Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 15 of 130
Found at i:4167496 original size:22 final size:22
Alignment explanation
Indices: 4167433--4167577 Score: 94
Period size: 22 Copynumber: 6.5 Consensus size: 22
4167423 TTAATCATTA
* * *
4167433 ATAATTTAATAATTAATTATTG
1 ATAATTTAATAGTAAATTAGTG
* *
4167455 ATAACTTAATAATAAATTAGTG
1 ATAATTTAATAGTAAATTAGTG
*
4167477 ATAATTTAATAGTAAATTAGTT
1 ATAATTTAATAGTAAATTAGTG
* * ** * * *
4167499 TTAGTTTGGTGGTAATTTATTG
1 ATAATTTAATAGTAAATTAGTG
* * *
4167521 ATCAATTTAGTAGTAAATCA-TAA
1 AT-AATTTAATAGTAAATTAGT-G
* * *
4167544 ATAATTTAATAATAAATTAATA
1 ATAATTTAATAGTAAATTAGTG
4167566 ATAATTTAATAG
1 ATAATTTAATAG
4167578 ACAATCATTG
Statistics
Matches: 95, Mismatches: 25, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
22 80 0.84
23 15 0.16
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (22 bp):
ATAATTTAATAGTAAATTAGTG
Found at i:4167563 original size:11 final size:11
Alignment explanation
Indices: 4167543--4167576 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
4167533 GTAAATCATA
4167543 AATAATTTAAT
1 AATAATTTAAT
*
4167554 AATAAATTAAT
1 AATAATTTAAT
4167565 AATAATTTAAT
1 AATAATTTAAT
4167576 A
1 A
4167577 GACAATCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AATAATTTAAT
Found at i:4167674 original size:22 final size:22
Alignment explanation
Indices: 4167647--4167730 Score: 100
Period size: 22 Copynumber: 3.9 Consensus size: 22
4167637 GCTTAGTAGT
* *
4167647 TAAATAACTCAATAATAAATTA
1 TAAATAATTTAATAATAAATTA
4167669 TAAATAATTTAAT-ATAAATTA
1 TAAATAATTTAATAATAAATTA
*
4167690 -ATGATAATTTAATAATAAATTA
1 TA-AATAATTTAATAATAAATTA
* *
4167712 TGATTAATTTAATAATAAA
1 TAAATAATTTAATAATAAA
4167731 CCTACGATGA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.02
21 18 0.34
22 34 0.64
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
TAAATAATTTAATAATAAATTA
Found at i:4167696 original size:11 final size:11
Alignment explanation
Indices: 4167657--4167730 Score: 64
Period size: 11 Copynumber: 6.8 Consensus size: 11
4167647 TAAATAACTC
4167657 AATAATAAATT
1 AATAATAAATT
*
4167668 -ATAAATAATTT
1 AAT-AATAAATT
4167679 AAT-ATAAATT
1 AATAATAAATT
* *
4167689 AATGATAATTT
1 AATAATAAATT
4167700 AATAATAAATT
1 AATAATAAATT
* *
4167711 -ATGATTAATTT
1 AAT-AATAAATT
4167722 AATAATAAA
1 AATAATAAA
4167731 CCTACGATGA
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
10 13 0.27
11 32 0.65
12 4 0.08
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (11 bp):
AATAATAAATT
Found at i:4167743 original size:22 final size:22
Alignment explanation
Indices: 4167673--4167752 Score: 67
Period size: 22 Copynumber: 3.7 Consensus size: 22
4167663 AAATTATAAA
* *
4167673 TAATTTAAT-ATAAATTAATGA-
1 TAATTTAATAATAAACT-ACGAT
* *
4167694 TAATTTAATAATAAATTATGAT
1 TAATTTAATAATAAACTACGAT
4167716 TAATTTAATAATAAACCTACGA-
1 TAATTTAATAATAAA-CTACGAT
* *
4167738 TGATTTTATAATAAA
1 TAATTTAATAATAAA
4167753 TAACTGAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
21 13 0.25
22 35 0.67
23 4 0.08
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (22 bp):
TAATTTAATAATAAACTACGAT
Found at i:4173787 original size:7 final size:7
Alignment explanation
Indices: 4173775--4173808 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
4173765 ACCTGCGGCC
4173775 ATATATT
1 ATATATT
4173782 ATATATT
1 ATATATT
*
4173789 ATATTTT
1 ATATATT
*
4173796 ATATTTT
1 ATATATT
4173803 ATATAT
1 ATATAT
4173809 ACAGACACAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
ATATATT
Found at i:4176582 original size:14 final size:13
Alignment explanation
Indices: 4176550--4176592 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
4176540 TAAATATTGA
4176550 TTTTAATAAAATT
1 TTTTAATAAAATT
*
4176563 TATTTAGTATAAATT
1 T-TTTAATA-AAATT
4176578 TTTTAATAAAATT
1 TTTTAATAAAATT
4176591 TT
1 TT
4176593 ATTTTTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 8 0.31
14 12 0.46
15 6 0.23
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (13 bp):
TTTTAATAAAATT
Found at i:4183315 original size:25 final size:26
Alignment explanation
Indices: 4183281--4183338 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
4183271 TTTTGTTGAA
4183281 AAATTTTTTT-AATCGTAATTATAAT
1 AAATTTTTTTCAATCGTAATTATAAT
*
4183306 AAATTTTTTTCAATTGTAATTATAAT
1 AAATTTTTTTCAATCGTAATTATAAT
*
4183332 TAATTTT
1 AAATTTT
4183339 ATTATTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 10 0.33
26 20 0.67
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.55
Consensus pattern (26 bp):
AAATTTTTTTCAATCGTAATTATAAT
Found at i:4183425 original size:12 final size:12
Alignment explanation
Indices: 4183408--4183433 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
4183398 AATTGCTTTT
4183408 GAAAAAAAAAAA
1 GAAAAAAAAAAA
4183420 GAAAAAAAAAAA
1 GAAAAAAAAAAA
4183432 GA
1 GA
4183434 GATTTTCCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
GAAAAAAAAAAA
Found at i:4192658 original size:21 final size:21
Alignment explanation
Indices: 4192634--4192728 Score: 61
Period size: 21 Copynumber: 4.5 Consensus size: 21
4192624 CCTTTGACAC
4192634 AATTTTAGTAACTTATGATAT
1 AATTTTAGTAACTTATGATAT
* * *
4192655 AATTGTAATAAC-TATTGATAC
1 AATTTTAGTAACTTA-TGATAT
* * * *
4192676 AATTTTGGTAA-TTTTTATAA
1 AATTTTAGTAACTTATGATAT
* *
4192696 AATTTTAGTAAACACT-TGATGT
1 AATTTTAGT-AAC-TTATGATAT
4192718 AATTTTAGTAA
1 AATTTTAGTAA
4192729 TTTTTTGGTA
Statistics
Matches: 55, Mismatches: 14, Indels: 10
0.70 0.18 0.13
Matches are distributed among these distances:
20 14 0.25
21 28 0.51
22 12 0.22
23 1 0.02
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (21 bp):
AATTTTAGTAACTTATGATAT
Found at i:4193048 original size:23 final size:24
Alignment explanation
Indices: 4193005--4193050 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
4192995 AACTTTAAGT
4193005 ATAAATAAATTTATCAATAATTTG
1 ATAAATAAATTTATCAATAATTTG
* *
4193029 ATAATTAAA-TTATCATTAATTT
1 ATAAATAAATTTATCAATAATTT
4193051 ACTATTATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (24 bp):
ATAAATAAATTTATCAATAATTTG
Found at i:4193063 original size:22 final size:22
Alignment explanation
Indices: 4193015--4193098 Score: 71
Period size: 22 Copynumber: 3.8 Consensus size: 22
4193005 ATAAATAAAT
**
4193015 TTATCAATAATTTGA-TAATTAAA
1 TTATCAATAATTT-ACT-ATTATG
*
4193038 TTATCATTAATTTACTATTATG
1 TTATCAATAATTTACTATTATG
* **
4193060 TTATTAATAATTTACTATTAAA
1 TTATCAATAATTTACTATTATG
* *
4193082 CTATCAATAATATACTA
1 TTATCAATAATTTACTA
4193099 CTAAATTACT
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
22 37 0.74
23 13 0.26
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.46
Consensus pattern (22 bp):
TTATCAATAATTTACTATTATG
Found at i:4193087 original size:44 final size:44
Alignment explanation
Indices: 4193010--4193295 Score: 181
Period size: 44 Copynumber: 6.5 Consensus size: 44
4193000 TAAGTATAAA
*
4193010 TAAATTTATCAATAATTTGA-TAATTAAATTATCATTAATTTACTAT
1 TAAA-TTATTAATAATTT-ACT-ATTAAATTATCATTAATTTACTAT
** * * * *
4193056 TATGTTATTAATAATTTACTATTAAACTATCAATAATATACTAC
1 TAAATTATTAATAATTTACTATTAAATTATCATTAATTTACTAT
* * * * * *
4193100 TAAATTACTAATGATTTACTACTAAATTAACATTGATTTACTAC
1 TAAATTATTAATAATTTACTATTAAATTATCATTAATTTACTAT
* * * * * *
4193144 TAATTTATGAA-AGACTTACTAGTAAATTATGATTAATTTACTAC
1 TAAATTATTAATA-ATTTACTATTAAATTATCATTAATTTACTAT
* * * * **
4193188 TAAATTATTGATGATTTACTACTAAATTACTAATT-ATTTGTTA-
1 TAAATTATTAATAATTTACTATTAAATTA-TCATTAATTTACTAT
* * *
4193231 TAAAGTTA-TAATAAGTTTACTATTAATTTATCA-TGATTTATTA-
1 TAAA-TTATTAATAA-TTTACTATTAAATTATCATTAATTTACTAT
* *
4193274 TAAAGTTATCAATAATTAACTA
1 TAAA-TTATTAATAATTTACTA
4193296 ATTTTTCTTA
Statistics
Matches: 189, Mismatches: 43, Indels: 19
0.75 0.17 0.08
Matches are distributed among these distances:
42 1 0.01
43 31 0.16
44 138 0.73
45 17 0.09
46 2 0.01
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (44 bp):
TAAATTATTAATAATTTACTATTAAATTATCATTAATTTACTAT
Found at i:4193103 original size:22 final size:22
Alignment explanation
Indices: 4193064--4193226 Score: 75
Period size: 22 Copynumber: 7.4 Consensus size: 22
4193054 ATTATGTTAT
*
4193064 TAATAATTTACTATTAAACTA-
1 TAATAATTTACTACTAAACTAC
* *
4193085 TCAATAATATACTACTAAATTAC
1 T-AATAATTTACTACTAAACTAC
* *
4193108 TAATGATTTACTACTAAATTAAC
1 TAATAATTTACTACTAAACT-AC
* * **
4193131 -ATTGATTTACTACTAATTTA-
1 TAATAATTTACTACTAAACTAC
* * *
4193151 TGAA-AGACTTACTAGTAAATTA-
1 T-AATA-ATTTACTACTAAACTAC
* * *
4193173 TGATTAATTTACTACTAAATTAT
1 T-AATAATTTACTACTAAACTAC
* * *
4193196 TGATGATTTACTACTAAATTAC
1 TAATAATTTACTACTAAACTAC
*
4193218 TAATTATTT
1 TAATAATTT
4193227 GTTATAAAGT
Statistics
Matches: 113, Mismatches: 21, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
21 2 0.02
22 106 0.94
23 5 0.04
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (22 bp):
TAATAATTTACTACTAAACTAC
Found at i:4193547 original size:22 final size:22
Alignment explanation
Indices: 4193521--4193575 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
4193511 CACTGATTTA
4193521 TATTAAATTATCCA-TAATGT-AC
1 TATTAAATTAT-CATTAAT-TAAC
* *
4193543 TATTAAGTTATCATTGATTAAC
1 TATTAAATTATCATTAATTAAC
4193565 TATTAAATTAT
1 TATTAAATTAT
4193576 TTATGATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 3 0.11
22 25 0.89
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.45
Consensus pattern (22 bp):
TATTAAATTATCATTAATTAAC
Found at i:4193665 original size:22 final size:22
Alignment explanation
Indices: 4193640--4193719 Score: 72
Period size: 22 Copynumber: 3.6 Consensus size: 22
4193630 AACAATTGAA
* *
4193640 TTATCATTGATTTACTGCTAAT
1 TTATCATTGATTTATTGTTAAT
** *
4193662 TTATTTTTGATTTATTATTGAA-
1 TTATCATTGATTTATTGTT-AAT
*
4193684 TTATCATTGAATTATTGTTAAT
1 TTATCATTGATTTATTGTTAAT
**
4193706 TTATTTTTGATTTA
1 TTATCATTGATTTA
4193720 ATACTAAGTT
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
21 2 0.05
22 40 0.91
23 2 0.05
ACGTcount: A:0.28, C:0.05, G:0.09, T:0.59
Consensus pattern (22 bp):
TTATCATTGATTTATTGTTAAT
Found at i:4193674 original size:11 final size:11
Alignment explanation
Indices: 4193660--4193719 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
4193650 TTTACTGCTA
*
4193660 ATTTATTTTTG
1 ATTTATTATTG
4193671 ATTTATTATTG
1 ATTTATTATTG
* *
4193682 AATTATCATTG
1 ATTTATTATTG
* * *
4193693 AATTATTGTTA
1 ATTTATTATTG
*
4193704 ATTTATTTTTG
1 ATTTATTATTG
4193715 ATTTA
1 ATTTA
4193720 ATACTAAGTT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 40 1.00
ACGTcount: A:0.28, C:0.02, G:0.08, T:0.62
Consensus pattern (11 bp):
ATTTATTATTG
Found at i:4193683 original size:44 final size:44
Alignment explanation
Indices: 4193634--4193719 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 44
4193624 ACGATTAACA
*
4193634 ATTGAATTATCATTGATTTACTGCTAATTTATTTTTGATTTATT
1 ATTGAATTATCATTGAATTACTGCTAATTTATTTTTGATTTATT
* *
4193678 ATTGAATTATCATTGAATTATTGTTAATTTATTTTTGATTTA
1 ATTGAATTATCATTGAATTACTGCTAATTTATTTTTGATTTA
4193720 ATACTAAGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.29, C:0.05, G:0.09, T:0.57
Consensus pattern (44 bp):
ATTGAATTATCATTGAATTACTGCTAATTTATTTTTGATTTATT
Found at i:4193782 original size:22 final size:22
Alignment explanation
Indices: 4193756--4193798 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
4193746 TTAAACTGAA
4193756 ACTAATTTACT-TCTAAGCTATT
1 ACTAATTTACTAT-TAAGCTATT
4193778 ACTAATTTACTATTAAGCTAT
1 ACTAATTTACTATTAAGCTAT
4193799 CATTATCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.44
Consensus pattern (22 bp):
ACTAATTTACTATTAAGCTATT
Found at i:4194138 original size:22 final size:22
Alignment explanation
Indices: 4194108--4194177 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 22
4194098 ATTAATTATT
* *
4194108 TTTATTACTAAATTATCAATAA
1 TTTACTACTAAATTATAAATAA
* *
4194130 TTTACTACTAATTTATGAATAA
1 TTTACTACTAAATTATAAATAA
* * *
4194152 TTTACCATTAAATTATAAATGA
1 TTTACTACTAAATTATAAATAA
4194174 TTTA
1 TTTA
4194178 ACATTATTAG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.46
Consensus pattern (22 bp):
TTTACTACTAAATTATAAATAA
Found at i:4194369 original size:19 final size:20
Alignment explanation
Indices: 4194274--4194377 Score: 75
Period size: 22 Copynumber: 5.0 Consensus size: 20
4194264 AATCATTAAC
*
4194274 TAATTTACTACTAAATTATCA
1 TAATTTACTACTAAGTTAT-A
* *
4194295 TAGATTTACAACTAAGTCATTA
1 TA-ATTTACTACTAAGTTA-TA
* *
4194317 GTAATTTACTATTATGTTACTA
1 -TAATTTACTACTAAGTTA-TA
**
4194339 GTAATTCGCTACTAAGTTAT-
1 -TAATTTACTACTAAGTTATA
*
4194359 TAATTTACTACTAAATTAT
1 TAATTTACTACTAAGTTAT
4194378 CAATGATTTA
Statistics
Matches: 65, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
19 16 0.25
21 3 0.05
22 43 0.66
23 3 0.05
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (20 bp):
TAATTTACTACTAAGTTATA
Found at i:4195503 original size:22 final size:22
Alignment explanation
Indices: 4195456--4195504 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
4195446 TTATTGATTA
* *
4195456 TATTAAATTATGCATGATTTAT
1 TATTAAATTATGCATGATTAAC
4195478 TATTAAATTAT-CACTGATTAAC
1 TATTAAATTATGCA-TGATTAAC
4195500 TATTA
1 TATTA
4195505 TGTTATCGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (22 bp):
TATTAAATTATGCATGATTAAC
Found at i:4195560 original size:43 final size:44
Alignment explanation
Indices: 4195472--4195577 Score: 115
Period size: 43 Copynumber: 2.4 Consensus size: 44
4195462 ATTATGCATG
* * *
4195472 ATTTATTATTAAATTATCACTGATTAACTATTATGTTATCGATA
1 ATTTATTACTAAATTATCACTGATTAACTATTAAGTTATCAATA
* * * *
4195516 ATTTATTACTAAGTTAT-ACTGATTTACTTTTAAGTTTTCAATA
1 ATTTATTACTAAATTATCACTGATTAACTATTAAGTTATCAATA
* * *
4195559 ATTAACTACTGAATTATCA
1 ATTTATTACTAAATTATCA
4195578 ATTATTTATT
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
43 34 0.68
44 16 0.32
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (44 bp):
ATTTATTACTAAATTATCACTGATTAACTATTAAGTTATCAATA
Found at i:4195696 original size:61 final size:61
Alignment explanation
Indices: 4195571--4195696 Score: 137
Period size: 61 Copynumber: 2.1 Consensus size: 61
4195561 TAACTACTGA
* * ** * * * *
4195571 ATTATCAATTATTTATTACTAATTTATAATTGACTTACTATTAAATTATTTATGATTTATT
1 ATTATCAATTAATTACTACTAAACTAAAATTGACTTACAATTAAATTATTCATGATTTACT
* * *
4195632 ATTATCAATTAATTACTATTAAACTAAAATTGATTTACAATTAAATT-TTCATTATTTCACT
1 ATTATCAATTAATTACTACTAAACTAAAATTGACTTACAATTAAATTATTCATGATTT-ACT
4195693 ATTA
1 ATTA
4195697 AGTTATTATT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
60 8 0.15
61 45 0.85
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (61 bp):
ATTATCAATTAATTACTACTAAACTAAAATTGACTTACAATTAAATTATTCATGATTTACT
Found at i:4195912 original size:22 final size:22
Alignment explanation
Indices: 4195887--4195959 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 22
4195877 TATTAATTAC
* *
4195887 TAAGTTATCATTCATTTTCTAT
1 TAAGTTATCATTAATTTACTAT
* *
4195909 TAAGTTATCACTAATTTAGTAT
1 TAAGTTATCATTAATTTACTAT
* * *
4195931 TAAGTTATCATTGA-TTGCTAC
1 TAAGTTATCATTAATTTACTAT
4195952 TAAGTTAT
1 TAAGTTAT
4195960 ACTAATTACA
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
21 12 0.29
22 30 0.71
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.48
Consensus pattern (22 bp):
TAAGTTATCATTAATTTACTAT
Found at i:4199167 original size:17 final size:16
Alignment explanation
Indices: 4199135--4199187 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
4199125 AAGCTTAATT
4199135 TTTTTATT-TAAAAAA
1 TTTTTATTATAAAAAA
*
4199150 TTTTTATTATACATAAA
1 TTTTTATTATA-AAAAA
* *
4199167 TTTTCATTATATGAAAA
1 TTTTTATTATA-AAAAA
4199184 TTTT
1 TTTT
4199188 AAAATATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
15 8 0.26
16 2 0.06
17 21 0.68
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTTTATTATAAAAAA
Found at i:4199204 original size:16 final size:16
Alignment explanation
Indices: 4199174--4199215 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 16
4199164 AAATTTTCAT
4199174 TATATGAAAATTTTAAAA
1 TATAT-AAAA-TTTAAAA
4199192 TATATAAAATTTAAAA
1 TATATAAAATTTAAAA
4199208 -A-ATAAAAT
1 TATATAAAAT
4199216 AAAATAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 7 0.29
15 1 0.04
16 7 0.29
17 4 0.17
18 5 0.21
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
TATATAAAATTTAAAA
Found at i:4199211 original size:18 final size:18
Alignment explanation
Indices: 4199174--4199208 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
4199164 AAATTTTCAT
*
4199174 TATATGAAAATTTTAAAA
1 TATATGAAAATTTAAAAA
4199192 TATAT-AAAATTTAAAAA
1 TATATGAAAATTTAAAAA
4199209 ATAAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
TATATGAAAATTTAAAAA
Found at i:4200243 original size:21 final size:22
Alignment explanation
Indices: 4200210--4200259 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
4200200 ATTCGATATG
* * *
4200210 AAAAAGTATTCTACTTATAAAA
1 AAAAAGTAGTCTAATAATAAAA
4200232 AAAAAG-AGTCTAATAATAAAA
1 AAAAAGTAGTCTAATAATAAAA
*
4200253 ATAAAGT
1 AAAAAGT
4200260 CATTTAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.60, C:0.06, G:0.08, T:0.26
Consensus pattern (22 bp):
AAAAAGTAGTCTAATAATAAAA
Found at i:4200622 original size:2 final size:2
Alignment explanation
Indices: 4200615--4200650 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4200605 ATCACTGTTA
4200615 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4200651 TTCCAATGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4201752 original size:550 final size:548
Alignment explanation
Indices: 4200714--4201813 Score: 2110
Period size: 550 Copynumber: 2.0 Consensus size: 548
4200704 AATGTTAATG
4200714 GGAGATGTGTCCGCTGTCCAGAGTCCATCACGATGTGACTCAAGAGATAACGAATTTAGCAGAGA
1 GGAGATGTGTCCGCTGTCCAGAGTCCATCACGATGTGACTCAAGAGATAACGAATTTAGCAGAGA
*
4200779 CATCAAATCAGAATTGTGGGTCAATCTCCGCATGTGGGATGTCGTCGTCGGTTACCTACATTCTA
66 CATCAAATCAGAATTGTGGGTCAATCTCCGCATGTGGGATGTCGTCGTCCGTTACCTACATTCTA
*
4200844 TACATTGTTTCAATTTGTTTGATTCAAGGGAAAGTGCAAAAGAAAATAATGCAGCTGGAAACTGT
131 TACATTGTTTCAATTTGTTTGATTCAAGGGAAAGTGCAAAAGAAAATAATGCAGCTGAAAACTGT
*
4200909 ATTTCATCACATTTTCATGGGTTTTTTTCGTTCATTTAGAATCTATAGTAAAGAATCATTTTGAT
196 ATTTCATCACATTTTCATGGGATTTTTTCGTTCATTTAGAATCTATAGTAAAGAATCATTTTGAT
4200974 TTACCCTAACCAAGAAACTCTGACCAAGGCTTTAAGTGCCTGGTTTTGTTGGTTAATATAAAAAC
261 TTACCCTAACCAAGAAACTCTGACCAAGGCTTTAAGTGCCTGGTTTTGTTGGTTAATATAAAAAC
4201039 TAGAAAATTGCAAAGAGAAACCAATCCTCGTTGTTTAAAACCCAGATTTTCTTGTTATAGAGACC
326 TAGAAAATTGCAAAGAGAAACCAATCCTCGTTGTTTAAAACCCAGATTTTCTTGTTATAGAGACC
*
4201104 ACAGCTTGATTACGTGATTACCGAGCTGGCAACACAGGTTTGTAAGGCAAAAAGGTGATGAAACA
391 ACAGCTTGATTACGTGATTACCGAGCTGGCAACACAGGTTTGTAAGGCAAAAAGGTAATGAAACA
4201169 ATGGCTCTTATCCACCTAGTCGGGTCCTCAAAGTTGGTTAATTTTGGCCTGCCTACCCTAGCAAT
456 ATGGCTCTTATCCACCTAGTCGGGTCCTCAAAGTTGGTTAATTTTGGCCTGCCTACCCTAGCAAT
4201234 GAGTTGAACCGAAGCCTGAATCCCAAAA
521 GAGTTGAACCGAAGCCTGAATCCCAAAA
*
4201262 GGAGATGTGTCCGTTGTCCAGAGTCCATCACGATGTGACTCAAGAGATAACGAATTTAGCAGAGA
1 GGAGATGTGTCCGCTGTCCAGAGTCCATCACGATGTGACTCAAGAGATAACGAATTTAGCAGAGA
4201327 CATCAAATCAGAATTGTGGGTCAATCTCCGCATGTGGGATGTCGTCGTCCGTTACCTACATTCTA
66 CATCAAATCAGAATTGTGGGTCAATCTCCGCATGTGGGATGTCGTCGTCCGTTACCTACATTCTA
*
4201392 TACATTGTTTCAATTTGTTTGATTCAAGGGAAAGTGTAAAAGAAAATAATGCAGCTGAAAACTGT
131 TACATTGTTTCAATTTGTTTGATTCAAGGGAAAGTGCAAAAGAAAATAATGCAGCTGAAAACTGT
*
4201457 ATTTCATCACATTTTCGTGGGATTTTTTCGTTCATTTTAGAATCTATAGTAAAAGAATCATTTTG
196 ATTTCATCACATTTTCATGGGATTTTTTCGTTCA-TTTAGAATCTATAGT-AAAGAATCATTTTG
4201522 ATTTACCCTAACCAAGAAACTCTGACCAAGGCTTTAAGTGCCTGGTTTTGTTGGTTAATATAAAA
259 ATTTACCCTAACCAAGAAACTCTGACCAAGGCTTTAAGTGCCTGGTTTTGTTGGTTAATATAAAA
4201587 ACTAGAAAATTGCAAAGAGAAACCAATCCTCGTTGTTTAAAACCCAGATTTTCTTGTTATAGAGA
324 ACTAGAAAATTGCAAAGAGAAACCAATCCTCGTTGTTTAAAACCCAGATTTTCTTGTTATAGAGA
*
4201652 CCACAGCTTGATTACGTGATTACCGAGCTGGCAACGCAGGTTTGTAAGGCAAAAAGGTAATGAAA
389 CCACAGCTTGATTACGTGATTACCGAGCTGGCAACACAGGTTTGTAAGGCAAAAAGGTAATGAAA
4201717 CAATGGCTCTTATCCACCTAGTCGGGTCCTCAAAGTTGGTTAATTTTGGCCTGCCTACCCTAGCA
454 CAATGGCTCTTATCCACCTAGTCGGGTCCTCAAAGTTGGTTAATTTTGGCCTGCCTACCCTAGCA
4201782 ATGAGTTGAACCGAAGCCTGAATCCCAAAA
519 ATGAGTTGAACCGAAGCCTGAATCCCAAAA
4201812 GG
1 GG
4201814 CGTTTGAACT
Statistics
Matches: 542, Mismatches: 8, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
548 223 0.41
549 15 0.03
550 304 0.56
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (548 bp):
GGAGATGTGTCCGCTGTCCAGAGTCCATCACGATGTGACTCAAGAGATAACGAATTTAGCAGAGA
CATCAAATCAGAATTGTGGGTCAATCTCCGCATGTGGGATGTCGTCGTCCGTTACCTACATTCTA
TACATTGTTTCAATTTGTTTGATTCAAGGGAAAGTGCAAAAGAAAATAATGCAGCTGAAAACTGT
ATTTCATCACATTTTCATGGGATTTTTTCGTTCATTTAGAATCTATAGTAAAGAATCATTTTGAT
TTACCCTAACCAAGAAACTCTGACCAAGGCTTTAAGTGCCTGGTTTTGTTGGTTAATATAAAAAC
TAGAAAATTGCAAAGAGAAACCAATCCTCGTTGTTTAAAACCCAGATTTTCTTGTTATAGAGACC
ACAGCTTGATTACGTGATTACCGAGCTGGCAACACAGGTTTGTAAGGCAAAAAGGTAATGAAACA
ATGGCTCTTATCCACCTAGTCGGGTCCTCAAAGTTGGTTAATTTTGGCCTGCCTACCCTAGCAAT
GAGTTGAACCGAAGCCTGAATCCCAAAA
Found at i:4203203 original size:30 final size:30
Alignment explanation
Indices: 4203144--4203204 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
4203134 GTCGTGCGAA
4203144 TTCGTAACTTAAATCTCAACTCGTGACACG
1 TTCGTAACTTAAATCTCAACTCGTGACACG
* *
4203174 TTCGTAACTTAAATCTTATCTCGTGACACG
1 TTCGTAACTTAAATCTCAACTCGTGACACG
4203204 T
1 T
4203205 GACACGTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (30 bp):
TTCGTAACTTAAATCTCAACTCGTGACACG
Found at i:4207341 original size:2 final size:2
Alignment explanation
Indices: 4207334--4207365 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4207324 TACATACTAC
4207334 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4207366 CAAAGCCAAT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4207752 original size:13 final size:14
Alignment explanation
Indices: 4207726--4207754 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
4207716 TATATTTATA
4207726 TAATTATAATATTT
1 TAATTATAATATTT
4207740 TAATTAT-ATATTT
1 TAATTATAATATTT
4207753 TA
1 TA
4207755 TTTAGATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTATAATATTT
Found at i:4214600 original size:2 final size:2
Alignment explanation
Indices: 4214593--4214623 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4214583 TTTTTAACTT
*
4214593 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4214624 TTATTTCTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4223964 original size:3 final size:3
Alignment explanation
Indices: 4223911--4223946 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
4223901 CCCTTAATTG
4223911 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4223947 ATTCATTGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4224650 original size:6 final size:6
Alignment explanation
Indices: 4224640--4224674 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
4224630 GAAAGACATG
* *
4224640 CCACAG CCACAG CCACAC CCACAC CCACAC CCACA
1 CCACAC CCACAC CCACAC CCACAC CCACAC CCACA
4224675 ATTTTTGCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.34, C:0.60, G:0.06, T:0.00
Consensus pattern (6 bp):
CCACAC
Found at i:4234264 original size:21 final size:21
Alignment explanation
Indices: 4234238--4234277 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
4234228 AATTTAAAAC
4234238 TATTAAG-TTTAATATATTTAA
1 TATTAAGATTTAA-ATATTTAA
4234259 TATTAAGATTTAAATATTT
1 TATTAAGATTTAAATATTT
4234278 TTATAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
TATTAAGATTTAAATATTTAA
Found at i:4234353 original size:22 final size:21
Alignment explanation
Indices: 4234328--4234388 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 21
4234318 TAAAATTTTT
4234328 AAAATATAATTTTAAAATCTAA
1 AAAATATAATTTT-AAATCTAA
* *
4234350 AAAATAAAAAATTTAAATCTAA
1 AAAAT-ATAATTTTAAATCTAA
4234372 AAAA-ATAATTTTGAAAT
1 AAAATATAATTTT-AAAT
4234389 GTACCAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 6 0.18
21 4 0.12
22 17 0.52
23 6 0.18
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAATATAATTTTAAATCTAA
Found at i:4235212 original size:3 final size:3
Alignment explanation
Indices: 4235204--4235238 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4235194 GATAACATAG
4235204 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
4235239 TATGAAATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4240610 original size:2 final size:2
Alignment explanation
Indices: 4240603--4240638 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4240593 TTTTTAAGGC
4240603 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4240639 TTGCCCAAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4242941 original size:22 final size:22
Alignment explanation
Indices: 4242899--4242942 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4242889 ATGCACTATT
* *
4242899 TTCTTGAATATTATGTGTTAAA
1 TTCTTAAATATTATATGTTAAA
*
4242921 TTCTTAAATATTATATTTTAAA
1 TTCTTAAATATTATATGTTAAA
4242943 AAAATTATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (22 bp):
TTCTTAAATATTATATGTTAAA
Found at i:4248277 original size:2 final size:2
Alignment explanation
Indices: 4248270--4248304 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4248260 AGTTTAGCTT
4248270 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4248305 TTATTTTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4250939 original size:6 final size:6
Alignment explanation
Indices: 4250928--4250954 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4250918 AAATACTATA
4250928 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
4250955 TGGTTTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:4251338 original size:14 final size:13
Alignment explanation
Indices: 4251289--4251341 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
4251279 TTATATAACG
4251289 ATATTTTTTAATTT
1 ATATTTTTT-ATTT
*
4251303 ATTTATTTTTATTT
1 ATAT-TTTTTATTT
* *
4251317 TTACTTTTTATTT
1 ATATTTTTTATTT
4251330 AATATTTTTTAT
1 -ATATTTTTTAT
4251342 AAAAAATTTC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
13 9 0.29
14 17 0.55
15 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (13 bp):
ATATTTTTTATTT
Found at i:4251585 original size:164 final size:162
Alignment explanation
Indices: 4251317--4251644 Score: 523
Period size: 164 Copynumber: 2.0 Consensus size: 162
4251307 ATTTTTATTT
* * * *
4251317 TTACTTTTTATTTAATATTTTTTATAAAAAATTTCATAAATTTCGTCTTAAAAGTTTTATCTAAA
1 TTACTTTTTATTTAATATTTTTTATAAAAAATTTCACAAATTGCATCTAAAAAGTTTTATCTAAA
*
4251382 TTTTTTCCGTTTACCAAAGGGCGGGAAATAACATGTATCAGCCGACAATTGGCTACAG-AAAAAA
66 TTTTTTCCGTTTACCAAAGGGCGGGAAATAAAATGTATCAGCCGACAATTGGCTACAGAAAAAAA
*
4251446 CAAGGGAAATTTATGTAGTAAAAAACGGGTAA
131 CAAGGGAAATTTATGTACTAAAAAACGGGTAA
* *
4251478 TTACTTTTTATTTAATTATTTTTTATAAAAATTTTCACAAATTGCATCTAAAAAAATTTTTATCT
1 TTACTTTTTATTTAA-TATTTTTTATAAAAAATTTCACAAATTGCATCT--AAAAAGTTTTATCT
* *
4251543 AAATTTTTTCCGTTTTCGAAAGGGCGGGAAATAAAATGTATCAGCCGACAATTGGCTACAGAAAA
63 AAATTTTTTCCGTTTACCAAAGGGCGGGAAATAAAATGTATCAGCCGACAATTGGCTACAGAAAA
*
4251608 AAACAAGGGAAATTTATGTACTAAAACACGGGTAA
128 AAACAAGGGAAATTTATGTACTAAAAAACGGGTAA
4251643 TT
1 TT
4251645 CTGCAGAGTT
Statistics
Matches: 152, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
161 15 0.10
162 29 0.19
164 70 0.46
165 38 0.25
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.36
Consensus pattern (162 bp):
TTACTTTTTATTTAATATTTTTTATAAAAAATTTCACAAATTGCATCTAAAAAGTTTTATCTAAA
TTTTTTCCGTTTACCAAAGGGCGGGAAATAAAATGTATCAGCCGACAATTGGCTACAGAAAAAAA
CAAGGGAAATTTATGTACTAAAAAACGGGTAA
Found at i:4254335 original size:12 final size:11
Alignment explanation
Indices: 4254293--4254333 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
4254283 TTTAAATTTT
4254293 AATATTTTTAAA
1 AATATTTTT-AA
*
4254305 AATATTATTAA
1 AATATTTTTAA
4254316 AATA--TTTAA
1 AATATTTTTAA
4254325 AATATTTTT
1 AATATTTTT
4254334 TATTAAGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
9 8 0.32
11 9 0.36
12 8 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
AATATTTTTAA
Found at i:4266875 original size:3 final size:3
Alignment explanation
Indices: 4266867--4266898 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
4266857 TTGAATTATA
4266867 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
4266899 ATATAGTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:4271478 original size:2 final size:2
Alignment explanation
Indices: 4271432--4271463 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4271422 TTTGGATTTC
4271432 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
4271464 TGATATTGTT
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:4271923 original size:2 final size:2
Alignment explanation
Indices: 4271916--4271947 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4271906 AAATTCCATC
4271916 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
4271948 TCGTTCTTTC
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:4273475 original size:49 final size:48
Alignment explanation
Indices: 4273422--4273520 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 48
4273412 ACTTATTGTT
* * *
4273422 TGTGAGTGAATTAGAGGAGATTGAAAA-AGTTCCGCATAGGTTTGGTACA
1 TGTGAGTGAATTAGAGGAGATT-AAAAGAG-TCCACATAGGTATGATACA
*
4273471 TGTGAGTGGATTAGAGGAGATTAAAAGAGTCCACATAGGTATGATACA
1 TGTGAGTGAATTAGAGGAGATTAAAAGAGTCCACATAGGTATGATACA
4273519 TG
1 TG
4273521 ATAGTACATG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
48 22 0.49
49 23 0.51
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.27
Consensus pattern (48 bp):
TGTGAGTGAATTAGAGGAGATTAAAAGAGTCCACATAGGTATGATACA
Found at i:4274080 original size:2 final size:2
Alignment explanation
Indices: 4274075--4274106 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4274065 TCTCTCCTTT
4274075 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4274107 CTTTACCTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4276807 original size:2 final size:2
Alignment explanation
Indices: 4276800--4276843 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
4276790 ACCCTACAAG
4276800 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4276842 AT
1 AT
4276844 TGGGTCCTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4288555 original size:23 final size:23
Alignment explanation
Indices: 4288512--4288555 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
4288502 AAGACATTCA
*
4288512 TTTAAAATCTAAGAATATTTACT
1 TTTAAAATCTAAAAATATTTACT
*
4288535 TTTAAAATTTTAAAAAT-TTTA
1 TTTAAAA-TCTAAAAATATTTA
4288556 AATTTATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (23 bp):
TTTAAAATCTAAAAATATTTACT
Found at i:4289549 original size:36 final size:36
Alignment explanation
Indices: 4289509--4289581 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
4289499 TAAAATAAAC
4289509 ATTGTTAAATTTACTTTAAAACCAAGATTGTGATGT
1 ATTGTTAAATTTACTTTAAAACCAAGATTGTGATGT
*
4289545 ATTGTTAAATTTACTTTAAACCCAAGATTGTGATGT
1 ATTGTTAAATTTACTTTAAAACCAAGATTGTGATGT
4289581 A
1 A
4289582 ATGTGAGGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.41
Consensus pattern (36 bp):
ATTGTTAAATTTACTTTAAAACCAAGATTGTGATGT
Found at i:4305902 original size:18 final size:18
Alignment explanation
Indices: 4305858--4305902 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
4305848 TTTCTGATTC
* *
4305858 TTTATTGTCATGATTATT
1 TTTATTGTTATAATTATT
*
4305876 TTTATTGTTATAATTTTT
1 TTTATTGTTATAATTATT
4305894 TTTATTGTT
1 TTTATTGTT
4305903 TCACTAATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.20, C:0.02, G:0.09, T:0.69
Consensus pattern (18 bp):
TTTATTGTTATAATTATT
Found at i:4307439 original size:13 final size:13
Alignment explanation
Indices: 4307421--4307446 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4307411 TTGAGTCGAA
4307421 TGTTTCATAATTT
1 TGTTTCATAATTT
4307434 TGTTTCATAATTT
1 TGTTTCATAATTT
4307447 GATCTTATAA
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:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (13 bp):
TGTTTCATAATTT
Found at i:4312179 original size:18 final size:17
Alignment explanation
Indices: 4312156--4312192 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
4312146 ATATAAAATT
4312156 ATGATATGATAAGATAAG
1 ATGATATGATAA-ATAAG
*
4312174 ATGATATTATAAATAAG
1 ATGATATGATAAATAAG
4312191 AT
1 AT
4312193 TAAATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.32
Consensus pattern (17 bp):
ATGATATGATAAATAAG
Found at i:4313190 original size:25 final size:23
Alignment explanation
Indices: 4313153--4313200 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
4313143 ATTATAATTA
4313153 TAATCAAAGATTATATTTAAAAAAT
1 TAATCAAAGATTA-A-TTAAAAAAT
4313178 TAATGCAAA-ATTAATTAAAAAAT
1 TAAT-CAAAGATTAATTAAAAAAT
4313201 ATATAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 9 0.41
24 1 0.05
25 8 0.36
26 4 0.18
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (23 bp):
TAATCAAAGATTAATTAAAAAAT
Found at i:4317370 original size:32 final size:32
Alignment explanation
Indices: 4317333--4317397 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
4317323 TTAACACCTA
* *
4317333 AAAAGAGTCAGTAAGGTTTGTTCATTTAACTT
1 AAAAGAGTCAGAAAGATTTGTTCATTTAACTT
*
4317365 AAAAGAGTCAGAAAGATTTGTTTATTTAACTT
1 AAAAGAGTCAGAAAGATTTGTTCATTTAACTT
4317397 A
1 A
4317398 CTCTGGTGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (32 bp):
AAAAGAGTCAGAAAGATTTGTTCATTTAACTT
Found at i:4323291 original size:17 final size:16
Alignment explanation
Indices: 4323248--4323292 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
4323238 AATGAATGAG
4323248 ATATAATTAAAAAAAT
1 ATATAATTAAAAAAAT
4323264 ATAATAAATTAAAAAAATT
1 AT-AT-AATTAAAAAAA-T
*
4323283 ATATTATTAA
1 ATATAATTAA
4323293 TGTATCGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 2 0.08
17 7 0.28
18 13 0.52
19 3 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATATAATTAAAAAAAT
Found at i:4325868 original size:20 final size:21
Alignment explanation
Indices: 4325822--4325869 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
4325812 AAGTTAAATC
4325822 ATGA-AAATGATAATATCAAA
1 ATGACAAATGATAATATCAAA
***
4325842 GCAACAAAT-ATAATATCAAA
1 ATGACAAATGATAATATCAAA
4325862 ATGACAAA
1 ATGACAAA
4325870 CAAAAAAATC
Statistics
Matches: 21, Mismatches: 6, Indels: 2
0.72 0.21 0.07
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.60, C:0.10, G:0.08, T:0.21
Consensus pattern (21 bp):
ATGACAAATGATAATATCAAA
Found at i:4330659 original size:18 final size:18
Alignment explanation
Indices: 4330613--4330656 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
4330603 AGATCTTAAC
4330613 TTAAATA-TAAA-A-TTA
1 TTAAATATTAAATATTTA
4330628 TTAAATATTAAATATTTA
1 TTAAATATTAAATATTTA
4330646 TTAAAT-TTAAA
1 TTAAATATTAAA
4330657 ATAACATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.27
16 4 0.15
17 6 0.23
18 9 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTAAATATTAAATATTTA
Found at i:4332720 original size:21 final size:21
Alignment explanation
Indices: 4332696--4332740 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
4332686 TTATAGAATT
* *
4332696 ATTATGA-ACTTATTTGATTTA
1 ATTATGATAATTACTTGA-TTA
4332717 ATTATGATAATTACTTGATTA
1 ATTATGATAATTACTTGATTA
4332738 ATT
1 ATT
4332741 TTACTTGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (21 bp):
ATTATGATAATTACTTGATTA
Found at i:4334641 original size:17 final size:17
Alignment explanation
Indices: 4334619--4334725 Score: 53
Period size: 17 Copynumber: 6.3 Consensus size: 17
4334609 TGTGCTCTTT
4334619 AATTTTCTTGTAATTTA
1 AATTTTCTTGTAATTTA
*
4334636 AATTTTATATGTAATTT-
1 AATTTTCT-TGTAATTTA
** *
4334653 -ATGTTTC--AAACATTTT
1 AAT-TTTCTTGTA-ATTTA
* *
4334669 AATTTTTTATGTTATTTA
1 AATTTTCT-TGTAATTTA
*
4334687 AATTTAC-TGTAATTTTA
1 AATTTTCTTGTAA-TTTA
* *
4334704 AATTTTCATGTTATTTA
1 AATTTTCTTGTAATTTA
4334721 AATTT
1 AATTT
4334726 ATGCAATTTT
Statistics
Matches: 66, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
14 1 0.02
15 4 0.06
16 9 0.14
17 31 0.47
18 21 0.32
ACGTcount: A:0.32, C:0.05, G:0.06, T:0.58
Consensus pattern (17 bp):
AATTTTCTTGTAATTTA
Found at i:4334690 original size:18 final size:17
Alignment explanation
Indices: 4334666--4334725 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
4334656 TTTCAAACAT
*
4334666 TTTAATTTTTTATGTTA
1 TTTAAATTTTTATGTTA
*
4334683 TTTAAA--TTTACTGTAA
1 TTTAAATTTTTA-TGTTA
*
4334699 TTTTAAATTTTCATGTTA
1 -TTTAAATTTTTATGTTA
4334717 TTTAAATTT
1 TTTAAATTT
4334726 ATGCAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 4 0.11
16 4 0.11
17 20 0.57
18 4 0.11
19 3 0.09
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (17 bp):
TTTAAATTTTTATGTTA
Found at i:4334702 original size:34 final size:33
Alignment explanation
Indices: 4334664--4334757 Score: 111
Period size: 34 Copynumber: 2.9 Consensus size: 33
4334654 TGTTTCAAAC
*
4334664 ATTTTAATTTTTTATGTTATTTAAATTTACTGTA
1 ATTTTAATTTTTTATGTTATTTAAATTTA-TGCA
* *
4334698 ATTTTAAATTTTCATGTTATTTAAATTTATGCA
1 ATTTTAATTTTTTATGTTATTTAAATTTATGCA
* * *
4334731 ATTTT--TTTTTTTTGTAATTTAATTTTA
1 ATTTTAATTTTTTATGTTATTTAAATTTA
4334758 AGTGTTTAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
31 17 0.33
33 8 0.15
34 27 0.52
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (33 bp):
ATTTTAATTTTTTATGTTATTTAAATTTATGCA
Found at i:4334816 original size:16 final size:16
Alignment explanation
Indices: 4334780--4334810 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4334770 TCATGGCCTC
4334780 ATTTACTTTTTATGCA
1 ATTTACTTTTTATGCA
*
4334796 ATTTATTTTTTATGC
1 ATTTACTTTTTATGC
4334811 GCTTTAAATT
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:0.23, C:0.10, G:0.06, T:0.61
Consensus pattern (16 bp):
ATTTACTTTTTATGCA
Found at i:4346152 original size:14 final size:14
Alignment explanation
Indices: 4346133--4346178 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
4346123 AATTATAATT
4346133 TAAAAAATTTTATA
1 TAAAAAATTTTATA
4346147 T-AAAAA-TTTATA
1 TAAAAAATTTTATA
4346159 TTAAATAAATTTTAT-
1 -TAAA-AAATTTTATA
4346174 TAAAA
1 TAAAA
4346179 TTATTATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 6 0.21
13 7 0.25
14 7 0.25
15 3 0.11
16 5 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAAAAATTTTATA
Found at i:4350608 original size:12 final size:12
Alignment explanation
Indices: 4350591--4350617 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4350581 GGCCATAAAC
4350591 AAGCTCCAAGGG
1 AAGCTCCAAGGG
4350603 AAGCTCCAAGGG
1 AAGCTCCAAGGG
4350615 AAG
1 AAG
4350618 GCTCTGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.22, G:0.33, T:0.07
Consensus pattern (12 bp):
AAGCTCCAAGGG
Found at i:4356795 original size:24 final size:23
Alignment explanation
Indices: 4356768--4356816 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
4356758 TAATAAATAT
4356768 ATTT-AAATTATATTATATTTTAAA
1 ATTTAAAATT-TATTATA-TTTAAA
*
4356792 ATTTAAAATTTTTTATATTTAAA
1 ATTTAAAATTTATTATATTTAAA
4356815 AT
1 AT
4356817 AAATTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 8 0.35
24 10 0.43
25 5 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTTAAAATTTATTATATTTAAA
Found at i:4356933 original size:13 final size:15
Alignment explanation
Indices: 4356917--4356948 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4356907 AATGTGTTTA
4356917 AATTTTA-TA-TTTC
1 AATTTTATTATTTTC
4356930 AATTTTATTATTTTC
1 AATTTTATTATTTTC
4356945 AATT
1 AATT
4356949 ATAATTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 2 0.12
15 8 0.47
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (15 bp):
AATTTTATTATTTTC
Found at i:4356954 original size:21 final size:21
Alignment explanation
Indices: 4356930--4356969 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4356920 TTTATATTTC
*
4356930 AATTTT-ATTATTTTCAATTAT
1 AATTTTGATTAATTT-AATTAT
4356951 AATTTTGATTAATTTAATT
1 AATTTTGATTAATTTAATT
4356970 TTAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (21 bp):
AATTTTGATTAATTTAATTAT
Found at i:4357047 original size:15 final size:14
Alignment explanation
Indices: 4357029--4357080 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
4357019 AATCAATCAA
4357029 AATTAATTCAATTAC
1 AATTAATT-AATTAC
4357044 AATTAATTAATTA-
1 AATTAATTAATTAC
* *
4357057 AATCAATATAATTAA
1 AATTAAT-TAATTAC
4357072 AATTGAATT
1 AATT-AATT
4357081 TTGAACATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 6 0.19
14 11 0.34
15 12 0.38
16 3 0.09
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (14 bp):
AATTAATTAATTAC
Found at i:4365559 original size:23 final size:23
Alignment explanation
Indices: 4365535--4365586 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
4365525 AAATAATTAT
4365535 TTTTTAAA-TATAATATTAATAA
1 TTTTTAAATTATAATATTAATAA
* *
4365557 -TTTTAAATTTTAATATTTATAAA
1 TTTTTAAATTATAATATTAAT-AA
4365580 TTTTTAA
1 TTTTTAA
4365587 TTTTCAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 7 0.28
22 10 0.40
23 2 0.08
24 6 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTTAAATTATAATATTAATAA
Found at i:4365569 original size:16 final size:16
Alignment explanation
Indices: 4365550--4365596 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 16
4365540 AAATATAATA
4365550 TTAATAATTTTAAATT
1 TTAATAATTTTAAATT
4365566 TTAAT-ATTTATAAATT
1 TTAATAATTT-TAAATT
4365582 TT--TAATTTTCAAATT
1 TTAATAATTTT-AAATT
4365597 ACAAATTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
14 2 0.07
15 13 0.46
16 13 0.46
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAATAATTTTAAATT
Found at i:4365570 original size:22 final size:23
Alignment explanation
Indices: 4365536--4365590 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
4365526 AATAATTATT
*
4365536 TTTTAAA-TATAATATTAAT-AA
1 TTTTAAATTTTAATATTAATAAA
*
4365557 TTTTAAATTTTAATATTTATAAA
1 TTTTAAATTTTAATATTAATAAA
*
4365580 TTTTTAATTTT
1 TTTTAAATTTT
4365591 CAAATTACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 7 0.24
22 10 0.34
23 12 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTTAAATTTTAATATTAATAAA
Found at i:4369301 original size:2 final size:2
Alignment explanation
Indices: 4369294--4369321 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4369284 TAATCGATTA
4369294 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
4369322 TAACAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4384747 original size:2 final size:2
Alignment explanation
Indices: 4384740--4384793 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
4384730 CTTCACAAAT
4384740 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
4384782 TC TC TC TC TC TC
1 TC TC TC TC TC TC
4384794 CATTTAGCTC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:4391042 original size:10 final size:10
Alignment explanation
Indices: 4391027--4391052 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
4391017 CTTTAATAAT
4391027 TTTATTCAAA
1 TTTATTCAAA
4391037 TTTATTCAAA
1 TTTATTCAAA
4391047 TTTATT
1 TTTATT
4391053 AATTTGGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (10 bp):
TTTATTCAAA
Found at i:4391137 original size:20 final size:20
Alignment explanation
Indices: 4391101--4391138 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4391091 ACTTACGTCG
**
4391101 ATATAATTTTTTTTAATTTT
1 ATATAATTTTTAATAATTTT
4391121 ATATAATTTTTAATAATT
1 ATATAATTTTTAATAATT
4391139 GATTTTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATATAATTTTTAATAATTTT
Found at i:4392863 original size:17 final size:17
Alignment explanation
Indices: 4392841--4392874 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4392831 GTAAGGGGAT
4392841 GTCTTAAAACCTGCCAA
1 GTCTTAAAACCTGCCAA
4392858 GTCTTAAAACCTGCCAA
1 GTCTTAAAACCTGCCAA
4392875 AACTTGGTCA
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:0.35, C:0.29, G:0.12, T:0.24
Consensus pattern (17 bp):
GTCTTAAAACCTGCCAA
Found at i:4400241 original size:34 final size:34
Alignment explanation
Indices: 4400197--4400277 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
4400187 TAATTGTAAT
4400197 GTTTTACAAAAATAAAATTTTAG-TAAAATT-AATAA
1 GTTTT-CAAAAAT-AAATTTTAGAT-AAATTAAATAA
* * *
4400232 GTTTTCAAAAATCAATTTTCGATACATTAAATAA
1 GTTTTCAAAAATAAATTTTAGATAAATTAAATAA
4400266 GTTTTCAAAAAT
1 GTTTTCAAAAAT
4400278 TCATTTCCAG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
33 11 0.27
34 25 0.61
35 5 0.12
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.38
Consensus pattern (34 bp):
GTTTTCAAAAATAAATTTTAGATAAATTAAATAA
Found at i:4400978 original size:22 final size:24
Alignment explanation
Indices: 4400946--4400989 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
4400936 GATATGTGTG
4400946 ATAAGATAAGATAAGA-TAATACT
1 ATAAGATAAGATAAGATTAATACT
*
4400969 ATAA-ATAAGATTAGATTAATA
1 ATAAGATAAGATAAGATTAATA
4400990 ATGTTATCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.57, C:0.02, G:0.11, T:0.30
Consensus pattern (24 bp):
ATAAGATAAGATAAGATTAATACT
Found at i:4401911 original size:20 final size:20
Alignment explanation
Indices: 4401868--4401911 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
4401858 TCGAAAATGA
4401868 ATTTTTAAAAATTATATAAT
1 ATTTTTAAAAATTATATAAT
*
4401888 -TTTTTGAAAGATTATA-AAT
1 ATTTTT-AAAAATTATATAAT
4401907 ATTTT
1 ATTTT
4401912 ATTTTCATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (20 bp):
ATTTTTAAAAATTATATAAT
Found at i:4402342 original size:14 final size:14
Alignment explanation
Indices: 4402323--4402350 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4402313 TAAATCAAAT
4402323 TATATATATTTTAA
1 TATATATATTTTAA
4402337 TATATATATTTTAA
1 TATATATATTTTAA
4402351 ATTTATATAA
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:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATATATATTTTAA
Found at i:4402359 original size:15 final size:15
Alignment explanation
Indices: 4402319--4402359 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
4402309 AAAATAAATC
4402319 AAATTATATATATTTT
1 AAATT-TATATATTTT
*
4402335 -AATATATATATTTT
1 AAATTTATATATTTT
4402349 AAATTTATATA
1 AAATTTATATA
4402360 AATTAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AAATTTATATATTTT
Found at i:4402365 original size:29 final size:30
Alignment explanation
Indices: 4402319--4402378 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
4402309 AAAATAAATC
** *
4402319 AAATTATATATATTTTAATAT-ATATATTTT
1 AAATTATATATAAATTAAAATAATA-ATTTT
4402349 AAATT-TATATAAATTAAAATAATAATTTT
1 AAATTATATATAAATTAAAATAATAATTTT
4402378 A
1 A
4402379 TATCAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
AAATTATATATAAATTAAAATAATAATTTT
Found at i:4402414 original size:33 final size:35
Alignment explanation
Indices: 4402349--4402430 Score: 96
Period size: 33 Copynumber: 2.4 Consensus size: 35
4402339 TATATATTTT
4402349 AAATTTATATAAATTAAAATAATAATTTTATATCA
1 AAATTTATATAAATTAAAATAATAATTTTATATCA
* * * *
4402384 AAATTTATTTAAA-TATATTAA-AATTTTATATTA
1 AAATTTATATAAATTAAAATAATAATTTTATATCA
*
4402417 AAATAATATATAAA
1 AAAT-TTATATAAA
4402431 AATTAAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
33 15 0.38
34 13 0.32
35 12 0.30
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (35 bp):
AAATTTATATAAATTAAAATAATAATTTTATATCA
Found at i:4402415 original size:13 final size:13
Alignment explanation
Indices: 4402396--4402445 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
4402386 ATTTATTTAA
4402396 ATATATTAAAATT
1 ATATATTAAAATT
* *
4402409 TTATATTAAAATA
1 ATATATTAAAATT
*
4402422 ATATATAAAAATT
1 ATATATTAAAATT
* *
4402435 AAAAATTAAAA
1 ATATATTAAAA
4402446 ATTAATAAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATATTAAAATT
Found at i:4402440 original size:33 final size:32
Alignment explanation
Indices: 4402355--4402441 Score: 79
Period size: 33 Copynumber: 2.7 Consensus size: 32
4402345 TTTTAAATTT
* * *
4402355 ATATAAATTAAAA-TAATAATTTTATATCAAA
1 ATATATATAAAAATTAAAAATTTTATATCAAA
* * *
4402386 ATTTATTTAAATATATT-AAAATTTTATATTAAA
1 ATATATATAAA-A-ATTAAAAATTTTATATCAAA
4402419 ATAATATATAAAAATTAAAAATT
1 AT-ATATATAAAAATTAAAAATT
4402442 AAAAATTAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
31 7 0.16
32 4 0.09
33 24 0.56
34 8 0.19
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (32 bp):
ATATATATAAAAATTAAAAATTTTATATCAAA
Found at i:4402442 original size:26 final size:26
Alignment explanation
Indices: 4402395--4402445 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
4402385 AATTTATTTA
* ** *
4402395 AATATATTAAAATTTTATATTAAAAT
1 AATATATAAAAATTAAAAATTAAAAT
4402421 AATATATAAAAATTAAAAATTAAAA
1 AATATATAAAAATTAAAAATTAAAA
4402446 ATTAATAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
AATATATAAAAATTAAAAATTAAAAT
Found at i:4402446 original size:14 final size:15
Alignment explanation
Indices: 4402427--4402455 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4402417 AAATAATATA
4402427 TAAAAATTAA-AAAT
1 TAAAAATTAATAAAT
4402441 TAAAAATTAATAAAT
1 TAAAAATTAATAAAT
4402456 CAAATTGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAAATTAATAAAT
Found at i:4409094 original size:31 final size:31
Alignment explanation
Indices: 4409056--4409118 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
4409046 CAACACTTCA
*
4409056 ACTAACTTCCAGAATTGCATGGAAGAAACCC
1 ACTAACTTCCAGAATTGCATGAAAGAAACCC
*
4409087 ACTAACTTCCAGAATTTCATGAAAGAAACCC
1 ACTAACTTCCAGAATTGCATGAAAGAAACCC
4409118 A
1 A
4409119 TGTTACCCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.41, C:0.25, G:0.13, T:0.21
Consensus pattern (31 bp):
ACTAACTTCCAGAATTGCATGAAAGAAACCC
Found at i:4416963 original size:15 final size:15
Alignment explanation
Indices: 4416939--4416968 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4416929 AGAAAATAAC
*
4416939 GTAAACTATCTTATG
1 GTAAAATATCTTATG
4416954 GTAAAATATCTTATG
1 GTAAAATATCTTATG
4416969 ATATGCTACG
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:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (15 bp):
GTAAAATATCTTATG
Found at i:4422940 original size:14 final size:14
Alignment explanation
Indices: 4422921--4422958 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
4422911 TGGAATATGC
4422921 AAAAAATAAAAATA
1 AAAAAATAAAAATA
4422935 AAAAAATAAAAATA
1 AAAAAATAAAAATA
4422949 AAAAAATAAA
1 AAAAAATAAA
4422959 TATATATAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAAAATAAAAATA
Found at i:4423506 original size:24 final size:26
Alignment explanation
Indices: 4423461--4423533 Score: 96
Period size: 24 Copynumber: 2.8 Consensus size: 26
4423451 AAATAATTTT
*
4423461 TTATATTTTAAAAATATAAAAATACTC
1 TTATATTAT-AAAATATAAAAATACTC
* *
4423488 TTATA-T-TAAGATATAAAAATATTC
1 TTATATTATAAAATATAAAAATACTC
4423512 TTATATTATAAAATATAAAAAT
1 TTATATTATAAAATATAAAAAT
4423534 GCGCCTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
24 20 0.49
25 2 0.05
26 14 0.34
27 5 0.12
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (26 bp):
TTATATTATAAAATATAAAAATACTC
Found at i:4427205 original size:50 final size:50
Alignment explanation
Indices: 4427151--4427249 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 50
4427141 CAATGACAAG
* * *
4427151 ATATATAAAAAAAAGAAAATGATACGATTTAAAATTGATAAAAATTGTAC
1 ATATATAAAAAAAAGAAAATAATACAATTTAAAATTAATAAAAATTGTAC
** *
4427201 ATATATAAAAAAATTAAAGTAATACAATTTAAAATTAATAAAAATTGTA
1 ATATATAAAAAAAAGAAAATAATACAATTTAAAATTAATAAAAATTGTA
4427250 TATGAATTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (50 bp):
ATATATAAAAAAAAGAAAATAATACAATTTAAAATTAATAAAAATTGTAC
Found at i:4440339 original size:14 final size:14
Alignment explanation
Indices: 4440320--4440348 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4440310 TTGGGTTCAT
4440320 TATTATTATTTTTC
1 TATTATTATTTTTC
4440334 TATTATTATTTTTC
1 TATTATTATTTTTC
4440348 T
1 T
4440349 TCTTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (14 bp):
TATTATTATTTTTC
Found at i:4443822 original size:23 final size:23
Alignment explanation
Indices: 4443790--4443840 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
4443780 AAATAATAAT
*
4443790 AAAAATTATTATAATTATGATTA
1 AAAAAATATTATAATTATGATTA
4443813 AAAAAATATTATAATTATGATTA
1 AAAAAATATTATAATTATGATTA
4443836 AAAAA
1 AAAAA
4443841 TAAATTTTTA
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:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (23 bp):
AAAAAATATTATAATTATGATTA
Found at i:4443975 original size:20 final size:20
Alignment explanation
Indices: 4443950--4443988 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4443940 TGTGATAGAA
* *
4443950 TCCAAACTTAATCCTAGTCC
1 TCCAAACCTAACCCTAGTCC
4443970 TCCAAACCTAACCCTAGTC
1 TCCAAACCTAACCCTAGTC
4443989 TTGATCAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.38, G:0.05, T:0.26
Consensus pattern (20 bp):
TCCAAACCTAACCCTAGTCC
Found at i:4450845 original size:8 final size:8
Alignment explanation
Indices: 4450824--4450866 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
4450814 AAGAGGATTG
4450824 AAAA-TTC
1 AAAATTTC
4450831 AACAATTTC
1 AA-AATTTC
4450840 AAAATTTC
1 AAAATTTC
4450848 AAAA-TTC
1 AAAATTTC
4450855 -AAATTTC
1 AAAATTTC
4450862 AAAAT
1 AAAAT
4450867 ATTTTCAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 3 0.09
7 8 0.25
8 16 0.50
9 5 0.16
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (8 bp):
AAAATTTC
Found at i:4450857 original size:7 final size:7
Alignment explanation
Indices: 4450824--4450866 Score: 50
Period size: 7 Copynumber: 5.7 Consensus size: 7
4450814 AAGAGGATTG
4450824 AAAATTC
1 AAAATTC
4450831 AACAATTTC
1 AA-AA-TTC
4450840 AAAATTTC
1 AAAA-TTC
4450848 AAAATTC
1 AAAATTC
*
4450855 AAATTTC
1 AAAATTC
4450862 AAAAT
1 AAAAT
4450867 ATTTTCAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 15 0.47
8 12 0.38
9 5 0.16
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (7 bp):
AAAATTC
Found at i:4451480 original size:25 final size:25
Alignment explanation
Indices: 4451447--4451498 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
4451437 ATGAAATTTC
4451447 ATAAAATTCATA-ATGATAAATTTTT
1 ATAAAATTCATAGATGA-AAATTTTT
* *
4451472 ATAAAATTCTTAGGTGAAAATTTTT
1 ATAAAATTCATAGATGAAAATTTTT
4451497 AT
1 AT
4451499 CTAAATTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 21 0.88
26 3 0.12
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (25 bp):
ATAAAATTCATAGATGAAAATTTTT
Found at i:4454220 original size:16 final size:17
Alignment explanation
Indices: 4454199--4454230 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4454189 AATGATAAGT
4454199 TAAAAAGAG-AAAAAAC
1 TAAAAAGAGTAAAAAAC
4454215 TAAAAAGAGTAAAAAA
1 TAAAAAGAGTAAAAAA
4454231 AGAAAGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.75, C:0.03, G:0.12, T:0.09
Consensus pattern (17 bp):
TAAAAAGAGTAAAAAAC
Found at i:4455503 original size:11 final size:11
Alignment explanation
Indices: 4455487--4455537 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
4455477 GATCAAAAGT
4455487 AAAAAAAACAA
1 AAAAAAAACAA
4455498 AAAAAAAACAA
1 AAAAAAAACAA
*
4455509 AAAAGCAAA-AA
1 AAAA-AAAACAA
*
4455520 AAAAAAAAGAA
1 AAAAAAAACAA
*
4455531 AATAAAA
1 AAAAAAA
4455538 TGAATGTCAC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
10 3 0.09
11 29 0.83
12 3 0.09
ACGTcount: A:0.88, C:0.06, G:0.04, T:0.02
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:4455510 original size:19 final size:18
Alignment explanation
Indices: 4455487--4455537 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
4455477 GATCAAAAGT
4455487 AAAAAAAACAAAAAAAAA
1 AAAAAAAACAAAAAAAAA
*
4455505 ACAAAAAAGCAAAAAAAAA
1 A-AAAAAAACAAAAAAAAA
*
4455524 AAAAGAAAATAAAA
1 AAAA-AAAACAAAA
4455538 TGAATGTCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.88, C:0.06, G:0.04, T:0.02
Consensus pattern (18 bp):
AAAAAAAACAAAAAAAAA
Found at i:4455521 original size:28 final size:27
Alignment explanation
Indices: 4455481--4455537 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
4455471 CTCAAAGATC
*
4455481 AAAAGTAAAAAAAACAAAAAAAAAACAA
1 AAAAGCAAAAAAAA-AAAAAAAAAACAA
* *
4455509 AAAAGCAAAAAAAAAAAAAGAAAATAA
1 AAAAGCAAAAAAAAAAAAAAAAAACAA
4455536 AA
1 AA
4455538 TGAATGTCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 13 0.50
28 13 0.50
ACGTcount: A:0.86, C:0.05, G:0.05, T:0.04
Consensus pattern (27 bp):
AAAAGCAAAAAAAAAAAAAAAAAACAA
Found at i:4455939 original size:32 final size:32
Alignment explanation
Indices: 4455900--4456000 Score: 98
Period size: 32 Copynumber: 3.1 Consensus size: 32
4455890 ATCAATAGTA
* *
4455900 AAAAAAATATAAAAAATATAAAATA-AAAAAAG
1 AAAAAAATA-AAAAAATAAAAAAGAGAAAAAAG
* *
4455932 AAAAAAATAAAAAGAA-AAAAAAGAGAAGAAAT
1 AAAAAAATAAAAA-AATAAAAAAGAGAAAAAAG
* * *
4455964 AAAAAAATAAAAAAATGAAAAGGAAATAAAAAG
1 AAAAAAATAAAAAAATAAAAAAGAGA-AAAAAG
4455997 AAAA
1 AAAA
4456001 CTCAAATTTA
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
31 12 0.21
32 36 0.64
33 8 0.14
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.10
Consensus pattern (32 bp):
AAAAAAATAAAAAAATAAAAAAGAGAAAAAAG
Found at i:4455951 original size:8 final size:8
Alignment explanation
Indices: 4455900--4455995 Score: 88
Period size: 8 Copynumber: 11.6 Consensus size: 8
4455890 ATCAATAGTA
4455900 AAAAAAAT
1 AAAAAAAT
4455908 ATAAAAAAT
1 A-AAAAAAT
*
4455917 -ATAAAAT
1 AAAAAAAT
*
4455924 AAAAAAAG
1 AAAAAAAT
4455932 AAAAAAAT
1 AAAAAAAT
*
4455940 AAAAAGA-
1 AAAAAAAT
*
4455947 AAAAAAAG
1 AAAAAAAT
*
4455955 AGAAGAAAT
1 A-AAAAAAT
4455964 AAAAAAAT
1 AAAAAAAT
4455972 AAAAAAAT
1 AAAAAAAT
4455980 GAAAAGGAAAT
1 -AAAA--AAAT
4455991 AAAAA
1 AAAAA
4455996 GAAAACTCAA
Statistics
Matches: 72, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
7 12 0.17
8 35 0.49
9 17 0.24
10 4 0.06
11 4 0.06
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:4455964 original size:40 final size:42
Alignment explanation
Indices: 4455920--4455997 Score: 124
Period size: 40 Copynumber: 1.9 Consensus size: 42
4455910 AAAAAATATA
4455920 AAATAAAAAAAGAAAAAAAT-AAAAAGAAA-AAAAAGAGAAG
1 AAATAAAAAAAGAAAAAAATGAAAAAGAAATAAAAAGAGAAG
* *
4455960 AAATAAAAAAATAAAAAAATGAAAAGGAAATAAAAAGA
1 AAATAAAAAAAGAAAAAAATGAAAAAGAAATAAAAAGA
4455998 AAACTCAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 19 0.56
41 8 0.24
42 7 0.21
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.08
Consensus pattern (42 bp):
AAATAAAAAAAGAAAAAAATGAAAAAGAAATAAAAAGAGAAG
Found at i:4455984 original size:14 final size:13
Alignment explanation
Indices: 4455899--4455995 Score: 67
Period size: 14 Copynumber: 7.3 Consensus size: 13
4455889 TATCAATAGT
*
4455899 AAAAAA-AATATA
1 AAAAAAGAAAATA
*
4455911 AAAAATATAAAATA
1 AAAAA-AGAAAATA
*
4455925 AAAAAAGAAAAAA
1 AAAAAAGAAAATA
4455938 ATAAAAAGAAAA-A
1 A-AAAAAGAAAATA
4455951 AAAGAGAAG-AAATA
1 AAA-A-AAGAAAATA
*
4455965 AAAAAATAAAA-A
1 AAAAAAGAAAATA
*
4455977 AATGAAAAGGAAATA
1 AA--AAAAGAAAATA
4455992 AAAA
1 AAAA
4455996 GAAAACTCAA
Statistics
Matches: 69, Mismatches: 6, Indels: 19
0.73 0.06 0.20
Matches are distributed among these distances:
12 12 0.17
13 20 0.29
14 34 0.49
15 3 0.04
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.10
Consensus pattern (13 bp):
AAAAAAGAAAATA
Found at i:4456872 original size:20 final size:20
Alignment explanation
Indices: 4456840--4456880 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
4456830 GAATTTCATG
4456840 ACATTATTGACATCTGCATT
1 ACATTATTGACATCTGCATT
*
4456860 ACATGTATT-ACATTTGCATT
1 ACAT-TATTGACATCTGCATT
4456880 A
1 A
4456881 TAAGTTGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (20 bp):
ACATTATTGACATCTGCATT
Found at i:4457599 original size:14 final size:14
Alignment explanation
Indices: 4457580--4457637 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
4457570 TGCGAATCTG
4457580 AAATTTTGTGAATC
1 AAATTTTGTGAATC
* *
4457594 AAATTTTTGTAAAACTA
1 AAA-TTTTGT-GAA-TC
*
4457611 AAATTTTGAGAATC
1 AAATTTTGTGAATC
*
4457625 AAATTTTATGAAT
1 AAATTTTGTGAAT
4457638 TCTTGCAAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
14 15 0.44
15 8 0.24
16 7 0.21
17 4 0.12
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.41
Consensus pattern (14 bp):
AAATTTTGTGAATC
Found at i:4457603 original size:15 final size:15
Alignment explanation
Indices: 4457583--4457631 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
4457573 GAATCTGAAA
4457583 TTTTGTGAATCAAAT
1 TTTTGTGAATCAAAT
* * *
4457598 TTTTGTAAAACTAAAA
1 TTTTGTGAATC-AAAT
*
4457614 TTTTGAGAATCAAAT
1 TTTTGTGAATCAAAT
4457629 TTT
1 TTT
4457632 ATGAATTCTT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (15 bp):
TTTTGTGAATCAAAT
Found at i:4457923 original size:84 final size:84
Alignment explanation
Indices: 4457786--4457940 Score: 213
Period size: 84 Copynumber: 1.8 Consensus size: 84
4457776 GCTTTATTTA
* * * * * *
4457786 TTTTTTTCAAAGTTGTTGAGCCTCTGTTTAAAGGAGTATTTATTTTTCTAAAGTTGTTGAGCCTC
1 TTTTTTTCAAAGTTATTGAGCCTCTGTTTAAAGAAGCATTTATTTTTCTAAAGTTATTAAACCTC
4457851 TGTTTAGAAGAACAATTAT
66 TGTTTAGAAGAACAATTAT
* * *
4457870 TTTTTTTCAAAGTTATTGAGCCTCTGTTT-ATGAAGCATTTGTTTTTTTCAAAGTTATTAAACCT
1 TTTTTTTCAAAGTTATTGAGCCTCTGTTTAAAGAAGCATTTATTTTTCT-AAAGTTATTAAACCT
4457934 CTGTTTA
65 CTGTTTA
4457941 TAGGAGTTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
83 14 0.23
84 47 0.77
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.48
Consensus pattern (84 bp):
TTTTTTTCAAAGTTATTGAGCCTCTGTTTAAAGAAGCATTTATTTTTCTAAAGTTATTAAACCTC
TGTTTAGAAGAACAATTAT
Found at i:4457941 original size:41 final size:41
Alignment explanation
Indices: 4457781--4457941 Score: 182
Period size: 41 Copynumber: 3.9 Consensus size: 41
4457771 GATAAGCTTT
* * * *
4457781 ATTTATTTTTTTCAAAGTTGTTGAGCCTCTGTTTAAAGGAGT
1 ATTTATTTTTTTCAAAGTTATTGAGCCTCTGTTT-ATGAAGC
* *
4457823 ATTTATTTTTCT-AAAGTTGTTGAGCCTCTGTTTA-GAAGAAC
1 ATTTATTTTTTTCAAAGTTATTGAGCCTCTGTTTATGAAG--C
*
4457864 AATTATTTTTTTTCAAAGTTATTGAGCCTCTGTTTATGAAGC
1 ATTTA-TTTTTTTCAAAGTTATTGAGCCTCTGTTTATGAAGC
* * *
4457906 ATTTGTTTTTTTCAAAGTTATTAAACCTCTGTTTAT
1 ATTTATTTTTTTCAAAGTTATTGAGCCTCTGTTTAT
4457942 AGGAGTTTTT
Statistics
Matches: 104, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
39 3 0.03
40 1 0.01
41 54 0.52
42 21 0.20
43 21 0.20
44 4 0.04
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.48
Consensus pattern (41 bp):
ATTTATTTTTTTCAAAGTTATTGAGCCTCTGTTTATGAAGC
Found at i:4458120 original size:8 final size:8
Alignment explanation
Indices: 4458106--4458157 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
4458096 TGATTTTGTT
4458106 AATAAAAA
1 AATAAAAA
*
4458114 GATAAAAA
1 AATAAAAA
4458122 AATAATAAA
1 AATAA-AAA
4458131 AA-ATAAAA
1 AATA-AAAA
4458139 AAT-AAAA
1 AATAAAAA
*
4458146 AATGAAAA
1 AATAAAAA
4458154 AATA
1 AATA
4458158 GGTGTTGAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
7 7 0.19
8 24 0.65
9 6 0.16
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (8 bp):
AATAAAAA
Found at i:4458129 original size:19 final size:18
Alignment explanation
Indices: 4458105--4458140 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
4458095 TTGATTTTGT
4458105 TAATAAAAAGATAAAAAAA
1 TAATAAAAA-ATAAAAAAA
4458124 TAATAAAAAATAAAAAA
1 TAATAAAAAATAAAAAA
4458141 TAAAAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.17
Consensus pattern (18 bp):
TAATAAAAAATAAAAAAA
Found at i:4458135 original size:7 final size:7
Alignment explanation
Indices: 4458120--4458157 Score: 58
Period size: 7 Copynumber: 5.1 Consensus size: 7
4458110 AAAAGATAAA
4458120 AAAATAAT
1 AAAA-AAT
4458128 AAAAAAT
1 AAAAAAT
4458135 AAAAAAT
1 AAAAAAT
4458142 AAAAAAT
1 AAAAAAT
4458149 GAAAAAAT
1 -AAAAAAT
4458157 A
1 A
4458158 GGTGTTGAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 18 0.62
8 11 0.38
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.16
Consensus pattern (7 bp):
AAAAAAT
Done.