Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000738.1 Hibiscus syriacus cultivar Beakdansim tig00001428_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: 104846
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:4730 original size:15 final size:16
Alignment explanation
Indices: 4710--4740 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4700 CATTAACTGG
4710 TTTTATT-TTTTATTT
1 TTTTATTATTTTATTT
4725 TTTTATTATTTTATTT
1 TTTTATTATTTTATTT
4741 AAATGGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTATTATTTTATTT
Found at i:5336 original size:2 final size:2
Alignment explanation
Indices: 5329--5374 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
5319 GAATTGAATA
5329 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
5371 AT AT
1 AT AT
5375 TGTAATTGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6440 original size:27 final size:29
Alignment explanation
Indices: 6357--6442 Score: 90
Period size: 29 Copynumber: 3.1 Consensus size: 29
6347 AGGCTCTCAA
* **
6357 TTTT-ATATTTATAATTAGGGCCTCCAAT
1 TTTTAATATTTATAATTAGGACCTATAAT
*
6385 TTTTAATATTTATAATTAGGACCTTTAAT
1 TTTTAATATTTATAATTAGGACCTATAAT
*
6414 TTTT-ATGTTTA-AATT-GGAGCCTATAAT
1 TTTTAATATTTATAATTAGGA-CCTATAAT
6441 TT
1 TT
6443 CTTTGATTCC
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
26 3 0.06
27 13 0.25
28 10 0.20
29 25 0.49
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.50
Consensus pattern (29 bp):
TTTTAATATTTATAATTAGGACCTATAAT
Found at i:7538 original size:76 final size:76
Alignment explanation
Indices: 7407--7563 Score: 287
Period size: 76 Copynumber: 2.1 Consensus size: 76
7397 ATTTTTATTT
* *
7407 TTGTAGAAATTTTGTGTGACCATTGTCTCCATTTTTTTCTCTATGCTTGAATGTGTTGTAATTAT
1 TTGTTGAAATTTTGTGTGACCATTGTCTCCATTTTTCTCTCTATGCTTGAATGTGTTGTAATTAT
7472 GATTCGTTCTA
66 GATTCGTTCTA
7483 TTGTTGAAATTTTGTGTGACCATTGTCTCCATTTTTCTCTCTATGCTTGAATGTGTTGTAATTAT
1 TTGTTGAAATTTTGTGTGACCATTGTCTCCATTTTTCTCTCTATGCTTGAATGTGTTGTAATTAT
*
7548 GATTGGTTCTA
66 GATTCGTTCTA
7559 TTGTT
1 TTGTT
7564 TTTATTAAAG
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.51
Consensus pattern (76 bp):
TTGTTGAAATTTTGTGTGACCATTGTCTCCATTTTTCTCTCTATGCTTGAATGTGTTGTAATTAT
GATTCGTTCTA
Found at i:10727 original size:4 final size:4
Alignment explanation
Indices: 10720--10810 Score: 84
Period size: 4 Copynumber: 23.8 Consensus size: 4
10710 AGCACAAAAA
* * * **
10720 AAAG AAAG AAAG AAAG AAAG ACAG AAAT AAAT AAAG AAAG GGAG -AAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
*
10767 AGAG AAAGG AAAG -AAG -AAG -AAG -AAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAA-G AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
10811 AGTTCCAAAC
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
3 14 0.19
4 57 0.76
5 4 0.05
ACGTcount: A:0.69, C:0.01, G:0.27, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:20973 original size:36 final size:36
Alignment explanation
Indices: 20931--21033 Score: 197
Period size: 36 Copynumber: 2.9 Consensus size: 36
20921 ACGATGCTGG
20931 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
*
20967 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
21003 ACATTGATACACGAATGTACCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
21034 CTACTCAACT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.23
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATAGGATA
Found at i:23771 original size:18 final size:18
Alignment explanation
Indices: 23748--23801 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
23738 ACTGAATATT
23748 TGTCCCGAAAGACCACTA
1 TGTCCCGAAAGACCACTA
*
23766 TGTCCCGAAGGACCACTA
1 TGTCCCGAAAGACCACTA
23784 TGTCCCGAAAGACCACTA
1 TGTCCCGAAAGACCACTA
23802 ATAATCCCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAAGACCACTA
Found at i:26961 original size:76 final size:77
Alignment explanation
Indices: 26873--27223 Score: 338
Period size: 76 Copynumber: 4.5 Consensus size: 77
26863 ATTGGATAAT
* * * *
26873 GGATTTCGACATAGTCCCATATTC-AGCACTCACTGGACTCC-CAAAA-ACAGACTAAAAGTTAG
1 GGATTGCGACATA-TCTCATATTCGA-CACTCACTGGACTCCGCAAAACATAGACGAAAAGTTAG
*
26935 AAAATTCGATCATA
64 AAAATTCGAGCATA
** * * *
26949 GGATTGCGACATATTCTTGTATTCGGCACTCACTGGACTCTCGGAAAACATAGACGAAATGTTTA
1 GGATTGCGACATA-TCTCATATTCGACACTCACTGGACTC-CGCAAAACATAGACGAAAAG-TTA
* *
27014 GAAAATTTGAGAATA
63 GAAAATTCGAGCATA
* *
27029 GGATTGCGACATA-CTCATATTCGACAC-CACTGGACTCCTGGAAAACATAGACGAAAACTTAGA
1 GGATTGCGACATATCTCATATTCGACACTCACTGGACTCC-GCAAAACATAGACGAAAAGTTAGA
27092 AAATTCGAGCAT-
65 AAATTCGAGCATA
** * * *
27104 GGTATTGCGACATACTCTTGTATTTGACACTCACTGGACTCCCGGAAAACATAGACGAAAACTTT
1 GG-ATTGCGACATA-TCTCATATTCGACACTCACTGGACT-CCGCAAAACATAGACGAAAA-GTT
27169 AGAAAATTCGAGCATA
62 AGAAAATTCGAGCATA
** ** * *
27185 GGATTATGACAT-TCTTGTATTTGACACTAACTGGACTCC
1 GGATTGCGACATATCTCATATTCGACACTCACTGGACTCC
27224 CGATAAACAT
Statistics
Matches: 235, Mismatches: 27, Indels: 25
0.82 0.09 0.09
Matches are distributed among these distances:
75 2 0.01
76 60 0.26
77 30 0.13
78 50 0.21
79 36 0.15
80 55 0.23
81 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (77 bp):
GGATTGCGACATATCTCATATTCGACACTCACTGGACTCCGCAAAACATAGACGAAAAGTTAGAA
AATTCGAGCATA
Found at i:27224 original size:78 final size:78
Alignment explanation
Indices: 26899--27233 Score: 389
Period size: 78 Copynumber: 4.3 Consensus size: 78
26889 CCATATTCAG
* * * *
26899 CACTCACTGGACTCCC--AAAA-ACAGACTAAAA-GTTAGAAAATTCGATCATAGGATTGCGACA
1 CACTCACTGGACTCCCGGAAAACATAGACGAAAACTTTAGAAAATTCGAGCATAGGATTGCGAC-
*
26960 TATTCTTGTATTCGG
65 -ATTCTTGTATTCGA
* ** * *
26975 CACTCACTGGACTCTCGGAAAACATAGACGAAATGTTTAGAAAATTTGAGAATAGGATTGCGACA
1 CACTCACTGGACTCCCGGAAAACATAGACGAAAACTTTAGAAAATTCGAGCATAGGATTGCGACA
* **
27040 TACTCATATTCGA
66 TTCTTGTATTCGA
*
27053 CAC-CACTGGACTCCTGGAAAACATAGACGAAAAC-TTAGAAAATTCGAGCAT-GGTATTGCGAC
1 CACTCACTGGACTCCCGGAAAACATAGACGAAAACTTTAGAAAATTCGAGCATAGG-ATTGCGAC
*
27115 ATACTCTTGTATTTGA
65 AT--TCTTGTATTCGA
**
27131 CACTCACTGGACTCCCGGAAAACATAGACGAAAACTTTAGAAAATTCGAGCATAGGATTATGACA
1 CACTCACTGGACTCCCGGAAAACATAGACGAAAACTTTAGAAAATTCGAGCATAGGATTGCGACA
*
27196 TTCTTGTATTTGA
66 TTCTTGTATTCGA
*
27209 CACTAACTGGACTCCC-GATAAACAT
1 CACTCACTGGACTCCCGGA-AAACAT
27234 CGACAAACAA
Statistics
Matches: 222, Mismatches: 26, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
75 2 0.01
76 40 0.18
77 29 0.13
78 61 0.27
79 38 0.17
80 50 0.23
81 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (78 bp):
CACTCACTGGACTCCCGGAAAACATAGACGAAAACTTTAGAAAATTCGAGCATAGGATTGCGACA
TTCTTGTATTCGA
Found at i:37904 original size:122 final size:123
Alignment explanation
Indices: 37685--37931 Score: 417
Period size: 122 Copynumber: 2.0 Consensus size: 123
37675 TTTGTTTTTC
*
37685 TCTGTGTTTGAGTAATATTTTTTTTGTTAAATCTATGATATCAATCTACCATCAAGTAGAAACAA
1 TCTGTGTTTGAGTAATA-TTTTTTTGTTAAATCTATGATATCAATATACCATCAAGTAGAAACAA
*
37750 AATTTAAGGACGAAATTTCATTAAGGTGGGGAGAGTTGTCATACCCAAAATCGAGGTTA
65 AATTTAAGGACGAAATTTCATTAAGGAGGGGAGAGTTGTCATACCCAAAATCGAGGTTA
*
37809 TCTGTGTTTGAGTAATA-TTTTTTGTTAAATCTATGATATCAATATACCATCAAGTCGGAAA-AA
1 TCTGTGTTTGAGTAATATTTTTTTGTTAAATCTATGATATCAATATACCATCAAGT-AGAAACAA
* *
37872 AATTTGAGGACGAAATTTCATTAAGGAGGGGAGAGTTGTCATACCCAAAATTGAGGTTA
65 AATTTAAGGACGAAATTTCATTAAGGAGGGGAGAGTTGTCATACCCAAAATCGAGGTTA
37931 T
1 T
37932 ATTTTTGTTT
Statistics
Matches: 117, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
122 96 0.82
123 4 0.03
124 17 0.15
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.34
Consensus pattern (123 bp):
TCTGTGTTTGAGTAATATTTTTTTGTTAAATCTATGATATCAATATACCATCAAGTAGAAACAAA
ATTTAAGGACGAAATTTCATTAAGGAGGGGAGAGTTGTCATACCCAAAATCGAGGTTA
Found at i:38239 original size:25 final size:25
Alignment explanation
Indices: 38211--38275 Score: 112
Period size: 25 Copynumber: 2.6 Consensus size: 25
38201 TTTATAGTTA
* *
38211 TTTGTTTATTTTATTTATCAATTAC
1 TTTGTCTATTATATTTATCAATTAC
38236 TTTGTCTATTATATTTATCAATTAC
1 TTTGTCTATTATATTTATCAATTAC
38261 TTTGTCTATTATATT
1 TTTGTCTATTATATT
38276 ATGTATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.25, C:0.09, G:0.05, T:0.62
Consensus pattern (25 bp):
TTTGTCTATTATATTTATCAATTAC
Found at i:42751 original size:81 final size:82
Alignment explanation
Indices: 42634--42826 Score: 228
Period size: 81 Copynumber: 2.3 Consensus size: 82
42624 AAAATTCGCT
* * * * *
42634 CTTTAGTGGTGTTTTTTAACAAACGCCGTAATAGGGTACATATATCGTGGCATTTTTAGACAAAT
1 CTTTAGTGGTGTTTTTTAACAAACGCCGCAACAGGGTACAAATATCATGGCATTTTTAGACAAAC
* *
42699 GCCGCTAAAACCTAGTA
66 ACCACTAAAACCTAGTA
* **
42716 CTTTAGTGGCT-TTTTTT-ATAAACGCCGCAACAGGGTACAAATATCATGGTGTTTTTAGACAAA
1 CTTTAGTGG-TGTTTTTTAACAAACGCCGCAACAGGGTACAAATATCATGGCATTTTTAGACAAA
42779 CACCACTAAAACCTAGTA
65 CACCACTAAAACCTAGTA
* *
42797 CTTTTTATTGGTGTTTTTCTTACAAACGCC
1 C--TTTAGTGGTGTTTTT-TAACAAACGCC
42827 ACAATAGACG
Statistics
Matches: 93, Mismatches: 12, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
81 55 0.59
82 16 0.17
83 13 0.14
84 1 0.01
85 8 0.09
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (82 bp):
CTTTAGTGGTGTTTTTTAACAAACGCCGCAACAGGGTACAAATATCATGGCATTTTTAGACAAAC
ACCACTAAAACCTAGTA
Found at i:42958 original size:42 final size:42
Alignment explanation
Indices: 42809--42951 Score: 191
Period size: 42 Copynumber: 3.5 Consensus size: 42
42799 TTTTATTGGT
* *
42809 GTTTTTCTTACAAACGCCACAATAGAC-GGTACATT-GTGGC
1 GTTTTTCTTACAAACGCCGCAATAGACTAGTACATTAGTGGC
* * *
42849 GTTTTTCTTGCAAACGTCGCAATAGACTAGTATATTAGTGGC
1 GTTTTTCTTACAAACGCCGCAATAGACTAGTACATTAGTGGC
* * *
42891 GTTTTTCTCACAAACGCCGCAATAGGCTAGTACATTAGTGAC
1 GTTTTTCTTACAAACGCCGCAATAGACTAGTACATTAGTGGC
*
42933 ATTTTTCTTACAAACGCCG
1 GTTTTTCTTACAAACGCCG
42952 TCATAGGATG
Statistics
Matches: 88, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 24 0.27
41 6 0.07
42 58 0.66
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (42 bp):
GTTTTTCTTACAAACGCCGCAATAGACTAGTACATTAGTGGC
Found at i:43121 original size:21 final size:21
Alignment explanation
Indices: 43095--43149 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
43085 ACGTCGCCGT
* *
43095 TCACCACCATCGTGCCATCAA
1 TCACCACTATCGCGCCATCAA
*
43116 TCACCACTATCACGCCATCAA
1 TCACCACTATCGCGCCATCAA
43137 TCACCACTATCGC
1 TCACCACTATCGC
43150 ACCTCCATCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.44, G:0.07, T:0.20
Consensus pattern (21 bp):
TCACCACTATCGCGCCATCAA
Found at i:44016 original size:20 final size:20
Alignment explanation
Indices: 43980--44017 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
43970 ATCCTATTTC
**
43980 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
44000 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
44018 GTCGTGAACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:50954 original size:13 final size:13
Alignment explanation
Indices: 50936--50974 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
50926 CATAGTTGAA
50936 CAGTCTTCATATG
1 CAGTCTTCATATG
50949 CAGTCTTCATATG
1 CAGTCTTCATATG
50962 CAGTCTTCATATG
1 CAGTCTTCATATG
50975 TACGTCTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:51653 original size:20 final size:20
Alignment explanation
Indices: 51605--51657 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
51595 TAATACAAAA
* *
51605 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
51625 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
51645 TCGCAACGCGATT
1 TCGCAACGCGATT
51658 TACATAGCGC
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:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:52276 original size:20 final size:19
Alignment explanation
Indices: 52230--52381 Score: 152
Period size: 20 Copynumber: 8.1 Consensus size: 19
52220 GAAACCAAAA
*
52230 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
52249 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
52268 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
52288 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
52304 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
52321 TCGCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCA-TT
*
52341 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
52360 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
52380 TC
1 TC
52382 AACCAAAAGA
Statistics
Matches: 114, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
14 10 0.09
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 48 0.42
20 52 0.46
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:52311 original size:39 final size:39
Alignment explanation
Indices: 52235--52311 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
52225 CAAAATCGCA
* **
52235 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
52274 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
52312 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:55843 original size:14 final size:14
Alignment explanation
Indices: 55824--55859 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
55814 ATTGTTTAAT
55824 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
55838 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
55852 TGATTTGT
1 TGATTTGT
55860 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:55990 original size:19 final size:19
Alignment explanation
Indices: 55966--56019 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
55956 AAAAAGTACT
* *
55966 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATAAAA
*
55985 ATCGCAACGAGAAAATAAAA
1 ATCGCAACGCG-AAATAAAA
56005 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
56020 TAAATTTGCG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.50, C:0.19, G:0.19, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATAAAA
Found at i:56070 original size:33 final size:32
Alignment explanation
Indices: 56028--56154 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
56018 ATTAAATTTG
56028 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
56061 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
56094 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
56127 CGTTACGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
56155 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:56117 original size:66 final size:66
Alignment explanation
Indices: 56021--56153 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
56011 ACGCGAAATT
* *
56021 AAATTTGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTACGATTTTCATTTCGCATTGC
56086 G
66 G
*
56087 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTACGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTACGATTTTCATTTCGCATTGC
56152 G
66 G
56153 A
1 A
56154 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTACGATTTTCATTTCGCATTGC
G
Found at i:58678 original size:24 final size:24
Alignment explanation
Indices: 58644--58697 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
58634 CTGAAACATC
* * *
58644 ATCAAAATCCGTGTATTTACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
58668 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
58692 ATCAAA
1 ATCAAA
58698 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:59782 original size:20 final size:20
Alignment explanation
Indices: 59757--59814 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
59747 ATTCATTTGA
59757 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
59777 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
59797 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
59815 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:59857 original size:14 final size:14
Alignment explanation
Indices: 59838--59891 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
59828 GAAAATCGCA
59838 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
59852 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
59869 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
59885 TTGCGAT
1 TTGCGAT
59892 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:59857 original size:33 final size:33
Alignment explanation
Indices: 59820--59890 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
59810 AAAATCGCAA
59820 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
59853 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
59886 TGCGA
1 TGCGA
59891 TAGCCATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:59891 original size:33 final size:33
Alignment explanation
Indices: 59833--59910 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
59823 GAAATGAAAA
***
59833 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
59866 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
59899 TCGCGTTGCGAT
1 TCGCATTGCGAT
59911 AGTCTGTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:60017 original size:14 final size:14
Alignment explanation
Indices: 59998--60034 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
59988 CATCAATTAA
59998 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
60012 ACAAATCATCTTTT
1 ACAAATCAACATTT
60026 ACAAATCAA
1 ACAAATCAA
60035 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:61938 original size:20 final size:19
Alignment explanation
Indices: 61907--61958 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
61897 CTTAAAATCG
61907 CAACGCGAAATGACTATCA
1 CAACGCGAAATGACTATCA
* *
61926 CAACGCGGAAATGGCTATCG
1 CAACGC-GAAATGACTATCA
*
61946 CAATGCGAAATGA
1 CAACGCGAAATGA
61959 AAATCGCAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (19 bp):
CAACGCGAAATGACTATCA
Found at i:61964 original size:19 final size:19
Alignment explanation
Indices: 61900--62001 Score: 81
Period size: 19 Copynumber: 5.6 Consensus size: 19
61890 CACGAAACTT
61900 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
** *
61919 ACTATCACAACGCGGAAATG
1 AAAATCGCAACGC-GAAATG
*** *
61939 GCTATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
*
61958 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAATG
61972 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
61991 -AAATCGCAACG
1 AAAATCGCAACG
62002 ACAAAATCGC
Statistics
Matches: 66, Mismatches: 11, Indels: 13
0.73 0.12 0.14
Matches are distributed among these distances:
14 10 0.15
15 1 0.02
16 2 0.03
17 2 0.03
18 12 0.18
19 23 0.35
20 16 0.24
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:61977 original size:14 final size:14
Alignment explanation
Indices: 61958--62015 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
61948 ATGCGAAATG
61958 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
61972 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
61988 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
62004 AAAATCGCAACG
1 AAAATCGCAACG
62016 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:62000 original size:32 final size:33
Alignment explanation
Indices: 61942--62020 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
61932 GGAAATGGCT
*
61942 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
61975 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
62007 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
62021 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:62049 original size:19 final size:17
Alignment explanation
Indices: 62027--62122 Score: 69
Period size: 19 Copynumber: 5.6 Consensus size: 17
62017 GAAACACAAA
62027 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
62046 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
62062 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
* *
62078 TTGCTTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
62094 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
62111 TCGCATTGCGAT
1 TCGC-TTGCGAT
62123 AGCCATTTCC
Statistics
Matches: 61, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
14 15 0.25
15 3 0.05
16 10 0.16
17 4 0.07
18 13 0.21
19 16 0.26
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:62087 original size:32 final size:33
Alignment explanation
Indices: 62032--62122 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
62022 ACAAATCGCA
*
62032 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
* *
62065 TTGCGA-TTTCATTTTGCTTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
62097 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
62123 AGCCATTTCC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 30 0.57
33 23 0.43
ACGTcount: A:0.11, C:0.18, G:0.22, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:62091 original size:13 final size:14
Alignment explanation
Indices: 62049--62106 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
62039 TTTCATTTCG
62049 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
62063 CGTTGCGATTTCATTTT
1 CGTTGCGA-TT--TTGT
*
62080 GCTTTGCGATTTTGT
1 -CGTTGCGATTTTGT
62095 CGTTGCGATTTT
1 CGTTGCGATTTT
62107 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.53
15 5 0.14
17 5 0.14
18 7 0.19
ACGTcount: A:0.09, C:0.16, G:0.24, T:0.52
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:62141 original size:20 final size:19
Alignment explanation
Indices: 62107--62161 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
62097 TTGCGATTTT
*
62107 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
62126 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
62146 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
62162 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:62669 original size:18 final size:18
Alignment explanation
Indices: 62643--62687 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
62633 GTCGATCAGA
*
62643 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
62661 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
62679 TGATGGCTC
1 TGATGGCTC
62688 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:64032 original size:20 final size:20
Alignment explanation
Indices: 64007--64044 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
63997 AATAGTTTCT
64007 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
64027 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
64045 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:64605 original size:41 final size:41
Alignment explanation
Indices: 64560--64637 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
64550 CGAAAGTCAG
* *
64560 TATCGCATTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
64601 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
64638 CCCAATTCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:64634 original size:20 final size:20
Alignment explanation
Indices: 64520--64634 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
64510 CGCTTTGAAA
*
64520 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
64541 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* *
64561 ATCGCATTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
64581 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
64602 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
64622 ATCGCATTGCGAT
1 ATCGCATTGCGAT
64635 TTTCCCAATT
Statistics
Matches: 74, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
19 2 0.03
20 48 0.65
21 24 0.32
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:76129 original size:31 final size:31
Alignment explanation
Indices: 76093--76215 Score: 196
Period size: 31 Copynumber: 4.0 Consensus size: 31
76083 CCCGAAGGAC
* *
76093 CAGTCCATA-GATTCCGAAGAATC-TAGGTAAT
1 CAGTCCATATG-TCCCGAAGAA-CATAGGTAAA
76124 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
76155 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
76186 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
76216 CCCTCGACCC
Statistics
Matches: 88, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
30 1 0.01
31 86 0.98
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:80254 original size:31 final size:31
Alignment explanation
Indices: 80216--80338 Score: 203
Period size: 31 Copynumber: 4.0 Consensus size: 31
80206 CCCGAAGGAC
* * *
80216 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
80247 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
80278 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
80309 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
80339 CCCTCGACCC
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:96810 original size:28 final size:27
Alignment explanation
Indices: 96739--96813 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 27
96729 ATTTAAGATG
*
96739 TATGATTTTAGTG-TTTAGGGTTTTGGTT
1 TATGA-TTTA-TGATTTAAGGTTTTGGTT
* **
96767 TCAAGATTTAAAATTTAAGGTTTATGGTT
1 T-ATGATTTATGATTTAAGGTTT-TGGTT
96796 TATGATTTATGATTTAAG
1 TATGATTTATGATTTAAG
96814 ATTGTAAGAT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
28 28 0.76
29 9 0.24
ACGTcount: A:0.27, C:0.01, G:0.21, T:0.51
Consensus pattern (27 bp):
TATGATTTATGATTTAAGGTTTTGGTT
Found at i:96823 original size:8 final size:7
Alignment explanation
Indices: 96769--96847 Score: 59
Period size: 7 Copynumber: 11.1 Consensus size: 7
96759 TTTTGGTTTC
96769 AAGATTT
1 AAGATTT
*
96776 AAAATTT
1 AAGATTT
*
96783 AAGGTTT
1 AAGATTT
* *
96790 ATGGTTT
1 AAGATTT
*
96797 ATGATTT
1 AAGATTT
*
96804 ATGATTT
1 AAGATTT
96811 AAGATTGT
1 AAGATT-T
96819 AAGATTT
1 AAGATTT
* *
96826 AGGTTTT
1 AAGATTT
* *
96833 AGGGTTT
1 AAGATTT
96840 AAGATTT
1 AAGATTT
96847 A
1 A
96848 TAACTTAGGC
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
7 53 0.88
8 7 0.12
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (7 bp):
AAGATTT
Found at i:97127 original size:22 final size:23
Alignment explanation
Indices: 97099--97152 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 23
97089 ATCAATATTC
*
97099 TAAGGTTTTAGGGTTTAT-GCTT
1 TAAGGTTTTAGGGGTTATAGCTT
* *
97121 T-AGGGTTTAGGGGTTATAGGTT
1 TAAGGTTTTAGGGGTTATAGCTT
97143 TAAGGTTTTA
1 TAAGGTTTTA
97153 ATGTTCATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 14 0.54
22 5 0.19
23 7 0.27
ACGTcount: A:0.20, C:0.02, G:0.31, T:0.46
Consensus pattern (23 bp):
TAAGGTTTTAGGGGTTATAGCTT
Found at i:97202 original size:30 final size:30
Alignment explanation
Indices: 97168--97224 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
97158 CATACTTTAA
* *
97168 GATTTATGGTTTCATGGTTTATGATTTTGG
1 GATTTATGGTTTCAGGGTTTAGGATTTTGG
*
97198 GATTTATGGTTTTAGGGTTTAGGATTT
1 GATTTATGGTTTCAGGGTTTAGGATTT
97225 ATGATTTTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.18, C:0.02, G:0.28, T:0.53
Consensus pattern (30 bp):
GATTTATGGTTTCAGGGTTTAGGATTTTGG
Found at i:97203 original size:15 final size:15
Alignment explanation
Indices: 97183--97224 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
97173 ATGGTTTCAT
97183 GGTTTATGATTTT-G
1 GGTTTATGATTTTAG
*
97197 GGATTTATGGTTTTAG
1 GG-TTTATGATTTTAG
*
97213 GGTTTAGGATTT
1 GGTTTATGATTT
97225 ATGATTTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 2 0.09
15 18 0.78
16 3 0.13
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.52
Consensus pattern (15 bp):
GGTTTATGATTTTAG
Found at i:97222 original size:22 final size:22
Alignment explanation
Indices: 97197--97260 Score: 89
Period size: 21 Copynumber: 3.0 Consensus size: 22
97187 TATGATTTTG
97197 GGATTTATGGTTTTAGGGTTTA
1 GGATTTATGGTTTTAGGGTTTA
*
97219 GGATTTATGATTTTA-GGTTTA
1 GGATTTATGGTTTTAGGGTTTA
97240 -GATTTCATGG-TTTAGGGTTTA
1 GGATTT-ATGGTTTTAGGGTTTA
97261 TGGCTTAGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
20 9 0.24
21 15 0.39
22 14 0.37
ACGTcount: A:0.20, C:0.02, G:0.28, T:0.50
Consensus pattern (22 bp):
GGATTTATGGTTTTAGGGTTTA
Found at i:97263 original size:14 final size:14
Alignment explanation
Indices: 97105--97274 Score: 69
Period size: 14 Copynumber: 11.8 Consensus size: 14
97095 ATTCTAAGGT
*
97105 TTTAGGGTTTATGC
1 TTTAGGGTTTATGG
*
97119 TTTAGGGTTTAGGGG
1 TTTAGGGTTTA-TGG
*
97134 TTATA-GGTTTAAGG
1 TT-TAGGGTTTATGG
** * **
97148 TTTTAATGTTCATAC
1 -TTTAGGGTTTATGG
* *
97163 TTTAAGATTTATGG
1 TTTAGGGTTTATGG
* *
97177 TTTCATGGTTTATGA
1 TTT-AGGGTTTATGG
*
97192 TTTTGGGATTTATGG
1 TTTAGGG-TTTATGG
97207 TTTTAGGGTTTA-GG
1 -TTTAGGGTTTATGG
* *
97221 ATTTATGATTT-TAGG
1 -TTTAGGGTTTAT-GG
*
97236 TTTA-GATTTCATGG
1 TTTAGGGTTT-ATGG
97250 TTTAGGGTTTATGG
1 TTTAGGGTTTATGG
* *
97264 CTTAGGATTTA
1 TTTAGGGTTTA
97275 AGATCTATGG
Statistics
Matches: 118, Mismatches: 26, Indels: 24
0.70 0.15 0.14
Matches are distributed among these distances:
13 5 0.04
14 62 0.53
15 43 0.36
16 8 0.07
ACGTcount: A:0.21, C:0.04, G:0.26, T:0.49
Consensus pattern (14 bp):
TTTAGGGTTTATGG
Found at i:97341 original size:21 final size:21
Alignment explanation
Indices: 97296--97335 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
97286 CATGGTCAGT
*
97296 GTTTAAGTTTTAGGGTTTATA
1 GTTTAAGTTTTAGGGTATATA
97317 GTTT-AGTGTTTAGGGTATA
1 GTTTAAGT-TTTAGGGTATA
97336 AGGTTTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.50
Consensus pattern (21 bp):
GTTTAAGTTTTAGGGTATATA
Found at i:97506 original size:22 final size:21
Alignment explanation
Indices: 97478--97526 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
97468 ATGACTCAAT
*
97478 TTTTAGGGTGCATGGTTTATAG
1 TTTTAGGGTGCAAGGTTT-TAG
*
97500 TTTTAGGGTTCAAGGTTTTAG
1 TTTTAGGGTGCAAGGTTTTAG
97521 TGTTTA
1 T-TTTA
97527 TGATTTAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.18, C:0.04, G:0.29, T:0.49
Consensus pattern (21 bp):
TTTTAGGGTGCAAGGTTTTAG
Found at i:97549 original size:22 final size:22
Alignment explanation
Indices: 97523--97569 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
97513 GGTTTTAGTG
97523 TTTATGATTTAAAGTATATGGT
1 TTTATGATTTAAAGTATATGGT
* *
97545 TTTATGGTTTAAGGTATATGGT
1 TTTATGATTTAAAGTATATGGT
97567 TTT
1 TTT
97570 GAGCTTTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (22 bp):
TTTATGATTTAAAGTATATGGT
Found at i:97577 original size:22 final size:22
Alignment explanation
Indices: 97523--97577 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
97513 GGTTTTAGTG
*
97523 TTTATGATTTAAAGTATATGGT
1 TTTATGCTTTAAAGTATATGGT
* *
97545 TTTATGGTTTAAGGTATATGGT
1 TTTATGCTTTAAAGTATATGGT
97567 TTTGA-GCTTTA
1 TTT-ATGCTTTA
97578 GGGTGTAGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.22, T:0.51
Consensus pattern (22 bp):
TTTATGCTTTAAAGTATATGGT
Found at i:97734 original size:37 final size:36
Alignment explanation
Indices: 97670--97767 Score: 94
Period size: 37 Copynumber: 2.7 Consensus size: 36
97660 TATGGTTATA
* * *
97670 GTTTTATGATTTAGTGTTTAAG-GTTTATAGCTTA-
1 GTTTTATGGTTTAGGGTTTAAGATTTTATAGCTTAG
* * *
97704 GTGTTTA-GTGTTTAGGGATTTATGATTTTATGGTTTAG
1 GT-TTTATG-GTTTAGGG-TTTAAGATTTTATAGCTTAG
97742 GTTTTATGGTTTAGGGTTTAAGATTT
1 GTTTTATGGTTTAGGGTTTAAGATTT
97768 AAGATTTATG
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
34 3 0.06
35 10 0.20
36 14 0.27
37 21 0.41
38 3 0.06
ACGTcount: A:0.20, C:0.01, G:0.26, T:0.53
Consensus pattern (36 bp):
GTTTTATGGTTTAGGGTTTAAGATTTTATAGCTTAG
Found at i:97748 original size:14 final size:14
Alignment explanation
Indices: 97729--97761 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
97719 GGATTTATGA
97729 TTTTATGGTTTAGG
1 TTTTATGGTTTAGG
97743 TTTTATGGTTTAGG
1 TTTTATGGTTTAGG
*
97757 GTTTA
1 TTTTA
97762 AGATTTAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (14 bp):
TTTTATGGTTTAGG
Found at i:97768 original size:14 final size:14
Alignment explanation
Indices: 97751--97794 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
97741 GGTTTTATGG
*
97751 TTTAGGGTTTAAGA
1 TTTAAGGTTTAAGA
* *
97765 TTTAAGATTTATGA
1 TTTAAGGTTTAAGA
97779 TTTAAGGTTT-AGA
1 TTTAAGGTTTAAGA
97792 TTT
1 TTT
97795 TTAAGATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 5 0.20
14 20 0.80
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (14 bp):
TTTAAGGTTTAAGA
Found at i:97775 original size:21 final size:20
Alignment explanation
Indices: 97751--97794 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
97741 GGTTTTATGG
*
97751 TTTAGGGTTTAAGATTTAAGA
1 TTTAGGATTTAAGATTT-AGA
* *
97772 TTTATGATTTAAGGTTTAGA
1 TTTAGGATTTAAGATTTAGA
97792 TTT
1 TTT
97795 TTAAGATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTAGGATTTAAGATTTAGA
Found at i:97846 original size:14 final size:14
Alignment explanation
Indices: 97829--97869 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
97819 GGGTCATTGA
97829 TTTAGGGTTTAGAG
1 TTTAGGGTTTAGAG
*
97843 TTTAGGGTTTATAG
1 TTTAGGGTTTAGAG
97857 TTTAGGGTTTAGA
1 TTTAGGGTTTAGA
97870 ACTTATGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (14 bp):
TTTAGGGTTTAGAG
Found at i:97847 original size:28 final size:28
Alignment explanation
Indices: 97816--97869 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
97806 TTTTGAGTGG
*
97816 TTAGGG-TCATTGATTTAGGGTTTAGAGT
1 TTAGGGTTCATAG-TTTAGGGTTTAGAGT
*
97844 TTAGGGTTTATAGTTTAGGGTTTAGA
1 TTAGGGTTCATAGTTTAGGGTTTAGA
97870 ACTTATGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.22, C:0.02, G:0.31, T:0.44
Consensus pattern (28 bp):
TTAGGGTTCATAGTTTAGGGTTTAGAGT
Found at i:97853 original size:21 final size:21
Alignment explanation
Indices: 97829--97868 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
97819 GGGTCATTGA
*
97829 TTTAGGGTTTAGAGTTTAGGG
1 TTTAGAGTTTAGAGTTTAGGG
* *
97850 TTTATAGTTTAGGGTTTAG
1 TTTAGAGTTTAGAGTTTAG
97869 AACTTATGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (21 bp):
TTTAGAGTTTAGAGTTTAGGG
Found at i:98137 original size:8 final size:8
Alignment explanation
Indices: 98126--98176 Score: 54
Period size: 7 Copynumber: 6.8 Consensus size: 8
98116 AGGATTTAGG
98126 GTTTATGA
1 GTTTATGA
98134 GTTTAT-A
1 GTTTATGA
*
98141 GTTTAGGA
1 GTTTATGA
98149 -TTTATGA
1 GTTTATGA
* *
98156 TTTTAGGA
1 GTTTATGA
98164 -TTTATGA
1 GTTTATGA
98171 GTTTAT
1 GTTTAT
98177 TGGTTCAAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
7 18 0.50
8 18 0.50
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.53
Consensus pattern (8 bp):
GTTTATGA
Found at i:98138 original size:15 final size:15
Alignment explanation
Indices: 98116--98175 Score: 70
Period size: 15 Copynumber: 4.1 Consensus size: 15
98106 TTAGGATTTA
*
98116 AGGATTTA-GGGTTT
1 AGGATTTATGAGTTT
*
98130 ATGAGTTTAT-AGTTT
1 AGGA-TTTATGAGTTT
*
98145 AGGATTTATGATTTT
1 AGGATTTATGAGTTT
98160 AGGATTTATGAGTTT
1 AGGATTTATGAGTTT
98175 A
1 A
98176 TTGGTTCAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
14 8 0.21
15 30 0.79
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (15 bp):
AGGATTTATGAGTTT
Found at i:98161 original size:37 final size:37
Alignment explanation
Indices: 98104--98176 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
98094 GGATATTTGT
*
98104 GTTTAGGATTTAAGGATTTAGGGTTTATGAGTTTATA
1 GTTTAGGATTTAAGGATTTAGGATTTATGAGTTTATA
*
98141 GTTTAGGATTT-ATGATTTTAGGATTTATGAGTTTAT
1 GTTTAGGATTTAAGGA-TTTAGGATTTATGAGTTTAT
98177 TGGTTCAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 3 0.09
37 30 0.91
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (37 bp):
GTTTAGGATTTAAGGATTTAGGATTTATGAGTTTATA
Found at i:98267 original size:15 final size:14
Alignment explanation
Indices: 98249--98303 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
98239 GGGCTTATGG
98249 TTTTAGGATTTAAGA
1 TTTT-GGATTTAAGA
* *
98264 TTTTGGGTTTATGA
1 TTTTGGATTTAAGA
*
98278 TTTTGGGTTTTAAGA
1 TTTT-GGATTTAAGA
*
98293 TTTTGGGTTTA
1 TTTTGGATTTA
98304 TGGTTTATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 18 0.53
15 16 0.47
ACGTcount: A:0.20, C:0.00, G:0.25, T:0.55
Consensus pattern (14 bp):
TTTTGGATTTAAGA
Found at i:98276 original size:29 final size:29
Alignment explanation
Indices: 98243--98309 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
98233 GTTATAGGGC
98243 TTATGGTTTTAGGATTTAAGATTTTGGGT
1 TTATGGTTTTAGGATTTAAGATTTTGGGT
* * *
98272 TTATGATTTTGGGTTTTAAGATTTTGGGT
1 TTATGGTTTTAGGATTTAAGATTTTGGGT
98301 TTATGGTTT
1 TTATGGTTT
98310 ATTATTTTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.18, C:0.00, G:0.27, T:0.55
Consensus pattern (29 bp):
TTATGGTTTTAGGATTTAAGATTTTGGGT
Found at i:98279 original size:14 final size:14
Alignment explanation
Indices: 98243--98305 Score: 72
Period size: 15 Copynumber: 4.4 Consensus size: 14
98233 GTTATAGGGC
* *
98243 TTATGGTTTTAGGAT
1 TTATGATTTT-GGGT
*
98258 TTAAGATTTTGGGT
1 TTATGATTTTGGGT
98272 TTATGATTTTGGGTT
1 TTATGATTTTGGG-T
*
98287 TTAAGATTTTGGGT
1 TTATGATTTTGGGT
98301 TTATG
1 TTATG
98306 GTTTATTATT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
14 20 0.49
15 21 0.51
ACGTcount: A:0.19, C:0.00, G:0.27, T:0.54
Consensus pattern (14 bp):
TTATGATTTTGGGT
Found at i:98382 original size:22 final size:22
Alignment explanation
Indices: 98314--98383 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
98304 TGGTTTATTA
* *
98314 TTTTAGAGTTTTAAGGTTTTG-G
1 TTTTAGA-ATTTAGGGTTTTGAG
* * *
98336 ATTTTAGGATCTAGGGGTTAT-AG
1 -TTTTAGAATTTA-GGGTTTTGAG
98359 TTTTAGAATTTAGGGTTTTGAG
1 TTTTAGAATTTAGGGTTTTGAG
98381 TTT
1 TTT
98384 ATGATATAGG
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
21 6 0.17
22 18 0.50
23 12 0.33
ACGTcount: A:0.21, C:0.01, G:0.27, T:0.50
Consensus pattern (22 bp):
TTTTAGAATTTAGGGTTTTGAG
Found at i:104302 original size:2 final size:2
Alignment explanation
Indices: 104295--104321 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
104285 TGATGATACA
104295 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
104322 GATAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:104330 original size:2 final size:2
Alignment explanation
Indices: 104325--104356 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
104315 ATATATAGAT
104325 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
104357 CTTGAAGAAG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.