Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020198.1 Corchorus olitorius cultivar O-4 contig20231, whole genome shotgun sequence
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: 48486
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:122 original size:51 final size:51
Alignment explanation
Indices: 31--268 Score: 218
Period size: 51 Copynumber: 5.0 Consensus size: 51
21 TGGGAACAGG
31 TAGACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGTAGACAACTC
1 TAGACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGTAGACAACTC
* * * *
82 TAGAAAACACCTTCCGATGAGGAAGGGCAATCTGGTAAAAGTTGACAACTC
1 TAGACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGTAGACAACTC
* * * * * * *
133 TGGACAACACCTTCCGATGGGGAAGGGCAAATTGGG-TAA--AGCCGA-TT
1 TAGACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGTAGACAACTC
* * * *
180 TAAACAACACCTTCCGGTGAGGAAGTGCAAA-T-TG----GT--A-AA--C
1 TAGACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGTAGACAACTC
* *
220 TAAACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAAAAGTAGACAAC
1 TAGACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGTAGACAAC
269 AACTTCCGAT
Statistics
Matches: 149, Mismatches: 26, Indels: 25
0.75 0.13 0.12
Matches are distributed among these distances:
40 30 0.20
41 2 0.01
42 1 0.01
45 1 0.01
46 3 0.02
47 27 0.18
48 4 0.03
49 2 0.01
50 2 0.01
51 77 0.52
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.17
Consensus pattern (51 bp):
TAGACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAAAGTAGACAACTC
Found at i:204 original size:47 final size:42
Alignment explanation
Indices: 136--331 Score: 179
Period size: 40 Copynumber: 4.7 Consensus size: 42
126 ACAACTCTGG
* *
136 ACAACACCTTCCGATGGGGAAGGGCAAATTGGGTAAAGCCGATTTAA
1 ACAACACCTTCCGGTGAGGAAGGGCAAATTGGGTAAAG-C----TAA
*
183 ACAACACCTTCCGGTGAGGAAGTGCAAATT-GGTAAA-CTAA
1 ACAACACCTTCCGGTGAGGAAGGGCAAATTGGGTAAAGCTAA
* * *
223 ACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAAAAG-TAG
1 ACAACACCTTCCGGTGAGGAAGGGCAAATTGGGTAAAGCTAA
* * * * **
264 ACAACAACTTCCGATG-GAGAAGGGCAAACTAGG--AAGCTCG
1 ACAACACCTTCCGGTGAG-GAAGGGCAAATTGGGTAAAGCTAA
*
304 ACAACACCTTCCGGTGAGGATGGGCAAA
1 ACAACACCTTCCGGTGAGGAAGGGCAAA
332 ACAGGAAGAG
Statistics
Matches: 130, Mismatches: 14, Indels: 17
0.81 0.09 0.11
Matches are distributed among these distances:
39 3 0.02
40 57 0.44
41 36 0.28
44 1 0.01
46 6 0.05
47 27 0.21
ACGTcount: A:0.36, C:0.21, G:0.28, T:0.16
Consensus pattern (42 bp):
ACAACACCTTCCGGTGAGGAAGGGCAAATTGGGTAAAGCTAA
Found at i:338 original size:40 final size:41
Alignment explanation
Indices: 183--349 Score: 168
Period size: 40 Copynumber: 4.1 Consensus size: 41
173 GCCGATTTAA
* * *
183 ACAACACCTTCCGGTGAGGAAGTGCAAA-TTGGTAAA-CTAA
1 ACAACACCTTCCGGTGAGGAAGGGCAAACTAGG-AAAGCTAG
*
223 ACAACACCTTCCGGTGAGGAAGGGCAAACTGGGAAAAG-TAG
1 ACAACACCTTCCGGTGAGGAAGGGCAAACTAGG-AAAGCTAG
* * *
264 ACAACAACTTCCGATG-GAGAAGGGCAAACTAGG-AAGCTCG
1 ACAACACCTTCCGGTGAG-GAAGGGCAAACTAGGAAAGCTAG
*
304 ACAACACCTTCCGGTGAGGATGGGCAAAAC-AGGAAGAG-TAG
1 ACAACACCTTCCGGTGAGGAAGGGC-AAACTAGGAA-AGCTAG
345 ACAAC
1 ACAAC
350 TTTGGGCAAC
Statistics
Matches: 107, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
39 3 0.03
40 53 0.50
41 49 0.46
42 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.28, T:0.14
Consensus pattern (41 bp):
ACAACACCTTCCGGTGAGGAAGGGCAAACTAGGAAAGCTAG
Found at i:8017 original size:13 final size:13
Alignment explanation
Indices: 7999--8025 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
7989 CTCTATAACC
7999 TCATAAATCATAT
1 TCATAAATCATAT
8012 TCATAAATCATAT
1 TCATAAATCATAT
8025 T
1 T
8026 TATTATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (13 bp):
TCATAAATCATAT
Found at i:18285 original size:18 final size:18
Alignment explanation
Indices: 18262--18298 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
18252 TATATTCAAT
18262 GAATAACTAGTAATTGAA
1 GAATAACTAGTAATTGAA
18280 GAATAACTAGTAATTGAA
1 GAATAACTAGTAATTGAA
18298 G
1 G
18299 TATTAAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.27
Consensus pattern (18 bp):
GAATAACTAGTAATTGAA
Found at i:19086 original size:108 final size:105
Alignment explanation
Indices: 18734--19087 Score: 523
Period size: 105 Copynumber: 3.3 Consensus size: 105
18724 GAAAGTTGTT
* *
18734 GTTTGATATC-TGAACTTGAGGAACCAGAGTAAGTTGATGAGGAGCCTCCTCCTGCCCCAAGATT
1 GTTTGAT-TCTTGAACTTGAGGAACCAGAGTAAGTTGATGAAGAGACTCCTCCTGCCCCAAGATT
**
18798 AAATTACCATAATATGTTTCATGATCTTCATCATCGTAGTG
65 AAATTACCATAGCATGTTTCATGATCTTCATCATCGTAGTG
* *
18839 GTTTGATTCTTGACCTTGAGGAACCAGAGTAAGTTGATGAAGAGACTCCTGCTGCCCCAAGATTA
1 GTTTGATTCTTGAACTTGAGGAACCAGAGTAAGTTGATGAAGAGACTCCTCCTGCCCCAAGATTA
18904 AATTACCATAGCATGTTTCATGATCTTCATCATCGTAGTG
66 AATTACCATAGCATGTTTCATGATCTTCATCATCGTAGTG
* *
18944 ATTTGATTCTTGAACTTGAGGAACCAGAGTAAGTTGATGAAGAGTCTCCTCCTGCCCCAAGATTA
1 GTTTGATTCTTGAACTTGAGGAACCAGAGTAAGTTGATGAAGAGACTCCTCCTGCCCCAAGATTA
* * * *
19009 AATTACCATAGCATGTTTCATCATATTGGGATTGAAT-GTAGTG
66 AATTACCATAGCATGTTTCATGATCTT--CA-T-CATCGTAGTG
* *
19052 GTTTGATTCTTGAACTTGAGGAACCATAGAAAGTTG
1 GTTTGATTCTTGAACTTGAGGAACCAGAGTAAGTTG
19088 GTGAGGCCCC
Statistics
Matches: 227, Mismatches: 17, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
104 2 0.01
105 182 0.80
107 1 0.00
108 40 0.18
109 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (105 bp):
GTTTGATTCTTGAACTTGAGGAACCAGAGTAAGTTGATGAAGAGACTCCTCCTGCCCCAAGATTA
AATTACCATAGCATGTTTCATGATCTTCATCATCGTAGTG
Found at i:19121 original size:96 final size:99
Alignment explanation
Indices: 18997--19182 Score: 252
Period size: 105 Copynumber: 1.8 Consensus size: 99
18987 GTCTCCTCCT
* *
18997 GCCCCAAGATTAAATTACCATAGCA-TG-T-TTCATCATATTGGGATTGAATGTAGTGGTTTGAT
1 GCCCCAAGATTAAATTACCATAGCATTGATCTTCATCATATTGGGATTGAACGTAGTAGTTTGAT
19059 TCTTGAACTTGAGGAACCATAGAAAGTTGGTGAG
66 TCTTGAACTTGAGGAACCATAGAAAGTTGGTGAG
** *
19093 GCCCCAAGATTAAATTACCATCGTATGTTCCGTGATCTTCATCATCTTGGGATTGAACGTAGTAG
1 GCCCCAAGATTAAATTACCA---TA-G--CATTGATCTTCATCATATTGGGATTGAACGTAGTAG
19158 TTTGATTCTTGAACTTGAGGAACCA
60 TTTGATTCTTGAACTTGAGGAACCA
19183 GAGCATGTTG
Statistics
Matches: 77, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
96 20 0.26
99 2 0.03
100 1 0.01
102 1 0.01
103 2 0.03
104 1 0.01
105 50 0.65
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (99 bp):
GCCCCAAGATTAAATTACCATAGCATTGATCTTCATCATATTGGGATTGAACGTAGTAGTTTGAT
TCTTGAACTTGAGGAACCATAGAAAGTTGGTGAG
Found at i:21509 original size:20 final size:20
Alignment explanation
Indices: 21472--21510 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
21462 TACTATTATT
21472 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
21492 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
21511 AATGCCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:21704 original size:22 final size:22
Alignment explanation
Indices: 21676--22338 Score: 190
Period size: 22 Copynumber: 29.9 Consensus size: 22
21666 TGTCTCTGTG
21676 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
21698 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
21721 T-GTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
21742 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-AGA
* * **
21765 -AGTTATCAAAATTTGATGGGA
1 TGGTTATCAAAATTTCATAAGA
*
21786 AGGTTATCAAAATTTCAT-AGTA
1 TGGTTATCAAAATTTCATAAG-A
* **
21808 TGGTTACCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAAGA
* ** *
21830 TCAGGTTATTAAAATTTTTTAGGA
1 T--GGTTATCAAAATTTCATAAGA
* ** *
21854 AGGTTATTGAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
21876 TGGTTATCACAATTTTAT-AGAA
1 TGGTTATCAAAATTTCATAAG-A
*
21898 AGGTTATCAAAGAGATTATCA-AAGA
1 TGGTTATC-AA-A-ATT-TCATAAGA
*
21923 -GGTTATCAAAGAGGTT-ATCAA-A
1 TGGTTATCAAA-A-TTTCAT-AAGA
*
21945 -GGTTAACAAAATTTCATAAGGA
1 TGGTTATCAAAATTTCATAA-GA
* *
21967 -GGTTA-CTAATATTTCATAGGA
1 TGGTTATC-AAAATTTCATAAGA
*
21988 AGGTTATCAAAATTTCAT-AG-
1 TGGTTATCAAAATTTCATAAGA
* * *
22008 TGTGATTATTAAAATTT-TTTAG-
1 TG-G-TTATCAAAATTTCATAAGA
*
22030 TGTAGTTATCAAAATTTCATATGA
1 TG--GTTATCAAAATTTCATAAGA
* *
22054 AGGTTATAAAAGTCTTAATTTCATAAG-
1 TGGTTAT-CAA-----AATTTCATAAGA
* *
22081 -GAG-TACCAAAATTTGAT-AGA
1 TG-GTTATCAAAATTTCATAAGA
* *
22101 AGGTTATC-AAATCTCAT-AGA
1 TGGTTATCAAAATTTCATAAGA
* *
22121 GTGATTATCGAAATTTCATAGAGA
1 -TGGTTATCAAAATTTCATA-AGA
*
22145 TCGGATTATCAAAATTT-ATAGGA
1 T-GG-TTATCAAAATTTCATAAGA
* *
22168 AGATTATCAAAATTTCAT-AG-
1 TGGTTATCAAAATTTCATAAGA
22188 TGTTGTTATCAAAATTTCA-AAGCGA
1 TG--GTTATCAAAATTTCATAA--GA
*
22213 -GGTTATCAAAATTACATAATGA
1 TGGTTATCAAAATTTCATAA-GA
***
22235 -AAATATCAAAATTTCAT-AGA
1 TGGTTATCAAAATTTCATAAGA
* * * *
22255 GGGGTA-AAAAATTTTATAGAGA
1 TGGTTATCAAAATTTCATA-AGA
* *
22277 -AGTTATCAAAATTTTATAAAGA
1 TGGTTATCAAAATTTCAT-AAGA
*
22299 -GGTTATCAAATTTTCA-AA-A
1 TGGTTATCAAAATTTCATAAGA
*
22318 TGTGATTACCAAAATTTCATA
1 TG-G-TTATCAAAATTTCATA
22339 GTGGTATTTC
Statistics
Matches: 480, Mismatches: 97, Indels: 127
0.68 0.14 0.18
Matches are distributed among these distances:
19 3 0.01
20 39 0.08
21 46 0.10
22 298 0.62
23 24 0.05
24 35 0.07
25 17 0.04
26 7 0.01
27 1 0.00
28 10 0.02
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:21792 original size:66 final size:67
Alignment explanation
Indices: 21673--22064 Score: 251
Period size: 66 Copynumber: 5.9 Consensus size: 67
21663 TCTTGTCTCT
* * * * * *
21673 GTGTGGTTATCAAAATTTCATAAGAT-GGTTATTATAATTTCATGAGG-ATGTTATCAAAATTCC
1 GTGTGGTTACCAAAATTTCATAGGATAGGTTATCAAAATTTCATG-GGAAGGTTATCAAAATTTC
21736 ATA
65 ATA
*
21739 GTGTGGTTACCAAAATTTCATATGGA-A-GTTATCAAAATTTGATGGGAAGGTTATCAAAATTTC
1 GTGTGGTTACCAAAATTTCATA-GGATAGGTTATCAAAATTTCATGGGAAGGTTATCAAAATTTC
21802 ATA
65 ATA
* * * ** * **
21805 GTATGGTTACCAAAATTTCATGGGATCAGGTTATTAAAATTTTTTAGGAAGGTTATTGAAATTTC
1 GTGTGGTTACCAAAATTTCATAGGAT-AGGTTATCAAAATTTCATGGGAAGGTTATCAAAATTTC
21870 ATA
65 ATA
* * * * **
21873 GTGTGGTTATCACAATTTTATA-GAAAGGTTATCAAAGAGATTATCA-AAG-AGGTTATCAAAGA
1 GTGTGGTTACCAAAATTTCATAGGATAGGTTATC-AA-A-ATT-TCATGGGAAGGTTATCAAA-A
21935 GGTTATCA-A
61 --TT-TCATA
* * * *
21944 ---AGGTTAACAAAATTTCATAAGG--AGGTTA-CTAATATTTCATAGGAAGGTTATCAAAATTT
1 GTGTGGTTACCAAAATTTCAT-AGGATAGGTTATC-AAAATTTCATGGGAAGGTTATCAAAATTT
22003 CATA
64 CATA
* ** ** **
22007 GTGTGATTATTAAAATTTTTTAGTG-TA-GTTATCAAAATTTCATATGAAGGTTAT-AAAA
1 GTGTGGTTACCAAAATTTCATAG-GATAGGTTATCAAAATTTCATGGGAAGGTTATCAAAA
22065 GTCTTAATTT
Statistics
Matches: 259, Mismatches: 42, Indels: 51
0.74 0.12 0.14
Matches are distributed among these distances:
62 3 0.01
63 3 0.01
64 3 0.01
65 17 0.07
66 126 0.49
67 12 0.05
68 80 0.31
69 7 0.03
70 2 0.01
71 3 0.01
72 3 0.01
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (67 bp):
GTGTGGTTACCAAAATTTCATAGGATAGGTTATCAAAATTTCATGGGAAGGTTATCAAAATTTCA
TA
Found at i:21918 original size:12 final size:12
Alignment explanation
Indices: 21898--21945 Score: 87
Period size: 12 Copynumber: 4.0 Consensus size: 12
21888 TTTTATAGAA
21898 AGGTTATCAAAG
1 AGGTTATCAAAG
*
21910 AGATTATCAAAG
1 AGGTTATCAAAG
21922 AGGTTATCAAAG
1 AGGTTATCAAAG
21934 AGGTTATCAAAG
1 AGGTTATCAAAG
21946 GTTAACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.44, C:0.08, G:0.23, T:0.25
Consensus pattern (12 bp):
AGGTTATCAAAG
Found at i:21949 original size:10 final size:10
Alignment explanation
Indices: 21896--21954 Score: 55
Period size: 12 Copynumber: 5.3 Consensus size: 10
21886 AATTTTATAG
21896 AAAGGTTATC
1 AAAGGTTATC
21906 AAAGAGATTATC
1 AAAG-G-TTATC
21918 AAAGAGGTTATC
1 -AA-AGGTTATC
21930 AAAGAGGTTATC
1 -AA-AGGTTATC
*
21942 AAAGGTTAAC
1 AAAGGTTATC
21952 AAA
1 AAA
21955 ATTTCATAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
10 14 0.32
11 3 0.07
12 22 0.50
13 3 0.07
14 2 0.05
ACGTcount: A:0.47, C:0.08, G:0.20, T:0.24
Consensus pattern (10 bp):
AAAGGTTATC
Found at i:22467 original size:22 final size:22
Alignment explanation
Indices: 22393--22884 Score: 191
Period size: 22 Copynumber: 22.7 Consensus size: 22
22383 CAAATTAGGA
* * *
22393 AGGTTATTAAACTTTTACTATGG
1 AGGTTATCAAAATTTCA-TATGG
* *
22416 A-GTAATCAAAATTTC--AGGG
1 AGGTTATCAAAATTTCATATGG
* *
22435 AGGATATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATATGG
**
22457 AGGTTATCAAAATTTCATAGTTT
1 AGGTTATCAAAATTTCATA-TGG
* *
22480 A-GTTTTCAAAATTTCATA-AG
1 AGGTTATCAAAATTTCATATGG
*
22500 AGGGTTATCAAAATTTCATAGGG
1 A-GGTTATCAAAATTTCATATGG
* * *
22523 AGATTAACAAAATTCCATAAT-G
1 AGGTTATCAAAATTTCAT-ATGG
* ** *
22545 AGATTATCAAAAAATCATAGGG
1 AGGTTATCAAAATTTCATATGG
*
22567 AGGTTATCAAAA--T--T-TGT
1 AGGTTATCAAAATTTCATATGG
* *
22584 A-GTTATCAAGATTTCATAAGG
1 AGGTTATCAAAATTTCATATGG
* * *
22605 AGGTTATTAAAATTTTATAGGG
1 AGGTTATCAAAATTTCATATGG
* * *
22627 AGGTTTGTTAAAATTTTATA-GCG
1 AGG-TTATCAAAATTTCATATG-G
* *
22650 AGGTTATCACAATTTCATGTGTG
1 AGGTTATCAAAATTTCATATG-G
*
22673 A--TTATCAAAATTTCAGA-GTG
1 AGGTTATCAAAATTTCATATG-G
* *
22693 TGTTTA-CTAACAA-TTCATATGG
1 AGGTTATC-AA-AATTTCATATGG
* * * **
22715 AGGTTTTTAAATTTTCATAACG
1 AGGTTATCAAAATTTCATATGG
* * *
22737 TGGTTAT-AAATATATCTTATGG
1 AGGTTATCAAA-ATTTCATATGG
* * *
22759 AGGTTATCAACATCTCATAGTGT
1 AGGTTATCAAAATTTCATA-TGG
*
22782 TGGTTATCAAAATTTCAT-TCGG
1 AGGTTATCAAAATTTCATAT-GG
* *
22804 AAGTTATTAAAATTTCATA-GTG
1 AGGTTATCAAAATTTCATATG-G
* * *
22826 AGGTCT-TCAAAATTCCTTAGGG
1 AGGT-TATCAAAATTTCATATGG
** * *
22848 AGGTTAAAAAAATTTCATAAGA
1 AGGTTATCAAAATTTCATATGG
**
22870 AGGTTAAAAAAATTT
1 AGGTTATCAAAATTT
22885 ATAAAAGGGT
Statistics
Matches: 351, Mismatches: 84, Indels: 69
0.70 0.17 0.14
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
18 2 0.01
19 4 0.01
20 18 0.05
21 24 0.07
22 240 0.68
23 52 0.15
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATATGG
Found at i:22641 original size:23 final size:23
Alignment explanation
Indices: 22594--22654 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
22584 AGTTATCAAG
* *
22594 ATTTCATAAGGAGG-TTATTAAA
1 ATTTTATAGGGAGGTTTATTAAA
*
22616 ATTTTATAGGGAGGTTTGTTAAA
1 ATTTTATAGGGAGGTTTATTAAA
*
22639 ATTTTATAGCGAGGTT
1 ATTTTATAGGGAGGTT
22655 ATCACAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 12 0.35
23 22 0.65
ACGTcount: A:0.33, C:0.03, G:0.23, T:0.41
Consensus pattern (23 bp):
ATTTTATAGGGAGGTTTATTAAA
Found at i:22895 original size:21 final size:22
Alignment explanation
Indices: 22848--22892 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
22838 TTCCTTAGGG
22848 AGGTTAAAAAAATTTCATAAGA
1 AGGTTAAAAAAATTTCATAAGA
22870 AGGTTAAAAAAATTT-ATAA-A
1 AGGTTAAAAAAATTTCATAAGA
22890 AGG
1 AGG
22893 GTTCTCGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 4 0.17
21 4 0.17
22 15 0.65
ACGTcount: A:0.56, C:0.02, G:0.16, T:0.27
Consensus pattern (22 bp):
AGGTTAAAAAAATTTCATAAGA
Found at i:24563 original size:2 final size:2
Alignment explanation
Indices: 24550--24602 Score: 81
Period size: 2 Copynumber: 26.5 Consensus size: 2
24540 TTCTAGTCAA
*
24550 TC TC TAC TC TC TC T- TC TC TC TC TC TC TC TC TC TC AC TC TC TC
1 TC TC T-C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
24592 TC TC TC TC TC T
1 TC TC TC TC TC T
24603 GCAAAAGCAT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 44 0.94
3 2 0.04
ACGTcount: A:0.04, C:0.47, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:25045 original size:12 final size:12
Alignment explanation
Indices: 25000--25052 Score: 65
Period size: 12 Copynumber: 4.5 Consensus size: 12
24990 ATTGTCCACT
25000 AAAAAAGCAAA-
1 AAAAAAGCAAAC
*
25011 AAAAAAGCATAC
1 AAAAAAGCAAAC
25023 AAACAAA-CAAAC
1 AAA-AAAGCAAAC
*
25035 AAAAAAGCAAAT
1 AAAAAAGCAAAC
25047 AAAAAA
1 AAAAAA
25053 ATTGGAGGCC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 13 0.36
12 20 0.56
13 3 0.08
ACGTcount: A:0.77, C:0.13, G:0.06, T:0.04
Consensus pattern (12 bp):
AAAAAAGCAAAC
Found at i:26243 original size:2 final size:2
Alignment explanation
Indices: 26236--26264 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
26226 ATTCTCCATC
26236 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26265 ATGATAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28573 original size:23 final size:24
Alignment explanation
Indices: 28547--28592 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
28537 AATTAATTTT
*
28547 TAGTT-TAATATGCTGTTAGTTCA
1 TAGTTCTAATATGCGGTTAGTTCA
28570 TAGTTGCTAATATGCGGTTAGTT
1 TAGTT-CTAATATGCGGTTAGTT
28593 TAATTCTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
25 15 0.75
ACGTcount: A:0.24, C:0.09, G:0.22, T:0.46
Consensus pattern (24 bp):
TAGTTCTAATATGCGGTTAGTTCA
Found at i:30463 original size:64 final size:64
Alignment explanation
Indices: 30357--30485 Score: 231
Period size: 64 Copynumber: 2.0 Consensus size: 64
30347 CTAATAGTCT
*
30357 ACCAAAAAGTCTCTTCAAATATAGATATAATCATGAAAAGTAAGTATAAAAAATGTCAATCTCG
1 ACCAAAAAGTCTCTTCAAATATAGATATAATCATGAAAAGTAAGTACAAAAAATGTCAATCTCG
* *
30421 ACCAGAAAGTCTCTTCAAATATAGATATAATCTTGAAAAGTAAGTACAAAAAATGTCAATCTCG
1 ACCAAAAAGTCTCTTCAAATATAGATATAATCATGAAAAGTAAGTACAAAAAATGTCAATCTCG
30485 A
1 A
30486 AAGAATTTGG
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (64 bp):
ACCAAAAAGTCTCTTCAAATATAGATATAATCATGAAAAGTAAGTACAAAAAATGTCAATCTCG
Found at i:30848 original size:219 final size:216
Alignment explanation
Indices: 30468--31211 Score: 816
Period size: 219 Copynumber: 3.5 Consensus size: 216
30458 AAGTAAGTAC
* * *
30468 AAAAAATGTCAATCTCGAAAGAATTTGGGGAAGGTGCATATGATTATTTGGGGATGTTGAGAAAT
1 AAAAAATGTCAATCTCGAAAGAATTTGGGGATGGTGCAAATGATTATTTGGGGATGATGAG-AAT
* * * * * *
30533 GATTTGGGTATAAATTATATCAGTTTGGAGATGCTGAATTTTGCATGTTGTTTAATTATTAGATG
65 GAGTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGTATTTTGTTTAATTATTAGATG
* * *
30598 GCACTAAATTCATTTAGACTGGGTTTATTCAATTAATTAGAATGAAAATATGGATTAAAACACGT
130 ACACTAAATTCATATAGACT-GGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACGT
30663 TTAAAGCCAATTTTGGCTATATA
194 TTAAAGCCAATTTTGGCTATATA
*
30686 ATAAAAATGGCAATCTCGAAAGAATTTGGGGATGGTGCAAATGATTATTTGGGGATGATGAGAAA
1 A-AAAAATGTCAATCTCGAAAGAATTTGGGGATGGTGCAAATGATTATTTGGGGATGATGAG-AA
* * *
30751 TGAGTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATATTGTATTTTGTTGAACTATTAGAT
64 TGAGTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGTATTTTGTTTAATTATTAGAT
*
30816 GACACTAAATTCATATAGACATGGTTTATTCAATTAATTAGGATGAAAATATGGTTTAAAACACG
129 GACACTAAATTCATATAGAC-TGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACG
*
30881 TTTAAAGTCAATTTTGGGC-ATATA
193 TTTAAAGCCAATTTT-GGCTATATA
* * * * *
30905 AAAAAATGTCAAACTCTAAAAAATTTGGGGATGATG-AGAA--ATGATTT-GGG-T-AT---AA-
1 AAAAAATGTCAATCTCGAAAGAATTTGGGGATGGTGCA-AATGATTATTTGGGGATGATGAGAAT
* * *
30960 -AG-T--ATAT-CAGT-T-T-A-----GGGATACTGAATTTTGTATTTTGTTTAATTATTAGATA
65 GAGTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGTATTTTGTTTAATTATTAGATG
* * * *
31012 ACACTAAATTCTTATAGACGGGGTTTATTTAATTAATTAGGATGAAAATATGGATTAAAGCACGT
130 ACACTAAATTCATATAGAC-TGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACGT
* *
31077 TTAAAGGCAATTTTGGGTATATA
194 TTAAAGCCAATTTTGGCTATATA
** * * ** *
31100 AGATATGATGTCAATCTCTAATGAATTTGGGGATGGGGGTGCTTATGATTATTTGGGAATGATGA
1 A-A-AAAATGTCAATCTCGAAAGAATTTGGGGAT---GGTGCAAATGATTATTTGGGGATGATGA
* * * *
31165 GAATGATTTGGGTATAGAGTATATCACTTTGGGGATGCTGAATTTTG
61 GAATGAGTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTG
31212 CGCATGCCTC
Statistics
Matches: 441, Mismatches: 52, Indels: 62
0.79 0.09 0.11
Matches are distributed among these distances:
194 2 0.00
195 112 0.25
196 1 0.00
197 25 0.06
200 5 0.01
201 1 0.00
202 7 0.02
203 5 0.01
204 4 0.01
205 2 0.00
206 1 0.00
207 2 0.00
208 2 0.00
209 2 0.00
210 1 0.00
211 1 0.00
213 5 0.01
214 4 0.01
215 4 0.01
216 7 0.02
217 2 0.00
218 33 0.07
219 194 0.44
220 4 0.01
222 15 0.03
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.36
Consensus pattern (216 bp):
AAAAAATGTCAATCTCGAAAGAATTTGGGGATGGTGCAAATGATTATTTGGGGATGATGAGAATG
AGTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATTTTGTATTTTGTTTAATTATTAGATGA
CACTAAATTCATATAGACTGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACGTTT
AAAGCCAATTTTGGCTATATA
Found at i:31064 original size:195 final size:197
Alignment explanation
Indices: 30732--31134 Score: 621
Period size: 195 Copynumber: 2.1 Consensus size: 197
30722 GCAAATGATT
*
30732 ATTTGGGGATGATGAGAAATGAGTTGGGTATAAAGTATATCAGTTTGGGGATACTGAATATTGTA
1 ATTTGGGGATGATGAGAAATGAGTTGGGTATAAAGTATATCAGTTTAGGGATACTGAATATTGTA
* *
30797 TTTTGTTGAACTATTAGATGACACTAAATTCATATAGACATGGTTTATTCAATTAATTAGGATGA
66 TTTTGTTGAACTATTAGATAACACTAAATTCATATAGACAGGGTTTATTCAATTAATTAGGATGA
* *
30862 AAATATGGTTTAAAACACGTTTAAAGTCAATTTTGGGCATATAA-A-AAAATGTCAAACTCTAAA
131 AAATATGGATTAAAACACGTTTAAAGGCAATTTTGGGCATATAAGATAAAATGTCAAACTCTAAA
30925 AA
196 AA
* *
30927 ATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTAGGGATACTGAATTTTGTA
1 ATTTGGGGATGATGAGAAATGAGTTGGGTATAAAGTATATCAGTTTAGGGATACTGAATATTGTA
* * * * *
30992 TTTTGTTTAATTATTAGATAACACTAAATTCTTATAGACGGGGTTTATTTAATTAATTAGGATGA
66 TTTTGTTGAACTATTAGATAACACTAAATTCATATAGACAGGGTTTATTCAATTAATTAGGATGA
* * ** * *
31057 AAATATGGATTAAAGCACGTTTAAAGGCAATTTTGGGTATATAAGATATGATGTCAATCTCTAAT
131 AAATATGGATTAAAACACGTTTAAAGGCAATTTTGGGCATATAAGATAAAATGTCAAACTCTAAA
*
31122 GA
196 AA
31124 ATTTGGGGATG
1 ATTTGGGGATG
31135 GGGGTGCTTA
Statistics
Matches: 187, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
195 160 0.86
196 1 0.01
197 26 0.14
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (197 bp):
ATTTGGGGATGATGAGAAATGAGTTGGGTATAAAGTATATCAGTTTAGGGATACTGAATATTGTA
TTTTGTTGAACTATTAGATAACACTAAATTCATATAGACAGGGTTTATTCAATTAATTAGGATGA
AAATATGGATTAAAACACGTTTAAAGGCAATTTTGGGCATATAAGATAAAATGTCAAACTCTAAA
AA
Found at i:32073 original size:219 final size:219
Alignment explanation
Indices: 31693--32424 Score: 1132
Period size: 219 Copynumber: 3.3 Consensus size: 219
31683 CTTGATATTA
* *
31693 CTCATCATCCCCAAATAATCATAAGCACCATCCCCAAATTCATTAGACATTGACATTTTTTCTTA
1 CTCATCATCCCCAAATAATCATAAGCACCATCCCAAAATTCATTAGAGATTGACATTTTTTCTTA
* *
31758 TAGACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAATCC
66 TATACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAA-AC
* * * *
31823 CAGTCTATATGAATGTAGTGCCATCTAATAATTAAACAACATGCAAAATTCAATATTCCCAAAGT
130 CAGTCTATATGAATTTTGTGCCATCTAATAATTAAACAAAATGCAAAATTCAATATTCCCAAACT
31888 GATATACTTTATACCCAAATCATTT
195 GATATACTTTATACCCAAATCATTT
* * * *
31913 CTCATCATCCCCACATAATCATATGCACCATCCCCAAATTCTTTAGAGATTGACATTTTTT-TTA
1 CTCATCATCCCCAAATAATCATAAGCACCATCCCAAAATTCATTAGAGATTGACATTTTTTCTTA
* * * *
31977 TATACCTAAAATTGGGTTTAAACGTGTTTTAATCCATATTTTCATCCTAATTCATTGAATAAACC
66 TATACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACC
32042 ATGTCTATATGAATTTTGTGCCATCTAATAATTAAACAAAATGCAAAATTCAATA-TCTCCAAAC
131 A-GTCTATATGAATTTTGTGCCATCTAATAATTAAACAAAATGCAAAATTCAATATTC-CCAAAC
32106 TGATATACTTTATACCCAAATCATTT
194 TGATATACTTTATACCCAAATCATTT
* * * *
32132 CTCATCATCCCCACATAATCATATGCACCATCCCAAAATTCTTTAGAGATTGTCA--TTTT-TTA
1 CTCATCATCCCCAAATAATCATAAGCACCATCCCAAAATTCATTAGAGATTGACATTTTTTCTTA
32194 TATACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACC
66 TATACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAA-C
* * * * *
32259 CCGTCTATATGAATTTTGTGTCATCTAATAATTAAACAAAATGCAATATTCAGTATCCCCAAACT
130 CAGTCTATATGAATTTTGTGCCATCTAATAATTAAACAAAATGCAAAATTCAATATTCCCAAACT
*
32324 GATATACTTTATACCCAGATCATTT
195 GATATACTTTATACCCAAATCATTT
* *
32349 CTCATCATCCCCAAATAATTATAAGCACCGTACCCAAAATTCATTAGAGATTGACATTTTTTCTT
1 CTCATCATCCCCAAATAATCATAAGCACCAT-CCCAAAATTCATTAGAGATTGACATTTTTTCTT
32414 ATATACCCAAA
65 ATATACCCAAA
32425 CTGATATACT
Statistics
Matches: 472, Mismatches: 32, Indels: 15
0.91 0.06 0.03
Matches are distributed among these distances:
217 174 0.37
218 30 0.06
219 194 0.41
220 61 0.13
221 13 0.03
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (219 bp):
CTCATCATCCCCAAATAATCATAAGCACCATCCCAAAATTCATTAGAGATTGACATTTTTTCTTA
TATACCCAAAATTGGCTTTAAACGTGCTTTAATCCATATTTTCATCCTAATTAATTGAATAAACC
AGTCTATATGAATTTTGTGCCATCTAATAATTAAACAAAATGCAAAATTCAATATTCCCAAACTG
ATATACTTTATACCCAAATCATTT
Found at i:32512 original size:103 final size:101
Alignment explanation
Indices: 32316--32524 Score: 321
Period size: 103 Copynumber: 2.1 Consensus size: 101
32306 ATTCAGTATC
* * * *
32316 CCCAAACTGATATACTTTATACCCAGATCATTTCTCATCATCCCCAAATAATTATAAGCACCGTA
1 CCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATCATAAGCAACATA
32381 CCCAAAATTCATTAGAGATTGACATTTTTTCTTATATA
66 CCCAAAATTCATTAGAGATTGACA-TTTTT-TTATATA
*
32419 CCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATCATATGCAACAT-
1 CCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATCATAAGCAACATA
* * *
32483 CCCCAAATTCTTTAGAGATTGGCATTTTTTTATATA
66 CCCAAAATTCATTAGAGATTGACATTTTTTTATATA
32519 CCCAAA
1 CCCAAA
32525 ATTGGCTTCA
Statistics
Matches: 98, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
100 13 0.13
101 5 0.05
102 21 0.21
103 59 0.60
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.33
Consensus pattern (101 bp):
CCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATCATAAGCAACATA
CCCAAAATTCATTAGAGATTGACATTTTTTTATATA
Found at i:32689 original size:317 final size:319
Alignment explanation
Indices: 32100--32741 Score: 1112
Period size: 317 Copynumber: 2.0 Consensus size: 319
32090 TTCAATATCT
* *
32100 CCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCCACATAATCATATGCACCATCC
1 CCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATCATATGCAACATCC
* *
32165 CAAAATTCTTTAGAGATTGTCATTTTTTATATACCCAAAATTGGCTTTAAACGTGCTTTAATCCA
66 CAAAATTCTTTAGAGATTGGCATTTTTTATATACCCAAAATTGGCTTCAAACGTGCTTTAATCCA
* *
32230 TATTTTCATCCTAATTAATTGAATAAACCCCGTCTATATGAATTTTGTGTCATCTAATAATTAAA
131 TATTTTCATCCTAATT-ATTGAATAAACCCCATCCATATGAATTTTGTGTCATCTAATAATTAAA
*
32295 CAAAATGCAATATTCAGTATCCCCAAACTGATATACTTTATACCCAGATCATTTCTCATCATCCC
195 CAAAATGCAATATTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCC
32360 CAAATAATTATAAGCACCGTACCCAAAATTCATTAGAGATTGACATTTTTTCTTATATAC
260 CAAATAATTATAAGCACCGTACCCAAAATTCATTAGAGATTGACATTTTTTCTTATATAC
32420 CCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATCATATGCAACATCC
1 CCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATCATATGCAACATCC
*
32485 CCAAATTCTTTAGAGATTGGCATTTTTTTATATACCCAAAATTGGCTTCAAACGTG-TTTAATCC
66 CAAAATTCTTTAGAGATTGGCA-TTTTTTATATACCCAAAATTGGCTTCAAACGTGCTTTAATCC
*
32549 ATATTTTTCATCCTAA-T-TTGAATAAA-CCCATCCGTATGAATTTTGTGTCATCTAATAATTAA
130 ATA-TTTTCATCCTAATTATTGAATAAACCCCATCCATATGAATTTTGTGTCATCTAATAATTAA
* *
32611 ACAAAATGCAATATTTAGTATCGCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCC
194 ACAAAATGCAATATTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCC
* *
32676 CCAAATAATTATAAGCACCGTATCGAAAATTCATTAGAGATTGACATTTTTTCTTATATAC
259 CCAAATAATTATAAGCACCGTACCCAAAATTCATTAGAGATTGACATTTTTTCTTATATAC
32737 CCAAA
1 CCAAA
32742 ATTAGTTTTA
Statistics
Matches: 307, Mismatches: 13, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
317 159 0.52
318 9 0.03
320 95 0.31
321 44 0.14
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.35
Consensus pattern (319 bp):
CCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATCATATGCAACATCC
CAAAATTCTTTAGAGATTGGCATTTTTTATATACCCAAAATTGGCTTCAAACGTGCTTTAATCCA
TATTTTCATCCTAATTATTGAATAAACCCCATCCATATGAATTTTGTGTCATCTAATAATTAAAC
AAAATGCAATATTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCC
AAATAATTATAAGCACCGTACCCAAAATTCATTAGAGATTGACATTTTTTCTTATATAC
Found at i:32874 original size:222 final size:214
Alignment explanation
Indices: 32420--32883 Score: 619
Period size: 222 Copynumber: 2.1 Consensus size: 214
32410 TCTTATATAC
*
32420 CCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATCATATGCAACATCC
1 CCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATCATAAGCAACATCC
* * * * *
32485 CCAAATTCTTTAGAGATTGGCATTTTTTTATATACCCAAAATTGGCTTCAAACGTGTTTAATCCA
66 CAAAATTCATTAGAGATTGACATTTTTTTATATACCCAAAATTGGCTTAAAAAGTGTTTAATCCA
* * * * *
32550 TATTTTTCATCCTAATTTGAATAAACCCATCCGTATGAATTTTGTGTCATCTAATAATTAAACAA
131 TATTTTTCATCATAATTTGAATAAACCCATACATATGAATTTAGTGTCATCTAATAATGAAACAA
* *
32615 AATGCAATATTTAGTATCG
196 AACGCAAAATTTAGTATCG
* *
32634 CCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATTATAAGCACCGTAT
1 CCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATCATAAGCAAC--AT
* **
32699 -CGAAAATTCATTAGAGATTGACATTTTTTCTTATATACCCAAAATTAGTTTTAAAAAGTGCTTT
64 CCCAAAATTCATTAGAGATTGACA-TTTTT-TTATATACCCAAAATT-GGCTTAAAAAGTG-TTT
* * *
32763 AATCCATA-TTTTCATCATAATTAATTGAATAAACCCCATATATATTAGTTTAGTGTCATCTAAT
125 AATCCATATTTTTCATCATAA-T--TTGAATAAA-CCCATACATATGAATTTAGTGTCATCTAAT
32827 AATGAAACAAAACGCAAAATTTAGTATC-
186 AATGAAACAAAACGCAAAATTTAGTATCG
32855 CTCAAACTGATATACTTTATACCCAAATC
1 C-CAAACTGATATACTTTATACCCAAATC
32884 TTGTGATGCC
Statistics
Matches: 218, Mismatches: 21, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
214 58 0.27
215 19 0.09
216 7 0.03
217 16 0.07
218 20 0.09
219 12 0.06
221 10 0.05
222 76 0.35
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (214 bp):
CCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCCAAATAATCATAAGCAACATCC
CAAAATTCATTAGAGATTGACATTTTTTTATATACCCAAAATTGGCTTAAAAAGTGTTTAATCCA
TATTTTTCATCATAATTTGAATAAACCCATACATATGAATTTAGTGTCATCTAATAATGAAACAA
AACGCAAAATTTAGTATCG
Found at i:36084 original size:25 final size:25
Alignment explanation
Indices: 36028--36090 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
36018 CAAAAATTAT
**
36028 TTTTCAAATTATTCTTTTCAAGTAAA
1 TTTTCAAATT-TTCTTTGAAAGTAAA
36054 TTTTCAAATTTT-TTTGAAAGATAAA
1 TTTTCAAATTTTCTTTGAAAG-TAAA
36079 TTTTCAAATTTT
1 TTTTCAAATTTT
36091 ATTTACAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
24 6 0.18
25 18 0.53
26 10 0.29
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (25 bp):
TTTTCAAATTTTCTTTGAAAGTAAA
Found at i:36504 original size:41 final size:41
Alignment explanation
Indices: 36401--36606 Score: 234
Period size: 41 Copynumber: 5.0 Consensus size: 41
36391 ATCATCACCC
* * * * **
36401 TGATAATCTAATTCAAGGGTCTTGACGGCTTGGTCTTGAAT
1 TGATAATTTAATTCAAGGGTCTCGATGACTTAATCTTGAAT
* **
36442 TGATAATAATTCGATTCAAGGGTCTCGATGACTTGTTCTTGAAT
1 TGATAAT--TT-AATTCAAGGGTCTCGATGACTTAATCTTGAAT
* *
36486 TGATAATTTAATTCAAGGGTTTCGATGACTCAATCTT-AAT
1 TGATAATTTAATTCAAGGGTCTCGATGACTTAATCTTGAAT
* * *
36526 TGATAATTTGATTCAAGGGTCTCGATGACTCAATATTGAAT
1 TGATAATTTAATTCAAGGGTCTCGATGACTTAATCTTGAAT
* *
36567 TCATAATTTAATTCAAGGGTCTTGATGACTTAATCTTGAA
1 TGATAATTTAATTCAAGGGTCTCGATGACTTAATCTTGAA
36607 CAAACGAAAA
Statistics
Matches: 142, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
40 37 0.26
41 68 0.48
42 2 0.01
43 1 0.01
44 34 0.24
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (41 bp):
TGATAATTTAATTCAAGGGTCTCGATGACTTAATCTTGAAT
Found at i:36547 original size:81 final size:81
Alignment explanation
Indices: 36447--36603 Score: 235
Period size: 81 Copynumber: 1.9 Consensus size: 81
36437 TGAATTGATA
*** * *
36447 ATAATTCGATTCAAGGGTCTCGATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGT-TTCGA
1 ATAATTCGATTCAAGGGTCTCGATGACTCAATATTGAATTCATAATTTAATTCAAGGGTCTT-GA
36511 TGACTCAATCTTAATTG
65 TGACTCAATCTTAATTG
*
36528 ATAATTTGATTCAAGGGTCTCGATGACTCAATATTGAATTCATAATTTAATTCAAGGGTCTTGAT
1 ATAATTCGATTCAAGGGTCTCGATGACTCAATATTGAATTCATAATTTAATTCAAGGGTCTTGAT
*
36593 GACTTAATCTT
66 GACTCAATCTT
36604 GAACAAACGA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
81 66 0.97
82 2 0.03
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (81 bp):
ATAATTCGATTCAAGGGTCTCGATGACTCAATATTGAATTCATAATTTAATTCAAGGGTCTTGAT
GACTCAATCTTAATTG
Found at i:37436 original size:63 final size:63
Alignment explanation
Indices: 37363--37493 Score: 199
Period size: 63 Copynumber: 2.1 Consensus size: 63
37353 AGTTCATTTA
* * * * * *
37363 TTTTTGTGCTCTAAGTTTTGCCAAAGTCGTCCTTTGCAGGATTTTCAACTTCGCGAGCTTTTT
1 TTTTTGTGCTCTAACTTTTGCCAAAGTCATCCTTTACAGGATTTTCAACTTAGCGAGCTCTTC
*
37426 TTTTTGTGCTCTAACTTTTGCCTAAGTCATCCTTTACAGGATTTTCAACTTAGCGAGCTCTTC
1 TTTTTGTGCTCTAACTTTTGCCAAAGTCATCCTTTACAGGATTTTCAACTTAGCGAGCTCTTC
37489 TTTTT
1 TTTTT
37494 CCCCCGTTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.46
Consensus pattern (63 bp):
TTTTTGTGCTCTAACTTTTGCCAAAGTCATCCTTTACAGGATTTTCAACTTAGCGAGCTCTTC
Found at i:39359 original size:41 final size:41
Alignment explanation
Indices: 39219--39462 Score: 276
Period size: 41 Copynumber: 5.9 Consensus size: 41
39209 GAGTTTGATT
* **
39219 TAATTTGATTCAAGGG--TCGAATGACTTGGTCTTGAATTGA
1 TAATTTAATTCAAGGGTCTCG-ATGACTTAATCTTGAATTGA
* * ** * * * *
39259 CAATCTAATTCAAGGGTCAAGACGGCTTAGTTTTGAATTGA
1 TAATTTAATTCAAGGGTCTCGATGACTTAATCTTGAATTGA
* **
39300 TAATAATTCGATTCAAGGGTCTCGATGACTTGTTCTTGAATTGA
1 TAAT--TT-AATTCAAGGGTCTCGATGACTTAATCTTGAATTGA
*
39344 TAATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGA
1 TAATTTAATTCAAGGGTCTCGATGACTTAATCTTGAATTGA
* * *
39385 TAATTTAATCCAAGGGTCTTGATGACTCAATCTTGAATTGA
1 TAATTTAATTCAAGGGTCTCGATGACTTAATCTTGAATTGA
39426 TAATTTAATTCAAGGGTCTCGATGACTTAATCTTGAA
1 TAATTTAATTCAAGGGTCTCGATGACTTAATCTTGAA
39463 CAAACGAAAA
Statistics
Matches: 171, Mismatches: 28, Indels: 9
0.82 0.13 0.04
Matches are distributed among these distances:
40 13 0.08
41 123 0.72
42 3 0.02
43 1 0.01
44 31 0.18
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (41 bp):
TAATTTAATTCAAGGGTCTCGATGACTTAATCTTGAATTGA
Found at i:39579 original size:16 final size:16
Alignment explanation
Indices: 39558--39608 Score: 93
Period size: 16 Copynumber: 3.2 Consensus size: 16
39548 TCTGAAAATA
39558 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
39574 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
*
39590 CTTCAGACCTTTTCTG
1 CTTCAGAGCTTTTCTG
39606 CTT
1 CTT
39609 TCTGAATTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.12, C:0.27, G:0.16, T:0.45
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTG
Found at i:43700 original size:60 final size:61
Alignment explanation
Indices: 43583--43733 Score: 189
Period size: 60 Copynumber: 2.5 Consensus size: 61
43573 GACAGCATGG
* * * * * *
43583 ACTTATTTGAGCAATTTTC-TAAAAGTTGGACCCTTATTTGAGCCTTTTTTTTTCTTTGGGC
1 ACTTATTTGAGC-ATTTTCGCAAACGTTGGACCCTGATTTAAGCCATTTTTTTTCTTTGAGC
*
43644 ACTTATTTGAGCATTTTCGCAAACGTTGGGCCCTGATTTAAG-CATTTTTTTTCTTTGAGC
1 ACTTATTTGAGCATTTTCGCAAACGTTGGACCCTGATTTAAGCCATTTTTTTTCTTTGAGC
* * *
43704 CCTTATTTAAGCATTTTCGCAAACGATGGA
1 ACTTATTTGAGCATTTTCGCAAACGTTGGA
43734 GAAAAAAAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
60 48 0.62
61 30 0.38
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.43
Consensus pattern (61 bp):
ACTTATTTGAGCATTTTCGCAAACGTTGGACCCTGATTTAAGCCATTTTTTTTCTTTGAGC
Found at i:44632 original size:22 final size:22
Alignment explanation
Indices: 44587--44644 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
44577 AATAAGGGCC
*
44587 TGAAAATTTGATAATCTCCATA
1 TGAAATTTTGATAATCTCCATA
*
44609 TGAAATTTTGATAATCT-TATTA
1 TGAAATTTTGATAATCTCCA-TA
*
44631 TGGAATTTTGATAA
1 TGAAATTTTGATAA
44645 CCACACGACG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 1 0.03
22 31 0.97
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAATCTCCATA
Found at i:44802 original size:59 final size:59
Alignment explanation
Indices: 44661--44808 Score: 176
Period size: 59 Copynumber: 2.5 Consensus size: 59
44651 GACGACAGAG
* * *
44661 ACTTATTTGAGCAATTTTCTA-AAA-GTTGGATCCTTATTTGAGCATTTTTTTCTTTGGTC
1 ACTTATTTGAGC-ATTTTC-ACAAACGTTGGACCCTGATTTAAGCATTTTTTTCTTTGGTC
* *
44720 ACTTATTTGAGCATTTTCGCAAACGTTGGGCCCTGATTTAAGCATTTTTTTCTTTGAG-C
1 ACTTATTTGAGCATTTTCACAAACGTTGGACCCTGATTTAAGCATTTTTTTCTTTG-GTC
* * *
44779 CCTTATTTAAGCATTTTCACAAACGATGGA
1 ACTTATTTGAGCATTTTCACAAACGTTGGA
44809 GAAAAAAAAG
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
58 9 0.12
59 66 0.87
60 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.43
Consensus pattern (59 bp):
ACTTATTTGAGCATTTTCACAAACGTTGGACCCTGATTTAAGCATTTTTTTCTTTGGTC
Found at i:46471 original size:14 final size:14
Alignment explanation
Indices: 46452--46480 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
46442 TCATGTTAAA
46452 ACGCCAACGATCAC
1 ACGCCAACGATCAC
46466 ACGCCAACGATCAC
1 ACGCCAACGATCAC
46480 A
1 A
46481 ATAAATTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.41, G:0.14, T:0.07
Consensus pattern (14 bp):
ACGCCAACGATCAC
Found at i:48218 original size:16 final size:16
Alignment explanation
Indices: 48184--48303 Score: 174
Period size: 16 Copynumber: 7.6 Consensus size: 16
48174 CGGGCTCGGG
*
48184 CGGGTTCGGGTA-CTT
1 CGGGTTCGGGTATTTT
48199 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
48215 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
*
48231 CGGGCTT-GGATATTTT
1 CGGG-TTCGGGTATTTT
48247 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
*
48263 CGGGTTCGGGT-TATGT
1 CGGGTTCGGGTAT-TTT
48279 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
48295 CGGGTTCGG
1 CGGGTTCGG
48304 TCTCGGGTAG
Statistics
Matches: 95, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
15 15 0.16
16 77 0.81
17 3 0.03
ACGTcount: A:0.07, C:0.14, G:0.39, T:0.40
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:48318 original size:17 final size:17
Alignment explanation
Indices: 48296--48342 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
48286 GGGTATTTTC
*
48296 GGGTTCGGTCTCGGGTA
1 GGGTTCGGGCTCGGGTA
*
48313 GGGTTCGGGCTCGGGTC
1 GGGTTCGGGCTCGGGTA
*
48330 GGGTTTGGGCTCG
1 GGGTTCGGGCTCG
48343 AGTTTGATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.02, C:0.19, G:0.51, T:0.28
Consensus pattern (17 bp):
GGGTTCGGGCTCGGGTA
Done.