Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007008.1 Hibiscus syriacus cultivar Beakdansim tig00018085_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: 61384
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:1373 original size:18 final size:18
Alignment explanation
Indices: 1350--1394 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1340 TAGTTTGATT
1350 AATGAACTAAAATTATTC
1 AATGAACTAAAATTATTC
**
1368 AATGAACTAACTTTATTC
1 AATGAACTAAAATTATTC
1386 AATGAACTA
1 AATGAACTA
1395 GATATGAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (18 bp):
AATGAACTAAAATTATTC
Found at i:7865 original size:23 final size:23
Alignment explanation
Indices: 7835--7882 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
7825 CATCCAACGG
7835 TCCAAATTGATTATAGAAAACTA
1 TCCAAATTGATTATAGAAAACTA
7858 TCCAAATTGATTATAGAAAACTA
1 TCCAAATTGATTATAGAAAACTA
7881 TC
1 TC
7883 TTAAATCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (23 bp):
TCCAAATTGATTATAGAAAACTA
Found at i:8693 original size:22 final size:22
Alignment explanation
Indices: 8668--8709 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
8658 TTTAACCAAA
8668 GTTGACTTT-AACTTTGACCAGC
1 GTTGACTTTGAA-TTTGACCAGC
*
8690 GTTGATTTTGAATTTGACCA
1 GTTGACTTTGAATTTGACCA
8710 AAAAGTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (22 bp):
GTTGACTTTGAATTTGACCAGC
Found at i:13381 original size:28 final size:27
Alignment explanation
Indices: 13342--13427 Score: 102
Period size: 28 Copynumber: 3.1 Consensus size: 27
13332 AAACATAACT
*
13342 AAACTTTTATCATAATAAATATCAAGTA
1 AAACTTTCATCATAA-AAATATCAAGTA
*
13370 AAACTTTCATCAATGAAAATATCAAGTA
1 AAACTTTCATC-ATAAAAATATCAAGTA
* *
13398 AAACTTTCATCAATGAAAATAT-AACTA
1 AAACTTTCATC-ATAAAAATATCAAGTA
13425 AAA
1 AAA
13428 TTTAATAGCT
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
27 7 0.13
28 44 0.81
29 3 0.06
ACGTcount: A:0.52, C:0.13, G:0.05, T:0.30
Consensus pattern (27 bp):
AAACTTTCATCATAAAAATATCAAGTA
Found at i:13388 original size:16 final size:16
Alignment explanation
Indices: 13369--13416 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
13359 AATATCAAGT
13369 AAAACTTTCATCAATG
1 AAAACTTTCATCAATG
13385 AAAA---T-ATCAA-G
1 AAAACTTTCATCAATG
13396 TAAAACTTTCATCAATG
1 -AAAACTTTCATCAATG
13413 AAAA
1 AAAA
13417 TATAACTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 12
0.68 0.00 0.32
Matches are distributed among these distances:
11 1 0.04
12 9 0.35
13 1 0.04
15 1 0.04
16 13 0.50
17 1 0.04
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.27
Consensus pattern (16 bp):
AAAACTTTCATCAATG
Found at i:15525 original size:27 final size:26
Alignment explanation
Indices: 15467--15517 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
15457 ATTTTGTTTC
*
15467 GAAATAACTATATAAATATCAAAATA
1 GAAATAACTATATAAAAATCAAAATA
*
15493 TGAAATAATTATATAAAAATCAAAA
1 -GAAATAACTATATAAAAATCAAAA
15518 CTCAAAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (26 bp):
GAAATAACTATATAAAAATCAAAATA
Found at i:16768 original size:75 final size:75
Alignment explanation
Indices: 16603--16768 Score: 235
Period size: 75 Copynumber: 2.2 Consensus size: 75
16593 AAATAAACGT
* *
16603 TACCTATTACGTTAAACTAGCTATCGGTTTGTTTAAAGATTAATAATAATGTAAACGGTAAAATA
1 TACCTATTACGTTAAAATAGCTATCGGTTTGTTTAAAGATTAATAAAAATGTAAACGGTAAAATA
16668 AAATAGGCGA
66 AAATAGGCGA
* * *
16678 TACCTATTACATTAAAATATCTA-CAGGTTTGTTTAAAGATTACTAAAAATGTAAACGGTAAAAT
1 TACCTATTACGTTAAAATAGCTATC-GGTTTGTTTAAAGATTAATAAAAATGTAAACGGTAAAAT
***
16742 AAAATAGGTTC
65 AAAATAGGCGA
*
16753 TACCTATTATGTTAAA
1 TACCTATTACGTTAAA
16769 TAGGCACTGC
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
74 1 0.01
75 79 0.99
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (75 bp):
TACCTATTACGTTAAAATAGCTATCGGTTTGTTTAAAGATTAATAAAAATGTAAACGGTAAAATA
AAATAGGCGA
Found at i:16772 original size:23 final size:22
Alignment explanation
Indices: 16743--16814 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 22
16733 CGGTAAAATA
*
16743 AAATAGGTTCTACCTATTATGTT
1 AAATAGG-TCTACCTATTACGTT
* *
16766 AAATAGGCACTGCCTATTACGTT
1 AAATAGG-TCTACCTATTACGTT
16789 AAATAAGCGT-TACCTATTACGTT
1 AAAT-AG-GTCTACCTATTACGTT
16812 AAA
1 AAA
16815 CTAGCTATCG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
23 38 0.93
24 2 0.05
25 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (22 bp):
AAATAGGTCTACCTATTACGTT
Found at i:16802 original size:196 final size:196
Alignment explanation
Indices: 16465--16863 Score: 586
Period size: 196 Copynumber: 2.0 Consensus size: 196
16455 CTTAACCGGT
* * ** * * * * *
16465 TAAAATAAAATAGTCGCTACCTATTATGTTAAATTACCTACCGGTTTGTTTGAAGGTTACTAATA
1 TAAAATAAAATAGGCGATACCTATTACATTAAAATACCTACAGGTTTGTTTAAAGATTACTAAAA
* * **
16530 ATGCAACTAGTAAAATAAAATAGGTCTTACATATTATGTTAAATATGTGCTACCTATTACGTTAA
66 ATGAAACTAGTAAAATAAAATAGGTCTTACATATTATGTTAAATAGGCACTACCTATTACGTTAA
16595 ATAAACGTTACCTATTACGTTAAACTAGCTATCGGTTTGTTTAAAGATTAATAATAATGTAAACG
131 ATAAACGTTACCTATTACGTTAAACTAGCTATCGGTTTGTTTAAAGATTAATAATAATGTAAACG
*
16660 G
196 A
*
16661 TAAAATAAAATAGGCGATACCTATTACATTAAAATATCTACAGGTTTGTTTAAAGATTACTAAAA
1 TAAAATAAAATAGGCGATACCTATTACATTAAAATACCTACAGGTTTGTTTAAAGATTACTAAAA
* * *
16726 ATGTAAAC-GGTAAAATAAAATAGGT-TCTACCTATTATGTTAAATAGGCACTGCCTATTACGTT
66 ATG-AAACTAGTAAAATAAAATAGGTCT-TACATATTATGTTAAATAGGCACTACCTATTACGTT
* *
16789 AAATAAGCGTTACCTATTACGTTAAACTAGCTATCGGTTTGTTTAAAGGTTAATAATAATGTAAA
129 AAATAAACGTTACCTATTACGTTAAACTAGCTATCGGTTTGTTTAAAGATTAATAATAATGTAAA
16854 CGA
194 CGA
16857 TAAAATA
1 TAAAATA
16864 TATACAACTT
Statistics
Matches: 181, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
195 1 0.01
196 177 0.98
197 3 0.02
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (196 bp):
TAAAATAAAATAGGCGATACCTATTACATTAAAATACCTACAGGTTTGTTTAAAGATTACTAAAA
ATGAAACTAGTAAAATAAAATAGGTCTTACATATTATGTTAAATAGGCACTACCTATTACGTTAA
ATAAACGTTACCTATTACGTTAAACTAGCTATCGGTTTGTTTAAAGATTAATAATAATGTAAACG
A
Found at i:19044 original size:22 final size:22
Alignment explanation
Indices: 19014--19067 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
19004 CAAAAAACTC
19014 TTTTT-AAAAACTA-TATTATAT
1 TTTTTCAAAAACTATTA-TATAT
19035 TTTTTCAAAAA-TATTATATAT
1 TTTTTCAAAAACTATTATATAT
*
19056 GTTTTCAAAAAC
1 TTTTTCAAAAAC
19068 CGTTTTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 22 0.76
22 7 0.24
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTCAAAAACTATTATATAT
Found at i:19086 original size:57 final size:57
Alignment explanation
Indices: 18954--19101 Score: 153
Period size: 57 Copynumber: 2.5 Consensus size: 57
18944 ATTATATTTA
* *
18954 TTTTAAAACTATATAACATACATTATATTTCAAAAACTATATTATGTTTTCAAAAAACTCT
1 TTTTAAAACTATAT-A-TTATATT-T-TTTCAAAAACTATATTATGTTTTCAAAAAACTCT
19015 TTTTAAAA--ACTATATTATATTTTTTCAAAAA-TATTATATATGTTTTC-AAAAAC-CGT
1 TTTTAAAACTA-TATATTATATTTTTTCAAAAACTA-TAT-TATGTTTTCAAAAAACTC-T
**
19071 TTTTAAAACTATATATTATACGTTTTCAAAA
1 TTTTAAAACTATATATTATATTTTTTCAAAA
19102 TAATGTTTTC
Statistics
Matches: 77, Mismatches: 4, Indels: 16
0.79 0.04 0.16
Matches are distributed among these distances:
55 3 0.04
56 27 0.35
57 28 0.36
58 6 0.08
59 2 0.03
60 3 0.04
61 8 0.10
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.44
Consensus pattern (57 bp):
TTTTAAAACTATATATTATATTTTTTCAAAAACTATATTATGTTTTCAAAAAACTCT
Found at i:19087 original size:38 final size:38
Alignment explanation
Indices: 19045--19176 Score: 150
Period size: 36 Copynumber: 3.6 Consensus size: 38
19035 TTTTTCAAAA
*
19045 ATATTATATATGTTTTCAAAAACCGTTTTTAAAACTAT
1 ATATTATATATGTTTTCAAAAACCGTTTTAAAAACTAT
* **
19083 ATA-T-TATACGTTTTCAAAATAATGTTTTCAAAAAC--T
1 ATATTATATATGTTTTCAAAA-ACCGTTTT-AAAAACTAT
* *
19119 ATATTATATATGTTTTAAAAAACCATTTTAAAAACTAT
1 ATATTATATATGTTTTCAAAAACCGTTTTAAAAACTAT
19157 ATATTATATA--TTTTCAAAAA
1 ATATTATATATGTTTTCAAAAA
19177 TATATTTTCA
Statistics
Matches: 78, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
36 33 0.42
37 13 0.17
38 32 0.41
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (38 bp):
ATATTATATATGTTTTCAAAAACCGTTTTAAAAACTAT
Found at i:19123 original size:74 final size:74
Alignment explanation
Indices: 19045--19203 Score: 248
Period size: 74 Copynumber: 2.1 Consensus size: 74
19035 TTTTTCAAAA
* * * * *
19045 ATATTATATATGTTTTCAAAAACCGTTTTTAAAACTATATATTATACGTTTTC-AAAATAATGTT
1 ATATTATATATGTTTTAAAAAACCATTTTAAAAACTATATATTATACATTTTCAAAAAT-ATATT
19109 TTCAAAAACT
65 TTCAAAAACT
*
19119 ATATTATATATGTTTTAAAAAACCATTTTAAAAACTATATATTATATATTTTCAAAAATATATTT
1 ATATTATATATGTTTTAAAAAACCATTTTAAAAACTATATATTATACATTTTCAAAAATATATTT
19184 TCAAAAACT
66 TCAAAAACT
19193 ATATTATATAT
1 ATATTATATAT
19204 CTTCAAAAGC
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
74 73 0.94
75 5 0.06
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (74 bp):
ATATTATATATGTTTTAAAAAACCATTTTAAAAACTATATATTATACATTTTCAAAAATATATTT
TCAAAAACT
Found at i:19190 original size:38 final size:38
Alignment explanation
Indices: 19031--19211 Score: 145
Period size: 36 Copynumber: 5.0 Consensus size: 38
19021 AAACTATATT
* *
19031 ATATTTTTTCAAAAA-TAT-TA-TATATGTTTTCAAAA
1 ATATATTTTCAAAAACTATATATTATATATTTTCAAAA
** **
19066 ACCGT-TTTT--AAAACTATATATTATACGTTTTC-AAA
1 A-TATATTTTCAAAAACTATATATTATATATTTTCAAAA
* *
19101 ATAATGTTTTCAAAAAC--TATATTATATATGTTTTAAAA
1 AT-ATATTTTCAAAAACTATATATTATATAT-TTTCAAAA
*
19139 A-ACCATTTT-AAAAACTATATATTATATATTTTCAAAA
1 ATA-TATTTTCAAAAACTATATATTATATATTTTCAAAA
*
19176 ATATATTTTCAAAAAC--TATATTATATATCTTCAAAA
1 ATATATTTTCAAAAACTATATATTATATATTTTCAAAA
19212 GCTATATATT
Statistics
Matches: 118, Mismatches: 13, Indels: 29
0.74 0.08 0.18
Matches are distributed among these distances:
33 4 0.03
34 3 0.03
35 12 0.10
36 51 0.43
37 20 0.17
38 28 0.24
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (38 bp):
ATATATTTTCAAAAACTATATATTATATATTTTCAAAA
Found at i:19195 original size:15 final size:14
Alignment explanation
Indices: 19162--19197 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
19152 ACTATATATT
19162 ATATATTTTCAAAA
1 ATATATTTTCAAAA
19176 ATATATTTTCAAAA
1 ATATATTTTCAAAA
19190 ACTATATT
1 A-TATATT
19198 ATATATCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATATTTTCAAAA
Found at i:19203 original size:22 final size:23
Alignment explanation
Indices: 19176--19230 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
19166 ATTTTCAAAA
19176 ATATATTTTCAAAAAC-TATATT
1 ATATATTTTCAAAAACATATATT
* *
19198 ATATATCTTCAAAAGCTATATATT
1 ATATATTTTCAAAAAC-ATATATT
19222 ATATATTTT
1 ATATATTTT
19231 TGAAATTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 14 0.50
24 14 0.50
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (23 bp):
ATATATTTTCAAAAACATATATT
Found at i:19593 original size:108 final size:109
Alignment explanation
Indices: 19312--19837 Score: 379
Period size: 108 Copynumber: 4.8 Consensus size: 109
19302 GAGTGTCTAC
* * * * * * * * *
19312 ACCTAGTATGTTAATATTTATTTATAACAAAATAAGAAATTAACATATTTTGTTGTCATGGGATA
1 ACCTAATATGTTGATA-ATATTGATAACAAATTAAGTAATTAACATATTTTGTTATCATCGGATT
* * *
19377 TCGAAGGTTCC-AT-AAGCTTAAACTTT-AGTAACATTTTAGGCACT
65 TCTAAGG-ACCTATCAA-CTTAAACTTTGACTAACATTTTAGGCACT
* * * *
19421 ACATAATATGTTGATAATATTAATAACAAAATAAGTAATTAACATATTTTGTTATCATCAGATTT
1 ACCTAATATGTTGATAATATTGATAACAAATTAAGTAATTAACATATTTTGTTATCATCGGATTT
*
19486 CTAAGGACCTATCAACTTAAACTTTGA-TAATATTTTAGGCGA-T
66 CTAAGGACCTATCAACTTAAACTTTGACTAACATTTTAGGC-ACT
* * *
19529 ACCTAATAAGTTGATAATATTGATAACAAATTAAGTAATTAACCTATTTTGTTATCTTCGGATTT
1 ACCTAATATGTTGATAATATTGATAACAAATTAAGTAATTAACATATTTTGTTATCATCGGATTT
* * * * * * * **
19594 TTAAGGCCCTATCAGCTTTAAAAATGTGTTACCTATTACATTAAATAAGCGTT
66 CTAAGGACCTATCAAC-TT-AAACT-T-TGA-CTA--ACATT--TTAGGCACT
** ** * * *** * * * * *
19647 ATTTGTTATGTT-ATTATGGTTGATAA-TGTTTCGAGTAATTAACCTATTTTTTTATCGTCAGAT
1 ACCTAATATGTTGATAAT-ATTGATAACAAATT-AAGTAATTAACATATTTTGTTATCATCGGAT
* * * *
19710 TTCTAAGG-CTCCATCAGCTTAAACTTTG-GTAACATTTTAGACACT
64 TTCTAAGGAC-CTATCAACTTAAACTTTGACTAACATTTTAGGCACT
* * *
19755 ACCTAATATGTGGATAATATTGATAACAAATCAAGTAATTAACATATTTTGTTATCGTCGGATTT
1 ACCTAATATGTTGATAATATTGATAACAAATTAAGTAATTAACATATTTTGTTATCATCGGATTT
19820 CTAA-GACCCTATCAACTT
66 CTAAGGA-CCTATCAACTT
19838 TAAAAATGCA
Statistics
Matches: 325, Mismatches: 70, Indels: 45
0.74 0.16 0.10
Matches are distributed among these distances:
107 3 0.01
108 202 0.62
109 25 0.08
110 9 0.03
111 1 0.00
112 4 0.01
114 3 0.01
115 1 0.00
116 8 0.02
117 9 0.03
118 60 0.18
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (109 bp):
ACCTAATATGTTGATAATATTGATAACAAATTAAGTAATTAACATATTTTGTTATCATCGGATTT
CTAAGGACCTATCAACTTAAACTTTGACTAACATTTTAGGCACT
Found at i:19749 original size:226 final size:223
Alignment explanation
Indices: 19454--19913 Score: 645
Period size: 226 Copynumber: 2.0 Consensus size: 223
19444 TAACAAAATA
* * *
19454 AGTAATTAACATATTTTGTTATCATCAGATTTCTAAGGACCTATCAACTTAAACTTTGATAATAT
1 AGTAATTAACCTATTTTGTTATCATCAGATTTCTAAGGACCCATCAACTTAAACTTTGATAACAT
* * * *
19519 TTTAGGCGA-TACCTAATAAGTTGATAATATTGATAACAAATTAAGTAATTAACCTATTTTGTTA
66 TTTAGAC-ACTACCTAATAAGTGGATAATATTGATAACAAATCAAGTAATTAACATATTTTGTTA
* * * * *** *
19583 TCTTCGGATTTTTAAGGCCCTATCAGCTTTAAAAATGTGTTACCTATTACATTAAATAAGCGTTA
130 TCGTCGGATTTCTAAGACCCTATCAACTTTAAAAATGCACTACCTATTACATTAAATAAGCGCTA
* *
19648 TTTGTTATGTTATTATGGTTGATAATGTTTCG
195 TTTGTTA---TATTATAGTTAATAATGTTTCG
* * * *
19680 AGTAATTAACCTATTTTTTTATCGTCAGATTTCTAAGG-CTCCATCAGCTTAAACTTTGGTAACA
1 AGTAATTAACCTATTTTGTTATCATCAGATTTCTAAGGAC-CCATCAACTTAAACTTTGATAACA
*
19744 TTTTAGACACTACCTAATATGTGGATAATATTGATAACAAATCAAGTAATTAACATATTTTGTTA
65 TTTTAGACACTACCTAATAAGTGGATAATATTGATAACAAATCAAGTAATTAACATATTTTGTTA
* *
19809 TCGTCGGATTTCTAAGACCCTATCAACTTTAAAAATGCACTACCTATTACGTTACATAAGCGCTA
130 TCGTCGGATTTCTAAGACCCTATCAACTTTAAAAATGCACTACCTATTACATTAAATAAGCGCTA
19874 TTTGTTATATTATAGTTAATAATGTTTCG
195 TTTGTTATATTATAGTTAATAATGTTTCG
19903 AGTAATTAACC
1 AGTAATTAACC
19914 GGTTATGTTA
Statistics
Matches: 208, Mismatches: 24, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
223 31 0.15
225 2 0.01
226 175 0.84
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (223 bp):
AGTAATTAACCTATTTTGTTATCATCAGATTTCTAAGGACCCATCAACTTAAACTTTGATAACAT
TTTAGACACTACCTAATAAGTGGATAATATTGATAACAAATCAAGTAATTAACATATTTTGTTAT
CGTCGGATTTCTAAGACCCTATCAACTTTAAAAATGCACTACCTATTACATTAAATAAGCGCTAT
TTGTTATATTATAGTTAATAATGTTTCG
Found at i:20060 original size:16 final size:16
Alignment explanation
Indices: 20039--20083 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
20029 TTATAGCACT
*
20039 TTTAACAAGTCACCTA
1 TTTAACTAGTCACCTA
20055 TTTAACTAGTCACCTA
1 TTTAACTAGTCACCTA
20071 TTTAACTAGTCAC
1 TTTAACTAGTCAC
20084 GCCTTTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (16 bp):
TTTAACTAGTCACCTA
Found at i:20533 original size:58 final size:59
Alignment explanation
Indices: 20470--20581 Score: 142
Period size: 58 Copynumber: 1.9 Consensus size: 59
20460 ATTATGACTA
*
20470 TTATTCTAAATTAGT-CTTCAAA-TTTTTAAAT-TTTC-ATTTTCATCCTCAAACTAGACCT
1 TTATTCTAAATTAGTCCAT-AAACTTTTTAAATATTTCAATTTT-ATCC-CAAACTAGACCT
* *
20528 TTATTCTAAATTGGTCCATAAACTTTTTGAATATTTCAATTTTATCCCAAACTA
1 TTATTCTAAATTAGTCCATAAACTTTTTAAATATTTCAATTTTATCCCAAACTA
20582 TATGTATATA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
58 17 0.36
59 17 0.36
60 8 0.17
61 5 0.11
ACGTcount: A:0.32, C:0.18, G:0.04, T:0.46
Consensus pattern (59 bp):
TTATTCTAAATTAGTCCATAAACTTTTTAAATATTTCAATTTTATCCCAAACTAGACCT
Found at i:20842 original size:60 final size:59
Alignment explanation
Indices: 20735--20864 Score: 145
Period size: 60 Copynumber: 2.2 Consensus size: 59
20725 TTTGGTGAGC
* * * * *
20735 AATTTAGAATG-AGTCATAGTTTGGGGATGAAATTGTAATGTTCAAAAGTATAAGAACT
1 AATTTAGAATGAAGTAATAGTTTGAGAATGAAATTGGAATATTCAAAAGTATAAGAACT
* * * * *
20793 AATTTAGAATGAAAGTAATATTTTGAGAATGAAATTGGAATATTTAAAAGTTTAAGGATT
1 AATTTAGAATG-AAGTAATAGTTTGAGAATGAAATTGGAATATTCAAAAGTATAAGAACT
*
20853 AATTTAAAATGA
1 AATTTAGAATGA
20865 GGGTCGTAGT
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
58 11 0.19
59 1 0.02
60 47 0.80
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.35
Consensus pattern (59 bp):
AATTTAGAATGAAGTAATAGTTTGAGAATGAAATTGGAATATTCAAAAGTATAAGAACT
Found at i:21401 original size:23 final size:24
Alignment explanation
Indices: 21353--21420 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 24
21343 ATCGAAAATG
21353 TGTCATAAAAATAGAGAAAAAAACA
1 TGTCATAAAAATA-AGAAAAAAACA
* *
21378 TGTCATAAAGAT-AGATAAAAACA
1 TGTCATAAAAATAAGAAAAAAACA
21401 TG--ATAAAAATTAA-AAAAAAA
1 TGTCATAAAAA-TAAGAAAAAAA
21421 TAAAAAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
21 6 0.16
22 7 0.19
23 13 0.35
25 11 0.30
ACGTcount: A:0.65, C:0.06, G:0.10, T:0.19
Consensus pattern (24 bp):
TGTCATAAAAATAAGAAAAAAACA
Found at i:21450 original size:11 final size:11
Alignment explanation
Indices: 21407--21452 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
21397 AACATGATAA
* *
21407 AAATTAAAAAA
1 AAATGAAAAAT
*
21418 AAATAAAAAAT
1 AAATGAAAAAT
21429 AAATGAAAAAT
1 AAATGAAAAAT
21440 AAATGAAAAAT
1 AAATGAAAAAT
21451 AA
1 AA
21453 GAAAGATCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.17
Consensus pattern (11 bp):
AAATGAAAAAT
Found at i:21450 original size:18 final size:18
Alignment explanation
Indices: 21403--21442 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
21393 TAAAAACATG
* *
21403 ATAAAAATTAAA-AAAAA
1 ATAAAAAATAAATGAAAA
21420 ATAAAAAATAAATGAAAA
1 ATAAAAAATAAATGAAAA
21438 ATAAA
1 ATAAA
21443 TGAAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (18 bp):
ATAAAAAATAAATGAAAA
Found at i:26553 original size:23 final size:23
Alignment explanation
Indices: 26523--26575 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
26513 ATGTAAACTC
26523 ATAAAATGATTTATGAATACAAA
1 ATAAAATGATTTATGAATACAAA
26546 ATAAAATGATTTATGAATACAAA
1 ATAAAATGATTTATGAATACAAA
26569 ATAAAAT
1 ATAAAAT
26576 TTATCAGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.30
Consensus pattern (23 bp):
ATAAAATGATTTATGAATACAAA
Found at i:27243 original size:24 final size:24
Alignment explanation
Indices: 27216--27324 Score: 78
Period size: 24 Copynumber: 4.5 Consensus size: 24
27206 AAACGGAGAT
* * *
27216 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACATAATCCAA
*
27240 ATCAGATAT-AAGAACATAATCCAA
1 ATCAGAAATCAA-AACATAATCCAA
* * *
27264 ATTAGAAATCAGAACATAATCCAG
1 ATCAGAAATCAAAACATAATCCAA
* * * *
27288 GTCA-AGTATCAGAACATAATTCAA
1 ATCAGA-AATCAAAACATAATCCAA
*
27312 ATCGGAAATCAAA
1 ATCAGAAATCAAA
27325 TAAAACATTC
Statistics
Matches: 64, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
23 3 0.05
24 59 0.92
25 2 0.03
ACGTcount: A:0.51, C:0.17, G:0.12, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAAAACATAATCCAA
Found at i:27302 original size:48 final size:48
Alignment explanation
Indices: 27216--27324 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 48
27206 AAACGGAGAT
*
27216 ATCAGAAATCAAAACAGAATTCAGATCAGATATAAGAACATAATCCAA
1 ATCAGAAATCAAAACAGAATCCAGATCAGATATAAGAACATAATCCAA
* * * * * *
27264 ATTAGAAATCAGAACATAATCCAGGTCA-AGTATCAGAACATAATTCAA
1 ATCAGAAATCAAAACAGAATCCAGATCAGA-TATAAGAACATAATCCAA
*
27312 ATCGGAAATCAAA
1 ATCAGAAATCAAA
27325 TAAAACATTC
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
47 1 0.02
48 49 0.98
ACGTcount: A:0.51, C:0.17, G:0.12, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATCCAGATCAGATATAAGAACATAATCCAA
Found at i:32963 original size:20 final size:20
Alignment explanation
Indices: 32935--32982 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
32925 TAAATTGTGT
*
32935 TCCATTACTTTTAAAGGTAA
1 TCCAATACTTTTAAAGGTAA
*
32955 TCCAATACTTTTAAAGGTAG
1 TCCAATACTTTTAAAGGTAA
32975 TCCAATAC
1 TCCAATAC
32983 CTATGCTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (20 bp):
TCCAATACTTTTAAAGGTAA
Found at i:38355 original size:20 final size:20
Alignment explanation
Indices: 38308--38356 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
38298 ATGCACTAAA
*
38308 TTTTTCTCCCTTCTCCTTAG
1 TTTTTCTTCCTTCTCCTTAG
38328 TTTTTCTTCCTTCTCCTTAG
1 TTTTTCTTCCTTCTCCTTAG
38348 TTTTTCTTC
1 TTTTTCTTC
38357 ATAACAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.04, C:0.31, G:0.04, T:0.61
Consensus pattern (20 bp):
TTTTTCTTCCTTCTCCTTAG
Found at i:41172 original size:22 final size:22
Alignment explanation
Indices: 41127--41173 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
41117 CCTCTTATGC
* *
41127 TTTTATGACACGTTTTTCTCTG
1 TTTTATAACACGTTTTGCTCTG
41149 TTTTATAACACGTTTTCGCT-TG
1 TTTTATAACACGTTTT-GCTCTG
41171 TTT
1 TTT
41174 GGCTATTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.15, C:0.17, G:0.13, T:0.55
Consensus pattern (22 bp):
TTTTATAACACGTTTTGCTCTG
Found at i:42447 original size:6 final size:6
Alignment explanation
Indices: 42436--42509 Score: 116
Period size: 6 Copynumber: 12.5 Consensus size: 6
42426 CCTAATCTCT
*
42436 CCCTCA CCCTCA CCCTCA CCTCTC- CCC-CA CCCCCA CCCTCA CCCTCA
1 CCCTCA CCCTCA CCCTCA CC-CTCA CCCTCA CCCTCA CCCTCA CCCTCA
42483 CCCTCA CCCTCA CCCTCA CCCTCA CCC
1 CCCTCA CCCTCA CCCTCA CCCTCA CCC
42510 ATTACTCTTG
Statistics
Matches: 64, Mismatches: 1, Indels: 6
0.90 0.01 0.08
Matches are distributed among these distances:
4 1 0.02
5 4 0.06
6 56 0.88
7 3 0.05
ACGTcount: A:0.15, C:0.70, G:0.00, T:0.15
Consensus pattern (6 bp):
CCCTCA
Found at i:44449 original size:33 final size:35
Alignment explanation
Indices: 44385--44450 Score: 93
Period size: 33 Copynumber: 1.9 Consensus size: 35
44375 AAAATATTTA
*
44385 TATATTTTCTTTAAAAAAATTAAATTCATAAAATT
1 TATATTTTCTTTAAAAAAATTAAAATCATAAAATT
44420 TATA-TTT-TTTAAAAAAATTGAAAAT-ATAAAA
1 TATATTTTCTTTAAAAAAATT-AAAATCATAAAA
44451 AGGTTTAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 18 0.62
34 7 0.24
35 4 0.14
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (35 bp):
TATATTTTCTTTAAAAAAATTAAAATCATAAAATT
Found at i:45579 original size:2 final size:2
Alignment explanation
Indices: 45574--45613 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
45564 CATGAACTTT
45574 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
45614 AGATTATTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47680 original size:15 final size:15
Alignment explanation
Indices: 47660--47710 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
47650 TTCCGGAAAA
*
47660 TGAATTACTGCAATT
1 TGAATTACTGGAATT
**
47675 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
*
47690 TGAATTACTGGATTT
1 TGAATTACTGGAATT
47705 TGAATT
1 TGAATT
47711 CTAGAAAATG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:47718 original size:29 final size:30
Alignment explanation
Indices: 47655--47726 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
47645 TGGTTTTCCG
*
47655 GAAAATGAATTACTGCAATTTGAATTACTG
1 GAAAATGAATTACTGCAATTTGAATTACTA
* *
47685 GAAAATGAATTACTGGATTTTGAATT-CTA
1 GAAAATGAATTACTGCAATTTGAATTACTA
47714 GAAAATGAATTAC
1 GAAAATGAATTAC
47727 ATTTCTGGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 15 0.38
30 24 0.62
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (30 bp):
GAAAATGAATTACTGCAATTTGAATTACTA
Found at i:47931 original size:50 final size:50
Alignment explanation
Indices: 47833--47932 Score: 116
Period size: 50 Copynumber: 2.0 Consensus size: 50
47823 TACAAATATT
*
47833 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATTATTTTA
1 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
* * *
47883 AAATATTAA-AAATAAT-TTATTTATTATTAAATA-TTATTTTTATAATTTTA
1 AAATA-TAATAAATAATATTATTTATCA-TAAA-ACTTAATATTATAATTTTA
47933 TTAATAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
49 9 0.21
50 30 0.70
51 4 0.09
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (50 bp):
AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
Found at i:48034 original size:90 final size:87
Alignment explanation
Indices: 47881--48051 Score: 202
Period size: 90 Copynumber: 1.9 Consensus size: 87
47871 ATTATTATTT
* * * * *
47881 TAAAATATTAAAAATAATTTATTTATTATTAAATATTATTTTTATAATTTTATTAATAAAAATAT
1 TAAAATATTAAAAATAATTTAATTATTATTAAATAATAGTGTTATAATTATATTAATAAAAATAT
*
47946 TAATATTGGTATATTTTAGTGAAA
66 TAA-A-TAGTATATTTTAGTGAAA
* * *
47970 TAAAATATTATAAATTATATTAATTATTTATTAAAGTAATAGTGTTAT-ATTATATT-TTAAAAA
1 TAAAATATTAAAAATAAT-TTAATTA-TTATTAAA-TAATAGTGTTATAATTATATTAATAAAAA
48033 TATTAAATAGTATATTTTA
63 TATTAAATAGTATATTTTA
48052 AATATATTTA
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
88 11 0.16
89 17 0.24
90 18 0.26
91 15 0.21
92 9 0.13
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (87 bp):
TAAAATATTAAAAATAATTTAATTATTATTAAATAATAGTGTTATAATTATATTAATAAAAATAT
TAAATAGTATATTTTAGTGAAA
Found at i:48070 original size:23 final size:23
Alignment explanation
Indices: 48021--48089 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
48011 GTGTTATATT
* **
48021 ATATTTTAAAAATATTAAATAGT
1 ATATTTTAAATATATTAAATAAA
* *
48044 ATATTTTAAATATATTTACTAAA
1 ATATTTTAAATATATTAAATAAA
48067 ATATTATTTAAATATA-TAAATAA
1 ATA-T-TTTAAATATATTAAATAA
48090 TATTATTTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
23 21 0.57
24 6 0.16
25 10 0.27
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (23 bp):
ATATTTTAAATATATTAAATAAA
Found at i:48101 original size:29 final size:30
Alignment explanation
Indices: 48067--48142 Score: 97
Period size: 28 Copynumber: 2.7 Consensus size: 30
48057 ATTTACTAAA
* *
48067 ATATTATTTAAATATATAAATAA-TATTAT
1 ATATTATTTAAATATAAAAAAAATTATTAT
*
48096 TTATTA-TTAAATATAAAAAAAATTATTAT
1 ATATTATTTAAATATAAAAAAAATTATTAT
48125 ATATTA-TTAAA-ATAAAAA
1 ATATTATTTAAATATAAAAA
48143 TATAATATCT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 21 0.50
29 21 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
ATATTATTTAAATATAAAAAAAATTATTAT
Found at i:48150 original size:24 final size:23
Alignment explanation
Indices: 48109--48155 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
48099 TTATTAAATA
* *
48109 TAAAAAAAATTATTATATATTAT
1 TAAAAAAAAATATAATATATTAT
*
48132 TAAAATAAAAATATAATATCTTAT
1 TAAAA-AAAAATATAATATATTAT
48156 ATTATATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAAAAAAAATATAATATATTAT
Found at i:48156 original size:29 final size:28
Alignment explanation
Indices: 48067--48160 Score: 102
Period size: 29 Copynumber: 3.2 Consensus size: 28
48057 ATTTACTAAA
* *
48067 ATATTATTTAAATATATAAATAATATTAT
1 ATATTATTAAAATA-AAAAATAATATTAT
*
48096 TTATTATTAAATATAAAAAA-AATTATTAT
1 ATATTATTAAA-ATAAAAAATAA-TATTAT
48125 ATATTATTAAAATAAAAATATAATATCT-T
1 ATATTATTAAAATAAAAA-ATAATAT-TAT
48154 ATATTAT
1 ATATTAT
48161 ATTATATTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
28 9 0.16
29 41 0.73
30 6 0.11
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (28 bp):
ATATTATTAAAATAAAAAATAATATTAT
Found at i:48176 original size:31 final size:31
Alignment explanation
Indices: 48124--48240 Score: 109
Period size: 31 Copynumber: 3.8 Consensus size: 31
48114 AAAATTATTA
* *
48124 TATATTAT-TAA-AATAAAAATATAATAT-CT
1 TATATTATATAATATTAAAAATATAAT-TGAT
* **
48153 TATATTATATTATATTATTAATATAATTGAT
1 TATATTATATAATATTAAAAATATAATTGAT
*
48184 TATTTTATATAATATTAAAAATATAA-TG-T
1 TATATTATATAATATTAAAAATATAATTGAT
48213 TATATTATTATAAATATTAATAAATATA
1 TATATTA-TAT-AATATTAA-AAATATA
48241 TTTTAAATAT
Statistics
Matches: 72, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
29 15 0.21
30 8 0.11
31 42 0.58
32 7 0.10
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.48
Consensus pattern (31 bp):
TATATTATATAATATTAAAAATATAATTGAT
Found at i:48231 original size:12 final size:12
Alignment explanation
Indices: 48214--48266 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
48204 ATATAATGTT
48214 ATATTATTATAA
1 ATATTATTATAA
48226 ATATTA--ATAA
1 ATATTATTATAA
*
48236 ATA-TATTTTAA
1 ATATTATTATAA
48247 ATATT-TTAATAA
1 ATATTATT-ATAA
*
48259 ATAATATT
1 ATATTATT
48267 TTGATGAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
9 2 0.06
10 7 0.21
11 8 0.24
12 14 0.42
13 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
ATATTATTATAA
Found at i:48247 original size:21 final size:23
Alignment explanation
Indices: 48218--48268 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
48208 AATGTTATAT
*
48218 TATTATAAATA-TTAATAAAT-A
1 TATTTTAAATATTTAATAAATAA
48239 TATTTTAAATATTTTAATAAATAA
1 TATTTTAAATA-TTTAATAAATAA
48263 TATTTT
1 TATTTT
48269 GATGAAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 10 0.38
23 9 0.35
24 7 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTTTAAATATTTAATAAATAA
Found at i:48472 original size:42 final size:42
Alignment explanation
Indices: 48426--48506 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
48416 CTGTTACTAA
* * *
48426 GAAAATGAATTACGTGAAACAAACAC-AGGAAAACATTTTCCG
1 GAAAACGAATTACGTAAAAAAAACACGA-GAAAACATTTTCCG
48468 GAAAACGAATTACGTAAAAAAAACACGAGAAAACATTTT
1 GAAAACGAATTACGTAAAAAAAACACGAGAAAACATTTT
48507 TTCAAAAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 34 0.97
43 1 0.03
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.19
Consensus pattern (42 bp):
GAAAACGAATTACGTAAAAAAAACACGAGAAAACATTTTCCG
Found at i:48515 original size:42 final size:42
Alignment explanation
Indices: 48427--48521 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
48417 TGTTACTAAG
* * * *
48427 AAAATGAATTACGTGAAACAAACACAGGAAAACATTTTCCGG
1 AAAACGAATTACGTAAAAAAAACACAGGAAAACATTTTCCGA
*
48469 AAAACGAATTACGTAAAAAAAACAC-GAGAAAACATTTTTTC-A
1 AAAACGAATTACGTAAAAAAAACACAG-GAAAACA-TTTTCCGA
48511 AAAACGAATTA
1 AAAACGAATTA
48522 TATGAAATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
41 1 0.02
42 40 0.87
43 5 0.11
ACGTcount: A:0.53, C:0.15, G:0.13, T:0.20
Consensus pattern (42 bp):
AAAACGAATTACGTAAAAAAAACACAGGAAAACATTTTCCGA
Found at i:49688 original size:23 final size:24
Alignment explanation
Indices: 49648--49694 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
49638 TGATTACTTA
*
49648 AATATCATTTTTTAAATTATATTT
1 AATATCATGTTTTAAATTATATTT
* *
49672 AATATTATGTTTT-AATTCTATTT
1 AATATCATGTTTTAAATTATATTT
49695 TGGTCGTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (24 bp):
AATATCATGTTTTAAATTATATTT
Found at i:50170 original size:22 final size:22
Alignment explanation
Indices: 50145--50190 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
50135 AAATTGAATT
*
50145 TAATTACAAATAAT-TAATAAAA
1 TAATTAAAAAT-ATGTAATAAAA
*
50167 TAATTAAAAATGTGTAATAAAA
1 TAATTAAAAATATGTAATAAAA
50189 TA
1 TA
50191 TTATTTTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (22 bp):
TAATTAAAAATATGTAATAAAA
Found at i:50590 original size:31 final size:31
Alignment explanation
Indices: 50555--50618 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
50545 AGGGTACATG
*
50555 GTCCCTAATGTTATCGATCCG-TCTGATTTTA
1 GTCCCAAATGTTATCGATCCGTTCT-ATTTTA
50586 GTCCCAAATGTTATCGATCCGTTCTATTTTA
1 GTCCCAAATGTTATCGATCCGTTCTATTTTA
50617 GT
1 GT
50619 TCCTCAGTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 28 0.90
32 3 0.10
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (31 bp):
GTCCCAAATGTTATCGATCCGTTCTATTTTA
Found at i:50888 original size:15 final size:16
Alignment explanation
Indices: 50870--50899 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
50860 TATGTTGTTA
50870 TTATATTA-TTATATG
1 TTATATTATTTATATG
50885 TTATATTATTTATAT
1 TTATATTATTTATAT
50900 ATGAATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
TTATATTATTTATATG
Found at i:50896 original size:47 final size:49
Alignment explanation
Indices: 50845--50953 Score: 134
Period size: 47 Copynumber: 2.2 Consensus size: 49
50835 TTTCATTTGG
*
50845 ATTTATTAT-TAAATATATGTTGTTATTATATTATTATATGT-TATATT
1 ATTTATTATATAAATATATGTTGTTATTATATTATTATATATCTATATT
* * *
50892 ATTTA-TATATGAATATTTGTTTTTATTATATTATTATATATCGTATATT
1 ATTTATTATATAAATATATGTTGTTATTATATTATTATATATC-TATATT
50941 ATATTATTTATAT
1 AT-TTA-TTATAT
50954 GAAAAATTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
46 3 0.06
47 33 0.63
49 8 0.15
50 3 0.06
52 5 0.10
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.60
Consensus pattern (49 bp):
ATTTATTATATAAATATATGTTGTTATTATATTATTATATATCTATATT
Found at i:50900 original size:18 final size:20
Alignment explanation
Indices: 50857--50902 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
50847 TTATTATTAA
*
50857 ATATATGTTGTTATTATATT
1 ATATATGTTGATATTATATT
50877 ATTATATGTT-ATATTAT-TT
1 A-TATATGTTGATATTATATT
50896 ATATATG
1 ATATATG
50903 AATATTTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.25
19 3 0.12
20 7 0.29
21 8 0.33
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.59
Consensus pattern (20 bp):
ATATATGTTGATATTATATT
Found at i:51097 original size:16 final size:17
Alignment explanation
Indices: 51076--51108 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
51066 GTTTATTTAA
51076 AATTAAA-TATAATTTT
1 AATTAAATTATAATTTT
51092 AATTAAATTATAATTTT
1 AATTAAATTATAATTTT
51109 TTGGGTAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTAAATTATAATTTT
Found at i:55780 original size:18 final size:19
Alignment explanation
Indices: 55757--55834 Score: 65
Period size: 18 Copynumber: 4.3 Consensus size: 19
55747 GTTCTTAAGG
55757 AGTGGTTC-TTCGGGACAT
1 AGTGGTTCATTCGGGACAT
* * *
55775 AGTGG-TCCTTCAGAACAT
1 AGTGGTTCATTCGGGACAT
*
55793 AGTGG-TCATTCGGGACAC
1 AGTGGTTCATTCGGGACAT
* * *
55811 AGTGG-TCTTTTGGTACAT
1 AGTGGTTCATTCGGGACAT
55829 AGTGGT
1 AGTGGT
55835 CCTACGGGGC
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
17 2 0.04
18 46 0.96
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.32
Consensus pattern (19 bp):
AGTGGTTCATTCGGGACAT
Found at i:55805 original size:36 final size:35
Alignment explanation
Indices: 55757--55835 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 35
55747 GTTCTTAAGG
*
55757 AGTGGTTCTTCGGGACATAGTGGTCCTTCAGAACAT
1 AGTGG-TCTTCGGGACACAGTGGTCCTTCAGAACAT
* ** *
55793 AGTGGTCATTCGGGACACAGTGGTCTTTTGGTACAT
1 AGTGGTC-TTCGGGACACAGTGGTCCTTCAGAACAT
55829 AGTGGTC
1 AGTGGTC
55836 CTACGGGGCA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 2 0.05
36 35 0.95
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (35 bp):
AGTGGTCTTCGGGACACAGTGGTCCTTCAGAACAT
Found at i:55835 original size:18 final size:18
Alignment explanation
Indices: 55765--55835 Score: 79
Period size: 18 Copynumber: 3.9 Consensus size: 18
55755 GGAGTGGTTC
*
55765 TTCGGGACATAGTGGTCC
1 TTCGGGACATAGTGGTCA
* *
55783 TTCAGAACATAGTGGTCA
1 TTCGGGACATAGTGGTCA
* *
55801 TTCGGGACACAGTGGTCT
1 TTCGGGACATAGTGGTCA
* *
55819 TTTGGTACATAGTGGTC
1 TTCGGGACATAGTGGTC
55836 CTACGGGGCA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (18 bp):
TTCGGGACATAGTGGTCA
Found at i:58115 original size:23 final size:23
Alignment explanation
Indices: 58089--58133 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
58079 CACCACAGCT
*
58089 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
58112 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
58134 ATATAATGAT
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:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:58372 original size:149 final size:149
Alignment explanation
Indices: 58101--58414 Score: 569
Period size: 149 Copynumber: 2.1 Consensus size: 149
58091 TATAATTGCA
* *
58101 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTACTGCCATATAATGATGTCCATAAAGACCACATAGAA
58165 TTCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTT
58230 CCAAAGAATATACATATGTC
130 CCAAAGAATATACATATGTC
*
58250 TCGAAGGACCGCGTAGAATTGCACCGTACTGCCATATAATGATGTCCATAAAGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTACTGCCATATAATGATGTCCATAAAGACCACATAGAAT
*
58315 TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCTAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
58380 CAAAGAATATACATATGTC
131 CAAAGAATATACATATGTC
58399 CCGAAGGA-CGCGTAGA
1 CCGAAGGACCGCGTAGA
58415 CCCTCGACTC
Statistics
Matches: 159, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
148 9 0.06
149 150 0.94
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTACTGCCATATAATGATGTCCATAAAGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
CAAAGAATATACATATGTC
Found at i:59265 original size:18 final size:18
Alignment explanation
Indices: 59244--59278 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
59234 TCCCATCTAG
59244 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
59262 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
59279 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:59883 original size:21 final size:21
Alignment explanation
Indices: 59859--59903 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
59849 TGTTGTTCGT
* *
59859 TTGAAAGGGTATCGGTTCCCC
1 TTGAAAGGGTACCGATTCCCC
*
59880 TTGAATGGGTACCGATTCCCC
1 TTGAAAGGGTACCGATTCCCC
59901 TTG
1 TTG
59904 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAAGGGTACCGATTCCCC
Found at i:60996 original size:72 final size:76
Alignment explanation
Indices: 60892--61084 Score: 279
Period size: 76 Copynumber: 2.6 Consensus size: 76
60882 GTTGTACAAG
* * *
60892 GGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGG-AAT-TC-GAG-C
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCC
**
60952 AAAACTGTTTA
66 AAAACCATTTA
* *
60963 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGCC
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCC
61028 AAAACCATTTA
66 AAAACCATTTA
*
61039 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCA
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCA
61085 ATCTGTAATT
Statistics
Matches: 109, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
71 17 0.16
72 30 0.28
73 3 0.03
74 2 0.02
75 2 0.02
76 55 0.50
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.23
Consensus pattern (76 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCC
AAAACCATTTA
Done.