Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002934.1 Hibiscus syriacus cultivar Beakdansim tig00006062_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: 77625
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:1863 original size:12 final size:13
Alignment explanation
Indices: 1846--1878 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1836 ACGTATATGA
1846 TTTTCAAACCT-G
1 TTTTCAAACCTAG
*
1858 TTTTCAAACTTAG
1 TTTTCAAACCTAG
1871 TTTTCAAA
1 TTTTCAAA
1879 ATTTCCCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (13 bp):
TTTTCAAACCTAG
Found at i:19662 original size:21 final size:21
Alignment explanation
Indices: 19637--19676 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
19627 CCGTTAGACA
19637 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
*
19658 GGGGGAATCTGTACCCCCT
1 GGGGGAATCGGTACCCCCT
19677 AGACATTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.30, G:0.38, T:0.17
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTGG
Found at i:20775 original size:21 final size:21
Alignment explanation
Indices: 20658--20775 Score: 71
Period size: 21 Copynumber: 5.7 Consensus size: 21
20648 ACGCGAAATA
**
20658 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
20678 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
*
20698 AAAATCGCAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* ** *
20719 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* * **
20740 AAATTTGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
20761 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
20776 ACACATAAAT
Statistics
Matches: 70, Mismatches: 24, Indels: 7
0.69 0.24 0.07
Matches are distributed among these distances:
19 1 0.01
20 24 0.34
21 43 0.61
22 2 0.03
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:20787 original size:20 final size:20
Alignment explanation
Indices: 20762--20935 Score: 217
Period size: 20 Copynumber: 8.7 Consensus size: 20
20752 CGATTTTCCA
* *
20762 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
20782 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
20802 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
20822 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
20842 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
20862 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
20882 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
20902 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
20923 AAATCGCAACGCG
1 AAATCGCAACGCG
20936 ATATTTAAAG
Statistics
Matches: 132, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
19 1 0.01
20 113 0.86
21 17 0.13
22 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:21276 original size:10 final size:10
Alignment explanation
Indices: 21261--21304 Score: 72
Period size: 10 Copynumber: 4.5 Consensus size: 10
21251 TTTTCATATT
21261 GAAAACTTAA
1 GAAAACTTAA
21271 GAAAACTTAA
1 GAAAACTTAA
*
21281 GAAAA-ATAA
1 GAAAACTTAA
21290 GAAAACTTAA
1 GAAAACTTAA
21300 GAAAA
1 GAAAA
21305 ATAAAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
9 8 0.26
10 23 0.74
ACGTcount: A:0.66, C:0.07, G:0.11, T:0.16
Consensus pattern (10 bp):
GAAAACTTAA
Found at i:21292 original size:19 final size:19
Alignment explanation
Indices: 21268--21308 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
21258 ATTGAAAACT
21268 TAAGAAAACTTAAGAAAAA
1 TAAGAAAACTTAAGAAAAA
21287 TAAGAAAACTTAAGAAAAA
1 TAAGAAAACTTAAGAAAAA
21306 TAA
1 TAA
21309 AAATATACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.68, C:0.05, G:0.10, T:0.17
Consensus pattern (19 bp):
TAAGAAAACTTAAGAAAAA
Found at i:22267 original size:14 final size:14
Alignment explanation
Indices: 22248--22283 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
22238 ATTGTTTAAT
22248 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
22262 TGATTTGTATAAGT
1 TGATTTGTAAAAGA
22276 TGATTTGT
1 TGATTTGT
22284 GTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:22406 original size:19 final size:19
Alignment explanation
Indices: 22390--22487 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
22380 AAAAATGACT
22390 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
22409 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
22428 ATCGCAA--CG--A-GATA
1 ATCGCAATGCGAAATGAAA
22442 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
22461 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
22481 ATCGCAA
1 ATCGCAA
22488 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:22519 original size:53 final size:53
Alignment explanation
Indices: 22390--22505 Score: 216
Period size: 53 Copynumber: 2.2 Consensus size: 53
22380 AAAAATGACT
*
22390 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
22442 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
22495 ATCGCAATGCG
1 ATCGCAATGCG
22506 TTTATAATTT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:22558 original size:19 final size:19
Alignment explanation
Indices: 22534--22698 Score: 189
Period size: 19 Copynumber: 9.4 Consensus size: 19
22524 GATTCTCTCG
22534 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
22553 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
22572 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
22586 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
22605 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
22624 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
22638 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
22658 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
22672 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
22691 TTGCGATT
1 TTGCGATT
22699 CTCTCGTTGC
Statistics
Matches: 124, Mismatches: 6, Indels: 32
0.77 0.04 0.20
Matches are distributed among these distances:
14 23 0.19
16 16 0.13
17 13 0.10
18 3 0.02
19 57 0.46
20 12 0.10
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:22569 original size:52 final size:52
Alignment explanation
Indices: 22512--22670 Score: 309
Period size: 52 Copynumber: 3.0 Consensus size: 52
22502 TGCGTTTATA
22512 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
22564 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
22616 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
22669 AT
1 AT
22671 GTTGGGATTT
Statistics
Matches: 106, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 89 0.84
53 17 0.16
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:22720 original size:33 final size:33
Alignment explanation
Indices: 22512--22712 Score: 212
Period size: 33 Copynumber: 5.9 Consensus size: 33
22502 TGCGTTTATA
22512 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
22545 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
22585 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
22616 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
22649 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTC
22683 ATTTCGCATTGCGATTCTCTCGTTGCGATT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATT
22713 GTAATTTCCG
Statistics
Matches: 138, Mismatches: 16, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
31 9 0.07
32 6 0.04
33 62 0.45
34 29 0.21
35 6 0.04
36 4 0.03
37 2 0.01
38 8 0.06
39 3 0.02
40 9 0.07
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:25227 original size:24 final size:24
Alignment explanation
Indices: 25193--25239 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
25183 CTGAAACATC
25193 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
25217 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
25240 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:26152 original size:20 final size:20
Alignment explanation
Indices: 25922--26151 Score: 237
Period size: 20 Copynumber: 11.5 Consensus size: 20
25912 AAATTTCAGT
* * *
25922 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
* *
25942 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
* *
25962 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
25982 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
26002 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
26022 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
26042 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
26062 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
26082 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
26102 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
26122 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
26142 GTTGCGATTT
1 GTTGCGATTT
26152 TGGAAAATCG
Statistics
Matches: 186, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 185 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:26168 original size:21 final size:21
Alignment explanation
Indices: 26138--26220 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
26128 ATTTTCATAT
*
26138 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
26159 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
26180 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
26201 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
26221 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:26211 original size:42 final size:43
Alignment explanation
Indices: 26118--26216 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
26108 ATTTATGTGT
* *
26118 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
26159 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
26201 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
26217 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:26964 original size:19 final size:20
Alignment explanation
Indices: 26917--26964 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
26907 TCTAAATCCT
*
26917 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* * *
26937 CTTTGAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
26956 TTTTCAAAA
1 TTTTCAAAA
26965 GAAAATCGTT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:28267 original size:20 final size:22
Alignment explanation
Indices: 28242--28301 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
28232 CCGTTAGACA
28242 GGGGGGAATCTGTTCCCCT-TGG
1 GGGGGGAATCTGTTCCCCTCT-G
* *
28264 GGGGGGAATCAG-TACCCTCT-
1 GGGGGGAATCTGTTCCCCTCTG
*
28284 GGGGGGAATCTGTACCCC
1 GGGGGGAATCTGTTCCCC
28302 ATGGACATTC
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 11 0.35
21 8 0.26
22 12 0.39
ACGTcount: A:0.15, C:0.25, G:0.38, T:0.22
Consensus pattern (22 bp):
GGGGGGAATCTGTTCCCCTCTG
Found at i:28286 original size:22 final size:22
Alignment explanation
Indices: 28242--28301 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 22
28232 CCGTTAGACA
* *
28242 GGGGGGAATCTGTTCCCCTTGG
1 GGGGGGAATCAGTACCCCTTGG
28264 GGGGGGAATCAGTA-CCCTCT--
1 GGGGGGAATCAGTACCCCT-TGG
*
28284 GGGGGGAATCTGTACCCC
1 GGGGGGAATCAGTACCCC
28302 ATGGACATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 13 0.39
21 7 0.21
22 13 0.39
ACGTcount: A:0.15, C:0.25, G:0.38, T:0.22
Consensus pattern (22 bp):
GGGGGGAATCAGTACCCCTTGG
Found at i:30836 original size:18 final size:19
Alignment explanation
Indices: 30804--30839 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
30794 TCAAAATTTA
*
30804 AAAACTATTAGAAAATAAT
1 AAAACTATTAAAAAATAAT
30823 AAAA-TATTAAAAAATAA
1 AAAACTATTAAAAAATAA
30840 AAATAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (19 bp):
AAAACTATTAAAAAATAAT
Found at i:31719 original size:3 final size:3
Alignment explanation
Indices: 31711--31756 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
31701 TCTAAGGTGT
*
31711 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AAA AGAA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA
31757 CGTTTTTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:34405 original size:2 final size:2
Alignment explanation
Indices: 34400--34425 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
34390 CTAATAAAAA
34400 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
34426 TTATTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35777 original size:22 final size:22
Alignment explanation
Indices: 35746--35807 Score: 115
Period size: 22 Copynumber: 2.8 Consensus size: 22
35736 AACACTTAAT
*
35746 ATATATAAATATTTTATTTGAA
1 ATATAAAAATATTTTATTTGAA
35768 ATATAAAAATATTTTATTTGAA
1 ATATAAAAATATTTTATTTGAA
35790 ATATAAAAATATTTTATT
1 ATATAAAAATATTTTATT
35808 AATATATATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (22 bp):
ATATAAAAATATTTTATTTGAA
Found at i:53595 original size:23 final size:23
Alignment explanation
Indices: 53505--53595 Score: 69
Period size: 23 Copynumber: 4.0 Consensus size: 23
53495 TTAAGGAATT
* *
53505 TTCTACGTGGTCATTATGG-ACAA
1 TTCTACGTGG-CACTATGGTGCAA
* * *
53528 -TCTTACATGGCACTCTGGTGCAT
1 TTC-TACGTGGCACTATGGTGCAA
* * *
53551 TTCTACGCGGCACTACGATGCAA
1 TTCTACGTGGCACTATGGTGCAA
*
53574 TTCTACGTGGCACTTTGGTGCA
1 TTCTACGTGGCACTATGGTGCA
53596 TTTATATGAG
Statistics
Matches: 50, Mismatches: 15, Indels: 6
0.70 0.21 0.08
Matches are distributed among these distances:
22 8 0.16
23 40 0.80
24 2 0.04
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (23 bp):
TTCTACGTGGCACTATGGTGCAA
Found at i:63126 original size:35 final size:35
Alignment explanation
Indices: 63085--63155 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
63075 AAGAAATAAG
*
63085 TTTATGGGCCCTGCTTTTAATTTAGTTTATTAATA
1 TTTATGGGCCCTGCTTTTAATTTAGTATATTAATA
63120 TTTATGGGCCCTGCTTTTAATTTAGTATATTAATA
1 TTTATGGGCCCTGCTTTTAATTTAGTATATTAATA
63155 T
1 T
63156 AGTTTTTAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.24, C:0.11, G:0.14, T:0.51
Consensus pattern (35 bp):
TTTATGGGCCCTGCTTTTAATTTAGTATATTAATA
Found at i:66226 original size:4 final size:4
Alignment explanation
Indices: 66217--66241 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
66207 GGATATATAA
66217 CTAG CTAG CTAG CTAG CTAG CTAG C
1 CTAG CTAG CTAG CTAG CTAG CTAG C
66242 AAAACTAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (4 bp):
CTAG
Found at i:70628 original size:27 final size:26
Alignment explanation
Indices: 70589--70676 Score: 76
Period size: 31 Copynumber: 3.3 Consensus size: 26
70579 GATTTTTTTA
70589 ATTAATTTTTT--TTATTAAA-AAAAT
1 ATTAATTTTTTAATT-TTAAATAAAAT
*
70613 -TAAATTTTTTAATTTTAAATAAAAT
1 ATTAATTTTTTAATTTTAAATAAAAT
*
70638 ATTAATTTTTTATTTAAAATTTAAATAAAAT
1 ATTAA---TTT-TTT-AATTTTAAATAAAAT
70669 ATTAATTT
1 ATTAATTT
70677 AATCTTATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
23 9 0.17
24 5 0.10
25 7 0.13
26 3 0.06
28 3 0.06
29 3 0.06
30 3 0.06
31 19 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
ATTAATTTTTTAATTTTAAATAAAAT
Found at i:70630 original size:24 final size:22
Alignment explanation
Indices: 70588--70656 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 22
70578 AGATTTTTTT
70588 AATTAATTTTTT-TTATTAAAAA
1 AATTAATTTTTTATT-TTAAAAA
70610 AATTAAATTTTTTAATTTTAAATAAA
1 AATT-AATTTTTT-ATTTT-AA-AAA
70636 ATATTAATTTTTTA-TTTAAAA
1 A-ATTAATTTTTTATTTTAAAA
70657 TTTAAATAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
22 6 0.15
23 10 0.24
24 5 0.12
25 5 0.12
26 12 0.29
27 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATTAATTTTTTATTTTAAAAA
Found at i:70664 original size:26 final size:26
Alignment explanation
Indices: 70606--70657 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
70596 TTTTTTATTA
* *
70606 AAAAAATTAAATTTTTTAATTTTAAAT
1 AAAATATT-AATTTTTTAATTTAAAAT
70633 AAAATATTAATTTTTT-ATTTAAAAT
1 AAAATATTAATTTTTTAATTTAAAAT
70658 TTAAATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 8 0.35
26 8 0.35
27 7 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
AAAATATTAATTTTTTAATTTAAAAT
Found at i:72741 original size:71 final size:71
Alignment explanation
Indices: 72644--72789 Score: 213
Period size: 71 Copynumber: 2.1 Consensus size: 71
72634 GAATTGTTAT
* *
72644 TAAGCATCTCATCGTGATTAAATGACTGCTGTCTAATTTCATAGTTCAAACTGGGAGACATTTCA
1 TAAGCATCTCATCGTGATCAAATGACTGCTGTCTAATTTCATAGCTCAAACTGGGAGACATTTCA
72709 GGAGTG
66 GGAGTG
* * * *
72715 TAAGCAT-TACATCTTGATCAACTGACTGCTGTCTAATTTCATAGCTCAAACTGGGGGACATTTG
1 TAAGCATCT-CATCGTGATCAAATGACTGCTGTCTAATTTCATAGCTCAAACTGGGAGACATTTC
*
72779 TGGAGTG
65 AGGAGTG
72786 TAAG
1 TAAG
72790 TAACGTCGGT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
70 1 0.01
71 66 0.99
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (71 bp):
TAAGCATCTCATCGTGATCAAATGACTGCTGTCTAATTTCATAGCTCAAACTGGGAGACATTTCA
GGAGTG
Found at i:72885 original size:37 final size:37
Alignment explanation
Indices: 72831--72911 Score: 121
Period size: 37 Copynumber: 2.2 Consensus size: 37
72821 TGGCAATCAA
72831 CTTTG-AAAAATATTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAAATATTTTTCAAAGTTTGGTAAATGTTT
* *
72867 CTTTGAAAAAATGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAATATTTTTCAAAGTTTGGTAAATGTTT
*
72904 -GTTGAAAA
1 CTTTGAAAA
72912 TAGGAATGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
36 12 0.29
37 29 0.71
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAAATATTTTTCAAAGTTTGGTAAATGTTT
Found at i:77097 original size:54 final size:55
Alignment explanation
Indices: 77015--77138 Score: 207
Period size: 55 Copynumber: 2.3 Consensus size: 55
77005 AGGCGTTCAG
*
77015 ATGATTCATGAATAAGAACATCCGATGAATGAAG-AATTTGAACCTGACTGAAGA
1 ATGATTCATGAAGAAGAACATCCGATGAATGAAGAAATTTGAACCTGACTGAAGA
77069 ATGATTCATGAAGAAGGAA-ATCCGATGAATGAAGAAATTTGAACCTGACTGAAGA
1 ATGATTCATGAAGAA-GAACATCCGATGAATGAAGAAATTTGAACCTGACTGAAGA
*
77124 ACGATTCATGAAGAA
1 ATGATTCATGAAGAA
77139 TGACAACCGA
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
54 29 0.44
55 37 0.56
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.23
Consensus pattern (55 bp):
ATGATTCATGAAGAAGAACATCCGATGAATGAAGAAATTTGAACCTGACTGAAGA
Done.