Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 13 of 193
Found at i:4547428 original size:13 final size:13
Alignment explanation
Indices: 4547410--4547435 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4547400 TCTTCCGATC
4547410 ACAGAAATGACAG
1 ACAGAAATGACAG
4547423 ACAGAAATGACAG
1 ACAGAAATGACAG
4547436 TAGATTTGCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.23, T:0.08
Consensus pattern (13 bp):
ACAGAAATGACAG
Found at i:4547927 original size:22 final size:22
Alignment explanation
Indices: 4547893--4547936 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
4547883 TAACAATAAA
*
4547893 AGAAATTGAGAGAAAAGAAATG
1 AGAAAATGAGAGAAAAGAAATG
*
4547915 AGAAAATGGGAGAAAAGAAATG
1 AGAAAATGAGAGAAAAGAAATG
4547937 TAACGAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.30, T:0.11
Consensus pattern (22 bp):
AGAAAATGAGAGAAAAGAAATG
Found at i:4548159 original size:66 final size:66
Alignment explanation
Indices: 4548077--4548206 Score: 251
Period size: 66 Copynumber: 2.0 Consensus size: 66
4548067 TATCACTGTT
4548077 GAAGAGAACATAAAATTGTATCATTCAATCTGATACCAAATAATTCAATTAATAACCATAAAAAA
1 GAAGAGAACATAAAATTGTATCATTCAATCTGATACCAAATAATTCAATTAATAACCATAAAAAA
4548142 C
66 C
*
4548143 GAAGAGAACATAAAATTGTATCATTCTATCTGATACCAAATAATTCAATTAATAACCATAAAAA
1 GAAGAGAACATAAAATTGTATCATTCAATCTGATACCAAATAATTCAATTAATAACCATAAAAA
4548207 GCGTTGAGCA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.27
Consensus pattern (66 bp):
GAAGAGAACATAAAATTGTATCATTCAATCTGATACCAAATAATTCAATTAATAACCATAAAAAA
C
Found at i:4548646 original size:32 final size:32
Alignment explanation
Indices: 4548610--4548677 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
4548600 AAAATCTAAC
*
4548610 AAATACATGAAAAAGCCTAGAAGAAGATTGAA
1 AAATACATGAAAAAGCCTAGAAGAAAATTGAA
4548642 AAATACATGAAAAAGCCTAGAAGAAAATTGAA
1 AAATACATGAAAAAGCCTAGAAGAAAATTGAA
4548674 AAAT
1 AAAT
4548678 TGAAAATACT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.59, C:0.09, G:0.16, T:0.16
Consensus pattern (32 bp):
AAATACATGAAAAAGCCTAGAAGAAAATTGAA
Found at i:4556488 original size:79 final size:79
Alignment explanation
Indices: 4556392--4556549 Score: 316
Period size: 79 Copynumber: 2.0 Consensus size: 79
4556382 GTTATTTAAA
4556392 AATTATTTTATGCTTTTCAAAGAGAATATTTCAACAAAAACAATTTGATCAATAGAAAATAATTT
1 AATTATTTTATGCTTTTCAAAGAGAATATTTCAACAAAAACAATTTGATCAATAGAAAATAATTT
4556457 TAAAACTCAGAAAG
66 TAAAACTCAGAAAG
4556471 AATTATTTTATGCTTTTCAAAGAGAATATTTCAACAAAAACAATTTGATCAATAGAAAATAATTT
1 AATTATTTTATGCTTTTCAAAGAGAATATTTCAACAAAAACAATTTGATCAATAGAAAATAATTT
4556536 TAAAACTCAGAAAG
66 TAAAACTCAGAAAG
4556550 TATATAAAGT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.48, C:0.10, G:0.09, T:0.33
Consensus pattern (79 bp):
AATTATTTTATGCTTTTCAAAGAGAATATTTCAACAAAAACAATTTGATCAATAGAAAATAATTT
TAAAACTCAGAAAG
Found at i:4557660 original size:21 final size:21
Alignment explanation
Indices: 4557634--4557694 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
4557624 AACCCATAAT
4557634 AACCCTCGTATCTGCAGGAAA
1 AACCCTCGTATCTGCAGGAAA
* * *
4557655 AACCCTCGAATGTGCAGGAAT
1 AACCCTCGTATCTGCAGGAAA
4557676 AACCCTCGTATCTGCAGGA
1 AACCCTCGTATCTGCAGGA
4557695 GTCGCTGCAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.20
Consensus pattern (21 bp):
AACCCTCGTATCTGCAGGAAA
Found at i:4558392 original size:32 final size:32
Alignment explanation
Indices: 4558289--4558393 Score: 88
Period size: 32 Copynumber: 3.1 Consensus size: 32
4558279 AATTGTGTGC
4558289 GTTATAGAGTGCACCCTTGACAGCACAATTGG
1 GTTATAGAGTGCACCCTTGACAGCACAATTGG
* * * * *
4558321 GTTA-AGATTTCATTGAGCATTAGAGCAGCAC-ATACGG
1 GTTATAGAGTGC----ACCCTT-GA-CAGCACAAT-TGG
4558358 GTTATAGAGTGCACCCTTGACAGCACAATTGG
1 GTTATAGAGTGCACCCTTGACAGCACAATTGG
4558390 GTTA
1 GTTA
4558394 AGGTTTCATT
Statistics
Matches: 54, Mismatches: 10, Indels: 18
0.66 0.12 0.22
Matches are distributed among these distances:
31 5 0.09
32 16 0.30
33 4 0.07
34 4 0.07
35 4 0.07
36 4 0.07
37 12 0.22
38 5 0.09
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.27
Consensus pattern (32 bp):
GTTATAGAGTGCACCCTTGACAGCACAATTGG
Found at i:4559053 original size:21 final size:21
Alignment explanation
Indices: 4559028--4559071 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
4559018 AGAAAAAGGG
4559028 TCAGCTCAAAAGAAATGTATT
1 TCAGCTCAAAAGAAATGTATT
4559049 TCAGCTCAAAAGAAATGTATT
1 TCAGCTCAAAAGAAATGTATT
4559070 TC
1 TC
4559072 TGCATACGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (21 bp):
TCAGCTCAAAAGAAATGTATT
Found at i:4559786 original size:26 final size:26
Alignment explanation
Indices: 4559750--4559801 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
4559740 GTAGATCCAT
4559750 CTCAAACACTCACACCTGAGTCAAAA
1 CTCAAACACTCACACCTGAGTCAAAA
4559776 CTCAAACACTCACACCTGAGTCAAAA
1 CTCAAACACTCACACCTGAGTCAAAA
4559802 TAAGGGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.35, G:0.08, T:0.15
Consensus pattern (26 bp):
CTCAAACACTCACACCTGAGTCAAAA
Found at i:4560023 original size:27 final size:27
Alignment explanation
Indices: 4559984--4560038 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
4559974 CCTTATCTTC
4559984 CCGTTCTCGCTTGCTGCATTCAGGTTG
1 CCGTTCTCGCTTGCTGCATTCAGGTTG
*
4560011 CCGTTCTCTCTTGCTGCATTCAGGTTG
1 CCGTTCTCGCTTGCTGCATTCAGGTTG
4560038 C
1 C
4560039 TTCATCAAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.07, C:0.31, G:0.24, T:0.38
Consensus pattern (27 bp):
CCGTTCTCGCTTGCTGCATTCAGGTTG
Found at i:4561076 original size:15 final size:15
Alignment explanation
Indices: 4561056--4561085 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4561046 AAACACTGAA
4561056 TCCAATCACATCCCC
1 TCCAATCACATCCCC
4561071 TCCAATCACATCCCC
1 TCCAATCACATCCCC
4561086 CTTTTTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.53, G:0.00, T:0.20
Consensus pattern (15 bp):
TCCAATCACATCCCC
Found at i:4561228 original size:594 final size:591
Alignment explanation
Indices: 4560372--4561664 Score: 1851
Period size: 594 Copynumber: 2.2 Consensus size: 591
4560362 CAACAAATAC
4560372 TACCCATGTCGATCCATCTCAGACACT--CA-C----TCAAAGTAAGGGCAAAGGCAAAAGCCAA
1 TACCCATGTCGATCCATCTCAGACACTCACACCTGAGTCAAAGTAAGGGCAAAGGCAAAAGCCAA
* * * *
4560430 ATAAAACTCGCGCCATACAAAAAGAAAATGCTAAACACTG------AATCCAATCGCGTCCCCCT
66 ATAAAACTCGCGCCAAACAAAAAGAAAAAGCTAAACACTGAATCCAAATCCAATCACATCCCCCT
*
4560489 TTTTCTTTTTGGACCATCCTATATTTCCTTAGTAAAGGAAAAAAGAAAAGAAAAGAAGATGACTA
131 TTTTCTTTTTGGACCATCCTATATTTCCTAAGTAAAGGAAAAAAG---AGAAAAGAAGATGACTA
4560554 CAGAATTCAAGAAATACCTTTGAGTTCCTTATCTTCCCCTTCCCCCATGTTGCATTCAGGTTGCT
193 CAGAATTCAAGAAATACCTTTGAGTTCCTTATCTTCCCCTTCCCCCATGTTGCATTCAGGTTGCT
* **
4560619 TCATCAAGCTGGAGTCTGTTTCAATTGCATTTCGTATGTGAAAATATTCAATCAATTGAAGAAAA
258 TCATCAAACTGGAGTCTG-TTCAATTGCATTTAATATGTGAAAATATTCAATCAATTGAAGAAAA
*
4560684 TAAAAAACCTAAAGCGATGGAAATAAATAAATAACATGATA-CTTCAAA-CTTCTATTTCGGGGA
322 TAAAAAACCTAAAGCGATGGAAATAAATAAATAACATGATAGC-TAAAATCTTCTATTTCGGGGA
* **
4560747 GTTTAGGTTCTGATCAGTCCCCAAAAATCCAAACCAGATGATTT-GAAATTAAATTTATTAGAAA
386 GTTTACGTTCCAATCAGTCCCCAAAAATCCAAACCAGATGATTTGGAAA-TAAATTTATTAGAAA
*
4560811 CATGGTC-GGGGTAAAAGGTTATGTTGTTCTAACTC-TCTATATTTATTAAAGTGCCCCTTACAT
450 CATGGTCAGGGGTAAAAGGTTATGTTGTTCTAACTCTTC-ATATTTATTAAAGTACCCCTTACAT
*
4560874 CCACATCCAATG-C-ATA-TAGATATGACCATCTAAACATCCAACAAATACATGAAAAAGCCTAG
514 CCACATCCAATGACGATAGTAGATATGACCATCTAAAAATCCAACAAATACATGAAAAAGCCTA-
4560936 AAA-AAATTGAAAA
578 AAAGAAATTGAAAA
*
4560949 TACCTATGTCGATCCATCTCAGACACTCACACCTGAGTCAAAGTAAGGGCAAAGGCAAAAGCCAA
1 TACCCATGTCGATCCATCTCAGACACTCACACCTGAGTCAAAGTAAGGGCAAAGGCAAAAGCCAA
*
4561014 ATAAAACTCGTGCCAAACAAAAAGAAAAAGCTAAACACTGAATCCAATCACATCCCCTCCAATCA
66 ATAAAACTCGCGCCAAACAAAAAGAAAAAGCTAAACACTGAATCC-A--A-A-----TCCAATCA
* * *
4561079 CATCCCCCTTTTTCTTTTTGGACCATCTTATATTTCCTAAGTAAA-TAGAAAAG-GAAAAGAAGA
122 CATCCCCCTTTTTCTTTTTGGACCATCCTATATTTCCTAAGTAAAGGAAAAAAGAGAAAAGAAGA
*
4561142 TGACTACAGAATTCAAGAAATACCTTTGAGTTCCTTATCTTCCCCTTCCCCCATTTTGCATTCAG
187 TGACTACAGAATTCAAGAAATACCTTTGAGTTCCTTATCTTCCCCTTCCCCCATGTTGCATTCAG
* * *
4561207 GTTGCTTCATCAAATTGGAGTCTGTTCAATTGCATTTAATTTGTGAAAATATTCCATCAATTGAA
252 GTTGCTTCATCAAACTGGAGTCTGTTCAATTGCATTTAATATGTGAAAATATTCAATCAATTGAA
* * * * *
4561272 GAAAATAAAAAGCCTAAGGGGATGGAAATAAATAAATAATATGATAGCTAAAATCTTCTATTTTG
317 GAAAATAAAAAACCTAAAGCGATGGAAATAAATAAATAACATGATAGCTAAAATCTTCTATTTCG
* *
4561337 GGGAGTTTACTTTCCAATCAGTCCTCAAAAATCCAAACCAGATGATTTGGAAATAAATTTATTAG
382 GGGAGTTTACGTTCCAATCAGTCCCCAAAAATCCAAACCAGATGATTTGGAAATAAATTTATTAG
* *
4561402 AAACATGGTCATGGGTAAAAGGTTATGTTGTTCTAACTCTTCATATTTCTTAAAGTACCCCTTAC
447 AAACATGGTCAGGGGTAAAAGGTTATGTTGTTCTAACTCTTCATATTTATTAAAGTACCCCTTAC
*
4561467 ATCCACATCCAATGCATACATGGATATGTAGATATGACCCTCTAAAAATCCAACAAATACATGAA
512 ATCCACATCCAATG---AC---GATA-GTAGATATGACCATCTAAAAATCCAACAAATACATGAA
4561532 AAAGCCTAAAAGAAATTGAAAA
570 AAAGCCTAAAAGAAATTGAAAA
* * *
4561554 TACCCATGTAGATCCATCTCAGACACTCACACCTGAGACAGAGTAAGGGCAAAGGCAAAAGCCAA
1 TACCCATGTCGATCCATCTCAGACACTCACACCTGAGTCAAAGTAAGGGCAAAGGCAAAAGCCAA
* * *
4561619 ATAAAACTCGCGCCAAACCAATAGAAAAAGCTATACACTGAATCCA
66 ATAAAACTCGCGCCAAACAAAAAGAAAAAGCTAAACACTGAATCCA
4561665 GTTGCATCCC
Statistics
Matches: 637, Mismatches: 41, Indels: 49
0.88 0.06 0.07
Matches are distributed among these distances:
577 26 0.04
579 2 0.00
580 1 0.00
584 65 0.10
593 84 0.13
594 173 0.27
595 66 0.10
596 2 0.00
598 6 0.01
599 50 0.08
603 3 0.00
604 4 0.01
605 155 0.24
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (591 bp):
TACCCATGTCGATCCATCTCAGACACTCACACCTGAGTCAAAGTAAGGGCAAAGGCAAAAGCCAA
ATAAAACTCGCGCCAAACAAAAAGAAAAAGCTAAACACTGAATCCAAATCCAATCACATCCCCCT
TTTTCTTTTTGGACCATCCTATATTTCCTAAGTAAAGGAAAAAAGAGAAAAGAAGATGACTACAG
AATTCAAGAAATACCTTTGAGTTCCTTATCTTCCCCTTCCCCCATGTTGCATTCAGGTTGCTTCA
TCAAACTGGAGTCTGTTCAATTGCATTTAATATGTGAAAATATTCAATCAATTGAAGAAAATAAA
AAACCTAAAGCGATGGAAATAAATAAATAACATGATAGCTAAAATCTTCTATTTCGGGGAGTTTA
CGTTCCAATCAGTCCCCAAAAATCCAAACCAGATGATTTGGAAATAAATTTATTAGAAACATGGT
CAGGGGTAAAAGGTTATGTTGTTCTAACTCTTCATATTTATTAAAGTACCCCTTACATCCACATC
CAATGACGATAGTAGATATGACCATCTAAAAATCCAACAAATACATGAAAAAGCCTAAAAGAAAT
TGAAAA
Found at i:4562209 original size:13 final size:13
Alignment explanation
Indices: 4562191--4562216 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4562181 CAGAAAGTAG
4562191 ACTCATAATGAAA
1 ACTCATAATGAAA
4562204 ACTCATAATGAAA
1 ACTCATAATGAAA
4562217 CGAAAACCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (13 bp):
ACTCATAATGAAA
Found at i:4573699 original size:27 final size:27
Alignment explanation
Indices: 4573659--4573712 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
4573649 TATAAGGGGG
4573659 TGGTGCCTACCTGTCAGGCGGCACCAA
1 TGGTGCCTACCTGTCAGGCGGCACCAA
** *
4573686 TGGTGCCTTTCTGTCAGGTGGCACCAA
1 TGGTGCCTACCTGTCAGGCGGCACCAA
4573713 CTCGTATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.24
Consensus pattern (27 bp):
TGGTGCCTACCTGTCAGGCGGCACCAA
Found at i:4573775 original size:15 final size:14
Alignment explanation
Indices: 4573729--4573776 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
4573719 TTTTTATTAC
*
4573729 AAAACTAATACAAA
1 AAAAATAATACAAA
* *
4573743 AAAAATTATACACCA
1 AAAAATAATACA-AA
*
4573758 AAATATAATACAAA
1 AAAAATAATACAAA
4573772 AAAAA
1 AAAAA
4573777 AGTAATAACT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAAATAATACAAA
Found at i:4577142 original size:26 final size:26
Alignment explanation
Indices: 4577050--4577142 Score: 80
Period size: 26 Copynumber: 3.5 Consensus size: 26
4577040 TCTGTTGGAA
* *
4577050 TTAATTAAGTTTATGATTGAATTTGGAA
1 TTAATTATGTTTATGATTGAATTT--AT
* * *
4577078 TTAATTCTATTTA-AATTTGAATTTAT
1 TTAATTATGTTTATGA-TTGAATTTAT
* *
4577104 TTAATAATTTTTATGATTGAATTTAT
1 TTAATTATGTTTATGATTGAATTTAT
*
4577130 TTAATTAGGTTTA
1 TTAATTATGTTTA
4577143 GCAAATGACA
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
26 31 0.61
27 2 0.04
28 18 0.35
ACGTcount: A:0.34, C:0.01, G:0.11, T:0.54
Consensus pattern (26 bp):
TTAATTATGTTTATGATTGAATTTAT
Found at i:4577219 original size:6 final size:6
Alignment explanation
Indices: 4577208--4577242 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
4577198 ATATTTGCAT
*
4577208 ACATAA ACATAA ACATAA ACATAA ATATAA ACATA
1 ACATAA ACATAA ACATAA ACATAA ACATAA ACATA
4577243 TTTAATGGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.66, C:0.14, G:0.00, T:0.20
Consensus pattern (6 bp):
ACATAA
Found at i:4579685 original size:17 final size:17
Alignment explanation
Indices: 4579656--4579703 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
4579646 TTCATTTTAA
4579656 AAAATATTT-AATATAT
1 AAAATATTTAAATATAT
4579672 AAAATATTTAAATATAT
1 AAAATATTTAAATATAT
* *
4579689 CAAATGAATTAAATA
1 AAAAT-ATTTAAATA
4579704 AAATAATCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.32
17 11 0.39
18 8 0.29
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (17 bp):
AAAATATTTAAATATAT
Found at i:4581799 original size:1 final size:1
Alignment explanation
Indices: 4581795--4581824 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
4581785 AAGGAAAAGT
4581795 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
4581825 ATACAGGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:4595326 original size:15 final size:16
Alignment explanation
Indices: 4595306--4595340 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4595296 GACCCATGAG
*
4595306 TTTAAT-TTTTTTAAA
1 TTTAATCTTTTATAAA
4595321 TTTAATCTTTTATAAA
1 TTTAATCTTTTATAAA
4595337 TTTA
1 TTTA
4595341 CACTATATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTAATCTTTTATAAA
Found at i:4598089 original size:3 final size:3
Alignment explanation
Indices: 4598041--4598074 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
4598031 GGATCTATCC
4598041 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
4598075 TTCGAAGTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:4599092 original size:31 final size:31
Alignment explanation
Indices: 4599057--4599116 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
4599047 ACAGTCCAAC
4599057 GACTTAAATAAAAACTTTT-GAATAGTTCAAT
1 GACTTAAATAAAAA-TTTTCGAATAGTTCAAT
*
4599088 GACTTAAATGAAAATTTTCGAATAGTTCA
1 GACTTAAATAAAAATTTTCGAATAGTTCA
4599117 TGATCAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (31 bp):
GACTTAAATAAAAATTTTCGAATAGTTCAAT
Found at i:4599598 original size:21 final size:22
Alignment explanation
Indices: 4599574--4599614 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
4599564 GTTTTATTAC
*
4599574 TGTTTTTC-ACTATTTTGCTCA
1 TGTTTTCCTACTATTTTGCTCA
*
4599595 TGTTTTCCTATTATTTTGCT
1 TGTTTTCCTACTATTTTGCT
4599615 GTCATTTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.12, C:0.17, G:0.10, T:0.61
Consensus pattern (22 bp):
TGTTTTCCTACTATTTTGCTCA
Found at i:4607259 original size:23 final size:23
Alignment explanation
Indices: 4607233--4607277 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
4607223 AAAAATGTAT
4607233 ATAAAATCATAGCTAATTGAGTA
1 ATAAAATCATAGCTAATTGAGTA
4607256 ATAAAATCATAGCTAATTGAGT
1 ATAAAATCATAGCTAATTGAGT
4607278 CTTAGTTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (23 bp):
ATAAAATCATAGCTAATTGAGTA
Found at i:4608679 original size:11 final size:11
Alignment explanation
Indices: 4608648--4608680 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
4608638 ACGTTCTATA
4608648 TAGAAGGAAAG
1 TAGAAGGAAAG
4608659 TAGTAA-GAAAG
1 TAG-AAGGAAAG
4608670 TAGAAGGAAAG
1 TAGAAGGAAAG
4608681 AAAGAGAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.10
11 16 0.80
12 2 0.10
ACGTcount: A:0.55, C:0.00, G:0.33, T:0.12
Consensus pattern (11 bp):
TAGAAGGAAAG
Found at i:4616567 original size:7 final size:7
Alignment explanation
Indices: 4616555--4616595 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
4616545 GAGAAGGATC
4616555 AGCCATA
1 AGCCATA
4616562 AGCCATA
1 AGCCATA
4616569 AGCCATA
1 AGCCATA
4616576 AGCCATA
1 AGCCATA
4616583 AGCCATA
1 AGCCATA
4616590 AGCCAT
1 AGCCAT
4616596 TAGTAGCATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.41, C:0.29, G:0.15, T:0.15
Consensus pattern (7 bp):
AGCCATA
Found at i:4623612 original size:18 final size:20
Alignment explanation
Indices: 4623585--4623624 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
4623575 TACATGATTT
*
4623585 ATGTATATGTGA-ATA-GAA
1 ATGTAAATGTGATATATGAA
4623603 ATGTAAATGTGATATATGAA
1 ATGTAAATGTGATATATGAA
4623623 AT
1 AT
4623625 TATGAGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 3 0.16
20 5 0.26
ACGTcount: A:0.45, C:0.00, G:0.20, T:0.35
Consensus pattern (20 bp):
ATGTAAATGTGATATATGAA
Found at i:4623634 original size:24 final size:26
Alignment explanation
Indices: 4623607--4623654 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
4623597 ATAGAAATGT
4623607 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
4623631 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
4623655 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:4623799 original size:22 final size:23
Alignment explanation
Indices: 4623738--4623817 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
4623728 AGCACGTTTC
* *
4623738 GTGCCCTCTGTTCAGCATTGTGT
1 GTGCCTTCTGTTCAGCACTGTGT
*
4623761 GTGCCCTCTGTTCAGCACTGTGT
1 GTGCCTTCTGTTCAGCACTGTGT
* *
4623784 GTG-CTTCTGTTTAGCACTTTGT
1 GTGCCTTCTGTTCAGCACTGTGT
*
4623806 GTGCCTACTGTT
1 GTGCCTTCTGTT
4623818 TTTCCTGCAC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
22 19 0.37
23 32 0.63
ACGTcount: A:0.09, C:0.25, G:0.25, T:0.41
Consensus pattern (23 bp):
GTGCCTTCTGTTCAGCACTGTGT
Found at i:4627053 original size:21 final size:22
Alignment explanation
Indices: 4627029--4627070 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4627019 ATTGTATTTA
*
4627029 AAAAAAAT-ATTATTAAAAATT
1 AAAAAAATAATAATTAAAAATT
4627050 AAAAAAATAATAATTAAAAAT
1 AAAAAAATAATAATTAAAAAT
4627071 ATAACATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAAAATAATAATTAAAAATT
Found at i:4627074 original size:12 final size:12
Alignment explanation
Indices: 4627031--4627148 Score: 58
Period size: 12 Copynumber: 10.2 Consensus size: 12
4627021 TGTATTTAAA
*
4627031 AAAAATATTATT
1 AAAAATATAATT
4627043 AAAAAT-TAA--
1 AAAAATATAATT
4627052 AAAAATAATAATT
1 AAAAAT-ATAATT
4627065 AAAAATATAACATT
1 AAAAATAT-A-ATT
* *
4627079 GTAAATTAGTAATT
1 -AAAAATA-TAATT
*
4627093 --AAATATTATT
1 AAAAATATAATT
4627103 -AAAA-A-AATT
1 AAAAATATAATT
4627112 AAAAA-ATAAATT
1 AAAAATAT-AATT
*
4627124 -AAAATATTATT
1 AAAAATATAATT
*
4627135 AAAAATATACTT
1 AAAAATATAATT
4627147 AA
1 AA
4627149 CAATGCAAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 28
0.69 0.08 0.23
Matches are distributed among these distances:
9 9 0.11
10 10 0.12
11 19 0.23
12 25 0.30
13 7 0.08
14 6 0.07
15 6 0.07
16 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (12 bp):
AAAAATATAATT
Found at i:4632590 original size:19 final size:19
Alignment explanation
Indices: 4632557--4632637 Score: 69
Period size: 19 Copynumber: 4.2 Consensus size: 19
4632547 CAAAATTTTC
*
4632557 AAAATT-TATATTTTTAAA
1 AAAATTATAAATTTTTAAA
4632575 AAAATTATAAATTTTTAAA
1 AAAATTATAAATTTTTAAA
* * *
4632594 AAAATCTAAAAAATATATAAAA
1 AAAAT-T-ATAAAT-TTTTAAA
4632616 AAAAGTTA-AAA-TTTTAAA
1 AAAA-TTATAAATTTTTAAA
4632634 AAAA
1 AAAA
4632638 AATTAAAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
18 15 0.29
19 16 0.31
20 4 0.08
21 6 0.12
22 10 0.19
23 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (19 bp):
AAAATTATAAATTTTTAAA
Found at i:4632638 original size:19 final size:18
Alignment explanation
Indices: 4632566--4632646 Score: 72
Period size: 19 Copynumber: 4.1 Consensus size: 18
4632556 CAAAATTTAT
*
4632566 ATTTTTAAAAAAATTATAA
1 ATTTTAAAAAAAATTA-AA
*
4632585 ATTTTTAAAAAAATCTAAAAA
1 ATTTTAAAAAAAAT-T--AAA
*
4632606 ATATATAAAAAAAAGTTAAA
1 AT-TTTAAAAAAAA-TTAAA
4632626 ATTTTAAAAAAAAATTAAA
1 ATTTT-AAAAAAAATTAAA
4632645 AT
1 AT
4632647 AATAATTTTG
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
19 23 0.43
20 14 0.26
21 4 0.08
22 11 0.21
23 1 0.02
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (18 bp):
ATTTTAAAAAAAATTAAA
Found at i:4632925 original size:2 final size:2
Alignment explanation
Indices: 4632918--4632949 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4632908 AGCTGATCCC
4632918 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
4632950 AAGTAGAAAG
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):
TA
Found at i:4639174 original size:41 final size:41
Alignment explanation
Indices: 4639129--4639215 Score: 138
Period size: 41 Copynumber: 2.1 Consensus size: 41
4639119 AAGGGTTGTC
4639129 TATTTGGATATGTATAAATCAACATTTTAATCCAAATGAAG
1 TATTTGGATATGTATAAATCAACATTTTAATCCAAATGAAG
* * * *
4639170 TATTTGGGTATGTATACATCAGCCTTTTAATCCAAATGAAG
1 TATTTGGATATGTATAAATCAACATTTTAATCCAAATGAAG
4639211 TATTT
1 TATTT
4639216 TAATGGTGCC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (41 bp):
TATTTGGATATGTATAAATCAACATTTTAATCCAAATGAAG
Found at i:4645705 original size:31 final size:31
Alignment explanation
Indices: 4645643--4645723 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
4645633 GAACCCCAAA
* * *
4645643 AAGTTCAAGTACCAACTTAAAAAAATATGTC
1 AAGTTTAAATACCAAATTAAAAAAATATGTC
*
4645674 AAGTTTAAATACCAAATTAAGAAAAA-GTGTC
1 AAGTTTAAATACCAAATTAA-AAAAATATGTC
* *
4645705 AAATTTGAATACCAAATTA
1 AAGTTTAAATACCAAATTA
4645724 GACCAAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 38 0.88
32 5 0.12
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (31 bp):
AAGTTTAAATACCAAATTAAAAAAATATGTC
Found at i:4649864 original size:5 final size:5
Alignment explanation
Indices: 4649846--4649885 Score: 66
Period size: 5 Copynumber: 8.4 Consensus size: 5
4649836 GTCTTGCTGG
4649846 CTTG- CTTG- CTTGC CTTGC CTTGC CTTGC CTTGC CTTGC CT
1 CTTGC CTTGC CTTGC CTTGC CTTGC CTTGC CTTGC CTTGC CT
4649886 GCGTTTAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 8 0.23
5 27 0.77
ACGTcount: A:0.00, C:0.38, G:0.20, T:0.42
Consensus pattern (5 bp):
CTTGC
Found at i:4654653 original size:19 final size:19
Alignment explanation
Indices: 4654626--4654671 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
4654616 CTCGCAAAGG
4654626 AAAAA-GAAA-AAAGAAATT
1 AAAAAGGAAAGAAA-AAATT
* *
4654644 AATAAGGAAAGAAAACATT
1 AAAAAGGAAAGAAAAAATT
4654663 AAAAAGGAA
1 AAAAAGGAA
4654672 GATGAAAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 4 0.17
19 16 0.70
20 3 0.13
ACGTcount: A:0.72, C:0.02, G:0.15, T:0.11
Consensus pattern (19 bp):
AAAAAGGAAAGAAAAAATT
Found at i:4659653 original size:21 final size:21
Alignment explanation
Indices: 4659628--4659681 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
4659618 CATTCCAAAT
4659628 AACAAAACAAAAAATAAAAAC
1 AACAAAACAAAAAATAAAAAC
4659649 AACAAAACAAAAAATAAAAAC
1 AACAAAACAAAAAATAAAAAC
* *
4659670 AATATAACAAAA
1 AACAAAACAAAA
4659682 GTCAAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.80, C:0.13, G:0.00, T:0.07
Consensus pattern (21 bp):
AACAAAACAAAAAATAAAAAC
Found at i:4660270 original size:23 final size:23
Alignment explanation
Indices: 4660227--4660271 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4660217 AAAAAAATTC
**
4660227 AACTCGATTCGTTTAACTCGAAT
1 AACTCGATTCGAATAACTCGAAT
*
4660250 AACTCGATTCGAATAATTCGAA
1 AACTCGATTCGAATAACTCGAA
4660272 ATTCAAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (23 bp):
AACTCGATTCGAATAACTCGAAT
Found at i:4670010 original size:18 final size:18
Alignment explanation
Indices: 4669969--4670011 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
4669959 ACACAATAAA
4669969 AATAGTATTTTAATTTTAG
1 AATA-TATTTTAATTTTAG
* * *
4669988 GATATATTTTATTTTTAT
1 AATATATTTTAATTTTAG
4670006 AATATA
1 AATATA
4670012 ATTATATATA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (18 bp):
AATATATTTTAATTTTAG
Found at i:4673181 original size:6 final size:6
Alignment explanation
Indices: 4673160--4673275 Score: 112
Period size: 6 Copynumber: 19.8 Consensus size: 6
4673150 TGCTCAGCAA
* * * * *
4673160 CAACAG CAGCAG CAACAA CAACAG CAGCAG CAACAG CAGCAG CAGCAG
1 CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG
* * * * * *
4673208 CAACAA CAACAG CAACAG CAGCAG CAGCAA CAACAA CAACAA CAACAG
1 CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG
4673256 CAACAG ---CAG CAACAG CAACA
1 CAACAG CAACAG CAACAG CAACA
4673276 ACAGCAGCCG
Statistics
Matches: 93, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
3 3 0.03
6 90 0.97
ACGTcount: A:0.49, C:0.34, G:0.17, T:0.00
Consensus pattern (6 bp):
CAACAG
Found at i:4673293 original size:30 final size:30
Alignment explanation
Indices: 4673154--4673294 Score: 192
Period size: 30 Copynumber: 4.6 Consensus size: 30
4673144 GAGGCATGCT
*
4673154 CAGCAACAACAGCAGCAGCAACAACAACAGCA
1 CAGCAACAGCAGCAGCAGCAACAACAACA--A
*
4673186 GCAGCAACAGCAGCAGCAGCAGCAACAACAA
1 -CAGCAACAGCAGCAGCAGCAACAACAACAA
4673217 CAGCAACAGCAGCAGCAGCAACAACAACAA
1 CAGCAACAGCAGCAGCAGCAACAACAACAA
* * *
4673247 CAACAACAGCAACAGCAGCAACAGCAACAA
1 CAGCAACAGCAGCAGCAGCAACAACAACAA
* *
4673277 CAGCAGCCGCAGCAGCAG
1 CAGCAACAGCAGCAGCAG
4673295 TCGCCCCAGC
Statistics
Matches: 98, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
30 70 0.71
31 1 0.01
33 27 0.28
ACGTcount: A:0.47, C:0.34, G:0.19, T:0.00
Consensus pattern (30 bp):
CAGCAACAGCAGCAGCAGCAACAACAACAA
Found at i:4673307 original size:3 final size:3
Alignment explanation
Indices: 4673163--4673294 Score: 93
Period size: 3 Copynumber: 44.0 Consensus size: 3
4673153 TCAGCAACAA
* * * * *
4673163 CAG CAG CAG CAA CAA CAA CAG CAG CAG CAA CAG CAG CAG CAG CAG CAA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
* * * * * * * * * *
4673211 CAA CAA CAG CAA CAG CAG CAG CAG CAA CAA CAA CAA CAA CAA CAG CAA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
* * * *
4673259 CAG CAG CAA CAG CAA CAA CAG CAG CCG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
4673295 TCGCCCCAGC
Statistics
Matches: 111, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 111 1.00
ACGTcount: A:0.46, C:0.34, G:0.20, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:4674073 original size:14 final size:13
Alignment explanation
Indices: 4674054--4674092 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
4674044 GGTTTGTTTA
4674054 ATCTCTTTCACTTG
1 ATCTCTTTCA-TTG
4674068 ATCTCTTAT-ATTG
1 ATCTCTT-TCATTG
4674081 ATCTCTTTCATT
1 ATCTCTTTCATT
4674093 TGATGCTTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 13 0.57
14 8 0.35
15 1 0.04
ACGTcount: A:0.18, C:0.23, G:0.05, T:0.54
Consensus pattern (13 bp):
ATCTCTTTCATTG
Found at i:4675058 original size:6 final size:6
Alignment explanation
Indices: 4675047--4675097 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
4675037 TGGCTCAGTT
* *
4675047 GCAACA GCAACA G---CA GCAACT GCAACA ACAACA GCAACA GCAACA
1 GCAACA GCAACA GCAACA GCAACA GCAACA GCAACA GCAACA GCAACA
4675092 G-AACA G
1 GCAACA G
4675098 TAGCTCACAG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
3 3 0.08
5 5 0.13
6 30 0.79
ACGTcount: A:0.49, C:0.31, G:0.18, T:0.02
Consensus pattern (6 bp):
GCAACA
Found at i:4680152 original size:18 final size:20
Alignment explanation
Indices: 4680117--4680155 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
4680107 AAATGCAAAA
4680117 ATAATATAAAATATAAATTT
1 ATAATATAAAATATAAATTT
4680137 ATAA-ATAAAA-ATAAATTT
1 ATAATATAAAATATAAATTT
4680155 A
1 A
4680156 ATTAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
19 6 0.32
20 4 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAATATAAAATATAAATTT
Found at i:4684943 original size:22 final size:22
Alignment explanation
Indices: 4684915--4684958 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
4684905 AACTAGTTTC
4684915 TGTACAATATATCAATGAATAA
1 TGTACAATATATCAATGAATAA
4684937 TGTACAATATATCAATGAATAA
1 TGTACAATATATCAATGAATAA
4684959 ACTAGTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.32
Consensus pattern (22 bp):
TGTACAATATATCAATGAATAA
Found at i:4691412 original size:9 final size:8
Alignment explanation
Indices: 4691396--4691422 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
4691386 TGTATATTTT
4691396 ATAAAAAA
1 ATAAAAAA
4691404 ATAAAAAA
1 ATAAAAAA
4691412 ATAAAAAA
1 ATAAAAAA
4691420 ATA
1 ATA
4691423 CTTTCTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (8 bp):
ATAAAAAA
Found at i:4692366 original size:25 final size:25
Alignment explanation
Indices: 4692329--4692383 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
4692319 AGCTTCTTTT
*
4692329 TTTTTCCCATCTTTACT-TTTCTCTA
1 TTTTTCCCATCTTCACTCTTTCT-TA
** *
4692354 TTTTTCCTTTCTTCATTCTTTCTTA
1 TTTTTCCCATCTTCACTCTTTCTTA
4692379 TTTTT
1 TTTTT
4692384 GTTTTTGCTG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 20 0.80
26 5 0.20
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTTTCCCATCTTCACTCTTTCTTA
Found at i:4693115 original size:16 final size:18
Alignment explanation
Indices: 4693083--4693122 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
4693073 TGGTGAGATG
4693083 CTGTTTTGGACTTGTGTA
1 CTGTTTTGGACTTGTGTA
*
4693101 -TGTTTT-GATTTGTGTA
1 CTGTTTTGGACTTGTGTA
4693117 CTGTTT
1 CTGTTT
4693123 GCTGTAGTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.10, C:0.07, G:0.25, T:0.57
Consensus pattern (18 bp):
CTGTTTTGGACTTGTGTA
Found at i:4695376 original size:57 final size:59
Alignment explanation
Indices: 4695296--4695449 Score: 192
Period size: 59 Copynumber: 2.6 Consensus size: 59
4695286 TATATTATAA
* * *
4695296 TTTTTACT-AATTCATATTTTAATAACAATTATATTAAAATATTATTAAATT-A-T-ATAT
1 TTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAATATAATTAAATTAATTAATAT
* *
4695353 TATTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATTAATTAATAT
1 T-TTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAATTAATAT
4695413 TTTTTATTAAATTATATTTAATAATAATCT-TATTAAA
1 TTTTTATTAAATTATATTTAATAATAAT-TATATTAAA
4695450 TTAATAACAA
Statistics
Matches: 84, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
57 32 0.38
58 9 0.11
59 37 0.44
60 6 0.07
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (59 bp):
TTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAATTAATAT
Found at i:4695630 original size:16 final size:16
Alignment explanation
Indices: 4695609--4695646 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
4695599 TGAATTATTA
4695609 ATTACAG-TCTTATTCC
1 ATTACAGCTC-TATTCC
*
4695625 ATTACAGCTCTATTCT
1 ATTACAGCTCTATTCC
4695641 ATTACA
1 ATTACA
4695647 ACGAACCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.42
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:4696525 original size:12 final size:12
Alignment explanation
Indices: 4696508--4696532 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4696498 AATTAATAAA
4696508 ATTAAAAATTAT
1 ATTAAAAATTAT
4696520 ATTAAAAATTAT
1 ATTAAAAATTAT
4696532 A
1 A
4696533 AAACCCGGTT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTAAAAATTAT
Found at i:4701855 original size:2 final size:2
Alignment explanation
Indices: 4701848--4701873 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4701838 AACTTTTAGT
4701848 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
4701874 AATCCTATAA
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):
TA
Found at i:4704939 original size:13 final size:13
Alignment explanation
Indices: 4704921--4704949 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
4704911 GTTACCGGCT
4704921 CCCGTATGATGTA
1 CCCGTATGATGTA
4704934 CCCGTATGATGTA
1 CCCGTATGATGTA
4704947 CCC
1 CCC
4704950 AGTCCTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.28
Consensus pattern (13 bp):
CCCGTATGATGTA
Found at i:4718180 original size:31 final size:31
Alignment explanation
Indices: 4718144--4718206 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
4718134 ACAAGAATAG
*
4718144 ATCAATTGAATCAGGAATCGAGTGAAGTATC
1 ATCAATTGAATCAGGAACCGAGTGAAGTATC
4718175 ATCAATTGAATCAGGAACCGAGTGAAGTATC
1 ATCAATTGAATCAGGAACCGAGTGAAGTATC
4718206 A
1 A
4718207 ATTCGAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (31 bp):
ATCAATTGAATCAGGAACCGAGTGAAGTATC
Found at i:4718962 original size:17 final size:17
Alignment explanation
Indices: 4718942--4718975 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4718932 TCATTAAGTA
4718942 GTACAAGTAATTAACAT
1 GTACAAGTAATTAACAT
4718959 GTACAAGTAATTAACAT
1 GTACAAGTAATTAACAT
4718976 TGTTAATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (17 bp):
GTACAAGTAATTAACAT
Found at i:4725149 original size:2 final size:2
Alignment explanation
Indices: 4725142--4725169 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4725132 TGGACTAAGG
4725142 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
4725170 ACACACACAC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:4745973 original size:3 final size:3
Alignment explanation
Indices: 4745967--4746001 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
4745957 TTTAAAAAAA
4745967 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
4746002 GCAATGGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:4775077 original size:31 final size:31
Alignment explanation
Indices: 4775040--4775106 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
4775030 AACAACTTAG
**
4775040 TGACTTATGTAAAAACTTTCGAATAATTTAA
1 TGACTTAAATAAAAACTTTCGAATAATTTAA
*
4775071 TGACTTAAATGAAAACTTTCGAATAATTTAA
1 TGACTTAAATAAAAACTTTCGAATAATTTAA
4775102 TGACT
1 TGACT
4775107 ATTTTGTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.37
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCGAATAATTTAA
Found at i:4779722 original size:30 final size:30
Alignment explanation
Indices: 4779675--4779767 Score: 100
Period size: 30 Copynumber: 3.1 Consensus size: 30
4779665 CTGTACTGGT
* * *
4779675 AACCTCGA-TATAGTGTCAACTTATGTGAGC
1 AACC-CGATTATAATGTCAGCTTGTGTGAGC
* *
4779705 AACCCGATTATATTGTCAGCTTGTGCGAGC
1 AACCCGATTATAATGTCAGCTTGTGTGAGC
*
4779735 ATCCCTG-TTATAATGTCAGCTTGTGTGAGC
1 AACCC-GATTATAATGTCAGCTTGTGTGAGC
4779765 AAC
1 AAC
4779768 TTATTCACTC
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
29 3 0.06
30 49 0.92
31 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (30 bp):
AACCCGATTATAATGTCAGCTTGTGTGAGC
Found at i:4780619 original size:18 final size:18
Alignment explanation
Indices: 4780586--4780632 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
4780576 AATGATGTAT
*
4780586 TTGAATTTAAATAGATGGA
1 TTGAATTT-GATAGATGGA
4780605 TTGAATTTGATAGATGGA
1 TTGAATTTGATAGATGGA
4780623 TTGAATTTGA
1 TTGAATTTGA
4780633 ATTTAAATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 19 0.70
19 8 0.30
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.40
Consensus pattern (18 bp):
TTGAATTTGATAGATGGA
Found at i:4788928 original size:20 final size:19
Alignment explanation
Indices: 4788894--4788935 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
4788884 CTGAAAATGG
4788894 TTTTTGAAAAATAAT-TTT
1 TTTTTGAAAAATAATATTT
4788912 TTTTTGAAAAAATTAATATTT
1 TTTTTG-AAAAA-TAATATTT
4788933 TTT
1 TTT
4788936 GTTGTTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.29
19 5 0.24
20 4 0.19
21 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTTTGAAAAATAATATTT
Found at i:4788936 original size:19 final size:18
Alignment explanation
Indices: 4788894--4788936 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
4788884 CTGAAAATGG
*
4788894 TTTTTGAAAAATAATTTT
1 TTTTTGAAAAATAATTAT
4788912 TTTTTGAAAAAATTAA-TAT
1 TTTTTG-AAAAA-TAATTAT
4788931 TTTTTG
1 TTTTTG
4788937 TTGTTTGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 6 0.27
19 13 0.59
20 3 0.14
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (18 bp):
TTTTTGAAAAATAATTAT
Found at i:4790625 original size:152 final size:152
Alignment explanation
Indices: 4790349--4790649 Score: 514
Period size: 152 Copynumber: 2.0 Consensus size: 152
4790339 ATAAACTATG
*
4790349 CAAATGAAGAAATTATATTTTTACTATCGTAAAAATCACAATTTAATTTCGACTCTCTCAAAAAA
1 CAAATGAAGAAATTATATTTTTACTATCGTAAAAATCACAATTTAATTTCGACTCCCTCAAAAAA
* *
4790414 AATTCTAATTTCTCCCGTGCAACCACACTCAAGGAGATAGCTAGAACGTGGTGGTATTCACTCAT
66 AATTCTAATTTCTCCCATGCAACCACACTCAAGGAGATAGCTAGAACCTGGTGGTATTCACTCAT
4790479 CA-AAGGATTGATTGTGAATATA
131 CATAA-GATTGATTGTGAATATA
* * **
4790501 CAAATGATGAAATTATATTTTTACTATTGTAAAAATCACAATTTAATTTCGACTCCCTTGAAAAA
1 CAAATGAAGAAATTATATTTTTACTATCGTAAAAATCACAATTTAATTTCGACTCCCTCAAAAAA
*
4790566 AATTCTAATTTCTCCCATGCAACCACACTCAAGGAGATAGCTATAACCTGGTGGTATTCACTCAT
66 AATTCTAATTTCTCCCATGCAACCACACTCAAGGAGATAGCTAGAACCTGGTGGTATTCACTCAT
4790631 CATAAGATTGATTGTGAAT
131 CATAAGATTGATTGTGAAT
4790650 TTCGATGAAT
Statistics
Matches: 140, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
152 138 0.99
153 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (152 bp):
CAAATGAAGAAATTATATTTTTACTATCGTAAAAATCACAATTTAATTTCGACTCCCTCAAAAAA
AATTCTAATTTCTCCCATGCAACCACACTCAAGGAGATAGCTAGAACCTGGTGGTATTCACTCAT
CATAAGATTGATTGTGAATATA
Found at i:4793298 original size:57 final size:58
Alignment explanation
Indices: 4793209--4793319 Score: 170
Period size: 57 Copynumber: 1.9 Consensus size: 58
4793199 TAAGTTTTTC
* *
4793209 AATGTAATTTTTTTTTAATTTGAATCGATCCAACTCGACTCATGAACAACTCTATTTG
1 AATGTAATTTTTCTCTAATTTGAATCGATCCAACTCGACTCATGAACAACTCTATTTG
** *
4793267 AATGTAA-TTTTCTCTAATTTGGGTCGATCCAACTCGACTCATGGACAACTCTA
1 AATGTAATTTTTCTCTAATTTGAATCGATCCAACTCGACTCATGAACAACTCTA
4793320 ATTACTGATA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 41 0.85
58 7 0.15
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.38
Consensus pattern (58 bp):
AATGTAATTTTTCTCTAATTTGAATCGATCCAACTCGACTCATGAACAACTCTATTTG
Found at i:4800591 original size:16 final size:17
Alignment explanation
Indices: 4800558--4800591 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4800548 TGACACGATG
4800558 TCAAGGTCTTTTTATTC
1 TCAAGGTCTTTTTATTC
*
4800575 TCAAGGT-TTTTTTTTC
1 TCAAGGTCTTTTTATTC
4800591 T
1 T
4800592 TAATCCCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.59
Consensus pattern (17 bp):
TCAAGGTCTTTTTATTC
Found at i:4821937 original size:25 final size:25
Alignment explanation
Indices: 4821903--4821953 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
4821893 ATATTAATTA
4821903 TATTATTGTAAAGAGATTTATATTG
1 TATTATTGTAAAGAGATTTATATTG
4821928 TATTATTGTAAAGAGATTTATATTG
1 TATTATTGTAAAGAGATTTATATTG
4821953 T
1 T
4821954 TATATAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (25 bp):
TATTATTGTAAAGAGATTTATATTG
Found at i:4825645 original size:3 final size:3
Alignment explanation
Indices: 4825639--4825669 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4825629 GAGGAGGAGG
4825639 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
4825670 AGATCGGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:4837684 original size:18 final size:18
Alignment explanation
Indices: 4837661--4837697 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
4837651 ATATAAGACA
4837661 AAATAGTGCCACGACAGC
1 AAATAGTGCCACGACAGC
*
4837679 AAATAGTGCCACGTCAGC
1 AAATAGTGCCACGACAGC
4837697 A
1 A
4837698 GCTGCATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.27, G:0.22, T:0.14
Consensus pattern (18 bp):
AAATAGTGCCACGACAGC
Found at i:4841894 original size:3 final size:3
Alignment explanation
Indices: 4841886--4841910 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4841876 AAACGAGTAG
4841886 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
4841911 CTTAGTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4844121 original size:25 final size:23
Alignment explanation
Indices: 4844085--4844182 Score: 144
Period size: 23 Copynumber: 4.2 Consensus size: 23
4844075 ACACTAGCGC
4844085 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
4844108 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
4844133 GCTCTCCGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
4844156 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
4844179 GCTC
1 GCTC
4844183 AGTACTTTGT
Statistics
Matches: 69, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
22 1 0.01
23 45 0.65
24 1 0.01
25 22 0.32
ACGTcount: A:0.12, C:0.24, G:0.23, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:4844156 original size:48 final size:46
Alignment explanation
Indices: 4844085--4844182 Score: 144
Period size: 48 Copynumber: 2.1 Consensus size: 46
4844075 ACACTAGCGC
*
4844085 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCCGATTAGCACTGTGTGTGCTCTCTG--ATTAGCACTGTGTGT
*
4844133 GCTCTCCGATTAGCACT-TCGTGTGCTCTCTGATTAGCACTTTGTGT
1 GCTCTCCGATTAGCACTGT-GTGTGCTCTCTGATTAGCACTGTGTGT
4844179 GCTC
1 GCTC
4844183 AGTACTTTGT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
46 18 0.38
47 1 0.02
48 28 0.60
ACGTcount: A:0.12, C:0.24, G:0.23, T:0.40
Consensus pattern (46 bp):
GCTCTCCGATTAGCACTGTGTGTGCTCTCTGATTAGCACTGTGTGT
Found at i:4844211 original size:39 final size:39
Alignment explanation
Indices: 4844147--4844221 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
4844137 TCCGATTAGC
*
4844147 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
4844186 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
4844222 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:4844216 original size:23 final size:23
Alignment explanation
Indices: 4844181--4844274 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
4844171 CTTTGTGTGC
*
4844181 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
4844204 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
4844227 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
4844252 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
4844274 T
1 T
4844275 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:4849958 original size:30 final size:30
Alignment explanation
Indices: 4849922--4849985 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
4849912 GTGAGATTTG
** *
4849922 AATTTTAAAATCTAAAAAATA-AAAGAATTA
1 AATTTTAAAAAAT-AAAAATACAAAAAATTA
4849952 AATTTTAAAAAATAAAAATACAAAAAATTA
1 AATTTTAAAAAATAAAAATACAAAAAATTA
4849982 AATT
1 AATT
4849986 CCAAACTTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 7 0.23
30 23 0.77
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (30 bp):
AATTTTAAAAAATAAAAATACAAAAAATTA
Found at i:4857904 original size:28 final size:24
Alignment explanation
Indices: 4857853--4857938 Score: 64
Period size: 25 Copynumber: 3.2 Consensus size: 24
4857843 AAGAGATATT
*
4857853 AAAAATTATAGAATTATTTAAAATATGA
1 AAAAATTATA-AA-AATTT-AAATA-GA
*
4857881 AAAAAGTTATAAAAAATTATAAATAGT
1 AAAAA-TTAT-AAAAATT-TAAATAGA
* *
4857908 AAAAATTATACAAATTTAAATAAGT
1 AAAAATTATAAAAATTTAAAT-AGA
4857933 AAAAAT
1 AAAAAT
4857939 ACTATTAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
24 5 0.10
25 15 0.29
26 4 0.08
27 6 0.12
28 13 0.25
29 7 0.14
30 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (24 bp):
AAAAATTATAAAAATTTAAATAGA
Found at i:4858223 original size:30 final size:30
Alignment explanation
Indices: 4858187--4858245 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
4858177 TTTGTGCAAT
4858187 TATGTAATATAATTTTGATTTTAATTCAAA
1 TATGTAATATAATTTTGATTTTAATTCAAA
4858217 TATGTAATATAATTTTGATTTTAATTCAA
1 TATGTAATATAATTTTGATTTTAATTCAA
4858246 TTGTACATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.39, C:0.03, G:0.07, T:0.51
Consensus pattern (30 bp):
TATGTAATATAATTTTGATTTTAATTCAAA
Found at i:4866484 original size:15 final size:15
Alignment explanation
Indices: 4866463--4866499 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
4866453 AGATTTAATA
*
4866463 ATTTTTATTCACATT
1 ATTTTTATTCAAATT
*
4866478 TTTTTTATTCAAATT
1 ATTTTTATTCAAATT
4866493 ATTTTTA
1 ATTTTTA
4866500 AAAAAAATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTTTTATTCAAATT
Found at i:4869841 original size:22 final size:22
Alignment explanation
Indices: 4869799--4869843 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
4869789 AATTATTAAA
*
4869799 TATTATTTAAATTTAATATATC
1 TATTATTTAAATGTAATATATC
*
4869821 TATTATTTATATAGTAAATATAT
1 TATTATTTAAAT-GT-AATATAT
4869844 TATATGGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.58
23 1 0.05
24 7 0.37
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TATTATTTAAATGTAATATATC
Found at i:4877564 original size:16 final size:16
Alignment explanation
Indices: 4877541--4877580 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
4877531 CGTTTGATTC
4877541 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
4877557 GGTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
4877573 GCTGTAAT
1 GCTGTAAT
4877581 CAGTAATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.35, C:0.05, G:0.33, T:0.28
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:4877780 original size:26 final size:26
Alignment explanation
Indices: 4877751--4877833 Score: 76
Period size: 26 Copynumber: 3.0 Consensus size: 26
4877741 TTTTAATGAT
4877751 TATTATTAAATATAATTTAATAAAAA
1 TATTATTAAATATAATTTAATAAAAA
* * * *
4877777 TATTAATTTATTTAATTATATTTTAACATAAT
1 TATT-A-TTA---AA-TATAATTTAATAAAAA
4877809 TATTATTAAATATAATTTAATAAAA
1 TATTATTAAATATAATTTAATAAAA
4877834 TAATATGTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
26 16 0.36
27 3 0.07
28 3 0.07
30 3 0.07
31 3 0.07
32 16 0.36
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (26 bp):
TATTATTAAATATAATTTAATAAAAA
Found at i:4877818 original size:58 final size:56
Alignment explanation
Indices: 4877749--4877894 Score: 188
Period size: 58 Copynumber: 2.5 Consensus size: 56
4877739 AATTTTAATG
*
4877749 ATTATTATTAAATATAATTTAATAAAAATAT-TAATTTATTTAATTATATTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATATGTAATTTA-ATAA-TAT-TTTTAACATA
*
4877807 ATTATTATTAAATATAATTTAATAAAATAATATGTAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAATTTAAT-AAA-AATATGTAATTTAATAATATTTTTAACATA
*
4877865 ATTATTATTAAAATATGAA-TTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTTAATAAAAAT
4877895 TATAATAATA
Statistics
Matches: 80, Mismatches: 3, Indels: 11
0.85 0.03 0.12
Matches are distributed among these distances:
57 3 0.04
58 44 0.55
59 16 0.20
60 10 0.12
61 7 0.09
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (56 bp):
ATTATTATTAAATATAATTTAATAAAAATATGTAATTTAATAATATTTTTAACATA
Found at i:4887422 original size:22 final size:22
Alignment explanation
Indices: 4887397--4887438 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
4887387 TCCAAAAATT
*
4887397 ATGATTAAAAAGATATAAATAA
1 ATGAATAAAAAGATATAAATAA
**
4887419 ATGAATAAAGTGATATAAAT
1 ATGAATAAAAAGATATAAAT
4887439 TGGAGTAGAG
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:0.60, C:0.00, G:0.12, T:0.29
Consensus pattern (22 bp):
ATGAATAAAAAGATATAAATAA
Found at i:4890471 original size:20 final size:20
Alignment explanation
Indices: 4890428--4890473 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
4890418 CTGGTCTGAT
* **
4890428 ATTTCATTATTTTTCTCTTT
1 ATTTTATTATTTTTCTCTAC
*
4890448 ATTTTATTATTTTTTTCTAC
1 ATTTTATTATTTTTCTCTAC
4890468 ATTTTA
1 ATTTTA
4890474 ATTTCGTTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.70
Consensus pattern (20 bp):
ATTTTATTATTTTTCTCTAC
Found at i:4892104 original size:9 final size:9
Alignment explanation
Indices: 4892075--4892114 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
4892065 TGTATATATT
4892075 TATTTTA-A
1 TATTTTATA
*
4892083 TATTTAATA
1 TATTTTATA
4892092 -ATTTTATA
1 TATTTTATA
4892100 TATTTTATA
1 TATTTTATA
4892109 TATTTT
1 TATTTT
4892115 CTTATTGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 13 0.46
9 15 0.54
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TATTTTATA
Found at i:4892104 original size:17 final size:17
Alignment explanation
Indices: 4892075--4892114 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
4892065 TGTATATATT
4892075 TATTTTAATATTTAATA
1 TATTTTAATATTTAATA
*
4892092 -ATTTTATATATTTTATA
1 TATTTTA-ATATTTAATA
4892109 TATTTT
1 TATTTT
4892115 CTTATTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 6 0.30
17 9 0.45
18 5 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTAATA
Found at i:4900394 original size:1 final size:1
Alignment explanation
Indices: 4900388--4900412 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
4900378 AGCGGACAAA
4900388 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
4900413 ATCTTTGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:4908276 original size:13 final size:12
Alignment explanation
Indices: 4908253--4908292 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
4908243 TTATAAAAGA
4908253 AAAAATTAATAT
1 AAAAATTAATAT
*
4908265 AAAAATTGA-AT
1 AAAAATTAATAT
4908276 --AAATTAATAT
1 AAAAATTAATAT
4908286 AAAAATT
1 AAAAATT
4908293 GAATGTGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
9 6 0.26
10 2 0.09
11 2 0.09
12 13 0.57
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (12 bp):
AAAAATTAATAT
Found at i:4908281 original size:21 final size:21
Alignment explanation
Indices: 4908255--4908296 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
4908245 ATAAAAGAAA
4908255 AAATTAATATAAAAATTGAAT
1 AAATTAATATAAAAATTGAAT
4908276 AAATTAATATAAAAATTGAAT
1 AAATTAATATAAAAATTGAAT
4908297 GTGATTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (21 bp):
AAATTAATATAAAAATTGAAT
Found at i:4908980 original size:20 final size:20
Alignment explanation
Indices: 4908939--4908982 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
4908929 AAAAAGTATA
**
4908939 TAAAGATATATAAATATTTT
1 TAAAGATATATAAATAAATT
4908959 TAAAGATATA-ATAATAAATT
1 TAAAGATATATA-AATAAATT
4908979 TAAA
1 TAAA
4908983 AAATATGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (20 bp):
TAAAGATATATAAATAAATT
Found at i:4908982 original size:51 final size:51
Alignment explanation
Indices: 4908926--4909034 Score: 130
Period size: 51 Copynumber: 2.1 Consensus size: 51
4908916 TCTGAAATTT
* * * *
4908926 TTTAAAAAGTATATAAAGATATATAAATATTTTT-AAAGATATAATAATAAA
1 TTTAAAAAATATATAAAAATAAATAAAT-TTTTTAAAAAATATAATAATAAA
* * *
4908977 TTTAAAAAATATGTAAAAATAAATATATTTTTTGAAAAAATATAATAGTAAA
1 TTTAAAAAATATATAAAAATAAATAAATTTTTT-AAAAAATATAATAATAAA
4909029 TTTAAA
1 TTTAAA
4909035 TTTTATATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
50 5 0.10
51 23 0.47
52 21 0.43
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.38
Consensus pattern (51 bp):
TTTAAAAAATATATAAAAATAAATAAATTTTTTAAAAAATATAATAATAAA
Found at i:4913534 original size:21 final size:21
Alignment explanation
Indices: 4913494--4913534 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4913484 TTTGGGTTTG
* * *
4913494 TTTAAATATTAATGTTAAATA
1 TTTAAATACTAATATAAAATA
4913515 TTTAAATACTAATATAAAAT
1 TTTAAATACTAATATAAAAT
4913535 TTCATTTTAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
TTTAAATACTAATATAAAATA
Found at i:4922789 original size:20 final size:20
Alignment explanation
Indices: 4922763--4922814 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
4922753 ATGTATTGAT
*
4922763 GTATTGATATCT-TATTAAA
1 GTATTGATATCTGGATTAAA
*
4922782 GTTATTGATAT-TGGATTCAA
1 G-TATTGATATCTGGATTAAA
4922802 GTATTGATATCTG
1 GTATTGATATCTG
4922815 AATATAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (20 bp):
GTATTGATATCTGGATTAAA
Found at i:4931484 original size:92 final size:93
Alignment explanation
Indices: 4931196--4931508 Score: 301
Period size: 96 Copynumber: 3.3 Consensus size: 93
4931186 GGGACCCCGT
* * * *
4931196 TGATCCCTTGAAATCATTAAAAGACACGTCACTGCATCTTCACTAAATTAAGGCTCAAGAGGAAG
1 TGATCCCTTGAAAGCATTAAAAGACACATCACAGCATCTTCACTAAA-T-AGGATCAAGAGGAAG
*
4931261 TGCTTCAGATTGGTTTGGTTTTGGACTCCAC
64 TGCTTCA-ATTGGTTTTGTTTTGGACTCCAC
* * * * * * *
4931292 TAATCCTTTGAAAACATTAAAAGATACATCACAACATCTTCACTAGATAAAGGTTCATA-AGGAA
1 TGATCCCTTGAAAGCATTAAAAGACACATCACAGCATCTTCACTA-A-ATAGGATCA-AGAGGAA
* * *
4931356 GTGCTTCAGTTCGGTCTTGTTTGGGACTCCAC
63 GTGCTTCAATT-GGTTTTGTTTTGGACTCCAC
* * * *
4931388 TGATCCCTTGAAAGCA-TAAAAGGCGCATCGCAGCATCTTCACTAAATA-GATCACGAGGAAGTG
1 TGATCCCTTGAAAGCATTAAAAGACACATCACAGCATCTTCACTAAATAGGATCAAGAGGAAGTG
*
4931451 CTTCAACTTGGTTTTGTTTTGGAC-CCAAT
66 CTTCAA-TTGGTTTTGTTTTGGACTCC-AC
* * * *
4931480 TGATCCTTTGAAAGTACTAAAAAACACAT
1 TGATCCCTTGAAAGCATTAAAAGACACAT
4931509 TTCAACATTT
Statistics
Matches: 176, Mismatches: 33, Indels: 19
0.77 0.14 0.08
Matches are distributed among these distances:
91 2 0.01
92 45 0.26
93 13 0.07
94 1 0.01
95 25 0.14
96 87 0.49
97 2 0.01
98 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.29
Consensus pattern (93 bp):
TGATCCCTTGAAAGCATTAAAAGACACATCACAGCATCTTCACTAAATAGGATCAAGAGGAAGTG
CTTCAATTGGTTTTGTTTTGGACTCCAC
Found at i:4931488 original size:188 final size:192
Alignment explanation
Indices: 4931182--4931537 Score: 445
Period size: 188 Copynumber: 1.9 Consensus size: 192
4931172 AAGTGCTTTA
** * * *
4931182 GTTTGGGACCCCGTTGATCCCTTGAAATCATTAAAAGACACGTCACTGCATCTTCACTAAATTAA
1 GTTTGGGACCCCACTGATCCCTTGAAAGCATTAAAAGACACATCACAGCATCTTCACTAAATTAA
* *
4931247 GGCTCAAGAGGAAGTGCTTCAGATTGGTTTGGTTTTGGACTCCACTAATCCTTTGAAAACATTAA
66 GGATCAAGAGGAAGTGCTTCAGATTGGTTTGGTTTTGGACTCCACTAATCCTTTGAAAACACTAA
* * *
4931312 AAGATACATCACAACATCTTCACTAGATAAAGGTTCATAAGGAAGTGCTTCAGTTCGGTCTT
131 AAAACACATCACAACATCTTCACTAGATAAAGATTCATAAGGAAGTGCTTCAGTTCGGTCTT
* * * *
4931374 GTTTGGGACTCCACTGATCCCTTGAAAGCA-TAAAAGGCGCATCGCAGCATCTTCACTAAA-T-A
1 GTTTGGGACCCCACTGATCCCTTGAAAGCATTAAAAGACACATCACAGCATCTTCACTAAATTAA
* * * * **
4931436 -GATCACGAGGAAGTGCTTCA-ACTTGGTTTTGTTTTGGAC-CCAATTGATCCTTTGAAAGTACT
66 GGATCAAGAGGAAGTGCTTCAGA-TTGGTTTGGTTTTGGACTCC-ACTAATCCTTTGAAAACACT
** *
4931498 AAAAAACACATTTCAACATTTTCACTAGATAAAGATTCAT
129 AAAAAACACATCACAACATCTTCACTAGATAAAGATTCAT
4931538 GAGAAAGAGC
Statistics
Matches: 139, Mismatches: 23, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
187 3 0.02
188 83 0.60
189 1 0.01
190 1 0.01
191 25 0.18
192 26 0.19
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (192 bp):
GTTTGGGACCCCACTGATCCCTTGAAAGCATTAAAAGACACATCACAGCATCTTCACTAAATTAA
GGATCAAGAGGAAGTGCTTCAGATTGGTTTGGTTTTGGACTCCACTAATCCTTTGAAAACACTAA
AAAACACATCACAACATCTTCACTAGATAAAGATTCATAAGGAAGTGCTTCAGTTCGGTCTT
Found at i:4931718 original size:19 final size:19
Alignment explanation
Indices: 4931691--4931731 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
4931681 AAGTGAAGAA
4931691 AAGGCGGATTTAAAGATCT
1 AAGGCGGATTTAAAGATCT
* *
4931710 AAGGTGGATTTAAATATCT
1 AAGGCGGATTTAAAGATCT
4931729 AAG
1 AAG
4931732 TGAAGAAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.29
Consensus pattern (19 bp):
AAGGCGGATTTAAAGATCT
Found at i:4932184 original size:42 final size:42
Alignment explanation
Indices: 4932104--4932185 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
4932094 AATCTAGTGA
* * **
4932104 AGATGTTATAATGTGTCTTTAATACTTTCAGGTTATCAGCGG
1 AGATGTTACAATGCGTCTTTAATACTTTCAGGAGATCAGCGG
4932146 AGATGTTACAATGCGTCTTTAATACTTTCAGGAGATCAGC
1 AGATGTTACAATGCGTCTTTAATACTTTCAGGAGATCAGC
4932186 AGATTCCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.37
Consensus pattern (42 bp):
AGATGTTACAATGCGTCTTTAATACTTTCAGGAGATCAGCGG
Found at i:4934927 original size:26 final size:25
Alignment explanation
Indices: 4934855--4934927 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 25
4934845 GGTCGAAGGT
* * *
4934855 TCCTTGAGTTTAAGTAGGTTCGAGG
1 TCCTTGAGTTTGAGTTGGTTGGAGG
*
4934880 ATCCTTGAGTTTGAGATGGTTGGAGG
1 -TCCTTGAGTTTGAGTTGGTTGGAGG
4934906 TCCCTTGAGTTTGAGTTGGTTG
1 T-CCTTGAGTTTGAGTTGGTTG
4934928 AAGGACCATG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
25 1 0.02
26 40 0.98
ACGTcount: A:0.16, C:0.11, G:0.34, T:0.38
Consensus pattern (25 bp):
TCCTTGAGTTTGAGTTGGTTGGAGG
Found at i:4936103 original size:19 final size:21
Alignment explanation
Indices: 4936066--4936105 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
4936056 TTTAAAATCG
*
4936066 AAATTAATATGATTTAAACTT
1 AAATTAATATGATTGAAACTT
4936087 AAATTAA-A-GATTGAAACTT
1 AAATTAATATGATTGAAACTT
4936106 GTAATTTCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 1 0.06
21 7 0.39
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (21 bp):
AAATTAATATGATTGAAACTT
Found at i:4942733 original size:24 final size:24
Alignment explanation
Indices: 4942705--4942755 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
4942695 AGAGTGACTC
*
4942705 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAACTG
4942729 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAACTG
4942753 AAA
1 AAA
4942756 GATTATTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACTG
Found at i:4952287 original size:17 final size:17
Alignment explanation
Indices: 4952265--4952303 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
4952255 AGGTGGAGAA
* *
4952265 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
4952282 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
4952299 CTTGT
1 CTTGT
4952304 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:4956980 original size:17 final size:17
Alignment explanation
Indices: 4956958--4957002 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
4956948 TCCTCTATGT
* *
4956958 TAGAATAAATATTAAAA
1 TAGAATAAAAATCAAAA
4956975 TAGAATAAAAATCAAAA
1 TAGAATAAAAATCAAAA
*
4956992 TAAAATAAAAA
1 TAGAATAAAAA
4957003 AAAAAGCTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.22
Consensus pattern (17 bp):
TAGAATAAAAATCAAAA
Found at i:4958548 original size:27 final size:27
Alignment explanation
Indices: 4958500--4958573 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
4958490 AAATATATAG
*** **
4958500 AAAAAATTATAAATTTTATAAAGTCAT
1 AAAAAATTATAAAAAATATAAAGAAAT
*
4958527 AAAAAATTATAAAAAATGTAAAGAAAT
1 AAAAAATTATAAAAAATATAAAGAAAT
*
4958554 ATAAAATTCATAAAAAATAT
1 AAAAAATT-ATAAAAAATAT
4958574 CAAAATTATC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 28 0.74
28 10 0.26
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.30
Consensus pattern (27 bp):
AAAAAATTATAAAAAATATAAAGAAAT
Found at i:4958789 original size:27 final size:28
Alignment explanation
Indices: 4958759--4958829 Score: 67
Period size: 27 Copynumber: 2.5 Consensus size: 28
4958749 TTTTATAGAA
*
4958759 TTTTATAATTTTTTACTAT-TTTTATTTT
1 TTTTAT-ATTTTTTAATATATTTTATTTT
*
4958787 TTTTCTGA-TTTTTAATATATTTTA-TTT
1 TTTTAT-ATTTTTTAATATATTTTATTTT
*
4958814 TTATATATTTTATTAA
1 TTTTATATTTT-TTAA
4958830 AATTTAATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
26 1 0.03
27 19 0.54
28 15 0.43
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.70
Consensus pattern (28 bp):
TTTTATATTTTTTAATATATTTTATTTT
Found at i:4958790 original size:28 final size:28
Alignment explanation
Indices: 4958759--4958815 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
4958749 TTTTATAGAA
*
4958759 TTTTATAATTTTTTACTAT-TTTTATTTT
1 TTTTATAA-TTTTTAATATATTTTATTTT
* *
4958787 TTTTCTGATTTTTAATATATTTTATTTT
1 TTTTATAATTTTTAATATATTTTATTTT
4958815 T
1 T
4958816 ATATATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 9 0.36
28 16 0.64
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (28 bp):
TTTTATAATTTTTAATATATTTTATTTT
Found at i:4958819 original size:15 final size:16
Alignment explanation
Indices: 4958794--4958827 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
4958784 TTTTTTTCTG
4958794 ATTTTTAATATATTTT
1 ATTTTTAATATATTTT
4958810 ATTTTT-ATATATTTT
1 ATTTTTAATATATTTT
4958825 ATT
1 ATT
4958828 AAAATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTTTAATATATTTT
Found at i:4962660 original size:9 final size:10
Alignment explanation
Indices: 4962646--4962686 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
4962636 TCATCATTCG
4962646 AAAAT-TAAA
1 AAAATATAAA
4962655 AAAAT-T-AA
1 AAAATATAAA
*
4962663 AAAATATATA
1 AAAATATAAA
4962673 AAAATATAAA
1 AAAATATAAA
4962683 AAAA
1 AAAA
4962687 AATTATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 7 0.25
9 7 0.25
10 14 0.50
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (10 bp):
AAAATATAAA
Found at i:4986566 original size:16 final size:15
Alignment explanation
Indices: 4986545--4986575 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
4986535 GTTTGACGAA
4986545 TTTTTTTCAAATAATT
1 TTTTTTTCAAA-AATT
4986561 TTTTTTTCAAAAATT
1 TTTTTTTCAAAAATT
4986576 AATCCTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTTTTCAAAAATT
Found at i:4986828 original size:22 final size:23
Alignment explanation
Indices: 4986780--4986828 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
4986770 CATGATTTAA
*
4986780 ATAAATATTGATATTTATATAAT
1 ATAAATATTCATATTTATATAAT
*
4986803 -TAAATATTCATATTT-TATACT
1 ATAAATATTCATATTTATATAAT
4986824 ATAAA
1 ATAAA
4986829 ACATTTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (23 bp):
ATAAATATTCATATTTATATAAT
Found at i:4987825 original size:30 final size:28
Alignment explanation
Indices: 4987782--4987838 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 28
4987772 AAAATTTTAT
** *
4987782 TTTTAAATTTAAAAAGTAAATAAATTAAAA
1 TTTTAAAAATAAAAA-TAAA-AAACTAAAA
4987812 TTTTAAAAATAAAAATAAAAAACTAAA
1 TTTTAAAAATAAAAATAAAAAACTAAA
4987839 TTTCGAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 7 0.29
29 4 0.17
30 13 0.54
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (28 bp):
TTTTAAAAATAAAAATAAAAAACTAAAA
Found at i:4992891 original size:3 final size:3
Alignment explanation
Indices: 4992883--4992912 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4992873 GCCACCTTCA
4992883 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4992913 ATTTACTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5009794 original size:21 final size:23
Alignment explanation
Indices: 5009748--5009826 Score: 113
Period size: 23 Copynumber: 3.4 Consensus size: 23
5009738 AGCACGTCTC
5009748 GTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* *
5009771 GTGCTCTTTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* * *
5009794 GTACTCTCTGTTTAGCACTGTGT
1 GTGCTCTCTGATTAGCACTTTGT
5009817 GTGCTCTCTG
1 GTGCTCTCTG
5009827 TTGCCCAGCA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTTTGT
Found at i:5009827 original size:23 final size:23
Alignment explanation
Indices: 5009735--5009828 Score: 100
Period size: 23 Copynumber: 4.1 Consensus size: 23
5009725 GCACTCTTTA
*
5009735 TTTAGCAC-GTCTCGTGCTCTCTG
1 TTTAGCACTGTGT-GTGCTCTCTG
* * *
5009758 ATTAGCACTTTGTGTGCTCTTTG
1 TTTAGCACTGTGTGTGCTCTCTG
* * * *
5009781 ATTAGTACTTTGTGTACTCTCTG
1 TTTAGCACTGTGTGTGCTCTCTG
5009804 TTTAGCACTGTGTGTGCTCTCTG
1 TTTAGCACTGTGTGTGCTCTCTG
5009827 TT
1 TT
5009829 GCCCAGCACT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 57 0.97
24 2 0.03
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (23 bp):
TTTAGCACTGTGTGTGCTCTCTG
Found at i:5014202 original size:23 final size:23
Alignment explanation
Indices: 5014176--5014360 Score: 190
Period size: 23 Copynumber: 8.2 Consensus size: 23
5014166 ACACTAGCGC
5014176 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
5014199 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
5014222 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
5014247 GCTCTCTGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
5014270 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
5014293 G--CTC-----AGTACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
5014309 ACTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
5014334 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
5014357 GCTC
1 GCTC
5014361 AGTACTTTGT
Statistics
Matches: 137, Mismatches: 10, Indels: 30
0.77 0.06 0.17
Matches are distributed among these distances:
16 11 0.08
18 3 0.02
21 3 0.02
22 4 0.03
23 78 0.57
24 1 0.01
25 34 0.25
26 3 0.02
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:5014245 original size:48 final size:45
Alignment explanation
Indices: 5014176--5014355 Score: 194
Period size: 48 Copynumber: 4.0 Consensus size: 45
5014166 ACACTAGCGC
* *
5014176 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTCT-GT
5014222 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGATTAGCACTTC-TGT
* * * *
5014270 GCTCTCTGATTAGCACTTTGTGTG--CTC--AGTA-C-TTTGTGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTCTGT
*
5014309 ACTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTT-TGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGATTAGCACTTCTGT
5014355 G
1 G
5014356 TGCTCAGTAC
Statistics
Matches: 112, Mismatches: 11, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
39 10 0.09
40 2 0.02
41 16 0.14
42 3 0.03
43 3 0.03
44 3 0.03
45 3 0.03
46 27 0.24
47 2 0.02
48 42 0.38
49 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.23, T:0.42
Consensus pattern (45 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTCTGT
Found at i:5014326 original size:41 final size:39
Alignment explanation
Indices: 5014261--5014337 Score: 109
Period size: 41 Copynumber: 1.9 Consensus size: 39
5014251 TCTGATTAGC
* *
5014261 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTGTGTGTGCTCAGT
*
5014300 ACTTTGTGTACTCTCTGTTATTAGCACTGTGTGTGCTC
1 ACTTCGTGTACTCTCTG--ATTAGCACTGTGTGTGCTC
5014338 TCTGATTAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 15 0.45
41 18 0.55
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTGTGTGTGCTCAGT
Found at i:5014391 original size:87 final size:84
Alignment explanation
Indices: 5014194--5014405 Score: 232
Period size: 87 Copynumber: 2.4 Consensus size: 84
5014184 ATTAGCACTG
* *
5014194 TGTGTGCTCTCTGTTTAGCACGTCTCGTG-CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATT
1 TGTGTACTCTCTGTTTAGCAC-T-TTGTGTCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATT
5014258 AGCACTTCGTGTGCTCTCTGAT
64 AGCACTTCGTGTGCTCTCT-AT
* * * * * *
5014280 T-AGCACTTTGTGTGCTCAGTACTTTGTGTACTCTCTGTTATTAGCACTGTGTGTGCTCTCTGAT
1 TGTGTACTCTCTGT--TTAGCACTTTGTGT-CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGAT
*
5014344 TAGCACTTTGTGTGCTCAGTACT-T
63 TAGCACTTCGTGTGCTC--T-CTAT
5014368 TGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTT
1 TGTGTACTCTCTGTTTAGCACTTTGTGT-CTCTCTGTT
5014406 GCCCAGCACT
Statistics
Matches: 102, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
85 11 0.11
86 2 0.02
87 76 0.75
88 2 0.02
89 9 0.09
90 2 0.02
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (84 bp):
TGTGTACTCTCTGTTTAGCACTTTGTGTCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAG
CACTTCGTGTGCTCTCTAT
Found at i:5014394 original size:23 final size:23
Alignment explanation
Indices: 5014359--5014452 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
5014349 CTTTGTGTGC
*
5014359 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
5014382 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
5014405 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
5014430 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
5014452 T
1 T
5014453 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Done.