Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000306.1 Hibiscus syriacus cultivar Beakdansim tig00000575_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: 74953
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:3791 original size:31 final size:32
Alignment explanation
Indices: 3745--3816 Score: 110
Period size: 31 Copynumber: 2.3 Consensus size: 32
3735 ATAAATAAAA
* *
3745 ATAAAATATTAATTTTAACCTCTAAATTTTAT
1 ATAAAATATTAATTTTAACCTATAAATTTTAG
*
3777 ATAAAATATT-ATTTTATCCTATAAATTTTAG
1 ATAAAATATTAATTTTAACCTATAAATTTTAG
3808 ATAAAATAT
1 ATAAAATAT
3817 CGATTTAACC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
31 27 0.73
32 10 0.27
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (32 bp):
ATAAAATATTAATTTTAACCTATAAATTTTAG
Found at i:10129 original size:2 final size:2
Alignment explanation
Indices: 10041--10109 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
10031 ATAAAACTAA
10041 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
10083 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 A
10110 GAATGAATCA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11431 original size:11 final size:11
Alignment explanation
Indices: 11415--11501 Score: 63
Period size: 11 Copynumber: 7.8 Consensus size: 11
11405 TACGACCTCC
11415 AAATAAAGTA-T
1 AAATAAA-TAGT
11426 AAATAAATAGT
1 AAATAAATAGT
* *
11437 AAATATATAAAT
1 AAATAAAT-AGT
11449 AAATAAATAGT
1 AAATAAATAGT
*
11460 AAAT-TATA-T
1 AAATAAATAGT
* *
11469 AATTATAATAAAT
1 AAATA-AAT-AGT
11482 AAATAAATAGT
1 AAATAAATAGT
*
11493 AAATCAATA
1 AAATAAATA
11502 TTATATACTT
Statistics
Matches: 60, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
9 4 0.07
10 5 0.08
11 33 0.55
12 13 0.22
13 5 0.08
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.31
Consensus pattern (11 bp):
AAATAAATAGT
Found at i:11433 original size:4 final size:4
Alignment explanation
Indices: 11424--11490 Score: 57
Period size: 4 Copynumber: 16.8 Consensus size: 4
11414 CAAATAAAGT
* * * *
11424 ATAA ATAA AT-A GTAA ATAT ATAA ATAA ATAA AT-A GTAA ATTAT ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A-TAA ATAA
*
11471 TTATA ATAA ATAA ATAA ATA
1 ATA-A ATAA ATAA ATAA ATA
11491 GTAAATCAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
3 4 0.08
4 39 0.80
5 6 0.12
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (4 bp):
ATAA
Found at i:11451 original size:23 final size:24
Alignment explanation
Indices: 11424--11482 Score: 93
Period size: 23 Copynumber: 2.5 Consensus size: 24
11414 CAAATAAAGT
11424 ATAAATAAATAGTAAA-TATATAA
1 ATAAATAAATAGTAAATTATATAA
11447 ATAAATAAATAGTAAATTATATAA
1 ATAAATAAATAGTAAATTATATAA
*
11471 TTATAATAAATA
1 ATA-AATAAATA
11483 AATAAATAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 16 0.48
24 9 0.27
25 8 0.24
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (24 bp):
ATAAATAAATAGTAAATTATATAA
Found at i:15533 original size:3 final size:3
Alignment explanation
Indices: 15525--15551 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
15515 CACTCTTTCT
15525 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
15552 ACTGCTAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:20074 original size:17 final size:18
Alignment explanation
Indices: 20048--20084 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
20038 ACACGAGGTC
20048 CACCACCTTCT-GAATAT
1 CACCACCTTCTGGAATAT
*
20065 CACCAGCTTCTGGAATAT
1 CACCACCTTCTGGAATAT
20083 CA
1 CA
20085 GAAGTTGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.30, C:0.32, G:0.11, T:0.27
Consensus pattern (18 bp):
CACCACCTTCTGGAATAT
Found at i:28240 original size:29 final size:27
Alignment explanation
Indices: 28167--28240 Score: 69
Period size: 31 Copynumber: 2.6 Consensus size: 27
28157 TAAGGTAACT
* * *
28167 TTTTAATATATTCTTTAAAATTTATAA
1 TTTTAATATATTATTTAAAATCTAAAA
28194 TTATTAATA-ATGTAATTTAAAAAATCTAAAA
1 TT-TTAATATAT-T-ATTT--AAAATCTAAAA
28225 TTTTAATATATTATTT
1 TTTTAATATATTATTT
28241 TTTTTAGTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
27 4 0.11
28 7 0.18
29 7 0.18
30 7 0.18
31 13 0.34
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (27 bp):
TTTTAATATATTATTTAAAATCTAAAA
Found at i:29741 original size:3 final size:3
Alignment explanation
Indices: 29733--29778 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
29723 AGTTTCTTTG
* *
29733 TAA TAA TAA TAA TAA CAA CAA TAA TAA TAA TAA TATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
29779 ATATATATAT
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:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:30578 original size:11 final size:11
Alignment explanation
Indices: 30562--30587 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
30552 TATTAAAAAT
30562 AAAAAAAATTA
1 AAAAAAAATTA
30573 AAAAAAAATTA
1 AAAAAAAATTA
30584 AAAA
1 AAAA
30588 GTTAATCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAAAATTA
Found at i:30992 original size:47 final size:46
Alignment explanation
Indices: 30921--31047 Score: 147
Period size: 46 Copynumber: 2.8 Consensus size: 46
30911 TTTCGTTAGC
*
30921 TAAC-TTCCGGTA-AAAAAAATAATGTTTTAGGTAGCGCCTAAT-G
1 TAACATTCCGGTAGAAAAAAATAATGTTTTAGGTAGCGCCCAATAG
* *
30964 TAACATTTCCGGTAGGAAAAAAATAATG-TTTAGATAGCGCCCAATAT
1 TAACA-TTCCGGTA-GAAAAAAATAATGTTTTAGGTAGCGCCCAATAG
* * *
31011 TAACATTCCAGAAG-AACAAATAATGTTTTAGGTAGCG
1 TAACATTCCGGTAGAAAAAAATAATGTTTTAGGTAGCG
31048 TTTTACCGAA
Statistics
Matches: 71, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
43 4 0.06
44 10 0.14
45 19 0.27
46 21 0.30
47 17 0.24
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Consensus pattern (46 bp):
TAACATTCCGGTAGAAAAAAATAATGTTTTAGGTAGCGCCCAATAG
Found at i:32818 original size:29 final size:29
Alignment explanation
Indices: 32774--32848 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
32764 TAACGGAGGT
*
32774 AGGTCGCCATGTACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
32803 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
32832 AGGTCGCCATGCACGCC
1 AGGTCGCCATGCACGCC
32849 ATATACTCAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.20, C:0.43, G:0.28, T:0.09
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAACC
Found at i:32892 original size:17 final size:18
Alignment explanation
Indices: 32858--32893 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
32848 CATATACTCA
32858 CCATGCAGACGAGCCATAC
1 CCATGCAGAC-AGCCATAC
32877 CCATGCAGAC-GCCATAC
1 CCATGCAGACAGCCATAC
32894 AAGCCATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
19 10 0.59
ACGTcount: A:0.31, C:0.39, G:0.19, T:0.11
Consensus pattern (18 bp):
CCATGCAGACAGCCATAC
Found at i:32938 original size:28 final size:28
Alignment explanation
Indices: 32907--32962 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
32897 CCATATACTC
32907 ACCATGCAGACGAGCCAGCCAACGGAGA
1 ACCATGCAGACGAGCCAGCCAACGGAGA
32935 ACCATGCAGACGAGCCAGCCAACGGAGA
1 ACCATGCAGACGAGCCAGCCAACGGAGA
32963 GGTCGCCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.32, G:0.29, T:0.04
Consensus pattern (28 bp):
ACCATGCAGACGAGCCAGCCAACGGAGA
Found at i:32976 original size:28 final size:28
Alignment explanation
Indices: 32945--33001 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
32935 ACCATGCAGA
*
32945 CGAGCCAGCCAACGGAGAGGTCGCCATG
1 CGAGCCAGCCAACAGAGAGGTCGCCATG
*
32973 CGAGCCAGCCAATAGAGAGGTCGCCATG
1 CGAGCCAGCCAACAGAGAGGTCGCCATG
33001 C
1 C
33002 AGTCTGGGCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.26, C:0.32, G:0.33, T:0.09
Consensus pattern (28 bp):
CGAGCCAGCCAACAGAGAGGTCGCCATG
Found at i:33034 original size:29 final size:29
Alignment explanation
Indices: 32990--33084 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
32980 GCCAATAGAG
* **
32990 AGGTCGCCATGCAGTCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
33019 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
33048 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
33077 AGGTCGCC
1 AGGTCGCC
33085 CCCTGCGAAC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.14, C:0.31, G:0.33, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:33117 original size:19 final size:19
Alignment explanation
Indices: 33093--33129 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
33083 CCCCCTGCGA
33093 ACCATGCATGCACCAGCCG
1 ACCATGCATGCACCAGCCG
33112 ACCATGCATGCACCAGCC
1 ACCATGCATGCACCAGCC
33130 AAATAACTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.43, G:0.19, T:0.11
Consensus pattern (19 bp):
ACCATGCATGCACCAGCCG
Found at i:33189 original size:49 final size:48
Alignment explanation
Indices: 33127--33227 Score: 168
Period size: 49 Copynumber: 2.1 Consensus size: 48
33117 GCATGCACCA
*
33127 GCCAAATAACTTCACGTGCTCCTGCT-CCCGCTGCATGCCTGCATGCAT
1 GCCAAATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTACA-GCAT
33175 GCCAAGATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTACAGCAT
1 GCCAA-ATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTACAGCAT
33224 GCCA
1 GCCA
33228 TGTGATCCTA
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
48 5 0.10
49 29 0.58
50 16 0.32
ACGTcount: A:0.20, C:0.39, G:0.19, T:0.23
Consensus pattern (48 bp):
GCCAAATAACTTCACGTGCTCCTGCTCCCCGCTGCATGCCTACAGCAT
Found at i:33460 original size:16 final size:18
Alignment explanation
Indices: 33439--33477 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
33429 GGAGATAAGG
*
33439 TAAATTTGTTTA-TATT-
1 TAAATTAGTTTATTATTA
33455 TAAATTAGTTTATTATTA
1 TAAATTAGTTTATTATTA
33473 TAAAT
1 TAAAT
33478 GTTAATTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 4 0.20
18 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TAAATTAGTTTATTATTA
Found at i:33625 original size:47 final size:47
Alignment explanation
Indices: 33582--33672 Score: 127
Period size: 45 Copynumber: 2.0 Consensus size: 47
33572 TTATATAGTT
33582 AAAAAA-TAATTAATTAGTTTGTT-TT-GTT-AATAGTTAGTTATATA
1 AAAAAATTAATTAATTAGTTT-TTGTTAGTTAAATAGTTAGTTATATA
*
33626 AAAAAATTATTTAATTAGTTTTTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAATTAATTAATTAGTTTTTGTTAGTTAAATAGTT-AGTTATAT
33673 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
44 8 0.20
45 15 0.37
46 3 0.07
47 7 0.17
48 8 0.20
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (47 bp):
AAAAAATTAATTAATTAGTTTTTGTTAGTTAAATAGTTAGTTATATA
Found at i:33717 original size:12 final size:12
Alignment explanation
Indices: 33702--33754 Score: 63
Period size: 12 Copynumber: 4.3 Consensus size: 12
33692 TATATAAAAA
33702 ATTAGTTAGTTT
1 ATTAGTTAGTTT
33714 ATTAGTTAGTTTT
1 ATTAGTTAG-TTT
*
33727 AGTTAGTAAGTTT
1 A-TTAGTTAGTTT
*
33740 ATTAG-TAGTAT
1 ATTAGTTAGTTT
33751 ATTA
1 ATTA
33755 TAATGAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 8 0.22
12 13 0.36
13 8 0.22
14 7 0.19
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (12 bp):
ATTAGTTAGTTT
Found at i:33771 original size:32 final size:33
Alignment explanation
Indices: 33735--33811 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 33
33725 TTAGTTAGTA
*
33735 AGTTTATTAGTAG-TATA-TTATAATGAAAAAAT
1 AGTTTATTAGTAGTTATAGTTAT-ATAAAAAAAT
*
33767 AGTTTATTAGTTAGTTTTAGTTATATAAAAAAAT
1 AGTTTATTAG-TAGTTATAGTTATATAAAAAAAT
*
33801 ATTTTATTAGT
1 AGTTTATTAGT
33812 TGTTTAAGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
32 10 0.26
33 4 0.10
34 21 0.54
35 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (33 bp):
AGTTTATTAGTAGTTATAGTTATATAAAAAAAT
Found at i:34084 original size:28 final size:28
Alignment explanation
Indices: 34044--34099 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
34034 ACATATTTCC
34044 TCTCCGTTGGCTGGCTCGTCTGCATGGT
1 TCTCCGTTGGCTGGCTCGTCTGCATGGT
34072 TCTCCGTTGGCTGGCTCGTCTGCATGGT
1 TCTCCGTTGGCTGGCTCGTCTGCATGGT
34100 GAGTATATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.04, C:0.29, G:0.32, T:0.36
Consensus pattern (28 bp):
TCTCCGTTGGCTGGCTCGTCTGCATGGT
Found at i:34135 original size:17 final size:18
Alignment explanation
Indices: 34113--34148 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
34103 TATATGGCTT
34113 GTATGG-CGTCTGCATGG
1 GTATGGCCGTCTGCATGG
34130 GTATGGCTCGTCTGCATGG
1 GTATGGC-CGTCTGCATGG
34149 TGAGTATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
19 11 0.65
ACGTcount: A:0.11, C:0.19, G:0.39, T:0.31
Consensus pattern (18 bp):
GTATGGCCGTCTGCATGG
Found at i:34191 original size:29 final size:29
Alignment explanation
Indices: 34158--34232 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
34148 GTGAGTATAT
34158 GGCGTGCATGGCGACCTGGTTGGTCGCCG
1 GGCGTGCATGGCGACCTGGTTGGTCGCCG
34187 GGCGTGCATGGCGACCTGGTTGGTCGCCG
1 GGCGTGCATGGCGACCTGGTTGGTCGCCG
*
34216 GGCGTACATGGCGACCT
1 GGCGTGCATGGCGACCT
34233 ACCTCCGTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.09, C:0.28, G:0.43, T:0.20
Consensus pattern (29 bp):
GGCGTGCATGGCGACCTGGTTGGTCGCCG
Found at i:45708 original size:26 final size:25
Alignment explanation
Indices: 45656--45722 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
45646 GATTTTTTTT
45656 ACAGTTTCTTAAATAATATGAACAAAA
1 ACAGTTT-TTAAATAATATGAAC-AAA
* * *
45683 ACAGTTTTTAATTAATATGGAGAAA
1 ACAGTTTTTAAATAATATGAACAAA
* *
45708 ACCGTTTTTTAATAA
1 ACAGTTTTTAAATAA
45723 AAAAATTATA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 15 0.44
26 12 0.35
27 7 0.21
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36
Consensus pattern (25 bp):
ACAGTTTTTAAATAATATGAACAAA
Found at i:46068 original size:10 final size:10
Alignment explanation
Indices: 46053--46092 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
46043 AATGAAAGAC
46053 TAATTTATTT
1 TAATTTATTT
46063 TAATTTATTT
1 TAATTTATTT
* *
46073 TAATTTAATA
1 TAATTTATTT
46083 T-ATTTATTT
1 TAATTTATTT
46092 T
1 T
46093 TCCACCAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TAATTTATTT
Found at i:48939 original size:14 final size:16
Alignment explanation
Indices: 48922--48958 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
48912 CTATCAATAT
*
48922 TCTTATCATT-TAT-A
1 TCTTATAATTATATCA
48936 TCTTATAATTATATCA
1 TCTTATAATTATATCA
48952 TCTTATA
1 TCTTATA
48959 TATATTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 9 0.45
15 3 0.15
16 8 0.40
ACGTcount: A:0.32, C:0.14, G:0.00, T:0.54
Consensus pattern (16 bp):
TCTTATAATTATATCA
Found at i:49318 original size:23 final size:23
Alignment explanation
Indices: 49283--49339 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
49273 CTCATATAAA
* *
49283 TGCACCGATGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTACAAT
* *
49306 TTCACCGAAGTGCCGCGTACAAT
1 TGCACCGAAGTGCCACGTACAAT
*
49329 TGCACTGAAGT
1 TGCACCGAAGT
49340 TCCATATAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTACAAT
Found at i:54747 original size:23 final size:24
Alignment explanation
Indices: 54721--54776 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
54711 CGTATAAATG
*
54721 CACCGAAGTGTCACGTAGAATT-T
1 CACCGAAGTGACACGTAGAATTGT
*
54744 CACCGAAGTGACTCGTAGAATTGT
1 CACCGAAGTGACACGTAGAATTGT
54768 -ACCGAAGTG
1 CACCGAAGTG
54777 CCATATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 29 0.97
24 1 0.03
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.23
Consensus pattern (24 bp):
CACCGAAGTGACACGTAGAATTGT
Found at i:65759 original size:16 final size:18
Alignment explanation
Indices: 65738--65773 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
65728 AAGTTAATAT
65738 AATCTCAGAA-AA-AAAA
1 AATCTCAGAATAATAAAA
65754 AATCTCAGAATAATAAAA
1 AATCTCAGAATAATAAAA
65772 AA
1 AA
65774 AAATCATGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 2 0.11
18 6 0.33
ACGTcount: A:0.67, C:0.11, G:0.06, T:0.17
Consensus pattern (18 bp):
AATCTCAGAATAATAAAA
Done.