Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003799.1 Hibiscus syriacus cultivar Beakdansim tig00008126_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: 68517
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1470 original size:13 final size:13
Alignment explanation
Indices: 1452--1477 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1442 TACAAACGCA
1452 CATATGAAGACTG
1 CATATGAAGACTG
1465 CATATGAAGACTG
1 CATATGAAGACTG
1478 TTAATCTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
CATATGAAGACTG
Found at i:3605 original size:17 final size:17
Alignment explanation
Indices: 3583--3617 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3573 AAATTCAAGT
3583 TTGAGTTCGAGCTTGAA
1 TTGAGTTCGAGCTTGAA
3600 TTGAGTTCGAGCTTGAA
1 TTGAGTTCGAGCTTGAA
3617 T
1 T
3618 CGAGCTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.11, G:0.29, T:0.37
Consensus pattern (17 bp):
TTGAGTTCGAGCTTGAA
Found at i:3622 original size:11 final size:11
Alignment explanation
Indices: 3606--3673 Score: 66
Period size: 11 Copynumber: 5.9 Consensus size: 11
3596 TGAATTGAGT
3606 TCGAGCTTGAA
1 TCGAGCTTGAA
**
3617 TCGAGCTCAAAA
1 TCGAGCT-TGAA
3629 TCGAGCTTGAA
1 TCGAGCTTGAA
*
3640 TCGAGC-TCAA
1 TCGAGCTTGAA
3650 CTCTGGAGCTTGAA
1 -TC--GAGCTTGAA
3664 TCGAGCTTGA
1 TCGAGCTTGA
3674 CTCTGGAGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
10 3 0.07
11 25 0.54
12 9 0.20
13 6 0.13
14 3 0.07
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:3636 original size:23 final size:22
Alignment explanation
Indices: 3606--3670 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 22
3596 TGAATTGAGT
3606 TCGAGCTTGAATCGAGCTCAAAA
1 TCGAGCTTGAATCGAGCTC-AAA
*
3629 TCGAGCTTGAATCGAGCTCAAC
1 TCGAGCTTGAATCGAGCTCAAA
3651 TCTGGAGCTTGAATCGAGCT
1 TC--GAGCTTGAATCGAGCT
3671 TGACTCTGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
22 4 0.10
23 19 0.49
24 16 0.41
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (22 bp):
TCGAGCTTGAATCGAGCTCAAA
Found at i:3663 original size:24 final size:24
Alignment explanation
Indices: 3608--3719 Score: 129
Period size: 24 Copynumber: 4.7 Consensus size: 24
3598 AATTGAGTTC
*
3608 GAGCTTGAATCGAGCTCAAAATC--
1 GAGCTTGAATCGAGCTC-AACTCTG
3631 GAGCTTGAATCGAGCTCAACTCTG
1 GAGCTTGAATCGAGCTCAACTCTG
**
3655 GAGCTTGAATCGAGCTTGACTCTG
1 GAGCTTGAATCGAGCTCAACTCTG
* * **
3679 GAGTTTCAATCGAAATCAACTCTG
1 GAGCTTGAATCGAGCTCAACTCTG
*
3703 GAGCTTCAATCGAGCTC
1 GAGCTTGAATCGAGCTC
3720 CTGAAATTTT
Statistics
Matches: 75, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
22 4 0.05
23 17 0.23
24 54 0.72
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (24 bp):
GAGCTTGAATCGAGCTCAACTCTG
Found at i:5426 original size:20 final size:20
Alignment explanation
Indices: 5397--5434 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5387 TTTCAAAGTG
5397 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
5417 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
5435 TAATTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:5503 original size:45 final size:46
Alignment explanation
Indices: 5454--5542 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 46
5444 AAACATCGAA
* * *
5454 TGCATTTTATGCATCGATGCAC-ATACCATGCATTGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
*
5499 TGCATTTGATGTATCGATGCACAAGACCATGCATCGATGCACTC
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTC
5543 TGGCTTTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 20 0.51
46 19 0.49
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
Found at i:13067 original size:21 final size:21
Alignment explanation
Indices: 13025--13068 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
13015 ACCCTGGGAG
*
13025 CTAGCTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
13046 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
13067 CT
1 CT
13069 CCTCCTCCGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.16, T:0.34
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:14224 original size:20 final size:20
Alignment explanation
Indices: 14195--14232 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
14185 TTTCAAAGTG
14195 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
14215 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
14233 TAATTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:14301 original size:45 final size:46
Alignment explanation
Indices: 14252--14340 Score: 117
Period size: 46 Copynumber: 2.0 Consensus size: 46
14242 AAACATCGAA
* * * *
14252 TGCATTTTATGCATTGATGC-ACATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCAAAAGACCATGCATCGATGCACTCAG
* *
14297 TGCATTTGATGCATCGATGCAAAAGACCATGCATTGTTGCACTC
1 TGCATTTGATGCATCGATGCAAAAGACCATGCATCGATGCACTC
14341 TGGCTTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 18 0.49
46 19 0.51
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCAAAAGACCATGCATCGATGCACTCAG
Found at i:16129 original size:14 final size:14
Alignment explanation
Indices: 16110--16169 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
16100 TTCTAAAAAA
*
16110 AATAAAGAAAATTG
1 AATAAATAAAATTG
*
16124 AATAAATAAATTATG
1 AATAAATAAAAT-TG
**
16139 AA-AAA-AATAATAA
1 AATAAATAA-AATTG
16152 AATAAATAAAATTG
1 AATAAATAAAATTG
16166 AATA
1 AATA
16170 TGAAATTCTA
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
13 4 0.11
14 25 0.71
15 6 0.17
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (14 bp):
AATAAATAAAATTG
Found at i:18724 original size:25 final size:25
Alignment explanation
Indices: 18696--18743 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
18686 AAAATACACA
*
18696 AAAATAAA-AAGATAATGAATAATTC
1 AAAATAAATAAAATAAT-AATAATTC
18721 AAAATAAATAAAATAATAATAAT
1 AAAATAAATAAAATAATAATAAT
18744 AGGAATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (25 bp):
AAAATAAATAAAATAATAATAATTC
Found at i:20139 original size:38 final size:38
Alignment explanation
Indices: 20097--20192 Score: 122
Period size: 38 Copynumber: 2.5 Consensus size: 38
20087 TTAGTTAGGG
* *
20097 TTTAGGGTTAGAGAAGATAAAGAAT-ATTCTTAATTAGA
1 TTTAGGGTTAGAGAAGA-AAAGAATAATACTCAATTAGA
** * *
20135 TTTAGGGTTAGAGAAGAAGTGTATAATACTCAGTTAGA
1 TTTAGGGTTAGAGAAGAAAAGAATAATACTCAATTAGA
20173 TTTAGGGTTAGAGAAGAAAA
1 TTTAGGGTTAGAGAAGAAAA
20193 AGTTAGAAGA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
37 4 0.08
38 45 0.92
ACGTcount: A:0.41, C:0.03, G:0.25, T:0.31
Consensus pattern (38 bp):
TTTAGGGTTAGAGAAGAAAAGAATAATACTCAATTAGA
Found at i:20480 original size:95 final size:94
Alignment explanation
Indices: 20364--20552 Score: 243
Period size: 95 Copynumber: 2.0 Consensus size: 94
20354 TGTAAGAATC
* * * * ** * *
20364 AAACAAGGGTTTAGGGATGAACATAGATGAATATGGGTTGATGATTTGGGTGTTTGATCCAAAAA
1 AAACAAAGGTTAAGGGATGAACACAAATGAATAAAGGTTGAGGATTTGGGAGTTTG-TCCAAAAA
*
20429 AACAAGTTGGGTTTTGGGTTTGGGTATTTG
65 AACAAGTTGGATTTTGGGTTTGGGTATTTG
* * *
20459 AAACAAAGGTTAAGGGATGAACACAAATGAATAAAGGTTGAGGGTTTGGGAGTTTGTTCATAAAA
1 AAACAAAGGTTAAGGGATGAACACAAATGAATAAAGGTTGAGGATTTGGGAGTTTGTCCAAAAAA
* *
20524 ACAAGTTGGATTTTGGGTTTTGGTGTTTG
66 ACAAGTTGGATTTTGGGTTTGGGTATTTG
20553 TAAAGATTAA
Statistics
Matches: 80, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
94 33 0.41
95 47 0.59
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.33
Consensus pattern (94 bp):
AAACAAAGGTTAAGGGATGAACACAAATGAATAAAGGTTGAGGATTTGGGAGTTTGTCCAAAAAA
ACAAGTTGGATTTTGGGTTTGGGTATTTG
Found at i:21031 original size:31 final size:28
Alignment explanation
Indices: 20978--21089 Score: 92
Period size: 31 Copynumber: 4.1 Consensus size: 28
20968 AACTATAACT
20978 TATTAATAAACTATATAGTTTATATATA
1 TATTAATAAACTATATAGTTTATATATA
21006 TATTAATAAAC--TATAGTTTAGT-T-TA
1 TATTAATAAACTATATAGTTTA-TATATA
*** * *
21031 TA-T-ATAGTTTATATAATTTACATATAA
1 TATTAATAAACTATATAGTTTATATAT-A
*
21058 TTGATTAATAAACTATATAGTTTTTATATA
1 -T-ATTAATAAACTATATAGTTTATATATA
21088 TA
1 TA
21090 GTTTTTATAT
Statistics
Matches: 63, Mismatches: 11, Indels: 20
0.67 0.12 0.21
Matches are distributed among these distances:
23 3 0.05
24 1 0.02
25 13 0.21
26 11 0.17
27 2 0.03
28 13 0.21
29 2 0.03
30 2 0.03
31 16 0.25
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (28 bp):
TATTAATAAACTATATAGTTTATATATA
Found at i:21089 original size:13 final size:13
Alignment explanation
Indices: 21071--21100 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
21061 ATTAATAAAC
21071 TATATAGTTTTTA
1 TATATAGTTTTTA
21084 TATATAGTTTTTA
1 TATATAGTTTTTA
21097 TATA
1 TATA
21101 CAAACTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (13 bp):
TATATAGTTTTTA
Found at i:21118 original size:30 final size:30
Alignment explanation
Indices: 21082--21148 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
21072 ATATAGTTTT
*
21082 TATATATAGTTTTTATATACAAACTATATA
1 TATATATAGTTTGTATATACAAACTATATA
* *
21112 TATATATAGTTTGTATATATAAATTATATA
1 TATATATAGTTTGTATATACAAACTATATA
21142 -ATATATA
1 TATATATA
21149 AGTAGTATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 7 0.21
30 27 0.79
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (30 bp):
TATATATAGTTTGTATATACAAACTATATA
Found at i:21207 original size:11 final size:11
Alignment explanation
Indices: 21112--21354 Score: 82
Period size: 11 Copynumber: 22.6 Consensus size: 11
21102 AAACTATATA
21112 TATATATAGTTT
1 TATATATAG-TT
**
21124 GTATATATAAAT
1 -TATATATAGTT
*
21136 TATATA-A-TA
1 TATATATAGTT
*
21145 TATA-AGTAGTA
1 TATATA-TAGTT
*
21156 TATAAATAGTT
1 TATATATAGTT
* *
21167 TATACATAGTA
1 TATATATAGTT
* *
21178 TATAAATA-TA
1 TATATATAGTT
*
21188 AACTATATAGTT
1 TA-TATATAGTT
*
21200 TATATATA-AT
1 TATATATAGTT
21210 T-TATATAGTT
1 TATATATAGTT
*
21220 TTTATATAGTT
1 TATATATAGTT
*
21231 CATATATAGTT
1 TATATATAGTT
*
21242 TACATATA---
1 TATATATAGTT
*
21250 AACTATATAGTT
1 TA-TATATAGTT
21262 TATTAATATAGTT
1 TA-T-ATATAGTT
* *
21275 TATAT-TAATA
1 TATATATAGTT
* *
21285 AACTATATTGTT
1 TA-TATATAGTT
* *
21297 TATACAT--TG
1 TATATATAGTT
*
21306 TATATATAATT
1 TATATATAGTT
* *
21317 TATACATA--A
1 TATATATAGTT
*
21326 TATATATTGTT
1 TATATATAGTT
*
21337 CATATATAGTT
1 TATATATAGTT
21348 TATATAT
1 TATATAT
21355 TGTATATAAA
Statistics
Matches: 170, Mismatches: 41, Indels: 40
0.68 0.16 0.16
Matches are distributed among these distances:
8 2 0.01
9 28 0.16
10 13 0.08
11 99 0.58
12 10 0.06
13 18 0.11
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.48
Consensus pattern (11 bp):
TATATATAGTT
Found at i:21208 original size:20 final size:20
Alignment explanation
Indices: 21183--21264 Score: 92
Period size: 20 Copynumber: 4.0 Consensus size: 20
21173 TAGTATATAA
21183 ATATAAACTATATAGTTTAT
1 ATATAAACTATATAGTTTAT
** *
21203 ATATAATTTATATAGTTTTT
1 ATATAAACTATATAGTTTAT
** *
21223 ATATAGTTCATATATAGTTTAC
1 ATATA-AAC-TATATAGTTTAT
21245 ATATAAACTATATAGTTTAT
1 ATATAAACTATATAGTTTAT
21265 TAATATAGTT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
20 33 0.66
21 2 0.04
22 15 0.30
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.49
Consensus pattern (20 bp):
ATATAAACTATATAGTTTAT
Found at i:21278 original size:22 final size:20
Alignment explanation
Indices: 21191--21279 Score: 88
Period size: 20 Copynumber: 4.2 Consensus size: 20
21181 AAATATAAAC
21191 TATATAGTTTATATATAATT
1 TATATAGTTTATATATAATT
* *
21211 TATATAGTTTTTATATAGTT
1 TATATAGTTTATATATAATT
* **
21231 CATATATAGTTTACATATAAAC
1 --TATATAGTTTATATATAATT
*
21253 TATATAGTTTATTAATATAGTT
1 TATATAGTTTA-T-ATATAATT
21275 TATAT
1 TATAT
21280 TAATAAACTA
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
20 29 0.54
22 25 0.46
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.52
Consensus pattern (20 bp):
TATATAGTTTATATATAATT
Found at i:21298 original size:35 final size:33
Alignment explanation
Indices: 21183--21299 Score: 100
Period size: 31 Copynumber: 3.6 Consensus size: 33
21173 TAGTATATAA
* *
21183 ATATAAACTATATAGTTTA-T-ATATAATTTAT
1 ATATAAACTATATAGTTTATTAATATAGTTTAC
*** *
21214 ATAGT-TTTTATATAGTTCA-T-ATATAGTTTAC
1 ATA-TAAACTATATAGTTTATTAATATAGTTTAC
*
21245 ATATAAACTATATAGTTTATTAATATAGTTTAT
1 ATATAAACTATATAGTTTATTAATATAGTTTAC
*
21278 ATTAATAAACTATATTGTTTAT
1 A-T-ATAAACTATATAGTTTAT
21300 ACATTGTATA
Statistics
Matches: 68, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
30 1 0.01
31 36 0.53
32 2 0.03
33 11 0.16
34 1 0.01
35 17 0.25
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (33 bp):
ATATAAACTATATAGTTTATTAATATAGTTTAC
Found at i:21329 original size:20 final size:20
Alignment explanation
Indices: 21295--21332 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21285 AACTATATTG
**
21295 TTTATACATTGTATATATAA
1 TTTATACATAATATATATAA
21315 TTTATACATAATATATAT
1 TTTATACATAATATATAT
21333 TGTTCATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (20 bp):
TTTATACATAATATATATAA
Found at i:21419 original size:16 final size:16
Alignment explanation
Indices: 21400--21449 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
21390 TATAGTTTCC
21400 ATATAGTTTATAATAT
1 ATATAGTTTATAATAT
21416 ATATAGTTTAT-ATATT
1 ATATAGTTTATAATA-T
* *
21432 ATGTAGTTTATATTAT
1 ATATAGTTTATAATAT
21448 AT
1 AT
21450 TATATTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 3 0.10
16 25 0.83
17 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (16 bp):
ATATAGTTTATAATAT
Found at i:21439 original size:32 final size:34
Alignment explanation
Indices: 21403--21654 Score: 210
Period size: 35 Copynumber: 7.6 Consensus size: 34
21393 AGTTTCCATA
21403 TAGTTTATAATATA-TATAGTT-TA-TATATTATG
1 TAGTTTATAATATATTATA-TTATATTATATTATG
*
21435 TAGTTTATATTATATTATATTATATTATATTA--
1 TAGTTTATAATATATTATATTATATTATATTATG
* *
21467 TA--TTATATTATATTATATTATATTATATTATAT
1 TAGTTTATAATATATTATATTATATTATATTAT-G
* *
21500 TA-TATTATATTATATTATATTATATTATATTATAT
1 TAGT-TTATAATATATTATATTATATTATATTAT-G
* *
21535 TA-TATTATATTATATTATATTATATTATATTATAT
1 TAGT-TTATAATATATTATATTATATTATATTAT-G
* *
21570 TA-TATTATATTATATTATATTATATTATATTATAT
1 TAGT-TTATAATATATTATATTATATTATATTAT-G
* *
21605 TA-TATTAT-ATTTATTAT-TTATATTATATTATT
1 TAGT-TTATAATATATTATATTATATTATATTATG
21637 TA-TATTAT-ATATATTATA
1 TAGT-TTATAATATATTATA
21655 ATTTTTTCTC
Statistics
Matches: 207, Mismatches: 4, Indels: 17
0.91 0.02 0.07
Matches are distributed among these distances:
30 28 0.14
32 34 0.16
33 22 0.11
34 14 0.07
35 109 0.53
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (34 bp):
TAGTTTATAATATATTATATTATATTATATTATG
Found at i:21449 original size:5 final size:5
Alignment explanation
Indices: 21439--21654 Score: 404
Period size: 5 Copynumber: 44.0 Consensus size: 5
21429 ATTATGTAGT
21439 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
21489 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
21539 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
21589 TTATA TTATA TTATA TTATA TTATA TT-TA TTAT- TTATA TTATA TTAT-
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
21636 TTATA TTATA -TATA TTATA
1 TTATA TTATA TTATA TTATA
21655 ATTTTTTCTC
Statistics
Matches: 207, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
4 16 0.08
5 191 0.92
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:22805 original size:41 final size:41
Alignment explanation
Indices: 22705--22798 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
22695 TTTATTTAGA
22705 TACCTCATAAAGAATACGTCATTGCATGGATAGTTTATAGG
1 TACCTCATAAAGAATACGTCATTGCATGGATAGTTTATAGG
* *
22746 TATCACATAAAGAATACGTCATTGCATGGATAGTTTATAGG
1 TACCTCATAAAGAATACGTCATTGCATGGATAGTTTATAGG
22787 TACCTCATAAAG
1 TACCTCATAAAG
22799 GGTACGTATG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (41 bp):
TACCTCATAAAGAATACGTCATTGCATGGATAGTTTATAGG
Found at i:29428 original size:22 final size:22
Alignment explanation
Indices: 29400--29481 Score: 137
Period size: 22 Copynumber: 3.7 Consensus size: 22
29390 GCATGTGAAA
* *
29400 TATGTCCCGAATGACCTACGAG
1 TATGTCCCGAAGGACCTATGAG
*
29422 TATGTCCCGAAGGACCTGTGAG
1 TATGTCCCGAAGGACCTATGAG
29444 TATGTCCCGAAGGACCTATGAG
1 TATGTCCCGAAGGACCTATGAG
29466 TATGTCCCGAAGGACC
1 TATGTCCCGAAGGACC
29482 GCGTAGACCC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.26, C:0.26, G:0.27, T:0.22
Consensus pattern (22 bp):
TATGTCCCGAAGGACCTATGAG
Found at i:31480 original size:19 final size:20
Alignment explanation
Indices: 31456--31506 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
31446 AATGACCAAT
31456 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
31475 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
31495 AAAATCGCAACG
1 AAAATCGCAACG
31507 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:31500 original size:20 final size:20
Alignment explanation
Indices: 31456--31713 Score: 108
Period size: 20 Copynumber: 12.6 Consensus size: 20
31446 AATGACCAAT
* *
31456 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
31475 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
31495 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
31515 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
31535 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
31556 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
31579 AAAAGCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
31599 ATAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* * *
31619 AGAGTCCCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
31642 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
31662 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
31682 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
*
31702 AGAATCGCAACG
1 AAAATCGCAACG
31714 TTGAAAATCG
Statistics
Matches: 183, Mismatches: 44, Indels: 23
0.73 0.18 0.09
Matches are distributed among these distances:
19 17 0.09
20 124 0.68
21 14 0.08
23 28 0.15
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:31645 original size:63 final size:63
Alignment explanation
Indices: 31563--31700 Score: 195
Period size: 63 Copynumber: 2.2 Consensus size: 63
31553 TCCAAGTTCG
* * * * * *
31563 CAACGCGATTTAGAAGAAAAGCGCAATGCGATTTATATAATCGCAATGCGATTGAGAGAGTCC
1 CAACGCGATTTAGAAGAAAAGCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCC
* *
31626 CAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCG
1 CAACGCGATTTAGAAGAAAAGCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCC
*
31689 CAATGCGATTTA
1 CAACGCGATTTA
31701 TAGAATCGCA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (63 bp):
CAACGCGATTTAGAAGAAAAGCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCC
Found at i:31827 original size:6 final size:6
Alignment explanation
Indices: 31816--31847 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
31806 GACACGTATT
31816 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
31848 CGAGACGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:32567 original size:6 final size:6
Alignment explanation
Indices: 32535--32599 Score: 102
Period size: 6 Copynumber: 11.5 Consensus size: 6
32525 TCTCGTCTCG
32535 GGTCG- GGTCG- GGTCG- GGTCGT -GTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
32579 GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGT
32600 AATACGTGTC
Statistics
Matches: 58, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
5 20 0.34
6 38 0.66
ACGTcount: A:0.00, C:0.17, G:0.52, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:32702 original size:20 final size:20
Alignment explanation
Indices: 32677--32720 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
32667 TTTTTAACTA
*
32677 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
32697 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
32717 TTCT
1 TTCT
32721 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:32730 original size:20 final size:20
Alignment explanation
Indices: 32709--32960 Score: 279
Period size: 20 Copynumber: 12.3 Consensus size: 20
32699 CTTTTTAACG
* *
32709 TTGCGATTTTCTAAATCGCG
1 TTGCGATTCTCTAAATCGCA
*
32729 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCA
* *
32749 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCA
* *
32769 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCA
* *
32789 TTGCGATTCTATAAATTGCA
1 TTGCGATTCTCTAAATCGCA
*
32809 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCA
* *
32829 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCA
*
32849 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TCTAAATCGCA
* *
32872 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCA
*
32892 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCA
* *
32912 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTAAATCGCA
*
32932 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TCTAAATCGCA
32955 TTGCGA
1 TTGCGA
32961 ACTTGGAAGC
Statistics
Matches: 199, Mismatches: 27, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
20 163 0.82
21 2 0.01
22 6 0.03
23 28 0.14
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (20 bp):
TTGCGATTCTCTAAATCGCA
Found at i:32931 original size:83 final size:83
Alignment explanation
Indices: 32707--32960 Score: 388
Period size: 83 Copynumber: 3.1 Consensus size: 83
32697 TTCTTTTTAA
* *
32707 CGTTGCGATTTTCTAAATCGCGTTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTG
1 CGTTGCGATTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTG
* *
32772 CGA--TTC-TCTCAGTCG
66 CGATTTTCTTCTAAATCG
* * *
32787 CATTGCGATTCTATAAATTGCATTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTG
1 CGTTGCGATTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTG
32852 CGATTTTCTTCTAAATCG
66 CGATTTTCTTCTAAATCG
* * * *
32870 CGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
1 CGTTGCGATTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTG
32935 CGATTTTCTTCTAAATCG
66 CGATTTTCTTCTAAATCG
32953 CGTTGCGA
1 CGTTGCGA
32961 ACTTGGAAGC
Statistics
Matches: 157, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
80 63 0.40
82 3 0.02
83 91 0.58
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.37
Consensus pattern (83 bp):
CGTTGCGATTCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTG
CGATTTTCTTCTAAATCG
Found at i:32999 original size:20 final size:20
Alignment explanation
Indices: 32974--33027 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
32964 TGGAAGCTCG
*
32974 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAA
*
32994 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTTTTGAA
*
33014 CGTTGTGATTTTCT
1 CGTTGCGATTTTCT
33028 AAATCGCGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.11, C:0.17, G:0.19, T:0.54
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAA
Found at i:33037 original size:20 final size:19
Alignment explanation
Indices: 33014--33064 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
33004 TTCTTTTTAA
* *
33014 CGTTGTGATTTTCTAAATCG
1 CGTTGCGATTTT-GAAATCG
*
33034 CGTTGCGATTTTGATATCG
1 CGTTGCGATTTTGAAATCG
33053 CGTTGCGATTTT
1 CGTTGCGATTTT
33065 ATTGGTCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTGAAATCG
Found at i:37363 original size:19 final size:20
Alignment explanation
Indices: 37315--37364 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
37305 TTTTAGATAA
37315 TTTAATTTAAT--TCAAACT
1 TTTAATTTAATCATCAAACT
*
37333 TTT-ATTTAAATCAT-AAATT
1 TTTAATTT-AATCATCAAACT
37352 TTTAATTTAATCA
1 TTTAATTTAATCA
37365 AAGTATATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
17 4 0.15
18 6 0.22
19 12 0.44
20 5 0.19
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTAATTTAATCATCAAACT
Found at i:42314 original size:17 final size:18
Alignment explanation
Indices: 42294--42335 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
42284 TTATAAATCT
42294 ATTTAAAGTAAT-ATTAA
1 ATTTAAAGTAATGATTAA
* *
42311 ATTTTAATTAATGATTAA
1 ATTTAAAGTAATGATTAA
*
42329 TTTTAAA
1 ATTTAAA
42336 CAAATATTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (18 bp):
ATTTAAAGTAATGATTAA
Found at i:44780 original size:17 final size:17
Alignment explanation
Indices: 44746--44797 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
44736 ACCGAATAAA
* *
44746 TTTATTATTTTAGAGAG
1 TTTATTAATTTACAGAG
*
44763 TTTATTAATTTACCGAG
1 TTTATTAATTTACAGAG
*
44780 --TATTAATTTAAAGAG
1 TTTATTAATTTACAGAG
44795 TTT
1 TTT
44798 CTACTGCAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (17 bp):
TTTATTAATTTACAGAG
Found at i:45341 original size:60 final size:60
Alignment explanation
Indices: 45266--45387 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
45256 ATATTGAAAA
45266 CTTATAATTATAAAAAACATCATTTTGGACTCATGAAATTTTATAATTGAGCTATCTTCG
1 CTTATAATTATAAAAAACATCATTTTGGACTCATGAAATTTTATAATTGAGCTATCTTCG
45326 CTTATAATTATAAAAAACATCATTTTGGACTCATGAAATTTTATAATTGAGCTATCTTCG
1 CTTATAATTATAAAAAACATCATTTTGGACTCATGAAATTTTATAATTGAGCTATCTTCG
45386 CT
1 CT
45388 AAAATGACGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (60 bp):
CTTATAATTATAAAAAACATCATTTTGGACTCATGAAATTTTATAATTGAGCTATCTTCG
Found at i:45725 original size:17 final size:17
Alignment explanation
Indices: 45705--45741 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
45695 CGTCGATCGT
*
45705 GAAGTTTTCTTATGTAA
1 GAAGTTTTCTCATGTAA
*
45722 GAAGTTTTCTCGTGTAA
1 GAAGTTTTCTCATGTAA
45739 GAA
1 GAA
45742 TAAATCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.41
Consensus pattern (17 bp):
GAAGTTTTCTCATGTAA
Found at i:46671 original size:18 final size:18
Alignment explanation
Indices: 46638--46673 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
46628 ATATTTCAAG
**
46638 TTATTTGATTTTAATTTA
1 TTATTTGATTCAAATTTA
46656 TTATTTGATTCAAATTTA
1 TTATTTGATTCAAATTTA
46674 ATTTTTTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.61
Consensus pattern (18 bp):
TTATTTGATTCAAATTTA
Found at i:51596 original size:33 final size:33
Alignment explanation
Indices: 51521--51619 Score: 123
Period size: 33 Copynumber: 3.1 Consensus size: 33
51511 AACATGAAAT
* *
51521 ATAAGTTGGCCACCTA-CAA-AAG-ATTTTTCCA
1 ATAAGTTGGCCACCAACCAAGATGAATTTTT-CA
* *
51552 ATGAGTTGGCCACCAACCAAGATTAATTTTTCA
1 ATAAGTTGGCCACCAACCAAGATGAATTTTTCA
*
51585 ATAAGTTGGCCACCAACCAAGATGAAATTTTCA
1 ATAAGTTGGCCACCAACCAAGATGAATTTTTCA
51618 AT
1 AT
51620 CTTGCCAAAC
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
31 14 0.24
32 3 0.05
33 35 0.60
34 6 0.10
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.28
Consensus pattern (33 bp):
ATAAGTTGGCCACCAACCAAGATGAATTTTTCA
Found at i:56336 original size:33 final size:33
Alignment explanation
Indices: 56260--56359 Score: 125
Period size: 33 Copynumber: 3.1 Consensus size: 33
56250 AAACATGAAA
* *
56260 AATAAGTTGGCCACCTACCAAAGA-T--TTTTCC
1 AATAAGTTGGCCACCAACC-AAGATTAATTTTTC
*
56291 AATGAGTTGGCCACCAACCAAGATTAATTTTTC
1 AATAAGTTGGCCACCAACCAAGATTAATTTTTC
* *
56324 AATAAGTTGGCCACCAACCAAGATGAAATTTTC
1 AATAAGTTGGCCACCAACCAAGATTAATTTTTC
56357 AAT
1 AAT
56360 CTTGCCAAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
30 4 0.07
31 18 0.30
33 38 0.63
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (33 bp):
AATAAGTTGGCCACCAACCAAGATTAATTTTTC
Found at i:62191 original size:2 final size:2
Alignment explanation
Indices: 62184--62222 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
62174 AAGGGAACTT
62184 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
62223 TAACAACCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:62367 original size:13 final size:15
Alignment explanation
Indices: 62335--62366 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
62325 AATTAGAATA
62335 TTTTACTTTTATTTT
1 TTTTACTTTTATTTT
62350 TTTTA-TTTTATTTT
1 TTTTACTTTTATTTT
62364 TTT
1 TTT
62367 AGTATTGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTACTTTTATTTT
Found at i:62440 original size:15 final size:15
Alignment explanation
Indices: 62420--62449 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
62410 TTTAAAACAT
62420 AAAATATAAATTAAA
1 AAAATATAAATTAAA
*
62435 AAAATATAATTTAAA
1 AAAATATAAATTAAA
62450 TTTTTTTATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATATAAATTAAA
Found at i:62518 original size:22 final size:23
Alignment explanation
Indices: 62474--62534 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
62464 ATTATAACTT
* *
62474 AAAATTATAAAAAATTAATTATA
1 AAAATAATAAAAAATTAAATATA
*
62497 AAAATAATAAATAA-TAAATATA
1 AAAATAATAAAAAATTAAATATA
*
62519 AATATAATATAAAAAT
1 AAAATAATA-AAAAAT
62535 ATGAAATTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 15 0.48
23 16 0.52
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATAATAAAAAATTAAATATA
Found at i:63390 original size:9 final size:9
Alignment explanation
Indices: 63378--63429 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
63368 TAATATTTTG
63378 TATTTAATT
1 TATTTAATT
*
63387 TATTTAA-A
1 TATTTAATT
63395 TATTTAATT
1 TATTTAATT
63404 TATTTAA--
1 TATTTAATT
* *
63411 TATTTTACT
1 TATTTAATT
63420 TATTTAATT
1 TATTTAATT
63429 T
1 T
63430 TTTTGCAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:63400 original size:17 final size:17
Alignment explanation
Indices: 63378--63426 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
63368 TAATATTTTG
63378 TATTTAATTTATTTAAA
1 TATTTAATTTATTTAAA
63395 TATTTAATTTATTT-AA
1 TATTTAATTTATTTAAA
* *
63411 TATTTTACTTATTTAA
1 TATTTAATTTATTTAA
63427 TTTTTTTGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 14 0.48
17 15 0.52
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTTAATTTATTTAAA
Found at i:63414 original size:16 final size:16
Alignment explanation
Indices: 63378--63427 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
63368 TAATATTTTG
63378 TATTTAATTTATTTAAA
1 TATTTAATTTATTT-AA
63395 TATTTAATTTATTTAA
1 TATTTAATTTATTTAA
* *
63411 TATTTTACTTATTTAA
1 TATTTAATTTATTTAA
63427 T
1 T
63428 TTTTTTGCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 17 0.55
17 14 0.45
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTTAATTTATTTAA
Found at i:65470 original size:18 final size:18
Alignment explanation
Indices: 65443--65477 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
65433 CTCAGGACGA
*
65443 CGACGCCGACGACGATGC
1 CGACGCCGACAACGATGC
*
65461 CGACGTCGACAACGATG
1 CGACGCCGACAACGATG
65478 ATGATGGTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.31, T:0.09
Consensus pattern (18 bp):
CGACGCCGACAACGATGC
Found at i:65799 original size:34 final size:34
Alignment explanation
Indices: 65718--65799 Score: 80
Period size: 34 Copynumber: 2.4 Consensus size: 34
65708 TTCAGTTAAT
*
65718 TTTGTTTA-TTATCATTTAATATCAGTTATTGTAA
1 TTTGTTTATTTACCATTTAATATCA-TTATTGTAA
*
65752 TTTGGTATCATTTACCATTTAATA-C-TTATTGTAA
1 TTT-GT-TTATTTACCATTTAATATCATTATTGTAA
65786 GTTTGTTGTATTTA
1 -TTTGTT-TATTTA
65800 AAATTATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
33 1 0.03
34 19 0.47
35 5 0.12
36 3 0.08
37 12 0.30
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.55
Consensus pattern (34 bp):
TTTGTTTATTTACCATTTAATATCATTATTGTAA
Done.