Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 21 of 318
Found at i:5475517 original size:5 final size:5
Alignment explanation
Indices: 5475507--5475544 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
5475497 CTTTCACTGT
* *
5475507 TCTTC TCTTC TCTTC TCTTC TCTTC GCTTC TTTTC TCT
1 TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TCT
5475545 GCAACCAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.37, G:0.03, T:0.61
Consensus pattern (5 bp):
TCTTC
Found at i:5487452 original size:48 final size:48
Alignment explanation
Indices: 5487381--5487762 Score: 307
Period size: 48 Copynumber: 7.9 Consensus size: 48
5487371 TACTAGGGTT
* * * *
5487381 ATATGTGAGCTACTGTAAGACCATGTCTGGGACATGGCATCGGCCTCA
1 ATATGTGAGCCAGTGTAAGACCATGTCTGGAACATGGCATCGGCCTTA
* * * *
5487429 ATATGTGAGCCAGTGGAAGACCATGTTTGGAACATGGCATCGACATTA
1 ATATGTGAGCCAGTGTAAGACCATGTCTGGAACATGGCATCGGCCTTA
* * * * * *
5487477 TTATGAGAGCTAGTGTAAGACCATGTCT-GAGACATGGCATTGACCTTG
1 ATATGTGAGCCAGTGTAAGACCATGTCTGGA-ACATGGCATCGGCCTTA
* * * * ** *
5487525 ATATGTGAGCCAGTTTAAGACCATGTTTGGAATATGGCCTCGGTATTG
1 ATATGTGAGCCAGTGTAAGACCATGTCTGGAACATGGCATCGGCCTTA
* * * * * * *
5487573 TTATGAGAGCTAGTGTAAGACCATATCTGGGACATGACATCGGCCTCA
1 ATATGTGAGCCAGTGTAAGACCATGTCTGGAACATGGCATCGGCCTTA
* * * * * ** *
5487621 ATATATGAGCTAGTCTAAGACCATGTTTGGAACATGGCGTCGGTATTG
1 ATATGTGAGCCAGTGTAAGACCATGTCTGGAACATGGCATCGGCCTTA
* * * * * * * **
5487669 TTGTATGAGCCAGTATAAGACCATGTCTGGGACATGACATTGGCACCGA
1 ATATGTGAGCCAGTGTAAGACCATGTCTGGAACATGGCATCGGC-CTTA
* *
5487718 TATATGAGAGCCAGTGTAAGACCATGTCTAGAACATGGCATCGGC
1 -ATATGTGAGCCAGTGTAAGACCATGTCTGGAACATGGCATCGGC
5487763 ATCTTACCCT
Statistics
Matches: 253, Mismatches: 77, Indels: 6
0.75 0.23 0.02
Matches are distributed among these distances:
47 2 0.01
48 214 0.85
49 2 0.01
50 35 0.14
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (48 bp):
ATATGTGAGCCAGTGTAAGACCATGTCTGGAACATGGCATCGGCCTTA
Found at i:5487551 original size:96 final size:96
Alignment explanation
Indices: 5487382--5487761 Score: 440
Period size: 96 Copynumber: 3.9 Consensus size: 96
5487372 ACTAGGGTTA
* * * * *
5487382 TATGTGAGCTACTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAATATGTGAGCCAGTGGAA
1 TATGAGAGCTAGTGTAAGACCATGTCTGGGACATGACATCGACCTCAATATGTGAGCCAGTGTAA
** *
5487447 GACCATGTTTGGAACATGGCATCGACATTAT
66 GACCATGTTTGGAACATGGCATCGGTATTGT
* * * ** *
5487478 TATGAGAGCTAGTGTAAGACCATGTCTGAGACATGGCATTGACCTTGATATGTGAGCCAGTTTAA
1 TATGAGAGCTAGTGTAAGACCATGTCTGGGACATGACATCGACCTCAATATGTGAGCCAGTGTAA
* *
5487543 GACCATGTTTGGAATATGGCCTCGGTATTGT
66 GACCATGTTTGGAACATGGCATCGGTATTGT
* * * * *
5487574 TATGAGAGCTAGTGTAAGACCATATCTGGGACATGACATCGGCCTCAATATATGAGCTAGTCTAA
1 TATGAGAGCTAGTGTAAGACCATGTCTGGGACATGACATCGACCTCAATATGTGAGCCAGTGTAA
*
5487639 GACCATGTTTGGAACATGGCGTCGGTATTGT
66 GACCATGTTTGGAACATGGCATCGGTATTGT
* * * * * *
5487670 TGT-ATGAGCCAGTATAAGACCATGTCTGGGACATGACATTGGCACC-GATATATGAGAGCCAGT
1 TATGA-GAGCTAGTGTAAGACCATGTCTGGGACATGACA-TCG-ACCTCA-ATATGTGAGCCAGT
* *
5487733 GTAAGACCATGTCTAGAACATGGCATCGG
62 GTAAGACCATGTTTGGAACATGGCATCGG
5487762 CATCTTACCC
Statistics
Matches: 240, Mismatches: 40, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
95 1 0.00
96 198 0.82
97 3 0.01
98 38 0.16
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (96 bp):
TATGAGAGCTAGTGTAAGACCATGTCTGGGACATGACATCGACCTCAATATGTGAGCCAGTGTAA
GACCATGTTTGGAACATGGCATCGGTATTGT
Found at i:5493609 original size:14 final size:14
Alignment explanation
Indices: 5493584--5493624 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
5493574 GTAGTCTTAA
5493584 AATAAA-ATAAAAGT
1 AATAAATATAAAA-T
5493598 AA-AAATATAAAAT
1 AATAAATATAAAAT
*
5493611 AATAAATAAAAAAT
1 AATAAATATAAAAT
5493625 TTTAAACATC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 6 0.25
14 18 0.75
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (14 bp):
AATAAATATAAAAT
Found at i:5493609 original size:19 final size:20
Alignment explanation
Indices: 5493585--5493622 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5493575 TAGTCTTAAA
*
5493585 ATAAAATAA-AAGTAAAAAT
1 ATAAAATAATAAATAAAAAT
5493604 ATAAAATAATAAATAAAAA
1 ATAAAATAATAAATAAAAA
5493623 ATTTTAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (20 bp):
ATAAAATAATAAATAAAAAT
Found at i:5511970 original size:11 final size:11
Alignment explanation
Indices: 5511954--5511987 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
5511944 AAATCTTACG
5511954 AAAACAAAAAA
1 AAAACAAAAAA
*
5511965 AAAACAAAACA
1 AAAACAAAAAA
5511976 AAAACAAGAAAA
1 AAAACAA-AAAA
5511988 CACATCAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 17 0.85
12 3 0.15
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAACAAAAAA
Found at i:5513377 original size:48 final size:48
Alignment explanation
Indices: 5513298--5513681 Score: 412
Period size: 48 Copynumber: 7.9 Consensus size: 48
5513288 TACTAGGGTT
* * *
5513298 ATATGTGAGTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCG
1 ATATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTTG
* *
5513346 ATATGTGAGCCAGTGTAAGACAATGTTTGGGACATGGTC-TCGGCATTG
1 ATATGTGAGCCAGTGTAAGACCATGTTTGGGACATGG-CATCGGCCTTG
*
5513394 TTATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTTG
1 ATATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTTG
* * * * * ***
5513442 ATATGTGAGCCAATATAAGTCTC-TGTTTGGAACATGGCCTCGATATTG
1 ATATGTGAGCCAGTGTAAGAC-CATGTTTGGGACATGGCATCGGCCTTG
* * * *
5513490 TTATGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCG
1 ATATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTTG
* *
5513538 ATATTGTTATGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCG
1 ATA-TG---T--GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTTG
* * * * *
5513592 ATATGTGAGCTAGTGTAAGACCATGCTTGGAACATGGCATCGACATTG
1 ATATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTTG
* * * * *
5513640 TTGTATGAGCCAGTATAAGCCCATGTTTGGGACATGGCATCG
1 ATATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCG
5513682 ACACCGATAT
Statistics
Matches: 282, Mismatches: 44, Indels: 20
0.82 0.13 0.06
Matches are distributed among these distances:
47 2 0.01
48 228 0.81
49 4 0.01
50 1 0.00
53 2 0.01
54 45 0.16
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (48 bp):
ATATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTTG
Found at i:5513595 original size:150 final size:149
Alignment explanation
Indices: 5513298--5513710 Score: 456
Period size: 150 Copynumber: 2.8 Consensus size: 149
5513288 TACTAGGGTT
* * * * * * * * *
5513298 ATATGTGAGTCAGTGTAAGACCATG-TCTGGGACATGGCATCGGCCTCGATATGTGAGCCAGTGT
1 ATATGTGAGCCAATATAAGACCATGCT-TGGAACATGGCATCGACATTGTTATGAGAGCCAGTGT
* * *
5513362 AAGACAATGTTTGGGACATGGTC-TCGG--C---ATTGTTATGTGAGCCAGTGTAAGACCATGTT
65 AAGACCATGTTTGGGACATGG-CATCGGCCCGATATTGTTATGAGAGCTAGTGTAAGACCATGTT
*
5513421 TGGGACATGGCATCGGCCTTG
129 TGGGACATGGCATCGGCCTCG
* * * * *
5513442 ATATGTGAGCCAATATAAGTCTC-TGTTTGGAACATGGCCTCGATATTGTTATGAGAGCTAGTGT
1 ATATGTGAGCCAATATAAGAC-CATGCTTGGAACATGGCATCGACATTGTTATGAGAGCCAGTGT
5513506 AAGACCATGTTTGGGACATGGCATCGGCCTCGATATTGTTATGAGAGCTAGTGTAAGACCATGTT
65 AAGACCATGTTTGGGACATGGCATCGGCC-CGATATTGTTATGAGAGCTAGTGTAAGACCATGTT
5513571 TGGGACATGGCATCGGCCTCG
129 TGGGACATGGCATCGGCCTCG
* * * * *
5513592 ATATGTGAGCTAGTGTAAGACCATGCTTGGAACATGGCATCGACATTGTTGT-ATGAGCCAGTAT
1 ATATGTGAGCCAATATAAGACCATGCTTGGAACATGGCATCGACATTGTTATGA-GAGCCAGTGT
* *
5513656 AAGCCCATGTTTGGGACATGGCATCGACACCGATA----TATGAGAGCTAGTGTAAGAC
65 AAGACCATGTTTGGGACATGGCATCGGC-CCGATATTGTTATGAGAGCTAGTGTAAGAC
5513711 TAAGTCTAAA
Statistics
Matches: 228, Mismatches: 29, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
143 1 0.00
144 71 0.31
145 2 0.01
146 20 0.09
147 1 0.00
149 2 0.01
150 130 0.57
151 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (149 bp):
ATATGTGAGCCAATATAAGACCATGCTTGGAACATGGCATCGACATTGTTATGAGAGCCAGTGTA
AGACCATGTTTGGGACATGGCATCGGCCCGATATTGTTATGAGAGCTAGTGTAAGACCATGTTTG
GGACATGGCATCGGCCTCG
Found at i:5513727 original size:98 final size:96
Alignment explanation
Indices: 5513351--5513736 Score: 249
Period size: 96 Copynumber: 3.9 Consensus size: 96
5513341 CCTCGATATG
* * * * * * * *
5513351 TGAGCCAGTGTAAGACAATGTTTGGGACATGGTC-TCGGCATTGTTATGTGAGCCAGTGTAAGAC
1 TGAGCCAGTATAAGACCATGTTTGGGACATGG-CATCGACCTCGATATGAGAGCTAGTGTAAGAC
* * *** * * * * *
5513415 CATGTTTGGGACATGGCATCGGCCTTGATATG
65 CAAGCTTAAAACATGGCATCGACATTGTTGTA
* * * * ** * *
5513447 TGAGCCAATATAAGTCTC-TGTTTGGAACATGGCCTCGATATTGTTATGAGAGCTAGTGTAAGAC
1 TGAGCCAGTATAAGAC-CATGTTTGGGACATGGCATCGACCTCGATATGAGAGCTAGTGTAAGAC
* * *** * * *
5513511 CATGTTTGGGACATGGCATCGGCCTCGATATTGTTA
65 CAAGCTTAAAACATGGCATCGACAT---TGTTG-TA
* * * *
5513547 TGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGATATGTGAGCTAGTGTAAGA
1 T--GAGCCAGTATAAGACCATGTTTGGGACATGGCATCGACCTCGATATGAGAGCTAGTGTAAGA
* **
5513612 CCATGCTTGGAACATGGCATCGACATTGTTGTA
64 CCAAGCTTAAAACATGGCATCGACATTGTTGTA
*
5513645 TGAGCCAGTATAAGCCCATGTTTGGGACATGGCATCGACAC-CGATATATGAGAGCTAGTGTAAG
1 TGAGCCAGTATAAGACCATGTTTGGGACATGGCATCGAC-CTCG--ATATGAGAGCTAGTGTAAG
*
5513709 ACTAAG-TCTAAAACATGGCATCGACATT
63 ACCAAGCT-TAAAACATGGCATCGACATT
5513737 TTACCCTTTT
Statistics
Matches: 238, Mismatches: 39, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
95 1 0.00
96 113 0.47
97 2 0.01
98 43 0.18
99 6 0.03
100 2 0.01
101 1 0.00
102 70 0.29
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (96 bp):
TGAGCCAGTATAAGACCATGTTTGGGACATGGCATCGACCTCGATATGAGAGCTAGTGTAAGACC
AAGCTTAAAACATGGCATCGACATTGTTGTA
Found at i:5513942 original size:12 final size:12
Alignment explanation
Indices: 5513925--5513950 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5513915 TAAGTAAGTT
5513925 ATGTCTATGGTC
1 ATGTCTATGGTC
5513937 ATGTCTATGGTC
1 ATGTCTATGGTC
5513949 AT
1 AT
5513951 TCGAGAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.42
Consensus pattern (12 bp):
ATGTCTATGGTC
Found at i:5516301 original size:44 final size:43
Alignment explanation
Indices: 5516157--5516315 Score: 173
Period size: 44 Copynumber: 3.7 Consensus size: 43
5516147 AGCTCGTACA
* * * *
5516157 ATGCCAACGTCCCAGACATGGCCTT--ACATGCAATCAAGCATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACAT-AAATCAA-AATCG
* * * *
5516200 ATGCCACTGTCCCAGACAGGGTCTTACAC-GAAATC-ATATACG
1 ATGCCAATGTCCCAGACATGGTCTTACACATAAATCAAAAT-CG
5516242 ATGCCAATGTCCCAGACATGGTCTTACACATAAATCACAAATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACATAAATCA-AAATCG
*
5516286 ATGCCAATGTCCCAGACGTGGTCTTACACA
1 ATGCCAATGTCCCAGACATGGTCTTACACA
5516316 ATAACACATA
Statistics
Matches: 98, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
41 2 0.02
42 30 0.31
43 30 0.31
44 31 0.32
45 5 0.05
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACATAAATCAAAATCG
Found at i:5516309 original size:86 final size:85
Alignment explanation
Indices: 5516157--5516314 Score: 214
Period size: 86 Copynumber: 1.8 Consensus size: 85
5516147 AGCTCGTACA
* * *
5516157 ATGCCAACGTCCCAGACATGGCCTTACATGCAATCAAGCATCGATGCCACTGTCCCAGACAGGGT
1 ATGCCAACGTCCCAGACATGGCCTTACATGAAATCAAGAATCGATGCCAATGTCCCAGACAGGGT
5516222 CTTACACGAAATCATATACG
66 CTTACACGAAATCATATACG
* *
5516242 ATGCCAATGTCCCAGACATGGTCTTACACAT-AAATCACA-AATCGATGCCAATGTCCCAGAC-G
1 ATGCCAACGTCCCAGACATGGCCTT--ACATGAAATCA-AGAATCGATGCCAATGTCCCAGACAG
5516304 TGGTCTTACAC
63 -GGTCTTACAC
5516315 AATAACACAT
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
85 24 0.38
86 35 0.55
87 5 0.08
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.22
Consensus pattern (85 bp):
ATGCCAACGTCCCAGACATGGCCTTACATGAAATCAAGAATCGATGCCAATGTCCCAGACAGGGT
CTTACACGAAATCATATACG
Found at i:5516340 original size:44 final size:44
Alignment explanation
Indices: 5516157--5516315 Score: 175
Period size: 43 Copynumber: 3.7 Consensus size: 44
5516147 AGCTCGTACA
* * * *
5516157 ATGCCAACGTCCCAGACATGGCCTT--ACATGCAATCA-AGCATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACAT-AAATCACA-AATCG
* * * * *
5516200 ATGCCACTGTCCCAGACAGGGTCTTACAC-GAAATCATATA-CG
1 ATGCCAATGTCCCAGACATGGTCTTACACATAAATCACAAATCG
5516242 ATGCCAATGTCCCAGACATGGTCTTACACATAAATCACAAATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACATAAATCACAAATCG
*
5516286 ATGCCAATGTCCCAGACGTGGTCTTACACA
1 ATGCCAATGTCCCAGACATGGTCTTACACA
5516316 ATAACACATA
Statistics
Matches: 98, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
42 29 0.30
43 35 0.36
44 32 0.33
45 2 0.02
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (44 bp):
ATGCCAATGTCCCAGACATGGTCTTACACATAAATCACAAATCG
Found at i:5518966 original size:23 final size:23
Alignment explanation
Indices: 5518936--5518983 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
5518926 CGATTGACAA
5518936 TATGAAAACTTGAACAATCGAAC
1 TATGAAAACTTGAACAATCGAAC
5518959 TATGAAAACTTGAACAATCGAAC
1 TATGAAAACTTGAACAATCGAAC
5518982 TA
1 TA
5518984 ACTTTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.23
Consensus pattern (23 bp):
TATGAAAACTTGAACAATCGAAC
Found at i:5541739 original size:59 final size:59
Alignment explanation
Indices: 5541647--5541764 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
5541637 CTCAAGTAAG
5541647 GATTTTCATTTAGAACTAGTATGGTTCCTATCACTCTTCGCGTTGGATTAATTAACATT
1 GATTTTCATTTAGAACTAGTATGGTTCCTATCACTCTTCGCGTTGGATTAATTAACATT
*
5541706 GATTTTCATTTAGAACTAGTATGGTTCCTATCACTCTTCGCGTTGGGTTAATTAACATT
1 GATTTTCATTTAGAACTAGTATGGTTCCTATCACTCTTCGCGTTGGATTAATTAACATT
5541765 TAAAACAAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (59 bp):
GATTTTCATTTAGAACTAGTATGGTTCCTATCACTCTTCGCGTTGGATTAATTAACATT
Found at i:5543145 original size:33 final size:33
Alignment explanation
Indices: 5543107--5543171 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
5543097 ATGATTGAAA
5543107 ATCAACAGCTTGATTTATCTTATAATTTCTTTT
1 ATCAACAGCTTGATTTATCTTATAATTTCTTTT
5543140 ATCAACAGCTTGATTTATCTTATAATTTCTTT
1 ATCAACAGCTTGATTTATCTTATAATTTCTTT
5543172 CTTTTTCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.51
Consensus pattern (33 bp):
ATCAACAGCTTGATTTATCTTATAATTTCTTTT
Found at i:5545055 original size:131 final size:130
Alignment explanation
Indices: 5544688--5545132 Score: 443
Period size: 131 Copynumber: 3.4 Consensus size: 130
5544678 TTCTGAAGAG
* ** *
5544688 ATATTCGATTATTTTGAACAAACGGGAAATTGCAACCCAGCACGATAGGGTACT-ATTCCCCGAA
1 ATATTCGATTATTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCA-TGATT-CCCGAA
** * * * *
5544752 TTGCCAAGCATCGAA-TATTGCCTTCATTTTAAAGGGTTTTTTAGAAAACGTGAGTG-AAATTTC
64 TTATCAAACA-CCAAGTATTGCCTTCGTTTTAAA-GG-TTTTTAGAAAACATGAGTGAAAATTT-
5544815 GAAGGA
125 GAAGGA
* * * * * *
5544821 ATCTTCGATTGTTTTGAAAAAACAAGAAATCACAACCCAACACGTTAGGGCATGATTCCCGAATT
1 ATATTCGATTATTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCATGATTCCCGAATT
* * * * ** *
5544886 ATCAAACA-CAGAGTATTGTCTTTGTTTTGGAAGGTTTTT-GATAAACACGAGTGAAAACCTAAA
66 ATCAAACACCA-AGTATTGCCTTCGTTTT-AAAGGTTTTTAGA-AAACATGAGTGAAAATTTGAA
5544949 GGA
128 GGA
* * *
5544952 ATATTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGCACGATAAGGCATGATTCTCGAATT
1 ATATTCGATTATTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCATGATTCCCGAATT
* *
5545017 ATCAAACACCAAGTATTGCCTTCGTTTTAAAGGATTTTTAGAAGACATGAGTGAAATTTTGAAGG
66 ATCAAACACCAAGTATTGCCTTCGTTTTAAAGG-TTTTTAGAAAACATGAGTGAAAATTTGAAGG
*
5545082 G
130 A
* * ** *
5545083 ATATTTGATTATTTT-AAGCAAACGGGAAATTGCAACCCAGCACGTTAGGG
1 ATATTCGATTATTTTGAA-CAAACGAGAAATCACAACCCAGCACGATAGGG
5545133 TGCGATTCTG
Statistics
Matches: 255, Mismatches: 47, Indels: 22
0.79 0.15 0.07
Matches are distributed among these distances:
130 9 0.04
131 163 0.64
132 36 0.14
133 47 0.18
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.29
Consensus pattern (130 bp):
ATATTCGATTATTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCATGATTCCCGAATT
ATCAAACACCAAGTATTGCCTTCGTTTTAAAGGTTTTTAGAAAACATGAGTGAAAATTTGAAGGA
Found at i:5546949 original size:5 final size:6
Alignment explanation
Indices: 5546934--5546958 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5546924 TTTTAAAGAA
5546934 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
5546959 GATTTGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:5547092 original size:16 final size:16
Alignment explanation
Indices: 5547074--5547130 Score: 62
Period size: 18 Copynumber: 3.5 Consensus size: 16
5547064 AACAAATAAG
*
5547074 AAAATAAAGAGAAAAG
1 AAAATAAAGAGAAAAA
* *
5547090 AAAA-AACGGGAAAAA
1 AAAATAAAGAGAAAAA
5547105 AAAATCAGAAGAGAAAAA
1 AAAAT-A-AAGAGAAAAA
5547123 AAAATAAA
1 AAAATAAA
5547131 ATTACCTCTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
15 12 0.36
16 6 0.18
17 2 0.06
18 13 0.39
ACGTcount: A:0.75, C:0.04, G:0.16, T:0.05
Consensus pattern (16 bp):
AAAATAAAGAGAAAAA
Found at i:5550988 original size:46 final size:46
Alignment explanation
Indices: 5550933--5551113 Score: 233
Period size: 46 Copynumber: 3.9 Consensus size: 46
5550923 TAGGATGGTT
5550933 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* * *
5550979 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAAC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C
*
5551025 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* ** *
5551072 GAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5551114 GCGGGTTACA
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.03
45 2 0.02
46 71 0.61
47 33 0.28
48 2 0.02
50 4 0.03
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
Found at i:5551094 original size:93 final size:93
Alignment explanation
Indices: 5550935--5551105 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
5550925 GGATGGTTGA
* *
5550935 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
5551000 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
5551028 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
5551093 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
5551106 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:5554103 original size:15 final size:15
Alignment explanation
Indices: 5554064--5554142 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
5554054 GTATCTTGGG
*
5554064 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
5554079 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
5554094 TTTCTTTATTC-GGG
1 TTTCTTTATTCTGGA
*
5554108 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
5554123 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
5554137 TTTCTT
1 TTTCTT
5554143 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
13 2 0.04
14 17 0.32
15 32 0.60
16 2 0.04
ACGTcount: A:0.10, C:0.18, G:0.14, T:0.58
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:5554127 original size:29 final size:29
Alignment explanation
Indices: 5554055--5554141 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
5554045 CATAGTATCG
* * * *
5554055 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTC-GGATTTCTC
*
5554085 TAT-TCTGGATTTCTTTATTCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCGGATTTCTC
*
5554114 TATCTTGGATTTCTTTATTCGGTTTTCT
1 TATCTTGGATTTCTTTATTCGGATTTCT
5554142 TGTTATCTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 32 0.65
30 17 0.35
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.56
Consensus pattern (29 bp):
TATCTTGGATTTCTTTATTCGGATTTCTC
Found at i:5556572 original size:46 final size:46
Alignment explanation
Indices: 5556522--5556697 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
5556512 ATGGTTGGCA
5556522 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
5556568 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
5556615 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
5556661 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5556698 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:5556677 original size:93 final size:93
Alignment explanation
Indices: 5556518--5556689 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
5556508 TAGGATGGTT
* *
5556518 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
5556583 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
5556611 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
5556676 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
5556690 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:5559417 original size:17 final size:19
Alignment explanation
Indices: 5559384--5559421 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
5559374 AAATTTAAAG
5559384 AATATATTTTTATATTTTT
1 AATATATTTTTATATTTTT
5559403 AATA-ATTTTTA-ATTTTT
1 AATATATTTTTATATTTTT
5559420 AA
1 AA
5559422 AAGTAGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 7 0.37
19 4 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
AATATATTTTTATATTTTT
Found at i:5559439 original size:30 final size:31
Alignment explanation
Indices: 5559405--5559487 Score: 114
Period size: 32 Copynumber: 2.7 Consensus size: 31
5559395 ATATTTTTAA
* *
5559405 TAATTTTTAATTTTTAAAAGTAG-TTTTTTT
1 TAATTTTTAAATTTTAAAAATAGTTTTTTTT
* *
5559435 TAATTTTTAAACTATAAAAATAGTTTTTTTTT
1 TAATTTTTAAATTTTAAAAATAG-TTTTTTTT
5559467 TAATTTTTAAATTTTAAAAAT
1 TAATTTTTAAATTTTAAAAAT
5559488 TAATTAAATG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 19 0.42
32 26 0.58
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (31 bp):
TAATTTTTAAATTTTAAAAATAGTTTTTTTT
Found at i:5560555 original size:7 final size:7
Alignment explanation
Indices: 5560543--5560574 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
5560533 GACGTCATGG
5560543 CATTTGT
1 CATTTGT
5560550 CATTTGT
1 CATTTGT
5560557 CATTTGT
1 CATTTGT
*
5560564 CATTTGC
1 CATTTGT
5560571 CATT
1 CATT
5560575 CGCCATTTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.19, G:0.12, T:0.53
Consensus pattern (7 bp):
CATTTGT
Found at i:5560562 original size:14 final size:14
Alignment explanation
Indices: 5560543--5560585 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
5560533 GACGTCATGG
*
5560543 CATTTGTCATTTGT
1 CATTTGTCATTTGC
5560557 CATTTGTCATTTGC
1 CATTTGTCATTTGC
* *
5560571 CATTCGCCATTTGC
1 CATTTGTCATTTGC
5560585 C
1 C
5560586 CCATGTGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.14, C:0.26, G:0.14, T:0.47
Consensus pattern (14 bp):
CATTTGTCATTTGC
Found at i:5560568 original size:21 final size:21
Alignment explanation
Indices: 5560543--5560583 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5560533 GACGTCATGG
* * *
5560543 CATTTGTCATTTGTCATTTGT
1 CATTTGCCATTCGCCATTTGT
5560564 CATTTGCCATTCGCCATTTG
1 CATTTGCCATTCGCCATTTG
5560584 CCCCATGTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.49
Consensus pattern (21 bp):
CATTTGCCATTCGCCATTTGT
Found at i:5564140 original size:21 final size:20
Alignment explanation
Indices: 5564116--5564162 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
5564106 TACTTTACAA
*
5564116 TGATTCTTATATTTA-AATATG
1 TGATT-TTATAATTACAAT-TG
5564137 TGATATTTATAATTACAATTG
1 TGAT-TTTATAATTACAATTG
5564158 TGATT
1 TGATT
5564163 ATACTTGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 18 0.78
22 4 0.17
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.51
Consensus pattern (20 bp):
TGATTTTATAATTACAATTG
Found at i:5566431 original size:15 final size:16
Alignment explanation
Indices: 5566411--5566443 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5566401 ATATATTTTT
5566411 TTATTTT-ATTTTTAA
1 TTATTTTAATTTTTAA
5566426 TTATTTTAAATTTTTAA
1 TTATTTT-AATTTTTAA
5566443 T
1 T
5566444 ATAAATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTAATTTTTAA
Found at i:5566529 original size:22 final size:22
Alignment explanation
Indices: 5566490--5566548 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
5566480 ATTTTAAGAA
*
5566490 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
5566511 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
5566533 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
5566549 GATTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.47
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:5566565 original size:26 final size:24
Alignment explanation
Indices: 5566519--5566578 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
5566509 ATTTGTTTTA
*
5566519 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
5566543 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTT-TTATATTTTTAAAT
* *
5566569 TTTTTTATTT
1 ATATTTATTT
5566579 AATGAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:5568082 original size:22 final size:24
Alignment explanation
Indices: 5568057--5568107 Score: 79
Period size: 22 Copynumber: 2.2 Consensus size: 24
5568047 ATTTAATTGA
*
5568057 TTTAGGGTTATGA-TTTTTAA-GG
1 TTTAGGGTTAGGATTTTTTAAGGG
5568079 TTTAGGGTTAGGATTTTTTAAGGG
1 TTTAGGGTTAGGATTTTTTAAGGG
5568103 TTTAG
1 TTTAG
5568108 TTTTTTTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 12 0.46
23 7 0.27
24 7 0.27
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (24 bp):
TTTAGGGTTAGGATTTTTTAAGGG
Found at i:5568878 original size:124 final size:126
Alignment explanation
Indices: 5568563--5568942 Score: 543
Period size: 124 Copynumber: 3.0 Consensus size: 126
5568553 TTTCTGCAAG
*
5568563 AATAATTCTAAATAGACGTTTCT-AGACAAATAGTGTCAGAAAACGCTTCAAGCAGGATGCACTG
1 AATAATTCTGAATAGACGTTTCTGA-ACAAATAGTGTC-GAAAACGCTTCAAGCAGGATGCACTG
* * * *
5568627 TCAGTAAAATTTCTAGAAAAAA-CTCCTATGTGGACACTCTTTTGCTACAGTATTTCGTAGAAA
64 TCAGCAAAATTTCTA-AAAAAAGCTCCCATGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
* * * *
5568690 AATAATTCTGAGTAGACGTTTCTGAACAAATAGTGTTGAAAACGCTTCAAGTAGGATGCCCTGTC
1 AATAATTCTGAATAGACGTTTCTGAACAAATAGTGTCGAAAACGCTTCAAGCAGGATGCACTGTC
** *
5568755 AGCAAAATTTCTAAAAAAAGCTCCCATGTGGACGCTCTTTCACTACAATAGTTCGTAGAAA
66 AGCAAAATTTCTAAAAAAAGCTCCCATGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
*
5568816 AATAA-T-TGAATAGACGTTTCTGAACAAATAGTGTCGAAAATGCTTCAAGCAGGATGCACTGTC
1 AATAATTCTGAATAGACGTTTCTGAACAAATAGTGTCGAAAACGCTTCAAGCAGGATGCACTGTC
** * **
5568879 AGCAAAATTTCTGGAAAAAGCTTCCACATGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
66 AGCAAAATTTCTAAAAAAAGCTCCCATGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
5568940 AAT
1 AAT
5568943 GAGGCTATAA
Statistics
Matches: 226, Mismatches: 25, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
124 108 0.48
125 7 0.03
126 78 0.35
127 32 0.14
128 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (126 bp):
AATAATTCTGAATAGACGTTTCTGAACAAATAGTGTCGAAAACGCTTCAAGCAGGATGCACTGTC
AGCAAAATTTCTAAAAAAAGCTCCCATGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
Found at i:5572475 original size:18 final size:18
Alignment explanation
Indices: 5572438--5572475 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5572428 GGAAAAGGAA
* *
5572438 ACATATAAGGGTTAGGAT
1 ACATATAAGGGCTAGAAT
5572456 ACATATAAGGGCTAGAAT
1 ACATATAAGGGCTAGAAT
5572474 AC
1 AC
5572476 GCACATGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.24
Consensus pattern (18 bp):
ACATATAAGGGCTAGAAT
Found at i:5574140 original size:48 final size:46
Alignment explanation
Indices: 5574073--5574206 Score: 162
Period size: 48 Copynumber: 2.8 Consensus size: 46
5574063 TGCAAACATT
* **
5574073 ATAAATGAAAAAAAAATCAAGCAGTATTGAAATTGTAATTATAA-TTGC
1 ATAAATG-AAAAAATATCAAATAGTATTGAAATT-TAATTA-AATTTGC
5574121 ATAAATGAATAAAATATCAAATAGTATTGCAAATTTAATTAAATTTGC
1 ATAAATGAA-AAAATATCAAATAGTATTG-AAATTTAATTAAATTTGC
*
5574169 ATAAATTAAAATAATATCAAATAGTATTGAAAATTTAA
1 ATAAATGAAAA-AATATCAAATAGTATTG-AAATTTAA
5574207 AATTATAACT
Statistics
Matches: 77, Mismatches: 5, Indels: 8
0.86 0.06 0.09
Matches are distributed among these distances:
47 6 0.08
48 66 0.86
49 5 0.06
ACGTcount: A:0.53, C:0.05, G:0.09, T:0.33
Consensus pattern (46 bp):
ATAAATGAAAAAATATCAAATAGTATTGAAATTTAATTAAATTTGC
Found at i:5574358 original size:11 final size:11
Alignment explanation
Indices: 5574339--5574370 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
5574329 TTTTAAACAA
5574339 AGAATTTTGAT
1 AGAATTTTGAT
*
5574350 AGAAATTTGAT
1 AGAATTTTGAT
5574361 AGAATTTTGA
1 AGAATTTTGA
5574371 GAAAATTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (11 bp):
AGAATTTTGAT
Found at i:5579854 original size:44 final size:44
Alignment explanation
Indices: 5579637--5580381 Score: 368
Period size: 45 Copynumber: 16.7 Consensus size: 44
5579627 AAGATCGATG
* * * * *
5579637 AATTACAAGTCTTGTCTCTCTGAAGTTGCAGTGAAGCAGACTGA
1 AATTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
* * * * *
5579681 AGA-TAGCAAATCTTATTTCCTTAAAGTTGCAATGGAACAGATTGA
1 A-ATTA-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
* * * *
5579726 AGCTATAAGTATATATCTTATCTCTCTGAAGTTGCAGT--AG-AGA-GGA
1 A---AT---TACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
* * * * * * *
5579772 TCA-TAGCATACCTTATCTACTTGAAGTTGCAGTAGAGCAGGTTGA
1 -AATTA-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
* * * * *
5579817 AATTACAAGTCTTATCTCCCTGAAGTTCCAGTGGAGCAAACTAA
1 AATTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
** * * *
5579861 AGATGGCGAATCTTATCTCCCTGAAGTTACAGTGGAACAGATTACGA
1 A-ATTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT--GA
* * * *
5579908 CCATTAGC----CTTATCTCTCTGAAGTTACAGTGGAGTAGATTGA
1 -AATTA-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
* * ** ** * *
5579950 AGTTACAAGTCTTATCTCTTTGAAGTTGCAGTGGAATAAACTGA
1 AATTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
* * *
5579994 AAATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATA
1 AATTA-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT---G----A
* * * **
5580046 AATTACAAATCTTATCTCTCTGAAGTTGCAGTAGAGTAGA-ACA
1 AATTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
* ** ** *
5580089 AA--ACAAACCTTATCTCCCTGAAGTTATAGTGGAATAGGTTGA
1 AATTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
* *
5580131 AATTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAA
1 AATTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG-A
* * * *
5580176 AACTACAAACCTTATCTCTCTGAAGTTGTAGTGGAGCAGATTGAA
1 AATTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG-A
* * * * * *
5580221 AACTACAAACCTTATCTCTCTGAAGTTGCAGTAGAGTAGGTT-A
1 AATTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
** ** * * * *
5580264 AAGCCACAAGCCTTATCTCCCTAAAGTTGCAGTGGAGAAAACT-A
1 AA-TTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
** * * **
5580308 AAACACAAATCTCATATCCCTGAAGTTGCAGTGGAGCAGACTAAA
1 AATTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTGA
* * *
5580353 AACTACAAGTCTTATCTCTCTGAAGTTGC
1 AATTACAAATCTTATCTCCCTGAAGTTGC
5580382 GATGGAATGG
Statistics
Matches: 531, Mismatches: 131, Indels: 77
0.72 0.18 0.10
Matches are distributed among these distances:
40 3 0.01
41 54 0.10
42 5 0.01
43 38 0.07
44 162 0.31
45 200 0.38
46 2 0.00
47 7 0.01
48 3 0.01
50 20 0.04
51 32 0.06
52 5 0.01
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (44 bp):
AATTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGA
Found at i:5579950 original size:133 final size:133
Alignment explanation
Indices: 5579782--5580036 Score: 352
Period size: 133 Copynumber: 1.9 Consensus size: 133
5579772 TCATAGCATA
* *
5579782 CCTTATCTACTTGAAGTTGCAGTAGAGCAGGTTGAAATTACAAGTCTTATCTCCCTGAAGTTCCA
1 CCTTATCTACTTGAAGTTACAGTAGAGCAGATTGAAATTACAAGTCTTATCTCCCTGAAGTTCCA
* * *
5579847 GTGGAGCAAACT-AAAGATGGCGAATCTTATCTCCCTGAAGTTACAGTGGAACAGATTACGACCA
66 GTGGAACAAACTGAAA-ATAGCAAATCTTATCTCCCTGAAGTTACAGTGGAACAGATTACGACCA
5579911 TTAG
130 TTAG
* * * ** *
5579915 CCTTATCT-CTCTGAAGTTACAGTGGAGTAGATTGAAGTTACAAGTCTTATCTCTTTGAAGTTGC
1 CCTTATCTACT-TGAAGTTACAGTAGAGCAGATTGAAATTACAAGTCTTATCTCCCTGAAGTTCC
* * *
5579979 AGTGGAATAAACTGAAAATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATT
65 AGTGGAACAAACTGAAAATAGCAAATCTTATCTCCCTGAAGTTACAGTGGAACAGATT
5580037 GAAGCTATAA
Statistics
Matches: 106, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
132 2 0.02
133 101 0.95
134 3 0.03
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (133 bp):
CCTTATCTACTTGAAGTTACAGTAGAGCAGATTGAAATTACAAGTCTTATCTCCCTGAAGTTCCA
GTGGAACAAACTGAAAATAGCAAATCTTATCTCCCTGAAGTTACAGTGGAACAGATTACGACCAT
TAG
Found at i:5580009 original size:89 final size:88
Alignment explanation
Indices: 5579915--5580379 Score: 341
Period size: 89 Copynumber: 5.2 Consensus size: 88
5579905 CGACCATTAG
* ** * * *
5579915 CCTTATCTCTCTGAAGTTACAGTGGAGTAGATTGAAGTTACAAGTCTTATCTCTTTGAAGTTGCA
1 CCTTATCTCCCTGAAGTTACAGTGGAACAGATTGAAATTACAAATCTTATCTCTCTGAAGTTGCA
*
5579980 GTGGAATAAACTGAAAATAGCAAA
66 GTGGAGTAAACTGAAAATA-CAAA
* * *
5580004 TCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTACAAATCTTATCTCTCTGA
1 CCTTATCTCCCTGAAGTTACAGTGGAACAGATT---G----AAATTACAAATCTTATCTCTCTGA
*
5580069 AGTTGCAGTAGAGTAGAAC---AAA-ACAAA
59 AGTTGCAGTGGAGTA-AACTGAAAATACAAA
* * * * *
5580096 CCTTATCTCCCTGAAGTTATAGTGGAATAGGTTGAAATTACAAGTCTTATCTCCCTGAAGTTGCA
1 CCTTATCTCCCTGAAGTTACAGTGGAACAGATTGAAATTACAAATCTTATCTCTCTGAAGTTGCA
* *
5580161 GTGGAGCAGACTGAAAACTACAAA
66 GTGGAGTAAACTGAAAA-TACAAA
* ** * * *
5580185 CCTTATCTCTCTGAAGTTGTAGTGGAGCAGATTGAAAACTACAAACCTTATCTCTCTGAAGTTGC
1 CCTTATCTCCCTGAAGTTACAGTGGAACAGATTG-AAATTACAAATCTTATCTCTCTGAAGTTGC
* ** * ** *
5580250 AGTAGAGT-AGGTTAAAGCCACAAG
65 AGTGGAGTAAACTGAAA-ATACAAA
* * * * ** * * *
5580274 CCTTATCTCCCTAAAGTTGCAGTGGAGA-AAACT-AAAACACAAATCTCATATCCCTGAAGTTGC
1 CCTTATCTCCCTGAAGTTACAGTGGA-ACAGATTGAAATTACAAATCTTATCTCTCTGAAGTTGC
* * * *
5580337 AGTGGAGCAGACTAAAAACTACAAG
65 AGTGGAGTAAACTGAAAA-TACAAA
* *
5580362 TCTTATCTCTCTGAAGTT
1 CCTTATCTCCCTGAAGTT
5580380 GCGATGGAAT
Statistics
Matches: 295, Mismatches: 63, Indels: 37
0.75 0.16 0.09
Matches are distributed among these distances:
84 2 0.01
85 35 0.12
87 33 0.11
88 24 0.08
89 96 0.33
90 32 0.11
92 32 0.11
93 1 0.00
94 3 0.01
96 34 0.12
97 3 0.01
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (88 bp):
CCTTATCTCCCTGAAGTTACAGTGGAACAGATTGAAATTACAAATCTTATCTCTCTGAAGTTGCA
GTGGAGTAAACTGAAAATACAAA
Found at i:5580139 original size:181 final size:175
Alignment explanation
Indices: 5579915--5580381 Score: 490
Period size: 181 Copynumber: 2.6 Consensus size: 175
5579905 CGACCATTAG
* * * **
5579915 CCTTATCTCTCTGAAGTTACAGTGGAGTAGATTGAAGTTACAAGTCTTATCTCTTTGAAGTTGCA
1 CCTTATCTCCCTGAAGTTACAGTGGAATAGATTGAAATTACAAGTCTTATCTCCCTGAAGTTGCA
* * *
5579980 GTGGAATAAACTGAAAA-TAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTA
66 GTGGAACAAACTGAAAACTA-CAAACCTTATCTCCCTGAAGTTGCAGTGGAACAGATT---G--A
* *
5580044 TAAATTACAAATCTTATCTCTCTGAAGTTGCAGTAGAGTAGAACAAAACAAA
125 -AAACTACAAACCTTATCTCTCTGAAGTTGCAGTAGAGTAGAACAAAACAAA
* *
5580096 CCTTATCTCCCTGAAGTTATAGTGGAATAGGTTGAAATTACAAGTCTTATCTCCCTGAAGTTGCA
1 CCTTATCTCCCTGAAGTTACAGTGGAATAGATTGAAATTACAAGTCTTATCTCCCTGAAGTTGCA
* * * * *
5580161 GTGGAGCAGACTGAAAACTACAAACCTTATCTCTCTGAAGTTGTAGTGGAGCAGATTGAAAACTA
66 GTGGAACAAACTGAAAACTACAAACCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAAACTA
*** *
5580226 CAAACCTTATCTCTCTGAAGTTGCAGTAGAGTAGGTTAAAGCCACAAG
131 CAAACCTTATCTCTCTGAAGTTGCAGTAGAGTAGAACAAA---ACAAA
* * * * ** * * *
5580274 CCTTATCTCCCTAAAGTTGCAGTGGAGA-AAACT-AAAACACAAATCTCATATCCCTGAAGTTGC
1 CCTTATCTCCCTGAAGTTACAGTGGA-ATAGATTGAAATTACAAGTCTTATCTCCCTGAAGTTGC
* * * ** *
5580337 AGTGGAGCAGACTAAAAACTACAAGTCTTATCTCTCTGAAGTTGC
65 AGTGGAACAAACTGAAAACTACAAACCTTATCTCCCTGAAGTTGC
5580382 GATGGAATGG
Statistics
Matches: 245, Mismatches: 36, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
175 41 0.17
176 1 0.00
177 66 0.27
178 30 0.12
179 1 0.00
181 104 0.42
182 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (175 bp):
CCTTATCTCCCTGAAGTTACAGTGGAATAGATTGAAATTACAAGTCTTATCTCCCTGAAGTTGCA
GTGGAACAAACTGAAAACTACAAACCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAAACTA
CAAACCTTATCTCTCTGAAGTTGCAGTAGAGTAGAACAAAACAAA
Found at i:5580357 original size:177 final size:175
Alignment explanation
Indices: 5580049--5580380 Score: 443
Period size: 177 Copynumber: 1.9 Consensus size: 175
5580039 AGCTATAAAT
* *
5580049 TACAAATCTTATCTCTCTGAAGTTGCAGTAGAGTAGAACAAAACAAACCTTATCTCCCTGAAGTT
1 TACAAACCTTATCTCTCTGAAGTTGCAGTAGAGTAGAACAAAACAAACCTTATCTCCCTAAAGTT
* *** ** * * * *
5580114 ATAGTGGAATAGGTTGAAATTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAAAC
66 ACAGTGGAATAAACTGAAAACACAAATCTCATATCCCTGAAGTTGCAGTGGAGCAGACTAAAAAC
5580179 TACAAACCTTATCTCTCTGAAGTTGTAGTGGAGCAGATTGAAAAC
131 TACAAACCTTATCTCTCTGAAGTTGTAGTGGAGCAGATTGAAAAC
*** *
5580224 TACAAACCTTATCTCTCTGAAGTTGCAGTAGAGTAGGTTAAAGCCACAAGCCTTATCTCCCTAAA
1 TACAAACCTTATCTCTCTGAAGTTGCAGTAGAGTAGAACAAA---ACAAACCTTATCTCCCTAAA
*
5580289 GTTGCAGTGGAGA-AAACT-AAAACACAAATCTCATATCCCTGAAGTTGCAGTGGAGCAGACTAA
63 GTTACAGTGGA-ATAAACTGAAAACACAAATCTCATATCCCTGAAGTTGCAGTGGAGCAGACTAA
**
5580352 AAACTACAAGTCTTATCTCTCTGAAGTTG
127 AAACTACAAACCTTATCTCTCTGAAGTTG
5580381 CGATGGAATG
Statistics
Matches: 134, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
175 38 0.28
177 66 0.49
178 29 0.22
179 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (175 bp):
TACAAACCTTATCTCTCTGAAGTTGCAGTAGAGTAGAACAAAACAAACCTTATCTCCCTAAAGTT
ACAGTGGAATAAACTGAAAACACAAATCTCATATCCCTGAAGTTGCAGTGGAGCAGACTAAAAAC
TACAAACCTTATCTCTCTGAAGTTGTAGTGGAGCAGATTGAAAAC
Found at i:5580372 original size:132 final size:134
Alignment explanation
Indices: 5580091--5580381 Score: 372
Period size: 134 Copynumber: 2.2 Consensus size: 134
5580081 GTAGAACAAA
* ** * * ** * *
5580091 ACAAACCTTATCTCCCTGAAGTTATAGTGGAATAGGTTGAAA-TTACAAGTCTTATCTCCCTGAA
1 ACAAACCTTATCTCTCTGAAGTTGCAGTAGAGTAGGTT-AAAGCCACAAGCCTTATCTCCCTAAA
* * * * * * * *
5580155 GTTGCAGTGGAGCAGACTGAAAACTACAAACCTTATCTCTCTGAAGTTGTAGTGGAGCAGATTGA
65 GTTGCAGTGGAGAAAACTGAAAACTACAAACCTCATATCCCTGAAGTTGCAGTGGAGCAGACTAA
5580220 AAACT
130 AAACT
5580225 ACAAACCTTATCTCTCTGAAGTTGCAGTAGAGTAGGTTAAAGCCACAAGCCTTATCTCCCTAAAG
1 ACAAACCTTATCTCTCTGAAGTTGCAGTAGAGTAGGTTAAAGCCACAAGCCTTATCTCCCTAAAG
*
5580290 TTGCAGTGGAGAAAACT-AAAAC-ACAAATCTCATATCCCTGAAGTTGCAGTGGAGCAGACTAAA
66 TTGCAGTGGAGAAAACTGAAAACTACAAACCTCATATCCCTGAAGTTGCAGTGGAGCAGACTAAA
5580353 AACT
131 AACT
**
5580357 ACAAGTCTTATCTCTCTGAAGTTGC
1 ACAAACCTTATCTCTCTGAAGTTGC
5580382 GATGGAATGG
Statistics
Matches: 136, Mismatches: 20, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
132 61 0.45
133 8 0.06
134 67 0.49
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (134 bp):
ACAAACCTTATCTCTCTGAAGTTGCAGTAGAGTAGGTTAAAGCCACAAGCCTTATCTCCCTAAAG
TTGCAGTGGAGAAAACTGAAAACTACAAACCTCATATCCCTGAAGTTGCAGTGGAGCAGACTAAA
AACT
Found at i:5580399 original size:132 final size:134
Alignment explanation
Indices: 5580091--5580405 Score: 352
Period size: 132 Copynumber: 2.4 Consensus size: 134
5580081 GTAGAACAAA
* ** * * ** * *
5580091 ACAAACCTTATCTCCCTGAAGTTATAGTGGAATAGGTTGAAA-TTACAAGTCTTATCTCCCTGAA
1 ACAAACCTTATCTCTCTGAAGTTGCAGTAGAATAGG-TCAAAGCAACAAGCCTTATCTCCCTAAA
* * * * * * * *
5580155 GTTGCAGTGGAGCAGACTGAAAACTACAAACCTTATCTCTCTGAAGTTGTAGTGGAGCAGATTGA
65 GTTGCAGTGGAGAAAACTGAAAACTACAAACCTCATATCCCTGAAGTTGCAGTGGAGCAGACTAA
5580220 AAACT
130 AAACT
* * *
5580225 ACAAACCTTATCTCTCTGAAGTTGCAGTAGAGTAGGTTAAAGCCACAAGCCTTATCTCCCTAAAG
1 ACAAACCTTATCTCTCTGAAGTTGCAGTAGAATAGGTCAAAGCAACAAGCCTTATCTCCCTAAAG
*
5580290 TTGCAGTGGAGAAAACT-AAAAC-ACAAATCTCATATCCCTGAAGTTGCAGTGGAGCAGACTAAA
66 TTGCAGTGGAGAAAACTGAAAACTACAAACCTCATATCCCTGAAGTTGCAGTGGAGCAGACTAAA
5580353 AACT
131 AACT
** *
5580357 ACAAGTCTTATCTCTCTGAAGTTGC-GATGGAAT-GGATCAAAGCAACAAG
1 ACAAACCTTATCTCTCTGAAGTTGCAG-TAGAATAGG-TCAAAGCAACAAG
5580406 ATACAGTGGA
Statistics
Matches: 153, Mismatches: 25, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
131 3 0.02
132 76 0.50
133 9 0.06
134 65 0.42
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (134 bp):
ACAAACCTTATCTCTCTGAAGTTGCAGTAGAATAGGTCAAAGCAACAAGCCTTATCTCCCTAAAG
TTGCAGTGGAGAAAACTGAAAACTACAAACCTCATATCCCTGAAGTTGCAGTGGAGCAGACTAAA
AACT
Found at i:5580648 original size:13 final size:13
Alignment explanation
Indices: 5580609--5580653 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
5580599 CAAATAACCT
*
5580609 AAACCTAAACCCA
1 AAACCCAAACCCA
*
5580622 AAACCCAAAACCA
1 AAACCCAAACCCA
* *
5580635 AAACCCTAGCCCA
1 AAACCCAAACCCA
5580648 AAACCC
1 AAACCC
5580654 CAATAAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.51, C:0.42, G:0.02, T:0.04
Consensus pattern (13 bp):
AAACCCAAACCCA
Found at i:5581657 original size:3 final size:3
Alignment explanation
Indices: 5581651--5581777 Score: 139
Period size: 3 Copynumber: 42.7 Consensus size: 3
5581641 CAATTTAATA
* * * *
5581651 TAT TAT TAC TAT TAT TAT TAT TAT TAC CAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
5581699 TTT TAT TAC TAT TAT TAT TAC TAT TAT TAT TTT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
5581747 TAC TAT T-G TAT TAT TAT TAT TGT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5581778 CATTTTTTGT
Statistics
Matches: 99, Mismatches: 24, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
2 1 0.01
3 98 0.99
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:5581687 original size:30 final size:30
Alignment explanation
Indices: 5581651--5581778 Score: 195
Period size: 30 Copynumber: 4.3 Consensus size: 30
5581641 CAATTTAATA
*
5581651 TATTATTACTATTATTATTATTATTACCAT
1 TATTATTACTATTATTATTATTATTACTAT
*
5581681 TATTATTACTATTATTATTTTTATTACTAT
1 TATTATTACTATTATTATTATTATTACTAT
*
5581711 TATTATTACTATTATTATTTTTATTACTAT
1 TATTATTACTATTATTATTATTATTACTAT
* * *
5581741 TATTATTACTATT-GTATTATTATTATTGT
1 TATTATTACTATTATTATTATTATTACTAT
5581770 TATTATTAC
1 TATTATTAC
5581779 ATTTTTTGTT
Statistics
Matches: 92, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
29 21 0.23
30 71 0.77
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (30 bp):
TATTATTACTATTATTATTATTATTACTAT
Found at i:5581915 original size:3 final size:3
Alignment explanation
Indices: 5581909--5582004 Score: 106
Period size: 3 Copynumber: 32.7 Consensus size: 3
5581899 CAATTTAATA
* * * *
5581909 TAT TAT TAC TAT TAT TAT TAT TAT TAC CAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
5581957 T-T TAT TAC TAT TAT TAT TAC TAT T-G TAT TAT TAT TAT TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5582003 TA
1 TA
5582005 CATTTTTTGT
Statistics
Matches: 75, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
2 3 0.04
3 72 0.96
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:5582188 original size:3 final size:3
Alignment explanation
Indices: 5582167--5582243 Score: 84
Period size: 3 Copynumber: 25.0 Consensus size: 3
5582157 CAAACTTTAA
* *
5582167 ATT ATTT ATT ATT -TGT ATT ATT TTT GTT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
5582213 ATT ATT ATT ATC ATT ATT AATT AGT ATT ATT
1 ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
5582244 TTTAAAACTA
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
2 1 0.02
3 55 0.87
4 7 0.11
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5583441 original size:20 final size:21
Alignment explanation
Indices: 5583403--5583441 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
5583393 AAACAACTCC
*
5583403 ATTTTTATTTTGGTCATTTTA
1 ATTTTTATTTTGGTAATTTTA
*
5583424 ATTTTT-TTTTGTTAATTT
1 ATTTTTATTTTGGTAATTT
5583442 AGTCACTCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.18, C:0.03, G:0.08, T:0.72
Consensus pattern (21 bp):
ATTTTTATTTTGGTAATTTTA
Found at i:5584032 original size:49 final size:49
Alignment explanation
Indices: 5583960--5584059 Score: 155
Period size: 49 Copynumber: 2.0 Consensus size: 49
5583950 CCTAACCCCG
* * **
5583960 ACCTAGACAGGAATGCTTAGTTTAGAATGCCATGTTGTCCTATGAGAAC
1 ACCTAGACAGGAATGATTAGTTTAGAATGCCACGTTGTCCTACCAGAAC
*
5584009 ACCTAGACGGGAATGATTAGTTTAGAATGCCACGTTGTCCTACCAGAAC
1 ACCTAGACAGGAATGATTAGTTTAGAATGCCACGTTGTCCTACCAGAAC
5584058 AC
1 AC
5584060 AGTCATACTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (49 bp):
ACCTAGACAGGAATGATTAGTTTAGAATGCCACGTTGTCCTACCAGAAC
Found at i:5585971 original size:3 final size:3
Alignment explanation
Indices: 5585963--5586004 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
5585953 AAATAGATAT
* *
5585963 TTA TTA TTA -TA TTA TTA TAA TGTA TTA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
5586005 ACTAGTATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.88
4 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:5586017 original size:2 final size:2
Alignment explanation
Indices: 5586010--5586042 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5586000 TATTAACTAG
5586010 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 T
5586043 GAAATAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5586533 original size:3 final size:3
Alignment explanation
Indices: 5586525--5586584 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
5586515 TAGAAATTCA
5586525 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5586573 ATT ATT ATT ATT
1 ATT ATT ATT ATT
5586585 GTAATTAATA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5586926 original size:70 final size:75
Alignment explanation
Indices: 5586850--5587025 Score: 191
Period size: 70 Copynumber: 2.3 Consensus size: 75
5586840 ATGTGAACAA
* * * *
5586850 ATTGGAAATTAAAAGTGATTTAAATTGAGT-AATTGAATT-AT-G-AATTATGTGAATATTTGAA
1 ATTGGAAACTAAAAGTGATTTGAATTGAATAAATTGAATTAATAGAAAATATGTGAATATTTGAA
5586911 A-GTATATTG
66 ATGTATATTG
* *
5586920 ATTGGAAACTAAGAGTGATTTGAATTGAATCAAATTGAATTGAATGAAGAAAATATGTGAGTATT
1 ATTGGAAACTAAAAGTGATTTGAATTGAAT-AAATTGAATT-AAT--AGAAAATATGTGAATATT
5586985 TGAAATGTATATTG
62 TGAAATGTATATTG
* * *
5586999 ATTGAAAAGTAATTAGTGATTTGAATT
1 ATTGGAAACTAA-AAGTGATTTGAATT
5587026 TGATTGGAAA
Statistics
Matches: 87, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
70 26 0.30
72 9 0.10
74 2 0.02
77 1 0.01
78 18 0.21
79 18 0.21
80 13 0.15
ACGTcount: A:0.41, C:0.01, G:0.20, T:0.38
Consensus pattern (75 bp):
ATTGGAAACTAAAAGTGATTTGAATTGAATAAATTGAATTAATAGAAAATATGTGAATATTTGAA
ATGTATATTG
Found at i:5587827 original size:16 final size:16
Alignment explanation
Indices: 5587808--5587858 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
5587798 ATTGAACTAT
5587808 TGAAAGTATGAGAAAG
1 TGAAAGTATGAGAAAG
* *
5587824 TGAAATTAT--G-AAT
1 TGAAAGTATGAGAAAG
5587837 TGAAATGTATGAGAAAG
1 TGAAA-GTATGAGAAAG
5587854 TGAAA
1 TGAAA
5587859 TCATGAATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
13 7 0.26
14 4 0.15
16 9 0.33
17 7 0.26
ACGTcount: A:0.49, C:0.00, G:0.25, T:0.25
Consensus pattern (16 bp):
TGAAAGTATGAGAAAG
Found at i:5587849 original size:30 final size:30
Alignment explanation
Indices: 5587806--5587874 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
5587796 CGATTGAACT
*
5587806 ATTGAAA-GTATGAGAAAGTGAAATTATGA
1 ATTGAAATGTATGAGAAAGTGAAATCATGA
5587835 ATTGAAATGTATGAGAAAGTGAAATCATGA
1 ATTGAAATGTATGAGAAAGTGAAATCATGA
5587865 ATTGAAATGT
1 ATTGAAATGT
5587875 GAATTAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 7 0.18
30 31 0.82
ACGTcount: A:0.46, C:0.01, G:0.23, T:0.29
Consensus pattern (30 bp):
ATTGAAATGTATGAGAAAGTGAAATCATGA
Found at i:5589017 original size:24 final size:25
Alignment explanation
Indices: 5588949--5589018 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
5588939 GCCCTTTCTT
* **
5588949 GAGCCATATAACATGAAGCTCATCC
1 GAGCTATATAACGGGAAGCTCATCC
* *
5588974 GAGCTATATAATGGGAAGCTCATGC
1 GAGCTATATAACGGGAAGCTCATCC
*
5588999 GAGCTA-ATAACGGGTAGCTC
1 GAGCTATATAACGGGAAGCTC
5589019 TGAAGAGCTA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
24 12 0.32
25 26 0.68
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (25 bp):
GAGCTATATAACGGGAAGCTCATCC
Found at i:5589131 original size:26 final size:26
Alignment explanation
Indices: 5589095--5589154 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
5589085 GAAGCTCTGG
5589095 AGAGCCATTAATTAG-GAAGCTCACAA
1 AGAGCCATTAA-TAGAGAAGCTCACAA
* * *
5589121 AGAGCCTTTAATCGAGAAGCTCACGA
1 AGAGCCATTAATAGAGAAGCTCACAA
5589147 AGAGCCAT
1 AGAGCCAT
5589155 ATAACGGGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 2 0.07
26 27 0.93
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (26 bp):
AGAGCCATTAATAGAGAAGCTCACAA
Found at i:5589165 original size:26 final size:26
Alignment explanation
Indices: 5589109--5589169 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
5589099 CCATTAATTA
*
5589109 GGAAGCTCACAAAGAGCCTTTAATCG
1 GGAAGCTCACAAAGAGCCTATAATCG
* *
5589135 AGAAGCTCACGAAGAGCCATATAA-CG
1 GGAAGCTCACAAAGAGCC-TATAATCG
5589161 GGAAGCTCA
1 GGAAGCTCA
5589170 TAAGAGCTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 26 0.87
27 4 0.13
ACGTcount: A:0.38, C:0.23, G:0.25, T:0.15
Consensus pattern (26 bp):
GGAAGCTCACAAAGAGCCTATAATCG
Found at i:5593757 original size:5 final size:5
Alignment explanation
Indices: 5593728--5593766 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
5593718 TAAATTTAGC
* *
5593728 TCAAT TTAAT ACAAT TCATAT TCAAT TCAAT TCAAT TCA
1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCAAT TCAAT TCA
5593767 CATCTTAGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
TCAAT
Found at i:5601084 original size:19 final size:19
Alignment explanation
Indices: 5601038--5601084 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
5601028 ATTAAGATTG
* *
5601038 AAAAATATTTTTTAAGTCA
1 AAAAATAATTTTTAAGCCA
**
5601057 AATCA-AATTTTTAAGCCA
1 AAAAATAATTTTTAAGCCA
5601075 AAAAATAATT
1 AAAAATAATT
5601085 GTAAGTAGAT
Statistics
Matches: 21, Mismatches: 6, Indels: 2
0.72 0.21 0.07
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (19 bp):
AAAAATAATTTTTAAGCCA
Found at i:5602040 original size:6 final size:6
Alignment explanation
Indices: 5602029--5602063 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
5602019 TAACCTTCAA
*
5602029 ATAATT ATAATT ATAATT AGATATT ATAATT ATAA
1 ATAATT ATAATT ATAATT ATA-ATT ATAATT ATAA
5602064 AGGAATTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (6 bp):
ATAATT
Found at i:5603131 original size:23 final size:23
Alignment explanation
Indices: 5603105--5603150 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
5603095 ATTTTTAACT
5603105 TAGCCAAACCTCCATTAAACCAA
1 TAGCCAAACCTCCATTAAACCAA
*
5603128 TAGCCAAACCTCCATTAAGCCAA
1 TAGCCAAACCTCCATTAAACCAA
5603151 GGGCTATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.35, G:0.07, T:0.17
Consensus pattern (23 bp):
TAGCCAAACCTCCATTAAACCAA
Found at i:5616802 original size:24 final size:24
Alignment explanation
Indices: 5616768--5616820 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
5616758 ATTCATAGGT
* * *
5616768 TAAATAAATTATGCTGATAAATGC
1 TAAATAAATTATACTAATAAATAC
*
5616792 TAAATATATTATACTAATAAATAC
1 TAAATAAATTATACTAATAAATAC
5616816 TAAAT
1 TAAAT
5616821 TTTCTAGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.36
Consensus pattern (24 bp):
TAAATAAATTATACTAATAAATAC
Found at i:5622798 original size:95 final size:95
Alignment explanation
Indices: 5622633--5622821 Score: 279
Period size: 95 Copynumber: 2.0 Consensus size: 95
5622623 CATTTGGCCC
* * * * * *
5622633 ACGCCTGTGTGGCTTGGGTGTGTGGGCGCACACGGACGTAGTGTATGGCCGTGTCTTGCTTCGTT
1 ACGCCCGTGTGGCTTGGGCGTGTGGGCACACACGGACGTAGTGCACGGCCGTGTCTTGCTTCATT
*
5622698 CGCTTCTCCCACGCTCGTGTACATAGGTCT
66 CGCTTCTCCCACGCCCGTGTACATAGGTCT
* * *
5622728 ACGCCCGTGTGGCTTGGGCGTGTGGGCACACACGGTCGTGGTGCACGGCTGTGTCTTGCTTCATT
1 ACGCCCGTGTGGCTTGGGCGTGTGGGCACACACGGACGTAGTGCACGGCCGTGTCTTGCTTCATT
*
5622793 TGCTTCTCCCACGCCCGTGTACATAGGTC
66 CGCTTCTCCCACGCCCGTGTACATAGGTC
5622822 CATGCCTGTG
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
95 83 1.00
ACGTcount: A:0.11, C:0.28, G:0.32, T:0.29
Consensus pattern (95 bp):
ACGCCCGTGTGGCTTGGGCGTGTGGGCACACACGGACGTAGTGCACGGCCGTGTCTTGCTTCATT
CGCTTCTCCCACGCCCGTGTACATAGGTCT
Found at i:5628687 original size:40 final size:42
Alignment explanation
Indices: 5628637--5628726 Score: 116
Period size: 40 Copynumber: 2.2 Consensus size: 42
5628627 CTACCCCAAT
5628637 ACCCAATACAGCCCAA-TGCAAA-CA-CAACCCAAA-CAAACTA
1 ACCCAATACAGCCCAACT--AAATCACCAACCCAAACCAAACTA
* *
5628677 ACCCATTACAGCCCAACTAAATCACCAACCCAAACCCAACTA
1 ACCCAATACAGCCCAACTAAATCACCAACCCAAACCAAACTA
5628719 ACCCAATA
1 ACCCAATA
5628727 TTCAAACTAG
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
39 3 0.07
40 17 0.40
41 10 0.23
42 13 0.30
ACGTcount: A:0.47, C:0.40, G:0.03, T:0.10
Consensus pattern (42 bp):
ACCCAATACAGCCCAACTAAATCACCAACCCAAACCAAACTA
Found at i:5629770 original size:3 final size:3
Alignment explanation
Indices: 5629751--5629926 Score: 233
Period size: 3 Copynumber: 61.3 Consensus size: 3
5629741 AGTTATTTAG
*
5629751 TTA TT- TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
5629797 TTA -TA TTA -CA TTA TTA TTA TTA TTA TTA TTA CTA TTA -TA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
5629842 TTA TTA -TA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
5629889 TTA TTA TTA TTA TTA -TA TT- GTA TTA TTA CTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5629927 ATTTTCATCT
Statistics
Matches: 151, Mismatches: 14, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
2 14 0.09
3 137 0.91
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:5630025 original size:3 final size:3
Alignment explanation
Indices: 5630017--5630207 Score: 61
Period size: 3 Copynumber: 65.7 Consensus size: 3
5630007 TTTATATTTC
*
5630017 TAT TAT TAT TA- TAT T-T TAT GTAT TAT ATCT CTAT T-T ATATT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT -TAT -TAT TAT -TA-T TAT
* * *
5630061 GTAT TAA TAT CAT TAT T-T TAT TAT TAC TAT T-T T-T TA- TAT TAT
1 -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
5630103 TAT TAT TAG CAT TA- TATT TAT TAT T-T T-T TAC TAT TGTT TAT TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT TAT
* * * * * *
5630147 CT-T TAT TAA CAT TAT TAC TGT CAT T-T T-T TAC TAT TAT TAT TAT
1 -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
5630190 TAT TAC T-T TAT T-T TAT TA
1 TAT TAT TAT TAT TAT TAT TA
5630208 AATATTTTCT
Statistics
Matches: 137, Mismatches: 31, Indels: 40
0.66 0.15 0.19
Matches are distributed among these distances:
2 27 0.20
3 92 0.67
4 17 0.12
5 1 0.01
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:5630028 original size:17 final size:17
Alignment explanation
Indices: 5630008--5630042 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5629998 TCATATCTAT
5630008 TTATATTTCTAT-TATTA
1 TTATATTT-TATGTATTA
5630025 TTATATTTTATGTATTA
1 TTATATTTTATGTATTA
5630042 T
1 T
5630043 ATCTCTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (17 bp):
TTATATTTTATGTATTA
Found at i:5630030 original size:27 final size:30
Alignment explanation
Indices: 5629960--5630030 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
5629950 TATTCTAGAA
*
5629960 CTATTATTATT-TATCTAATTTTTATTTGT
1 CTATTATTATTATATCTAATTTATATTTGT
*
5629989 CTATTTATT-TCATATCT-ATTTATA-TT-T
1 CTA-TTATTATTATATCTAATTTATATTTGT
5630016 CTATTATTATTATAT
1 CTATTATTATTATAT
5630031 TTTATGTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
26 5 0.14
27 9 0.25
28 2 0.06
29 10 0.28
30 10 0.28
ACGTcount: A:0.27, C:0.08, G:0.01, T:0.63
Consensus pattern (30 bp):
CTATTATTATTATATCTAATTTATATTTGT
Found at i:5630077 original size:26 final size:25
Alignment explanation
Indices: 5630021--5630082 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 25
5630011 TATTTCTATT
5630021 ATTA-TTATATTTTATGTATTATATC
1 ATTATTTATA-TTTATGTATTATATC
5630046 -TCTATTTATATTTATGTATTAATATC
1 AT-TATTTATATTTATGTATT-ATATC
5630072 ATTATTT-TATT
1 ATTATTTATATT
5630083 ATTACTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
24 1 0.03
25 16 0.48
26 15 0.45
27 1 0.03
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (25 bp):
ATTATTTATATTTATGTATTATATC
Found at i:5640517 original size:46 final size:46
Alignment explanation
Indices: 5640450--5640665 Score: 315
Period size: 46 Copynumber: 4.7 Consensus size: 46
5640440 GGCAACCTGA
5640450 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
*
5640496 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
* *
5640542 GTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
*** * * *
5640588 GAACAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
* * * *
5640634 GAGTAAGACCATAGTTGAAAGACACTATGGCA
1 GTGTAAGACCATGGTTGAAAGATACCATGGCA
5640666 TCATGTCAAA
Statistics
Matches: 156, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 156 1.00
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
Found at i:5640645 original size:138 final size:130
Alignment explanation
Indices: 5640400--5640665 Score: 379
Period size: 138 Copynumber: 2.0 Consensus size: 130
5640390 AGTGTGCTCT
*
5640400 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGTGTAAGACCATGGT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGTGCAAGACCATGGT
* * * * * *
5640465 TGAAAGATACCATGGCAACCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
66 TGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAAC
*
5640530 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAACAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG--A-G---TG--CAAG
*
5640595 ACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACT
58 ACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACC
5640660 ATGGCA
123 ATGGCA
5640666 TCATGTCAAA
Statistics
Matches: 119, Mismatches: 9, Indels: 8
0.88 0.07 0.06
Matches are distributed among these distances:
130 48 0.40
132 1 0.01
133 1 0.01
136 2 0.02
138 67 0.56
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (130 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGTGCAAGACCATGGT
TGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAAC
Found at i:5645523 original size:181 final size:181
Alignment explanation
Indices: 5645217--5645621 Score: 587
Period size: 181 Copynumber: 2.2 Consensus size: 181
5645207 CGATGAATCC
* * * * * *
5645217 ACAAGTCTTATCTCCCTAAAATTGCAGTGGAGC-AGACTAAAGATAGTGAATCTTACTTCCCTGA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGA-CTAGACTGAAGATAGCGAATATTACTTCCCTCA
** * *
5645281 AGTTGCGGTGGAACAGATTGAAGCTATAAATTACAGATTTTATCTCTCTGAAGTTGCAGTAGAGC
65 AGTTGCAATGGAACAAATTGAAGCTATAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGC
* *
5645346 AAATCAAAACAAACCTTATCTCCCTGAGGTTGTAGTGGAGCAGGTTGAAATT
130 AAATCAAAACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATT
* * *
5645398 ATAAGTCTTATCTCCCTGAAGTTGAAGTGGACTAGACTGAAGATAGCGAATATTATTTCCCTCAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGACTAGACTGAAGATAGCGAATATTACTTCCCTCAA
* *
5645463 GTTGCAATGGAACAAATTGAAGCTATAAATTATAGATCTTATTTCTCTGAAGTTGCAGTAGAGCA
66 GTTGCAATGGAACAAATTGAAGCTATAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCA
* *
5645528 GATCAAAACAAACCTTATCTCCCTGAAGTTGCAGTGGAGTAGGTTGAAATT
131 AATCAAAACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATT
* * * *
5645579 ACAAATCTCATCTCCCTGAAGTTGCAGCGGAGTAGACTGAAGA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGACTAGACTGAAGA
5645622 AAGCTAATCC
Statistics
Matches: 198, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
180 1 0.01
181 197 0.99
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.29
Consensus pattern (181 bp):
ACAAGTCTTATCTCCCTGAAGTTGCAGTGGACTAGACTGAAGATAGCGAATATTACTTCCCTCAA
GTTGCAATGGAACAAATTGAAGCTATAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCA
AATCAAAACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAATT
Found at i:5645557 original size:41 final size:43
Alignment explanation
Indices: 5645500--5645605 Score: 117
Period size: 44 Copynumber: 2.5 Consensus size: 43
5645490 AATTATAGAT
* *
5645500 CTTATTTCTCTGAAGTTGCAGTAGAGCA-GATCAAA-ACAAAC
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGGATCAAATACAAAC
* * * * *
5645541 CTTATCTCCCTGAAGTTGCAGTGGAGTAGGTTGAAATTACAAAT
1 CTTATCTCCCTGAAGTTGCAGTAGAGCAGGATCAAA-TACAAAC
*
5645585 CTCATCTCCCTGAAGTTGCAG
1 CTTATCTCCCTGAAGTTGCAG
5645606 CGGAGTAGAC
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 24 0.44
42 5 0.09
44 25 0.46
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (43 bp):
CTTATCTCCCTGAAGTTGCAGTAGAGCAGGATCAAATACAAAC
Found at i:5645960 original size:88 final size:85
Alignment explanation
Indices: 5645733--5646010 Score: 258
Period size: 88 Copynumber: 3.2 Consensus size: 85
5645723 TCTTATCATT
* *
5645733 CTAAAGTTGCAGTGGAGCAGATTAAAG-CCACAAGTCTTATCTCCCTAAAGTTACAGAGGAGCAG
1 CTAAAGTTGCAGTGGAGTAGA-TAAAGAAC-CAA-TCTTATCTCCCTAAAGTTACAGAGGAGCAG
* * * * *
5645797 ACTG-GATACAGCTGATCTTTTCTCT
63 ATTGAAATACA--AG-TCTTATCTCC
* * * * * * *
5645822 CTGAAGTTGCAGTAGAGTAGATCAA-AACAAACCTTATCTCCCTAAAGTTACAGTGGAGCAAATT
1 CTAAAGTTGCAGTGGAGTAGATAAAGAACCAATCTTATCTCCCTAAAGTTACAGAGGAGCAGATT
5645886 GAAATTACAAGTCTTATCTCC
66 GAAA-TACAAGTCTTATCTCC
*
5645907 CTAAAGTTGCAGTGGAGTAGACTAAAGATACCAATCTTATCTCCCTAAAGTTACAGCGGAGCAGA
1 CTAAAGTTGCAGTGGAGTAGA-TAAAGA-ACCAATCTTATCTCCCTAAAGTTACAGAGGAGCAGA
* *
5645972 TTGAAGCTACTAA-TCCTATCTCC
64 TTGAA-ATAC-AAGTCTTATCTCC
* *
5645995 TTGAAGTTGCAGTGGA
1 CTAAAGTTGCAGTGGA
5646011 CCGAATTAAG
Statistics
Matches: 156, Mismatches: 25, Indels: 17
0.79 0.13 0.09
Matches are distributed among these distances:
85 27 0.17
86 34 0.22
87 4 0.03
88 71 0.46
89 20 0.13
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.27
Consensus pattern (85 bp):
CTAAAGTTGCAGTGGAGTAGATAAAGAACCAATCTTATCTCCCTAAAGTTACAGAGGAGCAGATT
GAAATACAAGTCTTATCTCC
Found at i:5645992 original size:44 final size:43
Alignment explanation
Indices: 5645733--5646010 Score: 199
Period size: 44 Copynumber: 6.4 Consensus size: 43
5645723 TCTTATCATT
* * **
5645733 CTAAAGTTGCAGTGGAGCAGATTAAAGCCACAAGTCTTATCTCC
1 CTAAAGTTACAGTGGAGCAGATTGAAGATACAA-TCTTATCTCC
* * * *
5645777 CTAAAGTTACAGAGGAGCAGACTG--GATACAGCTGATCTTTTCTCT
1 CTAAAGTTACAGTGGAGCAGATTGAAGATACA----ATCTTATCTCC
* * * * * *
5645822 CTGAAGTTGCAGTAGAGTAGA-TCAA-A-ACAAACCTTATCTCC
1 CTAAAGTTACAGTGGAGCAGATTGAAGATAC-AATCTTATCTCC
*
5645863 CTAAAGTTACAGTGGAGCAAATTGAA-ATTACAAGTCTTATCTCC
1 CTAAAGTTACAGTGGAGCAGATTGAAGA-TACAA-TCTTATCTCC
* * * *
5645907 CTAAAGTTGCAGTGGAGTAGACTAAAGATACCAATCTTATCTCC
1 CTAAAGTTACAGTGGAGCAGATTGAAGATA-CAATCTTATCTCC
* * *
5645951 CTAAAGTTACAGCGGAGCAGATTGAAGCTACTAATCCTATCTCC
1 CTAAAGTTACAGTGGAGCAGATTGAAGATAC-AATCTTATCTCC
* * *
5645995 TTGAAGTTGCAGTGGA
1 CTAAAGTTACAGTGGA
5646011 CCGAATTAAG
Statistics
Matches: 180, Mismatches: 40, Indels: 28
0.73 0.16 0.11
Matches are distributed among these distances:
41 24 0.13
42 8 0.04
43 3 0.02
44 114 0.63
45 30 0.17
46 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.27
Consensus pattern (43 bp):
CTAAAGTTACAGTGGAGCAGATTGAAGATACAATCTTATCTCC
Found at i:5647536 original size:3 final size:3
Alignment explanation
Indices: 5647528--5648016 Score: 198
Period size: 3 Copynumber: 163.0 Consensus size: 3
5647518 TTTAGTCATT
** *
5647528 TTA TTA TTA AAA TTAA TTAA TTTA TTA TT- TCTA TTA TTA TTA TTA TTG
1 TTA TTA TTA TTA TT-A TT-A TT-A TTA TTA T-TA TTA TTA TTA TTA TTA
* * * * ** **
5647576 CTA CTA TTA TCA TTA CTA TTTA TTA TTA CCA TTA TTA TTA CAA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * ** * *
5647622 TTT TTA TTT TTA TTA CCA TTA CTA -TA TTA TT- TT- TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
5647667 CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
5647715 TTA TTA -TA TT- TTCA TCTA -TA TTTA TT- TTC TTA TT- CTA GTA CTA
1 TTA TTA TTA TTA TT-A T-TA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
* *
5647758 TTA TTA TTTA TTTA TT- TATA TTTC TTA TCTA TT- TATA TT- TCTG TTA
1 TTA TTA -TTA -TTA TTA T-TA -TTA TTA T-TA TTA T-TA TTA T-TA TTA
*
5647804 TTA TTA -TA TT- TTA TGTA TTA TATC TCTA TT- TATA TTTA TATA TTA
1 TTA TTA TTA TTA TTA T-TA TTA T-TA T-TA TTA T-TA -TTA T-TA TTA
* * * * * *
5647849 ATA TCA TTA TT- TTA CTA TTG CTA TT- TT- TTA -TA TTA TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** * * * *
5647893 GCA TTA -TA GTTA TTA TT- TTT TTA CTA TTGT TTA TTA TCT- TTA CTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT-A TTA TTA T-TA TTA TTA
** * * *
5647938 ACA TTA TTA CTA TCA TT- TT- TTA CTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
5647984 TTA TTA TTA TTA TTA TTA TTT TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5648017 AATATTTTCT
Statistics
Matches: 366, Mismatches: 79, Indels: 82
0.69 0.15 0.16
Matches are distributed among these distances:
2 41 0.11
3 275 0.75
4 47 0.13
5 3 0.01
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:5647814 original size:17 final size:17
Alignment explanation
Indices: 5647765--5647799 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5647755 CTATTATTAT
*
5647765 TTATTTATTTATATTTC
1 TTATCTATTTATATTTC
5647782 TTATCTATTTATATTTC
1 TTATCTATTTATATTTC
5647799 T
1 T
5647800 GTTATTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATCTATTTATATTTC
Found at i:5647859 original size:26 final size:26
Alignment explanation
Indices: 5647803--5647860 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
5647793 TATTTCTGTT
*
5647803 ATTA-TTATATTTTATGTATTATATC
1 ATTATTTATATTTTATATATTATATC
5647828 -TCTATTTATA-TTTATATATTAATATC
1 AT-TATTTATATTTTATATATT-ATATC
5647854 ATTATTT
1 ATTATTT
5647861 TACTATTGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
24 1 0.04
25 11 0.39
26 15 0.54
27 1 0.04
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (26 bp):
ATTATTTATATTTTATATATTATATC
Found at i:5651322 original size:28 final size:28
Alignment explanation
Indices: 5651269--5651331 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
5651259 AGAAAATTTA
*
5651269 AAATTAAAACTAAGAAATGAAGAAAATT
1 AAATTAAAACTAAGAAATGAAAAAAATT
5651297 AAATTGAAAACT-AGCAAA-GAAAAAAA-T
1 AAATT-AAAACTAAG-AAATGAAAAAAATT
5651324 -AATTAAAA
1 AAATTAAAA
5651332 TTGGGAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
25 4 0.12
26 4 0.12
27 1 0.03
28 14 0.44
29 9 0.28
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.19
Consensus pattern (28 bp):
AAATTAAAACTAAGAAATGAAAAAAATT
Found at i:5651825 original size:23 final size:23
Alignment explanation
Indices: 5651798--5651845 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
5651788 TAAGAACACT
*
5651798 TTGATCTCACAAACTTTATAGAA
1 TTGATCTCACAAACTTTATAAAA
*
5651821 TTGATCTCACAAATTTTATAAAA
1 TTGATCTCACAAACTTTATAAAA
5651844 TT
1 TT
5651846 AAACTCCGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40
Consensus pattern (23 bp):
TTGATCTCACAAACTTTATAAAA
Found at i:5655494 original size:22 final size:22
Alignment explanation
Indices: 5655467--5655508 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
5655457 TTGTCAAAAG
5655467 GGGATATGTATTAAATGATAAA
1 GGGATATGTATTAAATGATAAA
5655489 GGGATATGTATTAAATGATA
1 GGGATATGTATTAAATGATA
5655509 TGTGGAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.24, T:0.33
Consensus pattern (22 bp):
GGGATATGTATTAAATGATAAA
Found at i:5657588 original size:16 final size:15
Alignment explanation
Indices: 5657567--5657618 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 15
5657557 TTCGTACGGT
5657567 TAAATTTAATATTTTA
1 TAAATTT-ATATTTTA
5657583 TAAATTTATGATTTATA
1 TAAATTTAT-ATTT-TA
**
5657600 TTATTTTTATATTTTA
1 -TAAATTTATATTTTA
5657616 TAA
1 TAA
5657619 TTGGAAATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
15 4 0.13
16 13 0.43
17 6 0.20
18 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
TAAATTTATATTTTA
Found at i:5669271 original size:21 final size:21
Alignment explanation
Indices: 5669247--5669287 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
5669237 CACACGTCCA
5669247 TGTGGAAGGCTAACACACCCG
1 TGTGGAAGGCTAACACACCCG
*
5669268 TGTGGAAGGGTAACACACCC
1 TGTGGAAGGCTAACACACCC
5669288 TTGTCCCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.27, G:0.29, T:0.15
Consensus pattern (21 bp):
TGTGGAAGGCTAACACACCCG
Found at i:5670515 original size:50 final size:48
Alignment explanation
Indices: 5670353--5670623 Score: 180
Period size: 47 Copynumber: 5.7 Consensus size: 48
5670343 TAAGATACCT
* * * *
5670353 ATGCCATGTCCCAGACATGGTCTTACATTGGCTT-ATATCTCAAGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTTCACATCCCAAGCCG
* ** * ***
5670400 ATGCCATGTCCCAGACATTGTCTTACACTAACTATCGTCAT-CGGGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCT-TC-ACATCCCAAGCCG
* * *
5670449 ACGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACATACCCATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCT-TCACAT-CCCAAGCCG
* * ** *
5670499 ATGCCATGTCCCAGACATGGTTTTACACTGG---CACATTTCGTAGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTTCACA-TCCCAAGCCG
* * * * *** *
5670545 ATG-CATGTCCCAGACAT-ATCTTACAGTAGC-ACTTGTCTCAATGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTTCACATCCCAA-GCCG
*
5670591 ATGCCATGTCCCATACATGGTCTTACACTGGCT
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCT
5670624 CTCATAATGT
Statistics
Matches: 167, Mismatches: 45, Indels: 22
0.71 0.19 0.09
Matches are distributed among these distances:
44 8 0.05
45 16 0.10
46 17 0.10
47 43 0.26
48 14 0.08
49 34 0.20
50 35 0.21
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCTTCACATCCCAAGCCG
Found at i:5675716 original size:47 final size:47
Alignment explanation
Indices: 5675658--5676027 Score: 224
Period size: 47 Copynumber: 7.8 Consensus size: 47
5675648 TGGGTAAGAT
5675658 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATATCTCAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATATCTCAA
* * * ** **
5675705 GTCAATGCCATGTCCCAGACATTGTCTTACACTAACT-ATCATCATCGGG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-ATC-TC-AA
* * * **
5675754 GCCGACGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACATACCCGT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGG--CTCATAT-CTCAA
* * * * *
5675804 GCCAATGTCGTGTCCCAGACATGGTCTTACACTGGCACAT-T-TCGTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATATCTC-AA
* * * * * * *
5675850 GCTGATG-CATGTCCCAGACAT-GTCTTATAGTAGCACTTGTCTCAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATATCTCAA
* * *
5675895 TGCCGATGCCATGTCCCAGACGTGGTCTTACACTGGCTCTCATAATGT--G
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGG--CTCAT-ATCTCAA
* * * * *
5675944 GCCTATG-CATGTCCCTGACATGGTCTTACATTGGCTC-TCATAAT-ATG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-AT-CTCA-A
* *
5675991 GCCGATG-CATGTCCCAAACAT-GTCTTACACTAGCTCA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCA
5676028 CACAAATGAC
Statistics
Matches: 249, Mismatches: 54, Indels: 40
0.73 0.16 0.12
Matches are distributed among these distances:
44 16 0.06
45 20 0.08
46 28 0.11
47 92 0.37
48 20 0.08
49 29 0.12
50 35 0.14
51 7 0.03
52 2 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATATCTCAA
Found at i:5681285 original size:20 final size:20
Alignment explanation
Indices: 5681260--5681298 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
5681250 CAACATATGT
5681260 TGCACTCATAATCACAGTTG
1 TGCACTCATAATCACAGTTG
5681280 TGCACTCATAATCACAGTT
1 TGCACTCATAATCACAGTT
5681299 CACATATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.26, G:0.13, T:0.31
Consensus pattern (20 bp):
TGCACTCATAATCACAGTTG
Found at i:5681445 original size:18 final size:18
Alignment explanation
Indices: 5681419--5681462 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5681409 CATAGTTTGA
* *
5681419 CAAATTAATTCAGCTCAC
1 CAAATTAATACAGATCAC
*
5681437 CATATTAATACAGATCAC
1 CAAATTAATACAGATCAC
5681455 CAAATTAA
1 CAAATTAA
5681463 CACAATTCTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.45, C:0.23, G:0.05, T:0.27
Consensus pattern (18 bp):
CAAATTAATACAGATCAC
Found at i:5683165 original size:23 final size:23
Alignment explanation
Indices: 5683122--5683165 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
5683112 TCTAATTATT
*
5683122 TTAATAATTTATTATATTAATTC
1 TTAATAATTTATTATACTAATTC
*
5683145 TTAATCATTTAATTAT-CTAAT
1 TTAATAATTT-ATTATACTAAT
5683166 CTAATTACGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAATAATTTATTATACTAATTC
Found at i:5718832 original size:25 final size:25
Alignment explanation
Indices: 5718798--5718850 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
5718788 ATCAGTTACT
5718798 TATTCATGATTGAGGTAAGCCACAC
1 TATTCATGATTGAGGTAAGCCACAC
5718823 TATTCATGATTGAGGTAAGCCACAC
1 TATTCATGATTGAGGTAAGCCACAC
5718848 TAT
1 TAT
5718851 GAACGTCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (25 bp):
TATTCATGATTGAGGTAAGCCACAC
Found at i:5721224 original size:6 final size:6
Alignment explanation
Indices: 5721208--5721252 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
5721198 TGATTTTCTC
* * *
5721208 AAAATG GAAATG AAAATG CAAACG AAAATG AAAATG AAAAATG AA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG -AAAATG AA
5721253 TTCATTTAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.64, C:0.04, G:0.18, T:0.13
Consensus pattern (6 bp):
AAAATG
Found at i:5722824 original size:5 final size:5
Alignment explanation
Indices: 5722814--5722886 Score: 137
Period size: 5 Copynumber: 14.4 Consensus size: 5
5722804 ATTTAAGTAA
5722814 ATATT ATATT ATATT ATATAT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATAT-T ATATT ATATT ATATT ATATT ATATT ATATT
5722865 ATATT ATATT ATATT ATATT AT
1 ATATT ATATT ATATT ATATT AT
5722887 TATAATAATT
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
5 62 0.93
6 5 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:5722951 original size:10 final size:10
Alignment explanation
Indices: 5722936--5722961 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5722926 AGATTAGAGA
5722936 AAGAAAGAAC
1 AAGAAAGAAC
5722946 AAGAAAGAAC
1 AAGAAAGAAC
5722956 AAGAAA
1 AAGAAA
5722962 AAAACGAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.08, G:0.19, T:0.00
Consensus pattern (10 bp):
AAGAAAGAAC
Found at i:5722981 original size:5 final size:5
Alignment explanation
Indices: 5722935--5723010 Score: 50
Period size: 6 Copynumber: 14.6 Consensus size: 5
5722925 AAGATTAGAG
* *
5722935 AAAG- AAAGA ACAAG- AAAGA ACAAGA AAA-A AACGA AACAGA AAGGAA
1 AAAGA AAAGA A-AAGA AAAGA A-AAGA AAAGA AAAGA AA-AGA AAAG-A
*
5722981 AAAGG AAAGA AAAGAA AAAGA GAAAGA AAA
1 AAAGA AAAGA AAAG-A AAAGA -AAAGA AAA
5723011 AGGAGAAAGC
Statistics
Matches: 57, Mismatches: 6, Indels: 17
0.71 0.08 0.21
Matches are distributed among these distances:
4 10 0.18
5 21 0.37
6 26 0.46
ACGTcount: A:0.74, C:0.05, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:5722994 original size:17 final size:17
Alignment explanation
Indices: 5722931--5723010 Score: 69
Period size: 16 Copynumber: 4.7 Consensus size: 17
5722921 GAAAAAGATT
*
5722931 AGAGAAAG-AAAG-AAC
1 AGAGAAAGAAAAGAAAA
5722946 A-AGAAAGAACAAGAAAA
1 AGAGAAAGAA-AAGAAAA
* *
5722963 AAACGAAACAGAAAGGAAAA
1 AGA-G-AA-AGAAAAGAAAA
5722983 AG-GAAAGAAAAGAAAA
1 AGAGAAAGAAAAGAAAA
5722999 AGAGAAAGAAAA
1 AGAGAAAGAAAA
5723011 AGGAGAAAGC
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
14 6 0.11
15 2 0.04
16 15 0.28
17 14 0.26
18 2 0.04
19 1 0.02
20 9 0.17
21 4 0.08
ACGTcount: A:0.72, C:0.05, G:0.23, T:0.00
Consensus pattern (17 bp):
AGAGAAAGAAAAGAAAA
Found at i:5723011 original size:13 final size:12
Alignment explanation
Indices: 5722986--5723019 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
5722976 AGGAAAAAGG
5722986 AAAGA-AAAGAA
1 AAAGAGAAAGAA
5722997 AAAGAGAAAGAA
1 AAAGAGAAAGAA
5723009 AAAGGAGAAAG
1 AAA-GAGAAAG
5723020 CTAGGGTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.24
12 9 0.43
13 7 0.33
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AAAGAGAAAGAA
Found at i:5731482 original size:3 final size:3
Alignment explanation
Indices: 5731476--5731528 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
5731466 ATAAAAGTAG
5731476 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5731524 TAA TA
1 TAA TA
5731529 TGAGTTTAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5738736 original size:67 final size:67
Alignment explanation
Indices: 5738628--5738764 Score: 274
Period size: 67 Copynumber: 2.0 Consensus size: 67
5738618 TTACCATCCA
5738628 AGTAAGATTCACATTGTGGAAGAAGCACCTCTTTAAGTGAACTTAAAGTTTCTTCTTTCACAAGT
1 AGTAAGATTCACATTGTGGAAGAAGCACCTCTTTAAGTGAACTTAAAGTTTCTTCTTTCACAAGT
5738693 AT
66 AT
5738695 AGTAAGATTCACATTGTGGAAGAAGCACCTCTTTAAGTGAACTTAAAGTTTCTTCTTTCACAAGT
1 AGTAAGATTCACATTGTGGAAGAAGCACCTCTTTAAGTGAACTTAAAGTTTCTTCTTTCACAAGT
5738760 AT
66 AT
5738762 AGT
1 AGT
5738765 GATTCTTTCT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 70 1.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (67 bp):
AGTAAGATTCACATTGTGGAAGAAGCACCTCTTTAAGTGAACTTAAAGTTTCTTCTTTCACAAGT
AT
Found at i:5743311 original size:2 final size:2
Alignment explanation
Indices: 5743304--5743332 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5743294 AAGCTGTTTC
5743304 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
5743333 TTTGGTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:5745211 original size:38 final size:38
Alignment explanation
Indices: 5745127--5745226 Score: 119
Period size: 38 Copynumber: 2.6 Consensus size: 38
5745117 ATAACCTAAA
* * *
5745127 AATCTGCAACAAGGCTAGATCTTGTTAAATCACTAGAG
1 AATCTGCAACAAGGCTAGATCTTATTAAATAACCAGAG
* * *
5745165 AATTTGCAACAAGGCTAGATCTTATTAAGTAACCCGAG
1 AATCTGCAACAAGGCTAGATCTTATTAAATAACCAGAG
* *
5745203 AGTCTGCAACAAATGCTAGATCTT
1 AATCTGCAAC-AAGGCTAGATCTT
5745227 TTTATAAACT
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
38 40 0.77
39 12 0.23
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (38 bp):
AATCTGCAACAAGGCTAGATCTTATTAAATAACCAGAG
Found at i:5751959 original size:39 final size:39
Alignment explanation
Indices: 5751916--5751993 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
5751906 AAGCACTAAA
5751916 AAAATAATTATAACAATGTTTATCACATACGAACTTACC
1 AAAATAATTATAACAATGTTTATCACATACGAACTTACC
*
5751955 AAAATAATTATAACAATGTTTATCACTTACGAACTTACC
1 AAAATAATTATAACAATGTTTATCACATACGAACTTACC
5751994 TCGTACTCGG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (39 bp):
AAAATAATTATAACAATGTTTATCACATACGAACTTACC
Found at i:5756717 original size:66 final size:66
Alignment explanation
Indices: 5756609--5756736 Score: 195
Period size: 66 Copynumber: 1.9 Consensus size: 66
5756599 TACCAATTAT
* ** *
5756609 ATGAAGGAATGAGCTTTAGTGTATAAAGAGGACCTCATTGTTTAAGAAGTAA-CAGTAGAAACTT
1 ATGAAAGAATGAGCTCCAGTGTATAAAGAGGACCTCACTGTTTAAGAAGTAACCA-TAGAAACTT
5756673 AA
65 AA
*
5756675 ATGAAAGAATGAGCTCCGGTGTATAAAGAGGACCTCACTGTTTAAGAAGTAACCATAGAAAC
1 ATGAAAGAATGAGCTCCAGTGTATAAAGAGGACCTCACTGTTTAAGAAGTAACCATAGAAAC
5756737 GATGGAACCC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 54 0.96
67 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.24
Consensus pattern (66 bp):
ATGAAAGAATGAGCTCCAGTGTATAAAGAGGACCTCACTGTTTAAGAAGTAACCATAGAAACTTA
A
Found at i:5758354 original size:20 final size:20
Alignment explanation
Indices: 5758314--5758354 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5758304 TTTACTAAAA
* *
5758314 TAATTAGATTTTTATTTTGT
1 TAATTAGATTTTAATTGTGT
5758334 TAATTAGATTTTAATTGTGT
1 TAATTAGATTTTAATTGTGT
5758354 T
1 T
5758355 GAAAAGGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (20 bp):
TAATTAGATTTTAATTGTGT
Found at i:5759271 original size:15 final size:15
Alignment explanation
Indices: 5759247--5759285 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
5759237 TAAATTTTAC
* *
5759247 ACTTAATTTTTGAGT
1 ACTTATTTTTTCAGT
5759262 ACTTATTTTTTCAGT
1 ACTTATTTTTTCAGT
*
5759277 ACTAATTTT
1 ACTTATTTT
5759286 CTTTTTAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.08, T:0.56
Consensus pattern (15 bp):
ACTTATTTTTTCAGT
Found at i:5771243 original size:33 final size:33
Alignment explanation
Indices: 5771193--5771290 Score: 160
Period size: 33 Copynumber: 3.0 Consensus size: 33
5771183 GTTTGAGTGA
* *
5771193 GAGTGTTTGATTACTGGACAGGAGCTGGAATGG
1 GAGTGTTTGGTTGCTGGACAGGAGCTGGAATGG
*
5771226 GAGTGTTTGGTTGCTGGACAGGAGCTGGAATTG
1 GAGTGTTTGGTTGCTGGACAGGAGCTGGAATGG
*
5771259 AAGTGTTTGGTTGCTGGACAGGAGCTGGAATG
1 GAGTGTTTGGTTGCTGGACAGGAGCTGGAATG
5771291 TCAAGAAGAA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.21, C:0.09, G:0.41, T:0.29
Consensus pattern (33 bp):
GAGTGTTTGGTTGCTGGACAGGAGCTGGAATGG
Found at i:5779114 original size:3 final size:3
Alignment explanation
Indices: 5779106--5779168 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
5779096 TATAGTTACT
5779106 ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5779153 ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
5779169 GGGAGAAAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 57 0.97
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5781828 original size:39 final size:39
Alignment explanation
Indices: 5781710--5781892 Score: 222
Period size: 39 Copynumber: 4.6 Consensus size: 39
5781700 TCGTTCAAAC
* * ** * **
5781710 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAG
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
* * * *
5781750 GCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
* *
5781790 GCCTTCGGGCTTAGCCTGGATATCATAACTCGCCCAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
*
5781829 GCCTTCAGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
5781868 GCCTTCGGGCTTAGCCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCA
5781893 CTCGAACATT
Statistics
Matches: 122, Mismatches: 21, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
39 84 0.69
40 38 0.31
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.25
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
Found at i:5784029 original size:50 final size:50
Alignment explanation
Indices: 5783946--5784068 Score: 126
Period size: 50 Copynumber: 2.5 Consensus size: 50
5783936 TGCTTCGCTA
* * * ** *
5783946 TAACTTTAGGAAGACAAGACTTAG-TGTTATAGTTTC-ATCTTGCTCCATTG
1 TAACTTAAGGAAGATAAGA-TTTGTTGTTATAGTTTCAATC-TAATCCACTG
*
5783996 TAACTTTAAGG-AGATAAGATTTGTTGTTGTAGTTTCAATCTAATCCACTG
1 TAAC-TTAAGGAAGATAAGATTTGTTGTTATAGTTTCAATCTAATCCACTG
*
5784046 TAACTTCAGGAAGATAAGATTTG
1 TAACTTAAGGAAGATAAGATTTG
5784069 GGACTATAAC
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
49 8 0.13
50 45 0.74
51 8 0.13
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (50 bp):
TAACTTAAGGAAGATAAGATTTGTTGTTATAGTTTCAATCTAATCCACTG
Found at i:5784441 original size:50 final size:42
Alignment explanation
Indices: 5784310--5784451 Score: 115
Period size: 44 Copynumber: 3.1 Consensus size: 42
5784300 CTAAGATAGA
*
5784310 TTCAATCCGACCCACTACAACTTCAGGGGTATAGAATTTGTAGT
1 TTCAATCTGACCCACTACAACTTCA-GGGTATAG-ATTTGTAGT
* *
5784354 TTCAATCTG-CTCCACTGCAACTTCAGGGAGATAAGATTTGCTATGGTGAT
1 TTCAATCTGAC-CCACTACAACTTCAGGG-TAT-AGATTTG-TA----G-T
* *
5784404 TTCAATCTGACCCACTACAACTTTAGAGGTATGAGATTTGTGGT
1 TTCAATCTGACCCACTACAACTTCAG-GGTAT-AGATTTGTAGT
5784448 TTCA
1 TTCA
5784452 CTGATTTGTT
Statistics
Matches: 79, Mismatches: 8, Indels: 22
0.72 0.07 0.20
Matches are distributed among these distances:
43 4 0.05
44 33 0.42
45 5 0.06
49 2 0.03
50 32 0.41
51 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (42 bp):
TTCAATCTGACCCACTACAACTTCAGGGTATAGATTTGTAGT
Found at i:5784450 original size:94 final size:94
Alignment explanation
Indices: 5784167--5784451 Score: 256
Period size: 94 Copynumber: 3.0 Consensus size: 94
5784157 GACTTGTAAC
* * * * ** * * * *
5784167 TTCAATCTACTCCACTGCAACTTGAGGGAGATAAGATTCGCCACTATAGTTTTAAT-CAACCCAT
1 TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTCGCTAAGATAGATTCAATCCGACCCAC
*
5784231 TGCAACTTCA-AGGTTATAGAATTTGTAG-
66 TACAACTTCAGAGG-TATAGAATTTGTAGT
* * * * * ** *
5784259 CTCTATTTTGTTCTACTAAAACTTCAGAGTGATAAGATTCGCTAAGATAGATTCAATCCGACCCA
1 TTC-AATCTGCTCCACTGCAACTTCAGAGAGATAAGATTCGCTAAGATAGATTCAATCCGACCCA
*
5784324 CTACAACTTCAGGGGTATAGAATTTGTAGT
65 CTACAACTTCAGAGGTATAGAATTTGTAGT
* * * * *
5784354 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATGGT-GATTTCAATCTGACCCA
1 TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTCGCTAAGATAGA-TTCAATCCGACCCA
* *
5784418 CTACAACTTTAGAGGTAT-GAGATTTGTGGT
65 CTACAACTTCAGAGGTATAGA-ATTTGTAGT
5784448 TTCA
1 TTCA
5784452 CTGATTTGTT
Statistics
Matches: 151, Mismatches: 36, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
92 2 0.01
93 42 0.28
94 103 0.68
95 4 0.03
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (94 bp):
TTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATTCGCTAAGATAGATTCAATCCGACCCAC
TACAACTTCAGAGGTATAGAATTTGTAGT
Found at i:5805723 original size:17 final size:17
Alignment explanation
Indices: 5805701--5805735 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5805691 TTTATATGTC
5805701 AATGAAAGTTGATTTTT
1 AATGAAAGTTGATTTTT
5805718 AATGAAAGTTGATTTTT
1 AATGAAAGTTGATTTTT
5805735 A
1 A
5805736 GAGGTGTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (17 bp):
AATGAAAGTTGATTTTT
Found at i:5808835 original size:63 final size:63
Alignment explanation
Indices: 5808736--5808862 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
5808726 CCAAGTCTTG
5808736 AGGGTTTGCTTTGTGCAAAGGATGGTTCGTGAAATCATAGGAATTCCTGTTGATAATGGCGAA
1 AGGGTTTGCTTTGTGCAAAGGATGGTTCGTGAAATCATAGGAATTCCTGTTGATAATGGCGAA
5808799 AGGGTTTGCTTTGTGCAAAGGATGGTTCGTGAAATCATAGGAATTCCTGTTGATAATGGCGAA
1 AGGGTTTGCTTTGTGCAAAGGATGGTTCGTGAAATCATAGGAATTCCTGTTGATAATGGCGAA
5808862 A
1 A
5808863 ACGAGGGCTG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.28, C:0.11, G:0.30, T:0.31
Consensus pattern (63 bp):
AGGGTTTGCTTTGTGCAAAGGATGGTTCGTGAAATCATAGGAATTCCTGTTGATAATGGCGAA
Found at i:5810090 original size:19 final size:19
Alignment explanation
Indices: 5810054--5810089 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5810044 ATTATAATGA
*
5810054 AATTTGATATAGTGAAAAT
1 AATTTAATATAGTGAAAAT
5810073 AATTTAATATA-TGAAAA
1 AATTTAATATAGTGAAAA
5810090 AAAAAATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (19 bp):
AATTTAATATAGTGAAAAT
Found at i:5811791 original size:8 final size:9
Alignment explanation
Indices: 5811771--5811799 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
5811761 CTTTAACATA
5811771 AAACATAAC
1 AAACATAAC
5811780 AAACAT-AC
1 AAACATAAC
5811788 AAACATAAC
1 AAACATAAC
5811797 AAA
1 AAA
5811800 GATTACACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.69, C:0.21, G:0.00, T:0.10
Consensus pattern (9 bp):
AAACATAAC
Found at i:5811793 original size:17 final size:16
Alignment explanation
Indices: 5811765--5811799 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
5811755 AATATTCTTT
5811765 AACATAAAACATAACA
1 AACATAAAACATAACA
5811781 AACATACAAACATAACA
1 AACATA-AAACATAACA
5811798 AA
1 AA
5811800 GATTACACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.69, C:0.20, G:0.00, T:0.11
Consensus pattern (16 bp):
AACATAAAACATAACA
Found at i:5814841 original size:2 final size:2
Alignment explanation
Indices: 5814834--5814881 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
5814824 ATGTCATGAT
5814834 TC TC TC TC TC TC TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5814875 TC TC TC T
1 TC TC TC T
5814882 ATATATATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Done.