Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000226.1 Hibiscus syriacus cultivar Beakdansim tig00000396_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: 64442
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1190 original size:22 final size:21
Alignment explanation
Indices: 1148--1187 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1138 GAGTTTATTT
*
1148 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1169 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1188 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:4723 original size:64 final size:65
Alignment explanation
Indices: 4613--4763 Score: 225
Period size: 64 Copynumber: 2.3 Consensus size: 65
4603 TTAATTGAAT
* * *
4613 TTTACATTGATTTATAAATGTTGATTTGTTTAATTGATGAGGAAATAATAATTA-TTTTTTACTT
1 TTTA-ATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTACTT
4677 G
65 G
* *
4678 TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGAT-ATGTAAATAAGAATTATTTTTTTTCTT
1 TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGA-GGAAATAAGAATTATTTTTTTACTT
4742 G
65 G
4743 TTTAATTGATTTGTAAAAGTT
1 TTTAATTGATTTGTAAAAGTT
4764 TATTGTTGTT
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
63 1 0.01
64 43 0.54
65 35 0.44
ACGTcount: A:0.32, C:0.02, G:0.14, T:0.52
Consensus pattern (65 bp):
TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTACTTG
Found at i:4934 original size:20 final size:20
Alignment explanation
Indices: 4906--4944 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4896 GATAATCACA
4906 TTGCAAATTTGACTTTCGCG
1 TTGCAAATTTGACTTTCGCG
*
4926 TTGCGAATTTGACTTTCGC
1 TTGCAAATTTGACTTTCGC
4945 ATCAATCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.41
Consensus pattern (20 bp):
TTGCAAATTTGACTTTCGCG
Found at i:7433 original size:24 final size:24
Alignment explanation
Indices: 7399--7452 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
7389 CTGAAACATC
7399 ATCAAAATCCGAGTATTGACAAAG
1 ATCAAAATCCGAGTATTGACAAAG
* * *
7423 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACAAAG
7447 ATCAAA
1 ATCAAA
7453 TTTCTAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACAAAG
Found at i:8446 original size:19 final size:19
Alignment explanation
Indices: 8405--8467 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
8395 TTAAATTTGT
* *
8405 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTTGAAATTC-A
*
8425 GTTGCGAATTTGAAATTTA
1 GTTGCGAATTTGAAATTCA
8444 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
8463 GTTGC
1 GTTGC
8468 AAAATTGGCA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 24 0.62
20 15 0.38
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:11065 original size:19 final size:20
Alignment explanation
Indices: 11028--11075 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
11018 TTATACATTT
*
11028 TTTTAAAAAAACACATAAA-
1 TTTTAAAATAACACATAAAC
* *
11047 TTTTAAAATAACCCCTAAAC
1 TTTTAAAATAACACATAAAC
*
11067 TTTGAAAAT
1 TTTTAAAAT
11076 TTTCATTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.52, C:0.15, G:0.02, T:0.31
Consensus pattern (20 bp):
TTTTAAAATAACACATAAAC
Found at i:16999 original size:29 final size:29
Alignment explanation
Indices: 16794--17005 Score: 179
Period size: 29 Copynumber: 7.4 Consensus size: 29
16784 GAAAATTACA
* * *
16794 AAAATATCACCTTTATTAAAAATAATTACC
1 AAAATGTCACCTTT-TTCAAAATAATTCCC
* *
16824 AAAATAT--CCTAGTTTT-ACAAATAATTTCC
1 AAAATGTCACCT--TTTTCA-AAATAATTCCC
* * * * *
16853 AAAATGTCATCGTTTTAAAAATAATTACT
1 AAAATGTCACCTTTTTCAAAATAATTCCC
* *
16882 AGAACGTCA-CTGTTTT-AAAA-AATTCCC
1 AAAATGTCACCT-TTTTCAAAATAATTCCC
* *
16909 AAAATGTCTCATTTTTC-AAATAATTCCC
1 AAAATGTCACCTTTTTCAAAATAATTCCC
16937 AAAATGTCACCTTTTTCAAAATAATTCCC
1 AAAATGTCACCTTTTTCAAAATAATTCCC
16966 AAAATGTCACCTTTTTCAAAATAAATT-CC
1 AAAATGTCACCTTTTTCAAAAT-AATTCCC
*
16995 AAAATATCACC
1 AAAATGTCACC
17006 GGGTCGGTCA
Statistics
Matches: 152, Mismatches: 18, Indels: 25
0.78 0.09 0.13
Matches are distributed among these distances:
27 18 0.12
28 32 0.21
29 87 0.57
30 14 0.09
31 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAATGTCACCTTTTTCAAAATAATTCCC
Found at i:17036 original size:10 final size:10
Alignment explanation
Indices: 17021--17048 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
17011 GGTCAACGGG
17021 TCGGACCGTT
1 TCGGACCGTT
17031 TCGGACCGTT
1 TCGGACCGTT
17041 TCGGACCG
1 TCGGACCG
17049 GTCAGATCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.32, G:0.32, T:0.25
Consensus pattern (10 bp):
TCGGACCGTT
Found at i:18069 original size:2 final size:2
Alignment explanation
Indices: 18021--18051 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18011 ATAGAAGTGG
18021 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 T
18052 GTTTTAAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18812 original size:18 final size:18
Alignment explanation
Indices: 18789--18823 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
18779 AGGGATTATC
18789 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
18807 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
18824 AATATTCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:21378 original size:32 final size:32
Alignment explanation
Indices: 21338--21412 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
21328 CCCGAAGGAC
* *
21338 CTATCCATATGTT-CTGAAGAACATAGGTAACA
1 CTATCCATATGTTCCCGAAGAACATAGGCAA-A
* *
21370 CTGTCCATAT-TTCCCGAAGGACATAGGCAAA
1 CTATCCATATGTTCCCGAAGAACATAGGCAAA
21401 CTATCCATATGT
1 CTATCCATATGT
21413 CTCGAAAGAC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 12 0.33
32 24 0.67
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (32 bp):
CTATCCATATGTTCCCGAAGAACATAGGCAAA
Found at i:21424 original size:31 final size:32
Alignment explanation
Indices: 21338--21426 Score: 94
Period size: 31 Copynumber: 2.8 Consensus size: 32
21328 CCCGAAGGAC
*
21338 CTATCCATATGT-TCTG-AAGAACATAGGTAACA
1 CTATCCATATGTCTC-GAAAG-ACATAGGCAACA
* * * *
21370 CTGTCCATATTTCCCGAAGGACATAGGCAA-A
1 CTATCCATATGTCTCGAAAGACATAGGCAACA
21401 CTATCCATATGTCTCGAAAGACATAG
1 CTATCCATATGTCTCGAAAGACATAG
21427 ATAACCCTTG
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
31 23 0.50
32 20 0.43
33 3 0.07
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (32 bp):
CTATCCATATGTCTCGAAAGACATAGGCAACA
Found at i:26473 original size:31 final size:31
Alignment explanation
Indices: 26390--26477 Score: 92
Period size: 31 Copynumber: 2.8 Consensus size: 31
26380 CCCGAAGGAC
*
26390 CTATCCATATGT-TCCGAAGAACATAGGTAACA
1 CTATCCATATGTCT-CGAAG-ACATAGGGAACA
* *
26422 CTGTACATATGTC-CTGAAGACATAGGGAA-A
1 CTATCCATATGTCTC-GAAGACATAGGGAACA
26452 CTATCCATATGTCTCGAAAGACATAG
1 CTATCCATATGTCTCG-AAGACATAG
26478 ATAACCCTCG
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
30 13 0.28
31 20 0.43
32 14 0.30
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (31 bp):
CTATCCATATGTCTCGAAGACATAGGGAACA
Found at i:27942 original size:3 final size:3
Alignment explanation
Indices: 27934--27975 Score: 57
Period size: 3 Copynumber: 13.3 Consensus size: 3
27924 CTTATGTAGT
*
27934 TAA TAA TAA GAA GTGAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA -T-AA TAA TAA TAA TAA TAA TAA TAA TAA T
27976 GAAGTATCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 32 0.91
4 1 0.03
5 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:28687 original size:23 final size:23
Alignment explanation
Indices: 28657--28729 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
28647 GTAAGCTCTA
28657 AGGCCCCGAGGACTTTCTTGGGT
1 AGGCCCCGAGGACTTTCTTGGGT
28680 AGGCCCCGAGGACTTTCTTGGGT
1 AGGCCCCGAGGACTTTCTTGGGT
* *
28703 AGGCCCCGAGAACTTTCTTGGAT
1 AGGCCCCGAGGACTTTCTTGGGT
28726 AGGC
1 AGGC
28730 TCTCAGGCCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (23 bp):
AGGCCCCGAGGACTTTCTTGGGT
Found at i:31084 original size:2 final size:2
Alignment explanation
Indices: 31077--31111 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
31067 TAAATAATTA
31077 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31112 CTTGGATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35445 original size:2 final size:2
Alignment explanation
Indices: 35438--35480 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
35428 TAAATAATTA
35438 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
35480 A
1 A
35481 CTTGGATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35645 original size:16 final size:16
Alignment explanation
Indices: 35624--35689 Score: 69
Period size: 16 Copynumber: 4.1 Consensus size: 16
35614 GTAAATTAAA
35624 TTCGGGTTACTTTCGG
1 TTCGGGTTACTTTCGG
* *
35640 TTCGGGTTAGTTTTGG
1 TTCGGGTTACTTTCGG
* * *
35656 TTAGGGTTGCTTTCGA
1 TTCGGGTTACTTTCGG
* *
35672 TTCAGGTTACTTTTGG
1 TTCGGGTTACTTTCGG
35688 TT
1 TT
35690 GGCTAAAATT
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.09, C:0.12, G:0.30, T:0.48
Consensus pattern (16 bp):
TTCGGGTTACTTTCGG
Found at i:35669 original size:32 final size:32
Alignment explanation
Indices: 35627--35689 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
35617 AATTAAATTC
* * *
35627 GGGTTACTTTCGGTTCGGGTTAGTTTTGGTTA
1 GGGTTACTTTCGATTCAGGTTACTTTTGGTTA
*
35659 GGGTTGCTTTCGATTCAGGTTACTTTTGGTT
1 GGGTTACTTTCGATTCAGGTTACTTTTGGTT
35690 GGCTAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.10, C:0.11, G:0.32, T:0.48
Consensus pattern (32 bp):
GGGTTACTTTCGATTCAGGTTACTTTTGGTTA
Found at i:39999 original size:12 final size:12
Alignment explanation
Indices: 39982--40007 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
39972 ACAGCAATCT
39982 AAAATATGTTCA
1 AAAATATGTTCA
39994 AAAATATGTTCA
1 AAAATATGTTCA
40006 AA
1 AA
40008 TACGTTAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (12 bp):
AAAATATGTTCA
Found at i:44479 original size:15 final size:15
Alignment explanation
Indices: 44459--44488 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
44449 AATGAACCCG
44459 CAGTCACCCCTGCTT
1 CAGTCACCCCTGCTT
44474 CAGTCACCCCTGCTT
1 CAGTCACCCCTGCTT
44489 TCTTCCCGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.13, T:0.27
Consensus pattern (15 bp):
CAGTCACCCCTGCTT
Found at i:50020 original size:26 final size:26
Alignment explanation
Indices: 49981--50035 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
49971 TAGCTGGTAG
*
49981 CTGATTTCAATAGCTGATTTGAACAA
1 CTGATTTCAATAGCTAATTTGAACAA
* * *
50007 CTGATTTGATTAGCTAATTTGAATAA
1 CTGATTTCAATAGCTAATTTGAACAA
50033 CTG
1 CTG
50036 TTTATATAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (26 bp):
CTGATTTCAATAGCTAATTTGAACAA
Found at i:50231 original size:20 final size:20
Alignment explanation
Indices: 50208--50254 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
50198 AATTCCTTAA
50208 GAAAATTAGTGAATAT-TTTT
1 GAAAATT-GTGAATATATTTT
*
50228 GAAAATTTTGAATATATTTT
1 GAAAATTGTGAATATATTTT
*
50248 TAAAATT
1 GAAAATT
50255 TAATATTTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.47
Consensus pattern (20 bp):
GAAAATTGTGAATATATTTT
Found at i:50241 original size:19 final size:20
Alignment explanation
Indices: 50217--50255 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
50207 AGAAAATTAG
50217 TGAATAT-TTTTGAAAATTT
1 TGAATATATTTTGAAAATTT
*
50236 TGAATATATTTTTAAAATTT
1 TGAATATATTTTGAAAATTT
50256 AATATTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (20 bp):
TGAATATATTTTGAAAATTT
Found at i:50737 original size:16 final size:15
Alignment explanation
Indices: 50690--50737 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
50680 ACCAAATAAT
50690 ATTTAA-TTTTTATA
1 ATTTAATTTTTTATA
* *
50704 ATTTAATTTATAATTA
1 ATTTAATTTTTTA-TA
50720 ATTTAATTATTTTATA
1 ATTTAATT-TTTTATA
50736 AT
1 AT
50738 ATAGAAATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
14 6 0.22
15 4 0.15
16 14 0.52
17 3 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTAATTTTTTATA
Found at i:52738 original size:24 final size:24
Alignment explanation
Indices: 52711--52769 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
52701 TGTGTATCAC
52711 ATAAAACTAATATGGAAAAGAA-TA
1 ATAAAACTAATAT-GAAAAGAAGTA
* **
52735 ATAAATACAAATATTCAAAGAAGTA
1 ATAAA-ACTAATATGAAAAGAAGTA
52760 A-AAAACTAAT
1 ATAAAACTAAT
52770 TTAAAATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
23 5 0.17
24 14 0.48
25 10 0.34
ACGTcount: A:0.63, C:0.07, G:0.08, T:0.22
Consensus pattern (24 bp):
ATAAAACTAATATGAAAAGAAGTA
Found at i:55078 original size:228 final size:224
Alignment explanation
Indices: 54676--55126 Score: 494
Period size: 228 Copynumber: 2.0 Consensus size: 224
54666 TGTAAAATGG
* * * ** **
54676 CTCCTCGCTGTTGAGTTAAACCAAAATGCAATCAGTTTTGGATGTGTTTTTAGGTCAAGAATCCT
1 CTCCTCGCTGCTGAGTTAAACCAAAATGCAATCAATTCTGGATGCATTTCCAGGTCAAGAATCCT
* * * * * *
54741 CCGCTATAAATTTGAAACTTGGCCTAAAACTTCAACTGGAGACTAGCTCTTCATCGCTAAGTTAA
66 CCGATATAAAGTTGAAACTTAGCCTAAAACTTCAACTGAAAACTAGCTCATCATCGCTAAGTTAA
* ** * *
54806 TCTAAAATGCAATCGATTCTGAATTGGTATTCAAACCCAATATCCTCTGTCGTGGAGTTGAAATT
131 GCTAAAATGCAATCGATTCTGAATTACTATTCAAACCCAATATCCTCCGTCGTGGAGTAGAAATT
54871 -AACTTCGAGAAAAAAATTTAACTGGAAGATGA
196 GAA-TTC--G-AAAAAATTTAACTGGAAGATGA
* * * *
54903 CTCCTCGCTGCTGAGTTAAGCCAAAATGCAGTCAATTCTGGATGCATTTCCAGGTGAATAATCCT
1 CTCCTCGCTGCTGAGTTAAACCAAAATGCAATCAATTCTGGATGCATTTCCAGGTCAAGAATCCT
* * * *
54968 TC-ATAGTGAAGTTGAAACTTAGCCTGAAAACTTCAACTGAAAACTAGCTCATCGTCGCTTAGTT
66 CCGATA-TAAAGTTGAAACTTAGCCT-AAAACTTCAACTGAAAACTAGCTCATCATCGCTAAGTT
* * * * *** *
55032 AAGCTAGACTGTAGTCGATTCTGAATTAACT-TTCAAATTTAATATCCTCCGTTGTGGAGTAGAA
129 AAGCTAAAATGCAATCGATTCTGAATT-ACTATTCAAACCCAATATCCTCCGTCGTGGAGTAGAA
* *
55096 ATTGAATTCGAAAAGATTTGACTGGAAGATG
193 ATTGAATTCGAAAAAATTTAACTGGAAGATG
55127 TGTAACACCC
Statistics
Matches: 184, Mismatches: 36, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
225 19 0.10
226 3 0.02
227 71 0.39
228 88 0.48
229 3 0.02
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (224 bp):
CTCCTCGCTGCTGAGTTAAACCAAAATGCAATCAATTCTGGATGCATTTCCAGGTCAAGAATCCT
CCGATATAAAGTTGAAACTTAGCCTAAAACTTCAACTGAAAACTAGCTCATCATCGCTAAGTTAA
GCTAAAATGCAATCGATTCTGAATTACTATTCAAACCCAATATCCTCCGTCGTGGAGTAGAAATT
GAATTCGAAAAAATTTAACTGGAAGATGA
Found at i:56469 original size:18 final size:18
Alignment explanation
Indices: 56446--56498 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
56436 CACTGAATAT
56446 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
56464 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
56482 TGTCCCGAAGGGCCACT
1 TGTCCCGAAGGACCACT
56499 GAAAATCCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.25, C:0.34, G:0.25, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:58618 original size:17 final size:19
Alignment explanation
Indices: 58580--58626 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
58570 ATATTCAGAG
58580 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
58599 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
58616 TGCATTCGATG
1 TGCA-TCGATG
58627 TTTAATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:58667 original size:65 final size:63
Alignment explanation
Indices: 58470--58677 Score: 228
Period size: 65 Copynumber: 3.2 Consensus size: 63
58460 GCACCAAGTG
* * *
58470 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATGGATTG-
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT-TCATGATGCATCGATGCATGGA-TGA
*
58534 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGA-G
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCATGGATG
58597 AA
63 -A
* * *
58599 TGCATCGGTGCATGGAATGCATTCGATGTTT-AATTAATTCATCGATGCATCGATGCATGGACTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATTCAT-GATGCATCGATGCATGGA-TG
58663 A
63 A
58664 TGCATC-AGTGCATG
1 TGCATCGA-TGCATG
58678 CCTTTGAATA
Statistics
Matches: 124, Mismatches: 9, Indels: 21
0.81 0.06 0.14
Matches are distributed among these distances:
63 8 0.06
64 48 0.39
65 65 0.52
66 3 0.02
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (63 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGGATGA
Done.