2505504 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
2505447 ATATTCTTAA
2505457 ATAAATAAATATCTTACTTTT
1 ATAAATAAATATC-TA-TTTT
*
2505478 ATAAAT-TATATCTATTTT
1 ATAAATAAATATCTATTTT
2505496 -TAAATAAAT
1 ATAAATAAAT
2505505 GTTTTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 5 0.21
18 6 0.25
19 2 0.08
20 5 0.21
21 6 0.25
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (19 bp):
ATAAATAAATATCTATTTT
Found at i:2505488 original size:129 final size:123
Alignment explanation
Indices: 2505324--2505641 Score: 306
Period size: 129 Copynumber: 2.5 Consensus size: 123
2505314 TATTTTAGTC
* * * * *
2505324 TTATAAATATATATATATGTATATATATATATATATATATATATTTGTTTAAATAATAATATTTA
1 TTATAAATAAATAAATATAT-TATTTATAAATATAT-TATATATTT-TTTAAATAATAATATTTA
* **
2505389 TTTATT-TTTAATATCAAAGAAAATGGGTTGTCTTAAAGCACCTAGAAGTCATTTTCTGATAT
63 TTTATTATTTAATAT-AAAGAAAA-GAGTTGTCTTAAAGCACCTAGAAACCATTTTCTGATAT
* *
2505451 TCT-TAAATAAATAAATATCTTACTTTTATAAAT-TA-TATCTA-TTTTTAAATAAATGTTTTAA
1 T-TATAAATAAATAAATATATTA--TTTATAAATATATTATATATTTTTTAAAT-AA-----TAA
* * *
2505512 TATTTATTTATTCATTTTATATTAAGAAAAGAGTTGTCTTAAAGCACCTAGAAACCCTTTTCTGA
57 TATTTATTTATT-ATTTAATATAAAGAAAAGAGTTGTCTTAAAGCACCTAGAAACCATTTTCTGA
2505577 TAT
121 TAT
* *
2505580 TTATAAATAAATAAATATATTATTTATATATATATTAATATATTTTTTATATTAATAA-ATTT
1 TTATAAATAAATAAATATATTATTTATAAATATATT-ATATATTTTTTA-AATAATAATATTT
2505642 GAAATAACAT
Statistics
Matches: 158, Mismatches: 16, Indels: 36
0.75 0.08 0.17
Matches are distributed among these distances:
123 7 0.04
124 4 0.03
125 9 0.06
126 5 0.03
127 25 0.16
128 11 0.07
129 69 0.44
130 11 0.07
131 15 0.09
132 2 0.01
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (123 bp):
TTATAAATAAATAAATATATTATTTATAAATATATTATATATTTTTTAAATAATAATATTTATTT
ATTATTTAATATAAAGAAAAGAGTTGTCTTAAAGCACCTAGAAACCATTTTCTGATAT
Found at i:2505604 original size:23 final size:23
Alignment explanation
Indices: 2505577--2505639 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
2505567 CCTTTTCTGA
2505577 TATTTATAAATAAATAAATATAT
1 TATTTATAAATAAATAAATATAT
* * *
2505600 TATTTATATATATATTAATATAT
1 TATTTATAAATAAATAAATATAT
*
2505623 TTTTTATATTAATAAAT
1 TATTTATA--AATAAAT
2505640 TTGAAATAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 27 0.84
25 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTTATAAATAAATAAATATAT
Found at i:2506131 original size:7 final size:7
Alignment explanation
Indices: 2506119--2506170 Score: 59
Period size: 7 Copynumber: 6.9 Consensus size: 7
2506109 TTTCAAATTT
2506119 TTTATTA
1 TTTATTA
2506126 TTTATTA
1 TTTATTA
*
2506133 TTTTTATA
1 TTTAT-TA
2506141 TATTATTA
1 T-TTATTA
2506149 TTTATTA
1 TTTATTA
2506156 TTTTATTTA
1 -TTTA-TTA
2506165 TTTATT
1 TTTATT
2506171 TTATTCAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
7 19 0.49
8 14 0.36
9 6 0.15
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTATTA
Found at i:2506138 original size:16 final size:16
Alignment explanation
Indices: 2506117--2506172 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 16
2506107 TCTTTCAAAT
2506117 TTTTTATTATTTATTA
1 TTTTTATTATTTATTA
2506133 TTTTTA-TATATTATTA
1 TTTTTATTAT-TTATTA
2506149 TTTATTATTTTATTTATTTA
1 TTT-TTA--TTATTTA-TTA
2506169 TTTT
1 TTTT
2506173 ATTCAAGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
15 3 0.09
16 15 0.44
17 3 0.09
19 4 0.12
20 9 0.26
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTATTATTTATTA
Found at i:2506139 original size:13 final size:14
Alignment explanation
Indices: 2506123--2506175 Score: 69
Period size: 13 Copynumber: 4.1 Consensus size: 14
2506113 AAATTTTTTA
2506123 TTATTTATTATT-T
1 TTATTTATTATTAT
*
2506136 TTATATATTATTAT
1 TTATTTATTATTAT
2506150 TTA-TTATT-TTAT
1 TTATTTATTATTAT
2506162 TTATTTATT-TTAT
1 TTATTTATTATTAT
2506175 T
1 T
2506176 CAAGAATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
12 7 0.19
13 25 0.69
14 4 0.11
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTTATTATTAT
Found at i:2506146 original size:20 final size:20
Alignment explanation
Indices: 2506115--2506175 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
2506105 TTTCTTTCAA
*
2506115 ATTTTTTATTATTTATTATT
1 ATTTTATATTATTTATTATT
2506135 -TTTATATATTA-TTATTTATT
1 ATTT-TATATTATTTA-TTATT
2506155 ATTTTAT-TTATTTATT-TT
1 ATTTTATATTATTTATTATT
2506173 ATT
1 ATT
2506176 CAAGAATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
18 5 0.14
19 11 0.31
20 17 0.47
21 3 0.08
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
ATTTTATATTATTTATTATT
Found at i:2506169 original size:23 final size:23
Alignment explanation
Indices: 2506115--2506170 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
2506105 TTTCTTTCAA
2506115 ATTT-TTTATTATTTATTATTTT
1 ATTTATTTATTATTTATTATTTT
*
2506137 -TATATATTATTATTTATTATTTT
1 ATTTAT-TTATTATTTATTATTTT
2506160 ATTTATTTATT
1 ATTTATTTATT
2506171 TTATTCAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 2 0.07
22 1 0.03
23 22 0.76
24 4 0.14
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (23 bp):
ATTTATTTATTATTTATTATTTT
Found at i:2507776 original size:14 final size:14
Alignment explanation
Indices: 2507757--2507809 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
2507747 TTTTAAATAA
*
2507757 TTTACATTTACATT
1 TTTACATTTGCATT
*
2507771 TTTACATTTGCATA
1 TTTACATTTGCATT
2507785 TTTACATTTGGCATT
1 TTTACATTT-GCATT
*
2507800 TTTGCATTTG
1 TTTACATTTG
2507810 TATTGCACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.23, C:0.13, G:0.09, T:0.55
Consensus pattern (14 bp):
TTTACATTTGCATT
Found at i:2510420 original size:13 final size:13
Alignment explanation
Indices: 2510402--2510455 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
2510392 CTCATCCAGC
2510402 AAAGAAAGAAGAA
1 AAAGAAAGAAGAA
2510415 AAAGAAAGAAGAA
1 AAAGAAAGAAGAA
* *
2510428 AAA-AAAAAAAAA
1 AAAGAAAGAAGAA
*
2510440 AAAAAAAGAAGGAA
1 AAAGAAAGAA-GAA
2510454 AA
1 AA
2510456 TCGAATAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
12 10 0.29
13 21 0.60
14 4 0.11
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAGAA
Found at i:2512786 original size:83 final size:83
Alignment explanation
Indices: 2512685--2512949 Score: 460
Period size: 83 Copynumber: 3.2 Consensus size: 83
2512675 AATGGAACAA
2512685 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
2512750 AATCATTGAATTTGGAAG
66 AATCATTGAATTTGGAAG
2512768 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
*
2512833 AATCATTGAATTTAGAAG
66 AATCATTGAATTTGGAAG
* * * *
2512851 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGG-TTGGACAGAAC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAAAAC
2512915 CAATCATTGAATTTGGAAG
65 CAATCATTGAATTTGGAAG
*
2512934 ATGAATTTGCTCATAG
1 ATGAATGTGCTCATAG
2512950 TAGAAATAAG
Statistics
Matches: 174, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
82 4 0.02
83 170 0.98
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (83 bp):
ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
AATCATTGAATTTGGAAG
Found at i:2515328 original size:54 final size:52
Alignment explanation
Indices: 2515178--2515378 Score: 212
Period size: 54 Copynumber: 3.8 Consensus size: 52
2515168 AGAAATCTTG
* * * *
2515178 GCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAACGCTTTATGAACGTCTGA
1 GCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTA-CAAC-TCTGA
* * *
2515232 GCAAAAACCACA-AGAAAGAATGAATGTGTTGTCAAATATTTTACAAACATCTGA
1 GCAGAAACCACAGA-AAAGGATGAATGTGTTGTCAAATGTTTTAC-AAC-TCTGA
* * * *
2515286 GCAGAAGCCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATC-CCGA
1 GCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACAACTCTGA
*
2515337 -CAGAAACCACAGGAAAA-GATGAATGTATTGTCAAATGTTTTA
1 GCAGAAACCACA-GAAAAGGATGAATGTGTTGTCAAATGTTTTA
2515379 TGAACCAGTG
Statistics
Matches: 125, Mismatches: 18, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
50 33 0.26
51 8 0.06
53 3 0.02
54 80 0.64
55 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.24
Consensus pattern (52 bp):
GCAGAAACCACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACAACTCTGA
Found at i:2515779 original size:22 final size:22
Alignment explanation
Indices: 2515750--2515804 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
2515740 ATCTACACTC
*
2515750 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
2515772 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
2515794 TTCAAAGATGA
1 TTCAAAGATGA
2515805 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:2516588 original size:166 final size:164
Alignment explanation
Indices: 2516307--2516628 Score: 513
Period size: 166 Copynumber: 1.9 Consensus size: 164
2516297 AGAATGAGCA
* * *
2516307 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAACATAATGAGAAAACGA
1 TTATCTGGAGATTGGGACATGTTACCCAATCAACAGGTTATTT-AAAAACATAATGAGAAAACGA
* **
2516372 TTTCCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGA-TTTT
65 TTTCCAAAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTT
2516436 CTTAGTTTTTTTACTTATTAAACTATTTCCAACAACC
130 CTTAG-TTTTTTACTTATTAAAC-ATTTCCAACAACC
*
2516473 TTATCTGGAGATTGGGACATGTTACCCAATCAACAGGTTATCTT-GAAACATAATGAGAAAACGA
1 TTATCTGGAGATTGGGACATGTTACCCAATCAACAGGTTAT-TTAAAAACATAATGAGAAAACGA
*
2516537 TTTCCAAAGTTTCTCATTCAATCTTTTCTGAAAATGAAATTGTTGAAAAGTAAGAAAACTATTTT
65 TTTCCAAAGTTTCTCATTCAATCTTTTCT-AAAATGAAATTGTTGAAAAGTAAGAAAACGATTTT
2516602 TCTTAGTTTTTTACTTATTAAACATTT
129 TCTTAGTTTTTTACTTATTAAACATTT
2516629 TCCTTCAAAA
Statistics
Matches: 145, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
165 49 0.34
166 85 0.59
167 11 0.08
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (164 bp):
TTATCTGGAGATTGGGACATGTTACCCAATCAACAGGTTATTTAAAAACATAATGAGAAAACGAT
TTCCAAAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTTC
TTAGTTTTTTACTTATTAAACATTTCCAACAACC
Found at i:2516689 original size:36 final size:36
Alignment explanation
Indices: 2516626--2516907 Score: 230
Period size: 36 Copynumber: 7.7 Consensus size: 36
2516616 TTATTAAACA
*
2516626 TTTTCCTTCAAAACAACAATTTATCTCACTTGAGATTG
1 TTTTTCTT-AAAACAA-AATTTATCTCACTTGAGATTG
* * **
2516664 TTTTTCTTAAAACAAAATTTGTCTCACTCGAGACAG
1 TTTTTCTTAAAACAAAATTTATCTCACTTGAGATTG
** **
2516700 TTTCACTCGAAACAACAATTTATCTCACTTGAGATTG
1 TTTTTCTTAAAACAA-AATTTATCTCACTTGAGATTG
* * **
2516737 TTTTTCTTAAAACAAAATTTGTCTCACTCGAGACAG
1 TTTTTCTTAAAACAAAATTTATCTCACTTGAGATTG
* *
2516773 --TTTCATTCGAAACAGCAATTTATCTCACTTGAGATTG
1 TTTTTC-TT-AAAACA-AAATTTATCTCACTTGAGATTG
* * * **
2516810 TTTTTCTTAAAACAAAATTTGTCTCGCTCGAGACAG
1 TTTTTCTTAAAACAAAATTTATCTCACTTGAGATTG
* * *
2516846 --TTTCATTCGAAACAGCAATTTATCTCACTTGAAATTG
1 TTTTTC-TT-AAAACA-AAATTTATCTCACTTGAGATTG
* *
2516883 TTTTCCTTAAAACAAAATTTGTCTC
1 TTTTTCTTAAAACAAAATTTATCTC
2516908 GCTCGAGACA
Statistics
Matches: 187, Mismatches: 46, Indels: 24
0.73 0.18 0.09
Matches are distributed among these distances:
34 8 0.04
35 4 0.02
36 80 0.43
37 77 0.41
38 11 0.06
39 7 0.04
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (36 bp):
TTTTTCTTAAAACAAAATTTATCTCACTTGAGATTG
Found at i:2516755 original size:73 final size:73
Alignment explanation
Indices: 2516636--2516932 Score: 522
Period size: 73 Copynumber: 4.1 Consensus size: 73
2516626 TTTTCCTTCA
2516636 AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCACTCGAGACAGT
1 AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCACTCGAGACAGT
2516701 TTCACTCG
66 TTCACTCG
2516709 AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCACTCGAGACAGT
1 AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCACTCGAGACAGT
*
2516774 TTCATTCG
66 TTCACTCG
* *
2516782 AAACAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTCGAGACAGT
1 AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCACTCGAGACAGT
*
2516847 TTCATTCG
66 TTCACTCG
* * * *
2516855 AAACAGCAATTTATCTCACTTGAAATTGTTTTCCTTAAAACAAAATTTGTCTCGCTCGAGACAGT
1 AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCACTCGAGACAGT
2516920 TTCACTCG
66 TTCACTCG
2516928 AAACA
1 AAACA
2516933 TAAATTTCCA
Statistics
Matches: 218, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 218 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (73 bp):
AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCACTCGAGACAGT
TTCACTCG
Found at i:2517284 original size:113 final size:113
Alignment explanation
Indices: 2516939--2517273 Score: 589
Period size: 113 Copynumber: 3.0 Consensus size: 113
2516929 AACATAAATT
* *
2516939 TCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAAAAGAACTCATCTGAAGAAG
1 TCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
2517004 GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAA
66 GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAA
*
2517052 TCCATTACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
1 TCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
2517117 GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAA
66 GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAA
* *
2517165 TCCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAATTCATCTGAAGAAG
1 TCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
* ** *
2517230 GAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCT
66 GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCT
2517274 AGATTTCATC
Statistics
Matches: 212, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 212 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (113 bp):
TCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAA
Found at i:2517558 original size:39 final size:39
Alignment explanation
Indices: 2517514--2517590 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
2517504 CCCTCCATCC
*
2517514 AGCAGCCCCTCCACACATCATTTCCAGCAGCTTCCAGCG
1 AGCAGCCCCTCCACACATCAGTTCCAGCAGCTTCCAGCG
* *
2517553 AGCAGCCCCTCCACGCATCAGTTGCAGCAGCTTCCAGC
1 AGCAGCCCCTCCACACATCAGTTCCAGCAGCTTCCAGC
2517591 ACTGCCAGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.22, C:0.43, G:0.18, T:0.17
Consensus pattern (39 bp):
AGCAGCCCCTCCACACATCAGTTCCAGCAGCTTCCAGCG
Found at i:2517933 original size:17 final size:17
Alignment explanation
Indices: 2517895--2517926 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2517885 CCAACAACAC
2517895 AAAAACCAGAAGAAAAA
1 AAAAACCAGAAGAAAAA
2517912 AAAAA-CAGAAGAAAA
1 AAAAACCAGAAGAAAA
2517927 GGAAAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.78, C:0.09, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAAACCAGAAGAAAAA
Found at i:2519041 original size:12 final size:11
Alignment explanation
Indices: 2519026--2519102 Score: 75
Period size: 12 Copynumber: 6.7 Consensus size: 11
2519016 ATTTCATTAT
2519026 TTATTTGTAATA
1 TTATTT-TAATA
*
2519038 TTATTTTATTA
1 TTATTTTAATA
2519049 TTACTTTTAAT-
1 TTA-TTTTAATA
*
2519060 GTATTTTAATTA
1 TTATTTTAA-TA
*
2519072 TTACTTTAATTA
1 TTATTTTAA-TA
*
2519084 TTATTTTATTA
1 TTATTTTAATA
2519095 TTATTTTA
1 TTATTTTA
2519103 GTCTTATAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
10 6 0.11
11 20 0.36
12 29 0.53
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:2519065 original size:34 final size:34
Alignment explanation
Indices: 2519027--2519091 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
2519017 TTTCATTATT
*
2519027 TATTTGTAA-TATTA-TTTTATTATTACTTTTAATG
1 TATTT-TAATTATTACTTTAATTATTA-TTTTAATG
2519061 TATTTTAATTATTACTTTAATTATTATTTTA
1 TATTTTAATTATTACTTTAATTATTATTTTA
2519092 TTATTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 3 0.11
34 15 0.54
35 10 0.36
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (34 bp):
TATTTTAATTATTACTTTAATTATTATTTTAATG
Found at i:2519071 original size:23 final size:21
Alignment explanation
Indices: 2519037--2519102 Score: 80
Period size: 23 Copynumber: 3.0 Consensus size: 21
2519027 TATTTGTAAT
2519037 ATTATTTTATTATTACTTTTA
1 ATTATTTTATTATTACTTTTA
*
2519058 ATGTATTTTAATTATTACTTTAATT
1 AT-TATTTT-ATTATTACTTT--TA
2519083 ATTATTTTATTATTA-TTTTA
1 ATTATTTTATTATTACTTTTA
2519103 GTCTTATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
20 1 0.03
21 2 0.05
22 9 0.23
23 18 0.46
24 6 0.15
25 3 0.08
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (21 bp):
ATTATTTTATTATTACTTTTA
Found at i:2519119 original size:2 final size:2
Alignment explanation
Indices: 2519107--2519159 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
2519097 ATTTTAGTCT
* *
2519107 TA TA AA TA TA TA TA TG 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
2519149 TA TA TA TA TA T
1 TA TA TA TA TA T
2519160 TTGTTTAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2519272 original size:21 final size:19
Alignment explanation
Indices: 2519248--2519295 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
2519238 ATATTCTTAA
2519248 ATAAATAAATATCTTACTTTT
1 ATAAATAAATATC-TA-TTTT
*
2519269 ATAAAT-TATATCTATTTT
1 ATAAATAAATATCTATTTT
2519287 -TAAATAAAT
1 ATAAATAAAT
2519296 GTTTTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 5 0.21
18 6 0.25
19 2 0.08
20 5 0.21
21 6 0.25
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (19 bp):
ATAAATAAATATCTATTTT
Found at i:2519833 original size:2 final size:2
Alignment explanation
Indices: 2519828--2519857 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2519818 CCTTAAAAAT
2519828 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2519858 CTATGGATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2524240 original size:164 final size:164
Alignment explanation
Indices: 2524047--2525122 Score: 804
Period size: 164 Copynumber: 6.5 Consensus size: 164
2524037 CTATTTGCCA
2524047 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGT
*
2524112 CGAGAAGGGCTATCTG-CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATT
66 CGAGAAGGGCTATCTGCCCAAAGACCCCCGAGTTCGACTACACTCAGC-TCGAGGGCATATCATT
* *
2524176 CACAGCATAACTCAAGTCTAGAAGGGTTATCTGTC
130 TACAGCATAACTCAAGTCTAAAAGGGTTATCTGTC
* * * *
2524211 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGT
* * * *** * * * * *
2524276 CTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTTGACTACGCTCAGCTCAACGGCACATCA
66 CGAGAAGGGCTATCTGCC--C-AAAGACCCCCGAGTTCGACTACACTCAGCTCGAGGGCATATCA
* * * * * *
2524341 TTTGCAGCATAGCTTAAGTCGAAAAGAGCTATCTG--
128 TTTACAGCATAACTCAAGTCTAAAAGGGTTATCTGTC
** * * * * * ** * *
2524376 -CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTCACAGCATAACTCAAG
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCAAAGGCACATCATTTGCAGCATAGCTTAAG
* * ** * * * *
2524440 TCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCTACTACGCTCAGCTCCAAGGCATATCA
65 TCGAGAAGGGCTATCTG-C-CCAAAGACCCCCGAGTTCGACTACACTCAGCTCGAGGGCATATCA
* * * * *
2524505 TTTGCAGTACAACTTAAGTCTAAAAGGGTTGTCT-TCC
128 TTTACAGCATAACTCAAGTCTAAAAGGGTTATCTGT-C
* * *
2524542 AACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCTTAAG
1 -ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAG
* * *
2524607 TCGAGAAGGGCTGTCT-TCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCAT
65 TCGAGAAGGGCTATCTGCCCAAAGACCCCCGAGTTCGACTACACTCAGC-TCGAGGGCATATCAT
* ** *
2524671 TTACAGCATAACTCAAGGCTAGGAGGGTTATCTGCC
129 TTACAGCATAACTCAAGTCTAAAAGGGTTATCTGTC
* * * *
2524707 AACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGA
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAG-
* * * * *** * * * * *
2524772 T-AAGAAGGGATATTTGCCAATAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGTACATC
65 TCGAGAAGGGCTATCTGCC---CAAAGACCCCCGAGTTCGACTACACTCAGCTCGAGGGCATATC
** * * * * * * *
2524836 ATTTGTAGTATAGCTTAAGTCGAGAAGGGCTAACT-T-
127 ATTTACAGCATAACTCAAGTCTAAAAGGGTTATCTGTC
* * * * * * * *
2524872 -CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGTATAACTCAAG
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCAAAGGCACATCATTTGCAGCATAGCTTAAG
* * * * ** * * *
2524936 GCTAGAAGGGTTATATGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCGAAGGCACATC
65 TCGAGAAGGGCTATCTG-C--CCAAAGACCCCCGAGTTCGACTACACTCAGCTCGAGGGCATATC
* * * * * * * * *
2525001 ATCTGCAGCATAGCTTAAGTCGATAAGAGCTATCTGCC
127 ATTTACAGCATAACTCAAGTCTAAAAGGGTTATCTGTC
* * * * * * * ** *
2525039 AACCGAGGACCTTTGAGTTCGATTACACTCATCTCAAAGGCAAATCAAGTTCACAGCATAGCTCA
1 -ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATC-A-TTTGCAGCATAGCTTA
* *
2525104 AGGCAAGAAGGGCTATCTG
63 AGTCGAGAAGGGCTATCTG
2525123 TCAATAAATT
Statistics
Matches: 729, Mismatches: 153, Indels: 54
0.78 0.16 0.06
Matches are distributed among these distances:
164 285 0.39
165 192 0.26
166 2 0.00
167 112 0.15
168 83 0.11
169 27 0.04
170 28 0.04
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (164 bp):
ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGT
CGAGAAGGGCTATCTGCCCAAAGACCCCCGAGTTCGACTACACTCAGCTCGAGGGCATATCATTT
ACAGCATAACTCAAGTCTAAAAGGGTTATCTGTC
Found at i:2524303 original size:84 final size:83
Alignment explanation
Indices: 2524042--2525085 Score: 948
Period size: 84 Copynumber: 12.6 Consensus size: 83
2524032 AATGGCTATT
* *
2524042 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCT
1 TGCCAA-CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
* *
2524107 TAAGTCGAGAAGGGCTATC
65 TAAGTCTAGAAGGGTTATC
** * * * * * **
2524126 TG-C--CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTCACAGCATAACT
1 TGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACT
*
2524188 CAAGTCTAGAAGGGTTATC
65 TAAGTCTAGAAGGGTTATC
* * * *
2524207 TGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTT
1 TGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTT
*
2524272 AAGTCTAGAAGGGTTGTC
66 AAGTCTAGAAGGGTTATC
* * *
2524290 TGCCAACAAAAGACCTTTGAGTTTGACTACGCTCAGCT-CAACGGCACATCATTTGCAGCATAGC
1 TGCCAAC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAAC
* * * *
2524354 TTAAGTCGAAAAGAGCTATC
64 TTAAGTCTAGAAGGGTTATC
** * * * * * **
2524374 TG-C--CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTCACAGCATAACT
1 TGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACT
*
2524436 CAAGTCTAGAAGGGTTATC
65 TAAGTCTAGAAGGGTTATC
* * * * * *
2524455 TGTCACCAAAGACCTTCGAGTTCTACTACGCTCAGCTCCAAGGCATATCATTTGCAGTACAACTT
1 TGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTT
* *
2524520 AAGTCTAAAAGGGTTGTC
66 AAGTCTAGAAGGGTTATC
* * *
2524538 TTCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGGCACATCATTTGCAGCATAGC
1 TGCCAAC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAAC
* * *
2524602 TTAAGTCGAGAAGGGCTGTC
64 TTAAGTCTAGAAGGGTTATC
* ** * * * * * *
2524622 T-TC--CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACT
1 TGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACT
* * *
2524684 CAAGGCTAGGAGGGTTATC
65 TAAGTCTAGAAGGGTTATC
* * *
2524703 TGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAGCTC
1 TGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTT
* * *
2524768 AAGAT-AAGAAGGGATATT
66 AAG-TCTAGAAGGGTTATC
* * * * * *
2524786 TGCCAATAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGTACATCATTTGTAGTATAGCT
1 TGCCAA-CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
* * *
2524851 TAAGTCGAGAAGGGCTAAC
65 TAAGTCTAGAAGGGTTATC
* * * * * * *
2524870 T-TC--CAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGTATAACT
1 TGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACT
* * *
2524932 CAAGGCTAGAAGGGTTATA
65 TAAGTCTAGAAGGGTTATC
* * *
2524951 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCGAAGGCACATCATCTGCAGCATAGCT
1 TGCCAA-CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
* * * *
2525016 TAAGTCGATAAGAGCTATC
65 TAAGTCTAGAAGGGTTATC
* * * * * * * *
2525035 TGCCAACCGAGGACCTTTGAGTTCGATTACACTCATCTCAAAGGCAAATCA
1 TGCCAA-CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCA
2525086 AGTTCACAGC
Statistics
Matches: 771, Mismatches: 163, Indels: 52
0.78 0.17 0.05
Matches are distributed among these distances:
80 98 0.13
81 150 0.19
82 6 0.01
83 139 0.18
84 351 0.46
85 27 0.04
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (83 bp):
TGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTT
AAGTCTAGAAGGGTTATC
Found at i:2524445 original size:248 final size:248
Alignment explanation
Indices: 2524042--2525122 Score: 1543
Period size: 248 Copynumber: 4.3 Consensus size: 248
2524032 AATGGCTATT
* *
2524042 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCT
1 TGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCT
2524107 TAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATAT
66 TAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATAT
* *
2524172 CATTCACAGCATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
131 CATTCACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
* *
2524237 CTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTC
196 CTCAGCTCCAAGGCACATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTATC
* *
2524290 TGCCAACAAAAGACCTTTGAGTTTGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCT
1 TGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCT
* *
2524355 TAAGTCGAAAAGAGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATAT
66 TAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATAT
* * *
2524420 CATTCACAGCATAACTCAAGTCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCTACTACG
131 CATTCACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
* * * *
2524485 CTCAGCTCCAAGGCATATCATTTGCAGTACAACTTAAGTCTAAAAGGGTTGTC
196 CTCAGCTCCAAGGCACATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTATC
* *
2524538 TTCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTGCAGCATAGCT
1 TGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCT
* *
2524603 TAAGTCGAGAAGGGCTGTCTTCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATAT
66 TAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATAT
* * *
2524668 CATTTACAGCATAACTCAAGGCTAGGAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
131 CATTCACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
* * * * * * *
2524733 CTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGAT-AAGAAGGGATATT
196 CTCAGCTCCAAGGCACATCATTTGCAGCACAACTTAAG-TCTAGAAGGGTTATC
* * * * *
2524786 TGCCAATAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGTACATCATTTGTAGTATAGCT
1 TGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCT
* * * *
2524851 TAAGTCGAGAAGGGCTAACTTCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
66 TAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATAT
** * *
2524916 CATTTGCAGTATAACTCAAGGCTAGAAGGGTTATATGCCAACCAAAGACCTTCGAGTTCGACTAC
131 CATTCACAGCATAACTCAAGGCTAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTAC
* * * * * * * *
2524981 GCTCAGCTCGAAGGCACATCATCTGCAGCATAGCTTAAGTCGATAAGAGCTATC
195 GCTCAGCTCCAAGGCACATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTATC
** * * * * * **
2525035 TGCCAACCGAGGACCTTTGAGTTCGATTACACTCATCTCAAAGGCAAATCAAGTTCACAGCATAG
1 TGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATC-A-TTTGCAGCATAG
* * *
2525100 CTCAAGGCAAGAAGGGCTATCTG
64 CTTAAGTCGAGAAGGGCTATCTG
2525123 TCAATAAATT
Statistics
Matches: 752, Mismatches: 76, Indels: 7
0.90 0.09 0.01
Matches are distributed among these distances:
248 617 0.82
249 108 0.14
250 1 0.00
251 26 0.03
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (248 bp):
TGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCT
TAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATAT
CATTCACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTATC
Found at i:2525724 original size:23 final size:22
Alignment explanation
Indices: 2525698--2525748 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 22
2525688 TTATTAATAC
* *
2525698 TACATATTATATTATATTTTGTT
1 TACATACTATAATATATTTT-TT
2525721 TACATTACTATAATATATTTTTT
1 TACA-TACTATAATATATTTTTT
2525744 TACAT
1 TACAT
2525749 GATTCAGGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 1 0.04
23 10 0.40
24 14 0.56
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.57
Consensus pattern (22 bp):
TACATACTATAATATATTTTTT
Found at i:2526762 original size:2 final size:2
Alignment explanation
Indices: 2526755--2526789 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2526745 TCTCATATCC
2526755 AT AT AT AT AT 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 AT AT AT AT AT A
2526790 CGCTCTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2526995 original size:19 final size:19
Alignment explanation
Indices: 2526973--2527015 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
2526963 AGATGTAAGT
2526973 AATTTAAATTGAAATTTTA
1 AATTTAAATTGAAATTTTA
** * *
2526992 AATTTCGATTTAAATTTTT
1 AATTTAAATTGAAATTTTA
2527011 AATTT
1 AATTT
2527016 TCGCTATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (19 bp):
AATTTAAATTGAAATTTTA
Found at i:2527764 original size:21 final size:21
Alignment explanation
Indices: 2527740--2527783 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2527730 GGTAAAAAAA
2527740 TATTTAAAATATT-ATTATTTT
1 TATTTAAAATATTAATT-TTTT
2527761 TATTTAAAATATTAATTTTTT
1 TATTTAAAATATTAATTTTTT
2527782 TA
1 TA
2527784 ATATTTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTTAAAATATTAATTTTTT
Found at i:2529855 original size:44 final size:43
Alignment explanation
Indices: 2529767--2529869 Score: 136
Period size: 44 Copynumber: 2.4 Consensus size: 43
2529757 GTTATTACAC
* * *
2529767 CAATTATAAATGT-AAAAAGTAAGATTGTAAAAATTAAGGGCT
1 CAATTATAATTGTAAAAAAATAAGATTATAAAAATTAAGGGCT
* * *
2529809 CAATTATAATTGTAAAAAAATGAGATTATAACAATTGAGTGGCT
1 CAATTATAATTGTAAAAAAATAAGATTATAAAAATTAAG-GGCT
2529853 CAATTATAATTGTAAAA
1 CAATTATAATTGTAAAA
2529870 TGTGATATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
42 12 0.23
43 20 0.38
44 21 0.40
ACGTcount: A:0.49, C:0.06, G:0.15, T:0.31
Consensus pattern (43 bp):
CAATTATAATTGTAAAAAAATAAGATTATAAAAATTAAGGGCT
Found at i:2531544 original size:2 final size:2
Alignment explanation
Indices: 2531537--2531590 Score: 58
Period size: 2 Copynumber: 28.0 Consensus size: 2
2531527 TCGTGCCGGG
* * * *
2531537 TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- 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
2531577 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
2531591 ATAATTATTT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2531755 original size:30 final size:30
Alignment explanation
Indices: 2531682--2531772 Score: 119
Period size: 30 Copynumber: 3.0 Consensus size: 30
2531672 CCCTGCTTAG
* * *
2531682 TATAAACAGTTTTCCCCCGTCCCCGTTTAG
1 TATAAACAGTTTTTCTCCGTCCCCGTTTAA
* *
2531712 CATAAACAGTTTTTTTCCGTCCCCGTTTAA
1 TATAAACAGTTTTTCTCCGTCCCCGTTTAA
* *
2531742 TATAAACAGTTTTTCTCCGTCTCTGTTTAA
1 TATAAACAGTTTTTCTCCGTCCCCGTTTAA
2531772 T
1 T
2531773 TCGGTTTTCG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.22, C:0.26, G:0.11, T:0.41
Consensus pattern (30 bp):
TATAAACAGTTTTTCTCCGTCCCCGTTTAA
Found at i:2535696 original size:12 final size:12
Alignment explanation
Indices: 2535679--2535718 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
2535669 TCATATACGA
2535679 TATTTTTAATAT
1 TATTTTTAATAT
* *
2535691 TATTTTTATTAA
1 TATTTTTAATAT
2535703 TATTTTTAATAT
1 TATTTTTAATAT
2535715 TATT
1 TATT
2535719 GACACTCCTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTTTTAATAT
Found at i:2537641 original size:17 final size:20
Alignment explanation
Indices: 2537611--2537649 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
2537601 ATTTACCAGA
2537611 TTTATTATTCTTTTAA-ATT
1 TTTATTATTCTTTTAATATT
2537630 TTTATT-TT-TTTTAATATT
1 TTTATTATTCTTTTAATATT
2537648 TT
1 TT
2537650 AGACTTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 7 0.37
19 6 0.32
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTATTATTCTTTTAATATT
Found at i:2550175 original size:12 final size:12
Alignment explanation
Indices: 2550158--2550192 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
2550148 CTCAATTTGA
2550158 TTATTTTAAAAT
1 TTATTTTAAAAT
2550170 TTATTTTAAAAT
1 TTATTTTAAAAT
2550182 TTATTTTAAAA
1 TTATTTTAAAA
2550193 AATATATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTATTTTAAAAT
Found at i:2551970 original size:76 final size:76
Alignment explanation
Indices: 2551819--2552024 Score: 288
Period size: 76 Copynumber: 2.7 Consensus size: 76
2551809 CAAAGCCAAA
* * * **
2551819 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
2551884 TTGGCCCCGAG
66 TTGGCCCCGAG
* * *
2551895 ATTTTCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAATCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
2551960 TTTGCTCCGAG
66 TTGGCCCCGAG
* * *
2551971 AATTCCAGTATGCTCGGAGGGAACCGATTCCCCCCA-AGGGGGTACCGATTCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCC
2552025 TCTTGTACAA
Statistics
Matches: 114, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
75 15 0.13
76 99 0.87
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTGGCCCCGAG
Found at i:2557800 original size:21 final size:21
Alignment explanation
Indices: 2557774--2557836 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
2557764 TTTTGGTGCA
*
2557774 GAGGGAATCGATCCCCCCCCT
1 GAGGGAACCGATCCCCCCCCT
* **
2557795 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCCT
*
2557816 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATCCCCCCC
2557837 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 18 0.51
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.38, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCCT
Found at i:2557844 original size:21 final size:21
Alignment explanation
Indices: 2557818--2557857 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2557808 CCCCCTTTGA
*
2557818 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
2557839 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
2557858 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:2559810 original size:9 final size:8
Alignment explanation
Indices: 2559788--2559838 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
2559778 AGTTTAAACA
2559788 TTTTGGAT
1 TTTTGGAT
2559796 ATTTTGGAT
1 -TTTTGGAT
2559805 TGTTT-GAT
1 T-TTTGGAT
2559813 TTTGTGGAT
1 TTT-TGGAT
*
2559822 TGTTGGA-
1 TTTTGGAT
2559829 TTTTGGAT
1 TTTTGGAT
2559837 TT
1 TT
2559839 ATGAATTGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 8 0.22
8 12 0.33
9 16 0.44
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (8 bp):
TTTTGGAT
Found at i:2559822 original size:17 final size:17
Alignment explanation
Indices: 2559790--2559833 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
2559780 TTTAAACATT
2559790 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
2559807 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
2559824 TTGGATTTTG
1 TTGGATTTTG
2559834 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:2560553 original size:76 final size:76
Alignment explanation
Indices: 2560425--2560633 Score: 303
Period size: 76 Copynumber: 2.8 Consensus size: 76
2560415 CAAAGCCAAA
* * * **
2560425 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
2560490 TTGGCCCCGAG
66 TTGGCCCCGAG
* *
2560501 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCAATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
2560566 TTTGCTCCGAG
66 TTGGCCCCGAG
* * *
2560577 AATTCCAGTATGCTCGGAGGGAACCGATTCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
2560634 TGTACAACGG
Statistics
Matches: 119, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
75 18 0.15
76 101 0.85
ACGTcount: A:0.24, C:0.33, G:0.23, T:0.20
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTGGCCCCGAG
Found at i:2563489 original size:2 final size:2
Alignment explanation
Indices: 2563482--2563509 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2563472 AATGATGAAT
2563482 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
2563510 ATTATTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2579949 original size:2 final size:2
Alignment explanation
Indices: 2579942--2579977 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2579932 CAAATTAATA
2579942 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2579978 GTCTGTGTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2581371 original size:6 final size:6
Alignment explanation
Indices: 2581360--2581385 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2581350 GACACGTATT
2581360 ACCACG ACCACG ACCACG ACCACG AC
1 ACCACG ACCACG ACCACG ACCACG AC
2581386 ATGAGACGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.50, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2582146 original size:21 final size:21
Alignment explanation
Indices: 2582120--2582234 Score: 76
Period size: 21 Copynumber: 5.5 Consensus size: 21
2582110 ATTTGAAATA
2582120 AATCGCAACGCGAACTTCGAC
1 AATCGCAACGCGAACTTCGAC
* * *
2582141 AATCGCAA--CGAATTTGGAATA
1 AATCGCAACGCGAACTTCG-A-C
* *
2582162 AATCACAATGCGAACTTCGAC
1 AATCGCAACGCGAACTTCGAC
* * * *
2582183 TATCGCAA--CGAATTTGGAATA
1 AATCGCAACGCGAACTTCG-A-C
2582204 AATCGCAACGCGAACTTCGAC
1 AATCGCAACGCGAACTTCGAC
*
2582225 TATCGCAACG
1 AATCGCAACG
2582235 AATTTGGAAA
Statistics
Matches: 69, Mismatches: 17, Indels: 16
0.68 0.17 0.16
Matches are distributed among these distances:
19 14 0.20
20 2 0.03
21 37 0.54
22 2 0.03
23 14 0.20
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (21 bp):
AATCGCAACGCGAACTTCGAC
Found at i:2582175 original size:42 final size:42
Alignment explanation
Indices: 2582109--2582250 Score: 234
Period size: 42 Copynumber: 3.4 Consensus size: 42
2582099 TTAAGAAACA
* *
2582109 AATTTGAAATAAATCGCAACGCGAACTTCGACAATCGCAACG
1 AATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACG
* *
2582151 AATTTGGAATAAATCACAATGCGAACTTCGACTATCGCAACG
1 AATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACG
2582193 AATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACG
1 AATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACG
2582235 AATTTGG-A-AAATCGCA
1 AATTTGGAATAAATCGCA
2582251 TTGCGATAGT
Statistics
Matches: 94, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
40 8 0.09
41 1 0.01
42 85 0.90
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.22
Consensus pattern (42 bp):
AATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACG
Found at i:2583528 original size:17 final size:17
Alignment explanation
Indices: 2583505--2583547 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
2583495 CTACTTGATA
2583505 AAATATTTAATAAATTT
1 AAATATTTAATAAATTT
* **
2583522 TAATATTTTTTAAATTT
1 AAATATTTAATAAATTT
2583539 AAATATTTA
1 AAATATTTA
2583548 TTTTACATGG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAATATTTAATAAATTT
Found at i:2583765 original size:16 final size:15
Alignment explanation
Indices: 2583737--2583778 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
2583727 ATAGTAGTTT
2583737 TTTTATA-TTTAAAA
1 TTTTATATTTTAAAA
2583751 TTATTATATTTTAAAA
1 TT-TTATATTTTAAAA
2583767 TTTTAATATTTT
1 TTTT-ATATTTT
2583779 TATTGAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 2 0.08
15 7 0.28
16 16 0.64
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTATATTTTAAAA
Found at i:2585098 original size:35 final size:35
Alignment explanation
Indices: 2585052--2585166 Score: 212
Period size: 35 Copynumber: 3.3 Consensus size: 35
2585042 ACAATAGAGA
*
2585052 ATGCATGTCTTATGATGATCGATATTTATGGTACC
1 ATGCATATCTTATGATGATCGATATTTATGGTACC
2585087 ATGCATATCTTATGATGATCGATATTTATGGTACC
1 ATGCATATCTTATGATGATCGATATTTATGGTACC
*
2585122 ATGCATATCTTATGATGATTGATATTTATGGTACC
1 ATGCATATCTTATGATGATCGATATTTATGGTACC
2585157 ATGCATATCT
1 ATGCATATCT
2585167 AAAATAACAA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 78 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (35 bp):
ATGCATATCTTATGATGATCGATATTTATGGTACC
Found at i:2586007 original size:23 final size:22
Alignment explanation
Indices: 2585959--2586007 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
2585949 TAAACTACCA
* *
2585959 AAAGGCAAAGAAAACATGTTAC
1 AAAGGCAAAGAAAACATATCAC
*
2585981 AAAGGCAAAGATAAACATATCAT
1 AAAGGCAAAGA-AAACATATCAC
2586004 AAAG
1 AAAG
2586008 ACAGAGAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.57, C:0.12, G:0.16, T:0.14
Consensus pattern (22 bp):
AAAGGCAAAGAAAACATATCAC
Found at i:2591595 original size:15 final size:15
Alignment explanation
Indices: 2591572--2591601 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2591562 CCGTAATCAT
*
2591572 AAATTTTAATTTTAA
1 AAATATTAATTTTAA
2591587 AAATATTAATTTTAA
1 AAATATTAATTTTAA
2591602 GTTTTTTTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAATATTAATTTTAA
Found at i:2592411 original size:19 final size:21
Alignment explanation
Indices: 2592369--2592412 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
2592359 TGATAAAATA
2592369 TTATCTAAAATATTATTATTT
1 TTATCTAAAATATTATTATTT
2592390 TTATCTAAAATATT-TT-TTT
1 TTATCTAAAATATTATTATTT
2592409 TTAT
1 TTAT
2592413 ATTTCCGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 7 0.30
20 2 0.09
21 14 0.61
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATCTAAAATATTATTATTT
Found at i:2592472 original size:31 final size:30
Alignment explanation
Indices: 2592411--2592519 Score: 121
Period size: 30 Copynumber: 3.6 Consensus size: 30
2592401 ATTTTTTTTT
* *
2592411 ATATTTCCGGTTATTTTTTAGTGCTT-AATA
1 ATATTTTC-GTTATTTTTTAGCGCTTAAATA
2592441 ATATTTTCGTTTATTTTTTAGCGCTTAAATA
1 ATATTTTCG-TTATTTTTTAGCGCTTAAATA
* * * *
2592472 ATGTTTTCGATAATTTTTAGCGCCTAAATA
1 ATATTTTCGTTATTTTTTAGCGCTTAAATA
*
2592502 ATATTTTCAGTCATTTTT
1 ATATTTTC-GTTATTTTT
2592520 AACCGGTTTG
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
29 1 0.02
30 47 0.71
31 18 0.27
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.52
Consensus pattern (30 bp):
ATATTTTCGTTATTTTTTAGCGCTTAAATA
Found at i:2594614 original size:4 final size:4
Alignment explanation
Indices: 2594605--2594686 Score: 109
Period size: 4 Copynumber: 21.5 Consensus size: 4
2594595 CCATTTCGCA
* * *
2594605 ATGT ATGT ATGT ATGT ATGT CTCT CTGT ATG- -TGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2594651 ATGT ATGT ATGT ATGT ATG- -TGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
2594687 ATGTATTTGT
Statistics
Matches: 70, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.06
4 66 0.94
ACGTcount: A:0.22, C:0.04, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:2594648 original size:34 final size:34
Alignment explanation
Indices: 2594605--2594686 Score: 137
Period size: 34 Copynumber: 2.4 Consensus size: 34
2594595 CCATTTCGCA
* *
2594605 ATGTATGTATGTATGTATGTCTCTCTGTATGTGT
1 ATGTATGTATGTATGTATGTATCTATGTATGTGT
*
2594639 ATGTATGTATGTATGTATGTATGTATGTATGTGT
1 ATGTATGTATGTATGTATGTATCTATGTATGTGT
2594673 ATGTATGTATGTAT
1 ATGTATGTATGTAT
2594687 ATGTATTTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.22, C:0.04, G:0.24, T:0.50
Consensus pattern (34 bp):
ATGTATGTATGTATGTATGTATCTATGTATGTGT
Found at i:2595468 original size:13 final size:14
Alignment explanation
Indices: 2595441--2595470 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2595431 ATCAACATTC
2595441 ATGCATGTGTATGT
1 ATGCATGTGTATGT
2595455 ATGCATGT-TATGT
1 ATGCATGTGTATGT
2595468 ATG
1 ATG
2595471 TAGAGCGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.23, C:0.07, G:0.27, T:0.43
Consensus pattern (14 bp):
ATGCATGTGTATGT
Found at i:2595756 original size:31 final size:31
Alignment explanation
Indices: 2595737--2595829 Score: 159
Period size: 31 Copynumber: 3.0 Consensus size: 31
2595727 TACAGTCTCT
*
2595737 CAACATTTAGTCTGTTTGCAATATGATCCCC
1 CAACATTTAGTCCGTTTGCAATATGATCCCC
2595768 CAACATTTAGTCCGTTTGCAATATGATCCCC
1 CAACATTTAGTCCGTTTGCAATATGATCCCC
* *
2595799 CAACATTTAGTCCATTTGCAATATGGTCCCC
1 CAACATTTAGTCCGTTTGCAATATGATCCCC
2595830 GATGTAACTG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.33
Consensus pattern (31 bp):
CAACATTTAGTCCGTTTGCAATATGATCCCC
Found at i:2598514 original size:2 final size:2
Alignment explanation
Indices: 2598507--2598531 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2598497 AGACAAGCCT
2598507 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
2598532 TTTACCGTTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2605033 original size:45 final size:44
Alignment explanation
Indices: 2604970--2605060 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 44
2604960 GAGTATGGAT
*
2604970 TACTAGTTTTAAGTAGTCCACAAATGTTCATCAATATATATATA
1 TACTAGTTTTAAGTAGTCCAAAAATGTTCATCAATATATATATA
2605014 TACTAGTTTTTAAGTAGTCCAAAAATGTTCATCAATATATATATA
1 TACTAG-TTTTAAGTAGTCCAAAAATGTTCATCAATATATATATA
2605059 TA
1 TA
2605061 TACCTTCAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 6 0.13
45 39 0.87
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (44 bp):
TACTAGTTTTAAGTAGTCCAAAAATGTTCATCAATATATATATA
Found at i:2605076 original size:43 final size:45
Alignment explanation
Indices: 2604980--2605076 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 45
2604970 TACTAGTTTT
* ** **
2604980 AAGTAGTCCACAAATGTTCATCAATATATATATATACTAGTTTTT
1 AAGTAGTCCAAAAATGTTCATCAATATATATATATACTACCTTCA
2605025 AAGTAGTCCAAAAATGTTCATCAATATATATATATA-TACCTTCA
1 AAGTAGTCCAAAAATGTTCATCAATATATATATATACTACCTTCA
2605069 AAG-AGTCC
1 AAGTAGTCC
2605077 CATACTTGGA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 5 0.11
44 7 0.15
45 35 0.74
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.35
Consensus pattern (45 bp):
AAGTAGTCCAAAAATGTTCATCAATATATATATATACTACCTTCA
Found at i:2605838 original size:30 final size:30
Alignment explanation
Indices: 2605804--2605864 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
2605794 AGATTAATTG
*
2605804 CTGAAATGGGGTGAATTCTACAGTAATGGT
1 CTGAAATGGGGGGAATTCTACAGTAATGGT
2605834 CTGAAATGGGGGGAATTCTACAGTAATGGT
1 CTGAAATGGGGGGAATTCTACAGTAATGGT
2605864 C
1 C
2605865 ATGGGTCGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.11, G:0.31, T:0.28
Consensus pattern (30 bp):
CTGAAATGGGGGGAATTCTACAGTAATGGT
Found at i:2605963 original size:20 final size:20
Alignment explanation
Indices: 2605938--2605976 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2605928 TGACATACGA
2605938 ATACGAGCCATACAAGCCAT
1 ATACGAGCCATACAAGCCAT
*
2605958 ATACGAGCCATACGAGCCA
1 ATACGAGCCATACAAGCCA
2605977 ATGGAGAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.31, G:0.18, T:0.13
Consensus pattern (20 bp):
ATACGAGCCATACAAGCCAT
Found at i:2605970 original size:9 final size:9
Alignment explanation
Indices: 2605938--2605976 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
2605928 TGACATACGA
2605938 ATACGAGCC
1 ATACGAGCC
*
2605947 ATACAAGCC
1 ATACGAGCC
2605956 ATATACGAGCC
1 --ATACGAGCC
2605967 ATACGAGCC
1 ATACGAGCC
2605976 A
1 A
2605977 ATGGAGAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 18 0.69
11 8 0.31
ACGTcount: A:0.38, C:0.31, G:0.18, T:0.13
Consensus pattern (9 bp):
ATACGAGCC
Found at i:2606027 original size:29 final size:29
Alignment explanation
Indices: 2605983--2606086 Score: 145
Period size: 29 Copynumber: 3.6 Consensus size: 29
2605973 GCCAATGGAG
** **
2605983 AGGTCGCCATACAGTCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
*
2606012 AGGTCACCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
**
2606041 AGGTCGCCATGTAGTCCCGGCGACCAAGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
2606070 AGGTCGCCATGTAGTCC
1 AGGTCGCCATGTAGTCC
2606087 TAGCTCACGA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.18, C:0.30, G:0.30, T:0.22
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:2606428 original size:22 final size:23
Alignment explanation
Indices: 2606386--2606428 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2606376 CTTGGTCGCC
2606386 GAGATTGCAGCCGAAGAAAGAGA
1 GAGATTGCAGCCGAAGAAAGAGA
2606409 GAGATTGCAGCCG-AGAAAGA
1 GAGATTGCAGCCGAAGAAAGA
2606429 AAGAAAGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.42, C:0.14, G:0.35, T:0.09
Consensus pattern (23 bp):
GAGATTGCAGCCGAAGAAAGAGA
Found at i:2606827 original size:23 final size:24
Alignment explanation
Indices: 2606782--2606830 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
2606772 TTTAGTAGTA
2606782 TATTATAATGAAAAAATAGTTTAT
1 TATTATAATGAAAAAATAGTTTAT
*
2606806 TATTAT-AT-AAAAGAATATTTTAT
1 TATTATAATGAAAA-AATAGTTTAT
2606829 TA
1 TA
2606831 GTTGTTTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 13 0.57
24 6 0.26
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (24 bp):
TATTATAATGAAAAAATAGTTTAT
Found at i:2609051 original size:17 final size:17
Alignment explanation
Indices: 2609029--2609061 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2609019 CAATGATTTT
*
2609029 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
2609046 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
2609062 AATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:2609078 original size:24 final size:22
Alignment explanation
Indices: 2609046--2609111 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 22
2609036 AAATCATTAC
2609046 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
* *
2609068 TAGTAAATCAACT-ATTTAATCA-T
1 TAGT--ATCAAATAATTAAAT-ATT
2609091 TAGTATCAAATAA-TAAATATT
1 TAGTATCAAATAATTAAATATT
2609112 AACAATAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 11
0.70 0.08 0.22
Matches are distributed among these distances:
20 1 0.03
21 11 0.31
22 5 0.14
23 11 0.31
24 7 0.20
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (22 bp):
TAGTATCAAATAATTAAATATT
Found at i:2609262 original size:13 final size:12
Alignment explanation
Indices: 2609244--2609349 Score: 67
Period size: 13 Copynumber: 8.9 Consensus size: 12
2609234 TTAGTATTCT
2609244 ATAATTATTAGTA
1 ATAATTATTA-TA
2609257 ATAATTATTA-A
1 ATAATTATTATA
* *
2609268 ATCATTAGTATTA
1 ATAATTATTA-TA
*
2609281 ATCATTATTATAA
1 ATAATTATTAT-A
* *
2609294 ATAATTACTAAA
1 ATAATTATTATA
* *
2609306 AT-ATAACTA-A
1 ATAATTATTATA
*
2609316 ATAATTA-TAAA
1 ATAATTATTATA
*
2609327 ATCATTATTATA
1 ATAATTATTATA
*
2609339 ATGATTATTAT
1 ATAATTATTAT
2609350 CAAATCATTA
Statistics
Matches: 76, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
10 5 0.07
11 25 0.33
12 17 0.22
13 29 0.38
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (12 bp):
ATAATTATTATA
Found at i:2609333 original size:11 final size:12
Alignment explanation
Indices: 2609266--2609368 Score: 52
Period size: 11 Copynumber: 8.6 Consensus size: 12
2609256 AATAATTATT
*
2609266 AAATCATTAGTA
1 AAATCATTACTA
* *
2609278 TTAATCATTATTA
1 -AAATCATTACTA
*
2609291 TAAATAATTACTA
1 -AAATCATTACTA
*
2609304 AAAT-ATAACT-
1 AAATCATTACTA
*
2609314 AAATAATTA-TA
1 AAATCATTACTA
*
2609325 AAATCATTATTA
1 AAATCATTACTA
* * *
2609337 TAATGATTATTA
1 AAATCATTACTA
2609349 TCAAATCATTACT-
1 --AAATCATTACTA
2609362 AAATCAT
1 AAATCAT
2609369 CAAGTCATTA
Statistics
Matches: 72, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
10 5 0.07
11 23 0.32
12 16 0.22
13 20 0.28
14 8 0.11
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.40
Consensus pattern (12 bp):
AAATCATTACTA
Found at i:2609336 original size:14 final size:13
Alignment explanation
Indices: 2609319--2609720 Score: 155
Period size: 12 Copynumber: 30.1 Consensus size: 13
2609309 TAACTAAATA
2609319 ATTATAAAATCATT
1 ATTAT-AAATCATT
*
2609333 ATTAT-AATGATT
1 ATTATAAATCATT
2609345 ATTATCAAATCATT
1 ATTAT-AAATCATT
*
2609359 ACTAAATCATCAAGTCATT
1 A-T---T-AT-AAATCATT
* *
2609378 AAATATTTAATCATT
1 -ATTA-TAAATCATT
2609393 A-T-TA-ATCATT
1 ATTATAAATCATT
*
2609403 -TTAT-AATGATT
1 ATTATAAATCATT
2609414 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
2609428 ATTAT-AATGATT
1 ATTATAAATCATT
2609440 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
2609454 ACTAT-AATGATT
1 ATTATAAATCATT
*
2609466 ATTATCAATCATT
1 ATTATAAATCATT
*
2609479 ACTAATCACAAATCATT
1 A-T--T-ATAAATCATT
*
2609496 AAATATTTAAATCATT
1 --AT-TATAAATCATT
2609512 A-T-TAAATCATT
1 ATTATAAATCATT
*
2609523 -TT-T--ATGATT
1 ATTATAAATCATT
2609532 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
2609546 ATTAT-AATGATT
1 ATTATAAATCATT
2609558 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
2609572 ACTAT-AATGATT
1 ATTATAAATCATT
*
2609584 ATTATCAATCATT
1 ATTATAAATCATT
2609597 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
2609616 AAATATTTAAATCATT
1 --AT-TATAAATCATT
2609632 A-T-TAAATCATT
1 ATTATAAATCATT
* *
2609643 TTTAT-AATGATT
1 ATTATAAATCATT
2609655 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
2609669 ATTAT-AA-GATT
1 ATTATAAATCATT
2609680 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
2609694 ACTAT-AATGATT
1 ATTATAAATCATT
2609706 ATTATCAAATCATT
1 ATTAT-AAATCATT
2609720 A
1 A
2609721 CTAATCATCA
Statistics
Matches: 299, Mismatches: 39, Indels: 100
0.68 0.09 0.23
Matches are distributed among these distances:
9 5 0.02
10 9 0.03
11 35 0.12
12 81 0.27
13 23 0.08
14 80 0.27
15 8 0.03
16 19 0.06
17 12 0.04
18 6 0.02
19 18 0.06
20 2 0.01
21 1 0.00
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (13 bp):
ATTATAAATCATT
Found at i:2609354 original size:26 final size:26
Alignment explanation
Indices: 2609319--2609720 Score: 188
Period size: 26 Copynumber: 15.6 Consensus size: 26
2609309 TAACTAAATA
* *
2609319 ATTATAAAATCATTATTATAATGATT
1 ATTATCAAATCATTATTATAATCATT
* *
2609345 ATTATCAAATCATTACTA-AATCATC
1 ATTATCAAATCATTATTATAATCATT
* * *
2609370 A--AGTC-ATTAAATATT-TAATCATT
1 ATTA-TCAAATCATTATTATAATCATT
*
2609393 A-T-T--AATCATT-TTATAATGATT
1 ATTATCAAATCATTATTATAATCATT
*
2609414 ATTA-CTAAATCATTATTATAATGATT
1 ATTATC-AAATCATTATTATAATCATT
* *
2609440 ATTATCAAATCATTACTATAATGATT
1 ATTATCAAATCATTATTATAATCATT
*
2609466 ATTATC-AATCATTACTAATCACAAATCATT
1 ATTATCAAATCATTA-T--T-A-TAATCATT
* *
2609496 AAATATTTAAATCATTATTA-AATCATT
1 -ATTA-TCAAATCATTATTATAATCATT
* * * *
2609523 TTTAT--GATTATTACTA-AATCATT
1 ATTATCAAATCATTATTATAATCATT
*
2609546 ATTAT--AATGATTATTATCAAATCATT
1 ATTATCAAATCATTATTAT--AATCATT
* *
2609572 ACTAT--AATGATTATTATCAATCATT
1 ATTATCAAATCATTATTAT-AATCATT
*
2609597 ACTAAATCATCAAATCATTAAATATTTAAATCATT
1 A-T---T-ATCAAATCATT--AT-TAT-AATCATT
* *
2609632 A-T-T-AAATCATTTTTATAATGATT
1 ATTATCAAATCATTATTATAATCATT
*
2609655 ATTA-CTAAATCATTATTATAA-GATT
1 ATTATC-AAATCATTATTATAATCATT
* *
2609680 ATTATCAAATCATTACTATAATGATT
1 ATTATCAAATCATTATTATAATCATT
2609706 ATTATCAAATCATTA
1 ATTATCAAATCATTA
2609721 CTAATCATCA
Statistics
Matches: 299, Mismatches: 39, Indels: 76
0.72 0.09 0.18
Matches are distributed among these distances:
20 2 0.01
21 12 0.04
22 2 0.01
23 48 0.16
24 5 0.02
25 53 0.18
26 115 0.38
27 16 0.05
28 2 0.01
29 3 0.01
30 10 0.03
31 3 0.01
32 8 0.03
33 8 0.03
34 2 0.01
35 10 0.03
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (26 bp):
ATTATCAAATCATTATTATAATCATT
Found at i:2609538 original size:118 final size:123
Alignment explanation
Indices: 2609319--2609777 Score: 794
Period size: 122 Copynumber: 3.8 Consensus size: 123
2609309 TAACTAAATA
* * *
2609319 ATTATAAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAGTCATTAAATAT
1 ATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATAT
2609384 TT-AATCATTATT-AATCATTTTATAATGATTATTACTAAATCATTATTATAATGATT
66 TTAAATCATTATTAAATCATTTTATAATGATTATTACTAAATCATTATTATAATGATT
2609440 ATTATCAAATCATTACTATAATGATTATTATC-AATCATTACT-AATCA-CAAATCATTAAATAT
1 ATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATAT
2609502 TTAAATCATTATTAAATCATTTT-T-ATGATTATTACTAAATCATTATTATAATGATT
66 TTAAATCATTATTAAATCATTTTATAATGATTATTACTAAATCATTATTATAATGATT
2609558 ATTATCAAATCATTACTATAATGATTATTATC-AATCATTACTAAATCATCAAATCATTAAATAT
1 ATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATAT
2609622 TTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAA-GATT
66 TTAAATCATTATTAAATCA-TTTTATAATGATTATTACTAAATCATTATTATAATGATT
2609680 ATTATCAAATCATTACTATAATGATTATTATCAAATCATTACT-AATCATCAAATCATTAAATAT
1 ATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATAT
*
2609744 TTAAATCATTATTAAATAATTTTTATAATGATTA
66 TTAAATCATTATTAAATCA-TTTTATAATGATTA
2609778 ATAAATACAT
Statistics
Matches: 326, Mismatches: 4, Indels: 15
0.94 0.01 0.04
Matches are distributed among these distances:
118 90 0.28
119 21 0.06
120 53 0.16
121 34 0.10
122 91 0.28
123 37 0.11
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (123 bp):
ATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATAT
TTAAATCATTATTAAATCATTTTATAATGATTATTACTAAATCATTATTATAATGATT
Found at i:2609727 original size:15 final size:14
Alignment explanation
Indices: 2609677--2609723 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
2609667 TTATTATAAG
*
2609677 ATTATTATCAAATC
1 ATTACTATCAAATC
*
2609691 ATTACTAT--AATG
1 ATTACTATCAAATC
*
2609703 ATTATTATCAAATC
1 ATTACTATCAAATC
2609717 ATTACTA
1 ATTACTA
2609724 ATCATCAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
12 10 0.38
14 16 0.62
ACGTcount: A:0.43, C:0.13, G:0.02, T:0.43
Consensus pattern (14 bp):
ATTACTATCAAATC
Found at i:2613490 original size:28 final size:28
Alignment explanation
Indices: 2613442--2613502 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
2613432 ATTTTTTATA
*
2613442 TAATATATATATAACTTAACTAATAAAC
1 TAATATATATATAACTTAACTAACAAAC
2613470 TAATATA-ATATAACTTAAACTAACAAAC
1 TAATATATATATAACTT-AACTAACAAAC
2613498 TAATA
1 TAATA
2613503 ATTTATACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 9 0.29
28 22 0.71
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
TAATATATATATAACTTAACTAACAAAC
Found at i:2613509 original size:28 final size:27
Alignment explanation
Indices: 2613442--2613509 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 27
2613432 ATTTTTTATA
*
2613442 TAATATATATATAACTTAACTAATAAAC
1 TAATA-ATATATAACTTAACTAACAAAC
2613470 TAAT-ATAATATAACTTAAACTAACAAAC
1 TAATAAT-ATATAACTT-AACTAACAAAC
*
2613498 TAATAATTTATA
1 TAATAATATATA
2613510 CTAACAAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 2 0.06
27 9 0.26
28 22 0.63
29 2 0.06
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.35
Consensus pattern (27 bp):
TAATAATATATAACTTAACTAACAAAC
Found at i:2613512 original size:21 final size:21
Alignment explanation
Indices: 2613479--2613527 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
2613469 CTAATATAAT
2613479 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
2613500 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
2613521 ATTAACT
1 A-TAACT
2613528 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Done.