Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 128 of 203
Found at i:40623062 original size:23 final size:23
Alignment explanation
Indices: 40623029--40623074 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
40623019 ATCTCAGGCG
*
40623029 CATACTGACTAAGGCGCACAAAC
1 CATACTAACTAAGGCGCACAAAC
*
40623052 CATACTAACTAAGGTGCACAAAC
1 CATACTAACTAAGGCGCACAAAC
40623075 TCTAACTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.28, G:0.15, T:0.15
Consensus pattern (23 bp):
CATACTAACTAAGGCGCACAAAC
Found at i:40625018 original size:17 final size:18
Alignment explanation
Indices: 40624998--40625039 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
40624988 AGGCTCCTTT
*
40624998 TTATTTTTAATTAATA-A
1 TTATTTTTAATAAATATA
**
40625015 TTATAATTAATAAATATA
1 TTATTTTTAATAAATATA
40625033 TTATTTT
1 TTATTTT
40625040 CAAGTTTTTT
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATTTTTAATAAATATA
Found at i:40638723 original size:15 final size:17
Alignment explanation
Indices: 40638703--40638734 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
40638693 TGTTGCTTTG
40638703 TTGAT-ATGTG-TAAAT
1 TTGATAATGTGTTAAAT
40638718 TTGATAATGTGTTAAAT
1 TTGATAATGTGTTAAAT
40638735 CATGTTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 5 0.33
17 5 0.33
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (17 bp):
TTGATAATGTGTTAAAT
Found at i:40653168 original size:11 final size:11
Alignment explanation
Indices: 40653152--40653182 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
40653142 GCAAATCAGC
*
40653152 CCTTGAAGTAT
1 CCTTGAAATAT
40653163 CCTTGAAATAT
1 CCTTGAAATAT
40653174 CCTTGAAAT
1 CCTTGAAAT
40653183 CACATTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.35
Consensus pattern (11 bp):
CCTTGAAATAT
Found at i:40660187 original size:26 final size:26
Alignment explanation
Indices: 40660150--40660267 Score: 137
Period size: 26 Copynumber: 4.5 Consensus size: 26
40660140 TGGTAATCTA
* * *
40660150 TGAAATGGAAGCCTTTGTGGCGTATT
1 TGAAATGAAAGCCTTTGTGGCATATC
*
40660176 TGAAATGAAAGCCTTTGTGGCGTATC
1 TGAAATGAAAGCCTTTGTGGCATATC
* *
40660202 TAAAATGAAAGCCTTTGTGCCATATC
1 TGAAATGAAAGCCTTTGTGGCATATC
* * * *
40660228 TAAAATTAAAGTCTTTGTGGTATATC
1 TGAAATGAAAGCCTTTGTGGCATATC
*
40660254 TGAAATGGAAGCCT
1 TGAAATGAAAGCCT
40660268 CTATGGCAGT
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 79 1.00
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.33
Consensus pattern (26 bp):
TGAAATGAAAGCCTTTGTGGCATATC
Found at i:40660532 original size:54 final size:55
Alignment explanation
Indices: 40660416--40660533 Score: 132
Period size: 54 Copynumber: 2.2 Consensus size: 55
40660406 TATTCCTGGC
** * * * * *
40660416 GAACTCTGAAGGTGCAGTAAGTATGGTGAACTTTGAAGGAATAATATGTATGGCA
1 GAACTCTGAAGGCACAGTAAATATGGTGAACTCTAAAAGAATAATATGTACGGCA
* * *
40660471 -AAATCTGAAGGCACAGTAAATATGGTGAACTCTAAAAGAGTAATGTGTACGG-A
1 GAACTCTGAAGGCACAGTAAATATGGTGAACTCTAAAAGAATAATATGTACGGCA
40660524 GAACTCTGAA
1 GAACTCTGAA
40660534 AGAAAGGCTT
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
53 1 0.02
54 50 0.98
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (55 bp):
GAACTCTGAAGGCACAGTAAATATGGTGAACTCTAAAAGAATAATATGTACGGCA
Found at i:40660720 original size:18 final size:17
Alignment explanation
Indices: 40660692--40660725 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
40660682 GTGGTTTTTC
40660692 GAAATAGGAATGGGTAA
1 GAAATAGGAATGGGTAA
40660709 GAAATCAGGAATGGGTA
1 GAAAT-AGGAATGGGTA
40660726 GGGTGAAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.44, C:0.03, G:0.35, T:0.18
Consensus pattern (17 bp):
GAAATAGGAATGGGTAA
Found at i:40660767 original size:18 final size:21
Alignment explanation
Indices: 40660730--40660767 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 21
40660720 TGGGTAGGGT
40660730 GAAGGATGTGGAAGAGGTAAC
1 GAAGGATGTGGAAGAGGTAAC
40660751 GAAGG-TGT-GAA-AGGTAA
1 GAAGGATGTGGAAGAGGTAA
40660768 GTTATGTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
19 3 0.18
20 3 0.18
21 5 0.29
ACGTcount: A:0.39, C:0.03, G:0.42, T:0.16
Consensus pattern (21 bp):
GAAGGATGTGGAAGAGGTAAC
Found at i:40661177 original size:16 final size:16
Alignment explanation
Indices: 40661144--40661185 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
40661134 TGATATTCGC
* *
40661144 TTGTAAA-TCCTTATA
1 TTGTAAAGTCCTCAAA
40661159 TTGTAAAGTCCTCAAA
1 TTGTAAAGTCCTCAAA
40661175 TTGTAAAGTCC
1 TTGTAAAGTCC
40661186 AGCGCAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (16 bp):
TTGTAAAGTCCTCAAA
Found at i:40662604 original size:21 final size:21
Alignment explanation
Indices: 40662568--40662626 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
40662558 TAAAAAAATT
*
40662568 AAAACATTA-T-AAATTTGTA
1 AAAACATTATTAAAATTTATA
40662587 AAAACATTATTAAAATTTATA
1 AAAACATTATTAAAATTTATA
*
40662608 AAAATATTAAATTAAAATT
1 AAAACATT--ATTAAAATT
40662627 AAAATTTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.26
20 1 0.03
21 15 0.44
23 9 0.26
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (21 bp):
AAAACATTATTAAAATTTATA
Found at i:40662902 original size:20 final size:20
Alignment explanation
Indices: 40662877--40662920 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
40662867 TCTCAAACTC
40662877 TGGTATACATTTTAAGCATT
1 TGGTATACATTTTAAGCATT
40662897 TGGTATACATTTTAAGCATT
1 TGGTATACATTTTAAGCATT
40662917 TGGT
1 TGGT
40662921 GGCACTTCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.45
Consensus pattern (20 bp):
TGGTATACATTTTAAGCATT
Found at i:40663902 original size:26 final size:27
Alignment explanation
Indices: 40663852--40663909 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 27
40663842 TTGTATTAGA
40663852 TTTATATTAAATAATAACATATAAAAT
1 TTTATATTAAATAATAACATATAAAAT
40663879 TGTTATAATTAAATAAT-A-AT-TAAAAT
1 T-TTAT-ATTAAATAATAACATATAAAAT
40663905 TTTAT
1 TTTAT
40663910 TTCTACTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
25 4 0.14
26 7 0.24
27 3 0.10
28 5 0.17
29 10 0.34
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (27 bp):
TTTATATTAAATAATAACATATAAAAT
Found at i:40675597 original size:13 final size:12
Alignment explanation
Indices: 40675566--40675603 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
40675556 CCCTTTCTCC
*
40675566 TTTTCTTTC-CT
1 TTTTCTTTCTGT
40675577 TTTTCTTTCTGT
1 TTTTCTTTCTGT
40675589 TTTTCCTTTCTGT
1 TTTT-CTTTCTGT
40675602 TT
1 TT
40675604 CGTTTCTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 9 0.38
12 5 0.21
13 10 0.42
ACGTcount: A:0.00, C:0.21, G:0.05, T:0.74
Consensus pattern (12 bp):
TTTTCTTTCTGT
Found at i:40678190 original size:43 final size:43
Alignment explanation
Indices: 40678127--40678246 Score: 147
Period size: 43 Copynumber: 2.8 Consensus size: 43
40678117 TTGTACAATG
* * * *
40678127 CCAACGTCCTAGACGTGGTCTTACATGTAAACAC-AGATCGATG
1 CCAACGTCCCAGACGTGGTCTTACACGAAAACACAAG-TCGATA
*
40678170 CC-ACTGTCCCAGACAG-GGTCTTACACAAAAACACAAGTCGATA
1 CCAAC-GTCCCAGAC-GTGGTCTTACACGAAAACACAAGTCGATA
40678213 CCAACGTCCCAGACGTGGTCTTACACGAAAACAC
1 CCAACGTCCCAGACGTGGTCTTACACGAAAACAC
40678247 TTTTTGAAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
42 3 0.05
43 58 0.88
44 5 0.08
ACGTcount: A:0.33, C:0.30, G:0.18, T:0.18
Consensus pattern (43 bp):
CCAACGTCCCAGACGTGGTCTTACACGAAAACACAAGTCGATA
Found at i:40681600 original size:43 final size:43
Alignment explanation
Indices: 40681477--40681607 Score: 156
Period size: 43 Copynumber: 3.1 Consensus size: 43
40681467 TTACAACCAA
* * * *
40681477 AAACGCCGCTAAAGATCATGTTCTTTAACGGCGCTTTGTATAA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTTTAC
* ** *
40681520 AAACGCCGCTAGAGATCATAATATTTAGCGGCGCTTTTTTTAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTTTAC
* * *
40681563 AAACGCCGCTACAGAACATGTTCTTTAGCGGCAC-TTTTTTAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTTTAC
40681605 AAA
1 AAA
40681608 AATGCCACTA
Statistics
Matches: 74, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
42 11 0.15
43 63 0.85
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.31
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTTTAC
Found at i:40681745 original size:114 final size:113
Alignment explanation
Indices: 40681545--40681763 Score: 350
Period size: 114 Copynumber: 1.9 Consensus size: 113
40681535 TCATAATATT
* * *
40681545 TAGCGGCGCTTTTTTTACAAACGCCGCTACAGAACATGTTCTTTAGCGGCACTTTTTTACAAAAA
1 TAGCGGCGCTTTTTATACAAACGCCGCTAAAGAACATGTTCTTTAGCGGCACTTTTGTACAAAAA
*
40681610 TGCCACTATTTTTAGAATTTTTTTTATATTAAATTTTTCATATGATCTC
66 CGCCACTATTTTTAGAA-TTTTTTTATATTAAATTTTTCATATGATCTC
* * *
40681659 TAGCGGCG-TTTTTATACAAAGTGCCGTTAAAGAACATGTTCTTTAGCGGCGCTTTTGTACAAAA
1 TAGCGGCGCTTTTTATACAAA-CGCCGCTAAAGAACATGTTCTTTAGCGGCACTTTTGTACAAAA
40681723 ACGCCACTATTTTTAGAATTTTTTTATATTAAATTTTTCAT
65 ACGCCACTATTTTTAGAATTTTTTTATATTAAATTTTTCAT
40681764 TTTTTTAGCC
Statistics
Matches: 97, Mismatches: 7, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
113 34 0.35
114 63 0.65
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.42
Consensus pattern (113 bp):
TAGCGGCGCTTTTTATACAAACGCCGCTAAAGAACATGTTCTTTAGCGGCACTTTTGTACAAAAA
CGCCACTATTTTTAGAATTTTTTTATATTAAATTTTTCATATGATCTC
Found at i:40682115 original size:21 final size:21
Alignment explanation
Indices: 40682091--40682141 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
40682081 TTCTTTTGAA
**
40682091 CCTCTGCTTCTTTCGCTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
*
40682112 CCTCTGCTTCCCTCGCTGCCG
1 CCTCTGCTTCCCTCGCTGCAG
*
40682133 CGTCTGCTT
1 CCTCTGCTT
40682142 TAAGTTGTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.02, C:0.43, G:0.20, T:0.35
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Found at i:40682194 original size:87 final size:87
Alignment explanation
Indices: 40682026--40682194 Score: 241
Period size: 87 Copynumber: 1.9 Consensus size: 87
40682016 TTCTGCTCTG
* *
40682026 CTCTGCTTCTCTCGATGCCGCATCAGCTTTAAGTCGTAGCTGGAGTTCTTCATATTTCTTTTGAA
1 CTCTGCTTCCCTCGATGCCGCATCAGCTTTAAGTCGTAGCTGGAGTTCTTCATATTTCCTTTGAA
* **
40682091 CCTCTGCTTCTTTCGCTGCAGC
66 CCTCAGCTTCGGTCGCTGCAGC
* * * *
40682113 CTCTGCTTCCCTCGCTGCCGCGTCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATTTCCTTTGAA
1 CTCTGCTTCCCTCGATGCCGCATCAGCTTTAAGTCGTAGCTGGAGTTCTTCATATTTCCTTTGAA
40682178 CCTCAGCTGT-GGTCGCT
66 CCTCAGCT-TCGGTCGCT
40682195 TGCATCTGAG
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
87 71 0.99
88 1 0.01
ACGTcount: A:0.12, C:0.29, G:0.20, T:0.38
Consensus pattern (87 bp):
CTCTGCTTCCCTCGATGCCGCATCAGCTTTAAGTCGTAGCTGGAGTTCTTCATATTTCCTTTGAA
CCTCAGCTTCGGTCGCTGCAGC
Found at i:40684701 original size:582 final size:582
Alignment explanation
Indices: 40683597--40684760 Score: 2247
Period size: 582 Copynumber: 2.0 Consensus size: 582
40683587 GGTGTAATCG
40683597 GAACATTCGAAGATCCAATTGCTGTCTGTTGTTCAGTACTATTTGTTTCTGTCGAGTTTGGATCA
1 GAACATTCGAAGATCCAATTGCTGTCTGTTGTTCAGTACTATTTGTTTCTGTCGAGTTTGGATCA
40683662 TTTTGAACAATGCTTCCCCTTAGAATTTTTCTTCTAGGCATTTTATCTGCAATACACATAAAATA
66 TTTTGAACAATGCTTCCCCTTAGAATTTTTCTTCTAGGCATTTTATCTGCAATACACATAAAATA
*
40683727 GTTGAAAACTTAATAACTAATTACAACAATAATAGCACATATAAAATAGTTGAAATATATAATAA
131 GTTGAAAACTTAATAACTAATTACAACAATAACAGCACATATAAAATAGTTGAAATATATAATAA
40683792 GACCAAGATTTAAATTATGATATTACATATAATTAAACAATCGTAAAATCTTACTACATCATTAT
196 GACCAAGATTTAAATTATGATATTACATATAATTAAACAATCGTAAAATCTTACTACATCATTAT
40683857 TCGTAAATATCTTCATCCGTATCCTGACGAACCCATTGAAATTGTGCACTAGTACTAGGGATATT
261 TCGTAAATATCTTCATCCGTATCCTGACGAACCCATTGAAATTGTGCACTAGTACTAGGGATATT
40683922 ATCGTTTAAGTTTTGTTCTGGAAAGGGCAAAGTTTCTGATCTGTCGTCGATGTTATCTCTACTTC
326 ATCGTTTAAGTTTTGTTCTGGAAAGGGCAAAGTTTCTGATCTGTCGTCGATGTTATCTCTACTTC
40683987 CACTGCCCATGTCAAACAAGTCTCTAGGGATGTTACGGAGTACAACGTACCAACCCTCATCAGTT
391 CACTGCCCATGTCAAACAAGTCTCTAGGGATGTTACGGAGTACAACGTACCAACCCTCATCAGTT
*
40684052 GGATCTTTTGAGTAAAAAACTTGTTTGACTTGAGATGAGAATACATATAGCTCATCTATCAGTTG
456 GGATCTTTTGAGTAAAAAACTTGTTTGACTTGAGATGAGAATACATACAGCTCATCTATCAGTTG
* *
40684117 TTGTCTTGTGTGAATCAATTGGTCAAAGTTCACCATTGTAAAACCAAATTGATCTTGCTTAA
521 TTGTCCTGTGTGAATCAATCGGTCAAAGTTCACCATTGTAAAACCAAATTGATCTTGCTTAA
* * * *
40684179 GAACATTCGAAGATCCAATTGCTGTCTTTTGTTCAGTACTATTTGTTTTTGTTGAGTTTGTATCA
1 GAACATTCGAAGATCCAATTGCTGTCTGTTGTTCAGTACTATTTGTTTCTGTCGAGTTTGGATCA
40684244 TTTTGAACAATGCTTCCCCTTAGAATTTTTCTTCTAGGCATTTTATCTGCAATACACATAAAATA
66 TTTTGAACAATGCTTCCCCTTAGAATTTTTCTTCTAGGCATTTTATCTGCAATACACATAAAATA
40684309 GTTGAAAACTTAATAACTAATTACAACAATAACAGCACATATAAAATAGTTGAAATATATAATAA
131 GTTGAAAACTTAATAACTAATTACAACAATAACAGCACATATAAAATAGTTGAAATATATAATAA
40684374 GACCAAGATTTAAATTATGATATTACATATAATTAAACAATCGTAAAATCTTACTACATCATTAT
196 GACCAAGATTTAAATTATGATATTACATATAATTAAACAATCGTAAAATCTTACTACATCATTAT
40684439 TCGTAAATATCTTCATCCGTATCCTGACGAACCCATTGAAATTGTGCACTAGTACTAGGGATATT
261 TCGTAAATATCTTCATCCGTATCCTGACGAACCCATTGAAATTGTGCACTAGTACTAGGGATATT
40684504 ATCGTTTAAGTTTTGTTCTGGAAAGGGCAAAGTTTCTGATCTGTCGTCGATGTTATCTCTACTTC
326 ATCGTTTAAGTTTTGTTCTGGAAAGGGCAAAGTTTCTGATCTGTCGTCGATGTTATCTCTACTTC
40684569 CACTGCCCATGTCAAACAAGTCTCTAGGGATGTTACGGAGTACAACGTACCAACCCTCATCAGTT
391 CACTGCCCATGTCAAACAAGTCTCTAGGGATGTTACGGAGTACAACGTACCAACCCTCATCAGTT
*
40684634 GGATCTTTTGAGTAAAAAACTTGTTTGACTTGAGATGAGAATACATACGGCTCATCTATCAGTTG
456 GGATCTTTTGAGTAAAAAACTTGTTTGACTTGAGATGAGAATACATACAGCTCATCTATCAGTTG
40684699 TTGTCCTGTGTGAATCAATCGGTCAAAGTTCACCATTGTAAAACCAAATTGATCTTGCTTAA
521 TTGTCCTGTGTGAATCAATCGGTCAAAGTTCACCATTGTAAAACCAAATTGATCTTGCTTAA
40684761 TTCCACGAGC
Statistics
Matches: 573, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
582 573 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (582 bp):
GAACATTCGAAGATCCAATTGCTGTCTGTTGTTCAGTACTATTTGTTTCTGTCGAGTTTGGATCA
TTTTGAACAATGCTTCCCCTTAGAATTTTTCTTCTAGGCATTTTATCTGCAATACACATAAAATA
GTTGAAAACTTAATAACTAATTACAACAATAACAGCACATATAAAATAGTTGAAATATATAATAA
GACCAAGATTTAAATTATGATATTACATATAATTAAACAATCGTAAAATCTTACTACATCATTAT
TCGTAAATATCTTCATCCGTATCCTGACGAACCCATTGAAATTGTGCACTAGTACTAGGGATATT
ATCGTTTAAGTTTTGTTCTGGAAAGGGCAAAGTTTCTGATCTGTCGTCGATGTTATCTCTACTTC
CACTGCCCATGTCAAACAAGTCTCTAGGGATGTTACGGAGTACAACGTACCAACCCTCATCAGTT
GGATCTTTTGAGTAAAAAACTTGTTTGACTTGAGATGAGAATACATACAGCTCATCTATCAGTTG
TTGTCCTGTGTGAATCAATCGGTCAAAGTTCACCATTGTAAAACCAAATTGATCTTGCTTAA
Found at i:40688214 original size:16 final size:16
Alignment explanation
Indices: 40688193--40688290 Score: 94
Period size: 16 Copynumber: 6.0 Consensus size: 16
40688183 ATTATGTAAG
40688193 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
40688209 TTATGTAAGTTATTTA
1 TTATGTAAGTTATGTA
*
40688225 TTATG-AATATTATGTAA
1 TTATGTAA-GTTATGT-A
*
40688242 GTTATGT-A-TTATGAAAA
1 -TTATGTAAGTTATG--TA
*
40688259 TTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTA
40688275 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
40688291 NTTGAAGCAT
Statistics
Matches: 67, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
15 2 0.03
16 52 0.78
17 3 0.04
18 10 0.15
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:40688240 original size:41 final size:41
Alignment explanation
Indices: 40688184--40688290 Score: 128
Period size: 41 Copynumber: 2.6 Consensus size: 41
40688174 AAGATATACA
* * *
40688184 TTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTAT-TTA-
1 TTATGT-A-TTATGTAAGTTATGTATTATGAAAATTATGTAAG
40688225 TTATGAATATTATGTAAGTTATGTATTATGAAAATTATGTAAG
1 TTATG--TATTATGTAAGTTATGTATTATGAAAATTATGTAAG
*
40688268 TTGTGTATTATGTAAGTTATGTA
1 TTATGTATTATGTAAGTTATGTA
40688291 NTTGAAGCAT
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
41 50 0.86
42 3 0.05
43 5 0.09
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.49
Consensus pattern (41 bp):
TTATGTATTATGTAAGTTATGTATTATGAAAATTATGTAAG
Found at i:40688287 original size:25 final size:25
Alignment explanation
Indices: 40688183--40688290 Score: 130
Period size: 25 Copynumber: 4.3 Consensus size: 25
40688173 CAAGATATAC
*
40688183 ATTATGTAAGTTATGTAAGTTATG--T
1 ATTATGTAAGTTATGT-A-TTATGAAA
* *
40688208 ATTATGTAAGTTATTTATTATGAAT
1 ATTATGTAAGTTATGTATTATGAAA
40688233 ATTATGTAAGTTATGTATTATGAAA
1 ATTATGTAAGTTATGTATTATGAAA
* *
40688258 ATTATGTAAGTTGTGTATTATGTAA
1 ATTATGTAAGTTATGTATTATGAAA
*
40688283 GTTATGTA
1 ATTATGTA
40688291 NTTGAAGCAT
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
23 5 0.07
24 1 0.01
25 69 0.92
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (25 bp):
ATTATGTAAGTTATGTATTATGAAA
Found at i:40690969 original size:41 final size:40
Alignment explanation
Indices: 40690901--40690980 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 40
40690891 TTTAACTCAC
40690901 TTTTGCGGCGTTTCTTGTACAAACGCCGCT-ATTGCTTAAT
1 TTTTGCGGCGTTTCTTGTACAAACGCCGCTAATTG-TTAAT
40690941 TTTTAGCGGCGTTT-TTAGTA-AAATCGCCGCTAATTGTTAA
1 TTTT-GCGGCGTTTCTT-GTACAAA-CGCCGCTAATTGTTAA
40690981 AGTTATAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
40 9 0.25
41 23 0.64
42 4 0.11
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (40 bp):
TTTTGCGGCGTTTCTTGTACAAACGCCGCTAATTGTTAAT
Found at i:40691404 original size:14 final size:15
Alignment explanation
Indices: 40691367--40691407 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
40691357 CCCTGATTTG
40691367 ACCCTAAAATCCCTAA
1 ACCCT-AAATCCCTAA
*
40691383 ACCTTAAATCCC-AA
1 ACCCTAAATCCCTAA
40691397 ACCCTAAATCC
1 ACCCTAAATCC
40691408 ATACAAGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 12 0.52
15 7 0.30
16 4 0.17
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.20
Consensus pattern (15 bp):
ACCCTAAATCCCTAA
Found at i:40691899 original size:63 final size:63
Alignment explanation
Indices: 40691829--40691954 Score: 225
Period size: 63 Copynumber: 2.0 Consensus size: 63
40691819 ACTCCTAACC
*
40691829 CATAACGTCTAACCCAGCTCCTGACCCCTAAACATTAAATCTGATCAGCTCTTACATCATATA
1 CATAACGTCTAACCCAGCTCCTGACCCCTAAACATTAAATCTGATAAGCTCTTACATCATATA
* *
40691892 CATAACGTCTAACCTAGCTCTTGACCCCTAAACATTAAATCTGATAAGCTCTTACATCATATA
1 CATAACGTCTAACCCAGCTCCTGACCCCTAAACATTAAATCTGATAAGCTCTTACATCATATA
40691955 TATACAGTAC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.34, C:0.29, G:0.08, T:0.29
Consensus pattern (63 bp):
CATAACGTCTAACCCAGCTCCTGACCCCTAAACATTAAATCTGATAAGCTCTTACATCATATA
Found at i:40691944 original size:31 final size:30
Alignment explanation
Indices: 40691844--40691944 Score: 80
Period size: 31 Copynumber: 3.2 Consensus size: 30
40691834 CGTCTAACCC
*
40691844 AGCTCCTGACCCCTAAACATTAAATCTGAT
1 AGCTCTTGACCCCTAAACATTAAATCTGAT
* * * * *
40691874 CAGCTCTT-ACATCATATACA-TAACGTCTAACCT
1 -AGCTCTTGAC-CCCTAAACATTAA-ATCTGA--T
40691907 AGCTCTTGACCCCTAAACATTAAATCTGAT
1 AGCTCTTGACCCCTAAACATTAAATCTGAT
40691937 AAGCTCTT
1 -AGCTCTT
40691945 ACATCATATA
Statistics
Matches: 52, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
30 6 0.12
31 23 0.44
32 17 0.33
33 6 0.12
ACGTcount: A:0.33, C:0.29, G:0.09, T:0.30
Consensus pattern (30 bp):
AGCTCTTGACCCCTAAACATTAAATCTGAT
Found at i:40692264 original size:21 final size:20
Alignment explanation
Indices: 40692240--40692324 Score: 53
Period size: 21 Copynumber: 4.0 Consensus size: 20
40692230 ATTAGTTAAT
40692240 CTAAACTGTAAACCATAAACC
1 CTAAACT-TAAACCATAAACC
* * *
40692261 CTAAAATCATAAACCCTTAACAC
1 CT-AAA-CTTAAACCATAAAC-C
* * *
40692284 ATAACCTTAAACCTTAAACC
1 CTAAACTTAAACCATAAACC
* *
40692304 CCAACCTTTAAACCATAAACC
1 CTAAAC-TTAAACCATAAACC
40692325 ATAGACCAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
20 5 0.10
21 26 0.53
22 15 0.31
23 3 0.06
ACGTcount: A:0.46, C:0.32, G:0.01, T:0.21
Consensus pattern (20 bp):
CTAAACTTAAACCATAAACC
Found at i:40692265 original size:14 final size:14
Alignment explanation
Indices: 40692248--40692327 Score: 56
Period size: 14 Copynumber: 5.6 Consensus size: 14
40692238 ATCTAAACTG
40692248 TAAACCATAAACCC
1 TAAACCATAAACCC
*
40692262 TAAAATCATAAACCC
1 T-AAACCATAAACCC
* *
40692277 TTAACACAT-AACCT
1 TAAAC-CATAAACCC
*
40692291 TAAACCTTAAACCC
1 TAAACCATAAACCC
* * *
40692305 -CAACCTTTAAACCA
1 TAAACC-ATAAACCC
40692319 TAAACCATA
1 TAAACCATA
40692328 GACCAAATAC
Statistics
Matches: 50, Mismatches: 11, Indels: 10
0.70 0.15 0.14
Matches are distributed among these distances:
13 6 0.12
14 24 0.48
15 20 0.40
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:40692595 original size:115 final size:114
Alignment explanation
Indices: 40692384--40692941 Score: 464
Period size: 115 Copynumber: 4.9 Consensus size: 114
40692374 ATGCATGGTT
* * * * *
40692384 AAGACCAAAACTCTGCGTTTTGGTTAAGATATTTTCCGGCGTTTCTCAAAAAGCGCCACTAATAC
1 AAGACAAAAACTCTGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATAC
* * * *
40692449 TATGCTTTAGCGACGCTTTCTCGT-GGACGCCACTAATTCTAGTATACATC
66 TATGCTTTAGCGGCG-TTTCCCATAAG-CGCCACTAATTCTAGTATACATC
** * * * * *
40692499 AAGACTTAAACGCTGCGTTTTTGTTAATATATTTTGTGGCGCTTCTCAAAAAGCGCCGCTAATAG
1 AAGACAAAAACTCTGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATAC
* * * *
40692564 TATGCTTTAACGGCGTTCTCCCATAAGCGCCACTAATTCTAATATACTTG
66 TATGCTTTAGCGGCGTT-TCCCATAAGCGCCACTAATTCTAGTATACATC
* * * * * ****
40692614 ATGA-AAAAACTCTGCGTTTTGGTGAGCATATGTTGCGGCGCTTTTTGCCAAGCGCCGCTAATAC
1 AAGACAAAAACTCTGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATAC
* * *** ** *
40692678 TATGGTTTAGCGGTGTTTTTTAATATTCGCCACTAATAACT-GTATACATC
66 TATGCTTTAGCGGCG-TTTCCCATAAGCGCCACTAAT-TCTAGTATACATC
* * *** *
40692728 AAGACAAAAACGT-TGCGTTTTGGTTACCAAATTTTGCGGCGCTTCTTTTAAAGTGCCGCTAATA
1 AAGACAAAAAC-TCTGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATA
* * ** *
40692792 GTATGCCTTAGCGGCGTGTTCCC-TTTGCGCCACTAATTCTAGTATACCTC
65 CTATGCTTTAGCGGCGT-TTCCCATAAGCGCCACTAATTCTAGTATACATC
* * * * * *
40692842 ATGAC-CAAACTCTGCATTTTGGTTAAGATATTTTGCGGCGCTTCACACAAAA-CGCCCCTAATA
1 AAGACAAAAACTCTGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCA-AAAAGCGCCGCTAATA
* * * *
40692905 TTATGCTTTAGCGACGTTTTCCCTTAAACGCCACTAA
65 CTATGCTTTAGCGGCG-TTTCCCATAAGCGCCACTAA
40692942 CTGTAAATAC
Statistics
Matches: 346, Mismatches: 85, Indels: 25
0.76 0.19 0.05
Matches are distributed among these distances:
112 1 0.00
113 61 0.18
114 121 0.35
115 161 0.47
116 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (114 bp):
AAGACAAAAACTCTGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATAC
TATGCTTTAGCGGCGTTTCCCATAAGCGCCACTAATTCTAGTATACATC
Found at i:40695435 original size:68 final size:68
Alignment explanation
Indices: 40695342--40695621 Score: 207
Period size: 68 Copynumber: 4.1 Consensus size: 68
40695332 CCGATCCATG
* * * *
40695342 GTCTTACACATTGTAATCT-CATGTTTAATGT-TTGGACA-AGCTTTATTAGTT-TCCATAGTCA
1 GTCTTACAC-TTGTAACCTCCATGTTTAATGTCCTGG-CAGA-ATCTATTAGTTAT-CATAGTCA
*
40695403 AGCTATA
62 AGATATA
* * *
40695410 TTCTTACACTTGTAACCTCCATGTTTAATGTCCTGGCAGAATCTATTGGTTATCATAGTCGAGAT
1 GTCTTACACTTGTAACCTCCATGTTTAATGTCCTGGCAGAATCTATTAGTTATCATAGTCAAGAT
*
40695475 ATG
66 ATA
* * * * *
40695478 GTCTTACACTTGTAACC-CCATGTTTAATATCCTGGCA-AACTCT-CTATGTTGTCATAGCCGAG
1 GTCTTACACTTGTAACCTCCATGTTTAATGTCCTGGCAGAA-TCTATTA-GTTATCATAGTCAAG
* *
40695540 CTATG
64 ATATA
* * * * * * * * *
40695545 GTCTTACATATTATAACC-CCATGTTTAATGTCCTAGCAGACTATATTAATTGTCATAATCAAGC
1 GTCTTACA-CTTGTAACCTCCATGTTTAATGTCCTGGCAGAATCTATTAGTTATCATAGTCAAGA
*
40695609 TATC
65 TATA
40695613 GTCTTACAC
1 GTCTTACAC
40695622 CTTAAACCTC
Statistics
Matches: 174, Mismatches: 29, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
66 3 0.02
67 55 0.32
68 108 0.62
69 8 0.05
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.38
Consensus pattern (68 bp):
GTCTTACACTTGTAACCTCCATGTTTAATGTCCTGGCAGAATCTATTAGTTATCATAGTCAAGAT
ATA
Found at i:40695533 original size:67 final size:67
Alignment explanation
Indices: 40695411--40695584 Score: 226
Period size: 67 Copynumber: 2.6 Consensus size: 67
40695401 CAAGCTATAT
*
40695411 TCTTACACTTGTAACCTCCATGTTTAATGTCCTGGCAGAATCTATTGGTTATCATAGTCGAGATA
1 TCTTACACTTGTAACC-CCATGTTTAATGTCCTGGCAGAATCTATTGGTTATCATAGCCGAGATA
40695476 TGG
65 TGG
* * * *
40695479 TCTTACACTTGTAACCCCATGTTTAATATCCTGGCA-AACTCTCTAT-GTTGTCATAGCCGAGCT
1 TCTTACACTTGTAACCCCATGTTTAATGTCCTGGCAGAA-TCTAT-TGGTTATCATAGCCGAGAT
40695542 ATGG
64 ATGG
* * *
40695546 TCTTACATATTATAACCCCATGTTTAATGTCCTAGCAGA
1 TCTTACA-CTTGTAACCCCATGTTTAATGTCCTGGCAGA
40695585 CTATATTAAT
Statistics
Matches: 93, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
66 2 0.02
67 48 0.52
68 42 0.45
69 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (67 bp):
TCTTACACTTGTAACCCCATGTTTAATGTCCTGGCAGAATCTATTGGTTATCATAGCCGAGATAT
GG
Found at i:40701918 original size:24 final size:24
Alignment explanation
Indices: 40701872--40701919 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
40701862 TGTTTACCTC
*
40701872 CGGTGAGATTAAAAACAGCGGTGG
1 CGGTGAGATTAAAAACAACGGTGG
* *
40701896 CGGTGAGATTAGAAACAATGGTGG
1 CGGTGAGATTAAAAACAACGGTGG
40701920 AGTGTGTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.38, T:0.19
Consensus pattern (24 bp):
CGGTGAGATTAAAAACAACGGTGG
Found at i:40702037 original size:29 final size:29
Alignment explanation
Indices: 40702001--40702060 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
40701991 ATTAAAATTT
40702001 TTTTTAAAATACACTACATATATTTTTTA
1 TTTTTAAAATACACTACATATATTTTTTA
40702030 TTTTTAAAATACACTACATATATTTTTTA
1 TTTTTAAAATACACTACATATATTTTTTA
40702059 TT
1 TT
40702061 GAAGCAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (29 bp):
TTTTTAAAATACACTACATATATTTTTTA
Found at i:40708235 original size:66 final size:66
Alignment explanation
Indices: 40708124--40708268 Score: 236
Period size: 66 Copynumber: 2.2 Consensus size: 66
40708114 TGCCTAATGG
* * * *
40708124 CATATACAAAACTGAGACAAACTCAGTATGCCAATGGTGTGTCACATGGGCAAATACTATACACC
1 CATA-ACAAAACTCAGACAAACTCAATATGCCAATGGTGTGTCACATAGGAAAATACTATACACC
40708189 AA
65 AA
*
40708191 CATAACAAAACTCTGACAAACTCAATATGCCAATGGTGTGTCACATAGGAAAATACTATACACCA
1 CATAACAAAACTCAGACAAACTCAATATGCCAATGGTGTGTCACATAGGAAAATACTATACACCA
40708256 A
66 A
40708257 CATAACAAAACT
1 CATAACAAAACT
40708269 TCGACATTCC
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
66 69 0.95
67 4 0.05
ACGTcount: A:0.43, C:0.23, G:0.13, T:0.21
Consensus pattern (66 bp):
CATAACAAAACTCAGACAAACTCAATATGCCAATGGTGTGTCACATAGGAAAATACTATACACCA
A
Found at i:40710972 original size:7 final size:7
Alignment explanation
Indices: 40710962--40710997 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
40710952 TTAAAAATTT
40710962 GAAACTA
1 GAAACTA
40710969 GAAACTA
1 GAAACTA
40710976 GAAACTA
1 GAAACTA
*
40710983 GAAACAA
1 GAAACTA
40710990 GGAAACTA
1 -GAAACTA
40710998 AAATAAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.58, C:0.14, G:0.17, T:0.11
Consensus pattern (7 bp):
GAAACTA
Found at i:40716957 original size:27 final size:27
Alignment explanation
Indices: 40716899--40716964 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
40716889 GCTAATAAAT
*
40716899 GCCTTTGTGGCGAAATCTAAAAGGAAT
1 GCCTTTGTGGCGAAATCTAAAAGGAAC
* * *
40716926 TCCTTTGTGGC-AAATTCTGAATGGAAC
1 GCCTTTGTGGCGAAA-TCTAAAAGGAAC
*
40716953 GCCTTGGTGGCG
1 GCCTTTGTGGCG
40716965 TACTCTATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
26 3 0.10
27 28 0.90
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (27 bp):
GCCTTTGTGGCGAAATCTAAAAGGAAC
Found at i:40729315 original size:28 final size:27
Alignment explanation
Indices: 40729220--40729322 Score: 82
Period size: 28 Copynumber: 3.6 Consensus size: 27
40729210 AAAACTCAGG
* * *
40729220 AAAGGTAAGTCTTTGTAGTGAACCTATT
1 AAAGG-AAGCCTTTGTGGTGAACCTGTT
* ** *
40729248 AAAGGAAAACCTTTGTGGCAAAACTCTG-G
1 AAAGG-AAGCCTTTGTGG-TGAAC-CTGTT
40729277 AAAGGTAAGCCTTTGTGGTGAACCTGTT
1 AAAGG-AAGCCTTTGTGGTGAACCTGTT
40729305 AAAGGACAGCCTTTGTGG
1 AAAGGA-AGCCTTTGTGG
40729323 CAAAACTCTA
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
27 4 0.07
28 33 0.57
29 19 0.33
30 2 0.03
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (27 bp):
AAAGGAAGCCTTTGTGGTGAACCTGTT
Found at i:40729337 original size:28 final size:28
Alignment explanation
Indices: 40729196--40729377 Score: 102
Period size: 29 Copynumber: 6.4 Consensus size: 28
40729186 TTTGGAAAGA
*
40729196 TAAGCCTTTGTGGAAAAACTC-AGGAAAGG
1 TAAGCCTTTGTGGCAAAACTCTA-G-AAGG
* * ** * *
40729225 TAAGTCTTTGTAGTGAACCTATTA-AAGG
1 TAAGCCTTTGTGGCAAAACT-CTAGAAGG
* * *
40729253 AAAACCTTTGTGGCAAAACTCTGGAAAGG
1 TAAGCCTTTGTGGCAAAACTCTAG-AAGG
** * *
40729282 TAAGCCTTTGTGGTGAACCTGTTA-AAGG
1 TAAGCCTTTGTGGCAAAACT-CTAGAAGG
40729310 -ACAGCCTTTGTGGCAAAACTCTAGAAGGG
1 TA-AGCCTTTGTGGCAAAACTCTAGAA-GG
* * *
40729339 TAAACCTTTGTGCCAAAACTCTGGAAGGG
1 TAAGCCTTTGTGGCAAAACTCTAGAA-GG
*
40729368 TAAACCTTTG
1 TAAGCCTTTG
40729378 CGGTGAACCT
Statistics
Matches: 115, Mismatches: 29, Indels: 18
0.71 0.18 0.11
Matches are distributed among these distances:
27 4 0.03
28 38 0.33
29 70 0.61
30 2 0.02
31 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.26
Consensus pattern (28 bp):
TAAGCCTTTGTGGCAAAACTCTAGAAGG
Found at i:40729344 original size:86 final size:85
Alignment explanation
Indices: 40729254--40729422 Score: 239
Period size: 86 Copynumber: 2.0 Consensus size: 85
40729244 TATTAAAGGA
* * * *
40729254 AAACCTTTGTGGCAAAACTCTGGAAAGGTAAGCCTTTGTGGTGAACCTGTTAAAGGACAGCCTTT
1 AAACCTTTGTGCCAAAACTCTGGAAAGGTAAACCTTTGCGGTGAACCTCTTAAAGGA-AGCCTTT
*
40729319 GTGGCAAAACTCTAGAAGGGT
65 GTGGCAAAACTCTAAAAGGGT
* * * *
40729340 AAACCTTTGTGCCAAAACTCTGGAAGGGTAAACCTTTGCGGTGAACCTCTTAAATGATGGCTTTG
1 AAACCTTTGTGCCAAAACTCTGGAAAGGTAAACCTTTGCGGTGAACCTCTTAAAGGAAGCCTTTG
*
40729405 TGGCAAGACTCTAAAAGG
66 TGGCAAAACTCTAAAAGG
40729423 AAATACCTTA
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
85 22 0.30
86 51 0.70
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.26
Consensus pattern (85 bp):
AAACCTTTGTGCCAAAACTCTGGAAAGGTAAACCTTTGCGGTGAACCTCTTAAAGGAAGCCTTTG
TGGCAAAACTCTAAAAGGGT
Found at i:40729350 original size:29 final size:29
Alignment explanation
Indices: 40729254--40729377 Score: 119
Period size: 29 Copynumber: 4.3 Consensus size: 29
40729244 TATTAAAGGA
* *
40729254 AAACCTTTGTGGCAAAACTCTGGAAAGGT
1 AAACCTTTGTGGCAAAACTCTAGAAGGGT
* ** * *
40729283 AAGCCTTTGTGGTGAACCTGTTA-AA-GG-
1 AAACCTTTGTGGCAAAACT-CTAGAAGGGT
*
40729310 ACAGCCTTTGTGGCAAAACTCTAGAAGGGT
1 A-AACCTTTGTGGCAAAACTCTAGAAGGGT
* *
40729340 AAACCTTTGTGCCAAAACTCTGGAAGGGT
1 AAACCTTTGTGGCAAAACTCTAGAAGGGT
40729369 AAACCTTTG
1 AAACCTTTG
40729378 CGGTGAACCT
Statistics
Matches: 77, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
27 3 0.04
28 19 0.25
29 53 0.69
30 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.26
Consensus pattern (29 bp):
AAACCTTTGTGGCAAAACTCTAGAAGGGT
Found at i:40729350 original size:57 final size:57
Alignment explanation
Indices: 40729197--40729350 Score: 211
Period size: 57 Copynumber: 2.7 Consensus size: 57
40729187 TTGGAAAGAT
* * *
40729197 AAGCCTTTGTGGAAAAACTC-AGGAAAGGTAAGTCTTTGTAGTGAACCTATTAAAGGA
1 AAGCCTTTGTGGCAAAACTCTA-GAAAGGTAAGCCTTTGTGGTGAACCTATTAAAGGA
* * *
40729254 AAACCTTTGTGGCAAAACTCTGGAAAGGTAAGCCTTTGTGGTGAACCTGTTAAAGGA
1 AAGCCTTTGTGGCAAAACTCTAGAAAGGTAAGCCTTTGTGGTGAACCTATTAAAGGA
* * *
40729311 CAGCCTTTGTGGCAAAACTCTAGAAGGGTAAACCTTTGTG
1 AAGCCTTTGTGGCAAAACTCTAGAAAGGTAAGCCTTTGTG
40729351 CCAAAACTCT
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
57 85 1.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (57 bp):
AAGCCTTTGTGGCAAAACTCTAGAAAGGTAAGCCTTTGTGGTGAACCTATTAAAGGA
Found at i:40739683 original size:47 final size:47
Alignment explanation
Indices: 40739630--40740040 Score: 750
Period size: 47 Copynumber: 8.7 Consensus size: 47
40739620 TTAGGATTCT
40739630 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
40739677 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
40739724 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
40739771 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
40739818 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
40739865 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
40739912 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
40739959 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
40740006 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
40740041 TCCCGAAGGG
Statistics
Matches: 354, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 354 1.00
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:40740215 original size:37 final size:37
Alignment explanation
Indices: 40740159--40740237 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
40740149 CCGAGCTCTA
* * *
40740159 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
40740196 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
40740233 AAGAC
1 AAGAC
40740238 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:40741066 original size:55 final size:55
Alignment explanation
Indices: 40741000--40741110 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
40740990 CTAAAAATAG
40741000 TAGGATTGGAATTAAATAATGAATAAATTATGTAAACGAACCTTGATGAATCTAT
1 TAGGATTGGAATTAAATAATGAATAAATTATGTAAACGAACCTTGATGAATCTAT
40741055 TAGGATTGGAATTAAATAATGAATAAATTATGTAAACGAACCTTGATGAATCTAT
1 TAGGATTGGAATTAAATAATGAATAAATTATGTAAACGAACCTTGATGAATCTAT
40741110 T
1 T
40741111 TTCATAGGAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.33
Consensus pattern (55 bp):
TAGGATTGGAATTAAATAATGAATAAATTATGTAAACGAACCTTGATGAATCTAT
Found at i:40742195 original size:43 final size:43
Alignment explanation
Indices: 40742147--40742246 Score: 191
Period size: 43 Copynumber: 2.3 Consensus size: 43
40742137 TTGGTTTTCA
40742147 GCACTAAGTGTGCGGGCAAGAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAAGAAGTGTTCACGGTTGTGAGATTG
*
40742190 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAAGAAGTGTTCACGGTTGTGAGATTG
40742233 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
40742247 TGGTTGATTA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.23, C:0.15, G:0.36, T:0.26
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAAGAAGTGTTCACGGTTGTGAGATTG
Found at i:40742829 original size:40 final size:40
Alignment explanation
Indices: 40742555--40742815 Score: 287
Period size: 40 Copynumber: 6.5 Consensus size: 40
40742545 TCGAATGATG
* *
40742555 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCT-AGTGA-TATA
* * * * *
40742595 TCCGGACTAAGAT-CCGAAG-GCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGAGCATTCGTGCTAGTGA-TATA
*
40742635 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
* * *
40742675 TTCGGGCTAAGTCCCGAGGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
*
40742715 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
* ** * * *
40742755 TCCGTGCTAAACCCCAAAGAGCATTCGTGCTGGTGTTATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
*
40742795 TCCGGGCTAGGTCCCGAAGAG
1 TCCGGGCTAAGTCCCGAAGAG
40742816 TAATCATGCT
Statistics
Matches: 185, Mismatches: 32, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 165 0.89
41 19 0.10
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
Found at i:40746493 original size:49 final size:47
Alignment explanation
Indices: 40746294--40746516 Score: 392
Period size: 47 Copynumber: 4.7 Consensus size: 47
40746284 ATGATAGTAT
40746294 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
40746341 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
* *
40746388 TGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
*
40746435 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAA
40746484 GGCCTAATGGCCGATGTGATGAATGTGATAAGT
1 GGCCTAATGGCCGATGTGATGAATGTGA-AAGT
40746517 CCCGAAGGGC
Statistics
Matches: 170, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
47 124 0.73
49 42 0.25
50 4 0.02
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.30
Consensus pattern (47 bp):
GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
Found at i:40746690 original size:37 final size:37
Alignment explanation
Indices: 40746634--40746712 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
40746624 CCGAGCTCTA
* * *
40746634 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
40746671 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
40746708 AAGAC
1 AAGAC
40746713 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:40747805 original size:48 final size:48
Alignment explanation
Indices: 40747747--40747842 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
40747737 TTGAAGCTCT
40747747 GTGCAGGGAGATATCCAAGTCGTAATGCGAAAAGGTCAGTGTAGTCGA
1 GTGCAGGGAGATATCCAAGTCGTAATGCGAAAAGGTCAGTGTAGTCGA
*
40747795 GTGCAGGGAGATATCCAAGTCGTAATGCGCAAAGGTCAGTGTAGTCGA
1 GTGCAGGGAGATATCCAAGTCGTAATGCGAAAAGGTCAGTGTAGTCGA
40747843 TCCCTGTAAC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.30, C:0.16, G:0.33, T:0.21
Consensus pattern (48 bp):
GTGCAGGGAGATATCCAAGTCGTAATGCGAAAAGGTCAGTGTAGTCGA
Found at i:40748711 original size:29 final size:29
Alignment explanation
Indices: 40748652--40748721 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
40748642 GTTGTGAGAT
* *
40748652 TGGCACTAAGTGTGCGGGCTTGAAATGCA
1 TGGCACTAAGTGTGCGAGCTTGAAATACA
*
40748681 TGGCACTAAGTGTGCGAG-TTTAAAGTACA
1 TGGCACTAAGTGTGCGAGCTTGAAA-TACA
*
40748710 TGGCAATAAGTG
1 TGGCACTAAGTG
40748722 GGCGTGGTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
28 5 0.14
29 31 0.86
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGAAATACA
Found at i:40749350 original size:40 final size:40
Alignment explanation
Indices: 40749036--40749336 Score: 354
Period size: 40 Copynumber: 7.5 Consensus size: 40
40749026 TCGAATGATG
* * *
40749036 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCAAAGAGCATTCGTGCT-AGTGA-TATA
* * * *
40749076 TCCGGACTAAGTTCCGAAGAGCATTCATGCTAGTGATATA
1 TCCGGGCTAAGTCCCAAAGAGCATTCGTGCTAGTGATATA
* * *
40749116 TCCGGGCTAAGTCCCGAGGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCCCAAAGAGCATTCGTGCTAGTGATATA
*
40749156 TCCGGGCTAAGTTCCAAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCAAAGAGCATTCGTGCTAGTGATATA
* ** *
40749196 TCCGTGCTAAACCCCAAAGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCCCAAAGAGCATTCGTGCTAGTGATATA
* *
40749236 TCTGGGCTAAGTTCCAAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCAAAGAGCATTCGTGCTAGTGATATA
* ** * *
40749276 TCCGTGCTAAACCCCAAAGAGCATTCGTGCTGGTGTTATA
1 TCCGGGCTAAGTCCCAAAGAGCATTCGTGCTAGTGATATA
* *
40749316 TCCGGGCTAGGTCCCGAAGAG
1 TCCGGGCTAAGTCCCAAAGAG
40749337 TAATCATGCT
Statistics
Matches: 222, Mismatches: 37, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
40 209 0.94
41 7 0.03
42 6 0.03
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCAAAGAGCATTCGTGCTAGTGATATA
Found at i:40750236 original size:50 final size:50
Alignment explanation
Indices: 40750178--40750277 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
40750168 TTAATATGTG
40750178 CTCAATATGTGTTTGAAATGCATTTGTGAATTAAGTTAAGTGATTATTGC
1 CTCAATATGTGTTTGAAATGCATTTGTGAATTAAGTTAAGTGATTATTGC
40750228 CTCAATATGTGTTTGAAATGCATTTGTGAATTAAGTTAAGTGATTATTGC
1 CTCAATATGTGTTTGAAATGCATTTGTGAATTAAGTTAAGTGATTATTGC
40750278 TTATGAAATC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (50 bp):
CTCAATATGTGTTTGAAATGCATTTGTGAATTAAGTTAAGTGATTATTGC
Found at i:40752834 original size:25 final size:25
Alignment explanation
Indices: 40752806--40752884 Score: 74
Period size: 25 Copynumber: 3.3 Consensus size: 25
40752796 CTAATGGCCG
40752806 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
*** ****
40752831 ATGTGAT-AATGCCTAA-TG-GCCG
1 ATGTGATGAATGTGAAAGTGTATAT
40752853 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
40752878 ATGTGAT
1 ATGTGAT
40752885 AAGCCCTAAT
Statistics
Matches: 37, Mismatches: 14, Indels: 6
0.65 0.25 0.11
Matches are distributed among these distances:
22 7 0.19
23 8 0.22
24 8 0.22
25 14 0.38
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.34
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:40752992 original size:49 final size:47
Alignment explanation
Indices: 40752793--40753015 Score: 383
Period size: 47 Copynumber: 4.7 Consensus size: 47
40752783 ATGATAGTAT
40752793 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
*
40752840 TGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
*
40752887 GCCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
* *
40752934 GGCCTAATGGCCGATTTGATGAATGTGAAAGTGTATATATATGTGATAG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAA
40752983 GGCCTAATGGCCGATGTGATGAATGTGATAAGT
1 GGCCTAATGGCCGATGTGATGAATGTGA-AAGT
40753016 CCCGAAGGGC
Statistics
Matches: 166, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
47 122 0.73
49 40 0.24
50 4 0.02
ACGTcount: A:0.31, C:0.09, G:0.29, T:0.30
Consensus pattern (47 bp):
GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
Found at i:40753189 original size:37 final size:37
Alignment explanation
Indices: 40753133--40753211 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
40753123 CCGAGCTCTA
* * * *
40753133 AAGACCTGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
40753170 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
40753207 AAGAC
1 AAGAC
40753212 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:40755125 original size:43 final size:43
Alignment explanation
Indices: 40755077--40755179 Score: 197
Period size: 43 Copynumber: 2.4 Consensus size: 43
40755067 TTGGTTTTCA
*
40755077 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAAGAAGTGTTCACGGTTGTGAGATTG
40755120 GCACTAAGTGTGCGGGCAAGAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAAGAAGTGTTCACGGTTGTGAGATTG
40755163 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
40755180 TTGAAATGCA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.22, C:0.16, G:0.37, T:0.25
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAAGAAGTGTTCACGGTTGTGAGATTG
Found at i:40755195 original size:29 final size:29
Alignment explanation
Indices: 40755161--40755234 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
40755151 GTTGTGAGAT
* *
40755161 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
40755190 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
40755219 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
40755235 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:40755674 original size:40 final size:40
Alignment explanation
Indices: 40755547--40755902 Score: 369
Period size: 40 Copynumber: 8.9 Consensus size: 40
40755537 TCGAATGATG
** *
40755547 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGA-TATA
* ** * * *
40755587 TCCGGACTAAGAT-CCGAAG-GCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGAGCATTCATGCTAGTGA-TATA
* * *
40755627 CCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* *
40755667 TCTGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
*
40755707 TCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* * *
40755747 TCCGGGCTAAGTCCCGAGGAGCATTCGTGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* *
40755787 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* ** * * * *
40755827 TCCGTGCTAAACCCCAAAGAGCATTCGTGCTGGTGTTATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* * * *
40755867 TCCGGGCTAGGTCCCGAAGAGTAATCATGCTGGTGA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
40755903 CGTGTATTCG
Statistics
Matches: 268, Mismatches: 44, Indels: 8
0.84 0.14 0.03
Matches are distributed among these distances:
39 1 0.00
40 249 0.93
41 18 0.07
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
Found at i:40755763 original size:120 final size:120
Alignment explanation
Indices: 40755547--40755897 Score: 413
Period size: 120 Copynumber: 2.9 Consensus size: 120
40755537 TCGAATGATG
* * *
40755547 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAG-GCA
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCT-AGTGA-TATATCCGGGCTAAGATCCGAAGAGCA
* * * * *
40755609 TTGGTGCGAGTTACTAAACCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATGTA
64 TTCGTGCTAGTGA-TATATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATGTA
* * * *
40755667 TCTGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATT
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGATCCGAAGAGCATT
* * * *
40755732 CATGCTAGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCTAGTGATGTA
66 CGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATGTA
* * * *
40755787 TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGTGCTAA-ACCCCAAAGAGCAT
1 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGA-TCCGAAGAGCAT
* * * * *
40755851 TCGTGCTGGTGTTATATCCGGGCTAGGTCCCGAAGAGTAATCATGCT
65 TCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCATGCT
40755898 GGTGACGTGT
Statistics
Matches: 195, Mismatches: 32, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
120 170 0.87
121 19 0.10
122 6 0.03
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGATCCGAAGAGCATT
CGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGCGATGTA
Found at i:40761698 original size:45 final size:45
Alignment explanation
Indices: 40761553--40761699 Score: 111
Period size: 45 Copynumber: 3.2 Consensus size: 45
40761543 TAGGGGTGTT
*
40761553 ACACCTCAATTACAATGAAAAAACATCTCAA-TTTCTAGCAACTAA
1 ACACCTCAATTACAGTGAAAAAACATCTCAATTTTC-AGCAACTAA
* * *** * ** * ** *
40761598 ACACTTCAATT--TGCTGCACTTTAACATCTTAATTAACAACATTTAT
1 ACACCTCAATTACAG-TG-A-AAAAACATCTCAATTTTCAGCAACTAA
40761644 ACACCTCAATTACAGTGAAAAAACATCTCAATTTTCAGCAACTAA
1 ACACCTCAATTACAGTGAAAAAACATCTCAATTTTCAGCAACTAA
*
40761689 ACACTTCAATT
1 ACACCTCAATT
40761700 TGCAGTACTT
Statistics
Matches: 70, Mismatches: 26, Indels: 12
0.65 0.24 0.11
Matches are distributed among these distances:
44 2 0.03
45 38 0.54
46 25 0.36
47 4 0.06
48 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.30
Consensus pattern (45 bp):
ACACCTCAATTACAGTGAAAAAACATCTCAATTTTCAGCAACTAA
Found at i:40761745 original size:91 final size:91
Alignment explanation
Indices: 40761552--40761733 Score: 287
Period size: 91 Copynumber: 2.0 Consensus size: 91
40761542 TTAGGGGTGT
*
40761552 TACACCTCAATTACAATGAAAAAACATCTCAATTTCTAGCAACTAAACACTTCAATTTGCTGCAC
1 TACACCTCAATTACAATGAAAAAACATCTCAATTTCTAGCAACTAAACACTTCAATTTGCAGCAC
*
40761617 TTTAACATCTTAATTAACAACATTTA
66 TTAAACATCTTAATTAACAACATTTA
* *
40761643 TACACCTCAATTACAGTGAAAAAACATCTCAATTT-TCAGCAACTAAACACTTCAATTTGCAGTA
1 TACACCTCAATTACAATGAAAAAACATCTCAATTTCT-AGCAACTAAACACTTCAATTTGCAGCA
*
40761707 CTTAAACA-CTTTAATTTACAACATTTA
65 CTTAAACATC-TTAATTAACAACATTTA
40761734 AGCACTTCAA
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
90 2 0.02
91 82 0.98
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.32
Consensus pattern (91 bp):
TACACCTCAATTACAATGAAAAAACATCTCAATTTCTAGCAACTAAACACTTCAATTTGCAGCAC
TTAAACATCTTAATTAACAACATTTA
Found at i:40761766 original size:69 final size:69
Alignment explanation
Indices: 40761671--40761987 Score: 320
Period size: 69 Copynumber: 4.6 Consensus size: 69
40761661 AAAAAACATC
* ** * * *
40761671 TCAATTTTCAGCAACTAAACACTTCAATTTGCAGTACTTAAACACTTTAATTTACAACATTTAAG
1 TCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAACATTTAAA
40761736 CACT
66 CACT
* * *
40761740 TCAATTTAAAGCATTTAAACACTTCAATTTGCAGCACTTGAACACTTCAATTTACAACATTTAAG
1 TCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAACATTTAAA
40761805 CACT
66 CACT
* ** * * * * * *
40761809 TCAATTTGCAGCACTTT-AACA-TCTCAATTAACAACATTTATACACCTCAA-TTACAGCGA-TA
1 TCAATTTACAGCA-TTTAAACACT-TCAATTTGCAGCACTTAAACACTTCAATTTACAAC-ATTT
40761870 AAACA-T
63 AAACACT
* ** *
40761876 CTCAATTTCCAGCAACTAAACACTTCAATTTGCAGTACTTAAACACTTCAATTTACAACATTTAA
1 -TCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAACATTTAA
*
40761941 ACAAT
65 ACACT
* * * *
40761946 TTAATTTACAGTATTTAAACACTTCAATTTACAGCATTTAAA
1 TCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTAAA
40761988 TAGCAACAAC
Statistics
Matches: 200, Mismatches: 39, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
67 2 0.01
68 49 0.25
69 145 0.73
70 4 0.02
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (69 bp):
TCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAACATTTAAA
CACT
Found at i:40761934 original size:206 final size:206
Alignment explanation
Indices: 40761599--40761981 Score: 658
Period size: 206 Copynumber: 1.9 Consensus size: 206
40761589 AGCAACTAAA
* * *
40761599 CACTTCAATTTGCTGCACTTTAACATCTTAATTAACAACATTTATACACCTCAATTACAGTGAAA
1 CACTTCAATTTGCAGCACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGCGAAA
* *
40761664 AAACATCTCAATTTTCAGCAACTAAACACTTCAATTTGCAGTACTTAAACACTTTAATTTACAAC
66 AAACATCTCAATTTCCAGCAACTAAACACTTCAATTTGCAGTACTTAAACACTTCAATTTACAAC
* * *
40761729 ATTTAAGCACTTCAATTTAAAGCATTTAAACACTTCAATTTGCAGCACTTGAACACTTCAATTTA
131 ATTTAAACAATTCAATTTAAAGCATTTAAACACTTCAATTTACAGCACTTGAACACTTCAATTTA
40761794 CAACATTTAAG
196 CAACATTTAAG
*
40761805 CACTTCAATTTGCAGCACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGCGATA
1 CACTTCAATTTGCAGCACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGCGAAA
40761870 AAACATCTCAATTTCCAGCAACTAAACACTTCAATTTGCAGTACTTAAACACTTCAATTTACAAC
66 AAACATCTCAATTTCCAGCAACTAAACACTTCAATTTGCAGTACTTAAACACTTCAATTTACAAC
* * *
40761935 ATTTAAACAATTTAATTTACAGTATTTAAACACTTCAATTTACAGCA
131 ATTTAAACAATTCAATTTAAAGCATTTAAACACTTCAATTTACAGCA
40761982 TTTAAATAGC
Statistics
Matches: 165, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
206 165 1.00
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (206 bp):
CACTTCAATTTGCAGCACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGCGAAA
AAACATCTCAATTTCCAGCAACTAAACACTTCAATTTGCAGTACTTAAACACTTCAATTTACAAC
ATTTAAACAATTCAATTTAAAGCATTTAAACACTTCAATTTACAGCACTTGAACACTTCAATTTA
CAACATTTAAG
Found at i:40761984 original size:23 final size:23
Alignment explanation
Indices: 40761595--40761987 Score: 284
Period size: 23 Copynumber: 17.2 Consensus size: 23
40761585 TTCTAGCAAC
* *
40761595 TAAACACTTCAATTTGCTGCACTT
1 TAAACACTTCAATTTACAGCA-TT
* *
40761619 T-AACATCTT-AATTAACAACATT
1 TAAACA-CTTCAATTTACAGCATT
* * *
40761641 TATACACCTCAA-TTACAG--TG
1 TAAACACTTCAATTTACAGCATT
* * * **
40761661 AAAAAACATCTCAATTTTCAGCAAC
1 TAAACAC-T-TCAATTTACAGCATT
* * *
40761686 TAAACACTTCAATTTGCAGTACT
1 TAAACACTTCAATTTACAGCATT
* *
40761709 TAAACACTTTAATTTACAACATT
1 TAAACACTTCAATTTACAGCATT
* *
40761732 TAAGCACTTCAATTTAAAGCATT
1 TAAACACTTCAATTTACAGCATT
* *
40761755 TAAACACTTCAATTTGCAGCACT
1 TAAACACTTCAATTTACAGCATT
* *
40761778 TGAACACTTCAATTTACAACATT
1 TAAACACTTCAATTTACAGCATT
* *
40761801 TAAGCACTTCAATTTGCAGCACTT
1 TAAACACTTCAATTTACAGCA-TT
* *
40761825 T-AACA-TCTCAATTAACAACATT
1 TAAACACT-TCAATTTACAGCATT
* *
40761847 TATACACCTCAA-TTACAGCGA-T
1 TAAACACTTCAATTTACAGC-ATT
* * **
40761869 AAAACA-TCTCAATTTCCAGCAAC
1 TAAACACT-TCAATTTACAGCATT
* * *
40761892 TAAACACTTCAATTTGCAGTACT
1 TAAACACTTCAATTTACAGCATT
*
40761915 TAAACACTTCAATTTACAACATT
1 TAAACACTTCAATTTACAGCATT
* * *
40761938 TAAACAATTTAATTTACAGTATT
1 TAAACACTTCAATTTACAGCATT
40761961 TAAACACTTCAATTTACAGCATT
1 TAAACACTTCAATTTACAGCATT
40761984 TAAA
1 TAAA
40761988 TAGCAACAAC
Statistics
Matches: 280, Mismatches: 72, Indels: 35
0.72 0.19 0.09
Matches are distributed among these distances:
20 5 0.02
22 32 0.11
23 229 0.82
24 9 0.03
25 5 0.02
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (23 bp):
TAAACACTTCAATTTACAGCATT
Found at i:40763903 original size:21 final size:18
Alignment explanation
Indices: 40763877--40763915 Score: 51
Period size: 21 Copynumber: 2.0 Consensus size: 18
40763867 CAATTATACA
40763877 TAAAATGCTTAATATCATGAC
1 TAAAATG-TT-ATAT-ATGAC
40763898 TAAAATGTTATATATGAC
1 TAAAATGTTATATATGAC
40763916 CACTAAACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 4 0.22
20 2 0.11
21 7 0.39
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (18 bp):
TAAAATGTTATATATGAC
Found at i:40765676 original size:40 final size:40
Alignment explanation
Indices: 40765562--40765774 Score: 239
Period size: 40 Copynumber: 5.3 Consensus size: 40
40765552 TAAAAAAATA
* * * *
40765562 TTTT-CGGCATTTATGAAAAAATGCCGCTATTGCTTTAGC
1 TTTTGCGGCGTTTATGCAAAAACGCCGCTATTGCTTTACC
* *
40765601 TTTTGCGGCGTTTATGAGAAAAACACCGCTATTGCTTTACC
1 TTTTGCGGCGTTTATG-CAAAAACGCCGCTATTGCTTTACC
* * *
40765642 TTTTGTGGCGTTTATGCAAAAATGCCGCTCTTGCTTTACC
1 TTTTGCGGCGTTTATGCAAAAACGCCGCTATTGCTTTACC
* * * * *
40765682 TTTTTCAGCGTTTATGCAAAAACACCACTAATGCTTTACC
1 TTTTGCGGCGTTTATGCAAAAACGCCGCTATTGCTTTACC
* * * *
40765722 TTTTACGGCATTTATTCAAAAACGCCGCTAATGCTTTACC
1 TTTTGCGGCGTTTATGCAAAAACGCCGCTATTGCTTTACC
*
40765762 TTTTGCGGTGTTT
1 TTTTGCGGCGTTT
40765775 TTAATCCAAA
Statistics
Matches: 145, Mismatches: 27, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 4 0.03
40 106 0.73
41 35 0.24
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (40 bp):
TTTTGCGGCGTTTATGCAAAAACGCCGCTATTGCTTTACC
Found at i:40765749 original size:80 final size:80
Alignment explanation
Indices: 40765562--40765767 Score: 270
Period size: 80 Copynumber: 2.6 Consensus size: 80
40765552 TAAAAAAATA
* * * *
40765562 TTTTCGGCATTTATGAAAAAATGCCGCTATTGCTTTAGCTTTTGCGGCGTTTATGAGAAAAACAC
1 TTTTCGGCATTTATGCAAAAATGCCGCTATTGCTTTACCTTTTGCAGCGTTTATGACAAAAACAC
* *
40765627 CGCTATTGCTTTACC
66 CACTAATGCTTTACC
* * * *
40765642 TTTTGTGGCGTTTATGCAAAAATGCCGCTCTTGCTTTACCTTTTTCAGCGTTTATG-CAAAAACA
1 TTTT-CGGCATTTATGCAAAAATGCCGCTATTGCTTTACCTTTTGCAGCGTTTATGACAAAAACA
40765706 CCACTAATGCTTTACC
65 CCACTAATGCTTTACC
* * *
40765722 TTTTACGGCATTTATTCAAAAACGCCGCTAATGCTTTACCTTTTGC
1 TTTT-CGGCATTTATGCAAAAATGCCGCTATTGCTTTACCTTTTGC
40765768 GGTGTTTTTA
Statistics
Matches: 107, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
80 63 0.59
81 44 0.41
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.37
Consensus pattern (80 bp):
TTTTCGGCATTTATGCAAAAATGCCGCTATTGCTTTACCTTTTGCAGCGTTTATGACAAAAACAC
CACTAATGCTTTACC
Found at i:40765800 original size:13 final size:13
Alignment explanation
Indices: 40765782--40765809 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
40765772 TTTTTAATCC
40765782 AAATGCCGCTAAA
1 AAATGCCGCTAAA
40765795 AAATGCCGCTAAA
1 AAATGCCGCTAAA
40765808 AA
1 AA
40765810 CCTATTTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.21, G:0.14, T:0.14
Consensus pattern (13 bp):
AAATGCCGCTAAA
Found at i:40779873 original size:111 final size:110
Alignment explanation
Indices: 40779670--40779887 Score: 240
Period size: 111 Copynumber: 2.0 Consensus size: 110
40779660 ATGCATATTT
* * * * * *
40779670 TGTAACAGCCCATTTTTAGTGAAATCGGAATAGTGGTTTTGGGACCACAAATCCTAGCCGGAAAG
1 TGTAACAGCCCATTTTTAGTGAAATCAGAACAGTGGTTTTGGGACAACAAATCCGAGCCGAAAAA
* * **
40779735 GAAATTTGTTTTAATATTATGGCATGGTTTGCATTATGTTAGGAA
66 GAAATTTATTTTAATATTATGACATGGTCCGCATTATGTTAGGAA
* * *
40779780 TGTAACGGCCCATTTTTCAGTGAAATCAGAACAGTGGTTTTGGGACAACAAATTCGATCC-AAAA
1 TGTAACAGCCCATTTTT-AGTGAAATCAGAACAGTGGTTTTGGGACAACAAATCCGAGCCGAAAA
* * * * * *
40779844 ATAAAGTTTATTTTTATCTTATTATATGGTCCGTATTATGTTAG
65 AGAAA-TTTATTTTAATATTATGACATGGTCCGCATTATGTTAG
40779888 ATATGTCGTG
Statistics
Matches: 87, Mismatches: 19, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
110 22 0.25
111 65 0.75
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (110 bp):
TGTAACAGCCCATTTTTAGTGAAATCAGAACAGTGGTTTTGGGACAACAAATCCGAGCCGAAAAA
GAAATTTATTTTAATATTATGACATGGTCCGCATTATGTTAGGAA
Found at i:40780506 original size:20 final size:20
Alignment explanation
Indices: 40780472--40780516 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
40780462 AGGGATTAAA
*
40780472 ATGAAAAGTTGTGAAATTTG
1 ATGAAAAATTGTGAAATTTG
* * *
40780492 ATGAAAAATTTTGAATTTTT
1 ATGAAAAATTGTGAAATTTG
40780512 ATGAA
1 ATGAA
40780517 TACATGTCTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.40
Consensus pattern (20 bp):
ATGAAAAATTGTGAAATTTG
Found at i:40783261 original size:41 final size:41
Alignment explanation
Indices: 40783217--40783389 Score: 224
Period size: 41 Copynumber: 4.2 Consensus size: 41
40783207 ACCAAAAATG
* * * *
40783217 CCGCTAAAAACCAGAGCATTAGCGACGCTTTTGGTAAAACG
1 CCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGATAAAACA
*
40783258 CCGCTAAAAACTAGAGCATTAGCGGCGCTTTCGATAAAACA
1 CCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGATAAAACA
*
40783299 CCGCTAAAAACCAGAGCATTAGCGGCGCTTTC-ATTAATACA
1 CCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGA-TAAAACA
* * *
40783340 CTGCTAAAAATCAAAGCATTAGCGGCGCTTTC-ATTAAAACA
1 CCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGA-TAAAACA
*
40783381 CCGATAAAA
1 CCGCTAAAA
40783390 GTCAGGTAAT
Statistics
Matches: 118, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
40 1 0.01
41 117 0.99
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (41 bp):
CCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGATAAAACA
Found at i:40783468 original size:54 final size:54
Alignment explanation
Indices: 40783410--40783516 Score: 126
Period size: 54 Copynumber: 2.0 Consensus size: 54
40783400 CCCTAAAATC
* *
40783410 CTAAA-CCCTAAAAAATAATAAACACTAATCTATAACCCCTAAAACACTAAACCT
1 CTAAATCCC-AAAAAACAATAAACACTAAACTATAACCCCTAAAACACTAAACCT
* ** ** *
40783464 CTAAATCCCAAAAACCCTTAAACACTAAACTATAACCTTTAAAACCCTAAACC
1 CTAAATCCCAAAAAACAATAAACACTAAACTATAACCCCTAAAACACTAAACC
40783517 CCAAAAAAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
54 41 0.93
55 3 0.07
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.21
Consensus pattern (54 bp):
CTAAATCCCAAAAAACAATAAACACTAAACTATAACCCCTAAAACACTAAACCT
Found at i:40783755 original size:71 final size:71
Alignment explanation
Indices: 40783661--40783803 Score: 277
Period size: 71 Copynumber: 2.0 Consensus size: 71
40783651 TTGAAAGAGT
40783661 ATAGCTTAAAACTGAATGGGGTTTGAAAGGGAAGAAAAAGGTCTAAACCTTTGAAACATGAACTA
1 ATAGCTTAAAACTGAATGGGGTTTGAAAGGGAAGAAAAAGGTCTAAACCTTTGAAACATGAACTA
40783726 CAATTG
66 CAATTG
*
40783732 ATAGCTTAAAACTGAATTGGGTTTGAAAGGGAAGAAAAAGGTCTAAACCTTTGAAACATGAACTA
1 ATAGCTTAAAACTGAATGGGGTTTGAAAGGGAAGAAAAAGGTCTAAACCTTTGAAACATGAACTA
40783797 CAATTG
66 CAATTG
40783803 A
1 A
40783804 ACAACATTGG
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.24
Consensus pattern (71 bp):
ATAGCTTAAAACTGAATGGGGTTTGAAAGGGAAGAAAAAGGTCTAAACCTTTGAAACATGAACTA
CAATTG
Found at i:40796552 original size:49 final size:49
Alignment explanation
Indices: 40796480--40796611 Score: 142
Period size: 49 Copynumber: 2.7 Consensus size: 49
40796470 GCACATCATA
* * * * *
40796480 GTCGATGTCATGTTCCAGGCAGGTTTTACACTGAATTTCATATATTGAG-
1 GTCGATGTCATGTCCCAGACAGGTCTTACACTGAATCTCATATATCG-GT
* * * *
40796529 G-CTGATGTCGTGTCCCAGACAGGTCTTGCACTGACTCTCATCTATCGGT
1 GTC-GATGTCATGTCCCAGACAGGTCTTACACTGAATCTCATATATCGGT
*
40796578 GTCGATGCCATGTCCCAGACAGGTCTTACACTGA
1 GTCGATGTCATGTCCCAGACAGGTCTTACACTGA
40796612 CACACAACAA
Statistics
Matches: 68, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
48 2 0.03
49 65 0.96
50 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.31
Consensus pattern (49 bp):
GTCGATGTCATGTCCCAGACAGGTCTTACACTGAATCTCATATATCGGT
Found at i:40796738 original size:46 final size:45
Alignment explanation
Indices: 40796670--40796795 Score: 166
Period size: 46 Copynumber: 2.8 Consensus size: 45
40796660 TATATCTCGA
* *
40796670 GGCCGATGCATGTCTCAGACATGTCTTACACTAGCTCTCGTCTCAA-T
1 GGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTC--AT-AAGT
* *
40796717 -GCCGATGCATGTCCCAAACATGTCTTACACTGGCTCTCATAATGT
1 GGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATAA-GT
40796762 GGCCGATGCATGTCCCAGACATGTCTTACACTAG
1 GGCCGATGCATGTCCCAGACATGTCTTACACTAG
40796796 TACACATATC
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
43 2 0.03
44 1 0.01
45 1 0.01
46 66 0.94
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (45 bp):
GGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATAAGT
Found at i:40801973 original size:48 final size:49
Alignment explanation
Indices: 40801919--40802056 Score: 154
Period size: 48 Copynumber: 2.8 Consensus size: 49
40801909 ATCACTTAAC
* * * * *
40801919 GATGCCGAAGCCATATCCCTGATATGGTTTTATACGGGATCACATATTG
1 GATGCCGATGCCATGTCCCTGATATGGTCTTACACGGGATCACATATCG
* * * * *
40801968 G-TGCCGATGTCATGTCCCAGACATGGTCTTACACGGGATCTCATCTCG
1 GATGCCGATGCCATGTCCCTGATATGGTCTTACACGGGATCACATATCG
*
40802016 GATGCCGATGCCATGT-CCTAGATATGGTCTTACACAGGATC
1 GATGCCGATGCCATGTCCCT-GATATGGTCTTACACGGGATC
40802057 TCATTAACCA
Statistics
Matches: 73, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
48 40 0.55
49 33 0.45
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (49 bp):
GATGCCGATGCCATGTCCCTGATATGGTCTTACACGGGATCACATATCG
Found at i:40802031 original size:49 final size:49
Alignment explanation
Indices: 40801919--40802060 Score: 169
Period size: 49 Copynumber: 2.9 Consensus size: 49
40801909 ATCACTTAAC
* * * * * * *
40801919 GATGCCGAAGCCATATCCCTGATATGGTTTTATACGGGATCACATATTG
1 GATGCCGATGCCATGTCCCAGATATGGTCTTACACGGGATCTCATATCG
* * *
40801968 G-TGCCGATGTCATGTCCCAGACATGGTCTTACACGGGATCTCATCTCG
1 GATGCCGATGCCATGTCCCAGATATGGTCTTACACGGGATCTCATATCG
* *
40802016 GATGCCGATGCCATGTCCTAGATATGGTCTTACACAGGATCTCAT
1 GATGCCGATGCCATGTCCCAGATATGGTCTTACACGGGATCTCAT
40802061 TAACCATGGT
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
48 38 0.49
49 40 0.51
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (49 bp):
GATGCCGATGCCATGTCCCAGATATGGTCTTACACGGGATCTCATATCG
Found at i:40822683 original size:91 final size:92
Alignment explanation
Indices: 40822514--40822711 Score: 254
Period size: 91 Copynumber: 2.2 Consensus size: 92
40822504 TTGGATGCAA
* *
40822514 CCAACAATTGAATAGAACCAATTGCAACAGCCACCAATTGCCGAAAAATAAAAAATAATAGCAGC
1 CCAACAATTGAATAGAACCAATTGCAACAGCCACCAAATGCCGAAAAACAAAAAATAATAGCAGC
40822579 AAGGAACAATTGCAAAGACCTGAAGAG
66 AAGGAACAATTGCAAAGACCTGAAGAG
* * * ** * *
40822606 CCAGCGATTGAATAGAACCAATT-TAGTAGCCACCAAATGCCGAAAAACAAAAAATAATAGTAGT
1 CCAACAATTGAATAGAACCAATTGCAACAGCCACCAAATGCCGAAAAACAAAAAATAATAGCAGC
* * * * **
40822670 AGGGAGCAGTTGCAGAGATGTGAAGAG
66 AAGGAACAATTGCAAAGACCTGAAGAG
40822697 CCAACAATTGAATAG
1 CCAACAATTGAATAG
40822712 CAAAACAGTT
Statistics
Matches: 89, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
91 68 0.76
92 21 0.24
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.16
Consensus pattern (92 bp):
CCAACAATTGAATAGAACCAATTGCAACAGCCACCAAATGCCGAAAAACAAAAAATAATAGCAGC
AAGGAACAATTGCAAAGACCTGAAGAG
Found at i:40823177 original size:10 final size:10
Alignment explanation
Indices: 40823162--40823201 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
40823152 CAAAAATCAC
40823162 AAAATAATTT
1 AAAATAATTT
40823172 AAAATAATTTT
1 AAAATAA-TTT
*
40823183 CAAA-AATTT
1 AAAATAATTT
40823192 AAAATAATTT
1 AAAATAATTT
40823202 TTAAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 6 0.23
10 14 0.54
11 6 0.23
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (10 bp):
AAAATAATTT
Found at i:40823192 original size:20 final size:20
Alignment explanation
Indices: 40823167--40823207 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
40823157 ATCACAAAAT
40823167 AATTTAAAATAATTTTCAAA
1 AATTTAAAATAATTTTCAAA
*
40823187 AATTTAAAATAATTTTTAAA
1 AATTTAAAATAATTTTCAAA
40823207 A
1 A
40823208 TTTTGAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
AATTTAAAATAATTTTCAAA
Found at i:40830037 original size:14 final size:14
Alignment explanation
Indices: 40830018--40830045 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40830008 ATGTCACTAT
40830018 AACAAATTTAACAA
1 AACAAATTTAACAA
40830032 AACAAATTTAACAA
1 AACAAATTTAACAA
40830046 TATTAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.21
Consensus pattern (14 bp):
AACAAATTTAACAA
Found at i:40830378 original size:15 final size:14
Alignment explanation
Indices: 40830343--40830381 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
40830333 TTGGGAATAT
40830343 AAAATTTCAAATTAA
1 AAAATTT-AAATTAA
*
40830358 ATAATTTAAATTAA
1 AAAATTTAAATTAA
*
40830372 AAAAATTAAA
1 AAAATTTAAA
40830382 ATGAATGAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATTTAAATTAA
Found at i:40838264 original size:151 final size:150
Alignment explanation
Indices: 40837990--40838293 Score: 574
Period size: 151 Copynumber: 2.0 Consensus size: 150
40837980 ACATGTTTTG
40837990 TTAATGGAAGAATAAAATAAGGAGTATGGGTAATAAAGAAATGGAAACAAAAGAAAAAAAATGTG
1 TTAATGGAAGAATAAAATAAGGAGTATGGGTAATAAAGAAATGGAAACAAAAGAAAAAAAATGTG
*
40838055 TGGTTGCCCCCCCCATTGCCGTGAGCTAAAGAGAAGAAAGGAGAAAAATTTGTGTTCATCCTTTC
66 TGGTTGCCCCCCCCATTGCCGTGAGCTAAAGAGAAGAAAAGAGAAAAATTTGTGTTCATCCTTTC
40838120 TCACCTTCATTTTAGCCTAAA
131 TCACCTTCA-TTTAGCCTAAA
40838141 TTAATGGAAGAATAAAATAAGGAGTATGGGTAATAAAGAAATGGAAACAAAAGAAAAAAAATGTG
1 TTAATGGAAGAATAAAATAAGGAGTATGGGTAATAAAGAAATGGAAACAAAAGAAAAAAAATGTG
40838206 TGGTTG-CCCCCCCATTGCCGTGAGCTAAAGAGAAGAAAAGAGAAAAAATTTGTGTTCATCCTTT
66 TGGTTGCCCCCCCCATTGCCGTGAGCTAAAGAGAAGAAAAGAG-AAAAATTTGTGTTCATCCTTT
40838270 CTCACCTTCATTTAGCCTAAA
130 CTCACCTTCATTTAGCCTAAA
40838291 TTA
1 TTA
40838294 GAAAGAAAAA
Statistics
Matches: 151, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
150 49 0.32
151 102 0.68
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (150 bp):
TTAATGGAAGAATAAAATAAGGAGTATGGGTAATAAAGAAATGGAAACAAAAGAAAAAAAATGTG
TGGTTGCCCCCCCCATTGCCGTGAGCTAAAGAGAAGAAAAGAGAAAAATTTGTGTTCATCCTTTC
TCACCTTCATTTAGCCTAAA
Found at i:40839388 original size:40 final size:40
Alignment explanation
Indices: 40839358--40839527 Score: 216
Period size: 40 Copynumber: 4.3 Consensus size: 40
40839348 GGACTAAGAT
* *
40839358 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* *
40839398 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* ** *
40839438 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTACGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* * * * *
40839478 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
40839517 CCGAAGGCATT
1 CCGAAGGCATT
40839528 TGAACGAGGA
Statistics
Matches: 118, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 33 0.28
40 85 0.72
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:40839442 original size:80 final size:79
Alignment explanation
Indices: 40839305--40839529 Score: 236
Period size: 80 Copynumber: 2.8 Consensus size: 79
40839295 TTGAATGCGG
* * * ** * * * * *
40839305 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGCGAATATATCCGGACTAAGAT-CCGAAGGCCTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAAACCGGGCTAAG-TCCCGAAGGCATT
40839369 TGTGCGAGATACTAAA
64 TGTGCGAGATACTAAA
* * * *
40839385 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTT
* **
40839450 GTGCGAGTTGTTAAA
65 GTGCGAGATACTAAA
* * *
40839465 TCCGGGTTACGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
40839530 AACGAGGAGC
Statistics
Matches: 122, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
79 36 0.30
80 82 0.67
81 4 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATACTAAA
Found at i:40839547 original size:79 final size:80
Alignment explanation
Indices: 40839380--40839562 Score: 226
Period size: 79 Copynumber: 2.3 Consensus size: 80
40839370 GTGCGAGATA
* * *
40839380 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
40839445 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
40839460 TTAAATCCGGGTTACGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
40839524 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
40839539 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
40839563 TACGTGATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:40847324 original size:40 final size:40
Alignment explanation
Indices: 40847293--40847542 Score: 292
Period size: 40 Copynumber: 6.3 Consensus size: 40
40847283 GGACTAAGAT
* *
40847293 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATATCAAA-TCCGGGTTAAGTC
* *
40847333 CCGAAGGCCTTTGTGCGAGATA-CTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATATC-AAATCCGGGTTAAGTC
* *
40847373 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATATCAAATCCGGGTTAAGTC
* *
40847413 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATATCAAATCCGGGTTAAGTC
* * * *
40847453 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATATCAAATCCGGGTTAAGTC
* * * * *
40847493 CCGAAGGCATT-GTGTGAGTTA-CTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATATC-AAATCCGGGTTAAGTC
40847532 CCGAAGGCATT
1 CCGAAGGCATT
40847543 TGAACGAGGA
Statistics
Matches: 194, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
39 33 0.17
40 158 0.81
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGATATCAAATCCGGGTTAAGTC
Found at i:40847377 original size:80 final size:79
Alignment explanation
Indices: 40847240--40847542 Score: 342
Period size: 80 Copynumber: 3.8 Consensus size: 79
40847230 TTGAATGCTG
* * * * * **
40847240 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
* * *
40847303 TTGTGCGAGATACAAA
64 TCGTGCGAGTTATAAA
* *
40847319 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 -TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
40847384 CGTGCGAGTTATTAAA
65 CGTGCGAGTTA-TAAA
* * *
40847400 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTC
*
40847465 GTGCGAGTTGTTAAA
66 GTGCGAGTT-ATAAA
* * * * * *
40847480 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
40847543 TGAACGAGGA
Statistics
Matches: 192, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
79 36 0.19
80 145 0.76
81 11 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTC
GTGCGAGTTATAAA
Found at i:40847456 original size:120 final size:119
Alignment explanation
Indices: 40847240--40847542 Score: 358
Period size: 120 Copynumber: 2.5 Consensus size: 119
40847230 TTGAATGCTG
* * * * * *
40847240 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTAATAAATCCGGGCTAAG-TCCCGAAGGCATT
* * *
40847304 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
64 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTCGTGCGAGATACTAAA
* *
40847360 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATTC
* * * * **
40847425 GTGCGAGTTATTAAA-TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
65 GTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTCGTGCGAGATACTAAA
* * * * *
40847480 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATT
40847543 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
119 35 0.22
120 115 0.73
121 7 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATTCG
TGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTCGTGCGAGATACTAAA
Found at i:40858931 original size:22 final size:20
Alignment explanation
Indices: 40858881--40858919 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40858871 AAGCAATTGC
*
40858881 TTTATTTAAACTATTATTAT
1 TTTATTTAAACTATAATTAT
40858901 TTTATTTAAA-TATAATTAT
1 TTTATTTAAACTATAATTAT
40858920 AAATTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATTTAAACTATAATTAT
Found at i:40864816 original size:15 final size:17
Alignment explanation
Indices: 40864780--40864813 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40864770 TTAGATAAAA
*
40864780 TTAAAATATATATATTT
1 TTAAAAAATATATATTT
40864797 TTAAAAAATAT-TATTT
1 TTAAAAAATATATATTT
40864813 T
1 T
40864814 AAATAGTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAAAAATATATATTT
Found at i:40878072 original size:45 final size:45
Alignment explanation
Indices: 40878003--40878097 Score: 163
Period size: 45 Copynumber: 2.1 Consensus size: 45
40877993 TACTATGTGA
* *
40878003 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
*
40878048 ACCGGACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
40878093 ACCGA
1 ACCGA
40878098 GTATATGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
Found at i:40878167 original size:23 final size:22
Alignment explanation
Indices: 40878141--40878184 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
40878131 AATTAACTAA
40878141 GTGT-AATTGAATAATGAATATAG
1 GTGTGAATTGAAT--TGAATATAG
40878164 GTGTGGAATTGAATTGAATAT
1 GTGT-GAATTGAATTGAATAT
40878185 CGACTTAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.25, T:0.36
Consensus pattern (22 bp):
GTGTGAATTGAATTGAATATAG
Found at i:40880464 original size:24 final size:25
Alignment explanation
Indices: 40880428--40880562 Score: 127
Period size: 24 Copynumber: 5.6 Consensus size: 25
40880418 ATCTGGGATT
* *
40880428 TATAATAGAAAGCTCATAAGAGCCA
1 TATAATGGGAAGCTCATAAGAGCCA
**
40880453 TA-AATGGGAAGCTCATGCGAGCCA
1 TATAATGGGAAGCTCATAAGAGCCA
*
40880477 -ATAATGGGTAGCTCATAAGAGCCA
1 TATAATGGGAAGCTCATAAGAGCCA
**
40880501 TA-AATGGGAAGCTCATGCGAGCCA
1 TATAATGGGAAGCTCATAAGAGCCA
* **
40880525 -ATAATGGGTAGCTCCGAAGAGCCA
1 TATAATGGGAAGCTCATAAGAGCCA
*
40880549 T-TAATCGAGAAGCT
1 TATAAT-GGGAAGCT
40880563 TTGGATACCA
Statistics
Matches: 88, Mismatches: 17, Indels: 10
0.77 0.15 0.09
Matches are distributed among these distances:
23 2 0.02
24 77 0.88
25 9 0.10
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (25 bp):
TATAATGGGAAGCTCATAAGAGCCA
Found at i:40880490 original size:48 final size:48
Alignment explanation
Indices: 40880438--40880549 Score: 206
Period size: 48 Copynumber: 2.3 Consensus size: 48
40880428 TATAATAGAA
40880438 AGCTCATAAGAGCCATAAATGGGAAGCTCATGCGAGCCAATAATGGGT
1 AGCTCATAAGAGCCATAAATGGGAAGCTCATGCGAGCCAATAATGGGT
40880486 AGCTCATAAGAGCCATAAATGGGAAGCTCATGCGAGCCAATAATGGGT
1 AGCTCATAAGAGCCATAAATGGGAAGCTCATGCGAGCCAATAATGGGT
**
40880534 AGCTCCGAAGAGCCAT
1 AGCTCATAAGAGCCAT
40880550 TAATCGAGAA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 62 1.00
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.18
Consensus pattern (48 bp):
AGCTCATAAGAGCCATAAATGGGAAGCTCATGCGAGCCAATAATGGGT
Found at i:40881698 original size:13 final size:13
Alignment explanation
Indices: 40881680--40881707 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
40881670 CTTTATTTGA
40881680 TTATTTATCATCT
1 TTATTTATCATCT
40881693 TTATTTATCATCT
1 TTATTTATCATCT
40881706 TT
1 TT
40881708 CCAATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTTATCATCT
Found at i:40887981 original size:124 final size:124
Alignment explanation
Indices: 40887759--40888001 Score: 407
Period size: 124 Copynumber: 2.0 Consensus size: 124
40887749 TCCATACCTG
* *
40887759 TCCTAAGCCTCAAAACATTACAAGCCGAAAAGTCCTATGTGACCTAAACATCCTTATGCATGAAT
1 TCCTAAGCCTCAAAACATTACAAACCGAAAAGTCCTATGTGACCTAAACATCCTTACGCATGAAT
*
40887824 AGACATCATACTAAACATACGCATAAATTACTATTTGTATTCTAATCAGAGAATTAAAT
66 AGACATCATACTAAACATACGCATAAATGACTATTTGTATTCTAATCAGAGAATTAAAT
* *
40887883 TCCTAAGCCTTAGAACATTACAAACCGAAAAGTCCTATGTGACCTAAACATCCTTACGCATGAA-
1 TCCTAAGCCTCAAAACATTACAAACCGAAAAGTCCTATGTGACCTAAACATCCTTACGCATGAAT
**
40887947 AGGACATCATACTAAACATACGCATAAATGACTATTTGTATTCTGCTCAGAGAAT
66 A-GACATCATACTAAACATACGCATAAATGACTATTTGTATTCTAATCAGAGAAT
40888002 CAAAGTACTT
Statistics
Matches: 111, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
123 1 0.01
124 110 0.99
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (124 bp):
TCCTAAGCCTCAAAACATTACAAACCGAAAAGTCCTATGTGACCTAAACATCCTTACGCATGAAT
AGACATCATACTAAACATACGCATAAATGACTATTTGTATTCTAATCAGAGAATTAAAT
Found at i:40904373 original size:15 final size:16
Alignment explanation
Indices: 40904353--40904382 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40904343 TGGCGCCTTA
40904353 TTGATA-TGTGTTAAT
1 TTGATATTGTGTTAAT
40904368 TTGATATTGTGTTAA
1 TTGATATTGTGTTAA
40904383 AGCATGGTTG
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:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (16 bp):
TTGATATTGTGTTAAT
Found at i:40907063 original size:13 final size:13
Alignment explanation
Indices: 40907045--40907070 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40907035 CATGTGTGAC
40907045 ACACGACCATGTG
1 ACACGACCATGTG
40907058 ACACGACCATGTG
1 ACACGACCATGTG
40907071 TCCCCTGTAG
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:0.31, C:0.31, G:0.23, T:0.15
Consensus pattern (13 bp):
ACACGACCATGTG
Found at i:40917180 original size:43 final size:43
Alignment explanation
Indices: 40917127--40917215 Score: 133
Period size: 43 Copynumber: 2.1 Consensus size: 43
40917117 AAGATGACTA
* ** *
40917127 AGAGATCTTTTAATCCTAAAGGAACGAGAGCCAAAAAACCCCT
1 AGAGACCTTTTAATCAAAAAGGAACAAGAGCCAAAAAACCCCT
*
40917170 AGAGACCTTTTAATCAAAAAGGAACAAGAGCCGAAAAACCCCT
1 AGAGACCTTTTAATCAAAAAGGAACAAGAGCCAAAAAACCCCT
40917213 AGA
1 AGA
40917216 ACTTGTGTAC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.45, C:0.22, G:0.17, T:0.16
Consensus pattern (43 bp):
AGAGACCTTTTAATCAAAAAGGAACAAGAGCCAAAAAACCCCT
Found at i:40922755 original size:25 final size:25
Alignment explanation
Indices: 40922725--40922791 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
40922715 TTCAACTTAC
*
40922725 AGCTCGTGTGAGCATACCGATTTAT
1 AGCTCGTGTGAGCATACCGATTCAT
**
40922750 AGCTCGTGTGAGCATATTGATTCAT
1 AGCTCGTGTGAGCATACCGATTCAT
*
40922775 AGCTCGTATGAGCATAC
1 AGCTCGTGTGAGCATAC
40922792 ATGTACATGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (25 bp):
AGCTCGTGTGAGCATACCGATTCAT
Found at i:40929129 original size:46 final size:46
Alignment explanation
Indices: 40929076--40929167 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
40929066 TCCAGCTTCT
40929076 ATTTCTTGAATCTAACTTGACATTCTAGCTCCCCATTATCTCCTTA
1 ATTTCTTGAATCTAACTTGACATTCTAGCTCCCCATTATCTCCTTA
40929122 ATTTCTTGAATCTAACTTGACATTCTAGCTCCCCATTATCTCCTTA
1 ATTTCTTGAATCTAACTTGACATTCTAGCTCCCCATTATCTCCTTA
40929168 TTATTTTTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.24, C:0.28, G:0.07, T:0.41
Consensus pattern (46 bp):
ATTTCTTGAATCTAACTTGACATTCTAGCTCCCCATTATCTCCTTA
Found at i:40930071 original size:27 final size:26
Alignment explanation
Indices: 40930013--40930088 Score: 75
Period size: 27 Copynumber: 2.9 Consensus size: 26
40930003 ATGAATTTTC
* *
40930013 TCAAAATTTTACTAGGGTTAAAATTG
1 TCAAAATTTTACTAGGGGTAAAATCG
*
40930039 TTAAAATTTTA-TCAGGGAGTAAAATCG
1 TCAAAATTTTACT-AGGG-GTAAAATCG
* *
40930066 TCAAAATTTAACTA-GAGTAAAAT
1 TCAAAATTTTACTAGGGGTAAAAT
40930089 TAGGATGAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
25 8 0.20
26 15 0.37
27 17 0.41
28 1 0.02
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.34
Consensus pattern (26 bp):
TCAAAATTTTACTAGGGGTAAAATCG
Found at i:40936233 original size:29 final size:28
Alignment explanation
Indices: 40936142--40936234 Score: 66
Period size: 29 Copynumber: 3.2 Consensus size: 28
40936132 GCTAAAGGGT
* *
40936142 AGCCTTTGTGACAAAACTCTGGAAAGGTA
1 AGCCTTTGTGGCAAAACT-TTGAAAGGTA
* * *
40936171 AGCCCTTGTGGCGAACCTACTT--AAGG-A
1 AGCCTTTGTGGCAAAACT--TTGAAAGGTA
*
40936198 CAACCTTTGTGGCAAAACTTTAGAAAGGTA
1 -AGCCTTTGTGGCAAAACTTT-GAAAGGTA
40936228 AGCCTTT
1 AGCCTTT
40936235 TTGGTGAATG
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
26 2 0.04
27 1 0.02
28 18 0.38
29 24 0.50
30 3 0.06
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (28 bp):
AGCCTTTGTGGCAAAACTTTGAAAGGTA
Found at i:40938070 original size:57 final size:56
Alignment explanation
Indices: 40937996--40938165 Score: 180
Period size: 57 Copynumber: 3.0 Consensus size: 56
40937986 TCTGTTTACA
* * *
40937996 GTGAACTTGTGAAAGGATAGCCTTTGTGGCAAAACTCTAGAAAGGCAAGCCTTTGTG
1 GTGAACCTGTTAAAGGATAGCCTTTGTGGCAAAACTCT-GAAAGGAAAGCCTTTGTG
* * * * *
40938053 GTGAACCTGTTAAAGGATAACCTTTGTGGAAAAACTCTGGAAGAGTAAGCCTTTATG
1 GTGAACCTGTTAAAGGATAGCCTTTGTGGCAAAACTCTGAAAG-GAAAGCCTTTGTG
* * * * * * *
40938110 GTGAACCTCTTAAAGGA-CGTCTTTATGGCGAGACTCTGAAAGGAAAGCATTTGTG
1 GTGAACCTGTTAAAGGATAGCCTTTGTGGCAAAACTCTGAAAGGAAAGCCTTTGTG
40938165 G
1 G
40938166 CAAGTACTTA
Statistics
Matches: 93, Mismatches: 19, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
55 11 0.12
56 21 0.23
57 61 0.66
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (56 bp):
GTGAACCTGTTAAAGGATAGCCTTTGTGGCAAAACTCTGAAAGGAAAGCCTTTGTG
Found at i:40945035 original size:47 final size:47
Alignment explanation
Indices: 40944970--40945180 Score: 244
Period size: 47 Copynumber: 4.4 Consensus size: 47
40944960 CAGCCAAGAG
*
40944970 AGTGTATATATGTGATAAGGCCTAATGACCGATGTGATGAATGTGGA
1 AGTGTATATATGTGATAAGGCCTAATGACCGATGTGATGAATGTGAA
* * *
40945017 AGTGTATGTATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGACCGATGTGATGAATGTGAA
40945064 AGTGTATGTATATGTGTGATAAGGCCTAAT-AGCCGATGTGATGAATGTGAA
1 AGTGTA--TATA--TGTGATAAGGCCTAATGA-CCGATGTGATGAATGTGAA
* * * * * * * *
40945115 AGTGTATATATGTGACAAGGCCGAGTGGCCAACGTAATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGACCGATGTGATGAATGTGAA
* *
40945162 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
40945181 TCCCGAAAGG
Statistics
Matches: 140, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
47 93 0.66
49 7 0.05
51 40 0.29
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGACCGATGTGATGAATGTGAA
Found at i:40945099 original size:51 final size:50
Alignment explanation
Indices: 40944972--40945128 Score: 218
Period size: 51 Copynumber: 3.2 Consensus size: 50
40944962 GCCAAGAGAG
* *
40944972 TGTATATATGTGATAAGGCCTAATGACCGATGTGATGAATGTGGAAGTGTA
1 TGTATATGTGTGATAAGGCCTAATG-CCGATGTGATGAATGTGAAAGTGTA
*
40945023 TG--TA--TGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TGTATATGTGTGATAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGTA
40945070 TGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTA
1 TGTATATGTGTGATAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGTA
40945121 --TATATGTG
1 TGTATATGTG
40945129 ACAAGGCCGA
Statistics
Matches: 97, Mismatches: 4, Indels: 12
0.86 0.04 0.11
Matches are distributed among these distances:
47 41 0.42
48 1 0.01
49 12 0.12
51 43 0.44
ACGTcount: A:0.31, C:0.08, G:0.29, T:0.32
Consensus pattern (50 bp):
TGTATATGTGTGATAAGGCCTAATGCCGATGTGATGAATGTGAAAGTGTA
Found at i:40945144 original size:98 final size:98
Alignment explanation
Indices: 40944972--40945165 Score: 273
Period size: 98 Copynumber: 2.0 Consensus size: 98
40944962 GCCAAGAGAG
* * *
40944972 TGTATATATGTGATAAGGCCTAATGACCGATGTGATGAATGTGGAAGTGTATGTATGTAATAAGG
1 TGTATATATGTGATAAGGCCTAATGACCGATGTGATGAATGTGAAAGTGTATATATGTAACAAGG
* * * *
40945037 CCTAATGGCCGATGTGATGAATGTGAAAGTGTA
66 CCGAATGGCCAACGTAATGAATGTGAAAGTGTA
* *
40945070 TGTATATGTGTGATAAGGCCTAAT-AGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAG
1 TGTATATATGTGATAAGGCCTAATGA-CCGATGTGATGAATGTGAAAGTGTATATATGTAACAAG
* *
40945134 GCCGAGTGGCCAACGTAATGGATGTGAAAGTG
65 GCCGAATGGCCAACGTAATGAATGTGAAAGTG
40945166 CATAAATGTG
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
97 1 0.01
98 83 0.99
ACGTcount: A:0.31, C:0.09, G:0.30, T:0.29
Consensus pattern (98 bp):
TGTATATATGTGATAAGGCCTAATGACCGATGTGATGAATGTGAAAGTGTATATATGTAACAAGG
CCGAATGGCCAACGTAATGAATGTGAAAGTGTA
Found at i:40945354 original size:36 final size:37
Alignment explanation
Indices: 40945299--40945376 Score: 113
Period size: 36 Copynumber: 2.1 Consensus size: 37
40945289 CCGAGCTCTA
* * *
40945299 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGG-
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
40945335 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
40945372 AAGAC
1 AAGAC
40945377 TTTGTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 32 0.86
37 5 0.14
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.24
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:40947384 original size:20 final size:20
Alignment explanation
Indices: 40947355--40947394 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40947345 TAAAGGTCTT
* *
40947355 TAATGTATATGATGTGATGC
1 TAATGCATATGATGCGATGC
40947375 TAATGCATATGATGCGATGC
1 TAATGCATATGATGCGATGC
40947395 ACGAGGTGAA
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:0.30, C:0.10, G:0.25, T:0.35
Consensus pattern (20 bp):
TAATGCATATGATGCGATGC
Found at i:40950551 original size:40 final size:39
Alignment explanation
Indices: 40950487--40950858 Score: 431
Period size: 40 Copynumber: 9.3 Consensus size: 39
40950477 TCTTCGGAAT
* *
40950487 TTAG-CCGGATATAACCACAAGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATAT-ATCACTAGCACAAATGCCTTCGGGTC
*
40950526 TTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATATC-ACTAGCACAAATGCCTTCGGGTC
* *
40950566 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGAT-ATATCACTAGCACAAATGCCTTCGGGTC
* * * *
40950606 TTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATATC-ACTAGCACAAATGCCTTCGGGTC
* *
40950646 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGAT-ATATCACTAGCACAAATGCCTTCGGGTC
* * * *
40950686 TTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATATC-ACTAGCACAAATGCCTTCGGGTC
* *
40950726 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGAT-ATATCACTAGCACAAATGCCTTCGGGTC
* * * *
40950766 TTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATATC-ACTAGCACAAATGCCTTCGGGTC
* * *
40950806 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGAC
1 TTAGCCCGGAT-ATATCACTAGCACAAATGCCTTCGGGTC
*
40950846 TTAGCCTGGATAT
1 TTAGCCCGGATAT
40950859 CATTCAAATG
Statistics
Matches: 279, Mismatches: 45, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
39 16 0.06
40 250 0.90
41 13 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (39 bp):
TTAGCCCGGATATATCACTAGCACAAATGCCTTCGGGTC
Found at i:40950614 original size:80 final size:80
Alignment explanation
Indices: 40950487--40950848 Score: 645
Period size: 80 Copynumber: 4.5 Consensus size: 80
40950477 TCTTCGGAAT
* * * * * * *
40950487 TTAG-CCGGATATAACCACAAGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
40950551 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
40950566 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
40950631 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
40950646 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
40950711 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
40950726 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
40950791 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
*
40950806 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTA
1 TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTA
40950849 GCCTGGATAT
Statistics
Matches: 274, Mismatches: 8, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
79 4 0.01
80 270 0.99
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
TTAGCCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
AAATGCCTTCGGGTC
Found at i:40953896 original size:62 final size:63
Alignment explanation
Indices: 40953798--40953920 Score: 212
Period size: 62 Copynumber: 2.0 Consensus size: 63
40953788 CACCAAAACT
* * *
40953798 GACGTTTCAAGTCGTTGTACATTTTCGTGCTCCCCGGGTGAATTGACATTCGGCTACAATGTC
1 GACGTTTCAAATCATTGTACATTTTCGTACTCCCCGGGTGAATTGACATTCGGCTACAATGTC
40953861 GACGTTT-AAATCATTGTACATTTTCGTACTCCCCGGGTGAATTGACATTCGGCTACAATG
1 GACGTTTCAAATCATTGTACATTTTCGTACTCCCCGGGTGAATTGACATTCGGCTACAATG
40953921 GGCTTCGTTC
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
62 50 0.88
63 7 0.12
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (63 bp):
GACGTTTCAAATCATTGTACATTTTCGTACTCCCCGGGTGAATTGACATTCGGCTACAATGTC
Found at i:40955172 original size:145 final size:145
Alignment explanation
Indices: 40954909--40955196 Score: 567
Period size: 145 Copynumber: 2.0 Consensus size: 145
40954899 CAACACTTGC
40954909 CTCAGATGCTCAGCATGTTCGGTCTCATCTCTTGAATAGACCAAGATGTCATCAATGAACACAAC
1 CTCAGATGCTCAGCATGTTCGGTCTCATCTCTTGAATAGACCAAGATGTCATCAATGAACACAAC
40954974 TACGAACCGATCCAAATATGGTCTGAAGATCCGATTCATCAAATCCATAAACACCGCAGGGGCAT
66 TACGAACCGATCCAAATATGGTCTGAAGATCCGATTCATCAAATCCATAAACACCGCAGGGGCAT
40955039 TAGTGAGCCCAAAAT
131 TAGTGAGCCCAAAAT
*
40955054 CTCAGGTGCTCAGCATGTTCGGTCTCATCTCTTGAATAGACCAAGATGTCATCAATGAACACAAC
1 CTCAGATGCTCAGCATGTTCGGTCTCATCTCTTGAATAGACCAAGATGTCATCAATGAACACAAC
40955119 TACGAACCGATCCAAATATGGTCTGAAGATCCGATTCATCAAATCCATAAACACCGCAGGGGCAT
66 TACGAACCGATCCAAATATGGTCTGAAGATCCGATTCATCAAATCCATAAACACCGCAGGGGCAT
40955184 TAGTGAGCCCAAA
131 TAGTGAGCCCAAA
40955197 CGGCATCACT
Statistics
Matches: 142, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
145 142 1.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (145 bp):
CTCAGATGCTCAGCATGTTCGGTCTCATCTCTTGAATAGACCAAGATGTCATCAATGAACACAAC
TACGAACCGATCCAAATATGGTCTGAAGATCCGATTCATCAAATCCATAAACACCGCAGGGGCAT
TAGTGAGCCCAAAAT
Found at i:40958262 original size:47 final size:47
Alignment explanation
Indices: 40958208--40958410 Score: 261
Period size: 47 Copynumber: 4.3 Consensus size: 47
40958198 AGCTTAAGAT
*
40958208 CGAATGGCCAATGTGATGAATGTGAAAGTGTGTATTTGTGATAAGGC
1 CGAATGGCCAATGTGATGAATGTGAAAGTGTGTATATGTGATAAGGC
40958255 CGAATGGCCAATGTGATGAATGTGAAAGTGTGTATATGTGATAAGGC
1 CGAATGGCCAATGTGATGAATGTGAAAGTGTGTATATGTGATAAGGC
* * ** *
40958302 TGAATGGCCAATGTGATGAATGTGATAGTGCATACATGTGATAAGGC
1 CGAATGGCCAATGTGATGAATGTGAAAGTGTGTATATGTGATAAGGC
* * *
40958349 CGAATGTG-AAATGTGAT-ATATGTGTAA--GTGAATATGTGATAAGGC
1 CGAATG-GCCAATGTGATGA-ATGTGAAAGTGTGTATATGTGATAAGGC
*
40958394 CGAATGACCAATTGTGA
1 CGAATGGCCAA-TGTGA
40958411 AAAGTGTGCA
Statistics
Matches: 136, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
45 22 0.16
46 6 0.04
47 107 0.79
48 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
CGAATGGCCAATGTGATGAATGTGAAAGTGTGTATATGTGATAAGGC
Found at i:40958305 original size:25 final size:25
Alignment explanation
Indices: 40958230--40958305 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
40958220 GTGATGAATG
*
40958230 TGAAAGTGTGTATTTGTGATAAGGC
1 TGAAAGTGTGTATATGTGATAAGGC
* * *
40958255 CG-AA-TG-GCCA-ATGTGATGAATG-
1 TGAAAGTGTG-TATATGTGAT-AAGGC
40958277 TGAAAGTGTGTATATGTGATAAGGC
1 TGAAAGTGTGTATATGTGATAAGGC
40958302 TGAA
1 TGAA
40958306 TGGCCAATGT
Statistics
Matches: 37, Mismatches: 7, Indels: 14
0.64 0.12 0.24
Matches are distributed among these distances:
22 8 0.22
23 8 0.22
24 8 0.22
25 13 0.35
ACGTcount: A:0.32, C:0.07, G:0.32, T:0.30
Consensus pattern (25 bp):
TGAAAGTGTGTATATGTGATAAGGC
Found at i:40958318 original size:22 final size:22
Alignment explanation
Indices: 40958244--40958318 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
40958234 AGTGTGTATT
*
40958244 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCTGAATGGCCAA
* *
40958266 TGTGATGAATG-TGAAAGTGTG-TATA
1 TGTGAT-AAGGCTG-AA-TG-GCCA-A
40958291 TGTGATAAGGCTGAATGGCCAA
1 TGTGATAAGGCTGAATGGCCAA
40958313 TGTGAT
1 TGTGAT
40958319 GAATGTGATA
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
22 15 0.37
23 8 0.20
24 8 0.20
25 10 0.24
ACGTcount: A:0.31, C:0.09, G:0.32, T:0.28
Consensus pattern (22 bp):
TGTGATAAGGCTGAATGGCCAA
Found at i:40958365 original size:22 final size:23
Alignment explanation
Indices: 40958337--40958399 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
40958327 TAGTGCATAC
40958337 ATGTGATAAGGCCGAATGTGAA-
1 ATGTGATAAGGCCGAATGTGAAT
* *
40958359 ATGTGATATATG-TGTAA-GTGAAT
1 ATGTGATA-AGGCCG-AATGTGAAT
40958382 ATGTGATAAGGCCGAATG
1 ATGTGATAAGGCCGAATG
40958400 ACCAATTGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
22 18 0.56
23 14 0.44
ACGTcount: A:0.35, C:0.06, G:0.30, T:0.29
Consensus pattern (23 bp):
ATGTGATAAGGCCGAATGTGAAT
Found at i:40958372 original size:31 final size:30
Alignment explanation
Indices: 40958319--40958376 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
40958309 CCAATGTGAT
*
40958319 GAATGTGATAGTGCATACATGTGATAAGGCC
1 GAATGTGAAAGTGCATACATGTG-TAAGGCC
*
40958350 GAATGTGAAATGTG-ATATATGTGTAAG
1 GAATGTGAAA-GTGCATACATGTGTAAG
40958377 TGAATATGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 4 0.17
31 17 0.71
32 3 0.12
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.29
Consensus pattern (30 bp):
GAATGTGAAAGTGCATACATGTGTAAGGCC
Found at i:40958385 original size:14 final size:16
Alignment explanation
Indices: 40958352--40958391 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
40958342 ATAAGGCCGA
40958352 ATGTGA-AATGTGATAT
1 ATGTGATAA-GTGATAT
40958368 ATGTG-TAAGTGA-AT
1 ATGTGATAAGTGATAT
40958382 ATGTGATAAG
1 ATGTGATAAG
40958392 GCCGAATGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 7 0.32
15 8 0.36
16 7 0.32
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.35
Consensus pattern (16 bp):
ATGTGATAAGTGATAT
Done.