Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015161.1 Kokia drynarioides strain JFW-HI SEQ_130205, 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: 994981
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 641 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:2380 original size:27 final size:27
Alignment explanation
Indices: 2325--2388 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
2315 TTTTATATAT
*
2325 ATATTTTTTATGAATGTCTTGAGGTTA
1 ATATTTTTTATGAATATCTTGAGGTTA
* *
2352 ATATTATTTTATGTATATCTTTAGG-TA
1 ATATT-TTTTATGAATATCTTGAGGTTA
2379 AT-TTTTTTAT
1 ATATTTTTTAT
2389 ACATTTATGC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 6 0.18
26 2 0.06
27 9 0.27
28 16 0.48
ACGTcount: A:0.27, C:0.03, G:0.12, T:0.58
Consensus pattern (27 bp):
ATATTTTTTATGAATATCTTGAGGTTA
Found at i:6844 original size:41 final size:41
Alignment explanation
Indices: 6784--6876 Score: 114
Period size: 41 Copynumber: 2.3 Consensus size: 41
6774 ATTTATGGGA
* ** * **
6784 AAACGCCGTTATTGCTTGACTTTTAGCGGTGTTTTCCCCAT
1 AAACGCCGCTATTATTTGACCTTTAGCGACGTTTTCCCCAT
* *
6825 AAACGTCGCTATTATTTGACCTTTAGCGACGTTTTTCCCAT
1 AAACGCCGCTATTATTTGACCTTTAGCGACGTTTTCCCCAT
6866 AAACGCCGCTA
1 AAACGCCGCTA
6877 ATGCTCTTTC
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (41 bp):
AAACGCCGCTATTATTTGACCTTTAGCGACGTTTTCCCCAT
Found at i:8996 original size:41 final size:41
Alignment explanation
Indices: 8791--8999 Score: 229
Period size: 41 Copynumber: 5.1 Consensus size: 41
8781 AAATAAATTA
* **
8791 AACCTTTAGCGGTGCTTTTCCATAAGCGCCGCTATTGCTCT
1 AACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCT
* * * * ** *
8832 GACATTTAACGGCTCTTGCCCATAAATGCCGCTATTGATCT
1 AACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCT
* * * * *
8873 GACCTTTAGCGGCGCTTGACCATAAGCGTCGCTATTTCTCG
1 AACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCT
* * * *
8914 AACTTTTAGCAGCGCTTTCCCATAAGCGCTGCTATTGCTCT
1 AACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCT
* *
8955 AACCTTTAGCGGCACTTGCCCATAAGCGTCGCTATTGCTCT
1 AACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCT
8996 AACC
1 AACC
9000 ACCCATAAGT
Statistics
Matches: 133, Mismatches: 35, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
41 133 1.00
ACGTcount: A:0.20, C:0.30, G:0.19, T:0.31
Consensus pattern (41 bp):
AACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCT
Found at i:13124 original size:9 final size:9
Alignment explanation
Indices: 13110--13135 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
13100 GCTGCTAGCA
13110 AGACATGGC
1 AGACATGGC
13119 AGACATGGC
1 AGACATGGC
13128 AGACATGG
1 AGACATGG
13136 GCATTTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.19, G:0.35, T:0.12
Consensus pattern (9 bp):
AGACATGGC
Found at i:17941 original size:19 final size:19
Alignment explanation
Indices: 17917--17954 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
17907 AACCCACACC
17917 AATTGAATTAATAAAACCT
1 AATTGAATTAATAAAACCT
17936 AATTGAATTAATAAAACCT
1 AATTGAATTAATAAAACCT
17955 TAAATTTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.32
Consensus pattern (19 bp):
AATTGAATTAATAAAACCT
Found at i:42577 original size:26 final size:26
Alignment explanation
Indices: 42528--42577 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
42518 AAAGTTTTAG
* *
42528 AAAAATAATAAACCTTAAAGAAAATA
1 AAAAATAATAAACATTAAAAAAAATA
42554 AAAAATAATAAA-ATTAGAAAAAAA
1 AAAAATAATAAACATTA-AAAAAAA
42578 AATTAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.18
Consensus pattern (26 bp):
AAAAATAATAAACATTAAAAAAAATA
Found at i:42584 original size:22 final size:23
Alignment explanation
Indices: 42528--42589 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 23
42518 AAAGTTTTAG
*
42528 AAAAATAATAAACCTTAAAGAAAATA
1 AAAAATAATAAA-ATT--AGAAAATA
42554 AAAAATAATAAAATTAGAAAA-A
1 AAAAATAATAAAATTAGAAAATA
* *
42576 AAAATTAATTAAAT
1 AAAAATAATAAAAT
42590 GATAATTTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 13 0.39
23 6 0.18
25 2 0.06
26 12 0.36
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (23 bp):
AAAAATAATAAAATTAGAAAATA
Found at i:56309 original size:27 final size:27
Alignment explanation
Indices: 56279--56333 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
56269 AGAGCCTCAA
56279 AGGTAGAATCAGGAGGGTAAAATGTAG
1 AGGTAGAATCAGGAGGGTAAAATGTAG
56306 AGGTAGAATCAGGAGGGTAAAATGTAG
1 AGGTAGAATCAGGAGGGTAAAATGTAG
56333 A
1 A
56334 CACTGTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.42, C:0.04, G:0.36, T:0.18
Consensus pattern (27 bp):
AGGTAGAATCAGGAGGGTAAAATGTAG
Found at i:59214 original size:3 final size:3
Alignment explanation
Indices: 59201--59235 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
59191 AAAAGACATG
59201 ATA ATTA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
59236 AACCCCCTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:60649 original size:31 final size:31
Alignment explanation
Indices: 60611--60797 Score: 112
Period size: 31 Copynumber: 6.3 Consensus size: 31
60601 AAAAAATTAC
*
60611 GTACCAAATTAGGAAAAAATGTCAAGTTCAA
1 GTACCAAATTAGGAAAAAATGTCAAGTTTAA
**
60642 GTACCAAATT-GGACCCCAAA----AAGTTTAA
1 GTACCAAATTAGGA--AAAAATGTCAAGTTTAA
* * * *
60670 GTATCAACTTA-AAAAAAAGTGTCAAGTTTAG
1 GTACCAAATTAGGAAAAAA-TGTCAAGTTTAA
**
60701 GTACCAAATTA-GAAAAAAAATCAAGTTTAA
1 GTACCAAATTAGGAAAAAATGTCAAGTTTAA
60731 GTACCAAATT-GGATAAAAA----AAGTTTAA
1 GTACCAAATTAGGA-AAAAATGTCAAGTTTAA
** * *
60758 GTATTAAA-TAAGAAAAAAGTGTCAAGTTCAA
1 GTACCAAATTAGGAAAAAA-TGTCAAGTTTAA
*
60789 GTATCAAAT
1 GTACCAAAT
60798 GTTATATTAA
Statistics
Matches: 119, Mismatches: 20, Indels: 33
0.69 0.12 0.19
Matches are distributed among these distances:
26 9 0.08
27 16 0.13
28 16 0.13
30 24 0.20
31 51 0.43
32 3 0.03
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.25
Consensus pattern (31 bp):
GTACCAAATTAGGAAAAAATGTCAAGTTTAA
Found at i:60725 original size:30 final size:31
Alignment explanation
Indices: 60691--60751 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
60681 AAAAAAAGTG
*
60691 TCAAGTTTAGGTACCAAATTAGA-AAAAAAA
1 TCAAGTTTAAGTACCAAATTAGATAAAAAAA
*
60721 TCAAGTTTAAGTACCAAATTGGATAAAAAAA
1 TCAAGTTTAAGTACCAAATTAGATAAAAAAA
60752 GTTTAAGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 21 0.75
31 7 0.25
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.25
Consensus pattern (31 bp):
TCAAGTTTAAGTACCAAATTAGATAAAAAAA
Found at i:60782 original size:88 final size:90
Alignment explanation
Indices: 60611--60785 Score: 248
Period size: 88 Copynumber: 2.0 Consensus size: 90
60601 AAAAAATTAC
** **
60611 GTACCAAATTAGGAAAAAATGTCAAGTTCAAGTACCAAATTGGACCCCAAAAAGTTTAAGTATCA
1 GTACCAAATTAGGAAAAAAAATCAAGTTCAAGTACCAAATTGGACCAAAAAAAGTTTAAGTATCA
*
60676 ACTTAAAAAAAAGTGTCAAGTTTAG
66 ACATAAAAAAAAGTGTCAAGTTTAG
* * *
60701 GTACCAAATTA-GAAAAAAAATCAAGTTTAAGTACCAAATTGGA-TAAAAAAAGTTTAAGTATTA
1 GTACCAAATTAGGAAAAAAAATCAAGTTCAAGTACCAAATTGGACCAAAAAAAGTTTAAGTATCA
60764 A-ATAAGAAAAAAGTGTCAAGTT
66 ACATAA-AAAAAAGTGTCAAGTT
60786 CAAGTATCAA
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
87 3 0.04
88 33 0.43
89 29 0.38
90 11 0.14
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (90 bp):
GTACCAAATTAGGAAAAAAAATCAAGTTCAAGTACCAAATTGGACCAAAAAAAGTTTAAGTATCA
ACATAAAAAAAAGTGTCAAGTTTAG
Found at i:61990 original size:21 final size:21
Alignment explanation
Indices: 61938--61991 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
61928 ACCTACAAAA
* *
61938 CATTATATTTGTAACTCTCTT
1 CATTATGTTTGTAACTCTCAT
*
61959 CA-TAAGTTTTGTAACTCTCAT
1 CATTATG-TTTGTAACTCTCAT
61980 CATTATGTTTGT
1 CATTATGTTTGT
61992 TTTAAATTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 2 0.07
21 22 0.81
22 3 0.11
ACGTcount: A:0.24, C:0.17, G:0.09, T:0.50
Consensus pattern (21 bp):
CATTATGTTTGTAACTCTCAT
Found at i:69563 original size:25 final size:23
Alignment explanation
Indices: 69534--69579 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
69524 ATTTGATCCA
69534 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
69559 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
69580 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:69665 original size:13 final size:13
Alignment explanation
Indices: 69644--69677 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
69634 ATAATATAAT
69644 AATAATAATCCTA
1 AATAATAATCCTA
*
69657 AATATTAATCCTA
1 AATAATAATCCTA
*
69670 AAAAATAA
1 AATAATAA
69678 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:70599 original size:20 final size:21
Alignment explanation
Indices: 70574--70617 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
70564 CACTTTTGTA
70574 TTTTTTTTTCTC-AGTTTTCT
1 TTTTTTTTTCTCAAGTTTTCT
* *
70594 TTTTTTTTTTTCAATTTTTCT
1 TTTTTTTTTCTCAAGTTTTCT
70615 TTT
1 TTT
70618 AAACTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.07, C:0.11, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTTTTTTCTCAAGTTTTCT
Found at i:70624 original size:29 final size:28
Alignment explanation
Indices: 70593--70649 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
70583 CTCAGTTTTC
70593 TTTTTT-TTTTTTCAATTTTTCTTTTAAACT
1 TTTTTTCTTTTTTC--TTTTT-TTTTAAACT
70623 TTTTTTCTTTTTTCTTTTTTTTTAAAC
1 TTTTTTCTTTTTTCTTTTTTTTTAAAC
70650 AATAAAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 8 0.31
29 5 0.19
30 6 0.23
31 7 0.27
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (28 bp):
TTTTTTCTTTTTTCTTTTTTTTTAAACT
Found at i:71858 original size:25 final size:25
Alignment explanation
Indices: 71805--71851 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
71795 GTTGGATTCA
71805 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAATTCTAAAAAGATAATTTG
*
71830 AATTAAA-TCTAAACA-ATAATTT
1 AATTAAATTCTAAAAAGATAATTT
71852 CCTAATTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 7 0.33
25 7 0.33
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.36
Consensus pattern (25 bp):
AATTAAATTCTAAAAAGATAATTTG
Found at i:71943 original size:13 final size:13
Alignment explanation
Indices: 71922--71955 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
71912 TAATAATAAT
71922 AATAATAATCCTA
1 AATAATAATCCTA
*
71935 AATATTAATCCTA
1 AATAATAATCCTA
*
71948 AAAAATAA
1 AATAATAA
71956 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:73375 original size:22 final size:23
Alignment explanation
Indices: 73337--73379 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
73327 CATACCCTTT
73337 AAAATTACATAAATATTTTTTGA
1 AAAATTACATAAATATTTTTTGA
73360 AAAATTA-A-AAATTATTTTTT
1 AAAATTACATAAA-TATTTTTT
73380 TCGTATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.16
22 9 0.47
23 7 0.37
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
AAAATTACATAAATATTTTTTGA
Found at i:74059 original size:16 final size:17
Alignment explanation
Indices: 74033--74064 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
74023 AATATTTTTT
74033 TAAAAATATTTTAAAAA
1 TAAAAATATTTTAAAAA
74050 TAAAAA-ATTTTAAAA
1 TAAAAATATTTTAAAA
74065 TTCAATGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAAAATATTTTAAAAA
Found at i:74574 original size:3 final size:3
Alignment explanation
Indices: 74566--74624 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
74556 TTTCCTAGAA
74566 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
74614 ATT ATT ATT AT
1 ATT ATT ATT AT
74625 CATAAGGATA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:74848 original size:6 final size:6
Alignment explanation
Indices: 74839--74868 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
74829 CAGTAGCAGA
*
74839 GAAAGC GAAAGG GAAAGG GAAAGG GAAAGG
1 GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG
74869 TAAAAGGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (6 bp):
GAAAGG
Found at i:76500 original size:6 final size:7
Alignment explanation
Indices: 76480--76513 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
76470 TTAGAACATG
76480 ATTAAAA
1 ATTAAAA
76487 ATTAAAA
1 ATTAAAA
76494 ATTAAAA
1 ATTAAAA
76501 ATTAAAA
1 ATTAAAA
76508 A-TAAAA
1 ATTAAAA
76514 TCATCATTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
ATTAAAA
Found at i:79469 original size:3 final size:3
Alignment explanation
Indices: 79461--79486 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
79451 TTCTAAACTT
79461 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
79487 CTCTAAGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:82875 original size:18 final size:16
Alignment explanation
Indices: 82838--82886 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 16
82828 TTCAAATAGG
82838 ATTAGAATAAATTTTTA
1 ATTA-AATAAATTTTTA
82855 ATTAAATAAA--TTTA
1 ATTAAATAAATTTTTA
*
82869 ATTAATTAAAATTTTTA
1 ATTAAAT-AAATTTTTA
82886 A
1 A
82887 ATCATAAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.36
15 3 0.11
16 6 0.21
17 9 0.32
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
ATTAAATAAATTTTTA
Found at i:86291 original size:24 final size:24
Alignment explanation
Indices: 86256--86309 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
86246 TTTCATTATA
*
86256 CAATACAA-TTCATA-TATCATTT
1 CAATTCAATTTCATAGTATCATTT
*
86278 CACATTCAATTTCATAGTCTCATTT
1 CA-ATTCAATTTCATAGTATCATTT
86303 CAATTCA
1 CAATTCA
86310 TCATCAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 2 0.07
23 5 0.19
24 11 0.41
25 9 0.33
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.41
Consensus pattern (24 bp):
CAATTCAATTTCATAGTATCATTT
Found at i:88632 original size:19 final size:20
Alignment explanation
Indices: 88595--88634 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
88585 AGATTACAGG
* *
88595 AAATAATTTTGTTTTGTAGA
1 AAATAATATTGTTTAGTAGA
88615 AAATAATATT-TTTAGTAGA
1 AAATAATATTGTTTAGTAGA
88634 A
1 A
88635 TGATGAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (20 bp):
AAATAATATTGTTTAGTAGA
Found at i:88821 original size:15 final size:15
Alignment explanation
Indices: 88801--88852 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
88791 TTTAAGATTT
88801 TTCATAATTTATATA
1 TTCATAATTTATATA
* *
88816 TTCATAATTT-TTTT
1 TTCATAATTTATATA
* *
88830 TTGATCAAATTATATA
1 TTCAT-AATTTATATA
88846 TTCATAA
1 TTCATAA
88853 ATTAAATTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
14 6 0.21
15 16 0.57
16 6 0.21
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.54
Consensus pattern (15 bp):
TTCATAATTTATATA
Found at i:93929 original size:23 final size:23
Alignment explanation
Indices: 93898--94032 Score: 105
Period size: 23 Copynumber: 6.0 Consensus size: 23
93888 AGTGCTGGGT
*
93898 AACAGAGGGCACACAAAATGCTA
1 AACAGAGGGCACACAAAGTGCTA
* * *
93921 ATCAGAGGGCACACGAAGTGCTG
1 AACAGAGGGCACACAAAGTGCTA
** *
93944 ATTAGAGGGCACGA-AACGTGCTA
1 AACAGAGGGCAC-ACAAAGTGCTA
* *
93967 AACAGAGAGCACACACAGTGCTA
1 AACAGAGGGCACACAAAGTGCTA
* * *
93990 AACAGA-AGCACACACAGTGCTG
1 AACAGAGGGCACACAAAGTGCTA
** *
94012 AACA-AAAGCACACACAGTGCT
1 AACAGAGGGCACACAAAGTGCT
94033 GATCAGTAAG
Statistics
Matches: 95, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
21 1 0.01
22 35 0.37
23 58 0.61
24 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (23 bp):
AACAGAGGGCACACAAAGTGCTA
Found at i:94002 original size:22 final size:22
Alignment explanation
Indices: 93961--94032 Score: 117
Period size: 22 Copynumber: 3.2 Consensus size: 22
93951 GGCACGAAAC
93961 GTGCTAAACAGAGAGCACACACA
1 GTGCTAAACAGA-AGCACACACA
93984 GTGCTAAACAGAAGCACACACA
1 GTGCTAAACAGAAGCACACACA
* *
94006 GTGCTGAACAAAAGCACACACA
1 GTGCTAAACAGAAGCACACACA
94028 GTGCT
1 GTGCT
94033 GATCAGTAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
22 35 0.74
23 12 0.26
ACGTcount: A:0.42, C:0.26, G:0.21, T:0.11
Consensus pattern (22 bp):
GTGCTAAACAGAAGCACACACA
Found at i:96357 original size:14 final size:16
Alignment explanation
Indices: 96338--96371 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
96328 TTAAATAAAA
96338 ATAATATA-AA-TTTT
1 ATAATATATAACTTTT
96352 ATAATATATAACTTTT
1 ATAATATATAACTTTT
96368 ATAA
1 ATAA
96372 AAAAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 2 0.11
16 8 0.44
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAATATATAACTTTT
Found at i:96362 original size:16 final size:16
Alignment explanation
Indices: 96341--96371 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
96331 AATAAAAATA
96341 ATATAAATTTTATAAT
1 ATATAAATTTTATAAT
*
96357 ATATAACTTTTATAA
1 ATATAAATTTTATAA
96372 AAAAAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATAAATTTTATAAT
Found at i:97935 original size:30 final size:33
Alignment explanation
Indices: 97901--97973 Score: 100
Period size: 32 Copynumber: 2.3 Consensus size: 33
97891 AAGTTTCAAT
97901 TCAGTCACTCAA-CTT-TC-AAAAAATAACAAA
1 TCAGTCACTCAATCTTATCAAAAAAATAACAAA
* *
97931 TCAGTCACT-AATGTTATCAAAAAAATGACAAA
1 TCAGTCACTCAATCTTATCAAAAAAATAACAAA
97963 TCAGTCACTCA
1 TCAGTCACTCA
97974 TTAACATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
29 2 0.05
30 11 0.30
31 2 0.05
32 21 0.57
33 1 0.03
ACGTcount: A:0.47, C:0.22, G:0.07, T:0.25
Consensus pattern (33 bp):
TCAGTCACTCAATCTTATCAAAAAAATAACAAA
Found at i:101141 original size:19 final size:19
Alignment explanation
Indices: 101105--101158 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
101095 ATGTTTCGTT
101105 TTTTAGTTTT-TTAATTTTA
1 TTTTA-TTTTATTAATTTTA
*
101124 TTTTATTTTATTATTTTTA
1 TTTTATTTTATTAATTTTA
* *
101143 TGTTATATT-TTAATTT
1 TTTTATTTTATTAATTT
101159 CGTTTATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 10 0.33
19 20 0.67
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (19 bp):
TTTTATTTTATTAATTTTA
Found at i:103069 original size:23 final size:22
Alignment explanation
Indices: 103027--103075 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
103017 TGATCTATTA
*
103027 CATTATGCATTTTAGATAAGTG
1 CATTATGCATGTTAGATAAGTG
103049 CATTCATGCATGTTA-ATTAAGTG
1 CATT-ATGCATGTTAGA-TAAGTG
103072 -ATTA
1 CATTA
103076 CTAAATTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 1 0.04
22 8 0.33
23 15 0.62
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (22 bp):
CATTATGCATGTTAGATAAGTG
Found at i:104205 original size:10 final size:11
Alignment explanation
Indices: 104187--104215 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
104177 AAACACACCT
104187 AAAAGAGAAAG
1 AAAAGAGAAAG
104198 AAAA-AGAAAG
1 AAAAGAGAAAG
104208 AAAAGAGA
1 AAAAGAGA
104216 CAGCCTGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:106920 original size:23 final size:25
Alignment explanation
Indices: 106894--106939 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
106884 CCAATTAGGG
106894 AATTA-TTGTTTAG-ATTTAATTCT
1 AATTATTTGTTTAGAATTTAATTCT
*
106917 AATTATTTTTTTAGAATTTAATT
1 AATTATTTGTTTAGAATTTAATT
106940 TGGATCAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 7 0.35
25 8 0.40
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.59
Consensus pattern (25 bp):
AATTATTTGTTTAGAATTTAATTCT
Found at i:120249 original size:16 final size:16
Alignment explanation
Indices: 120225--120256 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
120215 TCCTTACAAA
*
120225 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
120241 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
120257 AAAAATTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:122638 original size:18 final size:19
Alignment explanation
Indices: 122579--122657 Score: 99
Period size: 19 Copynumber: 4.2 Consensus size: 19
122569 TAGAAAGTGT
122579 AATACTAGCTCGAAAGAGC
1 AATACTAGCTCGAAAGAGC
122598 AATACTAGCTCGAAAGAGC
1 AATACTAGCTCGAAAGAGC
* * *
122617 AATACTGGCT-GTAAGAGT
1 AATACTAGCTCGAAAGAGC
*
122635 AATACTGGCTC-ATAAGAGC
1 AATACTAGCTCGA-AAGAGC
122654 AATA
1 AATA
122658 TTGTAATGGC
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
18 16 0.30
19 37 0.70
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.20
Consensus pattern (19 bp):
AATACTAGCTCGAAAGAGC
Found at i:126922 original size:19 final size:19
Alignment explanation
Indices: 126894--126936 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
126884 CTAACTTAAC
* *
126894 AAAAATGCAATGGCAAAAT
1 AAAAAAGCAATGACAAAAT
126913 AAAAAAGCAATGACAAAAT
1 AAAAAAGCAATGACAAAAT
126932 AAAAA
1 AAAAA
126937 TGCATGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.67, C:0.09, G:0.12, T:0.12
Consensus pattern (19 bp):
AAAAAAGCAATGACAAAAT
Found at i:137963 original size:53 final size:53
Alignment explanation
Indices: 137832--137964 Score: 153
Period size: 53 Copynumber: 2.5 Consensus size: 53
137822 TGTGCCAAAG
* * * * *
137832 ATTAAAGATCTGATGACTCTGTGTCATTGTGAGTTATATAAATCCTGTAACGG
1 ATTAAAGGTCCGATGACTCTGTGTCATAGTGAGTTATATAAATCCTATAACGA
*
137885 ATTAAAGGTCCGATGACTCTATGTCATAGTGAGTTATATAAATCCTA-ATACGA
1 ATTAAAGGTCCGATGACTCTGTGTCATAGTGAGTTATATAAATCCTATA-ACGA
* * *
137938 ATTCAAA-GTCCGTTGATTTTGTGTCAT
1 ATT-AAAGGTCCGATGACTCTGTGTCAT
137965 CGTAAGATAC
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
52 1 0.01
53 64 0.94
54 3 0.04
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (53 bp):
ATTAAAGGTCCGATGACTCTGTGTCATAGTGAGTTATATAAATCCTATAACGA
Found at i:162909 original size:25 final size:25
Alignment explanation
Indices: 162875--162926 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
162865 GCCTTTGGAG
162875 TTAGAACACAAAGCTTACTAGGCTC
1 TTAGAACACAAAGCTTACTAGGCTC
162900 TTAGAACACAAAGCTTACTAGGCTC
1 TTAGAACACAAAGCTTACTAGGCTC
162925 TT
1 TT
162927 CAGCAGCTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (25 bp):
TTAGAACACAAAGCTTACTAGGCTC
Found at i:165227 original size:3 final size:3
Alignment explanation
Indices: 165219--165248 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
165209 ACAGCAAGTT
165219 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
165249 TATCTTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:166054 original size:16 final size:15
Alignment explanation
Indices: 166029--166081 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
166019 TACTGGAATT
166029 GAATAGGGTTGTAATG
1 GAATA-GGTTGTAATG
*
166045 GAATATGGTTGTAATA
1 GAATA-GGTTGTAATG
*
166061 GAATAGAGCTGTAATG
1 GAATAG-GTTGTAATG
166077 GAATA
1 GAATA
166082 AAGCTGTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 1 0.03
16 31 0.97
ACGTcount: A:0.38, C:0.02, G:0.30, T:0.30
Consensus pattern (15 bp):
GAATAGGTTGTAATG
Found at i:166086 original size:16 final size:16
Alignment explanation
Indices: 166038--166091 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
166028 TGAATAGGGT
** *
166038 TGTAATGGAATATGGT
1 TGTAATGGAATAAAGC
* *
166054 TGTAATAGAATAGAGC
1 TGTAATGGAATAAAGC
166070 TGTAATGGAATAAAGC
1 TGTAATGGAATAAAGC
166086 TGTAAT
1 TGTAAT
166092 CAATAATTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAAAGC
Found at i:166090 original size:32 final size:32
Alignment explanation
Indices: 166029--166091 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
166019 TACTGGAATT
* * ** *
166029 GAATAGGGTTGTAATGGAATATGGTTGTAATA
1 GAATAGAGCTGTAATGGAATAAAGCTGTAATA
166061 GAATAGAGCTGTAATGGAATAAAGCTGTAAT
1 GAATAGAGCTGTAATGGAATAAAGCTGTAAT
166092 CAATAATTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.38, C:0.03, G:0.29, T:0.30
Consensus pattern (32 bp):
GAATAGAGCTGTAATGGAATAAAGCTGTAATA
Found at i:166330 original size:24 final size:24
Alignment explanation
Indices: 166274--166330 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
166264 ATAGGATTAT
166274 TATTAA-ATATAATTTAATAAAAA
1 TATTAATATATAATTTAATAAAAA
* * *
166297 TAATATTATATAATTTAATAAAAT
1 TATTAATATATAATTTAATAAAAA
*
166321 TCTTAATATA
1 TATTAATATA
166331 ATTATTTTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
TATTAATATATAATTTAATAAAAA
Found at i:171054 original size:26 final size:25
Alignment explanation
Indices: 171007--171063 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
170997 TAATAATGAT
* *
171007 TTTAAAATTTTTATATTTAAATT-A
1 TTTAAAATTTTTATACTAAAATTAA
171031 TTTAAAATTATTATATACTAAAATTAA
1 TTTAAAATT-TT-TATACTAAAATTAA
171058 TTTAAA
1 TTTAAA
171064 TTCTTATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 9 0.32
25 2 0.07
26 10 0.36
27 7 0.25
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
TTTAAAATTTTTATACTAAAATTAA
Found at i:174848 original size:6 final size:6
Alignment explanation
Indices: 174825--174867 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
174815 AATTCATATT
* * * *
174825 ACTTTC AATTCC AATTTC ACTTTC ATTTTC ACTTTC ACTTTC A
1 ACTTTC ACTTTC ACTTTC ACTTTC ACTTTC ACTTTC ACTTTC A
174868 ATTTTGATCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.49
Consensus pattern (6 bp):
ACTTTC
Found at i:174848 original size:18 final size:18
Alignment explanation
Indices: 174825--174870 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
174815 AATTCATATT
174825 ACTTTCAATTCCAATTTC
1 ACTTTCAATTCCAATTTC
* * *
174843 ACTTTCATTTTCACTTTC
1 ACTTTCAATTCCAATTTC
174861 ACTTTCAATT
1 ACTTTCAATT
174871 TTGATCACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.24, C:0.26, G:0.00, T:0.50
Consensus pattern (18 bp):
ACTTTCAATTCCAATTTC
Found at i:178953 original size:21 final size:22
Alignment explanation
Indices: 178906--178960 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 22
178896 CTCTATCCTT
*
178906 TTATTTTATAATAATATTTTAC
1 TTATTTTTTAATAATATTTTAC
178928 --A--TTTTAATAAT-TTTTAC
1 TTATTTTTTAATAATATTTTAC
178945 TTATTTTTTAA-AATAT
1 TTATTTTTTAATAATAT
178961 CAAAATTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 11
0.69 0.03 0.28
Matches are distributed among these distances:
17 6 0.22
18 9 0.33
19 1 0.04
20 4 0.15
21 7 0.26
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATTTTTTAATAATATTTTAC
Found at i:179366 original size:30 final size:29
Alignment explanation
Indices: 179332--179390 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
179322 GAATTGAATC
* *
179332 AAATCAAATTTTCACGTATACAATTGCACA
1 AAATCAAA-GTTCACATATACAATTGCACA
*
179362 AAATCAAAGTTCATATATACAATTGCACA
1 AAATCAAAGTTCACATATACAATTGCACA
179391 TTAAACTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.46, C:0.19, G:0.07, T:0.29
Consensus pattern (29 bp):
AAATCAAAGTTCACATATACAATTGCACA
Found at i:180433 original size:15 final size:15
Alignment explanation
Indices: 180403--180433 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
180393 CCAATCCTCC
*
180403 ATTAAAAAACAAAAA
1 ATTAAAAAAAAAAAA
180418 ATTAAAAAAAAAAAA
1 ATTAAAAAAAAAAAA
180433 A
1 A
180434 AAAAGTTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.13
Consensus pattern (15 bp):
ATTAAAAAAAAAAAA
Found at i:188212 original size:15 final size:15
Alignment explanation
Indices: 188187--188221 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
188177 TGTGTCCTAA
188187 TTCAG-GCTAAAAGT
1 TTCAGAGCTAAAAGT
188201 TTCAGAGCTAAAAGT
1 TTCAGAGCTAAAAGT
188216 TTCAGA
1 TTCAGA
188222 TTCTCCTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (15 bp):
TTCAGAGCTAAAAGT
Found at i:195740 original size:122 final size:122
Alignment explanation
Indices: 195369--196047 Score: 849
Period size: 122 Copynumber: 5.6 Consensus size: 122
195359 ACTGTTTTGC
* * * * * **
195369 ACCCACTTCTCTGTAACTCACCAGGAAGATAAGATTCGAAGTTTCACTCATATTGAGCTTCACTT
1 ACCCACTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTTTCACTCATATTGAGCTTTGCTT
* * * * * * * * **
195434 CATTGTTTTGATCCACTTTTCTATATCTCA-TCAGGAAGATGATTGCTTTGTTGTCTG
66 CATTGATTTGGTCTACTTCTCTGTACCTCACT-AAGAAGATGACTGCTTCATTGTCTG
* * * * *
195491 ACCCATTTCTCTGTATCTCATCAGGAAGATAAGGTTTGAAGTTTTACTCACA-TGAGCTCTGCTT
1 ACCCACTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTTTCACTCATATTGAGCTTTGCTT
* * * * * *
195555 CATTGATTTGGTCTACTTTTCTATACCTCACTAGGAAGATGATTGTTTCATTATCTG
66 CATTGATTTGGTCTACTTCTCTGTACCTCACTAAGAAGATGACTGCTTCATTGTCTG
* * *
195612 ATCCACTTCTCTGTATCTTATCAGGAAGATGAGGTTTGAAGTTTCACTCATATTGAGCTTTGTTT
1 ACCCACTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTTTCACTCATATTGAGCTTTGCTT
* * *
195677 TAATGATTTGGTCTACTTCTCTGTACCTCACTAAGAAGATGACTGCTTCATTGTCTA
66 CATTGATTTGGTCTACTTCTCTGTACCTCACTAAGAAGATGACTGCTTCATTGTCTG
* * * * *
195734 ACCCACTTCTCTGTATCTCATTAGGAAGATGGGGTTTGAAGTTTCACTCACATTAAGCTCTGCTT
1 ACCCACTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTTTCACTCATATTGAGCTTTGCTT
* * *
195799 CATTGATTTGATCTACTTCTCTGTATCTCACCAAGAAGATGACTGCTTCATTGTCTG
66 CATTGATTTGGTCTACTTCTCTGTACCTCACTAAGAAGATGACTGCTTCATTGTCTG
* * * * * *
195856 ACCCACTTCTCTATATCTCATCAAGAAGATGGGGTTTGAAGTTTCAATCATATTGAGATTCGCTT
1 ACCCACTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTTTCACTCATATTGAGCTTTGCTT
* *
195921 CATTGATTTGGTCTACTTCTCTGTACCTCACCAAGAAGATGACTACTTCATTGTCTG
66 CATTGATTTGGTCTACTTCTCTGTACCTCACTAAGAAGATGACTGCTTCATTGTCTG
* * *
195978 ATCCACTTCTCTGTATCTCATCAGGAAGATGGAGGTTTGAAGTTTCACTCATCTTGAGCTTCGCT
1 ACCCACTTCTCTGTATCTCATCAGGAAGAT-GAGGTTTGAAGTTTCACTCATATTGAGCTTTGCT
196043 TCATT
65 TCATT
196048 TAATTAGTAT
Statistics
Matches: 486, Mismatches: 68, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
121 102 0.21
122 349 0.72
123 35 0.07
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (122 bp):
ACCCACTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTTTCACTCATATTGAGCTTTGCTT
CATTGATTTGGTCTACTTCTCTGTACCTCACTAAGAAGATGACTGCTTCATTGTCTG
Found at i:195873 original size:47 final size:48
Alignment explanation
Indices: 195793--195886 Score: 136
Period size: 47 Copynumber: 2.0 Consensus size: 48
195783 ACATTAAGCT
* * * *
195793 CTGCTTCATTGATTTGATCTACTTCTCTGTATCTCACCAAGAAGATGA
1 CTGCTTCATTGATCTGACCCACTTCTCTATATCTCACCAAGAAGATGA
*
195841 CTGCTTCATTG-TCTGACCCACTTCTCTATATCTCATCAAGAAGATG
1 CTGCTTCATTGATCTGACCCACTTCTCTATATCTCACCAAGAAGATG
195887 GGGTTTGAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
47 30 0.73
48 11 0.27
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (48 bp):
CTGCTTCATTGATCTGACCCACTTCTCTATATCTCACCAAGAAGATGA
Found at i:196350 original size:49 final size:50
Alignment explanation
Indices: 196291--196400 Score: 118
Period size: 49 Copynumber: 2.2 Consensus size: 50
196281 CATTACGGTC
* * * * *
196291 TCAACGTTTCCCTTT-ATATCTTTATGGTACT-GAGTTCGCCGTTGCGACA
1 TCAACCTTTCCCTTTCAAATCTTCATAGTACTAG-GTTCGCCGTTACGACA
* * *
196340 TCAACCTTT-CCTTTCAAATCTTCGTAGTACTAGGTTTGCCGTTACGACC
1 TCAACCTTTCCCTTTCAAATCTTCATAGTACTAGGTTCGCCGTTACGACA
196389 TCAACCTTTCCC
1 TCAACCTTTCCC
196401 ATCATGTCTT
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
48 5 0.10
49 42 0.84
50 3 0.06
ACGTcount: A:0.19, C:0.29, G:0.15, T:0.37
Consensus pattern (50 bp):
TCAACCTTTCCCTTTCAAATCTTCATAGTACTAGGTTCGCCGTTACGACA
Found at i:196453 original size:50 final size:50
Alignment explanation
Indices: 196378--196686 Score: 230
Period size: 50 Copynumber: 6.2 Consensus size: 50
196368 ACTAGGTTTG
* * * ** **
196378 CCGTTACGACCTCAACCTTTCCCATCATGTCTTCTAAGGTACCGAGTTTG
1 CCGTTGCGGCCTCAACCTTTTCCATCACATCTTCTAAGGTACCGAGTTCA
* * * ** * * *
196428 CCATTGTGGCCTCAACATTTTCCATCATGT-TTC-ATGGTACCGAATTTA
1 CCGTTGCGGCCTCAACCTTTTCCATCACATCTTCTAAGGTACCGAGTTCA
** * * * * * *
196476 CTATTACGGCCTTAATCTTTTCCATCACATCTTTTAAGGTATCGAGTTCG
1 CCGTTGCGGCCTCAACCTTTTCCATCACATCTTCTAAGGTACCGAGTTCA
* * * *
196526 CCGTTGCGGCCTCAA-CTTTTCCCTTCAAATCTT-TATGGTACCGGGTTCA
1 CCGTTGCGGCCTCAACCTTTT-CCATCACATCTTCTAAGGTACCGAGTTCA
* ** ** * *
196575 CCGTTGTGGCCTCAACCTTTTTTATCAGGTCTTCTAAGGTATCGAATTCA
1 CCGTTGCGGCCTCAACCTTTTCCATCACATCTTCTAAGGTACCGAGTTCA
* * * *
196625 TCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGGTTTA
1 CCGTTGCGGCCTCAACCTTTTCCATCACATCTTCTAAGGTACCGAGTTCA
*
196675 CCGTTGTGGCCT
1 CCGTTGCGGCCT
196687 TAAGCTTTCC
Statistics
Matches: 198, Mismatches: 56, Indels: 10
0.75 0.21 0.04
Matches are distributed among these distances:
48 34 0.17
49 43 0.22
50 121 0.61
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (50 bp):
CCGTTGCGGCCTCAACCTTTTCCATCACATCTTCTAAGGTACCGAGTTCA
Found at i:196613 original size:99 final size:100
Alignment explanation
Indices: 196505--196686 Score: 276
Period size: 99 Copynumber: 1.8 Consensus size: 100
196495 TTCCATCACA
* * * * * *
196505 TCTTTTAAGGTATCGAGTTCGCCGTTGCGGCCTCAACTTTTCCCTTCAAATCTT-TATGGTACCG
1 TCTTCTAAGGTATCGAATTCACCGTTGCGGCCTCAACCTTTCCCATCAAATCTTCTAAGGTACCG
196569 GGTTCACCGTTGTGGCCTCAACCTTTTTTATCAGG
66 GGTTCACCGTTGTGGCCTCAACCTTTTTTATCAGG
* *
196604 TCTTCTAAGGTATCGAATTCATCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTACCG
1 TCTTCTAAGGTATCGAATTCACCGTTGCGGCCTCAACCTTTCCCATCAAATCTTCTAAGGTACCG
*
196669 GGTTTACCGTTGTGGCCT
66 GGTTCACCGTTGTGGCCT
196687 TAAGCTTTCC
Statistics
Matches: 73, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
99 47 0.64
100 26 0.36
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.36
Consensus pattern (100 bp):
TCTTCTAAGGTATCGAATTCACCGTTGCGGCCTCAACCTTTCCCATCAAATCTTCTAAGGTACCG
GGTTCACCGTTGTGGCCTCAACCTTTTTTATCAGG
Found at i:198655 original size:11 final size:12
Alignment explanation
Indices: 198632--198664 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
198622 CAACCCCTCT
198632 TTTCTTATTTTC
1 TTTCTTATTTTC
198644 TTTCTT-TTTTC
1 TTTCTTATTTTC
198655 TTT-TTATTTT
1 TTTCTTATTTT
198665 TATTTTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 2 0.10
11 12 0.60
12 6 0.30
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTCTTATTTTC
Found at i:202870 original size:140 final size:146
Alignment explanation
Indices: 202722--203015 Score: 329
Period size: 146 Copynumber: 2.0 Consensus size: 146
202712 TAAAAATAAC
* * * * *
202722 ATATTTTTAAAACAAAAGTATGAGGATC-AA-AATAAAA-AAAAAGGAAAATTG-ATTTGCTAAT
1 ATATTTTTAAAACAAAAGTATAAGGATCAAATAAAAAAAGAAAAAGAAAAAATGAATTTGCCAAT
* **
202783 CTAAAAA-ACGATTTAAAC-AAAATGGACCGAGTTTT-AAATAAATAAAAAAAAGG-AGGACTTG
66 CTAAAAATA--ATTTAAACTAAAATGGACAGA-TTTTAAAATAAATAAAAAAAAGGTAGGACTAA
* *
202844 GCCAAG-AATTCTCCTTTT
128 ACCAAGAAATTATCCTTTT
* *
202862 ATATTTTTAAAATAAAGGTATAAGGATCAAATTTAAAAAAAGAAAAAGAAAAAATGAATTTGCCA
1 ATATTTTTAAAACAAAAGTATAAGGATCAAA--TAAAAAAAGAAAAAGAAAAAATGAATTTGCCA
* * * *
202927 ATTTAAAAATAATTTAAGCTACAATGGTCAGATTTTAAAATAAATAAAAAAAAGGTAGGACTAAA
64 ATCTAAAAATAATTTAAACTAAAATGGACAGATTTTAAAATAAATAAAAAAAAGGTAGGACTAAA
202992 CCAAGAAATTATCCTTTT
129 CCAAGAAATTATCCTTTT
203010 AT-TTTT
1 ATATTTT
203016 CAAAGCAGTG
Statistics
Matches: 127, Mismatches: 16, Indels: 15
0.80 0.10 0.09
Matches are distributed among these distances:
140 25 0.20
141 2 0.02
144 6 0.05
145 23 0.18
146 42 0.33
147 16 0.13
148 13 0.10
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.29
Consensus pattern (146 bp):
ATATTTTTAAAACAAAAGTATAAGGATCAAATAAAAAAAGAAAAAGAAAAAATGAATTTGCCAAT
CTAAAAATAATTTAAACTAAAATGGACAGATTTTAAAATAAATAAAAAAAAGGTAGGACTAAACC
AAGAAATTATCCTTTT
Found at i:203880 original size:19 final size:18
Alignment explanation
Indices: 203854--203891 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
203844 TTTTGCTATT
203854 TGTTTTTTTTCTTGTCTC
1 TGTTTTTTTTCTTGTCTC
203872 TGTTCTTTTTTCTTGTCTC
1 TGTT-TTTTTTCTTGTCTC
203891 T
1 T
203892 TGCAAGTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.00, C:0.18, G:0.11, T:0.71
Consensus pattern (18 bp):
TGTTTTTTTTCTTGTCTC
Found at i:205252 original size:3 final size:3
Alignment explanation
Indices: 205244--205275 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
205234 TTCCTCTATC
205244 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
205276 AAATAGTGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:209371 original size:16 final size:16
Alignment explanation
Indices: 209350--209385 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
209340 CCGACCCAAT
209350 AAAAAACAAAAAAAAC
1 AAAAAACAAAAAAAAC
209366 AAAAAACAAAAAAAAC
1 AAAAAACAAAAAAAAC
209382 AAAA
1 AAAA
209386 CCAAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAACAAAAAAAAC
Found at i:209396 original size:16 final size:15
Alignment explanation
Indices: 209351--209400 Score: 66
Period size: 16 Copynumber: 3.3 Consensus size: 15
209341 CGACCCAATA
209351 AAAAACAAAAAAAAC
1 AAAAACAAAAAAAAC
209366 AAAAAACAAAAAAAAC
1 -AAAAACAAAAAAAAC
*
209382 AAAACCAAAATAAAA-
1 AAAAACAAAA-AAAAC
209397 AAAA
1 AAAA
209401 TATGCAGTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
15 13 0.41
16 19 0.59
ACGTcount: A:0.86, C:0.12, G:0.00, T:0.02
Consensus pattern (15 bp):
AAAAACAAAAAAAAC
Found at i:209402 original size:9 final size:9
Alignment explanation
Indices: 209350--209400 Score: 61
Period size: 9 Copynumber: 5.7 Consensus size: 9
209340 CCGACCCAAT
209350 AAAAAACAA
1 AAAAAACAA
209359 AAAAAAC--
1 AAAAAACAA
209366 AAAAAACAA
1 AAAAAACAA
209375 AAAAAACAA
1 AAAAAACAA
*
209384 AACCAAAATAA
1 AA--AAAACAA
209395 AAAAAA
1 AAAAAA
209401 TATGCAGTCC
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
7 7 0.19
9 22 0.59
11 8 0.22
ACGTcount: A:0.86, C:0.12, G:0.00, T:0.02
Consensus pattern (9 bp):
AAAAAACAA
Found at i:216193 original size:19 final size:18
Alignment explanation
Indices: 216169--216222 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
216159 AATACAGCCC
216169 TTTATTTTTATCTTATTT
1 TTTATTTTTATCTTATTT
*
216187 GTTTATTTTTATTTTATTT
1 -TTTATTTTTATCTTATTT
216206 TTT-TTTCTTATC-TATTT
1 TTTATTT-TTATCTTATTT
216223 ATTTTATTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 8 0.25
18 7 0.22
19 17 0.53
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTATTTTTATCTTATTT
Found at i:216215 original size:32 final size:32
Alignment explanation
Indices: 216173--216236 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
216163 CAGCCCTTTA
* *
216173 TTTTTATCTTATTTGTTTATTTTTATTT-TATT
1 TTTTTATCTTATCTATTTA-TTTTATTTGTATT
*
216205 TTTTTTTCTTATCTATTTATTTTATTTGTATT
1 TTTTTATCTTATCTATTTATTTTATTTGTATT
216237 CCATTTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 8 0.29
32 20 0.71
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.77
Consensus pattern (32 bp):
TTTTTATCTTATCTATTTATTTTATTTGTATT
Found at i:228676 original size:21 final size:21
Alignment explanation
Indices: 228650--228719 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
228640 AATAGTGCAA
228650 ACTTCTACCAATACAAATGAC
1 ACTTCTACCAATACAAATGAC
* * * *
228671 AGTTCTATCGATACAAGTGAC
1 ACTTCTACCAATACAAATGAC
* * * **
228692 TCTTTTACCTATACAAATGTT
1 ACTTCTACCAATACAAATGAC
228713 ACTTCTA
1 ACTTCTA
228720 TTGATACTAA
Statistics
Matches: 35, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (21 bp):
ACTTCTACCAATACAAATGAC
Found at i:235143 original size:41 final size:41
Alignment explanation
Indices: 235067--235291 Score: 252
Period size: 41 Copynumber: 5.4 Consensus size: 41
235057 TTATGCTCTT
* * *
235067 TCGAGTCATAAGTCTTCCTTTAATCATATTCTCATTCTCATC
1 TCGAGACATAAGTCTTCC-TTAATCAAAATCTCATTCTCATC
* *
235109 TCAAGACATAAGTCTTCCTTAATCAAAATCTCATTCTCATT
1 TCGAGACATAAGTCTTCCTTAATCAAAATCTCATTCTCATC
* * *
235150 TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTCATC
1 TCGAGACATAAGTCTTCCTTAATCAAAATCTCATTCTCATC
* *
235191 TCGAGACATGAGTCTTCCTTAAATCAAAATCTCATTCTCATT
1 TCGAGACATAAGTCTTCCTT-AATCAAAATCTCATTCTCATC
* * ** * *
235233 TCGAGACATTAGTCTTCCATTTATACAATTTCTCATGCTCAAC
1 TCGAGACATAAGTCTTCC-TTAAT-CAAAATCTCATTCTCATC
* *
235276 CCGAGACATGAGTCTT
1 TCGAGACATAAGTCTT
235292 ACTTTTTATA
Statistics
Matches: 158, Mismatches: 22, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
41 76 0.48
42 53 0.34
43 29 0.18
ACGTcount: A:0.28, C:0.25, G:0.09, T:0.37
Consensus pattern (41 bp):
TCGAGACATAAGTCTTCCTTAATCAAAATCTCATTCTCATC
Found at i:235224 original size:83 final size:83
Alignment explanation
Indices: 235065--235291 Score: 314
Period size: 83 Copynumber: 2.7 Consensus size: 83
235055 CCTTATGCTC
* * * *
235065 TTTCGAGTCATAAGTCTTCCTTTAATCATATTCTCATTCTCATCTCAAGACATAAGTCTTCCTTA
1 TTTCGAGACATAAGTCTTCCTTTATTCATATTCTCATTCTCATCTCGAGACATGAGTCTTCCTTA
235130 ATCAAAATCTCATTCTCA
66 ATCAAAATCTCATTCTCA
* *
235148 TTTCGAGACATGAGTCTTCC-TTATTCATAATCTCATTCTCATCTCGAGACATGAGTCTTCCTTA
1 TTTCGAGACATAAGTCTTCCTTTATTCATATTCTCATTCTCATCTCGAGACATGAGTCTTCCTT-
235212 AATCAAAATCTCATTCTCA
65 AATCAAAATCTCATTCTCA
* * * * *
235231 TTTCGAGACATTAGTCTTCCATTTATACA-ATTTCTCATGCTCAACCCGAGACATGAGTCTT
1 TTTCGAGACATAAGTCTTCC-TTTATTCATA-TTCTCATTCTCATCTCGAGACATGAGTCTT
235292 ACTTTTTATA
Statistics
Matches: 128, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
82 39 0.30
83 56 0.44
84 1 0.01
85 32 0.25
ACGTcount: A:0.28, C:0.25, G:0.09, T:0.38
Consensus pattern (83 bp):
TTTCGAGACATAAGTCTTCCTTTATTCATATTCTCATTCTCATCTCGAGACATGAGTCTTCCTTA
ATCAAAATCTCATTCTCA
Found at i:236005 original size:3 final size:3
Alignment explanation
Indices: 235997--236039 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
235987 AACCGTGTAG
235997 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
236040 AGAAAATGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:236167 original size:22 final size:21
Alignment explanation
Indices: 236120--236167 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
236110 GACTTTCATA
*
236120 ATTAACTTAATTAATCATCTT
1 ATTAACTTAATTAATCATATT
* * *
236141 TTTAACCTTAATTTATCCTATT
1 ATTAA-CTTAATTAATCATATT
236163 ATTAA
1 ATTAA
236168 TCAATATTTG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTAACTTAATTAATCATATT
Found at i:239606 original size:16 final size:15
Alignment explanation
Indices: 239585--239618 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
239575 AGTAAAAATT
239585 AAAAAAAAATTATTTA
1 AAAAAAAAATTA-TTA
239601 AAAAAAAAATTATTA
1 AAAAAAAAATTATTA
239616 AAA
1 AAA
239619 GTTACAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAAAAAATTATTA
Found at i:239898 original size:18 final size:17
Alignment explanation
Indices: 239827--239911 Score: 68
Period size: 19 Copynumber: 4.8 Consensus size: 17
239817 AAAAATTCTA
*
239827 AAATTTTAATTTTTTAT
1 AAATTTTAAATTTTTAT
239844 ATATATTTTAGAATTTTTAT
1 A-A-ATTTTA-AATTTTTAT
**
239864 -AATTTTAAA--AATAT
1 AAATTTTAAATTTTTAT
239878 AAATTTTATAATTTTTAT
1 AAATTTTA-AATTTTTAT
239896 AAATATTTTAAATTTT
1 -AA-ATTTTAAATTTT
239912 AAAAATTATT
Statistics
Matches: 54, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
14 3 0.06
15 7 0.13
16 4 0.07
17 7 0.13
18 5 0.09
19 14 0.26
20 14 0.26
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (17 bp):
AAATTTTAAATTTTTAT
Found at i:239912 original size:18 final size:18
Alignment explanation
Indices: 239825--239930 Score: 69
Period size: 18 Copynumber: 5.9 Consensus size: 18
239815 AGAAAAATTC
*
239825 TAAA-ATTTTAATTTTTTA
1 TAAATATTTTAA-ATTTTA
*
239843 TATATATTTTAGAATTTT-
1 TAAATATTTTA-AATTTTA
* **
239861 TATA-ATTTTAAA-AATA
1 TAAATATTTTAAATTTTA
*
239877 TAAAT-TTTATAATTTTTA
1 TAAATATTT-TAAATTTTA
239895 TAAATATTTTAAATTTTA
1 TAAATATTTTAAATTTTA
* *
239913 AAAATTATTTTGAATTTT
1 TAAA-TATTTTAAATTTT
239931 TTTGTAATAT
Statistics
Matches: 69, Mismatches: 11, Indels: 15
0.73 0.12 0.16
Matches are distributed among these distances:
15 1 0.01
16 8 0.12
17 9 0.13
18 25 0.36
19 25 0.36
20 1 0.01
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TAAATATTTTAAATTTTA
Found at i:241117 original size:441 final size:437
Alignment explanation
Indices: 240218--241518 Score: 1391
Period size: 441 Copynumber: 3.0 Consensus size: 437
240208 AAACTTGAAA
* **
240218 TTTTGCATTAATTAAAGAATATT-TGAATTTTTTGTTTTTAAATAAAATGTGATTTACTCTAAAA
1 TTTTGCATTAATTGAAGAATATTCAAAATTTTTTGTTTTTAAATAAAATGTGATTTACTCTAAAA
* * * *
240282 ATATATAAATTTATGATGTTTTATTTTACGAGGTCACATTTAAATACTAAAGTTGAACTTGTATT
66 ATATAT-AATATATGAAGTTTAATTTTAC-AGGTCACATTTAAATACTAAAATTGAACTTGTA-T
* * *
240347 TTTTTTCTAAATTAAGATAACATGCGTTTAATAAGATATTGATTTTGAGCGTTGCAAAAGTGCTA
128 TTTTTT-TAAATTAAGATAACATGTGTTTAATAAGATATCGATTTTGAACGTTGCAAAAGTGCTA
* ** * * * * *
240412 AAATATTTATTGTGCGTAATTGACT-TTCGAACTTAAATTTTTCTTTGGATTTTAACGTAGGCTC
192 AAAT-TTTAATGCACGTAATTGACTCTT-GAACTCAAATATTTCTTTGGA--TTAAAGCAGGCCC
* * * * * * * * *
240476 AAAATTATCTTTTTTAAAGGAGTTCTAAAATTTCA-TTTTAAAGGATGGTTTTGTAAGTATTTGG
253 AAATTTTTTTTTTTTAAAGGAATTTTAAAATTTCATTTTTAAAAGATGGTTTTATAGGTGTTTGG
* *
240540 TCACACCCAATAAAAAAAGATAGATGGCAACTCCTCGTTTTTAAATAAAATCTCGTATTTTTCTT
318 TCACACCCAATAAAAAAAGAT-GAT-GCAACTCCTCATTTTTAAATAAAATCTCGTGTTTTTCTT
**
240605 AAAATAAAA-C-CATATTTTCAAATATCCATCAAGCTTATTG--TTTTTTTTTAAAT
381 AAAATAAAACCTCATATTTTCAAATATCTGTCAAGCTTATTGTTTTTTTTTTTAAAT
* *
240658 TATTGCATTAACTGAAGAATATTCAAAATTTTTTGTTTTTAAATAAAATGTGATTTACTCTAAAA
1 TTTTGCATTAATTGAAGAATATTCAAAATTTTTTGTTTTTAAATAAAATGTGATTTACTCTAAAA
* * * *
240723 ATATATGAATATATGAAGTTTCATTTTACAGATCACATTTAAATACTAAAATTGAATTTGTATAA
66 ATATAT-AATATATGAAGTTTAATTTTACAGGTCACATTTAAATACTAAAATTGAACTTGTAT-T
* * * * *
240788 TTTTTTAAATTAAAATAACATGTGTTTAATAAGGTATCAATTTTGAACGTTACAAGAGTGCTAAA
129 TTTTTTAAATTAAGATAACATGTGTTTAATAAGATATCGATTTTGAACGTTGCAAAAGTGCTAAA
*
240853 ATCTTTAATGCACGTAATTGACTCTTGAACTCATATATTT-TTTGGA-TAAAGCAGGCCCAAATT
194 AT-TTTAATGCACGTAATTGACTCTTGAACTCAAATATTTCTTTGGATTAAAGCAGGCCCAAATT
*
240916 TTTTTTTTTTAAAGGAATTTTAAAATTTCATTTTTAAAAGATGGTTTTTTAGGTGTTTGGTCACA
258 TTTTTTTTTTAAAGGAATTTTAAAATTTCATTTTTAAAAGATGGTTTTATAGGTGTTTGGTCACA
* * * * *
240981 -CTAATAAAAAAAGATCGATGACAACTTCTCACTTTTAAATAAAATATTGTGTTTTTCTTAAAAT
323 CCCAATAAAAAAAGAT-GATG-CAACTCCTCATTTTTAAATAAAATCTCGTGTTTTTCTTAAAAT
* * ***
241045 AAAACCTTCATGTTTTCAAATATCTGTGAAGCTTATTGTTTTTTTTTTTTTTTT
386 AAAACC-TCATATTTTCAAATATCTGTCAAGCTTATTG-TTTTTTTTTTTAAAT
**
241099 TTTTGCATTAATTGAAGAATATTCAAAAAATTTTGTTTTTAAAT--AA----A---A-TCT---A
1 TTTTGCATTAATTGAAGAATATTCAAAATTTTTTGTTTTTAAATAAAATGTGATTTACTCTAAAA
* * * * * * **
241151 GT-T-T-TTATATGAAGTTTAATTTTATGAGGTCACAATTAAACATTAAAATTGAACACGTATTT
66 ATATATAATATATGAAGTTTAATTTTA-CAGGTCACATTTAAATACTAAAATTGAACTTGTATTT
* * * *
241213 TTTTTAAATTAAGATAACATGTGTTTAACAAGATACCGATTTTGAACGTTGTAAAAATGCTAAAA
130 TTTTTAAATTAAGATAACATGTGTTTAATAAGATATCGATTTTGAACGTTGCAAAAGTGCTAAAA
* ** * *
241278 TTTTTAT-CTTGTATAATTGACTCTCGAACTCAAATATTTCTTTGGATTTTAATGCAGGCCCAAA
195 TTTTAATGCACG--TAATTGACTCTTGAACTCAAATATTTCTTTGGA--TTAAAGCAGGCCC-AA
* * * * ** * *
241342 ATTATATTTTTTTAAAGGAATTTTAAATTTTCATTTTTAAAAGATGGTTTTAAAGGTGTACGATT
255 ATTTTTTTTTTTTAAAGGAATTTTAAAATTTCATTTTTAAAAGATGGTTTTATAGGTGTTTGGTC
* * *
241407 ACACCCAATAAAAAAAGGTGATG--ACTCCTCATTTTTATATAAAATCCCGTGTTTTTCTTAAAA
320 ACACCCAATAAAAAAAGATGATGCAACTCCTCATTTTTAAATAAAATCTCGTGTTTTTCTTAAAA
* * * *
241470 TAAAACCTCCATATTTTCAAATATATGTCAAGTTTATTATTATTTTTTT
385 TAAAACCT-CATATTTTCAAATATCTGTCAAGCTTATTGTTTTTTTTTT
241519 CAGCTGAAAA
Statistics
Matches: 731, Mismatches: 109, Indels: 57
0.81 0.12 0.06
Matches are distributed among these distances:
422 2 0.00
423 5 0.01
424 100 0.14
425 43 0.06
426 67 0.09
427 1 0.00
428 13 0.02
429 65 0.09
430 13 0.02
431 3 0.00
432 1 0.00
434 1 0.00
435 98 0.13
436 31 0.04
438 32 0.04
439 85 0.12
440 57 0.08
441 114 0.16
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (437 bp):
TTTTGCATTAATTGAAGAATATTCAAAATTTTTTGTTTTTAAATAAAATGTGATTTACTCTAAAA
ATATATAATATATGAAGTTTAATTTTACAGGTCACATTTAAATACTAAAATTGAACTTGTATTTT
TTTTAAATTAAGATAACATGTGTTTAATAAGATATCGATTTTGAACGTTGCAAAAGTGCTAAAAT
TTTAATGCACGTAATTGACTCTTGAACTCAAATATTTCTTTGGATTAAAGCAGGCCCAAATTTTT
TTTTTTTAAAGGAATTTTAAAATTTCATTTTTAAAAGATGGTTTTATAGGTGTTTGGTCACACCC
AATAAAAAAAGATGATGCAACTCCTCATTTTTAAATAAAATCTCGTGTTTTTCTTAAAATAAAAC
CTCATATTTTCAAATATCTGTCAAGCTTATTGTTTTTTTTTTTAAAT
Found at i:241300 original size:424 final size:423
Alignment explanation
Indices: 240732--241518 Score: 1001
Period size: 424 Copynumber: 1.9 Consensus size: 423
240722 AATATATGAA
* * * ***
240732 TATATGAAGTTTCATTTTACAGATCACATTTAAATACTAAAATTGAATTTGTATAATTTTTTAAA
1 TATATGAAGTTTAATTTTACAGATCACAATTAAACACTAAAATTGAACACGTATAATTTTTTAAA
* * * * *
240797 TTAAAATAACATGTGTTTAATAAGGTATCAATTTTGAACGTTACAAGAGTGCTAAAATCTTTAAT
66 TTAAAATAACATGTGTTTAACAAGATACCAATTTTGAACGTTACAAAAATGCTAAAATCTTTAAT
* * * *
240862 GCACGTAATTGACTCTTGAACTCATATATTT-TTTGGA-TAAAGCAGGCCC-AAATTTTTTTTTT
131 GCAC-TAATTGACTCTCGAACTCAAATATTTCTTTGGATTAAAGCAGGCCCAAAATTATATTTTT
** ** * *
240924 TTAAAGGAATTTTAAAATTTCATTTTTAAAAGATGGTTTTTTAGGTGTTTGGTCACA-CTAATAA
195 TTAAAGGAATTTTAAAATTTCATTTTTAAAAGATGGTTTTAAAGGTGTACGATCACACCCAATAA
* ** *
240988 AAAAAGATCGATGACAACTTCTCACTTTTAAATAAAATATTGTGTTTTTCTTAAAATAAAACCTT
260 AAAAAGAT-GATG---ACTCCTCACTTTTAAATAAAATACCGTGTTTTTCTTAAAATAAAACCTC
* * * * *
241053 CATGTTTTCAAATATCTGTGAAGCTTATTGTTTTTTTTTTTTTTTTTTTTGCATTAATTGAAGAA
321 CATATTTTCAAATATATGTCAAGCTTATTATTATTTTTTTTTTTTTTTTTGCATTAATTGAAGAA
241118 TATTCAAAAAATTTTGTTTTTAAATAAAATCTAGTTTT
386 TATTCAAAAAATTTTGTTTTTAAATAAAATCTAGTTTT
* * * *
241156 TATATGAAGTTTAATTTTATGAGGTCACAATTAAACATTAAAATTGAACACGTAT-TTTTTTTAA
1 TATATGAAGTTTAATTTTA-CAGATCACAATTAAACACTAAAATTGAACACGTATAATTTTTTAA
* * ** *
241220 ATTAAGATAACATGTGTTTAACAAGATACCGATTTTGAACGTTGTAAAAATGCTAAAATTTTTAT
65 ATTAAAATAACATGTGTTTAACAAGATACCAATTTTGAACGTTACAAAAATGCTAAAATCTTTA-
* * *
241285 CTTGTA-TAATTGACTCTCGAACTCAAATATTTCTTTGGATTTTAATGCAGGCCCAAAATTATAT
129 -ATGCACTAATTGACTCTCGAACTCAAATATTTCTTTGGA--TTAAAGCAGGCCCAAAATTATAT
* *
241349 TTTTTTAAAGGAATTTTAAATTTTCATTTTTAAAAGATGGTTTTAAAGGTGTACGATTACACCCA
191 TTTTTTAAAGGAATTTTAAAATTTCATTTTTAAAAGATGGTTTTAAAGGTGTACGATCACACCCA
* * * *
241414 ATAAAAAAAGGTGATGACTCCTCATTTTTATATAAAATCCCGTGTTTTTCTTAAAATAAAACCTC
256 ATAAAAAAAGATGATGACTCCTCACTTTTAAATAAAATACCGTGTTTTTCTTAAAATAAAACCTC
*
241479 CATATTTTCAAATATATGTCAAGTTTATTATTATTTTTTT
321 CATATTTTCAAATATATGTCAAGCTTATTATTATTTTTTT
241519 CAGCTGAAAA
Statistics
Matches: 305, Mismatches: 49, Indels: 16
0.82 0.13 0.04
Matches are distributed among these distances:
424 104 0.34
425 33 0.11
426 79 0.26
428 11 0.04
429 65 0.21
430 13 0.04
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (423 bp):
TATATGAAGTTTAATTTTACAGATCACAATTAAACACTAAAATTGAACACGTATAATTTTTTAAA
TTAAAATAACATGTGTTTAACAAGATACCAATTTTGAACGTTACAAAAATGCTAAAATCTTTAAT
GCACTAATTGACTCTCGAACTCAAATATTTCTTTGGATTAAAGCAGGCCCAAAATTATATTTTTT
TAAAGGAATTTTAAAATTTCATTTTTAAAAGATGGTTTTAAAGGTGTACGATCACACCCAATAAA
AAAAGATGATGACTCCTCACTTTTAAATAAAATACCGTGTTTTTCTTAAAATAAAACCTCCATAT
TTTCAAATATATGTCAAGCTTATTATTATTTTTTTTTTTTTTTTTGCATTAATTGAAGAATATTC
AAAAAATTTTGTTTTTAAATAAAATCTAGTTTT
Found at i:244130 original size:31 final size:31
Alignment explanation
Indices: 244061--244130 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
244051 CTTAAGAGTC
*
244061 CAGTAACTTAAATAAAATCTTTCGAATAATT
1 CAGTGACTTAAATAAAATCTTTCGAATAATT
* *
244092 TAGTGACTTAAATGAAAAT-TTTTGAATAATT
1 CAGTGACTTAAAT-AAAATCTTTCGAATAATT
*
244123 CATTGACT
1 CAGTGACT
244131 ACTTTGTAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 28 0.85
32 5 0.15
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (31 bp):
CAGTGACTTAAATAAAATCTTTCGAATAATT
Found at i:244369 original size:73 final size:73
Alignment explanation
Indices: 244281--244428 Score: 269
Period size: 73 Copynumber: 2.0 Consensus size: 73
244271 ATTAATTAGA
* *
244281 AATAAGTAAACAAATTATTTACACAATCTTTCAAAGTTGACAACAAATTTTTCTCCCTTAGATTG
1 AATAAGTAAACAAATTATTTACACAATCTGTCAAAGTTGACAACAAATTATTCTCCCTTAGATTG
244346 CTCATGCC
66 CTCATGCC
*
244354 AATAAGTAAACAAATTATTTACACAATCTGTCAAATTTGACAACAAATTATTCTCCCTTAGATTG
1 AATAAGTAAACAAATTATTTACACAATCTGTCAAAGTTGACAACAAATTATTCTCCCTTAGATTG
244419 CTCATGCC
66 CTCATGCC
244427 AA
1 AA
244429 CACTCCCCCT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (73 bp):
AATAAGTAAACAAATTATTTACACAATCTGTCAAAGTTGACAACAAATTATTCTCCCTTAGATTG
CTCATGCC
Found at i:245300 original size:17 final size:17
Alignment explanation
Indices: 245280--245314 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
245270 TTCCACTTTA
245280 CTTTATTCA-TTTATTTT
1 CTTTATT-ATTTTATTTT
245297 CTTTATTATTTTATTTT
1 CTTTATTATTTTATTTT
245314 C
1 C
245315 ATAAAACCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 16 0.94
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.71
Consensus pattern (17 bp):
CTTTATTATTTTATTTT
Found at i:249716 original size:19 final size:18
Alignment explanation
Indices: 249678--249716 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
249668 TGTCGAGACA
*
249678 TATCTGCGTAAAATTAAC
1 TATCTGCGTAAAACTAAC
*
249696 TATCTGGGTAAACACTAAC
1 TATCTGCGTAAA-ACTAAC
249715 TA
1 TA
249717 CTAACGTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (18 bp):
TATCTGCGTAAAACTAAC
Found at i:250417 original size:20 final size:20
Alignment explanation
Indices: 250389--250429 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
250379 GGACTAAAAT
*
250389 AAAATAAATCAGAAATTTTC
1 AAAAAAAATCAGAAATTTTC
**
250409 AAAAAAAATTGGAAATTTTC
1 AAAAAAAATCAGAAATTTTC
250429 A
1 A
250430 TCTACAAGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.29
Consensus pattern (20 bp):
AAAAAAAATCAGAAATTTTC
Found at i:255812 original size:16 final size:17
Alignment explanation
Indices: 255786--255829 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
255776 TTCTTCGAAT
255786 CCCTAAAATATTAAAA-C
1 CCCT-AAATATTAAAATC
*
255803 CCCTAAATATCAAAATC
1 CCCTAAATATTAAAATC
255820 CCC-AAATATT
1 CCCTAAATATT
255830 TGAATCCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (17 bp):
CCCTAAATATTAAAATC
Found at i:256780 original size:33 final size:33
Alignment explanation
Indices: 256698--256872 Score: 142
Period size: 33 Copynumber: 5.3 Consensus size: 33
256688 TGTAGATTGT
* ***
256698 TGGGGAGGGTGATGATAAAGTTATAGAAGTTGA
1 TGGGGAGGGTGATGATGAAGGGGTAGAAGTTGA
*
256731 TAGGGAGGGTGATGATGAAGGGGTAGAAGTTGA
1 TGGGGAGGGTGATGATGAAGGGGTAGAAGTTGA
*
256764 TGGGGAGGGTGATGATGAAGAGGTAGAA-TCTGA
1 TGGGGAGGGTGATGATGAAGGGGTAGAAGT-TGA
* ** * * *
256797 TGGTGAATGTGAT-CTGAAAAGGGTAGAAGCT-A
1 TGGGGAGGGTGATGATG-AAGGGGTAGAAGTTGA
* * *
256829 TTGAGGAAGGTGATG-TAAGAGGGGTAGAAGTTGA
1 -TGGGGAGGGTGATGATGA-AGGGGTAGAAGTTGA
*
256863 TGTGGAGGGT
1 TGGGGAGGGT
256873 TAATTAGAAG
Statistics
Matches: 113, Mismatches: 22, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
32 5 0.04
33 107 0.95
34 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.43, T:0.24
Consensus pattern (33 bp):
TGGGGAGGGTGATGATGAAGGGGTAGAAGTTGA
Found at i:257010 original size:51 final size:51
Alignment explanation
Indices: 256930--257028 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
256920 TGCTAATGAT
* * * *
256930 TATGCTGCTGATTTTGCAACATTAGATGGAGAGGATAATTTTACTGATAAA
1 TATGATGCTAATTTTGCAACATCAGATGGAGAGGATAATGTTACTGATAAA
* *
256981 TATGATGCTAATTTTGCAACATCAGATGGAGTGGATAATGTTGCTGAT
1 TATGATGCTAATTTTGCAACATCAGATGGAGAGGATAATGTTACTGAT
257029 GAAGTTGCTG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.35
Consensus pattern (51 bp):
TATGATGCTAATTTTGCAACATCAGATGGAGAGGATAATGTTACTGATAAA
Found at i:261306 original size:15 final size:15
Alignment explanation
Indices: 261286--261319 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
261276 TTTTCGGAAT
*
261286 GATTAGGGATTTCAC
1 GATTAGAGATTTCAC
*
261301 GATTAGAGATTTCAT
1 GATTAGAGATTTCAC
261316 GATT
1 GATT
261320 TTTGTTCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (15 bp):
GATTAGAGATTTCAC
Found at i:263060 original size:20 final size:20
Alignment explanation
Indices: 263027--263078 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
263017 CATATATTTT
263027 TTTTCTTCTTTTTCTTCTCTC-
1 TTTTCTT-TTTTTCTT-TCTCA
263048 TTTTCTTTTTTTCTTTCTCA
1 TTTTCTTTTTTTCTTTCTCA
263068 TTTTCCTTTTT
1 TTTT-CTTTTT
263079 ACGTGACTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.14
20 12 0.41
21 13 0.45
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTCTTTTTTTCTTTCTCA
Found at i:273470 original size:17 final size:17
Alignment explanation
Indices: 273450--273484 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
273440 TTCCACTTTA
273450 CTTTATTCA-TTTATTTT
1 CTTTATT-ATTTTATTTT
273467 CTTTATTATTTTATTTT
1 CTTTATTATTTTATTTT
273484 C
1 C
273485 ATAAAAACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 16 0.94
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.71
Consensus pattern (17 bp):
CTTTATTATTTTATTTT
Found at i:279311 original size:3 final size:3
Alignment explanation
Indices: 279305--279345 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
279295 TAATAATAAT
279305 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
279346 AATAAAGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:282515 original size:17 final size:17
Alignment explanation
Indices: 282493--282535 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
282483 CTATAACAAC
*
282493 ATAAACATGGATTAAAT
1 ATAAACAAGGATTAAAT
282510 ATAAACAAGGATTAAAT
1 ATAAACAAGGATTAAAT
282527 ATAAACAAG
1 ATAAACAAG
282536 CTCTTCATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.58, C:0.07, G:0.12, T:0.23
Consensus pattern (17 bp):
ATAAACAAGGATTAAAT
Found at i:284638 original size:21 final size:21
Alignment explanation
Indices: 284614--284658 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
284604 TCAATCTCCA
*
284614 CAGGATCCTCTTCTTCTTCTT
1 CAGGATACTCTTCTTCTTCTT
* * *
284635 CAGGGTATTTTTCTTCTTCTT
1 CAGGATACTCTTCTTCTTCTT
284656 CAG
1 CAG
284659 CTTGTTGTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.11, C:0.27, G:0.13, T:0.49
Consensus pattern (21 bp):
CAGGATACTCTTCTTCTTCTT
Found at i:289653 original size:15 final size:15
Alignment explanation
Indices: 289620--289653 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
289610 CCACTTCTAG
*
289620 TTCTGGTGAAACCGG
1 TTCTGGTGAAACCGA
*
289635 TTCTGGTGAAATCGA
1 TTCTGGTGAAACCGA
289650 TTCT
1 TTCT
289654 ACTTCTGGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (15 bp):
TTCTGGTGAAACCGA
Found at i:293908 original size:21 final size:21
Alignment explanation
Indices: 293884--293928 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
293874 TCAATCTCCA
*
293884 CAGGATCCTCTTCTTCTTCTT
1 CAGGATACTCTTCTTCTTCTT
* * *
293905 CAGGGTATTTTTCTTCTTCTT
1 CAGGATACTCTTCTTCTTCTT
293926 CAG
1 CAG
293929 CTTGTTGTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.11, C:0.27, G:0.13, T:0.49
Consensus pattern (21 bp):
CAGGATACTCTTCTTCTTCTT
Found at i:298923 original size:15 final size:15
Alignment explanation
Indices: 298890--298923 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
298880 CCACTTCTAG
*
298890 TTCTGGTGAAACCGG
1 TTCTGGTGAAACCGA
*
298905 TTCTGGTGAAATCGA
1 TTCTGGTGAAACCGA
298920 TTCT
1 TTCT
298924 ACTTCTGGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (15 bp):
TTCTGGTGAAACCGA
Found at i:323211 original size:14 final size:14
Alignment explanation
Indices: 323192--323221 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
323182 TTCGTCATCA
*
323192 ATCTTTTATTTTTG
1 ATCTTTTATTGTTG
323206 ATCTTTTATTGTTG
1 ATCTTTTATTGTTG
323220 AT
1 AT
323222 AAATTCAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.67
Consensus pattern (14 bp):
ATCTTTTATTGTTG
Found at i:328875 original size:3 final size:3
Alignment explanation
Indices: 328867--328911 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
328857 GTTTATTTTC
328867 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
328912 TAGGCTATAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:347224 original size:39 final size:39
Alignment explanation
Indices: 347170--347249 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
347160 ACATATAATG
*
347170 TCAGCCAAATTTTCTTCATTTGGCTCTTTCAAACACAAC
1 TCAGCCAAATTTTCTTCATTTGGCTCCTTCAAACACAAC
347209 TCAGCCAAATTTTCTTCATTTGGCTCCTTCAAACACAAC
1 TCAGCCAAATTTTCTTCATTTGGCTCCTTCAAACACAAC
347248 TC
1 TC
347250 TTCAATTTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.28, C:0.30, G:0.07, T:0.35
Consensus pattern (39 bp):
TCAGCCAAATTTTCTTCATTTGGCTCCTTCAAACACAAC
Found at i:357927 original size:20 final size:21
Alignment explanation
Indices: 357902--357942 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
357892 ATATCGTATA
357902 AAATATTA-TCTAA-TTTTACT
1 AAATATTACT-TAACTTTTACT
357922 AAATATTACTTAACTTTTACT
1 AAATATTACTTAACTTTTACT
357943 TCTATTTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATATTACTTAACTTTTACT
Found at i:364165 original size:78 final size:77
Alignment explanation
Indices: 364002--364195 Score: 250
Period size: 78 Copynumber: 2.5 Consensus size: 77
363992 CTTTTGCACT
* *
364002 CAACGCTAGTTGGATAATCGACGA-ATATATAAGGTGTGCCCAACACTAGTTAGATAAATTGACA
1 CAACGCTAGTCGGATAATCGACGATATATATAAGGTGTGCCCAACACTAGCTAGATAAATTGACA
364066 AGGATTTACGCC
66 AGGATTTACGCC
* * * *
364078 CAGCACTAGTCAGATAACCGACGAGTATATATAAGGTGTGCCCAGA-ACTAGCTAGATAAATTGA
1 CAACGCTAGTCGGATAATCGACGA-TATATATAAGGTGTGCCCA-ACACTAGCTAGATAAATTGA
*
364142 CAAGGATTTATGCC
64 CAAGGATTTACGCC
* *
364156 TAACGCTAGTCGGATAATTGACGA-ATATATAGAGTGTGTG
1 CAACGCTAGTCGGATAATCGACGATATATATA-AG-GTGTG
364196 TAACAGCTCG
Statistics
Matches: 100, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
76 26 0.26
77 2 0.02
78 71 0.71
79 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (77 bp):
CAACGCTAGTCGGATAATCGACGATATATATAAGGTGTGCCCAACACTAGCTAGATAAATTGACA
AGGATTTACGCC
Found at i:372165 original size:22 final size:20
Alignment explanation
Indices: 372130--372173 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
372120 AAATGTAATG
* *
372130 TTATGTTTTGTACTTGATCACA
1 TTATGTTATATACTT-AT-ACA
372152 TTATGTTATATACTTATACA
1 TTATGTTATATACTTATACA
372172 TT
1 TT
372174 TGGCTATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 2 0.10
22 13 0.65
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.52
Consensus pattern (20 bp):
TTATGTTATATACTTATACA
Found at i:372899 original size:76 final size:76
Alignment explanation
Indices: 372770--372912 Score: 191
Period size: 76 Copynumber: 1.9 Consensus size: 76
372760 ACAGTGTACT
372770 CAACACTAATCAGATAAACTGACAAGAATTTGCGTCCAACGCTAGTCGAATAACCAACGAATATA
1 CAACACTAATCAGATAAACTGACAAGAATTTGCGTCCAACGCTAGTCGAATAACCAACGAATATA
372835 TAGGGTGTGCC
66 TAGGGTGTGCC
* * * * * * *
372846 CAACACTAGTCAGATAAATTGACAAGGATTTGTG-CTCAACAG-TAGTCGGATAACCGATGAATA
1 CAACACTAATCAGATAAACTGACAAGAATTTGCGTC-CAAC-GCTAGTCGAATAACCAACGAATA
372909 TATA
64 TATA
372913 TACGTATTCA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
75 1 0.02
76 56 0.97
77 1 0.02
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (76 bp):
CAACACTAATCAGATAAACTGACAAGAATTTGCGTCCAACGCTAGTCGAATAACCAACGAATATA
TAGGGTGTGCC
Found at i:380761 original size:30 final size:30
Alignment explanation
Indices: 380725--380797 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
380715 AAATAGTAAA
*
380725 TATAAAAATATATTTTAATTTTCTAAAAAT
1 TATAAAAATATAATTTAATTTTCTAAAAAT
* *
380755 TATAAAAATTTAATTTAATTTTTTAAAAAT
1 TATAAAAATATAATTTAATTTTCTAAAAAT
*
380785 TATAAAGATATAA
1 TATAAAAATATAA
380798 ACTATTTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (30 bp):
TATAAAAATATAATTTAATTTTCTAAAAAT
Found at i:382234 original size:22 final size:23
Alignment explanation
Indices: 382177--382239 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
382167 TTAGTAATCG
*
382177 AAATTAAATTATAATTTTTATGA
1 AAATTAAATTATAATTTTTATAA
* * * *
382200 TAGTAAAAATATAATTTTTA-AA
1 AAATTAAATTATAATTTTTATAA
382222 AAATTAAATTATAATTTT
1 AAATTAAATTATAATTTT
382240 ATTATTTTTA
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
22 15 0.48
23 16 0.52
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (23 bp):
AAATTAAATTATAATTTTTATAA
Found at i:386590 original size:151 final size:151
Alignment explanation
Indices: 386316--386602 Score: 513
Period size: 151 Copynumber: 1.9 Consensus size: 151
386306 GTTAGAGTTT
*
386316 TGGCTGGGGCAGAGTGTTAGCATTTTGTTGTTGAGTAATCAGGAACATTTTCTTTTGTTGTCTAA
1 TGGCTGGGGCAGAGTGTTAGCATTTTGTTGTTGAGTAATCAGGAACATTTTCTTTCGTTGTCTAA
*
386381 ATGTTTCTTGGTCACTCTGCACTAACCTTTAATCCTCACTATATCTAGGTAACAAGTCAGGAGAC
66 ATGATTCTTGGTCACTCTGCACTAACCTTTAATCCTCACTATATCTAGGTAACAAGTCAGGAGAC
386446 CAACCTCTCTCTCTCTCTCTG
131 CAACCTCTCTCTCTCTCTCTG
* *
386467 TGGCTGGAGG-AGAGTGTTAGGATTTTGTTGTTGAGTAATCGGGAACATTTTCTTTCGTTGTCTA
1 TGGCTGG-GGCAGAGTGTTAGCATTTTGTTGTTGAGTAATCAGGAACATTTTCTTTCGTTGTCTA
*
386531 AATGATTCTTGGTCACTCTGCACTAACCTTTAATCTTCACTATATCTAGGTAACAAGTCAGGAGA
65 AATGATTCTTGGTCACTCTGCACTAACCTTTAATCCTCACTATATCTAGGTAACAAGTCAGGAGA
386596 CCAACCT
130 CCAACCT
386603 AGTGGCTAGA
Statistics
Matches: 130, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
151 128 0.98
152 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (151 bp):
TGGCTGGGGCAGAGTGTTAGCATTTTGTTGTTGAGTAATCAGGAACATTTTCTTTCGTTGTCTAA
ATGATTCTTGGTCACTCTGCACTAACCTTTAATCCTCACTATATCTAGGTAACAAGTCAGGAGAC
CAACCTCTCTCTCTCTCTCTG
Found at i:391764 original size:29 final size:29
Alignment explanation
Indices: 391709--391791 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
391699 GATTTGTCAT
* * *
391709 TTTTTTAAAGTTTAGTAATTGA-GTTGTAA
1 TTTTTCAAAGTTTAGTGATT-ATTTTGTAA
*
391738 TTTTTCAAAGTTTAGTGATTATTTTGTTA
1 TTTTTCAAAGTTTAGTGATTATTTTGTAA
* *
391767 TTATCATCAAAGTTGAGTGATTATT
1 TT-T-TTCAAAGTTTAGTGATTATT
391792 AGTGTATTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
28 1 0.02
29 25 0.56
30 1 0.02
31 18 0.40
ACGTcount: A:0.29, C:0.04, G:0.16, T:0.52
Consensus pattern (29 bp):
TTTTTCAAAGTTTAGTGATTATTTTGTAA
Found at i:394418 original size:22 final size:25
Alignment explanation
Indices: 394390--394436 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 25
394380 TTATTTTTTG
394390 TTAAAT-AATATATT-TTA-TAATT
1 TTAAATAAATATATTATTACTAATT
394412 TTAAATAAATATATTATTACTAATT
1 TTAAATAAATATATTATTACTAATT
394437 AAATAAGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.27
23 8 0.36
24 3 0.14
25 5 0.23
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
TTAAATAAATATATTATTACTAATT
Found at i:394438 original size:23 final size:22
Alignment explanation
Indices: 394390--394442 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
394380 TTATTTTTTG
394390 TTAAAT-AATATATTTTATAATT
1 TTAAATAAATATATTTTATAA-T
394412 TTAAATAAATATATTATTACTAA-
1 TTAAATAAATATATT-TTA-TAAT
394435 TTAAATAA
1 TTAAATAA
394443 GTATTAGTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.21
23 16 0.57
24 3 0.11
25 3 0.11
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TTAAATAAATATATTTTATAAT
Found at i:396285 original size:19 final size:18
Alignment explanation
Indices: 396258--396307 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
396248 AATTTTATGT
*
396258 TTTTAAATTTTTTTAAAA
1 TTTTAAATTTTTCTAAAA
*
396276 TTTTAGAATTTTTCTCAAA
1 TTTTA-AATTTTTCTAAAA
396295 TTTTAAGATTTTT
1 TTTTAA-ATTTTT
396308 AATTTTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (18 bp):
TTTTAAATTTTTCTAAAA
Found at i:396493 original size:19 final size:18
Alignment explanation
Indices: 396469--396505 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
396459 TTAAAATTGG
396469 AATTTATTTTAAAACATAT
1 AATTTATTTTAAAA-ATAT
396488 AATTTATTTTAAAAATAT
1 AATTTATTTTAAAAATAT
396506 TCTTAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
AATTTATTTTAAAAATAT
Found at i:399062 original size:28 final size:28
Alignment explanation
Indices: 399009--399063 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
398999 GGCTGGGAAC
*
399009 AAAGAAGAAGGATAAATTCTTTTTACAG
1 AAAGAAGAAGGATAAATTCTTCTTACAG
399037 AAAGAAGAGAGG-TAAATT-TTGCTTACA
1 AAAGAAGA-AGGATAAATTCTT-CTTACA
399064 TTGTGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 2 0.08
28 19 0.79
29 3 0.12
ACGTcount: A:0.45, C:0.07, G:0.20, T:0.27
Consensus pattern (28 bp):
AAAGAAGAAGGATAAATTCTTCTTACAG
Found at i:399520 original size:66 final size:66
Alignment explanation
Indices: 399414--399606 Score: 323
Period size: 66 Copynumber: 2.9 Consensus size: 66
399404 CAAAGACTAC
* * * * *
399414 TCAAGTGTCACGGTTTGTGACCAAGAATGGAGGTCCTTATTACAGGGGGCTGAAGGAACGGGCTA
1 TCAAGTTTCACAGTTGGTGACCAAGAATGGAGGTCCTTATTACAGGGAGCTGATGGAACGGGCTA
399479 T
66 T
*
399480 TCAAGTTTCACAGTTGGTGACCAAGAATGGAGGTCCTTATTGCAGGGAGCTGATGGAACGGGCTA
1 TCAAGTTTCACAGTTGGTGACCAAGAATGGAGGTCCTTATTACAGGGAGCTGATGGAACGGGCTA
399545 T
66 T
*
399546 TCAAGTTTCACAGTTGGTGACCAAGAATGGAGGTTCTTATTACAGGGAGCTGATGGAACGG
1 TCAAGTTTCACAGTTGGTGACCAAGAATGGAGGTCCTTATTACAGGGAGCTGATGGAACGG
399607 AACAAGACAT
Statistics
Matches: 119, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 119 1.00
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.25
Consensus pattern (66 bp):
TCAAGTTTCACAGTTGGTGACCAAGAATGGAGGTCCTTATTACAGGGAGCTGATGGAACGGGCTA
T
Found at i:406344 original size:24 final size:24
Alignment explanation
Indices: 406317--406374 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
406307 AGCTCAAATA
*
406317 AGCCCA-AATAGGTTAGCTCTCATG
1 AGCCCAGAAT-GGTTAGCTCTCACG
*
406341 AGCCCAGAATGGTTAGCTCTTACG
1 AGCCCAGAATGGTTAGCTCTCACG
*
406365 AGCCCGGAAT
1 AGCCCAGAAT
406375 CAGAATAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 27 0.90
25 3 0.10
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (24 bp):
AGCCCAGAATGGTTAGCTCTCACG
Found at i:410571 original size:24 final size:23
Alignment explanation
Indices: 410544--410629 Score: 84
Period size: 24 Copynumber: 3.6 Consensus size: 23
410534 CAAAAAAAAA
*
410544 TAGCTCATACGAGCTCAG-ATAGGT
1 TAGCTC-TACGAGCCCAGAAT-GGT
410568 TAGCTCTCACGAGCCCAGAATGGT
1 TAGCTCT-ACGAGCCCAGAATGGT
* *
410592 TAGCTCTTACGAGCCCAAAATGAT
1 TAGCTC-TACGAGCCCAGAATGGT
*
410616 TAGCTATTACGAGC
1 TAGCT-CTACGAGC
410630 TCGGAATCAG
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
23 1 0.02
24 50 0.93
25 3 0.06
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (23 bp):
TAGCTCTACGAGCCCAGAATGGT
Found at i:412999 original size:52 final size:52
Alignment explanation
Indices: 412921--413024 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
412911 TAAAAAATGT
412921 CATTTTATACAATCTAAGGGACTTCTACTGGTACCTGTTGGGCAAGTATCGG
1 CATTTTATACAATCTAAGGGACTTCTACTGGTACCTGTTGGGCAAGTATCGG
412973 CATTTTATACAATCTAAGGGACTTCTACTGGTACCTGTTGGGCAAGTATCGG
1 CATTTTATACAATCTAAGGGACTTCTACTGGTACCTGTTGGGCAAGTATCGG
413025 TAAAAGTCAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (52 bp):
CATTTTATACAATCTAAGGGACTTCTACTGGTACCTGTTGGGCAAGTATCGG
Found at i:413841 original size:34 final size:34
Alignment explanation
Indices: 413785--413873 Score: 117
Period size: 34 Copynumber: 2.6 Consensus size: 34
413775 TCCAATAGAT
*
413785 CTCTTCAAG-TCTCCTAGTAATTTAACTCATACGAG
1 CTCTTCAAGAT-TCC-AGTAATTTAACTCATAAGAG
*
413820 TTCTTCAAGATTCCAGTAATTTAACTCATAAGAG
1 CTCTTCAAGATTCCAGTAATTTAACTCATAAGAG
*
413854 CTCTTTAAGATTCCCAGTAA
1 CTCTTCAAGATT-CCAGTAA
413874 ATTTTAGCTC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
34 29 0.60
35 18 0.38
36 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.35
Consensus pattern (34 bp):
CTCTTCAAGATTCCAGTAATTTAACTCATAAGAG
Found at i:413950 original size:38 final size:38
Alignment explanation
Indices: 413907--414035 Score: 150
Period size: 38 Copynumber: 3.4 Consensus size: 38
413897 CAGTAAATTG
* * *
413907 CTCTTACGAGCCAATGTCACTCTTTCAAGCCAGTATCA
1 CTCTTACGAGCCAATATCACTCTTTCGAGCCAATATCA
* * * *
413945 CTCTTACGAACCAGTATCGCTCTTTCGAGCCAATATCT
1 CTCTTACGAGCCAATATCACTCTTTCGAGCCAATATCA
* * * *
413983 CTTTTACGAGCCAGTATTACTCTTTCGAGCCAATATCG
1 CTCTTACGAGCCAATATCACTCTTTCGAGCCAATATCA
*
414021 CTTTTACGAGCCAAT
1 CTCTTACGAGCCAAT
414036 CTTCAGTAAA
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 78 1.00
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (38 bp):
CTCTTACGAGCCAATATCACTCTTTCGAGCCAATATCA
Found at i:413958 original size:19 final size:19
Alignment explanation
Indices: 413907--414035 Score: 123
Period size: 19 Copynumber: 6.8 Consensus size: 19
413897 CAGTAAATTG
*
413907 CTCTTACGAGCCAATGTCA
1 CTCTTACGAGCCAATATCA
* * *
413926 CTCTTTCAAGCCAGTATCA
1 CTCTTACGAGCCAATATCA
* * *
413945 CTCTTACGAACCAGTATCG
1 CTCTTACGAGCCAATATCA
* *
413964 CTCTTTCGAGCCAATATCT
1 CTCTTACGAGCCAATATCA
* * *
413983 CTTTTACGAGCCAGTATTA
1 CTCTTACGAGCCAATATCA
* *
414002 CTCTTTCGAGCCAATATCG
1 CTCTTACGAGCCAATATCA
*
414021 CTTTTACGAGCCAAT
1 CTCTTACGAGCCAAT
414036 CTTCAGTAAA
Statistics
Matches: 86, Mismatches: 24, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 86 1.00
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (19 bp):
CTCTTACGAGCCAATATCA
Found at i:413995 original size:57 final size:57
Alignment explanation
Indices: 413906--414035 Score: 156
Period size: 57 Copynumber: 2.3 Consensus size: 57
413896 TCAGTAAATT
* * *
413906 GCTCTTACGAGCCAATGTCACTCTTTCAAGCCAGTATCACTCTTACGAACCAGTATC
1 GCTCTTTCGAGCCAATATCACTCTTTCAAGCCAGTATCACTCTTACGAACCAATATC
* * * * *
413963 GCTCTTTCGAGCCAATATCTCT-TTTACGAGCCAGTATTACTCTTTCGAGCCAATATC
1 GCTCTTTCGAGCCAATATCACTCTTT-CAAGCCAGTATCACTCTTACGAACCAATATC
414020 GCT-TTTACGAGCCAAT
1 GCTCTTT-CGAGCCAAT
414036 CTTCAGTAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
56 6 0.10
57 57 0.90
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.32
Consensus pattern (57 bp):
GCTCTTTCGAGCCAATATCACTCTTTCAAGCCAGTATCACTCTTACGAACCAATATC
Done.