Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001677.1 Hibiscus syriacus cultivar Beakdansim tig00003354_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 162409
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:40 original size:26 final size:25
Alignment explanation
Indices: 2--59 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
1 G
* *
2 ATTTTATGATAGTCTAAATTTCTAAA
1 ATTTTATGATAGTC-AAACTTATAAA
*
28 ATTTTA-GAGTAGTCGAACTTATAAA
1 ATTTTATGA-TAGTCAAACTTATAAA
53 ATTTTAT
1 ATTTTAT
60 AGAGTTGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 16 0.59
26 11 0.41
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (25 bp):
ATTTTATGATAGTCAAACTTATAAA
Found at i:1264 original size:2 final size:2
Alignment explanation
Indices: 1257--1287 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1247 CTTCTATTTA
1257 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1288 TGTTTTAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:10484 original size:12 final size:13
Alignment explanation
Indices: 10464--10490 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
10454 TTCGTCCAAA
10464 TTTGTTTTTTTTT
1 TTTGTTTTTTTTT
10477 TTTGTTTTTTTTT
1 TTTGTTTTTTTTT
10490 T
1 T
10491 ATATTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (13 bp):
TTTGTTTTTTTTT
Found at i:10639 original size:39 final size:38
Alignment explanation
Indices: 10593--10882 Score: 249
Period size: 39 Copynumber: 7.6 Consensus size: 38
10583 GTTTTTGAAA
*
10593 ATATATATTATATAGTTTTGAAAACATTTTT-AAA-AT
1 ATATATAATATATAGTTTTGAAAACATTTTTAAAACAT
* **
10629 ATGTAT--TATATAGTTTTG-AAATTTTTTTGAAAAC--
1 ATATATAATATATAGTTTTGAAAACATTTTT-AAAACAT
* * * * * *
10663 ATATATGATATATAGTTTTTCAAAAAAATTTGAAAAAAT
1 ATATATAATATATAG-TTTTGAAAACATTTTTAAAACAT
* * *
10702 ATATATATATATATATATATATTGAAAATATTTTTAAAATAT
1 ATATATA-ATATATA-GT-T-TTGAAAACATTTTTAAAACAT
**
10744 ATATATAATATATAGAAATTGAAAACATTTTTGAAAACAT
1 ATATATAATATATAG-TTTTGAAAACATTTTT-AAAACAT
* *
10784 ATATATAATATATAGTTTTTAAAAACATTTTGAAAACAT
1 ATATATAATATATAG-TTTTGAAAACATTTTTAAAACAT
*
10823 ATATATAATATATAGTTTCT-AAAACATTTTGAAAA-A-
1 ATATATAATATATAGTTT-TGAAAACATTTTTAAAACAT
*
10859 ATATATAATATATAGTTTTTAAAA
1 ATATATAATATATAGTTTTGAAAA
10883 TGTTTTGAAA
Statistics
Matches: 210, Mismatches: 27, Indels: 34
0.77 0.10 0.13
Matches are distributed among these distances:
33 8 0.04
34 17 0.08
35 4 0.02
36 34 0.16
37 9 0.04
38 24 0.11
39 42 0.20
40 41 0.20
41 8 0.04
42 23 0.11
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (38 bp):
ATATATAATATATAGTTTTGAAAACATTTTTAAAACAT
Found at i:12877 original size:99 final size:99
Alignment explanation
Indices: 12758--12959 Score: 323
Period size: 99 Copynumber: 2.0 Consensus size: 99
12748 TTATAATATT
* * * *
12758 ATATATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTTGTTAAACACCCTGGCTTTATGG
1 ATATATATACAATAAAGCTTGAGATGTCCCTCTAAAGCAATTGGTTAAACACCCCGGCTTTATGG
* *
12823 ATAAGATTCAGCTAGCCTGATCAAGGTGATTATA
66 ATAAGATTCAGCTAGCCTAATAAAGGTGATTATA
* *
12857 ATATCTATACAATAAAGCTTGAGATGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGG
1 ATATATATACAATAAAGCTTGAGATGTCCCTCTAAAGCAATTGGTTAAACACCCCGGCTTTATGG
*
12922 ATAAGATTGAGCTAGCCTAATAAAGGTGATTATA
66 ATAAGATTCAGCTAGCCTAATAAAGGTGATTATA
12956 ATAT
1 ATAT
12960 TGAGATGTCC
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
99 94 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (99 bp):
ATATATATACAATAAAGCTTGAGATGTCCCTCTAAAGCAATTGGTTAAACACCCCGGCTTTATGG
ATAAGATTCAGCTAGCCTAATAAAGGTGATTATA
Found at i:14488 original size:85 final size:85
Alignment explanation
Indices: 14339--14656 Score: 313
Period size: 85 Copynumber: 3.8 Consensus size: 85
14329 CTCAGCTTAG
* * *
14339 TACAACATAACTCAAGGCGATAAAGGTTATATATCAACAGAAACCTTTGAGTTCGATT-CTATTC
1 TACAACATAACTCAAGGCGAGAAAGGTTATATATCAACAAAAACCTTCGAGTTCGATTAC-ATTC
* * * *
14403 AGCTCAAAGACATAACAAGTT
65 AGCTCAAGGGCATATCAAATT
* * * * * * *
14424 TACAGCATAACTTAAGGTGAGAAAGGTTATCTGTCAATAAAAATCTTCGAGTTCGATTACATTCA
1 TACAACATAACTCAAGGCGAGAAAGGTTATATATCAACAAAAACCTTCGAGTTCGATTACATTCA
14489 GCTCAAGGGCATATCAAATT
66 GCTCAAGGGCATATCAAATT
* * * * * *
14509 TACAGCATAGCTCAAGGCGAGAAGGGCTATATGTCAAC---AACCTTCGAGTTTGATTACATTCA
1 TACAACATAACTCAAGGCGAGAAAGGTTATATATCAACAAAAACCTTCGAGTTCGATTACATTCA
*
14571 ACTCAAGGGCATATCAAATT
66 GCTCAAGGGCATATCAAATT
* * * * * * * *
14591 TACAAACATAGCTTAAGGAGAGAAGGGTTATCTATCAACAAAAA-TTGTCGAGTTTGATTCCATT
1 TAC-AACATAACTCAAGGCGAGAAAGGTTATATATCAACAAAAACCT-TCGAGTTCGATTACATT
14655 CA
64 CA
14657 ACTCGATGAC
Statistics
Matches: 195, Mismatches: 32, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
82 44 0.23
83 29 0.15
85 101 0.52
86 21 0.11
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (85 bp):
TACAACATAACTCAAGGCGAGAAAGGTTATATATCAACAAAAACCTTCGAGTTCGATTACATTCA
GCTCAAGGGCATATCAAATT
Found at i:15829 original size:36 final size:36
Alignment explanation
Indices: 15789--15925 Score: 151
Period size: 34 Copynumber: 3.9 Consensus size: 36
15779 GCGATTTTCA
15789 AAAATATATATATTATATAGTTTTGAAAACATTTTG
1 AAAATATATATATTATATAGTTTTGAAAACATTTTG
* **
15825 -AAA-ATATATATTATAAAGTTTT-AAAA-AAATTG
1 AAAATATATATATTATATAGTTTTGAAAACATTTTG
* * *
15857 AAAACATATATAATATATAGGTTTTGAAAATATTTTTG
1 AAAATATATATATTATATA-GTTTTGAAAACA-TTTTG
15895 AAAATATATA-A-TATATAGTTTTTGAAAACAT
1 AAAATATATATATTATATAG-TTTTGAAAACAT
15926 ATATATATAG
Statistics
Matches: 85, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
32 4 0.05
33 7 0.08
34 30 0.35
35 10 0.12
36 20 0.24
37 2 0.02
38 12 0.14
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (36 bp):
AAAATATATATATTATATAGTTTTGAAAACATTTTG
Found at i:15837 original size:34 final size:34
Alignment explanation
Indices: 15746--15925 Score: 159
Period size: 36 Copynumber: 5.0 Consensus size: 34
15736 TGAAAATATT
* *
15746 TTTTGGAAAA-ATATAATATATAATTTTTAGAAAGCGA
1 TTTT-GAAAATATATAATATAT-AGTTTT-GAAAAC-A
*
15783 TTTTCAAAAATATATATATTATATAGTTTTGAAAACA
1 TTTT-GAAAATATATA-A-TATATAGTTTTGAAAACA
* *
15820 TTTTGAAAATATATATTATAAAGTTTT-AAAA-A
1 TTTTGAAAATATATAATATATAGTTTTGAAAACA
** *
15852 AATTGAAAACATATATAATATATAGGTTTTGAAAATA
1 TTTTG-AAA-ATATATAATATATA-GTTTTGAAAACA
15889 TTTTTGAAAATATATAATATATAGTTTTTGAAAACA
1 -TTTTGAAAATATATAATATATAG-TTTTGAAAACA
15925 T
1 T
15926 ATATATATAG
Statistics
Matches: 119, Mismatches: 14, Indels: 22
0.77 0.09 0.14
Matches are distributed among these distances:
32 4 0.03
33 7 0.06
34 22 0.18
35 7 0.06
36 38 0.32
37 17 0.14
38 13 0.11
39 6 0.05
40 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (34 bp):
TTTTGAAAATATATAATATATAGTTTTGAAAACA
Found at i:15939 original size:58 final size:61
Alignment explanation
Indices: 15854--15984 Score: 173
Period size: 59 Copynumber: 2.2 Consensus size: 61
15844 TTTAAAAAAA
*
15854 TTGAAAACATATATAATATATAGGTTTTGAAAATATTTTTG-AAA-ATATATA-ATATATAGTTT
1 TTGAAAAC--ATATAATATATAGGTTTTGAAAACA-TTTTGAAAACATATATATATATATAG-TT
15916 TTGAAAACATAT-ATATATA-GTTTTGAAAACATTTTGAAAACATATATATATATATAGTT
1 TTGAAAACATATAATATATAGGTTTTGAAAACATTTTGAAAACATATATATATATATAGTT
*
15975 TTAAAAACAT
1 TTGAAAACAT
15985 TTTGAAAACA
Statistics
Matches: 64, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
57 5 0.08
58 14 0.22
59 25 0.39
60 12 0.19
62 8 0.12
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (61 bp):
TTGAAAACATATAATATATAGGTTTTGAAAACATTTTGAAAACATATATATATATATAGTT
Found at i:15942 original size:22 final size:24
Alignment explanation
Indices: 15889--15947 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
15879 TTTGAAAATA
*
15889 TTTTTGAAAATATATAATATATAG
1 TTTTTGAAAACATATAATATATAG
15913 TTTTTGAAAACATAT-ATATATAG
1 TTTTTGAAAACATATAATATATAG
15936 -TTTTGAAAACAT
1 TTTTTGAAAACAT
15948 TTTGAAAACA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 12 0.35
23 8 0.24
24 14 0.41
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (24 bp):
TTTTTGAAAACATATAATATATAG
Found at i:15998 original size:35 final size:35
Alignment explanation
Indices: 15914--16015 Score: 163
Period size: 37 Copynumber: 2.9 Consensus size: 35
15904 AATATATAGT
*
15914 TTTTGAAAAC--ATATATATATAGTTTTGAAAACA
1 TTTTGAAAACATATATATATATAGTTTTAAAAACA
15947 TTTTGAAAACATATATATATATATAGTTTTAAAAACA
1 TTTTGAAAAC--ATATATATATATAGTTTTAAAAACA
15984 TTTTGAAAACATATATATATATAGTTTTAAAA
1 TTTTGAAAACATATATATATATAGTTTTAAAA
16016 TGTTTTTGAA
Statistics
Matches: 64, Mismatches: 1, Indels: 6
0.90 0.01 0.08
Matches are distributed among these distances:
33 10 0.16
35 22 0.34
37 32 0.50
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (35 bp):
TTTTGAAAACATATATATATATAGTTTTAAAAACA
Found at i:17305 original size:16 final size:16
Alignment explanation
Indices: 17286--17413 Score: 57
Period size: 16 Copynumber: 7.8 Consensus size: 16
17276 AATTTAACAC
17286 TTTTTTATTTTATTTT
1 TTTTTTATTTTATTTT
* * *
17302 TTTTTTCA-CTCA-GTT
1 TTTTTT-ATTTTATTTT
*
17317 TTATTTATCTTT-TTTT
1 TTTTTTAT-TTTATTTT
17333 ATCTATTTTA-TTTATTTT
1 -T-T-TTTTATTTTATTTT
* * *
17351 ATTATTATTATATTAATAT
1 -TT-TT-TTATTTTATTTT
* *
17370 TTTTTTATATTATTAT
1 TTTTTTATTTTATTTT
* *
17386 TTTATTATTTTATTTA
1 TTTTTTATTTTATTTT
17402 TTTTTTATTTTA
1 TTTTTTATTTTA
17414 CAATATAACA
Statistics
Matches: 85, Mismatches: 17, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
14 1 0.01
15 7 0.08
16 45 0.53
17 11 0.13
18 12 0.14
19 9 0.11
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.73
Consensus pattern (16 bp):
TTTTTTATTTTATTTT
Found at i:17329 original size:11 final size:11
Alignment explanation
Indices: 17315--17411 Score: 69
Period size: 11 Copynumber: 8.7 Consensus size: 11
17305 TTTCACTCAG
*
17315 TTTTATTTATC
1 TTTTATTTATA
17326 TTTT-TTTATCTA
1 TTTTATTTA--TA
17338 TTTTA-TT-TA
1 TTTTATTTATA
17347 TTTTA-TTATTA
1 TTTTATTTA-TA
* *
17358 TTATATTAATA
1 TTTTATTTATA
17369 TTTT-TTTATA
1 TTTTATTTATA
17379 TTATTATTTTATTA
1 TT-TTA-TTTA-TA
*
17393 TTTTATTTATT
1 TTTTATTTATA
17404 TTTTATTT
1 TTTTATTT
17412 TACAATATAA
Statistics
Matches: 70, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
9 9 0.13
10 11 0.16
11 26 0.37
12 13 0.19
13 7 0.10
14 4 0.06
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTATTTATA
Found at i:17341 original size:23 final size:22
Alignment explanation
Indices: 17291--17411 Score: 78
Period size: 24 Copynumber: 5.5 Consensus size: 22
17281 AACACTTTTT
*
17291 TATTTTATTT-TTTTTTTCA-C
1 TATTTTATTTATTTTTTTTATC
17311 TCAGTTTTATTTATCTTTTTTTATC
1 T-A-TTTTATTTAT-TTTTTTTATC
17336 TATTTTATTTATTTTATTATTAT-
1 TATTTTATTTATTTT-TT-TTATC
*
17359 TATATTAATATTT-TTTTATATTAT-
1 TAT-TT--TATTTATTTT-TTTTATC
*
17383 TATTTTA-TTATTTTATTTAT-
1 TATTTTATTTATTTTTTTTATC
17403 T-TTTTATTT
1 TATTTTATTT
17412 TACAATATAA
Statistics
Matches: 85, Mismatches: 4, Indels: 24
0.75 0.04 0.21
Matches are distributed among these distances:
19 5 0.06
20 10 0.12
21 7 0.08
22 11 0.13
23 18 0.21
24 21 0.25
25 8 0.09
26 5 0.06
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.73
Consensus pattern (22 bp):
TATTTTATTTATTTTTTTTATC
Found at i:17364 original size:8 final size:8
Alignment explanation
Indices: 17340--17403 Score: 53
Period size: 8 Copynumber: 8.2 Consensus size: 8
17330 TTTATCTATT
17340 TTATT-TA
1 TTATTATA
17347 TT-TTATTA
1 TTATTA-TA
17355 TTATTATA
1 TTATTATA
* *
17363 TTAATATT
1 TTATTATA
*
17371 TTTTTATA
1 TTATTATA
*
17379 TTATTATT
1 TTATTATA
*
17387 TTATTATT
1 TTATTATA
17395 TTATT-TA
1 TTATTATA
17402 TT
1 TT
17404 TTTTATTTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
6 2 0.04
7 5 0.11
8 36 0.78
9 3 0.07
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
TTATTATA
Found at i:17374 original size:24 final size:24
Alignment explanation
Indices: 17341--17402 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
17331 TTATCTATTT
17341 TATTTATTTTATTATTATTATATTAA
1 TATTT-TTTTA-TATTATTATATTAA
* *
17367 TATTTTTTTATATTATTATTTTAT
1 TATTTTTTTATATTATTATATTAA
17391 TATTTTATTTAT
1 TATTTT-TTTAT
17403 TTTTTATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
24 18 0.55
25 10 0.30
26 5 0.15
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (24 bp):
TATTTTTTTATATTATTATATTAA
Found at i:17383 original size:35 final size:32
Alignment explanation
Indices: 17338--17411 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 32
17328 TTTTTATCTA
17338 TTTTATTTATT-TTATTATTATTATATTAATATTT
1 TTTTATTTATTATT-TTATTATTATATT--TATTT
*
17372 TTTTATATTATTATTTTATTATTTTATTTA-TT
1 TTTTAT-TTATTATTTTATTATTATATTTATTT
17404 TTTTATTT
1 TTTTATTT
17412 TACAATATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
31 2 0.05
32 8 0.22
33 2 0.05
34 6 0.16
35 17 0.46
36 2 0.05
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (32 bp):
TTTTATTTATTATTTTATTATTATATTTATTT
Found at i:17406 original size:32 final size:29
Alignment explanation
Indices: 17315--17411 Score: 67
Period size: 32 Copynumber: 3.3 Consensus size: 29
17305 TTTCACTCAG
*
17315 TTTTATTTATCT-TTTTTTA-TCTATT-TT
1 TTTTATTTAT-TATTTTTTATTTTATTATT
* * * *
17342 ATTTATTTTATTA-TTATTATATTAATATTT
1 TTTTA-TTTATTATTTTTTATTTTATTA-TT
17372 TTTTATATTATTATTTTATTATTTTATTTATT
1 TTTTAT-TTATTATTTT-TTATTTTA-TTATT
17404 TTTTATTT
1 TTTTATTT
17412 TACAATATAA
Statistics
Matches: 52, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
27 10 0.19
28 8 0.15
29 1 0.02
30 12 0.23
31 4 0.08
32 15 0.29
33 2 0.04
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (29 bp):
TTTTATTTATTATTTTTTATTTTATTATT
Found at i:27577 original size:26 final size:26
Alignment explanation
Indices: 27540--27589 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
27530 TCTTACGAAT
27540 TTATATAATTATAAATTAATTAAAAA
1 TTATATAATTATAAATTAATTAAAAA
*
27566 TTATATAGTTATAAATTAATTAAA
1 TTATATAATTATAAATTAATTAAA
27590 TGAAAAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
TTATATAATTATAAATTAATTAAAAA
Found at i:31361 original size:14 final size:14
Alignment explanation
Indices: 31342--31383 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
31332 GATCAAAGTT
31342 AACGGGTTGACTCA
1 AACGGGTTGACTCA
31356 AACGGGTTG-CTCA
1 AACGGGTTGACTCA
**
31369 GTCTGGGTTGACTCA
1 AAC-GGGTTGACTCA
31384 GTTGAGTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 5 0.21
14 15 0.62
15 4 0.17
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.26
Consensus pattern (14 bp):
AACGGGTTGACTCA
Found at i:31392 original size:14 final size:15
Alignment explanation
Indices: 31361--31410 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 15
31351 ACTCAAACGG
*
31361 GTTG-CTCAGTCTGG
1 GTTGACTCAGTCTGA
31375 GTTGACTCAGT-TGA
1 GTTGACTCAGTCTGA
* *
31389 GTTGACTCA-ACCGA
1 GTTGACTCAGTCTGA
31403 GTTGACTC
1 GTTGACTC
31411 GGTTTAGACC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
14 25 0.81
15 6 0.19
ACGTcount: A:0.18, C:0.22, G:0.28, T:0.32
Consensus pattern (15 bp):
GTTGACTCAGTCTGA
Found at i:34091 original size:98 final size:98
Alignment explanation
Indices: 33922--34120 Score: 335
Period size: 98 Copynumber: 2.0 Consensus size: 98
33912 ATATGTTGAA
* * *
33922 AGAGTCGTTGTTTTTACTCTTATATCACAATATTTTGTCTCCTATAGCTGGCTTATTTTCTTTTC
1 AGAGTCATTGTTTTTACTCTTAGATCACAATATTTTGTCTCCTATAGCTGGCTTATTGTCTTTTC
*
33987 TGCAATTATGTGATGCTAAGGTCAACCCAGCCT
66 TGCAATTATGTGATGCCAAGGTCAACCCAGCCT
* *
34020 AGAGTCATTGTTTTTACTCTTGGATCACAATATTTTTTCTCCTATAGCTGGCTTATTGTCTTTTC
1 AGAGTCATTGTTTTTACTCTTAGATCACAATATTTTGTCTCCTATAGCTGGCTTATTGTCTTTTC
*
34085 TGCAATTATGTGATGCCATGGTCAACCCAGCCT
66 TGCAATTATGTGATGCCAAGGTCAACCCAGCCT
34118 AGA
1 AGA
34121 TAGCTGGGGT
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.42
Consensus pattern (98 bp):
AGAGTCATTGTTTTTACTCTTAGATCACAATATTTTGTCTCCTATAGCTGGCTTATTGTCTTTTC
TGCAATTATGTGATGCCAAGGTCAACCCAGCCT
Found at i:34643 original size:2 final size:2
Alignment explanation
Indices: 34636--34675 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
34626 GGGTTTTCTC
34636 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34676 GAAGACCCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37615 original size:33 final size:31
Alignment explanation
Indices: 37578--37640 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
37568 CAGACAGAGG
37578 GGGGACTCATTCGGAGATTTCCAGAAAAAAAAA
1 GGGGACTCATTCGG-G-TTTCCAGAAAAAAAAA
* * *
37611 GGGGATTCATTCGGGTTTTCAGAGAAAAAA
1 GGGGACTCATTCGGGTTTCCAGAAAAAAAA
37641 TTCCATTCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 13 0.48
32 1 0.04
33 13 0.48
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.22
Consensus pattern (31 bp):
GGGGACTCATTCGGGTTTCCAGAAAAAAAAA
Found at i:42385 original size:26 final size:25
Alignment explanation
Indices: 42356--42433 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
42346 AATTTTTGAC
42356 ATTCTATCTCTTTGAGACCTTGAAAT
1 ATTCT-TCTCTTTGAGACCTTGAAAT
* *
42382 A---TTCT-TTT-CGACCTTGAAAC
1 ATTCTTCTCTTTGAGACCTTGAAAT
*
42402 ATTCCCTCTCTTTGAGACCTTGAAAT
1 ATT-CTTCTCTTTGAGACCTTGAAAT
42428 ATTCTT
1 ATTCTT
42434 TCCACATTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
20 11 0.28
21 3 0.08
22 3 0.08
23 1 0.03
24 3 0.08
25 5 0.12
26 14 0.35
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.42
Consensus pattern (25 bp):
ATTCTTCTCTTTGAGACCTTGAAAT
Found at i:43078 original size:14 final size:14
Alignment explanation
Indices: 43059--43102 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
43049 GATAAAAGAA
43059 AAACAAAGAGAAAG
1 AAACAAAGAGAAAG
*
43073 AAACAAAGTGAAA-
1 AAACAAAGAGAAAG
43086 AAA-AAAGAGAAGAG
1 AAACAAAGAGAA-AG
43100 AAA
1 AAA
43103 GTGGACAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 7 0.27
13 4 0.15
14 15 0.58
ACGTcount: A:0.73, C:0.05, G:0.20, T:0.02
Consensus pattern (14 bp):
AAACAAAGAGAAAG
Found at i:44287 original size:4 final size:4
Alignment explanation
Indices: 44280--44323 Score: 60
Period size: 4 Copynumber: 12.0 Consensus size: 4
44270 ATACATCAAC
44280 ACAT ACAT ACAT ACAT ACAT --AT ACAT ACAT AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
44324 GATACATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 4 0.11
4 32 0.89
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:44305 original size:14 final size:14
Alignment explanation
Indices: 44284--44323 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
44274 ATCAACACAT
44284 ACATACATACATAC
1 ACATACATACATAC
*
44298 ATATACATACATAC
1 ACATACATACATAC
44312 ACATACATACAT
1 ACATACATACAT
44324 GATACATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (14 bp):
ACATACATACATAC
Found at i:44305 original size:18 final size:17
Alignment explanation
Indices: 44268--44323 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 17
44258 GATTGAGAAA
44268 ACATACAT-CAACACAT
1 ACATACATACAACACAT
*
44284 ACATACATACATACATAT
1 ACATACATACA-ACACAT
*
44302 ACATACATACACATACAT
1 ACATACATACA-ACACAT
44320 ACAT
1 ACAT
44324 GATACATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
16 8 0.24
17 2 0.06
18 24 0.71
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (17 bp):
ACATACATACAACACAT
Found at i:44321 original size:10 final size:10
Alignment explanation
Indices: 44268--44322 Score: 65
Period size: 10 Copynumber: 5.1 Consensus size: 10
44258 GATTGAGAAA
44268 ACATACATCAAC
1 ACATACAT--AC
44280 ACATACATAC
1 ACATACATAC
*
44290 ATACATACATAT
1 --ACATACATAC
44302 ACATACATAC
1 ACATACATAC
44312 ACATACATAC
1 ACATACATAC
44322 A
1 A
44323 TGATACATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
10 22 0.56
12 17 0.44
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (10 bp):
ACATACATAC
Found at i:44860 original size:105 final size:105
Alignment explanation
Indices: 44673--44862 Score: 283
Period size: 105 Copynumber: 1.8 Consensus size: 105
44663 TGAGAATTTT
* *
44673 AAAACAAATTGCGTATCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACT
1 AAAACAAATTGCGTATCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
44738 TAAAACAAAATTAATCTCACCTTAGATTGTTGTTTCTTTC
66 TAAAACAAAATTAATCTCACCTTAGATTGTTGTTTCTTTC
* * * * *
44778 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACA
1 AAAACAAATTGCGTATCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCAC-
* *
44843 TT-AAACAAAGTTGATCTCAC
65 TTAAAACAAAATTAATCTCAC
44863 TTGAGATCGT
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
105 73 0.97
106 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.38
Consensus pattern (105 bp):
AAAACAAATTGCGTATCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
TAAAACAAAATTAATCTCACCTTAGATTGTTGTTTCTTTC
Found at i:44919 original size:36 final size:36
Alignment explanation
Indices: 44873--44976 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
44863 TTGAGATCGT
* *
44873 TTTCTC-AAAAACAAACTTTGTCTCGCTTAAGACAA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
** *
44908 TTTCTCTAAAAACAAATTTTGTCTCATTTGAGACTA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
* *
44944 TATCT-T-AAAGCAAATTTTGTCTCGCTTGAGACA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACA
44977 TCATTTTCTC
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 23 0.40
35 7 0.12
36 28 0.48
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.37
Consensus pattern (36 bp):
TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
Found at i:45284 original size:26 final size:27
Alignment explanation
Indices: 45221--45317 Score: 115
Period size: 27 Copynumber: 3.5 Consensus size: 27
45211 TCTTGAGACA
* *
45221 GTTTCTCTTGAGATAAATCTTTGAGTCT
1 GTTTCTTTTGA-AAAAATCTTTGAGTCT
*
45249 GTTCCTTTTGAAAAAATCTTTGAGT-T
1 GTTTCTTTTGAAAAAATCTTTGAGTCT
45275 GTTTCTTTTGAAACAAATATCTTTGAGTCT
1 GTTTCTTTTG-AA-AAA-ATCTTTGAGTCT
*
45305 ATTTCTTTTGAAA
1 GTTTCTTTTGAAA
45318 CAAAGTTTTG
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
26 10 0.17
27 15 0.25
28 13 0.22
29 12 0.20
30 10 0.17
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.47
Consensus pattern (27 bp):
GTTTCTTTTGAAAAAATCTTTGAGTCT
Found at i:45312 original size:30 final size:29
Alignment explanation
Indices: 45235--45321 Score: 126
Period size: 30 Copynumber: 3.1 Consensus size: 29
45225 CTCTTGAGAT
*
45235 AAATCTTTGAGTCTGTTCCTTTTG-AA-A
1 AAATCTTTGAGTCTGTTTCTTTTGAAACA
45262 AAATCTTTGAGT-TGTTTCTTTTGAAACA
1 AAATCTTTGAGTCTGTTTCTTTTGAAACA
*
45290 AATATCTTTGAGTCTATTTCTTTTGAAACA
1 AA-ATCTTTGAGTCTGTTTCTTTTGAAACA
45320 AA
1 AA
45322 GTTTTGTCTC
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
26 10 0.19
27 14 0.26
28 3 0.06
29 10 0.19
30 17 0.31
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.45
Consensus pattern (29 bp):
AAATCTTTGAGTCTGTTTCTTTTGAAACA
Found at i:45440 original size:30 final size:30
Alignment explanation
Indices: 45400--45536 Score: 116
Period size: 30 Copynumber: 4.3 Consensus size: 30
45390 GACAATTTTG
*
45400 TGAAAAAAAAATCTTTGAGAT-TGTTTCTTT
1 TGAAACAAAAATCTTTGAG-TCTGTTTCTTT
45430 TGAAACAAAAATCTTTGAGTCTGTTTCTTT
1 TGAAACAAAAATCTTTGAGTCTGTTTCTTT
* * * **
45460 GGAAACAAAATTTGGTCTCTCTTAAGAT-AATTTCTTT
1 TGAAACAAAA------ATCT-TTGAG-TCTGTTTCTTT
45497 TGAAACAAAAATCTTTGAGTCTGTTTCTTT
1 TGAAACAAAAATCTTTGAGTCTGTTTCTTT
*
45527 GGAAACAAAA
1 TGAAACAAAA
45537 TTTTGTCTCT
Statistics
Matches: 85, Mismatches: 12, Indels: 20
0.73 0.10 0.17
Matches are distributed among these distances:
29 2 0.02
30 56 0.66
31 3 0.04
36 3 0.04
37 20 0.24
38 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (30 bp):
TGAAACAAAAATCTTTGAGTCTGTTTCTTT
Found at i:45531 original size:67 final size:67
Alignment explanation
Indices: 45423--45589 Score: 284
Period size: 67 Copynumber: 2.5 Consensus size: 67
45413 TTTGAGATTG
45423 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTGGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTGGTCTCTCTTAAGAT
45488 AA
66 AA
*
45490 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTGGTCTCTCTTAAGAT
*
45555 AT
66 AA
* *
45557 TTTCTTTT-AAA-AAAAATCTTTGAATTTGTTTCT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCT
45590 CTTAAAATGA
Statistics
Matches: 96, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
65 20 0.21
66 3 0.03
67 73 0.76
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.46
Consensus pattern (67 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTGGTCTCTCTTAAGAT
AA
Found at i:45613 original size:67 final size:65
Alignment explanation
Indices: 45423--45653 Score: 196
Period size: 67 Copynumber: 3.5 Consensus size: 65
45413 TTTGAGATTG
* * * *
45423 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAAT-TTGGTCTCTCTTAAGA
1 TTTCTTTT-AAA-AAAAATCTTTGAATATGTTTCTTTGAAAACAAAATGTT-ATCTCTCTTAAGA
45487 TAA
63 TAA
* * * * *
45490 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTT-AAA-AAAAATCTTTGAATATGTTTCTTTGAAAACAAAATGTTATCTCTCTTAAGAT
*
45555 AT
64 AA
* * * *
45557 TTTCTTTTAAAAAAAATCTTTGAATTTGTTTCTCTT-AAAATGAATTATGTTATCTCTCTTGAGA
1 TTTCTTTTAAAAAAAATCTTTGAATATGTTTCT-TTGAAAA-CAA-AATGTTATCTCTCTTAAGA
* *
45621 CAG
63 TAA
* * **
45624 TTTCTCTTGAAGTAAATCTTTGAATATGTT
1 TTTCTTTTAAAAAAAATCTTTGAATATGTT
45654 CATTTTGAAA
Statistics
Matches: 144, Mismatches: 16, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
65 23 0.16
66 7 0.05
67 112 0.78
68 2 0.01
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (65 bp):
TTTCTTTTAAAAAAAATCTTTGAATATGTTTCTTTGAAAACAAAATGTTATCTCTCTTAAGATAA
Found at i:46601 original size:28 final size:28
Alignment explanation
Indices: 46551--46633 Score: 107
Period size: 28 Copynumber: 2.9 Consensus size: 28
46541 TGTCGAGACA
46551 GTTTCTTTTGAAACACATTATCTTTGAG-CTT
1 GTTTCTTTTGAAACA-A--ATCTTTGAGTC-T
46582 GTTT-TTCTTGAAACAAATCTTTGAGTCT
1 GTTTCTT-TTGAAACAAATCTTTGAGTCT
46610 GTTTCTTTTGAAACAAATCTTTGA
1 GTTTCTTTTGAAACAAATCTTTGA
46634 ATCAATTTCT
Statistics
Matches: 49, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
28 31 0.63
29 3 0.06
30 3 0.06
31 12 0.24
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.47
Consensus pattern (28 bp):
GTTTCTTTTGAAACAAATCTTTGAGTCT
Found at i:46642 original size:28 final size:28
Alignment explanation
Indices: 46589--46643 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
46579 CTTGTTTTTC
* **
46589 TTGAAACAAATCTTTGAGTCTGTTTCTT
1 TTGAAACAAATCTTTGAATCAATTTCTT
46617 TTGAAACAAATCTTTGAATCAATTTCT
1 TTGAAACAAATCTTTGAATCAATTTCT
46644 CCTGAAGCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.44
Consensus pattern (28 bp):
TTGAAACAAATCTTTGAATCAATTTCTT
Found at i:46859 original size:40 final size:41
Alignment explanation
Indices: 46677--47151 Score: 191
Period size: 40 Copynumber: 10.9 Consensus size: 41
46667 TGGCCAGTCG
* *
46677 TCCTCATCACGTAGGAACCGTGTCATCCCCT-GACCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCATCCCCTAGACCAGAAC
* * * * *
46717 TCCTCATCATGTAGGAGCCATGTCA-ACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATCCCCTAG---ACCAGAAC
* *
46759 GTCCTCATCACGTAGGAACCGTGTTATCGCCCTACCTAAAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAGCCGTGTCAT---CC--CCT--AGA---CCAGAAC
* * * *
46811 TCTTCATCACGTATGAGCCGTGCCATCCCCT-GACCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCATCCCCTAGACCAGAAC
* * * * *
46851 TCCTCATCATGTAGGAGCCATGTCA-ACCATAGATAACCAG-TC
1 TCCTCATCACGTAGGAGCCGTGTCATCCCCTAG---ACCAGAAC
* *
46893 GTCCTCATCACGTAGGAACCGTGTTATCGCCCTACCTAAAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAGCCGTGTCAT---CC--CCT--AGA---CCAGAAC
* * * *
46945 TCTTCATCACGTATGAGCCGTGCCATCCCCT-GACCAGACC
1 TCCTCATCACGTAGGAGCCGTGTCATCCCCTAGACCAGAAC
*
46985 TCCTCATCACGTAGGAGCCGTGTCAT--CCTAGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATCCCCTAG---ACCAGAAC
* * *
47026 GTCCTCATCACGTAGGAATCGGGTTATCACTCCTCCTAAAGATGACCAGAAC
1 -TCCTCATCACGTAGG-AGC-CG-TGTCA-TCC-CCT----A-GACCAGAAC
* * * *
47078 TCTTCATCACGTATGAGCAGTGTCATCCCCT-GACCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCATCCCCTAGACCAGAAC
*
47118 TCCTCATCACGTAGGAGCCGTGTCA-CCCTTAGAC
1 TCCTCATCACGTAGGAGCCGTGTCATCCCCTAGAC
47152 GACCAGACCT
Statistics
Matches: 326, Mismatches: 56, Indels: 106
0.67 0.11 0.22
Matches are distributed among these distances:
38 3 0.01
39 11 0.03
40 112 0.34
41 2 0.01
42 23 0.07
43 58 0.18
44 1 0.00
45 4 0.01
46 10 0.03
47 5 0.02
48 10 0.03
49 8 0.02
50 2 0.01
51 72 0.22
52 3 0.01
53 1 0.00
54 1 0.00
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (41 bp):
TCCTCATCACGTAGGAGCCGTGTCATCCCCTAGACCAGAAC
Found at i:47121 original size:133 final size:134
Alignment explanation
Indices: 46659--47142 Score: 767
Period size: 134 Copynumber: 3.6 Consensus size: 134
46649 AGCCATGATC
* * * * *
46659 CCTAAAGATGGCCAG-TCGTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGATCTCCTCA
1 CCTAAAGATGGCCAGAAC-TCTTCATCACGTATGAGCCGTGCCATCCCCTGACCAGATCTCCTCA
*
46723 TCATGTAGGAGCCATGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCG
65 TCACGTAGGAGCCATGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCG
46788 CCCTA
130 CCCTA
46793 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGCCATCCCCTGACCAGATCTCCTCAT
1 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGCCATCCCCTGACCAGATCTCCTCAT
* *
46858 CATGTAGGAGCCATGTCAACCATAGATAACCAGTCGTCCTCATCACGTAGGAACCGTGTTATCGC
66 CACGTAGGAGCCATGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCGC
46923 CCTA
131 CCTA
*
46927 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGCCATCCCCTGACCAGACCTCCTCAT
1 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGCCATCCCCTGACCAGATCTCCTCAT
* * * * *
46992 CACGTAGGAGCCGTGTCATCC-TAGATAACCAGCCGTCCTCATCACGTAGGAATCGGGTTATCAC
66 CACGTAGGAGCCATGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCGC
47056 TCCT-
131 -CCTA
* * *
47060 CCTAAAGATGACCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGATCTCCTCAT
1 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGCCATCCCCTGACCAGATCTCCTCAT
*
47125 CACGTAGGAGCCGTGTCA
66 CACGTAGGAGCCATGTCA
47143 CCCTTAGACG
Statistics
Matches: 330, Mismatches: 18, Indels: 5
0.93 0.05 0.01
Matches are distributed among these distances:
133 118 0.36
134 211 0.64
135 1 0.00
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (134 bp):
CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGCCATCCCCTGACCAGATCTCCTCAT
CACGTAGGAGCCATGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCGC
CCTA
Found at i:47135 original size:267 final size:268
Alignment explanation
Indices: 46659--47142 Score: 776
Period size: 267 Copynumber: 1.8 Consensus size: 268
46649 AGCCATGATC
* * *
46659 CCTAAAGATGGCCAGTCGTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGATCTCCTCAT
1 CCTAAAGATGGCCAGACGTCCTCATCACGTAGGAACCGTGCCATCCCCTGACCAGACCTCCTCAT
* * *
46724 CATGTAGGAGCCATGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCGC
66 CACGTAGGAGCCATGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGGGTTATCAC
* *
46789 CCTACCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGCCATCCCCTGACCAGATCTCC
131 CCTACCTAAAGATGACCAGAACTCTTCATCACGTATGAGCAGTGCCATCCCCTGACCAGATCTCC
*
46854 TCATCATGTAGGAGCCATGTCAACCATAGATAACCAGTCGTCCTCATCACGTAGGAACCGTGTTA
196 TCATCACGTAGGAGCCATGTCAACCATAGATAACCAGTCGTCCTCATCACGTAGGAACCGTGTTA
46919 TCGCCCTA
261 TCGCCCTA
* * *
46927 CCTAAAGATGGCCAGAAC-TCTTCATCACGTATGAGCCGTGCCATCCCCTGACCAGACCTCCTCA
1 CCTAAAGATGGCCAG-ACGTCCTCATCACGTAGGAACCGTGCCATCCCCTGACCAGACCTCCTCA
* * *
46991 TCACGTAGGAGCCGTGTCATCC-TAGATAACCAGCCGTCCTCATCACGTAGGAATCGGGTTATCA
65 TCACGTAGGAGCCATGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGGGTTATCA
*
47055 CTCCT-CCTAAAGATGACCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCTGACCAGATCT
130 C-CCTACCTAAAGATGACCAGAACTCTTCATCACGTATGAGCAGTGCCATCCCCTGACCAGATCT
*
47119 CCTCATCACGTAGGAGCCGTGTCA
194 CCTCATCACGTAGGAGCCATGTCA
47143 CCCTTAGACG
Statistics
Matches: 197, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
267 118 0.60
268 78 0.40
269 1 0.01
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (268 bp):
CCTAAAGATGGCCAGACGTCCTCATCACGTAGGAACCGTGCCATCCCCTGACCAGACCTCCTCAT
CACGTAGGAGCCATGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGGGTTATCAC
CCTACCTAAAGATGACCAGAACTCTTCATCACGTATGAGCAGTGCCATCCCCTGACCAGATCTCC
TCATCACGTAGGAGCCATGTCAACCATAGATAACCAGTCGTCCTCATCACGTAGGAACCGTGTTA
TCGCCCTA
Found at i:47184 original size:43 final size:40
Alignment explanation
Indices: 47068--47190 Score: 122
Period size: 40 Copynumber: 3.0 Consensus size: 40
47058 CTCCTAAAGA
47068 TGACCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCC
1 TGACCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCC
* * * * *
47108 TGACCAGATCTCCTCATCACGTAGGAGCCGTGTCA-CCCT
1 TGACCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCC
* ** *
47147 TAGACGACCAGACCTCTTCATTGCGTATGAGCAGTGTCGTCCCC
1 T----GACCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCC
47191 ACCAACAAAA
Statistics
Matches: 65, Mismatches: 13, Indels: 6
0.77 0.15 0.07
Matches are distributed among these distances:
39 4 0.06
40 31 0.48
43 27 0.42
44 3 0.05
ACGTcount: A:0.22, C:0.33, G:0.20, T:0.24
Consensus pattern (40 bp):
TGACCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCC
Found at i:47347 original size:3 final size:3
Alignment explanation
Indices: 47341--47389 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
47331 CTTTTTTTAA
** *
47341 TAT TAT TAT TAT TAT CGT TA- TAT TAT TAT TAT TAC TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
47388 TA
1 TA
47390 ATTTACAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:47868 original size:33 final size:31
Alignment explanation
Indices: 47831--47893 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
47821 CAGACAGAGG
47831 GGGGACTCATTCGGAGATTTCCAGAAAAAAAAA
1 GGGGACTCATTCGG-G-TTTCCAGAAAAAAAAA
* * *
47864 GGGGATTCATTCGGGTTTTCAGAGAAAAAA
1 GGGGACTCATTCGGGTTTCCAGAAAAAAAA
47894 TTCCATTCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 13 0.48
32 1 0.04
33 13 0.48
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.22
Consensus pattern (31 bp):
GGGGACTCATTCGGGTTTCCAGAAAAAAAAA
Found at i:53378 original size:88 final size:88
Alignment explanation
Indices: 53219--53395 Score: 273
Period size: 88 Copynumber: 2.0 Consensus size: 88
53209 ACAGCATCAG
* * * * *
53219 CCACAGATCTTACTCATATGTCAAATGTTGGGTTAACTGGTTTTAATGCTAATTTGAAGATGCGC
1 CCACAGATCTTACTCACATGTCAAATGGTGGGTTAACTGGTTTTAATGATAATTTGAAGACGCGA
*
53284 GTTTTTCATTCCCTTTTGGGTAT
66 GGTTTTCATTCCCTTTTGGGTAT
* *
53307 CCACAGATCTTACTCACATGTCAAGTGGTGGGTTAACTGGTTTTAATGATATTTTGAAGACGCGA
1 CCACAGATCTTACTCACATGTCAAATGGTGGGTTAACTGGTTTTAATGATAATTTGAAGACGCGA
*
53372 GGTTTTCATTCCTTTTTGGGTAT
66 GGTTTTCATTCCCTTTTGGGTAT
53395 C
1 C
53396 TCCAACCATA
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 80 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (88 bp):
CCACAGATCTTACTCACATGTCAAATGGTGGGTTAACTGGTTTTAATGATAATTTGAAGACGCGA
GGTTTTCATTCCCTTTTGGGTAT
Found at i:60924 original size:18 final size:18
Alignment explanation
Indices: 60901--60947 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
60891 TTACGGAATG
*
60901 TAAGATTATTAA-AGGAAA
1 TAAGATTACTAACA-GAAA
60919 TAAGATTACTAACAGAAA
1 TAAGATTACTAACAGAAA
*
60937 TAAAATTACTA
1 TAAGATTACTA
60948 CGAATGTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 25 0.96
19 1 0.04
ACGTcount: A:0.55, C:0.06, G:0.11, T:0.28
Consensus pattern (18 bp):
TAAGATTACTAACAGAAA
Found at i:62384 original size:2 final size:2
Alignment explanation
Indices: 62372--62403 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
62362 GATTAGATTT
62372 TA TA T- 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 T
62404 TGGAAAATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:63821 original size:31 final size:31
Alignment explanation
Indices: 63785--63843 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
63775 AACTTAAAAG
*
63785 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
63816 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
63844 ACATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:63892 original size:22 final size:22
Alignment explanation
Indices: 63867--64401 Score: 763
Period size: 22 Copynumber: 24.4 Consensus size: 22
63857 ATAATAAATT
63867 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
63889 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
63911 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
63933 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
***
63955 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
63977 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
63999 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
64021 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* **
64043 TTTTTAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
64065 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* *
64087 TTTTATAATAAATTAATCCATA
1 TTTTAAAATAAATCAATCCATA
64109 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
64131 TTTTAAAATAATTCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*** *
64153 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
*
64175 -TTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
* *** *
64196 -TTTAAAATAATTTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
64217 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
64239 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
64261 TTTTAAAATAAACCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
64283 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
*
64305 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
***
64327 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
64349 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
64371 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
64393 TTTTAAAAT
1 TTTTAAAAT
64402 TTTAAAATTT
Statistics
Matches: 457, Mismatches: 51, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
21 43 0.09
22 406 0.89
23 8 0.02
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:71479 original size:31 final size:31
Alignment explanation
Indices: 71444--71518 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
71434 TCAAAAAACA
*
71444 TAAGATATGGTC-CCTTTCATTTTTATTTAAT
1 TAAGATATGGTCACCTTT-AGTTTTATTTAAT
* * *
71475 TAAGATAGGGTCACCTTTGGTTTTATTTTAT
1 TAAGATATGGTCACCTTTAGTTTTATTTAAT
*
71506 TAAGATGTGGTCA
1 TAAGATATGGTCA
71519 TCACGGGTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
31 32 0.86
32 5 0.14
ACGTcount: A:0.25, C:0.11, G:0.17, T:0.47
Consensus pattern (31 bp):
TAAGATATGGTCACCTTTAGTTTTATTTAAT
Found at i:73648 original size:44 final size:45
Alignment explanation
Indices: 73582--73673 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 45
73572 GAGTCGAGGG
* *
73582 TTCTACGAGGTCCTTCGGGAC-ATATATGTGGTCATTCGGGACAA
1 TTCTACGAGGTCCTCCGGGACAATATATGTGGTCATCCGGGACAA
* * *
73626 TTCTACTAGGTCCTCCGTGACATATATATGTGGTCCTCCGGGACAA
1 TTCTACGAGGTCCTCCGGGACA-ATATATGTGGTCATCCGGGACAA
73672 TT
1 TT
73674 TTATATGACA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
44 18 0.44
46 23 0.56
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.32
Consensus pattern (45 bp):
TTCTACGAGGTCCTCCGGGACAATATATGTGGTCATCCGGGACAA
Found at i:73930 original size:18 final size:18
Alignment explanation
Indices: 73887--73930 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
73877 TAAAAGGAAT
73887 TAATGATAAAAATATTGA
1 TAATGATAAAAATATTGA
* * *
73905 TAACGATAAGAATGTTGA
1 TAATGATAAAAATATTGA
*
73923 TGATGATA
1 TAATGATA
73931 TATATGTATG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.48, C:0.02, G:0.18, T:0.32
Consensus pattern (18 bp):
TAATGATAAAAATATTGA
Found at i:74525 original size:30 final size:30
Alignment explanation
Indices: 74467--74526 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
74457 CAATCTGGTC
* *
74467 ATATTTTTAAATAAATTTTAACATAAAATAT
1 ATATTTTTAAATAAA-TATAAAATAAAATAT
74498 ATATTTTTAAATGAAA-ATAAAATAAAATA
1 ATATTTTTAAAT-AAATATAAAATAAAATA
74527 ATTTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.42
31 12 0.46
32 3 0.12
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (30 bp):
ATATTTTTAAATAAATATAAAATAAAATAT
Found at i:74547 original size:26 final size:26
Alignment explanation
Indices: 74518--74584 Score: 77
Period size: 25 Copynumber: 2.6 Consensus size: 26
74508 ATGAAAATAA
*
74518 AATAAAATAATTTTAAATTAGTTAAT
1 AATAAAATAATTTTAAATAAGTTAAT
74544 AATAAAAT-ATATTT-AATAAGTTAAT
1 AATAAAATAAT-TTTAAATAAGTTAAT
*
74569 -ATAAAAATATTTTTAA
1 AAT-AAAATAATTTTAA
74585 GTTAATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
24 2 0.06
25 20 0.57
26 13 0.37
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (26 bp):
AATAAAATAATTTTAAATAAGTTAAT
Found at i:74575 original size:25 final size:23
Alignment explanation
Indices: 74537--74604 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 23
74527 ATTTTAAATT
74537 AGTTAATA-ATAAAATATATTTAATA
1 AGTTAATATATAAAATAT-TTT--TA
74562 AGTTAATATA-AAAATATTTTTA
1 AGTTAATATATAAAATATTTTTA
74584 AGTTAATATATATAAAATATT
1 AGTT-A-ATATATAAAATATT
74605 ATGAATTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.15
23 1 0.03
24 8 0.21
25 23 0.59
26 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
AGTTAATATATAAAATATTTTTA
Found at i:74585 original size:22 final size:24
Alignment explanation
Indices: 74519--74593 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 24
74509 TGAAAATAAA
*
74519 ATAAAATA-ATTTTAAATTAGTTAAT
1 ATAAAATATA-TTT-AATAAGTTAAT
74544 AATAAAATATATTTAATAAGTTAAT
1 -ATAAAATATATTTAATAAGTTAAT
*
74569 ATAAAA-ATATTT-TTAAGTTAAT
1 ATAAAATATATTTAATAAGTTAAT
74591 ATA
1 ATA
74594 TATAAAATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
22 12 0.26
23 6 0.13
24 6 0.13
25 10 0.22
26 11 0.24
27 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
ATAAAATATATTTAATAAGTTAAT
Found at i:74614 original size:25 final size:24
Alignment explanation
Indices: 74537--74615 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 24
74527 ATTTTAAATT
74537 AGTTAATA-ATAAAATATATTTAAT-A
1 AGTTAATATATAAAA-ATA-TT-ATGA
* *
74562 AGTT-A-ATATAAAAATATTTTTA
1 AGTTAATATATAAAAATATTATGA
74584 AGTTAATATATATAAAATATTATGA
1 AGTTAATATATA-AAAATATTATGA
*
74609 ATTTAAT
1 AGTTAAT
74616 TATTATACAC
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
21 1 0.02
22 7 0.16
23 5 0.11
24 12 0.27
25 20 0.44
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (24 bp):
AGTTAATATATAAAAATATTATGA
Found at i:82375 original size:10 final size:9
Alignment explanation
Indices: 82356--82390 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 9
82346 CATATAATTA
82356 TTTATTTAT
1 TTTATTTAT
82365 TTTATTTTAT
1 TTTA-TTTAT
82375 TTTATTTAT
1 TTTATTTAT
82384 TATTATT
1 T-TTATT
82391 GTTAATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 10 0.42
10 14 0.58
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTATTTAT
Found at i:83218 original size:38 final size:38
Alignment explanation
Indices: 83167--83242 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
83157 AAGGGAGAAA
83167 GGCTTTGGTTATAAAGGTTATGCTTTCCATCGTGTCAT
1 GGCTTTGGTTATAAAGGTTATGCTTTCCATCGTGTCAT
*
83205 GGCTTTGGTTATAAAGGTTCTGCTTTCCATCGTGTCAT
1 GGCTTTGGTTATAAAGGTTATGCTTTCCATCGTGTCAT
83243 TAAAGATTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.42
Consensus pattern (38 bp):
GGCTTTGGTTATAAAGGTTATGCTTTCCATCGTGTCAT
Found at i:83468 original size:10 final size:9
Alignment explanation
Indices: 83453--83523 Score: 52
Period size: 10 Copynumber: 7.3 Consensus size: 9
83443 ATGGTATTTG
83453 TTTTATTTTA
1 TTTT-TTTTA
83463 TTTTATTATTA
1 TTTT-TT-TTA
83474 TTTTTTTTA
1 TTTTTTTTA
*
83483 ATTTTTTTA
1 TTTTTTTTA
* *
83492 ATTTTTTAA
1 TTTTTTTTA
*
83501 TATTTGTTTA
1 T-TTTTTTTA
*
83511 TTGTTTATTA
1 TT-TTTTTTA
83521 TTT
1 TTT
83524 AATATTTTTG
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
9 21 0.41
10 23 0.45
11 7 0.14
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:85958 original size:16 final size:17
Alignment explanation
Indices: 85937--85977 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
85927 CTAAAAATTA
*
85937 TATATTTTTA-AATGAT
1 TATATTTTTATAATAAT
85953 TATATTTTTATAATAAT
1 TATATTTTTATAATAAT
*
85970 AATATTTT
1 TATATTTT
85978 CACCTTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
TATATTTTTATAATAAT
Found at i:86065 original size:15 final size:16
Alignment explanation
Indices: 86053--86093 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
86043 CAAATTTTTA
86053 ATATT-TTATTTTTGT
1 ATATTATTATTTTTGT
* *
86068 ATATTATTATTATTAT
1 ATATTATTATTTTTGT
86084 -TATTATTATT
1 ATATTATTATT
86094 ATTATTAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
ATATTATTATTTTTGT
Found at i:86077 original size:3 final size:3
Alignment explanation
Indices: 86069--86100 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
86059 TATTTTTGTA
86069 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
86101 AGTTTATAAT
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):
TAT
Found at i:87065 original size:22 final size:22
Alignment explanation
Indices: 87025--87066 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
87015 TTTTTGGTCC
*
87025 TTAAATTGTTTAACTTTTTTAT
1 TTAAATTGTTTAAATTTTTTAT
87047 TTAAATT-TTTAAATCTTTTT
1 TTAAATTGTTTAAAT-TTTTT
87067 GGTATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (22 bp):
TTAAATTGTTTAAATTTTTTAT
Found at i:87315 original size:32 final size:32
Alignment explanation
Indices: 87279--87347 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
87269 TAAGGGTCAA
*
87279 GAAAGTCATATACCCTTTTATTATGTCATTTT
1 GAAAGTCATATACCCTTTTATTACGTCATTTT
87311 GAAAGTCATATACCCTTTTATTACGTCATTTT
1 GAAAGTCATATACCCTTTTATTACGTCATTTT
87343 GAAAG
1 GAAAG
87348 CTAAATAAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (32 bp):
GAAAGTCATATACCCTTTTATTACGTCATTTT
Found at i:88785 original size:19 final size:19
Alignment explanation
Indices: 88761--88797 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
88751 CAATCCTAAC
88761 AATTAGGCCATAATTTAGT
1 AATTAGGCCATAATTTAGT
*
88780 AATTAGGCTATAATTTAG
1 AATTAGGCCATAATTTAG
88798 GCAACTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (19 bp):
AATTAGGCCATAATTTAGT
Found at i:92068 original size:45 final size:45
Alignment explanation
Indices: 92004--92090 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
91994 AGAGAGACAT
*
92004 GGTGTGCATGGCGGACTCAATATCCGTCATAGCCCACTGGGACGC
1 GGTGTGCATGGCGGACTCAATATCCGTCAGAGCCCACTGGGACGC
* *
92049 GGTGTGTATGGCGGACTCAATATCCGTCGGAGCCCACTGGGA
1 GGTGTGCATGGCGGACTCAATATCCGTCAGAGCCCACTGGGA
92091 TGCTGTAGCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.20, C:0.26, G:0.33, T:0.21
Consensus pattern (45 bp):
GGTGTGCATGGCGGACTCAATATCCGTCAGAGCCCACTGGGACGC
Found at i:92153 original size:23 final size:24
Alignment explanation
Indices: 92120--92176 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 24
92110 TACTGTTGGG
*
92120 GTCGTGCTCCTAGAATACCA-GCT
1 GTCGTGGTCCTAGAATACCAGGCT
* *
92143 GTCGTGGTCCTAGAATACTAGGTT
1 GTCGTGGTCCTAGAATACCAGGCT
92167 GTCGTGGTCC
1 GTCGTGGTCC
92177 AACTTGTCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 18 0.60
24 12 0.40
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.30
Consensus pattern (24 bp):
GTCGTGGTCCTAGAATACCAGGCT
Found at i:93327 original size:19 final size:19
Alignment explanation
Indices: 93303--93339 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
93293 CAATCCTTAC
93303 AATTAGGCTATAATTTAGT
1 AATTAGGCTATAATTTAGT
93322 AATTAGGCTATAATTTAG
1 AATTAGGCTATAATTTAG
93340 GCAACTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.41
Consensus pattern (19 bp):
AATTAGGCTATAATTTAGT
Found at i:93757 original size:32 final size:32
Alignment explanation
Indices: 93720--93786 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
93710 ACACTAGTTA
93720 TAGTATTGCATCTCGATGGATATAAATTTAGT
1 TAGTATTGCATCTCGATGGATATAAATTTAGT
*
93752 TAGTATTGCATCTCGATGGATATAGATTTAGT
1 TAGTATTGCATCTCGATGGATATAAATTTAGT
93784 TAG
1 TAG
93787 GCTTGATACA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (32 bp):
TAGTATTGCATCTCGATGGATATAAATTTAGT
Found at i:95024 original size:52 final size:52
Alignment explanation
Indices: 94941--95046 Score: 194
Period size: 52 Copynumber: 2.0 Consensus size: 52
94931 AAAATTGAAG
*
94941 TACCAATCTCTCATTTTCTCTAACGAATATTTCTAGCACTCGTCATCTTAAA
1 TACCAATCTCTCATTTTCTCTAACGAATATTTCCAGCACTCGTCATCTTAAA
*
94993 TACCGATCTCTCATTTTCTCTAACGAATATTTCCAGCACTCGTCATCTTAAA
1 TACCAATCTCTCATTTTCTCTAACGAATATTTCCAGCACTCGTCATCTTAAA
95045 TA
1 TA
95047 AGGAATCACG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.28, C:0.27, G:0.07, T:0.38
Consensus pattern (52 bp):
TACCAATCTCTCATTTTCTCTAACGAATATTTCCAGCACTCGTCATCTTAAA
Found at i:97869 original size:27 final size:27
Alignment explanation
Indices: 97831--98085 Score: 314
Period size: 27 Copynumber: 9.4 Consensus size: 27
97821 CTTATAGATA
*
97831 CAGATCACCATCAACTGTCCGACGTCG
1 CAGATCACCATCACCTGTCCGACGTCG
* *
97858 CAGATCACCATCAACTATCCGACGTCG
1 CAGATCACCATCACCTGTCCGACGTCG
97885 CAGATCACCATCACCTGTCCGACGTCG
1 CAGATCACCATCACCTGTCCGACGTCG
97912 CAGATCACCATCACCTGTCCGACGTCG
1 CAGATCACCATCACCTGTCCGACGTCG
*
97939 CAGATCACCATCACCTGTCCAACGTCG
1 CAGATCACCATCACCTGTCCGACGTCG
*
97966 CAGATCACCATCACCTGTCCGACATCG
1 CAGATCACCATCACCTGTCCGACGTCG
* * * ** *
97993 TAGGTCACCTTCACCAATCCGGCGTCG
1 CAGATCACCATCACCTGTCCGACGTCG
* ** * *
98020 CAGATCA-CAGTCTCCTAACCGGCGTCA
1 CAGATCACCA-TCACCTGTCCGACGTCG
* ** *
98047 CAGATCACCATCTCCCATCCGGCGTCG
1 CAGATCACCATCACCTGTCCGACGTCG
98074 CAGATCACCATC
1 CAGATCACCATC
98086 TCCCATCCGA
Statistics
Matches: 203, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 1 0.00
27 200 0.99
28 2 0.01
ACGTcount: A:0.24, C:0.40, G:0.17, T:0.19
Consensus pattern (27 bp):
CAGATCACCATCACCTGTCCGACGTCG
Found at i:98107 original size:27 final size:27
Alignment explanation
Indices: 98044--98109 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
98034 CTAACCGGCG
* * *
98044 TCACAGATCACCATCTCCCATCCGGCG
1 TCACAAATCACCATCTCCCATCCGACA
* *
98071 TCGCAGATCACCATCTCCCATCCGACA
1 TCACAAATCACCATCTCCCATCCGACA
*
98098 TCATAAATCACC
1 TCACAAATCACC
98110 GGTATCAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.27, C:0.42, G:0.11, T:0.20
Consensus pattern (27 bp):
TCACAAATCACCATCTCCCATCCGACA
Found at i:98249 original size:24 final size:24
Alignment explanation
Indices: 98222--98290 Score: 120
Period size: 24 Copynumber: 2.9 Consensus size: 24
98212 TTCGTCAACA
98222 CATCGTAGATCTCCATTACCTGTT
1 CATCGTAGATCTCCATTACCTGTT
98246 CATCGTAGATCTCCATTACCTGTT
1 CATCGTAGATCTCCATTACCTGTT
* *
98270 CATTGTAGATCTCCATCACCT
1 CATCGTAGATCTCCATTACCT
98291 TTGCAAAACA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.22, C:0.30, G:0.12, T:0.36
Consensus pattern (24 bp):
CATCGTAGATCTCCATTACCTGTT
Found at i:101494 original size:22 final size:23
Alignment explanation
Indices: 101454--101496 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
101444 ACTTTTAAAT
* *
101454 TTTTTATTTTTTAAGAAATAATA
1 TTTTTATTATTCAAGAAATAATA
101477 TTTTTATTATTCAA-AAATAA
1 TTTTTATTATTCAAGAAATAA
101497 AAAATATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
TTTTTATTATTCAAGAAATAATA
Found at i:102470 original size:32 final size:32
Alignment explanation
Indices: 102429--102550 Score: 210
Period size: 32 Copynumber: 3.8 Consensus size: 32
102419 GAGTCAAGGG
*
102429 TTACCTATGTCCTTTGGGACATATGGACATGA
1 TTACCTATGTCCTTCGGGACATATGGACATGA
102461 TTACCTATGTCCTTCGGGACATATGGACATGA
1 TTACCTATGTCCTTCGGGACATATGGACATGA
102493 TTACCTATGTCCTTCGGGACATATGGACATG-
1 TTACCTATGTCCTTCGGGACATATGGACATGA
* *
102524 TTACCTATGTTCTTCGGAACATATGGA
1 TTACCTATGTCCTTCGGGACATATGGA
102551 TAGGTCCTTA
Statistics
Matches: 87, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
31 25 0.29
32 62 0.71
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (32 bp):
TTACCTATGTCCTTCGGGACATATGGACATGA
Found at i:102807 original size:17 final size:16
Alignment explanation
Indices: 102782--102819 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
102772 ATGATTATAC
102782 GATAAAATAT-ATTAAT
1 GATAAAATATGA-TAAT
102798 GATAATAATATGATAAT
1 GATAA-AATATGATAAT
102815 GATAA
1 GATAA
102820 GAAAGAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 5 0.25
17 14 0.70
18 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (16 bp):
GATAAAATATGATAAT
Found at i:105856 original size:16 final size:16
Alignment explanation
Indices: 105831--105864 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
105821 TGTAAATGAA
*
105831 AAAAAGGAAATAAAAC
1 AAAAAGGAAAGAAAAC
*
105847 AAAAATGAAAGAAAAC
1 AAAAAGGAAAGAAAAC
105863 AA
1 AA
105865 GTCAATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.76, C:0.06, G:0.12, T:0.06
Consensus pattern (16 bp):
AAAAAGGAAAGAAAAC
Found at i:107294 original size:34 final size:32
Alignment explanation
Indices: 107241--107310 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
107231 CCTTACAAAC
*
107241 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
107273 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
107307 TCCC
1 TCCC
107311 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:107687 original size:20 final size:20
Alignment explanation
Indices: 107658--107719 Score: 97
Period size: 20 Copynumber: 3.1 Consensus size: 20
107648 CCGTTAGACA
*
107658 GGGGGAAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
107678 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
* *
107698 GGGGGGGATCTGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
107718 GG
1 GG
107720 ACATTCTGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.15, C:0.29, G:0.40, T:0.16
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCCCT
Found at i:109241 original size:19 final size:20
Alignment explanation
Indices: 109198--109245 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
109188 TCTAAATCCT
*
109198 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
109218 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
109237 TTTTCAAAA
1 TTTTCAAAA
109246 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:110546 original size:20 final size:20
Alignment explanation
Indices: 110521--110560 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
110511 CGTTAGACAA
110521 GGGGGAATCGGTACCCCTGG
1 GGGGGAATCGGTACCCCTGG
*
110541 GGGGGAATCTGTACCCCTGG
1 GGGGGAATCGGTACCCCTGG
110561 ACATTCTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.25, G:0.42, T:0.17
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCTGG
Found at i:110974 original size:37 final size:37
Alignment explanation
Indices: 110890--110967 Score: 138
Period size: 37 Copynumber: 2.1 Consensus size: 37
110880 TGGACTTGCC
* *
110890 TTTGACTTGGACCGGGATGGACTTTGTTGGACTTTTA
1 TTTGACTTGGACCAGGATGGACTTTGTTCGACTTTTA
110927 TTTGACTTGGACCAGGATGGACTTTGTTCGACTTTTA
1 TTTGACTTGGACCAGGATGGACTTTGTTCGACTTTTA
110964 TTTG
1 TTTG
110968 GATTGGATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.17, C:0.14, G:0.27, T:0.42
Consensus pattern (37 bp):
TTTGACTTGGACCAGGATGGACTTTGTTCGACTTTTA
Found at i:111004 original size:3 final size:3
Alignment explanation
Indices: 110996--111114 Score: 146
Period size: 3 Copynumber: 41.3 Consensus size: 3
110986 AAATAAACTG
110996 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
111044 AAT AAT AAT AAT AAT -AT AAT -AT AAT -AT AAT AA- ATAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
*
111085 -AT AA- AAT AAT -AT ATAT TAT AAT AAAT AAT A
1 AAT AAT AAT AAT AAT A-AT AAT AAT -AAT AAT A
111115 CATACACTAT
Statistics
Matches: 103, Mismatches: 2, Indels: 22
0.81 0.02 0.17
Matches are distributed among these distances:
2 15 0.15
3 82 0.80
4 6 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:111141 original size:16 final size:17
Alignment explanation
Indices: 111120--111215 Score: 65
Period size: 16 Copynumber: 5.5 Consensus size: 17
111110 TAATACATAC
*
111120 ACTATAT-TATTTTAAA
1 ACTATATATATTTCAAA
111136 ACTATATATATTTCAAA
1 ACTATATATATTTCAAA
* *
111153 ATTATAATATGTTTTCAAAA
1 ACTAT-ATAT-ATTTC-AAA
*
111173 ATTATATATATATTTTCAAA
1 A--CTATATATA-TTTCAAA
111193 A--ATATAT-TTTCAAA
1 ACTATATATATTTCAAA
*
111207 ACCATATAT
1 ACTATATAT
111216 TATATACATT
Statistics
Matches: 66, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
14 8 0.12
16 19 0.29
17 12 0.18
18 4 0.06
19 4 0.06
20 8 0.12
21 8 0.12
22 3 0.05
ACGTcount: A:0.46, C:0.08, G:0.01, T:0.45
Consensus pattern (17 bp):
ACTATATATATTTCAAA
Found at i:111162 original size:20 final size:20
Alignment explanation
Indices: 111139--111198 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
111129 TTTTAAAACT
111139 ATATATATTTCAAAATTATA
1 ATATATATTTCAAAATTATA
*
111159 ATATGT-TTTCAAAAATTAT-
1 ATATATATTTC-AAAATTATA
*
111178 ATATATATTTTCAAAAATATA
1 ATATATA-TTTCAAAATTATA
111199 TTTTCAAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 9 0.27
20 20 0.61
21 4 0.12
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (20 bp):
ATATATATTTCAAAATTATA
Found at i:111199 original size:18 final size:18
Alignment explanation
Indices: 111122--111199 Score: 72
Period size: 18 Copynumber: 4.3 Consensus size: 18
111112 ATACATACAC
*
111122 TATAT-TATTTT-AAAAC
1 TATATATATTTTCAAAAA
*
111138 TATATATA-TTTCAAAAT
1 TATATATATTTTCAAAAA
*
111155 TATAATATGTTTTCAAAAATTA
1 TAT-ATATATTTTC-AAAA--A
111177 TATATATATTTTCAAAAA
1 TATATATATTTTCAAAAA
111195 TATAT
1 TATAT
111200 TTTCAAAACC
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
16 8 0.16
17 9 0.18
18 10 0.20
19 4 0.08
20 8 0.16
21 9 0.18
22 3 0.06
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.47
Consensus pattern (18 bp):
TATATATATTTTCAAAAA
Found at i:111199 original size:20 final size:20
Alignment explanation
Indices: 111138--111199 Score: 83
Period size: 21 Copynumber: 3.1 Consensus size: 20
111128 ATTTTAAAAC
*
111138 TATATATA-TTTCAAAATTA
1 TATATATATTTTCAAAAATA
*
111157 TA-ATATGTTTTCAAAAATTA
1 TATATATATTTTCAAAAA-TA
111177 TATATATATTTTCAAAAATA
1 TATATATATTTTCAAAAATA
111197 TAT
1 TAT
111200 TTTCAAAACC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 4 0.11
19 10 0.27
20 9 0.24
21 14 0.38
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (20 bp):
TATATATATTTTCAAAAATA
Found at i:111216 original size:16 final size:14
Alignment explanation
Indices: 111180--111207 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
111170 AAAATTATAT
111180 ATATATTTTCAAAA
1 ATATATTTTCAAAA
111194 ATATATTTTCAAAA
1 ATATATTTTCAAAA
111208 CCATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATATTTTCAAAA
Found at i:111843 original size:4 final size:4
Alignment explanation
Indices: 111834--111869 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
111824 TATTACGGTA
111834 TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG
111870 CTTTTCATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:117618 original size:2 final size:2
Alignment explanation
Indices: 117611--117635 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
117601 CTATAAAATG
117611 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
117636 GTTTTGAAAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:118714 original size:5 final size:5
Alignment explanation
Indices: 118704--118732 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
118694 CACACAAATA
118704 ACTAT ACTAT ACTAT ACTAT ACTAT ACTA
1 ACTAT ACTAT ACTAT ACTAT ACTAT ACTA
118733 CGTGTATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (5 bp):
ACTAT
Found at i:120729 original size:19 final size:19
Alignment explanation
Indices: 120705--120742 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
120695 GAATTGAAGT
120705 TTAGGAGATGATGGTTATG
1 TTAGGAGATGATGGTTATG
120724 TTAGGAGATGATGGTTATG
1 TTAGGAGATGATGGTTATG
120743 ATTCTTACCT
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:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (19 bp):
TTAGGAGATGATGGTTATG
Found at i:122590 original size:21 final size:21
Alignment explanation
Indices: 122564--122621 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
122554 ACTATTGTCC
**
122564 AAGGGATCGATCCTTTTTTCA
1 AAGGGATCGATCCTTTGGTCA
** *
122585 AAGGGATATATCATTTGGTCA
1 AAGGGATCGATCCTTTGGTCA
*
122606 AATGGATCGATCCTTT
1 AAGGGATCGATCCTTT
122622 AAGCTAGAGA
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.36
Consensus pattern (21 bp):
AAGGGATCGATCCTTTGGTCA
Found at i:129035 original size:15 final size:15
Alignment explanation
Indices: 129017--129078 Score: 58
Period size: 15 Copynumber: 4.3 Consensus size: 15
129007 CAATCATCAC
* *
129017 CACCTCCATCACCAT
1 CACCACCATCAACAT
*
129032 CACCACCATGAACAT
1 CACCACCATCAACAT
*
129047 ---CACCATCACCAT
1 CACCACCATCAACAT
*
129059 CACCACCATGAACAT
1 CACCACCATCAACAT
129074 CACCA
1 CACCA
129079 TCACAGCAGC
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
12 10 0.27
15 27 0.73
ACGTcount: A:0.35, C:0.47, G:0.03, T:0.15
Consensus pattern (15 bp):
CACCACCATCAACAT
Found at i:129038 original size:21 final size:21
Alignment explanation
Indices: 129009--129078 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
128999 TTTGGGGACA
* *
129009 ATCATCACCACCTCCATCACC
1 ATCACCACCACCACCATCACC
** *
129030 ATCACCACCATGAACATCACC
1 ATCACCACCACCACCATCACC
* * *
129051 ATCACCATCACCACCATGAAC
1 ATCACCACCACCACCATCACC
129072 ATCACCA
1 ATCACCA
129079 TCACAGCAGC
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.36, C:0.46, G:0.03, T:0.16
Consensus pattern (21 bp):
ATCACCACCACCACCATCACC
Found at i:129060 original size:27 final size:27
Alignment explanation
Indices: 129022--129082 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
129012 ATCACCACCT
129022 CCATCACCATCACCACCATGAACATCA
1 CCATCACCATCACCACCATGAACATCA
129049 CCATCACCATCACCACCATGAACATCA
1 CCATCACCATCACCACCATGAACATCA
129076 CCATCAC
1 CCATCAC
129083 AGCAGCAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.36, C:0.46, G:0.03, T:0.15
Consensus pattern (27 bp):
CCATCACCATCACCACCATGAACATCA
Found at i:131925 original size:19 final size:19
Alignment explanation
Indices: 131887--131925 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
131877 ATTAAATAGT
* **
131887 AAAATTAATATTTTCGATA
1 AAAAGTAATATTTTAAATA
131906 AAAAGTAATATTTTAAATA
1 AAAAGTAATATTTTAAATA
131925 A
1 A
131926 GATTTTACCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (19 bp):
AAAAGTAATATTTTAAATA
Found at i:132603 original size:31 final size:31
Alignment explanation
Indices: 132566--132648 Score: 166
Period size: 31 Copynumber: 2.7 Consensus size: 31
132556 TGATAGTTGA
132566 ATATAGTGTAGGGATAAAAGACAAATGGACT
1 ATATAGTGTAGGGATAAAAGACAAATGGACT
132597 ATATAGTGTAGGGATAAAAGACAAATGGACT
1 ATATAGTGTAGGGATAAAAGACAAATGGACT
132628 ATATAGTGTAGGGATAAAAGA
1 ATATAGTGTAGGGATAAAAGA
132649 AGAATATATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.46, C:0.05, G:0.27, T:0.23
Consensus pattern (31 bp):
ATATAGTGTAGGGATAAAAGACAAATGGACT
Found at i:135138 original size:24 final size:24
Alignment explanation
Indices: 135111--135183 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
135101 CGTTCATTTG
135111 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * *
135135 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
* * * *
135159 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
135183 C
1 C
135184 ATTCATTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 42 0.95
25 2 0.05
ACGTcount: A:0.11, C:0.15, G:0.25, T:0.49
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:135140 original size:14 final size:14
Alignment explanation
Indices: 135121--135176 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
135111 CGTTCGTGAA
135121 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
135135 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
135149 CG-T---TTATGTT
1 CGTTCGGTTATGTT
*
135159 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
135173 CGTT
1 CGTT
135177 TATGTTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:135193 original size:24 final size:23
Alignment explanation
Indices: 135122--135196 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 23
135112 GTTCGTGAAC
* *
135122 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
135146 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
*
135170 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCGTTCA-TTAT
135194 GTT
1 GTT
135197 TAACCCAATC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.02
24 46 0.98
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.55
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTCATTAT
Found at i:135947 original size:16 final size:16
Alignment explanation
Indices: 135926--135993 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
135916 GTCTCCAACG
135926 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
135942 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
135958 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
135974 TTTATGTTCGT-TTTA
1 TTTATGTTCGTGTTCA
135989 TTTAT
1 TTTAT
135994 TAAATGAACG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
15 7 0.14
16 42 0.86
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:135965 original size:32 final size:32
Alignment explanation
Indices: 135924--135984 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
135914 GGGTCTCCAA
135924 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
*
135956 CGTTTATGTTCGTGTTCGTTTATGTTCGT
1 CGTTTATGTTCGTGTTCATTTATGTTCGT
135985 TTTATTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (32 bp):
CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
Found at i:136076 original size:16 final size:16
Alignment explanation
Indices: 136055--136087 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
136045 AAAAAATTTT
136055 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
136071 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
136087 T
1 T
136088 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:136199 original size:3 final size:3
Alignment explanation
Indices: 136191--136236 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
136181 AAAAATGAAT
136191 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
136237 ACTTAATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:136283 original size:26 final size:25
Alignment explanation
Indices: 136241--136291 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
136231 TAATAAACTT
136241 AATATATATTTAAAAAA-CTATATAA
1 AATATATATTTAAAAAATC-ATATAA
**
136266 AATATTATATTTTCAAAATCATATAA
1 AATA-TATATTTAAAAAATCATATAA
136292 TATGTTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 4 0.18
26 17 0.77
27 1 0.05
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (25 bp):
AATATATATTTAAAAAATCATATAA
Found at i:136317 original size:24 final size:23
Alignment explanation
Indices: 136275--136369 Score: 81
Period size: 24 Copynumber: 4.2 Consensus size: 23
136265 AAATATTATA
*
136275 TTTTCAAAATCATAT--AATATG
1 TTTTCAAAATTATATACAATATG
136296 TTTTCAAAATTATATAACAATATG
1 TTTTCAAAATTATAT-ACAATATG
* * *
136320 TTTTTAAAA--ACTATACTATATA
1 TTTTCAAAATTA-TATACAATATG
**
136342 TTTTCAAAAATTATATATTATATG
1 TTTTC-AAAATTATATACAATATG
136366 TTTT
1 TTTT
136370 TTAAAAACCG
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
21 14 0.23
22 11 0.18
23 7 0.12
24 27 0.45
25 1 0.02
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (23 bp):
TTTTCAAAATTATATACAATATG
Found at i:136345 original size:22 final size:21
Alignment explanation
Indices: 136315--136369 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
136305 TTATATAACA
*
136315 ATATGTTTTTAAAAACTATACT
1 ATATATTTTTAAAAACTATA-T
* *
136337 ATATATTTTCAAAAATTATAT
1 ATATATTTTTAAAAACTATAT
136358 ATTATATGTTTT
1 A-TATAT-TTTT
136370 TTAAAAACCG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 2 0.07
22 22 0.81
23 3 0.11
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (21 bp):
ATATATTTTTAAAAACTATAT
Found at i:138575 original size:6 final size:6
Alignment explanation
Indices: 138553--138630 Score: 60
Period size: 6 Copynumber: 14.0 Consensus size: 6
138543 TGGGGACAAT
* * * *
138553 CATCAC CACCTC CATCAC CATCA- C--CAC CATGAA CATCAC CATCAC
1 CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC
* *
138598 CATCA- C--CAC CATGAA CATCAC CATCAC CATCAC
1 CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC
138631 AGCAGCAAAC
Statistics
Matches: 54, Mismatches: 12, Indels: 12
0.69 0.15 0.15
Matches are distributed among these distances:
3 4 0.07
4 2 0.04
5 2 0.04
6 46 0.85
ACGTcount: A:0.35, C:0.47, G:0.03, T:0.15
Consensus pattern (6 bp):
CATCAC
Found at i:138580 original size:21 final size:21
Alignment explanation
Indices: 138551--138626 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
138541 TTTGGGGACA
* *
138551 ATCATCACCACCTCCATCACC
1 ATCACCACCACCACCATCACC
** *
138572 ATCACCACCATGAACATCACC
1 ATCACCACCACCACCATCACC
* * *
138593 ATCACCATCACCACCATGAAC
1 ATCACCACCACCACCATCACC
*
138614 ATCACCATCACCA
1 ATCACCACCACCA
138627 TCACAGCAGC
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.36, C:0.46, G:0.03, T:0.16
Consensus pattern (21 bp):
ATCACCACCACCACCATCACC
Found at i:138602 original size:27 final size:27
Alignment explanation
Indices: 138564--138630 Score: 134
Period size: 27 Copynumber: 2.5 Consensus size: 27
138554 ATCACCACCT
138564 CCATCACCATCACCACCATGAACATCA
1 CCATCACCATCACCACCATGAACATCA
138591 CCATCACCATCACCACCATGAACATCA
1 CCATCACCATCACCACCATGAACATCA
138618 CCATCACCATCAC
1 CCATCACCATCAC
138631 AGCAGCAAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.36, C:0.46, G:0.03, T:0.15
Consensus pattern (27 bp):
CCATCACCATCACCACCATGAACATCA
Found at i:141497 original size:29 final size:29
Alignment explanation
Indices: 141451--141508 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
141441 GTGTTGGCAG
* *
141451 TAGGTCGCCATGCCTTCCAGGCGACCTAC
1 TAGGTCGCCATACCTTCCAGGCGAACTAC
** *
141480 TAGGTCGCCATATTTTCCCGGCGAACTAC
1 TAGGTCGCCATACCTTCCAGGCGAACTAC
141509 AAGAGATTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.19, C:0.34, G:0.22, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATACCTTCCAGGCGAACTAC
Found at i:141561 original size:10 final size:10
Alignment explanation
Indices: 141548--141618 Score: 56
Period size: 10 Copynumber: 6.7 Consensus size: 10
141538 ACACGCTGGG
141548 CATCCGAGGC
1 CATCCGAGGC
141558 CATCCGACCGAGGC
1 CAT-C--C-GAGGC
141572 CATCCGAGAG-
1 CATCCGAG-GC
*
141582 CATCCGAGGT
1 CATCCGAGGC
*
141592 CATCCAAGAG-
1 CATCCGAG-GC
141602 CATCCGAGGC
1 CATCCGAGGC
141612 CATCCGA
1 CATCCGA
141619 CCGAGGCCAT
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
9 2 0.04
10 35 0.69
11 4 0.08
13 2 0.04
14 8 0.16
ACGTcount: A:0.25, C:0.37, G:0.27, T:0.11
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:141570 original size:14 final size:14
Alignment explanation
Indices: 141551--141578 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
141541 CGCTGGGCAT
141551 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
141565 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
141579 GAGCATCCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.29, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:141590 original size:20 final size:20
Alignment explanation
Indices: 141565--141618 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
141555 GGCCATCCGA
141565 CCGAGGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAGAGCAT
* *
141585 CCGAGGTCATCCAAGAGCAT
1 CCGAGGCCATCCGAGAGCAT
141605 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
141619 CCGAGGCCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.35, G:0.28, T:0.11
Consensus pattern (20 bp):
CCGAGGCCATCCGAGAGCAT
Found at i:141753 original size:29 final size:29
Alignment explanation
Indices: 141707--141762 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
141697 GAACGAGGGT
*
141707 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
141736 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
141763 TGTGTTGGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.20, C:0.30, G:0.38, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:141808 original size:12 final size:12
Alignment explanation
Indices: 141791--141815 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
141781 TGCCATGCAA
141791 CACGTTCATTCT
1 CACGTTCATTCT
141803 CACGTTCATTCT
1 CACGTTCATTCT
141815 C
1 C
141816 TCTGTTTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (12 bp):
CACGTTCATTCT
Found at i:141875 original size:29 final size:29
Alignment explanation
Indices: 141833--141889 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
141823 GATCAATGGT
* *
141833 AGGTCGCCCGGAGTGTATGGTGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
141862 AGGTCGCCCGGAGTGCATGGCGACCTAC
1 AGGTCGCCCGGAGTGCATGGCGACCTAC
141890 GACCAACACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.19, C:0.28, G:0.35, T:0.18
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Done.