Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015098.1 Kokia drynarioides strain JFW-HI SEQ_130142, 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: 196537
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 514 characters in sequence are not A, C, G, or T
Found at i:11189 original size:2 final size:2
Alignment explanation
Indices: 11182--11207 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
11172 TAATCTATTT
11182 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
11208 ATTCCTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14219 original size:4 final size:4
Alignment explanation
Indices: 14210--14235 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
14200 TCGAAACAAA
14210 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
14236 AAAATAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:20944 original size:29 final size:30
Alignment explanation
Indices: 20889--20959 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 30
20879 GTTTAATTTA
* *
20889 TAATTGTATACATAAACTTTGATTTTG-TT
1 TAATTTTATACATAAACTTTGAATTTGATT
*
20918 TAATTTTATACATGAAA-TTTTAATTTGATT
1 TAATTTTATACAT-AAACTTTGAATTTGATT
20948 TAAATTCTTATA
1 T-AATT-TTATA
20960 AATTATTAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 20 0.57
30 6 0.17
31 4 0.11
32 5 0.14
ACGTcount: A:0.35, C:0.06, G:0.07, T:0.52
Consensus pattern (30 bp):
TAATTTTATACATAAACTTTGAATTTGATT
Found at i:21592 original size:31 final size:29
Alignment explanation
Indices: 21546--21620 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
21536 GATAAATTTC
* *
21546 ATTATTATACATGAACATTGATTTAATGTGCA
1 ATTA-TATATATGAACATTAATTTAA--TGCA
* *
21578 ATTATATATATGAACTTTAATTTGATGCA
1 ATTATATATATGAACATTAATTTAATGCA
*
21607 ATTATATATGTGAA
1 ATTATATATATGAA
21621 TTTTTAATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 17 0.45
31 17 0.45
32 4 0.11
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.43
Consensus pattern (29 bp):
ATTATATATATGAACATTAATTTAATGCA
Found at i:22988 original size:27 final size:26
Alignment explanation
Indices: 22954--23042 Score: 76
Period size: 27 Copynumber: 3.4 Consensus size: 26
22944 TAATGGATTG
22954 ATGGGTTTTGTTTGTGATGTTAATTAT
1 ATGGGTTTTGTTTGTGATGTTAATT-T
* * *
22981 ATGGGTTTTGCATTATAATG---ATTT
1 ATGGGTTTTG-TTTGTGATGTTAATTT
*
23005 GATGGGTGTTGTTTGTGATGTTAATTTT
1 -ATGGGTTTTGTTTGTGATGTTAA-TTT
*
23033 CTGGGTTTTG
1 ATGGGTTTTG
23043 CATTGTAGTG
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
24 7 0.15
25 12 0.26
27 19 0.40
28 9 0.19
ACGTcount: A:0.17, C:0.02, G:0.28, T:0.53
Consensus pattern (26 bp):
ATGGGTTTTGTTTGTGATGTTAATTT
Found at i:23000 original size:52 final size:52
Alignment explanation
Indices: 22944--23068 Score: 180
Period size: 52 Copynumber: 2.4 Consensus size: 52
22934 TTTTGTGTTC
22944 TAATGGATTGATGGGTTTTGTTTGTGATGTTAATTATATGGGTTTTGCATTA
1 TAATGGATTGATGGGTTTTGTTTGTGATGTTAATTATATGGGTTTTGCATTA
* * * *
22996 TAAT-GATTTGATGGGTGTTGTTTGTGATGTTAATTTTCTGGGTTTTGCATTG
1 TAATGGA-TTGATGGGTTTTGTTTGTGATGTTAATTATATGGGTTTTGCATTA
* *
23048 TAGTGGATTGATGAGTTTTGT
1 TAATGGATTGATGGGTTTTGT
23069 GATTTTTTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
51 2 0.03
52 60 0.94
53 2 0.03
ACGTcount: A:0.18, C:0.02, G:0.29, T:0.50
Consensus pattern (52 bp):
TAATGGATTGATGGGTTTTGTTTGTGATGTTAATTATATGGGTTTTGCATTA
Found at i:25806 original size:2 final size:2
Alignment explanation
Indices: 25799--25833 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
25789 GGTTGTTCTT
25799 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25834 TTTTTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33811 original size:38 final size:37
Alignment explanation
Indices: 33769--33866 Score: 106
Period size: 38 Copynumber: 2.6 Consensus size: 37
33759 ATATAGACTT
*
33769 ACATCCTATGACAAATCACTATCCTTAAAACTAGAGAC
1 ACATCC-ATGACAAACCACTATCCTTAAAACTAGAGAC
* * * * * *
33807 ACATCCCATGACAAGCTACTACCCTTAAAATTAGGGAT
1 ACAT-CCATGACAAACCACTATCCTTAAAACTAGAGAC
33845 ACATCGCATGACAAACCACTAT
1 ACATC-CATGACAAACCACTAT
33867 GCTAGAAAAC
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
37 1 0.02
38 45 0.94
39 2 0.04
ACGTcount: A:0.40, C:0.28, G:0.10, T:0.22
Consensus pattern (37 bp):
ACATCCATGACAAACCACTATCCTTAAAACTAGAGAC
Found at i:37498 original size:21 final size:20
Alignment explanation
Indices: 37435--37500 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 20
37425 TTAACTTCGT
37435 CAACTAAGCCCACAATTTCTG
1 CAACTAAGCCCAC-ATTTCTG
* * * *
37456 CAGCCAAGACTC-CATCTCCTG
1 CAACTAAG-CCCACAT-TTCTG
37477 CAACTAAGCCCACAGTTTCTG
1 CAACTAAGCCCACA-TTTCTG
37498 CAA
1 CAA
37501 GATCCTCCAC
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
20 4 0.12
21 26 0.79
22 3 0.09
ACGTcount: A:0.30, C:0.36, G:0.12, T:0.21
Consensus pattern (20 bp):
CAACTAAGCCCACATTTCTG
Found at i:46752 original size:36 final size:36
Alignment explanation
Indices: 46712--46783 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
46702 AAATTAACAA
* * *
46712 GAAAAAATAAATTGAAAGGAGAGTGGGGATTTTTTC
1 GAAAAAAGAAAGTGAAAGGAGAGTGGGGATGTTTTC
* * *
46748 GAAAAAAGAAGGTGAAGGGTGAGTGGGGATGTTTTC
1 GAAAAAAGAAAGTGAAAGGAGAGTGGGGATGTTTTC
46784 TTTGATAATC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.38, C:0.03, G:0.35, T:0.25
Consensus pattern (36 bp):
GAAAAAAGAAAGTGAAAGGAGAGTGGGGATGTTTTC
Found at i:49736 original size:27 final size:27
Alignment explanation
Indices: 49671--49746 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
49661 AATGAAGCCG
* *
49671 ATCGAGATAGTAAACACG-GAGTATTCT
1 ATCGGGATAGTAAACACGAG-GTAATCT
* * *
49698 GTCAGGACAGTAAACACGAGGTAATCT
1 ATCGGGATAGTAAACACGAGGTAATCT
49725 ATCGGGATAGTAAACACGAGGT
1 ATCGGGATAGTAAACACGAGGT
49747 TATACTAGGA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 39 0.98
28 1 0.03
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (27 bp):
ATCGGGATAGTAAACACGAGGTAATCT
Found at i:57596 original size:19 final size:19
Alignment explanation
Indices: 57574--57620 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
57564 AAATTACAAA
*
57574 AAAAATCAAAATAATTTTC
1 AAAATTCAAAATAATTTTC
** *
57593 AAAATTTGAAATAATTTTT
1 AAAATTCAAAATAATTTTC
57612 AAAATTCAA
1 AAAATTCAA
57621 GTTATTCGAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.36
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTC
Found at i:58820 original size:22 final size:22
Alignment explanation
Indices: 58780--58821 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
58770 ATATATAAGC
**
58780 TCTTTAGTATTGTAATTTCAGT
1 TCTTTAGTACCGTAATTTCAGT
*
58802 TCTTTAGTACCGTATTTTCA
1 TCTTTAGTACCGTAATTTCA
58822 ATACCATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.21, C:0.14, G:0.12, T:0.52
Consensus pattern (22 bp):
TCTTTAGTACCGTAATTTCAGT
Found at i:67137 original size:21 final size:21
Alignment explanation
Indices: 67113--67165 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
67103 TCCATATTAT
67113 TTTTATTTTTTAA-AATTTTTA
1 TTTTATTTTTTAATAA-TTTTA
* *
67134 TTTTAATATTTAATAATTTTA
1 TTTTATTTTTTAATAATTTTA
*
67155 -TATATTTTTTA
1 TTTTATTTTTTA
67166 TTTATTGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 8 0.31
21 16 0.62
22 2 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTATTTTTTAATAATTTTA
Found at i:67168 original size:16 final size:16
Alignment explanation
Indices: 67112--67168 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
67102 GTCCATATTA
* * *
67112 TTTTTATTTTTTAAAA
1 TTTTTATTTTATATAT
67128 TTTTTATTTTA-ATAT
1 TTTTTATTTTATATAT
* *
67143 TTAATAATTTTATATAT
1 TT-TTTATTTTATATAT
67160 TTTTTATTT
1 TTTTTATTT
67169 ATTGAAATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 4 0.12
16 22 0.69
17 6 0.19
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTATTTTATATAT
Found at i:67835 original size:26 final size:24
Alignment explanation
Indices: 67792--67842 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
67782 TTATGAATTC
*
67792 TTTTTAGAGTTTATTATTATATAT
1 TTTTTAGAGTTTATTATTAAATAT
*
67816 TTTTTAGATTTTACTATATTAAATAT
1 TTTTTAGAGTTTA-T-TATTAAATAT
67842 T
1 T
67843 CATCTTGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 12 0.52
25 1 0.04
26 10 0.43
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (24 bp):
TTTTTAGAGTTTATTATTAAATAT
Found at i:72161 original size:3 final size:3
Alignment explanation
Indices: 72147--72204 Score: 53
Period size: 3 Copynumber: 19.3 Consensus size: 3
72137 CAAGCAAATT
* ** * * *
72147 TGC TGT TGC TGC TGC CCC TGT TGC TGC TGC TGC TGC TGG TGC TGC TCC
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
*
72195 GGC TGC TGC T
1 TGC TGC TGC T
72205 ACCCCTGTGG
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.34
Consensus pattern (3 bp):
TGC
Found at i:78537 original size:24 final size:25
Alignment explanation
Indices: 78510--78565 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
78500 TTTTTAAAAA
*
78510 TATTTATTTTATTTTA-ATATTTAG
1 TATTTATTTAATTTTATATATTTAG
* **
78534 TATTTA-ATAATTTTATATATTTTT
1 TATTTATTTAATTTTATATATTTAG
78558 TATTTATT
1 TATTTATT
78566 GAAAAATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (25 bp):
TATTTATTTAATTTTATATATTTAG
Found at i:80526 original size:18 final size:18
Alignment explanation
Indices: 80503--80566 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 18
80493 TTTATGTTAA
80503 AATTTTTAATTAAATTAT
1 AATTTTTAATTAAATTAT
*
80521 AATTTTTAAATATGTAATTAT
1 AATTTTT-AAT-T-AAATTAT
*
80542 CACAGTTTT-ATTAAATTAT
1 -A-ATTTTTAATTAAATTAT
80561 AATTTT
1 AATTTT
80567 CTAACTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
17 4 0.11
18 8 0.22
19 9 0.24
20 2 0.05
21 8 0.22
22 1 0.03
23 5 0.14
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
AATTTTTAATTAAATTAT
Found at i:87646 original size:10 final size:9
Alignment explanation
Indices: 87599--87668 Score: 54
Period size: 10 Copynumber: 7.6 Consensus size: 9
87589 AACATGTGGG
87599 AAAAATTAT
1 AAAAATTAT
87608 AAAAA-T-T
1 AAAAATTAT
*
87615 AAAAATCAAT
1 AAAAAT-TAT
87625 AAAAATTAT
1 AAAAATTAT
*
87634 AAAAGTTATT
1 AAAAATTA-T
**
87644 AAATTTTAAT
1 AAAAATT-AT
87654 AAAAATATAT
1 AAAAAT-TAT
87664 AAAAA
1 AAAAA
87669 AGAACCCAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
7 6 0.12
8 1 0.02
9 14 0.29
10 25 0.52
11 2 0.04
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:87835 original size:13 final size:13
Alignment explanation
Indices: 87819--87843 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
87809 AGTATATTCA
87819 AAAAATATAAAAT
1 AAAAATATAAAAT
87832 AAAAATATAAAA
1 AAAAATATAAAA
87844 GAATTAAGTT
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAAATATAAAAT
Found at i:88144 original size:95 final size:96
Alignment explanation
Indices: 88021--88217 Score: 245
Period size: 95 Copynumber: 2.1 Consensus size: 96
88011 ACTTAATTGC
* * * * * * *
88021 TTTTTTTGAAAAAGTTTGAGGGTCTTTTTGATACATTTTGAAAGTTCAAATACCCAATTGAATGT
1 TTTTTTTGAAAAAATTTGAAGGTCTTTTTAATACATTTTAAAAGTTCAAATACCAAAGTGAATGC
*
88086 AAAAT-AAAACAG-GATCTTAATTGCTTTTTT
66 AAAATAAAAACAGAGA-CTTAATTACTTTTTT
* * * ** *
88116 TTTTTTTGAAAAAATTTGAAGGTTTTTTTAATGCATTTTAAAAGTTCAAGTATTAAAGTGAGTGC
1 TTTTTTTGAAAAAATTTGAAGGTCTTTTTAATACATTTTAAAAGTTCAAATACCAAAGTGAATGC
88181 AAAATAAAAACAGAGACTTAATTACTTTTTT
66 AAAATAAAAACAGAGACTTAATTACTTTTTT
88212 TTTTTT
1 TTTTTT
88218 AAATTTTGAG
Statistics
Matches: 86, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
95 57 0.66
96 27 0.31
97 2 0.02
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.44
Consensus pattern (96 bp):
TTTTTTTGAAAAAATTTGAAGGTCTTTTTAATACATTTTAAAAGTTCAAATACCAAAGTGAATGC
AAAATAAAAACAGAGACTTAATTACTTTTTT
Found at i:98331 original size:7 final size:7
Alignment explanation
Indices: 98319--98350 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
98309 TTTTTTTACA
98319 AAAAAAG
1 AAAAAAG
98326 AAAAAAG
1 AAAAAAG
98333 AAAAAAG
1 AAAAAAG
98340 AAAAAAG
1 AAAAAAG
98347 AAAA
1 AAAA
98351 GAAAAGCACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:98620 original size:22 final size:22
Alignment explanation
Indices: 98595--98639 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
98585 TCAAGTTCGC
*
98595 ATATTTTTGAGTGTTCATAGAT
1 ATATTTTTGAGTGTTCACAGAT
*
98617 ATATTTTTGGGTGTTCACAGAT
1 ATATTTTTGAGTGTTCACAGAT
98639 A
1 A
98640 AAAGGTGCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.47
Consensus pattern (22 bp):
ATATTTTTGAGTGTTCACAGAT
Found at i:103022 original size:8 final size:8
Alignment explanation
Indices: 103009--103033 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
102999 GAGCATCCGG
103009 CTCATGTA
1 CTCATGTA
103017 CTCATGTA
1 CTCATGTA
103025 CTCATGTA
1 CTCATGTA
103033 C
1 C
103034 CACTTACTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (8 bp):
CTCATGTA
Found at i:111729 original size:6 final size:6
Alignment explanation
Indices: 111718--111752 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
111708 TGACCTCCCT
111718 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
111753 TGATTTTTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:111939 original size:2 final size:2
Alignment explanation
Indices: 111920--111954 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
111910 AAATCATATG
* *
111920 GT GT GG GT GT GA GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
111955 AAGGTCAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.00, G:0.54, T:0.43
Consensus pattern (2 bp):
GT
Found at i:118685 original size:34 final size:33
Alignment explanation
Indices: 118646--118710 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 33
118636 ATTATATTGT
118646 TGTTTTGGTG-CTATTTTTTTACTATTTTGGTTAC
1 TGTTTTGGTGCCT-TTTTTTTACT-TTTTGGTTAC
118680 TGTTTTGGTGCCTTTTTTTTACTTTTTGGTT
1 TGTTTTGGTGCCTTTTTTTTACTTTTTGGTT
118711 GTTATTTTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
33 8 0.27
34 20 0.67
35 2 0.07
ACGTcount: A:0.08, C:0.09, G:0.18, T:0.65
Consensus pattern (33 bp):
TGTTTTGGTGCCTTTTTTTTACTTTTTGGTTAC
Found at i:118736 original size:31 final size:29
Alignment explanation
Indices: 118695--118760 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 29
118685 TGGTGCCTTT
118695 TTTTTACTTTTTGGTTGT-TATTTTCGTGTTG
1 TTTTTACTTTTTGGTT-TCTATTTT--TGTTG
* *
118726 TTTTTGCTTTTTTGTTTCTATTTTTGTTG
1 TTTTTACTTTTTGGTTTCTATTTTTGTTG
118755 TTTTTA
1 TTTTTA
118761 ATGTTGTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 10 0.32
30 1 0.03
31 20 0.65
ACGTcount: A:0.06, C:0.06, G:0.15, T:0.73
Consensus pattern (29 bp):
TTTTTACTTTTTGGTTTCTATTTTTGTTG
Found at i:118959 original size:26 final size:28
Alignment explanation
Indices: 118930--118988 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 28
118920 TGCAACTATC
118930 TTAATATAAATTT-TTTTTAATG-TATT
1 TTAATATAAATTTATTTTTAATGTTATT
**
118956 TTAA-ATTTATTTATTTTTAATGTTTATT
1 TTAATATAAATTTATTTTTAATG-TTATT
118984 TTAAT
1 TTAAT
118989 GTTTTTAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 6 0.22
26 13 0.48
28 8 0.30
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.64
Consensus pattern (28 bp):
TTAATATAAATTTATTTTTAATGTTATT
Found at i:129205 original size:59 final size:58
Alignment explanation
Indices: 129130--129250 Score: 154
Period size: 58 Copynumber: 2.1 Consensus size: 58
129120 ACCCATCAAC
* * * *
129130 AAACTAAATCCAAATATTTTTAAACCCAAAATCTAATTTCATTCTTCAAA-AATACTCAT
1 AAACTAAACCCAAATATTTTTAAACCC-AAATATAATTTCATTCCT-AAATAACACTCAT
* * *
129189 AAACTAAACCCGAATATTTTTAAACTCAAATATAATTTTATTCCTAAATAACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAATAACACTCAT
129247 AAAC
1 AAAC
129251 AACTCTTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 3 0.06
58 27 0.50
59 24 0.44
ACGTcount: A:0.46, C:0.20, G:0.01, T:0.33
Consensus pattern (58 bp):
AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAATAACACTCAT
Found at i:129590 original size:69 final size:72
Alignment explanation
Indices: 129517--129665 Score: 164
Period size: 72 Copynumber: 2.1 Consensus size: 72
129507 TTGCCGTGTA
*
129517 GATTTTTACTGTATT-TTGAACTTTTGCTCA-TGTTTTT-TTATAATCTTGTTGTGTTAT-TGTT
1 GATTTTTACTGT-TTATTAAACTTTTGCTCATTGTTTTTATTATAATCTTGTTGTGTTATCT-TT
*
129578 G-TTATTTG
64 GTTTACTTG
* ** * * *
129586 GATTTATGTTGTTTACTTAAACTTTTGCTTATTTTTTTTATTATAATCTTGTTGTGTTGTCTTTG
1 GATTTTTACTGTTTA-TTAAACTTTTGCTCATTGTTTTTATTATAATCTTGTTGTGTTATCTTTG
129651 TTTACTTG
65 TTTACTTG
129659 GATTTTT
1 GATTTTT
129666 TCACTTATTT
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
68 2 0.03
69 9 0.14
70 13 0.20
71 6 0.09
72 22 0.34
73 13 0.20
ACGTcount: A:0.16, C:0.07, G:0.15, T:0.62
Consensus pattern (72 bp):
GATTTTTACTGTTTATTAAACTTTTGCTCATTGTTTTTATTATAATCTTGTTGTGTTATCTTTGT
TTACTTG
Found at i:136764 original size:47 final size:47
Alignment explanation
Indices: 136710--136805 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 47
136700 TAGAAATATG
*
136710 TTAGCTCAATTTTGGATACAAAATTCAAGAGAATTGAATTGCTTTTC
1 TTAGCTCAATTTTAGATACAAAATTCAAGAGAATTGAATTGCTTTTC
136757 TTAGCTCAATTTTAGATACAAAATTCAAGAGAATTGAATTGCTTTTC
1 TTAGCTCAATTTTAGATACAAAATTCAAGAGAATTGAATTGCTTTTC
136804 TT
1 TT
136806 TTAATTAGGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (47 bp):
TTAGCTCAATTTTAGATACAAAATTCAAGAGAATTGAATTGCTTTTC
Found at i:142000 original size:16 final size:15
Alignment explanation
Indices: 141971--142002 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
141961 CTCAACTTAA
141971 ATTTAAGATTTTTTT
1 ATTTAAGATTTTTTT
141986 ATTTAAGATTTTTTT
1 ATTTAAGATTTTTTT
142001 AT
1 AT
142003 CTTTCTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (15 bp):
ATTTAAGATTTTTTT
Found at i:142425 original size:31 final size:30
Alignment explanation
Indices: 142372--142437 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 30
142362 AATAATTTAT
*
142372 ATTTTTATAATTTTTAAAAATTAAATTA-A
1 ATTTTTATAATTTTTAAAAATTAAAATATA
*
142401 ATTTTTATTATTTTTTAAAAAATTAAAATATA
1 ATTTTTA-TAATTTTT-AAAAATTAAAATATA
142433 ATTTT
1 ATTTT
142438 ATTTATATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 7 0.22
30 7 0.22
31 12 0.38
32 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
ATTTTTATAATTTTTAAAAATTAAAATATA
Found at i:144403 original size:30 final size:29
Alignment explanation
Indices: 144368--144433 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 29
144358 CTAATAAATC
*
144368 ATATTAATA-A-ATTTATTAATAATTTTAAA
1 ATATTAATATATAGTTATT-AT-ATTTTAAA
144397 ATTATTAAATATATAGTTATTATATTTTAAA
1 A-TATT-AATATATAGTTATTATATTTTAAA
144428 ATATTA
1 ATATTA
144434 TTTTAAATAG
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
29 2 0.06
30 8 0.25
31 13 0.41
32 3 0.09
33 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (29 bp):
ATATTAATATATAGTTATTATATTTTAAA
Found at i:146450 original size:2 final size:2
Alignment explanation
Indices: 146445--146469 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
146435 TCTCTCTCTT
146445 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
146470 TTAAATGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:147123 original size:17 final size:17
Alignment explanation
Indices: 147096--147134 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
147086 GCGTGAAAAG
147096 ATAAAATATTATC-TTA
1 ATAAAATATTATCATTA
147112 ATAAATATATTATCATTA
1 ATAAA-ATATTATCATTA
147130 A-AAAA
1 ATAAAA
147135 AAAAGGAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 6 0.29
17 11 0.52
18 4 0.19
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAAAATATTATCATTA
Found at i:147613 original size:22 final size:21
Alignment explanation
Indices: 147561--147613 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
147551 TTGAGTACAA
147561 GATTCGAGATTTTAGATTTAG
1 GATTCGAGATTTTAGATTTAG
** *
147582 GATTTAAGATTTTAGGGTTTAG
1 GATTCGAGATTTTA-GATTTAG
147604 GATTCGAGAT
1 GATTCGAGAT
147614 AAAAAATTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.28, C:0.04, G:0.26, T:0.42
Consensus pattern (21 bp):
GATTCGAGATTTTAGATTTAG
Found at i:149959 original size:103 final size:102
Alignment explanation
Indices: 149685--149966 Score: 314
Period size: 102 Copynumber: 2.8 Consensus size: 102
149675 GGAGCACATA
* * * *
149685 ATGGTGGCCATGGCAACAGGACAGAGCCTGAAATAGACGAAGATGTAGGAGCTGAGCTCATCGGA
1 ATGGTGGCCATGGCAACAGGACGGAGCCTGAAATAGACGAAGATGAAGGAGCTCAACTCATCGGA
* * * *
149750 GTCGCGCTTTATAACTATATTAACACAGGTGTAGAGG
66 ATCGAGCTTTATAACTATATTAACACAGGAGCAGAGG
* * * * *
149787 ATGGCGGCCATGAG-AACACGAGGGAGCCTGAAATAGAGGAAGATGAAGGAGCTCAACTTATCGG
1 ATGGTGGCCATG-GCAACAGGACGGAGCCTGAAATAGACGAAGATGAAGGAGCTCAACTCATCGG
* * *
149851 CATCGAGCTTTATAACTATATTAACGCTGGAGCAGAGG
65 AATCGAGCTTTATAACTATATTAACACAGGAGCAGAGG
* * * * ** * *
149889 CTGGGTGGTCATGGCAACAGGACGGATCCTGAAGTAGACGAAGGCGAAGGAGCCCATCTCATCGG
1 AT-GGTGGCCATGGCAACAGGACGGAGCCTGAAATAGACGAAGATGAAGGAGCTCAACTCATCGG
*
149954 AATCGAGCCTTAT
65 AATCGAGCTTTAT
149967 CACCTTATTC
Statistics
Matches: 146, Mismatches: 31, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
102 86 0.59
103 60 0.41
ACGTcount: A:0.31, C:0.19, G:0.31, T:0.19
Consensus pattern (102 bp):
ATGGTGGCCATGGCAACAGGACGGAGCCTGAAATAGACGAAGATGAAGGAGCTCAACTCATCGGA
ATCGAGCTTTATAACTATATTAACACAGGAGCAGAGG
Found at i:151645 original size:17 final size:18
Alignment explanation
Indices: 151623--151660 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
151613 TATTATTTTG
*
151623 AAATTAATAAATAT-TAT
1 AAATTAATAAAAATATAT
151640 AAATTAATAAAAATATAT
1 AAATTAATAAAAATATAT
151658 AAA
1 AAA
151661 ATACAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATTAATAAAAATATAT
Found at i:155809 original size:44 final size:44
Alignment explanation
Indices: 155754--155840 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
155744 TTTGGCCTTA
*
155754 GTGCGGTTCTTCAACAGTTGAGACGCCTAATAACTTATTTTAGG
1 GTGCGGTTCTTCAACAGTTGAGACGCATAATAACTTATTTTAGG
*
155798 GTGCGGTTCTTCAACAGTTGAGACGCATAATAGCTTATTTTAG
1 GTGCGGTTCTTCAACAGTTGAGACGCATAATAACTTATTTTAG
155841 TAAAGCTTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.34
Consensus pattern (44 bp):
GTGCGGTTCTTCAACAGTTGAGACGCATAATAACTTATTTTAGG
Found at i:157057 original size:30 final size:29
Alignment explanation
Indices: 157023--157283 Score: 184
Period size: 29 Copynumber: 8.9 Consensus size: 29
157013 AAATGGTAAC
*
157023 TTTTGAAAGTTTCGGGATCAAAAATGAGAT
1 TTTTGAAAG-TTCGGGGTCAAAAATGAGAT
*
157053 TTTTGGAAGTTCGAGGG-C-AAAATG-GTAT
1 TTTTGAAAGTTCG-GGGTCAAAAATGAG-AT
* *
157081 TTTTTAGAAGTTTTAGGGGTCAAAAATGAGAT
1 TTTTGA-AAG--TTCGGGGTCAAAAATGAGAT
*
157113 TTTTGAAAGTTTAGGGGT--AAAATG-GTAAT
1 TTTTGAAAG-TTCGGGGTCAAAAATGAG--AT
* * *
157142 TTTTGGAAGTTCGGGGTAAAAAAGGA-AT
1 TTTTGAAAGTTCGGGGTCAAAAATGAGAT
* *
157170 TTTTAGAAGGTTCGAGGTCAAAAATGAGAT
1 TTTT-GAAAGTTCGGGGTCAAAAATGAGAT
*
157200 TTTTGGAAGTTCGAGGGT-AAAAATG-GAAT
1 TTTTGAAAGTTCG-GGGTCAAAAATGAG-AT
* * *
157229 TTTT-AGAAGTTTTGGGGTCAAAATTGGGAT
1 TTTTGA-AAG-TTCGGGGTCAAAAATGAGAT
157259 TTTTGAAAGTTCGGGGGT-AAAAATG
1 TTTTGAAAGTTC-GGGGTCAAAAATG
157284 GAATCAAGAA
Statistics
Matches: 186, Mismatches: 22, Indels: 47
0.73 0.09 0.18
Matches are distributed among these distances:
27 2 0.01
28 32 0.17
29 70 0.38
30 59 0.32
31 9 0.05
32 13 0.07
33 1 0.01
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (29 bp):
TTTTGAAAGTTCGGGGTCAAAAATGAGAT
Found at i:157114 original size:60 final size:58
Alignment explanation
Indices: 157012--157239 Score: 173
Period size: 60 Copynumber: 3.9 Consensus size: 58
157002 ATCCGGGAGT
* * *
157012 AAAATGGTAACTTTT-GAAAGTTTCGGGATCAAAAATGAGATTTTTGGAAGTTCGAGGGC
1 AAAATGGTAATTTTTAG-AAG-TTAGGGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGC
* * * *
157071 AAAATGGTATTTTTTAGAAGTTTTAGGGGTCAAAAATGAGATTTTTGAAAGTT-TAGGGGT
1 AAAATGGTAATTTTTAGAAG--TTAGGGGTCAAAAATGAGATTTTTGGAAGTTCGA-GGGC
* * * * * *
157131 AAAATGGTAATTTTTGGAAGTTCGGGGTAAAAAAGGA-ATTTTTAGAAGGTTCGAGGTC
1 AAAATGGTAATTTTTAGAAGTTAGGGGTCAAAAATGAGATTTTTGGAA-GTTCGAGGGC
* * *
157189 AAAAAT-G-AGATTTTTGGAAGTTCGAGGGT-AAAAATG-GAATTTTTAGAAGTT
1 -AAAATGGTA-ATTTTTAGAAGTTAG-GGGTCAAAAATGAG-ATTTTTGGAAGTT
157240 TTGGGGTCAA
Statistics
Matches: 141, Mismatches: 18, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
57 9 0.06
58 44 0.31
59 37 0.26
60 51 0.36
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTTAGAAGTTAGGGGTCAAAAATGAGATTTTTGGAAGTTCGAGGGC
Found at i:157210 original size:87 final size:89
Alignment explanation
Indices: 157042--157239 Score: 237
Period size: 87 Copynumber: 2.2 Consensus size: 89
157032 TTTCGGGATC
* * * * *
157042 AAAAAT-GAGATTTTTGGAAGTTCGAGGGCAAAATGGTATTTTTTAGAAGTTTTAGGGGTCAAAA
1 AAAAATGGA-ATTTTTGGAAGTTCGAGGGAAAAAAGGTAATTTTTAGAAGTGTTAGAGGTCAAAA
157106 ATGAGATTTTTGAAAGTTTAG-GGGT
65 ATGAGATTTTTGAAAG-TTAGAGGGT
*
157131 -AAAATGGTAATTTTTGGAAGTTCG-GGGTAAAAAAGG-AATTTTTAGAAG-GTTCGAGGTCAAA
1 AAAAATGG-AATTTTTGGAAGTTCGAGGG-AAAAAAGGTAATTTTTAGAAGTGTTAGAGGTCAAA
* *
157192 AATGAGATTTTTGGAAGTTCGAGGGT
64 AATGAGATTTTTGAAAGTTAGAGGGT
*
157218 AAAAATGGAATTTTTAGAAGTT
1 AAAAATGGAATTTTTGGAAGTT
157240 TTGGGGTCAA
Statistics
Matches: 95, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
86 3 0.03
87 43 0.45
88 26 0.27
89 22 0.23
90 1 0.01
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (89 bp):
AAAAATGGAATTTTTGGAAGTTCGAGGGAAAAAAGGTAATTTTTAGAAGTGTTAGAGGTCAAAAA
TGAGATTTTTGAAAGTTAGAGGGT
Found at i:157228 original size:59 final size:58
Alignment explanation
Indices: 157140--157287 Score: 215
Period size: 59 Copynumber: 2.5 Consensus size: 58
157130 TAAAATGGTA
*
157140 ATTTTTGGAAGTTCGGGGTAAAAAAGGAATTTTTAGAAGGTTCGAGGTCAAAAATGAG
1 ATTTTTGGAAGTTCGGGGTAAAAATGGAATTTTTAGAAGGTTCGAGGTCAAAAATGAG
* * * * *
157198 ATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAATTGGG
1 ATTTTTGGAAGTTCG-GGGTAAAAATGGAATTTTTAGAAGGTTCGAGGTCAAAAATGAG
*
157257 ATTTTTGAAAGTTCGGGGGTAAAAATGGAAT
1 ATTTTTGGAAGTTC-GGGGTAAAAATGGAAT
157288 CAAGAAGATA
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
58 15 0.19
59 65 0.80
60 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (58 bp):
ATTTTTGGAAGTTCGGGGTAAAAATGGAATTTTTAGAAGGTTCGAGGTCAAAAATGAG
Found at i:157665 original size:170 final size:168
Alignment explanation
Indices: 157316--157669 Score: 464
Period size: 170 Copynumber: 2.1 Consensus size: 168
157306 TTTTTTCCCC
* * *
157316 GTATTTCATCAGGAAGCTAACCGTTTTATTACTTCGATCTGCTTATCAGTCTCTCATTAGGAAGC
1 GTATCTCATCAGGAAGCTAACCGTTTTATTACTTCGACCTGCTTATCAGTCTCTCATCAGGAAGC
* * *
157381 TGGGGTTTGAAGATTCGTTCATCGCGCGTGGGTTTGACTTGGTCTTCTTCTCAGTATCTTTATCA
66 TGGGGTTCGAAGATTCGTTCATCGAGCGTGGGTTTGACTTGGTCTTCTTCTCAGTATCTTCATCA
* * *
157446 GGAAGATGACCGTATCGTTTGTCTCAATCTGCTTCTCT
131 GGAAGATGACCGCATCGTTTGTCTCAATCCGCTTCTCG
* * *
157484 GTATCTCATCAGGAAGCTAACC-TTTTATTGCTTCGACCTGCTTCTCAGTTGTCTTC-TCAGGAA
1 GTATCTCATCAGGAAGCTAACCGTTTTATTACTTCGACCTGCTTATCAG-TCTC-TCATCAGGAA
* * * *
157547 GCTGGGGTTCGAAGATTTTGCTTGCTTTGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTAT-TT
64 GCTGGGGTTCGAAGA-TTCG-TT-CATCGAGCGTGGGTTTGACTTGGTCTTCTTCTCAGTATCTT
* *
157611 CATCAGGAAGATGACCGCGTCGTTTGTCTTAATCCG-TCTCTCG
126 CATCAGGAAGATGACCGCATCGTTTGTCTCAATCCGCT-TCTCG
157654 GTATCTCATCAGGAAG
1 GTATCTCATCAGGAAG
157670 ACGAATTTGG
Statistics
Matches: 162, Mismatches: 18, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
167 23 0.14
168 44 0.27
169 6 0.04
170 55 0.34
171 34 0.21
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (168 bp):
GTATCTCATCAGGAAGCTAACCGTTTTATTACTTCGACCTGCTTATCAGTCTCTCATCAGGAAGC
TGGGGTTCGAAGATTCGTTCATCGAGCGTGGGTTTGACTTGGTCTTCTTCTCAGTATCTTCATCA
GGAAGATGACCGCATCGTTTGTCTCAATCCGCTTCTCG
Found at i:157839 original size:206 final size:206
Alignment explanation
Indices: 157484--158035 Score: 1014
Period size: 206 Copynumber: 2.7 Consensus size: 206
157474 CTGCTTCTCT
157484 GTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTTGTCTTCTCAGGAAGC
1 GTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAG-TGTCTTCTCAGGAAGC
* *
157549 TGGGGTTCGAAGATTTTGCTTGCTTTGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATTTCAT
65 TGGGGTTCGAAGATTTTGCTCGCTTTGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCAT
*
157614 CAGGAAGATGACCGCGTCGTTTGTCTTAATCCGTCTCTCGGTATCTCATCAGGAAGACGAATTTG
130 CAGGAAGATGACCGCGTCGTTTGTCTTAATCCATCTCTCGGTATCTCATCAGGAAGACGAATTTG
157679 GTTCACTCCTCA
195 GTTCACTCCTCA
*
157691 GTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGTCCTGCTTCTCAGTGTCTTCTCAGGAAGCT
1 GTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTTCTCAGGAAGCT
*
157756 GGGGTTCGAAGATTTTGCTCGCTTTGAGCGTAGGTTTGATTTGGTCTTCTTCTCAGTATCTCATC
66 GGGGTTCGAAGATTTTGCTCGCTTTGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATC
157821 AGGAAGATGACCGCGTCGTTTGTCTTAATCCATCTCTCGGTATCTCATCAGGAAGACGAATTTGG
131 AGGAAGATGACCGCGTCGTTTGTCTTAATCCATCTCTCGGTATCTCATCAGGAAGACGAATTTGG
157886 TTCACTCCTCA
196 TTCACTCCTCA
* *
157897 ATATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTTCTCAAGAAGCT
1 GTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTTCTCAGGAAGCT
* *
157962 GGGGTTCGAGGATTTTTCTCGCTTTGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATC
66 GGGGTTCGAAGATTTTGCTCGCTTTGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATC
158027 AGGAAGATG
131 AGGAAGATG
158036 CCCGTGAAAT
Statistics
Matches: 334, Mismatches: 11, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
206 287 0.86
207 47 0.14
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (206 bp):
GTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTTCTCAGGAAGCT
GGGGTTCGAAGATTTTGCTCGCTTTGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATC
AGGAAGATGACCGCGTCGTTTGTCTTAATCCATCTCTCGGTATCTCATCAGGAAGACGAATTTGG
TTCACTCCTCA
Found at i:169951 original size:59 final size:58
Alignment explanation
Indices: 169888--170032 Score: 229
Period size: 58 Copynumber: 2.5 Consensus size: 58
169878 ACATCCGAGA
* *
169888 GTAAAATGGTAACTTTTGGAAGTTTCGAGATCAAAAATGGGATTTTTGGAAGTTCGGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGAGATCAAAAATAGGA-TTTTGGAAGTTCGGGG
* * *
169947 GTAAAATGGTAATTTTTAGAAGTTTCGGGGTCAAAAATAGGATTTTGGAAGTTCGGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGAGATCAAAAATAGGATTTTGGAAGTTCGGGG
170005 GTAAAATGGTAATTTTTGGAAG-TTCGAG
1 GTAAAATGGTAATTTTTGGAAGTTTCGAG
170033 GGTAAAAACA
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
57 5 0.06
58 37 0.47
59 37 0.47
ACGTcount: A:0.31, C:0.06, G:0.30, T:0.33
Consensus pattern (58 bp):
GTAAAATGGTAATTTTTGGAAGTTTCGAGATCAAAAATAGGATTTTGGAAGTTCGGGG
Found at i:169952 original size:29 final size:29
Alignment explanation
Indices: 169920--170275 Score: 333
Period size: 29 Copynumber: 12.4 Consensus size: 29
169910 TTTCGAGATC
* *
169920 AAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAAATGGAATTTTTAGAAGTTCGGGGGT
169949 -AAAATGGTAATTTTTAGAAGTTTC-GGGGT
1 AAAAATGG-AATTTTTAGAAG-TTCGGGGGT
*
169978 CAAAAATAGG-A-TTTTGGAAGTTCGGGGGT
1 -AAAAAT-GGAATTTTTAGAAGTTCGGGGGT
* *
170007 -AAAATGGTAATTTTTGGAAGTTCGAGGGT
1 AAAAATGG-AATTTTTAGAAGTTCGGGGGT
*** *
170036 AAAAACAAAATTTTTAGAAGTCTCGGGGTT
1 AAAAATGGAATTTTTAGAAGT-TCGGGGGT
* *
170066 AAAAAT-GAGATTTTTGGAAGTTCGGGGAT
1 AAAAATGGA-ATTTTTAGAAGTTCGGGGGT
* * * *
170095 AAAAATGAAATTTTTAGAGGTTTTGAGGGT
1 AAAAATGGAATTTTTAGAAG-TTCGGGGGT
*
170125 AAAAATGGAATTTTTAAAAGTTC-GGGGT
1 AAAAATGGAATTTTTAGAAGTTCGGGGGT
* * *
170153 AAAAAT-AAGATTTTTAGAAGTT-GAGGAT
1 AAAAATGGA-ATTTTTAGAAGTTCGGGGGT
170181 AAAAAT-GAGATTTTTAGAAGTTCGGGGGT
1 AAAAATGGA-ATTTTTAGAAGTTCGGGGGT
* *
170210 AAAAATGAAATTTTTAGAAGTTCGAGGGT
1 AAAAATGGAATTTTTAGAAGTTCGGGGGT
*
170239 AAAAATGGAATTTTT---AGTTCGAGGGT
1 AAAAATGGAATTTTTAGAAGTTCGGGGGT
170265 AAAAATGGAAT
1 AAAAATGGAAT
170276 NNNNNNNNNN
Statistics
Matches: 274, Mismatches: 35, Indels: 39
0.79 0.10 0.11
Matches are distributed among these distances:
26 24 0.09
27 6 0.02
28 57 0.21
29 125 0.46
30 55 0.20
31 5 0.02
32 2 0.01
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.32
Consensus pattern (29 bp):
AAAAATGGAATTTTTAGAAGTTCGGGGGT
Found at i:179578 original size:59 final size:58
Alignment explanation
Indices: 179515--179659 Score: 229
Period size: 58 Copynumber: 2.5 Consensus size: 58
179505 ACATCCGAGA
* *
179515 GTAAAATGGTAACTTTTGGAAGTTTCGAGATCAAAAATGGGATTTTTGGAAGTTCGGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGAGATCAAAAATAGGA-TTTTGGAAGTTCGGGG
* * *
179574 GTAAAATGGTAATTTTTAGAAGTTTCGGGGTCAAAAATAGGATTTTGGAAGTTCGGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGAGATCAAAAATAGGATTTTGGAAGTTCGGGG
179632 GTAAAATGGTAATTTTTGGAAG-TTCGAG
1 GTAAAATGGTAATTTTTGGAAGTTTCGAG
179660 GGTAAAAACA
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
57 5 0.06
58 37 0.47
59 37 0.47
ACGTcount: A:0.31, C:0.06, G:0.30, T:0.33
Consensus pattern (58 bp):
GTAAAATGGTAATTTTTGGAAGTTTCGAGATCAAAAATAGGATTTTGGAAGTTCGGGG
Found at i:179579 original size:29 final size:29
Alignment explanation
Indices: 179547--179945 Score: 371
Period size: 29 Copynumber: 13.9 Consensus size: 29
179537 TTTCGAGATC
* *
179547 AAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAAATGGAATTTTTAGAAGTTCGGGGGT
179576 -AAAATGGTAATTTTTAGAAGTTTC-GGGGT
1 AAAAATGG-AATTTTTAGAAG-TTCGGGGGT
*
179605 CAAAAATAGG-A-TTTTGGAAGTTCGGGGGT
1 -AAAAAT-GGAATTTTTAGAAGTTCGGGGGT
* *
179634 -AAAATGGTAATTTTTGGAAGTTCGAGGGT
1 AAAAATGG-AATTTTTAGAAGTTCGGGGGT
*** *
179663 AAAAACAAAATTTTTAGAAGTCTCGGGGTT
1 AAAAATGGAATTTTTAGAAGT-TCGGGGGT
* *
179693 AAAAAT-GAGATTTTTGGAAGTTCGGGGAT
1 AAAAATGGA-ATTTTTAGAAGTTCGGGGGT
* * * *
179722 AAAAATGAAATTTTTAGAGGTTTTGAGGGT
1 AAAAATGGAATTTTTAGAAG-TTCGGGGGT
*
179752 AAAAATGGAATTTTTAAAAGTTC-GGGGT
1 AAAAATGGAATTTTTAGAAGTTCGGGGGT
* * *
179780 AAAAAT-AAGATTTTTAGAAGTT-GAGGAT
1 AAAAATGGA-ATTTTTAGAAGTTCGGGGGT
179808 AAAAAT-GAGATTTTTAGAAGTTCGGGGGT
1 AAAAATGGA-ATTTTTAGAAGTTCGGGGGT
* *
179837 AAAAATGAAATTTTTAGAAGTTCGAGGGT
1 AAAAATGGAATTTTTAGAAGTTCGGGGGT
*
179866 AAAAATGGAATTTTT---AGTTCGAGGGT
1 AAAAATGGAATTTTTAGAAGTTCGGGGGT
*
179892 AAAAATGGAATTTTT---AGTTCGAGGGT
1 AAAAATGGAATTTTTAGAAGTTCGGGGGT
*
179918 AAAAATGGAATATTTAGAAGTTTCGGGG
1 AAAAATGGAATTTTTAGAAG-TTCGGGG
179946 ACCTCCAGGG
Statistics
Matches: 311, Mismatches: 37, Indels: 43
0.80 0.09 0.11
Matches are distributed among these distances:
26 53 0.17
27 6 0.02
28 57 0.18
29 127 0.41
30 61 0.20
31 5 0.02
32 2 0.01
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (29 bp):
AAAAATGGAATTTTTAGAAGTTCGGGGGT
Found at i:179934 original size:52 final size:53
Alignment explanation
Indices: 179652--179934 Score: 204
Period size: 59 Copynumber: 5.0 Consensus size: 53
179642 AATTTTTGGA
** *
179652 AGTTCGAGGGTAAAAACAAAATTTTTAGAAGTCTCG-GGGTTAAAAAT-GAGATTTTT
1 AGTTCGAGGGTAAAAATGAAATTTTT--AAGT-TCGAGGG-TAAAAATGGA-ATATTT
* *
179708 GGAAGTTCG-GGGATAAAAATGAAATTTTTAGAGGTTTTGAGGGTAAAAATGGAATTTTT
1 ---AGTTCGAGGG-TAAAAATGAAATTTTTA-A-G-TTCGAGGGTAAAAATGGAATATTT
* *
179767 AAAAGTTCG-GGGTAAAAAT-AAGATTTTTAGAAGTT-GAGGATAAAAAT-GAGATTTTT
1 ---AGTTCGAGGGTAAAAATGAA-ATTTTT--AAGTTCGAGGGTAAAAATGGA-ATATTT
* *
179823 AGAAGTTCGGGGGTAAAAATGAAATTTTTAGAAGTTCGAGGGTAAAAATGGAATTTTT
1 ---AGTTCGAGGGTAAAAATGAAATTTTT--AAGTTCGAGGGTAAAAATGGAATATTT
*
179881 AGTTCGAGGGTAAAAATGGAATTTTT-AGTTCGAGGGTAAAAATGGAATATTT
1 AGTTCGAGGGTAAAAATGAAATTTTTAAGTTCGAGGGTAAAAATGGAATATTT
179933 AG
1 AG
179935 AAGTTTCGGG
Statistics
Matches: 199, Mismatches: 11, Indels: 35
0.81 0.04 0.14
Matches are distributed among these distances:
52 27 0.14
55 26 0.13
56 25 0.13
57 28 0.14
58 37 0.19
59 49 0.25
60 7 0.04
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (53 bp):
AGTTCGAGGGTAAAAATGAAATTTTTAAGTTCGAGGGTAAAAATGGAATATTT
Found at i:181717 original size:19 final size:19
Alignment explanation
Indices: 181701--181749 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 19
181691 TTATTTTGGA
181701 CTTTTAAATTTAATTTGAG
1 CTTTTAAATTTAATTTGAG
* *
181720 CTTTTAATTTTAAATATTAAG
1 CTTTTAAATTT-AAT-TTGAG
181741 CTTTTAAAT
1 CTTTTAAAT
181750 CTATTCAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 10 0.40
20 3 0.12
21 12 0.48
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (19 bp):
CTTTTAAATTTAATTTGAG
Found at i:181788 original size:17 final size:17
Alignment explanation
Indices: 181766--181798 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
181756 AAATTTAATT
181766 AAATTTAAATTTAAAAC
1 AAATTTAAATTTAAAAC
181783 AAATTTAAATTTAAAA
1 AAATTTAAATTTAAAA
181799 AGATAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATTTAAATTTAAAAC
Found at i:181907 original size:45 final size:45
Alignment explanation
Indices: 181848--181942 Score: 181
Period size: 45 Copynumber: 2.1 Consensus size: 45
181838 AATTTAAACT
181848 TAATTTTAAAATCAAAACTTGATCCAAAATCTGGATCCGGTTAAA
1 TAATTTTAAAATCAAAACTTGATCCAAAATCTGGATCCGGTTAAA
181893 TAATTTTAAAATCAAAACTTGATCCAAAATCTGGATCCGGTTAAA
1 TAATTTTAAAATCAAAACTTGATCCAAAATCTGGATCCGGTTAAA
*
181938 AAATT
1 TAATT
181943 GGGCTTCAAC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.32
Consensus pattern (45 bp):
TAATTTTAAAATCAAAACTTGATCCAAAATCTGGATCCGGTTAAA
Found at i:188270 original size:2 final size:2
Alignment explanation
Indices: 188263--188291 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
188253 TCCGAGTTTT
188263 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
188292 TTGTGAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:191884 original size:4 final size:4
Alignment explanation
Indices: 191868--191897 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
191858 GCACAATTAC
191868 AAAG AAA- AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
191898 TCAGAGAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:194965 original size:29 final size:30
Alignment explanation
Indices: 194923--194979 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
194913 GTTTGAGAGG
194923 GGGAGAGACCTTAAA-TATAAAAGAAAACT
1 GGGAGAGACCTTAAATTATAAAAGAAAACT
** *
194952 GGGAGAGATGTTAAATTATCAAAGAAAA
1 GGGAGAGACCTTAAATTATAAAAGAAAA
194980 AAGAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.51, C:0.07, G:0.23, T:0.19
Consensus pattern (30 bp):
GGGAGAGACCTTAAATTATAAAAGAAAACT
Done.