Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008732.1 Hibiscus syriacus cultivar Beakdansim tig00111802_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: 47988
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3756 original size:18 final size:18
Alignment explanation
Indices: 3735--3776 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
3725 TTAAAAAAAT
*
3735 ATTTT-TTTTTTTGTGAAA
1 ATTTTATTTTATT-TGAAA
3753 ATTTTGATTTTATTTGAAA
1 ATTTT-ATTTTATTTGAAA
3772 ATTTT
1 ATTTT
3777 GAGGGAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 10 0.48
20 6 0.29
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (18 bp):
ATTTTATTTTATTTGAAA
Found at i:4710 original size:131 final size:131
Alignment explanation
Indices: 4463--4708 Score: 370
Period size: 131 Copynumber: 1.9 Consensus size: 131
4453 TAATTTTAAG
* * *
4463 AGTGAAAACGATAATATATAATTACTTCCAATCGAGAATAAATGACCTTTCGTGCATTAAAACAT
1 AGTGAAAACAATAATATATAATGACTTCCAATCGAGAATAAACGACCTTTCGTGCATTAAAACAT
* * * *
4528 TCATTTATTACTCCAATTGAAATAAAGAGATATTACTATTTCATCTTAAAATTTAATATCGATTC
66 TCATTTATTACCCCAATTGAAATAAAGAGATATTAATATTCCATCTAAAAATTTAATATCGATTC
4593 A
131 A
* * *
4594 AGTGAAAATAATAATATCTAATGATTTCCAATCGAGAATAAACGACCTTTCGTGCATT-AAACAG
1 AGTGAAAACAATAATATATAATGACTTCCAATCGAGAATAAACGACCTTTCGTGCATTAAAACA-
*
4658 TT-ATTTATTACCCCAATTGAAATAAAGAGATATTAATATTCCGTCTAAAAA
65 TTCATTTATTACCCCAATTGAAATAAAGAGATATTAATATTCCATCTAAAAA
4709 ATCGATATTA
Statistics
Matches: 103, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
130 49 0.48
131 54 0.52
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (131 bp):
AGTGAAAACAATAATATATAATGACTTCCAATCGAGAATAAACGACCTTTCGTGCATTAAAACAT
TCATTTATTACCCCAATTGAAATAAAGAGATATTAATATTCCATCTAAAAATTTAATATCGATTC
A
Found at i:4740 original size:130 final size:131
Alignment explanation
Indices: 4488--4799 Score: 371
Period size: 130 Copynumber: 2.4 Consensus size: 131
4478 ATATAATTAC
*
4488 TTCCAATCGAGAATAAATGACCTTTCGTGCATTAAAACATTCATTTATTACTCCAATTGAAATAA
1 TTCCAATCGAGAATAAATGACCTTTCGTGCATTAAAACATTCATTTATTACCCCAATTGAAATAA
* * * * * * * * *
4553 AGAGATATTACTATTTCATCTTAAAATTTAATATCGATTCAAGTGAAAATAATAATATCTAATGA
66 AGAGATATTAATATTCCATCTAAAAAATCAATATCAATTCAAGAGAAAATAACAATATCAAATGA
4618 T
131 T
*
4619 TTCCAATCGAGAATAAACGACCTTTCGTGCATT-AAACAGTT-ATTTATTACCCCAATTGAAATA
1 TTCCAATCGAGAATAAATGACCTTTCGTGCATTAAAACA-TTCATTTATTACCCCAATTGAAATA
* * * * *
4682 AAGAGATATTAATATTCCGTCTAAAAAATCGATATTAATTCGAGAGAAAA-AGGCAATATCAAAT
65 AAGAGATATTAATATTCCATCTAAAAAATCAATATCAATTCAAGAGAAAATA-ACAATATCAAAT
*
4746 TAT
129 GAT
* * * * *
4749 TTCCAATTGAAAATAAATGACCTCTT-ATGCCTTAAAGCATTCATTTATTAC
1 TTCCAATCGAGAATAAATGACCT-TTCGTGCATTAAAACATTCATTTATTAC
4800 TCCGACCGAA
Statistics
Matches: 153, Mismatches: 23, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
129 1 0.01
130 103 0.67
131 49 0.32
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (131 bp):
TTCCAATCGAGAATAAATGACCTTTCGTGCATTAAAACATTCATTTATTACCCCAATTGAAATAA
AGAGATATTAATATTCCATCTAAAAAATCAATATCAATTCAAGAGAAAATAACAATATCAAATGA
T
Found at i:6899 original size:21 final size:22
Alignment explanation
Indices: 6869--7093 Score: 165
Period size: 21 Copynumber: 10.6 Consensus size: 22
6859 GATTTACATA
* *
6869 TTCGCATTGCGA-TAGTCCAAG
1 TTCGCGTTGCGATTATTCCAAG
6890 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA-TTATTCCAAG
* *
6913 TT--CGTTGCGA-TAGTCGAAG
1 TTCGCGTTGCGATTATTCCAAG
*
6932 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA-TTATTCCAAG
* *
6955 TT--CGTTACGATTTATTCCAAA
1 TTCGCGTTGCGA-TTATTCCAAG
6976 TT--CGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA-TTATTCCAAG
* *
6997 TTCGCGTTGCGATTTATTACAAA
1 TTCGCGTTGCGA-TTATTCCAAG
* *
7020 TT--CGTTGCGA-TAGTCGAAG
1 TTCGCGTTGCGATTATTCCAAG
*
7039 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA-TTATTCCAAG
*
7062 TT--CGTTGCGATTTATTCTAAG
1 TTCGCGTTGCGA-TTATTCCAAG
7083 TT--CGTTGCGAT
1 TTCGCGTTGCGAT
7094 AGTCCAAAAT
Statistics
Matches: 171, Mismatches: 21, Indels: 25
0.79 0.10 0.12
Matches are distributed among these distances:
19 16 0.09
20 1 0.01
21 109 0.64
23 45 0.26
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (22 bp):
TTCGCGTTGCGATTATTCCAAG
Found at i:6926 original size:42 final size:41
Alignment explanation
Indices: 6875--7101 Score: 212
Period size: 42 Copynumber: 5.4 Consensus size: 41
6865 CATATTCGCA
*
6875 TTGCGA-TAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATTAGTCCAAATT--CGTTGCGATTTATTCCAAGTTCG
* * *
6917 TTGCGA-TAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATTAGTCCAAATT--CGTTGCGATTTATTCCAAGTTCG
* *
6959 TTACGATTTATTCCAAATTCGTTGCGATTTATTCCAAGTTCGCG
1 TTGCGA-TTAGTCCAAATTCGTTGCGATTTATTCCAAGTT--CG
* * * *
7003 TTGCGATTTATTACAAATTCGTTGCGA--TAGTCGAAGTTCGCG
1 TTGCGA-TTAGTCCAAATTCGTTGCGATTTATTCCAAGTT--CG
* *
7045 TTGCGATTTATTCCAAATTCGTTGCGATTTATTCTAAGTTCG
1 TTGCGA-TTAGTCCAAATTCGTTGCGATTTATTCCAAGTTCG
7087 TTGCGA-TAGTCCAAA
1 TTGCGATTAGTCCAAA
7102 ATCGCAACGA
Statistics
Matches: 164, Mismatches: 15, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
40 8 0.05
42 112 0.68
44 44 0.27
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (41 bp):
TTGCGATTAGTCCAAATTCGTTGCGATTTATTCCAAGTTCG
Found at i:6998 original size:107 final size:107
Alignment explanation
Indices: 6884--7093 Score: 375
Period size: 107 Copynumber: 2.0 Consensus size: 107
6874 ATTGCGATAG
* *
6884 TCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
6949 TCCAAATTCGTTACGATTTATTCCAAATTCGTTGCGATTTAT
66 TCCAAATTCGTTACGATTTATTCCAAATTCGTTGCGATTTAT
6991 TCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* * *
7056 TCCAAATTCGTTGCGATTTATTCTAAGTTCGTTGCGAT
66 TCCAAATTCGTTACGATTTATTCCAAATTCGTTGCGAT
7094 AGTCCAAAAT
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
107 98 1.00
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.39
Consensus pattern (107 bp):
TCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
TCCAAATTCGTTACGATTTATTCCAAATTCGTTGCGATTTAT
Found at i:7196 original size:6 final size:6
Alignment explanation
Indices: 7186--7246 Score: 99
Period size: 6 Copynumber: 10.5 Consensus size: 6
7176 GACACGTATT
*
7186 ACCACT ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
7234 ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACC
7247 CGAGACGAGA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
5 10 0.19
6 44 0.81
ACGTcount: A:0.31, C:0.52, G:0.15, T:0.02
Consensus pattern (6 bp):
ACCACG
Found at i:7255 original size:5 final size:5
Alignment explanation
Indices: 7247--7279 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
7237 CGACCCGACC
*
7247 CGAGA CGAGA CGAGA CGAGA CGAGA TGAGA CGA
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGA
7280 ACGGCAGCGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.18, G:0.39, T:0.03
Consensus pattern (5 bp):
CGAGA
Found at i:7796 original size:6 final size:6
Alignment explanation
Indices: 7770--7817 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
7760 TCTCGTCTCG
7770 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
7815 GGT
1 GGT
7818 AATACGTGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.36
6 27 0.64
ACGTcount: A:0.00, C:0.17, G:0.54, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:7963 original size:21 final size:21
Alignment explanation
Indices: 7934--8070 Score: 163
Period size: 21 Copynumber: 6.6 Consensus size: 21
7924 GATTTACATA
*
7934 TTCGTATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
7955 TTCGCATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* *
7975 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
7996 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
8017 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
8038 CTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
8059 TTCGCGTTGCGA
1 TTCGCATTGCGA
8071 ATCTGGAAAC
Statistics
Matches: 100, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
20 17 0.17
21 82 0.82
22 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:8007 original size:62 final size:62
Alignment explanation
Indices: 7910--8033 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
7900 TGTGATTTTG
*
7910 GACTATCGCATTGCGATTTACATATTCGTATTGCGATAGTCCAAGTTCGCATTGCGATAGTC
1 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTC
7972 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTC
1 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTC
8034 CAAGCTCGCA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (62 bp):
GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTC
Found at i:8043 original size:62 final size:62
Alignment explanation
Indices: 7914--8050 Score: 229
Period size: 62 Copynumber: 2.2 Consensus size: 62
7904 ATTTTGGACT
* * **
7914 ATCGCATTGCGATTTACATATTCGTATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACT
1 ATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAG
7976 ATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAG
1 ATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAG
*
8038 CTCGCATTGCGAT
1 ATCGCATTGCGAT
8051 AGTCGAAGTT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 70 1.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (62 bp):
ATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAG
Found at i:10069 original size:2 final size:2
Alignment explanation
Indices: 10062--10133 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
10052 AGTATCTACA
10062 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
10104 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
10134 CATTATAAGC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10868 original size:21 final size:21
Alignment explanation
Indices: 10816--10868 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
10806 GTTAACCGTT
* * *
10816 ACAGTGTGGATGTGGTAGTTC
1 ACAGTGTTGACGTGGTAGTCC
* **
10837 ACGGTACTGACGTGGTAGTCC
1 ACAGTGTTGACGTGGTAGTCC
10858 ACAGTGTTGAC
1 ACAGTGTTGAC
10869 ATGACAGTCC
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.17, G:0.34, T:0.28
Consensus pattern (21 bp):
ACAGTGTTGACGTGGTAGTCC
Found at i:11284 original size:29 final size:30
Alignment explanation
Indices: 11251--11308 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
11241 TATCATTTAT
11251 ATCAT-AAATTTTTAAT-TTAATCAAATTAC
1 ATCATCAAATTTTTAATATTAAT-AAATTAC
* *
11280 ATCATCTAATTTTTATTATTAATAAATTA
1 ATCATCAAATTTTTAATATTAATAAATTA
11309 AGTCGCTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.20
30 15 0.60
31 5 0.20
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (30 bp):
ATCATCAAATTTTTAATATTAATAAATTAC
Found at i:12614 original size:39 final size:36
Alignment explanation
Indices: 12571--12667 Score: 90
Period size: 37 Copynumber: 2.6 Consensus size: 36
12561 TACAAACGGT
12571 TTTTGAAAATACGTATATAATATATAGTTTTT-AAAATCA
1 TTTTGAAAAT--GTATATAATATAT-GTTTTTGAAAAT-A
* * *
12610 TTTTGAACATTTATATATTATATGTTTTTGAAAATA
1 TTTTGAAAATGTATATAATATATGTTTTTGAAAATA
* * *
12646 TTTT-TATATATATATAATATAT
1 TTTTGAAAATGTATATAATATAT
12668 TATTATTTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
35 14 0.28
36 11 0.22
37 16 0.32
39 9 0.18
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (36 bp):
TTTTGAAAATGTATATAATATATGTTTTTGAAAATA
Found at i:12667 original size:35 final size:37
Alignment explanation
Indices: 12584--12667 Score: 102
Period size: 37 Copynumber: 2.3 Consensus size: 37
12574 TGAAAATACG
*
12584 TATATAATATATAGTTTTTAAAATCATTTTGAACATT
1 TATATAATATATAGTTTTTAAAATCATTTTGAACATA
* * *
12621 TATATATTATAT-GTTTTTGAAAAT-ATTTT-TATATA
1 TATATAATATATAGTTTTT-AAAATCATTTTGAACATA
12656 TATATAATATAT
1 TATATAATATAT
12668 TATTATTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
35 14 0.34
36 11 0.27
37 16 0.39
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (37 bp):
TATATAATATATAGTTTTTAAAATCATTTTGAACATA
Found at i:12673 original size:3 final size:3
Alignment explanation
Indices: 12665--12702 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
12655 ATATATAATA
12665 TAT TAT TATT TAT TAT TAT TAT TAT TACT T-T TAT TAT T
1 TAT TAT TA-T TAT TAT TAT TAT TAT TA-T TAT TAT TAT T
12703 TTGTAGACCT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 2 0.06
3 25 0.78
4 5 0.16
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:17365 original size:96 final size:96
Alignment explanation
Indices: 17190--17380 Score: 269
Period size: 96 Copynumber: 2.0 Consensus size: 96
17180 TACTATTATA
* *
17190 TATACAATAAAGCTTAAGTTGTCCCTCTAAAGCAATTGGTTAAACGCACCGACTTTATGGATAAG
1 TATACAATAAAGCTTAAGCTATCCCTCTAAAGCAATTGGTTAAACGCACCGACTTTATGGATAAG
*
17255 AACCAACTAGCCTGATAAAGGTGA-TTATATC
66 AACCAACTAACCTGATAAAGGT-ATTTATATC
* * *
17286 TATACAATAAAGCTTGAA-CTATCCCTCTAAGGCAATTGGTTAAATGCCCCGACTTTATGGATAA
1 TATACAATAAAGCTT-AAGCTATCCCTCTAAAGCAATTGGTTAAACGCACCGACTTTATGGATAA
** *
17350 GATTCAGCTAACCTGATAAAGGTATTTATAT
65 GAACCAACTAACCTGATAAAGGTATTTATAT
17381 ATTGAGTTGT
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
95 1 0.01
96 81 0.96
97 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (96 bp):
TATACAATAAAGCTTAAGCTATCCCTCTAAAGCAATTGGTTAAACGCACCGACTTTATGGATAAG
AACCAACTAACCTGATAAAGGTATTTATATC
Found at i:18915 original size:21 final size:21
Alignment explanation
Indices: 18889--18950 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
18879 GACAGTTTCC
18889 CTTGAAACAAATTTTGTCTCT
1 CTTGAAACAAATTTTGTCTCT
*
18910 CTTGAAAC--A----GTTTCT
1 CTTGAAACAAATTTTGTCTCT
18925 CTTGAAACAAATTTTGTCTCT
1 CTTGAAACAAATTTTGTCTCT
18946 CTTGA
1 CTTGA
18951 GATAGTTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
15 13 0.39
17 1 0.03
19 1 0.03
21 18 0.55
ACGTcount: A:0.27, C:0.19, G:0.11, T:0.42
Consensus pattern (21 bp):
CTTGAAACAAATTTTGTCTCT
Found at i:18922 original size:36 final size:36
Alignment explanation
Indices: 18856--19041 Score: 286
Period size: 36 Copynumber: 5.2 Consensus size: 36
18846 AATTTACTCA
* * *
18856 AAACAAAGTTTAGTCTTTCCTGAGACAGTTTCCCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
18893 AAACAAATTTTGTCTCTCTTGAAACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
18929 AAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
18965 AAACAAA--TTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
18999 AAACAAATTTGGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
19035 AAACAAA
1 AAACAAA
19042 ATCTTTGAAT
Statistics
Matches: 137, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
34 33 0.24
36 97 0.71
37 7 0.05
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:19003 original size:70 final size:71
Alignment explanation
Indices: 18856--19242 Score: 372
Period size: 70 Copynumber: 5.6 Consensus size: 71
18846 AATTTACTCA
* *
18856 AAACAAAGTTTAGTCTTTCCTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAAACAGT
1 AAACAAA-TTTAGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-TTTGTCTCTCTTGAAACAGT
*
18921 TTCTCTTG
64 TTCCCTTG
* * *
18929 AAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAA-TTGTCTCTCTTGAGACAGTTT
1 AAACAAATTTAGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTGTCTCTCTTGAAACAGTTT
18993 CCCTTG
66 CCCTTG
* * * *
18999 AAACAAATTTGGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-----ATCT-TTGAATCTGTTT
1 AAACAAATTTAGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTGTCTCTCTTGAAACAGTTT
*
19058 TCCTTG
66 CCCTTG
* * * * * *
19064 AAACAAA---A---TCT-TTGA-ATCTGTTTTCCTTGAAACAAATTTATTCTCCCTTGAGAGAGT
1 AAACAAATTTAGTCTCTCTTGAGA-CAGTTTCCCTTGAAACAAATTT-GTCTCTCTTGAAACAGT
**
19121 TTCTTTTG
64 TTCCCTTG
* * * * *
19129 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGACACGGG
1 AAACAAA-TTTAGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-TTTGTCTCTCTTGAAACAGT
19194 TTCCCTTG
64 TTCCCTTG
** *
19202 AAACAAATTTTTTCTCTCTTAAGACAGTTTCCCTTGAAACA
1 AAACAAATTTAGTCTCTCTTGAGACAGTTTCCCTTGAAACA
19243 GTTTCCCTTG
Statistics
Matches: 256, Mismatches: 40, Indels: 37
0.77 0.12 0.11
Matches are distributed among these distances:
57 1 0.00
58 21 0.08
59 3 0.01
64 2 0.01
65 39 0.15
66 3 0.01
70 66 0.26
72 66 0.26
73 51 0.20
74 4 0.02
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.39
Consensus pattern (71 bp):
AAACAAATTTAGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTGTCTCTCTTGAAACAGTTT
CCCTTG
Found at i:19057 original size:29 final size:29
Alignment explanation
Indices: 19025--19099 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
19015 TCTTGAGACA
*
19025 GTTTCCCTTGAAACAAAATCTTTGAATCT
1 GTTTTCCTTGAAACAAAATCTTTGAATCT
19054 GTTTTCCTTGAAACAAAATCTTTGAATCT
1 GTTTTCCTTGAAACAAAATCTTTGAATCT
19083 GTTTTCCTTGAAACAAA
1 GTTTTCCTTGAAACAAA
19100 TTTATTCTCC
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:0.32, C:0.19, G:0.11, T:0.39
Consensus pattern (29 bp):
GTTTTCCTTGAAACAAAATCTTTGAATCT
Found at i:19174 original size:73 final size:71
Alignment explanation
Indices: 19085--19242 Score: 194
Period size: 73 Copynumber: 2.2 Consensus size: 71
19075 TTGAATCTGT
* * **
19085 TTTCCTTGAAACAAATTTAT-TCTCCCTTGAGA-GAGTTTCTTTTGAAACAAAGTTTTGTCTCTC
1 TTTCCTTGAAACAAATTT-TGTCTCCCTTGACACG-GGTTCCCTTGAAACAAA-TTTTGTCTCTC
*
19148 TTGAGACAG
63 TTAAGACAG
* *
19157 TTTCTCTTGAAACAAATTTTGTCTCTCTTGACACGGGTTCCCTTGAAACAAATTTTTTCTCTCTT
1 TTTC-CTTGAAACAAATTTTGTCTCCCTTGACACGGGTTCCCTTGAAACAAATTTTGTCTCTCTT
19222 AAGACAG
65 AAGACAG
19229 TTTCCCTTGAAACA
1 TTT-CCTTGAAACA
19243 GTTTCCCTTG
Statistics
Matches: 75, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
72 35 0.47
73 39 0.52
74 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (71 bp):
TTTCCTTGAAACAAATTTTGTCTCCCTTGACACGGGTTCCCTTGAAACAAATTTTGTCTCTCTTA
AGACAG
Found at i:19184 original size:36 final size:36
Alignment explanation
Indices: 19083--19242 Score: 196
Period size: 36 Copynumber: 4.4 Consensus size: 36
19073 CTTTGAATCT
* * *
19083 GTTTTCCTTGAAACAAATTTAT-TCTCCCTTGAGAGA
1 GTTTCCCTTGAAACAAATTT-TGTCTCTCTTGAGACA
**
19119 GTTTCTTTTGAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
* * *
19156 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGACACG
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
19192 GGTTCCCTTGAAACAAATTTTTTCTCTCTTAAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
19228 GTTTCCCTTGAAACA
1 GTTTCCCTTGAAACA
19243 GTTTCCCTTG
Statistics
Matches: 107, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
36 76 0.71
37 31 0.29
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:19245 original size:15 final size:15
Alignment explanation
Indices: 19225--19257 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
19215 CTCTCTTAAG
19225 ACAGTTTCCCTTGAA
1 ACAGTTTCCCTTGAA
19240 ACAGTTTCCCTTGAA
1 ACAGTTTCCCTTGAA
19255 ACA
1 ACA
19258 AAATCTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.30
Consensus pattern (15 bp):
ACAGTTTCCCTTGAA
Found at i:19410 original size:21 final size:21
Alignment explanation
Indices: 19385--19449 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
19375 TGAGACAGTT
19385 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
* *
19406 TCTCTTGAGAC--A-GTT-TC
1 TCTCTTGAAACAAATTTTGTC
19423 -C-CTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
19442 TCTCTTGA
1 TCTCTTGA
19450 GACAGTTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 7 0.21
16 1 0.03
17 3 0.09
18 4 0.12
19 3 0.09
20 1 0.03
21 15 0.44
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.42
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:19410 original size:36 final size:37
Alignment explanation
Indices: 19273--19472 Score: 271
Period size: 36 Copynumber: 5.5 Consensus size: 37
19263 TTTGAATCTA
* * *
19273 TTTCCCTTGAAAC-AAATTTCGTCTCCCTTGAGACAA
1 TTTCCCTTGAAACTAAATTTTGTCTCTCTTGAGACAG
** * *
19309 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACTAAATTTTGTCTCTCTTGAGACAG
** * *
19346 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACTAAATTTTGTCTCTCTTGAGACAG
*
19383 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACTAAATTTTGTCTCTCTTGAGACAG
19419 TTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACTAAATTTTGTCTCTCTTGAGACAG
19455 TTTCCCTTGAAACTAAAT
1 TTTCCCTTGAAACTAAAT
19473 CTTTTGGAAC
Statistics
Matches: 151, Mismatches: 11, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
36 80 0.53
37 71 0.47
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.41
Consensus pattern (37 bp):
TTTCCCTTGAAACTAAATTTTGTCTCTCTTGAGACAG
Found at i:19484 original size:124 final size:125
Alignment explanation
Indices: 19348--19589 Score: 405
Period size: 124 Copynumber: 1.9 Consensus size: 125
19338 TGAGACAGTT
19348 TCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTG
1 TCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTG
*
19413 AGACAGTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACTAAA
66 AGACAGTTTCCCTTAAAACAAATTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACTAAA
* * * *
19472 TCTTTTGGAACTAAGTTTTGTCTCTCTTTAGATAGTTTCTTTTGAAACAAATTTTGTGTCTCTTG
1 TCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTG
* * *
19537 AGATAGTTTCCCTTAAAACAAATTTTTGTCTCTCTTGAGACATTTTCTCTTGA
66 AGACAGTTTCCCTTAAAACAAATTTTTGTCTCTCTTGAGACAGTTTCCCTTGA
19590 GATATTTTCT
Statistics
Matches: 109, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
124 81 0.74
125 28 0.26
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (125 bp):
TCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTG
AGACAGTTTCCCTTAAAACAAATTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACTAAA
Found at i:19499 original size:88 final size:86
Alignment explanation
Indices: 19399--19564 Score: 251
Period size: 88 Copynumber: 1.9 Consensus size: 86
19389 TTGAAACAAA
*
19399 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTA
19464 AAACTAAATCTTTTGGAACTAAG
66 AAAC-AAAT-TTTTGGAACTAAG
* * ** * *
19487 TTTTGTCTCTCTTTAGATAGTTTCTTTTGAAACAAATTTTGTGTCTCTTGAGATAGTTTCCCTTA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTA
19552 AAACAAATTTTTG
66 AAACAAATTTTTG
19565 TCTCTCTTGA
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
86 5 0.07
87 4 0.06
88 62 0.87
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (86 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTA
AAACAAATTTTTGGAACTAAG
Found at i:19513 original size:37 final size:36
Alignment explanation
Indices: 19472--19576 Score: 129
Period size: 36 Copynumber: 2.9 Consensus size: 36
19462 TGAAACTAAA
* * *
19472 TCTTTTGGAACTAAGTTTTGTCTCTCTTTAGATAGTT
1 TCTTTTGAAAC-AAATTTTGTCTCTCTTGAGATAGTT
*
19509 TCTTTTGAAACAAATTTTGTGTCTCTTGAGATAGTT
1 TCTTTTGAAACAAATTTTGTCTCTCTTGAGATAGTT
** *
19545 TCCCTTAAAACAAATTTTTGTCTCTCTTGAGA
1 TCTTTTGAAACAAA-TTTTGTCTCTCTTGAGA
19577 CATTTTCTCT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
36 33 0.56
37 26 0.44
ACGTcount: A:0.24, C:0.15, G:0.14, T:0.47
Consensus pattern (36 bp):
TCTTTTGAAACAAATTTTGTCTCTCTTGAGATAGTT
Found at i:19587 original size:15 final size:15
Alignment explanation
Indices: 19567--19604 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
19557 AATTTTTGTC
19567 TCTCTTGAGACATTT
1 TCTCTTGAGACATTT
*
19582 TCTCTTGAGATATTT
1 TCTCTTGAGACATTT
19597 TCTCTTGA
1 TCTCTTGA
19605 AACACCAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.13, T:0.50
Consensus pattern (15 bp):
TCTCTTGAGACATTT
Found at i:19713 original size:30 final size:30
Alignment explanation
Indices: 19677--19749 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
19667 CTTGAAACAC
* * *
19677 AAAAAAAACCTTTGAAATTGTTTCTCTTGA
1 AAAAAAAACCTTGGAAAATGTTTCTATTGA
*
19707 AAAAAAAATCTTGGAAAATGTTTCTATTGA
1 AAAAAAAACCTTGGAAAATGTTTCTATTGA
*
19737 AACACAAAACCTT
1 AA-AAAAAACCTT
19750 CGAGTGAGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 28 0.78
31 8 0.22
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.32
Consensus pattern (30 bp):
AAAAAAAACCTTGGAAAATGTTTCTATTGA
Found at i:20447 original size:29 final size:27
Alignment explanation
Indices: 20412--20494 Score: 107
Period size: 27 Copynumber: 3.0 Consensus size: 27
20402 TTTGTAAATG
20412 GTTTTTGAAAATATGTATATAATATATA
1 GTTTTTGAAAATAT-TATATAATATATA
*
20440 GTTTTTTGAAAAT-TTATATATTATAT-
1 G-TTTTTGAAAATATTATATAATATATA
20466 GTTTTTGAAAATATTTATATATATATATA
1 GTTTTTGAAAATA-TTATATA-ATATATA
20495 TATAATATTA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
25 11 0.23
26 1 0.02
27 18 0.38
28 7 0.15
29 11 0.23
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (27 bp):
GTTTTTGAAAATATTATATAATATATA
Found at i:20512 original size:3 final size:3
Alignment explanation
Indices: 20500--20548 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
20490 ATATATATAA
* * *
20500 TAT TATT TAT TAT TAT TAT TAT GATT TAA TAT TAT AAT TAT TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
20547 TA
1 TA
20549 CTTTTAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
3 33 0.87
4 5 0.13
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:20532 original size:19 final size:19
Alignment explanation
Indices: 20490--20540 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
20480 TTATATATAT
*
20490 ATATATATAA-TATTATTTA
1 ATAT-TATAATTATGATTTA
* *
20509 TTATTATTATTATGATTTA
1 ATATTATAATTATGATTTA
20528 ATATTATAATTAT
1 ATATTATAATTAT
20541 TATTATTACT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
ATATTATAATTATGATTTA
Found at i:28735 original size:2 final size:2
Alignment explanation
Indices: 28728--28774 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
28718 TAGATAACAA
28728 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
28770 AT AT A
1 AT AT A
28775 AGATTAAGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29802 original size:3 final size:3
Alignment explanation
Indices: 29789--29861 Score: 128
Period size: 3 Copynumber: 24.3 Consensus size: 3
29779 TTTTACCCAC
*
29789 ATT ACT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
29837 ATT ATC ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
29862 AATATATATT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:29888 original size:14 final size:15
Alignment explanation
Indices: 29860--29894 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
29850 TTATTATTAT
29860 TAAATATATATTAAA
1 TAAATATATATTAAA
29875 TAAATATATA-TAAA
1 TAAATATATATTAAA
29889 TAAATA
1 TAAATA
29895 ATTACAGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATATATATTAAA
Found at i:42646 original size:12 final size:12
Alignment explanation
Indices: 42629--42666 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
42619 ATGCTTGAAG
42629 AAAAAAAAAG--
1 AAAAAAAAAGAA
42639 AAAAAAAAAGAA
1 AAAAAAAAAGAA
*
42651 AAAAAAAGAGAA
1 AAAAAAAAAGAA
42663 AAAA
1 AAAA
42667 GAGGGGTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.40
12 15 0.60
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:42669 original size:9 final size:10
Alignment explanation
Indices: 42626--42666 Score: 73
Period size: 10 Copynumber: 4.0 Consensus size: 10
42616 ATTATGCTTG
42626 AAGAAAAAAA
1 AAGAAAAAAA
42636 AAGAAAAAAA
1 AAGAAAAAAA
42646 AAGAAAAAAA
1 AAGAAAAAAA
42656 AAGAGAAAAAA
1 AAGA-AAAAAA
42667 GAGGGGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 24 0.80
11 6 0.20
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:43003 original size:16 final size:16
Alignment explanation
Indices: 42977--43021 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
42967 TTTGAATACA
*
42977 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
42994 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
43009 ATTCAATTTATTT
1 ATTCAATTTATTT
43022 TTGGAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:44214 original size:82 final size:83
Alignment explanation
Indices: 43801--44515 Score: 1133
Period size: 83 Copynumber: 8.7 Consensus size: 83
43791 CATTAACTGA
**
43801 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
1 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
43866 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
*
43884 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGA
1 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
43949 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
* *
43967 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCCGGTTTAGCAGA
1 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
**
44032 ACCAATCATTGAATTGGG
66 ACCAATCATTGAATTTAG
* *
44050 AAGATGAATGTATTAATAGCATCTTCTGGAAGTGTTCTTTGAG---T-T-ATCTGGTTTAGCAGA
1 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
44110 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
*
44128 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTC-TTGAGTTATCTGACCTGGTTTAGCAGA
1 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
**
44192 ACCAATCATTGAATTGGG
66 ACCAATCATTGAATTTAG
* * * *
44210 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAG-CAG
44274 AACC-ATCATTGAATTTAG
65 AACCAATCATTGAATTTAG
44292 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
1 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
**
44357 ACCAATCATTGAATTGGG
66 ACCAATCATTGAATTTAG
* * *
44375 AAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTC-TTGAGTTATCTGATCTGGTTTAGCAGA
1 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
*
44439 ACCAATCATTGAATTTGG
66 ACCAATCATTGAATTTAG
* * *
44457 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
44516 GGTAAGAACT
Statistics
Matches: 587, Mismatches: 35, Indels: 20
0.91 0.05 0.03
Matches are distributed among these distances:
77 5 0.01
78 64 0.11
79 1 0.00
80 2 0.00
81 1 0.00
82 219 0.37
83 295 0.50
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (83 bp):
AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
ACCAATCATTGAATTTAG
Found at i:44446 original size:247 final size:248
Alignment explanation
Indices: 43801--44514 Score: 1181
Period size: 247 Copynumber: 2.9 Consensus size: 248
43791 CATTAACTGA
**
43801 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
1 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
43866 ACCAATCATTGAATTTAGAAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
66 ACCAATCATTGAATTTAGAAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTC-TTGAGTTAT
* * * *
43931 CTGACCTGGTTTAGCAGAACCAATCATTGAATTTAGAAGATGAATTTGTTAATAGCATCTTCTGG
130 CTGACCTGGTTTAGCAGAACCAATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGG
* * * *
43996 AAGTGTTCTTTGAGTTATCTGACCCGGTTTAGCAGAACCAATCATTGAATTGGG
195 AAGTGTTCTTTGAGTTATCTGATCTGGTTGAGCAGAACCAATCATTGAATTGAG
* *
44050 AAGATGAATGTATTAATAGCATCTTCTGGAAGTGTTCTTTGAG---T-T-ATCTGGTTTAGCAGA
1 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
44110 ACCAATCATTGAATTTAGAAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTGAGTTATC
66 ACCAATCATTGAATTTAGAAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTGAGTTATC
*
44175 TGACCTGGTTTAGCAGAACCAATCATTGAATTGGGAAGATGAATGTGCTCATAGCATCTTCTGGA
131 TGACCTGGTTTAGCAGAACCAATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGA
*
44240 AGTGTTCTTTGAGTTATCTGATCTGGTTG-GACAGAACC-ATCATTGAATTTAG
196 AGTGTTCTTTGAGTTATCTGATCTGGTTGAG-CAGAACCAATCATTGAATTGAG
44292 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
1 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
** * * *
44357 ACCAATCATTGAATTGGGAAGATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTGAGTTATC
66 ACCAATCATTGAATTTAGAAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTGAGTTATC
*
44422 TGATCTGGTTTAGCAGAACCAATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGA
131 TGACCTGGTTTAGCAGAACCAATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGA
44487 AGTGTTCTTTGAGTTATCTGATCTGGTT
196 AGTGTTCTTTGAGTTATCTGATCTGGTT
44515 TGGTAAGAAC
Statistics
Matches: 436, Mismatches: 23, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
242 54 0.12
243 103 0.24
244 70 0.16
245 2 0.00
246 2 0.00
247 166 0.38
249 39 0.09
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (248 bp):
AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGA
ACCAATCATTGAATTTAGAAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTGAGTTATC
TGACCTGGTTTAGCAGAACCAATCATTGAATTTGGAAGATGAATGTGCTCATAGCATCTTCTGGA
AGTGTTCTTTGAGTTATCTGATCTGGTTGAGCAGAACCAATCATTGAATTGAG
Found at i:45242 original size:24 final size:24
Alignment explanation
Indices: 45198--45243 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
45188 GTTCATAATG
*
45198 AGAAGAAACTCATCTGAAGAAGGA
1 AGAAGAAACTCATATGAAGAAGGA
*
45222 AGAAGAAATTCATAATG-AGAAG
1 AGAAGAAACTCAT-ATGAAGAAG
45244 AATTTGTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.52, C:0.09, G:0.24, T:0.15
Consensus pattern (24 bp):
AGAAGAAACTCATATGAAGAAGGA
Found at i:45548 original size:114 final size:113
Alignment explanation
Indices: 45158--45794 Score: 839
Period size: 111 Copynumber: 5.6 Consensus size: 113
45148 ATTCAAATCT
*
45158 ATCATTTGATGGATTGA-CATTT-CAGAGAAGGTTCATAATGAGAAGAAACTCATCTGAAGAAGG
1 ATCAATTGATGGATT-ATCATTTCCAGAGAAGGTTCATAATGAGAAG-AACTCATCTGAAGAAGG
* * *
45221 AAGAAGAAATTCATAATGAGAAGAATTTGTTAAACC-TTCTGCCT-AATTC
64 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTG-CTGAATTC
* * *
45270 TATCACTTGATGGA-TAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 -ATCAATTGATGGATTATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
45334 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTTCTGAATTC
65 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTGCTGAATTC
*
45383 ATCAAATTGATGG---ATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATC-AATTGATGGATTATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
45445 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTTCTGAATTC
65 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTGCTGAATTC
*
45494 ATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATC-AATTGATGGATTATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
45559 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAATC-TTTTGCTTGAATTC
65 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTGC-TGAATTC
* * * * *
45608 ATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 ATCAATTGATGGATTATCATTTCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGAA
* *
45672 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATC-TTTTGCTTGAATTC
62 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTGC-TGAATTC
* * ** * *
45724 ATCATTTGATGGATCATCATCCCCAGCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-
1 ATCAATTGATGGATTATCATTTCCAG-AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
45788 AGAAGAA
65 AGAAGAA
45795 TTTATTCAAT
Statistics
Matches: 486, Mismatches: 23, Indels: 30
0.90 0.04 0.06
Matches are distributed among these distances:
111 111 0.23
112 64 0.13
113 98 0.20
114 105 0.22
115 2 0.00
116 87 0.18
117 17 0.03
118 2 0.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.29
Consensus pattern (113 bp):
ATCAATTGATGGATTATCATTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTGCTGAATTC
Found at i:45941 original size:3 final size:3
Alignment explanation
Indices: 45928--46049 Score: 165
Period size: 3 Copynumber: 39.3 Consensus size: 3
45918 TTTTACCCAC
*
45928 ATT ACT ATT ATT ATT ATT ATT ATT ATTT ATT ATT A-T ATT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT AT-T ATT
*
45974 ATT ATT ATT ATT ATAT ATAT ATT ATT ATT ATT ATT ATT ATT ATT ATC
1 ATT ATT ATT ATT AT-T AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
46021 ATT ATT ATT ATT ATT ATT AAAT ATT ATT A
1 ATT ATT ATT ATT ATT ATT -ATT ATT ATT A
46050 AATAAATATA
Statistics
Matches: 108, Mismatches: 6, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
2 2 0.02
3 91 0.84
4 15 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Done.