Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007230.1 Hibiscus syriacus cultivar Beakdansim tig00019139_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: 61073
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6290 original size:36 final size:35
Alignment explanation
Indices: 6249--6320 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 35
6239 ATGATATTTA
6249 AGAGGAATTTGTTCCTACAGATTTAGTAACGATATT
1 AGAGGAATTTGTTCCTACAGATTTAGT-ACGATATT
* * *
6285 AGAGGAATTTGTTCTTATAGATTTAGTACGGTATT
1 AGAGGAATTTGTTCCTACAGATTTAGTACGATATT
6320 A
1 A
6321 TAGACACACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 8 0.24
36 25 0.76
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (35 bp):
AGAGGAATTTGTTCCTACAGATTTAGTACGATATT
Found at i:7245 original size:18 final size:18
Alignment explanation
Indices: 7217--7270 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 18
7207 TAATATTATA
7217 TTAATGGATTAAATAATTT
1 TTAA-GGATTAAATAATTT
7236 TTAAGGATTAATTAAATAATTT
1 TTAAGG----ATTAAATAATTT
7258 TTAAGGATTAAAT
1 TTAAGGATTAAAT
7271 TAAATAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
18 9 0.29
19 4 0.13
22 18 0.58
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (18 bp):
TTAAGGATTAAATAATTT
Found at i:7252 original size:22 final size:23
Alignment explanation
Indices: 7224--7277 Score: 101
Period size: 22 Copynumber: 2.4 Consensus size: 23
7214 ATATTAATGG
7224 ATTAAATAATTTTTAAGGATT-A
1 ATTAAATAATTTTTAAGGATTAA
7246 ATTAAATAATTTTTAAGGATTAA
1 ATTAAATAATTTTTAAGGATTAA
7269 ATTAAATAA
1 ATTAAATAA
7278 ATTTAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 21 0.68
23 10 0.32
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (23 bp):
ATTAAATAATTTTTAAGGATTAA
Found at i:7289 original size:22 final size:23
Alignment explanation
Indices: 7224--7290 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 23
7214 ATATTAATGG
* **
7224 ATTAAATAATTTTTAAGGATT-A
1 ATTAAATAATATTTAAAAATTAA
* **
7246 ATTAAATAATTTTTAAGGATTAA
1 ATTAAATAATATTTAAAAATTAA
7269 ATTAAATAA-ATTTAAAAATTAA
1 ATTAAATAATATTTAAAAATTAA
7291 GAGACATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 31 0.76
23 10 0.24
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (23 bp):
ATTAAATAATATTTAAAAATTAA
Found at i:8129 original size:20 final size:21
Alignment explanation
Indices: 8096--8141 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
8086 ATCCGACTCG
8096 AAATAATATATTTATT-AAAA
1 AAATAATATATTTATTCAAAA
* * *
8116 AAATATTATTTTTATTCAATA
1 AAATAATATATTTATTCAAAA
8137 AAATA
1 AAATA
8142 GGGATTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AAATAATATATTTATTCAAAA
Found at i:11795 original size:19 final size:19
Alignment explanation
Indices: 11767--11820 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
11757 TTAATTAGTC
11767 TGTTTATTTATGATTT-GAA
1 TGTTTATTTATGATTTAG-A
* * *
11786 TGTTTCTTTATAATTTAGT
1 TGTTTATTTATGATTTAGA
11805 TGTTTATTTATGATTT
1 TGTTTATTTATGATTT
11821 TATTCATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 28 0.97
20 1 0.03
ACGTcount: A:0.22, C:0.02, G:0.13, T:0.63
Consensus pattern (19 bp):
TGTTTATTTATGATTTAGA
Found at i:13581 original size:3 final size:3
Alignment explanation
Indices: 13573--13625 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
13563 ATTACATTGA
13573 ATT ATT ATT ATT ATT ATT ATT 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
13621 ATT AT
1 ATT AT
13626 ATCTAGGGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:13954 original size:43 final size:43
Alignment explanation
Indices: 13868--13954 Score: 97
Period size: 42 Copynumber: 2.0 Consensus size: 43
13858 TCATTTCTAA
* **
13868 TTTCAAAATTATTTCACCCTAACATTCTAAATCTCTATTTTTT
1 TTTCAAAATTATTTCACCCTAACATTCTAAATCTATAAATTTT
* *
13911 TTTC-AAATTATTTCACCTTAACATT-TAATTATTTATAAATTTT
1 TTTCAAAATTATTTCACCCTAACATTCTAA--ATCTATAAATTTT
13954 T
1 T
13955 AAGTTTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
41 3 0.08
42 20 0.54
43 14 0.38
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (43 bp):
TTTCAAAATTATTTCACCCTAACATTCTAAATCTATAAATTTT
Found at i:15093 original size:20 final size:21
Alignment explanation
Indices: 15068--15119 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
15058 TTTTCCCAAT
*
15068 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
15088 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
15109 TCGCAATGCGA
1 TCGCAATGCGA
15120 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:15133 original size:20 final size:19
Alignment explanation
Indices: 15108--15222 Score: 95
Period size: 20 Copynumber: 5.7 Consensus size: 19
15098 AATTGGGAAA
15108 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACT-ACT
*
15128 ATCGCATTGCGATACTTACT
1 ATCGCAATGCGATAC-TACT
* *
15148 ATCGCAATGCGATAATACAAA
1 ATCGCAATGCGATACTAC--T
* *
15169 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACT-ACT
* * *
15189 TTCGCAACGCGATAATACAT
1 ATCGCAATGCGATACTAC-T
15209 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
15223 TTTCAAAGCG
Statistics
Matches: 76, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
19 5 0.07
20 44 0.58
21 25 0.33
22 2 0.03
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.24
Consensus pattern (19 bp):
ATCGCAATGCGATACTACT
Found at i:15173 original size:41 final size:41
Alignment explanation
Indices: 15128--15222 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
15118 GATACTGACT
* * *
15128 ATCGCATTGCGATACTTACTATCGCAATGCGATAATACAAA
1 ATCGCAATGCGATACTGACTATCGCAACGCGATAATACAAA
* * * *
15169 ATCGCAACGAGATACTGACTTTCGCAACGCGATAATACATA
1 ATCGCAATGCGATACTGACTATCGCAACGCGATAATACAAA
15210 ATCGCAATGCGAT
1 ATCGCAATGCGAT
15223 TTTCAAAGCG
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (41 bp):
ATCGCAATGCGATACTGACTATCGCAACGCGATAATACAAA
Found at i:15174 original size:21 final size:20
Alignment explanation
Indices: 15148--15222 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
15138 GATACTTACT
*
15148 ATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATAATAC-AA
* * *
15169 ATCGCAACGAGATACTGAC-T
1 ATCGCAACGCGATAAT-ACAA
*
15189 TTCGCAACGCGATAATACATA
1 ATCGCAACGCGATAATACA-A
*
15210 ATCGCAATGCGAT
1 ATCGCAACGCGAT
15223 TTTCAAAGCG
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
19 2 0.05
20 13 0.32
21 24 0.59
22 2 0.05
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGATAATACAA
Found at i:15201 original size:61 final size:62
Alignment explanation
Indices: 15105--15222 Score: 159
Period size: 61 Copynumber: 1.9 Consensus size: 62
15095 GCGAATTGGG
* * ** *
15105 AAAATCGCAATGCGATACTGACTATCGCATTGCGATACTTAC-T-ATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA-ATACATAATCGCAATGCGATAATAC
*
15166 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATAATACATAATCGCAATGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATACATAATCGCAATGCGAT
15223 TTTCAAAGCG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
60 3 0.06
61 33 0.67
62 13 0.27
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (62 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATACATAATCGCAATGCGATAATAC
Found at i:15418 original size:22 final size:22
Alignment explanation
Indices: 15390--15433 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
15380 CACTCTCTCA
15390 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
15412 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
15434 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:15733 original size:20 final size:20
Alignment explanation
Indices: 15697--15753 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
15687 ATTCTCTCGT
**
15697 TGCGATAGTCAAATTCACGC
1 TGCGATAGTCATTTTCACGC
* *
15717 TGCGATAGTCATTTTCATGT
1 TGCGATAGTCATTTTCACGC
**
15737 TGCGATTTTCATTTTCA
1 TGCGATAGTCATTTTCA
15754 GAAACTATTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (20 bp):
TGCGATAGTCATTTTCACGC
Found at i:15943 original size:25 final size:24
Alignment explanation
Indices: 15889--15943 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
15879 TGTTTATTAT
* *
15889 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
15913 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
15939 TGTTT
1 TGTTT
15944 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:17094 original size:18 final size:18
Alignment explanation
Indices: 17073--17117 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
17063 TCCACTTCGG
*
17073 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
17091 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
17109 GAGCCATCA
1 GAGCCATCA
17118 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:17652 original size:19 final size:20
Alignment explanation
Indices: 17598--17664 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
17588 TAGTTTACTT
* *
17598 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
17618 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
17638 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
17657 TCGCAACG
1 TCGCAACG
17665 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:17672 original size:14 final size:14
Alignment explanation
Indices: 17653--17707 Score: 65
Period size: 14 Copynumber: 3.6 Consensus size: 14
17643 ATGCGAAATG
17653 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
17667 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
17683 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
17699 AAAATCGCA
1 AAAATCGCA
17708 TCGCGAAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
14 18 0.51
16 8 0.23
18 9 0.26
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:17695 original size:32 final size:33
Alignment explanation
Indices: 17637--17727 Score: 159
Period size: 32 Copynumber: 2.8 Consensus size: 33
17627 GGAAATGGCT
17637 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
17670 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
17702 ATCGC-ATCGCGAAATGAAAATCGCAA
1 ATCGCAAT-GCGAAATGAAAATCGCAA
17728 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
31 2 0.04
32 29 0.52
33 25 0.45
ACGTcount: A:0.46, C:0.22, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:17763 original size:14 final size:14
Alignment explanation
Indices: 17744--17834 Score: 74
Period size: 14 Copynumber: 5.9 Consensus size: 14
17734 TTGTGTTTCG
17744 CGTTGCGATTTTAT
1 CGTTGCGATTTTAT
*
17758 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TAT
*
17774 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTAT
17790 CGTTGCGATTTTCATTT
1 CGTTGCGATTTT-A--T
*
17807 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTAT
17823 CGTTGCGATTTT
1 CGTTGCGATTTT
17835 CATTTCGCAT
Statistics
Matches: 64, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 31 0.48
16 11 0.17
17 3 0.05
18 9 0.14
19 10 0.16
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTAT
Found at i:17782 original size:32 final size:33
Alignment explanation
Indices: 17739--17850 Score: 199
Period size: 33 Copynumber: 3.4 Consensus size: 33
17729 GCGATTTGTG
* *
17739 TTTCGCGTTGCGATTTTATCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
17771 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
17804 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
17837 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
17851 AGCTATTTCC
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 25 0.32
33 52 0.68
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:17869 original size:20 final size:20
Alignment explanation
Indices: 17823--17890 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
17813 GCGATTTTGT
**
17823 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
17842 CATTGCGATAG-CTATTTCCG
1 CGTTGCGATAGTC-ATTTCCG
*
17862 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
17882 CGTTGCGAT
1 CGTTGCGAT
17891 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
18 1 0.02
19 12 0.29
20 27 0.66
21 1 0.02
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:18464 original size:16 final size:16
Alignment explanation
Indices: 18443--18479 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
18433 TGATGGATGA
18443 GAGTTGGCTCTCATAT
1 GAGTTGGCTCTCATAT
18459 GAGTTGGCTCTCATAT
1 GAGTTGGCTCTCATAT
18475 GAGTT
1 GAGTT
18480 ATCGGCTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.19, C:0.16, G:0.27, T:0.38
Consensus pattern (16 bp):
GAGTTGGCTCTCATAT
Found at i:19795 original size:14 final size:14
Alignment explanation
Indices: 19776--19811 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
19766 ATTGTTTAAT
19776 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
19790 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
19804 TGATTTGT
1 TGATTTGT
19812 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:19972 original size:19 final size:19
Alignment explanation
Indices: 19948--20015 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
19938 ATCGCAACGA
19948 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
19967 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
19986 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
20000 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
20016 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:20067 original size:34 final size:36
Alignment explanation
Indices: 20022--20111 Score: 103
Period size: 40 Copynumber: 2.4 Consensus size: 36
20012 GCGATTTTCA
* * *
20022 TTTCGCATTGCGATTTTC-T-AGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCTTCAATTGCGATAACCAT
20056 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAACCAT
1 TTTCGCGTTGCGA-TTTTC--TTC-AATTGCGATAACCAT
20096 TTTCGCGTTGCGATTT
1 TTTCGCGTTGCGATTT
20112 CCCCGTTACG
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
34 12 0.26
35 5 0.11
38 1 0.02
39 3 0.06
40 26 0.55
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.43
Consensus pattern (36 bp):
TTTCGCGTTGCGATTTTCTTCAATTGCGATAACCAT
Found at i:20079 original size:20 final size:21
Alignment explanation
Indices: 20052--20111 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 21
20042 GTTGCGATAG
*
20052 CCATTTTCGCGTTGCGATTTT
1 CCATTTTCGCGTTGCGATTTA
* ** *
20073 TCA-TTTCGAATTGCGA-TAA
1 CCATTTTCGCGTTGCGATTTA
20092 CCATTTTCGCGTTGCGATTT
1 CCATTTTCGCGTTGCGATTT
20112 CCCCGTTACG
Statistics
Matches: 28, Mismatches: 9, Indels: 4
0.68 0.22 0.10
Matches are distributed among these distances:
19 3 0.11
20 22 0.79
21 3 0.11
ACGTcount: A:0.17, C:0.22, G:0.18, T:0.43
Consensus pattern (21 bp):
CCATTTTCGCGTTGCGATTTA
Found at i:20443 original size:20 final size:21
Alignment explanation
Indices: 20399--20450 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
20389 ATAGTCAGTA
*
20399 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
20420 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
20440 TCGCATTGCGA
1 TCGCATTGCGA
20451 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:20666 original size:12 final size:12
Alignment explanation
Indices: 20647--20680 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
20637 CTCTCCGGTG
20647 ACATCCGTTCCT
1 ACATCCGTTCCT
*
20659 ATATCCGTTCCT
1 ACATCCGTTCCT
20671 ACATCC-TTCC
1 ACATCCGTTCC
20681 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:21262 original size:24 final size:24
Alignment explanation
Indices: 21235--21288 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
21225 GTATTCGAAA
*
21235 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
21259 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
21283 TTTGAT
1 TTTGAT
21289 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:21480 original size:12 final size:12
Alignment explanation
Indices: 21463--21499 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
21453 ATATAATCCT
21463 GAAGAAGAAAAA
1 GAAGAAGAAAAA
21475 GAAGAAGAAAAA
1 GAAGAAGAAAAA
21487 GAAGAAGAAAAA
1 GAAGAAGAAAAA
21499 G
1 G
21500 TCCCCGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:23832 original size:33 final size:33
Alignment explanation
Indices: 23790--23916 Score: 204
Period size: 33 Copynumber: 3.8 Consensus size: 33
23780 GGAAATTACT
23790 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
**
23823 ATCGCAATGCGAAATGAAAATCGCAAC--GCTA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
23854 ATTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 A--TCGCAATGCGAAATGAAAATCGCAACGAGGGA
23889 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
23917 CGAATTTAAT
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
Found at i:23897 original size:66 final size:66
Alignment explanation
Indices: 23791--23923 Score: 257
Period size: 66 Copynumber: 2.0 Consensus size: 66
23781 GAAATTACTA
*
23791 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
23856 T
66 T
23857 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
23922 T
66 T
23923 T
1 T
23924 AATTTCGCGT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:23948 original size:14 final size:14
Alignment explanation
Indices: 23931--23987 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
23921 TTTAATTTCG
23931 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
23945 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
23962 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
23978 CGTTGCGATT
1 CGTTGCGATT
23988 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:23970 original size:33 final size:33
Alignment explanation
Indices: 23916--24005 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
23906 AAATCGCAAC
* * *
23916 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCATTGCGATTCTCTCGTT
23949 GCGATTTTCATTTCGCATTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCATTGCGATTCTCTCGTT
23982 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCATTGCGAT
24006 AGTACTTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.43
Consensus pattern (33 bp):
GCGATTTTCATTTCGCATTGCGATTCTCTCGTT
Found at i:23971 original size:19 final size:19
Alignment explanation
Indices: 23947--24005 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
23937 GATTCTCTCG
23947 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
23966 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
23980 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
23999 TTGCGAT
1 TTGCGAT
24006 AGTACTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:24130 original size:14 final size:14
Alignment explanation
Indices: 24111--24147 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
24101 ACATCAATTA
24111 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
24125 ACAAATCACCTTTT
1 ACAAATCAACTTTT
24139 ACAAATCAA
1 ACAAATCAA
24148 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:27796 original size:33 final size:33
Alignment explanation
Indices: 27739--27837 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
27729 ACGAGATAAT
27739 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
27773 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
27806 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
27838 CGAAATGAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 47 0.77
34 14 0.23
ACGTcount: A:0.39, C:0.23, G:0.26, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:27831 original size:19 final size:19
Alignment explanation
Indices: 27714--27859 Score: 105
Period size: 19 Copynumber: 8.1 Consensus size: 19
27704 TCTTTTGGTT
* *
27714 GAAATGAAAATTGCAACGA
1 GAAATGAAAATCGCAACGC
*
27733 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
27753 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
27771 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
27787 GAAATGACTATCGCGA--C
1 GAAATGAAAATCGCAACGC
*
27804 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
27820 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
27839 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
27858 GA
1 GA
27860 TTTTGGTTTC
Statistics
Matches: 100, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
14 17 0.17
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 43 0.43
20 26 0.26
21 2 0.02
ACGTcount: A:0.42, C:0.20, G:0.25, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:27888 original size:19 final size:19
Alignment explanation
Indices: 27855--27899 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
27845 AAAATCGCAA
*
27855 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
27874 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
27893 TGCGATT
1 TGCGATT
27900 CTCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:28475 original size:20 final size:20
Alignment explanation
Indices: 28450--28502 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
28440 GCGCTATGTA
28450 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
28470 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
28490 TATCTCGTTGCGA
1 AATCGCGTTGCGA
28503 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:28536 original size:20 final size:20
Alignment explanation
Indices: 28511--28564 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
28501 GATTTTGTAT
28511 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
28531 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
28551 TATCGCATTGCGAT
1 TATCGCATTGCGAT
28565 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:28549 original size:61 final size:61
Alignment explanation
Indices: 28451--28567 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
28441 CGCTATGTAA
* * * * *
28451 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
28512 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
28568 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:28583 original size:61 final size:61
Alignment explanation
Indices: 28451--28585 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
28441 CGCTATGTAA
* * * * * ** *
28451 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
28512 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
28574 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
28586 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:31266 original size:49 final size:49
Alignment explanation
Indices: 31166--31263 Score: 121
Period size: 49 Copynumber: 2.0 Consensus size: 49
31156 TGAAATAATA
*
31166 TAATTAAATCTAAATATAAAACTTAATTTTTGAATTGAAACAATGAATT
1 TAATTAAATCTAAATATAAAACTTAATTTATGAATTGAAACAATGAATT
* * *
31215 TAATTGAATCTAAA-ACTAAAACTT-ATATTAT-AATTGAAATAATTAATT
1 TAATTAAATCTAAATA-TAAAACTTAAT-TTATGAATTGAAACAATGAATT
31263 T
1 T
31264 TAACACGTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
48 19 0.44
49 24 0.56
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.40
Consensus pattern (49 bp):
TAATTAAATCTAAATATAAAACTTAATTTATGAATTGAAACAATGAATT
Found at i:41533 original size:2 final size:2
Alignment explanation
Indices: 41526--41550 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41516 GGACCTCTTG
41526 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 T
41551 GGATGAATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41680 original size:24 final size:24
Alignment explanation
Indices: 41652--41698 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
41642 ATTTTTACAA
* *
41652 TTTAAAATTTTATAAGTTTGTTCC
1 TTTAAAATTATACAAGTTTGTTCC
41676 TTTAAAATTATACAAGTTTGTTC
1 TTTAAAATTATACAAGTTTGTTC
41699 TTCTAACGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.51
Consensus pattern (24 bp):
TTTAAAATTATACAAGTTTGTTCC
Found at i:42675 original size:23 final size:23
Alignment explanation
Indices: 42628--42675 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
42618 AATAACATAT
* **
42628 TAGGTAACGTTTATATAATGTAA
1 TAGGTAACGATTATATAATAAAA
*
42651 TAGGTAGCGATTATATAATAAAA
1 TAGGTAACGATTATATAATAAAA
42674 TA
1 TA
42676 TGCATTTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (23 bp):
TAGGTAACGATTATATAATAAAA
Found at i:42737 original size:87 final size:86
Alignment explanation
Indices: 42587--42753 Score: 253
Period size: 87 Copynumber: 1.9 Consensus size: 86
42577 CGGTTATGTT
* * *
42587 ATATCATTTAACCGGAAATATTATCAAGCACAATAACATATTAGGTAACGTTTATATAATGTAAT
1 ATATCATTTAACCAGAAATATTACCAAGCACAATAACATATTAGGTAACGCTTATATAATGTAAT
42652 AGGTAGCGATTATATAATAAA
66 AGGTAGCGATTATATAATAAA
* * *
42673 ATATGCATTTAATCAGAAATATTACCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAA
1 ATAT-CATTTAACCAGAAATATTACCAAGCACAATAACATATTAGGTAACGCTTATATAATGTAA
* *
42738 TAGGTAGTGCTTATAT
65 TAGGTAGCGATTATAT
42754 TGACCTATTT
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
86 4 0.06
87 68 0.94
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.34
Consensus pattern (86 bp):
ATATCATTTAACCAGAAATATTACCAAGCACAATAACATATTAGGTAACGCTTATATAATGTAAT
AGGTAGCGATTATATAATAAA
Found at i:43888 original size:183 final size:183
Alignment explanation
Indices: 43433--43984 Score: 822
Period size: 182 Copynumber: 3.0 Consensus size: 183
43423 TGTTTACTAA
*
43433 TTTTTTTAAAGTATCGACACTTTATATGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTC
1 TTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTC
* * * *
43498 GTTACTTATATTAAAATATCGACACTTTCAACATATCCGGTAGTTCTTTATCGGTTTTGTCATTT
66 GATACTTATATTAAATTATCGACACTTTCAACATATCCGGTAGTGCTTTACCGGTTTTGTCATTT
* * *
43563 TGAGACCGATTTTGTCATATTTTTAGCTGTTATATCGTTATGGATCGATACA-
131 TGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAT
** * * * *
43615 TTTTCATAAAGTATCGACACTTTTTAGGCGCTATAACTTATTCTCTTTTAAATTCAAAAAGTGTT
1 TTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTC
* *
43680 GATACTTATATTAAATTATCGACACTTTCAACATATCCGGTAGAGCTTTACCGGATTTGTCATTT
66 GATACTTATATTAAATTATCGACACTTTCAACATATCCGGTAGTGCTTTACCGGTTTTGTCATTT
* *
43745 TGGGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATATAT
131 TGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAT
43798 TTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTTCCTT-TCTTTTAAATTCCAAAAGTGT
1 TTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTT-CTTCTCTTTTAAATTCCAAAAGTGT
* ** * * *
43862 CGATACTTATATTAAATTATCGACACTTTCAACATATTCAATATTGTTTTACCGGTTTTATCATT
65 CGATACTTATATTAAATTATCGACACTTTCAACATATCCGGTAGTGCTTTACCGGTTTTGTCATT
* * *
43927 TCGAGACCGGTTTTGTCATATTTTTACCTGTAATATT-TCTATGGAGCGATACAT
130 TTGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGT-TATGGATCGATACAT
43981 TTTT
1 TTTT
43985 CATTTGTATC
Statistics
Matches: 330, Mismatches: 37, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
182 165 0.50
183 163 0.49
184 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (183 bp):
TTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTC
GATACTTATATTAAATTATCGACACTTTCAACATATCCGGTAGTGCTTTACCGGTTTTGTCATTT
TGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACAT
Found at i:58757 original size:16 final size:15
Alignment explanation
Indices: 58724--58783 Score: 54
Period size: 17 Copynumber: 4.0 Consensus size: 15
58714 TAAGCAAAAT
*
58724 GAAATAAGAAACAGAAA
1 GAAATAA-AAA-ATAAA
58741 GAAATAGAAAAATAAA
1 GAAATA-AAAAATAAA
*
58757 G-AA-AATAAAT-AA
1 GAAATAAAAAATAAA
58769 GAAATAAAAAATAAA
1 GAAATAAAAAATAAA
58784 AATAAGACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
12 3 0.08
13 7 0.19
14 7 0.19
15 4 0.11
16 5 0.14
17 9 0.25
18 1 0.03
ACGTcount: A:0.75, C:0.02, G:0.12, T:0.12
Consensus pattern (15 bp):
GAAATAAAAAATAAA
Found at i:58773 original size:20 final size:20
Alignment explanation
Indices: 58750--58801 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
58740 AGAAATAGAA
*
58750 AAATAAAGAAA-ATAAATAAG
1 AAATAAA-AAATAAAAATAAG
58770 AAATAAAAAATAAAAATAAG
1 AAATAAAAAATAAAAATAAG
58790 ACAATAGAAAAA
1 A-AATA-AAAAA
58802 ATTTAATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 3 0.11
20 16 0.57
21 4 0.14
22 5 0.18
ACGTcount: A:0.77, C:0.02, G:0.08, T:0.13
Consensus pattern (20 bp):
AAATAAAAAATAAAAATAAG
Found at i:58795 original size:14 final size:13
Alignment explanation
Indices: 58742--58788 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
58732 AAACAGAAAG
58742 AAATAGAAAAATAA
1 AAATA-AAAAATAA
*
58756 AGAA-AATAAATAA
1 A-AATAAAAAATAA
58769 GAAATAAAAAATAA
1 -AAATAAAAAATAA
58783 AAATAA
1 AAATAA
58789 GACAATAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 15 0.54
14 11 0.39
15 2 0.07
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (13 bp):
AAATAAAAAATAA
Found at i:58798 original size:27 final size:28
Alignment explanation
Indices: 58739--58799 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
58729 AAGAAACAGA
*
58739 AAGAAATAGAAAAATAAAGAAAATAAAT
1 AAGAAATAGAAAAATAAAGAAAAGAAAT
58767 AAGAAATA-AAAAATAAA-AATAAGACAAT
1 AAGAAATAGAAAAATAAAGAA-AAGA-AAT
58795 -AGAAA
1 AAGAAA
58800 AAATTTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 2 0.07
27 17 0.57
28 11 0.37
ACGTcount: A:0.75, C:0.02, G:0.10, T:0.13
Consensus pattern (28 bp):
AAGAAATAGAAAAATAAAGAAAAGAAAT
Found at i:59097 original size:33 final size:36
Alignment explanation
Indices: 59032--59125 Score: 92
Period size: 37 Copynumber: 2.7 Consensus size: 36
59022 AATATCAACT
*
59032 AAAATAATTAATATATATAT--TATAGTAGTATAC-C
1 AAAATAA-TAATATATATATAAAATAGTAGTATACAC
59066 -AAATAA-AATATATATATAAAATACGTA-TATACAAC
1 AAAATAATAATATATATATAAAATA-GTAGTATAC-AC
* *
59101 AAAATAATAATATAAATATACAATA
1 AAAATAATAATATATATATAAAATA
59126 TAATATAGGG
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
31 11 0.22
33 14 0.28
34 3 0.06
35 1 0.02
36 6 0.12
37 15 0.30
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (36 bp):
AAAATAATAATATATATATAAAATAGTAGTATACAC
Done.