Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004304.1 Hibiscus syriacus cultivar Beakdansim tig00009438_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: 71008
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Found at i:14491 original size:13 final size:12
Alignment explanation
Indices: 14475--14522 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
14465 TTTTCCCATT
14475 TTTTTTCCTTTTC
1 TTTTTT-CTTTTC
14488 TTTTTTCTTTTC
1 TTTTTTCTTTTC
14500 --TTTTCTTTTC
1 TTTTTTCTTTTC
**
14510 CCTTTTCTTTTC
1 TTTTTTCTTTTC
14522 T
1 T
14523 CTTACTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
10 10 0.31
12 16 0.50
13 6 0.19
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTTCTTTTC
Found at i:14502 original size:17 final size:17
Alignment explanation
Indices: 14473--14522 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
14463 ATTTTTCCCA
*
14473 TTTTT-TTTCCTTTTCT
1 TTTTTCTTTTCTTTTCT
14489 TTTTTCTTTTCTTTTCT
1 TTTTTCTTTTCTTTTCT
**
14506 TTTCCCTTTTCTTTTCT
1 TTTTTCTTTTCTTTTCT
14523 CTTACTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 5 0.17
17 25 0.83
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTCTTTTCTTTTCT
Found at i:22342 original size:76 final size:76
Alignment explanation
Indices: 22235--22426 Score: 357
Period size: 76 Copynumber: 2.5 Consensus size: 76
22225 ATTTTAAATA
22235 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
22300 GGATATTATTT
66 GGATATTATTT
* *
22311 TTATATTTTATCTCTGTTTTAGGTATTTTAGTTTAAATAGGTTTTTGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
22376 GGATATTATTT
66 GGATATTATTT
*
22387 TTATTTTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAG
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAG
22427 TGTTAACTGT
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 112 1.00
ACGTcount: A:0.25, C:0.02, G:0.13, T:0.60
Consensus pattern (76 bp):
TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTA
GGATATTATTT
Found at i:23106 original size:23 final size:25
Alignment explanation
Indices: 23057--23106 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
23047 TTTACTACTA
*
23057 TTATTAATTATTTTATTTCCCTTTTAT
1 TTATTAATTATTTTATTT--CTATTAT
23084 TTATT-ATTATTTTATTT-TATTAT
1 TTATTAATTATTTTATTTCTATTAT
23107 ACCTTTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 5 0.23
26 12 0.55
27 5 0.23
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (25 bp):
TTATTAATTATTTTATTTCTATTAT
Found at i:28658 original size:5 final size:5
Alignment explanation
Indices: 28638--28678 Score: 57
Period size: 5 Copynumber: 8.0 Consensus size: 5
28628 AAGGCAACCC
28638 ATTTT -TTTT CATTTT ATTTT ATTTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT -ATTTT ATTTT A-TTTT ATTTT ATTTT ATTTT
28679 TCAGCAAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 4 0.12
5 20 0.61
6 9 0.27
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:28667 original size:16 final size:16
Alignment explanation
Indices: 28638--28679 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
28628 AAGGCAACCC
*
28638 ATTTT-TTTTCATTTT
1 ATTTTATTTTTATTTT
28653 ATTTTATTTTTATTTT
1 ATTTTATTTTTATTTT
28669 ATTTTATTTTT
1 ATTTTATTTTT
28680 CAGCAAACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 5 0.20
16 20 0.80
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (16 bp):
ATTTTATTTTTATTTT
Found at i:30699 original size:51 final size:51
Alignment explanation
Indices: 30642--30759 Score: 202
Period size: 51 Copynumber: 2.3 Consensus size: 51
30632 GTTTAAATAA
30642 GTTTTAGTATTTTA-ATAGAGTTTTAGGATATTATTTTTATATTTTATCTTT
1 GTTTTAGTATTTTAGATA-AGTTTTAGGATATTATTTTTATATTTTATCTTT
*
30693 GTTTTAGTATTTTAGTTAAGTTTTAGGATATTATTTTTATATTTTATCTTT
1 GTTTTAGTATTTTAGATAAGTTTTAGGATATTATTTTTATATTTTATCTTT
30744 GTTTTAGGTATTTTAG
1 GTTTTA-GTATTTTAG
30760 TTTAAATAGT
Statistics
Matches: 64, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
51 53 0.83
52 11 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.61
Consensus pattern (51 bp):
GTTTTAGTATTTTAGATAAGTTTTAGGATATTATTTTTATATTTTATCTTT
Found at i:30703 original size:19 final size:18
Alignment explanation
Indices: 30670--30758 Score: 57
Period size: 19 Copynumber: 5.1 Consensus size: 18
30660 AGTTTTAGGA
30670 TATTAT-TTTTA-TATTT
1 TATTATGTTTTAGTATTT
*
30686 TATCTTTGTTTTAGTATTT
1 TAT-TATGTTTTAGTATTT
* *
30705 TAGTTAAGTTTTAGGA---
1 TA-TTATGTTTTAGTATTT
30721 TATTAT-TTTTA-TATTT
1 TATTATGTTTTAGTATTT
*
30737 TATCTTTGTTTTAGGTATTT
1 TAT-TATGTTTTA-GTATTT
30757 TA
1 TA
30759 GTTTAAATAG
Statistics
Matches: 55, Mismatches: 7, Indels: 18
0.69 0.09 0.22
Matches are distributed among these distances:
13 1 0.02
14 5 0.09
15 3 0.05
16 8 0.15
17 4 0.07
18 10 0.18
19 16 0.29
20 8 0.15
ACGTcount: A:0.22, C:0.02, G:0.10, T:0.65
Consensus pattern (18 bp):
TATTATGTTTTAGTATTT
Found at i:31402 original size:17 final size:18
Alignment explanation
Indices: 31380--31421 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
31370 CTTTAGATTG
31380 TTTATTTAATTATTAT-T
1 TTTATTTAATTATTATCT
*
31397 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
31415 TTTATTT
1 TTTATTT
31422 TAAAAAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:31506 original size:16 final size:17
Alignment explanation
Indices: 31465--31516 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 17
31455 TATTTATTAC
31465 TATTATTTATTATTTTAT
1 TATTATTT-TTATTTTAT
**
31483 T-TCCTTTTTA-TTTAT
1 TATTATTTTTATTTTAT
31498 TATTA-TTTTATTTTAT
1 TATTATTTTTATTTTAT
31514 TAT
1 TAT
31517 ACCTTTTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 11 0.39
16 12 0.43
17 4 0.14
18 1 0.04
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (17 bp):
TATTATTTTTATTTTAT
Found at i:32275 original size:7 final size:7
Alignment explanation
Indices: 32211--32326 Score: 58
Period size: 7 Copynumber: 15.9 Consensus size: 7
32201 TAAGTAATAT
32211 TATATAA
1 TATATAA
*
32218 TAAAATAA
1 T-ATATAA
* *
32226 AATCTAA
1 TATATAA
*
32233 TATATGA
1 TATATAA
*
32240 TATATGA
1 TATATAA
*
32247 TGTATAA
1 TATATAA
*
32254 TAT-TGA
1 TATATAA
*
32260 T-TGTAA
1 TATATAA
32266 TATATAA
1 TATATAA
32273 TATA-ATA
1 TATATA-A
32280 TAATATAA
1 T-ATATAA
32288 TATACATAA
1 TAT--ATAA
*
32297 TATATATG
1 TATATA-A
32305 TCATATAA
1 T-ATATAA
32313 TATAGTAA
1 TATA-TAA
32321 TATATA
1 TATATA
32327 TCAATGAGTG
Statistics
Matches: 83, Mismatches: 15, Indels: 22
0.69 0.12 0.18
Matches are distributed among these distances:
5 1 0.01
6 7 0.08
7 43 0.52
8 19 0.23
9 13 0.16
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.41
Consensus pattern (7 bp):
TATATAA
Found at i:32277 original size:5 final size:5
Alignment explanation
Indices: 32267--32316 Score: 57
Period size: 5 Copynumber: 10.0 Consensus size: 5
32257 TGATTGTAAT
* * *
32267 ATATA ATATA ATATA ATATA ATAT- ACATA ATATA TATGTC ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA -ATATA ATATA ATATA
32317 GTAATATATA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
4 3 0.08
5 31 0.84
6 3 0.08
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:32321 original size:55 final size:55
Alignment explanation
Indices: 32211--32326 Score: 130
Period size: 55 Copynumber: 2.1 Consensus size: 55
32201 TAAGTAATAT
* * * *
32211 TATATAATAAAATAAAATCTAATATATGATATATGATGTATAATATTGATTGTAA
1 TATATAATAAAATAAAATATAATATATAATATATGATGTATAATAATGATAGTAA
* *
32266 TATATAATATAATATAATATAATATACATAATATAT-ATGTCAT-ATAAT-ATAGTAA
1 TATATAATAAAATAAAATATAATAT--ATAATATATGATGT-ATAATAATGATAGTAA
32321 TATATA
1 TATATA
32327 TCAATGAGTG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
55 34 0.65
56 8 0.15
57 10 0.19
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.41
Consensus pattern (55 bp):
TATATAATAAAATAAAATATAATATATAATATATGATGTATAATAATGATAGTAA
Found at i:32974 original size:113 final size:112
Alignment explanation
Indices: 32768--32975 Score: 335
Period size: 113 Copynumber: 1.8 Consensus size: 112
32758 TCAACAAGTC
* **
32768 ATGTCACTTTTTTTAGATAAAATTACTATTTTCGGTATGAATTACTTTGGGTTATTCTCATTGGA
1 ATGTCACTTTTTTTAGATAAAACTACTATTTTCGGTATGAATTACTTTCAGTTATTCTCATTGGA
*
32833 CTTTTGTTTATATTTTGGATTTATTATTTATCTAACCATGACAGTGG
66 CTTTTGTTTATAATTTGGATTTATTATTTATCTAACCATGACAGTGG
* * *
32880 ATGTCATTATTTTTTAGATAAAACTGCTATTTTCGGTATGAATTACTTTCAGTTTTTCTCATTGG
1 ATGTCACT-TTTTTTAGATAAAACTACTATTTTCGGTATGAATTACTTTCAGTTATTCTCATTGG
*
32945 ACTTTTGTTTATAATTTGGGTTTATTATTTA
65 ACTTTTGTTTATAATTTGGATTTATTATTTA
32976 CGCATGCATT
Statistics
Matches: 87, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
112 7 0.08
113 80 0.92
ACGTcount: A:0.25, C:0.10, G:0.14, T:0.51
Consensus pattern (112 bp):
ATGTCACTTTTTTTAGATAAAACTACTATTTTCGGTATGAATTACTTTCAGTTATTCTCATTGGA
CTTTTGTTTATAATTTGGATTTATTATTTATCTAACCATGACAGTGG
Found at i:36838 original size:3 final size:3
Alignment explanation
Indices: 36825--36865 Score: 57
Period size: 3 Copynumber: 13.3 Consensus size: 3
36815 AATGTAATTT
36825 ATA ATTA ATA ATA A-A CATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA A-TA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA A
36866 AATTAAATAG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.03
3 30 0.86
4 4 0.11
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:37350 original size:28 final size:27
Alignment explanation
Indices: 37318--37385 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
37308 GAAATCGAAA
37318 CAAAGATAAGTTTCAA-AAGAAACAGACT
1 CAAAGATAA-TTTCAAGAA-AAACAGACT
* * *
37346 TAAAGATCTATTTCAAGAAAAACAGAGT
1 CAAAGAT-AATTTCAAGAAAAACAGACT
37374 CAAAGATAATTT
1 CAAAGATAATTT
37386 GTTTCAAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
27 4 0.12
28 26 0.79
29 3 0.09
ACGTcount: A:0.51, C:0.12, G:0.13, T:0.24
Consensus pattern (27 bp):
CAAAGATAATTTCAAGAAAAACAGACT
Found at i:37911 original size:36 final size:36
Alignment explanation
Indices: 37823--37923 Score: 99
Period size: 36 Copynumber: 3.0 Consensus size: 36
37813 TGAGAAAAGG
* * * *
37823 TCTCAAGGAAAAAAAGATTTGTTTTAAGTGAAACGA
1 TCTCAAGGAAAATAAGATTTGTTTCAAGAGAAACAA
*
37859 TCTC-A--AAAAT--G-GTTGTTTCATAG-GAAACAA
1 TCTCAAGGAAAATAAGATTTGTTTCA-AGAGAAACAA
37889 TCTCAAGGAAAATAAGATTTGTTTCAAGAGAAACA
1 TCTCAAGGAAAATAAGATTTGTTTCAAGAGAAACA
37924 TACTGAAAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
30 17 0.33
31 4 0.08
33 9 0.17
35 4 0.08
36 18 0.35
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.28
Consensus pattern (36 bp):
TCTCAAGGAAAATAAGATTTGTTTCAAGAGAAACAA
Found at i:38216 original size:36 final size:36
Alignment explanation
Indices: 38170--38272 Score: 120
Period size: 36 Copynumber: 2.8 Consensus size: 36
38160 AATTTGTGGA
38170 AAAATGTCTCAAGCGAGATCGAA-TTTGTTTTTAGAG
1 AAAATGTCTCAAGCGAGATC-AACTTTGTTTTTAGAG
* * *
38206 AAAATGTCTCAAGCGAGA-CAAAGTTTATTTTTTGAG
1 AAAATGTCTCAAGCGAGATC-AACTTTGTTTTTAGAG
* *
38242 AAAACGATCTCAAGTGAGATCAACTTTGTTT
1 AAAATG-TCTCAAGCGAGATCAACTTTGTTT
38273 ACTGTGAAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
35 3 0.05
36 34 0.60
37 19 0.33
38 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (36 bp):
AAAATGTCTCAAGCGAGATCAACTTTGTTTTTAGAG
Found at i:38363 original size:36 final size:37
Alignment explanation
Indices: 38288--38448 Score: 145
Period size: 36 Copynumber: 4.4 Consensus size: 37
38278 GAAACAAATT
* * * *
38288 CAAAATTTGTATCTCAAAGGAAAAATGTCTCAAGCGAGA
1 CAAAATTTGTTTTTC-AA-GAAAATTGTCTAAAGCGAGA
* *
38327 CGAAATTTGTTTTTCAAG-AAATTGTCTGAAA-TGAGA
1 CAAAATTTGTTTTTCAAGAAAATTGTCT-AAAGCGAGA
*
38363 CAAAATTTGTTTTT--AGAAAATTGTCTAAAGCGATA
1 CAAAATTTGTTTTTCAAGAAAATTGTCTAAAGCGAGA
**
38398 CAAAATTTGTTTTTCAA-AAGAAGTTGTCTCTAGCGAGA
1 CAAAATTTGTTTTTCAAGAA-AA-TTGTCTAAAGCGAGA
*
38436 CAACATTT-TTTTT
1 CAAAATTTGTTTTT
38449 GAGAAAAACA
Statistics
Matches: 102, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
34 5 0.05
35 26 0.25
36 27 0.26
37 11 0.11
38 21 0.21
39 12 0.12
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (37 bp):
CAAAATTTGTTTTTCAAGAAAATTGTCTAAAGCGAGA
Found at i:38447 original size:71 final size:71
Alignment explanation
Indices: 38307--38456 Score: 176
Period size: 71 Copynumber: 2.1 Consensus size: 71
38297 TATCTCAAAG
* * * *
38307 GAAAAATGTCTCAAGCGAGACGAAATTTGTTTTTCAAGAAATTGTCTGAAATGAGACAAAATTTG
1 GAAAAATGTCTAAAGCGAGACAAAATTTGTTTTTCAAGAAATTGTCTCAAACGAGACAAAATTTG
38372 TTTTTA
66 TTTTTA
* * * * * *
38378 GAAAATTGTCTAAAGCGATACAAAATTTGTTTTTCAAAAGAAGTTGTCTCTAGCGAGACAACATT
1 GAAAAATGTCTAAAGCGAGACAAAATTTGTTTTTC--AAGAAATTGTCTCAAACGAGACAAAATT
38443 T-TTTTTGA
64 TGTTTTT-A
38451 GAAAAA
1 GAAAAA
38457 CAACATCAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
71 31 0.48
72 5 0.08
73 29 0.45
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (71 bp):
GAAAAATGTCTAAAGCGAGACAAAATTTGTTTTTCAAGAAATTGTCTCAAACGAGACAAAATTTG
TTTTTA
Found at i:38979 original size:4 final size:4
Alignment explanation
Indices: 38752--38967 Score: 342
Period size: 4 Copynumber: 54.0 Consensus size: 4
38742 TGTAAATTTC
38752 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
38800 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATAT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * *
38848 ATAT ATAT ATAT ATGT ATAT ATGT ATGT ATGT ATGT ATGT ATGT ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
38896 ATGT ATGT ATGT ATGT ATGT ATAT ATGT ATAT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
38944 ATGT ATAT ATGT ATGT ATAT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT
38968 GTTGATGTAT
Statistics
Matches: 196, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 196 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:47883 original size:15 final size:16
Alignment explanation
Indices: 47858--47887 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
47848 AATGTAATTT
47858 ATAATTAATAATAAAC
1 ATAATTAATAATAAAC
47874 ATAA-TAATAATAAA
1 ATAATTAATAATAAA
47888 ATTAAATAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAATTAATAATAAAC
Found at i:48147 original size:40 final size:40
Alignment explanation
Indices: 48042--48157 Score: 119
Period size: 43 Copynumber: 2.8 Consensus size: 40
48032 TGTTAGTTGT
* *
48042 TGGGGATTACACTGCTCATACGCGATGAAGATGTATGGTCG
1 TGGGGATGACACTGCTCATACGTGATGAAGA-GTATGGTCG
* * * *
48083 TCTAAGGG-TGACACGGCTCCTACGTGATGAAGAGATCTGGTCG
1 --T-GGGGATGACACTGCTCATACGTGATGAAGAG-TATGGTCG
48126 -GGGGATGACACTGCTCATACGTGATGAAGAGT
1 TGGGGATGACACTGCTCATACGTGATGAAGAGT
48158 TCTTGGCCAT
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
39 4 0.07
40 24 0.39
42 1 0.02
43 29 0.48
44 3 0.05
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (40 bp):
TGGGGATGACACTGCTCATACGTGATGAAGAGTATGGTCG
Found at i:48348 original size:28 final size:28
Alignment explanation
Indices: 48332--48399 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
48322 AGAGAATCTG
48332 ACTCAAAGATAAGTTTCAAAAGAAACAT
1 ACTCAAAGATAAGTTTCAAAAGAAACAT
** * *
48360 ACTCAAAGATCTGTTTTAAGAA-AAACAA
1 ACTCAAAGATAAGTTTCAA-AAGAAACAT
48388 ACTCAAAGATAA
1 ACTCAAAGATAA
48400 TGTGTTTCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 31 0.94
29 2 0.06
ACGTcount: A:0.53, C:0.15, G:0.10, T:0.22
Consensus pattern (28 bp):
ACTCAAAGATAAGTTTCAAAAGAAACAT
Found at i:48937 original size:36 final size:36
Alignment explanation
Indices: 48819--48938 Score: 105
Period size: 36 Copynumber: 3.5 Consensus size: 36
48809 AAGATGATTT
* *
48819 TTTGTTTCATGAGAAA-AGTTCTCAAGGAAAATAAGA
1 TTTGTTTCAAGAGAAACAG-ACTCAAGGAAAATAAGA
* *
48855 TTTGTTTTAAGTGAAAC-GATCTC-A--AAAAT--G-
1 TTTGTTTCAAGAGAAACAGA-CTCAAGGAAAATAAGA
*
48885 GTTGTTTCATA-AGAAACAGACTCAAGGAAAATAAGA
1 TTTGTTTCA-AGAGAAACAGACTCAAGGAAAATAAGA
48921 TTTGTTTCAAGAGAAACA
1 TTTGTTTCAAGAGAAACA
48939 TACTGAAAGA
Statistics
Matches: 65, Mismatches: 8, Indels: 22
0.68 0.08 0.23
Matches are distributed among these distances:
30 15 0.23
31 5 0.08
33 10 0.15
35 3 0.05
36 32 0.49
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.30
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACAGACTCAAGGAAAATAAGA
Found at i:49417 original size:35 final size:36
Alignment explanation
Indices: 49329--49447 Score: 120
Period size: 36 Copynumber: 3.3 Consensus size: 36
49319 AAAGGAAAAA
49329 TGTCTCAAGCGAAACAAAATTTGTTTTTCAAGAAAT
1 TGTCTCAAGCGAAACAAAATTTGTTTTTCAAGAAAT
** *
49365 TGTCTCAAATGAGACAAAATTTGTTTTT--AGAAAAT
1 TGTCTCAAGCGAAACAAAATTTGTTTTTCAAG-AAAT
* * *
49400 TTTCTCAAGCGATAC-AAATTT-TTTTTCAAAAGAAGT
1 TGTCTCAAGCGAAACAAAATTTGTTTTTC--AAGAAAT
*
49436 TGTCTCTAGCGA
1 TGTCTCAAGCGA
49448 GACGACATTT
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
33 5 0.07
34 8 0.12
35 15 0.22
36 38 0.56
37 2 0.03
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (36 bp):
TGTCTCAAGCGAAACAAAATTTGTTTTTCAAGAAAT
Found at i:49775 original size:4 final size:4
Alignment explanation
Indices: 49766--51468 Score: 3148
Period size: 4 Copynumber: 427.2 Consensus size: 4
49756 ATGCAAATTT
49766 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
49814 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
49862 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
49910 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
49958 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
50006 TATG TATG TATG TATG TATG TATG TATA TATG TATG TATG TATA TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
50054 TATG TATG TATG TATG TATG TATA TATG TATG TATG TATG TATG TGTG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
50102 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA-- TATA TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
50148 TTTG TATG TATG TATA TATG TATG TATA TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
50196 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
50244 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
50292 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
50340 TATG TATG TATG TATG TATG TATG TATG TTTG TATG --TG TGTG TGTG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
50386 TGTG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
50434 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
50482 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
50530 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATT TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
50578 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
50626 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
50674 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
50722 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
50770 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
50818 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG CATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
50866 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
50914 TA-- TATA TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
50960 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
51008 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
51056 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * *
51104 TATG TATG TATG TATG TATG TATG TTTA TATG CATG TATG CATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
51152 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
51200 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
51248 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
51296 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
51344 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
51392 TATG TATG TATG TATG TATG TATG TATG TATG TTTG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
51440 CATG TATG TATA TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
51469 GTTGATGTAT
Statistics
Matches: 1652, Mismatches: 41, Indels: 12
0.97 0.02 0.01
Matches are distributed among these distances:
2 6 0.00
4 1646 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:54529 original size:13 final size:13
Alignment explanation
Indices: 54511--54535 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54501 ATCGCTTAAA
54511 ACACTTATAGCAT
1 ACACTTATAGCAT
54524 ACACTTATAGCA
1 ACACTTATAGCA
54536 ATAATGCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (13 bp):
ACACTTATAGCAT
Found at i:55151 original size:14 final size:15
Alignment explanation
Indices: 55126--55154 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
55116 TTAATTTATG
55126 TTTCCGTTTAACTTT
1 TTTCCGTTTAACTTT
55141 TTTCC-TTTAACTTT
1 TTTCCGTTTAACTTT
55155 ATTTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.14, C:0.21, G:0.03, T:0.62
Consensus pattern (15 bp):
TTTCCGTTTAACTTT
Found at i:55489 original size:7 final size:7
Alignment explanation
Indices: 55459--55516 Score: 55
Period size: 7 Copynumber: 8.1 Consensus size: 7
55449 TTAATACTAA
55459 ATATTAT
1 ATATTAT
*
55466 ATAATAT
1 ATATTAT
*
55473 AGT-TTTT
1 A-TATTAT
55480 ATATTAT
1 ATATTAT
55487 ATATTTAT
1 ATA-TTAT
55495 ATATTAT
1 ATATTAT
*
55502 ATTTTAT
1 ATATTAT
*
55509 ATTTTAT
1 ATATTAT
55516 A
1 A
55517 AGTATAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
6 1 0.02
7 34 0.79
8 8 0.19
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (7 bp):
ATATTAT
Found at i:55502 original size:29 final size:27
Alignment explanation
Indices: 55462--55516 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
55452 ATACTAAATA
55462 TTATATAATATAGTTTTTATATTATATAT
1 TTATATAATATA--TTTTATATTATATAT
* *
55491 TTATATATTATATTTTATATTTTATA
1 TTATATAATATATTTTATATTATATA
55517 AGTATAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 13 0.54
29 11 0.46
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (27 bp):
TTATATAATATATTTTATATTATATAT
Found at i:55503 original size:20 final size:19
Alignment explanation
Indices: 55478--55516 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
55468 AATATAGTTT
55478 TTATATTATATATTTATATA
1 TTATATTATATATTT-TATA
*
55498 TTATATTTTATATTTTATA
1 TTATATTATATATTTTATA
55517 AGTATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATATTATATATTTTATA
Found at i:55522 original size:20 final size:20
Alignment explanation
Indices: 55479--55522 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
55469 ATATAGTTTT
*
55479 TATATTATATATTTATATAT
1 TATATTATATATTTATATAG
*
55499 TATATTTTATATTT-TATAAG
1 TATATTATATATTTATAT-AG
55519 TATA
1 TATA
55523 AAATTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TATATTATATATTTATATAG
Found at i:55840 original size:22 final size:22
Alignment explanation
Indices: 55812--55858 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
55802 ACGTTACCAA
* *
55812 CCATTAACTTCTTCTTCTTCTT
1 CCATTAACTTCTTATCCTTCTT
55834 CCATTAACTTCTTATCCTTCTT
1 CCATTAACTTCTTATCCTTCTT
55856 CCA
1 CCA
55859 ATACGCGCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.49
Consensus pattern (22 bp):
CCATTAACTTCTTATCCTTCTT
Found at i:57477 original size:34 final size:34
Alignment explanation
Indices: 57434--57500 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
57424 AATAGAAATT
*
57434 ACAACTTCTCTC-GATCTAACAAAGAGAAAACAATA
1 ACAACTTCTCTCTGA--TAAAAAAGAGAAAACAATA
57469 ACAA-TTCTCTCTTGATAAAAAAGAGAAAACAA
1 ACAACTTCTCTC-TGATAAAAAAGAGAAAACAA
57501 CTCTCAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 23 0.79
35 4 0.14
36 2 0.07
ACGTcount: A:0.51, C:0.19, G:0.09, T:0.21
Consensus pattern (34 bp):
ACAACTTCTCTCTGATAAAAAAGAGAAAACAATA
Found at i:57721 original size:15 final size:15
Alignment explanation
Indices: 57701--57732 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
57691 TTTTTTCAAC
*
57701 TTTCGGTGCCACTAA
1 TTTCGGTGCCACCAA
57716 TTTCGGTGCCACCAA
1 TTTCGGTGCCACCAA
57731 TT
1 TT
57733 GTTGAATTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.34
Consensus pattern (15 bp):
TTTCGGTGCCACCAA
Found at i:61753 original size:16 final size:16
Alignment explanation
Indices: 61732--61787 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
61722 TTTCATTGCC
*
61732 ATAGCTTCTATTACGA
1 ATAGCTCCTATTACGA
61748 ATAGCTCCTATTACGA
1 ATAGCTCCTATTACGA
*
61764 ATGGCTCCTATTACGA
1 ATAGCTCCTATTACGA
61780 ATAGCTCC
1 ATAGCTCC
61788 CACTATTTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (16 bp):
ATAGCTCCTATTACGA
Found at i:64621 original size:261 final size:261
Alignment explanation
Indices: 64157--64687 Score: 1048
Period size: 261 Copynumber: 2.0 Consensus size: 261
64147 CCTTTACGAC
64157 ATGCACCCATAACAAAACCTTTGTTTCGAATTACAACACTTGACCATGATCTTTGTTGTCCTTGC
1 ATGCACCCATAACAAAACCTTTGTTTCGAATTACAACACTTGACCATGATCTTTGTTGTCCTTGC
64222 AAAAAATTTAAATCAAAGTTAACCTTCGTTGCTTGAGATAGGAGAGGCTTCCAAAAGACCACCGA
66 AAAAAATTTAAATCAAAGTTAACCTTCGTTGCTTGAGATAGGAGAGGCTTCCAAAAGACCACCGA
64287 CAGCAAAAGAGGTCCACGAAGGTTGGTATTGGCCGAGTGAAAATCTAAATACTGTACTCTAACCA
131 CAGCAAAAGAGGTCCACGAAGGTTGGTATTGGCCGAGTGAAAATCTAAATACTGTACTCTAACCA
64352 AGGTAATTATCTCTTCAAGCCTCACAATTTGTCCCTCATGAAGAAGTCGGTTGCTTGCATACCGT
196 AGGTAATTATCTCTTCAAGCCTCACAATTTGTCCCTCATGAAGAAGTCGGTTGCTTGCATACCGT
64417 A
261 A
64418 ATGCACCCATAACAAAACCTTTGTTTCGAATTACAACACTTGACCATGATCTTTGTTGTCCTTGC
1 ATGCACCCATAACAAAACCTTTGTTTCGAATTACAACACTTGACCATGATCTTTGTTGTCCTTGC
64483 AAAAAATTTAAATCAAAGTTAACCTTCGTTGCTTGAGATAGGAGAGGCTTCCAAAAGACCACCGA
66 AAAAAATTTAAATCAAAGTTAACCTTCGTTGCTTGAGATAGGAGAGGCTTCCAAAAGACCACCGA
64548 CAGCAAAAGAGGTCCACGAAGGTTGGTATTGGCCGAGTGAAAATCTAAATACTGTACTCTAACCA
131 CAGCAAAAGAGGTCCACGAAGGTTGGTATTGGCCGAGTGAAAATCTAAATACTGTACTCTAACCA
64613 AGGTAATTATCTCTTCAAGCCTCACAATTTGTCCCTCATGAAGAAGTCGGTTGCTTGCATACCGT
196 AGGTAATTATCTCTTCAAGCCTCACAATTTGTCCCTCATGAAGAAGTCGGTTGCTTGCATACCGT
64678 A
261 A
64679 AT--ACCCATA
1 ATGCACCCATA
64688 GAATTACTAT
Statistics
Matches: 270, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
259 7 0.03
261 263 0.97
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.27
Consensus pattern (261 bp):
ATGCACCCATAACAAAACCTTTGTTTCGAATTACAACACTTGACCATGATCTTTGTTGTCCTTGC
AAAAAATTTAAATCAAAGTTAACCTTCGTTGCTTGAGATAGGAGAGGCTTCCAAAAGACCACCGA
CAGCAAAAGAGGTCCACGAAGGTTGGTATTGGCCGAGTGAAAATCTAAATACTGTACTCTAACCA
AGGTAATTATCTCTTCAAGCCTCACAATTTGTCCCTCATGAAGAAGTCGGTTGCTTGCATACCGT
A
Found at i:64896 original size:121 final size:121
Alignment explanation
Indices: 64682--64921 Score: 462
Period size: 121 Copynumber: 2.0 Consensus size: 121
64672 TACCGTAATA
64682 CCCATAGAATTACTATTATCTCTGTATGCTTTGTATCTGTATAATTCTAAAACATCCATTTCATC
1 CCCATAGAATTACTATTATCTCTGTATGCTTTGTATCTGTATAATTCTAAAACATCCATTTCATC
64747 TATTCGAATAACGACACATCTACCACATGTTGAGGCCAATGGTAACCCATGGAATG
66 TATTCGAATAACGACACATCTACCACATGTTGAGGCCAATGGTAACCCATGGAATG
*
64803 CCCATAGAATTACTATTATCTCTTTATGCTTTGTATCTGTATAATTCTAAAACATCCATTTCATC
1 CCCATAGAATTACTATTATCTCTGTATGCTTTGTATCTGTATAATTCTAAAACATCCATTTCATC
*
64868 TATTCGAATAACGACACATCTACCACATGTTGAGGCCAATGTTAACCCATGGAA
66 TATTCGAATAACGACACATCTACCACATGTTGAGGCCAATGGTAACCCATGGAA
64922 AGCCATACTA
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
121 117 1.00
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.34
Consensus pattern (121 bp):
CCCATAGAATTACTATTATCTCTGTATGCTTTGTATCTGTATAATTCTAAAACATCCATTTCATC
TATTCGAATAACGACACATCTACCACATGTTGAGGCCAATGGTAACCCATGGAATG
Found at i:65756 original size:37 final size:36
Alignment explanation
Indices: 65713--65811 Score: 137
Period size: 35 Copynumber: 2.7 Consensus size: 36
65703 CATTTTTCAA
65713 CAAACTTTGAAAAACTATTTTTCAAAGAAACATTTAC
1 CAAACTTTGAAAAAC-ATTTTTCAAAGAAACATTTAC
* * *
65750 CAAACTTTGAAAACCA-TTTTCAAAAAAATATTTAC
1 CAAACTTTGAAAAACATTTTTCAAAGAAACATTTAC
*
65785 CAAACTTTGAAAATCATATTTTCAAAG
1 CAAACTTTGAAAAACAT-TTTTCAAAG
65812 TTGGTTGCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 32 0.58
36 1 0.02
37 22 0.40
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.32
Consensus pattern (36 bp):
CAAACTTTGAAAAACATTTTTCAAAGAAACATTTAC
Found at i:70232 original size:36 final size:36
Alignment explanation
Indices: 70185--70300 Score: 155
Period size: 35 Copynumber: 3.2 Consensus size: 36
70175 TTATCCCATT
* * *
70185 ATCATTTTTC-AACAAACATCTACCAAACCTTGAAAA
1 ATCATTTTTCAAAAAAACATTTACCAAACTTTG-AAA
* *
70221 ATTATTTTTCAAAGAAACATTTACCAAACTTTGAAA
1 ATCATTTTTCAAAAAAACATTTACCAAACTTTGAAA
*
70257 ACCA-TTTTCAAAAAAACATTTACCAAACTTTGAAA
1 ATCATTTTTCAAAAAAACATTTACCAAACTTTGAAA
70292 ATCATTTTT
1 ATCATTTTT
70301 TCCAAGTTGG
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
35 33 0.47
36 18 0.26
37 19 0.27
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (36 bp):
ATCATTTTTCAAAAAAACATTTACCAAACTTTGAAA
Found at i:70262 original size:21 final size:20
Alignment explanation
Indices: 70235--70298 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
70225 TTTTTCAAAG
70235 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
70255 AAACCATTT-TCAAA-----A
1 AAA-CATTTACCAAACTTTGA
70270 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
70290 AAATCATTT
1 AAA-CATTT
70299 TTTCCAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 8 0.24
20 11 0.32
21 10 0.29
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Done.