Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006815.1 Hibiscus syriacus cultivar Beakdansim tig00017319_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: 89746
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:1435 original size:19 final size:19
Alignment explanation
Indices: 1411--1453 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
1401 CGGTACAGGG
1411 GGCGCGCTATACTCCACGT
1 GGCGCGCTATACTCCACGT
*
1430 GGCGCGTTATACTCCACGT
1 GGCGCGCTATACTCCACGT
1449 GGCGC
1 GGCGC
1454 CAAATCAGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.14, C:0.35, G:0.30, T:0.21
Consensus pattern (19 bp):
GGCGCGCTATACTCCACGT
Found at i:1795 original size:45 final size:43
Alignment explanation
Indices: 1749--1877 Score: 151
Period size: 45 Copynumber: 3.0 Consensus size: 43
1739 ACATTAAAAT
*
1749 ATATATTTTATTATATCTTAATTTTAAAATATTATAAGAAT-AA
1 ATATATTTTATT-TATCTTAATTTTAAAATATTATAAGATTAAA
* **
1792 ATATA---T-TTTATCTTAAATTTTAAAATATTTTAATTTTAAA
1 ATATATTTTATTTATCTT-AATTTTAAAATATTATAAGATTAAA
1832 ATATATTTTATTTTTATCTTAATTTTAAAATATTATAAGATTAAA
1 ATATATTTTA--TTTATCTTAATTTTAAAATATTATAAGATTAAA
1877 A
1 A
1878 ATAAATATTT
Statistics
Matches: 71, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
38 6 0.08
39 20 0.28
40 8 0.11
43 6 0.08
45 23 0.32
46 8 0.11
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (43 bp):
ATATATTTTATTTATCTTAATTTTAAAATATTATAAGATTAAA
Found at i:1826 original size:16 final size:16
Alignment explanation
Indices: 1807--1865 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
1797 TTTTATCTTA
1807 AATTTTAAAATATTTT
1 AATTTTAAAATATTTT
1823 AATTTTAAAATATATTT
1 AATTTTAAAATAT-TTT
* *
1840 TATTTT----TATCTT
1 AATTTTAAAATATTTT
1852 AATTTTAAAATATT
1 AATTTTAAAATATT
1866 ATAAGATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
12 7 0.21
13 3 0.09
16 16 0.47
17 8 0.24
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTTTAAAATATTTT
Found at i:1839 original size:18 final size:17
Alignment explanation
Indices: 1807--1847 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
1797 TTTTATCTTA
1807 AATTTT-AAAATATTTT
1 AATTTTAAAAATATTTT
1823 AATTTTAAAATATATTTT
1 AATTTTAAAA-ATATTTT
*
1841 ATTTTTA
1 AATTTTA
1848 TCTTAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.27
17 3 0.14
18 13 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTTTAAAAATATTTT
Found at i:1961 original size:43 final size:40
Alignment explanation
Indices: 1921--2087 Score: 135
Period size: 42 Copynumber: 4.0 Consensus size: 40
1911 ATTTTTAAGT
1921 TAAATTAAAATTAGATAAAAAATAAAATATA-TTTAATTTAA
1 TAAATTAAAATTAGAT--AAAATAAAATATATTTTAATTTAA
* * *
1962 TTTAAATCAAAAGTAAGATAAAATAAAATA-ATTTTAAAATTAA
1 --TAAATTAAAA-TTAGATAAAATAAAATATATTTT-AATTTAA
** * * *
2005 TATTTTAAATTTAAGATAAAAATAAAATATACTTT-ATTCTTA
1 TAAATTAAAATT-AGAT-AAAATAAAATATATTTTAATT-TAA
2047 TAATATT-AAATTAGATAAAATAAAATATATTTTAATGTTAA
1 TAA-ATTAAAATTAGATAAAATAAAATATATTTTAAT-TTAA
2088 GATGTTAATT
Statistics
Matches: 98, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
40 17 0.17
41 21 0.21
42 34 0.35
43 21 0.21
44 5 0.05
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.39
Consensus pattern (40 bp):
TAAATTAAAATTAGATAAAATAAAATATATTTTAATTTAA
Found at i:8359 original size:17 final size:17
Alignment explanation
Indices: 8337--8376 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
8327 CTCGAATCGA
8337 GTGTTCGGTACAAGTAC
1 GTGTTCGGTACAAGTAC
8354 GTGTTCGGTACAAGTAC
1 GTGTTCGGTACAAGTAC
8371 GTGTTC
1 GTGTTC
8377 TTGGATTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (17 bp):
GTGTTCGGTACAAGTAC
Found at i:16069 original size:21 final size:22
Alignment explanation
Indices: 16044--16094 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
16034 AGTTGTGGGG
16044 ATGTTTTTAGT-TTTTTATTAA
1 ATGTTTTTAGTATTTTTATTAA
* *
16065 ATGTTTTTGGTATTTTTATTTA
1 ATGTTTTTAGTATTTTTATTAA
16087 AT-TTTTTA
1 ATGTTTTTA
16095 AATGATTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.22, C:0.00, G:0.10, T:0.69
Consensus pattern (22 bp):
ATGTTTTTAGTATTTTTATTAA
Found at i:17486 original size:24 final size:24
Alignment explanation
Indices: 17459--17511 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
17449 AAGAAAATAT
*
17459 GAAACCTAATTTGATTGAAACTAA
1 GAAACCTAATTTGATTAAAACTAA
* * *
17483 GAAATCTAGTTTGATTAAAAGTAA
1 GAAACCTAATTTGATTAAAACTAA
17507 GAAAC
1 GAAAC
17512 ATATTTCTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.28
Consensus pattern (24 bp):
GAAACCTAATTTGATTAAAACTAA
Found at i:19044 original size:20 final size:20
Alignment explanation
Indices: 19016--19073 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
19006 ATGTGAAAAT
* *
19016 TGTCTCGAATGACCTATGTA
1 TGTCCCGAAGGACCTATGTA
*
19036 TGTCCCGAAGGACCTCTGTA
1 TGTCCCGAAGGACCTATGTA
19056 TGTCCCGAAGGACCTATG
1 TGTCCCGAAGGACCTATG
19074 AACCCTCGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (20 bp):
TGTCCCGAAGGACCTATGTA
Found at i:22292 original size:24 final size:24
Alignment explanation
Indices: 22246--22290 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
22236 TTATTTGACA
22246 ACATTAATATAAATAAATATATAC
1 ACATTAATATAAATAAATATATAC
*
22270 ACATT-ATA-AAATATATATATA
1 ACATTAATATAAATAAATATATA
22291 TATATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 3 0.15
24 5 0.25
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (24 bp):
ACATTAATATAAATAAATATATAC
Found at i:22855 original size:34 final size:35
Alignment explanation
Indices: 22775--23071 Score: 294
Period size: 34 Copynumber: 8.2 Consensus size: 35
22765 TATATATAAC
** *
22775 ATATATAATATATAATTTCGAAAATATTTTTGAAAA
1 ATATATAATATATAATTTTTAAAACATTTTTG-AAA
*
22811 TATATATAATATATAGTTTTTAAAACA-TTTTGAAA
1 -ATATATAATATATAATTTTTAAAACATTTTTGAAA
*
22846 ATATATAATATATAGTTTTTAAAACA-TTTTGAAA
1 ATATATAATATATAATTTTTAAAACATTTTTGAAA
* * *
22880 ACATATAATATATAATTTTAAAAATATTTTTTGAAAA
1 ATATATAATATATAATTTTTAAAACA-TTTTTG-AAA
*
22917 TATATATAATATATAGTTTTTAAAACA-TTTTGAAA
1 -ATATATAATATATAATTTTTAAAACATTTTTGAAA
* * * * *
22952 ACATATAATATATAGTTTTGAAAGCATTTTTAAAA
1 ATATATAATATATAATTTTTAAAACATTTTTGAAA
* *
22987 ACGTATATAATATATAATCTTTAATAGGATATTTTTGAAA
1 A--TATATAATATATAATTTTTAA-A--ACATTTTTGAAA
**
23027 ACGTATAATATATAATTTTTAAAAACGATTTTTGAAA
1 ATATATAATATATAATTTTT-AAAAC-ATTTTTGAAA
23064 CATATATA
1 -ATATATA
23072 TTTTGAAAAT
Statistics
Matches: 218, Mismatches: 29, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
34 79 0.36
35 14 0.06
36 16 0.07
37 52 0.24
38 45 0.21
39 2 0.01
40 10 0.05
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (35 bp):
ATATATAATATATAATTTTTAAAACATTTTTGAAA
Found at i:22941 original size:106 final size:107
Alignment explanation
Indices: 22777--23071 Score: 391
Period size: 106 Copynumber: 2.7 Consensus size: 107
22767 TATATAACAT
**
22777 ATATAATATATAATTTCGAAAATATTTTTGAAAATATATATAATATATAGTTTTTAAAACATTTT
1 ATATAATATATAATTTTAAAAATATTTTTGAAAATATATATAATATATAGTTTTTAAAACATTTT
* *
22842 GAAAATATATAATATATAGTTTTTAAAACA-TTTTGAAAAC-
66 GAAAATATATAATATATAGTTTTGAAAACATTTTTAAAAACG
22882 ATATAATATATAATTTTAAAAATATTTTTTGAAAATATATATAATATATAGTTTTTAAAACATTT
1 ATATAATATATAATTTTAAAAATA-TTTTTGAAAATATATATAATATATAGTTTTTAAAACATTT
* *
22947 TGAAAACATATAATATATAGTTTTGAAAGCATTTTTAAAAACG
65 TGAAAATATATAATATATAGTTTTGAAAACATTTTTAAAAACG
* ** *
22990 TATATAATATATAATCTTTAATAGGATATTTTTG-AAA-ACGTATAATATATAATTTTTAAAAAC
1 -ATATAATATATAAT-TTTAA-A-AATATTTTTGAAAATATATATAATATATAGTTTTT-AAAAC
23053 GATTTTTGAAACATATATA
61 -A-TTTTGAAA-ATATATA
23072 TTTTGAAAAT
Statistics
Matches: 168, Mismatches: 11, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
105 22 0.13
106 68 0.40
107 9 0.05
109 31 0.18
110 13 0.08
111 8 0.05
112 11 0.07
113 6 0.04
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (107 bp):
ATATAATATATAATTTTAAAAATATTTTTGAAAATATATATAATATATAGTTTTTAAAACATTTT
GAAAATATATAATATATAGTTTTGAAAACATTTTTAAAAACG
Found at i:23035 original size:24 final size:24
Alignment explanation
Indices: 23008--23053 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
22998 ATATAATCTT
*
23008 TAATAGGAT-ATTTTTGAAAACGTA
1 TAATA-GATAATTTTTAAAAACGTA
*
23032 TAATATATAATTTTTAAAAACG
1 TAATAGATAATTTTTAAAAACG
23054 ATTTTTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.46, C:0.04, G:0.11, T:0.39
Consensus pattern (24 bp):
TAATAGATAATTTTTAAAAACGTA
Found at i:23142 original size:13 final size:13
Alignment explanation
Indices: 23124--23148 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23114 AGTTACATTA
23124 TATTTATTTATTG
1 TATTTATTTATTG
23137 TATTTATTTATT
1 TATTTATTTATT
23149 TGTTTTGTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TATTTATTTATTG
Found at i:25445 original size:56 final size:56
Alignment explanation
Indices: 25374--25490 Score: 173
Period size: 56 Copynumber: 2.1 Consensus size: 56
25364 TAAGTGACAC
* *
25374 AACATGATTAGAGATTTTTTCTTAATGTTATTTTATTCTCCATCCAATTAGATATT
1 AACATGATTAGAGATTTTTTCTTAATGTTATTTTATTCTCAATCCAATCAGATATT
* *
25430 AACATGATT-GAAGATTTTTTCTTACTGTTATTTTATTCTCAATCCAGTCAGATATT
1 AACATGATTAG-AGATTTTTTCTTAATGTTATTTTATTCTCAATCCAATCAGATATT
*
25486 GACAT
1 AACAT
25491 CACCGTTAAG
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
55 1 0.02
56 54 0.98
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (56 bp):
AACATGATTAGAGATTTTTTCTTAATGTTATTTTATTCTCAATCCAATCAGATATT
Found at i:27482 original size:22 final size:22
Alignment explanation
Indices: 27455--27503 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
27445 ATATTTTTTT
*
27455 ATATTT-ATAATATTAATTATA
1 ATATTTAATAATATAAATTATA
*
27476 GATATTTAATATTATAAATTATA
1 -ATATTTAATAATATAAATTATA
27499 ATATT
1 ATATT
27504 ATTTTATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
ATATTTAATAATATAAATTATA
Found at i:27513 original size:7 final size:7
Alignment explanation
Indices: 27503--27536 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
27493 ATTATAATAT
27503 TATTTTA
1 TATTTTA
27510 TATTTTA
1 TATTTTA
27517 TATTTTA
1 TATTTTA
27524 TATTTTA
1 TATTTTA
27531 TATTTT
1 TATTTT
27537 TTAATTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TATTTTA
Found at i:44118 original size:22 final size:21
Alignment explanation
Indices: 44071--44128 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
44061 AAGGACTTAT
* * *
44071 TTAATTTTTTAGAAATAATATT
1 TTAAATTTTTA-AAATAAAATA
44093 TTAAATTTTTAAAATTAAAATA
1 TTAAATTTTTAAAA-TAAAATA
* *
44115 TTAAAATATTAAAA
1 TTAAATTTTTAAAA
44129 AATATCAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 3 0.10
22 27 0.90
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
TTAAATTTTTAAAATAAAATA
Found at i:44174 original size:2 final size:2
Alignment explanation
Indices: 44167--44218 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
44157 AAATTAATAA
44167 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
*
44209 AT AT TT AT AT
1 AT AT AT AT AT
44219 TAAAAATAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:48287 original size:20 final size:20
Alignment explanation
Indices: 48262--48396 Score: 94
Period size: 20 Copynumber: 6.8 Consensus size: 20
48252 GTAACACAGA
*
48262 AGTCAAATTCGCAACGTGAT
1 AGTCAAATTCGCAACGCGAT
* * * *
48282 AGTCAAATTTGCAACACAAA
1 AGTCAAATTCGCAACGCGAT
* * *
48302 AGTTAAATTAGCAATGCGAT
1 AGTCAAATTCGCAACGCGAT
48322 AGTCAAATTCGCAACGCGA-
1 AGTCAAATTCGCAACGCGAT
* * * * *
48341 ATTTATAAATCGTAACACAGA-
1 AGTCA-AATTCGCAACGC-GAT
** *
48362 AGTCAAATTCATAATGCGAT
1 AGTCAAATTCGCAACGCGAT
48382 AGTCAAATTCGCAAC
1 AGTCAAATTCGCAAC
48397 ACAAAAGTTA
Statistics
Matches: 84, Mismatches: 28, Indels: 6
0.71 0.24 0.05
Matches are distributed among these distances:
19 5 0.06
20 74 0.88
21 5 0.06
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAT
Found at i:48298 original size:40 final size:40
Alignment explanation
Indices: 48232--48336 Score: 115
Period size: 40 Copynumber: 2.6 Consensus size: 40
48222 TTCTAATTTC
* * *
48232 GCAACGCGAATATGT-AAA-TCGTAACACAGAAGTCAAATTC
1 GCAACGCG-ATA-GTCAAATTCGCAACACAAAAGTCAAATTA
* * *
48272 GCAACGTGATAGTCAAATTTGCAACACAAAAGTTAAATTA
1 GCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAATTA
*
48312 GCAATGCGATAGTCAAATTCGCAAC
1 GCAACGCGATAGTCAAATTCGCAAC
48337 GCGAATTTAT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
38 2 0.04
39 6 0.11
40 46 0.85
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (40 bp):
GCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAATTA
Found at i:48326 original size:60 final size:60
Alignment explanation
Indices: 48262--48396 Score: 157
Period size: 60 Copynumber: 2.2 Consensus size: 60
48252 GTAACACAGA
* * * *
48262 AGTCAAATTCGCAACGTGATAGTCA-AATTTGCAACACAAAAGTTAAATT-AGCAATGCGAT
1 AGTCAAATTCGCAACGCGA-AGTCATAAATCGCAACACAAAAGTCAAATTCA-CAATGCGAT
* * * * *
48322 AGTCAAATTCGCAACGCGAATTTATAAATCGTAACACAGAAGTCAAATTCATAATGCGAT
1 AGTCAAATTCGCAACGCGAAGTCATAAATCGCAACACAAAAGTCAAATTCACAATGCGAT
48382 AGTCAAATTCGCAAC
1 AGTCAAATTCGCAAC
48397 ACAAAAGTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 3 0.05
60 60 0.94
61 1 0.02
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (60 bp):
AGTCAAATTCGCAACGCGAAGTCATAAATCGCAACACAAAAGTCAAATTCACAATGCGAT
Found at i:48365 original size:100 final size:100
Alignment explanation
Indices: 48229--48408 Score: 297
Period size: 100 Copynumber: 1.8 Consensus size: 100
48219 AATTTCTAAT
* * * *
48229 TTCGCAACGCGAATATGTAAATCGTAACACAGAAGTCAAATTCGCAACGTGATAGTCAAATTTGC
1 TTCGCAACGCGAATATATAAATCGTAACACAGAAGTCAAATTCACAACGCGATAGTCAAATTCGC
48294 AACACAAAAGTTAAATTAGCAATGCGATAGTCAAA
66 AACACAAAAGTTAAATTAGCAATGCGATAGTCAAA
* * *
48329 TTCGCAACGCGAATTTATAAATCGTAACACAGAAGTCAAATTCATAATGCGATAGTCAAATTCGC
1 TTCGCAACGCGAATATATAAATCGTAACACAGAAGTCAAATTCACAACGCGATAGTCAAATTCGC
48394 AACACAAAAGTTAAA
66 AACACAAAAGTTAAA
48409 ATGCGGAATT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 73 1.00
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (100 bp):
TTCGCAACGCGAATATATAAATCGTAACACAGAAGTCAAATTCACAACGCGATAGTCAAATTCGC
AACACAAAAGTTAAATTAGCAATGCGATAGTCAAA
Found at i:48504 original size:20 final size:19
Alignment explanation
Indices: 48414--48510 Score: 113
Period size: 19 Copynumber: 4.9 Consensus size: 19
48404 TTAAAATGCG
*
48414 GAATTTCAAATTCGTAATGT
1 GAATTTCAAATTCGTAA-CT
* *
48434 GGAATTTCAAATTCGCAATT
1 -GAATTTCAAATTCGTAACT
*
48454 GAATTTCAAATTCGCAACT
1 GAATTTCAAATTCGTAACT
48473 GAATTTCAAATTCGTAACT
1 GAATTTCAAATTCGTAACT
* *
48492 AGATTTTCGAATTCGTAAC
1 -GAATTTCAAATTCGTAAC
48511 ACGAATTTAA
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
19 36 0.52
20 17 0.25
21 16 0.23
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.36
Consensus pattern (19 bp):
GAATTTCAAATTCGTAACT
Found at i:48517 original size:59 final size:58
Alignment explanation
Indices: 48414--48529 Score: 135
Period size: 58 Copynumber: 2.0 Consensus size: 58
48404 TTAAAATGCG
* * **
48414 GAATTTCAAATTCGTAATGTGGAATTTCAAATTCGCAATTGAATTTCAAATTCGCAACT
1 GAATTTCAAATTCGTAATCTAGAATTTCAAATTCGCAAACGAATTT-AAATTCGCAACT
* * * *
48473 GAATTTCAAATTCGTAA-CTAGATTTTCGAATTCGTAACACGAATTTAATTTCGCAAC
1 GAATTTCAAATTCGTAATCTAGAATTTCAAATTCGCAA-ACGAATTTAAATTCGCAAC
48530 AGGTTTTAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
58 25 0.52
59 23 0.48
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (58 bp):
GAATTTCAAATTCGTAATCTAGAATTTCAAATTCGCAAACGAATTTAAATTCGCAACT
Found at i:48530 original size:19 final size:19
Alignment explanation
Indices: 48503--48549 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
48493 GATTTTCGAA
*
48503 TTCGTAACACGAATTTAAT
1 TTCGCAACACGAATTTAAT
** *
48522 TTCGCAACA-GGTTTTAGT
1 TTCGCAACACGAATTTAAT
48540 TTCGCAACAC
1 TTCGCAACAC
48550 AAATGTTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (19 bp):
TTCGCAACACGAATTTAAT
Found at i:49498 original size:24 final size:24
Alignment explanation
Indices: 49447--49500 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
49437 GTATTTGAAA
*
49447 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
49471 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
49495 TTTGAT
1 TTTGAT
49501 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:51340 original size:20 final size:20
Alignment explanation
Indices: 51317--51367 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
51307 AGCAGTTTCT
*
51317 GAAACTTAAATTCGCAACGC
1 GAAACTAAAATTCGCAACGC
*
51337 GAAAATGAAAA-TCGCAACGC
1 GAAACT-AAAATTCGCAACGC
*
51357 AAAACTAAAAT
1 GAAACTAAAAT
51368 CGCGTTGCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 4 0.16
20 18 0.72
21 3 0.12
ACGTcount: A:0.51, C:0.20, G:0.14, T:0.16
Consensus pattern (20 bp):
GAAACTAAAATTCGCAACGC
Found at i:51366 original size:19 final size:20
Alignment explanation
Indices: 51318--51370 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 20
51308 GCAGTTTCTG
*
51318 AAACTTAAATTCGCAACGCGA
1 AAAC-TAAAATCGCAACGCGA
51339 AAA-TGAAAATCGCAACGC-A
1 AAACT-AAAATCGCAACGCGA
51358 AAACTAAAATCGC
1 AAACTAAAATCGC
51371 GTTGCGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 13 0.45
20 13 0.45
21 3 0.10
ACGTcount: A:0.49, C:0.23, G:0.13, T:0.15
Consensus pattern (20 bp):
AAACTAAAATCGCAACGCGA
Found at i:51910 original size:20 final size:20
Alignment explanation
Indices: 51881--52013 Score: 155
Period size: 20 Copynumber: 6.7 Consensus size: 20
51871 TAATATTGTG
*
51881 TTTCGCGTTGCGAATTTGAC
1 TTTCGTGTTGCGAATTTGAC
51901 TTTCGTGTTGCGAATTTGAC
1 TTTCGTGTTGCGAATTTGAC
51921 TTTCGTGTTGCGAATTTGAC
1 TTTCGTGTTGCGAATTTGAC
*
51941 TTTTGTGTTGCG-ATTT-AC
1 TTTCGTGTTGCGAATTTGAC
* * *
51959 AAATTCGCGTTGCGGATTTGAC
1 --TTTCGTGTTGCGAATTTGAC
* *
51981 TATCGCGTTGCGAATTTGA-
1 TTTCGTGTTGCGAATTTGAC
52000 TTTCTGTGTTGCGA
1 TTTC-GTGTTGCGA
52014 TTTACAGATT
Statistics
Matches: 98, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
18 2 0.02
19 7 0.07
20 83 0.85
21 4 0.04
22 2 0.02
ACGTcount: A:0.16, C:0.16, G:0.26, T:0.43
Consensus pattern (20 bp):
TTTCGTGTTGCGAATTTGAC
Found at i:51980 original size:60 final size:60
Alignment explanation
Indices: 51902--52053 Score: 202
Period size: 60 Copynumber: 2.5 Consensus size: 60
51892 GAATTTGACT
* * * *
51902 TTCGTGTTGCGAATTTGACTTTCGTGTTGCGAATTTGACTTT-TGTGTTGCGATTTACAAA
1 TTCGCGTTGCGGATTTGACTATCGCGTTGCGAATTTGA-TTTCTGTGTTGCGATTTACAAA
*
51962 TTCGCGTTGCGGATTTGACTATCGCGTTGCGAATTTGATTTCTGTGTTGCGATTTACAGA
1 TTCGCGTTGCGGATTTGACTATCGCGTTGCGAATTTGATTTCTGTGTTGCGATTTACAAA
*
52022 TTCGCGTTGC-GATTT-ACAGATTCGCGTTGCGA
1 TTCGCGTTGCGGATTTGAC-TA-TCGCGTTGCGA
52054 TTTACAAATT
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
58 2 0.02
59 9 0.11
60 72 0.87
ACGTcount: A:0.17, C:0.16, G:0.26, T:0.41
Consensus pattern (60 bp):
TTCGCGTTGCGGATTTGACTATCGCGTTGCGAATTTGATTTCTGTGTTGCGATTTACAAA
Found at i:52030 original size:20 final size:20
Alignment explanation
Indices: 51947--52072 Score: 136
Period size: 20 Copynumber: 6.3 Consensus size: 20
51937 TGACTTTTGT
*
51947 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAGATTCGC
*
51967 GTTGCGGATTTGAC-TA-TCGC
1 GTTGC-GATTT-ACAGATTCGC
*
51987 GTTGCGAATTT---GATTTCTGT
1 GTTGCG-ATTTACAGA-TTC-GC
52007 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
52027 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
*
52047 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAGATTCGC
52067 GTTGCG
1 GTTGCG
52073 TTGCGAATTT
Statistics
Matches: 92, Mismatches: 5, Indels: 18
0.80 0.04 0.16
Matches are distributed among these distances:
17 1 0.01
19 7 0.08
20 71 0.77
21 9 0.10
22 4 0.04
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCGC
Found at i:52071 original size:60 final size:60
Alignment explanation
Indices: 51902--52072 Score: 152
Period size: 60 Copynumber: 2.9 Consensus size: 60
51892 GAATTTGACT
* * ** * * * * *
51902 TTCGTGTTGCGAATTTGACTTTCGTGTTGCGAATTTGACTTTTGTGTTGCGATTTACAAA
1 TTCGCGTTGCGGATTTGACGATCGCGTTGCGAATTTAAATTCTGCGTTGCGATTTACAAA
* * * * *
51962 TTCGCGTTGCGGATTTGACTATCGCGTTGCGAATTTGATTTCTGTGTTGCGATTTACAGA
1 TTCGCGTTGCGGATTTGACGATCGCGTTGCGAATTTAAATTCTGCGTTGCGATTTACAAA
52022 TTCGCGTTGC-GATTT-ACAGATTCGCGTTGCG-ATTTACAAATTC-GCGTTGCG
1 TTCGCGTTGCGGATTTGAC-GA-TCGCGTTGCGAATTT--AAATTCTGCGTTGCG
52073 TTGCGAATTT
Statistics
Matches: 96, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
58 2 0.02
59 10 0.10
60 80 0.83
61 4 0.04
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.40
Consensus pattern (60 bp):
TTCGCGTTGCGGATTTGACGATCGCGTTGCGAATTTAAATTCTGCGTTGCGATTTACAAA
Found at i:59488 original size:14 final size:15
Alignment explanation
Indices: 59462--59491 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
59452 TGTATATAAT
59462 TTTATATATTTTATA
1 TTTATATATTTTATA
59477 TTTATA-ATTTTATA
1 TTTATATATTTTATA
59491 T
1 T
59492 ACAGTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTATATATTTTATA
Found at i:59499 original size:23 final size:23
Alignment explanation
Indices: 59456--59500 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
59446 ATATAGTGTA
***
59456 TATAATTTTATATATTTTATATT
1 TATAATTTTATATACAGTATATT
59479 TATAATTTTATATACAGTATAT
1 TATAATTTTATATACAGTATAT
59501 AAACTATGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (23 bp):
TATAATTTTATATACAGTATATT
Found at i:59617 original size:33 final size:33
Alignment explanation
Indices: 59579--59744 Score: 160
Period size: 33 Copynumber: 5.0 Consensus size: 33
59569 ATTAATAAAC
*
59579 TATATATTTCATTAGTATATATAAATTATATAT
1 TATATATTTCATTAGTATATATAAACTATATAT
*
59612 TATATAGTTT-ATTAGTATATATAACCTATATAT
1 TATATA-TTTCATTAGTATATATAAACTATATAT
* * * *
59645 TATAAAGTTCAATAGTATAT-T-AACTATATAG
1 TATATATTTCATTAGTATATATAAACTATATAT
* *
59676 TAAATAGTTT-ATTAGTATATATAAACTATTTATAAAC
1 TATATA-TTTCATTAGTATATATAAACTA--TAT--AT
* *
59713 TATATAGTTCATTAGTTTATATAAACTATATA
1 TATATATTTCATTAGTATATATAAACTATATA
59745 GTTCATTAGT
Statistics
Matches: 108, Mismatches: 15, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
31 21 0.19
32 6 0.06
33 47 0.44
34 3 0.03
35 6 0.06
36 2 0.02
37 23 0.21
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (33 bp):
TATATATTTCATTAGTATATATAAACTATATAT
Found at i:59716 original size:22 final size:22
Alignment explanation
Indices: 59655--59807 Score: 67
Period size: 26 Copynumber: 6.4 Consensus size: 22
59645 TATAAAGTTC
*
59655 AATAGTATATTAACTATATAGTA
1 AATAGTTTA-TAACTATATAGTA
* *
59678 AATAGTTTATTAGTATATA-TA
1 AATAGTTTATAACTATATAGTA
*
59699 AACTA-TTTATAAACTATATAGTTC
1 AA-TAGTTTAT-AACTATATAG-TA
* *
59723 ATTAGTTTATATAAACTATATAGTTC
1 AATAG-TT-TAT-AACTATATAG-TA
* *
59749 ATTAGTTTATATAAACTATATAGTTC
1 AATAG-TT-TAT-AACTATATAG-TA
*
59775 ATTAGTTTATATAAACTATATAGTA
1 AATAG-TT-TAT-AACTATATAGTA
*
59800 TATAGTTT
1 AATAGTTT
59808 TGTTTATTAG
Statistics
Matches: 113, Mismatches: 10, Indels: 14
0.82 0.07 0.10
Matches are distributed among these distances:
21 9 0.08
22 17 0.15
23 11 0.10
24 4 0.04
25 6 0.05
26 66 0.58
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (22 bp):
AATAGTTTATAACTATATAGTA
Found at i:59741 original size:26 final size:26
Alignment explanation
Indices: 59706--59798 Score: 186
Period size: 26 Copynumber: 3.6 Consensus size: 26
59696 ATAAACTATT
59706 TATAAACTATATAGTTCATTAGTTTA
1 TATAAACTATATAGTTCATTAGTTTA
59732 TATAAACTATATAGTTCATTAGTTTA
1 TATAAACTATATAGTTCATTAGTTTA
59758 TATAAACTATATAGTTCATTAGTTTA
1 TATAAACTATATAGTTCATTAGTTTA
59784 TATAAACTATATAGT
1 TATAAACTATATAGT
59799 ATATAGTTTT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 67 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.45
Consensus pattern (26 bp):
TATAAACTATATAGTTCATTAGTTTA
Found at i:61342 original size:17 final size:17
Alignment explanation
Indices: 61320--61355 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
61310 TGAATCACTA
*
61320 TTTTAATTATCCAAATT
1 TTTTAAATATCCAAATT
*
61337 TTTTAAATATTCAAATT
1 TTTTAAATATCCAAATT
61354 TT
1 TT
61356 CGGATCGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAAATATCCAAATT
Found at i:76240 original size:18 final size:17
Alignment explanation
Indices: 76214--76416 Score: 63
Period size: 19 Copynumber: 11.2 Consensus size: 17
76204 CAAATAAAAT
*
76214 AAATAAAATAAAGATTAA
1 AAATAAAATAAA-AATAA
*
76232 AAATGAAATAAAAATAA
1 AAATAAAATAAAAATAA
*
76249 AAATTAAAA-AATAATATA
1 AAA-TAAAATAAAAATA-A
* *
76267 ATATAATATAAGAAAATAA
1 AAATAAAAT-A-AAAATAA
*
76286 TAATAATAATAATAATATATA
1 AAATAA-AATAA-AA-ATA-A
**
76307 CCAT-AAATAAATAAATAA
1 AAATAAAAT-AA-AAATAA
* *
76325 GAACAAGAATAAAAAGTAA
1 AAATAA-AATAAAAA-TAA
**
76344 AAATAAATATAGTAAT-A
1 AAATAAA-ATAAAAATAA
* *
76361 AAATAAATATAAAGAGAA
1 AAATAAA-ATAAAAATAA
* * *
76379 AAAGAGTAAATATAAAGAA
1 AAATA--AAATAAAAATAA
*
76398 AAAT-AAATAATAATAA
1 AAATAAAATAAAAATAA
76414 AAA
1 AAA
76417 AACCGAAAAA
Statistics
Matches: 138, Mismatches: 30, Indels: 36
0.68 0.15 0.18
Matches are distributed among these distances:
16 12 0.09
17 30 0.22
18 31 0.22
19 41 0.30
20 21 0.15
21 3 0.02
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.23
Consensus pattern (17 bp):
AAATAAAATAAAAATAA
Found at i:76254 original size:24 final size:22
Alignment explanation
Indices: 76209--76272 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 22
76199 GGAAGCAAAT
*
76209 AAAATAAATAAAATAAAGATTA
1 AAAATAAATAAAATAAAAATTA
76231 AAAATGAAATAAAAATAAAAATTAA
1 AAAAT-AAAT-AAAATAAAAATT-A
*
76256 AAAATAATATAATATAA
1 AAAATAA-ATAAAATAA
76273 TATAAGAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
22 5 0.14
23 4 0.11
24 19 0.53
25 8 0.22
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (22 bp):
AAAATAAATAAAATAAAAATTA
Found at i:76264 original size:17 final size:17
Alignment explanation
Indices: 76214--76252 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
76204 CAAATAAAAT
* *
76214 AAATAAAATAAAGATTAA
1 AAATGAAATAAA-AATAA
76232 AAATGAAATAAAAATAA
1 AAATGAAATAAAAATAA
76249 AAAT
1 AAAT
76253 TAAAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (17 bp):
AAATGAAATAAAAATAA
Found at i:76289 original size:3 final size:3
Alignment explanation
Indices: 76258--76302 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
76248 AAAATTAAAA
*
76258 AAT AAT -AT AAT -AT AAT -AT AAG AA- AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
76302 A
1 A
76303 TATACCATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
2 8 0.22
3 29 0.78
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:76300 original size:23 final size:22
Alignment explanation
Indices: 76238--76300 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
76228 TTAAAAATGA
* *
76238 AATAAAAATAAAAATTAAAAAAT
1 AATAATAATAATAA-TAAAAAAT
76261 AAT-ATAAT-ATAATATAAGAAAAT
1 AATAATAATAAT-A-ATAA-AAAAT
76284 AATAATAATAATAATAA
1 AATAATAATAATAATAA
76301 TATATACCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
21 1 0.03
22 8 0.24
23 16 0.48
24 6 0.18
25 2 0.06
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (22 bp):
AATAATAATAATAATAAAAAAT
Found at i:76320 original size:32 final size:28
Alignment explanation
Indices: 76253--76324 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 28
76243 AAATAAAAAT
*
76253 TAAA-AAATAATATAATATAATATAAGA
1 TAAATAAATAATATAATATAATATAACA
76280 -AAAT-AATAATAATAATAATAATATATACCA
1 TAAATAAATAAT-ATAAT-ATAATATA-A-CA
76310 TAAATAAATAA-ATAA
1 TAAATAAATAATATAA
76325 GAACAAGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
26 9 0.24
27 5 0.14
28 8 0.22
29 1 0.03
30 5 0.14
31 4 0.11
32 5 0.14
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (28 bp):
TAAATAAATAATATAATATAATATAACA
Found at i:76416 original size:17 final size:17
Alignment explanation
Indices: 76209--76417 Score: 56
Period size: 17 Copynumber: 12.2 Consensus size: 17
76199 GGAAGCAAAT
76209 AAAATAAATAA-AATAA
1 AAAATAAATAATAATAA
* *
76225 AGATTAAA-AATGAA-ATA
1 AAAATAAATAAT-AATA-A
76242 AAAATAAA-AAT--TAA
1 AAAATAAATAATAATAA
76256 AAAATAATATAAT-ATAA
1 AAAATAA-ATAATAATAA
76273 TATAAGA-AAATAATAATAA
1 -A-AA-ATAAATAATAATAA
76292 TAATAAT-AATATATACCATAA
1 -AA-AATAAATA-ATA--ATAA
* *
76313 ATAAATAAATAAGAA-CA
1 A-AAATAAATAATAATAA
* *
76330 AGAAT-AA-AA-AGT-A
1 AAAATAAATAATAATAA
*
76343 AAAATAAAT-ATAGTAA
1 AAAATAAATAATAATAA
* *
76359 TAAAATAAATATAAAGAGAA
1 -AAAATAAATA-ATA-ATAA
76379 AAAGAGTAAAT-ATAA-AGA
1 AAA-A-TAAATAATAATA-A
76397 AAAATAAATAATAATAA
1 AAAATAAATAATAATAA
76414 AAAA
1 AAAA
76418 ACCGAAAAAA
Statistics
Matches: 148, Mismatches: 13, Indels: 63
0.66 0.06 0.28
Matches are distributed among these distances:
13 6 0.04
14 13 0.09
15 9 0.06
16 19 0.13
17 37 0.25
18 19 0.13
19 21 0.14
20 10 0.07
21 14 0.09
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.22
Consensus pattern (17 bp):
AAAATAAATAATAATAA
Found at i:77971 original size:37 final size:37
Alignment explanation
Indices: 77884--78029 Score: 176
Period size: 38 Copynumber: 4.0 Consensus size: 37
77874 CAAAGCTTTG
77884 GTGTTTCAAGAGAAAC-ATGTTCAAAGGTTTTCTTTTTT
1 GTGTTTCAAGAGAAACGAT-TTCAAAGGTTTTC-TTTTT
* * *
77922 TTATTTCAAGAGAAACAATTTCAAAGGTTTTCTTTTT
1 GTGTTTCAAGAGAAACGATTTCAAAGGTTTTCTTTTT
* *
77959 GTGTTCCCAGAGAAACGATTTCAAAGG---T-TTTTT
1 GTGTTTCAAGAGAAACGATTTCAAAGGTTTTCTTTTT
*
77992 GTGTTTCAAGAGAAAACGATTTCAAAGGTTTTTTTTTT
1 GTGTTTCAAGAG-AAACGATTTCAAAGGTTTTCTTTTT
78030 TCAAGAGAAA
Statistics
Matches: 93, Mismatches: 9, Indels: 12
0.82 0.08 0.11
Matches are distributed among these distances:
33 15 0.16
34 16 0.17
37 28 0.30
38 32 0.34
39 2 0.02
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (37 bp):
GTGTTTCAAGAGAAACGATTTCAAAGGTTTTCTTTTT
Found at i:77996 original size:33 final size:33
Alignment explanation
Indices: 77928--78040 Score: 129
Period size: 33 Copynumber: 3.3 Consensus size: 33
77918 TTTTTTATTT
*
77928 CAAGAGAAACAATTTCAAAGGTTTTCTTTTTGTGTTC
1 CAAGAGAAACGATTTCAAAGG---T-TTTTTGTGTTC
* *
77965 CCAGAGAAACGATTTCAAAGGTTTTTTGTGTTT
1 CAAGAGAAACGATTTCAAAGGTTTTTTGTGTTC
* *
77998 CAAGAGAAAACGATTTCAAAGGTTTTTT-TTTTT
1 CAAGAG-AAACGATTTCAAAGGTTTTTTGTGTTC
78031 CAAGAGAAAC
1 CAAGAGAAAC
78041 TGTCTCCATG
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
32 4 0.06
33 25 0.36
34 22 0.31
37 19 0.27
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (33 bp):
CAAGAGAAACGATTTCAAAGGTTTTTTGTGTTC
Found at i:78014 original size:34 final size:33
Alignment explanation
Indices: 77884--78040 Score: 147
Period size: 37 Copynumber: 4.5 Consensus size: 33
77874 CAAAGCTTTG
77884 GTGTTTCAAGAGAAAC-ATGTTCAAAGGTTTTCTTTTTT
1 GTGTTTCAAGAGAAACGAT-TTCAAAGG-----TTTTTT
* * *
77922 TTATTTCAAGAGAAACAATTTCAAAGGTTTTCTTTTT
1 GTGTTTCAAGAGAAACGATTTCAAAGG---T-TTTTT
* *
77959 GTGTTCCCAGAGAAACGATTTCAAAGGTTTTTT
1 GTGTTTCAAGAGAAACGATTTCAAAGGTTTTTT
77992 GTGTTTCAAGAGAAAACGATTTCAAAGGTTTTTT
1 GTGTTTCAAGAG-AAACGATTTCAAAGGTTTTTT
*
78026 -TTTTTCAAGAGAAAC
1 GTGTTTCAAGAGAAAC
78041 TGTCTCCATG
Statistics
Matches: 105, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
32 4 0.04
33 25 0.24
34 22 0.21
36 3 0.03
37 27 0.26
38 22 0.21
39 2 0.02
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (33 bp):
GTGTTTCAAGAGAAACGATTTCAAAGGTTTTTT
Found at i:78117 original size:30 final size:30
Alignment explanation
Indices: 78055--78139 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 30
78045 TCCATGGAGG
* ** *
78055 CAAAATTT-TGTTTCAAGAGAAA-AATATT
1 CAAAGTTTATGTTTCAAGAGAAACTGTTTT
*
78083 CAAAGGTTT-TGTTTCAAGGGAAACTGTTTT
1 CAAA-GTTTATGTTTCAAGAGAAACTGTTTT
78113 CAAAGTTTATGTTTCAAGAGAAACTGT
1 CAAAGTTTATGTTTCAAGAGAAACTGT
78140 CTCAAGGGAG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.08
29 20 0.42
30 24 0.50
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (30 bp):
CAAAGTTTATGTTTCAAGAGAAACTGTTTT
Found at i:78187 original size:36 final size:36
Alignment explanation
Indices: 78139--78208 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
78129 AGAGAAACTG
* **
78139 TCTCAAGGGAGACAAAATTTGTTCCAAGGGAAATTA
1 TCTCAAGAGAGACAAAATTCATTCCAAGGGAAATTA
*
78175 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAAT
1 TCTCAAGAGAGACAAAATTCATTCCAAGGGAAAT
78209 GTTTTCAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.24
Consensus pattern (36 bp):
TCTCAAGAGAGACAAAATTCATTCCAAGGGAAATTA
Found at i:78273 original size:36 final size:36
Alignment explanation
Indices: 78223--78408 Score: 151
Period size: 36 Copynumber: 5.4 Consensus size: 36
78213 TCAATGTTTA
* *
78223 TGTTTCAAGAGAAACTGCCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
* *
78259 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
** * * * *
78295 CATTTTAAGGGAAA-TGTTTTCAA---TG-----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGGGAGACAAAATT
*
78323 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA-TT
78361 TGTTTCAA-GGAAACTGTCTCAA-GGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
**
78395 CATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
78409 TGTTTTCAAT
Statistics
Matches: 116, Mismatches: 21, Indels: 27
0.71 0.13 0.16
Matches are distributed among these distances:
28 2 0.02
29 15 0.13
30 2 0.02
32 1 0.01
33 1 0.01
34 8 0.07
35 16 0.14
36 61 0.53
37 8 0.07
38 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
Found at i:78445 original size:100 final size:101
Alignment explanation
Indices: 78094--78498 Score: 643
Period size: 101 Copynumber: 4.0 Consensus size: 101
78084 AAAGGTTTTG
*
78094 TTTCAAGGGAAACTGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TTTCAAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* *
78159 GTTCCAAGGGAAATTATCTCAAGAGAGACAAAATTCA
65 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
*
78196 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGCCTCAAGGGAGACAAAATTTG
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTG
78261 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
66 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
*
78297 TTTTAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTT
*
78362 GTTTCAA-GGAAACTGTCTCAAG-GAGACAAAATTCA
65 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
* *
78397 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGACACTATCTCAAGGGAGACAAAAAAAA
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAC----AAAA
* * *
78462 TTTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAAT
62 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
78499 CTTGTTTTAA
Statistics
Matches: 283, Mismatches: 13, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
100 67 0.24
101 158 0.56
102 22 0.08
103 9 0.03
104 18 0.06
105 9 0.03
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.30
Consensus pattern (101 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTG
TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
Found at i:78621 original size:36 final size:36
Alignment explanation
Indices: 78495--78984 Score: 140
Period size: 36 Copynumber: 13.7 Consensus size: 36
78485 AAGCGAGATA
* *
78495 AAATCTTGTTTTAAG-AAAA-AATCTTGAGGGAAAT
1 AAATCTTCTTTCAAGTAAAACAATCTTGAGGGAAAT
* ** ** * * *
78529 AAATCTTCTTTCGAGTAAAACAGCCTCAAGTGAGAC
1 AAATCTTCTTTCAAGTAAAACAATCTTGAGGGAAAT
* *
78565 AAAGTATGT-TTT-AAGAAAAACAATCTTGAGGGAAAT
1 AAA-TCT-TCTTTCAAGTAAAACAATCTTGAGGGAAAT
* * ** * * *
78601 AAATCTTCTTTCGAGTAAAACAGTCTCAAGTGAGAC
1 AAATCTTCTTTCAAGTAAAACAATCTTGAGGGAAAT
*
78637 AAAGTCTGT-TTT-AAGAAAAACAATCTTGAGGGAAAT
1 AAA-TCT-TCTTTCAAGTAAAACAATCTTGAGGGAAAT
* * ** * * *
78673 -AATCCTCTTTCAAGTAAAACAGTCTCAAGTGAGAC
1 AAATCTTCTTTCAAGTAAAACAATCTTGAGGGAAAT
* * **
78708 AAAGTC--CGTTTTAAG-AATGACAATCTCAAGGGAAAT
1 AAA-TCTTC-TTTCAAGTAA-AACAATCTTGAGGGAAAT
* * * *
78744 -AATCTTCTTTCAAGTAAAACAGTC-TCAAGGAAGAC
1 AAATCTTCTTTCAAGTAAAACAATCTTGAGGGAA-AT
* * *
78779 AAGGTCTGT-TTT-AAG-AATGACAATCTTAAGGGAAAT
1 AA-ATCT-TCTTTCAAGTAA-AACAATCTTGAGGGAAAT
* * ** * * *
78815 AAATATTCTTTCAAGTAAAACAGTCTCAAGTGAGAC
1 AAATCTTCTTTCAAGTAAAACAATCTTGAGGGAAAT
* * **
78851 AAGGTCTGT-TTT-AAG-AATGACAATCTCAAGGGAAAT
1 AA-ATCT-TCTTTCAAGTAA-AACAATCTTGAGGGAAAT
* * ** * * *
78887 AAATCTTCTTTCAAGTAAAATAGTCTCAAGTGAGAC
1 AAATCTTCTTTCAAGTAAAACAATCTTGAGGGAAAT
* * **
78923 AAGGTCTGT-TTT-AAG-AATGACAATCTCAAGGGAAAT
1 AA-ATCT-TCTTTCAAGTAA-AACAATCTTGAGGGAAAT
78959 AAATCTTCTTTCAAGTAAAACAATCT
1 AAATCTTCTTTCAAGTAAAACAATCT
78985 CAAGTGAGAC
Statistics
Matches: 323, Mismatches: 95, Indels: 74
0.66 0.19 0.15
Matches are distributed among these distances:
33 1 0.00
34 28 0.09
35 68 0.21
36 179 0.55
37 42 0.13
38 5 0.02
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (36 bp):
AAATCTTCTTTCAAGTAAAACAATCTTGAGGGAAAT
Found at i:78689 original size:143 final size:144
Alignment explanation
Indices: 78481--78997 Score: 747
Period size: 143 Copynumber: 3.6 Consensus size: 144
78471 AGGGAAACTA
* * * * *
78481 TCTCAAGCGAGATAAAATCTTGTTTTAAG-AAAA-AATCTTGAGGGAAATAAATCTTCTTTCGAG
1 TCTCAAGTGAGACAAAGTC-TGTTTTAAGAAAAACAATCTTAAGGGAAATAAATCTTCTTTCAAG
* * ** **
78544 TAAAACAGCCTCAAGTGAGACAAAGTATGTTTTAAGAAAAACAATCTTGAGGGAAATAAATCTTC
65 TAAAACAGTCTCAAGTGAGACAAAGTCTGTTTTAAGAATGACAATCTCAAGGGAAATAAATCTTC
*
78609 TTTCGAGTAAAACAG
130 TTTCAAGTAAAACAG
* *
78624 TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAACAATCTTGAGGGAAAT-AATCCTCTTTCAAGT
1 TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAACAATCTTAAGGGAAATAAATCTTCTTTCAAGT
*
78688 AAAACAGTCTCAAGTGAGACAAAGTCCGTTTTAAGAATGACAATCTCAAGGGAAAT-AATCTTCT
66 AAAACAGTCTCAAGTGAGACAAAGTCTGTTTTAAGAATGACAATCTCAAGGGAAATAAATCTTCT
78752 TTCAAGTAAAACAG
131 TTCAAGTAAAACAG
* ** *
78766 TCTCAAG-GAAGACAAGGTCTGTTTTAAGAATGACAATCTTAAGGGAAATAAATATTCTTTCAAG
1 TCTCAAGTG-AGACAAAGTCTGTTTTAAGAAAAACAATCTTAAGGGAAATAAATCTTCTTTCAAG
*
78830 TAAAACAGTCTCAAGTGAGACAAGGTCTGTTTTAAGAATGACAATCTCAAGGGAAATAAATCTTC
65 TAAAACAGTCTCAAGTGAGACAAAGTCTGTTTTAAGAATGACAATCTCAAGGGAAATAAATCTTC
*
78895 TTTCAAGTAAAATAG
130 TTTCAAGTAAAACAG
* ** *
78910 TCTCAAGTGAGACAAGGTCTGTTTTAAGAATGACAATCTCAAGGGAAATAAATCTTCTTTCAAGT
1 TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAACAATCTTAAGGGAAATAAATCTTCTTTCAAGT
*
78975 AAAACAATCTCAAGTGAGACAAA
66 AAAACAGTCTCAAGTGAGACAAA
78998 TCATCTATAT
Statistics
Matches: 342, Mismatches: 26, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
141 1 0.00
142 73 0.21
143 149 0.44
144 118 0.35
145 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (144 bp):
TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAACAATCTTAAGGGAAATAAATCTTCTTTCAAGT
AAAACAGTCTCAAGTGAGACAAAGTCTGTTTTAAGAATGACAATCTCAAGGGAAATAAATCTTCT
TTCAAGTAAAACAG
Found at i:78713 original size:71 final size:72
Alignment explanation
Indices: 78481--78997 Score: 747
Period size: 72 Copynumber: 7.2 Consensus size: 72
78471 AGGGAAACTA
* * * * * *
78481 TCTCAAGCGAGATAAAATCTTGTTTTAAGAA--AAAATCTTGAGGGAAATAAATCTTCTTTCGAG
1 TCTCAAGTGAGACAAAGTC-TGTTTTAAGAATGACAATCTTAAGGGAAATAAATCTTCTTTCAAG
78544 TAAAACAG
65 TAAAACAG
* * ** * *
78552 CCTCAAGTGAGACAAAGTATGTTTTAAGAAAAACAATCTTGAGGGAAATAAATCTTCTTTCGAGT
1 TCTCAAGTGAGACAAAGTCTGTTTTAAGAATGACAATCTTAAGGGAAATAAATCTTCTTTCAAGT
78617 AAAACAG
66 AAAACAG
** * *
78624 TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAACAATCTTGAGGGAAAT-AATCCTCTTTCAAGT
1 TCTCAAGTGAGACAAAGTCTGTTTTAAGAATGACAATCTTAAGGGAAATAAATCTTCTTTCAAGT
78688 AAAACAG
66 AAAACAG
* *
78695 TCTCAAGTGAGACAAAGTCCGTTTTAAGAATGACAATCTCAAGGGAAAT-AATCTTCTTTCAAGT
1 TCTCAAGTGAGACAAAGTCTGTTTTAAGAATGACAATCTTAAGGGAAATAAATCTTCTTTCAAGT
78759 AAAACAG
66 AAAACAG
* *
78766 TCTCAAG-GAAGACAAGGTCTGTTTTAAGAATGACAATCTTAAGGGAAATAAATATTCTTTCAAG
1 TCTCAAGTG-AGACAAAGTCTGTTTTAAGAATGACAATCTTAAGGGAAATAAATCTTCTTTCAAG
78830 TAAAACAG
65 TAAAACAG
* *
78838 TCTCAAGTGAGACAAGGTCTGTTTTAAGAATGACAATCTCAAGGGAAATAAATCTTCTTTCAAGT
1 TCTCAAGTGAGACAAAGTCTGTTTTAAGAATGACAATCTTAAGGGAAATAAATCTTCTTTCAAGT
*
78903 AAAATAG
66 AAAACAG
* *
78910 TCTCAAGTGAGACAAGGTCTGTTTTAAGAATGACAATCTCAAGGGAAATAAATCTTCTTTCAAGT
1 TCTCAAGTGAGACAAAGTCTGTTTTAAGAATGACAATCTTAAGGGAAATAAATCTTCTTTCAAGT
*
78975 AAAACAA
66 AAAACAG
78982 TCTCAAGTGAGACAAA
1 TCTCAAGTGAGACAAA
78998 TCATCTATAT
Statistics
Matches: 415, Mismatches: 26, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
70 12 0.03
71 143 0.34
72 259 0.62
73 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (72 bp):
TCTCAAGTGAGACAAAGTCTGTTTTAAGAATGACAATCTTAAGGGAAATAAATCTTCTTTCAAGT
AAAACAG
Found at i:84440 original size:5 final size:5
Alignment explanation
Indices: 84430--84507 Score: 57
Period size: 5 Copynumber: 14.2 Consensus size: 5
84420 ATAGGGAAGC
*
84430 AAATA AAATA AAGATAAA AAATG AAATAA AAATA AAATA TAAATA TAAATA
1 AAATA AAATA AA-AT--A AAATA AAAT-A AAATA AAATA -AAATA -AAATA
* * *
84481 AAATA TAATA TAAGA AAATA ATAATA A
1 AAATA AAATA AAATA AAATA A-AATA A
84508 TATATACCAT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
5 34 0.56
6 22 0.36
7 2 0.03
8 3 0.05
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (5 bp):
AAATA
Found at i:84456 original size:18 final size:16
Alignment explanation
Indices: 84430--84648 Score: 67
Period size: 17 Copynumber: 12.8 Consensus size: 16
84420 ATAGGGAAGC
84430 AAATAAAATAAAGATAAA
1 AAAT-AAATAAA-ATAAA
84448 AAATGAAATAAAAATAAA
1 AAAT-AAAT-AAAATAAA
*
84466 ATATAAATATAAATAAA
1 AAATAAATA-AAATAAA
*
84483 ATATAATATAAGAA-AATA
1 AAATAA-ATAA-AATAA-A
*
84501 ATAATAATATATACCATAAA
1 A-AATAA-ATA-A-AATAAA
84521 TAAATAAAT-AAATAAGA
1 -AAATAAATAAAATAA-A
* *
84538 CAA-GAATAAAAGT-AA
1 AAATAAATAAAA-TAAA
* *
84553 AAATAAATACAGTAATA
1 AAATAAATAAAATAA-A
*
84570 AAATAAATATAATGGAAA
1 AAATAAATAAAAT--AAA
* *
84588 AAA-AGAGTAATATAAAA
1 AAATA-AATAAAAT-AAA
84605 GAAATAAAT--AATAAA
1 -AAATAAATAAAATAAA
* *
84620 AAACAGA-AAAATAAA
1 AAATAAATAAAATAAA
84635 ATGAATAAATAAAA
1 A--AATAAATAAAA
84649 ATAATAATTA
Statistics
Matches: 152, Mismatches: 24, Indels: 50
0.67 0.11 0.22
Matches are distributed among these distances:
14 5 0.03
15 17 0.11
16 19 0.12
17 43 0.28
18 41 0.27
19 16 0.11
20 8 0.05
21 3 0.02
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.21
Consensus pattern (16 bp):
AAATAAATAAAATAAA
Found at i:84501 original size:24 final size:23
Alignment explanation
Indices: 84430--84532 Score: 86
Period size: 23 Copynumber: 4.3 Consensus size: 23
84420 ATAGGGAAGC
*
84430 AAATAAAATA-AAGATAAAAAAT
1 AAATAAAATATAAAATAAAAAAT
*
84452 GAAATAAAA-ATAAAATATAAATAT
1 -AAATAAAATATAAAATA-AAAAAT
*
84476 AAATAAAATATAATATAAGAAAAT
1 AAATAAAATATAAAATAA-AAAAT
*
84500 -AATAATAATATATACCATAAATAAAT
1 AAATAA-AATATA-A-AATAAA-AAAT
84526 AAATAAA
1 AAATAAA
84533 TAAGACAAGA
Statistics
Matches: 66, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
22 1 0.02
23 27 0.41
24 22 0.33
25 2 0.03
26 9 0.14
27 5 0.08
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (23 bp):
AAATAAAATATAAAATAAAAAAT
Found at i:84601 original size:88 final size:87
Alignment explanation
Indices: 84454--84619 Score: 187
Period size: 88 Copynumber: 1.9 Consensus size: 87
84444 TAAAAAATGA
* * * ** *
84454 AATAAAAATAAAATATAAATATAAATAAAATATAATATAAGAAAATAATAATAATATATACCATA
1 AATAAAAATAAAATATAAATACAAATAAAATATAATATAAGAAAAAAAGAATAATATATAAAAGA
84519 AATAAATAAATAAATAAGACAAG
66 AATAAAT-AATAAATAAGACAAG
* *
84542 AATAAAAGTAAAA-ATAAATACAGTAATAAAATA-AATATAATGGAAAAAAAGAGT-A-ATATAA
1 AATAAAAATAAAATATAAATACA--AATAAAATATAATATAA--GAAAAAAAGAATAATATATAA
84603 AAGAAATAAATAATAAA
62 AAGAAATAAATAATAAA
84620 AAACAGAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
87 14 0.21
88 33 0.50
89 10 0.15
90 9 0.14
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.23
Consensus pattern (87 bp):
AATAAAAATAAAATATAAATACAAATAAAATATAATATAAGAAAAAAAGAATAATATATAAAAGA
AATAAATAATAAATAAGACAAG
Found at i:86392 original size:25 final size:24
Alignment explanation
Indices: 86364--86411 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
86354 GTATAAATAC
*
86364 TTAAATTCATAATATTTTTTATATA
1 TTAAATTCAAAATA-TTTTTATATA
*
86389 TTAACTTCAAAATATTTTTATAT
1 TTAAATTCAAAATATTTTTATAT
86412 TAACTTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (24 bp):
TTAAATTCAAAATATTTTTATATA
Found at i:86424 original size:23 final size:22
Alignment explanation
Indices: 86380--86432 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 22
86370 TCATAATATT
86380 TTTTATATATTAACTTCAAAATA
1 TTTT-TATATTAACTTCAAAATA
86403 TTTTTATATTAACTT-ATTAAATA
1 TTTTTATATTAACTTCA--AAATA
86426 TTTTTAT
1 TTTTTAT
86433 TTTTTATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 1 0.04
22 11 0.39
23 16 0.57
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTTATATTAACTTCAAAATA
Found at i:87304 original size:13 final size:13
Alignment explanation
Indices: 87280--87320 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
87270 AATTGAATAC
87280 AAAATTAAAATTT
1 AAAATTAAAATTT
* *
87293 AATATTATAATTT
1 AAAATTAAAATTT
87306 AAAATTAAAATTT
1 AAAATTAAAATTT
87319 AA
1 AA
87321 CGATATAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:87789 original size:21 final size:21
Alignment explanation
Indices: 87760--87812 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
87750 ATTCTGACTA
87760 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
87781 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
87802 TCGCAATGCGA
1 TCGCATTGCGA
87813 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:87827 original size:20 final size:20
Alignment explanation
Indices: 87802--88061 Score: 152
Period size: 20 Copynumber: 12.7 Consensus size: 20
87792 TTTTCCTAAT
87802 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
87822 TCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
87842 TCGCAATGCGAATTCGGAAAA
1 TCGCAATGCGAATAC-GTAAA
*
87863 TCGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
87883 TCGCAATGC-AATTTTC-TAAT
1 TCGCAATGCGAA--TACGTAAA
* * * *
87903 TCGCATTGCG-ATTCCTAAT
1 TCGCAATGCGAATACGTAAA
* * *
87922 TCGCATTGCGATTTATTCGT-AT
1 TCGCAATGCGA---ATACGTAAA
** * * * *
87944 TCGTATTCGTTGCGATTTTCCTAAT
1 TCG----CAATGCGA-ATACGTAAA
87969 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
87989 TCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
88009 TTGCAATGCGAATTA-GGAAA
1 TCGCAATGCGAA-TACGTAAA
*
88029 TCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
88049 TCGCAATGCGAAT
1 TCGCAATGCGAAT
88062 CTGACTATCG
Statistics
Matches: 191, Mismatches: 33, Indels: 32
0.75 0.13 0.12
Matches are distributed among these distances:
18 3 0.02
19 18 0.09
20 116 0.61
21 27 0.14
22 5 0.03
23 5 0.03
24 5 0.03
25 5 0.03
26 7 0.04
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:87848 original size:40 final size:40
Alignment explanation
Indices: 87802--88061 Score: 179
Period size: 40 Copynumber: 6.3 Consensus size: 40
87792 TTTTCCTAAT
87802 TCGCAATGCGAATACGTAAATCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGATTACGTAAA
* * ** *
87842 TCGCAATGCGAATTCGGAAAATCGCAATACGAATACGTAAA
1 TCGCAATGCGAATAC-GTAAATCGCAACGCGATTACGTAAA
* * ** * *
87883 TCGCAATGC-AATTTTC-TAATTCGCATTGCGATT-CCTAAT
1 TCGCAATGCGAA--TACGTAAATCGCAACGCGATTACGTAAA
* * * * * * * *
87922 TCGCATTGCGATTTATTCGT-ATTCGTATTCGTTGCGATTTTCCTAAT
1 TCGCAATGCGA---ATACGTAAATCGCA-AC---GCGA-TTACGTAAA
87969 TCGCAATGCGAATACGTAAATCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGATTACGTAAA
* * *
88009 TTGCAATGCGAATTA-GGAAATCGCAACGCGAATACGTAAA
1 TCGCAATGCGAA-TACGTAAATCGCAACGCGATTACGTAAA
88049 TCGCAATGCGAAT
1 TCGCAATGCGAAT
88062 CTGACTATCG
Statistics
Matches: 177, Mismatches: 27, Indels: 33
0.75 0.11 0.14
Matches are distributed among these distances:
39 13 0.07
40 80 0.45
41 45 0.25
42 5 0.03
43 1 0.01
44 6 0.03
45 9 0.05
46 2 0.01
47 16 0.09
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGATTACGTAAA
Found at i:87922 original size:19 final size:19
Alignment explanation
Indices: 87898--87934 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
87888 ATGCAATTTT
87898 CTAATTCGCATTGCGATTC
1 CTAATTCGCATTGCGATTC
87917 CTAATTCGCATTGCGATT
1 CTAATTCGCATTGCGATT
87935 TATTCGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (19 bp):
CTAATTCGCATTGCGATTC
Found at i:88633 original size:20 final size:19
Alignment explanation
Indices: 88608--88679 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
88598 TTCTAAACTT
88608 AAAATCGCAACATGAAAATG
1 AAAATCGCAACA-GAAAATG
88628 AAAATCGCAACACGAAAATG
1 AAAATCGCAACA-GAAAATG
** *
88648 ACTATCGCAATGAGAGAAATG
1 AAAATCGCAA-CAGA-AAATG
88669 AAAATCGCAAC
1 AAAATCGCAAC
88680 GCGAAATGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 29 0.67
21 14 0.33
ACGTcount: A:0.51, C:0.18, G:0.17, T:0.14
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:88709 original size:16 final size:16
Alignment explanation
Indices: 88669--88710 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
88659 GAGAGAAATG
*
88669 AAAATCGCAACGCGAA
1 AAAATCGCAACACGAA
*
88685 ATGAATCGCAACACGAA
1 A-AAATCGCAACACGAA
88702 AAAATCGCA
1 AAAATCGCA
88711 TTGCGATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.50, C:0.24, G:0.17, T:0.10
Consensus pattern (16 bp):
AAAATCGCAACACGAA
Done.