Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 51 of 103
Found at i:19152313 original size:20 final size:20
Alignment explanation
Indices: 19152288--19152328 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
19152278 ATAAGCCTTG
*
19152288 TTGATTTTTATGAAATGAAA
1 TTGATTTATATGAAATGAAA
19152308 TTGATTTATATGAAATGAAA
1 TTGATTTATATGAAATGAAA
19152328 T
1 T
19152329 GAGATTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (20 bp):
TTGATTTATATGAAATGAAA
Found at i:19155482 original size:121 final size:121
Alignment explanation
Indices: 19155236--19155483 Score: 270
Period size: 121 Copynumber: 2.0 Consensus size: 121
19155226 GTGCTTGAAT
* * * * *
19155236 TATTTTGGATCCAGATTGATTCAGGTTCATGTTGTGTTATTCTAAATCCGGGTTCTTGATTCGAG
1 TATTTTGGATCCAAATTGATTCAGGTTCATATTGTGTTATTCTAAATCCAGGTTCTCGATTCAAG
* * * ** * * *
19155301 TCTGGATTGTTAACTTTTAGTGACAAATCAACTTGGATAGAATTTTGTGTTTGGAT
66 TCTGGATTATTAACTTTAAGTGACAAATCAACTTGGATAGAATATTAAGCTTAGAC
* * **
19155357 TATTTTGGATCCAAATTGATTCATGTTCGA-ATTGTGTTGTTCTAAATGTTAGGTTCTCGATTCA
1 TATTTTGGATCCAAATTGATTCAGGTTC-ATATTGTGTTATTCTAAAT-CCAGGTTCTCGATTCA
*
19155421 AGTTTGTG-TTATTAACCTTTAAGTGACAAATCAACTTGGATA-AA-ATTAAGCTTAGAC
64 AGTCTG-GATTATTAA-CTTTAAGTGACAAATCAACTTGGATAGAATATTAAGCTTAGAC
19155478 TATTTT
1 TATTTT
19155484 CTCAAGTTCA
Statistics
Matches: 105, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
121 54 0.51
122 25 0.24
123 26 0.25
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.43
Consensus pattern (121 bp):
TATTTTGGATCCAAATTGATTCAGGTTCATATTGTGTTATTCTAAATCCAGGTTCTCGATTCAAG
TCTGGATTATTAACTTTAAGTGACAAATCAACTTGGATAGAATATTAAGCTTAGAC
Found at i:19163164 original size:2 final size:2
Alignment explanation
Indices: 19163157--19163188 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
19163147 TAGGGTTAAC
19163157 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19163189 TAATTGTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19176591 original size:26 final size:26
Alignment explanation
Indices: 19176528--19176593 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
19176518 AACTTTCGGC
* *
19176528 AATA-AATATGTTATTATTAAATTAT
1 AATATAATATGTTATCATTAAAATAT
*
19176553 AATTTAATATGTTATCATTAAAATATT
1 AATATAATATGTTATCATTAAAATA-T
*
19176580 AATATGAT-TGTTAT
1 AATATAATATGTTAT
19176594 TTTAATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 3 0.09
26 24 0.71
27 7 0.21
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (26 bp):
AATATAATATGTTATCATTAAAATAT
Found at i:19176621 original size:9 final size:8
Alignment explanation
Indices: 19176603--19176642 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
19176593 TTTTAATTTC
19176603 TTTTTCTT
1 TTTTTCTT
19176611 TTTTTCTT
1 TTTTTCTT
*
19176619 TTTTTCAT
1 TTTTTCTT
*
19176627 TTTTCCTT
1 TTTTTCTT
*
19176635 TTCTTCTT
1 TTTTTCTT
19176643 GTCTTTCCTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTCTT
Found at i:19188575 original size:13 final size:13
Alignment explanation
Indices: 19188557--19188581 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19188547 GAGATTTGTA
19188557 TTTACATTGGATG
1 TTTACATTGGATG
19188570 TTTACATTGGAT
1 TTTACATTGGAT
19188582 TATTGGTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (13 bp):
TTTACATTGGATG
Found at i:19199620 original size:11 final size:11
Alignment explanation
Indices: 19199606--19199637 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
19199596 AAATATCAGT
19199606 ATAAAATCAAC
1 ATAAAATCAAC
19199617 ATAAAATCAAC
1 ATAAAATCAAC
*
19199628 AAAAAATCAA
1 ATAAAATCAA
19199638 AGGAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.69, C:0.16, G:0.00, T:0.16
Consensus pattern (11 bp):
ATAAAATCAAC
Found at i:19199775 original size:23 final size:22
Alignment explanation
Indices: 19199725--19199806 Score: 96
Period size: 21 Copynumber: 3.8 Consensus size: 22
19199715 ACTAATAGAG
* * *
19199725 AAAATCAAGATAACATTA-CAA
1 AAAATCAACATAAAATCAGCAA
*
19199746 AATATCAACATAAAATCAGCGAA
1 AAAATCAACATAAAATCAGC-AA
19199769 AAAATCAACATAAAATCAGCAA
1 AAAATCAACATAAAATCAGCAA
*
19199791 AAAATCAA-AGAAAATC
1 AAAATCAACATAAAATC
19199807 GAGATGCTGA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
21 21 0.40
22 11 0.21
23 21 0.40
ACGTcount: A:0.62, C:0.16, G:0.06, T:0.16
Consensus pattern (22 bp):
AAAATCAACATAAAATCAGCAA
Found at i:19199794 original size:11 final size:11
Alignment explanation
Indices: 19199742--19199798 Score: 60
Period size: 11 Copynumber: 5.1 Consensus size: 11
19199732 AGATAACATT
*
19199742 ACAAAATATCA
1 ACAAAAAATCA
*
19199753 ACATAAAATCA
1 ACAAAAAATCA
*
19199764 GCGAAAAAATCA
1 AC-AAAAAATCA
*
19199776 ACATAAAATCA
1 ACAAAAAATCA
*
19199787 GCAAAAAATCA
1 ACAAAAAATCA
19199798 A
1 A
19199799 AGAAAATCGA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
11 27 0.75
12 9 0.25
ACGTcount: A:0.63, C:0.18, G:0.05, T:0.14
Consensus pattern (11 bp):
ACAAAAAATCA
Found at i:19199845 original size:26 final size:26
Alignment explanation
Indices: 19199816--19199893 Score: 129
Period size: 26 Copynumber: 3.0 Consensus size: 26
19199806 CGAGATGCTG
19199816 AGTCAAATAACCTTTAACAAATATCA
1 AGTCAAATAACCTTTAACAAATATCA
19199842 AGTCAAATAACCTTTAACAAATATCA
1 AGTCAAATAACCTTTAACAAATATCA
** *
19199868 AGTCAAATAACGGTTAAGAAATATCA
1 AGTCAAATAACCTTTAACAAATATCA
19199894 GGCAACAAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.50, C:0.17, G:0.08, T:0.26
Consensus pattern (26 bp):
AGTCAAATAACCTTTAACAAATATCA
Found at i:19200132 original size:146 final size:146
Alignment explanation
Indices: 19199868--19200306 Score: 646
Period size: 146 Copynumber: 3.0 Consensus size: 146
19199858 ACAAATATCA
*
19199868 AGTCAAATAACGGTTAAGAAATATCAGGCAACAAACTAACAGAAAAGCTTTAGAGGAGATGAGTG
1 AGTCAAATAACGGTTAAGAAATATCAGGCAACAAACTAACAAAAAAGCTTTAGAGGAGATGAGTG
* * * *
19199933 GGTGTTTTGAGATTGACGTAGATAGGTTGTATTTATAGGCTGGAGCAGAGAGTTAACATTACTGA
66 GGTGTCTTGAGATTGAGGTAGATAGGCTGTATTTATAGGCTGGAGCAGAGAGTTAACATTACTAA
19199998 ATATCAGCATAAAATC
131 ATATCAGCATAAAATC
* *
19200014 AGTCAAATAACGATTAAGAAATATCAGGCAACAAACTAACATAAAAGCTTTAGAGGAGATGAGTG
1 AGTCAAATAACGGTTAAGAAATATCAGGCAACAAACTAACAAAAAAGCTTTAGAGGAGATGAGTG
* * * *
19200079 GGTGTCTTGAGATTGAGGTAAATAGACTGTATTTATATGCTGGAGCATAGAGTTAACATTACTAA
66 GGTGTCTTGAGATTGAGGTAGATAGGCTGTATTTATAGGCTGGAGCAGAGAGTTAACATTACTAA
19200144 ATATCAGCATAAAATC
131 ATATCAGCATAAAATC
* * * * *
19200160 AGTCAAATAATGGTTAAGAAATGTCAGGCAACAGAC-ATACAAAAAAGCTTTATAAGAGATGAGT
1 AGTCAAATAACGGTTAAGAAATATCAGGCAACAAACTA-ACAAAAAAGCTTTAGAGGAGATGAGT
* * * * * * *
19200224 GGGTGTCTTGTGACTAAGGTCGGTAGGCTGTATTTATAGGCTAGAGCAGAGAGTTAACATTACTT
65 GGGTGTCTTGAGATTGAGGTAGATAGGCTGTATTTATAGGCTGGAGCAGAGAGTTAACATTACTA
*
19200289 AATATCAGCATAAGATC
130 AATATCAGCATAAAATC
19200306 A
1 A
19200307 ACATAAAATA
Statistics
Matches: 263, Mismatches: 29, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
145 1 0.00
146 262 1.00
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.26
Consensus pattern (146 bp):
AGTCAAATAACGGTTAAGAAATATCAGGCAACAAACTAACAAAAAAGCTTTAGAGGAGATGAGTG
GGTGTCTTGAGATTGAGGTAGATAGGCTGTATTTATAGGCTGGAGCAGAGAGTTAACATTACTAA
ATATCAGCATAAAATC
Found at i:19201510 original size:54 final size:53
Alignment explanation
Indices: 19201452--19201659 Score: 335
Period size: 54 Copynumber: 3.8 Consensus size: 53
19201442 TGGCATTAAC
* *
19201452 TGTGCATGATGTGGAGGGATGCACACGAGCTGGGTGAGATAGGGTGTCCGGCTA
1 TGTGCACGATGTGGGGGGATGCACACGAGCTGGGTGAGAT-GGGTGTCCGGCTA
19201506 TGTGCACGATGTGGGGGGATGCACACGAGCTGGGTGAGATGGGGTGTCCGGCTA
1 TGTGCACGATGTGGGGGGATGCACACGAGCTGGGTGAGAT-GGGTGTCCGGCTA
*
19201560 TGTGCACGATGTAGGGGGATGCACACGAGCTGGGTGAGATGGGATGTCCGGCTA
1 TGTGCACGATGTGGGGGGATGCACACGAGCTGGGTGAGATGGG-TGTCCGGCTA
* *
19201614 TGTGCACGATGTGGGGGGATGCACATGAGCTGGATGAGATGTGGTG
1 TGTGCACGATGTGGGGGGATGCACACGAGCTGGGTGAGATG-GGTG
19201660 GTATACTAAT
Statistics
Matches: 145, Mismatches: 7, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
53 3 0.02
54 140 0.97
55 2 0.01
ACGTcount: A:0.19, C:0.15, G:0.44, T:0.22
Consensus pattern (53 bp):
TGTGCACGATGTGGGGGGATGCACACGAGCTGGGTGAGATGGGTGTCCGGCTA
Found at i:19203714 original size:26 final size:26
Alignment explanation
Indices: 19203683--19203761 Score: 113
Period size: 26 Copynumber: 3.0 Consensus size: 26
19203673 TGGGTTAGGG
19203683 TATCCATCCACTTCTAGTGGTAAAAT
1 TATCCATCCACTTCTAGTGGTAAAAT
**
19203709 TATCCATATACTTCTAGTGGTAAAAT
1 TATCCATCCACTTCTAGTGGTAAAAT
* * *
19203735 TATCCATCCACTTTTGGTGGCAAAAT
1 TATCCATCCACTTCTAGTGGTAAAAT
19203761 T
1 T
19203762 TTTCATAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (26 bp):
TATCCATCCACTTCTAGTGGTAAAAT
Found at i:19205124 original size:15 final size:15
Alignment explanation
Indices: 19205106--19205136 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
19205096 ATATTTCTAA
19205106 TATTTCTATTTCATT
1 TATTTCTATTTCATT
*
19205121 TATTTCTTTTTCATT
1 TATTTCTATTTCATT
19205136 T
1 T
19205137 CGAATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTTCTATTTCATT
Found at i:19206860 original size:2 final size:2
Alignment explanation
Indices: 19206849--19206883 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
19206839 TTCTACATGA
*
19206849 AT AT -T AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19206884 GATTTCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:19213229 original size:20 final size:19
Alignment explanation
Indices: 19213201--19213238 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
19213191 ACAGTCTTCA
19213201 ATTACTCAATTTCTAAAATC
1 ATTACTCAATTTC-AAAATC
*
19213221 ATTATTCAATTTCAAAAT
1 ATTACTCAATTTCAAAAT
19213239 GATTTAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTACTCAATTTCAAAATC
Found at i:19218713 original size:21 final size:21
Alignment explanation
Indices: 19218675--19218714 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19218665 ATATATGTAC
**
19218675 CTTGTCTAAATTTGGACAACT
1 CTTGTCTAAATTAAGACAACT
*
19218696 CTTGTCTTAATTAAGACAA
1 CTTGTCTAAATTAAGACAA
19218715 TATCTAAAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (21 bp):
CTTGTCTAAATTAAGACAACT
Found at i:19221648 original size:20 final size:19
Alignment explanation
Indices: 19221618--19221655 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
19221608 TTTCTAAATC
19221618 ATTTTGAAATTGAATAATG
1 ATTTTGAAATTGAATAATG
*
19221637 ATTTTAGAAATTGAGTAAT
1 ATTTT-GAAATTGAATAAT
19221656 TGAAGACTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (19 bp):
ATTTTGAAATTGAATAATG
Found at i:19222949 original size:2 final size:2
Alignment explanation
Indices: 19222942--19222974 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
19222932 TCATGACATT
19222942 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19222975 GTAAATGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19227952 original size:41 final size:39
Alignment explanation
Indices: 19227862--19227958 Score: 106
Period size: 39 Copynumber: 2.5 Consensus size: 39
19227852 ATAGTGCTTG
* * **
19227862 TGTGCACGATGTGG-GGGGATGTACACAATGGCATTGAT
1 TGTGCATGATGTGGAGGGGATGCACACAATGGCACCGAT
* *
19227900 TGTGCATGATGTGGAGGGGATGCACACGATGGCGCCGACT
1 TGTGCATGATGTGGAGGGGATGCACACAATGGCACCGA-T
*
19227940 ATGTGCATGATGTGAAGGG
1 -TGTGCATGATGTGGAGGG
19227959 ATGTACATGA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
38 13 0.27
39 18 0.37
40 1 0.02
41 17 0.35
ACGTcount: A:0.23, C:0.14, G:0.39, T:0.24
Consensus pattern (39 bp):
TGTGCATGATGTGGAGGGGATGCACACAATGGCACCGAT
Found at i:19236591 original size:19 final size:19
Alignment explanation
Indices: 19236567--19236605 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
19236557 ACAAGTGAAA
19236567 AATTTTAAAATAAAATAAT
1 AATTTTAAAATAAAATAAT
***
19236586 AATTTTTGGATAAAATAAT
1 AATTTTAAAATAAAATAAT
19236605 A
1 A
19236606 TTAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
AATTTTAAAATAAAATAAT
Found at i:19237730 original size:18 final size:17
Alignment explanation
Indices: 19237707--19237740 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
19237697 AGCTTCCACC
19237707 TGAGAGGAGAGGAAAGAT
1 TGAGAGGA-AGGAAAGAT
19237725 TGAGAGGAAGGAAAGA
1 TGAGAGGAAGGAAAGA
19237741 AAGAGAAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.44, T:0.09
Consensus pattern (17 bp):
TGAGAGGAAGGAAAGAT
Found at i:19237746 original size:17 final size:18
Alignment explanation
Indices: 19237708--19237746 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
19237698 GCTTCCACCT
**
19237708 GAGAGGAGAGGAAAGATT
1 GAGAGGAGAGGAAAGAAA
19237726 GAGAGGA-AGGAAAGAAA
1 GAGAGGAGAGGAAAGAAA
19237743 GAGA
1 GAGA
19237747 AACGACTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.51, C:0.00, G:0.44, T:0.05
Consensus pattern (18 bp):
GAGAGGAGAGGAAAGAAA
Found at i:19238826 original size:108 final size:108
Alignment explanation
Indices: 19238594--19238804 Score: 344
Period size: 108 Copynumber: 2.0 Consensus size: 108
19238584 TTGGAAAATT
19238594 GTTTG-TGTAGACTATATATATATATATATATACGTACATATATAGTAAAGTAGTTTAGAAACCG
1 GTTTGTTGTAGACTATATATATATATATATATACGTACATATATAGTAAAGTAGTTTAGAAACCG
*
19238658 AAAATAAGTCCTTTTATACTTGTTTTGCATACAAAATCTGTNA
66 AAAATAAGTCCTTTTATACTTGTTTTGCATACAAAATCTGTTA
19238701 GTTTGTTGTAGACTATATATATATATATATATACGTACATATAT-GTAAAG-AGTTTTAGAAACC
1 GTTTGTTGTAGACTATATATATATATATATATACGTACATATATAGTAAAGTAG-TTTAGAAACC
19238764 GAAAAATAAG-CCTTTTATAC-TGTTTTGCAT-CAAAAATCTGT
65 G-AAAATAAGTCCTTTTATACTTGTTTTGCATAC-AAAATCTGT
19238805 GCCTTGTATT
Statistics
Matches: 100, Mismatches: 0, Indels: 9
0.92 0.00 0.08
Matches are distributed among these distances:
105 1 0.01
106 21 0.21
107 32 0.32
108 46 0.46
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.38
Consensus pattern (108 bp):
GTTTGTTGTAGACTATATATATATATATATATACGTACATATATAGTAAAGTAGTTTAGAAACCG
AAAATAAGTCCTTTTATACTTGTTTTGCATACAAAATCTGTTA
Found at i:19245221 original size:15 final size:14
Alignment explanation
Indices: 19245191--19245225 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
19245181 ATTTTTTCAT
*
19245191 TTTCTTTTCCTTCC
1 TTTCTTCTCCTTCC
19245205 TTTCTTCTCCTTTCC
1 TTTCTTCTCC-TTCC
19245220 TTTCTT
1 TTTCTT
19245226 TTCTTACTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTCTTCTCCTTCC
Found at i:19245223 original size:24 final size:25
Alignment explanation
Indices: 19245191--19245241 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 25
19245181 ATTTTTTCAT
* *
19245191 TTTCTTTTCCTTCCTTTCTTC-TCC
1 TTTCCTTTCCTTCCTTACTTCTTCC
* *
19245215 TTTCCTTTCTTTTCTTACTTCTTCC
1 TTTCCTTTCCTTCCTTACTTCTTCC
19245240 TT
1 TT
19245242 CTCTTATCTC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTCCTTTCCTTCCTTACTTCTTCC
Found at i:19247309 original size:19 final size:19
Alignment explanation
Indices: 19247285--19247387 Score: 82
Period size: 19 Copynumber: 5.3 Consensus size: 19
19247275 ACCCGGCTGA
19247285 TGCACATCCCCCCACATCG
1 TGCACATCCCCCCACATCG
**
19247304 TGCACATACCCGACACCATCG
1 TGCACAT-CCCCCCA-CATCG
** *
19247325 TGTGCATCCCCCCACATTG
1 TGCACATCCCCCCACATCG
****
19247344 TGCACAATCAGTGC-CATCG
1 TGCAC-ATCCCCCCACATCG
*
19247363 TGTACATCCCCCCACATCG
1 TGCACATCCCCCCACATCG
19247382 TGCACA
1 TGCACA
19247388 CGGGCACTAT
Statistics
Matches: 60, Mismatches: 20, Indels: 8
0.68 0.23 0.09
Matches are distributed among these distances:
18 4 0.07
19 32 0.53
20 14 0.23
21 10 0.17
ACGTcount: A:0.23, C:0.43, G:0.15, T:0.19
Consensus pattern (19 bp):
TGCACATCCCCCCACATCG
Found at i:19247333 original size:40 final size:38
Alignment explanation
Indices: 19247288--19247387 Score: 128
Period size: 38 Copynumber: 2.6 Consensus size: 38
19247278 CGGCTGATGC
*
19247288 ACATCCCCCCACATCGTGCACATACCCGACACCATCGTGT
1 ACATCCCCCCACATCGTGCACA-ACCAG-CACCATCGTGT
* * * **
19247328 GCATCCCCCCACATTGTGCACAATCAGTGCCATCGTGT
1 ACATCCCCCCACATCGTGCACAACCAGCACCATCGTGT
19247366 ACATCCCCCCACATCGTGCACA
1 ACATCCCCCCACATCGTGCACA
19247388 CGGGCACTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
38 29 0.56
39 3 0.06
40 20 0.38
ACGTcount: A:0.24, C:0.43, G:0.14, T:0.19
Consensus pattern (38 bp):
ACATCCCCCCACATCGTGCACAACCAGCACCATCGTGT
Found at i:19249474 original size:35 final size:36
Alignment explanation
Indices: 19249435--19249511 Score: 93
Period size: 36 Copynumber: 2.2 Consensus size: 36
19249425 GCACACGATG
** * *
19249435 ATGATGATGTTTACCATGT-GGGTATGGGAGTGCAC
1 ATGATGACATTTACCATGTGGGGTATGGGACTACAC
* *
19249470 ATGATGACATTTGCCATGTGGGGTGTGGGACTACAC
1 ATGATGACATTTACCATGTGGGGTATGGGACTACAC
19249506 ATGATG
1 ATGATG
19249512 GTATTAGCTA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
35 16 0.46
36 19 0.54
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (36 bp):
ATGATGACATTTACCATGTGGGGTATGGGACTACAC
Found at i:19249525 original size:36 final size:36
Alignment explanation
Indices: 19249448--19249535 Score: 88
Period size: 36 Copynumber: 2.5 Consensus size: 36
19249438 ATGATGTTTA
* * * *
19249448 CCATGT-GGGTATGGGAGTGCACATGATGACATTTG
1 CCATGTGGGGTGTGGGACTACACATGATGACATTAG
**
19249483 CCATGTGGGGTGTGGGACTACACATGATGGTATTAG
1 CCATGTGGGGTGTGGGACTACACATGATGACATTAG
* **
19249519 CTATGTGCAGTGTGGGA
1 CCATGTGGGGTGTGGGA
19249536 GAGCACATGA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
35 6 0.14
36 37 0.86
ACGTcount: A:0.22, C:0.14, G:0.36, T:0.28
Consensus pattern (36 bp):
CCATGTGGGGTGTGGGACTACACATGATGACATTAG
Found at i:19249543 original size:36 final size:36
Alignment explanation
Indices: 19249459--19249545 Score: 86
Period size: 36 Copynumber: 2.4 Consensus size: 36
19249449 CATGTGGGTA
* * **
19249459 TGGGAGTGCACATGATGACATTTGCCATGTGGGGTG
1 TGGGAGAGCACATGATGACATTAGCCATGTGCAGTG
* ** *
19249495 TGGGACTA-CACATGATGGTATTAGCTATGTGCAGTG
1 TGGGA-GAGCACATGATGACATTAGCCATGTGCAGTG
19249531 TGGGAGAGCACATGA
1 TGGGAGAGCACATGA
19249546 GCTGAGTTGA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
35 1 0.03
36 39 0.98
ACGTcount: A:0.24, C:0.14, G:0.36, T:0.26
Consensus pattern (36 bp):
TGGGAGAGCACATGATGACATTAGCCATGTGCAGTG
Found at i:19250647 original size:2 final size:2
Alignment explanation
Indices: 19250640--19250667 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19250630 ATCGAGGTAC
19250640 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19250668 CTGGATTCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19252492 original size:2 final size:2
Alignment explanation
Indices: 19252485--19252518 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
19252475 TTGAAATGTC
19252485 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19252519 GTACATAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19262589 original size:25 final size:25
Alignment explanation
Indices: 19262561--19262620 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
19262551 GTGGTCGCAA
* *
19262561 CCACGTATATCAACTCGTGGCCTTG
1 CCACGTATAACAACCCGTGGCCTTG
19262586 CCACGTATAACAACCCGTGGCCTTG
1 CCACGTATAACAACCCGTGGCCTTG
19262611 CCACGTATAA
1 CCACGTATAA
19262621 TCACAGACCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.23
Consensus pattern (25 bp):
CCACGTATAACAACCCGTGGCCTTG
Found at i:19278853 original size:37 final size:37
Alignment explanation
Indices: 19278810--19278884 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
19278800 TGTTACAAAA
19278810 TGCACTAACTCACTTGTCTTGATAGTTGTTCTTAAAT
1 TGCACTAACTCACTTGTCTTGATAGTTGTTCTTAAAT
19278847 TGCACTAACTCACTTGTCTTGATAGTTGTTCTTAAAT
1 TGCACTAACTCACTTGTCTTGATAGTTGTTCTTAAAT
19278884 T
1 T
19278885 ACTACTCCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (37 bp):
TGCACTAACTCACTTGTCTTGATAGTTGTTCTTAAAT
Found at i:19284892 original size:20 final size:20
Alignment explanation
Indices: 19284833--19284892 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
19284823 AAAAATCGGT
*
19284833 GAAATGTATCAATACAATTG
1 GAAATGTATCAATACATTTG
19284853 GAAATGTATCAATACATTTG
1 GAAATGTATCAATACATTTG
* * *
19284873 GTAATGTATCGATACTTTTG
1 GAAATGTATCAATACATTTG
19284893 TTTCTAGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (20 bp):
GAAATGTATCAATACATTTG
Found at i:19285180 original size:15 final size:17
Alignment explanation
Indices: 19285156--19285192 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
19285146 GGATTCAATA
19285156 AAAATATCAAAA-AAT-
1 AAAATATCAAAAGAATC
*
19285171 AAAATTTCAAAAGAATC
1 AAAATATCAAAAGAATC
19285188 AAAAT
1 AAAAT
19285193 CTAAATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 11 0.58
16 3 0.16
17 5 0.26
ACGTcount: A:0.68, C:0.08, G:0.03, T:0.22
Consensus pattern (17 bp):
AAAATATCAAAAGAATC
Found at i:19287278 original size:18 final size:18
Alignment explanation
Indices: 19287257--19287295 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
19287247 CTAATATATA
19287257 TATATATATATATGTATG
1 TATATATATATATGTATG
* *
19287275 TATATGTATGTATGTATG
1 TATATATATATATGTATG
19287293 TAT
1 TAT
19287296 TGTATATAGT
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:0.33, C:0.00, G:0.15, T:0.51
Consensus pattern (18 bp):
TATATATATATATGTATG
Found at i:19287284 original size:14 final size:14
Alignment explanation
Indices: 19287250--19287300 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
19287240 ATATTTGCTA
* *
19287250 ATATATATATATAT
1 ATATATGTATGTAT
19287264 ATATATGTATGTAT
1 ATATATGTATGTAT
*
19287278 ATGTATGTATGTAT
1 ATATATGTATGTAT
*
19287292 GTAT-TGTAT
1 ATATATGTAT
19287301 ATAGTGACTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
13 5 0.16
14 27 0.84
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (14 bp):
ATATATGTATGTAT
Found at i:19294422 original size:39 final size:36
Alignment explanation
Indices: 19294374--19294483 Score: 91
Period size: 34 Copynumber: 3.0 Consensus size: 36
19294364 CACACAGTAC
*
19294374 ACCACTATCACCGTCATGTGCACTTCCACATCGCACA
1 ACCAATATCACCGTCATGTGCACTTCCACA-CGCACA
* * * **
19294411 AGGCATATATCATCATTGTGTGCAC-T-CACACAGCAC-
1 A-CCA-ATATCACCGTCATGTGCACTTCCACAC-GCACA
*
19294447 ACCACTATCACCGTCATGTGCACTTCCACACCGCACA
1 ACCAATATCACCGTCATGTGCACTTCCACA-CGCACA
19294484 TGCACGGTCA
Statistics
Matches: 54, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
34 14 0.26
35 3 0.06
36 10 0.19
37 10 0.19
38 3 0.06
39 14 0.26
ACGTcount: A:0.28, C:0.37, G:0.13, T:0.22
Consensus pattern (36 bp):
ACCAATATCACCGTCATGTGCACTTCCACACGCACA
Found at i:19294439 original size:73 final size:73
Alignment explanation
Indices: 19294346--19294483 Score: 249
Period size: 73 Copynumber: 1.9 Consensus size: 73
19294336 AGGCAATGTC
* *
19294346 ATCATCAATGTGTGCACTCACACAGTACACCACTATCACCGTCATGTGCACTTCCACATCGCACA
1 ATCATCAATGTGTGCACTCACACAGCACACCACTATCACCGTCATGTGCACTTCCACACCGCACA
19294411 AGGCATAT
66 AGGCATAT
*
19294419 ATCATCATTGTGTGCACTCACACAGCACACCACTATCACCGTCATGTGCACTTCCACACCGCACA
1 ATCATCAATGTGTGCACTCACACAGCACACCACTATCACCGTCATGTGCACTTCCACACCGCACA
19294484 TGCACGGTCA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 62 1.00
ACGTcount: A:0.29, C:0.36, G:0.13, T:0.22
Consensus pattern (73 bp):
ATCATCAATGTGTGCACTCACACAGCACACCACTATCACCGTCATGTGCACTTCCACACCGCACA
AGGCATAT
Found at i:19294483 original size:36 final size:34
Alignment explanation
Indices: 19294356--19294470 Score: 106
Period size: 34 Copynumber: 3.2 Consensus size: 34
19294346 ATCATCAATG
*
19294356 TGTGCACTCACACAGTACACCACTATCACCGTCA
1 TGTGCACTCACACAGCACACCACTATCACCGTCA
* * * * **
19294390 TGTGCACTTC-CACATCGCACAAGGCATATATCATCATTG
1 TGTGCAC-TCACACA--GCAC-A-CCA-CTATCACCGTCA
19294429 TGTGCACTCACACAGCACACCACTATCACCGTCA
1 TGTGCACTCACACAGCACACCACTATCACCGTCA
19294463 TGTGCACT
1 TGTGCACT
19294471 TCCACACCGC
Statistics
Matches: 61, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
34 26 0.43
35 4 0.07
36 4 0.07
37 5 0.08
38 4 0.07
39 18 0.30
ACGTcount: A:0.28, C:0.35, G:0.14, T:0.23
Consensus pattern (34 bp):
TGTGCACTCACACAGCACACCACTATCACCGTCA
Found at i:19295115 original size:20 final size:20
Alignment explanation
Indices: 19295090--19295128 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
19295080 TAGGAGAAGG
19295090 AAGGAATAAGAAAA-GAAAAC
1 AAGGAA-AAGAAAATGAAAAC
19295110 AAGGAAAAGAAAATGAAAA
1 AAGGAAAAGAAAATGAAAA
19295129 TCTTGATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.72, C:0.03, G:0.21, T:0.05
Consensus pattern (20 bp):
AAGGAAAAGAAAATGAAAAC
Found at i:19310920 original size:10 final size:11
Alignment explanation
Indices: 19310893--19310927 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
19310883 TGTGGCTGGC
*
19310893 CAAAGCAAGAA
1 CAAAGGAAGAA
19310904 CAAAGGAAGAA
1 CAAAGGAAGAA
19310915 -AAAGGAAGAA
1 CAAAGGAAGAA
19310925 CAA
1 CAA
19310928 GAACCCTAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.66, C:0.11, G:0.23, T:0.00
Consensus pattern (11 bp):
CAAAGGAAGAA
Found at i:19313564 original size:63 final size:62
Alignment explanation
Indices: 19313406--19313573 Score: 234
Period size: 63 Copynumber: 2.7 Consensus size: 62
19313396 TTGATGTAAC
*
19313406 CGTGCATGTGCGGAGTGGGCAGTGCATATGCCAGTTGAATGATGATGTTGTGACAACTACAAT
1 CGTGCATGTGCGGAGTGGGCAGTGCATATGCC-GGTGAATGATGATGTTGTGACAACTACAAT
* * *
19313469 CGTGCATATGCGGAGTGAGTAGTGCATATGCCGGTCGAATGATGATGTTGTGAC-ACTTACAA-
1 CGTGCATGTGCGGAGTGGGCAGTGCATATGCCGGT-GAATGATGATGTTGTGACAAC-TACAAT
*
19313531 CTGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGT-AATGATG
1 C-GTGCATGTGCGGAGTGGGCAGTGCATATGCCGGTGAATGATG
19313574 TGCGTGTGGG
Statistics
Matches: 94, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
61 7 0.07
62 5 0.05
63 82 0.87
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (62 bp):
CGTGCATGTGCGGAGTGGGCAGTGCATATGCCGGTGAATGATGATGTTGTGACAACTACAAT
Found at i:19320475 original size:2 final size:2
Alignment explanation
Indices: 19320468--19320493 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19320458 ATTGCTTAAG
19320468 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
19320494 CTTAACAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19321527 original size:40 final size:40
Alignment explanation
Indices: 19321469--19321574 Score: 135
Period size: 38 Copynumber: 2.7 Consensus size: 40
19321459 CACACCCAAC
*
19321469 TCATGTGCATCCCCCCACATCGTTCACATAGCCAGAGTCA
1 TCATGTGCATCCCCCCACATCGTTCACATAGCCAGAGCCA
* * * *
19321509 TCGTGTGCATCCCCCCACATC-AT-GCATAGCCAGTGCCA
1 TCATGTGCATCCCCCCACATCGTTCACATAGCCAGAGCCA
* *
19321547 TCATGTACATCCCCCCACATCGTGCACA
1 TCATGTGCATCCCCCCACATCGTTCACA
19321575 CGGGGCACTA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
38 31 0.57
39 1 0.02
40 22 0.41
ACGTcount: A:0.24, C:0.40, G:0.15, T:0.22
Consensus pattern (40 bp):
TCATGTGCATCCCCCCACATCGTTCACATAGCCAGAGCCA
Found at i:19330913 original size:18 final size:19
Alignment explanation
Indices: 19330887--19330922 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
19330877 TTTTTATTAA
*
19330887 TAATCAATTAA-ATAAAAC
1 TAATAAATTAACATAAAAC
19330905 TAATAAATTAACATAAAA
1 TAATAAATTAACATAAAA
19330923 TTAGATGAAA
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (19 bp):
TAATAAATTAACATAAAAC
Found at i:19331074 original size:32 final size:30
Alignment explanation
Indices: 19331038--19331106 Score: 70
Period size: 30 Copynumber: 2.2 Consensus size: 30
19331028 TGGTCTTTAA
*
19331038 AATTT-AACATAAATATTATTTTTTGTCCTTAC
1 AATTTCAA-ATAAA-ATT-TTTTTTATCCTTAC
*
19331070 AATTTCAAATATAATTTTTTTTATCCTTA-
1 AATTTCAAATAAAATTTTTTTTATCCTTAC
19331099 AACTTTCA
1 AA-TTTCA
19331107 GTTTGTATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 2 0.06
30 17 0.52
31 3 0.09
32 9 0.27
33 2 0.06
ACGTcount: A:0.35, C:0.13, G:0.01, T:0.51
Consensus pattern (30 bp):
AATTTCAAATAAAATTTTTTTTATCCTTAC
Found at i:19337390 original size:15 final size:15
Alignment explanation
Indices: 19337370--19337398 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
19337360 AGAAGAGAAA
19337370 GATGGATCACCATAG
1 GATGGATCACCATAG
19337385 GATGGATCACCATA
1 GATGGATCACCATA
19337399 AGCATTACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (15 bp):
GATGGATCACCATAG
Found at i:19342215 original size:2 final size:2
Alignment explanation
Indices: 19342208--19342246 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
19342198 TATTAAACAT
19342208 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19342247 TTATGTCTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19342605 original size:2 final size:2
Alignment explanation
Indices: 19342598--19342625 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19342588 TAGAGAAATA
19342598 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19342626 TTTATTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19343784 original size:22 final size:24
Alignment explanation
Indices: 19343759--19343808 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
19343749 GGACATTAAT
*
19343759 AAAATA-GAAAAAGCATAAAATA-
1 AAAATAGGAAAAAGAATAAAATAG
*
19343781 AAAA-AGGAAAAATAATAAAATAG
1 AAAATAGGAAAAAGAATAAAATAG
19343804 AAAAT
1 AAAAT
19343809 GATAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 1 0.04
22 18 0.78
23 4 0.17
ACGTcount: A:0.74, C:0.02, G:0.10, T:0.14
Consensus pattern (24 bp):
AAAATAGGAAAAAGAATAAAATAG
Found at i:19343792 original size:14 final size:15
Alignment explanation
Indices: 19343757--19343800 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
19343747 AAGGACATTA
19343757 ATAAAATAGAAAAAGC
1 ATAAAATA-AAAAAGC
*
19343773 ATAAAATAAAAAAGG
1 ATAAAATAAAAAAGC
19343788 A-AAAATAATAAAA
1 ATAAAATAA-AAAA
19343801 TAGAAAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 7 0.27
15 11 0.42
16 8 0.31
ACGTcount: A:0.75, C:0.02, G:0.09, T:0.14
Consensus pattern (15 bp):
ATAAAATAAAAAAGC
Found at i:19343817 original size:21 final size:20
Alignment explanation
Indices: 19343755--19343819 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 20
19343745 AAAAGGACAT
19343755 TAATAAAATAGAAAAAGCATAA
1 TAATAAAATAG-AAAAG-ATAA
* *
19343777 -AATAAAAAAG-GAA-A-AA
1 TAATAAAATAGAAAAGATAA
19343793 TAATAAAATAGAAAATGATAA
1 TAATAAAATAGAAAA-GATAA
19343814 TAATAA
1 TAATAA
19343820 TAATGAACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 11
0.69 0.08 0.22
Matches are distributed among these distances:
16 2 0.06
17 10 0.29
18 2 0.06
19 2 0.06
20 1 0.03
21 17 0.50
ACGTcount: A:0.71, C:0.02, G:0.09, T:0.18
Consensus pattern (20 bp):
TAATAAAATAGAAAAGATAA
Found at i:19343819 original size:38 final size:38
Alignment explanation
Indices: 19343739--19343819 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 38
19343729 TTTAAAATAT
* *
19343739 TAATAAAAAAGGACATTAATAAAATAGAAAAAGCATAA
1 TAATAAAAAAGGAAAATAATAAAATAGAAAAAGCATAA
*
19343777 -AATAAAAAAGGAAAAATAATAAAATAGAAAATG-ATAA
1 TAATAAAAAAGG-AAAATAATAAAATAGAAAAAGCATAA
19343814 TAATAA
1 TAATAA
19343820 TAATGAACAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 15 0.39
38 23 0.61
ACGTcount: A:0.69, C:0.02, G:0.10, T:0.19
Consensus pattern (38 bp):
TAATAAAAAAGGAAAATAATAAAATAGAAAAAGCATAA
Found at i:19351136 original size:12 final size:12
Alignment explanation
Indices: 19351119--19351152 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
19351109 AAGACAAGGG
19351119 AGAAAGAGAAAA
1 AGAAAGAGAAAA
19351131 AGAAAGA-AAAA
1 AGAAAGAGAAAA
19351142 AGGAAAGAGAA
1 A-GAAAGAGAA
19351153 GGAAGAGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 5 0.25
12 13 0.65
13 2 0.10
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAGAGAAAA
Found at i:19351242 original size:54 final size:57
Alignment explanation
Indices: 19351182--19351323 Score: 164
Period size: 54 Copynumber: 2.5 Consensus size: 57
19351172 GAGGGATAGA
19351182 GAAAGAGAAAGAGAAGAAAAAAAAGAGAGAGCGAGCACGAC-A-G-AGCAGAAAAAG
1 GAAAGAGAAAGAGAAGAAAAAAAAGAGAGAGCGAGCACGACGATGAAGCAGAAAAAG
* * * * * *
19351236 GAAAGAGAAAGAGAAGAAAAAAAGGGGAGAGGGAGCATGGCGATGAAGTAGAAAAAG
1 GAAAGAGAAAGAGAAGAAAAAAAAGAGAGAGCGAGCACGACGATGAAGCAGAAAAAG
* *
19351293 GGAAGAAAGAAGAGAAAGAAAAAGAAAGAGA
1 GAAAGAGA-AAGAG-AAGAAAAA-AAAGAGA
19351324 AGGAAAGAGG
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
54 36 0.50
55 1 0.01
56 1 0.01
57 16 0.22
58 5 0.07
59 8 0.11
60 5 0.07
ACGTcount: A:0.58, C:0.05, G:0.35, T:0.02
Consensus pattern (57 bp):
GAAAGAGAAAGAGAAGAAAAAAAAGAGAGAGCGAGCACGACGATGAAGCAGAAAAAG
Found at i:19351389 original size:8 final size:9
Alignment explanation
Indices: 19351353--19351394 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
19351343 GATGAGGGAA
19351353 AAGAAAAAG
1 AAGAAAAAG
*
19351362 AGGGAAGAAAG
1 A-AGAA-AAAG
19351373 AAGAAAAAG
1 AAGAAAAAG
19351382 AA-AAAAAG
1 AAGAAAAAG
19351390 AAGAA
1 AAGAA
19351395 GAAAAAGCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
8 8 0.29
9 9 0.32
10 6 0.21
11 5 0.18
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:19352028 original size:60 final size:60
Alignment explanation
Indices: 19351933--19352234 Score: 419
Period size: 60 Copynumber: 5.0 Consensus size: 60
19351923 TTTGATTGTA
*
19351933 AAAAGGAGGACCTT-AAGCCCCGATTTATATATGGTGACGTGGGCAGATCCCACGAGTAGGC
1 AAAAGG-GGA-CTTGAAGCCCCGATTTATATATGGTGGCGTGGGCAGATCCCACGAGTAGGC
* * * *
19351994 AAAAGGAGACTTGAAGCCCCGATTTATATTTGGTGGCATGGGCAGATCCCTCGAGTAGGC
1 AAAAGGGGACTTGAAGCCCCGATTTATATATGGTGGCGTGGGCAGATCCCACGAGTAGGC
* * *
19352054 AAAAAGGGGGACTTGAAGGCCCGATTTATATATCGTGGCGTGGGCAGATCCCACAAGTCA-GC
1 -AAAA-GGGGACTTGAAGCCCCGATTTATATATGGTGGCGTGGGCAGATCCCACGAGT-AGGC
* * *
19352116 AAAAGGGGACCTGAAGCCTCGATTTATATATGGTGACGTGGGCAGATCCCACGAGTAGGC
1 AAAAGGGGACTTGAAGCCCCGATTTATATATGGTGGCGTGGGCAGATCCCACGAGTAGGC
* * *
19352176 AAAGGGGGACCTGAAGCCCCGATTTATATATGGTGGCGTGGACAGATCCCACGAGTAGG
1 AAAAGGGGACTTGAAGCCCCGATTTATATATGGTGGCGTGGGCAGATCCCACGAGTAGG
19352235 TGATGATGCC
Statistics
Matches: 214, Mismatches: 22, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
59 4 0.02
60 148 0.69
61 14 0.07
62 47 0.22
63 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.31, T:0.20
Consensus pattern (60 bp):
AAAAGGGGACTTGAAGCCCCGATTTATATATGGTGGCGTGGGCAGATCCCACGAGTAGGC
Found at i:19352150 original size:122 final size:122
Alignment explanation
Indices: 19351932--19352234 Score: 425
Period size: 122 Copynumber: 2.5 Consensus size: 122
19351922 ATTTGATTGT
* * *
19351932 AAAAAGGAGGACCTT-AAGCCCCGATTTATATATGGTGACGTGGGCAGATCCCACGAGTAGGCAA
1 AAAAAGGGGGA-CTTGAAGCCCCGATTTATATATGGTGGCGTGGGCAGATCCCACAAGTAGGCAA
* * * *
19351996 AAGGAGACTTGAAGCCCCGATTTATATTTGGTGGCATGGGCAGATCCCTCGAGTAGGC
65 AAGGAGACCTGAAGCCCCGATTTATATATGGTGACATGGGCAGATCCCACGAGTAGGC
* *
19352054 AAAAAGGGGGACTTGAAGGCCCGATTTATATATCGTGGCGTGGGCAGATCCCACAAGTCA-GCAA
1 AAAAAGGGGGACTTGAAGCCCCGATTTATATATGGTGGCGTGGGCAGATCCCACAAGT-AGGCAA
* * *
19352118 AAGGGGACCTGAAGCCTCGATTTATATATGGTGACGTGGGCAGATCCCACGAGTAGGC
65 AAGGAGACCTGAAGCCCCGATTTATATATGGTGACATGGGCAGATCCCACGAGTAGGC
* * *
19352176 --AAAGGGGGACCTGAAGCCCCGATTTATATATGGTGGCGTGGACAGATCCCACGAGTAGG
1 AAAAAGGGGGACTTGAAGCCCCGATTTATATATGGTGGCGTGGGCAGATCCCACAAGTAGG
19352235 TGATGATGCC
Statistics
Matches: 161, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
119 1 0.01
120 52 0.32
121 3 0.02
122 104 0.65
123 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.31, T:0.20
Consensus pattern (122 bp):
AAAAAGGGGGACTTGAAGCCCCGATTTATATATGGTGGCGTGGGCAGATCCCACAAGTAGGCAAA
AGGAGACCTGAAGCCCCGATTTATATATGGTGACATGGGCAGATCCCACGAGTAGGC
Found at i:19360200 original size:29 final size:28
Alignment explanation
Indices: 19360159--19360220 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 28
19360149 ATTTTCAATT
*
19360159 TTTGGGGTAAAAATGTAATTTTTGAAAAG
1 TTTGGGGTAAAAATGTAA-TTTTGAAAAA
19360188 TTTGGAGGTAAAAATGTAATTTTGAAAAA
1 TTTGG-GGTAAAAATGTAATTTTGAAAAA
19360217 TTTG
1 TTTG
19360221 CTCCACCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 18 0.58
30 13 0.42
ACGTcount: A:0.39, C:0.00, G:0.23, T:0.39
Consensus pattern (28 bp):
TTTGGGGTAAAAATGTAATTTTGAAAAA
Found at i:19361323 original size:9 final size:10
Alignment explanation
Indices: 19361302--19361330 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
19361292 CTAAGGTAGT
19361302 TTTTATGAAA
1 TTTTATGAAA
19361312 TTTTAT-AAA
1 TTTTATGAAA
19361321 TTTTATGAAA
1 TTTTATGAAA
19361331 AATGGATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (10 bp):
TTTTATGAAA
Found at i:19366619 original size:24 final size:23
Alignment explanation
Indices: 19366575--19366624 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
19366565 TCCTTCAATG
* * *
19366575 GGGAGCTTGGTACTCCCTCGATA
1 GGGAGCTTGGCACTCCATCGAGA
*
19366598 GGGAGCTTTGGCACTCTATCGAGA
1 GGGAGC-TTGGCACTCCATCGAGA
19366622 GGG
1 GGG
19366625 GAGTTCGATG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.18, C:0.22, G:0.36, T:0.24
Consensus pattern (23 bp):
GGGAGCTTGGCACTCCATCGAGA
Found at i:19368312 original size:35 final size:35
Alignment explanation
Indices: 19368246--19368318 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
19368236 CTTGCTCAGC
*
19368246 TCATGTGCACTCCCTACACGCCTAAGACAATATCA
1 TCATGTGCACTCCCTACACGCATAAGACAATATCA
* ***
19368281 TCATGTGCACTCCTTACACGCATATTTCAATATCA
1 TCATGTGCACTCCCTACACGCATAAGACAATATCA
19368316 TCA
1 TCA
19368319 CACGCACTCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.30, C:0.32, G:0.10, T:0.29
Consensus pattern (35 bp):
TCATGTGCACTCCCTACACGCATAAGACAATATCA
Found at i:19369071 original size:19 final size:19
Alignment explanation
Indices: 19369047--19369088 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
19369037 GGTGGTAAAG
19369047 TGAAAATAGCATGGGAGCA
1 TGAAAATAGCATGGGAGCA
*
19369066 TGAAAATGGCATGGGAGCA
1 TGAAAATAGCATGGGAGCA
19369085 TGAA
1 TGAA
19369089 GGAGAAGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.33, T:0.17
Consensus pattern (19 bp):
TGAAAATAGCATGGGAGCA
Found at i:19369496 original size:11 final size:11
Alignment explanation
Indices: 19369482--19369511 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
19369472 TTGAATAAAA
19369482 TATTAATATTT
1 TATTAATATTT
19369493 TATTAATATTT
1 TATTAATATTT
19369504 TATTAATA
1 TATTAATA
19369512 AAATATTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTAATATTT
Found at i:19369968 original size:18 final size:18
Alignment explanation
Indices: 19369907--19369969 Score: 51
Period size: 18 Copynumber: 3.5 Consensus size: 18
19369897 TTCTTTAGTG
* *
19369907 AATT-TTTACTCTTCATT
1 AATTATTTAGTCTTAATT
*
19369924 AATTAGTTTAGTTTTCTAATT
1 AATTA-TTTAG-TCT-TAATT
19369945 AA--ATTTAGTCTTAATT
1 AATTATTTAGTCTTAATT
19369961 AATTATTTA
1 AATTATTTA
19369970 TGAAATCGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
16 7 0.19
17 6 0.17
18 10 0.28
19 5 0.14
20 2 0.06
21 6 0.17
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.56
Consensus pattern (18 bp):
AATTATTTAGTCTTAATT
Found at i:19375811 original size:23 final size:23
Alignment explanation
Indices: 19375768--19375811 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
19375758 ATATTTTTAA
*
19375768 AATATAAATTTTGAATATATTGT
1 AATATAAATTTTAAATATATTGT
*
19375791 AATATTAATTTATAAAT-TATT
1 AATATAAATTT-TAAATATATT
19375812 CAATACTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (23 bp):
AATATAAATTTTAAATATATTGT
Found at i:19375846 original size:154 final size:154
Alignment explanation
Indices: 19375672--19375972 Score: 523
Period size: 154 Copynumber: 2.0 Consensus size: 154
19375662 CTAAATCATA
*
19375672 AAATTTGAAATATAAATAATTGAAATTTTGTAACGCTGCACATAAATAC-TTTTTTATTTATTTT
1 AAATTTGAAACATAAATAATTGAAATTTTGTAACGCTGCACATAAATACTTTTTTTATTT-TTTT
*
19375736 TAAATATTATATATAAGTAAAAATATTTTTAAAATATAAATTTTGAATATATTGTAATATTAATT
65 TAAATATTATATATAAGAAAAAATATTTTTAAAATATAAATTTTGAATATATTGTAATATTAATT
*
19375801 TATAAATTATTCAATACTTTTTATG
130 TATAAATTAATCAATACTTTTTATG
* *
19375826 AAATTTGAAACATATATAATTGAAATTTTTTAACGCTGCACATAAATACTTTTTTTATTTTTTTT
1 AAATTTGAAACATAAATAATTGAAATTTTGTAACGCTGCACATAAATACTTTTTTTATTTTTTTT
* *
19375891 AAATATTATATATAAGAAAAAATATTTTTAAAATATAAATTTTGCATATATTGTGATATTAATTT
66 AAATATTATATATAAGAAAAAATATTTTTAAAATATAAATTTTGAATATATTGTAATATTAATTT
19375956 ATAAATTAATCAATACT
131 ATAAATTAATCAATACT
19375973 ATTATAATTA
Statistics
Matches: 139, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
154 129 0.93
155 10 0.07
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (154 bp):
AAATTTGAAACATAAATAATTGAAATTTTGTAACGCTGCACATAAATACTTTTTTTATTTTTTTT
AAATATTATATATAAGAAAAAATATTTTTAAAATATAAATTTTGAATATATTGTAATATTAATTT
ATAAATTAATCAATACTTTTTATG
Found at i:19377581 original size:12 final size:12
Alignment explanation
Indices: 19377564--19377588 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19377554 CTAATCAAAC
19377564 TAAATAAAATAT
1 TAAATAAAATAT
19377576 TAAATAAAATAT
1 TAAATAAAATAT
19377588 T
1 T
19377589 TCATTTACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAATAAAATAT
Found at i:19378380 original size:35 final size:35
Alignment explanation
Indices: 19378332--19378405 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
19378322 CCACCAAATC
19378332 AATA-AAAATTTTGACAACATGACATGACTAATAT
1 AATATAAAATTTTGACAACATGACATGACTAATAT
*
19378366 AATATAAAATTTTGACAACATGACATGGCTAATAT
1 AATATAAAATTTTGACAACATGACATGACTAATAT
19378401 AATAT
1 AATAT
19378406 CACCCAGCCT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 4 0.11
35 34 0.89
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.31
Consensus pattern (35 bp):
AATATAAAATTTTGACAACATGACATGACTAATAT
Found at i:19378514 original size:2 final size:2
Alignment explanation
Indices: 19378507--19378535 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19378497 AATTCAAACC
19378507 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 A
19378536 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19388877 original size:38 final size:40
Alignment explanation
Indices: 19388827--19388932 Score: 126
Period size: 38 Copynumber: 2.7 Consensus size: 40
19388817 ATAGTGCCCG
**
19388827 TGTGCACGATGTGGGGGGATGTACATGATGGCACTGA-T-
1 TGTGCACGATGTGGGGGGATGTACATGATGGCACCAACTA
* * * ** *
19388865 TTTGCAAGATGTGGGGGGATGCACACAATGGCGCCAACTA
1 TGTGCACGATGTGGGGGGATGTACATGATGGCACCAACTA
19388905 TGTGCACGATGTGGGGGGATGTACATGA
1 TGTGCACGATGTGGGGGGATGTACATGA
19388933 GCCAGGTGTG
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
38 29 0.55
39 1 0.02
40 23 0.43
ACGTcount: A:0.24, C:0.15, G:0.38, T:0.24
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACATGATGGCACCAACTA
Found at i:19389242 original size:21 final size:22
Alignment explanation
Indices: 19389196--19389242 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
19389186 ACCAGTTTGG
*
19389196 TTCTCGCTGTAGCGAGAACGCA
1 TTCTCGCTGTAGCGAGAACACA
19389218 TTCTCGCTGTAGCGAGAA-ACA
1 TTCTCGCTGTAGCGAGAACACA
19389239 TTCT
1 TTCT
19389243 GTTTTAGGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (22 bp):
TTCTCGCTGTAGCGAGAACACA
Found at i:19397082 original size:13 final size:13
Alignment explanation
Indices: 19397064--19397090 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19397054 TATATCATAG
19397064 AGTAGGGCTTGAC
1 AGTAGGGCTTGAC
19397077 AGTAGGGCTTGAC
1 AGTAGGGCTTGAC
19397090 A
1 A
19397091 TCACTCAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.15, G:0.37, T:0.22
Consensus pattern (13 bp):
AGTAGGGCTTGAC
Found at i:19402739 original size:73 final size:73
Alignment explanation
Indices: 19402613--19402788 Score: 271
Period size: 73 Copynumber: 2.4 Consensus size: 73
19402603 GAACTACCAG
* *
19402613 AGAGTTTTTCGCTGCAGCGAGAATGCATTTTCGCTGCAGCAAAAATCTGGGCTAGTCAAGCCCCT
1 AGAGTTTCTCGCTGCAGCGAGAATGCATTTTCGCTGCAGCAAAAATCTAGGCTAGTCAAGCCCCT
* *
19402678 AGCACTCA
66 AACACCCA
* *
19402686 AGAGTTTCTCGCTGCAGCGAGAATGCATTTTCGCTGTAGCAAAATTCTAGGCTAGTCAAGCCCCT
1 AGAGTTTCTCGCTGCAGCGAGAATGCATTTTCGCTGCAGCAAAAATCTAGGCTAGTCAAGCCCCT
*
19402751 AACACCCG
66 AACACCCA
* *
19402759 AGAGTTTCTCGCTGTAGCGAGAATGAATTT
1 AGAGTTTCTCGCTGCAGCGAGAATGCATTT
19402789 CGTTACAGCG
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 94 1.00
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.26
Consensus pattern (73 bp):
AGAGTTTCTCGCTGCAGCGAGAATGCATTTTCGCTGCAGCAAAAATCTAGGCTAGTCAAGCCCCT
AACACCCA
Found at i:19411770 original size:9 final size:9
Alignment explanation
Indices: 19411734--19411775 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
19411724 ACAACCCCAG
19411734 CTTTCTCTT
1 CTTTCTCTT
* *
19411743 TTTTCTTTT
1 CTTTCTCTT
19411752 CTTTCT-TT
1 CTTTCTCTT
19411760 CTTTCTCTT
1 CTTTCTCTT
*
19411769 CTCTCTC
1 CTTTCTC
19411776 GATTTTTGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 8 0.29
9 20 0.71
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (9 bp):
CTTTCTCTT
Found at i:19411959 original size:14 final size:14
Alignment explanation
Indices: 19411940--19411999 Score: 59
Period size: 14 Copynumber: 4.2 Consensus size: 14
19411930 AACTTTGACT
19411940 TTTCTTTTCTTTTC
1 TTTCTTTTCTTTTC
*
19411954 TTTCTTATCTTTTC
1 TTTCTTTTCTTTTC
*
19411968 TATC-TTTCATCTTTC
1 TTTCTTTTC-T-TTTC
* *
19411983 ATTCATTTCTTTTC
1 TTTCTTTTCTTTTC
19411997 TTT
1 TTT
19412000 TATATGGCCT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 3 0.08
14 23 0.62
15 7 0.19
16 4 0.11
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTCTTTTCTTTTC
Found at i:19412474 original size:10 final size:10
Alignment explanation
Indices: 19412461--19412485 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
19412451 TCCAAAAATT
19412461 TCCTTTTGTC
1 TCCTTTTGTC
19412471 TCCTTTTGTC
1 TCCTTTTGTC
19412481 TCCTT
1 TCCTT
19412486 GATACCCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.32, G:0.08, T:0.60
Consensus pattern (10 bp):
TCCTTTTGTC
Found at i:19413176 original size:42 final size:42
Alignment explanation
Indices: 19413124--19413288 Score: 233
Period size: 42 Copynumber: 3.9 Consensus size: 42
19413114 AACTCTGTCT
* * *
19413124 CAGCTTATGTGCACTACC-ACACCGCACATAGCCAGGTCAGCA
1 CAGCTCATGTGCACT-CCTACACCGCACATGGCTAGGTCAGCA
*
19413166 CAGCTCATGTGCACTCATACACCGCACATGGCTAGGTCAGCA
1 CAGCTCATGTGCACTCCTACACCGCACATGGCTAGGTCAGCA
* * *
19413208 CAGCTCATGTGCACTCCTACACTGCACATGGCTGGGTCAACA
1 CAGCTCATGTGCACTCCTACACCGCACATGGCTAGGTCAGCA
* *
19413250 CAGCTCATGTGCACTCCTATACCGCACATGGCTGGGTCA
1 CAGCTCATGTGCACTCCTACACCGCACATGGCTAGGTCA
19413289 TAATTATCAC
Statistics
Matches: 112, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
41 1 0.01
42 111 0.99
ACGTcount: A:0.25, C:0.34, G:0.21, T:0.20
Consensus pattern (42 bp):
CAGCTCATGTGCACTCCTACACCGCACATGGCTAGGTCAGCA
Found at i:19414620 original size:92 final size:92
Alignment explanation
Indices: 19414476--19414705 Score: 309
Period size: 92 Copynumber: 2.5 Consensus size: 92
19414466 TCAACCTCAA
* * * *
19414476 AAAAATTAGCAGCCT-AAGCTACTCATTTCACCCTCAAAATCGGTAGCCAAAACCTTAAAAATCA
1 AAAAATCAGCAG-CTAAAACTACTCATATCACCCTCAAAATCGGTAGCCAAAACCTCAAAAATCA
19414540 ACAGCTAAAGCTGCTCCTTTCAGCCTTC
65 ACAGCTAAAGCTGCTCCTTTCAGCCTTC
* *
19414568 AAAAATCAGTAGCTAAAACTACTCATATCACCCTCAAAATCGGTAGCCAAAACCTCAAAAATCAG
1 AAAAATCAGCAGCTAAAACTACTCATATCACCCTCAAAATCGGTAGCCAAAACCTCAAAAATCAA
* **
19414633 CAGTTAAAGCTGCTTTTTTCAGCCTTC
66 CAGCTAAAGCTGCTCCTTTCAGCCTTC
** * * * *
19414660 AAAAATCAGCAGCTAAAGTTGCTCATATCATCCTCAAGACCGGTAG
1 AAAAATCAGCAGCTAAAACTACTCATATCACCCTCAAAATCGGTAG
19414706 AAAAATAGCT
Statistics
Matches: 121, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
91 2 0.02
92 119 0.98
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (92 bp):
AAAAATCAGCAGCTAAAACTACTCATATCACCCTCAAAATCGGTAGCCAAAACCTCAAAAATCAA
CAGCTAAAGCTGCTCCTTTCAGCCTTC
Found at i:19416460 original size:14 final size:15
Alignment explanation
Indices: 19416441--19416469 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
19416431 CTATAGATTA
19416441 CATTTCCTT-GATAT
1 CATTTCCTTGGATAT
19416455 CATTTCCTTGGATAT
1 CATTTCCTTGGATAT
19416470 TCCTCCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (15 bp):
CATTTCCTTGGATAT
Found at i:19416823 original size:14 final size:14
Alignment explanation
Indices: 19416804--19416831 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19416794 AGATTACCCT
19416804 TTTTATATGTTTAA
1 TTTTATATGTTTAA
19416818 TTTTATATGTTTAA
1 TTTTATATGTTTAA
19416832 ATCACCATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (14 bp):
TTTTATATGTTTAA
Found at i:19419766 original size:21 final size:20
Alignment explanation
Indices: 19419726--19419766 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
19419716 TGAGCTGATT
19419726 TTGGTGATTTTAGTGAGTTA
1 TTGGTGATTTTAGTGAGTTA
19419746 TTGGCTGATATTTAGTG-GTTA
1 TTGG-TGAT-TTTAGTGAGTTA
19419767 GAAATGTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 8 0.42
22 7 0.37
ACGTcount: A:0.20, C:0.02, G:0.29, T:0.49
Consensus pattern (20 bp):
TTGGTGATTTTAGTGAGTTA
Found at i:19429138 original size:26 final size:26
Alignment explanation
Indices: 19429103--19429186 Score: 159
Period size: 26 Copynumber: 3.2 Consensus size: 26
19429093 GTTTCAATCA
19429103 TTTTCACCACAAGGGTAAAATGGTCAT
1 TTTTC-CCACAAGGGTAAAATGGTCAT
19429130 TTTTCCCACAAGGGTAAAATGGTCAT
1 TTTTCCCACAAGGGTAAAATGGTCAT
19429156 TTTTCCCACAAGGGTAAAATGGTCAT
1 TTTTCCCACAAGGGTAAAATGGTCAT
19429182 TTTTC
1 TTTTC
19429187 ACCTCCAGTA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
26 52 0.91
27 5 0.09
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (26 bp):
TTTTCCCACAAGGGTAAAATGGTCAT
Found at i:19432619 original size:60 final size:60
Alignment explanation
Indices: 19432541--19432707 Score: 192
Period size: 60 Copynumber: 2.8 Consensus size: 60
19432531 TAGGAGACCA
* * *
19432541 AAACAGAAAGTTTTTCGCTGCAGCGAGATTGAATCTTGCTGCAGTGAAATT-ATAACCCAG
1 AAACAGAAAGTTTCTCGCTGCAGAGAGATTGAATCTTGCTGCAGCGAAATTGAT-ACCCAG
* * * * * * * *
19432601 AAACAGAATGTTTCTCGCTGCAGTGAAATTCAATCTCGTTGCAACGAAATTGCTACCCAG
1 AAACAGAAAGTTTCTCGCTGCAGAGAGATTGAATCTTGCTGCAGCGAAATTGATACCCAG
* * *
19432661 AAACAGAAAGTTTCTCGCTGCAGAGAGAATGTATTTTGCTGCAGCGA
1 AAACAGAAAGTTTCTCGCTGCAGAGAGATTGAATCTTGCTGCAGCGA
19432708 GAAGCTGCAG
Statistics
Matches: 86, Mismatches: 20, Indels: 2
0.80 0.19 0.02
Matches are distributed among these distances:
60 85 0.99
61 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (60 bp):
AAACAGAAAGTTTCTCGCTGCAGAGAGATTGAATCTTGCTGCAGCGAAATTGATACCCAG
Found at i:19433124 original size:43 final size:43
Alignment explanation
Indices: 19433063--19433151 Score: 133
Period size: 43 Copynumber: 2.1 Consensus size: 43
19433053 CCCATCATCA
* *
19433063 TCATCACCAGCTCATGCGCACTCCCTACTCGCACATGGCTGGG
1 TCATCACCAGCTCATGCGCACTCCCTACTCGCACATAGCTGAG
* * *
19433106 TCATCACCAGGTTATGCGCACTCCCTACTTGCACATAGCTGAG
1 TCATCACCAGCTCATGCGCACTCCCTACTCGCACATAGCTGAG
19433149 TCA
1 TCA
19433152 ATATAATTAC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (43 bp):
TCATCACCAGCTCATGCGCACTCCCTACTCGCACATAGCTGAG
Found at i:19437893 original size:19 final size:19
Alignment explanation
Indices: 19437852--19437893 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
19437842 GAAGAAGGAG
* *
19437852 AAGAAGCTGTTGGAGAATG
1 AAGAAGCTGCTGGAGAATA
19437871 AAGAAGCTGCTGGAAGAA-A
1 AAGAAGCTGCTGG-AGAATA
19437890 AAGA
1 AAGA
19437894 TATTTATAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.45, C:0.07, G:0.33, T:0.14
Consensus pattern (19 bp):
AAGAAGCTGCTGGAGAATA
Found at i:19439248 original size:21 final size:22
Alignment explanation
Indices: 19439217--19439262 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
19439207 TATTTATTAA
19439217 TCTTCACAATTAAGTCCTCCAT
1 TCTTCACAATTAAGTCCTCCAT
*
19439239 TCTTC-CAATTAAGTCTTCCAT
1 TCTTCACAATTAAGTCCTCCAT
19439260 TCT
1 TCT
19439263 CTAATTTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.24, C:0.30, G:0.04, T:0.41
Consensus pattern (22 bp):
TCTTCACAATTAAGTCCTCCAT
Found at i:19439290 original size:3 final size:3
Alignment explanation
Indices: 19439282--19439307 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
19439272 CTTTATTCTT
19439282 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
19439308 TGACATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:19440033 original size:19 final size:19
Alignment explanation
Indices: 19440009--19440046 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
19439999 CAACCCTAAA
*
19440009 TTCAATGTTAACATAAAAG
1 TTCAATGCTAACATAAAAG
19440028 TTCAATGCTAACATAAAAG
1 TTCAATGCTAACATAAAAG
19440047 GTCGATCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (19 bp):
TTCAATGCTAACATAAAAG
Found at i:19440928 original size:21 final size:21
Alignment explanation
Indices: 19440902--19440956 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
19440892 GAAAGACAAA
19440902 TATCGATACTTGATGCCTAAG
1 TATCGATACTTGATGCCTAAG
* *
19440923 TATCGATACTTAATGCCTAGG
1 TATCGATACTTGATGCCTAAG
19440944 TAGT-GATACTTGA
1 TA-TCGATACTTGA
19440957 AACCTAGAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (21 bp):
TATCGATACTTGATGCCTAAG
Found at i:19442142 original size:43 final size:43
Alignment explanation
Indices: 19442060--19442142 Score: 96
Period size: 43 Copynumber: 1.9 Consensus size: 43
19442050 CAAAAACCCA
* * ** *
19442060 ATATTTGTAAAGGAAAGAATTGATTCTCAGTCAAGAAGAAATG
1 ATATTTGGAAAGGAAAGAATCGATTCTCAGAAAAAAAGAAATG
*
19442103 ATATTTGGAAA-GACAAGAATCGATTCTTAGAAAAAAAGAA
1 ATATTTGGAAAGGA-AAGAATCGATTCTCAGAAAAAAAGAA
19442143 CTGACTTCTC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
42 2 0.06
43 31 0.94
ACGTcount: A:0.48, C:0.07, G:0.19, T:0.25
Consensus pattern (43 bp):
ATATTTGGAAAGGAAAGAATCGATTCTCAGAAAAAAAGAAATG
Found at i:19442243 original size:72 final size:72
Alignment explanation
Indices: 19442156--19442309 Score: 182
Period size: 72 Copynumber: 2.1 Consensus size: 72
19442146 ACTTCTCAGC
* * * *
19442156 AATGAAGAATCGATTCCATGAAAGCAGAAAGCTCCAGACGTTAAGAATGACGTGAAGAATTGACA
1 AATGAAGAATCGATTCCATGAAAACAGAAAGCTCCAGACGTTAAGAATGACATGAAGAACTAACA
* *
19442221 CCTTAAG
66 CATCAAG
* ** * * * *
19442228 AATGAAGAATTGATTCTTTGAAAACAGAAAGTTGCAGACTTTAGGAATGACATGAAGAACTAACA
1 AATGAAGAATCGATTCCATGAAAACAGAAAGCTCCAGACGTTAAGAATGACATGAAGAACTAACA
19442293 CATCAAG
66 CATCAAG
*
19442300 AATAAAGAAT
1 AATGAAGAAT
19442310 GGGTTATTAG
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.21
Consensus pattern (72 bp):
AATGAAGAATCGATTCCATGAAAACAGAAAGCTCCAGACGTTAAGAATGACATGAAGAACTAACA
CATCAAG
Found at i:19444791 original size:2 final size:2
Alignment explanation
Indices: 19444786--19444816 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
19444776 ATATAGTACC
*
19444786 AT AT AT AA 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
19444817 GCCTTTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:19445841 original size:31 final size:30
Alignment explanation
Indices: 19445801--19445939 Score: 111
Period size: 31 Copynumber: 4.5 Consensus size: 30
19445791 TTTATTATCC
* *
19445801 CTTTGCAATTTAGTCCTCCAGTATTTTCTTT
1 CTTTTCAATTTAGTCCTCTA-TATTTTCTTT
* * *
19445832 CTTTTCAATTTAGCCCTTTAATGTTTTCTTT
1 CTTTTCAATTTAGTCCTCT-ATATTTTCTTT
* * *
19445863 CTATTCAATTTAGTACTCTA-ACTTTTTTTT
1 CTTTTCAATTTAGTCCTCTATA-TTTTCTTT
* * *
19445893 CTTTTCAATTTAATCTTTCAACT-TTTTCTTT
1 CTTTTCAATTTAGTC-CTCTA-TATTTTCTTT
*
19445924 CTTTTCAATTAAGTCC
1 CTTTTCAATTTAGTCC
19445940 CTTTCCCAAA
Statistics
Matches: 83, Mismatches: 20, Indels: 11
0.73 0.18 0.10
Matches are distributed among these distances:
30 20 0.24
31 62 0.75
32 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.05, T:0.55
Consensus pattern (30 bp):
CTTTTCAATTTAGTCCTCTATATTTTCTTT
Found at i:19445900 original size:30 final size:30
Alignment explanation
Indices: 19445824--19445938 Score: 135
Period size: 31 Copynumber: 3.8 Consensus size: 30
19445814 TCCTCCAGTA
*
19445824 TTTTCTTTCTTTTCAATTTAGCCCTTTAA-T
1 TTTTCTTTCTTTTCAATTTAG-TCTTTAACT
* *
19445854 GTTTTCTTTCTATTCAATTTAGTACTCTAACT
1 -TTTTCTTTCTTTTCAATTTAGT-CTTTAACT
*
19445886 TTTT-TTTCTTTTCAATTTAATCTTTCAACT
1 TTTTCTTTCTTTTCAATTTAGTCTTT-AACT
*
19445916 TTTTCTTTCTTTTCAATTAAGTC
1 TTTTCTTTCTTTTCAATTTAGTC
19445939 CCTTTCCCAA
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
29 3 0.04
30 23 0.32
31 45 0.62
32 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.03, T:0.59
Consensus pattern (30 bp):
TTTTCTTTCTTTTCAATTTAGTCTTTAACT
Found at i:19456757 original size:38 final size:40
Alignment explanation
Indices: 19456715--19456817 Score: 131
Period size: 38 Copynumber: 2.6 Consensus size: 40
19456705 ATAGTGCTCG
* * *
19456715 TGTGCATGATGTGGGGGGATGTACACGAT-G-GCACTGAT-
1 TGTGCACGATGTGGGGGGATGTACACAATGGTGC-CGGATA
* *
19456753 TGTGCACGATGTGGGGGGATGCACACAATGGTGCCGGCTA
1 TGTGCACGATGTGGGGGGATGTACACAATGGTGCCGGATA
19456793 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
19456818 TGAGCGGGGT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
38 26 0.46
39 4 0.07
40 26 0.46
ACGTcount: A:0.20, C:0.16, G:0.41, T:0.23
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACACAATGGTGCCGGATA
Found at i:19461658 original size:32 final size:32
Alignment explanation
Indices: 19461620--19461764 Score: 114
Period size: 35 Copynumber: 4.3 Consensus size: 32
19461610 TATCGGGATT
* *
19461620 AACCAAAACCCAAAGTGTTTTTTCAAAGGCTT
1 AACCAAAACCCAAAGTGGTTTTTCAAAGGCTC
* *
19461652 AGCCAAAACCTTTCACAA-TGGTTTTTC-ACGAGCTC
1 AACCAAAACC---CA-AAGTGGTTTTTCAAAG-GCTC
19461687 AACCAAAACCCAAAGTGGTTTTTCAAAGGCTC
1 AACCAAAACCCAAAGTGGTTTTTCAAAGGCTC
* * * * *
19461719 AAGCACAACCTACAACAATGGTTTTTCACACGGATC
1 AACCAAAACC--CAA-AGTGGTTTTTCA-AAGGCTC
19461755 AACCAAAACC
1 AACCAAAACC
19461765 AAACAACTAA
Statistics
Matches: 89, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
31 2 0.02
32 32 0.36
33 2 0.02
34 5 0.06
35 33 0.37
36 15 0.17
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (32 bp):
AACCAAAACCCAAAGTGGTTTTTCAAAGGCTC
Found at i:19461691 original size:67 final size:67
Alignment explanation
Indices: 19461579--19461764 Score: 227
Period size: 67 Copynumber: 2.8 Consensus size: 67
19461569 GACTTTTACT
* * * *
19461579 AGGCTTAGCCAAAACCTTTCACAATCGTTTTT-ATCGGGATTAACCAAAACCCAAAGTGTTTTTT
1 AGGCTTAGCCAAAACCTTTCACAATGGTTTTTCA-CGAGATCAACCAAAACCCAAAGTGGTTTTT
19461643 CAA
65 CAA
*
19461646 AGGCTTAGCCAAAACCTTTCACAATGGTTTTTCACGAGCTCAACCAAAACCCAAAGTGGTTTTTC
1 AGGCTTAGCCAAAACCTTTCACAATGGTTTTTCACGAGATCAACCAAAACCCAAAGTGGTTTTTC
19461711 AA
66 AA
* * *
19461713 AGGCTCAAG-CACAACC-TACAACAATGGTTTTTCAC-ACGGATCAACCAAAACC
1 AGGCT-TAGCCAAAACCTTTC-ACAATGGTTTTTCACGA--GATCAACCAAAACC
19461765 AAACAACTAA
Statistics
Matches: 105, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
66 3 0.03
67 86 0.82
68 16 0.15
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (67 bp):
AGGCTTAGCCAAAACCTTTCACAATGGTTTTTCACGAGATCAACCAAAACCCAAAGTGGTTTTTC
AA
Found at i:19465882 original size:17 final size:19
Alignment explanation
Indices: 19465841--19465882 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
19465831 GTATATATAT
19465841 ATGAATATATGTTGTGCATTG
1 ATGAATATATGTTGTG-A-TG
19465862 ATGAATA-ATGTTGTG-TG
1 ATGAATATATGTTGTGATG
19465879 ATGA
1 ATGA
19465883 TATTGACCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.29
20 8 0.38
21 7 0.33
ACGTcount: A:0.31, C:0.02, G:0.26, T:0.40
Consensus pattern (19 bp):
ATGAATATATGTTGTGATG
Found at i:19465931 original size:49 final size:49
Alignment explanation
Indices: 19465877--19465996 Score: 170
Period size: 49 Copynumber: 2.4 Consensus size: 49
19465867 TAATGTTGTG
* *
19465877 TGATGAT-ATTGACCCGGCTATGTGCCAGTAGGGAGTGCGCATAAGCCGA
1 TGATGATGA-TGACCCGACTATGTGCCAGTAGGGAGTACGCATAAGCCGA
* * *
19465926 TGATGATGATGACCCGACTATGTGCGAGTTGGGAGTACGCATAAGTCGA
1 TGATGATGATGACCCGACTATGTGCCAGTAGGGAGTACGCATAAGCCGA
*
19465975 TGATGATGATGACCCGAATATG
1 TGATGATGATGACCCGACTATG
19465997 ACGATGAATG
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
49 63 0.98
50 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (49 bp):
TGATGATGATGACCCGACTATGTGCCAGTAGGGAGTACGCATAAGCCGA
Found at i:19474903 original size:42 final size:42
Alignment explanation
Indices: 19474836--19474961 Score: 173
Period size: 42 Copynumber: 3.0 Consensus size: 42
19474826 GTAATGATAT
* * *
19474836 TGACCCGACTATGTGCGATTAGGAGTGCACATAAGCAGTTGC
1 TGACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCAGTTGC
* *
19474878 TGACCCGGCTATGTGCAAGTGGGAGTTCACATAAGCCA-TTGC
1 TGACCCGGCTATGTGCGAGTGGGAGTGCACATAAG-CAGTTGC
* *
19474920 TGACCCGGCTATGTGCGAGTGGGAGTGCGCATAAGCCGTTGC
1 TGACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCAGTTGC
19474962 ATATGAGATG
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
41 1 0.01
42 70 0.96
43 2 0.03
ACGTcount: A:0.22, C:0.23, G:0.32, T:0.23
Consensus pattern (42 bp):
TGACCCGGCTATGTGCGAGTGGGAGTGCACATAAGCAGTTGC
Found at i:19480799 original size:29 final size:28
Alignment explanation
Indices: 19480750--19480825 Score: 89
Period size: 29 Copynumber: 2.7 Consensus size: 28
19480740 TTCCTGTCTT
** *
19480750 AAATTAAGACAAATGTATTTTCTGGTAA
1 AAATTAAGACAAACATGTTTTCTGGTAA
* * *
19480778 AAATTAGGACTAAACATGTTTTCTTGTCA
1 AAATTAAGAC-AAACATGTTTTCTGGTAA
19480807 AAATTAAGACAAACATGTT
1 AAATTAAGACAAACATGTT
19480826 AAAGCTATCA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
28 18 0.45
29 22 0.55
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (28 bp):
AAATTAAGACAAACATGTTTTCTGGTAA
Found at i:19488692 original size:40 final size:40
Alignment explanation
Indices: 19488637--19488736 Score: 120
Period size: 36 Copynumber: 2.6 Consensus size: 40
19488627 CCCAGCTCAT
*
19488637 GTGCATCCCCCCACATCGTGCACATAGCCAGA-GTCATCGC
1 GTGCATCCCCCCACATCGTGCACATAGCCA-ATGCCATCGC
** *
19488677 GTGCATCCCCCCACATCGTG----TAGGTAATGCCATCGT
1 GTGCATCCCCCCACATCGTGCACATAGCCAATGCCATCGC
19488713 GTGCATCCCCCCACATCGTGCACA
1 GTGCATCCCCCCACATCGTGCACA
19488737 CGGGCAATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
35 1 0.02
36 30 0.59
40 20 0.39
ACGTcount: A:0.21, C:0.39, G:0.20, T:0.20
Consensus pattern (40 bp):
GTGCATCCCCCCACATCGTGCACATAGCCAATGCCATCGC
Found at i:19499614 original size:17 final size:17
Alignment explanation
Indices: 19499588--19499624 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
19499578 TTGAACATGC
*
19499588 TTAGACATTCGCAAGGT
1 TTAGAAATTCGCAAGGT
*
19499605 TTAGAAATTCTCAAGGT
1 TTAGAAATTCGCAAGGT
19499622 TTA
1 TTA
19499625 ACATACAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (17 bp):
TTAGAAATTCGCAAGGT
Found at i:19499696 original size:2 final size:2
Alignment explanation
Indices: 19499686--19499782 Score: 133
Period size: 2 Copynumber: 48.5 Consensus size: 2
19499676 TATAACACAC
*
19499686 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
19499728 ACN AT A- AC AC AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19499770 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
19499783 CACATCATCA
Statistics
Matches: 88, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
1 1 0.01
2 86 0.98
3 1 0.01
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:19499897 original size:42 final size:42
Alignment explanation
Indices: 19499809--19499940 Score: 185
Period size: 42 Copynumber: 3.1 Consensus size: 42
19499799 CCATCCCTCG
* * **
19499809 ATCATCAGCTCATGTGCACTCCCAACTCACACATAGCCAGGTC
1 ATCATCAGCTCATGTGCACTCCC-ACACGCACATAGCTGGGTC
*
19499852 ATCATCAGCTCATGTGCACT-CCACACCGCACATAGTTGGGTC
1 ATCATCAGCTCATGTGCACTCCCACA-CGCACATAGCTGGGTC
*
19499894 ATCATCAACTCATGTGCACTCCCACACGCACATAGCTGGGTC
1 ATCATCAGCTCATGTGCACTCCCACACGCACATAGCTGGGTC
19499936 ATCAT
1 ATCAT
19499941 TATCACATTA
Statistics
Matches: 80, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
41 2 0.03
42 53 0.66
43 25 0.31
ACGTcount: A:0.27, C:0.35, G:0.16, T:0.23
Consensus pattern (42 bp):
ATCATCAGCTCATGTGCACTCCCACACGCACATAGCTGGGTC
Found at i:19504120 original size:2 final size:2
Alignment explanation
Indices: 19504066--19504108 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
19504056 TATGACATAG
19504066 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19504108 T
1 T
19504109 CAACATTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19506876 original size:23 final size:23
Alignment explanation
Indices: 19506828--19506885 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
19506818 CATGTGGAGG
* * *
19506828 AAGGCTGTGGCCTTGAGGAAGTC
1 AAGGCTGTAGCATTGAGGAAGAC
19506851 AAGGCTGTAGCATTGAGG-AGAAC
1 AAGGCTGTAGCATTGAGGAAG-AC
19506874 AAGGCTGTAGCA
1 AAGGCTGTAGCA
19506886 GTGGTGAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 2 0.06
23 29 0.94
ACGTcount: A:0.29, C:0.16, G:0.36, T:0.19
Consensus pattern (23 bp):
AAGGCTGTAGCATTGAGGAAGAC
Found at i:19509804 original size:38 final size:40
Alignment explanation
Indices: 19509716--19509818 Score: 140
Period size: 38 Copynumber: 2.6 Consensus size: 40
19509706 CACATCTAGC
* * *
19509716 TCATGTGCAT-CCCCTACATCGTGCACATAGCTGGTGTCA
1 TCATGTGCATCCCCCCACATCGTGCACATAGCTAGTGCCA
*
19509755 TCATGTGCATCCCCCCACATCGTGCACA-ATC-AGTGCCA
1 TCATGTGCATCCCCCCACATCGTGCACATAGCTAGTGCCA
*
19509793 TCATGTACATCCCCCCACATCGTGCA
1 TCATGTGCATCCCCCCACATCGTGCA
19509819 TAGGGGCACT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
38 30 0.52
39 12 0.21
40 16 0.28
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.24
Consensus pattern (40 bp):
TCATGTGCATCCCCCCACATCGTGCACATAGCTAGTGCCA
Found at i:19509943 original size:2 final size:2
Alignment explanation
Indices: 19509936--19509974 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
19509926 CATGCACAAC
*
19509936 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19509975 CCAACATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19513749 original size:43 final size:43
Alignment explanation
Indices: 19513686--19513815 Score: 138
Period size: 43 Copynumber: 3.0 Consensus size: 43
19513676 GTAATTATGT
* * **
19513686 TGACTCGGCTATGTGTGAGTAAGGAGTGCGCATAAGTCGAG-GA
1 TGACTCGGTTATGTGCGAGTAAGGAGTGCGCATAACCCG-GTGA
* * *
19513729 TGACTTGGTTATGTGCGAGT-AGAGAGTACACATAACCCGGTGA
1 TGACTCGGTTATGTGCGAGTAAG-GAGTGCGCATAACCCGGTGA
* * *
19513772 TGACTCGGTTATGTGCGAGTAGGGAATGCGCATAACCCGATGA
1 TGACTCGGTTATGTGCGAGTAAGGAGTGCGCATAACCCGGTGA
19513815 T
1 T
19513816 AACCCAACCA
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
42 3 0.04
43 67 0.94
44 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.33, T:0.25
Consensus pattern (43 bp):
TGACTCGGTTATGTGCGAGTAAGGAGTGCGCATAACCCGGTGA
Found at i:19513871 original size:20 final size:20
Alignment explanation
Indices: 19513846--19513888 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
19513836 GAGAGTGCGC
19513846 ATGAGCTAGTGATGATGATG
1 ATGAGCTAGTGATGATGATG
*
19513866 ATGAGCTGGTGATGATGATG
1 ATGAGCTAGTGATGATGATG
19513886 ATG
1 ATG
19513889 GGTATATACG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.28, C:0.05, G:0.37, T:0.30
Consensus pattern (20 bp):
ATGAGCTAGTGATGATGATG
Found at i:19513904 original size:2 final size:2
Alignment explanation
Indices: 19513899--19513945 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
19513889 GGTATATACG
* *
19513899 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
19513941 CA TA T
1 TA TA T
19513946 GTAAATGTGT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:19513906 original size:10 final size:10
Alignment explanation
Indices: 19513891--19513937 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
19513881 TGATGATGGG
*
19513891 TATATACGTA
1 TATATATGTA
*
19513901 TATATATATA
1 TATATATGTA
19513911 TATATATGTA
1 TATATATGTA
*
19513921 TATATATATA
1 TATATATGTA
*
19513931 TAAATAT
1 TATATAT
19513938 ATACATATGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (10 bp):
TATATATGTA
Found at i:19513945 original size:16 final size:16
Alignment explanation
Indices: 19513902--19513951 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
19513892 ATATACGTAT
*
19513902 ATATATATATATATAT
1 ATATATATATATATAA
*
19513918 GTATATATATATATAA
1 ATATATATATATATAA
* *
19513934 ATATATACATATGTAA
1 ATATATATATATATAA
19513950 AT
1 AT
19513952 GTGTGTGTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (16 bp):
ATATATATATATATAA
Found at i:19521204 original size:16 final size:16
Alignment explanation
Indices: 19521183--19521224 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
19521173 GTAAACTTGA
*
19521183 TGTCATACTCTGACAC
1 TGTCATACTCCGACAC
19521199 TGTCATACTCCGACAC
1 TGTCATACTCCGACAC
19521215 TGTCATACTC
1 TGTCATACTC
19521225 GAAGTTTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.24, C:0.33, G:0.12, T:0.31
Consensus pattern (16 bp):
TGTCATACTCCGACAC
Found at i:19522950 original size:20 final size:20
Alignment explanation
Indices: 19522893--19522955 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
19522883 TATATACCCA
*
19522893 TCATCATCATC-TCACCAAC
1 TCATCATCATCATCACCAGC
*
19522912 CCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
19522932 TCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
19522952 TCAT
1 TCAT
19522956 GCGCACTCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.30, C:0.41, G:0.03, T:0.25
Consensus pattern (20 bp):
TCATCATCATCATCACCAGC
Done.