Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 110 of 150
Found at i:34146466 original size:20 final size:22
Alignment explanation
Indices: 34146433--34146472 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
34146423 ATTTAATCCC
*
34146433 TCTACCTTTTAAATT-TATAAA
1 TCTACCTTTCAAATTATATAAA
34146454 TCTA-CTTTCAAATTATATA
1 TCTACCTTTCAAATTATATA
34146473 TAACTACTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (22 bp):
TCTACCTTTCAAATTATATAAA
Found at i:34146472 original size:21 final size:21
Alignment explanation
Indices: 34146433--34146480 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
34146423 ATTTAATCCC
*
34146433 TCTACCTTTTAAATTTATA-AA
1 TCTA-CTTTCAAATTTATATAA
34146454 TCTACTTTCAAATTATATATAA
1 TCTACTTTCAAATT-TATATAA
34146476 -CTACT
1 TCTACT
34146481 AGCATTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 9 0.38
21 13 0.54
22 2 0.08
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.46
Consensus pattern (21 bp):
TCTACTTTCAAATTTATATAA
Found at i:34146554 original size:29 final size:29
Alignment explanation
Indices: 34146520--34146575 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
34146510 TAACTATTTG
*
34146520 AACTAATTAATTATATTATAAAAATATTA
1 AACTAATTAATAATATTATAAAAATATTA
34146549 AACTAATTAATAATATTATAAAAATAT
1 AACTAATTAATAATATTATAAAAATAT
34146576 AAAAACCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (29 bp):
AACTAATTAATAATATTATAAAAATATTA
Found at i:34146592 original size:29 final size:29
Alignment explanation
Indices: 34146524--34146589 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
34146514 TATTTGAACT
* * *
34146524 AATTAATTATATTATAAAAATATTAAACT
1 AATTAATAATATTATAAAAATATAAAACA
34146553 AATTAATAATATTATAAAAATATAAAAACCA
1 AATTAATAATATTATAAAAATAT-AAAA-CA
34146584 AATTAA
1 AATTAA
34146590 ATAAAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 22 0.69
30 3 0.09
31 7 0.22
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.35
Consensus pattern (29 bp):
AATTAATAATATTATAAAAATATAAAACA
Found at i:34147048 original size:19 final size:19
Alignment explanation
Indices: 34147026--34147070 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
34147016 TTAAATTATC
34147026 AAAAAATAATAAAAATTGT
1 AAAAAATAATAAAAATTGT
* *
34147045 AAAAAAT-TTAAATATTGT
1 AAAAAATAATAAAAATTGT
*
34147063 TAAAAATA
1 AAAAAATA
34147071 TTTTTAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (19 bp):
AAAAAATAATAAAAATTGT
Found at i:34147056 original size:18 final size:18
Alignment explanation
Indices: 34147004--34147112 Score: 69
Period size: 20 Copynumber: 5.8 Consensus size: 18
34146994 TAATATGTAT
*
34147004 ATTGT-AAAAATTT-TAA
1 ATTGTAAAAAATTTAAAA
* *
34147020 ATTATCAAAAAATAATAAAA
1 ATTGT-AAAAAAT-TTAAAA
*
34147040 ATTGTAAAAAATTTAAAT
1 ATTGTAAAAAATTTAAAA
**
34147058 ATTGTTAAAAATATTTTTAA
1 ATTG-TAAAAA-ATTTAAAA
*
34147078 ATTGTAAAAATTTATTAAAA
1 ATTGTAAAAA-AT-TTAAAA
**
34147098 ATAATAAAAAATTTA
1 ATTGTAAAAAATTTA
34147113 TTTAAATTTT
Statistics
Matches: 71, Mismatches: 15, Indels: 12
0.72 0.15 0.12
Matches are distributed among these distances:
16 4 0.06
18 17 0.24
19 23 0.32
20 27 0.38
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.39
Consensus pattern (18 bp):
ATTGTAAAAAATTTAAAA
Found at i:34147129 original size:21 final size:20
Alignment explanation
Indices: 34147050--34147135 Score: 59
Period size: 21 Copynumber: 4.2 Consensus size: 20
34147040 ATTGTAAAAA
34147050 ATTTAAATATTGTTAAAAATATT
1 ATTTAAAT-TT-TTAAAAAT-TT
*
34147073 -TTTAAA-TTGTAAAAATTT
1 ATTTAAATTTTTAAAAATTT
* ** *
34147091 ATTAAAAATAATAAAAAATTT
1 ATT-TAAATTTTTAAAAATTT
*
34147112 ATTTAAATTTTTAGAAAAATT
1 ATTTAAATTTTTA-AAAATTT
34147133 ATT
1 ATT
34147136 CAAAACCATA
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
18 2 0.04
19 9 0.19
20 11 0.23
21 20 0.42
22 6 0.12
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
ATTTAAATTTTTAAAAATTT
Found at i:34152154 original size:10 final size:10
Alignment explanation
Indices: 34152075--34152216 Score: 66
Period size: 10 Copynumber: 14.6 Consensus size: 10
34152065 ATGATTCTAT
34152075 ATTTTTAATA
1 ATTTTTAATA
*
34152085 ATTATTT-GTA
1 ATT-TTTAATA
34152095 ATTTTTTAATA
1 A-TTTTTAATA
**
34152106 A--TTTACCA
1 ATTTTTAATA
* *
34152114 GTTTTTAATC
1 ATTTTTAATA
*
34152124 A-TTTTAAAA
1 ATTTTTAATA
** *
34152133 AAATTAAATA
1 ATTTTTAATA
34152143 ATTTTTAATA
1 ATTTTTAATA
*
34152153 ATTTTT-TTA
1 ATTTTTAATA
*
34152162 CAATTTTAA-A
1 -ATTTTTAATA
*
34152172 ATATTTTAACA
1 AT-TTTTAATA
*
34152183 ATATTTAAT-
1 ATTTTTAATA
*
34152192 ATTTTTTATA
1 ATTTTTAATA
34152202 ATTTTTAAT-
1 ATTTTTAATA
34152211 ATTTTT
1 ATTTTT
34152217 TTACAATTTC
Statistics
Matches: 95, Mismatches: 26, Indels: 23
0.66 0.18 0.16
Matches are distributed among these distances:
8 5 0.05
9 23 0.24
10 56 0.59
11 11 0.12
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:34152168 original size:40 final size:38
Alignment explanation
Indices: 34152124--34152206 Score: 94
Period size: 40 Copynumber: 2.1 Consensus size: 38
34152114 GTTTTTAATC
* *
34152124 ATTTTAAAAAAATTAAATAATTTTTAATAATTTTTTTACA
1 ATTTTAAAAAAATTAAACAATATTTAAT-A-TTTTTTACA
* * * *
34152164 ATTTTAAAATATTTTAACAATATTTAATATTTTTTATA
1 ATTTTAAAAAAATTAAACAATATTTAATATTTTTTACA
34152202 ATTTT
1 ATTTT
34152207 TAATATTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
38 13 0.35
39 1 0.03
40 23 0.62
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (38 bp):
ATTTTAAAAAAATTAAACAATATTTAATATTTTTTACA
Found at i:34152231 original size:19 final size:19
Alignment explanation
Indices: 34152145--34152225 Score: 92
Period size: 19 Copynumber: 4.2 Consensus size: 19
34152135 ATTAAATAAT
34152145 TTTTAATAATTTTTTTACAA
1 TTTTAAT-ATTTTTTTACAA
* * *
34152165 TTTTAAAATATTTTAACAA
1 TTTTAATATTTTTTTACAA
*
34152184 TATTTAATATTTTTTATA-AT
1 T-TTTAATATTTTTT-TACAA
34152204 TTTTAATATTTTTTTACAA
1 TTTTAATATTTTTTTACAA
34152223 TTT
1 TTT
34152226 CTATATGTAT
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
18 2 0.04
19 28 0.56
20 19 0.38
21 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTAATATTTTTTTACAA
Found at i:34160567 original size:31 final size:33
Alignment explanation
Indices: 34160512--34160582 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 33
34160502 TAAACTTATG
*
34160512 ATATATATACATGGGCTTTATTTTATATATA-GT
1 ATATATATACATGGGCTTTATTTTA-ATATACAT
34160545 ATATATATTA-ATGGG-TTT-TTTTAATATACAT
1 ATATATA-TACATGGGCTTTATTTTAATATACAT
34160576 ATATATA
1 ATATATA
34160583 AGCGTGTGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
30 5 0.14
31 13 0.37
32 3 0.09
33 12 0.34
34 2 0.06
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (33 bp):
ATATATATACATGGGCTTTATTTTAATATACAT
Found at i:34161760 original size:17 final size:17
Alignment explanation
Indices: 34161740--34161807 Score: 55
Period size: 17 Copynumber: 4.0 Consensus size: 17
34161730 TTATTTTGCG
34161740 TGAATTGTTATTTGGTA
1 TGAATTGTTATTTGGTA
* **
34161757 TGAATTGATATTTCATA
1 TGAATTGTTATTTGGTA
* * * *
34161774 TGAACTATTATTTTGCA
1 TGAATTGTTATTTGGTA
* *
34161791 TGAGTTGTCATTTGGTA
1 TGAATTGTTATTTGGTA
34161808 AGAACTATTA
Statistics
Matches: 36, Mismatches: 15, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.49
Consensus pattern (17 bp):
TGAATTGTTATTTGGTA
Found at i:34161777 original size:51 final size:51
Alignment explanation
Indices: 34161722--34161833 Score: 136
Period size: 51 Copynumber: 2.2 Consensus size: 51
34161712 ATGATGGAGC
* * * * *
34161722 ATGAAATGTTATTTTGCGTGAATTGTTATTTGGTATGAATTGA-TATTTCAT
1 ATGAAATATTATTTTGCATGAATTGTCATTTGGTAAGAACT-ATTATTTCAT
* *
34161773 ATGAACTATTATTTTGCATGAGTTGTCATTTGGTAAGAACTATTATTTCAT
1 ATGAAATATTATTTTGCATGAATTGTCATTTGGTAAGAACTATTATTTCAT
34161824 ATGAACATAT
1 ATGAA-ATAT
34161834 GTTTGGTGCG
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
50 1 0.02
51 47 0.92
52 3 0.06
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (51 bp):
ATGAAATATTATTTTGCATGAATTGTCATTTGGTAAGAACTATTATTTCAT
Found at i:34161894 original size:18 final size:18
Alignment explanation
Indices: 34161873--34161919 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
34161863 CTGCCCATTT
*
34161873 TATGTGAATTGCTTATTA
1 TATGTGAACTGCTTATTA
* *
34161891 TATGTGCACTGCTTATTG
1 TATGTGAACTGCTTATTA
*
34161909 TATGAGAACTG
1 TATGTGAACTG
34161920 TTGTGTTGTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.43
Consensus pattern (18 bp):
TATGTGAACTGCTTATTA
Found at i:34168395 original size:59 final size:58
Alignment explanation
Indices: 34168278--34168460 Score: 141
Period size: 59 Copynumber: 3.2 Consensus size: 58
34168268 ATCACTTTAA
* * * * *
34168278 TATTAAATTAATGTAATATTTATCTTGATAAATATTAGATTAAATTTAATATTAAATC
1 TATTAAAATAATATAATATTTATCTTGATAAATATAAGATTAAATTAAATAATAAATC
* * *
34168336 TTATTAAAATAATATAATGTTTATCTTG-TAAAT-TAAGTTTAATATTAAGATAATCAATC
1 -TATTAAAATAATATAATATTTATCTTGATAAATATAAGATTAA-ATTAA-ATAATAAATC
* * * * * *
34168395 TATTAAGATAAAATACTA-TTA---AGATAAGTATTAA-ATTAAATT-AATATTAAA-C
1 TATTAAAATAATATAATATTTATCTTGATAAATA-TAAGATTAAATTAAATAATAAATC
34168447 TATTAAAATAATAT
1 TATTAAAATAATAT
34168461 TATTAAGATA
Statistics
Matches: 100, Mismatches: 19, Indels: 17
0.74 0.14 0.12
Matches are distributed among these distances:
52 13 0.13
53 6 0.06
54 2 0.02
55 7 0.07
56 4 0.04
57 13 0.13
58 23 0.23
59 32 0.32
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (58 bp):
TATTAAAATAATATAATATTTATCTTGATAAATATAAGATTAAATTAAATAATAAATC
Found at i:34168415 original size:16 final size:16
Alignment explanation
Indices: 34168378--34168421 Score: 63
Period size: 16 Copynumber: 2.7 Consensus size: 16
34168368 TTAAGTTTAA
34168378 TATTAAGATAATCAATC
1 TATTAAGATAA-CAATC
34168395 TATTAAGATAA-AATAC
1 TATTAAGATAACAAT-C
34168411 TATTAAGATAA
1 TATTAAGATAA
34168422 GTATTAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 3 0.12
16 12 0.46
17 11 0.42
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (16 bp):
TATTAAGATAACAATC
Found at i:34174184 original size:23 final size:23
Alignment explanation
Indices: 34174158--34174204 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
34174148 GTAAGAATAC
34174158 TAATAAGATGAGTAGGAGACATA
1 TAATAAGATGAGTAGGAGACATA
*
34174181 TAATAAGATGAGTGGGAGACATA
1 TAATAAGATGAGTAGGAGACATA
34174204 T
1 T
34174205 TTGAACTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.04, G:0.28, T:0.23
Consensus pattern (23 bp):
TAATAAGATGAGTAGGAGACATA
Found at i:34176307 original size:20 final size:18
Alignment explanation
Indices: 34176257--34176367 Score: 68
Period size: 19 Copynumber: 6.0 Consensus size: 18
34176247 CTACAAGATA
34176257 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
34176274 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
**
34176294 AATATTAAATTAATAAAAT
1 AATATTAAATTAAT-ATTT
*
34176313 ACTATTAAGA-TAAGTATTT
1 AATATTAA-ATTAA-TATTT
* *
34176332 AAT-TTAATTTAATATTAA
1 AATATTAAATTAATATT-T
* *
34176350 AATTTTAAAATAATATTT
1 AATATTAAATTAATATTT
34176368 TTTTGGAATA
Statistics
Matches: 72, Mismatches: 12, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
17 15 0.21
18 11 0.15
19 28 0.39
20 18 0.25
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:34178414 original size:19 final size:20
Alignment explanation
Indices: 34178392--34178432 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
34178382 CTTCCTTGTA
34178392 TTTAAT-TCTTTTACTCTTT
1 TTTAATATCTTTTACTCTTT
* *
34178411 TTTAATATTTTTTTCTCTTT
1 TTTAATATCTTTTACTCTTT
34178431 TT
1 TT
34178433 AATGAAGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTAATATCTTTTACTCTTT
Found at i:34179458 original size:2 final size:2
Alignment explanation
Indices: 34179451--34179495 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
34179441 TTTAATTCCT
34179451 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34179493 TA T
1 TA T
34179496 CCAAACAAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34181673 original size:14 final size:14
Alignment explanation
Indices: 34181650--34181683 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
34181640 AGGGTGCATT
*
34181650 TGTTTCACGAAAAA
1 TGTTTTACGAAAAA
34181664 TGTTTTACGAAAAA
1 TGTTTTACGAAAAA
*
34181678 TATTTT
1 TGTTTT
34181684 CTGCATTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (14 bp):
TGTTTTACGAAAAA
Found at i:34183174 original size:9 final size:9
Alignment explanation
Indices: 34183160--34183190 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
34183150 GTTAAACGAA
34183160 TCGAGTTAT
1 TCGAGTTAT
*
34183169 TCGAGTTAA
1 TCGAGTTAT
34183178 TCGAGTTAT
1 TCGAGTTAT
34183187 TCGA
1 TCGA
34183191 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:34183261 original size:9 final size:9
Alignment explanation
Indices: 34183244--34183280 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
34183234 TGAGTTTTCG
34183244 AATTCGAAT
1 AATTCGAAT
*
34183253 AACTCGAAT
1 AATTCGAAT
34183262 AATTCGAAT
1 AATTCGAAT
34183271 AATTCGAAT
1 AATTCGAAT
34183280 A
1 A
34183281 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:34184381 original size:5 final size:5
Alignment explanation
Indices: 34184371--34184396 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
34184361 CTCGAAAATT
34184371 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
34184397 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:34185060 original size:23 final size:23
Alignment explanation
Indices: 34185034--34185078 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
34185024 GATTCGATCA
34185034 ATTAATTTGATTTTAATCAAACG
1 ATTAATTTGATTTTAATCAAACG
34185057 ATTAATTTGATTTTAATCAAAC
1 ATTAATTTGATTTTAATCAAAC
34185079 TATGAACACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (23 bp):
ATTAATTTGATTTTAATCAAACG
Found at i:34188524 original size:21 final size:21
Alignment explanation
Indices: 34188498--34188539 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
34188488 GTCGCTTAAA
*
34188498 TTTTGACGGATCCATATTGCC
1 TTTTGACGGATCCACATTGCC
* *
34188519 TTTTGATGGATTCACATTGCC
1 TTTTGACGGATCCACATTGCC
34188540 ATCAATTTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (21 bp):
TTTTGACGGATCCACATTGCC
Found at i:34188968 original size:15 final size:15
Alignment explanation
Indices: 34188944--34188973 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34188934 CATCGCTAAA
34188944 AATAGGAAAAACAAC
1 AATAGGAAAAACAAC
*
34188959 AATAGTAAAAACAAC
1 AATAGGAAAAACAAC
34188974 CAAGAGCATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.13, G:0.10, T:0.10
Consensus pattern (15 bp):
AATAGGAAAAACAAC
Found at i:34191517 original size:26 final size:26
Alignment explanation
Indices: 34191481--34191542 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
34191471 ACATATTTTT
*
34191481 TCAAAATTTTACCA-AGGTCAAAATCG
1 TCAAAATTTTACCAGAGGT-AAAATCA
*
34191507 TCAAAATTTTACCAGGGGTAAAATCA
1 TCAAAATTTTACCAGAGGTAAAATCA
34191533 TCAAAATTTT
1 TCAAAATTTT
34191543 GTTGGGGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 30 0.91
27 3 0.09
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (26 bp):
TCAAAATTTTACCAGAGGTAAAATCA
Found at i:34193538 original size:18 final size:18
Alignment explanation
Indices: 34193488--34193553 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 18
34193478 TTCATGACAT
*
34193488 ATTTCACATTTCATTTTCC
1 ATTTCACATATCA-TTTCC
* *
34193507 A-TCCACTATCTCATTTCC
1 ATTTCAC-ATATCATTTCC
*
34193525 ATTTCACATATCA-TGCC
1 ATTTCACATATCATTTCC
34193542 ATTTCA-ATATCA
1 ATTTCACATATCA
34193554 ACTATAGAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
16 6 0.15
17 9 0.22
18 15 0.38
19 10 0.25
ACGTcount: A:0.27, C:0.29, G:0.02, T:0.42
Consensus pattern (18 bp):
ATTTCACATATCATTTCC
Found at i:34200689 original size:24 final size:24
Alignment explanation
Indices: 34200650--34200719 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
34200640 AATACCAACC
*
34200650 TTTTCATT-ACTATCCTTTTTGACA
1 TTTTCATTGA-TATCCTTTTCGACA
* *
34200674 TTTTCATTGATTTCCTTTTCGACC
1 TTTTCATTGATATCCTTTTCGACA
34200698 TTTTCATTGATATCCTTTTCGA
1 TTTTCATTGATATCCTTTTCGA
34200720 ATAACGTCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 40 0.98
25 1 0.02
ACGTcount: A:0.17, C:0.21, G:0.07, T:0.54
Consensus pattern (24 bp):
TTTTCATTGATATCCTTTTCGACA
Found at i:34200770 original size:40 final size:40
Alignment explanation
Indices: 34200686--34200824 Score: 142
Period size: 40 Copynumber: 3.5 Consensus size: 40
34200676 TTCATTGATT
*
34200686 TCCTTTTCGACCTTTTCA-TTGATATCCTTTTCGAATAAC
1 TCCTTTTCAACCTTTTCATTTGATATCCTTTTCGAATAAC
*
34200725 GTCCTTTTCAACCTTTTCATTTGATATCCTTTTTGGACAT-A-
1 -TCCTTTTCAACCTTTTCATTTGATATCC-TTTTCGA-ATAAC
* * * *
34200766 TCCTTTTCAACATTTTCATGTGTTATCCCTTTC-AAGTAACC
1 TCCTTTTCAACCTTTTCATTTGATATCCTTTTCGAA-TAA-C
*
34200807 TCCTTTTCAAACTTTTCA
1 TCCTTTTCAACCTTTTCA
34200825 AGTATTCAGA
Statistics
Matches: 83, Mismatches: 9, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
37 1 0.01
38 2 0.02
39 4 0.05
40 42 0.51
41 25 0.30
42 7 0.08
43 2 0.02
ACGTcount: A:0.21, C:0.25, G:0.07, T:0.47
Consensus pattern (40 bp):
TCCTTTTCAACCTTTTCATTTGATATCCTTTTCGAATAAC
Found at i:34205132 original size:13 final size:13
Alignment explanation
Indices: 34205114--34205139 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34205104 AACAATAGGG
34205114 GTAAATTCATTTT
1 GTAAATTCATTTT
34205127 GTAAATTCATTTT
1 GTAAATTCATTTT
34205140 TTCTCATGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (13 bp):
GTAAATTCATTTT
Found at i:34220122 original size:22 final size:22
Alignment explanation
Indices: 34220096--34220137 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
34220086 CCTCAGCTAC
34220096 CCAAACACAACCAAACCCAAAT
1 CCAAACACAACCAAACCCAAAT
* *
34220118 CCAAACAGAACCAGACCCAA
1 CCAAACACAACCAAACCCAA
34220138 CTAGCCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.40, G:0.05, T:0.02
Consensus pattern (22 bp):
CCAAACACAACCAAACCCAAAT
Found at i:34221237 original size:3 final size:3
Alignment explanation
Indices: 34221231--34221269 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
34221221 TTAATAATAA
* *
34221231 TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
34221270 AATTGCCCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:34221511 original size:39 final size:39
Alignment explanation
Indices: 34221449--34221526 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
34221439 TATATGTGTT
* * *
34221449 CTTTATATTTTATGATTCATACATATATCTATATATATA
1 CTTTATATTTTATGATACATACATACATATATATATATA
* ** *
34221488 CTTTTTATTTTATGATAGTTACATACATATATATGTATA
1 CTTTATATTTTATGATACATACATACATATATATATATA
34221527 TGCTTACTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.51
Consensus pattern (39 bp):
CTTTATATTTTATGATACATACATACATATATATATATA
Found at i:34221713 original size:18 final size:17
Alignment explanation
Indices: 34221690--34221725 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
34221680 TTTAATTTTA
*
34221690 TATTTGTTTATTTACTTT
1 TATTTGTTGATTT-CTTT
34221708 TATTTGTTGATTTCTTT
1 TATTTGTTGATTTCTTT
34221725 T
1 T
34221726 CATTATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.72
Consensus pattern (17 bp):
TATTTGTTGATTTCTTT
Found at i:34222026 original size:110 final size:110
Alignment explanation
Indices: 34221833--34222375 Score: 855
Period size: 110 Copynumber: 5.0 Consensus size: 110
34221823 TATCAAAAAC
*
34221833 AAAAATTTTCAAATAAGGCAATGTTTTACGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
*
34221898 GGGTGTCGATTTTTCTCATTCAACCAAATGGTTAAATATCCTTTT
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
*
34221943 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGACAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
34222008 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
* * *
34222053 AAAAATTTTAAAATAAGGCAATGTTTTGCATTTGGGAAATTCGAGAGAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
* *
34222118 AGGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTT
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
* * *
34222163 AAAAAATTTTCGAAATAAAGCAATGATTTGCATTTGGGAAATTCGAG-----GTGCCCTAAGGTG
1 -AAAAATTTTC-AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTG
*
34222223 CTGGGTGTCGATTTTTCTCGTTCAACCAAATGGCTAAATATCCTTTT
64 CTGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
* * *
34222270 AAAATTTTTAAAATAAGGCAATGTTTTGCGTTT-GAAAATTCGAGAAAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
* * * *
34222334 GGGTGTCGATTTTTCTCATTTAACCGAATAGCCAAATATCCT
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCT
34222376 CTTGAATTTC
Statistics
Matches: 403, Mismatches: 23, Indels: 15
0.91 0.05 0.03
Matches are distributed among these distances:
104 10 0.02
105 20 0.05
106 8 0.02
107 59 0.15
109 52 0.13
110 212 0.53
111 9 0.02
112 33 0.08
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.34
Consensus pattern (110 bp):
AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
Found at i:34226385 original size:9 final size:9
Alignment explanation
Indices: 34226371--34226400 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
34226361 CTCGAAAGAA
34226371 AAATAAAAT
1 AAATAAAAT
*
34226380 AAATAAAAC
1 AAATAAAAT
34226389 AAATAAAAT
1 AAATAAAAT
34226398 AAA
1 AAA
34226401 AATAAAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (9 bp):
AAATAAAAT
Found at i:34226422 original size:20 final size:20
Alignment explanation
Indices: 34226371--34226412 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 20
34226361 CTCGAAAGAA
34226371 AAATAAAAT--AAATAAAAC
1 AAATAAAATAAAAATAAAAC
34226389 AAATAAAATAAAAATAAAAAC
1 AAATAAAATAAAAAT-AAAAC
34226410 AAA
1 AAA
34226413 AAATCAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.43
20 4 0.19
21 8 0.38
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (20 bp):
AAATAAAATAAAAATAAAAC
Found at i:34228397 original size:34 final size:34
Alignment explanation
Indices: 34228354--34228418 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
34228344 GGAGGAGATT
*
34228354 GAAGATAGCAGATCTTGTCTTCCTATATTTGATC
1 GAAGATAGCAGATCTTATCTTCCTATATTTGATC
*
34228388 GAAGATAGCAGATCTTATCTTCCTGTATTTG
1 GAAGATAGCAGATCTTATCTTCCTATATTTG
34228419 GCAGCGGAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.38
Consensus pattern (34 bp):
GAAGATAGCAGATCTTATCTTCCTATATTTGATC
Found at i:34228817 original size:46 final size:46
Alignment explanation
Indices: 34228384--34228807 Score: 713
Period size: 46 Copynumber: 9.2 Consensus size: 46
34228374 TCCTATATTT
*
34228384 GATCGAAGATAGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGA
1 GATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGA
*
34228430 GATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAACGGAGGA
1 GATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGA
*
34228476 GATAGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGA
1 GATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGA
* *
34228522 GATCAAAGATAGCAGATCTTTTCTTCCTGTATTTGGCAGCGGAGGA
1 GATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGA
* * *
34228568 GATCAAAGATAGTAGATCTTGTCTTCCTGTATTTGGCAGCGAAGGA
1 GATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGA
*
34228614 GATCGAAGATAGTAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGA
1 GATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGA
* *
34228660 GATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGACAGTGGAGGA
1 GATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGA
34228706 GATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGA
1 GATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGA
* * * *
34228752 GATCGAAGATAGCAAATCTTGTCTTTCTGTATTTGGCAGCAGAGTA
1 GATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGA
34228798 GATCGAAGAT
1 GATCGAAGAT
34228808 GGTGAATCTT
Statistics
Matches: 357, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 357 1.00
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (46 bp):
GATCGAAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGA
Found at i:34229035 original size:132 final size:132
Alignment explanation
Indices: 34228797--34229117 Score: 441
Period size: 132 Copynumber: 2.4 Consensus size: 132
34228787 GCAGCAGAGT
* *
34228797 AGATCGAAGATGGTGAATCTTATCTTCCCAATACAGCGGAGAAGCAGATTTAAGCCATTAGTCCT
1 AGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAACCATTAGTCCT
* * ** * *
34228862 ATCACTCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCA-CCCTAAGCAGTAGTGG
66 ATCACTCTAAGCAGTAGTGGAATAGATCAAAGACTGCAGATTCTGT-ATCCCTAAACAGTAGTGG
34228926 AGC
130 AGC
*
34228929 AGATCGAATATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAACCATTAGTCCT
1 AGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAACCATTAGTCCT
*
34228994 ATCAC-CTTAAGCAGTAGTGGAATAGATCAAAGACTGTAGATTCTGTATCCCTAAACAGTAGTGG
66 ATCACTC-TAAGCAGTAGTGGAATAGATCAAAGACTGCAGATTCTGTATCCCTAAACAGTAGTGG
34229058 AGC
130 AGC
* * * * * * *
34229061 AGATCAAAGACGGTGAATTTTATCTTCCCAAGATAGTAGG-GAAGTAAATTTAAACCA
1 AGATCGAAGATGGTGAATCTTATCTTCCCAATACAGT-GGAGAAGCAGATTTAAACCA
34229118 CAAACCTCCC
Statistics
Matches: 168, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
131 2 0.01
132 164 0.98
133 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (132 bp):
AGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAACCATTAGTCCT
ATCACTCTAAGCAGTAGTGGAATAGATCAAAGACTGCAGATTCTGTATCCCTAAACAGTAGTGGA
GC
Found at i:34229431 original size:22 final size:22
Alignment explanation
Indices: 34229405--34229446 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
34229395 CCTCAGCTAC
34229405 CCAAACACAACCAAACCCAAAT
1 CCAAACACAACCAAACCCAAAT
* * *
34229427 CCAAATAGAACCAGACCCAA
1 CCAAACACAACCAAACCCAA
34229447 CTAGCCTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.38, G:0.05, T:0.05
Consensus pattern (22 bp):
CCAAACACAACCAAACCCAAAT
Found at i:34230576 original size:3 final size:3
Alignment explanation
Indices: 34230570--34230611 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
34230560 TTACTAATAA
* *
34230570 TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
34230612 AATTGCCCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:34230683 original size:24 final size:22
Alignment explanation
Indices: 34230634--34230694 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 22
34230624 ATATATACGT
* * *
34230634 TTTTTTATATATATACATATAT
1 TTTTTTATATATACACACATAC
34230656 TTTTTTATATACTTACACACATAC
1 TTTTTTATATA--TACACACATAC
34230680 TTTTTGTAATATATA
1 TTTTT-T-ATATATA
34230695 TGTACACTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
22 11 0.34
24 15 0.47
25 1 0.03
26 5 0.16
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTTTTATATATACACACATAC
Found at i:34231017 original size:18 final size:17
Alignment explanation
Indices: 34230994--34231029 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
34230984 TTTAATTTTA
*
34230994 TATTTGTTTATTTACTTT
1 TATTTGTTGATTT-CTTT
34231012 TATTTGTTGATTTCTTT
1 TATTTGTTGATTTCTTT
34231029 T
1 T
34231030 CATTATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.72
Consensus pattern (17 bp):
TATTTGTTGATTTCTTT
Found at i:34231548 original size:112 final size:110
Alignment explanation
Indices: 34231137--34231575 Score: 761
Period size: 110 Copynumber: 4.0 Consensus size: 110
34231127 TATCAAAAAC
* *
34231137 AAAAATTTTCAAATAAGGCAATGTTTTACGTTTGGAAAATTCGAGAAAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
34231202 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
34231247 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
34231312 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
* *
34231357 AAAAATTTTAAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAGAACGTGCCCTAAGGTGCT
1 AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
* *
34231422 GGGTGTCGATTTTTCTCGTACAACCAAATGGCTAAATATCCTTTT
66 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
*
34231467 AAAAAATTTTCGAAATAAGGCAATGTTTTGCATTTGGGAAATTCGAGAAAACGTGCCCTAAGGTG
1 -AAAAATTTTC-AAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTG
* * * *
34231532 CTGGGTGTCGATTTTTCTCATTTAACCGAATAGCCAAATATCCT
64 CTGGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCT
34231576 CTTGAATTTC
Statistics
Matches: 312, Mismatches: 15, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
110 214 0.69
111 9 0.03
112 89 0.29
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (110 bp):
AAAAATTTTCAAATAAGGCAATGTTTTGCGTTTGGGAAATTCGAGAAAACGTGCCCTAAGGTGCT
GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
Found at i:34232911 original size:139 final size:139
Alignment explanation
Indices: 34232661--34232938 Score: 547
Period size: 139 Copynumber: 2.0 Consensus size: 139
34232651 TAAATAACTT
*
34232661 GGCTCTTGACACTATTTCGAGACCAATGTCGTGACGTTGCACCTTGGTTGCTAATGAATCAATGA
1 GGCTCTTGACACTATTTCAAGACCAATGTCGTGACGTTGCACCTTGGTTGCTAATGAATCAATGA
34232726 AATAGTTGGGTGAATCAATGAAATAGTGCCCAACATCATGGCATCATATACACAACATTGTGAGA
66 AATAGTTGGGTGAATCAATGAAATAGTGCCCAACATCATGGCATCATATACACAACATTGTGAGA
34232791 TCACTTTGG
131 TCACTTTGG
34232800 GGCTCTTGACACTATTTCAAGACCAATGTCGTGACGTTGCACCTTGGTTGCTAATGAATCAATGA
1 GGCTCTTGACACTATTTCAAGACCAATGTCGTGACGTTGCACCTTGGTTGCTAATGAATCAATGA
34232865 AATAGTTGGGTGAATCAATGAAATAGTGCCCAACATCATGGCATCATATACACAACATTGTGAGA
66 AATAGTTGGGTGAATCAATGAAATAGTGCCCAACATCATGGCATCATATACACAACATTGTGAGA
34232930 TCACTTTGG
131 TCACTTTGG
34232939 TCATTAATAA
Statistics
Matches: 138, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 138 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (139 bp):
GGCTCTTGACACTATTTCAAGACCAATGTCGTGACGTTGCACCTTGGTTGCTAATGAATCAATGA
AATAGTTGGGTGAATCAATGAAATAGTGCCCAACATCATGGCATCATATACACAACATTGTGAGA
TCACTTTGG
Found at i:34233514 original size:63 final size:63
Alignment explanation
Indices: 34233435--34233561 Score: 164
Period size: 63 Copynumber: 2.0 Consensus size: 63
34233425 ATCACACGCA
* *
34233435 CACACACACACACACACACAAAGACATACTTTTTTCAACCCAAACTCTCAATTTGCATAAGTC
1 CACACACACACACACACACAAAGACATACTTCTTTCAACCCAAACTATCAATTTGCATAAGTC
* * ** * * * *
34233498 CACACACGCACGCACACACAGTGACATACTTCTTTCGATCCACACTATGAATTTGCATAAGTC
1 CACACACACACACACACACAAAGACATACTTCTTTCAACCCAAACTATCAATTTGCATAAGTC
34233561 C
1 C
34233562 TATCAAATCC
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.35, C:0.33, G:0.09, T:0.23
Consensus pattern (63 bp):
CACACACACACACACACACAAAGACATACTTCTTTCAACCCAAACTATCAATTTGCATAAGTC
Found at i:34235251 original size:38 final size:38
Alignment explanation
Indices: 34235199--34235313 Score: 178
Period size: 38 Copynumber: 3.1 Consensus size: 38
34235189 TAGAAGCATA
* *
34235199 ATGTTATTCGGGCTCTGTGCCTAGCAGGCTTTGTGCCG
1 ATGTTATTCAGGCTCTGTGCCTAGTAGGCTTTGTGCCG
34235237 ATGTTATTCAGGCTCTGTGCCTAGTAGGCTTTGTGCCG
1 ATGTTATTCAGGCTCTGTGCCTAGTAGGCTTTGTGCCG
* * *
34235275 GTGTTATTCAGGCTTTGTGCGTAGTAGGC-TTGTGCCG
1 ATGTTATTCAGGCTCTGTGCCTAGTAGGCTTTGTGCCG
34235312 AT
1 AT
34235314 ATATTGAAAG
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
37 9 0.13
38 62 0.87
ACGTcount: A:0.12, C:0.20, G:0.31, T:0.37
Consensus pattern (38 bp):
ATGTTATTCAGGCTCTGTGCCTAGTAGGCTTTGTGCCG
Found at i:34235290 original size:22 final size:21
Alignment explanation
Indices: 34235223--34235294 Score: 73
Period size: 22 Copynumber: 3.6 Consensus size: 21
34235213 CTGTGCCTAG
34235223 CAGGCTTTGTGCCGATGTTATT
1 CAGGCTTTGTGCCG-TGTTATT
* *
34235245 CAGGCTCTGTGCC----TAGT
1 CAGGCTTTGTGCCGTGTTATT
34235262 -AGGCTTTGTGCCGGTGTTATT
1 CAGGCTTTGTGCC-GTGTTATT
34235283 CAGGCTTTGTGC
1 CAGGCTTTGTGC
34235295 GTAGTAGGCT
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
16 11 0.28
17 3 0.08
21 3 0.08
22 23 0.57
ACGTcount: A:0.11, C:0.21, G:0.31, T:0.38
Consensus pattern (21 bp):
CAGGCTTTGTGCCGTGTTATT
Found at i:34237234 original size:50 final size:50
Alignment explanation
Indices: 34237156--34237398 Score: 360
Period size: 50 Copynumber: 4.8 Consensus size: 50
34237146 ATTTGGGTAA
** * *
34237156 AGAGGTCCCATGTAAGACCATGAATGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
34237206 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
**
34237256 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
34237306 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
34237356 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
34237399 TGTTATTATT
Statistics
Matches: 178, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 143 0.80
51 35 0.20
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:34241828 original size:38 final size:38
Alignment explanation
Indices: 34241786--34241902 Score: 164
Period size: 38 Copynumber: 3.1 Consensus size: 38
34241776 TAGAAGCATA
* * *
34241786 ATGTTATTCCGGCTCTATGCCTAGCAGGCTTTGTGCTG
1 ATGTTATTCAGGCTCTGTGCCTAGCAGGCTTTGTGCCG
* *
34241824 ATGTTATTCGGGCTCTGTGCCTAGCAGGTTTTGTGCCG
1 ATGTTATTCAGGCTCTGTGCCTAGCAGGCTTTGTGCCG
* *
34241862 GTGTTATTCAGGCTCTGTGCCTAGTAGGC-TTGTGCCG
1 ATGTTATTCAGGCTCTGTGCCTAGCAGGCTTTGTGCCG
34241899 ATGT
1 ATGT
34241903 ATTGAAAGTT
Statistics
Matches: 70, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
37 11 0.16
38 59 0.84
ACGTcount: A:0.12, C:0.21, G:0.30, T:0.37
Consensus pattern (38 bp):
ATGTTATTCAGGCTCTGTGCCTAGCAGGCTTTGTGCCG
Found at i:34243390 original size:55 final size:55
Alignment explanation
Indices: 34243306--34243412 Score: 178
Period size: 55 Copynumber: 1.9 Consensus size: 55
34243296 TTATAGATTA
* * *
34243306 CAAATTAATTATTCATGAGCCCTATTCAAATTAAAAGTGATGATTTATCATCTTG
1 CAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATAATTTATCATCTTG
*
34243361 CAAATTAATTATTCATAAGTACTATTCAAATTAAAAGTGATAATTTATCATC
1 CAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATAATTTATCATC
34243413 CAATGGATAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.38
Consensus pattern (55 bp):
CAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATAATTTATCATCTTG
Found at i:34246738 original size:55 final size:55
Alignment explanation
Indices: 34246678--34246787 Score: 175
Period size: 55 Copynumber: 2.0 Consensus size: 55
34246668 AAATTATAGA
* * * *
34246678 TTGCAAATTAATTTTTCATGAGTACTATTCAAATTAAAAGTGATGATTTATCATC
1 TTGCAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATGATCTATCATC
*
34246733 TTGCAAATTAATTATTCATAAGCACTATTCAAATTAAAATTGATGATCTATCATC
1 TTGCAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATGATCTATCATC
34246788 CAATGGATAC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (55 bp):
TTGCAAATTAATTATTCATAAGCACTATTCAAATTAAAAGTGATGATCTATCATC
Found at i:34251781 original size:10 final size:10
Alignment explanation
Indices: 34251739--34251786 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
34251729 TAAAAATTGT
34251739 ATTTTTTATA
1 ATTTTTTATA
*
34251749 ATTTTATATA
1 ATTTTTTATA
* *
34251759 ATTCTTAATA
1 ATTTTTTATA
*
34251769 ATTTTTTAGA
1 ATTTTTTATA
*
34251779 ATTATTTA
1 ATTTTTTA
34251787 AAAAACACAG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:34251844 original size:32 final size:32
Alignment explanation
Indices: 34251808--34251885 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 32
34251798 ATAAACCTAG
*
34251808 AAAAATATTTTTTTAAGATTTGTTATCTGTTA
1 AAAAATATTTTTTTAAGATTTGTTATCTATTA
*
34251840 AAAAATA-TTTTTTAAGATTTTTTATCTATTA
1 AAAAATATTTTTTTAAGATTTGTTATCTATTA
*
34251871 AAAAATATTTGTTTA
1 AAAAATATTTTTTTA
34251886 CTTAACATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
31 29 0.69
32 13 0.31
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (32 bp):
AAAAATATTTTTTTAAGATTTGTTATCTATTA
Found at i:34257163 original size:188 final size:186
Alignment explanation
Indices: 34256830--34257182 Score: 485
Period size: 188 Copynumber: 1.9 Consensus size: 186
34256820 GGTGTTTTAC
* *** * * *
34256830 TTTGATATTCTTGAAATTTTTATTATTTGTTAAATTTTATTTACTTAATTTTTTTTTCAAAATAT
1 TTTGATATTCTTGAAAATTTTATTATTTGTTAAAACATATTTACTAAAATTTATTTTCAAAATAT
* * * *
34256895 ATTTTTAAGGTTAATTCGACACTTTTGAGTATTGAGTACAGTGCATTATCAAATCATTATAAGAA
66 ATTTTTAAGGTTAACTCGACACCTTTGAGTATTGAGTACAATGCATTATCAAATCATTACAAGAA
*
34256960 TGCATCCATTATATGTCAAGAGAAAAGGATTGTTGTAACGTCCCAATTTTTTTTTT
131 TGCATCCACTATATGTCAAGAGAAAAGGATTGTTGTAACGTCCCAATTTTTTTTTT
* *
34257016 TTTGATATTGTTGAAAATTTTATTATTTGTTAAAACATATTTGCTCAAAATTTATTTTCAAAATG
1 TTTGATATTCTTGAAAATTTTATTATTTGTTAAAACATATTTACT-AAAATTTATTTTCAAAAT-
* * * *
34257081 CAT-TTTTTAAGGTTAACTCGACACCTTTGATTGTTGAGTACAATGCGTTGTCAAATCATTACAA
64 -ATATTTTTAAGGTTAACTCGACACCTTTGAGTATTGAGTACAATGCATTATCAAATCATTACAA
*
34257145 -AAGTGCATGCACTATATGTCAAGAGAAAAGGATTGTTG
128 GAA-TGCATCCACTATATGTCAAGAGAAAAGGATTGTTG
34257183 AAACACCCTA
Statistics
Matches: 144, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
186 39 0.27
187 17 0.12
188 86 0.60
189 2 0.01
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (186 bp):
TTTGATATTCTTGAAAATTTTATTATTTGTTAAAACATATTTACTAAAATTTATTTTCAAAATAT
ATTTTTAAGGTTAACTCGACACCTTTGAGTATTGAGTACAATGCATTATCAAATCATTACAAGAA
TGCATCCACTATATGTCAAGAGAAAAGGATTGTTGTAACGTCCCAATTTTTTTTTT
Found at i:34265356 original size:26 final size:27
Alignment explanation
Indices: 34265321--34265373 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
34265311 ACCATAGCAC
34265321 AAATCAGTCATTTACCC-TCGAGGGGCA
1 AAATCAGTCATTTACCCTTC-AGGGGCA
34265348 AAAT-AGTCATTTACCCTTCAGGGGCA
1 AAATCAGTCATTTACCCTTCAGGGGCA
34265374 TTACGATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (27 bp):
AAATCAGTCATTTACCCTTCAGGGGCA
Found at i:34271852 original size:43 final size:44
Alignment explanation
Indices: 34271804--34271902 Score: 112
Period size: 44 Copynumber: 2.3 Consensus size: 44
34271794 GTACGAGATT
* *
34271804 GCATTTTGGTGC-CACTGAT-TCGCACTACAGTGCCTACTATTTA
1 GCATTTTGATGCTCACT-ATCTAGCACTACAGTGCCTACTATTTA
* * * *
34271847 GCATTTTGATGCTTACTATCTAGCACTTCAGTGCCTACTAATCA
1 GCATTTTGATGCTCACTATCTAGCACTACAGTGCCTACTATTTA
*
34271891 GCACTTTGATGC
1 GCATTTTGATGC
34271903 CTACTGTTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
43 13 0.28
44 34 0.72
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.35
Consensus pattern (44 bp):
GCATTTTGATGCTCACTATCTAGCACTACAGTGCCTACTATTTA
Found at i:34271885 original size:22 final size:22
Alignment explanation
Indices: 34271825--34271896 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
34271815 CCACTGATTC
* *
34271825 GCACTACAGTGCCTACTATTTA
1 GCACTTCAGTGCCTACTATCTA
** *
34271847 GCA-TTTTGATGCTTACTATCTA
1 GCACTTCAG-TGCCTACTATCTA
34271869 GCACTTCAGTGCCTACTAATC-A
1 GCACTTCAGTGCCTACT-ATCTA
34271891 GCACTT
1 GCACTT
34271897 TGATGCCTAC
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
21 2 0.05
22 31 0.79
23 6 0.15
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (22 bp):
GCACTTCAGTGCCTACTATCTA
Found at i:34271903 original size:22 final size:22
Alignment explanation
Indices: 34271834--34271907 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
34271824 CGCACTACAG
* * *
34271834 TGCCTACTATTTAGCATTTTGA
1 TGCCTACTAATCAGCACTTTGA
* *
34271856 TGCTTACT-ATCTAGCAC-TTCA
1 TGCCTACTAATC-AGCACTTTGA
34271877 GTGCCTACTAATCAGCACTTTGA
1 -TGCCTACTAATCAGCACTTTGA
34271900 TGCCTACT
1 TGCCTACT
34271908 GTTTAAACTC
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
21 4 0.10
22 31 0.76
23 6 0.15
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.38
Consensus pattern (22 bp):
TGCCTACTAATCAGCACTTTGA
Found at i:34280885 original size:44 final size:44
Alignment explanation
Indices: 34280822--34280971 Score: 166
Period size: 43 Copynumber: 3.5 Consensus size: 44
34280812 GATGTGTTAT
* *
34280822 CGTGTAAGACCACATCTGGGACGTTGGCATCGATTTGTGATTTA
1 CGTGTAAGACCATATCTGGGACGTTGGCATCGATATGTGATTTA
* * * *
34280866 CGTGTAAGACCATGTCTGGGACATCGGCATCG-TATATGATTT-
1 CGTGTAAGACCATATCTGGGACGTTGGCATCGATATGTGATTTA
* *
34280908 CGTGTAAGACTC-TGTCTGGGACAG-TGGCATCGATATGTGA-TAA
1 CGTGTAAGAC-CATATCTGGGAC-GTTGGCATCGATATGTGATTTA
*
34280951 CATGTAAGACCATATCTGGGA
1 CGTGTAAGACCATATCTGGGA
34280972 TATGGCGTTG
Statistics
Matches: 89, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
42 29 0.33
43 32 0.36
44 28 0.31
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (44 bp):
CGTGTAAGACCATATCTGGGACGTTGGCATCGATATGTGATTTA
Found at i:34282530 original size:2 final size:2
Alignment explanation
Indices: 34282523--34282565 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
34282513 GTTAATGTCG
34282523 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34282565 T
1 T
34282566 TAACATTTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34283621 original size:14 final size:14
Alignment explanation
Indices: 34283602--34283648 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
34283592 CACGGGCTTC
34283602 GTTTGTCTTTCTAA
1 GTTTGTCTTTCTAA
34283616 GTTTG----TCTAA
1 GTTTGTCTTTCTAA
34283626 GTTTGTCTTTCTAA
1 GTTTGTCTTTCTAA
34283640 GTTTGTCTT
1 GTTTGTCTT
34283649 CTTCCTCCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 10 0.34
14 19 0.66
ACGTcount: A:0.13, C:0.13, G:0.17, T:0.57
Consensus pattern (14 bp):
GTTTGTCTTTCTAA
Found at i:34283634 original size:24 final size:24
Alignment explanation
Indices: 34283602--34283647 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
34283592 CACGGGCTTC
34283602 GTTTGTCTTTCTAAGTTTGTCTAA
1 GTTTGTCTTTCTAAGTTTGTCTAA
34283626 GTTTGTCTTTCTAAGTTTGTCT
1 GTTTGTCTTTCTAAGTTTGTCT
34283648 TCTTCCTCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.13, C:0.13, G:0.17, T:0.57
Consensus pattern (24 bp):
GTTTGTCTTTCTAAGTTTGTCTAA
Found at i:34283920 original size:25 final size:25
Alignment explanation
Indices: 34283886--34283946 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
34283876 AGCCACCCCT
* *
34283886 TTTATTTTATTTTATTTATTTATTA
1 TTTATTTTATTTTATTTACTAATTA
* * *
34283911 TTTATATTATTTTTTTTACTAATTT
1 TTTATTTTATTTTATTTACTAATTA
34283936 TTTATTTTATT
1 TTTATTTTATT
34283947 ATTCTTATAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTATTTTATTTTATTTACTAATTA
Found at i:34288885 original size:42 final size:42
Alignment explanation
Indices: 34288838--34288923 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 42
34288828 TCCTTCTTTT
* * *
34288838 GTGGAAAAAATGTTATAATT-TATGTGCTAATTTTGTATTTAA
1 GTGGAAAAAATGTAATAATTGTAAG-GCTAATTTTGTACTTAA
* *
34288880 GTGGAAATAATGTAATAGTTGTAAGGCTAATTTTGTACTTAA
1 GTGGAAAAAATGTAATAATTGTAAGGCTAATTTTGTACTTAA
34288922 GT
1 GT
34288924 CTACAATAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
42 35 0.92
43 3 0.08
ACGTcount: A:0.35, C:0.03, G:0.20, T:0.42
Consensus pattern (42 bp):
GTGGAAAAAATGTAATAATTGTAAGGCTAATTTTGTACTTAA
Found at i:34290911 original size:23 final size:23
Alignment explanation
Indices: 34290861--34290917 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
34290851 TAAAATAGTG
*
34290861 GAAAAACAACAAGAAAATATAAA
1 GAAAAACAACAAGAAAACATAAA
* *
34290884 GAAAAAAAACAAGAAAACAGTGAA
1 GAAAAACAACAAGAAAACA-TAAA
34290908 -AAAAACAACA
1 GAAAAACAACA
34290918 GTTTTTTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 26 0.90
24 3 0.10
ACGTcount: A:0.74, C:0.11, G:0.11, T:0.05
Consensus pattern (23 bp):
GAAAAACAACAAGAAAACATAAA
Found at i:34300770 original size:22 final size:22
Alignment explanation
Indices: 34300723--34300771 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
34300713 TAAATATTTT
* * *
34300723 TAAATAAATTTTTATTTTTATT
1 TAAATAAATGTTTATTTTGATA
34300745 TAAATAAATGTTTATATTTGA-A
1 TAAATAAATGTTTAT-TTTGATA
34300767 TAAAT
1 TAAAT
34300772 TAAAACTCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (22 bp):
TAAATAAATGTTTATTTTGATA
Found at i:34303498 original size:18 final size:18
Alignment explanation
Indices: 34303475--34303511 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
34303465 TGAATTTTCG
34303475 AATTTGAATAACTCGAAT
1 AATTTGAATAACTCGAAT
*
34303493 AATTTGAATAATTCGAAT
1 AATTTGAATAACTCGAAT
34303511 A
1 A
34303512 TCAAACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.35
Consensus pattern (18 bp):
AATTTGAATAACTCGAAT
Found at i:34305331 original size:18 final size:19
Alignment explanation
Indices: 34305308--34305352 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
34305298 ATATATATTG
34305308 TATATATTTTAAATGTT-T
1 TATATATTTTAAATGTTAT
* *
34305326 TATATATGTTATATGTTAT
1 TATATATTTTAAATGTTAT
34305345 TAT-TATTT
1 TATATATTT
34305353 ATTTGCAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (19 bp):
TATATATTTTAAATGTTAT
Found at i:34305513 original size:2 final size:2
Alignment explanation
Indices: 34305508--34305539 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
34305498 TTTTACATTC
34305508 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34305540 TTATTTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34305809 original size:22 final size:22
Alignment explanation
Indices: 34305767--34305809 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
34305757 TATTTTTATT
* *
34305767 TTTATTTTTTACTTTATTATAC
1 TTTATATTTTACTATATTATAC
34305789 TTTATATTTTA-TATATATATA
1 TTTATATTTTACTATAT-TATA
34305810 TATTAATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTATATTTTACTATATTATAC
Found at i:34307832 original size:19 final size:18
Alignment explanation
Indices: 34307808--34307853 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
34307798 AACGTCTCTT
*
34307808 TTTGCATTCATTTCATGCA
1 TTTGCATTCATTGCAT-CA
34307827 TTTGCATTTCATTGCATCA
1 TTTGCA-TTCATTGCATCA
*
34307846 TATGCATT
1 TTTGCATT
34307854 AAACACCTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 13 0.54
20 9 0.38
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.48
Consensus pattern (18 bp):
TTTGCATTCATTGCATCA
Found at i:34310598 original size:44 final size:46
Alignment explanation
Indices: 34310538--34310625 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 46
34310528 AAAGGTGGGA
* *
34310538 CCAATGTGAAAGCCTACAAA-GGGCGCTTTGAGT-AAAAAAAAAGG
1 CCAAGGTGAAACCCTACAAAGGGGCGCTTTGAGTCAAAAAAAAAGG
*
34310582 CCAAGGTGAAACCCTACAAAGGGGCTCTTTGAGTCAAAAAAAAA
1 CCAAGGTGAAACCCTACAAAGGGGCGCTTTGAGTCAAAAAAAAA
34310626 AGAGACCAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
44 18 0.46
45 12 0.31
46 9 0.23
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (46 bp):
CCAAGGTGAAACCCTACAAAGGGGCGCTTTGAGTCAAAAAAAAAGG
Found at i:34312181 original size:132 final size:132
Alignment explanation
Indices: 34311964--34312457 Score: 704
Period size: 132 Copynumber: 3.7 Consensus size: 132
34311954 ATGGAGCAGG
*
34311964 TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGTAGATCAAAGATGGTGGATTTTACC
1 TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACC
* *
34312029 TCCCTGTGGTTACAGCGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCAGTGGAATA
66 TCCCTGAGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCAGTGGAATA
34312094 GA
131 GA
** * * * ***
34312096 TTGAAGATTTTGGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGACAGATTTTACC
1 TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACC
* * * *
34312161 T-CCTCGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTTTACTTCCCTGGACAGCAGTGGAAT
66 TCCCT-GAGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCAGTGGAAT
34312225 AGA
130 AGA
* * *
34312228 TTGAAGATTTTAGATCTTGCCTCTCTAAGCAGTAGTGGAGAAGATCAAAGATGGTGGATTTTACC
1 TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACC
** *
34312293 TCCCTGAGGTTACAGTGGAGTACATTGAAGCCAATAATTCTA-TCTCCCTCAGCAACAGTGGAAT
66 TCCCTGAGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACT-TCCCTGGGCAGCAGTGGAAT
*
34312357 AAA
130 AGA
* ** * *
34312360 TTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGATGGTGGATTTTACC
1 TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACC
*
34312425 TCCCTGAGGTTACAGTAGAGTACATTGAAGCCA
66 TCCCTGAGGTTACAGTGGAGTACATTGAAGCCA
34312458 GTTATCCTAT
Statistics
Matches: 320, Mismatches: 39, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
131 4 0.01
132 313 0.98
133 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (132 bp):
TTGAAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACC
TCCCTGAGGTTACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCAGTGGAATA
GA
Found at i:34312507 original size:132 final size:132
Alignment explanation
Indices: 34311975--34312514 Score: 628
Period size: 132 Copynumber: 4.1 Consensus size: 132
34311965 TGAAGATTTC
* * * *
34311975 AGATCTTGCCTCCCTAAGCAGTAGTGGAGTAGATCAAAGATGGTGGATTTTACCTCCCTGTGGTT
1 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAAATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
* * *
34312040 ACAGCGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATT
66 ACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGAGCAGCAGTGGAATAGATTGAA-AAT
*
34312105 TTG
130 TAG
* * * *** *
34312108 -GATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGACAGATTTTACCT-CCTCGTGGT
1 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAAATCAAAGATGGTGGATTTTACCTCCCT-GAGGT
* * *
34312171 TACAGTGGAGTACATTGAAGCCAGTAATTTTACTTCCCTG-GACAGCAGTGGAATAGATTGAAGA
65 TACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGAG-CAGCAGTGGAATAGATTGAAAA
**
34312235 TTTT
129 TTAG
* *
34312239 AGATCTTGCCTCTCTAAGCAGTAGTGGAG-AAGATCAAAGATGGTGGATTTTACCTCCCTGAGGT
1 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAA-ATCAAAGATGGTGGATTTTACCTCCCTGAGGT
* * * *
34312303 TACAGTGGAGTACATTGAAGCCAATAATTCTA-TCTCCCTCAGCAACAGTGGAATAAATTGAAGA
65 TACAGTGGAGTACATTGAAGCCAATAATTCTACT-TCCCTGAGCAGCAGTGGAATAGATTGAAAA
*
34312367 TTAC
129 TTAG
* *
34312371 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGATGGTGGATTTTACCTCCCTGAGGTT
1 AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAAATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
* * * * * *
34312436 ACAGTAGAGTACATTGAAGCCAGTTATCCTATTTCCCTGA-TATCGCAGT-GAAGTAGATT-AAA
66 ACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGAGCA--GCAGTGGAA-TAGATTGAAA
*
34312498 ATGAG
128 ATTAG
34312503 AGATCTTGTCTC
1 AGATCTTGTCTC
34312515 TCTGAAGTTG
Statistics
Matches: 350, Mismatches: 45, Indels: 25
0.83 0.11 0.06
Matches are distributed among these distances:
131 10 0.03
132 324 0.93
133 16 0.05
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (132 bp):
AGATCTTGTCTCCCTAAGCAGTAGTGGAGCAAATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
ACAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTGAGCAGCAGTGGAATAGATTGAAAATT
AG
Found at i:34312509 original size:264 final size:264
Alignment explanation
Indices: 34311975--34312517 Score: 727
Period size: 264 Copynumber: 2.1 Consensus size: 264
34311965 TGAAGATTTC
* * *
34311975 AGATCTTGCCTCCCTAAGCAGTAGTGGAGTAGATCAAAGATGGTGGATTTTACCTCCCTGTGGTT
1 AGATCTTGCCTCTCTAAGCAGTAGTGGAGAAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
** * *
34312040 ACAGCGGAGTACATTGAAGCCAATAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATT
66 ACAGCGGAGTACATTGAAGCCAATAATTCTACTTCCCTCAGCAACAGTGGAATAAATTGAAGATT
*** * * * *
34312105 TTGGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATTAAAGACGACAGATTTTACCTCCTCGTGG
131 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCAAAGACGACAGATTTTACCTCCTCGAGG
* ** *
34312170 TTACAGTGGAGTACATTGAAGCCAGTAATTTTACTTCCCTGGACAGCAGTGGAATAGATTGAAGA
196 TTACAGTAGAGTACATTGAAGCCAGTAATCCTACTTCCCTGGACAGCAGTGGAATAGATTGAAAA
***
34312235 TTTT
261 TGAG
34312239 AGATCTTGCCTCTCTAAGCAGTAGTGGAGAAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
1 AGATCTTGCCTCTCTAAGCAGTAGTGGAGAAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
*
34312304 ACAGTGGAGTACATTGAAGCCAATAATTCTA-TCTCCCTCAGCAACAGTGGAATAAATTGAAGAT
66 ACAGCGGAGTACATTGAAGCCAATAATTCTACT-TCCCTCAGCAACAGTGGAATAAATTGAAGAT
* * ***
34312368 TACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGATGGTGGATTTTACCTCC-CTGA
130 TACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCAAAGACGACAGATTTTACCTCCTC-GA
* * *
34312432 GGTTACAGTAGAGTACATTGAAGCCAGTTATCCTATTTCCCT-GATATCGCAGT-GAAGTAGATT
194 GGTTACAGTAGAGTACATTGAAGCCAGTAATCCTACTTCCCTGGACA--GCAGTGGAA-TAGATT
34312495 -AAAATGAG
256 GAAAATGAG
*
34312503 AGATCTTGTCTCTCT
1 AGATCTTGCCTCTCT
34312518 GAAGTTGCAG
Statistics
Matches: 243, Mismatches: 31, Indels: 10
0.86 0.11 0.04
Matches are distributed among these distances:
263 5 0.02
264 227 0.93
265 11 0.05
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (264 bp):
AGATCTTGCCTCTCTAAGCAGTAGTGGAGAAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
ACAGCGGAGTACATTGAAGCCAATAATTCTACTTCCCTCAGCAACAGTGGAATAAATTGAAGATT
ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCAAAGACGACAGATTTTACCTCCTCGAGG
TTACAGTAGAGTACATTGAAGCCAGTAATCCTACTTCCCTGGACAGCAGTGGAATAGATTGAAAA
TGAG
Found at i:34314007 original size:18 final size:19
Alignment explanation
Indices: 34313984--34314028 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
34313974 ATATATATTG
34313984 TATATATTTTAAATGTT-T
1 TATATATTTTAAATGTTAT
* *
34314002 TATATATGTTATATGTTAT
1 TATATATTTTAAATGTTAT
34314021 TAT-TATTT
1 TATATATTT
34314029 ATTTGCAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (19 bp):
TATATATTTTAAATGTTAT
Found at i:34314382 original size:44 final size:43
Alignment explanation
Indices: 34314328--34314417 Score: 110
Period size: 44 Copynumber: 2.1 Consensus size: 43
34314318 ATATACATAC
* **
34314328 TTTGTGAATATATGTACATATACTTATACATTTT-ATTTTTCTAT
1 TTTGTAAATATATACACATATAC--ATACATTTTCATTTTTCTAT
* *
34314372 TTTGTAAATATATACGCATATACATACATTTTCATTTTTTTAT
1 TTTGTAAATATATACACATATACATACATTTTCATTTTTCTAT
34314415 TTT
1 TTT
34314418 TATTTTTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
42 9 0.22
43 12 0.30
44 19 0.47
ACGTcount: A:0.30, C:0.10, G:0.06, T:0.54
Consensus pattern (43 bp):
TTTGTAAATATATACACATATACATACATTTTCATTTTTCTAT
Found at i:34314464 original size:22 final size:22
Alignment explanation
Indices: 34314422--34314464 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
34314412 TATTTTTATT
* *
34314422 TTTATTTTTTACTTTATTATAC
1 TTTATATTTTACTATATTATAC
34314444 TTTATATTTTA-TATATATATA
1 TTTATATTTTACTATAT-TATA
34314465 TATATTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTATATTTTACTATATTATAC
Found at i:34317429 original size:23 final size:23
Alignment explanation
Indices: 34317403--34317453 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
34317393 ATAGGCTCAT
*
34317403 ATTGGTAGGGTTAGATTCTTAGA
1 ATTGCTAGGGTTAGATTCTTAGA
34317426 ATTGCTAGGGTTAGATTCTTAGA
1 ATTGCTAGGGTTAGATTCTTAGA
34317449 ATTGC
1 ATTGC
34317454 AAATCAGTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.39
Consensus pattern (23 bp):
ATTGCTAGGGTTAGATTCTTAGA
Found at i:34318816 original size:4 final size:4
Alignment explanation
Indices: 34318804--34318837 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
34318794 AATTAAACTC
*
34318804 AATT AAATT AATT AATT AATT ACTT AATT AATT A
1 AATT -AATT AATT AATT AATT AATT AATT AATT A
34318838 TCCTTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (4 bp):
AATT
Found at i:34318830 original size:12 final size:12
Alignment explanation
Indices: 34318792--34318837 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
34318782 AGTTTAATGT
34318792 TTAATTAA--AC
1 TTAATTAATTAC
* *
34318802 TCAATTAAATTAA
1 TTAATT-AATTAC
34318815 TTAATTAATTAC
1 TTAATTAATTAC
34318827 TTAATTAATTA
1 TTAATTAATTA
34318838 TCCTTATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 5 0.17
11 2 0.07
12 16 0.55
13 6 0.21
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (12 bp):
TTAATTAATTAC
Found at i:34319693 original size:16 final size:17
Alignment explanation
Indices: 34319672--34319706 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
34319662 TAGGGTTGAA
*
34319672 AAGAAA-GATTTAGAAG
1 AAGAAAGGATTGAGAAG
34319688 AAGAAAGGATTGAGAAG
1 AAGAAAGGATTGAGAAG
34319705 AA
1 AA
34319707 AGAACTGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (17 bp):
AAGAAAGGATTGAGAAG
Found at i:34325688 original size:24 final size:25
Alignment explanation
Indices: 34325643--34325690 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
34325633 TTTTATGTTC
* * *
34325643 TTTTAACATTCTTTTTTTTTTCTTA
1 TTTTAACATTCTGTTCTGTTTCTTA
34325668 TTTT-ACATTCTGTTCTGTTTCTT
1 TTTTAACATTCTGTTCTGTTTCTT
34325691 CCTCTGTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.12, C:0.15, G:0.04, T:0.69
Consensus pattern (25 bp):
TTTTAACATTCTGTTCTGTTTCTTA
Found at i:34328704 original size:19 final size:21
Alignment explanation
Indices: 34328666--34328706 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
34328656 TATTATACTT
*
34328666 TATTTCATTTTTTCTTAAAAA
1 TATTTCATTTTTTCTCAAAAA
34328687 TATTTC-TTTTTT-TCAAAAA
1 TATTTCATTTTTTCTCAAAAA
34328706 T
1 T
34328707 TCCAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 6 0.32
21 6 0.32
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTCATTTTTTCTCAAAAA
Found at i:34328705 original size:20 final size:21
Alignment explanation
Indices: 34328666--34328705 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
34328656 TATTATACTT
*
34328666 TATTTCATTTTTTCTTAAAAA
1 TATTTCATTTTTTCTAAAAAA
*
34328687 TATTTCTTTTTTTC-AAAAA
1 TATTTCATTTTTTCTAAAAA
34328706 TTCCAGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTCATTTTTTCTAAAAAA
Found at i:34339926 original size:17 final size:17
Alignment explanation
Indices: 34339904--34339937 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
34339894 TTGGGTTGGG
34339904 AGCTTAACTCAATTAAC
1 AGCTTAACTCAATTAAC
34339921 AGCTTAACTCAATTAAC
1 AGCTTAACTCAATTAAC
34339938 CTTTACACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.29
Consensus pattern (17 bp):
AGCTTAACTCAATTAAC
Found at i:34340362 original size:104 final size:104
Alignment explanation
Indices: 34340090--34340906 Score: 742
Period size: 104 Copynumber: 7.9 Consensus size: 104
34340080 GTTAAAATTT
* * * * * * * ** * *
34340090 ATCAGCTGGGAACGTAGGTCTGCGAGCTGTTTTGGATTTGTGAGCTTAGCTCAACTAACTCAAAG
1 ATCAGTTGGGAACGTAGGTCCGCGAGCTATTTGGGAGTTGCGATCTTAAATCAGCTAACTCAGAG
* * * * * *
34340155 AAATGA-AGGCTGTGAACATAACTCAACTAACCTTTAAAC
66 AGAT-ATAGGTTGCGATCTTAAATCAACTAACCTTTAAAC
* * * * * * * * *
34340194 ATCAGCT-AGAAGCTTAGGT---CAAGTTATTTTGGAGTTGCGAGT-TTAACTCTGCTAACTCAA
1 ATCAGTTGGGAA-CGTAGGTCCGCGAGCTATTTGGGAGTTGCGA-TCTTAAATCAGCTAACTCAG
**
34340254 AGAGATATAGGTTGCGATCTTAAATCAGTTAACCTTTAAAC
64 AGAGATATAGGTTGCGATCTTAAATCAACTAACCTTTAAAC
* * *
34340295 ATCAGTTGGGAACGTAGGTCCGTGAGCTATTTGGGAGTTGTGATCTTAAATCAGTTAACTCAGAG
1 ATCAGTTGGGAACGTAGGTCCGCGAGCTATTTGGGAGTTGCGATCTTAAATCAGCTAACTCAGAG
* *
34340360 AGATATAGGTTGTGATATTAAATCAACTAACC-TTAAAC
66 AGATATAGGTTGCGATCTTAAATCAACTAACCTTTAAAC
* * ** * * * * *
34340398 ATCAATTGGGAATGTAGGTCTACGAGTTGTTTGGGAGTTGCAATCTTAAATCAACTATCT-AGAG
1 ATCAGTTGGGAACGTAGGTCCGCGAGCTATTTGGGAGTTGCGATCTTAAATCAGCTAACTCAGAG
* * *
34340462 AGATATAGGTTGCAATCTTAAGTCAAATAACCTTTAAAC
66 AGATATAGGTTGCGATCTTAAATCAACTAACCTTTAAAC
** * * * * *
34340501 ATCAACTGGGAGCGTAGGTCCGCGAGTTGTTTGGAAGTTGCGATCTTAAATCAACTAACTCAGAG
1 ATCAGTTGGGAACGTAGGTCCGCGAGCTATTTGGGAGTTGCGATCTTAAATCAGCTAACTCAGAG
* * *
34340566 AGATATAGGTTGCAATATTAAATCAGCTAACCTTTAAAC
66 AGATATAGGTTGCGATCTTAAATCAACTAACCTTTAAAC
* * * * **
34340605 ATCAGCTGGGAACATAGGTCTGTGAGCTATTTGGGAGTTAAGATCTTAAATCAGCTAACTCAGAG
1 ATCAGTTGGGAACGTAGGTCCGCGAGCTATTTGGGAGTTGCGATCTTAAATCAGCTAACTCAGAG
* * **
34340670 AGATTTAGGTTGCGATATTAAATCAGTTAACCTTTAAAC
66 AGATATAGGTTGCGATCTTAAATCAACTAACCTTTAAAC
* * * * * *
34340709 ATCA-TCTGGGAACGTAAGTCCGAGAGCTGTTTAGGAGTTGCGATCTTAAAT-ATGTTAACTCAA
1 ATCAGT-TGGGAACGTAGGTCCGCGAGCTATTTGGGAGTTGCGATCTTAAATCA-GCTAACTCAG
* * *
34340772 ATAGATTTA-GTTGCGATCTTAAATCAACTAATCTTTAAAC
64 AGAGATATAGGTTGCGATCTTAAATCAACTAACCTTTAAAC
* * ** * * *
34340812 ATCAGTTGGAAACGTAAGTTTGCGAGCTATTTAGGAGTT-CTGATCTTAAATCTG-TCAACTTAG
1 ATCAGTTGGGAACGTAGGTCCGCGAGCTATTTGGGAGTTGC-GATCTTAAATCAGCT-AACTCAG
*
34340875 AGAGATTTAGGTTGCGATCTTAAATCAACTAA
64 AGAGATATAGGTTGCGATCTTAAATCAACTAA
34340907 ATCGGAGAGA
Statistics
Matches: 593, Mismatches: 103, Indels: 34
0.81 0.14 0.05
Matches are distributed among these distances:
100 1 0.00
101 74 0.12
102 36 0.06
103 200 0.34
104 282 0.48
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31
Consensus pattern (104 bp):
ATCAGTTGGGAACGTAGGTCCGCGAGCTATTTGGGAGTTGCGATCTTAAATCAGCTAACTCAGAG
AGATATAGGTTGCGATCTTAAATCAACTAACCTTTAAAC
Found at i:34347236 original size:16 final size:17
Alignment explanation
Indices: 34347217--34347252 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
34347207 TTTCACATTC
34347217 TTTTTC-TTTCTCA-TA
1 TTTTTCTTTTCTCACTA
34347232 TTTTTCTTTTCTCACT-
1 TTTTTCTTTTCTCACTA
34347248 TTTTT
1 TTTTT
34347253 TTCATTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 12 0.63
17 1 0.05
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTCTTTTCTCACTA
Found at i:34347250 original size:15 final size:15
Alignment explanation
Indices: 34347215--34347255 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
34347205 TTTTTCACAT
34347215 TCTTTTTCTTTCTCA
1 TCTTTTTCTTTCTCA
*
34347230 TATTTTTCTTTTCTCA
1 TCTTTTTC-TTTCTCA
34347246 -CTTTTT-TTTC
1 TCTTTTTCTTTC
34347256 ATTTTCTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 4 0.17
15 12 0.52
16 7 0.30
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (15 bp):
TCTTTTTCTTTCTCA
Found at i:34349420 original size:14 final size:15
Alignment explanation
Indices: 34349377--34349422 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
34349367 TTTTTTTTCT
* *
34349377 TTTTTTAATCACGAT
1 TTTTTTAATTACGAA
34349392 TTTTTTAATTACGAA
1 TTTTTTAATTACGAA
*
34349407 TTTTTT-ATTTCGAA
1 TTTTTTAATTACGAA
34349421 TT
1 TT
34349423 CTTCTCTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 9 0.32
15 19 0.68
ACGTcount: A:0.26, C:0.09, G:0.07, T:0.59
Consensus pattern (15 bp):
TTTTTTAATTACGAA
Found at i:34357941 original size:20 final size:21
Alignment explanation
Indices: 34357918--34357969 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
34357908 AATCTTGGTT
34357918 TTATCGATACTT-A-ATAAAAA
1 TTATCGATACTTGACA-AAAAA
*
34357938 TTATTGATACTTGACAAAAAA
1 TTATCGATACTTGACAAAAAA
34357959 TTATCGATACT
1 TTATCGATACT
34357970 GGATCGGTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 11 0.39
21 16 0.57
22 1 0.04
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.37
Consensus pattern (21 bp):
TTATCGATACTTGACAAAAAA
Found at i:34364655 original size:13 final size:13
Alignment explanation
Indices: 34364637--34364663 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
34364627 CAAGAATCAG
34364637 ATCATAATTTAAC
1 ATCATAATTTAAC
34364650 ATCATAATTTAAC
1 ATCATAATTTAAC
34364663 A
1 A
34364664 ACTTCAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
ATCATAATTTAAC
Found at i:34365560 original size:20 final size:21
Alignment explanation
Indices: 34365517--34365560 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
34365507 TGAATTTTAT
** *
34365517 ATTTTTTTAATTTGGTACTTA
1 ATTTTTTTAATTTAATACTAA
34365538 ATTTTTTTAATTTAATAC-AA
1 ATTTTTTTAATTTAATACTAA
34365558 ATT
1 ATT
34365561 ACTTCAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (21 bp):
ATTTTTTTAATTTAATACTAA
Found at i:34382143 original size:49 final size:49
Alignment explanation
Indices: 34382035--34382156 Score: 147
Period size: 49 Copynumber: 2.5 Consensus size: 49
34382025 ATATTTGCAA
* * * * * *
34382035 ATCTGGTGGCTTGACCATAATATTCTGTATCTTGCAGTTTGTTTGCATT
1 ATCTAGTGGCTTGACCACAATATTCTGTATCTGGCAGCTTGTCTGCACT
*
34382084 AT-TTGATGGCTTGACCACAATATTCTGTATCTGGCAGCTTGTCTGCACT
1 ATCTAG-TGGCTTGACCACAATATTCTGTATCTGGCAGCTTGTCTGCACT
* *
34382133 ATCTAGTGGCTTAACCACATTATT
1 ATCTAGTGGCTTGACCACAATATT
34382157 GGTGTGATAT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
48 2 0.03
49 58 0.94
50 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (49 bp):
ATCTAGTGGCTTGACCACAATATTCTGTATCTGGCAGCTTGTCTGCACT
Found at i:34390123 original size:13 final size:13
Alignment explanation
Indices: 34390105--34390135 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
34390095 AGGGTGAATG
*
34390105 ATAACACTCTAGA
1 ATAACACTCTAAA
34390118 ATAACACTCTAAA
1 ATAACACTCTAAA
34390131 ATAAC
1 ATAAC
34390136 GTATTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.52, C:0.23, G:0.03, T:0.23
Consensus pattern (13 bp):
ATAACACTCTAAA
Found at i:34391286 original size:10 final size:9
Alignment explanation
Indices: 34391271--34391295 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
34391261 AATTCTGTTA
34391271 TTTTTTTAT
1 TTTTTTTAT
34391280 TTTTTTTAT
1 TTTTTTTAT
34391289 TTTTTTT
1 TTTTTTT
34391296 CCAGTAACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:34392850 original size:13 final size:13
Alignment explanation
Indices: 34392832--34392892 Score: 77
Period size: 13 Copynumber: 4.7 Consensus size: 13
34392822 AGTTATTCAT
34392832 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
34392845 TGCTTTTGAGATG
1 TGCTTTTGAGAAG
* * *
34392858 TGCTGTGGAAAAG
1 TGCTTTTGAGAAG
*
34392871 TACTTTTGAGAAG
1 TGCTTTTGAGAAG
34392884 TGCTTTTGA
1 TGCTTTTGA
34392893 AAAATTTGAG
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.23, C:0.08, G:0.30, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:34397706 original size:44 final size:44
Alignment explanation
Indices: 34397658--34397756 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 44
34397648 TTATGTGAAA
* * *
34397658 AAACGCTGCTAAAGATCACGACCTTTAGCGGCGCTTTTTATCAC
1 AAACGCCGCTAAAGATCACGACCTTTAGCGACGCTTTTTACCAC
* * * *
34397702 AAACGCCGCTAAAGGTCATGATCTTTAGCGACGCTTTTTGCCAC
1 AAACGCCGCTAAAGATCACGACCTTTAGCGACGCTTTTTACCAC
34397746 AAACGCCGCTA
1 AAACGCCGCTA
34397757 TAAAACAAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.25
Consensus pattern (44 bp):
AAACGCCGCTAAAGATCACGACCTTTAGCGACGCTTTTTACCAC
Found at i:34397841 original size:18 final size:19
Alignment explanation
Indices: 34397818--34397855 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
34397808 CATTTAAAAA
*
34397818 TTTTATTTAAATATT-TAT
1 TTTTATATAAATATTATAT
34397836 TTTTATATAAATATTATAT
1 TTTTATATAAATATTATAT
34397855 T
1 T
34397856 ATGTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTATATAAATATTATAT
Found at i:34398849 original size:16 final size:16
Alignment explanation
Indices: 34398828--34398858 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
34398818 AGTCCCAAAC
34398828 TATTGTAAACATCAGT
1 TATTGTAAACATCAGT
34398844 TATTGTAAACATCAG
1 TATTGTAAACATCAG
34398859 ATAGGTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (16 bp):
TATTGTAAACATCAGT
Found at i:34401632 original size:39 final size:39
Alignment explanation
Indices: 34401571--34401682 Score: 145
Period size: 30 Copynumber: 3.1 Consensus size: 39
34401561 ATGCAAATGA
34401571 AATGGGT-AAAAAAAAAGAAAAGAAGATGAACAATTTTT
1 AATGGGTAAAAAAAAAAGAAAAGAAGATGAACAATTTTT
34401609 AATGGGTAAAAAAAAAAGAAAAGAAGATG----A-----
1 AATGGGTAAAAAAAAAAGAAAAGAAGATGAACAATTTTT
*
34401639 AATGGGTAAAAGAAAAAGAAAAGAAGATGAACAATTTTT
1 AATGGGTAAAAAAAAAAGAAAAGAAGATGAACAATTTTT
34401678 AATGG
1 AATGG
34401683 AGAAACCAAA
Statistics
Matches: 63, Mismatches: 1, Indels: 19
0.76 0.01 0.23
Matches are distributed among these distances:
30 28 0.44
34 1 0.02
35 1 0.02
38 7 0.11
39 26 0.41
ACGTcount: A:0.59, C:0.02, G:0.21, T:0.18
Consensus pattern (39 bp):
AATGGGTAAAAAAAAAAGAAAAGAAGATGAACAATTTTT
Found at i:34402109 original size:41 final size:41
Alignment explanation
Indices: 34402057--34402260 Score: 263
Period size: 41 Copynumber: 5.0 Consensus size: 41
34402047 GCCACTATTG
* *
34402057 CCCTGAGCATTAGCGGCACTTTTTCAAAAACGCCACTAAAGA
1 CCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAA-A
* *
34402099 CCC-GATCATTAGTGGCGCTTTTT-AAAAAGCGCCGCTAAAA
1 CCCTGAGCATTAGCGGCGCTTTTTCAAAAA-CGCCGCTAAAA
*
34402139 CCCTGAGCATTAGCGGCGCATTTTCAAAAACGCCGCTAAATA
1 CCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAA-A
* *
34402181 -TCTGAGCATTAGCGGCGC-TTTACAAAAAACGCCGCTAAAA
1 CCCTGAGCATTAGCGGCGCTTTTTC-AAAAACGCCGCTAAAA
* *
34402221 CCCTGAGCATTAGCGGCGCTTTTTAAAAAACGCCACTAAA
1 CCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAA
34402261 TCCCCGAATA
Statistics
Matches: 142, Mismatches: 13, Indels: 15
0.84 0.08 0.09
Matches are distributed among these distances:
40 14 0.10
41 116 0.82
42 12 0.08
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (41 bp):
CCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAA
Found at i:34402261 original size:82 final size:82
Alignment explanation
Indices: 34402057--34402267 Score: 305
Period size: 82 Copynumber: 2.6 Consensus size: 82
34402047 GCCACTATTG
* * * * **
34402057 CCCTGAGCATTAGCGGCACTTTTTCAAAAACGCCACTAAAGACCCGATCATTAGTGGCGCTTTTT
1 CCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCACTAAATACCCGAGCATTAGCGGCGCTTTAC
*
34402122 AAAAAGCGCCGCTAAAA
66 AAAAAACGCCGCTAAAA
* * * *
34402139 CCCTGAGCATTAGCGGCGCATTTTCAAAAACGCCGCTAAATATCTGAGCATTAGCGGCGCTTTAC
1 CCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCACTAAATACCCGAGCATTAGCGGCGCTTTAC
34402204 AAAAAACGCCGCTAAAA
66 AAAAAACGCCGCTAAAA
* *
34402221 CCCTGAGCATTAGCGGCGCTTTTTAAAAAACGCCACTAAATCCCCGA
1 CCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCACTAAATACCCGA
34402268 ATACCAAAAA
Statistics
Matches: 112, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
82 112 1.00
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (82 bp):
CCCTGAGCATTAGCGGCGCTTTTTCAAAAACGCCACTAAATACCCGAGCATTAGCGGCGCTTTAC
AAAAAACGCCGCTAAAA
Found at i:34402295 original size:43 final size:43
Alignment explanation
Indices: 34402247--34402332 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
34402237 CGCTTTTTAA
34402247 AAAACGCCACTAAATCCCCGAATACCAAAAAAAGGTGTCGTAG
1 AAAACGCCACTAAATCCCCGAATACCAAAAAAAGGTGTCGTAG
34402290 AAAACGCCACTAAATCCCCGAATACCAAAAAAAGGTGTCGTAG
1 AAAACGCCACTAAATCCCCGAATACCAAAAAAAGGTGTCGTAG
34402333 GGCTTAGGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.44, C:0.26, G:0.16, T:0.14
Consensus pattern (43 bp):
AAAACGCCACTAAATCCCCGAATACCAAAAAAAGGTGTCGTAG
Found at i:34402448 original size:40 final size:40
Alignment explanation
Indices: 34402341--34402479 Score: 140
Period size: 40 Copynumber: 3.5 Consensus size: 40
34402331 AGGGCTTAGG
* * * *
34402341 TTTTTTGCGGCGCTTTTTGAAAAACGCCGCTAATGCTC-A
1 TTTTTAGCGGCGTTTTTTTAAAAGCGCCGCTAATGCTCAA
* * ***
34402380 TTTTTAGCGACATTTTCCAAAAAGCGCCGCTAATAG-TCAA
1 TTTTTAGCGGCGTTTTTTTAAAAGCGCCGCTAAT-GCTCAA
* *
34402420 TCTTTT-GCTGCGTTTTTTTAAAAGCGCCGCTAATGCTTAA
1 T-TTTTAGCGGCGTTTTTTTAAAAGCGCCGCTAATGCTCAA
34402460 TTTTTAGCGGCGTTTTTTTA
1 TTTTTAGCGGCGTTTTTTTA
34402480 TCCAAACGCC
Statistics
Matches: 79, Mismatches: 16, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
39 33 0.42
40 42 0.53
41 4 0.05
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTTTAAAAGCGCCGCTAATGCTCAA
Found at i:34406548 original size:21 final size:21
Alignment explanation
Indices: 34406522--34406567 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
34406512 CGAGCTTCTA
34406522 TTCAACTCAT-ATGAGTTTTCG
1 TTCAAC-CATAATGAGTTTTCG
* *
34406543 TTCAACCCTAATGGGTTTTCG
1 TTCAACCATAATGAGTTTTCG
34406564 TTCA
1 TTCA
34406568 GCTCTTTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (21 bp):
TTCAACCATAATGAGTTTTCG
Found at i:34406606 original size:21 final size:21
Alignment explanation
Indices: 34406538--34406648 Score: 68
Period size: 21 Copynumber: 5.4 Consensus size: 21
34406528 TCATATGAGT
*
34406538 TTTC-GTTCAACCCTAATGGG
1 TTTCTGTTCAACCCTTATGGG
* * * *
34406558 TTT-TCGTTCAGCTCTTTTGAG
1 TTTCT-GTTCAACCCTTATGGG
* *
34406579 -CTCTGTTTAACCCTTATGGG
1 TTTCTGTTCAACCCTTATGGG
* * *
34406599 TTTCTGTTCAGCTCTTATGAGC
1 TTTCTGTTCAACCCTTATG-GG
* *
34406621 TTCCAG-TCAACCCTTATGGG
1 TTTCTGTTCAACCCTTATGGG
34406641 TTTCTGTT
1 TTTCTGTT
34406649 TAGCACTTAT
Statistics
Matches: 62, Mismatches: 23, Indels: 11
0.65 0.24 0.11
Matches are distributed among these distances:
20 20 0.32
21 37 0.60
22 5 0.08
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.43
Consensus pattern (21 bp):
TTTCTGTTCAACCCTTATGGG
Found at i:34406645 original size:42 final size:41
Alignment explanation
Indices: 34406542--34406658 Score: 139
Period size: 41 Copynumber: 2.8 Consensus size: 41
34406532 ATGAGTTTTC
* * *
34406542 GTTCAACCCTAATGGGTTT-TCGTTCAGCTCTTTTGAGCTCT
1 GTTCAACCCTTATGGGTTTCT-GTTCAGCTCTTATGAGCTCA
*
34406583 GTTTAACCCTTATGGGTTTCTGTTCAGCTCTTATGAGCTTCCA
1 GTTCAACCCTTATGGGTTTCTGTTCAGCTCTTATGAGC-T-CA
* *
34406626 G-TCAACCCTTATGGGTTTCTGTTTAGCACTTAT
1 GTTCAACCCTTATGGGTTTCTGTTCAGCTCTTAT
34406659 ATGCTTCTGT
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
41 33 0.50
42 31 0.47
43 2 0.03
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.42
Consensus pattern (41 bp):
GTTCAACCCTTATGGGTTTCTGTTCAGCTCTTATGAGCTCA
Found at i:34406657 original size:21 final size:21
Alignment explanation
Indices: 34406580--34406674 Score: 66
Period size: 21 Copynumber: 4.5 Consensus size: 21
34406570 TCTTTTGAGC
*
34406580 TCTGTTTAACCCTTATGGGTT
1 TCTGTTTAGCCCTTATGGGTT
* * *
34406601 TCTGTTCAGCTCTTATGAGCTT
1 TCTGTTTAGCCCTTATG-GGTT
* * * *
34406623 CCAG-TCAACCCTTATGGGTT
1 TCTGTTTAGCCCTTATGGGTT
* ** *
34406643 TCTGTTTAGCACTTATATGCT
1 TCTGTTTAGCCCTTATGGGTT
34406664 TCTGTTTAGCC
1 TCTGTTTAGCC
34406675 TTTGGACTTC
Statistics
Matches: 54, Mismatches: 18, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
20 5 0.09
21 44 0.81
22 5 0.09
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (21 bp):
TCTGTTTAGCCCTTATGGGTT
Found at i:34408727 original size:10 final size:10
Alignment explanation
Indices: 34408712--34408736 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
34408702 AACTGATGGT
34408712 CATAAACAAA
1 CATAAACAAA
34408722 CATAAACAAA
1 CATAAACAAA
34408732 CATAA
1 CATAA
34408737 GCAATACTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.20, G:0.00, T:0.12
Consensus pattern (10 bp):
CATAAACAAA
Found at i:34411735 original size:34 final size:35
Alignment explanation
Indices: 34411680--34411746 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
34411670 CAAACACCAA
*
34411680 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
34411715 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
34411747 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:34421559 original size:29 final size:29
Alignment explanation
Indices: 34421526--34421582 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
34421516 TTACTTTGTC
34421526 ATTTATGTTTGAAATATTACGTTTTAGTT
1 ATTTATGTTTGAAATATTACGTTTTAGTT
*
34421555 ATTTATGTTTGAAATGTTACGTTTTAGT
1 ATTTATGTTTGAAATATTACGTTTTAGT
34421583 CACATACGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.26, C:0.04, G:0.16, T:0.54
Consensus pattern (29 bp):
ATTTATGTTTGAAATATTACGTTTTAGTT
Found at i:34428809 original size:24 final size:20
Alignment explanation
Indices: 34428760--34428808 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
34428750 CAGCCATACA
34428760 GTAGTAAGTTGCAATATATG
1 GTAGTAAGTTGCAATATATG
34428780 GTAGTAAGTTGCAATATATG
1 GTAGTAAGTTGCAATATATG
*
34428800 GTAGAAAGT
1 GTAGTAAGT
34428809 ACATCATTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.33
Consensus pattern (20 bp):
GTAGTAAGTTGCAATATATG
Found at i:34432680 original size:15 final size:15
Alignment explanation
Indices: 34432660--34432697 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
34432650 TAACCTATAA
*
34432660 CCCTAAACCCCAAAC
1 CCCTAAACCACAAAC
*
34432675 CCCT-AACCACTAAC
1 CCCTAAACCACAAAC
34432689 CCCTAAACC
1 CCCTAAACC
34432698 TTATTTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.37, C:0.53, G:0.00, T:0.11
Consensus pattern (15 bp):
CCCTAAACCACAAAC
Found at i:34432681 original size:21 final size:22
Alignment explanation
Indices: 34432657--34432697 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
34432647 TCTTAACCTA
34432657 TAACC-CTAAACCCC-AAACCCC
1 TAACCACT-AACCCCTAAACCCC
34432678 TAACCACTAACCCCTAAACC
1 TAACCACTAACCCCTAAACC
34432698 TTATTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.39, C:0.49, G:0.00, T:0.12
Consensus pattern (22 bp):
TAACCACTAACCCCTAAACCCC
Found at i:34432776 original size:88 final size:89
Alignment explanation
Indices: 34432669--34432853 Score: 291
Period size: 88 Copynumber: 2.1 Consensus size: 89
34432659 ACCCTAAACC
* * *
34432669 CCAAACCCCTAACCACTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATC
1 CCAAATCCTTAACCACTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATC
*
34432734 TAAA-CCTAAACCCTAACCCGACC
66 TAAACCCTAAACCCTAACCCGACA
* * * *
34432757 CCGAATCCTTAACCCCTAACCCTTAAACATTATTTAATATATAAATTAAAACACACTAATTAATC
1 CCAAATCCTTAACCACTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATC
34432822 TAAACCCTAAACCCTAACCCGACA
66 TAAACCCTAAACCCTAACCCGACA
34432846 CCAAATCC
1 CCAAATCC
34432854 ATAAACTCTA
Statistics
Matches: 87, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
88 62 0.71
89 25 0.29
ACGTcount: A:0.43, C:0.31, G:0.02, T:0.24
Consensus pattern (89 bp):
CCAAATCCTTAACCACTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATC
TAAACCCTAAACCCTAACCCGACA
Done.