Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008225.1 Hibiscus syriacus cultivar Beakdansim tig00110858_pilon, 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: 1890193
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 10
Found at i:1363763 original size:22 final size:23
Alignment explanation
Indices: 1363737--1363839 Score: 75
Period size: 20 Copynumber: 4.9 Consensus size: 23
1363727 TTTATTTTTC
1363737 ATTTATTATTATTATTAT-TACT
1 ATTTATTATTATTATTATATACT
*
1363759 ATTTA-T-TT-TTATTATACA-T
1 ATTTATTATTATTATTATATACT
* *
1363778 TTTTA-TATTTTTA-TATATA-T
1 ATTTATTATTATTATTATATACT
*
1363798 -TTTTTTATTATTATT-TATACT
1 ATTTATTATTATTATTATATACT
1363819 ATTTATTTATT-TTCATTATAT
1 ATTTA-TTATTATT-ATTATAT
1363840 TTTTTTCTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
19 16 0.25
20 22 0.34
21 6 0.09
22 10 0.15
23 8 0.12
24 3 0.05
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (23 bp):
ATTTATTATTATTATTATATACT
Found at i:1363826 original size:13 final size:12
Alignment explanation
Indices: 1363723--1363828 Score: 50
Period size: 13 Copynumber: 9.1 Consensus size: 12
1363713 TATATATATG
1363723 TATATTTATTT-
1 TATATTTATTTA
1363734 T-TCATTTA-TTA
1 TAT-ATTTATTTA
1363745 T-TA-TTA-TTA
1 TATATTTATTTA
*
1363754 TTACTATTTATTTT
1 -TA-TATTTATTTA
** *
1363768 TATTATACATTTT
1 TA-TATTTATTTA
1363781 TATATTT-TTATA
1 TATATTTATT-TA
*
1363793 TATATTTTTTTA
1 TATATTTATTTA
1363805 T-TA-TTATTTA
1 TATATTTATTTA
1363815 TACTATTTATTTA
1 TA-TATTTATTTA
1363828 T
1 T
1363829 TTTCATTATA
Statistics
Matches: 75, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
9 6 0.08
10 12 0.16
11 12 0.16
12 18 0.24
13 25 0.33
14 2 0.03
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (12 bp):
TATATTTATTTA
Found at i:1363839 original size:42 final size:41
Alignment explanation
Indices: 1363760--1363845 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 41
1363750 ATTATTACTA
* *
1363760 TTTATTTTTATTATACATTTTTATATTTTTATATATATTTT
1 TTTATTATTATTATACATTTTTATATTTTCATATATATTTT
1363801 TTTATTATTATTTATACTATTTATT-TATTTTCAT-TATATTTT
1 TTTATTATTA-TTATAC-ATTT-TTATATTTTCATATATATTTT
1363843 TTT
1 TTT
1363846 CTTTGCTCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
41 9 0.22
42 17 0.43
43 12 0.30
44 2 0.05
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (41 bp):
TTTATTATTATTATACATTTTTATATTTTCATATATATTTT
Found at i:1365681 original size:3 final size:3
Alignment explanation
Indices: 1365673--1365717 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1365663 TCAGGCTGCA
1365673 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1365718 CCATAGATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1378959 original size:2 final size:2
Alignment explanation
Indices: 1378952--1378983 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1378942 AGTACAAGTA
1378952 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1378984 GTATGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1380948 original size:2 final size:2
Alignment explanation
Indices: 1380943--1380979 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1380933 TTTTATGATT
1380943 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1380980 AAATTTAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1384703 original size:31 final size:31
Alignment explanation
Indices: 1384668--1384729 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1384658 GTTTCGGTTT
1384668 GGTCACCCAACTATTTTTTGTTTCAAAATCA
1 GGTCACCCAACTATTTTTTGTTTCAAAATCA
1384699 GGTCACCCAACTATTTTTTGTTTCAAAATCA
1 GGTCACCCAACTATTTTTTGTTTCAAAATCA
1384730 TACCTAACGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.39
Consensus pattern (31 bp):
GGTCACCCAACTATTTTTTGTTTCAAAATCA
Found at i:1385742 original size:12 final size:12
Alignment explanation
Indices: 1385725--1385789 Score: 53
Period size: 12 Copynumber: 5.6 Consensus size: 12
1385715 ACTATACAGT
1385725 ATGAACAATACC
1 ATGAACAATACC
*
1385737 ATGAACAGTA--
1 ATGAACAATACC
* *
1385747 ATGAACAACATC
1 ATGAACAATACC
* * *
1385759 GTGAACAGTATC
1 ATGAACAATACC
*
1385771 ATGAACAACACC
1 ATGAACAATACC
1385783 ATGAACA
1 ATGAACA
1385790 GTGCTGCAGT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
10 8 0.20
12 33 0.80
ACGTcount: A:0.48, C:0.22, G:0.14, T:0.17
Consensus pattern (12 bp):
ATGAACAATACC
Found at i:1385779 original size:24 final size:22
Alignment explanation
Indices: 1385720--1385791 Score: 92
Period size: 22 Copynumber: 3.2 Consensus size: 22
1385710 ACAGTACTAT
*
1385720 ACAGT-ATGAACAATACCATGA
1 ACAGTAATGAACAACACCATGA
* *
1385741 ACAGTAATGAACAACATCGTGA
1 ACAGTAATGAACAACACCATGA
1385763 ACAGTATCATGAACAACACCATGA
1 ACAGTA--ATGAACAACACCATGA
1385787 ACAGT
1 ACAGT
1385792 GCTGCAGTGC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
21 5 0.12
22 19 0.44
24 19 0.44
ACGTcount: A:0.46, C:0.21, G:0.15, T:0.18
Consensus pattern (22 bp):
ACAGTAATGAACAACACCATGA
Found at i:1388434 original size:20 final size:20
Alignment explanation
Indices: 1388402--1388439 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1388392 GTGAATTATT
*
1388402 GTTGTTGTATTTTTTTAATA
1 GTTGTTGTATTTTATTAATA
1388422 GTTGTTAGT-TTTTATTAA
1 GTTGTT-GTATTTTATTAA
1388440 AAATAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.21, C:0.00, G:0.16, T:0.63
Consensus pattern (20 bp):
GTTGTTGTATTTTATTAATA
Found at i:1388963 original size:20 final size:20
Alignment explanation
Indices: 1388934--1388977 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1388924 TCCAATTTCA
1388934 CAACGCGAATCTGTAAATCG
1 CAACGCGAATCTGTAAATCG
* *
1388954 CAACGTGAATTTGTAAATCG
1 CAACGCGAATCTGTAAATCG
1388974 CAAC
1 CAAC
1388978 ACATAAGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (20 bp):
CAACGCGAATCTGTAAATCG
Found at i:1388994 original size:20 final size:20
Alignment explanation
Indices: 1388971--1389037 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
1388961 AATTTGTAAA
1388971 TCGCAACACATAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
**
1388991 TCGCAATGCGAT-AGTCAAAT
1 TCGCAACAC-ATAAGTCAAAT
*
1389011 TCGCAACACAAAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
1389031 TCGCAAC
1 TCGCAAC
1389038 GCGGAATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.03
20 37 0.93
21 2 0.05
ACGTcount: A:0.42, C:0.25, G:0.13, T:0.19
Consensus pattern (20 bp):
TCGCAACACATAAGTCAAAT
Found at i:1389065 original size:19 final size:20
Alignment explanation
Indices: 1389025--1389097 Score: 85
Period size: 19 Copynumber: 3.6 Consensus size: 20
1389015 AACACAAAAG
**
1389025 TCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAAC-TAGAATT
*
1389046 TCAAATTCACAACT-GAATT
1 TCAAATTCGCAACTAGAATT
*
1389065 TCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACTAGAATT
*
1389085 TCGAATTCGCAAC
1 TCAAATTCGCAAC
1389098 ACGAATTTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
19 18 0.39
20 16 0.35
21 12 0.26
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (20 bp):
TCAAATTCGCAACTAGAATT
Found at i:1389104 original size:40 final size:41
Alignment explanation
Indices: 1389005--1389105 Score: 107
Period size: 40 Copynumber: 2.5 Consensus size: 41
1388995 AATGCGATAG
* ** *
1389005 TCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAACACGAATTTCAAATTCGCAACGCAGAATT
* * * *
1389046 TCAAATTCACAAC-TGAATTTCAAATTCGCAAC-TAGATTT
1 TCAAATTCGCAACACGAATTTCAAATTCGCAACGCAGAATT
*
1389085 TCGAATTCGCAACACGAATTT
1 TCAAATTCGCAACACGAATTT
1389106 AATTTCGTAA
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
39 15 0.31
40 21 0.44
41 12 0.25
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.27
Consensus pattern (41 bp):
TCAAATTCGCAACACGAATTTCAAATTCGCAACGCAGAATT
Found at i:1389292 original size:14 final size:15
Alignment explanation
Indices: 1389273--1389310 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1389263 TCCCCATCTC
1389273 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
1389287 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1389303 TAATTTTT
1 TAATTTTT
1389311 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1390101 original size:24 final size:24
Alignment explanation
Indices: 1390050--1390103 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1390040 GTATTCGAAA
*
1390050 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
1390074 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
1390098 TTTGAT
1 TTTGAT
1390104 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:1392831 original size:20 final size:20
Alignment explanation
Indices: 1392806--1392844 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1392796 GCAACGCTTA
1392806 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
*
1392826 TTTCGCGTTGTGAATTTGA
1 TTTCGCGTTGCGAATTTGA
1392845 ACATTGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:1393258 original size:24 final size:24
Alignment explanation
Indices: 1393207--1393259 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1393197 TTTCATATGT
* * *
1393207 AATTGGAGTTTGAATTTCAATTTC
1 AATTTGAGTTTGAATTTCAATATA
*
1393231 AATTTGAGTTTGAATTTTAATATA
1 AATTTGAGTTTGAATTTCAATATA
1393255 AATTT
1 AATTT
1393260 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTCAATATA
Found at i:1393934 original size:13 final size:14
Alignment explanation
Indices: 1393916--1393948 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1393906 TTCGGAAGGC
1393916 ATTTTTT-TACATA
1 ATTTTTTCTACATA
*
1393929 ATTTTTTCTATATA
1 ATTTTTTCTACATA
1393943 ATTTTT
1 ATTTTT
1393949 CAATGATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTTTTTCTACATA
Found at i:1394225 original size:18 final size:18
Alignment explanation
Indices: 1394202--1394237 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1394192 AAGCAAAAGG
1394202 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
1394220 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
1394238 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:1394442 original size:13 final size:13
Alignment explanation
Indices: 1394424--1394461 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
1394414 ATTTACATTT
1394424 TCGCAACGCGAAA
1 TCGCAACGCGAAA
1394437 TCGCAAAC-CGAAA
1 TCGC-AACGCGAAA
1394450 TCGCAACGCGAA
1 TCGCAACGCGAA
1394462 TTTGACTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.13
13 17 0.74
14 3 0.13
ACGTcount: A:0.39, C:0.32, G:0.21, T:0.08
Consensus pattern (13 bp):
TCGCAACGCGAAA
Found at i:1394612 original size:64 final size:63
Alignment explanation
Indices: 1394491--1394615 Score: 200
Period size: 63 Copynumber: 2.0 Consensus size: 63
1394481 ATTTACCTTT
1394491 CAAATCAATTAAACAAGCAAAAAAATAATCTTATTTACATCAAATTAAACAAATCAACTTTTA
1 CAAATCAATTAAACAAGCAAAAAAATAATCTTATTTACATCAAATTAAACAAATCAACTTTTA
*
1394554 CAAATCAATTAAACAAGC-AAAAAATAATTCTTATTTTC-TCATCAATTAAACAAATCAACTTT
1 CAAATCAATTAAACAAGCAAAAAAATAA-TCTTATTTACATCA--AATTAAACAAATCAACTTT
1394616 CAATGTAAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
62 12 0.21
63 27 0.47
64 19 0.33
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.30
Consensus pattern (63 bp):
CAAATCAATTAAACAAGCAAAAAAATAATCTTATTTACATCAAATTAAACAAATCAACTTTTA
Found at i:1395678 original size:4 final size:4
Alignment explanation
Indices: 1395657--1395698 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
1395647 AGGCCGTTGA
* * *
1395657 AAAT AAAT TAAT ACAT AAAT AAGT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1395699 TGCCGAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:1396251 original size:45 final size:44
Alignment explanation
Indices: 1396057--1396253 Score: 115
Period size: 45 Copynumber: 4.6 Consensus size: 44
1396047 GGTGATGGTG
* * *
1396057 GAGAAGAGGCTTGATGATGTGATGGAATATGTGATGGTGGAGGTA
1 GAGAAGAGGCTCGATCAGGTGATGG-ATATGTGATGGTGGAGGTA
* * ** * * *
1396102 GAG-AGAGGCTCTATCAGGTGATGGCTCCG-GGT-GTCGAGCT-
1 GAGAAGAGGCTCGATCAGGTGATGGATATGTGATGGTGGAGGTA
** * * * *
1396142 GTAGAATCGGCTCGATCAGGCG-T--CTATCATGA-GGT-GATGGTG
1 G-AGAAGAGGCTCGATCAGGTGATGGATAT-GTGATGGTGGA-GGTA
* * *
1396184 GAGAAGAGGCTTGATGATGTGATGGAATATGTGATGGTGGAGGTA
1 GAGAAGAGGCTCGATCAGGTGATGG-ATATGTGATGGTGGAGGTA
1396229 GAGAAGAGGCTCGATCAGGTGATGG
1 GAGAAGAGGCTCGATCAGGTGATGG
1396254 CTCCGGGTGT
Statistics
Matches: 108, Mismatches: 31, Indels: 26
0.65 0.19 0.16
Matches are distributed among these distances:
39 2 0.02
40 3 0.03
41 28 0.26
42 17 0.16
43 2 0.02
44 20 0.19
45 34 0.31
46 2 0.02
ACGTcount: A:0.25, C:0.10, G:0.41, T:0.24
Consensus pattern (44 bp):
GAGAAGAGGCTCGATCAGGTGATGGATATGTGATGGTGGAGGTA
Found at i:1397753 original size:20 final size:19
Alignment explanation
Indices: 1397715--1397753 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1397705 TGCGATTTTG
* *
1397715 GTGTTGCGATTTCATTTTC
1 GTGTTGCGATTTAAGTTTC
1397734 GTGTTGCGAATTTAAGTTTC
1 GTGTTGCG-ATTTAAGTTTC
1397754 AGAAACTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.15, C:0.13, G:0.23, T:0.49
Consensus pattern (19 bp):
GTGTTGCGATTTAAGTTTC
Found at i:1398102 original size:21 final size:22
Alignment explanation
Indices: 1398076--1398122 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1398066 GATGGAGATA
1398076 GACGGA-TTCG-CTGGAGATGGG
1 GACGGATTTCGTC-GGAGATGGG
1398097 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
1398119 GACG
1 GACG
1398123 TATGTCGCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 6 0.25
22 17 0.71
23 1 0.04
ACGTcount: A:0.19, C:0.15, G:0.47, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:1398264 original size:20 final size:20
Alignment explanation
Indices: 1398239--1398322 Score: 87
Period size: 20 Copynumber: 4.2 Consensus size: 20
1398229 TGTGTTTCGC
1398239 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* * * *
1398259 GTTGCGAATTTGGCTATCGC
1 GTTGCGAATTTGACTTTTGT
* *
1398279 ATTGCGAATTTGACTTATGT
1 GTTGCGAATTTGACTTTTGT
* * *
1398299 GTTGCGATTTTAACTTCTGT
1 GTTGCGAATTTGACTTTTGT
1398319 GTTG
1 GTTG
1398323 TGATTTACAA
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.17, C:0.13, G:0.25, T:0.45
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:1398327 original size:20 final size:20
Alignment explanation
Indices: 1398280--1398328 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1398270 GGCTATCGCA
* *
1398280 TTGCGAATTTGACTTATGTG
1 TTGCGATTTTAACTTATGTG
*
1398300 TTGCGATTTTAACTTCTGTG
1 TTGCGATTTTAACTTATGTG
*
1398320 TTGTGATTT
1 TTGCGATTT
1398329 ACAAATTCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.16, C:0.10, G:0.22, T:0.51
Consensus pattern (20 bp):
TTGCGATTTTAACTTATGTG
Found at i:1400298 original size:35 final size:35
Alignment explanation
Indices: 1400251--1400336 Score: 109
Period size: 35 Copynumber: 2.5 Consensus size: 35
1400241 AAAACAGTCA
* * *
1400251 TCAATTTCATTCTAAACCCCAATTTCTAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCTAAAATAAT
* * *
1400286 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCTAAAATAAT
*
1400321 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
1400337 ATACTTCAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.41, C:0.20, G:0.01, T:0.38
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCTAAAATAAT
Found at i:1400330 original size:21 final size:21
Alignment explanation
Indices: 1400305--1400347 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1400295 TTCTAAACCC
1400305 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
1400326 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
1400347 T
1 T
1400348 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:1400499 original size:16 final size:18
Alignment explanation
Indices: 1400467--1400500 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1400457 ATATTAAGTA
1400467 TGAATGATTTATATTTTT
1 TGAATGATTTATATTTTT
1400485 TGAAT-ATTT-TATTTTT
1 TGAATGATTTATATTTTT
1400501 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (18 bp):
TGAATGATTTATATTTTT
Found at i:1401169 original size:128 final size:128
Alignment explanation
Indices: 1400962--1401205 Score: 416
Period size: 128 Copynumber: 1.9 Consensus size: 128
1400952 TTTTCTTCTA
* * *
1400962 ATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGATCC
1 ATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGATCC
*
1401027 TGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAT
66 TAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAT
* * * *
1401090 ATTAGGTGGTAACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGATCC
1 ATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGATCC
1401155 TAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
66 TAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
1401206 TATATAAATA
Statistics
Matches: 108, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
128 108 1.00
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.36
Consensus pattern (128 bp):
ATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGATCC
TAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAT
Found at i:1406914 original size:131 final size:130
Alignment explanation
Indices: 1406739--1407055 Score: 340
Period size: 126 Copynumber: 2.5 Consensus size: 130
1406729 GTTGTTCTTA
* * * * **
1406739 AAGGTAGATCATATCTAAAAACGTTGATTCACTCCACTGCTCTTCAGGGAATGTTGAATTGGGTT
1 AAGGTATATCAGATCCAAAAACTTTGATTCACTCCACTGCTCTTCAGGGAA-GTTGAATCAGGTT
* * * * * *
1406804 TGATTTGCTACACTGCTCTTCAGGGAATG-TCAAATTTGAGAAAATG-GATCTTCTTCGCTGCGT
65 TGATTTGCTACACTGCTCTTCA-AGAAAGATAAAATCTGAGAAAA-GAGATCTGCTCCGCTGCGT
1406867 TTC
128 TTC
* * ** *
1406870 AGGGTATATCAGATCCGAAAACTTTGATTCACTCCACTATTCTTCA-GG--G-TGAATCATGTTT
1 AAGGTATATCAGATCCAAAAACTTTGATTCACTCCACTGCTCTTCAGGGAAGTTGAATCAGGTTT
* * *
1406931 GATTTGCTTCACTGCTTTTCAAGAAAGATAAAATCTGAGAAAAGAGATCTGCTCCGCTGTGTTTC
66 GATTTGCTACACTGCTCTTCAAGAAAGATAAAATCTGAGAAAAGAGATCTGCTCCGCTGCGTTTC
** * *
1406996 AAGGTATATTGGATCCAAAAACTTTTATTCGCTCCACTGCTCTTCAGGGAAGATTGAATC
1 AAGGTATATCAGATCCAAAAACTTTGATTCACTCCACTGCTCTTCAGGGAAG-TTGAATC
1407056 TAAAAATTAA
Statistics
Matches: 151, Mismatches: 28, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
125 5 0.03
126 96 0.64
127 3 0.02
129 1 0.01
130 2 0.01
131 44 0.29
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (130 bp):
AAGGTATATCAGATCCAAAAACTTTGATTCACTCCACTGCTCTTCAGGGAAGTTGAATCAGGTTT
GATTTGCTACACTGCTCTTCAAGAAAGATAAAATCTGAGAAAAGAGATCTGCTCCGCTGCGTTTC
Found at i:1407865 original size:16 final size:17
Alignment explanation
Indices: 1407836--1407870 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1407826 GGTCGGAAAG
1407836 TAAAAAAAACCCCAAAA
1 TAAAAAAAACCCCAAAA
*
1407853 TAAAATAAA-CCCAAAA
1 TAAAAAAAACCCCAAAA
1407869 TA
1 TA
1407871 TCTTTTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.69, C:0.20, G:0.00, T:0.11
Consensus pattern (17 bp):
TAAAAAAAACCCCAAAA
Found at i:1408078 original size:16 final size:15
Alignment explanation
Indices: 1408057--1408100 Score: 63
Period size: 14 Copynumber: 2.9 Consensus size: 15
1408047 TCCTTTTGAA
*
1408057 TTTCTCTATTTTATTT
1 TTTCTCTATTTT-TTC
1408073 TTTCTCTA-TTTTTC
1 TTTCTCTATTTTTTC
1408087 TTTCTCTATTTTTT
1 TTTCTCTATTTTTT
1408101 AAAAGTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 10 0.38
15 8 0.31
16 8 0.31
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTCTCTATTTTTTC
Found at i:1408576 original size:3 final size:3
Alignment explanation
Indices: 1408568--1408631 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
1408558 TGCTTGTAAC
1408568 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1408616 ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
1408632 AATGGTTATA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1411189 original size:2 final size:2
Alignment explanation
Indices: 1411182--1411207 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1411172 ACTCTAAATA
1411182 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1411208 CACAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1412052 original size:47 final size:46
Alignment explanation
Indices: 1411946--1412041 Score: 131
Period size: 46 Copynumber: 2.1 Consensus size: 46
1411936 AAACGTTACC
* ** * *
1411946 TAAAACA-TAATTTTTTTATCGAAAATGTTAATATTAGGCGCTACT
1 TAAAACATTATTTTTTTTATAAAAAATGTTAATATTAGACGATACT
1411991 TAAAACATTATTTTTTTTATAAAAAATGTTAATATTAGACGATACCT
1 TAAAACATTATTTTTTTTATAAAAAATGTTAATATTAGACGATA-CT
1412038 TAAA
1 TAAA
1412042 TGTTATTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
45 7 0.16
46 31 0.70
47 6 0.14
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (46 bp):
TAAAACATTATTTTTTTTATAAAAAATGTTAATATTAGACGATACT
Found at i:1413553 original size:14 final size:15
Alignment explanation
Indices: 1413534--1413562 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1413524 TTTGGTTTAG
1413534 TAATTAT-ATTAATT
1 TAATTATAATTAATT
1413548 TAATTATAATTAATT
1 TAATTATAATTAATT
1413563 ATATAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTATAATTAATT
Found at i:1413918 original size:28 final size:28
Alignment explanation
Indices: 1413885--1413976 Score: 166
Period size: 28 Copynumber: 3.3 Consensus size: 28
1413875 TACAAATGGC
*
1413885 CAAAACCCGTTCAGCATACAATCCATTA
1 CAAAACCCGTTCAGCACACAATCCATTA
*
1413913 CAAAACCCGTTCAGCACACAATCTATTA
1 CAAAACCCGTTCAGCACACAATCCATTA
1413941 CAAAACCCGTTCAGCACACAATCCATTA
1 CAAAACCCGTTCAGCACACAATCCATTA
1413969 CAAAACCC
1 CAAAACCC
1413977 ACTACTAGCC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 61 1.00
ACGTcount: A:0.40, C:0.35, G:0.07, T:0.18
Consensus pattern (28 bp):
CAAAACCCGTTCAGCACACAATCCATTA
Found at i:1416829 original size:24 final size:23
Alignment explanation
Indices: 1416775--1416843 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 23
1416765 TGTCCGTTTA
*
1416775 TTTATTGTTCGCGAACGTATTCTT
1 TTTA-TGTTCGCGAACATATTCTT
* * *
1416799 TTAATGTTCGTGAACATTTTCATT
1 TTTATGTTCGCGAACATATTC-TT
**
1416823 TTTATGTTAACGAACATATTC
1 TTTATGTTCGCGAACATATTC
1416844 ATTTAATATT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
23 14 0.40
24 21 0.60
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.48
Consensus pattern (23 bp):
TTTATGTTCGCGAACATATTCTT
Found at i:1417914 original size:2 final size:2
Alignment explanation
Indices: 1417907--1417933 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1417897 TGTCATTAGA
1417907 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 A
1417934 AAGGTTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1418632 original size:33 final size:34
Alignment explanation
Indices: 1418590--1418656 Score: 127
Period size: 33 Copynumber: 2.0 Consensus size: 34
1418580 AGTTGACAAG
1418590 TTGGAAATTTCATCTTGGTTGGTGGCC-AACTTT
1 TTGGAAATTTCATCTTGGTTGGTGGCCAAACTTT
1418623 TTGGAAATTTCATCTTGGTTGGTGGCCAAACTTT
1 TTGGAAATTTCATCTTGGTTGGTGGCCAAACTTT
1418657 GAACATGTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 27 0.82
34 6 0.18
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.42
Consensus pattern (34 bp):
TTGGAAATTTCATCTTGGTTGGTGGCCAAACTTT
Found at i:1426780 original size:31 final size:30
Alignment explanation
Indices: 1426734--1426822 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 30
1426724 TTCGATAATA
*
1426734 TAATAATTATTTTATAGTATTTAAATAAATT
1 TAATAA-TATTTTATAATATTTAAATAAATT
* * *
1426765 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATATTTAAATAAATT
*
1426796 TAATAAGTATTTTATAATTTTTTAAAT
1 TAATAA-TATTTTATAA-TATTTAAAT
1426823 TTTATTGAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
30 1 0.02
31 39 0.81
32 8 0.17
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAATATTTAAATAAATT
Found at i:1426791 original size:19 final size:20
Alignment explanation
Indices: 1426767--1426816 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1426757 AATAAATTTA
*
1426767 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
1426786 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
1426807 TT-ATAATTTT
1 TTAATAATTTT
1426817 TTAAATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:1426812 original size:11 final size:10
Alignment explanation
Indices: 1426736--1426827 Score: 52
Period size: 11 Copynumber: 9.2 Consensus size: 10
1426726 CGATAATATA
1426736 ATAATTATTTT
1 ATAA-TATTTT
*
1426747 ATAGTA-TTT
1 ATAATATTTT
*
1426756 A-AATAAATTT
1 ATAAT-ATTTT
1426766 ATTAATAATTTT
1 A-TAAT-ATTTT
*
1426778 ATAATCTTTT
1 ATAATATTTT
*
1426788 AATAA-ATTTA
1 -ATAATATTTT
1426798 ATAAGTATTTT
1 ATAA-TATTTT
1426809 ATAAT-TTTT
1 ATAATATTTT
1426818 -TAA-ATTTT
1 ATAATATTTT
1426826 AT
1 AT
1426828 TGAAAAAAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 20
0.71 0.08 0.22
Matches are distributed among these distances:
8 9 0.14
9 14 0.22
10 14 0.22
11 19 0.29
12 9 0.14
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (10 bp):
ATAATATTTT
Found at i:1428164 original size:30 final size:30
Alignment explanation
Indices: 1428128--1428230 Score: 188
Period size: 30 Copynumber: 3.4 Consensus size: 30
1428118 CCCGAAGGAC
1428128 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1428158 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1428188 CTATCCAGAGGTCATAAAGATCCTCGATAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1428218 CTATCCATAGGTC
1 CTATCCAGAGGTC
1428231 CCGAAGAACC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 71 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1428247 original size:60 final size:61
Alignment explanation
Indices: 1428128--1428255 Score: 186
Period size: 60 Copynumber: 2.1 Consensus size: 61
1428118 CCCGAAGGAC
* * * *
1428128 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGT-AA
1 CTATCCAGAGGTCATAAAGATCCTCGATAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
* * *
1428188 CTATCCAGAGGTCATAAAGATCCTCGATAACTATCCATAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCAGAGGTCATAAAGATCCTCGATAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
1428249 CTATCCA
1 CTATCCA
1428256 TATGTTCCTT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
60 51 0.85
61 9 0.15
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (61 bp):
CTATCCAGAGGTCATAAAGATCCTCGATAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
Found at i:1428915 original size:7 final size:7
Alignment explanation
Indices: 1428903--1428931 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1428893 ATATAGTTCA
1428903 ATATCAC
1 ATATCAC
1428910 ATATCAC
1 ATATCAC
1428917 ATATCAC
1 ATATCAC
1428924 ATAT-AC
1 ATATCAC
1428930 AT
1 AT
1428932 GTAATCATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (7 bp):
ATATCAC
Found at i:1429400 original size:64 final size:64
Alignment explanation
Indices: 1429248--1429404 Score: 151
Period size: 64 Copynumber: 2.5 Consensus size: 64
1429238 CAATGAAAGT
* * * ** *
1429248 ATGCATCGATGCACTA-CTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATCACTGGG
1 ATGCATCGATGCACTACCTG-TGCATCGATGCATAAAATGCATTCGATGTTCTATTATAAAAGAG
* * * * *
1429312 ATACATCGATGCA-TGCCTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATTTTAAAAG
1 ATGCATCGATGCACTACC-TGTGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATAAAAG
1429375 AG
63 AG
1429377 -TGCATCGATGCACTACCTGTGCATCGAT
1 ATGCATCGATGCACTACCTGTGCATCGAT
1429405 ACACCTTCAA
Statistics
Matches: 74, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
63 1 0.01
64 58 0.78
65 15 0.20
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTGTGCATCGATGCATAAAATGCATTCGATGTTCTATTATAAAAGAG
Found at i:1429952 original size:3 final size:3
Alignment explanation
Indices: 1429944--1429979 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
1429934 TCTCGTACAT
* *
1429944 GAA GAA GAA GAA GAA GAA GAA GAA GAT GAT GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1429980 AATATCTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.61, C:0.00, G:0.33, T:0.06
Consensus pattern (3 bp):
GAA
Found at i:1432585 original size:30 final size:30
Alignment explanation
Indices: 1432515--1432616 Score: 170
Period size: 30 Copynumber: 3.4 Consensus size: 30
1432505 CCCGAAGGAC
1432515 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1432545 CTAT-CAGAGGTCATAAAGATCCTTGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1432574 CTATCCAGAGGTCATAAAGATCCTCGATAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1432604 CTATCCATAGGTC
1 CTATCCAGAGGTC
1432617 CCGAAGAACC
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
29 28 0.42
30 39 0.58
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1432661 original size:30 final size:31
Alignment explanation
Indices: 1432602--1432693 Score: 89
Period size: 30 Copynumber: 3.0 Consensus size: 31
1432592 GATCCTCGAT
* *
1432602 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
**
1432633 AACTATCCATATGT-CCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* * * *
1432663 TACTGTCCATATATCTCGAA-AGACATAGGTA
1 AACTATCCATATGTCCCGAAGA-ACATAGGTA
1432694 GTTCTTTGAC
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
30 25 0.51
31 24 0.49
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:1450413 original size:172 final size:167
Alignment explanation
Indices: 1450134--1450472 Score: 585
Period size: 172 Copynumber: 2.0 Consensus size: 167
1450124 GAGAGAGCTT
1450134 CTTCGTCCAGTGGCTTCTTCATTTCCCTCTCTCCTCCTCAGTGTTAGACGTCTCCTCTTCCTCTG
1 CTTCGTCCAGTGGCTTCTTCATTTCCCTCTCTCCTCCTCAGTGTTAGACGTCTCCTCTTCCTCTG
1450199 CGCGGCCCTCAACTTATCCTTCGGTTGTAGCTTCGAAAGCCAACT-CTCGCTGAATCCATTTTCT
66 CGCGGCCCTCAACTTATCCTTCGGTTGTAGCTTCGAAAGCCAACTCCTCGCTGAATCCATTTTCT
1450263 CTCATCAAAATCAAATCTCACGAAAAT-AAAATTCCC
131 CTCATCAAAATCAAATCTCACGAAAATAAAAATTCCC
1450299 CTTCGTCCAGATTGGCTTCTTCATTTCCCTCTC-CTCTCCACTTCCAGTGTTAGACGTCTCCTCA
1 CTTCGTCCAG--TGGCTTCTTCATTTCCCTCTCTC-CT-C-C-T-CAGTGTTAGACGTCTCCTC-
1450363 TTCCTCTGCGCGGCCCTCAACTTATCCTTCGGTTGTAGCTTCGAAAGCCAACTCCTCGCTGAATC
58 TTCCTCTGCGCGGCCCTCAACTTATCCTTCGGTTGTAGCTTCGAAAGCCAACTCCTCGCTGAATC
1450428 CATTTTCTCTCATCAAAATCAAATCTCACGAAAATAAAAATTCCC
123 CATTTTCTCTCATCAAAATCAAATCTCACGAAAATAAAAATTCCC
1450473 TCGCATTCTG
Statistics
Matches: 164, Mismatches: 0, Indels: 11
0.94 0.00 0.06
Matches are distributed among these distances:
165 10 0.06
166 1 0.01
167 23 0.14
168 1 0.01
169 1 0.01
170 1 0.01
171 19 0.12
172 53 0.32
173 46 0.28
174 9 0.05
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.32
Consensus pattern (167 bp):
CTTCGTCCAGTGGCTTCTTCATTTCCCTCTCTCCTCCTCAGTGTTAGACGTCTCCTCTTCCTCTG
CGCGGCCCTCAACTTATCCTTCGGTTGTAGCTTCGAAAGCCAACTCCTCGCTGAATCCATTTTCT
CTCATCAAAATCAAATCTCACGAAAATAAAAATTCCC
Found at i:1452173 original size:64 final size:63
Alignment explanation
Indices: 1452066--1452205 Score: 165
Period size: 64 Copynumber: 2.2 Consensus size: 63
1452056 ACATTCAATA
* * * * *
1452066 TGTACCGATGCACTCTTTAAAGAAGAAACATCGAATGCCATGAGTGAATCGATACACAGTTAG
1 TGTATCGATGCACTCTTGAAAGAAGAAACATCGAATGCAATGAGTGAACCGATACACAGGTAG
* * * *
1452129 TGTATCGATGCACTCCTTGAAA-TAGAAAACATCGAATGCAATGAGTGTACCGATGCATAGGTAG
1 TGTATCGATGCACT-CTTGAAAGAAG-AAACATCGAATGCAATGAGTGAACCGATACACAGGTAG
*
1452193 TGTATCGTTGCAC
1 TGTATCGATGCAC
1452206 ACGTTAAGGG
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
63 15 0.23
64 50 0.77
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.26
Consensus pattern (63 bp):
TGTATCGATGCACTCTTGAAAGAAGAAACATCGAATGCAATGAGTGAACCGATACACAGGTAG
Found at i:1452960 original size:31 final size:31
Alignment explanation
Indices: 1452921--1453076 Score: 201
Period size: 31 Copynumber: 5.0 Consensus size: 31
1452911 AGAGTCGAGG
*
1452921 GTTTACCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1452952 CTTTACCTATGTTCTTCGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1452983 GTTTACCTATGTTCTTCGGGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1453014 GATTACCTA-GATTCTTCGGGATATATGGACT
1 GTTTACCTATG-TTCTTCGGGACATATGGACT
*
1453045 GATTACCTA-GATTCTTCGGGATC-TATGGACT
1 GTTTACCTATG-TTCTTCGGGA-CATATGGACT
1453076 G
1 G
1453077 GTCTTTCGGG
Statistics
Matches: 113, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
30 1 0.01
31 112 0.99
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1457200 original size:15 final size:15
Alignment explanation
Indices: 1457180--1457211 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1457170 TAGCAGAAAC
1457180 GAAAAACATTGTACT
1 GAAAAACATTGTACT
1457195 GAAAAACATTGTACT
1 GAAAAACATTGTACT
1457210 GA
1 GA
1457212 TTTTTCCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (15 bp):
GAAAAACATTGTACT
Found at i:1460073 original size:45 final size:45
Alignment explanation
Indices: 1459969--1460109 Score: 155
Period size: 45 Copynumber: 3.1 Consensus size: 45
1459959 ATTTATTTTC
* * *
1459969 ATTTTTCGAATAAATGCTTGCGAACTAGATATCA--A-GATAGGTTT
1 ATTTTTCGAA-CAA-GCATGCGAACTAGATATCATGAGGTTAGGTTT
*
1460013 ATTTTTCGAACAAGCATGCGAACTAGATATCATGCGGTTAGGTTT
1 ATTTTTCGAACAAGCATGCGAACTAGATATCATGAGGTTAGGTTT
* *
1460058 A-TTTTCTGAATAAGCATGCGAATTAGATATCATGAGGTTAGGATTT
1 ATTTTTC-GAACAAGCATGCGAACTAGATATCATGAGGTTAGG-TTT
*
1460104 CTTTTT
1 ATTTTT
1460110 GTGGATAATA
Statistics
Matches: 83, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
42 18 0.22
43 2 0.02
44 15 0.18
45 41 0.49
46 3 0.04
47 4 0.05
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (45 bp):
ATTTTTCGAACAAGCATGCGAACTAGATATCATGAGGTTAGGTTT
Found at i:1469924 original size:25 final size:25
Alignment explanation
Indices: 1469870--1469925 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
1469860 AGAAGAAATA
**
1469870 AAAAAGAAAAAATGAGAAAATGAGG
1 AAAAAGAAAAAATGAGAAAACAAGG
1469895 AAAAAGAAAAAATG-GAAAAACAATGG
1 AAAAAGAAAAAATGAG-AAAACAA-GG
1469921 AAAAA
1 AAAAA
1469926 AAATGAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 1 0.04
25 19 0.70
26 7 0.26
ACGTcount: A:0.71, C:0.02, G:0.20, T:0.07
Consensus pattern (25 bp):
AAAAAGAAAAAATGAGAAAACAAGG
Found at i:1469930 original size:11 final size:11
Alignment explanation
Indices: 1469901--1469935 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
1469891 GAGGAAAAAG
1469901 AAAAAATGGAA
1 AAAAAATGGAA
*
1469912 AAACAATGGAA
1 AAAAAATGGAA
1469923 AAAAAAT-GAA
1 AAAAAATGGAA
1469933 AAA
1 AAA
1469936 TGAAAAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 6 0.27
11 16 0.73
ACGTcount: A:0.74, C:0.03, G:0.14, T:0.09
Consensus pattern (11 bp):
AAAAAATGGAA
Found at i:1469942 original size:8 final size:8
Alignment explanation
Indices: 1469865--1469957 Score: 54
Period size: 7 Copynumber: 11.2 Consensus size: 8
1469855 CTTGAAGAAG
1469865 AAAT-AAA
1 AAATGAAA
1469872 AAA-GAAA
1 AAATGAAA
*
1469879 AAATGAGA
1 AAATGAAA
1469887 AAATGAGGAA
1 AAATGA--AA
1469897 AAA-GAAA
1 AAATGAAA
1469904 AAATGGAAAA
1 AAAT-G-AAA
1469914 ACAATGGAAAAA
1 A-AAT-G--AAA
1469926 AAATG-AA
1 AAATGAAA
1469933 AAATGAAA
1 AAATGAAA
1469941 AAA-GAAA
1 AAATGAAA
1469948 TAAAT-AAA
1 -AAATGAAA
1469956 AA
1 AA
1469958 GGAGGGTTCA
Statistics
Matches: 72, Mismatches: 2, Indels: 24
0.73 0.02 0.24
Matches are distributed among these distances:
7 27 0.38
8 20 0.28
9 3 0.04
10 9 0.12
11 8 0.11
12 5 0.07
ACGTcount: A:0.74, C:0.01, G:0.15, T:0.10
Consensus pattern (8 bp):
AAATGAAA
Found at i:1471290 original size:37 final size:36
Alignment explanation
Indices: 1471229--1471338 Score: 130
Period size: 36 Copynumber: 3.0 Consensus size: 36
1471219 CCAAAACAGG
* * * * *
1471229 TCAATCTTAAGTCATCATGAAAGAGCAGTGAAGCAAT
1 TCAA-CTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
*
1471266 TCAAACTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
1 TC-AACTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
* *
1471303 TCATCTTAAGCCTTCATGAAAGAGTAGTGAAGCAAA
1 TCAACTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
1471339 CTCGTTTGTT
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
36 31 0.49
37 30 0.48
38 2 0.03
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (36 bp):
TCAACTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
Found at i:1471318 original size:36 final size:37
Alignment explanation
Indices: 1471229--1471338 Score: 132
Period size: 37 Copynumber: 3.0 Consensus size: 37
1471219 CCAAAACAGG
* * * * * *
1471229 TCAATCTTAAGTCATCATGAAAGAGCAGTGAAGCAAT
1 TCAAACTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
*
1471266 TCAAACTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
1 TCAAACTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
* *
1471303 TC-ATCTTAAGCCTTCATGAAAGAGTAGTGAAGCAAA
1 TCAAACTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
1471339 CTCGTTTGTT
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
36 31 0.49
37 32 0.51
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (37 bp):
TCAAACTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
Found at i:1471649 original size:51 final size:51
Alignment explanation
Indices: 1471341--1471804 Score: 484
Period size: 51 Copynumber: 8.9 Consensus size: 51
1471331 GAAGCAAACT
*
1471341 CGTTTGTTGAAGATCGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
1471392 AGTTCGTTGAAGATTGAGTCCTATA--CTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * *
1471441 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACA
1 CGTTTGTTGAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
1471492 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
1471543 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * *
1471594 CGTTTATTGAAGATCGAGTCTTATACTCTCTGAAGGAATAGCGAGCGGACC
1 CGTTTGTTGAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * * * *
1471645 CGTTTTTTGAAGATTGTTCGAGTCTTATACTCCCTAAACGAATAGGGAGCAGACA
1 CGTTTGTTGAAGA----TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
** * * * *
1471700 CGTTTACTGAAGATTATTCGAGTCTTATACTCCCTGAATGAATAGGGAGCAGACA
1 CGTTTGTTGAAG---A-TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
** * *
1471755 CGTTTACTGAAGATTGTTCGAGTCTTATACTC-CATGAAAGAATAGGGAGC
1 CGTTTGTTGAAGA----TCGAGTCCTATACTCTC-TGAAGGAATAGGGAGC
1471805 AGACCCGCCA
Statistics
Matches: 375, Mismatches: 25, Indels: 22
0.89 0.06 0.05
Matches are distributed among these distances:
49 48 0.13
51 202 0.54
52 1 0.00
54 1 0.00
55 122 0.33
58 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (51 bp):
CGTTTGTTGAAGATCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
Found at i:1471824 original size:110 final size:109
Alignment explanation
Indices: 1471578--1471808 Score: 301
Period size: 110 Copynumber: 2.1 Consensus size: 109
1471568 CTCTCTGAAG
* * *
1471578 GAATAGGGAGCGGACACGTTTATTGAAG---A-TCGAGTCTTATACTCTCTGAAGGAATAGCGAG
1 GAATAGGGAGCAGACACGATTA-TGAAGATTATTCGAGTCTTATACTCCCTGAAGGAATAGCGAG
* * ** *
1471639 CGGACCCGTTTTTTGAAGATTGTTCGAGTCTTATACTCCCTAAAC
65 CAGACACGTTTACTGAAGATTGTTCGAGTCTTATACTCCATAAAC
* * *
1471684 GAATAGGGAGCAGACACGTTTACTGAAGATTATTCGAGTCTTATACTCCCTGAATGAATAGGGAG
1 GAATAGGGAGCAGACACGATTA-TGAAGATTATTCGAGTCTTATACTCCCTGAAGGAATAGCGAG
1471749 CAGACACGTTTACTGAAGATTGTTCGAGTCTTATACTCCATGAAA-
65 CAGACACGTTTACTGAAGATTGTTCGAGTCTTATACTCCAT-AAAC
1471794 GAATAGGGAGCAGAC
1 GAATAGGGAGCAGAC
1471809 CCGCCATTTG
Statistics
Matches: 110, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
106 26 0.24
109 1 0.01
110 80 0.73
111 3 0.03
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (109 bp):
GAATAGGGAGCAGACACGATTATGAAGATTATTCGAGTCTTATACTCCCTGAAGGAATAGCGAGC
AGACACGTTTACTGAAGATTGTTCGAGTCTTATACTCCATAAAC
Found at i:1472219 original size:15 final size:15
Alignment explanation
Indices: 1472199--1472229 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1472189 ATCAGAAACA
1472199 AAAAACATTGTACTG
1 AAAAACATTGTACTG
1472214 AAAAACATTGTACTG
1 AAAAACATTGTACTG
1472229 A
1 A
1472230 TTTTTCCGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (15 bp):
AAAAACATTGTACTG
Found at i:1475233 original size:31 final size:31
Alignment explanation
Indices: 1475194--1475349 Score: 208
Period size: 31 Copynumber: 5.0 Consensus size: 31
1475184 AGAGTCGAGG
1475194 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1475225 CTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
**
1475256 GTTTACCTATGTTCTTCGGGACATATATACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1475287 GTTTACTTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1475318 GATTATCTA-GATTCTTCAGGATC-TATGGACT
1 GTTTACCTATG-TTCTTCGGGA-CATATGGACT
1475349 G
1 G
1475350 GTCTTTCGGG
Statistics
Matches: 110, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
30 1 0.01
31 109 0.99
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1476072 original size:21 final size:21
Alignment explanation
Indices: 1476046--1476086 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1476036 CCGAAATTAC
* *
1476046 TGTAGCATTGTATCGATACAT
1 TGTAGCAGTGCATCGATACAT
1476067 TGTAGCAGTGCATCGATACA
1 TGTAGCAGTGCATCGATACA
1476087 CTGTTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (21 bp):
TGTAGCAGTGCATCGATACAT
Found at i:1476133 original size:20 final size:20
Alignment explanation
Indices: 1476104--1476143 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1476094 TTATTGTTCA
*
1476104 CGGTACTATTTACACATTAT
1 CGGTACTATTCACACATTAT
* *
1476124 CGGTATTATTCATACATTAT
1 CGGTACTATTCACACATTAT
1476144 ATTACTATTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.42
Consensus pattern (20 bp):
CGGTACTATTCACACATTAT
Found at i:1480424 original size:106 final size:105
Alignment explanation
Indices: 1480234--1480973 Score: 1239
Period size: 105 Copynumber: 7.0 Consensus size: 105
1480224 GTTGTGAAGT
* * *
1480234 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGT
1 TGAAATTGAGAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* * *
1480299 CTGGAGTCCAATATTCTTCGCTGTGAAGTTGAAATTGACTC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
1480340 TGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
1480405 CTTGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
1480446 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1480511 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
1480552 AG-AATTCGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATT-GAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
1480616 CTGGAGTTCAATATCCTTCATTGTGAAGTTGAAATTGGCTC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
1480657 TGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
1480722 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
1480762 TGAATTTGAGAAATGTTTGTTGACAACTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1480827 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
1480867 TGAATTTGAGAAATGTTTGTTGACAACTAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
1480932 TAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
1480972 TG
1 TG
1480974 GGTAAAACCT
Statistics
Matches: 606, Mismatches: 25, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
105 398 0.66
106 208 0.34
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
Found at i:1491243 original size:10 final size:10
Alignment explanation
Indices: 1491218--1491251 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1491208 AACGTTAGTA
*
1491218 AAATAGAAAT
1 AAATAAAAAT
*
1491228 AGATAAAAAT
1 AAATAAAAAT
1491238 AAATAAAAAT
1 AAATAAAAAT
1491248 AAAT
1 AAAT
1491252 GGTAAATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:1492486 original size:13 final size:13
Alignment explanation
Indices: 1492461--1492506 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
1492451 ATAAATATTT
1492461 AAAA-AAACAAAA
1 AAAATAAACAAAA
*
1492473 AAAATAAACGAAA
1 AAAATAAACAAAA
* *
1492486 ACAATAAATAAAA
1 AAAATAAACAAAA
1492499 AAAATAAA
1 AAAATAAA
1492507 GAAACGTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 4 0.14
13 24 0.86
ACGTcount: A:0.83, C:0.07, G:0.02, T:0.09
Consensus pattern (13 bp):
AAAATAAACAAAA
Found at i:1492570 original size:12 final size:13
Alignment explanation
Indices: 1492553--1492609 Score: 50
Period size: 12 Copynumber: 4.6 Consensus size: 13
1492543 GTAAAAAAAG
1492553 ATAATAATA-ATA
1 ATAATAATATATA
*
1492565 ATAATAGT-TATA
1 ATAATAATATATA
*
1492577 TTAAT-ATATATA
1 ATAATAATATATA
*
1492589 A-AAAAATATATA
1 ATAATAATATATA
1492601 TATAATAAT
1 -ATAATAAT
1492610 TTGTAAGCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
11 3 0.09
12 25 0.74
13 1 0.03
14 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (13 bp):
ATAATAATATATA
Found at i:1502802 original size:57 final size:57
Alignment explanation
Indices: 1502735--1502865 Score: 235
Period size: 57 Copynumber: 2.3 Consensus size: 57
1502725 ATGGAAATTT
* *
1502735 TCGCAACGCGAATTTCGTTTTCGCAACATTAATTACCGATATTGGTAAACACAACTA
1 TCGCAACGCGAATTTCGTTTTCGCAACACTAATTACCGATATAGGTAAACACAACTA
1502792 TCGCAACGCGAATTTCGTTTTCGCAACACTAATTACCGATATAGGTAAACACAACTA
1 TCGCAACGCGAATTTCGTTTTCGCAACACTAATTACCGATATAGGTAAACACAACTA
*
1502849 TCGCAACGCAAATTTCG
1 TCGCAACGCGAATTTCG
1502866 CAAATCGAAT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 71 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (57 bp):
TCGCAACGCGAATTTCGTTTTCGCAACACTAATTACCGATATAGGTAAACACAACTA
Found at i:1519635 original size:749 final size:754
Alignment explanation
Indices: 1517860--1520083 Score: 3942
Period size: 749 Copynumber: 2.9 Consensus size: 754
1517850 AATAAAAGAT
1517860 TATTGGAATGCATATTTTACTAAATTGTCCTTATGATATTTTTTTAACAAGTTGAATTCCAAATA
1 TATTGGAATGCATATTTTACTAAATTGTCCTTATGATATTTTTTTAACAAGTTGAATTCCAAATA
1517925 TTTAAATGAAAATATTTATATAAAAATTCATAGAAAATATATTATTGTATTATTTTCAATTTATA
66 TTTAAATGAAAATATTTATATAAAAATTCATAGAAAATATATTATTGTATTATTTTCAATTTATA
* *
1517990 CATTTTTTATTAAATTTAAATTCATAAAATTTATATAATTTTTTACAATAATTAAAAGATAAATG
131 TATTTTTTATTAAATTTAAATTCATAAAATTTATAT-ATTTTTTACAATATTTAAAAGATAAATG
1518055 GGCATATTAAAAGAGTAAATATACCATATATTATTTTAAACTTAATTAATATTTAAAAAGTTATA
195 GGCATATTAAAAGAGTAAATATACCATATATTATTTTAAACTTAATTAATATTTAAAAAGTTATA
1518120 ATAATTTGTGAAAATAAATTTTTGAAATAAATATGTGAAACAAAAGATTATAGCTTTTGAAATAA
260 ATAATTTGTGAAAATAAATTTTTGAAATAAATATGTGAAACAAAAGATTATAGCTTTTGAAATAA
*
1518185 AAGTAAGGATATTTTTGAAACAAATCTTTTGTTTCAAAGGCATTTTAATCCAAGTTGAAGGGAAA
325 AAGTAAGGATATTTTTGAAACAAATCTTTTGTTTCAAGGGCATTTTAATCCAAGTTGAAGGGAAA
* * *
1518250 CAAAAAATACCTAAGAAAAACA-GGGATTAACATTCCCGGCTATTGGGAATATTTTATTACTCCC
390 CAAAAAATACCTAAGAAAAACAGGGGATTAGCATTCCCGGGTGTTGGGAATATTTTATTACTCCC
*
1518314 TATTGGGAATATTTCTCATCCAAACGTGGGAATTTGAATCTGGAAAGAAAAATTCCTACCAAGAA
455 TATTGGGAATATTTCTCATCCAAACATGGGAATTTGAATCTGGAAAGAAAAATTCCTACCAAGAA
*
1518379 TCTTGAATTCCATGATCCAATC-ACCCATTAGATTCGATGAAGCTGACATGATTAATTCATAAGC
520 TCTTGAATTCCATGATCCAATCAACCC-TTAGAGTCGATGAAGCTGACATGATTAATTCATAAGC
* *
1518443 TACCTGACCAAAACACGCATTAATAACGTGCCATAGAAAATTGCTGAAGTTTTGCAAAATCTTAG
584 TACCTGACCAAAACACACATTAATCACGTGCCATAGAAAATTGCTGAAGTTTTGCAAAATCTTAG
1518508 GCTAATAATTTTGTTTTGGGTTGAGGGTTGAGGGTTTTTGATATTCTACATATGTGGGTCTTTCT
649 GCTAATAATTTTG-TTT--GTT-AGGGTTGAGGGTTTTTGATATTCTACATA--T--G-------
1518573 CAATAATTTTGGGGGATTTAAAAAAAAATCCTTCATGTATTAGGGTTATGTCAGAAAATA
699 ---TAATTTTGGGGGATTT-AAAAAAAATCCTTCATGTATTAGGGTTATGTCAGAAAATA
1518633 TATTGGAATGCATATTTTACTAAATTGTCCTTATGATATTTTTTTAACAAGTTGAATTCCAAATA
1 TATTGGAATGCATATTTTACTAAATTGTCCTTATGATATTTTTTTAACAAGTTGAATTCCAAATA
1518698 TTTAAATGAAAATATTTATATAAAAATTCATAGAAAATATATTATTGTATTATTTTCAATTTATA
66 TTTAAATGAAAATATTTATATAAAAATTCATAGAAAATATATTATTGTATTATTTTCAATTTATA
1518763 TATTTTTTATTAAATTTAAATTCATAAAATTTATATATTTTTTACAATATTTAAAAGATAAATGG
131 TATTTTTTATTAAATTTAAATTCATAAAATTTATATATTTTTTACAATATTTAAAAGATAAATGG
*
1518828 GCATATTAAAAGAATAAATATACCATATATTATTTTAAACTTAATTAATATTTAAAAAGTTATAA
196 GCATATTAAAAGAGTAAATATACCATATATTATTTTAAACTTAATTAATATTTAAAAAGTTATAA
1518893 TAATTTGTGAAAATAAATTTTTGAAATAAATATGTGAAACAAAAGATTATAGCTTTTGAAATAAA
261 TAATTTGTGAAAATAAATTTTTGAAATAAATATGTGAAACAAAAGATTATAGCTTTTGAAATAAA
1518958 AGTAAGGATATTTTTGAAACAAATCTTTTGTTTCAAGGGCATTTTAATCCAAGTTGAAGGGAAAC
326 AGTAAGGATATTTTTGAAACAAATCTTTTGTTTCAAGGGCATTTTAATCCAAGTTGAAGGGAAAC
* *
1519023 AAAAAAAACCTAAGAAAAATAGGGGATTAGCATTCCCGGGTGTTGGGAATATTTTATTACTCCCT
391 AAAAAATACCTAAGAAAAACAGGGGATTAGCATTCCCGGGTGTTGGGAATATTTTATTACTCCCT
* *
1519088 ATTGGGAATATTTCTCATCCAAACATGGGAATTTGAATCTGAAAAGAAAGATTCCTACCAAGAAT
456 ATTGGGAATATTTCTCATCCAAACATGGGAATTTGAATCTGGAAAGAAAAATTCCTACCAAGAAT
1519153 CTTGAATTCCATGATCCAATCAACCCTTAGAGTCGATGAAGCTGACATGATTAATTCATAAGCTA
521 CTTGAATTCCATGATCCAATCAACCCTTAGAGTCGATGAAGCTGACATGATTAATTCATAAGCTA
* *
1519218 CCTGACCAAAACACACATCAATCACGTGCCATAGAAAATTGCTGAAGTTTCGCAAAATCTTAGGC
586 CCTGACCAAAACACACATTAATCACGTGCCATAGAAAATTGCTGAAGTTTTGCAAAATCTTAGGC
1519283 TAATAATTTTG-TT-TT-GGGTTGAGGGTTTTTGATATTCTACATATGT-ATTTTGGGGGATTT-
651 TAATAATTTTGTTTGTTAGGGTTGAGGGTTTTTGATATTCTACATATGTAATTTTGGGGGATTTA
1519343 AAAAAAATCCTTCATGTATTAGGGTTATGTCAGAAAATA
716 AAAAAAATCCTTCATGTATTAGGGTTATGTCAGAAAATA
1519382 TATTGGAATGCATATTTTACTAAATTGTCCTTATGATA-TTTTTTAACAAGTTGAATTCCAAATA
1 TATTGGAATGCATATTTTACTAAATTGTCCTTATGATATTTTTTTAACAAGTTGAATTCCAAATA
1519446 TTTAAATGAAAATATTTATATAAAAATTCATAGAAAATATATTATTGTATTATTTTCAATTTATA
66 TTTAAATGAAAATATTTATATAAAAATTCATAGAAAATATATTATTGTATTATTTTCAATTTATA
1519511 TATTTTTTATTAAATTTAAATTCATAAAATTTATATATTTTTTTACAATATTTAAAAGATAAATG
131 TATTTTTTATTAAATTTAAATTCATAAAATTTATATA-TTTTTTACAATATTTAAAAGATAAATG
1519576 GGCATATTAAAAGAGTAAATATACCATATATTATTTTAAACTTAATTAATATTTAAAAAGTTATA
195 GGCATATTAAAAGAGTAAATATACCATATATTATTTTAAACTTAATTAATATTTAAAAAGTTATA
1519641 ATAATTTGTGAAAATAAATTTTTGAAATAAATATGTGAAACAAAAGATTATAGCTTTTGAAATAA
260 ATAATTTGTGAAAATAAATTTTTGAAATAAATATGTGAAACAAAAGATTATAGCTTTTGAAATAA
*
1519706 AAGTAAGGATATTTTTGAAATAAATCTTTTGTTTCAAGGGCATTTTAATCCAAGTTGAAGGGAAA
325 AAGTAAGGATATTTTTGAAACAAATCTTTTGTTTCAAGGGCATTTTAATCCAAGTTGAAGGGAAA
1519771 CAAAAAATACCTAAGAAAAACAGGGGATTAGCATTCCCGGGTGTTGGGAATATTTTATTACTCCC
390 CAAAAAATACCTAAGAAAAACAGGGGATTAGCATTCCCGGGTGTTGGGAATATTTTATTACTCCC
* * *
1519836 TATTGGGAATATTCCTCATCCAAACATGGGAATTTGAATCTGGAAAGAAAAATTCCTACAAAAAA
455 TATTGGGAATATTTCTCATCCAAACATGGGAATTTGAATCTGGAAAGAAAAATTCCTACCAAGAA
* * *
1519901 TCTTGAATTTCATGATCCAATCACCCCTTAGAGTCGATGAAGCTGACAGGATTAATTCATAAGCT
520 TCTTGAATTCCATGATCCAATCAACCCTTAGAGTCGATGAAGCTGACATGATTAATTCATAAGCT
*
1519966 ACCTGACCAAAACACACATTAATCACGTGCCATAGAAAATTGCTGAAGTTTTTCAAAATCTTAGG
585 ACCTGACCAAAACACACATTAATCACGTGCCATAGAAAATTGCTGAAGTTTTGCAAAATCTTAGG
1520031 CTAATAATTTTGTTTTGGGTTAGGGTTGAGGGTTTTTGATATTCTACATATGT
650 CTAATAATTTTG-TTT--GTTAGGGTTGAGGGTTTTTGATATTCTACATATGT
1520084 GGGTCTTTCT
Statistics
Matches: 1410, Mismatches: 32, Indels: 36
0.95 0.02 0.02
Matches are distributed among these distances:
748 128 0.09
749 556 0.39
751 16 0.01
752 1 0.00
754 2 0.00
755 31 0.02
762 1 0.00
764 1 0.00
766 28 0.02
768 2 0.00
771 2 0.00
772 240 0.17
773 398 0.28
774 4 0.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.37
Consensus pattern (754 bp):
TATTGGAATGCATATTTTACTAAATTGTCCTTATGATATTTTTTTAACAAGTTGAATTCCAAATA
TTTAAATGAAAATATTTATATAAAAATTCATAGAAAATATATTATTGTATTATTTTCAATTTATA
TATTTTTTATTAAATTTAAATTCATAAAATTTATATATTTTTTACAATATTTAAAAGATAAATGG
GCATATTAAAAGAGTAAATATACCATATATTATTTTAAACTTAATTAATATTTAAAAAGTTATAA
TAATTTGTGAAAATAAATTTTTGAAATAAATATGTGAAACAAAAGATTATAGCTTTTGAAATAAA
AGTAAGGATATTTTTGAAACAAATCTTTTGTTTCAAGGGCATTTTAATCCAAGTTGAAGGGAAAC
AAAAAATACCTAAGAAAAACAGGGGATTAGCATTCCCGGGTGTTGGGAATATTTTATTACTCCCT
ATTGGGAATATTTCTCATCCAAACATGGGAATTTGAATCTGGAAAGAAAAATTCCTACCAAGAAT
CTTGAATTCCATGATCCAATCAACCCTTAGAGTCGATGAAGCTGACATGATTAATTCATAAGCTA
CCTGACCAAAACACACATTAATCACGTGCCATAGAAAATTGCTGAAGTTTTGCAAAATCTTAGGC
TAATAATTTTGTTTGTTAGGGTTGAGGGTTTTTGATATTCTACATATGTAATTTTGGGGGATTTA
AAAAAAATCCTTCATGTATTAGGGTTATGTCAGAAAATA
Found at i:1522097 original size:17 final size:16
Alignment explanation
Indices: 1522055--1522115 Score: 55
Period size: 15 Copynumber: 4.2 Consensus size: 16
1522045 ATAAATATAC
1522055 AAAT-CATATATTTAT
1 AAATACATATATTTAT
1522070 AAATACA-ATATTTAT
1 AAATACATATATTTAT
* *
1522085 AAA-A-TTA-ATATAT
1 AAATACATATATTTAT
1522098 AAA-A-ATATATTTAT
1 AAATACATATATTTAT
1522112 AAAT
1 AAAT
1522116 TGGGTAAACT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 11 0.29
14 10 0.26
15 15 0.39
16 2 0.05
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATACATATATTTAT
Found at i:1522242 original size:31 final size:30
Alignment explanation
Indices: 1522183--1522256 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
1522173 TTTAAAAAAA
* *
1522183 ATTAAGTTTTGATCATTTACATTTTTGATTT
1 ATTAAATTTTGATCATTTACATTATTGA-TT
*
1522214 ATTAAATTTTGATCACTTT-TATTATTGATT
1 ATTAAATTTTGATCA-TTTACATTATTGATT
* *
1522244 GTTACATTTTGAT
1 ATTAAATTTTGAT
1522257 AACTGAATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 13 0.35
31 21 0.57
32 3 0.08
ACGTcount: A:0.27, C:0.07, G:0.09, T:0.57
Consensus pattern (30 bp):
ATTAAATTTTGATCATTTACATTATTGATT
Found at i:1524975 original size:21 final size:21
Alignment explanation
Indices: 1524949--1524998 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1524939 GGGTTTACGC
1524949 GGTCCTTC-GGACATATACAGA
1 GGTCCTTCGGGACA-ATACAGA
*
1524970 GGTCCTTCGGGACAATACATA
1 GGTCCTTCGGGACAATACAGA
1524991 GGTCCTTC
1 GGTCCTTC
1524999 AGGATAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (21 bp):
GGTCCTTCGGGACAATACAGA
Found at i:1525873 original size:21 final size:21
Alignment explanation
Indices: 1525847--1525893 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1525837 AGCAGTACTA
1525847 TAGCAGTGCATCGATACACTG
1 TAGCAGTGCATCGATACACTG
*
1525868 TAGCAGTGCATCGGTACACTG
1 TAGCAGTGCATCGATACACTG
1525889 TAGCA
1 TAGCA
1525894 TTGTTCATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (21 bp):
TAGCAGTGCATCGATACACTG
Found at i:1526675 original size:36 final size:34
Alignment explanation
Indices: 1526618--1526731 Score: 174
Period size: 35 Copynumber: 3.2 Consensus size: 34
1526608 CTCAGTCGAT
1526618 TTGAACCTATATAAGGAATTACCAGTTTGACTGAG
1 TTGAACCTATATAAGGAATTACCAGTTTGA-TGAG
* *
1526653 TTGAACCTATCATAAGGAATTACCAGTTCGATCAG
1 TTGAACCTAT-ATAAGGAATTACCAGTTTGATGAG
1526688 TCTGAACCTATATAAGGAATTACCAGTTTGATCGAG
1 T-TGAACCTATATAAGGAATTACCAGTTTGAT-GAG
1526724 TTGAACCT
1 TTGAACCT
1526732 GTAGAAACTT
Statistics
Matches: 72, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
35 41 0.57
36 31 0.43
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (34 bp):
TTGAACCTATATAAGGAATTACCAGTTTGATGAG
Found at i:1528509 original size:16 final size:13
Alignment explanation
Indices: 1528475--1528516 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 13
1528465 TTTACTTTTT
1528475 TGGTCAAAGTCAA
1 TGGTCAAAGTCAA
1528488 TGGTCAACAGTCAGA
1 TGGTCAA-AGTCA-A
1528503 CTGGTCAAAGTCAA
1 -TGGTCAAAGTCAA
1528517 CGATTAACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.27
14 6 0.23
15 6 0.23
16 7 0.27
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (13 bp):
TGGTCAAAGTCAA
Found at i:1528525 original size:29 final size:30
Alignment explanation
Indices: 1528475--1528531 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
1528465 TTTACTTTTT
* *
1528475 TGGTCAAAGTCAATGGTCAACA-GTCAGAC
1 TGGTCAAAGTCAACGATCAACAGGTCAGAC
*
1528504 TGGTCAAAGTCAACGATTAACAGGTCAG
1 TGGTCAAAGTCAACGATCAACAGGTCAG
1528532 GTCAAAGTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (30 bp):
TGGTCAAAGTCAACGATCAACAGGTCAGAC
Found at i:1531102 original size:35 final size:35
Alignment explanation
Indices: 1531051--1531143 Score: 125
Period size: 35 Copynumber: 2.7 Consensus size: 35
1531041 AACACAATCA
* *
1531051 TCAATTACATTATAAACCCCAAAATCCAAAATGCT
1 TCAATTACATTCTAAACCCCAAAATCCAAAATACT
* *
1531086 TCAATTACATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAAATCCAAAATACT
*
1531121 TCAATTACATGCCT-AACCCCAAA
1 TCAATTACAT-TCTAAACCCCAAA
1531144 TTCATAATCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
35 49 0.96
36 2 0.04
ACGTcount: A:0.43, C:0.28, G:0.02, T:0.27
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAAATCCAAAATACT
Found at i:1531486 original size:150 final size:148
Alignment explanation
Indices: 1531295--1531589 Score: 511
Period size: 150 Copynumber: 2.0 Consensus size: 148
1531285 AAATACTCAA
* * *
1531295 TTCAGTTTATAAAATAGTTGACTCGAAATTTTTTTGATTTGAGTTTATAAAATTTAAATCAAATC
1 TTCAGTTTATAAAATAGCTGACTCAAAATTTTTCTGATTTGAGTTTATAAAATTTAAATCAAATC
*
1531360 GAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATCATATATTATAAT
66 GAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTAT-A-ATACTATAAT
1531425 ATTATTTGATTCTAATTCAG
129 ATTATTTGATTCTAATTCAG
*
1531445 TTCAGTTTATAAAATAGCTGACTCAAAATGTTTTCT-ATTTGAGTTTATAAAATTTAAATCAAGT
1 TTCAGTTTATAAAATAGCTGACTCAAAAT-TTTTCTGATTTGAGTTTATAAAATTTAAATCAAAT
1531509 CGAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATA
65 CGAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATA
1531574 TTATTTGATTCTAATT
130 TTATTTGATTCTAATT
1531590 TAAATAGTTT
Statistics
Matches: 139, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
148 26 0.19
149 1 0.01
150 107 0.77
151 5 0.04
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.47
Consensus pattern (148 bp):
TTCAGTTTATAAAATAGCTGACTCAAAATTTTTCTGATTTGAGTTTATAAAATTTAAATCAAATC
GAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATAT
TATTTGATTCTAATTCAG
Found at i:1532123 original size:36 final size:34
Alignment explanation
Indices: 1532074--1532177 Score: 109
Period size: 35 Copynumber: 3.0 Consensus size: 34
1532064 TTTTGAGAAT
* * *
1532074 GTATTATGAATTTGGGGTTGGGTATGTAATTGAA
1 GTATTATGAATTTGAGGTTGAGAATGTAATTGAA
*
1532108 GTATTATTGGAATTTGAGGTTTAGAATGTAATTGAA
1 GTATTA-T-GAATTTGAGGTTGAGAATGTAATTGAA
* * * *
1532144 TTATTTTAAAATTTGAGGTTTAGAATGTAATTGA
1 GTATTAT-GAATTTGAGGTTGAGAATGTAATTGA
1532178 TGAAAAGTTG
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
34 6 0.10
35 27 0.45
36 27 0.45
ACGTcount: A:0.32, C:0.00, G:0.25, T:0.43
Consensus pattern (34 bp):
GTATTATGAATTTGAGGTTGAGAATGTAATTGAA
Found at i:1532163 original size:35 final size:36
Alignment explanation
Indices: 1532097--1532177 Score: 128
Period size: 35 Copynumber: 2.3 Consensus size: 36
1532087 GGGGTTGGGT
**
1532097 ATGTAATTGAAGTATTATTGGAATTTGAGGTTTAGA
1 ATGTAATTGAAGTATTATTAAAATTTGAGGTTTAGA
*
1532133 ATGTAATTGAATTATT-TTAAAATTTGAGGTTTAGA
1 ATGTAATTGAAGTATTATTAAAATTTGAGGTTTAGA
1532168 ATGTAATTGA
1 ATGTAATTGA
1532178 TGAAAAGTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 27 0.64
36 15 0.36
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.43
Consensus pattern (36 bp):
ATGTAATTGAAGTATTATTAAAATTTGAGGTTTAGA
Found at i:1532512 original size:3 final size:3
Alignment explanation
Indices: 1532504--1532555 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
1532494 TTTCGTCCCG
1532504 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1532552 TTA T
1 TTA T
1532556 GTTGTTTTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1533300 original size:13 final size:13
Alignment explanation
Indices: 1533263--1533302 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
1533253 TCGATATTGA
1533263 AAAATAAATA-TT
1 AAAATAAATATTT
*
1533275 AAAATAATTTATTT
1 AAAATAA-ATATTT
1533289 AAAATAAATATTT
1 AAAATAAATATTT
1533302 A
1 A
1533303 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:1534542 original size:3 final size:3
Alignment explanation
Indices: 1534534--1534608 Score: 123
Period size: 3 Copynumber: 25.0 Consensus size: 3
1534524 TTAATATATT
* *
1534534 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1534582 TAA TAA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1534609 ATCAATATGG
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1535253 original size:116 final size:114
Alignment explanation
Indices: 1534924--1535377 Score: 551
Period size: 113 Copynumber: 4.0 Consensus size: 114
1534914 AGAATTATGC
* ** * ** *
1534924 AAAAAGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTT-CTTC-AGATGACGAGTTCTTCTCA
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA-GATGAGTTCTTCTCA
* * * *
1534987 TTATGAACTCT-ACCTGGCAATGTTAATCCATCAAATGATGAATTTAAAT
65 TTATGAACTCTCATCTGGAAAAGCTAATCCATCAAATGATGAATTTAAAT
* *
1535036 AAAAGGTAGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * **
1535101 TATGAACTTTC-TCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGC
66 TATGAACTCTCATCTGGAAAAGCTAATCCATCAAATGATGAATTTAAAT
* * * * *
1535149 AAAAGATTGAACAAATTCTCCTCATTATGAATTTCTTTTTCTTTCTTCAGATGACGAGTTCTTCT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCT
* * *
1535214 CATTATGAACTCTCAT-TGGCAATGTTAATCCATCAAATGATGAATTTAAAT
63 CATTATGAACTCTCATCTGGAAAAGCTAATCCATCAAATGATGAATTTAAAT
*
1535265 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
1535330 TATGAACT-TCCTCTGGAAAAGCTGATCCATCAAATGATGGATTTAAAT
66 TATGAACTCTCATCTGGAAAAGCTAATCCATCAAATGATGAATTTAAAT
1535378 CTTTGCTAAG
Statistics
Matches: 287, Mismatches: 47, Indels: 15
0.82 0.13 0.04
Matches are distributed among these distances:
112 37 0.13
113 152 0.53
114 1 0.00
116 96 0.33
117 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (114 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTCTCATCTGGAAAAGCTAATCCATCAAATGATGAATTTAAAT
Found at i:1536176 original size:83 final size:83
Alignment explanation
Indices: 1536081--1536712 Score: 983
Period size: 83 Copynumber: 7.7 Consensus size: 83
1536071 GTAGTTCCTA
1536081 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTCCAA
1536146 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* * * *
1536164 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGATATTG-GCAAATTCATCTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCCTCCA
* *
1536228 AATTCAATAATTGGTT-TA
65 AATTCAATGATTGGTTCTG
*
1536246 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCACCCTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTCCAA
1536311 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* * * *
1536329 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGATATTG-GCAAATTCATCTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCCTCCA
* * *
1536393 AATTCAATAATTAGTT-TA
65 AATTCAATGATTGGTTCTG
*
1536411 CCAAACCAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTCCAA
1536476 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* * *
1536494 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAACACATTCCT-CT-CA
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTCCA
* *
1536556 AATTCAATGATTGGTTTTA
65 AATTCAATGATTGGTTCTG
1536575 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTCCAA
1536640 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
1536658 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGTACATT
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
1536713 GCATTTATTC
Statistics
Matches: 497, Mismatches: 41, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
80 2 0.00
81 75 0.15
82 147 0.30
83 265 0.53
84 8 0.02
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTCCAA
ATTCAATGATTGGTTCTG
Found at i:1536351 original size:165 final size:165
Alignment explanation
Indices: 1536079--1536699 Score: 1099
Period size: 165 Copynumber: 3.8 Consensus size: 165
1536069 CTGTAGTTCC
1536079 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTCC
1536144 AAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGAT
66 AAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGAT
1536208 ATTGGCAAATTCATCTTCTAAATTCAATAATTGGTT
130 ATTGGCAAATTCATCTTCTAAATTCAATAATTGGTT
*
1536244 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCACCCTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTCC
1536309 AAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGAT
66 AAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGAT
*
1536373 ATTGGCAAATTCATCTTCTAAATTCAATAATTAGTT
130 ATTGGCAAATTCATCTTCTAAATTCAATAATTGGTT
*
1536409 TACCAAACCAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTCC
*
1536474 AAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTA
66 AAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGATA
* * * *
1536539 -TGAACACATTCCTC-TC-AAATTCAATGATTGGTTT
131 TTG-GCAAATTCATCTTCTAAATTCAATAATTGG-TT
1536573 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTCC
1536638 AAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
66 AAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
1536700 CTATGAGTAC
Statistics
Matches: 442, Mismatches: 11, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
163 13 0.03
164 132 0.30
165 295 0.67
166 2 0.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (165 bp):
TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCCTCC
AAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGATA
TTGGCAAATTCATCTTCTAAATTCAATAATTGGTT
Found at i:1537435 original size:16 final size:16
Alignment explanation
Indices: 1537400--1537436 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1537390 GAATTTTTGA
*
1537400 AAATAAATTGAATTTC
1 AAATAAATTGAACTTC
*
1537416 AAATAAATTGAACTTG
1 AAATAAATTGAACTTC
1537432 AAATA
1 AAATA
1537437 GATAGAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.32
Consensus pattern (16 bp):
AAATAAATTGAACTTC
Found at i:1537770 original size:7 final size:7
Alignment explanation
Indices: 1537758--1537838 Score: 76
Period size: 7 Copynumber: 11.1 Consensus size: 7
1537748 TGACCTCCCC
1537758 TTTTTCT
1 TTTTTCT
1537765 TTTTTCT
1 TTTTTCT
1537772 TTTTCTCTT
1 TTTT-TC-T
1537781 TTTTTCT
1 TTTTTCT
1537788 TTTTTCT
1 TTTTTCT
1537795 CTTTTT-T
1 -TTTTTCT
*
1537802 CTTTTCTT
1 TTTTTC-T
*
1537810 TTTTTCC
1 TTTTTCT
*
1537817 CTTTTCT
1 TTTTTCT
1537824 TTCTTT-T
1 TT-TTTCT
1537831 TTTTTCT
1 TTTTTCT
1537838 T
1 T
1537839 CAAGCATAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
6 7 0.11
7 31 0.51
8 18 0.30
9 5 0.08
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTCT
Found at i:1537775 original size:8 final size:8
Alignment explanation
Indices: 1537758--1537833 Score: 77
Period size: 8 Copynumber: 9.6 Consensus size: 8
1537748 TGACCTCCCC
1537758 TTTTTC-T
1 TTTTTCTT
1537765 TTTTTCTT
1 TTTTTCTT
*
1537773 TTTCTCTT
1 TTTTTCTT
1537781 TTTTTC-T
1 TTTTTCTT
1537788 TTTTTCTCT
1 TTTTTCT-T
1537797 TTTTTCTT
1 TTTTTCTT
*
1537805 TTCTT-TT
1 TTTTTCTT
**
1537812 TTTCCCTT
1 TTTTTCTT
1537820 TTCTTTCTT
1 TT-TTTCTT
1537829 TTTTT
1 TTTTT
1537834 TTCTTCAAGC
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
7 17 0.30
8 25 0.45
9 14 0.25
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTCTT
Found at i:1537807 original size:31 final size:31
Alignment explanation
Indices: 1537758--1537832 Score: 100
Period size: 31 Copynumber: 2.4 Consensus size: 31
1537748 TGACCTCCCC
*
1537758 TTTTTCTTTTTTCTTTTTCTCTTTTTT-TCTT
1 TTTTTCTTTTTTCTTTTTCT-TTTTTTCCCTT
1537789 TTTTCTCTTTTTTC-TTTTCTTTTTTTCCCTT
1 TTTT-TCTTTTTTCTTTTTCTTTTTTTCCCTT
1537820 TTCTTTCTTTTTT
1 TT-TTTCTTTTTT
1537833 TTTCTTCAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
30 6 0.15
31 23 0.57
32 11 0.28
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (31 bp):
TTTTTCTTTTTTCTTTTTCTTTTTTTCCCTT
Found at i:1537835 original size:23 final size:24
Alignment explanation
Indices: 1537759--1537833 Score: 84
Period size: 23 Copynumber: 3.2 Consensus size: 24
1537749 GACCTCCCCT
1537759 TTTTCTTTTTTCT-TTTTCTCTTT
1 TTTTCTTTTTTCTCTTTTCTCTTT
*
1537782 TTTTCTTTTTTCTCTTTTTTC-TT
1 TTTTCTTTTTTCTCTTTTCTCTTT
* *
1537805 TTCT-TTTTTTCCCTTTTCTTTCTTT
1 TTTTCTTTTTTCTCTTTTC--TCTTT
1537830 TTTT
1 TTTT
1537834 TTCTTCAAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
22 12 0.28
23 18 0.42
24 8 0.19
25 5 0.12
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (24 bp):
TTTTCTTTTTTCTCTTTTCTCTTT
Found at i:1537835 original size:29 final size:28
Alignment explanation
Indices: 1537759--1537838 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 28
1537749 GACCTCCCCT
**
1537759 TTTTCTTTTTTCTTTTTCTCTTTTTTTCTT
1 TTTTCTTTTTT-TTTTT-TCTTTTTTTCCC
*
1537789 TTTTCTCTTTTTTCTTTTCTTTTTTTCCC
1 TTTTCT-TTTTTTTTTTTCTTTTTTTCCC
1537818 TTTTCTTTCTTTTTTTTTCTT
1 TTTTCTTT-TTTTTTTTTCTT
1537839 CAAGCATAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
28 2 0.05
29 27 0.61
30 10 0.23
31 5 0.11
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (28 bp):
TTTTCTTTTTTTTTTTTCTTTTTTTCCC
Found at i:1549246 original size:13 final size:13
Alignment explanation
Indices: 1549209--1549248 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
1549199 TCGATATTGA
1549209 AAAATAAATA-TT
1 AAAATAAATATTT
*
1549221 AAAATAATTTATTT
1 AAAATAA-ATATTT
1549235 AAAATAAATATTT
1 AAAATAAATATTT
1549248 A
1 A
1549249 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:1552450 original size:15 final size:15
Alignment explanation
Indices: 1552432--1552461 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1552422 TCTAAAGTTT
*
1552432 AAAAAAGAGAAAAAA
1 AAAAAAAAGAAAAAA
1552447 AAAAAAAAGAAAAAA
1 AAAAAAAAGAAAAAA
1552462 GGTTGTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAAAA
Found at i:1553884 original size:131 final size:131
Alignment explanation
Indices: 1553615--1553972 Score: 491
Period size: 131 Copynumber: 2.7 Consensus size: 131
1553605 GAGAATAGTA
* * * * *
1553615 ATATCTTTTCATTTCGGTTGGAGTAATAAATGATTGCTTTAAGGCACGAGATGTCATTTTATTCT
1 ATATCTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGTATGAGAGGTCA-TTTATTCT
* * * * * * * * * *
1553680 CAATTGGAAATAATTCGATATTATCATTTTCTCTCAAATTAATATTGATTTTTAAGATGTAATAG
65 CGATTGGAAATAATTAGATATTATCGTTTTCACTCAAATCAATAATGAATTTTAAGACGGAATAA
1553745 TG
130 TG
* *
1553747 ATATCTCTTCATTTCGATTGGAGCAATAAATGACTGCTTTAAGGTATGAGAGGTCATTTATTCTC
1 ATATCTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGTATGAGAGGTCATTTATTCTC
* **
1553812 GATTGGAAATCATTAGATATTATCGTTTTCACTTGAATCAATAATGAATTTTAAGACGGAATAAT
66 GATTGGAAATAATTAGATATTATCGTTTTCACTCAAATCAATAATGAATTTTAAGACGGAATAAT
1553877 G
131 G
* * *
1553878 ATATCTCTTCATTTCGATTGGAGTAATAAACGATTGTTTTAATGTATGAGAGGTCATTTATTCTC
1 ATATCTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGTATGAGAGGTCATTTATTCTC
*
1553943 GATTGGAAATAATTAGATATCATCGTTTTC
66 GATTGGAAATAATTAGATATTATCGTTTTC
1553973 TCTCTTAAAA
Statistics
Matches: 199, Mismatches: 27, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
131 150 0.75
132 49 0.25
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.41
Consensus pattern (131 bp):
ATATCTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGTATGAGAGGTCATTTATTCTC
GATTGGAAATAATTAGATATTATCGTTTTCACTCAAATCAATAATGAATTTTAAGACGGAATAAT
G
Found at i:1554142 original size:159 final size:159
Alignment explanation
Indices: 1553844--1554142 Score: 345
Period size: 159 Copynumber: 1.9 Consensus size: 159
1553834 TCGTTTTCAC
* * * *
1553844 TTGAATCAATAATGAATTTTAAGACGGAATAATGATATCTCTTCATTTCGATTGGAGTAATAAAC
1 TTGAATCAATAATGAACTTTAAGACGGAATAATAATATCTCTTCATTTCGATTAGAGTAAGAAAC
* * * * * *
1553909 GATTGTTTTAATGTATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATCATCGTTTTCT
66 GATTGCTTTAAGGTATGAGAGATCATTTATTCTCGATAGGAAATAATTAAATATCATCATTTTCT
**
1553974 CTCTTAAAATTATTTTGGGTGTTGTTATT
131 CTCAAAAAATTATTTTGGGTGTTGTTATT
* * * * * *
1554003 TTGAATTAATAATGAACTTT-AGAATGGAATATTAATATTTCTTTATTTCGATTAGAGTAAGAAT
1 TTGAATCAATAATGAACTTTAAG-ACGGAATAATAATATCTCTTCATTTCGATTAGAGTAAGAAA
* *
1554067 CGATTGCTTTAAGGTATGCA-AGATCGATTT-TTTTCGATAGGAAATAATTAAATATTATCATGT
65 CGATTGCTTTAAGGTATG-AGAGATC-ATTTATTCTCGATAGGAAATAATTAAATATCATCAT-T
*
1554130 TTC-GTCAAAAAAT
127 TTCTCTCAAAAAAT
1554143 CCAAAGAATA
Statistics
Matches: 115, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
158 2 0.02
159 104 0.90
160 9 0.08
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (159 bp):
TTGAATCAATAATGAACTTTAAGACGGAATAATAATATCTCTTCATTTCGATTAGAGTAAGAAAC
GATTGCTTTAAGGTATGAGAGATCATTTATTCTCGATAGGAAATAATTAAATATCATCATTTTCT
CTCAAAAAATTATTTTGGGTGTTGTTATT
Found at i:1554764 original size:130 final size:130
Alignment explanation
Indices: 1554586--1554846 Score: 468
Period size: 130 Copynumber: 2.0 Consensus size: 130
1554576 GAGTTCTTAT
**
1554586 GATATTAGGTAATTTGCTCATTTTAATTTGAACAGAGAGCCGTGACCTATGATTTATGGTAGAAT
1 GATATTAGGTAATTTGCTCATTTTAATTTGAACAGAGAGCCGCAACCTATGATTTATGGTAGAAT
* *
1554651 TACATATAATTAATGTAGTCTGATTTAAAAGAATTTCAAAAAGTTTGAGAAAAGAAGAAGTAGTA
66 TACATATAATTAATGTAGTCTGATCTAAAAGAATTTCAAAAAGTTTGAGAAAAGAAGAAGCAGTA
*
1554716 GATATTAGGTAATTTGCTCATTTTGATTTGAACAGAGAGCCGCAACCTATGATTTATGGTAGAAT
1 GATATTAGGTAATTTGCTCATTTTAATTTGAACAGAGAGCCGCAACCTATGATTTATGGTAGAAT
*
1554781 TACATATAATTAATGTAGTCTGATCTAAAAGAATTTCAAAAAGTTTGAGAAAAGAAGTAGCAGTA
66 TACATATAATTAATGTAGTCTGATCTAAAAGAATTTCAAAAAGTTTGAGAAAAGAAGAAGCAGTA
1554846 G
1 G
1554847 TTCTCTCCCT
Statistics
Matches: 125, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
130 125 1.00
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.33
Consensus pattern (130 bp):
GATATTAGGTAATTTGCTCATTTTAATTTGAACAGAGAGCCGCAACCTATGATTTATGGTAGAAT
TACATATAATTAATGTAGTCTGATCTAAAAGAATTTCAAAAAGTTTGAGAAAAGAAGAAGCAGTA
Found at i:1556225 original size:22 final size:22
Alignment explanation
Indices: 1556193--1556237 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1556183 GATGTATGCT
1556193 ACCCATATATTTTTTAATCTAA
1 ACCCATATATTTTTTAATCTAA
*
1556215 ACCCATCTATTTTTTAATCTAA
1 ACCCATATATTTTTTAATCTAA
1556237 A
1 A
1556238 GTAGCATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.20, G:0.00, T:0.44
Consensus pattern (22 bp):
ACCCATATATTTTTTAATCTAA
Found at i:1557546 original size:41 final size:43
Alignment explanation
Indices: 1557488--1557593 Score: 128
Period size: 43 Copynumber: 2.5 Consensus size: 43
1557478 TGGGGCTCTC
* *
1557488 ATTTTTTCATCTTTATAATT-AGGTTCTTAA-CTT-TTAAATCTT
1 ATTTTTT-ATCTTTATAATTGAGG-TCTTAATATTATTAAATCTA
* *
1557530 ATTTTTTACCTTTATAATTGAGGTCTTAATATTATTCAATCTA
1 ATTTTTTATCTTTATAATTGAGGTCTTAATATTATTAAATCTA
*
1557573 ACTTTTTATCTTTATAATTGA
1 ATTTTTTATCTTTATAATTGA
1557594 AATCTCTAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
41 17 0.31
42 12 0.22
43 26 0.47
ACGTcount: A:0.28, C:0.11, G:0.06, T:0.55
Consensus pattern (43 bp):
ATTTTTTATCTTTATAATTGAGGTCTTAATATTATTAAATCTA
Found at i:1557586 original size:43 final size:40
Alignment explanation
Indices: 1557498--1557763 Score: 166
Period size: 41 Copynumber: 6.3 Consensus size: 40
1557488 ATTTTTTCAT
* * *
1557498 CTTTATAATT-AGGTTCTTAACTTTTAAATCTTATTTTTTAC
1 CTTTATAATTGAGG-TCTTAATTTTTCAATC-TACTTTTTAC
*
1557539 CTTTATAATTGAGGTCTTAATATTATTCAATCTAACTTTTTAT
1 CTTTATAATTGAGGTCTTAAT-TT-TTCAATCT-ACTTTTTAC
** *
1557582 CTTTATAATTGAAATCTCTAATTTTTCAATC-CCTTTTTTAC
1 CTTTATAATTGAGGTCT-TAATTTTTCAATCTAC-TTTTTAC
** * * *
1557623 CTTTATAATTGATGCCCCTAATTTTGT-AATAT-CATTTTTAA
1 CTTTATAATTGA-GGTCTTAATTTT-TCAATCTAC-TTTTTAC
* * *
1557664 CTTTACAATTGAGGCTTTTAAGTTTTTTCAATTTCACTTTTTAC
1 CTTTATAATTGAGG-TCTTAA--TTTTTCAATCT-ACTTTTTAC
* * *
1557708 CTTT-TCAATTAAGGAC-TAAGTTTTTTCAATCTCAATTTTTAC
1 CTTTAT-AATTGAGGTCTTAA--TTTTTCAATCT-ACTTTTTAC
1557750 CTTTATAATTGAGG
1 CTTTATAATTGAGG
1557764 CCTCTAAGAA
Statistics
Matches: 179, Mismatches: 29, Indels: 33
0.74 0.12 0.14
Matches are distributed among these distances:
40 2 0.01
41 65 0.36
42 51 0.28
43 39 0.22
44 21 0.12
45 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.51
Consensus pattern (40 bp):
CTTTATAATTGAGGTCTTAATTTTTCAATCTACTTTTTAC
Found at i:1557628 original size:41 final size:43
Alignment explanation
Indices: 1557531--1557634 Score: 126
Period size: 43 Copynumber: 2.5 Consensus size: 43
1557521 TTAAATCTTA
**
1557531 TTTTTTACCTTTATAATTGAGGTCTTAATATTATTCAATCTAAC
1 TTTTTTACCTTTATAATTGAAATCTTAATATTATTCAATC-AAC
* *
1557575 -TTTTTATCTTTATAATTGAAATCTCTAAT-TT-TTCAATC-CC
1 TTTTTTACCTTTATAATTGAAATCT-TAATATTATTCAATCAAC
1557615 TTTTTTACCTTTATAATTGA
1 TTTTTTACCTTTATAATTGA
1557635 TGCCCCTAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
40 1 0.02
41 18 0.34
42 7 0.13
43 23 0.43
44 4 0.08
ACGTcount: A:0.28, C:0.14, G:0.05, T:0.53
Consensus pattern (43 bp):
TTTTTTACCTTTATAATTGAAATCTTAATATTATTCAATCAAC
Found at i:1557841 original size:43 final size:42
Alignment explanation
Indices: 1557618--1557867 Score: 161
Period size: 42 Copynumber: 5.9 Consensus size: 42
1557608 CAATCCCTTT
* * * *
1557618 TTTACCTTTATAATTGATGCCCCTAA-TTTTGT-AATATCATT
1 TTTACCTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCA-A
* * *** * *
1557659 TTTAACTTTACAATTGAGGCTTTTAAGTTTTTTCAATTTCACTT
1 TTTACCTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCA--A
* *
1557703 TTTACCTTT-TCAATTAAGG--ACTAAGTTTTTTCAATCTCAA
1 TTTACCTTTAT-AATTGAGGCCCCTAAGTTTTTTCAATCTCAA
* ** *
1557743 TTTTTACCTTTATAATTGAGGCCTCTAAGAATTTTCGATCTCAA
1 --TTTACCTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCAA
** *
1557787 TTATAATTTTATAATTGAGGCCCCT-ATTTTTTTCAATCTCAA
1 TT-TACCTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCAA
* * * *
1557829 TTTCCACCTTTATAATTAAGGCCTCTAACTTTTTACAAT
1 TTT--ACCTTTATAATTGAGGCCCCTAAGTTTTTTCAAT
1557868 TTCATAAAAT
Statistics
Matches: 163, Mismatches: 33, Indels: 23
0.74 0.15 0.11
Matches are distributed among these distances:
41 21 0.13
42 55 0.34
43 43 0.26
44 44 0.27
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.47
Consensus pattern (42 bp):
TTTACCTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCAA
Found at i:1558703 original size:31 final size:32
Alignment explanation
Indices: 1558659--1558722 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
1558649 ATTCTTTAAA
*
1558659 ATGATGAAATTATATATAAT-TTTTTTAAAAC
1 ATGATGAAATTATATATAATCTTTATTAAAAC
*
1558690 ATGAT-AAACTTATATTTAATCTTTATTAAAAC
1 ATGATGAAA-TTATATATAATCTTTATTAAAAC
1558722 A
1 A
1558723 ATATTATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 3 0.10
31 15 0.52
32 11 0.38
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (32 bp):
ATGATGAAATTATATATAATCTTTATTAAAAC
Found at i:1561212 original size:30 final size:30
Alignment explanation
Indices: 1561188--1561254 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
1561178 TAACTTCTCT
1561188 TATGTATGTATGTAAATGACTAACTATATG
1 TATGTATGTATGTAAATGACTAACTATATG
* *
1561218 TATGTATGTATGTAAATGACTTATTATATG
1 TATGTATGTATGTAAATGACTAACTATATG
*
1561248 TGTGTAT
1 TATGTAT
1561255 AGGAAGAGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.45
Consensus pattern (30 bp):
TATGTATGTATGTAAATGACTAACTATATG
Found at i:1570168 original size:21 final size:21
Alignment explanation
Indices: 1570119--1570197 Score: 110
Period size: 21 Copynumber: 3.9 Consensus size: 21
1570109 GAGTCGAGGG
* *
1570119 TCTACGCGGTCCTTCGGGACA
1 TCTACGTGGTCATTCGGGACA
1570140 --TA-GTGGTCATTCGGGACA
1 TCTACGTGGTCATTCGGGACA
1570158 TCTACGTGGTCATTCGGGACA
1 TCTACGTGGTCATTCGGGACA
*
1570179 TCTACGTGGTCCTTCGGGA
1 TCTACGTGGTCATTCGGGA
1570198 TAAATTCTAC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
18 14 0.27
19 2 0.04
20 2 0.04
21 34 0.65
ACGTcount: A:0.16, C:0.25, G:0.30, T:0.28
Consensus pattern (21 bp):
TCTACGTGGTCATTCGGGACA
Found at i:1570174 original size:39 final size:41
Alignment explanation
Indices: 1570119--1570197 Score: 108
Period size: 39 Copynumber: 2.0 Consensus size: 41
1570109 GAGTCGAGGG
*
1570119 TCTACGCGGTCCTTCGGGACA-TA-GTGGTCATTCGGGACA
1 TCTACGCGGTCATTCGGGACACTACGTGGTCATTCGGGACA
* *
1570158 TCTACGTGGTCATTCGGGACATCTACGTGGTCCTTCGGGA
1 TCTACGCGGTCATTCGGGACA-CTACGTGGTCATTCGGGA
1570198 TAAATTCTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 19 0.56
41 2 0.06
42 13 0.38
ACGTcount: A:0.16, C:0.25, G:0.30, T:0.28
Consensus pattern (41 bp):
TCTACGCGGTCATTCGGGACACTACGTGGTCATTCGGGACA
Found at i:1572005 original size:190 final size:190
Alignment explanation
Indices: 1571682--1572064 Score: 766
Period size: 190 Copynumber: 2.0 Consensus size: 190
1571672 GTAAAAAAGG
1571682 ATGAATACATGGTAAGTTTGTCCAAAATGCATCAAATGAGGAAATTCACAAGCTTAGGAATGATC
1 ATGAATACATGGTAAGTTTGTCCAAAATGCATCAAATGAGGAAATTCACAAGCTTAGGAATGATC
1571747 TAAAAAAAGAATTGAGAGAGAACAAGGAATTCCACAGAAAAAAGATGAAAGCACGTGTACCATCC
66 TAAAAAAAGAATTGAGAGAGAACAAGGAATTCCACAGAAAAAAGATGAAAGCACGTGTACCATCC
1571812 TTTGACTTTACTATTGACGCAATTATAAAAATTACCACCAAATTTTTAGAACTATTGGTA
131 TTTGACTTTACTATTGACGCAATTATAAAAATTACCACCAAATTTTTAGAACTATTGGTA
1571872 ATGAATACATGGTAAGTTTGTCCAAAATGCATCAAATGAGGAAATTCACAAGCTTAGGAATGATC
1 ATGAATACATGGTAAGTTTGTCCAAAATGCATCAAATGAGGAAATTCACAAGCTTAGGAATGATC
1571937 TAAAAAAAGAATTGAGAGAGAACAAGGAATTCCACAGAAAAAAGATGAAAGCACGTGTACCATCC
66 TAAAAAAAGAATTGAGAGAGAACAAGGAATTCCACAGAAAAAAGATGAAAGCACGTGTACCATCC
1572002 TTTGACTTTACTATTGACGCAATTATAAAAATTACCACCAAATTTTTAGAACTATTGGTA
131 TTTGACTTTACTATTGACGCAATTATAAAAATTACCACCAAATTTTTAGAACTATTGGTA
1572062 ATG
1 ATG
1572065 TTGCATGTCC
Statistics
Matches: 193, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
190 193 1.00
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.26
Consensus pattern (190 bp):
ATGAATACATGGTAAGTTTGTCCAAAATGCATCAAATGAGGAAATTCACAAGCTTAGGAATGATC
TAAAAAAAGAATTGAGAGAGAACAAGGAATTCCACAGAAAAAAGATGAAAGCACGTGTACCATCC
TTTGACTTTACTATTGACGCAATTATAAAAATTACCACCAAATTTTTAGAACTATTGGTA
Found at i:1576916 original size:8 final size:7
Alignment explanation
Indices: 1576894--1576924 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
1576884 CCATTTACCC
1576894 GACCGTT
1 GACCGTT
1576901 GACCGTT
1 GACCGTT
1576908 GACCCGTT
1 GA-CCGTT
1576916 GACCGTT
1 GACCGTT
1576923 GA
1 GA
1576925 TCGGAGTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:1576916 original size:15 final size:15
Alignment explanation
Indices: 1576896--1576924 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1576886 ATTTACCCGA
1576896 CCGTTGACCGTTGAC
1 CCGTTGACCGTTGAC
1576911 CCGTTGACCGTTGA
1 CCGTTGACCGTTGA
1576925 TCGGAGTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.31, G:0.28, T:0.28
Consensus pattern (15 bp):
CCGTTGACCGTTGAC
Found at i:1578254 original size:18 final size:18
Alignment explanation
Indices: 1578228--1578263 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1578218 TTCGAAGGAC
*
1578228 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1578246 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1578264 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1579538 original size:2 final size:2
Alignment explanation
Indices: 1579531--1579560 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1579521 TATTTTGTAG
1579531 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1579561 GGAAATATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1587339 original size:16 final size:17
Alignment explanation
Indices: 1587301--1587340 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1587291 TATTATATAT
**
1587301 ATATTTTAAATATTTGT
1 ATATTTTAAATATTTCA
1587318 ATATTTTAAATA-TTCA
1 ATATTTTAAATATTTCA
1587334 ATATTTT
1 ATATTTT
1587341 TATTTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (17 bp):
ATATTTTAAATATTTCA
Found at i:1608224 original size:28 final size:28
Alignment explanation
Indices: 1608185--1608247 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
1608175 GTTCGGGTCA
1608185 GGTCGGG-TTTTTTAAGTGTGATATTCG
1 GGTCGGGTTTTTTTAAGTGTGATATTCG
1608212 GGTCGGGTTTTTTTAAGTGTGATATTCG
1 GGTCGGGTTTTTTTAAGTGTGATATTCG
*
1608240 GGTTGGGT
1 GGTCGGGT
1608248 CGGGTTCGGG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 7 0.21
28 27 0.79
ACGTcount: A:0.13, C:0.06, G:0.37, T:0.44
Consensus pattern (28 bp):
GGTCGGGTTTTTTTAAGTGTGATATTCG
Found at i:1608873 original size:18 final size:18
Alignment explanation
Indices: 1608850--1608886 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1608840 AATTTTTGAC
1608850 AGATTCTAATTCCTTCAT
1 AGATTCTAATTCCTTCAT
1608868 AGATTCTAATTCCTTCAT
1 AGATTCTAATTCCTTCAT
1608886 A
1 A
1608887 AACATTCCAG
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:0.30, C:0.22, G:0.05, T:0.43
Consensus pattern (18 bp):
AGATTCTAATTCCTTCAT
Done.