Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001792.1 Hibiscus syriacus cultivar Beakdansim tig00003620_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: 47614
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2090 original size:27 final size:28
Alignment explanation
Indices: 2052--2116 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
2042 TATAACTCAA
2052 AAACCCAAAATCA-AAACCCCATTCGTG
1 AAACCCAAAATCAGAAACCCCATTCGTG
*
2079 AAACCCAAAATCAGAACCCCCATTCGTG
1 AAACCCAAAATCAGAAACCCCATTCGTG
2107 AAACCCAAAA
1 AAACCCAAAA
2117 AACCTCTCTG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 13 0.36
28 23 0.64
ACGTcount: A:0.46, C:0.34, G:0.08, T:0.12
Consensus pattern (28 bp):
AAACCCAAAATCAGAAACCCCATTCGTG
Found at i:7897 original size:25 final size:25
Alignment explanation
Indices: 7852--7921 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
7842 AAAGCCCGAA
*
7852 GCTTTGTTTATTTTTTTCTTTCGATT
1 GCTTTGGTTA-TTTTTTCTTTCGATT
* *
7878 GCTTTGGTTATTTTTGCTTTCGGTT
1 GCTTTGGTTATTTTTTCTTTCGATT
*
7903 GCCTT-GTTATTTTTTCTTT
1 GCTTTGGTTATTTTTTCTTT
7922 TGGTTGTGGC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
24 13 0.33
25 17 0.44
26 9 0.23
ACGTcount: A:0.06, C:0.13, G:0.16, T:0.66
Consensus pattern (25 bp):
GCTTTGGTTATTTTTTCTTTCGATT
Found at i:7911 original size:24 final size:25
Alignment explanation
Indices: 7863--7927 Score: 87
Period size: 24 Copynumber: 2.6 Consensus size: 25
7853 CTTTGTTTAT
* *
7863 TTTTTTCTTTCGATTGCTTTGGTTA
1 TTTTTTCTTTCGGTTGCCTTGGTTA
*
7888 TTTTTGCTTTCGGTTGCCTT-GTTA
1 TTTTTTCTTTCGGTTGCCTTGGTTA
*
7912 TTTTTTCTTTTGGTTG
1 TTTTTTCTTTCGGTTG
7928 TGGCTTTGCT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
24 18 0.51
25 17 0.49
ACGTcount: A:0.05, C:0.12, G:0.18, T:0.65
Consensus pattern (25 bp):
TTTTTTCTTTCGGTTGCCTTGGTTA
Found at i:8432 original size:2 final size:2
Alignment explanation
Indices: 8425--8685 Score: 166
Period size: 2 Copynumber: 137.5 Consensus size: 2
8415 CAAATGAATA
* * * *
8425 AT AT AT AT AT AT AT AT AT A- AT AT AT GT GT -T AT AA AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
8465 -T AT A- AC AA AT AA AA AT AT AT A- AT AT AC ACT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* *
8505 AT ACT AT A- AT AT A- AA AT AA AT AT A- AT A- AT AT AT AT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8544 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * * * *
8586 AT AA AT AT ACT AT A- AC AT AT AA AA AT AT A- AT AT AT -T AT GT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
8626 A- AT AT AA AT AT GCT AT A- AT AT AT A- AT -T A- AT AT AT -T AT
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8663 AT AT AT AT AT ACT AT AT -T AT AT A
1 AT AT AT AT AT A-T AT AT AT AT AT A
8686 AATTTACTAC
Statistics
Matches: 208, Mismatches: 25, Indels: 52
0.73 0.09 0.18
Matches are distributed among these distances:
1 20 0.10
2 178 0.86
3 10 0.05
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:8633 original size:109 final size:111
Alignment explanation
Indices: 8421--8686 Score: 272
Period size: 107 Copynumber: 2.5 Consensus size: 111
8411 AAAACAAATG
* * * *
8421 AATAATATATATATATATATATA-ATATATGTGT-TATAAATAAAT-TATAACAAATAAAAATAT
1 AATAATATATATATATATATATATATATATATATATATATATATATATATAACAAATAAAAATAT
* *
8483 ATAATATACACTATATATATATATACTATAATATAAAATAAATAT-
66 ATAATATACACTATAAAAATATATACTATAATATAAAATAAATATC
* *
8528 AATAATATATATATATATATATATATATATATATATATATATATATATACTATA-TAATATAAAT
1 AATAATATATATATATATATATATATATATATATATATATATATATATA-TA-ACAAATAAAAAT
* * *
8592 ATACT-ATA-ACA-TATAAAAATATAATA-TATTATGTAATATAAATATGC
64 ATA-TAATATACACTATAAAAATAT-ATACTATAATATAAAATAAATAT-C
*
8639 TATAATATATA-AT-TA-ATATAT-TATATATATATATACTATAT-TATATAA
1 AATAATATATATATATATATATATATATATATATATATA-TATATATATATAA
8687 ATTTACTACA
Statistics
Matches: 137, Mismatches: 12, Indels: 22
0.80 0.07 0.13
Matches are distributed among these distances:
105 1 0.01
106 2 0.01
107 41 0.30
108 19 0.14
109 36 0.26
110 10 0.07
111 26 0.19
112 2 0.01
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (111 bp):
AATAATATATATATATATATATATATATATATATATATATATATATATATAACAAATAAAAATAT
ATAATATACACTATAAAAATATATACTATAATATAAAATAAATATC
Found at i:8642 original size:23 final size:23
Alignment explanation
Indices: 8616--8673 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 23
8606 AAAAATATAA
* *
8616 TATATTATGTAATATAA-ATATGC
1 TATAATATATAAT-TAATATATGC
**
8639 TATAATATATAATTAATATATTA
1 TATAATATATAATTAATATATGC
8662 TATATATATATA
1 TATA-ATATATA
8674 CTATATTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 3 0.10
23 19 0.66
24 7 0.24
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (23 bp):
TATAATATATAATTAATATATGC
Found at i:9559 original size:25 final size:25
Alignment explanation
Indices: 9530--9595 Score: 96
Period size: 25 Copynumber: 2.6 Consensus size: 25
9520 AAGCCCCAAA
* *
9530 CTTTGTTGATTTTTTCCTTCGGTTG
1 CTTTGTTTATTTTTGCCTTCGGTTG
*
9555 CTTTGTTTATTTTTGCTTTCGGTTG
1 CTTTGTTTATTTTTGCCTTCGGTTG
*
9580 CTTTATTTATTTTTGC
1 CTTTGTTTATTTTTGC
9596 TTTCAGTTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.06, C:0.14, G:0.17, T:0.64
Consensus pattern (25 bp):
CTTTGTTTATTTTTGCCTTCGGTTG
Found at i:9596 original size:25 final size:25
Alignment explanation
Indices: 9538--9599 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
9528 AACTTTGTTG
* * *
9538 ATTTTTTCCTTCGGTTGCTTTGTTT
1 ATTTTTGCTTTCGGTTGCTTTATTT
9563 ATTTTTGCTTTCGGTTGCTTTATTT
1 ATTTTTGCTTTCGGTTGCTTTATTT
9588 ATTTTTGCTTTC
1 ATTTTTGCTTTC
9600 AGTTTGTGGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.06, C:0.15, G:0.15, T:0.65
Consensus pattern (25 bp):
ATTTTTGCTTTCGGTTGCTTTATTT
Found at i:10125 original size:2 final size:2
Alignment explanation
Indices: 10118--10145 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10108 AAGCAAATGA
10118 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10146 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10150 original size:2 final size:2
Alignment explanation
Indices: 10145--10201 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
10135 TATATATATA
10145 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
10187 TA TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG T
10202 TATAAATAAG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.02, C:0.00, G:0.47, T:0.51
Consensus pattern (2 bp):
TG
Found at i:10235 original size:2 final size:2
Alignment explanation
Indices: 10219--10432 Score: 146
Period size: 2 Copynumber: 114.5 Consensus size: 2
10209 AAGTTATAAC
* *
10219 AT AT A- AT AA AT AT AT AT AT AT TT AT AT ACT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * *
10261 AT AT AT AT AT AT AT AT A- AT AG A- AT AT AG A- AT AA AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
10299 AT A- AT AT A- AT AT AT AT AT ACT AT AT A- AT AT AA AT AT ACT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT
* *
10340 A- AC AT AT ACT A- AT AT A- AT AT AT -T AT AT A- AT AT AA AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
10378 ACT AT A- AT AT AT A- AT -T A- AT AA AT A- AT AT -T AT A- AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10414 AT AT AT ACT AT AT -T AT AT A
1 AT AT AT A-T AT AT AT AT AT A
10433 AATTTACTAC
Statistics
Matches: 170, Mismatches: 15, Indels: 54
0.71 0.06 0.23
Matches are distributed among these distances:
1 21 0.12
2 137 0.81
3 12 0.07
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (2 bp):
AT
Found at i:10254 original size:23 final size:23
Alignment explanation
Indices: 10219--10471 Score: 155
Period size: 23 Copynumber: 11.3 Consensus size: 23
10209 AAGTTATAAC
* *
10219 ATATAATAAATATATATATATTT
1 ATATAATATATATATATATATAT
*
10242 ATATACTATATATATATATATAT
1 ATATAATATATATATATATATAT
*
10265 ATAT-ATATATATA-ATAGA-AT
1 ATATAATATATATATATATATAT
* *
10285 ATAGAATAAATATA-ATA-ATAT
1 ATATAATATATATATATATATAT
10306 A-AT-ATATATATACTATATA-AT
1 ATATAATATATATA-TATATATAT
*
10327 ATA-AATATACTATA-ACATATACT
1 ATATAATATA-TATATATATATA-T
*
10350 AATATAATATAT-TATATAATATAA
1 -ATATAATATATATATAT-ATATAT
*
10374 ATATACTATA-ATATATA-AT-T
1 ATATAATATATATATATATATAT
10394 A-ATAA-ATA-ATATTATAATATAT
1 ATATAATATATATA-TAT-ATATAT
* * *
10416 ATATACTATAT-TATATAAATTT
1 ATATAATATATATATATATATAT
* * *
10438 ACTACACATAAAAACTATATATATAT
1 A-TATA-ATATATA-TATATATATAT
10464 ATATAATA
1 ATATAATA
10472 AAAAAGATCG
Statistics
Matches: 179, Mismatches: 25, Indels: 51
0.70 0.10 0.20
Matches are distributed among these distances:
18 6 0.03
19 14 0.08
20 9 0.05
21 32 0.18
22 24 0.13
23 54 0.30
24 16 0.09
25 14 0.08
26 10 0.06
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (23 bp):
ATATAATATATATATATATATAT
Found at i:10410 original size:103 final size:101
Alignment explanation
Indices: 10242--10468 Score: 289
Period size: 103 Copynumber: 2.2 Consensus size: 101
10232 ATATATATTT
* *
10242 ATATACTATATATATATATATATATATATATATATAATAGAATATAGAATAAATATAATAATATA
1 ATATACTATATATATATATATATATATATAAATATAATAGAATATAGAATAAAAATAATAATATA
10307 ATATATATATACTATATAATATAAATATACTATAAC
66 ATATATATATACTATATAATATAAATATACTATAAC
* * * *
10343 ATATACTA-ATATA-ATATATTATATAATATAAATATACTATAATATATAATTAATAAATAATAT
1 ATATACTATATATATATATA-TATAT-ATATAAATATAATAGAATATAGAA-TAA-AAATAATAA
* * *
10406 TATAATATATATATACTATATTATATAAATTTACTA-CAC
62 TATAATATATATATACTATATAATATAAATATACTATAAC
*
10445 ATAAAAACTATATATATATATATA
1 AT--ATACTATATATATATATATA
10469 ATAAAAAAGA
Statistics
Matches: 108, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
99 5 0.05
100 10 0.09
101 28 0.26
102 7 0.06
103 41 0.38
104 5 0.05
105 7 0.06
106 5 0.05
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.41
Consensus pattern (101 bp):
ATATACTATATATATATATATATATATATAAATATAATAGAATATAGAATAAAAATAATAATATA
ATATATATATACTATATAATATAAATATACTATAAC
Found at i:11848 original size:5 final size:5
Alignment explanation
Indices: 11840--12061 Score: 138
Period size: 5 Copynumber: 43.2 Consensus size: 5
11830 AAAACAAAGG
* **
11840 AATAT AATAT -ATAT -ATAT AATAT ATATGT GTTAT AGATA- AACTAT
1 AATAT AATAT AATAT AATAT AATAT A-ATAT AATAT A-ATAT AA-TAT
*
11885 AACATAT AATA- AATAT AATAT -ATAT -ATAT ATATAT ACTAT AATAT
1 -A-ATAT AATAT AATAT AATAT AATAT AATAT A-ATAT AATAT AATAT
* *
11930 AATAT AAAAT AAATAT AATAT ATATAT ATATAT AATAT AAATAT ACTAT
1 AATAT AATAT -AATAT AATAT A-ATAT A-ATAT AATAT -AATAT AATAT
* * *
11979 AACAT -ATAAT AATAT AATAT ATTAT AATAT AAATAT ACTAT AATAT -ATAATT
1 AATAT AAT-AT AATAT AATAT AATAT AATAT -AATAT AATAT AATAT AAT-A-T
* * *
12031 AATA- AATAAT ATTAT AATAT ACTAT ATTAT A
1 AATAT AAT-AT AATAT AATAT AATAT AATAT A
12062 TAAATTTACT
Statistics
Matches: 174, Mismatches: 22, Indels: 42
0.73 0.09 0.18
Matches are distributed among these distances:
4 27 0.16
5 98 0.56
6 42 0.24
7 6 0.03
8 1 0.01
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (5 bp):
AATAT
Found at i:11851 original size:2 final size:2
Alignment explanation
Indices: 11841--12063 Score: 118
Period size: 2 Copynumber: 121.5 Consensus size: 2
11831 AAACAAAGGA
* * * *
11841 AT AT A- AT AT AT AT AT AT A- AT AT AT AT GT GT -T AT AG AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
11880 ACT AT A- AC AT AT A- AT AA AT AT A- AT AT AT AT AT AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
11920 ACT AT A- AT AT A- AT AT A- AA AT AA AT AT A- AT AT AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
11959 AT AT A- AT AT AA AT AT ACT AT A- AC AT AT A- AT A- AT AT A- AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
*
11997 AT AT -T AT A- AT AT AA AT AT ACT AT A- AT AT AT A- AT -T A- AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
*
12034 AA AT A- AT AT -T AT A- AT AT ACT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A
12064 AATTTACTAC
Statistics
Matches: 173, Mismatches: 18, Indels: 60
0.69 0.07 0.24
Matches are distributed among these distances:
1 25 0.14
2 139 0.80
3 9 0.05
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (2 bp):
AT
Found at i:16200 original size:13 final size:13
Alignment explanation
Indices: 16182--16236 Score: 83
Period size: 13 Copynumber: 4.2 Consensus size: 13
16172 TGCGTCATAA
16182 ATTTATGACGTGC
1 ATTTATGACGTGC
* *
16195 ATTTATGACATAC
1 ATTTATGACGTGC
16208 ATTTATGACGTGC
1 ATTTATGACGTGC
*
16221 ATTTATGACGTTC
1 ATTTATGACGTGC
16234 ATT
1 ATT
16237 GAGCATCATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (13 bp):
ATTTATGACGTGC
Found at i:16236 original size:26 final size:26
Alignment explanation
Indices: 16177--16229 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
16167 AACTGTGCGT
*
16177 CATAAATTTATGACGTGCATTTATGA
1 CATACATTTATGACGTGCATTTATGA
16203 CATACATTTATGACGTGCATTTATGA
1 CATACATTTATGACGTGCATTTATGA
16229 C
1 C
16230 GTTCATTGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (26 bp):
CATACATTTATGACGTGCATTTATGA
Found at i:20843 original size:14 final size:14
Alignment explanation
Indices: 20824--20858 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
20814 AAATTAGCGA
20824 GTGTCATCGTTCGT
1 GTGTCATCGTTCGT
20838 GTGTCATCGTTCGT
1 GTGTCATCGTTCGT
20852 GTGTCAT
1 GTGTCAT
20859 TAAAGGTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.09, C:0.20, G:0.29, T:0.43
Consensus pattern (14 bp):
GTGTCATCGTTCGT
Found at i:32933 original size:2 final size:2
Alignment explanation
Indices: 32923--33147 Score: 122
Period size: 2 Copynumber: 122.5 Consensus size: 2
32913 AAACAAATAA
* *
32923 AT AT A- AT AT AT AT TT A- AT A- AT AT A- AT AT A- AC AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
32959 AT A- AC AT AT A- AT AA AT AT A- AT AT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
32998 AT AT AT ACT AT AT -T AT AT AA AT AT A- AT GT A- AC AT AT A- AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
33037 -T AT AT A- AT AT AT AT AT AT ACT AT GT A- AT AT A- AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
*
33076 AT ACT AT A- AT AT AT A- AT AA AT A- AGT A- AT AT -T AT A- AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
*
33114 AT AT AT AT AT ACT AT AT -T AT AT AA AT AT A- AT AT A
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A
33148 CATAAAAACT
Statistics
Matches: 172, Mismatches: 21, Indels: 60
0.68 0.08 0.24
Matches are distributed among these distances:
1 25 0.15
2 138 0.80
3 9 0.05
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:32987 original size:6 final size:6
Alignment explanation
Indices: 32923--33147 Score: 122
Period size: 5 Copynumber: 40.8 Consensus size: 6
32913 AAACAAATAA
* * *
32923 ATATA- ATATAT ATTTA- ATA-AT ATA-AT ATA-AC ATAT-T ATA-AC
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* *
32964 ATATA- ATAAAT ATA-AT ATGTAT ATATAT ATATAT ATATAT ACTATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT A-TATAT
* * *
33011 -TATAT AAATAT A-ATGT A-ACAT ATA-AT -TATAT A-ATAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * *
33053 ATACTAT GTA-AT ATA-AT ATAAAT ATACTAT A-ATAT ATA-AT AAATA-
1 ATA-TAT ATATAT ATATAT ATATAT ATA-TAT ATATAT ATATAT ATATAT
*
33098 AGTA-AT AT-TAT A-ATAT ATATAT ATATACT ATAT-T ATATAA ATATA-
1 A-TATAT ATATAT ATATAT ATATAT ATATA-T ATATAT ATATAT ATATAT
33143 ATATA
1 ATATA
33148 CATAAAAACT
Statistics
Matches: 177, Mismatches: 18, Indels: 50
0.72 0.07 0.20
Matches are distributed among these distances:
4 3 0.02
5 91 0.51
6 65 0.37
7 18 0.10
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (6 bp):
ATATAT
Found at i:32996 original size:50 final size:54
Alignment explanation
Indices: 32918--33145 Score: 211
Period size: 56 Copynumber: 4.1 Consensus size: 54
32908 TTAAAAAACA
* *
32918 AATAAATATAATATATATTTA-ATA-ATATA-ATATAAC-ATATTATA-ACATAT
1 AATAAATATAATATATATATATATATATATATATAT-ACTATATTATATAAATAT
*
32968 AATAAATATAATATGTATATATATATATATATATATACTATATTATATAAATAT
1 AATAAATATAATATATATATATATATATATATATATACTATATTATATAAATAT
* *
33022 AATGTAACATATAAT-TATATA-ATATATATATATACTAT-GTAATATAATATAAATAT
1 AA--TAA-ATATAATATATATATATATATATATATA-TATACT-ATATTATATAAATAT
33078 ACTATAATATATAATAAATAAGTAATATTATAATATATATATATATACTATATTATATAAATAT
1 A--ATAA-ATATAAT--AT-A-T-ATA-TAT-ATATATATATATATACTATATTATATAAATAT
33142 AATA
1 AATA
33146 TACATAAAAA
Statistics
Matches: 147, Mismatches: 9, Indels: 32
0.78 0.05 0.17
Matches are distributed among these distances:
50 19 0.13
51 3 0.02
52 7 0.05
53 12 0.08
54 7 0.05
55 14 0.10
56 36 0.24
57 7 0.05
58 1 0.01
59 1 0.01
60 1 0.01
61 1 0.01
62 6 0.04
64 20 0.14
65 12 0.08
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (54 bp):
AATAAATATAATATATATATATATATATATATATATACTATATTATATAAATAT
Found at i:33052 original size:51 final size:48
Alignment explanation
Indices: 32922--33148 Score: 176
Period size: 46 Copynumber: 4.8 Consensus size: 48
32912 AAAACAAATA
* *
32922 AATATAATATATA-TTTAATAATATAATATAACATATTATAAC-ATATAATA-
1 AATATAA-ATATACTATAAT-ATATAATAT-ATATA-TAT-ACTATATAATAT
* *
32972 AATAT-AATAT-GTAT-ATATAT-ATATATATATATACTATATTATAT
1 AATATAAATATACTATAATATATAATATATATATATACTATATAATAT
* *
33016 AA-ATATAATGTAACATATAATTATATAATATATATATATACTATGTAATAT
1 AATATA-AATAT-AC-TATAA-TATATAATATATATATATACTATATAATAT
*
33067 AATATAAATATACTATAATATATAATA-A-ATA-AGTAATATTATAATAT
1 AATATAAATATACTATAATATATAATATATATATA-TACTA-TATAATAT
* *
33114 -ATATATATATACTATATTATATAA-ATATA-ATATAC
1 AATATAAATATACTATAATATATAATATATATATATAC
33149 ATAAAAACTA
Statistics
Matches: 147, Mismatches: 13, Indels: 38
0.74 0.07 0.19
Matches are distributed among these distances:
42 2 0.01
43 12 0.08
44 6 0.04
45 10 0.07
46 37 0.25
47 12 0.08
48 18 0.12
49 7 0.05
50 12 0.08
51 28 0.19
52 3 0.02
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (48 bp):
AATATAAATATACTATAATATATAATATATATATATACTATATAATAT
Found at i:33161 original size:46 final size:46
Alignment explanation
Indices: 33062--33167 Score: 108
Period size: 46 Copynumber: 2.3 Consensus size: 46
33052 TATACTATGT
* * *
33062 AATATAATATAAATATACTATAATATATAATAAATAAGTAATATTAT
1 AATAT-ATATAAATATACTATAATATATAATAAATAAGTAACATAAA
* * *
33109 AATATATATATATATACTATATTATATAA-ATATAA-TATACATAAA
1 AATATATATAAATATACTATAATATATAATAAATAAGTA-ACATAAA
33154 AACTATATAATAAA
1 AA-TATAT-ATAAA
33168 AAGATTGGAC
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
44 2 0.04
45 11 0.22
46 27 0.55
47 9 0.18
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.38
Consensus pattern (46 bp):
AATATATATAAATATACTATAATATATAATAAATAAGTAACATAAA
Found at i:33161 original size:120 final size:120
Alignment explanation
Indices: 32940--33165 Score: 327
Period size: 120 Copynumber: 1.9 Consensus size: 120
32930 ATATATTTAA
32940 TAATATAATATAACATATTATAACATATAATAAATATAATATGTATATATATATATATATATATA
1 TAATATAATATAACATATTATAACATATAATAAATATAATA-GTATATATATATATATATATATA
* * *
33005 CTATATTATATAAATATAATGTAACATATAATTATATAATATATATATATACTATG
65 CTATATTATATAAATATAATATAACATAAAACTATATAATATATATATATACTATG
*
33061 TAATATAATATAA-ATATACTATAATATATAATAAATAAGTAATA-T-TATA-ATATATATATAT
1 TAATATAATATAACATAT--TATAACATATAATAAAT-A-TAATAGTATATATATATATATATAT
33122 ATACTATATTATATAAATATAATAT-ACATAAAAACTATATAATA
62 ATACTATATTATATAAATATAATATAACAT-AAAACTATATAATA
33166 AAAAGATTGG
Statistics
Matches: 96, Mismatches: 4, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
119 4 0.04
120 52 0.54
121 17 0.18
122 17 0.18
123 1 0.01
124 5 0.05
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (120 bp):
TAATATAATATAACATATTATAACATATAATAAATATAATAGTATATATATATATATATATATAC
TATATTATATAAATATAATATAACATAAAACTATATAATATATATATATACTATG
Found at i:43529 original size:20 final size:19
Alignment explanation
Indices: 43495--43533 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
43485 CAAACATTAA
*
43495 ATTTACACCGGTAGAACAT
1 ATTTACACCGATAGAACAT
43514 ATTTATCACCGATAGAACAT
1 ATTTA-CACCGATAGAACAT
43534 GAAATAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (19 bp):
ATTTACACCGATAGAACAT
Done.