Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 47 of 113
Found at i:12659100 original size:20 final size:21
Alignment explanation
Indices: 12659072--12659111 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
12659062 TTGATCCAAT
12659072 GATTAAATAAATTGT-TATTA
1 GATTAAATAAATTGTATATTA
* *
12659092 GATTTAATAATTTGTATATT
1 GATTAAATAAATTGTATATT
12659112 TATATTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (21 bp):
GATTAAATAAATTGTATATTA
Found at i:12659136 original size:32 final size:32
Alignment explanation
Indices: 12659100--12659173 Score: 105
Period size: 32 Copynumber: 2.3 Consensus size: 32
12659090 TAGATTTAAT
*
12659100 AATTTGTATATTTATATTATATAAAATATAAA
1 AATTTATATATTTATATTATATAAAATATAAA
***
12659132 AATTTATATATTTATATTATATTTTATATAAA
1 AATTTATATATTTATATTATATAAAATATAAA
12659164 AA-TTATATAT
1 AATTTATATAT
12659174 CACAATTAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
31 8 0.21
32 30 0.79
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (32 bp):
AATTTATATATTTATATTATATAAAATATAAA
Found at i:12660561 original size:26 final size:26
Alignment explanation
Indices: 12660532--12660616 Score: 102
Period size: 26 Copynumber: 3.2 Consensus size: 26
12660522 AACTGGATGC
12660532 CACCATATTAAGTAGTAGGATATTAG
1 CACCATATTAAGTAGTAGGATATTAG
*
12660558 CACCAAGTGAGTTTAAATA-TA-GATATTAG
1 CACC-A-T-A--TTAAGTAGTAGGATATTAG
12660587 CACCATATTAAGTAGTAGGATATTAG
1 CACCATATTAAGTAGTAGGATATTAG
12660613 CACC
1 CACC
12660617 GTATCATGCC
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
24 6 0.12
25 2 0.04
26 17 0.34
27 2 0.04
28 2 0.04
29 13 0.26
30 2 0.04
31 6 0.12
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (26 bp):
CACCATATTAAGTAGTAGGATATTAG
Found at i:12673131 original size:12 final size:12
Alignment explanation
Indices: 12673114--12673154 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
12673104 TAAAAATAAT
12673114 AATTTATATTAA
1 AATTTATATTAA
12673126 AATTTATATTAA
1 AATTTATATTAA
* *
12673138 AATAATATATAAA
1 AAT-TTATATTAA
12673151 AATT
1 AATT
12673155 AAAAAACTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AATTTATATTAA
Found at i:12675527 original size:17 final size:18
Alignment explanation
Indices: 12675487--12675527 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
12675477 AAAATAAAAT
12675487 AATTTATTTATTAGTCAA
1 AATTTATTTATTAGTCAA
**
12675505 AA-TTATTT-TTCTTCAA
1 AATTTATTTATTAGTCAA
12675521 AATTTAT
1 AATTTAT
12675528 AAATTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 8 0.40
17 10 0.50
18 2 0.10
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (18 bp):
AATTTATTTATTAGTCAA
Found at i:12676046 original size:28 final size:28
Alignment explanation
Indices: 12676015--12676071 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
12676005 AAGAACCAAA
12676015 TCAAGATTAATAGTATTTAAATTGAGAG
1 TCAAGATTAATAGTATTTAAATTGAGAG
12676043 TCAAGATTAATAGTATTTAAATTGAGAG
1 TCAAGATTAATAGTATTTAAATTGAGAG
12676071 T
1 T
12676072 AACTTATGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.42, C:0.04, G:0.18, T:0.37
Consensus pattern (28 bp):
TCAAGATTAATAGTATTTAAATTGAGAG
Found at i:12677012 original size:20 final size:19
Alignment explanation
Indices: 12676983--12677030 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 19
12676973 GTTTTTATTC
12676983 TTTT-AATTTGGTGATGATT
1 TTTTAAATTT-GTGATGATT
12677002 TTTTAAA-TT-TGATGATT
1 TTTTAAATTTGTGATGATT
12677019 TTTTAAATTTGT
1 TTTTAAATTTGT
12677031 AGCAACTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 15 0.58
18 2 0.08
19 7 0.27
20 2 0.08
ACGTcount: A:0.25, C:0.00, G:0.15, T:0.60
Consensus pattern (19 bp):
TTTTAAATTTGTGATGATT
Found at i:12677014 original size:17 final size:17
Alignment explanation
Indices: 12676994--12677029 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
12676984 TTTAATTTGG
12676994 TGATGATTTTTTAAATT
1 TGATGATTTTTTAAATT
12677011 TGATGATTTTTTAAATT
1 TGATGATTTTTTAAATT
12677028 TG
1 TG
12677030 TAGCAACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (17 bp):
TGATGATTTTTTAAATT
Found at i:12682806 original size:23 final size:25
Alignment explanation
Indices: 12682780--12682834 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 25
12682770 TCAAAACAAG
*
12682780 AATAAT-AAAC-AACCAAAATCATA
1 AATAATAAAACTAACAAAAATCATA
12682803 AATAATGCAAAACTAACAAAAATCATA
1 AATAAT--AAAACTAACAAAAATCATA
12682830 AATAA
1 AATAA
12682835 ACAAGCAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 6 0.22
26 4 0.15
27 17 0.63
ACGTcount: A:0.65, C:0.15, G:0.02, T:0.18
Consensus pattern (25 bp):
AATAATAAAACTAACAAAAATCATA
Found at i:12684176 original size:18 final size:16
Alignment explanation
Indices: 12684155--12684221 Score: 71
Period size: 18 Copynumber: 3.9 Consensus size: 16
12684145 AAATGTTTTT
12684155 AAAAATTAAATAATTTC
1 AAAAATTAAA-AATTTC
*
12684172 AAAAATCTAAAACATTTT
1 AAAAAT-TAAAA-ATTTC
12684190 AAAAATTAAAAAAATTTC
1 AAAAATT--AAAAATTTC
*
12684208 GAAAATTAAAAATT
1 AAAAATTAAAAATT
12684222 AAAAGGTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
16 7 0.16
17 8 0.19
18 24 0.56
19 4 0.09
ACGTcount: A:0.61, C:0.06, G:0.01, T:0.31
Consensus pattern (16 bp):
AAAAATTAAAAATTTC
Found at i:12684195 original size:35 final size:35
Alignment explanation
Indices: 12684151--12684218 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
12684141 TTTAAAATGT
*
12684151 TTTTAAAAATT-AAATAATTTCAAAAATCTAAAACA
1 TTTTAAAAATTAAAAAAATTTCAAAAAT-TAAAACA
*
12684186 TTTTAAAAATTAAAAAAATTTCGAAAATTAAAA
1 TTTTAAAAATTAAAAAAATTTCAAAAATTAAAA
12684219 ATTAAAAGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 16 0.53
36 14 0.47
ACGTcount: A:0.59, C:0.06, G:0.01, T:0.34
Consensus pattern (35 bp):
TTTTAAAAATTAAAAAAATTTCAAAAATTAAAACA
Found at i:12684259 original size:21 final size:20
Alignment explanation
Indices: 12684230--12684276 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
12684220 TTAAAAGGTT
*
12684230 AAAAA-TTTAATAATAATACA
1 AAAAATTTTAAAAAT-ATACA
*
12684250 AAAAATTTTAAAAATATATA
1 AAAAATTTTAAAAATATACA
12684270 AAAAATT
1 AAAAATT
12684277 AAAATTGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAATTTTAAAAATATACA
Found at i:12684325 original size:19 final size:19
Alignment explanation
Indices: 12684301--12684375 Score: 114
Period size: 19 Copynumber: 3.9 Consensus size: 19
12684291 CAAAAAAATG
*
12684301 AAAAAAATTTTGAATTTTA
1 AAAAAAATTTTAAATTTTA
12684320 AAAAAAATTTTAAATTTTA
1 AAAAAAATTTTAAATTTTA
12684339 AAAAAAATTTTAAATTTTA
1 AAAAAAATTTTAAATTTTA
* * *
12684358 TAAAAATTTTTATATTTT
1 AAAAAAATTTTAAATTTT
12684376 TTAATTTAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (19 bp):
AAAAAAATTTTAAATTTTA
Found at i:12684445 original size:18 final size:17
Alignment explanation
Indices: 12684417--12684499 Score: 78
Period size: 17 Copynumber: 4.8 Consensus size: 17
12684407 TTTTTTTGAA
* *
12684417 TTTTTAGAAATTTTTAT
1 TTTTTAAAAATTTTCAT
* *
12684434 TTTTGTTAAAATTTGCAT
1 TTTT-TAAAAATTTTCAT
*
12684452 TTTTTGAAAATTTTCAT
1 TTTTTAAAAATTTTCAT
*
12684469 TTTTTAAAAA-TTTCAGA
1 TTTTTAAAAATTTTCA-T
*
12684486 TTTTAAAAAATTTT
1 TTTTTAAAAATTTT
12684500 TTAAGTTTCC
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
16 5 0.09
17 33 0.61
18 16 0.30
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.57
Consensus pattern (17 bp):
TTTTTAAAAATTTTCAT
Found at i:12684477 original size:16 final size:16
Alignment explanation
Indices: 12684417--12684493 Score: 73
Period size: 16 Copynumber: 4.6 Consensus size: 16
12684407 TTTTTTTGAA
*
12684417 TTTTTAGAAATTTTTATT
1 TTTTTA-AAATTTTCA-T
*
12684435 TTTGTTAAAATTTGCAT
1 TTT-TTAAAATTTTCAT
12684452 TTTTTGAAAATTTTCAT
1 TTTTT-AAAATTTTCAT
* *
12684469 TTTTTAAAAATTTCAG
1 TTTTTAAAATTTTCAT
*
12684485 ATTTTAAAA
1 TTTTTAAAA
12684494 AATTTTTTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
16 19 0.37
17 19 0.37
18 10 0.20
19 3 0.06
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (16 bp):
TTTTTAAAATTTTCAT
Found at i:12684479 original size:34 final size:34
Alignment explanation
Indices: 12684411--12684499 Score: 90
Period size: 34 Copynumber: 2.6 Consensus size: 34
12684401 GTGAACTTTT
* *
12684411 TTTGAATTTTTAGAAATTTTTATTTTTGTTAAAA
1 TTTGAATTTTTAGAAATTTTCATTTTTGTAAAAA
* *
12684445 TTTGCATTTTTTGAAAATTTTCATTTTT-TAAAAA
1 TTTGAATTTTTAG-AAATTTTCATTTTTGTAAAAA
* * *
12684479 TTTCAGATTTTAAAAAATTTT
1 TTTGA-ATTTTTAGAAATTTT
12684500 TTAAGTTTCC
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
34 26 0.59
35 18 0.41
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.56
Consensus pattern (34 bp):
TTTGAATTTTTAGAAATTTTCATTTTTGTAAAAA
Found at i:12684536 original size:19 final size:19
Alignment explanation
Indices: 12684512--12684581 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
12684502 AAGTTTCCTT
*
12684512 TTTTAAAATTTTTAGAATG
1 TTTTAAAATTTTTAGAATC
* * *
12684531 TTTTAAACTTTTTAGAGTT
1 TTTTAAAATTTTTAGAATC
*
12684550 TTTTAAAATTTTTAGAAAC
1 TTTTAAAATTTTTAGAATC
*
12684569 TTTTATAATTTTT
1 TTTTAAAATTTTT
12684582 TAAAAAGTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (19 bp):
TTTTAAAATTTTTAGAATC
Found at i:12684573 original size:38 final size:39
Alignment explanation
Indices: 12684510--12684583 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 39
12684500 TTAAGTTTCC
**
12684510 TTTTTTAAAATTTTTAGAATGTTTTA-AACTTTTTAGAG
1 TTTTTTAAAATTTTTAGAAACTTTTATAACTTTTTAGAG
*
12684548 TTTTTTAAAATTTTTAGAAACTTTTATAATTTTTTA
1 TTTTTTAAAATTTTTAGAAACTTTTATAACTTTTTA
12684584 AAAAGTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 24 0.75
39 8 0.25
ACGTcount: A:0.32, C:0.03, G:0.07, T:0.58
Consensus pattern (39 bp):
TTTTTTAAAATTTTTAGAAACTTTTATAACTTTTTAGAG
Found at i:12684582 original size:10 final size:9
Alignment explanation
Indices: 12684510--12684645 Score: 65
Period size: 10 Copynumber: 14.0 Consensus size: 9
12684500 TTAAGTTTCC
12684510 TTTTTTAAA
1 TTTTTTAAA
*
12684519 ATTTTTAGAA
1 TTTTTTA-AA
*
12684529 TGTTTTAAA
1 TTTTTTAAA
* *
12684538 CTTTTTAGAG
1 TTTTTTA-AA
12684548 TTTTTTAAA
1 TTTTTTAAA
*
12684557 ATTTTTAGAA
1 TTTTTTA-AA
**
12684567 ACTTTTATAA
1 TTTTTTA-AA
12684577 TTTTTTAAAAA
1 TTTTTT--AAA
*
12684588 GTTTTTTGAA
1 -TTTTTTAAA
* *
12684598 TTTTCTAAT
1 TTTTTTAAA
*
12684607 TTTTTTGAA
1 TTTTTTAAA
*
12684616 TTTTTAAGAA
1 TTTTTTA-AA
*
12684626 TTTTCTAAAA
1 TTTT-TTAAA
12684636 CTTTTTTAAA
1 -TTTTTTAAA
12684646 AGTTTCACAA
Statistics
Matches: 95, Mismatches: 23, Indels: 17
0.70 0.17 0.13
Matches are distributed among these distances:
9 37 0.39
10 42 0.44
11 9 0.09
12 7 0.07
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:12684601 original size:29 final size:29
Alignment explanation
Indices: 12684535--12684621 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
12684525 AGAATGTTTT
12684535 AAACTTTT-TAGAGTTTTTTAAAATTTTTAG
1 AAACTTTTATA-A-TTTTTTAAAATTTTTAG
*
12684565 AAACTTTTATAATTTTTTAAAAAGTTTTTTG
1 AAACTTTTATAATTTTTT-AAAA-TTTTTAG
* **
12684596 -AA-TTTTCTAATTTTTTTGAATTTTTA
1 AAACTTTTATAATTTTTTAAAATTTTTA
12684622 AGAATTTTCT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
27 5 0.10
28 2 0.04
29 19 0.39
30 15 0.31
31 8 0.16
ACGTcount: A:0.32, C:0.03, G:0.07, T:0.57
Consensus pattern (29 bp):
AAACTTTTATAATTTTTTAAAATTTTTAG
Found at i:12684629 original size:19 final size:18
Alignment explanation
Indices: 12684510--12684634 Score: 81
Period size: 19 Copynumber: 6.5 Consensus size: 18
12684500 TTAAGTTTCC
12684510 TTTTTTAAAATTTTTAGAA
1 TTTTTT-AAATTTTTAGAA
* *
12684529 TGTTTTAAACTTTTTAGAG
1 TTTTTTAAA-TTTTTAGAA
12684548 TTTTTTAAAATTTTTAGAAA
1 TTTTTT-AAATTTTTAG-AA
* * *
12684568 CTTTTATAATTTTTTAAAAA
1 -TTTTTTAAATTTTT-AGAA
* *
12684588 GTTTTTTGAATTTTCTA-AT
1 -TTTTTTAAATTTT-TAGAA
*
12684607 TTTTTTGAATTTTTAAGAA
1 TTTTTTAAATTTTT-AGAA
*
12684626 TTTTCTAAA
1 TTTTTTAAA
12684635 ACTTTTTTAA
Statistics
Matches: 83, Mismatches: 15, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
17 1 0.01
18 17 0.20
19 34 0.41
20 24 0.29
21 7 0.08
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (18 bp):
TTTTTTAAATTTTTAGAA
Found at i:12684645 original size:11 final size:10
Alignment explanation
Indices: 12684510--12684646 Score: 65
Period size: 9 Copynumber: 14.0 Consensus size: 10
12684500 TTAAGTTTCC
12684510 TTTTTTAAAA
1 TTTTTTAAAA
*
12684520 -TTTTTAGAA
1 TTTTTTAAAA
*
12684529 TGTTTT-AAA
1 TTTTTTAAAA
* * *
12684538 CTTTTTAGAG
1 TTTTTTAAAA
12684548 TTTTTTAAAA
1 TTTTTTAAAA
12684558 -TTTTTAGAAA
1 TTTTTTA-AAA
* *
12684568 -CTTTTATAA
1 TTTTTTAAAA
12684577 TTTTTTAAAAA
1 TTTTTT-AAAA
*
12684588 GTTTTTT-GAA
1 -TTTTTTAAAA
*
12684598 TTTTCT--AA
1 TTTTTTAAAA
**
12684606 TTTTTTTGAA
1 TTTTTTAAAA
12684616 -TTTTTAAGAA
1 TTTTTTAA-AA
*
12684626 TTTTCTAAAA
1 TTTTTTAAAA
12684636 CTTTTTTAAAA
1 -TTTTTTAAAA
12684647 GTTTCACAAC
Statistics
Matches: 95, Mismatches: 21, Indels: 21
0.69 0.15 0.15
Matches are distributed among these distances:
8 7 0.07
9 32 0.34
10 32 0.34
11 18 0.19
12 6 0.06
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.56
Consensus pattern (10 bp):
TTTTTTAAAA
Found at i:12684736 original size:28 final size:28
Alignment explanation
Indices: 12684672--12684736 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
12684662 AAAATTAGAA
*
12684672 TTTTAAAAAAATTTAAAGTCTTTATAAT
1 TTTTAAAAAAATTTAAACTCTTTATAAT
12684700 TTTTAAAAAAATTTTAAACT-TGTTGA-AAT
1 TTTTAAAAAAA-TTTAAACTCT-TT-ATAAT
12684729 TTTTAAAA
1 TTTTAAAA
12684737 GTTTTTGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
28 12 0.36
29 20 0.61
30 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (28 bp):
TTTTAAAAAAATTTAAACTCTTTATAAT
Found at i:12684749 original size:17 final size:16
Alignment explanation
Indices: 12684726--12684776 Score: 75
Period size: 18 Copynumber: 3.0 Consensus size: 16
12684716 AACTTGTTGA
12684726 AATTTTTAAAAGTTTTT
1 AATTTTTAAAA-TTTTT
12684743 GAATTTTTCAAAATTTTT
1 -AATTTTT-AAAATTTTT
12684761 AATTTTTAAAATTTTT
1 AATTTTTAAAATTTTT
12684777 TTAACATTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.28
17 7 0.22
18 12 0.38
19 4 0.12
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (16 bp):
AATTTTTAAAATTTTT
Found at i:12684780 original size:18 final size:17
Alignment explanation
Indices: 12684726--12684777 Score: 70
Period size: 17 Copynumber: 3.0 Consensus size: 17
12684716 AACTTGTTGA
*
12684726 AATTTTTAAAAGTTTTTG
1 AATTTTTAAAA-TTTTTT
12684744 AATTTTTCAAAA-TTTTT
1 AATTTTT-AAAATTTTTT
12684761 AATTTTTAAAATTTTTT
1 AATTTTTAAAATTTTTT
12684778 TAACATTGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
16 4 0.13
17 16 0.52
18 7 0.23
19 4 0.13
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (17 bp):
AATTTTTAAAATTTTTT
Found at i:12684825 original size:19 final size:19
Alignment explanation
Indices: 12684803--12684842 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12684793 ATTGATGATG
*
12684803 TGACACTTATTAGATTTTT
1 TGACACATATTAGATTTTT
* *
12684822 TGACACATGTTAGTTTTTT
1 TGACACATATTAGATTTTT
12684841 TG
1 TG
12684843 GATATGTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.53
Consensus pattern (19 bp):
TGACACATATTAGATTTTT
Found at i:12691720 original size:3 final size:3
Alignment explanation
Indices: 12691712--12691755 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
12691702 TAAACAAAAG
12691712 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
12691756 GAAAAATGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:12703624 original size:2 final size:2
Alignment explanation
Indices: 12703617--12703642 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12703607 CTTCTATCTA
12703617 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
12703643 GCTTTCTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12713210 original size:21 final size:21
Alignment explanation
Indices: 12713181--12713238 Score: 107
Period size: 21 Copynumber: 2.7 Consensus size: 21
12713171 TTTTTAAAGT
12713181 ATAATGTAAAAAATAAAAAAAA
1 ATAA-GTAAAAAATAAAAAAAA
12713203 ATAAGTAAAAAATAAAAAAAA
1 ATAAGTAAAAAATAAAAAAAA
12713224 ATAAGTAAAAAATAA
1 ATAAGTAAAAAATAA
12713239 GATTAATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 32 0.89
22 4 0.11
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (21 bp):
ATAAGTAAAAAATAAAAAAAA
Found at i:12713212 original size:11 final size:11
Alignment explanation
Indices: 12713181--12713239 Score: 77
Period size: 11 Copynumber: 5.5 Consensus size: 11
12713171 TTTTTAAAGT
12713181 ATAATGTAAAAA
1 ATAA-GTAAAAA
*
12713193 ATAA-AAAAAA
1 ATAAGTAAAAA
12713203 ATAAGTAAAAA
1 ATAAGTAAAAA
*
12713214 ATAA-AAAAAA
1 ATAAGTAAAAA
12713224 ATAAGTAAAAA
1 ATAAGTAAAAA
12713235 ATAAG
1 ATAAG
12713240 ATTAATTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
10 18 0.44
11 19 0.46
12 4 0.10
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (11 bp):
ATAAGTAAAAA
Found at i:12713565 original size:24 final size:24
Alignment explanation
Indices: 12713525--12713585 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
12713515 TATAAGGAGG
12713525 CATTAAAATTTT-T-TTGTGAATTT
1 CATTAAAATTTTATATTGT-AATTT
**
12713548 -ATTTTAATTTTATATTGTAATTT
1 CATTAAAATTTTATATTGTAATTT
12713571 CATTAAAATTTTATA
1 CATTAAAATTTTATA
12713586 ATTATGACTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
22 9 0.29
23 6 0.19
24 16 0.52
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.57
Consensus pattern (24 bp):
CATTAAAATTTTATATTGTAATTT
Found at i:12713683 original size:24 final size:22
Alignment explanation
Indices: 12713655--12713702 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
12713645 ATGAAAGAGC
*
12713655 TTAATTATATATAAAAAAAATTAA
1 TTAATTAAAT-TAAAAAAAA-TAA
*
12713679 TTAATTAAATTAAAACAAATAA
1 TTAATTAAATTAAAAAAAATAA
12713701 TT
1 TT
12713703 TTAATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 5 0.23
23 8 0.36
24 9 0.41
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
TTAATTAAATTAAAAAAAATAA
Found at i:12715146 original size:30 final size:29
Alignment explanation
Indices: 12715110--12715191 Score: 74
Period size: 30 Copynumber: 2.7 Consensus size: 29
12715100 TCCTAAATTT
12715110 TTTATTTTAAATCAATTGAGCCATTAAACA
1 TTTATTTT-AATCAATTGAGCCATTAAACA
* ** * *
12715140 TTTATTTTTATCTAATTGAATCTTTATACA
1 TTTATTTTAATC-AATTGAGCCATTAAACA
* *
12715170 TTTATTTTCATTCAATTAAGCC
1 TTTATTTT-AATCAATTGAGCC
12715192 TTCCATTGGA
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
29 3 0.08
30 35 0.88
31 2 0.05
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.49
Consensus pattern (29 bp):
TTTATTTTAATCAATTGAGCCATTAAACA
Found at i:12715416 original size:2 final size:2
Alignment explanation
Indices: 12715406--12715450 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
12715396 TTCATGTGTG
* * * *
12715406 TA TA CA TA TA TA TA TA TA TA TA CA CA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12715448 TA T
1 TA T
12715451 GTAAAGGATC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (2 bp):
TA
Found at i:12716657 original size:15 final size:15
Alignment explanation
Indices: 12716637--12716666 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12716627 ATTGAAAATT
*
12716637 GTTTAAAGTTATCAA
1 GTTTAAAGTGATCAA
12716652 GTTTAAAGTGATCAA
1 GTTTAAAGTGATCAA
12716667 CTTACACAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.37
Consensus pattern (15 bp):
GTTTAAAGTGATCAA
Found at i:12720437 original size:2 final size:2
Alignment explanation
Indices: 12720430--12720460 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12720420 CAAAGATGCA
12720430 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12720461 CACAACATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12722763 original size:7 final size:7
Alignment explanation
Indices: 12722750--12722783 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
12722740 TGCAAAAGGG
12722750 GAAAAAA
1 GAAAAAA
*
12722757 AAAAAAA
1 GAAAAAA
*
12722764 GAAAAAG
1 GAAAAAA
12722771 GAAAAAA
1 GAAAAAA
12722778 GAAAAA
1 GAAAAA
12722784 CTACTAGTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:12725080 original size:34 final size:35
Alignment explanation
Indices: 12725025--12725097 Score: 89
Period size: 34 Copynumber: 2.1 Consensus size: 35
12725015 GCAAAGAGGT
* *
12725025 TTGATTTTTTAAATTTTAATTTTTATTAT-TTTTAG
1 TTGATTTTTTAAATTTTAA-TTTAATTATATTTAAG
12725060 TTGA-TTTTT-AATTTTAAATTTAATTATATTTAAG
1 TTGATTTTTTAAATTTT-AATTTAATTATATTTAAG
12725094 TTGA
1 TTGA
12725098 GGATTTCACT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
33 14 0.41
34 16 0.47
35 4 0.12
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (35 bp):
TTGATTTTTTAAATTTTAATTTAATTATATTTAAG
Found at i:12725086 original size:33 final size:36
Alignment explanation
Indices: 12725025--12725097 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 36
12725015 GCAAAGAGGT
* * *
12725025 TTGATTTTTTAAATTTTAATTTTTATTAT-TTTTAG
1 TTGATTTTTTAAATTTTAAATTTAATTATATTTAAG
12725060 TTGA-TTTTT-AATTTTAAATTTAATTATATTTAAG
1 TTGATTTTTTAAATTTTAAATTTAATTATATTTAAG
12725094 TTGA
1 TTGA
12725098 GGATTTCACT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 16 0.47
34 14 0.41
35 4 0.12
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (36 bp):
TTGATTTTTTAAATTTTAAATTTAATTATATTTAAG
Found at i:12725819 original size:19 final size:19
Alignment explanation
Indices: 12725782--12725833 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
12725772 ATTTATATCA
*
12725782 AAATAATATTA-TATAATAC
1 AAATAATATAATTAT-ATAC
* *
12725801 GATTAATATAATTATATAC
1 AAATAATATAATTATATAC
12725820 AAATAATATAATTA
1 AAATAATATAATTA
12725834 GACATAATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 24 0.89
20 3 0.11
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (19 bp):
AAATAATATAATTATATAC
Found at i:12725845 original size:19 final size:19
Alignment explanation
Indices: 12725802--12725845 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
12725792 ATATAATACG
* *
12725802 ATTAATATAATTATATACA
1 ATTAATATAATTAGACACA
* *
12725821 AATAATATAATTAGACATA
1 ATTAATATAATTAGACACA
12725840 ATTAAT
1 ATTAAT
12725846 TACTCAAATA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (19 bp):
ATTAATATAATTAGACACA
Found at i:12725906 original size:19 final size:19
Alignment explanation
Indices: 12725882--12725919 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12725872 TATATTTAAC
*
12725882 ATAATTATATACGAATAAT
1 ATAATTAGATACGAATAAT
*
12725901 ATAATTAGATACGATTAAT
1 ATAATTAGATACGAATAAT
12725920 TTATTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (19 bp):
ATAATTAGATACGAATAAT
Found at i:12725977 original size:28 final size:29
Alignment explanation
Indices: 12725925--12725987 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
12725915 TTAATTTATT
12725925 TATTTAAACAAAAAATAATTTAAATT-AA
1 TATTTAAACAAAAAATAATTTAAATTAAA
*
12725953 TATTTAAA-TAAAAAT-ATTTAAAAATTAAA
1 TATTTAAACAAAAAATAATTT--AAATTAAA
12725982 TATTTA
1 TATTTA
12725988 TAATCTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
26 4 0.13
27 6 0.19
28 13 0.42
29 8 0.26
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (29 bp):
TATTTAAACAAAAAATAATTTAAATTAAA
Found at i:12725984 original size:15 final size:15
Alignment explanation
Indices: 12725946--12725987 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
12725936 AAAATAATTT
12725946 AAATT-AATATTTAA
1 AAATTAAATATTTAA
12725960 ATAA--AAATATTTAA
1 A-AATTAAATATTTAA
12725974 AAATTAAATATTTA
1 AAATTAAATATTTA
12725988 TAATCTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 2 0.08
14 11 0.46
15 11 0.46
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATTAAATATTTAA
Found at i:12726047 original size:25 final size:25
Alignment explanation
Indices: 12726016--12726073 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 25
12726006 AAATAATATG
12726016 ATAAATATAATTATT-AATTTATTT-TT
1 ATAAATA-AATT-TTAAATTT-TTTATT
12726042 -TAAATAAATTTTAAATTTTTTATT
1 ATAAATAAATTTTAAATTTTTTATT
12726066 ATAAATAA
1 ATAAATAA
12726074 TATCGTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
23 5 0.17
24 11 0.38
25 13 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
ATAAATAAATTTTAAATTTTTTATT
Found at i:12726152 original size:31 final size:33
Alignment explanation
Indices: 12726093--12726156 Score: 89
Period size: 31 Copynumber: 2.0 Consensus size: 33
12726083 TTAAATATAT
12726093 TATTATTATTTTATATGAATATGATACAAATAA
1 TATTATTATTTTATATGAATATGATACAAATAA
*
12726126 TATTA-TATTTTA-AT-TATATCGATACAAATAA
1 TATTATTATTTTATATGAATAT-GATACAAATAA
12726157 AATATAAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 4 0.14
31 13 0.45
32 7 0.24
33 5 0.17
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (33 bp):
TATTATTATTTTATATGAATATGATACAAATAA
Found at i:12726205 original size:14 final size:15
Alignment explanation
Indices: 12726181--12726210 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
12726171 TTATATTAAA
12726181 TTTATATATAATTTT
1 TTTATATATAATTTT
12726196 TTTA-ATATAATTTT
1 TTTATATATAATTTT
12726210 T
1 T
12726211 ATATTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTATATATAATTTT
Found at i:12726218 original size:14 final size:13
Alignment explanation
Indices: 12726181--12726214 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
12726171 TTATATTAAA
12726181 TTTATATATAATT
1 TTTATATATAATT
*
12726194 TTTTTAATATAATT
1 TTTAT-ATATAATT
12726208 TTTATAT
1 TTTATAT
12726215 TATATTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTATATATAATT
Found at i:12727394 original size:21 final size:21
Alignment explanation
Indices: 12727368--12727409 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
12727358 GGGTAATGTC
12727368 TCTGTTGTAGCTAAGTAGGAT
1 TCTGTTGTAGCTAAGTAGGAT
12727389 TCTGTTGTAGCTAAGTAGGAT
1 TCTGTTGTAGCTAAGTAGGAT
12727410 ATCTTATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.29, T:0.38
Consensus pattern (21 bp):
TCTGTTGTAGCTAAGTAGGAT
Found at i:12730907 original size:2 final size:2
Alignment explanation
Indices: 12730902--12730935 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12730892 TTTTTAAGTA
12730902 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12730936 TACAAAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12735309 original size:29 final size:29
Alignment explanation
Indices: 12735244--12735309 Score: 71
Period size: 33 Copynumber: 2.1 Consensus size: 29
12735234 TCCCAGTGCT
*
12735244 TTCTTGATTGAACATAAAAAAGTGGCGAATTAT
1 TTCTTGATTGAACATAAAAAAGTGGC--A--AG
12735277 TTCTTGATTGAACATAAAAAAGTGAGC-AG
1 TTCTTGATTGAACATAAAAAAGTG-GCAAG
12735306 TTCT
1 TTCT
12735310 AAATTCTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
29 5 0.16
33 24 0.77
34 2 0.06
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (29 bp):
TTCTTGATTGAACATAAAAAAGTGGCAAG
Found at i:12738393 original size:20 final size:22
Alignment explanation
Indices: 12738368--12738428 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
12738358 ATATATTTAA
12738368 AATA-TTTATA-TTTAAAAAAT
1 AATACTTTATATTTTAAAAAAT
*
12738388 AATATTTTATATTTTAAAAAAT
1 AATACTTTATATTTTAAAAAAT
12738410 AATACTTTATTAATTTTAA
1 AATACTTTA-T-ATTTTAA
12738429 GTCGAATCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 4 0.11
21 6 0.17
22 18 0.50
23 1 0.03
24 7 0.19
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
AATACTTTATATTTTAAAAAAT
Found at i:12739993 original size:12 final size:12
Alignment explanation
Indices: 12739950--12739993 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
12739940 AATATAATAC
12739950 TAAATTTTAATT
1 TAAATTTTAATT
*
12739962 TTAA-TTTAATT
1 TAAATTTTAATT
*
12739973 TAAAATTTAATT
1 TAAATTTTAATT
*
12739985 CAAATTTTA
1 TAAATTTTA
12739994 TCGAATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (12 bp):
TAAATTTTAATT
Found at i:12740250 original size:38 final size:33
Alignment explanation
Indices: 12740207--12740290 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 33
12740197 AAATACTTTG
*
12740207 AATTTAATTTGATTAATAAGTTAAATTATTTAAATTTA
1 AATTTAATTTGAATAATAA-TTAAA-TA---AAATTTA
*
12740245 AATTTAA-TTAAATAATAATTAAATAAAATTTA
1 AATTTAATTTGAATAATAATTAAATAAAATTTA
*
12740277 AATTTTATTTGAAT
1 AATTTAATTTGAAT
12740291 TGAATTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
32 13 0.32
33 5 0.12
35 2 0.05
36 5 0.12
37 9 0.22
38 7 0.17
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.48
Consensus pattern (33 bp):
AATTTAATTTGAATAATAATTAAATAAAATTTA
Found at i:12740257 original size:16 final size:16
Alignment explanation
Indices: 12740227--12740281 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
12740217 GATTAATAAG
*
12740227 TTAAA-TTATTTAAAT
1 TTAAATTTAATTAAAT
12740242 TTAAATTTAATTAAA-
1 TTAAATTTAATTAAAT
* * *
12740257 TAATAATTAAATAAAAT
1 TTA-AATTTAATTAAAT
12740274 TTAAATTT
1 TTAAATTT
12740282 TATTTGAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
15 7 0.23
16 22 0.71
17 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAATTTAATTAAAT
Found at i:12740907 original size:8 final size:8
Alignment explanation
Indices: 12740894--12740938 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
12740884 ATTTTTATTA
12740894 TATATAAT
1 TATATAAT
12740902 TATATAAT
1 TATATAAT
*
12740910 TATACAAT
1 TATATAAT
12740918 TATATTAAT
1 TATA-TAAT
*
12740927 TTTATAA-
1 TATATAAT
12740934 TATAT
1 TATAT
12740939 TAAACTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
7 4 0.12
8 22 0.69
9 6 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (8 bp):
TATATAAT
Found at i:12746371 original size:72 final size:72
Alignment explanation
Indices: 12746279--12746424 Score: 292
Period size: 72 Copynumber: 2.0 Consensus size: 72
12746269 ATAGTGGAAA
12746279 GGGAATAAACTATTCTATTGAAATGGGAATGAATACTACTAAACGTTTTTGTTTGTGGAAACAAT
1 GGGAATAAACTATTCTATTGAAATGGGAATGAATACTACTAAACGTTTTTGTTTGTGGAAACAAT
12746344 TTGCGTT
66 TTGCGTT
12746351 GGGAATAAACTATTCTATTGAAATGGGAATGAATACTACTAAACGTTTTTGTTTGTGGAAACAAT
1 GGGAATAAACTATTCTATTGAAATGGGAATGAATACTACTAAACGTTTTTGTTTGTGGAAACAAT
12746416 TTGCGTT
66 TTGCGTT
12746423 GG
1 GG
12746425 AAACAGGTAT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.36
Consensus pattern (72 bp):
GGGAATAAACTATTCTATTGAAATGGGAATGAATACTACTAAACGTTTTTGTTTGTGGAAACAAT
TTGCGTT
Found at i:12752444 original size:13 final size:13
Alignment explanation
Indices: 12752426--12752459 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
12752416 AATTTTATGA
12752426 ATTTTAAAAATTT
1 ATTTTAAAAATTT
12752439 ATTTTAAAAATTT
1 ATTTTAAAAATTT
*
12752452 AATTTAAA
1 ATTTTAAA
12752460 TTTAAATCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTTTAAAAATTT
Found at i:12752494 original size:15 final size:15
Alignment explanation
Indices: 12752453--12752496 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
12752443 TAAAAATTTA
12752453 ATTTAAATTTAAATCG
1 ATTTAAA-TTAAATCG
**
12752469 ATTTATTTTAAATCG
1 ATTTAAATTAAATCG
12752484 ATTTAAATTAAAT
1 ATTTAAATTAAAT
12752497 TTTATTTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (15 bp):
ATTTAAATTAAATCG
Found at i:12752596 original size:18 final size:17
Alignment explanation
Indices: 12752548--12752607 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
12752538 TATTATTTTG
*
12752548 GTATAAATTTTTTATAT
1 GTATAAATTATTTATAT
* *
12752565 GTTTAAATAAATTTATAT
1 GTATAAAT-TATTTATAT
12752583 GTATAATATTATTTTATAT
1 GTATAA-ATTA-TTTATAT
12752602 -TATAAA
1 GTATAAA
12752608 ATTTTAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 8 0.23
18 18 0.51
19 9 0.26
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (17 bp):
GTATAAATTATTTATAT
Found at i:12753295 original size:15 final size:16
Alignment explanation
Indices: 12753275--12753304 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12753265 GAAGACTTAG
12753275 TTTGTTGT-TATTATT
1 TTTGTTGTATATTATT
12753290 TTTGTTGTATATTAT
1 TTTGTTGTATATTAT
12753305 AAAATTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.17, C:0.00, G:0.13, T:0.70
Consensus pattern (16 bp):
TTTGTTGTATATTATT
Found at i:12754035 original size:22 final size:25
Alignment explanation
Indices: 12754015--12754069 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 25
12754005 GTTGATTATT
12754015 TAATAATT-ATAATTTAATTATGATA
1 TAATAATTAATAATTTAATTAT-ATA
*
12754040 TAATAATTAATTATTTAATTGATTATA
1 TAATAATTAATAATTTAATT-A-TATA
12754067 TAA
1 TAA
12754070 ATATATTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 8 0.31
26 10 0.38
27 7 0.27
28 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (25 bp):
TAATAATTAATAATTTAATTATATA
Found at i:12754066 original size:25 final size:25
Alignment explanation
Indices: 12754006--12754096 Score: 73
Period size: 25 Copynumber: 3.6 Consensus size: 25
12753996 AAATAGTTAG
*
12754006 TTGATTATTTAATAATT-ATAATTTAA
1 TTGATTA--TAATAATTAATTATTTAA
12754032 TT-ATGATATAATAATTAATTATTTAA
1 TTGAT--TATAATAATTAATTATTTAA
*
12754058 TTGATTAT-ATAAATATATTATTTAA
1 TTGATTATAATAATTA-ATTATTTAA
* *
12754083 -TGATAATTATAATT
1 TTGATTATAATAATT
12754097 TTAAAAAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
24 12 0.22
25 27 0.49
26 12 0.22
27 4 0.07
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (25 bp):
TTGATTATAATAATTAATTATTTAA
Found at i:12765951 original size:24 final size:26
Alignment explanation
Indices: 12765897--12765953 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 26
12765887 AAAATTTTTA
*
12765897 AAAACCTAACAAATTGTCTAGAAAAC
1 AAAACCTAACAAATTGCCTAGAAAAC
* **
12765923 TAAACCTAA-AAATT-CCTAGAATGC
1 AAAACCTAACAAATTGCCTAGAAAAC
12765947 AAAACCT
1 AAAACCT
12765954 TACAGAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 13 0.50
25 5 0.19
26 8 0.31
ACGTcount: A:0.51, C:0.21, G:0.07, T:0.21
Consensus pattern (26 bp):
AAAACCTAACAAATTGCCTAGAAAAC
Found at i:12766321 original size:51 final size:51
Alignment explanation
Indices: 12766188--12766453 Score: 322
Period size: 51 Copynumber: 5.2 Consensus size: 51
12766178 TATTTGATTT
* * *
12766188 TCATTTTAATGAGAATTGATTATAAAATTAAATCCCAAAAATCTCTCC-ACA
1 TCATTTTAATGCGAATTGATTCTAGAATTAAATCCCAAAAATCTC-CCAACA
* ***
12766239 TCATTCTTAATGCCAATTGATTCTAGAATTAAATTTGAAAAATCTCCCAACA
1 TCATT-TTAATGCGAATTGATTCTAGAATTAAATCCCAAAAATCTCCCAACA
*
12766291 TCATTTTAATGTGAATTGATTCTAGAATTAAATCCCAAAAATCTCTCC--CTA
1 TCATTTTAATGCGAATTGATTCTAGAATTAAATCCCAAAAATCTC-CCAAC-A
* **
12766342 TCATTTTTAATGCCAATTGATTCTAGAATTAAATCTGAAAAATCTCCCAACA
1 TCA-TTTTAATGCGAATTGATTCTAGAATTAAATCCCAAAAATCTCCCAACA
* * * **
12766394 TCATTTTAATGTGAATTGATTCTGGAATTAAATCCAAAAAATCTCTTAACA
1 TCATTTTAATGCGAATTGATTCTAGAATTAAATCCCAAAAATCTCCCAACA
12766445 TCATTTTAA
1 TCATTTTAA
12766454 CTAGATTTCA
Statistics
Matches: 185, Mismatches: 23, Indels: 14
0.83 0.10 0.06
Matches are distributed among these distances:
50 1 0.01
51 98 0.53
52 85 0.46
53 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.36
Consensus pattern (51 bp):
TCATTTTAATGCGAATTGATTCTAGAATTAAATCCCAAAAATCTCCCAACA
Found at i:12766367 original size:103 final size:103
Alignment explanation
Indices: 12766188--12766453 Score: 428
Period size: 103 Copynumber: 2.6 Consensus size: 103
12766178 TATTTGATTT
* * *
12766188 TCATTTTAATGAGAATTGATTATAAAATTAAATCCCAAAAATCTCTCCACATCATTCTTAATGCC
1 TCATTTTAATGTGAATTGATTCTAGAATTAAATCCCAAAAATCTCTCCACATCATTCTTAATGCC
*
12766253 AATTGATTCTAGAATTAAATTTGAAAAATCTCCCAACA
66 AATTGATTCTAGAATTAAATCTGAAAAATCTCCCAACA
*
12766291 TCATTTTAATGTGAATTGATTCTAGAATTAAATCCCAAAAATCTCTCC-CTATCATTTTTAATGC
1 TCATTTTAATGTGAATTGATTCTAGAATTAAATCCCAAAAATCTCTCCAC-ATCATTCTTAATGC
12766355 CAATTGATTCTAGAATTAAATCTGAAAAATCTCCCAACA
65 CAATTGATTCTAGAATTAAATCTGAAAAATCTCCCAACA
* * **
12766394 TCATTTTAATGTGAATTGATTCTGGAATTAAATCCAAAAAATCTCTTAACATCATT-TTAA
1 TCATTTTAATGTGAATTGATTCTAGAATTAAATCCCAAAAATCTCTCCACATCATTCTTAA
12766454 CTAGATTTCA
Statistics
Matches: 152, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
102 5 0.03
103 146 0.96
104 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.36
Consensus pattern (103 bp):
TCATTTTAATGTGAATTGATTCTAGAATTAAATCCCAAAAATCTCTCCACATCATTCTTAATGCC
AATTGATTCTAGAATTAAATCTGAAAAATCTCCCAACA
Found at i:12767298 original size:59 final size:55
Alignment explanation
Indices: 12767241--12767428 Score: 182
Period size: 55 Copynumber: 3.4 Consensus size: 55
12767231 TAGGAAAATG
* *
12767241 AAATGATCTAGA-TGAGCTAAGATCAGATGATCGAGACTGAGCCACAAGTTAAAA
1 AAATAATCTAGACTGAGCCAAGATCAGATGATCGAGACTGAGCCACAAGTTAAAA
* * *
12767295 AAATAATCTAGACTGAGCCAAGATCGGATG-GCTGAGACTAAGCCACAAGTTAAAA
1 AAATAATCTAGACTGAGCCAAGATCAGATGATC-GAGACTGAGCCACAAGTTAAAA
* * * * * * * * * * **
12767350 AAATAATTTGGACTAAGCCAAGATCAAATTATCAAGATTGAACCATAAGTCAGGA
1 AAATAATCTAGACTGAGCCAAGATCAGATGATCGAGACTGAGCCACAAGTTAAAA
* *
12767405 AAATAATCTAGATTGAGTCAAGAT
1 AAATAATCTAGACTGAGCCAAGAT
12767429 TGAAAATAAG
Statistics
Matches: 106, Mismatches: 25, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
54 12 0.11
55 93 0.88
56 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.22
Consensus pattern (55 bp):
AAATAATCTAGACTGAGCCAAGATCAGATGATCGAGACTGAGCCACAAGTTAAAA
Found at i:12768169 original size:5 final size:5
Alignment explanation
Indices: 12768159--12768192 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
12768149 TTTTCTCTTT
*
12768159 TTTTG TTTTG TTTTG TTTTG TTTT- TTTTT TTTTG
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG
12768193 CACACCTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (5 bp):
TTTTG
Found at i:12772843 original size:22 final size:20
Alignment explanation
Indices: 12772818--12772866 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
12772808 AATTCATGAA
12772818 TTTATTTGAAAAGATTTTTTAT
1 TTTATTTGAAAA-ATTTTTT-T
**
12772840 TTTATTTTTAAAATTTTTTT
1 TTTATTTGAAAAATTTTTTT
12772860 TTTATTT
1 TTTATTT
12772867 TTTAGATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.32
21 7 0.28
22 10 0.40
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (20 bp):
TTTATTTGAAAAATTTTTTT
Found at i:12772993 original size:15 final size:15
Alignment explanation
Indices: 12772973--12773023 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
12772963 AAATGAAACT
12772973 TAAAATATAAAATAA
1 TAAAATATAAAATAA
12772988 TAAAATATAAATATAAA
1 TAAAATATAAA-AT-AA
*
12773005 TAAAATCAAAAAAT-A
1 TAAAAT-ATAAAATAA
12773020 TAAA
1 TAAA
12773024 TAAAAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 16 0.50
16 2 0.06
17 10 0.31
18 4 0.12
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (15 bp):
TAAAATATAAAATAA
Found at i:12773007 original size:25 final size:25
Alignment explanation
Indices: 12772973--12773034 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 25
12772963 AAATGAAACT
12772973 TAAAATATAAAAT-AATAAAATATAAA
1 TAAAA-ATAAAATCAA-AAAATATAAA
*
12772999 TATAAATAAAATCAAAAAATATAAA
1 TAAAAATAAAATCAAAAAATATAAA
*
12773024 TAAAAAAAAAA
1 TAAAAATAAAA
12773035 ACCTTTGATC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 26 0.81
26 6 0.19
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.23
Consensus pattern (25 bp):
TAAAAATAAAATCAAAAAATATAAA
Found at i:12773034 original size:19 final size:19
Alignment explanation
Indices: 12772974--12773035 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
12772964 AATGAAACTT
*
12772974 AAAATATAAAATAATAAAATA
1 AAAATAT-AAATAA-AAAAAA
* **
12772995 TAAATATAAATAAAATCAA
1 AAAATATAAATAAAAAAAA
12773014 AAAATATAAATAAAAAAAA
1 AAAATATAAATAAAAAAAA
12773033 AAA
1 AAA
12773036 CCTTTGATCG
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 22 0.65
20 6 0.18
21 6 0.18
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAATATAAATAAAAAAAA
Found at i:12773567 original size:52 final size:50
Alignment explanation
Indices: 12773508--12773668 Score: 171
Period size: 51 Copynumber: 3.1 Consensus size: 50
12773498 TATTTGATTT
* * **
12773508 TCATTTTAATGAGAATGGATTCTGAAATTAAATCCCAAAATCCTTTCCCCA
1 TCATTTTAATGAGAATTGATTCTGAAATTAAATCCCAAAAT-CTCTCAACA
** ** *
12773559 TCATTTTTAATGCCAATTGATTCTTG-AATTAAATCTAAAAAATCTCTCAATA
1 TCA-TTTTAATGAGAATTGATTC-TGAAATTAAATC-CCAAAATCTCTCAACA
* *
12773611 TCATTTTAATGTGAATTGATTCTGAAATTAAATCCCAAAAATCTCTTAACA
1 TCATTTTAATGAGAATTGATTCTGAAATTAAATCCC-AAAATCTCTCAACA
12773662 TCATTTT
1 TCATTTT
12773669 GACCATATTT
Statistics
Matches: 90, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
50 2 0.02
51 48 0.53
52 33 0.37
53 7 0.08
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (50 bp):
TCATTTTAATGAGAATTGATTCTGAAATTAAATCCCAAAATCTCTCAACA
Found at i:12773992 original size:51 final size:51
Alignment explanation
Indices: 12773937--12774045 Score: 130
Period size: 51 Copynumber: 2.1 Consensus size: 51
12773927 CACAAAAAAT
**
12773937 ATTTTAATGCCAATTAATTCTTGAATTAAAT-TTAAAAAATCTCTCAACATC
1 ATTTTAATGCCAATTAATTCTAAAATTAAATCTT-AAAAATCTCTCAACATC
** * * * *
12773988 ATTTTAATGTGAATTGATTCTAAAATTAAATCTTAAAACTCTCTTAATATC
1 ATTTTAATGCCAATTAATTCTAAAATTAAATCTTAAAAATCTCTCAACATC
12774039 ATTTTAA
1 ATTTTAA
12774046 CCATATTTCA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 47 0.96
52 2 0.04
ACGTcount: A:0.40, C:0.13, G:0.05, T:0.42
Consensus pattern (51 bp):
ATTTTAATGCCAATTAATTCTAAAATTAAATCTTAAAAATCTCTCAACATC
Found at i:12782900 original size:9 final size:9
Alignment explanation
Indices: 12782886--12782976 Score: 50
Period size: 9 Copynumber: 10.2 Consensus size: 9
12782876 AAATATAATT
12782886 TTTTAAAAA
1 TTTTAAAAA
12782895 TTTTAAAAAA
1 TTTT-AAAAA
12782905 TATATTAAAAA
1 T-T-TTAAAAA
*
12782916 GTTT-AAAA
1 TTTTAAAAA
*
12782924 TTGTTACAAA
1 TT-TTAAAAA
**
12782934 TAATAAAAA
1 TTTTAAAAA
12782943 TTTCT-AAAA
1 TTT-TAAAAA
12782952 -TTT-AAAA
1 TTTTAAAAA
*
12782959 --TTAATAA
1 TTTTAAAAA
12782966 TTTTAAAAA
1 TTTTAAAAA
12782975 TT
1 TT
12782977 AATAATTTTA
Statistics
Matches: 63, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
6 2 0.03
7 8 0.13
8 7 0.11
9 26 0.41
10 12 0.19
11 6 0.10
12 2 0.03
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:12782983 original size:23 final size:24
Alignment explanation
Indices: 12782932--12782983 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
12782922 AATTGTTACA
*
12782932 AATAA-TAAAAATTTCTAAAATTT
1 AATAATTAAAAATTTCTAAAAATT
*
12782955 AA-AATTAATAATTT-TAAAAATT
1 AATAATTAAAAATTTCTAAAAATT
12782977 AATAATT
1 AATAATT
12782984 TTATTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
AATAATTAAAAATTTCTAAAAATT
Found at i:12782997 original size:19 final size:18
Alignment explanation
Indices: 12782953--12782994 Score: 70
Period size: 16 Copynumber: 2.4 Consensus size: 18
12782943 TTTCTAAAAT
12782953 TTAAAATTAATAATTTTA
1 TTAAAATTAATAATTTTA
12782971 --AAAATTAATAATTTTA
1 TTAAAATTAATAATTTTA
12782987 TTAAAATT
1 TTAAAATT
12782995 TAAAAGATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 16 0.73
18 6 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAAAATTAATAATTTTA
Found at i:12790888 original size:17 final size:17
Alignment explanation
Indices: 12790875--12790909 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
12790865 TATAAAAGAG
*
12790875 GAAAAATAAAAAAAAAA
1 GAAAAAGAAAAAAAAAA
12790892 GAAAAAGAAAAAGAAAAA
1 GAAAAAGAAAAA-AAAAA
12790910 CATTTTGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (17 bp):
GAAAAAGAAAAAAAAAA
Found at i:12790891 original size:6 final size:6
Alignment explanation
Indices: 12790875--12790909 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
12790865 TATAAAAGAG
*
12790875 GAAAAA TAAAAA -AAAAA GAAAAA GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
12790910 CATTTTGGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (6 bp):
GAAAAA
Found at i:12800081 original size:13 final size:14
Alignment explanation
Indices: 12800065--12800093 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12800055 TTTAAAAAAT
12800065 AAAATA-ATTTCAA
1 AAAATATATTTCAA
12800078 AAAATATATTTCAA
1 AAAATATATTTCAA
12800092 AA
1 AA
12800094 TAAATGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAATATATTTCAA
Found at i:12800112 original size:76 final size:72
Alignment explanation
Indices: 12800001--12800141 Score: 194
Period size: 76 Copynumber: 1.9 Consensus size: 72
12799991 CTTAAAATAA
*
12800001 AAAAAATTTATTTAAAAAAATTATTTTAAGAAAAAGTTGAAAATATCAAATTTCTTTAAAAAATA
1 AAAAAATATATTTAAAAAAATTATTTTAAGAAAAAGTTGAAAATATC-AATTT-TTT-AAAAATA
12800066 AAATAATTTC
63 AAATAATTTC
* * *
12800076 AAAAAATATATTTCAAAATAAA-TGTTTTAAGGAAAAGTTGAAAGTATCAATTTTTTAAAAATAA
1 AAAAAATATATTT-AAAA-AAATTATTTTAAGAAAAAGTTGAAAATATCAATTTTTTAAAAATAA
12800140 AA
64 AA
12800142 AGTAATAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
73 10 0.17
74 3 0.05
75 17 0.28
76 27 0.45
77 3 0.05
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (72 bp):
AAAAAATATATTTAAAAAAATTATTTTAAGAAAAAGTTGAAAATATCAATTTTTTAAAAATAAAA
TAATTTC
Found at i:12801415 original size:19 final size:19
Alignment explanation
Indices: 12801391--12801430 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
12801381 GATTATTTTT
12801391 ATAATCCTTCTTTTATGGC
1 ATAATCCTTCTTTTATGGC
12801410 ATAATCCTTCTTTTATGGC
1 ATAATCCTTCTTTTATGGC
12801429 AT
1 AT
12801431 GAGTATGCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.47
Consensus pattern (19 bp):
ATAATCCTTCTTTTATGGC
Found at i:12804195 original size:16 final size:17
Alignment explanation
Indices: 12804185--12804229 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
12804175 GAAAAAAATG
12804185 AAAAATGAAAAATG-AA
1 AAAAATGAAAAATGTAA
* *
12804201 AAAAATAAAAAATGTGA
1 AAAAATGAAAAATGTAA
*
12804218 TAAAATGAAAAA
1 AAAAATGAAAAA
12804230 AAAAAAGATG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (17 bp):
AAAAATGAAAAATGTAA
Found at i:12804196 original size:8 final size:8
Alignment explanation
Indices: 12804177--12804230 Score: 51
Period size: 7 Copynumber: 6.8 Consensus size: 8
12804167 AATAAAGTGA
12804177 AAAAAATG
1 AAAAAATG
12804185 -AAAAATG
1 AAAAAATG
12804192 -AAAAATG
1 AAAAAATG
12804199 AAAAAAAT-
1 -AAAAAATG
12804207 AAAAAATGTG
1 AAAAAA--TG
*
12804217 ATAAAATG
1 AAAAAATG
12804225 AAAAAA
1 AAAAAA
12804231 AAAAAGATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 20 0.51
8 7 0.18
9 7 0.18
10 5 0.13
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (8 bp):
AAAAAATG
Found at i:12804229 original size:7 final size:7
Alignment explanation
Indices: 12804178--12804203 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
12804168 ATAAAGTGAA
12804178 AAAAATG
1 AAAAATG
12804185 AAAAATG
1 AAAAATG
12804192 AAAAATG
1 AAAAATG
12804199 AAAAA
1 AAAAA
12804204 AATAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:12804235 original size:25 final size:26
Alignment explanation
Indices: 12804168--12804253 Score: 90
Period size: 25 Copynumber: 3.5 Consensus size: 26
12804158 TAAATCATGA
* *
12804168 ATAAAGTGAAAAAAATGAAAAA--TG
1 ATAAAATGAAAAAAATAAAAAATGTG
12804192 A-AAAATGAAAAAAATAAAAAATGTG
1 ATAAAATGAAAAAAATAAAAAATGTG
* *
12804217 ATAAAATGAAAAAAA-AAAAGATGAG
1 ATAAAATGAAAAAAATAAAAAATGTG
* *
12804242 AGAAAAGGAAAA
1 ATAAAATGAAAA
12804254 CTCAATTGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
23 18 0.34
24 1 0.02
25 21 0.40
26 13 0.25
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (26 bp):
ATAAAATGAAAAAAATAAAAAATGTG
Found at i:12805593 original size:23 final size:23
Alignment explanation
Indices: 12805483--12805593 Score: 77
Period size: 22 Copynumber: 4.8 Consensus size: 23
12805473 GATGAAATCC
*
12805483 TAAAATTTTTGAATGAGAACCTT
1 TAAAATTTTTGAATGTGAACCTT
* * *
12805506 TAAAA-TATT-ATATGTGAATCTC
1 TAAAATTTTTGA-ATGTGAACCTT
** *
12805528 TAAAACTTTTTTGAAT-AAAGATCTT
1 TAAAA--TTTTTGAATGTGA-ACCTT
* *
12805553 TGAAATATTT-AATGTGAACCTT
1 TAAAATTTTTGAATGTGAACCTT
12805575 TAAAATTTTTGAATGTGAA
1 TAAAATTTTTGAATGTGAA
12805594 TTTTTGAATT
Statistics
Matches: 65, Mismatches: 15, Indels: 16
0.68 0.16 0.17
Matches are distributed among these distances:
21 1 0.02
22 31 0.48
23 18 0.28
24 1 0.02
25 13 0.20
26 1 0.02
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (23 bp):
TAAAATTTTTGAATGTGAACCTT
Found at i:12805600 original size:45 final size:45
Alignment explanation
Indices: 12805439--12805601 Score: 127
Period size: 47 Copynumber: 3.6 Consensus size: 45
12805429 ATATGAATCC
* * * * ** * *
12805439 CTAAAGTTTTTAAATCAGAATCTTTGAAATTTTGGATG-AAATC-
1 CTAAAATTTTTGAATGAGAATCTTTGAAATATTATATGTGAACCT
* * *
12805482 CTAAAATTTTTGAATGAGAACCTTTAAAATATTATATGTGAATCT
1 CTAAAATTTTTGAATGAGAATCTTTGAAATATTATATGTGAACCT
*
12805527 CTAAAACTTTTTTGAAT-AAAGATCTTTGAAATATT-TAATGTGAACCT
1 CTAAAA--TTTTTGAATGAGA-ATCTTTGAAATATTAT-ATGTGAACCT
* * *
12805574 TTAAAATTTTTGAATGTGAATTTTTGAA
1 CTAAAATTTTTGAATGAGAATCTTTGAA
12805602 TTTTGGAGGT
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
43 30 0.31
44 4 0.04
45 23 0.24
46 4 0.04
47 35 0.36
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (45 bp):
CTAAAATTTTTGAATGAGAATCTTTGAAATATTATATGTGAACCT
Found at i:12805858 original size:17 final size:17
Alignment explanation
Indices: 12805811--12805865 Score: 67
Period size: 16 Copynumber: 3.2 Consensus size: 17
12805801 TGCAAACCTG
*
12805811 AAATTCTTACGAATCTAA
1 AAATT-TTAAGAATCTAA
* *
12805829 AAAGTTGAA-AATCTAA
1 AAATTTTAAGAATCTAA
12805845 AAATTTTAAGAATCTAA
1 AAATTTTAAGAATCTAA
12805862 AAAT
1 AAAT
12805866 CTTGCAAACC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 14 0.45
17 13 0.42
18 4 0.13
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.31
Consensus pattern (17 bp):
AAATTTTAAGAATCTAA
Found at i:12805920 original size:18 final size:18
Alignment explanation
Indices: 12805897--12806008 Score: 72
Period size: 17 Copynumber: 6.5 Consensus size: 18
12805887 GCGAACATTC
12805897 AATTCTTGCAAATCTTAA
1 AATTCTTGCAAATCTTAA
* *
12805915 AATTCTTGCAAAGCTAAA
1 AATTCTTGCAAATCTTAA
*
12805933 AATT-TTGCGAATC-TAA
1 AATTCTTGCAAATCTTAA
* ** **
12805949 AATTTTTGTGAAT-TTTC
1 AATTCTTGCAAATCTTAA
* **
12805966 AATTCTTACAAAT-TTTC
1 AATTCTTGCAAATCTTAA
* *
12805983 AATTCTTACAAATCTT-C
1 AATTCTTGCAAATCTTAA
12806000 AATTCTTGC
1 AATTCTTGC
12806009 GAATTTGTGT
Statistics
Matches: 78, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
16 6 0.08
17 50 0.64
18 22 0.28
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (18 bp):
AATTCTTGCAAATCTTAA
Found at i:12805940 original size:17 final size:18
Alignment explanation
Indices: 12805897--12805950 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
12805887 GCGAACATTC
*
12805897 AATTCTTGCAAATCTTAA
1 AATTCTTGCAAATCTAAA
*
12805915 AATTCTTGCAAAGCTAAA
1 AATTCTTGCAAATCTAAA
*
12805933 AATT-TTGCGAATCTAAA
1 AATTCTTGCAAATCTAAA
12805950 A
1 A
12805951 TTTTTGTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 12 0.38
18 20 0.62
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (18 bp):
AATTCTTGCAAATCTAAA
Found at i:12805979 original size:17 final size:17
Alignment explanation
Indices: 12805959--12806006 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
12805949 AATTTTTGTG
12805959 AATTTTCAATTCTTACA
1 AATTTTCAATTCTTACA
12805976 AATTTTCAATTCTTACA
1 AATTTTCAATTCTTACA
*
12805993 AATCTTCAATTCTT
1 AATTTTCAATTCTT
12806007 GCGAATTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTTTCAATTCTTACA
Found at i:12812057 original size:121 final size:122
Alignment explanation
Indices: 12811838--12812229 Score: 305
Period size: 122 Copynumber: 3.2 Consensus size: 122
12811828 GCGTTTTTTA
* * * *
12811838 TTATTCAAGGTGTTTCTAACCAAAAATGCATTTAATAATCCCTTTCTATTTTTAGGGAATTATTC
1 TTATTCAAGGGGTTTCTAACAAAAAATACATTCAATAATCCCTTTCTATTTTTAGGGAATTATTC
* ** *
12811903 AAGGCATTTTTGGCCAAAAAATGCCTTGAATAATTTCTTATA-A-AAAATTGAATAGGG
66 AAGGCATTTTTGACCAAAAAACACCTTGAATAA-TCCTT-TACAGAAAATTGAATAGGG
* **
12811960 TTATTCAAGGCGGTTTCT-ACAAAAAATACCTTCAATAATCCC-TTCTTATTTTTTTGG-ATTAT
1 TTATTCAAGG-GGTTTCTAACAAAAAATACATTCAATAATCCCTTTC-TATTTTTAGGGAATTAT
** *
12812022 TCAAGGTGTTTTTGACCAGAAAACACCTTGAATAATCCTTTACAGAAAATTGAATAGGG
64 TCAAGGCATTTTTGACCAAAAAACACCTTGAATAATCCTTTACAGAAAATTGAATAGGG
* * * ** * * * * ***
12812081 TTATTCAATGTGTTTTTGGTC-AAAAATGTC-TTGAACAATCCCTTTCAATTTTTTTTAGAATTA
1 TTATTCAAGGGGTTTCT-AACAAAAAAT-ACATTCAATAATCCCTTTCTA-TTTTTAGGGAATTA
* * * * ** * * *
12812144 TTCAAAGCATTTTTG-GCTAGAAATGCCTTGAATAATTCTTTACAAAAAATTGAATGGGAG
63 TTCAAGGCATTTTTGACCAAAAAACACCTTGAATAATCCTTTACAGAAAATTGAATAGG-G
* ** *
12812204 TTATTCAATGTATTTCTAGCAAAAAA
1 TTATTCAAGGGGTTTCTAACAAAAAA
12812230 GGCCTTAAAT
Statistics
Matches: 219, Mismatches: 39, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
119 2 0.01
120 10 0.05
121 77 0.35
122 87 0.40
123 43 0.20
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (122 bp):
TTATTCAAGGGGTTTCTAACAAAAAATACATTCAATAATCCCTTTCTATTTTTAGGGAATTATTC
AAGGCATTTTTGACCAAAAAACACCTTGAATAATCCTTTACAGAAAATTGAATAGGG
Found at i:12812251 original size:123 final size:122
Alignment explanation
Indices: 12811838--12812254 Score: 386
Period size: 121 Copynumber: 3.4 Consensus size: 122
12811828 GCGTTTTTTA
* * * * *
12811838 TTATTCAAGGTGTTTCTAACCAAAAATGCATTTAATAATCCCTT---TCTA-TTTTTAGGGAATT
1 TTATTCAATGTGTTTCTAGCAAAAAATGCCTTAAATAATCCCTTCAAT-TATTTTTTA--GAATT
* *
12811899 ATTCAAGGCATTTTTGGCCAAAAAATGCCTTGAATAATT-TCTTATAAAAAATTGAATAGGG
63 ATTCAAGGCATTTTTGG-CAAGAAATGCCTTGAATAATTCT-TTACAAAAAATTGAATAGGG
* * * * * *
12811960 TTATTCAAGGCGGTTTCTA-CAAAAAATACCTTCAATAATCCCTTC--TTATTTTTTTGGATTAT
1 TTATTCAATG-TGTTTCTAGCAAAAAATGCCTTAAATAATCCCTTCAATTATTTTTTAGAATTAT
** * * ** * *
12812022 TCAAGGTGTTTTTGACCAGAAAACACCTTGAATAATCCTTTACAGAAAATTGAATAGGG
65 TCAAGGCATTTTTGGCAAG-AAATGCCTTGAATAATTCTTTACAAAAAATTGAATAGGG
* * * * *
12812081 TTATTCAATGTGTTTTTGGTC-AAAAATGTCTTGAACAATCCCTTTCAATT-TTTTTTAGAATTA
1 TTATTCAATGTGTTTCTAG-CAAAAAATGCCTTAAATAATCCC-TTCAATTATTTTTTAGAATTA
* * *
12812144 TTCAAAGCATTTTTGGCTAGAAATGCCTTGAATAATTCTTTACAAAAAATTGAATGGGAG
64 TTCAAGGCATTTTTGGCAAGAAATGCCTTGAATAATTCTTTACAAAAAATTGAATAGG-G
* *
12812204 TTATTCAATGTATTTCTAGCAAAAAAGGCCTTAAATAATTCCCTTCAATTA
1 TTATTCAATGTGTTTCTAGCAAAAAATGCCTTAAATAA-TCCCTTCAATTA
12812255 AAAGTTAAAG
Statistics
Matches: 237, Mismatches: 44, Indels: 26
0.77 0.14 0.08
Matches are distributed among these distances:
120 7 0.03
121 76 0.32
122 72 0.30
123 76 0.32
124 6 0.03
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.38
Consensus pattern (122 bp):
TTATTCAATGTGTTTCTAGCAAAAAATGCCTTAAATAATCCCTTCAATTATTTTTTAGAATTATT
CAAGGCATTTTTGGCAAGAAATGCCTTGAATAATTCTTTACAAAAAATTGAATAGGG
Found at i:12814707 original size:46 final size:47
Alignment explanation
Indices: 12814655--12814743 Score: 135
Period size: 46 Copynumber: 1.9 Consensus size: 47
12814645 AAATAAACGT
*
12814655 TTTAAAGAAAAGTTAAAAGTAT-TAGTTTTTTTTAAATAAAAAAAAA
1 TTTAAAGAAAAGTTAAAAGTATCAAGTTTTTTTTAAATAAAAAAAAA
** *
12814701 TTTAAAGAAAAGTTGTAAGTATCAATTTTTTTTTAAATAAAAA
1 TTTAAAGAAAAGTTAAAAGTATCAAGTTTTTTTTAAATAAAAA
12814744 TCTTTTCAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
46 20 0.53
47 18 0.47
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.39
Consensus pattern (47 bp):
TTTAAAGAAAAGTTAAAAGTATCAAGTTTTTTTTAAATAAAAAAAAA
Found at i:12814821 original size:23 final size:24
Alignment explanation
Indices: 12814795--12814850 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
12814785 AAGAAAAAGT
12814795 TAAAAATATCAA-TTTTTTAAAAA
1 TAAAAATATCAATTTTTTTAAAAA
** *
12814818 TAAAAGCATTAATTTTTTTAAAAA
1 TAAAAATATCAATTTTTTTAAAAA
*
12814842 AATAAAATA
1 TA-AAAATA
12814851 AGAAAAGAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 9 0.36
24 12 0.48
25 4 0.16
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.38
Consensus pattern (24 bp):
TAAAAATATCAATTTTTTTAAAAA
Found at i:12819045 original size:22 final size:22
Alignment explanation
Indices: 12819017--12819100 Score: 89
Period size: 22 Copynumber: 3.7 Consensus size: 22
12819007 GAAATATGAA
12819017 ATATATATTTTTTAAAATTTAT
1 ATATATATTTTTTAAAATTTAT
***
12819039 ATATATATTTTTGCTAATTTAT
1 ATATATATTTTTTAAAATTTAT
*
12819061 ATAT-TATTTTTATTAAAATTTTAA
1 ATATATA-TTTT-TTAAAA-TTTAT
12819085 ATCATATATTTTTTAA
1 AT-ATATATTTTTTAA
12819101 TTTTTTTTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
21 2 0.04
22 27 0.54
23 3 0.06
24 10 0.20
25 6 0.12
26 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.58
Consensus pattern (22 bp):
ATATATATTTTTTAAAATTTAT
Found at i:12819102 original size:45 final size:41
Alignment explanation
Indices: 12819017--12819103 Score: 104
Period size: 45 Copynumber: 2.0 Consensus size: 41
12819007 GAAATATGAA
*
12819017 ATATATATTTTTTAAAATTTATATATATATTTTTGCTAATTT
1 ATATATATTTTTTAAAATTTAAATATATATTTTT-CTAATTT
12819059 ATATATTATTTTTATTAAAATTTTAAATCATATATTTTT-TAATTT
1 ATATA-TA-TTTT-TTAAAA-TTTAAAT-ATATATTTTTCTAATTT
12819104 TTTTTATATC
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
42 5 0.13
43 2 0.05
44 4 0.10
45 12 0.31
46 6 0.15
47 10 0.26
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (41 bp):
ATATATATTTTTTAAAATTTAAATATATATTTTTCTAATTT
Found at i:12820113 original size:32 final size:33
Alignment explanation
Indices: 12820070--12820135 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
12820060 TCATAAGAAA
*
12820070 ATATAAAA-TTTTATAAGTCCTTAAAAATAAAT
1 ATATAAAATTTTTATAAATCCTTAAAAATAAAT
* *
12820102 ATATAATATTTTTATAAATCTTTAAAAATAAAT
1 ATATAAAATTTTTATAAATCCTTAAAAATAAAT
12820135 A
1 A
12820136 CAAAAAAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 7 0.23
33 23 0.77
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (33 bp):
ATATAAAATTTTTATAAATCCTTAAAAATAAAT
Found at i:12823102 original size:14 final size:15
Alignment explanation
Indices: 12823083--12823111 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12823073 TTTCAAATTT
12823083 AAATTAAT-ATTTTA
1 AAATTAATAATTTTA
12823097 AAATTAATAATTTTA
1 AAATTAATAATTTTA
12823112 TTTAAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATTAATAATTTTA
Found at i:12833041 original size:18 final size:18
Alignment explanation
Indices: 12833018--12833056 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
12833008 TAGTATAAGA
*
12833018 ATATGCATGTCTATGCTC
1 ATATGCATGTCTATGCAC
12833036 ATATGCATGTCTATGCAC
1 ATATGCATGTCTATGCAC
12833054 ATA
1 ATA
12833057 AGGCTCCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (18 bp):
ATATGCATGTCTATGCAC
Found at i:12834068 original size:26 final size:26
Alignment explanation
Indices: 12834031--12834092 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
12834021 TTACGACTTG
* *
12834031 GTTTGAGTTTCAAAGTGAAACTCATT
1 GTTTGAGCTTCAAACTGAAACTCATT
12834057 GTTTGAGCTTCAAACTGAAACTCATT
1 GTTTGAGCTTCAAACTGAAACTCATT
12834083 GTTTGAGCTT
1 GTTTGAGCTT
12834093 GAGCTACGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (26 bp):
GTTTGAGCTTCAAACTGAAACTCATT
Found at i:12840274 original size:13 final size:14
Alignment explanation
Indices: 12840258--12840286 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12840248 TTTAAAAAAT
12840258 AAAATA-ATTTCAA
1 AAAATATATTTCAA
12840271 AAAATATATTTCAA
1 AAAATATATTTCAA
12840285 AA
1 AA
12840287 TAAACATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAATATATTTCAA
Found at i:12842333 original size:121 final size:120
Alignment explanation
Indices: 12842121--12842361 Score: 292
Period size: 121 Copynumber: 2.0 Consensus size: 120
12842111 CATTTTTAGG
** * *
12842121 GGATTATTCAAGGTGTTTTTGGTAAAAAAATGCCTTGAATAATTCCTTATAAAAAATTAAATGGG
1 GGATTATTCAAGGTGTTTTTGGTAAAAAAACACCTTGAATAATCCCTTACAAAAAATTAAATGGG
* * *
12842186 GTTATTCAAGGCGGTTTCTACAAAAAATGCCTTCAATAAT-CCTTTCTCATTTTTT
66 GTTATTCAAGGCGGTTTCTACAAAAAATACCTTCAACAATCCCTTTC-AATTTTTT
* *
12842241 GGATTATTCAAGGTGTTTTT-TTACCAGAAAACACCTTGAATAATCCCTTACAAAAAATTAAATG
1 GGATTATTCAAGGTGTTTTTGGTA--AAAAAACACCTTGAATAATCCCTTACAAAAAATTAAATG
* * * *
12842305 GGGTTATTCAATGC-GTTTTTGGTC-AAAAATACCTTGAACAATCCCTTTCAATTTTTT
64 GGGTTATTCAAGGCGGTTTCT--ACAAAAAATACCTTCAACAATCCCTTTCAATTTTTT
12842362 TAGAGTATTT
Statistics
Matches: 103, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
119 2 0.02
120 25 0.24
121 69 0.67
122 7 0.07
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (120 bp):
GGATTATTCAAGGTGTTTTTGGTAAAAAAACACCTTGAATAATCCCTTACAAAAAATTAAATGGG
GTTATTCAAGGCGGTTTCTACAAAAAATACCTTCAACAATCCCTTTCAATTTTTT
Found at i:12843007 original size:13 final size:13
Alignment explanation
Indices: 12842989--12843027 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
12842979 ATTATTCTAA
12842989 AAAAAAAAATGAT
1 AAAAAAAAATGAT
12843002 AAAAAAAAAT-AT
1 AAAAAAAAATGAT
*
12843014 -AAAACAAATGAT
1 AAAAAAAAATGAT
12843026 AA
1 AA
12843028 GATTTGGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
11 8 0.35
12 4 0.17
13 11 0.48
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (13 bp):
AAAAAAAAATGAT
Found at i:12845040 original size:23 final size:24
Alignment explanation
Indices: 12845013--12845071 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
12845003 GTTAAAAAGA
*
12845013 AAAAATTAAAAATATCAA-TTTTTT
1 AAAAA-TAAAAACATCAATTTTTTT
* *
12845037 AAAAATAAAAGCATTAATTTTTTT
1 AAAAATAAAAACATCAATTTTTTT
12845061 AAAAAATAAAA
1 -AAAAATAAAA
12845072 TAGGAAAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.30
24 11 0.37
25 10 0.33
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (24 bp):
AAAAATAAAAACATCAATTTTTTT
Found at i:12845985 original size:14 final size:15
Alignment explanation
Indices: 12845966--12845998 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
12845956 TCAAATATTG
12845966 ATTTTGCCTTTTGC-
1 ATTTTGCCTTTTGCT
12845980 ATTTTGCCTTTTGCT
1 ATTTTGCCTTTTGCT
12845995 ATTT
1 ATTT
12845999 GCTATTAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.09, C:0.18, G:0.12, T:0.61
Consensus pattern (15 bp):
ATTTTGCCTTTTGCT
Found at i:12845999 original size:7 final size:7
Alignment explanation
Indices: 12845992--12846022 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
12845982 TTTGCCTTTT
*
12845992 GCTATTT
1 GCTATTA
12845999 GCTATTA
1 GCTATTA
12846006 GCTATTA
1 GCTATTA
12846013 GCTATTA
1 GCTATTA
12846020 GCT
1 GCT
12846023 TTTGTTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (7 bp):
GCTATTA
Found at i:12846009 original size:14 final size:14
Alignment explanation
Indices: 12845992--12846026 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
12845982 TTTGCCTTTT
12845992 GCTATTTGCTATTA
1 GCTATTTGCTATTA
*
12846006 GCTATTAGCTATTA
1 GCTATTTGCTATTA
12846020 GCT-TTTG
1 GCTATTTG
12846027 TTTTTGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 3 0.16
14 16 0.84
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.49
Consensus pattern (14 bp):
GCTATTTGCTATTA
Found at i:12850383 original size:32 final size:33
Alignment explanation
Indices: 12850340--12850405 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
12850330 TCATAAGAAA
*
12850340 ATATAAAA-TTTTATAAGTCCTTAAAAATAAAT
1 ATATAAAATTTTTATAAATCCTTAAAAATAAAT
* *
12850372 ATATAATATTTTTATAAATCTTTAAAAATAAAT
1 ATATAAAATTTTTATAAATCCTTAAAAATAAAT
12850405 A
1 A
12850406 CAAAAAAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 7 0.23
33 23 0.77
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (33 bp):
ATATAAAATTTTTATAAATCCTTAAAAATAAAT
Found at i:12851947 original size:21 final size:19
Alignment explanation
Indices: 12851919--12851957 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 19
12851909 AATAATATAA
12851919 TTTAAAATTTTAATAAAAAG
1 TTTAAAA-TTTAATAAAAAG
12851939 TTTACAAATTTAATAAAAA
1 TTTA-AAATTTAATAAAAA
12851958 TAAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
TTTAAAATTTAATAAAAAG
Found at i:12853516 original size:15 final size:15
Alignment explanation
Indices: 12853498--12853546 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 15
12853488 TGAAATTTAG
*
12853498 TAATTTATATAAATT
1 TAATTTATATAATTT
12853513 TAATTCTCATAT-ATTT
1 TAATT-T-ATATAATTT
12853529 TAATTTAT-TAATTT
1 TAATTTATATAATTT
12853543 TAAT
1 TAAT
12853547 GTAATCACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 1 0.03
14 10 0.33
15 6 0.20
16 9 0.30
17 4 0.13
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (15 bp):
TAATTTATATAATTT
Found at i:12853746 original size:31 final size:31
Alignment explanation
Indices: 12853696--12853755 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
12853686 ATGCAAATAA
* *
12853696 TTTTACACTCATTTTAAATTTTAAATTTAAT
1 TTTTACACTCATTTAAAATTTGAAATTTAAT
* *
12853727 TTTTATACTCGTTTAAAATTTGAAATTTA
1 TTTTACACTCATTTAAAATTTGAAATTTA
12853756 GTCTTTGTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.53
Consensus pattern (31 bp):
TTTTACACTCATTTAAAATTTGAAATTTAAT
Found at i:12854286 original size:33 final size:35
Alignment explanation
Indices: 12854243--12854312 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 35
12854233 TTATTTTTAT
*
12854243 TTAAATATTAAAAAATAAAGAAAA-TTTCTAAAAA
1 TTAAATATTAAAAAATAAAGAAAATTTTATAAAAA
**
12854277 TTAAA-ATTAAAAAATATGGAAAATTTTATAAAAA
1 TTAAATATTAAAAAATAAAGAAAATTTTATAAAAA
12854311 TT
1 TT
12854313 TTAAAAACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 16 0.50
34 16 0.50
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (35 bp):
TTAAATATTAAAAAATAAAGAAAATTTTATAAAAA
Found at i:12856970 original size:2 final size:2
Alignment explanation
Indices: 12856963--12857019 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
12856953 TACTAATCGA
12856963 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12857005 AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG A
12857020 AATTAAAAAC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12857340 original size:2 final size:2
Alignment explanation
Indices: 12857333--12857363 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12857323 TGGAAATGTC
12857333 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12857364 CTTGTTTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12859502 original size:8 final size:8
Alignment explanation
Indices: 12859489--12859513 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
12859479 TAAGTGTTGT
12859489 TGTTCATA
1 TGTTCATA
12859497 TGTTCATA
1 TGTTCATA
12859505 TGTTCATA
1 TGTTCATA
12859513 T
1 T
12859514 ATTTTAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.52
Consensus pattern (8 bp):
TGTTCATA
Found at i:12862012 original size:13 final size:13
Alignment explanation
Indices: 12861982--12862014 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
12861972 TCACGTCTCA
12861982 TTTTTTTTGTATC
1 TTTTTTTTGTATC
*
12861995 TTTTTCTTGT-TC
1 TTTTTTTTGTATC
12862007 TTTTTTTT
1 TTTTTTTT
12862015 TTTTTTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.03, C:0.09, G:0.06, T:0.82
Consensus pattern (13 bp):
TTTTTTTTGTATC
Found at i:12863133 original size:20 final size:21
Alignment explanation
Indices: 12863095--12863134 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
12863085 GACATGTTTA
* *
12863095 TTTTCCTTTTTTTTTTTTGTG
1 TTTTCCTTTTTTATCTTTGTG
12863116 TTTT-CTTTTTTATCTTTGT
1 TTTTCCTTTTTTATCTTTGT
12863135 TAATTGCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.03, C:0.10, G:0.07, T:0.80
Consensus pattern (21 bp):
TTTTCCTTTTTTATCTTTGTG
Found at i:12865338 original size:2 final size:2
Alignment explanation
Indices: 12865331--12865358 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12865321 TTCCTACCCC
12865331 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12865359 GTACACAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.