Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 100 of 328
Found at i:27965860 original size:16 final size:16
Alignment explanation
Indices: 27965822--27965860 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
27965812 TCTTCAAAAA
*
27965822 AAAAACTAGCCTCTCC
1 AAAAACTAGCCTCTAC
*
27965838 AAAAACTAGCCTTTAC
1 AAAAACTAGCCTCTAC
*
27965854 AATAACT
1 AAAAACT
27965861 TTTCTCCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.28, G:0.05, T:0.23
Consensus pattern (16 bp):
AAAAACTAGCCTCTAC
Found at i:27966063 original size:18 final size:17
Alignment explanation
Indices: 27966036--27966095 Score: 58
Period size: 18 Copynumber: 3.7 Consensus size: 17
27966026 GTAGGTACAA
27966036 GTGGTAGTGGAGCAAGT
1 GTGGTAGTGGAGCAAGT
27966053 GTGGCTAGT-G-G--AGT
1 GTGG-TAGTGGAGCAAGT
*
27966067 -AGGTAGTGGAGCAAGT
1 GTGGTAGTGGAGCAAGT
27966083 GTGGCTAGTGGAG
1 GTGG-TAGTGGAG
27966096 TTGGTGGTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 13
0.69 0.04 0.27
Matches are distributed among these distances:
12 4 0.12
13 3 0.09
14 4 0.12
16 4 0.12
17 7 0.21
18 12 0.35
ACGTcount: A:0.22, C:0.07, G:0.48, T:0.23
Consensus pattern (17 bp):
GTGGTAGTGGAGCAAGT
Found at i:27966074 original size:30 final size:30
Alignment explanation
Indices: 27966037--27966135 Score: 162
Period size: 30 Copynumber: 3.3 Consensus size: 30
27966027 TAGGTACAAG
27966037 TGGTAGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTAGTGGAGCAAGTGTGGCTAGTGGAGT
*
27966067 AGGTAGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTAGTGGAGCAAGTGTGGCTAGTGGAGT
* *
27966097 TGGTGGTGGAGCAATTGTGGCTAGTGGAGT
1 TGGTAGTGGAGCAAGTGTGGCTAGTGGAGT
*
27966127 TGGTGGTGG
1 TGGTAGTGG
27966136 CAAAGGCTAG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.18, C:0.06, G:0.48, T:0.27
Consensus pattern (30 bp):
TGGTAGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:27966125 original size:18 final size:16
Alignment explanation
Indices: 27966036--27966125 Score: 52
Period size: 18 Copynumber: 5.8 Consensus size: 16
27966026 GTAGGTACAA
27966036 GTGGTAGTGGAGCAAGT
1 GTGGTAGTGGAGCAA-T
27966053 GTGGCTAGTGGAG---T
1 GTGG-TAGTGGAGCAAT
*
27966067 -AGGTAGTGGAGCAAGT
1 GTGGTAGTGGAGCAA-T
27966083 GTGGCTAGTGGAG---T
1 GTGG-TAGTGGAGCAAT
*
27966097 -TGGTGGTGGAGCAATT
1 GTGGTAGTGGAGCAA-T
27966113 GTGGCTAGTGGAG
1 GTGG-TAGTGGAG
27966126 TTGGTGGTGG
Statistics
Matches: 56, Mismatches: 4, Indels: 25
0.66 0.05 0.29
Matches are distributed among these distances:
12 15 0.27
13 5 0.09
14 2 0.04
16 2 0.04
17 9 0.16
18 23 0.41
ACGTcount: A:0.20, C:0.07, G:0.48, T:0.26
Consensus pattern (16 bp):
GTGGTAGTGGAGCAAT
Found at i:27968411 original size:28 final size:28
Alignment explanation
Indices: 27968378--27968463 Score: 100
Period size: 28 Copynumber: 3.0 Consensus size: 28
27968368 AAAACACACC
* *
27968378 AATATAATCTTCCAAAACACACCAGTAT
1 AATATAATCATCCAAAACACACCAGAAT
* * *
27968406 TATATAATCCTCCCAAACACACCAGAAT
1 AATATAATCATCCAAAACACACCAGAAT
* *
27968434 AATATAATCCATCCAAAAAACAACAGAAT
1 AATATAAT-CATCCAAAACACACCAGAAT
27968463 A
1 A
27968464 GCACAGAATG
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
28 31 0.65
29 17 0.35
ACGTcount: A:0.50, C:0.26, G:0.03, T:0.21
Consensus pattern (28 bp):
AATATAATCATCCAAAACACACCAGAAT
Found at i:27968435 original size:23 final size:24
Alignment explanation
Indices: 27968366--27968436 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 24
27968356 AAATGTCCAA
*
27968366 CCAAAACACACCA-ATATAATCTT
1 CCAAAACACACCAGATATAATCCT
27968389 CCAAAACACACCAGTATTATATAATCCT
1 CCAAAACACACCAG----ATATAATCCT
*
27968417 CCCAAACACACCAGA-ATAAT
1 CCAAAACACACCAGATATAAT
27968437 ATAATCCATC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
23 18 0.44
24 1 0.02
28 22 0.54
ACGTcount: A:0.46, C:0.31, G:0.03, T:0.20
Consensus pattern (24 bp):
CCAAAACACACCAGATATAATCCT
Found at i:27968526 original size:13 final size:13
Alignment explanation
Indices: 27968508--27968533 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27968498 ATAAACATCA
27968508 ACATCTCCAAATC
1 ACATCTCCAAATC
27968521 ACATCTCCAAATC
1 ACATCTCCAAATC
27968534 CCTTCTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.23
Consensus pattern (13 bp):
ACATCTCCAAATC
Found at i:27968638 original size:17 final size:17
Alignment explanation
Indices: 27968618--27968656 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
27968608 TTTTTTTATT
*
27968618 TCAATTTCATTTCCATA
1 TCAATTTCAATTCCATA
*
27968635 TCAATTTCAATTCCATT
1 TCAATTTCAATTCCATA
27968652 TCAAT
1 TCAAT
27968657 ATACAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (17 bp):
TCAATTTCAATTCCATA
Found at i:27968641 original size:23 final size:24
Alignment explanation
Indices: 27968615--27968663 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
27968605 TTTTTTTTTT
* *
27968615 ATTTCAATTTCATTTCCATAT-CA
1 ATTTCAATTCCATTTCAATATACA
27968638 ATTTCAATTCCATTTCAATATACA
1 ATTTCAATTCCATTTCAATATACA
27968662 AT
1 AT
27968664 CAATTCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.45
Consensus pattern (24 bp):
ATTTCAATTCCATTTCAATATACA
Found at i:27969910 original size:16 final size:16
Alignment explanation
Indices: 27969889--27969925 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
27969879 TTTATTCACT
27969889 AATATAAT-ATCAATTA
1 AATATAATAATCAA-TA
27969905 AATATAATAATCAATA
1 AATATAATAATCAATA
27969921 AATAT
1 AATAT
27969926 CTTTTACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (16 bp):
AATATAATAATCAATA
Found at i:27974642 original size:28 final size:27
Alignment explanation
Indices: 27974590--27974642 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
27974580 CTATTCAGAA
* *
27974590 ATCAGTGTTAACTAGGCCTTAGCCCAT
1 ATCAGTATTAACTAGGCCATAGCCCAT
*
27974617 ATCAGTATTAATCTGGGCCATAGCCC
1 ATCAGTATTAA-CTAGGCCATAGCCC
27974643 CTTACAGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (27 bp):
ATCAGTATTAACTAGGCCATAGCCCAT
Found at i:27974727 original size:60 final size:59
Alignment explanation
Indices: 27974604--27974738 Score: 157
Period size: 60 Copynumber: 2.2 Consensus size: 59
27974594 GTGTTAACTA
* *
27974604 GGCCTTAGCCCATATCAGTATTAATCTGGGCCATAGCCCCTTACAGTAACAGAGTATACTG
1 GGCC-TAGCCCATATCAGTATCAATCTGGGCCATAGCCCATTACAGT-ACAGAGTATACTG
* * *
27974665 GGCCTAGCCCATATCAGTATCAATCTGGGTCGTAGCCCTATTACAAGT-C-GAGATATATTG
1 GGCCTAGCCCATATCAGTATCAATCTGGGCCATAGCCC-ATTAC-AGTACAGAG-TATACTG
*
27974725 GGCCTTGCCCATAT
1 GGCCTAGCCCATAT
27974739 TAACACAGTT
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
59 3 0.05
60 51 0.78
61 8 0.12
62 3 0.05
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (59 bp):
GGCCTAGCCCATATCAGTATCAATCTGGGCCATAGCCCATTACAGTACAGAGTATACTG
Found at i:27974774 original size:19 final size:20
Alignment explanation
Indices: 27974731--27974786 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
27974721 ATTGGGCCTT
27974731 GCCCATATTAACACAGTTGG
1 GCCCATATTAACACAGTTGG
* *
27974751 GCCCATTTTAATACAGTT-G
1 GCCCATATTAACACAGTTGG
* *
27974770 GCCCATAATAAAACAGT
1 GCCCATATTAACACAGT
27974787 CTCATATGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (20 bp):
GCCCATATTAACACAGTTGG
Found at i:27974835 original size:22 final size:22
Alignment explanation
Indices: 27974810--27974851 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
27974800 TGCATGATAA
*
27974810 CTCCATCCAACCCTGCACTTGC
1 CTCCATCCAACCCTACACTTGC
* *
27974832 CTCCGTCCATCCCTACACTT
1 CTCCATCCAACCCTACACTT
27974852 CCTGTGGGGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.17, C:0.50, G:0.07, T:0.26
Consensus pattern (22 bp):
CTCCATCCAACCCTACACTTGC
Found at i:27979685 original size:15 final size:16
Alignment explanation
Indices: 27979653--27979687 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
27979643 TAAATATTTT
27979653 TTATAAAGATTATATA
1 TTATAAAGATTATATA
*
27979669 TTATAAAG-TTTTATA
1 TTATAAAGATTATATA
27979684 TTAT
1 TTAT
27979688 TTTTATTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (16 bp):
TTATAAAGATTATATA
Found at i:27980412 original size:19 final size:18
Alignment explanation
Indices: 27980388--27980430 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
27980378 TTAGAAATTA
27980388 TTTTTATCA-TACTAATAAT
1 TTTTTAT-AGTACTAAT-AT
*
27980407 TTTTTATAGTATTAATAT
1 TTTTTATAGTACTAATAT
27980425 TTTTTA
1 TTTTTA
27980431 AAATTATGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTTATAGTACTAATAT
Found at i:27984723 original size:26 final size:26
Alignment explanation
Indices: 27984666--27984772 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
27984656 TGAAATGCCC
*
27984666 ATCATGGAACATTTACCTAA-ACATT
1 ATCATGGAACATTTACCTAACCCATT
27984691 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
27984717 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
27984743 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
27984769 ATCA
1 ATCA
27984773 ATTTGTATCA
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
25 20 0.26
26 56 0.74
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:27988823 original size:16 final size:17
Alignment explanation
Indices: 27988785--27988830 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
27988775 GAGTTTTTCG
27988785 CATTCTTTATAAAATTTT
1 CATT-TTTATAAAATTTT
27988803 CATTTTTA-AAAATCTTT
1 CATTTTTATAAAAT-TTT
*
27988820 -ATTTTTGTAAA
1 CATTTTTATAAA
27988831 CCCATTCCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 11 0.44
17 10 0.40
18 4 0.16
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.54
Consensus pattern (17 bp):
CATTTTTATAAAATTTT
Found at i:27991567 original size:26 final size:26
Alignment explanation
Indices: 27991531--27991638 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
27991521 TGAAATGCTC
* *
27991531 ATCATGGAACATTTACCTAAACAATT
1 ATCATGGAACATTTACCTAACCCATT
27991557 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
27991583 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
27991609 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
27991635 ATCA
1 ATCA
27991639 ATTTGTATCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:27995219 original size:12 final size:12
Alignment explanation
Indices: 27995202--27995230 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
27995192 TGCTTCTGTA
27995202 TTTAATTTTATT
1 TTTAATTTTATT
27995214 TTTAA-TTTATT
1 TTTAATTTTATT
27995225 TTTAAT
1 TTTAAT
27995231 AATTTAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTAATTTTATT
Found at i:27998233 original size:25 final size:25
Alignment explanation
Indices: 27998186--27998233 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
27998176 TTCCATATAC
* * * *
27998186 TTATACTTATTTCGTTTATCTATCG
1 TTATAATTATTTCATATAACTATCG
27998211 TTATAATTATTTCATATAACTAT
1 TTATAATTATTTCATATAACTAT
27998234 TTTGTACATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.54
Consensus pattern (25 bp):
TTATAATTATTTCATATAACTATCG
Found at i:27998669 original size:137 final size:138
Alignment explanation
Indices: 27998399--27998738 Score: 538
Period size: 137 Copynumber: 2.5 Consensus size: 138
27998389 TGCCACAGTG
* * *
27998399 TCTTTCAACTATGGTCTTCCTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
1 TCTTTCAACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
* * ** *
27998464 TTCTTTTCATGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGCTG
66 TTCTTTTCATGTCAAGTTCCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGCTG
27998529 CCATGGTA
131 CCATGGTA
* *
27998537 TCTTTCAACCATGGTCTTATTCATTTCCCGTCATGTTGCCATGGTATCTTTCAACCATGG-CTTA
1 TCTTTCAACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
* *
27998601 TTCTTTTCATGTCAAGTTCCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTG
66 TTCTTTTCATGTCAAGTTCCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGCTG
27998666 CCATGGTA
131 CCATGGTA
* * *
27998674 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
1 TCTTTCAACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
27998739 CATATTTCAT
Statistics
Matches: 184, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
137 125 0.68
138 59 0.32
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (138 bp):
TCTTTCAACCATGGTCTTACTCATTTCCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
TTCTTTTCATGTCAAGTTCCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGCTG
CCATGGTA
Found at i:27998739 original size:46 final size:46
Alignment explanation
Indices: 27998399--27998748 Score: 499
Period size: 46 Copynumber: 7.6 Consensus size: 46
27998389 TGCCACAGTG
* *
27998399 TCTTTCAACTATGGTCTTCCTCATTTTC-TGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCA-TTTCATGTCATGTTGCCATGGTA
* *
27998445 TCTTTCAACCATGGTCTTATTCTTTTCATGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATGGTA
* * *
27998491 TCTTTCAACCATGGTCTTATTCATTTCATGTCACGCTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATGGTA
* **
27998537 TCTTTCAACCATGGTCTTATTCATTTCCCGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATGGTA
* * * *
27998583 TCTTTCAACCATGG-CTTATTCTTTTCATGTCAAGTTCCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATGGTA
* *
27998628 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATGGTA
* *
27998674 TCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATGGTA
27998720 TCTTTCAACCATGGTCTTACAT-ATTTCAT
1 TCTTTCAACCATGGTCTTAC-TCATTTCAT
27998749 TTTAGAGAGT
Statistics
Matches: 278, Mismatches: 23, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
45 44 0.16
46 234 0.84
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATGGTA
Found at i:28001114 original size:15 final size:15
Alignment explanation
Indices: 28001086--28001119 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28001076 GGATTGAATG
28001086 TTGTAAATGTTATGA
1 TTGTAAATGTTATGA
28001101 TTGTGAAATG-TATGA
1 TTGT-AAATGTTATGA
28001116 TTGT
1 TTGT
28001120 CGGACAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (15 bp):
TTGTAAATGTTATGA
Found at i:28003394 original size:38 final size:38
Alignment explanation
Indices: 28003352--28003425 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
28003342 TAAAAAGCCG
28003352 TATCTAAGGACCGAGGTGAGGAGGTAAAAGAAGCCTAT
1 TATCTAAGGACCGAGGTGAGGAGGTAAAAGAAGCCTAT
28003390 TATCTAAGGACCGAGGTGAGGAGGTAAAAGAAGCCT
1 TATCTAAGGACCGAGGTGAGGAGGTAAAAGAAGCCT
28003426 TCTTTCAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.36, C:0.14, G:0.32, T:0.18
Consensus pattern (38 bp):
TATCTAAGGACCGAGGTGAGGAGGTAAAAGAAGCCTAT
Found at i:28008338 original size:15 final size:16
Alignment explanation
Indices: 28008312--28008341 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28008302 TGAATGTTAT
28008312 AAATGTTATGATTGTG
1 AAATGTTATGATTGTG
28008328 AAATG-TATGATTGT
1 AAATGTTATGATTGT
28008342 CGGACAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.43
Consensus pattern (16 bp):
AAATGTTATGATTGTG
Found at i:28009477 original size:20 final size:20
Alignment explanation
Indices: 28009441--28009486 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
28009431 TCGGATCACC
*
28009441 TAAAA-ATTTAGTTATTTTAA
1 TAAAACATTTAGTGA-TTTAA
*
28009461 TAAAACATTTA-TGATTTAC
1 TAAAACATTTAGTGATTTAA
28009480 TAAAACA
1 TAAAACA
28009487 ACAATTTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 11 0.48
20 7 0.30
21 5 0.22
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (20 bp):
TAAAACATTTAGTGATTTAA
Found at i:28010133 original size:132 final size:132
Alignment explanation
Indices: 28009896--28010135 Score: 354
Period size: 132 Copynumber: 1.8 Consensus size: 132
28009886 TCTTGCTTTG
* * * * * *
28009896 GAAAACGTGAATGAAATTCCAAAGGGATATTCGATTATTTTGCACAAACGAGAAATTGCAACCCA
1 GAAAACATGAACGAAATTCCAAAGAGACATCCGATTATTTTGCACAAACAAGAAATTGCAACCCA
* * * *
28009961 GCACGATAGGGCACGATTCCCTGAATTGCCGAACGTCGAACATTTCCTTCGTTTTAAAAGGTTTT
66 ACACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTTCCTTCGTTTTAAAAGGTTTT
28010026 TA
131 TA
* **
28010028 GAAAACATGAACGAAATTCTAAAGAGACATCCGATTATTTTGGGCAAACAAGAAATTGCAACCCA
1 GAAAACATGAACGAAATTCCAAAGAGACATCCGATTATTTTGCACAAACAAGAAATTGCAACCCA
*
28010093 ACACGATAGGGCACGATTCCCCGAATTGCTAAACATCGAACAT
66 ACACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACAT
28010136 CGTCTCCGTT
Statistics
Matches: 94, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
132 94 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.24
Consensus pattern (132 bp):
GAAAACATGAACGAAATTCCAAAGAGACATCCGATTATTTTGCACAAACAAGAAATTGCAACCCA
ACACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTTCCTTCGTTTTAAAAGGTTTT
TA
Found at i:28010451 original size:3 final size:3
Alignment explanation
Indices: 28010438--28010497 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
28010428 ACAAACAATG
*
28010438 ATA AAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28010486 ATA ATA ATA ATA
1 ATA ATA ATA ATA
28010498 TAGAAATACA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:28010558 original size:2 final size:2
Alignment explanation
Indices: 28010553--28010577 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28010543 ATAAAAAACA
28010553 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
28010578 CATAAAAATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28010829 original size:3 final size:3
Alignment explanation
Indices: 28010816--28010895 Score: 53
Period size: 3 Copynumber: 26.3 Consensus size: 3
28010806 GAGGGCATAT
28010816 ATA AT- ATA ATA AT- ATAA ATA ATA ATA TATA CATGA GA-A ATA ATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA -ATA -AT-A -ATA ATA ATA
* *
28010860 ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA A
28010896 AAAAAATAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
2 9 0.15
3 42 0.68
4 9 0.15
5 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:28010838 original size:12 final size:12
Alignment explanation
Indices: 28010814--28010896 Score: 71
Period size: 12 Copynumber: 6.6 Consensus size: 12
28010804 GAGAGGGCAT
28010814 ATATAATATAATA
1 ATATAA-ATAATA
28010827 ATATAAATAATA
1 ATATAAATAATA
28010839 ATATATACATGAGA-A
1 ATATA-A-AT-A-ATA
28010854 ATA-ATAATAATA
1 ATATA-AATAATA
28010866 ATATAAATAATA
1 ATATAAATAATA
* *
28010878 GTAAAAATAATA
1 ATATAAATAATA
*
28010890 AAATAAA
1 ATATAAA
28010897 AAAAATAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
11 1 0.02
12 37 0.63
13 10 0.17
14 5 0.08
15 5 0.08
16 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (12 bp):
ATATAAATAATA
Found at i:28010857 original size:21 final size:18
Alignment explanation
Indices: 28010816--28010877 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 18
28010806 GAGGGCATAT
*
28010816 ATAAT-ATAATAATATAA
1 ATAATAATAATAATAGAA
28010833 ATAATAATATATACATGAGAA
1 ATAATAATA-ATA-AT-AGAA
*
28010854 ATAATAATAATAATATAA
1 ATAATAATAATAATAGAA
28010872 ATAATA
1 ATAATA
28010878 GTAAAAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.13
18 12 0.31
19 5 0.13
20 5 0.13
21 12 0.31
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (18 bp):
ATAATAATAATAATAGAA
Found at i:28010886 original size:27 final size:27
Alignment explanation
Indices: 28010814--28010903 Score: 73
Period size: 27 Copynumber: 3.4 Consensus size: 27
28010804 GAGAGGGCAT
* *
28010814 ATATAATATAATAATATAAATAATAAT-
1 ATATAA-ATAATAGTAAAAATAATAATA
* *
28010841 ATATACAT--GAG-AAATAATAATAATA
1 ATATAAATAATAGTAAA-AATAATAATA
28010866 ATATAAATAATAGTAAAAATAATAA-A
1 ATATAAATAATAGTAAAAATAATAATA
* *
28010892 ATAAAAAAAATA
1 ATATAAATAATA
28010904 AAACAAAGCT
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
23 2 0.04
24 10 0.20
25 7 0.14
26 13 0.26
27 15 0.30
28 3 0.06
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (27 bp):
ATATAAATAATAGTAAAAATAATAATA
Found at i:28011261 original size:18 final size:18
Alignment explanation
Indices: 28011240--28011289 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 18
28011230 CTCTAAAAAA
*
28011240 CAAAAAACAAACCTCCTC
1 CAAAAAACAAACCCCCTC
28011258 CAAAAAACAAAAAACCCCCTC
1 CAAAAAAC---AAACCCCCTC
28011279 CAAAAAACAAA
1 CAAAAAACAAA
28011290 AAAAAACACC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 11 0.39
21 17 0.61
ACGTcount: A:0.60, C:0.34, G:0.00, T:0.06
Consensus pattern (18 bp):
CAAAAAACAAACCCCCTC
Found at i:28011293 original size:24 final size:24
Alignment explanation
Indices: 28011211--28011313 Score: 108
Period size: 25 Copynumber: 4.3 Consensus size: 24
28011201 TAGCCTTTCC
* *
28011211 AAAACAAAAAACAACCCTCCTCTAA
1 AAAACAAAAAAAAACCC-CCTCCAA
*
28011236 AAAACAAAAAACAAACCTCCTCCAA
1 AAAACAAAAAA-AAACCCCCTCCAA
28011261 AAAAC---AAAAAACCCCCTCCAA
1 AAAACAAAAAAAAACCCCCTCCAA
28011282 AAAACAAAAAAAAACACCCC-CTC-A
1 AAAACAAAAAAAAAC-CCCCTC-CAA
28011306 AAAACAAA
1 AAAACAAA
28011314 GTCTTGAATG
Statistics
Matches: 68, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
21 17 0.25
22 3 0.04
24 17 0.25
25 27 0.40
26 4 0.06
ACGTcount: A:0.61, C:0.32, G:0.00, T:0.07
Consensus pattern (24 bp):
AAAACAAAAAAAAACCCCCTCCAA
Found at i:28011406 original size:13 final size:13
Alignment explanation
Indices: 28011388--28011447 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
28011378 GGGTGGTTTA
28011388 GGTGGCCAAGGTG
1 GGTGGCCAAGGTG
***
28011401 GGTGGCCAACAAG
1 GGTGGCCAAGGTG
*** *
28011414 GGTGGTGGA-GTA
1 GGTGGCCAAGGTG
28011426 GGTGGCCAAGGTG
1 GGTGGCCAAGGTG
28011439 GGTGGCCAA
1 GGTGGCCAA
28011448 CAAGGGTGGT
Statistics
Matches: 33, Mismatches: 13, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
12 6 0.18
13 27 0.82
ACGTcount: A:0.20, C:0.15, G:0.50, T:0.15
Consensus pattern (13 bp):
GGTGGCCAAGGTG
Found at i:28011428 original size:38 final size:38
Alignment explanation
Indices: 28011386--28011465 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
28011376 TGGGGTGGTT
28011386 TAGGTGGCCAAGGTGGGTGGCCAACAAGGGTGGTGGAG
1 TAGGTGGCCAAGGTGGGTGGCCAACAAGGGTGGTGGAG
28011424 TAGGTGGCCAAGGTGGGTGGCCAACAAGGGTGGTGGAG
1 TAGGTGGCCAAGGTGGGTGGCCAACAAGGGTGGTGGAG
28011462 TAGG
1 TAGG
28011466 CTTAATTTGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.21, C:0.12, G:0.50, T:0.16
Consensus pattern (38 bp):
TAGGTGGCCAAGGTGGGTGGCCAACAAGGGTGGTGGAG
Found at i:28011764 original size:44 final size:44
Alignment explanation
Indices: 28011701--28012561 Score: 1050
Period size: 44 Copynumber: 20.2 Consensus size: 44
28011691 AGGAGCACTG
* * *
28011701 ATCTGTTATTTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAA
* * * *
28011745 ATCTGTTATCTTTGATCTGCTCTCTGCCGCTACGGAGAAGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAA
*
28011789 ATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGACTGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGA-TGCCAA
*
28011834 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAAAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAA
* **
28011878 ATCTGTTATCTTCGATCTGCTCTCCGCCTCTACAGAGACACCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAA
* *
28011922 ATCTATTATCTTCGATCTGCTCTCTGCCGCTACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAA
28011966 ATC----ATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAA
* *
28012006 ATC----ATCTTCGATCTGTTCTCCGCCGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAA
* * **
28012046 ATCTTGTTA-CTTTCAATCGGCTCTTTGCCGCTACAGAGATGCCAA
1 ATC-TGTTATC-TTCGATCTGCTCTCCGCCGCTACAGAGATGCCAA
* *
28012091 ATCTGTTATTTTCGATCTGGTCTCCGCCGCTACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAA
* * *
28012135 A----TAATCTTCGATCTGCTCTCCGCCACTCCAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAA
* *
28012175 ATCTGTTATTTTCGATTTGCTCTCCGCCGCTACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAA
* * * *
28012219 ATC----ATCTTCGATCTACTCTCTGCCGCTATAAAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAA
*
28012259 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCGA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAA
* * *
28012303 ATCTGTTATCTTCGATCTACTCTCTGCCGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAA
* * *
28012347 ATCTATTATTTTTGATCTGCTCTCCGCCGCTACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAA
*
28012391 ATC----ATCTTCGATCTGCTCTCCGCCACTACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAA
* * *
28012431 ATC----ATCTTCGATTTGCTCTCTGCCGCTACAGAAATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAA
*
28012471 ATC----ATCTTCGATCTGCTCTCCGCAGCTACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAA
* *
28012511 A----TTATCTTTGATCTGCTCTCCGCCGCTACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAA
*
28012551 AACTGTTATCT
1 ATCTGTTATCT
28012562 GTTTCAAGGA
Statistics
Matches: 717, Mismatches: 78, Indels: 44
0.85 0.09 0.05
Matches are distributed among these distances:
40 288 0.40
44 356 0.50
45 73 0.10
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.30
Consensus pattern (44 bp):
ATCTGTTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAA
Found at i:28024640 original size:3 final size:3
Alignment explanation
Indices: 28024632--28024691 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
28024622 ACAAACAATG
28024632 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28024680 ATA ATA ATA ATA
1 ATA ATA ATA ATA
28024692 TAGAAATACA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:28024795 original size:20 final size:18
Alignment explanation
Indices: 28024638--28024800 Score: 60
Period size: 18 Copynumber: 9.1 Consensus size: 18
28024628 AATGATAATA
*
28024638 ATAATAATA-ATAATAAT
1 ATAATAATATATAAAAAT
*
28024655 AATAATAATA-ATAATAAT
1 -ATAATAATATATAAAAAT
*
28024673 AATAATAATA-ATAATAAT
1 -ATAATAATATATAAAAAT
* **
28024691 ATAGA-AATACA-AAAAGC
1 ATA-ATAATATATAAAAAT
28024708 A-AAT-ATA-ATAAAAAT
1 ATAATAATATATAAAAAT
28024723 ATTAAATTAA-AGTAATAAAAA-
1 A-T-AA-TAATA-T-ATAAAAAT
* *
28024744 ATAATACTATATAAATAT
1 ATAATAATATATAAAAAT
*
28024762 AT-ATATATACATAAAAAT
1 ATAATA-ATATATAAAAAT
*
28024780 ATACATTAATATATAATAAT
1 ATA-A-TAATATATAAAAAT
28024800 A
1 A
28024801 ATAGTAATAG
Statistics
Matches: 115, Mismatches: 12, Indels: 34
0.71 0.07 0.21
Matches are distributed among these distances:
14 1 0.01
15 9 0.08
16 1 0.01
17 20 0.17
18 55 0.48
19 5 0.04
20 14 0.12
21 3 0.03
22 7 0.06
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (18 bp):
ATAATAATATATAAAAAT
Found at i:28025027 original size:12 final size:13
Alignment explanation
Indices: 28025003--28025032 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
28024993 GAGAGAGCAT
28025003 ATATAATATAATA
1 ATATAATATAATA
28025016 ATATAA-ATAATA
1 ATATAATATAATA
28025028 ATATA
1 ATATA
28025033 TGCATGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATATAATATAATA
Found at i:28025056 original size:9 final size:9
Alignment explanation
Indices: 28025042--28025087 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
28025032 ATGCATGAGA
28025042 AATAATAAT
1 AATAATAAT
28025051 AATAATAAT
1 AATAATAAT
28025060 AGA-AATAAT
1 A-ATAATAAT
* *
28025069 AGTAAAAAT
1 AATAATAAT
28025078 AATAA-AAT
1 AATAATAAT
28025086 AA
1 AA
28025088 AAAATAAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
8 5 0.16
9 26 0.81
10 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (9 bp):
AATAATAAT
Found at i:28025063 original size:21 final size:21
Alignment explanation
Indices: 28025005--28025094 Score: 84
Period size: 21 Copynumber: 4.5 Consensus size: 21
28024995 GAGAGCATAT
*
28025005 ATAAT-ATAATAATATAAATA
1 ATAATAATAATAATAGAAATA
*
28025025 ATAAT-AT-ATGCATGAGAAATA
1 ATAATAATAAT-AAT-AGAAATA
28025046 ATAATAATAATAATAGAAATA
1 ATAATAATAATAATAGAAATA
* *
28025067 ATAGTAAAAATAATA-AAATA
1 ATAATAATAATAATAGAAATA
28025087 A-AA-AATAA
1 ATAATAATAA
28025095 AACAAAGCTC
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
18 4 0.07
19 3 0.05
20 15 0.25
21 31 0.53
22 4 0.07
23 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.28
Consensus pattern (21 bp):
ATAATAATAATAATAGAAATA
Found at i:28025093 original size:12 final size:13
Alignment explanation
Indices: 28025041--28025096 Score: 53
Period size: 12 Copynumber: 4.2 Consensus size: 13
28025031 TATGCATGAG
28025041 AAATAATAATAATA
1 AAATAA-AATAATA
28025055 ATAATAGAAATAATA
1 A-AATA-AAATAATA
**
28025070 GTA-AAAATAATA
1 AAATAAAATAATA
28025082 AAATAAAA-AATA
1 AAATAAAATAATA
28025094 AAA
1 AAA
28025097 CAAAGCTCTC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
12 16 0.46
13 5 0.14
14 2 0.06
15 11 0.31
16 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (13 bp):
AAATAAAATAATA
Found at i:28025432 original size:25 final size:25
Alignment explanation
Indices: 28025400--28025481 Score: 105
Period size: 25 Copynumber: 3.3 Consensus size: 25
28025390 TAGCCTTTCC
* *
28025400 AAAACAAAAAACAACCCTCCTCTAA
1 AAAACAAAAAACAAACCTCCTCCAA
28025425 AAAACAAAAAACAAACCTCCTCCAA
1 AAAACAAAAAACAAACCTCCTCCAA
* *
28025450 AAAACAAAAAAAAAACACCCCT-C-A
1 AAAACAAAAAACAAAC-CTCCTCCAA
28025474 AAAACAAA
1 AAAACAAA
28025482 GTCTTGAATG
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
24 9 0.17
25 39 0.75
26 4 0.08
ACGTcount: A:0.63, C:0.29, G:0.00, T:0.07
Consensus pattern (25 bp):
AAAACAAAAAACAAACCTCCTCCAA
Found at i:28025574 original size:13 final size:13
Alignment explanation
Indices: 28025556--28025615 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
28025546 GGGTGGTTTA
28025556 GGTGGCCAAGGTG
1 GGTGGCCAAGGTG
***
28025569 GGTGGCCAACAAG
1 GGTGGCCAAGGTG
*** *
28025582 GGTGGTGGA-GTA
1 GGTGGCCAAGGTG
28025594 GGTGGCCAAGGTG
1 GGTGGCCAAGGTG
28025607 GGTGGCCAA
1 GGTGGCCAA
28025616 CAAGGGTGGT
Statistics
Matches: 33, Mismatches: 13, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
12 6 0.18
13 27 0.82
ACGTcount: A:0.20, C:0.15, G:0.50, T:0.15
Consensus pattern (13 bp):
GGTGGCCAAGGTG
Found at i:28025596 original size:38 final size:38
Alignment explanation
Indices: 28025554--28025634 Score: 162
Period size: 38 Copynumber: 2.1 Consensus size: 38
28025544 TGGGGTGGTT
28025554 TAGGTGGCCAAGGTGGGTGGCCAACAAGGGTGGTGGAG
1 TAGGTGGCCAAGGTGGGTGGCCAACAAGGGTGGTGGAG
28025592 TAGGTGGCCAAGGTGGGTGGCCAACAAGGGTGGTGGAG
1 TAGGTGGCCAAGGTGGGTGGCCAACAAGGGTGGTGGAG
28025630 TAGGT
1 TAGGT
28025635 TTAATTTGGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.21, C:0.12, G:0.49, T:0.17
Consensus pattern (38 bp):
TAGGTGGCCAAGGTGGGTGGCCAACAAGGGTGGTGGAG
Found at i:28026862 original size:64 final size:64
Alignment explanation
Indices: 28026652--28026862 Score: 151
Period size: 64 Copynumber: 3.2 Consensus size: 64
28026642 CTGGGCCAGA
*
28026652 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
* * * *** * ** *
28026716 GCCCATTTCAAAATAC-ATGCAACATCAGTAAACATATGCAAGCCC--ATTTGGGTAACAGTGGT
1 GCCCATTTCAGATTACAAT--AA-A-CTG-GGCCTTA-GC---CCCTTATTCAGATAACA---GT
* *
28026778 ACTGGGCCAGA-
54 A-TGGCCCATAG
*
28026789 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
28026853 GCCCATTTCA
1 GCCCATTTCA
28026863 AAATACATGC
Statistics
Matches: 103, Mismatches: 27, Indels: 34
0.63 0.16 0.21
Matches are distributed among these distances:
63 9 0.09
64 25 0.24
65 5 0.05
66 1 0.01
67 11 0.11
68 5 0.05
69 5 0.05
70 11 0.11
71 1 0.01
72 5 0.05
73 16 0.16
74 9 0.09
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (64 bp):
GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
Found at i:28026883 original size:137 final size:138
Alignment explanation
Indices: 28026632--28026904 Score: 539
Period size: 137 Copynumber: 2.0 Consensus size: 138
28026622 ACATTCAGGT
28026632 ACAGCTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAG
1 ACAGCTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAG
28026697 ATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCCCA
66 ATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCCCA
28026762 TTTGGGTA
131 TTTGGGTA
28026770 ACAG-TGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAG
1 ACAGCTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAG
28026834 ATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCCCA
66 ATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCCCA
28026899 TTTGGG
131 TTTGGG
28026905 GAGACTACTC
Statistics
Matches: 135, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
137 131 0.97
138 4 0.03
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (138 bp):
ACAGCTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAG
ATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGCCCA
TTTGGGTA
Found at i:28028716 original size:26 final size:26
Alignment explanation
Indices: 28028680--28028803 Score: 207
Period size: 26 Copynumber: 4.8 Consensus size: 26
28028670 ACATGAATTC
28028680 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28028706 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
28028732 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
28028758 TTATCATGAAACATTTACCTAA-CCA
1 TTATCATGAAACATTTACCTAACCCA
*
28028783 TTATCATG-TACATTTACCTAA
1 TTATCATGAAACATTTACCTAA
28028804 ATTATATATC
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
24 12 0.13
25 10 0.11
26 71 0.76
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:28032757 original size:136 final size:136
Alignment explanation
Indices: 28032513--28032930 Score: 736
Period size: 136 Copynumber: 3.1 Consensus size: 136
28032503 CATTGGGCCT
** *
28032513 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGTCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
28032578 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
28032643 ATATGC
131 ATATGC
* *
28032649 AAGCCCATTTGGGTAACAGTGATACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
28032714 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAAT-AA
28032779 CATATGC
130 CATATGC
*
28032786 -AGGCCATTTGGGTAACAGTGGTACTGGG-CAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
28032849 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATC-A-AAC
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
28032912 ATATGC
131 ATATGC
28032918 AAGCCCATTTGGG
1 AAGCCCATTTGGG
28032931 AGACTACTCA
Statistics
Matches: 269, Mismatches: 11, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
132 9 0.03
133 11 0.04
135 93 0.35
136 147 0.55
137 9 0.03
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (136 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
ATATGC
Found at i:28034734 original size:26 final size:26
Alignment explanation
Indices: 28034698--28034833 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
28034688 CATGATATTC
28034698 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28034724 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
28034750 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
28034776 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
28034802 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
28034828 TTATCA
1 TTATCA
28034834 AAAGTGTACA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:28042610 original size:6 final size:6
Alignment explanation
Indices: 28042593--28042632 Score: 71
Period size: 6 Copynumber: 6.5 Consensus size: 6
28042583 GAAAACAAAT
28042593 GGGAGAA GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA GGG
1 GGGAG-A GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA GGG
28042633 GAAGGAGGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 28 0.85
7 5 0.15
ACGTcount: A:0.33, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GGGAGA
Found at i:28042620 original size:18 final size:19
Alignment explanation
Indices: 28042593--28042637 Score: 76
Period size: 18 Copynumber: 2.5 Consensus size: 19
28042583 GAAAACAAAT
28042593 GGGAGAAGGGAGAGGGAGA
1 GGGAGAAGGGAGAGGGAGA
28042612 GGGAG-AGGGAGAGGGAGA
1 GGGAGAAGGGAGAGGGAGA
28042630 GGG-GAAGG
1 GGGAGAAGG
28042638 AGGATGGCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.04
18 19 0.76
19 5 0.20
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (19 bp):
GGGAGAAGGGAGAGGGAGA
Found at i:28043005 original size:14 final size:14
Alignment explanation
Indices: 28042986--28043026 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
28042976 ATTCAGCCCA
28042986 TTTATATTAAAATT
1 TTTATATTAAAATT
28043000 TTTATATTAAAATT
1 TTTATATTAAAATT
*
28043014 TTTATATAAAAAT
1 TTTATATTAAAAT
28043027 AAATTTTAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTATATTAAAATT
Found at i:28045679 original size:14 final size:14
Alignment explanation
Indices: 28045660--28045696 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
28045650 ATTTCTTGTC
28045660 TCATGCTTTTAATA
1 TCATGCTTTTAATA
28045674 TCATGCTTTTAATA
1 TCATGCTTTTAATA
28045688 TCATGCTTT
1 TCATGCTTT
28045697 CATGCTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.51
Consensus pattern (14 bp):
TCATGCTTTTAATA
Found at i:28046165 original size:37 final size:37
Alignment explanation
Indices: 28046112--28046184 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
28046102 AATACACATA
*
28046112 AATGTGCCTAGCACCTCATCAATATG-TCCAAAGTAG
1 AATGTGCCTAGCACCTCATCAATATGAACCAAAGTAG
*
28046148 AATGTGCGCTTGCACCTCATCAATATGAACCAAAGTA
1 AATGTGC-CTAGCACCTCATCAATATGAACCAAAGTA
28046185 AACCTCGTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 7 0.21
37 18 0.55
38 8 0.24
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (37 bp):
AATGTGCCTAGCACCTCATCAATATGAACCAAAGTAG
Found at i:28048425 original size:34 final size:34
Alignment explanation
Indices: 28048382--28048454 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
28048372 GTAATACTAA
28048382 CATTCTTTCTTCGGAATATTATAAAGTTAAATAG
1 CATTCTTTCTTCGGAATATTATAAAGTTAAATAG
28048416 CATTCTTTCTTCGGAATATTATAAAGTTAAATAG
1 CATTCTTTCTTCGGAATATTATAAAGTTAAATAG
28048450 CATTC
1 CATTC
28048455 AACAAATCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (34 bp):
CATTCTTTCTTCGGAATATTATAAAGTTAAATAG
Found at i:28050074 original size:26 final size:26
Alignment explanation
Indices: 28050037--28050172 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
28050027 TGATACAAAT
* *
28050037 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
28050063 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
28050089 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
28050115 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
28050141 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
28050167 TGATAA
1 TGATAA
28050173 GAATATCATG
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:28051674 original size:25 final size:26
Alignment explanation
Indices: 28051646--28051697 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
28051636 TTTACAGTTT
28051646 TACCCCTAGAGATAAATT-ACCGAAA
1 TACCCCTAGAGATAAATTGACCGAAA
* * *
28051671 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGAGATAAATTGACCGAAA
28051697 T
1 T
28051698 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (26 bp):
TACCCCTAGAGATAAATTGACCGAAA
Found at i:28055935 original size:26 final size:26
Alignment explanation
Indices: 28055848--28055981 Score: 218
Period size: 26 Copynumber: 5.2 Consensus size: 26
28055838 TGATACAAAT
28055848 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
28055874 TGATAAT-GGTTAGGTAAATGTT-CA
1 TGATAATAGGTTAGGTAAATGTTCCA
28055898 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
28055924 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
28055950 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
28055976 TGATAA
1 TGATAA
28055982 GAATTCATGT
Statistics
Matches: 104, Mismatches: 2, Indels: 4
0.95 0.02 0.04
Matches are distributed among these distances:
24 9 0.09
25 30 0.29
26 65 0.62
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:28057482 original size:25 final size:26
Alignment explanation
Indices: 28057454--28057505 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
28057444 TTTACAGTTT
28057454 TACCCCTAGAGATAAATT-ACCGAAA
1 TACCCCTAGAGATAAATTGACCGAAA
* * *
28057479 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGAGATAAATTGACCGAAA
28057505 T
1 T
28057506 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (26 bp):
TACCCCTAGAGATAAATTGACCGAAA
Found at i:28061699 original size:26 final size:26
Alignment explanation
Indices: 28061662--28061797 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
28061652 TGATACAAAT
* *
28061662 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
28061688 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
28061714 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
28061740 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
28061766 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
28061792 TGATAA
1 TGATAA
28061798 GAATTCATGT
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:28063301 original size:25 final size:26
Alignment explanation
Indices: 28063273--28063324 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
28063263 TTTACAGTTT
28063273 TACCCCTAGAGATAAATT-ACCGAAA
1 TACCCCTAGAGATAAATTGACCGAAA
* * *
28063298 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGAGATAAATTGACCGAAA
28063324 T
1 T
28063325 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (26 bp):
TACCCCTAGAGATAAATTGACCGAAA
Found at i:28063710 original size:32 final size:33
Alignment explanation
Indices: 28063633--28063724 Score: 91
Period size: 32 Copynumber: 2.9 Consensus size: 33
28063623 TATGGGCCAT
**
28063633 ACTGTTATCTGAATAAGGGCTAAGGCCCAGTTT
1 ACTGTTATCTGAATAAGGGCTAAGGCCCAGTAC
* * **
28063666 ATTGTAATCTGAA-AAGGGCTCTGGCCCAGTAC
1 ACTGTTATCTGAATAAGGGCTAAGGCCCAGTAC
* *
28063698 ACTGTTACCTGAAT--GGGCTTAGGCCCA
1 ACTGTTATCTGAATAAGGGCTAAGGCCCA
28063725 ATGGGCTTGA
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
31 11 0.23
32 25 0.53
33 11 0.23
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (33 bp):
ACTGTTATCTGAATAAGGGCTAAGGCCCAGTAC
Found at i:28064836 original size:125 final size:126
Alignment explanation
Indices: 28064707--28064988 Score: 296
Period size: 130 Copynumber: 2.2 Consensus size: 126
28064697 CCCAAACTGT
* * * * *** *
28064707 AAATCGAAACACAGCACGATTGGGCACGATATATCGAATTTCCAAATACAAAACATTGCCTCATT
1 AAATCGAAACCCAGCACGATTGGGCACGACATACCAAACCCCCAAACACAAAACATTGCCTCATT
* * ** * * *
28064772 TTAA-TTTGAGAAAACATGGATGAAATTTCAAAAGGATATTTTGTATTTTAGTCGAATGGA
66 TTAATTTTAAAAAAACATGGATGAAATTTCAAAAGGATATTCCGCATTTTAGTCGAACGAA
* * * * ** *
28064832 AAATCGAAGCCCAGCACGATTGGACACGACCTCCCAAACCCCCAAACACAAAATGTTGCCTCGTT
1 AAATCGAAACCCAGCACGATTGGGCACGACATACCAAACCCCCAAACACAAAACATTGCCTCATT
*
28064897 TTAATTTTTTTTAAAAAAACATGGATGAAATTTCAAAAGGATATTCCGCATTTTAGTTGAACGAA
66 TTAA----TTTTAAAAAAACATGGATGAAATTTCAAAAGGATATTCCGCATTTTAGTCGAACGAA
* *
28064962 AAATTGAAACCCAGCACGATAGGGCAC
1 AAATCGAAACCCAGCACGATTGGGCAC
28064989 AATTCCTCGA
Statistics
Matches: 125, Mismatches: 27, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
125 54 0.43
130 71 0.57
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.26
Consensus pattern (126 bp):
AAATCGAAACCCAGCACGATTGGGCACGACATACCAAACCCCCAAACACAAAACATTGCCTCATT
TTAATTTTAAAAAAACATGGATGAAATTTCAAAAGGATATTCCGCATTTTAGTCGAACGAA
Found at i:28065006 original size:130 final size:130
Alignment explanation
Indices: 28064782--28065015 Score: 317
Period size: 130 Copynumber: 1.8 Consensus size: 130
28064772 TTAATTTGAG
** * * * *
28064782 AAAACATGGATGAAATTTCAAAAGGATATTTTGTATTTTAGTCGAATGGAAAATCGAAGCCCAGC
1 AAAACATGGATGAAATTTCAAAAGGATATTCCGCATTTTAGTCGAACGAAAAATCGAAACCCAGC
* *
28064847 ACGATTGGACACGACCTCCCAAACCCCCAAACACAAAATGTTGCCTCGTTTTAATTTTTTTTAAA
66 ACGATAGGACACGAACTCCCAAACCCCCAAACACAAAATGTTGCCTCGTTTTAATTTTTTTTAAA
* *
28064912 AAAACATGGATGAAATTTCAAAAGGATATTCCGCATTTTAGTTGAACGAAAAATTGAAACCCAGC
1 AAAACATGGATGAAATTTCAAAAGGATATTCCGCATTTTAGTCGAACGAAAAATCGAAACCCAGC
* * * * *
28064977 ACGATAGGGCAC-AATTCCTCGAACTCCCAAACACGAAAT
66 ACGATAGGACACGAACTCC-CAAACCCCCAAACACAAAAT
28065016 ATTTCCTTAT
Statistics
Matches: 88, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
129 4 0.05
130 84 0.95
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (130 bp):
AAAACATGGATGAAATTTCAAAAGGATATTCCGCATTTTAGTCGAACGAAAAATCGAAACCCAGC
ACGATAGGACACGAACTCCCAAACCCCCAAACACAAAATGTTGCCTCGTTTTAATTTTTTTTAAA
Found at i:28065165 original size:21 final size:23
Alignment explanation
Indices: 28065118--28065171 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
28065108 CATTCAAGAT
**
28065118 AAAATAATATATAAAACTCTTTA
1 AAAATAATATATAAAACTAATTA
*
28065141 AAAATAATATAT-AAAC-AATTC
1 AAAATAATATATAAAACTAATTA
28065162 AAAAT-ATATA
1 AAAATAATATA
28065172 ATGTGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 4 0.14
23 12 0.43
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATAATATATAAAACTAATTA
Found at i:28065224 original size:51 final size:49
Alignment explanation
Indices: 28065144--28065241 Score: 128
Period size: 51 Copynumber: 2.0 Consensus size: 49
28065134 CTCTTTAAAA
*
28065144 ATAATATATAAACAATTCAAAATATATAATGTGTAAAAAAGTTTGAAATAC
1 ATAATATATAAACAATTCAAAATAAATAATGTGT-AAAAA-TTTGAAATAC
*
28065195 ATAATATATGAAA-ATATT-AAAGTAAATAATGTGTAAAAATTTGAAAT
1 ATAATATAT-AAACA-ATTCAAAATAAATAATGTGTAAAAATTTGAAAT
28065242 GAGCATTGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
49 8 0.19
50 5 0.12
51 24 0.56
52 6 0.14
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (49 bp):
ATAATATATAAACAATTCAAAATAAATAATGTGTAAAAATTTGAAATAC
Found at i:28065403 original size:25 final size:23
Alignment explanation
Indices: 28065348--28065403 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
28065338 ATAATAATGA
*
28065348 AAATAATAATAGTATATAAATAG
1 AAATAATAATAGTATAGAAATAG
*
28065371 AAAT-ATAATAGTAGTAGAAATAT
1 AAATAATAATAGTA-TAGAAATAG
28065394 AAATAGATAA
1 AAATA-ATAA
28065404 ATAAAATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 9 0.32
23 15 0.54
25 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.29
Consensus pattern (23 bp):
AAATAATAATAGTATAGAAATAG
Found at i:28065414 original size:14 final size:13
Alignment explanation
Indices: 28065388--28065426 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
28065378 ATAGTAGTAG
28065388 AAATATAAATAGAT
1 AAATA-AAATAGAT
28065402 AAATAAAATTAGAT
1 AAATAAAA-TAGAT
28065416 AAATAATAATA
1 AAATAA-AATA
28065427 ATATTAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.13
14 18 0.78
15 2 0.09
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (13 bp):
AAATAAAATAGAT
Found at i:28065433 original size:20 final size:22
Alignment explanation
Indices: 28065392--28065434 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
28065382 TAGTAGAAAT
28065392 ATAAATAGATAAATAAAATTAG
1 ATAAATAGATAAATAAAATTAG
*
28065414 ATAAATA-AT-AATAATATTAG
1 ATAAATAGATAAATAAAATTAG
28065434 A
1 A
28065435 ATAAGAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 2 0.10
22 7 0.35
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (22 bp):
ATAAATAGATAAATAAAATTAG
Found at i:28065720 original size:17 final size:17
Alignment explanation
Indices: 28065698--28065737 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
28065688 TTTTAGGGCC
*
28065698 AATTAAGAATAATGAAA
1 AATTAAGAATAACGAAA
28065715 AATTAAGAATAACGAAA
1 AATTAAGAATAACGAAA
*
28065732 ACTTAA
1 AATTAA
28065738 TTGCAAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.23
Consensus pattern (17 bp):
AATTAAGAATAACGAAA
Found at i:28066522 original size:43 final size:45
Alignment explanation
Indices: 28066428--28066522 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 45
28066418 AACTTAAAGA
* * * * * *
28066428 AGATAAAATCTAGTAATCTTCAGTCTGCTTCACTACTGCTTAGGG
1 AGATAAGATCTAGTAATCTTCAGCCTACTCCACTACTACTCAGGG
*
28066473 AGATAAGATCTA-TAATTTTCAGCCTACTCCA-TACTACTCAGGG
1 AGATAAGATCTAGTAATCTTCAGCCTACTCCACTACTACTCAGGG
28066516 AGATAAG
1 AGATAAG
28066523 GCTCACTGTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 17 0.40
44 15 0.35
45 11 0.26
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Consensus pattern (45 bp):
AGATAAGATCTAGTAATCTTCAGCCTACTCCACTACTACTCAGGG
Found at i:28066645 original size:43 final size:44
Alignment explanation
Indices: 28066549--28066653 Score: 142
Period size: 43 Copynumber: 2.4 Consensus size: 44
28066539 CTGCTCCGTT
* * *
28066549 ACTGCTTAGGGAGATAAGATATGTAATTTTCACCTTGTTTCCCT
1 ACTGCTTAGGGAGATAAGATATCTAATATTCACCTTGTTTCCCC
*
28066593 ACTGCTTAGGGAGATAAGATTTCTAA-ATTCAGCC-TGTTTCCCC
1 ACTGCTTAGGGAGATAAGATATCTAATATTCA-CCTTGTTTCCCC
*
28066636 ACTGCTTAGGGGGATAAG
1 ACTGCTTAGGGAGATAAG
28066654 GTTCACCGTC
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
43 29 0.53
44 26 0.47
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (44 bp):
ACTGCTTAGGGAGATAAGATATCTAATATTCACCTTGTTTCCCC
Found at i:28066674 original size:131 final size:131
Alignment explanation
Indices: 28066460--28066734 Score: 363
Period size: 131 Copynumber: 2.1 Consensus size: 131
28066450 GTCTGCTTCA
* *
28066460 CTACTGCTTAGGGAGATAAGATCTATAATTTTCAGCCTACTCCATACTACTCAGGGAGATAAGGC
1 CTACTGCTTAGGGAGATAAGATCTATAATATTCAGCCTACTCCACACTACTCAGGGAGATAAGGC
* * ** *
28066525 TCACTGTTTTCGATCTGCTCCGTTACTGCTTAGGGAGATAAGATATGTAATTTTCACCTTGTTTC
66 TCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATATGTAATTTTCACCTTGTTAC
28066590 C
131 C
* * ** * * * *
28066591 CTACTGCTTAGGGAGATAAGATTTCTAA-ATTCAGCCTGTTTCCCCACTGCTTAGGGGGATAAGG
1 CTACTGCTTAGGGAGATAAGATCTATAATATTCAGCCT-ACTCCACACTACTCAGGGAGATAAGG
* * * *
28066655 TTCACCGTCTTCGATCTGCTCCACTACTGCTTATGGAGATAAGATCTGTAATTTTCAGCTTGTTA
65 CTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATATGTAATTTTCACCTTGTTA
28066720 CC
130 CC
28066722 CTACTGCTTAGGG
1 CTACTGCTTAGGG
28066735 GGTTAAGGCT
Statistics
Matches: 124, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
130 8 0.06
131 116 0.94
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (131 bp):
CTACTGCTTAGGGAGATAAGATCTATAATATTCAGCCTACTCCACACTACTCAGGGAGATAAGGC
TCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATATGTAATTTTCACCTTGTTAC
C
Found at i:28066726 original size:44 final size:43
Alignment explanation
Indices: 28066548--28066734 Score: 157
Period size: 44 Copynumber: 4.3 Consensus size: 43
28066538 TCTGCTCCGT
*
28066548 TACTGCTTAGGGAGATAAGATATGTAATTTTCACCTTGTTTCCC
1 TACTGCTTAGGGAGATAAGAT-TGTAATTTTCAGCTTGTTTCCC
* * *
28066592 TACTGCTTAGGGAGATAAGATTTCTAA-ATTCAGCCTGTTTCCC
1 TACTGCTTAGGGAGATAAGA-TTGTAATTTTCAGCTTGTTTCCC
* * * * * * * *
28066635 CACTGCTTAGGGGGATAAGGTT-CACCGTCTTC-GATCTG-CTCCAC
1 TACTGCTTAGGGAGATAAGATTGTA--ATTTTCAGCT-TGTTTCC-C
* *
28066679 TACTGCTTATGGAGATAAGATCTGTAATTTTCAGCTTGTTACCC
1 TACTGCTTAGGGAGATAAGAT-TGTAATTTTCAGCTTGTTTCCC
28066723 TACTGCTTAGGG
1 TACTGCTTAGGG
28066735 GGTTAAGGCT
Statistics
Matches: 109, Mismatches: 24, Indels: 20
0.71 0.16 0.13
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
43 34 0.31
44 65 0.60
45 6 0.06
46 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (43 bp):
TACTGCTTAGGGAGATAAGATTGTAATTTTCAGCTTGTTTCCC
Found at i:28066742 original size:88 final size:87
Alignment explanation
Indices: 28066591--28067196 Score: 739
Period size: 88 Copynumber: 7.0 Consensus size: 87
28066581 CCTTGTTTCC
* * * * * *
28066591 CTACTGCTTAGGGAGATAAGATTTCTAA-ATTCAGCCTGTTTCCCCACTGCTTAGGGGGATAAGG
1 CTACTGCTTA-GGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
28066655 -TTCACCGTCTTCGATCTGCTCCA
65 CTT-ACCGTCTTCGATCTGCTCCA
*
28066678 CTACTGCTTATGGAGATAAGATCTGTAATTTTCAGCTTGTTACCCTACTGCTTAGGGGGTTAAGG
1 CTACTGCTTA-GGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
*
28066743 CTTACCCTCTTCGATCTGCTCCA
65 CTTACCGTCTTCGATCTGCTCCA
* * * *
28066766 CTACTGCTTAGAGAGATAATATCTGTAATTTTTAGCCTGTTACCCTACTACTTAAGGGGTTAAGG
1 CTACTGCTTAG-GAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
* * *
28066831 CTCACCCTCTTCGATCTGCTCCG
65 CTTACCGTCTTCGATCTGCTCCA
*
28066854 CTACTGCTTAGAGAGATAAGATTTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
1 CTACTGCTTAG-GAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
** * * *
28066919 CTCGCTGTCTTCAATCTGTTCCA
65 CTTACCGTCTTCGATCTGCTCCA
* * *
28066942 CTACTGTTTAGG-GATAAGATCTGTAATTTTCTAGCCTATTACCCTACTGCTTAGAGGGTTAAGG
1 CTACTGCTTAGGAGATAAGATCTGTAATTTTC-AGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
* *
28067006 CTTACTGTCTTCGATTTGCTCCA
65 CTTACCGTCTTCGATCTGCTCCA
* * *
28067029 CTACTGTTTAGG-G--GAGATCTGT-ATTTTCCAGCCTGTTACCTTACTGCTTAGGGGGTTAAGG
1 CTACTGCTTAGGAGATAAGATCTGTAATTTT-CAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
* *
28067090 CTTGCTGTCTTCGATCTGCTCCA
65 CTTACCGTCTTCGATCTGCTCCA
*
28067113 CTACTGTTTAGG-G--AAGATCTGT-ATTTTCTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
1 CTACTGCTTAGGAGATAAGATCTGTAATTTTC-AGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
* ** *
28067174 CTTGCTATCTTTGATCTGCTCCA
65 CTTACCGTCTTCGATCTGCTCCA
28067197 TTATTGTTTA
Statistics
Matches: 467, Mismatches: 46, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
83 1 0.00
84 133 0.28
85 9 0.02
86 18 0.04
87 88 0.19
88 216 0.46
89 2 0.00
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.35
Consensus pattern (87 bp):
CTACTGCTTAGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
TTACCGTCTTCGATCTGCTCCA
Found at i:28066770 original size:44 final size:44
Alignment explanation
Indices: 28066636--28066776 Score: 121
Period size: 44 Copynumber: 3.2 Consensus size: 44
28066626 CTGTTTCCCC
*
28066636 ACTGCTTAGGGGGATAAGG-TTCACCGTCTTCGATCTGCTCCACT
1 ACTGCTTAGGGGGATAAGGCTT-ACCATCTTCGATCTGCTCCACT
* * * * * *
28066680 ACTGCTTATGGAGATAAGATCTGTA--ATTTTC-AGCTTGTTACC-CT
1 ACTGCTTAGGGGGATAAG-GCT-TACCATCTTCGATC-TGCT-CCACT
* *
28066724 ACTGCTTAGGGGGTTAAGGCTTACCCTCTTCGATCTGCTCCACT
1 ACTGCTTAGGGGGATAAGGCTTACCATCTTCGATCTGCTCCACT
28066768 ACTGCTTAG
1 ACTGCTTAG
28066777 AGAGATAATA
Statistics
Matches: 73, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
42 2 0.03
43 6 0.08
44 58 0.79
45 4 0.05
46 2 0.03
47 1 0.01
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (44 bp):
ACTGCTTAGGGGGATAAGGCTTACCATCTTCGATCTGCTCCACT
Found at i:28067537 original size:179 final size:177
Alignment explanation
Indices: 28067215--28067704 Score: 592
Period size: 179 Copynumber: 2.7 Consensus size: 177
28067205 TAGGGGAGAT
* * * *
28067215 CTGTATTTTTCAGTCTGCTCCATAGCTGATACATGAAGATAAGACCTGTAATTTTCAACCTGCTC
1 CTGTAATTTTCAGTCTGCTCCATAGCCGATTCATGGAGATAAGACCTG-AATTTTCAACCTGCTC
* * * * * * *
28067280 TCCTGCTACCTCAAAGAGATAAGGTTGGTAGCTAAAATCTGCTCCATAGCTGAGACATGGAGATA
65 TCTTGCTACCTCAGAGAGATAAGGCTGGT-GCTAAAATCTACTCTATAGCCGATACATGGAGATA
*
28067345 GGACTCGCCATTTTCGATCTGCTCCATAGCCGATACATAGAGATAAGAA
129 AGACTCGCCATTTTCGATCTGCTCCATAGCCGATACATAGAGATAAGAA
* * *
28067394 CTGTAATTCTCAGTCTGCTCCATAGCCGATTCATGGAGTTAAAACCTGCAATTTTCAACCTGCTC
1 CTGTAATTTTCAGTCTGCTCCATAGCCGATTCATGGAGATAAGACCTG-AATTTTCAACCTGCTC
* *
28067459 TCTTGCTACTTCAGAGAGATAAGGCTGGTGTCTAAAATCTACTCTGTAGCCGATACATGGAGATA
65 TCTTGCTACCTCAGAGAGATAAGGCTGGTG-CTAAAATCTACTCTATAGCCGATACATGGAGATA
** * *
28067524 AGACTTTCCATTTTCGATCTGCTCCATAGCCGATACATGGAGATAAGAT
129 AGACTCGCCATTTTCGATCTGCTCCATAGCCGATACATAGAGATAAGAA
* * * * * * * *
28067573 TTGTAATTTTTAGTCTGCTTCC-TTG-CTACCTCA-GGAAGATAAGACTTGTATCTTT-AACTTG
1 CTGTAATTTTCAGTCTGC-TCCATAGCCGA-TTCATGG-AGATAAGACCTGAAT-TTTCAACCTG
* *
28067634 CTCTCTTACTACCTCAGAAAGATAAGGCTGGTGGCTAAAATCTACTCTATAGCCGATACATGGAG
62 CTCTCTTGCTACCTCAGAGAGATAAGGCTGGT-GCTAAAATCTACTCTATAGCCGATACATGGAG
28067699 ATAAGA
126 ATAAGA
28067705 TCTGTAATTT
Statistics
Matches: 268, Mismatches: 37, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
178 77 0.29
179 188 0.70
180 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (177 bp):
CTGTAATTTTCAGTCTGCTCCATAGCCGATTCATGGAGATAAGACCTGAATTTTCAACCTGCTCT
CTTGCTACCTCAGAGAGATAAGGCTGGTGCTAAAATCTACTCTATAGCCGATACATGGAGATAAG
ACTCGCCATTTTCGATCTGCTCCATAGCCGATACATAGAGATAAGAA
Found at i:28067582 original size:45 final size:45
Alignment explanation
Indices: 28067315--28067591 Score: 168
Period size: 45 Copynumber: 6.2 Consensus size: 45
28067305 TGGTAGCTAA
* * * * *
28067315 AATCTGCTCCATAGCTGAGACATGGAGATAGGACTCGCCATTTTC
1 AATCTGCTCCATAGCCGATACATGGAGATAAGACTTGCAATTTTC
* * * *
28067360 GATCTGCTCCATAGCCGATACATAGAGATAAGAAC-TGTAATTCTC
1 AATCTGCTCCATAGCCGATACATGGAGATAAG-ACTTGCAATTTTC
* * * * *
28067405 AGTCTGCTCCATAGCCGATTCATGGAGTTAAAACCTGCAATTTTC
1 AATCTGCTCCATAGCCGATACATGGAGATAAGACTTGCAATTTTC
* * * * * *** * **
28067450 AACCTGCTCTC-TTG-CTACTTCA-GAGAGATAAGGC-TGGTGTCTAA
1 AATCTGCTC-CATAGCCGA-TACATG-GAGATAAGACTTGCAATTTTC
* ** * *
28067494 AATCTACTCTGTAGCCGATACATGGAGATAAGACTTTCCATTTTC
1 AATCTGCTCCATAGCCGATACATGGAGATAAGACTTGCAATTTTC
* * * *
28067539 GATCTGCTCCATAGCCGATACATGGAGATAAGATTTGTAATTTTT
1 AATCTGCTCCATAGCCGATACATGGAGATAAGACTTGCAATTTTC
*
28067584 AGTCTGCT
1 AATCTGCT
28067592 TCCTTGCTAC
Statistics
Matches: 168, Mismatches: 55, Indels: 18
0.70 0.23 0.07
Matches are distributed among these distances:
44 30 0.18
45 135 0.80
46 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (45 bp):
AATCTGCTCCATAGCCGATACATGGAGATAAGACTTGCAATTTTC
Found at i:28074173 original size:21 final size:23
Alignment explanation
Indices: 28074126--28074179 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
28074116 CATTCAAGAT
**
28074126 AAAATAATATATAAAACTCTTTA
1 AAAATAATATATAAAACTAATTA
*
28074149 AAAATAATATAT-AAAC-AATTC
1 AAAATAATATATAAAACTAATTA
28074170 AAAAT-ATATA
1 AAAATAATATA
28074180 ATGTGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 4 0.14
23 12 0.43
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATAATATATAAAACTAATTA
Found at i:28074412 original size:25 final size:23
Alignment explanation
Indices: 28074357--28074412 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
28074347 ATAATAATGA
*
28074357 AAATAATAATAGTATATAAATAG
1 AAATAATAATAGTATAGAAATAG
*
28074380 AAAT-ATAATAGTAGTAGAAATAT
1 AAATAATAATAGTA-TAGAAATAG
28074403 AAATAGATAA
1 AAATA-ATAA
28074413 ATAAAATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 9 0.32
23 15 0.54
25 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.29
Consensus pattern (23 bp):
AAATAATAATAGTATAGAAATAG
Found at i:28074423 original size:14 final size:13
Alignment explanation
Indices: 28074397--28074472 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 13
28074387 ATAGTAGTAG
28074397 AAATATAAATAGAT
1 AAATA-AAATAGAT
28074411 AAATAAAATTAGAT
1 AAATAAAA-TAGAT
*
28074425 AAATAATAATA-TT
1 AAATAA-AATAGAT
28074438 AGAATAAGAA-A-AT
1 A-AATAA-AATAGAT
28074451 AAATATAAATAGA-
1 AAATA-AAATAGAT
28074464 AACATAAAA
1 AA-ATAAAA
28074473 ATAATAGCAA
Statistics
Matches: 52, Mismatches: 3, Indels: 15
0.74 0.04 0.21
Matches are distributed among these distances:
12 6 0.12
13 15 0.29
14 29 0.56
15 2 0.04
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.25
Consensus pattern (13 bp):
AAATAAAATAGAT
Found at i:28074479 original size:17 final size:17
Alignment explanation
Indices: 28074401--28074476 Score: 55
Period size: 18 Copynumber: 4.2 Consensus size: 17
28074391 TAGTAGAAAT
28074401 ATAAATAGATAAATAAAA
1 ATAAATAGA-AAATAAAA
* * *
28074419 TTAGATA-AATAATAATA
1 ATAAATAGAA-AATAAAA
* *
28074436 TTAGAATAAGAAAATAAAT
1 ATA-AAT-AGAAAATAAAA
28074455 ATAAATAGAAACATAAAA
1 ATAAATAGAAA-ATAAAA
28074473 ATAA
1 ATAA
28074477 TAGCAATAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
16 1 0.02
17 15 0.33
18 19 0.42
19 8 0.18
20 2 0.04
ACGTcount: A:0.67, C:0.01, G:0.07, T:0.25
Consensus pattern (17 bp):
ATAAATAGAAAATAAAA
Found at i:28074729 original size:17 final size:17
Alignment explanation
Indices: 28074707--28074748 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
28074697 TTTTAGAGCC
*
28074707 AAAATTAAGAATAATGA
1 AAAATTAAGAATAACGA
28074724 AAAATTAAGAATAACGA
1 AAAATTAAGAATAACGA
*
28074741 AAACTTAA
1 AAAATTAA
28074749 TTGCAAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (17 bp):
AAAATTAAGAATAACGA
Found at i:28077553 original size:6 final size:6
Alignment explanation
Indices: 28077538--28077572 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
28077528 CTAAAAAATT
* *
28077538 CTACTA CTACTC CTACTC CTACTC TTACTC CTACT
1 CTACTC CTACTC CTACTC CTACTC CTACTC CTACT
28077573 TAAGATAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.20, C:0.43, G:0.00, T:0.37
Consensus pattern (6 bp):
CTACTC
Found at i:28079030 original size:35 final size:36
Alignment explanation
Indices: 28078971--28079044 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 36
28078961 TGCTATTTTC
28078971 TTTTATTATTATAAAAACCCTAAAAATTCCCTTTAT
1 TTTTATTATTATAAAAACCCTAAAAATTCCCTTTAT
28079007 TTTTATTATTAT-AAAACCCTAAAAATTCCCTTTAT
1 TTTTATTATTATAAAAACCCTAAAAATTCCCTTTAT
28079042 TTT
1 TTT
28079045 AACTTTGTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 26 0.68
36 12 0.32
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.47
Consensus pattern (36 bp):
TTTTATTATTATAAAAACCCTAAAAATTCCCTTTAT
Found at i:28083543 original size:40 final size:40
Alignment explanation
Indices: 28083394--28083579 Score: 218
Period size: 40 Copynumber: 4.7 Consensus size: 40
28083384 TCGAATGATG
* * *
28083394 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
28083434 TCCGGACTAAGAT-CCAAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28083474 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
28083514 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
28083555 -CCGGGCTATGTCCCGAAGGTATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28083580 AACGAGTAGC
Statistics
Matches: 130, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
39 1 0.01
40 119 0.92
41 10 0.08
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28083586 original size:80 final size:79
Alignment explanation
Indices: 28083450--28083602 Score: 186
Period size: 80 Copynumber: 1.9 Consensus size: 79
28083440 CTAAGATCCA
* **
28083450 AAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTA-CTAAA
1 AAGGCATTTGTGCGAGCTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAG-TAGCTAAA
28083514 TCCGGGTTAAGTCCCG
65 TCC-GGTTAAGTCCCG
* * * *
28083530 AAGGCATTTGTGCGAGCTACTATAA-CCGGGCTATG-TCCCGAAGGTATTTGAACGAGTAGCTAT
1 AAGGCATTTGTGCGAGCTACTA-AATCCGGACTAAGAT-CCGAAGGCATTTGAACGAGTAGCTAA
28083593 ATCCGGTTAA
64 ATCCGGTTAA
28083603 ACTCCGAAGG
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
79 9 0.14
80 52 0.83
81 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (79 bp):
AAGGCATTTGTGCGAGCTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTAGCTAAAT
CCGGTTAAGTCCCG
Found at i:28090084 original size:18 final size:17
Alignment explanation
Indices: 28090052--28090092 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
28090042 TAATGTTAAC
*
28090052 ATTTATTATTAAAATAA
1 ATTTATAATTAAAATAA
28090069 ATTTATAATATAAAATAA
1 ATTTATAAT-TAAAATAA
28090087 ATTTAT
1 ATTTAT
28090093 TAAAATAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTATAATTAAAATAA
Found at i:28090096 original size:14 final size:15
Alignment explanation
Indices: 28090057--28090100 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 15
28090047 TTAACATTTA
28090057 TTATTAAAATAAATT
1 TTATTAAAATAAATT
28090072 TATAATATAAAATAAA-T
1 T-T-AT-TAAAATAAATT
28090089 TTATTAAAATAA
1 TTATTAAAATAA
28090101 TCATTTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 8 0.31
15 3 0.12
16 2 0.08
17 4 0.15
18 9 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TTATTAAAATAAATT
Found at i:28093113 original size:25 final size:25
Alignment explanation
Indices: 28093083--28093132 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
28093073 CTAGAAAGTA
*
28093083 TGACTTGAGAACGTATAGGTGATTT
1 TGACTTGAGAACGTATAAGTGATTT
28093108 TGACTTGAGAACGTATAAGTGATTT
1 TGACTTGAGAACGTATAAGTGATTT
28093133 AACATAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.26, T:0.36
Consensus pattern (25 bp):
TGACTTGAGAACGTATAAGTGATTT
Found at i:28099489 original size:3 final size:3
Alignment explanation
Indices: 28099481--28099536 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
28099471 CTTCATTGTG
28099481 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28099529 TTA TTA TT
1 TTA TTA TT
28099537 TGTTTCAATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28099752 original size:19 final size:19
Alignment explanation
Indices: 28099730--28099766 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
28099720 TTAAATATAG
28099730 TTTATTA-TACTCATTATTA
1 TTTATTATTA-TCATTATTA
28099749 TTTATTATTATCATTATT
1 TTTATTATTATCATTATT
28099767 GTTAGCTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATTATTATCATTATTA
Found at i:28100275 original size:115 final size:113
Alignment explanation
Indices: 28100052--28100261 Score: 314
Period size: 115 Copynumber: 1.8 Consensus size: 113
28100042 GACATAAAAA
*
28100052 CAATTTTCTATACTTAATCGTTTTAAAAAACGAGCCCTACCGTATTGGGTTCGTTTTTTTATTCG
1 CAATTTTCTATACTTAATCGTTTTAAAAAACGAGCCCTACCGTACTGGGTTCGTTTTTTTATTCG
** *
28100117 ATTTAAGTATTTTATTCAACGTCTTATTCCCAAATAGTTTTTAATAAAGG
66 ATTTAAGTATTGAATTC-ACGTCTTAAT-CCAAATAGTTTTTAATAAAGG
*
28100167 CAATTTTCTATACTTAATCGTTTTAAAAAACGTGCCCTACCGTACTGGGTTTCGTTTTTTTATTC
1 CAATTTTCTATACTTAATCGTTTTAAAAAACGAGCCCTACCGTACTGGG-TTCGTTTTTTTATTC
*
28100232 GATTTAAGTATTCGAATATC-CTTCTTAATC
65 GATTTAAGTATT-GAAT-TCACGTCTTAATC
28100262 AATTTATTCT
Statistics
Matches: 86, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
115 48 0.56
116 34 0.40
117 2 0.02
118 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (113 bp):
CAATTTTCTATACTTAATCGTTTTAAAAAACGAGCCCTACCGTACTGGGTTCGTTTTTTTATTCG
ATTTAAGTATTGAATTCACGTCTTAATCCAAATAGTTTTTAATAAAGG
Found at i:28113642 original size:18 final size:18
Alignment explanation
Indices: 28113619--28113655 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
28113609 CATATGCGAC
28113619 TTTGATGCCTAATGAGTA
1 TTTGATGCCTAATGAGTA
28113637 TTTGATGCCTAATGAGTA
1 TTTGATGCCTAATGAGTA
28113655 T
1 T
28113656 ATATATTGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.41
Consensus pattern (18 bp):
TTTGATGCCTAATGAGTA
Found at i:28114113 original size:39 final size:40
Alignment explanation
Indices: 28114014--28114203 Score: 138
Period size: 40 Copynumber: 4.8 Consensus size: 40
28114004 CGAATGATGT
* * * * * *
28114014 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTTAATAAAC
* * *
28114054 CCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAAT
1 CCGGGCTAAG-TCCCGAAGGCATTCGTGCGAGTTAATAAAC
* * *
28114094 CCGGGCTAAG-CCTGAAGGCATT-GTGCAAGTTACTAAAC
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTAATAAAC
* ***
28114132 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCGCTATAA-
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTAATA-AAC
** * *
28114172 CCGGGCTTCGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGT
28114204 CGTTATATCC
Statistics
Matches: 121, Mismatches: 23, Indels: 12
0.78 0.15 0.08
Matches are distributed among these distances:
38 22 0.18
39 21 0.17
40 69 0.57
41 9 0.07
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.23
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTAATAAAC
Found at i:28114155 original size:78 final size:80
Alignment explanation
Indices: 28114013--28114194 Score: 201
Period size: 78 Copynumber: 2.3 Consensus size: 80
28114003 TCGAATGATG
* * * *
28114013 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
28114078 GTGCGAGTTAATAAA
66 GTGCGAGTTAATAAA
* * **
28114093 TCCGGGCTAAG-CCTGAAGGCATTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCATT
***
28114155 CGTGCGAGTCGCTATAA
65 CGTGCGAGTTAATA-AA
**
28114172 -CCGGGCTTCGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
28114195 TGAGCGAGTC
Statistics
Matches: 85, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
77 1 0.01
78 46 0.54
79 27 0.32
80 11 0.13
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
GTGCGAGTTAATAAA
Found at i:28115820 original size:44 final size:44
Alignment explanation
Indices: 28115604--28115999 Score: 197
Period size: 44 Copynumber: 8.9 Consensus size: 44
28115594 CGAGAAAATG
* *
28115604 ACAGATCTTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGT
1 ACAGATC-TTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAT--T
* * * * * *
28115651 -GAG-TCTTAAC-CCCTAGGCAGTAG-GGTAACTGA-CTGAA-AAT
1 ACAGATCTTATCTCCCTAAGCAGTAGTGG-AGCAGATC-GAAGATT
* * * * *
28115691 ACAGATCCTATTTCCCTAAGCAATAGTGGAGCGGATCGAAAATGGT
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAT--T
* * * *
28115737 A-AGCT-TTATCTCCCTGAGCAGCAGTGGAGCA-AGCTGAAGATT
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC-GAAGATT
*
28115779 ACAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGATGAT
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAT--T
* * * ** * * *
28115825 GAGCAGGTTTTAACTCCCTAAGCAGTAG-GGTAAAAAGCTGGAGGATT
1 -A-CAGATCTTATCTCCCTAAGCAGTAGTGG--AGCAGATCGAAGATT
* *
28115872 ACAAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATG
1 AC-AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATT
* * * * ** * * * *
28115917 GCAAACCTTATCTCTCTGAAGTTGCAG-AGAGCAGGTTGAAG-TT
1 ACAGATCTTATCTCCCT-AAGCAGTAGTGGAGCAGATCGAAGATT
*
28115960 ACA-AGTCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAA
1 ACAGA-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAA
28116000 AATACCAAAA
Statistics
Matches: 256, Mismatches: 68, Indels: 54
0.68 0.18 0.14
Matches are distributed among these distances:
40 1 0.00
41 2 0.01
42 17 0.07
43 64 0.25
44 86 0.34
45 24 0.09
46 26 0.10
47 6 0.02
48 21 0.08
49 9 0.04
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (44 bp):
ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATT
Found at i:28115930 original size:182 final size:173
Alignment explanation
Indices: 28115604--28115999 Score: 420
Period size: 182 Copynumber: 2.2 Consensus size: 173
28115594 CGAGAAAATG
* * * *
28115604 ACAGATCTTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGTGAGTCTTAACCCCTAGGC
1 ACAGATC-TTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGAGAGTCTTAACCCCTAAGC
** * *
28115669 AGTAGGGTAACTGACTGAAAATACAGATCCTATTTCCCTAAGCAATAGTGGAGCGGATCGAAAAT
65 AGTAGGGTAAAAGACTGAAAATACAGATCCTATCTCCCTAAGCAATAGTGGAGCAGATCGAAAAT
* * * *
28115734 GGTAAGCTTTATCTCCCTG-AGCAGCAGTGGAGCAAGCTGAAGATT
130 GGCAAACCTTATCTCCCTGAAGCAGCAG-AGAGCAAGCTGAAG-TT
* *
28115779 ACAGATCTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGATGATGAGCAGGTTTTAACTCCCT
1 ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATG--GAG-A-GTCTTAAC-CCCT
* * * * *
28115844 AAGCAGTAGGGTAAAA-AGCTGGAGGATTACAAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGA
61 AAGCAGTAGGGTAAAAGA-CT-GA-AAATAC-AGATCCTATCTCCCTAAGCAATAGTGGAGCAGA
* * ** * *
28115908 TCGAAGATGGCAAACCTTATCTCTCTGAAGTTGCAGAGAGCAGGTTGAAGTT
122 TCGAAAATGGCAAACCTTATCTCCCTGAAGCAGCAGAGAGCAAGCTGAAGTT
*
28115960 ACA-AGTCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAA
1 ACAGA-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAA
28116000 AATACCAAAA
Statistics
Matches: 183, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
174 34 0.19
175 7 0.04
176 2 0.01
177 1 0.01
178 8 0.04
179 19 0.10
180 3 0.02
181 42 0.23
182 61 0.33
183 6 0.03
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (173 bp):
ACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGAGAGTCTTAACCCCTAAGCA
GTAGGGTAAAAGACTGAAAATACAGATCCTATCTCCCTAAGCAATAGTGGAGCAGATCGAAAATG
GCAAACCTTATCTCCCTGAAGCAGCAGAGAGCAAGCTGAAGTT
Found at i:28116034 original size:87 final size:87
Alignment explanation
Indices: 28115870--28116076 Score: 279
Period size: 87 Copynumber: 2.4 Consensus size: 87
28115860 AGCTGGAGGA
* ** *
28115870 TTACAAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAAACCTTATCTCTCTG
1 TTACAAG-TCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAAATACCAAAACTTATCTCTCTG
*
28115935 AAGTTGCAGAGAGCAGGTTGAAG
65 AAGTTGCAGAGAGCAAGTTGAAG
* * * * *
28115958 TTACAAGTCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAAAATACCAAAACTTGTTTCTTTGA
1 TTACAAGTCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAAATACCAAAACTTATCTCTCTGA
28116023 AGTTGCAGAGAGCAAGTTGAAG
66 AGTTGCAGAGAGCAAGTTGAAG
* ** *
28116045 ATACAAACCTTGTGTCCCTAAGCAGTAGTGGA
1 TTACAAGTCTTGTCTCCCTAAGCAGTAGTGGA
28116077 ACAGGTTGAA
Statistics
Matches: 103, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
87 96 0.93
88 7 0.07
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (87 bp):
TTACAAGTCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAAATACCAAAACTTATCTCTCTGA
AGTTGCAGAGAGCAAGTTGAAG
Found at i:28117537 original size:3 final size:3
Alignment explanation
Indices: 28117529--28117594 Score: 116
Period size: 3 Copynumber: 22.0 Consensus size: 3
28117519 CTTCATTGTG
28117529 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28117577 ATT ATT ATTT ATT -TT ATT
1 ATT ATT A-TT ATT ATT ATT
28117595 TATTTGTTTC
Statistics
Matches: 61, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
3 56 0.92
4 3 0.05
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:28118334 original size:115 final size:113
Alignment explanation
Indices: 28118111--28118320 Score: 298
Period size: 116 Copynumber: 1.8 Consensus size: 113
28118101 AACATAAAAA
*
28118111 CAATTTTCTATACTTAATCGTTTTAAAAAAACGAGCCCTACCGTATTGGGTTTGTTTTTTATTCG
1 CAATTTTCTATACTTAATCGTTTTAAAAAAACGAGCCCTACCGTACTGGGTTTGTTTTTTATTCG
** *
28118176 ATTTAAGTATTTTATTCAACGTCTTATTCCCAAATAGTTTTTAATAAAGG
66 ATTTAAGTATTGGATTC-ACGTCTTAAT-CCAAATAGTTTTTAATAAAGG
*
28118226 CAATTTTCTATACTTAATCGTTTT-AAAAAACGTGCCCTACCGTACTGGGTTTCGTTTTTTTATT
1 CAATTTTCTATACTTAATCGTTTTAAAAAAACGAGCCCTACCGTACTGGGTTT-G-TTTTTTATT
*
28118290 CGATTTAAGTATTCGGATATC-CTTCTTAATC
64 CGATTTAAGTATT-GGAT-TCACGTCTTAATC
28118321 AATTTATTCT
Statistics
Matches: 85, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
114 26 0.31
115 26 0.31
116 29 0.34
117 2 0.02
118 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (113 bp):
CAATTTTCTATACTTAATCGTTTTAAAAAAACGAGCCCTACCGTACTGGGTTTGTTTTTTATTCG
ATTTAAGTATTGGATTCACGTCTTAATCCAAATAGTTTTTAATAAAGG
Found at i:28119262 original size:16 final size:15
Alignment explanation
Indices: 28119241--28119288 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
28119231 ATTTTGAATA
28119241 TTATTTAATATTATTT
1 TTATTT-ATATTATTT
* *
28119257 TTATTTATGTAATTT
1 TTATTTATATTATTT
*
28119272 TTATTTTATAATATTT
1 TTA-TTTATATTATTT
28119288 T
1 T
28119289 ATAACAGCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 10 0.38
16 16 0.62
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (15 bp):
TTATTTATATTATTT
Found at i:28120834 original size:18 final size:18
Alignment explanation
Indices: 28120811--28120849 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
28120801 ATGCCAGGTG
* *
28120811 TGTATCCTAGCCTTTATA
1 TGTATCCTAACCCTTATA
28120829 TGTATCCTAACCCTTATA
1 TGTATCCTAACCCTTATA
28120847 TGT
1 TGT
28120850 TTTCTTTTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (18 bp):
TGTATCCTAACCCTTATA
Found at i:28125027 original size:24 final size:26
Alignment explanation
Indices: 28124978--28125027 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
28124968 ACAAAGAACT
28124978 TTTAATCAGAAAGCTCATGAAGAGCC
1 TTTAATCAGAAAGCTCATGAAGAGCC
* *
28125004 TTTAATCA-AGAGCTC-TGAATAGCC
1 TTTAATCAGAAAGCTCATGAAGAGCC
28125028 ATATATCGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 8 0.36
25 6 0.27
26 8 0.36
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (26 bp):
TTTAATCAGAAAGCTCATGAAGAGCC
Found at i:28127776 original size:125 final size:124
Alignment explanation
Indices: 28127613--28128131 Score: 476
Period size: 125 Copynumber: 4.2 Consensus size: 124
28127603 GGCCAATCAA
* ** * *
28127613 GAACTACTGTAGAAAAAGAGCATCCACATGGGAGCTTTTTTTAATAATTTTACTGACAGTGCATC
1 GAACTACTATAGAAAAA-AAAATCCACATGGGAGCTTTTTTCAATAATTTTACTAACAGTGCATC
28127678 CTGCTTGAAGCGTTTTTGACACTTTTTTTCCAGAACCATCTTCTCAAAATTATTTTTCTAG
65 CTGCTTGAAGCGTTTTTGACA-TTTTTTTCCAGAACCATCTTCTCAAAATTATTTTTCTAG
* ** * * * *
28127739 GAACTAGTATAGAAAAAAAAATCCACATAAGAGCTTTTTTCAGTAATTTTGCTAACAATACATCC
1 GAACTACTATAGAAAAAAAAATCCACATGGGAGCTTTTTTCAATAATTTTACTAACAGTGCATCC
* * *
28127804 TGCTTGAAGTGTTTTTGACACTATTTTTT--AGAACCGTCTTCTCAAAATTATTTTT-TCAA
66 TGCTTGAAGCGTTTTTGACA-T-TTTTTTCCAGAACCATCTTCTCAAAATTATTTTTCT-AG
* *** * * * * * *
28127863 GAACTACTATAGGAAAAAGCGTCCAC--GTGAGTTTTTTTTAGTAATTTTACTGACACTGCATCC
1 GAACTACTATAGAAAAAAAAATCCACATGGGAGCTTTTTTCAATAATTTTACTAACAGTGCATCC
* * * * * *** *
28127926 CGCTTGAAGCATTTTTTACATTATTTTTTCAAAATTGTCTTCTCAAAATTATTTTTTTAG
66 TGCTTGAAGCGTTTTTGACATT-TTTTTCCAGAACCATCTTCTCAAAATTATTTTTCTAG
* *** * * * * *
28127986 GAACTAC-GTAGAAAAAGAGTGTCCACGTGGGAGCTTCTTTCAAAAATTTTGCTAACAGTGTATC
1 GAACTACTATAGAAAAA-AAAATCCACATGGGAGCTTTTTTCAATAATTTTACTAACAGTGCATC
* * * *
28128050 CTGCTTAAAGCGTTTTTGACATTATCTTCTCAGAACTATCTTCTCAAAATTAATTTTTCTA-
65 CTGCTTGAAGCGTTTTTGACATTTTTTTC-CAGAACCATCTTCTCAAAATT-ATTTTTCTAG
*
28128111 AAACTACTATAGAAAAAAAAA
1 GAACTACTATAGAAAAAAAAA
28128132 ACAAAAGCCT
Statistics
Matches: 316, Mismatches: 65, Indels: 25
0.78 0.16 0.06
Matches are distributed among these distances:
120 1 0.00
121 6 0.02
122 52 0.16
123 40 0.13
124 51 0.16
125 129 0.41
126 37 0.12
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.37
Consensus pattern (124 bp):
GAACTACTATAGAAAAAAAAATCCACATGGGAGCTTTTTTCAATAATTTTACTAACAGTGCATCC
TGCTTGAAGCGTTTTTGACATTTTTTTCCAGAACCATCTTCTCAAAATTATTTTTCTAG
Found at i:28128269 original size:34 final size:33
Alignment explanation
Indices: 28128214--28128342 Score: 149
Period size: 34 Copynumber: 3.9 Consensus size: 33
28128204 TAAACACAAA
* *
28128214 AATTATTTTAAAAA-ACTAAACCCTAATTTAATC
1 AATT-TTTTAAAAACTCTAAACCCTAATTTAATT
28128247 AATTTTCTTAAAAACTCTAAACCCTAATTTAATT
1 AATTTT-TTAAAAACTCTAAACCCTAATTTAATT
* *
28128281 AATTTATTT-AAAACCCTTAAAACCTAATTTAATT
1 AATTT-TTTAAAAACTC-TAAACCCTAATTTAATT
*
28128315 AA--TTTAAAAAACTCTAAACCCTAATTTA
1 AATTTTTTAAAAACTCTAAACCCTAATTTA
28128343 TTTTTTAAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 12
0.82 0.07 0.12
Matches are distributed among these distances:
31 15 0.18
32 9 0.11
33 17 0.20
34 42 0.50
35 1 0.01
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.38
Consensus pattern (33 bp):
AATTTTTTAAAAACTCTAAACCCTAATTTAATT
Found at i:28132936 original size:2 final size:2
Alignment explanation
Indices: 28132929--28132959 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28132919 AAATAAATAA
28132929 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28132960 AAAGTTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28133393 original size:18 final size:21
Alignment explanation
Indices: 28133356--28133398 Score: 65
Period size: 18 Copynumber: 2.2 Consensus size: 21
28133346 GAAGTTTTGG
28133356 TACCATTGTTGTAGGTATCGA
1 TACCATTGTTGTAGGTATCGA
28133377 TACC-TTGTT-TA-GTATCGA
1 TACCATTGTTGTAGGTATCGA
28133395 TACC
1 TACC
28133399 GTTTTTAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 11 0.50
19 2 0.09
20 5 0.23
21 4 0.18
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.40
Consensus pattern (21 bp):
TACCATTGTTGTAGGTATCGA
Found at i:28136250 original size:21 final size:22
Alignment explanation
Indices: 28136226--28136269 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
28136216 TTAAATCAGT
*
28136226 TTTAATTTAAGAGTTT-GTTTA
1 TTTAATTAAAGAGTTTAGTTTA
*
28136247 TTTAATTAAAGTGTTTAGTTTA
1 TTTAATTAAAGAGTTTAGTTTA
28136269 T
1 T
28136270 ACTTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.57
Consensus pattern (22 bp):
TTTAATTAAAGAGTTTAGTTTA
Found at i:28140674 original size:10 final size:10
Alignment explanation
Indices: 28140642--28140678 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
28140632 GGAAAAATAT
28140642 AAAAAATTTAC
1 AAAAAATTT-C
28140653 AAAAAA-TT-
1 AAAAAATTTC
28140661 AAAAAATTTC
1 AAAAAATTTC
28140671 AAAAAATT
1 AAAAAATT
28140679 ATTTAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 6 0.25
9 2 0.08
10 10 0.42
11 6 0.25
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAAAATTTC
Found at i:28140674 original size:29 final size:28
Alignment explanation
Indices: 28140625--28140703 Score: 63
Period size: 29 Copynumber: 2.8 Consensus size: 28
28140615 AAATAACCTT
**
28140625 AAAAAATGGAAAAATATAAAAAATT-TAC
1 AAAAAATTAAAAAAT-TAAAAAATTATAC
*
28140653 AAAAAATTAAAAAATTTCAAAAAATTAT-T
1 AAAAAATTAAAAAA-TT-AAAAAATTATAC
* *
28140682 TAAAAATTACAAACATTAAAAA
1 AAAAAATTA-AAAAATTAAAAA
28140704 CTGATCCAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
28 18 0.43
29 19 0.45
30 5 0.12
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.25
Consensus pattern (28 bp):
AAAAAATTAAAAAATTAAAAAATTATAC
Found at i:28140675 original size:18 final size:19
Alignment explanation
Indices: 28140634--28140679 Score: 76
Period size: 18 Copynumber: 2.4 Consensus size: 19
28140624 TAAAAAATGG
28140634 AAAAATATAAAAAATTTACA
1 AAAAAT-TAAAAAATTTACA
28140654 AAAAATTAAAAAATTT-CA
1 AAAAATTAAAAAATTTACA
28140672 AAAAATTA
1 AAAAATTA
28140680 TTTAAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 10 0.38
19 10 0.38
20 6 0.23
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAAATTAAAAAATTTACA
Found at i:28140878 original size:10 final size:10
Alignment explanation
Indices: 28140859--28140914 Score: 55
Period size: 10 Copynumber: 5.5 Consensus size: 10
28140849 TGTAAAAATA
28140859 TTAA-ATTTT
1 TTAATATTTT
28140868 TTAATATTTT
1 TTAATATTTT
28140878 TTAATAATTTT
1 TTAAT-ATTTT
28140889 ATTAA-A-TTT
1 -TTAATATTTT
28140898 TTATATATTTT
1 TTA-ATATTTT
28140909 TATAAT
1 T-TAAT
28140915 TTTGTAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
8 3 0.08
9 8 0.20
10 12 0.30
11 11 0.28
12 6 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTAATATTTT
Found at i:28140895 original size:31 final size:29
Alignment explanation
Indices: 28140857--28140917 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 29
28140847 AATGTAAAAA
28140857 TATTAAATTTTT-TAATATTTTTTAATAATTT
1 TATTAAATTTTTAT-ATA-TTTTT-ATAATTT
28140888 TATTAAATTTTTATATATTTTTATAATTT
1 TATTAAATTTTTATATATTTTTATAATTT
28140917 T
1 T
28140918 GTAATTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 8 0.28
30 5 0.17
31 15 0.52
32 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (29 bp):
TATTAAATTTTTATATATTTTTATAATTT
Found at i:28140915 original size:19 final size:19
Alignment explanation
Indices: 28140865--28140964 Score: 57
Period size: 19 Copynumber: 5.3 Consensus size: 19
28140855 AATATTAAAT
*
28140865 TTTTTAATATTTTTTA-ATA
1 TTTTT-ATAATTTTTATATA
*
28140884 ATTTTATTAAATTTTTATATA
1 TTTTTA-T-AATTTTTATATA
*
28140905 TTTTTATAA-TTTTGTA-A
1 TTTTTATAATTTTTATATA
* * *
28140922 -TTTTATACTTTTTTTCTA
1 TTTTTATAATTTTTATATA
* *
28140940 TTTTTAATCATTTTTGTA-A
1 TTTTT-ATAATTTTTATATA
28140959 TTTTTA
1 TTTTTA
28140965 AATAACTCTT
Statistics
Matches: 63, Mismatches: 11, Indels: 15
0.71 0.12 0.17
Matches are distributed among these distances:
16 7 0.11
17 6 0.10
18 9 0.14
19 17 0.27
20 16 0.25
21 8 0.13
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTTATAATTTTTATATA
Found at i:28140942 original size:26 final size:25
Alignment explanation
Indices: 28140896--28140947 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
28140886 TTTATTAAAT
28140896 TTTTATATATTTTTATAATTTTGTAA
1 TTTTATATATTTTTATAATTTT-TAA
* *
28140922 TTTTATACTTTTTTTCT-ATTTTTAA
1 TTTTATA-TATTTTTATAATTTTTAA
28140947 T
1 T
28140948 CATTTTTGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 4 0.17
26 12 0.52
27 7 0.30
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (25 bp):
TTTTATATATTTTTATAATTTTTAA
Done.