Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006698.1 Hibiscus syriacus cultivar Beakdansim tig00016665_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: 58308
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:7043 original size:36 final size:36
Alignment explanation
Indices: 7002--7104 Score: 179
Period size: 36 Copynumber: 2.9 Consensus size: 36
6992 ATTTATCCAT
*
7002 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
7038 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
* *
7074 TATCAGCTTTGGTATATTCGTGTACCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
7105 CCAGTACCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:13577 original size:19 final size:19
Alignment explanation
Indices: 13546--13598 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
13536 ACCAACAAAA
*
13546 TCGCAATGCGATCTCTAAT
1 TCGCATTGCGATCTCTAAT
*
13565 TCGCATTGTGATCTCTAAT
1 TCGCATTGCGATCTCTAAT
13584 TCGCATTGCGATCTC
1 TCGCATTGCGATCTC
13599 CATTATCGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (19 bp):
TCGCATTGCGATCTCTAAT
Found at i:13670 original size:21 final size:21
Alignment explanation
Indices: 13644--13697 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
13634 ATTTTCCAGT
13644 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
13665 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
13686 TAGCGTTGCGAT
1 TCGCGTTGCGAT
13698 TTTCCATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:13754 original size:19 final size:19
Alignment explanation
Indices: 13730--13792 Score: 126
Period size: 19 Copynumber: 3.3 Consensus size: 19
13720 TCTACAGTTG
13730 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
13749 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
13768 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
13787 TCGTTG
1 TCGTTG
13793 TGATAGTCTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.43
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:13819 original size:22 final size:22
Alignment explanation
Indices: 13787--13839 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
13777 TTTTCCAAAT
*
13787 TCGTTGTGATAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
*
13809 TTGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
13831 TCGTTGCGA
1 TCGTTGCGA
13840 AAATCCGTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.17, C:0.15, G:0.28, T:0.40
Consensus pattern (22 bp):
TCGTTGCGATAGTCTACAGTTG
Found at i:13932 original size:6 final size:6
Alignment explanation
Indices: 13921--13953 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
13911 GACAAGTATT
13921 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
13954 CGAGACGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:14604 original size:22 final size:22
Alignment explanation
Indices: 14577--14629 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
14567 AATTTGGAAA
14577 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
14599 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
14621 ATTGCAACG
1 ATCGCAACG
14630 CGAAATGGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:14669 original size:41 final size:41
Alignment explanation
Indices: 14618--14758 Score: 255
Period size: 41 Copynumber: 3.4 Consensus size: 41
14608 ACAACTGTAG
*
14618 ACTATTGCAACGCGAAATGGAAAATCGCGTTGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCGTTGCGATTTTCA
*
14659 ACTATCGCAACTCGAAATGGAAAATCGCGTTGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCGTTGCGATTTTCA
*
14700 ACTATCGCAACGCGAAATGGAAAATCGCATTGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCGTTGCGATTTTCA
14741 ACTATCGCAACGCGAAAT
1 ACTATCGCAACGCGAAAT
14759 ACAACGCGAA
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 96 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCGTTGCGATTTTCA
Found at i:14714 original size:21 final size:21
Alignment explanation
Indices: 14690--14755 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
14680 AAATCGCGTT
14690 GCGATTTTCAACTATCGCAAC
1 GCGATTTTCAACTATCGCAAC
** ** * **
14711 GCGAAATGGAA-AATCGCATT
1 GCGATTTTCAACTATCGCAAC
14731 GCGATTTTCAACTATCGCAAC
1 GCGATTTTCAACTATCGCAAC
14752 GCGA
1 GCGA
14756 AATACAACGC
Statistics
Matches: 30, Mismatches: 14, Indels: 2
0.65 0.30 0.04
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (21 bp):
GCGATTTTCAACTATCGCAAC
Found at i:14763 original size:21 final size:21
Alignment explanation
Indices: 14698--14763 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
14688 TTGCGATTTT
*
14698 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATA
* * ** ** *
14719 GAA-AATCGCATTGCGATTTT
1 CAACTATCGCAACGCGAAATA
14739 CAACTATCGCAACGCGAAATA
1 CAACTATCGCAACGCGAAATA
14760 CAAC
1 CAAC
14764 GCGAATTTGC
Statistics
Matches: 30, Mismatches: 14, Indels: 2
0.65 0.30 0.04
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.20
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATA
Found at i:14800 original size:28 final size:28
Alignment explanation
Indices: 14760--14826 Score: 125
Period size: 28 Copynumber: 2.4 Consensus size: 28
14750 ACGCGAAATA
14760 CAACGCGAATTTGCGATAGTGGAGATCG
1 CAACGCGAATTTGCGATAGTGGAGATCG
14788 CAACGCGAATTTGCGATAGTGGAGATCG
1 CAACGCGAATTTGCGATAGTGGAGATCG
*
14816 CAATGCGAATT
1 CAACGCGAATT
14827 AGAGATCGCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.22
Consensus pattern (28 bp):
CAACGCGAATTTGCGATAGTGGAGATCG
Found at i:14833 original size:19 final size:19
Alignment explanation
Indices: 14809--14861 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
14799 TGCGATAGTG
14809 GAGATCGCAATGCGAATTA
1 GAGATCGCAATGCGAATTA
14828 GAGATCGCAATGCGAATTA
1 GAGATCGCAATGCGAATTA
*
14847 GAGATCGCATTGCGA
1 GAGATCGCAATGCGA
14862 TTTTGTTGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (19 bp):
GAGATCGCAATGCGAATTA
Found at i:16182 original size:36 final size:36
Alignment explanation
Indices: 16141--16243 Score: 179
Period size: 36 Copynumber: 2.9 Consensus size: 36
16131 ATTTATCCAT
*
16141 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
16177 TATCAGCTTTGGTACATTCGTGTATCAATATTATCA
1 TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
*
16213 TATCAGCTTTGGTACATTCGTGTACCAATGT
1 TATCAGCTTTGGTACATTCGTGTATCAATGT
16244 CCAGCACCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 63 1.00
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (36 bp):
TATCAGCTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:26875 original size:23 final size:23
Alignment explanation
Indices: 26845--26893 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
26835 TCCTTCGACT
26845 GCCGCTTGTGTGGAGGGATGTAA
1 GCCGCTTGTGTGGAGGGATGTAA
26868 GCCGCTTGTGTGGAGGGATGTAA
1 GCCGCTTGTGTGGAGGGATGTAA
26891 GCC
1 GCC
26894 ATGTATGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.16, C:0.16, G:0.43, T:0.24
Consensus pattern (23 bp):
GCCGCTTGTGTGGAGGGATGTAA
Found at i:29322 original size:22 final size:22
Alignment explanation
Indices: 29294--29338 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
29284 CTATTTTATA
29294 ATTTCTAATAGTTAGGAGACTC
1 ATTTCTAATAGTTAGGAGACTC
29316 ATTTCTAATAGTTAGGAGACTC
1 ATTTCTAATAGTTAGGAGACTC
29338 A
1 A
29339 GTAACCTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (22 bp):
ATTTCTAATAGTTAGGAGACTC
Found at i:30204 original size:29 final size:29
Alignment explanation
Indices: 30160--30348 Score: 317
Period size: 29 Copynumber: 6.5 Consensus size: 29
30150 GTTGACTCGA
* *
30160 GTGTTATTTTCGTAAATATTGTTAAAAGG
1 GTGTTAGTTTCGTAAATATTTTTAAAAGG
*
30189 GTGTTAGTTTCATAAATATTTTTAAAAGG
1 GTGTTAGTTTCGTAAATATTTTTAAAAGG
30218 GTGTTAGTTTCGTAAATATTTTTAAAAGG
1 GTGTTAGTTTCGTAAATATTTTTAAAAGG
*
30247 GTGTTAGTTTTGTAAATATTTTTAAAA-G
1 GTGTTAGTTTCGTAAATATTTTTAAAAGG
30275 GTGTTAGTTTCGTAAATATTTTTAAAAAGG
1 GTGTTAGTTTCGTAAATATTTTT-AAAAGG
30305 GTGTTAGTTTCGTAAATATTTTTAAAAGG
1 GTGTTAGTTTCGTAAATATTTTTAAAAGG
*
30334 GTGTTAGTTTTGTAA
1 GTGTTAGTTTCGTAA
30349 TTAATTTCTG
Statistics
Matches: 151, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
28 23 0.15
29 104 0.69
30 24 0.16
ACGTcount: A:0.31, C:0.03, G:0.20, T:0.46
Consensus pattern (29 bp):
GTGTTAGTTTCGTAAATATTTTTAAAAGG
Found at i:33293 original size:25 final size:25
Alignment explanation
Indices: 33258--33310 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
33248 AAGGCAACTC
* *
33258 TTTTATAAGATTTACTGCATTATGA
1 TTTTATAAGATTTACTGAACTATGA
*
33283 TTTTATGAGATTTACTGAACTATGA
1 TTTTATAAGATTTACTGAACTATGA
33308 TTT
1 TTT
33311 GTTTAGTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.13, T:0.49
Consensus pattern (25 bp):
TTTTATAAGATTTACTGAACTATGA
Found at i:39901 original size:35 final size:35
Alignment explanation
Indices: 39855--39922 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
39845 CGTCACGTCC
* *
39855 AGTAAGGCCCTGAGCACACAGTCGAGGAGCCGCTA
1 AGTAAGGCCCTGAGCAAAAAGTCGAGGAGCCGCTA
*
39890 AGTAAGGCCCTGAGTAAAAAGTCGAGGAGCCGC
1 AGTAAGGCCCTGAGCAAAAAGTCGAGGAGCCGC
39923 CATGTATTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.31, C:0.25, G:0.32, T:0.12
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCAAAAAGTCGAGGAGCCGCTA
Found at i:40018 original size:24 final size:24
Alignment explanation
Indices: 40005--40123 Score: 177
Period size: 24 Copynumber: 5.0 Consensus size: 24
39995 AAACATAATT
* *
40005 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCAGATCAGAATC
*
40029 CAGGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCAGATCAGAATC
*
40053 CAAGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCAGATCAGAATC
40077 CATGTC-AGATATCAGATCAGAATC
1 CATGTCAAG-TATCAGATCAGAATC
*
40101 CATGTCAAGTATCAAATCAGAAT
1 CATGTCAAGTATCAGATCAGAAT
40124 TCAAATCGCA
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
23 2 0.02
24 83 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
CATGTCAAGTATCAGATCAGAATC
Found at i:40139 original size:48 final size:48
Alignment explanation
Indices: 40008--40141 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 48
39998 CATAATTCAT
* * ** *
40008 GTCAAGTATCATATCAAAATCCAGGTCA-AGTATCAGATCAGAATCCAA
1 GTCAAGTATCAAATCAGAATCCAAATCAGA-AATCAGATCAGAATCCAA
* ** * *
40056 GTCAAGTATCAGATCAGAATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAAATCAGAATCCAAATCAGAAATCAGATCAGAATCCAA
*
40104 GTCAAGTATCAAATCAGAATTCAAATC-GCAAATCAGAT
1 GTCAAGTATCAAATCAGAATCCAAATCAG-AAATCAGAT
40142 AAAAATATTC
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
47 1 0.01
48 73 0.97
49 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (48 bp):
GTCAAGTATCAAATCAGAATCCAAATCAGAAATCAGATCAGAATCCAA
Found at i:43763 original size:30 final size:29
Alignment explanation
Indices: 43698--43831 Score: 189
Period size: 30 Copynumber: 4.6 Consensus size: 29
43688 CATTGACTCG
* *
43698 GGTGTTACTTTCGTAAATATTGTT-AAAA
1 GGTGTTAGTTTCGTAAATATTTTTAAAAA
43726 GGATGTTAGTTTCGTAAATATTTTTTAAAAA
1 GG-TGTTAGTTTCGTAAATA-TTTTTAAAAA
43757 GGTGTTAGTTTCGTAAATATTTTTAAAAAA
1 GGTGTTAGTTTCGTAAATATTTTT-AAAAA
*
43787 GGTGTTAGTTTCGTAAATATTTTTAAAAG
1 GGTGTTAGTTTCGTAAATATTTTTAAAAA
* *
43816 GGTATTAGTTTTGTAA
1 GGTGTTAGTTTCGTAA
43832 TTAATTTATA
Statistics
Matches: 97, Mismatches: 5, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
28 2 0.02
29 39 0.40
30 50 0.52
31 6 0.06
ACGTcount: A:0.33, C:0.04, G:0.19, T:0.45
Consensus pattern (29 bp):
GGTGTTAGTTTCGTAAATATTTTTAAAAA
Found at i:43810 original size:59 final size:59
Alignment explanation
Indices: 43698--43831 Score: 191
Period size: 59 Copynumber: 2.3 Consensus size: 59
43688 CATTGACTCG
*
43698 GGTGTTACTTTCGTAAATATTGTTAAAAGGATGTTAGTTTCGTAAATATTTTTTAAAAA
1 GGTGTTAGTTTCGTAAATATTGTTAAAAGGATGTTAGTTTCGTAAATATTTTTTAAAAA
* *
43757 GGTGTTAGTTTCGTAAATATTTTTAAAAAAGG-TGTTAGTTTCGTAAATA-TTTTTAAAAG
1 GGTGTTAGTTTCGTAAATATTGTT--AAAAGGATGTTAGTTTCGTAAATATTTTTTAAAAA
* *
43816 GGTATTAGTTTTGTAA
1 GGTGTTAGTTTCGTAA
43832 TTAATTTATA
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
59 45 0.66
60 17 0.25
61 6 0.09
ACGTcount: A:0.33, C:0.04, G:0.19, T:0.45
Consensus pattern (59 bp):
GGTGTTAGTTTCGTAAATATTGTTAAAAGGATGTTAGTTTCGTAAATATTTTTTAAAAA
Found at i:44920 original size:25 final size:25
Alignment explanation
Indices: 44892--44942 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
44882 AGAGTAACTC
*
44892 TTTTATAAGATTTACTGCAGTATGA
1 TTTTATAAGATTTACTGCACTATGA
* *
44917 TTTTATGAGATTTACTGGACTATGA
1 TTTTATAAGATTTACTGCACTATGA
44942 T
1 T
44943 ATGTTTAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (25 bp):
TTTTATAAGATTTACTGCACTATGA
Found at i:48978 original size:22 final size:22
Alignment explanation
Indices: 48953--48996 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
48943 AATTTATTAG
48953 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
48975 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
48997 AATTTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:49055 original size:31 final size:31
Alignment explanation
Indices: 49020--49078 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
49010 AGTTGTATGG
* *
49020 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
49051 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
49079 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:49201 original size:22 final size:22
Alignment explanation
Indices: 49176--49219 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
49166 AATTTATTAG
*
49176 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTAAAAA
49198 TATGGATTGATTTATTTAAAAA
1 TATGGATTGATTTATTTAAAAA
49220 AAATTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.48
Consensus pattern (22 bp):
TATGGATTGATTTATTTAAAAA
Found at i:49229 original size:223 final size:223
Alignment explanation
Indices: 48828--49365 Score: 1004
Period size: 223 Copynumber: 2.4 Consensus size: 223
48818 AGTTGTATGG
48828 ATTATTTAAATTTCAGTATTGCAAAACTCTTTTAAGTTTAAAAAATCAGTTTATTTATATTTCAG
1 ATTATTTAAATTTCAGTATTGCAAAACTCTTTTAAGTTTAAAAAATCAGTTTATTTATATTTCAG
48893 TTTATTTTAGCAGTCTGCAGACGTTAATTTAATAAGGTTATTTATTAAATAATTTATTAGTATGG
66 TTTATTTTAGCAGTCTGCAGACGTTAATTTAATAAGGTTATTTATTAAATAATTTATTAGTATGG
* *
48958 ATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAAAATTTATTATTGTAGTTGTATGGATT
131 ATTGATTTATTTTAAAATATGGATTGATTTATTTAAAAAAAATTATTATTGTAGTTGTATGGATT
*
49023 ATTTAAATTTCAGTATTGTAAAACTAAA
196 ATTTAAATTTCAGTATTATAAAACTAAA
* *
49051 ATTATTTAAATCTCAGTATTGCAAAACTCTTTTAAGTTTAAAAAATCAGTTTATTTATATTTTAG
1 ATTATTTAAATTTCAGTATTGCAAAACTCTTTTAAGTTTAAAAAATCAGTTTATTTATATTTCAG
* *
49116 TTTATTTTAGCAGTATGCAGATGTTAATTTAATAAGGTTATTTATTAAATAATTTATTAGTATGG
66 TTTATTTTAGCAGTCTGCAGACGTTAATTTAATAAGGTTATTTATTAAATAATTTATTAGTATGG
49181 ATTGATTTATTTTAAAATATGGATTGATTTATTTAAAAAAAATTATTATTGTAGTTGTATGGATT
131 ATTGATTTATTTTAAAATATGGATTGATTTATTTAAAAAAAATTATTATTGTAGTTGTATGGATT
*
49246 ATTTAAATTTCAGTTTTATAAAACTAAA
196 ATTTAAATTTCAGTATTATAAAACTAAA
49274 ATTATTTAAATTTCAGTATTGCAAAACTCTTTTAAGTTTAAAAAATCAGTTTATTTATATTTCAG
1 ATTATTTAAATTTCAGTATTGCAAAACTCTTTTAAGTTTAAAAAATCAGTTTATTTATATTTCAG
49339 TTTATTTTAGCAGTCTGCAGACGTTAA
66 TTTATTTTAGCAGTCTGCAGACGTTAA
49366 AAAACAAACA
Statistics
Matches: 303, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
223 303 1.00
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (223 bp):
ATTATTTAAATTTCAGTATTGCAAAACTCTTTTAAGTTTAAAAAATCAGTTTATTTATATTTCAG
TTTATTTTAGCAGTCTGCAGACGTTAATTTAATAAGGTTATTTATTAAATAATTTATTAGTATGG
ATTGATTTATTTTAAAATATGGATTGATTTATTTAAAAAAAATTATTATTGTAGTTGTATGGATT
ATTTAAATTTCAGTATTATAAAACTAAA
Found at i:49300 original size:31 final size:31
Alignment explanation
Indices: 49243--49301 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
49233 AGTTGTATGG
* *
49243 ATTATTTAAATTTCAGTTTTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
*
49274 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
49302 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.44
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:52907 original size:33 final size:34
Alignment explanation
Indices: 52850--52918 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 34
52840 TAATTTTAAA
* * *
52850 TTTAAAAAATATTATTATATTTAAAATAT-ATTT
1 TTTAAAAAATATAAGTATATTTAAAAAATCATTT
52883 TTTAAAAAATATAAGTAT-TATTAAAAAATCATTT
1 TTTAAAAAATATAAGTATAT-TTAAAAAATCATTT
52917 TT
1 TT
52919 AGGAAAAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 1 0.03
33 24 0.77
34 6 0.19
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (34 bp):
TTTAAAAAATATAAGTATATTTAAAAAATCATTT
Found at i:56883 original size:20 final size:20
Alignment explanation
Indices: 56832--56874 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
56822 GAACCGATTT
* *
56832 GAACCAGTCCGAGTCAACCC
1 GAACCAATCTGAGTCAACCC
56852 GAACCAATCTGAGTCAACCC
1 GAACCAATCTGAGTCAACCC
56872 GAA
1 GAA
56875 TCGGTCTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.35, G:0.19, T:0.12
Consensus pattern (20 bp):
GAACCAATCTGAGTCAACCC
Found at i:56961 original size:19 final size:19
Alignment explanation
Indices: 56900--56968 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 19
56890 GAATTTGACC
* *
56900 CATTAACTTTGACCTGA-T
1 CATTGACTTTGACCCGACT
56918 CCATT-ACTTTGACCCGACT
1 -CATTGACTTTGACCCGACT
* * *
56937 TATTGAGTTTGACCTGACT
1 CATTGACTTTGACCCGACT
*
56956 CGTTGACTTTGAC
1 CATTGACTTTGAC
56969 ATAAAAAGTA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
18 14 0.34
19 27 0.66
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.38
Consensus pattern (19 bp):
CATTGACTTTGACCCGACT
Found at i:58248 original size:13 final size:13
Alignment explanation
Indices: 58214--58251 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
58204 GAGTCAACCT
58214 ATTAACTTTGACCC
1 ATTAACTTTGA-CC
*
58228 ATT-GCTTTGACC
1 ATTAACTTTGACC
58240 ATTAACTTTGAC
1 ATTAACTTTGAC
58252 GAAAAGTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 5 0.24
13 13 0.62
14 3 0.14
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (13 bp):
ATTAACTTTGACC
Done.