Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003543.1 Hibiscus syriacus cultivar Beakdansim tig00007474_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: 69864
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:6479 original size:15 final size:15
Alignment explanation
Indices: 6461--6490 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6451 CAATCTCTTT
6461 TTCGTTATCTAAACC
1 TTCGTTATCTAAACC
6476 TTCGTTATCTAAACC
1 TTCGTTATCTAAACC
6491 AAATGTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.40
Consensus pattern (15 bp):
TTCGTTATCTAAACC
Found at i:9175 original size:15 final size:15
Alignment explanation
Indices: 9157--9186 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
9147 CAATCTCTTT
9157 TTCGTTATCTAAACC
1 TTCGTTATCTAAACC
9172 TTCGTTATCTAAACC
1 TTCGTTATCTAAACC
9187 AAATGTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.40
Consensus pattern (15 bp):
TTCGTTATCTAAACC
Found at i:13302 original size:23 final size:24
Alignment explanation
Indices: 13276--13325 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
13266 TTCCCTAAAG
*
13276 GGGGGAATCGGTTCCCATTCAA-A
1 GGGGGAATAGGTTCCCATTCAAGA
* *
13299 GGGGGAATATGTTCCCCTTCAAGA
1 GGGGGAATAGGTTCCCATTCAAGA
13323 GGG
1 GGG
13326 TATCGATTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.24, C:0.20, G:0.34, T:0.22
Consensus pattern (24 bp):
GGGGGAATAGGTTCCCATTCAAGA
Found at i:19511 original size:24 final size:24
Alignment explanation
Indices: 19479--19526 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
19469 AAAACATCAA
* * *
19479 ATTTTAAAATCAAAACATTTTTTT
1 ATTTCAAAATCAAAAAAATTTTTT
*
19503 ATTTCAAAATGAAAAAAATTTTTT
1 ATTTCAAAATCAAAAAAATTTTTT
19527 GATAAAATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (24 bp):
ATTTCAAAATCAAAAAAATTTTTT
Found at i:21676 original size:20 final size:20
Alignment explanation
Indices: 21651--21693 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
21641 TACCAGGTTT
21651 TTCAACTAATCATAATTTAC
1 TTCAACTAATCATAATTTAC
*
21671 TTCAACTAATCATACTTTAC
1 TTCAACTAATCATAATTTAC
21691 TTC
1 TTC
21694 TCTCAAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (20 bp):
TTCAACTAATCATAATTTAC
Found at i:22823 original size:16 final size:15
Alignment explanation
Indices: 22797--22826 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
22787 TTAGATCATG
22797 CATTACAAATTTTAT
1 CATTACAAATTTTAT
22812 CATTATCAAATTTTA
1 CATTA-CAAATTTTA
22827 GCTTTGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (15 bp):
CATTACAAATTTTAT
Found at i:26280 original size:21 final size:21
Alignment explanation
Indices: 26256--26298 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
26246 GAAGAAGTCA
26256 ATCATCTCCTCTTCAATGGCT
1 ATCATCTCCTCTTCAATGGCT
26277 ATCATCTCCTCTTCAATGGCT
1 ATCATCTCCTCTTCAATGGCT
26298 A
1 A
26299 CTCTATATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.33, G:0.09, T:0.37
Consensus pattern (21 bp):
ATCATCTCCTCTTCAATGGCT
Found at i:32602 original size:46 final size:45
Alignment explanation
Indices: 32549--32664 Score: 121
Period size: 46 Copynumber: 2.5 Consensus size: 45
32539 GGTATATTTT
32549 CTCCACTACTCTTCAGAGAAGATTAAATCTTGGAAAAA-TAT-A-TCTA
1 CTCCACTACTCTTCAG-GAAGATTAAATC-T-GAAAAATTATGATTC-A
* * *
32595 CTCCACTACTCTTTAGGGAAGATCAGATCTGAAAAATTATGATTCA
1 CTCCACTACTCTTCA-GGAAGATTAAATCTGAAAAATTATGATTCA
*
32641 CTTCACTACTCTTCAGGAAAGATT
1 CTCCACTACTCTTCAGG-AAGATT
32665 GAATTGAGGT
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
44 6 0.10
45 6 0.10
46 44 0.75
47 3 0.05
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (45 bp):
CTCCACTACTCTTCAGGAAGATTAAATCTGAAAAATTATGATTCA
Found at i:32613 original size:134 final size:133
Alignment explanation
Indices: 32462--32716 Score: 352
Period size: 134 Copynumber: 1.9 Consensus size: 133
32452 AGAAATCTTT
* * *
32462 TCCACTATTCTTTAGGGAAGATCATATATGAAAAATTATGATTCACTT-AATGACTCTCCATGAA
1 TCCACTACTCTTTAGGGAAGATCAGATATGAAAAATTATGATTCACTTCAAT-ACTCTCCAGGAA
* * *
32526 AGATTGAATCTGAGGTATATTTTCTCCAC-TACTCTTCAGAGAAGATTAAATCTTGGAAAAATAT
65 AGATTGAAT-TGAGGTAGATTTGCTCCACTTA-TCTTCAGAGAAGATCAAATCTTGGAAAAATAT
32590 ATCTAC
128 ATCTAC
* * *
32596 TCCACTACTCTTTAGGGAAGATCAGATCTGAAAAATTATGATTCACTTCACTACTCTTCAGGAAA
1 TCCACTACTCTTTAGGGAAGATCAGATATGAAAAATTATGATTCACTTCAATACTCTCCAGGAAA
** * *
32661 GATTGAATTGAGGTAGATTTGCTGTACTTATCTTCAGGGAATATCAAATCTTGGAA
66 GATTGAATTGAGGTAGATTTGCTCCACTTATCTTCAGAGAAGATCAAATCTTGGAA
32717 GAAGGGGTAT
Statistics
Matches: 106, Mismatches: 13, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
133 38 0.36
134 66 0.62
135 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (133 bp):
TCCACTACTCTTTAGGGAAGATCAGATATGAAAAATTATGATTCACTTCAATACTCTCCAGGAAA
GATTGAATTGAGGTAGATTTGCTCCACTTATCTTCAGAGAAGATCAAATCTTGGAAAAATATATC
TAC
Found at i:33607 original size:12 final size:12
Alignment explanation
Indices: 33590--33615 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
33580 TAAAAAGTTT
33590 TTGGATAAATAC
1 TTGGATAAATAC
33602 TTGGATAAATAC
1 TTGGATAAATAC
33614 TT
1 TT
33616 AATTTATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (12 bp):
TTGGATAAATAC
Found at i:33752 original size:8 final size:8
Alignment explanation
Indices: 33739--33787 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
33729 CTTGAACCCC
33739 TTTTATTA
1 TTTTATTA
*
33747 TTTTATTC
1 TTTTATTA
*
33755 TTATATT-
1 TTTTATTA
*
33762 TTTT-TTC
1 TTTTATTA
33769 TTTTATTA
1 TTTTATTA
33777 TTTT-TTA
1 TTTTATTA
33784 TTTT
1 TTTT
33788 TCTCTATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
6 2 0.06
7 14 0.40
8 19 0.54
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTATTA
Found at i:33780 original size:14 final size:14
Alignment explanation
Indices: 33738--33781 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
33728 TCTTGAACCC
33738 CTTTTATTATTTTATT
1 CTTTTATTA-TTT-TT
* *
33754 CTTATATTTTTTTT
1 CTTTTATTATTTTT
33768 CTTTTATTATTTTT
1 CTTTTATTATTTTT
33782 TATTTTTCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 14 0.58
15 3 0.12
16 7 0.29
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (14 bp):
CTTTTATTATTTTT
Found at i:33788 original size:16 final size:16
Alignment explanation
Indices: 33741--33800 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
33731 TGAACCCCTT
*
33741 TTATTATTTTATTCTTA
1 TTATT-TTTTATTTTTA
*
33758 -TATTTTTTTTCTTTTA
1 TTATTTTTTAT-TTTTA
*
33774 TTATTTTTTATTTTTC
1 TTATTTTTTATTTTTA
33790 TCTATTTTTTA
1 T-TATTTTTTA
33801 GGCAAAGTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 5 0.14
16 13 0.36
17 18 0.50
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.77
Consensus pattern (16 bp):
TTATTTTTTATTTTTA
Found at i:43282 original size:34 final size:34
Alignment explanation
Indices: 43234--43310 Score: 120
Period size: 34 Copynumber: 2.3 Consensus size: 34
43224 AAGTTTAGGC
*
43234 AGAGTTTCAGCATAAAATGGGCGGAATTTTGGGT
1 AGAGTTTCAGCATAAAATGGGCAGAATTTTGGGT
*
43268 AGAGTTTC-GACATAAAATGGGCATAATTTTGGGT
1 AGAGTTTCAG-CATAAAATGGGCAGAATTTTGGGT
43302 AGAGTTTCA
1 AGAGTTTCA
43311 ACGAAAAACA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
33 1 0.03
34 38 0.97
ACGTcount: A:0.31, C:0.09, G:0.29, T:0.31
Consensus pattern (34 bp):
AGAGTTTCAGCATAAAATGGGCAGAATTTTGGGT
Found at i:45842 original size:19 final size:18
Alignment explanation
Indices: 45813--45851 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
45803 AGTCATTTTC
45813 TTGTTTTTATTTTTTTAT
1 TTGTTTTTATTTTTTTAT
45831 TTGTTGTTTATTTTTTTAT
1 TTGTT-TTTATTTTTTTAT
45850 TT
1 TT
45852 TTATCTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.10, C:0.00, G:0.08, T:0.82
Consensus pattern (18 bp):
TTGTTTTTATTTTTTTAT
Found at i:45939 original size:3 final size:3
Alignment explanation
Indices: 45927--45955 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
45917 GTTTTCCTAA
45927 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
45956 ATATATACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:46023 original size:31 final size:29
Alignment explanation
Indices: 45964--46028 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 29
45954 ATATATATAC
*
45964 ATTTTTTTACTATTATTTTCTTTCTTTTT
1 ATTTTTTTACTATTATTTTCTTTATTTTT
* *
45993 ATTTTTTATTCTATTTATTTTTTTTATTTTT
1 ATTTTTT-TACTA-TTATTTTCTTTATTTTT
46024 ATTTT
1 ATTTT
46029 CACTTTGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 7 0.23
30 4 0.13
31 20 0.65
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.78
Consensus pattern (29 bp):
ATTTTTTTACTATTATTTTCTTTATTTTT
Found at i:46140 original size:17 final size:17
Alignment explanation
Indices: 46111--46249 Score: 67
Period size: 18 Copynumber: 7.7 Consensus size: 17
46101 TTGTATATGT
46111 TTTTATTATTTTATTTA
1 TTTTATTATTTTATTTA
46128 TTTT-TTATCTTTATTTTA
1 TTTTATTAT-TTTA-TTTA
*
46146 TTCTTATTTCTTTTATTT-
1 TT-TTA-TTATTTTATTTA
46164 TCTTTATCTCATTTT-TTTA
1 T-TTTAT-T-ATTTTATTTA
*
46183 TTTCATT-TGTTT-TCTTA
1 TTTTATTAT-TTTAT-TTA
*
46200 TCTTCT-TTACTTTATTTTA
1 T-TT-TATTATTTTA-TTTA
46219 TTTGCT-TTATTTTATTTA
1 TTT--TATTATTTTATTTA
46237 TTTTCATTATTTT
1 TTTT-ATTATTTT
46250 TTATTCTTTT
Statistics
Matches: 97, Mismatches: 6, Indels: 37
0.69 0.04 0.26
Matches are distributed among these distances:
15 1 0.01
16 9 0.09
17 14 0.14
18 41 0.42
19 24 0.25
20 5 0.05
21 3 0.03
ACGTcount: A:0.16, C:0.09, G:0.01, T:0.73
Consensus pattern (17 bp):
TTTTATTATTTTATTTA
Found at i:46144 original size:11 final size:10
Alignment explanation
Indices: 45996--46264 Score: 57
Period size: 9 Copynumber: 26.1 Consensus size: 10
45986 TCTTTTTATT
*
45996 TTTTATTCTA
1 TTTTATTTTA
46006 -TTTATTTT-
1 TTTTATTTTA
46014 TTTTATTTTTA
1 TTTTA-TTTTA
46025 TTTTCACTTTGT-
1 TTTT-A-TTT-TA
*
46037 TTTTA-TTTC
1 TTTTATTTTA
* *
46046 CTTTATATTAA
1 TTTTAT-TTTA
46057 TTTTATTTCTTCA
1 TTTTA-TT-TT-A
46070 TTTTTATTTTA
1 -TTTTATTTTA
46081 TTCCTGT-TTTTA
1 TT--T-TATTTTA
46093 -TTTA-TTTA
1 TTTTATTTTA
46101 TTGTATATGTTT-
1 TT-T-TAT-TTTA
46113 TTATTATTTTA
1 TT-TTATTTTA
*
46124 TTTATTTTTTA
1 TTT-TATTTTA
46135 TCTTTATTTTA
1 T-TTTATTTTA
*
46146 TTCTTA-TTTC
1 TT-TTATTTTA
46156 TTTTATTTT-
1 TTTTATTTTA
* * *
46165 CTTTATCTCA
1 TTTTATTTTA
46175 -TTT-TTTTA
1 TTTTATTTTA
* *
46183 TTTCATTTGTT
1 TTTTATTT-TA
*
46194 TTCTTATCTT-
1 TT-TTATTTTA
* *
46204 CTTTACTTTA
1 TTTTATTTTA
*
46214 TTTTA-TTTG
1 TTTTATTTTA
*
46223 CTTTATTTTA
1 TTTTATTTTA
46233 -TTTATTTTCA
1 TTTTATTTT-A
46243 TTATT-TTTTA
1 TT-TTATTTTA
*
46253 TTCTTTTTTTA
1 TT-TTATTTTA
46264 T
1 T
46265 AACGCTTTTC
Statistics
Matches: 194, Mismatches: 28, Indels: 73
0.66 0.09 0.25
Matches are distributed among these distances:
8 9 0.05
9 53 0.27
10 37 0.19
11 53 0.27
12 29 0.15
13 8 0.04
14 5 0.03
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.73
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:46214 original size:31 final size:31
Alignment explanation
Indices: 46120--46222 Score: 83
Period size: 31 Copynumber: 3.4 Consensus size: 31
46110 TTTTTATTAT
* *
46120 TTTATTT-ATTT-TTTATCTTTATTTTA-TTC
1 TTTATTTCATTTGTTT-TCTTTATCTCATTTC
* * *
46149 -TTATTTCTTTTATTTTCTTTATCTCATTTT
1 TTTATTTCATTTGTTTTCTTTATCTCATTTC
46179 TTTATTTCATTTGTTTTC-TTATCTTC-TTTAC
1 TTTATTTCATTTGTTTTCTTTATC-TCATTT-C
*
46210 TTTATTTTATTTG
1 TTTATTTCATTTG
46223 CTTTATTTTA
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
28 6 0.10
29 12 0.20
30 13 0.22
31 29 0.48
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.73
Consensus pattern (31 bp):
TTTATTTCATTTGTTTTCTTTATCTCATTTC
Found at i:49855 original size:27 final size:30
Alignment explanation
Indices: 49817--49897 Score: 96
Period size: 33 Copynumber: 2.7 Consensus size: 30
49807 AAATAATTTA
* *
49817 TTTATT-ATTAAAATATTAT-TT-TTATAT
1 TTTATTAATAAAAATATTATATTGGTATAT
49844 TTTATTAATAAAAATATTAATATTGGTATAT
1 TTTATTAATAAAAATATT-ATATTGGTATAT
49875 TTTATTGAAATAAAAATATTATA
1 TTTATT--AATAAAAATATTATA
49898 AATTATATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
27 6 0.13
28 10 0.22
29 2 0.04
30 2 0.04
31 11 0.24
32 3 0.07
33 12 0.26
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (30 bp):
TTTATTAATAAAAATATTATATTGGTATAT
Found at i:49905 original size:31 final size:29
Alignment explanation
Indices: 49797--49967 Score: 82
Period size: 28 Copynumber: 5.8 Consensus size: 29
49787 TATTATTTTT
* * * *
49797 AAAATATTAAAAATAATTTATTTATT-ATT
1 AAAATATTAATAATTATAT-TTTATTAATA
**
49826 AAAATATT-ATTTTTATATTTTATTAATA
1 AAAATATTAATAATTATATTTTATTAATA
*
49854 AAAATATTAATATTGGTATATTTTATTGAAATA
1 AAAATATTAATAAT--TATATTTTATT--AATA
* *
49887 AAAATATT-ATAAATTATATTAATTATTTATT
1 AAAATATTAAT-AATTATATT--TTATTAATA
* * * * * *
49918 AAAGTAATAGT-GTTATATTATATT-TTA
1 AAAATATTAATAATTATATTTTATTAATA
* *
49945 AAAATATTAATTAGTATATTTTA
1 AAAATATTAATAATTATATTTTA
49968 AATATATTTA
Statistics
Matches: 108, Mismatches: 23, Indels: 23
0.70 0.15 0.15
Matches are distributed among these distances:
27 15 0.14
28 27 0.25
29 12 0.11
30 7 0.06
31 25 0.23
32 3 0.03
33 19 0.18
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (29 bp):
AAAATATTAATAATTATATTTTATTAATA
Found at i:49934 original size:92 final size:87
Alignment explanation
Indices: 49797--49967 Score: 207
Period size: 92 Copynumber: 1.9 Consensus size: 87
49787 TATTATTTTT
* * * * *
49797 AAAATATTAAAAATAATTTATTTATTATTAAAATATTATTTTTATATTTTATTAATAAAAATATT
1 AAAATATTAAAAATAATTTAATTATTATTAAAATAATAGTGTTATATTATATT-ATAAAAATATT
*
49862 AATATTGGTATATTTTATTGAAATA
65 -A-ATTAGTATATTTTATTGAAATA
* * * *
49887 AAAATATTATAAATTATATTAATTATTTATTAAAGTAATAGTGTTATATTATATTTTAAAAATAT
1 AAAATATTAAAAATAAT-TTAATTA-TTATTAAAATAATAGTGTTATATTATATTATAAAAATAT
49952 TAATTAGTATATTTTA
64 TAATTAGTATATTTTA
49968 AATATATTTA
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
89 13 0.19
90 16 0.23
91 16 0.23
92 24 0.35
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (87 bp):
AAAATATTAAAAATAATTTAATTATTATTAAAATAATAGTGTTATATTATATTATAAAAATATTA
ATTAGTATATTTTATTGAAATA
Found at i:49965 original size:23 final size:23
Alignment explanation
Indices: 49936--49980 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
49926 AGTGTTATAT
49936 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAG
* *
49959 TATATTTTAAATATATTTATTA
1 TATATTTTAAAAATATTAATTA
49981 AAATATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAG
Found at i:49986 original size:23 final size:23
Alignment explanation
Indices: 49937--49987 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
49927 GTGTTATATT
**
49937 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* *
49960 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
49983 ATATT
1 ATATT
49988 ATAGATTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:50014 original size:24 final size:26
Alignment explanation
Indices: 49960--50024 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 26
49950 ATTAATTAGT
*
49960 ATATTTTAAAT-ATATT--TATTAAA
1 ATATTATAAATAATATTAATATTAAA
* *
49983 ATATTATAGATTATATTAATATT-AA
1 ATATTATAAATAATATTAATATTAAA
50008 ATA-TATAAATAATATTA
1 ATATTATAAATAATATTA
50025 TTCATTAGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 9 0.26
24 17 0.49
25 5 0.14
26 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
ATATTATAAATAATATTAATATTAAA
Found at i:50182 original size:22 final size:23
Alignment explanation
Indices: 50157--50201 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
50147 TGATTATTTT
50157 TTATAATATTAAAAATA-TAATA
1 TTATAATATTAAAAATATTAATA
* *
50179 TTATATTATTAGAAATATTAATA
1 TTATAATATTAAAAATATTAATA
50202 AAAATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TTATAATATTAAAAATATTAATA
Found at i:50217 original size:52 final size:52
Alignment explanation
Indices: 50100--50272 Score: 121
Period size: 52 Copynumber: 3.3 Consensus size: 52
50090 AGTTTATTAT
* * **
50100 ATATTATTAAA-A-TAAAAATATAATATCTTATATTATTATAATATAATTGATT
1 ATATT-TTAAATATTAAAAATATAATA-CTTATATTATTAAAATATAATTAAAA
*
50152 ATTTTTTATAATATTAAAAATATAATA-TTATATTATTAGAAATATTAA-TAAAA
1 ATATTTTA-AATATTAAAAATATAATACTTATATTATTA-AAATA-TAATTAAAA
** * *
50205 ATATTTTAAATATT-TTAATA-ATTA-TTATTTTGATTAAAATGAT-ATT-AAA
1 ATATTTTAAATATTAAAAATATAATACTTATATT-ATTAAAAT-ATAATTAAAA
50254 ATATTTTATTAATATTAAA
1 ATATTTTA--AATATTAAA
50273 TTCATAAAAT
Statistics
Matches: 98, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
49 12 0.12
50 15 0.15
51 18 0.18
52 23 0.23
53 14 0.14
54 16 0.16
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (52 bp):
ATATTTTAAATATTAAAAATATAATACTTATATTATTAAAATATAATTAAAA
Found at i:55764 original size:17 final size:16
Alignment explanation
Indices: 55736--55774 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
55726 GATATTACCC
* *
55736 GACCAGTTTTAAACCT
1 GACCTGTTTTTAACCT
55752 GACCTGTTTTTAACCT
1 GACCTGTTTTTAACCT
55768 GACCTGT
1 GACCTGT
55775 AAATGATCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (16 bp):
GACCTGTTTTTAACCT
Found at i:55992 original size:13 final size:13
Alignment explanation
Indices: 55976--56002 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55966 TACCTATTAT
55976 ATAAAATTATTTA
1 ATAAAATTATTTA
55989 ATAAAATTATTTA
1 ATAAAATTATTTA
56002 A
1 A
56003 ATGTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:56012 original size:15 final size:14
Alignment explanation
Indices: 55976--56018 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
55966 TACCTATTAT
55976 ATAAAATTATTT-A
1 ATAAAATTATTTAA
55989 ATAAAATTATTTAA
1 ATAAAATTATTTAA
* *
56003 ATGTAAATTATATAA
1 AT-AAAATTATTTAA
56018 A
1 A
56019 ACATGATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 12 0.46
14 3 0.12
15 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
ATAAAATTATTTAA
Found at i:56101 original size:23 final size:24
Alignment explanation
Indices: 56058--56111 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 24
56048 CAATGATTAA
*
56058 ATGTAAATTAATATAGTTTAATTT
1 ATGTAAATTAATATAGCTTAATTT
56082 ATGTAAATT-ATATAGCTTAATTT
1 ATGTAAATTAATATAGCTTAATTT
56105 ATGTAAA
1 ATGTAAA
56112 GAAAAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 20 0.69
24 9 0.31
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (24 bp):
ATGTAAATTAATATAGCTTAATTT
Found at i:56387 original size:12 final size:11
Alignment explanation
Indices: 56361--56402 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
56351 GATAATGATA
*
56361 ATTTAAATAAC
1 ATTTGAATAAC
*
56372 ATTTGATATAAA
1 ATTTGA-ATAAC
56384 ATTTGAATAAC
1 ATTTGAATAAC
56395 ATTTGAAT
1 ATTTGAAT
56403 TAATTCAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (11 bp):
ATTTGAATAAC
Found at i:57001 original size:13 final size:14
Alignment explanation
Indices: 56952--57027 Score: 67
Period size: 13 Copynumber: 5.9 Consensus size: 14
56942 TATTAAATAA
56952 TAATTGCATGTTAT
1 TAATTGCATGTTAT
**
56966 TAATT-CATG-TGG
1 TAATTGCATGTTAT
56978 T-ATTGCATGTTAT
1 TAATTGCATGTTAT
56991 TAATT-CATG-T-T
1 TAATTGCATGTTAT
**
57002 GCATTGCATGTTAT
1 TAATTGCATGTTAT
57016 TAATT-CATGTTA
1 TAATTGCATGTTA
57028 CATTAGGTGT
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
11 7 0.15
12 11 0.23
13 18 0.38
14 12 0.25
ACGTcount: A:0.26, C:0.09, G:0.16, T:0.49
Consensus pattern (14 bp):
TAATTGCATGTTAT
Found at i:57026 original size:25 final size:25
Alignment explanation
Indices: 56954--57031 Score: 129
Period size: 25 Copynumber: 3.1 Consensus size: 25
56944 TTAAATAATA
* *
56954 ATTGCATGTTATTAATTCATGTGGT
1 ATTGCATGTTATTAATTCATGTTGC
56979 ATTGCATGTTATTAATTCATGTTGC
1 ATTGCATGTTATTAATTCATGTTGC
*
57004 ATTGCATGTTATTAATTCATGTTAC
1 ATTGCATGTTATTAATTCATGTTGC
57029 ATT
1 ATT
57032 AGGTGTTAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.26, C:0.10, G:0.15, T:0.49
Consensus pattern (25 bp):
ATTGCATGTTATTAATTCATGTTGC
Found at i:57735 original size:26 final size:28
Alignment explanation
Indices: 57719--57782 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
57709 AACTATTTAT
57719 AATTAATAATAATATAAATTATATATTAG
1 AATTAATAATAATATAAA-TATATATTAG
* *
57748 AATTAATATTAATATAATTA-ATATTA-
1 AATTAATAATAATATAAATATATATTAG
57774 ATATTAATA
1 A-ATTAATA
57783 TTAACTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 1 0.03
27 13 0.41
28 2 0.06
29 16 0.50
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (28 bp):
AATTAATAATAATATAAATATATATTAG
Found at i:57743 original size:24 final size:24
Alignment explanation
Indices: 57690--57743 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
57680 ATTTCATCCC
* *
57690 TATATAATTTATATTAATAAACTAT
1 TATATAATTAATAATAATAAAC-AT
57715 T-TATAATTAATAATAATATAA-AT
1 TATATAATTAATAATAATA-AACAT
57738 TATATA
1 TATATA
57744 TTAGAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 3 0.12
24 19 0.76
25 3 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
TATATAATTAATAATAATAAACAT
Found at i:57758 original size:6 final size:6
Alignment explanation
Indices: 57720--57798 Score: 66
Period size: 6 Copynumber: 14.2 Consensus size: 6
57710 ACTATTTATA
*
57720 ATTAAT AATAAT A-TAA- ATTATAT ATTAGA- ATTAAT ATTAAT A-T-A-
1 ATTAAT ATTAAT ATTAAT ATTA-AT ATTA-AT ATTAAT ATTAAT ATTAAT
*
57764 ATTAAT ATTAAT ATTAAT ATTAA- CTT-AT ATTAAT A
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT A
57799 GAATATAGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
3 1 0.02
4 4 0.07
5 12 0.20
6 38 0.63
7 5 0.08
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (6 bp):
ATTAAT
Found at i:57768 original size:15 final size:15
Alignment explanation
Indices: 57716--57777 Score: 74
Period size: 15 Copynumber: 4.2 Consensus size: 15
57706 ATAAACTATT
*
57716 TATAATTAATAATAA
1 TATAATTAATATTAA
*
57731 TATAAATT-ATA-TAT
1 TAT-AATTAATATTAA
*
57745 TAGAATTAATATTAA
1 TATAATTAATATTAA
57760 TATAATTAATATTAA
1 TATAATTAATATTAA
57775 TAT
1 TAT
57778 TAATATTAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
13 4 0.10
14 7 0.17
15 25 0.62
16 4 0.10
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
TATAATTAATATTAA
Found at i:57794 original size:37 final size:37
Alignment explanation
Indices: 57724--57803 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
57714 TTTATAATTA
57724 ATAATAATATAAATTATATATTAGAATTAATATTAAT
1 ATAATAATATAAATTATATATTAGAATTAATATTAAT
*
57761 ATAATTAATATTAATATTA-ATATTA-ACTT-ATATTAAT
1 ATAA-TAATA-TAA-ATTATATATTAGAATTAATATTAAT
*
57798 AGAATA
1 ATAATA
57804 TAGTTTATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
36 2 0.05
37 15 0.39
38 8 0.21
39 9 0.24
40 4 0.11
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.44
Consensus pattern (37 bp):
ATAATAATATAAATTATATATTAGAATTAATATTAAT
Found at i:57803 original size:27 final size:27
Alignment explanation
Indices: 57720--57804 Score: 77
Period size: 27 Copynumber: 3.1 Consensus size: 27
57710 ACTATTTATA
* *
57720 ATTAATAATAATATAAATTATATATTAGA-
1 ATTAATATTAATAT-AATTA-ATATGA-AT
*
57749 ATTAATATTAATATAATTAATATTAAT
1 ATTAATATTAATATAATTAATATGAAT
57776 ATTAATATTAACT-TATATTAATA-GAAT
1 ATTAATATTAA-TATA-ATTAATATGAAT
57803 AT
1 AT
57805 AGTTTATAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
26 1 0.02
27 24 0.47
28 13 0.25
29 13 0.25
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (27 bp):
ATTAATATTAATATAATTAATATGAAT
Found at i:57841 original size:29 final size:30
Alignment explanation
Indices: 57809--57872 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
57799 GAATATAGTT
*
57809 TATAATTTGT-AATTAATATCAATATAAAA
1 TATAATCTGTAAATTAATATCAATATAAAA
* * *
57838 TATAGTCTGTAAAATTAATATTAATATAAAC
1 TATAATCTGT-AAATTAATATCAATATAAAA
57869 TATA
1 TATA
57873 TTTTATAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 8 0.28
31 21 0.72
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (30 bp):
TATAATCTGTAAATTAATATCAATATAAAA
Found at i:58006 original size:19 final size:19
Alignment explanation
Indices: 57982--58082 Score: 69
Period size: 21 Copynumber: 5.0 Consensus size: 19
57972 AAGAAATTAA
*
57982 CATTAATGTAAACTATAGT
1 CATTAATATAAACTATAGT
58001 CATTAATATAAACTATAGTT
1 CATTAATATAAACTATAG-T
* * *
58021 TATAAATTATATACTATAGTT
1 CATTAA-TATAAACTATAG-T
* *
58042 TATAAAGTAT-AACTATATAGT
1 CATTAA-TATAAAC--TATAGT
*
58063 ACACTAATATAAACTATAGT
1 -CATTAATATAAACTATAGT
58083 TTATAAATGA
Statistics
Matches: 67, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
19 17 0.25
20 13 0.19
21 26 0.39
22 11 0.16
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.39
Consensus pattern (19 bp):
CATTAATATAAACTATAGT
Found at i:58036 original size:21 final size:20
Alignment explanation
Indices: 58011--58121 Score: 111
Period size: 21 Copynumber: 5.3 Consensus size: 20
58001 CATTAATATA
*
58011 AACTATAGTTTATAAATTAT
1 AACTATAGTTTATAAAGTAT
58031 ATACTATAGTTTATAAAGTAT
1 A-ACTATAGTTTATAAAGTAT
* *
58052 AACTATA-TAGTACACTAA-TAT
1 AACTATAGT-TTATA--AAGTAT
58073 AAACTATAGTTTATAAA-TGAT
1 -AACTATAGTTTATAAAGT-AT
58094 ATACTATAGTTTATAAAGTAT
1 A-ACTATAGTTTATAAAGTAT
58115 AACTATA
1 AACTATA
58122 TAGTACACTA
Statistics
Matches: 77, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
19 1 0.01
20 20 0.26
21 42 0.55
22 13 0.17
23 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (20 bp):
AACTATAGTTTATAAAGTAT
Found at i:58071 original size:63 final size:63
Alignment explanation
Indices: 57995--58157 Score: 274
Period size: 63 Copynumber: 2.6 Consensus size: 63
57985 TAATGTAAAC
*
57995 TATAGT-CATTAATATAAACTATAGTTTATAAATTATATACTATAGTTTATAAAGTATAACTA
1 TATAGTACACTAATATAAACTATAGTTTATAAATTATATACTATAGTTTATAAAGTATAACTA
*
58057 TATAGTACACTAATATAAACTATAGTTTATAAATGATATACTATAGTTTATAAAGTATAACTA
1 TATAGTACACTAATATAAACTATAGTTTATAAATTATATACTATAGTTTATAAAGTATAACTA
** *
58120 TATAGTACACTAATATAAACTATTTTTTATAAACTATA
1 TATAGTACACTAATATAAACTATAGTTTATAAATTATA
58158 GGTTACATAT
Statistics
Matches: 94, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
62 6 0.06
63 88 0.94
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.40
Consensus pattern (63 bp):
TATAGTACACTAATATAAACTATAGTTTATAAATTATATACTATAGTTTATAAAGTATAACTA
Found at i:58139 original size:145 final size:144
Alignment explanation
Indices: 57857--58142 Score: 321
Period size: 145 Copynumber: 2.0 Consensus size: 144
57847 TAAAATTAAT
* * ** *
57857 ATTAATATAAACTATATTTTATAAATTATATAGTATAATTTATAAACTATAGTTAATATAATATT
1 ATTAATATAAACTATAGTTTATAAATTATATACTATAATTTATAAACTATAACTAATATAATAAT
* * * ** * *
57922 AATAGAGTATAGTTTATAAACTATATACTATATTAATATAAATTATAGTTAAGAAATTAACATTA
66 AATAAACTATAGTTTATAAACTATATACTATATT-ATATAAAGTATAACTAAGAAAGTAACACTA
*
57987 ATGTAAACTATAGTC
130 ATATAAACTATAGTC
* *
58002 ATTAATATAAACTATAGTTTATAAATTATATACTATAGTTTATAAAGTATAACTATATAGTACAC
1 ATTAATATAAACTATAGTTTATAAATTATATACTATAATTTATAAACTATAACTA-ATA-TA-A-
* *
58067 TAAT-ATAAACTATAGTTTATAAA-TGATATACTATAGTT-TATAAAGTATAACT-ATATAGT-A
62 TAATAATAAACTATAGTTTATAAACT-ATATACTATA-TTATATAAAGTATAACTAAGAAAGTAA
58127 CACTAATATAAACTAT
125 CACTAATATAAACTAT
58143 TTTTTATAAA
Statistics
Matches: 118, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
145 64 0.54
146 7 0.06
147 14 0.12
148 28 0.24
149 5 0.04
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.40
Consensus pattern (144 bp):
ATTAATATAAACTATAGTTTATAAATTATATACTATAATTTATAAACTATAACTAATATAATAAT
AATAAACTATAGTTTATAAACTATATACTATATTATATAAAGTATAACTAAGAAAGTAACACTAA
TATAAACTATAGTC
Found at i:58238 original size:15 final size:15
Alignment explanation
Indices: 58218--58249 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
58208 TACTATAAGT
*
58218 TATATATATAGTTTA
1 TATATACATAGTTTA
58233 TATATACATAGTTTA
1 TATATACATAGTTTA
58248 TA
1 TA
58250 CACACATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (15 bp):
TATATACATAGTTTA
Found at i:58589 original size:7 final size:7
Alignment explanation
Indices: 58575--58612 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
58565 TACATATATA
58575 GTTTAGG
1 GTTTAGG
*
58582 GGTTAGG
1 GTTTAGG
58589 GTTTAGG
1 GTTTAGG
*
58596 ATTTAGG
1 GTTTAGG
58603 GTTTAGG
1 GTTTAGG
58610 GTT
1 GTT
58613 AAGGATTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (7 bp):
GTTTAGG
Found at i:58600 original size:21 final size:21
Alignment explanation
Indices: 58576--58621 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
58566 ACATATATAG
*
58576 TTTAGGGGTTAGGGTTTAGGA
1 TTTAGGGGTTAGGGTTAAGGA
*
58597 TTTAGGGTTTAGGGTTAAGGA
1 TTTAGGGGTTAGGGTTAAGGA
58618 TTTA
1 TTTA
58622 ATGATGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (21 bp):
TTTAGGGGTTAGGGTTAAGGA
Found at i:58709 original size:2 final size:2
Alignment explanation
Indices: 58702--58860 Score: 70
Period size: 2 Copynumber: 83.5 Consensus size: 2
58692 TTCTATAAAC
* *
58702 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA AA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
58743 TA TA TA GA TT TC T- TA TA T- TA -A T- TA TA CA TA CA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
58781 CA TA CA TA TA TA CTA TA T- TA -A TA TA AA T- TA TA -A TT TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
58820 AA CTA TA TA T- TT TA TA TA GTT TA TA CA TA TA TA TA TA -A TA T
1 TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA T
58861 TAATATAAAT
Statistics
Matches: 114, Mismatches: 29, Indels: 28
0.67 0.17 0.16
Matches are distributed among these distances:
1 11 0.10
2 99 0.87
3 4 0.04
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.45
Consensus pattern (2 bp):
TA
Found at i:58865 original size:62 final size:63
Alignment explanation
Indices: 58778--58914 Score: 233
Period size: 62 Copynumber: 2.2 Consensus size: 63
58768 ACATACATAC
*
58778 ATACATACATATATACTATATTAATATAAATTATAATTTATAAACTATATA-TTTTATATAGTTT
1 ATACATATATATATAC-ATATTAATATAAATTATAATTTATAAACTATATACTTTT-TATAGTTT
58842 ATACATATATATATA-ATATTAATATAAATTATAATTTATAAACTATATACTTTTTATAGTTT
1 ATACATATATATATACATATTAATATAAATTATAATTTATAAACTATATACTTTTTATAGTTT
58904 ATACATATATA
1 ATACATATATA
58915 GTTTACGTAC
Statistics
Matches: 71, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
62 53 0.75
63 4 0.06
64 14 0.20
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.47
Consensus pattern (63 bp):
ATACATATATATATACATATTAATATAAATTATAATTTATAAACTATATACTTTTTATAGTTT
Found at i:58941 original size:13 final size:13
Alignment explanation
Indices: 58896--58975 Score: 61
Period size: 13 Copynumber: 5.8 Consensus size: 13
58886 ATATACTTTT
58896 TATAGTTTATACATA
1 TATAGTTTAT--ATA
**
58911 TATAGTTTACGTA
1 TATAGTTTATATA
*
58924 CATAGTTTATATA
1 TATAGTTTATATA
*
58937 TATAGTTCATATAAA
1 TATAGTT--TATATA
* *
58952 CATAATTTATATA
1 TATAGTTTATATA
*
58965 TATAGCTTATA
1 TATAGTTTATA
58976 ATAATTATAT
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
13 31 0.62
15 19 0.38
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:59003 original size:18 final size:17
Alignment explanation
Indices: 58959--59017 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
58949 AAACATAATT
* *
58959 TATATATATAGCTTATA
1 TATAAATATAGTTTATA
*
58976 -ATAATTATATAGTTTGTAA
1 TATAA--ATATAGTTTAT-A
58995 TATAAATATAGTTTATA
1 TATAAATATAGTTTATA
59012 TATAAA
1 TATAAA
59018 CTTATATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 3 0.09
17 7 0.21
18 19 0.56
19 1 0.03
20 4 0.12
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (17 bp):
TATAAATATAGTTTATA
Found at i:59027 original size:17 final size:16
Alignment explanation
Indices: 58994--59041 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
58984 ATAGTTTGTA
58994 ATATAAA-TATAGTTTAT
1 ATATAAATTATA--TTAT
59011 ATATAAACTTATATTAT
1 ATATAAA-TTATATTAT
*
59028 ATATATATTATATT
1 ATATAAATTATATT
59042 TTTTTTCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 7 0.25
17 17 0.61
19 4 0.14
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (16 bp):
ATATAAATTATATTAT
Found at i:61503 original size:27 final size:22
Alignment explanation
Indices: 61438--61494 Score: 114
Period size: 22 Copynumber: 2.6 Consensus size: 22
61428 TGTTTAAGGT
61438 TGTTTTAAAAATATTAATTTAA
1 TGTTTTAAAAATATTAATTTAA
61460 TGTTTTAAAAATATTAATTTAA
1 TGTTTTAAAAATATTAATTTAA
61482 TGTTTTAAAAATA
1 TGTTTTAAAAATA
61495 AATTATTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (22 bp):
TGTTTTAAAAATATTAATTTAA
Found at i:62694 original size:18 final size:19
Alignment explanation
Indices: 62671--62720 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
62661 TTAGCAAAAG
*
62671 AATCGATCCCTTTG-ACCA
1 AATCGATCCCTTTGAAACA
*
62689 AATCGATCCCCTTGAAACA
1 AATCGATCCCTTTGAAACA
62708 AGATCGATCCCTT
1 A-ATCGATCCCTT
62721 GGATTCTAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 13 0.48
19 4 0.15
20 10 0.37
ACGTcount: A:0.30, C:0.32, G:0.12, T:0.26
Consensus pattern (19 bp):
AATCGATCCCTTTGAAACA
Found at i:62719 original size:19 final size:17
Alignment explanation
Indices: 62671--62721 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 17
62661 TTAGCAAAAG
*
62671 AATCGATCCCTTTGACCA
1 AATCGATCCC-TTGAACA
62689 AATCGATCCCCTTGAAACA
1 AATCGAT-CCCTTG-AACA
62708 AGATCGATCCCTTG
1 A-ATCGATCCCTTG
62722 GATTCTAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 10 0.34
19 13 0.45
20 6 0.21
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.25
Consensus pattern (17 bp):
AATCGATCCCTTGAACA
Found at i:62779 original size:21 final size:21
Alignment explanation
Indices: 62755--62822 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
62745 TCCTTTCACC
62755 AAAAGGATCAGTCCCTCGATG
1 AAAAGGATCAGTCCCTCGATG
* * * **
62776 AAAACGGTTGA-TCCTTTC-ACC
1 AAAA-GGATCAGTCC-CTCGATG
62797 AAAAGGATCAGTCCCTCGATG
1 AAAAGGATCAGTCCCTCGATG
62818 AAAAG
1 AAAAG
62823 AATTTATCCC
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
20 6 0.18
21 21 0.64
22 6 0.18
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.21
Consensus pattern (21 bp):
AAAAGGATCAGTCCCTCGATG
Found at i:65673 original size:18 final size:17
Alignment explanation
Indices: 65641--65674 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
65631 AATTTTTAAA
65641 TTTTAATATTTTTATTC
1 TTTTAATATTTTTATTC
*
65658 TTTTTATATTTATTATT
1 TTTTAATATTT-TTATT
65675 AATTAAATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTAATATTTTTATTC
Found at i:68749 original size:56 final size:56
Alignment explanation
Indices: 68672--68785 Score: 194
Period size: 57 Copynumber: 2.0 Consensus size: 56
68662 GGAAGGCACA
*
68672 TTTGCCATCCAATAGATTTTACACTTTTCTCAA-AGAAAGAGAAGCCTAGGCATTC
1 TTTGCCATCCAATAGATTTTACACTTCTCTCAATAGAAAGAGAAGCCTAGGCATTC
*
68727 TTTGTCATCCAAATAGATTTTACACTTCTCTCAATAGAAAGAGAAGCCTAGGCATTC
1 TTTGCCATCC-AATAGATTTTACACTTCTCTCAATAGAAAGAGAAGCCTAGGCATTC
68784 TT
1 TT
68786 CGTCGCATCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
55 9 0.16
56 22 0.40
57 24 0.44
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (56 bp):
TTTGCCATCCAATAGATTTTACACTTCTCTCAATAGAAAGAGAAGCCTAGGCATTC
Done.