Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_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: 6984689
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 29
Found at i:4626634 original size:16 final size:16
Alignment explanation
Indices: 4626613--4626660 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
4626603 AAGTTTTTCA
4626613 TATTATTAATTAATAT
1 TATTATTAATTAATAT
4626629 TATTATTAATT-ATA-
1 TATTATTAATTAATAT
*
4626643 -ATTATTAATTATTAT
1 TATTATTAATTAATAT
4626658 TAT
1 TAT
4626661 AGATAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 10 0.36
14 2 0.07
15 3 0.11
16 13 0.46
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTATTAATTAATAT
Found at i:4628458 original size:19 final size:19
Alignment explanation
Indices: 4628434--4628470 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4628424 ATGACCAACA
*
4628434 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
4628453 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
4628471 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:4628561 original size:21 final size:21
Alignment explanation
Indices: 4628515--4628568 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
4628505 GATTTTGACT
*
4628515 ATCGCATTGCGATTTTCCAAA
1 ATCGCATTGCGATTTTACAAA
* * *
4628536 TTCGCGTTGCGATTTTAGAAA
1 ATCGCATTGCGATTTTACAAA
*
4628557 ATCGCAATGCGA
1 ATCGCATTGCGA
4628569 ATATGTAAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (21 bp):
ATCGCATTGCGATTTTACAAA
Found at i:4628620 original size:41 final size:41
Alignment explanation
Indices: 4628575--4628718 Score: 180
Period size: 41 Copynumber: 3.4 Consensus size: 41
4628565 GCGAATATGT
* *
4628575 AAATCACAACACGATTCTGACTATCGTAATGCAATAATACA
1 AAATCACAACACGATTCTGACTATCGCAATGCGATAATACA
* *
4628616 AAATCGCAACGCGATTCTGACTATCGCAATGCGATAATACA
1 AAATCACAACACGATTCTGACTATCGCAATGCGATAATACA
*
4628657 AAATCACAATGCAACGCGATTCTGACTATCGCAATGCGATAACACA
1 AAATCACAA--C-A--CGATTCTGACTATCGCAATGCGATAATACA
* *
4628703 AAATCGCAATACGATT
1 AAATCACAACACGATT
4628719 TTCCAAATTC
Statistics
Matches: 89, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
41 50 0.56
43 2 0.02
46 37 0.42
ACGTcount: A:0.40, C:0.24, G:0.14, T:0.22
Consensus pattern (41 bp):
AAATCACAACACGATTCTGACTATCGCAATGCGATAATACA
Found at i:4628688 original size:46 final size:45
Alignment explanation
Indices: 4628581--4628712 Score: 182
Period size: 46 Copynumber: 3.0 Consensus size: 45
4628571 ATGTAAATCA
* * *
4628581 CAACACGATTCTGACTATCGTAATGCAATAATACAAAAT-C---G
1 CAACGCGATTCTGACTATCGCAATGCGATAATACAAAATCCAATG
4628622 CAACGCGATTCTGACTATCGCAATGCGATAATACAAAATCACAATG
1 CAACGCGATTCTGACTATCGCAATGCGATAATACAAAATC-CAATG
*
4628668 CAACGCGATTCTGACTATCGCAATGCGATAACACAAAATCGCAAT
1 CAACGCGATTCTGACTATCGCAATGCGATAATACAAAATC-CAAT
4628713 ACGATTTTCC
Statistics
Matches: 81, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
41 36 0.44
43 1 0.01
46 44 0.54
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.22
Consensus pattern (45 bp):
CAACGCGATTCTGACTATCGCAATGCGATAATACAAAATCCAATG
Found at i:4628742 original size:19 final size:19
Alignment explanation
Indices: 4628720--4628769 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 19
4628710 AATACGATTT
*
4628720 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
4628739 TCCAAGTTCACGTTGCGATAG
1 TCCAAGTT--CGTTGCGATAG
4628760 TCCAAGTTCG
1 TCCAAGTTCG
4628770 CGTTACGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 9 0.32
21 19 0.68
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (19 bp):
TCCAAGTTCGTTGCGATAG
Found at i:4628754 original size:21 final size:21
Alignment explanation
Indices: 4628728--4628778 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
4628718 TTTCCAAATT
4628728 CGTTGCGATAGTCCAAGTTCA
1 CGTTGCGATAGTCCAAGTTCA
*
4628749 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCA
*
4628770 CGTTACGAT
1 CGTTGCGAT
4628779 TTTGGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCA
Found at i:4628952 original size:41 final size:41
Alignment explanation
Indices: 4628889--4628985 Score: 149
Period size: 41 Copynumber: 2.4 Consensus size: 41
4628879 CGACCTATGT
*
4628889 AAATCGCAACGCGATTCTGACTATCGTAACGCGATAATACA
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
* * *
4628930 GAATCACAACGCGATTCTGACTATCGCAATGCGATAATACA
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
*
4628971 AAATCGCAATGCGAT
1 AAATCGCAACGCGAT
4628986 AATACAAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.22
Consensus pattern (41 bp):
AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
Found at i:4629014 original size:21 final size:21
Alignment explanation
Indices: 4628952--4629006 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
4628942 GATTCTGACT
4628952 ATCGCAATGCGATAATACAAA
1 ATCGCAATGCGATAATACAAA
4628973 ATCGCAATGCGATAATACAAA
1 ATCGCAATGCGATAATACAAA
4628994 ATCGCAATGCGAT
1 ATCGCAATGCGAT
4629007 TTTCCAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (21 bp):
ATCGCAATGCGATAATACAAA
Found at i:4629025 original size:19 final size:20
Alignment explanation
Indices: 4629001--4629049 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
4628991 AAAATCGCAA
4629001 TGCGATTTTCCAAATT-CGT
1 TGCGATTTTCCAAATTCCGT
** *
4629020 TGCGATAGTCCAAGTTCGCGT
1 TGCGATTTTCCAAATTC-CGT
4629041 TGCGATTTT
1 TGCGATTTT
4629050 GGAAATTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 13 0.57
21 10 0.43
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.39
Consensus pattern (20 bp):
TGCGATTTTCCAAATTCCGT
Found at i:4629098 original size:268 final size:270
Alignment explanation
Indices: 4628616--4629151 Score: 837
Period size: 268 Copynumber: 2.0 Consensus size: 270
4628606 CAATAATACA
*
4628616 AAATCGCAACGCGATTCTGACTATCGCAATGCGATAATACAAAATCACAATGCAACGCGATTCTG
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAAAT-ACAA-GCAACGCGATTCTG
** * * * *
4628681 ACTATCGCAATGCGATAACACAAAATCGCAATACGATTTTCCAAATTCGTTGCGATAGTCCAAGT
64 ACTATCGCAATGCGATAACACAAAATCGCAATACGATAATACAAAATCGATGCGATAGTCCAAAT
*
4628746 TCACGTTGCGATAGTCCAAGTTCGCGTTACGATTTTGGAAAATCGCAACGACTGGTGGTATTGCA
129 T-ACGTTGCGATAGTCCAAGTTCGCGTTACGATTTTGGAAAATCACAACGACTGGTGGTATTGCA
*
4628811 TTTGTTTCTTAAGAAATTTCTCTAAAAAGATAGTATCCGCGCGGACGTGTCGAAGACACGTATTA
193 TTTGTTTCTTAAGAAATTTCTCTAAAAAGATAGTATCCGCACGGACGTGTCGAAGACACGTATTA
4628876 CCACGACCTATGT
258 CCACGACCTATGT
* *
4628889 AAATCGCAACGCGATTCTGACTATCGTAACGCGATAATACAGAAT-C-A-CAACGCGATTCTGAC
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAAATACAAGCAACGCGATTCTGAC
* * **
4628951 TATCGCAATGCGATAATACAAAATCGCAATGCGATAATACAAAATCGCAATGCGATTTTCCAAAT
66 TATCGCAATGCGATAACACAAAATCGCAATACGATAATACAAAATCG--ATGCGATAGTCCAAAT
* *
4629016 T-CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTGGAAATTCACAACGACTGGTGGTATTGCAT
129 TACGTTGCGATAGTCCAAGTTCGCGTTACGATTTTGGAAAATCACAACGACTGGTGGTATTGCAT
4629080 TTGTTTCTTAAGAAATTTCTCTAAAAAGATAGTATCCGCACGGACGTGTCGAAGACACGTATTAC
194 TTGTTTCTTAAGAAATTTCTCTAAAAAGATAGTATCCGCACGGACGTGTCGAAGACACGTATTAC
*
4629145 CATGACC
259 CACGACC
4629152 ACGACCCGAG
Statistics
Matches: 243, Mismatches: 18, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
268 186 0.77
270 14 0.06
271 1 0.00
273 42 0.17
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (270 bp):
AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAAATACAAGCAACGCGATTCTGAC
TATCGCAATGCGATAACACAAAATCGCAATACGATAATACAAAATCGATGCGATAGTCCAAATTA
CGTTGCGATAGTCCAAGTTCGCGTTACGATTTTGGAAAATCACAACGACTGGTGGTATTGCATTT
GTTTCTTAAGAAATTTCTCTAAAAAGATAGTATCCGCACGGACGTGTCGAAGACACGTATTACCA
CGACCTATGT
Found at i:4629474 original size:19 final size:20
Alignment explanation
Indices: 4629449--4629539 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 20
4629439 CTTATTTTGG
4629449 ATTTTTCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
4629469 -TTTTTCACTATCGCAACAAC
1 ATTTTTCACTATCGCAAC-AC
*
4629489 AAGTTTTTCAAACTCTCGCAACAC
1 -A-TTTTTC--ACTATCGCAACAC
*
4629513 A-TTTTAACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
4629532 ATTTTTCA
1 ATTTTTCA
4629540 AAATCGCGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
19 30 0.50
20 7 0.12
21 4 0.07
23 7 0.12
24 2 0.03
25 10 0.17
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.35
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:4629511 original size:44 final size:41
Alignment explanation
Indices: 4629460--4629541 Score: 119
Period size: 44 Copynumber: 1.9 Consensus size: 41
4629450 TTTTTCACTA
* *
4629460 TCGCAACACTTTTTCACTATCGCAACAACAAGTTTTTCAAACTC
1 TCGCAACACATTTTAACTATCGCAAC-AC-A-TTTTTCAAACTC
4629504 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
1 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
4629542 ATCGCGTTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 9 0.25
42 1 0.03
43 2 0.06
44 24 0.67
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.32
Consensus pattern (41 bp):
TCGCAACACATTTTAACTATCGCAACACATTTTTCAAACTC
Found at i:4632126 original size:2 final size:2
Alignment explanation
Indices: 4632119--4632145 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4632109 TCAATCTACA
4632119 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4632146 ATTTACGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4632235 original size:13 final size:13
Alignment explanation
Indices: 4632217--4632257 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
4632207 AATGACACGC
*
4632217 AATGTAAGTCGTA
1 AATGTAAGTCATA
4632230 AATGTAAGTCATA
1 AATGTAAGTCATA
* *
4632243 AATGCATGTCATA
1 AATGTAAGTCATA
4632256 AA
1 AA
4632258 CTTATGACAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (13 bp):
AATGTAAGTCATA
Found at i:4642629 original size:11 final size:11
Alignment explanation
Indices: 4642598--4642643 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 11
4642588 ATTACACCTG
*
4642598 AATAAAAGGAA
1 AATAAAAGAAA
*
4642609 AA-AGAAGAAA
1 AATAAAAGAAA
4642619 AATAAAAGAAA
1 AATAAAAGAAA
*
4642630 AATAAGA-AAA
1 AATAAAAGAAA
4642640 AATA
1 AATA
4642644 GAAAAACAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
10 15 0.50
11 15 0.50
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (11 bp):
AATAAAAGAAA
Found at i:4642643 original size:21 final size:21
Alignment explanation
Indices: 4642598--4642640 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
4642588 ATTACACCTG
4642598 AATAAAAGGAAAAAGAAGAAA
1 AATAAAAGGAAAAAGAAGAAA
*
4642619 AATAAAA-GAAAAATAAGAAA
1 AATAAAAGGAAAAAGAAGAAA
4642639 AA
1 AA
4642641 ATAGAAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (21 bp):
AATAAAAGGAAAAAGAAGAAA
Found at i:4642656 original size:16 final size:14
Alignment explanation
Indices: 4642601--4642705 Score: 68
Period size: 17 Copynumber: 6.8 Consensus size: 14
4642591 ACACCTGAAT
*
4642601 AAAAGGAAAAAGAA
1 AAAAGAAAAAAGAA
*
4642615 GAAAA-ATAAAAGAAA
1 -AAAAGAAAAAAG-AA
4642630 AATAAGAAAAAATAGAA
1 AA-AAG-AAAAA-AGAA
4642647 AAACAGAAAAACAGAAA
1 AAA-AGAAAAA-AG-AA
4642664 AAAGAGAAAAAAGAGA
1 AAA-AGAAAAAAGA-A
* *
4642680 AGAGAGAAAAAAGGA
1 A-AAAGAAAAAAGAA
4642695 AAAAGAAAAAA
1 AAAAGAAAAAA
4642706 ATGAAAAATG
Statistics
Matches: 73, Mismatches: 8, Indels: 19
0.73 0.08 0.19
Matches are distributed among these distances:
14 16 0.22
15 11 0.15
16 21 0.29
17 23 0.32
18 2 0.03
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (14 bp):
AAAAGAAAAAAGAA
Found at i:4642662 original size:25 final size:24
Alignment explanation
Indices: 4642622--4642713 Score: 98
Period size: 25 Copynumber: 3.8 Consensus size: 24
4642612 GAAGAAAAAT
*
4642622 AAAAGAAAAATAAGAAAAAATAGAA
1 AAAAGAAAAA-AAGAAAAAAGAGAA
*
4642647 AAACAGAAAAACAGAAAAAAGAGAA
1 AAA-AGAAAAAAAGAAAAAAGAGAA
* *
4642672 AAAAGAGAAGAGAGAAAAAAG-G-A
1 AAAAGA-AAAAAAGAAAAAAGAGAA
4642695 AAAAGAAAAAAATGAAAAA
1 AAAAGAAAAAAA-GAAAAA
4642714 TGAATAAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
22 4 0.07
23 13 0.22
24 4 0.07
25 30 0.52
26 7 0.12
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.03
Consensus pattern (24 bp):
AAAAGAAAAAAAGAAAAAAGAGAA
Found at i:4642705 original size:7 final size:7
Alignment explanation
Indices: 4642601--4642705 Score: 68
Period size: 8 Copynumber: 13.6 Consensus size: 7
4642591 ACACCTGAAT
*
4642601 AAAAGGA
1 AAAAGAA
4642608 AAAAGAA
1 AAAAGAA
*
4642615 GAAAA-AT
1 -AAAAGAA
4642622 AAAAGAAA
1 AAAAG-AA
4642630 AATAAGAAA
1 AA-AAG-AA
4642639 AAATAGAA
1 AAA-AGAA
4642647 AAACAGAA
1 AAA-AGAA
4642655 AAACAGAAA
1 AAA-AG-AA
4642664 AAAGAGAA
1 AAA-AGAA
4642672 AAAAGAGA
1 AAAAGA-A
*
4642680 AGAGAGAA
1 A-AAAGAA
*
4642688 AAAAGGA
1 AAAAGAA
4642695 AAAAGAA
1 AAAAGAA
4642702 AAAA
1 AAAA
4642706 ATGAAAAATG
Statistics
Matches: 81, Mismatches: 9, Indels: 16
0.76 0.08 0.15
Matches are distributed among these distances:
6 4 0.05
7 24 0.30
8 32 0.40
9 21 0.26
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (7 bp):
AAAAGAA
Found at i:4642706 original size:16 final size:16
Alignment explanation
Indices: 4642613--4642725 Score: 59
Period size: 16 Copynumber: 6.8 Consensus size: 16
4642603 AAGGAAAAAG
*
4642613 AAGAAAAATAAAAGAAA
1 AAGAAAAA-AAAGGAAA
* *
4642630 AATAAGAAAAAATAGAAA
1 AAGAA-AAAAAA-GGAAA
* * *
4642648 AACAGAAAAACAGAAAA
1 AAGA-AAAAAAAGGAAA
*
4642665 AAGAGAAAAAA-GAGAA
1 AAGAAAAAAAAGGA-AA
* *
4642681 GAGAGAAAAAAGGAAA
1 AAGAAAAAAAAGGAAA
*
4642697 AAG-AAAAAAATGAAA
1 AAGAAAAAAAAGGAAA
*
4642712 AATGAATAAAAAGG
1 AA-GAAAAAAAAGG
4642726 GGTTCAAGAT
Statistics
Matches: 74, Mismatches: 15, Indels: 14
0.72 0.15 0.14
Matches are distributed among these distances:
15 13 0.18
16 22 0.30
17 22 0.30
18 16 0.22
19 1 0.01
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.05
Consensus pattern (16 bp):
AAGAAAAAAAAGGAAA
Found at i:4642711 original size:9 final size:8
Alignment explanation
Indices: 4642622--4642713 Score: 73
Period size: 9 Copynumber: 11.2 Consensus size: 8
4642612 GAAGAAAAAT
4642622 AAAAGAAA
1 AAAAGAAA
4642630 AATAAGAAA
1 AA-AAGAAA
4642639 AAATAGAAA
1 AAA-AGAAA
*
4642648 AACAGAAA
1 AAAAGAAA
*
4642656 AACAG-AA
1 AAAAGAAA
4642663 AAAAGAGAA
1 AAAAGA-AA
*
4642672 AAAAG-AG
1 AAAAGAAA
*
4642679 AAGAGAGAA
1 AAAAGA-AA
*
4642688 AAAAG-GA
1 AAAAGAAA
4642695 AAAAGAAA
1 AAAAGAAA
4642703 AAAATGAAA
1 AAAA-GAAA
4642712 AA
1 AA
4642714 TGAATAAAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
7 17 0.25
8 18 0.26
9 33 0.49
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.03
Consensus pattern (8 bp):
AAAAGAAA
Found at i:4645131 original size:15 final size:15
Alignment explanation
Indices: 4645095--4645137 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
4645085 GAGTGACACT
4645095 AGTTACCTAGCT-CA
1 AGTTACCTAGCTACA
* *
4645109 GGTCTACCCAGCTACA
1 AGT-TACCTAGCTACA
4645125 AGTTACCTAGCTA
1 AGTTACCTAGCTA
4645138 GCTATATATG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 2 0.09
15 17 0.74
16 4 0.17
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (15 bp):
AGTTACCTAGCTACA
Found at i:4646546 original size:2 final size:2
Alignment explanation
Indices: 4646484--4646528 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
4646474 TGGGTTATTA
4646484 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4646526 AT A
1 AT A
4646529 CATACATACA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4646547 original size:10 final size:10
Alignment explanation
Indices: 4646484--4646555 Score: 67
Period size: 10 Copynumber: 7.4 Consensus size: 10
4646474 TGGGTTATTA
*
4646484 ATATATATAT
1 ATATACATAT
*
4646494 ATATATATAT
1 ATATACATAT
*
4646504 ATATATATAT
1 ATATACATAT
*
4646514 ATATATATAT
1 ATATACATAT
4646524 ATATAC--AT
1 ATATACATAT
* *
4646532 ACATACATGT
1 ATATACATAT
*
4646542 ATATACATAA
1 ATATACATAT
4646552 ATAT
1 ATAT
4646556 TAAATAATTA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
8 7 0.13
10 47 0.87
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (10 bp):
ATATACATAT
Found at i:4648436 original size:25 final size:26
Alignment explanation
Indices: 4648385--4648436 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
4648375 CCTAGTACGA
*
4648385 TGCTTATGGTTTTATTTTGTTTCTAT
1 TGCTTATGGTTTTATTTTATTTCTAT
* *
4648411 TGCTTGTGG-TTTATTTTATTTTTAT
1 TGCTTATGGTTTTATTTTATTTCTAT
4648436 T
1 T
4648437 TTAATCCTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.12, C:0.06, G:0.15, T:0.67
Consensus pattern (26 bp):
TGCTTATGGTTTTATTTTATTTCTAT
Found at i:4650289 original size:27 final size:27
Alignment explanation
Indices: 4650259--4650332 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
4650249 TAGATGAAAG
* * *
4650259 AAAAGGACTAAAATACCCTTGAATTGT
1 AAAATGACTAAAATACCCCTGAAGTGT
4650286 AAAATGACTAAAATACCCCTGAAGTGT
1 AAAATGACTAAAATACCCCTGAAGTGT
*
4650313 AAAATAACCTAAAATACCCC
1 AAAATGA-CTAAAATACCCC
4650333 AAGCCTTGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 30 0.71
28 12 0.29
ACGTcount: A:0.47, C:0.20, G:0.11, T:0.22
Consensus pattern (27 bp):
AAAATGACTAAAATACCCCTGAAGTGT
Found at i:4651631 original size:22 final size:22
Alignment explanation
Indices: 4651603--4651645 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
4651593 ATGTAGTTTT
4651603 AGGGAACTGCATATTGGTGTTC
1 AGGGAACTGCATATTGGTGTTC
4651625 AGGGAACTGCATATTGGTGTT
1 AGGGAACTGCATATTGGTGTT
4651646 TGGTTGGAGG
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:0.23, C:0.12, G:0.33, T:0.33
Consensus pattern (22 bp):
AGGGAACTGCATATTGGTGTTC
Found at i:4654271 original size:25 final size:25
Alignment explanation
Indices: 4654242--4654293 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
4654232 TATCTCCCGA
4654242 TTCAATACGAATTTTCATGTTTAAG
1 TTCAATACGAATTTTCATGTTTAAG
4654267 TTCAATACGAATTTTCATGTTTAAG
1 TTCAATACGAATTTTCATGTTTAAG
4654292 TT
1 TT
4654294 ATGTCTAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (25 bp):
TTCAATACGAATTTTCATGTTTAAG
Found at i:4655037 original size:27 final size:28
Alignment explanation
Indices: 4655005--4655069 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 28
4654995 AAAGAAAGGA
*
4655005 CTAAAATACCATTGAACTGTAAAATAAC
1 CTAAAATACCACTGAACTGTAAAATAAC
* * *
4655033 C-AAAATACCCCTGAAGTGTGAAATAAC
1 CTAAAATACCACTGAACTGTAAAATAAC
4655060 CTAAAATACC
1 CTAAAATACC
4655070 CCCAAGCCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 23 0.72
28 9 0.28
ACGTcount: A:0.48, C:0.22, G:0.09, T:0.22
Consensus pattern (28 bp):
CTAAAATACCACTGAACTGTAAAATAAC
Found at i:4656201 original size:32 final size:32
Alignment explanation
Indices: 4656155--4656240 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 32
4656145 CCTATGGTGA
* * *
4656155 CCTTAGGTAGGCTCTTAGGCCCCAACGCATTT
1 CCTTGGGTAGGCTCTTAGGCCCCAAAGCACTT
* *
4656187 CCTTGGGTAGGCTCTAAGGCCCCAAAGTACTT
1 CCTTGGGTAGGCTCTTAGGCCCCAAAGCACTT
*
4656219 -ATATGGGTAGGCTCTTAGGCCC
1 CCT-TGGGTAGGCTCTTAGGCCC
4656241 TATGGTACTC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
31 1 0.02
32 45 0.98
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.27
Consensus pattern (32 bp):
CCTTGGGTAGGCTCTTAGGCCCCAAAGCACTT
Found at i:4660599 original size:36 final size:35
Alignment explanation
Indices: 4660559--4660668 Score: 102
Period size: 36 Copynumber: 3.1 Consensus size: 35
4660549 ATACATATAT
*
4660559 TTTTTAAATATTTTAAATTAAAATATATTGATTATC
1 TTTTTAAATATATTAAATTAAAATATATT-ATTATC
4660595 TTTTTAAATGTAAATATT-AA-TAAAATA-ATTA-TATC
1 TTTTTAAA--T--ATATTAAATTAAAATATATTATTATC
* * *
4660630 TTTTTAAATATCTCAAATTAAAAGATATTTATTATC
1 TTTTTAAATATATTAAATTAAAATATA-TTATTATC
4660666 TTT
1 TTT
4660669 CAAAATTTGA
Statistics
Matches: 61, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
31 3 0.05
32 2 0.03
33 7 0.11
34 1 0.02
35 15 0.25
36 16 0.26
37 3 0.05
38 8 0.13
39 2 0.03
40 4 0.07
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.50
Consensus pattern (35 bp):
TTTTTAAATATATTAAATTAAAATATATTATTATC
Found at i:4660699 original size:71 final size:70
Alignment explanation
Indices: 4660554--4660728 Score: 199
Period size: 71 Copynumber: 2.5 Consensus size: 70
4660544 ACTAAATACA
* * ** * *
4660554 TATATTTTTTAAATATTTTAAATTAAAATATATTGATTATCTTTTTAAATGTAAATATTAATAAA
1 TATATTTTTTAAATATTTCAAATTAAAAAATATTGATTATCTTTCAAAATGTAAATAATAACAAA
4660619 ATAAT
66 ATAAT
* * * * *
4660624 TATATCTTTTTAAATATCTCAAATTAAAAGATATTTATTATCTTTCAAAATTTGAATAATAACAA
1 TATAT-TTTTTAAATATTTCAAATTAAAAAATATTGATTATCTTTCAAAATGTAAATAATAACAA
*
4660689 GAT-AT
65 AATAAT
* *
4660694 CTATATATTTTAAATATTTCATATTAAAAAATATT
1 -TATATTTTTTAAATATTTCAAATTAAAAAATATT
4660729 ATCTATTCAA
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
70 32 0.36
71 56 0.64
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (70 bp):
TATATTTTTTAAATATTTCAAATTAAAAAATATTGATTATCTTTCAAAATGTAAATAATAACAAA
ATAAT
Found at i:4672386 original size:10 final size:10
Alignment explanation
Indices: 4672367--4672400 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
4672357 AAGTATGATT
4672367 AATGCAACTA
1 AATGCAACTA
4672377 AATG-AGACTA
1 AATGCA-ACTA
4672387 AATGCAACTA
1 AATGCAACTA
4672397 AATG
1 AATG
4672401 GGCTTTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 1 0.05
10 20 0.91
11 1 0.05
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.21
Consensus pattern (10 bp):
AATGCAACTA
Found at i:4675282 original size:16 final size:16
Alignment explanation
Indices: 4675261--4675294 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
4675251 TGATCACTGG
4675261 TTATCAT-ATATGATAT
1 TTATCATGA-ATGATAT
4675277 TTATCATGAATGATAT
1 TTATCATGAATGATAT
4675293 TT
1 TT
4675295 TGGGTATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 16 0.94
17 1 0.06
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (16 bp):
TTATCATGAATGATAT
Found at i:4678613 original size:21 final size:21
Alignment explanation
Indices: 4678589--4678637 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
4678579 ATGAAGCAAG
4678589 GGAAGCAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* ** *
4678610 GGAAGTAGCTAGAGCAGTAGC
1 GGAAGCAGAGAGAGCAGCAGC
4678631 GGAAGCA
1 GGAAGCA
4678638 AAGAAAAAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.37, C:0.16, G:0.41, T:0.06
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:4678652 original size:21 final size:21
Alignment explanation
Indices: 4678628--4678672 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4678618 CTAGAGCAGT
4678628 AGCGGAAGCAAAGAAAAAAGC
1 AGCGGAAGCAAAGAAAAAAGC
* * * *
4678649 AGCGGTAGCACAGACAGAAGC
1 AGCGGAAGCAAAGAAAAAAGC
4678670 AGC
1 AGC
4678673 ATATCAGCAT
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:0.47, C:0.20, G:0.31, T:0.02
Consensus pattern (21 bp):
AGCGGAAGCAAAGAAAAAAGC
Found at i:4679339 original size:31 final size:31
Alignment explanation
Indices: 4679299--4679361 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
4679289 TTGTCATAAT
* *
4679299 GTCGTAGGTGTTTTTAGCGGTGCTTAAAAAC
1 GTCGCAGGTGTTTTTAGCGGCGCTTAAAAAC
4679330 GTCGCAGGTGTTTTTAGCGGCGCTTAAAAAC
1 GTCGCAGGTGTTTTTAGCGGCGCTTAAAAAC
4679361 G
1 G
4679362 CCGCTATACG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (31 bp):
GTCGCAGGTGTTTTTAGCGGCGCTTAAAAAC
Found at i:4683415 original size:25 final size:25
Alignment explanation
Indices: 4683387--4683480 Score: 80
Period size: 25 Copynumber: 3.4 Consensus size: 25
4683377 ATTTCCAAAG
4683387 CTAGTGGGATAACCAATATCCAATA
1 CTAGTGGGATAACCAATATCCAATA
* * *
4683412 CTAGTGGGATATTGAGTCATTACCAACAAAATA
1 CTAGTGGGATA---A-CCAATATC--C--AATA
*
4683445 CTAGTTGGATAACCAATATCCAATA
1 CTAGTGGGATAACCAATATCCAATA
4683470 CTAGTGGGATA
1 CTAGTGGGATA
4683481 TTGAGTCATT
Statistics
Matches: 53, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
25 25 0.47
27 1 0.02
28 1 0.02
29 10 0.19
30 1 0.02
31 1 0.02
33 14 0.26
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (25 bp):
CTAGTGGGATAACCAATATCCAATA
Found at i:4683445 original size:33 final size:32
Alignment explanation
Indices: 4683408--4683529 Score: 98
Period size: 33 Copynumber: 4.0 Consensus size: 32
4683398 ACCAATATCC
4683408 AATACTAGTGGGATATTGAGTCATTACCAACAA
1 AATACTAGTGGGATATTGAGTCATTACCAAC-A
* * * *
4683441 AATACTAGTTGGATA---A-CCAATATC--C-
1 AATACTAGTGGGATATTGAGTCATTACCAACA
4683466 AATACTAGTGGGATATTGAGTCATTACCAACA
1 AATACTAGTGGGATATTGAGTCATTACCAACA
** * *
4683498 TCTAATAAGTGGGATATTGAG-CATTATCAACA
1 AATACT-AGTGGGATATTGAGTCATTACCAACA
4683530 TTCCCCCACT
Statistics
Matches: 69, Mismatches: 12, Indels: 17
0.70 0.12 0.17
Matches are distributed among these distances:
25 14 0.20
27 1 0.01
28 1 0.01
29 10 0.14
30 1 0.01
31 1 0.01
32 13 0.19
33 28 0.41
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.29
Consensus pattern (32 bp):
AATACTAGTGGGATATTGAGTCATTACCAACA
Found at i:4683458 original size:58 final size:58
Alignment explanation
Indices: 4683387--4683497 Score: 213
Period size: 58 Copynumber: 1.9 Consensus size: 58
4683377 ATTTCCAAAG
4683387 CTAGTGGGATAACCAATATCCAATACTAGTGGGATATTGAGTCATTACCAACAAAATA
1 CTAGTGGGATAACCAATATCCAATACTAGTGGGATATTGAGTCATTACCAACAAAATA
*
4683445 CTAGTTGGATAACCAATATCCAATACTAGTGGGATATTGAGTCATTACCAACA
1 CTAGTGGGATAACCAATATCCAATACTAGTGGGATATTGAGTCATTACCAACA
4683498 TCTAATAAGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (58 bp):
CTAGTGGGATAACCAATATCCAATACTAGTGGGATATTGAGTCATTACCAACAAAATA
Found at i:4688887 original size:35 final size:35
Alignment explanation
Indices: 4688841--4688965 Score: 128
Period size: 35 Copynumber: 3.9 Consensus size: 35
4688831 TAGTGGGATA
*
4688841 ACCAATATCCAATACTAGTGGAATATTGAGTCATT
1 ACCAACATCCAATACTAGTGGAATATTGAGTCATT
4688876 ACCAACATCCAATACTAGTGG------GA-T-A--
1 ACCAACATCCAATACTAGTGGAATATTGAGTCATT
* *
4688901 ACCAATATCCAATACTAGTGGGATATTGAGTCATT
1 ACCAACATCCAATACTAGTGGAATATTGAGTCATT
*
4688936 ACCAACATCTAATACTAGT-GAGATATTGAG
1 ACCAACATCCAATACTAGTGGA-ATATTGAG
4688966 CTTTATCAAC
Statistics
Matches: 74, Mismatches: 5, Indels: 22
0.73 0.05 0.22
Matches are distributed among these distances:
25 20 0.27
27 1 0.01
28 1 0.01
29 2 0.03
31 2 0.03
32 1 0.01
33 1 0.01
34 1 0.01
35 45 0.61
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (35 bp):
ACCAACATCCAATACTAGTGGAATATTGAGTCATT
Found at i:4688898 original size:60 final size:60
Alignment explanation
Indices: 4688830--4688960 Score: 235
Period size: 60 Copynumber: 2.2 Consensus size: 60
4688820 ATTTCCAAAG
4688830 CTAGTGGGATAACCAATATCCAATACTAGTGGAATATTGAGTCATTACCAACATCCAATA
1 CTAGTGGGATAACCAATATCCAATACTAGTGGAATATTGAGTCATTACCAACATCCAATA
* *
4688890 CTAGTGGGATAACCAATATCCAATACTAGTGGGATATTGAGTCATTACCAACATCTAATA
1 CTAGTGGGATAACCAATATCCAATACTAGTGGAATATTGAGTCATTACCAACATCCAATA
*
4688950 CTAGTGAGATA
1 CTAGTGGGATA
4688961 TTGAGCTTTA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 68 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.27
Consensus pattern (60 bp):
CTAGTGGGATAACCAATATCCAATACTAGTGGAATATTGAGTCATTACCAACATCCAATA
Found at i:4688904 original size:25 final size:25
Alignment explanation
Indices: 4688876--4688925 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
4688866 TTGAGTCATT
4688876 ACCAACATCCAATACTAGTGGGATA
1 ACCAACATCCAATACTAGTGGGATA
*
4688901 ACCAATATCCAATACTAGTGGGATA
1 ACCAACATCCAATACTAGTGGGATA
4688926 TTGAGTCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (25 bp):
ACCAACATCCAATACTAGTGGGATA
Found at i:4698638 original size:25 final size:26
Alignment explanation
Indices: 4698590--4698645 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
4698580 AAAATCTTAT
*
4698590 TTTAATTATTTCAAAATTTAATATTC
1 TTTAATTATTTCAAAATTAAATATTC
**
4698616 TTTAATTATTT-TTAATTAAATATTC
1 TTTAATTATTTCAAAATTAAATATTC
*
4698641 ATTAA
1 TTTAA
4698646 AAGAGTTGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTAATTATTTCAAAATTAAATATTC
Found at i:4699693 original size:38 final size:38
Alignment explanation
Indices: 4699642--4699720 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
4699632 GGTTAATAAA
4699642 ATATGTCCATACAATCATCATATGGTTGGTCTTTGGAC
1 ATATGTCCATACAATCATCATATGGTTGGTCTTTGGAC
4699680 ATATGTCCATACAATCATCATATGGTTGGTCTTTGGAC
1 ATATGTCCATACAATCATCATATGGTTGGTCTTTGGAC
4699718 ATA
1 ATA
4699721 CTCTAAGAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (38 bp):
ATATGTCCATACAATCATCATATGGTTGGTCTTTGGAC
Found at i:4704274 original size:22 final size:22
Alignment explanation
Indices: 4704236--4704277 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4704226 TCTTAGTATT
*
4704236 GGATTAAATGGTAATTATGGAA
1 GGATTAAAGGGTAATTATGGAA
4704258 GGATTGAAAGGGT-ATTATGG
1 GGATT-AAAGGGTAATTATGG
4704278 TCTTTTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.31
Consensus pattern (22 bp):
GGATTAAAGGGTAATTATGGAA
Found at i:4712174 original size:22 final size:22
Alignment explanation
Indices: 4712136--4712177 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4712126 TCTTAGTATT
*
4712136 GGATTAAATGGTAATTATGGAA
1 GGATTAAAGGGTAATTATGGAA
4712158 GGATTGAAAGGGT-ATTATGG
1 GGATT-AAAGGGTAATTATGG
4712178 TCTTTTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.31
Consensus pattern (22 bp):
GGATTAAAGGGTAATTATGGAA
Found at i:4715835 original size:26 final size:26
Alignment explanation
Indices: 4715799--4715849 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
4715789 AATTAATTAA
*
4715799 AATCTTACTTTAATTAATTTAAAATTT
1 AATCTTACTTTAATT-ATTCAAAATTT
4715826 AATCTT-CTTTAATTATTCAAAATT
1 AATCTTACTTTAATTATTCAAAATT
4715850 AATTATTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.39
26 8 0.35
27 6 0.26
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (26 bp):
AATCTTACTTTAATTATTCAAAATTT
Found at i:4715862 original size:25 final size:26
Alignment explanation
Indices: 4715808--4715862 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 26
4715798 AAATCTTACT
* * *
4715808 TTAATTAATTTAAAATTTAATCTTCT
1 TTAATTAATTCAAAATTTAATATTCA
4715834 TTAATT-ATTCAAAA-TTAATTATTCA
1 TTAATTAATTCAAAATTTAA-TATTCA
4715859 TTAA
1 TTAA
4715863 AAGAGTTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 4 0.16
25 15 0.60
26 6 0.24
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (26 bp):
TTAATTAATTCAAAATTTAATATTCA
Found at i:4717301 original size:20 final size:20
Alignment explanation
Indices: 4717271--4717446 Score: 149
Period size: 20 Copynumber: 8.7 Consensus size: 20
4717261 GTTTCCAGAT
*
4717271 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* ** *
4717291 TCGCATTGCGATT-TTCCAAA
1 TCGCAATGCGATTCTGAC-TA
**
4717311 TTCGCTTTGCGATTTTCTGACTA
1 -TCGCAATGCGA--TTCTGACTA
* * *
4717334 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
*
4717354 TCGCAATGCGATTATGACTA
1 TCGCAATGCGATTCTGACTA
*
4717374 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* *
4717394 TCGCAACGCGATGCTGACTA
1 TCGCAATGCGATTCTGACTA
* *
4717414 TCGCAACGCGATGCTGACTA
1 TCGCAATGCGATTCTGACTA
4717434 TCGCAATGCGATT
1 TCGCAATGCGATT
4717447 TTCAAAGCGC
Statistics
Matches: 128, Mismatches: 21, Indels: 14
0.79 0.13 0.09
Matches are distributed among these distances:
19 3 0.02
20 100 0.78
21 11 0.09
22 9 0.07
23 3 0.02
24 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:4717563 original size:22 final size:22
Alignment explanation
Indices: 4717535--4717584 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
4717525 CTAAGGTAAC
*
4717535 ATCCGTCCCCATCTCCGATGAA
1 ATCCGTCCCCATCTCCGACGAA
*
4717557 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
4717579 ATCCGT
1 ATCCGT
4717585 TATCTCCATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.20, C:0.42, G:0.16, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:4718004 original size:20 final size:20
Alignment explanation
Indices: 4717979--4718030 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
4717969 CGATTTTAGT
4717979 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
**
4717999 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCAAA
*
4718019 TTCGTGTTGCGA
1 TTCGCGTTGCGA
4718031 ATTTCATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:4718061 original size:20 final size:20
Alignment explanation
Indices: 4718018--4718061 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4718008 CGATAGTCAT
* *
4718018 TTTCGTGTTGCGAATTTCAT
1 TTTCGTGTTGCGAATTTAAG
*
4718038 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGAATTTAAG
4718058 TTTC
1 TTTC
4718062 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGAATTTAAG
Found at i:4719803 original size:18 final size:18
Alignment explanation
Indices: 4719780--4719829 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
4719770 TTTACTCGTA
4719780 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
*
4719798 ATTTCACTTAGATTAATC
1 ATTTCACTTAGATTAACC
4719816 ATTTCACTTAGATT
1 ATTTCACTTAGATT
4719830 GCTTAGTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:4720002 original size:20 final size:20
Alignment explanation
Indices: 4719977--4720042 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
4719967 TAGTTTACTT
4719977 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
4719997 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* * **
4720017 TCGCAATGGGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
4720037 TCGCAA
1 TCGCAA
4720043 TGAAAGAATC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:4720115 original size:20 final size:20
Alignment explanation
Indices: 4720087--4720142 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
4720077 GCGATTCTCT
*
4720087 CGTTACGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
4720107 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
4720127 TGTTGCGATAGTCATT
1 CGTTGCGATAGTCATT
4720143 CGTGTTGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:4720146 original size:18 final size:19
Alignment explanation
Indices: 4720092--4720153 Score: 90
Period size: 20 Copynumber: 3.2 Consensus size: 19
4720082 TCTCTCGTTA
*
4720092 CGATAGTCATTTTCGCGTTG
1 CGATAGTCA-TTTCGTGTTG
4720112 CGATAGTCATTTTCGTGTTG
1 CGATAGTCA-TTTCGTGTTG
4720132 CGATAGTCA-TTCGTGTTG
1 CGATAGTCATTTCGTGTTG
4720150 CGAT
1 CGAT
4720154 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
18 13 0.32
20 28 0.68
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.40
Consensus pattern (19 bp):
CGATAGTCATTTCGTGTTG
Found at i:4720684 original size:18 final size:19
Alignment explanation
Indices: 4720645--4720686 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
4720635 CTCACCTGTC
4720645 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
4720666 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
4720684 ATC
1 ATC
4720687 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:4720740 original size:42 final size:42
Alignment explanation
Indices: 4720670--4720761 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
4720660 TCCCCTATCG
* * *
4720670 TTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCACCA
1 TTCAAGAGGCCACTATCATCACTCAAGAGGT-CCCTCCCAACA
* * *
4720712 TTCAAGAGGCCACTGTCATCATTGAAGAGGTCCCTCCCAACA
1 TTCAAGAGGCCACTATCATCACTCAAGAGGTCCCTCCCAACA
*
4720754 TTCTAGAG
1 TTCAAGAG
4720762 CCCGATTCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 40 0.95
43 2 0.05
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (42 bp):
TTCAAGAGGCCACTATCATCACTCAAGAGGTCCCTCCCAACA
Found at i:4722186 original size:14 final size:14
Alignment explanation
Indices: 4722149--4722211 Score: 63
Period size: 14 Copynumber: 4.4 Consensus size: 14
4722139 TTGCTTGTTT
*
4722149 AATTGATTTATAAA
1 AATTGATTTGTAAA
4722163 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
4722177 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
4722192 TATTGATGTGTAAA
1 AATTGATTTGTAAA
4722206 TAATTG
1 -AATTG
4722212 TTATTTGTGC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.64
15 14 0.36
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:4722334 original size:20 final size:20
Alignment explanation
Indices: 4722309--4722362 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
4722299 AGGTACACTT
*
4722309 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
*
4722329 TCGCAATGCGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
4722349 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
4722363 TCAATTCGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.43, C:0.28, G:0.19, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:4722428 original size:54 final size:54
Alignment explanation
Indices: 4722356--4722507 Score: 207
Period size: 54 Copynumber: 2.8 Consensus size: 54
4722346 AAATCGCAAC
* * * *
4722356 GCGAAAGTC-AATTCGCGTTGCGATAGTCTAATACGCTTTGCGATTTTCTCATT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTTCTCATT
* *
4722409 GCGATAGTCAAATTCGCGTTGCGATAGTAAAATTCGCATTGCGATTTTCTCGTT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTTCTCATT
* * * *
4722463 GCGATAGTCAAATACCCGTTGCGATAATCAAATTCGCGTTGCGAT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGAT
4722508 AGTCAAATTC
Statistics
Matches: 87, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
53 8 0.09
54 79 0.91
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (54 bp):
GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCATTGCGATTTTCTCATT
Found at i:4722432 original size:20 final size:20
Alignment explanation
Indices: 4722407--4722697 Score: 207
Period size: 20 Copynumber: 15.8 Consensus size: 20
4722397 GATTTTCTCA
4722407 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
* *
4722427 TTGCGATAGTAAAATTCGCA
1 TTGCGATAGTCAAATTCGCG
*
4722447 TTGCGAT--T----TTCTCG
1 TTGCGATAGTCAAATTCGCG
* *
4722461 TTGCGATAGTCAAATACCCG
1 TTGCGATAGTCAAATTCGCG
*
4722481 TTGCGATAATCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
4722501 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
*
4722521 TTGCGATAGACAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
*
4722541 TTGCGAT--T----TTTGCG
1 TTGCGATAGTCAAATTCGCG
* * *
4722555 TTGTGATAGTCATATTCGTG
1 TTGCGATAGTCAAATTCGCG
* *
4722575 TTGCAATAGTCAAATTCACG
1 TTGCGATAGTCAAATTCGCG
* * *
4722595 TTGC-A-A-T---TTTTGAG
1 TTGCGATAGTCAAATTCGCG
* *
4722609 TTGCGATAATCAAATTCGCA
1 TTGCGATAGTCAAATTCGCG
* *
4722629 TTGCGAT--T----TTTGAG
1 TTGCGATAGTCAAATTCGCG
* *
4722643 TTGCGATAATCAAATTCTCG
1 TTGCGATAGTCAAATTCGCG
4722663 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
*
4722683 TTGCGATATTCAAAT
1 TTGCGATAGTCAAAT
4722698 GAATGTGTAA
Statistics
Matches: 209, Mismatches: 38, Indels: 48
0.71 0.13 0.16
Matches are distributed among these distances:
14 39 0.19
15 1 0.00
16 4 0.02
17 2 0.01
18 3 0.01
19 1 0.00
20 159 0.76
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:4722514 original size:40 final size:40
Alignment explanation
Indices: 4722407--4722697 Score: 182
Period size: 34 Copynumber: 7.9 Consensus size: 40
4722397 GATTTTCTCA
* * *
4722407 TTGCGATAGTCAAATTCGCGTTGCGATAGTAAAATTCGCA
1 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCG
* * *
4722447 TTGCGAT--T----TTCTCGTTGCGATAGTCAAATACCCG
1 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCG
4722481 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCG
1 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCG
*
4722521 TTGCGATAGA-CAAATTCGCGTTGCGAT--T----TTTGCG
1 TTGCGATA-ATCAAATTCGCGTTGCGATAGTCAAATTCGCG
* * * * * *
4722555 TTGTGATAGTCATATTCGTGTTGCAATAGTCAAATTCACG
1 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCG
* * * * *
4722595 TTGC---AAT---TTTTGAGTTGCGATAATCAAATTCGCA
1 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCG
* * * *
4722629 TTGCGAT--T----TTTGAGTTGCGATAATCAAATTCTCG
1 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCG
* *
4722663 TTGCGATAGTCAAATTCGCGTTGCGATATTCAAAT
1 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAAT
4722698 GAATGTGTAA
Statistics
Matches: 198, Mismatches: 30, Indels: 46
0.72 0.11 0.17
Matches are distributed among these distances:
34 109 0.55
35 1 0.01
36 3 0.02
37 2 0.01
38 2 0.01
40 80 0.40
41 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (40 bp):
TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCG
Found at i:4722556 original size:54 final size:54
Alignment explanation
Indices: 4722498--4722635 Score: 186
Period size: 54 Copynumber: 2.6 Consensus size: 54
4722488 AATCAAATTC
* *
4722498 GCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTTGCGATTTTT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCACGTTGCAATTTTT
* * * * *
4722552 GCGTTGTGATAGTCATATTCGTGTTGCAATAGTCAAATTCACGTTGCAATTTTT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCACGTTGCAATTTTT
* * *
4722606 GAGTTGCGATAATCAAATTCGCATTGCGAT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGAT
4722636 TTTTGAGTTG
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 70 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.36
Consensus pattern (54 bp):
GCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCACGTTGCAATTTTT
Found at i:4722557 original size:74 final size:73
Alignment explanation
Indices: 4722356--4722598 Score: 220
Period size: 74 Copynumber: 3.3 Consensus size: 73
4722346 AAATCGCAAC
* * * *
4722356 GCGAAAGTC-AATTCGCGTTGCGATAGTCTAATACGCTTTGCGATTTTCTCATTGCGATAGTCAA
1 GCGATAGTCAAATTCGCGTTGCGATAGTCTAATTCGCGTTGCGATTTT-TCGTTGCGATAGTCAA
4722420 ATTCGCGTT
65 ATTCGCGTT
* * ** ** * * * *** *
4722429 GCGATAGTAAAATTCGCATTGCGATTTTCTCGTT-GCGATAGTCAAATACCCGTTGCGATAATCA
1 GCGATAGTCAAATTCGCGTTGCGATAGTCTAATTCGCG-TTG-CGATTTTTCGTTGCGATAGTCA
4722493 AATTCGCGTT
64 AATTCGCGTT
* * * *
4722503 GCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCGTTGCGATTTTTGCGTTGTGATAGTCAT
1 GCGATAGTCAAATTCGCGTTGCGATAGTCTAATTCGCGTTGCGATTTTT-CGTTGCGATAGTCAA
*
4722568 ATTCGTGTT
65 ATTCGCGTT
* *
4722577 GCAATAGTCAAATTCACGTTGC
1 GCGATAGTCAAATTCGCGTTGC
4722599 AATTTTTGAG
Statistics
Matches: 128, Mismatches: 37, Indels: 9
0.74 0.21 0.05
Matches are distributed among these distances:
73 12 0.09
74 110 0.86
75 6 0.05
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (73 bp):
GCGATAGTCAAATTCGCGTTGCGATAGTCTAATTCGCGTTGCGATTTTTCGTTGCGATAGTCAAA
TTCGCGTT
Found at i:4722920 original size:140 final size:140
Alignment explanation
Indices: 4722668--4722937 Score: 486
Period size: 140 Copynumber: 1.9 Consensus size: 140
4722658 TCTCGTTGCG
* *
4722668 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAAAAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGGGTAATAAGTGATAAAAACTGAACAGATCA
*
4722733 TAGCAATGTTCAAACTCAAGCTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTCCAAACTCAAGCTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
4722798 AATACACATA
131 AATACACATA
*
4722808 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGGGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGGGTAATAAGTGATAAAAACTGAACAGATCA
* *
4722873 TAGCAATGTCCAAACTCAAGTTATTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTCCAAACTCAAGCTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
4722938 TACAACGTTT
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 124 1.00
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.28
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGGGTAATAAGTGATAAAAACTGAACAGATCA
TAGCAATGTCCAAACTCAAGCTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:4725088 original size:14 final size:14
Alignment explanation
Indices: 4725069--4725105 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
4725059 TCTCGTGGCA
4725069 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
4725083 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
4725097 TTCTTCTTC
1 TT-TTCTTC
4725106 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:4726176 original size:20 final size:20
Alignment explanation
Indices: 4726152--4726218 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
4726142 AAATTCAGTG
* *
4726152 TTGCGACAGTCAAAATCGCG
1 TTGCGATAGTCAAAATCGCA
*
4726172 TTGCGATAGTCAGAATCGCA
1 TTGCGATAGTCAAAATCGCA
*
4726192 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCAAAATCGCA
4726212 TTGCGAT
1 TTGCGAT
4726219 TTACATATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (20 bp):
TTGCGATAGTCAAAATCGCA
Found at i:4726225 original size:20 final size:20
Alignment explanation
Indices: 4726185--4726258 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
4726175 CGATAGTCAG
*
4726185 AATCGCATTGCGATAGT-CAT
1 AATCGCATTGCGAT-TTACAT
4726205 AATCGCATTGCGATTTACAT
1 AATCGCATTGCGATTTACAT
*
4726225 ATTCGCATTGCGATTTACAT
1 AATCGCATTGCGATTTACAT
* *
4726245 ATTCACATTGCGAT
1 AATCGCATTGCGAT
4726259 AGTCGGAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
19 1 0.02
20 49 0.98
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.35
Consensus pattern (20 bp):
AATCGCATTGCGATTTACAT
Found at i:4733527 original size:22 final size:22
Alignment explanation
Indices: 4733502--4733553 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
4733492 TCAAAAAGGA
4733502 AGATGTCGGATCTAAAGAATAT
1 AGATGTCGGATCTAAAGAATAT
4733524 AGATGTCGGATCTAAAGAATAT
1 AGATGTCGGATCTAAAGAATAT
4733546 AGATGTCG
1 AGATGTCG
4733554 TACTATGTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.27
Consensus pattern (22 bp):
AGATGTCGGATCTAAAGAATAT
Found at i:4742443 original size:17 final size:16
Alignment explanation
Indices: 4742417--4742450 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
4742407 TTTCACTAAT
*
4742417 AGAGGAAATATTACAA
1 AGAGGAAATAGTACAA
4742433 AGAGAGAAATAGTACAA
1 AGAG-GAAATAGTACAA
4742450 A
1 A
4742451 TAGCCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.59, C:0.06, G:0.21, T:0.15
Consensus pattern (16 bp):
AGAGGAAATAGTACAA
Found at i:4747185 original size:16 final size:18
Alignment explanation
Indices: 4747157--4747209 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
4747147 AAATGTGTAA
*
4747157 ATAATATATATATATATT
1 ATAAAATATATATATATT
4747175 ATAAAATATATATATATT
1 ATAAAATATATATATATT
*
4747193 ATAAAATATATACATAT
1 ATAAAATATATATATAT
4747210 AATCATATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAAAATATATATATATT
Found at i:4749986 original size:18 final size:17
Alignment explanation
Indices: 4749950--4749983 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
4749940 ATTAAAGATC
4749950 AAAATATTAAAAAAATT
1 AAAATATTAAAAAAATT
4749967 AAAA-ATTAAAAGAAATT
1 AAAATATTAAAA-AAATT
4749984 TAATCAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAATATTAAAAAAATT
Found at i:4750380 original size:29 final size:29
Alignment explanation
Indices: 4750338--4750394 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
4750328 TAAAAATTAA
4750338 ATTAGAAGCATAAAACATTTAGTATAAGT
1 ATTAGAAGCATAAAACATTTAGTATAAGT
4750367 ATTAGAAGCATAAAACATTTAGTATAAG
1 ATTAGAAGCATAAAACATTTAGTATAAG
4750395 CATAAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.49, C:0.07, G:0.14, T:0.30
Consensus pattern (29 bp):
ATTAGAAGCATAAAACATTTAGTATAAGT
Found at i:4750608 original size:64 final size:63
Alignment explanation
Indices: 4750524--4750643 Score: 170
Period size: 64 Copynumber: 1.9 Consensus size: 63
4750514 ATGTATTTAT
* * *
4750524 TATCTATTTAACTTTTAATAGTAAAAGATGATTATATAT-TTTTAAATATTTCAAATTAACATAA
1 TATCTATTTAAATTTAAATAGTAAAAGAAG-TT-TATATCTTTTAAATATTTCAAATTAACATAA
* *
4750588 TATCTATTTAAATTTAAATAGTAAAAGAAGTTTATATCTTTTGAATATTTTAAATT
1 TATCTATTTAAATTTAAATAGTAAAAGAAGTTTATATCTTTTAAATATTTCAAATT
4750644 GAAAGATATT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
62 5 0.10
63 18 0.36
64 27 0.54
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (63 bp):
TATCTATTTAAATTTAAATAGTAAAAGAAGTTTATATCTTTTAAATATTTCAAATTAACATAA
Found at i:4750660 original size:64 final size:64
Alignment explanation
Indices: 4750521--4750660 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 64
4750511 AATATGTATT
* * *
4750521 TATTATCTATTTAACTTTTAATAGTAAAAGATGATTATATATTTTTAAATATTTCAAATTAACA
1 TATTATCTATTTAAATTTAAATAGTAAAAGAAGATTATATATTTTTAAATATTTCAAATTAACA
* * *
4750585 TAATATCTATTTAAATTTAAATAGTAAAAGAAG-TT-TATATCTTTTGAATATTTTAAATTGAAA
1 TATTATCTATTTAAATTTAAATAGTAAAAGAAGATTATATAT-TTTTAAATATTTCAAATT--AA
*
4750648 GA
63 CA
4750650 TATTAT-TATTT
1 TATTATCTATTT
4750661 TTTAAAATTA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
62 5 0.08
63 18 0.28
64 34 0.52
65 8 0.12
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.47
Consensus pattern (64 bp):
TATTATCTATTTAAATTTAAATAGTAAAAGAAGATTATATATTTTTAAATATTTCAAATTAACA
Found at i:4751517 original size:20 final size:20
Alignment explanation
Indices: 4751492--4751550 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
4751482 AGATGAGGTA
4751492 CGCCGAGTT-ATGTCGAGCCG
1 CGCCGAGTTGA-GTCGAGCCG
*
4751512 CGCCGAGTTGAGTCGAACCG
1 CGCCGAGTTGAGTCGAGCCG
4751532 CGCCGAGTTGAGTCGAGCC
1 CGCCGAGTTGAGTCGAGCC
4751551 ATGTCGAGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 35 0.97
21 1 0.03
ACGTcount: A:0.17, C:0.31, G:0.36, T:0.17
Consensus pattern (20 bp):
CGCCGAGTTGAGTCGAGCCG
Found at i:4754749 original size:20 final size:20
Alignment explanation
Indices: 4754726--4754768 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
4754716 TCAAAATCAT
*
4754726 TTTTCAAAATTTC-ATTTTGC
1 TTTTCAAAA-TCCAATTTTGC
4754746 TTTTCAAAATCCAATTTTGC
1 TTTTCAAAATCCAATTTTGC
4754766 TTT
1 TTT
4754769 CAAGAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTTCAAAATCCAATTTTGC
Found at i:4756275 original size:90 final size:90
Alignment explanation
Indices: 4756122--4756299 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 90
4756112 CCTAACACAC
* * * *
4756122 CCTTTAATAGCCAAGTTACCTTAGTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTAATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
* *
4756187 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
* *
4756212 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTAATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
4756277 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
4756300 TTCGGGATTA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.44
Consensus pattern (90 bp):
CCTTTAATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:4760968 original size:22 final size:20
Alignment explanation
Indices: 4760943--4760986 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
4760933 TTTGTGCTCA
*
4760943 AATTATAGTTTAATGAACTTTG
1 AATTAT-GTTTAA-AAACTTTG
*
4760965 AATTATTTTTAAAAACTTTG
1 AATTATGTTTAAAAACTTTG
4760985 AA
1 AA
4760987 CAAATTCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 9 0.45
21 5 0.25
22 6 0.30
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (20 bp):
AATTATGTTTAAAAACTTTG
Found at i:4762621 original size:13 final size:13
Alignment explanation
Indices: 4762603--4762646 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
4762593 GTCATAAATC
*
4762603 TATGACGCACATT
1 TATGACGCGCATT
*
4762616 TATGACGCGTATT
1 TATGACGCGCATT
*
4762629 TATGACGTGCATT
1 TATGACGCGCATT
4762642 TATGA
1 TATGA
4762647 TGCTCATTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.36
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:4762654 original size:13 final size:13
Alignment explanation
Indices: 4762603--4762654 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
4762593 GTCATAAATC
*
4762603 TATGACGCACATT
1 TATGACGCTCATT
4762616 TATGACGCGT-ATT
1 TATGACGC-TCATT
4762629 TATGACG-TGCATT
1 TATGACGCT-CATT
*
4762642 TATGATGCTCATT
1 TATGACGCTCATT
4762655 GTGCGTCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
11 1 0.03
13 31 0.94
14 1 0.03
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.38
Consensus pattern (13 bp):
TATGACGCTCATT
Found at i:4767806 original size:21 final size:19
Alignment explanation
Indices: 4767764--4767803 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
4767754 AGAAAAATTT
4767764 AATATTTTATCTTTTTATA
1 AATATTTTATCTTTTTATA
*
4767783 AATATTTTA-CTTCTT-TA
1 AATATTTTATCTTTTTATA
4767800 AATA
1 AATA
4767804 AATTTCCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 5 0.25
19 9 0.45
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (19 bp):
AATATTTTATCTTTTTATA
Found at i:4767843 original size:29 final size:29
Alignment explanation
Indices: 4767776--4767846 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
4767766 TATTTTATCT
4767776 TTTTATAAATATTTTACTTCTTTAAATAA
1 TTTTATAAATATTTTACTTCTTTAAATAA
* **
4767805 ATTTCCAAATATTTTA-TAAT-TTTAAATAA
1 TTTTATAAATATTTTACT--TCTTTAAATAA
4767834 TTTTATAAATATT
1 TTTTATAAATATT
4767847 AATTTATTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
28 1 0.03
29 32 0.94
30 1 0.03
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.54
Consensus pattern (29 bp):
TTTTATAAATATTTTACTTCTTTAAATAA
Found at i:4768347 original size:7 final size:7
Alignment explanation
Indices: 4768331--4768387 Score: 71
Period size: 7 Copynumber: 8.3 Consensus size: 7
4768321 TACACTTGAA
*
4768331 AAATTAT
1 AAATTTT
*
4768338 AAATCTT
1 AAATTTT
4768345 AAATTTT
1 AAATTTT
* *
4768352 AGA-TAT
1 AAATTTT
4768358 AAATTTT
1 AAATTTT
4768365 AAATTTT
1 AAATTTT
4768372 AAATTTT
1 AAATTTT
4768379 AAATTTT
1 AAATTTT
4768386 AA
1 AA
4768388 GTAAGAGGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
6 4 0.10
7 38 0.90
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (7 bp):
AAATTTT
Found at i:4768360 original size:20 final size:20
Alignment explanation
Indices: 4768335--4768372 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4768325 CTTGAAAAAT
4768335 TATAAATCTTAAATTTTAGA
1 TATAAATCTTAAATTTTAGA
*
4768355 TATAAATTTTAAATTTTA
1 TATAAATCTTAAATTTTA
4768373 AATTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (20 bp):
TATAAATCTTAAATTTTAGA
Found at i:4768767 original size:23 final size:23
Alignment explanation
Indices: 4768737--4768803 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
4768727 ACTTTGATGT
* * *
4768737 TGAATCATTCAACACTGTTTTTC
1 TGAATCATTCAACACAGTCTTGC
4768760 TGAATCATTCAACACAGTCTTGC
1 TGAATCATTCAACACAGTCTTGC
*
4768783 TAAATCATTCAACACAGTCTT
1 TGAATCATTCAACACAGTCTT
4768804 CATTCAGAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (23 bp):
TGAATCATTCAACACAGTCTTGC
Found at i:4771654 original size:38 final size:38
Alignment explanation
Indices: 4771611--4771724 Score: 165
Period size: 38 Copynumber: 3.0 Consensus size: 38
4771601 TATGCGATGT
* * *
4771611 GAACAAATAATGTTAAATTTATGGTACTTTTCGGAGTC
1 GAACAAATCATGTTAAATTTATGGTACTTGTAGGAGTC
* *
4771649 GAACAAATCATGTTAAATTTATGGTACTCGTAGGAGAC
1 GAACAAATCATGTTAAATTTATGGTACTTGTAGGAGTC
* *
4771687 GAACAAATCATTTTAAATTTATAGTACTTGTAGGAGTC
1 GAACAAATCATGTTAAATTTATGGTACTTGTAGGAGTC
4771725 CCTGAAATTT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 67 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.34
Consensus pattern (38 bp):
GAACAAATCATGTTAAATTTATGGTACTTGTAGGAGTC
Found at i:4775804 original size:3 final size:3
Alignment explanation
Indices: 4775796--4775868 Score: 139
Period size: 3 Copynumber: 24.7 Consensus size: 3
4775786 CTCATGTTAC
4775796 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4775843 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
4775869 GATATCCACA
Statistics
Matches: 69, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 67 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4784526 original size:13 final size:13
Alignment explanation
Indices: 4784508--4784536 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
4784498 AGGAGGTGAA
4784508 AGACCAAAGGACT
1 AGACCAAAGGACT
4784521 AGACCAAAGGACT
1 AGACCAAAGGACT
4784534 AGA
1 AGA
4784537 AATTAAGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.21, G:0.24, T:0.07
Consensus pattern (13 bp):
AGACCAAAGGACT
Found at i:4787812 original size:27 final size:30
Alignment explanation
Indices: 4787781--4787840 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
4787771 AATATCTTTT
*
4787781 ATATAAAAGTAT-TA-AA-TTTAATTAAAG
1 ATATAAAAATATATATAACTTTAATTAAAG
4787808 ATATAAAAATATGATATAACTTTAATTAAAG
1 ATATAAAAATAT-ATATAACTTTAATTAAAG
4787839 AT
1 AT
4787841 TCTCCAGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 11 0.39
29 2 0.07
30 2 0.07
31 13 0.46
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.37
Consensus pattern (30 bp):
ATATAAAAATATATATAACTTTAATTAAAG
Found at i:4788344 original size:27 final size:27
Alignment explanation
Indices: 4788314--4788401 Score: 149
Period size: 27 Copynumber: 3.3 Consensus size: 27
4788304 TCGGGTTGGA
*
4788314 TCGGGTTTTTTAATTGTGATGTTTGGG
1 TCGGGTTTTTTAATTGTGATGTTCGGG
4788341 TCGGGTTTTTTAATTGTGATGTTCGGG
1 TCGGGTTTTTTAATTGTGATGTTCGGG
* *
4788368 CCGGGTGTTTTAATTGTGATGTTCGGG
1 TCGGGTTTTTTAATTGTGATGTTCGGG
4788395 TCGGGTT
1 TCGGGTT
4788402 CGAGTTTATG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.10, C:0.08, G:0.35, T:0.47
Consensus pattern (27 bp):
TCGGGTTTTTTAATTGTGATGTTCGGG
Found at i:4790331 original size:21 final size:21
Alignment explanation
Indices: 4790291--4790332 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4790281 TAATAAACTT
*
4790291 AAATAAAAAAAATACTAAAAA
1 AAATAAAAAAAATACAAAAAA
* *
4790312 AAATAAAAACAGTACAAAAAA
1 AAATAAAAAAAATACAAAAAA
4790333 CAACATAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.79, C:0.07, G:0.02, T:0.12
Consensus pattern (21 bp):
AAATAAAAAAAATACAAAAAA
Found at i:4792788 original size:57 final size:56
Alignment explanation
Indices: 4792678--4792788 Score: 143
Period size: 57 Copynumber: 2.0 Consensus size: 56
4792668 AGAGTGCATC
* * *
4792678 GATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCT
1 GATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAATGCATCGATGCATGGCT
* * *
4792734 GATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAATGCATCGGTGCATGG
1 GATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAATGCATCGATGCATGG
4792789 TAAGTGCATC
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
56 21 0.45
57 23 0.49
58 3 0.06
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (56 bp):
GATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAATGCATCGATGCATGGCT
Found at i:4799421 original size:22 final size:21
Alignment explanation
Indices: 4799379--4799418 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4799369 GAGTTTATTT
*
4799379 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
4799400 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
4799419 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:4801358 original size:17 final size:18
Alignment explanation
Indices: 4801336--4801371 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4801326 GTGCACTAAG
4801336 AGTGCA-TCGATGTATCA
1 AGTGCATTCGATGTATCA
*
4801353 AGTGCATTCGATGTTTCA
1 AGTGCATTCGATGTATCA
4801371 A
1 A
4801372 AATAGCCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (18 bp):
AGTGCATTCGATGTATCA
Found at i:4802430 original size:36 final size:36
Alignment explanation
Indices: 4802336--4802511 Score: 120
Period size: 36 Copynumber: 4.8 Consensus size: 36
4802326 TTGTCTCAAG
* * **
4802336 GGTTTTAAGAAAAACGATCTCAAATGAGATAAATTT
1 GGTTTTAAGAAAAACCATCTCAAGTGAGACGAATTT
* * * ** *
4802372 TGTTTCAAGGGAAAACTGTCTCAAGTGAGACGAAGTT
1 GGTTTTAA-GAAAAACCATCTCAAGTGAGACGAATTT
*
4802409 GGTTTTAAGAAAAACCATCTCAAGTGAGATTC-ATTTCT
1 GGTTTTAAGAAAAACCATCTCAAGTGAGA--CGAATT-T
* * ** ** * * **
4802447 TGTTTCAAGGGAAACTTTCTCCAGTGAGATGAAAAT
1 GGTTTTAAGAAAAACCATCTCAAGTGAGACGAATTT
4802483 GGTTTTAAGAAAAACCATCTCAAGTGAGA
1 GGTTTTAAGAAAAACCATCTCAAGTGAGA
4802512 TAAAATTTCT
Statistics
Matches: 101, Mismatches: 34, Indels: 10
0.70 0.23 0.07
Matches are distributed among these distances:
36 47 0.47
37 30 0.30
38 24 0.24
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (36 bp):
GGTTTTAAGAAAAACCATCTCAAGTGAGACGAATTT
Found at i:4802528 original size:75 final size:74
Alignment explanation
Indices: 4802336--4802790 Score: 323
Period size: 78 Copynumber: 6.0 Consensus size: 74
4802326 TTGTCTCAAG
* * *
4802336 GGTTTTAAGAAAAACGATCTCAAATGAGATAAA-TT-TTGTTTCAAGGGAAAACTGTCTCAAGTG
1 GGTTTTAAGAAAAACCATCTCAAGTGAGATAAATTTCTTGTTTCAAGGG-AAACTATCTCAAGTG
**
4802399 AGACGAAGTT
65 AGACGAAAAT
** * *
4802409 GGTTTTAAGAAAAACCATCTCAAGTGAGATTCATTTCTTGTTTCAAGGGAAACTTTCTCCAGTGA
1 GGTTTTAAGAAAAACCATCTCAAGTGAGATAAATTTCTTGTTTCAAGGGAAACTATCTCAAGTGA
*
4802474 GATGAAAAT
66 GACGAAAAT
* * *
4802483 GGTTTTAAGAAAAACCATCTCAAGTGAGATAAAATTTCTTATTTCAATGGAAACTATCTCAAGCG
1 GGTTTTAAGAAAAACCATCTCAAGTGAGAT-AAATTTCTTGTTTCAAGGGAAACTATCTCAAGTG
4802548 AGAC-AAAATCTTT
65 AGACGAAAA----T
* ** * * ** * *
4802561 TGTTTCGAGGAAAACTATCTCAAACGAGATAAAATCTT-TTGTTTCGAGGGAAACTATCTCAAGC
1 GGTTTTAAGAAAAACCATCTCAAGTGAGAT-AAAT-TTCTTGTTTCAAGGGAAACTATCTCAAGT
**
4802625 GAGATAAAATCAT
64 GAGACGAAA--AT
** * ** * *
4802638 TTTTTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTT-TTGTTTCAAGGGAAACTATCTCAAG
1 GGTTTT-AAGAAAAACCATCTCAAGTGAGAT-AAAT-TTCTTGTTTCAAGGGAAACTATCTCAAG
*
4802702 CGAGAC-AAAATCTTT
63 TGAGACGAAAA----T
* * ** * * **
4802717 TGTTTCAAGGGAAACTATATCAAACGAGATACAATCTT-TTGTTTCAAGGGAAACTATCTCAAGT
1 GGTTTTAAGAAAAACCATCTCAAGTGAGATA-AAT-TTCTTGTTTCAAGGGAAACTATCTCAAGT
4802781 GAGAC-AAAAT
64 GAGACGAAAAT
4802791 CTTTTGTTTC
Statistics
Matches: 325, Mismatches: 40, Indels: 33
0.82 0.10 0.08
Matches are distributed among these distances:
73 29 0.09
74 57 0.18
75 43 0.13
77 9 0.03
78 176 0.54
79 10 0.03
81 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (74 bp):
GGTTTTAAGAAAAACCATCTCAAGTGAGATAAATTTCTTGTTTCAAGGGAAACTATCTCAAGTGA
GACGAAAAT
Found at i:4802545 original size:39 final size:39
Alignment explanation
Indices: 4802494--4802833 Score: 477
Period size: 39 Copynumber: 8.7 Consensus size: 39
4802484 GTTTTAAGAA
* * * *
4802494 AAACCATCTCAAGTGAGATAAAAT-TTCTTATTTCAATGG
1 AAACTATCTCAAGCGAGATAAAATCTT-TTGTTTCAAGGG
* * *
4802533 AAACTATCTCAAGCGAGACAAAATCTTTTGTTTCGAGGA
1 AAACTATCTCAAGCGAGATAAAATCTTTTGTTTCAAGGG
* *
4802572 AAACTATCTCAAACGAGATAAAATCTTTTGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTTTGTTTCAAGGG
*
4802611 AAACTATCTCAAGCGAGATAAAATCATTTT-TTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATC-TTTTGTTTCAAGGG
4802650 AAACTATCTCAAGCGAGATAAAATCTTTTGTTTCAAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTTTGTTTCAAGGG
*
4802689 AAACTATCTCAAGCGAGACAAAATCTTTTGTTTCAAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTTTGTTTCAAGGG
* * *
4802728 AAACTATATCAAACGAGATACAATCTTTTGTTTCAAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTTTGTTTCAAGGG
* *
4802767 AAACTATCTCAAGTGAGACAAAATCTTTTGTTTCAAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTTTGTTTCAAGGG
* *
4802806 AAACTATCTCAAGTGATATAAAAATCTT
1 AAACTATCTCAAGCGAGAT-AAAATCTT
4802834 CTTTAAAAAC
Statistics
Matches: 273, Mismatches: 24, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
38 4 0.01
39 255 0.93
40 14 0.05
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (39 bp):
AAACTATCTCAAGCGAGATAAAATCTTTTGTTTCAAGGG
Found at i:4802892 original size:73 final size:72
Alignment explanation
Indices: 4802827--4803046 Score: 252
Period size: 73 Copynumber: 3.0 Consensus size: 72
4802817 AGTGATATAA
*
4802827 AAATCTTCTTT-AAAAACAATCTTGAGTGAAATGAAATGTCTT-TTTCGAGTAACAACCGTCTCA
1 AAATCTTCTTTAAAAAACAATCTTGAGTGAAATGAAATGTCTTCTTTCGAGTAA-AACTGTCTCA
4802890 AGTGAGAC
65 AGTGAGAC
* * * * * * * *
4802898 AAATCTTGTTTAAGAAAACAATCTTGAGTG-AA-CAAATCTTATTGTTTCAAGTAAAAAT-TATC
1 AAATCTTCTTTAA-AAAACAATCTTGAGTGAAATGAAAT-GTCTTCTTTCGAGTAAAACTGTCT-
*
4802960 CAAGCGAGAC
63 CAAGTGAGAC
*
4802970 AAATCTTCTTTAAGAAAAACAATCTTGAGTCAAATGAAATGTCTTCTTTCGAGTAAAACTGTCTC
1 AAATCTTCTTT-A-AAAAACAATCTTGAGTGAAATGAAATGTCTTCTTTCGAGTAAAACTGTCTC
4803035 AAGTGAGAC
64 AAGTGAGAC
4803044 AAA
1 AAA
4803047 GTCTGTTTTA
Statistics
Matches: 120, Mismatches: 19, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
71 16 0.13
72 27 0.22
73 41 0.34
74 30 0.25
75 6 0.05
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (72 bp):
AAATCTTCTTTAAAAAACAATCTTGAGTGAAATGAAATGTCTTCTTTCGAGTAAAACTGTCTCAA
GTGAGAC
Found at i:4808744 original size:18 final size:18
Alignment explanation
Indices: 4808722--4808759 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
4808712 AATAAAATAT
4808722 TAAAAATATAAT-TATAA
1 TAAAAATATAATGTATAA
*
4808739 TAAAAATATATTGTATAA
1 TAAAAATATAATGTATAA
4808757 TAA
1 TAA
4808760 CTCATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
TAAAAATATAATGTATAA
Found at i:4812816 original size:20 final size:21
Alignment explanation
Indices: 4812791--4812829 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4812781 TTTCCCTTAA
4812791 TCAT-CCAATATCAATATTTT
1 TCATCCCAATATCAATATTTT
*
4812811 TCATCCCAATATCGATATT
1 TCATCCCAATATCAATATT
4812830 CAAACCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.41
Consensus pattern (21 bp):
TCATCCCAATATCAATATTTT
Found at i:4818105 original size:14 final size:15
Alignment explanation
Indices: 4818082--4818119 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
4818072 TGAAAACTAT
*
4818082 TTTG-AAAAACCATG
1 TTTGAAAAAACAATG
4818096 TTT-AAAAAACAATG
1 TTTGAAAAAACAATG
4818110 TTTGAAAAAA
1 TTTGAAAAAA
4818120 AAATCATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.29
Consensus pattern (15 bp):
TTTGAAAAAACAATG
Found at i:4830778 original size:36 final size:35
Alignment explanation
Indices: 4830703--4830837 Score: 173
Period size: 36 Copynumber: 3.8 Consensus size: 35
4830693 AGATGAACAA
* *
4830703 TTGAATCGAAAAGTGCTGACGCTTCCTTCCGTTCAC
1 TTGAATCG-AAAGTGCAGATGCTTCCTTCCGTTCAC
* *
4830739 TTGAATCGAAAGTGTCAG-TGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTG-CAGATGCTTCCTTCCGTTC-AC
*
4830775 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGCAGATGCTTCCTTCCGTTCAC
*
4830810 TTTGAATCGAAAGTGCTGATGCTTCCTT
1 -TTGAATCGAAAGTGCAGATGCTTCCTT
4830838 TCCTTCTTCT
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
35 22 0.25
36 65 0.75
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (35 bp):
TTGAATCGAAAGTGCAGATGCTTCCTTCCGTTCAC
Found at i:4830824 original size:72 final size:72
Alignment explanation
Indices: 4830703--4830848 Score: 224
Period size: 72 Copynumber: 2.0 Consensus size: 72
4830693 AGATGAACAA
*
4830703 TTGAATCGAAAAGTGCTGACGCTTCCTTCCGTTCACTTGAATCGAAAGTGTCAG-TGCTTCCTTT
1 TTGAATCGAAAAGTGCCGACGCTTCCTTCCGTTCACTTGAATCGAAAGTG-CAGATGCTTCCTTT
*
4830767 CGTTCTTC
65 CCTTCTTC
* *
4830775 TTGAATCG-AAAGTGCCGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGCTGATGCTTCCTTT
1 TTGAATCGAAAAGTGCCGACGCTTCCTTCCGTTCAC-TTGAATCGAAAGTGCAGATGCTTCCTTT
4830839 CCTTCTTC
65 CCTTCTTC
4830847 TT
1 TT
4830849 ATTCACCTTC
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
71 27 0.40
72 41 0.60
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.38
Consensus pattern (72 bp):
TTGAATCGAAAAGTGCCGACGCTTCCTTCCGTTCACTTGAATCGAAAGTGCAGATGCTTCCTTTC
CTTCTTC
Found at i:4837379 original size:3 final size:3
Alignment explanation
Indices: 4837371--4837402 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
4837361 GGGTTCTAAT
4837371 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4837403 CTAATTACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4837500 original size:30 final size:29
Alignment explanation
Indices: 4837466--4837530 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 29
4837456 CCCACTGATT
* *
4837466 CAAGCCTGCAAAGAAACAAGCCCATCAACC
1 CAAGCCTACAAAGAAACAAG-CCAGCAACC
*
4837496 CAAGCCTATAAAGAAACAAGCCAGCAACC
1 CAAGCCTACAAAGAAACAAGCCAGCAACC
4837525 CAAGCC
1 CAAGCC
4837531 ATAACCAACC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.45, C:0.35, G:0.14, T:0.06
Consensus pattern (29 bp):
CAAGCCTACAAAGAAACAAGCCAGCAACC
Found at i:4837544 original size:28 final size:29
Alignment explanation
Indices: 4837479--4837545 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
4837469 GCCTGCAAAG
* *
4837479 AAACAAGCCCATCAACCCAAGCCTATAAAG
1 AAACAAG-CCAGCAACCCAAGCCTATAAAC
*
4837509 AAACAAGCCAGCAACCCAAGCC-ATAACC
1 AAACAAGCCAGCAACCCAAGCCTATAAAC
*
4837537 AACCAAGCC
1 AAACAAGCC
4837546 CGCCCGGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 12 0.36
29 14 0.42
30 7 0.21
ACGTcount: A:0.46, C:0.37, G:0.10, T:0.06
Consensus pattern (29 bp):
AAACAAGCCAGCAACCCAAGCCTATAAAC
Found at i:4845100 original size:66 final size:63
Alignment explanation
Indices: 4844901--4845139 Score: 214
Period size: 66 Copynumber: 3.7 Consensus size: 63
4844891 TTGATCTCAC
* * * * * * *
4844901 TTGAGATAGTTTTCCTAAAAACAAATTTTGTCTCGCTTGAGACATTTGTCTTGAACATAAACAT
1 TTGAGATTGTTTTTCTCAAAACAAATTTTATCTCACTTGAGACATTT-CCTTAAACATAAACAT
* * * *
4844965 TTGAGATTGTTTCTT-TGAAATA-AAGTTTTATCTCATTTGAGACATTTTCTTTTAAAACATAAG
1 TTGAGATTGTTT-TTCTCAAA-ACAAATTTTATCTCACTTGAGACA-TTTC-CTT-AAACATAA-
4845028 AC-T
60 ACAT
* *
4845031 TTGATATTGTTTTTCTCAAAACAAATTTTATCTCACTTGAGACAGTCTTCCTTAAGACACAAACA
1 TTGAGATTGTTTTTCTCAAAACAAATTTTATCTCACTTGAGACA-T-TTCCTTAA-ACATAAACA
4845096 T
63 T
* **
4845097 TTGAGATTGTTTTTCCTCAAAACAAATTTCATCTTGCTTGAGA
1 TTGAGATTGTTTTT-CTCAAAACAAATTTTATCTCACTTGAGA
4845140 TAATTCTCCT
Statistics
Matches: 142, Mismatches: 21, Indels: 21
0.77 0.11 0.11
Matches are distributed among these distances:
64 33 0.23
65 14 0.10
66 65 0.46
67 30 0.21
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (63 bp):
TTGAGATTGTTTTTCTCAAAACAAATTTTATCTCACTTGAGACATTTCCTTAAACATAAACAT
Found at i:4845150 original size:67 final size:67
Alignment explanation
Indices: 4845030--4845175 Score: 165
Period size: 67 Copynumber: 2.2 Consensus size: 67
4845020 AACATAAGAC
* * *
4845030 TTTGATATTGTTTTTCTCAAAACAAATTTTATCTCACTTGAGACAGTCTTCC-T-TAAGACACAA
1 TTTGAAATTGTTTTTCTCAAAACAAATTTCATCTCACTTGAGAAAGTCTTCCTTCTAA-ACACAA
4845093 ACA-
65 A-AT
* ** *
4845096 TTTGAGATTGTTTTTCCTCAAAACAAATTTCATCTTGCTTGAGATAATTC-TCCTTCTAAACACA
1 TTTGAAATTGTTTTT-CTCAAAACAAATTTCATCTCACTTGAGA-AAGTCTTCCTTCTAAACACA
4845160 AAAT
64 AAAT
4845164 TTTGAAATTGTT
1 TTTGAAATTGTT
4845176 CTCAGTTAAG
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
66 14 0.21
67 29 0.43
68 22 0.32
69 3 0.04
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (67 bp):
TTTGAAATTGTTTTTCTCAAAACAAATTTCATCTCACTTGAGAAAGTCTTCCTTCTAAACACAAA
AT
Found at i:4845262 original size:84 final size:84
Alignment explanation
Indices: 4845100--4845258 Score: 182
Period size: 84 Copynumber: 1.9 Consensus size: 84
4845090 CAAACATTTG
* ** * * *
4845100 AGATTGTTTTTCCTCAAAACAAATTTCATCTTGCTTGAGATAATTCTCCTTCTAAACACAAAATT
1 AGATTGTTTTTCCTAAAAACAAATTTCATCTCCCTTGAGAAAATTCTCCTTCGAAACACAAAATC
4845165 TTGAAATTGTTCTCAGTTA
66 TTGAAATTGTTCTCAGTTA
**
4845184 AGATTG-TTTTCTCTAAAAACAAATTTTGTCTCCCTTGAGAAAATT-TCTCTT-GAAACAC-AAA
1 AGATTGTTTTTC-CTAAAAACAAATTTCATCTCCCTTGAGAAAATTCTC-CTTCGAAACACAAAA
*
4845245 TCCTTGAGATTGTT
64 T-CTTGAAATTGTT
4845259 TCTCTTGAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
82 4 0.06
83 23 0.37
84 36 0.57
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.40
Consensus pattern (84 bp):
AGATTGTTTTTCCTAAAAACAAATTTCATCTCCCTTGAGAAAATTCTCCTTCGAAACACAAAATC
TTGAAATTGTTCTCAGTTA
Found at i:4845832 original size:138 final size:139
Alignment explanation
Indices: 4845623--4845890 Score: 380
Period size: 138 Copynumber: 1.9 Consensus size: 139
4845613 TCAGGCAACC
* * *
4845623 AGACTTCCTCATCACGTAGGAATCGTGTTGTCTACAAATTATCCCTAAATACAGATAGACGTCCT
1 AGACTTCCTCATCAAGCAGGAATCGTGTTGTCTACAAATTATCCCTAAAGACAGATAGACGTCCT
* * * * *
4845688 CATCACATAGGAACAATGTCGTCCACTGATTC-GATCTCCTCAACGCGTAGGAGCAGTGTCATCC
66 CATCACATAGGAACAATGTCATCCACCGA-CCAGATCTCCTCAACACGAAGGAGCAGTGTCATCC
4845752 TCTGACATTA
130 TCTGACATTA
* * *
4845762 AGACTTCCTCATCAAGCAGGAA-CTGTGTTGTCTCCAAATTA-CCCTAAAGACGGCTAGACGTCC
1 AGACTTCCTCATCAAGCAGGAATC-GTGTTGTCTACAAATTATCCCTAAAGACAGATAGACGTCC
* *
4845825 TCATCACATAGGAACAATGTCATCCACCGACCAGATCTCTTTAACACGAAGGAGCAGTGTCATCC
65 TCATCACATAGGAACAATGTCATCCACCGACCAGATCTCCTCAACACGAAGGAGCAGTGTCATCC
4845890 T
130 T
4845891 TAGTCAATCA
Statistics
Matches: 114, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
137 1 0.01
138 77 0.68
139 36 0.32
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (139 bp):
AGACTTCCTCATCAAGCAGGAATCGTGTTGTCTACAAATTATCCCTAAAGACAGATAGACGTCCT
CATCACATAGGAACAATGTCATCCACCGACCAGATCTCCTCAACACGAAGGAGCAGTGTCATCCT
CTGACATTA
Found at i:4846202 original size:3 final size:3
Alignment explanation
Indices: 4846185--4846221 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
4846175 GGGTTCTAAT
*
4846185 TTA TCA TTA -TA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4846222 ATAATATTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:4848297 original size:19 final size:19
Alignment explanation
Indices: 4848273--4848318 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
4848263 CGACTACAAT
4848273 TCAAAATCTTTCTAATTAA
1 TCAAAATCTTTCTAATTAA
4848292 TCAAAATCTTTCTAATTAA
1 TCAAAATCTTTCTAATTAA
4848311 TCAAAATC
1 TCAAAATC
4848319 ATCAAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.39
Consensus pattern (19 bp):
TCAAAATCTTTCTAATTAA
Found at i:4848641 original size:2 final size:2
Alignment explanation
Indices: 4848636--4848671 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
4848626 AAAAGTAATA
*
4848636 AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4848672 TTAACTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4849298 original size:12 final size:12
Alignment explanation
Indices: 4849281--4849305 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4849271 AATATTGCTT
4849281 CTAAAAGCAAAG
1 CTAAAAGCAAAG
4849293 CTAAAAGCAAAG
1 CTAAAAGCAAAG
4849305 C
1 C
4849306 AATGTAGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.20, G:0.16, T:0.08
Consensus pattern (12 bp):
CTAAAAGCAAAG
Found at i:4851951 original size:16 final size:16
Alignment explanation
Indices: 4851930--4851961 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4851920 TTTGAAACAA
4851930 ATTTATAAAATTTTAT
1 ATTTATAAAATTTTAT
*
4851946 ATTTATAAAGTTTTAT
1 ATTTATAAAATTTTAT
4851962 GAGATGAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
ATTTATAAAATTTTAT
Found at i:4855570 original size:20 final size:19
Alignment explanation
Indices: 4855545--4855595 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
4855535 GCGAAATAAA
4855545 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
*
4855565 AATCGCAAATC-CGTTCCCAG
1 AATCGC-AA-CGCGATCCCAG
4855585 AATCGCAACGC
1 AATCGCAACGC
4855596 AATTATGATG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 1 0.04
19 3 0.11
20 16 0.59
21 6 0.22
22 1 0.04
ACGTcount: A:0.31, C:0.35, G:0.18, T:0.16
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Done.