Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000576.1 Hibiscus syriacus cultivar Beakdansim tig00001128_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: 58507
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2491 original size:2 final size:2
Alignment explanation
Indices: 2486--2533 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
2476 AAAAAATAGC
2486 AT AT AT AT AT A- 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 AT AT AT AT AT
2527 AT AT AT A
1 AT AT AT A
2534 ATTTATTCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6957 original size:2 final size:2
Alignment explanation
Indices: 6950--6990 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
6940 TGTAACACAT
6950 TA TA TA TA 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 TA TA TA TA T
6991 TCGTATTCGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9631 original size:3 final size:3
Alignment explanation
Indices: 9625--9744 Score: 188
Period size: 3 Copynumber: 40.3 Consensus size: 3
9615 TTTTTTATCC
* *
9625 ATT ATT ATT ATT AAT ATT ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
9673 ATT ATT ATT ATT ATT ACT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
9720 ATT ATC ATT ATT ACT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
9745 AATATATTAA
Statistics
Matches: 107, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
2 2 0.02
3 105 0.98
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:10262 original size:23 final size:25
Alignment explanation
Indices: 10232--10282 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
10222 AGAACGAGAC
* *
10232 AGAGAGACA-A-AAAAAAAGAATAG
1 AGAGAGACATAGAAAAAAAAAACAG
10255 AGAGAGACATAGAAAAAAAAAACAG
1 AGAGAGACATAGAAAAAAAAAACAG
10280 AGA
1 AGA
10283 AAATACAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 9 0.38
24 1 0.04
25 14 0.58
ACGTcount: A:0.69, C:0.06, G:0.22, T:0.04
Consensus pattern (25 bp):
AGAGAGACATAGAAAAAAAAAACAG
Found at i:11166 original size:12 final size:12
Alignment explanation
Indices: 11151--11184 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
11141 TTTTATTATA
11151 TTATTAAATATT
1 TTATTAAATATT
11163 TTATTAAATATT
1 TTATTAAATATT
11175 TTA-TAAATAT
1 TTATTAAATAT
11185 ATAATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TTATTAAATATT
Found at i:11183 original size:11 final size:11
Alignment explanation
Indices: 11155--11194 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
11145 ATTATATTAT
11155 TAAATATTTTA
1 TAAATATTTTA
11166 TTAAATATTTTA
1 -TAAATATTTTA
* *
11178 TAAATATATAA
1 TAAATATTTTA
11189 TAAATA
1 TAAATA
11195 GTATTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TAAATATTTTA
Found at i:11918 original size:18 final size:18
Alignment explanation
Indices: 11871--11918 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
11861 CTTTTCAAAT
11871 TTTTTA-TTTATTTATTA
1 TTTTTATTTTATTTATTA
**
11888 TTTTTATAATATTTA-TA
1 TTTTTATTTTATTTATTA
11905 TGTTTTATTTTATT
1 T-TTTTATTTTATT
11919 GCAAGTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTTTATTTTATTTATTA
Found at i:23955 original size:84 final size:84
Alignment explanation
Indices: 23702--23938 Score: 458
Period size: 84 Copynumber: 2.8 Consensus size: 84
23692 ATATCTTAGT
23702 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
23767 CTGATCTGGTTTGGCAGAA
66 CTGATCTGGTTTGGCAGAA
23786 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
23851 CTGATCTGGTTTGGCAGAA
66 CTGATCTGGTTTGGCAGAA
*
23870 CCAATCATTGAATTTGGAAGATGAATTTG-TTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
23934 CTGAT
66 CTGAT
23939 TTGATTCAGT
Statistics
Matches: 152, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
83 39 0.26
84 113 0.74
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.38
Consensus pattern (84 bp):
CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGGTTTGGCAGAA
Found at i:24771 original size:113 final size:113
Alignment explanation
Indices: 24574--25355 Score: 1272
Period size: 113 Copynumber: 6.9 Consensus size: 113
24564 ATTCAAATCT
* * *
24574 ATCATTTGATGGGTTAGCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
24638 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
24686 ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
24751 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
24799 ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAAT--G-AGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
24861 GCAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
* * * * *
24909 ATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAATTCGTTATCTGAAGAA
1 ATCATTTGATGGATCATCTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
24973 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
62 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
25025 ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
25090 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
* * * * *
25138 ATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAATTCGTTATCTGAAGAA
1 ATCATTTGATGGATCATCTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
25202 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
62 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
* * *
25254 ATCAATTGATGGATTATCTTTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAA
1 ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
25318 GAAGAAGTTCATAATAAGAAGAATTTATTCAACCTTTT
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
25356 GAATGACTCT
Statistics
Matches: 626, Mismatches: 30, Indels: 28
0.92 0.04 0.04
Matches are distributed among these distances:
109 1 0.00
110 102 0.16
111 1 0.00
112 77 0.12
113 234 0.37
114 1 0.00
115 21 0.03
116 188 0.30
117 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (113 bp):
ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
Found at i:25149 original size:229 final size:229
Alignment explanation
Indices: 24574--25355 Score: 1366
Period size: 229 Copynumber: 3.4 Consensus size: 229
24564 ATTCAAATCT
* * *
24574 ATCATTTGATGGGTTAGCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
24638 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCATTTGATGGATCAT
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCATTTGATGGATCAA
* * * *
24703 CTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATA
131 CATTGCCAG-GTAGAGTTCATAATGAGAAGAATTCGTTATCTGAAGAAGGAAGAAGAAGTTCATA
24764 ATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
195 ATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
24799 ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAAT--G-AGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
24861 GCAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCATTTGATGGATCAA
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCATTTGATGGATCAA
24926 CATTGCCAGGTAGAGTTCATAATGAGAAGAATTCGTTATCTGAAGAAGGAAGAAGAAGTTCATAA
131 CATTGCCAGGTAGAGTTCATAATGAGAAGAATTCGTTATCTGAAGAAGGAAGAAGAAGTTCATAA
24991 TGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
196 TGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
25025 ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
25090 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCATTTGATGGATCAA
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCATTTGATGGATCAA
25155 CATTGCCAGGTAGAGTTCATAATGAGAAGAATTCGTTATCTGAAGAAGGAAGAAGAAGTTCATAA
131 CATTGCCAGGTAGAGTTCATAATGAGAAGAATTCGTTATCTGAAGAAGGAAGAAGAAGTTCATAA
25220 TGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
196 TGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
* * *
25254 ATCAATTGATGGATTATCTTTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAA
1 ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
25318 GAAGAAGTTCATAATAAGAAGAATTTATTCAACCTTTT
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
25356 GAATGACTCT
Statistics
Matches: 534, Mismatches: 15, Indels: 13
0.95 0.03 0.02
Matches are distributed among these distances:
222 1 0.00
223 110 0.21
224 1 0.00
225 26 0.05
226 114 0.21
228 73 0.14
229 209 0.39
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (229 bp):
ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCATTTGATGGATCAA
CATTGCCAGGTAGAGTTCATAATGAGAAGAATTCGTTATCTGAAGAAGGAAGAAGAAGTTCATAA
TGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
Found at i:25682 original size:3 final size:3
Alignment explanation
Indices: 25674--25801 Score: 211
Period size: 3 Copynumber: 42.7 Consensus size: 3
25664 TTTTTATCCA
* *
25674 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
25722 TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
25770 TAT TAT TAT TAT CAT TAT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
25802 AATATATTAA
Statistics
Matches: 115, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 115 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:26306 original size:24 final size:25
Alignment explanation
Indices: 26274--26325 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
26264 AGAACGAGAC
*
26274 AGAGAGACA-A-AAAAAAAAGAATAG
1 AGAGAGACATAGAAAAAAAA-AACAG
26298 AGAGAGACATAGAAAAAAAAAACAG
1 AGAGAGACATAGAAAAAAAAAACAG
26323 AGA
1 AGA
26326 AAATACAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 9 0.36
25 8 0.32
26 8 0.32
ACGTcount: A:0.69, C:0.06, G:0.21, T:0.04
Consensus pattern (25 bp):
AGAGAGACATAGAAAAAAAAAACAG
Found at i:27154 original size:19 final size:18
Alignment explanation
Indices: 27118--27166 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
27108 TAGATTTTTA
*
27118 ATTTTATT-TTTTCGTTT
1 ATTTTATTGTTTTCATTT
27135 ATTTTATATGTTTTCATTT
1 ATTTTAT-TGTTTTCATTT
27154 ATTTTATTGTTTT
1 ATTTTATTGTTTT
27167 TAAATATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
19 15 0.52
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.73
Consensus pattern (18 bp):
ATTTTATTGTTTTCATTT
Found at i:27235 original size:13 final size:13
Alignment explanation
Indices: 27207--27241 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
27197 TTTTATTATA
27207 TTATTAAATA-TT
1 TTATTAAATATTT
27219 TTATTAAATATTT
1 TTATTAAATATTT
27232 TTA-TAAATAT
1 TTATTAAATAT
27242 ATAATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATTAAATATTT
Found at i:28334 original size:17 final size:17
Alignment explanation
Indices: 28312--28358 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
28302 ATAATATTTT
28312 AAAATAAGAATTCAAAA
1 AAAATAAGAATTCAAAA
* *
28329 AAAATAAAAATT-ATAA
1 AAAATAAGAATTCAAAA
* *
28345 AATATATGAATTCA
1 AAAATAAGAATTCA
28359 TAATCTATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (17 bp):
AAAATAAGAATTCAAAA
Found at i:30174 original size:66 final size:66
Alignment explanation
Indices: 30092--30223 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
30082 CACAATTCTT
30092 GGTCAGATTATCTTGCACATAGTTTTAGATGTATTTGACTAAAAGAAATGATAAAATCAACTTTA
1 GGTCAGATTATCTTGCACATAGTTTTAGATGTATTTGACTAAAAGAAATGATAAAATCAACTTTA
30157 A
66 A
30158 GGTCAGATTATCTTGCACATAGTTTTAGATGTATTTGACTAAAAGAAATGATAAAATCAACTTTA
1 GGTCAGATTATCTTGCACATAGTTTTAGATGTATTTGACTAAAAGAAATGATAAAATCAACTTTA
30223 A
66 A
30224 AAACGATTGA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (66 bp):
GGTCAGATTATCTTGCACATAGTTTTAGATGTATTTGACTAAAAGAAATGATAAAATCAACTTTA
A
Found at i:33747 original size:3 final size:3
Alignment explanation
Indices: 33734--33773 Score: 55
Period size: 3 Copynumber: 13.0 Consensus size: 3
33724 AATTTTTAAA
33734 ATT ATT AATT ATT ATT ATT ATT A-T ATT ATTT ATT ATT ATT
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
33774 TATATATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 2 0.06
3 26 0.76
4 6 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:33774 original size:10 final size:10
Alignment explanation
Indices: 33735--33791 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
33725 ATTTTTAAAA
33735 TTATTAATTA-
1 TTATT-ATTAT
33745 TTATTATTA-
1 TTATTATTAT
33754 TTA-TATTAT
1 TTATTATTAT
33763 TTATTATTAT
1 TTATTATTAT
33773 TTA-TATATAT
1 TTATTAT-TAT
33783 TTATATATT
1 TTAT-TATT
33792 TCTATTTATA
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
8 5 0.12
9 13 0.31
10 20 0.48
11 1 0.02
12 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTATTATTAT
Found at i:33786 original size:14 final size:15
Alignment explanation
Indices: 33751--33815 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
33741 ATTATTATTA
*
33751 TTAT-TATATTATTT
1 TTATATATATTATAT
*
33765 ATTATTATTTATATATAT
1 -TTA-TATATAT-TATAT
*
33783 TTATATAT-TTCTAT
1 TTATATATATTATAT
*
33797 TTATATATTTTATAT
1 TTATATATATTATAT
33812 TTAT
1 TTAT
33816 GTTTCATTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
14 12 0.29
15 13 0.32
16 5 0.12
17 7 0.17
18 4 0.10
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATATATATTATAT
Found at i:33786 original size:24 final size:24
Alignment explanation
Indices: 33742--33815 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
33732 AAATTATTAA
33742 TTATTATTA-TTAT-TATA-TTAT
1 TTATTATTATTTATATATATTTAT
33763 TTATTATTATTTATATATATTTAT
1 TTATTATTATTTATATATATTTAT
* *
33787 ATATT-TCTATTTATATATTTTATAT
1 TTATTAT-TATTTATATATATT-TAT
33812 TTAT
1 TTAT
33816 GTTTCATTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
21 9 0.20
22 4 0.09
23 5 0.11
24 21 0.47
25 6 0.13
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (24 bp):
TTATTATTATTTATATATATTTAT
Found at i:33841 original size:9 final size:10
Alignment explanation
Indices: 33810--33843 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
33800 TATATTTTAT
33810 ATTTATGTTTC
1 ATTTAT-TTTC
33821 ATTTATTTTC
1 ATTTATTTTC
33831 ATTTA-TTTC
1 ATTTATTTTC
33840 ATTT
1 ATTT
33844 GCATTTGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 8 0.35
10 9 0.39
11 6 0.26
ACGTcount: A:0.21, C:0.09, G:0.03, T:0.68
Consensus pattern (10 bp):
ATTTATTTTC
Found at i:35638 original size:16 final size:16
Alignment explanation
Indices: 35615--35653 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
35605 CCTTATTGTC
35615 TATATTTTT-TATAGA
1 TATATTTTTATATAGA
*
35630 TATATTTTTATCTAGA
1 TATATTTTTATATAGA
35646 TATATTTT
1 TATATTTT
35654 AAATACAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (16 bp):
TATATTTTTATATAGA
Found at i:39669 original size:36 final size:36
Alignment explanation
Indices: 39616--39819 Score: 338
Period size: 36 Copynumber: 5.7 Consensus size: 36
39606 AATTACATCC
*
39616 ACTTTAGC-TTAGGTAAAAGCTTAAATGTAATATGA
1 ACTTTAGCTTTAGGTAAAAGCTTAAACGTAATATGA
* *
39651 ACTTTAGCTTTAGGTAAAAGCTTATACATAATATGA
1 ACTTTAGCTTTAGGTAAAAGCTTAAACGTAATATGA
39687 ACTTTAGCTTTAGGTAAAAGCTTAAACGTAATATGA
1 ACTTTAGCTTTAGGTAAAAGCTTAAACGTAATATGA
*
39723 ACTTTAGCTTTAGGTAAAAGCTTAAACGTAATATAA
1 ACTTTAGCTTTAGGTAAAAGCTTAAACGTAATATGA
* * *
39759 ACTTTAGCTTTAAGTAAAATCTTAAACATAATATGA
1 ACTTTAGCTTTAGGTAAAAGCTTAAACGTAATATGA
39795 ACTTTAGCTTTAGGTAAAAGCTTAA
1 ACTTTAGCTTTAGGTAAAAGCTTAA
39820 TACTTCATAT
Statistics
Matches: 156, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
35 8 0.05
36 148 0.95
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (36 bp):
ACTTTAGCTTTAGGTAAAAGCTTAAACGTAATATGA
Found at i:42884 original size:15 final size:15
Alignment explanation
Indices: 42866--42894 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
42856 TTCATTTCAA
42866 AATTTTATAAAATAC
1 AATTTTATAAAATAC
42881 AATTTTATAAAATA
1 AATTTTATAAAATA
42895 ACTTAAAAAA
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:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTTTATAAAATAC
Found at i:42918 original size:25 final size:23
Alignment explanation
Indices: 42890--42938 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
42880 CAATTTTATA
*
42890 AAATAACTTAAAAAAATTTAAAAAT
1 AAATAAC--AAAAAAATATAAAAAT
*
42915 AAATAACAAGAAAATATAAAAAT
1 AAATAACAAAAAAATATAAAAAT
42938 A
1 A
42939 TATACATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 15 0.68
25 7 0.32
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (23 bp):
AAATAACAAAAAAATATAAAAAT
Found at i:54205 original size:19 final size:19
Alignment explanation
Indices: 54164--54205 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
54154 TAAAACTAAT
*
54164 AAAATAATAATAATAAACG
1 AAAATAATAATAATAAAAG
54183 -AAATAAATAATAA-AAAAG
1 AAAAT-AATAATAATAAAAG
54201 AAAAT
1 AAAAT
54206 CAAAATGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (19 bp):
AAAATAATAATAATAAAAG
Found at i:56022 original size:15 final size:15
Alignment explanation
Indices: 56003--56033 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
55993 TATGTAAGAA
56003 AAAAATAATTAATAAT
1 AAAAATAA-TAATAAT
56019 AAAAATAATAATAAT
1 AAAAATAATAATAAT
56034 TAATAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAAATAATAATAAT
Found at i:56028 original size:19 final size:18
Alignment explanation
Indices: 56001--56039 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
55991 CATATGTAAG
56001 AAAAAAATAATTAA-TAAT
1 AAAAAAATAA-TAATTAAT
56019 AAAAATAATAATAATTAAT
1 AAAAA-AATAATAATTAAT
56038 AA
1 AA
56040 TATAACATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAAAAATAATAATTAAT
Found at i:56034 original size:22 final size:23
Alignment explanation
Indices: 56006--56060 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 23
55996 GTAAGAAAAA
56006 AATAATTAATAATA-AAAATAAT
1 AATAATTAATAATATAAAATAAT
*
56028 AATAATTAATAATATAACATAAT
1 AATAATTAATAATATAAAATAAT
56051 -ATAATATAAT
1 AATAAT-TAAT
56061 GTTTTTGTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
AATAATTAATAATATAAAATAAT
Found at i:56531 original size:81 final size:79
Alignment explanation
Indices: 56391--56662 Score: 319
Period size: 81 Copynumber: 3.3 Consensus size: 79
56381 ATATGCCCTC
* * * *
56391 GAGCTGAATGGAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCCTAAGCTATGCTGC
1 GAGCTGAGTGGAGTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTATG-TGC
*
56456 AAATGATGATGCATTT
65 AAATGATG-TGCCTTT
* *
56472 GAGCTGAGTGGAGTCGAATTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGGGCTATGTCGC
1 GAGCTGAGTGGAGTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGT-GC
*
56537 AAATGATGGTTCCTTT
65 AAATGAT-GTGCCTTT
* * * *
56553 GAGTTGAGTGGAGTCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGT
1 GAGCTGAGTGGAGTCGAACTCGAAGGTCTTTG--G-CAGATAGCCCTTCTTGCCTTGAGCTATG-
* * *
56618 TGTAAATGACGTGCCTTG
62 TGCAAATGATGTGCCTTT
* *
56636 GAGCTGAGCGTAGTCGAACTCGAAGGT
1 GAGCTGAGTGGAGTCGAACTCGAAGGT
56663 TTGGTGTTTC
Statistics
Matches: 164, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
80 1 0.01
81 99 0.60
82 1 0.01
83 31 0.19
84 31 0.19
85 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (79 bp):
GAGCTGAGTGGAGTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGTGCA
AATGATGTGCCTTT
Found at i:56699 original size:30 final size:30
Alignment explanation
Indices: 56663--56778 Score: 110
Period size: 30 Copynumber: 3.6 Consensus size: 30
56653 ACTCGAAGGT
56663 TTGGTGTTTCAAGAGAAACATTTTCAAAGA
1 TTGGTGTTTCAAGAGAAACATTTTCAAAGA
*
56693 TTGGTGTTTCAAGAGAAAC-TATCTCAAGGGAGGCAAAA
1 TTGGTGTTTCAAGAGAAACAT-TTTCAA---A-G----A
* *
56731 TT-TTGTTTCAAGAGAAACATATTCAAAGA
1 TTGGTGTTTCAAGAGAAACATTTTCAAAGA
56760 TTGGTGTTTCAAGAGAAAC
1 TTGGTGTTTCAAGAGAAAC
56779 TATCTCAAGA
Statistics
Matches: 70, Mismatches: 5, Indels: 22
0.72 0.05 0.23
Matches are distributed among these distances:
29 4 0.06
30 39 0.56
33 2 0.03
34 2 0.03
37 19 0.27
38 4 0.06
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (30 bp):
TTGGTGTTTCAAGAGAAACATTTTCAAAGA
Found at i:56747 original size:37 final size:35
Alignment explanation
Indices: 56697--56846 Score: 145
Period size: 37 Copynumber: 4.3 Consensus size: 35
56687 CAAAGATTGG
*
56697 TGTTTCAAGAGAAACTATCTCAAGGGAGGCAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGA-G-AAAATTT
*
56734 TGTTTCAAGAGAAACATAT-TC-A-A-AG---ATTGG
1 TGTTTCAAGAGAAAC-TATCTCAAGAGAGAAAATT-T
56764 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAG--AAAATTT
* * *
56801 TGTTTCAAGGGAAATTGTCTCAAGAGAGAAAA-TT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGAAAATTT
56835 TGTTTCAAGAGA
1 TGTTTCAAGAGA
56847 GACAAAACTT
Statistics
Matches: 95, Mismatches: 7, Indels: 25
0.75 0.06 0.20
Matches are distributed among these distances:
29 6 0.06
30 17 0.18
31 1 0.01
32 1 0.01
33 3 0.03
34 14 0.15
35 4 0.04
36 1 0.01
37 42 0.44
38 6 0.06
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (35 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGAAAATTT
Found at i:56775 original size:67 final size:67
Alignment explanation
Indices: 56667--56814 Score: 260
Period size: 67 Copynumber: 2.2 Consensus size: 67
56657 GAAGGTTTGG
* * *
56667 TGTTTCAAGAGAAACATTTTCAAAGATTGGTGTTTCAAGAGAAACTATCTCAAGGGAGGCAAAAT
1 TGTTTCAAGAGAAACATATTCAAAGATTGGTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAAT
56732 TT
66 TT
56734 TGTTTCAAGAGAAACATATTCAAAGATTGGTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAAT
1 TGTTTCAAGAGAAACATATTCAAAGATTGGTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAAT
56799 TT
66 TT
*
56801 TGTTTCAAGGGAAA
1 TGTTTCAAGAGAAA
56815 TTGTCTCAAG
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 77 1.00
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.29
Consensus pattern (67 bp):
TGTTTCAAGAGAAACATATTCAAAGATTGGTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAAT
TT
Found at i:56842 original size:19 final size:19
Alignment explanation
Indices: 56783--56848 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
56773 AGAAACTATC
56783 TCAAGAGAGACAAAATTTTGTT
1 TCAAGAGAG--AAAA-TTTGTT
*
56805 TCAAG-G-G-AAA-TTGTC
1 TCAAGAGAGAAAATTTGTT
56820 TCAAGAGAGAAAATTTGTT
1 TCAAGAGAGAAAATTTGTT
56839 TCAAGAGAGA
1 TCAAGAGAGA
56849 CAAAACTTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
15 9 0.24
16 1 0.03
17 4 0.11
18 3 0.08
19 14 0.37
20 1 0.03
21 1 0.03
22 5 0.13
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (19 bp):
TCAAGAGAGAAAATTTGTT
Found at i:56965 original size:21 final size:21
Alignment explanation
Indices: 56936--57005 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
56926 TTAAGGGAAA
56936 TTGTCTCAAGAGAGACAAAAT
1 TTGTCTCAAGAGAGACAAAAT
*
56957 TTGTTTCAAG-G-G---AAA-
1 TTGTCTCAAGAGAGACAAAAT
*
56972 CTGTCTCAAGAGAGACAAAAT
1 TTGTCTCAAGAGAGACAAAAT
*
56993 TTGTTTCAAGAGA
1 TTGTCTCAAGAGA
57006 AATTGTATCA
Statistics
Matches: 38, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
15 8 0.21
16 4 0.11
17 1 0.03
19 1 0.03
20 4 0.11
21 20 0.53
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (21 bp):
TTGTCTCAAGAGAGACAAAAT
Found at i:56968 original size:36 final size:36
Alignment explanation
Indices: 56920--57312 Score: 430
Period size: 36 Copynumber: 11.0 Consensus size: 36
56910 ATTCAAAGAT
* *
56920 TTTGTTTTAAGGGAAATTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
56956 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
56992 TTTGTTTCAAGAGAAATTGTATCAAGAGAGACAAAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTC-A-AGAG----AGACAAAA
* * * *
57034 TTTGTTTCGAGAGAAACTATCTCAAGAGATACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** * *
57070 CTTAGTTCCAAAAGAAACTATCTCAAGAGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
** * *
57107 TTTGTTT-AATGTAAAACATAT-TC-A-A-AG----AT
1 TTTGTTTCAA-GGGAAAC-TGTCTCAAGAGAGACAAAA
57136 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
57172 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACATAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
57208 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
57244 TTTGTTTCAAGGGAAACTGTCTTAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
57280 TTTGTTT-AAGAGAAACTGTCTC-AGAGAGACAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
57313 CTTGTTTTGA
Statistics
Matches: 308, Mismatches: 31, Indels: 38
0.82 0.08 0.10
Matches are distributed among these distances:
28 2 0.01
29 15 0.05
30 3 0.01
31 1 0.00
32 2 0.01
33 2 0.01
34 12 0.04
35 16 0.05
36 185 0.60
37 34 0.11
38 4 0.01
40 4 0.01
41 1 0.00
42 27 0.09
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:57035 original size:42 final size:42
Alignment explanation
Indices: 56948--57068 Score: 146
Period size: 42 Copynumber: 3.0 Consensus size: 42
56938 GTCTCAAGAG
*
56948 AGACAAAATTTGTTTCAAGGGAAACTGTCTC-A-AGAG----
1 AGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
* *
56984 AGACAAAATTTGTTTCAAGAGAAATTGTATCAAGAGAGACAA
1 AGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
* * *
57026 AGACAAAATTTGTTTCGAGAGAAACTATCTCAAGAGATACAA
1 AGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
57068 A
1 A
57069 ACTTAGTTCC
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
36 28 0.39
37 1 0.01
38 4 0.06
42 38 0.54
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.24
Consensus pattern (42 bp):
AGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
Found at i:57074 original size:216 final size:216
Alignment explanation
Indices: 56839--57319 Score: 680
Period size: 216 Copynumber: 2.3 Consensus size: 216
56829 AAAATTTGTT
* * *
56839 TCAAGAGAGACAAAACTTAGTTCCGAAATAAACTGTCTCAA-AGGAGACGAAATTTGTTTCAA-G
1 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTATCTCAAGA-GAGACGAAATTTGTTT-AATG
* *
56902 GAAAACATATTCAAAGATTTTGTTTTAAGGGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAG
64 GAAAACATATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAG
*
56967 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATTGTATCAAGAGAGACAAAGACAA
129 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTATCAAGAGAGACAAAGACAA
57032 AATTTGTTTCGAGAGAAACTATC
194 AATTTGTTTCGAGAGAAACTATC
* *
57055 TCAAGAGATACAAAACTTAGTTCCAAAAGAAACTATCTCAAGAGAGACGAAATTTGTTTAATGTA
1 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTATCTCAAGAGAGACGAAATTTGTTTAATGGA
57120 AAACATATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGG
66 AAACATATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGG
* * *
57185 AAACTGTCTCAAGAGAGACATAATTTGTTTCAAGGGAAACTGTCTC-A-AGAG----AGACAAAA
131 AAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTATCAAGAGAGACAAAGACAAAA
* * *
57244 TTTGTTTCAAGGGAAACTGTC
196 TTTGTTTCGAGAGAAACTATC
* * * * * *
57265 TTAAGAGAGACAAAA-TTTGTT-TAAGAGAAACTGTCTC-AGAGAGAC-AAACTTGTTT
1 TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTATCTCAAGAGAGACGAAATTTGTTT
57320 TGAGTAAATT
Statistics
Matches: 242, Mismatches: 21, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
206 9 0.04
207 8 0.03
208 13 0.05
209 5 0.02
210 39 0.16
214 4 0.02
215 3 0.01
216 160 0.66
217 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (216 bp):
TCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTATCTCAAGAGAGACGAAATTTGTTTAATGGA
AAACATATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGG
AAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTATCAAGAGAGACAAAGACAAAA
TTTGTTTCGAGAGAAACTATC
Found at i:57748 original size:123 final size:121
Alignment explanation
Indices: 57497--57960 Score: 509
Period size: 123 Copynumber: 3.8 Consensus size: 121
57487 ACTTCATCAG
** * ** * * * * * *
57497 GCACGATAGCCTTCCTCGTGAAGTTGAAATTGTGGATGGCTCTTTCGCTGTGAAATTGAGCTTTT
1 GCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGC-CTG
** * * *
57562 AA-TTGACGTCCTTCATTGTGAAGTTAAAATCCACACTGAAGATGATGTTGCTGGTGG
65 AACTTGATATCCTTCGTCGTGAAGTTAAAATCCA-ACTGAAGATGATGTTGCTGGTGA
* * * * * *
57619 GTACGATTCCCTTCTTTGTGAAGTTAAAATCGTGGATGGCCCATTCGTTGCGAAGTTGAGCCTCG
1 GCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCT-G
* * *
57684 AA-TTGGATATCCTTCGTCGTGAAGTTAAAATTCAATCTAAAGATGATGTTGTTGGTGA
65 AACTT-GATATCCTTCGTCGTGAAGTTAAAATCCAA-CTGAAGATGATGTTGCTGGTGA
* *
57742 GCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCTCATTCGTTGTGAAGTTGAGCCTTA
1 GCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTGA
** * *
57807 ACTTGATATCCTTCGTCGTGAAAATGAAATCCAAGCTGAAGATGAATGTTACTGGTGA
66 ACTTGATATCCTTCGTCGTGAAGTTAAAATCCAA-CTGAAGATG-ATGTTGCTGGTGA
* *
57865 ACACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTA
1 GCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTGA
* * * *
57930 GCTTGAATATCCTTCGCCGCGAAGTTGAAAT
66 ACTTG-ATATCCTTCGTCGTGAAGTTAAAAT
57961 TGGTTCTGAA
Statistics
Matches: 291, Mismatches: 45, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
121 1 0.00
122 90 0.31
123 179 0.62
124 21 0.07
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (121 bp):
GCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTGA
ACTTGATATCCTTCGTCGTGAAGTTAAAATCCAACTGAAGATGATGTTGCTGGTGA
Found at i:57942 original size:246 final size:245
Alignment explanation
Indices: 57497--57961 Score: 594
Period size: 246 Copynumber: 1.9 Consensus size: 245
57487 ACTTCATCAG
* ** * *
57497 GCACGATAGCCTTCCTCGTGAAGTTGAAATTGTGGATGGCTCTTTCGCTGTGAAATTGAGCTTTT
1 GCACGATACCCTTCCTCGTGAAGTTGAAACCGTGGATGGCTCATTCGCTGTGAAATTGAGCTCTT
* * ** * ***
57562 AATTGACGTCCTTCATTGTGAAGTTAAAATCCACACTGAAGATGATGTTGCTGGTGGGTACGATT
66 AATTGACATCCTTCATCGTGAAAATAAAATCCACACTGAAGATGATGTTACTGGTGAACACGATT
* * * * *
57627 CCCTTCTTTGTGAAGTTAAAATCGTGGATGGCCCATTCGTTGCGAAGTTGAGCCTCGAATTGGAT
131 CCCTTCGTCGTGAAGTTAAAACCGTGGATGGCCCATTCGTTGCGAAGTTGAGCCTAGAATTGAAT
* *
57692 ATCCTTCGTCGTGAAGTTAAAATTCAATCTAAAGATGATGTTGTTGGTGA
196 ATCCTTCGCCGCGAAGTTAAAATTCAATCTAAAGATGATGTTGTTGGTGA
* * * *
57742 GCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCTCATTCGTTGTGAAGTTGAGC-CTT
1 GCACGATACCCTTCCTCGTGAAGTTGAAACCGTGGATGGCTCATTCGCTGTGAAATTGAGCTCTT
* * *
57806 AACTTGATATCCTTCGTCGTGAAAATGAAATCCA-AGCTGAAGATGAATGTTACTGGTGAACACG
66 AA-TTGACATCCTTCATCGTGAAAATAAAATCCACA-CTGAAGATG-ATGTTACTGGTGAACACG
* * *
57870 ATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGAGCCTTAG-CTT
128 ATTCCCTTCGTCGTGAAGTTAAAACCGTGGATGGCCCATTCGTTGCGAAGTTGAGCC-TAGAATT
*
57934 GAATATCCTTCGCCGCGAAGTTGAAATT
192 GAATATCCTTCGCCGCGAAGTTAAAATT
57962 GGTTCTGAAT
Statistics
Matches: 185, Mismatches: 31, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
244 5 0.03
245 86 0.46
246 92 0.50
247 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (245 bp):
GCACGATACCCTTCCTCGTGAAGTTGAAACCGTGGATGGCTCATTCGCTGTGAAATTGAGCTCTT
AATTGACATCCTTCATCGTGAAAATAAAATCCACACTGAAGATGATGTTACTGGTGAACACGATT
CCCTTCGTCGTGAAGTTAAAACCGTGGATGGCCCATTCGTTGCGAAGTTGAGCCTAGAATTGAAT
ATCCTTCGCCGCGAAGTTAAAATTCAATCTAAAGATGATGTTGTTGGTGA
Found at i:58247 original size:63 final size:64
Alignment explanation
Indices: 58169--58297 Score: 215
Period size: 63 Copynumber: 2.0 Consensus size: 64
58159 GTATTATTTC
58169 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACT-GAAAATTATTTGTT
1 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAATTATTTGTT
* * * *
58232 GAGTCGAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAATTATTTGTT
58296 GA
1 GA
58298 AAGTCGCCCC
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
63 47 0.77
64 14 0.23
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (64 bp):
GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAATTATTTGTT
Found at i:58310 original size:63 final size:61
Alignment explanation
Indices: 58180--58323 Score: 191
Period size: 63 Copynumber: 2.3 Consensus size: 61
58170 AGTCCAATAT
* *
58180 CCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAATTATTTGTTGAGTCGAATAT
1 CCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAATTATTTGTTGAGTCG-A-AC
* * *
58243 CCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTGAAAGTCG-CC
1 CCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACT-GAAAATTATTTGTTG--AGTCGAAC
58306 CCTTCGCTGTGAAGTTGA
1 CCTTCGCTGTGAAGTTGA
58324 GAAACCACCA
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
63 55 0.75
64 13 0.18
66 5 0.07
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.33
Consensus pattern (61 bp):
CCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAATTATTTGTTGAGTCGAAC
Done.