Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007923.1 Hibiscus syriacus cultivar Beakdansim tig00110328_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8415618
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 40
Found at i:4167024 original size:19 final size:19
Alignment explanation
Indices: 4166988--4167054 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
4166978 AAAATCGCAA
*
4166988 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
4167007 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
4167026 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
4167046 TGCGATTTT
1 TGCGATTTT
4167055 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 28 0.70
20 12 0.30
ACGTcount: A:0.09, C:0.16, G:0.24, T:0.51
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:4167596 original size:20 final size:20
Alignment explanation
Indices: 4167571--4167623 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
4167561 ACGCTATATA
4167571 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
4167591 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
4167611 TATCTCGTTGCGA
1 AATCGCGTTGCGA
4167624 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:4167657 original size:20 final size:20
Alignment explanation
Indices: 4167632--4167685 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
4167622 GATTTTGTAT
4167632 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
4167652 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
4167672 TATCGCATTGCGAT
1 TATCGCATTGCGAT
4167686 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:4167670 original size:61 final size:61
Alignment explanation
Indices: 4167572--4167688 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
4167562 CGCTATATAA
* * * * *
4167572 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
4167633 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
4167689 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:4167704 original size:61 final size:61
Alignment explanation
Indices: 4167572--4167706 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
4167562 CGCTATATAA
* * * * * ** *
4167572 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
4167633 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
4167695 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
4167707 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:4167796 original size:21 final size:21
Alignment explanation
Indices: 4167756--4167796 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4167746 ATTGTATACC
**
4167756 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
4167777 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
4167797 GCGAATTTGC
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:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:4169739 original size:18 final size:21
Alignment explanation
Indices: 4169718--4169758 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 21
4169708 TTGTTGTAAG
4169718 ATATTT-TTTTA-ATAT-ATT
1 ATATTTATTTTATATATGATT
4169736 ATATTTATTTTATATATGATT
1 ATATTTATTTTATATATGATT
4169757 AT
1 AT
4169759 TTGAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.30
19 5 0.25
20 4 0.20
21 5 0.25
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
ATATTTATTTTATATATGATT
Found at i:4173282 original size:15 final size:15
Alignment explanation
Indices: 4173264--4173304 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
4173254 TTCCTCACTT
*
4173264 TCATTATCATCACCA
1 TCATAATCATCACCA
4173279 TCATAATCATCACCA
1 TCATAATCATCACCA
* *
4173294 TAATCATCATC
1 TCATAATCATC
4173305 GTCGTCGTCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.37, C:0.32, G:0.00, T:0.32
Consensus pattern (15 bp):
TCATAATCATCACCA
Found at i:4174916 original size:5 final size:5
Alignment explanation
Indices: 4174902--4174941 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
4174892 GCAAAAAATA
*
4174902 ATAA- ATAAT ATAAT ATAATT ATTAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAA-T ATAAT ATAAT ATAAT ATAAT
4174942 TTATTATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
4 4 0.12
5 24 0.75
6 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATAAT
Found at i:4174932 original size:21 final size:22
Alignment explanation
Indices: 4174906--4174950 Score: 83
Period size: 21 Copynumber: 2.1 Consensus size: 22
4174896 AAAATAATAA
4174906 ATAATATAATATAA-TTATTAT
1 ATAATATAATATAATTTATTAT
4174927 ATAATATAATATAATTTATTAT
1 ATAATATAATATAATTTATTAT
4174949 AT
1 AT
4174951 TACATTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAATATAATATAATTTATTAT
Found at i:4175024 original size:10 final size:10
Alignment explanation
Indices: 4175011--4175044 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
4175001 TTTGATATGG
4175011 TTTGAGAGGA
1 TTTGAGAGGA
4175021 TTTGAGAGGA
1 TTTGAGAGGA
*
4175031 TTTGAGAGAA
1 TTTGAGAGGA
4175041 TTTG
1 TTTG
4175045 GTGTGATTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.35
Consensus pattern (10 bp):
TTTGAGAGGA
Found at i:4180897 original size:39 final size:39
Alignment explanation
Indices: 4180854--4180932 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
4180844 ATCTAAAAAG
*
4180854 TGAAAGCACTTCTTGATATAGTGGACTGATTGGCAGAGT
1 TGAAAGCACTTCTTGATAAAGTGGACTGATTGGCAGAGT
4180893 TGAAAGCACTTCTTGATAAAGTGGACTGATTGGCAGAGT
1 TGAAAGCACTTCTTGATAAAGTGGACTGATTGGCAGAGT
4180932 T
1 T
4180933 AAAAACTTGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (39 bp):
TGAAAGCACTTCTTGATAAAGTGGACTGATTGGCAGAGT
Found at i:4182205 original size:58 final size:58
Alignment explanation
Indices: 4182106--4182227 Score: 219
Period size: 58 Copynumber: 2.1 Consensus size: 58
4182096 ATAAGTGCAG
*
4182106 GGATATTACCTCCAAAGACATGGAAAAACTTAAAAAGGAAATTGAACATACCTGTGTT
1 GGATATTACCTCCAAACACATGGAAAAACTTAAAAAGGAAATTGAACATACCTGTGTT
4182164 GGATATTACCTCCAAACACATGGAAAAACTTGAAAAA-GAAATTGAACATACCTGTGTT
1 GGATATTACCTCCAAACACATGGAAAAACTT-AAAAAGGAAATTGAACATACCTGTGTT
4182222 GGATAT
1 GGATAT
4182228 AACCCATGTC
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
58 57 0.92
59 5 0.08
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.25
Consensus pattern (58 bp):
GGATATTACCTCCAAACACATGGAAAAACTTAAAAAGGAAATTGAACATACCTGTGTT
Found at i:4186861 original size:17 final size:17
Alignment explanation
Indices: 4186835--4186876 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
4186825 AAAATATTAT
4186835 TTTC-CAATTAATCATC
1 TTTCTCAATTAATCATC
4186851 TTTCTCAATTAATCATC
1 TTTCTCAATTAATCATC
4186868 TTTCTCAAT
1 TTTCTCAAT
4186877 CAAAAACCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTCTCAATTAATCATC
Found at i:4203040 original size:18 final size:18
Alignment explanation
Indices: 4203017--4203053 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
4203007 TATTGCTTTC
4203017 TGTTATTTTAGTTTGACT
1 TGTTATTTTAGTTTGACT
4203035 TGTTATTTTAGTTTGACT
1 TGTTATTTTAGTTTGACT
4203053 T
1 T
4203054 TATGTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.05, G:0.16, T:0.62
Consensus pattern (18 bp):
TGTTATTTTAGTTTGACT
Found at i:4206783 original size:66 final size:66
Alignment explanation
Indices: 4206677--4206809 Score: 232
Period size: 66 Copynumber: 2.0 Consensus size: 66
4206667 CTCTGGGAGC
*
4206677 GATTGAGGTACTAATATGCATATTTCATGTTAGTGCTTTTGAGTTGAAAGTATTTTATCCCATTT
1 GATTGAGGTACTAATATGCATATTTCATGTTAGTGCTTTTGAGTTGAAAGTATCTTATCCCATTT
4206742 T
66 T
*
4206743 GATTGAGGTACTAATATGCAT-TTGTCATGTTAGTGCTTTTGATTTGAAAGTATCTTATCCCATT
1 GATTGAGGTACTAATATGCATATT-TCATGTTAGTGCTTTTGAGTTGAAAGTATCTTATCCCATT
4206807 TT
65 TT
4206809 G
1 G
4206810 CTTCTGCACA
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
65 2 0.03
66 62 0.97
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45
Consensus pattern (66 bp):
GATTGAGGTACTAATATGCATATTTCATGTTAGTGCTTTTGAGTTGAAAGTATCTTATCCCATTT
T
Found at i:4209258 original size:19 final size:19
Alignment explanation
Indices: 4209234--4209304 Score: 74
Period size: 19 Copynumber: 3.7 Consensus size: 19
4209224 AATGCATTTT
4209234 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
*
4209253 ATGCATCGATGCACTTA--
1 ATGCATCGATGCACATACC
* * *
4209270 GTGCATTTGATGCACAAGACC
1 ATGCA-TCGATGCAC-ATACC
4209291 ATGCATCGATGCAC
1 ATGCATCGATGCAC
4209305 TCAGGCTATT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
17 4 0.10
18 8 0.20
19 17 0.41
20 8 0.20
21 4 0.10
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.24
Consensus pattern (19 bp):
ATGCATCGATGCACATACC
Found at i:4217349 original size:21 final size:21
Alignment explanation
Indices: 4217320--4217364 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4217310 GATTTCTGGG
* *
4217320 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
* *
4217341 CAAGTGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
4217362 CAA
1 CAA
4217365 ACGAACAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:4218851 original size:23 final size:23
Alignment explanation
Indices: 4218783--4218851 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
4218773 CATTATTATA
* *
4218783 TGGCACTTCCGTGCATTTATACA
1 TGGCACTTCGGTGCATTTATACG
* * * *
4218806 CGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTATACG
4218829 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTATACG
4218852 AGTTGTGGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTATACG
Found at i:4219325 original size:15 final size:15
Alignment explanation
Indices: 4219304--4219350 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
4219294 TTTCCGAAAA
4219304 ATGAATTACTGGAAT
1 ATGAATTACTGGAAT
* *
4219319 TTGAATTACTGGAAA
1 ATGAATTACTGGAAT
4219334 ATGAATTACTGGAAT
1 ATGAATTACTGGAAT
4219349 AT
1 AT
4219351 TAAAATGAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.34
Consensus pattern (15 bp):
ATGAATTACTGGAAT
Found at i:4219533 original size:37 final size:41
Alignment explanation
Indices: 4219482--4219557 Score: 106
Period size: 38 Copynumber: 2.0 Consensus size: 41
4219472 TAAATACAAT
4219482 AAATAATATTATTTATCA-TAAA-ACT-TTTTTATTATTAA
1 AAATAATATTATTTATCATTAAATACTATTTTTATTATTAA
* *
4219520 AAATAAT-TTATTTATTATTAAATAGTATTTTTATTATT
1 AAATAATATTATTTATCATTAAATACTATTTTTATTATT
4219558 TTTGTATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 9 0.27
38 11 0.33
39 2 0.06
40 11 0.33
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (41 bp):
AAATAATATTATTTATCATTAAATACTATTTTTATTATTAA
Found at i:4219549 original size:21 final size:19
Alignment explanation
Indices: 4219507--4219557 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
4219497 TCATAAAACT
4219507 TTTTTATTATTAAAAATAA
1 TTTTTATTATTAAAAATAA
*
4219526 TTTATTTATTATTAAATAGT-A
1 -TT-TTTATTATTAAA-AATAA
4219547 TTTTTATTATT
1 TTTTTATTATT
4219558 TTTGTATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 9 0.32
20 4 0.14
21 13 0.46
22 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTTATTATTAAAAATAA
Found at i:4219678 original size:23 final size:23
Alignment explanation
Indices: 4219629--4219691 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
4219619 GTGTTATATT
**
4219629 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
4219652 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
4219675 ATATTATTAAAATATAT
1 ATATT-TTAAAA-ATAT
4219692 AAATAATATT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
23 23 0.74
24 5 0.16
25 3 0.10
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:4219683 original size:11 final size:11
Alignment explanation
Indices: 4219667--4219704 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
4219657 TTAAATATCT
4219667 TTATTAAAATA
1 TTATTAAAATA
4219678 TTATTAAAATA
1 TTATTAAAATA
*
4219689 -TATAAATAATA
1 TTATTAA-AATA
4219700 TTATT
1 TTATT
4219705 CATAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 5 0.22
11 15 0.65
12 3 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TTATTAAAATA
Found at i:4219719 original size:19 final size:20
Alignment explanation
Indices: 4219668--4219719 Score: 54
Period size: 22 Copynumber: 2.6 Consensus size: 20
4219658 TAAATATCTT
4219668 TATTAAA-ATATTATTAAAA
1 TATTAAATATATTATTAAAA
* *
4219687 TATATAAATAATATTATTCATA
1 TAT-TAAAT-ATATTATTAAAA
4219709 -ATTAAATATAT
1 TATTAAATATAT
4219720 AAATTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 2 0.07
22 10 0.36
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
TATTAAATATATTATTAAAA
Found at i:4219731 original size:28 final size:28
Alignment explanation
Indices: 4219679--4219740 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
4219669 ATTAAAATAT
4219679 TATTAAAATATATAAATAATATTATTCATA
1 TATT-AAATATATAAATAATATTATT-ATA
** *
4219709 -ATTAAATATATAAATTTTTTTATTATA
1 TATTAAATATATAAATAATATTATTATA
4219736 TATTA
1 TATTA
4219741 TTAAAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
27 3 0.11
28 22 0.79
29 3 0.11
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (28 bp):
TATTAAATATATAAATAATATTATTATA
Found at i:4219810 original size:31 final size:33
Alignment explanation
Indices: 4219764--4219843 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 33
4219754 ATAATATCTT
* *
4219764 ATATTATTATAATATAATTGATTATTTTA-TAT-A
1 ATATTAATA-AATATAATT-ATTATATTATTATAA
4219797 ATATTAA-AAATATAA-TATTATATTATTATAA
1 ATATTAATAAATATAATTATTATATTATTATAA
4219828 ATATTAATAAAT-TAAT
1 ATATTAATAAATATAAT
4219844 AAATAATATT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
29 8 0.20
30 4 0.10
31 18 0.44
32 5 0.12
33 6 0.15
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (33 bp):
ATATTAATAAATATAATTATTATATTATTATAA
Found at i:4219818 original size:22 final size:23
Alignment explanation
Indices: 4219793--4219836 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
4219783 GATTATTTTA
4219793 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
4219815 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
4219837 AATTAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:4219850 original size:52 final size:52
Alignment explanation
Indices: 4219747--4219853 Score: 128
Period size: 52 Copynumber: 2.0 Consensus size: 52
4219737 ATTATTAAAA
** * *
4219747 TAAAAATATAATATCTTATATTATTATAATATAATTGATTATTTTATATAATAT
1 TAAAAATATAATA-CTTATATTATTATAATATAATAAATTA-TATAAATAATAT
4219801 TAAAAATATAATA-TTATATTATTATAAATATTAATAAATTA-ATAAATAATAT
1 TAAAAATATAATACTTATATTATTAT-AATA-TAATAAATTATATAAATAATAT
4219853 T
1 T
4219854 TTGATGAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
52 22 0.47
53 4 0.09
54 21 0.45
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (52 bp):
TAAAAATATAATACTTATATTATTATAATATAATAAATTATATAAATAATAT
Found at i:4219980 original size:16 final size:17
Alignment explanation
Indices: 4219946--4219980 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
4219936 AAAAGTTCGG
4219946 AAAATGACTTACAGAAA
1 AAAATGACTTACAGAAA
*
4219963 AAAATGACTTACGGAAA
1 AAAATGACTTACAGAAA
4219980 A
1 A
4219981 TGAATCCGTA
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:0.57, C:0.11, G:0.14, T:0.17
Consensus pattern (17 bp):
AAAATGACTTACAGAAA
Found at i:4220108 original size:42 final size:42
Alignment explanation
Indices: 4220049--4220164 Score: 178
Period size: 42 Copynumber: 2.8 Consensus size: 42
4220039 ATTATGTTCA
* * * *
4220049 GGAAAACCAATTACGTGAAACAAACACTGGAAAATATTTTTC
1 GGAAAACGAATTACGTGAAACAAACACAGGAAAACATTTTCC
*
4220091 GGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTCC
1 GGAAAACGAATTACGTGAAACAAACACAGGAAAACATTTTCC
*
4220133 GGAAAACGAATTACGTGAAATAAACACAGGAA
1 GGAAAACGAATTACGTGAAACAAACACAGGAA
4220165 TTCGGGGAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.47, C:0.16, G:0.18, T:0.18
Consensus pattern (42 bp):
GGAAAACGAATTACGTGAAACAAACACAGGAAAACATTTTCC
Found at i:4225561 original size:26 final size:26
Alignment explanation
Indices: 4225507--4225595 Score: 83
Period size: 26 Copynumber: 3.4 Consensus size: 26
4225497 CTTTCAGTGA
* *
4225507 AAAAAAAAAGAAAAAAATGAG-AAAAG
1 AAAAAAAAAG-AAAAATTGTGCAAAAG
*
4225533 AAAAAAAAAGAAAAATTGTGCAAAGG
1 AAAAAAAAAGAAAAATTGTGCAAAAG
* * *
4225559 AAATAAAGAAAGAGAGATTGTGC-AATG
1 AAA-AAA-AAAGAAAAATTGTGCAAAAG
4225586 AAAAAAAAAG
1 AAAAAAAAAG
4225596 TTATATGGCT
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
25 12 0.22
26 20 0.37
27 9 0.17
28 13 0.24
ACGTcount: A:0.69, C:0.02, G:0.19, T:0.10
Consensus pattern (26 bp):
AAAAAAAAAGAAAAATTGTGCAAAAG
Found at i:4228272 original size:24 final size:24
Alignment explanation
Indices: 4228245--4228325 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
4228235 ACACTTAACA
4228245 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
* *
4228269 GTGCATCGATTCAT-CATGTTG-A-
1 GTGCATCGATGCATCCCT-TTGAAT
*
4228291 -TGCACCGATGCA-CGCC-TTGAAT
1 GTGCATCGATGCATC-CCTTTGAAT
4228313 GTGCATCGATGCA
1 GTGCATCGATGCA
4228326 CAAGGTCATG
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
20 3 0.07
21 11 0.24
22 1 0.02
23 14 0.31
24 16 0.36
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTTGAAT
Found at i:4231106 original size:45 final size:46
Alignment explanation
Indices: 4231057--4231144 Score: 124
Period size: 45 Copynumber: 1.9 Consensus size: 46
4231047 GAACATCGAA
* * * *
4231057 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTTAG
1 TGCATTTGATGCATCAATGCACAAGACCATCCATCGATGCACTTAG
*
4231102 TGCATTTGATGTATCAATGCACAAGACCATCCATCGATGCACT
1 TGCATTTGATGCATCAATGCACAAGACCATCCATCGATGCACT
4231145 CAAGCTATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 19 0.51
46 18 0.49
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (46 bp):
TGCATTTGATGCATCAATGCACAAGACCATCCATCGATGCACTTAG
Found at i:4232011 original size:21 final size:21
Alignment explanation
Indices: 4231985--4232026 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4231975 GATATATTGG
4231985 GGGTTTCTTTAAGAGGGGGTC
1 GGGTTTCTTTAAGAGGGGGTC
* *
4232006 GGGTTTTTTTCAGAGGGGGTC
1 GGGTTTCTTTAAGAGGGGGTC
4232027 AAAGATTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.10, G:0.43, T:0.36
Consensus pattern (21 bp):
GGGTTTCTTTAAGAGGGGGTC
Found at i:4238269 original size:18 final size:19
Alignment explanation
Indices: 4238225--4238293 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 19
4238215 TTTGTCCCAA
*
4238225 AAGACCACTGATTGTTCCG
1 AAGACCACTGATTGTCCCG
4238244 AAGAACCACT-A-TGTCCCG
1 AAG-ACCACTGATTGTCCCG
4238262 AATGACCACTGTATATGTCCCG
1 AA-GACCACTG-AT-TGTCCCG
4238284 AAGGACCACT
1 AA-GACCACT
4238294 CCTTAAGAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
18 14 0.33
19 5 0.12
20 7 0.17
22 16 0.38
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (19 bp):
AAGACCACTGATTGTCCCG
Found at i:4238269 original size:38 final size:40
Alignment explanation
Indices: 4238217--4238293 Score: 104
Period size: 38 Copynumber: 2.0 Consensus size: 40
4238207 ACTGAATATT
*
4238217 TGTCCCAAAAGACCACTG-AT-TGTTCCGAAGAACCACTA
1 TGTCCCAAAAGACCACTGTATATGTCCCGAAGAACCACTA
* * *
4238255 TGTCCCGAATGACCACTGTATATGTCCCGAAGGACCACT
1 TGTCCCAAAAGACCACTGTATATGTCCCGAAGAACCACT
4238294 CCTTAAGAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 16 0.48
39 2 0.06
40 15 0.45
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (40 bp):
TGTCCCAAAAGACCACTGTATATGTCCCGAAGAACCACTA
Found at i:4244110 original size:18 final size:19
Alignment explanation
Indices: 4244087--4244180 Score: 84
Period size: 18 Copynumber: 4.8 Consensus size: 19
4244077 CTGAATATTT
4244087 GTCCCGAAGGACCACTA-A
1 GTCCCGAAGGACCACTATA
* *
4244105 GTCCCGAAGGATCACTGATT
1 GTCCCGAAGGACCACT-ATA
** *
4244125 GTTTCGAAGAACCACTATA
1 GTCCCGAAGGACCACTATA
4244144 -TCCCGAAGGACCACTGTATA
1 GTCCCGAAGGACCAC--TATA
*
4244164 TGTCCCGAAAGACCACT
1 -GTCCCGAAGGACCACT
4244181 CCTTAAGAAC
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
18 26 0.44
19 3 0.05
20 17 0.29
22 13 0.22
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (19 bp):
GTCCCGAAGGACCACTATA
Found at i:4244433 original size:24 final size:21
Alignment explanation
Indices: 4244377--4244434 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 21
4244367 ATATATTCTC
4244377 ATCACTTTTCATATAAACATGT
1 ATCAC-TTTCATATAAACATGT
4244399 ATTTCAC-TTCATATACATACATGT
1 A--TCACTTTCATATA-A-ACATGT
4244423 GATCACTTTCAT
1 -ATCACTTTCAT
4244435 TATTTCACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
22 9 0.30
23 5 0.17
24 15 0.50
25 1 0.03
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (21 bp):
ATCACTTTCATATAAACATGT
Found at i:4252766 original size:333 final size:334
Alignment explanation
Indices: 4252158--4252822 Score: 1260
Period size: 333 Copynumber: 2.0 Consensus size: 334
4252148 TTATACCGAT
*
4252158 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAATGA
1 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
*
4252223 TCGATATTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTATTTCATGTTTTC
66 TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTTTTAATAGTATTTCATGTTTTC
4252288 CACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTA
130 CACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTA
* *
4252353 TAAAATATTATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATT
195 TAAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGAAAAAAATAAATCATT
4252418 AGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTT
260 AGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTT
4252483 TTCCACAATG
325 TTCCACAATG
4252493 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
1 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
*
4252558 TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTTTAATAGTGTTTCATGTTTTCC
66 TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTATTTCATGTTTTCC
4252622 ACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTAT
131 ACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTAT
*
4252687 AAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAATGAAAAAAATAAATCATTA
196 AAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGAAAAAAATAAATCATTA
4252752 GACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTT
261 GACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTT
4252817 TCCACA
326 TCCACA
4252823 GTGAAAAAAG
Statistics
Matches: 324, Mismatches: 6, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
333 223 0.69
335 101 0.31
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (334 bp):
AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTATTTCATGTTTTCC
ACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTAT
AAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGAAAAAAATAAATCATTA
GACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTT
TCCACAATG
Found at i:4252905 original size:23 final size:23
Alignment explanation
Indices: 4252879--4252941 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
4252869 ATATAACCAC
4252879 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
4252902 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
4252925 TACCTATTACATCATAT
1 TACCTATTACATTATAT
4252942 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:4253397 original size:39 final size:39
Alignment explanation
Indices: 4253343--4253425 Score: 139
Period size: 39 Copynumber: 2.1 Consensus size: 39
4253333 TCAAGTTGTA
* *
4253343 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTGGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
4253382 GATTTGGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTGGATTTCCTTTTGCTTGGCACCATATGAGATTTG
4253421 GATTT
1 GATTT
4253426 TGATGAGCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.17, C:0.14, G:0.22, T:0.47
Consensus pattern (39 bp):
GATTTGGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:4253710 original size:18 final size:18
Alignment explanation
Indices: 4253687--4253723 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4253677 CGAAATATAT
4253687 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
4253705 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
4253723 A
1 A
4253724 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:4254567 original size:182 final size:183
Alignment explanation
Indices: 4253991--4254698 Score: 1301
Period size: 183 Copynumber: 3.9 Consensus size: 183
4253981 TTAAAATTAC
* *
4253991 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
* *
4254056 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
4254121 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
*
4254174 CGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
4254239 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
4254304 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
4254357 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
4254422 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCAT-AAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
4254486 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
4254539 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
4254604 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* * * **
4254669 ATATTGCAAATTTACCTATTTTATTATAAT
131 ATATTACAAAATTATCTATTACATTATAAT
4254699 ATGTTGAAAG
Statistics
Matches: 511, Mismatches: 13, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
182 182 0.36
183 329 0.64
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.35
Consensus pattern (183 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:4254662 original size:365 final size:366
Alignment explanation
Indices: 4253991--4254698 Score: 1301
Period size: 365 Copynumber: 1.9 Consensus size: 366
4253981 TTAAAATTAC
* *
4253991 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
* *
4254056 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
4254121 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGTCGATACTTTTTT
131 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGTCGACACTTTTTT
4254186 AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGT
196 AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGT
4254251 CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAAT
261 CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAAT
*
4254316 TATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
326 TACCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
4254357 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
4254422 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCAT-AAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
4254486 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTT
131 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGTCGACACTTTTTT
4254551 AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGT
196 AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGT
* *
4254616 CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTGCAAATT
261 CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAAT
**
4254681 TACCTATTTTATTATAAT
326 TACCTATTACATTATAAT
4254699 ATGTTGAAAG
Statistics
Matches: 330, Mismatches: 12, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
365 228 0.69
366 102 0.31
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.35
Consensus pattern (366 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGTCGACACTTTTTT
AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGT
CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAAT
TACCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:4256173 original size:3 final size:3
Alignment explanation
Indices: 4256165--4256245 Score: 72
Period size: 3 Copynumber: 27.0 Consensus size: 3
4256155 AATTGTTTGG
* * * **
4256165 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
4256213 AGC TTC ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
4256246 GTCAGCTTCA
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.23, C:0.35, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:4256182 original size:12 final size:12
Alignment explanation
Indices: 4256169--4256257 Score: 88
Period size: 12 Copynumber: 7.4 Consensus size: 12
4256159 GTTTGGATCA
* *
4256169 TCATCTTCATCA
1 TCATCGTCATCT
* *
4256181 TCATCATCATCA
1 TCATCGTCATCT
* *
4256193 TCGTCATCATCT
1 TCATCGTCATCT
* *
4256205 TCATCGCCAGCT
1 TCATCGTCATCT
*
4256217 TCATCGTCATCA
1 TCATCGTCATCT
4256229 TCATCGTCATCT
1 TCATCGTCATCT
*
4256241 TCATCGTCAGCT
1 TCATCGTCATCT
4256253 TCATC
1 TCATC
4256258 TTCTGCGATC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:4256188 original size:18 final size:18
Alignment explanation
Indices: 4256169--4256260 Score: 76
Period size: 18 Copynumber: 5.1 Consensus size: 18
4256159 GTTTGGATCA
* *
4256169 TCATCTTCATCATCATCA
1 TCATCATCATCATCATCT
*
4256187 TCATCATCGTCATCATCT
1 TCATCATCATCATCATCT
** * * *
4256205 TCATCGCCAGCTTCATCG
1 TCATCATCATCATCATCT
*
4256223 TCATCATCATCGTCATCT
1 TCATCATCATCATCATCT
* * *
4256241 TCATCGTCAGCTTCATCT
1 TCATCATCATCATCATCT
4256259 TC
1 TC
4256261 TGCGATCGCT
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.37
Consensus pattern (18 bp):
TCATCATCATCATCATCT
Found at i:4256221 original size:36 final size:36
Alignment explanation
Indices: 4256181--4256257 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
4256171 ATCTTCATCA
*
4256181 TCATCATCATCATCGTCATCATCTTCATCGCCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
* * *
4256217 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
4256253 TCATC
1 TCATC
4256258 TTCTGCGATC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.21, C:0.35, G:0.09, T:0.35
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGCCAGCT
Found at i:4256260 original size:6 final size:6
Alignment explanation
Indices: 4256169--4256260 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
4256159 GTTTGGATCA
* * * * * * * *
4256169 TCATCT TCATCA TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * * *
4256217 TCATCG TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
4256261 TGCGATCGCT
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:4257424 original size:15 final size:15
Alignment explanation
Indices: 4257406--4257434 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4257396 AGAAGGAGGT
4257406 GGTTGAGAAGAACTG
1 GGTTGAGAAGAACTG
4257421 GGTTGAGAAGAACT
1 GGTTGAGAAGAACT
4257435 TTGAGAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.07, G:0.38, T:0.21
Consensus pattern (15 bp):
GGTTGAGAAGAACTG
Found at i:4258189 original size:197 final size:198
Alignment explanation
Indices: 4257714--4259073 Score: 2522
Period size: 197 Copynumber: 6.9 Consensus size: 198
4257704 TTTAAATTAG
*
4257714 TATCGACACAAACTATATTAGTGTCGACATATTA--TAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
4257777 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
4257842 CGACA-TCTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGTAAA
131 CGACACT-TTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAA
4257906 AAAA
195 AAAA
4257910 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
4257975 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
4258040 CGACACTTTTTATATATGGATCGACAC-TTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
4258104 AAA
196 AAA
*
4258107 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
4258172 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
4258237 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
4258302 AAA
196 AAA
4258305 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
4258370 ATTTTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
4258434 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
4258499 AAA
196 AAA
* *
4258502 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCAGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
4258567 ATTGTACTGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTAGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
4258632 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
4258697 AAAA
195 AAAA
4258701 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
4258766 ATTGTACCGGTTAGATTGAAAAATTACATATTACATT-TACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
4258830 CGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
4258894 AAAA
195 AAAA
4258898 TATCGACACAAACTATATTAGTGTCGACACATTA-TTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
4258962 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATG-TTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
*
4259026 TTGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
130 TCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
4259074 GGCCATATTG
Statistics
Matches: 1138, Mismatches: 16, Indels: 17
0.97 0.01 0.01
Matches are distributed among these distances:
196 100 0.09
197 507 0.45
198 385 0.34
199 146 0.13
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (198 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAA
Found at i:4258481 original size:395 final size:395
Alignment explanation
Indices: 4257714--4259073 Score: 2518
Period size: 395 Copynumber: 3.4 Consensus size: 395
4257704 TTTAAATTAG
*
4257714 TATCGACACAAACTATATTAGTGTCGACATATTA-TAGACATATTCTCTCATAAAACCGGTATAA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTAGACATATTCTCTCATAAAACCGGTATAA
4257778 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
*
4257843 GACA-TCTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGTAAAA
131 GACACT-TTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
4257907 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGT
195 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGT
4257972 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
260 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
4258037 GATCGACACTTTTTATATATGGATCGACAC-TTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
325 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
4258101 AAAAAA
390 AAAAAA
*
4258107 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTA-TTAGACATATTCTCTCATAAAACCGGTATA
4258172 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
65 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
4258237 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
130 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
4258302 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGT
195 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGT
*
4258367 ATAATTTTACCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGG
260 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
4258431 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
325 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
4258496 AAAAAA
390 AAAAAA
* *
4258502 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCAGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTA-TTAGACATATTCTCTCATAAAACCGGTATA
* *
4258567 ATTGTACTGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTAGGAT
65 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
4258632 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
130 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
4258697 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
194 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
4258762 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATT-TACTTTTGGGTTCGATGATTTTG
259 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
4258826 GGATCGACAC-TTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG
324 GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG
4258890 AAAAAAAA
389 -AAAAAAA
4258898 TATCGACACAAACTATATTAGTGTCGACACATTATTAGACATATTCTCTCATAAAACCGGTATAA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTAGACATATTCTCTCATAAAACCGGTATAA
*
4258963 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATG-TTTTGGGAT
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGAT
*
4259027 TGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
130 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
4259074 GGCCATATTG
Statistics
Matches: 944, Mismatches: 14, Indels: 15
0.97 0.01 0.02
Matches are distributed among these distances:
393 33 0.03
394 50 0.05
395 635 0.67
396 226 0.24
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (395 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTAGACATATTCTCTCATAAAACCGGTATAA
TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAA
AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAA
AAAAA
Found at i:4259238 original size:19 final size:19
Alignment explanation
Indices: 4259192--4259240 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
4259182 TTATATTCAC
*
4259192 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
4259211 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
4259230 ATACAAAATTA
1 ATACAAAATTA
4259241 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:4261074 original size:32 final size:32
Alignment explanation
Indices: 4261032--4261092 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
4261022 TTAATATCAC
*
4261032 CCCTTAACACCCCAACTTCTTTCACCACTTCA
1 CCCTCAACACCCCAACTTCTTTCACCACTTCA
* *
4261064 CCCTCAACACCTCTACTTCTTTCACCACT
1 CCCTCAACACCCCAACTTCTTTCACCACT
4261093 CCATCTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.30
Consensus pattern (32 bp):
CCCTCAACACCCCAACTTCTTTCACCACTTCA
Found at i:4263470 original size:20 final size:19
Alignment explanation
Indices: 4263424--4263470 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
4263414 TCCGGTATCA
*
4263424 TTTTACTGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
4263443 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
4263464 TTTTACC
1 TTTTACC
4263471 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.15, G:0.11, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:4263618 original size:20 final size:20
Alignment explanation
Indices: 4263592--4263637 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
4263582 CACTTTTAAA
4263592 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
4263611 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
4263632 TTTACC
1 TTTACC
4263638 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:4272372 original size:37 final size:37
Alignment explanation
Indices: 4272321--4272391 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
4272311 GGAGCCCATT
*
4272321 TTTTAAATTATTTTTAAGTTT-AATAATTAAAAAATA
1 TTTTAAAATATTTTTAAGTTTAAATAATTAAAAAATA
* * *
4272357 TTTTAAACATATTTTTTATTTTAAATATTTAAAAA
1 TTTTAAA-ATATTTTTAAGTTTAAATAATTAAAAA
4272392 TATGGTAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 7 0.24
37 11 0.38
38 11 0.38
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (37 bp):
TTTTAAAATATTTTTAAGTTTAAATAATTAAAAAATA
Found at i:4272476 original size:73 final size:71
Alignment explanation
Indices: 4272342--4272480 Score: 197
Period size: 73 Copynumber: 1.9 Consensus size: 71
4272332 TTTTAAGTTT
* * * * **
4272342 AATAATTAAAAAATATTTTAAACATATTTTTTATTTTAAATATTTAAAAATATGGTAATTTAGTG
1 AATAATTAAAAAATATTTTAAACATATTTTTTATTTAAAAAACTCAAAAATATAATAATTTAGTG
4272407 GGTCCC
66 GGTCCC
*
4272413 AATAATTAAAAAATATTTTTAAACATTATTTTTTATTTAAAAAACTCGAAAATATAATAATTTAG
1 AATAATTAAAAAATA-TTTTAAACA-TATTTTTTATTTAAAAAACTCAAAAATATAATAATTTAG
4272478 TGG
64 TGG
4272481 ACCCCATTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
71 15 0.25
72 9 0.15
73 35 0.59
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (71 bp):
AATAATTAAAAAATATTTTAAACATATTTTTTATTTAAAAAACTCAAAAATATAATAATTTAGTG
GGTCCC
Found at i:4284931 original size:31 final size:29
Alignment explanation
Indices: 4284895--4284993 Score: 90
Period size: 31 Copynumber: 3.2 Consensus size: 29
4284885 TATTTTTTGG
4284895 TTTCAATTTGATACTTGAATTTAATTTTAA
1 TTTCAATTTGATACTT-AATTTAATTTTAA
* * *
4284925 TGTTCAATGTGATGCTTAATTTTCATTTTAA
1 T-TTCAATTTGATACTTAA-TTTAATTTTAA
* *
4284956 TCTCTAATTAGATACTTCAATTTAACTTTTAA
1 TTTC-AATTTGATACTT-AATTTAA-TTTTAA
*
4284988 ATTCAA
1 TTTCAA
4284994 AACATAGTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
30 5 0.09
31 39 0.72
32 10 0.19
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.49
Consensus pattern (29 bp):
TTTCAATTTGATACTTAATTTAATTTTAA
Found at i:4287409 original size:30 final size:29
Alignment explanation
Indices: 4287372--4287472 Score: 121
Period size: 30 Copynumber: 3.4 Consensus size: 29
4287362 TTAATTTTAC
*
4287372 ATCTTAACGCTAAAAATATATTTTATTTTT
1 ATCTTAAC-TTAAAAATATATTTTATTTTT
* * *
4287402 ATTTTAACTTAAAAACATATTTTAGTATTT
1 ATCTTAACTTAAAAATATATTTTA-TTTTT
* *
4287432 ATCTAAACTTAAAAAATATATTTTATTATT
1 ATCTTAACTT-AAAAATATATTTTATTTTT
4287462 ATCTTAACTTA
1 ATCTTAACTTA
4287473 TTGCATAAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
29 15 0.25
30 31 0.53
31 13 0.22
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.49
Consensus pattern (29 bp):
ATCTTAACTTAAAAATATATTTTATTTTT
Found at i:4287515 original size:12 final size:12
Alignment explanation
Indices: 4287498--4287523 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4287488 TCTTAAAAAA
4287498 TATTATATAATT
1 TATTATATAATT
4287510 TATTATATAATT
1 TATTATATAATT
4287522 TA
1 TA
4287524 AGTTAAAATA
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTATATAATT
Found at i:4287577 original size:30 final size:30
Alignment explanation
Indices: 4287506--4287577 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
4287496 AATATTATAT
* *
4287506 AATTTATTATATAATTTAAGTTAAAATAAG
1 AATTAATTATATAATTTAAGTTAAAATAAA
* * **
4287536 AATAAAATATATGTTTTAAGTTAAAATAAA
1 AATTAATTATATAATTTAAGTTAAAATAAA
4287566 AATTAATTATAT
1 AATTAATTATAT
4287578 TTAATAATTT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (30 bp):
AATTAATTATATAATTTAAGTTAAAATAAA
Found at i:4287675 original size:30 final size:30
Alignment explanation
Indices: 4287641--4287708 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
4287631 ATTTATGTAA
4287641 TAAGTTAAGAT-GAGAATAAAATATATTTTT
1 TAAGTTAAGATAGAGAATAAAATATA-TTTT
* *
4287671 TAAGTTAAGATATAGATTAAAATATATTTT
1 TAAGTTAAGATAGAGAATAAAATATATTTT
4287701 TAAGTTAA
1 TAAGTTAA
4287709 AACAAAAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 23 0.66
31 12 0.34
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (30 bp):
TAAGTTAAGATAGAGAATAAAATATATTTT
Found at i:4287723 original size:119 final size:119
Alignment explanation
Indices: 4287522--4287738 Score: 265
Period size: 119 Copynumber: 1.8 Consensus size: 119
4287512 TTATATAATT
* *
4287522 TAAGTTAAAATAAGAATAAAATATATGTTTTAAGTTAAAATAAAAATTAATTATATTTAATAATT
1 TAAGTTAAAATAAGAATAAAATATATGTTTTAAGTTAAAATAAAAATTAAATATATTTAATAAGT
* ** * ** *
4287587 TGAGGCAAGAATGAAATATATTAAATAATTTAACTTAAAACATAATTTATGTAA
66 TAAAACAAAAACAAAATATATTAAATAAGTTAACTTAAAACATAATTTATGTAA
* * * * * * *
4287641 TAAGTTAAGATGAGAATAAAATATATTTTTTAAGTTAAGATATAGATTAAAATATATTT-TTAAG
1 TAAGTTAAAATAAGAATAAAATATATGTTTTAAGTTAAAATAAAAATT-AAATATATTTAATAAG
*
4287705 TTAAAACAAAAACAAAATATATTTAATAAGTTAA
65 TTAAAACAAAAACAAAATATATTAAATAAGTTAA
4287739 AAAAAATATA
Statistics
Matches: 80, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
119 71 0.89
120 9 0.11
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.37
Consensus pattern (119 bp):
TAAGTTAAAATAAGAATAAAATATATGTTTTAAGTTAAAATAAAAATTAAATATATTTAATAAGT
TAAAACAAAAACAAAATATATTAAATAAGTTAACTTAAAACATAATTTATGTAA
Found at i:4287751 original size:29 final size:30
Alignment explanation
Indices: 4287689--4287744 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
4287679 GATATAGATT
*
4287689 AAAATATATTT-TTAAGTTAAAACAAAAAC
1 AAAATATATTTAATAAGTTAAAACAAAAAC
4287718 AAAATATATTTAATAAGTTAAAA-AAAA
1 AAAATATATTTAATAAGTTAAAACAAAA
4287745 TATAAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (30 bp):
AAAATATATTTAATAAGTTAAAACAAAAAC
Found at i:4290205 original size:20 final size:20
Alignment explanation
Indices: 4290168--4290205 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4290158 CTTAAACTTC
*
4290168 TTAACAATCATATCATTCAT
1 TTAACAATAATATCATTCAT
4290188 TTAACAATTAATAT-ATTC
1 TTAACAA-TAATATCATTC
4290206 GACATTACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAACAATAATATCATTCAT
Found at i:4290404 original size:23 final size:23
Alignment explanation
Indices: 4290367--4290430 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
4290357 CAGCTCGTAT
4290367 AAATGCACCGAAGTGCCACATAG
1 AAATGCACCGAAGTGCCACATAG
* * * * *
4290390 AATTGCAGCGTAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACATAG
4290413 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
4290431 TATAATATGT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.33, C:0.25, G:0.27, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACATAG
Found at i:4295660 original size:23 final size:23
Alignment explanation
Indices: 4295595--4295663 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
4295585 CCCCACAGCT
* *
4295595 CGTATAAATGCACCGAAGTACCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
4295618 CGTAGAATTGCACC-ATAGTGCCG
1 CGTAGAAATGCACCGA-AGTGCCA
4295641 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
4295664 TATAATATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 1 0.03
23 36 0.95
24 1 0.03
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:4297956 original size:35 final size:34
Alignment explanation
Indices: 4297916--4297994 Score: 85
Period size: 33 Copynumber: 2.4 Consensus size: 34
4297906 AATTAATCAT
*
4297916 TAATTAAATTT-TAATTTTACTTTTAATAGAAAAT-A
1 TAATTAAATTTATAATTCT--TTTTAATA-AAAATAA
*
4297951 TAATT-AATTTATAATTCTTTTTATTAAAAATAA
1 TAATTAAATTTATAATTCTTTTTAATAAAAATAA
4297984 TAATT-AATTTA
1 TAATTAAATTTA
4297995 AGTAATATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
32 5 0.12
33 19 0.47
34 5 0.12
35 11 0.28
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.51
Consensus pattern (34 bp):
TAATTAAATTTATAATTCTTTTTAATAAAAATAA
Found at i:4299148 original size:15 final size:15
Alignment explanation
Indices: 4299124--4299159 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
4299114 ATATTTAGCT
*
4299124 GGGC-GGCGGATGTG
1 GGGCGGGCGGATGCG
4299138 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
4299153 GGGCGGG
1 GGGCGGG
4299160 TAATGTCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.06, C:0.17, G:0.69, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:4299985 original size:23 final size:23
Alignment explanation
Indices: 4299959--4300003 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
4299949 CAAATTTTTA
*
4299959 TATAAAAGTTTAAAAAATAAAAT
1 TATAAAAGTTTAAAAAAGAAAAT
* **
4299982 TATATATTTTTAAAAAAGAAAA
1 TATAAAAGTTTAAAAAAGAAAA
4300004 AACATAAATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (23 bp):
TATAAAAGTTTAAAAAAGAAAAT
Found at i:4301030 original size:21 final size:21
Alignment explanation
Indices: 4300992--4301031 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4300982 TCGAAGTACC
* *
4300992 ACATATATGTTCCAAAGGATT
1 ACATATATATCCCAAAGGATT
*
4301013 ACATATATATCCCTAAGGA
1 ACATATATATCCCAAAGGA
4301032 CCACGTAGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.30
Consensus pattern (21 bp):
ACATATATATCCCAAAGGATT
Found at i:4301931 original size:163 final size:164
Alignment explanation
Indices: 4301661--4301984 Score: 605
Period size: 163 Copynumber: 2.0 Consensus size: 164
4301651 TGATTCGAAT
4301661 CCTTAATTTCTTAAGCTAGAAGAAAGAGTTAATCCAAATTTTCTCTTGCAGTGGTATCGATACCC
1 CCTTAATTTCTTAAGCTAGAAGAAAGAGTTAATCCAAATTTTCTCTTGCAGTGGTATCGATACCC
* *
4301726 CCATAGGGTATCGATATTTCCCTAATTGTAGTATCGATACCAATCCG-GTATCGATACCAATTTT
66 CCATAGGGTATCGATACTTCCCTAACTGTAGTATCGATACCAATCCGAGTATCGATACCAATTTT
4301790 GCATTCGATGTTTTTGTTTCAAGCATGGTATAGA
131 GCATTCGATGTTTTTGTTTCAAGCATGGTATAGA
*
4301824 CCTTAATTTCTTAAGCTAGAAGAAAGAGTTAATCCAAATTTTCTCTTGCAGTGGTATCGGTACCC
1 CCTTAATTTCTTAAGCTAGAAGAAAGAGTTAATCCAAATTTTCTCTTGCAGTGGTATCGATACCC
*
4301889 CCATAGGGTATCGATACTTCCCTAACTGTGGTATCGATACCAATCCGAGTATCGATACCAATTTT
66 CCATAGGGTATCGATACTTCCCTAACTGTAGTATCGATACCAATCCGAGTATCGATACCAATTTT
4301954 GCATTCGATGTTTTTGTTTCAAGCATGGTAT
131 GCATTCGATGTTTTTGTTTCAAGCATGGTAT
4301985 CGATAATGTC
Statistics
Matches: 156, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
163 108 0.69
164 48 0.31
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (164 bp):
CCTTAATTTCTTAAGCTAGAAGAAAGAGTTAATCCAAATTTTCTCTTGCAGTGGTATCGATACCC
CCATAGGGTATCGATACTTCCCTAACTGTAGTATCGATACCAATCCGAGTATCGATACCAATTTT
GCATTCGATGTTTTTGTTTCAAGCATGGTATAGA
Found at i:4303088 original size:19 final size:20
Alignment explanation
Indices: 4303052--4303094 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
4303042 AAGTTAGGGT
4303052 TTTTTTATAAACATAATAATA
1 TTTTTTATAAACATAATAA-A
4303073 TTTTTTATAAA-A-AATAAA
1 TTTTTTATAAACATAATAAA
4303091 TTTT
1 TTTT
4303095 AAAATTATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.23
19 5 0.23
20 1 0.05
21 11 0.50
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTTTATAAACATAATAAA
Found at i:4305070 original size:23 final size:23
Alignment explanation
Indices: 4305026--4305070 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4305016 AACATATTAG
**
4305026 GTAGCGCTTATATAATGTAATAT
1 GTAGCGCTTATATAATAAAATAT
*
4305049 GTAGCGTTTATATAATAAAATA
1 GTAGCGCTTATATAATAAAATA
4305071 GGCATTTAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.38
Consensus pattern (23 bp):
GTAGCGCTTATATAATAAAATAT
Found at i:4305132 original size:87 final size:87
Alignment explanation
Indices: 4304986--4305148 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
4304976 AATGTTATAT
* * *
4304986 CATTTAACTGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATATGT
1 CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
*
4305051 AGCGTTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
*
4305073 CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCTCTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
4305138 AGCGCTTATAT
66 AGCGCTTATAT
4305149 TTACATATTT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.34
Consensus pattern (87 bp):
CATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
AGCGCTTATATAATAAAATAGG
Found at i:4308745 original size:230 final size:231
Alignment explanation
Indices: 4308381--4308815 Score: 619
Period size: 230 Copynumber: 1.9 Consensus size: 231
4308371 GCTTTCGATG
* *
4308381 CTTTTGGGATCGACACTTTTTGAAAATGTATTGACACTTTATGCGTTCACCCTTTTTGGCATCCA
1 CTTTTGGGATCGACACTCTATGAAAATGTATTGACACTTTATGCGTTCACCCTTTTTGGCATCCA
* * * * *
4308446 TTATGGACAAAAATTATCGATACAATATTAATAAGAGTCGATACATATTATAGACCTATTCTCTC
66 TTATGGACAAAAAGTATCGACACAATACTAATAAGAGTCGATAAATATTATAGACATATTCTCTC
*
4308511 ATAAAACCGGTATATGTATACCGATTATATTACAAAAA-TACCTATTACATTATAATTATGGGTT
131 ATAAAACCGGTATATGTATACCGATTATATTA-AAAAATTACCCATTACATTATAATTATGGGTT
* *
4308575 TTGGTGTTTTTGGGATCGACACTTTATGCGTGCAACC
195 TCGATGTTTTTGGGATCGACACTTTATGCGTGCAACC
* *
4308612 CTTTT-GGATCGACACTCTATGAAAATGTATCT-ACACTTTGTAG-GTTCCCCCTTTTTGGCATC
1 CTTTTGGGATCGACACTCTATGAAAATGTAT-TGACACTTTAT-GCGTTCACCCTTTTTGGCATC
* * * *
4308674 CATTCTGGACAAAAAAGTATCGACACAATACTAATAAGTGTCGATAAATGTTGTAGACATATT-T
64 CATTATGGAC-AAAAAGTATCGACACAATACTAATAAGAGTCGATAAATATTATAGACATATTCT
* * * *
4308738 TTCATAAAACCGGTATATTTATACCGGTTATATTAAAAAATTACCCATTGCATTATAATTATGGG
128 CTCATAAAACCGGTATATGTATACCGATTATATTAAAAAATTACCCATTACATTATAATTATGGG
4308803 TTTCGATGTTTTT
193 TTTCGATGTTTTT
4308816 TGGGTCGTTA
Statistics
Matches: 180, Mismatches: 20, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
229 5 0.03
230 124 0.69
231 51 0.28
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (231 bp):
CTTTTGGGATCGACACTCTATGAAAATGTATTGACACTTTATGCGTTCACCCTTTTTGGCATCCA
TTATGGACAAAAAGTATCGACACAATACTAATAAGAGTCGATAAATATTATAGACATATTCTCTC
ATAAAACCGGTATATGTATACCGATTATATTAAAAAATTACCCATTACATTATAATTATGGGTTT
CGATGTTTTTGGGATCGACACTTTATGCGTGCAACC
Found at i:4312522 original size:21 final size:21
Alignment explanation
Indices: 4312496--4312535 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4312486 CAGAACCCCA
4312496 GGGGGGTATCGATTCCCCTGT
1 GGGGGGTATCGATTCCCCTGT
*
4312517 GGGGGGTATCGGTTCCCCT
1 GGGGGGTATCGATTCCCCT
4312536 TCAAAGGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.07, C:0.25, G:0.40, T:0.28
Consensus pattern (21 bp):
GGGGGGTATCGATTCCCCTGT
Found at i:4312571 original size:21 final size:21
Alignment explanation
Indices: 4312516--4312579 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
4312506 GATTCCCCTG
*
4312516 TGGGGGGTATCGGTTCCCCTTCA
1 TGGGGGGAATCGGTT-CCC-TCA
**
4312539 AAGGGGGAATCGGTTCCCTCA
1 TGGGGGGAATCGGTTCCCTCA
* *
4312560 TGGGGGGGATCGATTCCCTC
1 TGGGGGGAATCGGTTCCCTC
4312580 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 19 0.56
22 3 0.09
23 12 0.35
ACGTcount: A:0.14, C:0.25, G:0.36, T:0.25
Consensus pattern (21 bp):
TGGGGGGAATCGGTTCCCTCA
Found at i:4316424 original size:22 final size:21
Alignment explanation
Indices: 4316382--4316421 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4316372 GAGTTTGTTT
*
4316382 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
4316403 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
4316422 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:4319796 original size:12 final size:12
Alignment explanation
Indices: 4319749--4319794 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
4319739 TGGATTATCA
*
4319749 TCATCATCATCG
1 TCATCTTCATCG
4319761 TCATCTTCATCG
1 TCATCTTCATCG
*
4319773 TCATCTTCATTG
1 TCATCTTCATCG
4319785 TCATCTTCAT
1 TCATCTTCAT
4319795 TGACCGCTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.20, C:0.30, G:0.07, T:0.43
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:4321613 original size:201 final size:201
Alignment explanation
Indices: 4321261--4322220 Score: 1359
Period size: 201 Copynumber: 4.7 Consensus size: 201
4321251 TATTTAAATT
* *
4321261 AGTATCGACACAAAATTAAAAACGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACTGGT
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
* * * * * *
4321326 ATATTTATACCAGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTC-GATGTTTTT
66 ATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATACTTAT-GGATGCATATGTTTCT
* * * *
4321390 GGGATCGACAATTTTCGAAAATGTATCGACACTTTATGCGTTTACCCTTTTTAGCATCCATTCTG
130 GGGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTG
4321455 GACCAAA
195 GACCAAA
* * *
4321462 AGTATTGACACAAAATTAAAAACGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAATCGGT
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
*
4321527 ATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
66 ATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
*
4321592 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTATGG
131 GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
4321657 ACCAAA
196 ACCAAA
* *
4321663 AGTATCGACACAAAATTTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCAGT
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
* * *
4321728 ATATTTATACCGGTTACATTGTAAATTTATCTATTACATTATACTTATGGATGCATATGTTTTTG
66 ATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
* * * * *
4321793 GGATCGACACTTTTTGAAAATGTATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCAC
131 GGATCGACACTTTTTGAAAATGTATCGACACTTTATG----CGT-TC-ACCCTTTTTG-G--CAT
* *
4321858 CCTTTTTGGCATCCATTCTAA
187 CCATTCTGG-A-CCA----AA
** ** *
4321879 ACCAAAAGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAA
1 A-GTATCG-A-C-ACA-AAAT-TAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAA
* *
4321944 ACCGGTATATTTATACCAATTACATTGTAAATTTATCTATTACATTATACTTATGGATGCATATG
60 ACCGGTATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATG
*
4322009 TTTCTGGGATCGACACTTTTTGAAAATGTATCGACACTTTATGTGTTCACCCTTTTTGGCATCCA
125 TTTCTGGGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCA
4322074 TTCTGGACCAAA
190 TTCTGGACCAAA
4322086 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTA-T-TCTCATAAAACCGGT
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
*
4322149 ATATTTATACCAGTTACATTGTAAATTTACCTATTACTTTATACTTATGGATGCATATGTTTCTG
66 ATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
4322214 GGATCGA
131 GGATCGA
4322221 TAAATTTTAC
Statistics
Matches: 684, Mismatches: 53, Indels: 46
0.87 0.07 0.06
Matches are distributed among these distances:
199 84 0.12
200 5 0.01
201 371 0.54
202 3 0.00
203 3 0.00
204 1 0.00
205 3 0.00
206 4 0.01
207 11 0.02
208 1 0.00
210 9 0.01
211 4 0.01
212 4 0.01
213 9 0.01
215 1 0.00
216 11 0.02
217 4 0.01
218 4 0.01
219 1 0.00
220 3 0.00
221 3 0.00
222 145 0.21
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.36
Consensus pattern (201 bp):
AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
ATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
GGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
ACCAAA
Found at i:4321821 original size:21 final size:21
Alignment explanation
Indices: 4321795--4321847 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
4321785 TGTTTTTGGG
4321795 ATCGACACTTTTTGAAAATGT
1 ATCGACACTTTTTGAAAATGT
4321816 ATCGACACTTTTTGAAAATGT
1 ATCGACACTTTTTGAAAATGT
4321837 ATCGACACTTT
1 ATCGACACTTT
4321848 ATGCGTTCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (21 bp):
ATCGACACTTTTTGAAAATGT
Found at i:4321980 original size:222 final size:222
Alignment explanation
Indices: 4321594--4322220 Score: 994
Period size: 222 Copynumber: 2.9 Consensus size: 222
4321584 TGTTTCTGGG
*
4321594 ATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTATGGAC
1 ATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGGAC
*
4321659 CAAAAGTATCGACACAAAATTTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAAC
66 CAAAAGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAAC
* *
4321724 CAGTATATTTATACCGGTTACATTGTAAATTTATCTATTACATTATACTTATGGATGCATATGTT
131 CGGTATATTTATACCAGTTACATTGTAAATTTATCTATTACATTATACTTATGGATGCATATGTT
*
4321789 TTTGGGATCGACACTTTTTGAAAATGT
196 TCTGGGATCGACACTTTTTGAAAATGT
**
4321816 ATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTAAAC
1 ATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGGAC
4321881 CAAAAGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAAC
66 CAAAAGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAAC
*
4321946 CGGTATATTTATACCAATTACATTGTAAATTTATCTATTACATTATACTTATGGATGCATATGTT
131 CGGTATATTTATACCAGTTACATTGTAAATTTATCTATTACATTATACTTATGGATGCATATGTT
4322011 TCTGGGATCGACACTTTTTGAAAATGT
196 TCTGGGATCGACACTTTTTGAAAATGT
*
4322038 ATCGACACTTTATG----TGT-TC-AC-C------C--T-----TTT-TGGCATCCATTCTGGAC
1 ATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGGAC
4322082 CAAAAGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTA-T-TCTCATAAAAC
66 CAAAAGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAAC
* *
4322145 CGGTATATTTATACCAGTTACATTGTAAATTTACCTATTACTTTATACTTATGGATGCATATGTT
131 CGGTATATTTATACCAGTTACATTGTAAATTTATCTATTACATTATACTTATGGATGCATATGTT
4322210 TCTGGGATCGA
196 TCTGGGATCGA
4322221 TAAATTTTAC
Statistics
Matches: 391, Mismatches: 14, Indels: 23
0.91 0.03 0.05
Matches are distributed among these distances:
199 84 0.21
200 1 0.00
201 66 0.17
202 3 0.01
207 1 0.00
209 1 0.00
215 1 0.00
216 2 0.01
217 2 0.01
218 3 0.01
222 227 0.58
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (222 bp):
ATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGGAC
CAAAAGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAAC
CGGTATATTTATACCAGTTACATTGTAAATTTATCTATTACATTATACTTATGGATGCATATGTT
TCTGGGATCGACACTTTTTGAAAATGT
Found at i:4324333 original size:33 final size:33
Alignment explanation
Indices: 4324291--4324357 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4324281 TTAAGATCAC
* * *
4324291 CCCTTAACACCTCAACTTCTTTCACCACTTCAT
1 CCCTCAACACCTCAACTTCTTTAACCACTCCAT
*
4324324 CCCTCAACACCTCTACTTCTTTAACCACTCCAT
1 CCCTCAACACCTCAACTTCTTTAACCACTCCAT
4324357 C
1 C
4324358 TATTTTTCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.24, C:0.45, G:0.00, T:0.31
Consensus pattern (33 bp):
CCCTCAACACCTCAACTTCTTTAACCACTCCAT
Found at i:4324411 original size:21 final size:21
Alignment explanation
Indices: 4324386--4324429 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4324376 CCCCTTATGC
*
4324386 CTCTCAAGTGTATCTTTGACT
1 CTCTCAAGTGTATCTTCGACT
* *
4324407 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
4324428 CT
1 CT
4324430 TGATTGTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.30, G:0.11, T:0.43
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:4331350 original size:21 final size:21
Alignment explanation
Indices: 4331325--4331367 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
4331315 AAAGAATATA
4331325 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
4331346 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
4331367 T
1 T
4331368 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:4332972 original size:20 final size:19
Alignment explanation
Indices: 4332917--4332963 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
4332907 ATCCGATAGA
4332917 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
4332936 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
4332957 TTTTACC
1 TTTTACC
4332964 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:4338332 original size:20 final size:21
Alignment explanation
Indices: 4338286--4338346 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
4338276 TTCCCCTGTG
4338286 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
4338309 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
4338329 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
4338347 TGCACCAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:4344111 original size:20 final size:20
Alignment explanation
Indices: 4344086--4344124 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4344076 CGTTATACAA
4344086 GGGGGGAATCGGTACCCTCT
1 GGGGGGAATCGGTACCCTCT
*
4344106 GGGGGGAATCGGTTCCCTC
1 GGGGGGAATCGGTACCCTC
4344125 CGAGCATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.26, G:0.41, T:0.21
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCTCT
Found at i:4345085 original size:225 final size:223
Alignment explanation
Indices: 4344692--4345118 Score: 617
Period size: 225 Copynumber: 1.9 Consensus size: 223
4344682 GACTATATGG
* * * *
4344692 TGTTACTTTGTTGAGTCCCTCGACTATTTAAAGTTACAAAATTGTTACTGACTATTTATTATGTT
1 TGTTACTTTATTGAGTCCCTCGACTATTTAAAATTACAAAATGGTTACTGACTATTCATTATGTT
* * * * *
4344757 TCAAACTCATTTTTTTTATTAAAAGATTAACGATAATATGAGTTGGATGTTAATCTATTGTCTGA
66 TCAAACTCATTTTTTCTATTAAAAGATCAACGACAATATGAGTTAGATGTTAATCTACTGTCTGA
* * * *
4344822 GATATTATAGTCGTTTGAGATTCTAGTATCAAATTTTATCATAACTCAGAGAAAATATTAACATT
131 GATATGATAGCCGTTTGAGATTCTAGAATCAAATTTTATCATAACTCAGAGAAAATATTAACAAT
4344887 CAGCTCATATTACCGTCAATTTTTTGAA
196 CAGCTCATATTACCGTCAATTTTTTGAA
* *
4344915 TGTTACTTTATTGAGTCCAC-CGACTGTTTAAAATTATAAAATGGTTACATGACTATTCATTATG
1 TGTTACTTTATTGAGTCC-CTCGACTATTTAAAATTACAAAATGGTTAC-TGACTATTCATTATG
*
4344979 TTTCAAACTCGTCTTTTTCTATTAAAAGATCAACGACAATCA-GAGTTAGATGTTAATCTACTGT
64 TTTCAAACTCAT-TTTTTCTATTAAAAGATCAACGACAAT-ATGAGTTAGATGTTAATCTACTGT
* * *
4345043 TTGAGATATGATAGCCGTTTGAGATTCT-GAAATTAGATTTTATCATAACTCAGAGAAAATATTA
127 CTGAGATATGATAGCCGTTTGAGATTCTAG-AATCAAATTTTATCATAACTCAGAGAAAATATTA
4345107 ACAATCAGCTCA
191 ACAATCAGCTCA
4345119 GACTGTCGTA
Statistics
Matches: 180, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
223 41 0.23
224 27 0.15
225 111 0.62
226 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (223 bp):
TGTTACTTTATTGAGTCCCTCGACTATTTAAAATTACAAAATGGTTACTGACTATTCATTATGTT
TCAAACTCATTTTTTCTATTAAAAGATCAACGACAATATGAGTTAGATGTTAATCTACTGTCTGA
GATATGATAGCCGTTTGAGATTCTAGAATCAAATTTTATCATAACTCAGAGAAAATATTAACAAT
CAGCTCATATTACCGTCAATTTTTTGAA
Found at i:4352044 original size:23 final size:23
Alignment explanation
Indices: 4352013--4352057 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
4352003 AAATGATAAA
4352013 CGAACATAAACGAACAAAACAAG
1 CGAACATAAACGAACAAAACAAG
* *
4352036 CGAATATAAACGAACAACACAA
1 CGAACATAAACGAACAAAACAA
4352058 ACACAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.60, C:0.22, G:0.11, T:0.07
Consensus pattern (23 bp):
CGAACATAAACGAACAAAACAAG
Found at i:4361600 original size:10 final size:10
Alignment explanation
Indices: 4361585--4361614 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
4361575 ATATGGTTTT
4361585 ATGTCTTCAA
1 ATGTCTTCAA
4361595 ATGTCTTCAA
1 ATGTCTTCAA
*
4361605 ATCTCTTCAA
1 ATGTCTTCAA
4361615 GAACAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (10 bp):
ATGTCTTCAA
Found at i:4361649 original size:23 final size:25
Alignment explanation
Indices: 4361623--4361678 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
4361613 AAGAACAATT
* *
4361623 ATAAAATATGGTTATTTATTAAAATA
1 ATAAAATAAGGTTATTTATTATAA-A
**
4361649 ATTTAATAAGGTTATTTATTATAAA
1 ATAAAATAAGGTTATTTATTATAAA
4361674 ATAAA
1 ATAAA
4361679 TTATTTTAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (25 bp):
ATAAAATAAGGTTATTTATTATAAA
Found at i:4361682 original size:15 final size:15
Alignment explanation
Indices: 4361664--4361706 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
4361654 ATAAGGTTAT
4361664 TTATTATAAAATAAA
1 TTATTATAAAATAAA
*
4361679 TTATTTTAAAATAAA
1 TTATTATAAAATAAA
4361694 TTATTATAAAATA
1 TTATTATAAAATA
4361707 TGGATTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATTATAAAATAAA
Found at i:4361734 original size:15 final size:14
Alignment explanation
Indices: 4361714--4361749 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
4361704 ATATGGATTG
4361714 ATTTATTTTAAAATA
1 ATTTATTTT-AAATA
4361729 ATTTATTTTAAATA
1 ATTTATTTTAAATA
4361743 ATTTATT
1 ATTTATT
4361750 AGTATAGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:4361743 original size:14 final size:15
Alignment explanation
Indices: 4361662--4361749 Score: 70
Period size: 15 Copynumber: 5.5 Consensus size: 15
4361652 TAATAAGGTT
*
4361662 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
4361677 AATTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
4361692 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
4361711 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
4361729 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
4361743 ATTTATT
1 ATTTATT
4361750 AGTATAGATT
Statistics
Matches: 61, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
14 12 0.20
15 29 0.48
16 4 0.07
17 2 0.03
18 1 0.02
19 1 0.02
20 2 0.03
21 4 0.07
22 6 0.10
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:4361767 original size:32 final size:32
Alignment explanation
Indices: 4361729--4361881 Score: 164
Period size: 32 Copynumber: 5.4 Consensus size: 32
4361719 TTTTAAAATA
4361729 ATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
4361761 ATTTA--TT--ATAA---A--A-TATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
4361783 ATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
*
4361815 ATTTATTTT---TAA---A--A-TATAAATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
4361838 ATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTG
4361870 ATTTATTTTAAA
1 ATTTATTTTAAA
4361882 ATATGAATTT
Statistics
Matches: 100, Mismatches: 2, Indels: 38
0.71 0.01 0.27
Matches are distributed among these distances:
22 14 0.14
23 18 0.18
24 3 0.03
25 1 0.01
26 8 0.08
28 4 0.04
29 5 0.05
30 2 0.02
31 2 0.02
32 43 0.43
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATAGATTG
Found at i:4361777 original size:22 final size:22
Alignment explanation
Indices: 4361752--4361794 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
4361742 AATTTATTAG
4361752 TATAGATTGATTTATTATAAAA
1 TATAGATTGATTTATTATAAAA
*
4361774 TATAGATTGATTTATTTTAAA
1 TATAGATTGATTTATTATAAA
4361795 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (22 bp):
TATAGATTGATTTATTATAAAA
Found at i:4361853 original size:55 final size:54
Alignment explanation
Indices: 4361729--4361898 Score: 295
Period size: 54 Copynumber: 3.1 Consensus size: 54
4361719 TTTTAAAATA
* *
4361729 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTATAAAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAAATTG
4361783 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTTAAAATATAAATTG
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTA-TTTTAAAATATAAATTG
* *
4361838 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGAATTT
1 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAAATTG
4361892 ATTTATT
1 ATTTATT
4361899 ATTGTAGTTG
Statistics
Matches: 111, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
54 59 0.53
55 52 0.47
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAAATTG
Found at i:4361950 original size:80 final size:80
Alignment explanation
Indices: 4361829--4361978 Score: 257
Period size: 80 Copynumber: 1.9 Consensus size: 80
4361819 ATTTTTAAAA
* *
4361829 TATAAATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATAT-GAATTTA
1 TATAAATTAATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAG-ATTGA
4361893 TTTATTATTGTAGTTG
65 TTTATTATTGTAGTTG
*
4361909 TATAGATTAATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGAT
1 TATAAATTAATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGAT
4361974 TTATT
66 TTATT
4361979 TTAAATAATT
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
80 65 0.98
81 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (80 bp):
TATAAATTAATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGAT
TTATTATTGTAGTTG
Found at i:4361957 original size:22 final size:22
Alignment explanation
Indices: 4361941--4361983 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
4361931 AATTTATTAG
4361941 TATAGATTGATTTATTTTAAAA
1 TATAGATTGATTTATTTTAAAA
4361963 TATAGATTGATTTATTTTAAA
1 TATAGATTGATTTATTTTAAA
4361984 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TATAGATTGATTTATTTTAAAA
Found at i:4362043 original size:31 final size:31
Alignment explanation
Indices: 4362008--4362066 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
4361998 AGTTGTATGG
*
4362008 ATTATTTAAAT-TTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTT-AGTATTGCAAAACTAAA
4362039 ATTATTTAAATCTTAGTATTGCAAAACT
1 ATTATTTAAATCTTAGTATTGCAAAACT
4362067 GTTTTAAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATCTTAGTATTGCAAAACTAAA
Found at i:4363602 original size:14 final size:14
Alignment explanation
Indices: 4363580--4363631 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
4363570 GATTTTGTTT
*
4363580 TTACGTAAAATGAA
1 TTACCTAAAATGAA
* **
4363594 TTACCTAAATTGTT
1 TTACCTAAAATGAA
**
4363608 TTAAGTAAAATGAA
1 TTACCTAAAATGAA
4363622 TTACCTAAAA
1 TTACCTAAAA
4363632 CTATTTTACG
Statistics
Matches: 27, Mismatches: 11, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.35
Consensus pattern (14 bp):
TTACCTAAAATGAA
Found at i:4363618 original size:28 final size:29
Alignment explanation
Indices: 4363549--4363650 Score: 125
Period size: 29 Copynumber: 3.5 Consensus size: 29
4363539 TGAAAAATAA
* * **
4363549 TTTACGTAAAATAAATTACCTGATTTTGTT
1 TTTACGTAAAATGAATTACCTAAAATTG-T
4363579 TTTACGTAAAATGAATTACCT-AAATTGT
1 TTTACGTAAAATGAATTACCTAAAATTGT
* * *
4363607 TTTAAGTAAAATGAATTACCTAAAACTAT
1 TTTACGTAAAATGAATTACCTAAAATTGT
4363636 TTTACGTAAAATGAA
1 TTTACGTAAAATGAA
4363651 CAAGAAATAG
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
28 21 0.33
29 23 0.36
30 20 0.31
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (29 bp):
TTTACGTAAAATGAATTACCTAAAATTGT
Found at i:4363648 original size:29 final size:28
Alignment explanation
Indices: 4363578--4363650 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
4363568 CTGATTTTGT
* *
4363578 TTTTACGTAAAATGAATTACCTAAATTG
1 TTTTACGTAAAATGAATTACCTAAACTA
*
4363606 TTTTAAGTAAAATGAATTACCTAAAACTA
1 TTTTACGTAAAATGAATTACCT-AAACTA
4363635 TTTTACGTAAAATGAA
1 TTTTACGTAAAATGAA
4363651 CAAGAAATAG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 21 0.52
29 19 0.47
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (28 bp):
TTTTACGTAAAATGAATTACCTAAACTA
Found at i:4364047 original size:11 final size:12
Alignment explanation
Indices: 4363983--4364076 Score: 58
Period size: 11 Copynumber: 8.1 Consensus size: 12
4363973 TTATTATTAC
*
4363983 TTATTATTAATA
1 TTATTAATAATA
4363995 TT-TTAATAATA
1 TTATTAATAATA
*
4364006 TTATTATTAACTA
1 TTATTAATAA-TA
*
4364019 TTAATAGATAA-A
1 TTATTA-ATAATA
4364031 -TATTAATAAT-
1 TTATTAATAATA
*
4364041 TTATTAAAAAT-
1 TTATTAATAATA
*
4364052 TTAAT-ATCATATA
1 TTATTAAT-A-ATA
4364065 TTATT-ATAATA
1 TTATTAATAATA
4364076 T
1 T
4364077 ATCTGAGTAT
Statistics
Matches: 65, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
10 5 0.08
11 32 0.49
12 12 0.18
13 13 0.20
14 3 0.05
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (12 bp):
TTATTAATAATA
Found at i:4364115 original size:19 final size:18
Alignment explanation
Indices: 4364091--4364134 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
4364081 GAGTATTGAT
4364091 TAATATAATATTAAAAATA
1 TAATAT-ATATTAAAAATA
*
4364110 TAATAT-TATTAAAATTA
1 TAATATATATTAAAAATA
*
4364127 TATTATAT
1 TAATATAT
4364135 GTGTATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 15 0.68
18 1 0.05
19 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAATATATATTAAAAATA
Found at i:4364334 original size:18 final size:18
Alignment explanation
Indices: 4364311--4364345 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4364301 ACAAAGGAAC
*
4364311 TAGGAAAATGAATTACAT
1 TAGGAAAATCAATTACAT
4364329 TAGGAAAATCAATTACA
1 TAGGAAAATCAATTACA
4364346 ACTATCAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.09, G:0.14, T:0.26
Consensus pattern (18 bp):
TAGGAAAATCAATTACAT
Found at i:4364609 original size:30 final size:27
Alignment explanation
Indices: 4364552--4364609 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 27
4364542 CTCAAAACAT
**
4364552 TATTATTTTATATATTTAATATTAATA
1 TATTATTTTATATATTTAATAAAAATA
4364579 TATTATTTTAGTATCAATTTAATAAAAATA
1 TATTATTTTA-TAT--ATTTAATAAAAATA
4364609 T
1 T
4364610 TAATTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 3 0.12
30 13 0.50
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (27 bp):
TATTATTTTATATATTTAATAAAAATA
Found at i:4364698 original size:29 final size:29
Alignment explanation
Indices: 4364666--4364723 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
4364656 TATTTTATTG
4364666 TTATAATTATATTATT-ATAATATATAATA
1 TTATAATTATATT-TTAATAATATATAATA
* *
4364695 TTATACTTTTATTTTAATAATATATAATA
1 TTATAATTATATTTTAATAATATATAATA
4364724 AATTATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (29 bp):
TTATAATTATATTTTAATAATATATAATA
Found at i:4364749 original size:21 final size:22
Alignment explanation
Indices: 4364704--4364751 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
4364694 ATTATACTTT
*
4364704 TATT-TTAATAATATATAATAA
1 TATTATTAATAAAATATAATAA
*
4364725 -ATTATTAATAAAAT-TAGTAA
1 TATTATTAATAAAATATAATAA
4364745 TATTATT
1 TATTATT
4364752 GAAATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TATTATTAATAAAATATAATAA
Found at i:4364806 original size:26 final size:27
Alignment explanation
Indices: 4364759--4364826 Score: 68
Period size: 26 Copynumber: 2.5 Consensus size: 27
4364749 ATTGAAATTT
*
4364759 TAATATAATATATATTTCTTAA-AATA
1 TAATATAATATTTATTTCTTAATAATA
* *
4364785 TAATATAATATTTGTATT-TTAATATTA
1 TAATATAATATTTAT-TTCTTAATAATA
4364812 TAATTTATAATATTT
1 TAA--TATAATATTT
4364827 TAACAATATT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 17 0.49
27 8 0.23
29 10 0.29
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (27 bp):
TAATATAATATTTATTTCTTAATAATA
Found at i:4365036 original size:19 final size:18
Alignment explanation
Indices: 4365009--4365048 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
4364999 CAATATTAAA
*
4365009 TAAATTATTATAATATTTT
1 TAAAATATTATAAT-TTTT
*
4365028 TAAAATATTATTATTTTT
1 TAAAATATTATAATTTTT
4365046 TAA
1 TAA
4365049 TAAATAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TAAAATATTATAATTTTT
Found at i:4367965 original size:18 final size:17
Alignment explanation
Indices: 4367932--4367966 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
4367922 GTGTAATCAG
*
4367932 TAAATTTATGTAAATCT
1 TAAATTTATATAAATCT
4367949 TAAATTTATATATAATCT
1 TAAATTTATATA-AATCT
4367967 CAATTAGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (17 bp):
TAAATTTATATAAATCT
Found at i:4369632 original size:22 final size:21
Alignment explanation
Indices: 4369602--4369645 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
4369592 AAGTTGGACT
4369602 TAAGCTGGTATTAAAGTTTGCA
1 TAAGCTGGTATTAAAG-TTGCA
*
4369624 TAAGTTGGTATTAAAGTTGCA
1 TAAGCTGGTATTAAAGTTGCA
4369645 T
1 T
4369646 TATTATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.39
Consensus pattern (21 bp):
TAAGCTGGTATTAAAGTTGCA
Found at i:4370250 original size:18 final size:19
Alignment explanation
Indices: 4370198--4370251 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 19
4370188 CAAATACTCT
*
4370198 TATATTTTA-T-TATTAAGG
1 TATATTTTAGTATATTTA-G
*
4370216 TATATTTTATTATATTTAG
1 TATATTTTAGTATATTTAG
*
4370235 TATTTTTTAGTA-ATTTA
1 TATATTTTAGTATATTTA
4370252 TTTTATTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 14 0.45
19 12 0.39
20 5 0.16
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.61
Consensus pattern (19 bp):
TATATTTTAGTATATTTAG
Found at i:4370982 original size:2 final size:2
Alignment explanation
Indices: 4370973--4371001 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4370963 AAATTTTTTA
4370973 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4371002 TATTTTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:4371152 original size:29 final size:30
Alignment explanation
Indices: 4371083--4371157 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
4371073 CGTCCCCGTC
*
4371083 CCCCATCCCCGTTTAACATAAACAGTTTTT
1 CCCCGTCCCCGTTTAACATAAACAGTTTTT
* *
4371113 CCCCGTCCCCGTTTAGCATAAACATTTTTT
1 CCCCGTCCCCGTTTAACATAAACAGTTTTT
*
4371143 CTCCGT-CCCGTTTAA
1 CCCCGTCCCCGTTTAA
4371158 TTCGATTTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 8 0.20
30 32 0.80
ACGTcount: A:0.21, C:0.35, G:0.09, T:0.35
Consensus pattern (30 bp):
CCCCGTCCCCGTTTAACATAAACAGTTTTT
Done.