Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 25 of 325
Found at i:5817619 original size:15 final size:16
Alignment explanation
Indices: 5817594--5817627 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
5817584 TGGGAGTTTA
5817594 TTTTTGTTTTTTTGTT
1 TTTTTGTTTTTTTGTT
5817610 TTTTTG-TTTTTTGTT
1 TTTTTGTTTTTTTGTT
5817625 TTT
1 TTT
5817628 ACTGGTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (16 bp):
TTTTTGTTTTTTTGTT
Found at i:5820909 original size:132 final size:131
Alignment explanation
Indices: 5820579--5820921 Score: 357
Period size: 131 Copynumber: 2.6 Consensus size: 131
5820569 GCAAAATTGT
* ** * * *
5820579 GCCCTAACGTGCTGGGTTGCAATTTCTCGTTTCCTCAAAATAACCGAATGTCCCTTTAGAATTTC
1 GCCCTATCGTGCTGGGTTGCAATTTCTCGTTTGTTCAAAATAATCGAATATCTCTTTAGAATTTC
* * * * ** *
5820644 ATTCACGTTTTCTAAAAACTCTTTGAAACGAAGGAAATGTTCGATGTTTGGCTATTTGAGAATCG
66 ACTCATGTTTTCTAAAAACTCTTTAAAACGAAGGAAATGTTCGATGTCTGGAAATTTGAGAATAG
*
5820709 T
131 C
* ** * ** * * *
5820710 GCCCTATCGTGTTGGGTTGCGCTTTTTTATTTGTTCAAAACAATCGAAGAT-TCCTTTAAAATTT
1 GCCCTATCGTGCTGGGTTGCAATTTCTCGTTTGTTCAAAATAATCGAATATCT-CTTTAGAATTT
* *
5820774 CACTCATGTTTTCTAATAACTCTTTAAAACGAGGGAAATGTTCGATGTCTGGAAATTCATG-GAA
65 CACTCATGTTTTCTAAAAACTCTTTAAAACGAAGGAAATGTTCGATGTCTGGAAATT--TGAGAA
5820838 TAGC
128 TAGC
* * * **
5820842 GCCCTATCGTGCTGGATTGCAATCTCCCGTTTGTTCAAAATAATCGAATATCTCTTCGGAATTTC
1 GCCCTATCGTGCTGGGTTGCAATTTCTCGTTTGTTCAAAATAATCGAATATCTCTTTAGAATTTC
* *
5820907 ACTCGTATTTTCTAA
66 ACTCATGTTTTCTAA
5820922 GGCGAGGCAA
Statistics
Matches: 167, Mismatches: 41, Indels: 7
0.78 0.19 0.03
Matches are distributed among these distances:
131 97 0.58
132 67 0.40
133 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (131 bp):
GCCCTATCGTGCTGGGTTGCAATTTCTCGTTTGTTCAAAATAATCGAATATCTCTTTAGAATTTC
ACTCATGTTTTCTAAAAACTCTTTAAAACGAAGGAAATGTTCGATGTCTGGAAATTTGAGAATAG
C
Found at i:5834950 original size:64 final size:64
Alignment explanation
Indices: 5834860--5834980 Score: 170
Period size: 64 Copynumber: 1.9 Consensus size: 64
5834850 ATCATTCATT
* * * *
5834860 TAGTTAGGAGCACTTGATTCACTTTGATCATAGCATTCTAATTATTTGACATAAGCACCACATC
1 TAGTTAGGAGCACTTGACTCACTTTGAGCATAGCATCCTAATTATTTGACACAAGCACCACATC
* * * *
5834924 TAGTTAGGAGCATTTGACTCATTTTGAGCATGGCATCCTAATTATTTGGCACAAGCA
1 TAGTTAGGAGCACTTGACTCACTTTGAGCATAGCATCCTAATTATTTGACACAAGCA
5834981 TAGATACGAG
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 49 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (64 bp):
TAGTTAGGAGCACTTGACTCACTTTGAGCATAGCATCCTAATTATTTGACACAAGCACCACATC
Found at i:5838259 original size:131 final size:132
Alignment explanation
Indices: 5838102--5838448 Score: 373
Period size: 131 Copynumber: 2.6 Consensus size: 132
5838092 GATATTTGAC
* *
5838102 AATTCGTG-GAATCGTGCCCTAATGTGCTGGGTTGCAATTTCTCATTT-TCTCAAAATAACCGAA
1 AATTCG-GAGAATCGTGCCCTATTGTGCTGGGTTGCAATTTCTCATTTGT-TCAAAATAATCGAA
** * * *
5838165 TGTCCCTTTAGAATTTCATTC-TCGTTTTCTAAAAACTATTTGAAACGAAGGAAATGTTCGATGT
64 TGTCCCTTCGGAATTTCACTCAT-GTTTCCTAAAAACTATTTAAAACGAAGGAAATGTTCGATGT
* *
5838229 TTGGC
128 CTGGA
* * * * * *
5838234 GATT-TGAGAATCGTGCCCTATTGTGCTGGGTTGCACTTTTTCATTTGTTCAAAACAATC-AAAG
1 AATTCGGAGAATCGTGCCCTATTGTGCTGGGTTGCAATTTCTCATTTGTTCAAAATAATCGAATG
* * * *
5838297 ATTCCTTCGGAATTTCACTCATGTTTCCTAATAACTCTTTAAAACGAGGGAAATGTTCGATGTCT
66 -TCCCTTCGGAATTTCACTCATGTTTCCTAAAAACTATTTAAAACGAAGGAAATGTTCGATGTCT
5838362 GGA
130 GGA
* * * * * *
5838365 AATTCGGGGAATAGCGCTCTATCGTGCTGGGTTGCAATCTTC-CGTTTGTTCAAAATAATCGAAT
1 AATTCGGAGAATCGTGCCCTATTGTGCTGGGTTGCAAT-TTCTCATTTGTTCAAAATAATCGAAT
*
5838429 ATCCCTTCGGAATTTCACTC
65 GTCCCTTCGGAATTTCACTC
5838449 GTATTTTCTA
Statistics
Matches: 175, Mismatches: 33, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
130 4 0.02
131 102 0.58
132 65 0.37
133 4 0.02
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (132 bp):
AATTCGGAGAATCGTGCCCTATTGTGCTGGGTTGCAATTTCTCATTTGTTCAAAATAATCGAATG
TCCCTTCGGAATTTCACTCATGTTTCCTAAAAACTATTTAAAACGAAGGAAATGTTCGATGTCTG
GA
Found at i:5842337 original size:23 final size:23
Alignment explanation
Indices: 5842307--5842354 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
5842297 ACTTACATGT
5842307 TATCAAAACCGGATTATATTAGC
1 TATCAAAACCGGATTATATTAGC
5842330 TATCAAAACCGGATTATATTAGC
1 TATCAAAACCGGATTATATTAGC
5842353 TA
1 TA
5842355 ACCTATGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (23 bp):
TATCAAAACCGGATTATATTAGC
Found at i:5845215 original size:32 final size:32
Alignment explanation
Indices: 5845179--5845275 Score: 176
Period size: 32 Copynumber: 3.0 Consensus size: 32
5845169 TGTATGCATT
**
5845179 TTAGCATTTTAATAGTTAATATATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
5845211 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
5845243 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
5845275 T
1 T
5845276 GGTAAGCATT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 63 1.00
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.39
Consensus pattern (32 bp):
TTAGCATTTTAATAGTTAATGGATGATGGGCA
Found at i:5846809 original size:26 final size:26
Alignment explanation
Indices: 5846759--5846809 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
5846749 ACAGTTTTAC
5846759 CCCCTAGGAGGTAAATTACCGAAATA
1 CCCCTAGGAGGTAAATTACCGAAATA
* *
5846785 CCCCTAGG-GTTAAATTGACCTAAAT
1 CCCCTAGGAGGTAAATT-ACCGAAAT
5846810 GCATGTTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (26 bp):
CCCCTAGGAGGTAAATTACCGAAATA
Found at i:5848420 original size:12 final size:12
Alignment explanation
Indices: 5848403--5848433 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
5848393 ACTCGGGGAA
5848403 GAGGCCGTGGTC
1 GAGGCCGTGGTC
5848415 GAGGCCGTGGTC
1 GAGGCCGTGGTC
5848427 GAGGCCG
1 GAGGCCG
5848434 AGGTAGTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.10, C:0.26, G:0.52, T:0.13
Consensus pattern (12 bp):
GAGGCCGTGGTC
Found at i:5853291 original size:32 final size:32
Alignment explanation
Indices: 5853255--5853319 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
5853245 TGTATGCATT
5853255 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
5853287 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
5853319 T
1 T
5853320 GGTAAGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (32 bp):
TTAGCATTTTAATAGTTAATGGATGATGGGCA
Found at i:5854826 original size:26 final size:26
Alignment explanation
Indices: 5854796--5854848 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
5854786 TTTATAGTTT
5854796 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
5854822 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
5854848 T
1 T
5854849 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:5861367 original size:13 final size:13
Alignment explanation
Indices: 5861345--5861376 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
5861335 CCAATTTGAG
5861345 AAAAAT-AAAATA
1 AAAAATAAAAATA
5861357 AAAAATAAAAATA
1 AAAAATAAAAATA
5861370 AAAAATA
1 AAAAATA
5861377 CACAAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:5862466 original size:26 final size:26
Alignment explanation
Indices: 5862437--5862497 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
5862427 TCATTTAATG
* * *
5862437 TTTAAAATATTAAATTAATTTTAT-TT
1 TTTAAAAAATTAAAATAA-ATTATGTT
5862463 TTTAAAAAATTAAAATAAATTATGTT
1 TTTAAAAAATTAAAATAAATTATGTT
5862489 TTTAAAAAA
1 TTTAAAAAA
5862498 ATGAAATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 4 0.13
26 27 0.87
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
TTTAAAAAATTAAAATAAATTATGTT
Found at i:5862478 original size:27 final size:26
Alignment explanation
Indices: 5862437--5862505 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 26
5862427 TCATTTAATG
* * *
5862437 TTTAAAATATTAAATTAATTTTATTT
1 TTTAAAAAATTAAATAAATTATATTT
*
5862463 TTTAAAAAATTAAAATAAATTATGTTT
1 TTTAAAAAATT-AAATAAATTATATTT
* *
5862490 TTAAAAAAATGAAATA
1 TTTAAAAAATTAAATA
5862506 TAAAAAATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
26 15 0.42
27 21 0.58
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (26 bp):
TTTAAAAAATTAAATAAATTATATTT
Found at i:5862504 original size:26 final size:25
Alignment explanation
Indices: 5862457--5862505 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
5862447 TAAATTAATT
*
5862457 TTATTTTTTAAAAAATTAAAATAAA
1 TTATTTTTTAAAAAAATAAAATAAA
*
5862482 TTATGTTTTTAAAAAAATGAAATA
1 TTAT-TTTTTAAAAAAATAAAATA
5862506 TAAAAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (25 bp):
TTATTTTTTAAAAAAATAAAATAAA
Found at i:5862590 original size:22 final size:22
Alignment explanation
Indices: 5862537--5862590 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
5862527 CTAAAATTAA
*
5862537 AAAATAATAATCTTTTAAAAAC
1 AAAATAATTATCTTTTAAAAAC
* *
5862559 -AAATATTTAT-TTTTATCAAAC
1 AAAATAATTATCTTTTA-AAAAC
5862580 AAAATAATTAT
1 AAAATAATTAT
5862591 ATTCCGTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 5 0.19
21 12 0.46
22 9 0.35
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATAATTATCTTTTAAAAAC
Found at i:5863241 original size:17 final size:17
Alignment explanation
Indices: 5863221--5863253 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5863211 ATTATTTTAA
5863221 TATT-TATATTATAGTAG
1 TATTATATATT-TAGTAG
5863238 TATTATATATTTAGTA
1 TATTATATATTTAGTA
5863254 TAGCTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (17 bp):
TATTATATATTTAGTAG
Found at i:5864890 original size:21 final size:21
Alignment explanation
Indices: 5864837--5864890 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
5864827 CATAAATTTG
5864837 AAACTTTAAACCTTAAACCTC
1 AAACTTTAAACCTTAAACCTC
5864858 AAA-TTTCAAACCTTAAACACT-
1 AAACTTT-AAACCTTAAAC-CTC
*
5864879 AAACTTTGAACC
1 AAACTTTAAACC
5864891 AAAACTCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 3 0.10
21 21 0.72
22 5 0.17
ACGTcount: A:0.44, C:0.26, G:0.02, T:0.28
Consensus pattern (21 bp):
AAACTTTAAACCTTAAACCTC
Found at i:5868665 original size:19 final size:18
Alignment explanation
Indices: 5868622--5868666 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 18
5868612 AATTTGGAAT
*
5868622 TATTTATTATATGTTTTTC
1 TATTT-TTATATGATTTTC
5868641 TAATTTTTATCATGATTTTC
1 T-ATTTTTAT-ATGATTTTC
5868661 TATTTT
1 TATTTT
5868667 CATTATGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.67
Consensus pattern (18 bp):
TATTTTTATATGATTTTC
Found at i:5868678 original size:19 final size:20
Alignment explanation
Indices: 5868631--5868678 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
5868621 TTATTTATTA
*
5868631 TATGTTTTTCTAATTTTTAT
1 TATGTTTTTCTAATTTTCAT
* *
5868651 CATGATTTTCT-ATTTTCAT
1 TATGTTTTTCTAATTTTCAT
5868670 TATGTTTTT
1 TATGTTTTT
5868679 TTGGGGGAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.67
Consensus pattern (20 bp):
TATGTTTTTCTAATTTTCAT
Found at i:5870478 original size:40 final size:38
Alignment explanation
Indices: 5870434--5870521 Score: 90
Period size: 40 Copynumber: 2.2 Consensus size: 38
5870424 CTTTAAACTG
*
5870434 TTTTTATTTAATT-TCATTTTCT-TTTTATTATTGTAATATA
1 TTTTTATTTAATTAT-ATTTT-TATTTAATTATT-TAAT-TA
* *
5870474 TTTTTAATAAATTATATTTTTATTTAATTATTTAATTA
1 TTTTTATTTAATTATATTTTTATTTAATTATTTAATTA
5870512 TTTTTCATTT
1 TTTTT-ATTT
5870522 CTATTTTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
38 7 0.17
39 7 0.17
40 25 0.62
41 1 0.03
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.67
Consensus pattern (38 bp):
TTTTTATTTAATTATATTTTTATTTAATTATTTAATTA
Found at i:5870502 original size:16 final size:16
Alignment explanation
Indices: 5870461--5870504 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
5870451 TTTCTTTTTA
5870461 TTATTGTAA-TATATTT
1 TTATT-TAATTATATTT
* *
5870477 TTAATAAATTATATTT
1 TTATTTAATTATATTT
5870493 TTATTTAATTAT
1 TTATTTAATTAT
5870505 TTAATTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 2 0.09
16 21 0.91
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
TTATTTAATTATATTT
Found at i:5870642 original size:27 final size:25
Alignment explanation
Indices: 5870612--5870661 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
5870602 TATTTTTCAA
5870612 TTTTCAAAAAATAGAAAATGAAAACTG
1 TTTTCAAAAAATA-AAAAT-AAAACTG
**
5870639 TTTTCTGAAAATAAAAATAAAAC
1 TTTTCAAAAAATAAAAATAAAAC
5870662 AGAAAATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 5 0.24
27 11 0.52
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (25 bp):
TTTTCAAAAAATAAAAATAAAACTG
Found at i:5875733 original size:19 final size:20
Alignment explanation
Indices: 5875711--5875751 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
5875701 TTTTATATAT
5875711 TTTTAAAAATATA-TAAAAA
1 TTTTAAAAATATATTAAAAA
*
5875730 TTTTAAATATATATTAAAAA
1 TTTTAAAAATATATTAAAAA
5875750 TT
1 TT
5875752 CCAAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTTAAAAATATATTAAAAA
Found at i:5875760 original size:19 final size:18
Alignment explanation
Indices: 5875716--5875760 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
5875706 TATATTTTTA
**
5875716 AAAATATATAAAAATTTT
1 AAAATATATAAAAATTCC
5875734 AAATATATATTAAAAATTCC
1 AAA-ATATA-TAAAAATTCC
5875754 AAAATAT
1 AAAATAT
5875761 TCTCAAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 3 0.13
19 9 0.39
20 11 0.48
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATATATAAAAATTCC
Found at i:5875796 original size:17 final size:18
Alignment explanation
Indices: 5875768--5875810 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
5875758 TATTCTCAAG
5875768 AATATATAAAAAAGT-TAA
1 AATATATAAAAAA-TATAA
5875786 AATAT-TAAAAAATATAA
1 AATATATAAAAAATATAA
5875803 AATA-ATAA
1 AATATATAA
5875811 TTTTGGGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 1 0.04
17 17 0.74
18 5 0.22
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (18 bp):
AATATATAAAAAATATAA
Found at i:5881762 original size:31 final size:31
Alignment explanation
Indices: 5881724--5881786 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
5881714 CAAAGTTGAA
5881724 AATAATGCATTGAAACTTGAAAGTTACTCTT
1 AATAATGCATTGAAACTTGAAAGTTACTCTT
5881755 AATAATGCATTGAAACTTGAAAGTTACTCTT
1 AATAATGCATTGAAACTTGAAAGTTACTCTT
5881786 A
1 A
5881787 CACTCTTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (31 bp):
AATAATGCATTGAAACTTGAAAGTTACTCTT
Found at i:5883179 original size:22 final size:22
Alignment explanation
Indices: 5883151--5883197 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
5883141 TTTTTGTTCC
*
5883151 ATTATTAAATATTGTTATTATT
1 ATTATTAAATATTGTCATTATT
5883173 ATTATTAAATATTGTCATTATT
1 ATTATTAAATATTGTCATTATT
5883195 ATT
1 ATT
5883198 CTAATATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (22 bp):
ATTATTAAATATTGTCATTATT
Found at i:5883726 original size:27 final size:26
Alignment explanation
Indices: 5883673--5883729 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 26
5883663 AGAATGTGTT
*
5883673 TATTTTTTTAATACTATATGTTGTACG
1 TATTTTTTTAATACTATA-GTTATACG
5883700 TATTTTTTTATATAACTATA-TTATACG
1 TATTTTTTTA-AT-ACTATAGTTATACG
5883727 TAT
1 TAT
5883730 ATATGTGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 19 0.70
28 2 0.07
29 6 0.22
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (26 bp):
TATTTTTTTAATACTATAGTTATACG
Found at i:5884125 original size:2 final size:2
Alignment explanation
Indices: 5884118--5884150 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
5884108 ATTATGTAGG
*
5884118 TA TA TA TA TA TA TA TA TT TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5884151 CATTTTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:5892149 original size:13 final size:13
Alignment explanation
Indices: 5892131--5892170 Score: 80
Period size: 13 Copynumber: 3.1 Consensus size: 13
5892121 AATATCGCAA
5892131 AATCCGGTTTTAT
1 AATCCGGTTTTAT
5892144 AATCCGGTTTTAT
1 AATCCGGTTTTAT
5892157 AATCCGGTTTTAT
1 AATCCGGTTTTAT
5892170 A
1 A
5892171 TTCCAAATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (13 bp):
AATCCGGTTTTAT
Found at i:5897031 original size:22 final size:23
Alignment explanation
Indices: 5897003--5897046 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5896993 TCTCGAGGCC
*
5897003 AAAATTT-AATTATAATTTTATA
1 AAAATTTAAAATATAATTTTATA
5897025 AAAATTTAAAATATAATTTTAT
1 AAAATTTAAAATATAATTTTAT
5897047 CATTTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAATTTAAAATATAATTTTATA
Found at i:5900441 original size:22 final size:22
Alignment explanation
Indices: 5900416--5900464 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
5900406 TAGTAGTAAT
*
5900416 ATAATAGCAAAATGACAGCAAA
1 ATAACAGCAAAATGACAGCAAA
* * *
5900438 ATAACAGTAATATGGCAGCAAA
1 ATAACAGCAAAATGACAGCAAA
5900460 A-AACA
1 ATAACA
5900465 ACAGGAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (22 bp):
ATAACAGCAAAATGACAGCAAA
Found at i:5900749 original size:12 final size:12
Alignment explanation
Indices: 5900728--5900757 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5900718 GGTCAAAGCC
*
5900728 CCTTGGTTACTT
1 CCTTGATTACTT
5900740 CCTTGATTACTT
1 CCTTGATTACTT
5900752 CCTTGA
1 CCTTGA
5900758 CTTTCCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.27, G:0.13, T:0.47
Consensus pattern (12 bp):
CCTTGATTACTT
Found at i:5902762 original size:21 final size:20
Alignment explanation
Indices: 5902720--5902762 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
5902710 AAGTTTTTTC
** *
5902720 TTTTTCTCTTCTTTTGTTTT
1 TTTTTCTCTTCTTAAGTCTT
5902740 TTTTTCTTCTTCTTAAGTCTT
1 TTTTTC-TCTTCTTAAGTCTT
5902761 TT
1 TT
5902763 CATTTTGTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTTTCTCTTCTTAAGTCTT
Found at i:5904099 original size:77 final size:77
Alignment explanation
Indices: 5903972--5904125 Score: 290
Period size: 77 Copynumber: 2.0 Consensus size: 77
5903962 TATATATTGA
*
5903972 ACCGCATCGCATAGTACAGAGCAGGCGATAGAAAAGAGTGTAATACTATGGACTAGAAAAAGTTT
1 ACCGCATCGCATAGTACAGAGCAGGCGAAAGAAAAGAGTGTAATACTATGGACTAGAAAAAGTTT
5904037 AACATGGAGGAG
66 AACATGGAGGAG
*
5904049 ACCGCATCGCATAGTACAGAGCAGGTGAAAGAAAAGAGTGTAATACTATGGACTAGAAAAAGTTT
1 ACCGCATCGCATAGTACAGAGCAGGCGAAAGAAAAGAGTGTAATACTATGGACTAGAAAAAGTTT
5904114 AACATGGAGGAG
66 AACATGGAGGAG
5904126 GGAATTTACC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.41, C:0.14, G:0.27, T:0.18
Consensus pattern (77 bp):
ACCGCATCGCATAGTACAGAGCAGGCGAAAGAAAAGAGTGTAATACTATGGACTAGAAAAAGTTT
AACATGGAGGAG
Found at i:5909725 original size:17 final size:17
Alignment explanation
Indices: 5909703--5909737 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5909693 TTAATCCTCA
5909703 ACGTTTACACAATACCT
1 ACGTTTACACAATACCT
5909720 ACGTTTACACAATACCT
1 ACGTTTACACAATACCT
5909737 A
1 A
5909738 ATATAGTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.29, G:0.06, T:0.29
Consensus pattern (17 bp):
ACGTTTACACAATACCT
Found at i:5916358 original size:25 final size:26
Alignment explanation
Indices: 5916298--5916346 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
5916288 ATTTATTTTA
*
5916298 ATATTTG-TTT-TTATGTTTTTAAAT
1 ATATTTGATTTATTATATTTTTAAAT
5916322 ATATTTGATTTATTATATTTTTAAA
1 ATATTTGATTTATTATATTTTTAAA
5916347 ATTTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (26 bp):
ATATTTGATTTATTATATTTTTAAAT
Found at i:5916743 original size:41 final size:41
Alignment explanation
Indices: 5916693--5916870 Score: 252
Period size: 41 Copynumber: 4.4 Consensus size: 41
5916683 CGTTTTACCA
* * ** *
5916693 AAAATGCCGCTAAAAA-CAGAGCAATAGCGGCTTTTTTTGTT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGC-GCTTTTGGT
5916734 AAAACGCCGCTAAAAA-CAGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
*
5916774 AAAACGCCGCTAAAAACCAGAGCATTAGCGGTGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
* * *
5916815 AAAACGCCGCTAAAAACCAGAGCAGTAGCGGCGCTTTCGAT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
5916856 AAAACGCCGCTAAAA
1 AAAACGCCGCTAAAA
5916871 GTCATATAAT
Statistics
Matches: 126, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
40 22 0.17
41 104 0.83
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.20
Consensus pattern (41 bp):
AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
Found at i:5916849 original size:82 final size:81
Alignment explanation
Indices: 5916664--5916870 Score: 265
Period size: 81 Copynumber: 2.5 Consensus size: 81
5916654 AAAAATTATA
* * * * * **
5916664 AAAAACGGAGCAATAGCGGCGTTTTACCA-AAAATGCCGCTAAAAACAGAGCAATAGCGGCTTTT
1 AAAAACAGAGCAGTAGCGGCGCTTT-CGATAAAACGCCGCTAAAAACAGAGCAATAGCGGCTGCT
*
5916728 TTTGTTAAAACGCCGCT
65 TTTGGTAAAACGCCGCT
* * * *
5916745 AAAAACAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCATTAGCGG-TGCT
1 AAAAACAGAGCAGTAGCGGCGCTTTCGATAAAACGCCGCTAAAAA-CAGAGCAATAGCGGCTGCT
5916809 TTTGGTAAAACGCCGCT
65 TTTGGTAAAACGCCGCT
5916826 AAAAACCAGAGCAGTAGCGGCGCTTTCGATAAAACGCCGCTAAAA
1 AAAAA-CAGAGCAGTAGCGGCGCTTTCGATAAAACGCCGCTAAAA
5916871 GTCATATAAT
Statistics
Matches: 109, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
81 60 0.55
82 49 0.45
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (81 bp):
AAAAACAGAGCAGTAGCGGCGCTTTCGATAAAACGCCGCTAAAAACAGAGCAATAGCGGCTGCTT
TTGGTAAAACGCCGCT
Found at i:5917399 original size:7 final size:7
Alignment explanation
Indices: 5917389--5917439 Score: 75
Period size: 7 Copynumber: 7.3 Consensus size: 7
5917379 GGTTTAAGAT
*
5917389 TTAGGTG
1 TTAGGGG
5917396 TTAGGGG
1 TTAGGGG
5917403 TTAGGGG
1 TTAGGGG
5917410 TTAGGGG
1 TTAGGGG
5917417 TTAGGGG
1 TTAGGGG
*
5917424 TTAAGGG
1 TTAGGGG
*
5917431 TGAGGGG
1 TTAGGGG
5917438 TT
1 TT
5917440 CATGGTTCAG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.16, C:0.00, G:0.53, T:0.31
Consensus pattern (7 bp):
TTAGGGG
Found at i:5917419 original size:21 final size:21
Alignment explanation
Indices: 5917372--5917439 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
5917362 GGTGGTTTAA
**
5917372 GGGTT-GGGGTTTAAGATTTAG
1 GGGTTAGGGG-TTAAGGGTTAG
* *
5917393 GTGTTAGGGGTTAGGGGTTAG
1 GGGTTAGGGGTTAAGGGTTAG
*
5917414 GGGTTAGGGGTTAAGGGTGAG
1 GGGTTAGGGGTTAAGGGTTAG
5917435 GGGTT
1 GGGTT
5917440 CATGGTTCAG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 35 0.90
22 4 0.10
ACGTcount: A:0.16, C:0.00, G:0.51, T:0.32
Consensus pattern (21 bp):
GGGTTAGGGGTTAAGGGTTAG
Found at i:5917664 original size:15 final size:15
Alignment explanation
Indices: 5917646--5917688 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
5917636 ATTATTTTAA
5917646 GGTTTATGGATTATG
1 GGTTTATGGATTATG
*
5917661 GGTTTAGGGATTAT-
1 GGTTTATGGATTATG
*
5917675 GATTTATGG-TTATG
1 GGTTTATGGATTATG
5917689 TAAGAGATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 4 0.17
14 7 0.29
15 13 0.54
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.47
Consensus pattern (15 bp):
GGTTTATGGATTATG
Found at i:5917666 original size:22 final size:22
Alignment explanation
Indices: 5917641--5917683 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
5917631 GAGTTATTAT
*
5917641 TTTAAGGTTTATGGA-TTATGGG
1 TTTAAGGATTAT-GATTTATGGG
*
5917663 TTTAGGGATTATGATTTATGG
1 TTTAAGGATTATGATTTATGG
5917684 TTATGTAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (22 bp):
TTTAAGGATTATGATTTATGGG
Found at i:5918298 original size:7 final size:7
Alignment explanation
Indices: 5918283--5918336 Score: 99
Period size: 7 Copynumber: 7.7 Consensus size: 7
5918273 AAAAAATTTT
*
5918283 AAAATTA
1 AAAAATA
5918290 AAAAATA
1 AAAAATA
5918297 AAAAATA
1 AAAAATA
5918304 AAAAATA
1 AAAAATA
5918311 AAAAATA
1 AAAAATA
5918318 AAAAATA
1 AAAAATA
5918325 AAAAATA
1 AAAAATA
5918332 AAAAA
1 AAAAA
5918337 CTTAAAAATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAATA
Found at i:5918321 original size:21 final size:21
Alignment explanation
Indices: 5918283--5918345 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
5918273 AAAAAATTTT
*
5918283 AAAATTAAAAAATAAAAAATA
1 AAAAATAAAAAATAAAAAATA
5918304 AAAAATAAAAAATAAAAAATA
1 AAAAATAAAAAATAAAAAATA
*
5918325 AAAAATAAAAAACTTAAAAAT
1 AAAAATAAAAAA-TAAAAAAT
5918346 TTAATATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 32 0.82
22 7 0.18
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (21 bp):
AAAAATAAAAAATAAAAAATA
Found at i:5920228 original size:138 final size:138
Alignment explanation
Indices: 5919980--5920249 Score: 470
Period size: 138 Copynumber: 2.0 Consensus size: 138
5919970 ATAATGTATA
* * *
5919980 GATGCTTTGTGGAGTCCCTGTTTTGAATTTTAGAATCATATGTAATCTCTTTAAAAATTGGCATT
1 GATGCTTTGTGGAGTACCTGTTTTGAATTTTAGAACCATATGTAATCTCCTTAAAAATTGGCATT
5920045 AAATTGTTTTTAGGTTTTATAATAACATTTCTCTTTGTTATGTTATTATGCAACTTATTTGATTT
66 AAATTGTTTTTAGGTTTTATAATAACATTTCTCTTTGTTATGTTATTATGCAACTTATTTGATTT
5920110 AACGTCTG
131 AACGTCTG
* *
5920118 GATGCTTT-TAGGAGTACTTGTTTTGAATTTTAGAACCATATGTAATTTCCTTAAAAATTGGCAT
1 GATGCTTTGT-GGAGTACCTGTTTTGAATTTTAGAACCATATGTAATCTCCTTAAAAATTGGCAT
*
5920182 TAAATTGTTTTTAGGTTTTATATTAACATTTCTCTTTGTTATGTTATTATGCAACTTATTTGATT
65 TAAATTGTTTTTAGGTTTTATAATAACATTTCTCTTTGTTATGTTATTATGCAACTTATTTGATT
5920247 TAA
130 TAA
5920250 AATTTTAAAA
Statistics
Matches: 125, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
137 1 0.01
138 124 0.99
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (138 bp):
GATGCTTTGTGGAGTACCTGTTTTGAATTTTAGAACCATATGTAATCTCCTTAAAAATTGGCATT
AAATTGTTTTTAGGTTTTATAATAACATTTCTCTTTGTTATGTTATTATGCAACTTATTTGATTT
AACGTCTG
Found at i:5921352 original size:43 final size:43
Alignment explanation
Indices: 5921291--5921478 Score: 270
Period size: 43 Copynumber: 4.4 Consensus size: 43
5921281 AAATTTCATT
5921291 ACCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTAAAG
1 ACCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTAAAG
* *
5921334 ACCTTTAGCGGCGTTTGTGGGGAAAGCACCGCTAAAGGTCAAA-
1 ACCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT-AAAG
* * ***
5921377 ACCTCTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGGTCTTG
1 ACCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTAAAG
* * *
5921420 ACCTCTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATG
1 ACCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTAAAG
5921463 ACCTTTAGCGGCGTTT
1 ACCTTTAGCGGCGTTT
5921479 TTTTAAATAA
Statistics
Matches: 133, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
43 130 0.98
44 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.32, T:0.23
Consensus pattern (43 bp):
ACCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTAAAG
Found at i:5929184 original size:24 final size:24
Alignment explanation
Indices: 5929139--5929185 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
5929129 TTTAGAGAAT
*
5929139 TTTGTGTTTACGTTTTGAGGGTTC
1 TTTGTGTTTACGTTTTCAGGGTTC
* * *
5929163 TTTGTTTTTAGGTTTTCTGGGTT
1 TTTGTGTTTACGTTTTCAGGGTT
5929186 TAGTTTTTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.06, C:0.06, G:0.28, T:0.60
Consensus pattern (24 bp):
TTTGTGTTTACGTTTTCAGGGTTC
Found at i:5930676 original size:21 final size:21
Alignment explanation
Indices: 5930650--5930697 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
5930640 CAATATAGGT
*
5930650 TTTAATTAGAAAGAGATTTTA
1 TTTAATTAGAAAAAGATTTTA
5930671 TTTAATTAGAAAAAGATTTTA
1 TTTAATTAGAAAAAGATTTTA
*
5930692 ATTAAT
1 TTTAAT
5930698 CAACCTAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (21 bp):
TTTAATTAGAAAAAGATTTTA
Found at i:5934926 original size:13 final size:13
Alignment explanation
Indices: 5934908--5934941 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
5934898 TGCACGACCC
5934908 TTCCCCCTCTCTT
1 TTCCCCCTCTCTT
*
5934921 TT-CCCCTTTCTT
1 TTCCCCCTCTCTT
5934933 TTCCCCCTC
1 TTCCCCCTC
5934942 CCTCAGAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (13 bp):
TTCCCCCTCTCTT
Found at i:5935117 original size:18 final size:17
Alignment explanation
Indices: 5935096--5935131 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
5935086 ACTCTTATTA
*
5935096 TTGTTATTTCTTTTTTAT
1 TTGTTATTT-TTATTTAT
5935114 TTGTTATTTTTATTTAT
1 TTGTTATTTTTATTTAT
5935131 T
1 T
5935132 CCTTTTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.78
Consensus pattern (17 bp):
TTGTTATTTTTATTTAT
Found at i:5935130 original size:28 final size:28
Alignment explanation
Indices: 5935099--5935164 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
5935089 CTTATTATTG
* * *
5935099 TTATTTCTTTTTTATTTGTTATTTT-TAT
1 TTATTTCTTTTCTAATTATTATTTTCT-T
*
5935127 TTATTCCTTTTCTAATTATTATTTTCTT
1 TTATTTCTTTTCTAATTATTATTTTCTT
*
5935155 TAATTTCTTT
1 TTATTTCTTT
5935165 CCTAGTTTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
28 30 0.97
29 1 0.03
ACGTcount: A:0.17, C:0.09, G:0.02, T:0.73
Consensus pattern (28 bp):
TTATTTCTTTTCTAATTATTATTTTCTT
Found at i:5936423 original size:20 final size:20
Alignment explanation
Indices: 5936398--5936447 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
5936388 CACTTTGGTC
* *
5936398 TCCTCCACACATCGGAGCAG
1 TCCTCCACACACCGGAACAG
5936418 TCCTCCACACACCGGAACAG
1 TCCTCCACACACCGGAACAG
5936438 TCCTCCACAC
1 TCCTCCACAC
5936448 TCATTTTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.26, C:0.46, G:0.14, T:0.14
Consensus pattern (20 bp):
TCCTCCACACACCGGAACAG
Found at i:5936859 original size:12 final size:12
Alignment explanation
Indices: 5936842--5936875 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5936832 ATTTGTTTCC
*
5936842 TTTTATTTTTAT
1 TTTTATTTTCAT
*
5936854 TTTTATGTTCAT
1 TTTTATTTTCAT
5936866 TTTTATTTTC
1 TTTTATTTTC
5936876 TTAGACTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (12 bp):
TTTTATTTTCAT
Found at i:5947559 original size:41 final size:43
Alignment explanation
Indices: 5947501--5947614 Score: 142
Period size: 41 Copynumber: 2.7 Consensus size: 43
5947491 ATATTTTCAC
* * * *
5947501 ATATCGATGCCATTGTCCTAGACAGGGTCTTATACG-AATCGT
1 ATATCGATGCCAATGTCCCAGACATGGTCTTACACGTAATCGT
* * * *
5947543 ATA-CGATGCTAATGTCCCAGACATAGTCTTACATGTAATCTT
1 ATATCGATGCCAATGTCCCAGACATGGTCTTACACGTAATCGT
5947585 ATATCGATGCCAATGTCCCAGACATGGTCT
1 ATATCGATGCCAATGTCCCAGACATGGTCT
5947615 CACATGAAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
41 25 0.42
42 11 0.18
43 24 0.40
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (43 bp):
ATATCGATGCCAATGTCCCAGACATGGTCTTACACGTAATCGT
Found at i:5947600 original size:43 final size:42
Alignment explanation
Indices: 5947501--5947622 Score: 147
Period size: 43 Copynumber: 2.9 Consensus size: 42
5947491 ATATTTTCAC
* * * * *
5947501 ATATCGATGCCATTGTCCTAGACAGGGTCTTATACGAATCGT
1 ATATCGATGCCAATGTCCCAGACATGGTCTTACATGAATCGT
* * *
5947543 ATA-CGATGCTAATGTCCCAGACATAGTCTTACATGTAATCTT
1 ATATCGATGCCAATGTCCCAGACATGGTCTTACATG-AATCGT
*
5947585 ATATCGATGCCAATGTCCCAGACATGGTCTCACATGAA
1 ATATCGATGCCAATGTCCCAGACATGGTCTTACATGAA
5947623 ATCACACCTC
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 25 0.37
42 13 0.19
43 29 0.43
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (42 bp):
ATATCGATGCCAATGTCCCAGACATGGTCTTACATGAATCGT
Found at i:5950707 original size:26 final size:26
Alignment explanation
Indices: 5950678--5950785 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
5950668 TGGTACAAAT
5950678 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
5950704 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
5950730 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
5950756 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
5950782 TGAT
1 TGAT
5950786 GGGCATTTCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.32, C:0.07, G:0.25, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:5955312 original size:40 final size:40
Alignment explanation
Indices: 5955268--5955347 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
5955258 TTTGACATTT
*
5955268 TTATAAAAATTAGTCTGTAATTAATTGATTCTAAAATTAA
1 TTATAAAAATTAGTCTCTAATTAATTGATTCTAAAATTAA
5955308 TTATAAAAATTAGTCTCTAATTAATTGATTCTAAAATTAA
1 TTATAAAAATTAGTCTCTAATTAATTGATTCTAAAATTAA
5955348 CTGAGATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (40 bp):
TTATAAAAATTAGTCTCTAATTAATTGATTCTAAAATTAA
Found at i:5958939 original size:4 final size:4
Alignment explanation
Indices: 5958930--5958976 Score: 51
Period size: 4 Copynumber: 11.5 Consensus size: 4
5958920 TTTACTTGTC
* *
5958930 TTAT TTAT TTAT TTGT TTAT TT-T TTAT GTTAT TTGT TTGAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TT-AT TTAT TT
5958977 TATTATTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 3 0.08
4 26 0.72
5 7 0.19
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:5958945 original size:17 final size:16
Alignment explanation
Indices: 5958919--5958976 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 16
5958909 ATTTAGAATC
*
5958919 ATTTACTTGTCTTATTT
1 ATTTATTTGT-TTATTT
5958936 ATTTATTTGTTTATTT
1 ATTTATTTGTTTATTT
* *
5958952 -TTTATGTTATTTGTTT
1 ATTTAT-TTGTTTATTT
5958968 GATTTATTT
1 -ATTTATTT
5958977 TATTATTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
15 5 0.14
16 14 0.40
17 11 0.31
18 5 0.14
ACGTcount: A:0.17, C:0.03, G:0.09, T:0.71
Consensus pattern (16 bp):
ATTTATTTGTTTATTT
Found at i:5958963 original size:20 final size:20
Alignment explanation
Indices: 5958933--5958972 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5958923 ACTTGTCTTA
5958933 TTTATTTATTTGTTT-ATTT
1 TTTATTTATTTGTTTGATTT
5958952 TTTATGTTATTTGTTTGATTT
1 TTTAT-TTATTTGTTTGATTT
5958973 ATTTTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 10 0.53
21 4 0.21
ACGTcount: A:0.15, C:0.00, G:0.10, T:0.75
Consensus pattern (20 bp):
TTTATTTATTTGTTTGATTT
Found at i:5958974 original size:13 final size:12
Alignment explanation
Indices: 5958919--5958976 Score: 55
Period size: 13 Copynumber: 4.7 Consensus size: 12
5958909 ATTTAGAATC
*
5958919 ATTTACTTGTCTT
1 ATTTATTTGT-TT
*
5958932 ATTTATTTATTT
1 ATTTATTTGTTT
*
5958944 GTTTATTT-TTT
1 ATTTATTTGTTT
5958955 ATGTTATTTGTTT
1 AT-TTATTTGTTT
5958968 GATTTATTT
1 -ATTTATTT
5958977 TATTATTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
11 4 0.11
12 15 0.39
13 17 0.45
14 2 0.05
ACGTcount: A:0.17, C:0.03, G:0.09, T:0.71
Consensus pattern (12 bp):
ATTTATTTGTTT
Found at i:5958985 original size:24 final size:23
Alignment explanation
Indices: 5958934--5958987 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
5958924 CTTGTCTTAT
5958934 TTATTTATTTGTTTATTTTTTATG
1 TTATTTATTTGTTTATTTTTTA-G
*
5958958 TTATTTGTTTGATTTATTTTATTA-
1 TTATTTATTTG-TTTATTTT-TTAG
5958982 TTATTT
1 TTATTT
5958988 TTACTCTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 16 0.59
25 8 0.30
26 3 0.11
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (23 bp):
TTATTTATTTGTTTATTTTTTAG
Found at i:5960479 original size:99 final size:99
Alignment explanation
Indices: 5960308--5960614 Score: 280
Period size: 99 Copynumber: 3.2 Consensus size: 99
5960298 ATCTACTCCA
* ** * * * *
5960308 CTGCAACTTC-AGGAAGATAAGATTCATCGTAATTTGTAGCTTTAATCTGTTCTACCACAACATC
1 CTGCAACTTCAAGG-AGATAAGATCCGCCATAATTTGTAGCTTCAATCTATTCCACCACAACATC
* * *
5960372 AGGGAAATAAGATTCGCTGTCTTCAGTTTGCTTCG
65 AGGGAAATAAGATTCGCTATATTCAGTTTGCTGCG
* * *
5960407 CTGCAACTTCAAGGAGGTAAGATCCGCCATAATTTGTAGCTTCAATCTATTCCA-CAGCAACTTT
1 CTGCAACTTCAAGGAGATAAGATCCGCCATAATTTGTAGCTTCAATCTATTCCACCA-CAACATC
* *
5960471 TGGGAAATAAGATTTGCTATATTCAGTTTGCTGCG
65 AGGGAAATAAGATTCGCTATATTCAGTTTGCTGCG
* * * ** *
5960506 CTGCAACTTCAAGGAGATAAG----G-C-----TGGTGGCTTCAATCTGTTCCACTGCAACGTCA
1 CTGCAACTTCAAGGAGATAAGATCCGCCATAATTTGTAGCTTCAATCTATTCCACCACAACATCA
* *
5960561 GGGAAATAAGATCCGCTATCTTCAGTTTGCT-CTG
66 GGGAAATAAGATTCGCTATATTCAGTTTGCTGC-G
*
5960595 CTGCAACTTCAGGGAGATAA
1 CTGCAACTTCAAGGAGATAA
5960615 AGTTTGTGTC
Statistics
Matches: 176, Mismatches: 28, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
88 1 0.01
89 71 0.40
94 1 0.01
95 1 0.01
98 2 0.01
99 97 0.55
100 3 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (99 bp):
CTGCAACTTCAAGGAGATAAGATCCGCCATAATTTGTAGCTTCAATCTATTCCACCACAACATCA
GGGAAATAAGATTCGCTATATTCAGTTTGCTGCG
Found at i:5960640 original size:89 final size:89
Alignment explanation
Indices: 5960445--5960640 Score: 250
Period size: 89 Copynumber: 2.2 Consensus size: 89
5960435 ATAATTTGTA
* * ** **
5960445 GCTTCAATCTATTCCACAGCAACTTTTGGGAAATAAGATTTGCTATATTCAGTTTGCTGCGCTGC
1 GCTTCAATCTATTCCACTGCAACGTCAGGGAAATAAGATCCGCTATATTCAGTTTGCTGCGCTGC
*
5960510 AACTTCAAGGAGATAAGGCTGGTG
66 AACTTCAAGGAGATAAAGCTGGTG
* *
5960534 GCTTCAATCTGTTCCACTGCAACGTCAGGGAAATAAGATCCGCTATCTTCAGTTTGCT-CTGCTG
1 GCTTCAATCTATTCCACTGCAACGTCAGGGAAATAAGATCCGCTATATTCAGTTTGCTGC-GCTG
* * *
5960598 CAACTTCAGGGAGATAAAGTTTGTG
65 CAACTTCAAGGAGATAAAGCTGGTG
* *
5960623 TCTTCAATCTACTCCACT
1 GCTTCAATCTATTCCACT
5960641 AAAACTTCAA
Statistics
Matches: 91, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
88 1 0.01
89 90 0.99
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (89 bp):
GCTTCAATCTATTCCACTGCAACGTCAGGGAAATAAGATCCGCTATATTCAGTTTGCTGCGCTGC
AACTTCAAGGAGATAAAGCTGGTG
Found at i:5961111 original size:46 final size:46
Alignment explanation
Indices: 5961014--5961115 Score: 125
Period size: 46 Copynumber: 2.2 Consensus size: 46
5961004 AAAATTTGGT
* * *
5961014 TTCTTCCATCCATCCCACTACAACTCAAGGGTATAGGATTTGTATC
1 TTCTTCAATCCATCCCACTACAACTCAAGGGTACAGGATTTGTAGC
* * * *
5961060 ATCTTCAATCCAAT-CCATTACAGCTCAAGGGTACAGGATTTGTGGC
1 TTCTTCAATCC-ATCCCACTACAACTCAAGGGTACAGGATTTGTAGC
5961106 TTCTTCAATC
1 TTCTTCAATC
5961116 AATTGGTCTA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
46 45 0.96
47 2 0.04
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (46 bp):
TTCTTCAATCCATCCCACTACAACTCAAGGGTACAGGATTTGTAGC
Found at i:5961660 original size:53 final size:53
Alignment explanation
Indices: 5961525--5961662 Score: 213
Period size: 53 Copynumber: 2.6 Consensus size: 53
5961515 TCAAAATGAA
* ** * *
5961525 TTAATCAAATATAGCAAATACAATAAGAAAGAAGTTAACTCGAAATGAATAAG
1 TTAATCAAAGATAGCAAATGTAATAAGAAGGAAATTAACTCGAAATGAATAAG
*
5961578 TTAATCAAAGATAGAAAATGTAATAAGAAGGAAATTAACTCGAAATGAATAAG
1 TTAATCAAAGATAGCAAATGTAATAAGAAGGAAATTAACTCGAAATGAATAAG
*
5961631 TTAATCAAGGATAGCAAATGTAATAAGAAGGA
1 TTAATCAAAGATAGCAAATGTAATAAGAAGGA
5961663 TATTGATTGG
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 77 1.00
ACGTcount: A:0.54, C:0.07, G:0.17, T:0.22
Consensus pattern (53 bp):
TTAATCAAAGATAGCAAATGTAATAAGAAGGAAATTAACTCGAAATGAATAAG
Found at i:5963860 original size:38 final size:38
Alignment explanation
Indices: 5963770--5963861 Score: 98
Period size: 38 Copynumber: 2.4 Consensus size: 38
5963760 AGAATTTATA
*
5963770 AAATAATTATATAATATATAAAAATATCAGTTAAAAATG
1 AAATAA-TATATAATACATAAAAATATCAGTTAAAAATG
* * *
5963809 AAATAACACATAATACATAAATAA-AT-AGTTAATAATG
1 AAATAATATATAATACATAAA-AATATCAGTTAAAAATG
*
5963846 AAATATGTATATAATA
1 AAATA-ATATATAATA
5963862 TGAGTTAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
37 15 0.34
38 21 0.48
39 8 0.18
ACGTcount: A:0.59, C:0.04, G:0.05, T:0.32
Consensus pattern (38 bp):
AAATAATATATAATACATAAAAATATCAGTTAAAAATG
Found at i:5964108 original size:24 final size:24
Alignment explanation
Indices: 5964081--5964144 Score: 65
Period size: 26 Copynumber: 2.6 Consensus size: 24
5964071 AAAATTTTGT
5964081 ATAAATATATAAATAGTATTTTTA
1 ATAAATATATAAATAGTATTTTTA
** *
5964105 ATAATAATATATGTATAGTTTTTTTA
1 AT-A-AATATATAAATAGTATTTTTA
* *
5964131 AAAAATAAATAAAT
1 ATAAATATATAAAT
5964145 TATATATATA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
24 10 0.32
25 2 0.06
26 19 0.61
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.44
Consensus pattern (24 bp):
ATAAATATATAAATAGTATTTTTA
Found at i:5964113 original size:26 final size:24
Alignment explanation
Indices: 5964083--5964161 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
5964073 AATTTTGTAT
5964083 AAATATATAAATAGTATTTTTAATA
1 AAATATATAAATAGTATTTTTAA-A
** *
5964108 ATAATATATGTATAGTTTTTTTAAA
1 A-AATATATAAATAGTATTTTTAAA
* * *
5964133 AAATAAATAAATTA-TATATATAAA
1 AAATATATAAA-TAGTATTTTTAAA
5964157 AAATA
1 AAATA
5964162 ACAATATTTG
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
24 19 0.44
25 5 0.12
26 19 0.44
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
AAATATATAAATAGTATTTTTAAA
Found at i:5965926 original size:206 final size:204
Alignment explanation
Indices: 5965691--5966412 Score: 1079
Period size: 206 Copynumber: 3.5 Consensus size: 204
5965681 TACAGAGATG
* * *
5965691 CTTAGATTTGCTTCAGCGTAAACACGTGAAAGCCAAATCTA-CTATGTCTTTGATTTGCTCCTTG
1 CTTAGATTTGCTTCAACGTAAGCACGTGAAAGCCAAATC-AGCTATGTCTTCGATTTGCTCCTTG
* * * * * * * * *
5965755 TGACCACAAGGATGCCAAATCATCTTGGATCTGCTTTAGTCTAATCGTCTGAAAGTTAGATCTGC
65 TAAGCACAAGGATACCAAACCATCTTGGATCTGCTTCAGTATAA-CATCTGAAGGTTGGATCTGC
* * * *
5965820 TATGTGTCTGCTCTCTGTTGAATATGGAAACGTCAAACTTCGATTTGTTCTCTGACAATACAGAG
129 TATGTGTCTGC-CTCAGTCGAATATGGAGACGCCAAACTTCGATTTGTTCTCTGACAATACAGAG
5965885 ATGCCAAATCAT
193 ATGCCAAATCAT
5965897 CTTAGATTTGCTTCAACGTAAGCACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGT
1 CTTAGATTTGCTTCAACGTAAGCACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGT
5965962 AAGCACAAGGATACCAAACCATCTTGGATCTGCTTCAGTATAGACATCTGAAGGTTGGATCTGCT
66 AAGCACAAGGATACCAAACCATCTTGGATCTGCTTCAGTATA-ACATCTGAAGGTTGGATCTGCT
5966027 ATGTGTCTGCCCTCAGTCGAATATGGAGACGCCAAACTTCGATTTGTTCTCTGACAATACAGAGA
130 ATGTGTCTG-CCTCAGTCGAATATGGAGACGCCAAACTTCGATTTGTTCTCTGACAATACAGAGA
*
5966092 TGCCAAATTAT
194 TGCCAAATCAT
* *
5966103 CTTAGATTTGCTTCAACGTAAGCACGTGAAAGCCAAATCAACTATGTCTTCGATTTCCTCCTTGT
1 CTTAGATTTGCTTCAACGTAAGCACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGT
*
5966168 AAGCACAAGGATACCAAACCATCTTGGATCTACTTCAGTATAAACATCTGAAGGTTGGATCTGCT
66 AAGCACAAGGATACCAAACCATCTTGGATCTGCTTCAGTAT-AACATCTGAAGGTTGGATCTGCT
* ** *
5966233 ATGTGTCTGGCCTCCGTCGAATATGGAGACGCCAAACTTTTATTTGTTCTCTAACAATACAGAGA
130 ATGTGTCT-GCCTCAGTCGAATATGGAGACGCCAAACTTCGATTTGTTCTCTGACAATACAGAGA
5966298 TGCCAAATCAT
194 TGCCAAATCAT
** * *
5966309 CTTAGATTTGCTTCTGCGTAAGCACGCGGAAA-CCAAATCAGCTATGTCTTCGATTTTCTCCTTG
1 CTTAGATTTGCTTCAACGTAAGCACG-TGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTG
* *
5966373 TAAGGACAAGGATGCCAAACCATCTTGGATCTTGCTTCAG
65 TAAGCACAAGGATACCAAACCATCTTGGATC-TGCTTCAG
5966413 CCAGATCTGC
Statistics
Matches: 476, Mismatches: 33, Indels: 13
0.91 0.06 0.02
Matches are distributed among these distances:
205 1 0.00
206 460 0.97
207 15 0.03
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (204 bp):
CTTAGATTTGCTTCAACGTAAGCACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGT
AAGCACAAGGATACCAAACCATCTTGGATCTGCTTCAGTATAACATCTGAAGGTTGGATCTGCTA
TGTGTCTGCCTCAGTCGAATATGGAGACGCCAAACTTCGATTTGTTCTCTGACAATACAGAGATG
CCAAATCAT
Found at i:5974630 original size:46 final size:49
Alignment explanation
Indices: 5974545--5974743 Score: 181
Period size: 54 Copynumber: 3.9 Consensus size: 49
5974535 TCTTGCACAT
* * * *
5974545 AATCACAT-ATCACACACCGAAGCCATAGCCCAGCCATGGTCTTACACGG
1 AATCACATAAT-ACACACTGATGCCATAGCCCAGCTATGGTCTTATACGG
* * *
5974594 -ATCACAT-AT-CACACTGATGCCATATCCCAGATATGGTTTTATACGG
1 AATCACATAATACACACTGATGCCATAGCCCAGCTATGGTCTTATACGG
* * * *
5974640 AAGCACATAATCACATATCTCTGATGCCATAGCCCAGTTATGGTCTTATATGG
1 AATCACATAAT-AC--A-CACTGATGCCATAGCCCAGCTATGGTCTTATACGG
5974693 AAATCACATAATCACATCACATTGATGCCATAGCCCAGCTATGGTCTTATA
1 -AATCACATAAT-ACA-CAC--TGATGCCATAGCCCAGCTATGGTCTTATA
5974744 TGAAAATCAC
Statistics
Matches: 124, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
46 30 0.24
47 6 0.05
48 11 0.09
50 1 0.01
52 5 0.04
53 30 0.24
54 41 0.33
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (49 bp):
AATCACATAATACACACTGATGCCATAGCCCAGCTATGGTCTTATACGG
Found at i:5974723 original size:54 final size:54
Alignment explanation
Indices: 5974601--5974762 Score: 206
Period size: 54 Copynumber: 3.0 Consensus size: 54
5974591 CGGATCACAT
* * * * *
5974601 ATCACACTGATGCCATATCCCAGATATGGTTTTATACGG-AAGCACATAATCAC
1 ATCACATTGATGCCATAGCCCAGATATGGTCTTATATGGAAATCACATAATCAC
*
5974654 AT-ATC-TCTGATGCCATAGCCCAGTTATGGTCTTATATGGAAATCACATAATCAC
1 ATCA-CAT-TGATGCCATAGCCCAGATATGGTCTTATATGGAAATCACATAATCAC
* *
5974708 ATCACATTGATGCCATAGCCCAGCTATGGTCTTATATGAAAATCACAT-ATCAC
1 ATCACATTGATGCCATAGCCCAGATATGGTCTTATATGGAAATCACATAATCAC
5974761 AT
1 AT
5974763 GTTGCCATGG
Statistics
Matches: 96, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
52 1 0.01
53 38 0.40
54 55 0.57
55 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.29
Consensus pattern (54 bp):
ATCACATTGATGCCATAGCCCAGATATGGTCTTATATGGAAATCACATAATCAC
Found at i:5976079 original size:39 final size:39
Alignment explanation
Indices: 5976034--5976173 Score: 253
Period size: 39 Copynumber: 3.6 Consensus size: 39
5976024 ATCGTGATCT
* *
5976034 GAAGCCCGAAGTCTAACTGAAGTACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
5976073 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
*
5976112 GAAGCCCGAAGGCTAACAGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
5976151 GAAGCCCGAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
5976174 TCACCAGAGC
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 97 1.00
ACGTcount: A:0.39, C:0.23, G:0.26, T:0.13
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
Found at i:5983609 original size:44 final size:44
Alignment explanation
Indices: 5983327--5983609 Score: 144
Period size: 44 Copynumber: 6.4 Consensus size: 44
5983317 ACTTCTTCAA
* * * * * * * *
5983327 GTAGCCTCGTTCTAATCCACTGCAACTTTAGGGAGATGAGACTT
1 GTAGCTTCGATCTACTCCAATGTAACTTCAGGGAGATAAGATTT
* * * *
5983371 GTGGCTTCGATTTACTCCAATGTAATTTCAGGGAGATGAGATTT
1 GTAGCTTCGATCTACTCCAATGTAACTTCAGGGAGATAAGATTT
** * * * *
5983415 GTAGCTTCGATCTACTCCGCTGGAACTTAAAGGAGATAAGAATTG
1 GTAGCTTCGATCTACTCCAATGTAACTTCAGGGAGATAAG-ATTT
** * * ** * * *
5983460 GTAATTTCAACCTGTTCCATTGCAACTTCAGGGAGATAAGGTTT
1 GTAGCTTCGATCTACTCCAATGTAACTTCAGGGAGATAAGATTT
** * * * * *
5983504 GT-G-TAT-TTTCCTGCTTCACTGTAACTTCAAGGAAATAAGGA-TT
1 GTAGCT-TCGAT-CTACTCCAATGTAACTTCAGGGAGATAA-GATTT
* * * *
5983547 GTGGCTTCGAT-TCGCTCCAATGTAATTTCAGGGAGAAAAGATTT
1 GTAGCTTCGATCT-ACTCCAATGTAACTTCAGGGAGATAAGATTT
5983591 GTAGCTTCGATCTACTCCA
1 GTAGCTTCGATCTACTCCA
5983610 CTGGTGTAAT
Statistics
Matches: 175, Mismatches: 54, Indels: 20
0.70 0.22 0.08
Matches are distributed among these distances:
42 1 0.01
43 30 0.17
44 109 0.62
45 35 0.20
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (44 bp):
GTAGCTTCGATCTACTCCAATGTAACTTCAGGGAGATAAGATTT
Found at i:5985179 original size:24 final size:26
Alignment explanation
Indices: 5985151--5985199 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
5985141 TTTACTTGTC
*
5985151 TTATTTATTTG-TTTGTTTT-TTATG
1 TTATTTATTTGATTTATTTTATTATG
*
5985175 TTATTTGTTTGATTTATTTTATTAT
1 TTATTTATTTGATTTATTTTATTAT
5985200 TATTTTTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.48
25 7 0.33
26 4 0.19
ACGTcount: A:0.16, C:0.00, G:0.10, T:0.73
Consensus pattern (26 bp):
TTATTTATTTGATTTATTTTATTATG
Found at i:5985204 original size:24 final size:20
Alignment explanation
Indices: 5985151--5985200 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
5985141 TTTACTTGTC
5985151 TTAT-TTATTTGTTTGTTTT
1 TTATATTATTTGTTTGTTTT
*
5985170 TTATGTTATTTGTTTGATTTAT
1 TTATATTATTTGTTTG-TTT-T
5985192 TT-TATTATT
1 TTATATTATT
5985201 ATTTTTACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 4 0.15
20 11 0.41
21 9 0.33
22 3 0.11
ACGTcount: A:0.16, C:0.00, G:0.10, T:0.74
Consensus pattern (20 bp):
TTATATTATTTGTTTGTTTT
Found at i:5985299 original size:40 final size:37
Alignment explanation
Indices: 5985255--5985330 Score: 91
Period size: 40 Copynumber: 2.0 Consensus size: 37
5985245 TCTTCATTTA
*
5985255 TTATTAT-TATTAGTATTCATGTTTTATTTACATATTTCAC
1 TTATTATGTATT-CTATTCAT-TTTT-TTTACAT-TTTCAC
*
5985295 TTATTATGTATTCTATTCATTTTTTTTATATTTTCA
1 TTATTATGTATTCTATTCATTTTTTTTACATTTTCA
5985331 TATTCTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
37 5 0.15
38 6 0.18
39 4 0.12
40 14 0.42
41 4 0.12
ACGTcount: A:0.25, C:0.09, G:0.04, T:0.62
Consensus pattern (37 bp):
TTATTATGTATTCTATTCATTTTTTTTACATTTTCAC
Found at i:5985363 original size:3 final size:3
Alignment explanation
Indices: 5985355--5985389 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5985345 CTTTTATCTT
5985355 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5985390 GTAATTTATT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5986640 original size:143 final size:140
Alignment explanation
Indices: 5986407--5986671 Score: 343
Period size: 143 Copynumber: 1.9 Consensus size: 140
5986397 TATTTTCCTA
* * * * * * * *
5986407 CTCCACTGCAACTTCAGGGAGATAAGGATTGTGACTTGTAGCTTCAATTTGTTTCGCTGCATCTT
1 CTCCACTGCAACTTCAGGAAGATAAGGATTGTAACTTGTAGCTTCAATCTGTTCCACCGCAACAT
* *
5986472 CAGGGAAATGAGATTCACTATCTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGGCTGGTGG
66 CAGGGAAATAAGATCCACTATCTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGGCTGGTGG
5986537 CTTCAATATG
131 CTTCAATATG
* *
5986547 CTCCACTGCAACTTCAGGAAGATAA-GATTCACCGTAATTTGTAGCTTTAATCTGTTCCACCGCA
1 CTCCACTGCAACTTCAGGAAGATAAGGATT----GTAACTTGTAGCTTCAATCTGTTCCACCGCA
* * * *
5986611 ACATCAGGGAAATAAGATCCGCTGTCTTCAGTCTGCTTCACTGCAACTTCAGGGAGATAAG
62 ACATCAGGGAAATAAGATCCACTATCTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAG
5986672 ATCTGCCATA
Statistics
Matches: 105, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
139 4 0.04
140 24 0.23
143 77 0.73
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (140 bp):
CTCCACTGCAACTTCAGGAAGATAAGGATTGTAACTTGTAGCTTCAATCTGTTCCACCGCAACAT
CAGGGAAATAAGATCCACTATCTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGGCTGGTGG
CTTCAATATG
Found at i:5986684 original size:99 final size:99
Alignment explanation
Indices: 5986545--5986770 Score: 267
Period size: 99 Copynumber: 2.3 Consensus size: 99
5986535 GGCTTCAATA
* * * * *
5986545 TGCTCCACTGCAACTTCAGGAAGATAAGATTCACCGTAATTTGTAGCTTTAATCTGTTCCACCGC
1 TGCTTCACTGCAACTTCAGGGAGATAAGATTCACCATAATTTGTAGCTTCAATATGTTCCACCGC
*
5986610 AACATCAGGGAAATAAGATCCGCTGTCTTCAGTC
66 AACATCAGGGAAATAAGATCCGCTATCTTCAGTC
* * *
5986644 TGCTTCACTGCAACTTCAGGGAGATAAGA-TCTGCCATAATTTGTAGCTTCAATATGTTCCGCTG
1 TGCTTCACTGCAACTTCAGGGAGATAAGATTC-ACCATAATTTGTAGCTTCAATATGTTCCACCG
* * * **
5986708 CAACTTTAGGGAAATGAGATTTGCTATCTTCAGTC
65 CAACATCAGGGAAATAAGATCCGCTATCTTCAGTC
* **
5986743 TGC-TCTGCTATAACTTCAGGGAGATAAG
1 TGCTTC-ACTGCAACTTCAGGGAGATAAG
5986771 GCTGGTGGCT
Statistics
Matches: 108, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
98 4 0.04
99 104 0.96
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (99 bp):
TGCTTCACTGCAACTTCAGGGAGATAAGATTCACCATAATTTGTAGCTTCAATATGTTCCACCGC
AACATCAGGGAAATAAGATCCGCTATCTTCAGTC
Found at i:5986803 original size:143 final size:143
Alignment explanation
Indices: 5986636--5986960 Score: 436
Period size: 143 Copynumber: 2.3 Consensus size: 143
5986626 GATCCGCTGT
*
5986636 CTTCAGTCTGCTTCACTGCAACTTCAGGGAGATAAGA-TCTGCCATAATTTGTAGCTTCAATATG
1 CTTCAATCTGCTTCACTGCAACTTCAGGGAGATAAGATTC-GCCATAATTTGTAGCTTCAATATG
* * * * * * * *
5986700 TTCCGCTGCAACTTTAGGGAAATGAGATTTGCTATCTTCAGTCTGCTCTGCTATAACTTCAGGGA
65 TTCCACTGCAACGTCAGGGAAATAAGATATGCTATCTTCAGTCTGCTCCGCTACAACTTCAGAGA
5986765 GATAAGGCTGGTGG
130 GATAAGGCTGGTGG
* * * *
5986779 CTTCAATCTACTTCACTGCAACTTCAGGAAAATAAGATTCGCCATAATTTGTAGCTTCAATCTGT
1 CTTCAATCTGCTTCACTGCAACTTCAGGGAGATAAGATTCGCCATAATTTGTAGCTTCAATATGT
* * *
5986844 TCCACTGCAACGTCAGGGAAATAAGATATGCTATCTTCAGTCTGTTCCGTTGCAACTTCAGAGAG
66 TCCACTGCAACGTCAGGGAAATAAGATATGCTATCTTCAGTCTGCTCCGCTACAACTTCAGAGAG
* ** *
5986909 ATAAGGTTTTTGT
131 ATAAGGCTGGTGG
* *
5986922 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATGAGATT
1 CTTCAATCTGCTTCACTGCAACTTCAGGGAGATAAGATT
5986961 TATGGATTCA
Statistics
Matches: 156, Mismatches: 25, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
143 154 0.99
144 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.32
Consensus pattern (143 bp):
CTTCAATCTGCTTCACTGCAACTTCAGGGAGATAAGATTCGCCATAATTTGTAGCTTCAATATGT
TCCACTGCAACGTCAGGGAAATAAGATATGCTATCTTCAGTCTGCTCCGCTACAACTTCAGAGAG
ATAAGGCTGGTGG
Found at i:5986867 original size:242 final size:237
Alignment explanation
Indices: 5986410--5986960 Score: 702
Period size: 242 Copynumber: 2.3 Consensus size: 237
5986400 TTTCCTACTC
* * * *
5986410 CACTGCAACTTCAGGGAGATAAGGATTGTGACTTGTAGCTTCAATTTGTTTCGCTGCATCTTCAG
1 CACTGCAACTTCAGGGAGATAA-GATTGTAACTTGTAGCTTCAATATGTTCCGCTGCAACTTCAG
*
5986475 GGAAATGAGATTCACTATCTTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGGCTGGTGGCTT
65 GGAAATGAGATTCACTATCTTCAGTCTACTCCACTACAACTTCAGGGAGATAAGGCTGGTGGCTT
* * * *
5986540 CAATATGCTCCACTGCAACTTCAGGAAGATAAGATTCACCGTAATTTGTAGCTTTAATCTGTTCC
130 CAATATACTCCACTGCAACTTCAGGAAAATAAGATTCACCATAATTTGTAGCTTCAATCTGTTCC
* *
5986605 ACCGCAACATCAGGGAAATAAGATCCGCTGTCTTCAGTCTGCTT
195 ACCGCAACATCAGGGAAATAAGATACGCTATCTTCAGTCTG-TT
*
5986649 CACTGCAACTTCAGGGAGATAAGATCTGCCATAATTTGTAGCTTCAATATGTTCCGCTGCAACTT
1 CACTGCAACTTCAGGGAGATAAGAT-TG---TAACTTGTAGCTTCAATATGTTCCGCTGCAACTT
* ** * ** *
5986714 TAGGGAAATGAGATTTGCTATCTTCAGTCTGCTCTGCTATAACTTCAGGGAGATAAGGCTGGTGG
62 CAGGGAAATGAGATTCACTATCTTCAGTCTACTCCACTACAACTTCAGGGAGATAAGGCTGGTGG
* * *
5986779 CTTCAATCTACTTCACTGCAACTTCAGGAAAATAAGATTCGCCATAATTTGTAGCTTCAATCTGT
127 CTTCAATATACTCCACTGCAACTTCAGGAAAATAAGATTCACCATAATTTGTAGCTTCAATCTGT
* * *
5986844 TCCACTGCAACGTCAGGGAAATAAGATATGCTATCTTCAGTCTGTT
192 TCCACCGCAACATCAGGGAAATAAGATACGCTATCTTCAGTCTGTT
* * * * *
5986890 C-CGTTGCAACTTCAGAGAGATAAGGTT-T---TTGT--CTTCAATCTGCTCCACTGCAACTTCA
1 CAC--TGCAACTTCAGGGAGATAAGATTGTAACTTGTAGCTTCAATATGTTCCGCTGCAACTTCA
*
5986948 GGGAGATGAGATT
64 GGGAAATGAGATT
5986961 TATGGATTCA
Statistics
Matches: 274, Mismatches: 32, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
232 34 0.12
234 4 0.01
237 1 0.00
238 3 0.01
239 24 0.09
240 1 0.00
241 4 0.01
242 203 0.74
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (237 bp):
CACTGCAACTTCAGGGAGATAAGATTGTAACTTGTAGCTTCAATATGTTCCGCTGCAACTTCAGG
GAAATGAGATTCACTATCTTCAGTCTACTCCACTACAACTTCAGGGAGATAAGGCTGGTGGCTTC
AATATACTCCACTGCAACTTCAGGAAAATAAGATTCACCATAATTTGTAGCTTCAATCTGTTCCA
CCGCAACATCAGGGAAATAAGATACGCTATCTTCAGTCTGTT
Found at i:5986942 original size:44 final size:45
Alignment explanation
Indices: 5986833--5986959 Score: 139
Period size: 44 Copynumber: 2.8 Consensus size: 45
5986823 TAATTTGTAG
* *
5986833 CTTCAATCTGTTCCACTGCAACGTCAGGGAAATAAGATATGCTAT
1 CTTCAATCTGTTCCACTGCAACTTCAGGGAGATAAGATATGCTAT
* ** * * ** *
5986878 CTTCAGTCTGTTCCGTTGCAACTTCAGAGAGATAAGGT-TTTTGT
1 CTTCAATCTGTTCCACTGCAACTTCAGGGAGATAAGATATGCTAT
* *
5986922 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATGAGAT
1 CTTCAATCTGTTCCACTGCAACTTCAGGGAGATAAGAT
5986960 TTATGGATTC
Statistics
Matches: 65, Mismatches: 17, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
44 34 0.52
45 31 0.48
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (45 bp):
CTTCAATCTGTTCCACTGCAACTTCAGGGAGATAAGATATGCTAT
Found at i:5987454 original size:46 final size:46
Alignment explanation
Indices: 5987313--5987460 Score: 190
Period size: 46 Copynumber: 3.2 Consensus size: 46
5987303 AAAATTTTGT
* * *
5987313 TTCTTCCATCCATCCCACTACAACTCAAGGGTATAGGATTTGTATC
1 TTCTTCAATCCATCCCACTGCAACTCAGGGGTATAGGATTTGTATC
* * *
5987359 ATCTTCAATCCATCCCACAGCAACGT-AGAGGTATAGGATTTGTATC
1 TTCTTCAATCCATCCCACTGCAAC-TCAGGGGTATAGGATTTGTATC
* * **
5987405 TTCTTCAATCCATCCCACTGCAGCTCAGGGGTATAAGATTTGTGGC
1 TTCTTCAATCCATCCCACTGCAACTCAGGGGTATAGGATTTGTATC
5987451 TTCTTCAATC
1 TTCTTCAATC
5987461 AATTGGTCTA
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
45 1 0.01
46 85 0.98
47 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (46 bp):
TTCTTCAATCCATCCCACTGCAACTCAGGGGTATAGGATTTGTATC
Found at i:5987939 original size:53 final size:53
Alignment explanation
Indices: 5987868--5988009 Score: 203
Period size: 53 Copynumber: 2.7 Consensus size: 53
5987858 TCAAAATGAA
* * * *
5987868 TTAATCAAATATAAAAAATGCAATAAGAAGGAAATTAACTTGAAATGAATAAG
1 TTAATCAAAGATAGAAAATGTAATAAGAAGGAAATTAACTCGAAATGAATAAG
*
5987921 TTAATCAAAGATAGAAAATATAATAAGAAGGAAATTAACTCGAAATGAATAAG
1 TTAATCAAAGATAGAAAATGTAATAAGAAGGAAATTAACTCGAAATGAATAAG
* * * *
5987974 TTAATTAAGGATAGCAAATGTAATAAAAAGGAAATT
1 TTAATCAAAGATAGAAAATGTAATAAGAAGGAAATT
5988010 GATTGGGAGT
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 79 1.00
ACGTcount: A:0.56, C:0.05, G:0.15, T:0.25
Consensus pattern (53 bp):
TTAATCAAAGATAGAAAATGTAATAAGAAGGAAATTAACTCGAAATGAATAAG
Found at i:5989340 original size:19 final size:19
Alignment explanation
Indices: 5989316--5989352 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
5989306 TGCCTGGCCA
5989316 TTGTAAAACCATTAACATG
1 TTGTAAAACCATTAACATG
5989335 TTGTAAAACCATTAACAT
1 TTGTAAAACCATTAACAT
5989353 ATGTTCTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.32
Consensus pattern (19 bp):
TTGTAAAACCATTAACATG
Found at i:5991807 original size:14 final size:14
Alignment explanation
Indices: 5991774--5991833 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
5991764 TAAACACTAG
5991774 ACCCTAACCCATAA
1 ACCCTAACCCATAA
* *
5991788 ATCCTAACCCATTA
1 ACCCTAACCCATAA
*
5991802 ACCCTAAATCC-TAA
1 ACCCT-AACCCATAA
* *
5991816 CCCCTAACCCTTAA
1 ACCCTAACCCATAA
5991830 ACCC
1 ACCC
5991834 ATAAACTATA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
13 4 0.11
14 28 0.78
15 4 0.11
ACGTcount: A:0.37, C:0.43, G:0.00, T:0.20
Consensus pattern (14 bp):
ACCCTAACCCATAA
Found at i:5991830 original size:21 final size:20
Alignment explanation
Indices: 5991775--5991826 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
5991765 AAACACTAGA
5991775 CCCTAACCCATAAATCCTAAC
1 CCCTAACCC-TAAATCCTAAC
*
5991796 CCATTAACCCTAAATCCTAAC
1 CC-CTAACCCTAAATCCTAAC
5991817 CCCTAACCCT
1 CCCTAACCCT
5991827 TAAACCCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 7 0.25
21 15 0.54
22 6 0.21
ACGTcount: A:0.35, C:0.44, G:0.00, T:0.21
Consensus pattern (20 bp):
CCCTAACCCTAAATCCTAAC
Found at i:5991874 original size:14 final size:14
Alignment explanation
Indices: 5991835--5991882 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
5991825 CTTAAACCCA
*
5991835 TAAACTATAGACCT
1 TAAACTATAAACCT
*
5991849 TAAATCT-CAAACCT
1 TAAA-CTATAAACCT
*
5991863 TAAACTATAAACCC
1 TAAACTATAAACCT
5991877 TAAACT
1 TAAACT
5991883 CTTAAATCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 2 0.07
14 24 0.86
15 2 0.07
ACGTcount: A:0.46, C:0.25, G:0.02, T:0.27
Consensus pattern (14 bp):
TAAACTATAAACCT
Found at i:5991894 original size:22 final size:22
Alignment explanation
Indices: 5991857--5991910 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
5991847 CTTAAATCTC
5991857 AAAC-CTTAAACTATAAACCCT
1 AAACTCTTAAACTATAAACCCT
5991878 AAACTCTTAAA-TCATAAACCCT
1 AAACTCTTAAACT-ATAAACCCT
*
5991900 AAAATCTTAAA
1 AAACTCTTAAA
5991911 AATAAATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 5 0.17
22 25 0.83
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (22 bp):
AAACTCTTAAACTATAAACCCT
Found at i:5992328 original size:34 final size:36
Alignment explanation
Indices: 5992289--5992363 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 36
5992279 GTGCATGGAA
5992289 TTAGGGGT-TAAGGTTTAAAATTTAGGTT-CAAGGT
1 TTAGGGGTATAAGGTTTAAAATTTAGGTTACAAGGT
* * * *
5992323 TTA-GGGTATTAGGTTTGAAATTTAGTTTATAAGGT
1 TTAGGGGTATAAGGTTTAAAATTTAGGTTACAAGGT
5992358 TTAGGG
1 TTAGGG
5992364 TATTGGGTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
33 4 0.12
34 20 0.59
35 8 0.24
36 2 0.06
ACGTcount: A:0.28, C:0.01, G:0.29, T:0.41
Consensus pattern (36 bp):
TTAGGGGTATAAGGTTTAAAATTTAGGTTACAAGGT
Found at i:5992364 original size:35 final size:34
Alignment explanation
Indices: 5992299--5992367 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
5992289 TTAGGGGTTA
5992299 AGGTTTAAAATTTAGGTTCAAGGTTTAGGGTATT
1 AGGTTTAAAATTTAGGTTCAAGGTTTAGGGTATT
* * *
5992333 AGGTTTGAAATTTAGTTTATAAGGTTTAGGGTATT
1 AGGTTTAAAATTTAGGTT-CAAGGTTTAGGGTATT
5992368 GGGTATTGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
34 16 0.52
35 15 0.48
ACGTcount: A:0.29, C:0.01, G:0.26, T:0.43
Consensus pattern (34 bp):
AGGTTTAAAATTTAGGTTCAAGGTTTAGGGTATT
Found at i:5992380 original size:49 final size:49
Alignment explanation
Indices: 5992326--5992466 Score: 205
Period size: 49 Copynumber: 2.9 Consensus size: 49
5992316 TCAAGGTTTA
** *
5992326 GGGTATTAGGTTT-GAAATTTAGTTTATAAGGTTTAGGGTATTGGGTATT
1 GGGTATTAGGTTTAG-GGTTTAGTTTATAGGGTTTAGGGTATTGGGTATT
* *
5992375 GGGTATTGGGTTTAGGGTTTAGTCTATAGGGTTTAGGGTATTGGGTATT
1 GGGTATTAGGTTTAGGGTTTAGTTTATAGGGTTTAGGGTATTGGGTATT
5992424 GGGT-TTAGGGTTTAGGGTTTAGTTTATAGGGTTTAGGGTATTG
1 GGGTATTA-GGTTTAGGGTTTAGTTTATAGGGTTTAGGGTATTG
5992467 AGGTTTAGTC
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
48 2 0.02
49 80 0.96
50 1 0.01
ACGTcount: A:0.19, C:0.01, G:0.36, T:0.44
Consensus pattern (49 bp):
GGGTATTAGGTTTAGGGTTTAGTTTATAGGGTTTAGGGTATTGGGTATT
Found at i:5992434 original size:7 final size:7
Alignment explanation
Indices: 5992355--5992462 Score: 84
Period size: 7 Copynumber: 15.4 Consensus size: 7
5992345 TAGTTTATAA
5992355 GGTTTAG
1 GGTTTAG
5992362 GGTATT-G
1 GGT-TTAG
5992369 GGTATT-G
1 GGT-TTAG
5992376 GGTATT-G
1 GGT-TTAG
5992383 GGTTTAG
1 GGTTTAG
5992390 GGTTTAG
1 GGTTTAG
** *
5992397 TCTATAG
1 GGTTTAG
5992404 GGTTTAG
1 GGTTTAG
5992411 GGTATT-G
1 GGT-TTAG
5992418 GGTATT-G
1 GGT-TTAG
5992425 GGTTTAG
1 GGTTTAG
5992432 GGTTTAG
1 GGTTTAG
5992439 GGTTTA-
1 GGTTTAG
*
5992445 GTTTATAG
1 GGTT-TAG
5992453 GGTTTAG
1 GGTTTAG
5992460 GGT
1 GGT
5992463 ATTGAGGTTT
Statistics
Matches: 87, Mismatches: 8, Indels: 12
0.81 0.07 0.11
Matches are distributed among these distances:
6 7 0.08
7 73 0.84
8 7 0.08
ACGTcount: A:0.16, C:0.01, G:0.40, T:0.44
Consensus pattern (7 bp):
GGTTTAG
Found at i:5992434 original size:14 final size:14
Alignment explanation
Indices: 5992355--5992474 Score: 99
Period size: 14 Copynumber: 8.5 Consensus size: 14
5992345 TAGTTTATAA
5992355 GGTTTAGGGTATTG
1 GGTTTAGGGTATTG
5992369 GGTATT-GGGTATTG
1 GGT-TTAGGGTATTG
5992383 GGTTTAGGGT-TT-
1 GGTTTAGGGTATTG
*
5992395 AGTCTATAGGGT-TTAG
1 GGT-T-TAGGGTATT-G
5992411 GGTATT-GGGTATTG
1 GGT-TTAGGGTATTG
5992425 GGTTTAGGGT-TTAG
1 GGTTTAGGGTATT-G
** *
5992439 GGTTTAGTTTATAG
1 GGTTTAGGGTATTG
5992453 GGTTTAGGGTATTG
1 GGTTTAGGGTATTG
5992467 AGGTTTAG
1 -GGTTTAG
5992475 TCTATTGGTT
Statistics
Matches: 86, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
12 2 0.02
13 9 0.10
14 59 0.69
15 13 0.15
16 3 0.03
ACGTcount: A:0.17, C:0.01, G:0.39, T:0.43
Consensus pattern (14 bp):
GGTTTAGGGTATTG
Found at i:5992484 original size:28 final size:27
Alignment explanation
Indices: 5992401--5992485 Score: 75
Period size: 28 Copynumber: 3.0 Consensus size: 27
5992391 GTTTAGTCTA
**
5992401 TAGGGTTTAGGGTATT-GGGTATTGGGTT
1 TAGGGTTTAGGGT-TTAGTCTATT-GGTT
* *
5992429 TAGGGTTTAGGGTTTAGTTTATAGGGTT
1 TAGGGTTTAGGGTTTAGTCTAT-TGGTT
5992457 TAGGGTATT-GAGGTTTAGTCTATTGGTT
1 TAGGGT-TTAG-GGTTTAGTCTATTGGTT
5992485 T
1 T
5992486 TGGGCTTAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
27 2 0.04
28 33 0.69
29 13 0.27
ACGTcount: A:0.16, C:0.01, G:0.36, T:0.46
Consensus pattern (27 bp):
TAGGGTTTAGGGTTTAGTCTATTGGTT
Found at i:5992485 original size:49 final size:48
Alignment explanation
Indices: 5992343--5992485 Score: 173
Period size: 49 Copynumber: 2.9 Consensus size: 48
5992333 AGGTTTGAAA
* **
5992343 TTTAGTTTATAAGGTTTAGGGTATTGGGTATTGGGTATTGGGTTTAGGG
1 TTTAGTTTATAGGGTTTAGGGTATTGGGTATTGTCTATT-GGTTTAGGG
* * *
5992392 TTTAGTCTATAGGGTTTAGGGTATTGGGTATTGGGTTTA-GGGTTTAGGG
1 TTTAGTTTATAGGGTTTAGGGTATTGGGTATT--GTCTATTGGTTTAGGG
5992441 TTTAGTTTATAGGGTTTAGGGTATTGAGGT-TTAGTCTATTGGTTT
1 TTTAGTTTATAGGGTTTAGGGTATTG-GGTATT-GTCTATTGGTTT
5992486 TGGGCTTAAT
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
48 4 0.05
49 71 0.88
50 3 0.04
51 3 0.04
ACGTcount: A:0.17, C:0.01, G:0.35, T:0.46
Consensus pattern (48 bp):
TTTAGTTTATAGGGTTTAGGGTATTGGGTATTGTCTATTGGTTTAGGG
Found at i:5993317 original size:16 final size:16
Alignment explanation
Indices: 5993292--5993324 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5993282 AGAACGCAGA
5993292 TTTCTATTGTTAATGC
1 TTTCTATTGTTAATGC
*
5993308 TTTCTGTTGTTAATGC
1 TTTCTATTGTTAATGC
5993324 T
1 T
5993325 CAGCACTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.58
Consensus pattern (16 bp):
TTTCTATTGTTAATGC
Found at i:5995263 original size:20 final size:21
Alignment explanation
Indices: 5995204--5995262 Score: 111
Period size: 20 Copynumber: 2.9 Consensus size: 21
5995194 TATTCGGTCA
5995204 AATATATTTTTTCATAAAATC
1 AATATATTTTTTCATAAAATC
5995225 AATATA-TTTTTCATAAAATC
1 AATATATTTTTTCATAAAATC
5995245 AATATATTTTTTCATAAA
1 AATATATTTTTTCATAAA
5995263 TTATTTTCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (21 bp):
AATATATTTTTTCATAAAATC
Found at i:5995828 original size:3 final size:3
Alignment explanation
Indices: 5995822--5995860 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
5995812 AATAATAATA
5995822 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5995861 TGTTGTTGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5995866 original size:3 final size:3
Alignment explanation
Indices: 5995860--5995905 Score: 83
Period size: 3 Copynumber: 15.0 Consensus size: 3
5995850 TTATTATTAT
5995860 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG -TTG TTG
5995906 ATTCGAGTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:5996348 original size:13 final size:13
Alignment explanation
Indices: 5996330--5996359 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
5996320 CCACGTAATA
5996330 CATAAATATATAT
1 CATAAATATATAT
5996343 CATAAATATATAT
1 CATAAATATATAT
5996356 CATA
1 CATA
5996360 TCATAAGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (13 bp):
CATAAATATATAT
Found at i:5996373 original size:9 final size:9
Alignment explanation
Indices: 5996361--5996442 Score: 76
Period size: 9 Copynumber: 9.1 Consensus size: 9
5996351 TATATCATAT
*
5996361 CATAAGTTA
1 CATAACTTA
5996370 CATAACTTA
1 CATAACTTA
*
5996379 CATACCTTA
1 CATAACTTA
*
5996388 CATAAATGTA
1 CATAACT-TA
* * *
5996398 TATCA-TAA
1 CATAACTTA
5996406 CATAACTTA
1 CATAACTTA
5996415 CATAACTTA
1 CATAACTTA
*
5996424 CAAAACTTA
1 CATAACTTA
*
5996433 CTTAACTTA
1 CATAACTTA
5996442 C
1 C
5996443 GTAATACATA
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
8 4 0.07
9 49 0.84
10 5 0.09
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.33
Consensus pattern (9 bp):
CATAACTTA
Found at i:5996433 original size:45 final size:45
Alignment explanation
Indices: 5996343--5996433 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
5996333 AAATATATAT
* * * *
5996343 CATAAATATATATCATATCATAAGTTACATAACTTACATACCTTA
1 CATAAATATATATCATAACATAACTTACATAACTTACAAAACTTA
*
5996388 CATAAATGTATATCATAACATAACTTACATAACTTACAAAACTTA
1 CATAAATATATATCATAACATAACTTACATAACTTACAAAACTTA
5996433 C
1 C
5996434 TTAACTTACG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (45 bp):
CATAAATATATATCATAACATAACTTACATAACTTACAAAACTTA
Found at i:6002026 original size:21 final size:21
Alignment explanation
Indices: 6002001--6002047 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
6001991 GAGCGAAAGG
*
6002001 AGCAGCGAAGGAGACAGCGGC
1 AGCAGCGAAGGAGACAGAGGC
* *
6002022 AGCAGCGAGGGAGGCAGAGGC
1 AGCAGCGAAGGAGACAGAGGC
6002043 AGCAG
1 AGCAG
6002048 TGATGGCAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.21, G:0.47, T:0.00
Consensus pattern (21 bp):
AGCAGCGAAGGAGACAGAGGC
Found at i:6002456 original size:43 final size:42
Alignment explanation
Indices: 6002409--6002542 Score: 119
Period size: 43 Copynumber: 3.1 Consensus size: 42
6002399 TCTTCTAAAA
*
6002409 TTAGCAGCGTTTGTAAAAAAAGCGCCGCTAAAAGCCATGACTT
1 TTAGCAGCCTTT-TAAAAAAAGCGCCGCTAAAAGCCATGACTT
** * * *
6002452 TTAGC-GACGCTTTTCTCACAAA-CACCGTTAAAAGCCATGACTT
1 TTAGCAG-C-CTTTT-AAAAAAAGCGCCGCTAAAAGCCATGACTT
* ** *
6002495 TTAGCGGCACTTTTATCACAAGCGCCGCTAAAAGCCATGACTT
1 TTAGCAGC-CTTTTAAAAAAAGCGCCGCTAAAAGCCATGACTT
6002538 TTAGC
1 TTAGC
6002543 GGTGTTTTTT
Statistics
Matches: 72, Mismatches: 14, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
42 3 0.04
43 61 0.85
44 8 0.11
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (42 bp):
TTAGCAGCCTTTTAAAAAAAGCGCCGCTAAAAGCCATGACTT
Found at i:6002592 original size:42 final size:42
Alignment explanation
Indices: 6002431--6002594 Score: 186
Period size: 43 Copynumber: 3.9 Consensus size: 42
6002421 GTAAAAAAAG
* *
6002431 CGCCGCTAAAAGCCATGACTTTTAGCGACGCTTTTCTCACAAA
1 CGCCGCTAAAAGCCATGACTTTTAGCGGCG-TTTTTTCACAAA
* * * * *
6002474 CACCGTTAAAAGCCATGACTTTTAGCGGCACTTTTATCACAAG
1 CGCCGCTAAAAGCCATGACTTTTAGCGGC-GTTTTTTCACAAA
*
6002517 CGCCGCTAAAAGCCATGACTTTTAGCGGTGTTTTTTCACAAA
1 CGCCGCTAAAAGCCATGACTTTTAGCGGCGTTTTTTCACAAA
* * * *
6002559 CGCTGCTAAAAGTCTTGATCTTTT-GTGGCGTTTTTT
1 CGCCGCTAAAAGCCATGA-CTTTTAGCGGCGTTTTTT
6002595 TCAGATAAAC
Statistics
Matches: 102, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
42 35 0.34
43 67 0.66
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32
Consensus pattern (42 bp):
CGCCGCTAAAAGCCATGACTTTTAGCGGCGTTTTTTCACAAA
Found at i:6008230 original size:23 final size:23
Alignment explanation
Indices: 6008204--6008253 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
6008194 TATTCCTTCA
6008204 ATACCATATT-GGAGAATATTTGT
1 ATACCATATTCGGA-AATATTTGT
* *
6008227 ATA-CATATTCGGAACTATTTTT
1 ATACCATATTCGGAAATATTTGT
6008249 ATACC
1 ATACC
6008254 CTAAACTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (23 bp):
ATACCATATTCGGAAATATTTGT
Found at i:6011226 original size:28 final size:28
Alignment explanation
Indices: 6011195--6011253 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
6011185 TTTAAAAATA
*
6011195 TTAAG-ATGATTTTTATTTATTA-ATTTTT
1 TTAAGCATGAATTTTA-TTA-TAGATTTTT
*
6011223 TTAAGCATTAATTTTATTATAGATTTTT
1 TTAAGCATGAATTTTATTATAGATTTTT
6011251 TTA
1 TTA
6011254 TATATAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 2 0.07
28 17 0.63
29 8 0.30
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.61
Consensus pattern (28 bp):
TTAAGCATGAATTTTATTATAGATTTTT
Found at i:6011647 original size:14 final size:16
Alignment explanation
Indices: 6011613--6011649 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
6011603 TTTTTAATAT
6011613 AATTTAAGTAATTATAA
1 AATTT-AGTAATTATAA
6011630 AATTTAGT-ATTA-AA
1 AATTTAGTAATTATAA
6011644 AATTTA
1 AATTTA
6011650 ATACTTAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
15 4 0.20
16 3 0.15
17 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (16 bp):
AATTTAGTAATTATAA
Found at i:6014598 original size:15 final size:14
Alignment explanation
Indices: 6014574--6014604 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
6014564 CTATGTTTTG
6014574 TATTTTATTATTCA
1 TATTTTATTATTCA
6014588 TATTCTTATTATTCA
1 TATT-TTATTATTCA
6014603 TA
1 TA
6014605 ATATTTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTTTATTATTCA
Found at i:6015986 original size:31 final size:31
Alignment explanation
Indices: 6015948--6016011 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
6015938 GAAATGAAAA
6015948 CTGAATAAAACCATTCATTTATGGATCCTTT
1 CTGAATAAAACCATTCATTTATGGATCCTTT
6015979 CTGAATAAAACCATTCATTTATGGATCCTTT
1 CTGAATAAAACCATTCATTTATGGATCCTTT
6016010 CT
1 CT
6016012 TAAATTTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.39
Consensus pattern (31 bp):
CTGAATAAAACCATTCATTTATGGATCCTTT
Found at i:6025798 original size:138 final size:138
Alignment explanation
Indices: 6025550--6025808 Score: 376
Period size: 138 Copynumber: 1.9 Consensus size: 138
6025540 TGCCATAGTG
* *
6025550 TCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCATAGTCTTA
1 TCTTTCAACCATGGTCTTACTCATTTTCTGTCATGTTACCATGGTATCTTTCAACCATAGTCTTA
** * * * * **
6025615 TTCATTTCCTGTCATGTTTCCATGGTATCTTTCGACCATGGTCTTATTCATTTCATATCACGTTG
66 CACATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTG
6025680 TCATGGTA
131 TCATGGTA
* * * *
6025688 TCTTTCAACCATTGTCTTATTCA-TTTCTCGTCATGTTACCATGGTATTTTTCAACCATGGTCTT
1 TCTTTCAACCATGGTCTTACTCATTTTCT-GTCATGTTACCATGGTATCTTTCAACCATAGTCTT
6025752 ACACATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
65 ACACATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
6025809 TTCAGAAAAT
Statistics
Matches: 106, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
137 5 0.05
138 101 0.95
ACGTcount: A:0.20, C:0.23, G:0.12, T:0.44
Consensus pattern (138 bp):
TCTTTCAACCATGGTCTTACTCATTTTCTGTCATGTTACCATGGTATCTTTCAACCATAGTCTTA
CACATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGTTG
TCATGGTA
Found at i:6025807 original size:46 final size:46
Alignment explanation
Indices: 6025535--6025808 Score: 336
Period size: 46 Copynumber: 6.0 Consensus size: 46
6025525 TTATCTTCGA
* * * *
6025535 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGT
* * *
6025581 CATGTTGCCATGGTATCTTTCAACCATAGTCTTATTCATTTCCTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * * *
6025627 CATGTTTCCATGGTATCTTTCGACCATGGTCTTATTCATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * * *
6025673 CACGTTGTCATGGTATCTTTCAACCATTGTCTTATTCATTTC-TCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT-GT
* * * *
6025719 CATGTTACCATGGTATTTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
*
6025765 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
6025809 TTCAGAAAAT
Statistics
Matches: 198, Mismatches: 27, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
45 5 0.03
46 192 0.97
47 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.43
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
Found at i:6027701 original size:11 final size:11
Alignment explanation
Indices: 6027685--6027722 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
6027675 CTAAATAATA
6027685 AATAATAAAAT
1 AATAATAAAAT
*
6027696 AATAATGAAAT
1 AATAATAAAAT
*
6027707 AATAATAAATT
1 AATAATAAAAT
6027718 AATAA
1 AATAA
6027723 AATATCTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:6027745 original size:19 final size:19
Alignment explanation
Indices: 6027723--6027761 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
6027713 AAATTAATAA
6027723 AATATCTTAT-TAATAAAAT
1 AATAT-TTATCTAATAAAAT
*
6027742 AATATTTATCTAATTAAAT
1 AATATTTATCTAATAAAAT
6027761 A
1 A
6027762 GTTATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
AATATTTATCTAATAAAAT
Found at i:6042869 original size:55 final size:55
Alignment explanation
Indices: 6042803--6042908 Score: 203
Period size: 55 Copynumber: 1.9 Consensus size: 55
6042793 GCAAGCCTAT
*
6042803 TTTAGATCTCATCTATATTATTTTTAAAAATTTAAAATATGTTTATATTACCCAA
1 TTTAGATCTCATCCATATTATTTTTAAAAATTTAAAATATGTTTATATTACCCAA
6042858 TTTAGATCTCATCCATATTATTTTTAAAAATTTAAAATATGTTTATATTAC
1 TTTAGATCTCATCCATATTATTTTTAAAAATTTAAAATATGTTTATATTAC
6042909 TTTTTAATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.48
Consensus pattern (55 bp):
TTTAGATCTCATCCATATTATTTTTAAAAATTTAAAATATGTTTATATTACCCAA
Found at i:6043541 original size:2 final size:2
Alignment explanation
Indices: 6043536--6043560 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6043526 ATTACTAATT
6043536 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 T
6043561 TACAACACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6043755 original size:47 final size:47
Alignment explanation
Indices: 6043701--6043794 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
6043691 TTGCATATCC
6043701 ATGTGTAGGTTACCTTTTCTCATTTATGATAAAATGTATGGTAAAGT
1 ATGTGTAGGTTACCTTTTCTCATTTATGATAAAATGTATGGTAAAGT
*
6043748 ATGTGTAGGTTCCCTTTTCTCATTTATGATAAAATGTATGGTAAAGT
1 ATGTGTAGGTTACCTTTTCTCATTTATGATAAAATGTATGGTAAAGT
6043795 GTTAAAGTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.43
Consensus pattern (47 bp):
ATGTGTAGGTTACCTTTTCTCATTTATGATAAAATGTATGGTAAAGT
Done.