Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 355 of 378
Found at i:106476034 original size:35 final size:36
Alignment explanation
Indices: 106475971--106476107 Score: 190
Period size: 35 Copynumber: 3.8 Consensus size: 36
106475961 CAATGATATG
*
106475971 CAATCTTAAATATGATATGCAATCTTAGATATGATA
1 CAATCTTAGATATGATATGCAATCTTAGATATGATA
106476007 CAATCTTAGATATGAT-TGCAATCTTAGATATGATA
1 CAATCTTAGATATGATATGCAATCTTAGATATGATA
* * *
106476042 TGTAATCTTAGATATGATAT--AATCTTAGATATAATTG
1 --CAATCTTAGATATGATATGCAATCTTAGATATGA-TA
106476079 CAATCTTAGATATGATATGCAATCTTAGA
1 CAATCTTAGATATGATATGCAATCTTAGA
106476108 AGATATGATT
Statistics
Matches: 90, Mismatches: 5, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
35 36 0.40
36 28 0.31
37 25 0.28
38 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (36 bp):
CAATCTTAGATATGATATGCAATCTTAGATATGATA
Found at i:106476057 original size:14 final size:15
Alignment explanation
Indices: 106475991--106476095 Score: 75
Period size: 17 Copynumber: 6.1 Consensus size: 15
106475981 TATGATATGC
106475991 AATCTTAGATATGAT
1 AATCTTAGATATGAT
106476006 ACAATCTTAGATATGATT
1 --AATCTTAGATATGA-T
106476024 GCAATCTTAGATATGATATGT
1 --AATCTTAGATATG--A--T
106476045 AATCTTAGATATGATAT
1 AATCTTAGATATG--AT
*
106476062 AATCTTAGATATAATT
1 AATCTTAGATATGA-T
106476078 GCAATCTTAGATATGAT
1 --AATCTTAGATATGAT
106476095 A
1 A
106476096 TGCAATCTTA
Statistics
Matches: 77, Mismatches: 4, Indels: 16
0.79 0.04 0.16
Matches are distributed among these distances:
15 2 0.03
16 1 0.01
17 28 0.36
18 28 0.36
19 16 0.21
20 1 0.01
21 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (15 bp):
AATCTTAGATATGAT
Found at i:106476100 original size:73 final size:73
Alignment explanation
Indices: 106475963--106476130 Score: 223
Period size: 73 Copynumber: 2.2 Consensus size: 73
106475953 ATAATCTTCA
* * *
106475963 ATGATATGCAATCTTAAATATGATATGCAATCTTAGATATGATACAATCTTAGATATGATTGCAA
1 ATGATATGTAATCTTAGATATGATAT-CAATCTTAGATATAATACAATCTTAGATATGATTGCAA
106476028 TCTT-AGAT
65 TCTTAAGAT
*
106476036 ATGATATGTAATCTTAGATATGATAT-AATCTTAGATATAATTGCAATCTTAGATATGATATGCA
1 ATGATATGTAATCTTAGATATGATATCAATCTTAGATATAA-TACAATCTTAGATATGAT-TGCA
106476100 ATCTTAGAAGAT
64 ATCTT--AAGAT
*
106476112 ATGATTTTGTAATCTTAGA
1 ATGA-TATGTAATCTTAGA
106476131 GATTTAATTT
Statistics
Matches: 84, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
71 13 0.15
72 17 0.20
73 33 0.39
76 8 0.10
77 13 0.15
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (73 bp):
ATGATATGTAATCTTAGATATGATATCAATCTTAGATATAATACAATCTTAGATATGATTGCAAT
CTTAAGAT
Found at i:106476133 original size:22 final size:22
Alignment explanation
Indices: 106475963--106476130 Score: 102
Period size: 19 Copynumber: 8.8 Consensus size: 22
106475953 ATAATCTTCA
106475963 ATGATATGCAATCTT--AA-AT
1 ATGATATGCAATCTTAGAAGAT
106475982 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
106476001 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
106476018 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
*
106476036 ATGATATGTAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
106476055 ATGATAT--AATCTTAG---AT
1 ATGATATGCAATCTTAGAAGAT
*
106476072 ATAAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
106476090 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
106476112 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
106476131 GATTTAATTT
Statistics
Matches: 129, Mismatches: 5, Indels: 26
0.81 0.03 0.16
Matches are distributed among these distances:
16 1 0.01
17 28 0.22
18 29 0.22
19 51 0.40
22 8 0.06
23 12 0.09
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:106476421 original size:19 final size:19
Alignment explanation
Indices: 106476397--106476433 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
106476387 GTTTCCTGTT
* *
106476397 TTTTTTTATATATTTTTAA
1 TTTTTTTAAATAATTTTAA
106476416 TTTTTTTAAATAATTTTA
1 TTTTTTTAAATAATTTTA
106476434 GTATTATATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTTTTAAATAATTTTAA
Found at i:106477669 original size:22 final size:23
Alignment explanation
Indices: 106477621--106477669 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
106477611 TGTACTTTTT
*
106477621 TATTTCTTTTAGGTTTGTCTTAC
1 TATTTCTTTTAGGTTTGCCTTAC
*
106477644 TATTT-TTTTAGTTTTAGCCTTA-
1 TATTTCTTTTAGGTTT-GCCTTAC
106477666 TATT
1 TATT
106477670 ATGCTGAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.16, C:0.10, G:0.10, T:0.63
Consensus pattern (23 bp):
TATTTCTTTTAGGTTTGCCTTAC
Found at i:106488892 original size:11 final size:11
Alignment explanation
Indices: 106488876--106488905 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
106488866 TAACATTAAG
106488876 AATATATATAT
1 AATATATATAT
*
106488887 AATATAAATAT
1 AATATATATAT
106488898 AATATATA
1 AATATATA
106488906 CAATATACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AATATATATAT
Found at i:106489439 original size:18 final size:18
Alignment explanation
Indices: 106489404--106489457 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
106489394 CGAAAAAAGG
106489404 AAAAA-AATAAA-AA-AT
1 AAAAATAATAAAGAAGAT
*
106489419 AAAAATAA-AAATAAGAGT
1 AAAAATAATAAAGAAGA-T
106489437 -AAAATAATAAAGAAGAT
1 AAAAATAATAAAGAAGAT
106489454 AAAA
1 AAAA
106489458 TCACCTTTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
15 8 0.25
16 4 0.12
17 9 0.28
18 11 0.34
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (18 bp):
AAAAATAATAAAGAAGAT
Found at i:106489442 original size:17 final size:17
Alignment explanation
Indices: 106489420--106489458 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
106489410 ATAAAAAATA
*
106489420 AAAATAA-AAATAAGAGT
1 AAAATAATAAAGAAGA-T
106489437 AAAATAATAAAGAAGAT
1 AAAATAATAAAGAAGAT
106489454 AAAAT
1 AAAAT
106489459 CACCTTTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (17 bp):
AAAATAATAAAGAAGAT
Found at i:106489715 original size:15 final size:15
Alignment explanation
Indices: 106489697--106489730 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
106489687 TTTCTTCTTT
*
106489697 TTTTTTTGGGTTAGG
1 TTTTTTTGGGGTAGG
106489712 TTTTTTTGGGGTAGG
1 TTTTTTTGGGGTAGG
106489727 TTTT
1 TTTT
106489731 CTTTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.00, G:0.32, T:0.62
Consensus pattern (15 bp):
TTTTTTTGGGGTAGG
Found at i:106489756 original size:16 final size:16
Alignment explanation
Indices: 106489696--106489735 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
106489686 TTTTCTTCTT
*
106489696 TTTTTTTTGGGTTAGG
1 TTTTTTTTGGGGTAGG
106489712 -TTTTTTTGGGGTAGG
1 TTTTTTTTGGGGTAGG
106489727 TTTTCTTTT
1 TTTT-TTTT
106489736 TTTTTTGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 14 0.67
16 3 0.14
17 4 0.19
ACGTcount: A:0.05, C:0.03, G:0.28, T:0.65
Consensus pattern (16 bp):
TTTTTTTTGGGGTAGG
Found at i:106490705 original size:13 final size:13
Alignment explanation
Indices: 106490672--106490726 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
106490662 TAGCCTATTC
106490672 TAAATTAAT-AAAA
1 TAAA-TAATAAAAA
106490685 TAAA-AATAAAAA
1 TAAATAATAAAAA
106490697 TAAATAATAAAACA
1 TAAATAATAAAA-A
*
106490711 -AAATAAAACAAAA
1 TAAATAATA-AAAA
106490724 TAA
1 TAA
106490727 TATCTTCTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
11 3 0.08
12 8 0.22
13 19 0.53
14 6 0.17
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (13 bp):
TAAATAATAAAAA
Found at i:106490715 original size:10 final size:10
Alignment explanation
Indices: 106490702--106490726 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
106490692 AAAAATAAAT
106490702 AATAAAACAA
1 AATAAAACAA
106490712 AATAAAACAA
1 AATAAAACAA
106490722 AATAA
1 AATAA
106490727 TATCTTCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (10 bp):
AATAAAACAA
Found at i:106503803 original size:17 final size:17
Alignment explanation
Indices: 106503765--106503796 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
106503755 GGTCGTTTTC
106503765 TCTTTGCAAGTCTCAAG
1 TCTTTGCAAGTCTCAAG
106503782 TCTTTG-AAG-CTCAAG
1 TCTTTGCAAGTCTCAAG
106503797 CTTCTTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (17 bp):
TCTTTGCAAGTCTCAAG
Found at i:106504228 original size:35 final size:35
Alignment explanation
Indices: 106504179--106504248 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
106504169 ACGGGGCTGT
106504179 TTCTAAAATACCGTATGAATCATTTTGTTATGCCA
1 TTCTAAAATACCGTATGAATCATTTTGTTATGCCA
* **
106504214 TTCTAAAATGCCGTATGAATTGTTTTGTTATGCCA
1 TTCTAAAATACCGTATGAATCATTTTGTTATGCCA
106504249 AATATCTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (35 bp):
TTCTAAAATACCGTATGAATCATTTTGTTATGCCA
Found at i:106509831 original size:35 final size:35
Alignment explanation
Indices: 106509787--106509953 Score: 201
Period size: 35 Copynumber: 4.6 Consensus size: 35
106509777 TCCTCATTGA
** *
106509787 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
106509822 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
106509862 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
106509897 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
106509932 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
106509954 CTTTGCCATG
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
35 87 0.74
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:106509870 original size:75 final size:73
Alignment explanation
Indices: 106509782--106509953 Score: 226
Period size: 75 Copynumber: 2.4 Consensus size: 73
106509772 GGTTTTCCTC
** * * **
106509782 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
106509846 TCAGTATGG
65 TCAGTATGG
*
106509855 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
106509920 CTCAGTATGG
64 CTCAGTATGG
106509930 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
106509954 CTTTGCCATG
Statistics
Matches: 89, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 58 0.65
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:106521994 original size:18 final size:18
Alignment explanation
Indices: 106521954--106521996 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
106521944 ATTTATGTTA
106521954 TTTTATATTAATAATAAT
1 TTTTATATTAATAATAAT
*
106521972 ATTTATATTAATTAAT-AT
1 TTTTATATTAA-TAATAAT
106521990 TTTTATA
1 TTTTATA
106521997 ACAGTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTATATTAATAATAAT
Found at i:106522709 original size:15 final size:15
Alignment explanation
Indices: 106522661--106522711 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
106522651 ATAAAATAAT
106522661 AATATAAGTGACTAA
1 AATATAAGTGACTAA
* * *
106522676 AACAT-AGT-ATTTCA
1 AATATAAGTGA-CTAA
106522690 AATATAAGTGACTAA
1 AATATAAGTGACTAA
106522705 AATATAA
1 AATATAA
106522712 TTTGAGTCAA
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 1 0.04
14 9 0.33
15 16 0.59
16 1 0.04
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (15 bp):
AATATAAGTGACTAA
Found at i:106527527 original size:16 final size:16
Alignment explanation
Indices: 106527507--106527544 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
106527497 AAATTGGTTG
106527507 AAATTTAAGA-TATTTT
1 AAATTTAA-ATTATTTT
*
106527523 GAATTTAAATTATTTT
1 AAATTTAAATTATTTT
106527539 AAATTT
1 AAATTT
106527545 TGAAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 1 0.05
16 18 0.95
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (16 bp):
AAATTTAAATTATTTT
Found at i:106527722 original size:22 final size:21
Alignment explanation
Indices: 106527693--106527733 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
106527683 TCTAATTCGG
106527693 TTAATCGGTCA-ATGGTCGAAT
1 TTAATCGGTCAGA-GGTCGAAT
106527714 TTAACTCGGTCAGAGGTCGA
1 TTAA-TCGGTCAGAGGTCGA
106527734 TTAATGATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 13 0.72
23 1 0.06
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (21 bp):
TTAATCGGTCAGAGGTCGAAT
Found at i:106527891 original size:14 final size:14
Alignment explanation
Indices: 106527854--106527895 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
106527844 CTATTATTTT
106527854 TTATAT-TAATATA
1 TTATATATAATATA
* *
106527867 -AATAAATAATATA
1 TTATATATAATATA
106527880 TTATATATAATATA
1 TTATATATAATATA
106527894 TT
1 TT
106527896 TTTGAACTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
12 3 0.13
13 7 0.30
14 13 0.57
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTATATATAATATA
Found at i:106534253 original size:15 final size:16
Alignment explanation
Indices: 106534233--106534262 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
106534223 CAACAAGAAC
106534233 AATTTACA-TAAAATG
1 AATTTACATTAAAATG
106534248 AATTTACATTAAAAT
1 AATTTACATTAAAAT
106534263 AGGTTCCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (16 bp):
AATTTACATTAAAATG
Found at i:106539412 original size:17 final size:17
Alignment explanation
Indices: 106539390--106539422 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
106539380 TTTTCTGATG
106539390 AATAAAATTAAGCTAAC
1 AATAAAATTAAGCTAAC
*
106539407 AATAAAATTAATCTAA
1 AATAAAATTAAGCTAA
106539423 AGCTTCTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.09, G:0.03, T:0.27
Consensus pattern (17 bp):
AATAAAATTAAGCTAAC
Found at i:106554507 original size:29 final size:30
Alignment explanation
Indices: 106554474--106554532 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
106554464 TGAAGAACCC
*
106554474 TAATTTAAACTAAATTAACA-ATAAAAATT
1 TAATTTAAACTAAATTAAAATATAAAAATT
***
106554503 TAATTTATTTTAAATTAAAATATAAAAATT
1 TAATTTAAACTAAATTAAAATATAAAAATT
106554533 AAATCATCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (30 bp):
TAATTTAAACTAAATTAAAATATAAAAATT
Found at i:106555553 original size:24 final size:24
Alignment explanation
Indices: 106555520--106555566 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
106555510 AGAGAAGAAA
*
106555520 CGATGGATTAATCTTAAAGGAATG
1 CGATGCATTAATCTTAAAGGAATG
106555544 CGATGCATTAATCTTAAAGGAAT
1 CGATGCATTAATCTTAAAGGAAT
106555567 TACTTGTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (24 bp):
CGATGCATTAATCTTAAAGGAATG
Found at i:106556590 original size:19 final size:18
Alignment explanation
Indices: 106556568--106556664 Score: 58
Period size: 19 Copynumber: 5.3 Consensus size: 18
106556558 CTAAAAATAT
106556568 TAAAAATATATAAACTTTA
1 TAAAAATATATAAAC-TTA
106556587 TAAAAA-ATAATAAAACTTA
1 TAAAAATAT-AT-AAACTTA
* **
106556606 TAAATAT-TATAAAAATA
1 TAAAAATATATAAACTTA
* *
106556623 TAAAAATCTAGTAAA-TTC
1 TAAAAATATA-TAAACTTA
*
106556641 TAATAAAT-TATAAAATTAA
1 TAA-AAATATATAAACTT-A
106556660 TAAAA
1 TAAAA
106556665 CATGTTTAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
17 15 0.24
18 16 0.25
19 28 0.44
20 4 0.06
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (18 bp):
TAAAAATATATAAACTTA
Found at i:106556594 original size:20 final size:19
Alignment explanation
Indices: 106556569--106556609 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
106556559 TAAAAATATT
106556569 AAAAAT-ATATAAACTTTATA
1 AAAAATAATA-AAAC-TTATA
106556589 AAAAATAATAAAACTTATA
1 AAAAATAATAAAACTTATA
106556608 AA
1 AA
106556610 TATTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 10 0.50
21 3 0.15
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAATAATAAAACTTATA
Found at i:106556637 original size:28 final size:26
Alignment explanation
Indices: 106556559--106556639 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 26
106556549 TATTAAATTC
*
106556559 TAAAAATATTAAAAATATATAAACTTTA
1 TAAAAATA-TAAAAATCTATAAA-TTTA
*
106556587 TAAAAA-ATAATAAAACTTATAAATATTA
1 TAAAAATATAA-AAATC-TATAAAT-TTA
106556615 TAAAAATATAAAAATCTAGTAAATT
1 TAAAAATATAAAAATCTA-TAAATT
106556640 CTAATAAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
26 3 0.07
27 8 0.18
28 30 0.67
29 4 0.09
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (26 bp):
TAAAAATATAAAAATCTATAAATTTA
Found at i:106556701 original size:47 final size:45
Alignment explanation
Indices: 106556650--106556741 Score: 107
Period size: 45 Copynumber: 2.0 Consensus size: 45
106556640 CTAATAAATT
* *
106556650 ATAAAATTAATA-AAACATGTTTAAAATTTTATAAAAACAT-ATAAAAA
1 ATAAAATTAATATAAAC-T-TTGAAAA-ATTATAAAAA-ATCATAAAAA
*
106556697 ATAAATTTAATATAAACTTTGAAAAATTATAAAAAATCATAAAAA
1 ATAAAATTAATATAAACTTTGAAAAATTATAAAAAATCATAAAAA
106556742 CTTGAATTGG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
44 2 0.05
45 16 0.40
46 6 0.15
47 12 0.30
48 4 0.10
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (45 bp):
ATAAAATTAATATAAACTTTGAAAAATTATAAAAAATCATAAAAA
Found at i:106557404 original size:31 final size:30
Alignment explanation
Indices: 106557369--106557447 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 30
106557359 TTTTTATAAC
*
106557369 TTTTATAATTTGTATATAACTTATTA-GAATT
1 TTTTATAATTT-TATATAA-ATATTAGGAATT
106557400 TTTTAT-ATTATT-TATAAATATTAGGAATT
1 TTTTATAATT-TTATATAAATATTAGGAATT
106557429 TTTTATAAGTTTT-TATAAA
1 TTTTATAA-TTTTATATAAA
106557448 ATTTTAAATG
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
28 5 0.12
29 16 0.37
30 13 0.30
31 9 0.21
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.56
Consensus pattern (30 bp):
TTTTATAATTTTATATAAATATTAGGAATT
Found at i:106557406 original size:20 final size:19
Alignment explanation
Indices: 106557357--106557406 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
106557347 TTAATTTTTT
*
106557357 ATTTTTTATAACTTTTATA
1 ATTTTTTATAACTTTTAGA
*
106557376 ATTTGTATATAACTTATTAGA
1 ATTT-TTTATAACTT-TTAGA
106557397 ATTTTTTATA
1 ATTTTTTATA
106557407 TTATTTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 4 0.15
20 14 0.54
21 8 0.31
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTTTTATAACTTTTAGA
Found at i:106557528 original size:9 final size:9
Alignment explanation
Indices: 106557348--106557531 Score: 56
Period size: 9 Copynumber: 19.3 Consensus size: 9
106557338 TTAAAAATTT
106557348 TAATTTTT-
1 TAATTTTTA
*
106557356 TATTTTTTA
1 TAATTTTTA
*
106557365 TAACTTTTA
1 TAATTTTTA
106557374 TAATTTGTATA
1 TAATTT-T-TA
*
106557385 TAACTTATTA
1 TAA-TTTTTA
*
106557395 GAATTTTT-
1 TAATTTTTA
106557403 TATATTATTTA
1 TA-ATT-TTTA
* *
106557414 TAAATATTA
1 TAATTTTTA
*
106557423 GGAATTTTTTA
1 -TAA-TTTTTA
106557434 TAAGTTTTTA
1 TAA-TTTTTA
*
106557444 TAAAATTTTA
1 T-AATTTTTA
*
106557454 -AATGCATTTCA
1 TAAT---TTTTA
*
106557465 TTAA-ATTTA
1 -TAATTTTTA
*
106557474 T-ATTTTTT
1 TAATTTTTA
106557482 TACATATTATTA
1 TA-AT-TT-TTA
*
106557494 T-ATTATTA
1 TAATTTTTA
106557502 TAATTTTTA
1 TAATTTTTA
* *
106557511 TAGTATTTA
1 TAATTTTTA
106557520 TAATTTTTA
1 TAATTTTTA
106557529 TAA
1 TAA
106557532 GTGTATATTT
Statistics
Matches: 126, Mismatches: 29, Indels: 41
0.64 0.15 0.21
Matches are distributed among these distances:
7 1 0.01
8 19 0.15
9 49 0.39
10 30 0.24
11 20 0.16
12 5 0.04
13 2 0.02
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (9 bp):
TAATTTTTA
Found at i:106557572 original size:20 final size:20
Alignment explanation
Indices: 106557558--106557599 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
106557548 TTTTAATGAC
106557558 TTTTATAAGTTTTTAAAAAA
1 TTTTATAAGTTTTTAAAAAA
*
106557578 TTTTATACGTTTTTATAAAAA
1 TTTTATAAGTTTTTA-AAAAA
106557599 T
1 T
106557600 AGATTAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (20 bp):
TTTTATAAGTTTTTAAAAAA
Found at i:106559259 original size:15 final size:16
Alignment explanation
Indices: 106559239--106559283 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
106559229 ATAACAATCC
106559239 ATAATTTAAAATT-AA
1 ATAATTTAAAATTAAA
*
106559254 ATAATTTAAATTTAAA
1 ATAATTTAAAATTAAA
106559270 ATATATTTTAAAAT
1 ATA-A-TTTAAAAT
106559284 AGTAATAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 12 0.48
16 5 0.20
17 1 0.04
18 7 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATTTAAAATTAAA
Found at i:106561958 original size:24 final size:24
Alignment explanation
Indices: 106561920--106561968 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
106561910 GGTTCCCTCG
* *
106561920 GCCTCTTAGGAGAATCTGTTGGAA
1 GCCTCTCAGGAGAATCAGTTGGAA
*
106561944 GCCTCTCAGGCGAATCAGTTGGAA
1 GCCTCTCAGGAGAATCAGTTGGAA
106561968 G
1 G
106561969 TCTTTGCTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (24 bp):
GCCTCTCAGGAGAATCAGTTGGAA
Found at i:106568149 original size:26 final size:26
Alignment explanation
Indices: 106568113--106568194 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 26
106568103 AACACACCAA
*
106568113 TATCACAGCAAGGCTGCCAGTAACAG
1 TATCGCAGCAAGGCTGCCAGTAACAG
* * **
106568139 TATCGCAGCAAAGCTGTCAGTATTAG
1 TATCGCAGCAAGGCTGCCAGTAACAG
* * **
106568165 TATATGTAGCAAGGCCACCAGTAACAG
1 TAT-CGCAGCAAGGCTGCCAGTAACAG
106568192 TAT
1 TAT
106568195 ATGTGGCGAA
Statistics
Matches: 42, Mismatches: 13, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
26 24 0.57
27 18 0.43
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (26 bp):
TATCGCAGCAAGGCTGCCAGTAACAG
Found at i:106578736 original size:40 final size:40
Alignment explanation
Indices: 106578673--106578748 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
106578663 CGGTACTTTA
* * *
106578673 TGGTATGTAGGGTTGGATGGGTCGATTTTATCCCCATATT
1 TGGTATGCAGGGATGGATAGGTCGATTTTATCCCCATATT
*
106578713 TGGTATGCAGGGATGGGTAGGTCGATTTTATCCCCA
1 TGGTATGCAGGGATGGATAGGTCGATTTTATCCCCA
106578749 CGTGGTGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.18, C:0.14, G:0.32, T:0.36
Consensus pattern (40 bp):
TGGTATGCAGGGATGGATAGGTCGATTTTATCCCCATATT
Found at i:106579953 original size:18 final size:16
Alignment explanation
Indices: 106579923--106579972 Score: 73
Period size: 16 Copynumber: 3.0 Consensus size: 16
106579913 CAGTTAGGGT
106579923 GGGAAAAAGAAAAAGA
1 GGGAAAAAGAAAAAGA
*
106579939 GGGAAAATGAGAAAAAAA
1 GGGAAAA--AGAAAAAGA
106579957 GGGAAAAAGAAAAAGA
1 GGGAAAAAGAAAAAGA
106579973 AAAATGAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 15 0.50
18 15 0.50
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (16 bp):
GGGAAAAAGAAAAAGA
Found at i:106585247 original size:24 final size:24
Alignment explanation
Indices: 106585191--106585250 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
106585181 TTTTCTCACA
**
106585191 TTTTTAGTTCTTGTTTTCTTTTTAT
1 TTTTTA-TTCTTCCTTTCTTTTTAT
*
106585216 TTTCTATTCTTCCTTT-TTTTTATT
1 TTTTTATTCTTCCTTTCTTTTTA-T
106585240 TTTTTATTCTT
1 TTTTTATTCTT
106585251 TTCTGCAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 6 0.20
24 19 0.63
25 5 0.17
ACGTcount: A:0.08, C:0.12, G:0.03, T:0.77
Consensus pattern (24 bp):
TTTTTATTCTTCCTTTCTTTTTAT
Found at i:106592281 original size:19 final size:20
Alignment explanation
Indices: 106592235--106592288 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
106592225 AGATAGGGGC
*
106592235 ACATGCCCGTGTGGCTTGGG
1 ACATGCCCGTGTGGCTTGGA
*
106592255 ACACGCCC-TGTGG-TCTGGA
1 ACATGCCCGTGTGGCT-TGGA
106592274 ACATGCCCGTGTGGC
1 ACATGCCCGTGTGGC
106592289 CTGCCCATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 1 0.04
19 15 0.54
20 12 0.43
ACGTcount: A:0.13, C:0.30, G:0.35, T:0.22
Consensus pattern (20 bp):
ACATGCCCGTGTGGCTTGGA
Found at i:106593175 original size:53 final size:52
Alignment explanation
Indices: 106593043--106593252 Score: 197
Period size: 52 Copynumber: 4.1 Consensus size: 52
106593033 TTCATTATCA
* *
106593043 CACATCACACACTGAAGCCATAGCCCT-GCCATGGTCTTATACGG-ATCACATAT
1 CACATCACAC-C-GATGCCATAG-CCTAGCTATGGTCTTATACGGAATCACATAT
* * *
106593096 --CAT---ACCGATGCAATATCCTAGATATGGTCTTATACGGAATCACATTAT
1 CACATCACACCGATGCCATAGCCTAGCTATGGTCTTATACGGAATCACA-TAT
*
106593144 CACATCACACCGATGCCATAG-CTCAGCTATGGTCTTATACGAGAA-CACAAAT
1 CACATCACACCGATGCCATAGCCT-AGCTATGGTCTTATACG-GAATCACATAT
*** * *
106593196 CACATTGTACCGATGCCATAGCCTGGCTATAGTCTTATACGG-ATCACATAT
1 CACATCACACCGATGCCATAGCCTAGCTATGGTCTTATACGGAATCACATAT
106593247 CACATC
1 CACATC
106593253 TTTTTCGTCA
Statistics
Matches: 129, Mismatches: 16, Indels: 26
0.75 0.09 0.15
Matches are distributed among these distances:
45 3 0.02
46 22 0.17
47 7 0.05
48 5 0.04
50 4 0.03
51 15 0.12
52 37 0.29
53 33 0.26
54 3 0.02
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (52 bp):
CACATCACACCGATGCCATAGCCTAGCTATGGTCTTATACGGAATCACATAT
Found at i:106595542 original size:13 final size:13
Alignment explanation
Indices: 106595526--106595558 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
106595516 TTTAATTTAA
*
106595526 TTAGTTAATTAGT
1 TTAGATAATTAGT
106595539 TTAGATAATTAGT
1 TTAGATAATTAGT
106595552 TTA-ATAA
1 TTAGATAA
106595559 ACAAACCCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:106595982 original size:23 final size:24
Alignment explanation
Indices: 106595952--106596018 Score: 127
Period size: 24 Copynumber: 2.8 Consensus size: 24
106595942 TTTTCATGAT
106595952 TTTTGTTCATCTT-TAATTCCATA
1 TTTTGTTCATCTTCTAATTCCATA
106595975 TTTTGTTCATCTTCTAATTCCATA
1 TTTTGTTCATCTTCTAATTCCATA
106595999 TTTTGTTCATCTTCTAATTC
1 TTTTGTTCATCTTCTAATTC
106596019 GATTCCTACA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
23 13 0.30
24 30 0.70
ACGTcount: A:0.19, C:0.19, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTTGTTCATCTTCTAATTCCATA
Found at i:106606209 original size:130 final size:130
Alignment explanation
Indices: 106605976--106606236 Score: 522
Period size: 130 Copynumber: 2.0 Consensus size: 130
106605966 TGTGACTCAA
106605976 GTGGCGGAGGTGTGCATACAGAATACCAACCCTTCAATCCTACAACTGAAGAAGAATAAGTCAAC
1 GTGGCGGAGGTGTGCATACAGAATACCAACCCTTCAATCCTACAACTGAAGAAGAATAAGTCAAC
106606041 TATATGGGTAACAATAACTTTCGATCTCAAAATAACCCATACAGTAATACTTATAATGCAGGTTG
66 TATATGGGTAACAATAACTTTCGATCTCAAAATAACCCATACAGTAATACTTATAATGCAGGTTG
106606106 GTGGCGGAGGTGTGCATACAGAATACCAACCCTTCAATCCTACAACTGAAGAAGAATAAGTCAAC
1 GTGGCGGAGGTGTGCATACAGAATACCAACCCTTCAATCCTACAACTGAAGAAGAATAAGTCAAC
106606171 TATATGGGTAACAATAACTTTCGATCTCAAAATAACCCATACAGTAATACTTATAATGCAGGTTG
66 TATATGGGTAACAATAACTTTCGATCTCAAAATAACCCATACAGTAATACTTATAATGCAGGTTG
106606236 G
1 G
106606237 AGGAACCACC
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
130 131 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.25
Consensus pattern (130 bp):
GTGGCGGAGGTGTGCATACAGAATACCAACCCTTCAATCCTACAACTGAAGAAGAATAAGTCAAC
TATATGGGTAACAATAACTTTCGATCTCAAAATAACCCATACAGTAATACTTATAATGCAGGTTG
Found at i:106610156 original size:6 final size:6
Alignment explanation
Indices: 106610145--106610239 Score: 82
Period size: 6 Copynumber: 15.0 Consensus size: 6
106610135 TCCTCCTATC
* * *
106610145 TTTTTA TTTTTA TTTATTA TTATTA TTATTA TTATTTA TTATTTTA TTATTA
1 TTTTTA TTTTTA TTT-TTA TTTTTA TTTTTA TT-TTTA -T-TTTTA TTTTTA
* * **
106610197 TTTTTC TTTTTA TTTTTA TTTTCA TTTCAA TTTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA -TTTTTA TTTTTA
106610240 AAGACATGTC
Statistics
Matches: 73, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
6 54 0.74
7 13 0.18
8 5 0.07
9 1 0.01
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTTTA
Found at i:106610166 original size:3 final size:3
Alignment explanation
Indices: 106610148--106610198 Score: 68
Period size: 3 Copynumber: 16.7 Consensus size: 3
106610138 TCCTATCTTT
*
106610148 TTA TTT TTA TTTA TTA TTA TTA TTA TTA TTA TTTA TTA TT- TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
106610194 TTA TT
1 TTA TT
106610199 TTTCTTTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 35 0.81
4 6 0.14
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:106613168 original size:13 final size:13
Alignment explanation
Indices: 106613152--106613184 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
106613142 TTTAATTAAA
*
106613152 TTAGTTAATTAGT
1 TTAGATAATTAGT
106613165 TTAGATAATTAGT
1 TTAGATAATTAGT
106613178 TTA-ATAA
1 TTAGATAA
106613185 ACAAACCCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:106615438 original size:24 final size:24
Alignment explanation
Indices: 106615410--106615460 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
106615400 TTCAAATATG
*
106615410 AAAATTAAAAAAAGAAT-GATTAGA
1 AAAATGAAAAAAA-AATAGATTAGA
* *
106615434 AAAATGAAAATAAAATAGATTTGA
1 AAAATGAAAAAAAAATAGATTAGA
106615458 AAA
1 AAA
106615461 TAATGAGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.22
Consensus pattern (24 bp):
AAAATGAAAAAAAAATAGATTAGA
Found at i:106616667 original size:20 final size:19
Alignment explanation
Indices: 106616618--106616665 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
106616608 TAAACCTTAA
106616618 AAATAAAAATAATATAATT
1 AAATAAAAATAATATAATT
106616637 AGAATAAAAATAA-ACTAATT
1 A-AATAAAAATAATA-TAATT
106616657 AAATAAAAA
1 AAATAAAAA
106616666 ATTGGACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (19 bp):
AAATAAAAATAATATAATT
Found at i:106618481 original size:27 final size:26
Alignment explanation
Indices: 106618405--106618471 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
106618395 TTATATAATT
* **
106618405 TATTTATTTTAAAAA-ACTATACATA
1 TATTTATATTAAAAATACTATTTATA
106618430 TA-TTATTATTAAAAATACTATTTATA
1 TATTTA-TATTAAAAATACTATTTATA
106618456 TATTTATATTAAAAAT
1 TATTTATATTAAAAAT
106618472 TTTTATTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 3 0.08
25 10 0.28
26 20 0.56
27 3 0.08
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (26 bp):
TATTTATATTAAAAATACTATTTATA
Found at i:106618492 original size:27 final size:25
Alignment explanation
Indices: 106618402--106618492 Score: 73
Period size: 26 Copynumber: 3.6 Consensus size: 25
106618392 TTTTTATATA
106618402 ATTTAT-T-TATT-TTAAAAA-ACT
1 ATTTATATATATTATTAAAAATACT
**
106618423 ATACATATATTATTATTAAAAATACT
1 ATTTATATA-TATTATTAAAAATACT
* **
106618449 ATTTATATATTTATATTAAAAATTTTT
1 ATTTATATATAT-TATTAAAAA-TACT
106618476 ATTTATCATATATTATT
1 ATTTAT-ATATATTATT
106618493 TTCCTATATA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
21 4 0.07
22 1 0.02
24 4 0.07
25 9 0.17
26 19 0.35
27 12 0.22
28 5 0.09
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (25 bp):
ATTTATATATATTATTAAAAATACT
Found at i:106618558 original size:24 final size:24
Alignment explanation
Indices: 106618451--106618559 Score: 68
Period size: 24 Copynumber: 4.7 Consensus size: 24
106618441 AAAATACTAT
* *
106618451 TTATATATT-TATATTAAAAATTT-
1 TTATATATTATATATT-ATATTTTA
* * *
106618474 TTATTTATCATATA-T-TATTTTC
1 TTATATATTATATATTATATTTTA
*
106618496 CTATATATT-TATATTATATTTTA
1 TTATATATTATATATTATATTTTA
** *
106618519 TTATATAACATTTATTATATTTTTA
1 TTATATATTATATATTATA-TTTTA
*
106618544 TTGT-TATTATATATTA
1 TTATATATTATATATTA
106618560 CTTATTATAT
Statistics
Matches: 64, Mismatches: 16, Indels: 11
0.70 0.18 0.12
Matches are distributed among these distances:
21 8 0.12
22 7 0.11
23 20 0.31
24 21 0.33
25 8 0.12
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.61
Consensus pattern (24 bp):
TTATATATTATATATTATATTTTA
Found at i:106618586 original size:31 final size:29
Alignment explanation
Indices: 106618504--106618585 Score: 92
Period size: 31 Copynumber: 2.8 Consensus size: 29
106618494 TCCTATATAT
* *
106618504 TTATATTATATTTTATTATATAACATTTA
1 TTATATTATTTTTTATTATATAACACTTA
* **
106618533 TTATATTTTTATTGTTATTATATATTACTTA
1 TTATATTATT-TT-TTATTATATAACACTTA
*
106618564 TTATATTATTTTTTATTCTATA
1 TTATATTATTTTTTATTATATA
106618586 TTATGTATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 17 0.39
30 4 0.09
31 23 0.52
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (29 bp):
TTATATTATTTTTTATTATATAACACTTA
Found at i:106621880 original size:30 final size:29
Alignment explanation
Indices: 106621846--106621952 Score: 88
Period size: 30 Copynumber: 3.6 Consensus size: 29
106621836 GTAACCAAAG
*
106621846 CTATCCCTTTTCATAGTTCGACAGTCGAAA
1 CTATCCCTTTTCATAGTTCGATAGTCG-AA
** * * *
106621876 CTATCTATTTTCATTGTTCGATGGTCGTCA
1 CTATCCCTTTTCATAGTTCGATAGTCG-AA
* * * *
106621906 CCATCCCTTTTCATAATTTGATAGCCGAA
1 CTATCCCTTTTCATAGTTCGATAGTCGAA
*
106621935 GTCATCCCTTTTCATAGT
1 CT-ATCCCTTTTCATAGT
106621953 GCAATAACCG
Statistics
Matches: 57, Mismatches: 19, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 56 0.98
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.39
Consensus pattern (29 bp):
CTATCCCTTTTCATAGTTCGATAGTCGAA
Found at i:106621948 original size:60 final size:60
Alignment explanation
Indices: 106621883--106622068 Score: 173
Period size: 60 Copynumber: 3.1 Consensus size: 60
106621873 AAACTATCTA
*
106621883 TTTTCATTGTTCGATGGTCGTCACCATCCCTTTTCATAATTTGATAGCCGAAGTCATCCC
1 TTTTCATAGTTCGATGGTCGTCACCATCCCTTTTCATAATTTGATAGCCGAAGTCATCCC
* * *** * * * * * *
106621943 TTTTCATAGTGCAATAACCG-AAGCCATCCCATTTCATAATTTAATAGTCGTCA-CCATCCC
1 TTTTCATAGTTCGATGGTCGTCA-CCATCCCTTTTCATAATTTGATAGCCG-AAGTCATCCC
* * * *
106622003 TTTTCATAATAT-GATGGTCGTCACCATCTCTTTTCATGA-TTGATAGCCGAAGTTATCCC
1 TTTTCATAGT-TCGATGGTCGTCACCATCCCTTTTCATAATTTGATAGCCGAAGTCATCCC
106622062 TTTTCAT
1 TTTTCAT
106622069 TCGTCATTGA
Statistics
Matches: 94, Mismatches: 27, Indels: 11
0.71 0.20 0.08
Matches are distributed among these distances:
58 1 0.01
59 21 0.22
60 70 0.74
61 2 0.02
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.38
Consensus pattern (60 bp):
TTTTCATAGTTCGATGGTCGTCACCATCCCTTTTCATAATTTGATAGCCGAAGTCATCCC
Found at i:106622000 original size:30 final size:30
Alignment explanation
Indices: 106621899--106622039 Score: 106
Period size: 30 Copynumber: 4.7 Consensus size: 30
106621889 TTGTTCGATG
* *
106621899 GTCGTCACCATCCCTTTTCATAATTTGATA
1 GTCGTCACCATCCCTTTTCATAATATAATA
* * * * **
106621929 GCCG-AAGTCATCCCTTTTCATAGTGCAATA
1 GTCGTCA-CCATCCCTTTTCATAATATAATA
** * * *
106621959 ACCG-AAGCCATCCCATTTCATAATTTAATA
1 GTCGTCA-CCATCCCTTTTCATAATATAATA
* *
106621989 GTCGTCACCATCCCTTTTCATAATATGATG
1 GTCGTCACCATCCCTTTTCATAATATAATA
*
106622019 GTCGTCACCATCTCTTTTCAT
1 GTCGTCACCATCCCTTTTCAT
106622040 GATTGATAGC
Statistics
Matches: 88, Mismatches: 21, Indels: 4
0.78 0.19 0.04
Matches are distributed among these distances:
29 1 0.01
30 86 0.98
31 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.35
Consensus pattern (30 bp):
GTCGTCACCATCCCTTTTCATAATATAATA
Found at i:106628829 original size:33 final size:33
Alignment explanation
Indices: 106628792--106628856 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
106628782 TGACTATGAC
106628792 TCAAGTAGACATCTTTGAATGAACTATAAATAT
1 TCAAGTAGACATCTTTGAATGAACTATAAATAT
106628825 TCAAGTAGACATCTTTGAATGAACTATAAATA
1 TCAAGTAGACATCTTTGAATGAACTATAAATA
106628857 ATAGTGGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (33 bp):
TCAAGTAGACATCTTTGAATGAACTATAAATAT
Found at i:106638451 original size:46 final size:45
Alignment explanation
Indices: 106638384--106638555 Score: 177
Period size: 46 Copynumber: 3.7 Consensus size: 45
106638374 AACCCGCCCT
* *
106638384 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCAT-CA
* *
106638430 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATC-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C-ATTTGCATCA
* * * ** *
106638478 TCA-CGAACTCGAACTCAACTCAACGAGTTCGAACATTCGCATTCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCA-TCA
*
106638523 TAGGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
106638556 ATGCTCAACT
Statistics
Matches: 102, Mismatches: 17, Indels: 14
0.77 0.13 0.11
Matches are distributed among these distances:
43 4 0.04
44 3 0.03
45 1 0.01
46 58 0.57
47 26 0.25
48 3 0.03
49 2 0.02
50 5 0.05
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCATCA
Found at i:106638498 original size:93 final size:93
Alignment explanation
Indices: 106638389--106638559 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
106638379 GCCCTTAAGT
* ** * *
106638389 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
106638454 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
106638482 GAACTCGAACTCAACTCAACGAGTTCGAACATTCGCATTCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
106638547 CGAGTTCGGATGC
66 CGAGTTCGGATGC
106638560 TCAACTCAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGAACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:106638969 original size:30 final size:30
Alignment explanation
Indices: 106638935--106638994 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
106638925 ATTTAATACG
106638935 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
106638965 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
106638995 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:106639934 original size:40 final size:40
Alignment explanation
Indices: 106639873--106639948 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
106639863 CGATACTTTA
* *
106639873 TGGTGCGTAGGGTTAGATGGGTTGATTTTATCCCCATATT
1 TGGTGCGTAGGGATAGATGGGTCGATTTTATCCCCATATT
* *
106639913 TGGTGTGTAGGGATAGGTGGGTCGATTTTATCCCCA
1 TGGTGCGTAGGGATAGATGGGTCGATTTTATCCCCA
106639949 CATGGTGTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.17, C:0.13, G:0.33, T:0.37
Consensus pattern (40 bp):
TGGTGCGTAGGGATAGATGGGTCGATTTTATCCCCATATT
Found at i:106645386 original size:5 final size:5
Alignment explanation
Indices: 106645365--106645417 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
106645355 TGTTAAAATA
* *
106645365 TATAT TAAAT TATTAT TATAT TATAG TATAT TATATT ATATAT TATAT
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TATA-T -TATAT TATAT
106645413 TATAT
1 TATAT
106645418 AAATAAGTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 31 0.76
6 6 0.15
7 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:106645396 original size:10 final size:9
Alignment explanation
Indices: 106645362--106645418 Score: 59
Period size: 8 Copynumber: 6.6 Consensus size: 9
106645352 ATGTGTTAAA
106645362 ATATATATT
1 ATATATATT
*
106645371 AAAT-TATT
1 ATATATATT
106645379 AT-TATATT
1 ATATATATT
106645387 ATAGTATATT
1 ATA-TATATT
106645397 ATAT-TA-T
1 ATATATATT
106645404 ATATTATATT
1 ATA-TATATT
106645414 ATATA
1 ATATA
106645419 AATAAGTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.35
9 8 0.20
10 13 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (9 bp):
ATATATATT
Found at i:106645408 original size:12 final size:12
Alignment explanation
Indices: 106645363--106645418 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
106645353 TGTGTTAAAA
*
106645363 TATATATTAAAT
1 TATATATTATAT
106645375 TAT-TATTATATT
1 TATATATTATA-T
106645387 ATAGTATATTATAT
1 -TA-TATATTATAT
106645401 TATATATTATAT
1 TATATATTATAT
106645413 TATATA
1 TATATA
106645419 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:106646754 original size:18 final size:19
Alignment explanation
Indices: 106646733--106646771 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
106646723 ATATATAGAT
106646733 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
106646751 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
106646770 AT
1 AT
106646772 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:106647120 original size:39 final size:39
Alignment explanation
Indices: 106647010--106647144 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 39
106647000 GACCTCGAGT
* * * *
106647010 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
106647051 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
106647089 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
106647128 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
106647145 CCATATTGGT
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:106647288 original size:18 final size:19
Alignment explanation
Indices: 106647267--106647307 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
106647257 AATGAAATGA
106647267 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
106647285 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
106647304 GAAA
1 GAAA
106647308 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:106651824 original size:5 final size:5
Alignment explanation
Indices: 106651798--106651855 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
106651788 ATGTGTTAAA
* *
106651798 ATATAT ATATT AAATT ATTATT ATATT ATAGT ATATT ATATTAT ATATT
1 ATAT-T ATATT ATATT A-TATT ATATT ATATT ATATT ATA-T-T ATATT
106651847 ATATT ATAT
1 ATATT ATAT
106651856 AAATAAGTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
5 31 0.69
6 10 0.22
7 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (5 bp):
ATATT
Found at i:106651834 original size:10 final size:9
Alignment explanation
Indices: 106651799--106651856 Score: 61
Period size: 8 Copynumber: 6.7 Consensus size: 9
106651789 TGTGTTAAAA
106651799 TATATATAT
1 TATATATAT
*
106651808 TAAAT-TAT
1 TATATATAT
106651816 TAT-TATAT
1 TATATATAT
106651824 TATAGTATAT
1 TATA-TATAT
106651834 TATAT-TA-
1 TATATATAT
106651841 TATATTATAT
1 TATA-TATAT
106651851 TATATA
1 TATATA
106651857 AATAAGTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.34
9 9 0.22
10 13 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (9 bp):
TATATATAT
Found at i:106651846 original size:12 final size:12
Alignment explanation
Indices: 106651801--106651856 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
106651791 TGTTAAAATA
*
106651801 TATATATTAAAT
1 TATATATTATAT
106651813 TAT-TATTATATT
1 TATATATTATA-T
106651825 ATAGTATATTATAT
1 -TA-TATATTATAT
106651839 TATATATTATAT
1 TATATATTATAT
106651851 TATATA
1 TATATA
106651857 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:106653191 original size:18 final size:19
Alignment explanation
Indices: 106653170--106653208 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
106653160 ATATATAGAT
106653170 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
106653188 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
106653207 AT
1 AT
106653209 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:106653724 original size:18 final size:19
Alignment explanation
Indices: 106653703--106653743 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
106653693 AATGAAATGA
106653703 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
106653721 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
106653740 GAAA
1 GAAA
106653744 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:106655383 original size:17 final size:19
Alignment explanation
Indices: 106655361--106655395 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
106655351 CTAAAATATT
106655361 AACAAAA-TTA-ACAATAA
1 AACAAAAGTTATACAATAA
106655378 AACAAAAGTTATACAATA
1 AACAAAAGTTATACAATA
106655396 TCCAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (19 bp):
AACAAAAGTTATACAATAA
Found at i:106658973 original size:10 final size:9
Alignment explanation
Indices: 106658942--106658974 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
106658932 ATAGTAAAAA
106658942 ATAATAAAT
1 ATAATAAAT
106658951 A-AATAAAT
1 ATAATAAAT
106658959 ATAATCAAAT
1 ATAAT-AAAT
106658969 ATAATA
1 ATAATA
106658975 CTTTGCTCGC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.36
9 5 0.23
10 9 0.41
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (9 bp):
ATAATAAAT
Found at i:106661963 original size:2 final size:2
Alignment explanation
Indices: 106661956--106661980 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
106661946 AATCTATTTT
106661956 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
106661981 TAGATTATCG
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:106663953 original size:10 final size:10
Alignment explanation
Indices: 106663940--106663965 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
106663930 TAACAAACTC
106663940 TTTTAATTTA
1 TTTTAATTTA
106663950 TTTTAATTTA
1 TTTTAATTTA
106663960 TTTTAA
1 TTTTAA
106663966 AATTTTGGGT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTAATTTA
Found at i:106673244 original size:14 final size:16
Alignment explanation
Indices: 106673210--106673248 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
106673200 CTCTCATTCC
106673210 TCTTCTTTT-TGTTCT
1 TCTTCTTTTCTGTTCT
106673225 TC-TCTTTTCT-TT-T
1 TCTTCTTTTCTGTTCT
106673238 TCTTCTTTTCT
1 TCTTCTTTTCT
106673249 CTTTAGTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.14
14 16 0.73
15 3 0.14
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.74
Consensus pattern (16 bp):
TCTTCTTTTCTGTTCT
Found at i:106681905 original size:55 final size:55
Alignment explanation
Indices: 106681758--106681891 Score: 259
Period size: 55 Copynumber: 2.4 Consensus size: 55
106681748 CCGCCACAAG
*
106681758 ACACACCCATATGCCTTGACCGTGGTCGAATCTGACTTTGGCCACACGGCTAGCC
1 ACACACCCATGTGCCTTGACCGTGGTCGAATCTGACTTTGGCCACACGGCTAGCC
106681813 ACACACCCATGTGCCTTGACCGTGGTCGAATCTGACTTTGGCCACACGGCTAGCC
1 ACACACCCATGTGCCTTGACCGTGGTCGAATCTGACTTTGGCCACACGGCTAGCC
106681868 ACACACCCATGTGCCTTGACCGTG
1 ACACACCCATGTGCCTTGACCGTG
106681892 CTCAAGCCTG
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
55 78 1.00
ACGTcount: A:0.21, C:0.35, G:0.22, T:0.22
Consensus pattern (55 bp):
ACACACCCATGTGCCTTGACCGTGGTCGAATCTGACTTTGGCCACACGGCTAGCC
Found at i:106682960 original size:40 final size:39
Alignment explanation
Indices: 106682911--106683025 Score: 169
Period size: 40 Copynumber: 2.9 Consensus size: 39
106682901 GCTATCTCAG
*
106682911 TTCGTACACTTAGTGCCTCA-TACAGCCGAAGCTATACCAT
1 TTCGCACACTTAGTG-CT-ATTACAGCCGAAGCTATACCAT
*
106682951 TTCGCACACTTAGTGCTATTTATAGCCGAAGCTATACCAT
1 TTCGCACACTTAGTGCTA-TTACAGCCGAAGCTATACCAT
106682991 TTCGCACACTTAGTGCTATTTACAGCCGAAGCTAT
1 TTCGCACACTTAGTGCTA-TTACAGCCGAAGCTAT
106683026 TTTGAACCGC
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
38 1 0.01
39 2 0.03
40 67 0.96
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (39 bp):
TTCGCACACTTAGTGCTATTACAGCCGAAGCTATACCAT
Found at i:106686084 original size:38 final size:38
Alignment explanation
Indices: 106686009--106686085 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
106685999 TATTGCATCA
* *
106686009 AAACACATCCCAAACCGATCAACGATGCATCACTGTAG
1 AAACACATCCCAAACCGATCAACAATACATCACTGTAG
* * * *
106686047 AAACACATCCCAGATCGATCAACAATACATTATTGTAG
1 AAACACATCCCAAACCGATCAACAATACATCACTGTAG
106686085 A
1 A
106686086 TCAAAAATTC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.42, C:0.27, G:0.12, T:0.19
Consensus pattern (38 bp):
AAACACATCCCAAACCGATCAACAATACATCACTGTAG
Found at i:106691104 original size:52 final size:52
Alignment explanation
Indices: 106690957--106691105 Score: 163
Period size: 52 Copynumber: 2.8 Consensus size: 52
106690947 TTCATTTATT
* * * * * *
106690957 TGCCATATCTCAGATATAGTCTCATACGGAAGCACATAATCACATCTCACCGA
1 TGCCATAGCCCAGCTATGGTCTTATACGGAAGCACAT-ATCACATCACACCGA
* * *
106691010 TGCCATAGCCCAGCTATGATCTTATACAGAAGCATATATCACATCACACCGA
1 TGCCATAGCCCAGCTATGGTCTTATACGGAAGCACATATCACATCACACCGA
* * * * *
106691062 TTCCATAGTCTAGCTATGGTCTTATACGGAAACACATGTCACAT
1 TGCCATAGCCCAGCTATGGTCTTATACGGAAGCACATATCACAT
106691106 ATTGCCAAGG
Statistics
Matches: 79, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
52 50 0.63
53 29 0.37
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.26
Consensus pattern (52 bp):
TGCCATAGCCCAGCTATGGTCTTATACGGAAGCACATATCACATCACACCGA
Found at i:106693863 original size:3 final size:3
Alignment explanation
Indices: 106693857--106693897 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
106693847 GTTGTTTATA
*
106693857 TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
106693898 TTTTGCAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:106699612 original size:17 final size:17
Alignment explanation
Indices: 106699573--106699613 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
106699563 ATGAAATGTT
* *
106699573 AATAATTTAAATTTTAA
1 AATATTTTAAATTTGAA
106699590 AATATTTTAAATTTGAA
1 AATATTTTAAATTTGAA
*
106699607 ATTATTT
1 AATATTT
106699614 AATTAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
AATATTTTAAATTTGAA
Found at i:106699722 original size:32 final size:31
Alignment explanation
Indices: 106699686--106699781 Score: 93
Period size: 32 Copynumber: 3.0 Consensus size: 31
106699676 TGATTATAAT
*
106699686 TTAAATTAAATCAAATTTAAAATAATTTAAAC
1 TTAAAATAAA-CAAATTTAAAATAATTTAAAC
* * * *
106699718 TTAAAATAACCAAAATCTAAAATAATTAAAAT
1 TTAAAATAAAC-AAATTTAAAATAATTTAAAC
* *
106699750 TTAAAGCTAACACAAATTTAAAATATTTTAAA
1 TTAAA-ATAA-ACAAATTTAAAATAATTTAAA
106699782 ATTTTTAAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
31 1 0.02
32 30 0.59
33 19 0.37
34 1 0.02
ACGTcount: A:0.57, C:0.08, G:0.01, T:0.33
Consensus pattern (31 bp):
TTAAAATAAACAAATTTAAAATAATTTAAAC
Found at i:106699748 original size:16 final size:16
Alignment explanation
Indices: 106699698--106699754 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
106699688 AAATTAAATC
* *
106699698 AAATTTAAAATAATTT
1 AAATCTAAAATAATTA
**
106699714 AAA-CTTAAAATAACCA
1 AAATC-TAAAATAATTA
106699730 AAATCTAAAATAATTA
1 AAATCTAAAATAATTA
*
106699746 AAATTTAAA
1 AAATCTAAA
106699755 GCTAACACAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
16 31 0.97
17 1 0.03
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATCTAAAATAATTA
Found at i:106707335 original size:16 final size:17
Alignment explanation
Indices: 106707311--106707343 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
106707301 TTAAAAATTA
106707311 AAATATTATAT-TATTG
1 AAATATTATATATATTG
*
106707327 AAATGTTATATATATTG
1 AAATATTATATATATTG
106707344 TGTTATTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (17 bp):
AAATATTATATATATTG
Found at i:106710178 original size:6 final size:6
Alignment explanation
Indices: 106710167--106710193 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
106710157 CTTATATACA
106710167 CTCCCT CTCCCT CTCCCT CTCCCT CTC
1 CTCCCT CTCCCT CTCCCT CTCCCT CTC
106710194 ACCACTCTTC
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:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCCCT
Found at i:106711245 original size:2 final size:2
Alignment explanation
Indices: 106711240--106711265 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
106711230 AAAAAAAAAA
106711240 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
106711266 TTAAGGTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:106715308 original size:2 final size:2
Alignment explanation
Indices: 106715301--106715333 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
106715291 GTGGTTATTT
106715301 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 T
106715334 GATCAGTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:106719814 original size:17 final size:16
Alignment explanation
Indices: 106719788--106719822 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
106719778 TCAATTAACC
*
106719788 AATCAACTTAAATCTT
1 AATCAACTTAAACCTT
106719804 AATCAAACTTAAACCTT
1 AATC-AACTTAAACCTT
106719821 AA
1 AA
106719823 CTGATTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (16 bp):
AATCAACTTAAACCTT
Found at i:106731991 original size:30 final size:28
Alignment explanation
Indices: 106731945--106732000 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
106731935 ATTTTACCAA
*
106731945 TTTTTTTTAAAAAAAATTCATATAAACT
1 TTTTTTTTAAAAAAAATGCATATAAACT
*
106731973 TTTTTTTTAAAAGTAAAATGCTTATAAA
1 TTTTTTTTAAAA--AAAATGCATATAAA
106732001 ATATAGAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 12 0.50
30 12 0.50
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (28 bp):
TTTTTTTTAAAAAAAATGCATATAAACT
Found at i:106734372 original size:13 final size:13
Alignment explanation
Indices: 106734354--106734378 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
106734344 AATTTTTTTA
106734354 TTTTTAATTAATC
1 TTTTTAATTAATC
106734367 TTTTTAATTAAT
1 TTTTTAATTAAT
106734379 AACTCTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATC
Found at i:106739584 original size:17 final size:18
Alignment explanation
Indices: 106739547--106739585 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
106739537 AAAATTTTAA
* *
106739547 ATTAATTTATATTGTTGC
1 ATTAAATTATATTGGTGC
106739565 ATTAAATTAT-TTGGTGC
1 ATTAAATTATATTGGTGC
106739582 ATTA
1 ATTA
106739586 CCATTTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.51
Consensus pattern (18 bp):
ATTAAATTATATTGGTGC
Found at i:106739637 original size:25 final size:24
Alignment explanation
Indices: 106739594--106739659 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 24
106739584 TACCATTTAT
106739594 TTTAAAAATAATTTATATTTATTA
1 TTTAAAAATAATTTATATTTATTA
*
106739618 TTTAAAATATATATTT-TATTTATCA
1 TTTAAAA-ATA-ATTTATATTTATTA
*
106739643 TTATATTAAATAATTTA
1 TT-TA-AAAATAATTTA
106739660 AAATCTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
24 7 0.20
25 17 0.49
26 9 0.26
27 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTAAAAATAATTTATATTTATTA
Found at i:106740028 original size:32 final size:32
Alignment explanation
Indices: 106739992--106740054 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
106739982 AATTCAGACA
*
106739992 AATTTAAACACAAAACAATATAAACCTAAATT
1 AATTTAAACACAAAACAATATAAACCCAAATT
* * *
106740024 AATTTGAACTCAAAACAATTTAAACCCAAAT
1 AATTTAAACACAAAACAATATAAACCCAAAT
106740055 CATCAAACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.56, C:0.17, G:0.02, T:0.25
Consensus pattern (32 bp):
AATTTAAACACAAAACAATATAAACCCAAATT
Found at i:106740053 original size:16 final size:16
Alignment explanation
Indices: 106739992--106740053 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 16
106739982 AATTCAGACA
*
106739992 AATTTAAACACAAAAC
1 AATTTAAACCCAAAAC
* * **
106740008 AATATAAACCTAAATT
1 AATTTAAACCCAAAAC
* *
106740024 AATTTGAACTCAAAAC
1 AATTTAAACCCAAAAC
106740040 AATTTAAACCCAAA
1 AATTTAAACCCAAA
106740054 TCATCAAACT
Statistics
Matches: 33, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.56, C:0.18, G:0.02, T:0.24
Consensus pattern (16 bp):
AATTTAAACCCAAAAC
Found at i:106744059 original size:22 final size:22
Alignment explanation
Indices: 106744031--106744076 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
106744021 TTCTAGGCTT
106744031 AAGCTTTGTCCAAAAATGACCA
1 AAGCTTTGTCCAAAAATGACCA
106744053 AAGCTTTGTCCAAAAATGACCA
1 AAGCTTTGTCCAAAAATGACCA
106744075 AA
1 AA
106744077 AATGAGCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.22, G:0.13, T:0.22
Consensus pattern (22 bp):
AAGCTTTGTCCAAAAATGACCA
Found at i:106747977 original size:2 final size:2
Alignment explanation
Indices: 106747970--106748006 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
106747960 TAATATACAT
106747970 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
106748007 AAAGTACAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:106751767 original size:6 final size:6
Alignment explanation
Indices: 106751756--106751784 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
106751746 GGAATACACC
106751756 GTAACA GTAACA GTAACA GTAACA GTAAC
1 GTAACA GTAACA GTAACA GTAACA GTAAC
106751785 GATACACAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
GTAACA
Found at i:106760028 original size:15 final size:16
Alignment explanation
Indices: 106760003--106760032 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
106759993 AATATGTGAA
106760003 TATATTATACTAAAAT
1 TATATTATACTAAAAT
106760019 TATA-TATACTAAAA
1 TATATTATACTAAAA
106760033 CCATGTTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
TATATTATACTAAAAT
Found at i:106760394 original size:9 final size:8
Alignment explanation
Indices: 106760365--106760394 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
106760355 TATCGTTATT
106760365 AAAATTTC
1 AAAATTTC
106760373 AAAATTTC
1 AAAATTTC
106760381 AAAATTTGC
1 AAAATTT-C
106760390 AAAAT
1 AAAAT
106760395 ACAACTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 15 0.71
9 6 0.29
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.33
Consensus pattern (8 bp):
AAAATTTC
Found at i:106771055 original size:3 final size:3
Alignment explanation
Indices: 106771047--106771090 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
106771037 GGAATTTGAA
106771047 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
106771091 AGATGACGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:106772075 original size:26 final size:27
Alignment explanation
Indices: 106772021--106772077 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
106772011 GCCTGCTGGA
* *
106772021 GCTGGGTTCAACCATGGTGTTGCTCCT
1 GCTGGGTTCAACCATGGAGTGGCTCCT
* *
106772048 GCTGGGTT-AACCCTGGAGTGGCTGCT
1 GCTGGGTTCAACCATGGAGTGGCTCCT
106772074 GCTG
1 GCTG
106772078 CTGCACCGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.11, C:0.25, G:0.35, T:0.30
Consensus pattern (27 bp):
GCTGGGTTCAACCATGGAGTGGCTCCT
Found at i:106784866 original size:13 final size:13
Alignment explanation
Indices: 106784848--106784872 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
106784838 CCCCCCAAAA
106784848 AAAAAAAAAAACC
1 AAAAAAAAAAACC
106784861 AAAAAAAAAAAC
1 AAAAAAAAAAAC
106784873 GTTGTAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAACC
Found at i:106787287 original size:30 final size:30
Alignment explanation
Indices: 106787229--106787293 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
106787219 CATAAATTTC
* *
106787229 AAATTTAATCTCCCTACTTTTATTTTTTAA
1 AAATTTAATCACCCTACTTTTATATTTTAA
* *
106787259 GAATTTAATCACTCTACTTTTCA-ATTTTAA
1 AAATTTAATCACCCTACTTTT-ATATTTTAA
106787289 AAATT
1 AAATT
106787294 CAAGTCTAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.34, C:0.15, G:0.02, T:0.49
Consensus pattern (30 bp):
AAATTTAATCACCCTACTTTTATATTTTAA
Found at i:106787821 original size:14 final size:14
Alignment explanation
Indices: 106787802--106787833 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
106787792 CAATTTATTT
106787802 TAAAAATTAAATTA
1 TAAAAATTAAATTA
*
106787816 TAAAAATTAAATTT
1 TAAAAATTAAATTA
106787830 TAAA
1 TAAA
106787834 TTTAAGCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAAAATTAAATTA
Found at i:106792325 original size:35 final size:35
Alignment explanation
Indices: 106792279--106792349 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
106792269 TTTAGGATCA
* * *
106792279 CATATCTTTGAAGATCCCCTTCCATATTTGCCAAG
1 CATATATTTGAAGATCACCTTCCATATTTACCAAG
* *
106792314 CATATATTTGAAGATCACTTTTCATATTTACCAAG
1 CATATATTTGAAGATCACCTTCCATATTTACCAAG
106792349 C
1 C
106792350 TCTAGAGATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.37
Consensus pattern (35 bp):
CATATATTTGAAGATCACCTTCCATATTTACCAAG
Found at i:106796873 original size:48 final size:49
Alignment explanation
Indices: 106796802--106796926 Score: 159
Period size: 48 Copynumber: 2.6 Consensus size: 49
106796792 TTAGGGAATT
* * *
106796802 CATTGATTTTGCTCCGG-GCCATGATATCGGCACTTCAGG-TGCTAGTTA
1 CATTGATTTGGCTTCGGAGCCATGATATCGGCACTTC-GGATGCGAGTTA
106796850 CATTGATTTGGCTTCGGAG-CATGATATCGGCACTTCGGATGCGAGTTA
1 CATTGATTTGGCTTCGGAGCCATGATATCGGCACTTCGGATGCGAGTTA
* * *
106796898 TATTGATTTGGTTTC-GAGCCATGTTATCG
1 CATTGATTTGGCTTCGGAGCCATGATATCG
106796927 AAACTTAAAG
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
47 5 0.07
48 62 0.91
49 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.35
Consensus pattern (49 bp):
CATTGATTTGGCTTCGGAGCCATGATATCGGCACTTCGGATGCGAGTTA
Found at i:106799653 original size:22 final size:24
Alignment explanation
Indices: 106799623--106799666 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
106799613 CTATCTAGAT
106799623 ATCAAATC-TCT-AAGATTACAGA
1 ATCAAATCTTCTAAAGATTACAGA
*
106799645 ATCATATCTTCTAAAGATTACA
1 ATCAAATCTTCTAAAGATTACA
106799667 TTTAATGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 3 0.16
24 9 0.47
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (24 bp):
ATCAAATCTTCTAAAGATTACAGA
Found at i:106799742 original size:35 final size:35
Alignment explanation
Indices: 106799684--106799754 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
106799674 CCTAGGATCA
* *
106799684 CATATATTTGAAGATACCCTTCCATGTTTGCCAAG
1 CATATATTTGAAGATACCCTTCCATATTTCCCAAG
*
106799719 CATATATTTGAAGAT-CACTTTCCATATTTCCCAAG
1 CATATATTTGAAGATAC-CCTTCCATATTTCCCAAG
106799754 C
1 C
106799755 TCCGAAGGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 1 0.03
35 31 0.97
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (35 bp):
CATATATTTGAAGATACCCTTCCATATTTCCCAAG
Found at i:106805921 original size:2 final size:2
Alignment explanation
Indices: 106805910--106805943 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
106805900 AATCAACCAT
106805910 TA TA -A 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
106805944 CCTGAATCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:106806474 original size:57 final size:55
Alignment explanation
Indices: 106806394--106806540 Score: 154
Period size: 57 Copynumber: 2.6 Consensus size: 55
106806384 AACTTCACAC
* *
106806394 TTTTCTTAATTTGGTAT-TTAGTTTTTTTTTTTAATTTAGTACT-TGAATTTGATACAT
1 TTTTC-TAATTTGGTATCTAAGTTTTTTTTTTTAATTTAATA-TATGAATTTGA-A-AT
* **
106806451 TTTTCTAATTTGGTATCTAAGTTTTCTTTGTCCAATTTAATATATGAATTTGAAAT
1 TTTTCTAATTTGGTATCTAAGTTTT-TTTTTTTAATTTAATATATGAATTTGAAAT
* *
106806507 TTTTCCTAATTTGATACCTAAGGTTTTTTTTTTT
1 TTTT-CTAATTTGGTATCTAA-GTTTTTTTTTTT
106806541 TGTGTGTGTT
Statistics
Matches: 75, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
56 17 0.23
57 32 0.43
58 26 0.35
ACGTcount: A:0.24, C:0.08, G:0.10, T:0.58
Consensus pattern (55 bp):
TTTTCTAATTTGGTATCTAAGTTTTTTTTTTTAATTTAATATATGAATTTGAAAT
Found at i:106808433 original size:46 final size:44
Alignment explanation
Indices: 106808374--106808488 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
106808364 ACAGGACAGA
* *
106808374 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
106808420 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
106808464 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
106808489 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:106808469 original size:44 final size:45
Alignment explanation
Indices: 106808374--106808507 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
106808364 ACAGGACAGA
* *
106808374 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
106808420 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
106808464 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
106808508 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:106811945 original size:19 final size:19
Alignment explanation
Indices: 106811905--106811951 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
106811895 ATTTTATTTT
* *
106811905 ATTTTTTAAATTTTTATGA
1 ATTTTTTTAATTTTTATAA
106811924 ATTTTTTTAATATTTTA-AA
1 ATTTTTTTAAT-TTTTATAA
*
106811943 ATTTATTTA
1 ATTTTTTTA
106811952 TTTATTGACG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTTTTTTAATTTTTATAA
Found at i:106812831 original size:17 final size:19
Alignment explanation
Indices: 106812797--106812845 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
106812787 GTCCACGTGT
*
106812797 ATATTATAAAAATTTTAAA
1 ATATTATAAAAATCTTAAA
106812816 ATATTA-AAAAA-CTTAAA
1 ATATTATAAAAATCTTAAA
*
106812833 AAATTCATAAAAA
1 ATATT-ATAAAAA
106812846 AAAGTTAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 9 0.35
18 6 0.23
19 11 0.42
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
ATATTATAAAAATCTTAAA
Found at i:106813022 original size:24 final size:22
Alignment explanation
Indices: 106812970--106813022 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 22
106812960 GGATAAACAT
*
106812970 TAAAAAGCTAAAATTTTTAAAT
1 TAAAAAGCTAAAATTTTTAAAA
106812992 TAGAAAAGGACTAAAA-TTTTAGAAA
1 TA-AAAA-G-CTAAAATTTTTA-AAA
106813017 TAAAAA
1 TAAAAA
106813023 TAGAAAGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 2 0.08
23 4 0.15
24 10 0.38
25 10 0.38
ACGTcount: A:0.58, C:0.04, G:0.09, T:0.28
Consensus pattern (22 bp):
TAAAAAGCTAAAATTTTTAAAA
Found at i:106813236 original size:2 final size:2
Alignment explanation
Indices: 106813229--106813258 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
106813219 TAAACAATAA
*
106813229 CT CT CT CT CT CT CT TT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
106813259 ACACTAGTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:106813315 original size:2 final size:2
Alignment explanation
Indices: 106813308--106813336 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
106813298 GGGATAATAT
106813308 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
106813337 GAAATTCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Done.