Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 55 of 199
Found at i:16162694 original size:50 final size:50
Alignment explanation
Indices: 16162579--16162827 Score: 282
Period size: 50 Copynumber: 4.8 Consensus size: 50
16162569 GATAATAACA
* * ** * *
16162579 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* *
16162630 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
16162680 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * * *
16162730 TGCCCATGTCATGTCCTAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
16162785 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
16162828 TTACCCAAAT
Statistics
Matches: 167, Mismatches: 25, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
50 92 0.55
51 33 0.20
53 2 0.01
54 1 0.01
55 2 0.01
56 37 0.22
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:16162766 original size:100 final size:104
Alignment explanation
Indices: 16162578--16162827 Score: 337
Period size: 100 Copynumber: 2.4 Consensus size: 104
16162568 TGATAATAAC
** * *
16162578 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCCATGCCATG
* *
16162643 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* * *
16162680 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGTCATGT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
*
16162744 CCTAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
16162785 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
16162828 TTACCCAAAT
Statistics
Matches: 130, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
100 48 0.37
101 36 0.28
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.31
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.27
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:16162943 original size:13 final size:13
Alignment explanation
Indices: 16162922--16162952 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
16162912 GCTTAGATCA
*
16162922 TCATCAAATAAAT
1 TCATAAAATAAAT
16162935 TCATAAAATAAAT
1 TCATAAAATAAAT
16162948 TCATA
1 TCATA
16162953 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:16167073 original size:18 final size:19
Alignment explanation
Indices: 16167038--16167074 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
16167028 TATAGTAGAA
16167038 GAGAAAGTAAATAATTTAG
1 GAGAAAGTAAATAATTTAG
*
16167057 GAGAAATTAAA-AATTTAG
1 GAGAAAGTAAATAATTTAG
16167075 ATTTAAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.19, T:0.27
Consensus pattern (19 bp):
GAGAAAGTAAATAATTTAG
Found at i:16167156 original size:27 final size:27
Alignment explanation
Indices: 16167112--16167163 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
16167102 TAACTAGTGT
* *
16167112 TAATAATAAATTAGATCAGGTTATAAA
1 TAATAATAAATTAAATCAGGATATAAA
16167139 TAATAAT-AATATAAATCAGGATATA
1 TAATAATAAAT-TAAATCAGGATATA
16167164 GATTTAGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.33
Consensus pattern (27 bp):
TAATAATAAATTAAATCAGGATATAAA
Found at i:16168645 original size:22 final size:22
Alignment explanation
Indices: 16168605--16168646 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
16168595 TTTACATTAA
16168605 TTTTCTCTTTAGTTTTTTCTAC
1 TTTTCTCTTTAGTTTTTTCTAC
*
16168627 TTTTC-CTTTATTTTCTTTCT
1 TTTTCTCTTTAGTTT-TTTCT
16168647 TCGTCCTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.07, C:0.19, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTCTCTTTAGTTTTTTCTAC
Found at i:16168985 original size:19 final size:21
Alignment explanation
Indices: 16168949--16168987 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
16168939 TTCTATTTTA
*
16168949 AATTATTTTATTATATTTATG
1 AATTATTTTAATATATTTATG
16168970 AATT-TTTTAATA-ATTTAT
1 AATTATTTTAATATATTTAT
16168988 TTGATCGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
AATTATTTTAATATATTTATG
Found at i:16170677 original size:14 final size:15
Alignment explanation
Indices: 16170646--16170678 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
16170636 AAATTTTAAG
16170646 AAAAATGAATATTGT
1 AAAAATGAATATTGT
*
16170661 AAAAATGGATATT-T
1 AAAAATGAATATTGT
16170675 AAAA
1 AAAA
16170679 CAATTCTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.30
Consensus pattern (15 bp):
AAAAATGAATATTGT
Found at i:16170770 original size:18 final size:18
Alignment explanation
Indices: 16170732--16170775 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
16170722 TAGTTCACTC
16170732 TTACTTTATTTTTTTAGTT
1 TTACTTTA-TTTTTTAGTT
16170751 TTACTTTA-TTTTTAGTTT
1 TTACTTTATTTTTTAG-TT
16170769 TTACTTT
1 TTACTTT
16170776 TACAATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.29
18 9 0.38
19 8 0.33
ACGTcount: A:0.16, C:0.07, G:0.05, T:0.73
Consensus pattern (18 bp):
TTACTTTATTTTTTAGTT
Found at i:16170777 original size:19 final size:18
Alignment explanation
Indices: 16170732--16170777 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 18
16170722 TAGTTCACTC
*
16170732 TTACTTTATTTTTTTAGTT
1 TTACTTT-TATTTTTAGTT
16170751 TTAC-TTTATTTTTAGTTT
1 TTACTTTTATTTTTAG-TT
16170769 TTACTTTTA
1 TTACTTTTA
16170778 CAATTTATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 8 0.33
18 8 0.33
19 8 0.33
ACGTcount: A:0.17, C:0.07, G:0.04, T:0.72
Consensus pattern (18 bp):
TTACTTTTATTTTTAGTT
Found at i:16174911 original size:9 final size:9
Alignment explanation
Indices: 16174897--16174921 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
16174887 AATTTTCACA
16174897 TCTAACTGC
1 TCTAACTGC
16174906 TCTAACTGC
1 TCTAACTGC
16174915 TCTAACT
1 TCTAACT
16174922 CAAAGTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.32, G:0.08, T:0.36
Consensus pattern (9 bp):
TCTAACTGC
Found at i:16183249 original size:3 final size:3
Alignment explanation
Indices: 16183241--16183290 Score: 91
Period size: 3 Copynumber: 16.3 Consensus size: 3
16183231 TAAAACGTGG
16183241 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
16183287 TAA T
1 TAA T
16183291 GATACAAGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:16183792 original size:19 final size:19
Alignment explanation
Indices: 16183768--16183823 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
16183758 AATCATATCT
16183768 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
16183787 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
16183806 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
16183824 TGAAGATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:16183817 original size:38 final size:40
Alignment explanation
Indices: 16183745--16183823 Score: 117
Period size: 38 Copynumber: 2.0 Consensus size: 40
16183735 AAATTAAATC
16183745 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTACAAAATCATA--TTCTAAGATTGCATATCATA
*
16183787 TCTAAGATTAC-ATATCATA-TCTAAGATTGCATATCAT
1 TCTAAGATTACAAAATCATATTCTAAGATTGCATATCAT
16183824 TGAAGATTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
38 18 0.50
41 7 0.19
42 11 0.31
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (40 bp):
TCTAAGATTACAAAATCATATTCTAAGATTGCATATCATA
Found at i:16183830 original size:36 final size:36
Alignment explanation
Indices: 16183761--16183832 Score: 103
Period size: 38 Copynumber: 2.0 Consensus size: 36
16183751 ATTACAAAAT
*
16183761 CATATCTTCTAAGATTGCATATCATATCTAAGATTA
1 CATATCTTCTAAGATTGCATATCATATCGAAGATTA
16183797 CATATCATATCTAAGATTGCATATCAT-T-GAAGATTA
1 CATATC-T-TCTAAGATTGCATATCATATCGAAGATTA
16183833 TGTTTCCATA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
36 13 0.39
37 2 0.06
38 18 0.55
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (36 bp):
CATATCTTCTAAGATTGCATATCATATCGAAGATTA
Found at i:16187259 original size:3 final size:3
Alignment explanation
Indices: 16187251--16187308 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
16187241 ATTTGTATTT
16187251 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
16187299 ATA ATA ATA A
1 ATA ATA ATA A
16187309 AGTAAACAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:16194600 original size:2 final size:2
Alignment explanation
Indices: 16194593--16194640 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
16194583 AAAACTGAAA
16194593 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
16194635 AC AC AC
1 AC AC AC
16194641 TTTTAGTTGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:16195328 original size:5 final size:5
Alignment explanation
Indices: 16195318--16195349 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
16195308 TTGCCACTTA
16195318 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
16195350 AAATATTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:16199174 original size:2 final size:2
Alignment explanation
Indices: 16199167--16199197 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
16199157 CTTTGAAGTA
16199167 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16199198 TAAAAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16202741 original size:18 final size:19
Alignment explanation
Indices: 16202714--16202749 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
16202704 CTTGAAAAGT
*
16202714 ATATTGTGTGA-TGTGATG
1 ATATTATGTGATTGTGATG
16202732 ATATTATGTGATTGTGAT
1 ATATTATGTGATTGTGAT
16202750 TTTTGTACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (19 bp):
ATATTATGTGATTGTGATG
Found at i:16202981 original size:22 final size:22
Alignment explanation
Indices: 16202949--16202990 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
16202939 AAGAAAGATA
*
16202949 TGTGGCAGTTTATCTACAATCG
1 TGTGGCAGTTTATCGACAATCG
*
16202971 TGTGGCCGTTTATCGACAAT
1 TGTGGCAGTTTATCGACAAT
16202991 TATATGGTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (22 bp):
TGTGGCAGTTTATCGACAATCG
Found at i:16207005 original size:7 final size:7
Alignment explanation
Indices: 16206983--16207017 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
16206973 TTTAATTGAC
16206983 ACCCTCAA
1 ACCCT-AA
16206991 ACCCTAA
1 ACCCTAA
*
16206998 ACCTTAA
1 ACCCTAA
16207005 ACCCTAA
1 ACCCTAA
16207012 ACCCTA
1 ACCCTA
16207018 CTCGGTTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 20 0.80
8 5 0.20
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (7 bp):
ACCCTAA
Found at i:16211716 original size:39 final size:39
Alignment explanation
Indices: 16211659--16211733 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
16211649 TACTTTCTGT
** * *
16211659 TTGGCGTGATTCGGGTGGATCAGCTCTTATGAGCTTTTG
1 TTGGCGTGATTCAAGTGGACCAACTCTTATGAGCTTTTG
*
16211698 TTGGCGTGTTTCAAGTGGACCAACTCTTATGAGCTT
1 TTGGCGTGATTCAAGTGGACCAACTCTTATGAGCTT
16211734 CTATTTGGCG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.16, C:0.17, G:0.29, T:0.37
Consensus pattern (39 bp):
TTGGCGTGATTCAAGTGGACCAACTCTTATGAGCTTTTG
Found at i:16212290 original size:15 final size:17
Alignment explanation
Indices: 16212262--16212293 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
16212252 TTCATTATTG
16212262 AAAGGTGATATGATGAA
1 AAAGGTGATATGATGAA
16212279 AAAGG-GAT-TGATGAA
1 AAAGGTGATATGATGAA
16212294 TTGAATGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (17 bp):
AAAGGTGATATGATGAA
Found at i:16217364 original size:124 final size:124
Alignment explanation
Indices: 16217139--16217418 Score: 499
Period size: 124 Copynumber: 2.3 Consensus size: 124
16217129 TTATTTCGAG
* * *
16217139 TTGACGTTTCTG-GTCAAATAGCATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGT
1 TTGATGTTTCTGAG-CAAATAGTATAAAATCGCTTCTACCAAGATGCTATTTGAGAAGAAATTGT
*
16217203 GAAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAGATAATTTTTT
65 GAAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
*
16217263 TTGATGTTTCTGAGCAAATAGTATAAAATTGCTTCTACCAAGATGCTATTTGAGAAGAAATTGTG
1 TTGATGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAAGATGCTATTTGAGAAGAAATTGTG
16217328 AAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
66 AAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
16217387 TTGATGTTTCTGAGCAAATAGTATAAAATCGC
1 TTGATGTTTCTGAGCAAATAGTATAAAATCGC
16217419 GCCCTCGTGG
Statistics
Matches: 149, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
124 148 0.99
125 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.34
Consensus pattern (124 bp):
TTGATGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAAGATGCTATTTGAGAAGAAATTGTG
AAATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTTT
Found at i:16219482 original size:56 final size:56
Alignment explanation
Indices: 16219422--16219579 Score: 280
Period size: 56 Copynumber: 2.8 Consensus size: 56
16219412 ACATTATGTA
*
16219422 AAACTATGTAAAATTATTAAGCCCAAAAACTTCTGTTAATGGTTAGTAAAATTATC
1 AAACTATGTAAAATTATTAAGCCCAAAAACTTTTGTTAATGGTTAGTAAAATTATC
** *
16219478 AAACTATGTAAAATTATTAATTCCAAAAACTTTTGTTAATGTTTAGTAAAATTATC
1 AAACTATGTAAAATTATTAAGCCCAAAAACTTTTGTTAATGGTTAGTAAAATTATC
16219534 AAACTATGTAAAATTATTAAGCCCAAAAACTTTTGTTAATGGTTAG
1 AAACTATGTAAAATTATTAAGCCCAAAAACTTTTGTTAATGGTTAG
16219580 GGTTTTTAAT
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 95 1.00
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (56 bp):
AAACTATGTAAAATTATTAAGCCCAAAAACTTTTGTTAATGGTTAGTAAAATTATC
Found at i:16219695 original size:29 final size:29
Alignment explanation
Indices: 16219574--16219830 Score: 323
Period size: 29 Copynumber: 8.9 Consensus size: 29
16219564 TTTTGTTAAT
*
16219574 GGTTAGGGTTTTTAATTAAATTAAGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
16219603 GGTTTATGGTTTTTAATTAAATTAGGTT--
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
* *
16219631 -GCTAGGGTTTTTAATTAAATTAAGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
16219659 GGTTTAGGGTTTTTAATTAAATTAGGTTAG
1 GG-TTAGGGTTTTTAATTAAATTAGGTTAG
16219689 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAG
1 GGTTAGGGTTTTTAATT-AA--A--TTA-GGTTAG
16219724 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
*
16219753 GGTTAGGG----T-ATTAAATTAGGTTGG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
16219777 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* *
16219806 AGTTAGGGTTTTTAATTAAGTTAGG
1 GGTTAGGGTTTTTAATTAAATTAGG
16219831 GTTTTTAATT
Statistics
Matches: 201, Mismatches: 11, Indels: 32
0.82 0.05 0.13
Matches are distributed among these distances:
24 22 0.11
25 1 0.00
26 22 0.11
27 1 0.00
28 1 0.00
29 69 0.34
30 55 0.27
32 2 0.01
34 5 0.02
35 23 0.11
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.45
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:16219727 original size:35 final size:35
Alignment explanation
Indices: 16219633--16219761 Score: 172
Period size: 35 Copynumber: 4.0 Consensus size: 35
16219623 ATTAGGTTGC
*
16219633 TAGGGTTTTTAATTAAATTAAGTTAGGG-T----T
1 TAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGT
16219663 TAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGT
1 TAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGT
16219692 TAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGT
1 TAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGT
16219727 TAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGT
1 TAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGT
16219762 ATTAAATTAG
Statistics
Matches: 88, Mismatches: 0, Indels: 17
0.84 0.00 0.16
Matches are distributed among these distances:
24 2 0.02
25 4 0.05
27 1 0.01
29 17 0.19
30 16 0.18
32 1 0.01
34 3 0.03
35 44 0.50
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (35 bp):
TAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGT
Found at i:16219780 original size:47 final size:47
Alignment explanation
Indices: 16219725--16219895 Score: 243
Period size: 47 Copynumber: 3.5 Consensus size: 47
16219715 TAGGGTTAGG
* * **
16219725 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTATTAAATTAGGTTGGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGT-TT---TTA-ATT-AA
16219778 GTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTTAATTAA
*
16219825 GTTAGGGTTTTTAATTAAGTTAGGTTAGAGTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTTAATTAA
16219872 GTTAGGGTTTTTAATTAAATTAGG
1 GTTAGGGTTTTTAATTAAATTAGG
16219896 ATTTTTATTA
Statistics
Matches: 112, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
47 69 0.62
48 2 0.02
49 3 0.03
52 2 0.02
53 36 0.32
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.45
Consensus pattern (47 bp):
GTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTTAATTAA
Found at i:16219829 original size:18 final size:18
Alignment explanation
Indices: 16219806--16219902 Score: 118
Period size: 18 Copynumber: 5.8 Consensus size: 18
16219796 ATTAGGTTAG
16219806 AGTTAGGGTTTTTAATTA
1 AGTTAGGGTTTTTAATTA
16219824 AGTTAGGGTTTTTAATTA
1 AGTTAGGGTTTTTAATTA
*
16219842 AGTTA-GG---TT-A--G
1 AGTTAGGGTTTTTAATTA
16219853 AGTTAGGGTTTTTAATTA
1 AGTTAGGGTTTTTAATTA
16219871 AGTTAGGGTTTTTAATTA
1 AGTTAGGGTTTTTAATTA
* *
16219889 AATTAGGATTTTTA
1 AGTTAGGGTTTTTA
16219903 TTACATCAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
11 5 0.07
12 2 0.03
13 1 0.01
14 2 0.03
15 2 0.03
16 1 0.01
17 2 0.03
18 53 0.78
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (18 bp):
AGTTAGGGTTTTTAATTA
Found at i:16219950 original size:25 final size:26
Alignment explanation
Indices: 16219898--16219961 Score: 103
Period size: 25 Copynumber: 2.5 Consensus size: 26
16219888 AAATTAGGAT
16219898 TTTTATTACATCAAATAGAACTTCTA
1 TTTTATTACATCAAATAGAACTTCTA
* *
16219924 TTTTATTATATTAAATA-AACTTCTA
1 TTTTATTACATCAAATAGAACTTCTA
16219949 TTTTATTACATCA
1 TTTTATTACATCA
16219962 GATAATAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 19 0.56
26 15 0.44
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (26 bp):
TTTTATTACATCAAATAGAACTTCTA
Found at i:16221824 original size:25 final size:25
Alignment explanation
Indices: 16221774--16221829 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
16221764 CTTTTATAAC
*
16221774 AAATAATAAATTAATAATTATCTAA
1 AAATAATAAATTAATAAATATCTAA
*
16221799 AAATACATAAA-TAA-AAATATCT-T
1 AAATA-ATAAATTAATAAATATCTAA
16221822 AAATAATA
1 AAATAATA
16221830 TTTAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 3 0.11
23 5 0.18
24 7 0.25
25 8 0.29
26 5 0.18
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (25 bp):
AAATAATAAATTAATAAATATCTAA
Found at i:16221935 original size:10 final size:10
Alignment explanation
Indices: 16221920--16221986 Score: 62
Period size: 10 Copynumber: 6.6 Consensus size: 10
16221910 GCCATTGATG
*
16221920 AAAAATATAA
1 AAAAATTTAA
16221930 AAAAATTTAA
1 AAAAATTTAA
** *
16221940 ATTATTTTAA
1 AAAAATTTAA
*
16221950 AAAAATATAA
1 AAAAATTTAA
16221960 AAAAATTTAA
1 AAAAATTTAA
* *
16221970 AATTATTTTAA
1 AA-AAATTTAA
16221981 AAAAAT
1 AAAAAT
16221987 GAAATTGAGG
Statistics
Matches: 43, Mismatches: 13, Indels: 2
0.74 0.22 0.03
Matches are distributed among these distances:
10 35 0.81
11 8 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
AAAAATTTAA
Found at i:16221954 original size:30 final size:31
Alignment explanation
Indices: 16221920--16221986 Score: 127
Period size: 30 Copynumber: 2.2 Consensus size: 31
16221910 GCCATTGATG
16221920 AAAAATATAAAAAAATTT-AAATTATTTTAA
1 AAAAATATAAAAAAATTTAAAATTATTTTAA
16221950 AAAAATATAAAAAAATTTAAAATTATTTTAA
1 AAAAATATAAAAAAATTTAAAATTATTTTAA
16221981 AAAAAT
1 AAAAAT
16221987 GAAATTGAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 18 0.50
31 18 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (31 bp):
AAAAATATAAAAAAATTTAAAATTATTTTAA
Found at i:16222056 original size:22 final size:23
Alignment explanation
Indices: 16222021--16222070 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
16222011 AATATGGATT
16222021 TGAGA-GATTCTTGGAAGGAAAC
1 TGAGAGGATTCTTGGAAGGAAAC
*
16222043 TGAGAGGATT-TTGGAAGGAAAT
1 TGAGAGGATTCTTGGAAGGAAAC
16222065 TGAGAG
1 TGAGAG
16222071 TTTGAGAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.36, C:0.04, G:0.36, T:0.24
Consensus pattern (23 bp):
TGAGAGGATTCTTGGAAGGAAAC
Found at i:16222078 original size:30 final size:30
Alignment explanation
Indices: 16222043--16222100 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
16222033 GGAAGGAAAC
*
16222043 TGAGAGGATTTTGGAAGGAAATTGAGAGTT
1 TGAGAGAATTTTGGAAGGAAATTGAGAGTT
16222073 TGAGAGAATTTTGGAAGGAAATTGAGAG
1 TGAGAGAATTTTGGAAGGAAATTGAGAG
16222101 GATTTTGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.28
Consensus pattern (30 bp):
TGAGAGAATTTTGGAAGGAAATTGAGAGTT
Found at i:16222087 original size:52 final size:52
Alignment explanation
Indices: 16222019--16222121 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 52
16222009 TTAATATGGA
16222019 TTTGAGAGATTCTTGGAAGGAAACTGAGAGGATTTTGGAAGGAAATTGAGAG
1 TTTGAGAGATTCTTGGAAGGAAACTGAGAGGATTTTGGAAGGAAATTGAGAG
* *
16222071 TTTGAGAGAATT-TTGGAAGGAAATTGAGAGGATTTTGGAATGAAATTGAGA
1 TTTGAGAG-ATTCTTGGAAGGAAACTGAGAGGATTTTGGAAGGAAATTGAGA
16222122 TAGGATTTGT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 45 0.94
53 3 0.06
ACGTcount: A:0.36, C:0.02, G:0.33, T:0.29
Consensus pattern (52 bp):
TTTGAGAGATTCTTGGAAGGAAACTGAGAGGATTTTGGAAGGAAATTGAGAG
Found at i:16222100 original size:22 final size:22
Alignment explanation
Indices: 16222072--16222121 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
16222062 AATTGAGAGT
16222072 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
* *
16222094 TTGAGAGGATTTTGGAATGAAA
1 TTGAGAGAATTTTGGAAGGAAA
16222116 TTGAGA
1 TTGAGA
16222122 TAGGATTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.30
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:16227004 original size:19 final size:19
Alignment explanation
Indices: 16226982--16227018 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16226972 TAAAATATTT
*
16226982 AAAAATTACAAAAAATATA
1 AAAAAATACAAAAAATATA
*
16227001 AAAAAATGCAAAAAATAT
1 AAAAAATACAAAAAATAT
16227019 TTTGAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (19 bp):
AAAAAATACAAAAAATATA
Found at i:16227755 original size:30 final size:28
Alignment explanation
Indices: 16227685--16227758 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 28
16227675 TAGTAAATCT
*
16227685 GATTTATAAA-A-TTTTAAAAATATTAA
1 GATTTATAAATATTTTTAAAAAAATTAA
* *
16227711 GATTTATAATTATTTTTAAAAAAATTTA
1 GATTTATAAATATTTTTAAAAAAATTAA
*
16227739 GTAATTTTTAAATATTTTTA
1 G--ATTTATAAATATTTTTA
16227759 TAATGCTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
26 9 0.23
27 1 0.03
28 14 0.36
30 15 0.38
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (28 bp):
GATTTATAAATATTTTTAAAAAAATTAA
Found at i:16227817 original size:21 final size:21
Alignment explanation
Indices: 16227792--16227837 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 21
16227782 AATTTTTCCT
16227792 ATTTTTT-AATAATTTTTT-TA
1 ATTTTTTAAAT-ATTTTTTGTA
16227812 ATTTTTTAAATATTTTTTGTA
1 ATTTTTTAAATATTTTTTGTA
16227833 ATTTT
1 ATTTT
16227838 CACAATTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
ATTTTTTAAATATTTTTTGTA
Found at i:16233680 original size:19 final size:19
Alignment explanation
Indices: 16233658--16233718 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
16233648 ATTAAAGTAG
16233658 GAAAGAAAGAGATATGGGA
1 GAAAGAAAGAGATATGGGA
*
16233677 GAAAGATAGAG--A-GGCGA
1 GAAAGAAAGAGATATGG-GA
* *
16233694 GAGAGAAAGAGATATGAGA
1 GAAAGAAAGAGATATGGGA
16233713 GAAAGA
1 GAAAGA
16233719 TAGAAAGACG
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 2 0.06
17 12 0.36
19 18 0.55
20 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.38, T:0.08
Consensus pattern (19 bp):
GAAAGAAAGAGATATGGGA
Found at i:16233701 original size:36 final size:36
Alignment explanation
Indices: 16233661--16233734 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
16233651 AAAGTAGGAA
* * *
16233661 AGAAAGAGATATGGGAGAAAGATAGAGAGGCGAGAG
1 AGAAAGAGATATGAGAGAAAGATAGAAAGACGAGAG
16233697 AGAAAGAGATATGAGAGAAAGATAGAAAGACGAGAG
1 AGAAAGAGATATGAGAGAAAGATAGAAAGACGAGAG
16233733 AG
1 AG
16233735 GGAAAGGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.38, T:0.08
Consensus pattern (36 bp):
AGAAAGAGATATGAGAGAAAGATAGAAAGACGAGAG
Found at i:16235505 original size:50 final size:50
Alignment explanation
Indices: 16235450--16235643 Score: 196
Period size: 50 Copynumber: 3.9 Consensus size: 50
16235440 CATTGAGGTT
* *
16235450 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
1 ATGAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
** * * *
16235500 ATGAGAGATCCCCCGTAAGACCATGTCTGGGAGATGGCATGGGCACCGAT
1 ATGAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
* * **
16235550 ATGAGA-ACTCCCATGTAAAACCATATCTGGGTTATGGCATTGGCA--GTAC
1 ATGAGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AC
* * * * * *
16235599 AAGAAACATCCCATGTAAGACCATGTTTGGGACATGACTTTGGCA
1 ATGAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
16235644 TGTTATTATC
Statistics
Matches: 118, Mismatches: 23, Indels: 7
0.80 0.16 0.05
Matches are distributed among these distances:
48 1 0.01
49 36 0.31
50 81 0.69
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (50 bp):
ATGAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
Found at i:16239928 original size:5 final size:5
Alignment explanation
Indices: 16239918--16239965 Score: 80
Period size: 5 Copynumber: 9.6 Consensus size: 5
16239908 GTAATTTGAT
16239918 AAATA AAATA AAATA AAATA AAAT- AAATA AAATA AAATAA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAAT-A AAATA AAA
16239966 GCTATCATCT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
4 4 0.10
5 32 0.78
6 5 0.12
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:16239945 original size:14 final size:14
Alignment explanation
Indices: 16239918--16239958 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
16239908 GTAATTTGAT
16239918 AAATAAAATAAAATA
1 AAATAAAAT-AAATA
16239933 AAATAAAATAAATA
1 AAATAAAATAAATA
16239947 AAATAAAATAAA
1 AAATAAAATAAA
16239959 AATAAAAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 17 0.65
15 9 0.35
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATAAAATAAATA
Found at i:16239945 original size:24 final size:25
Alignment explanation
Indices: 16239916--16239965 Score: 93
Period size: 24 Copynumber: 2.0 Consensus size: 25
16239906 TGGTAATTTG
16239916 ATAAATAAAATAAAAT-AAAATAAA
1 ATAAATAAAATAAAATAAAAATAAA
16239940 ATAAATAAAATAAAATAAAAATAAA
1 ATAAATAAAATAAAATAAAAATAAA
16239965 A
1 A
16239966 GCTATCATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (25 bp):
ATAAATAAAATAAAATAAAAATAAA
Found at i:16244927 original size:21 final size:21
Alignment explanation
Indices: 16244881--16244927 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
16244871 AAGTAGTTTT
*
16244881 GAAATGGAAAAGTAATGGATT
1 GAAATGGAAAAGTAATGGATG
16244902 GAAAT-GAAAAGT-ATGGTATG
1 GAAATGGAAAAGTAATGG-ATG
16244922 GTAAAT
1 G-AAAT
16244928 AGTTACATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 4 0.17
20 10 0.43
21 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.28, T:0.26
Consensus pattern (21 bp):
GAAATGGAAAAGTAATGGATG
Found at i:16250327 original size:38 final size:38
Alignment explanation
Indices: 16250285--16250358 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
16250275 CAGTTCAAGC
* *
16250285 TAATAAGCTCTTGAATCAAGGTTGTGAAGCTTTCCTGG
1 TAATAAGCTCCTGAATCAAGGTTGTGAAGCATTCCTGG
*
16250323 TAATAAGTTCCTGAATCAAGGTTGTGAAGCATTCCT
1 TAATAAGCTCCTGAATCAAGGTTGTGAAGCATTCCT
16250359 AGCCTACGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (38 bp):
TAATAAGCTCCTGAATCAAGGTTGTGAAGCATTCCTGG
Found at i:16252575 original size:56 final size:50
Alignment explanation
Indices: 16252495--16252685 Score: 190
Period size: 50 Copynumber: 3.7 Consensus size: 50
16252485 GGAATGAGAT
*
16252495 TCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C---GAGA-TATGAGAGG
* *
16252550 TCTCATGTAAGACCATGTCTGGGACATGACGTTGGCACCGAG--ATGAGAGG
1 TC-CATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGAGATATGAGAGG
** * * **
16252600 TCCCCGTAAGACCATGTCTGGGACATGGCATGGGCAC-CGATATGAGAAC
1 TCCATGTAAGACCATGTCTGGGACATGGCATTGGCACGAGATATGAGAGG
* *
16252649 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 T-CCATGTAAGACCATGTCTGGGACATGGCATTGGCA
16252686 GTATAGAAAA
Statistics
Matches: 115, Mismatches: 17, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
47 1 0.01
48 1 0.01
49 36 0.31
50 40 0.35
53 3 0.03
55 2 0.02
56 32 0.28
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
TCCATGTAAGACCATGTCTGGGACATGGCATTGGCACGAGATATGAGAGG
Found at i:16252678 original size:50 final size:50
Alignment explanation
Indices: 16252496--16252734 Score: 216
Period size: 49 Copynumber: 4.7 Consensus size: 50
16252486 GAATGAGATT
* * **
16252496 CCATGTAAGACCATGTCTAGGACATGGCATTGGCATCATTGAGATTATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C----CGA-TATGAGAACTC
* * * * **
16252552 TCATGTAAGACCATGTCTGGGACATGACGTTGGCACCGAGATGAGAGGTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAACTC
* *
16252602 CC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAACTC
* * *
16252651 CCATGTAAGACCATATCTGGGATATGGCATTGGCA--G-TATAGAAAACATC
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATAT-GAGAAC-TC
* * *
16252700 CCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA
16252735 TGTATTATCA
Statistics
Matches: 156, Mismatches: 24, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
47 3 0.02
48 6 0.04
49 74 0.47
50 39 0.25
51 2 0.01
55 1 0.01
56 31 0.20
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (50 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAACTC
Found at i:16252951 original size:12 final size:12
Alignment explanation
Indices: 16252934--16252972 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
16252924 ATGAGTTATT
16252934 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
16252946 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
16252958 TAAGTGAGTAAG
1 TAAGTAAGCAAG
16252970 TAA
1 TAA
16252973 ACAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:16252960 original size:20 final size:20
Alignment explanation
Indices: 16252935--16252977 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
16252925 TGAGTTATTT
16252935 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
**
16252955 AAGTAAGTGAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
16252975 AAG
1 AAG
16252978 CGAGTAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.53, C:0.07, G:0.23, T:0.16
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:16259131 original size:50 final size:50
Alignment explanation
Indices: 16259016--16259414 Score: 451
Period size: 50 Copynumber: 7.8 Consensus size: 50
16259006 GATCATAACA
* * ** * *
16259016 TGCCAAAGCCATGTCCTAGACATGGTCTTACATGGGATGTTCTCATATTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
16259067 TGCCCATGCCATGTCCCAGACATGGTCTTA-AGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACA-TGGGACCTCTCATCTCGG
* * *
16259117 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGATCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
16259167 TGCTAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCA-CTTTGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATC-TCGG
* * * *
16259217 TGCCAACACCATGTCCCAGACATGGTATTACATGGAACCTCTTATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
16259267 TACCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
16259317 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATGATCTCAAGAA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--G-G
* * * *
16259373 TTCCAATGCCATGTCCTAGACATGGTCTTACATGGGATCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
16259415 TTACCTAAAT
Statistics
Matches: 298, Mismatches: 40, Indels: 15
0.84 0.11 0.04
Matches are distributed among these distances:
49 1 0.00
50 222 0.74
51 33 0.11
53 4 0.01
55 1 0.00
56 37 0.12
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:16266534 original size:11 final size:11
Alignment explanation
Indices: 16266518--16266546 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
16266508 ATTTAAAATA
16266518 AAAATTATTTT
1 AAAATTATTTT
16266529 AAAATTATTTT
1 AAAATTATTTT
16266540 AAAATTA
1 AAAATTA
16266547 AAAATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AAAATTATTTT
Found at i:16266569 original size:29 final size:28
Alignment explanation
Indices: 16266506--16266569 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
16266496 AAACATTAAA
* ** *
16266506 ATATTTAAAATAAAAATTATTTTAAAAT
1 ATATTTAAAATAAAAATAAAATAAAAAT
16266534 -TATTTTAAAATTAAAAATAAAATAAAAAT
1 ATA-TTTAAAA-TAAAAATAAAATAAAAAT
16266563 ATATTTA
1 ATATTTA
16266570 TTATATTCGA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
27 2 0.07
28 7 0.24
29 18 0.62
30 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
ATATTTAAAATAAAAATAAAATAAAAAT
Found at i:16267267 original size:38 final size:38
Alignment explanation
Indices: 16267194--16267278 Score: 102
Period size: 38 Copynumber: 2.2 Consensus size: 38
16267184 ATAAATATAT
*
16267194 ATTTTTTAATTTTAAAATATTTTTTACATACTTTTTTA
1 ATTTTTTAATTTTAAAATATTTTTTACATACTTTTTAA
* *
16267232 ATTTTTTTATTTTAAAATACTTTTTTTA-A-ATTTTTTAA
1 ATTTTTTAATTTTAAAATA--TTTTTTACATACTTTTTAA
*
16267270 AATTTTTAA
1 ATTTTTTAA
16267279 AATAAAAATG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 32 0.80
39 1 0.03
40 7 0.17
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (38 bp):
ATTTTTTAATTTTAAAATATTTTTTACATACTTTTTAA
Found at i:16268800 original size:50 final size:51
Alignment explanation
Indices: 16268693--16268939 Score: 256
Period size: 50 Copynumber: 4.8 Consensus size: 51
16268683 ATTTGGGTAA
*
16268693 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAAGTTATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAAG--ATG
*
16268749 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAAGATG
* *
16268799 AGAGGTCCC-TCGTAAGACCATGTCTGGGACATGGCA-TGTGCACCG-ATATG
1 AGAGATCCCAT-GTAAGACCATGTCTGGGACATGGCATTG-GCACCGAAGATG
* * * * *
16268849 AGA-ACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAAG
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAAGATG
* * * *
16268898 AAACATCCCATGTAAGACCATGTTTGGGACATGGCTTTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
16268940 TGTTATTATC
Statistics
Matches: 171, Mismatches: 13, Indels: 21
0.83 0.06 0.10
Matches are distributed among these distances:
48 1 0.01
49 41 0.24
50 81 0.47
51 3 0.02
52 2 0.01
53 1 0.01
55 1 0.01
56 41 0.24
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (51 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAAGATG
Found at i:16274558 original size:26 final size:26
Alignment explanation
Indices: 16274522--16274573 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
16274512 TTGCCAACTG
*
16274522 AGTTATAGAAGATTCATAATGTATTC
1 AGTTAGAGAAGATTCATAATGTATTC
16274548 AGTTAGAGAAGATTCATAATGTATTC
1 AGTTAGAGAAGATTCATAATGTATTC
16274574 TATGTGTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (26 bp):
AGTTAGAGAAGATTCATAATGTATTC
Found at i:16276172 original size:50 final size:50
Alignment explanation
Indices: 16276061--16276255 Score: 221
Period size: 50 Copynumber: 3.8 Consensus size: 50
16276051 ATTTGGGTAA
* *
16276061 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAAGTTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CG-AG--ATG
* *
16276117 AGAGGTCCCATGTAAGACCATGTCTTGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
16276167 AGAGGTCCCCCT-TAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGT-CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
16276217 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATTG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTG
16276256 ACAGTACAAG
Statistics
Matches: 122, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
49 4 0.03
50 71 0.58
51 4 0.03
52 2 0.02
53 1 0.01
55 1 0.01
56 39 0.32
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:16293250 original size:50 final size:50
Alignment explanation
Indices: 16293135--16293383 Score: 282
Period size: 50 Copynumber: 4.8 Consensus size: 50
16293125 GATAATAACA
* * ** * *
16293135 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* *
16293186 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
16293236 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
16293286 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* * * *
16293341 ATGCCAATACCATGTCCCAGGCATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
16293384 TTACCCAAAT
Statistics
Matches: 169, Mismatches: 23, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
50 94 0.56
51 33 0.20
53 2 0.01
54 1 0.01
55 2 0.01
56 37 0.22
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:16293321 original size:100 final size:104
Alignment explanation
Indices: 16293134--16293383 Score: 339
Period size: 100 Copynumber: 2.4 Consensus size: 104
16293124 TGATAATAAC
** * *
16293134 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCCATGCCATG
* *
16293199 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
16293236 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
16293300 CCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
16293341 ATGCCAATA-CCATGTCCCAGGCATGGTCTTACATGGGATCTCT
1 ATGCCAA-AGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
16293384 TTACCCAAAT
Statistics
Matches: 130, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
100 50 0.38
101 36 0.28
103 3 0.02
104 1 0.01
105 2 0.02
106 38 0.29
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:16293499 original size:13 final size:13
Alignment explanation
Indices: 16293478--16293509 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
16293468 GCTTGAATCA
*
16293478 TCATCAAATAAAT
1 TCATAAAATAAAT
16293491 TCATAAAATAAAT
1 TCATAAAATAAAT
16293504 TCATAA
1 TCATAA
16293510 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:16296712 original size:41 final size:45
Alignment explanation
Indices: 16296638--16296721 Score: 113
Period size: 46 Copynumber: 1.9 Consensus size: 45
16296628 TTTAAAAATC
*
16296638 TATATTTAAATTAAAATATTAATAAATAAAAATGTTACAAAAAGTT
1 TATATTTAAATTAAAATATTAATAAAT-AAAATGTAACAAAAAGTT
*
16296684 TATATTTAAATTCAAA-A-T-ATAAAT-AAATGTAACAAAAA
1 TATATTTAAATTAAAATATTAATAAATAAAATGTAACAAAAA
16296722 TCTAATCTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
41 13 0.36
43 6 0.17
44 1 0.03
45 1 0.03
46 15 0.42
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (45 bp):
TATATTTAAATTAAAATATTAATAAATAAAATGTAACAAAAAGTT
Found at i:16297261 original size:32 final size:32
Alignment explanation
Indices: 16297221--16297291 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
16297211 CTTTTAGGTC
*
16297221 ACCA-AACCCTACCTGAACGCAAGCAATCCAT
1 ACCACAACCCTACCTGAACGCAAGCAACCCAT
*
16297252 ACCACAACCCTACCTGAATGCAAGCAACCCAT
1 ACCACAACCCTACCTGAACGCAAGCAACCCAT
*
16297284 ACCGCAAC
1 ACCACAAC
16297292 TCAGAAGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 4 0.11
32 32 0.89
ACGTcount: A:0.38, C:0.41, G:0.10, T:0.11
Consensus pattern (32 bp):
ACCACAACCCTACCTGAACGCAAGCAACCCAT
Found at i:16300522 original size:9 final size:9
Alignment explanation
Indices: 16300505--16300541 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
16300495 TGAGTTTTCG
16300505 AATTCGAAT
1 AATTCGAAT
*
16300514 AACTCGAAT
1 AATTCGAAT
16300523 AATTCGAAT
1 AATTCGAAT
16300532 AATTCGAAT
1 AATTCGAAT
16300541 A
1 A
16300542 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:16301555 original size:5 final size:5
Alignment explanation
Indices: 16301545--16301570 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
16301535 CTCAAAAATT
16301545 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
16301571 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:16306395 original size:7 final size:7
Alignment explanation
Indices: 16306376--16306408 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
16306366 GCAGACCAGA
16306376 AAAAAAT
1 AAAAAAT
16306383 AGAAAAAT
1 A-AAAAAT
16306391 AAAAAAT
1 AAAAAAT
16306398 -AAAAAT
1 AAAAAAT
16306404 AAAAA
1 AAAAA
16306409 GCCAAACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.25
7 11 0.46
8 7 0.29
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:16310835 original size:29 final size:29
Alignment explanation
Indices: 16310793--16310860 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
16310783 TATTTAATTA
16310793 ATGTTAAATGATTTTATTGAGTTGTTTTG
1 ATGTTAAATGATTTTATTGAGTTGTTTTG
16310822 ATGTTAAATGATTTTATTGAGTTGTTTTG
1 ATGTTAAATGATTTTATTGAGTTGTTTTG
16310851 ATGTTAAATG
1 ATGTTAAATG
16310861 TTACACCCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (29 bp):
ATGTTAAATGATTTTATTGAGTTGTTTTG
Found at i:16325241 original size:14 final size:14
Alignment explanation
Indices: 16325209--16325235 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16325199 CAAATTTAAC
16325209 TATACTAAAATGAA
1 TATACTAAAATGAA
16325223 TATACTAAAATGA
1 TATACTAAAATGA
16325236 TCATACAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (14 bp):
TATACTAAAATGAA
Found at i:16325696 original size:24 final size:24
Alignment explanation
Indices: 16325650--16325696 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
16325640 GGCTCTTCAG
* *
16325650 TAGCAGTTAGATTGGGCTGCTCGA
1 TAGCAGTTAGAGTGGCCTGCTCGA
* *
16325674 TAGCAGTTTGAGTGGCCTTCTCG
1 TAGCAGTTAGAGTGGCCTGCTCG
16325697 GCAGCATAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.17, C:0.19, G:0.32, T:0.32
Consensus pattern (24 bp):
TAGCAGTTAGAGTGGCCTGCTCGA
Found at i:16330343 original size:27 final size:27
Alignment explanation
Indices: 16330300--16330663 Score: 373
Period size: 27 Copynumber: 13.5 Consensus size: 27
16330290 CTTTCGATTT
*
16330300 GAAGGGTAAAATGATTGAAATACCCTC
1 GAAGGGTAAAATGATCGAAATACCCTC
* * * *
16330327 GAAAGGTAAAATAATTGAAATACCCCC
1 GAAGGGTAAAATGATCGAAATACCCTC
* *
16330354 GAAGGGTAAAATGATTGAAATACCCTT
1 GAAGGGTAAAATGATCGAAATACCCTC
* * *
16330381 AAAGGGTAAAATGACCGAAATACGCTC
1 GAAGGGTAAAATGATCGAAATACCCTC
* *
16330408 AAAGAGTAAAATGA-CAGAAATACCCTC
1 GAAGGGTAAAATGATC-GAAATACCCTC
* * *
16330435 AAAGGGTAAAATGA-CTAAAATACCCAC
1 GAAGGGTAAAATGATC-GAAATACCCTC
*
16330462 GAAGGGTAAAATGATCGAAATACCCCC
1 GAAGGGTAAAATGATCGAAATACCCTC
16330489 GAAGGGTAAAATGA-CGAAAATACCCTC
1 GAAGGGTAAAATGATCG-AAATACCCTC
* * * *
16330516 GAAGGGTAAAATGACCAAAACACCCCC
1 GAAGGGTAAAATGATCGAAATACCCTC
* *
16330543 GAAGGGTAAAATGATCAAAATACCCTA
1 GAAGGGTAAAATGATCGAAATACCCTC
16330570 GAAGGGTAAAATGATCGAAATACCC-C
1 GAAGGGTAAAATGATCGAAATACCCTC
* ** *
16330596 TGAAGGGTAAACTGGCCAAAATACCC-C
1 -GAAGGGTAAAATGATCGAAATACCCTC
* *
16330623 -ACAGGGTAAAATGATTGAAATACCTTC
1 GA-AGGGTAAAATGATCGAAATACCCTC
16330650 -ATAGGGTAAAATGA
1 GA-AGGGTAAAATGA
16330664 CCATTATACC
Statistics
Matches: 288, Mismatches: 42, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
25 1 0.00
26 20 0.07
27 265 0.92
28 2 0.01
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.17
Consensus pattern (27 bp):
GAAGGGTAAAATGATCGAAATACCCTC
Found at i:16336855 original size:11 final size:11
Alignment explanation
Indices: 16336839--16336863 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16336829 ACAGTTGTGG
16336839 GGATTTTGAAT
1 GGATTTTGAAT
16336850 GGATTTTGAAT
1 GGATTTTGAAT
16336861 GGA
1 GGA
16336864 GTTGTTGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.32, T:0.40
Consensus pattern (11 bp):
GGATTTTGAAT
Found at i:16337908 original size:27 final size:27
Alignment explanation
Indices: 16337875--16338351 Score: 502
Period size: 27 Copynumber: 17.7 Consensus size: 27
16337865 AACTTTTGAT
* *
16337875 TCGAAGGGTAAAATGATCGAAATATCC
1 TCGAAGGGTAAAATGACCGAAATACCC
*
16337902 TTGAAGGGTAAAATGACCGAAATACCC
1 TCGAAGGGTAAAATGACCGAAATACCC
* * *
16337929 CCAAAGGGTAAAATGATCGAAATACCC
1 TCGAAGGGTAAAATGACCGAAATACCC
* *
16337956 TCGAAGGGTAAAATAATCGAAATATCCC
1 TCGAAGGGTAAAATGACCGAAATA-CCC
* * *
16337984 T-AAATGGTAAAAT-AGCTGAAATACCC
1 TCGAAGGGTAAAATGA-CCGAAATACCC
** *
16338010 TTAAAGGGTAAAAT-AGCTGAAATACCC
1 TCGAAGGGTAAAATGA-CCGAAATACCC
*
16338037 TTGAAGGGTAAAATGACCGAAATACCC
1 TCGAAGGGTAAAATGACCGAAATACCC
* *
16338064 TAGAATGGTAAAATGACCGAAATACCC
1 TCGAAGGGTAAAATGACCGAAATACCC
* * *
16338091 CCGAAAGGTAAAATGACCGAAATAACCA
1 TCGAAGGGTAAAATGACCGAAAT-ACCC
* *
16338119 T-GAAGGGTAAAATAATCGAAATACCC
1 TCGAAGGGTAAAATGACCGAAATACCC
*
16338145 TCGAAGGGTAAAATGATCGAAATACCC
1 TCGAAGGGTAAAATGACCGAAATACCC
* *
16338172 TCGAAGGGTAAAATGATCGAAATACTC
1 TCGAAGGGTAAAATGACCGAAATACCC
* * *
16338199 TCAAAGGGTAAAATGATCGAAACACCC
1 TCGAAGGGTAAAATGACCGAAATACCC
* **
16338226 CCTGAAGGGTAAAATGACTAAAATACCC
1 TC-GAAGGGTAAAATGACCGAAATACCC
* * *
16338254 TCGAAAGGTAATATGACCAAAATACCAC
1 TCGAAGGGTAAAATGACCGAAATACC-C
*
16338282 -CGAAGGGTAAAATGACCAAAATACCC
1 TCGAAGGGTAAAATGACCGAAATACCC
16338308 -C-ACAGGGTAAAATGACCGAAATACCC
1 TCGA-AGGGTAAAATGACCGAAATACCC
*
16338334 T-TATAGGGTAAAATGACC
1 TCGA-AGGGTAAAATGACC
16338352 ATTATACCCC
Statistics
Matches: 392, Mismatches: 47, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
25 1 0.00
26 33 0.08
27 328 0.84
28 30 0.08
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.18
Consensus pattern (27 bp):
TCGAAGGGTAAAATGACCGAAATACCC
Found at i:16338681 original size:28 final size:28
Alignment explanation
Indices: 16338640--16338731 Score: 123
Period size: 28 Copynumber: 3.3 Consensus size: 28
16338630 GTTGCATTAT
* * *
16338640 CACACTGTTACTGTAATAGGCTAAGGTC
1 CACACTGTTTCTGTATTAGGCTAAGGCC
*
16338668 CACACTGTTTCTGTATTGGGCTAAGGCC
1 CACACTGTTTCTGTATTAGGCTAAGGCC
*
16338696 CACATTGTTAT-TGTATTAGGCTAAGGCC
1 CACACTGTT-TCTGTATTAGGCTAAGGCC
16338724 CACACTGT
1 CACACTGT
16338732 ACTATTATTG
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
28 55 0.98
29 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.32
Consensus pattern (28 bp):
CACACTGTTTCTGTATTAGGCTAAGGCC
Found at i:16338740 original size:28 final size:27
Alignment explanation
Indices: 16338656--16338740 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 27
16338646 GTTACTGTAA
* * *
16338656 TAGGCTAAGGTCCACACTGTTTCTGTAT
1 TAGGCTAAGGCCCACACTGTCTAT-TAT
* *
16338684 TGGGCTAAGGCCCACATTGT-TATTGTAT
1 TAGGCTAAGGCCCACACTGTCTA-T-TAT
16338712 TAGGCTAAGGCCCACACTGTACTATTAT
1 TAGGCTAAGGCCCACACTGT-CTATTAT
16338740 T
1 T
16338741 GCGTTGGGCT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
27 1 0.02
28 44 0.92
29 1 0.02
30 2 0.04
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (27 bp):
TAGGCTAAGGCCCACACTGTCTATTAT
Found at i:16348569 original size:16 final size:16
Alignment explanation
Indices: 16348548--16348621 Score: 96
Period size: 16 Copynumber: 4.6 Consensus size: 16
16348538 CGTTTGGTTC
16348548 GCTGTAATAGAATAGA
1 GCTGTAATAGAATAGA
*
16348564 GCTGTAATTGAATAGA
1 GCTGTAATAGAATAGA
*
16348580 GCTGTAATAGAATAAA
1 GCTGTAATAGAATAGA
16348596 GCTGTAAT-GTAATAGA
1 GCTGTAATAG-AATAGA
**
16348612 ATTGTAATAG
1 GCTGTAATAG
16348622 TAATTCAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
15 1 0.02
16 48 0.96
17 1 0.02
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.30
Consensus pattern (16 bp):
GCTGTAATAGAATAGA
Found at i:16348691 original size:44 final size:45
Alignment explanation
Indices: 16348601--16348693 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 45
16348591 ATAAAGCTGT
* *
16348601 AATGTAATAGAATTGTAATAGTAATTCAATTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTAATTCAATTGTTTGGTTGAATGG
*
16348646 AATGGAATAGAACTGTAATAGT-ATTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
16348690 AATG
1 AATG
16348694 ATGTTGTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.52
45 20 0.45
ACGTcount: A:0.33, C:0.03, G:0.25, T:0.39
Consensus pattern (45 bp):
AATGGAATAGAACTGTAATAGTAATTCAATTGTTTGGTTGAATGG
Found at i:16354811 original size:22 final size:22
Alignment explanation
Indices: 16354781--16354823 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
16354771 ACAACAAAAC
*
16354781 AGGCTTTTAGCGGCACTTTTTT
1 AGGCCTTTAGCGGCACTTTTTT
*
16354803 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCACTTTTT
16354824 AGCGCCACGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.21, G:0.26, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGGCACTTTTTT
Found at i:16354968 original size:43 final size:43
Alignment explanation
Indices: 16354915--16355229 Score: 350
Period size: 43 Copynumber: 7.3 Consensus size: 43
16354905 GTTTCTAGGA
*
16354915 ACAAATGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCAAAC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCAAAC
16354958 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCAAAC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCAAAC
* *
16355001 ACAAACGCCGCTAAATACCAAGACCTTTAGCGGCGCTTCAAGC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCAAAC
* *
16355044 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCAT-ATTAC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCA-AAC
* * * * ***
16355087 ATAAACGCCGCTAAATACTAAGATCTTTAGCGGCGCTTCTCTC
1 ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCAAAC
* * * ****
16355130 GCAAACGCCGCTAAATG-CTAAGTCCTTTAGCGGCGCTTTTCTC
1 ACAAACGCCGCTAAA-GACCAAGACCTTTAGCGGCGCTTCAAAC
* ****
16355173 ACAAACGCCGCTAAATG-CTAAGTA-CTTTAGCGGCGCTTTTCCC
1 ACAAACGCCGCTAAA-GACCAAG-ACCTTTAGCGGCGCTTCAAAC
16355216 ACAAACGCCGCTAA
1 ACAAACGCCGCTAA
16355230 TTTTGGCAGA
Statistics
Matches: 244, Mismatches: 24, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
42 1 0.00
43 243 1.00
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (43 bp):
ACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCAAAC
Found at i:16361260 original size:22 final size:21
Alignment explanation
Indices: 16361235--16361367 Score: 84
Period size: 22 Copynumber: 6.4 Consensus size: 21
16361225 GTTACATATC
16361235 ATATTAATGTAAGTTATGTATT
1 ATATTAATGTAAGTTATGTA-T
* *
16361257 ATATAAGTTATTTAAGTTATGTA-
1 ATAT---TAATGTAAGTTATGTAT
* *
16361280 A-GTT-GTGTAAGTTATGTAT
1 ATATTAATGTAAGTTATGTAT
**
16361299 AATATTACGGTAAGTTATG---
1 -ATATTAATGTAAGTTATGTAT
16361318 -TATT-ATGTAAGTTATGTAT
1 ATATTAATGTAAGTTATGTAT
16361337 AATATTAATGTAAGTTATGTATT
1 -ATATTAATGTAAGTTATGTA-T
*
16361360 ATGTTAAT
1 ATATTAAT
16361368 ATTTAGAAAA
Statistics
Matches: 86, Mismatches: 11, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
16 10 0.12
17 4 0.05
18 12 0.14
19 1 0.01
20 1 0.01
21 6 0.07
22 36 0.42
23 2 0.02
25 14 0.16
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.47
Consensus pattern (21 bp):
ATATTAATGTAAGTTATGTAT
Found at i:16361267 original size:9 final size:9
Alignment explanation
Indices: 16361241--16361335 Score: 81
Period size: 9 Copynumber: 10.6 Consensus size: 9
16361231 TATCATATTA
16361241 ATGTAAGTT
1 ATGTAAGTT
16361250 ATGT-A-TT
1 ATGTAAGTT
*
16361257 ATATAAGTT
1 ATGTAAGTT
*
16361266 ATTTAAGTT
1 ATGTAAGTT
16361275 ATGTAAGTT
1 ATGTAAGTT
*
16361284 GTGTAAGTT
1 ATGTAAGTT
*
16361293 ATGTATAATATT
1 ATG--TAA-GTT
*
16361305 ACGGTAAGTT
1 A-TGTAAGTT
16361315 ATGT-A-TT
1 ATGTAAGTT
16361322 ATGTAAGTT
1 ATGTAAGTT
16361331 ATGTA
1 ATGTA
16361336 TAATATTAAT
Statistics
Matches: 69, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
7 11 0.16
8 4 0.06
9 41 0.59
10 3 0.04
11 6 0.09
12 3 0.04
13 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.19, T:0.46
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:16361281 original size:18 final size:18
Alignment explanation
Indices: 16361241--16361335 Score: 81
Period size: 16 Copynumber: 5.3 Consensus size: 18
16361231 TATCATATTA
16361241 ATGTAAGTTATGT-A-TT
1 ATGTAAGTTATGTAAGTT
* *
16361257 ATATAAGTTATTTAAGTT
1 ATGTAAGTTATGTAAGTT
*
16361275 ATGTAAGTTGTGTAAGTT
1 ATGTAAGTTATGTAAGTT
* *
16361293 ATGTATAATATTACGGTAAGTT
1 ATG--TAA-GTTA-TGTAAGTT
16361315 ATGT-A-TTATGTAAGTT
1 ATGTAAGTTATGTAAGTT
16361331 ATGTA
1 ATGTA
16361336 TAATATTAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
16 22 0.35
17 4 0.06
18 20 0.32
19 1 0.02
20 4 0.06
21 2 0.03
22 10 0.16
ACGTcount: A:0.34, C:0.01, G:0.19, T:0.46
Consensus pattern (18 bp):
ATGTAAGTTATGTAAGTT
Found at i:16361327 original size:38 final size:38
Alignment explanation
Indices: 16361269--16361363 Score: 145
Period size: 38 Copynumber: 2.4 Consensus size: 38
16361259 ATAAGTTATT
* *
16361269 TAAGTTATGTAAGTTGTGTAAGTTATGTATAATATTACGG
1 TAAGTTATGT-A-TTATGTAAGTTATGTATAATATTAAGG
*
16361309 TAAGTTATGTATTATGTAAGTTATGTATAATATTAATG
1 TAAGTTATGTATTATGTAAGTTATGTATAATATTAAGG
16361347 TAAGTTATGTATTATGT
1 TAAGTTATGTATTATGT
16361364 TAATATTTAG
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
38 41 0.79
39 1 0.02
40 10 0.19
ACGTcount: A:0.34, C:0.01, G:0.19, T:0.46
Consensus pattern (38 bp):
TAAGTTATGTATTATGTAAGTTATGTATAATATTAAGG
Found at i:16361490 original size:21 final size:21
Alignment explanation
Indices: 16361457--16361496 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
16361447 TAACATTTAC
*
16361457 AATTATTTCTGAAATTATAAA
1 AATTATTTCTGAAAATATAAA
16361478 AATTATTAT-TGAAAATATA
1 AATTATT-TCTGAAAATATA
16361497 GGTTTAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (21 bp):
AATTATTTCTGAAAATATAAA
Found at i:16361519 original size:69 final size:69
Alignment explanation
Indices: 16361360--16361554 Score: 220
Period size: 69 Copynumber: 2.8 Consensus size: 69
16361350 GTTATGTATT
* * *
16361360 ATGTTAATATTTAG-AAAATAGCAATTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAA
1 ATGTTAATCTTT-GCAAAATAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAA
16361424 TATAG
65 TATAG
* * *
16361429 ATGTTAATCTTTGGAAAATAACATTTACAATTATTTCTGAAATTATAAAAATTATTATTGAAAAT
1 ATGTTAATCTTTGCAAAATAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAAT
16361494 ATAG
66 ATAG
* *** *
16361498 GT-TTAAT-TGTTGTCTTCATAACATTTATC-ATTATTTTTAAAATTA-AAAATTTATTAT
1 ATGTTAATCT-TTG-CAAAATAACATTTA-CAATTATTTCTAAAATTATAAAATTTATTAT
16361555 CAATAAAATT
Statistics
Matches: 109, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
67 1 0.01
68 20 0.18
69 87 0.80
70 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (69 bp):
ATGTTAATCTTTGCAAAATAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAAT
ATAG
Found at i:16363169 original size:24 final size:22
Alignment explanation
Indices: 16363131--16363176 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 22
16363121 CTAGGGTTCT
16363131 AAATTTGGGGGATTTTTGGGGA
1 AAATTTGGGGGATTTTTGGGGA
16363153 AAATTTGGGGGGAATTTTTGGGGA
1 AAATTT-GGGGG-ATTTTTGGGGA
16363177 GAAAACTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 6 0.27
23 5 0.23
24 11 0.50
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.35
Consensus pattern (22 bp):
AAATTTGGGGGATTTTTGGGGA
Found at i:16364015 original size:19 final size:20
Alignment explanation
Indices: 16363988--16364028 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
16363978 AAAATTTTAA
16363988 TTAAATAAT-TATTAAAA-TT
1 TTAAATAATAT-TTAAAAGTT
*
16364007 TTAAGTAATATTTAAAAGTT
1 TTAAATAATATTTAAAAGTT
16364027 TT
1 TT
16364029 TGATAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TTAAATAATATTTAAAAGTT
Found at i:16364752 original size:7 final size:7
Alignment explanation
Indices: 16364740--16364814 Score: 51
Period size: 7 Copynumber: 9.9 Consensus size: 7
16364730 ACCCTTGACA
16364740 CCCTAAC
1 CCCTAAC
*
16364747 CCCTAAAT
1 CCCT-AAC
16364755 CCCTAAC
1 CCCTAAC
16364762 CCCTAAC
1 CCCTAAC
*
16364769 CCTTAAATC
1 CCCT-AA-C
16364778 TCCCTAACCC
1 -CCCTAA--C
* *
16364788 CCCAAAT
1 CCCTAAC
*
16364795 CACTAAC
1 CCCTAAC
16364802 CCCTAAC
1 CCCTAAC
16364809 CCCTAA
1 CCCTAA
16364815 ATTCCTAACC
Statistics
Matches: 52, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
7 32 0.62
8 8 0.15
9 8 0.15
10 4 0.08
ACGTcount: A:0.32, C:0.49, G:0.00, T:0.19
Consensus pattern (7 bp):
CCCTAAC
Found at i:16364768 original size:22 final size:22
Alignment explanation
Indices: 16364740--16364836 Score: 98
Period size: 22 Copynumber: 4.6 Consensus size: 22
16364730 ACCCTTGACA
16364740 CCCTAACCCCTAAATCCCTAAC
1 CCCTAACCCCTAAATCCCTAAC
*
16364762 CCCTAACCCTTAAAT--CT---
1 CCCTAACCCCTAAATCCCTAAC
* *
16364779 CCCTAACCCCCCAAATCACTAAC
1 CCCTAA-CCCCTAAATCCCTAAC
*
16364802 CCCTAACCCCTAAATTCCTAAC
1 CCCTAACCCCTAAATCCCTAAC
*
16364824 CCAT-ACCCCTAAA
1 CCCTAACCCCTAAA
16364837 CCTTAATCCC
Statistics
Matches: 62, Mismatches: 7, Indels: 13
0.76 0.09 0.16
Matches are distributed among these distances:
17 6 0.10
18 7 0.11
20 4 0.06
21 9 0.15
22 30 0.48
23 6 0.10
ACGTcount: A:0.33, C:0.47, G:0.00, T:0.20
Consensus pattern (22 bp):
CCCTAACCCCTAAATCCCTAAC
Found at i:16364801 original size:40 final size:39
Alignment explanation
Indices: 16364740--16364825 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 39
16364730 ACCCTTGACA
* * *
16364740 CCCTAA-CCCCTAAATCCCTAACCCCTAACCCTTAAATCT
1 CCCTAACCCCCCAAATCACTAACCCCTAACCCCTAAAT-T
16364779 CCCTAACCCCCCAAATCACTAACCCCTAACCCCTAAATT
1 CCCTAACCCCCCAAATCACTAACCCCTAACCCCTAAATT
16364818 -CCTAACCC
1 CCCTAACCC
16364826 ATACCCCTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
38 8 0.19
39 7 0.16
40 28 0.65
ACGTcount: A:0.31, C:0.49, G:0.00, T:0.20
Consensus pattern (39 bp):
CCCTAACCCCCCAAATCACTAACCCCTAACCCCTAAATT
Found at i:16365142 original size:2 final size:2
Alignment explanation
Indices: 16365135--16365169 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
16365125 GACAAACAAC
*
16365135 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16365170 GGCATTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:16365534 original size:42 final size:40
Alignment explanation
Indices: 16365478--16365633 Score: 127
Period size: 41 Copynumber: 3.8 Consensus size: 40
16365468 GCTAAAACTC
*
16365478 CAACATTAGTGGCGCTTTATAAACAAACGCCACTAAAAACCT
1 CAACATTAGCGGCGC-TTATAAA-AAACGCCACTAAAAACCT
* * * * *
16365520 CAACTTTAGCGGCGCATTATCAAAAATGCCGCTAAAAGCC-
1 CAACATTAGCGGCGC-TTATAAAAAACGCCACTAAAAACCT
* * *
16365560 CTAAAATTAGCGGCGCTCAGGAAAAAACGCCACTAAAAACCAT
1 C-AACATTAGCGGCGCTTA-TAAAAAACGCCACTAAAAACC-T
* * *
16365603 -AACATTAGCGGCGTTTGTTTAAAAACGCCAC
1 CAACATTAGCGGCGCTT-ATAAAAAACGCCAC
16365634 GAAAGCCCTC
Statistics
Matches: 88, Mismatches: 21, Indels: 11
0.73 0.17 0.09
Matches are distributed among these distances:
40 3 0.03
41 66 0.75
42 19 0.22
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.20
Consensus pattern (40 bp):
CAACATTAGCGGCGCTTATAAAAAACGCCACTAAAAACCT
Found at i:16365555 original size:41 final size:42
Alignment explanation
Indices: 16365461--16365575 Score: 112
Period size: 41 Copynumber: 2.8 Consensus size: 42
16365451 GTTTCCATCG
* *
16365461 AAATGCCGCT-AAAACTCCAACATTAGTGGCGCTTTATAAAC
1 AAATGCCGCTAAAAACTCCAACATTAGCGGCGCATTATAAAC
* * * *
16365502 AAACGCCACTAAAAAC-CTCAACTTTAGCGGCGCATTATCAA-
1 AAATGCCGCTAAAAACTC-CAACATTAGCGGCGCATTATAAAC
* *
16365543 AAATGCCGCTAAAAGC-CCTAAAATTAGCGGCGC
1 AAATGCCGCTAAAAACTCC-AACATTAGCGGCGC
16365576 TCAGGAAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
40 1 0.02
41 35 0.58
42 24 0.40
ACGTcount: A:0.37, C:0.27, G:0.16, T:0.20
Consensus pattern (42 bp):
AAATGCCGCTAAAAACTCCAACATTAGCGGCGCATTATAAAC
Found at i:16368459 original size:17 final size:18
Alignment explanation
Indices: 16368437--16368470 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16368427 TTATTTATAA
16368437 TTTAAA-AAATTAATTAT
1 TTTAAATAAATTAATTAT
*
16368454 TTTAAATAATTTAATTA
1 TTTAAATAAATTAATTA
16368471 AATTAAGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATAAATTAATTAT
Found at i:16371985 original size:22 final size:22
Alignment explanation
Indices: 16371950--16372056 Score: 142
Period size: 22 Copynumber: 4.9 Consensus size: 22
16371940 CTTAATTCAA
16371950 GTACTAAGCTCTCATGTTTAAC
1 GTACTAAGCTCTCATGTTTAAC
* * * **
16371972 GAACTAAACCCTCATGGCTAAC
1 GTACTAAGCTCTCATGTTTAAC
**
16371994 GTACTAAGCTCTCATGGCTAAC
1 GTACTAAGCTCTCATGTTTAAC
*
16372016 GTACTAAGCTCTCATGTTTCAC
1 GTACTAAGCTCTCATGTTTAAC
16372038 GTACTAAGCTCTCATGTTT
1 GTACTAAGCTCTCATGTTT
16372057 GAACAATAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 74 1.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (22 bp):
GTACTAAGCTCTCATGTTTAAC
Found at i:16382078 original size:31 final size:27
Alignment explanation
Indices: 16382035--16382098 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 27
16382025 AATACAATAA
16382035 ATTTTTTTATTTTTTTAAATTTTAAAAT
1 ATTTTTTTATTTTTTT-AATTTTAAAAT
16382063 ACTTTTTTTAAATTTTTTTAATTTTAAAAT
1 A-TTTTTTT--ATTTTTTTAATTTTAAAAT
16382093 ATTTTT
1 ATTTTT
16382099 AAAATAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
28 1 0.03
29 12 0.36
30 12 0.36
31 8 0.24
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (27 bp):
ATTTTTTTATTTTTTTAATTTTAAAAT
Found at i:16382079 original size:30 final size:28
Alignment explanation
Indices: 16382035--16382098 Score: 92
Period size: 30 Copynumber: 2.2 Consensus size: 28
16382025 AATACAATAA
*
16382035 ATTTTTTTATTTTTTTAAATTTTAAAAT
1 ATTTTTTTAATTTTTTAAATTTTAAAAT
*
16382063 ACTTTTTTTAAATTTTTTTAATTTTAAAAT
1 A-TTTTTTT-AATTTTTTAAATTTTAAAAT
16382093 ATTTTT
1 ATTTTT
16382099 AAAATAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 1 0.03
29 12 0.38
30 19 0.59
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (28 bp):
ATTTTTTTAATTTTTTAAATTTTAAAAT
Found at i:16382112 original size:32 final size:32
Alignment explanation
Indices: 16382045--16382144 Score: 86
Period size: 32 Copynumber: 3.2 Consensus size: 32
16382035 ATTTTTTTAT
* *
16382045 TTTTTTAAATTTTAAAATACTTTTT---TTAAAT
1 TTTTTT-AATTTTAAAATA-TTTTTAAAATAAAA
16382076 TTTTTTAATTTTAAAATATTTTTAAAATAAAA
1 TTTTTTAATTTTAAAATATTTTTAAAATAAAA
**
16382108 TTTTTTATTATTTT-TTA-ATTTTTAAAAT-AAA
1 TTTTTTA--ATTTTAAAATATTTTTAAAATAAAA
16382139 TTTTTT
1 TTTTTT
16382145 GTATTTATTT
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
29 5 0.08
30 12 0.20
31 15 0.25
32 22 0.37
33 1 0.02
34 5 0.08
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (32 bp):
TTTTTTAATTTTAAAATATTTTTAAAATAAAA
Found at i:16382156 original size:31 final size:32
Alignment explanation
Indices: 16382093--16382156 Score: 96
Period size: 31 Copynumber: 2.0 Consensus size: 32
16382083 ATTTTAAAAT
*
16382093 ATTTTTAAAATAAAATTTTTTATTATTTTTTA
1 ATTTTTAAAATAAAATTTTTTAGTATTTTTTA
16382125 ATTTTTAAAAT-AAATTTTTT-GTATTTATTTA
1 ATTTTTAAAATAAAATTTTTTAGTATTT-TTTA
16382156 A
1 A
16382157 AAAACGGGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 5 0.17
31 14 0.47
32 11 0.37
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (32 bp):
ATTTTTAAAATAAAATTTTTTAGTATTTTTTA
Found at i:16382807 original size:14 final size:14
Alignment explanation
Indices: 16382788--16382873 Score: 52
Period size: 14 Copynumber: 6.0 Consensus size: 14
16382778 TTCCTTCTAG
16382788 TTTATTTTATTATT
1 TTTATTTTATTATT
16382802 TTTATTATTA-TATT
1 TTTATT-TTATTATT
* *
16382816 AGTTT-TATTATTAGT
1 --TTTATTTTATTATT
* *
16382831 TTTATTATATTGTT
1 TTTATTTTATTATT
*
16382845 TTTATATTATT-TAT
1 TTTATTTTATTAT-T
*
16382859 CTTATTTTCATTATT
1 TTTATTTT-ATTATT
16382874 AGGATTAGTT
Statistics
Matches: 54, Mismatches: 10, Indels: 15
0.68 0.13 0.19
Matches are distributed among these distances:
13 4 0.07
14 35 0.65
15 11 0.20
16 4 0.07
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.70
Consensus pattern (14 bp):
TTTATTTTATTATT
Found at i:16382811 original size:12 final size:12
Alignment explanation
Indices: 16382792--16382897 Score: 53
Period size: 12 Copynumber: 8.8 Consensus size: 12
16382782 TTCTAGTTTA
16382792 TTTTATTATT-T
1 TTTTATTATTAT
*
16382803 TTATTATTATATTAG
1 TT-TTA-T-TATTAT
*
16382818 TTTTATTATTAG
1 TTTTATTATTAT
16382830 TTTTATTA-TAT
1 TTTTATTATTAT
16382841 TGTTT-TTA-TAT
1 T-TTTATTATTAT
*
16382852 TATTTA-TCTTAT
1 T-TTTATTATTAT
* *
16382864 TTTCATTATTAG
1 TTTTATTATTAT
**
16382876 GATTAGTT-TTAT
1 TTTTA-TTATTAT
16382888 TTTTATTATT
1 TTTTATTATT
16382898 GCTATAGTTA
Statistics
Matches: 72, Mismatches: 13, Indels: 19
0.69 0.12 0.18
Matches are distributed among these distances:
11 21 0.29
12 38 0.53
13 4 0.06
14 7 0.10
15 2 0.03
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.68
Consensus pattern (12 bp):
TTTTATTATTAT
Found at i:16382835 original size:26 final size:25
Alignment explanation
Indices: 16382792--16382846 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
16382782 TTCTAGTTTA
*
16382792 TTTTATTATTTTTATTATTATATTAG
1 TTTTATTATTGTTATTATTATATT-G
16382818 TTTTATTATTAGTT-TTATTATATTG
1 TTTTATTATT-GTTATTATTATATTG
16382843 TTTT
1 TTTT
16382847 TATATTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 5 0.19
26 20 0.74
27 2 0.07
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (25 bp):
TTTTATTATTGTTATTATTATATTG
Found at i:16382837 original size:9 final size:8
Alignment explanation
Indices: 16382789--16382827 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 8
16382779 TCCTTCTAGT
16382789 TTATTTTA
1 TTATTTTA
16382797 TTATTTTTA
1 TTA-TTTTA
*
16382806 TTATTATA
1 TTATTTTA
16382814 TTAGTTTTA
1 TTA-TTTTA
16382823 TTATT
1 TTATT
16382828 AGTTTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 12 0.44
9 15 0.56
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (8 bp):
TTATTTTA
Found at i:16383054 original size:16 final size:16
Alignment explanation
Indices: 16383018--16383057 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
16383008 ATTACGTGCC
*
16383018 GATTTGTTTTATTTGTT
1 GATTTG-TTTATTTATT
*
16383035 GATTTGTTTCTTTATT
1 GATTTGTTTATTTATT
16383051 GATTTGT
1 GATTTGT
16383058 ACTGATATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.12, C:0.03, G:0.17, T:0.68
Consensus pattern (16 bp):
GATTTGTTTATTTATT
Found at i:16384581 original size:35 final size:35
Alignment explanation
Indices: 16384542--16384608 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
16384532 GCACTATTTT
* *
16384542 TTTAT-TTTTTCAGTTTTTTTCTAGTTTT-TTATCTC
1 TTTATATTATTCA-TTTTTGTCTA-TTTTCTTATCTC
16384577 TTTATATTATTCATTTTTGTCTATTTTCTTAT
1 TTTATATTATTCATTTTTGTCTATTTTCTTAT
16384609 TAGTTTGCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 4 0.14
35 18 0.64
36 6 0.21
ACGTcount: A:0.15, C:0.10, G:0.04, T:0.70
Consensus pattern (35 bp):
TTTATATTATTCATTTTTGTCTATTTTCTTATCTC
Found at i:16385325 original size:35 final size:35
Alignment explanation
Indices: 16385279--16385348 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
16385269 GTTGTATTAA
16385279 CCCCTAGTAAACATTGCTGATCCTAACACATTTTT
1 CCCCTAGTAAACATTGCTGATCCTAACACATTTTT
*
16385314 CCCCTAGTAAACATTGTTGATCCTAACACATTTTT
1 CCCCTAGTAAACATTGCTGATCCTAACACATTTTT
16385349 TTTTCTCTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.36
Consensus pattern (35 bp):
CCCCTAGTAAACATTGCTGATCCTAACACATTTTT
Found at i:16391616 original size:18 final size:18
Alignment explanation
Indices: 16391589--16391674 Score: 75
Period size: 18 Copynumber: 4.6 Consensus size: 18
16391579 CACATTTTTC
16391589 TTCATTTCATATTTTTCAT
1 TTCA-TTCATATTTTTCAT
* **
16391608 TTCAGTCATATATACTCAT
1 TTCATTCATAT-TTTTCAT
* **
16391627 TCCAATTCCCATTTTTC-T
1 TTC-ATTCATATTTTTCAT
16391645 TTCATTTCATATTTTTCAT
1 TTCA-TTCATATTTTTCAT
16391664 TTCATTCATAT
1 TTCATTCATAT
16391675 ATCCTTATTC
Statistics
Matches: 51, Mismatches: 12, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
17 1 0.02
18 26 0.51
19 19 0.37
20 5 0.10
ACGTcount: A:0.23, C:0.21, G:0.01, T:0.55
Consensus pattern (18 bp):
TTCATTCATATTTTTCAT
Found at i:16391661 original size:56 final size:56
Alignment explanation
Indices: 16391581--16391703 Score: 194
Period size: 56 Copynumber: 2.2 Consensus size: 56
16391571 TTCCATGTCA
16391581 CATTTTTC-TTCATTTCATATTTTTCATTTCAGTCATATATACTCATTCCAATTCC
1 CATTTTTCTTTCATTTCATATTTTTCATTTCAGTCATATATACTCATTCCAATTCC
* * * *
16391636 CATTTTTCTTTCATTTCATATTTTTCATTTCATTCATATATCCTTATTCCAATTCT
1 CATTTTTCTTTCATTTCATATTTTTCATTTCAGTCATATATACTCATTCCAATTCC
*
16391692 CATTTTTATTTC
1 CATTTTTCTTTC
16391704 CCTATTAACG
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
55 8 0.13
56 54 0.87
ACGTcount: A:0.22, C:0.22, G:0.01, T:0.55
Consensus pattern (56 bp):
CATTTTTCTTTCATTTCATATTTTTCATTTCAGTCATATATACTCATTCCAATTCC
Found at i:16399918 original size:11 final size:11
Alignment explanation
Indices: 16399902--16399928 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
16399892 CGTCCCTAGA
16399902 AAGTTAGAATT
1 AAGTTAGAATT
16399913 AAGTTAGAATT
1 AAGTTAGAATT
16399924 AAGTT
1 AAGTT
16399929 TTCTAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.37
Consensus pattern (11 bp):
AAGTTAGAATT
Found at i:16404655 original size:101 final size:102
Alignment explanation
Indices: 16404540--16404724 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 102
16404530 AAAGTGATGG
*
16404540 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACCACGTGTACCAGATAGTGAT-GGTCGCATGTGTAGT
*
16404603 ACTATGTGTAGGCTACTATGCGTACCGGATAGCTTCGA
65 ACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
* * * *
16404641 TCACGTGTGTAGTACTATGTGCAGGCTACCATGTGTATCGGATAGTGATGGTCTCATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACCACGTGTACCAGATAGTGATGGTCGCATGTGTAGTA
16404706 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
16404725 TGAACCGATA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 38 0.50
102 34 0.45
103 4 0.05
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACCACGTGTACCAGATAGTGATGGTCGCATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:16404660 original size:51 final size:49
Alignment explanation
Indices: 16404537--16404731 Score: 212
Period size: 51 Copynumber: 3.9 Consensus size: 49
16404527 GTGAAAGTGA
* * *
16404537 TGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-ATGAT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATA-G-T
* * * *
16404587 AGGTCGCATGTGTAGTACTATGTGTAGGCTACTATGCGTACCGGATAGCT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAG-T
* * * *
16404637 TCGATCACGTGTGTAGTACTATGTGCAGGCTACCATGTGTATCGGATAGT
1 T-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGT
* *
16404687 GATGGTCTCATGTGTAGTACTATGTGCAGGCTACTATGTGAACCG
1 --TGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCG
16404732 ATATCATTAA
Statistics
Matches: 119, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
50 41 0.34
51 77 0.65
52 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.31
Consensus pattern (49 bp):
TGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGT
Found at i:16404971 original size:16 final size:16
Alignment explanation
Indices: 16404950--16404981 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
16404940 TGATTGAAAG
*
16404950 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
16404966 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
16404982 GCAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:16408936 original size:20 final size:21
Alignment explanation
Indices: 16408891--16408938 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
16408881 ATAGGTAAAT
*
16408891 TCATC-CACAGTATAAGTAGA
1 TCATCTCACAGTATAAGTACA
*
16408911 T-TTCTCACA-TATAAGTACA
1 TCATCTCACAGTATAAGTACA
16408930 TCATCTCAC
1 TCATCTCAC
16408939 CAATCCTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.31
Consensus pattern (21 bp):
TCATCTCACAGTATAAGTACA
Found at i:16423425 original size:3 final size:3
Alignment explanation
Indices: 16423346--16423410 Score: 60
Period size: 3 Copynumber: 21.0 Consensus size: 3
16423336 TTAGGACACC
* * * *
16423346 TTA TCTA TT- TTA TTA TTA TTA TGA TGTGA TTA TTA ATA TTA ATA TTG
1 TTA T-TA TTA TTA TTA TTA TTA TTA T-T-A TTA TTA TTA TTA TTA TTA
16423393 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
16423411 CATTACTGTT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 2 0.04
3 42 0.84
4 4 0.08
5 2 0.04
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:16424655 original size:23 final size:23
Alignment explanation
Indices: 16424625--16424677 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
16424615 ATGTACATCT
16424625 TTATTTTGATCATTTTAGGAAGA
1 TTATTTTGATCATTTTAGGAAGA
16424648 TTATTTTGATCATTTTAGGAAGA
1 TTATTTTGATCATTTTAGGAAGA
16424671 TTATTTT
1 TTATTTT
16424678 AAGAGACGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.28, C:0.04, G:0.15, T:0.53
Consensus pattern (23 bp):
TTATTTTGATCATTTTAGGAAGA
Found at i:16439598 original size:27 final size:22
Alignment explanation
Indices: 16439545--16439590 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
16439535 ATGAGTTAAG
16439545 AAAGGAAATTAGGATTGGAACA
1 AAAGGAAATTAGGATTGGAACA
16439567 AAAGGAAATTAGGATTGGAACA
1 AAAGGAAATTAGGATTGGAACA
16439589 AA
1 AA
16439591 TCTCAAGGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.52, C:0.04, G:0.26, T:0.17
Consensus pattern (22 bp):
AAAGGAAATTAGGATTGGAACA
Found at i:16444472 original size:42 final size:42
Alignment explanation
Indices: 16444409--16444580 Score: 231
Period size: 42 Copynumber: 4.1 Consensus size: 42
16444399 GAAAGCATTT
*
16444409 ATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTTTTC
1 ATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTC
* *
16444451 ATTGCATTTAGAGGCCCAGGTGTGGAGGTTCATTTACCTTTC
1 ATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTC
* *
16444493 ATTGCATTTAGAGGCCCAGGGGTGGCA-GACCATTTACTTTTC
1 ATTGCATTTAGAGGCCCAGGTGTGG-AGGTCCATTTACTTTTC
* ** *
16444535 ATTGCATTTAGAGGCTCAGGAATGGAGGTTCATTTA-TTTATC
1 ATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTT-TC
16444577 ATTG
1 ATTG
16444581 TATATGAAAG
Statistics
Matches: 115, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
41 4 0.03
42 110 0.96
43 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.36
Consensus pattern (42 bp):
ATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTC
Found at i:16451094 original size:30 final size:30
Alignment explanation
Indices: 16451058--16451145 Score: 131
Period size: 30 Copynumber: 2.9 Consensus size: 30
16451048 CTGGGCACTT
*
16451058 CCACACGAGCTGGCCACACACCCATGTGAG
1 CCACACGAGCTGGCCACACGCCCATGTGAG
* * *
16451088 CCACACGAGATGGCCACATGCCCCTGTGAG
1 CCACACGAGCTGGCCACACGCCCATGTGAG
*
16451118 CCACACGGGCTGGCCACACGCCCATGTG
1 CCACACGAGCTGGCCACACGCCCATGTG
16451146 CCAGCCTGTG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.23, C:0.40, G:0.26, T:0.11
Consensus pattern (30 bp):
CCACACGAGCTGGCCACACGCCCATGTGAG
Found at i:16458573 original size:6 final size:5
Alignment explanation
Indices: 16458567--16458639 Score: 51
Period size: 6 Copynumber: 13.6 Consensus size: 5
16458557 ATTGAGTTTA
*
16458567 TTATT ATTATT ATTATT TTCGTT TTATTT TTATT TTATT TTATT TT-TAT
1 TTATT -TTATT -TTATT TT-ATT TTA-TT TTATT TTATT TTATT TTAT-T
*
16458616 TTATCT TT-TT TTAATT TTGTT TTA
1 TTAT-T TTATT TT-ATT TTATT TTA
16458640 GTTGCTTTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
4 4 0.07
5 24 0.43
6 28 0.50
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (5 bp):
TTATT
Done.