Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008505.1 Corchorus capsularis cultivar CVL-1 contig08526, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 68197
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:786 original size:21 final size:18
Alignment explanation
Indices: 761--801 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
751 GCTTGAAGAC
761 CATTGAAGATCAATTGGAGAG
1 CATTGAAG-TC-ATTGGA-AG
782 CATTGAAGTCATTGGAAG
1 CATTGAAGTCATTGGAAG
800 CA
1 CA
802 AGAATATTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 6 0.30
20 2 0.10
21 8 0.40
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (18 bp):
CATTGAAGTCATTGGAAG
Found at i:6311 original size:2 final size:2
Alignment explanation
Indices: 6299--6340 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
6289 ATAGTCCATC
6299 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6340 A
1 A
6341 ATCAACAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7719 original size:21 final size:20
Alignment explanation
Indices: 7673--7721 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
7663 CCATACAAAA
7673 TCAACTTCCTCAAAATCATT
1 TCAACTTCCTCAAAATCATT
* *
7693 TGAACTTACCTC-AAATTATTT
1 TCAACTT-CCTCAAAATCA-TT
7714 TCAACTTC
1 TCAACTTC
7722 AAACTTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.33, C:0.27, G:0.02, T:0.39
Consensus pattern (20 bp):
TCAACTTCCTCAAAATCATT
Found at i:14077 original size:54 final size:54
Alignment explanation
Indices: 14010--14118 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
14000 CATCTCTTTG
14010 ACAATCTGAGTGCTTTTGCATTTAGATATTATTTCAATCATCATTACTATTCTC
1 ACAATCTGAGTGCTTTTGCATTTAGATATTATTTCAATCATCATTACTATTCTC
*
14064 ACAATCTGAGTGCTTTTGCATTTAGATATTATTTCAATCATCATTACTGTTCTC
1 ACAATCTGAGTGCTTTTGCATTTAGATATTATTTCAATCATCATTACTATTCTC
14118 A
1 A
14119 TCAAAAGGTT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.44
Consensus pattern (54 bp):
ACAATCTGAGTGCTTTTGCATTTAGATATTATTTCAATCATCATTACTATTCTC
Found at i:15753 original size:27 final size:29
Alignment explanation
Indices: 15683--15758 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 29
15673 TAGCAACAGT
15683 CAACAATGAGAATATATTTTGAAACTCAAAAG
1 CAACAATGAGAATATATTTTGAAACT---AAG
15715 TCAACAATGAGAATATATTTTGAAACT-A-
1 -CAACAATGAGAATATATTTTGAAACTAAG
*
15743 CAACATTGAGAATATA
1 CAACAATGAGAATATA
15759 ACAAAAGATT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
27 15 0.36
29 1 0.02
33 26 0.62
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.28
Consensus pattern (29 bp):
CAACAATGAGAATATATTTTGAAACTAAG
Found at i:18357 original size:90 final size:90
Alignment explanation
Indices: 18257--18429 Score: 244
Period size: 90 Copynumber: 1.9 Consensus size: 90
18247 CATTGTTTAA
* *
18257 ACTTTTATAGTTTTAG-TCAATTAAAAACTCT-TTATTTATTTAATTAAATCTAGTATCCTTATA
1 ACTTTTATAGTTTT-GCTCAACTAAAAACTCTATT-TTTATTTAATTAAATCTAATATCCTTATA
18320 ACTATTTT-ATTTCTACCATACTGTTTT
64 ACTATTTTAATTT-TACCATACTGTTTT
* * * *
18347 ACTTTTATAGTTTTGCTTAGCTAAAAACTCTATTTTTATTTGATTAAATCTAATATCCTTATACC
1 ACTTTTATAGTTTTGCTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
18412 TATTTTAATTTTACCATA
66 TATTTTAATTTTACCATA
18430 TTACTAATTT
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
89 1 0.01
90 67 0.91
91 6 0.08
ACGTcount: A:0.31, C:0.14, G:0.05, T:0.50
Consensus pattern (90 bp):
ACTTTTATAGTTTTGCTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAC
TATTTTAATTTTACCATACTGTTTT
Found at i:23063 original size:105 final size:105
Alignment explanation
Indices: 22876--23136 Score: 393
Period size: 106 Copynumber: 2.5 Consensus size: 105
22866 AATTTTTCTA
**
22876 ACCCTTAAAATAAAATCTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTAGTTATATATTTTA
1 ACCCTTAAAATAAAAT-AAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
* *
22939 TTTCTAAAACCCTATAACAAT-ATTATTAATTATGGAATTT
65 TTTCTAAAACCCTACAACAATAATTATTAATTATGAAATTT
* *
22979 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAAT-AAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
* *
23044 TTTTTAAAACCCTACAACAATAAATTATTAATTTTGAAATTT
65 TTTCTAAAACCCTACAACAAT-AATTATTAATTATGAAATTT
*
23086 ACCCTTAAAATAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTA
1 ACCCTTAAAATAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
23137 AAGTTAAAAT
Statistics
Matches: 144, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
103 22 0.15
104 20 0.14
105 35 0.24
106 39 0.27
107 28 0.19
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.40
Consensus pattern (105 bp):
ACCCTTAAAATAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTAT
TTCTAAAACCCTACAACAATAATTATTAATTATGAAATTT
Found at i:23132 original size:106 final size:103
Alignment explanation
Indices: 22876--23136 Score: 389
Period size: 105 Copynumber: 2.5 Consensus size: 103
22866 AATTTTTCTA
**
22876 ACCCTTAAAATAAAATCTTAATTTTAATTTGGGCTAAACTTAGTG-AATTAGTTATATATTTTAT
1 ACCCTTAAAATAAAAT-AAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTATATATTTTAT
* *
22940 TTCTAAAACCCTATAACAATATTATTAATTATGGAATTT
65 TTCTAAAACCCTACAACAATATTATTAATTATGAAATTT
* *
22979 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAAT-AAAATAAAATTTTAATTT-GGGCTAAACTTAGTGAAATTAGTTATATATTTTA
* *
23044 TTTTTAAAACCCTACAACAATAAATTATTAATTTTGAAATTT
64 TTTCTAAAACCCTACAACAAT--ATTATTAATTATGAAATTT
23086 ACCCTTAAAATAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTA
1 ACCCTTAAAATAAAATAAAATTTTAATTTGGG-CTAAACTTAGTGAAATTA
23137 AAGTTAAAAT
Statistics
Matches: 144, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
103 22 0.15
104 20 0.14
105 38 0.26
106 36 0.25
107 28 0.19
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.40
Consensus pattern (103 bp):
ACCCTTAAAATAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTATATATTTTATT
TCTAAAACCCTACAACAATATTATTAATTATGAAATTT
Found at i:30494 original size:21 final size:21
Alignment explanation
Indices: 30470--30536 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
30460 TTTTATTGAA
30470 TTACTGATTACCATTACTATT
1 TTACTGATTACCATTACTATT
* *
30491 TTACTGATTATTCTTTACT-TT
1 TTACTGATTA-CCATTACTATT
* * *
30512 GTACTGATTACTACTTACCATT
1 TTACTGATTACCA-TTACTATT
30534 TTA
1 TTA
30537 TTCTTTGCTG
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
21 25 0.71
22 10 0.29
ACGTcount: A:0.25, C:0.18, G:0.06, T:0.51
Consensus pattern (21 bp):
TTACTGATTACCATTACTATT
Found at i:30615 original size:35 final size:34
Alignment explanation
Indices: 30576--30675 Score: 107
Period size: 35 Copynumber: 2.9 Consensus size: 34
30566 GATTAATATT
30576 TTACTCTTTACCATTTTTCTTTACTGGATTACTCC
1 TTACTCTTTACCATTTTTCTTTACTGGATTACT-C
* * *
30611 TTACTCTTCT-TCATTCTTCTTTACTGGCTT-CTC
1 TTACTCTT-TACCATTTTTCTTTACTGGATTACTC
* *
30644 TTCACTCTTTACCATTTTCCTTTGCT-GATTAC
1 TT-ACTCTTTACCATTTTTCTTTACTGGATTAC
30676 CATTTCCTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
33 7 0.13
34 20 0.38
35 25 0.47
36 1 0.02
ACGTcount: A:0.14, C:0.28, G:0.06, T:0.52
Consensus pattern (34 bp):
TTACTCTTTACCATTTTTCTTTACTGGATTACTC
Found at i:30683 original size:19 final size:20
Alignment explanation
Indices: 30652--30694 Score: 79
Period size: 19 Copynumber: 2.2 Consensus size: 20
30642 TCTTCACTCT
30652 TTACCATTTTCCTTTGCTGA
1 TTACCATTTTCCTTTGCTGA
30672 TTACCA-TTTCCTTTGCTGA
1 TTACCATTTTCCTTTGCTGA
30691 TTAC
1 TTAC
30695 TCTTTACTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.16, C:0.26, G:0.09, T:0.49
Consensus pattern (20 bp):
TTACCATTTTCCTTTGCTGA
Found at i:30703 original size:7 final size:7
Alignment explanation
Indices: 30691--30742 Score: 61
Period size: 7 Copynumber: 7.6 Consensus size: 7
30681 CCTTTGCTGA
30691 TTACTCT
1 TTACTCT
30698 TTACTCT
1 TTACTCT
30705 TTACTCT
1 TTACTCT
30712 TT-CTCT
1 TTACTCT
**
30718 TTACTGA
1 TTACTCT
*
30725 TTACTTT
1 TTACTCT
*
30732 TTGCTCT
1 TTACTCT
30739 TTAC
1 TTAC
30743 GATTTTTTTC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
6 6 0.16
7 31 0.84
ACGTcount: A:0.13, C:0.25, G:0.04, T:0.58
Consensus pattern (7 bp):
TTACTCT
Found at i:30739 original size:34 final size:34
Alignment explanation
Indices: 30678--30805 Score: 107
Period size: 34 Copynumber: 3.5 Consensus size: 34
30668 CTGATTACCA
* * *
30678 TTTC-CTTTGCTGATTACTCTTTACTCTTTACTC
1 TTTCTCTTTACTGATTACTTTTTGCTCTTTACTC
*
30711 TTTCTCTTTACTGATTACTTTTTGCTCTTTACGATT
1 TTTCTCTTTACTGATTACTTTTTGCTCTTTAC--TC
*
30747 TTTTTCTTTACTGATTACCATTTCCTTTGCT-TGATTACTC
1 TTTCTCTTTACTGATTA-C--TT--TTTGCTCT--TTACTC
30787 TTTACTCTTTACTGATTAC
1 TTT-CTCTTTACTGATTAC
30806 CATTTTACTC
Statistics
Matches: 77, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
33 4 0.05
34 24 0.31
36 17 0.22
37 1 0.01
39 2 0.03
40 6 0.08
41 19 0.25
42 4 0.05
ACGTcount: A:0.15, C:0.23, G:0.07, T:0.55
Consensus pattern (34 bp):
TTTCTCTTTACTGATTACTTTTTGCTCTTTACTC
Found at i:30746 original size:20 final size:20
Alignment explanation
Indices: 30694--30916 Score: 117
Period size: 20 Copynumber: 11.0 Consensus size: 20
30684 TTGCTGATTA
**
30694 CTCTTTACTCTTTACTCTTT
1 CTCTTTACTGATTACTCTTT
*
30714 CTCTTTACTGATTACTTTTT
1 CTCTTTACTGATTACTCTTT
30734 GCTCTTTAC-GATT--T-TTT
1 -CTCTTTACTGATTACTCTTT
30751 -TCTTTACTGATTAC-CATTT
1 CTCTTTACTGATTACTC-TTT
*
30770 C-CTTTGCTTGATTACTCTTT
1 CTCTTTAC-TGATTACTCTTT
30790 ACTCTTTACTGATTAC-CATTTT
1 -CTCTTTACTGATTACTC--TTT
* * *
30812 ACTCTTTTCTAATTACTATTTT
1 -CTCTTTACTGATTACT-CTTT
* * *
30834 AGTTTTTACTGATTACCTTTTT
1 -CTCTTTACTGATTA-CTCTTT
* *
30856 ACTTTTTACTGATTAC-CATTG
1 -CTCTTTACTGATTACTC-TTT
* *
30877 CT-TCTTACTGATTACTATTA
1 CTCT-TTACTGATTACTCTTT
30897 CT-TTCTACTGATTACTCTTT
1 CTCTT-TACTGATTACTCTTT
30917 TAATTTTTAC
Statistics
Matches: 164, Mismatches: 19, Indels: 40
0.74 0.09 0.18
Matches are distributed among these distances:
15 7 0.04
16 4 0.02
17 3 0.02
18 1 0.01
19 10 0.06
20 63 0.38
21 20 0.12
22 54 0.33
23 2 0.01
ACGTcount: A:0.18, C:0.21, G:0.06, T:0.55
Consensus pattern (20 bp):
CTCTTTACTGATTACTCTTT
Found at i:30812 original size:22 final size:22
Alignment explanation
Indices: 30751--30991 Score: 168
Period size: 22 Copynumber: 11.3 Consensus size: 22
30741 ACGATTTTTT
30751 TCTTTACTGATTACCA-TTT-C
1 TCTTTACTGATTACCATTTTAC
*
30771 -CTTTGCTTGATTA-C-TCTTTAC
1 TCTTTAC-TGATTACCAT-TTTAC
30792 TCTTTACTGATTACCATTTTAC
1 TCTTTACTGATTACCATTTTAC
* * * *
30814 TCTTTTCTAATTACTATTTTAG
1 TCTTTACTGATTACCATTTTAC
* *
30836 TTTTTACTGATTACCTTTTTAC
1 TCTTTACTGATTACCATTTTAC
* *
30858 TTTTTACTGATTACCA--TTGC
1 TCTTTACTGATTACCATTTTAC
*
30878 T-TCTTACTGATTA-C-TATTAC
1 TCT-TTACTGATTACCATTTTAC
*
30898 T-TTCTACTGATTACTC-TTTTAA
1 TCTT-TACTGATTAC-CATTTTAC
*
30920 TTTTTACTGATTACCATTTTAC
1 TCTTTACTGATTACCATTTTAC
* * *
30942 TTTTTGA-TAATTGCCATTTTAC
1 TCTTT-ACTGATTACCATTTTAC
* *
30964 CCTTTACTAATTACC-TTTTAC
1 TCTTTACTGATTACCATTTTAC
*
30985 TTTTTAC
1 TCTTTAC
30992 CATTTTACCT
Statistics
Matches: 179, Mismatches: 25, Indels: 33
0.76 0.11 0.14
Matches are distributed among these distances:
19 9 0.05
20 37 0.21
21 20 0.11
22 109 0.61
23 4 0.02
ACGTcount: A:0.21, C:0.20, G:0.05, T:0.54
Consensus pattern (22 bp):
TCTTTACTGATTACCATTTTAC
Found at i:30924 original size:62 final size:64
Alignment explanation
Indices: 30751--30937 Score: 190
Period size: 62 Copynumber: 3.0 Consensus size: 64
30741 ACGATTTTTT
* * * * *
30751 TCTTTACTGATTACCATTTCCTTTGCT--TGATTACTC-TTTACTCTTTACTGATTACCATTTTA
1 TCTTTACTAATTACTATTTACTTT-CTACTGATTACTCTTTTACTTTTTACTGATTACCATTCTA
* * *
30813 CTCTTTTCTAATTACTATTTTAGTTTTTACTGATTAC-CTTTTTACTTTTTACTGATTACCATTG
1 -TCTTTACTAATTACTA-TTTACTTTCTACTGATTACTC-TTTTACTTTTTACTGATTACCATT-
30877 CT-
62 CTA
* *
30879 TC-TTACTGATTACTA-TTACTTTCTACTGATTACTCTTTTAATTTTTACTGATTACCATT
1 TCTTTACTAATTACTATTTACTTTCTACTGATTACTCTTTTACTTTTTACTGATTACCATT
30938 TTACTTTTTG
Statistics
Matches: 104, Mismatches: 13, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
62 39 0.38
63 15 0.14
64 18 0.17
65 9 0.09
66 22 0.21
67 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.06, T:0.53
Consensus pattern (64 bp):
TCTTTACTAATTACTATTTACTTTCTACTGATTACTCTTTTACTTTTTACTGATTACCATTCTA
Found at i:30962 original size:106 final size:107
Alignment explanation
Indices: 30752--30978 Score: 241
Period size: 106 Copynumber: 2.1 Consensus size: 107
30742 CGATTTTTTT
* * * *
30752 CTTTACTGATTACCATTTCCTTTGCTTGATTACTCTTTACTCTTTACTGATTACCATTTTACTCT
1 CTTTACTGATTACCATTGCCTTTACTTGATTACTCATTACTCTTTACTGATTACCATTTTAATCT
* * * * *
30817 TTTCTAATTACTATTTTAGTTTTTACTGATTACCTTTTTACT
66 TTTCTAATTACCATTTTACTTTTTACTAATTACCATTTTACC
* *
30859 TTTTACTGATTACCATTGCTTCTTAC-TGATTACT-ATTACT-TTCTACTGATTACTC-TTTTAA
1 CTTTACTGATTACCATTGCCT-TTACTTGATTACTCATTACTCTT-TACTGATTAC-CATTTTAA
* *
30920 T-TTTTACTGATTACCATTTTACTTTTTGA-TAATTGCCATTTTACC
63 TCTTTT-CTAATTACCATTTTACTTTTT-ACTAATTACCATTTTACC
*
30965 CTTTACTAATTACC
1 CTTTACTGATTACC
30979 TTTTACTTTT
Statistics
Matches: 100, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
105 6 0.06
106 63 0.63
107 28 0.28
108 3 0.03
ACGTcount: A:0.22, C:0.20, G:0.06, T:0.52
Consensus pattern (107 bp):
CTTTACTGATTACCATTGCCTTTACTTGATTACTCATTACTCTTTACTGATTACCATTTTAATCT
TTTCTAATTACCATTTTACTTTTTACTAATTACCATTTTACC
Found at i:31061 original size:15 final size:14
Alignment explanation
Indices: 31039--31075 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
31029 ATCATTTTTA
31039 TCTTTACTGATCAC
1 TCTTTACTGATCAC
*
31053 TCTTCTACTGATTAC
1 TCTT-TACTGATCAC
31068 TCTTTACT
1 TCTTTACT
31076 CTTTACAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.19, C:0.27, G:0.05, T:0.49
Consensus pattern (14 bp):
TCTTTACTGATCAC
Found at i:31184 original size:34 final size:33
Alignment explanation
Indices: 31145--31247 Score: 127
Period size: 34 Copynumber: 3.1 Consensus size: 33
31135 ACTTCACACC
* *
31145 TTACTCTTTGCCATTTTTCTTTGCTGATTTCTCT
1 TTACTCTTTG-CATTTTTCTTTACTGATTACTCT
* *
31179 TTACTCTTTGCATTTCTCTTTACTGATTACTTT
1 TTACTCTTTGCATTTTTCTTTACTGATTACTCT
*
31212 TTACTCTTTATG-ATTTTTTTTTACTGATTACTCT
1 TTACTC-TT-TGCATTTTTCTTTACTGATTACTCT
31246 TT
1 TT
31248 TACTTTTTAC
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
33 25 0.42
34 33 0.55
35 2 0.03
ACGTcount: A:0.14, C:0.19, G:0.07, T:0.60
Consensus pattern (33 bp):
TTACTCTTTGCATTTTTCTTTACTGATTACTCT
Found at i:31232 original size:20 final size:21
Alignment explanation
Indices: 31194--31387 Score: 101
Period size: 22 Copynumber: 9.6 Consensus size: 21
31184 CTTTGCATTT
31194 CTCTTTACTGATTACTTTTTA
1 CTCTTTACTGATTACTTTTTA
31215 CTCTTTA-TG---A-TTTTT-
1 CTCTTTACTGATTACTTTTTA
31230 -T-TTTACTGATTACTCTTTTA
1 CTCTTTACTGATTACT-TTTTA
* * *
31250 CTTTTTACTGACTACCATTTTA
1 CTCTTTACTGATTA-CTTTTTA
* * *
31272 CCCTTT-CCGA-TACCTTTTA
1 CTCTTTACTGATTACTTTTTA
* *
31291 CTTTTTAGTGATTACCTTTTTA
1 CTCTTTACTGATTA-CTTTTTA
* * * *
31313 CTTTTTACCGTTTAC-TATTA
1 CTCTTTACTGATTACTTTTTA
* *
31333 CT-TCTTACTGATTTC-TATTA
1 CTCT-TTACTGATTACTTTTTA
*
31353 CTCTTTACTGATTACCATTTTA
1 CTCTTTACTGATTA-CTTTTTA
31375 C-CTTTTACTGATT
1 CTC-TTTACTGATT
31388 GCATCTTTCT
Statistics
Matches: 135, Mismatches: 20, Indels: 35
0.71 0.11 0.18
Matches are distributed among these distances:
13 4 0.03
14 3 0.02
16 5 0.04
17 2 0.01
18 1 0.01
19 15 0.11
20 36 0.27
21 17 0.13
22 51 0.38
23 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.06, T:0.55
Consensus pattern (21 bp):
CTCTTTACTGATTACTTTTTA
Found at i:31256 original size:22 final size:21
Alignment explanation
Indices: 31229--31387 Score: 137
Period size: 22 Copynumber: 7.6 Consensus size: 21
31219 TTATGATTTT
31229 TTTTTACTGATTACTCTTTTAC
1 TTTTTACTGATTAC-CTTTTAC
*
31251 TTTTTACTGACTACCATTTTAC
1 TTTTTACTGATTACC-TTTTAC
** *
31273 CCTTT-CCGA-TACCTTTTAC
1 TTTTTACTGATTACCTTTTAC
*
31292 TTTTTAGTGATTACCTTTTTAC
1 TTTTTACTGATTACC-TTTTAC
* * *
31314 TTTTTACCGTTTA-CTATTAC
1 TTTTTACTGATTACCTTTTAC
* * *
31334 TTCTTACTGATT-TCTATTAC
1 TTTTTACTGATTACCTTTTAC
*
31354 TCTTTACTGATTACCATTTTAC
1 TTTTTACTGATTACC-TTTTAC
*
31376 CTTTTACTGATT
1 TTTTTACTGATT
31388 GCATCTTTCT
Statistics
Matches: 109, Mismatches: 21, Indels: 14
0.76 0.15 0.10
Matches are distributed among these distances:
19 9 0.08
20 37 0.34
21 10 0.09
22 53 0.49
ACGTcount: A:0.19, C:0.21, G:0.06, T:0.53
Consensus pattern (21 bp):
TTTTTACTGATTACCTTTTAC
Found at i:31449 original size:30 final size:32
Alignment explanation
Indices: 31379--31449 Score: 94
Period size: 30 Copynumber: 2.3 Consensus size: 32
31369 ATTTTACCTT
*
31379 TTACTGATTGCATCTTTCTTATTGAACTTAAA
1 TTACTGATTACATCTTTCTTATTGAACTTAAA
*
31411 TCACTGATTAC-T-TTTCCTTATTGAACTT-AA
1 TTACTGATTACATCTTT-CTTATTGAACTTAAA
31441 TTACTGATT
1 TTACTGATT
31450 GCCCTTTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 13 0.37
31 13 0.37
32 9 0.26
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (32 bp):
TTACTGATTACATCTTTCTTATTGAACTTAAA
Found at i:32738 original size:14 final size:13
Alignment explanation
Indices: 32719--32750 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
32709 TTCTTTGAGC
32719 TTTTTCTGTATAT
1 TTTTTCTGTATAT
32732 ATTTTTCTGTATAT
1 -TTTTTCTGTATAT
32746 TTTTT
1 TTTTT
32751 GGTGCCGCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.72
Consensus pattern (13 bp):
TTTTTCTGTATAT
Found at i:43165 original size:24 final size:24
Alignment explanation
Indices: 43138--43206 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 24
43128 TTTGTTTTTC
*
43138 TTTTTTATTAGATAAGTTACATTA
1 TTTTTTATAAGATAAGTTACATTA
* *
43162 -TTTTTAAAAG-TCAAGTTACATTC
1 TTTTTTATAAGAT-AAGTTACATTA
*
43185 TTTTTTATCAGATAAGTTACAT
1 TTTTTTATAAGATAAGTTACAT
43207 CAATAAAGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
22 1 0.03
23 18 0.49
24 17 0.46
25 1 0.03
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (24 bp):
TTTTTTATAAGATAAGTTACATTA
Found at i:48851 original size:19 final size:19
Alignment explanation
Indices: 48829--48889 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
48819 CAGCGAATTA
48829 AATAATTAAGAGTCAAAGT
1 AATAATTAAGAGTCAAAGT
* * * *
48848 AAT-AGTAACCAGTAAAATT
1 AATAATTAA-GAGTCAAAGT
*
48867 GATAATTAAGAGTCAAAGT
1 AATAATTAAGAGTCAAAGT
48886 AATA
1 AATA
48890 GTAATTAGTA
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
18 4 0.13
19 22 0.73
20 4 0.13
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (19 bp):
AATAATTAAGAGTCAAAGT
Found at i:48921 original size:37 final size:38
Alignment explanation
Indices: 48830--48924 Score: 147
Period size: 38 Copynumber: 2.5 Consensus size: 38
48820 AGCGAATTAA
*
48830 ATAATTAAGAGTCAAAGTAATAGTAACCAGTAAAATTG
1 ATAATTAAGAGTCAAAGTAATAGTAACCAGTAAAATCG
**
48868 ATAATTAAGAGTCAAAGTAATAGTAATTAGT-AAATCG
1 ATAATTAAGAGTCAAAGTAATAGTAACCAGTAAAATCG
*
48905 ATGATTAAGAGTCAAAGTAA
1 ATAATTAAGAGTCAAAGTAA
48925 GAAGATTAAC
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 24 0.45
38 29 0.55
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.27
Consensus pattern (38 bp):
ATAATTAAGAGTCAAAGTAATAGTAACCAGTAAAATCG
Found at i:49021 original size:71 final size:71
Alignment explanation
Indices: 48712--49133 Score: 247
Period size: 71 Copynumber: 5.8 Consensus size: 71
48702 AAAGTAATGG
* * * *
48712 TAATCAGTAAATTGATAATTAAGAGTAAAAG----TAG-AAATAGT-AATCAGTAAATCAGTAAA
1 TAATCAGTAAATTGATAGTTAAGAG-AAAAGAAAATAGTAATTAGTAAATCAGTAATTAAGTAAA
48771 AAGAGAT
65 AAGAGAT
* * *** * ** * * * *
48778 TAATCAGTAAATTGGTAATTAAGAGCCGAGATAATAGTAACCAGCGAATTAAATAATTAAG-AGT
1 TAATCAGTAAATTGATAGTTAAGAGAAAAGAAAATAGTAATTAG-TAAATCAGTAATTAAGTA--
*
48842 CAAAGTA-AT
63 AAAAG-AGAT
* * * * *
48851 AGTAACCAGTAAAATTGATAATTAAGAGTCAAAG-TAATAGTAATTAGTAAATC-GATGATTAAG
1 --TAATCAGT-AAATTGATAGTTAAGAG-AAAAGAAAATAGTAATTAGTAAATCAG-TAATT-A-
48914 AGTCAAAGTAAGAAGAT
59 AGT-AAA--AAG-AGAT
* * * *
48931 TAACCAAGTGAATTAATAGTTAAG-GAAAATAAAAGTAGTAATTAGTAAATCAGTAATTAAGTAA
1 TAATC-AGTAAATTGATAGTTAAGAGAAAAGAAAA-TAGTAATTAGTAAATCAGTAATTAAGTAA
48995 AAAGAGAT
64 AAAGAGAT
** ** * *
49003 TAATCAGTAAATTGATAGTTAAGAGTCAAGGTAATAGTAGTTAGTAAATCGGTAATTAAGTAAAA
1 TAATCAGTAAATTGATAGTTAAGAGAAAAGAAAATAGTAATTAGTAAATCAGTAATTAAGTAAAA
49068 AGAGAT
66 AGAGAT
* ** ** *
49074 TAATCAGTAGATTGATAGTTAAGAGTCAAGGTAATAGTAATCAGTAAATC-GATAATTAAG
1 TAATCAGTAAATTGATAGTTAAGAGAAAAGAAAATAGTAATTAGTAAATCAG-TAATTAAG
49134 AGTCAAGGTA
Statistics
Matches: 282, Mismatches: 46, Indels: 51
0.74 0.12 0.13
Matches are distributed among these distances:
65 2 0.01
66 24 0.09
69 3 0.01
70 5 0.02
71 107 0.38
72 22 0.08
73 9 0.03
74 1 0.00
75 17 0.06
76 34 0.12
77 10 0.04
78 37 0.13
79 9 0.03
80 2 0.01
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.27
Consensus pattern (71 bp):
TAATCAGTAAATTGATAGTTAAGAGAAAAGAAAATAGTAATTAGTAAATCAGTAATTAAGTAAAA
AGAGAT
Found at i:49025 original size:34 final size:34
Alignment explanation
Indices: 48987--49096 Score: 89
Period size: 34 Copynumber: 3.1 Consensus size: 34
48977 AAATCAGTAA
48987 TTAAGTAAAAAGAGATTAATCAGTAAATTGATAG
1 TTAAGTAAAAAGAGATTAATCAGTAAATTGATAG
** * * * * *
49021 TTAAG-AGTCAAG-GTAATAGTAGTTAGTAAATCGGTAA
1 TTAAGTA-AAAAGAG--AT--TAATCAGTAAATTGATAG
*
49058 TTAAGTAAAAAGAGATTAATCAGTAGATTGATAG
1 TTAAGTAAAAAGAGATTAATCAGTAAATTGATAG
49092 TTAAG
1 TTAAG
49097 AGTCAAGGTA
Statistics
Matches: 54, Mismatches: 15, Indels: 14
0.65 0.18 0.17
Matches are distributed among these distances:
33 2 0.04
34 25 0.46
35 2 0.04
36 2 0.04
37 21 0.39
38 2 0.04
ACGTcount: A:0.45, C:0.04, G:0.21, T:0.30
Consensus pattern (34 bp):
TTAAGTAAAAAGAGATTAATCAGTAAATTGATAG
Found at i:49161 original size:40 final size:37
Alignment explanation
Indices: 48778--49179 Score: 191
Period size: 37 Copynumber: 10.8 Consensus size: 37
48768 AAAAAGAGAT
* * * * *
48778 TAATCAGTAAATTGGTAATTAAGAGCCGAGATAATAG
1 TAATCAGTAAATCGATAATTAAGAGTCAAGGTAATAG
* * * ** *
48815 TAACCAGCGAATTAAATAATTAAGAGTCAAAGTAATAG
1 TAATCAG-TAAATCGATAATTAAGAGTCAAGGTAATAG
* * *
48853 TAACCAGTAAAATTGATAATTAAGAGTCAAAGTAATAG
1 TAATCAGT-AAATCGATAATTAAGAGTCAAGGTAATAG
* * * *
48891 TAATTAGTAAATCGATGATTAAGAGTCAAAGTAAGAAG
1 TAATCAGTAAATCGATAATTAAGAGTCAAGGTAA-TAG
* * ** * ** ***
48929 ATTAACCAAGTGAATTAATAGTTAAG-GAAAATAAAAGTAG
1 --TAATC-AGTAAATCGATAATTAAGAGTCAAGGTAA-TAG
* * *
48969 TAATTAGTAAATC-AGTAATT-A-AGT-AA--AAAGAG
1 TAATCAGTAAATCGA-TAATTAAGAGTCAAGGTAATAG
* *
49001 ATTAATCAGTAAATTGATAGTTAAGAGTCAAGGTAATAG
1 --TAATCAGTAAATCGATAATTAAGAGTCAAGGTAATAG
* * * * *
49040 TAGTTAGTAAATCGGTAATT-A-AGT-AA--AAAGAG
1 TAATCAGTAAATCGATAATTAAGAGTCAAGGTAATAG
* * *
49072 ATTAATCAGTAGATTGATAGTTAAGAGTCAAGGTAATAG
1 --TAATCAGTAAATCGATAATTAAGAGTCAAGGTAATAG
49111 TAATCAGTAAATCGATAATTAAGAGTCAAGGTAAAAATAG
1 TAATCAGTAAATCGATAATTAAGAGTCAAGGT---AATAG
*
49151 TAATCAGTAAATC-AGTAATTAAAAGTCAA
1 TAATCAGTAAATCGA-TAATTAAGAGTCAA
49180 TGGATTAATC
Statistics
Matches: 275, Mismatches: 63, Indels: 51
0.71 0.16 0.13
Matches are distributed among these distances:
32 6 0.02
33 3 0.01
34 31 0.11
35 8 0.03
36 10 0.04
37 88 0.32
38 65 0.24
39 9 0.03
40 42 0.15
41 13 0.05
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.27
Consensus pattern (37 bp):
TAATCAGTAAATCGATAATTAAGAGTCAAGGTAATAG
Found at i:49199 original size:111 final size:108
Alignment explanation
Indices: 49003--49207 Score: 261
Period size: 111 Copynumber: 1.9 Consensus size: 108
48993 AAAAAGAGAT
* * * * *
49003 TAATCAGTAAATTGATAGTTAAGAGTCAAGGTAATAGTAGTTAGTAAATCGGTAATTAAGTAAAA
1 TAATCAGTAAATCGATAATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAA
* *
49068 AGAGATTAATCAGTAGATTGATAGTTAAGAGTCAAGGTAATAG
66 AGAGATTAATCAGTAAATTGATACTTAAGAGTCAAGGTAATAG
49111 TAATCAGTAAATCGATAATTAAGAGTCAAGGTAAAAATAGTAATCAGTAAATCAGTAATTAAAAG
1 TAATCAGTAAATCGATAATTAAGAGTCAAGGT---AATAGTAATCAGTAAATCAGTAATT--AAG
* * *
49176 T-CAATG-GATTAATCGGTAAATTGATACTTAAG
61 TAAAAAGAGATTAATCAGTAAATTGATACTTAAG
49208 GGAGAAAGTA
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
108 30 0.37
111 45 0.55
112 3 0.04
113 4 0.05
ACGTcount: A:0.45, C:0.06, G:0.20, T:0.29
Consensus pattern (108 bp):
TAATCAGTAAATCGATAATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGTAAAA
AGAGATTAATCAGTAAATTGATACTTAAGAGTCAAGGTAATAG
Found at i:49304 original size:21 final size:21
Alignment explanation
Indices: 49274--49313 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
49264 TCAAGAAAGT
*
49274 AAAATAGTAATCAGTAAAGGA
1 AAAATAGTAAACAGTAAAGGA
* *
49295 AAAATGGTAAAGAGTAAAG
1 AAAATAGTAAACAGTAAAG
49314 AATAATCAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.23, T:0.17
Consensus pattern (21 bp):
AAAATAGTAAACAGTAAAGGA
Found at i:49321 original size:35 final size:35
Alignment explanation
Indices: 49281--49347 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
49271 AGTAAAATAG
* *
49281 TAATCAGTAAAGGA-AAAATGGTAAAGAGTAAAGAA
1 TAATCAAT-AAGGAGAAAATAGTAAAGAGTAAAGAA
* *
49316 TAATCAATAAGGAGTAATTAGTAAAGAGTAAA
1 TAATCAATAAGGAGAAAATAGTAAAGAGTAAA
49348 ATGATAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 5 0.19
35 22 0.81
ACGTcount: A:0.55, C:0.03, G:0.21, T:0.21
Consensus pattern (35 bp):
TAATCAATAAGGAGAAAATAGTAAAGAGTAAAGAA
Found at i:49338 original size:56 final size:55
Alignment explanation
Indices: 49210--49339 Score: 131
Period size: 56 Copynumber: 2.3 Consensus size: 55
49200 TACTTAAGGG
* ** *
49210 AGAAAGTAAAATTAGTGATCAGTAAAGAGAAAAATGGTAAAATGGTAATTAAATTCA
1 AGAAAGT-AAATTAGTAATCAGTAAAGAGAAAAATGGTAAAA-GGTAAAGAAAATCA
*
49267 AGAAAGTAAAATAGTAATCAGTAAAG-GAAAAATGGT-AAAGAGTAAAGAATAATCA
1 AGAAAGTAAATTAGTAATCAGTAAAGAGAAAAATGGTAAAAG-GTAAAGAA-AATCA
*
49322 ATAAGGAGT-AATTAGTAA
1 AGAA--AGTAAATTAGTAA
49340 AGAGTAAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
53 1 0.02
54 9 0.15
55 17 0.27
56 25 0.40
57 10 0.16
ACGTcount: A:0.55, C:0.03, G:0.20, T:0.22
Consensus pattern (55 bp):
AGAAAGTAAATTAGTAATCAGTAAAGAGAAAAATGGTAAAAGGTAAAGAAAATCA
Found at i:49370 original size:50 final size:52
Alignment explanation
Indices: 49279--49397 Score: 131
Period size: 50 Copynumber: 2.4 Consensus size: 52
49269 AAAGTAAAAT
* * * *
49279 AGTAATCAGTAAAG-GAAAAATGGTAAAGAGTAAAGAATAATCAAT-AAGG-
1 AGTAATTAGTAAAGAGTAAAATGATAAAAAGTAAAGAATAATCAATAAAGGA
* * *
49328 AGTAATTAGTAAAGAGTAAAATGATAAAAAGTAAGGAGTAATCAGTAAAGGA
1 AGTAATTAGTAAAGAGTAAAATGATAAAAAGTAAAGAATAATCAATAAAGGA
*
49380 AG-AA-TGGTAAAGAGTAAA
1 AGTAATTAGTAAAGAGTAAA
49398 GGGTAATCAG
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
49 13 0.22
50 38 0.64
51 6 0.10
52 2 0.03
ACGTcount: A:0.55, C:0.03, G:0.24, T:0.19
Consensus pattern (52 bp):
AGTAATTAGTAAAGAGTAAAATGATAAAAAGTAAAGAATAATCAATAAAGGA
Found at i:49404 original size:35 final size:36
Alignment explanation
Indices: 49323--49425 Score: 122
Period size: 36 Copynumber: 2.9 Consensus size: 36
49313 GAATAATCAA
*
49323 TAAGGAGTAATTAGTAAAGAGTAAAATGATAAAAAG
1 TAAGGAGTAATCAGTAAAGAGTAAAATGATAAAAAG
* *
49359 TAAGGAGTAATCAGTAAAG-G-AAGAATGGTAAAGAG
1 TAAGGAGTAATCAGTAAAGAGTAA-AATGATAAAAAG
* *
49394 TAAAGG-GTAATCAGTAAAAAGTAAAAAGATAA
1 T-AAGGAGTAATCAGTAAAGAGTAAAATGATAA
49426 TCAGTAAAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
34 2 0.04
35 24 0.42
36 29 0.51
37 2 0.04
ACGTcount: A:0.54, C:0.02, G:0.24, T:0.19
Consensus pattern (36 bp):
TAAGGAGTAATCAGTAAAGAGTAAAATGATAAAAAG
Found at i:49429 original size:22 final size:21
Alignment explanation
Indices: 49386--49620 Score: 116
Period size: 22 Copynumber: 10.5 Consensus size: 21
49376 AGGAAGAATG
* **
49386 GTAAAGAGTAAAGGGTAATCA
1 GTAAAAAGTAAAAAGTAATCA
49407 GTAAAAAGTAAAAAGATAATCA
1 GTAAAAAGTAAAAAG-TAATCA
49429 GTAAAGAATGAAATAGTAAAAGGTAATCA
1 GTAAA-AA-G---TA--AAAA-GTAATCA
* **
49458 ATAAAAAAAGTAATGA-TAATCA
1 GTAAA--AAGTAAAAAGTAATCA
* *
49480 GTAAAAGGTAAAATAATAATCA
1 GTAAAAAGTAAAA-AGTAATCA
* * *
49502 GT-AAGAGCAAAATGGTAATCA
1 GTAAAAAGTAAAA-AGTAATCA
* * *
49523 AT-GAGAGTAAAATAGTAATCA
1 GTAAAAAGTAAAA-AGTAATCA
* *
49544 GCAAAGAGTAAAATAGTAATCA
1 GTAAAAAGTAAAA-AGTAATCA
*
49566 GTAAAAAGTAAGAAGGTAATCA
1 GTAAAAAGTAA-AAAGTAATCA
* *
49588 GTGAAGAGTAAAATAGTAATCA
1 GTAAAAAGTAAAA-AGTAATCA
*
49610 GTAAAAGGTAA
1 GTAAAAAGTAA
49621 TCAGTAAGAG
Statistics
Matches: 167, Mismatches: 32, Indels: 29
0.73 0.14 0.13
Matches are distributed among these distances:
20 5 0.03
21 46 0.28
22 87 0.52
23 4 0.02
24 3 0.02
26 2 0.01
27 2 0.01
29 15 0.09
30 3 0.02
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (21 bp):
GTAAAAAGTAAAAAGTAATCA
Found at i:49520 original size:21 final size:21
Alignment explanation
Indices: 49474--49699 Score: 175
Period size: 22 Copynumber: 10.9 Consensus size: 21
49464 AAAGTAATGA
* *
49474 TAATCAGTAAAAGGTAAAATAA
1 TAATCAGTAAGA-GTAAAATAG
* *
49496 TAATCAGTAAGAGCAAAATGG
1 TAATCAGTAAGAGTAAAATAG
* *
49517 TAATCAATGAGAGTAAAATAG
1 TAATCAGTAAGAGTAAAATAG
*
49538 TAATCAGCAAAGAGTAAAATAG
1 TAATCAG-TAAGAGTAAAATAG
* *
49560 TAATCAGTAAAAAGTAAGAA-GG
1 TAATCAGT-AAGAGTAA-AATAG
49582 TAATCAGTGAAGAGTAAAATAG
1 TAATCAGT-AAGAGTAAAATAG
*
49604 TAATCAGTAAAAGGT--AATCAG
1 TAATCAGTAAGA-GTAAAAT-AG
* *
49625 T-A--AG----AGTAAAACAA
1 TAATCAGTAAGAGTAAAATAG
* *
49639 TAATCAGTAAGAGCAAAATGG
1 TAATCAGTAAGAGTAAAATAG
*
49660 TAATTAGTAAGAGTAAAATAG
1 TAATCAGTAAGAGTAAAATAG
49681 TAATCAGTAAAGAGTAAAA
1 TAATCAGT-AAGAGTAAAA
49700 CGTGATCAGT
Statistics
Matches: 160, Mismatches: 28, Indels: 32
0.73 0.13 0.15
Matches are distributed among these distances:
13 2 0.01
14 3 0.02
15 3 0.02
17 2 0.01
18 2 0.01
20 4 0.03
21 68 0.43
22 74 0.46
23 2 0.01
ACGTcount: A:0.53, C:0.06, G:0.19, T:0.21
Consensus pattern (21 bp):
TAATCAGTAAGAGTAAAATAG
Found at i:49643 original size:35 final size:37
Alignment explanation
Indices: 49572--49650 Score: 126
Period size: 35 Copynumber: 2.2 Consensus size: 37
49562 ATCAGTAAAA
* *
49572 AGTAAGAAGGTAATCAGTGAAGAGTAAAATAGTAATC
1 AGTAAGAAGGTAATCAGTGAAGAGTAAAACAATAATC
49609 AGTAA-AAGGTAATCAGT-AAGAGTAAAACAATAATC
1 AGTAAGAAGGTAATCAGTGAAGAGTAAAACAATAATC
49644 AGTAAGA
1 AGTAAGA
49651 GCAAAATGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
35 21 0.54
36 13 0.33
37 5 0.13
ACGTcount: A:0.52, C:0.06, G:0.22, T:0.20
Consensus pattern (37 bp):
AGTAAGAAGGTAATCAGTGAAGAGTAAAACAATAATC
Found at i:49707 original size:21 final size:20
Alignment explanation
Indices: 49496--49711 Score: 129
Period size: 21 Copynumber: 10.5 Consensus size: 20
49486 GGTAAAATAA
* *
49496 TAATCAGTAAGAGCAAAATGG
1 TAATCAGTAAGAGTAAAA-CG
* * *
49517 TAATCAATGAGAGTAAAATAG
1 TAATCAGTAAGAGTAAAA-CG
* *
49538 TAATCAGCAAAGAGTAAAATAG
1 TAATCAG-TAAGAGTAAAA-CG
* *
49560 TAATCAGTAAAAAGTAAGAAGG
1 TAATCAGT-AAGAGTAA-AACG
49582 TAATCAGTGAAGAGT--AA--
1 TAATCAGT-AAGAGTAAAACG
* *
49599 -AAT-AGTAATCAGTAAAAGG
1 TAATCAGTAA-GAGTAAAACG
*
49618 TAATCAGTAAGAGTAAAACAA
1 TAATCAGTAAGAGTAAAAC-G
* *
49639 TAATCAGTAAGAGCAAAATGG
1 TAATCAGTAAGAGTAAAA-CG
* *
49660 TAATTAGTAAGAGTAAAATAG
1 TAATCAGTAAGAGTAAAA-CG
49681 TAATCAGTAAAGAGTAAAACG
1 TAATCAGT-AAGAGTAAAACG
*
49702 TGATCAGTAA
1 TAATCAGTAA
49712 TTCAAAGAGT
Statistics
Matches: 157, Mismatches: 25, Indels: 27
0.75 0.12 0.13
Matches are distributed among these distances:
14 2 0.01
15 6 0.04
16 3 0.02
17 2 0.01
19 2 0.01
20 12 0.08
21 78 0.50
22 50 0.32
23 2 0.01
ACGTcount: A:0.51, C:0.07, G:0.20, T:0.21
Consensus pattern (20 bp):
TAATCAGTAAGAGTAAAACG
Found at i:50390 original size:21 final size:21
Alignment explanation
Indices: 50366--50432 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
50356 TTTTACTGAA
50366 TTACTGATTACCATTACTATT
1 TTACTGATTACCATTACTATT
* *
50387 TTACTGATTATTCTTTACT-TT
1 TTACTGATTA-CCATTACTATT
* * *
50408 GTACTGATTACTAGTTACCATT
1 TTACTGATTACCA-TTACTATT
50430 TTA
1 TTA
50433 TTCTTTGCTG
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
21 25 0.71
22 10 0.29
ACGTcount: A:0.25, C:0.16, G:0.07, T:0.51
Consensus pattern (21 bp):
TTACTGATTACCATTACTATT
Found at i:50556 original size:34 final size:34
Alignment explanation
Indices: 50474--50827 Score: 185
Period size: 39 Copynumber: 9.9 Consensus size: 34
50464 TTAATATTTT
* *
50474 ACTCTTTACCATTTTTTTCTTTACTGGATTACTCTTT
1 ACTCTTTACCA--TTTTTCTTTACT-GATTACCCTTC
* *
50511 ACTCTTCACCATTCTTCTTTACTGACTT-CCCTTC
1 ACTCTTTACCATTTTTCTTTACTGA-TTACCCTTC
*
50545 ACTCTTTACCATTTTTCTTTACTGATTACTCTT-
1 ACTCTTTACCATTTTTCTTTACTGATTACCCTTC
** * ** * * *
50578 TTTCTTTACTGATTACTCTTTACT--CTACTCTTT
1 ACTCTTTAC-CATTTTTCTTTACTGATTACCCTTC
* * *
50611 ACCCTTTGCCATTTTTTCTTTACTGATTACTCTTCACTC
1 ACTCTTTACCA-TTTTTCTTTACTGATTAC-C--C-TTC
* * *
50650 TACTCTTTACCCTTTTTCTTTACTGATTACTCTTTT
1 -ACTCTTTACCATTTTTCTTTACTGATTAC-CCTTC
* * * * *
50686 ACTTTTTACCATTTTACTTTGCTGATTACTATTTACTTT
1 ACTCTTTACCATTTTTCTTTACTGATTAC-----CCTTC
*
50725 ACTCTTTACCATTTTTCTTTACTGATTACTCTTCACTC
1 ACTCTTTACCATTTTTCTTTACTGATTAC-C--C-TTC
* * *
50763 TACTCTTTACCCTTTTTCTTTACTGATTACTCTTTT
1 -ACTCTTTACCATTTTTCTTTACTGATTAC-CCTTC
* * * *
50799 ATTTTTTACCATTTTACTTTGCTGATTAC
1 ACTCTTTACCATTTTTCTTTACTGATTAC
50828 TATTTACTTT
Statistics
Matches: 246, Mismatches: 51, Indels: 42
0.73 0.15 0.12
Matches are distributed among these distances:
32 8 0.03
33 24 0.10
34 44 0.18
35 66 0.27
36 2 0.01
37 11 0.04
38 2 0.01
39 81 0.33
40 8 0.03
ACGTcount: A:0.17, C:0.25, G:0.04, T:0.54
Consensus pattern (34 bp):
ACTCTTTACCATTTTTCTTTACTGATTACCCTTC
Found at i:50600 original size:7 final size:7
Alignment explanation
Indices: 50560--50946 Score: 85
Period size: 7 Copynumber: 58.0 Consensus size: 7
50550 TTACCATTTT
50560 TCTTTAC
1 TCTTTAC
**
50567 TGATTAC
1 TCTTTAC
*
50574 TCTTT-T
1 TCTTTAC
50580 TCTTTAC
1 TCTTTAC
**
50587 TGATTAC
1 TCTTTAC
50594 TCTTTAC
1 TCTTTAC
50601 TC--TAC
1 TCTTTAC
50606 TCTTTAC
1 TCTTTAC
* *
50613 CCTTTGC
1 TCTTTAC
**
50620 -CATTTTT
1 TC-TTTAC
50627 TCTTTAC
1 TCTTTAC
**
50634 TGATTAC
1 TCTTTAC
*
50641 TCTTCAC
1 TCTTTAC
50648 TC--TAC
1 TCTTTAC
50653 TCTTTAC
1 TCTTTAC
* *
50660 CCTTT-T
1 TCTTTAC
50666 TCTTTAC
1 TCTTTAC
**
50673 TGATTAC
1 TCTTTAC
50680 TCTTTTAC
1 TC-TTTAC
*
50688 TTTTTAC
1 TCTTTAC
50695 -CATTT--
1 TC-TTTAC
*
50700 TACTTTGC
1 T-CTTTAC
**
50708 TGATTAC
1 TCTTTAC
*
50715 TATTTA-
1 TCTTTAC
50721 -CTTTAC
1 TCTTTAC
50727 TCTTTAC
1 TCTTTAC
*
50734 -CATTT-T
1 TC-TTTAC
50740 TCTTTAC
1 TCTTTAC
**
50747 TGATTAC
1 TCTTTAC
*
50754 TCTTCAC
1 TCTTTAC
50761 TC--TAC
1 TCTTTAC
50766 TCTTTAC
1 TCTTTAC
* *
50773 CCTTT-T
1 TCTTTAC
50779 TCTTTAC
1 TCTTTAC
**
50786 TGATTAC
1 TCTTTAC
*
50793 TCTTTTAT
1 TC-TTTAC
*
50801 TTTTTAC
1 TCTTTAC
50808 -CATTT--
1 TC-TTTAC
*
50813 TACTTTGC
1 T-CTTTAC
**
50821 TGATTAC
1 TCTTTAC
*
50828 TATTTA-
1 TCTTTAC
50834 -CTTTAC
1 TCTTTAC
50840 TCTTTAC
1 TCTTTAC
50847 TCTTTAC
1 TCTTTAC
*
50854 -CATTT-T
1 TC-TTTAC
50860 TCTTTAC
1 TCTTTAC
**
50867 TGATTAC
1 TCTTTAC
50874 TCTTTAC
1 TCTTTAC
50881 TC--TAC
1 TCTTTAC
50886 TCTTTAC
1 TCTTTAC
*
50893 CCTTTAC
1 TCTTTAC
**
50900 -CATTTTT
1 TC-TTTAC
50907 TCTTTAC
1 TCTTTAC
**
50914 TGATTAC
1 TCTTTAC
50921 TC-TT-C
1 TCTTTAC
50926 TCTTTAC
1 TCTTTAC
*
50933 TCTGTAC
1 TCTTTAC
50940 TCTTTAC
1 TCTTTAC
50947 CATTTTTTTT
Statistics
Matches: 261, Mismatches: 80, Indels: 78
0.62 0.19 0.19
Matches are distributed among these distances:
5 29 0.11
6 33 0.13
7 186 0.71
8 13 0.05
ACGTcount: A:0.17, C:0.25, G:0.04, T:0.55
Consensus pattern (7 bp):
TCTTTAC
Found at i:50674 original size:39 final size:39
Alignment explanation
Indices: 50614--50974 Score: 308
Period size: 39 Copynumber: 8.8 Consensus size: 39
50604 ACTCTTTACC
* *
50614 CTTTGCCATTTTTTCTTTACTGATTACTCTTCACTCTACT
1 CTTTACCA-TTTTTCTTTACTGATTACTCTTTACTCTACT
*
50654 CTTTACCCTTTTTCTTTACTGATTACTC-TT--T-TACT
1 CTTTACCATTTTTCTTTACTGATTACTCTTTACTCTACT
* * * * *
50689 TTTTACCATTTTACTTTGCTGATTACTATTTACTTTACT
1 CTTTACCATTTTTCTTTACTGATTACTCTTTACTCTACT
*
50728 CTTTACCATTTTTCTTTACTGATTACTCTTCACTCTACT
1 CTTTACCATTTTTCTTTACTGATTACTCTTTACTCTACT
*
50767 CTTTACCCTTTTTCTTTACTGATTACTCTTTTA-T-T--T
1 CTTTACCATTTTTCTTTACTGATTACTC-TTTACTCTACT
* *
50803 -TTTACCATTTTACTTTGCTGATTACTATTTACTTTACTCTTTACT
1 CTTTACCATTTTTCTTTACTGATTAC----T-CTTTACTC--TACT
50848 CTTTACCATTTTTCTTTACTGATTACTCTTTACTCTACTCTTT
1 CTTTACCATTTTTCTTTACTGATTACTCTTTACTCTA--C--T
50891 ACCCTTTACCATTTTTTCTTTACTGATTACTCTTCTCTTTACTCTGTACT
1 ---CTTTACCA-TTTTTCTTTACTGATTA-----CTCTTTACTC--TACT
50941 CTTTACCATTTTTTTTCTTTACTGATTACTCTTT
1 CTTTACCA---TTTTTCTTTACTGATTACTCTTT
50975 TACTTTTTAC
Statistics
Matches: 266, Mismatches: 21, Indels: 64
0.76 0.06 0.18
Matches are distributed among these distances:
35 49 0.18
36 4 0.02
38 3 0.01
39 92 0.35
40 11 0.04
41 9 0.03
42 1 0.00
43 2 0.01
44 6 0.02
45 1 0.00
46 31 0.12
47 25 0.09
49 18 0.07
50 1 0.00
52 11 0.04
54 2 0.01
ACGTcount: A:0.17, C:0.24, G:0.04, T:0.56
Consensus pattern (39 bp):
CTTTACCATTTTTCTTTACTGATTACTCTTTACTCTACT
Found at i:50766 original size:113 final size:116
Alignment explanation
Indices: 50597--50897 Score: 482
Period size: 113 Copynumber: 2.6 Consensus size: 116
50587 TGATTACTCT
* * *
50597 TTACTCTACTCTTTACCCTTTGCCATTTTTTCTTTACTGATTACTCTTCACTCTACTCTTTACCC
1 TTACTTTAC-CTTTACTCTTTACCA-TTTTTCTTTACTGATTACTCTTCACTCTACTCTTTACCC
50662 TTTTTCTTTACTGATTACTCTTTTACTTTTTACCATTTTACTTTGCTGATTAC
64 TTTTTCTTTACTGATTACTCTTTTACTTTTTACCATTTTACTTTGCTGATTAC
50715 -TA-TTTA-CTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTCACTCTACTCTTTACCCTT
1 TTACTTTACCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTCACTCTACTCTTTACCCTT
*
50777 TTTCTTTACTGATTACTCTTTTATTTTTTACCATTTTACTTTGCTGATTAC
66 TTTCTTTACTGATTACTCTTTTACTTTTTACCATTTTACTTTGCTGATTAC
*
50828 TATTTACTTTACTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTTACTCTACTCTTTAC
1 ---TTACTTTAC-CTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTCACTCTACTCTTTAC
50893 CCTTT
62 CCTTT
50898 ACCATTTTTT
Statistics
Matches: 171, Mismatches: 5, Indels: 12
0.91 0.03 0.06
Matches are distributed among these distances:
113 91 0.53
114 13 0.08
116 3 0.02
117 4 0.02
118 4 0.02
120 56 0.33
ACGTcount: A:0.17, C:0.25, G:0.03, T:0.55
Consensus pattern (116 bp):
TTACTTTACCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTCACTCTACTCTTTACCCTT
TTTCTTTACTGATTACTCTTTTACTTTTTACCATTTTACTTTGCTGATTAC
Found at i:50843 original size:47 final size:46
Alignment explanation
Indices: 50779--50980 Score: 244
Period size: 46 Copynumber: 4.2 Consensus size: 46
50769 TTACCCTTTT
* * * *
50779 TCTTTACTGATTACTCTTTTATTTTTTACCATTTTACTTTGCTGATTAC
1 TCTTTACT--TTACTC-TTTACTCTTTACCATTTTTCTTTACTGATTAC
*
50828 TATTTACTTTACTCTTTACTCTTTACCATTTTTCTTTACTGATTAC
1 TCTTTACTTTACTCTTTACTCTTTACCATTTTTCTTTACTGATTAC
* *
50874 TCTTTACTCTACTCTTTACCCTTTACCATTTTTTCTTTACTGATTAC
1 TCTTTACTTTACTCTTTACTCTTTACCA-TTTTTCTTTACTGATTAC
*
50921 TCTTCT-CTTTACTCTGTACTCTTTACCATTTTTTTTCTTTACTGATTAC
1 TCTT-TACTTTACTCTTTACTCTTTACCA---TTTTTCTTTACTGATTAC
50970 TCTTTTACTTT
1 TC-TTTACTTT
50981 TTACTGATTA
Statistics
Matches: 136, Mismatches: 11, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
46 53 0.39
47 47 0.35
48 1 0.01
49 29 0.21
50 6 0.04
ACGTcount: A:0.17, C:0.23, G:0.03, T:0.57
Consensus pattern (46 bp):
TCTTTACTTTACTCTTTACTCTTTACCATTTTTCTTTACTGATTAC
Found at i:50892 original size:19 final size:19
Alignment explanation
Indices: 50870--50943 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
50860 TCTTTACTGA
*
50870 TTACTCTTTACTCTACTCT
1 TTACTCTTTACTCTTCTCT
* * *
50889 TTACCCTTTACCATTTTTTCT
1 TTACTCTTTA-C-TCTTCTCT
**
50910 TTACTGATTACTCTTCTCT
1 TTACTCTTTACTCTTCTCT
*
50929 TTACTCTGTACTCTT
1 TTACTCTTTACTCTT
50944 TACCATTTTT
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
19 27 0.66
20 2 0.05
21 12 0.29
ACGTcount: A:0.15, C:0.28, G:0.03, T:0.54
Consensus pattern (19 bp):
TTACTCTTTACTCTTCTCT
Found at i:50912 original size:74 final size:75
Alignment explanation
Indices: 50596--50924 Score: 244
Period size: 74 Copynumber: 4.3 Consensus size: 75
50586 CTGATTACTC
* * * *
50596 TTTACTCTACTCTTTACCCTTTGCCATTTTTTCTTTACTGATTACTCTTCACTCTACTCTTTACC
1 TTTACTTTACTCTTTACTCTTTACCA-TTTTTCTTTACTGATTACTCTTTACTCTACTCTTTACC
*
50661 CTTTTTCTTTA
65 CTTTTCCTTTA
* * * * * * *
50672 CTGA--TTACTCTTTTACTTTTTACCATTTTACTTTGCTGATTACTATTTACTTTACTCTTTACC
1 TTTACTTTACTC-TTTACTCTTTACCATTTTTCTTTACTGATTACTCTTTACTCTACTCTTTACC
* *
50735 ATTTTTCTTTA
65 CTTTTCCTTTA
* * *
50746 CTGATTACTCTTCACTC--TACTCTTTACCCTTTTTCTTTACTGATTACTCTTTTATTTTTTAC-
1 -T--TTACT-TT-ACTCTTTACTCTTTACCATTTTTCTTTACTGATTACTC-TTTA--CTCTACT
**
50808 CATTTTA--CTTTGCTGATTACTA
58 C--TTTACCCTTT--TCCTT--TA
50830 TTTACTTTACTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTTACTCTACTCTTTACCC
1 TTTACTTTACTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTTACTCTACTCTTTACCC
*
50895 TTTACCATTT-
66 TTTTCC-TTTA
**
50905 TTT-CTTTACTGATTACTCTT
1 TTTACTTTACTCTTTACTCTT
50925 CTCTTTACTC
Statistics
Matches: 199, Mismatches: 31, Indels: 48
0.72 0.11 0.17
Matches are distributed among these distances:
74 63 0.32
75 14 0.07
76 3 0.02
77 6 0.03
78 33 0.17
79 13 0.07
80 12 0.06
81 45 0.23
82 7 0.04
83 1 0.01
84 2 0.01
ACGTcount: A:0.17, C:0.25, G:0.03, T:0.55
Consensus pattern (75 bp):
TTTACTTTACTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTTACTCTACTCTTTACCC
TTTTCCTTTA
Found at i:50983 original size:22 final size:21
Alignment explanation
Indices: 50958--51154 Score: 161
Period size: 22 Copynumber: 9.3 Consensus size: 21
50948 ATTTTTTTTC
50958 TTTACTGATTACTCTTTTACTT
1 TTTACTGATTAC-CTTTTACTT
*
50980 TTTACTGATTACCATTTTCCTAT
1 TTTACTGATTACC-TTTTACT-T
* * *
51003 TTT-CTAATTACTATTTTACCT
1 TTTACTGATTAC-CTTTTACTT
51024 TTTACTGATTACCTTTGTACTT
1 TTTACTGATTACCTTT-TACTT
*
51046 TTTACTGATTA-CTATTAC-T
1 TTTACTGATTACCTTTTACTT
* *
51065 CTTACTGATTACC-ATTACTT
1 TTTACTGATTACCTTTTACTT
* * * *
51085 CTTACTGATCA-CTATTACTC
1 TTTACTGATTACCTTTTACTT
* *
51105 TTTACTGACTACTCTTTTAATT
1 TTTACTGATTAC-CTTTTACTT
* *
51127 TTCAATGATTACCATTTTACTT
1 TTTACTGATTACC-TTTTACTT
51149 TTTACT
1 TTTACT
51155 AAACCCTTTT
Statistics
Matches: 140, Mismatches: 24, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
19 17 0.12
20 29 0.21
21 12 0.09
22 78 0.56
23 4 0.03
ACGTcount: A:0.23, C:0.20, G:0.05, T:0.52
Consensus pattern (21 bp):
TTTACTGATTACCTTTTACTT
Found at i:51082 original size:13 final size:13
Alignment explanation
Indices: 51047--51110 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
51037 TTTGTACTTT
*
51047 TTACTGATTACTA
1 TTACTCATTACTA
51060 TTACTC-TTACTGA
1 TTACTCATTACT-A
*
51073 TTAC-CATTACTTC
1 TTACTCATTAC-TA
* *
51086 TTACTGATCACTA
1 TTACTCATTACTA
*
51099 TTACTCTTTACT
1 TTACTCATTACT
51111 GACTACTCTT
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
12 6 0.15
13 28 0.72
14 5 0.13
ACGTcount: A:0.25, C:0.23, G:0.05, T:0.47
Consensus pattern (13 bp):
TTACTCATTACTA
Found at i:51092 original size:39 final size:42
Alignment explanation
Indices: 51024--51112 Score: 130
Period size: 39 Copynumber: 2.2 Consensus size: 42
51014 TATTTTACCT
* * *
51024 TTTACTGATTACCTTTGTACTTTTTACTGATTACTATTACTC
1 TTTACTGATTACCTATGTACTTCTTACTGATCACTATTACTC
51066 -TTACTGATTACC-AT-TACTTCTTACTGATCACTATTACTC
1 TTTACTGATTACCTATGTACTTCTTACTGATCACTATTACTC
51105 TTTACTGA
1 TTTACTGA
51113 CTACTCTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
39 23 0.53
40 8 0.19
41 12 0.28
ACGTcount: A:0.24, C:0.21, G:0.07, T:0.48
Consensus pattern (42 bp):
TTTACTGATTACCTATGTACTTCTTACTGATCACTATTACTC
Found at i:55113 original size:27 final size:27
Alignment explanation
Indices: 55075--55144 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
55065 GGCTATTAAT
* * *
55075 TGACTAAAATGCCCCTGAATATGCAAA
1 TGACCAAAATGCCCCTGAACATGAAAA
*
55102 TGACCAAAATGCCCCTGAACGTGAAAA
1 TGACCAAAATGCCCCTGAACATGAAAA
* *
55129 TGATCAAAATGTCCCT
1 TGACCAAAATGCCCCT
55145 ATGTTACCCT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (27 bp):
TGACCAAAATGCCCCTGAACATGAAAA
Found at i:57984 original size:11 final size:11
Alignment explanation
Indices: 57953--57989 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
57943 ACACCCTTAG
57953 GAAAAACTAGAA
1 GAAAAA-TAGAA
57965 G-AAAA-AGAA
1 GAAAAATAGAA
57974 GAAAAATAGAA
1 GAAAAATAGAA
57985 GAAAA
1 GAAAA
57990 GAAATTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 5 0.22
10 4 0.17
11 13 0.57
12 1 0.04
ACGTcount: A:0.73, C:0.03, G:0.19, T:0.05
Consensus pattern (11 bp):
GAAAAATAGAA
Found at i:58503 original size:8 final size:8
Alignment explanation
Indices: 58490--58514 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
58480 CCAATAATTC
58490 CAGGGCTT
1 CAGGGCTT
58498 CAGGGCTT
1 CAGGGCTT
58506 CAGGGCTT
1 CAGGGCTT
58514 C
1 C
58515 TTGTCTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.28, G:0.36, T:0.24
Consensus pattern (8 bp):
CAGGGCTT
Done.