Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003956.1 Hibiscus syriacus cultivar Beakdansim tig00008555_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: 51636
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:7314 original size:12 final size:12
Alignment explanation
Indices: 7291--7322 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
7281 AGTGCATTAG
7291 CAACATGTACCTC
1 CAACA-GTACCTC
7304 CAACAGTACCTC
1 CAACAGTACCTC
7316 CAACAGT
1 CAACAGT
7323 TCACGACTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.34, C:0.38, G:0.09, T:0.19
Consensus pattern (12 bp):
CAACAGTACCTC
Found at i:9560 original size:140 final size:140
Alignment explanation
Indices: 9308--9585 Score: 432
Period size: 140 Copynumber: 2.0 Consensus size: 140
9298 CCTGAAACTA
* * * *
9308 TTCTTCATACTTTAAAGGCCTATCGTAGTTCGCGCTCTATTCTTGCTCTGTCCGGACTTGGTACA
1 TTCTTCATACTTTAAAGGCCTATCCTAGATCGCGCTCCATTCTTGCTCTGTCCGGACTTGATACA
* *
9373 TTGCTGTTGGACTGGCAAGCTAACACATGCAAAGATTGGCTTGAAAAGGTAGCAGCTTCTCGTGA
66 TTGCTGGTGAACTGGCAAGCTAACACATGCAAAGATTGGCTTGAAAAGGTAGCAGCTTCTCGTGA
9438 TCACCTAGGT
131 TCACCTAGGT
* * *
9448 TTCTTCATA-TATTAAAGGCCTATCCTAGATCTCGCTCCATTCTTGCTCTTTCTGGACTTGATAC
1 TTCTTCATACT-TTAAAGGCCTATCCTAGATCGCGCTCCATTCTTGCTCTGTCCGGACTTGATAC
* * *
9512 ATTGCTGGTGAACTGGCAAGCTAACACATGCAAAGATTGGCTTGAAAAGGTAGTATCTTCTCTTG
65 ATTGCTGGTGAACTGGCAAGCTAACACATGCAAAGATTGGCTTGAAAAGGTAGCAGCTTCTCGTG
9577 ATCACCTAG
130 ATCACCTAG
9586 ATTTTACTAA
Statistics
Matches: 125, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
139 1 0.01
140 124 0.99
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.33
Consensus pattern (140 bp):
TTCTTCATACTTTAAAGGCCTATCCTAGATCGCGCTCCATTCTTGCTCTGTCCGGACTTGATACA
TTGCTGGTGAACTGGCAAGCTAACACATGCAAAGATTGGCTTGAAAAGGTAGCAGCTTCTCGTGA
TCACCTAGGT
Found at i:12080 original size:23 final size:24
Alignment explanation
Indices: 12045--12089 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
12035 AACTCACTGG
* *
12045 GTCAACTCATTGACT-TTGACCGA
1 GTCAACCCATTGAATGTTGACCGA
*
12068 GTCAACCCGTTGAATGTTGACC
1 GTCAACCCATTGAATGTTGACC
12090 ATTGACTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (24 bp):
GTCAACCCATTGAATGTTGACCGA
Found at i:14859 original size:43 final size:43
Alignment explanation
Indices: 14726--15122 Score: 323
Period size: 43 Copynumber: 9.1 Consensus size: 43
14716 TCCTTTTCCA
* * * *
14726 TGTGCAAGGGTAAGCCTCACAGTTTCCCCCAGGTTCATTTGTTG
1 TGTGCAAGGGTAAGCCTTACAGTTT-TCCCAGGTTCCTTTGCTG
* * *
14770 TGTGCAAGAGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTGTTG
1 TGTGCAAGGGTAAGCCTTACAGTTT-TCCCAGGTTCCTTTGCTG
* *
14814 TGTGCAAGGGGAAGCCTTATAGTTTTCCCAGGTTCCTTTGCTG
1 TGTGCAAGGGTAAGCCTTACAGTTTTCCCAGGTTCCTTTGCTG
* ** * * **
14857 TGTGAAAACGTAAGCCTTACATTTTTCCAAGGTTCCTTTATTG
1 TGTGCAAGGGTAAGCCTTACAGTTTTCCCAGGTTCCTTTGCTG
* * *
14900 AGTACAAGGGTAAGCCTTACAGTTTTCCCCAGGTTCCTTTGTTG
1 TGTGCAAGGGTAAGCCTTACAGTTTT-CCCAGGTTCCTTTGCTG
* * * * * *
14944 GGTTCAAGGGTAAGACCTTATAGTTTT-ACAGGCTCCTTTGCTA
1 TGTGCAAGGGTAAG-CCTTACAGTTTTCCCAGGTTCCTTTGCTG
* * ** * *
14987 TGTGCAAAGGTAAGACCTTATAGTTTT-ATAGGCTCCTTTGCTA
1 TGTGCAAGGGTAAG-CCTTACAGTTTTCCCAGGTTCCTTTGCTG
* * * * * *
15030 TGTGCAAGGGTAAGACCTTATAG-TTTCTCAGGCTCTTTTTCTA
1 TGTGCAAGGGTAAG-CCTTACAGTTTTCCCAGGTTCCTTTGCTG
* ** * * *
15073 TGTGCAAGGGTAAGACCTTACCGTTTTTGCATGCTCCTTTGCTT
1 TGTGCAAGGGTAAG-CCTTACAGTTTTCCCAGGTTCCTTTGCTG
15117 TGTGCA
1 TGTGCA
15123 CATTGTAAAT
Statistics
Matches: 300, Mismatches: 49, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
42 3 0.01
43 176 0.59
44 110 0.37
45 11 0.04
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (43 bp):
TGTGCAAGGGTAAGCCTTACAGTTTTCCCAGGTTCCTTTGCTG
Found at i:14877 original size:87 final size:86
Alignment explanation
Indices: 14726--14940 Score: 270
Period size: 87 Copynumber: 2.5 Consensus size: 86
14716 TCCTTTTCCA
* * * * *
14726 TGTGCAAGGGTAAGCCTCACAGTTTCCCCCAGGTTCATTTGTTGTGTGCAAGAGTAAGCCTTACA
1 TGTGCAAGGGTAAGCCTTACAGTTT-TCCCAGGTTCCTTTGCTGTGTGCAAAAGTAAGCCTTACA
* *
14791 GTTTCCCCCAGGTTCCTTTGTTG
65 -TTTCCCCAAGGTTCCTTTATTG
* *
14814 TGTGCAAGGGGAAGCCTTATAGTTTTCCCAGGTTCCTTTGCTGTGTG-AAAACGTAAGCCTTACA
1 TGTGCAAGGGTAAGCCTTACAGTTTTCCCAGGTTCCTTTGCTGTGTGCAAAA-GTAAGCCTTACA
**
14878 TTTTTCCAAGGTTCCTTTATTG
65 TTTCCCCAAGGTTCCTTTATTG
* *
14900 AGTACAAGGGTAAGCCTTACAGTTTTCCCCAGGTTCCTTTG
1 TGTGCAAGGGTAAGCCTTACAGTTTT-CCCAGGTTCCTTTG
14941 TTGGGTTCAA
Statistics
Matches: 110, Mismatches: 15, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
86 43 0.39
87 45 0.41
88 22 0.20
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (86 bp):
TGTGCAAGGGTAAGCCTTACAGTTTTCCCAGGTTCCTTTGCTGTGTGCAAAAGTAAGCCTTACAT
TTCCCCAAGGTTCCTTTATTG
Found at i:14952 original size:130 final size:131
Alignment explanation
Indices: 14756--15006 Score: 353
Period size: 130 Copynumber: 1.9 Consensus size: 131
14746 AGTTTCCCCC
* * * *
14756 AGGTTCATTTGTTGTGTGCAAGAGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTGTTGTGTGCAA
1 AGGTTCATTTATTGAGTACAAGAGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTGTTGGGTGCAA
* * *
14821 GGGGAAG-CCTTATAGTTTTCCCAGGTTCCTTTGCTGTGTGAAAACGTAAG-CCTTACATTTTTC
66 GGGGAAGACCTTATAGTTTT-ACAGGCTCCTTTGCTATGTGAAAACGTAAGACCTTACATTTTTC
14884 CA
130 CA
* * * *
14886 AGGTTCCTTTATTGAGTACAAGGGTAAGCCTTACAGTTTTCCCCAGGTTCCTTTGTTGGGTTCAA
1 AGGTTCATTTATTGAGTACAAGAGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTGTTGGGTGCAA
* * *
14951 GGGTAAGACCTTATAGTTTTACAGGCTCCTTTGCTATGTGCAAAGGTAAGACCTTA
66 GGGGAAGACCTTATAGTTTTACAGGCTCCTTTGCTATGTGAAAACGTAAGACCTTA
15007 TAGTTTTATA
Statistics
Matches: 105, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
130 88 0.84
131 17 0.16
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (131 bp):
AGGTTCATTTATTGAGTACAAGAGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTGTTGGGTGCAA
GGGGAAGACCTTATAGTTTTACAGGCTCCTTTGCTATGTGAAAACGTAAGACCTTACATTTTTCC
A
Found at i:15038 original size:130 final size:130
Alignment explanation
Indices: 14770--15056 Score: 348
Period size: 130 Copynumber: 2.2 Consensus size: 130
14760 TCATTTGTTG
* *
14770 TGTGCAAGAGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTGTTGTGTGCAAGGGGAAGCCTTATA
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTGTTGGGTGCAAGGGGAAGCCTTATA
* * * * * *
14835 GTTTTCCCAGGTTCCTTTGCTGTGTGAAAACGTAAGCCTTACATTTTTCCAAGGTTCCTTTATTG
66 GTTTTCACAGGCTCCTTTGCTATGTGAAAACGTAAGCCTTACAGTTTT-CAAGGCTCCTTTACTG
14900 A
130 A
* * * *
14901 -GTACAAGGGTAAGCCTTACAGTTTTCCCCAGGTTCCTTTGTTGGGTTCAAGGGTAAGACCTTAT
1 TGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTGTTGGGTGCAAGGGGAAG-CCTTAT
* * * *
14965 AGTTTT-ACAGGCTCCTTTGCTATGTGCAAAGGTAAGACCTTATAGTTTT-ATAGGCTCCTTTGC
65 AGTTTTCACAGGCTCCTTTGCTATGTGAAAACGTAAG-CCTTACAGTTTTCA-AGGCTCCTTTAC
15028 T-A
128 TGA
*
15030 TGTGCAAGGGTAAGACCTTATAGTTTC
1 TGTGCAAGGGTAAG-CCTTACAGTTTC
15057 TCAGGCTCTT
Statistics
Matches: 132, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
129 2 0.02
130 98 0.74
131 32 0.24
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.36
Consensus pattern (130 bp):
TGTGCAAGGGTAAGCCTTACAGTTTCCCCCAGGTTCCTTTGTTGGGTGCAAGGGGAAGCCTTATA
GTTTTCACAGGCTCCTTTGCTATGTGAAAACGTAAGCCTTACAGTTTTCAAGGCTCCTTTACTGA
Found at i:19828 original size:43 final size:43
Alignment explanation
Indices: 19764--20099 Score: 374
Period size: 43 Copynumber: 7.8 Consensus size: 43
19754 CCGCAGGCTT
* *
19764 CTTTGTTGTGTGCAAGGGTAAGCCTTATAGTTTCCCCAGGTTC
1 CTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTC
* *
19807 CTTTGCTGTGTGCAAGAGTAAGCCTTACAGTTTCCCCTGGGTTC
1 CTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC-AGGTTC
* * * *
19851 CTTTGTTGTGTGCAAGGGAAAGCTTTACAGTTTGCCCAGGTTC
1 CTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTC
* * * *
19894 CTTTGCTGTGAGCAAGTGTAAGCCTTACATTTTCCCCAAGTTC
1 CTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTC
* *
19937 CTTTGCTATGTGCAAGGGTAATCCTTACAGTTTTCCCCAGGTTC
1 CTTTGCTGTGTGCAAGGGTAAGCCTTACAG-TTTCCCCAGGTTC
* *
19981 CTTTGTTGTGTGCAAGGGTAAGACCTTATAGTTT-CCCAGGTTC
1 CTTTGCTGTGTGCAAGGGTAAG-CCTTACAGTTTCCCCAGGTTC
* ** * *
20024 CTTTTCCAT-TGAAAGGGTAAGACCTTATAGTTT-CCCA-GTCTC
1 CTTTGCTGTGTGCAAGGGTAAG-CCTTACAGTTTCCCCAGGT-TC
* * *
20066 TTTTGCTATGTGCAAGGGTAAGACCTTACCGTTT
1 CTTTGCTGTGTGCAAGGGTAAG-CCTTACAGTTT
20100 TTGCATGCTC
Statistics
Matches: 249, Mismatches: 39, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
41 2 0.01
42 35 0.14
43 134 0.54
44 71 0.29
45 7 0.03
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (43 bp):
CTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTC
Found at i:19915 original size:87 final size:86
Alignment explanation
Indices: 19764--20099 Score: 358
Period size: 87 Copynumber: 3.9 Consensus size: 86
19754 CCGCAGGCTT
*
19764 CTTTGTTGTGTGCAAGGGTAAGCCTTATAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGAGTAAG
1 CTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGAGTAAG
**
19829 CCTTACAGTTTCCCCTGGGTTC
66 CCTTACAGTTTCCCC-AAGTTC
* * * * *
19851 CTTTGTTGTGTGCAAGGGAAAGCTTTACAGTTTGCCCAGGTTCCTTTGCTGTGAGCAAGTGTAAG
1 CTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGAGTAAG
*
19916 CCTTACATTTTCCCCAAGTTC
66 CCTTACAGTTTCCCCAAGTTC
* * * * *
19937 CTTTGCTATGTGCAAGGGTAATCCTTACAGTTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAA
1 CTTTGTTGTGTGCAAGGGTAAGCCTTACAG-TTTCCCCAGGTTCCTTTGCTGTGTGCAAGAGTAA
* *
20002 GACCTTATAGTTT-CCCAGGTTC
65 G-CCTTACAGTTTCCCCAAGTTC
** * * * * *
20024 CTTT-TCCAT-TGAAAGGGTAAGACCTTATAGTTT-CCCA-GTCTCTTTTGCTATGTGCAAGGGT
1 CTTTGT-TGTGTGCAAGGGTAAG-CCTTACAGTTTCCCCAGGT-TCCTTTGCTGTGTGCAAGAGT
*
20085 AAGACCTTACCGTTT
63 AAG-CCTTACAGTTT
20100 TTGCATGCTC
Statistics
Matches: 213, Mismatches: 31, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
84 2 0.01
85 35 0.16
86 42 0.20
87 125 0.59
88 9 0.04
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (86 bp):
CTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGAGTAAG
CCTTACAGTTTCCCCAAGTTC
Found at i:19997 original size:130 final size:131
Alignment explanation
Indices: 19764--20100 Score: 411
Period size: 130 Copynumber: 2.6 Consensus size: 131
19754 CCGCAGGCTT
* * * * * *
19764 CTTTGTTGTGTGCAAGGGTAAGCCTTATAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGAGTAAG
1 CTTTGCTGTGAGCAAGGGTAAGCCTTATAGTTTCCCCAAGTTCCTTTGCTATGTGCAAGGGTAAA
* *
19829 CCTTACAG-TTTCCCCTGGGTTCCTTTGTTGTGTGCAAGGGAAAG-CTTTACAGTTTGCCCAGGT
66 CCTTACAGTTTTCCCCTAGGTTCCTTTGTTGTGTGCAAGGGAAAGACCTTACAGTTT-CCCAGGT
19892 TC
130 TC
* * * *
19894 CTTTGCTGTGAGCAAGTGTAAGCCTTACATTTTCCCCAAGTTCCTTTGCTATGTGCAAGGGTAAT
1 CTTTGCTGTGAGCAAGGGTAAGCCTTATAGTTTCCCCAAGTTCCTTTGCTATGTGCAAGGGTAAA
* *
19959 CCTTACAGTTTTCCCC-AGGTTCCTTTGTTGTGTGCAAGGGTAAGACCTTATAGTTTCCCAGGTT
66 CCTTACAGTTTTCCCCTAGGTTCCTTTGTTGTGTGCAAGGGAAAGACCTTACAGTTTCCCAGGTT
20023 C
131 C
* *
20024 CTTTTCCAT-TGA--AAGGGTAAGACCTTATAGTTT-CCC-AGTCTCTTTTGCTATGTGCAAGGG
1 C-TTTGC-TGTGAGCAAGGGTAAG-CCTTATAGTTTCCCCAAGT-TCCTTTGCTATGTGCAAGGG
*
20084 TAAGACCTTACCGTTTT
62 TAA-ACCTTACAGTTTT
20101 TGCATGCTCA
Statistics
Matches: 180, Mismatches: 20, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
128 3 0.02
129 33 0.18
130 120 0.67
131 23 0.13
132 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (131 bp):
CTTTGCTGTGAGCAAGGGTAAGCCTTATAGTTTCCCCAAGTTCCTTTGCTATGTGCAAGGGTAAA
CCTTACAGTTTTCCCCTAGGTTCCTTTGTTGTGTGCAAGGGAAAGACCTTACAGTTTCCCAGGTT
C
Found at i:20048 original size:42 final size:43
Alignment explanation
Indices: 19989--20093 Score: 144
Period size: 42 Copynumber: 2.5 Consensus size: 43
19979 TCCTTTGTTG
*
19989 TGTGCAAGGGTAAGACCTTATAGTTTCCCAGGT-TCCTTTT-CCA
1 TGTGAAAGGGTAAGACCTTATAGTTTCCCA-GTCT-CTTTTGCCA
*
20032 T-TGAAAGGGTAAGACCTTATAGTTTCCCAGTCTCTTTTGCTA
1 TGTGAAAGGGTAAGACCTTATAGTTTCCCAGTCTCTTTTGCCA
*
20074 TGTGCAAGGGTAAGACCTTA
1 TGTGAAAGGGTAAGACCTTA
20094 CCGTTTTTGC
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
41 7 0.12
42 31 0.55
43 18 0.32
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (43 bp):
TGTGAAAGGGTAAGACCTTATAGTTTCCCAGTCTCTTTTGCCA
Found at i:24874 original size:32 final size:32
Alignment explanation
Indices: 24814--24874 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
24804 AGGCATGTAA
* * *
24814 AGAAAATGTCTCCAGTGAGACAATTTTTTAAG
1 AGAAAATATCTCAAGTGAGACAAATTTTTAAG
* *
24846 AGAAAATATCTCAAGTGTGATAAATTTTT
1 AGAAAATATCTCAAGTGAGACAAATTTTT
24875 TTTGAGAGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.34
Consensus pattern (32 bp):
AGAAAATATCTCAAGTGAGACAAATTTTTAAG
Found at i:24965 original size:70 final size:68
Alignment explanation
Indices: 24891--25101 Score: 188
Period size: 70 Copynumber: 3.0 Consensus size: 68
24881 AGAAAACATC
* ** *
24891 TCGAGCAGACAAAAAATTTCAATAGAAAATATTTTAAATGAGATGAAATTTTGTTTCAAGAGAAA
1 TCGAG-AGA-AAAAATTTTCAAGGGAAAATATTTCAAATGAGATGAAATTTTGTTTCAAGAGAAA
24956 TTGTA
64 TTGTA
** * * * * * *
24961 TCGAGTGAGAAAACTTTTTTAAGGGAAAATATCTCAAGTTAGTTGAAATTTTGTTTCGAGAGAAA
1 TCGA--GAGAAAAAATTTTCAAGGGAAAATATTTCAAATGAGATGAAATTTTGTTTCAAGAGAAA
* * *
25026 ATATC
64 TTGTA
* * * *
25031 TCGATTGAGATGAAAATTTTCAAGGGAAAATATTTCGACTGAGATAAAATTTTGTTTCAAGAGAA
1 TCGA--GAGA-AAAAATTTTCAAGGGAAAATATTTCAAATGAGATGAAATTTTGTTTCAAGAGAA
25096 ATTGTA
63 ATTGTA
25102 GAGAAACTAT
Statistics
Matches: 108, Mismatches: 30, Indels: 5
0.76 0.21 0.03
Matches are distributed among these distances:
70 58 0.54
71 49 0.45
72 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (68 bp):
TCGAGAGAAAAAATTTTCAAGGGAAAATATTTCAAATGAGATGAAATTTTGTTTCAAGAGAAATT
GTA
Found at i:25081 original size:141 final size:137
Alignment explanation
Indices: 24827--25101 Score: 356
Period size: 141 Copynumber: 2.0 Consensus size: 137
24817 AAATGTCTCC
* *
24827 AGTGAGACAATTTTTTAAGAGAAAATATCTCAAGTGTGATAAATTTTTTTTGAGAGAAAACATCT
1 AGTGAGAAAATTTTTTAAGAGAAAATATCTCAAGTGTGATAAATTTTTTTCGAGAGAAAACATCT
* * *
24892 CGAGCAGACAAAAAATTTCAATAGAAAATATTTTAAATGAGATGAAATTTTGTTTCAAGAGAAAT
66 CGAGCAGACAAAAAATTTCAAGAGAAAATATTTCAAATGAGATAAAATTTTGTTTCAAGAGAAAT
24957 TGTATCG
131 TGTATCG
* * *
24964 AGTGAGAAAACTTTTTTAAGGGAAAATATCTCAAGT-TAGTTGAAATTTTGTTTCGAGAGAAAAT
1 AGTGAGAAAA-TTTTTTAAGAGAAAATATCTCAAGTGT-GAT-AAATTTT-TTTCGAGAGAAAAC
** * * * *
25028 ATCTCGATTG-AGATGAAAATTTTCAAGGGAAAATATTTCGACTGAGATAAAATTTTGTTTCAAG
62 ATCTCGA--GCAGACAAAAAATTTCAAGAGAAAATATTTCAAATGAGATAAAATTTTGTTTCAAG
25092 AGAAATTGTA
125 AGAAATTGTA
25102 GAGAAACTAT
Statistics
Matches: 118, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
137 10 0.08
138 26 0.22
139 7 0.06
140 19 0.16
141 55 0.47
142 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (137 bp):
AGTGAGAAAATTTTTTAAGAGAAAATATCTCAAGTGTGATAAATTTTTTTCGAGAGAAAACATCT
CGAGCAGACAAAAAATTTCAAGAGAAAATATTTCAAATGAGATAAAATTTTGTTTCAAGAGAAAT
TGTATCG
Found at i:25345 original size:75 final size:74
Alignment explanation
Indices: 25214--25636 Score: 334
Period size: 74 Copynumber: 5.7 Consensus size: 74
25204 TCAAAAGAAG
* ** * * ** * *
25214 ACTATCTCAAGCGAGAT-AAAGTTTTTTTTCGAGAGAAACCGCCTCGAGTGAGATGATACTTGTT
1 ACTATCTCAAGTGAGATAAAAAATTTATTTCGAGGGAAATTGTCTCAAGTGAGATGATACTTGTT
25278 TTAAGGAAA
66 TTAAGGAAA
*
25287 ACTATCTCAAGTAAGATAAAAAAATTTATTTCGAGGGAAATTGTCTCAAGTGAGATGATACTTGT
1 ACTATCTCAAGTGAGAT-AAAAAATTTATTTCGAGGGAAATTGTCTCAAGTGAGATGATACTTGT
*
25352 TTTAAGAAAA
65 TTTAAGGAAA
* * ** * * * * *
25362 ACTATCTCGAGCGAGATAAAATTTTTGTATCGAGAGAAACTGTCT-AGAATGAGATGATACTTGT
1 ACTATCTCAAGTGAGATAAAAAATTTATTTCGAGGGAAATTGTCTCA-AGTGAGATGATACTTGT
*
25426 CTTAAGGAAA
65 TTTAAGGAAA
* * * * * *
25436 ACTATCTCAAGTGAGATAAAAAA-TTATTTTGAAGGAAATTATGTCAAGTGAGAGGA-AATTGTT
1 ACTATCTCAAGTGAGATAAAAAATTTATTTCGAGGGAAATTGTCTCAAGTGAGATGATACTTGTT
*
25499 TTTAGGAAA
66 TTAAGGAAA
***** * * * * * ** * *
25508 ACTATCTCAAGTGAGATATTTTTTTTTGTTTCAAGAGAAATTATCTCGAGTGAGACAAAACTTAT
1 ACTATCTCAAGTGAGATA-AAAAATTTATTTCGAGGGAAATTGTCTCAAGTGAGATGATACTTGT
25573 TTTAAGGAAA
65 TTTAAGGAAA
* * * * ** *
25583 ACTATATCAAGTGAGAT-ATAATTATTATTTTGAGAAAAAATGTCTCAAGTGAGA
1 ACTATCTCAAGTGAGATAAAAAAT-TTATTTCGAGGGAAATTGTCTCAAGTGAGA
25637 CAAAATTCAT
Statistics
Matches: 274, Mismatches: 68, Indels: 15
0.77 0.19 0.04
Matches are distributed among these distances:
72 31 0.11
73 40 0.15
74 113 0.41
75 90 0.33
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.32
Consensus pattern (74 bp):
ACTATCTCAAGTGAGATAAAAAATTTATTTCGAGGGAAATTGTCTCAAGTGAGATGATACTTGTT
TTAAGGAAA
Found at i:25421 original size:74 final size:73
Alignment explanation
Indices: 25214--25636 Score: 322
Period size: 75 Copynumber: 5.7 Consensus size: 73
25204 TCAAAAGAAG
* * * *
25214 ACTATCTCAAGCGAGATAAAGTTTTTTTTCGAGAGAAACCGCCTCGAGTGAGATGATACTTGTTT
1 ACTATCTCAAGCGAGATAAAATTTTTTTTCGAGAGAAACTGTCTAGAGTGAGATGATACTTGTTT
25279 TAAGGAAA
66 TAAGGAAA
** * * * *
25287 ACTATCTCAAGTAAGATAAAAAAATTTATTTCGAGGGAAATTGTCTCA-AGTGAGATGATACTTG
1 ACTATCTCAAGCGAGAT--AAAATTTTTTTTCGAGAGAAACTGTCT-AGAGTGAGATGATACTTG
*
25351 TTTTAAGAAAA
63 TTTTAAGGAAA
* * * *
25362 ACTATCTCGAGCGAGATAAAATTTTTGTATCGAGAGAAACTGTCTAGAATGAGATGATACTTGTC
1 ACTATCTCAAGCGAGATAAAATTTTT-TTTCGAGAGAAACTGTCTAGAGTGAGATGATACTTGTT
25427 TTAAGGAAA
65 TTAAGGAAA
* * * * * *
25436 ACTATCTCAAGTGAGATAAAAAATTATTTT-GA-AGGAAATTATGTC-A-AGTGAGAGGA-AATT
1 ACTATCTCAAGCGAGAT-AAAATTTTTTTTCGAGA-GAAA--CTGTCTAGAGTGAGATGATACTT
*
25496 GTTTTTAGGAAA
62 GTTTTAAGGAAA
* *** * * * * ** * *
25508 ACTATCTCAAGTGAGATATTTTTTTTTGTTTCAAGAGAAATTATCTCGAGTGAGACAAAACTTAT
1 ACTATCTCAAGCGAGATA-AAATTTTT-TTTCGAGAGAAACTGTCTAGAGTGAGATGATACTTGT
25573 TTTAAGGAAA
64 TTTAAGGAAA
* * * * *
25583 ACTATATCAAGTGAGATATAATTATTATTTT-GAGAAAAAATGTCTCA-AGTGAGA
1 ACTATCTCAAGCGAGATAAAATT-TT-TTTTCGAGAGAAACTGTCT-AGAGTGAGA
25637 CAAAATTCAT
Statistics
Matches: 276, Mismatches: 55, Indels: 37
0.75 0.15 0.10
Matches are distributed among these distances:
71 1 0.00
72 37 0.13
73 40 0.14
74 90 0.33
75 107 0.39
76 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.32
Consensus pattern (73 bp):
ACTATCTCAAGCGAGATAAAATTTTTTTTCGAGAGAAACTGTCTAGAGTGAGATGATACTTGTTT
TAAGGAAA
Found at i:25431 original size:149 final size:145
Alignment explanation
Indices: 25214--25525 Score: 426
Period size: 149 Copynumber: 2.1 Consensus size: 145
25204 TCAAAAGAAG
* * * * *
25214 ACTATCTCAAGCGAGATAAAGTTTTTTTTCGAGAGAAACCGCCTCGAGTGAGATGATACTTGTTT
1 ACTATCTCAAGCGAGATAAAATTTTTTATCGAGAGAAACCGCCTAGAATGAGATGATACTTGTCT
* * *
25279 TAAGGAAAACTATCTCAAGTAAGATAAAAAAATTTATTTCGAGGGAAATTGTCTCAAGTGAGATG
66 TAAGGAAAACTATCTCAAGTAAGAT-AAAAAA-TTATTTCGAAGGAAATTATCTCAAGTGAGAGG
*
25344 ATACTTGTTTTAAGAAAA
129 A-AATTGTTTTAAGAAAA
* * *
25362 ACTATCTCGAGCGAGATAAAATTTTTGTATCGAGAGAAACTGTCTAGAATGAGATGATACTTGTC
1 ACTATCTCAAGCGAGATAAAATTTTT-TATCGAGAGAAACCGCCTAGAATGAGATGATACTTGTC
* * *
25427 TTAAGGAAAACTATCTCAAGTGAGATAAAAAATTATTTTGAAGGAAATTATGTCAAGTGAGAGGA
65 TTAAGGAAAACTATCTCAAGTAAGATAAAAAATTATTTCGAAGGAAATTATCTCAAGTGAGAGGA
* *
25492 AATTGTTTTTAGGAAA
130 AATTGTTTTAAGAAAA
*
25508 ACTATCTCAAGTGAGATA
1 ACTATCTCAAGCGAGATA
25526 TTTTTTTTTG
Statistics
Matches: 144, Mismatches: 19, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
146 29 0.20
147 28 0.19
148 30 0.21
149 57 0.40
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (145 bp):
ACTATCTCAAGCGAGATAAAATTTTTTATCGAGAGAAACCGCCTAGAATGAGATGATACTTGTCT
TAAGGAAAACTATCTCAAGTAAGATAAAAAATTATTTCGAAGGAAATTATCTCAAGTGAGAGGAA
ATTGTTTTAAGAAAA
Found at i:25562 original size:147 final size:147
Alignment explanation
Indices: 25214--25615 Score: 448
Period size: 147 Copynumber: 2.7 Consensus size: 147
25204 TCAAAAGAAG
* * * ***
25214 ACTATCTCAAGCGAGATAAAGTTTTT-TTTCGAGAGAAACCGCCTCGAGTGAGATGATACTTGTT
1 ACTATCTCAAGCGAGATAAAATTTTTGTATCAAGAGAAACTATCTCGAGTGAGATGATACTTGTT
* * * * *
25278 TTAAGGAAAACTATCTCAAGTAAGATAAAAAAATTTATTTCGAGGGAAATTGTCTCAAGTGAGAT
66 TTAAGGAAAACTATCTCAAGTGAGAT-AAAAAA-TTATTTTGAAGGAAATTATCTCAAGTGAGAG
*
25343 GATACTTGTTTTAAGAAAA
129 GATAATTGTTTTAAGAAAA
* * * * * *
25362 ACTATCTCGAGCGAGATAAAATTTTTGTATCGAGAGAAACTGTCTAGAATGAGATGATACTTGTC
1 ACTATCTCAAGCGAGATAAAATTTTTGTATCAAGAGAAACTATCTCGAGTGAGATGATACTTGTT
*
25427 TTAAGGAAAACTATCTCAAGTGAGATAAAAAATTATTTTGAAGGAAATTATGTCAAGTGAGAGGA
66 TTAAGGAAAACTATCTCAAGTGAGATAAAAAATTATTTTGAAGGAAATTATCTCAAGTGAGAGGA
* *
25492 -AATTGTTTTTAGGAAA
131 TAATTGTTTTAAGAAAA
* *** * * ** * *
25508 ACTATCTCAAGTGAGATATTTTTTTTTGTTTCAAGAGAAATTATCTCGAGTGAGACAAAACTTAT
1 ACTATCTCAAGCGAGATA-AAATTTTTGTATCAAGAGAAACTATCTCGAGTGAGATGATACTTGT
* **
25573 TTTAAGGAAAACTATATCAAGTGAGATATAATTATTATTTTGA
65 TTTAAGGAAAACTATCTCAAGTGAGATA-AAAAATTATTTTGA
25616 GAAAAAATGT
Statistics
Matches: 215, Mismatches: 36, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
146 29 0.13
147 87 0.40
148 42 0.20
149 57 0.27
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (147 bp):
ACTATCTCAAGCGAGATAAAATTTTTGTATCAAGAGAAACTATCTCGAGTGAGATGATACTTGTT
TTAAGGAAAACTATCTCAAGTGAGATAAAAAATTATTTTGAAGGAAATTATCTCAAGTGAGAGGA
TAATTGTTTTAAGAAAA
Found at i:25613 original size:38 final size:37
Alignment explanation
Indices: 25427--25636 Score: 146
Period size: 38 Copynumber: 5.7 Consensus size: 37
25417 GATACTTGTC
**
25427 TTAAGGAAAACTATCTCAAGTGAGATAAAAAATTATT
1 TTAAGGAAAACTATCTCAAGTGAGATAAATTATTATT
* * * *
25464 TTGAAGG-AAATTATGTCAAGTGAGAGGAAATT-GT-TT
1 TT-AAGGAAAACTATCTCAAGTGAGA-TAAATTATTATT
** * *
25500 TT-AGGAAAACTATCTCAAGTGAGATATTTTTTTTTGT
1 TTAAGGAAAACTATCTCAAGTGAGATAAATTATTAT-T
* * *
25537 TTCAA-GAGAAATTATCTCGAGTGAGACAAA--ACTTATT
1 TT-AAGGA-AAACTATCTCAAGTGAGATAAATTA-TTATT
*
25574 TTAAGGAAAACTATATCAAGTGAGATATAATTATTATT
1 TTAAGGAAAACTATCTCAAGTGAGATA-AATTATTATT
* * * *
25612 TTGAGAAAAAATGTCTCAAGTGAGA
1 TTAAGGAAAACTATCTCAAGTGAGA
25637 CAAAATTCAT
Statistics
Matches: 131, Mismatches: 28, Indels: 27
0.70 0.15 0.15
Matches are distributed among these distances:
34 6 0.05
35 17 0.13
36 23 0.18
37 29 0.22
38 37 0.28
39 19 0.15
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34
Consensus pattern (37 bp):
TTAAGGAAAACTATCTCAAGTGAGATAAATTATTATT
Found at i:29342 original size:31 final size:32
Alignment explanation
Indices: 29302--29361 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
29292 GGGCATATGA
*
29302 CATACTATATATAGT-TTTAAAAATATAAGTT
1 CATACTATATATAATATTTAAAAATATAAGTT
*
29333 CATATTATATATAATATTTAAAAATATAA
1 CATACTATATATAATATTTAAAAATATAA
29362 CATATAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (32 bp):
CATACTATATATAATATTTAAAAATATAAGTT
Found at i:29366 original size:22 final size:23
Alignment explanation
Indices: 29341--29393 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
29331 TTCATATTAT
29341 ATATAATATTTAAAAATAT-AAC
1 ATATAATATTTAAAAATATAAAC
* ** *
29363 ATATAGT-TTTGTAAATATAAAT
1 ATATAATATTTAAAAATATAAAC
29385 ATATAATAT
1 ATATAATAT
29394 ATATAGTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
21 9 0.38
22 14 0.58
23 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (23 bp):
ATATAATATTTAAAAATATAAAC
Found at i:29379 original size:53 final size:52
Alignment explanation
Indices: 29310--29412 Score: 127
Period size: 53 Copynumber: 2.0 Consensus size: 52
29300 GACATACTAT
* *
29310 ATATAGTTTTAAAAATATAAGT-TCATATTATATATAATATTTAAAAATATAAC
1 ATATAGTTTTAAAAATATAAATAT-ATAATATATATAAT-TTTAAAAATATAAC
** * *
29363 ATATAGTTTTGTAAATATAAATATATAATATATATAGTTTTGAAAATATA
1 ATATAGTTTTAAAAATATAAATATATAATATATATAATTTTAAAAATATA
29413 TGCATAGTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
52 11 0.26
53 31 0.72
54 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.43
Consensus pattern (52 bp):
ATATAGTTTTAAAAATATAAATATATAATATATATAATTTTAAAAATATAAC
Found at i:29383 original size:29 final size:31
Alignment explanation
Indices: 29351--29412 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
29341 ATATAATATT
*
29351 TAAAAATAT-A-ACATATAGTTTTGTAAATA
1 TAAAAATATAATACATATAGTTTTGAAAATA
* *
29380 TAAATATATAATATATATAGTTTTGAAAATA
1 TAAAAATATAATACATATAGTTTTGAAAATA
29411 TA
1 TA
29413 TGCATAGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 8 0.29
30 1 0.04
31 19 0.68
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (31 bp):
TAAAAATATAATACATATAGTTTTGAAAATA
Found at i:29551 original size:31 final size:29
Alignment explanation
Indices: 29449--29581 Score: 139
Period size: 28 Copynumber: 4.6 Consensus size: 29
29439 CTGTATAGTT
*
29449 AAAATAATATAT-TATATAGATAGTTTTG
1 AAAATAATATATATATATATATAGTTTTG
* *
29477 AAAATAATATATATGTATATA-A-TTTTA
1 AAAATAATATATATATATATATAGTTTTG
**
29504 AAAATAATATGCATATAT-TATAGTTTTG
1 AAAATAATATATATATATATATAGTTTTG
**
29532 AAAATAATATATTATATATATTATAACTTTG
1 AAAATAATATA-TATATATA-TATAGTTTTG
*
29563 AAAATAACATATATCATAT
1 AAAATAATATATAT-ATAT
29582 GTACATTATA
Statistics
Matches: 86, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
26 2 0.02
27 20 0.23
28 27 0.31
29 12 0.14
30 3 0.03
31 22 0.26
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (29 bp):
AAAATAATATATATATATATATAGTTTTG
Found at i:29568 original size:28 final size:26
Alignment explanation
Indices: 29473--29576 Score: 61
Period size: 31 Copynumber: 3.7 Consensus size: 26
29463 TATAGATAGT
*
29473 TTTGAAAATA-ATATATATGTATATAA
1 TTTGAAAATATATATATATAT-TATAA
* *
29499 TTTTAAAA-ATAATATGCATATATTATAGT
1 TTTGAAAATAT-ATAT--ATATATTATA-A
29528 TTTGAAAATAATATATTATATATATTATAA
1 TTTG--AA-AATATA-TATATATATTATAA
*
29558 CTTTGAAAATA-ACATATAT
1 -TTTGAAAATATATATATAT
29577 CATATGTACA
Statistics
Matches: 61, Mismatches: 6, Indels: 22
0.69 0.07 0.25
Matches are distributed among these distances:
25 1 0.02
26 13 0.21
27 5 0.08
28 8 0.13
29 10 0.16
31 16 0.26
32 3 0.05
33 5 0.08
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (26 bp):
TTTGAAAATATATATATATATTATAA
Found at i:29694 original size:5 final size:5
Alignment explanation
Indices: 29684--29745 Score: 51
Period size: 5 Copynumber: 13.0 Consensus size: 5
29674 ATATGTATAT
* *
29684 TTTTA TTTTA TTTTA TTTTA TTTT- TATGTA -TTTA -TTTA TTTT- TATTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA
* *
29731 TTTAA TTTAA TTTTA
1 TTTTA TTTTA TTTTA
29746 GGTTCATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
4 11 0.23
5 36 0.77
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:29700 original size:29 final size:29
Alignment explanation
Indices: 29668--29731 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
29658 AGTATTAGTG
*
29668 TATTATATATGTATATTTTTATTT-TATTT
1 TATTATATATGTATATATTTATTTAT-TTT
* * * *
29697 TATTTTATTTTTATGTATTTATTTATTTT
1 TATTATATATGTATATATTTATTTATTTT
29726 TATTAT
1 TATTAT
29732 TTAATTTAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (29 bp):
TATTATATATGTATATATTTATTTATTTT
Found at i:29712 original size:33 final size:32
Alignment explanation
Indices: 29675--29738 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
29665 GTGTATTATA
* *
29675 TATGTATATT-TTTATTTTATTTTATTTTATTTT
1 TATGTAT-TTATTTATTTT-TATTATTTAATTTT
29708 TATGTATTTATTTATTTTTATTATTTAATTT
1 TATGTATTTATTTATTTTTATTATTTAATTT
29739 AATTTTAGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (32 bp):
TATGTATTTATTTATTTTTATTATTTAATTTT
Found at i:29723 original size:18 final size:17
Alignment explanation
Indices: 29681--29745 Score: 67
Period size: 18 Copynumber: 3.5 Consensus size: 17
29671 TATATATGTA
29681 TATTTTTATTTTATTTTATTT
1 TATTTTTA--TTA-TTTA-TT
29702 TATTTTTATGTATTTATT
1 TATTTTTAT-TATTTATT
29720 TATTTTTATTATTTAATT
1 TATTTTTATTATTT-ATT
*
29738 TAATTTTA
1 TATTTTTA
29746 GGTTCATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
17 5 0.12
18 21 0.51
19 5 0.12
20 2 0.05
21 8 0.20
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (17 bp):
TATTTTTATTATTTATT
Found at i:30067 original size:2 final size:2
Alignment explanation
Indices: 30060--30100 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
30050 ATTAAAGAGT
30060 TA TA TA TA TA 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 TA TA TA TA TA T
30101 TTGAATACAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33335 original size:13 final size:13
Alignment explanation
Indices: 33319--33343 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33309 ATCCTAAACA
33319 ATTCGATTAGGTC
1 ATTCGATTAGGTC
33332 ATTCGATTAGGT
1 ATTCGATTAGGT
33344 TATCCTTCAA
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:0.24, C:0.12, G:0.24, T:0.40
Consensus pattern (13 bp):
ATTCGATTAGGTC
Found at i:37845 original size:12 final size:12
Alignment explanation
Indices: 37830--37855 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
37820 TGATCAGAAA
37830 GTTGAGCTCGTT
1 GTTGAGCTCGTT
37842 GTTGAGCTCGTT
1 GTTGAGCTCGTT
37854 GT
1 GT
37856 GTAGGTTTAT
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:0.08, C:0.15, G:0.35, T:0.42
Consensus pattern (12 bp):
GTTGAGCTCGTT
Found at i:38852 original size:2 final size:2
Alignment explanation
Indices: 38845--38872 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38835 CTTATTCAAT
38845 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
38873 TATATATATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:41212 original size:29 final size:30
Alignment explanation
Indices: 41152--41214 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
41142 ACTTTGGTCC
* *
41152 CTAAACTTTTCTAAACTTTATACTTGGTCA
1 CTAAACTTTTCTAAAATTTATACTTGATCA
*
41182 CTAAAC-TTTC-AAAATTTATGATTTGATCA
1 CTAAACTTTTCTAAAATTTAT-ACTTGATCA
41211 CTAA
1 CTAA
41215 CCAAAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 8 0.28
29 15 0.52
30 6 0.21
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.41
Consensus pattern (30 bp):
CTAAACTTTTCTAAAATTTATACTTGATCA
Found at i:51374 original size:116 final size:116
Alignment explanation
Indices: 51253--51512 Score: 294
Period size: 116 Copynumber: 2.2 Consensus size: 116
51243 TCATACCATT
** *
51253 AGTATGATTTTGTTACCATTTTAGCACATGAA-ATGCCCTATATGAAAATCCATACCATT-AGTA
1 AGTATGATTTCCTTACCATTTTAGCACAT-AATATGCCCTATATGAAAATCC-TA-CATTCAATA
* * * * * * *
51316 TGA-TTCCTTATCCTTGTAGCACCCTTAGTGCTCTATCTGGAAA-CCATACACTC
63 TCATTTCCTTATCATT-TAGCACACTCAGCGCTCCATATGGAAATCCATACACTC
* * * **
51369 AGTATGATTCCCTTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCTATTTTCAATATCA
1 AGTATGATTTCCTTACCATTTTAGCACATAATATGCCCTATATGAAAATCCTACATTCAATATCA
* *
51434 TTTCCTTATCATTTAGTACACTCAGCGCTCCATATGGAAATCTATACACTC
66 TTTCCTTATCATTTAGCACACTCAGCGCTCCATATGGAAATCCATACACTC
*
51485 AGTATGATTTCCTTATCATTTTAGCACA
1 AGTATGATTTCCTTACCATTTTAGCACA
51513 CAAAGTGTCA
Statistics
Matches: 121, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
114 2 0.02
115 30 0.25
116 89 0.74
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.36
Consensus pattern (116 bp):
AGTATGATTTCCTTACCATTTTAGCACATAATATGCCCTATATGAAAATCCTACATTCAATATCA
TTTCCTTATCATTTAGCACACTCAGCGCTCCATATGGAAATCCATACACTC
Found at i:51411 original size:58 final size:58
Alignment explanation
Indices: 51239--51419 Score: 167
Period size: 58 Copynumber: 3.1 Consensus size: 58
51229 TGCCCTATTC
* * ** * *
51239 AAATTCATACCATTAGTATGATTTTGTTACCATTTTAGCACATGAA-ATGCCCTATATGA
1 AAATCCATACCATCAGTATGA-TTCCTTACCATTTTAGCACAT-AATATGCCCTATCTGG
* * * *
51298 AAATCCATACCATTAGTATGATTCCTTATCC-TTGTAGCACCCT--TAGTGCTCTATCTGG
1 AAATCCATACCATCAGTATGATTCCTTA-CCATTTTAGCA-CATAATA-TGCCCTATCTGG
51356 AAA-CCATA-CACTCAGTATGATTCCCTTACCATTTTAGCACATAATATGCCCTATCTGG
1 AAATCCATACCA-TCAGTATGATT-CCTTACCATTTTAGCACATAATATGCCCTATCTGG
51414 AAATCC
1 AAATCC
51420 TATTTTCAAT
Statistics
Matches: 100, Mismatches: 12, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
56 2 0.02
57 20 0.20
58 50 0.50
59 28 0.28
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (58 bp):
AAATCCATACCATCAGTATGATTCCTTACCATTTTAGCACATAATATGCCCTATCTGG
Done.