Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001547.1 Hibiscus syriacus cultivar Beakdansim tig00003041_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: 10425128
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 51
Found at i:4508952 original size:24 final size:24
Alignment explanation
Indices: 4508877--4508990 Score: 128
Period size: 24 Copynumber: 4.8 Consensus size: 24
4508867 CATAAATCAA
*
4508877 GTCAAGTATCATATCA-AACTCCAG
1 GTCAAGTATCATATCAGAA-TCCAT
* *
4508901 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAT
*
4508925 GTCAAGTATCATATCAGAATCTAT
1 GTCAAGTATCATATCAGAATCCAT
*
4508949 GTC-AGATATCAGATC--AATCCAT
1 GTCAAG-TATCATATCAGAATCCAT
*
4508971 GTCAAATATCATATCAGAAT
1 GTCAAGTATCATATCAGAAT
4508991 TCAAATCGAA
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
22 17 0.22
23 3 0.04
24 54 0.71
25 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAT
Found at i:4508959 original size:48 final size:46
Alignment explanation
Indices: 4508874--4508990 Score: 148
Period size: 48 Copynumber: 2.5 Consensus size: 46
4508864 AAACATAAAT
4508874 CAAGTCAAGTATCATATCA-AACTCCAGGTCAAGTATCAGATCAGAATC
1 CAAGTCAAGTATCATATCAGAA-TCCAGGTCAAGTATCAGATC--AATC
* *
4508922 CAAGTCAAGTATCATATCAGAATCTATGTC-AGATATCAGATCAATC
1 CAAGTCAAGTATCATATCAGAATCCAGGTCAAG-TATCAGATCAATC
* *
4508968 CATGTCAAATATCATATCAGAAT
1 CAAGTCAAGTATCATATCAGAAT
4508991 TCAAATCGAA
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
46 25 0.40
47 2 0.03
48 34 0.54
49 2 0.03
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (46 bp):
CAAGTCAAGTATCATATCAGAATCCAGGTCAAGTATCAGATCAATC
Found at i:4509997 original size:26 final size:26
Alignment explanation
Indices: 4509968--4510020 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
4509958 TCTGTTTTAT
*
4509968 TCCATTCATTTCAGAGCTCGAGGATA
1 TCCAATCATTTCAGAGCTCGAGGATA
* * *
4509994 TCCAATCATTTCTGAGCTTGATGATA
1 TCCAATCATTTCAGAGCTCGAGGATA
4510020 T
1 T
4510021 TCTTGGGTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (26 bp):
TCCAATCATTTCAGAGCTCGAGGATA
Found at i:4511458 original size:18 final size:18
Alignment explanation
Indices: 4511422--4511458 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4511412 AACGGGTAAA
*
4511422 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTAAACAGGT
*
4511440 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACAGGT
4511458 C
1 C
4511459 TGGTTATGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.16, C:0.22, G:0.46, T:0.16
Consensus pattern (18 bp):
CGGGTCGGGTAAACAGGT
Found at i:4513422 original size:24 final size:24
Alignment explanation
Indices: 4513395--4513470 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
4513385 TATATCAAAA
4513395 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* * *
4513419 ATCATATCAAACTCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
4513443 ATCATATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
4513467 ATCA
1 ATCA
4513471 GATCAGAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 3 0.07
24 42 0.93
ACGTcount: A:0.43, C:0.21, G:0.12, T:0.24
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:4513475 original size:24 final size:24
Alignment explanation
Indices: 4513412--4513527 Score: 155
Period size: 24 Copynumber: 4.8 Consensus size: 24
4513402 CATAAATCAG
*
4513412 GTCAAGTATCATATCA-AACTCCAG
1 GTCAAGTATCATATCAGAA-TCCAT
*
4513436 GTCAAGTATCATATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAT
* *
4513460 GTCAAGTATCAGATCAGAATCTAT
1 GTCAAGTATCATATCAGAATCCAT
*
4513484 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCATATCAGAATCCAT
4513508 GTCAAGTATCATATCAGAAT
1 GTCAAGTATCATATCAGAAT
4513528 TCAAATCGAA
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
23 2 0.02
24 77 0.93
25 4 0.05
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAT
Found at i:4513543 original size:48 final size:48
Alignment explanation
Indices: 4513443--4513545 Score: 120
Period size: 48 Copynumber: 2.1 Consensus size: 48
4513433 CAGGTCAAGT
* ** *
4513443 ATCATATCAGAATCCAAGTCAAGTATCAGATCAGAATCTATGTCAGAT
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTAAATCAGAA
* *
4513491 ATCAGATCAGAATCCATGTCAAGTATCATATCAGAAT-TCAAATC-GAAA
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCT-AAATCAG-AA
4513539 ATCAGAT
1 ATCAGAT
4513546 AAAATATTCA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
47 2 0.04
48 45 0.96
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (48 bp):
ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTAAATCAGAA
Found at i:4514534 original size:26 final size:26
Alignment explanation
Indices: 4514505--4514557 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
4514495 TCAGTTTTAT
*
4514505 TCCATTCATTTCAGAGCTCGAGGATA
1 TCCAATCATTTCAGAGCTCGAGGATA
* * *
4514531 TCCAATCATTTCTGAGCTTGATGATA
1 TCCAATCATTTCAGAGCTCGAGGATA
4514557 T
1 T
4514558 TCTTGGGTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (26 bp):
TCCAATCATTTCAGAGCTCGAGGATA
Found at i:4515943 original size:15 final size:15
Alignment explanation
Indices: 4515923--4515955 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
4515913 GTCAACGCTT
4515923 GTCAACGGCCAACGG
1 GTCAACGGCCAACGG
*
4515938 GTCAACGGTCAACGG
1 GTCAACGGCCAACGG
4515953 GTC
1 GTC
4515956 GTGTCAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.30, G:0.33, T:0.12
Consensus pattern (15 bp):
GTCAACGGCCAACGG
Found at i:4515973 original size:18 final size:18
Alignment explanation
Indices: 4515950--4515996 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
4515940 CAACGGTCAA
*
4515950 CGGGTCGTGTCAACAGGT
1 CGGGTCGGGTCAACAGGT
*
4515968 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACAGGT
*
4515986 CAGGTCGGGTC
1 CGGGTCGGGTC
4515997 GGGTTATGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.13, C:0.23, G:0.45, T:0.19
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:4516750 original size:30 final size:30
Alignment explanation
Indices: 4516679--4516751 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
4516669 TTAAAAGTAT
*
4516679 ACCCCTAATAACAAATATTAAAAAAATTAG
1 ACCCCTAATAATAAATATTAAAAAAATTAG
* * *
4516709 ACCCCTGATAATAAGTATTGAAAAAATTAG
1 ACCCCTAATAATAAATATTAAAAAAATTAG
* *
4516739 TCCCTTAATAATA
1 ACCCCTAATAATA
4516752 CATGTTAGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.27
Consensus pattern (30 bp):
ACCCCTAATAATAAATATTAAAAAAATTAG
Found at i:4527858 original size:21 final size:20
Alignment explanation
Indices: 4527828--4527945 Score: 101
Period size: 20 Copynumber: 5.8 Consensus size: 20
4527818 GATTCTGACT
4527828 ATCGCATTGCGATTTCCCAA
1 ATCGCATTGCGATTTCCCAA
* *
4527848 ATTCGCGTTGCGATTTTCCTAA
1 A-TCGCATTGCGA-TTTCCCAA
* * * **
4527870 ATCGCAATGCGAATACGTAA
1 ATCGCATTGCGATTTCCCAA
*
4527890 ATCGCATTGCGATTTTCCTAA
1 ATCGCATTGCGA-TTTCCCAA
* * **
4527911 TTCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTCCCAA
4527931 ATCGCATTGCGATTT
1 ATCGCATTGCGATTT
4527946 AGTAAATCGC
Statistics
Matches: 79, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
20 36 0.46
21 35 0.44
22 8 0.10
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.35
Consensus pattern (20 bp):
ATCGCATTGCGATTTCCCAA
Found at i:4527900 original size:41 final size:41
Alignment explanation
Indices: 4527850--4527945 Score: 140
Period size: 41 Copynumber: 2.3 Consensus size: 41
4527840 TTTCCCAAAT
*
4527850 TCGCGTTGCGATTTTCCTAAATCGCAATGCGA-ATACGTAAA
1 TCGCATTGCGATTTTCCTAAATCGCAATGCGATATACGT-AA
* * *
4527891 TCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTTCCTAAATCGCAATGCGATATACGTAA
4527932 TCGCATTGCGATTT
1 TCGCATTGCGATTT
4527946 AGTAAATCGC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 45 0.90
42 5 0.10
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCTAAATCGCAATGCGATATACGTAA
Found at i:4527937 original size:20 final size:21
Alignment explanation
Indices: 4527828--4527956 Score: 131
Period size: 21 Copynumber: 6.3 Consensus size: 21
4527818 GATTCTGACT
*
4527828 ATCGCATTGCGATTT-CCCAA
1 ATCGCATTGCGATTTACCTAA
* *
4527848 ATTCGCGTTGCGATTTTCCTAA
1 A-TCGCATTGCGATTTACCTAA
* * *
4527870 ATCGCAATGCGA-ATACGTAA
1 ATCGCATTGCGATTTACCTAA
*
4527890 ATCGCATTGCGATTTTCCTAA
1 ATCGCATTGCGATTTACCTAA
* *
4527911 TTCGCATTGCGATTTACGT-A
1 ATCGCATTGCGATTTACCTAA
*
4527931 ATCGCATTGCGATTTA-GTAA
1 ATCGCATTGCGATTTACCTAA
4527951 ATCGCA
1 ATCGCA
4527957 ACGAGATTCT
Statistics
Matches: 90, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.02
20 40 0.44
21 43 0.48
22 5 0.06
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.33
Consensus pattern (21 bp):
ATCGCATTGCGATTTACCTAA
Found at i:4528850 original size:24 final size:24
Alignment explanation
Indices: 4528823--4528872 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
4528813 TCGAAATTTA
4528823 ATCTTGGTCAATACCCGGACTTTG
1 ATCTTGGTCAATACCCGGACTTTG
* *
4528847 ATCTTGGTCAATACTCGGATTTTG
1 ATCTTGGTCAATACCCGGACTTTG
4528871 AT
1 AT
4528873 GATTTTTCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (24 bp):
ATCTTGGTCAATACCCGGACTTTG
Found at i:4531428 original size:19 final size:19
Alignment explanation
Indices: 4531404--4531469 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
4531394 AATTATTACT
4531404 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4531423 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
4531437 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4531456 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
4531470 CTAAATTCGC
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 23 0.59
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4531497 original size:19 final size:19
Alignment explanation
Indices: 4531475--4531572 Score: 63
Period size: 19 Copynumber: 5.7 Consensus size: 19
4531465 CGAAACTAAA
4531475 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
4531494 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
4531509 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
4531527 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
4531542 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
4531560 TTCACATTGCGAT
1 TTCGCGTTGCGAT
4531573 AGTCATTTTT
Statistics
Matches: 58, Mismatches: 11, Indels: 20
0.65 0.12 0.22
Matches are distributed among these distances:
14 17 0.29
16 6 0.10
17 6 0.10
19 29 0.50
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.45
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:4531521 original size:33 final size:33
Alignment explanation
Indices: 4531479--4531572 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
4531469 ACTAAATTCG
*
4531479 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
4531512 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
4531545 CGTTGCGATTTTCATTTCACATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
4531573 AGTCATTTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:4531698 original size:14 final size:13
Alignment explanation
Indices: 4531679--4531717 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 13
4531669 CATCAATTAA
4531679 ACAAATCAACTTTT
1 ACAAATCAA-TTTT
4531693 ACAAATCATATTTT
1 ACAAATCA-ATTTT
4531707 ACAAATCAATT
1 ACAAATCAATT
4531718 AAACAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 3 0.12
14 20 0.83
15 1 0.04
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (13 bp):
ACAAATCAATTTT
Found at i:4533608 original size:19 final size:19
Alignment explanation
Indices: 4533568--4533727 Score: 124
Period size: 19 Copynumber: 8.8 Consensus size: 19
4533558 TCTAGAACTT
*
4533568 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
**
4533589 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
4533608 AAAATCGCAACGAGAGAATG
1 AAAATCGCAACGCGA-AATG
* *
4533628 AAAATCACAACGCGAAACG
1 AAAATCGCAACGCGAAATG
4533647 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
*
4533661 AGAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
4533680 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
* * * *
4533694 AGAATTGCAATGCGGAATG
1 AAAATCGCAACGCGAAATG
4533713 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
4533728 TTATAGTTTC
Statistics
Matches: 110, Mismatches: 18, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
14 19 0.17
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 51 0.46
20 17 0.15
21 11 0.10
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:4533639 original size:39 final size:38
Alignment explanation
Indices: 4533568--4533698 Score: 155
Period size: 39 Copynumber: 3.5 Consensus size: 38
4533558 TCTAGAACTT
* * *
4533568 AAAATCGCAACGTGAAAAATGACTATCGCAACGCGAAATG
1 AAAATCGCAACGAG-AGAATGA-AATCGCAACGCGAAATG
* *
4533608 AAAATCGCAACGAGAGAATGAAAATCACAACGCGAAACG
1 AAAATCGCAACGAGAGAATG-AAATCGCAACGCGAAATG
4533647 AAAATCGCAAC--GAG-A-G-AATCGCAACGCGAAATG
1 AAAATCGCAACGAGAGAATGAAATCGCAACGCGAAATG
4533680 AAAATCGCAACGAGAGAAT
1 AAAATCGCAACGAGAGAAT
4533699 TGCAATGCGG
Statistics
Matches: 79, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
33 26 0.33
35 4 0.05
36 2 0.03
37 3 0.04
39 30 0.38
40 14 0.18
ACGTcount: A:0.48, C:0.20, G:0.21, T:0.11
Consensus pattern (38 bp):
AAAATCGCAACGAGAGAATGAAATCGCAACGCGAAATG
Found at i:4533677 original size:33 final size:33
Alignment explanation
Indices: 4533592--4533724 Score: 167
Period size: 33 Copynumber: 3.8 Consensus size: 33
4533582 AAAAATGACT
4533592 ATCGCAACGCGAAATGAAAATCGCAACGAGAGAATGAAA
1 ATCGCAACGCGAAATGAAAATCGCAAC--GAG-A-G--A
* *
4533631 ATCACAACGCGAAACGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
4533664 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* * *
4533697 ATTGCAATGCGGAATGAAAATCGCAACG
1 ATCGCAACGCGAAATGAAAATCGCAACG
4533725 CGATTATAGT
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
33 57 0.66
35 1 0.01
36 1 0.01
37 3 0.03
39 25 0.29
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:4533758 original size:20 final size:20
Alignment explanation
Indices: 4533733--4533770 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
4533723 CGCGATTATA
4533733 GTTTCGCGTTGCGATTTTTG
1 GTTTCGCGTTGCGATTTTTG
4533753 GTTTCGCGTTGCGATTTT
1 GTTTCGCGTTGCGATTTT
4533771 GTCGTTGCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.16, G:0.29, T:0.50
Consensus pattern (20 bp):
GTTTCGCGTTGCGATTTTTG
Found at i:4533994 original size:94 final size:94
Alignment explanation
Indices: 4533881--4534348 Score: 770
Period size: 94 Copynumber: 5.1 Consensus size: 94
4533871 ATGGATTGCA
* *
4533881 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
4533945 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
4533974 TTACTTTCAACCAAATGACAAAACAAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
4534039 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
4534068 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
4534133 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
4534162 TTACTTTCAGCCAACAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
4534227 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* * *
4534256 TTAC-TTCAACTAAAAGACAACA-AAAGACAAATACTAACTTCACAGTGTT----AATAAACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
4534315 TTAGCAGTATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
4534344 TTACT
1 TTACT
4534349 AAGCAATCTA
Statistics
Matches: 359, Mismatches: 14, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
88 41 0.11
92 27 0.08
93 18 0.05
94 273 0.76
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:4536435 original size:75 final size:76
Alignment explanation
Indices: 4536308--4536499 Score: 266
Period size: 75 Copynumber: 2.5 Consensus size: 76
4536298 CCGTTGTACA
* * *
4536308 AGGGGGGAATCGGTACCCCCT-TGGGGGG-ATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGGAATC-GTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
**
4536371 -CAAAACTGTTT
65 CCAAAACCATTT
* *
4536382 AGGGGGGAATCGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGC
1 AGGGGGGAATCGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGC
4536447 CAAAACCATTT
66 CAAAACCATTT
4536458 A-GGGGGAATCGATTCCTCCTATGGGGGGGAATCGGTTCCCTC
1 AGGGGGGAATCG-TTCCTCCTAT-GGGGGGAATCGGTTCCCTC
4536500 TTAGCAATCT
Statistics
Matches: 106, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
73 7 0.07
74 18 0.17
75 42 0.40
76 20 0.19
77 19 0.18
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.23
Consensus pattern (76 bp):
AGGGGGGAATCGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGC
CAAAACCATTT
Found at i:4542971 original size:22 final size:21
Alignment explanation
Indices: 4542929--4542968 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4542919 TAGTTTGTTT
*
4542929 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
4542950 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
4542969 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:4545007 original size:76 final size:77
Alignment explanation
Indices: 4544895--4545095 Score: 266
Period size: 76 Copynumber: 2.6 Consensus size: 77
4544885 CCGTTGTACA
* * *
4544895 AGGGGGGAATCGGTACCCCCT-TGGGAGGG-ATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
1 AGGGGGGAATCGGTTCCTCCTATGGG-GGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGA
**
4544958 G-CAAAACTGTTT
65 GCCAAAACCATTT
* * *
4544970 AGGGGGGAGTCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
4545035 CCAAAACCATTT
66 CCAAAACCATTT
*
4545047 A-GGGGGAATCGGTTCCTCCTATGGGGGGGGAATCGGTTCCCTCTGAGCA
1 AGGGGGGAATCGGTTCCTCCTAT--GGGGGGAATCGGTTCCCTCCGAGCA
4545096 ATCTGTAATT
Statistics
Matches: 111, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
75 21 0.19
76 56 0.50
77 10 0.09
78 24 0.22
ACGTcount: A:0.19, C:0.24, G:0.34, T:0.23
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
CCAAAACCATTT
Found at i:4545562 original size:20 final size:20
Alignment explanation
Indices: 4545537--4545599 Score: 101
Period size: 20 Copynumber: 3.1 Consensus size: 20
4545527 TTTTGGTTGA
4545537 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
4545557 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
4545576 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
4545597 AAT
1 AAT
4545600 CGCAACACGA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 1 0.03
20 37 0.95
21 1 0.03
ACGTcount: A:0.49, C:0.16, G:0.24, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:4545602 original size:14 final size:14
Alignment explanation
Indices: 4545583--4545639 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
4545573 CGGAAATGAA
4545583 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
4545597 AATCGCAACACGAAATTAA
1 AATCGC-A-ACG--A-GAG
4545616 AATCGCAACGAGAG
1 AATCGCAACGAGAG
4545630 AATCGCAACG
1 AATCGCAACG
4545640 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 17 0.50
15 2 0.06
16 3 0.09
17 3 0.09
18 2 0.06
19 7 0.21
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:4545618 original size:33 final size:33
Alignment explanation
Indices: 4545535--4545653 Score: 157
Period size: 33 Copynumber: 3.4 Consensus size: 33
4545525 TCTTTTGGTT
4545535 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-G--AATCGCAACGC
*
4545574 GGAAATGAAAATCGCAACGAGAGAATCGCAACAC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
4545608 GAAATTAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
4545641 GAAATGAAAATCG
1 GAAATGAAAATCG
4545654 TAATGCGATT
Statistics
Matches: 75, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
33 43 0.57
34 10 0.13
36 1 0.01
37 1 0.01
38 3 0.04
40 17 0.23
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:4545694 original size:33 final size:33
Alignment explanation
Indices: 4545657--4545737 Score: 99
Period size: 33 Copynumber: 2.5 Consensus size: 33
4545647 AAAATCGTAA
** * *
4545657 TGCGATTTTGGTTTCGCGTTGCGATTATATCGT
1 TGCGATTTTCATTTCACGTTGCAATTATATCGT
* *
4545690 TGCGATTTTCATTTCACGTTGCAATTCTCTCGT
1 TGCGATTTTCATTTCACGTTGCAATTATATCGT
*
4545723 TACGATTTTCATTTC
1 TGCGATTTTCATTTC
4545738 TCTCGTTGCG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.15, C:0.20, G:0.19, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCACGTTGCAATTATATCGT
Found at i:4545755 original size:21 final size:21
Alignment explanation
Indices: 4545714--4545769 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
4545704 CACGTTGCAA
* **
4545714 TTCTCTCGTTACGATTTTCAT
1 TTCTCTCGTTGCGATAGTCAT
4545735 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATAGTCAT
4545756 TT-TCGT-GTTGCGAT
1 TTCTC-TCGTTGCGAT
4545770 TTTTATTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.32
21 21 0.68
ACGTcount: A:0.12, C:0.21, G:0.18, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATAGTCAT
Found at i:4545767 original size:20 final size:20
Alignment explanation
Indices: 4545742--4545789 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
4545732 CATTTCTCTC
*
4545742 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCAT
** *
4545762 GTTGCGATTTTTATTTTCAT
1 GTTGCGATAGTCATTTTCAT
4545782 GTTGCGAT
1 GTTGCGAT
4545790 TTTAAGTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.12, G:0.23, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCAT
Found at i:4545790 original size:20 final size:20
Alignment explanation
Indices: 4545754--4545792 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4545744 TGCGATAGTC
*
4545754 ATTTTCGTGTTGCGATTTTT
1 ATTTTCATGTTGCGATTTTT
4545774 ATTTTCATGTTGCGATTTT
1 ATTTTCATGTTGCGATTTT
4545793 AAGTTTAGAA
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:0.13, C:0.10, G:0.18, T:0.59
Consensus pattern (20 bp):
ATTTTCATGTTGCGATTTTT
Found at i:4546348 original size:13 final size:14
Alignment explanation
Indices: 4546327--4546359 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
4546317 CTATGTAAAT
4546327 CGTAATGCGA-TTA
1 CGTAATGCGATTTA
*
4546340 CGTATTGCGATTTA
1 CGTAATGCGATTTA
4546354 CGTAAT
1 CGTAAT
4546360 CGCGTTGCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (14 bp):
CGTAATGCGATTTA
Found at i:4546369 original size:20 final size:20
Alignment explanation
Indices: 4546343--4546393 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
4546333 GCGATTACGT
4546343 ATTGCGATTTACGTAATCGC
1 ATTGCGATTTACGTAATCGC
* *
4546363 GTTGCGATTTACGTATTCGC
1 ATTGCGATTTACGTAATCGC
4546383 ATTGCGATTTA
1 ATTGCGATTTA
4546394 GGGAAATCGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
ATTGCGATTTACGTAATCGC
Found at i:4546811 original size:3 final size:3
Alignment explanation
Indices: 4546803--4546830 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4546793 CTGTTTCTAA
4546803 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
4546831 CAAATTAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:4562877 original size:17 final size:18
Alignment explanation
Indices: 4562838--4562878 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
4562828 AAATTCTTTT
4562838 CTTTATTATCTCATAAATA
1 CTTTATTATCT-ATAAATA
4562857 --TTATTATCT-TAAATA
1 CTTTATTATCTATAAATA
4562872 CTTTATT
1 CTTTATT
4562879 TTATATTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
15 6 0.30
17 14 0.70
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.54
Consensus pattern (18 bp):
CTTTATTATCTATAAATA
Found at i:4565317 original size:2 final size:2
Alignment explanation
Indices: 4565312--4565354 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
4565302 GTGAGTAATA
4565312 AT AT AT 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 AT AT AT
4565354 A
1 A
4565355 GTTGAGGTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4566840 original size:32 final size:32
Alignment explanation
Indices: 4566799--4566884 Score: 136
Period size: 32 Copynumber: 2.7 Consensus size: 32
4566789 CTAATCGGGT
4566799 AAATGTGAAAGATGACCGGAGACTGTAAAAAG
1 AAATGTGAAAGATGACCGGAGACTGTAAAAAG
4566831 AAATGTGAAAGATGACCGGAGACTGTAAAAAG
1 AAATGTGAAAGATGACCGGAGACTGTAAAAAG
* * * *
4566863 AAAAGTAAAAGACGACCAGAGA
1 AAATGTGAAAGATGACCGGAGA
4566885 GATAAAGACG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.50, C:0.10, G:0.27, T:0.13
Consensus pattern (32 bp):
AAATGTGAAAGATGACCGGAGACTGTAAAAAG
Found at i:4567497 original size:17 final size:17
Alignment explanation
Indices: 4567471--4567511 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
4567461 TTCCAATATA
*
4567471 ATATTAATTATTAAAAT
1 ATATTAATTAATAAAAT
*
4567488 ATATTTATTAATAAAAT
1 ATATTAATTAATAAAAT
4567505 -TATTAAT
1 ATATTAAT
4567512 ATTATATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATTAATTAATAAAAT
Found at i:4567733 original size:22 final size:21
Alignment explanation
Indices: 4567700--4567743 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
4567690 TTAAAATATA
*
4567700 ATATAATTTTATTGTTTTAAT
1 ATATAATTTTATTATTTTAAT
*
4567721 ATATTATTATTATTATTTTAAT
1 ATATAATT-TTATTATTTTAAT
4567743 A
1 A
4567744 AGTGATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
ATATAATTTTATTATTTTAAT
Found at i:4567751 original size:22 final size:22
Alignment explanation
Indices: 4567700--4567751 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
4567690 TTAAAATATA
* *
4567700 ATATAATT-TTATTGTTTTAAT
1 ATATGATTATTATTATTTTAAT
*
4567721 ATATTATTATTATTATTTTAAT
1 ATATGATTATTATTATTTTAAT
4567743 A-AGTGATTA
1 ATA-TGATTA
4567752 ATATAATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.58
Consensus pattern (22 bp):
ATATGATTATTATTATTTTAAT
Found at i:4567753 original size:33 final size:32
Alignment explanation
Indices: 4567716--4567814 Score: 108
Period size: 37 Copynumber: 2.9 Consensus size: 32
4567706 TTTTATTGTT
* *
4567716 TTAATATATTATTATTATTATTTTAATAAGTGA
1 TTAATATATTATTATT-TTATTTTAATAAATAA
4567749 TTAATATAATTAATAATATTTTATTATTAATAAATAA
1 TTAATAT-ATT-AT--TATTTTATT-TTAATAAATAA
* *
4567786 TTAATATAATAATATTTTATTTTAATAAA
1 TTAATATATTATTATTTTATTTTAATAAA
4567815 ATATACTAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
32 8 0.14
33 16 0.28
34 3 0.05
35 3 0.05
36 7 0.12
37 20 0.35
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (32 bp):
TTAATATATTATTATTTTATTTTAATAAATAA
Found at i:4567789 original size:37 final size:32
Alignment explanation
Indices: 4567716--4567814 Score: 110
Period size: 33 Copynumber: 2.9 Consensus size: 32
4567706 TTTTATTGTT
* *
4567716 TTAATATATTATTATTATTATTTTAATAAGTGATTAA
1 TTAATATAATAATATT-TTATTTTAATAA---A-TAA
4567753 TATAAT-TAATAATATTTTATTATTAATAAATAA
1 T-TAATATAATAATATTTTATT-TTAATAAATAA
4567786 TTAATATAATAATATTTTATTTTAATAAA
1 TTAATATAATAATATTTTATTTTAATAAA
4567815 ATATACTAGT
Statistics
Matches: 57, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
32 12 0.21
33 19 0.33
34 1 0.02
36 5 0.09
37 16 0.28
38 4 0.07
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (32 bp):
TTAATATAATAATATTTTATTTTAATAAATAA
Found at i:4569869 original size:22 final size:22
Alignment explanation
Indices: 4569844--4569896 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
4569834 GTATATTTAG
4569844 AAAATCCTCATTGTAAGACGAC
1 AAAATCCTCATTGTAAGACGAC
4569866 AAAATCCTCATTGTAAGACGAC
1 AAAATCCTCATTGTAAGACGAC
*
4569888 AAAAGCCTC
1 AAAATCCTC
4569897 GTTATAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.42, C:0.25, G:0.13, T:0.21
Consensus pattern (22 bp):
AAAATCCTCATTGTAAGACGAC
Found at i:4572569 original size:54 final size:54
Alignment explanation
Indices: 4572330--4572552 Score: 260
Period size: 54 Copynumber: 4.2 Consensus size: 54
4572320 AGATGGCGTC
* * * ** * * * *
4572330 CCCACGCCATAACTGAATATTTCTTCTGCGAAAGATGTGGGTGAATAA---GTT
1 CCCACGCCTTAACTGAAGACTTCTTCTGCGTTAGCTCTGGATGAATAAGCCGTG
* * * *
4572381 CCCACGCCTTAAGT-ATAGA-TTCTTTTGCAG-TAGCTCGGGATGGATAAGCCGTG
1 CCCACGCCTTAACTGA-AGACTTCTTCTGC-GTTAGCTCTGGATGAATAAGCCGTG
4572434 CCCACGCCTTAACTGAAGACTTCTTCTGCGTTAGCTCTGGATGAATAAGCCGTG
1 CCCACGCCTTAACTGAAGACTTCTTCTGCGTTAGCTCTGGATGAATAAGCCGTG
*
4572488 CCCAAGCCTTAACTGAAGACTTCTTCTGCGTTAGCTCTGGATGAATAAGCCGTG
1 CCCACGCCTTAACTGAAGACTTCTTCTGCGTTAGCTCTGGATGAATAAGCCGTG
4572542 CCCACGCCTTA
1 CCCACGCCTTA
4572553 TGCGAACGCC
Statistics
Matches: 147, Mismatches: 17, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
50 20 0.14
51 15 0.10
53 19 0.13
54 93 0.63
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (54 bp):
CCCACGCCTTAACTGAAGACTTCTTCTGCGTTAGCTCTGGATGAATAAGCCGTG
Found at i:4574026 original size:21 final size:20
Alignment explanation
Indices: 4573966--4574032 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
4573956 AATCAGCTAC
*
4573966 CATAAATT-TCATATAAATAT
1 CATAAATTATCAT-TTAATAT
*
4573986 CATGAATTATTACA-TTAATAT
1 CATAAATTA-T-CATTTAATAT
4574007 CATAAATTATCATTTCAATAT
1 CATAAATTATCATTT-AATAT
4574028 CATAA
1 CATAA
4574033 TAATTCATGA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 2 0.05
20 10 0.26
21 24 0.62
22 1 0.03
23 2 0.05
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.40
Consensus pattern (20 bp):
CATAAATTATCATTTAATAT
Found at i:4574040 original size:21 final size:20
Alignment explanation
Indices: 4573981--4574040 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 20
4573971 ATTTCATATA
*
4573981 AATATCATGAATTATTACA-TT
1 AATATCAT-AATAATT-CATTT
*
4574002 AATATCATAA-ATTATCATTT
1 AATATCATAATAAT-TCATTT
4574022 CAATATCATAATAATTCAT
1 -AATATCATAATAATTCAT
4574041 GATAAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 3 0.09
20 5 0.16
21 22 0.69
22 2 0.06
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.42
Consensus pattern (20 bp):
AATATCATAATAATTCATTT
Found at i:4579372 original size:67 final size:65
Alignment explanation
Indices: 4579263--4579397 Score: 218
Period size: 67 Copynumber: 2.0 Consensus size: 65
4579253 ATTTTCAAAA
*
4579263 TAATTACCATTTTAAAATCCATATTTTTTAAAACATTATAATTTTTTAAAACATAATTATAATGG
1 TAATTACCATTTAAAAATCCATATTTTTTAAAACATTATAATTTTTTAAAACATAATTATAATGG
*
4579328 TAATTACCACTTTAAAAAT-CATATATTCTTTAATACATTATAATTTTTTAAAACATAATTATAA
1 TAATTACCA-TTTAAAAATCCATAT-TT-TTTAAAACATTATAATTTTTTAAAACATAATTATAA
4579392 TGG
63 TGG
4579395 TAA
1 TAA
4579398 AACATAAATC
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
65 14 0.22
66 10 0.15
67 41 0.63
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.44
Consensus pattern (65 bp):
TAATTACCATTTAAAAATCCATATTTTTTAAAACATTATAATTTTTTAAAACATAATTATAATGG
Found at i:4580201 original size:4 final size:4
Alignment explanation
Indices: 4580194--4580252 Score: 72
Period size: 4 Copynumber: 15.8 Consensus size: 4
4580184 CTTACACACA
4580194 CACG CACG CACG CACG CACG CACG CACG CA-- CACG CACG CA-- CACG
1 CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG CACG
* *
4580238 CACG CGCG CGCG CAC
1 CACG CACG CACG CAC
4580253 ACACACACAC
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
2 4 0.08
4 45 0.92
ACGTcount: A:0.24, C:0.51, G:0.25, T:0.00
Consensus pattern (4 bp):
CACG
Found at i:4580215 original size:16 final size:16
Alignment explanation
Indices: 4580194--4580252 Score: 72
Period size: 14 Copynumber: 3.9 Consensus size: 16
4580184 CTTACACACA
4580194 CACGCACGCACGCACG
1 CACGCACGCACGCACG
4580210 CACGCACGCACGCA--
1 CACGCACGCACGCACG
4580224 CACGCACGCA--CACG
1 CACGCACGCACGCACG
* *
4580238 CACGCGCGCGCGCAC
1 CACGCACGCACGCAC
4580253 ACACACACAC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
12 2 0.05
14 18 0.49
16 17 0.46
ACGTcount: A:0.24, C:0.51, G:0.25, T:0.00
Consensus pattern (16 bp):
CACGCACGCACGCACG
Found at i:4580255 original size:2 final size:2
Alignment explanation
Indices: 4580250--4580279 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4580240 CGCGCGCGCG
4580250 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
4580280 TGTCATCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:4580701 original size:32 final size:32
Alignment explanation
Indices: 4580626--4580778 Score: 186
Period size: 32 Copynumber: 4.8 Consensus size: 32
4580616 GAAGGACCTA
** * *
4580626 TCCATATGTTTCGAAGAACATAGGTAA-CATG
1 TCCATATGTCCCGAAGGACATAGGTAATCCTG
* *
4580657 TACATATATCCCGAAGGACATAGGTAATCCTG
1 TCCATATGTCCCGAAGGACATAGGTAATCCTG
*
4580689 TCCATATGTCCCGAATGACATAGGTAATCCTG
1 TCCATATGTCCCGAAGGACATAGGTAATCCTG
*
4580721 TCCATATGTCCCGAATGACATAGGTAAAT--TG
1 TCCATATGTCCCGAAGGACATAGGT-AATCCTG
* *
4580752 TCCATATGTCTCGAAAGACATAGGTAA
1 TCCATATGTCCCGAAGGACATAGGTAA
4580779 CCCTCGACTC
Statistics
Matches: 109, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
30 2 0.02
31 47 0.43
32 57 0.52
33 3 0.03
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (32 bp):
TCCATATGTCCCGAAGGACATAGGTAATCCTG
Found at i:4580712 original size:63 final size:61
Alignment explanation
Indices: 4580626--4580779 Score: 193
Period size: 63 Copynumber: 2.4 Consensus size: 61
4580616 GAAGGACCTA
*
4580626 TCCATATGTTTCGAAGAACATAGGTAACATGTACATATATCCCGAAGGACATAGGT-AATCCTG
1 TCCATATGTCTCGAAG-ACATAGGTAACATGTACATATATCCCGAAGGACATAGGTAAAT--TG
* * * * *
4580689 TCCATATGTCCCGAATGACATAGGTAATCCTGTCCATATGTCCCGAATGACATAGGTAAATTG
1 TCCATATGTCTCGAA-GACATAGGTAA-CATGTACATATATCCCGAAGGACATAGGTAAATTG
4580752 TCCATATGTCTCGAAAGACATAGGTAAC
1 TCCATATGTCTCG-AAGACATAGGTAAC
4580780 CCTCGACTCT
Statistics
Matches: 80, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
62 1 0.01
63 48 0.60
64 28 0.35
65 3 0.04
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (61 bp):
TCCATATGTCTCGAAGACATAGGTAACATGTACATATATCCCGAAGGACATAGGTAAATTG
Found at i:4582752 original size:36 final size:36
Alignment explanation
Indices: 4582708--4582778 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
4582698 GTCTTAGGTC
* * **
4582708 TATAAGAAATTATCAGCTTGATCGGTGCTGAACCTA
1 TATAAGAAATTACCAGCTTAATCGAAGCTGAACCTA
4582744 TATAAGAAATTACCAGCTTAATCGAAGCTGAACCT
1 TATAAGAAATTACCAGCTTAATCGAAGCTGAACCT
4582779 GCAGAGACTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (36 bp):
TATAAGAAATTACCAGCTTAATCGAAGCTGAACCTA
Found at i:4583501 original size:16 final size:17
Alignment explanation
Indices: 4583476--4583508 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4583466 TCGAAAAACG
*
4583476 TAAAATATT-ACTTTTT
1 TAAAAAATTAACTTTTT
4583492 TAAAAAATTAACTTTTT
1 TAAAAAATTAACTTTTT
4583509 GGTCAAAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
TAAAAAATTAACTTTTT
Found at i:4584725 original size:31 final size:31
Alignment explanation
Indices: 4584687--4584749 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
4584677 TTTAAGGAAG
* *
4584687 GATAATCTATTTCAATGACAACTTAATTTAA
1 GATAATCTAATTCAAGGACAACTTAATTTAA
*
4584718 GATAATCTAATTCAAGGATAACTTAATTTAA
1 GATAATCTAATTCAAGGACAACTTAATTTAA
4584749 G
1 G
4584750 GTTAAAAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.37
Consensus pattern (31 bp):
GATAATCTAATTCAAGGACAACTTAATTTAA
Found at i:4584745 original size:16 final size:16
Alignment explanation
Indices: 4584684--4584738 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
4584674 AATTTTAAGG
*
4584684 AAGGATAATCTATTTC
1 AAGGATAATCTAATTC
* * *
4584700 AATGACAA-CTTAATTT
1 AAGGATAATC-TAATTC
4584716 AA-GATAATCTAATTC
1 AAGGATAATCTAATTC
4584731 AAGGATAA
1 AAGGATAA
4584739 CTTAATTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
15 12 0.40
16 18 0.60
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (16 bp):
AAGGATAATCTAATTC
Found at i:4584750 original size:16 final size:16
Alignment explanation
Indices: 4584706--4584750 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
4584696 TTTCAATGAC
4584706 AACTTAATTTAA-GAT
1 AACTTAATTTAAGGAT
*
4584721 AA-TCTAATTCAAGGAT
1 AACT-TAATTTAAGGAT
4584737 AACTTAATTTAAGG
1 AACTTAATTTAAGG
4584751 TTAAAAGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 1 0.04
15 9 0.36
16 14 0.56
17 1 0.04
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (16 bp):
AACTTAATTTAAGGAT
Found at i:4585778 original size:29 final size:29
Alignment explanation
Indices: 4585736--4585799 Score: 128
Period size: 29 Copynumber: 2.2 Consensus size: 29
4585726 GTTTACATTG
4585736 TAAAAATTCTTCATAGATATTCATAATAA
1 TAAAAATTCTTCATAGATATTCATAATAA
4585765 TAAAAATTCTTCATAGATATTCATAATAA
1 TAAAAATTCTTCATAGATATTCATAATAA
4585794 TAAAAA
1 TAAAAA
4585800 GATGTAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (29 bp):
TAAAAATTCTTCATAGATATTCATAATAA
Found at i:4588313 original size:24 final size:24
Alignment explanation
Indices: 4588281--4588336 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
4588271 AGACCGATGG
4588281 TACGAGAGGAGGCTCCTCATATCA
1 TACGAGAGGAGGCTCCTCATATCA
4588305 TACGAGAGGAGGCTCCTCATATCA
1 TACGAGAGGAGGCTCCTCATATCA
4588329 TACGAGAG
1 TACGAGAG
4588337 CACAAGAGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (24 bp):
TACGAGAGGAGGCTCCTCATATCA
Found at i:4594451 original size:2 final size:2
Alignment explanation
Indices: 4594444--4594471 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4594434 ATGCAACTCC
4594444 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
4594472 ATCCAGCCCA
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:4599889 original size:6 final size:6
Alignment explanation
Indices: 4599872--4599911 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
4599862 TCGTTAAGAA
*
4599872 CTCGAG -TCGAG CTCGAG CTCGAG CTCGAG ATCGAG -TCGAG
1 CTCGAG CTCGAG CTCGAG CTCGAG CTCGAG CTCGAG CTCGAG
4599912 TCCATTCGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
5 10 0.31
6 22 0.69
ACGTcount: A:0.20, C:0.28, G:0.35, T:0.17
Consensus pattern (6 bp):
CTCGAG
Found at i:4611854 original size:45 final size:45
Alignment explanation
Indices: 4611755--4611858 Score: 129
Period size: 45 Copynumber: 2.3 Consensus size: 45
4611745 ATGCACAAGA
* *
4611755 AGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATT
1 AGTGCATCGATGCACCCATTAAAAATGAAAACATCGAAGGCAATT
* **
4611800 AGTGCATCGATGCACCCCCTT-AAAATGAAAACATCGAAGGTGATT
1 AGTGCATCGATGCA-CCCATTAAAAATGAAAACATCGAAGGCAATT
* *
4611845 TGTGTATCGATGCA
1 AGTGCATCGATGCA
4611859 TGGGTAGTGT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
45 46 0.90
46 5 0.10
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (45 bp):
AGTGCATCGATGCACCCATTAAAAATGAAAACATCGAAGGCAATT
Found at i:4612301 original size:20 final size:21
Alignment explanation
Indices: 4612276--4612326 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
4612266 TGATATAAAC
*
4612276 TATATGATATGATAAGA-AA-T
1 TATATGATAT-AAAAGAGAAGT
4612296 TATATGAATATAAAAGAGAAGT
1 TATATG-ATATAAAAGAGAAGT
4612318 TATATGATA
1 TATATGATA
4612327 AGACACAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 11 0.41
21 9 0.33
22 7 0.26
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.33
Consensus pattern (21 bp):
TATATGATATAAAAGAGAAGT
Found at i:4612774 original size:24 final size:24
Alignment explanation
Indices: 4612729--4612774 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
4612719 TTCGGTGCAT
* *
4612729 TTCTACGTGGCACTACGGTGCAAA
1 TTCTAAGTGGCACTACGATGCAAA
* *
4612753 TTCTAAGTGGCGCTTCGATGCA
1 TTCTAAGTGGCACTACGATGCA
4612775 TTTATACGAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (24 bp):
TTCTAAGTGGCACTACGATGCAAA
Found at i:4613751 original size:12 final size:11
Alignment explanation
Indices: 4613716--4613749 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
4613706 ATATGTTTAA
*
4613716 ATTATTACTTTA
1 ATTATTA-TTTT
4613728 ATTATTATTTT
1 ATTATTATTTT
4613739 ATTATTATTTT
1 ATTATTATTTT
4613750 TAGTCATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:4613892 original size:2 final size:2
Alignment explanation
Indices: 4613885--4613951 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
4613875 AGAAAAACAA
4613885 AT AT AT 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 AT AT AT
4613927 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
4613952 GTTGCTTTAG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4615331 original size:15 final size:13
Alignment explanation
Indices: 4615288--4615363 Score: 72
Period size: 12 Copynumber: 5.9 Consensus size: 13
4615278 CTCGAAGTAA
4615288 GAAGAAGAAAAAA-
1 GAAG-AGAAAAAAG
4615301 GAAGA-AGAAAAA-
1 GAAGAGA-AAAAAG
4615313 GAA-AGAAAAAAG
1 GAAGAGAAAAAAG
4615325 GAAGA-AAAAAAG
1 GAAGAGAAAAAAG
4615337 GAAGAGAAAAAAAG
1 GAAGAG-AAAAAAG
*
4615351 AAAAGAGAAAAAA
1 -GAAGAGAAAAAA
4615364 AGAGATTGAT
Statistics
Matches: 55, Mismatches: 1, Indels: 13
0.80 0.01 0.19
Matches are distributed among these distances:
11 7 0.13
12 25 0.45
13 5 0.09
14 13 0.24
15 5 0.09
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
GAAGAGAAAAAAG
Found at i:4615361 original size:12 final size:13
Alignment explanation
Indices: 4615286--4615366 Score: 77
Period size: 13 Copynumber: 6.5 Consensus size: 13
4615276 TGCTCGAAGT
4615286 AAGAAGAAGAAAA
1 AAGAAGAAGAAAA
4615299 AAGAAGAAG-AAA
1 AAGAAGAAGAAAA
4615311 AAG-A-AAGAAAA
1 AAGAAGAAGAAAA
4615322 AAGGAAGAA-AAAA
1 AA-GAAGAAGAAAA
*
4615335 AGGAAG-AGAAAAA
1 AAGAAGAAG-AAAA
4615348 AAGAA-AAGAGAAA
1 AAGAAGAAGA-AAA
4615361 AA-AAGA
1 AAGAAGA
4615367 GATTGATTTA
Statistics
Matches: 57, Mismatches: 2, Indels: 18
0.74 0.03 0.23
Matches are distributed among these distances:
10 3 0.05
11 7 0.12
12 14 0.25
13 31 0.54
14 2 0.04
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAGAAGAAGAAAA
Found at i:4615364 original size:15 final size:15
Alignment explanation
Indices: 4615305--4615366 Score: 67
Period size: 15 Copynumber: 4.3 Consensus size: 15
4615295 AAAAAAGAAG
*
4615305 AAGAAAA-AGAAAGA
1 AAGAAAAGAGAAAAA
*
4615319 AA-AAAGGAAGAAAAA
1 AAGAAAAG-AGAAAAA
*
4615334 AAG-GAAGAGAAAAA
1 AAGAAAAGAGAAAAA
4615348 AAGAAAAGAGAAAAA
1 AAGAAAAGAGAAAAA
4615363 AAGA
1 AAGA
4615367 GATTGATTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
13 3 0.08
14 12 0.31
15 24 0.62
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAGAAAAGAGAAAAA
Found at i:4615844 original size:10 final size:9
Alignment explanation
Indices: 4615824--4615906 Score: 51
Period size: 9 Copynumber: 9.9 Consensus size: 9
4615814 TCATCTATTA
4615824 GAAAAAAAT
1 GAAAAAAAT
4615833 GAAAACAAAT
1 GAAAA-AAAT
4615843 G--AAAAAT
1 GAAAAAAAT
4615850 GAAAAAAA-
1 GAAAAAAAT
4615858 G--AAAAAT
1 GAAAAAAAT
4615865 --AAAAAAT
1 GAAAAAAAT
4615872 GAAAAATAA-
1 GAAAAA-AAT
*
4615881 -AAAAGAAAA
1 GAAAA-AAAT
4615890 GAAAAAAA-
1 GAAAAAAAT
4615898 GAAGAAAAA
1 GAA-AAAAA
4615907 AAGAAATTGA
Statistics
Matches: 62, Mismatches: 0, Indels: 24
0.72 0.00 0.28
Matches are distributed among these distances:
6 5 0.08
7 11 0.18
8 12 0.19
9 23 0.37
10 11 0.18
ACGTcount: A:0.80, C:0.01, G:0.12, T:0.07
Consensus pattern (9 bp):
GAAAAAAAT
Found at i:4615854 original size:6 final size:7
Alignment explanation
Indices: 4615839--4615889 Score: 59
Period size: 7 Copynumber: 7.3 Consensus size: 7
4615829 AAATGAAAAC
4615839 AAATGAA
1 AAATGAA
4615846 AAATGAAA
1 AAATG-AA
*
4615854 AAAAGAA
1 AAATGAA
*
4615861 AAATAAA
1 AAATGAA
4615868 AAATGAA
1 AAATGAA
4615875 AAAT-AA
1 AAATGAA
*
4615881 AAAAGAA
1 AAATGAA
4615888 AA
1 AA
4615890 GAAAAAAAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
6 5 0.14
7 26 0.70
8 6 0.16
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (7 bp):
AAATGAA
Found at i:4615870 original size:13 final size:12
Alignment explanation
Indices: 4615851--4615912 Score: 72
Period size: 13 Copynumber: 4.9 Consensus size: 12
4615841 ATGAAAAATG
4615851 AAAAAAAGAAAA
1 AAAAAAAGAAAA
4615863 ATAAAAAATGAAAA
1 A-AAAAAA-GAAAA
4615877 ATAAAAAAGAAAA
1 A-AAAAAAGAAAA
*
4615890 GAAAAAAAG-AAG
1 -AAAAAAAGAAAA
4615902 AAAAAAAGAAA
1 AAAAAAAGAAA
4615913 TTGAATCAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
11 8 0.18
12 5 0.11
13 18 0.40
14 14 0.31
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.05
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:4615897 original size:8 final size:8
Alignment explanation
Indices: 4615823--4615912 Score: 60
Period size: 8 Copynumber: 10.6 Consensus size: 8
4615813 CTCATCTATT
4615823 AGAAAAAA
1 AGAAAAAA
4615831 ATGAAAACAA
1 A-GAAAA-AA
4615841 ATG-AAAAA
1 A-GAAAAAA
*
4615849 TGAAAAAA
1 AGAAAAAA
4615857 AGAAAAATA
1 AGAAAAA-A
4615866 A-AAAATGAA
1 AGAAAA--AA
*
4615875 AAATAAAAA
1 AGA-AAAAA
4615884 AGAAAAGAA
1 AGAAAA-AA
*
4615893 A-AAAAGA
1 AGAAAAAA
4615900 AGAAAAAA
1 AGAAAAAA
4615908 AGAAA
1 AGAAA
4615913 TTGAATCAAG
Statistics
Matches: 67, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
7 3 0.04
8 35 0.52
9 19 0.28
10 7 0.10
11 3 0.04
ACGTcount: A:0.80, C:0.01, G:0.12, T:0.07
Consensus pattern (8 bp):
AGAAAAAA
Found at i:4619360 original size:222 final size:221
Alignment explanation
Indices: 4618974--4619457 Score: 824
Period size: 222 Copynumber: 2.2 Consensus size: 221
4618964 CCATGATGTT
*
4618974 TAAATCCTTCGGGTCATATGTGATCCTTTCGAGCAAGATGATAAGACCTTCAAGCCATCCATCAG
1 TAAATCCTTCGGGTCATCTGTGAT-CTTTCGAGCAAGATGATAAGACCTTCAAGCCATCCATCAG
*
4619039 ACCTTCTGGCATGATGTTTTCAAATGAGATATTAGAAACTAAGCCTAATTTTAAGGGGTTTCTTA
65 ACCTTCGGGCATGATGTTTTCAAATGAGATATTAGAAACTAAGCCTAATTTTAAGGGGTTTCTTA
* *
4619104 ATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAATAAAGGGGTTCATTGATAACTAAGAAA
130 ATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAACAAAGGGGTTCATTGACAACTAAGAAA
* *
4619169 CTAAGCTTTTGAGGGTTTCTTGATTTG
195 CTAAGCTTTCGAGGGTTTCTTGATTCG
*
4619196 TAAATCCTTCGGGTCATCTGTGATCTTTTCGAGCAAGATGATAAGACCTTCAGGCCATCCATCAG
1 TAAATCCTTCGGGTCATCTGTGATC-TTTCGAGCAAGATGATAAGACCTTCAAGCCATCCATCAG
4619261 ACCTTCGGGCATGATGTTTTCAAATGAGATATTAGAAACTAAGCCTAATTTTAAGGGGTTTCTTA
65 ACCTTCGGGCATGATGTTTTCAAATGAGATATTAGAAACTAAGCCTAATTTTAAGGGGTTTCTTA
*
4619326 ATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAACAAAGGGGTTCCTTGACAACTAAGAAA
130 ATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAACAAAGGGGTTCATTGACAACTAAGAAA
4619391 CTAAGCTTTCGAGGGTTTCTTGATTCG
195 CTAAGCTTTCGAGGGTTTCTTGATTCG
* * * * *
4619418 TAAGTCCTTTGGGCCATCTGTAAGTCTTTCGAGCATGATG
1 TAAATCCTTCGGGTCATCTGTGA-TCTTTCGAGCAAGATG
4619458 CTTAAATCCT
Statistics
Matches: 247, Mismatches: 13, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
221 1 0.00
222 244 0.99
223 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (221 bp):
TAAATCCTTCGGGTCATCTGTGATCTTTCGAGCAAGATGATAAGACCTTCAAGCCATCCATCAGA
CCTTCGGGCATGATGTTTTCAAATGAGATATTAGAAACTAAGCCTAATTTTAAGGGGTTTCTTAA
TTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAACAAAGGGGTTCATTGACAACTAAGAAAC
TAAGCTTTCGAGGGTTTCTTGATTCG
Found at i:4619481 original size:42 final size:42
Alignment explanation
Indices: 4619422--4619518 Score: 149
Period size: 42 Copynumber: 2.3 Consensus size: 42
4619412 GATTCGTAAG
* * *
4619422 TCCTTTGGGCCATCTGTAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTAGGGTCATCTGTAAGTCTTTCAAGCATGATGCTTAAA
* *
4619464 TCCTTCGGGTCATCTGTAAGTCTTTCAAGCATGATGTTTAAA
1 TCCTTAGGGTCATCTGTAAGTCTTTCAAGCATGATGCTTAAA
4619506 TCCTTAGGGTCAT
1 TCCTTAGGGTCAT
4619519 TCATAAGACC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.37
Consensus pattern (42 bp):
TCCTTAGGGTCATCTGTAAGTCTTTCAAGCATGATGCTTAAA
Found at i:4619944 original size:12 final size:12
Alignment explanation
Indices: 4619927--4619964 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
4619917 TCCATTTGTT
*
4619927 TTATTAGTATTA
1 TTATTAATATTA
*
4619939 TTATTAATTTTA
1 TTATTAATATTA
4619951 TTA-TAATATTA
1 TTATTAATATTA
4619962 TTA
1 TTA
4619965 CTATTAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (12 bp):
TTATTAATATTA
Found at i:4619962 original size:20 final size:21
Alignment explanation
Indices: 4619925--4619964 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
4619915 TATCCATTTG
*
4619925 TTTTATTAGTATTATTATTAA
1 TTTTATTAGTAATATTATTAA
4619946 TTTTATTA-TAATATTATTA
1 TTTTATTAGTAATATTATTA
4619965 CTATTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
TTTTATTAGTAATATTATTAA
Found at i:4620329 original size:36 final size:36
Alignment explanation
Indices: 4620278--4620363 Score: 118
Period size: 36 Copynumber: 2.4 Consensus size: 36
4620268 AATTTCAGCC
*
4620278 GCTGCCACGATGCCACTCTCACCGAAGATTCCAGTA
1 GCTGCCACGACGCCACTCTCACCGAAGATTCCAGTA
* * * *
4620314 GCTGCCAAGACGCCACTCTCGCCGAAGATTTCGGTA
1 GCTGCCACGACGCCACTCTCACCGAAGATTCCAGTA
*
4620350 GCTGACACGACGCC
1 GCTGCCACGACGCC
4620364 GCACACGTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.23, C:0.36, G:0.23, T:0.17
Consensus pattern (36 bp):
GCTGCCACGACGCCACTCTCACCGAAGATTCCAGTA
Found at i:4621324 original size:19 final size:19
Alignment explanation
Indices: 4621302--4621345 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
4621292 ACCATAAGTT
4621302 TTATTTTTTTAATTTACTC
1 TTATTTTTTTAATTTACTC
** *
4621321 TTATAGTTTTAATTTTCTC
1 TTATTTTTTTAATTTACTC
4621340 -TATTTT
1 TTATTTT
4621346 AGTCACTATT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.68
Consensus pattern (19 bp):
TTATTTTTTTAATTTACTC
Found at i:4622955 original size:38 final size:37
Alignment explanation
Indices: 4622904--4623028 Score: 187
Period size: 37 Copynumber: 3.4 Consensus size: 37
4622894 TTTTCACCCT
* * *
4622904 AAACCTGACCCGACCCGACCTGAATAACACACTTAAAA
1 AAACCCGACCCGACCCGACCCGAATATCACACTT-AAA
*
4622942 AAACCCGACCCGACTCGACCCGAATATCACACTTAAA
1 AAACCCGACCCGACCCGACCCGAATATCACACTTAAA
* *
4622979 AAACCCTACCCGACCTGACCCGAATATCACACTTAAA
1 AAACCCGACCCGACCCGACCCGAATATCACACTTAAA
4623016 AAACCCGACCCGA
1 AAACCCGACCCGA
4623029 ACAAAATAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
37 49 0.62
38 30 0.38
ACGTcount: A:0.39, C:0.38, G:0.10, T:0.13
Consensus pattern (37 bp):
AAACCCGACCCGACCCGACCCGAATATCACACTTAAA
Found at i:4623060 original size:31 final size:31
Alignment explanation
Indices: 4623018--4623087 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
4623008 CACTTAAAAA
4623018 ACCCGACCCGAACAAAATAAAGTTTCACCCG
1 ACCCGACCCGAACAAAATAAAGTTTCACCCG
*
4623049 ACCTGACCCGAACAAAATAAAGTTTCACCCG
1 ACCCGACCCGAACAAAATAAAGTTTCACCCG
4623080 ACCCGACC
1 ACCCGACC
4623088 TGAATATATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.37, C:0.37, G:0.13, T:0.13
Consensus pattern (31 bp):
ACCCGACCCGAACAAAATAAAGTTTCACCCG
Found at i:4623787 original size:16 final size:16
Alignment explanation
Indices: 4623756--4623807 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
4623746 ACATTCGCAA
4623756 ATATGTTCG-T-ATAT
1 ATATGTTCGCTAATAT
4623770 ATATGTTCGCTAATAT
1 ATATGTTCGCTAATAT
* * *
4623786 ATTTATTCGCGAATAT
1 ATATGTTCGCTAATAT
*
4623802 GTATGT
1 ATATGT
4623808 ATAAGCTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
14 9 0.30
15 1 0.03
16 20 0.67
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (16 bp):
ATATGTTCGCTAATAT
Found at i:4629843 original size:2 final size:2
Alignment explanation
Indices: 4629836--4629890 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
4629826 TTCAAACACG
4629836 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
4629878 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
4629891 TACTCGATGC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4644258 original size:17 final size:18
Alignment explanation
Indices: 4644236--4644271 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
4644226 AGGTTAGGGC
4644236 TAGGGATTTGA-GATTTT
1 TAGGGATTTGAGGATTTT
4644253 TAGGGATTTGAGGATTTT
1 TAGGGATTTGAGGATTTT
4644271 T
1 T
4644272 TTTTGTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (18 bp):
TAGGGATTTGAGGATTTT
Found at i:4649212 original size:2 final size:2
Alignment explanation
Indices: 4649200--4649243 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
4649190 TTCAGTCAGG
*
4649200 TA TA TA CA TA TA TA TA T- 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
4649241 TA T
1 TA T
4649244 TGATGGTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4653237 original size:41 final size:41
Alignment explanation
Indices: 4653122--4653278 Score: 172
Period size: 41 Copynumber: 3.8 Consensus size: 41
4653112 AATACCGCTA
* ** *
4653122 GTACTTTAGTGGCCGTTTTTATACAAATGATGCAAAAGACTC
1 GTACTTTAGTGG-CGTTTTTATACAAACGCCGCTAAAGACTC
* * *
4653164 GTACTTTAGTGCCGTTTTTTTCAATAAACGCCGCTAAAGACTC
1 GTACTTTAGTGGCGTTTTTAT--ACAAACGCCGCTAAAGACTC
* * *
4653207 GTACTTTAGTGGCATTTTT-TAACAAACGCCGCTAAAGAATT
1 GTACTTTAGTGGCGTTTTTAT-ACAAACGCCGCTAAAGACTC
*
4653248 GTACTTTAGTGGCGCTTTTATACAAACGCCG
1 GTACTTTAGTGGCGTTTTTATACAAACGCCG
4653279 TCATTTTCCT
Statistics
Matches: 98, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
41 53 0.54
42 13 0.13
43 32 0.33
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (41 bp):
GTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTC
Found at i:4656356 original size:43 final size:41
Alignment explanation
Indices: 4656308--4656603 Score: 245
Period size: 43 Copynumber: 7.0 Consensus size: 41
4656298 TTTGTATCCC
*
4656308 AAAACGTCGCTATAGATCTGACCTTTTGCGGCGTTT-TTATA
1 AAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTA-A
* * *
4656349 TACAAACGCCGCTATAGATATGACCTTTTACGGCATTT-TTAGA
1 -A-AAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTA-A
* *
4656392 TACAAACGCCGCTATAGATCTAACCTTTTACGGCGTTTGTTAA
1 -A-AAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTAA
* * * * *
4656435 AAAACACCGCTATATATCTCGACATTTTGCGGCATTTGTTCCA
1 AAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGTT-AA
* *
4656478 AAAACGCCGCTATAGATCTTGACCTATGGCGGCGTTTGTTCAA
1 AAAACGCCGCTATAGATC-TGACCTTTTGCGGCGTTTGTT-AA
* * * ** *
4656521 AAAATGCAGCTATATATCTCGATATTTTGCGGCGTTTGTTCCA
1 AAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGTT-AA
* * * **
4656564 AAAACGCCGCTAGAGATATCAATTTTTTGCGGCGTTTGTT
1 AAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGTT
4656604 CCAAAAATGT
Statistics
Matches: 211, Mismatches: 37, Indels: 11
0.81 0.14 0.04
Matches are distributed among these distances:
41 16 0.08
42 19 0.09
43 172 0.82
44 4 0.02
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (41 bp):
AAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTAA
Found at i:4656596 original size:86 final size:85
Alignment explanation
Indices: 4656298--4656612 Score: 298
Period size: 86 Copynumber: 3.7 Consensus size: 85
4656288 ATTAGTGGCG
* * * * *
4656298 TTTGTATCCCAAAACGTCGCTATAGATCTGACCTTTTGCGGCGTTT-TT-ATATACAAACGCCGC
1 TTTGT-TCCAAAAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTGTTCA-A-A-AAATGCAGC
* * * *
4656361 TATAGATAT-GACCTTTTACGGCA
62 TATATATCTCGACATTTTGCGGCA
** * ** *
4656384 TTT-TTAGATACAAACGCCGCTATAGATCTAACCTTTTACGGCGTTTGTT-AAAAAACACCGCTA
1 TTTGTTCCA-A-AAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTGTTCAAAAAATGCAGCTA
4656447 TATATCTCGACATTTTGCGGCA
64 TATATCTCGACATTTTGCGGCA
* * *
4656469 TTTGTTCCAAAAACGCCGCTATAGATCTTGACCTATGGCGGCGTTTGTTCAAAAAATGCAGCTAT
1 TTTGTTCCAAAAACGCCGCTATAGATC-TAACCTTTTGCGGCGTTTGTTCAAAAAATGCAGCTAT
* *
4656534 ATATCTCGATATTTTGCGGCG
65 ATATCTCGACATTTTGCGGCA
* * ** *
4656555 TTTGTTCCAAAAACGCCGCTAGAGATATCAATTTTTTGCGGCGTTTGTTCCAAAAATG
1 TTTGTTCCAAAAACGCCGCTATAGATCT-AACCTTTTGCGGCGTTTGTTCAAAAAATG
4656613 TCGCTAACTT
Statistics
Matches: 191, Mismatches: 30, Indels: 16
0.81 0.13 0.07
Matches are distributed among these distances:
84 33 0.17
85 37 0.19
86 118 0.62
87 3 0.02
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (85 bp):
TTTGTTCCAAAAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTGTTCAAAAAATGCAGCTATA
TATCTCGACATTTTGCGGCA
Found at i:4656618 original size:43 final size:42
Alignment explanation
Indices: 4656506--4656618 Score: 136
Period size: 43 Copynumber: 2.6 Consensus size: 42
4656496 TTGACCTATG
* * * * *
4656506 GCGGCGTTTGTTCAAAAAATGCAGCTATATATCTCGATATTTT
1 GCGGCGTTTGTTCCAAAAATGC-GCTAGAGATATCAATATTTT
* *
4656549 GCGGCGTTTGTTCCAAAAACGCCGCTAGAGATATCAATTTTTT
1 GCGGCGTTTGTTCCAAAAATG-CGCTAGAGATATCAATATTTT
4656592 GCGGCGTTTGTTCCAAAAATGTCGCTA
1 GCGGCGTTTGTTCCAAAAATG-CGCTA
4656619 ACTTTAGCGG
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
43 59 0.98
44 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAATGCGCTAGAGATATCAATATTTT
Found at i:4663666 original size:180 final size:177
Alignment explanation
Indices: 4663358--4663716 Score: 643
Period size: 180 Copynumber: 2.0 Consensus size: 177
4663348 TAGGTTCAGG
4663358 AGATCAGAATAGGTTATCTAGTGTGTTCCCATAAAATCAGTGAAGAGATACAAATCTTTTCTTTT
1 AGATCAGAATAGGTTATCTAGTGTGTTCCCATAAAATCAGTGAAGAGATACAAATCTTTTCTTTT
4663423 TAAAGTAGTAGTTTAAAACATTTTTTATTCAAAAACCATATTAATCCCTCCAACCAAACTCTCCA
66 TAAAGTAGTAGTTTAAAACATTTTTTATTCAAAAACCATATTAATCCCTCCAACCAAACTCTCCA
4663488 TAATGTGTA-GTTCCCTAGAACCATACACCCACATACACACACCAAATA
131 TAATGTGTAGGTTCCCTAGAACCATACACCCACAT--ACACACCAAATA
4663536 AGATCA-AATAGGTTATCTAGTGTG-TCCCATAAAATCAGTGAAGAGATACAAATCTTTTCTTTT
1 AGATCAGAATAGGTTATCTAGTGTGTTCCCATAAAATCAGTGAAGAGATACAAATCTTTTCTTTT
4663599 TAAACAGTAGTAGTTTAAAAACATATTTTTATTCAAAAACCATATTAATCCCTCCAACCAAACTC
66 T-AA-AGTAGTAGTTT-AAAACAT-TTTTTATTCAAAAACCATATTAATCCCTCCAACCAAACTC
4663664 TCCATAATGTGTAGGTTCCCTAGAACCATACACCCACATACACACCAAATA
127 TCCATAATGTGTAGGTTCCCTAGAACCATACACCCACATACACACCAAATA
4663715 AG
1 AG
4663717 GACTTACCCT
Statistics
Matches: 176, Mismatches: 0, Indels: 9
0.95 0.00 0.05
Matches are distributed among these distances:
176 40 0.23
177 20 0.11
178 17 0.10
179 21 0.12
180 53 0.30
181 25 0.14
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.30
Consensus pattern (177 bp):
AGATCAGAATAGGTTATCTAGTGTGTTCCCATAAAATCAGTGAAGAGATACAAATCTTTTCTTTT
TAAAGTAGTAGTTTAAAACATTTTTTATTCAAAAACCATATTAATCCCTCCAACCAAACTCTCCA
TAATGTGTAGGTTCCCTAGAACCATACACCCACATACACACCAAATA
Found at i:4672647 original size:24 final size:22
Alignment explanation
Indices: 4672604--4672655 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
4672594 ATTTATCTTT
*
4672604 TAAATTTATAAAAAATTATATA
1 TAAATTTATAAAAAAATATATA
*
4672626 TAAATTTTATTAAAAAA-ATATA
1 TAAA-TTTATAAAAAAATATATA
4672648 TAAATTTA
1 TAAATTTA
4672656 AAATAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 4 0.15
22 13 0.48
23 10 0.37
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATTTATAAAAAAATATATA
Found at i:4674747 original size:18 final size:19
Alignment explanation
Indices: 4674724--4674759 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
4674714 ACATTTTAAA
4674724 AAATAAAATAA-AATATTT
1 AAATAAAATAATAATATTT
4674742 AAATAAAATAATAATATT
1 AAATAAAATAATAATATT
4674760 CATAAATTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATAAAATAATAATATTT
Found at i:4674965 original size:14 final size:14
Alignment explanation
Indices: 4674948--4674974 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4674938 TTGAAATTTA
4674948 AAATTTTAATTTTC
1 AAATTTTAATTTTC
4674962 AAATTTTAATTTT
1 AAATTTTAATTTT
4674975 AAAAATTAAA
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:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (14 bp):
AAATTTTAATTTTC
Found at i:4675138 original size:43 final size:43
Alignment explanation
Indices: 4675090--4675869 Score: 478
Period size: 43 Copynumber: 18.1 Consensus size: 43
4675080 GAGCATGAGA
* * *
4675090 ATGTCATATTGGTTAATGATGATATGCTCCTTCAAATACGAGG
1 ATGTCATATTGGTTGATGATGATATGCTCCTTCGAACACGAGG
* * * **
4675133 ATGTCATATTGG-T--TGATGATATGCTCATTCAAATATAAGG
1 ATGTCATATTGGTTGATGATGATATGCTCCTTCGAACACGAGG
* * * * ** *
4675173 ATGACAGATTGGTTGACGATAATATTTTCCTTCAAACAC-AGG
1 ATGTCATATTGGTTGATGATGATATGCTCCTTCGAACACGAGG
* * * * *
4675215 ATGTCAGATTGGTTGACT-ATGACATGCTCTTTTGGACACGAGG
1 ATGTCATATTGGTTGA-TGATGATATGCTCCTTCGAACACGAGG
* * ** * * *
4675258 AAGTCAAATTAATTGATGATGATATGCTTCTTCGAATACGAGA
1 ATGTCATATTGGTTGATGATGATATGCTCCTTCGAACACGAGG
** ** ** ** * * * *
4675301 ACATCGGATTTATCAATGATAATGTACTCATTCGAACACGAGG
1 ATGTCATATTGGTTGATGATGATATGCTCCTTCGAACACGAGG
* * * * *
4675344 ATGTCAAATTGTTTGACGATGATATGCTACTTGGAACACGAGG
1 ATGTCATATTGGTTGATGATGATATGCTCCTTCGAACACGAGG
* * ** * * *
4675387 ATGCCAAATTTATCGATGATGATTTGTTCCTTCGAACACGAGG
1 ATGTCATATTGGTTGATGATGATATGCTCCTTCGAACACGAGG
*** * *
4675430 ACACCATATTGGTCGATGATGATGTGCAT-CTTCGAACACGAGG
1 ATGTCATATTGGTTGATGATGATATGC-TCCTTCGAACACGAGG
* * * * * * *
4675473 ATGCCATATTGGTTGAAGATTATATGTTCTTTTGAACATGAGG
1 ATGTCATATTGGTTGATGATGATATGCTCCTTCGAACACGAGG
* * * * *
4675516 ATGTCATATTAGTCGATGATGATCTGCTCCTTCAAACACAAGG
1 ATGTCATATTGGTTGATGATGATATGCTCCTTCGAACACGAGG
* * *
4675559 AT-TCCATATTAGTTGATGATGATATGCTCATTCGAACACTAGG
1 ATGT-CATATTGGTTGATGATGATATGCTCCTTCGAACACGAGG
* *
4675602 AATTAGTCATATTGGTTGATGATGATCATGCTCCTTCAAACACAAGG
1 -A-T-GTCATATTGGTTGATGATGAT-ATGCTCCTTCGAACACGAGG
* * **
4675649 AT-TCCATATTAGTTGACGACAATATGCTCCTTCGAACACGAGG
1 ATGT-CATATTGGTTGATGATGATATGCTCCTTCGAACACGAGG
* * *
4675692 AAGTCATATTGGTTGATGATGATCATGCTCCTTCAAACTCGAGG
1 ATGTCATATTGGTTGATGATGAT-ATGCTCCTTCGAACACGAGG
* * * ** * * * *
4675736 AAGCCAGATTTATCGATTATGATATACTCATTCGAACACGAGG
1 ATGTCATATTGGTTGATGATGATATGCTCCTTCGAACACGAGG
* * * * * * * **
4675779 ATGCCAAATTGATTGATGATGATGTACTCATTCGAATATAAGG
1 ATGTCATATTGGTTGATGATGATATGCTCCTTCGAACACGAGG
* * ** * * *
4675822 AGGTCAAATTGGTTGATGACAATCTACTCTTTCGAACACGAGG
1 ATGTCATATTGGTTGATGATGATATGCTCCTTCGAACACGAGG
4675865 ATGTC
1 ATGTC
4675870 GACTAAACTG
Statistics
Matches: 568, Mismatches: 152, Indels: 34
0.75 0.20 0.05
Matches are distributed among these distances:
40 34 0.06
41 1 0.00
42 35 0.06
43 406 0.71
44 53 0.09
45 2 0.00
46 19 0.03
47 18 0.03
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (43 bp):
ATGTCATATTGGTTGATGATGATATGCTCCTTCGAACACGAGG
Found at i:4675164 original size:40 final size:40
Alignment explanation
Indices: 4675090--4675193 Score: 127
Period size: 40 Copynumber: 2.5 Consensus size: 40
4675080 GAGCATGAGA
* *
4675090 ATGTCATATTGGTTAATGATGATATGCTCCTTCAAATACGAGG
1 ATGTCATATTGG-T--TGATGATATGCTCATTCAAATACAAGG
*
4675133 ATGTCATATTGGTTGATGATATGCTCATTCAAATATAAGG
1 ATGTCATATTGGTTGATGATATGCTCATTCAAATACAAGG
* * *
4675173 ATGACAGATTGGTTGACGATA
1 ATGTCATATTGGTTGATGATA
4675194 ATATTTTCCT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
40 42 0.76
42 1 0.02
43 12 0.22
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.35
Consensus pattern (40 bp):
ATGTCATATTGGTTGATGATATGCTCATTCAAATACAAGG
Found at i:4676109 original size:34 final size:34
Alignment explanation
Indices: 4676064--4676130 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
4676054 AATAGGAATT
*
4676064 ACAACTTCTCTC-GATATAACAAGGAGAAAACAATA
1 ACAACTTCTCTCTGATA-AA-AAAGAGAAAACAATA
4676099 ACAA-TTCTCTCTTGATAAAAAAGAGAAAACAA
1 ACAACTTCTCTC-TGATAAAAAAGAGAAAACAA
4676131 CTCTCAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 19 0.66
35 6 0.21
36 4 0.14
ACGTcount: A:0.51, C:0.18, G:0.10, T:0.21
Consensus pattern (34 bp):
ACAACTTCTCTCTGATAAAAAAGAGAAAACAATA
Found at i:4679131 original size:76 final size:76
Alignment explanation
Indices: 4679044--4679217 Score: 187
Period size: 76 Copynumber: 2.3 Consensus size: 76
4679034 TATGGAAGAC
* * *
4679044 AAATTGATGTTTGAAGAGAAATAATTTTAA-AGAAGACGGAAA-TGATG-TTCTAA-GAGAAACG
1 AAATTGGTGTTTCAAGAGAAATAATATTAAGA-AAGA-GGAAATTGATGTTTC-AACGA-AAACG
*
4679105 GTCTTAAG-GAAGATG
62 GTCTT-AGTGAAGATA
* * * *
4679120 AAATTGGTGTTTCAAGAGAAATGATATTAAGAAAGATGAAATTGATGTTTCAACGAAATCGTTCT
1 AAATTGGTGTTTCAAGAGAAATAATATTAAGAAAGAGGAAATTGATGTTTCAACGAAAACGGTCT
4679185 TAGTGAAGATA
66 TAGTGAAGATA
*
4679196 AAATTGGTGTTTCAAGATAAAT
1 AAATTGGTGTTTCAAGAGAAAT
4679218 GGGCTTAAAG
Statistics
Matches: 84, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
75 6 0.07
76 72 0.86
77 6 0.07
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.30
Consensus pattern (76 bp):
AAATTGGTGTTTCAAGAGAAATAATATTAAGAAAGAGGAAATTGATGTTTCAACGAAAACGGTCT
TAGTGAAGATA
Found at i:4679137 original size:38 final size:38
Alignment explanation
Indices: 4679095--4679212 Score: 132
Period size: 38 Copynumber: 3.1 Consensus size: 38
4679085 ATGATGTTCT
*
4679095 AAGAGAAACGGTCTTAAGGAAGATGAAATTGGTGTTTC
1 AAGAGAAACGATCTTAAGGAAGATGAAATTGGTGTTTC
* * * *
4679133 AAGAGAAATGATATTAAGAAAGATGAAATTGATGTTTC
1 AAGAGAAACGATCTTAAGGAAGATGAAATTGGTGTTTC
* * *
4679171 AACGA-AATCGTTCTT-AGTGAAGATAAAATTGGTGTTTC
1 AA-GAGAAACGATCTTAAG-GAAGATGAAATTGGTGTTTC
4679209 AAGA
1 AAGA
4679213 TAAATGGGCT
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
37 4 0.06
38 60 0.91
39 2 0.03
ACGTcount: A:0.41, C:0.07, G:0.24, T:0.29
Consensus pattern (38 bp):
AAGAGAAACGATCTTAAGGAAGATGAAATTGGTGTTTC
Found at i:4679246 original size:76 final size:76
Alignment explanation
Indices: 4679113--4679253 Score: 167
Period size: 76 Copynumber: 1.9 Consensus size: 76
4679103 CGGTCTTAAG
* * * ** *
4679113 GAAGATGAAATTGGTGTTTCAAGAGAAATGATATTAAGAAAGATGAAATTGATGTTTCAACGAAA
1 GAAGATAAAATTGGTGTTTCAAGAGAAATGAGATTAAGAAAGATAAAATCAAAGTTTCAACGAAA
4679178 TCGTTCTTAGT
66 TCGTTCTTAGT
* * * * *
4679189 GAAGATAAAATTGGTGTTTCAAGATAAATGGGCTTAA-AGAATATAAAATCAAAGTTTCAAGGAA
1 GAAGATAAAATTGGTGTTTCAAGAGAAATGAGATTAAGA-AAGATAAAATCAAAGTTTCAACGAA
4679253 A
65 A
4679254 ACATCTTAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
75 1 0.02
76 52 0.98
ACGTcount: A:0.43, C:0.06, G:0.21, T:0.29
Consensus pattern (76 bp):
GAAGATAAAATTGGTGTTTCAAGAGAAATGAGATTAAGAAAGATAAAATCAAAGTTTCAACGAAA
TCGTTCTTAGT
Found at i:4679448 original size:19 final size:19
Alignment explanation
Indices: 4679419--4679464 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
4679409 CGTGCCTAAC
* *
4679419 TTTAAAAAATA-ATTATTT
1 TTTATAAAATATATTATTA
4679437 TTTCATAAAATATATTATTA
1 TTT-ATAAAATATATTATTA
4679457 TTTATAAA
1 TTTATAAA
4679465 GATCTTATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 3 0.12
19 12 0.50
20 9 0.38
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTATAAAATATATTATTA
Found at i:4687704 original size:32 final size:32
Alignment explanation
Indices: 4687668--4687817 Score: 221
Period size: 32 Copynumber: 4.7 Consensus size: 32
4687658 AAATATCTTG
*
4687668 GGGCCTGAGAGCCTACCCAAGGGAGTACCTTA
1 GGGCCTAAGAGCCTACCCAAGGGAGTACCTTA
4687700 GGGCCTAAGAGCCTACCCAAGGGAGTACCTTA
1 GGGCCTAAGAGCCTACCCAAGGGAGTACCTTA
*
4687732 GGGCCTAAGAGCCTACCTAAGGGAGTACCTTA
1 GGGCCTAAGAGCCTACCCAAGGGAGTACCTTA
* * * * *
4687764 GGACCTAAAAGCCTACCAAAGGAAGTACCTTG
1 GGGCCTAAGAGCCTACCCAAGGGAGTACCTTA
4687796 GGGCCCT-AGAGCCTACCCAAGG
1 GGG-CCTAAGAGCCTACCCAAGG
4687818 TCACCTTAGG
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
32 104 0.97
33 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.15
Consensus pattern (32 bp):
GGGCCTAAGAGCCTACCCAAGGGAGTACCTTA
Found at i:4692811 original size:31 final size:31
Alignment explanation
Indices: 4692776--4692854 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
4692766 GGAGCCAACA
* * *
4692776 CAAGAAAGTTCTCGGGGCTATGGGGCCTACT
1 CAAGAAAGATCTCGGGGCTATAGGGCCTACC
*
4692807 CAAGAAAGATCTCGGGGCTGTAGGGCCTACC
1 CAAGAAAGATCTCGGGGCTATAGGGCCTACC
4692838 CAAGAAAGATCTCGGGG
1 CAAGAAAGATCTCGGGG
4692855 TCAAAAAGCC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.27, C:0.23, G:0.33, T:0.18
Consensus pattern (31 bp):
CAAGAAAGATCTCGGGGCTATAGGGCCTACC
Found at i:4692866 original size:31 final size:31
Alignment explanation
Indices: 4692776--4692868 Score: 80
Period size: 31 Copynumber: 3.0 Consensus size: 31
4692766 GGAGCCAACA
* **** *
4692776 CAAGAAAGTTCTCGGGGCTATGGGGCCTACT
1 CAAGAAAGATCTCGGGGCTAAAAAGCCTACC
** **
4692807 CAAGAAAGATCTCGGGGCTGTAGGGCCTACC
1 CAAGAAAGATCTCGGGGCTAAAAAGCCTACC
4692838 CAAGAAAGATCTCGGGG-TCAAAAAGCCTACC
1 CAAGAAAGATCTCGGGGCT-AAAAAGCCTACC
4692869 TAAGGTTAGG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
30 1 0.02
31 52 0.98
ACGTcount: A:0.29, C:0.25, G:0.29, T:0.17
Consensus pattern (31 bp):
CAAGAAAGATCTCGGGGCTAAAAAGCCTACC
Found at i:4693582 original size:22 final size:22
Alignment explanation
Indices: 4693556--4693612 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
4693546 GATCAGTCAA
*
4693556 ATCAAAGTCAACGATCTGACTAG
1 ATCAAAGTCAACAATCTGA-TAG
* *
4693579 -TCAAAGTTAACAATCTGATTG
1 ATCAAAGTCAACAATCTGATAG
4693600 ATCAAAGTCAACA
1 ATCAAAGTCAACA
4693613 GTCAGACCGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 2 0.07
22 27 0.93
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (22 bp):
ATCAAAGTCAACAATCTGATAG
Found at i:4694668 original size:32 final size:32
Alignment explanation
Indices: 4694632--4694805 Score: 226
Period size: 32 Copynumber: 5.4 Consensus size: 32
4694622 TTGGGCGTAG
* * * *
4694632 GAGCCAACCTAAGGGAATATCTTGGGGCCTGA
1 GAGCCTACCCAAGGAAATATCTTGGGGCCTTA
* * *
4694664 GAGCCTACCCAATGG-AGTATCTTAGGGCCTAA
1 GAGCCTACCCAA-GGAAATATCTTGGGGCCTTA
*
4694696 GAGCCTACCCAA-GAAAGTACCTTGGGGCCTTA
1 GAGCCTACCCAAGGAAA-TATCTTGGGGCCTTA
*
4694728 GAGCCTACCCAAGGAAATGTCTTGGGGCCTTA
1 GAGCCTACCCAAGGAAATATCTTGGGGCCTTA
*
4694760 GAGCCTACCCAAGGAAATGTCTTGGGGCCTTA
1 GAGCCTACCCAAGGAAATATCTTGGGGCCTTA
4694792 GAGCCTACCCAAGG
1 GAGCCTACCCAAGG
4694806 TCACCTTAGG
Statistics
Matches: 127, Mismatches: 11, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
30 1 0.01
31 1 0.01
32 119 0.94
33 6 0.05
ACGTcount: A:0.27, C:0.26, G:0.28, T:0.20
Consensus pattern (32 bp):
GAGCCTACCCAAGGAAATATCTTGGGGCCTTA
Found at i:4702358 original size:26 final size:25
Alignment explanation
Indices: 4702288--4702413 Score: 81
Period size: 25 Copynumber: 5.0 Consensus size: 25
4702278 ATTGAACCTT
* * *
4702288 ACCCTAAACCTCTTTAACCTACACA
1 ACCCTAAACCACTTTAACCTAAAAA
** * * *
4702313 ACCCTTGATCACTCTCACCTTAAAAA
1 ACCCTAAACCACTTTAACC-TAAAAA
*
4702339 ACCCTAAACCACTTTAACCTATAAA
1 ACCCTAAACCACTTTAACCTAAAAA
* ** * * *
4702364 ATCCTTCACTACTTTTACCTTAATAA
1 ACCCTAAACCACTTTAACC-TAAAAA
* *
4702390 ACTCTATACCACTTTAACCTAAAA
1 ACCCTAAACCACTTTAACCTAAAA
4702414 TCACTCTAAC
Statistics
Matches: 71, Mismatches: 28, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
25 36 0.51
26 35 0.49
ACGTcount: A:0.37, C:0.33, G:0.01, T:0.29
Consensus pattern (25 bp):
ACCCTAAACCACTTTAACCTAAAAA
Found at i:4702384 original size:51 final size:51
Alignment explanation
Indices: 4702288--4702410 Score: 140
Period size: 51 Copynumber: 2.4 Consensus size: 51
4702278 ATTGAACCTT
* * *
4702288 ACCCTAAACCTCTTTAACCTACACAACCCTTGATCACTCTCACCTTAAAAA
1 ACCCTAAACCACTTTAACCTACAAAACCCTTCATCACTCTCACCTTAAAAA
* * * * *
4702339 ACCCTAAACCACTTTAACCTATAAAATCCTTCA-CTACTTTTACCTTAATAA
1 ACCCTAAACCACTTTAACCTACAAAACCCTTCATC-ACTCTCACCTTAAAAA
* *
4702390 ACTCTATACCACTTTAACCTA
1 ACCCTAAACCACTTTAACCTA
4702411 AAATCACTCT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
50 1 0.02
51 60 0.98
ACGTcount: A:0.36, C:0.33, G:0.01, T:0.30
Consensus pattern (51 bp):
ACCCTAAACCACTTTAACCTACAAAACCCTTCATCACTCTCACCTTAAAAA
Found at i:4710116 original size:16 final size:15
Alignment explanation
Indices: 4710080--4710119 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
4710070 CCTAAATCTT
4710080 AAATTTTAAAAATTA
1 AAATTTTAAAAATTA
* *
4710095 ACATTTTTAAAATTA
1 AAATTTTAAAAATTA
*
4710110 AAAATTTAAA
1 AAATTTTAAA
4710120 TTCTAATACT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATTTTAAAAATTA
Found at i:4713452 original size:2 final size:2
Alignment explanation
Indices: 4713435--4713480 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
4713425 AAAAATTAAC
* *
4713435 AT AT AC AT AC 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 AT AT AT
4713477 AT AT
1 AT AT
4713481 TATCCATGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4713659 original size:2 final size:2
Alignment explanation
Indices: 4713652--4713806 Score: 167
Period size: 2 Copynumber: 78.5 Consensus size: 2
4713642 CATAAAAACT
4713652 TA TA TA TA TA 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 TA TA TA TA TA TA
* * * * * * ** *
4713693 TCA AA TA TA GT- TG TT TA -A TA AA AA TA -A TA -A TA TG CG TA AA
1 T-A TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4713733 TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4713776 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
4713807 GCGTAAATTA
Statistics
Matches: 133, Mismatches: 12, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
1 5 0.04
2 125 0.94
3 3 0.02
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:4716180 original size:134 final size:134
Alignment explanation
Indices: 4715837--4717391 Score: 1658
Period size: 134 Copynumber: 11.7 Consensus size: 134
4715827 ATGGATGAGT
* * * ** * * *
4715837 GAAATAAAAACGTCGATCCCCCTCATTCTGTGATATAATCGAACGAGATGTAGGTACTGATCTAC
1 GAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGATATGTTGGTGCTGATCTAC
*
4715902 CTCCTTCTATGATAGAATCGAGCT-AAAAGTTGAC-ACTGATCCAACTCCTTCTGCGATGGATTT
66 CTCCTTCTGTGATAGAATCGAGCTAAAAAGTTGACGA-TGATCCAACTCCTTCTGCGATGGATTT
*
4715965 GAGAG
130 GAGCG
* * * * *
4715970 AAAATAAAAATGT-GAATCCACCTCCTTCTGTGATGGAATCGAATGAGATATCGGTG-TCGATCT
1 GAAATAAAAATGTCG-ATCCACCTCCTTCTGTGATGGAATCGAACGATATGTTGGTGCT-GATCT
* * *
4716033 ACCTCATTATGTGATAGAATCGAGCTAAAAAGTTGACGATGATACAACTCCTTCTGCGATGGATT
64 ACCTCCTTCTGTGATAGAATCGAGCTAAAAAGTTGACGATGATCCAACTCCTTCTGCGATGGATT
4716098 TGAGCG
129 TGAGCG
* * * *
4716104 GAAA-AAAAATGTCGATCCACCTCGTTCTGTGATGGAAATCAAACGATATGTTGATGTTGATCTA
1 GAAATAAAAATGTCGATCCACCTCCTTCTGTGATGG-AATCGAACGATATGTTGGTGCTGATCTA
* * * * *
4716168 CCTCCTTCTGTGATAGAATCAAGCT-AAAAGTTGA-TACTGATCTAACTCCTTCGGCAATGGATT
65 CCTCCTTCTGTGATAGAATCGAGCTAAAAAGTTGACGA-TGATCCAACTCCTTCTGCGATGGATT
*
4716231 TGAGTG
129 TGAGCG
* * * *** **
4716237 AAAATAAAAATGTCGATCCACCTCATTCTGTGATGGAAATCAAACGATATGTCAATATTGATCTA
1 GAAATAAAAATGTCGATCCACCTCCTTCTGTGATGG-AATCGAACGATATGTTGGTGCTGATCTA
* * *
4716302 CCTCTTTCTGTGATAGAATCAAGCT-AAAAGTTGAC-ACTGATCCAATTCCTTCTGCGATGGATT
65 CCTCCTTCTGTGATAGAATCGAGCTAAAAAGTTGACGA-TGATCCAACTCCTTCTGCGATGGATT
4716365 TGAGCG
129 TGAGCG
* * * * * * * *
4716371 AAAATAAAAATAATTGATCCACCTCTTTCTATGATGGAATC-AAGCGAAATGTTGGCGTTGATCT
1 GAAATAAAAAT-GTCGATCCACCTCCTTCTGTGATGGAATCGAA-CGATATGTTGGTGCTGATCT
* * * *
4716435 ACCTCATTCTGTGATAGAATCGAG-TAAAAAGTTCACGTTGATCCAAATCCTTCTGCGATGGATT
64 ACCTCCTTCTGTGATAGAATCGAGCTAAAAAGTTGACGATGATCCAACTCCTTCTGCGATGGATT
4716499 TGAGCG
129 TGAGCG
* * * * * * *
4716505 GAAAAAAAAATTATCGATCAATCTCCTTCTGTGATGGAATCAAACGATATGTCGATGCTGATCTA
1 GAAATAAAAA-TGTCGATCCACCTCCTTCTGTGATGGAATCGAACGATATGTTGGTGCTGATCTA
* * * *
4716570 CCTCCTTCTGTGATAGAATCTAGC-AAAAAGTTGACGCTGATCCAACTCTTTCTACGATGGATTT
65 CCTCCTTCTGTGATAGAATCGAGCTAAAAAGTTGACGATGATCCAACTCCTTCTGCGATGGATTT
4716634 GAGC-
130 GAGCG
* * * * *
4716638 G--A-ACAAATGTCGATCCACCTCTTTTTGTGATGGAATCGAATGATATGTCGGTGCTGATCTAC
1 GAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGATATGTTGGTGCTGATCTAC
* * *
4716700 CTCCTTCTGTGATAGAATCGAG-TTAAAAGTTGACGCTGATCCAACTCATTCTGCGATGGATTTG
66 CTCCTTCTGTGATAGAATCGAGCTAAAAAGTTGACGATGATCCAACTCCTTCTGCGATGGATTTG
4716764 AGCG
131 AGCG
* * * * ** * * * *
4716768 AAAATAAAAAAGTCGAT-CATCTCCTTCTTTGATCCAATTGAACGATATGTTGATGTTGATATAC
1 GAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGATATGTTGGTGCTGATCTAC
* * * *
4716832 CTCATTCTGTGATAGAATCAAGCT-AAAACTTGACGCTGATCCAACTCCTTCTGCGATGGATTTG
66 CTCCTTCTGTGATAGAATCGAGCTAAAAAGTTGACGATGATCCAACTCCTTCTGCGATGGATTTG
**
4716896 AGTA
131 AGCG
* * * * * * *
4716900 AAAATAAAAATGTCGATCCACCTCATTTTATGATGGAATCGAATGAAATGTTGGTGTTGATCTAC
1 GAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGATATGTTGGTGCTGATCTAC
* * * *
4716965 CTCCTTCTATGATAGAAACGAGC-AAAAAGTTGA-TACTGATCCAACTCATTCTGCGATGGATTT
66 CTCCTTCTGTGATAGAATCGAGCTAAAAAGTTGACGA-TGATCCAACTCCTTCTGCGATGGATTT
4717028 GA---
130 GAGCG
* * * * *
4717030 GTAA-ACAAATGTCGATCCACCTCCTTCTGTGATGGAATCAAATGAAATGTTGGTGCTGATCTAC
1 GAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGATATGTTGGTGCTGATCTAC
* * * *
4717094 CTCCTTTTGTGATAGAATCGAGC-AAAAAGTTGACGTTGATCCAACTTCTTCTGCGATCGATTTG
66 CTCCTTCTGTGATAGAATCGAGCTAAAAAGTTGACGATGATCCAACTCCTTCTGCGATGGATTTG
4717158 AGC-
131 AGCG
* * * *
4717161 GAAATAAAAATGTTGATCCACCTCCTTCTGTGATGGAAACGAACGAGATGTTGGTGCTAATCTAC
1 GAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGATATGTTGGTGCTGATCTAC
* * * *** * * *
4717226 CTCCTTTTGTGATAAAATCACAAAAAAAAAGTTGATGCTGATCCAACTCTTTCTGCGATGGATTT
66 CTCCTTCTGTGATAGAATC-GAGCTAAAAAGTTGACGATGATCCAACTCCTTCTGCGATGGATTT
*
4717291 GAAC-
130 GAGCG
* ***
4717295 GAAA-AAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATACCGGTGCTGATCTAC
1 GAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGATATGTTGGTGCTGATCTAC
* *
4717359 CTCTTTCTGTGATAGAATCAAGCT-AAAAGTTGA
66 CTCCTTCTGTGATAGAATCGAGCTAAAAAGTTGA
4717392 ACAATTTCTT
Statistics
Matches: 1212, Mismatches: 178, Indels: 66
0.83 0.12 0.05
Matches are distributed among these distances:
129 219 0.18
130 6 0.00
131 13 0.01
132 187 0.15
133 316 0.26
134 445 0.37
135 26 0.02
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (134 bp):
GAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGATATGTTGGTGCTGATCTAC
CTCCTTCTGTGATAGAATCGAGCTAAAAAGTTGACGATGATCCAACTCCTTCTGCGATGGATTTG
AGCG
Found at i:4717044 original size:394 final size:394
Alignment explanation
Indices: 4715848--4717391 Score: 1851
Period size: 394 Copynumber: 3.9 Consensus size: 394
4715838 AAATAAAAAC
* ** * * * *
4715848 GTCGATCCCCCTCATTCTGTGATATAATCGAACGAGATGTAGGTACTGATCTACCTCCTTCTATG
1 GTCGATCCACCTCATTCTGTGATGGAATCAAACGATATGTCGGTACTGATCTACCTCCTTCTGTG
*
4715913 ATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGAGAGAAAATAAA
66 ATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAA
* * * * * *
4715978 AATG-TGAATCCACCTCCTTCTGTGATGGAATCGAATGAGATATCGGTGTCGATCTACCTCATTA
131 AAAGTTG-ATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTTGGTGTTGATCTACCTCATTC
* * * **
4716042 TGTGATAGAATCGAGCTAAAAAGTTGACGATGATACAACTCCTTCTGCGATGGATTTGAGCGGAA
195 TGTGATAGAATCAAGCTAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAG-AAAA
* * *
4716107 AAAAAATGTCGATCCACCTCGTTCTGTGATGGAAATCAAACGATATGTTGATGTTGATCTACCTC
259 AAAAAATGTCGATCCACCTCCTTCTGTGATGG-AATCAAACGATATGTCGATGCTGATCTACCTC
* * * * *
4716172 CTTCTGTGATAGAATCAAGCTAAAAGTTGATACTGATCTAACTCCTTCGGCAATGGATTTGAGTG
323 CTTCTGTGATAGAATCAAGCAAAAAGTTGATACTGATCCAACTCATTCTGCGATGGATTTGAGT-
*
4716237 AAAATAAAAAT
387 --AA-ACAAAT
** * *
4716248 GTCGATCCACCTCATTCTGTGATGGAAATCAAACGATATGTCAATATTGATCTACCTCTTTCTGT
1 GTCGATCCACCTCATTCTGTGATGG-AATCAAACGATATGTCGGTACTGATCTACCTCCTTCTGT
* *
4716313 GATAGAATCAAGCTAAAAGTTGACACTGATCCAATTCCTTCTGCGATGGATTTGAGCGAAAATAA
65 GATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAA
* * * * *
4716378 AAATAATTGATCCACCTCTTTCTATGATGGAATC-AAGCGAAATGTTGGCGTTGATCTACCTCAT
130 AAA-AGTTGATCCACCTCCTTCTGTGATGGAATCGAA-CGAGATGTTGGTGTTGATCTACCTCAT
* * * *
4716442 TCTGTGATAGAATCGAG-TAAAAAGTTCACGTTGATCCAAATCCTTCTGCGATGGATTTGAGCGG
193 TCTGTGATAGAATCAAGCTAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA---G
* * * *
4716506 AAAAAAAAATTATCGATCAATCTCCTTCTGTGATGGAATCAAACGATATGTCGATGCTGATCTAC
255 AAAAAAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCAAACGATATGTCGATGCTGATCTAC
* ** * *
4716571 CTCCTTCTGTGATAGAATCTAGCAAAAAGTTGACGCTGATCCAACTCTTTCTACGATGGATTTGA
320 CTCCTTCTGTGATAGAATCAAGCAAAAAGTTGATACTGATCCAACTCATTCTGCGATGGATTTGA
**
4716636 GCGAACAAAT
385 GTAAACAAAT
* * * * *
4716646 GTCGATCCACCTCTTTTTGTGATGGAATCGAATGATATGTCGGTGCTGATCTACCTCCTTCTGTG
1 GTCGATCCACCTCATTCTGTGATGGAATCAAACGATATGTCGGTACTGATCTACCTCCTTCTGTG
* * *
4716711 ATAGAATCGAGTTAAAAGTTGACGCTGATCCAACTCATTCTGCGATGGATTTGAGCGAAAATAAA
66 ATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAA
* * * ** * * * *
4716776 AAAGTCGAT-CATCTCCTTCTTTGATCCAATTGAACGATATGTTGATGTTGATATACCTCATTCT
131 AAAGTTGATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTTGGTGTTGATCTACCTCATTCT
*
4716840 GTGATAGAATCAAGCT-AAAACTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAGTAAAAA
196 GTGATAGAATCAAGCTAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAG-AAAAA
* * * * * * * * *
4716904 TAAAAATGTCGATCCACCTCATTTTATGATGGAATCGAATGAAATGTTGGTGTTGATCTACCTCC
260 -AAAAATGTCGATCCACCTCCTTCTGTGATGGAATCAAACGATATGTCGATGCTGATCTACCTCC
* * *
4716969 TTCTATGATAGAAACGAGCAAAAAGTTGATACTGATCCAACTCATTCTGCGATGGATTTGAGTAA
324 TTCTGTGATAGAATCAAGCAAAAAGTTGATACTGATCCAACTCATTCTGCGATGGATTTGAGTAA
4717034 ACAAAT
389 ACAAAT
* * * * * *
4717040 GTCGATCCACCTCCTTCTGTGATGGAATCAAATGAAATGTTGGTGCTGATCTACCTCCTTTTGTG
1 GTCGATCCACCTCATTCTGTGATGGAATCAAACGATATGTCGGTACTGATCTACCTCCTTCTGTG
* ** * *
4717105 ATAGAATCGAGCAAAAAGTTGACGTTGATCCAACTTCTTCTGCGATCGATTTGAGCG-AAATAAA
66 ATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAA
* * * * * *
4717169 AATGTTGATCCACCTCCTTCTGTGATGGAAACGAACGAGATGTTGGTGCTAATCTACCTCCTTTT
131 AAAGTTGATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTTGGTGTTGATCTACCTCATTCT
* *** * * *
4717234 GTGATAAAATCACAAAAAAAAAGTTGATGCTGATCCAACTCTTTCTGCGATGGATTTGA-ACGAA
196 GTGATAGAATCA-AGCTAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAGA-AAA
* * ** * *
4717298 AAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATACCGGTGCTGATCTACCTCT
259 AAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCAAACGATATGTCGATGCTGATCTACCTCC
*
4717363 TTCTGTGATAGAATCAAGCTAAAAGTTGA
324 TTCTGTGATAGAATCAAGCAAAAAGTTGA
4717392 ACAATTTCTT
Statistics
Matches: 977, Mismatches: 152, Indels: 36
0.84 0.13 0.03
Matches are distributed among these distances:
392 1 0.00
393 19 0.02
394 356 0.36
395 96 0.10
396 46 0.05
397 95 0.10
398 28 0.03
399 1 0.00
400 22 0.02
401 137 0.14
402 144 0.15
403 31 0.03
404 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (394 bp):
GTCGATCCACCTCATTCTGTGATGGAATCAAACGATATGTCGGTACTGATCTACCTCCTTCTGTG
ATAGAATCGAGCTAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAA
AAAGTTGATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTTGGTGTTGATCTACCTCATTCT
GTGATAGAATCAAGCTAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGAGAAAAAA
AAAATGTCGATCCACCTCCTTCTGTGATGGAATCAAACGATATGTCGATGCTGATCTACCTCCTT
CTGTGATAGAATCAAGCAAAAAGTTGATACTGATCCAACTCATTCTGCGATGGATTTGAGTAAAC
AAAT
Found at i:4717786 original size:37 final size:37
Alignment explanation
Indices: 4717731--4717914 Score: 164
Period size: 37 Copynumber: 5.3 Consensus size: 37
4717721 TATTTCGAGG
*
4717731 GAAACTGTCTCTAA-AGAGACAAAACTTTGTTTTAAGA
1 GAAACTGTCTC-AAGAGAGACAAAACTTTGTTTCAAGA
*
4717768 GAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGA
* * *
4717804 GAAACAGAT-TC-A-A-AG-----ATTTTGTTTCAAGG
1 GAAACTG-TCTCAAGAGAGACAAAACTTTGTTTCAAGA
4717833 GAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAA-A
1 GAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGA
* * *
4717869 -AAA-TGTCTCAAGGGAGA-TAAACTTTGTTTCAAAA
1 GAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGA
*
4717903 GAAACTGACTCA
1 GAAACTGTCTCA
4717915 GGCTTTTGTT
Statistics
Matches: 123, Mismatches: 9, Indels: 31
0.75 0.06 0.19
Matches are distributed among these distances:
28 2 0.02
29 20 0.16
30 1 0.01
31 1 0.01
32 2 0.02
33 16 0.13
34 15 0.12
35 7 0.06
36 26 0.21
37 33 0.27
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.27
Consensus pattern (37 bp):
GAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGA
Found at i:4717896 original size:33 final size:34
Alignment explanation
Indices: 4717838--4717902 Score: 105
Period size: 33 Copynumber: 1.9 Consensus size: 34
4717828 CAAGGGAAAC
4717838 TGTCTCAAGAGAGACAAAACTTTGTTTCAAAAAA
1 TGTCTCAAGAGAGACAAAACTTTGTTTCAAAAAA
* *
4717872 TGTCTCAAGGGAGA-TAAACTTTGTTTCAAAA
1 TGTCTCAAGAGAGACAAAACTTTGTTTCAAAA
4717903 GAAACTGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 16 0.55
34 13 0.45
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (34 bp):
TGTCTCAAGAGAGACAAAACTTTGTTTCAAAAAA
Found at i:4717954 original size:98 final size:102
Alignment explanation
Indices: 4717731--4717980 Score: 267
Period size: 99 Copynumber: 2.5 Consensus size: 102
4717721 TATTTCGAGG
* * *
4717731 GAAACTGTCTCTAAAGAGACAAAACTTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
1 GAAACTATCTCAAAAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
** * *
4717796 TTTCAAGGGAAACAGATTCAAAGATTTTGTTTCAAGG
66 TTTCAAAAGAAACAGACTCAAAGATTTTGTTTCAAGA
* * * * *
4717833 GAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAA-A-AAA-TGTCTCAAGGGAGATAAACTTTG
1 GAAACTATCTCAAAAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
* * * **
4717895 TTTCAAAAGAAACTGACTC-AGGCTTTTGTTTTGAGA
66 TTTCAAAAGAAACAGACTCAAAGATTTTGTTTCAAGA
* * * *
4717931 GAAATTATCTCAAAAGAGACAAAAC-TTGTTTTAAGTAAAAATTGTCTCAA
1 GAAACTATCTCAAAAGAGACAAAACTTTGTTTCAAG-AGAAACTGTCTCAA
4717981 TTTTTTTTTG
Statistics
Matches: 125, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
97 8 0.06
98 34 0.27
99 36 0.29
100 6 0.05
101 9 0.07
102 32 0.26
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (102 bp):
GAAACTATCTCAAAAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
TTTCAAAAGAAACAGACTCAAAGATTTTGTTTCAAGA
Found at i:4718166 original size:90 final size:89
Alignment explanation
Indices: 4718020--4718378 Score: 436
Period size: 90 Copynumber: 4.1 Consensus size: 89
4718010 CCTAAAAATC
* * *
4718020 AGGCTTAGTTTTTAAAA-CTCATTTGAAAACATCCTGCCCT-AGGGTCTTATGGATGGCCCGAAG
1 AGGCTTAGTTTCTAAAATCTCATTTGAAAACAT-CTGCACTGAAGGTCTTATGGATGGCCCGAAG
*
4718083 GACTTACAAATAAAGAAACCCCCGA
65 GACTTACAAATCAAGAAACCCCCGA
*
4718108 AGGCTTGGTTTCTAAAATCTCATTTGAAAACATACTGCACTGAAGGTCTTATGGATGGCCCGAAG
1 AGGCTTAGTTTCTAAAATCTCATTTGAAAACAT-CTGCACTGAAGGTCTTATGGATGGCCCGAAG
4718173 GACTTACAAATCAAGAAACCCCCGA
65 GACTTACAAATCAAGAAACCCCCGA
* * *
4718198 AGGTTTAGTTTCTAAAATCTCATTTGAAAACATCTTGAACTGAAGGTCTTATGGATGGTCCGAAG
1 AGGCTTAGTTTCTAAAATCTCATTTGAAAACATC-TGCACTGAAGGTCTTATGGATGGCCCGAAG
**
4718263 GACTTA-AAATCAAGAAACCTTCGA
65 GACTTACAAATCAAGAAACCCCCGA
* * *** *
4718287 A-G---A--TT-T--AGTTTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAG
1 AGGCTTAGTTTCTAAAATCTCATTTGAAAA-CATCTGCACTGAAGGTCTTATGGATGGCCCGAAG
* *
4718343 GACTTACAAATCGAGAAACCCCTGA
65 GACTTACAAATCAAGAAACCCCCGA
4718368 AGGCTTAGTTT
1 AGGCTTAGTTT
4718379 TTTAAAAAAT
Statistics
Matches: 236, Mismatches: 24, Indels: 23
0.83 0.08 0.08
Matches are distributed among these distances:
80 46 0.19
81 16 0.07
82 2 0.01
83 2 0.01
85 2 0.01
87 2 0.01
88 16 0.07
89 39 0.17
90 111 0.47
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (89 bp):
AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCTGCACTGAAGGTCTTATGGATGGCCCGAAGG
ACTTACAAATCAAGAAACCCCCGA
Found at i:4719663 original size:28 final size:28
Alignment explanation
Indices: 4719623--4719713 Score: 137
Period size: 28 Copynumber: 3.2 Consensus size: 28
4719613 GATAAAAGGC
*
4719623 TCAGGTTGACTTGGGAATGTAATGTATT
1 TCAGGTTGACTTGGGAAGGTAATGTATT
4719651 TCAGGTTGACTTGGGAAGGTAATGTATT
1 TCAGGTTGACTTGGGAAGGTAATGTATT
* * * *
4719679 TCAGGTTAATTTGGGGAGGTAATGTGTT
1 TCAGGTTGACTTGGGAAGGTAATGTATT
4719707 TCAGGTT
1 TCAGGTT
4719714 TGCCTCTTGC
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.23, C:0.07, G:0.32, T:0.38
Consensus pattern (28 bp):
TCAGGTTGACTTGGGAAGGTAATGTATT
Done.