Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 86 of 325
Found at i:29094995 original size:23 final size:24
Alignment explanation
Indices: 29094967--29095018 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
29094957 TCTTTAATAT
*
29094967 TATATTATGCATACATAT-TTTTA
1 TATATTACGCATACATATCTTTTA
* *
29094990 TATATTACGTATATATATCTTTTA
1 TATATTACGCATACATATCTTTTA
29095014 -ATATT
1 TATATT
29095019 GTATTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.54
Consensus pattern (24 bp):
TATATTACGCATACATATCTTTTA
Found at i:29095046 original size:36 final size:36
Alignment explanation
Indices: 29094982--29095051 Score: 88
Period size: 38 Copynumber: 1.9 Consensus size: 36
29094972 TATGCATACA
*
29094982 TATTTTTATATATTACGTATATATATCTTTTAATATTG
1 TATTTTTATATATTAC-TATATACATC-TTTAATATTG
* *
29095020 TATTTTTATATGTTA-TGTATACATCTTTAATA
1 TATTTTTATATATTACTATATACATCTTTAATA
29095052 CTATATTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 7 0.24
36 8 0.28
38 14 0.48
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (36 bp):
TATTTTTATATATTACTATATACATCTTTAATATTG
Found at i:29095244 original size:28 final size:27
Alignment explanation
Indices: 29095189--29095246 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
29095179 TTATTCCTAG
* *
29095189 TATATATACATTTTTTAAATACTATAT
1 TATATATACATTTTTAAAATACCATAT
* *
29095216 TATATATATATATTTTAAAATACCGTAT
1 TATATATACAT-TTTTAAAATACCATAT
29095244 TAT
1 TAT
29095247 GTACATGTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (27 bp):
TATATATACATTTTTAAAATACCATAT
Found at i:29095518 original size:21 final size:20
Alignment explanation
Indices: 29095478--29095540 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 20
29095468 ATAATAATTA
29095478 TTATTAT-TA-GTATAT-GT
1 TTATTATATATGTATATAGT
29095495 TTATTATATATGTATATAGCT
1 TTATTATATATGTATATAG-T
*
29095516 TTAATACATATATGTATATA-T
1 TT-AT-TATATATGTATATAGT
29095537 TTAT
1 TTAT
29095541 GTAGTATTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
17 7 0.18
18 2 0.05
19 6 0.15
20 3 0.08
21 6 0.15
22 2 0.05
23 13 0.33
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.54
Consensus pattern (20 bp):
TTATTATATATGTATATAGT
Found at i:29095608 original size:13 final size:13
Alignment explanation
Indices: 29095526--29095644 Score: 76
Period size: 13 Copynumber: 9.5 Consensus size: 13
29095516 TTAATACATA
29095526 TATGTATATAT-T
1 TATGTATATATAT
29095538 TATGTAGTAT-TAT
1 TATGTA-TATATAT
* * *
29095551 TAATATATATTTTT
1 T-ATGTATATATAT
29095565 TATGT-TATTAGTAT
1 TATGTATA-TA-TAT
*
29095579 T-TCTA-ATATAT
1 TATGTATATATAT
29095590 T-T-TATATATAT
1 TATGTATATATAT
29095601 TATGTATATATAT
1 TATGTATATATAT
*
29095614 CATGTATATATA-
1 TATGTATATATAT
*
29095626 TATTTAGTAT-TAT
1 TATGTA-TATATAT
29095639 TATGTA
1 TATGTA
29095645 GACACTTCTC
Statistics
Matches: 85, Mismatches: 10, Indels: 23
0.72 0.08 0.19
Matches are distributed among these distances:
10 2 0.02
11 12 0.14
12 18 0.21
13 43 0.51
14 10 0.12
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.56
Consensus pattern (13 bp):
TATGTATATATAT
Found at i:29099433 original size:4 final size:4
Alignment explanation
Indices: 29099426--29099482 Score: 66
Period size: 4 Copynumber: 15.0 Consensus size: 4
29099416 TTCATGACTA
* * *
29099426 CATT CATT CA-T CATT TATT CA-A CATT CATT TA-T CATT CATT CATT
1 CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT CATT
29099471 CATT CATT CATT
1 CATT CATT CATT
29099483 GCATGTACAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
3 7 0.16
4 37 0.84
ACGTcount: A:0.28, C:0.23, G:0.00, T:0.49
Consensus pattern (4 bp):
CATT
Found at i:29099445 original size:11 final size:11
Alignment explanation
Indices: 29099426--29099481 Score: 76
Period size: 11 Copynumber: 5.0 Consensus size: 11
29099416 TTCATGACTA
29099426 CATTCATTCAT
1 CATTCATTCAT
* *
29099437 CATTTATTCAA
1 CATTCATTCAT
*
29099448 CATTCATTTAT
1 CATTCATTCAT
29099459 CATTCATTCATT
1 CATTCATTCA-T
29099471 CATTCATTCAT
1 CATTCATTCAT
29099482 TGCATGTACA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
11 27 0.71
12 11 0.29
ACGTcount: A:0.29, C:0.23, G:0.00, T:0.48
Consensus pattern (11 bp):
CATTCATTCAT
Found at i:29099454 original size:15 final size:16
Alignment explanation
Indices: 29099427--29099482 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 16
29099417 TCATGACTAC
*
29099427 ATTCATTCA-TCATTT
1 ATTCATACATTCATTT
29099442 ATTCA-ACATTCATTT
1 ATTCATACATTCATTT
* *
29099457 A-TCATTCATTCATTC
1 ATTCATACATTCATTT
*
29099472 ATTCATTCATT
1 ATTCATACATT
29099483 GCATGTACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 5 0.14
15 21 0.60
16 9 0.26
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTCATACATTCATTT
Found at i:29107999 original size:75 final size:75
Alignment explanation
Indices: 29107785--29108086 Score: 385
Period size: 75 Copynumber: 4.0 Consensus size: 75
29107775 TTTCTGTTAC
* * * *
29107785 AAAAATCAATTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGACACGCTGAGGTATTTTCAATTTC
* *
29107850 TATCTTTCAAAAA
66 TGTTTTTC---AA
*
29107863 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGACACGCTGAGGTATTTTCAATTTC
*
29107926 TGTTTTGCAA
66 TGTTTTTCAA
* * * * *
29107936 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAACCTCGGGATATGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGACACGCTGAGGTATTTTCAATTTC
29108001 TGTTTTTC-A
66 TGTTTTTCAA
* * * * *
29108010 AAAAATCAAGCTCATATTGCGAGAGGTGAGTTGAACTTCGGGACATGCTGAGGCATTTTCAGTTT
1 AAAAATCAA-CTCATATTGCGAGAGGTGAGTTGAACCTCAGGACACGCTGAGGTATTTTCAATTT
29108075 CTGTTTTTCAA
65 CTGTTTTTCAA
29108086 A
1 A
29108087 TTTTGTTTTT
Statistics
Matches: 202, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
73 40 0.20
74 10 0.05
75 85 0.42
76 28 0.14
78 39 0.19
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.33
Consensus pattern (75 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGACACGCTGAGGTATTTTCAATTTC
TGTTTTTCAA
Found at i:29110064 original size:23 final size:22
Alignment explanation
Indices: 29110038--29110081 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
29110028 TCGTTATTAT
*
29110038 TATTATTATTAGTATTTTTTTAC
1 TATTATTA-AAGTATTTTTTTAC
*
29110061 TATTATTAAATTATTTTTTTA
1 TATTATTAAAGTATTTTTTTA
29110082 GTTTCAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (22 bp):
TATTATTAAAGTATTTTTTTAC
Found at i:29110077 original size:20 final size:21
Alignment explanation
Indices: 29110031--29110078 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
29110021 ACCATTATCG
* * *
29110031 TTATTATTATTATTATTAGTA
1 TTATTTTTACTATTATTAGAA
29110052 TT-TTTTTACTATTATTA-AA
1 TTATTTTTACTATTATTAGAA
29110071 TTATTTTT
1 TTATTTTT
29110079 TTAGTTTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 3 0.13
20 18 0.78
21 2 0.09
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TTATTTTTACTATTATTAGAA
Found at i:29110541 original size:21 final size:21
Alignment explanation
Indices: 29110509--29110556 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
29110499 TGCGTTTCAT
29110509 TATATGTATATATCTTTAATG-AA
1 TATATGTATATA--TTT-ATGTAA
29110532 TATATGTATATATTTATGTAA
1 TATATGTATATATTTATGTAA
29110553 TATA
1 TATA
29110557 ATTAATAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.12
21 9 0.38
23 12 0.50
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (21 bp):
TATATGTATATATTTATGTAA
Found at i:29110634 original size:25 final size:25
Alignment explanation
Indices: 29110601--29110681 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 25
29110591 CTAATATGTA
*
29110601 TATACTATGTAAATATCTTTAATAT
1 TATATTATGTAAATATCTTTAATAT
* * *
29110626 TATATTATGTATACATATTT--TA-
1 TATATTATGTAAATATCTTTAATAT
*
29110648 TATATTACGTATATATATCTTTTAATAT
1 TATATTATGTA-A-ATATC-TTTAATAT
29110676 TATATT
1 TATATT
29110682 TTTATATGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
22 10 0.24
23 2 0.05
24 3 0.07
25 19 0.45
27 2 0.05
28 6 0.14
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (25 bp):
TATATTATGTAAATATCTTTAATAT
Found at i:29110687 original size:38 final size:35
Alignment explanation
Indices: 29110636--29110727 Score: 98
Period size: 36 Copynumber: 2.6 Consensus size: 35
29110626 TATATTATGT
*
29110636 ATAC-ATA-TTTTATATATTACGTATATATATCTTTTA
1 ATACTATATTTTTATATATTA--TATATACATC-TTTA
* * *
29110672 ATATTATATTTTTATATGTTATGTATACATCTTTA
1 ATACTATATTTTTATATATTATATATACATCTTTA
29110707 ATACTATATTATTTATATATT
1 ATACTATATT-TTTATATATT
29110728 TTTTTTCATA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
35 13 0.28
36 20 0.43
37 3 0.06
38 11 0.23
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (35 bp):
ATACTATATTTTTATATATTATATATACATCTTTA
Found at i:29111173 original size:21 final size:20
Alignment explanation
Indices: 29111133--29111195 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 20
29111123 GTAATTATTA
29111133 TTATTAT-TA-GTATAT-GT
1 TTATTATATATGTATATAGT
29111150 TTATTATATATGTATATAGCT
1 TTATTATATATGTATATAG-T
*
29111171 TTAATACATATATGTATATA-T
1 TT-AT-TATATATGTATATAGT
29111192 TTAT
1 TTAT
29111196 GTAGTATTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
17 7 0.18
18 2 0.05
19 6 0.15
20 3 0.08
21 6 0.15
22 2 0.05
23 13 0.33
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.54
Consensus pattern (20 bp):
TTATTATATATGTATATAGT
Found at i:29111253 original size:11 final size:12
Alignment explanation
Indices: 29111239--29111284 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 12
29111229 AGTATTTCTA
29111239 ATATATTT-TAT
1 ATATATTTGTAT
29111250 ATATATTATGTAT
1 ATATATT-TGTAT
29111263 ATATATTTAGTAT
1 ATATATTT-GTAT
29111276 -TAT-TTTGTA
1 ATATATTTGTA
29111285 GACACTTCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
10 3 0.09
11 10 0.31
12 5 0.16
13 14 0.44
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.59
Consensus pattern (12 bp):
ATATATTTGTAT
Found at i:29113232 original size:20 final size:20
Alignment explanation
Indices: 29113189--29113229 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
29113179 TTATCTATAT
*
29113189 TTAT-TATTTAATACTAAAA
1 TTATCTATTTAATACCAAAA
29113208 TTATCTATTTAATATCCAAAA
1 TTATCTATTTAATA-CCAAAA
29113229 T
1 T
29113230 ATCAATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (20 bp):
TTATCTATTTAATACCAAAA
Found at i:29115240 original size:24 final size:24
Alignment explanation
Indices: 29115213--29115266 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
29115203 AAATATTTTT
* *
29115213 ATAATTTTTGAATAATTCAAAAAA
1 ATAATTTTTAAAAAATTCAAAAAA
* *
29115237 ATAAATTTTAAAAAATTTAAAAAA
1 ATAATTTTTAAAAAATTCAAAAAA
*
29115261 TTAATT
1 ATAATT
29115267 AAATGCTTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (24 bp):
ATAATTTTTAAAAAATTCAAAAAA
Found at i:29116225 original size:3 final size:3
Alignment explanation
Indices: 29116217--29116254 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
29116207 ACTAGGAGTT
29116217 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
29116255 TGCTTAGAAC
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:29119375 original size:15 final size:15
Alignment explanation
Indices: 29119343--29119385 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
29119333 ATTAAATTTG
*
29119343 TAATATTAATTCTATT
1 TAATATT-ATTATATT
29119359 TAATATTATTATATT
1 TAATATTATTATATT
*
29119374 TACTATTATTAT
1 TAATATTATTAT
29119386 TTATAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (15 bp):
TAATATTATTATATT
Found at i:29119430 original size:17 final size:16
Alignment explanation
Indices: 29119407--29119455 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
29119397 ACTGTACTTT
29119407 GTATGTATATATTATTA
1 GTATGTATATATT-TTA
*
29119424 TTATGTATAT-TTTTA
1 GTATGTATATATTTTA
29119439 GTATGTATATATATTTA
1 GTATGTATATAT-TTTA
29119456 TGAAGTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 12 0.43
16 3 0.11
17 13 0.46
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (16 bp):
GTATGTATATATTTTA
Found at i:29119434 original size:15 final size:15
Alignment explanation
Indices: 29119414--29119453 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
29119404 TTTGTATGTA
*
29119414 TATATTATTATTATG
1 TATATTATTAGTATG
*
29119429 TATATTTTTAGTATG
1 TATATTATTAGTATG
29119444 TATATATATT
1 TATAT-TATT
29119454 TATGAAGTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 18 0.86
16 3 0.14
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (15 bp):
TATATTATTAGTATG
Found at i:29119536 original size:24 final size:24
Alignment explanation
Indices: 29119499--29119576 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
29119489 TATTCTTTAA
*
29119499 TATATTATGCATATATTTTAATAC
1 TATATTATACATATATTTTAATAC
* *
29119523 TATATTATATATATACATTTTTATAC
1 TATATTATACATAT--ATTTTAATAC
* * *
29119549 TAT-GTATACATA-CTTTTAATAT
1 TATATTATACATATATTTTAATAC
29119571 TATATT
1 TATATT
29119577 TCATATGTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
22 10 0.24
23 1 0.02
24 12 0.29
25 7 0.17
26 12 0.29
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.53
Consensus pattern (24 bp):
TATATTATACATATATTTTAATAC
Found at i:29126985 original size:5 final size:5
Alignment explanation
Indices: 29126975--29127009 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
29126965 AATAATTAAG
29126975 TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT
29127010 ATAAAAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:29127079 original size:31 final size:30
Alignment explanation
Indices: 29127044--29127104 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
29127034 GAAACAGAAT
*
29127044 GAAAGCAAACGAAAC-AGAGAAGAACAGGGGA
1 GAAAG-AAACGAAACAAGA-AAGAAAAGGGGA
* *
29127075 GAAAGAAAGGAAAGAAGAAAGAAAAGGGGA
1 GAAAGAAACGAAACAAGAAAGAAAAGGGGA
29127105 AATAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.59, C:0.07, G:0.34, T:0.00
Consensus pattern (30 bp):
GAAAGAAACGAAACAAGAAAGAAAAGGGGA
Found at i:29128680 original size:39 final size:39
Alignment explanation
Indices: 29128573--29128707 Score: 123
Period size: 39 Copynumber: 3.4 Consensus size: 39
29128563 GACCTCGAGT
* * *
29128573 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGCTAG-TC
** ** *
29128614 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
29128652 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
29128691 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
29128708 CCATATTGGT
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 19 0.25
39 36 0.47
40 4 0.05
41 15 0.20
42 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:29134770 original size:5 final size:5
Alignment explanation
Indices: 29134760--29134792 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
29134750 AATAATTAAG
29134760 TATAT TATAT TATA- TATAT TATAT TATTAT TAT
1 TATAT TATAT TATAT TATAT TATAT TA-TAT TAT
29134793 TATATATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 17 0.65
6 5 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:29134777 original size:14 final size:13
Alignment explanation
Indices: 29134760--29134797 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
29134750 AATAATTAAG
29134760 TATATTATATTAT
1 TATATTATATTAT
29134773 ATATATTATATTAT
1 -TATATTATATTAT
29134787 TATTATTATAT
1 TA-TATTATAT
29134798 ATAAAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 2 0.09
14 21 0.91
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TATATTATATTAT
Found at i:29134867 original size:31 final size:30
Alignment explanation
Indices: 29134832--29134892 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
29134822 GAAACAGAAT
*
29134832 GAAAGCAAACGAAAC-AGAGAAGAACAGGGGA
1 GAAAG-AAACGAAACAAGA-AAGAAAAGGGGA
* *
29134863 GAAAGAAAGGAAAGAAGAAAGAAAAGGGGA
1 GAAAGAAACGAAACAAGAAAGAAAAGGGGA
29134893 AATAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.59, C:0.07, G:0.34, T:0.00
Consensus pattern (30 bp):
GAAAGAAACGAAACAAGAAAGAAAAGGGGA
Found at i:29136467 original size:39 final size:39
Alignment explanation
Indices: 29136360--29136494 Score: 123
Period size: 39 Copynumber: 3.4 Consensus size: 39
29136350 GACCTCGAGT
* * *
29136360 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGCTAG-TC
** ** *
29136401 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
29136439 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
29136478 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
29136495 CCATATTGGT
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 19 0.25
39 36 0.47
40 4 0.05
41 15 0.20
42 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:29140833 original size:46 final size:43
Alignment explanation
Indices: 29140782--29140958 Score: 192
Period size: 46 Copynumber: 3.9 Consensus size: 43
29140772 ATGTTTGGGC
29140782 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GA
*** * *
29140826 ATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGC
1 A--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GGA
*
29140875 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGA
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GA
* *
29140919 ACACCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 A-TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29140959 GCGGGTTATA
Statistics
Matches: 112, Mismatches: 12, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 3 0.03
46 67 0.60
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.29
Consensus pattern (43 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGA
Found at i:29140938 original size:93 final size:93
Alignment explanation
Indices: 29140779--29140950 Score: 283
Period size: 93 Copynumber: 1.8 Consensus size: 93
29140769 AGGATGTTTG
* **
29140779 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATCACCGAACTCGTTGAG
29140844 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
29140872 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAA-CACCTGAGCTCGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATCACC-GAACTCGTTGA
29140936 GTTGAGTCCGAGTTC
65 GTTGAGTCCGAGTTC
29140951 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATCACCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:29148078 original size:251 final size:249
Alignment explanation
Indices: 29147628--29148354 Score: 874
Period size: 251 Copynumber: 2.9 Consensus size: 249
29147618 GCTTTTCAAA
* * *
29147628 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCT-TGGCTCACATGTCGAGGTATTTTCAGT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGT-GAGGTATTTTCA--
* *
29147692 TTTTATTTATTTCAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
60 ---AATTTATTTCAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC
* *
29147757 GGGTTGCATGACGAGGTATTTTCAAAAGCTACTTTTTAAATTAAGTTTCAAAAAAGACCAACTCA
122 GGGTTACATGACGAGGTATTTTCAAAAGCTACTTTTCAAATTAAGTTTCAAAAAAGACCAACTCA
* *
29147822 TATTGCTAGAAGTGAGTTGAGCCTTGGCTCACGTGTTGAGCTATTTTCAATTTCTGTCTGTTT
187 TATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATTTCTGTCTGTTT
29147885 CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAAATT
1 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG-TGAGGTATTTTCAAATT
*
29147950 CTATTT-AATTTATACTTTTCAAAAATCAATTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTTA
64 -TATTTCAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTTA
*
29148014 CATGACGAGGTATTTTCAAAAGCTACTTTTCAAATTAAGTTTCAAAAACGACCAACTCATATTGC
128 CATGACGAGGTATTTTCAAAAGCTACTTTTCAAATTAAGTTTCAAAAAAGACCAACTCATATTGC
*
29148079 GAGAAGTGAGTTGAGCCTTGGCTTACGTGCTGAGCTATTTTCAATTTCTGTCTGTTT
193 GAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATTTCTGTCTGTTT
* *
29148136 -TAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGTTGAGGTATTTT--AA---
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG-TGAGGTATTTTCAAATTT
* * * *
29148195 ATTTC----TGT--TTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACA
65 ATTTCAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTTACA
* * * * *
29148252 -CACTGAGGTATTTTC-AAA--TTCTGTTT-AATTTATACTTTTC--AAAA-ATCAACTCATATT
130 TGAC-GAGGTATTTTCAAAAGCTACT-TTTCAAATTA-A-GTTTCAAAAAAGACCAACTCATATT
* * * *
29148309 GCGAGAAGTGAGTTGAGCCTCGGGTCACATGAC-GAGGTATTTTCAA
191 GCGAGAAGTGAGTTGAGCCTTGGCTCACGTG-CTGAGCTATTTTCAA
29148355 AACCTACTTT
Statistics
Matches: 429, Mismatches: 31, Indels: 44
0.85 0.06 0.09
Matches are distributed among these distances:
232 51 0.12
233 12 0.03
234 4 0.01
235 9 0.02
236 14 0.03
238 42 0.10
240 2 0.00
243 4 0.01
247 2 0.00
249 54 0.13
251 175 0.41
252 5 0.01
256 16 0.04
257 1 0.00
258 36 0.08
259 2 0.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.34
Consensus pattern (249 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGTGAGGTATTTTCAAATTTA
TTTCAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTTACAT
GACGAGGTATTTTCAAAAGCTACTTTTCAAATTAAGTTTCAAAAAAGACCAACTCATATTGCGAG
AAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAATTTCTGTCTGTTT
Found at i:29148083 original size:90 final size:86
Alignment explanation
Indices: 29147881--29148122 Score: 260
Period size: 90 Copynumber: 2.8 Consensus size: 86
29147871 ATTTCTGTCT
* * * *
29147881 GTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCTGAGGTATTTT
1 GTTTCAAAAACCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTTACATGCTGAGGTATTTT
** *
29147944 CAAATTCTATTTAATTTATAC
66 CAAAAGCTATTTAAATTATAC
* * *
29147965 TTTTCAAAAATCAATTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTTACATGAC-GAGGTATTT
1 GTTTCAAAAACCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTTACATG-CTGAGGTATTT
29148029 TCAAAAGCTACTTTTCAAATTA-A-
65 TCAAAAGCTA--TTT-AAATTATAC
* * * *
29148052 GTTTCAAAAACGACCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTTACGTGCTGAGCTAT
1 GTTTC-AAAA--ACCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTTACATGCTGAGGTAT
29148117 TTTCAA
63 TTTCAA
29148123 TTTCTGTCTG
Statistics
Matches: 133, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
84 42 0.32
86 21 0.16
87 5 0.04
88 8 0.06
89 6 0.05
90 51 0.38
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (86 bp):
GTTTCAAAAACCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTTACATGCTGAGGTATTTT
CAAAAGCTATTTAAATTATAC
Found at i:29148229 original size:73 final size:73
Alignment explanation
Indices: 29148066--29148277 Score: 266
Period size: 73 Copynumber: 2.9 Consensus size: 73
29148056 CAAAAACGAC
* * * * *
29148066 CAACTCATATTGCGAGAAGTGAGTTGAGCCT-TGGCTTACGTGCTGAGCTATTTTCAATTTCTGT
1 CAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ATACGT--TGAGGTATTTTAAATTTCTGT
* ***
29148130 CTGTTTTAAAT
63 TTGTCAAAAAT
29148141 CAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGTTGAGGTATTTTAAATTTCTGTTTG
1 CAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGTTGAGGTATTTTAAATTTCTGTTTG
29148206 TCAAAAAT
66 TCAAAAAT
* **
29148214 CAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCAAA-TTCTGTTT
1 CAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGTTGAGGTATTTT-AAATTTCTGTTT
29148278 AATTTATACT
Statistics
Matches: 123, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
73 83 0.67
74 3 0.02
75 35 0.28
76 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.35
Consensus pattern (73 bp):
CAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGTTGAGGTATTTTAAATTTCTGTTTG
TCAAAAAT
Found at i:29148249 original size:322 final size:324
Alignment explanation
Indices: 29147815--29148450 Score: 1064
Period size: 322 Copynumber: 2.0 Consensus size: 324
29147805 CAAAAAAGAC
* * * *
29147815 CAACTCATATTGCTAGAAGTGAGTTGAGCCTTGGCTCACGTGTTGAGCTATTTTCAATTTCTGTC
1 CAACTCATATTGCGAGAAGTGAGTTGAGCCTAGGATCACG-GTTGAGCTATTTTAAATTTCTGTC
* *
29147880 TGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
65 TGTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTC
*
29147945 AAATTCTATTTAATTTATACTTTTCAAAAATCAATTCATATTGCGAGAAGTGAGTTGAGCCTCGG
130 AAATTCTATTTAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGG
* * *
29148010 GTTACATGACGAGGTATTTTCAAAAGCTACTTTTCAAATTAAGTTTCAAAAACGACCAACTCATA
195 GTCACATGACGAGGTATTTTCAAAACCTACTTTTCAAATTAAGTTTCAAAAA-AACCAACTCATA
* *
29148075 TTGCGAGAAGTGAGTTGAGCCTTGGCTTACGTGCTGAGCTATTTTCAATTTCTGTCTGTTTTAAA
259 TTGCGAGAAGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATTTTCAATTTCTGTCTGTTTTAAA
29148140 T
324 T
* *
29148141 CAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAT-AC-GTTGAGGTATTTTAAATTTCTGT-
1 CAACTCATATTGCGAGAAGTGAGTTGAGCCT-AGGATCACGGTTGAGCTATTTTAAATTTCTGTC
29148203 T-TGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTC
65 TGTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTC
*
29148267 AAATTCTGTTTAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGG
130 AAATTCTATTTAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGG
*
29148332 GTCACATGACGAGGTATTTTCAAAACCTACTTTTCAAATTAAGTTTCAAAAAAATCAACTCATAT
195 GTCACATGACGAGGTATTTTCAAAACCTACTTTTCAAATTAAGTTTCAAAAAAACCAACTCATAT
*
29148397 TGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATTTTCAATTTCTGT
260 TGCGAGAAGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATTTTCAATTTCTGT
29148451 TTTTTAGTTT
Statistics
Matches: 292, Mismatches: 17, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
321 62 0.21
322 174 0.60
323 1 0.00
324 21 0.07
326 31 0.11
327 3 0.01
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (324 bp):
CAACTCATATTGCGAGAAGTGAGTTGAGCCTAGGATCACGGTTGAGCTATTTTAAATTTCTGTCT
GTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCA
AATTCTATTTAATTTATACTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGG
TCACATGACGAGGTATTTTCAAAACCTACTTTTCAAATTAAGTTTCAAAAAAACCAACTCATATT
GCGAGAAGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATTTTCAATTTCTGTCTGTTTTAAAT
Found at i:29148398 original size:89 final size:84
Alignment explanation
Indices: 29148206--29148417 Score: 261
Period size: 84 Copynumber: 2.5 Consensus size: 84
29148196 TTTCTGTTTG
29148206 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCAAAT
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCAAAT
* * *
29148271 TCTGTTTAATTTATACTTT
66 ACTGTTTAAATTATACGTT
* * *
29148290 TCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACA-TGACGAGGTATTTTCA
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACT---GAGGTATTTTC-
29148354 AAACCTACT-TTTCAAATTA-A-GTT
62 AAA--TACTGTTT-AAATTATACGTT
29148377 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
29148418 TGGCTCACGC
Statistics
Matches: 112, Mismatches: 7, Indels: 13
0.85 0.05 0.10
Matches are distributed among these distances:
83 1 0.01
84 45 0.40
86 11 0.10
87 7 0.06
88 4 0.04
89 44 0.39
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (84 bp):
TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCAAAT
ACTGTTTAAATTATACGTT
Found at i:29148439 original size:89 final size:86
Alignment explanation
Indices: 29148206--29148443 Score: 256
Period size: 89 Copynumber: 2.7 Consensus size: 86
29148196 TTTCTGTTTG
*
29148206 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACACTGAGGTATTTTC-A
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGTCACACGCTGAGGTATTTTCAA
* * *
29148268 AATTCTGTTTAATTTATACTTT
65 AATACTGTTTAAATTATACGTT
* * *
29148290 TCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACATGAC-GAGGTATTTTCA
1 TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGTCACACG-CTGAGGTATTTTCA
29148354 AAACCTACT-TTTCAAATTA-A-GTT
64 AAA--TACTGTTT-AAATTATACGTT
* * *
29148377 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTATTTTC
1 TC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGG-TCACACGCTGAGGTATTTTC
29148442 AA
63 AA
29148444 TTTCTGTTTT
Statistics
Matches: 131, Mismatches: 12, Indels: 17
0.82 0.08 0.11
Matches are distributed among these distances:
84 41 0.31
86 14 0.11
87 8 0.06
88 7 0.05
89 61 0.47
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (86 bp):
TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGTCACACGCTGAGGTATTTTCAAA
ATACTGTTTAAATTATACGTT
Found at i:29150306 original size:15 final size:15
Alignment explanation
Indices: 29150274--29150316 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
29150264 ATTAAATTTG
*
29150274 TAATATTAATTCTATT
1 TAATATT-ATTATATT
29150290 TAATATTATTATATT
1 TAATATTATTATATT
*
29150305 TACTATTATTAT
1 TAATATTATTAT
29150317 TTATAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 18 0.72
16 7 0.28
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (15 bp):
TAATATTATTATATT
Found at i:29150373 original size:15 final size:15
Alignment explanation
Indices: 29150339--29150381 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
29150329 GTGTACTTTT
*
29150339 TATGTATA-TATTAT
1 TATGTATATTATTAG
*
29150353 TATGTATATTTTTAG
1 TATGTATATTATTAG
29150368 TATGTATATATATT
1 TATGTATAT-TATT
29150382 TATGAAGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 8 0.33
15 13 0.54
16 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (15 bp):
TATGTATATTATTAG
Found at i:29160695 original size:54 final size:54
Alignment explanation
Indices: 29160609--29160713 Score: 174
Period size: 54 Copynumber: 1.9 Consensus size: 54
29160599 ATGAAGAAAC
* *
29160609 TGGACGTTTCCAAGAATCCCAGTTCAACGAAACTCCGTTTCAGGAGATCAAAGG
1 TGGACGTGTCCAAGAATCCCAGTTCAACGAAACTCCATTTCAGGAGATCAAAGG
* *
29160663 TGGACGTGTCCAAGAATCCCAGTTCCAGGAAACTCCATTTCAGGAGATCAA
1 TGGACGTGTCCAAGAATCCCAGTTCAACGAAACTCCATTTCAGGAGATCAA
29160714 CAACGTCAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (54 bp):
TGGACGTGTCCAAGAATCCCAGTTCAACGAAACTCCATTTCAGGAGATCAAAGG
Found at i:29160817 original size:36 final size:36
Alignment explanation
Indices: 29160772--29160841 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
29160762 GAAGAAGAAT
*
29160772 GAACCAGAAGTGAGGACTTTTCATTCTATAGGGAAA
1 GAACCAGAAGTGAGGACTTTTCACTCTATAGGGAAA
*
29160808 GAACCAGAAGTGAGGACTTTTCACTCTGTAGGGA
1 GAACCAGAAGTGAGGACTTTTCACTCTATAGGGA
29160842 CTGGAACTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (36 bp):
GAACCAGAAGTGAGGACTTTTCACTCTATAGGGAAA
Found at i:29167103 original size:29 final size:28
Alignment explanation
Indices: 29167039--29167100 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
29167029 TCTATTTTAT
* * *
29167039 TAAATACATAATTTAATTTAACTTTAGTT
1 TAAATATAT-ATTTAATTTAACTTTAATA
29167068 TAAATATATATTTAAATTTAACTATTAATA
1 TAAATATATATTT-AATTTAACT-TTAATA
29167098 TAA
1 TAA
29167101 TATGATTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 4 0.14
29 17 0.61
30 7 0.25
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (28 bp):
TAAATATATATTTAATTTAACTTTAATA
Found at i:29169339 original size:4 final size:4
Alignment explanation
Indices: 29169326--29169361 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
29169316 TGTTCATATA
* *
29169326 TATG TGTG TATG TATG CATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG
29169362 CAACTATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.22, C:0.03, G:0.28, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:29170570 original size:46 final size:46
Alignment explanation
Indices: 29170517--29170610 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
29170507 AAAAAAAGAT
29170517 AAAATTATTAAAAAAATATAAGCATGGATACCAAAAATAGTGTTTG
1 AAAATTATTAAAAAAATATAAGCATGGATACCAAAAATAGTGTTTG
29170563 AAAATTATTAAAAAAATATAAGCATGGATACCAAAAATAGTGTTTG
1 AAAATTATTAAAAAAATATAAGCATGGATACCAAAAATAGTGTTTG
29170609 AA
1 AA
29170611 GGGAATATAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.53, C:0.06, G:0.13, T:0.28
Consensus pattern (46 bp):
AAAATTATTAAAAAAATATAAGCATGGATACCAAAAATAGTGTTTG
Found at i:29177816 original size:24 final size:24
Alignment explanation
Indices: 29177789--29177838 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
29177779 ACCACCAACT
*
29177789 CCACTTCCGTATCCGGATCCAGAC
1 CCACTTCCGTATCCAGATCCAGAC
* *
29177813 CCACTTTCTTATCCAGATCCAGAC
1 CCACTTCCGTATCCAGATCCAGAC
29177837 CC
1 CC
29177839 TTCTCCACTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.22, C:0.42, G:0.12, T:0.24
Consensus pattern (24 bp):
CCACTTCCGTATCCAGATCCAGAC
Found at i:29177866 original size:15 final size:15
Alignment explanation
Indices: 29177848--29177876 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29177838 CTTCTCCACT
29177848 GCCACCACCTCCGCC
1 GCCACCACCTCCGCC
29177863 GCCACCACCTCCGC
1 GCCACCACCTCCGC
29177877 TACCACCGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.66, G:0.14, T:0.07
Consensus pattern (15 bp):
GCCACCACCTCCGCC
Found at i:29177882 original size:15 final size:15
Alignment explanation
Indices: 29177849--29177883 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
29177839 TTCTCCACTG
*
29177849 CCACCACCTCCGCCG
1 CCACCACCTCCGCCA
*
29177864 CCACCACCTCCGCTA
1 CCACCACCTCCGCCA
29177879 CCACC
1 CCACC
29177884 GCCACCTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.66, G:0.09, T:0.09
Consensus pattern (15 bp):
CCACCACCTCCGCCA
Found at i:29177962 original size:12 final size:12
Alignment explanation
Indices: 29177942--29178000 Score: 55
Period size: 12 Copynumber: 4.9 Consensus size: 12
29177932 TCCCGATCCT
*
29177942 GACCTATACCCA
1 GACCCATACCCA
*
29177954 GACCCATACCCC
1 GACCCATACCCA
* * * * *
29177966 GATCTAGATCCT
1 GACCCATACCCA
29177978 GACCCATACCCA
1 GACCCATACCCA
29177990 GACCCATACCC
1 GACCCATACCC
29178001 CGATCCGGAT
Statistics
Matches: 35, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.29, C:0.46, G:0.10, T:0.15
Consensus pattern (12 bp):
GACCCATACCCA
Found at i:29177962 original size:36 final size:36
Alignment explanation
Indices: 29177915--29178024 Score: 175
Period size: 36 Copynumber: 3.1 Consensus size: 36
29177905 TATGCCACCA
* * *
29177915 CCAGACCCATACCACGATCCCGATCCTGACCTATAC
1 CCAGACCCATACCCCGATCCAGATCCTGACCCATAC
*
29177951 CCAGACCCATACCCCGATCTAGATCCTGACCCATAC
1 CCAGACCCATACCCCGATCCAGATCCTGACCCATAC
*
29177987 CCAGACCCATACCCCGATCCGGATCCTGACCCATAC
1 CCAGACCCATACCCCGATCCAGATCCTGACCCATAC
29178023 CC
1 CC
29178025 TGATCCTTCA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 68 1.00
ACGTcount: A:0.26, C:0.46, G:0.12, T:0.15
Consensus pattern (36 bp):
CCAGACCCATACCCCGATCCAGATCCTGACCCATAC
Found at i:29178173 original size:15 final size:15
Alignment explanation
Indices: 29178155--29178195 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
29178145 GGCACCACCC
*
29178155 CCTCCGCCACCTCCA
1 CCTCCACCACCTCCA
* *
29178170 CCTCCACCACTTCCT
1 CCTCCACCACCTCCA
29178185 CCTCCACCACC
1 CCTCCACCACC
29178196 ACTAAGTGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.15, C:0.66, G:0.02, T:0.17
Consensus pattern (15 bp):
CCTCCACCACCTCCA
Found at i:29178185 original size:18 final size:18
Alignment explanation
Indices: 29178164--29178198 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29178154 CCCTCCGCCA
*
29178164 CCTCCACCTCCACCACTT
1 CCTCCACCACCACCACTT
*
29178182 CCTCCTCCACCACCACT
1 CCTCCACCACCACCACT
29178199 AAGTGACCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.63, G:0.00, T:0.20
Consensus pattern (18 bp):
CCTCCACCACCACCACTT
Found at i:29186016 original size:4 final size:4
Alignment explanation
Indices: 29186007--29186054 Score: 55
Period size: 4 Copynumber: 12.0 Consensus size: 4
29185997 TATATAGTTG
*
29186007 ATTT ATTT A-TT ATTT ATTT ATTT CTTT -TTGT ATATT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATT-T AT-TT ATTT ATTT ATTT
29186055 TTAAAACTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
3 5 0.13
4 29 0.74
5 4 0.10
6 1 0.03
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:29186023 original size:11 final size:11
Alignment explanation
Indices: 29186007--29186057 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
29185997 TATATAGTTG
29186007 ATTTATTTATT
1 ATTTATTTATT
29186018 ATTTATTTATTT
1 ATTTATTTA-TT
* *
29186030 CTTTTTGTATATT
1 ATTTAT-T-TATT
29186043 ATTTATTTATT
1 ATTTATTTATT
29186054 -TTTA
1 ATTTA
29186058 AAACTCATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
10 4 0.12
11 13 0.39
12 7 0.21
13 7 0.21
14 2 0.06
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (11 bp):
ATTTATTTATT
Found at i:29186984 original size:15 final size:14
Alignment explanation
Indices: 29186956--29186982 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29186946 ATGCTGCCAA
29186956 AATTTTTATAAAAT
1 AATTTTTATAAAAT
29186970 AATTTTTATAAAA
1 AATTTTTATAAAA
29186983 ATGGAAAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATTTTTATAAAAT
Found at i:29188990 original size:33 final size:32
Alignment explanation
Indices: 29188927--29188992 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 32
29188917 AAAAATAATA
* *
29188927 AATTTAAAAATAAAAATTAATTAAAGAGAAAT
1 AATTTAAAAATAAAAATAAACTAAAGAGAAAT
*
29188959 AATTTAATAAGTAAAAATAAACTAGAA-AGAAAT
1 AATTTAA-AAATAAAAATAAACTA-AAGAGAAAT
29188992 A
1 A
29188993 TTAAAATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
32 7 0.24
33 20 0.69
34 2 0.07
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.26
Consensus pattern (32 bp):
AATTTAAAAATAAAAATAAACTAAAGAGAAAT
Found at i:29190349 original size:29 final size:29
Alignment explanation
Indices: 29190307--29190363 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
29190297 CATAGCCTTG
29190307 ACCTCGGATATTTTGTATGTCAAAACTAA
1 ACCTCGGATATTTTGTATGTCAAAACTAA
29190336 ACCTCGGATATTTTGTATGTCAAAACTA
1 ACCTCGGATATTTTGTATGTCAAAACTA
29190364 CGTTGCAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (29 bp):
ACCTCGGATATTTTGTATGTCAAAACTAA
Found at i:29191312 original size:21 final size:21
Alignment explanation
Indices: 29191288--29191339 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
29191278 AAAGTGATAA
*
29191288 AAAAGTAAAA-ACAATAAAAAC
1 AAAA-TAAAATACAAAAAAAAC
*
29191309 AAAATAAAATACAAAAAAAAT
1 AAAATAAAATACAAAAAAAAC
29191330 AAAA-AAAATA
1 AAAATAAAATA
29191340 TTTTGTGGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.81, C:0.06, G:0.02, T:0.12
Consensus pattern (21 bp):
AAAATAAAATACAAAAAAAAC
Found at i:29191319 original size:16 final size:15
Alignment explanation
Indices: 29191300--29191337 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
29191290 AAGTAAAAAC
29191300 AATAAAAACAAAATAA
1 AATAAAAA-AAAATAA
29191316 AATACAAAAAAAATAA
1 AATA-AAAAAAAATAA
29191332 AA-AAAA
1 AATAAAA
29191338 TATTTTGTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 3 0.14
15 1 0.05
16 13 0.62
17 4 0.19
ACGTcount: A:0.84, C:0.05, G:0.00, T:0.11
Consensus pattern (15 bp):
AATAAAAAAAAATAA
Found at i:29195954 original size:9 final size:9
Alignment explanation
Indices: 29195942--29195972 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
29195932 TTAATCAAAC
29195942 AATTAAATT
1 AATTAAATT
29195951 AATTAAATT
1 AATTAAATT
*
29195960 AACTAAATT
1 AATTAAATT
29195969 AATT
1 AATT
29195973 TTTCAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (9 bp):
AATTAAATT
Found at i:29198572 original size:24 final size:24
Alignment explanation
Indices: 29198514--29198574 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
29198504 GACCCTCCTG
*
29198514 CACTGCCACCACCTCCACCACCGC
1 CACTGCCACCACCTCCACCACCAC
* * *
29198538 CACTGCTACCACCTCCTCCTCCAC
1 CACTGCCACCACCTCCACCACCAC
**
29198562 CGTTGCCACCACC
1 CACTGCCACCACC
29198575 AACTCCACTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.18, C:0.59, G:0.08, T:0.15
Consensus pattern (24 bp):
CACTGCCACCACCTCCACCACCAC
Found at i:29198606 original size:24 final size:24
Alignment explanation
Indices: 29198579--29198625 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
29198569 ACCACCAACT
*
29198579 CCACTTCCGTATCCGGATCCAGAA
1 CCACTTCCATATCCGGATCCAGAA
*
29198603 CCACTTCCATATCTGGATCCAGA
1 CCACTTCCATATCCGGATCCAGA
29198626 CCCTTCTCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.36, G:0.15, T:0.23
Consensus pattern (24 bp):
CCACTTCCATATCCGGATCCAGAA
Found at i:29198749 original size:12 final size:12
Alignment explanation
Indices: 29198705--29198754 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
29198695 TATGCCACCA
29198705 CCAGACCCATAC
1 CCAGACCCATAC
* * * *
29198717 CCCGATCCAGAT
1 CCAGACCCATAC
*
29198729 CCTGACCCATAC
1 CCAGACCCATAC
29198741 CCAGACCCATAC
1 CCAGACCCATAC
29198753 CC
1 CC
29198755 CGATCCGGAT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.28, C:0.50, G:0.10, T:0.12
Consensus pattern (12 bp):
CCAGACCCATAC
Found at i:29198752 original size:36 final size:36
Alignment explanation
Indices: 29198705--29198778 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
29198695 TATGCCACCA
29198705 CCAGACCCATACCCCGATCCAGATCCTGACCCATAC
1 CCAGACCCATACCCCGATCCAGATCCTGACCCATAC
*
29198741 CCAGACCCATACCCCGATCCGGATCCTGACCCATAC
1 CCAGACCCATACCCCGATCCAGATCCTGACCCATAC
29198777 CC
1 CC
29198779 TGATCCTTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.26, C:0.49, G:0.12, T:0.14
Consensus pattern (36 bp):
CCAGACCCATACCCCGATCCAGATCCTGACCCATAC
Found at i:29198826 original size:24 final size:24
Alignment explanation
Indices: 29198782--29198845 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 24
29198772 CATACCCTGA
*
29198782 TCCTTCACCC-CTACCATCACCGCC
1 TCCTTCACCCTCT-CCACCACCGCC
* *
29198806 TCCTTCACCCTCTCCCCCACCTCC
1 TCCTTCACCCTCTCCACCACCGCC
* * *
29198830 ACCTCCACCTTCTCCA
1 TCCTTCACCCTCTCCA
29198846 AGACCACCAG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
24 30 0.94
25 2 0.06
ACGTcount: A:0.14, C:0.61, G:0.02, T:0.23
Consensus pattern (24 bp):
TCCTTCACCCTCTCCACCACCGCC
Found at i:29198881 original size:23 final size:23
Alignment explanation
Indices: 29198855--29198915 Score: 104
Period size: 23 Copynumber: 2.6 Consensus size: 23
29198845 AAGACCACCA
29198855 GCTCCCGAACCATATCCGGAGCC
1 GCTCCCGAACCATATCCGGAGCC
29198878 GCTCCCGAACCATATCCGGAGCC
1 GCTCCCGAACCATATCCGGAGCC
*
29198901 ACTCCCGAAACCATA
1 GCTCCCG-AACCATA
29198916 CCCTAAACCA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 29 0.81
24 7 0.19
ACGTcount: A:0.26, C:0.43, G:0.18, T:0.13
Consensus pattern (23 bp):
GCTCCCGAACCATATCCGGAGCC
Found at i:29198968 original size:15 final size:15
Alignment explanation
Indices: 29198950--29198990 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
29198940 GGCACCATCC
*
29198950 CCTCCGCCACCTCCA
1 CCTCCACCACCTCCA
* *
29198965 CCTCCACCACTTCCT
1 CCTCCACCACCTCCA
29198980 CCTCCACCACC
1 CCTCCACCACC
29198991 ACTAAGTGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.15, C:0.66, G:0.02, T:0.17
Consensus pattern (15 bp):
CCTCCACCACCTCCA
Found at i:29200368 original size:18 final size:17
Alignment explanation
Indices: 29200345--29200390 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
29200335 AATAAAATAT
*
29200345 TTATTTATATTTTAGTAA
1 TTATTTATAATTTA-TAA
29200363 TTATTTATAATTTATAA
1 TTATTTATAATTTATAA
*
29200380 -TATATATAATT
1 TTATTTATAATT
29200391 AGTTAGGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 10 0.38
17 3 0.12
18 13 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
TTATTTATAATTTATAA
Found at i:29212617 original size:21 final size:22
Alignment explanation
Indices: 29212591--29212643 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
29212581 AAAATGGATT
29212591 AATAAAATAAA-TATAATGAA-A-
1 AATAAAATAAAGTA-AAT-AATAG
*
29212612 AATAAAAAAAAGTAAATAATAG
1 AATAAAATAAAGTAAATAATAG
29212634 AATAAAATAA
1 AATAAAATAA
29212644 TATGCTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 2 0.07
21 14 0.52
22 11 0.41
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (22 bp):
AATAAAATAAAGTAAATAATAG
Found at i:29215246 original size:53 final size:53
Alignment explanation
Indices: 29215182--29215289 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
29215172 AAGGGTTTTA
29215182 TGTAGCAAAATTACCCTTTTATTTGATAGTGGTCGGTTGTTATATGTTTTAGT
1 TGTAGCAAAATTACCCTTTTATTTGATAGTGGTCGGTTGTTATATGTTTTAGT
29215235 TGTAGCAAAATTACCCTTTTATTTGATAGTGGTCGGTTGTTATATGTTTTAGT
1 TGTAGCAAAATTACCCTTTTATTTGATAGTGGTCGGTTGTTATATGTTTTAGT
29215288 TG
1 TG
29215290 AACTTTATAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.22, C:0.09, G:0.21, T:0.47
Consensus pattern (53 bp):
TGTAGCAAAATTACCCTTTTATTTGATAGTGGTCGGTTGTTATATGTTTTAGT
Found at i:29216485 original size:14 final size:14
Alignment explanation
Indices: 29216466--29216496 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29216456 AGAGTTTTTT
*
29216466 TAATCTAAATTTAC
1 TAATCTAAATTGAC
29216480 TAATCTAAATTGAC
1 TAATCTAAATTGAC
29216494 TAA
1 TAA
29216497 GAACGCAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTGAC
Found at i:29226589 original size:6 final size:7
Alignment explanation
Indices: 29226541--29226572 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
29226531 TAAACACAAG
*
29226541 AAAACGT
1 AAAAAGT
29226548 AAAAAGT
1 AAAAAGT
29226555 AAAAAGT
1 AAAAAGT
29226562 AAAAAGT
1 AAAAAGT
29226569 AAAA
1 AAAA
29226573 GATGAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.72, C:0.03, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAAGT
Found at i:29228699 original size:21 final size:22
Alignment explanation
Indices: 29228673--29228716 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
29228663 TTCTCAAGGG
*
29228673 TTGGATCGA-AGGCTTGGATCT
1 TTGGATCGACAGACTTGGATCT
29228694 TTGGATCGATCAGACTTGGATCT
1 TTGGATCGA-CAGACTTGGATCT
29228717 AGCCATCGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
23 11 0.55
ACGTcount: A:0.20, C:0.16, G:0.30, T:0.34
Consensus pattern (22 bp):
TTGGATCGACAGACTTGGATCT
Found at i:29229233 original size:28 final size:28
Alignment explanation
Indices: 29229201--29229267 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
29229191 ATTTACTATA
* *
29229201 ATACCCCTATGTATGCAATATTACAATT
1 ATACCCCTATGTATGCAAAATGACAATT
**
29229229 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACAATT
29229257 ATACCCCTATG
1 ATACCCCTATG
29229268 GTTAATTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.33
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACAATT
Found at i:29229412 original size:28 final size:27
Alignment explanation
Indices: 29229371--29229460 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 27
29229361 AGGAAGCGTC
29229371 CTGGTGG-CTATGCCACAAATTATCTGTT
1 CTGGTGGCCT-TGCCACAAA-TATCTGTT
**
29229399 CTGGTGGCCTTGCCACGTATATCTGTT
1 CTGGTGGCCTTGCCACAAATATCTGTT
*
29229426 CTGGTGGCAC-TGTCACAAAATATCTGTAT
1 CTGGTGGC-CTTGCCAC-AAATATCTGT-T
29229455 CTGGTG
1 CTGGTG
29229461 ACTCTGTCAT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
27 21 0.40
28 23 0.43
29 9 0.17
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.34
Consensus pattern (27 bp):
CTGGTGGCCTTGCCACAAATATCTGTT
Found at i:29232832 original size:22 final size:20
Alignment explanation
Indices: 29232791--29232850 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
29232781 GAAATTAGGG
*
29232791 ATTTTGTTTTTTTTTGTTTT
1 ATTTTCTTTTTTTTTGTTTT
29232811 AATTTTCTTTTTCTTCTT-TTTT
1 -ATTTTCTTTTT-TT-TTGTTTT
*
29232833 ATTTTC-CTTTTTTTGTTT
1 ATTTTCTTTTTTTTTGTTT
29232851 CTTTGGGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
18 2 0.06
19 5 0.15
20 3 0.09
21 16 0.47
22 6 0.18
23 2 0.06
ACGTcount: A:0.07, C:0.08, G:0.05, T:0.80
Consensus pattern (20 bp):
ATTTTCTTTTTTTTTGTTTT
Found at i:29233003 original size:15 final size:15
Alignment explanation
Indices: 29232983--29233011 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29232973 TTAATTGGGT
29232983 TTGGGTTGATGGATA
1 TTGGGTTGATGGATA
29232998 TTGGGTTGATGGAT
1 TTGGGTTGATGGAT
29233012 GGGTAGTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.41, T:0.41
Consensus pattern (15 bp):
TTGGGTTGATGGATA
Found at i:29238997 original size:18 final size:19
Alignment explanation
Indices: 29238969--29239008 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
29238959 ACGTAAAAAG
29238969 TAAAAAGTAAAAAATGAAA
1 TAAAAAGTAAAAAATGAAA
*
29238988 TAAAAA-TAAATAATGAAA
1 TAAAAAGTAAAAAATGAAA
29239006 TAA
1 TAA
29239009 TTTTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.20
Consensus pattern (19 bp):
TAAAAAGTAAAAAATGAAA
Found at i:29239922 original size:16 final size:16
Alignment explanation
Indices: 29239892--29239939 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
29239882 GAAAATTAAT
29239892 ATAAAATCT-AAAAT-A
1 ATAAAAT-TAAAAATAA
29239907 ATAATAATTAAAAATAA
1 ATAA-AATTAAAAATAA
29239924 ATAAAATT-AAAATAA
1 ATAAAATTAAAAATAA
29239939 A
1 A
29239940 CTTAAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.43
16 12 0.40
17 5 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAAATAA
Found at i:29239938 original size:11 final size:11
Alignment explanation
Indices: 29239883--29239953 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
29239873 ATAGATTAAG
*
29239883 AAAATTAATAT
1 AAAATTAAAAT
29239894 AAAATCTAAAAT
1 AAAAT-TAAAAT
*
29239906 AATAA-T-AATT
1 AA-AATTAAAAT
*
29239916 AAAAAT-AAAT
1 AAAATTAAAAT
29239926 AAAATTAAAAT
1 AAAATTAAAAT
*
29239937 AAACTTAAAAT
1 AAAATTAAAAT
*
29239948 AGAATT
1 AAAATT
29239954 TCCTATTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
9 2 0.04
10 14 0.29
11 24 0.49
12 7 0.14
13 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:29240954 original size:28 final size:27
Alignment explanation
Indices: 29240923--29240977 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
29240913 TTTATTATTT
*
29240923 TTCAATAGCAATAAATCAATCAGTAATA
1 TTCAATAACAATAAATCAATCAG-AATA
* * *
29240951 TTCATTAACAATCAGTCAATCAGAATA
1 TTCAATAACAATAAATCAATCAGAATA
29240978 ATTATTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.29
Consensus pattern (27 bp):
TTCAATAACAATAAATCAATCAGAATA
Found at i:29241004 original size:18 final size:18
Alignment explanation
Indices: 29240949--29241046 Score: 81
Period size: 18 Copynumber: 5.5 Consensus size: 18
29240939 CAATCAGTAA
* *
29240949 TATTCATTAACAATCAGT
1 TATTCAGTAATAATCAGT
* * * *
29240967 CAATCAG-AATAATTATT
1 TATTCAGTAATAATCAGT
*
29240984 TATTCAGTAATAGTCAGT
1 TATTCAGTAATAATCAGT
** * *
29241002 TATTTGGTAACAATCAAT
1 TATTCAGTAATAATCAGT
*
29241020 TATTCAATAATAATCAGT
1 TATTCAGTAATAATCAGT
29241038 TATTCAGTA
1 TATTCAGTA
29241047 TCAATCAATT
Statistics
Matches: 57, Mismatches: 22, Indels: 2
0.70 0.27 0.02
Matches are distributed among these distances:
17 12 0.21
18 45 0.79
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (18 bp):
TATTCAGTAATAATCAGT
Found at i:29241025 original size:36 final size:36
Alignment explanation
Indices: 29240983--29241056 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 36
29240973 GAATAATTAT
* * **
29240983 TTATTCAGTAATAGTCAGTTATTTGGTAACAATCAA
1 TTATTCAATAATAATCAGTTATTCAGTAACAATCAA
*
29241019 TTATTCAATAATAATCAGTTATTCAGTATCAATCAA
1 TTATTCAATAATAATCAGTTATTCAGTAACAATCAA
29241055 TT
1 TT
29241057 GATCGGCAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (36 bp):
TTATTCAATAATAATCAGTTATTCAGTAACAATCAA
Found at i:29241052 original size:18 final size:18
Alignment explanation
Indices: 29240937--29241053 Score: 60
Period size: 18 Copynumber: 6.4 Consensus size: 18
29240927 ATAGCAATAA
*
29240937 ATCAATCAGTAATATTCATT
1 ATCAATCAGT--TATTCAGT
* * * *
29240957 AACAATCAGTCAATCAGA
1 ATCAATCAGTTATTCAGT
* *
29240975 AT-AATTATTTATTCAGT
1 ATCAATCAGTTATTCAGT
* **
29240992 AAT-AGTCAGTTATTTGGT
1 -ATCAATCAGTTATTCAGT
* * *
29241010 AACAATCAATTATTCAAT
1 ATCAATCAGTTATTCAGT
29241028 AAT-AATCAGTTATTCAGT
1 -ATCAATCAGTTATTCAGT
29241046 ATCAATCA
1 ATCAATCA
29241054 ATTGATCGGC
Statistics
Matches: 68, Mismatches: 25, Indels: 10
0.66 0.24 0.10
Matches are distributed among these distances:
17 13 0.19
18 45 0.66
19 1 0.01
20 9 0.13
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.37
Consensus pattern (18 bp):
ATCAATCAGTTATTCAGT
Found at i:29241152 original size:18 final size:19
Alignment explanation
Indices: 29241106--29241152 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
29241096 TCGAGATAAT
*
29241106 GAAAAATAATTACTTTAAA
1 GAAAAATAATTACATTAAA
29241125 -AATAAA-AATTA-ATTAAA
1 GAA-AAATAATTACATTAAA
29241142 GAAAAATAATT
1 GAAAAATAATT
29241153 TAATAAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
17 8 0.33
18 13 0.54
19 3 0.12
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (19 bp):
GAAAAATAATTACATTAAA
Found at i:29243726 original size:56 final size:56
Alignment explanation
Indices: 29243651--29243771 Score: 201
Period size: 56 Copynumber: 2.2 Consensus size: 56
29243641 ATCTTAAAAG
* *
29243651 ATAAAAA-AAAATTAATAACTATAAAATAAAATTA-AACTTTAAACTTTAAAACACA
1 ATAAAAACAAAATTAATAACTACAAAATAAAATTACAA-TCTAAACTTTAAAACACA
29243706 ATAAAAACAAAATTAATAACTACAAAATAAAATTACAATCTAAACTTTAAAACACA
1 ATAAAAACAAAATTAATAACTACAAAATAAAATTACAATCTAAACTTTAAAACACA
29243762 ATAAAAACAA
1 ATAAAAACAA
29243772 TTGTAAAATT
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
55 7 0.11
56 53 0.85
57 2 0.03
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (56 bp):
ATAAAAACAAAATTAATAACTACAAAATAAAATTACAATCTAAACTTTAAAACACA
Found at i:29244314 original size:19 final size:19
Alignment explanation
Indices: 29244249--29244316 Score: 77
Period size: 18 Copynumber: 3.7 Consensus size: 19
29244239 TGTTGATCGG
* *
29244249 TTATCCAGTAACAGTC-AA
1 TTATTCAGTAACAATCAAA
*
29244267 TTATTCAGTAAAAATCAAA
1 TTATTCAGTAACAATCAAA
* *
29244286 -TATACAGTAACAATTAAA
1 TTATTCAGTAACAATCAAA
29244304 TTATTCAGTAACA
1 TTATTCAGTAACA
29244317 GTCGATCTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
18 28 0.68
19 13 0.32
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (19 bp):
TTATTCAGTAACAATCAAA
Found at i:29244508 original size:6 final size:6
Alignment explanation
Indices: 29244497--29244533 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
29244487 ACAAACCCGA
*
29244497 AACAGT AACAGT AACAGT AACGGT AACAGT AACAGT A
1 AACAGT AACAGT AACAGT AACAGT AACAGT AACAGT A
29244534 GTCGGCACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.49, C:0.16, G:0.19, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:29246934 original size:10 final size:10
Alignment explanation
Indices: 29246901--29246942 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
29246891 AAATCTGTCG
*
29246901 AAAA-TAATC
1 AAAATTAATT
29246910 AAAATTAATTAT
1 AAAATTAA-T-T
29246922 AAAATTAATT
1 AAAATTAATT
29246932 AAAATTAATT
1 AAAATTAATT
29246942 A
1 A
29246943 CGTTAATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 4 0.14
10 15 0.52
11 2 0.07
12 8 0.28
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAATTAATT
Found at i:29253217 original size:3 final size:3
Alignment explanation
Indices: 29253209--29253272 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
29253199 TTCTCGCCCA
29253209 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29253257 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
29253273 TACTTTGTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:29258709 original size:3 final size:3
Alignment explanation
Indices: 29258694--29258743 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
29258684 CCACAACTCG
*
29258694 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29258742 TT
1 TT
29258744 TACTTTGTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:29262503 original size:19 final size:19
Alignment explanation
Indices: 29262481--29262532 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
29262471 TTTAGAAAAT
29262481 TTTTAAATATTTTCATTAA
1 TTTTAAATATTTTCATTAA
* *
29262500 TTTTAAAT-TTATTTA-TAT
1 TTTTAAATATT-TTCATTAA
29262518 TTTTAAA-ATTTTCAT
1 TTTTAAATATTTTCAT
29262533 AATAAGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
17 3 0.11
18 13 0.48
19 11 0.41
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTAAATATTTTCATTAA
Found at i:29271548 original size:21 final size:20
Alignment explanation
Indices: 29271473--29271562 Score: 67
Period size: 21 Copynumber: 4.3 Consensus size: 20
29271463 CGTGGAATAA
*
29271473 AAAAATATATTATAAATATATT
1 AAAAAT-TATAATAAAT-TATT
* * *
29271495 AAAAATTAAAATGATTTA-T
1 AAAAATTATAATAAATTATT
*
29271514 AAATTATATATAATAATATT-TT
1 AAA-AAT-TATAATAA-ATTATT
29271536 ATAAAATTATAATAAATTATT
1 A-AAAATTATAATAAATTATT
29271557 AAAAAT
1 AAAAAT
29271563 AAATATTTAC
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
19 4 0.08
20 12 0.23
21 23 0.43
22 12 0.23
23 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (20 bp):
AAAAATTATAATAAATTATT
Found at i:29277265 original size:19 final size:20
Alignment explanation
Indices: 29277241--29277280 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
29277231 TTGCTACTGT
29277241 TTTGC-TTCGTTTCTGCTTC
1 TTTGCTTTCGTTTCTGCTTC
* *
29277260 TTTGCTTTCTTTTCTGTTTC
1 TTTGCTTTCGTTTCTGCTTC
29277280 T
1 T
29277281 ATTTTGCAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.00, C:0.23, G:0.12, T:0.65
Consensus pattern (20 bp):
TTTGCTTTCGTTTCTGCTTC
Found at i:29283696 original size:45 final size:45
Alignment explanation
Indices: 29283646--29283756 Score: 172
Period size: 45 Copynumber: 2.5 Consensus size: 45
29283636 CGACTACTGT
29283646 TACTGTTATCGTTACTGTTATCA-ATTC-GACACTTTGTGTGTTGAA
1 TACTGTTATCGTTACTGTTA-CAGATTCAG-CACTTTGTGTGTTGAA
29283691 TACTGTTATCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTATCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
* *
29283736 TACTGCTACCGTTACTGTTAC
1 TACTGTTATCGTTACTGTTAC
29283757 TGCTACCGTT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
44 2 0.03
45 59 0.95
46 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (45 bp):
TACTGTTATCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
Found at i:29291194 original size:9 final size:9
Alignment explanation
Indices: 29291180--29291220 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
29291170 TTAAATTTTT
29291180 AAAAATTAAA
1 AAAAATT-AA
29291190 AAAATATTAA
1 AAAA-ATTAA
29291200 AAAAATTAA
1 AAAAATTAA
*
29291209 AAACATTAA
1 AAAAATTAA
29291218 AAA
1 AAA
29291221 CATTTTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 16 0.55
10 10 0.34
11 3 0.10
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (9 bp):
AAAAATTAA
Found at i:29291221 original size:9 final size:9
Alignment explanation
Indices: 29291189--29291224 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
29291179 TAAAAATTAA
*
29291189 AAAAATATT
1 AAAAACATT
*
29291198 AAAAAAATT
1 AAAAACATT
29291207 AAAAACATT
1 AAAAACATT
29291216 AAAAACATT
1 AAAAACATT
29291225 TTTTAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (9 bp):
AAAAACATT
Found at i:29291821 original size:22 final size:20
Alignment explanation
Indices: 29291784--29291823 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
29291774 TTAAAATATT
*
29291784 TTTTTATTCATTAAACTTAA
1 TTTTTATTCATAAAACTTAA
29291804 TTTTTATTCTATCAAAACTT
1 TTTTTATTC-AT-AAAACTT
29291824 GTAAGAGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 2 0.12
22 6 0.35
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTTATTCATAAAACTTAA
Found at i:29310037 original size:10 final size:10
Alignment explanation
Indices: 29310022--29310072 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
29310012 TAATTTTAGG
29310022 ATTTATTTTT
1 ATTTATTTTT
*
29310032 ATTTATCTTT
1 ATTTATTTTT
*
29310042 ATTTATCTTT
1 ATTTATTTTT
* *
29310052 AATTATTTGT
1 ATTTATTTTT
29310062 ATTTATCTTTT
1 ATTTAT-TTTT
29310073 GAAATTTAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
10 31 0.91
11 3 0.09
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.71
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:29310047 original size:20 final size:20
Alignment explanation
Indices: 29310022--29310071 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
29310012 TAATTTTAGG
* * *
29310022 ATTTATTTTTATTTATCTTT
1 ATTTATCTTTAATTATCTGT
*
29310042 ATTTATCTTTAATTATTTGT
1 ATTTATCTTTAATTATCTGT
29310062 ATTTATCTTT
1 ATTTATCTTT
29310072 TGAAATTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.70
Consensus pattern (20 bp):
ATTTATCTTTAATTATCTGT
Found at i:29311451 original size:15 final size:16
Alignment explanation
Indices: 29311433--29311463 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
29311423 TTAGTGCTCC
29311433 CTCCAAAGTTT-AAAA
1 CTCCAAAGTTTGAAAA
29311448 CTCCAAAGTTTGAAAA
1 CTCCAAAGTTTGAAAA
29311464 GTATAATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (16 bp):
CTCCAAAGTTTGAAAA
Found at i:29316765 original size:24 final size:24
Alignment explanation
Indices: 29316732--29316781 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
29316722 AAGTCTGTCT
29316732 GGAGAAGATTTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
* *
29316756 GGAGAGGATTTAGGAGCTGATTAG
1 GGAGAAGATTTAGGAGCTGATAAG
29316780 GG
1 GG
29316782 TGAACTGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.32, C:0.04, G:0.42, T:0.22
Consensus pattern (24 bp):
GGAGAAGATTTAGGAGCTGATAAG
Found at i:29318232 original size:27 final size:26
Alignment explanation
Indices: 29318193--29318303 Score: 105
Period size: 27 Copynumber: 4.1 Consensus size: 26
29318183 GGAAGCGTCT
*
29318193 TGGTGGCTATGCCACAATTATCTGATC
1 TGGTGGCTCTGCCAC-ATTATCTGATC
*
29318220 TGGTGGCTCTGCCACATATATCTGTTC
1 TGGTGGCTCTGCCACAT-TATCTGATC
* * *
29318247 TAGTGGTTCTGACACGATTATCTGTATC
1 TGGTGGCTCTGCCAC-ATTATCTG-ATC
** * *
29318275 TGGTAACTCTGTCACATTATCTGTTC
1 TGGTGGCTCTGCCACATTATCTGATC
29318301 TGG
1 TGG
29318304 CAGCCATGCT
Statistics
Matches: 69, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
26 7 0.10
27 48 0.70
28 14 0.20
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.38
Consensus pattern (26 bp):
TGGTGGCTCTGCCACATTATCTGATC
Found at i:29320699 original size:44 final size:44
Alignment explanation
Indices: 29320594--29321130 Score: 321
Period size: 44 Copynumber: 11.8 Consensus size: 44
29320584 GATAATGGCG
* * * * *
29320594 AATCTCATCTCCCTAAAATTGCAGTGGAGTAAATTGAAGATAGCA
1 AATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGATA-CA
* * *
29320639 AATCTTATCTCTCTGAAATTGCAGTAGAGCAGATTAAAGCTACA
1 AATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGATACA
* * * * * *
29320683 AATCTTATCTCCCTGAAGTTGCAATGGGGCAGGTTGAAGTTACA
1 AATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGATACA
* * * *
29320727 AGTCTTATCTCCCT-AAAGTTGAAGTGGAGCAGACTAAAGATAGCG
1 AATCTTATCTCCCTGAAA-TTGCAGTGGAGCAGATTAAAGATA-CA
* * *
29320772 AGTTTTATTTCCCTGAAATTGCAGTGGA--ATGATTAAAGCTACAAATGACA
1 AATCTTATCTCCCTGAAATTGCAGTGGAGCA-GATTAAAG------AT-ACA
* * * *
29320822 AATCTAATCTCCCT-AAAGTTGCAGTCGAGTAGATTGAAGATAGCA
1 AATCTTATCTCCCTGAAA-TTGCAGTGGAGCAGATTAAAGATA-CA
* * * * * * *
29320867 AATCTTATCTCTCT-AAAGTTGCAATAGAGTAGATGAAAGTTATA
1 AATCTTATCTCCCTGAAA-TTGCAGTGGAGCAGATTAAAGATACA
* * * * * * * *
29320911 AACCTTATCTCTCTTAAGTTGTAGTGGGGCAGGTTAAAGTTACA
1 AATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGATACA
* * *
29320955 AGTCTTATCTCCCTGAAATTGCAGTGGAGCAGACTGAAA-ATAACG
1 AATCTTATCTCCCTGAAATTGCAGTGGAGCAGA-TTAAAGAT-ACA
* * *
29321000 AATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAATTACA
1 AATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAG------A-TACA
* * * * *
29321051 AATCTTATCTCTCTGAAATTGCAGTCGAGTAGATTAAAGCTATA
1 AATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGATACA
* * * *
29321095 AATCTTATCTCCATGAAGTCGCAATTGGAGCAGATT
1 AATCTTATCTCCCTGAAATTGC-AGTGGAGCAGATT
29321131 GAAGTTATTA
Statistics
Matches: 378, Mismatches: 87, Indels: 54
0.73 0.17 0.10
Matches are distributed among these distances:
43 3 0.01
44 159 0.42
45 142 0.38
46 3 0.01
49 3 0.01
50 22 0.06
51 44 0.12
52 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGATACA
Found at i:29320920 original size:184 final size:182
Alignment explanation
Indices: 29320637--29320982 Score: 417
Period size: 184 Copynumber: 1.9 Consensus size: 182
29320627 TTGAAGATAG
* * * *
29320637 CAAATCTTATCTCTCTGAAATTGCAGTAGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAGT
1 CAAATCTAATCTCCCTGAAATTGCAGTAGAGCAGATTAAAGATACAAATCTTATCTCCCTAAAGT
* * * **
29320702 TGCAATGGGGCAGGTTGAAGTTACAAGTCTTATCTCCCTAAAGTTGAAGTGGAGCAGACTAAAGA
66 TGCAATAGAGCAGGATGAAGTTACAAACCTTATCTCCCTAAAGTTGAAGTGGAGCAGACTAAAGA
* * *
29320767 TAGCGAGTTTTATTTCCCTGAAATTGCAGTGGAATGATTAAAGCTACAAATGA
131 TA-CAAGTCTTATCTCCCTGAAATTGCAGTGGAATGATTAAAGCTACAAATGA
* * * *
29320820 CAAATCTAATCTCCCT-AAAGTTGCAGTCGAGTAGATTGAAGATAGCAAATCTTATCTCTCTAAA
1 CAAATCTAATCTCCCTGAAA-TTGCAGTAGAGCAGATTAAAGATA-CAAATCTTATCTCCCTAAA
* * * * * * **
29320884 GTTGCAATAGAGTA-GATGAAAGTTATAAACCTTATCTCTCTTAAGTTGTAGTGGGGCAGGTTAA
64 GTTGCAATAGAGCAGGATG-AAGTTACAAACCTTATCTCCCTAAAGTTGAAGTGGAGCAGACTAA
*
29320948 AGTTACAAGTCTTATCTCCCTGAAATTGCAGTGGA
128 AGATACAAGTCTTATCTCCCTGAAATTGCAGTGGA
29320983 GCAGACTGAA
Statistics
Matches: 135, Mismatches: 25, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
182 3 0.02
183 64 0.47
184 68 0.50
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (182 bp):
CAAATCTAATCTCCCTGAAATTGCAGTAGAGCAGATTAAAGATACAAATCTTATCTCCCTAAAGT
TGCAATAGAGCAGGATGAAGTTACAAACCTTATCTCCCTAAAGTTGAAGTGGAGCAGACTAAAGA
TACAAGTCTTATCTCCCTGAAATTGCAGTGGAATGATTAAAGCTACAAATGA
Found at i:29320953 original size:228 final size:228
Alignment explanation
Indices: 29320594--29321105 Score: 692
Period size: 228 Copynumber: 2.2 Consensus size: 228
29320584 GATAATGGCG
* * *
29320594 AATCTCATCTCCCTAAAATTGCAGTGGAGTAAATTGAAGATAGCAAATCTTATCTCTCTGAAATT
1 AATCTAATCTCCCT-AAATTGCAGTCGAGTAGATTGAAGATAGCAAATCTTATCTCTCTGAAATT
* * * *
29320659 GCAGTAGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTGCAATGGGGCAGGTTGAAGTT
65 GCAATAGAGCAGATGAAAGCTACAAACCTTATCTCCCTGAAGTTGCAATGGGGCAGGTTAAAGTT
* * *
29320724 ACAAGTCTTATCTCCCT-AAAGTTGAAGTGGAGCAGACT-AAAGATAGCGAGTTTTATTTCCCTG
130 ACAAGTCTTATCTCCCTGAAA-TTGAAGTGGAGCAGACTGAAA-ATAACGAATCTTATTTCCCTG
*
29320787 AAATTGCAGTGGAA-TGATTAAAGCTACAAATGACA
193 AAATTGCAGTGGAACAGATTAAAGCTACAAATGACA
29320822 AATCTAATCTCCCTAAAGTTGCAGTCGAGTAGATTGAAGATAGCAAATCTTATCTCTCT-AAAGT
1 AATCTAATCTCCCTAAA-TTGCAGTCGAGTAGATTGAAGATAGCAAATCTTATCTCTCTGAAA-T
* * * * * * *
29320886 TGCAATAGAGTAGATGAAAGTTATAAACCTTATCTCTCTTAAGTTGTAGTGGGGCAGGTTAAAGT
64 TGCAATAGAGCAGATGAAAGCTACAAACCTTATCTCCCTGAAGTTGCAATGGGGCAGGTTAAAGT
*
29320951 TACAAGTCTTATCTCCCTGAAATTGCAGTGGAGCAGACTGAAAATAACGAATCTTATTTCCCTGA
129 TACAAGTCTTATCTCCCTGAAATTGAAGTGGAGCAGACTGAAAATAACGAATCTTATTTCCCTGA
* * *
29321016 AGTTGCAGTGGAACAGATTAAAGCTATAAATTACA
194 AATTGCAGTGGAACAGATTAAAGCTACAAATGACA
* * * * *
29321051 AATCTTATCTCTCTGAAATTGCAGTCGAGTAGATTAAAGCTA-TAAATCTTATCTC
1 AATCTAATCTCCCT-AAATTGCAGTCGAGTAGATTGAAGATAGCAAATCTTATCTC
29321106 CATGAAGTCG
Statistics
Matches: 251, Mismatches: 27, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
227 6 0.02
228 184 0.73
229 58 0.23
230 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (228 bp):
AATCTAATCTCCCTAAATTGCAGTCGAGTAGATTGAAGATAGCAAATCTTATCTCTCTGAAATTG
CAATAGAGCAGATGAAAGCTACAAACCTTATCTCCCTGAAGTTGCAATGGGGCAGGTTAAAGTTA
CAAGTCTTATCTCCCTGAAATTGAAGTGGAGCAGACTGAAAATAACGAATCTTATTTCCCTGAAA
TTGCAGTGGAACAGATTAAAGCTACAAATGACA
Found at i:29321085 original size:51 final size:51
Alignment explanation
Indices: 29320945--29321097 Score: 147
Period size: 51 Copynumber: 3.1 Consensus size: 51
29320935 TGGGGCAGGT
* * * *
29320945 TAAAGTTACAAGTCTTATCTCCCTGAAATTGCAGTGGAGCAGACT---G--A
1 TAAA-TTACAAATCTTATCTCCCTGAAATTGCAGTCGAACAGATTAAAGCTA
* * * * *
29320992 -AAATAACGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTA
1 TAAATTACAAATCTTATCTCCCTGAAATTGCAGTCGAACAGATTAAAGCTA
* **
29321042 TAAATTACAAATCTTATCTCTCTGAAATTGCAGTCGAGTAGATTAAAGCTA
1 TAAATTACAAATCTTATCTCCCTGAAATTGCAGTCGAACAGATTAAAGCTA
29321093 TAAAT
1 TAAAT
29321098 CTTATCTCCA
Statistics
Matches: 85, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
45 33 0.39
46 3 0.04
48 1 0.01
50 1 0.01
51 47 0.55
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (51 bp):
TAAATTACAAATCTTATCTCCCTGAAATTGCAGTCGAACAGATTAAAGCTA
Found at i:29321843 original size:15 final size:17
Alignment explanation
Indices: 29321820--29321858 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
29321810 AAGGTTGTTT
29321820 TTTTA-TTTTT-CT-GC
1 TTTTATTTTTTACTAGC
29321834 TTTTATTTTTTACTAGC
1 TTTTATTTTTTACTAGC
29321851 TTTT-TTTT
1 TTTTATTTT
29321859 AAAAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 5 0.23
15 5 0.23
16 6 0.27
17 6 0.27
ACGTcount: A:0.10, C:0.10, G:0.05, T:0.74
Consensus pattern (17 bp):
TTTTATTTTTTACTAGC
Found at i:29322060 original size:20 final size:20
Alignment explanation
Indices: 29322035--29322076 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
29322025 GGACGGTGGC
*
29322035 GCCGTCATCGGCCACCGACG
1 GCCGTCACCGGCCACCGACG
* *
29322055 GCCGTCACCGGCGATCGACG
1 GCCGTCACCGGCCACCGACG
29322075 GC
1 GC
29322077 AGCCACAGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.43, G:0.33, T:0.10
Consensus pattern (20 bp):
GCCGTCACCGGCCACCGACG
Found at i:29322716 original size:13 final size:13
Alignment explanation
Indices: 29322698--29322731 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
29322688 CTACTGCGCA
29322698 TTTTATTCTTATT
1 TTTTATTCTTATT
*
29322711 TTTTATTTTTATT
1 TTTTATTCTTATT
29322724 TTTT-TTCT
1 TTTTATTCT
29322732 ATTAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 3 0.16
13 16 0.84
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTATTCTTATT
Found at i:29322854 original size:14 final size:15
Alignment explanation
Indices: 29322828--29322868 Score: 66
Period size: 14 Copynumber: 2.8 Consensus size: 15
29322818 CTTGCACATT
*
29322828 TTATTAGTATTACCA
1 TTATTATTATTACCA
29322843 TT-TTATTATTACCA
1 TTATTATTATTACCA
29322857 TTATTATTATTA
1 TTATTATTATTA
29322869 TTGTTTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (15 bp):
TTATTATTATTACCA
Found at i:29323697 original size:19 final size:18
Alignment explanation
Indices: 29323673--29323708 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
29323663 ATGCATAATA
29323673 AAATTAAATAATCGAAATT
1 AAATTAAATAATC-AAATT
*
29323692 AAATTAGATAATCAAAT
1 AAATTAAATAATCAAAT
29323709 ATGCGAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (18 bp):
AAATTAAATAATCAAATT
Found at i:29328406 original size:20 final size:20
Alignment explanation
Indices: 29328364--29328410 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
29328354 AAAATTACAA
* *
29328364 AAAAAATTCAATATAATTTT
1 AAAAAATTCAAAATAATTAT
29328384 AAAAAATTCAAAAT-ATTCAT
1 AAAAAATTCAAAATAATT-AT
29328404 AAAAAAT
1 AAAAAAT
29328411 CTAAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTAT
Found at i:29329493 original size:13 final size:13
Alignment explanation
Indices: 29329475--29329527 Score: 70
Period size: 13 Copynumber: 4.1 Consensus size: 13
29329465 AGTTTGGCAA
29329475 TACTTTTGAAAAG
1 TACTTTTGAAAAG
* *
29329488 TACTTTTCAAGAG
1 TACTTTTGAAAAG
* *
29329501 TGCTTTTGATAAG
1 TACTTTTGAAAAG
29329514 TACTTTTGAAAAG
1 TACTTTTGAAAAG
29329527 T
1 T
29329528 TTGGTTTAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (13 bp):
TACTTTTGAAAAG
Found at i:29329806 original size:19 final size:20
Alignment explanation
Indices: 29329762--29329806 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
29329752 ATTAATTATT
*
29329762 TATAAAATTTAATTAGAATA
1 TATAAAATATAATTAGAATA
*
29329782 TATAAAATATATTTA-AATA
1 TATAAAATATAATTAGAATA
*
29329801 TTTAAA
1 TATAAA
29329807 TGTAACTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
TATAAAATATAATTAGAATA
Found at i:29338039 original size:25 final size:24
Alignment explanation
Indices: 29338010--29338071 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
29338000 ATAATTGATG
*
29338010 AATATTTTATATTTAAAATTTATTC
1 AATATTTTATATTTAAAATTTA-TA
* *
29338035 AATATCATT-TATTTAATATTTATA
1 AATAT-TTTATATTTAAAATTTATA
29338059 AATATTTTTATAT
1 AATA-TTTTATAT
29338072 ACAATAGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
24 7 0.23
25 21 0.70
26 2 0.07
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.56
Consensus pattern (24 bp):
AATATTTTATATTTAAAATTTATA
Found at i:29351403 original size:29 final size:31
Alignment explanation
Indices: 29351336--29351407 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 31
29351326 TTACATTTAA
*
29351336 ATATTTAAAATAAATCTTTAACTTTTAATTT
1 ATATTTAAAATAAAGCTTTAACTTTTAATTT
* * *
29351367 ATA-GTAAAAT-AAGC-TTCACTTTTTATTT
1 ATATTTAAAATAAAGCTTTAACTTTTAATTT
29351395 ATATTT-AAATAAA
1 ATATTTAAAATAAA
29351408 TTATTAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
28 19 0.56
29 6 0.18
30 6 0.18
31 3 0.09
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (31 bp):
ATATTTAAAATAAAGCTTTAACTTTTAATTT
Found at i:29353680 original size:17 final size:17
Alignment explanation
Indices: 29353658--29353703 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
29353648 AGAACAAGGA
29353658 AAGAAAAGAA-AGGAAG
1 AAGAAAAGAAGAGGAAG
29353674 AAGGAAAAGAAAAGAGGAAG
1 AA-GAAAAG--AAGAGGAAG
29353694 AAGAAAAGAA
1 AAGAAAAGAA
29353704 CTAACGTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 2 0.08
17 8 0.31
19 8 0.31
20 8 0.31
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (17 bp):
AAGAAAAGAAGAGGAAG
Found at i:29353688 original size:14 final size:15
Alignment explanation
Indices: 29353671--29353703 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
29353661 AAAAGAAAGG
29353671 AAGAAGGAA-AAGAA
1 AAGAAGGAAGAAGAA
29353685 AAG-AGGAAGAAGAA
1 AAGAAGGAAGAAGAA
29353699 AAGAA
1 AAGAA
29353704 CTAACGTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 5 0.29
14 11 0.65
15 1 0.06
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (15 bp):
AAGAAGGAAGAAGAA
Found at i:29354501 original size:16 final size:18
Alignment explanation
Indices: 29354469--29354501 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29354459 ATTAAGAGAA
29354469 TGAATTTAGTGTTAATTG
1 TGAATTTAGTGTTAATTG
29354487 TGAATTT-GT-TTAATT
1 TGAATTTAGTGTTAATT
29354502 TTATGTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (18 bp):
TGAATTTAGTGTTAATTG
Done.