Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 66 of 204
Found at i:20976686 original size:25 final size:27
Alignment explanation
Indices: 20976648--20976697 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
20976638 GATAAATTAT
*
20976648 TAAAAATAGGTAAAT-TTAT-TATTCA
1 TAAAAATAGATAAATGTTATATATTCA
*
20976673 TAAAAATATATAAATGTTATATATT
1 TAAAAATAGATAAATGTTATATATT
20976698 ATTTCTATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 13 0.62
26 4 0.19
27 4 0.19
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (27 bp):
TAAAAATAGATAAATGTTATATATTCA
Found at i:20978652 original size:20 final size:19
Alignment explanation
Indices: 20978627--20978702 Score: 68
Period size: 19 Copynumber: 4.0 Consensus size: 19
20978617 TAACTATTAG
20978627 AAATTATTAAAATATTATAA
1 AAATTATTAAAAT-TTATAA
* **
20978647 AAATTA-TGAACCTTATAGA
1 AAATTATTAAAATTTATA-A
*
20978666 AAAAT-TTAAAATTT-TAA
1 AAATTATTAAAATTTATAA
20978683 AAATTATTAGAAATTTATAA
1 AAATTATTA-AAATTTATAA
20978703 TATATAGAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
17 5 0.12
18 10 0.23
19 19 0.44
20 9 0.21
ACGTcount: A:0.55, C:0.03, G:0.04, T:0.38
Consensus pattern (19 bp):
AAATTATTAAAATTTATAA
Found at i:20978785 original size:24 final size:24
Alignment explanation
Indices: 20978748--20978822 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 24
20978738 ATTACTTATC
20978748 ATTTTATAAAATTTTAATAATTTT
1 ATTTTATAAAATTTTAATAATTTT
* * *
20978772 ATTTTGTAAGATTTCAATAATTTTT
1 ATTTTATAAAATTTTAATAA-TTTT
* ** *
20978797 ATTATTTTATTATTTTAACAATTTT
1 ATT-TTATAAAATTTTAATAATTTT
20978822 A
1 A
20978823 ATATAATTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
24 17 0.41
25 12 0.29
26 12 0.29
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (24 bp):
ATTTTATAAAATTTTAATAATTTT
Found at i:20978864 original size:18 final size:19
Alignment explanation
Indices: 20978841--20978888 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
20978831 TTCTATAAAA
*
20978841 AAATTTTTATAGTTT-TAT
1 AAATTTTTATAATTTCTAT
* *
20978859 AAATTTCTATAATTTCTCT
1 AAATTTTTATAATTTCTAT
20978878 -AATTTTTATAA
1 AAATTTTTATAA
20978889 ATTTTATGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 23 0.92
19 2 0.08
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.56
Consensus pattern (19 bp):
AAATTTTTATAATTTCTAT
Found at i:20981923 original size:15 final size:16
Alignment explanation
Indices: 20981894--20981923 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20981884 CAAACATGTT
20981894 TTAACACATTATCAAA
1 TTAACACATTATCAAA
20981910 TTAACACA-TATCAA
1 TTAACACATTATCAA
20981924 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:20984061 original size:5 final size:5
Alignment explanation
Indices: 20984053--20984084 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
20984043 AACAAAACAT
*
20984053 TTTAG TTTAA TTTAA TTTAA TTTAA TTTAA TT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TT
20984085 ATCAAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:20991382 original size:16 final size:16
Alignment explanation
Indices: 20991361--20991392 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20991351 TGTTGTTTTA
20991361 ATATAAATGAATCAAT
1 ATATAAATGAATCAAT
*
20991377 ATATAAATGTATCAAT
1 ATATAAATGAATCAAT
20991393 GCTATGATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.34
Consensus pattern (16 bp):
ATATAAATGAATCAAT
Found at i:20992591 original size:24 final size:24
Alignment explanation
Indices: 20992558--20992603 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
20992548 AATTTTGGGT
*
20992558 TCACATGGCCTGAG-ACACGAGCTG
1 TCACACGGCCTG-GCACACGAGCTG
20992582 TCACACGGCCTGGCACACGAGC
1 TCACACGGCCTGGCACACGAGC
20992604 ATGTGTGGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.24, C:0.35, G:0.28, T:0.13
Consensus pattern (24 bp):
TCACACGGCCTGGCACACGAGCTG
Found at i:20993831 original size:24 final size:26
Alignment explanation
Indices: 20993773--20993832 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 26
20993763 GACCAAAATT
* *
20993773 AGAATTAATAAAATAGAAAGGAATTAA
1 AGAATAAATAAAACAGAAA-GAATTAA
20993800 AGAAATAAATAAAACAGAAA-AATTAA
1 AG-AATAAATAAAACAGAAAGAATTAA
20993826 AG-ATAAA
1 AGAATAAA
20993833 AAGTAGTCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 5 0.17
26 8 0.27
27 2 0.07
28 15 0.50
ACGTcount: A:0.68, C:0.02, G:0.12, T:0.18
Consensus pattern (26 bp):
AGAATAAATAAAACAGAAAGAATTAA
Found at i:20997520 original size:15 final size:15
Alignment explanation
Indices: 20997502--20997532 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
20997492 GTTTGGATAG
20997502 GCGATTGGGTGCGGT
1 GCGATTGGGTGCGGT
20997517 GCGATTGGGTGCGGT
1 GCGATTGGGTGCGGT
20997532 G
1 G
20997533 TGGTACGGTG
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:0.06, C:0.13, G:0.55, T:0.26
Consensus pattern (15 bp):
GCGATTGGGTGCGGT
Found at i:20999469 original size:24 final size:24
Alignment explanation
Indices: 20999442--20999491 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
20999432 GAACGATTCA
*
20999442 TTTAGTATTTTAGGAACATGTTTG
1 TTTAGTATTTTAGGAACATGCTTG
*
20999466 TTTAGTGTTTTAGGAACATGCTTG
1 TTTAGTATTTTAGGAACATGCTTG
20999490 TT
1 TT
20999492 GAGTGTTCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.06, G:0.22, T:0.50
Consensus pattern (24 bp):
TTTAGTATTTTAGGAACATGCTTG
Found at i:20999496 original size:24 final size:24
Alignment explanation
Indices: 20999449--20999498 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
20999439 TCATTTAGTA
* *
20999449 TTTTAGGAACATGTTTGTTTAGTG
1 TTTTAGGAACATGCTTGTTGAGTG
20999473 TTTTAGGAACATGCTTGTTGAGTG
1 TTTTAGGAACATGCTTGTTGAGTG
20999497 TT
1 TT
20999499 CACAAATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.20, C:0.06, G:0.26, T:0.48
Consensus pattern (24 bp):
TTTTAGGAACATGCTTGTTGAGTG
Found at i:20999519 original size:23 final size:23
Alignment explanation
Indices: 20999456--20999522 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
20999446 GTATTTTAGG
* **
20999456 AACATGTTTGTTTAGTGTTTTAGG
1 AACATGTTTGTTTAGTG-TTCACA
* *
20999480 AACATGCTTGTTGAGTGTTCACA
1 AACATGTTTGTTTAGTGTTCACA
*
20999503 AATATGTTTGTTTAGTGTTC
1 AACATGTTTGTTTAGTGTTC
20999523 CTGAACAATT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 20 0.57
24 15 0.43
ACGTcount: A:0.22, C:0.09, G:0.22, T:0.46
Consensus pattern (23 bp):
AACATGTTTGTTTAGTGTTCACA
Found at i:21012100 original size:16 final size:16
Alignment explanation
Indices: 21012053--21012091 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
21012043 AGAGAACAAA
*
21012053 ATAATA-GAAAATAAAT
1 ATAATATGAAAAT-GAT
21012069 ATAATATGAAAATGAT
1 ATAATATGAAAATGAT
21012085 ATAATAT
1 ATAATAT
21012092 ATAGATGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (16 bp):
ATAATATGAAAATGAT
Found at i:21012712 original size:21 final size:23
Alignment explanation
Indices: 21012673--21012717 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
21012663 TGTGAATAGC
*
21012673 TTTTTTAACCTTTTATGAACTTT
1 TTTTTTAACATTTTATGAACTTT
21012696 TTTTTTAA-ATTTT-TGAACTTT
1 TTTTTTAACATTTTATGAACTTT
21012717 T
1 T
21012718 ATGAAGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 4 0.19
23 8 0.38
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.64
Consensus pattern (23 bp):
TTTTTTAACATTTTATGAACTTT
Found at i:21017661 original size:22 final size:22
Alignment explanation
Indices: 21017633--21017687 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
21017623 TAGTGCCTAG
* *
21017633 CAGGCTTAGTGTTGGTGTTATT
1 CAGGCTTAGTGTCGATGTTATT
*
21017655 CAGGCTTAGTGTCGATGTTGTT
1 CAGGCTTAGTGTCGATGTTATT
21017677 CAGGCTTAGTG
1 CAGGCTTAGTG
21017688 CCTAGTAGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.15, C:0.13, G:0.33, T:0.40
Consensus pattern (22 bp):
CAGGCTTAGTGTCGATGTTATT
Found at i:21020278 original size:43 final size:43
Alignment explanation
Indices: 21020180--21020348 Score: 184
Period size: 43 Copynumber: 3.9 Consensus size: 43
21020170 ATGAGACTTT
* * * *
21020180 GTGTAAGACCTTATCTGGGATA-TGGCATCGATATATGTGATTAC
1 GTGTAAGACCATGTCTGGGACATTGGCATCG--ATATGTGATTTC
* *
21020224 GTGTAATACCATGTCTGGGACATTGGCATCGTTATGTGATTTC
1 GTGTAAGACCATGTCTGGGACATTGGCATCGATATGTGATTTC
* * *
21020267 GAGTAAGACCATGTATGGGACATTGGCATCGATATATGA-TTC
1 GTGTAAGACCATGTCTGGGACATTGGCATCGATATGTGATTTC
*
21020309 GTGTAAGACCATAGT-TGGG-CTATTGGCATCAATATGTGAT
1 GTGTAAGACCAT-GTCTGGGAC-ATTGGCATCGATATGTGAT
21020349 AACATATAAA
Statistics
Matches: 107, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
41 1 0.01
42 34 0.32
43 46 0.43
44 18 0.17
45 8 0.07
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (43 bp):
GTGTAAGACCATGTCTGGGACATTGGCATCGATATGTGATTTC
Found at i:21020334 original size:42 final size:43
Alignment explanation
Indices: 21020141--21020348 Score: 164
Period size: 44 Copynumber: 4.8 Consensus size: 43
21020131 GATTTCGTAT
* * *
21020141 AGACCATAG-CTGGGCTA-TGGAATCAATATATGAGACTTTGTGTA
1 AGACCATAGTCTGGGCTATTGGCATCGATATAT--GA-TTCGTGTA
* *
21020185 AGACCTTA-TCTGGGATA-TGGCATCGATATATGTGATTACGTGTA
1 AGACCATAGTCTGGGCTATTGGCATCGATATA--TGATT-CGTGTA
* * * *
21020229 ATACCAT-GTCTGGGAC-ATTGGCATCGTTATGTGATTTCGAGTA
1 AGACCATAGTCTGGG-CTATTGGCATCGATATATGA-TTCGTGTA
*
21020272 AGACCAT-GTATGGGAC-ATTGGCATCGATATATGATTCGTGTA
1 AGACCATAGTCTGGG-CTATTGGCATCGATATATGATTCGTGTA
* *
21020314 AGACCATAGT-TGGGCTATTGGCATCAATATGTGAT
1 AGACCATAGTCTGGGCTATTGGCATCGATATATGAT
21020349 AACATATAAA
Statistics
Matches: 136, Mismatches: 18, Indels: 22
0.77 0.10 0.12
Matches are distributed among these distances:
41 1 0.01
42 35 0.26
43 42 0.31
44 46 0.34
45 11 0.08
46 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.32
Consensus pattern (43 bp):
AGACCATAGTCTGGGCTATTGGCATCGATATATGATTCGTGTA
Found at i:21020363 original size:85 final size:87
Alignment explanation
Indices: 21020202--21020363 Score: 190
Period size: 85 Copynumber: 1.9 Consensus size: 87
21020192 ATCTGGGATA
* ** **
21020202 TGGCATCGATATATGTGATTACGTGTAATACCATGTCTGGGACATTGGCATCGTTATGTGATTTC
1 TGGCATCGATATA-GTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCAATATGTGATAAC
* *
21020267 GAGTAAGACCATGTATGGGACAT
65 GAATAAAACCATGTATGGGACAT
21020290 TGGCATCGATATA-TGATT-CGTGTAAGACCATAGT-TGGG-CTATTGGCATCAATATGTGATAA
1 TGGCATCGATATAGTGATTACGTGTAAGACCAT-GTCTGGGAC-ATTGGCATCAATATGTGATAA
21020351 C-ATATAAAACCAT
64 CGA-ATAAAACCAT
21020364 ATTTGGGATA
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
84 2 0.03
85 42 0.66
86 7 0.11
88 13 0.20
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (87 bp):
TGGCATCGATATAGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCAATATGTGATAACG
AATAAAACCATGTATGGGACAT
Found at i:21025105 original size:34 final size:34
Alignment explanation
Indices: 21025046--21025235 Score: 247
Period size: 34 Copynumber: 5.6 Consensus size: 34
21025036 GTATACGGTT
* *
21025046 AACCATCCAACACACCAGAA-ACTCGTATGAGCCA
1 AACCAGCCAACACACC-GAATGCTCGTATGAGCCA
* * * * *
21025080 AACCAACCAATACATCAAATGCTCGTATAAGCCA
1 AACCAGCCAACACACCGAATGCTCGTATGAGCCA
*
21025114 AACCAACCAACACACCGAATGCTCGTATGAGCCA
1 AACCAGCCAACACACCGAATGCTCGTATGAGCCA
21025148 AACCAGCCAACACACCGAATGCTCGTATGAGCCA
1 AACCAGCCAACACACCGAATGCTCGTATGAGCCA
**
21025182 AACCAGCCAACACAATGAATGCTCGTATGAGCCA
1 AACCAGCCAACACACCGAATGCTCGTATGAGCCA
* * *
21025216 ATCCAGCCAACGCACTGAAT
1 AACCAGCCAACACACCGAAT
21025236 AACACTATAA
Statistics
Matches: 139, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
33 2 0.01
34 137 0.99
ACGTcount: A:0.39, C:0.33, G:0.14, T:0.14
Consensus pattern (34 bp):
AACCAGCCAACACACCGAATGCTCGTATGAGCCA
Found at i:21032038 original size:3 final size:3
Alignment explanation
Indices: 21032030--21032086 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
21032020 ATGTCTACCC
*
21032030 TTA TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21032078 TTA TTA TTA
1 TTA TTA TTA
21032087 ATTTTAAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:21036353 original size:24 final size:19
Alignment explanation
Indices: 21036307--21036344 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
21036297 GAAGTTAGGC
21036307 CATGGACATTAGAGGTTAG
1 CATGGACATTAGAGGTTAG
21036326 CATGGACATTAGAGGTTAG
1 CATGGACATTAGAGGTTAG
21036345 GTAGACATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.32, T:0.26
Consensus pattern (19 bp):
CATGGACATTAGAGGTTAG
Found at i:21042935 original size:122 final size:122
Alignment explanation
Indices: 21042718--21042957 Score: 349
Period size: 122 Copynumber: 2.0 Consensus size: 122
21042708 GTTCTATCAA
** * * * * *
21042718 TAGAACTCTGATGGTTTCATTTGGTATCAATAGAACCCATCAGAGTATCAGTAGAAGTGCAGGAT
1 TAGAACTCTGATGGTTTCAACTGGTATCAATAGAACCCAACAAAGTATCAGTAAAAGTACAGGAG
21042783 AGGCTAGACTTTGGCTACTGTTTTGACTTGTTTCGGTAGAAGTCCTCAAGGTAGCGG
66 AGGCTAGACTTTGGCTACTGTTTTGACTTGTTTCGGTAGAAGTCCTCAAGGTAGCGG
* * *
21042840 TAGAACTCT-AGTGGTTTCAACTGGTATCGATAGAATCCAACAAAGTATCGGTAAAAGTACAGGA
1 TAGAACTCTGA-TGGTTTCAACTGGTATCAATAGAACCCAACAAAGTATCAGTAAAAGTACAGGA
*
21042904 GAGGCT-GAACTTTGGCTACTTTTTTGACTTGTTTCGGTAGAAGTCCTCAAGGTA
65 GAGGCTAG-ACTTTGGCTACTGTTTTGACTTGTTTCGGTAGAAGTCCTCAAGGTA
21042958 TCGATATAAC
Statistics
Matches: 105, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
121 2 0.02
122 103 0.98
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (122 bp):
TAGAACTCTGATGGTTTCAACTGGTATCAATAGAACCCAACAAAGTATCAGTAAAAGTACAGGAG
AGGCTAGACTTTGGCTACTGTTTTGACTTGTTTCGGTAGAAGTCCTCAAGGTAGCGG
Found at i:21043458 original size:44 final size:44
Alignment explanation
Indices: 21043395--21043500 Score: 158
Period size: 44 Copynumber: 2.4 Consensus size: 44
21043385 GTTGCGGATT
* * * *
21043395 ATTCACAGCTCCTATGAGTAGCATCGTGTAATGGTTAATGTCTG
1 ATTCATAGCTCATGTGAGTAGCATCGTGTAATGGTTAATGTCTA
*
21043439 ATTCATAGCTCATGTGAGTAGCATCGTGTACTGGTTAATGTCTA
1 ATTCATAGCTCATGTGAGTAGCATCGTGTAATGGTTAATGTCTA
*
21043483 ATTCATAGCTCGTGTGAG
1 ATTCATAGCTCATGTGAG
21043501 CAATTTCATT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.35
Consensus pattern (44 bp):
ATTCATAGCTCATGTGAGTAGCATCGTGTAATGGTTAATGTCTA
Found at i:21045644 original size:24 final size:24
Alignment explanation
Indices: 21045593--21045644 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
21045583 TTTCTTTTCT
* ** *
21045593 TTTTCTTTTTCTTTTTAGTTTAGG
1 TTTTCTTTTTCCTTTTAGAGTAGA
21045617 TTTTCTTTTTCCTTTTAGAGTAGA
1 TTTTCTTTTTCCTTTTAGAGTAGA
21045641 TTTT
1 TTTT
21045645 ATTCTTGTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.67
Consensus pattern (24 bp):
TTTTCTTTTTCCTTTTAGAGTAGA
Found at i:21051264 original size:21 final size:21
Alignment explanation
Indices: 21051238--21051281 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
21051228 ATCTACCTCT
* *
21051238 TCCTCCTCTTCATCCTCATCC
1 TCCTCCTCCTCATCATCATCC
21051259 TCCTCCTCCTCATCATCATCC
1 TCCTCCTCCTCATCATCATCC
21051280 TC
1 TC
21051282 TACCCCATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.11, C:0.52, G:0.00, T:0.36
Consensus pattern (21 bp):
TCCTCCTCCTCATCATCATCC
Found at i:21051295 original size:27 final size:27
Alignment explanation
Indices: 21051233--21051305 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
21051223 TCATTATCTA
* *
21051233 CCTCTTCCTCCTCTTCATCCTCATCCT
1 CCTCTTCCTCATCATCATCCTCATCCT
*
21051260 CCTCCTCCTCATCATCATCCTC-TACC-
1 CCTCTTCCTCATCATCATCCTCAT-CCT
21051286 CCATCTTCCTCATCATCATC
1 CC-TCTTCCTCATCATCATC
21051306 ACTATCCCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
26 3 0.08
27 37 0.93
ACGTcount: A:0.14, C:0.51, G:0.00, T:0.36
Consensus pattern (27 bp):
CCTCTTCCTCATCATCATCCTCATCCT
Found at i:21051314 original size:27 final size:26
Alignment explanation
Indices: 21051235--21051315 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 26
21051225 ATTATCTACC
* *
21051235 TCTTCCTCCTCTTCATCCTCATCCTCC-
1 TCTTCCTCATCATCATCCT-ATCC-CCA
* *
21051262 TCCTCCTCATCATCATCCTCTACCCCA
1 TCTTCCTCATCATCATCCTAT-CCCCA
21051289 TCTTCCTCATCATCATCACTATCCCCA
1 TCTTCCTCATCATCATC-CTATCCCCA
21051316 ATATCATGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
26 3 0.07
27 39 0.87
28 3 0.07
ACGTcount: A:0.16, C:0.49, G:0.00, T:0.35
Consensus pattern (26 bp):
TCTTCCTCATCATCATCCTATCCCCA
Found at i:21051655 original size:18 final size:18
Alignment explanation
Indices: 21051628--21051662 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21051618 ATCATCCTCA
*
21051628 TCCTCATCCTCTTCATCT
1 TCCTCATCCTCCTCATCT
*
21051646 TCCTCTTCCTCCTCATC
1 TCCTCATCCTCCTCATC
21051663 ATCCGATTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.49, G:0.00, T:0.43
Consensus pattern (18 bp):
TCCTCATCCTCCTCATCT
Found at i:21056665 original size:34 final size:35
Alignment explanation
Indices: 21056627--21056693 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
21056617 TTAATTTTGA
21056627 AAAGTAATAA-TTATCATTCAATAGATACATTTAG
1 AAAGTAATAATTTATCATTCAATAGATACATTTAG
* *
21056661 AAAGTGATAATTTATCATTCAATGGATACATTT
1 AAAGTAATAATTTATCATTCAATAGATACATTT
21056694 TCATGAGACA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 9 0.30
35 21 0.70
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.37
Consensus pattern (35 bp):
AAAGTAATAATTTATCATTCAATAGATACATTTAG
Found at i:21062353 original size:14 final size:13
Alignment explanation
Indices: 21062325--21062361 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
21062315 AGTAGATAAT
21062325 GGGGAAA-AAATA
1 GGGGAAAGAAATA
21062337 GGGGAAAGAATATA
1 GGGGAAAGAA-ATA
21062351 GGGGAAAGAAA
1 GGGGAAAGAAA
21062362 AGAAATGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 3 0.13
14 13 0.57
ACGTcount: A:0.54, C:0.00, G:0.38, T:0.08
Consensus pattern (13 bp):
GGGGAAAGAAATA
Found at i:21062579 original size:22 final size:23
Alignment explanation
Indices: 21062545--21062588 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
21062535 ATAACATAAG
*
21062545 GAATGAGAGAAGAAAGA-GGAAA
1 GAATGAGAAAAGAAAGACGGAAA
* *
21062567 GAATGATAAAAGAGAGACGGAA
1 GAATGAGAAAAGAAAGACGGAA
21062589 GAAGGGGTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.57, C:0.02, G:0.34, T:0.07
Consensus pattern (23 bp):
GAATGAGAAAAGAAAGACGGAAA
Found at i:21072861 original size:25 final size:26
Alignment explanation
Indices: 21072807--21072867 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 26
21072797 GAGCAGCAAA
21072807 TAAATATTTATTCTTAGACAATGGCCAAT
1 TAAATATTTATTCTTAGACAAT---CAAT
* *
21072836 TTAATATTTATTTTTAGACAAT-AAT
1 TAAATATTTATTCTTAGACAATCAAT
21072861 TAAATAT
1 TAAATAT
21072868 GCAAAATTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 9 0.31
29 20 0.69
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (26 bp):
TAAATATTTATTCTTAGACAATCAAT
Found at i:21074259 original size:3 final size:3
Alignment explanation
Indices: 21074246--21074312 Score: 52
Period size: 3 Copynumber: 23.7 Consensus size: 3
21074236 TATACATAAA
* * * * **
21074246 TAT TA- TAT TAT TAT TAT TAT AAT TAT TA- AAC CAT TAT TAT GGT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
21074291 TA- TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
21074313 AATAAAGTAA
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
2 7 0.14
3 44 0.86
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:21075102 original size:16 final size:18
Alignment explanation
Indices: 21075069--21075102 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
21075059 TAGAAATTTT
21075069 GATTAGAATTGATAAAAG
1 GATTAGAATTGATAAAAG
21075087 GATTA-AATTG-TAAAAG
1 GATTAGAATTGATAAAAG
21075103 AAACTATAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 5 0.31
18 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
GATTAGAATTGATAAAAG
Found at i:21075956 original size:37 final size:39
Alignment explanation
Indices: 21075897--21075992 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
21075887 CGGATAGATT
* * * *
21075897 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
21075934 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
21075973 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
21075993 TTTTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:21076868 original size:41 final size:41
Alignment explanation
Indices: 21076851--21077004 Score: 281
Period size: 41 Copynumber: 3.8 Consensus size: 41
21076841 ACTTACAGCA
21076851 TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
1 TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
* *
21076892 TGATTCAAATCACTGGCACGTAGCCTGCTAGGTTTATAACC
1 TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
*
21076933 TGATTCAGATCACCGGCGCGTAGCCTGCTAGGTTTATAACC
1 TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
21076974 TGATTCAGATCACCGGCACGTAGCCTGCTAG
1 TGATTCAGATCACCGGCACGTAGCCTGCTAG
21077005 ACTTAAAGTT
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 107 1.00
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.27
Consensus pattern (41 bp):
TGATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACC
Found at i:21079014 original size:13 final size:13
Alignment explanation
Indices: 21078996--21079020 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21078986 CAATCAAATG
21078996 CACACAAAATAAA
1 CACACAAAATAAA
21079009 CACACAAAATAA
1 CACACAAAATAA
21079021 TATTAAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:21084875 original size:114 final size:114
Alignment explanation
Indices: 21084236--21084884 Score: 713
Period size: 114 Copynumber: 5.7 Consensus size: 114
21084226 GTGTTTCCAT
* *
21084236 AAAGCGCCGC-AAAATACCTAAGCCCAACGACGCCGTTTTTCT-AGCTTTCGGGGATTTAACGGC
1 AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCG-TTTTCTGAGCTTTCGGGGATTTAGCGGC
* * * *
21084299 GTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTCGCTGCGTTTTCGAG
65 GTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAG
* * * * * * * * * *
21084349 AAAGCGCCACAAAAAAACCAAAGCCTAACTACGCCATTTTTTGAGCGTTCAGGGATTTAGTGGCA
1 AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCG
* * *
21084414 CTTTTAAGTAAACGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGG
66 TTTTTAAGTAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAG
* *
21084463 AAAGCGCCG-AAAAGATACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGGC
1 AAAGCGCCGCAAAA-AAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGC
* *
21084527 ATTTTTAAGTAAGCGCCGCTAATGCTCAGGGCTTTAGCAGCGTTTTTGAG
65 GTTTTTAAGTAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAG
* * * * * * * *
21084577 AAAGCGCCACAAAAAAACCAAAGCTCAATGACGCTGTTTTTTGAGCTTTTGGGGATTTAGTGGCG
1 AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCG
21084642 TTTTTAAGTAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAG
66 TTTTTAAGTAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAG
* * * * * *
21084691 AAAGCGCTGCAATAAAAA-CTAAGCCCAACTACACCGCTTTCTGA-CAATTCGTGGGCTTTAGCG
1 AAAGCGCCGCAA-AAAAACCTAAGCCCAACGACGCCGTTTTCTGAGC-TTTCG-GGGATTTAGCG
* * * * *
21084754 GCG-TTTTAAG-AATGCGCCGCCAATGCTTAAGGCTTTAGCGGCTTTTTTGTTG
63 GCGTTTTTAAGTAA-GCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG-AG
* * * * * ** *
21084806 -AAGCGCCGCAAAAAAACCTAAGCCCAACGGCGTCATTTTCTAAACTTTTAGGGCTTTAGCGGCG
1 AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCG
*
21084870 TTTTTAA-AAAGCGCC
66 TTTTTAAGTAAGCGCC
21084885 ACAAAAACCT
Statistics
Matches: 451, Mismatches: 72, Indels: 26
0.82 0.13 0.05
Matches are distributed among these distances:
113 45 0.10
114 383 0.85
115 23 0.05
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (114 bp):
AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCG
TTTTTAAGTAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAG
Found at i:21084922 original size:19 final size:18
Alignment explanation
Indices: 21084898--21084937 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
21084888 AAAACCTTTT
21084898 ATTTG-TTATTTACTATTTA
1 ATTTGTTTATTTA-TA-TTA
21084917 ATTTGTTTATTTATATTA
1 ATTTGTTTATTTATATTA
21084935 ATT
1 ATT
21084938 AAAATTCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.30
19 7 0.35
20 7 0.35
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.65
Consensus pattern (18 bp):
ATTTGTTTATTTATATTA
Found at i:21085243 original size:14 final size:15
Alignment explanation
Indices: 21085215--21085247 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
21085205 AACGTTTATA
21085215 GATTATGGAATTAGG
1 GATTATGGAATTAGG
21085230 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
21085244 GATT
1 GATT
21085248 TTGGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:21085409 original size:81 final size:82
Alignment explanation
Indices: 21085320--21085477 Score: 230
Period size: 81 Copynumber: 1.9 Consensus size: 82
21085310 TTTGGTGTCA
* *
21085320 GGTTAGGATTTAGGGTTTAGATTAATTAGTGTGTTTTAATTT-T-TATGAAATAAGGTTTAAGGG
1 GGTTAGGATTTAGGGTTTAGATTAATTAATAT-TTTTAATTTGTATATGAAATAAGGTTTAAGGG
*
21085383 TTAGGGGTTAGGGATTCG
65 TTAGGAGTTAGGGATTCG
* * *
21085401 GGTTAGGATTTAGGGTTTTGATTAATTAATATTTTTAATTTGTATATTAAATAAGGTTTAGGGGT
1 GGTTAGGATTTAGGGTTTAGATTAATTAATATTTTTAATTTGTATATGAAATAAGGTTTAAGGGT
*
21085466 TAGTAGTTAGGG
66 TAGGAGTTAGGG
21085478 GTTAGTGGTT
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
80 9 0.13
81 30 0.44
82 29 0.43
ACGTcount: A:0.27, C:0.01, G:0.28, T:0.44
Consensus pattern (82 bp):
GGTTAGGATTTAGGGTTTAGATTAATTAATATTTTTAATTTGTATATGAAATAAGGTTTAAGGGT
TAGGAGTTAGGGATTCG
Found at i:21085477 original size:14 final size:14
Alignment explanation
Indices: 21085458--21085495 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
21085448 TAAATAAGGT
21085458 TTAGGGGTTAGTAG
1 TTAGGGGTTAGTAG
*
21085472 TTAGGGGTTAGTGG
1 TTAGGGGTTAGTAG
*
21085486 TTTGGGGTTA
1 TTAGGGGTTA
21085496 AGGGTTAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.16, C:0.00, G:0.45, T:0.39
Consensus pattern (14 bp):
TTAGGGGTTAGTAG
Found at i:21085509 original size:35 final size:35
Alignment explanation
Indices: 21085462--21085529 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
21085452 TAAGGTTTAG
* * * * *
21085462 GGGTTAGTAGTTAGGGGTTAGTGGTTTGGGGTTAA
1 GGGTTAGAAGTTAAGAGTTAGTGATTTAGGGTTAA
21085497 GGGTTAGAAGTTAAGAGTTAGTGATTTAGGGTT
1 GGGTTAGAAGTTAAGAGTTAGTGATTTAGGGTT
21085530 TAGAGATTCG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.22, C:0.00, G:0.41, T:0.37
Consensus pattern (35 bp):
GGGTTAGAAGTTAAGAGTTAGTGATTTAGGGTTAA
Found at i:21085930 original size:19 final size:21
Alignment explanation
Indices: 21085896--21085937 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
21085886 GGTTTGTGAT
21085896 TTGGGGTTTAGGATTTAGGGG
1 TTGGGGTTTAGGATTTAGGGG
*
21085917 TTGGGG-TT-GGATTTTGGGG
1 TTGGGGTTTAGGATTTAGGGG
21085936 TT
1 TT
21085938 TGGTTGTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
20 2 0.10
21 6 0.30
ACGTcount: A:0.10, C:0.00, G:0.48, T:0.43
Consensus pattern (21 bp):
TTGGGGTTTAGGATTTAGGGG
Found at i:21087024 original size:147 final size:145
Alignment explanation
Indices: 21086768--21087214 Score: 432
Period size: 147 Copynumber: 3.0 Consensus size: 145
21086758 TACGTTGCTA
* * * ** * * *
21086768 TTAGTGGCGCTTTACATCAAACGCTGCAAAATTGTAATTATGTTTATTGAAATGTTGTCGTTTTG
1 TTAGTGGCGCTTTAC-TCAAACGCCGCAAAATTGTTATAACATTTATTGAAACGATGCCGTTTTG
* * * * * **
21086833 TCTATGGTATTAGTGGTGTTTTTAT-GAAAACGCCACAAGCTTGAGTTAACTGTTGGGGAAACGA
65 T-TATGTTATTAGTGGCGTTTTT-TCGAAAACGCCACAGGTTTGAGCTAACTGTTGATGAAACGA
21086897 CTTCG-TTTGAGCTTATAG
128 CTTCGTTTTGA-CTTATAG
* * *
21086915 TTAGTGGCGCTTTACTCAAAACGCCGCAAAATTGTTCTAACATTTATAGAAACGCTGCCGTTTTG
1 TTAGTGGCGCTTTACTC-AAACGCCGCAAAATTGTTATAACATTTATTGAAACGATGCCGTTTTG
* * * * *
21086980 TAAATGTTATTAGTGGCGTTTTTTCGAAAACGCCACGGGTTTGAGGTAAGTGTTGATGAATCGAC
65 T-TATGTTATTAGTGGCGTTTTTTCGAAAACGCCACAGGTTTGAGCTAACTGTTGATGAAACGAC
* * *
21087045 TGCGTTTTGATTTACAG
129 TTCGTTTTGACTTATAG
*** * * * * *
21087062 TTAGTGGCGCTTCGGTTCAAACGCCGCAAAAATATTTTAACATTTATTGATACGAGGCCGTTTTG
1 TTAGTGGCGCTT-TACTCAAACGCCGCAAAATTGTTATAACATTTATTGAAACGATGCCGTTTTG
* * * * * **
21087127 TTGTATTATTAGTGGCGTTTATTCAAAAACGCCACAGGTGTGAGCTATTTGTTGATGAAAC-AGC
65 TTATGTTATTAGTGGCGTTTTTTCGAAAACGCCACAGGTTTGAGCTAACTGTTGATGAAACGA-C
21087191 TTCGTTTTGACTTATAG
129 TTCGTTTTGACTTATAG
21087208 TTAGTGG
1 TTAGTGG
21087215 TTCTTATTTA
Statistics
Matches: 246, Mismatches: 49, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
145 1 0.00
146 74 0.30
147 164 0.67
148 7 0.03
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (145 bp):
TTAGTGGCGCTTTACTCAAACGCCGCAAAATTGTTATAACATTTATTGAAACGATGCCGTTTTGT
TATGTTATTAGTGGCGTTTTTTCGAAAACGCCACAGGTTTGAGCTAACTGTTGATGAAACGACTT
CGTTTTGACTTATAG
Found at i:21087235 original size:146 final size:146
Alignment explanation
Indices: 21086859--21087237 Score: 372
Period size: 146 Copynumber: 2.6 Consensus size: 146
21086849 TGTTTTTATG
* * * **
21086859 AAAACGCCACAAGCT-TGAGTTAACTGTTGGGGAAACGACTTCG-TTTGAGCTTATAGTTAGTGG
1 AAAACGCCAC-AGGTGTGAGCTAAGTGTTGATGAAACGACTTCGTTTTGA-CTTATAGTTAGTGG
* * * ** *
21086922 CGCTTTACTCAAAACGCCGCAAAATTGTTCTAACATTTATAGAAACGCTGCCGTTTTGTAAATGT
64 CGC-TTACTTAAAACGCCGCAAAAATATTCTAACATTTATAGAAACGAGGCCGTTTTGTAAATAT
* *
21086987 TATTAGTGGCGTTTTTTCG
128 TATTAGTGGCGTTTATTCA
* * * * * * *
21087006 AAAACGCCACGGGTTTGAGGTAAGTGTTGATGAATCGACTGCGTTTTGATTTACAGTTAGTGGCG
1 AAAACGCCACAGGTGTGAGCTAAGTGTTGATGAAACGACTTCGTTTTGACTTATAGTTAGTGGCG
* * * * **
21087071 CTT-CGGTTCAAACGCCGCAAAAATATTTTAACATTTATTGATACGAGGCCGTTTTGT-TGTATT
66 CTTAC--TTAAAACGCCGCAAAAATATTCTAACATTTATAGAAACGAGGCCGTTTTGTAAATATT
21087134 ATTAGTGGCGTTTATTCA
129 ATTAGTGGCGTTTATTCA
** *
21087152 AAAACGCCACAGGTGTGAGCTATTTGTTGATGAAAC-AGCTTCGTTTTGACTTATAGTTAGTGGT
1 AAAACGCCACAGGTGTGAGCTAAGTGTTGATGAAACGA-CTTCGTTTTGACTTATAGTTAGTGGC
* * *
21087216 TCTTATTTATAAACACCGCAAA
65 GCTTACTTA-AAACGCCGCAAA
21087238 TGGTTAATTT
Statistics
Matches: 187, Mismatches: 38, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
145 4 0.02
146 89 0.48
147 89 0.48
148 5 0.03
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.34
Consensus pattern (146 bp):
AAAACGCCACAGGTGTGAGCTAAGTGTTGATGAAACGACTTCGTTTTGACTTATAGTTAGTGGCG
CTTACTTAAAACGCCGCAAAAATATTCTAACATTTATAGAAACGAGGCCGTTTTGTAAATATTAT
TAGTGGCGTTTATTCA
Found at i:21088589 original size:15 final size:15
Alignment explanation
Indices: 21088569--21088600 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
21088559 AGGGTTGAAG
21088569 TATTTGATACTAATT
1 TATTTGATACTAATT
*
21088584 TATTTGGTACTAATT
1 TATTTGATACTAATT
21088599 TA
1 TA
21088601 CTGTTATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.09, T:0.53
Consensus pattern (15 bp):
TATTTGATACTAATT
Found at i:21089403 original size:20 final size:19
Alignment explanation
Indices: 21089361--21089413 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
21089351 ACTTATTAAT
*
21089361 ATATATATTTTAA-AGTTA
1 ATATATATTTTAATATTTA
21089379 ATATATATTTTCAATATTTA
1 ATATATATTTT-AATATTTA
*
21089399 TTATAT-TTTTAATAT
1 ATATATATTTTAATAT
21089414 ATTTTTACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 16 0.52
19 6 0.19
20 9 0.29
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
ATATATATTTTAATATTTA
Found at i:21089590 original size:13 final size:13
Alignment explanation
Indices: 21089572--21089729 Score: 124
Period size: 13 Copynumber: 12.0 Consensus size: 13
21089562 AATTTATTTT
*
21089572 AATATATTACTTG
1 AATATATTACTTA
21089585 AATATATTACTTA
1 AATATATTACTTA
*
21089598 AATAAATTACTTA
1 AATATATTACTTA
* *
21089611 AAGACATTACTTA
1 AATATATTACTTA
* **
21089624 CTAAAAT-TTGGTTA
1 --AATATATTACTTA
*
21089638 AATTTATTACTTA
1 AATATATTACTTA
*
21089651 AATATGTTACTTA
1 AATATATTACTTA
*
21089664 AATACATTACTTA
1 AATATATTACTTA
*
21089677 CTAAAATATGT--TTA
1 --AATATAT-TACTTA
*
21089691 AATTTATTACTTA
1 AATATATTACTTA
*
21089704 AATATGTTACTTA
1 AATATATTACTTA
*
21089717 AATACATTACTTA
1 AATATATTACTTA
21089730 CTAAAATTAA
Statistics
Matches: 113, Mismatches: 24, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
11 1 0.01
12 8 0.07
13 87 0.77
14 8 0.07
15 8 0.07
16 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.44
Consensus pattern (13 bp):
AATATATTACTTA
Found at i:21089608 original size:66 final size:66
Alignment explanation
Indices: 21089538--21089674 Score: 166
Period size: 66 Copynumber: 2.1 Consensus size: 66
21089528 CTTACATTAC
* ** * * *
21089538 TTACTAAAACATATTTTTTACTAAAATTTATTTTAATATATTACTTGAATATATTACTTAAATAA
1 TTACTAAAACACATTACTTACTAAAATTTAGTTAAATATATTACTTAAATATATTACTTAAATAA
21089603 A
66 A
* * * * * *
21089604 TTACTTAAAGACATTACTTACTAAAATTTGGTTAAATTTATTACTTAAATATGTTACTTAAATAC
1 TTACTAAAACACATTACTTACTAAAATTTAGTTAAATATATTACTTAAATATATTACTTAAATAA
21089669 A
66 A
21089670 TTACT
1 TTACT
21089675 TACTAAAATA
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (66 bp):
TTACTAAAACACATTACTTACTAAAATTTAGTTAAATATATTACTTAAATATATTACTTAAATAA
A
Found at i:21089646 original size:53 final size:53
Alignment explanation
Indices: 21089589--21089737 Score: 253
Period size: 53 Copynumber: 2.8 Consensus size: 53
21089579 TACTTGAATA
** *
21089589 TATTACTTAAATAAATTACTTAAAGACATTACTTACTAAAATTTGGTTAAATT
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
* *
21089642 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATATGTTTAAATT
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
21089695 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATT
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATT
21089738 AAGTATATAT
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 90 1.00
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (53 bp):
TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
Found at i:21089706 original size:23 final size:23
Alignment explanation
Indices: 21089621--21089711 Score: 83
Period size: 23 Copynumber: 3.7 Consensus size: 23
21089611 AAGACATTAC
* *
21089621 TTACTAAAATTTGGTTAAATTTA
1 TTACTAAAATATGTTTAAATTTA
*
21089644 TTACTTAAATATGTTACTTAAATACATTA
1 TTACTAAAATATG-T--TTAAAT---TTA
21089673 CTTACTAAAATATGTTTAAATTTA
1 -TTACTAAAATATGTTTAAATTTA
*
21089697 TTACTTAAATATGTT
1 TTACTAAAATATGTT
21089712 ACTTAAATAC
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
23 25 0.45
24 3 0.05
26 6 0.11
27 6 0.11
29 4 0.07
30 12 0.21
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (23 bp):
TTACTAAAATATGTTTAAATTTA
Found at i:21089924 original size:16 final size:16
Alignment explanation
Indices: 21089903--21089952 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
21089893 CTTATATGTA
21089903 AACTTACATAATACAT
1 AACTTACATAATACAT
*
21089919 AACTTACAT-GT---T
1 AACTTACATAATACAT
21089931 AACTTACATAATACAT
1 AACTTACATAATACAT
21089947 AACTTA
1 AACTTA
21089953 TAAAATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 10 0.36
13 1 0.04
15 1 0.04
16 16 0.57
ACGTcount: A:0.46, C:0.18, G:0.02, T:0.34
Consensus pattern (16 bp):
AACTTACATAATACAT
Found at i:21089929 original size:28 final size:28
Alignment explanation
Indices: 21089886--21089952 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
21089876 CATAACTGTC
*
21089886 ACATAAACTTATATGTAAACTTACATAAT
1 ACAT-AACTTACATGTAAACTTACATAAT
*
21089915 ACATAACTTACATGTTAACTTACATAAT
1 ACATAACTTACATGTAAACTTACATAAT
21089943 ACATAACTTA
1 ACATAACTTA
21089953 TAAAATTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
28 32 0.89
29 4 0.11
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.34
Consensus pattern (28 bp):
ACATAACTTACATGTAAACTTACATAAT
Found at i:21096411 original size:679 final size:678
Alignment explanation
Indices: 21095111--21096468 Score: 2216
Period size: 679 Copynumber: 2.0 Consensus size: 678
21095101 GATATTGTTA
* *
21095111 TAAGCTAATCGACTATAACCGTTGCATTCAGATATCTTTACAATTCAAACATTATTCCACTAATT
1 TAAGCTAATCGACTATAACCGCTGCATTCAGATATCTTTACAATTCAAACATTATTCCACTAACT
* * *
21095176 ATTACAGTCTTCATTAATCCCACATTATCTCATTCACTCAAGAAATCAATGTAGAAGAAATTTTC
66 ATTACAGTCTTCATTAATCCCACATTATCCCATACACTAAAGAAATCAATGTAGAAGAAATTTTC
* * *
21095241 GGTTTATACATTCTTTAGATACCATACCTGAATAGGTTGATTACCCGAGAATAACCTTTTTTCAG
131 GGTTAATACATTATTTAGATACCATACCTGAATAGGTTGATTACCCGAGAATAACCTTTTTTCAA
*
21095306 CAATGACATTGCGTATCCCGAATAATCTTCAAAAAAATCTAATATCTCTTCTAAAACTCTCTTTA
196 CAACGACATTGCGTATCCCGAATAATCTTCAAAAAAATCTAATATCTCTTCTAAAACTCTCTTTA
*
21095371 TCTGCTAACCCATTCTCGGCTCTGACCGCATTATTATTCATTCATCCACTGAACTCTTCGATTTT
261 TCTGCTAACCCATTCTCGGCTCTGACCCCATTATTATTCATTCATCCACTGAACTCTTCGATTTT
* * *
21095436 ACACTTGTGAGCTTAATCAAGATAAATCTTGTAAATTATGTTATATAAAACTATACAGGTGAGGG
326 ACACTTGTGAGCATAATCAAGATAAATCTTGTAAATTACGTTATATAAAACTATACAGGTGAGGA
* *
21095501 GGTGAAGGTCGTAAAGCCTCTAAAGTTGACTCTCATATAAATACACATAACATAAAATTCATCAT
391 GGTAAAGGTCGTAAAGCCTCTAAAGTTAACTCTCATATAAATACACATAACATAAAATTCATCAT
* * * *
21095566 TAGCATACATTATAAAATATTTATTCATACCTTTATAAGTTTCTACTAATTATAAGCAACATTTT
456 CAGCATACATTATAAAACATTTATTCAAACCTTTATAAGTTTCTACTAATCATAAGCAACATTTT
* *
21095631 TACTCAAATACTTGAGTATCGCATTCAGCATTATCGGAATTAGCTCTGTTGGAAAACATCTCTAT
521 TACTCAAATACTTGAATATCGCATTCAGCATTATCGGAATTAGCTCGGTTGGAAAACATCTCTAT
* *
21095696 CTAAAAATGAAACAAATCTCATCAGGGTCAGGAGATATCACATTATCACAGGTAATATAATGGCA
586 CTAAAAATGAAACAAATCTCATCAGAGTCAGGAGATATCACACTATCACAGGTAATATAATGGCA
* *
21095761 TTTATTTCTAGACTTCACACATGTTATG
651 TGTATTTCTAGAATTCACACATGTTATG
* * *
21095789 TAAGCTACTCGACTATAACCGCTGCATTCAGATATCTTTGCAATTCAAACATTATTCCACTGACT
1 TAAGCTAATCGACTATAACCGCTGCATTCAGATATCTTTACAATTCAAACATTATTCCACTAACT
21095854 ATTACAGTCTTCATTAATCCCACATTATCCCATACACTAAAGAAATCAAT-TCAGAAGAAATTTT
66 ATTACAGTCTTCATTAATCCCACATTATCCCATACACTAAAGAAATCAATGT-AGAAGAAATTTT
*
21095918 TGGTTAATACATTATTTAGATACCATACCTGAATAGGTTGATTACCCGAGAATAACCTTTTTTTT
130 CGGTTAATACATTATTTAGATACCATACCTGAATAGGTTGATTACCCGAGAATAACC--TTTTTT
* * *
21095983 CAACAACGACATTGCGTATCCCGAATGATCTTCAGAAAAATCTAATATCTCTTCTAGAACTCTCT
193 CAACAACGACATTGCGTATCCCGAATAATCTTCAAAAAAATCTAATATCTCTTCTAAAACTCTCT
* * *
21096048 TTATTTGCTAACTCATTCTCGGCTCTGACCCCATTATTATTCATTCATCCATTGAACTCTTCGA-
258 TTATCTGCTAACCCATTCTCGGCTCTGACCCCATTATTATTCATTCATCCACTGAACTCTTCGAT
* * * * *
21096112 TTTACACTTGTGAGCATAATCAAGATAAATCTTGTGAATTCCGTTGTATAAAATTGTACAGGTGA
323 TTTACACTTGTGAGCATAATCAAGATAAATCTTGTAAATTACGTTATATAAAACTATACAGGTGA
* *
21096177 GGAGGTAAAGGTCGTAAAGCCTCTAAATTTAACTCTCATATAAATACACATAATATAAAATTCAT
388 GGAGGTAAAGGTCGTAAAGCCTCTAAAGTTAACTCTCATATAAATACACATAACATAAAATTCAT
* * *
21096242 CATCAGCATGCATTATAAAACATTTATTCAAACCTTTATCAGTTTCTACTCATCATAAGCAACAT
453 CATCAGCATACATTATAAAACATTTATTCAAACCTTTATAAGTTTCTACTAATCATAAGCAACAT
* *
21096307 TTTTACTCAAATACTTGAATATCGCATTCAGCATTATTGGAATTAGCTCGGTTGGAAAATATCTC
518 TTTTACTCAAATACTTGAATATCGCATTCAGCATTATCGGAATTAGCTCGGTTGGAAAACATCTC
* * * *
21096372 TGTCTAAAAATGAAACAAATCTCATCATAGTCGGGAGATATCACACTATCACAGGTTATATAATG
583 TATCTAAAAATGAAACAAATCTCATCAGAGTCAGGAGATATCACACTATCACAGGTAATATAATG
21096437 GCATGTATTTCTAGAATTCACACATGTTATG
648 GCATGTATTTCTAGAATTCACACATGTTATG
21096468 T
1 T
21096469 TCAGCCCAAG
Statistics
Matches: 626, Mismatches: 51, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
677 1 0.00
678 173 0.28
679 326 0.52
680 126 0.20
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (678 bp):
TAAGCTAATCGACTATAACCGCTGCATTCAGATATCTTTACAATTCAAACATTATTCCACTAACT
ATTACAGTCTTCATTAATCCCACATTATCCCATACACTAAAGAAATCAATGTAGAAGAAATTTTC
GGTTAATACATTATTTAGATACCATACCTGAATAGGTTGATTACCCGAGAATAACCTTTTTTCAA
CAACGACATTGCGTATCCCGAATAATCTTCAAAAAAATCTAATATCTCTTCTAAAACTCTCTTTA
TCTGCTAACCCATTCTCGGCTCTGACCCCATTATTATTCATTCATCCACTGAACTCTTCGATTTT
ACACTTGTGAGCATAATCAAGATAAATCTTGTAAATTACGTTATATAAAACTATACAGGTGAGGA
GGTAAAGGTCGTAAAGCCTCTAAAGTTAACTCTCATATAAATACACATAACATAAAATTCATCAT
CAGCATACATTATAAAACATTTATTCAAACCTTTATAAGTTTCTACTAATCATAAGCAACATTTT
TACTCAAATACTTGAATATCGCATTCAGCATTATCGGAATTAGCTCGGTTGGAAAACATCTCTAT
CTAAAAATGAAACAAATCTCATCAGAGTCAGGAGATATCACACTATCACAGGTAATATAATGGCA
TGTATTTCTAGAATTCACACATGTTATG
Found at i:21097771 original size:15 final size:16
Alignment explanation
Indices: 21097742--21097771 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21097732 CAAACATGCT
21097742 TTAACACATTATCAAA
1 TTAACACATTATCAAA
21097758 TTAACACA-TATCAA
1 TTAACACATTATCAA
21097772 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:21098955 original size:25 final size:25
Alignment explanation
Indices: 21098909--21098975 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 25
21098899 TAGTACATGT
* *
21098909 ATGCTCACACGAGCTGTGAATCAGA
1 ATGCTCACATGAGCTGTAAATCAGA
*
21098934 ATGCTCACATGAGTTGTAAATCAGA
1 ATGCTCACATGAGCTGTAAATCAGA
* *
21098959 ATGCTTACATGATCTGT
1 ATGCTCACATGAGCTGT
21098976 GAAAATGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (25 bp):
ATGCTCACATGAGCTGTAAATCAGA
Found at i:21105022 original size:16 final size:16
Alignment explanation
Indices: 21105009--21105041 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
21104999 TGTCACAAGT
21105009 GAAGTAATTCACAAAC
1 GAAGTAATTCACAAAC
21105025 GAAGTAATTCACAAAC
1 GAAGTAATTCACAAAC
21105041 G
1 G
21105042 GATTCAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (16 bp):
GAAGTAATTCACAAAC
Found at i:21107700 original size:10 final size:10
Alignment explanation
Indices: 21107685--21107734 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
21107675 AAAAGTAACA
21107685 TTCTTTCTTT
1 TTCTTTCTTT
21107695 TTCTTTCTTCT
1 TTCTTTCTT-T
21107706 TT-TTTCTTCT
1 TTCTTTCTT-T
*
21107716 TT-TTTCTTC
1 TTCTTTCTTT
21107725 TTCTTTCTTT
1 TTCTTTCTTT
21107735 CTTTTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
9 2 0.06
10 31 0.86
11 3 0.08
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (10 bp):
TTCTTTCTTT
Found at i:21107707 original size:13 final size:14
Alignment explanation
Indices: 21107685--21107737 Score: 67
Period size: 13 Copynumber: 3.9 Consensus size: 14
21107675 AAAAGTAACA
21107685 TTCTTTCTTT-TTC
1 TTCTTTCTTTCTTC
*
21107698 TT-TCTTCTTTTTTC
1 TTCT-TTCTTTCTTC
21107712 TTCTTT-TTTCTTC
1 TTCTTTCTTTCTTC
21107725 TTCTTTCTTTCTT
1 TTCTTTCTTTCTT
21107738 TTTTTGTTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
12 1 0.03
13 20 0.57
14 13 0.37
15 1 0.03
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (14 bp):
TTCTTTCTTTCTTC
Found at i:21107707 original size:17 final size:17
Alignment explanation
Indices: 21107685--21107737 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
21107675 AAAAGTAACA
21107685 TTCTTTCTTTTTCTTTC
1 TTCTTTCTTTTTCTTTC
*
21107702 TTCTTT-TTTCTTCTTTT
1 TTCTTTCTTT-TTCTTTC
21107719 TTC-TTCTTCTTTCTTTC
1 TTCTTTCTT-TTTCTTTC
21107736 TT
1 TT
21107738 TTTTTGTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 5 0.16
17 25 0.81
18 1 0.03
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (17 bp):
TTCTTTCTTTTTCTTTC
Found at i:21107713 original size:20 final size:19
Alignment explanation
Indices: 21107685--21107740 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
21107675 AAAAGTAACA
21107685 TTCTTTCTTTTTCTTTCTTC
1 TTCTTTCTTTTT-TTTCTTC
*
21107705 TTTTTTCTTCTTTTTTCTTC
1 TTCTTTCTT-TTTTTTCTTC
21107725 TTCTTTCTTTCTTTTT
1 TTCTTTCTTT-TTTTT
21107741 TTGTTGTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 28 0.88
21 3 0.09
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (19 bp):
TTCTTTCTTTTTTTTCTTC
Found at i:21113989 original size:43 final size:43
Alignment explanation
Indices: 21113885--21114108 Score: 387
Period size: 43 Copynumber: 5.2 Consensus size: 43
21113875 CGCTGTTGTG
* *
21113885 AACGCCGCTATAGAGCAGGACCTTTAGCGGCGCTTTT-CCACA
1 AACGCCGCTATAGACCAGGACCTTTAGCGGCGCTTTTAGCACA
*
21113927 AACGCCGCTATAGAGCAGGACCTTTAGCGGCGCTTTTAGCACA
1 AACGCCGCTATAGACCAGGACCTTTAGCGGCGCTTTTAGCACA
*
21113970 AACGCCGCTATAGACCAGGACCTTTAGCGGCGCTTTTCGCACA
1 AACGCCGCTATAGACCAGGACCTTTAGCGGCGCTTTTAGCACA
*
21114013 AACGCCGCTATAGACCAGGACCTTTAGCGGCGCTTTTCGCACA
1 AACGCCGCTATAGACCAGGACCTTTAGCGGCGCTTTTAGCACA
*
21114056 AACGCCGCTATAGACCAGGACCTTTAGCGGCGCTTTTACCACA
1 AACGCCGCTATAGACCAGGACCTTTAGCGGCGCTTTTAGCACA
21114099 AACGCCGCTA
1 AACGCCGCTA
21114109 AAAACATATC
Statistics
Matches: 176, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
42 37 0.21
43 139 0.79
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.21
Consensus pattern (43 bp):
AACGCCGCTATAGACCAGGACCTTTAGCGGCGCTTTTAGCACA
Found at i:21118517 original size:96 final size:96
Alignment explanation
Indices: 21118411--21118648 Score: 348
Period size: 89 Copynumber: 2.5 Consensus size: 96
21118401 TTTTGCGGCG
21118411 TTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAATCCTAAACCCTAACCCGAGCC
1 TTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAATCCTAAACCCTAACCCGA-CC
*
21118476 C-AAATCCCTAACCCTTAACCCCTAAACATTA
65 CTAAATCCCTAACCCCTAACCCCTAAACATTA
21118507 TTTAATATATAAATTAAAAAACAC----TAAT-T-AAT-CTAAATCCTAAACCCTAACCCGACCC
1 TTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAATCCTAAACCCTAACCCGACCC
21118565 TAAATCCCTAACCCCTAACCCCTAAACATTA
66 TAAATCCCTAACCCCTAACCCCTAAACATTA
* * *
21118596 TTTAATATATAAATTAAAACACAGTACTAATTAATCTAAACCCTAAACCCTAA
1 TTTAATATATAAATTAAAA-A-A-CACTAATTAATCTAAATCCTAAATCCTAA
21118649 CCTAACACTG
Statistics
Matches: 127, Mismatches: 4, Indels: 19
0.85 0.03 0.13
Matches are distributed among these distances:
88 3 0.02
89 71 0.56
90 4 0.03
91 2 0.02
92 6 0.05
96 28 0.22
97 1 0.01
98 2 0.02
99 10 0.08
ACGTcount: A:0.45, C:0.26, G:0.02, T:0.27
Consensus pattern (96 bp):
TTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAATCCTAAACCCTAACCCGACCC
TAAATCCCTAACCCCTAACCCCTAAACATTA
Found at i:21119159 original size:21 final size:19
Alignment explanation
Indices: 21119131--21119175 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
21119121 AATTTTAATT
21119131 AATATAAATAAACAAAATAA
1 AATATAAATAAAC-AAATAA
* *
21119151 AATAGTAAATAGACAGATAA
1 AATA-TAAATAAACAAATAA
21119171 AATAT
1 AATAT
21119176 TTTTGCGGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 13 0.59
21 8 0.36
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (19 bp):
AATATAAATAAACAAATAA
Found at i:21119225 original size:41 final size:41
Alignment explanation
Indices: 21119180--21119259 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
21119170 AAATATTTTT
*
21119180 GCGGCGCTTTTCTAAAAACGCCGCTATAGATCTGAGCATCA
1 GCGGCGCTTTTCTAAAAACGCCGCTACAGATCTGAGCATCA
*
21119221 GCGGCGCTTTTTTAAAAACGCCGCTACAGATCTGAGCAT
1 GCGGCGCTTTTCTAAAAACGCCGCTACAGATCTGAGCAT
21119260 ATTTTTCTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (41 bp):
GCGGCGCTTTTCTAAAAACGCCGCTACAGATCTGAGCATCA
Found at i:21119430 original size:231 final size:231
Alignment explanation
Indices: 21119027--21119490 Score: 883
Period size: 231 Copynumber: 2.0 Consensus size: 231
21119017 TTTTTAACAA
21119027 ATATTTTTCTATATTTTTTTATTTCAAATTATTTCTACGTGTCATTATTTCAAATTTATCCATTT
1 ATATTTTTCTATATTTTTTTATTTCAAATTATTTCTACGTGTCATTATTTCAAATTTATCCATTT
21119092 TTAACAAATATTCAATTAAAAATAAATTGAATTTTAATTAATATAAATAAACAAAATAAAATAGT
66 TTAACAAATATTCAATTAAAAATAAATTGAATTTTAATTAATATAAATAAACAAAATAAAATAGT
* *
21119157 AAATAGACAGATAAAATATTTTTGCGGCGCTTTTCTAAAAACGCCGCTATAGATCTGAGCATCAG
131 AAATAGACAGATAAAATATTTTTGCGGCGCTTTTCCAAAAACGCCGCTACAGATCTGAGCATCAG
* *
21119222 CGGCGCTTTTTTAAAAACGCCGCTACAGATCTGAGC
196 CGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGC
21119258 ATATTTTTCTATATTTTTTTATTTCAAATTATTTCTACGTGTCATTATTTCAAATTTATCCATTT
1 ATATTTTTCTATATTTTTTTATTTCAAATTATTTCTACGTGTCATTATTTCAAATTTATCCATTT
21119323 TTAACAAATATTCAATTAAAAATAAATTGAATTTTAATTAATATAAATAAACAAAATAAAATAGT
66 TTAACAAATATTCAATTAAAAATAAATTGAATTTTAATTAATATAAATAAACAAAATAAAATAGT
*
21119388 AAATAGACAGATAAAATGTTTTTGCGGCGCTTTTCCAAAAACGCCGCTACAGATCTGAGCATCAG
131 AAATAGACAGATAAAATATTTTTGCGGCGCTTTTCCAAAAACGCCGCTACAGATCTGAGCATCAG
21119453 CGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGC
196 CGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGC
21119489 AT
1 AT
21119491 TAGCGGCGCT
Statistics
Matches: 228, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
231 228 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.37
Consensus pattern (231 bp):
ATATTTTTCTATATTTTTTTATTTCAAATTATTTCTACGTGTCATTATTTCAAATTTATCCATTT
TTAACAAATATTCAATTAAAAATAAATTGAATTTTAATTAATATAAATAAACAAAATAAAATAGT
AAATAGACAGATAAAATATTTTTGCGGCGCTTTTCCAAAAACGCCGCTACAGATCTGAGCATCAG
CGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGC
Found at i:21119457 original size:41 final size:41
Alignment explanation
Indices: 21119411--21119562 Score: 225
Period size: 41 Copynumber: 3.7 Consensus size: 41
21119401 AAATGTTTTT
* *
21119411 GCGGCGCTT-TTCCAAAAACGCCGCTACAGATCTGAGCATCA
1 GCGGCGCTTCTT-CAAAAACGCCGCTAAAGATCTGAGCATTA
*
21119452 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGATCTGAGCATTA
* * *
21119493 GCGGCGCTTCTTAAAAAACGTCGTTAAAGATCTGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGATCTGAGCATTA
*
21119534 GCGGTGCTTCTTCAAAAACGCCGCTAAAG
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAG
21119563 CCCCGAAAGG
Statistics
Matches: 100, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
41 98 0.98
42 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (41 bp):
GCGGCGCTTCTTCAAAAACGCCGCTAAAGATCTGAGCATTA
Found at i:21119706 original size:40 final size:39
Alignment explanation
Indices: 21119599--21119734 Score: 150
Period size: 40 Copynumber: 3.4 Consensus size: 39
21119589 TTGGCTTAGG
* *
21119599 TTTTTTGCGGCGTTTT-CTAGAAAAACGCCGCTAATGCTGA
1 TTTTTAGCGGCGTTTTCCT-G-AAAGCGCCGCTAATGCTGA
* *
21119639 TTTTTAGCGACGCTTTCCTGAAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTCCTGAAAGCGCCGCTAATGCT-GA
* * *
21119679 TCTTTAGCGGCGTTTTAC-GTAATGCGCCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTTCCTG-AAAGCGCCGCTAATGC-TGA
21119719 TTTTTAGCGGCGTTTT
1 TTTTTAGCGGCGTTTT
21119735 TTGTCCAAGC
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
39 17 0.21
40 62 0.76
41 3 0.04
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTCCTGAAAGCGCCGCTAATGCTGA
Found at i:21121296 original size:27 final size:27
Alignment explanation
Indices: 21121272--21121327 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
21121262 ATCAAAATGT
21121272 TATA-AATTTTTTTATTTACCAAAATA
1 TATATAATTTTTTTATTTACCAAAATA
21121298 TATATAATTTTTTTATTTACCAAAATA
1 TATATAATTTTTTTATTTACCAAAATA
21121325 TAT
1 TAT
21121328 CAAAAAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 4 0.14
27 25 0.86
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (27 bp):
TATATAATTTTTTTATTTACCAAAATA
Found at i:21121437 original size:27 final size:27
Alignment explanation
Indices: 21121407--21121474 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
21121397 ACACCAATGG
21121407 CATTGGCGGCACCAAAGGTGCCAAAAC
1 CATTGGCGGCACCAAAGGTGCCAAAAC
* **
21121434 CATTGGCGGCACCAATGGTGCCAATGC
1 CATTGGCGGCACCAAAGGTGCCAAAAC
21121461 CATTGGCGGCACCA
1 CATTGGCGGCACCA
21121475 GTTGATAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.26, C:0.31, G:0.28, T:0.15
Consensus pattern (27 bp):
CATTGGCGGCACCAAAGGTGCCAAAAC
Found at i:21121527 original size:4 final size:4
Alignment explanation
Indices: 21121518--21121622 Score: 60
Period size: 4 Copynumber: 26.0 Consensus size: 4
21121508 GAAGGAGAGG
* *
21121518 GAAA GAAA GAAA GGAGAG GAAA GAAA G-AA -AAA GAAG GAAA GAAAA GGAAA
1 GAAA GAAA GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -GAAA
* * *
21121568 G-GA GAAGA GAAA AAAA GAAA GAAA G-AA G-AA GAAAA GGAAG GAAA GAAA
1 GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -GAAA GAAA GAAA
21121616 -AAA GAAA
1 GAAA GAAA
21121623 AAGGTAATTT
Statistics
Matches: 79, Mismatches: 10, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
3 15 0.19
4 43 0.54
5 18 0.23
6 3 0.04
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:21121550 original size:24 final size:24
Alignment explanation
Indices: 21121523--21121615 Score: 77
Period size: 24 Copynumber: 3.9 Consensus size: 24
21121513 AGAGGGAAAG
*
21121523 AAAGAAAGGAGAGGAAAGAAAGAA
1 AAAGAAAGGAAAGGAAAGAAAGAA
*
21121547 AAAG-AAGGAAAGAAAAGGAAAGGAGA
1 AAAGAAAGGAAAGGAAA-GAAA-GA-A
* *
21121573 AGAGAAA--AAAAGAAAGAAAGAA
1 AAAGAAAGGAAAGGAAAGAAAGAA
*
21121595 GAAGAAAAGG-AAGGAAAGAAA
1 AAAG-AAAGGAAAGGAAAGAAA
21121616 AAAGAAAAAG
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
22 3 0.06
23 15 0.28
24 22 0.41
25 8 0.15
26 4 0.07
27 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (24 bp):
AAAGAAAGGAAAGGAAAGAAAGAA
Found at i:21122536 original size:159 final size:154
Alignment explanation
Indices: 21122142--21122589 Score: 369
Period size: 159 Copynumber: 2.9 Consensus size: 154
21122132 TATTCCCCCT
* *
21122142 TAACACACTAAATTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAAGACTA
1 TAACACACT-AATTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATA-GA
* *
21122207 AGTTTATGATA--TTT-TTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAATGGCAAAAG
64 A-ATTATGATATTTTTATTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAAGGGCAAAAG
* * *
21122269 TAAGAGTATATTACTAACTTTTTTAAA
128 TAAGAGTATATTACCAAATTATTTAAA
* * * * ** * * **
21122296 -ATTCAGAAATAATTAATACAAAATATTTCAAAGAAAATGTACTGAAATAATTTAAAACAATAAA
1 TA-ACA-CACTAATTAAT----AA-ATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAA
* * *
21122360 ATACGAGAATAAT-ATATTTTTATTTAAAGTAATAAAAAT-C-GAGAAAATAATACGAGCAAAGG
59 ATA-GA-AATTATGATATTTTTATTTAAAGTAAT-AAAATGCGGAGAAAAAAATACGAACAAAGG
*** * * *
21122422 GCAGGGGTAAGGGTTTTTTTACACCAAATTAATTTAAA
121 GCAAAAGTAAGAG-TATATT--ACCAAATT-ATTTAAA
21122460 TAACACACTAGATTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATTAGA
1 TAACACACTA-ATTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAA-TAGA
* * * **
21122525 AATTATGATA---TT-TTTAAAGGAATAAAATGCGGAGAAAAAAATACGAATAAATGGCCGAAGT
64 AATTATGATATTTTTATTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAAGGGCAAAAGT
21122586 AAGA
129 AAGA
21122590 TTTTTTTACT
Statistics
Matches: 226, Mismatches: 46, Indels: 42
0.72 0.15 0.13
Matches are distributed among these distances:
153 1 0.00
154 14 0.06
155 13 0.06
156 28 0.12
158 10 0.04
159 79 0.35
160 36 0.16
161 16 0.07
162 5 0.02
163 9 0.04
164 14 0.06
165 1 0.00
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.29
Consensus pattern (154 bp):
TAACACACTAATTAATAAATTTCAAACATTATGCACTGAAATAATGTAAAATTATAAAATAGAAA
TTATGATATTTTTATTTAAAGTAATAAAATGCGGAGAAAAAAATACGAACAAAGGGCAAAAGTAA
GAGTATATTACCAAATTATTTAAA
Found at i:21125552 original size:18 final size:18
Alignment explanation
Indices: 21125529--21125573 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
21125519 ATCCCAATGA
21125529 TCGCCACCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
21125547 TCGCCAGCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
21125565 TCACCACCA
1 TCGCCACCA
21125574 ACCATGTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.49, G:0.07, T:0.29
Consensus pattern (18 bp):
TCGCCACCACCTTCTTCT
Found at i:21126454 original size:3 final size:3
Alignment explanation
Indices: 21126446--21126471 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
21126436 TCTTAATACT
21126446 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
21126472 TAATAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:21126562 original size:19 final size:21
Alignment explanation
Indices: 21126538--21126576 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
21126528 ACTAAAACAA
*
21126538 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
21126557 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
21126577 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:21126617 original size:10 final size:11
Alignment explanation
Indices: 21126600--21126628 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
21126590 AAAAAAAAAC
21126600 CTTCTTTTTCT
1 CTTCTTTTTCT
21126611 C-TCTTTTTCT
1 CTTCTTTTTCT
21126621 CTTCTTTT
1 CTTCTTTT
21126629 CCGCAGCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (11 bp):
CTTCTTTTTCT
Found at i:21126758 original size:27 final size:26
Alignment explanation
Indices: 21126712--21126786 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 26
21126702 AATACGAATA
21126712 GTGCCGCCAAT-CAGTATGGCACCATTG
1 GTGCCGCCAATGCA-T-TGGCACCATTG
21126739 GTGCCGCCAATGGCATTGGCACCATTG
1 GTGCCGCCAAT-GCATTGGCACCATTG
21126766 GTGCCGCCAATGCCATTGGCA
1 GTGCCGCCAATG-CATTGGCA
21126787 TGACCAAGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
26 1 0.02
27 41 0.91
28 1 0.02
29 2 0.04
ACGTcount: A:0.20, C:0.31, G:0.28, T:0.21
Consensus pattern (26 bp):
GTGCCGCCAATGCATTGGCACCATTG
Found at i:21126906 original size:28 final size:28
Alignment explanation
Indices: 21126846--21126911 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
21126836 TTTTTTTTAT
*
21126846 ATTTTGGTAAATAAAAAAAATTATATAT
1 ATTTTGGTAAATAAAAAAAATTATATAC
*
21126874 TTTTTGGTAAATAAAAAAAAGTTATA-AC
1 ATTTTGGTAAATAAAAAAAA-TTATATAC
21126902 ATTTTGGTAA
1 ATTTTGGTAA
21126912 TTTTTTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 29 0.85
29 5 0.15
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (28 bp):
ATTTTGGTAAATAAAAAAAATTATATAC
Found at i:21127081 original size:2 final size:2
Alignment explanation
Indices: 21127074--21127110 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
21127064 TCATCAATTG
21127074 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21127111 TAATGTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21127805 original size:31 final size:31
Alignment explanation
Indices: 21127737--21127808 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
21127727 TTAAATTTTT
* *
21127737 TATTAGTCCCTATACTTTTCAAATTAGTCAA
1 TATTAGTCCTTATACTTTTCAAATTAGTAAA
* *
21127768 TTTTAGTCCTTATACTTTTCAAATT-TTAAAA
1 TATTAGTCCTTATACTTTTCAAATTAGT-AAA
21127799 TATTAGTCCT
1 TATTAGTCCT
21127809 GACCCAGACA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 1 0.03
31 34 0.97
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.47
Consensus pattern (31 bp):
TATTAGTCCTTATACTTTTCAAATTAGTAAA
Found at i:21129296 original size:69 final size:69
Alignment explanation
Indices: 21129193--21129329 Score: 211
Period size: 69 Copynumber: 2.0 Consensus size: 69
21129183 TTTCGATTTT
* *
21129193 TTTCCCAGTTAAACTCTATTTTTAGTTTCCCACTTACACTTTCATTAGTGCAGGTTATTTTAATA
1 TTTCCCAGTTAAACTCTATTTTTAGTTTCCCACTTAAACTCTCATTAGTGCAGGTTATTTTAATA
21129258 TTAG
66 TTAG
* ** * *
21129262 TTTCCCAGTTAAACTCTGTTTTTAGTTTTTCACTTAAACTCTGATTAGTGTAGGTTATTTTAATA
1 TTTCCCAGTTAAACTCTATTTTTAGTTTCCCACTTAAACTCTCATTAGTGCAGGTTATTTTAATA
21129327 TTA
66 TTA
21129330 TTTGACCTAC
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.48
Consensus pattern (69 bp):
TTTCCCAGTTAAACTCTATTTTTAGTTTCCCACTTAAACTCTCATTAGTGCAGGTTATTTTAATA
TTAG
Found at i:21131215 original size:44 final size:44
Alignment explanation
Indices: 21131142--21131232 Score: 146
Period size: 44 Copynumber: 2.1 Consensus size: 44
21131132 AACTTTATTT
* * *
21131142 TTAGCTTCCTACTTAAGCTCTGATTAGTGTAGGTTATTTTAATA
1 TTAGCTTCCCACTTAAACTCTAATTAGTGTAGGTTATTTTAATA
*
21131186 TTAGTTTCCCACTTAAACTCTAATTAGTGTAGGTTATTTTAATA
1 TTAGCTTCCCACTTAAACTCTAATTAGTGTAGGTTATTTTAATA
21131230 TTA
1 TTA
21131233 TTTGACGTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.46
Consensus pattern (44 bp):
TTAGCTTCCCACTTAAACTCTAATTAGTGTAGGTTATTTTAATA
Found at i:21133314 original size:18 final size:18
Alignment explanation
Indices: 21133268--21133315 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
21133258 TTCCAGGCAT
*
21133268 TCTTCTCCCTTCATCCAG
1 TCTTCTCCCTTCATCCAA
*** *
21133286 TAAGCTTCCTTCATCCAA
1 TCTTCTCCCTTCATCCAA
21133304 TCTTCTCCCTTC
1 TCTTCTCCCTTC
21133316 CTTCATTCCT
Statistics
Matches: 21, Mismatches: 9, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.42, G:0.04, T:0.40
Consensus pattern (18 bp):
TCTTCTCCCTTCATCCAA
Found at i:21136774 original size:14 final size:15
Alignment explanation
Indices: 21136752--21136828 Score: 61
Period size: 14 Copynumber: 5.0 Consensus size: 15
21136742 CAATCAAACA
21136752 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
21136766 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
21136781 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
21136801 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
*
21136815 CC-GAAAAACATTTT
1 CCAGAAAATCATTTT
21136829 ACTAGTAATC
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
13 1 0.02
14 25 0.49
15 11 0.22
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:21136793 original size:20 final size:20
Alignment explanation
Indices: 21136768--21136807 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
21136758 AATATTTTCC
*
21136768 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
21136788 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
21136808 TCATTTTCCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:21137745 original size:21 final size:20
Alignment explanation
Indices: 21137721--21137759 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
21137711 TTATATATTC
*
21137721 TTTATAATTTTTTTAAAAAAA
1 TTTATAA-TATTTTAAAAAAA
21137742 TTTATAATATTTTAAAAA
1 TTTATAATATTTTAAAAA
21137760 TATAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTATAATATTTTAAAAAAA
Found at i:21137783 original size:18 final size:19
Alignment explanation
Indices: 21137760--21137796 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
21137750 ATTTTAAAAA
21137760 TATAAAT-TTTGGAATTTT
1 TATAAATATTTGGAATTTT
*
21137778 TATAAATATTTTGAATTTT
1 TATAAATATTTGGAATTTT
21137797 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:21137795 original size:19 final size:19
Alignment explanation
Indices: 21137760--21137817 Score: 66
Period size: 18 Copynumber: 3.1 Consensus size: 19
21137750 ATTTTAAAAA
*
21137760 TATAAAT-TTTGGAATTTT
1 TATAAATATTTTGAATTTT
21137778 TATAAATATTTTGAA-TTT
1 TATAAATATTTTGAATTTT
*
21137796 TAAAAATTATTTTGATATTTT
1 TATAAA-TATTTTGA-ATTTT
21137817 T
1 T
21137818 TTTGTAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 15 0.44
19 14 0.41
20 1 0.03
21 4 0.12
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:21145404 original size:17 final size:15
Alignment explanation
Indices: 21145372--21145402 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
21145362 AACCACTTCT
21145372 ATATAATTAAAAAAA
1 ATATAATTAAAAAAA
21145387 ATATAATTAAAAAAA
1 ATATAATTAAAAAAA
21145402 A
1 A
21145403 AAACACTACT
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
ATATAATTAAAAAAA
Found at i:21145895 original size:35 final size:37
Alignment explanation
Indices: 21145856--21145924 Score: 97
Period size: 35 Copynumber: 1.9 Consensus size: 37
21145846 TTTTAATTTA
*
21145856 AAATTTTTAAAAATAGAAAAATAT-TTA-AAAATTAT
1 AAATTATTAAAAATAGAAAAATATGTTATAAAATTAT
* *
21145891 AAATTATTAAAAATATATAAATATGTTATAAAAT
1 AAATTATTAAAAATAGAAAAATATGTTATAAAAT
21145925 AAATAAACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 21 0.72
36 3 0.10
37 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (37 bp):
AAATTATTAAAAATAGAAAAATATGTTATAAAATTAT
Found at i:21145898 original size:18 final size:18
Alignment explanation
Indices: 21145856--21145912 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
21145846 TTTTAATTTA
*
21145856 AAATT-TTTAAAAA-TAGA
1 AAATTATTTAAAAATTA-T
*
21145873 AAAATATTTAAAAATTAT
1 AAATTATTTAAAAATTAT
21145891 AAATTA-TTAAAAATATAT
1 AAATTATTTAAAAAT-TAT
21145909 AAAT
1 AAAT
21145913 ATGTTATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
17 12 0.35
18 20 0.59
19 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
AAATTATTTAAAAATTAT
Found at i:21149542 original size:21 final size:21
Alignment explanation
Indices: 21149518--21149572 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
21149508 GTGTCCCCTC
21149518 CACACGGGCGTGTGTGGCCTT
1 CACACGGGCGTGTGTGGCCTT
*
21149539 CACACGGGCGTATGTGGCCTT
1 CACACGGGCGTGTGTGGCCTT
*
21149560 CACATGGGCGTGT
1 CACACGGGCGTGT
21149573 AGACCCCTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.13, C:0.27, G:0.36, T:0.24
Consensus pattern (21 bp):
CACACGGGCGTGTGTGGCCTT
Found at i:21151516 original size:14 final size:15
Alignment explanation
Indices: 21151482--21151526 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
21151472 ATTAGTCTCC
21151482 AATTATAATAAATAT
1 AATTATAATAAATAT
21151497 AA-TATAATAAATA-
1 AATTATAATAAATAT
*
21151510 AATTATAGTAAAATAT
1 AATTATAAT-AAATAT
21151526 A
1 A
21151527 CCTGAGATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 2 0.08
14 16 0.62
15 7 0.27
16 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (15 bp):
AATTATAATAAATAT
Found at i:21153106 original size:40 final size:40
Alignment explanation
Indices: 21153053--21153183 Score: 181
Period size: 40 Copynumber: 3.3 Consensus size: 40
21153043 CGTTTGGATA
* * * **
21153053 AAAAATGCTGCTATAGATCGAGCATTAATGGCGCTTTTTG
1 AAAAACGCCGCTATAGATCGACCATTAGCGGCGCTTTTTG
*
21153093 AAAAACGCCGCTATAGATCGACCATTAGCGGTGCTTTTTG
1 AAAAACGCCGCTATAGATCGACCATTAGCGGCGCTTTTTG
* *
21153133 AAAAACGCCGCTATAGGTCAACCATTAGCGGCGCTTTTTG
1 AAAAACGCCGCTATAGATCGACCATTAGCGGCGCTTTTTG
*
21153173 AAAAATGCCGC
1 AAAAACGCCGC
21153184 CAAAAAAATA
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (40 bp):
AAAAACGCCGCTATAGATCGACCATTAGCGGCGCTTTTTG
Found at i:21153284 original size:40 final size:40
Alignment explanation
Indices: 21153229--21153332 Score: 136
Period size: 40 Copynumber: 2.6 Consensus size: 40
21153219 AGCTTTAGTG
21153229 GCATTAGTGGCGCTTTTTGAAAAACGCAGCTATAGATCGA
1 GCATTAGTGGCGCTTTTTGAAAAACGCAGCTATAGATCGA
* * * * *
21153269 GCATTAGCGGCGCTTTTTAAAAAATGCTGCTATAGGTCGA
1 GCATTAGTGGCGCTTTTTGAAAAACGCAGCTATAGATCGA
* * *
21153309 CCATTAGTGCCACTTTTTGAAAAA
1 GCATTAGTGGCGCTTTTTGAAAAA
21153333 AGCCGCAAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (40 bp):
GCATTAGTGGCGCTTTTTGAAAAACGCAGCTATAGATCGA
Found at i:21153363 original size:155 final size:155
Alignment explanation
Indices: 21153074--21153455 Score: 507
Period size: 155 Copynumber: 2.5 Consensus size: 155
21153064 TATAGATCGA
* * *
21153074 GCATTAATGGCGCTTTTTGAAAAACGCCGCTATAGATCGACCATTAGCGGTGCTTTTTGAAAAAC
1 GCATTAATGGCGCTTTTTGAAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTAAAAAAC
* * * * *
21153139 GCCGCTATAGGTCAACCATTAGCGGCGCTTTTTGAAAAATGCCGCCAAAAAAATAAGCACAATGT
66 GCCGCTATAGGTCAACCATTAGCGCCACTTTTTGAAAAAAGCCGCCAAAAAAATAAGCACAACGC
21153204 CGTCGTTTTATGTTAAGCTTTAGTG
131 CGTCGTTTTATGTTAAGCTTTAGTG
* * *
21153229 GCATTAGTGGCGCTTTTTGAAAAACGCAGCTATAGATCGAGCATTAGCGGCGCTTTTTAAAAAAT
1 GCATTAATGGCGCTTTTTGAAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTAAAAAAC
* * *
21153294 GCTGCTATAGGTCGACCATTAGTGCCACTTTTTGAAAAAAGCCG-CAAAAAAATTAAGCACAACG
66 GCCGCTATAGGTCAACCATTAGCGCCACTTTTTGAAAAAAGCCGCCAAAAAAA-TAAGCACAACG
*
21153358 CCGTCGTTTTATGTTGAGCTTTAGTG
130 CCGTCGTTTTATGTTAAGCTTTAGTG
** * ** * * * *
21153384 GCATTAACAGTGCTTTTTTGAAAAATACCGTTATAGGTCGAGCATTAGAGGCG-TTTCTTTAAAA
1 GCATTAATGGCGC-TTTTTGAAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTT-TTAAAAA
21153448 ACGCCGCT
64 ACGCCGCT
21153456 GCGCTTTTTG
Statistics
Matches: 196, Mismatches: 28, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
154 8 0.04
155 143 0.73
156 45 0.23
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (155 bp):
GCATTAATGGCGCTTTTTGAAAAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTTAAAAAAC
GCCGCTATAGGTCAACCATTAGCGCCACTTTTTGAAAAAAGCCGCCAAAAAAATAAGCACAACGC
CGTCGTTTTATGTTAAGCTTTAGTG
Found at i:21153959 original size:15 final size:15
Alignment explanation
Indices: 21153941--21154006 Score: 64
Period size: 14 Copynumber: 4.5 Consensus size: 15
21153931 TAAGGTTCAT
21153941 GGATTATGGGTTTAG
1 GGATTATGGGTTTAG
*
21153956 GGATTAT-GGTTTAT
1 GGATTATGGGTTTAG
* *
21153970 GGTTTA-AGGTTTAG
1 GGATTATGGGTTTAG
* *
21153984 GGGTTAAGGGTTTAG
1 GGATTATGGGTTTAG
*
21153999 GGTTTATG
1 GGATTATG
21154007 ATTTTATGAT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
14 22 0.52
15 20 0.48
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.42
Consensus pattern (15 bp):
GGATTATGGGTTTAG
Found at i:21153971 original size:7 final size:7
Alignment explanation
Indices: 21153929--21154026 Score: 52
Period size: 7 Copynumber: 13.6 Consensus size: 7
21153919 GAGTTACTAT
*
21153929 TTTAAGG
1 TTTATGG
*
21153936 TTCATGG
1 TTTATGG
*
21153943 ATTATGGG
1 TTTAT-GG
*
21153951 TTTAGGG
1 TTTATGG
*
21153958 ATTATGG
1 TTTATGG
21153965 TTTATGG
1 TTTATGG
*
21153972 TTTAAGG
1 TTTATGG
*
21153979 TTTAGGGG
1 TTTA-TGG
* *
21153987 TTAAGGG
1 TTTATGG
*
21153994 TTTAGGG
1 TTTATGG
*
21154001 TTTATGAT
1 TTTATG-G
*
21154009 TTTATGA
1 TTTATGG
*
21154016 TTTAGGG
1 TTTATGG
21154023 TTTA
1 TTTA
21154027 GGCGATAGGG
Statistics
Matches: 70, Mismatches: 18, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
7 54 0.77
8 16 0.23
ACGTcount: A:0.21, C:0.01, G:0.32, T:0.46
Consensus pattern (7 bp):
TTTATGG
Found at i:21153988 original size:22 final size:21
Alignment explanation
Indices: 21153892--21154028 Score: 80
Period size: 22 Copynumber: 6.3 Consensus size: 21
21153882 TATCATTATA
*
21153892 GTTTAGGGTTTACGGTTTAAG
1 GTTTAGGGTTTATGGTTTAAG
21153913 GTTTAGGAGTTACTAT--TTTAAG
1 GTTTAGG-GTT--TATGGTTTAAG
* * * *
21153935 GTTCATGGATTATGGGTTTAGG
1 GTTTAGGGTTTAT-GGTTTAAG
* *
21153957 GATTATGGTTTATGGTTTAAG
1 GTTTAGGGTTTATGGTTTAAG
* * *
21153978 GTTTAGGGGTTAAGGGTTTAGG
1 GTTTA-GGGTTTATGGTTTAAG
** * *
21154000 GTTTATGATTTTATGATTTAGG
1 GTTTA-GGGTTTATGGTTTAAG
21154022 GTTTAGG
1 GTTTAGG
21154029 CGATAGGGGA
Statistics
Matches: 88, Mismatches: 21, Indels: 14
0.72 0.17 0.11
Matches are distributed among these distances:
19 3 0.03
21 21 0.24
22 62 0.70
24 2 0.02
ACGTcount: A:0.21, C:0.02, G:0.32, T:0.45
Consensus pattern (21 bp):
GTTTAGGGTTTATGGTTTAAG
Found at i:21154027 original size:7 final size:7
Alignment explanation
Indices: 21153948--21154028 Score: 63
Period size: 7 Copynumber: 11.3 Consensus size: 7
21153938 CATGGATTAT
21153948 GGGTTTA
1 GGGTTTA
*
21153955 GGGATTA
1 GGGTTTA
*
21153962 TGGTTTA
1 GGGTTTA
*
21153969 TGGTTTA
1 GGGTTTA
*
21153976 AGGTTTA
1 GGGTTTA
*
21153983 GGGGTTAA
1 -GGGTTTA
21153991 GGGTTTA
1 GGGTTTA
21153998 GGGTTTA
1 GGGTTTA
**
21154005 TGATTTTA
1 -GGGTTTA
* *
21154013 TGATTTA
1 GGGTTTA
21154020 GGGTTTA
1 GGGTTTA
21154027 GG
1 GG
21154029 CGATAGGGGA
Statistics
Matches: 58, Mismatches: 14, Indels: 4
0.76 0.18 0.05
Matches are distributed among these distances:
7 48 0.83
8 10 0.17
ACGTcount: A:0.20, C:0.00, G:0.36, T:0.44
Consensus pattern (7 bp):
GGGTTTA
Found at i:21154045 original size:44 final size:44
Alignment explanation
Indices: 21153965--21154048 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 44
21153955 GGGATTATGG
* * * * *
21153965 TTTATGGTTTAAGGTTTAGGGGTTAAGGGTTTAGGGTTTATGAT
1 TTTATGATTTAAGGTTTAGGCGATAAGGGATAAGGGTTTATGAT
* *
21154009 TTTATGATTTAGGGTTTAGGCGATAGGGGATAAGGGTTTA
1 TTTATGATTTAAGGTTTAGGCGATAAGGGATAAGGGTTTA
21154049 AGGTTTAGAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
44 33 1.00
ACGTcount: A:0.23, C:0.01, G:0.35, T:0.42
Consensus pattern (44 bp):
TTTATGATTTAAGGTTTAGGCGATAAGGGATAAGGGTTTATGAT
Found at i:21155640 original size:66 final size:66
Alignment explanation
Indices: 21155529--21155665 Score: 159
Period size: 66 Copynumber: 2.1 Consensus size: 66
21155519 GCACCTATTG
* * * * *
21155529 AACTTAAACCGGAGGCAGCATCGAGAGAAGCTGAGGTTCAAAGAAAATATGAAGAACTCCAGCTA
1 AACTTAAACCGAAGGCAGCAGCGAGAGAAGCAGAGGTACAAAGAAAATACGAAGAACTCCAGCTA
21155594 C
66 C
* * * * * *
21155595 AACTTAAAGCGAAGGCAGCAGCGAGGGAAGCAGA-GTAGAACAGAAAGTACGACGTACTCCAGCT
1 AACTTAAACCGAAGGCAGCAGCGAGAGAAGCAGAGGTACAA-AGAAAATACGAAGAACTCCAGCT
21155659 AC
65 AC
21155661 AACTT
1 AACTT
21155666 TAGAATATGA
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 4 0.07
66 55 0.93
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (66 bp):
AACTTAAACCGAAGGCAGCAGCGAGAGAAGCAGAGGTACAAAGAAAATACGAAGAACTCCAGCTA
C
Found at i:21160105 original size:25 final size:25
Alignment explanation
Indices: 21160077--21160187 Score: 89
Period size: 25 Copynumber: 4.4 Consensus size: 25
21160067 CACAGCTCTT
*
21160077 ATGAGCTTCCCCATATTTAGCTCGC
1 ATGAGCTTCCCCATATTCAGCTCGC
** ** *
21160102 ATGAGCTTCCTGATATTTGGCTTGC
1 ATGAGCTTCCCCATATTCAGCTCGC
*** * *
21160127 ATGAGCTTCCTGTTATACAGCTTGC
1 ATGAGCTTCCCCATATTCAGCTCGC
*
21160152 ATGAGCTT-CCCATTATTCAGCTCGG
1 ATGAGCTTCCCCA-TATTCAGCTCGC
*
21160177 AGGAGCTTCCC
1 ATGAGCTTCCC
21160188 GTTTACAGCT
Statistics
Matches: 69, Mismatches: 15, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
24 1 0.01
25 66 0.96
26 2 0.03
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.33
Consensus pattern (25 bp):
ATGAGCTTCCCCATATTCAGCTCGC
Found at i:21174521 original size:2 final size:2
Alignment explanation
Indices: 21174514--21174556 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
21174504 CAATTTGGGT
21174514 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21174556 T
1 T
21174557 GATGAATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21177486 original size:20 final size:22
Alignment explanation
Indices: 21177449--21177488 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
21177439 TTTGGTATCG
21177449 TTTTTAAGAAAGGTATCGATTA
1 TTTTTAAGAAAGGTATCGATTA
21177471 TTTTTAA-AAA-GTATCGAT
1 TTTTTAAGAAAGGTATCGAT
21177489 ACCGAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 3 0.17
22 7 0.39
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (22 bp):
TTTTTAAGAAAGGTATCGATTA
Found at i:21177682 original size:20 final size:20
Alignment explanation
Indices: 21177651--21177712 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 20
21177641 TGAAAATCAT
*
21177651 TTAAAATGATTTTAACTTGA
1 TTAAAATCATTTTAACTTGA
* * *
21177671 TTGAAATCATTTTGACTTGG
1 TTAAAATCATTTTAACTTGA
**
21177691 TTAAAATCATTTGCACTTGA
1 TTAAAATCATTTTAACTTGA
21177711 TT
1 TT
21177713 TTAAAATTGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (20 bp):
TTAAAATCATTTTAACTTGA
Found at i:21179103 original size:3 final size:3
Alignment explanation
Indices: 21179095--21179132 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
21179085 CCCTAGGAAC
21179095 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
21179133 AAAACCAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:21183024 original size:24 final size:24
Alignment explanation
Indices: 21182997--21183048 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
21182987 TTAGTAAGTC
*
21182997 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
*
21183021 AAATATACTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
21183045 AAAT
1 AAAT
21183049 CTTCTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.31
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:21184850 original size:16 final size:16
Alignment explanation
Indices: 21184829--21184870 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
21184819 ATAAAAACTA
21184829 AACCCGAAAAACAAAG
1 AACCCGAAAAACAAAG
21184845 AACCCGAAAAACAAAG
1 AACCCGAAAAACAAAG
21184861 AACCCGAAAA
1 AACCCGAAAA
21184871 CGTAAGCACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.62, C:0.26, G:0.12, T:0.00
Consensus pattern (16 bp):
AACCCGAAAAACAAAG
Found at i:21185002 original size:24 final size:24
Alignment explanation
Indices: 21184975--21185026 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
21184965 TTAGTAAGTC
*
21184975 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
21184999 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
21185023 AAAT
1 AAAT
21185027 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:21186715 original size:11 final size:11
Alignment explanation
Indices: 21186699--21186736 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
21186689 CCAGGGCTTG
21186699 GAAAGACATGT
1 GAAAGACATGT
**
21186710 GAAAGA-ATCA
1 GAAAGACATGT
21186720 GAAAGACATGT
1 GAAAGACATGT
21186731 GAAAGA
1 GAAAGA
21186737 ATCAGGAGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.53, C:0.08, G:0.26, T:0.13
Consensus pattern (11 bp):
GAAAGACATGT
Found at i:21186723 original size:21 final size:21
Alignment explanation
Indices: 21186699--21186741 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
21186689 CCAGGGCTTG
21186699 GAAAGACATGTGAAAGAATCA
1 GAAAGACATGTGAAAGAATCA
21186720 GAAAGACATGTGAAAGAATCA
1 GAAAGACATGTGAAAGAATCA
21186741 G
1 G
21186742 GAGGAGGTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.09, G:0.26, T:0.14
Consensus pattern (21 bp):
GAAAGACATGTGAAAGAATCA
Found at i:21189407 original size:14 final size:14
Alignment explanation
Indices: 21189390--21189423 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
21189380 TCATCGTTTG
21189390 CCTATAACCAAAAC
1 CCTATAACCAAAAC
21189404 CCTATAACCAAAAC
1 CCTATAACCAAAAC
21189418 CC-ATAA
1 CCTATAA
21189424 ACTCATACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:21190192 original size:14 final size:14
Alignment explanation
Indices: 21190173--21190201 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
21190163 GCAGAGCCGA
21190173 AGGGAGAGGGAGAG
1 AGGGAGAGGGAGAG
21190187 AGGGAGAGGGAGAG
1 AGGGAGAGGGAGAG
21190201 A
1 A
21190202 AGAAGCTCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (14 bp):
AGGGAGAGGGAGAG
Found at i:21194412 original size:27 final size:26
Alignment explanation
Indices: 21194382--21194451 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 26
21194372 CTGGTAGCTC
21194382 CCTCTTCCTCTTCCCTCCTCCGAGCAT
1 CCTCTTCCTCTTCCCTCCTCCG-GCAT
* *
21194409 CCTCTTCCTC-T--CTCCTTCTGGCCT
1 CCTCTTCCTCTTCCCTCC-TCCGGCAT
21194433 CCTCTTCCTCTTCCCTCCT
1 CCTCTTCCTCTTCCCTCCT
21194452 AGCTTCTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
24 17 0.46
25 4 0.11
26 2 0.05
27 14 0.38
ACGTcount: A:0.03, C:0.53, G:0.06, T:0.39
Consensus pattern (26 bp):
CCTCTTCCTCTTCCCTCCTCCGGCAT
Found at i:21194435 original size:24 final size:24
Alignment explanation
Indices: 21194408--21194683 Score: 130
Period size: 24 Copynumber: 10.8 Consensus size: 24
21194398 CCTCCGAGCA
21194408 TCCTCTTCCTCTCTCCTTCTGGCC
1 TCCTCTTCCTCTCTCCTTCTGGCC
* *
21194432 TCCTCTTCCTCT-TCCCTCCTAGCTTC
1 TCCTCTTCCTCTCT-CCTTCTGGC--C
* * *
21194458 TTCTTCCTCCTCTCTCCTCCTGGCC
1 -TCCTCTTCCTCTCTCCTTCTGGCC
* * * * *
21194483 TCTTTTTCTTCTCTTCTCTTAGCT-TCT
1 TCCTCTTCCTCTC-TC-CTT--CTGGCC
21194510 TCCTCTTCCTCTCTCCTTCTGGCC
1 TCCTCTTCCTCTCTCCTTCTGGCC
* * * *
21194534 TCCTCTTCTTCCCTTCTCTTAGCT-TCT
1 TCCTCTTCCTCTC-TC-CTT--CTGGCC
21194561 TCCTCTTCCTCTCTCCTTCTGGCC
1 TCCTCTTCCTCTCTCCTTCTGGCC
*
21194585 TCCTCTTCCTCTTCCCTTCTCTTTTGGGCC
1 TCCTCTTCCTC-T--C-TC-CTTCT-GGCC
* * * *
21194615 TCTTCTTCCTCTTTCC-TCTTAGCT
1 TCCTCTTCCTCTCTCCTTC-TGGCC
* *
21194639 TCTTCCTCCTCTCTTCTCTTTCTGGCC
1 TCCTCTTCCTCTC-TC-C-TTCTGGCC
21194666 TCCTCTTCCTC-CTCCTTC
1 TCCTCTTCCTCTCTCCTTC
21194684 CTTTCCCTTT
Statistics
Matches: 190, Mismatches: 36, Indels: 53
0.68 0.13 0.19
Matches are distributed among these distances:
23 8 0.04
24 68 0.36
25 18 0.09
26 14 0.07
27 54 0.28
28 9 0.05
29 5 0.03
30 14 0.07
ACGTcount: A:0.01, C:0.45, G:0.06, T:0.47
Consensus pattern (24 bp):
TCCTCTTCCTCTCTCCTTCTGGCC
Found at i:21194440 original size:51 final size:52
Alignment explanation
Indices: 21194382--21194607 Score: 229
Period size: 51 Copynumber: 4.4 Consensus size: 52
21194372 CTGGTAGCTC
** *
21194382 CCTCTTCCTCTTCCCTCCTCCGAG-CATCCTCTTCCTCTCTCCTTCTGGCCT
1 CCTCTTCCTCTTCCCTCCTCTTAGTCTTCCTCTTCCTCTCTCCTTCTGGCCT
* * *
21194433 CCTCTTCCTCTTCCCT-C-C-TAGCTTCTTCTTCCTCCTCTCTCCTCCTGGCCT
1 CCTCTTCCTCTTCCCTCCTCTTAG--TCTTCCTCTTCCTCTCTCCTTCTGGCCT
* * *
21194484 -CT-TT-TTCTTCTCTTCTCTTAGCTTCTTCCTCTTCCTCTCTCCTTCTGGCCT
1 CCTCTTCCTCTTCCCTCCTCTTAG--TCTTCCTCTTCCTCTCTCCTTCTGGCCT
*
21194535 CCTC-T--TCTTCCCTTCTCTTAGCTTCTTCCTCTTCCTCTCTCCTTCTGGCCT
1 CCTCTTCCTCTTCCCTCCTCTTAG--TCTTCCTCTTCCTCTCTCCTTCTGGCCT
*
21194586 CCTCTTCCTCTTCCCTTCTCTT
1 CCTCTTCCTCTTCCCTCCTCTT
21194608 TTGGGCCTCT
Statistics
Matches: 153, Mismatches: 11, Indels: 19
0.84 0.06 0.10
Matches are distributed among these distances:
48 9 0.06
49 4 0.03
50 4 0.03
51 118 0.77
52 4 0.03
54 14 0.09
ACGTcount: A:0.02, C:0.47, G:0.06, T:0.45
Consensus pattern (52 bp):
CCTCTTCCTCTTCCCTCCTCTTAGTCTTCCTCTTCCTCTCTCCTTCTGGCCT
Done.