Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 66 of 135
Found at i:19664839 original size:69 final size:69
Alignment explanation
Indices: 19664728--19664875 Score: 278
Period size: 69 Copynumber: 2.1 Consensus size: 69
19664718 CGTCAAAGTT
19664728 CTGCTTGCATAGTAGATAGGGTGAAACACTTTGTTTCTTCTTTGACCCATCACAACTCTAACGAA
1 CTGCTTGCATAGTAGATAGGGTGAAACACTTTGTTTCTTCTTTGACCCATCACAACTCTAACGAA
19664793 AAAA
66 AAAA
* *
19664797 CTGCTTGCATAGTAGATAGGGTGAAACACTTTGTTTCTTCTTTGACTCATCACAACTCTAACGGA
1 CTGCTTGCATAGTAGATAGGGTGAAACACTTTGTTTCTTCTTTGACCCATCACAACTCTAACGAA
19664862 AAAA
66 AAAA
19664866 CTGCTTGCAT
1 CTGCTTGCAT
19664876 CACACATCAA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 77 1.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.32
Consensus pattern (69 bp):
CTGCTTGCATAGTAGATAGGGTGAAACACTTTGTTTCTTCTTTGACCCATCACAACTCTAACGAA
AAAA
Found at i:19668626 original size:8 final size:8
Alignment explanation
Indices: 19668610--19668649 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
19668600 AAAGGAATTT
19668610 AGAGAATG
1 AGAGAATG
*
19668618 AGAGTATG
1 AGAGAATG
*
19668626 AAAGAATG
1 AGAGAATG
19668634 AGAGAATG
1 AGAGAATG
19668642 A-AGAATG
1 AGAGAATG
19668649 A
1 A
19668650 TTGATGAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
7 7 0.25
8 21 0.75
ACGTcount: A:0.53, C:0.00, G:0.33, T:0.15
Consensus pattern (8 bp):
AGAGAATG
Found at i:19677059 original size:35 final size:35
Alignment explanation
Indices: 19677013--19677088 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
19677003 AAGTCCAGCT
* *
19677013 CTAGTTGGATAAACCAATGATGTT-TGTGCCCAACG
1 CTAGTCGGATAAACCAACGAT-TTATGTGCCCAACG
*
19677048 CTAGTCGGATAAACCGACGATTTATGTGCCCAACG
1 CTAGTCGGATAAACCAACGATTTATGTGCCCAACG
19677083 CTAGTC
1 CTAGTC
19677089 AAATTAACTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 2 0.05
35 35 0.95
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (35 bp):
CTAGTCGGATAAACCAACGATTTATGTGCCCAACG
Found at i:19677076 original size:110 final size:110
Alignment explanation
Indices: 19676878--19677077 Score: 278
Period size: 110 Copynumber: 1.8 Consensus size: 110
19676868 CGAATGAACC
* * *
19676878 GACGATATAAAAGGTGAGCCCAACTCTAGTTGGATATACCAACAATTATTGTGCCCAGCGCTAGT
1 GACGATATAAAAGGTAAGCCCAACTCTAGTTGGATAAACCAACAATTATTGTGCCCAACGCTAGT
*
19676943 CGGATAAACCGACAAGTTGTGTGCCTATCACTAGTTAGATAAACT
66 CGGATAAACCGACAAGTTATGTGCCTATCACTAGTTAGATAAACT
* * **
19676988 GACGATATAAATA-GTAAGTCCAGCTCTAGTTGGATAAACCAATGATGT-TTGTGCCCAACGCTA
1 GACGATATAAA-AGGTAAGCCCAACTCTAGTTGGATAAACCAACAAT-TATTGTGCCCAACGCTA
* *
19677051 GTCGGATAAACCGACGATTTATGTGCC
64 GTCGGATAAACCGACAAGTTATGTGCC
19677078 CAACGCTAGT
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
110 76 0.97
111 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.26
Consensus pattern (110 bp):
GACGATATAAAAGGTAAGCCCAACTCTAGTTGGATAAACCAACAATTATTGTGCCCAACGCTAGT
CGGATAAACCGACAAGTTATGTGCCTATCACTAGTTAGATAAACT
Found at i:19682298 original size:38 final size:38
Alignment explanation
Indices: 19682231--19682342 Score: 172
Period size: 38 Copynumber: 3.0 Consensus size: 38
19682221 GAACTTGGAG
*
19682231 TTCCAAAGTATTTT-TCGTAGTACGGGAAGGTTCAAAC
1 TTCCAAAGTATTTTCTCGTAGTACGAGAAGGTTCAAAC
*
19682268 TTCCAAAGCATTTTCTCGTAGTACGAGAAGGTTCAAAC
1 TTCCAAAGTATTTTCTCGTAGTACGAGAAGGTTCAAAC
* * *
19682306 TTCCAAAGTGTTTTCCCGTAGTATGAGAAGGTTCAAA
1 TTCCAAAGTATTTTCTCGTAGTACGAGAAGGTTCAAA
19682343 ATTCTTATTT
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
37 13 0.19
38 55 0.81
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (38 bp):
TTCCAAAGTATTTTCTCGTAGTACGAGAAGGTTCAAAC
Found at i:19684117 original size:16 final size:16
Alignment explanation
Indices: 19684096--19684126 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19684086 ATAATGTGAA
19684096 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
19684112 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
19684127 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:19685004 original size:38 final size:37
Alignment explanation
Indices: 19684925--19685022 Score: 119
Period size: 38 Copynumber: 2.6 Consensus size: 37
19684915 GGACATGTTC
19684925 ATGCAGCGACA-TTTCTGGGTGCAATTGAAGAATACTT
1 ATGCAGCGACAGTTT-TGGGTGCAATTGAAGAATACTT
* * *
19684962 ATGCAGCGATAGTTTTGGATGCAATTTGAATAATA-TT
1 ATGCAGCGACAGTTTTGGGTGCAA-TTGAAGAATACTT
*
19684999 AATGCAGCGACAGTCTTGGGTGCA
1 -ATGCAGCGACAGTTTTGGGTGCA
19685023 TTCCAGAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
37 20 0.38
38 32 0.62
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.31
Consensus pattern (37 bp):
ATGCAGCGACAGTTTTGGGTGCAATTGAAGAATACTT
Found at i:19685107 original size:37 final size:37
Alignment explanation
Indices: 19685049--19685119 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
19685039 GCGACAACGG
* *
19685049 TTTTGGCTGCAACCTAGAAGTGCTCATGCGGCGATGA
1 TTTTGGCTGCAACCTACAAGTGCTCATGCAGCGATGA
*
19685086 TTTTGGGC-GCAATCTACAAGTGCTCATGCAGCGA
1 TTTT-GGCTGCAACCTACAAGTGCTCATGCAGCGA
19685120 CATTAGTAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
37 27 0.90
38 3 0.10
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.27
Consensus pattern (37 bp):
TTTTGGCTGCAACCTACAAGTGCTCATGCAGCGATGA
Found at i:19685204 original size:20 final size:21
Alignment explanation
Indices: 19685169--19685208 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
19685159 GCCAAGCTTC
*
19685169 ACTAAGTTAGAAAATACTAAT
1 ACTAAATTAGAAAATACTAAT
19685190 ACTAAATTA-AAAATACTAA
1 ACTAAATTAGAAAATACTAA
19685209 AAATGCATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (21 bp):
ACTAAATTAGAAAATACTAAT
Found at i:19685580 original size:17 final size:18
Alignment explanation
Indices: 19685558--19685598 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
19685548 TATACACATA
19685558 TTTTTTC-TTCTTTTCCT
1 TTTTTTCTTTCTTTTCCT
19685575 TTTTTTCTTTCTTTTCCT
1 TTTTTTCTTTCTTTTCCT
19685593 TTTTTT
1 TTTTTT
19685599 ATGTGACTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTTCTTTCTTTTCCT
Found at i:19686200 original size:17 final size:17
Alignment explanation
Indices: 19686155--19686202 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
19686145 ATATATATGT
**
19686155 AAATGCAATGACAATGT
1 AAATGCAATGACAATAA
* * *
19686172 AGATGTAGTGACAATAA
1 AAATGCAATGACAATAA
19686189 AAATGCAATGACAA
1 AAATGCAATGACAA
19686203 AAGATATGTG
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.50, C:0.10, G:0.19, T:0.21
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:19687488 original size:16 final size:16
Alignment explanation
Indices: 19687467--19687497 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19687457 ATAATGTGAA
19687467 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
19687483 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
19687498 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:19688287 original size:36 final size:38
Alignment explanation
Indices: 19688247--19688333 Score: 99
Period size: 36 Copynumber: 2.3 Consensus size: 38
19688237 AGACATGTTC
*
19688247 ATGCAGCGACA-TTCCTGGATGCA-ATTGAAG-ATACTT
1 ATGCAGCGACAGTT-CTAGATGCAGATTGAAGAATACTT
* * *
19688283 ATGCAGCGATAGTTCTAGATGCAGTTTGAAGAATATTT
1 ATGCAGCGACAGTTCTAGATGCAGATTGAAGAATACTT
*
19688321 ATACAGCGACAGT
1 ATGCAGCGACAGT
19688334 CTTGGGTGCA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
36 18 0.43
37 8 0.19
38 16 0.38
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (38 bp):
ATGCAGCGACAGTTCTAGATGCAGATTGAAGAATACTT
Found at i:19688434 original size:37 final size:37
Alignment explanation
Indices: 19688363--19688442 Score: 106
Period size: 37 Copynumber: 2.2 Consensus size: 37
19688353 TATTCTTGCG
* * *
19688363 GCGACAGTTTTGGGTGTAATATAAAAGTACTCATGCA
1 GCGACAATTTTAGGTGCAATATAAAAGTACTCATGCA
* * *
19688400 GTGACAATTTTAGGTGCAATCTAAAAGTGCTCATGCA
1 GCGACAATTTTAGGTGCAATATAAAAGTACTCATGCA
19688437 GCGACA
1 GCGACA
19688443 TTAGTAGTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.28
Consensus pattern (37 bp):
GCGACAATTTTAGGTGCAATATAAAAGTACTCATGCA
Found at i:19692746 original size:13 final size:14
Alignment explanation
Indices: 19692719--19692755 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
19692709 CAAAAATTTC
19692719 TTCCTTCTCTCATT
1 TTCCTTCTCTCATT
19692733 TTCCTTCT-TCATT
1 TTCCTTCTCTCATT
*
19692746 TTCCTCCTCT
1 TTCCTTCTCT
19692756 TTCTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.05, C:0.38, G:0.00, T:0.57
Consensus pattern (14 bp):
TTCCTTCTCTCATT
Found at i:19701116 original size:17 final size:17
Alignment explanation
Indices: 19701094--19701129 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
19701084 GTTAGTGCAC
*
19701094 ATTTTCGTTGCATTTTA
1 ATTTTCATTGCATTTTA
19701111 ATTTTCATTGCATTTTA
1 ATTTTCATTGCATTTTA
19701128 AT
1 AT
19701130 GTAAGTACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.08, T:0.58
Consensus pattern (17 bp):
ATTTTCATTGCATTTTA
Found at i:19707723 original size:20 final size:20
Alignment explanation
Indices: 19707698--19707735 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
19707688 TCAGGAACCA
*
19707698 CAACTACAATCATCGTCTAC
1 CAACTACAAGCATCGTCTAC
*
19707718 CAACTATAAGCATCGTCT
1 CAACTACAAGCATCGTCT
19707736 TTCAATAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.32, G:0.08, T:0.26
Consensus pattern (20 bp):
CAACTACAAGCATCGTCTAC
Found at i:19711262 original size:20 final size:21
Alignment explanation
Indices: 19711234--19711273 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
19711224 TAAGATTGAG
19711234 AGGATTTTTTTTATTCAGAGA
1 AGGATTTTTTTTATTCAGAGA
*
19711255 AGGA-TTTTTTTGTTCAGAG
1 AGGATTTTTTTTATTCAGAG
19711274 GGGAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.25, C:0.05, G:0.23, T:0.47
Consensus pattern (21 bp):
AGGATTTTTTTTATTCAGAGA
Found at i:19711282 original size:19 final size:20
Alignment explanation
Indices: 19711240--19711285 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
19711230 TGAGAGGATT
*
19711240 TTTTTTATTCAGAGAAGGAT
1 TTTTTTATTCAGAGAAGGAA
* *
19711260 TTTTTTGTTCAGAG-GGGAA
1 TTTTTTATTCAGAGAAGGAA
19711279 TTTTTTA
1 TTTTTTA
19711286 ATGAGATTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.24, C:0.04, G:0.22, T:0.50
Consensus pattern (20 bp):
TTTTTTATTCAGAGAAGGAA
Found at i:19711572 original size:20 final size:21
Alignment explanation
Indices: 19711524--19711572 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
19711514 GTTCGTATTT
19711524 TTTATTATTATTCATATTTAA
1 TTTATTATTATTCATATTTAA
*
19711545 -TTATTTATT-TTGATATTTAA
1 TTTA-TTATTATTCATATTTAA
19711565 TTTATTAT
1 TTTATTAT
19711573 CTTGTTTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTATTATTATTCATATTTAA
Found at i:19715822 original size:15 final size:13
Alignment explanation
Indices: 19715798--19715836 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 13
19715788 TGCATATGCA
19715798 TACATGCATTCAT
1 TACATGCATTCAT
19715811 TAGCATTGCATTTCAT
1 TA-CA-TGCA-TTCAT
19715827 TACATGCATT
1 TACATGCATT
19715837 AAATTTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 4 0.17
14 6 0.26
15 6 0.26
16 7 0.30
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (13 bp):
TACATGCATTCAT
Found at i:19728610 original size:28 final size:28
Alignment explanation
Indices: 19728579--19728636 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
19728569 AAATCTGAAG
19728579 TATGTCTTTCTAGGTGACAATGACACAT
1 TATGTCTTTCTAGGTGACAATGACACAT
19728607 TATGTCTTTCTAGGTGACAATGACACAT
1 TATGTCTTTCTAGGTGACAATGACACAT
19728635 TA
1 TA
19728637 CACGTGATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (28 bp):
TATGTCTTTCTAGGTGACAATGACACAT
Found at i:19738433 original size:18 final size:18
Alignment explanation
Indices: 19738410--19738455 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
19738400 TCCAGACTTG
19738410 GATGTTGAAGCAAAAAGA
1 GATGTTGAAGCAAAAAGA
*
19738428 GATGTTAAAGCAAAAAGA
1 GATGTTGAAGCAAAAAGA
*
19738446 GAAGTTGAAG
1 GATGTTGAAG
19738456 ATATTATGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.50, C:0.04, G:0.28, T:0.17
Consensus pattern (18 bp):
GATGTTGAAGCAAAAAGA
Found at i:19779027 original size:18 final size:20
Alignment explanation
Indices: 19778991--19779027 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19778981 GGAAAGAAAT
*
19778991 AAAGAAAGAAAAGTTGATAA
1 AAAGAAAGAAAAGTAGATAA
19779011 AAAGAAA-AAAA-TAGATA
1 AAAGAAAGAAAAGTAGATA
19779028 TATATTAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 4 0.25
20 7 0.44
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (20 bp):
AAAGAAAGAAAAGTAGATAA
Found at i:19787393 original size:16 final size:16
Alignment explanation
Indices: 19787372--19787412 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
19787362 TTAAAAATAT
19787372 ATTTTTCTTTTTAAAA
1 ATTTTTCTTTTTAAAA
*
19787388 ATTTTTC-TTTTAACA
1 ATTTTTCTTTTTAAAA
*
19787403 TTTTTTCTTT
1 ATTTTTCTTT
19787413 CTTTTTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTTCTTTTTAAAA
Found at i:19815393 original size:24 final size:23
Alignment explanation
Indices: 19815358--19815404 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
19815348 AAGAGTTAAT
19815358 TTGTCAATGCAAATATAAAATAAA
1 TTGTCAATGCAAAT-TAAAATAAA
*
19815382 TTGTCAGA-GCAAATTAAGATAAA
1 TTGTCA-ATGCAAATTAAAATAAA
19815405 AATGAATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 12 0.57
25 1 0.05
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.28
Consensus pattern (23 bp):
TTGTCAATGCAAATTAAAATAAA
Found at i:19821482 original size:30 final size:29
Alignment explanation
Indices: 19821446--19821645 Score: 120
Period size: 29 Copynumber: 6.8 Consensus size: 29
19821436 AAAACGGTGA
*
19821446 TTTTGGACACTTTAGGGGCAAAATGGTAAT
1 TTTTGGACA-TTTAGGGGCAAAATGATAAT
** * * **
19821476 TTTTGGATGTTTGGGGGTAAAAACATAAT
1 TTTTGGACATTTAGGGGCAAAATGATAAT
*
19821505 TTTTGGAAAGTTT-GGGGTCAAAAAT-ATAAT
1 TTTTGGACA-TTTAGGGG-C-AAAATGATAAT
* * *
19821535 TTTTGGACA-TTCGAGGGTAAAATGGTAAT
1 TTTTGGACATTTAG-GGGCAAAATGATAAT
* * *
19821564 TTTTGGAAATTTCAGGGTCAAAAAT-AGAAT
1 TTTTGGACATTT-AGGGGC-AAAATGATAAT
** * *
19821594 TTTTGGACATCCAAGGGTAAAATGATAAT
1 TTTTGGACATTTAGGGGCAAAATGATAAT
* *
19821623 TTTTGGAAATTTTGGGGTCAAAA
1 TTTTGGACATTTAGGGG-CAAAA
19821646 ATTGAATTTT
Statistics
Matches: 126, Mismatches: 33, Indels: 22
0.70 0.18 0.12
Matches are distributed among these distances:
28 12 0.10
29 58 0.46
30 46 0.37
31 10 0.08
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.35
Consensus pattern (29 bp):
TTTTGGACATTTAGGGGCAAAATGATAAT
Found at i:19821535 original size:59 final size:58
Alignment explanation
Indices: 19821472--19821779 Score: 273
Period size: 59 Copynumber: 5.2 Consensus size: 58
19821462 GGCAAAATGG
** * * **
19821472 TAATTTTTGGATGTTTGGGGGTAAAAACATAATTTTTGGAAAGTTTGGGGTCAAAAATA
1 TAATTTTTGGACATTCGAGGGTAAAATGATAATTTTTGGAAA-TTTGGGGTCAAAAATA
* *
19821531 TAATTTTTGGACATTCGAGGGTAAAATGGTAATTTTTGGAAATTTCAGGGTCAAAAATA
1 TAATTTTTGGACATTCGAGGGTAAAATGATAATTTTTGGAAATTT-GGGGTCAAAAATA
* * *
19821590 GAATTTTTGGACATCCAAGGGTAAAATGATAATTTTTGGAAATTTTGGGGTCAAAAAT-
1 TAATTTTTGGACATTCGAGGGTAAAATGATAATTTTTGGAAA-TTTGGGGTCAAAAATA
* * * * **
19821648 TGAATTTTCGAACATCCGAGGGTAAAATTG-TAACTTTTGGAAAGTTCAGGGTCAAAAATGA
1 T-AATTTTTGGACATTCGAGGGTAAAA-TGATAATTTTTGGAAA-TTTGGGGTCAAAAAT-A
* ** * * * **
19821709 -AATTTTTGGACATCCG-GAGGTAAAATGGCAATTTTTGAAAAGTTCGGGATCAAAAAGG
1 TAATTTTTGGACATTCGAG-GGTAAAATGATAATTTTTGGAAA-TTTGGGGTCAAAAATA
*
19821767 GAATTTTTGGACA
1 TAATTTTTGGACA
19821780 ATTTAGGGAC
Statistics
Matches: 210, Mismatches: 30, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
58 6 0.03
59 199 0.95
60 5 0.02
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.33
Consensus pattern (58 bp):
TAATTTTTGGACATTCGAGGGTAAAATGATAATTTTTGGAAATTTGGGGTCAAAAATA
Found at i:19821622 original size:118 final size:116
Alignment explanation
Indices: 19821490--19821779 Score: 366
Period size: 118 Copynumber: 2.5 Consensus size: 116
19821480 GGATGTTTGG
** *
19821490 GGGTAAAAACATAATTTTTGGAAAGTTTGGGGTCAAAAATATAATTTTTGGACATTCGAGGGTAA
1 GGGTAAAATGATAATTTTTGGAAAGTTTGGGGTCAAAAAT-TAATTTTTGGACATCCGAGGGTAA
* *
19821555 AATGGTAATTTTTGGAAATTTCAGGGTCAAAAAT-AGAATTTTTGGACATCCAA
65 AATGGTAACTTTTGGAAAGTTCAGGGTCAAAAATGA-AATTTTTGGACATCC-A
* * *
19821608 GGGTAAAATGATAATTTTTGGAAATTTTGGGGTCAAAAATTGAATTTTCGAACATCCGAGGGTAA
1 GGGTAAAATGATAATTTTTGGAAAGTTTGGGGTCAAAAATT-AATTTTTGGACATCCGAGGGTAA
* *
19821673 AATTGTAACTTTTGGAAAGTTCAGGGTCAAAAATGAAATTTTTGGACATCCG
65 AATGGTAACTTTTGGAAAGTTCAGGGTCAAAAATGAAATTTTTGGACATCCA
** * * * **
19821725 GAGGTAAAATGGCAATTTTTGAAAAGTTCGGGATCAAAAAGGGAATTTTTGGACA
1 G-GGTAAAATGATAATTTTTGGAAAGTTTGGGGTCAAAAA-TTAATTTTTGGACA
19821780 ATTTAGGGAC
Statistics
Matches: 148, Mismatches: 20, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
117 2 0.01
118 145 0.98
119 1 0.01
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32
Consensus pattern (116 bp):
GGGTAAAATGATAATTTTTGGAAAGTTTGGGGTCAAAAATTAATTTTTGGACATCCGAGGGTAAA
ATGGTAACTTTTGGAAAGTTCAGGGTCAAAAATGAAATTTTTGGACATCCA
Found at i:19821718 original size:30 final size:29
Alignment explanation
Indices: 19821502--19821787 Score: 137
Period size: 30 Copynumber: 9.7 Consensus size: 29
19821492 GTAAAAACAT
**
19821502 AATTTTTGGAAAGTTTGGGGTCAAAAAT-A
1 AATTTTTGGAAA-TTCAGGGTCAAAAATGA
* *
19821531 TAATTTTTGGACATTCGAGGGT--AAAATGGT
1 -AATTTTTGGAAATTC-AGGGTCAAAAAT-GA
19821561 AATTTTTGGAAATTTCAGGGTCAAAAAT-A
1 AATTTTTGGAAA-TTCAGGGTCAAAAATGA
* *
19821590 GAATTTTTGGACATCCAAGGGT--AAAATGA
1 -AATTTTTGGAAATTC-AGGGTCAAAAATGA
**
19821619 TAATTTTTGGAAATTTTGGGGTCAAAAATTG-
1 -AATTTTTGGAAA-TTCAGGGTCAAAAA-TGA
* * * *
19821650 AA-TTTTCGAACATCCGAGGGT-AAAATTGT
1 AATTTTTGGAA-ATTC-AGGGTCAAAAATGA
*
19821679 AACTTTTGGAAAGTTCAGGGTCAAAAATGA
1 AATTTTTGGAAA-TTCAGGGTCAAAAATGA
* * * *
19821709 AATTTTTGGACATCCGGAGGT--AAAATGGC
1 AATTTTTGGAAATTCAG-GGTCAAAAAT-GA
* * *
19821738 AATTTTTGAAAAGTTC-GGGATCAAAAAGGG
1 AATTTTTGGAAA-TTCAGGG-TCAAAAATGA
*
19821768 AATTTTTGGACAATTTAGGG
1 AATTTTTGGA-AATTCAGGG
19821788 ACCTTTTGGG
Statistics
Matches: 195, Mismatches: 34, Indels: 53
0.69 0.12 0.19
Matches are distributed among these distances:
28 19 0.10
29 72 0.37
30 84 0.43
31 18 0.09
32 2 0.01
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.33
Consensus pattern (29 bp):
AATTTTTGGAAATTCAGGGTCAAAAATGA
Found at i:19822930 original size:16 final size:19
Alignment explanation
Indices: 19822894--19822931 Score: 55
Period size: 16 Copynumber: 2.2 Consensus size: 19
19822884 CTTGTAAAAA
19822894 TGGACACTTTGTTTGTATT
1 TGGACACTTTGTTTGTATT
19822913 TGGAC-CTTT-TTT-TATT
1 TGGACACTTTGTTTGTATT
19822929 TGG
1 TGG
19822932 GATTTTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 3 0.16
18 4 0.21
19 5 0.26
ACGTcount: A:0.13, C:0.11, G:0.21, T:0.55
Consensus pattern (19 bp):
TGGACACTTTGTTTGTATT
Found at i:19822965 original size:6 final size:6
Alignment explanation
Indices: 19822943--19823011 Score: 65
Period size: 6 Copynumber: 12.0 Consensus size: 6
19822933 ATTTTATTCT
* *
19822943 TTTAAA TTTAGAA --TAAA TTTAAA CTTAAA -ATAAA TTTAAA TTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
**
19822989 -ACAAA TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
19823012 ATAAACTTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
4 2 0.04
5 9 0.18
6 38 0.75
7 2 0.04
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:19823012 original size:23 final size:23
Alignment explanation
Indices: 19822973--19823021 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
19822963 AAACTTAAAA
*
19822973 TAAATTTAAATTTAAAACAAATT
1 TAAATTTAAATTTAAAACAAACT
*
19822996 TAAATTTAAATTTAAAATAAACT
1 TAAATTTAAATTTAAAACAAACT
19823019 TAA
1 TAA
19823022 TCTTAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (23 bp):
TAAATTTAAATTTAAAACAAACT
Found at i:19823021 original size:17 final size:17
Alignment explanation
Indices: 19822943--19823005 Score: 99
Period size: 17 Copynumber: 3.7 Consensus size: 17
19822933 ATTTTATTCT
*
19822943 TTTAAATTTAGAATAAA
1 TTTAAATTTAAAATAAA
*
19822960 TTTAAACTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
19822977 TTTAAATTTAAAACAAA
1 TTTAAATTTAAAATAAA
19822994 TTTAAATTTAAA
1 TTTAAATTTAAA
19823006 TTTAAAATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:19823027 original size:23 final size:22
Alignment explanation
Indices: 19822956--19823028 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 22
19822946 AAATTTAGAA
* *
19822956 TAAATTTAAACTTAAAATAAATT
1 TAAATTTAAA-ATAAAATTAATT
* *
19822979 TAAATTTAAAACAAATTTAAATT
1 TAAATTTAAAATAAAATT-AATT
*
19823002 TAAATTTAAAATAAACTTAATCT
1 TAAATTTAAAATAAAATTAAT-T
19823025 TAAA
1 TAAA
19823029 ATAAATTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
22 7 0.17
23 35 0.83
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATTTAAAATAAAATTAATT
Found at i:19823689 original size:209 final size:209
Alignment explanation
Indices: 19823329--19824087 Score: 1302
Period size: 209 Copynumber: 3.6 Consensus size: 209
19823319 TGGTTTGGTA
* ** *
19823329 TCATTGATTTGGTCTACTTCTCAGTGTCTCATCAAGAAGATGACCGCATCACTTGTTTCAATCCG
1 TCATTGATTTGGTCTTCTTCTCAGTACCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCG
*
19823394 CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAC
66 CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAGGAAGCTAAC
* **
19823459 CATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTCACTCA
131 CATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
*
19823524 CTTTGAGCCTGGCT
196 CTTTGAGCTTGGCT
* *
19823538 TCATTGATTTGGTCTTCTTCTCAGTACCTCATCAGGAAGATGACCGTATCACTTGTTTCAATCTG
1 TCATTGATTTGGTCTTCTTCTCAGTACCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCG
* *
19823603 CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGTTAAC
66 CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAGGAAGCTAAC
19823668 CATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
131 CATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
19823733 CTTTGAGCTTGGCT
196 CTTTGAGCTTGGCT
**
19823747 TCATTGATTTGGTCTTCTTCTCAGTACCTCATCAGGAAGATGATTGCATCACTTGTTTCAATCCG
1 TCATTGATTTGGTCTTCTTCTCAGTACCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCG
* * *
19823812 CTTCTCTATATCTCATCAGGAAGACGAATTTGGTCCAGTTCTCAATATCTTATCAGGAAGCTAAC
66 CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAGGAAGCTAAC
* * * *
19823877 CATTTTATTACTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTTGAAGATTTGCTCA
131 CATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
19823942 CTTTGAGCTTGGCT
196 CTTTGAGCTTGGCT
*
19823956 TCATTGATTTGGTCTTCTTCTCAATACCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCG
1 TCATTGATTTGGTCTTCTTCTCAGTACCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCG
*
19824021 CTTCTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAGGAAGCTAAC
66 CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAGGAAGCTAAC
19824086 CA
131 CA
19824088 GCTCATTGTT
Statistics
Matches: 519, Mismatches: 31, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
209 519 1.00
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (209 bp):
TCATTGATTTGGTCTTCTTCTCAGTACCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCG
CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATCAGGAAGCTAAC
CATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
CTTTGAGCTTGGCT
Found at i:19836327 original size:58 final size:59
Alignment explanation
Indices: 19836228--19836565 Score: 364
Period size: 59 Copynumber: 5.8 Consensus size: 59
19836218 CAAAAATGTA
* * * *
19836228 AAAAT-GTAATTTTTAGAAAGTTCGGGGTCAAAAATGCAATTTTTGGACATCCTAGGGT
1 AAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAAATGGAATTTTTGGACATCCGAGGGT
* * *
19836286 -AAATGGTAATTTTTGGAAATTTTGGAGT-AAATAATGGAATTTTTGAACATCCGAGGGT
1 AAAATGGTAATTTTTGGAAAGTTTGGGGTCAAA-AATGGAATTTTTGGACATCCGAGGGT
* ** * * ** * *
19836344 AAAATGGGAATTTTTAAAAATTTTAGGGTTTAAAATGGAATTTTCGGACATCCGA-GCT
1 AAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAAATGGAATTTTTGGACATCCGAGGGT
* ** * * *
19836402 AAAATGGTATTTTTTGGAAA-TTTCAAGGTCAAAAAAGGAATTTTTGAACATTCGAGGGT
1 AAAATGGTAATTTTTGGAAAGTTT-GGGGTCAAAAATGGAATTTTTGGACATCCGAGGGT
* * * *
19836461 AAAATGCTAACTTTTGGAAAGTTTGGGGTCAAAAATGAAATTTTTGGACAT-CTAGGGGT
1 AAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAAATGGAATTTTTGGACATCCGA-GGGT
*
19836520 AAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAAAGGGAATTTTTG
1 AAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAAATGGAATTTTTG
19836566 TCAGTTTATG
Statistics
Matches: 231, Mismatches: 41, Indels: 15
0.80 0.14 0.05
Matches are distributed among these distances:
57 10 0.04
58 86 0.37
59 130 0.56
60 5 0.02
ACGTcount: A:0.35, C:0.07, G:0.24, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAAGTTTGGGGTCAAAAATGGAATTTTTGGACATCCGAGGGT
Found at i:19836354 original size:29 final size:29
Alignment explanation
Indices: 19836321--19836466 Score: 93
Period size: 29 Copynumber: 5.0 Consensus size: 29
19836311 AGTAAATAAT
*
19836321 GGAATTTTTGAACATCCGAGGGTAAAATG
1 GGAATTTTTGAACATTCGAGGGTAAAATG
* * **
19836350 GGAATTTTTAAAAATTTTAGGGTTTAAAAT-
1 GGAATTTTTGAACATTCGAGGG--TAAAATG
* * * *
19836380 GGAATTTTCGGACATCCGA-GCTAAAATG
1 GGAATTTTTGAACATTCGAGGGTAAAATG
* * * **
19836408 GTATTTTTTGGAA-ATTTC-AAGGTCAAAAAA
1 GGAATTTTT-GAACA-TTCGAGGGT-AAAATG
19836438 GGAATTTTTGAACATTCGAGGGTAAAATG
1 GGAATTTTTGAACATTCGAGGGTAAAATG
19836467 CTAACTTTTG
Statistics
Matches: 82, Mismatches: 26, Indels: 18
0.65 0.21 0.14
Matches are distributed among these distances:
27 6 0.07
28 8 0.10
29 34 0.41
30 28 0.34
31 6 0.07
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.33
Consensus pattern (29 bp):
GGAATTTTTGAACATTCGAGGGTAAAATG
Found at i:19836379 original size:117 final size:117
Alignment explanation
Indices: 19836238--19836565 Score: 367
Period size: 117 Copynumber: 2.8 Consensus size: 117
19836228 AAAATGTAAT
* ** *
19836238 TTTTAGAAAGTTCGGGGTCAAAAATGCAATTTTTGGACATCCTAGGGT-AAATGGTAATTTTTGG
1 TTTTAAAAAGTTTAGGGTCAAAAATGAAATTTTTGGACATCCTAGGGTAAAATGGTAATTTTTGG
* * *
19836302 AAATTTTGGAGT-AAATAATGGAATTTTTGAACATCCGAGGGTAAAATGGGAAT
66 AAA-TTTGGAGTCAAA-AAAGGAATTTTTGAACATCCGAGGGTAAAATGCGAAC
* ** * * * * *
19836355 TTTTAAAAATTTTAGGGTTTAAAATGGAATTTTCGGACATCCGA-GCTAAAATGGTATTTTTTGG
1 TTTTAAAAAGTTTAGGGTCAAAAATGAAATTTTTGGACATCCTAGGGTAAAATGGTAATTTTTGG
** * *
19836419 AAATTTCAAGGTCAAAAAAGGAATTTTTGAACATTCGAGGGTAAAATGCTAAC
66 AAATTTGGA-GTCAAAAAAGGAATTTTTGAACATCCGAGGGTAAAATGCGAAC
** *
19836472 TTTTGGAAAGTTTGGGGTCAAAAATGAAATTTTTGGACAT-CTAGGGGTAAAATGGTAATTTTTG
1 TTTTAAAAAGTTTAGGGTCAAAAATGAAATTTTTGGACATCCTA-GGGTAAAATGGTAATTTTTG
* *
19836536 GAAAGTTTGGGGTCAAAAAGGGAATTTTTG
65 GAAA-TTTGGAGTCAAAAAAGGAATTTTTG
19836566 TCAGTTTATG
Statistics
Matches: 172, Mismatches: 33, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
116 8 0.05
117 119 0.69
118 42 0.24
119 3 0.02
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.34
Consensus pattern (117 bp):
TTTTAAAAAGTTTAGGGTCAAAAATGAAATTTTTGGACATCCTAGGGTAAAATGGTAATTTTTGG
AAATTTGGAGTCAAAAAAGGAATTTTTGAACATCCGAGGGTAAAATGCGAAC
Found at i:19836489 original size:29 final size:29
Alignment explanation
Indices: 19836457--19836553 Score: 101
Period size: 29 Copynumber: 3.3 Consensus size: 29
19836447 GAACATTCGA
*
19836457 GGGT-AAAATGCTAACTTTTGGAAAGTTTG
1 GGGTCAAAATG-TAATTTTTGGAAAGTTTG
* * *
19836486 GGGTCAAAAATGAAATTTTTGGACA-TCTAG
1 GGGTC-AAAATGTAATTTTTGGAAAGT-TTG
19836516 GGGT-AAAATGGTAATTTTTGGAAAGTTTG
1 GGGTCAAAAT-GTAATTTTTGGAAAGTTTG
19836545 GGGTCAAAA
1 GGGTCAAAA
19836554 AGGGAATTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
28 5 0.09
29 23 0.42
30 21 0.38
31 6 0.11
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.32
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTTGGAAAGTTTG
Found at i:19836508 original size:30 final size:30
Alignment explanation
Indices: 19836472--19836565 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
19836462 AAATGCTAAC
19836472 TTTTGGAAAGTTTGGGGTCAAAAATGAAAT
1 TTTTGGAAAGTTTGGGGTCAAAAATGAAAT
* * *
19836502 TTTTGGACA-TCTAGGGGT--AAAATGGTAAT
1 TTTTGGAAAGT-TTGGGGTCAAAAAT-GAAAT
* *
19836531 TTTTGGAAAGTTTGGGGTCAAAAAGGGAAT
1 TTTTGGAAAGTTTGGGGTCAAAAATGAAAT
19836561 TTTTG
1 TTTTG
19836566 TCAGTTTATG
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
28 5 0.10
29 19 0.37
30 24 0.46
31 4 0.08
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (30 bp):
TTTTGGAAAGTTTGGGGTCAAAAATGAAAT
Found at i:19838404 original size:6 final size:6
Alignment explanation
Indices: 19838382--19838450 Score: 74
Period size: 6 Copynumber: 12.0 Consensus size: 6
19838372 CTTTTATTCT
*
19838382 TTTAAA TTTAGAA --TAAA TTTAAA CTTAAA -TTAAA TTTAAA TTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
**
19838428 -ACAAA TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
19838451 ATAAACTTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
4 2 0.04
5 10 0.19
6 39 0.74
7 2 0.04
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:19838451 original size:23 final size:22
Alignment explanation
Indices: 19838395--19838469 Score: 80
Period size: 23 Copynumber: 3.2 Consensus size: 22
19838385 AAATTTAGAA
19838395 TAAATTT-AAACTTAAATTAAATT
1 TAAATTTAAAAC--AAATTAAATT
19838418 TAAATTTAAAACAAATTTAAATT
1 TAAATTTAAAACAAA-TTAAATT
*
19838441 TAAATTTAAAATAAACTTAATATT
1 TAAATTTAAAACAAA-TTAA-ATT
*
19838465 AAAAT
1 TAAAT
19838470 AAACTTAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
22 3 0.07
23 32 0.70
24 11 0.24
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATTTAAAACAAATTAAATT
Found at i:19838460 original size:17 final size:17
Alignment explanation
Indices: 19838382--19838444 Score: 90
Period size: 17 Copynumber: 3.7 Consensus size: 17
19838372 CTTTTATTCT
*
19838382 TTTAAATTTAGAATAAA
1 TTTAAATTTAAAATAAA
* *
19838399 TTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAA
*
19838416 TTTAAATTTAAAACAAA
1 TTTAAATTTAAAATAAA
19838433 TTTAAATTTAAA
1 TTTAAATTTAAA
19838445 TTTAAAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:19838479 original size:11 final size:11
Alignment explanation
Indices: 19838384--19838460 Score: 66
Period size: 11 Copynumber: 6.8 Consensus size: 11
19838374 TTTATTCTTT
*
19838384 TAAATTTAGAA
1 TAAATTTAAAA
*
19838395 TAAATTTAAACT
1 TAAATTTAAA-A
*
19838407 TAAA-TTAAATT
1 TAAATTTAAA-A
19838418 TAAATTTAAAA
1 TAAATTTAAAA
* *
19838429 CAAATTTAAATT
1 TAAATTTAAA-A
19838441 TAAATTTAAAA
1 TAAATTTAAAA
*
19838452 TAAACTTAA
1 TAAATTTAA
19838461 TATTAAAATA
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
11 36 0.67
12 18 0.33
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:19843225 original size:18 final size:18
Alignment explanation
Indices: 19843197--19843235 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
19843187 TATTTTTAGA
*
19843197 AAAATTAATTTTATAGTTT
1 AAAATTAATTTT-TAGGTT
19843216 AAAA-TAATTTTTAGGTT
1 AAAATTAATTTTTAGGTT
19843233 AAA
1 AAA
19843236 TAAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 7 0.37
19 4 0.21
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (18 bp):
AAAATTAATTTTTAGGTT
Found at i:19859694 original size:11 final size:11
Alignment explanation
Indices: 19859675--19859722 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
19859665 TCACACCAGC
*
19859675 AAATGATTTTA
1 AAATTATTTTA
19859686 AAATTATTTTTA
1 AAATTA-TTTTA
19859698 AAA--ATTATTA
1 AAATTATT-TTA
19859708 AAATTATTTTA
1 AAATTATTTTA
19859719 AAAT
1 AAAT
19859723 CATAATTATC
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
9 2 0.06
10 7 0.22
11 12 0.38
12 11 0.34
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:19859703 original size:13 final size:12
Alignment explanation
Indices: 19859681--19859722 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 12
19859671 CAGCAAATGA
19859681 TTTTAAAATTAT
1 TTTTAAAATTAT
19859693 TTTTAAAA--AT
1 TTTTAAAATTAT
*
19859703 TATTAAAATTA-
1 TTTTAAAATTAT
19859714 TTTTAAAAT
1 TTTTAAAAT
19859723 CATAATTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 9 0.35
11 8 0.31
12 9 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTTAAAATTAT
Found at i:19864315 original size:30 final size:30
Alignment explanation
Indices: 19864186--19864315 Score: 75
Period size: 30 Copynumber: 4.1 Consensus size: 30
19864176 ATAATTCTCA
* ** * **
19864186 ATATCTCGTTTAGGAATTTGAGAAGACACG
1 ATATCTCGTTCAGGAGCTTGGGAAGATTCG
**
19864216 ATATCTCAATCAGGAGCTTGGGAAGACTT-G
1 ATATCTCGTTCAGGAGCTTGGGAAGA-TTCG
* * *
19864246 ATATCTCGTTCAAGATCTTCGGATTGAGAAGA-CCTG
1 ATATCTCGTTCAGGAGCTT--G---G-GAAGATTC-G
19864282 ATATCTCGTTCAGGAGCTTGGGAAGATTCG
1 ATATCTCGTTCAGGAGCTTGGGAAGATTCG
19864312 ATAT
1 ATAT
19864316 TTGATTTTTC
Statistics
Matches: 74, Mismatches: 16, Indels: 20
0.67 0.15 0.18
Matches are distributed among these distances:
30 46 0.62
31 2 0.03
32 1 0.01
34 1 0.01
35 1 0.01
36 23 0.31
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (30 bp):
ATATCTCGTTCAGGAGCTTGGGAAGATTCG
Found at i:19873795 original size:36 final size:35
Alignment explanation
Indices: 19873749--19873823 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 35
19873739 TACAGCTTAG
19873749 AAAAATGTCAAATTCATATATCAAATTAAACAAAA
1 AAAAATGTCAAATTCATATATCAAATTAAACAAAA
*
19873784 AAAAATTGTCAAATTCATATATCAAATTAAACAAAT
1 AAAAA-TGTCAAATTCATATATCAAATTAAACAAAA
19873820 AAAA
1 AAAA
19873824 TTAAGTACAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 5 0.13
36 33 0.87
ACGTcount: A:0.60, C:0.11, G:0.03, T:0.27
Consensus pattern (35 bp):
AAAAATGTCAAATTCATATATCAAATTAAACAAAA
Found at i:19875610 original size:12 final size:13
Alignment explanation
Indices: 19875588--19875636 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
19875578 GTAGAAAAAT
*
19875588 AAGAGAAAAGGAG
1 AAGAGAAAAGGAA
19875601 AAGA-AAAAGGAA
1 AAGAGAAAAGGAA
19875613 AAGAAGAAAAGGAA
1 AAG-AGAAAAGGAA
*
19875627 AAGAAAAAAG
1 AAGAGAAAAG
19875637 AAGAGAAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 10 0.31
13 11 0.34
14 11 0.34
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (13 bp):
AAGAGAAAAGGAA
Found at i:19875619 original size:15 final size:15
Alignment explanation
Indices: 19875599--19875647 Score: 61
Period size: 14 Copynumber: 3.5 Consensus size: 15
19875589 AGAGAAAAGG
19875599 AGAAGAAAAAGGAAA
1 AGAAGAAAAAGGAAA
19875614 AGAAG-AAAAGGAAA
1 AGAAGAAAAAGGAAA
*
19875628 AG-A-AAAAA-GAAG
1 AGAAGAAAAAGGAAA
19875640 AGAAGAAA
1 AGAAGAAA
19875648 TGGAGATGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 5 0.17
13 6 0.20
14 14 0.47
15 5 0.17
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (15 bp):
AGAAGAAAAAGGAAA
Found at i:19875624 original size:26 final size:26
Alignment explanation
Indices: 19875591--19875653 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
19875581 GAAAAATAAG
*
19875591 AGAAAAGGAGAAGAAAAAGGAAAAGA
1 AGAAAAGGAGAAGAAAAAAGAAAAGA
* *
19875617 AGAAAAGGAAAAGAAAAAAGAAGAGA
1 AGAAAAGGAGAAGAAAAAAGAAAAGA
*
19875643 AGAAATGGAGA
1 AGAAAAGGAGA
19875654 TGTCATCCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (26 bp):
AGAAAAGGAGAAGAAAAAAGAAAAGA
Found at i:19877047 original size:23 final size:23
Alignment explanation
Indices: 19877015--19877114 Score: 119
Period size: 23 Copynumber: 4.3 Consensus size: 23
19877005 TAGCGCAAAT
* *
19877015 CAGTAGGCACACGAGGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
19877038 CAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
* *
19877061 CAGTAAGCACACAAAGTACGAAA
1 CAGTAAGCACACGAAGTGCGAAA
* * **
19877084 TAGTAAGCATAAAAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
*
19877107 CTGTAAGC
1 CAGTAAGC
19877115 GCGCTAGTGT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 67 1.00
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (23 bp):
CAGTAAGCACACGAAGTGCGAAA
Found at i:19884333 original size:23 final size:23
Alignment explanation
Indices: 19884188--19884336 Score: 108
Period size: 23 Copynumber: 6.5 Consensus size: 23
19884178 TAGTGCTGGG
19884188 GAAACAGTAAGCACACACAA-TGC
1 GAAACAGTAAGCACACA-AAGTGC
* * *
19884211 -AATCCAGTAGGCACACACAGTGC
1 GAA-ACAGTAAGCACACAAAGTGC
* * * * *
19884234 -CATCAGTAGGCATACATAGTGC
1 GAAACAGTAAGCACACAAAGTGC
* * * *
19884256 -AAATCAGCAGGCACACGAGGTGC
1 GAAA-CAGTAAGCACACAAAGTGC
*
19884279 GAAACAGTAAGCACACGAAGTGC
1 GAAACAGTAAGCACACAAAGTGC
*
19884302 GAAACAGTAAGCACGCAAAGTGC
1 GAAACAGTAAGCACACAAAGTGC
*
19884325 GAAATAGTAAGC
1 GAAACAGTAAGC
19884337 GCGCTAGTGT
Statistics
Matches: 102, Mismatches: 20, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
22 21 0.21
23 78 0.76
24 3 0.03
ACGTcount: A:0.40, C:0.23, G:0.24, T:0.12
Consensus pattern (23 bp):
GAAACAGTAAGCACACAAAGTGC
Found at i:19890849 original size:58 final size:58
Alignment explanation
Indices: 19890688--19890854 Score: 214
Period size: 58 Copynumber: 2.9 Consensus size: 58
19890678 ATATTATATA
* * *
19890688 TTATGATTTTTATT-AATTCATATTTTAATAATAATTATATTAAAAATGTTATTAAATTAT
1 TTATTATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAATTAT
* * *
19890748 ATATT-TTTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATTAT
1 TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAT
*
19890805 TTATTATTTTTATTAAATTATATTTAATAATAATCT-TATTAAAATTTAAT
1 TTATTATTTTTATTAAATTATATTTAATAATAAT-TATATTAAAATATAAT
19890855 AATAATAATC
Statistics
Matches: 94, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
57 20 0.21
58 56 0.60
59 11 0.12
60 7 0.07
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (58 bp):
TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAT
Found at i:19891572 original size:2 final size:2
Alignment explanation
Indices: 19891565--19891591 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19891555 TTGACCATAC
19891565 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 T
19891592 TCTATAGTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19896228 original size:51 final size:51
Alignment explanation
Indices: 19895985--19896220 Score: 305
Period size: 51 Copynumber: 4.6 Consensus size: 51
19895975 GCTATAAACG
*
19895985 AAAGAGTCTGATGACTAAGTGTCATCGTGAGTAAATGAAT-CATTTACGGATT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCA-TTACGGATT
* * * *
19896037 AAAGGTCTGATGACTAAGTGTCATCATGAGTAAACGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATTACGGATT
* *
19896088 AAAGGTCCGATAACTAAGTGTCATCGTGAGTAAACGAATCC-TCTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCAT-TACGGATT
* * * * *
19896139 AAAGGTCCGATGACTACGTGTCATTGTGAATAAATGAATCCATGACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATTACGGATT
* *
19896190 AAAAGTCCGATGACTCAGTGTCATCGTGAGT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGT
19896221 TTATGAATTT
Statistics
Matches: 163, Mismatches: 18, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
50 1 0.01
51 156 0.96
52 6 0.04
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.28
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATTACGGATT
Found at i:19900758 original size:15 final size:12
Alignment explanation
Indices: 19900721--19900745 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19900711 CGGCAAGCTC
19900721 TTCTTCTTCCTT
1 TTCTTCTTCCTT
19900733 TTCTTCTTCCTT
1 TTCTTCTTCCTT
19900745 T
1 T
19900746 CCCTCTTCTT
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (12 bp):
TTCTTCTTCCTT
Found at i:19908034 original size:25 final size:26
Alignment explanation
Indices: 19907978--19908036 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
19907968 TGAAAAGTGT
*
19907978 GCAAAGATGCAGCCACAAATTTAACC
1 GCAAAGATGCAGCCACAAATGTAACC
** * *
19908004 TAAAAG-TGCAGCCACAGATGTCACC
1 GCAAAGATGCAGCCACAAATGTAACC
19908029 GCAAAGAT
1 GCAAAGAT
19908037 ACCTTAACTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
25 20 0.80
26 5 0.20
ACGTcount: A:0.41, C:0.25, G:0.19, T:0.15
Consensus pattern (26 bp):
GCAAAGATGCAGCCACAAATGTAACC
Found at i:19909701 original size:19 final size:19
Alignment explanation
Indices: 19909677--19909761 Score: 107
Period size: 19 Copynumber: 4.5 Consensus size: 19
19909667 ATATGGAATT
* *
19909677 TGTGAACATGTGACATTAA
1 TGTGAATATGTGACATTTA
*
19909696 TGTGAATATGTGAAATTTA
1 TGTGAATATGTGACATTTA
*
19909715 TGTGAATATGTAACATTTA
1 TGTGAATATGTGACATTTA
* **
19909734 TGTGAATATGTGAAATAGA
1 TGTGAATATGTGACATTTA
19909753 TGTGAATAT
1 TGTGAATAT
19909762 CAAATGTGTT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 57 1.00
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.38
Consensus pattern (19 bp):
TGTGAATATGTGACATTTA
Found at i:19909731 original size:38 final size:38
Alignment explanation
Indices: 19909677--19909761 Score: 125
Period size: 38 Copynumber: 2.2 Consensus size: 38
19909667 ATATGGAATT
* * **
19909677 TGTGAACATGTGACATTAATGTGAATATGTGAAATTTA
1 TGTGAATATGTAACATTAATGTGAATATGTGAAATAGA
*
19909715 TGTGAATATGTAACATTTATGTGAATATGTGAAATAGA
1 TGTGAATATGTAACATTAATGTGAATATGTGAAATAGA
19909753 TGTGAATAT
1 TGTGAATAT
19909762 CAAATGTGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.38
Consensus pattern (38 bp):
TGTGAATATGTAACATTAATGTGAATATGTGAAATAGA
Found at i:19920899 original size:12 final size:11
Alignment explanation
Indices: 19920878--19920928 Score: 59
Period size: 12 Copynumber: 4.5 Consensus size: 11
19920868 CAATCACTTG
19920878 AAAAAGA-AAA
1 AAAAAGAGAAA
*
19920888 AAAATGAGAAA
1 AAAAAGAGAAA
19920899 AAGAAAGAGAAA
1 AA-AAAGAGAAA
19920911 AGAAAAGAAGAAA
1 A-AAAAG-AGAAA
19920924 AAAAA
1 AAAAA
19920929 ATTATTGCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 6 0.17
11 5 0.14
12 17 0.49
13 7 0.20
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (11 bp):
AAAAAGAGAAA
Found at i:19920909 original size:24 final size:25
Alignment explanation
Indices: 19920877--19920929 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
19920867 TCAATCACTT
19920877 GAAAAAGAAAA-AAAATG-AGAAAAA
1 GAAAAAGAAAAGAAAA-GAAGAAAAA
*
19920901 GAAAGAGAAAAGAAAAGAAGAAAAA
1 GAAAAAGAAAAGAAAAGAAGAAAAA
19920926 -AAAA
1 GAAAA
19920930 TTATTGCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (25 bp):
GAAAAAGAAAAGAAAAGAAGAAAAA
Found at i:19928249 original size:22 final size:22
Alignment explanation
Indices: 19928208--19928249 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
19928198 ATCAAATCTC
*
19928208 AATTTTTATTAAGTAGTTAATT
1 AATTTTTATTAAGTAATTAATT
* *
19928230 AATTTTTTTTAATTAATTAA
1 AATTTTTATTAAGTAATTAA
19928250 GTTAGTTCTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
AATTTTTATTAAGTAATTAATT
Found at i:19930529 original size:14 final size:15
Alignment explanation
Indices: 19930500--19930553 Score: 65
Period size: 14 Copynumber: 3.5 Consensus size: 15
19930490 ATACGGTCTT
19930500 TTTATTTTCTTATTTTA
1 TTTA-TTTCTT-TTTTA
19930517 TTTATTTCTTTTTTA
1 TTTATTTCTTTTTTA
*
19930532 -TTACTTCTTTTTTA
1 TTTATTTCTTTTTTA
*
19930546 TTTGTTTC
1 TTTATTTC
19930554 AATTTTAGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 13 0.39
15 10 0.30
16 6 0.18
17 4 0.12
ACGTcount: A:0.13, C:0.09, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTATTTCTTTTTTA
Found at i:19930559 original size:29 final size:28
Alignment explanation
Indices: 19930499--19930560 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
19930489 GATACGGTCT
**
19930499 TTTTATTTTCTTATTTTATTTATTTCTT
1 TTTTATTTTCTTATTTTATTTATTTCAA
*
19930527 TTTTATTACTTCTT-TTTTATTTGTTTCAA
1 TTTTATT--TTCTTATTTTATTTATTTCAA
19930556 TTTTA
1 TTTTA
19930561 GTTTATGACT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 7 0.24
29 17 0.59
30 5 0.17
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.74
Consensus pattern (28 bp):
TTTTATTTTCTTATTTTATTTATTTCAA
Found at i:19938835 original size:25 final size:24
Alignment explanation
Indices: 19938798--19938845 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
19938788 GAAATAATTC
19938798 ATGTTTAATTATTAAATATAATTTT
1 ATGTTTAATTATTAAAT-TAATTTT
*
19938823 ATGTCTTAA-TATTTAATTAATTT
1 ATGT-TTAATTATTAAATTAATTT
19938846 ATTTATGACT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 11 0.52
26 4 0.19
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (24 bp):
ATGTTTAATTATTAAATTAATTTT
Found at i:19940454 original size:22 final size:23
Alignment explanation
Indices: 19940424--19940467 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
19940414 AATGTTTTAT
*
19940424 TATGCAAG-AATAAAATCCTAAA
1 TATGAAAGAAATAAAATCCTAAA
*
19940446 TATGAAAGAAATAAACTCCTAA
1 TATGAAAGAAATAAAATCCTAA
19940468 GGACCTAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.55, C:0.14, G:0.09, T:0.23
Consensus pattern (23 bp):
TATGAAAGAAATAAAATCCTAAA
Found at i:19942609 original size:22 final size:23
Alignment explanation
Indices: 19942579--19942622 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
19942569 AGTGTTTTAT
*
19942579 TATGCAAG-AATAAAATCCTAAA
1 TATGAAAGAAATAAAATCCTAAA
*
19942601 TATGAAAGAAATAAACTCCTAA
1 TATGAAAGAAATAAAATCCTAA
19942623 GGACCTAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.55, C:0.14, G:0.09, T:0.23
Consensus pattern (23 bp):
TATGAAAGAAATAAAATCCTAAA
Found at i:19954690 original size:45 final size:45
Alignment explanation
Indices: 19954612--19954724 Score: 136
Period size: 45 Copynumber: 2.5 Consensus size: 45
19954602 TAACTGCATA
* * * *
19954612 TCGACATAAGTGGGCTATCATTGTCAAGTAACCCGGTGTAGCAAT
1 TCGACATAAGTGAGCTATCATTGCCAAGCAACCCGGGGTAGCAAT
* * *
19954657 TCGACATACGTGAGCTATCGTTGCCAGGCAACCCGGGGTAGCAAT
1 TCGACATAAGTGAGCTATCATTGCCAAGCAACCCGGGGTAGCAAT
* * *
19954702 TCAATATAAGTGAGCCATCATTG
1 TCGACATAAGTGAGCTATCATTG
19954725 TCGAGCAATT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (45 bp):
TCGACATAAGTGAGCTATCATTGCCAAGCAACCCGGGGTAGCAAT
Found at i:19955063 original size:19 final size:19
Alignment explanation
Indices: 19955039--19955082 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
19955029 ATTTGGAATT
* * *
19955039 TGTGAACATGTGACATTGA
1 TGTGAACATGTCAAATAGA
*
19955058 TGTGAATATGTCAAATAGA
1 TGTGAACATGTCAAATAGA
19955077 TGTGAA
1 TGTGAA
19955083 TATCAAATGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.32
Consensus pattern (19 bp):
TGTGAACATGTCAAATAGA
Found at i:19955090 original size:17 final size:18
Alignment explanation
Indices: 19955056--19955090 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19955046 ATGTGACATT
19955056 GATGTGAATATGTCAAATA
1 GATGTGAATA-GTCAAATA
19955075 GATGTGAATA-TCAAAT
1 GATGTGAATAGTCAAAT
19955091 GTGTTTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (18 bp):
GATGTGAATAGTCAAATA
Found at i:19956666 original size:18 final size:18
Alignment explanation
Indices: 19956640--19956677 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
19956630 TTGCCATCCA
* *
19956640 ATGTGCATGATATAATTT
1 ATGTCCATGAAATAATTT
19956658 ATGTCCATGAAATAATTT
1 ATGTCCATGAAATAATTT
19956676 AT
1 AT
19956678 ATCATGTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (18 bp):
ATGTCCATGAAATAATTT
Found at i:19958163 original size:24 final size:24
Alignment explanation
Indices: 19958131--19958228 Score: 196
Period size: 24 Copynumber: 4.1 Consensus size: 24
19958121 ATATGTATTT
19958131 TGTTAGGTGTTTGTACACCTGATA
1 TGTTAGGTGTTTGTACACCTGATA
19958155 TGTTAGGTGTTTGTACACCTGATA
1 TGTTAGGTGTTTGTACACCTGATA
19958179 TGTTAGGTGTTTGTACACCTGATA
1 TGTTAGGTGTTTGTACACCTGATA
19958203 TGTTAGGTGTTTGTACACCTGATA
1 TGTTAGGTGTTTGTACACCTGATA
19958227 TG
1 TG
19958229 CATTTTGTTT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 74 1.00
ACGTcount: A:0.20, C:0.12, G:0.26, T:0.42
Consensus pattern (24 bp):
TGTTAGGTGTTTGTACACCTGATA
Found at i:19984233 original size:21 final size:21
Alignment explanation
Indices: 19984209--19984304 Score: 131
Period size: 21 Copynumber: 4.6 Consensus size: 21
19984199 CTTATGACAG
*
19984209 TTCTACCAATACAAGTACA-GC
1 TTCTACCGATACAAGT-CATGC
* *
19984230 TTCTACAGAAACAAGTCATGC
1 TTCTACCGATACAAGTCATGC
*
19984251 TTCTACCGATATAAGTCATGC
1 TTCTACCGATACAAGTCATGC
*
19984272 TTCTACCGATATAAGTCATGC
1 TTCTACCGATACAAGTCATGC
19984293 TTCTACCGATAC
1 TTCTACCGATAC
19984305 TAAAAACTCT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 2 0.03
21 65 0.97
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.29
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATGC
Found at i:19985519 original size:19 final size:19
Alignment explanation
Indices: 19985495--19985531 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19985485 CACATTAAAT
19985495 ACACAATTAGATCATTTTA
1 ACACAATTAGATCATTTTA
* *
19985514 ACACAATTTGATCCTTTT
1 ACACAATTAGATCATTTT
19985532 TGGAAAAATT
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:0.35, C:0.19, G:0.05, T:0.41
Consensus pattern (19 bp):
ACACAATTAGATCATTTTA
Found at i:19997426 original size:17 final size:17
Alignment explanation
Indices: 19997401--19997438 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
19997391 ATGCATCTCA
19997401 TTTAATTGTCATTGCAT
1 TTTAATTGTCATTGCAT
*
19997418 TTTAGTTGTCATTGCAT
1 TTTAATTGTCATTGCAT
19997435 TTTA
1 TTTA
19997439 CTTATTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.11, G:0.13, T:0.55
Consensus pattern (17 bp):
TTTAATTGTCATTGCAT
Found at i:19998059 original size:16 final size:16
Alignment explanation
Indices: 19998026--19998064 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
19998016 ATCACGTATA
*
19998026 AAAAAAAGAGAAGAAG
1 AAAAAAAGAAAAGAAG
* *
19998042 AAAAAGAGAAAAGCAG
1 AAAAAAAGAAAAGAAG
19998058 AAAAAAA
1 AAAAAAA
19998065 ATATATTGCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.77, C:0.03, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAAGAAG
Found at i:19999863 original size:45 final size:45
Alignment explanation
Indices: 19999781--19999882 Score: 132
Period size: 45 Copynumber: 2.3 Consensus size: 45
19999771 GGCAGATCAG
* * * *
19999781 TGAGCTATCATTGCCAGGCAACCTGGGGTAGCAATTCAATATAAA
1 TGAGCCATCATTGCCAGGAAACCAGGGGTACCAATTCAATATAAA
* * * *
19999826 TGAGCCATCGTTGTCAGGAAACCAGGGGTACCTATTCAATATAAG
1 TGAGCCATCATTGCCAGGAAACCAGGGGTACCAATTCAATATAAA
19999871 TGAGCCATCATT
1 TGAGCCATCATT
19999883 ACCGGGCAAC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (45 bp):
TGAGCCATCATTGCCAGGAAACCAGGGGTACCAATTCAATATAAA
Found at i:20000220 original size:19 final size:19
Alignment explanation
Indices: 20000196--20000261 Score: 87
Period size: 19 Copynumber: 3.5 Consensus size: 19
20000186 ATATGGAATT
*
20000196 TGTGAACATGTGACATTGA
1 TGTGAATATGTGACATTGA
* *
20000215 TGTGAATATGTCACATTTA
1 TGTGAATATGTGACATTGA
* *
20000234 TGTGAATATGTGAAATAGA
1 TGTGAATATGTGACATTGA
20000253 TGTGAATAT
1 TGTGAATAT
20000262 CAAATGTGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.36
Consensus pattern (19 bp):
TGTGAATATGTGACATTGA
Found at i:20014438 original size:101 final size:102
Alignment explanation
Indices: 20014250--20014463 Score: 306
Period size: 101 Copynumber: 2.1 Consensus size: 102
20014240 AAATCAAGGC
* * ** *
20014250 AATATTATTTTATTTTAGGGAACTCGAGAAATTGTGTTCTAATGTATTAGGTATGGTTTTTCTTT
1 AATATTCTTTTATTTTAGGGAACTCAAGAAATTGTCCTCTAATGTACTAGGTATGGTTTTTCTTT
* *
20014315 GAACATAAGTGATTGAATATCCTATTTAAAATCGATA
66 GAACATAAGTAATTGAATATCCTATTTAAAATCAATA
* *
20014352 AATGTTCTTTTATTTTAGGGAACTCAAGAAATTGTACCT-TAATGT-CTGGGTATGGTTTTTCTT
1 AATATTCTTTTATTTTAGGGAACTCAAGAAATTGT-CCTCTAATGTACTAGGTATGGTTTTTCTT
* *
20014415 TGAACCTAAGTAATTTAATATCCTATTTAAAATCAATA
65 TGAACATAAGTAATTGAATATCCTATTTAAAATCAATA
20014453 AATATTCTTTT
1 AATATTCTTTT
20014464 CAAATATTCA
Statistics
Matches: 99, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
101 60 0.61
102 38 0.38
103 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (102 bp):
AATATTCTTTTATTTTAGGGAACTCAAGAAATTGTCCTCTAATGTACTAGGTATGGTTTTTCTTT
GAACATAAGTAATTGAATATCCTATTTAAAATCAATA
Found at i:20017584 original size:37 final size:37
Alignment explanation
Indices: 20017534--20017608 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
20017524 AGGGCATCTT
20017534 GAAAATCTATGTATCTCCTTCATCTCTTCACGTCATG
1 GAAAATCTATGTATCTCCTTCATCTCTTCACGTCATG
20017571 GAAAATCTATGTATCTCCTTCATCTCTTCACGTCATG
1 GAAAATCTATGTATCTCCTTCATCTCTTCACGTCATG
20017608 G
1 G
20017609 CTTCTTTCTA
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:0.27, G:0.12, T:0.37
Consensus pattern (37 bp):
GAAAATCTATGTATCTCCTTCATCTCTTCACGTCATG
Found at i:20018783 original size:11 final size:11
Alignment explanation
Indices: 20018755--20018784 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
20018745 TTCACCAACA
20018755 TTAGCCATTTT
1 TTAGCCATTTT
20018766 TTA-CCATTTT
1 TTAGCCATTTT
20018776 TTAGCCATT
1 TTAGCCATT
20018785 GATTAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (11 bp):
TTAGCCATTTT
Found at i:20021948 original size:26 final size:26
Alignment explanation
Indices: 20021896--20021949 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
20021886 ATTCTAGATG
* * * * *
20021896 CAATTCTAGGCGTGCTTATGCAGCGA
1 CAATTCTAGACATGCTCATACAACGA
20021922 CAATTCTAGACATGCTCATACAACGA
1 CAATTCTAGACATGCTCATACAACGA
20021948 CA
1 CA
20021950 TTAATAGTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (26 bp):
CAATTCTAGACATGCTCATACAACGA
Found at i:20022964 original size:60 final size:60
Alignment explanation
Indices: 20022843--20022956 Score: 142
Period size: 61 Copynumber: 1.9 Consensus size: 60
20022833 CTCCCACTAA
* * *
20022843 TTTTATTTTTTAAAATTGGCCCTCTATTCTATTTTGATTTCTAATTTAATCCCTCAACAT
1 TTTTATTTTTTAAAATTGCCCCTCTAATCTATTTTGATTTCTAATTAAATCCCTCAACAT
* * *
20022903 TTTTATTGTTTTAAATTTTCCCCTTTAATCTATTTT-ATTT-TCAATTAAATCCCT
1 TTTTATT-TTTTAAAATTGCCCCTCTAATCTATTTTGATTTCT-AATTAAATCCCT
20022957 TTTCATTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 1 0.02
60 22 0.48
61 23 0.50
ACGTcount: A:0.25, C:0.18, G:0.04, T:0.54
Consensus pattern (60 bp):
TTTTATTTTTTAAAATTGCCCCTCTAATCTATTTTGATTTCTAATTAAATCCCTCAACAT
Found at i:20023555 original size:102 final size:102
Alignment explanation
Indices: 20023379--20023586 Score: 357
Period size: 102 Copynumber: 2.0 Consensus size: 102
20023369 AGCAATATTA
*
20023379 TTTTATTTAAGGGAACTCGAGAAATTGTGTCCTAACGTACTGGATATAGTTTTTATTTGAACCTA
1 TTTTATTTAAGGGAACTCGAGAAATTGTGCCCTAACGTACTGGATATAGTTTTTATTTGAACCTA
20023444 AGTAATTGAATATCCTATTTAAAATCGATAAATGTTC
66 AGTAATTGAATATCCTATTTAAAATCGATAAATGTTC
* *
20023481 TTTTATTTTAGGGAACTCGAGAAATTGTGCCCTAACGTACTAGG-TAT-GATTTTTCTTTGAACC
1 TTTTATTTAAGGGAACTCGAGAAATTGTGCCCTAACGTACT-GGATATAG-TTTTTATTTGAACC
20023544 TAAGTAATTGAATATCCTATTTAAAATCGATAAATGTTC
64 TAAGTAATTGAATATCCTATTTAAAATCGATAAATGTTC
20023583 TTTT
1 TTTT
20023587 CGAATATTCG
Statistics
Matches: 101, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
101 1 0.01
102 98 0.97
103 2 0.02
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.40
Consensus pattern (102 bp):
TTTTATTTAAGGGAACTCGAGAAATTGTGCCCTAACGTACTGGATATAGTTTTTATTTGAACCTA
AGTAATTGAATATCCTATTTAAAATCGATAAATGTTC
Found at i:20040118 original size:24 final size:24
Alignment explanation
Indices: 20040068--20040118 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
20040058 GGACAGGCCC
* * *
20040068 AAAAAAAAGAATCTAAAAAAATAG
1 AAAAAAAAAAAACTAAAAAAACAG
* *
20040092 AAAAAAAAAAAACTTAAAAAACCG
1 AAAAAAAAAAAACTAAAAAAACAG
20040116 AAA
1 AAA
20040119 TATCCTAGCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.76, C:0.08, G:0.06, T:0.10
Consensus pattern (24 bp):
AAAAAAAAAAAACTAAAAAAACAG
Found at i:20068887 original size:20 final size:20
Alignment explanation
Indices: 20068829--20068891 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
20068819 ATGTTAAATT
20068829 CAAACAGGGGCACCAAAGTG
1 CAAACAGGGGCACCAAAGTG
* * * **
20068849 CAAATAAGGGTAATAAAGTG
1 CAAACAGGGGCACCAAAGTG
*
20068869 CAAACAGGGGCACCGAAGTG
1 CAAACAGGGGCACCAAAGTG
20068889 CAA
1 CAA
20068892 TAACAACCCA
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.43, C:0.19, G:0.29, T:0.10
Consensus pattern (20 bp):
CAAACAGGGGCACCAAAGTG
Found at i:20078829 original size:20 final size:20
Alignment explanation
Indices: 20078791--20078876 Score: 73
Period size: 20 Copynumber: 4.3 Consensus size: 20
20078781 ATGTTAAATT
* * *
20078791 CAAACAGAGGCATCGAAGTG
1 CAAACAGGGGCACCAAAGTG
*
20078811 CAAGCAGGGGCACCAAAGTG
1 CAAACAGGGGCACCAAAGTG
* * *
20078831 CAAATAGGGGCACTAAAATG
1 CAAACAGGGGCACCAAAGTG
* * *
20078851 CAAAAAGGGGCATCGAAGTG
1 CAAACAGGGGCACCAAAGTG
*
20078871 GAAACA
1 CAAACA
20078877 ACAACCAACA
Statistics
Matches: 51, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.42, C:0.19, G:0.30, T:0.09
Consensus pattern (20 bp):
CAAACAGGGGCACCAAAGTG
Found at i:20085739 original size:16 final size:16
Alignment explanation
Indices: 20085713--20085759 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
20085703 CACTGGAATG
*
20085713 GAATAGGGTTGTAATA
1 GAATAGAGTTGTAATA
* *
20085729 GAATATAGTTGTAATG
1 GAATAGAGTTGTAATA
*
20085745 GAATAGAGCTGTAAT
1 GAATAGAGTTGTAAT
20085760 CAGTAATTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.28, T:0.32
Consensus pattern (16 bp):
GAATAGAGTTGTAATA
Found at i:20112653 original size:18 final size:18
Alignment explanation
Indices: 20112627--20112664 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
20112617 TAAATTTTCA
20112627 AATTCGAAT-AACTCGAAT
1 AATTCGAATAAAC-CGAAT
*
20112645 AATTTGAATAAACCGAAT
1 AATTCGAATAAACCGAAT
20112663 AA
1 AA
20112665 AACTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (18 bp):
AATTCGAATAAACCGAAT
Found at i:20125516 original size:18 final size:18
Alignment explanation
Indices: 20125490--20125570 Score: 99
Period size: 18 Copynumber: 4.4 Consensus size: 18
20125480 GAAAGAATAA
20125490 CATACTGGCTCGTTTGAG
1 CATACTGGCTCGTTTGAG
* *
20125508 CATAGTGGCTCATTTGAG
1 CATACTGGCTCGTTTGAG
* *
20125526 CATATTGGCTCGTTAGAG
1 CATACTGGCTCGTTTGAG
**
20125544 CATACTGGCTCGTAAGAG
1 CATACTGGCTCGTTTGAG
20125562 CATTACTGG
1 CA-TACTGG
20125571 ATCAGGAGTT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
18 49 0.89
19 6 0.11
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (18 bp):
CATACTGGCTCGTTTGAG
Found at i:20126175 original size:21 final size:23
Alignment explanation
Indices: 20126149--20126204 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 23
20126139 GACTAGGGTT
20126149 GTATCGGTAGTTTCTT-AGA-AG
1 GTATCGGTAGTTTCTTCAGAGAG
* * *
20126170 GTATCGATAGATTTGTTCATAGAG
1 GTATCGGTAG-TTTCTTCAGAGAG
20126194 GTATCGGTAGT
1 GTATCGGTAGT
20126205 CTGGGTGCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 9 0.32
22 5 0.18
23 3 0.11
24 11 0.39
ACGTcount: A:0.25, C:0.09, G:0.29, T:0.38
Consensus pattern (23 bp):
GTATCGGTAGTTTCTTCAGAGAG
Found at i:20132549 original size:18 final size:18
Alignment explanation
Indices: 20132526--20132609 Score: 91
Period size: 18 Copynumber: 4.7 Consensus size: 18
20132516 AAGGAATAGT
20132526 ATACTGGCTCATTTGAGC
1 ATACTGGCTCATTTGAGC
*
20132544 ATACTGGCTCGTTTGAGC
1 ATACTGGCTCATTTGAGC
* *
20132562 AAACTGACTC-TCTTGAGC
1 ATACTGGCTCAT-TTGAGC
* *
20132580 ATACTGACT-AGTCTGAGC
1 ATACTGGCTCA-TTTGAGC
20132598 ATACTGGCTCAT
1 ATACTGGCTCAT
20132610 AAGAGCATTA
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
17 1 0.02
18 53 0.95
19 2 0.04
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (18 bp):
ATACTGGCTCATTTGAGC
Found at i:20132617 original size:36 final size:36
Alignment explanation
Indices: 20132526--20132609 Score: 107
Period size: 36 Copynumber: 2.3 Consensus size: 36
20132516 AAGGAATAGT
* * *
20132526 ATACTGGCTCATTTGAGCATACTGGCTCGTTTGAGC
1 ATACTGGCTCATTTGAGCATACTGACTAGTCTGAGC
* *
20132562 AAACTGACTC-TCTTGAGCATACTGACTAGTCTGAGC
1 ATACTGGCTCAT-TTGAGCATACTGACTAGTCTGAGC
20132598 ATACTGGCTCAT
1 ATACTGGCTCAT
20132610 AAGAGCATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
35 1 0.03
36 37 0.95
37 1 0.03
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (36 bp):
ATACTGGCTCATTTGAGCATACTGACTAGTCTGAGC
Found at i:20134372 original size:15 final size:15
Alignment explanation
Indices: 20134352--20134382 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
20134342 AAAGGCTTAA
20134352 AAAGAGATATAGGAC
1 AAAGAGATATAGGAC
20134367 AAAGAGATATAGGAC
1 AAAGAGATATAGGAC
20134382 A
1 A
20134383 GTAGCTGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.26, T:0.13
Consensus pattern (15 bp):
AAAGAGATATAGGAC
Found at i:20140114 original size:18 final size:17
Alignment explanation
Indices: 20140093--20140126 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
20140083 TCACAATTTC
20140093 TTTCAGTCTCTCTTTCTT
1 TTTCAGTCTCT-TTTCTT
*
20140111 TTTCATTCTCTTTTCT
1 TTTCAGTCTCTTTTCT
20140127 CACAACTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.06, C:0.26, G:0.03, T:0.65
Consensus pattern (17 bp):
TTTCAGTCTCTTTTCTT
Found at i:20142625 original size:17 final size:17
Alignment explanation
Indices: 20142594--20142626 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20142584 CAAACACTTA
20142594 TTAAACTAAAATAAAAC
1 TTAAACTAAAATAAAAC
20142611 TTAAA-TAAAATTAAAA
1 TTAAACTAAAA-TAAAA
20142627 AGTCCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAACTAAAATAAAAC
Found at i:20147844 original size:50 final size:51
Alignment explanation
Indices: 20147790--20147905 Score: 150
Period size: 51 Copynumber: 2.3 Consensus size: 51
20147780 TTTTGCCCTT
* *
20147790 TTAATCAATTTTTTTTTTCAAAATTAAACC-CTTCTATTCCTTTTTTTT-AA
1 TTAATCACTTTTTTTTTT-AAAATTAAACCTCTTCTATCCCTTTTTTTTAAA
*
20147840 TTAATC-CTTTAATTTTTTTAAAATTAAACCTCTTTTATCCCTTTTTTTTAAA
1 TTAATCACTTT--TTTTTTTAAAATTAAACCTCTTCTATCCCTTTTTTTTAAA
20147892 TTAAT-ACTTTTTTT
1 TTAATCACTTTTTTT
20147906 ATTTTTTCAT
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
49 3 0.05
50 21 0.36
51 23 0.40
52 11 0.19
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.58
Consensus pattern (51 bp):
TTAATCACTTTTTTTTTTAAAATTAAACCTCTTCTATCCCTTTTTTTTAAA
Found at i:20147886 original size:51 final size:52
Alignment explanation
Indices: 20147801--20147901 Score: 152
Period size: 51 Copynumber: 2.0 Consensus size: 52
20147791 TAATCAATTT
* *
20147801 TTTTTTTCAAAATTAAACCCTTCTATTCCTTTTTTTT-AATTAATCCTTTAA
1 TTTTTTTCAAAATTAAACCCTTCTATCCCTTTTTTTTAAATTAATACTTTAA
*
20147852 TTTTTTT-AAAATTAAACCTCTTTTATCCCTTTTTTTTAAATTAATACTTT
1 TTTTTTTCAAAATTAAACC-CTTCTATCCCTTTTTTTTAAATTAATACTTT
20147902 TTTTATTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
50 11 0.24
51 23 0.51
52 11 0.24
ACGTcount: A:0.28, C:0.16, G:0.00, T:0.56
Consensus pattern (52 bp):
TTTTTTTCAAAATTAAACCCTTCTATCCCTTTTTTTTAAATTAATACTTTAA
Found at i:20149159 original size:271 final size:269
Alignment explanation
Indices: 20148659--20149206 Score: 1033
Period size: 271 Copynumber: 2.0 Consensus size: 269
20148649 TCCAATCTAG
**
20148659 ATATTAAGGATAAAATGATATATGAAAAGATTATCACAAAAATGTTATGTTAAGTCACGACTTCT
1 ATATTAAAAATAAAATGATATATGAAAAGATTATCACAAAAATGTTATGTTAAGTCACGACTTCT
*
20148724 TCTAACTTGAGTGTAAATGATGCATTGCTAGATGTCATTCATTGCTTGTAATGTTAGAAACGTTC
66 TCTAACTTGAGTGTAAATGATGCATTGCTAGATGTCACTCATTGCTTGTAATGTTAGAAACGTTC
20148789 TAGTATTACTACCAACATCACAAGAGCCTACAGGGTCACACCCTATAGTTGAAACGAACAAAATC
131 TAGTATTACTACCAACATCACAAGAGCCTACAGGGTCACACCCTATAGTTGAAACGAACAAAATC
*
20148854 CAAATACATTTGGTATTTATTTAATTGTCACATTAATTAAATTAATTGTTGAATTAATTTAATTT
196 CAAATACATGTGGTATTTATTTAATTGTCACATTAATTAAATTAATTGTTGAATTAATTTAATTT
20148919 GACAGTTAA
261 GACAGTTAA
20148928 ATATTAAAAATAAAATGATATATATGAAAAGATTATCACAAAAATGTTATGTTAAGTCACGACTT
1 ATATTAAAAATAAAATG--ATATATGAAAAGATTATCACAAAAATGTTATGTTAAGTCACGACTT
20148993 CTTCTAACTTGAGTGTAAATGATGCATTGCTAGATGTCACTCATTGCTTGTAATGTTAGAAACGT
64 CTTCTAACTTGAGTGTAAATGATGCATTGCTAGATGTCACTCATTGCTTGTAATGTTAGAAACGT
*
20149058 TCTAGTATTACTACCAACATCACAAGAGCCTATAGGGTCACACCCTATAGTTGAAACGAACAAAA
129 TCTAGTATTACTACCAACATCACAAGAGCCTACAGGGTCACACCCTATAGTTGAAACGAACAAAA
20149123 TCCAAATACATGTGGTATTTATTTAATTGTCACATTAATTAAATTAATTGTTGAATTAATTTAAT
194 TCCAAATACATGTGGTATTTATTTAATTGTCACATTAATTAAATTAATTGTTGAATTAATTTAAT
20149188 TTGACAGTTAA
259 TTGACAGTTAA
20149199 ATATTAAA
1 ATATTAAA
20149207 CACATTATAT
Statistics
Matches: 272, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
269 15 0.06
271 257 0.94
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (269 bp):
ATATTAAAAATAAAATGATATATGAAAAGATTATCACAAAAATGTTATGTTAAGTCACGACTTCT
TCTAACTTGAGTGTAAATGATGCATTGCTAGATGTCACTCATTGCTTGTAATGTTAGAAACGTTC
TAGTATTACTACCAACATCACAAGAGCCTACAGGGTCACACCCTATAGTTGAAACGAACAAAATC
CAAATACATGTGGTATTTATTTAATTGTCACATTAATTAAATTAATTGTTGAATTAATTTAATTT
GACAGTTAA
Found at i:20149422 original size:137 final size:138
Alignment explanation
Indices: 20149270--20149671 Score: 653
Period size: 137 Copynumber: 2.9 Consensus size: 138
20149260 ATGTACGAAG
* * *
20149270 TTGATTCATACAAAATATTGATTGTATATATTTTACCGAATTTATTAATATAAACAGTTATATTA
1 TTGATTCATACAAAATATTAATTGTATATATTTTATCGAATTTATTAATATAAACAATTATATTA
* * * *
20149335 ATTAATTTTGATCAAAATATAAAAGATATAAAAATTAATATTCTTTTGGAAATAATATAATTAAT
66 ATTAATTTTGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAAGAATATAATTAAT
20149400 ATAT-AAT
131 ATATAAAT
* *
20149407 TTGATTTATACAAAATATTAATTGTATATATTTTATTGAATTTATTAATATAAACAATTATATTA
1 TTGATTCATACAAAATATTAATTGTATATATTTTATCGAATTTATTAATATAAACAATTATATTA
* *
20149472 ATTAATTTTGGTCAAAATATAAAAGACATGAAAATTAATATTATTTTGAAAAGAATATAATTAAT
66 ATTAATTTTGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAAGAATATAATTAAT
*
20149537 ATGTAAAT
131 ATATAAAT
* *
20149545 TTGAATCATACAAAATATTAATTGTATATATTTTATCGAATTTATTAATATAAACAATTATATTT
1 TTGATTCATACAAAATATTAATTGTATATATTTTATCGAATTTATTAATATAAACAATTATATTA
* *
20149610 ATTAATTTAGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTAGAAAGAATATAATT
66 ATTAATTTTGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAAGAATATAATT
20149672 CCTTTTTTCT
Statistics
Matches: 244, Mismatches: 20, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
137 122 0.50
138 122 0.50
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (138 bp):
TTGATTCATACAAAATATTAATTGTATATATTTTATCGAATTTATTAATATAAACAATTATATTA
ATTAATTTTGGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAAGAATATAATTAAT
ATATAAAT
Found at i:20150045 original size:21 final size:21
Alignment explanation
Indices: 20149999--20150046 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
20149989 ATTATTAAAT
20149999 ATAATTTAATAAATATATTAA
1 ATAATTTAATAAATATATTAA
* * *
20150020 TTAATTTAAT-TATATTTTAA
1 ATAATTTAATAAATATATTAA
20150040 CATAATT
1 -ATAATT
20150047 ATTATTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAATTTAATAAATATATTAA
Found at i:20150055 original size:58 final size:58
Alignment explanation
Indices: 20149986--20150144 Score: 189
Period size: 58 Copynumber: 2.7 Consensus size: 58
20149976 AATTTTAATG
* *
20149986 ATTATTATTAAATATAATTTAATAAATATATTA-ATTAATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATATAATTTAATAAA-ATAATATA-TAATTTAATAATATTTTTAACATA
* *
20150044 ATTATTATTAAATACAATTTAATAAAATAATATATAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAATATTTTTAACATA
20150102 ATTATTATTAAAATATGAATTAGTAA-AAATTATAATATATAAT
1 ATTATTATT-AAATAT-AATT--TAATAAA--ATAATATATAAT
20150145 ATTAGAAAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 11
0.85 0.05 0.11
Matches are distributed among these distances:
57 17 0.19
58 44 0.50
59 5 0.06
60 4 0.05
61 3 0.03
62 3 0.03
63 12 0.14
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (58 bp):
ATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAATATTTTTAACATA
Found at i:20150133 original size:25 final size:24
Alignment explanation
Indices: 20150105--20150155 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
20150095 TAATATAATT
*
20150105 ATTATTAAAATATGA-ATTAGTAAAA
1 ATTA-TAAAATATAATATTAG-AAAA
*
20150130 ATTATAATATATAATATTAGAAAA
1 ATTATAAAATATAATATTAGAAAA
20150154 AT
1 AT
20150156 AATATATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (24 bp):
ATTATAAAATATAATATTAGAAAA
Found at i:20153805 original size:59 final size:59
Alignment explanation
Indices: 20153733--20153919 Score: 338
Period size: 59 Copynumber: 3.2 Consensus size: 59
20153723 TATATATATA
*
20153733 TATAGGTACTGAGATTGAGAGTTCTATGGCTATTGTCAATTGTGTGTGATAAAGAAAGC
1 TATAGGTACTGAGATTGAGAGTTCTGTGGCTATTGTCAATTGTGTGTGATAAAGAAAGC
20153792 TATAGGTACTGAGATTGAGAGTTCTGTGGCTATTGTCAATTGTGTGTGATAAAGAAAGC
1 TATAGGTACTGAGATTGAGAGTTCTGTGGCTATTGTCAATTGTGTGTGATAAAGAAAGC
* *
20153851 TATAGGTACTGAGATTGAGAGTTCTGTGGCTACTGCCAATTGTGTGTGATAAAGAAAGC
1 TATAGGTACTGAGATTGAGAGTTCTGTGGCTATTGTCAATTGTGTGTGATAAAGAAAGC
*
20153910 TATGGGTACT
1 TATAGGTACT
20153920 ATGACTTGAT
Statistics
Matches: 124, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 124 1.00
ACGTcount: A:0.29, C:0.10, G:0.28, T:0.33
Consensus pattern (59 bp):
TATAGGTACTGAGATTGAGAGTTCTGTGGCTATTGTCAATTGTGTGTGATAAAGAAAGC
Found at i:20157060 original size:23 final size:23
Alignment explanation
Indices: 20157034--20157079 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
20157024 AAAAAGAGCG
*
20157034 AAAACCAGAAAATCAGAGGAAGC
1 AAAACCAAAAAATCAGAGGAAGC
20157057 AAAACCAAAAAATCAGAGGAAGC
1 AAAACCAAAAAATCAGAGGAAGC
20157080 TATAGGCGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.59, C:0.17, G:0.20, T:0.04
Consensus pattern (23 bp):
AAAACCAAAAAATCAGAGGAAGC
Found at i:20159732 original size:31 final size:30
Alignment explanation
Indices: 20159672--20159762 Score: 82
Period size: 31 Copynumber: 3.1 Consensus size: 30
20159662 TTATTTTAAT
* **
20159672 TTTATAAATTTTATAAAACATGTTTAAATTA
1 TTTA-AAATTTTATAAAACATATAAAAATTA
20159703 TTTAAAATTTTATAAAAACATATAAAAATT-
1 TTTAAAATTTTAT-AAAACATATAAAAATTA
* * *
20159733 CTTAAAA-ATTATAAAATAT-TAAAAA-TA
1 TTTAAAATTTTATAAAACATATAAAAATTA
20159760 TTT
1 TTT
20159763 CTCACCAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
26 1 0.02
27 8 0.16
28 6 0.12
29 4 0.08
30 15 0.29
31 17 0.33
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (30 bp):
TTTAAAATTTTATAAAACATATAAAAATTA
Found at i:20159747 original size:9 final size:9
Alignment explanation
Indices: 20159712--20159995 Score: 87
Period size: 10 Copynumber: 29.0 Consensus size: 9
20159702 ATTTAAAATT
20159712 TTATAAAAA
1 TTATAAAAA
*
20159721 CATATAAAAA
1 -TTATAAAAA
*
20159731 TTCTTAAAAA
1 TT-ATAAAAA
20159741 TTATAAAATA
1 TTATAAAA-A
20159751 TTA-AAAATA
1 TTATAAAA-A
*
20159760 TTTCTCACCAAAA
1 -TTAT-A--AAAA
20159773 GATTATTAAAAA
1 --TTA-TAAAAA
*
20159785 -TATTAAAA
1 TTATAAAAA
*
20159793 TTGATATAAAT
1 TT-ATA-AAAA
*
20159804 TTATAGAAA
1 TTATAAAAA
*
20159813 TGATAAAAAA
1 TTAT-AAAAA
*
20159823 TCATAAAAA
1 TTATAAAAA
*
20159832 CTAATAAAAA
1 -TTATAAAAA
20159842 TTATAAAAA
1 TTATAAAAA
*
20159851 -AATAATAAA
1 TTATAA-AAA
*
20159860 TTTTAACAAA
1 TTATAA-AAA
*
20159870 TTATTAAATA
1 TTA-TAAAAA
*
20159880 TT-T-ATAA
1 TTATAAAAA
20159887 TTAATAAAATA
1 TT-ATAAAA-A
* *
20159898 TATTTAAAATT
1 T-TATAAAA-A
20159909 TTATAAAAAA
1 TTAT-AAAAA
*
20159919 CTTGGTAAAAA
1 -TT-ATAAAAA
*
20159930 TTCATAAAATC
1 TT-ATAAAA-A
20159941 TTATAAATAA
1 TTATAAA-AA
20159951 -TATAAAAA
1 TTATAAAAA
*
20159959 TTCTAATAAA
1 TTATAA-AAA
20159969 TTATAAAAA
1 TTATAAAAA
20159978 -TATTAAAAA
1 TTA-TAAAAA
20159987 TTATAAAAA
1 TTATAAAAA
20159996 AAGTCATTTA
Statistics
Matches: 206, Mismatches: 37, Indels: 63
0.67 0.12 0.21
Matches are distributed among these distances:
7 4 0.02
8 14 0.07
9 62 0.30
10 80 0.39
11 31 0.15
12 7 0.03
13 1 0.00
14 6 0.03
15 1 0.00
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.35
Consensus pattern (9 bp):
TTATAAAAA
Found at i:20159969 original size:21 final size:19
Alignment explanation
Indices: 20159951--20159995 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 19
20159941 TTATAAATAA
20159951 TATAAAAATTCTAATAAAT
1 TATAAAAATTCTAATAAAT
20159970 TATAAAAATAT-TAA-AAAT
1 TATAAAAAT-TCTAATAAAT
20159988 TATAAAAA
1 TATAAAAA
20159996 AAGTCATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.48
19 12 0.48
20 1 0.04
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
TATAAAAATTCTAATAAAT
Found at i:20159973 original size:19 final size:18
Alignment explanation
Indices: 20159924--20159995 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 18
20159914 AAAAACTTGG
*
20159924 TAAAAATTCAT-AAAATCT
1 TAAAAATT-ATAAAAATAT
*
20159942 TATAAATAATATAAAAAT-T
1 TA-AAA-ATTATAAAAATAT
20159961 CTAATAAATTATAAAAATAT
1 -TAA-AAATTATAAAAATAT
20159981 TAAAAATTATAAAAA
1 TAAAAATTATAAAAA
20159996 AAGTCATTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
18 14 0.30
19 20 0.43
20 12 0.26
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAAATTATAAAAATAT
Found at i:20159973 original size:28 final size:29
Alignment explanation
Indices: 20159924--20159994 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 29
20159914 AAAAACTTGG
*
20159924 TAAAAATTCATAAAATCTTATAAATAATA-
1 TAAAAATTCATAAAATATTATAAA-AATAT
20159953 TAAAAATTC-TAATAA-ATTATAAAAATAT
1 TAAAAATTCATAA-AATATTATAAAAATAT
20159981 TAAAAATT-ATAAAA
1 TAAAAATTCATAAAA
20159995 AAAGTCATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
27 6 0.16
28 21 0.55
29 11 0.29
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (29 bp):
TAAAAATTCATAAAATATTATAAAAATAT
Found at i:20160126 original size:35 final size:35
Alignment explanation
Indices: 20160087--20160169 Score: 87
Period size: 35 Copynumber: 2.4 Consensus size: 35
20160077 CCTATCATTT
20160087 TTGTGTTTCTGGTCAAGTCCTCATA-CTCGTCATCC
1 TTGTGTTTCTGGTCAAGTCCTCATATC-CGTCATCC
* *** *
20160122 TTGTGTTTTTGGTTGGGTCGTCATATCCGTCATCC
1 TTGTGTTTCTGGTCAAGTCCTCATATCCGTCATCC
**
20160157 TCATGTTTCTGGT
1 TTGTGTTTCTGGT
20160170 TAGGTTGCCA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
35 38 0.97
36 1 0.03
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.45
Consensus pattern (35 bp):
TTGTGTTTCTGGTCAAGTCCTCATATCCGTCATCC
Found at i:20161999 original size:26 final size:26
Alignment explanation
Indices: 20161938--20162073 Score: 119
Period size: 26 Copynumber: 5.2 Consensus size: 26
20161928 TTTCTACTTG
* *
20161938 GTATTTTCATGCTGACGAGCGTAAAC
1 GTATATTCATGCTGACGAGCGTAAAT
* * * *
20161964 ATATAATCATGCTGACAAGTGTAAAT
1 GTATATTCATGCTGACGAGCGTAAAT
* * *
20161990 GTATTTTCATGCTAATGAGCGTAAAT
1 GTATATTCATGCTGACGAGCGTAAAT
* * * *
20162016 GTATATTCATACTGATGAGTGTAAAC
1 GTATATTCATGCTGACGAGCGTAAAT
* * * *
20162042 ATGTATTCAAGCTGACGAGCGTAAAC
1 GTATATTCATGCTGACGAGCGTAAAT
20162068 GTATAT
1 GTATAT
20162074 ATATATATAT
Statistics
Matches: 84, Mismatches: 26, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 84 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (26 bp):
GTATATTCATGCTGACGAGCGTAAAT
Found at i:20162073 original size:52 final size:51
Alignment explanation
Indices: 20161942--20162073 Score: 149
Period size: 52 Copynumber: 2.5 Consensus size: 51
20161932 TACTTGGTAT
* * *
20161942 TTTCATGCTGACGAGCGTAAACATATAATCATGCTGACAAGTGTAAATGTA
1 TTTCATGCTGACGAGCGTAAACGTATATTCATACTGACAAGTGTAAATGTA
* * * **
20161993 TTTTCATGCTAATGAGCGTAAATGTATATTCATACTGATGAGTGTAAACATGTA
1 -TTTCATGCTGACGAGCGTAAACGTATATTCATACTGACAAGTGT-AA-ATGTA
*
20162047 -TTCAAGCTGACGAGCGTAAACGTATAT
1 TTTCATGCTGACGAGCGTAAACGTATAT
20162074 ATATATATAT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
52 59 0.89
53 2 0.03
54 5 0.08
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (51 bp):
TTTCATGCTGACGAGCGTAAACGTATATTCATACTGACAAGTGTAAATGTA
Found at i:20166057 original size:9 final size:9
Alignment explanation
Indices: 20166045--20166100 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 9
20166035 AATTAATACA
20166045 AAAAATTTT
1 AAAAATTTT
20166054 -AAAATTTT
1 AAAAATTTT
20166062 AAAAA-TTT
1 AAAAATTTT
20166070 AAAAATTTCAT
1 AAAAATTT--T
*
20166081 AAAAACTTTC
1 AAAAA-TTTT
*
20166091 AAAAAATTT
1 AAAAATTTT
20166100 A
1 A
20166101 GACATATTAG
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
8 16 0.41
9 9 0.23
10 5 0.13
11 6 0.15
12 3 0.08
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (9 bp):
AAAAATTTT
Found at i:20166067 original size:17 final size:17
Alignment explanation
Indices: 20166045--20166100 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
20166035 AATTAATACA
*
20166045 AAAAATTTTAAAATTTT
1 AAAAATTTAAAAATTTT
20166062 AAAAATTTAAAAATTTCAT
1 AAAAATTTAAAAATTT--T
*
20166081 AAAAACTTTCAAAAAATTT
1 AAAAA-TTT-AAAAATTTT
20166100 A
1 A
20166101 GACATATTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 15 0.45
19 8 0.24
20 3 0.09
21 7 0.21
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAAATTTAAAAATTTT
Found at i:20169744 original size:20 final size:21
Alignment explanation
Indices: 20169716--20169768 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
20169706 CGTTGGAGTT
*
20169716 GTATAGATACTTGAT-AAAAG
1 GTATCGATACTTGATGAAAAG
**
20169736 GTATCGATACTTTTTGAAAAG
1 GTATCGATACTTGATGAAAAG
20169757 GTATCGATACTT
1 GTATCGATACTT
20169769 TTTGAAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (21 bp):
GTATCGATACTTGATGAAAAG
Found at i:20169757 original size:21 final size:21
Alignment explanation
Indices: 20169731--20169775 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
20169721 GATACTTGAT
20169731 AAAAGGTATCGATACTTTTTG
1 AAAAGGTATCGATACTTTTTG
20169752 AAAAGGTATCGATACTTTTTG
1 AAAAGGTATCGATACTTTTTG
20169773 AAA
1 AAA
20169776 TTGTTTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.36
Consensus pattern (21 bp):
AAAAGGTATCGATACTTTTTG
Done.