Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 87 of 143
Found at i:27447314 original size:58 final size:57
Alignment explanation
Indices: 27447243--27447488 Score: 191
Period size: 58 Copynumber: 4.2 Consensus size: 57
27447233 ACCCGGGGGG
* * *
27447243 AAAATGGTAATTTTGGTCTAACTTGGGATAAAAACGAGATTTTGGAAAGTTCGAGGGT
1 AAAATGGTAATTTTGGTCAAAATTGGG-TAAAAATGAGATTTTGGAAAGTTCGAGGGT
* *
27447301 AAAATGGTAATTTTTGG-CAAAATTAGGGTCAAAAATG-GAATTTTGGAAAGCTCGAGTGT
1 AAAATGGTAA-TTTTGGTCAAAATT-GGGT-AAAAATGAG-ATTTTGGAAAGTTCGAGGGT
* * * * * * * *
27447360 AAAGTGGTACTTTTGGT-GAAATCGAAGTTAAAAATGAAATTTTAGAAAGTTCGGGGGT
1 AAAATGGTAATTTTGGTCAAAATTG--GGTAAAAATGAGATTTTGGAAAGTTCGAGGGT
* * * *
27447418 AAAATGGTAATTTTGGT-GAAATCGGGGTGAAAAAT-AGAATTTTGGAAAATTTG-GGGTT
1 AAAATGGTAATTTTGGTCAAAAT-TGGGT-AAAAATGAG-ATTTTGGAAAGTTCGAGGG-T
27447476 AAAAT-GTAATTTT
1 AAAATGGTAATTTT
27447489 ACAAATTTTT
Statistics
Matches: 153, Mismatches: 23, Indels: 25
0.76 0.11 0.12
Matches are distributed among these distances:
57 15 0.10
58 94 0.61
59 44 0.29
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (57 bp):
AAAATGGTAATTTTGGTCAAAATTGGGTAAAAATGAGATTTTGGAAAGTTCGAGGGT
Found at i:27447344 original size:59 final size:59
Alignment explanation
Indices: 27447281--27447488 Score: 201
Period size: 58 Copynumber: 3.6 Consensus size: 59
27447271 TAAAAACGAG
**
27447281 ATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGCAAAATTAGGGTCAAAAATGGA
1 ATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTCAAAAATGGA
* * * * * * * *
27447340 ATTTTGGAAAGCTCGAGTGTAAAGTGGT-ACTTTTGGTGAAA-TCGAAGTTAAAAATGAA
1 ATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATTAG-GGTCAAAAATGGA
* * ** * *
27447398 ATTTTAGAAAGTTCGGGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTGAAAAATAGA
1 ATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTCAAAAATGGA
* *
27447456 ATTTTGGAAAATTTG-GGGTTAAAAT-GTAATTTT
1 ATTTTGGAAAGTTCGAGGG-TAAAATGGTAATTTT
27447489 ACAAATTTTT
Statistics
Matches: 120, Mismatches: 24, Indels: 11
0.77 0.15 0.07
Matches are distributed among these distances:
57 9 0.08
58 84 0.70
59 27 0.22
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (59 bp):
ATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTCAAAAATGGA
Found at i:27447442 original size:29 final size:28
Alignment explanation
Indices: 27447281--27447547 Score: 90
Period size: 29 Copynumber: 9.2 Consensus size: 28
27447271 TAAAAACGAG
* *
27447281 ATTTTGGAAAGTTCGAGGGTAAAATGGTA
1 ATTTTGGAAAATTCGGGGGTAAAAT-GTA
* *** *
27447310 ATTTTTGGCAAAATTAGGGTCAAAAATGGA
1 A-TTTTGG-AAAATTCGGGGGTAAAATGTA
** * * *
27447340 ATTTTGGAAAGCTCGAGTGTAAAGTGGTA
1 ATTTTGGAAAATTCGGGGGTAAAAT-GTA
* * ** * *
27447369 CTTTTGGTGAAA-TCGAAGTTAAAAATGAA
1 ATTTTGG-AAAATTCGGGGGT-AAAATGTA
* *
27447398 ATTTTAGAAAGTTCGGGGGTAAAATGGTA
1 ATTTTGGAAAATTCGGGGGTAAAAT-GTA
* *
27447427 ATTTTGGTGAAA-TCGGGGTGAAAAATAG-A
1 ATTTTGG-AAAATTCGGGG-GTAAAAT-GTA
* *
27447456 ATTTTGGAAAATTTGGGGTTAAAATGTA
1 ATTTTGGAAAATTCGGGGGTAAAATGTA
** * * * *
27447484 ATTTTACAAATTTTTGGGGTTAAAATATA
1 ATTTTGGAAA-ATTCGGGGGTAAAATGTA
* * * *
27447513 ATTTTTAGAAAGTTTTGGGGTTAAAATGTA
1 A-TTTTGGAAA-ATTCGGGGGTAAAATGTA
27447543 ATTTT
1 ATTTT
27447548 CAAAAAGTTT
Statistics
Matches: 178, Mismatches: 47, Indels: 26
0.71 0.19 0.10
Matches are distributed among these distances:
27 1 0.01
28 35 0.20
29 80 0.45
30 50 0.28
31 12 0.07
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (28 bp):
ATTTTGGAAAATTCGGGGGTAAAATGTA
Found at i:27447529 original size:30 final size:30
Alignment explanation
Indices: 27447467--27447729 Score: 255
Period size: 30 Copynumber: 8.9 Consensus size: 30
27447457 TTTTGGAAAA
* *
27447467 TTTGGGGTTAAAATGTAA-TTTTACAAATT
1 TTTGGGGTTAAAATGTAATTTTTAGAAAGT
*
27447496 TTTGGGGTTAAAATATAATTTTTAGAAAGT
1 TTTGGGGTTAAAATGTAATTTTTAGAAAGT
* *
27447526 TTTGGGGTTAAAATGTAATTTTCAAAAAGT
1 TTTGGGGTTAAAATGTAATTTTTAGAAAGT
* * * *
27447556 TTTAGGCTTAAAATGTAATATTCAGAAAGT
1 TTTGGGGTTAAAATGTAATTTTTAGAAAGT
* **
27447586 TTTGGGGTTAAAATATAATTTTGGGAAAG-
1 TTTGGGGTTAAAATGTAATTTTTAGAAAGT
* * * *
27447615 TTTAGGGTCAAAATGTAATTTTCAAAAAG-
1 TTTGGGGTTAAAATGTAATTTTTAGAAAGT
* * * *
27447644 TTTGAGGTCAAAATATAA-TTTTGGAAAAGT
1 TTTGGGGTTAAAATGTAATTTTTAG-AAAGT
** * *
27447674 TTAAGGGTCAAAATGTAATTTTTAAAAAGT
1 TTTGGGGTTAAAATGTAATTTTTAGAAAGT
**
27447704 TTTAAGGTTAAAATGTAATTTTTAGA
1 TTTGGGGTTAAAATGTAATTTTTAGA
27447730 CAGTCCAGGG
Statistics
Matches: 192, Mismatches: 38, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
28 3 0.02
29 59 0.31
30 126 0.66
31 4 0.02
ACGTcount: A:0.38, C:0.03, G:0.19, T:0.40
Consensus pattern (30 bp):
TTTGGGGTTAAAATGTAATTTTTAGAAAGT
Found at i:27447545 original size:59 final size:59
Alignment explanation
Indices: 27447467--27447725 Score: 281
Period size: 59 Copynumber: 4.4 Consensus size: 59
27447457 TTTTGGAAAA
* * * * * *
27447467 TTTGGGGTTAAAATGTAATTTT-ACAAATTTTTGGGGTTAAAATATAATTTTTAGAAAGT
1 TTTGGGGTTAAAATGTAATTTTGA-AAAGTTTTAGGGTCAAAATGTAATTTTCAAAAAGT
* * * * *
27447526 TTTGGGGTTAAAATGTAATTTTCAAAAAGTTTTAGGCTTAAAATGTAATATTCAGAAAGT
1 TTTGGGGTTAAAATGTAATTTT-GAAAAGTTTTAGGGTCAAAATGTAATTTTCAAAAAGT
* *
27447586 TTTGGGGTTAAAATATAATTTTGGGAAAG-TTTAGGGTCAAAATGTAATTTTCAAAAAG-
1 TTTGGGGTTAAAATGTAATTTT-GAAAAGTTTTAGGGTCAAAATGTAATTTTCAAAAAGT
* * * * *
27447644 TTTGAGGTCAAAATATAATTTTGGAAAAGTTTAAGGGTCAAAATGTAATTTTTAAAAAGT
1 TTTGGGGTTAAAATGTAATTTT-GAAAAGTTTTAGGGTCAAAATGTAATTTTCAAAAAGT
**
27447704 TTTAAGGTTAAAATGTAATTTT
1 TTTGGGGTTAAAATGTAATTTT
27447726 TAGACAGTCC
Statistics
Matches: 174, Mismatches: 22, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
58 26 0.15
59 74 0.43
60 73 0.42
61 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.19, T:0.40
Consensus pattern (59 bp):
TTTGGGGTTAAAATGTAATTTTGAAAAGTTTTAGGGTCAAAATGTAATTTTCAAAAAGT
Found at i:27448209 original size:12 final size:13
Alignment explanation
Indices: 27448181--27448213 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
27448171 TATTTTTTAG
27448181 TTTTTCATTCTAT
1 TTTTTCATTCTAT
27448194 TTTTTCATTCTAT
1 TTTTTCATTCTAT
27448207 TTTTTCA
1 TTTTTCA
27448214 AAAAAAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTCATTCTAT
Found at i:27448828 original size:3 final size:3
Alignment explanation
Indices: 27448779--27448812 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
27448769 TATTTAAACA
27448779 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
27448813 AAGCACTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:27449552 original size:6 final size:6
Alignment explanation
Indices: 27449541--27449602 Score: 53
Period size: 6 Copynumber: 11.2 Consensus size: 6
27449531 TTATAATAAT
* *
27449541 TTTAAA TTTAAA -TTAAA TCTAAA TTT-AA --TAAA TGTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
27449585 ATTAAA -ATAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA T
27449603 GGTTTGGTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
3 1 0.02
4 2 0.04
5 11 0.24
6 31 0.69
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:27449563 original size:17 final size:17
Alignment explanation
Indices: 27449543--27449602 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
27449533 ATAATAATTT
*
27449543 TAAATTTAAATTAAATC
1 TAAATTTAAATTAAATA
*
27449560 TAAATTT-AA-TAAATG
1 TAAATTTAAATTAAATA
27449575 TAAATTTAAAATTAAA-A
1 TAAATTT-AAATTAAATA
27449592 TAAATTTAAAT
1 TAAATTTAAAT
27449603 GGTTTGGTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
15 12 0.32
16 6 0.16
17 16 0.42
18 4 0.11
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTAAATA
Found at i:27449571 original size:32 final size:32
Alignment explanation
Indices: 27449534--27449600 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
27449524 ATTTTATTTA
* * *
27449534 TAATAATTTTAAATTT-AAATTAAATCTAAATT
1 TAATAAATGTAAATTTAAAATTAAA-ATAAATT
27449566 TAATAAATGTAAATTTAAAATTAAAATAAATT
1 TAATAAATGTAAATTTAAAATTAAAATAAATT
27449598 TAA
1 TAA
27449601 ATGGTTTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 23 0.74
33 8 0.26
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (32 bp):
TAATAAATGTAAATTTAAAATTAAAATAAATT
Found at i:27449578 original size:15 final size:16
Alignment explanation
Indices: 27449543--27449583 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
27449533 ATAATAATTT
27449543 TAAATTTAAATTAAATC
1 TAAATTT-AATTAAATC
*
27449560 TAAATTTAA-TAAATG
1 TAAATTTAATTAAATC
27449575 TAAATTTAA
1 TAAATTTAA
27449584 AATTAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
16 2 0.09
17 7 0.30
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (16 bp):
TAAATTTAATTAAATC
Found at i:27449579 original size:21 final size:20
Alignment explanation
Indices: 27449549--27449589 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
27449539 ATTTTAAATT
*
27449549 TAAATTAAATCTAAATTTAA
1 TAAATTAAATCTAAAATTAA
*
27449569 TAAATGTAAATTTAAAATTAA
1 TAAAT-TAAATCTAAAATTAA
27449590 AATAAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
TAAATTAAATCTAAAATTAA
Found at i:27449964 original size:92 final size:92
Alignment explanation
Indices: 27449855--27450632 Score: 1349
Period size: 92 Copynumber: 8.5 Consensus size: 92
27449845 GACGTCTAGG
* * *
27449855 CTTCATCTTGCTTTTACTACAACTTTAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTT
27449920 CAAGAGGATAAGAATTGACATTTGAAA
66 CAAGAGGATAAGAATTGACATTTGAAA
27449947 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTT
27450012 CAAGAGGATAAGAATTGACATTTGAAA
66 CAAGAGGATAAGAATTGACATTTGAAA
27450039 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTT
27450104 CAAGAGGATAAGAATTGACATTTGAAA
66 CAAGAGGATAAGAATTGACATTTGAAA
* *
27450131 CTTCATCTTGCTCTCACTATAACTACAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTT
27450196 CAAGAGGATAAGAATTGACATTTGAAA
66 CAAGAGGATAAGAATTGACATTTGAAA
* *
27450223 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCGTTATCCAACTTTACTGTAACTT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTT
*
27450288 CAAGAGGATAAGAATTGACATTTGAAG
66 CAAGAGGATAAGAATTGACATTTGAAA
*
27450315 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCGTTATCCAACTTTACTATAACTT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTT
* * * *
27450380 CAAGAGGTTAAGAAATGACGTTTGAAC
66 CAAGAGGATAAGAATTGACATTTGAAA
* *
27450407 CTTTATCTTGCTCTTACTATAACTTCAGAGAGATAAAGGTTCGTTATCCAACTTTACTATAACTT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTT
* *
27450472 CAAGAGGATAAGAATTGACGTTTGAAG
66 CAAGAGGATAAGAATTGACATTTGAAA
* * *
27450499 CTTCATCTGGCTCTTACTATAACTTCAGAGAGATAAAGGTTCGTTATCCAACGTTACTATAACTT
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTT
* * *
27450564 CAAAAGGATAAGAATTGACGTTTGAAG
66 CAAGAGGATAAGAATTGACATTTGAAA
27450591 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGATTC
1 CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGATTC
27450633 AATATTTTTG
Statistics
Matches: 661, Mismatches: 25, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 661 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Consensus pattern (92 bp):
CTTCATCTTGCTCTTACTATAACTTCAGAGAGATAAAGATTCGTTATCCAACTTTACTATAACTT
CAAGAGGATAAGAATTGACATTTGAAA
Found at i:27451584 original size:80 final size:80
Alignment explanation
Indices: 27451451--27451630 Score: 333
Period size: 80 Copynumber: 2.2 Consensus size: 80
27451441 TGAAATTTTA
*
27451451 TTGGAGGCAAAGCTCACATGAAAAAAAGTGACCCATATTGGTCAAAGGATGCCGAAAATAGAGTA
1 TTGGAGGCAAAGCTTACATGAAAAAAAGTGACCCATATTGGTCAAAGGATGCCGAAAATAGAGTA
27451516 AGCAAAGAGTATCAT
66 AGCAAAGAGTATCAT
*
27451531 TTGGAGGCAAAGCTTACATGAAAAAAAGTGACCCATATTGGTCAAAGGATGCCGAATATAGAGTA
1 TTGGAGGCAAAGCTTACATGAAAAAAAGTGACCCATATTGGTCAAAGGATGCCGAAAATAGAGTA
27451596 AGCAAAGAGTATCAT
66 AGCAAAGAGTATCAT
*
27451611 TTGGAGGCAAAGCTTGCATG
1 TTGGAGGCAAAGCTTACATG
27451631 GATGAAAAGA
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 97 1.00
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.21
Consensus pattern (80 bp):
TTGGAGGCAAAGCTTACATGAAAAAAAGTGACCCATATTGGTCAAAGGATGCCGAAAATAGAGTA
AGCAAAGAGTATCAT
Found at i:27458450 original size:58 final size:58
Alignment explanation
Indices: 27458387--27458690 Score: 427
Period size: 58 Copynumber: 5.2 Consensus size: 58
27458377 ACTCGAGAGC
* * * *
27458387 AAAATGGTAATTTTGGTCGAAATTG-GGATAAAAACGGGA-TTTGGAAAGTTTGAGGGT
1 AAAATGGTAATTTTGGT-GAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGT
* * *
27458444 AAAAATGGTAATTTTTGGTAAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGT
1 -AAAATGGTAA-TTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGT
* * *
27458504 AAAGTGGTAATTTTGGTGAAATCGAAGTTAAAAATGGAATTTTAGAAAGTTTGAGGGT
1 AAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGT
*
27458562 AAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTTGAGGGT
1 AAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGT
* *
27458620 AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAATTT-AGGGTT
1 AAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGAGGG-T
27458678 AAAAT-GTAATTTT
1 AAAATGGTAATTTT
27458691 ACAAAGTTTT
Statistics
Matches: 224, Mismatches: 18, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
57 12 0.05
58 169 0.75
59 26 0.12
60 17 0.08
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGT
Found at i:27458499 original size:29 final size:29
Alignment explanation
Indices: 27458426--27458690 Score: 189
Period size: 29 Copynumber: 9.1 Consensus size: 29
27458416 AAAAACGGGA
*
27458426 TTTGGAAAGTTTGAGGGTAAAAATGGTAATT
1 TTTGGAAA-TTCGAGGGTAAAAATGGTAA-T
*
27458457 TTTGGTAAAATCGA-GGTCAAAAATGG-AAT
1 TTTGG-AAATTCGAGGGT-AAAAATGGTAAT
*
27458486 TTTGGAAAGTTCGAGGGT-AAAGTGGTAAT
1 TTTGGAAA-TTCGAGGGTAAAAATGGTAAT
* *
27458515 TTTGGTGAAA-TCGAAGTTAAAAATGG-AAT
1 TTT-G-GAAATTCGAGGGTAAAAATGGTAAT
* *
27458544 TTTAGAAAGTTTGAGGGT-AAAATGGTAAT
1 TTTGGAAA-TTCGAGGGTAAAAATGGTAAT
*
27458573 TTTGGTGAAA-TCGAGGTTAAAAATGG-AAT
1 TTT-G-GAAATTCGAGGGTAAAAATGGTAAT
* *
27458602 TTTAGAAAGTTTGAGGGT-AAAATGGTAAT
1 TTTGGAAA-TTCGAGGGTAAAAATGGTAAT
27458631 TTTGGTGAAA-TCG-GGGTTAAAAATGG-AAT
1 TTT-G-GAAATTCGAGGG-TAAAAATGGTAAT
* *
27458660 TTTGGAAAATT-TAGGGTTAAAAT-GTAAT
1 TTTGG-AAATTCGAGGGTAAAAATGGTAAT
27458688 TTT
1 TTT
27458691 ACAAAGTTTT
Statistics
Matches: 188, Mismatches: 21, Indels: 53
0.72 0.08 0.20
Matches are distributed among these distances:
27 10 0.05
28 42 0.22
29 76 0.40
30 29 0.15
31 28 0.15
32 3 0.02
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (29 bp):
TTTGGAAATTCGAGGGTAAAAATGGTAAT
Found at i:27458721 original size:116 final size:114
Alignment explanation
Indices: 27458387--27458749 Score: 346
Period size: 116 Copynumber: 3.1 Consensus size: 114
27458377 ACTCGAGAGC
* * * * * * *
27458387 AAAATGGTAATTTTGGTCGAAATTG-GGATAAAAACGGGA-TTTGGAAAGTTTGAGGGTAAAAAT
1 AAAATGGTAATTTTGGT-GAAATCGAAGTTAAAAATGGAATTTTAGAAAATTTGAGGGT-AAAAT
* * *
27458450 GGTAATTTTTGGTA-AAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGT
64 GGTAA-TTTT-G-ACAAATCGAGGTTAAAAAT-GAATTTTAGAAAGTTTGAGGGT
* *
27458504 AAAGTGGTAATTTTGGTGAAATCGAAGTTAAAAATGGAATTTTAGAAAGTTTGAGGGTAAAATGG
1 AAAATGGTAATTTTGGTGAAATCGAAGTTAAAAATGGAATTTTAGAAAATTTGAGGGTAAAATGG
**
27458569 TAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTTGAGGGT
66 TAATTTT-GACAAATCGAGGTTAAAAAT-GAATTTTAGAAAGTTTGAGGGT
** *
27458620 AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAATTT-AGGGTTAAAAT-
1 AAAATGGTAATTTTGGTGAAATCGAAGTTAAAAATGGAATTTTAGAAAATTTGAGGG-TAAAATG
** * *
27458683 GTAATTTT-ACAAAGTTTTAGGGTTAAAATAT-AATTTTTAAAAAGTTTTAGGGTT
65 GTAATTTTGACAAA--TCGA-GGTTAAAA-ATGAA-TTTTAGAAAGTTTGAGGG-T
27458737 AAAAT-GTAATTTT
1 AAAATGGTAATTTT
27458750 CAAAAAGTTT
Statistics
Matches: 214, Mismatches: 22, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
113 3 0.01
115 16 0.07
116 134 0.63
117 44 0.21
118 17 0.08
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.34
Consensus pattern (114 bp):
AAAATGGTAATTTTGGTGAAATCGAAGTTAAAAATGGAATTTTAGAAAATTTGAGGGTAAAATGG
TAATTTTGACAAATCGAGGTTAAAAATGAATTTTAGAAAGTTTGAGGGT
Found at i:27458727 original size:30 final size:30
Alignment explanation
Indices: 27458644--27458871 Score: 266
Period size: 30 Copynumber: 7.6 Consensus size: 30
27458634 GGTGAAATCG
* **
27458644 GGGTTAAAAATGGAATTTTGGAAAA--TTTA
1 GGGTT-AAAATGTAATTTTTAAAAAGTTTTA
*
27458673 GGGTTAAAATGTAA-TTTTACAAAGTTTTA
1 GGGTTAAAATGTAATTTTTAAAAAGTTTTA
*
27458702 GGGTTAAAATATAATTTTTAAAAAGTTTTA
1 GGGTTAAAATGTAATTTTTAAAAAGTTTTA
*
27458732 GGGTTAAAATGTAATTTTCAAAAAGTTTTA
1 GGGTTAAAATGTAATTTTTAAAAAGTTTTA
* * * *
27458762 GGCTCAAAATGTAATATTCAAAAAGTTTTA
1 GGGTTAAAATGTAATTTTTAAAAAGTTTTA
* * *
27458792 GGGTCAAAATATAA-TTTTAGAAAAGTTTAA
1 GGGTTAAAATGTAATTTTTA-AAAAGTTTTA
* *
27458822 GGGGTTAAAATGTAATTTTCAAAAAGTTTTG
1 -GGGTTAAAATGTAATTTTTAAAAAGTTTTA
27458853 GGGTTAAAATGTAATTTTT
1 GGGTTAAAATGTAATTTTT
27458872 GGATAGTCTA
Statistics
Matches: 171, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
27 6 0.04
28 8 0.05
29 25 0.15
30 108 0.63
31 20 0.12
32 4 0.02
ACGTcount: A:0.40, C:0.03, G:0.18, T:0.39
Consensus pattern (30 bp):
GGGTTAAAATGTAATTTTTAAAAAGTTTTA
Found at i:27459876 original size:12 final size:12
Alignment explanation
Indices: 27459851--27459884 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
27459841 ATTTATAACC
*
27459851 TAATAAATATTGT
1 TAAT-AATAATGT
27459864 TAATAATAATGT
1 TAATAATAATGT
27459876 TAATAATAA
1 TAATAATAA
27459885 CAGTAATAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (12 bp):
TAATAATAATGT
Found at i:27460993 original size:59 final size:57
Alignment explanation
Indices: 27460925--27461266 Score: 262
Period size: 59 Copynumber: 5.8 Consensus size: 57
27460915 CGAACTTCTA
27460925 AAAATTACCATTTTACCCCAGAATATCCAAAAATTCCATTTTTAACCCTAAAACTTTC
1 AAAATTACCATTTTACCCC-GAATATCCAAAAATTCCATTTTTAACCCTAAAACTTTC
* ** * * *
27460983 AAGAATTACCATTTTACCCCTAAATATCCAAAACCTCCACTTTTGA-CCTCGAAACTTTC
1 AA-AATTACCATTTTACCCC-GAATATCCAAAAATTCCATTTTTAACCCT-AAAACTTTC
* * * *
27461042 AAAAATTACCATTTTACCCTCGAAT-GCCTAAAATTTCATTTTTAACCCT-AAATTTTCC
1 -AAAATTACCATTTTACCC-CGAATATCCAAAAATTCCATTTTTAACCCTAAAACTTT-C
* * * * *
27461100 TAAAATTATCATTTTACCCCCGGATGTCCAAAAACTT-CATTTTTGACCCTGAAACTTTC
1 -AAAATTACCATTTTA-CCCCGAATATCCAAAAA-TTCCATTTTTAACCCTAAAACTTTC
* * * ** * **
27461159 AAAAATTACCATTTTACTCTCGAATGT-CTAAAATTTTATTTTTAACCCCAAATTTTTCC
1 -AAAATTACCATTTTAC-CCCGAATATCCAAAAATTCCATTTTTAACCCTAAAACTTT-C
* * * * *
27461218 AAAATTACCATTTTGCCCCCGAGTATCCAAATAGTCTCATTTTCAACCC
1 AAAATTACCATTTT-ACCCCGAATATCCAAAAATTC-CATTTTTAACCC
27461267 CGATTGCTTT
Statistics
Matches: 224, Mismatches: 44, Indels: 30
0.75 0.15 0.10
Matches are distributed among these distances:
57 8 0.04
58 78 0.35
59 117 0.52
60 21 0.09
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCGAATATCCAAAAATTCCATTTTTAACCCTAAAACTTTC
Found at i:27461004 original size:30 final size:30
Alignment explanation
Indices: 27460924--27461060 Score: 106
Period size: 30 Copynumber: 4.6 Consensus size: 30
27460914 CCGAACTTCT
*
27460924 AAAAATTACCATTTTACCCC-AGAATATCC
1 AAAAATTACCATTTTACCCCTAAAATATCC
* *
27460953 AAAAATT-CCATTTTTAACCCTAAAACT-TTC
1 AAAAATTACCA-TTTTACCCCTAAAA-TATCC
*
27460983 AAGAATTACCATTTTACCCCT-AAATATCC
1 AAAAATTACCATTTTACCCCTAAAATATCC
** * * * *
27461012 AAAACCT-CCACTTTTGACCTCGAAACT-TTC
1 AAAAATTACCA-TTTT-ACCCCTAAAATATCC
27461042 AAAAATTACCATTTTACCC
1 AAAAATTACCATTTTACCC
27461061 TCGAATGCCT
Statistics
Matches: 83, Mismatches: 16, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
28 7 0.08
29 31 0.37
30 35 0.42
31 10 0.12
ACGTcount: A:0.38, C:0.28, G:0.03, T:0.31
Consensus pattern (30 bp):
AAAAATTACCATTTTACCCCTAAAATATCC
Found at i:27461063 original size:30 final size:31
Alignment explanation
Indices: 27460887--27461065 Score: 100
Period size: 29 Copynumber: 6.1 Consensus size: 31
27460877 AGAGGTCCCT
* * *
27460887 AAACTATCAAAAATTA-TATTTTGACCCCCG
1 AAACTTTCAAAAATTACCATTTTGACCCTCG
27460917 -AAC-TTCTAAAAATTACCATTTT-ACCC-C-
1 AAACTTTC-AAAAATTACCATTTTGACCCTCG
* * *
27460944 AGAA-TATCCAAAAATT-CCATTTTTAACCCT-A
1 A-AACT-TTCAAAAATTACCA-TTTTGACCCTCG
* *
27460975 AAACTTTCAAGAATTACCATTTT-ACCC-CT
1 AAACTTTCAAAAATTACCATTTTGACCCTCG
* **
27461004 AAA-TATCCAAAACCT-CCACTTTTGA-CCTCG
1 AAACT-TTCAAAAATTACCA-TTTTGACCCTCG
27461034 AAACTTTCAAAAATTACCATTTT-ACCCTCG
1 AAACTTTCAAAAATTACCATTTTGACCCTCG
27461064 AA
1 AA
27461066 TGCCTAAAAT
Statistics
Matches: 115, Mismatches: 14, Indels: 40
0.68 0.08 0.24
Matches are distributed among these distances:
28 10 0.09
29 48 0.42
30 48 0.42
31 9 0.08
ACGTcount: A:0.38, C:0.27, G:0.04, T:0.31
Consensus pattern (31 bp):
AAACTTTCAAAAATTACCATTTTGACCCTCG
Found at i:27461090 original size:29 final size:28
Alignment explanation
Indices: 27461053--27461202 Score: 74
Period size: 30 Copynumber: 5.2 Consensus size: 28
27461043 AAAATTACCA
27461053 TTTTACCCTCGAATGCCTAAAATTTCAT
1 TTTTACCCTCGAATGCCTAAAATTTCAT
* *
27461081 TTTTAACCCT-AAATTTTCCTAAAATTATCA-
1 TTTT-ACCCTCGAA--TGCCTAAAATT-TCAT
* * * *
27461111 TTTTACCCCCGGATGTCCAAAAACTTCAT
1 TTTTACCCTCGAATG-CCTAAAATTTCAT
** * *
27461140 TTTTGACCCT-GAAACTTTCAAAAATTACCA-
1 TTTT-ACCCTCG-AA-TGCCTAAAATT-TCAT
* * *
27461170 TTTTACTCTCGAATGTCTAAAATTTTAT
1 TTTTACCCTCGAATGCCTAAAATTTCAT
27461198 TTTTA
1 TTTTA
27461203 ACCCCAAATT
Statistics
Matches: 90, Mismatches: 19, Indels: 26
0.67 0.14 0.19
Matches are distributed among these distances:
27 1 0.01
28 24 0.27
29 27 0.30
30 32 0.36
31 6 0.07
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.41
Consensus pattern (28 bp):
TTTTACCCTCGAATGCCTAAAATTTCAT
Found at i:27461091 original size:117 final size:117
Alignment explanation
Indices: 27460924--27461248 Score: 397
Period size: 117 Copynumber: 2.8 Consensus size: 117
27460914 CCGAACTTCT
* * * *
27460924 AAAAATTACCATTTTACCC-CAGAATATCCAAAAATTCCATTTTTAACCCTAAAACTTT-CAAGA
1 AAAAATTACCATTTTACCCTC-GAAT-GCCTAAAATTTCATTTTTAACCCTAAAATTTTCCAA-A
* *
27460987 ATTACCATTTTACCCCTAAATATCCAAAACCTCCACTTTTGA-CCTCGAAACTTTC
63 ATTACCATTTTACCCCCAAATATCCAAAAACTCCACTTTTGACCCT-GAAACTTTC
27461042 AAAAATTACCATTTTACCCTCGAATGCCTAAAATTTCATTTTTAACCCT-AAATTTTCCTAAAAT
1 AAAAATTACCATTTTACCCTCGAATGCCTAAAATTTCATTTTTAACCCTAAAATTTTCC-AAAAT
* ** * * *
27461106 TATCATTTTACCCCCGGATGTCCAAAAACTTCATTTTTGACCCTGAAACTTTC
65 TACCATTTTACCCCCAAATATCCAAAAACTCCACTTTTGACCCTGAAACTTTC
* * * * *
27461159 AAAAATTACCATTTTACTCTCGAATGTCTAAAATTTTATTTTTAACCCCAAATTTTTCCAAAATT
1 AAAAATTACCATTTTACCCTCGAATGCCTAAAATTTCATTTTTAACCCTAAAATTTTCCAAAATT
* * *
27461224 ACCATTTTGCCCCCGAGTATCCAAA
66 ACCATTTTACCCCCAAATATCCAAA
27461249 TAGTCTCATT
Statistics
Matches: 180, Mismatches: 22, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
116 6 0.03
117 137 0.76
118 36 0.20
119 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.35
Consensus pattern (117 bp):
AAAAATTACCATTTTACCCTCGAATGCCTAAAATTTCATTTTTAACCCTAAAATTTTCCAAAATT
ACCATTTTACCCCCAAATATCCAAAAACTCCACTTTTGACCCTGAAACTTTC
Found at i:27465554 original size:7 final size:7
Alignment explanation
Indices: 27465542--27465579 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
27465532 AAACCTAATA
27465542 AAAAAAG
1 AAAAAAG
27465549 AAAAAAG
1 AAAAAAG
27465556 AAAAAAG
1 AAAAAAG
*
27465563 AAAGAA-
1 AAAAAAG
*
27465569 AAAAAGG
1 AAAAAAG
27465576 AAAA
1 AAAA
27465580 GTCAAGATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
6 4 0.15
7 23 0.85
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:27466415 original size:7 final size:7
Alignment explanation
Indices: 27466398--27466456 Score: 59
Period size: 7 Copynumber: 8.6 Consensus size: 7
27466388 TCAAATCTAA
27466398 AAAAAAGG
1 AAAAAA-G
27466406 AAAAAAG
1 AAAAAAG
27466413 AAAAAA-
1 AAAAAAG
*
27466419 AAAGAAG
1 AAAAAAG
*
27466426 GAAAAAG
1 AAAAAAG
*
27466433 AAAATAG
1 AAAAAAG
*
27466440 AAAAACG
1 AAAAAAG
27466447 -AAAAAG
1 AAAAAAG
27466453 AAAA
1 AAAA
27466457 TGAGAGGTCG
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
6 10 0.24
7 25 0.61
8 6 0.15
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:27466426 original size:21 final size:19
Alignment explanation
Indices: 27466396--27466456 Score: 77
Period size: 20 Copynumber: 3.1 Consensus size: 19
27466386 ACTCAAATCT
27466396 AAAAAAAAGGAAAAAAGAAA
1 AAAAAAAAGG-AAAAAGAAA
27466416 AAAAAAGAAGGAAAAAGAAA
1 AAAAAA-AAGGAAAAAGAAA
* *
27466436 ATAGAAAAACGAAAAAGAAA
1 A-AAAAAAAGGAAAAAGAAA
27466456 A
1 A
27466457 TGAGAGGTCG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 29 0.78
21 8 0.22
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (19 bp):
AAAAAAAAGGAAAAAGAAA
Found at i:27466442 original size:13 final size:14
Alignment explanation
Indices: 27466399--27466456 Score: 52
Period size: 13 Copynumber: 4.3 Consensus size: 14
27466389 CAAATCTAAA
*
27466399 AAAAAGGAAAAAAG
1 AAAAACGAAAAAAG
27466413 AAAAA--AAAAGAAGG
1 AAAAACGAAAA-AA-G
*
27466427 AAAAA-GAAAATAG
1 AAAAACGAAAAAAG
27466440 AAAAACG-AAAAAG
1 AAAAACGAAAAAAG
27466453 AAAA
1 AAAA
27466457 TGAGAGGTCG
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
12 4 0.11
13 17 0.45
14 13 0.34
15 4 0.11
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (14 bp):
AAAAACGAAAAAAG
Found at i:27467522 original size:51 final size:51
Alignment explanation
Indices: 27467357--27467845 Score: 525
Period size: 51 Copynumber: 9.8 Consensus size: 51
27467347 CAAGTTTAAC
* * ** * *
27467357 AGGGAATGATCTAAG-CCGCGACGGTGGATCCAGTACCACAAAAATA-TGA
1 AGGGAAAGATCTAAGACCGCAACGGCAGATCCAGTACCACAAAGATACAGA
* * * * *
27467406 CGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGCGAAG--ACACA
1 AGGGAAAGATCTAAGACCGCAACGGCAGATCCAGTACCACAAAGATACAGA
* * *
27467455 AGGGAAAGATTTAAGACTGCAACGGTAGATCCAGTACCACAAAGATACAGA
1 AGGGAAAGATCTAAGACCGCAACGGCAGATCCAGTACCACAAAGATACAGA
*
27467506 AGGGAAAGATTTAAGACCGCAACGGCAGATCCAGTACCACAAAG-TACAGA
1 AGGGAAAGATCTAAGACCGCAACGGCAGATCCAGTACCACAAAGATACAGA
* * * *
27467556 AGGAAAAGATCTAAGACCGCAACCGCAGATCTAATACCACAAAGATACAGA
1 AGGGAAAGATCTAAGACCGCAACGGCAGATCCAGTACCACAAAGATACAGA
* * *
27467607 AGGGAAAGATCTAAGATCGCAACGGCAGATCCAGTACCATAAAGATATAGA
1 AGGGAAAGATCTAAGACCGCAACGGCAGATCCAGTACCACAAAGATACAGA
* * *
27467658 AGGGAAAGATCTAAGACCGTAACGGTAGATCCGGTACCACAAAGATACAGA
1 AGGGAAAGATCTAAGACCGCAACGGCAGATCCAGTACCACAAAGATACAGA
* * * *
27467709 AGGGAAAGATCTAA-AGTCGTAACGACGGATCCAGTACCAC-AA-ATACACGA
1 AGGGAAAGATCTAAGA-CCGCAACGGCAGATCCAGTACCACAAAGATACA-GA
* * * * *** *
27467759 CGAGAAAGATCTAAGACCGCAACGACGGATCCAGTACCGTGAAG--ACACA
1 AGGGAAAGATCTAAGACCGCAACGGCAGATCCAGTACCACAAAGATACAGA
*
27467808 AGGGAAAGATCTAAG-CCGCAACAGC-GAATCCAGTACCA
1 AGGGAAAGATCTAAGACCGCAACGGCAG-ATCCAGTACCA
27467846 TGAAGATTTG
Statistics
Matches: 375, Mismatches: 54, Indels: 23
0.83 0.12 0.05
Matches are distributed among these distances:
47 1 0.00
48 19 0.05
49 70 0.19
50 108 0.29
51 177 0.47
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.13
Consensus pattern (51 bp):
AGGGAAAGATCTAAGACCGCAACGGCAGATCCAGTACCACAAAGATACAGA
Found at i:27467607 original size:101 final size:101
Alignment explanation
Indices: 27467364--27467845 Score: 525
Period size: 101 Copynumber: 4.8 Consensus size: 101
27467354 AACAGGGAAT
* * * * *
27467364 GATCTAAG-CCGCGACGGTGGATCCAGTACCACAAAAATA-TGACGGGAAAGATCTAAGACCGCA
1 GATCTAAGACCGCAACGGTAGATCCAGTACCACAAAGATACAGAAGGGAAAGATCTAAGACCGCA
* * * * *
27467427 ACGGCGGATCCAGTACCGCGAAG-ACACAAGGGAAA
66 ACGGCAGATCCAGTACCACAAAGTACAGAAGGAAAA
* * *
27467462 GATTTAAGACTGCAACGGTAGATCCAGTACCACAAAGATACAGAAGGGAAAGATTTAAGACCGCA
1 GATCTAAGACCGCAACGGTAGATCCAGTACCACAAAGATACAGAAGGGAAAGATCTAAGACCGCA
27467527 ACGGCAGATCCAGTACCACAAAGTACAGAAGGAAAA
66 ACGGCAGATCCAGTACCACAAAGTACAGAAGGAAAA
* * * * *
27467563 GATCTAAGACCGCAACCGCAGATCTAATACCACAAAGATACAGAAGGGAAAGATCTAAGATCGCA
1 GATCTAAGACCGCAACGGTAGATCCAGTACCACAAAGATACAGAAGGGAAAGATCTAAGACCGCA
* * *
27467628 ACGGCAGATCCAGTACCATAAAGATATAGAAGGGAAA
66 ACGGCAGATCCAGTACCACAAAG-TACAGAAGGAAAA
* * * *
27467665 GATCTAAGACCGTAACGGTAGATCCGGTACCACAAAGATACAGAAGGGAAAGATCTAA-AGTCGT
1 GATCTAAGACCGCAACGGTAGATCCAGTACCACAAAGATACAGAAGGGAAAGATCTAAGA-CCGC
* * *
27467729 AACGACGGATCCAGTACCACAAA-TACACG-ACGAGAAA
65 AACGGCAGATCCAGTACCACAAAGTACA-GAAGGA-AAA
*** *** *
27467766 GATCTAAGACCGCAACGACGGATCCAGTACCGTGAAG--ACACAAGGGAAAGATCTAAG-CCGCA
1 GATCTAAGACCGCAACGGTAGATCCAGTACCACAAAGATACAGAAGGGAAAGATCTAAGACCGCA
*
27467828 ACAGC-GAATCCAGTACCA
66 ACGGCAG-ATCCAGTACCA
27467846 TGAAGATTTG
Statistics
Matches: 325, Mismatches: 50, Indels: 18
0.83 0.13 0.05
Matches are distributed among these distances:
97 1 0.00
98 24 0.07
99 45 0.14
100 46 0.14
101 123 0.38
102 86 0.26
ACGTcount: A:0.41, C:0.23, G:0.24, T:0.13
Consensus pattern (101 bp):
GATCTAAGACCGCAACGGTAGATCCAGTACCACAAAGATACAGAAGGGAAAGATCTAAGACCGCA
ACGGCAGATCCAGTACCACAAAGTACAGAAGGAAAA
Found at i:27467659 original size:152 final size:149
Alignment explanation
Indices: 27467357--27467845 Score: 510
Period size: 152 Copynumber: 3.3 Consensus size: 149
27467347 CAAGTTTAAC
* * ** * * *
27467357 AGGGAATGATCTAAGCCGCGACGGTGGATCCAGTACCACAAAAATA-TGACGGGAAAGATCTAAG
1 AGGGAAAGATCTAAGCCGCAACGGCAGATCCAGTACCAC-AAAGTACAGAAGGGAAAGATCTAAG
* * * * *
27467421 ACCGCAACGGCGGATCCAGTACCGCGAAG--ACACAAGGGAAAGATTTAAGACTGCAACGGTAGA
65 ACCGCAACCGCGGATCCAGTACCAC-AAGATACAGAAGGGAAAGATCTAAGAC-GCAACGGCAGA
*
27467484 TCCAGTACCACAAAGATACAGA
128 TCCAGTACCATAAAGATACAGA
* *
27467506 AGGGAAAGATTTAAGACCGCAACGGCAGATCCAGTACCACAAAGTACAGAAGGAAAAGATCTAAG
1 AGGGAAAGATCTAAG-CCGCAACGGCAGATCCAGTACCACAAAGTACAGAAGGGAAAGATCTAAG
* * *
27467571 ACCGCAACCGCAGATCTAATACCACAAAGATACAGAAGGGAAAGATCTAAGATCGCAACGGCAGA
65 ACCGCAACCGCGGATCCAGTACCAC-AAGATACAGAAGGGAAAGATCTAAGA-CGCAACGGCAGA
*
27467636 TCCAGTACCATAAAGATATAGA
128 TCCAGTACCATAAAGATACAGA
* * *
27467658 AGGGAAAGATCTAAGACCGTAACGGTAGATCCGGTACCACAAAGATACAGAAGGGAAAGATCTAA
1 AGGGAAAGATCTAAG-CCGCAACGGCAGATCCAGTACCACAAAG-TACAGAAGGGAAAGATCTAA
* * * * *
27467723 -AGTCGTAA-CGACGGATCCAGTACCACAA-ATACACGACGAGAAAGATCTAAGACCGCAACGAC
64 GA-CCGCAACCG-CGGATCCAGTACCACAAGATACA-GAAGGGAAAGATCTAAGA-CGCAACGGC
* * * *
27467785 GGATCCAGTACCGTGAAG--ACACA
125 AGATCCAGTACCATAAAGATACAGA
*
27467808 AGGGAAAGATCTAAGCCGCAACAGC-GAATCCAGTACCA
1 AGGGAAAGATCTAAGCCGCAACGGCAG-ATCCAGTACCA
27467846 TGAAGATTTG
Statistics
Matches: 287, Mismatches: 43, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
148 1 0.00
149 35 0.12
150 77 0.27
151 5 0.02
152 133 0.46
153 36 0.13
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.13
Consensus pattern (149 bp):
AGGGAAAGATCTAAGCCGCAACGGCAGATCCAGTACCACAAAGTACAGAAGGGAAAGATCTAAGA
CCGCAACCGCGGATCCAGTACCACAAGATACAGAAGGGAAAGATCTAAGACGCAACGGCAGATCC
AGTACCATAAAGATACAGA
Found at i:27468625 original size:206 final size:206
Alignment explanation
Indices: 27468271--27470039 Score: 2768
Period size: 206 Copynumber: 8.6 Consensus size: 206
27468261 AGGAAGTCAT
*
27468271 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGGAT
1 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
** * * *
27468336 TGAAACAAGCAATACGGTCATCTTCCTGATGAGATACCGAGAAGAAGACTAAATCAAACCCACGC
66 TGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
* * **
27468401 TCGATGTGAGTAAATCTTCGAA-CCTCAGCTTCCTGATGAGATACCGAGAAGCAGGTTAAAGCAA
131 TCGATGTGAGCAAATCTTCGAACCCT-AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAA
27468465 TAAAATGGTTAG
195 TAAAATGGTTAG
27468477 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
1 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
*
27468542 TGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAATACCAAATCAAACCCACGC
66 TGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
*
27468607 TCGATGTGAGCAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGACGCAGGTCGAAGCAAT
131 TCGATGTGAGCAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT
27468672 AAAATGGTTAG
196 AAAATGGTTAG
** * * *
27468683 CTTTTTGATGAGATACTGAGAAGTGGACTAAATTCGTCTTCCTGATAAGATACAGAGAAGCAGAT
1 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
* *
27468748 TGAAACAAGTGATGCGGTCATCTTTCTGATTAGATACTGAGAAGAAGACCAAATCAAACCCACGC
66 TGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
* *
27468813 TTGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT
131 TCGATGTGAGCAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT
27468878 AAAATGGTTAG
196 AAAATGGTTAG
* * * *
27468889 CTTCCTGATGAGATAATGAGAAATGGACCAAAGTCGTCTTCCTGATGAGATACAAAGAAGCGGAT
1 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
* * ** *
27468954 TGAAATAAGCGATGCAATCACCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
66 TGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
* * * *
27469019 TTGATGTGAGCAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTAAA
131 TCGATGTGAGCAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT
27469084 AAAATGGTTAG
196 AAAATGGTTAG
*
27469095 CTTCCTGATGAGATATTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
1 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
*
27469160 TGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAATACCAAATCAAACCCACGC
66 TGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
* *
27469225 TCGATGTGAGCAAATCTTCGAACCCTAGCTTCCCGATGAGATACTGAGACGCAGGTCGAAGCAAT
131 TCGATGTGAGCAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT
27469290 AAAATGGTTAG
196 AAAATGGTTAG
** * * * *
27469301 CTTTTTGATGAGATATTGAGAAGTGCACCAAATTCGTCTTCCTGATAAGACACAGAGAAGCGGAT
1 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
* *
27469366 TGAAACAAGTGATGCGGTCATCTTTCTGATGAGATACTGAGAAGAAGACTAAATCAAACCCACGC
66 TGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
* * * * *
27469431 TAGATGTGAGCAAATCTTTGAACCCCAGCTTCTTGATGAGATACTGAGAAGCAGGTCAAAGCAAT
131 TCGATGTGAGCAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT
*
27469496 AAAATAGTTAG
196 AAAATGGTTAG
* * * *
27469507 CTTCCTGATGAGATAATGAGAAATGGACCAAAGTCGTCTTCCTGATGAGATACAAAGAAGCGGAT
1 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
* * ** *
27469572 TGAAATAAGCGATGCAATCACCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
66 TGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
* * * *
27469637 TTGATGTGAGCAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGTAAA
131 TCGATGTGAGCAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT
27469702 AAAATGGTTAG
196 AAAATGGTTAG
* *
27469713 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGGGAAGCGAAT
1 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
*
27469778 TGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCGAATC-AACCCACGC
66 TGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
* * * *
27469842 TCGATGTAAGCAAATCTTCGAACCCCAGCTTCTTGATGAGATACTGAGAAGCAGGTCGAAGTAAT
131 TCGATGTGAGCAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT
27469907 AAAATGGTTAG
196 AAAATGGTTAG
* * * * * * *
27469918 CTTCCTGATGAGATACGGAGAAGTGAACCAAATCCATCTTCCTGATGAAACACAGAGAAGTGGAT
1 CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
** * *
27469983 CAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAAGTCAA
66 TGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
27470040 TGAAATCAGA
Statistics
Matches: 1429, Mismatches: 132, Indels: 4
0.91 0.08 0.00
Matches are distributed among these distances:
205 185 0.13
206 1241 0.87
207 3 0.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (206 bp):
CTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGAT
TGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
TCGATGTGAGCAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAAT
AAAATGGTTAG
Found at i:27470388 original size:6 final size:6
Alignment explanation
Indices: 27470370--27470407 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
27470360 AAACTTTTCT
*
27470370 TTTAAA GTTTAAA TTTAAA -TTAAG TTTAAA TTTAAA TT
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT
27470408 GAATTCAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 4 0.14
6 18 0.64
7 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:27470396 original size:17 final size:17
Alignment explanation
Indices: 27470374--27470407 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
27470364 TTTTCTTTTA
27470374 AAGTTTAAATTTAAATT
1 AAGTTTAAATTTAAATT
27470391 AAGTTTAAATTTAAATT
1 AAGTTTAAATTTAAATT
27470408 GAATTCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
AAGTTTAAATTTAAATT
Found at i:27470417 original size:17 final size:17
Alignment explanation
Indices: 27470374--27470417 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
27470364 TTTTCTTTTA
*
27470374 AAGTTTAAATTTAAATT
1 AAGTTCAAATTTAAATT
*
27470391 AAGTTTAAATTTAAATT
1 AAGTTCAAATTTAAATT
27470408 GAA-TTCAAAT
1 -AAGTTCAAAT
27470418 CAAACATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 23 0.92
18 2 0.08
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (17 bp):
AAGTTCAAATTTAAATT
Found at i:27472330 original size:60 final size:58
Alignment explanation
Indices: 27472237--27472587 Score: 214
Period size: 59 Copynumber: 5.9 Consensus size: 58
27472227 AGGGGTCTCT
* **
27472237 AAACTATCCAAAAATTATATTTTAACCCCTAAACTTCTTGAAAATTA-CATTTTGACCCCC
1 AAACT-TCCAAAAATTACATTTTAACCCCTAAACTTC-CAAAAATTACCATTTT-ACCCCC
*
27472297 AAACTTCCTGAAAATTACATTTTAACCCCTAAACTTCCAAAAATTACCATTTTACCCCC
1 AAACTTCC-AAAAATTACATTTTAACCCCTAAACTTCCAAAAATTACCATTTTACCCCC
* * * * * *
27472356 GAACTTCCAAAAATTCCATTTTTGA-CCTTGAAACTTTCAAAAATTACCATTTTACCCTC
1 AAACTTCCAAAAATTACA-TTTTAACCCCT-AAACTTCCAAAAATTACCATTTTACCCCC
** * * * * * * ** * **
27472415 GGA-TATCCAATAACTCCACTTTTGACCCCCAAAATTTTAAAAATTACCATTTAACCCTT
1 AAACT-TCCAAAAATTACA-TTTTAACCCCTAAACTTCCAAAAATTACCATTTTACCCCC
* * * * * * *
27472474 GAA-TGCCTAAAATTTCATTTTTAACCCC-AAATTTTCCTAAAATTACCATTTTACCCTC
1 AAACTTCCAAAAATTACA-TTTTAACCCCTAAA-CTTCCAAAAATTACCATTTTACCCCC
* * * *
27472532 GAA-TGTCCAAAAACTCTA-TTTTTGA-CCCTAAAACTTTCAAAAATTACCATTTTACC
1 AAACT-TCCAAAAA-T-TACATTTTAACCCCT-AAACTTCCAAAAATTACCATTTTACC
27472588 TCGAATATCT
Statistics
Matches: 236, Mismatches: 43, Indels: 25
0.78 0.14 0.08
Matches are distributed among these distances:
57 3 0.01
58 56 0.24
59 133 0.56
60 43 0.18
61 1 0.00
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (58 bp):
AAACTTCCAAAAATTACATTTTAACCCCTAAACTTCCAAAAATTACCATTTTACCCCC
Found at i:27472340 original size:29 final size:29
Alignment explanation
Indices: 27472235--27472409 Score: 165
Period size: 30 Copynumber: 5.9 Consensus size: 29
27472225 TTAGGGGTCT
*
27472235 CTAAACTATCCAAAAATTATATTTTAACCC
1 CTAAACT-TCCAAAAATTACATTTTAACCC
** *
27472265 CTAAACTTCTTGAAAATTACATTTTGACCC
1 CTAAACTTC-CAAAAATTACATTTTAACCC
* *
27472295 CCAAACTTCCTGAAAATTACATTTTAACCC
1 CTAAACTTCC-AAAAATTACATTTTAACCC
27472325 CTAAACTTCCAAAAATTACCATTTT-ACCC
1 CTAAACTTCCAAAAATTA-CATTTTAACCC
** * *
27472354 CCGAACTTCCAAAAATTCCATTTTTGA-CC
1 CTAAACTTCCAAAAATTACA-TTTTAACCC
* *
27472383 TTGAAACTTTCAAAAATTACCATTTTA
1 CT-AAACTTCCAAAAATTA-CATTTTA
27472410 CCCTCGGATA
Statistics
Matches: 120, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
28 2 0.02
29 34 0.28
30 82 0.68
31 2 0.02
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (29 bp):
CTAAACTTCCAAAAATTACATTTTAACCC
Found at i:27472390 original size:59 final size:58
Alignment explanation
Indices: 27472323--27472669 Score: 310
Period size: 59 Copynumber: 5.9 Consensus size: 58
27472313 ACATTTTAAC
* *
27472323 CCCT-AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGA
1 CCCTCAAACTTTCAAAAATTACCATTTTACCCTCGAA-TTCCAAAAATTCCATTTTTGA
* * * * * *
27472381 CCTTGAAACTTTCAAAAATTACCATTTTACCCTCGGATATCCAATAACTCCACTTTTGA
1 CCCTCAAACTTTCAAAAATTACCATTTTACCCTCGAAT-TCCAAAAATTCCATTTTTGA
* * * * * * * * *
27472440 CCCCCAAAATTTTAAAAATTACCATTTAACCCTTGAATGCCTAAAATTTCATTTTTAA
1 CCCTCAAACTTTCAAAAATTACCATTTTACCCTCGAATTCCAAAAATTCCATTTTTGA
* * * *
27472498 CCC-CAAATTTTCCTAAAATTACCATTTTACCCTCGAATGTCCAAAAACTCTATTTTTGA
1 CCCTCAAACTTT-CAAAAATTACCATTTTACCCTCGAAT-TCCAAAAATTCCATTTTTGA
* * * *
27472557 CCCTAAAACTTTCAAAAATTACCATTTTA-CCTCGAATAT-CTAAAATTTCATTTTTAA
1 CCCTCAAACTTTCAAAAATTACCATTTTACCCTCGAAT-TCCAAAAATTCCATTTTTGA
* * * * *
27472614 CCCT-AAATTTTTCCAAAATTACCATTTTGCCCACGAGTGTCC-AAAATTACCATTTT
1 CCCTCAAA-CTTTCAAAAATTACCATTTTACCCTCGAAT-TCCAAAAATT-CCATTTT
27472670 GCCCCCGGGT
Statistics
Matches: 231, Mismatches: 49, Indels: 17
0.78 0.16 0.06
Matches are distributed among these distances:
56 3 0.01
57 42 0.18
58 64 0.28
59 116 0.50
60 6 0.03
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (58 bp):
CCCTCAAACTTTCAAAAATTACCATTTTACCCTCGAATTCCAAAAATTCCATTTTTGA
Found at i:27472528 original size:117 final size:116
Alignment explanation
Indices: 27472316--27472659 Score: 352
Period size: 117 Copynumber: 2.9 Consensus size: 116
27472306 GAAAATTACA
* * * * * * * * *
27472316 TTTTAACCCCTAAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGA
1 TTTTGACCCCAAAACTTTCAAAAATTACCA-TTTAACCTCGAA-TACCTAAAATTTCATTTTTAA
** * * * *
27472381 CCTTGAAA-CTTTCAAAAATTACCATTTTACCCTCGGATATCCAATAACTCCAC
64 CC-CCAAATTTTTCCAAAATTACCATTTTACCCTCGAATATCCAAAAACTCCAC
* * *
27472434 TTTTGACCCCCAAAA-TTTTAAAAATTACCATTTAACCCTTGAATGCCTAAAATTTCATTTTTAA
1 TTTTGA-CCCCAAAACTTTCAAAAATTACCATTTAA-CCTCGAATACCTAAAATTTCATTTTTAA
* * *
27472498 CCCCAAA-TTTTCCTAAAATTACCATTTTACCCTCGAATGTCCAAAAACTCTAT
64 CCCCAAATTTTTCC-AAAATTACCATTTTACCCTCGAATATCCAAAAACTCCAC
* * *
27472551 TTTTGACCCTAAAACTTTCAAAAATTACCATTTTACCTCGAATATCTAAAATTTCATTTTTAACC
1 TTTTGACCCCAAAACTTTCAAAAATTACCATTTAACCTCGAATACCTAAAATTTCATTTTTAACC
* * * * *
27472616 CTAAATTTTTCCAAAATTACCATTTTGCCCACGAGTGTCCAAAA
66 CCAAATTTTTCCAAAATTACCATTTTACCCTCGAATATCCAAAA
27472660 TTACCATTTT
Statistics
Matches: 191, Mismatches: 30, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
116 74 0.39
117 87 0.46
118 23 0.12
119 7 0.04
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.35
Consensus pattern (116 bp):
TTTTGACCCCAAAACTTTCAAAAATTACCATTTAACCTCGAATACCTAAAATTTCATTTTTAACC
CCAAATTTTTCCAAAATTACCATTTTACCCTCGAATATCCAAAAACTCCAC
Found at i:27472658 original size:28 final size:28
Alignment explanation
Indices: 27472625--27472687 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
27472615 CCTAAATTTT
*
27472625 TCCAAAATTACCATTTTGCCCACGAGTG
1 TCCAAAATTACCATTTTGCCCACGAGTA
* *
27472653 TCCAAAATTACCATTTTGCCCCCGGGTA
1 TCCAAAATTACCATTTTGCCCACGAGTA
27472681 TCCAAAA
1 TCCAAAA
27472688 AGTCTCATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.27
Consensus pattern (28 bp):
TCCAAAATTACCATTTTGCCCACGAGTA
Found at i:27482142 original size:11 final size:11
Alignment explanation
Indices: 27482128--27482175 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
27482118 ATTTTAAAAA
27482128 ATTATTAAATT
1 ATTATTAAATT
27482139 ATTATTAAATT
1 ATTATTAAATT
*
27482150 ATT-TCAAAGTT
1 ATTATTAAA-TT
*
27482161 TTTATTTAAATT
1 ATTA-TTAAATT
27482173 ATT
1 ATT
27482176 TCAGTGTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
10 4 0.13
11 18 0.60
12 4 0.13
13 4 0.13
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (11 bp):
ATTATTAAATT
Found at i:27484387 original size:3 final size:3
Alignment explanation
Indices: 27484379--27484419 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
27484369 TAATTGTTAT
27484379 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
27484420 TTCAAAACGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:27485571 original size:29 final size:29
Alignment explanation
Indices: 27485516--27485914 Score: 222
Period size: 29 Copynumber: 13.6 Consensus size: 29
27485506 CCTAAAAGGT
* * * * *
27485516 CCTCAAACTTTCTAAAAATCACGTTTTGAC
1 CCTCGAACTTTC-CAAAATTACATTTTTAC
*
27485546 CCTCGAACTTTCCAAAATTATATTTTTAC
1 CCTCGAACTTTCCAAAATTACATTTTTAC
* *** *
27485575 CCCCGAACTACTAAAAAAATTACATTTTCAC
1 CCTCGAACT--TTCCAAAATTACATTTTTAC
* * *
27485606 CCTTGAATTTCTCCAAAATTACATTTTTGC
1 CCTCGAACTT-TCCAAAATTACATTTTTAC
* * * *
27485636 CCCCAAACTTTCAAAAATCACA-TTTTAC
1 CCTCGAACTTTCCAAAATTACATTTTTAC
* * *
27485664 CCTTGAACTTTCAAAAATCACATTTTTAC
1 CCTCGAACTTTCCAAAATTACATTTTTAC
* * *
27485693 CC-CTAAATTTCTCTAAAATTACATTTTTGC
1 CCTCGAACTTTC-C-AAAATTACATTTTTAC
** *
27485723 CCTAAAAC-TTCCAAAAATCACATTTTTAC
1 CCTCGAACTTTCC-AAAATTACATTTTTAC
* *
27485752 TCTCGAAC-TTCCAAAAATCACATTTTTAC
1 CCTCGAACTTTCC-AAAATTACATTTTTAC
27485781 CCTCGAAC-TTCCAAAAATTACATTTTTAC
1 CCTCGAACTTTCC-AAAATTACATTTTTAC
** * *
27485810 CCTTAAAC-ATCCAAAAATTACCA-TTTTGC
1 CCTCGAACTTTCC-AAAATTA-CATTTTTAC
* * *
27485839 CCCCGAGC-ATCCAAAAATTACCATTTTTAC
1 CCTCGAACTTTCC-AAAATTA-CATTTTTAC
* * * * *
27485869 CCT-TAAATTTCCAAAAATCACATTTTCAA
1 CCTCGAACTTTCC-AAAATTACATTTTTAC
* *
27485898 CCTCAAAATTTCCAAAA
1 CCTCGAACTTTCCAAAA
27485915 GCTCGATTTT
Statistics
Matches: 293, Mismatches: 65, Indels: 23
0.77 0.17 0.06
Matches are distributed among these distances:
28 30 0.10
29 163 0.56
30 77 0.26
31 23 0.08
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
CCTCGAACTTTCCAAAATTACATTTTTAC
Found at i:27485711 original size:58 final size:57
Alignment explanation
Indices: 27485520--27485894 Score: 304
Period size: 58 Copynumber: 6.4 Consensus size: 57
27485510 AAAGGTCCTC
* * * *
27485520 AAACTTTCTAAAAATCACGTTTTGACCCTCGAACTTTCC-AAAATTATATTTTTACCCCC
1 AAAC-TTCCAAAAATCACATTTT-ACCCTCGAAC-TTCCAAAAATTACATTTTTACCCCT
* ** * * * * * *
27485579 GAACTACTAAAAAAATTACATTTTCACCCTTGAATTTCTCCAAAATTACATTTTTGCCCCC
1 AAACT--TCCAAAAATCACATTTT-ACCCTCGAACTTC-CAAAAATTACATTTTTACCCCT
* * * *
27485640 AAACTTTCAAAAATCACATTTTACCCTTGAACTTTCAAAAATCACATTTTTACCCCT
1 AAACTTCCAAAAATCACATTTTACCCTCGAACTTCCAAAAATTACATTTTTACCCCT
* * * * ** * *
27485697 AAATTTCTCTAAAATTACATTTTTGCCCTAAAACTTCCAAAAATCACATTTTTA-CTCT
1 AAACTTC-CAAAAATCACA-TTTTACCCTCGAACTTCCAAAAATTACATTTTTACCCCT
* *
27485755 CGAACTTCCAAAAATCACATTTTTACCCTCGAACTTCCAAAAATTACATTTTTACCCTT
1 -AAACTTCCAAAAATCACA-TTTTACCCTCGAACTTCCAAAAATTACATTTTTACCCCT
* * * * * * *
27485814 AAACATCCAAAAATTACCATTTTGCCCCCGAGCATCCAAAAATTACCATTTTTACCCTT
1 AAACTTCCAAAAATCA-CATTTTACCCTCGAACTTCCAAAAATTA-CATTTTTACCCCT
*
27485873 AAATTTCCAAAAATCACATTTT
1 AAACTTCCAAAAATCACATTTT
27485895 CAACCTCAAA
Statistics
Matches: 257, Mismatches: 49, Indels: 21
0.79 0.15 0.06
Matches are distributed among these distances:
57 23 0.09
58 105 0.41
59 85 0.33
60 22 0.09
61 22 0.09
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.35
Consensus pattern (57 bp):
AAACTTCCAAAAATCACATTTTACCCTCGAACTTCCAAAAATTACATTTTTACCCCT
Found at i:27485711 original size:87 final size:86
Alignment explanation
Indices: 27485589--27485894 Score: 326
Period size: 87 Copynumber: 3.5 Consensus size: 86
27485579 GAACTACTAA
* * * * * ** *
27485589 AAAAATTACATTTTCACCCTTGAATTTCTCCAAAATTACATTTTTGCCCCCAAACTTTCAAAAAT
1 AAAAATCACATTTTTACCCCTAAATTTC-CAAAAATTACATTTTTGCCCTAAAACTTCCAAAAAT
* *
27485654 CACATTTTACCCTTGAACTTTC
65 CACATTTTACCCTCGAACTTCC
*
27485676 AAAAATCACATTTTTACCCCTAAATTTCTCTAAAATTACATTTTTGCCCTAAAACTTCCAAAAAT
1 AAAAATCACATTTTTACCCCTAAATTTC-CAAAAATTACATTTTTGCCCTAAAACTTCCAAAAAT
*
27485741 CACATTTTTACTCTCGAACTTCC
65 CACA-TTTTACCCTCGAACTTCC
* * * * *
27485764 AAAAATCACATTTTTA-CCCTCGAACTTCCAAAAATTACATTTTTACCCTTAAACATCCAAAAAT
1 AAAAATCACATTTTTACCCCT-AAATTTCCAAAAATTACATTTTTGCCCTAAAACTTCCAAAAAT
* * * * *
27485828 TACCATTTTGCCCCCGAGCATCC
65 CA-CATTTTACCCTCGAACTTCC
* * *
27485851 AAAAATTACCATTTTTACCCTTAAATTTCCAAAAATCACATTTT
1 AAAAATCA-CATTTTTACCCCTAAATTTCCAAAAATTACATTTT
27485895 CAACCTCAAA
Statistics
Matches: 186, Mismatches: 28, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
87 118 0.63
88 65 0.35
89 3 0.02
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (86 bp):
AAAAATCACATTTTTACCCCTAAATTTCCAAAAATTACATTTTTGCCCTAAAACTTCCAAAAATC
ACATTTTACCCTCGAACTTCC
Found at i:27495433 original size:59 final size:58
Alignment explanation
Indices: 27495338--27495848 Score: 249
Period size: 59 Copynumber: 8.7 Consensus size: 58
27495328 GGACACTTTG
* * * * * * *
27495338 GGGGCAAAATGGTAATTTTT-ATAGGTTCGAGATCAAAAATGGAGTTTTTGGACATTC
1 GGGGTAAAATGGTAATTTTTGAAAAGTTCAAGGTCAAAAATGGAATTTTTAGACATTC
* *
27495395 GGGGATAAAATGGTAGTTTTTGAAAAGTTCAAGGTCAAAAAT-GACA-TTTTAGACATCC
1 GGGG-TAAAATGGTAATTTTTGAAAAGTTCAAGGTCAAAAATGGA-ATTTTTAGACATTC
* * * *** *
27495453 GAGGGTAAAATGGTAATATTTGGAAATTTTGGGGTCAAAAA-GAGAATTTTCAGACATTC
1 G-GGGTAAAATGGTAATTTTTGAAAAGTTCAAGGTCAAAAATG-GAATTTTTAGACATTC
* * *
27495512 GGGGGTAAAATGGTAATTTTT-AGAAAGTTTAGGGTCAAAAAGGGAATTTTTAGA-AGTTC
1 -GGGGTAAAATGGTAATTTTTGA-AAAGTTCAAGGTCAAAAATGGAATTTTTAGACA-TTC
* ** * * * * * *
27495571 GAGGGTAAAATGGTAATTTTTGGAGAA-TT-TGGGGCCAAAATGGAAATTTTGGAAATTTA
1 G-GGGTAAAATGGTAATTTTT-GAAAAGTTCAAGGTCAAAAATGGAATTTTTAGACA-TTC
* * * * * *
27495630 AGGGTAAAAAT-GTAATTTTTGGAGAA-TTCAAGGTTAAAAATGGAATTTTTGGAAATTTA
1 GGGGT-AAAATGGTAATTTTT-GAAAAGTTCAAGGTCAAAAATGGAATTTTTAGACA-TTC
* * * * * * ** * *
27495689 AGGGTAAAAAT-GTAATTTTTG-GAAGTTTAGGGGCAAAAATGTAGCTTTTGGAAAGTTC
1 GGGGT-AAAATGGTAATTTTTGAAAAGTTCAAGGTCAAAAATGGAATTTTTAGACA-TTC
* * * ** * * *
27495747 AAGGGTTAAAAT-GTAATTTTTAAAAAGTTTAAAGGTCAAAAATATAATTTTTGGAAAGTTTA
1 --GGGGTAAAATGGTAATTTTTGAAAAG-TTCAAGGTCAAAAATGGAATTTTTAGACA--TTC
*
27495809 GGGGTCAAAAT-GTAATTTTTAAAAAGTTCAAGGGTCAAAA
1 GGGGT-AAAATGGTAATTTTTGAAAAGTTCAA-GGTCAAAA
27495849 TATGATTTTT
Statistics
Matches: 367, Mismatches: 62, Indels: 46
0.77 0.13 0.10
Matches are distributed among these distances:
57 7 0.02
58 123 0.34
59 165 0.45
60 18 0.05
61 52 0.14
62 2 0.01
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.32
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGAAAAGTTCAAGGTCAAAAATGGAATTTTTAGACATTC
Found at i:27495529 original size:29 final size:28
Alignment explanation
Indices: 27495440--27495707 Score: 109
Period size: 29 Copynumber: 9.2 Consensus size: 28
27495430 CAAAAATGAC
* *
27495440 ATTTTAGACATCCGAGGGTAAAATGGTA
1 ATTTTAGAAATTCGAGGGTAAAATGGTA
* * *
27495468 ATATTTGGAAATTTTG-GGGTCAAAAAGAG-A
1 AT-TTTAGAAA-TTCGAGGGT-AAAATG-GTA
* *
27495498 ATTTTCAGACATTCGGGGGTAAAATGGTA
1 ATTTT-AGAAATTCGAGGGTAAAATGGTA
* * *
27495527 ATTTTTAGAAAGTT-TAGGGTCAAAAAGGGA
1 A-TTTTAGAAA-TTCGAGGGT-AAAATGGTA
*
27495557 ATTTTTAGAAGTTCGAGGGTAAAATGGTA
1 A-TTTTAGAAATTCGAGGGTAAAATGGTA
* * * *
27495586 ATTTTTGGAGAATTTG-GGGCCAAAATGGAA
1 A-TTTTAGA-AATTCGAGGG-TAAAATGGTA
* **
27495616 ATTTTGGAAATTTAAGGGTAAAAAT-GTA
1 ATTTTAGAAATTCGAGGGT-AAAATGGTA
* * *
27495644 ATTTTTGGAGAATTCAAGGTTAAAAATGG-A
1 A-TTTTAGA-AATTCGAGGGT-AAAATGGTA
* **
27495674 ATTTTTGGAAATTTAAGGGTAAAAAT-GTA
1 A-TTTTAGAAATTCGAGGGT-AAAATGGTA
27495703 ATTTT
1 ATTTT
27495708 TGGAAGTTTA
Statistics
Matches: 191, Mismatches: 30, Indels: 38
0.74 0.12 0.15
Matches are distributed among these distances:
28 16 0.08
29 90 0.47
30 83 0.43
31 2 0.01
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.33
Consensus pattern (28 bp):
ATTTTAGAAATTCGAGGGTAAAATGGTA
Found at i:27495560 original size:30 final size:30
Alignment explanation
Indices: 27495518--27495848 Score: 247
Period size: 30 Copynumber: 11.1 Consensus size: 30
27495508 ATTCGGGGGT
*
27495518 AAAATGGTAATTTTTAGAAAGTTTAGGGTCA
1 AAAAT-GTAATTTTTGGAAAGTTTAGGGTCA
* * * *
27495549 AAAAGGGAATTTTTAG-AAGTTCGAGGGT--
1 AAAATGTAATTTTTGGAAAGTT-TAGGGTCA
* *
27495577 AAAATGGTAATTTTTGGAGAA-TTT-GGGGCC
1 AAAAT-GTAATTTTTGGA-AAGTTTAGGGTCA
* *
27495607 AAAATGGAAATTTTGGAAA-TTTAAGGGT-A
1 AAAATGTAATTTTTGGAAAGTTT-AGGGTCA
* * *
27495636 AAAATGTAATTTTTGGAGAA-TTCAAGGTTA
1 AAAATGTAATTTTTGGA-AAGTTTAGGGTCA
*
27495666 AAAATGGAATTTTTGGAAA-TTTAAGGGT-A
1 AAAATGTAATTTTTGGAAAGTTT-AGGGTCA
*
27495695 AAAATGTAATTTTTGG-AAGTTTAGGGGCA
1 AAAATGTAATTTTTGGAAAGTTTAGGGTCA
** * *
27495724 AAAATGTAGCTTTTGGAAAGTTCAAGGGT-T
1 AAAATGTAATTTTTGGAAAGTT-TAGGGTCA
** *
27495754 AAAATGTAATTTTTAAAAAGTTTAAAGGTCA
1 AAAATGTAATTTTTGGAAAGTTT-AGGGTCA
*
27495785 AAAATATAATTTTTGGAAAGTTTAGGGGTC-
1 AAAATGTAATTTTTGGAAAGTTTA-GGGTCA
** *
27495815 AAAATGTAATTTTTAAAAAGTTCAAGGGTCA
1 AAAATGTAATTTTTGGAAAGTT-TAGGGTCA
27495846 AAA
1 AAA
27495849 TATGATTTTT
Statistics
Matches: 239, Mismatches: 41, Indels: 40
0.75 0.13 0.12
Matches are distributed among these distances:
28 18 0.08
29 81 0.34
30 102 0.43
31 38 0.16
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.34
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAAGTTTAGGGTCA
Found at i:27495708 original size:29 final size:29
Alignment explanation
Indices: 27495514--27495828 Score: 260
Period size: 29 Copynumber: 10.7 Consensus size: 29
27495504 AGACATTCGG
*
27495514 GGGT-AAAATGGTAATTTTTAGAAAGTTT-A
1 GGGTAAAAAT-GTAATTTTTGGAAA-TTTAA
* * * * **
27495543 GGGTCAAAAAGGGAATTTTTAGAAGTTCGA
1 GGGT-AAAAATGTAATTTTTGGAAATTTAA
*
27495573 GGGT-AAAATGGTAATTTTTGGAGAATTT-G
1 GGGTAAAAAT-GTAATTTTTGGA-AATTTAA
** * *
27495602 GGGCCAAAATGGAAATTTTGGAAATTTAA
1 GGGTAAAAATGTAATTTTTGGAAATTTAA
*
27495631 GGGTAAAAATGTAATTTTTGGAGAATTCAA
1 GGGTAAAAATGTAATTTTTGGA-AATTTAA
* *
27495661 GGTTAAAAATGGAATTTTTGGAAATTTAA
1 GGGTAAAAATGTAATTTTTGGAAATTTAA
* *
27495690 GGGTAAAAATGTAATTTTTGGAAGTTTAG
1 GGGTAAAAATGTAATTTTTGGAAATTTAA
* ** *
27495719 GGGCAAAAATGTAGCTTTTGGAAAGTTCAA
1 GGGTAAAAATGTAATTTTTGGAAA-TTTAA
* **
27495749 GGGTTAAAATGTAATTTTTAAAAAGTTTAA
1 GGGTAAAAATGTAATTTTTGGAAA-TTTAA
* * *
27495779 AGGTCAAAAATATAATTTTTGGAAAGTTTAG
1 GGGT-AAAAATGTAATTTTTGGAAA-TTTAA
*
27495810 GGGTCAAAATGTAATTTTT
1 GGGTAAAAATGTAATTTTT
27495829 AAAAAGTTCA
Statistics
Matches: 228, Mismatches: 48, Indels: 19
0.77 0.16 0.06
Matches are distributed among these distances:
28 9 0.04
29 98 0.43
30 93 0.41
31 28 0.12
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGGAAATTTAA
Found at i:27497770 original size:11 final size:10
Alignment explanation
Indices: 27497734--27497786 Score: 61
Period size: 11 Copynumber: 4.9 Consensus size: 10
27497724 TGGACATTTT
27497734 AATTTAAATA
1 AATTTAAATA
27497744 AATTTAAACTTA
1 AATTTAAA--TA
27497756 AATTTATAATA
1 AATTTA-AATA
27497767 AATTTAAAATA
1 AATTT-AAATA
*
27497778 TATTTAAAT
1 AATTTAAAT
27497787 TCTGTTGGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
10 12 0.32
11 15 0.39
12 9 0.24
13 2 0.05
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (10 bp):
AATTTAAATA
Found at i:27497782 original size:22 final size:22
Alignment explanation
Indices: 27497734--27497786 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
27497724 TGGACATTTT
*
27497734 AATTTAAATAAATTTAAACTTA
1 AATTTAAATAAATTTAAACATA
27497756 AATTTATAATAAATTTAAA-ATA
1 AATTTA-AATAAATTTAAACATA
*
27497778 TATTTAAAT
1 AATTTAAAT
27497787 TCTGTTGGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 3 0.11
22 13 0.46
23 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTTAAATAAATTTAAACATA
Found at i:27499250 original size:17 final size:17
Alignment explanation
Indices: 27499211--27499248 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
27499201 GAACCCATTC
*
27499211 TTAAATTTACTTTAAGT
1 TTAAATTTACTTTAAAT
27499228 TTAAATTTA-TTTAAAT
1 TTAAATTTACTTTAAAT
27499244 TTAAA
1 TTAAA
27499249 ATAAATAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (17 bp):
TTAAATTTACTTTAAAT
Found at i:27501037 original size:30 final size:29
Alignment explanation
Indices: 27500904--27501104 Score: 181
Period size: 29 Copynumber: 6.8 Consensus size: 29
27500894 CAAAAGGTCT
* *
27500904 CCAAACTTTCCAAAAATCACGTTTTGACCC
1 CCAAAC-TTCCAAAAATCACATTTTTACCC
* * *
27500934 CCGAATTTCTTC-AAAATTACA-TTTTACCC
1 CCAAACTTC--CAAAAATCACATTTTTACCC
* * *
27500963 CTAAACTTCCAAAAATCATATTTTTATCC
1 CCAAACTTCCAAAAATCACATTTTTACCC
*
27500992 CCAAACTTCCAAAAATCACATTTTTACCT
1 CCAAACTTCCAAAAATCACATTTTTACCC
* * * *
27501021 TCGAACTTCTCAAAAATTACATTTTTGCCC
1 CCAAACTTC-CAAAAATCACATTTTTACCC
* * *
27501051 CCAAACATCCAAAAATTACCATTTTTGCCC
1 CCAAACTTCCAAAAATCA-CATTTTTACCC
* *
27501081 TCAAATTTCCAAAAATCACATTTT
1 CCAAACTTCCAAAAATCACATTTT
27501105 CAACCTCAAA
Statistics
Matches: 138, Mismatches: 27, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
27 1 0.01
28 7 0.05
29 70 0.51
30 59 0.43
31 1 0.01
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.33
Consensus pattern (29 bp):
CCAAACTTCCAAAAATCACATTTTTACCC
Found at i:27501046 original size:59 final size:59
Alignment explanation
Indices: 27500955--27501104 Score: 178
Period size: 59 Copynumber: 2.5 Consensus size: 59
27500945 CAAAATTACA
* * *
27500955 TTTTACCC-CTAAACTTCCAAAAATCATATTTTTATCCCCAAACTTCCAAAAATCA-CAT
1 TTTTACCCTC-AAACTTCCAAAAATCACATTTTTACCCCCAAACATCCAAAAATCACCAT
* * * * *
27501013 TTTTACCTTCGAACTTCTCAAAAATTACATTTTTGCCCCCAAACATCCAAAAATTACCAT
1 TTTTACCCTCAAACTTC-CAAAAATCACATTTTTACCCCCAAACATCCAAAAATCACCAT
* *
27501073 TTTTGCCCTCAAATTTCCAAAAATCACATTTT
1 TTTTACCCTCAAACTTCCAAAAATCACATTTT
27501105 CAACCTCAAA
Statistics
Matches: 76, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
58 13 0.17
59 47 0.62
60 16 0.21
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.35
Consensus pattern (59 bp):
TTTTACCCTCAAACTTCCAAAAATCACATTTTTACCCCCAAACATCCAAAAATCACCAT
Found at i:27501111 original size:29 final size:29
Alignment explanation
Indices: 27500965--27501124 Score: 142
Period size: 30 Copynumber: 5.4 Consensus size: 29
27500955 TTTTACCCCT
* * *
27500965 AAACTTCCAAAAATCATATTTTTATCCCC
1 AAACTTCCAAAAATCACATTTTTAACCTC
27500994 AAACTTCCAAAAATCACATTTTT-ACCTTC
1 AAACTTCCAAAAATCACATTTTTAACC-TC
* * ** *
27501023 GAACTTCTCAAAAATTACATTTTTGCCCCC
1 AAACTTC-CAAAAATCACATTTTTAACCTC
* * **
27501053 AAACATCCAAAAATTACCATTTTTGCCCTC
1 AAACTTCCAAAAATCA-CATTTTTAACCTC
* *
27501083 AAATTTCCAAAAATCACATTTTCAACCTC
1 AAACTTCCAAAAATCACATTTTTAACCTC
*
27501112 AAATTTTCCAAAA
1 AAA-CTTCCAAAA
27501125 GCTCGATTTT
Statistics
Matches: 110, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
28 2 0.02
29 51 0.46
30 55 0.50
31 2 0.02
ACGTcount: A:0.38, C:0.28, G:0.02, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATCACATTTTTAACCTC
Found at i:27501134 original size:30 final size:30
Alignment explanation
Indices: 27500969--27501152 Score: 78
Period size: 29 Copynumber: 6.2 Consensus size: 30
27500959 ACCCCTAAAC
* * * *
27500969 TTCCAAAAATCATATTTTTATCCCCAAA-C
1 TTCCAAAAATCACATTTTAATCCTCAAATT
* * *
27500998 TTCCAAAAATCACATTTTTA-CCTTCGAA-C
1 TTCCAAAAATCACATTTTAATCC-TCAAATT
* *** * *
27501027 TTCTCAAAAATTACATTTTTGCCCCCAAA-C
1 TTC-CAAAAATCACATTTTAATCCTCAAATT
* * ***
27501057 ATCCAAAAATTACCATTTTTGCCCTCAAA-T
1 TTCCAAAAATCA-CATTTTAATCCTCAAATT
27501087 TTCCAAAAATCACATTTTCAA-CCTCAAATT
1 TTCCAAAAATCACATTTT-AATCCTCAAATT
* *
27501117 TTCCAAAAGCTC-GATTTTAATCC-CAAATT
1 TTCCAAAA-ATCACATTTTAATCCTCAAATT
*
27501146 CTCCAAA
1 TTCCAAA
27501153 TTTTCAATTT
Statistics
Matches: 130, Mismatches: 17, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
28 2 0.02
29 62 0.48
30 62 0.48
31 4 0.03
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (30 bp):
TTCCAAAAATCACATTTTAATCCTCAAATT
Found at i:27503120 original size:19 final size:19
Alignment explanation
Indices: 27503079--27503135 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
27503069 AAAAAAATAC
*
27503079 ATTTTGAAATTTTTATAAA-T
1 ATTTTG-AA-TTTTAAAAATT
27503099 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTAAAAATT
** *
27503118 ATTTAAAATTTTGAAAAT
1 ATTTTGAATTTTAAAAAT
27503136 GGACAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 8 0.25
19 18 0.56
20 6 0.19
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
ATTTTGAATTTTAAAAATT
Found at i:27503234 original size:18 final size:21
Alignment explanation
Indices: 27503213--27503258 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 21
27503203 ATATTTTTAA
27503213 AAAAAATTATAAT-AA-AT-T
1 AAAAAATTATAATGAATATAT
*
27503231 AAAAAATTCTAATGAATATAT
1 AAAAAATTATAATGAATATAT
27503252 AAAAAAT
1 AAAAAAT
27503259 CAAAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 12 0.50
19 2 0.08
20 2 0.08
21 8 0.33
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAAAATTATAATGAATATAT
Found at i:27503393 original size:16 final size:16
Alignment explanation
Indices: 27503374--27503408 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
27503364 TTGAAAAAGT
27503374 TTTCAAATATATATGA
1 TTTCAAATATATATGA
* *
27503390 TTTCAAATTTATGTGA
1 TTTCAAATATATATGA
27503406 TTT
1 TTT
27503409 AATATGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (16 bp):
TTTCAAATATATATGA
Found at i:27505089 original size:15 final size:15
Alignment explanation
Indices: 27505065--27505098 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
27505055 GTAGAGTGAG
27505065 AAAAAAATTGA-AAA
1 AAAAAAATTGAGAAA
27505079 AAAAAACATTGAGAAA
1 AAAAAA-ATTGAGAAA
27505095 AAAA
1 AAAA
27505099 GAAAGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 5 0.28
16 7 0.39
ACGTcount: A:0.76, C:0.03, G:0.09, T:0.12
Consensus pattern (15 bp):
AAAAAAATTGAGAAA
Found at i:27510753 original size:14 final size:15
Alignment explanation
Indices: 27510723--27510763 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
27510713 TGTAAGCTGG
27510723 TTTT-TTTATCATGT
1 TTTTATTTATCATGT
27510737 TTTTATTTATCAT-T
1 TTTTATTTATCATGT
*
27510751 TTTTATTTTTCAT
1 TTTTATTTATCAT
27510764 CATCCATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTTATTTATCATGT
Found at i:27512418 original size:28 final size:28
Alignment explanation
Indices: 27512375--27512428 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
27512365 TTTGCATACT
*
27512375 TGTATTTTTTGAACAAATTGGTTTAACC
1 TGTATTTTTTGAACAAATTGATTTAACC
*
27512403 TGTATTTTTTGGACAAATTGATTTAA
1 TGTATTTTTTGAACAAATTGATTTAA
27512429 TAATTGCATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (28 bp):
TGTATTTTTTGAACAAATTGATTTAACC
Found at i:27512631 original size:88 final size:88
Alignment explanation
Indices: 27512482--27512661 Score: 297
Period size: 88 Copynumber: 2.0 Consensus size: 88
27512472 TTTTCCATGC
*
27512482 AAAGCAAAATAGAAGCAAATATTGACTTATTAATTATCTAACATTTAACTAATACCATGCAAAAT
1 AAAGCAAAATAGAAGCAAATATTAACTTATTAATTATCTAACATTTAACTAATACCATGCAAAAT
* *
27512547 TACATGGTTAGATTGTAATACAA
66 TACATGGTTAGATCGAAATACAA
* * *
27512570 AAAGCAAAATAGAATCCAATATTAACTTATTAATTATCTAACATTTAACTATTACCATGCAAAAT
1 AAAGCAAAATAGAAGCAAATATTAACTTATTAATTATCTAACATTTAACTAATACCATGCAAAAT
*
27512635 TACATGGTTGGATCGAAATACAA
66 TACATGGTTAGATCGAAATACAA
27512658 AAAG
1 AAAG
27512662 ATAACTTGTA
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 85 1.00
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (88 bp):
AAAGCAAAATAGAAGCAAATATTAACTTATTAATTATCTAACATTTAACTAATACCATGCAAAAT
TACATGGTTAGATCGAAATACAA
Found at i:27520379 original size:221 final size:221
Alignment explanation
Indices: 27519996--27520436 Score: 873
Period size: 221 Copynumber: 2.0 Consensus size: 221
27519986 GTGCACTGGG
27519996 TAACAAAGCTTGGGTTAAAAGTTTCTCAAATAGCCTAATTATCCACCTCCCCAAGATCAAGTCTG
1 TAACAAAGCTTGGGTTAAAAGTTTCTCAAATAGCCTAATTATCCACCTCCCCAAGATCAAGTCTG
27520061 ACCATAGACCTCTCCTCCTTAACCTTAATCCGGAAATTGTCTTGCCAAGAGGAAGGCCCTTTCAG
66 ACCATAGACCTCTCCTCCTTAACCTTAATCCGGAAATTGTCTTGCCAAGAGGAAGGCCCTTTCAG
27520126 TTCTTGGCGGGTTGTACTGAACATCCTGACTTTGGTAGCCTCGTGAAAGAGAGATGGGACTTCAG
131 TTCTTGGCGGGTTGTACTGAACATCCTGACTTTGGTAGCCTCGTGAAAGAGAGATGGGACTTCAG
27520191 AGGCTTGATGATAGATTCTCTATCCT
196 AGGCTTGATGATAGATTCTCTATCCT
*
27520217 TAACAAAGCTTGGGTTAAAAGTTTCTCAAATAGCCTAATTATCCATCTCCCCAAGATCAAGTCTG
1 TAACAAAGCTTGGGTTAAAAGTTTCTCAAATAGCCTAATTATCCACCTCCCCAAGATCAAGTCTG
27520282 ACCATAGACCTCTCCTCCTTAACCTTAATCCGGAAATTGTCTTGCCAAGAGGAAGGCCCTTTCAG
66 ACCATAGACCTCTCCTCCTTAACCTTAATCCGGAAATTGTCTTGCCAAGAGGAAGGCCCTTTCAG
27520347 TTCTTGGCGGGTTGTACTGAACATCCTGACTTTGGTAGCCTCGTGAAAGAGAGATGGGACTTCAG
131 TTCTTGGCGGGTTGTACTGAACATCCTGACTTTGGTAGCCTCGTGAAAGAGAGATGGGACTTCAG
27520412 AGGCTTGATGATAGATTCTCTATCC
196 AGGCTTGATGATAGATTCTCTATCC
27520437 ATCCACTCTA
Statistics
Matches: 219, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
221 219 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (221 bp):
TAACAAAGCTTGGGTTAAAAGTTTCTCAAATAGCCTAATTATCCACCTCCCCAAGATCAAGTCTG
ACCATAGACCTCTCCTCCTTAACCTTAATCCGGAAATTGTCTTGCCAAGAGGAAGGCCCTTTCAG
TTCTTGGCGGGTTGTACTGAACATCCTGACTTTGGTAGCCTCGTGAAAGAGAGATGGGACTTCAG
AGGCTTGATGATAGATTCTCTATCCT
Found at i:27521405 original size:12 final size:12
Alignment explanation
Indices: 27521390--27521415 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27521380 CCGTGTGCAG
27521390 GATCATGTGTCA
1 GATCATGTGTCA
27521402 GATCATGTGTCA
1 GATCATGTGTCA
27521414 GA
1 GA
27521416 CCGTGTTCCT
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:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (12 bp):
GATCATGTGTCA
Found at i:27522790 original size:82 final size:82
Alignment explanation
Indices: 27522442--27522793 Score: 497
Period size: 82 Copynumber: 4.3 Consensus size: 82
27522432 AATGAGTTCG
* ** * * * *
27522442 GCTCTAGTTAGATTAACCAACAATAGTTTCGTCAATTCCTGGCACCAAGTGCTTAGTGGATAAAC
1 GCTCTAGTTGGATTAACCAATGATAGTTTCGTCAATTCCTAGCACCTAGTGCCTAGCGGATAAAC
*
27522507 TGCAATAAGTGAGCCTA
66 CGCAATAAGTGAGCCTA
*
27522524 TCTCTAGTTGGATTAACCAATGATAGTTTCGTCAATTCCTAGCACCTAGTGCCTAGCGGATAAAC
1 GCTCTAGTTGGATTAACCAATGATAGTTTCGTCAATTCCTAGCACCTAGTGCCTAGCGGATAAAC
27522589 CGCAATAAGTGAGCCTA
66 CGCAATAAGTGAGCCTA
* * * * * **
27522606 GCTCCAGTTGGATTAACCAACGATAGTTTCTTCAATTCCTAACACTTAGTGCCTAGCAAATAAAC
1 GCTCTAGTTGGATTAACCAATGATAGTTTCGTCAATTCCTAGCACCTAGTGCCTAGCGGATAAAC
*
27522671 CGCAATAAGTGAGCCCA
66 CGCAATAAGTGAGCCTA
* * * * *
27522688 GCTCTAGTTGGATTAACCAATGATAGTTTCGTCAATTCCTGGCACCCAGTACCTAACGGATAAAT
1 GCTCTAGTTGGATTAACCAATGATAGTTTCGTCAATTCCTAGCACCTAGTGCCTAGCGGATAAAC
*
27522753 CGCAATAAGTGAGCCTT
66 CGCAATAAGTGAGCCTA
27522770 GCTCTAGTTGGATTAACCAATGAT
1 GCTCTAGTTGGATTAACCAATGAT
27522794 TTTGCGCCTA
Statistics
Matches: 238, Mismatches: 32, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
82 238 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (82 bp):
GCTCTAGTTGGATTAACCAATGATAGTTTCGTCAATTCCTAGCACCTAGTGCCTAGCGGATAAAC
CGCAATAAGTGAGCCTA
Found at i:27524081 original size:22 final size:23
Alignment explanation
Indices: 27524038--27524081 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
27524028 TAAATCAACT
*
27524038 TAAACATTACTCTAATAATTAAG
1 TAAACATAACTCTAATAATTAAG
*
27524061 TAAACATAACT-TATTAATTAA
1 TAAACATAACTCTAATAATTAA
27524082 ATACTGACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (23 bp):
TAAACATAACTCTAATAATTAAG
Found at i:27526128 original size:22 final size:23
Alignment explanation
Indices: 27526083--27526134 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
27526073 GACCCAAACA
*
27526083 AAATTTAAATTTACATTTATTTG
1 AAATTTAAATTTAAATTTATTTG
*
27526106 AAATTTAATTTTAAATTTA-TTG
1 AAATTTAAATTTAAATTTATTTG
27526128 AAATTTA
1 AAATTTA
27526135 TTAATGTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (23 bp):
AAATTTAAATTTAAATTTATTTG
Found at i:27527947 original size:24 final size:24
Alignment explanation
Indices: 27527907--27527957 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
27527897 CTTTTTTTTC
*
27527907 TTTAAAAAATAATAAAACATGAGA
1 TTTAAAAAATAAGAAAACATGAGA
* * *
27527931 TTTAAAAAATAGGAAAACTTGTGA
1 TTTAAAAAATAAGAAAACATGAGA
27527955 TTT
1 TTT
27527958 TGAAAACATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.53, C:0.04, G:0.12, T:0.31
Consensus pattern (24 bp):
TTTAAAAAATAAGAAAACATGAGA
Found at i:27532424 original size:7 final size:7
Alignment explanation
Indices: 27532412--27532505 Score: 95
Period size: 7 Copynumber: 13.3 Consensus size: 7
27532402 GAGAGAAAAG
27532412 AAAGGAA
1 AAAGGAA
27532419 AAAGGAA
1 AAAGGAA
27532426 AAAGGAAA
1 AAAGG-AA
*
27532434 AAAAGAA
1 AAAGGAA
*
27532441 AAAGAAA
1 AAAGGAA
*
27532448 AAAAGAA
1 AAAGGAA
27532455 AAAGG-A
1 AAAGGAA
27532461 AAAGGAA
1 AAAGGAA
27532468 AAAGGAA
1 AAAGGAA
27532475 AAA-GAA
1 AAAGGAA
*
27532481 AATAGAAAA
1 AA-AG-GAA
27532490 AATAGGAA
1 AA-AGGAA
27532498 AAA-GAA
1 AAAGGAA
27532504 AA
1 AA
27532506 GGAGAGGTTG
Statistics
Matches: 74, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
6 16 0.22
7 41 0.55
8 10 0.14
9 7 0.09
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (7 bp):
AAAGGAA
Found at i:27532437 original size:36 final size:34
Alignment explanation
Indices: 27532396--27532505 Score: 100
Period size: 36 Copynumber: 3.1 Consensus size: 34
27532386 AAAAATAAAT
*
27532396 AAAAAAG-AGAGAAAAGAAAGGAAAAAGGAAAAAGGA
1 AAAAAAGAAAAGAAAA-AAA-GAAAAAGG-AAAAGGA
27532432 AAAAAAGAAAAAGAAAAAAAGAAAAAGGAAAAGG-
1 AAAAAAG-AAAAGAAAAAAAGAAAAAGGAAAAGGA
* *
27532466 AAAAAGGAAAAAGAAAATAGAA-AAAATAGGAAAAAGA
1 AAAAAAG-AAAAGAAAA-A-AAGAAAA-AGGAAAAGGA
27532503 AAA
1 AAA
27532506 GGAGAGGTTG
Statistics
Matches: 65, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
34 16 0.25
35 11 0.17
36 25 0.38
37 6 0.09
38 7 0.11
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (34 bp):
AAAAAAGAAAAGAAAAAAAGAAAAAGGAAAAGGA
Found at i:27532445 original size:42 final size:41
Alignment explanation
Indices: 27532397--27532508 Score: 131
Period size: 42 Copynumber: 2.7 Consensus size: 41
27532387 AAAATAAATA
*
27532397 AAAAAGAGAGAAAAG-AAAGGAAAAAGGAAAAAGGAAAAAAAG
1 AAAAAGA-AAAAAAGAAAAGG-AAAAGGAAAAAGGAAAAAAAG
27532439 AAAAAGAAAAAAAGAAAAAGGAAAAGGAAAAAGG--AAAAAG
1 AAAAAGAAAAAAAG-AAAAGGAAAAGGAAAAAGGAAAAAAAG
*
27532479 AAAATAGAAAAAATAGGAAAAAGAAAAGGA
1 AAAA-AGAAAAAA-A-GAAAAGGAAAAGGA
27532509 GAGGTTGAGG
Statistics
Matches: 63, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
40 10 0.16
41 14 0.22
42 33 0.52
43 6 0.10
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (41 bp):
AAAAAGAAAAAAAGAAAAGGAAAAGGAAAAAGGAAAAAAAG
Found at i:27532505 original size:49 final size:49
Alignment explanation
Indices: 27532396--27532490 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 49
27532386 AAAAATAAAT
27532396 AAAAAAGAGAGAAAA-G-AAAGGAAAAAGGAAAAAGGAAAAAAAGAAAAAG
1 AAAAAA-AGA-AAAAGGAAAAGGAAAAAGGAAAAAGGAAAAAAAGAAAAAG
*
27532445 AAAAAAAGAAAAAGGAAAAGGAAAAAGGAAAAA-G-AAAATAGAAAAA
1 AAAAAAAGAAAAAGGAAAAGGAAAAAGGAAAAAGGAAAAAAAGAAAAA
27532491 ATAGGAAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
47 15 0.35
48 5 0.12
49 23 0.53
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (49 bp):
AAAAAAAGAAAAAGGAAAAGGAAAAAGGAAAAAGGAAAAAAAGAAAAAG
Found at i:27533771 original size:91 final size:91
Alignment explanation
Indices: 27533593--27533774 Score: 240
Period size: 91 Copynumber: 2.0 Consensus size: 91
27533583 AGATTAAAGG
* *
27533593 GAAAGGTTGAGGCCGCAACTGCAAACCCGGTAACTTAAAAGATGTGATGAGAAGGACTGAGGCCG
1 GAAAGGTTGAGGCCGCAACGGCAAACCCGATAACTTAAAAGATGTGATGAGAAGGACTGAGGCCG
* *
27533658 CAATGATGAATTCGGTACCATGAAGA
66 CAACGACGAATTCGGTACCATGAAGA
** * * * * *
27533684 GAAAGGTTGAGGCCGCAACGGTGAACTCGATACCTTAAAAGATGTGATGGGAAGGATTGAGGCTG
1 GAAAGGTTGAGGCCGCAACGGCAAACCCGATAACTTAAAAGATGTGATGAGAAGGACTGAGGCCG
*
27533749 CAACGACGAA-TCTGGTAGCATGAAGA
66 CAACGACGAATTC-GGTACCATGAAGA
27533775 TGCGATGGGA
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
90 2 0.03
91 76 0.97
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.18
Consensus pattern (91 bp):
GAAAGGTTGAGGCCGCAACGGCAAACCCGATAACTTAAAAGATGTGATGAGAAGGACTGAGGCCG
CAACGACGAATTCGGTACCATGAAGA
Found at i:27534157 original size:39 final size:38
Alignment explanation
Indices: 27534096--27534465 Score: 160
Period size: 39 Copynumber: 9.5 Consensus size: 38
27534086 TTAAACTACA
*
27534096 TCAGCTAATCTCTTACCCCGAGCCTAGGTCAGATCACCG
1 TCAG-TAATCTCTTACCCCGAGCCTAGGGCAGATCACCG
* * *
27534135 TTAGTTAATCTCTTACCTCGAGCCTAGGGCAGATTACAACCA
1 TCAG-TAATCTCTTACCCCGAGCCTAGGGCAGA-T-C-ACCG
* * * * *
27534177 TCCG--ATCTTTTACCCCGAGCTTAAGGTAGATCACCG
1 TCAGTAATCTCTTACCCCGAGCCTAGGGCAGATCACCG
* * *
27534213 TCAGCCAATCTCTTACCTCGAGCCTAGGGCAGATTGCAGCCA
1 TCAG-TAATCTCTTACCCCGAGCCTAGGGCAGA-T-CA-CCG
* * * **
27534255 TCCG--ATCTCTTACCCCGATCACGA-GGCAGATCACAA
1 TCAGTAATCTCTTACCCCGAGC-CTAGGGCAGATCACCG
* * * **
27534291 TCATTCGATCTTTTACCCCGAGTTTAGGGCAGATCACCG
1 TCAGT-AATCTCTTACCCCGAGCCTAGGGCAGATCACCG
* ** * * * *
27534330 TTAGCCGATCTCTTATCCCGAGCCTAGGGAAGATTACAG
1 TCAG-TAATCTCTTACCCCGAGCCTAGGGCAGATCACCG
* * * * * * *
27534369 CCA-TCCAATCTCTTACCTCGATCATAAGGTAGATCACAG
1 TCAGT--AATCTCTTACCCCGAGCCTAGGGCAGATCACCG
* * * * *
27534408 TCA-TCCGATCTTTTACCCCGAGCCTAAGGTAGATCACCA
1 TCAGT--AATCTCTTACCCCGAGCCTAGGGCAGATCACCG
*
27534447 TCAGCCAATCTCTTACCCC
1 TCAG-TAATCTCTTACCCC
27534466 AAGCTTGGGA
Statistics
Matches: 246, Mismatches: 66, Indels: 38
0.70 0.19 0.11
Matches are distributed among these distances:
36 10 0.04
37 3 0.01
38 3 0.01
39 213 0.87
40 4 0.02
41 3 0.01
42 10 0.04
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (38 bp):
TCAGTAATCTCTTACCCCGAGCCTAGGGCAGATCACCG
Found at i:27534237 original size:78 final size:78
Alignment explanation
Indices: 27534103--27534892 Score: 566
Period size: 78 Copynumber: 10.1 Consensus size: 78
27534093 ACATCAGCTA
* * ** * *
27534103 ATCTCTTACCCCGAGCCT-AGGTCAGATCACCGTTAGTTAATCTCTTACCTCGAGCCTAGGGCAG
1 ATCTTTTACCCCGAGCCTAAGGT-AGATCACCGTCAGCCAATCTCTTACCCCGAGCCTAGGGTAG
*
27534167 ATTACAACCATCCG
65 ATTACAGCCATCCG
* * *
27534181 ATCTTTTACCCCGAGCTTAAGGTAGATCACCGTCAGCCAATCTCTTACCTCGAGCCTAGGGCAGA
1 ATCTTTTACCCCGAGCCTAAGGTAGATCACCGTCAGCCAATCTCTTACCCCGAGCCTAGGGTAGA
*
27534246 TTGCAGCCATCCG
66 TTACAGCCATCCG
* * * * ** ** * * ** *
27534259 ATCTCTTACCCCGATCAC-GAGGCAGATCACAATCATTCGATCTTTTACCCCGAGTTTAGGGCAG
1 ATCTTTTACCCCGAGC-CTAAGGTAGATCACCGTCAGCCAATCTCTTACCCCGAGCCTAGGGTAG
* * ** *
27534323 ATCACCGTTAGCCG
65 ATTACAGCCATCCG
* * * * * * * * * * * *
27534337 ATCTCTTATCCCGAGCCTAGGGAAGATTACAGCCATCCAATCTCTTACCTCGATCATAAGGTAGA
1 ATCTTTTACCCCGAGCCTAAGGTAGATCACCGTCAGCCAATCTCTTACCCCGAGCCTAGGGTAGA
* *
27534402 TCACAGTCATCCG
66 TTACAGCCATCCG
* * *
27534415 ATCTTTTACCCCGAGCCTAAGGTAGATCACCATCAGCCAATCTCTTACCCCAAG-CTTGGGATAG
1 ATCTTTTACCCCGAGCCTAAGGTAGATCACCGTCAGCCAATCTCTTACCCCGAGCCTAGGG-TAG
* *
27534479 ATTATAGCCATTCG
65 ATTACAGCCATCCG
* * * * * *
27534493 ATCTTTTACTCCGAGCCTAGGGTAAATTACACC--CATCCGATCTTTTACCCCGAGCCTAGGGTA
1 ATCTTTTACCCCGAGCCTAAGGTAGA-T-CACCGTCAGCCAATCTCTTACCCCGAGCCTAGGGTA
* * **
27534556 GATTGCAACCATTTG
64 GATTACAGCCATCCG
* ** * ** * * * * * * *
27534571 ATCTTTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTCTTACACCGATCAT-GGGATAG
1 ATCTTTTACCCCGAGCCTAAGGTAGATCACCGTCAGCCAATCTCTTACCCCGAGCCTAGGG-TAG
* *
27534635 ATCACAGTCATCCG
65 ATTACAGCCATCCG
* * * * ** * *
27534649 ATCTTTTACCTCGAGCCTAAGGTAAATCACCATCAGTCAATCTCTTACCCTAAGCTTAGGGCAGA
1 ATCTTTTACCCCGAGCCTAAGGTAGATCACCGTCAGCCAATCTCTTACCCCGAGCCTAGGGTAGA
27534714 TTACAGCCATCCG
66 TTACAGCCATCCG
** * ** * *
27534727 ATCTTTTACCTTGAGCTTGGGGCAGATCACCGTCAGCCAATCTCTTACCCCTAGCCTAGGGTAGA
1 ATCTTTTACCCCGAGCCTAAGGTAGATCACCGTCAGCCAATCTCTTACCCCGAGCCTAGGGTAGA
* * *
27534792 TTGCAGTCATCTG
66 TTACAGCCATCCG
* * ** * * * * *
27534805 ATCTTTTATCCCGAGCTTGGGGCAGATTATCGTCAGCCAATCTCTTACCCCGAGCCCAAGGTAGA
1 ATCTTTTACCCCGAGCCTAAGGTAGATCACCGTCAGCCAATCTCTTACCCCGAGCCTAGGGTAGA
*
27534870 TTGCAGCCATCCG
66 TTACAGCCATCCG
*
27534883 ATCTCTTACC
1 ATCTTTTACC
27534893 TCAATCATGG
Statistics
Matches: 556, Mismatches: 145, Indels: 22
0.77 0.20 0.03
Matches are distributed among these distances:
76 1 0.00
77 8 0.01
78 530 0.95
79 13 0.02
80 4 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (78 bp):
ATCTTTTACCCCGAGCCTAAGGTAGATCACCGTCAGCCAATCTCTTACCCCGAGCCTAGGGTAGA
TTACAGCCATCCG
Found at i:27534546 original size:39 final size:39
Alignment explanation
Indices: 27534142--27535005 Score: 477
Period size: 39 Copynumber: 22.2 Consensus size: 39
27534132 CCGTTAGTTA
* * *
27534142 ATCTCTTACCTCGAGCCTAGGGCAGATTACAACCATCCG
1 ATCTCTTACCCCGAGCCTAGGGTAGATTACAGCCATCCG
* * * * * * * *
27534181 ATCTTTTACCCCGAGCTTAAGGTAGATCACCGTCAGCCA
1 ATCTCTTACCCCGAGCCTAGGGTAGATTACAGCCATCCG
* * *
27534220 ATCTCTTACCTCGAGCCTAGGGCAGATTGCAGCCATCCG
1 ATCTCTTACCCCGAGCCTAGGGTAGATTACAGCCATCCG
* * * * ** *
27534259 ATCTCTTACCCCGATCACGA-GGCAGATCACAATCATTCG
1 ATCTCTTACCCCGAGC-CTAGGGTAGATTACAGCCATCCG
* ** * * * ** *
27534298 ATCTTTTACCCCGAGTTTAGGGCAGATCACCGTTAGCCG
1 ATCTCTTACCCCGAGCCTAGGGTAGATTACAGCCATCCG
* * *
27534337 ATCTCTTATCCCGAGCCTAGGGAAGATTACAGCCATCCA
1 ATCTCTTACCCCGAGCCTAGGGTAGATTACAGCCATCCG
* * * * * *
27534376 ATCTCTTACCTCGATCATAAGGTAGATCACAGTCATCCG
1 ATCTCTTACCCCGAGCCTAGGGTAGATTACAGCCATCCG
* * * * * *
27534415 ATCTTTTACCCCGAGCCTAAGGTAGATCACCA-TCAGCCA
1 ATCTCTTACCCCGAGCCTAGGGTAGATTA-CAGCCATCCG
* * * *
27534454 ATCTCTTACCCCAAG-CTTGGGATAGATTATAGCCATTCG
1 ATCTCTTACCCCGAGCCTAGGG-TAGATTACAGCCATCCG
* * * *
27534493 ATCTTTTACTCCGAGCCTAGGGTAAATTACACCCATCCG
1 ATCTCTTACCCCGAGCCTAGGGTAGATTACAGCCATCCG
* * * **
27534532 ATCTTTTACCCCGAGCCTAGGGTAGATTGCAACCATTTG
1 ATCTCTTACCCCGAGCCTAGGGTAGATTACAGCCATCCG
* * * * *
27534571 ATCTTTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCG
1 ATCTCTTACCCCGAGCCTAGGGTAGATTACAGCCATCCG
* * * * *
27534610 ATCTCTTACACCGATCAT-GGGATAGATCACAGTCATCCG
1 ATCTCTTACCCCGAGCCTAGGG-TAGATTACAGCCATCCG
* * * * *
27534649 ATCTTTTACCTCGAGCCTAAGGTA-AAT-CA-CCATCAGTCA
1 ATCTCTTACCCCGAGCCTAGGGTAGATTACAGCCATC---CG
** * *
27534688 ATCTCTTACCCTAAGCTTAGGGCAGATTACAGCCATCCG
1 ATCTCTTACCCCGAGCCTAGGGTAGATTACAGCCATCCG
* ** * * * * * * * *
27534727 ATCTTTTACCTTGAGCTTGGGGCAGATCACCGTCAGCCA
1 ATCTCTTACCCCGAGCCTAGGGTAGATTACAGCCATCCG
* * * *
27534766 ATCTCTTACCCCTAGCCTAGGGTAGATTGCAGTCATCTG
1 ATCTCTTACCCCGAGCCTAGGGTAGATTACAGCCATCCG
* * * * * * * *
27534805 ATCTTTTATCCCGAGCTTGGGGCAGATTATC-GTCAGCCA
1 ATCTCTTACCCCGAGCCTAGGGTAGATTA-CAGCCATCCG
* * *
27534844 ATCTCTTACCCCGAGCCCAAGGTAGATTGCAGCCATCCG
1 ATCTCTTACCCCGAGCCTAGGGTAGATTACAGCCATCCG
* * * * * * * ** *
27534883 ATCTCTTACCTCAATCATGGGGCAGATCACAATCATTCG
1 ATCTCTTACCCCGAGCCTAGGGTAGATTACAGCCATCCG
* * * * * *
27534922 ATCTTTTACCTCGAGCCTGGGGTAGATTACCA-TCAGCCA
1 ATCTCTTACCCCGAGCCTAGGGTAGATTA-CAGCCATCCG
* * * *
27534961 ATCTCTTACCCCGAGCTTAGGGCAGATTGCAACCATCCG
1 ATCTCTTACCCCGAGCCTAGGGTAGATTACAGCCATCCG
27535000 ATCTCT
1 ATCTCT
27535006 CTAAAAAAAT
Statistics
Matches: 610, Mismatches: 197, Indels: 36
0.72 0.23 0.04
Matches are distributed among these distances:
36 4 0.01
37 2 0.00
38 13 0.02
39 568 0.93
40 16 0.03
41 2 0.00
42 5 0.01
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.27
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTAGGGTAGATTACAGCCATCCG
Found at i:27534754 original size:117 final size:117
Alignment explanation
Indices: 27534142--27534792 Score: 616
Period size: 117 Copynumber: 5.6 Consensus size: 117
27534132 CCGTTAGTTA
* * ** *
27534142 ATCTCTTACCTCGAGCCTAGGGCAGATTACAACCATCCGATCTTTTACCCCGAGCTTAAGGTAGA
1 ATCTCTTACCTCGAGCATAGGGCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTAAGGTAGA
* * * *
27534207 TCACCGTCAGCCAATCTCTTACCTCGAGCCTAGGGCAGATTGCAGCCATCCG
66 TCACCATCAGCCAATCTCTTACCCCGAGCTTAGGGCAGATTACAGCCATCCG
* * * * * ** * *
27534259 ATCTCTTACCCCGATCA-CGAGGCAGATCACAATCATTCGATCTTTTACCCCGAGTTTAGGGCAG
1 ATCTCTTACCTCGAGCATAG-GGCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTAAGGTAG
* * * * * * *
27534323 ATCACCGTTAGCCGATCTCTTATCCCGAGCCTAGGGAAGATTACAGCCATCCA
65 ATCACCATCAGCCAATCTCTTACCCCGAGCTTAGGGCAGATTACAGCCATCCG
* * *
27534376 ATCTCTTACCTCGATCATAAGGTAGATCACAGTCATCCGATCTTTTACCCCGAGCCTAAGGTAGA
1 ATCTCTTACCTCGAGCATAGGGCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTAAGGTAGA
* * * *
27534441 TCACCATCAGCCAATCTCTTACCCCAAGCTT-GGGATAGATTATAGCCATTCG
66 TCACCATCAGCCAATCTCTTACCCCGAGCTTAGGG-CAGATTACAGCCATCCG
* * * * * ** *
27534493 ATCTTTTA-CTCCGAGCCTAGGGTAAATTACACCCATCCGATCTTTTACCCCGAGCCTAGGGTAG
1 ATCTCTTACCT-CGAGCATAGGGCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTAAGGTAG
** * * *
27534557 ATTGCAACCATTTG---ATCTTTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCG
65 A-T-C-ACCATCAGCCAATCTCTTACCCCGAGCTTAGGGCAGATTACAGCCATCCG
* * *
27534610 ATCTCTTACAC-CGATCAT-GGGATAGATCACAGTCATCCGATCTTTTACCTCGAGCCTAAGGTA
1 ATCTCTTAC-CTCGAGCATAGGG-CAGATCACAGTCATCCGATCTTTTACCCCGAGCCTAAGGTA
* * **
27534673 AATCACCATCAGTCAATCTCTTACCCTAAGCTTAGGGCAGATTACAGCCATCCG
64 GATCACCATCAGCCAATCTCTTACCCCGAGCTTAGGGCAGATTACAGCCATCCG
* * * * * * * * * *
27534727 ATCTTTTACCTTGAGCTTGGGGCAGATCACCGTCAGCCAATCTCTTACCCCTAGCCTAGGGTAGA
1 ATCTCTTACCTCGAGCATAGGGCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTAAGGTAGA
27534792 T
66 T
27534793 TGCAGTCATC
Statistics
Matches: 434, Mismatches: 84, Indels: 32
0.79 0.15 0.06
Matches are distributed among these distances:
114 6 0.01
115 1 0.00
116 11 0.03
117 401 0.92
118 7 0.02
119 2 0.00
120 6 0.01
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (117 bp):
ATCTCTTACCTCGAGCATAGGGCAGATCACAGTCATCCGATCTTTTACCCCGAGCCTAAGGTAGA
TCACCATCAGCCAATCTCTTACCCCGAGCTTAGGGCAGATTACAGCCATCCG
Found at i:27535614 original size:17 final size:16
Alignment explanation
Indices: 27535574--27535651 Score: 74
Period size: 17 Copynumber: 4.9 Consensus size: 16
27535564 ACCCAAACAG
*
27535574 AATTTAAATTTATTTT
1 AATTTAAATTTATTTA
27535590 AA--TAAATTTATTTGA
1 AATTTAAATTTATTT-A
27535605 AATTTAAATTTATTTTA
1 AATTTAAATTTA-TTTA
*
27535622 AATTTAAGTTTAAATTT-
1 AATTTAAATTT--ATTTA
27535639 -ATTTAAATTTATT
1 AATTTAAATTTATT
27535652 AATGTCCCTT
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
14 14 0.26
15 2 0.04
16 11 0.21
17 19 0.36
18 6 0.11
19 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
AATTTAAATTTATTTA
Found at i:27535615 original size:6 final size:6
Alignment explanation
Indices: 27535599--27535649 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
27535589 TAATAAATTT
* *
27535599 ATTTGAA ATTTAA ATTT-A TTTTAA ATTTAA GTTTAA ATTT-- ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
27535645 ATTTA
1 ATTTA
27535650 TTAATGTCCC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
4 4 0.11
5 4 0.11
6 25 0.68
7 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (6 bp):
ATTTAA
Found at i:27535635 original size:23 final size:22
Alignment explanation
Indices: 27535607--27535649 Score: 77
Period size: 22 Copynumber: 1.9 Consensus size: 22
27535597 TTATTTGAAA
27535607 TTTAAATTTATTTTAAATTTAAG
1 TTTAAATTTA-TTTAAATTTAAG
27535630 TTTAAATTTATTTAAATTTA
1 TTTAAATTTATTTAAATTTA
27535650 TTAATGTCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTAAATTTATTTAAATTTAAG
Found at i:27539655 original size:21 final size:21
Alignment explanation
Indices: 27539631--27539683 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
27539621 GAGCTTTTAA
*
27539631 TATCGGTAGATGTGAAACTTG
1 TATCGGTAGAAGTGAAACTTG
**
27539652 TATCGGTAGAAGTGTCACTTG
1 TATCGGTAGAAGTGAAACTTG
*
27539673 TATCAGTAGAA
1 TATCGGTAGAA
27539684 CTATCACTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.32
Consensus pattern (21 bp):
TATCGGTAGAAGTGAAACTTG
Found at i:27539690 original size:21 final size:21
Alignment explanation
Indices: 27539647--27539703 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
27539637 TAGATGTGAA
* * *
27539647 ACTTGTATCGGTAGAAGTGTC
1 ACTTGTATCAGTAGAACTATC
27539668 ACTTGTATCAGTAGAACTATC
1 ACTTGTATCAGTAGAACTATC
27539689 ACTTGTATCAGTAGA
1 ACTTGTATCAGTAGA
27539704 TATCCGCACT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (21 bp):
ACTTGTATCAGTAGAACTATC
Found at i:27545121 original size:22 final size:22
Alignment explanation
Indices: 27545078--27545121 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
27545068 AAATAAGTAT
* *
27545078 AAATAGGTTTGATTAAGGTTAA
1 AAATAGGTTTAATTAAGCTTAA
27545100 AAATAGG-TTAATTAAAGCTTAA
1 AAATAGGTTTAATT-AAGCTTAA
27545122 TGATGAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.45, C:0.02, G:0.18, T:0.34
Consensus pattern (22 bp):
AAATAGGTTTAATTAAGCTTAA
Found at i:27546901 original size:20 final size:20
Alignment explanation
Indices: 27546866--27546922 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
27546856 TAGAGGTGAA
27546866 ACTTGTATCGATAGAA-GAGTC
1 ACTTGTATC-ATAGAACGA-TC
*
27546887 ACTTGTATCATAGAACTATC
1 ACTTGTATCATAGAACGATC
27546907 ACTTGTATCAGTAGAA
1 ACTTGTATCA-TAGAA
27546923 ATCTACACTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 18 0.55
21 15 0.45
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Consensus pattern (20 bp):
ACTTGTATCATAGAACGATC
Found at i:27559471 original size:16 final size:18
Alignment explanation
Indices: 27559436--27559483 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
27559426 ATTTATATTT
27559436 TAAAAATATTAATTACTA
1 TAAAAATATTAATTACTA
*
27559454 TAAAAAT-TT-ATTAGTA
1 TAAAAATATTAATTACTA
27559470 TAATAAA-ATTAATT
1 TAA-AAATATTAATT
27559484 TGTAAACAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 9 0.35
17 7 0.27
18 10 0.38
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (18 bp):
TAAAAATATTAATTACTA
Found at i:27563608 original size:21 final size:21
Alignment explanation
Indices: 27563584--27563639 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
27563574 AAAGTTTTTA
*
27563584 GTATCGGTAGAAGTGAGACTT
1 GTATCGGTAGAAGTGACACTT
* *
27563605 GTATCGGTAGAACTGTCACTT
1 GTATCGGTAGAAGTGACACTT
*
27563626 GCATCGGTAGAAGT
1 GTATCGGTAGAAGT
27563640 CTGCACTATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.29
Consensus pattern (21 bp):
GTATCGGTAGAAGTGACACTT
Found at i:27567010 original size:24 final size:25
Alignment explanation
Indices: 27566982--27567067 Score: 65
Period size: 25 Copynumber: 3.6 Consensus size: 25
27566972 ATCGTATATT
*
27566982 GCTAAACCATT-TTGGCTCGTAAGA
1 GCTAAACCATTCTGGGCTCGTAAGA
**
27567006 GCT-AACCATTCTGGGCTCGTGTGA
1 GCTAAACCATTCTGGGCTCGTAAGA
** * *
27567030 GCTAATGTCA-TCTGTGCTCGTATGA
1 GCTAA-ACCATTCTGGGCTCGTAAGA
27567055 GCTAAA--ATTCTGG
1 GCTAAACCATTCTGG
27567068 AAGACTGAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
22 1 0.02
23 11 0.22
24 16 0.33
25 19 0.39
26 2 0.04
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.31
Consensus pattern (25 bp):
GCTAAACCATTCTGGGCTCGTAAGA
Found at i:27567013 original size:23 final size:24
Alignment explanation
Indices: 27566986--27567034 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
27566976 TATATTGCTA
*
27566986 AACCATT-TTGGCTCGTAAGAGCT
1 AACCATTCTGGGCTCGTAAGAGCT
**
27567009 AACCATTCTGGGCTCGTGTGAGCT
1 AACCATTCTGGGCTCGTAAGAGCT
27567033 AA
1 AA
27567035 TGTCATCTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (24 bp):
AACCATTCTGGGCTCGTAAGAGCT
Found at i:27567790 original size:21 final size:21
Alignment explanation
Indices: 27567731--27567796 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
27567721 GAAGTTTTTA
**
27567731 GTATCGGTAGAAGTGAGACTT
1 GTATCGGTAGAAGTGTCACTT
* *
27567752 ATATCGGTAGAAGAGTCACTT
1 GTATCGGTAGAAGTGTCACTT
*
27567773 GTATCGGTAGAACTGTCACTT
1 GTATCGGTAGAAGTGTCACTT
27567794 GTA
1 GTA
27567797 CTGGTAAAAG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (21 bp):
GTATCGGTAGAAGTGTCACTT
Found at i:27570288 original size:24 final size:23
Alignment explanation
Indices: 27570242--27570341 Score: 84
Period size: 21 Copynumber: 4.4 Consensus size: 23
27570232 CCTACAACAT
**
27570242 CTACCGATACAA-GTATACA-AA
1 CTACCGATACAACAAATACATAA
27570263 CTACCGATACAACAAATCACATAA
1 CTACCGATACAACAAAT-ACATAA
** *
27570287 CTACCGATACTTGC-AATTC--AA
1 CTACCGATAC-AACAAATACATAA
*
27570308 CTATCGATACAACAAATGACATAA
1 CTACCGATACAACAAAT-ACATAA
27570332 CTACCGATAC
1 CTACCGATAC
27570342 TTGCAATTTA
Statistics
Matches: 61, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
20 1 0.02
21 26 0.43
22 3 0.05
23 4 0.07
24 26 0.43
25 1 0.02
ACGTcount: A:0.44, C:0.27, G:0.08, T:0.21
Consensus pattern (23 bp):
CTACCGATACAACAAATACATAA
Found at i:27570310 original size:45 final size:45
Alignment explanation
Indices: 27570261--27570365 Score: 174
Period size: 45 Copynumber: 2.3 Consensus size: 45
27570251 CAAGTATACA
27570261 AACTACCGATACAACAAATCACATAACTACCGATACTTGCAATTC
1 AACTACCGATACAACAAATCACATAACTACCGATACTTGCAATTC
* * *
27570306 AACTATCGATACAACAAATGACATAACTACCGATACTTGCAATTT
1 AACTACCGATACAACAAATCACATAACTACCGATACTTGCAATTC
*
27570351 AATTACCGATACAAC
1 AACTACCGATACAAC
27570366 CCAAGTGAGT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.43, C:0.26, G:0.08, T:0.24
Consensus pattern (45 bp):
AACTACCGATACAACAAATCACATAACTACCGATACTTGCAATTC
Found at i:27570822 original size:17 final size:17
Alignment explanation
Indices: 27570793--27570826 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
27570783 AATATCTTTG
27570793 GTAAGCTTCATAGTTTA
1 GTAAGCTTCATAGTTTA
27570810 GTAAG-TTCGATAGTTTA
1 GTAAGCTTC-ATAGTTTA
27570827 AGGAGTTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (17 bp):
GTAAGCTTCATAGTTTA
Found at i:27575975 original size:16 final size:18
Alignment explanation
Indices: 27575941--27575982 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
27575931 GGGGTAAAAA
*
27575941 TCATATTTCACTTCAATTC
1 TCAT-TTTCACATCAATTC
27575960 T-ATTTTCACATC-ATTC
1 TCATTTTCACATCAATTC
27575976 TCATTTT
1 TCATTTT
27575983 TGTCTCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.24
17 13 0.62
18 2 0.10
19 1 0.05
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (18 bp):
TCATTTTCACATCAATTC
Found at i:27577021 original size:18 final size:18
Alignment explanation
Indices: 27576998--27577038 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
27576988 TTTTATTTTA
27576998 TATTATATAATAAAATAT
1 TATTATATAATAAAATAT
* * *
27577016 TATTATTTATTATAATAT
1 TATTATATAATAAAATAT
27577034 TATTA
1 TATTA
27577039 ATTAATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATTATATAATAAAATAT
Found at i:27577047 original size:18 final size:18
Alignment explanation
Indices: 27577005--27577047 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
27576995 TTATATTATA
* *
27577005 TAATAAAATATTATTATT
1 TAATATAATATTATTAAT
*
27577023 TATTATAATATTATTAAT
1 TAATATAATATTATTAAT
27577041 TAATATA
1 TAATATA
27577048 TCTTTTAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATATAATATTATTAAT
Found at i:27584395 original size:3 final size:3
Alignment explanation
Indices: 27584387--27584424 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
27584377 AATGATTGTT
27584387 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
27584425 TGGATAAGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:27587477 original size:24 final size:23
Alignment explanation
Indices: 27587398--27587479 Score: 94
Period size: 23 Copynumber: 3.5 Consensus size: 23
27587388 TTAATGTTCA
*
27587398 CGAATATGTTCATTTAAT-TTAAT
1 CGAACATGTTCA-TTAATATTAAT
** *
27587421 CGAACATGTTCACGAATATTAAA
1 CGAACATGTTCATTAATATTAAT
27587444 CGAACATGTTCATTAATATATAAT
1 CGAACATGTTCATTAATAT-TAAT
*
27587468 TGAACATGTTCA
1 CGAACATGTTCA
27587480 CGAACAATGT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
22 3 0.06
23 32 0.65
24 14 0.29
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (23 bp):
CGAACATGTTCATTAATATTAAT
Found at i:27588700 original size:3 final size:3
Alignment explanation
Indices: 27588692--27588723 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
27588682 TTTCTCTCGT
*
27588692 TTC TTC TTC TTC TTC TTC TAC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
27588724 TTGTCAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:27589338 original size:3 final size:3
Alignment explanation
Indices: 27589330--27589356 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
27589320 CTTCATTCCA
27589330 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
27589357 TCAAAGGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:27591929 original size:22 final size:22
Alignment explanation
Indices: 27591871--27591930 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
27591861 ATCAAATCGA
*
27591871 ATTGGG-TTTATGGTTTGGGTG
1 ATTGGGTTTTATGGTTTGGATG
** *
27591892 ATTTAGTTTTAGGGTTTGGAT-
1 ATTGGGTTTTATGGTTTGGATG
27591913 ATTGGGTTTTCATGGTTT
1 ATTGGGTTTT-ATGGTTT
27591931 TGGGTTTGCA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
21 12 0.40
22 18 0.60
ACGTcount: A:0.13, C:0.02, G:0.33, T:0.52
Consensus pattern (22 bp):
ATTGGGTTTTATGGTTTGGATG
Found at i:27597065 original size:7 final size:7
Alignment explanation
Indices: 27597032--27597089 Score: 55
Period size: 7 Copynumber: 8.3 Consensus size: 7
27597022 ACCCCAAAAA
27597032 GTCAACT
1 GTCAACT
27597039 GTCAA-T
1 GTCAACT
* *
27597045 AGTTAACA
1 -GTCAACT
27597053 GTCAACT
1 GTCAACT
*
27597060 GTCAACG
1 GTCAACT
27597067 GTCAACT
1 GTCAACT
* *
27597074 ATCAACG
1 GTCAACT
27597081 GTCAACT
1 GTCAACT
27597088 GT
1 GT
27597090 TAAATCGATT
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
6 1 0.03
7 38 0.97
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (7 bp):
GTCAACT
Found at i:27597070 original size:14 final size:14
Alignment explanation
Indices: 27597053--27597089 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
27597043 ATAGTTAACA
27597053 GTCAACTGTCAACG
1 GTCAACTGTCAACG
*
27597067 GTCAACTATCAACG
1 GTCAACTGTCAACG
27597081 GTCAACTGT
1 GTCAACTGT
27597090 TAAATCGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (14 bp):
GTCAACTGTCAACG
Found at i:27604277 original size:12 final size:12
Alignment explanation
Indices: 27604260--27604292 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
27604250 ACTTGGGTAA
27604260 TTAGTTTGGGGT
1 TTAGTTTGGGGT
*
27604272 TTAGTTT-AGGT
1 TTAGTTTGGGGT
27604283 TTAGTTTGGG
1 TTAGTTTGGG
27604293 TTTGTTGGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.12, C:0.00, G:0.36, T:0.52
Consensus pattern (12 bp):
TTAGTTTGGGGT
Found at i:27609267 original size:21 final size:21
Alignment explanation
Indices: 27609243--27609282 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
27609233 TAACCCAAAA
27609243 GTCAACAATCAACTGTCAATT
1 GTCAACAATCAACTGTCAATT
***
27609264 GTCAAGGGTCAACTGTCAA
1 GTCAACAATCAACTGTCAA
27609283 ATCGAATTGG
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:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (21 bp):
GTCAACAATCAACTGTCAATT
Found at i:27609314 original size:22 final size:20
Alignment explanation
Indices: 27609288--27609338 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
27609278 GTCAAATCGA
*
27609288 ATTGGGTCTAGGGTTTGGGT
1 ATTGGGTCTAAGGTTTGGGT
* *
27609308 GATTTGGTTTTAAGGTTTGGGT
1 -A-TTGGGTCTAAGGTTTGGGT
27609330 ATTGGGTCT
1 ATTGGGTCT
27609339 TTATGGTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
20 6 0.25
21 2 0.08
22 16 0.67
ACGTcount: A:0.12, C:0.04, G:0.39, T:0.45
Consensus pattern (20 bp):
ATTGGGTCTAAGGTTTGGGT
Found at i:27609341 original size:22 final size:22
Alignment explanation
Indices: 27609299--27609352 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
27609289 TTGGGTCTAG
*
27609299 GGTTTGGGTGATTTGGTTTTAA
1 GGTTTGGGTGATTGGGTTTTAA
*
27609321 GGTTTGGGT-ATTGGGTCTTTAT
1 GGTTTGGGTGATTGGGT-TTTAA
27609343 GGTTTTGGGT
1 GG-TTTGGGT
27609353 TTGCACACAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 6 0.21
22 15 0.54
23 7 0.25
ACGTcount: A:0.09, C:0.02, G:0.39, T:0.50
Consensus pattern (22 bp):
GGTTTGGGTGATTGGGTTTTAA
Found at i:27611943 original size:29 final size:29
Alignment explanation
Indices: 27611911--27612007 Score: 106
Period size: 29 Copynumber: 3.3 Consensus size: 29
27611901 GCTTAAGGGT
* *
27611911 TTATTTAGGTAAAAATATACTATAATAGC
1 TTATTTAAGTAAAAATATACTATAAGAGC
* *
27611940 TTATTTAAATAAATCATTATAGCTA-AAGAGC
1 TTATTTAAGTAAA--AATATA-CTATAAGAGC
* *
27611971 TTATTTAAGTAAAAAGATACTATAAGAAC
1 TTATTTAAGTAAAAATATACTATAAGAGC
27612000 TTATTTAA
1 TTATTTAA
27612008 ATAAGTCATT
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
28 3 0.05
29 28 0.50
31 22 0.39
32 3 0.05
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.37
Consensus pattern (29 bp):
TTATTTAAGTAAAAATATACTATAAGAGC
Found at i:27611945 original size:60 final size:60
Alignment explanation
Indices: 27611875--27612051 Score: 214
Period size: 60 Copynumber: 3.0 Consensus size: 60
27611865 ACTAGATTTG
* * * * * *
27611875 AGAGCTTATTTAAATAAATCGTTATAGCTTAAGGGTTTATTTAGGTAAAAATATACTATA
1 AGAGCTTATTTAAATAAATCATTATAGCTAAAGAGCTTATTTAAGTAAAAAGATACTATA
*
27611935 ATAGCTTATTTAAATAAATCATTATAGCTAAAGAGCTTATTTAAGTAAAAAGATACTATA
1 AGAGCTTATTTAAATAAATCATTATAGCTAAAGAGCTTATTTAAGTAAAAAGATACTATA
* * * * * *
27611995 AGAACTTATTTAAATAAGTCATTGTAGAATAAAGA-CTTATTTAATTACAAA-ATACTA
1 AGAGCTTATTTAAATAAATCATTATAG-CTAAAGAGCTTATTTAAGTAAAAAGATACTA
27612052 AAAAGACTTT
Statistics
Matches: 102, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
59 6 0.06
60 90 0.88
61 6 0.06
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (60 bp):
AGAGCTTATTTAAATAAATCATTATAGCTAAAGAGCTTATTTAAGTAAAAAGATACTATA
Found at i:27611975 original size:31 final size:31
Alignment explanation
Indices: 27611875--27612038 Score: 117
Period size: 31 Copynumber: 5.4 Consensus size: 31
27611865 ACTAGATTTG
* *
27611875 AGAGCTTATTTAAATAAATCGTTATAGCTTA
1 AGAGCTTATTTAAATAAATCATTATAGCTAA
* * ** *
27611906 AGGGTTTATTTAGGTAAA--AATATA-CTATA
1 AGAGCTTATTTAAATAAATCATTATAGCTA-A
*
27611935 ATAGCTTATTTAAATAAATCATTATAGCTAA
1 AGAGCTTATTTAAATAAATCATTATAGCTAA
* **
27611966 AGAGCTTATTTAAGTAAA--AAGATA-CTATA
1 AGAGCTTATTTAAATAAATCATTATAGCTA-A
* * * *
27611995 AGAACTTATTTAAATAAGTCATTGTAGAATAA
1 AGAGCTTATTTAAATAAATCATTATAG-CTAA
27612027 AGA-CTTATTTAA
1 AGAGCTTATTTAA
27612039 TTACAAAATA
Statistics
Matches: 100, Mismatches: 24, Indels: 18
0.70 0.17 0.13
Matches are distributed among these distances:
28 5 0.05
29 38 0.38
31 48 0.48
32 7 0.07
33 2 0.02
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (31 bp):
AGAGCTTATTTAAATAAATCATTATAGCTAA
Found at i:27616455 original size:2 final size:2
Alignment explanation
Indices: 27616448--27616494 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
27616438 TACATAGAAT
*
27616448 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
27616489 GA TA TA
1 TA TA TA
27616495 AAATAAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:27616470 original size:19 final size:19
Alignment explanation
Indices: 27616446--27616484 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
27616436 TTTACATAGA
27616446 ATTATATATATATATATAT
1 ATTATATATATATATATAT
27616465 ATTATATATATATATATAT
1 ATTATATATATATATATAT
27616484 A
1 A
27616485 AATAGATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTATATATATATATATAT
Found at i:27616472 original size:17 final size:17
Alignment explanation
Indices: 27616450--27616483 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
27616440 CATAGAATTA
27616450 TATATATATATATATAT
1 TATATATATATATATAT
27616467 TATATATATATATATAT
1 TATATATATATATATAT
27616484 AAATAGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:27625720 original size:14 final size:16
Alignment explanation
Indices: 27625696--27625738 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
27625686 TTAAAAATAT
* *
27625696 TAAGCATTGAATTT-T
1 TAAGTATTGAATTTGA
27625711 TAA-TATTGAATTTGA
1 TAAGTATTGAATTTGA
27625726 TAAGTATTGAATT
1 TAAGTATTGAATT
27625739 CATATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 9 0.38
15 6 0.25
16 9 0.38
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (16 bp):
TAAGTATTGAATTTGA
Found at i:27631241 original size:53 final size:53
Alignment explanation
Indices: 27631178--27631281 Score: 129
Period size: 53 Copynumber: 2.0 Consensus size: 53
27631168 TTTAAAAGAT
* * * *
27631178 TAAATCAAAATTTTATTACTTTT-AAGAGAACAAAATGTAATTTTACATTTTGC
1 TAAATCAAAATTCTATGAATTTTAAAGAG-ACAAAATGAAATTTTACATTTTGC
* * *
27631231 TAAATTAAAATTCTGTGAATTTTAAAGAGCCAAAATGAAATTTTACATTTT
1 TAAATCAAAATTCTATGAATTTTAAAGAGACAAAATGAAATTTTACATTTT
27631282 TATGGTGTCG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
53 38 0.88
54 5 0.12
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (53 bp):
TAAATCAAAATTCTATGAATTTTAAAGAGACAAAATGAAATTTTACATTTTGC
Found at i:27631877 original size:11 final size:11
Alignment explanation
Indices: 27631863--27631896 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
27631853 AAAATTGAGG
27631863 GAAAAAAGAAA
1 GAAAAAAGAAA
27631874 GAAAAAAGAGAA
1 GAAAAAAGA-AA
27631886 GAAAGAAAGAA
1 GAAA-AAAGAA
27631897 GAAGAATAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 9 0.43
12 7 0.33
13 5 0.24
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:27632400 original size:92 final size:91
Alignment explanation
Indices: 27632279--27632616 Score: 462
Period size: 93 Copynumber: 3.8 Consensus size: 91
27632269 TTAATTTTGC
* *
27632279 TAGTTAGTAATTTTATTTTATTGTTAGTAGTAGTAAGTAAAAAATATTGTTCATATTTATTGATT
1 TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAAGTAAAAAACATTGTTCATATTTATTGATT
**
27632344 TAAAATTTAATAATGTTTAAATTTTGT
66 TAAAATTTAATAATGTTTAAA-TTAAT
27632371 TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAAGTAAAAAAACATTGTTCATATTTATTGAT
1 TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAAGT-AAAAAACATTGTTCATATTTATTGAT
27632436 TTAAAATTTAATAATGTTTAAA--AAT
65 TTAAAATTTAATAATGTTTAAATTAAT
*
27632461 TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAATAGTAAGT-AAAAACATTATTCATATTTATTG
1 TAGTTAGTAATTTTATTTTGTTGTTAGTAG---TAGTAAGTAAAAAACATTGTTCATATTTATTG
* **
27632525 ATTTAAAA-TTAATAATGCTTAAAAAAAT
63 ATTTAAAATTTAATAATGTTTAAATTAAT
* * *
27632553 TAATTAGTAATTTTA--TT-TTATT-GT--TAGTAAGTAAAAAATATTGTTCATATTTATTGATT
1 TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAAGTAAAAAACATTGTTCATATTTATTGATT
27632612 TAAAA
66 TAAAA
27632617 AAATAATATA
Statistics
Matches: 229, Mismatches: 10, Indels: 22
0.88 0.04 0.08
Matches are distributed among these distances:
83 8 0.03
84 29 0.13
88 2 0.01
89 4 0.02
90 47 0.21
91 30 0.13
92 54 0.24
93 55 0.24
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (91 bp):
TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAAGTAAAAAACATTGTTCATATTTATTGATT
TAAAATTTAATAATGTTTAAATTAAT
Found at i:27632485 original size:93 final size:89
Alignment explanation
Indices: 27632279--27632616 Score: 458
Period size: 92 Copynumber: 3.8 Consensus size: 89
27632269 TTAATTTTGC
* *
27632279 TAGTTAGTAATTTTATTTTATTGTTAGTAGTAGTAAGTAAAAAATATTGTTCATATTTATTGATT
1 TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAAGTAAAAAACATTGTTCATATTTATTGATT
**
27632344 TAAAATTTAATAATGTTTAAATTTTGT
66 TAAAATTTAATAATGTTTAAA---AAT
27632371 TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAAGTAAAAAAACATTGTTCATATTTATTGAT
1 TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAAGT-AAAAAACATTGTTCATATTTATTGAT
27632436 TTAAAATTTAATAATGTTTAAAAAT
65 TTAAAATTTAATAATGTTTAAAAAT
*
27632461 TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAATAGTAAGT-AAAAACATTATTCATATTTATTG
1 TAGTTAGTAATTTTATTTTGTTGTTAGTAG---TAGTAAGTAAAAAACATTGTTCATATTTATTG
*
27632525 ATTTAAAA-TTAATAATGCTTAAAAAAAT
63 ATTTAAAATTTAATAATG-TT-TAAAAAT
* * *
27632553 TAATTAGTAATTTTA--TT-TTATT-GT--TAGTAAGTAAAAAATATTGTTCATATTTATTGATT
1 TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAAGTAAAAAACATTGTTCATATTTATTGATT
27632612 TAAAA
66 TAAAA
27632617 AAATAATATA
Statistics
Matches: 229, Mismatches: 10, Indels: 22
0.88 0.04 0.08
Matches are distributed among these distances:
83 8 0.03
84 29 0.13
88 2 0.01
89 4 0.02
90 42 0.18
91 32 0.14
92 57 0.25
93 55 0.24
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (89 bp):
TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAAGTAAAAAACATTGTTCATATTTATTGATT
TAAAATTTAATAATGTTTAAAAAT
Found at i:27632855 original size:16 final size:16
Alignment explanation
Indices: 27632810--27632859 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
27632800 TAAACCTAGT
*
27632810 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
27632826 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
27632840 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
27632856 TAAT
1 TAAT
27632860 ACTCCCATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:27634223 original size:43 final size:43
Alignment explanation
Indices: 27634141--27634225 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
27634131 ATTAACATGT
* * *
27634141 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAACTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
* *
27634184 TAAACTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAACTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA
27634226 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 3 0.08
43 33 0.92
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.46
Consensus pattern (43 bp):
TAAACTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Done.