Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002193.1 Hibiscus syriacus cultivar Beakdansim tig00004470_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: 83957
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:62 original size:29 final size:29
Alignment explanation
Indices: 16--100 Score: 136
Period size: 29 Copynumber: 2.9 Consensus size: 29
6 AGCAAGGGTA
*
16 GTCGCCCGGAGTGTATGGCGACCTACAAG
1 GTCGCCCGGAGTGCATGGCGACCTACAAG
*
45 GTCGCCTGGAGTGCATGGCGACCTACAAG
1 GTCGCCCGGAGTGCATGGCGACCTACAAG
74 GTCGCCCGGAAG-GCATGGCGACCTACA
1 GTCGCCCGG-AGTGCATGGCGACCTACA
101 GCCAACACTG
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
29 50 0.96
30 2 0.04
ACGTcount: A:0.21, C:0.29, G:0.34, T:0.15
Consensus pattern (29 bp):
GTCGCCCGGAGTGCATGGCGACCTACAAG
Found at i:1213 original size:18 final size:17
Alignment explanation
Indices: 1173--1217 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
1163 CTCCAAAACG
1173 AATTTATAAAAAAATTA
1 AATTTATAAAAAAATTA
1190 AA-TTATCAATAAAAA-TA
1 AATTTAT-AA-AAAAATTA
1207 AATTTATAAAA
1 AATTTATAAAA
1218 TTTTTCAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
16 6 0.24
17 10 0.40
18 9 0.36
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
AATTTATAAAAAAATTA
Found at i:11454 original size:22 final size:23
Alignment explanation
Indices: 11429--11476 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
11419 AATTTTATTT
11429 TATTTAAT-AAAAACAACTTTTA
1 TATTTAATAAAAAACAACTTTTA
*
11451 TATTTAATAAAAAATAACTTTTA
1 TATTTAATAAAAAACAACTTTTA
11474 TAT
1 TAT
11477 ATACTGTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (23 bp):
TATTTAATAAAAAACAACTTTTA
Found at i:12156 original size:2 final size:2
Alignment explanation
Indices: 12151--12175 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12141 ATAAATTTTA
12151 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 A
12176 AGATAAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14919 original size:34 final size:36
Alignment explanation
Indices: 14850--14920 Score: 101
Period size: 35 Copynumber: 2.0 Consensus size: 36
14840 GTTTGAAAAT
* *
14850 ATTTATATATTTTCTTTAAAAATTTAAATTAATAAA
1 ATTTATATATTTTCTTTAAAAATTGAAAATAATAAA
*
14886 ATTTATATATTTT-TTTATAAATTGAAAAT-ATAAA
1 ATTTATATATTTTCTTTAAAAATTGAAAATAATAAA
14920 A
1 A
14921 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 6 0.19
35 13 0.41
36 13 0.41
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTGAAAATAATAAA
Found at i:15335 original size:25 final size:25
Alignment explanation
Indices: 15307--15354 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
15297 CGTTATATAA
15307 CGATCAATACTCTAGTAACATAAAT
1 CGATCAATACTCTAGTAACATAAAT
*
15332 CGATCACTACTCTAGTAACATAA
1 CGATCAATACTCTAGTAACATAA
15355 CGCTATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (25 bp):
CGATCAATACTCTAGTAACATAAAT
Found at i:32476 original size:27 final size:27
Alignment explanation
Indices: 32446--32497 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
32436 ATTGTAAAAA
*
32446 AATAATAT-AATTTTAATATTTACATAT
1 AATAATATAAATTTAAAT-TTTACATAT
*
32473 AATATTATAAATTTAAATTTTACAT
1 AATAATATAAATTTAAATTTTACAT
32498 GATATAGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 14 0.64
28 8 0.36
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (27 bp):
AATAATATAAATTTAAATTTTACATAT
Found at i:32984 original size:59 final size:59
Alignment explanation
Indices: 32842--32985 Score: 188
Period size: 59 Copynumber: 2.4 Consensus size: 59
32832 TTTTTAGGGT
*
32842 AAAG-TACACAAATAGTC-CTTCGACTATAGGTGATGCTTTGTTGAGTCCCTCGACTATTA
1 AAAGTTACA-AAATGGTCACTT-GACTATAGGTGATGCTTTGTTGAGTCCCTCGACTATTA
* * *
32901 AAAGTTATAAAATGATCA-TCTGACTATAGGGTGTTGCTTTGTTGAGT-CCTCGACTATTA
1 AAAGTTACAAAATGGTCACT-TGACTATA-GGTGATGCTTTGTTGAGTCCCTCGACTATTA
32960 AAAGTTACAAAATGGTCACTTGACTA
1 AAAGTTACAAAATGGTCACTTGACTA
32986 ATTAGTATGT
Statistics
Matches: 74, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
59 52 0.70
60 22 0.30
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (59 bp):
AAAGTTACAAAATGGTCACTTGACTATAGGTGATGCTTTGTTGAGTCCCTCGACTATTA
Found at i:34098 original size:21 final size:21
Alignment explanation
Indices: 34074--34126 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
34064 ATTATGACTA
34074 TCGCAATGCGATTTT-CCAATT
1 TCGCAATGCGATTTTCCCAA-T
**
34095 TCGCGTTGCGATTTTCCCAAT
1 TCGCAATGCGATTTTCCCAAT
34116 TCGCAATGCGA
1 TCGCAATGCGA
34127 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCCAAT
Found at i:34159 original size:21 final size:20
Alignment explanation
Indices: 34116--34162 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
34106 TTTTCCCAAT
*
34116 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
34136 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
34157 TCGCAA
1 TCGCAA
34163 CGCAATACTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:34181 original size:20 final size:20
Alignment explanation
Indices: 34156--34250 Score: 102
Period size: 20 Copynumber: 4.7 Consensus size: 20
34146 AATTTGGAAA
*
34156 ATCGCAACGCAATACTGACT
1 ATCGCAACGCGATACTGACT
* *
34176 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
34197 ATCGCAACGCGATACTTACT
1 ATCGCAACGCGATACTGACT
*
34217 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
34237 TTCGCAACGAGATA
1 ATCGCAACGCGATA
34251 ATACATAATC
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.70
21 15 0.23
22 2 0.03
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:34229 original size:41 final size:41
Alignment explanation
Indices: 34153--34230 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
34143 GCGAATTTGG
34153 AAAATCGCAACGCAATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCAATACTGACTATCGCAACGCGATAATAC
* * *
34194 AAAATCGCAACGCGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGCAATACTGACTATCGCAACGCGATA
34231 CTGACTTTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.19
Consensus pattern (41 bp):
AAAATCGCAACGCAATACTGACTATCGCAACGCGATAATAC
Found at i:34264 original size:21 final size:19
Alignment explanation
Indices: 34156--34270 Score: 86
Period size: 20 Copynumber: 5.7 Consensus size: 19
34146 AATTTGGAAA
* *
34156 ATCGCAACGCAATACTGACT
1 ATCGCAACGCGATAAT-ACT
*
34176 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATAC--T
*
34197 ATCGCAACGCGATACTTACT
1 ATCGCAACGCGATA-ATACT
* *
34217 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATAAT-ACT
* *
34237 TTCGCAACGAGATAATACAT
1 ATCGCAACGCGATAATAC-T
*
34257 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
34271 TTTCAAAGCG
Statistics
Matches: 77, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
19 5 0.06
20 45 0.58
21 24 0.31
22 3 0.04
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.22
Consensus pattern (19 bp):
ATCGCAACGCGATAATACT
Found at i:34486 original size:22 final size:22
Alignment explanation
Indices: 34440--34486 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
34430 TCTCTCACCC
*
34440 ATCTCCGACGAAATCCGTCCCT
1 ATCTCCGACGAAATCCGTCCAT
* *
34462 ATCTCCGGCGAAATCCGTCTAT
1 ATCTCCGACGAAATCCGTCCAT
34484 ATC
1 ATC
34487 CGTCTCTCAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.36, G:0.15, T:0.26
Consensus pattern (22 bp):
ATCTCCGACGAAATCCGTCCAT
Found at i:34793 original size:20 final size:20
Alignment explanation
Indices: 34744--34802 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
34734 TTTATTCTCT
* **
34744 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
34764 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
34784 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
34803 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:36142 original size:18 final size:18
Alignment explanation
Indices: 36121--36186 Score: 114
Period size: 18 Copynumber: 3.7 Consensus size: 18
36111 TCCACTTCAG
36121 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
36139 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
36157 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
36175 GAGCCATCACCT
1 GAGCCATCACCT
36187 GATCGACCCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.27, C:0.45, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:36752 original size:20 final size:20
Alignment explanation
Indices: 36727--36772 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
36717 TAGTTTACTT
36727 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
** * *
36747 TCGCAATGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
36767 TCGCAA
1 TCGCAA
36773 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:36781 original size:19 final size:20
Alignment explanation
Indices: 36738--36782 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
36728 CGCAACACGA
36738 AAATGACTATCGCAATGCGG
1 AAATGACTATCGCAATGCGG
*
36758 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAATGCGG
36777 AAATGA
1 AAATGA
36783 AAATTGCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (20 bp):
AAATGACTATCGCAATGCGG
Found at i:36791 original size:19 final size:19
Alignment explanation
Indices: 36746--36848 Score: 108
Period size: 19 Copynumber: 5.6 Consensus size: 19
36736 GAAAATGACT
***
36746 ATCGCAATGCGGAAATGGCT
1 ATCGCAATGC-GAAATGAAA
36766 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
36785 ATTGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
36799 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
36818 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
36837 ATCGCAATGCGA
1 ATCGCAATGCGA
36849 TTTGTGTTTC
Statistics
Matches: 69, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 44 0.64
20 10 0.14
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:36920 original size:20 final size:19
Alignment explanation
Indices: 36886--36943 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 19
36876 TTGCGATTTT
*
36886 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
36905 CATTTCCGCGTTGCGATAGC
1 CATTT-CGCGTTGCGATAGC
36925 CATTTTCGCGTTGCGATAG
1 CA-TTTCGCGTTGCGATAG
36944 TAAGTTTCGT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 5 0.14
20 28 0.78
21 3 0.08
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:36951 original size:20 final size:19
Alignment explanation
Indices: 36887--36960 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
36877 TGCGATTTTC
* *
36887 ATTTCGCATTGCGATAGCC
1 ATTTCGCGTTGCGATAGCA
36906 ATTTCCGCGTTGCGATAGCCA
1 ATTT-CGCGTTGCGATAG-CA
* *
36927 TTTTCGCGTTGCGATAGTA
1 ATTTCGCGTTGCGATAGCA
*
36946 AGTTTCGTGTTGCGA
1 A-TTTCGCGTTGCGA
36961 AAGTAAACTA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
19 5 0.11
20 37 0.80
21 4 0.09
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.35
Consensus pattern (19 bp):
ATTTCGCGTTGCGATAGCA
Found at i:36965 original size:20 final size:20
Alignment explanation
Indices: 36928--36966 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
36918 CGATAGCCAT
*
36928 TTTCGCGTTGCGATAGTAAG
1 TTTCGCGTTGCGAAAGTAAG
*
36948 TTTCGTGTTGCGAAAGTAA
1 TTTCGCGTTGCGAAAGTAA
36967 ACTATTCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.36
Consensus pattern (20 bp):
TTTCGCGTTGCGAAAGTAAG
Found at i:37367 original size:42 final size:41
Alignment explanation
Indices: 37308--37386 Score: 122
Period size: 42 Copynumber: 1.9 Consensus size: 41
37298 GACTCACCTG
*
37308 TCATCCCTCAAGAGTCCCCTCAAATCGTTCAAGAGGCCCATA
1 TCATCCCTCAAGAGTCCCC-CAAACCGTTCAAGAGGCCCATA
**
37350 TCATCCCTCAAGAGTCCCCCCCACCGTTCAAGAGGCC
1 TCATCCCTCAAGAGTCCCCCAAACCGTTCAAGAGGCC
37387 ACTGTCATCG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
41 15 0.44
42 19 0.56
ACGTcount: A:0.25, C:0.41, G:0.15, T:0.19
Consensus pattern (41 bp):
TCATCCCTCAAGAGTCCCCCAAACCGTTCAAGAGGCCCATA
Found at i:37395 original size:41 final size:41
Alignment explanation
Indices: 37304--37395 Score: 123
Period size: 41 Copynumber: 2.2 Consensus size: 41
37294 GCCCGACTCA
*
37304 CCTGTCATCCCTCAAGAGTCCCCTCAAATCGTTCAAGAGGC
1 CCTGTCATCCCTCAAGAGTCCCCTCAAACCGTTCAAGAGGC
* **
37345 CCATATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGC
1 CC-TGTCATCCCTCAAGAGTCCCCTCAAACCGTTCAAGAGGC
37386 CACTGTCATC
1 C-CTGTCATC
37396 GTTGAAGAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
41 23 0.52
42 21 0.48
ACGTcount: A:0.24, C:0.40, G:0.15, T:0.21
Consensus pattern (41 bp):
CCTGTCATCCCTCAAGAGTCCCCTCAAACCGTTCAAGAGGC
Found at i:38825 original size:14 final size:14
Alignment explanation
Indices: 38791--38829 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
38781 TTGATTGTTT
38791 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
38805 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
38819 TGTTGATTTGT
1 AATTGATTTGT
38830 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:38993 original size:19 final size:19
Alignment explanation
Indices: 38969--39033 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
38959 GCAACGAGAG
38969 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
38988 AATCGCAATGCGAAATAAA
1 AATCGCAATGCGAAATGAA
39007 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
39021 AATCGCAATGCGA
1 AATCGCAATGCGA
39034 TTTTCTCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
14 10 0.24
15 1 0.02
16 2 0.05
17 2 0.05
19 26 0.63
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:39058 original size:20 final size:20
Alignment explanation
Indices: 39033--39108 Score: 125
Period size: 20 Copynumber: 3.8 Consensus size: 20
39023 TCGCAATGCG
* *
39033 ATTTTCTCGTTACGATAGCC
1 ATTTTCGCGTTGCGATAGCC
39053 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
39073 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGCC
39093 ATTTTCGCGTTGCGAT
1 ATTTTCGCGTTGCGAT
39109 TTCCCCGTTG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:39347 original size:20 final size:20
Alignment explanation
Indices: 39331--39383 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
39321 ATTGCGATTT
*
39331 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
39351 TCAGAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
*
39371 TCAGTATCGCGTT
1 TCAGAATCGCGTT
39384 ACGATTTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (20 bp):
TCAGAATCGCGTTGCGAAAG
Found at i:39447 original size:21 final size:20
Alignment explanation
Indices: 39421--39469 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
39411 GTCAGTATCA
*
39421 CATTGCGATTTTCCAAATTCG
1 CATTGCGA-TTTACAAATTCG
**
39442 CATTGCGATTTACTTATTCG
1 CATTGCGATTTACAAATTCG
39462 CATTGCGA
1 CATTGCGA
39470 ATTGGGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (20 bp):
CATTGCGATTTACAAATTCG
Found at i:39511 original size:21 final size:22
Alignment explanation
Indices: 39459--39511 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
39449 ATTTACTTAT
39459 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
** *
39480 TCGCAACGCGAAATT-GTAAAA
1 TCGCATTGCGAAATTGGGAAAA
39501 TCGCATTGCGA
1 TCGCATTGCGA
39512 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.23
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:42221 original size:27 final size:27
Alignment explanation
Indices: 42191--42244 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
42181 ACCAGAAATA
42191 TATGCATAATTATCTTAAAGTAACTTT
1 TATGCATAATTATCTTAAAGTAACTTT
*
42218 TATGCATAATTCTCTTAAAGTAACTTT
1 TATGCATAATTATCTTAAAGTAACTTT
42245 CTTTCATTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.44
Consensus pattern (27 bp):
TATGCATAATTATCTTAAAGTAACTTT
Found at i:44073 original size:2 final size:2
Alignment explanation
Indices: 44066--44095 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
44056 TCCAATCATC
44066 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
44096 TGTTCTAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47380 original size:16 final size:16
Alignment explanation
Indices: 47361--47399 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
47351 CAAACATAAA
*
47361 AAACATTTCCATTAAG
1 AAACATATCCATTAAG
47377 AAACATATCCATTAAG
1 AAACATATCCATTAAG
47393 AAACATA
1 AAACATA
47400 ATAAAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.51, C:0.18, G:0.05, T:0.26
Consensus pattern (16 bp):
AAACATATCCATTAAG
Found at i:51973 original size:24 final size:24
Alignment explanation
Indices: 51946--52001 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
51936 TTAAATAGTT
51946 ATTTTGGCATTTATTTTTTTTAGC
1 ATTTTGGCATTTATTTTTTTTAGC
* *
51970 ATTTTCGCTTTTATTTTTTTTAGC
1 ATTTTGGCATTTATTTTTTTTAGC
51994 ATTTTGGC
1 ATTTTGGC
52002 TACAATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.14, C:0.11, G:0.12, T:0.62
Consensus pattern (24 bp):
ATTTTGGCATTTATTTTTTTTAGC
Found at i:53341 original size:2 final size:2
Alignment explanation
Indices: 53334--53365 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
53324 ATTTAACATA
53334 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
53366 TGATGAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58025 original size:19 final size:19
Alignment explanation
Indices: 58001--58037 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
57991 ACCCTTCATT
58001 TTTTATCGTGGAACCATCC
1 TTTTATCGTGGAACCATCC
*
58020 TTTTATCTTGGAACCATC
1 TTTTATCGTGGAACCATC
58038 GAAACTAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (19 bp):
TTTTATCGTGGAACCATCC
Found at i:61361 original size:60 final size:59
Alignment explanation
Indices: 61196--61366 Score: 173
Period size: 60 Copynumber: 2.8 Consensus size: 59
61186 TTCGGATGAA
* * * * ** *
61196 TTTAGGGATATAATTGGAATATTTAAAAGTTTAGGGACCCATTTAGAAA-GAGGGTCATAG
1 TTTAGGGATA-AATTAGAATATTAAAAAGTTTAAGGACCAATTTA-AAATGAAAGCCATAG
* * ****
61256 TTTAGTGATAAAATTAGAATATTCAAAAGTTTAAGGATTGTTTTAAAATGAAAGCCATAG
1 TTTAGGGAT-AAATTAGAATATTAAAAAGTTTAAGGACCAATTTAAAATGAAAGCCATAG
*
61316 TTTAGGGATCAAATTAGAATATTAAAAAGTTTAAGTACCAATTTAAAATGA
1 TTTAGGGAT-AAATTAGAATATTAAAAAGTTTAAGGACCAATTTAAAATGA
61367 GGGTTATAGG
Statistics
Matches: 90, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
59 3 0.03
60 86 0.96
61 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (59 bp):
TTTAGGGATAAATTAGAATATTAAAAAGTTTAAGGACCAATTTAAAATGAAAGCCATAG
Found at i:61904 original size:2 final size:2
Alignment explanation
Indices: 61897--61932 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
61887 TATAAAAGAG
61897 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61933 GTTTCTTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:62095 original size:30 final size:29
Alignment explanation
Indices: 61999--62337 Score: 196
Period size: 30 Copynumber: 11.5 Consensus size: 29
61989 ATCTCAAAAT
61999 TTAAAAATATATTTTATTCTT-T-TTAAC
1 TTAAAAATATATTTTATTCTTATCTTAAC
** * *
62026 TTATTGAGTTTATTTTATTCTTATCTTAA-
1 TTA-AAAATATATTTTATTCTTATCTTAAC
* *
62055 TTGAAAAATGTATTTTAATCTTATCTTAAC
1 TT-AAAAATATATTTTATTCTTATCTTAAC
* * *
62085 TTATAAAATGTATTTTATTCCTAACTTAAC
1 TTA-AAAATATATTTTATTCTTATCTTAAC
*
62115 TTAAAAATATA-TTTATTTTTATCTTAAC
1 TTAAAAATATATTTTATTCTTATCTTAAC
** * ** *
62143 TTGTTACATATA--TTA-TCTTAAGTTAAA
1 TT-AAAAATATATTTTATTCTTATCTTAAC
* * * * *
62170 TTATTAAATATAATATATTCTTACCTTAAA
1 TTA-AAAATATATTTTATTCTTATCTTAAC
*
62200 TTATTAAATAT-TATTTATTCTTATCTTAAC
1 TTA-AAAATATAT-TTTATTCTTATCTTAAC
* *
62230 TTGAAAATATACATTTTATT-TTAAT-TTAAAAAA
1 TT-AAAA-ATATATTTTATTCTT-ATCTT---AAC
** * *
62263 TATATTAATATATTTTATTCTTATTTTTAAT
1 T-TAAAAATATATTTTATTCTTA-TCTTAAC
*
62294 TTAAAAATATATTTTATTTTTATCTTAAC
1 TTAAAAATATATTTTATTCTTATCTTAAC
62323 TATAAAAA-ATATTTT
1 T-TAAAAATATATTTT
62338 TTTATCTCAA
Statistics
Matches: 244, Mismatches: 44, Indels: 46
0.73 0.13 0.14
Matches are distributed among these distances:
27 20 0.08
28 33 0.14
29 52 0.21
30 100 0.41
31 15 0.06
32 13 0.05
33 8 0.03
34 3 0.01
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (29 bp):
TTAAAAATATATTTTATTCTTATCTTAAC
Found at i:62099 original size:59 final size:58
Alignment explanation
Indices: 61999--62144 Score: 172
Period size: 59 Copynumber: 2.5 Consensus size: 58
61989 ATCTCAAAAT
** * * * *
61999 TTAAAAATATATTTTATTCTT-T-TTAACTTATTGAGTTTATTTTATTCTTATCTTAA
1 TTAAAAATATATTTTATTCTTATCTTAACTTATAAAATGTATTTTATTCCTAACTTAA
* *
62055 TTGAAAAATGTATTTTAATCTTATCTTAACTTATAAAATGTATTTTATTCCTAACTTAA
1 TT-AAAAATATATTTTATTCTTATCTTAACTTATAAAATGTATTTTATTCCTAACTTAA
*
62114 CTTAAAAATATA-TTTATTTTTATCTTAACTT
1 -TTAAAAATATATTTTATTCTTATCTTAACTT
62145 GTTACATATA
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
56 2 0.03
57 17 0.23
58 18 0.24
59 36 0.48
60 2 0.03
ACGTcount: A:0.34, C:0.09, G:0.03, T:0.53
Consensus pattern (58 bp):
TTAAAAATATATTTTATTCTTATCTTAACTTATAAAATGTATTTTATTCCTAACTTAA
Found at i:65192 original size:2 final size:2
Alignment explanation
Indices: 65187--65214 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
65177 GACAAGGGGG
65187 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
65215 ACTTTAACGC
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:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:73634 original size:19 final size:20
Alignment explanation
Indices: 73596--73635 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
73586 TCTCTCTCAA
*
73596 TTTAACCTTCACTCTTTATT
1 TTTAACCTTCACTATTTATT
*
73616 TTTAGCCTTCA-TATTTATT
1 TTTAACCTTCACTATTTATT
73635 T
1 T
73636 GACACATTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.20, C:0.20, G:0.03, T:0.57
Consensus pattern (20 bp):
TTTAACCTTCACTATTTATT
Found at i:75849 original size:21 final size:21
Alignment explanation
Indices: 75783--75849 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
75773 AGAAACCATG
75783 GTTTTAGTCCATCATGTTCGA
1 GTTTTAGTCCATCATGTTCGA
** ** * *
75804 G-TTTAAACCATGGTTTTAGA
1 GTTTTAGTCCATCATGTTCGA
*
75824 CTTTTAGTCCATCATGTTCGA
1 GTTTTAGTCCATCATGTTCGA
75845 GTTTT
1 GTTTT
75850 TATCTCATTC
Statistics
Matches: 31, Mismatches: 14, Indels: 2
0.66 0.30 0.04
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.45
Consensus pattern (21 bp):
GTTTTAGTCCATCATGTTCGA
Found at i:83281 original size:15 final size:16
Alignment explanation
Indices: 83250--83282 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
83240 AGTGAGAATG
83250 TAAGATTATCAGGGAA
1 TAAGATTATCAGGGAA
*
83266 TAAGATTA-CTGGGAA
1 TAAGATTATCAGGGAA
83281 TA
1 TA
83283 TTGTATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.42, C:0.06, G:0.24, T:0.27
Consensus pattern (16 bp):
TAAGATTATCAGGGAA
Done.