Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 177 of 204
Found at i:52545146 original size:33 final size:33
Alignment explanation
Indices: 52545109--52545171 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
52545099 TAGTTAAGGG
*
52545109 TTAGGGTTAGGGTTTTTTAGTGAAGGGTTAGGA
1 TTAGGGTTAGGGTTTTTAAGTGAAGGGTTAGGA
* *
52545142 TTAGGGTTAGTGTTTTTAAGTTAAGGGTTA
1 TTAGGGTTAGGGTTTTTAAGTGAAGGGTTA
52545172 TGGTTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.43
Consensus pattern (33 bp):
TTAGGGTTAGGGTTTTTAAGTGAAGGGTTAGGA
Found at i:52545176 original size:27 final size:27
Alignment explanation
Indices: 52545088--52545176 Score: 90
Period size: 27 Copynumber: 3.1 Consensus size: 27
52545078 GGTTTAAGGT
*
52545088 TTAGGGTTTTTTAGTTAAGGGTTAGGG
1 TTAGGGTTTTTTAGTTAAGGGTTATGG
*
52545115 TTAGGGTTTTTTAGTGAAGGGTTA-GG
1 TTAGGGTTTTTTAGTTAAGGGTTATGG
52545141 ATTAGGGTTAGTGTTTTTAAGTTAAGGGTTATGG
1 -TTA-GG---GT-TTTTT-AGTTAAGGGTTATGG
52545175 TT
1 TT
52545177 TTTAGGTTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
26 2 0.04
27 26 0.50
28 2 0.04
31 2 0.04
32 5 0.10
33 13 0.25
34 2 0.04
ACGTcount: A:0.20, C:0.00, G:0.35, T:0.45
Consensus pattern (27 bp):
TTAGGGTTTTTTAGTTAAGGGTTATGG
Found at i:52545213 original size:15 final size:15
Alignment explanation
Indices: 52545162--52545232 Score: 65
Period size: 15 Copynumber: 4.8 Consensus size: 15
52545152 TGTTTTTAAG
*
52545162 TTAAGGGTTATGG-TT
1 TTAAGGTTTA-GGATT
*
52545177 TTTAGGTTTAGG-TT
1 TTAAGGTTTAGGATT
* **
52545191 TTATGGTTTTTGATT
1 TTAAGGTTTAGGATT
*
52545206 TTAAGGTTTAGGGTT
1 TTAAGGTTTAGGATT
52545221 TTAAGGTTTAGG
1 TTAAGGTTTAGG
52545233 GTTTAGGGTT
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
14 12 0.27
15 33 0.73
ACGTcount: A:0.18, C:0.00, G:0.30, T:0.52
Consensus pattern (15 bp):
TTAAGGTTTAGGATT
Found at i:52545215 original size:7 final size:7
Alignment explanation
Indices: 52545205--52545372 Score: 69
Period size: 7 Copynumber: 23.4 Consensus size: 7
52545195 GGTTTTTGAT
52545205 TTTAAGG
1 TTTAAGG
*
52545212 TTTAGGG
1 TTTAAGG
52545219 TTTTAAGG
1 -TTTAAGG
*
52545227 TTTAGGG
1 TTTAAGG
*
52545234 TTTAGGG
1 TTTAAGG
52545241 TTTAAGG
1 TTTAAGG
52545248 TTT-AGAG
1 TTTAAG-G
*
52545255 TTTATGG
1 TTTAAGG
52545262 TTTTTAA-G
1 --TTTAAGG
52545270 -TTAAGG
1 TTTAAGG
* * *
52545276 GTTATGA
1 TTTAAGG
*
52545283 TTTATGG
1 TTTAAGG
52545290 TTTAAGG
1 TTTAAGG
* *
52545297 TTTATGTTT
1 TTTAAG--G
52545306 TTTAA-G
1 TTTAAGG
52545312 TTT-AGAG
1 TTTAAG-G
**
52545319 TTTATGATTT
1 TTTA--A-GG
52545329 TTTAA-G
1 TTTAAGG
52545335 TTTAAGG
1 TTTAAGG
*
52545342 TTTAGGG
1 TTTAAGG
*
52545349 TTTAGGG
1 TTTAAGG
*
52545356 TTTAGGG
1 TTTAAGG
52545363 TTTAAGG
1 TTTAAGG
52545370 TTT
1 TTT
52545373 TTAAGTTAAA
Statistics
Matches: 125, Mismatches: 20, Indels: 32
0.71 0.11 0.18
Matches are distributed among these distances:
5 5 0.04
6 11 0.09
7 87 0.70
8 9 0.07
9 8 0.06
10 5 0.04
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (7 bp):
TTTAAGG
Found at i:52545278 original size:108 final size:108
Alignment explanation
Indices: 52545153--52545392 Score: 299
Period size: 108 Copynumber: 2.2 Consensus size: 108
52545143 TAGGGTTAGT
* * * *
52545153 GTTTTTAAGTTAAGGGTTATGGTTTTTAGGTTT-AGGTTTTATGGTTTTTGATTTTA-AGGTTTA
1 GTTTTTAAGTTAAGGGTTATGATTTAT-GGTTTAAGG-TTTATGGTTTTTAAGTTTAGA-GTTTA
* *
52545216 -G-GGTTTTAAGGTTTAGGGTTTAGGGTTTAAGGTTTAGAGTTTATG
63 TGAGGTTTTAA-GTTTAAGGTTTAGGGTTTAAGGTTTAGAGTTTAAG
*
52545261 GTTTTTAAGTTAAGGGTTATGATTTATGGTTTAAGGTTTATGTTTTTTAAGTTTAGAGTTTATGA
1 GTTTTTAAGTTAAGGGTTATGATTTATGGTTTAAGGTTTATGGTTTTTAAGTTTAGAGTTTATGA
** * *
52545326 TTTTTTAAGTTTAAGGTTTAGGGTTTAGGGTTTAGGGTTTAAG
66 GGTTTTAAGTTTAAGGTTTAGGGTTTAAGGTTTAGAGTTTAAG
* *
52545369 GTTTTTAAGTTAAAGGTTAAGATT
1 GTTTTTAAGTTAAGGGTTATGATT
52545393 AGGGTTAGGA
Statistics
Matches: 115, Mismatches: 13, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
107 26 0.23
108 83 0.72
109 6 0.05
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (108 bp):
GTTTTTAAGTTAAGGGTTATGATTTATGGTTTAAGGTTTATGGTTTTTAAGTTTAGAGTTTATGA
GGTTTTAAGTTTAAGGTTTAGGGTTTAAGGTTTAGAGTTTAAG
Found at i:52545280 original size:21 final size:21
Alignment explanation
Indices: 52545144--52545387 Score: 97
Period size: 21 Copynumber: 11.3 Consensus size: 21
52545134 GGTTAGGATT
52545144 AGGGTTA-GTGTTTTTAAGTTA
1 AGGGTTATG-GTTTTTAAGTTA
* *
52545165 AGGGTTATGGTTTTTAGGTTT
1 AGGGTTATGGTTTTTAAGTTA
* **
52545186 AGGTTTTATGGTTTTTGATTTTA
1 AGG-GTTATGGTTTTT-AAGTTA
* * *
52545209 AGGTTTA-GGGTTTTAAGGTTT
1 AGGGTTATGGTTTTTAA-GTTA
* *
52545230 AGGGTT-TAGG-GTTTAAGGTTT
1 AGGGTTAT-GGTTTTTAA-GTTA
*
52545251 AGAGTTTATGGTTTTTAAGTTA
1 AG-GGTTATGGTTTTTAAGTTA
* * *
52545273 AGGGTTATGATTTAT-GGTTTA
1 AGGGTTATGGTTTTTAAG-TTA
* * *
52545294 AGGTTTATGTTTTTTAAGTTT
1 AGGGTTATGGTTTTTAAGTTA
* *
52545315 AGAGTTTATGATTTTTTAAGTTTA
1 AG-GGTTATG-GTTTTTAAG-TTA
* * * *
52545339 AGGTTTA-GG-GTTTAGGGTTT
1 AGGGTTATGGTTTTTA-AGTTA
*
52545359 AGGGTTTAAGGTTTTTAAGTTA
1 AGGG-TTATGGTTTTTAAGTTA
*
52545381 AAGGTTA
1 AGGGTTA
52545388 AGATTAGGGT
Statistics
Matches: 171, Mismatches: 34, Indels: 36
0.71 0.14 0.15
Matches are distributed among these distances:
20 11 0.06
21 81 0.47
22 45 0.26
23 30 0.18
24 4 0.02
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (21 bp):
AGGGTTATGGTTTTTAAGTTA
Found at i:52545302 original size:14 final size:14
Alignment explanation
Indices: 52545162--52545372 Score: 83
Period size: 14 Copynumber: 14.6 Consensus size: 14
52545152 TGTTTTTAAG
*
52545162 TTAAGGGTTATGGTT
1 TTAAGGTTTATGG-T
*
52545177 TTTAGGTTTA-GGTT
1 TTAAGGTTTATGG-T
* * *
52545191 TTATGGTTTTTGATT
1 TTAAGGTTTATG-GT
*
52545206 TTAAGGTTTAGGGTT
1 TTAAGGTTTATGG-T
*
52545221 TTAAGGTTTAGGGT
1 TTAAGGTTTATGGT
* *
52545235 TTAGGGTTTAAGGT
1 TTAAGGTTTATGGT
52545249 TT-AGAGTTTATGGTTT
1 TTAAG-GTTTATGG--T
* *
52545265 TTAA-G-TTAAGGG
1 TTAAGGTTTATGGT
* *
52545277 TTATGATTTATGGT
1 TTAAGGTTTATGGT
*
52545291 TTAAGGTTTATGTTTT
1 TTAAGGTTTATG--GT
52545307 TTAA-GTTTA-GAGT
1 TTAAGGTTTATG-GT
* * * *
52545320 TTATGATTTTTTAAGT
1 TTAAG-GTTTAT-GGT
*
52545336 TTAAGGTTTAGGGT
1 TTAAGGTTTATGGT
* *
52545350 TTAGGGTTTAGGGT
1 TTAAGGTTTATGGT
52545364 TTAAGGTTT
1 TTAAGGTTT
52545373 TTAAGTTAAA
Statistics
Matches: 145, Mismatches: 36, Indels: 31
0.68 0.17 0.15
Matches are distributed among these distances:
12 3 0.02
13 5 0.03
14 77 0.53
15 45 0.31
16 14 0.10
17 1 0.01
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (14 bp):
TTAAGGTTTATGGT
Found at i:52545410 original size:33 final size:34
Alignment explanation
Indices: 52545357--52545439 Score: 109
Period size: 33 Copynumber: 2.5 Consensus size: 34
52545347 GGTTTAGGGT
52545357 TTAGGGTTTAAGGTTTTTAAGTTAAAGGTTAAGA
1 TTAGGGTTTAAGGTTTTTAAGTTAAAGGTTAAGA
*
52545391 TTAGGG-TT-AGGATTTTTAAGTTAAGGGTT-AGAA
1 TTAGGGTTTAAGG-TTTTTAAGTTAAAGGTTAAG-A
*
52545424 TTGGGGTTTAAGGTTT
1 TTAGGGTTTAAGGTTT
52545440 AGGGTTTATG
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
32 5 0.12
33 24 0.56
34 11 0.26
35 3 0.07
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (34 bp):
TTAGGGTTTAAGGTTTTTAAGTTAAAGGTTAAGA
Found at i:52545461 original size:22 final size:22
Alignment explanation
Indices: 52545434--52545668 Score: 118
Period size: 21 Copynumber: 10.9 Consensus size: 22
52545424 TTGGGGTTTA
*
52545434 AGGTTTAGGGTTTATGTTTTTT
1 AGGTTTAGGGTTTATGGTTTTT
52545456 AGGTTTAGGGTTT-TAGG-TTTT
1 AGGTTTAGGGTTTAT-GGTTTTT
* * *
52545477 AGGGTTTTTA-AG-TTAAGG--GTT
1 A-GG--TTTAGGGTTTATGGTTTTT
*
52545498 AGGATTAGGG-TTATGGTTTTT
1 AGGTTTAGGGTTTATGGTTTTT
* *
52545519 AAGTTAAGGG-TTATGGTTTTT
1 AGGTTTAGGGTTTATGGTTTTT
***
52545540 AGGTTTAGGGTTT-TTAATTTT
1 AGGTTTAGGGTTTATGGTTTTT
* ** **
52545561 ATGGTTTAGGGTTTTTAATGCTT
1 A-GGTTTAGGGTTTATGGTTTTT
* *
52545584 AGTGTTTAAGGTTTAAGGTTTTT
1 AG-GTTTAGGGTTTATGGTTTTT
*
52545607 AGGTTTAGGG-TTAAGAG--TTT
1 AGGTTTAGGGTTTATG-GTTTTT
*
52545627 AGAGTTTAGGGTTTAAGGTTTTT
1 AG-GTTTAGGGTTTATGGTTTTT
* *
52545650 AAG-TTAGGGTTTAAGGTTT
1 AGGTTTAGGGTTTATGGTTT
52545669 AGAGGTTATG
Statistics
Matches: 167, Mismatches: 29, Indels: 35
0.72 0.13 0.15
Matches are distributed among these distances:
18 3 0.02
19 6 0.04
20 7 0.04
21 73 0.44
22 49 0.29
23 25 0.15
24 4 0.02
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.49
Consensus pattern (22 bp):
AGGTTTAGGGTTTATGGTTTTT
Found at i:52545477 original size:15 final size:14
Alignment explanation
Indices: 52545452--52545484 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
52545442 GGTTTATGTT
52545452 TTTTAGGTTTAGGG
1 TTTTAGGTTTAGGG
52545466 TTTTAGGTTTTAGGG
1 TTTTAGG-TTTAGGG
52545481 TTTT
1 TTTT
52545485 TAAGTTAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.12, C:0.00, G:0.30, T:0.58
Consensus pattern (14 bp):
TTTTAGGTTTAGGG
Found at i:52545590 original size:23 final size:22
Alignment explanation
Indices: 52545538--52545597 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
52545528 GTTATGGTTT
*
52545538 TTAG-GTTTAGGGTTTTTAATT
1 TTAGTGTTTAGGGTTTTTAATC
52545559 TTA-TGGTTTAGGGTTTTTAATGC
1 TTAGT-GTTTAGGGTTTTTAAT-C
*
52545582 TTAGTGTTTAAGGTTT
1 TTAGTGTTTAGGGTTT
52545598 AAGGTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 3 0.09
22 16 0.48
23 13 0.39
24 1 0.03
ACGTcount: A:0.18, C:0.02, G:0.25, T:0.55
Consensus pattern (22 bp):
TTAGTGTTTAGGGTTTTTAATC
Found at i:52545599 original size:7 final size:7
Alignment explanation
Indices: 52545587--52545735 Score: 67
Period size: 7 Copynumber: 20.7 Consensus size: 7
52545577 AATGCTTAGT
52545587 GTTTAAG
1 GTTTAAG
52545594 GTTTAAG
1 GTTTAAG
*
52545601 GTTTTTAG
1 G-TTTAAG
52545609 GTTT-AG
1 GTTTAAG
*
52545615 GGTTAAG
1 GTTTAAG
52545622 AGTTT-AG
1 -GTTTAAG
*
52545629 AGTTTAGG
1 -GTTTAAG
52545637 GTTTAAG
1 GTTTAAG
52545644 GTTTTTAA-
1 G--TTTAAG
*
52545652 G-TTAGG
1 GTTTAAG
52545658 GTTTAAG
1 GTTTAAG
52545665 GTTTAGAG
1 GTTTA-AG
*
52545673 G-TTATG
1 GTTTAAG
*
52545679 TTTTTTAA-
1 --GTTTAAG
*
52545687 GTTTAGG
1 GTTTAAG
52545694 GTTTAAG
1 GTTTAAG
*
52545701 GTTTTAAA
1 G-TTTAAG
52545709 GTTTAAG
1 GTTTAAG
*
52545716 AGTTTATG
1 -GTTTAAG
* *
52545724 ATTTAGG
1 GTTTAAG
52545731 GTTTA
1 GTTTA
52545736 TGATTTAGTG
Statistics
Matches: 108, Mismatches: 19, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
5 3 0.03
6 11 0.10
7 60 0.56
8 26 0.24
9 8 0.07
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (7 bp):
GTTTAAG
Found at i:52545627 original size:36 final size:37
Alignment explanation
Indices: 52545587--52545735 Score: 112
Period size: 36 Copynumber: 3.9 Consensus size: 37
52545577 AATGCTTAGT
*
52545587 GTTTA-AGGTTTAAGGTTTTTAGGTTTAGGG-TTAAG
1 GTTTATAGGTTTAAGGTTTTTAAGTTTAGGGTTTAAG
52545622 AGTTTAGAGTTTAGGGTTTAAGGTTTTTAAG-TTAGGGTTTAAG
1 -GTTT--A---TA-GGTTTAAGGTTTTTAAGTTTAGGGTTTAAG
* * *
52545665 GTTTAGAGG-TTATGTTTTTTAAGTTTAGGGTTTAAG
1 GTTTATAGGTTTAAGGTTTTTAAGTTTAGGGTTTAAG
* * *
52545701 GTTT-TAAAGTTTAAGAGTTTATGA-TTTAGGGTTTA
1 GTTTAT-AGGTTTAAG-GTTTTTAAGTTTAGGGTTTA
52545736 TGATTTAGTG
Statistics
Matches: 91, Mismatches: 10, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
35 12 0.13
36 24 0.26
37 16 0.18
38 6 0.07
40 1 0.01
42 11 0.12
43 21 0.23
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (37 bp):
GTTTATAGGTTTAAGGTTTTTAAGTTTAGGGTTTAAG
Found at i:52545640 original size:43 final size:42
Alignment explanation
Indices: 52545582--52545672 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 42
52545572 TTTTTAATGC
* *
52545582 TTAGTGTTTAAGGTTTAAGGTTTTTAGGTTTAGGG-TTAAGAGT
1 TTAGAGTTTAAGGTTTAAGGTTTTTAAG-TTAGGGTTTAAG-GT
*
52545625 TTAGAGTTTAGGGTTTAAGGTTTTTAAGTTAGGGTTTAAGGT
1 TTAGAGTTTAAGGTTTAAGGTTTTTAAGTTAGGGTTTAAGGT
52545667 TTAGAG
1 TTAGAG
52545673 GTTATGTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
42 14 0.32
43 30 0.68
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (42 bp):
TTAGAGTTTAAGGTTTAAGGTTTTTAAGTTAGGGTTTAAGGT
Found at i:52545692 original size:22 final size:22
Alignment explanation
Indices: 52545659--52545723 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
52545649 TAAGTTAGGG
*
52545659 TTTAAGGTTTAGAGGTTATGTTT
1 TTTAA-GTTTAGAGGTTATGGTT
*
52545682 TTTAAGTTTAG-GGTTTAAGGTT
1 TTTAAGTTTAGAGG-TTATGGTT
* *
52545704 TTAAAGTTTAAGAGTTTATG
1 TTTAAGTTT-AGAGGTTATG
52545724 ATTTAGGGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
21 2 0.06
22 20 0.59
23 11 0.32
24 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (22 bp):
TTTAAGTTTAGAGGTTATGGTT
Found at i:52545734 original size:22 final size:21
Alignment explanation
Indices: 52545709--52545778 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 21
52545699 AGGTTTTAAA
52545709 GTTTAAGAGTTTATGATTTAGG
1 GTTTAAGA-TTTATGATTTAGG
* *
52545731 GTTTATGATTTAGTGTTTTAGG
1 GTTTAAGATTTA-TGATTTAGG
52545753 GTTTAA-ATTT-TAGAGTTTAGG
1 GTTTAAGATTTAT-GA-TTTAGG
52545774 GTTTA
1 GTTTA
52545779 GGGTTTTTAG
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 1 0.02
21 19 0.46
22 20 0.49
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (21 bp):
GTTTAAGATTTATGATTTAGG
Found at i:52545757 original size:7 final size:7
Alignment explanation
Indices: 52545687--52545811 Score: 54
Period size: 7 Copynumber: 17.6 Consensus size: 7
52545677 TGTTTTTTAA
52545687 GTTTAGG
1 GTTTAGG
52545694 GTTTAAGG
1 GTTT-AGG
* **
52545702 TTTTAAA
1 GTTTAGG
*
52545709 GTTTAAGA
1 GTTT-AGG
*
52545717 GTTTATG
1 GTTTAGG
*
52545724 ATTTAGG
1 GTTTAGG
*
52545731 GTTTATG
1 GTTTAGG
*
52545738 ATTTAGTG
1 GTTTAG-G
*
52545746 TTTTAGG
1 GTTTAGG
**
52545753 GTTTAAA
1 GTTTAGG
* *
52545760 TTTTAGA
1 GTTTAGG
52545767 GTTTAGG
1 GTTTAGG
52545774 GTTTAGG
1 GTTTAGG
***
52545781 GTTTTTA
1 GTTTAGG
* *
52545788 GTTAATG
1 GTTTAGG
52545795 G-TTAGG
1 GTTTAGG
52545801 GTTTAGG
1 GTTTAGG
52545808 GTTT
1 GTTT
52545812 TAAGTTAAGG
Statistics
Matches: 85, Mismatches: 29, Indels: 8
0.70 0.24 0.07
Matches are distributed among these distances:
6 4 0.05
7 63 0.74
8 18 0.21
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (7 bp):
GTTTAGG
Found at i:52545778 original size:14 final size:14
Alignment explanation
Indices: 52545604--52545824 Score: 56
Period size: 14 Copynumber: 16.1 Consensus size: 14
52545594 GTTTAAGGTT
52545604 TTTAG-GTTTAGGG
1 TTTAGAGTTTAGGG
* *
52545617 TTAAGAGTTTAGAG
1 TTTAGAGTTTAGGG
* *
52545631 TTTAGGGTTTAAGGTT
1 TTTAGAGTTT-AGG-G
52545647 TTTA-AG-TTAGGG
1 TTTAGAGTTTAGGG
52545659 TTTA-AGGTTTAGAGG
1 TTTAGA-GTTTAG-GG
*
52545674 -TTA-TGTTT----
1 TTTAGAGTTTAGGG
52545682 TTTA-AGTTTAGGG
1 TTTAGAGTTTAGGG
**
52545695 TTTA-AGGTTTTAAAG
1 TTTAGA-G-TTTAGGG
* *
52545710 TTTAAGAGTTTATGA
1 TTT-AGAGTTTAGGG
* * *
52545725 TTTAGGGTTTATGA
1 TTTAGAGTTTAGGG
*
52545739 TTTAGTGTTTTAGGG
1 TTTAGAG-TTTAGGG
* * *
52545754 TTTAAATTTTAGAG
1 TTTAGAGTTTAGGG
*
52545768 TTTAGGGTTTAGGG
1 TTTAGAGTTTAGGG
** * *
52545782 TTTTTAGTTAATGG
1 TTTAGAGTTTAGGG
*
52545796 -TTAGGGTTTAGGG
1 TTTAGAGTTTAGGG
*
52545809 TTTTA-AGTTAAGGG
1 -TTTAGAGTTTAGGG
52545823 TT
1 TT
52545825 ATGATTAGGG
Statistics
Matches: 151, Mismatches: 39, Indels: 36
0.67 0.17 0.16
Matches are distributed among these distances:
9 7 0.05
12 5 0.03
13 27 0.18
14 73 0.48
15 32 0.21
16 6 0.04
17 1 0.01
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.48
Consensus pattern (14 bp):
TTTAGAGTTTAGGG
Found at i:52545805 original size:27 final size:27
Alignment explanation
Indices: 52545769--52545825 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
52545759 ATTTTAGAGT
* *
52545769 TTAGGGTTTAGGGTTTTTAGTTAATGG
1 TTAGGGTTTAGGGTTTTAAGTTAAGGG
52545796 TTAGGGTTTAGGGTTTTAAGTTAAGGG
1 TTAGGGTTTAGGGTTTTAAGTTAAGGG
52545823 TTA
1 TTA
52545826 TGATTAGGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (27 bp):
TTAGGGTTTAGGGTTTTAAGTTAAGGG
Found at i:52545846 original size:33 final size:33
Alignment explanation
Indices: 52545796--52545860 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
52545786 TAGTTAATGG
52545796 TTAGGGTTTAGGGTTTTAAGTTAAGGGTTATGA
1 TTAGGGTTTAGGGTTTTAAGTTAAGGGTTATGA
* * *
52545829 TTAGGG-TTAGTGTTTTTAGGTTTAGGGTTATG
1 TTAGGGTTTAG-GGTTTTAAGTTAAGGGTTATG
52545861 GTTTTTAGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 4 0.14
33 24 0.86
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (33 bp):
TTAGGGTTTAGGGTTTTAAGTTAAGGGTTATGA
Found at i:52545885 original size:22 final size:22
Alignment explanation
Indices: 52545835--52545911 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
52545825 ATGATTAGGG
* *
52545835 TTAGTGTTTTTAGGTTTAG-GG
1 TTAGGGTTTTTAGGTTTAGTGT
*
52545856 TTATGGTTTTTAGGTTTAGTGT
1 TTAGGGTTTTTAGGTTTAGTGT
**
52545878 TTAGGGTTTTTAATTTTAAGT-T
1 TTAGGGTTTTTAGGTTT-AGTGT
*
52545900 TTAGGATTTTTA
1 TTAGGGTTTTTA
52545912 ATTTTTAGGG
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
21 17 0.36
22 27 0.57
23 3 0.06
ACGTcount: A:0.18, C:0.00, G:0.25, T:0.57
Consensus pattern (22 bp):
TTAGGGTTTTTAGGTTTAGTGT
Found at i:52545954 original size:14 final size:14
Alignment explanation
Indices: 52545915--52546059 Score: 71
Period size: 14 Copynumber: 10.8 Consensus size: 14
52545905 ATTTTTAATT
* *
52545915 TTTAGGGTTTACAA
1 TTTAGGGTTTAGAG
*
52545929 TTTAGGGTTTAGTG
1 TTTAGGGTTTAGAG
52545943 TTTAGGGTTTAGAG
1 TTTAGGGTTTAGAG
52545957 TTT-GGGTTTTTA-AG
1 TTTAGGG--TTTAGAG
*
52545971 TTAAGGG-TTACGA-
1 TTTAGGGTTTA-GAG
*
52545984 TTTATGGTTTA-AGG
1 TTTAGGGTTTAGA-G
52545998 TTTA-GGTTT----
1 TTTAGGGTTTAGAG
*
52546007 TTTA-GGTTTATAG
1 TTTAGGGTTTAGAG
*
52546020 TTTATGGTTTTTA-AG
1 TTTA-GG-GTTTAGAG
* *
52546035 TTTAAGGTTTAGGG
1 TTTAGGGTTTAGAG
52546049 TTTAGGGTTTA
1 TTTAGGGTTTA
52546060 AGGGTTTTAA
Statistics
Matches: 103, Mismatches: 12, Indels: 32
0.70 0.08 0.22
Matches are distributed among these distances:
9 9 0.09
12 4 0.04
13 21 0.20
14 51 0.50
15 14 0.14
16 4 0.04
ACGTcount: A:0.21, C:0.01, G:0.28, T:0.50
Consensus pattern (14 bp):
TTTAGGGTTTAGAG
Found at i:52546016 original size:22 final size:21
Alignment explanation
Indices: 52545929--52546062 Score: 82
Period size: 22 Copynumber: 6.3 Consensus size: 21
52545919 GGGTTTACAA
* *
52545929 TTTAGGGTTTA-GTGTTTAGGG
1 TTTAAGGTTTAGGTTTTTA-GG
* *
52545950 TTT-AGAGTTTGGGTTTTTAAG
1 TTTAAG-GTTTAGGTTTTTAGG
* * *
52545971 -TTAAGGGTTACG-ATTTATGG
1 TTTAAGGTTTAGGTTTTTA-GG
52545991 TTTAAGGTTTAGGTTTTTTAGG
1 TTTAAGGTTTAGG-TTTTTAGG
*
52546013 TTTATA-GTTTATGGTTTTTAAG
1 TTTA-AGGTTTA-GGTTTTTAGG
*
52546035 TTTAAGGTTTAGG-GTTTAGGG
1 TTTAAGGTTTAGGTTTTTA-GG
52546056 TTTAAGG
1 TTTAAGG
52546063 GTTTTAAGTT
Statistics
Matches: 87, Mismatches: 15, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
19 4 0.05
20 12 0.14
21 31 0.36
22 33 0.38
23 7 0.08
ACGTcount: A:0.20, C:0.01, G:0.30, T:0.49
Consensus pattern (21 bp):
TTTAAGGTTTAGGTTTTTAGG
Found at i:52546065 original size:8 final size:7
Alignment explanation
Indices: 52545915--52546066 Score: 53
Period size: 7 Copynumber: 21.4 Consensus size: 7
52545905 ATTTTTAATT
52545915 TTTAGGG
1 TTTAGGG
***
52545922 TTTACAA
1 TTTAGGG
52545929 TTTAGGG
1 TTTAGGG
*
52545936 TTTAGTG
1 TTTAGGG
52545943 TTTAGGG
1 TTTAGGG
*
52545950 TTTAGAG
1 TTTAGGG
52545957 TTT-GGG
1 TTTAGGG
*
52545963 TTTTTA-AG
1 --TTTAGGG
*
52545971 TTAAGGG
1 TTTAGGG
* *
52545978 -TTACGA
1 TTTAGGG
*
52545984 TTTATGG
1 TTTAGGG
*
52545991 TTTAAGG
1 TTTAGGG
*
52545998 TTTAGGTTT
1 TTTAGG--G
52546007 TTTA-GG
1 TTTAGGG
**
52546013 TTTATAG
1 TTTAGGG
*
52546020 TTTATGGTT
1 TTTA-GG-G
*
52546029 TTTA-AG
1 TTTAGGG
*
52546035 TTTAAGG
1 TTTAGGG
52546042 TTTAGGG
1 TTTAGGG
52546049 TTTAGGG
1 TTTAGGG
52546056 TTTAAGGG
1 TTT-AGGG
52546064 TTT
1 TTT
52546067 TAAGTTAAGG
Statistics
Matches: 103, Mismatches: 30, Indels: 23
0.66 0.19 0.15
Matches are distributed among these distances:
6 16 0.16
7 67 0.65
8 12 0.12
9 8 0.08
ACGTcount: A:0.20, C:0.01, G:0.29, T:0.49
Consensus pattern (7 bp):
TTTAGGG
Found at i:52546105 original size:33 final size:32
Alignment explanation
Indices: 52546025--52546342 Score: 193
Period size: 33 Copynumber: 9.6 Consensus size: 32
52546015 TATAGTTTAT
* *
52546025 GGTTTTTAAGTTTAAGGTTTAGGGTTTAGGGTTTAA
1 GGTTTTTAAG-TTAAGGGTTA-GGATTAGGG-TT-A
* *
52546061 GGGTTTTAAGTTAAGGGTTAAGATTAGGGTTA
1 GGTTTTTAAGTTAAGGGTTAGGATTAGGGTTA
*
52546093 GGATTTTTAAGTTAAGGGTTAGAATTAGGGTTTA
1 GG-TTTTTAAGTTAAGGGTTAGGATTAGGG-TTA
* * ** * *
52546127 GG-GTTTATGTT---TTTTAGGTTTAGGGTTTT
1 GGTTTTTAAGTTAAGGGTTAGGATTAGGG-TTA
* * *
52546156 TGTTTTTAAGTTTAGGGTTTA-GATTTTTAGGTTTTA
1 GGTTTTTAAGTTAAGGG-TTAGGA---TTAGG-GTTA
*
52546192 GAGTTTTTATA-TTAAGAGTTAGGATTAGGGTTA
1 G-GTTTTTA-AGTTAAGGGTTAGGATTAGGGTTA
* * *
52546225 GGGTTTTTAAGTTAAGTGTTAGGGTTAAGGTTA
1 -GGTTTTTAAGTTAAGGGTTAGGATTAGGGTTA
* *
52546258 GGGTTTTTTATGTTAAGGGTTGGGATTA-GGTTA
1 -GG-TTTTTAAGTTAAGGGTTAGGATTAGGGTTA
* * * *
52546291 GGGTTTTAGGTTATGGGTTATGATTAGGGTTA
1 GGTTTTTAAGTTAAGGGTTAGGATTAGGGTTA
52546323 GAGTTTTT-AGTTTAAGGGTT
1 G-GTTTTTAAG-TTAAGGGTT
52546343 TATGGTTTGT
Statistics
Matches: 221, Mismatches: 41, Indels: 43
0.72 0.13 0.14
Matches are distributed among these distances:
29 14 0.06
30 7 0.03
31 19 0.09
32 20 0.09
33 77 0.35
34 41 0.19
35 9 0.04
36 19 0.09
37 14 0.06
38 1 0.00
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (32 bp):
GGTTTTTAAGTTAAGGGTTAGGATTAGGGTTA
Found at i:52546145 original size:132 final size:132
Alignment explanation
Indices: 52545963--52546263 Score: 367
Period size: 132 Copynumber: 2.3 Consensus size: 132
52545953 AGAGTTTGGG
* * * *
52545963 TTTTTAAGTTAAGGGTTACGATTTATGGTTTAAGGTTTAGGTTTTTTAGGTTTATAGTTTATGGT
1 TTTTTAAGTTAAGGGTTA-GAATTAAGGTTTAGGGTTTAGGTTTTTTAGGTTTAGAGTTT-TGGT
*
52546028 TTTTAAGTTTAAGGTTTAG-GGTTTAGGGTTTAAG-GGTTTTA-AGTTAAGGGTTAAGATTAGGG
64 TTTTAAGTTTAAGGTTTAGAGGTTTA-GGTTTAAGAGGTTTTATA-TTAAGAGTTAAGATTAGGG
52546090 TTAGGA
127 TTAGGA
* * * *
52546096 TTTTTAAGTTAAGGGTTAGAATTAGGGTTTAGGGTTTATGTTTTTTAGGTTTAGGGTTTTTGTTT
1 TTTTTAAGTTAAGGGTTAGAATTAAGGTTTAGGGTTTAGGTTTTTTAGGTTTAGAGTTTTGGTTT
* ** * * *
52546161 TTAAGTTTAGGGTTTAGATTTTTAGGTTTTAGAGTTTTTATATTAAGAGTTAGGATTAGGGTTAG
66 TTAAGTTTAAGGTTTAGAGGTTTAGGTTTAAGAGGTTTTATATTAAGAGTTAAGATTAGGGTTAG
*
52546226 GG
131 GA
* **
52546228 TTTTTAAGTTAAGTGTTAGGGTTAAGG-TTAGGGTTT
1 TTTTTAAGTTAAGGGTTAGAATTAAGGTTTAGGGTTT
52546264 TTTATGTTAA
Statistics
Matches: 146, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
131 37 0.25
132 90 0.62
133 19 0.13
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (132 bp):
TTTTTAAGTTAAGGGTTAGAATTAAGGTTTAGGGTTTAGGTTTTTTAGGTTTAGAGTTTTGGTTT
TTAAGTTTAAGGTTTAGAGGTTTAGGTTTAAGAGGTTTTATATTAAGAGTTAAGATTAGGGTTAG
GA
Found at i:52546148 original size:22 final size:21
Alignment explanation
Indices: 52546121--52546189 Score: 95
Period size: 21 Copynumber: 3.2 Consensus size: 21
52546111 TTAGAATTAG
52546121 GGTTTAGGGTTTATGTTTTTTA
1 GGTTTAGGGTTTATG-TTTTTA
*
52546143 GGTTTAGGGTTTTTGTTTTTA
1 GGTTTAGGGTTTATGTTTTTA
*
52546164 AGTTTAGGGTTTA-GATTTTTA
1 GGTTTAGGGTTTATG-TTTTTA
52546185 GGTTT
1 GGTTT
52546190 TAGAGTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
20 1 0.02
21 27 0.64
22 14 0.33
ACGTcount: A:0.14, C:0.00, G:0.28, T:0.58
Consensus pattern (21 bp):
GGTTTAGGGTTTATGTTTTTA
Found at i:52546184 original size:15 final size:16
Alignment explanation
Indices: 52546166--52546200 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
52546156 TGTTTTTAAG
52546166 TTTAGGGTTTAGA-TT
1 TTTAGGGTTTAGAGTT
*
52546181 TTTAGGTTTTAGAGTT
1 TTTAGGGTTTAGAGTT
52546197 TTTA
1 TTTA
52546201 TATTAAGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (16 bp):
TTTAGGGTTTAGAGTT
Found at i:52546197 original size:22 final size:20
Alignment explanation
Indices: 52545434--52546189 Score: 91
Period size: 21 Copynumber: 36.3 Consensus size: 20
52545424 TTGGGGTTTA
52545434 AGGTTTAGGGTTTATGTTTTTT
1 AGGTTTAGGGTTTA-G-TTTTT
*
52545456 AGGTTTAGGGTTTTAGGTTTT
1 AGGTTTAGGG-TTTAGTTTTT
* * **
52545477 AGGGTTTTTA-AGTTAAG-GGTT
1 A-GG--TTTAGGGTTTAGTTTTT
* *
52545498 AGGATTAGGGTTATGGTTTTT
1 AGGTTTAGGGTT-TAGTTTTT
* * *
52545519 AAGTTAAGGGTTATGGTTTTT
1 AGGTTTAGGGTT-TAGTTTTT
*
52545540 AGGTTTAGGGTTTTTA-ATTTT
1 AGGTTTAGGG--TTTAGTTTTT
* **
52545561 ATGGTTTAGGGTTTTTAATGCTT
1 A-GGTTTAGGG--TTTAGTTTTT
*
52545584 AGTGTTTAAGGTTTAAGGTTTTT
1 AG-GTTTAGGGTTT-A-GTTTTT
* **
52545607 AGGTTTAGGGTTAAGAGTTT
1 AGGTTTAGGGTTTAGTTTTT
52545627 AGAGTTTAGGGTTTAAGGTTTTT
1 AG-GTTTAGGGTTT-A-GTTTTT
*
52545650 AAG-TTAGGGTTTA------
1 AGGTTTAGGGTTTAGTTTTT
52545663 AGGTTTAGAGG-TTATGTTTTTT
1 AGGTTTAG-GGTTTA-G-TTTTT
* *
52545685 AAGTTTAGGGTTTAAGGTTTTA
1 AGGTTTAGGGTTT-A-GTTTTT
* * *
52545707 AAGTTTAAGAGTTTA-TGATTT
1 AGGTTT-AGGGTTTAGT-TTTT
* *
52545728 AGGGTTTATGATTTAGTGTTTT
1 A-GGTTTAGGGTTTAGT-TTTT
*** **
52545750 AGGGTTTAAATTTTAGAGTTT
1 A-GGTTTAGGGTTTAGTTTTT
**
52545771 AGGGTTTAGGGTTTTTAGTTAAT
1 A-GGTTTAGGG--TTTAGTTTTT
*
52545794 -GG-TTAGGGTTTAGGGTTTT
1 AGGTTTAGGGTTTA-GTTTTT
* * **
52545813 AAGTTAAGGG-TTA-TGATT
1 AGGTTTAGGGTTTAGTTTTT
*
52545831 AGGGTTA--G--T-GTTTTT
1 AGGTTTAGGGTTTAGTTTTT
*
52545846 AGGTTTAGGGTTATGGTTTTT
1 AGGTTTAGGGTT-TAGTTTTT
*
52545867 AGGTTTAGTGTTTAGGGTTTTT
1 AGGTTTAGGGTTTA--GTTTTT
** * *
52545889 AATTTTAAGTTTTAGGATTTTT
1 AGGTTTAGGGTTTA-G-TTTTT
** *
52545911 AATTTTTAGGGTTTA-----C
1 -AGGTTTAGGGTTTAGTTTTT
* *
52545927 A-ATTTAGGGTTTAGTGTTT
1 AGGTTTAGGGTTTAGTTTTT
* *
52545946 AGGGTTTAGAGTTTGGGTTTTT
1 A-GGTTTAGGGTTT-AGTTTTT
* * *
52545968 AAGTTAAGGG-TTACG-ATTT
1 AGGTTTAGGGTTTA-GTTTTT
*
52545987 ATGGTTTAAGGTTTAGGTTTTTT
1 A-GGTTTAGGGTTTA-G-TTTTT
**
52546010 AGGTTTATAGTTTATGGTTTTT
1 AGGTTTAGGGTTTA--GTTTTT
* * **
52546032 AAGTTTAAGGTTTAGGGTTT
1 AGGTTTAGGGTTTAGTTTTT
*
52546052 AGGGTTTAAGGGTTTTAAGTTAAGGGTT
1 A-GGTTT-AGGG-TTT-AGTT----TTT
* *
52546080 AAGATTAGGG-TTAGGATTTTT
1 AGGTTTAGGGTTTA-G-TTTTT
* * **
52546101 AAGTTAAGGG-TTAG-AATT
1 AGGTTTAGGGTTTAGTTTTT
52546119 AGGGTTTAGGGTTTATGTTTTTT
1 A-GGTTTAGGGTTTA-G-TTTTT
*
52546142 AGGTTTAGGGTTTTTGTTTTT
1 AGGTTTAGGG-TTTAGTTTTT
*
52546163 AAGTTTAGGGTTTAGATTTTT
1 AGGTTTAGGGTTTAG-TTTTT
52546184 AGGTTT
1 AGGTTT
52546190 TAGAGTTTTT
Statistics
Matches: 529, Mismatches: 125, Indels: 161
0.65 0.15 0.20
Matches are distributed among these distances:
13 2 0.00
14 18 0.03
15 13 0.02
16 1 0.00
17 1 0.00
18 16 0.03
19 18 0.03
20 45 0.09
21 172 0.33
22 154 0.29
23 68 0.13
24 9 0.02
25 2 0.00
26 4 0.01
27 3 0.01
28 3 0.01
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (20 bp):
AGGTTTAGGGTTTAGTTTTT
Found at i:52546400 original size:8 final size:7
Alignment explanation
Indices: 52546371--52546408 Score: 58
Period size: 7 Copynumber: 5.1 Consensus size: 7
52546361 TTATGCATTT
52546371 AATTATA
1 AATTATA
52546378 AATTATA
1 AATTATA
52546385 AATTATA
1 AATTATA
52546392 AATTTATA
1 AA-TTATA
52546400 AATTTATA
1 AA-TTATA
52546408 A
1 A
52546409 TTTTTTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
AATTATA
Found at i:52546410 original size:15 final size:14
Alignment explanation
Indices: 52546371--52546411 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
52546361 TTATGCATTT
*
52546371 AATTATAAATTATA
1 AATTATAATTTATA
52546385 AATTATAAATTTATA
1 AATTAT-AATTTATA
52546400 AATTTATAATTT
1 AA-TTATAATTT
52546412 TTTAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 6 0.25
15 14 0.58
16 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AATTATAATTTATA
Found at i:52546919 original size:18 final size:18
Alignment explanation
Indices: 52546896--52546935 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
52546886 GACTCGGAAA
* *
52546896 AGGATACATATAAGGGTT
1 AGGATACATAAAAGGGCT
*
52546914 AGGATACCTAAAAGGGCT
1 AGGATACATAAAAGGGCT
52546932 AGGA
1 AGGA
52546936 AACGTACCTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.10, G:0.30, T:0.20
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:52547816 original size:20 final size:20
Alignment explanation
Indices: 52547779--52547816 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
52547769 TTTATTTTTA
*
52547779 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
52547799 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
52547817 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:52548855 original size:11 final size:12
Alignment explanation
Indices: 52548839--52548882 Score: 58
Period size: 11 Copynumber: 3.8 Consensus size: 12
52548829 ATTAAATATG
52548839 AATTTGAGA-GA
1 AATTTGAGAGGA
52548850 AATTTG-GAAGGA
1 AATTTGAG-AGGA
52548862 AA-TTGAGAGGA
1 AATTTGAGAGGA
52548873 AATTTGAGAG
1 AATTTGAGAG
52548883 AGGATTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 16 0.55
12 12 0.41
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (12 bp):
AATTTGAGAGGA
Found at i:52551250 original size:16 final size:16
Alignment explanation
Indices: 52551231--52551272 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
52551221 AGGATCGAAA
*
52551231 TATAATTTTATTATTG
1 TATAATTTTATTATTC
52551247 TAT-ATGTTTATTATTC
1 TATAAT-TTTATTATTC
*
52551263 TAGAATTTTA
1 TATAATTTTA
52551273 AAAGATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 2 0.09
16 18 0.82
17 2 0.09
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (16 bp):
TATAATTTTATTATTC
Found at i:52552546 original size:32 final size:33
Alignment explanation
Indices: 52552486--52552553 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 33
52552476 AATTTTCAAT
52552486 AAATAAAAAATATATAAAATTATTAAAT-ATTA
1 AAATAAAAAATATATAAAATTATTAAATAATTA
* * *
52552518 AAATAAAAAATGTAT-AATTTTTTAAAATAATTA
1 AAATAAAAAATATATAAAATTATT-AAATAATTA
52552551 AAA
1 AAA
52552554 ATAATATAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 6 0.19
32 18 0.58
33 7 0.23
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (33 bp):
AAATAAAAAATATATAAAATTATTAAATAATTA
Found at i:52572909 original size:10 final size:10
Alignment explanation
Indices: 52572894--52572921 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
52572884 TTTTAAAGAA
52572894 ATTTTAACCC
1 ATTTTAACCC
52572904 ATTTTAACCC
1 ATTTTAACCC
52572914 ATTTTAAC
1 ATTTTAAC
52572922 TTCCAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.25, G:0.00, T:0.43
Consensus pattern (10 bp):
ATTTTAACCC
Found at i:52574666 original size:32 final size:32
Alignment explanation
Indices: 52574626--52574686 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
52574616 TCTATCAAAA
*
52574626 AATTTTCTTCTCTCATTTTATCCCAACATCCT
1 AATTTTCTTCTCCCATTTTATCCCAACATCCT
*
52574658 AATTTTCTTCTCCCATTTTCTCCCAACAT
1 AATTTTCTTCTCCCATTTTATCCCAACAT
52574687 ATTTTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.21, C:0.33, G:0.00, T:0.46
Consensus pattern (32 bp):
AATTTTCTTCTCCCATTTTATCCCAACATCCT
Found at i:52577583 original size:49 final size:49
Alignment explanation
Indices: 52577454--52577585 Score: 137
Period size: 48 Copynumber: 2.7 Consensus size: 49
52577444 TCAACAGGCA
* *
52577454 TCCATCAATTCATGCAGAGATTTGTTTTATCAT-TGCACTCATCAAGCT
1 TCCATCAACTCATGCAGAGAATTGTTTTATCATCTGCACTCATCAAGCT
* * *
52577502 TCCATCAACTCATGCAGAGAAAAT-TTTAATCATCT-CAAC-CATCAGGCT
1 TCCATCAACTCATGCAGAG-AATTGTTTTATCATCTGC-ACTCATCAAGCT
* * *
52577550 TCCTTTCAACTCATGTAGAGACTTGTTTTATCATCT
1 TCC-ATCAACTCATGCAGAGAATTGTTTTATCATCT
52577586 TAGTCTTCCT
Statistics
Matches: 69, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
48 40 0.58
49 29 0.42
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (49 bp):
TCCATCAACTCATGCAGAGAATTGTTTTATCATCTGCACTCATCAAGCT
Found at i:52584638 original size:12 final size:14
Alignment explanation
Indices: 52584622--52584654 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
52584612 CAATTTTTTT
52584622 TATATTTTT-TAAA
1 TATATTTTTATAAA
52584635 -ATATTTTTATAAA
1 TATATTTTTATAAA
52584648 TATATTT
1 TATATTT
52584655 AAAAATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.44
13 4 0.22
14 6 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TATATTTTTATAAA
Found at i:52587790 original size:15 final size:16
Alignment explanation
Indices: 52587770--52587799 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
52587760 ATGTCTTGTG
52587770 TTCTTTTT-TTTTTCT
1 TTCTTTTTCTTTTTCT
52587785 TTCTTTTTCTTTTTC
1 TTCTTTTTCTTTTTC
52587800 CTTTTTTAAG
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:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTCTTTTTCTTTTTCT
Found at i:52592404 original size:16 final size:16
Alignment explanation
Indices: 52592383--52592413 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52592373 ATCATTGTGT
*
52592383 TATATATTTTATTTAG
1 TATATATATTATTTAG
52592399 TATATATATTATTTA
1 TATATATATTATTTA
52592414 TACTAGATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
TATATATATTATTTAG
Found at i:52592674 original size:2 final size:2
Alignment explanation
Indices: 52592667--52592697 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
52592657 TAGTTCAGGA
52592667 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
52592698 AATAGGAGTT
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:52593319 original size:21 final size:21
Alignment explanation
Indices: 52593290--52593346 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 21
52593280 TCAAACTAAG
* *
52593290 GTTTGAAATCAAGAGAACAAT
1 GTTTGAAATCAAAAGAACAAA
*
52593311 GTTTTAAATATCAAAAGAACAAA
1 G-TTTGAA-ATCAAAAGAACAAA
52593334 GTTTGAAATCAAA
1 GTTTGAAATCAAA
52593347 CTTTGTGGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 7 0.23
22 10 0.33
23 13 0.43
ACGTcount: A:0.51, C:0.09, G:0.14, T:0.26
Consensus pattern (21 bp):
GTTTGAAATCAAAAGAACAAA
Found at i:52595028 original size:30 final size:30
Alignment explanation
Indices: 52594975--52595033 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
52594965 TTTACTACTA
*
52594975 AACTTTGAATTTTATTAAAAATTT-CCACC
1 AACTTTGAATTTAATTAAAAATTTACCACC
52595004 AACTTTGATTATTTAATT-AAAATTTACCAC
1 AACTTTGA--ATTTAATTAAAAATTTACCAC
52595034 TCAGTATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 8 0.31
30 7 0.27
31 11 0.42
ACGTcount: A:0.39, C:0.15, G:0.03, T:0.42
Consensus pattern (30 bp):
AACTTTGAATTTAATTAAAAATTTACCACC
Found at i:52596592 original size:16 final size:18
Alignment explanation
Indices: 52596562--52596594 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52596552 ATCGAACTTA
52596562 TAAATATATTGTATTTTT
1 TAAATATATTGTATTTTT
52596580 TAAATAT-TT-TATTTT
1 TAAATATATTGTATTTT
52596595 ATTTTATTTT
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:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TAAATATATTGTATTTTT
Found at i:52597669 original size:29 final size:29
Alignment explanation
Indices: 52597620--52597678 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
52597610 CACGGCCGTG
* * *
52597620 TGTCCCCTATTTTTTAGATTTTATAATTT
1 TGTCCCCTACTTTATAAATTTTATAATTT
*
52597649 TGTCCCCTACTTTATAAATTTTATAGTTT
1 TGTCCCCTACTTTATAAATTTTATAATTT
52597678 T
1 T
52597679 ATCCAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.15, G:0.07, T:0.56
Consensus pattern (29 bp):
TGTCCCCTACTTTATAAATTTTATAATTT
Found at i:52597980 original size:34 final size:33
Alignment explanation
Indices: 52597936--52598048 Score: 111
Period size: 34 Copynumber: 3.3 Consensus size: 33
52597926 GGCTACCGAG
*
52597936 TTGATCTGTTATAAGCATATTATTTGCTACTGTA
1 TTGATTTGTTATAAGCATATTA-TTGCTACTGTA
* * *
52597970 TTGAATTGTTATAAGCATATTGATTGTTACCGTA
1 TTGATTTGTTATAAGCATATT-ATTGCTACTGTA
* * *
52598004 TTG-TTCTGTTAAAAGCATAATTACATGCTATTGTA
1 TTGATT-TGTTATAAGCAT-ATTA-TTGCTACTGTA
52598039 TTGATTTGTT
1 TTGATTTGTT
52598049 TGAGCTTGCC
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
33 1 0.02
34 43 0.67
35 18 0.28
36 2 0.03
ACGTcount: A:0.27, C:0.10, G:0.16, T:0.47
Consensus pattern (33 bp):
TTGATTTGTTATAAGCATATTATTGCTACTGTA
Found at i:52602676 original size:15 final size:15
Alignment explanation
Indices: 52602652--52602702 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
52602642 TATCATTACC
52602652 ATTATTTATAATATT
1 ATTATTTATAATATT
* *
52602667 ATTATCTATATTATT
1 ATTATTTATAATATT
* * *
52602682 TTTATTTATCATACT
1 ATTATTTATAATATT
52602697 ATTATT
1 ATTATT
52602703 ATATGATAGT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTATTTATAATATT
Found at i:52602704 original size:18 final size:19
Alignment explanation
Indices: 52602663--52602704 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
52602653 TTATTTATAA
*
52602663 TATTA-TTATCTATATTAT
1 TATTATTTATCTATACTAT
*
52602681 TTTTATTTATC-ATACTAT
1 TATTATTTATCTATACTAT
52602699 TATTAT
1 TATTAT
52602705 ATGATAGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTATTTATCTATACTAT
Found at i:52605983 original size:3 final size:3
Alignment explanation
Indices: 52605975--52606009 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
52605965 TCATTTTGTT
* *
52605975 TAA TAA TAA TAA TAA TAA CAA TAA TAA CAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
52606010 GGCTACCACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:52605989 original size:9 final size:9
Alignment explanation
Indices: 52605976--52606009 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
52605966 CATTTTGTTT
*
52605976 AATAATAAT
1 AATAATAAC
52605985 AATAATAAC
1 AATAATAAC
52605994 AATAATAAC
1 AATAATAAC
52606003 AATAATA
1 AATAATA
52606010 GGCTACCACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (9 bp):
AATAATAAC
Found at i:52607023 original size:16 final size:16
Alignment explanation
Indices: 52607002--52607071 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
52606992 TTTGGTTCGC
*
52607002 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
52607018 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
52607034 TGTAATGGATTAGAGG
1 TGTAATGGATTAGAGG
* *
52607050 TGTAATAGAATAGAGG
1 TGTAATGGATTAGAGG
52607066 TGTAAT
1 TGTAAT
52607072 AGCAAATCAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:52607106 original size:45 final size:41
Alignment explanation
Indices: 52607050--52607159 Score: 116
Period size: 45 Copynumber: 2.6 Consensus size: 41
52607040 GGATTAGAGG
*
52607050 TGTAATAGAATAGAGGTGTAATAGCAAATCAAATGTTTGGTT
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAAATGTTTGG-T
* * ***
52607092 GAATGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGT
1 ---TGTAATGGAATAGAGGTGTAATAGCAAATCAAATGTTTGGT
52607135 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
52607160 TAATGGAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
39 20 0.36
40 2 0.04
43 1 0.02
44 11 0.20
45 22 0.39
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (41 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAAATGTTTGGT
Found at i:52611117 original size:9 final size:9
Alignment explanation
Indices: 52611105--52611187 Score: 55
Period size: 9 Copynumber: 8.9 Consensus size: 9
52611095 AAAATTAGAA
52611105 AAAAATTAT
1 AAAAATTAT
52611114 AAAAA-T-T
1 AAAAATTAT
*
52611121 AAAAATTAA
1 AAAAATTAT
*
52611130 AAAAACTATAG
1 AAAAA-T-TAT
52611141 AAAAATTATT
1 AAAAATTA-T
*
52611151 AAATTATTAAT
1 AAA-AATT-AT
52611162 AAAAA-TAT
1 AAAAATTAT
*
52611170 AAAATTTATT
1 AAAAATTA-T
52611180 AAAAATTA
1 AAAAATTA
52611188 GAATTTTTTA
Statistics
Matches: 58, Mismatches: 7, Indels: 17
0.71 0.09 0.21
Matches are distributed among these distances:
7 6 0.10
8 8 0.14
9 15 0.26
10 14 0.24
11 14 0.24
12 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:52611165 original size:21 final size:21
Alignment explanation
Indices: 52611141--52611181 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
52611131 AAAACTATAG
*
52611141 AAAAATTATTAAA-TTATTAAT
1 AAAAA-TATAAAATTTATTAAT
52611162 AAAAATATAAAATTTATTAA
1 AAAAATATAAAATTTATTAA
52611182 AAATTAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAAATATAAAATTTATTAAT
Found at i:52611537 original size:19 final size:20
Alignment explanation
Indices: 52611515--52611564 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
52611505 TTTTAACAAT
52611515 TTTTTAATATTT-TTTACT-A
1 TTTTTAATATTTATTT-CTAA
52611534 TTTTT-ATATTTATTTCTAA
1 TTTTTAATATTTATTTCTAA
52611553 TTTTTAATATTT
1 TTTTTAATATTT
52611565 GAAATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.29
19 14 0.50
20 6 0.21
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTTAATATTTATTTCTAA
Found at i:52611557 original size:20 final size:20
Alignment explanation
Indices: 52611512--52611564 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
52611502 AAATTTTAAC
52611512 AATTTTTTAATATTTTTTACT
1 AATTTTTT-ATATTTTTTACT
52611533 -A-TTTTTATATTTATTT-CT
1 AATTTTTTATATTT-TTTACT
*
52611551 AATTTTTAATATTT
1 AATTTTTTATATTT
52611565 GAAATTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 8 0.29
19 9 0.32
20 11 0.39
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (20 bp):
AATTTTTTATATTTTTTACT
Found at i:52612003 original size:91 final size:92
Alignment explanation
Indices: 52611647--52612105 Score: 685
Period size: 93 Copynumber: 5.0 Consensus size: 92
52611637 TTTTAATAAA
* *
52611647 AGTAGGGGCTTAATTGCTTTTTTTTTTGAAAAAGTTTGAGGGCCTTTTTGATGGATTTTGAAAGT
1 AGTAGGGGCTTAATTGC--TTTTTTTTGAAAAGGTTTGAGGGCCTTTTTGATGCATTTTGAAAGT
* *
52611712 TCAAGTACCCAATTAAGTGCAAAAAAAAAG
64 TCAAGTACCCAATTGAGTAC-AAAAAAAAG
*
52611742 AGTAGGGGCTTAATTACTTTTTTTTGAAAAGGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTTC
1 AGTAGGGGCTTAATTGCTTTTTTTTGAAAAGGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTTC
* **
52611807 AAGTACCGAATTGAGTACAAATCAAAG
66 AAGTACCCAATTGAGTACAAAAAAAAG
*
52611834 AGTAGGGGCTTAATTGCTTTTTTTTTGAAAAGGTTTGAGGGCATTTTTGATGCATTTTGAAAGTT
1 AGTAGGGGCTTAATTGC-TTTTTTTTGAAAAGGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTT
* *
52611899 CAAGTACCAAATTGAGTACAAATAAAAG
65 CAAGTACCCAATTGAGTACAAAAAAAAG
*
52611927 AGTAGGGGCTTAATTGC-TTTTTTTGAAAAGGTTTGAGGGCATTTTTGATGCATTTTGAAAGTTC
1 AGTAGGGGCTTAATTGCTTTTTTTTGAAAAGGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTTC
*
52611991 AAGTACCGAATTGAGTAC--AAAAAA-
66 AAGTACCCAATTGAGTACAAAAAAAAG
* *
52612015 AGTAGGGGCTTAATTACTTTTTTTTGAAAAGGTTTGAGGGCCTTTTTGATGTATTTTGAAAGGTT
1 AGTAGGGGCTTAATTGCTTTTTTTTGAAAAGGTTTGAGGGCCTTTTTGATGCATTTTGAAA-GTT
* *
52612080 -AAGTACCCAAATGAGTGCAAAAAAAA
65 CAAGTACCCAATTGAGTACAAAAAAAA
52612106 AAAGAAAAAA
Statistics
Matches: 339, Mismatches: 20, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
88 16 0.05
89 61 0.18
90 3 0.01
91 70 0.21
92 23 0.07
93 150 0.44
95 16 0.05
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.36
Consensus pattern (92 bp):
AGTAGGGGCTTAATTGCTTTTTTTTGAAAAGGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTTC
AAGTACCCAATTGAGTACAAAAAAAAG
Found at i:52624385 original size:30 final size:30
Alignment explanation
Indices: 52624345--52624481 Score: 161
Period size: 30 Copynumber: 4.6 Consensus size: 30
52624335 AAAAATAAAA
* **
52624345 AAATTGCATTTTGACCCCTGTACTTTCT-T
1 AAATTACATTTTGACCCCTAAACTTTCTCT
**
52624374 GAAATTACATTTCAACCCCTAAACTTT-TCT
1 -AAATTACATTTTGACCCCTAAACTTTCTCT
*
52624404 AAATTACATTTTGACCCCTAAACTTTCTCA
1 AAATTACATTTTGACCCCTAAACTTTCTCT
**
52624434 AAATTACATTTCAACCCCTAAACTTTCTCT
1 AAATTACATTTTGACCCCTAAACTTTCTCT
* *
52624464 AAATTACGTTTTGGCCCC
1 AAATTACATTTTGACCCC
52624482 AAAAATTTTG
Statistics
Matches: 90, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
29 25 0.28
30 65 0.72
ACGTcount: A:0.29, C:0.27, G:0.06, T:0.38
Consensus pattern (30 bp):
AAATTACATTTTGACCCCTAAACTTTCTCT
Found at i:52624438 original size:59 final size:60
Alignment explanation
Indices: 52624345--52624481 Score: 204
Period size: 59 Copynumber: 2.3 Consensus size: 60
52624335 AAAAATAAAA
* ** **
52624345 AAATTGCATTTTGACCCCTGTACTTTCTTGAAATTACATTTCAACCCCTAAACTTT-TCT
1 AAATTACATTTTGACCCCTAAACTTTCTCAAAATTACATTTCAACCCCTAAACTTTCTCT
52624404 AAATTACATTTTGACCCCTAAACTTTCTCAAAATTACATTTCAACCCCTAAACTTTCTCT
1 AAATTACATTTTGACCCCTAAACTTTCTCAAAATTACATTTCAACCCCTAAACTTTCTCT
* *
52624464 AAATTACGTTTTGGCCCC
1 AAATTACATTTTGACCCC
52624482 AAAAATTTTG
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
59 51 0.73
60 19 0.27
ACGTcount: A:0.29, C:0.27, G:0.06, T:0.38
Consensus pattern (60 bp):
AAATTACATTTTGACCCCTAAACTTTCTCAAAATTACATTTCAACCCCTAAACTTTCTCT
Found at i:52624961 original size:15 final size:16
Alignment explanation
Indices: 52624943--52624975 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
52624933 CGAAGGGAAG
*
52624943 AAGGAAGAAGA-AGGA
1 AAGGAAAAAGAGAGGA
52624958 AAGGAAAAAGAGAGGA
1 AAGGAAAAAGAGAGGA
52624974 AA
1 AA
52624976 AAAGGAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (16 bp):
AAGGAAAAAGAGAGGA
Found at i:52624981 original size:24 final size:24
Alignment explanation
Indices: 52624940--52625014 Score: 82
Period size: 24 Copynumber: 3.1 Consensus size: 24
52624930 GGTCGAAGGG
52624940 AAGAAGGAAGAAGAAGGAAAGGAAA
1 AAGAAGGAAGAA-AAGGAAAGGAAA
52624965 AAGAGAGGAA-AAAAGGAAA-GAAGA
1 AAGA-AGGAAGAAAAGGAAAGGAA-A
* * *
52624989 AAGAAAGAAGAAAGGGAAAGAAAA
1 AAGAAGGAAGAAAAGGAAAGGAAA
52625013 AA
1 AA
52625015 AAATTACAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
23 7 0.16
24 23 0.53
25 8 0.19
26 5 0.12
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (24 bp):
AAGAAGGAAGAAAAGGAAAGGAAA
Found at i:52624994 original size:11 final size:11
Alignment explanation
Indices: 52624947--52625002 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
52624937 GGGAAGAAGG
*
52624947 AAGAAGAAGGA
1 AAGAAGAAAGA
52624958 AAGGAA-AAAGA
1 AA-GAAGAAAGA
* *
52624969 GAGGAAAAAAGGA
1 -AAGAAGAAA-GA
52624982 AAGAAGAAAGA
1 AAGAAGAAAGA
52624993 AAGAAGAAAG
1 AAGAAGAAAG
52625003 GGAAAGAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 21 0.57
12 14 0.38
13 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (11 bp):
AAGAAGAAAGA
Found at i:52631615 original size:9 final size:9
Alignment explanation
Indices: 52631602--52631672 Score: 56
Period size: 9 Copynumber: 7.8 Consensus size: 9
52631592 AAAACAAACA
52631602 AAAAAAATAG
1 AAAAAAA-AG
*
52631612 AAAAAAAAC
1 AAAAAAAAG
*
52631621 AAAAAACAG
1 AAAAAAAAG
52631630 AAAAAAACAG
1 AAAAAAA-AG
*
52631640 ACAAAACAA-
1 A-AAAAAAAG
*
52631649 AAAACAAA-
1 AAAAAAAAG
*
52631657 AAAAAAGAG
1 AAAAAAAAG
52631666 AAAAAAA
1 AAAAAAA
52631673 TCAAGATGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
8 11 0.23
9 21 0.44
10 11 0.23
11 5 0.10
ACGTcount: A:0.83, C:0.08, G:0.07, T:0.01
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:52631615 original size:10 final size:10
Alignment explanation
Indices: 52631592--52631672 Score: 59
Period size: 10 Copynumber: 8.7 Consensus size: 10
52631582 ATGCTTAAAA
52631592 AAAACAAACA-
1 AAAA-AAACAG
*
52631602 AAAAAAATAG
1 AAAAAAACAG
52631612 AAAAAAA-A-
1 AAAAAAACAG
*
52631620 CAAAAAACAG
1 AAAAAAACAG
52631630 AAAAAAACAG
1 AAAAAAACAG
*
52631640 -ACAAAAC--
1 AAAAAAACAG
*
52631647 -AAAAAACAA
1 AAAAAAACAG
*
52631656 AAAAAAAGAG
1 AAAAAAACAG
52631666 AAAAAAA
1 AAAAAAA
52631673 TCAAGATGAA
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
7 6 0.10
8 6 0.10
9 12 0.21
10 34 0.59
ACGTcount: A:0.83, C:0.10, G:0.06, T:0.01
Consensus pattern (10 bp):
AAAAAAACAG
Found at i:52631633 original size:26 final size:25
Alignment explanation
Indices: 52631588--52631672 Score: 91
Period size: 26 Copynumber: 3.3 Consensus size: 25
52631578 TATTATGCTT
* *
52631588 AAAAAAAACAAACAA-AAAAAATAG
1 AAAAAAAACAAAAAACAAAAAAAAG
*
52631612 AAAAAAAACAAAAAACAGAAAAAAAC
1 AAAAAAAACAAAAAACA-AAAAAAAG
* *
52631638 AGACAAAACAAAAAACAAAAAAAAAG
1 AAAAAAAACAAAAAAC-AAAAAAAAG
52631664 AGAAAAAAA
1 A-AAAAAAA
52631673 TCAAGATGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
24 14 0.29
25 1 0.02
26 28 0.57
27 6 0.12
ACGTcount: A:0.84, C:0.09, G:0.06, T:0.01
Consensus pattern (25 bp):
AAAAAAAACAAAAAACAAAAAAAAG
Found at i:52632872 original size:79 final size:78
Alignment explanation
Indices: 52632597--52633337 Score: 1247
Period size: 76 Copynumber: 9.6 Consensus size: 78
52632587 NNNNNNNNAA
*
52632597 TCTGTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
1 TCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
52632662 ATTTTTTTTAATT
66 ATTTTTTTTAATT
*
52632675 TCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGATGAGGT
1 TCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
*
52632740 A--TTTTTAAATT
66 ATTTTTTTTAATT
*
52632751 TCTACTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
1 TCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
52632816 ATTTTTTTTTAATT
66 A-TTTTTTTTAATT
52632830 TCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
1 TCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
52632895 A--TTTTTTAATT
66 ATTTTTTTTAATT
*
52632906 TCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTTGGGTCACGCTGAGGT
1 TCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
*
52632971 A--TTTTTAAATT
66 ATTTTTTTTAATT
* *
52632982 TCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCCGACGT
1 TCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
52633047 ATTTATTTTTAAATT
66 ATTT-TTTTT-AATT
*
52633062 TCTGCTTTTTCCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
1 TCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
52633127 ATTTTTTTTAATT
66 ATTTTTTTTAATT
52633140 TCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
1 TCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
52633205 ATTTTTTTTTAATT
66 A-TTTTTTTTAATT
*
52633219 TTTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
1 TCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
52633284 A---TTTTTAATT
66 ATTTTTTTTAATT
*
52633294 TATGTCTTTTTT---AAAATCAACTCAT-ATACAGAGGTGAGTTGAGC
1 TCTG-CTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGC
52633338 TTTGGTCACG
Statistics
Matches: 635, Mismatches: 19, Indels: 24
0.94 0.03 0.04
Matches are distributed among these distances:
72 19 0.03
73 13 0.02
75 12 0.02
76 227 0.36
78 134 0.21
79 160 0.25
80 70 0.11
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (78 bp):
TCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
ATTTTTTTTAATT
Found at i:52632883 original size:155 final size:154
Alignment explanation
Indices: 52632597--52633337 Score: 1212
Period size: 155 Copynumber: 4.8 Consensus size: 154
52632587 NNNNNNNNAA
*
52632597 TCTGTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
1 TCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
52632662 ATTTTTTTTAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
66 ATTTTTTTTAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
52632727 GTCACGATGAGGTATTTTTAAATT
131 GTCACGATGAGGTATTTTTAAATT
*
52632751 TCTACTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
1 TCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
52632816 ATTTTTTTTTAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCG
66 A-TTTTTTTTAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCG
* *
52632881 GGTCACGCTGAGGTATTTTTTAATT
130 GGTCACGATGAGGTATTTTTAAATT
*
52632906 TCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTTGGGTCACGCTGAGGT
1 TCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
*
52632971 A--TTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
66 ATTTTTTTTAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
* **
52633034 GTCACGCCGACGTATTTATTTTTAAATT
131 GTCA---CGATG-AGGTATTTTTAAATT
*
52633062 TCTGCTTTTTCCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
1 TCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
52633127 ATTTTTTTTAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
66 ATTTTTTTTAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
* *
52633192 GTCACGCTGAGGTATTTTTTTTTAATT
131 GTCACGATGAGGTA---TTTTTAAATT
*
52633219 TTTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
1 TCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
*
52633284 A---TTTTTAATTTATGTCTTTTTT---AAAATCAACTCAT-ATACAGAGGTGAGTTGAGC
66 ATTTTTTTTAATTTCTG-CTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGC
52633338 TTTGGTCACG
Statistics
Matches: 553, Mismatches: 23, Indels: 25
0.92 0.04 0.04
Matches are distributed among these distances:
151 19 0.03
152 78 0.14
154 79 0.14
155 163 0.29
156 76 0.14
157 73 0.13
158 65 0.12
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (154 bp):
TCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
ATTTTTTTTAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
GTCACGATGAGGTATTTTTAAATT
Found at i:52633570 original size:30 final size:30
Alignment explanation
Indices: 52633551--52633659 Score: 161
Period size: 29 Copynumber: 3.7 Consensus size: 30
52633541 TGACCCCTGT
52633551 ACTTTCT-TGAAATTACATTTCAACCCCTAA
1 ACTTTCTCT-AAATTACATTTCAACCCCTAA
**
52633581 ACTTT-TCTAAATTACATTTTGACCCCTAA
1 ACTTTCTCTAAATTACATTTCAACCCCTAA
52633610 ACTTTCTC-AAATTACATTTCAACCCCTAA
1 ACTTTCTCTAAATTACATTTCAACCCCTAA
*
52633639 ACTTTCTCTAAATTACGTTTC
1 ACTTTCTCTAAATTACATTTC
52633660 GGCCCCAAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
29 52 0.73
30 19 0.27
ACGTcount: A:0.31, C:0.27, G:0.03, T:0.39
Consensus pattern (30 bp):
ACTTTCTCTAAATTACATTTCAACCCCTAA
Found at i:52633649 original size:59 final size:59
Alignment explanation
Indices: 52633530--52633654 Score: 198
Period size: 59 Copynumber: 2.1 Consensus size: 59
52633520 AAAAATAAAA
* ** *
52633530 AAATTGCATTTTGACCCCTGTACTTTCTTGAAATTACATTTCAACCCCTAAACTTTTCT
1 AAATTACATTTTGACCCCTAAACTTTCTTCAAATTACATTTCAACCCCTAAACTTTTCT
52633589 AAATTACATTTTGACCCCTAAACTTTC-TCAAATTACATTTCAACCCCTAAACTTTCTCT
1 AAATTACATTTTGACCCCTAAACTTTCTTCAAATTACATTTCAACCCCTAAACTTT-TCT
52633648 AAATTAC
1 AAATTAC
52633655 GTTTCGGCCC
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
58 27 0.44
59 34 0.56
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.38
Consensus pattern (59 bp):
AAATTACATTTTGACCCCTAAACTTTCTTCAAATTACATTTCAACCCCTAAACTTTTCT
Found at i:52634138 original size:18 final size:18
Alignment explanation
Indices: 52634117--52634196 Score: 51
Period size: 18 Copynumber: 4.4 Consensus size: 18
52634107 GAGCAAGGTC
52634117 GAAGGGAAGAAGGAAGAA
1 GAAGGGAAGAAGGAAGAA
*
52634135 GAA-GG-A-AAGGAAAAA
1 GAAGGGAAGAAGGAAGAA
* *
52634150 GAGAGGAAAAAAGGAAAGAA
1 GA-AGGGAAGAAGG-AAGAA
* *
52634170 GAA-AGAAGAAAGAAAGAA
1 GAAGGGAAG-AAGGAAGAA
52634188 GAAAGGGAA
1 G-AAGGGAA
52634197 AGAAAAAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
15 10 0.22
16 2 0.04
17 3 0.07
18 12 0.26
19 10 0.22
20 9 0.20
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (18 bp):
GAAGGGAAGAAGGAAGAA
Found at i:52634144 original size:15 final size:16
Alignment explanation
Indices: 52634126--52634158 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
52634116 CGAAGGGAAG
*
52634126 AAGGAAGAAGA-AGGA
1 AAGGAAAAAGAGAGGA
52634141 AAGGAAAAAGAGAGGA
1 AAGGAAAAAGAGAGGA
52634157 AA
1 AA
52634159 AAAGGAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (16 bp):
AAGGAAAAAGAGAGGA
Found at i:52634164 original size:24 final size:25
Alignment explanation
Indices: 52634123--52634200 Score: 76
Period size: 24 Copynumber: 3.2 Consensus size: 25
52634113 GGTCGAAGGG
52634123 AAGAAGGAAGAAGAAGGAAAGGAA-A
1 AAGAAGGAAGAAGAAGGAAA-GAAGA
52634148 AAGAGAGGAA-AA-AAGGAAAGAAGA
1 AAGA-AGGAAGAAGAAGGAAAGAAGA
* *
52634172 AAGAAGAAAGAAAGAA-GAAAG-GGA
1 AAGAAGGAAG-AAGAAGGAAAGAAGA
52634196 AAGAA
1 AAGAA
52634201 AAAAAAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
23 7 0.15
24 19 0.41
25 13 0.28
26 7 0.15
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (25 bp):
AAGAAGGAAGAAGAAGGAAAGAAGA
Found at i:52634182 original size:31 final size:32
Alignment explanation
Indices: 52634133--52634200 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
52634123 AAGAAGGAAG
*
52634133 AAGAAGGAAAGGAAAAAGAGAGGAA-AAAAGGA
1 AAGAAGGAAAGGAAAAAGA-AAGAAGAAAAGGA
*
52634165 AAGAA-GAAA-GAAGAAAGAAAGAAGAAAGGGA
1 AAGAAGGAAAGGAA-AAAGAAAGAAGAAAAGGA
52634196 AAGAA
1 AAGAA
52634201 AAAAAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 7 0.22
31 20 0.62
32 5 0.16
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (32 bp):
AAGAAGGAAAGGAAAAAGAAAGAAGAAAAGGA
Found at i:52634184 original size:11 final size:11
Alignment explanation
Indices: 52634168--52634192 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
52634158 AAAAGGAAAG
52634168 AAGAAAGAAGA
1 AAGAAAGAAGA
52634179 AAGAAAGAAGA
1 AAGAAAGAAGA
52634190 AAG
1 AAG
52634193 GGAAAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (11 bp):
AAGAAAGAAGA
Found at i:52634203 original size:42 final size:42
Alignment explanation
Indices: 52634118--52634204 Score: 104
Period size: 42 Copynumber: 2.0 Consensus size: 42
52634108 AGCAAGGTCG
* * * *
52634118 AAGGGAAGAAGGAAGAAGAAGGAAAGGAAAAAGAGAGGAAAA
1 AAGGAAAGAAGAAAGAAGAAAGAAAGGAAAAAGAGAAGAAAA
*
52634160 AAGGAAAGAAGAAAGAAGAAAGAAA-GAAGAAAGGGAAAGAAAA
1 AAGGAAAGAAGAAAGAAGAAAGAAAGGAA-AAAGAG-AAGAAAA
52634203 AA
1 AA
52634205 AAAAAATTAC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
41 3 0.08
42 27 0.71
43 8 0.21
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (42 bp):
AAGGAAAGAAGAAAGAAGAAAGAAAGGAAAAAGAGAAGAAAA
Found at i:52634511 original size:8 final size:7
Alignment explanation
Indices: 52634489--52634563 Score: 96
Period size: 7 Copynumber: 10.0 Consensus size: 7
52634479 CAGCAGAGAG
52634489 GAAAAAA
1 GAAAAAA
52634496 GAAAAAA
1 GAAAAAA
52634503 GAAAGAAA
1 GAAA-AAA
52634511 GAAGAAAA
1 GAA-AAAA
*
52634519 AAAAAAA
1 GAAAAAA
52634526 GAAAAAGA
1 GAAAAA-A
52634534 GAGAAAAA
1 GA-AAAAA
52634542 GAAAAAAA
1 G-AAAAAA
52634550 GAAAAAA
1 GAAAAAA
52634557 GAAAAAA
1 GAAAAAA
52634564 CAAGAAAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
7 33 0.54
8 22 0.36
9 6 0.10
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:52634525 original size:25 final size:25
Alignment explanation
Indices: 52634489--52634573 Score: 91
Period size: 25 Copynumber: 3.3 Consensus size: 25
52634479 CAGCAGAGAG
* *
52634489 GAAAAAAGAAAAAAGAAAGAAAGAA
1 GAAAAAAAAAAAAAGAAAGAAAAAA
*
52634514 GAAAAAAAAAAAGAAAAAGAGAGAAAAA
1 GAAAAAAAAAAA-AAGAA-AGA-AAAAA
*
52634542 GAAAAAAAGAAAAAAGAAA-AAACAA
1 GAAAAAAA-AAAAAAGAAAGAAAAAA
52634567 GAAAAAA
1 GAAAAAA
52634574 GGGGTTAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
25 22 0.43
26 5 0.10
27 4 0.08
28 16 0.31
29 4 0.08
ACGTcount: A:0.82, C:0.01, G:0.16, T:0.00
Consensus pattern (25 bp):
GAAAAAAAAAAAAAGAAAGAAAAAA
Found at i:52634543 original size:31 final size:30
Alignment explanation
Indices: 52634489--52634563 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 30
52634479 CAGCAGAGAG
52634489 GAAAAAAGAAAAAAGAAAGAAAGAAGAAAAA
1 GAAAAAAGAAAAAAGAAAGAAAGAA-AAAAA
52634520 -AAAAAAGAAAAAGAGAGAA-AAAGAAAAAAA
1 GAAAAAAGAAAAA-AGA-AAGAAAGAAAAAAA
52634550 GAAAAAAGAAAAAA
1 GAAAAAAGAAAAAA
52634564 CAAGAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
30 18 0.44
31 21 0.51
32 2 0.05
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (30 bp):
GAAAAAAGAAAAAAGAAAGAAAGAAAAAAA
Found at i:52634570 original size:31 final size:31
Alignment explanation
Indices: 52634489--52634572 Score: 102
Period size: 31 Copynumber: 2.7 Consensus size: 31
52634479 CAGCAGAGAG
*
52634489 GAAAAAAGAAAAAAGAA-AGAAAGAAGAAAAA
1 GAAAAAAGAAAAAA-AAGAAAAAGAAGAAAAA
*
52634520 -AAAAAAGAAAAAGAGAGAAAAAGAA-AAAAA
1 GAAAAAAGAAAAA-AAAGAAAAAGAAGAAAAA
52634550 GAAAAAAGAAAAAACAAGAAAAA
1 GAAAAAAGAAAAAA-AAGAAAAA
52634573 AGGGGTTAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
30 19 0.41
31 27 0.59
ACGTcount: A:0.82, C:0.01, G:0.17, T:0.00
Consensus pattern (31 bp):
GAAAAAAGAAAAAAAAGAAAAAGAAGAAAAA
Found at i:52634739 original size:10 final size:10
Alignment explanation
Indices: 52634724--52634774 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
52634714 CATTTATATC
*
52634724 TTTAATTTCA
1 TTTAATTTTA
*
52634734 TTTAATTTAA
1 TTTAATTTTA
*
52634744 TTCAATTTTTA
1 TTTAA-TTTTA
52634755 TTTAATTTTA
1 TTTAATTTTA
*
52634765 TTTTATTTTA
1 TTTAATTTTA
52634775 AATACTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
10 27 0.77
11 8 0.23
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTAATTTTA
Found at i:52634744 original size:15 final size:15
Alignment explanation
Indices: 52634724--52634772 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
52634714 CATTTATATC
*
52634724 TTTAATTTCATTTAA
1 TTTAATTTCATTTTA
52634739 TTTAA-TTCAATTTTTA
1 TTTAATTTC-A-TTTTA
*
52634755 TTTAATTTTATTTTA
1 TTTAATTTCATTTTA
52634770 TTT
1 TTT
52634773 TAAATACTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 3 0.10
15 14 0.48
16 10 0.34
17 2 0.07
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTAATTTCATTTTA
Found at i:52634772 original size:21 final size:21
Alignment explanation
Indices: 52634715--52634773 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
52634705 ATATTTTGGC
*
52634715 ATTTATATCTTTAATTTCATTTA
1 ATTT-TAT-TTTATTTTCATTTA
* ** *
52634738 ATTTAATTCAATTTTTATTTA
1 ATTTTATTTTATTTTCATTTA
52634759 ATTTTATTTTATTTT
1 ATTTTATTTTATTTT
52634774 AAATACTTTT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 22 0.79
22 2 0.07
23 4 0.14
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (21 bp):
ATTTTATTTTATTTTCATTTA
Found at i:52634774 original size:16 final size:16
Alignment explanation
Indices: 52634724--52634775 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
52634714 CATTTATATC
*
52634724 TTTAATTTCA-TTTAA
1 TTTAATTTTATTTTAA
** *
52634739 TTTAATTCAATTTTTA
1 TTTAATTTTATTTTAA
*
52634755 TTTAATTTTATTTTAT
1 TTTAATTTTATTTTAA
52634771 TTTAA
1 TTTAA
52634776 ATACTTTTAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTAATTTTATTTTAA
Found at i:52634969 original size:22 final size:21
Alignment explanation
Indices: 52634936--52634978 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
52634926 TCGCGTTTCG
52634936 AAATTTTCGTGTCTTCAAAAA
1 AAATTTTCGTGTCTTCAAAAA
*
52634957 AAATTTCTCGTGTTTTCAAAAA
1 AAATTT-TCGTGTCTTCAAAAA
52634979 TAAGGTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (21 bp):
AAATTTTCGTGTCTTCAAAAA
Found at i:52634977 original size:20 final size:20
Alignment explanation
Indices: 52634936--52634978 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
52634926 TCGCGTTTCG
52634936 AAATTTTCGTGTCTTCAAAAA
1 AAATTTTCGTGTCTTC-AAAA
*
52634957 AAATTTCTCGTGTTTTCAAAA
1 AAATTT-TCGTGTCTTCAAAA
52634978 A
1 A
52634979 TAAGGTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (20 bp):
AAATTTTCGTGTCTTCAAAA
Found at i:52635112 original size:18 final size:19
Alignment explanation
Indices: 52635091--52635584 Score: 137
Period size: 17 Copynumber: 26.9 Consensus size: 19
52635081 AGAAAATTTT
52635091 TCGTGTTTT-AAAAAATTC
1 TCGTGTTTTCAAAAAATTC
52635109 TCGTGTTTTCAAAAAATTC
1 TCGTGTTTTCAAAAAATTC
* * *
52635128 -CAT-TTTTC-AAAATTTT
1 TCGTGTTTTCAAAAAATTC
* *
52635144 TCGTCTTTTCTAAAAATT-
1 TCGTGTTTTCAAAAAATTC
* * * *
52635162 TCCAT-ATTTC-TAAAATTT
1 T-CGTGTTTTCAAAAAATTC
*
52635180 TCGTG-TTTAAAAAAATT-
1 TCGTGTTTTCAAAAAATTC
* * *
52635197 TCGTATTTTCAAAATTTTTATTTT
1 TCGTGTTTTCAAAA-----AATTC
** * *
52635221 TATTTTTTTC-AACAATTC
1 TCGTGTTTTCAAAAAATTC
* *
52635239 TCGAG-TTTC-ACAAATTC
1 TCGTGTTTTCAAAAAATTC
* *
52635256 TCGTGTTTT--AAAATTTT
1 TCGTGTTTTCAAAAAATTC
** *
52635273 TTATGTTTTAAAAAATAAATTTC
1 TCGTGTTTT--CAAA-AAAT-TC
*
52635296 TCGTG-TTTCAAAAAAATTG
1 TCGTGTTTTC-AAAAAATTC
*
52635315 TCGTGTTTT--AAAAATTT
1 TCGTGTTTTCAAAAAATTC
* *
52635332 TCATG-TTTC-TAAAATGT-
1 TCGTGTTTTCAAAAAAT-TC
* *
52635349 TCGT-ATTTCAAAAAATCC
1 TCGTGTTTTCAAAAAATTC
52635367 TCGTGTTTTC-AAAAATTC
1 TCGTGTTTTCAAAAAATTC
**
52635385 TTATG-TTTC-AAAAA-TC
1 TCGTGTTTTCAAAAAATTC
52635401 TTCGTGTTTTC--AAAATTC
1 -TCGTGTTTTCAAAAAATTC
* *
52635419 TAGTG-TTTC-AAAAATTT
1 TCGTGTTTTCAAAAAATTC
* *
52635436 TCATGTTTTCAAAAATTTC
1 TCGTGTTTTCAAAAAATTC
* *
52635455 CCCTGTTTTC-AAAAATTC
1 TCGTGTTTTCAAAAAATTC
* * *
52635473 TCGTATTTT--GAAAATTT
1 TCGTGTTTTCAAAAAATTC
*
52635490 TCTTGTTTTCAAAAAAAAAAACTT-
1 TCGTGTTTTC-----AAAAAA-TTC
*
52635514 TCGTGTTTT--ATAAA-TC
1 TCGTGTTTTCAAAAAATTC
52635530 TCCGTGTTTTCAAAAAATTC
1 T-CGTGTTTTCAAAAAATTC
* *
52635550 TCGT-CTTTC-AAAAATTT
1 TCGTGTTTTCAAAAAATTC
52635567 TCGTGTTTTCAAAAAATT
1 TCGTGTTTTCAAAAAATT
52635585 GACCTTGTTT
Statistics
Matches: 352, Mismatches: 73, Indels: 101
0.67 0.14 0.19
Matches are distributed among these distances:
15 1 0.00
16 16 0.05
17 136 0.39
18 93 0.26
19 55 0.16
20 10 0.03
21 5 0.01
22 6 0.02
23 9 0.03
24 19 0.05
25 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (19 bp):
TCGTGTTTTCAAAAAATTC
Found at i:52635159 original size:35 final size:34
Alignment explanation
Indices: 52635109--52635215 Score: 108
Period size: 36 Copynumber: 3.0 Consensus size: 34
52635099 TAAAAAATTC
52635109 TCGTGTTTTCAAAAAATTCCATTTTTCAAAATTTT
1 TCGT-TTTTCAAAAAATTCCATTTTTCAAAATTTT
* *
52635144 TCGTCTTTTCTAAAAATTTCCATATTTCTAAAA-TTT
1 TCGT-TTTTC-AAAAAATTCCATTTTTC-AAAATTTT
* * * *
52635180 TCGTGTTTAAAAAAATTTCGTATTTTCAAAATTTT
1 TCGTTTTTCAAAAAATTCCAT-TTTTCAAAATTTT
52635215 T
1 T
52635216 ATTTTTATTT
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
34 13 0.22
35 20 0.34
36 22 0.37
37 4 0.07
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.50
Consensus pattern (34 bp):
TCGTTTTTCAAAAAATTCCATTTTTCAAAATTTT
Found at i:52635382 original size:53 final size:53
Alignment explanation
Indices: 52635296--52635504 Score: 184
Period size: 54 Copynumber: 3.9 Consensus size: 53
52635286 AATAAATTTC
* * * *
52635296 TCGTGTTTCAAAAAAATTGTCGTGTTTT-AAAAATTTTCATGTTTCTAAAATGT
1 TCGTATTTC-AAAAAATTCTCGTGTTTTCAAAAATTTTCATGTTTCAAAAATCT
*
52635349 TCGTATTTCAAAAAATCCTCGTGTTTTCAAAAATTCTT-ATGTTTCAAAAATCT
1 TCGTATTTCAAAAAATTCTCGTGTTTTCAAAAATT-TTCATGTTTCAAAAATCT
* *
52635402 TCGTGTTTTC--AAAATTCTAGTG-TTTCAAAAATTTTCATGTTTTCAAAAAT-T
1 TCGT-ATTTCAAAAAATTCTCGTGTTTTCAAAAATTTTCATG-TTTCAAAAATCT
* * *
52635453 TCCCCTGT-TTTC-AAAAATTCTCGTATTTT-GAAAATTTTCTTGTTTTCAAAAA
1 T---C-GTATTTCAAAAAATTCTCGTGTTTTCAAAAATTTTCATG-TTTCAAAAA
52635505 AAAAAACTTT
Statistics
Matches: 133, Mismatches: 12, Indels: 21
0.80 0.07 0.13
Matches are distributed among these distances:
50 2 0.02
51 16 0.12
52 36 0.27
53 36 0.27
54 38 0.29
55 5 0.04
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.45
Consensus pattern (53 bp):
TCGTATTTCAAAAAATTCTCGTGTTTTCAAAAATTTTCATGTTTCAAAAATCT
Found at i:52635503 original size:35 final size:35
Alignment explanation
Indices: 52635354--52635504 Score: 139
Period size: 35 Copynumber: 4.3 Consensus size: 35
52635344 AATGTTCGTA
* * *
52635354 TTTCAAAAAATCCTCGTGTTTTCAAAAATTCTTATG
1 TTTC-AAAAATTCTCGTGTTTTCAAAATTTCTTGTG
*
52635390 TTTCAAAAA-TCTTCGTGTTTTCAAAA-TTCTAGTG
1 TTTCAAAAATTC-TCGTGTTTTCAAAATTTCTTGTG
* * *
52635424 TTTCAAAAATTTTCATGTTTTCAAAAATTTCCCCTGT-
1 TTTCAAAAATTCTCGTGTTTTC-AAAATTT--CTTGTG
* *
52635461 TTTCAAAAATTCTCGTATTTTGAAAATTTTCTTGT-
1 TTTCAAAAATTCTCGTGTTTTCAAAA-TTTCTTGTG
52635496 TTTCAAAAA
1 TTTCAAAAA
52635505 AAAAAACTTT
Statistics
Matches: 96, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
34 25 0.26
35 37 0.39
36 10 0.10
37 21 0.22
38 3 0.03
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.45
Consensus pattern (35 bp):
TTTCAAAAATTCTCGTGTTTTCAAAATTTCTTGTG
Found at i:52635596 original size:37 final size:36
Alignment explanation
Indices: 52635442--52635618 Score: 119
Period size: 36 Copynumber: 4.8 Consensus size: 36
52635432 ATTTTCATGT
* *
52635442 TTTCAAAAATTTCCCCTGTTTTC-AAAAATTCTCGTA
1 TTTCAAAAATTT-CCGTGTTTTCAAAAAATTCTCGTC
** * * *
52635478 TTTTGAAAATTTTCTTGTTTTCAAAAAAAAAAACTT-TCGTG
1 TTTCAAAAATTTCCGTGTTTTC-----AAAAAA-TTCTCGTC
* * *
52635519 TTTTATAAATCTCCGTGTTTTCAAAAAATTCTCGTC
1 TTTCAAAAATTTCCGTGTTTTCAAAAAATTCTCGTC
* * *
52635555 TTTCAAAAATTTTCGTGTTTTCAAAAAATTGAC-CTTG
1 TTTCAAAAATTTCCGTGTTTTCAAAAAATT--CTCGTC
*
52635592 TTTCATAAATTTCCGTG-TTTCAAAAAA
1 TTTCAAAAATTTCCGTGTTTTCAAAAAA
52635619 AATCCTCGTG
Statistics
Matches: 112, Mismatches: 19, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
35 10 0.09
36 56 0.50
37 17 0.15
38 1 0.01
41 26 0.23
42 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (36 bp):
TTTCAAAAATTTCCGTGTTTTCAAAAAATTCTCGTC
Found at i:52635612 original size:17 final size:17
Alignment explanation
Indices: 52635289--52635617 Score: 107
Period size: 17 Copynumber: 18.2 Consensus size: 17
52635279 TTTAAAAAAT
52635289 AAATTTCTCGTGTTTCAAAA
1 AAATTTC-CGTGTTTC--AA
*
52635309 AAATTGT-CGTGTTTTAA
1 AAATT-TCCGTGTTTCAA
* * *
52635326 AAATTTTCATGTTTCTA
1 AAATTTCCGTGTTTCAA
*
52635343 AAATGTT-CGTATTTCAA
1 AAAT-TTCCGTGTTTCAA
* *
52635360 AAAATCCTCGTGTTTTCAA
1 AAATTTC-CGTG-TTTCAA
**
52635379 AAA-TTCTTATGTTTCAA
1 AAATTTC-CGTGTTTCAA
52635396 AAATCTT-CGTGTTTTC-A
1 AAAT-TTCCGTG-TTTCAA
*
52635413 AAA-TTCTAGTGTTTCAA
1 AAATTTC-CGTGTTTCAA
* *
52635430 AAATTTTCATGTTTTCAA
1 AAATTTCCGTG-TTTCAA
*
52635448 AAATTTCCCCTGTTTTCAA
1 AAATTT-CCGTG-TTTCAA
* **
52635467 AAA-TTCTCGTATTTTGA
1 AAATTTC-CGTGTTTCAA
* *
52635484 AAATTTTCTTGTTTTCAAAAAAAA
1 AAATTTCCGTG-TTTC------AA
* *
52635508 AAACTTT-CGTGTTTTAT
1 AAA-TTTCCGTGTTTCAA
*
52635525 AAATCTCCGTGTTTTCAA
1 AAATTTCCGTG-TTTCAA
* *
52635543 AAAATTCTCGTCTTTCAA
1 AAATTTC-CGTGTTTCAA
*
52635561 AAATTTTCGTGTTTTCAAA
1 AAATTTCCGTG-TTTC-AA
* * *
52635580 AAATTGACCTTGTTTCAT
1 AAATT-TCCGTGTTTCAA
52635598 AAATTTCCGTGTTTCAA
1 AAATTTCCGTGTTTCAA
52635615 AAA
1 AAA
52635618 AAATCCTCGT
Statistics
Matches: 229, Mismatches: 49, Indels: 65
0.67 0.14 0.19
Matches are distributed among these distances:
15 2 0.01
16 8 0.03
17 85 0.37
18 67 0.29
19 45 0.20
20 8 0.03
21 1 0.00
23 3 0.01
24 7 0.03
25 3 0.01
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (17 bp):
AAATTTCCGTGTTTCAA
Found at i:52635619 original size:37 final size:36
Alignment explanation
Indices: 52635505--52635636 Score: 135
Period size: 36 Copynumber: 3.6 Consensus size: 36
52635495 TTTTCAAAAA
* *
52635505 AAAAAACTT-TCGTGTTTTATAAATCTCCGTGTTTTC
1 AAAAAA-TTCTCGTGTTTCATAAATTTCCGTGTTTTC
* * *
52635541 AAAAAATTCTCGTCTTTCAAAAATTTTCGTGTTTTC
1 AAAAAATTCTCGTGTTTCATAAATTTCCGTGTTTTC
*
52635577 AAAAAATTGAC-CTTGTTTCATAAATTTCCGTG-TTTC
1 AAAAAATT--CTCGTGTTTCATAAATTTCCGTGTTTTC
*
52635613 AAAAAAAATCCTCGTGTTTCATAA
1 --AAAAAATTCTCGTGTTTCATAA
52635637 TTTATCAAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
35 2 0.03
36 41 0.52
37 28 0.35
38 8 0.10
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.41
Consensus pattern (36 bp):
AAAAAATTCTCGTGTTTCATAAATTTCCGTGTTTTC
Found at i:52635639 original size:36 final size:37
Alignment explanation
Indices: 52635514--52635636 Score: 128
Period size: 37 Copynumber: 3.4 Consensus size: 37
52635504 AAAAAAACTT
* * *
52635514 TCGTGTTTTATAAATCTCCGTGTTTTC-AAAAAATTC
1 TCGTGTTTCATAAATTTCCGTGTTTTCAAAAAAATCC
* * * *
52635550 TCGTCTTTCAAAAATTTTCGTGTTTTCAAAAAATTGACC
1 TCGTGTTTCATAAATTTCCGTGTTTTCAAAAAAAT--CC
52635589 T--TGTTTCATAAATTTCCGTG-TTTCAAAAAAAATCC
1 TCGTGTTTCATAAATTTCCGTGTTTTC-AAAAAAATCC
52635624 TCGTGTTTCATAA
1 TCGTGTTTCATAA
52635637 TTTATCAAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
35 3 0.04
36 26 0.37
37 39 0.56
39 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (37 bp):
TCGTGTTTCATAAATTTCCGTGTTTTCAAAAAAATCC
Found at i:52635685 original size:22 final size:22
Alignment explanation
Indices: 52635643--52635684 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
52635633 ATAATTTATC
*
52635643 AAAATTTTTGTGTTTTCAAAAT
1 AAAATTTTTGTGTTTTAAAAAT
52635665 AAAA-TTTTGTGTTTTAAAAA
1 AAAATTTTTGTGTTTTAAAAA
52635685 AGTCTCATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (22 bp):
AAAATTTTTGTGTTTTAAAAAT
Found at i:52635777 original size:18 final size:19
Alignment explanation
Indices: 52635745--52635798 Score: 85
Period size: 17 Copynumber: 2.9 Consensus size: 19
52635735 AAATTTTGTG
52635745 TTTTCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTCAAAAAA
52635764 TTTTCGTG-TTTC-AAAAA
1 TTTTCGTGTTTTCAAAAAA
*
52635781 TCTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
52635799 TTATTATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 12 0.38
18 8 0.25
19 12 0.38
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (19 bp):
TTTTCGTGTTTTCAAAAAA
Found at i:52635781 original size:17 final size:18
Alignment explanation
Indices: 52635745--52635800 Score: 87
Period size: 18 Copynumber: 3.1 Consensus size: 18
52635735 AAATTTTGTG
52635745 TTTTCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
52635764 TTTTCGTG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
52635781 TCTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
52635799 TT
1 TT
52635801 ATTATTTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 12 0.35
18 14 0.41
19 8 0.24
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:52637436 original size:21 final size:21
Alignment explanation
Indices: 52637412--52637455 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
52637402 CATCCACTAG
*
52637412 TATGATACTGACTACTTGATC
1 TATGATACTGAATACTTGATC
52637433 TATGATACTGAATACTTGATC
1 TATGATACTGAATACTTGATC
52637454 TA
1 TA
52637456 GAGAAGTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.39
Consensus pattern (21 bp):
TATGATACTGAATACTTGATC
Found at i:52648272 original size:14 final size:14
Alignment explanation
Indices: 52648253--52648280 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52648243 TTGAATCTAT
52648253 ACTTTGCTTGCTCA
1 ACTTTGCTTGCTCA
52648267 ACTTTGCTTGCTCA
1 ACTTTGCTTGCTCA
52648281 GAAGACAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.29, G:0.14, T:0.43
Consensus pattern (14 bp):
ACTTTGCTTGCTCA
Found at i:52654038 original size:31 final size:29
Alignment explanation
Indices: 52653969--52654042 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
52653959 ACAAAATAAT
*
52653969 AACATAAGTGACTAAAATGTAACATTTCA
1 AACATAAGTGACTAAAATGTAACATTGCA
52653998 AACATAAGTGACTAAAATGTAAC-TTAAGGCA
1 AACATAAGTGACTAAAATGTAACATT---GCA
*
52654029 AACAAAAGTGACTA
1 AACATAAGTGACTA
52654043 TTTTTGTAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 2 0.05
29 23 0.57
31 15 0.38
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.23
Consensus pattern (29 bp):
AACATAAGTGACTAAAATGTAACATTGCA
Found at i:52659661 original size:54 final size:53
Alignment explanation
Indices: 52659601--52659755 Score: 138
Period size: 53 Copynumber: 2.9 Consensus size: 53
52659591 CCAAACCCTT
*
52659601 TTACTTTTCCCAAAAAAATTTACTTTCC-CTCAAACCCTCAAAACATTTTTCCTA
1 TTACTTTTCCCAAAAAAATTTAC-TTCCTC-CAAACCCTAAAAACATTTTTCCTA
** ** * * *
52659655 TTACTTTTCCTTAAAACTTTTACTTCTTCCAAACCCTAAAAACATTTTTTCTT
1 TTACTTTTCCCAAAAAAATTTACTTCCTCCAAACCCTAAAAACATTTTTCCTA
* ** *
52659708 TTGCTTTTCCTC-AAAACTTTTACTT-CTCCAAA-CCTCAAAAACTTTTTT
1 TTACTTTTCC-CAAAAAAATTTACTTCCTCCAAACCCT-AAAAACATTTTT
52659756 TTGAATTTAT
Statistics
Matches: 86, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
51 3 0.03
52 17 0.20
53 46 0.53
54 20 0.23
ACGTcount: A:0.30, C:0.27, G:0.01, T:0.43
Consensus pattern (53 bp):
TTACTTTTCCCAAAAAAATTTACTTCCTCCAAACCCTAAAAACATTTTTCCTA
Found at i:52659701 original size:53 final size:52
Alignment explanation
Indices: 52659631--52659755 Score: 171
Period size: 53 Copynumber: 2.4 Consensus size: 52
52659621 TACTTTCCCT
* *
52659631 CAAACCCTCAAAACATTTTTCCTATTACTTTTCCTTAAAACTTTTACTTCTTC
1 CAAACCCTAAAAACATTTTTCCTATTACTTTTCCTCAAAACTTTTACTTC-TC
* * *
52659684 CAAACCCTAAAAACATTTTTTCTTTTGCTTTTCCTCAAAACTTTTACTTCTC
1 CAAACCCTAAAAACATTTTTCCTATTACTTTTCCTCAAAACTTTTACTTCTC
*
52659736 CAAA-CCTCAAAAACTTTTTT
1 CAAACCCT-AAAAACATTTTT
52659756 TTGAATTTAT
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
51 3 0.05
52 17 0.26
53 45 0.69
ACGTcount: A:0.30, C:0.27, G:0.01, T:0.42
Consensus pattern (52 bp):
CAAACCCTAAAAACATTTTTCCTATTACTTTTCCTCAAAACTTTTACTTCTC
Found at i:52662020 original size:14 final size:14
Alignment explanation
Indices: 52662001--52662028 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52661991 TTTAGAACAC
52662001 ATAATTTTGATACA
1 ATAATTTTGATACA
52662015 ATAATTTTGATACA
1 ATAATTTTGATACA
52662029 TACAAAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
ATAATTTTGATACA
Found at i:52665186 original size:40 final size:40
Alignment explanation
Indices: 52665142--52665240 Score: 128
Period size: 40 Copynumber: 2.5 Consensus size: 40
52665132 AACGCTGCTT
* *
52665142 AAGATCAAGCATTAGCGGCGCTTTACGGAAAACACCGCTA
1 AAGATCGAGAATTAGCGGCGCTTTACGGAAAACACCGCTA
* * * *
52665182 AAGATCGAGAATTAGCGGCGCTTTCCTGAAATCGCCGCTA
1 AAGATCGAGAATTAGCGGCGCTTTACGGAAAACACCGCTA
*
52665222 AAAAT-GAGAATTAGCGGCG
1 AAGATCGAGAATTAGCGGCG
52665241 TTTGTTTAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
39 14 0.27
40 38 0.73
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.19
Consensus pattern (40 bp):
AAGATCGAGAATTAGCGGCGCTTTACGGAAAACACCGCTA
Found at i:52665415 original size:41 final size:41
Alignment explanation
Indices: 52665304--52665463 Score: 212
Period size: 41 Copynumber: 3.9 Consensus size: 41
52665294 CTTTCGTGGA
* *
52665304 TTTAGCGGCGTTTTTGAATAAGCGCTGCTAATGCTCAGAGC
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCAGAGC
* * *
52665345 TTTAGCGGCATTTTTTGAATAAGCACCGCTAATGCTCAGAGC
1 TTTAGCGGC-GTTTTTGAAGAAGCGCCGCTAATGCTCAGAGC
* * *
52665387 TTTAACGGCTTTTTTGAAGAAGCGCCGCTAATGCTCAGAGG
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCAGAGC
** *
52665428 TTTAGCGGCGAATGTGAAGAAGCGCCGCTAATGCTC
1 TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
52665464 GGTTTTTTTA
Statistics
Matches: 106, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
41 69 0.65
42 37 0.35
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCAGAGC
Found at i:52665479 original size:83 final size:81
Alignment explanation
Indices: 52665304--52665501 Score: 211
Period size: 83 Copynumber: 2.4 Consensus size: 81
52665294 CTTTCGTGGA
* * * * *
52665304 TTTAGCGGCGTTTTTGAATAAGCGCTGCTAATGCTCAGAGCTTTAGCGGCATTTTTTGAATAAGC
1 TTTAGCGGCTTTTTTGAA-AAGCGCCGCTAATGCTCAGAGCTTTAGCGGCA-TATGTGAAGAAGC
52665369 ACCGCTAATGCTCAGAGC
64 ACCGCTAATGCTCAGAGC
* *
52665387 TTTAACGGCTTTTTTGAAGAAGCGCCGCTAATGCTCAGAGGTTTAGCGGCGA-ATGTGAAGAAGC
1 TTTAGCGGCTTTTTTGAA-AAGCGCCGCTAATGCTCAGAGCTTTAGCGGC-ATATGTGAAGAAGC
* * ***
52665451 GCCGCTAATGCTCGGTTTT
64 ACCGCTAATGCTCAG-AGC
52665470 TTTAGCGGCTTTTTTCAGAAAA-CGCCGCTAAT
1 TTTAGCGGCTTTTTT--GAAAAGCGCCGCTAAT
52665502 AGTCGGGGTT
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
82 22 0.23
83 69 0.71
84 3 0.03
85 3 0.03
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (81 bp):
TTTAGCGGCTTTTTTGAAAAGCGCCGCTAATGCTCAGAGCTTTAGCGGCATATGTGAAGAAGCAC
CGCTAATGCTCAGAGC
Found at i:52666139 original size:29 final size:29
Alignment explanation
Indices: 52666099--52666172 Score: 112
Period size: 29 Copynumber: 2.5 Consensus size: 29
52666089 TTGGGGTTTA
*
52666099 GGGTTTAAGATTTAGAAATTATGGTTTTG
1 GGGTTTAAGATTTAGAAATTATGATTTTG
*
52666128 GGGTTTAGGATTTAGAAATTATGATTTTG
1 GGGTTTAAGATTTAGAAATTATGATTTTG
*
52666157 GGGTTTTAGAGTTTAG
1 GGGTTTAAGA-TTTAG
52666173 GGTTTAAGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 35 0.88
30 5 0.12
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.45
Consensus pattern (29 bp):
GGGTTTAAGATTTAGAAATTATGATTTTG
Found at i:52673300 original size:40 final size:39
Alignment explanation
Indices: 52673232--52673348 Score: 148
Period size: 40 Copynumber: 3.0 Consensus size: 39
52673222 GGCGTTTGCA
*
52673232 TAAAAAATGCCGCTAAAAATAAGCATTAGCGGCGCTTTT
1 TAAAAAATGCCGCTAAAAATGAGCATTAGCGGCGCTTTT
* * *
52673271 TAAAAAACGCAGCTAAAAATCGAGTATTAG-GAGCGCTTTT
1 TAAAAAATGCCGCTAAAAAT-GAGCATTAGCG-GCGCTTTT
**
52673311 TGCAAAATGCCGCTAAAAATGAGCATTAGCGGCG-TTTT
1 TAAAAAATGCCGCTAAAAATGAGCATTAGCGGCGCTTTT
52673349 CCAAAAAGCG
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
38 4 0.06
39 30 0.45
40 32 0.48
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.26
Consensus pattern (39 bp):
TAAAAAATGCCGCTAAAAATGAGCATTAGCGGCGCTTTT
Found at i:52673362 original size:39 final size:38
Alignment explanation
Indices: 52673234--52673368 Score: 123
Period size: 39 Copynumber: 3.4 Consensus size: 38
52673224 CGTTTGCATA
* * *
52673234 AAAAATGCCGCTAAAAATAAGCATTAGCGGCGCTTTTTA
1 AAAAACGCCGCTAAAAATGAGCATTAGCGGCGC-TTTTC
* *
52673273 AAAAACGCAGCTAAAAATCGAGTATTAG-GAGCGCTTTTTGC
1 AAAAACGCCGCTAAAAAT-GAGCATTAGCG-GCGC-TTTT-C
*
52673314 -AAAATGCCGCTAAAAATGAGCATTAGCGGCG-TTTTCC
1 AAAAACGCCGCTAAAAATGAGCATTAGCGGCGCTTTT-C
*
52673351 AAAAAGCGCCGCAAAAAA
1 AAAAA-CGCCGCTAAAAA
52673369 CCTAAGCCCA
Statistics
Matches: 79, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
37 5 0.06
38 4 0.05
39 38 0.48
40 32 0.41
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.21
Consensus pattern (38 bp):
AAAAACGCCGCTAAAAATGAGCATTAGCGGCGCTTTTC
Found at i:52673459 original size:40 final size:40
Alignment explanation
Indices: 52673397--52673499 Score: 134
Period size: 40 Copynumber: 2.6 Consensus size: 40
52673387 TTCGGGGCTT
* ** *
52673397 TAGCAGCGTTTTTGAAGTAGCGCCGCTATTGCTCTATTTG
1 TAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTATTTG
* * *
52673437 TAGTGTCGTTTTTGAAAAAGCGCCGCTAATGCTCTATTTT
1 TAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTATTTG
*
52673477 TAGCGGCGTTTTTGAAAAGGCGC
1 TAGCGGCGTTTTTGAAAAAGCGC
52673500 TGCAAAAAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (40 bp):
TAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTATTTG
Found at i:52673749 original size:7 final size:7
Alignment explanation
Indices: 52673728--52673874 Score: 53
Period size: 7 Copynumber: 20.6 Consensus size: 7
52673718 TTAATTATCA
*
52673728 TTATTGT
1 TTATGGT
*
52673735 TTAGGGT
1 TTATGGT
52673742 TTATGGT
1 TTATGGT
* *
52673749 TAAGGGT
1 TTATGGT
*
52673756 ATATGGT
1 TTATGGT
*
52673763 TTAGGGT
1 TTATGGT
**
52673770 TTAAAGT
1 TTATGGT
*
52673777 TT-TGGAG
1 TTATGG-T
**
52673784 TTACTATT
1 TTA-TGGT
*
52673792 TTAAGGT
1 TTATGGT
* *
52673799 TTATAGA
1 TTATGGT
52673806 TTATGGGT
1 TTAT-GGT
* *
52673814 TTAAGGA
1 TTATGGT
*
52673821 TTATGAT
1 TTATGGT
*
52673828 TTACGGT
1 TTATGGT
52673835 TTATGCGT
1 TTATG-GT
*
52673843 TTAAGGT
1 TTATGGT
* *
52673850 TTAAGGG
1 TTATGGT
*
52673857 TTACGGT
1 TTATGGT
52673864 TTATGGT
1 TTATGGT
52673871 TTAT
1 TTAT
52673875 AGATTAATGG
Statistics
Matches: 96, Mismatches: 39, Indels: 10
0.66 0.27 0.07
Matches are distributed among these distances:
6 1 0.01
7 81 0.84
8 13 0.14
9 1 0.01
ACGTcount: A:0.23, C:0.03, G:0.27, T:0.47
Consensus pattern (7 bp):
TTATGGT
Found at i:52673778 original size:14 final size:14
Alignment explanation
Indices: 52673728--52673772 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
52673718 TTAATTATCA
*
52673728 TTATTGTTTAGGGT
1 TTATGGTTTAGGGT
*
52673742 TTATGGTTAAGGGT
1 TTATGGTTTAGGGT
*
52673756 ATATGGTTTAGGGT
1 TTATGGTTTAGGGT
52673770 TTA
1 TTA
52673773 AAGTTTTGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (14 bp):
TTATGGTTTAGGGT
Found at i:52673836 original size:36 final size:35
Alignment explanation
Indices: 52673791--52673886 Score: 93
Period size: 36 Copynumber: 2.7 Consensus size: 35
52673781 GAGTTACTAT
* *
52673791 TTTAAGGTTTATAGATTATGGGTTTAAGGATTATGA
1 TTTAAGGTTTATAGATTA-AGGTTTAAGGATTACGA
* * * * *
52673827 TTTACGGTTTATGCGTTTAAGGTTTAAGGGTTACGG
1 TTTAAGGTTTAT-AGATTAAGGTTTAAGGATTACGA
*
52673863 TTTATGGTTTATAGATTAATGGTT
1 TTTAAGGTTTATAGATTAA-GGTT
52673887 GGGGTTTAAG
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
35 5 0.10
36 39 0.81
37 4 0.08
ACGTcount: A:0.25, C:0.03, G:0.26, T:0.46
Consensus pattern (35 bp):
TTTAAGGTTTATAGATTAAGGTTTAAGGATTACGA
Found at i:52673838 original size:14 final size:14
Alignment explanation
Indices: 52673806--52673873 Score: 64
Period size: 14 Copynumber: 4.7 Consensus size: 14
52673796 GGTTTATAGA
* *
52673806 TTATGGGTTTAAGGA
1 TTAT-GGTTTACGGT
*
52673821 TTATGATTTACGGT
1 TTATGGTTTACGGT
*
52673835 TTATGCGTTTAAGGT
1 TTATG-GTTTACGGT
* *
52673850 TTAAGGGTTACGGT
1 TTATGGTTTACGGT
52673864 TTATGGTTTA
1 TTATGGTTTA
52673874 TAGATTAATG
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
14 27 0.64
15 15 0.36
ACGTcount: A:0.22, C:0.04, G:0.28, T:0.46
Consensus pattern (14 bp):
TTATGGTTTACGGT
Found at i:52673881 original size:28 final size:28
Alignment explanation
Indices: 52673806--52673914 Score: 94
Period size: 28 Copynumber: 3.8 Consensus size: 28
52673796 GGTTTATAGA
* **
52673806 TTATGGGTTTAAGGATTATGATTTACGGT
1 TTAT-GGTTTAAGGATTAAGGGTTACGGT
*
52673835 TTATGCGTTTAAGGTTTAAGGGTTACGGT
1 TTATG-GTTTAAGGATTAAGGGTTACGGT
* **
52673864 TTATGGTTTATA-GATTAATGGTTGGGGT
1 TTATGGTTTA-AGGATTAAGGGTTACGGT
* * *
52673892 TTAAGGTTTAGGGATTAGGGGTT
1 TTATGGTTTAAGGATTAAGGGTT
52673915 GAGGGTTAAG
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
28 36 0.55
29 29 0.45
ACGTcount: A:0.22, C:0.03, G:0.32, T:0.43
Consensus pattern (28 bp):
TTATGGTTTAAGGATTAAGGGTTACGGT
Found at i:52674075 original size:15 final size:15
Alignment explanation
Indices: 52674056--52674092 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
52674046 ACTATTTTAA
52674056 GGTTTATGA-ATTAT
1 GGTTTATGAGATTAT
52674070 GAGTTTA-GAGATTAT
1 G-GTTTATGAGATTAT
52674085 GGTTTATG
1 GGTTTATG
52674093 GTTTAAGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (15 bp):
GGTTTATGAGATTAT
Found at i:52674076 original size:22 final size:21
Alignment explanation
Indices: 52674051--52674101 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
52674041 GAGTTACTAT
52674051 TTTAAGGTTTATGAATTATGAG
1 TTTAAGGTTTATGAATTATG-G
* **
52674073 TTT-AGAGATTATGGTTTATGG
1 TTTAAG-GTTTATGAATTATGG
52674094 TTTAAGGT
1 TTTAAGGT
52674102 AGAGGTGCTC
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.47
Consensus pattern (21 bp):
TTTAAGGTTTATGAATTATGG
Found at i:52674325 original size:7 final size:7
Alignment explanation
Indices: 52674315--52674350 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
52674305 TTTATTATTA
52674315 CATTTCC
1 CATTTCC
52674322 CATTTCC
1 CATTTCC
52674329 CATTTCC
1 CATTTCC
52674336 CATTTCC
1 CATTTCC
52674343 CATTTCC
1 CATTTCC
52674350 C
1 C
52674351 GTGTATCTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.14, C:0.44, G:0.00, T:0.42
Consensus pattern (7 bp):
CATTTCC
Found at i:52676365 original size:16 final size:16
Alignment explanation
Indices: 52676344--52676377 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
52676334 ATATAAATTC
52676344 AATAACAATTAATTTT
1 AATAACAATTAATTTT
*
52676360 AATAACAATTAGTTTT
1 AATAACAATTAATTTT
52676376 AA
1 AA
52676378 CTTTTAAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (16 bp):
AATAACAATTAATTTT
Done.