Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004882.1 Hibiscus syriacus cultivar Beakdansim tig00011000_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: 136843
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:525 original size:20 final size:22
Alignment explanation
Indices: 482--534 Score: 83
Period size: 20 Copynumber: 2.5 Consensus size: 22
472 ATCTACACTC
482 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
504 TTTAAAGATGATAGA-T-TCTT
1 TTCAAAGATGATAGATTCTCTT
524 TTCAAAGATGA
1 TTCAAAGATGA
535 AAGCTTTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 14 0.48
21 1 0.03
22 14 0.48
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:1180 original size:76 final size:76
Alignment explanation
Indices: 1081--2594 Score: 2715
Period size: 76 Copynumber: 20.0 Consensus size: 76
1071 CTATTTCCCA
*
1081 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1146 ACCCTCAGGGT
66 ACCCTCAGGGT
* *
1157 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAGGCTTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1222 ACCCTAAGGGT
66 ACCCTCAGGGT
*
1233 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1298 ACCCTCAGGGT
66 ACCCTCAGGGT
*
1309 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
1374 AACCCTCAGGGT
65 AACCCTCAGGGT
*
1386 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1450 ACCCTCA-GGT
66 ACCCTCAGGGT
* *
1460 CATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1525 ACCCTCAGGGT
66 ACCCTCAGGGT
* *
1536 CATCTGTAAGTCCTGCAGTGCATCATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1600 ACCCTCAGGGT
66 ACCCTCAGGGT
*
1611 CATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1676 ACCCTCAGGGT
66 ACCCTCAGGGT
*
1687 CATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1752 ACCCTCAGGGT
66 ACCCTCAGGGT
*
1763 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAGGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1828 A-CCTCAGGGT
66 ACCCTCAGGGT
*
1838 CATCTGT-AGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1902 ACCCTCAGGGT
66 ACCCTCAGGGT
1913 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1978 ACCCTCAGGGT
66 ACCCTCAGGGT
*
1989 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2054 ACCCTCAGGGT
66 ACCCTCAGGGT
*
2065 CATCTGTAAGTCCTGCAGTGCATGATGTTTCC-AAAAGCCTTC-GGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2128 ACCCTCAGGGT
66 ACCCTCAGGGT
*
2139 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTAATG-TTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2202 ACCCTCAGGGT
66 ACCCTCAGGGT
2213 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2278 ACCCTCAGGGT
66 ACCCTCAGGGT
*
2289 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2354 ACCCTCAGGGT
66 ACCCTCAGGGT
* *
2365 CATCTGTAAGTCCTGCAGTGCATCATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
**
2429 ACCCTCAAAGT
66 ACCCTCAGGGT
*
2440 CATCTGTAAGTCCTGCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2505 ACCCTCAGGGT
66 ACCCTCAGGGT
*
2516 CATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2581 ACCCTTAGGGT
66 ACCCTCAGGGT
2592 CAT
1 CAT
2595 TCATAAGACC
Statistics
Matches: 1382, Mismatches: 45, Indels: 22
0.95 0.03 0.02
Matches are distributed among these distances:
74 235 0.17
75 238 0.17
76 849 0.61
77 60 0.04
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
ACCCTCAGGGT
Found at i:1538 original size:227 final size:228
Alignment explanation
Indices: 1081--2594 Score: 2715
Period size: 227 Copynumber: 6.7 Consensus size: 228
1071 CTATTTCCCA
*
1081 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
1146 ACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAGGCTTTCGGGAGCTTTTT
66 ACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
1211 GATGTTTTCAAACCCTAAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTC
1276 GGGAGCTTTTTAATGTTTTCAAACCCTCAGGGT
196 GGGAGCTTTTTAATGTTTTCAAACCCTCAGGGT
*
1309 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
*
1374 AACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGC-TTT
65 AACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
1438 TGATGTTTTCAAACCCTCA-GGTCATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTT
130 TGATGTTTTCAAACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTT
1502 CGGGAGCTTTTTAATGTTTTCAAACCCTCAGGGT
195 CGGGAGCTTTTTAATGTTTTCAAACCCTCAGGGT
* *
1536 CATCTGTAAGTCCTGCAGTGCATCATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1600 ACCCTCAGGGTCATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 ACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
1665 GATGTTTTCAAACCCTCAGGGTCATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTC
*
1730 GGGAGCTTTTTGATGTTTTCAAACCCTCAGGGT
196 GGGAGCTTTTTAATGTTTTCAAACCCTCAGGGT
*
1763 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAGGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1828 A-CCTCAGGGTCATCTGT-AGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 ACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
1891 AATGTTTTCAAACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTC
*
1956 GGGAGCTTTTTGATGTTTTCAAACCCTCAGGGT
196 GGGAGCTTTTTAATGTTTTCAAACCCTCAGGGT
*
1989 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2054 ACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCC-AAAAGCCTTC-GGAGCTTTTT
66 ACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
2117 AATGTTTTCAAACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTC
2182 GGGAGC-TTTTAATG-TTTCAAACCCTCAGGGT
196 GGGAGCTTTTTAATGTTTTCAAACCCTCAGGGT
2213 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2278 ACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 ACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
* * *
2343 AATGTTTTCAAACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATCATGTTTCCAAAAAGTCTTC
131 GATGTTTTCAAACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTC
* **
2408 GGGAGCTTTTTGATG-TTTCAAACCCTCAAAGT
196 GGGAGCTTTTTAATGTTTTCAAACCCTCAGGGT
*
2440 CATCTGTAAGTCCTGCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
2505 ACCCTCAGGGTCATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 ACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
2570 GATGTTTTCAAACCCTTAGGGTCAT
131 GATGTTTTCAAACCCTCAGGGTCAT
2595 TCATAAGACC
Statistics
Matches: 1245, Mismatches: 32, Indels: 19
0.96 0.02 0.01
Matches are distributed among these distances:
224 124 0.10
225 77 0.06
226 391 0.31
227 481 0.39
228 113 0.09
229 59 0.05
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (228 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
ACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAACCCTCAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTC
GGGAGCTTTTTAATGTTTTCAAACCCTCAGGGT
Found at i:2760 original size:3 final size:3
Alignment explanation
Indices: 2752--2811 Score: 59
Period size: 3 Copynumber: 19.0 Consensus size: 3
2742 TTTTACTTAA
* *
2752 ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT ATT ATT -TAT ATTT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T A-TT AT-T
2799 ATAT ATT ATT ATT
1 AT-T ATT ATT ATT
2812 TAATAAATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 1 0.02
3 38 0.78
4 9 0.18
5 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:2777 original size:18 final size:19
Alignment explanation
Indices: 2749--2786 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
2739 TTATTTTACT
2749 TAAATTATTATTATTATTA
1 TAAATTATTATTATTATTA
2768 TAAA-TATTATTATTATTA
1 TAAATTATTATTATTATTA
2786 T
1 T
2787 TTATATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TAAATTATTATTATTATTA
Found at i:2784 original size:24 final size:23
Alignment explanation
Indices: 2752--2823 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 23
2742 TTTTACTTAA
2752 ATTATTATTATTATTATAAATATT
1 ATTATTATTATT-TTATAAATATT
**
2776 ATTATTATTA-TTTATATTTATAT
1 ATTATTATTATTTTATAAATAT-T
*
2799 ATATATTATTATTTAATAAATATT
1 AT-TATTATTATTTTATAAATATT
2823 A
1 A
2824 CAAACCCAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
22 8 0.20
23 4 0.10
24 20 0.50
25 8 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTATTATTATTTTATAAATATT
Found at i:2792 original size:18 final size:18
Alignment explanation
Indices: 2754--2809 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 18
2744 TTACTTAAAT
*
2754 TATTATTATTATTATAAA
1 TATTATTATTATTATTAA
*
2772 TATTATTATTATTATTTA
1 TATTATTATTATTATTAA
2790 TATTTATATATATATTATTA
1 TA-TTAT-TAT-TATTATTA
2810 TTTAATAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
18 18 0.56
19 4 0.12
20 3 0.09
21 7 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTATTATTATTATTAA
Found at i:4162 original size:19 final size:17
Alignment explanation
Indices: 4137--4183 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 17
4127 TAGTTTTTAA
4137 TATTATTACTTTTAATTT
1 TATTATTACTTTT-ATTT
4155 TAATTATTATTCTTTTATTT
1 T-ATTATTA--CTTTTATTT
4175 TATTATTAC
1 TATTATTAC
4184 GTTTGATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 1 0.04
18 1 0.04
19 14 0.54
20 5 0.19
21 5 0.19
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTATTACTTTTATTT
Found at i:4162 original size:22 final size:20
Alignment explanation
Indices: 4131--4182 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
4121 ATCCATTAGT
4131 TTTTAA-TATTATTACTTTTAA
1 TTTTAATTATTATT-CTTTT-A
4152 TTTTAATTATTATTCTTTTA
1 TTTTAATTATTATTCTTTTA
4172 TTTT-ATTATTA
1 TTTTAATTATTA
4183 CGTTTGATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.23
20 5 0.17
21 11 0.37
22 7 0.23
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTAATTATTATTCTTTTA
Found at i:4256 original size:14 final size:15
Alignment explanation
Indices: 4239--4271 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4229 TATTATTAAG
4239 TTATATAA-ATATAT
1 TTATATAATATATAT
*
4253 TTATATAATATCTAT
1 TTATATAATATATAT
4268 TTAT
1 TTAT
4272 TTATTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATATAATATATAT
Found at i:4669 original size:17 final size:15
Alignment explanation
Indices: 4639--4674 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
4629 AAATTATAGT
4639 AATAAATTTAAATTA
1 AATAAATTTAAATTA
4654 AATAGAATTATAAATTA
1 AATA-AATT-TAAATTA
4671 AATA
1 AATA
4675 TATCTTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 4 0.21
17 11 0.58
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (15 bp):
AATAAATTTAAATTA
Found at i:27919 original size:31 final size:31
Alignment explanation
Indices: 27847--27919 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
27837 AATCATAAAC
* *
27847 CAAAATGTAA-CAATACATAATATAAGTGAT
1 CAAAATGTAATAAATACATAAGATAAGTGAT
* *
27877 CAAAATTTAATAAATAGATAAGATAAGTG-T
1 CAAAATGTAATAAATACATAAGATAAGTGAT
*
27907 CTGAAATGTAATA
1 C-AAAATGTAATA
27920 TTTTCAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
30 11 0.31
31 24 0.69
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.29
Consensus pattern (31 bp):
CAAAATGTAATAAATACATAAGATAAGTGAT
Found at i:28182 original size:31 final size:31
Alignment explanation
Indices: 28114--28208 Score: 149
Period size: 31 Copynumber: 3.1 Consensus size: 31
28104 TGCTTTAACG
*
28114 AAATATCTAATGTGATACCTATA-TTT-TTA
1 AAATATCTAATGTGATATCTATACTTTGTTA
*
28143 AAACATCTAATGTGATATCTATACTTTGTTA
1 AAATATCTAATGTGATATCTATACTTTGTTA
*
28174 AAATATCTAATGTGATATATATACTTTGTTA
1 AAATATCTAATGTGATATCTATACTTTGTTA
28205 AAAT
1 AAAT
28209 GTTCAAATAG
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
29 21 0.35
30 3 0.05
31 36 0.60
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.43
Consensus pattern (31 bp):
AAATATCTAATGTGATATCTATACTTTGTTA
Found at i:29582 original size:28 final size:28
Alignment explanation
Indices: 29547--29619 Score: 139
Period size: 28 Copynumber: 2.6 Consensus size: 28
29537 ACTTACGCCT
29547 AAACTTTATTTAGGTTTTTTGTACAATA
1 AAACTTTATTTAGGTTTTTTGTACAATA
29575 AAACTTTATTTAGGTTTTTTGTACAATA
1 AAACTTTATTTAGGTTTTTTGTACAATA
29603 AAACTTTATTTA-GTTTT
1 AAACTTTATTTAGGTTTT
29620 AAATATTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 5 0.11
28 40 0.89
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.52
Consensus pattern (28 bp):
AAACTTTATTTAGGTTTTTTGTACAATA
Found at i:29756 original size:57 final size:57
Alignment explanation
Indices: 29688--29801 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
29678 ATATTGTAGG
29688 TGAAAATTTTAAAACTTATTTCATAATGACAATTAGTTTAATAGTAAAGAATTTGTT
1 TGAAAATTTTAAAACTTATTTCATAATGACAATTAGTTTAATAGTAAAGAATTTGTT
29745 TGAAAATTTTAAAACTTATTTCATAATGACAATTAGTTTAATAGTAAAGAATTTGTT
1 TGAAAATTTTAAAACTTATTTCATAATGACAATTAGTTTAATAGTAAAGAATTTGTT
29802 AGCAAATCAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (57 bp):
TGAAAATTTTAAAACTTATTTCATAATGACAATTAGTTTAATAGTAAAGAATTTGTT
Found at i:32842 original size:13 final size:13
Alignment explanation
Indices: 32817--32922 Score: 103
Period size: 13 Copynumber: 8.5 Consensus size: 13
32807 ATAAATCTAC
*
32817 GACGCGCATTTAT
1 GACGCGTATTTAT
*
32830 GACACGTATTTAT
1 GACGCGTATTTAT
32843 GACGCGTATTTAT
1 GACGCGTATTTAT
*
32856 GACGCGCA--T-T
1 GACGCGTATTTAT
**
32866 G-CGTATATTTAT
1 GACGCGTATTTAT
*
32878 GACGCGTATTTAC
1 GACGCGTATTTAT
*
32891 GACGCGCATTTAT
1 GACGCGTATTTAT
**
32904 GATACGTATTTAT
1 GACGCGTATTTAT
32917 GACGCG
1 GACGCG
32923 CATTGCGTGT
Statistics
Matches: 72, Mismatches: 17, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
9 3 0.04
10 2 0.03
11 2 0.03
12 2 0.03
13 63 0.88
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (13 bp):
GACGCGTATTTAT
Found at i:33048 original size:2 final size:2
Alignment explanation
Indices: 33041--33073 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
33031 TGTCGTAAAT
33041 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33074 TGTATATTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34577 original size:18 final size:18
Alignment explanation
Indices: 34554--34591 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
34544 ATGTTACCTA
34554 AATCATATTAGAAGTTAG
1 AATCATATTAGAAGTTAG
34572 AATCATATTAGAAGTTAG
1 AATCATATTAGAAGTTAG
34590 AA
1 AA
34592 AAAGTTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.32
Consensus pattern (18 bp):
AATCATATTAGAAGTTAG
Found at i:44157 original size:47 final size:47
Alignment explanation
Indices: 44105--44196 Score: 168
Period size: 47 Copynumber: 2.0 Consensus size: 47
44095 GTACCGATAC
44105 CATAGGCAAAAATTAGGCTAAATCAT-CTGAGAAGTATCGATACTGAT
1 CATAGGCAAAAATTAGGCTAAATCATAC-GAGAAGTATCGATACTGAT
44152 CATAGGCAAAAATTAGGCTAAATCATACGAGAAGTATCGATACTG
1 CATAGGCAAAAATTAGGCTAAATCATACGAGAAGTATCGATACTG
44197 TTTCAATAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
47 43 0.98
48 1 0.02
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (47 bp):
CATAGGCAAAAATTAGGCTAAATCATACGAGAAGTATCGATACTGAT
Found at i:44514 original size:94 final size:94
Alignment explanation
Indices: 44232--44540 Score: 309
Period size: 95 Copynumber: 3.3 Consensus size: 94
44222 AAGTGATATT
* * * * *
44232 GATATCATGGTGAGGGTATCGATACCAGGTAACATCGAACCTAATTTTGGTATCGATATCAT-AT
1 GATACCATGGTAAGGGTATCGATACCAGGAAACATAGAACCTAATTTTGGTATCGATA-C-TGAA
*
44296 AGGGGTATCGGTACCATAGTATAGTGGTATC
64 AGGGGTATCGGTACCATAGTATAGTAGTATC
*** ** * ** * * *
44327 GATACCTATGGTAAGGGTA-CGATATGGGGCCACATTGAATATAATTTTGGTATCAATGCCGTAA
1 GATACC-ATGGTAAGGGTATCGATACCAGGAAACATAGAACCTAATTTTGGTATCGATACTG-AA
* * *
44391 GGGGGTATCGGTACCATAGCATGGTAGTATC
64 AGGGGTATCGGTACCATAGTATAGTAGTATC
44422 GATACCATGGTAAGGGTATCGATACCAGGAAACATAGAACCTAATTTTGGTATCGATACTGAAAG
1 GATACCATGGTAAGGGTATCGATACCAGGAAACATAGAACCTAATTTTGGTATCGATACTGAAAG
* * * *
44487 AGGTATCGATACCATAATATAGAAGTATC
66 GGGTATCGGTACCATAGTATAGTAGTATC
* * *
44516 GGTACCAGGGT-AGAAGTATCGATAC
1 GATACCATGGTAAG-GGTATCGATAC
44541 TTCAGAGACA
Statistics
Matches: 170, Mismatches: 39, Indels: 11
0.77 0.18 0.05
Matches are distributed among these distances:
93 2 0.01
94 58 0.34
95 99 0.58
96 11 0.06
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.28
Consensus pattern (94 bp):
GATACCATGGTAAGGGTATCGATACCAGGAAACATAGAACCTAATTTTGGTATCGATACTGAAAG
GGGTATCGGTACCATAGTATAGTAGTATC
Found at i:45065 original size:79 final size:79
Alignment explanation
Indices: 44927--45307 Score: 529
Period size: 79 Copynumber: 4.9 Consensus size: 79
44917 GGCACTGTGT
* * * *
44927 GTGCAGTATTGGCATGAAAAGAT-TCCATAGCTAAAATGTATATGGGTACATTATCGGCATAAAA
1 GTGCATTATTGGCATGAAAGGATGT-CATAGCTGAAATGTATATGGGTACATTATCAGCATAAAA
44991 GAATAATGCATATGG
65 GAATAATGCATATGG
* * * **
45006 GTGTATTATTGGCATGAAACGATGTCATAGTTGAAATGTATATGGGTACATTATTGGCAT--AAG
1 GTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGTATATGGGTACATTATCAGCATAAAAG
* *
45069 AATAAGGCATATGA
66 AATAATGCATATGG
45083 GTGCATTATTGGCATGAAAGGAT-TCCATAGCTGAAATGTATATGGGTACATTATCAGCATAAAA
1 GTGCATTATTGGCATGAAAGGATGT-CATAGCTGAAATGTATATGGGTACATTATCAGCATAAAA
*
45147 GAATAATTCATATGG
65 GAATAATGCATATGG
* *
45162 GTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATAGGTACATTATCAGCATAAAAG
1 GTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGTATATGGGTACATTATCAGCATAAAAG
*
45227 AATAATACATATGG
66 AATAATGCATATGG
* * * * *
45241 ATGCATTATTGGCATGAAAGGATGTCAAAGTTGAAATGAATATGGGTGCATTATCA-CATAAAAG
1 GTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGTATATGGGTACATTATCAGCATAAAAG
45305 AAT
66 AAT
45308 GCTATAATTA
Statistics
Matches: 271, Mismatches: 26, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
76 1 0.00
77 68 0.25
78 11 0.04
79 190 0.70
80 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (79 bp):
GTGCATTATTGGCATGAAAGGATGTCATAGCTGAAATGTATATGGGTACATTATCAGCATAAAAG
AATAATGCATATGG
Found at i:45211 original size:156 final size:156
Alignment explanation
Indices: 44927--45307 Score: 543
Period size: 156 Copynumber: 2.4 Consensus size: 156
44917 GGCACTGTGT
* * * *
44927 GTGCAGTATTGGCATGAAAAGATTCCATAGCTAAAATGTATATGGGTACATTATCGGCATAAAAG
1 GTGCATTATTGGCATGAAAGGATTCCATAGCTGAAATGTATATGGGTACATTATCAGCATAAAAG
* * * *
44992 AATAATGCATATGGGTGTATTATTGGCATGAAACGATGTCATAGTTGAAATGTATATGGGTACAT
66 AATAATGCATATGGGTGCATTATTGGCATGAAACGATGCCATAGCTGAAATGTATATAGGTACAT
** *
45057 TATTGGCAT-AAGAATAAGGCATATG
131 TATCAGCATAAAGAATAAGACATATG
45082 AGTGCATTATTGGCATGAAAGGATTCCATAGCTGAAATGTATATGGGTACATTATCAGCATAAAA
1 -GTGCATTATTGGCATGAAAGGATTCCATAGCTGAAATGTATATGGGTACATTATCAGCATAAAA
* *
45147 GAATAATTCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATAGGTACA
65 GAATAATGCATATGGGTGCATTATTGGCATGAAACGATGCCATAGCTGAAATGTATATAGGTACA
*
45212 TTATCAGCATAAAAGAATAATACATATG
130 TTATCAGCAT-AAAGAATAAGACATATG
* * * *
45240 GATGCATTATTGGCATGAAAGGATGT-CAAAGTTGAAATGAATATGGGTGCATTATCA-CATAAA
1 G-TGCATTATTGGCATGAAAGGAT-TCCATAGCTGAAATGTATATGGGTACATTATCAGCATAAA
45303 AGAAT
64 AGAAT
45308 GCTATAATTA
Statistics
Matches: 203, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
156 127 0.63
157 12 0.06
158 63 0.31
159 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (156 bp):
GTGCATTATTGGCATGAAAGGATTCCATAGCTGAAATGTATATGGGTACATTATCAGCATAAAAG
AATAATGCATATGGGTGCATTATTGGCATGAAACGATGCCATAGCTGAAATGTATATAGGTACAT
TATCAGCATAAAGAATAAGACATATG
Found at i:45721 original size:2 final size:2
Alignment explanation
Indices: 45714--45748 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
45704 GGAAGGGATG
45714 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
45749 ATGTACAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:59025 original size:12 final size:11
Alignment explanation
Indices: 58959--59026 Score: 52
Period size: 11 Copynumber: 6.3 Consensus size: 11
58949 AAAATTTTAT
58959 TATTAAAAATA
1 TATTAAAAATA
58970 TATTAAAAATA
1 TATTAAAAATA
* * ***
58981 CACTATTGATA
1 TATTAAAAATA
58992 -ATTATAAAA-A
1 TATTA-AAAATA
59002 T-TTAAAAATA
1 TATTAAAAATA
59012 TATTAAAAATTA
1 TATTAAAAA-TA
59024 TAT
1 TAT
59027 AATACAATCA
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
9 4 0.09
10 9 0.21
11 25 0.58
12 5 0.12
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.38
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:59993 original size:25 final size:25
Alignment explanation
Indices: 59964--60013 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
59954 ACTTGTTATG
59964 AGGCTTATATAATTGATTGATTGTA
1 AGGCTTATATAATTGATTGATTGTA
59989 AGGCTTATATAATTGATTGATTGTA
1 AGGCTTATATAATTGATTGATTGTA
60014 GGAAAACCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.04, G:0.20, T:0.44
Consensus pattern (25 bp):
AGGCTTATATAATTGATTGATTGTA
Found at i:60808 original size:12 final size:12
Alignment explanation
Indices: 60786--60831 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
60776 AAATGAGCTT
*
60786 AAATTGAGCTCA
1 AAATCGAGCTCA
*
60798 AAGTCGAGCTCA
1 AAATCGAGCTCA
*
60810 AAATCGAGTTCA
1 AAATCGAGCTCA
60822 AAATCGAGCT
1 AAATCGAGCT
60832 TGAGTCTTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (12 bp):
AAATCGAGCTCA
Found at i:66670 original size:16 final size:15
Alignment explanation
Indices: 66625--66667 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
66615 TTTGACTTCA
66625 TAAAATTATAAATAAT
1 TAAAATTATAAAT-AT
*
66641 TAATA-TATTAAATAT
1 TAAAATTA-TAAATAT
66656 TAAAATTATAAA
1 TAAAATTATAAA
66668 ATAAATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAAATTATAAATAT
Found at i:70108 original size:24 final size:25
Alignment explanation
Indices: 70081--70129 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
70071 AAAGAAATAA
70081 AAATAA-ATTATCAATAT-AAAATTT
1 AAATAATATTAT-AATATGAAAATTT
*
70105 AAATAATATTATAATTTGAAAATTT
1 AAATAATATTATAATATGAAAATTT
70130 TAAGAAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (25 bp):
AAATAATATTATAATATGAAAATTT
Found at i:72089 original size:17 final size:17
Alignment explanation
Indices: 72067--72123 Score: 96
Period size: 17 Copynumber: 3.4 Consensus size: 17
72057 TTGACCGAGT
*
72067 CGATCTCGAGTAGCTCA
1 CGATCTCGAATAGCTCA
*
72084 CGATCTCGAATAGCTAA
1 CGATCTCGAATAGCTCA
72101 CGATCTCGAATAGCTCA
1 CGATCTCGAATAGCTCA
72118 CGATCT
1 CGATCT
72124 ATCTCGTCTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (17 bp):
CGATCTCGAATAGCTCA
Found at i:74043 original size:23 final size:23
Alignment explanation
Indices: 73999--74044 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
73989 TAACATATTA
**
73999 GTAGAGCTTATATAATGTAATAG
1 GTAGAGCTTATATAATAAAATAG
*
74022 GTAGCGCTTATATAATAAAATAG
1 GTAGAGCTTATATAATAAAATAG
74045 ACATTTAACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.33
Consensus pattern (23 bp):
GTAGAGCTTATATAATAAAATAG
Found at i:74557 original size:200 final size:198
Alignment explanation
Indices: 74139--74847 Score: 770
Period size: 200 Copynumber: 3.5 Consensus size: 198
74129 TTTTTGAAAT
* * * * * **
74139 AAACCGCTATATTTATATCGGTAACATTGCAAATTTACCTATTACATTATTATTATCGGTGACGA
1 AAACCGGTATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATCGGTTTCGA
*** * *
74204 TGTTTTTTACATCGATA-TAATTT-TAAATGTATCGACACTTTATGCTTGCACCTGGTTGGGCAT
66 TGTTTTTGGGATCGATACT-TTTTATAAATGTATCGACACTTTATGGTTGCACCT-GTT-----T
** * *
74267 TCATATTTCATTCTGGAAAAAAGTATCGACACAAACTAACAACGTGTCGATACATTAT-TTAGAC
124 TGGTA-TTCATTCTGGACAAAAGTATCGACACAAATTAACAA-GTGTCGATACATTATGTT-GAC
* *
74331 ATATTCTCTCATA
186 CTATTTTCTCATA
* *
74344 AAACCGGTATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGGTTTCGA
1 AAACCGGTATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATCGGTTTCGA
* *
74409 TGTTTATGGGATCGATACTTTTTATAAATGTATCGACACTCTATGGTTGCACCCT-TTTTGGTAT
66 TGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCA-CCTGTTTTGGTAT
* * * *
74473 TCATTCTGGACCAAAAGTATCAACACAAATTTATCAAGTGTCGATACTTTATGCTGACCTATTTT
130 TCATTCTGGA-CAAAAGTATCGACACAAA-TTAACAAGTGTCGATACATTATGTTGACCTATTTT
*
74538 ATCATA
193 CTCATA
* * * *
74544 AAACCGGTATATTTATATCGGTTACATTGTAAATTTACCTAATACATTATAATTATCAGTTTCGA
1 AAACCGGTATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATCGGTTTCGA
* * *
74609 TGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGGGTGCACCTCG-TTTGTGCA
66 TGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCT-GTTTTG-GTA
* *
74673 TTCATCCTGGACAATAAGTATCGACACAAATTACACAAGTGTCGATACATTATGTTGACCTGTTT
129 TTCATTCTGGACAA-AAGTATCGACACAAATTA-ACAAGTGTCGATACATTATGTTGACCTATTT
*
74738 TCTAAT-
192 TCTCATA
* * * * * *
74744 TAACTGGTATATTTATACCAGTTACATT-ATTAATTTACCTATTACATTATAATTATTGGTTTTG
1 AAACCGGTATATTTATACCGGTTACATTGA-AAATTTACCTATTACATTATAATTATCGGTTTCG
* *
74808 ATATTTTTTGGG-TCGATAC-TTGTATAAAATGTATCGACAC
65 AT-GTTTTTGGGATCGATACTTTTTAT-AAATGTATCGACAC
74848 ATATTTAGGT
Statistics
Matches: 431, Mismatches: 59, Indels: 33
0.82 0.11 0.06
Matches are distributed among these distances:
199 18 0.04
200 239 0.55
201 71 0.16
205 74 0.17
206 26 0.06
207 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (198 bp):
AAACCGGTATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATCGGTTTCGA
TGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCTGTTTTGGTATT
CATTCTGGACAAAAGTATCGACACAAATTAACAAGTGTCGATACATTATGTTGACCTATTTTCTC
ATA
Found at i:79211 original size:6 final size:6
Alignment explanation
Indices: 79204--79237 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
79194 GTTTGGATCA
* *
79204 TCATCA TCATCT TCATCG TCATCT TCATCT TCAT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCAT
79238 TGACCGCTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.21, C:0.32, G:0.03, T:0.44
Consensus pattern (6 bp):
TCATCT
Found at i:81025 original size:128 final size:133
Alignment explanation
Indices: 80876--81140 Score: 477
Period size: 132 Copynumber: 2.0 Consensus size: 133
80866 TTGGCATCCA
80876 TTATGGAAAAAATTATCGACACAATATTAATAA-GTCGAT-ATATTATAGACATATTCTCTCATA
1 TTATGGAAAAAATTATCGACACAATATTAATAAGGTCGATAATATTATAGACATATTCTCTCATA
80939 AAACCGGTATATGTATACCGG-TATATTACAAAATTACCTATTACAA-ATAATTAT-GGTTTCGA
66 AAACCGGTATATGTATACCGGTTATATTACAAAATTACCTATTACAATATAATTATGGGTTTCGA
81001 TGT
131 TGT
81004 TTATGGAAAAAATTATCGACACAATATTAATAAGTGTCGATACATATTATAGACATATTCTCTCA
1 TTATGGAAAAAATTATCGACACAATATTAATAAG-GTCGATA-ATATTATAGACATATTCTCTCA
81069 TAAAACCGGTATATGTATACCGGTTATATTACAAAATTACCTATTACAATATAATTATGGGTTTC
64 TAAAACCGGTATATGTATACCGGTTATATTACAAAATTACCTATTACAATATAATTATGGGTTTC
81134 GATGT
129 GATGT
81139 TT
1 TT
81141 TTGGGATCGA
Statistics
Matches: 130, Mismatches: 0, Indels: 7
0.95 0.00 0.05
Matches are distributed among these distances:
128 33 0.25
130 6 0.05
132 45 0.35
133 25 0.19
134 8 0.06
135 13 0.10
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (133 bp):
TTATGGAAAAAATTATCGACACAATATTAATAAGGTCGATAATATTATAGACATATTCTCTCATA
AAACCGGTATATGTATACCGGTTATATTACAAAATTACCTATTACAATATAATTATGGGTTTCGA
TGT
Found at i:81224 original size:142 final size:142
Alignment explanation
Indices: 81060--81341 Score: 467
Period size: 142 Copynumber: 2.0 Consensus size: 142
81050 TTATAGACAT
*
81060 ATTCTCTCATAAAACCGGTATATGTATACCGGTTATATT-ACAAAATTACCTATTACAATATAAT
1 ATTCTCTCATAAAACCGGTATATGTATACCGGTTACATTGA-AAAATTACCTATTACAATATAAT
* *
81124 TATGGGTTTCGATGTTTTTGGGATCGACACGTTTTGAAAATGTATCGACACTTTATGCGTTCACC
65 TATGGGTTTCGATGTTTTTGGGATAGACACGTTTTGAAAATGTATCGACACTTTATGCATTCACC
*
81189 CTTTTTGGCATCC
130 CTTTCTGGCATCC
* * * *
81202 ATTCTCTCATAAAACTGGTATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATT
1 ATTCTCTCATAAAACCGGTATATGTATACCGGTTACATTGAAAAATTACCTATTACAATATAATT
*
81267 ATGGGTTTCGATGTTTTTGGGATAGACACTTTTTGAAAATGTATCGACACTTTATGCATTCACCC
66 ATGGGTTTCGATGTTTTTGGGATAGACACGTTTTGAAAATGTATCGACACTTTATGCATTCACCC
81332 TTTCTGGCAT
131 TTTCTGGCAT
81342 GTAAGTGTCG
Statistics
Matches: 130, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
142 129 0.99
143 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (142 bp):
ATTCTCTCATAAAACCGGTATATGTATACCGGTTACATTGAAAAATTACCTATTACAATATAATT
ATGGGTTTCGATGTTTTTGGGATAGACACGTTTTGAAAATGTATCGACACTTTATGCATTCACCC
TTTCTGGCATCC
Found at i:81485 original size:167 final size:167
Alignment explanation
Indices: 81202--81508 Score: 524
Period size: 167 Copynumber: 1.8 Consensus size: 167
81192 TTTGGCATCC
*
81202 ATTCTCTCATAAAACTGGTATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATT
1 ATTCTCTCATAAAACTGATATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATT
* *
81267 ATGGGTTTCGATGTTTTTGGGATAGACACTTTTTGAAAATGTATCGACACTTTATGCATTCACCC
66 ATGGGTTTCGACGTTTTTGGGATAGACACTTTTTGAAAATATATCGACACTTTATGCATTCACCC
81332 TTTCTGGCATGTAAGTGTCGATACATGTTGTAGACCT
131 TTTCTGGCATGTAAGTGTCGATACATGTTGTAGACCT
* *
81369 ATTCTCTCATAAAATTGATATATTTATATCGGTTACATTGAAAATTTACCTATTACATTATAATT
1 ATTCTCTCATAAAACTGATATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATT
* * * * *
81434 ATGGGTTTCGACGTTTTTGGGATCGATACTTTTTGGAAATATATTGACACTTTATGCGTTCACCC
66 ATGGGTTTCGACGTTTTTGGGATAGACACTTTTTGAAAATATATCGACACTTTATGCATTCACCC
81499 TTTCTGGCAT
131 TTTCTGGCAT
81509 CCATTATGGA
Statistics
Matches: 130, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
167 130 1.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (167 bp):
ATTCTCTCATAAAACTGATATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATT
ATGGGTTTCGACGTTTTTGGGATAGACACTTTTTGAAAATATATCGACACTTTATGCATTCACCC
TTTCTGGCATGTAAGTGTCGATACATGTTGTAGACCT
Found at i:83639 original size:21 final size:21
Alignment explanation
Indices: 83614--83676 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
83604 CCTCTTATGC
* *
83614 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
83635 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
83656 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
83677 TTTGATTGTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:86089 original size:174 final size:180
Alignment explanation
Indices: 85866--86308 Score: 510
Period size: 182 Copynumber: 2.5 Consensus size: 180
85856 CGTACTTATG
** *
85866 AAAGTATCGACACTTTCAATATATCCGGTAGTACTTTACCGGTTTTATCATTTTTATATC-GTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGTACTTTACCGGTTTTATCATTTCGATACCTG-TT
* * *
85930 TTATCATATTTTTACCTG-T-T-G-AG-G-ATCGATACATTTTTATAAAGTATCGACACTTTATA
65 TTATCATATTTTTACATGTTATCGTAGTGTATCGATACAATTTTATAAAGTACCGACACTTTATA
* *
85989 GGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATT
130 GGCGCTAAAAATACTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATT
* * * *
86040 AAAGTACCGACACTTTAAATATATCTGGTAGCT-CTTTACTGGTTTTATCATTTCGATACCTGTT
1 AAAGTATCGACACTTTCAATATATCCGGTAG-TACTTTACCGGTTTTATCATTTCGATACCTGTT
* * *
86104 TTGTCATATTTTTACATGTTATATCGTTGTGTATCGATACAATTTTATAAAGTACCGATACTTTA
65 TTATCATATTTTTACATG-T-TATCGTAGTGTATCGATACAATTTTATAAAGTACCGACACTTTA
* * *
86169 TAGGTGTTAAAAATACTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
128 TAGGCGCTAAAAATACTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATT
* * * * * * *
86222 AAAGTATCGACACGTTCAATATATCCGGTAAG-AATTTATCGGTATTGTCTTTTCG-TGACCGGT
1 AAAGTATCGACACTTTCAATATATCCGGT-AGTACTTTACCGGTTTTATCATTTCGAT-ACCTGT
* *
86285 TTTATCGATATTGTTACCTGTTAT
64 TTTATC-ATATTTTTACATGTTAT
86309 ATTGATATGG
Statistics
Matches: 223, Mismatches: 32, Indels: 21
0.81 0.12 0.08
Matches are distributed among these distances:
174 69 0.31
175 2 0.01
177 1 0.00
178 1 0.00
179 1 0.00
180 1 0.00
181 5 0.02
182 130 0.58
183 13 0.06
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (180 bp):
AAAGTATCGACACTTTCAATATATCCGGTAGTACTTTACCGGTTTTATCATTTCGATACCTGTTT
TATCATATTTTTACATGTTATCGTAGTGTATCGATACAATTTTATAAAGTACCGACACTTTATAG
GCGCTAAAAATACTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATT
Found at i:96783 original size:21 final size:23
Alignment explanation
Indices: 96745--96786 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
96735 AAAAAATACA
*
96745 AAAATAAAAAGAATGAGAGAAAG
1 AAAATAAAAACAATGAGAGAAAG
96768 AAAA-AAAAACAA-GAGAGAA
1 AAAATAAAAACAATGAGAGAA
96787 CTTATCTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (23 bp):
AAAATAAAAACAATGAGAGAAAG
Found at i:98569 original size:3 final size:3
Alignment explanation
Indices: 98561--98594 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
98551 GGTGTACATT
98561 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
98595 TATGTATGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:98802 original size:18 final size:19
Alignment explanation
Indices: 98781--98825 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
98771 AATCAAGCCC
98781 TTTTTTAAATAAAATG-TT
1 TTTTTTAAATAAAATGATT
*
98799 TTTTATAAAATAAAATGATT
1 TTTT-TTAAATAAAATGATT
98819 TTATTTT
1 TT-TTTT
98826 CCTACCTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 4 0.18
19 11 0.50
20 5 0.23
21 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (19 bp):
TTTTTTAAATAAAATGATT
Found at i:111846 original size:31 final size:31
Alignment explanation
Indices: 111808--111934 Score: 200
Period size: 31 Copynumber: 4.1 Consensus size: 31
111798 GAGTCGAGGG
*
111808 TTACCTATGTTCTTCGGGACATATGGACAGA
1 TTACCTATGTTCTTCGGGACATATAGACAGA
* *
111839 TTACCTATGTTCTTCAGGACATATAGACATA
1 TTACCTATGTTCTTCGGGACATATAGACAGA
111870 TTACCTATGTTCTTCGGGACATATAGACAGA
1 TTACCTATGTTCTTCGGGACATATAGACAGA
* * *
111901 TTACCTATGTTCTTCGGGATATATGGATAGA
1 TTACCTATGTTCTTCGGGACATATAGACAGA
111932 TTA
1 TTA
111935 TTATACGAGT
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 88 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATAGACAGA
Found at i:115077 original size:13 final size:13
Alignment explanation
Indices: 115047--115080 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
115037 TCATCTCTAC
* *
115047 TTTTATTTCTTTA
1 TTTTCTTTCATTA
115060 TTTTCTTTCATTA
1 TTTTCTTTCATTA
115073 TTTTCTTT
1 TTTTCTTT
115081 TCACAATGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTCTTTCATTA
Found at i:116114 original size:24 final size:23
Alignment explanation
Indices: 116087--116143 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
116077 TCTGTCTTTT
116087 TGGCACGTTTTAAATATGCTCTTG
1 TGGCACGTTTTAAAT-TGCTCTTG
**
116111 TGGCAC-TCTTTACGTTGCTCTTG
1 TGGCACGT-TTTAAATTGCTCTTG
*
116134 TGGCATGTTT
1 TGGCACGTTT
116144 CCTCTACCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 16 0.57
24 12 0.43
ACGTcount: A:0.14, C:0.19, G:0.23, T:0.44
Consensus pattern (23 bp):
TGGCACGTTTTAAATTGCTCTTG
Found at i:119538 original size:32 final size:32
Alignment explanation
Indices: 119484--119588 Score: 131
Period size: 32 Copynumber: 3.3 Consensus size: 32
119474 ACTCCTTAAA
*
119484 ACATAGGT-ATACTGTCCATATGTCTCAAAAG
1 ACATAGGTAATTCTGTCCATATGTCTCAAAAG
* * *
119515 ACATAGGTAATTCTCTCCATATGTCCCGAAAG
1 ACATAGGTAATTCTGTCCATATGTCTCAAAAG
* * *
119547 ACATAGGTAATTCTGTCCATAAGTCTTAAAAT
1 ACATAGGTAATTCTGTCCATATGTCTCAAAAG
*
119579 ATATAGGTAA
1 ACATAGGTAA
119589 CCCTCGACTC
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
31 8 0.13
32 54 0.87
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (32 bp):
ACATAGGTAATTCTGTCCATATGTCTCAAAAG
Found at i:123647 original size:30 final size:31
Alignment explanation
Indices: 123608--123674 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
123598 GAAGGACCTA
* * *
123608 TCCAGAGGTCATAAAGAACCTCGG-CAACTG
1 TCCATAGGTCATAAAGAACCTAGGTAAACTG
* *
123638 TCCATAGGTCCTGAAGAACCTAGGTAAACTG
1 TCCATAGGTCATAAAGAACCTAGGTAAACTG
123669 TCCATA
1 TCCATA
123675 TGCTCCTTAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 20 0.65
31 11 0.35
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (31 bp):
TCCATAGGTCATAAAGAACCTAGGTAAACTG
Found at i:123671 original size:31 final size:31
Alignment explanation
Indices: 123633--123790 Score: 101
Period size: 32 Copynumber: 5.0 Consensus size: 31
123623 GAACCTCGGC
* *
123633 AACTGTCCATA-GGTCCTGAAGAACCTAGGTA
1 AACTGTCCATATGCTCCT-AAGAACATAGGTA
*
123664 AACTGTCCATATGCTCCTTAGAACATAGGTA
1 AACTGTCCATATGCTCCTAAGAACATAGGTA
* * **
123695 TATTGTCCATATGTCTCAAAAG-ACATAGGTA
1 AACTGTCCATATG-CTCCTAAGAACATAGGTA
* * *
123726 ATTCTGTACATATG-TCCCGAA-AGACATAGGTA
1 A-ACTGTCCATATGCT-CCTAAGA-ACATAGGTA
* * *
123758 ATTCTGTCCATATG-TCTCAAAAAACATAGGTA
1 A-ACTGTCCATATGCTC-CTAAGAACATAGGTA
123790 A
1 A
123791 CCCTTGACTC
Statistics
Matches: 103, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
30 1 0.01
31 46 0.45
32 55 0.53
33 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (31 bp):
AACTGTCCATATGCTCCTAAGAACATAGGTA
Found at i:123749 original size:32 final size:32
Alignment explanation
Indices: 123686--123790 Score: 151
Period size: 32 Copynumber: 3.3 Consensus size: 32
123676 GCTCCTTAGA
123686 ACATAGGT-ATAT-TGTCCATATGTCTCAAAAG
1 ACATAGGTAAT-TCTGTCCATATGTCTCAAAAG
* * *
123717 ACATAGGTAATTCTGTACATATGTCCCGAAAG
1 ACATAGGTAATTCTGTCCATATGTCTCAAAAG
*
123749 ACATAGGTAATTCTGTCCATATGTCTCAAAAA
1 ACATAGGTAATTCTGTCCATATGTCTCAAAAG
123781 ACATAGGTAA
1 ACATAGGTAA
123791 CCCTTGACTC
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
31 9 0.14
32 56 0.86
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (32 bp):
ACATAGGTAATTCTGTCCATATGTCTCAAAAG
Found at i:136795 original size:2 final size:2
Alignment explanation
Indices: 136783--136820 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
136773 TCAATTGTAT
136783 TA TA TA T- 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 TA
136821 GTCAATGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Done.