Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001857.1 Hibiscus syriacus cultivar Beakdansim tig00003758_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: 59220
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:2879 original size:20 final size:19
Alignment explanation
Indices: 2839--2876 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2829 TTTTGGTGCA
*
2839 GAGGGAATCGATCCCCCTT
1 GAGGGAACCGATCCCCCTT
*
2858 GAGGGAACCGATTCCCCTT
1 GAGGGAACCGATCCCCCTT
2877 TGAAGGGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.32, G:0.26, T:0.21
Consensus pattern (19 bp):
GAGGGAACCGATCCCCCTT
Found at i:10260 original size:32 final size:31
Alignment explanation
Indices: 10219--10340 Score: 115
Period size: 31 Copynumber: 3.9 Consensus size: 31
10209 AGTCGAGGGT
10219 TTACCTATGTTCTACGGAACATATGGACAGAA
1 TTACCTATGTTCTACGGAACATATGGACA-AA
* * *
10251 TTACCTATG-TCTTTCGGGACATGTGGAC-AA
1 TTACCTATGTTC-TACGGAACATATGGACAAA
* * *
10281 TATACCTATGTTCTAAGGAACATATAGACAAT
1 T-TACCTATGTTCTACGGAACATATGGACAAA
* * *
10313 TTACCTAGGTTCTTCGG-ACATAGGGACA
1 TTACCTATGTTCTACGGAACATATGGACA
10341 GTTGCCGAGG
Statistics
Matches: 72, Mismatches: 14, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
30 12 0.17
31 34 0.47
32 26 0.36
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (31 bp):
TTACCTATGTTCTACGGAACATATGGACAAA
Found at i:11640 original size:2 final size:2
Alignment explanation
Indices: 11629--11695 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
11619 GTGACAAGCG
11629 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11670 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
11696 AAGTCATAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:14519 original size:31 final size:32
Alignment explanation
Indices: 14434--14523 Score: 103
Period size: 32 Copynumber: 2.8 Consensus size: 32
14424 AGTCGAGGGT
*
14434 TTACATATGTTCTACGGAACATATGGACAGAA
1 TTACCTATGTTCTACGGAACATATGGACAGAA
* * **
14466 TTACCTATG-TCTTTCGGGACATATGGACATTA
1 TTACCTATGTTC-TACGGAACATATGGACAGAA
*
14498 -TACCTATGTTCTAAGGAACATATGGA
1 TTACCTATGTTCTACGGAACATATGGA
14524 TAGTTTACGT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
31 22 0.46
32 26 0.54
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (32 bp):
TTACCTATGTTCTACGGAACATATGGACAGAA
Found at i:14542 original size:63 final size:61
Alignment explanation
Indices: 14439--14555 Score: 146
Period size: 63 Copynumber: 1.9 Consensus size: 61
14429 AGGGTTTACA
* *
14439 TATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGGGACATATGGACATTATACC
1 TATGTTCTAAGGAACATATGGACAGAATTACCTAGGTCTTT--GGACATATGGACATTATACC
* * * *
14502 TATGTTCTAAGGAACATATGGATAG-TTTACGTAGGTTCTTTGGACCTATGGACA
1 TATGTTCTAAGGAACATATGGACAGAATTACCTAGG-TCTTTGGACATATGGACA
14556 GTTGCCGAGG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
61 12 0.26
62 7 0.15
63 28 0.60
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.33
Consensus pattern (61 bp):
TATGTTCTAAGGAACATATGGACAGAATTACCTAGGTCTTTGGACATATGGACATTATACC
Found at i:17175 original size:18 final size:18
Alignment explanation
Indices: 17149--17191 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
17139 CTTCTTCTCC
*
17149 TCCTCCTCCTCATTATTT
1 TCCTTCTCCTCATTATTT
* *
17167 TCCTTCTCCTTATTCTTT
1 TCCTTCTCCTCATTATTT
*
17185 TTCTTCT
1 TCCTTCT
17192 TCTCCTTCTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.07, C:0.35, G:0.00, T:0.58
Consensus pattern (18 bp):
TCCTTCTCCTCATTATTT
Found at i:20765 original size:24 final size:24
Alignment explanation
Indices: 20738--20789 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
20728 CGTTCGTGAA
20738 CGTTCGGTTATGTT-TGTTTATGTT
1 CGTTCGGTTATGTTCT-TTTATGTT
20762 CGTTCGGTTATGTTCTTTTATGTT
1 CGTTCGGTTATGTTCTTTTATGTT
20786 CGTT
1 CGTT
20790 TATTTATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 26 0.96
25 1 0.04
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.58
Consensus pattern (24 bp):
CGTTCGGTTATGTTCTTTTATGTT
Found at i:20796 original size:24 final size:24
Alignment explanation
Indices: 20738--20800 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
20728 CGTTCGTGAA
*
20738 CGTTCGGTTATGTTTGTTTATGTT
1 CGTTCAGTTATGTTTGTTTATGTT
*
20762 CGTTCGGTTATGTTCT-TTTATGTT
1 CGTTCAGTTATGTT-TGTTTATGTT
* *
20786 CGTTTATTTATGTTT
1 CGTTCAGTTATGTTT
20801 AACTCAATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
23 1 0.03
24 33 0.94
25 1 0.03
ACGTcount: A:0.10, C:0.10, G:0.21, T:0.60
Consensus pattern (24 bp):
CGTTCAGTTATGTTTGTTTATGTT
Found at i:21168 original size:16 final size:16
Alignment explanation
Indices: 21149--21213 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
21139 CCAATGTTTA
*
21149 TGTTTGTTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
21165 TGTTCATTTATGTTCA
1 TGTTCGTTTATGTTCG
21181 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
21197 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
21213 T
1 T
21214 TTATTTATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.09, C:0.11, G:0.22, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:21195 original size:10 final size:10
Alignment explanation
Indices: 21144--21217 Score: 59
Period size: 10 Copynumber: 7.6 Consensus size: 10
21134 GGTCTCCAAT
*
21144 GTTTATGTTT
1 GTTTATGTTC
21154 GTTTATGTTC
1 GTTTATGTTC
*
21164 GTGTTCAT-TTAT
1 GT-TT-ATGTT-C
*
21176 GTTCATGTTC
1 GTTTATGTTC
21186 GTTTATGTTC
1 GTTTATGTTC
21196 G----TGTTC
1 GTTTATGTTC
21202 GTTTATGTTC
1 GTTTATGTTC
21212 GTTTAT
1 GTTTAT
21218 TTATTAAATG
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.11, C:0.09, G:0.20, T:0.59
Consensus pattern (10 bp):
GTTTATGTTC
Found at i:21773 original size:24 final size:22
Alignment explanation
Indices: 21706--21773 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 22
21696 TATATATTAT
21706 TTTTATTTTATATTACATTTTTA
1 TTTTATTTTATATTA-ATTTTTA
*
21729 TTTATAATATATATATT-ATTTTTA
1 TTT-T-AT-TTTATATTAATTTTTA
21753 CTTTTATTTTATATTGAATTT
1 -TTTTATTTTATATT-AATTT
21774 AATTTTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
22 7 0.19
23 5 0.14
24 13 0.35
25 5 0.14
26 7 0.19
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.66
Consensus pattern (22 bp):
TTTTATTTTATATTAATTTTTA
Found at i:21774 original size:42 final size:42
Alignment explanation
Indices: 21687--21774 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
21677 CGATACCCGG
* **
21687 TTTATTATATATATATTATTTTTATTTTATATTACATTTTTA
1 TTTATAATATATATATTATTTTTATTTTATATTACATTTGAA
* *
21729 TTTATAATATATATATTATTTTTACTTTTATTTTATA-TTGAA
1 TTTATAATATATATATTATTTTTA-TTTTATATTACATTTGAA
21771 TTTA
1 TTTA
21775 ATTTTTATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 30 0.75
43 10 0.25
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (42 bp):
TTTATAATATATATATTATTTTTATTTTATATTACATTTGAA
Found at i:21835 original size:39 final size:39
Alignment explanation
Indices: 21791--21898 Score: 159
Period size: 39 Copynumber: 2.8 Consensus size: 39
21781 ATTATAATTA
21791 TTAAATTATTTCACTCTAACATTCTAAATTCCTAATTTC
1 TTAAATTATTTCACTCTAACATTCTAAATTCCTAATTTC
*
21830 TTAAATT-TTTCCAC-CATAACATTCTAAATTCTTAATTTC
1 TTAAATTATTT-CACTC-TAACATTCTAAATTCCTAATTTC
21869 TTAAATTATTTCACAT-TAACATTCTAAATT
1 TTAAATTATTTCAC-TCTAACATTCTAAATT
21899 ATTTTTTAAA
Statistics
Matches: 63, Mismatches: 1, Indels: 10
0.85 0.01 0.14
Matches are distributed among these distances:
38 4 0.06
39 56 0.89
40 3 0.05
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.46
Consensus pattern (39 bp):
TTAAATTATTTCACTCTAACATTCTAAATTCCTAATTTC
Found at i:28670 original size:12 final size:11
Alignment explanation
Indices: 28655--28701 Score: 58
Period size: 12 Copynumber: 4.0 Consensus size: 11
28645 AATATTATAC
28655 TTATTATTACAT
1 TTATTATTA-AT
*
28667 TTATTATTATT
1 TTATTATTAAT
28678 TATATTATTAAT
1 T-TATTATTAAT
28690 ATTATTATTAAT
1 -TTATTATTAAT
28702 AATAATTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 2 0.06
12 28 0.90
13 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTATTAAT
Found at i:29760 original size:33 final size:33
Alignment explanation
Indices: 29696--29762 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
29686 AAAAATAAAA
*
29696 GAGTTTATTTGGGTTAGTAATATGATAATAATT
1 GAGTTTATTTAGGTTAGTAATATGATAATAATT
29729 GAGTTTATTTAGGTTAGTAATATGATAATAATT
1 GAGTTTATTTAGGTTAGTAATATGATAATAATT
29762 G
1 G
29763 TTTAATATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (33 bp):
GAGTTTATTTAGGTTAGTAATATGATAATAATT
Found at i:30300 original size:2 final size:2
Alignment explanation
Indices: 30293--30383 Score: 182
Period size: 2 Copynumber: 45.5 Consensus size: 2
30283 ATTTGTGACT
30293 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30335 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30377 TA TA TA T
1 TA TA TA T
30384 GTATGTATTA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31096 original size:13 final size:13
Alignment explanation
Indices: 31078--31107 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
31068 TTAAAATAAA
31078 AGTGTATCCTATC
1 AGTGTATCCTATC
31091 AGTGTATCCTATC
1 AGTGTATCCTATC
31104 AGTG
1 AGTG
31108 ACACCTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (13 bp):
AGTGTATCCTATC
Found at i:36178 original size:29 final size:28
Alignment explanation
Indices: 36145--36252 Score: 93
Period size: 29 Copynumber: 3.9 Consensus size: 28
36135 AAAAGAGAAA
*
36145 AAAAAAAAGAAAAAAAACAGAGCAAAAAG
1 AAAAAAAAGAAAAAAAA-AAAGCAAAAAG
*
36174 AAAAAAAA-AAAAGAAATTAAAGC--AAAG
1 AAAAAAAAGAAAA-AAA-AAAAGCAAAAAG
**
36201 --AAAAAAGAGCAAAAAAAAG-AAACAAG
1 AAAAAAAAGAAAAAAAAAAAGCAAA-AAG
36227 AAAAAAAAAGAAAAAAAAAAAGCAAA
1 -AAAAAAAAGAAAAAAAAAAAGCAAA
36253 GAAAAAGGGA
Statistics
Matches: 62, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
24 4 0.06
25 10 0.16
26 5 0.08
27 4 0.06
28 4 0.06
29 32 0.52
30 3 0.05
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.02
Consensus pattern (28 bp):
AAAAAAAAGAAAAAAAAAAAGCAAAAAG
Found at i:36184 original size:33 final size:33
Alignment explanation
Indices: 36133--36247 Score: 105
Period size: 33 Copynumber: 3.5 Consensus size: 33
36123 CCAATTAGAA
36133 CAAAAAGAGAAAAAAAAAAAGAAA-AAAAACAGAG
1 CAAAAAGA-AAAAAAAAAAAGAAACAAAAACA-AG
** *
36167 CAAAAAGAAAAAAAAAAAAGAAATTAAAGCAAAG
1 CAAAAAGAAAAAAAAAAAAGAAACAAAAAC-AAG
* ** *
36201 AAAAAAG-AGCAAAAAAAAGAAACAAGAA-AA-
1 CAAAAAGAAAAAAAAAAAAGAAACAAAAACAAG
36231 -AAAAAGAAAAAAAAAAA
1 CAAAAAGAAAAAAAAAAA
36248 GCAAAGAAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
29 6 0.09
30 8 0.12
31 2 0.03
33 30 0.45
34 20 0.30
35 1 0.01
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.02
Consensus pattern (33 bp):
CAAAAAGAAAAAAAAAAAAGAAACAAAAACAAG
Found at i:36253 original size:17 final size:16
Alignment explanation
Indices: 36142--36258 Score: 66
Period size: 17 Copynumber: 7.1 Consensus size: 16
36132 ACAAAAAGAG
36142 AAAAAAAA-AAAGAAA
1 AAAAAAAACAAAGAAA
*
36157 AAAAACAGAGCAAA-AAGA
1 AAAAA-A-AACAAAGAA-A
36175 AAAAAAAA-AAAG--A
1 AAAAAAAACAAAGAAA
** *
36188 AATTAAAGCAAAGAAA
1 AAAAAAAACAAAGAAA
*
36204 AAAGAGCAAAAAAAAGAAA
1 AAA-A--AAAACAAAGAAA
36223 CAAGAAAAAA-AAAGAAA
1 -AA-AAAAAACAAAGAAA
36240 AAAAAAAAGCAAAGAAA
1 AAAAAAAA-CAAAGAAA
36257 AA
1 AA
36259 GGGACGATAA
Statistics
Matches: 78, Mismatches: 9, Indels: 28
0.68 0.08 0.24
Matches are distributed among these distances:
13 6 0.08
14 4 0.05
15 14 0.18
16 7 0.09
17 20 0.26
18 13 0.17
19 10 0.13
20 3 0.04
21 1 0.01
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.02
Consensus pattern (16 bp):
AAAAAAAACAAAGAAA
Found at i:36254 original size:27 final size:28
Alignment explanation
Indices: 36144--36258 Score: 116
Period size: 27 Copynumber: 4.2 Consensus size: 28
36134 AAAAAGAGAA
* *
36144 AAAAAAAAAGAAAAAAAACAGAGCAAA-
1 AAAAAAAAAGAAAAAAAATAAAGCAAAG
36171 AAGAAAAAAA-AAAAAGAAATTAAAGCAAAG
1 AA-AAAAAAAGAAAAA-AAA-TAAAGCAAAG
* *
36201 -AAAAAAGAGCAAAAAAAAGAAA-C-AAG
1 AAAAAAAAAG-AAAAAAAATAAAGCAAAG
36227 AAAAAAAAAGAAAAAAAA-AAAGCAAAG
1 AAAAAAAAAGAAAAAAAATAAAGCAAAG
36254 AAAAA
1 AAAAA
36259 GGGACGATAA
Statistics
Matches: 74, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
25 3 0.04
26 12 0.16
27 24 0.32
28 19 0.26
29 11 0.15
30 5 0.07
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.02
Consensus pattern (28 bp):
AAAAAAAAAGAAAAAAAATAAAGCAAAG
Found at i:37286 original size:33 final size:33
Alignment explanation
Indices: 37236--37395 Score: 225
Period size: 33 Copynumber: 4.8 Consensus size: 33
37226 GGAGCAATAG
*
37236 AGGGTATCTTTGAAGATTCAACATCAAAAATTT
1 AGGGCATCTTTGAAGATTCAACATCAAAAATTT
* ** *
37269 AGGGCATCTTTGGAGATTCAACATCAAATGTTG
1 AGGGCATCTTTGAAGATTCAACATCAAAAATTT
37302 AGGGCATCTTTGAAGATTCAACATCAAAAATTT
1 AGGGCATCTTTGAAGATTCAACATCAAAAATTT
37335 GAGGGCATCTTTGAAGATTCAACATC--AAATGTT
1 -AGGGCATCTTTGAAGATTCAACATCAAAAAT-TT
* *
37368 GGGGCATCTTTGGAGATTCAACATCAAA
1 AGGGCATCTTTGAAGATTCAACATCAAA
37396 TGTTAGGACA
Statistics
Matches: 112, Mismatches: 11, Indels: 7
0.86 0.08 0.05
Matches are distributed among these distances:
32 27 0.24
33 59 0.53
34 26 0.23
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (33 bp):
AGGGCATCTTTGAAGATTCAACATCAAAAATTT
Found at i:37373 original size:66 final size:66
Alignment explanation
Indices: 37235--37395 Score: 279
Period size: 66 Copynumber: 2.4 Consensus size: 66
37225 TGGAGCAATA
* *
37235 GAGGGTATCTTTGAAGATTCAACATCAAAAATTTAGGGCATCTTTGGAGATTCAACATCAAATGT
1 GAGGGCATCTTTGAAGATTCAACATCAAAAATTTAGGGCATCTTTGAAGATTCAACATCAAATGT
37300 T
66 T
37301 GAGGGCATCTTTGAAGATTCAACATCAAAAATTTGAGGGCATCTTTGAAGATTCAACATCAAATG
1 GAGGGCATCTTTGAAGATTCAACATCAAAAATTT-AGGGCATCTTTGAAGATTCAACATCAAATG
37366 TT
65 TT
*
37368 G-GGGCATCTTTGGAGATTCAACATCAAA
1 GAGGGCATCTTTGAAGATTCAACATCAAA
37396 TGTTAGGACA
Statistics
Matches: 91, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
66 59 0.65
67 32 0.35
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (66 bp):
GAGGGCATCTTTGAAGATTCAACATCAAAAATTTAGGGCATCTTTGAAGATTCAACATCAAATGT
T
Found at i:37378 original size:32 final size:32
Alignment explanation
Indices: 37241--37418 Score: 227
Period size: 32 Copynumber: 5.4 Consensus size: 32
37231 AATAGAGGGT
*
37241 ATCTTTGAAGATTCAACATCAAAAAT-TTAGGGC
1 ATCTTTGAAGATTCAACATC--AAATGTTGGGGC
*
37274 ATCTTTGGAGATTCAACATCAAATGTTGAGGGC
1 ATCTTTGAAGATTCAACATCAAATGTTG-GGGC
37307 ATCTTTGAAGATTCAACATCAAAAAT-TTGAGGGC
1 ATCTTTGAAGATTCAACATC--AAATGTTG-GGGC
37341 ATCTTTGAAGATTCAACATCAAATGTTGGGGC
1 ATCTTTGAAGATTCAACATCAAATGTTGGGGC
* * *
37373 ATCTTTGGAGATTCAACATCAAATGTTAGGAC
1 ATCTTTGAAGATTCAACATCAAATGTTGGGGC
37405 ATCTTT-AGAGATTC
1 ATCTTTGA-AGATTC
37419 GAATATTGGG
Statistics
Matches: 132, Mismatches: 7, Indels: 13
0.87 0.05 0.09
Matches are distributed among these distances:
31 4 0.03
32 51 0.39
33 45 0.34
34 28 0.21
35 4 0.03
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Consensus pattern (32 bp):
ATCTTTGAAGATTCAACATCAAATGTTGGGGC
Found at i:37581 original size:34 final size:34
Alignment explanation
Indices: 37526--37654 Score: 197
Period size: 34 Copynumber: 3.8 Consensus size: 34
37516 TGTTTCTCTT
* * *
37526 AAAAAAAATTT-GTCTCACTTGAGATAATTTCTC
1 AAAACAAATTTCGTCTCGCTTGAGACAATTTCTC
37559 AAAACAAATTTCGTCTCGCTTGAGACAATTTCTC
1 AAAACAAATTTCGTCTCGCTTGAGACAATTTCTC
*
37593 AAAACAAATTTCTTCTCGCTTGAGACAATTTCTC
1 AAAACAAATTTCGTCTCGCTTGAGACAATTTCTC
* *
37627 AAAATAAATTTCATCTCGCTTGAGACAA
1 AAAACAAATTTCGTCTCGCTTGAGACAA
37655 GTTTTATTTA
Statistics
Matches: 89, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
33 10 0.11
34 79 0.89
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.33
Consensus pattern (34 bp):
AAAACAAATTTCGTCTCGCTTGAGACAATTTCTC
Found at i:37801 original size:40 final size:40
Alignment explanation
Indices: 37747--38234 Score: 724
Period size: 40 Copynumber: 12.4 Consensus size: 40
37737 ACTCGAAATA
* *
37747 AGAAGATTTAATCTCATTAAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
* * *
37787 AGAAGATTTTATCTCACTCAATATTGTTTTTCCTTGAAAT
1 AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
*
37827 AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGACA-
1 AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
*
37866 AGAAGATTTTATCTCATTCAAAATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
*
37906 --AAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
* * *
37944 ATAAGATTTTATCTCATTCAAAATTATTTTT--TTGAAAC
1 AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
* *
37982 AGAAGATTTTATCTCACTCAAGATTGTTTTTCATTGAAAC
1 AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
38022 AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
38062 AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
*
38102 A-AAGATTTTAACTCATTCAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
* *
38141 AAAAGATTTTATCT-AGCTCAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCA-TTCAAGATTGTTTTTCCTTGAAAC
* *
38181 AGAAGAATTTATCTCACTCAAGATTG-TTTTCTCTTGAAAC
1 AGAAGATTTTATCTCATTCAAGATTGTTTTTC-CTTGAAAC
*
38221 A-AAGATTTTGTCTC
1 AGAAGATTTTATCTC
38235 CTTGAGATAG
Statistics
Matches: 411, Mismatches: 28, Indels: 19
0.90 0.06 0.04
Matches are distributed among these distances:
38 70 0.17
39 92 0.22
40 248 0.60
41 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (40 bp):
AGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGAAAC
Found at i:37882 original size:119 final size:118
Alignment explanation
Indices: 37746--38234 Score: 695
Period size: 119 Copynumber: 4.1 Consensus size: 118
37736 TACTCGAAAT
* *
37746 AAGAAGATTTAATCTCATTAAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCAATAT
1 AAGAAGATTTTATCTCATTAAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCAAGAT
*
37811 TGTTTTTCCTTGAAATAGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGA
66 TGTTTTTCCTTGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGA
37864 CAAGAAGATTTTATCTCATTCAAA-ATTGTTTTTCCTTGAAAC--AAGATTTTATCTCACTCAAG
1 -AAGAAGATTTTATCTCATT-AAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCAAG
* * *
37926 ATTGTTTTTCCTTGAAACATAAGATTTTATCTCATTCAAAATTATTTTT--TTGAA
64 ATTGTTTTTCCTTGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTG-A
* * * *
37980 ACAGAAGATTTTATCTCACTCAAGATTGTTTTTCATTGAAACAGAAGATTTTATCTCATTCAAGA
1 A-AGAAGATTTTATCTCATTAAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCAAGA
38045 TTGTTTTTCCTTGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGA
65 TTGTTTTTCCTTGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGA
* * * *
38099 AACAAAGATTTTAACTCATTCAAGATTGTTTTTCCTTGAAACAAAAGATTTTATCT-AGCTCAAG
1 AA-GAAGATTTTATCTCATTAAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCA-CTCAAG
* *
38163 ATTGTTTTTCCTTGAAACAGAAGAATTTATCTCACTCAAGATTG-TTTTCTCTTGA
64 ATTGTTTTTCCTTGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTC-CTTGA
* *
38218 AACAAAGATTTTGTCTC
1 AA-GAAGATTTTATCTC
38235 CTTGAGATAG
Statistics
Matches: 336, Mismatches: 23, Indels: 22
0.88 0.06 0.06
Matches are distributed among these distances:
115 6 0.02
116 35 0.10
117 64 0.19
118 72 0.21
119 153 0.46
120 6 0.02
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (118 bp):
AAGAAGATTTTATCTCATTAAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTCAAGAT
TGTTTTTCCTTGAAACAGAAGATTTTATCTCATTCAAGATTGTTTTTCCTTGA
Found at i:38027 original size:23 final size:23
Alignment explanation
Indices: 38001--38069 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
37991 TATCTCACTC
38001 AAGATTGTTTTTCATTGAAACAG
1 AAGATTGTTTTTCATTGAAACAG
*
38024 AAGATT-TTATCTCATT----C--
1 AAGATTGTT-TTTCATTGAAACAG
*
38041 AAGATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCATTGAAACAG
38064 AAGATT
1 AAGATT
38070 TTATCTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 16
0.65 0.06 0.30
Matches are distributed among these distances:
17 11 0.31
18 2 0.06
19 1 0.03
21 1 0.03
22 2 0.06
23 18 0.51
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (23 bp):
AAGATTGTTTTTCATTGAAACAG
Found at i:38323 original size:15 final size:14
Alignment explanation
Indices: 38299--38351 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 14
38289 ATTTGTATCC
*
38299 CTTGAGACAATTTCT
1 CTTGAAACAATTT-T
*
38314 CTTGAAACAAGTTT
1 CTTGAAACAATTTT
*
38328 -TTGAGACAGATTTT
1 CTTGAAACA-ATTTT
38342 CTTGAAACAA
1 CTTGAAACAA
38352 AGTTTTGTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
13 7 0.23
14 6 0.19
15 18 0.58
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (14 bp):
CTTGAAACAATTTT
Found at i:38344 original size:28 final size:29
Alignment explanation
Indices: 38300--38357 Score: 93
Period size: 28 Copynumber: 2.0 Consensus size: 29
38290 TTTGTATCCC
38300 TTGAGACAATTTCTCTTGAAAC-AAGTTT
1 TTGAGACAATTTCTCTTGAAACAAAGTTT
38328 TTGAGACAGATTT-TCTTGAAACAAAGTTT
1 TTGAGACA-ATTTCTCTTGAAACAAAGTTT
38357 T
1 T
38358 GTCTCCCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 17 0.61
29 11 0.39
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (29 bp):
TTGAGACAATTTCTCTTGAAACAAAGTTT
Found at i:38472 original size:76 final size:72
Alignment explanation
Indices: 38328--38596 Score: 225
Period size: 76 Copynumber: 3.6 Consensus size: 72
38318 AAACAAGTTT
* * * * * * * *
38328 TTGAGACAGATTT-TCTTGAAACAAAGTTTTGTCTCCCTTAAGATGGTTTTTCTTAAAATCAACT
1 TTGAGACA-ATTTCCCTTGAAACAAA-ATGTATCTCACTTGAGATGGTTTTTCTTAAAACCTACT
*
38392 TCGTCTCAC
64 TCGTCTTAC
* *
38401 TTGAGACAACTTTCCCTTGAAACAAAATGTATCTCGCTTGAGATGGTTTTTTTTCATAAAACCTA
1 TTGAGACAA-TTTCCCTTGAAACAAAATGTATCTCACTTGAGATGG---TTTTTCTTAAAACCTA
38466 CTTCGTCTTAC
62 CTTCGTCTTAC
* * ** * *
38477 TTGAGATAGTTTTCTTTTGAAACAAAGAAATTGAATCTCACTTGAGATGGGTTTTCTTAAAACCT
1 TTGAGACA-ATTTCCCTTGAAAC--A-AAA-TGTATCTCACTTGAGATGGTTTTTCTTAAAACCT
38542 ACTTCGTCTTAC
61 ACTTCGTCTTAC
* * * * *
38554 TGGAGACAATTTTCCTTCGAAATAAAATTTATCTCACTCGAGA
1 TTGAGACAATTTCCCTT-GAAACAAAATGTATCTCACTTGAGA
38597 GAGCTTCTCT
Statistics
Matches: 157, Mismatches: 28, Indels: 22
0.76 0.14 0.11
Matches are distributed among these distances:
72 1 0.01
73 39 0.25
74 14 0.09
75 1 0.01
76 46 0.29
77 35 0.22
78 1 0.01
79 3 0.02
80 17 0.11
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (72 bp):
TTGAGACAATTTCCCTTGAAACAAAATGTATCTCACTTGAGATGGTTTTTCTTAAAACCTACTTC
GTCTTAC
Found at i:39026 original size:91 final size:91
Alignment explanation
Indices: 38871--39121 Score: 448
Period size: 91 Copynumber: 2.7 Consensus size: 91
38861 TTTCTAATAG
38871 AGAGTTCATAATGAGAAGAACTCATCCAACGAGAGAAAAGAAGTTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCAACGAGAGAAAAGAAGTTCATAATGAGAAGAACTTGTT
38936 CGATCTCGCATCAGTGTTTCCAATGA
66 CGATCTCGCATCAGTGTTTCCAATGA
38962 AGAGTTCATAATGAGAAGAACTCATCCAACGAGAGAAAAGAAGTTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCAACGAGAGAAAAGAAGTTCATAATGAGAAGAACTTGTT
*
39027 CGATCTCGCATCAGTGTTTCCAATGG
66 CGATCTCGCATCAGTGTTTCCAATGA
* * * *
39053 AGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGT
1 AGAGTTCATAATGAGAAGAACTCATCC-AACGAGAGAAAAGAAGTTCATAATGAGAAGAACTTGT
39118 TCGA
65 TCGA
39122 CTTATCACTC
Statistics
Matches: 154, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
91 117 0.76
92 37 0.24
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (91 bp):
AGAGTTCATAATGAGAAGAACTCATCCAACGAGAGAAAAGAAGTTCATAATGAGAAGAACTTGTT
CGATCTCGCATCAGTGTTTCCAATGA
Found at i:39205 original size:16 final size:16
Alignment explanation
Indices: 39184--39239 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
39174 TAACATTTCC
39184 AGAAGAGTTCATAATG
1 AGAAGAGTTCATAATG
* *
39200 AGAAGAACTCGTCATAAAG
1 AGAAG-AGT--TCATAATG
*
39219 -GAAAAGTTCATAATG
1 AGAAGAGTTCATAATG
39234 AGAAGA
1 AGAAGA
39240 ACTTGTTCCT
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
15 7 0.23
16 9 0.30
17 4 0.13
18 3 0.10
19 7 0.23
ACGTcount: A:0.48, C:0.09, G:0.23, T:0.20
Consensus pattern (16 bp):
AGAAGAGTTCATAATG
Found at i:39214 original size:19 final size:17
Alignment explanation
Indices: 39191--39243 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
39181 TCCAGAAGAG
39191 TTCATAATGAGAAGAAC
1 TTCATAATGAGAAGAAC
* *
39208 TCGTCATAAAG-GAA-AAG
1 T--TCATAATGAGAAGAAC
39225 TTCATAATGAGAAGAAC
1 TTCATAATGAGAAGAAC
39242 TT
1 TT
39244 GTTCCTTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
15 7 0.25
16 3 0.11
17 8 0.29
18 3 0.11
19 7 0.25
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.25
Consensus pattern (17 bp):
TTCATAATGAGAAGAAC
Found at i:39471 original size:240 final size:239
Alignment explanation
Indices: 39043--39648 Score: 1034
Period size: 240 Copynumber: 2.5 Consensus size: 239
39033 CGCATCAGTG
39043 TTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAG
1 TTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAG
* *
39108 AAGAGCTTGTTCGACTTATCACTCGATTCATGGCATTTCGAATCAGTGACGCCTCGTTTGAGGGA
66 AAGAGCTTGTTCGACTTATCACTCGATTCA-CGCATTTCGAATCAGTGACGCCTCGCTTGAGGGA
39173 TTAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCATAAAGGAAAAGTTCATAATGAGAA
130 TTAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCATAAAGGAAAAGTTCATAATGAGAA
* * *
39238 GAACTTGTTCCTTTCAATTCCATCACAGAATGAGATGTATCAACA
195 GAACTTGTTCATTTCAATTCCATCACAGAATAAGATGGATCAACA
*
39283 TTTCTAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAG
1 TTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAG
*
39348 AAGAGCTTGTTCGACTTATCACTCGATTCACAGCATTTCGAATTAGTGACGCCTCGCTTGAGGGA
66 AAGAGCTTGTTCGACTTATCACTCGATTCAC-GCATTTCGAATCAGTGACGCCTCGCTTGAGGGA
* * *
39413 TTGACATTTCCATAAGAGTTCATAATGAGAAGAACTCGTCATAAAGGAAAAGTTCATAATGAGGA
130 TTAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCATAAAGGAAAAGTTCATAATGAGAA
*
39478 GAATTTGTTCATTTCAATTCCATCACAGAATAAGATGGATCAACA
195 GAACTTGTTCATTTCAATTCCATCACAGAATAAGATGGATCAACA
* *
39523 TTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCC-AACGAGAGAGAAGAAGTTCATAATGAG
1 TTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAG
* * *
39587 AAGAGCTTGTTCGACCTATCACTCGACTCACGACATTTTGAATCAGTGACGCCTCGCTTGAG
66 AAGAGCTTGTTCGACTTATCACTCGATTCACG-CATTTCGAATCAGTGACGCCTCGCTTGAG
39649 AAACCATCAT
Statistics
Matches: 346, Mismatches: 18, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
238 1 0.00
239 81 0.23
240 264 0.76
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.26
Consensus pattern (239 bp):
TTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAG
AAGAGCTTGTTCGACTTATCACTCGATTCACGCATTTCGAATCAGTGACGCCTCGCTTGAGGGAT
TAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCATAAAGGAAAAGTTCATAATGAGAAG
AACTTGTTCATTTCAATTCCATCACAGAATAAGATGGATCAACA
Found at i:39705 original size:43 final size:43
Alignment explanation
Indices: 39642--39946 Score: 332
Period size: 43 Copynumber: 6.8 Consensus size: 43
39632 GTGACGCCTC
*
39642 GCTTG-AGAAACCATCATGATATGTAGGGGTTTCTTGATGAAAA
1 GCTTGAAG-AACCATCGTGATATGTAGGGGTTTCTTGATGAAAA
* * *
39685 GCTTGAAGGACCATCGTGATATGTAGGGGTTTTTTGATGACAA
1 GCTTGAAGAACCATCGTGATATGTAGGGGTTTCTTGATGAAAA
* *
39728 GTTTG-AGAAACCATCGTGATATGTAGGGGTTTCTTGATGACAA
1 GCTTGAAG-AACCATCGTGATATGTAGGGGTTTCTTGATGAAAA
*
39771 GCTTG-AGAAACCATCGTGATTTGTAGGGGTTTCTTGATGAAAA
1 GCTTGAAG-AACCATCGTGATATGTAGGGGTTTCTTGATGAAAA
* *
39814 ACTT-AAGGAACCATCGTGATATGTAGGGGTTCCTTGATGACAAACTTGA
1 GCTTGAA-GAACCATCGTGATATGTAGGGGTTTCTTGATG--AAA----A
39863 TGAATACTTGAAGAACCATCGTGATATGTAGGGGTTTCTTGATGAAAA
1 -G----CTTGAAGAACCATCGTGATATGTAGGGGTTTCTTGATGAAAA
* *
39911 GCTT-AAGGAACCATCATGATATGTAGGGGTTCCTTG
1 GCTTGAA-GAACCATCGTGATATGTAGGGGTTTCTTG
39947 GTGACAATTA
Statistics
Matches: 228, Mismatches: 17, Indels: 34
0.82 0.06 0.12
Matches are distributed among these distances:
42 4 0.02
43 176 0.77
44 3 0.01
45 3 0.01
47 1 0.00
48 1 0.00
49 1 0.00
52 3 0.01
54 34 0.15
55 2 0.01
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (43 bp):
GCTTGAAGAACCATCGTGATATGTAGGGGTTTCTTGATGAAAA
Found at i:39789 original size:86 final size:87
Alignment explanation
Indices: 39642--39953 Score: 367
Period size: 86 Copynumber: 3.5 Consensus size: 87
39632 GTGACGCCTC
* * * *
39642 GCTTGAGAAACCATCATGATATGTAGGGGTTTCTTGATGAAAAGCTTGA-AGGACCATCGTGATA
1 GCTTAAGAAACCATCATGATATGTAGGGGTTCCTTGATGACAAGCTTGAGAGAACCATCGTGATA
* *
39706 TGTAGGGGTTTTTTGATGACAA
66 TGTAGGGGTTTCTTGATGAAAA
* * * * *
39728 GTTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGACAAGCTTGAGA-AACCATCGTGATT
1 GCTTAAGAAACCATCATGATATGTAGGGGTTCCTTGATGACAAGCTTGAGAGAACCATCGTGATA
39792 TGTAGGGGTTTCTTGATGAAAA
66 TGTAGGGGTTTCTTGATGAAAA
* * * *
39814 ACTTAAGGAACCATCGTGATATGTAGGGGTTCCTTGATGACAAACTTGATGAATACTTGAAGAAC
1 GCTTAAGAAACCATCATGATATGTAGGGGTTCCTTGATGACAAGC-T--TG---A---G-AGAAC
39879 CATCGTGATATGTAGGGGTTTCTTGATGAAAA
56 CATCGTGATATGTAGGGGTTTCTTGATGAAAA
* *
39911 GCTTAAGGAACCATCATGATATGTAGGGGTTCCTTGGTGACAA
1 GCTTAAGAAACCATCATGATATGTAGGGGTTCCTTGATGACAA
39954 TTAAAAAATT
Statistics
Matches: 197, Mismatches: 17, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
86 116 0.59
87 2 0.01
89 2 0.01
92 1 0.01
95 1 0.01
96 1 0.01
97 74 0.38
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (87 bp):
GCTTAAGAAACCATCATGATATGTAGGGGTTCCTTGATGACAAGCTTGAGAGAACCATCGTGATA
TGTAGGGGTTTCTTGATGAAAA
Found at i:39886 original size:54 final size:55
Alignment explanation
Indices: 39803--39907 Score: 169
Period size: 54 Copynumber: 1.9 Consensus size: 55
39793 GTAGGGGTTT
39803 CTTGATGAAAAACTTAAGGAACCATCGTGATATGTAGGGGTTCCTTGATGACAAA
1 CTTGATGAAAAACTTAAGGAACCATCGTGATATGTAGGGGTTCCTTGATGACAAA
* *
39858 CTTGATG-AATACTTGAA-GAACCATCGTGATATGTAGGGGTTTCTTGATGA
1 CTTGATGAAAAACTT-AAGGAACCATCGTGATATGTAGGGGTTCCTTGATGA
39908 AAAGCTTAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
54 38 0.81
55 9 0.19
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.30
Consensus pattern (55 bp):
CTTGATGAAAAACTTAAGGAACCATCGTGATATGTAGGGGTTCCTTGATGACAAA
Found at i:40156 original size:88 final size:90
Alignment explanation
Indices: 39963--40272 Score: 486
Period size: 89 Copynumber: 3.5 Consensus size: 90
39953 ATTAAAAAAT
** *
39963 TGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTTGGGCCATCCATAAGACCTTCAATGCAGGA
1 TGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGA
40028 TG-TTTCAAATGAGATCTAAGAAAC
66 TGTTTTCAAATGAGATCTAAGAAAC
* *
40052 TGAGCCTTCTGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCAT-A-ACCTTCAGTGCAGGA
1 TGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGA
40115 TGTTTTCAAATGAGATCTAAGAAAC
66 TGTTTTCAAATGAGATCTAAGAAAC
40140 TGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGA
1 TGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGA
* *
40205 TGTTTTCAAATGATATTTTAA-AAAC
66 TGTTTTCAAATGAGA-TCTAAGAAAC
* * *
40230 TAACCCTTCGGGGG-TTCTTGATTTGTAAGTCCTCCGGGCCATC
1 TGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTCCGGGCCATC
40273 AGTAAGTCTT
Statistics
Matches: 207, Mismatches: 10, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
87 16 0.08
88 68 0.33
89 74 0.36
90 45 0.22
91 4 0.02
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (90 bp):
TGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGA
TGTTTTCAAATGAGATCTAAGAAAC
Found at i:40279 original size:20 final size:21
Alignment explanation
Indices: 40253--40314 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
40243 GTTCTTGATT
40253 TGTAAGTCCTCCGGGCCATCA
1 TGTAAGTCCTCCGGGCCATCA
* * *
40274 -GTAAGTCTTCCGAG-CATGA
1 TGTAAGTCCTCCGGGCCATCA
40293 TGCATAAGTCCTCCGGGCCATC
1 TG--TAAGTCCTCCGGGCCATC
40315 CATAAGACCT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
19 4 0.13
20 13 0.42
22 11 0.35
23 3 0.10
ACGTcount: A:0.21, C:0.31, G:0.24, T:0.24
Consensus pattern (21 bp):
TGTAAGTCCTCCGGGCCATCA
Found at i:40422 original size:131 final size:131
Alignment explanation
Indices: 40166--40422 Score: 403
Period size: 131 Copynumber: 2.0 Consensus size: 131
40156 TCTTGATTTT
*
40166 TAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGATATTTTAAAAACT
1 TAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAAAAACT
* *
40231 AACCCTTCGGGGGTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATGATGC
66 AACCCTTCGGGGGTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGCCTTCAGAGCATGATGC
40296 A
131 A
*
40297 TAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAGTGAGA-TTTAAAAACT
1 TAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAAAAACT
* * *
40361 AAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCCTCCA-TAAGACCTTCAG-GCATG
66 AACCCTTCGGGGG-TTCTTGATTTGTAAGTCCTCCGGGCCAT-CAGTAAG-CCTTCAGAGCATG
40423 GTGTTTTCAA
Statistics
Matches: 116, Mismatches: 7, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
130 22 0.19
131 87 0.75
132 7 0.06
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.30
Consensus pattern (131 bp):
TAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAAAAACT
AACCCTTCGGGGGTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGCCTTCAGAGCATGATGC
A
Found at i:41639 original size:36 final size:36
Alignment explanation
Indices: 41599--41670 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
41589 TTAATTTCAA
41599 TTTGAAAATGGGGAATGAAATATGTTAAAAATATAT
1 TTTGAAAATGGGGAATGAAATATGTTAAAAATATAT
*
41635 TTTGAAATTGGGGAATGAAATATGTTAAAAATATAT
1 TTTGAAAATGGGGAATGAAATATGTTAAAAATATAT
41671 ATGTATTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.19, T:0.35
Consensus pattern (36 bp):
TTTGAAAATGGGGAATGAAATATGTTAAAAATATAT
Found at i:46801 original size:12 final size:12
Alignment explanation
Indices: 46775--46817 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
46765 ATATACAAAT
46775 ACCTAACTC-TC
1 ACCTAACTCTTC
46786 ACCTAACTCTTC
1 ACCTAACTCTTC
*
46798 ACCTAATTCTTC
1 ACCTAACTCTTC
46810 ACCTAACT
1 ACCTAACT
46818 AAATTGATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 9 0.31
12 20 0.69
ACGTcount: A:0.28, C:0.40, G:0.00, T:0.33
Consensus pattern (12 bp):
ACCTAACTCTTC
Found at i:48177 original size:9 final size:9
Alignment explanation
Indices: 48165--48198 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
48155 TAATATTTTG
48165 TATTTAATT
1 TATTTAATT
*
48174 TATTTAA-G
1 TATTTAATT
48182 TATTTAATT
1 TATTTAATT
48191 TATTTAAT
1 TATTTAAT
48199 ATTTTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TATTTAATT
Found at i:48186 original size:17 final size:17
Alignment explanation
Indices: 48164--48215 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
48154 TTAATATTTT
48164 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
48181 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
* *
48198 -TATTTTATTTAATTAA
1 GTATTTAATTTATTTAA
48214 GT
1 GT
48216 TTTTTACAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 14 0.44
17 18 0.56
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:48220 original size:17 final size:17
Alignment explanation
Indices: 48164--48221 Score: 73
Period size: 17 Copynumber: 3.5 Consensus size: 17
48154 TTAATATTTT
*
48164 GTATTTAATTTATTTAA
1 GTATTTTATTTATTTAA
*
48181 GTATTTAATTTATTTAA
1 GTATTTTATTTATTTAA
*
48198 -TATTTTATTTAATTAA
1 GTATTTTATTTATTTAA
*
48214 GTTTTTTA
1 GTATTTTA
48222 CAGATATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 14 0.38
17 23 0.62
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
GTATTTTATTTATTTAA
Found at i:49105 original size:26 final size:26
Alignment explanation
Indices: 49076--49128 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
49066 TATGTCCCGT
*
49076 TGTGAAGAACTCATTCTTATTTCCGC
1 TGTGAAGAACCCATTCTTATTTCCGC
49102 TGTGAAGAACCCATTCTTATTTCCGC
1 TGTGAAGAACCCATTCTTATTTCCGC
49128 T
1 T
49129 ACTCTTGAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.38
Consensus pattern (26 bp):
TGTGAAGAACCCATTCTTATTTCCGC
Found at i:50483 original size:25 final size:25
Alignment explanation
Indices: 50443--50503 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
50433 AGATTTTGTT
* * *
50443 TTTTTATTATATTTGTATT-TAGTAC
1 TTTTTATTGTAGTTGT-TTATAGGAC
*
50468 TTTTTATTGTAGTTGTTTATTGGAC
1 TTTTTATTGTAGTTGTTTATAGGAC
50493 TTTTTATTGTA
1 TTTTTATTGTA
50504 ATTTTATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 2 0.06
25 29 0.94
ACGTcount: A:0.20, C:0.03, G:0.13, T:0.64
Consensus pattern (25 bp):
TTTTTATTGTAGTTGTTTATAGGAC
Found at i:50488 original size:13 final size:12
Alignment explanation
Indices: 50464--50508 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
50454 TTTGTATTTA
50464 GTACTTTTTATT
1 GTACTTTTTATT
*
50476 GTAGTTGTTTATT
1 GTACTT-TTTATT
*
50489 GGACTTTTTATT
1 GTACTTTTTATT
*
50501 GTAATTTT
1 GTACTTTT
50509 ATTATTATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.18, C:0.04, G:0.16, T:0.62
Consensus pattern (12 bp):
GTACTTTTTATT
Found at i:57710 original size:20 final size:20
Alignment explanation
Indices: 57685--57723 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
57675 ACGAGAAAGT
57685 AAGTGAATAAGGGCTTAGTC
1 AAGTGAATAAGGGCTTAGTC
57705 AAGTGAATAAGGGCTTAGT
1 AAGTGAATAAGGGCTTAGT
57724 TACCATGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.08, G:0.31, T:0.26
Consensus pattern (20 bp):
AAGTGAATAAGGGCTTAGTC
Done.