Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003350.1 Hibiscus syriacus cultivar Beakdansim tig00007054_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: 82446
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:387 original size:19 final size:19
Alignment explanation
Indices: 363--399 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
353 AAACCGATAT
*
363 TTTACCGGTACATTGTAAA
1 TTTACCGATACATTGTAAA
*
382 TTTACCTATACATTGTAA
1 TTTACCGATACATTGTAA
400 TTATCGGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (19 bp):
TTTACCGATACATTGTAAA
Found at i:742 original size:33 final size:31
Alignment explanation
Indices: 699--760 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 31
689 TATATTATTC
699 TTATTATAAT-AAATACTAAATATATTATAATAA
1 TTATTATAATAAAATA-T-AATA-ATTATAATAA
*
732 TTATTTTAATAAAATATAATAATTATAAT
1 TTATTATAATAAAATATAATAATTATAAT
761 TTTTTATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 8 0.30
32 4 0.15
33 10 0.37
34 5 0.19
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (31 bp):
TTATTATAATAAAATATAATAATTATAATAA
Found at i:754 original size:25 final size:26
Alignment explanation
Indices: 715--763 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
705 TAATAAATAC
* *
715 TAAATATATTATAATAATTATTTTAA
1 TAAATATATAATAATAATAATTTTAA
*
741 TAAA-ATATAATAATTATAATTTT
1 TAAATATATAATAATAATAATTTT
764 TTATTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TAAATATATAATAATAATAATTTTAA
Found at i:801 original size:14 final size:14
Alignment explanation
Indices: 725--805 Score: 58
Period size: 14 Copynumber: 5.8 Consensus size: 14
715 TAAATATATT
725 ATAATAATTATTTTA
1 ATAATAA-TATTTTA
**
740 ATAA-AATATAATA
1 ATAATAATATTTTA
* *
753 ATTATAATTTTTTA
1 ATAATAATATTTTA
* * * *
767 TTTATAAAATTATA
1 ATAATAATATTTTA
781 GAT-ATAATATTTTA
1 -ATAATAATATTTTA
795 ATAATAATATT
1 ATAATAATATT
806 GACATAAATA
Statistics
Matches: 50, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
13 10 0.20
14 35 0.70
15 5 0.10
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (14 bp):
ATAATAATATTTTA
Found at i:801 original size:28 final size:28
Alignment explanation
Indices: 728--801 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 28
718 ATATATTATA
*
728 ATAATTATTTTAATAA-AATATAATAATT
1 ATAA-TATTTTAATAATAAAATAATAATT
* * * *
756 ATAATTTTTTATTTATAAAATTATAGA-T
1 ATAATATTTTAATAATAAAATAATA-ATT
784 ATAATATTTTAATAATAA
1 ATAATATTTTAATAATAA
802 TATTGACATA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
27 8 0.22
28 27 0.75
29 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
ATAATATTTTAATAATAAAATAATAATT
Found at i:1245 original size:19 final size:20
Alignment explanation
Indices: 1215--1269 Score: 94
Period size: 19 Copynumber: 2.8 Consensus size: 20
1205 AATGCCCAAC
1215 AATAACAAAACCGGTAAAAA
1 AATAACAAAACCGGTAAAAA
*
1235 AATAA-AAAACCGATAAAAA
1 AATAACAAAACCGGTAAAAA
1254 AATAACAAAACCGGTA
1 AATAACAAAACCGGTA
1270 GCGTTTACCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.65, C:0.15, G:0.09, T:0.11
Consensus pattern (20 bp):
AATAACAAAACCGGTAAAAA
Found at i:1972 original size:23 final size:23
Alignment explanation
Indices: 1937--2016 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
1927 TTAGTAATTA
**
1937 ACCTATTTTATTATATAAGCTCT
1 ACCTATTACATTATATAAGCTCT
1960 ACCTATTACATTATATAAG-TGCT
1 ACCTATTACATTATATAAGCT-CT
* *
1983 ACATATTACATTATATAAGCGCT
1 ACCTATTACATTATATAAGCTCT
2006 ACCTATTACAT
1 ACCTATTACAT
2017 CATTTTTTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
22 1 0.02
23 49 0.98
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.40
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCTCT
Found at i:2647 original size:2 final size:2
Alignment explanation
Indices: 2640--2665 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2630 ATATCTTTTA
2640 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
2666 GATAATATCA
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:4344 original size:15 final size:15
Alignment explanation
Indices: 4280--4363 Score: 61
Period size: 15 Copynumber: 5.8 Consensus size: 15
4270 ATTATTATTA
4280 TATATATATATAATAT
1 TATATATATATAAT-T
* *
4296 TA-ATAAATTTAATT
1 TATATATATATAATT
* *
4310 TAAAT-TA-AT-ATA
1 TATATATATATAATT
4322 TATATATATATAATGT
1 TATATATATATAAT-T
*
4338 T-TATATATTTAATT
1 TATATATATATAATT
*
4352 TAAATATATATA
1 TATATATATATA
4364 TATACCCGGC
Statistics
Matches: 52, Mismatches: 10, Indels: 13
0.69 0.13 0.17
Matches are distributed among these distances:
12 6 0.12
13 3 0.06
14 8 0.15
15 32 0.62
16 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (15 bp):
TATATATATATAATT
Found at i:4348 original size:42 final size:42
Alignment explanation
Indices: 4269--4367 Score: 139
Period size: 42 Copynumber: 2.4 Consensus size: 42
4259 TATTAAAAAT
*
4269 AATTATTATTATATATATATATAATATTAATAAATTTAATTTA
1 AATTAATA-TATATATATATATAATATTAATAAATTTAATTTA
* * *
4312 AATTAATATATATATATATATAATGTTTATATATTTAATTTA
1 AATTAATATATATATATATATAATATTAATAAATTTAATTTA
4354 AA-T-ATATATATATA
1 AATTAATATATATATA
4368 CCCGGCCCGA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
40 11 0.21
41 1 0.02
42 33 0.63
43 7 0.13
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (42 bp):
AATTAATATATATATATATATAATATTAATAAATTTAATTTA
Found at i:5441 original size:18 final size:18
Alignment explanation
Indices: 5418--5458 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5408 GAGAGCCAAA
5418 TTAATAGTAAAGTAAAGT
1 TTAATAGTAAAGTAAAGT
* * *
5436 TTAATATTTAATTAAAGT
1 TTAATAGTAAAGTAAAGT
5454 TTAAT
1 TTAAT
5459 GACAAAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (18 bp):
TTAATAGTAAAGTAAAGT
Found at i:11130 original size:18 final size:19
Alignment explanation
Indices: 11101--11136 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
11091 TCTTTAGAGA
11101 ATTTTAAAATTTTCTTTAT
1 ATTTTAAAATTTTCTTTAT
*
11120 ATTTT-AAATTTTTTTTA
1 ATTTTAAAATTTTCTTTA
11137 AATATTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTTAAAATTTTCTTTAT
Found at i:11139 original size:29 final size:28
Alignment explanation
Indices: 11102--11166 Score: 103
Period size: 29 Copynumber: 2.3 Consensus size: 28
11092 CTTTAGAGAA
*
11102 TTTTAAAATTTTCTTTATATTTTAAATTT
1 TTTTAAAATATTCTTTATATTTT-AATTT
*
11131 TTTTTAAATATTCTTTATATTTTAATTT
1 TTTTAAAATATTCTTTATATTTTAATTT
11159 TTTTAAAA
1 TTTTAAAA
11167 AATATTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 12 0.36
29 21 0.64
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (28 bp):
TTTTAAAATATTCTTTATATTTTAATTT
Found at i:14942 original size:26 final size:26
Alignment explanation
Indices: 14869--14942 Score: 64
Period size: 26 Copynumber: 2.8 Consensus size: 26
14859 ATATTTTTAT
**
14869 TTACTTTATTTTGTTAAATTGTAATTT
1 TTACTTTATTTTGTTAAATT-TAATAC
*
14896 TTA-TATTATTATT-TCT-CATTTAATAC
1 TTACT-TTATT-TTGT-TAAATTTAATAC
14922 TTACTTTATTTTGTTAAATTT
1 TTACTTTATTTTGTTAAATTT
14943 GTTGGGCTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
25 3 0.08
26 18 0.49
27 13 0.35
28 3 0.08
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.62
Consensus pattern (26 bp):
TTACTTTATTTTGTTAAATTTAATAC
Found at i:18752 original size:51 final size:51
Alignment explanation
Indices: 18630--18752 Score: 167
Period size: 51 Copynumber: 2.4 Consensus size: 51
18620 CCCTACATGG
* ** * *
18630 CGTATAGCGCGCTGCAGGGGCCGCGCTATACCCACGTGTATGCCAGATCAC
1 CGTATAGCGCGGTGCAGGGGGAGCGCTATACCCACGTGTACGCCAAATCAC
* *
18681 CGTATAGCGCGGTGCAGGGGGAGCGCTATACCCCACGTG-GCGCCAAATCAT
1 CGTATAGCGCGGTGCAGGGGGAGCGCTATA-CCCACGTGTACGCCAAATCAC
18732 CGTATAGCGCGGTGCAGGGGG
1 CGTATAGCGCGGTGCAGGGGG
18753 CGTGCTTTAC
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
51 56 0.88
52 8 0.12
ACGTcount: A:0.20, C:0.29, G:0.35, T:0.16
Consensus pattern (51 bp):
CGTATAGCGCGGTGCAGGGGGAGCGCTATACCCACGTGTACGCCAAATCAC
Found at i:22988 original size:28 final size:29
Alignment explanation
Indices: 22937--22998 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 29
22927 TTGTATTGGT
22937 GTTTATGGATTAAATGTTTAAGCATTTAG
1 GTTTATGGATTAAATGTTTAAGCATTTAG
*
22966 GTTTATGGGTT-AATGTTTAAGCATTTAG
1 GTTTATGGATTAAATGTTTAAGCATTTAG
22994 GTTTA
1 GTTTA
22999 CTGCTTTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 22 0.69
29 10 0.31
ACGTcount: A:0.27, C:0.03, G:0.23, T:0.47
Consensus pattern (29 bp):
GTTTATGGATTAAATGTTTAAGCATTTAG
Found at i:25245 original size:3 final size:3
Alignment explanation
Indices: 25237--25275 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
25227 ATTTATTTAT
* * *
25237 TTA TTA TTA TTA TAA TTA TTA TAA TTA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
25276 AAATATATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:25254 original size:9 final size:9
Alignment explanation
Indices: 25237--25288 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
25227 ATTTATTTAT
*
25237 TTATTATTA
1 TTATAATTA
25246 TTATAATTA
1 TTATAATTA
25255 TTATAATTA
1 TTATAATTA
* *
25264 TAATTATTA
1 TTATAATTA
*
25273 TTA-AAATA
1 TTATAATTA
25281 TATATAAT
1 T-TATAAT
25289 AATAATAATA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
8 4 0.12
9 28 0.82
10 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
TTATAATTA
Found at i:26911 original size:23 final size:26
Alignment explanation
Indices: 26879--26928 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
26869 CCTTTTCTGA
*
26879 TATTTCTAAATA-A-ATAAA-TATTT
1 TATTTATAAATATATATAAATTATTT
26902 TATTTATAAATATATATAAATTATTT
1 TATTTATAAATATATATAAATTATTT
26928 T
1 T
26929 TTTTCTCTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 5 0.22
26 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTTATAAATATATATAAATTATTT
Found at i:38170 original size:19 final size:18
Alignment explanation
Indices: 38146--38200 Score: 76
Period size: 17 Copynumber: 3.0 Consensus size: 18
38136 ATTATGCTTG
38146 AAGAAAAAAAAGAATAAAA
1 AAGAAAAAAAAGAA-AAAA
38165 AAGAAAAAAAAAGAAAAAA
1 AAG-AAAAAAAAGAAAAAA
*
38184 AAG-GAAAAAAGAAAAAA
1 AAGAAAAAAAAGAAAAAA
38201 GAAAAAAGGG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
17 13 0.38
19 10 0.29
20 11 0.32
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (18 bp):
AAGAAAAAAAAGAAAAAA
Found at i:38173 original size:7 final size:7
Alignment explanation
Indices: 38161--38208 Score: 64
Period size: 7 Copynumber: 7.0 Consensus size: 7
38151 AAAAAAGAAT
38161 AAAAAAG
1 AAAAAAG
38168 AAAAAA-
1 AAAAAAG
38174 AAAGAAA-
1 AAA-AAAG
*
38181 AAAAAGG
1 AAAAAAG
38188 AAAAAAG
1 AAAAAAG
38195 AAAAAAG
1 AAAAAAG
38202 AAAAAAG
1 AAAAAAG
38209 GGGGTCCAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 5 0.14
7 32 0.86
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:38174 original size:20 final size:19
Alignment explanation
Indices: 38149--38208 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 19
38139 ATGCTTGAAG
38149 AAAAAAAAGAATAAAAAAGA
1 AAAAAAAAGAA-AAAAAAGA
38169 AAAAAAAAGAAAAAAAAGGA
1 AAAAAAAAGAAAAAAAA-GA
*
38189 AAAAAGAAAAAAGAAAAAAG
1 AAAAA-AAAGAA-AAAAAAG
38209 GGGGTCCAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
19 6 0.17
20 18 0.50
21 6 0.17
22 6 0.17
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (19 bp):
AAAAAAAAGAAAAAAAAGA
Found at i:38207 original size:9 final size:9
Alignment explanation
Indices: 38146--38200 Score: 76
Period size: 9 Copynumber: 6.0 Consensus size: 9
38136 ATTATGCTTG
38146 AAGAAAAAA
1 AAGAAAAAA
38155 AAGAATAAAA
1 AAGAA-AAAA
38165 AAGAAAAAAA
1 AAG-AAAAAA
38175 AAGAAAAAA
1 AAGAAAAAA
*
38184 AAG-GAAAA
1 AAGAAAAAA
38192 AAGAAAAAA
1 AAGAAAAAA
38201 GAAAAAAGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
8 7 0.17
9 18 0.44
10 14 0.34
11 2 0.05
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:39616 original size:44 final size:44
Alignment explanation
Indices: 39553--39643 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
39543 CAAGTGCCAT
39553 GTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAA
1 GTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAA
39597 GTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAA
1 GTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAA
39641 GTG
1 GTG
39644 TTCTTTGAGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (44 bp):
GTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAA
Found at i:39849 original size:115 final size:114
Alignment explanation
Indices: 39598--39828 Score: 349
Period size: 115 Copynumber: 2.0 Consensus size: 114
39588 CTTCTGGAAG
* *
39598 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAAAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATC
* * * * * *
39663 TGGTTTGGTATGAACCCTAAAAACCAATCATTGGATTTGAAAGATGAATG
66 TGGTTCGATAGGAACCC-AAAAACCAATCATTGGAATTAAAAGATGAATC
39713 TGCTCATAGTAAAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATC
1 TGCTCATAGTAAAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATC
*
39778 TGGTTCGATAGGAA-CCACATAACCAATCATTGGAATTAAAAGATGAA-C
66 TGGTTCGATAGGAACCCA-AAAACCAATCATTGGAATTAAAAGATGAATC
39826 TGC
1 TGC
39829 ATGATCGTCT
Statistics
Matches: 106, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
113 4 0.04
114 28 0.26
115 74 0.70
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (114 bp):
TGCTCATAGTAAAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATC
TGGTTCGATAGGAACCCAAAAACCAATCATTGGAATTAAAAGATGAATC
Found at i:40620 original size:24 final size:23
Alignment explanation
Indices: 40577--40621 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
40567 GTTCATAATG
*
40577 AGAAGAAATCATCTGAAGAAGGA
1 AGAAGAAATCATATGAAGAAGGA
40600 AGAAGAAATTCATAATG-AGAAG
1 AGAAGAAA-TCAT-ATGAAGAAG
40622 AATTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 9 0.47
25 2 0.11
ACGTcount: A:0.53, C:0.07, G:0.24, T:0.16
Consensus pattern (23 bp):
AGAAGAAATCATATGAAGAAGGA
Found at i:40756 original size:73 final size:73
Alignment explanation
Indices: 40600--40769 Score: 191
Period size: 73 Copynumber: 2.3 Consensus size: 73
40590 TGAAGAAGGA
** *
40600 AGAAGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATC
1 AGAA-AAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCAGATGGAAC
** *
40664 AGCTTTTCC
65 AGCAGTACC
** * *
40673 AGAAAAAGTTCATAATGAGAAGAATTTGTTCAATTTTTTGCTTAAATTCATCACTCAG-TGGAAC
1 AGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCA-TCAGATGGAAC
40737 AGCAGTACC
65 AGCAGTACC
** *
40746 AGTTAGAGTTCATAATGAGAAGAA
1 AGAAAAAGTTCATAATGAGAAGAA
40770 CTCACCTAAA
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
72 3 0.04
73 77 0.94
74 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (73 bp):
AGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATCAGATGGAACA
GCAGTACC
Found at i:40950 original size:116 final size:116
Alignment explanation
Indices: 40673--41114 Score: 543
Period size: 116 Copynumber: 3.8 Consensus size: 116
40663 CAGCTTTTCC
* ** * * *
40673 AGAAAAAGTTCATAATGAGAAGAATTTGTTCAATTTTTTGCTTAAATTCATCACTCAGTGGAACA
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTCAATGGATCA
* * *
40738 GCAGTACCAGTTAGAGTTCATAATGAGAAGAACTCA-C--CTAAAGAAAGA
66 ACATTACCAGTTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAAGA
* * *
40786 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTTTGCTTGAATTCATCATTCAATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTCAATGGATCA
* * * * * *
40851 GCATTACCAGTTCGAGTTCATAATAAAAAGAACTCATCATCGGAAGAAGGA
66 ACATTACCAGTTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAAGA
* * ** *
40902 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATTATTTGATGGATTA
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTCAATGGATCA
* *
40967 ACATTGCCA-TGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAATGA
66 ACATTACCAGT-TAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAAGA
* * * *
41018 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTT-GATGGATC
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCA-TTCAATGGATC
* * *
41082 AACTTTTCCAGTTCGAGTTCATAATGAGAAGAA
65 AACATTACCAGTTAGAGTTCATAATGAGAAGAA
41115 TTTGTTCAAC
Statistics
Matches: 284, Mismatches: 39, Indels: 9
0.86 0.12 0.03
Matches are distributed among these distances:
113 89 0.31
114 1 0.00
115 1 0.00
116 190 0.67
117 3 0.01
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (116 bp):
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTCAATGGATCA
ACATTACCAGTTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAAGA
Found at i:41174 original size:73 final size:73
Alignment explanation
Indices: 41018--41187 Score: 245
Period size: 73 Copynumber: 2.3 Consensus size: 73
41008 TGAAGAATGA
*
41018 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCA
41083 ACTTTTCC
66 ACTTTTCC
** * *
41091 AGTTCG-AGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCAAATCCATCACTTGATTGATC
1 AG-AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATC
**
41155 AGTTTTTTCC
65 A-ACTTTTCC
41165 A-AAGAAGTTCATAATGAGAAGAA
1 AGAAGAAGTTCATAATGAGAAGAA
41188 CTCATCTGAA
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
72 1 0.01
73 76 0.89
74 8 0.09
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (73 bp):
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCA
ACTTTTCC
Found at i:41210 original size:36 final size:36
Alignment explanation
Indices: 41166--41258 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
41156 GTTTTTTCCA
41166 AAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
1 AAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
41202 AAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
1 AAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
* *
41238 AAAAAGTTCACAATGAGAAGA
1 AAGAAGTTCATAATGAGAAGA
41259 GCTTATTCAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.49, C:0.11, G:0.22, T:0.18
Consensus pattern (36 bp):
AAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
Found at i:41222 original size:17 final size:17
Alignment explanation
Indices: 41166--41223 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
41156 GTTTTTTCCA
41166 AAGAAGTTCATAATGAG
1 AAGAAGTTCATAATGAG
*
41183 AAGAA-CTCATCTGAA-GAAG
1 AAGAAGTTCA--T-AATG-AG
41202 AAGAAGTTCATAATGAG
1 AAGAAGTTCATAATGAG
41219 AAGAA
1 AAGAA
41224 CTCATCTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
16 3 0.09
17 14 0.42
18 4 0.12
19 9 0.27
20 3 0.09
ACGTcount: A:0.50, C:0.09, G:0.22, T:0.19
Consensus pattern (17 bp):
AAGAAGTTCATAATGAG
Found at i:41424 original size:124 final size:118
Alignment explanation
Indices: 41205--41478 Score: 307
Period size: 124 Copynumber: 2.3 Consensus size: 118
41195 GAAGAAGAAG
* *
41205 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAGTTCACAATGAGAAGAGCTTATTCAAC
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAGTTCACAATAAGAAAAGCTTATTCAAC
* * * * * *
41270 CTTTTGCATAATTCTATCACATAAGCAAATAGATTAGCATCAACCTTTCCAG-AGA
66 CTTTTGAATAACTCTATCACAGAAGAAAATAGATCAACATCAACC---CCAGTAGA
* * *
41325 AAGTTCATAATGAGAAGAACTCATCTGAAGTAGAAAGAAGAAGTTCATAATAAGAAAATCTTATT
1 AAGTTCATAATGAGAAGAACTCATCTG-A--AG-AAGAAAAAGTTCACAATAAGAAAAGCTTATT
* * * * * *
41390 TAATCTTTTGAATGACTCTATCACAGAAGAAAATAGGTCAACATCATCCCCAGTGGA
62 CAACCTTTTGAATAACTCTATCACAGAAGAAAATAGATCAACATCAACCCCAGTAGA
* *
41447 AAGTTCATAATGAGAAGAACACATCTTAAGAA
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAA
41479 AGAGAAGGAT
Statistics
Matches: 130, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
118 2 0.02
119 2 0.02
120 27 0.21
121 6 0.05
122 27 0.21
123 2 0.02
124 64 0.49
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.26
Consensus pattern (118 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAAAGTTCACAATAAGAAAAGCTTATTCAAC
CTTTTGAATAACTCTATCACAGAAGAAAATAGATCAACATCAACCCCAGTAGA
Found at i:41651 original size:3 final size:3
Alignment explanation
Indices: 41643--41673 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
41633 ATTTATTTAT
*
41643 TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
41674 AAAAATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:41652 original size:18 final size:19
Alignment explanation
Indices: 41631--41671 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
41621 CCATTTTTAT
*
41631 TTATTTATT-TATTTATTA
1 TTATTTATTATAATTATTA
41649 TTA-TTATTATAATTATTA
1 TTATTTATTATAATTATTA
41667 TTATT
1 TTATT
41672 ATAAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 5 0.25
18 14 0.70
19 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTTATTATAATTATTA
Found at i:41663 original size:15 final size:15
Alignment explanation
Indices: 41645--41675 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
41635 TTATTTATTT
41645 ATTATTATTATTATA
1 ATTATTATTATTATA
41660 ATTATTATTATTATA
1 ATTATTATTATTATA
41675 A
1 A
41676 AAATAATAAT
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTATTATTATTATA
Found at i:41687 original size:12 final size:12
Alignment explanation
Indices: 41672--41727 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
41662 TATTATTATT
41672 ATAAAAATAATA
1 ATAAAAATAATA
* *
41684 ATAATAATAATT
1 ATAAAAATAATA
*
41696 ATTAAAAT-ATA
1 ATAAAAATAATA
*
41707 TATATAAATAATA
1 -ATAAAAATAATA
41720 ATAAAAAT
1 ATAAAAAT
41728 TACAAGCCCA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
11 2 0.06
12 29 0.85
13 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
ATAAAAATAATA
Found at i:43336 original size:23 final size:24
Alignment explanation
Indices: 43304--43351 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
43294 CCTTTTCTGA
*
43304 TATTTCTAAATAAATAAA-TATTT
1 TATTTATAAATAAATAAATTATTT
*
43327 TATTTATAAATATATAAATTATTT
1 TATTTATAAATAAATAAATTATTT
43351 T
1 T
43352 TTCTCTCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TATTTATAAATAAATAAATTATTT
Found at i:44040 original size:3 final size:3
Alignment explanation
Indices: 44034--44062 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
44024 TATATATATA
44034 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
44063 AAATAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:44529 original size:42 final size:41
Alignment explanation
Indices: 44441--44535 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 41
44431 TATAGACGGT
* *
44441 CCGAAGGACTTAACATCTTTCTCGAAAGACTGATAGATGAC
1 CCGAAGGACTTAACATCATGCTCGAAAGACTGATAGATGAC
* * *
44482 CCGAAGGATTTAATCATCATGCTCGAAAGACTTACT-GATGGC
1 CCGAAGGACTTAA-CATCATGCTCGAAAGACTGA-TAGATGAC
*
44524 TCGAAGGACTTA
1 CCGAAGGACTTA
44536 TTAAATTTGG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
41 12 0.27
42 32 0.71
43 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (41 bp):
CCGAAGGACTTAACATCATGCTCGAAAGACTGATAGATGAC
Found at i:45006 original size:41 final size:41
Alignment explanation
Indices: 44946--45052 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 41
44936 GCCCGAAGGT
* *
44946 CTTACAGATGGCCCAAAGGACTTATCATCTTGCTC-GAAAGA
1 CTTACAGATGGCCCGAAGGACTTATCATCATG-TCAGAAAGA
** * *
44987 CTTACAGATAACCCGAAGGATTTAATTATCATGTCAGAAAGA
1 CTTACAGATGGCCCGAAGGACTT-ATCATCATGTCAGAAAGA
45029 CTTACTA-ATGGCCCGAAGGACTTA
1 CTTAC-AGATGGCCCGAAGGACTTA
45053 CTAATTTTGG
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
41 22 0.41
42 31 0.57
43 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (41 bp):
CTTACAGATGGCCCGAAGGACTTATCATCATGTCAGAAAGA
Found at i:45007 original size:258 final size:258
Alignment explanation
Indices: 44218--45308 Score: 1442
Period size: 258 Copynumber: 4.3 Consensus size: 258
44208 TGAGAACGAT
* *
44218 AGATAACCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAA-GACTTACTA
1 AGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCC-AAAGGACTTACTA
* * * *
44282 ATTTTGGAAATAATTTAC-GGGAAAGAAACATTGGAAATCAATTTCTTACTTTTCAAAAATTTCA
65 ATTTTGGAAATAATTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCA
* * *
44346 TTTTCTGAAAACATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCGAAAATCATGTGGA
130 TTTTCAGAAAAGATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCGAAAATCATGAGGA
* ** * * * * * * *
44411 AATATCCTGCCCGAATATCTTATAGACGGTCCGAAGGACTTAACATCTTTCTCGAAAGACTGAT
195 AACATCCTGCCCGAAGGTCTTACAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTAC
* * *
44475 AGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCTCGAAGGACTTATTAA
1 AGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACTAA
*
44540 ATTTGGAAATAATTTACTAGGTAA-AAAGCTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCA
66 TTTTGGAAATAATTTACTAGGTAAGAAA-CTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCA
* * *
44604 TTTTCAGAAAACATTTAAATGAGAAACTTTGGAAATCGTTTTCTCATTTTTCAAAAATCATGAGG
130 TTTTCAGAAAAGA-TTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCGAAAATCATGAGG
* ** ** *
44669 AAACATCATGCCCGAAGGTCTTATGGATGATCCGAAGGACTTATAATCTTGCTCGAAAGA-TTGA
194 AAACATCCTGCCCGAAGGTCTTACAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTT-A
44733 C
258 C
* * *
44734 AGATGACCTGAAGGATTTAATCATCATGCTCAAAAGACTTACTGATGGCCCAAATGACTTACTAA
1 AGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACTAA
* *
44799 TTTAT-GAAATAATTTA-TCGGGTAAGAAACTTTGGAAATCACTTTCTTATTTTTCAAAAATTTC
66 TTT-TGGAAATAATTTACT-AGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTC
* *
44862 ATTTTCTGAAAAGTTTAAATGAGAAACTTTGGAAATCGCTTTGC-CATTTTTCGAAAATCATG-G
129 ATTTTCAGAAAAGATTAAATGAGAAACTTTGGAAATCGCTTT-CTCATTTTTCGAAAATCATGAG
*
44925 GAAAACATCCTGCCCGAAGGTCTTACAGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTT
193 G-AAACATCCTGCCCGAAGGTCTTACAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTT
44990 AC
257 AC
* * * *
44992 AGATAACCCGAAGGATTTAATTATCATG-TCAGAAAGACTTACTAATGGCCCGAAGGACTTACTA
1 AGATGACCCGAAGGATTTAATCATCATGCTC-GAAAGACTTACTGATGGCCCAAAGGACTTACTA
* *
45056 ATTTTGGAAATAATTTACTAGGTAAGAAACTTTGGAAATCATTTTCTTTA-TTTTCGAAAATTTC
65 ATTTTGGAAATAATTTACTAGGTAAGAAACTTTGGAAATCACTTTC-TTACTTTTCAAAAATTTC
* * * ** * *
45120 ATTTTCAGAAAAGATTAAATGATAAACATTGAAAATCATTTTCCCATTTTTC--AAA--GTGA--
129 ATTTTCAGAAAAGATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCGAAAATCATGAGG
* * *
45179 AAACATCCTACCCAAAGGTCTTACGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTAC
194 AAACATCCTGCCCGAAGGTCTTACAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTAC
* *
45244 AGATGACCTGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGG-CCAGAAGGACTTACTA
1 AGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCA-AAGGACTTACTA
45308 A
65 A
45309 GTAAGAAACT
Statistics
Matches: 740, Mismatches: 75, Indels: 43
0.86 0.09 0.05
Matches are distributed among these distances:
251 2 0.00
252 114 0.15
253 2 0.00
254 2 0.00
256 5 0.01
257 82 0.11
258 301 0.41
259 228 0.31
260 4 0.01
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (258 bp):
AGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACTAA
TTTTGGAAATAATTTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCAT
TTTCAGAAAAGATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCGAAAATCATGAGGAA
ACATCCTGCCCGAAGGTCTTACAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTAC
Found at i:58875 original size:20 final size:21
Alignment explanation
Indices: 58842--58884 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
58832 TGTTCATTTA
* *
58842 AATGATAAACGAACATAAACG
1 AATGATAAAAGAACACAAACG
58863 AATG-TAAAAGAACACAAACG
1 AATGATAAAAGAACACAAACG
58883 AA
1 AA
58885 CGAACATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.60, C:0.14, G:0.14, T:0.12
Consensus pattern (21 bp):
AATGATAAAAGAACACAAACG
Found at i:59189 original size:10 final size:10
Alignment explanation
Indices: 59174--59198 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
59164 GCCCTCTATT
59174 TGAACATAAA
1 TGAACATAAA
59184 TGAACATAAA
1 TGAACATAAA
59194 TGAAC
1 TGAAC
59199 GAACATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.20
Consensus pattern (10 bp):
TGAACATAAA
Found at i:60157 original size:16 final size:14
Alignment explanation
Indices: 60127--60160 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
60117 AGTTTTAAGG
60127 ATTAAATTTAATAA
1 ATTAAATTTAATAA
60141 ATTAATATTTAAATAA
1 ATTAA-ATTT-AATAA
60157 ATTA
1 ATTA
60161 CACAACATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 4 0.22
16 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTAAATTTAATAA
Found at i:72293 original size:23 final size:23
Alignment explanation
Indices: 72263--72307 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
72253 AGTGTAAACT
72263 GTTTGTATACTGAATTATGCTTG
1 GTTTGTATACTGAATTATGCTTG
72286 GTTTGTATACTGAATTATGCTT
1 GTTTGTATACTGAATTATGCTT
72308 CCAGTTCTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.09, G:0.20, T:0.49
Consensus pattern (23 bp):
GTTTGTATACTGAATTATGCTTG
Found at i:72584 original size:30 final size:30
Alignment explanation
Indices: 72526--72584 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
72516 ACCGAAATTT
** ** *
72526 GTTCGGTTCGGTTAATTTTTTCATAAAAAA
1 GTTCGGTTCGGTTAATGGTTAAAGAAAAAA
72556 GTTCGGTTCGGTTAATGGTTAAAGAAAAA
1 GTTCGGTTCGGTTAATGGTTAAAGAAAAA
72585 TAAATTCGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.37
Consensus pattern (30 bp):
GTTCGGTTCGGTTAATGGTTAAAGAAAAAA
Found at i:76154 original size:15 final size:14
Alignment explanation
Indices: 76114--76156 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
76104 TGATCATTGC
*
76114 TTTTCTTTCCTTCG
1 TTTTCTTTTCTTCG
*
76128 TGTTTCTGTTCTTCG
1 T-TTTCTTTTCTTCG
76143 TTTTCTTTTTCTTC
1 TTTTC-TTTTCTTC
76157 TAGATGCTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 5 0.21
15 19 0.79
ACGTcount: A:0.00, C:0.23, G:0.09, T:0.67
Consensus pattern (14 bp):
TTTTCTTTTCTTCG
Found at i:76558 original size:31 final size:31
Alignment explanation
Indices: 76523--76583 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
76513 AAGAATCATT
*
76523 AATTTAATGTTTAAATTTTAAATAAAATATC
1 AATTTAATGTTTAAATTTAAAATAAAATATC
* *
76554 AATTTAATTTTTAAATTTAAAATATAATAT
1 AATTTAATGTTTAAATTTAAAATAAAATAT
76584 TGCTTTATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (31 bp):
AATTTAATGTTTAAATTTAAAATAAAATATC
Found at i:77587 original size:30 final size:30
Alignment explanation
Indices: 77512--77597 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 30
77502 TTTGATCAGA
* *
77512 TTTAAAAGTTAAATTATTATTTTATTAAAAC
1 TTTAAAGGTTAAATTAATATTTTA-TAAAAC
* *
77543 TTTAAAGATTAAATTAATATTTTATATAA-
1 TTTAAAGGTTAAATTAATATTTTATAAAAC
* **
77572 TTGTAGAGGTTAAATTCGTATTTTAT
1 TT-TAAAGGTTAAATTAATATTTTAT
77598 CTTAAGTTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
29 2 0.04
30 23 0.50
31 21 0.46
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (30 bp):
TTTAAAGGTTAAATTAATATTTTATAAAAC
Found at i:79836 original size:15 final size:15
Alignment explanation
Indices: 79816--79846 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
79806 TTAACACAAG
79816 AAACTAACCAAATAA
1 AAACTAACCAAATAA
*
79831 AAACTAACTAAATAA
1 AAACTAACCAAATAA
79846 A
1 A
79847 CTCGAACAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (15 bp):
AAACTAACCAAATAA
Done.