Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003604.1 Hibiscus syriacus cultivar Beakdansim tig00007623_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: 117981
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:2597 original size:17 final size:17
Alignment explanation
Indices: 2575--2613 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2565 CGTCGAGCTA
*
2575 GAAGAGGCAGTTAGGAG
1 GAAGAGGCAGTAAGGAG
*
2592 GAAGAGGCAGTAAGGCG
1 GAAGAGGCAGTAAGGAG
2609 GAAGA
1 GAAGA
2614 AGATTTTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.08, G:0.46, T:0.08
Consensus pattern (17 bp):
GAAGAGGCAGTAAGGAG
Found at i:16906 original size:24 final size:25
Alignment explanation
Indices: 16855--16926 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 25
16845 TAATCTTATA
*
16855 TGGCACTACGGTGC--ATTTCTACG
1 TGGCACTACGGTGCAAATTTATACG
* *
16878 AGGCACTTCGGTGCAAATTT-TACG
1 TGGCACTACGGTGCAAATTTATACG
**
16902 TGGCACTAAAGTGCAAATTTATACG
1 TGGCACTACGGTGCAAATTTATACG
16927 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
23 12 0.30
24 20 0.50
25 8 0.20
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (25 bp):
TGGCACTACGGTGCAAATTTATACG
Found at i:19570 original size:3 final size:3
Alignment explanation
Indices: 19549--19613 Score: 59
Period size: 3 Copynumber: 23.0 Consensus size: 3
19539 TTTATTTCAT
* * *
19549 TTA TT- TTA TTTA CTA TTA TTA TT- TTG TT- TTA ATA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19592 TTA -TA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
19614 AATAAATAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
2 10 0.19
3 39 0.75
4 3 0.06
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:19584 original size:19 final size:20
Alignment explanation
Indices: 19549--19613 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 20
19539 TTTATTTCAT
*
19549 TTATT-TTA-TTTACTATTA
1 TTATTATTATTTTAATATTA
*
19567 TTATT-TTGTTTTAATATTA
1 TTATTATTATTTTAATATTA
*
19586 TTATTATTATATT-ATATTA
1 TTATTATTATTTTAATATTA
19605 TTATTATTA
1 TTATTATTA
19614 AATAAATAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
18 7 0.17
19 29 0.71
20 5 0.12
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (20 bp):
TTATTATTATTTTAATATTA
Found at i:19587 original size:22 final size:22
Alignment explanation
Indices: 19562--19613 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
19552 TTTTATTTAC
* * *
19562 TATTATTATTTTGTTTTAATAT
1 TATTATTATTATATTATAATAT
*
19584 TATTATTATTATATTATATTAT
1 TATTATTATTATATTATAATAT
19606 TATTATTA
1 TATTATTA
19614 AATAAATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TATTATTATTATATTATAATAT
Found at i:20839 original size:16 final size:16
Alignment explanation
Indices: 20820--20875 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 16
20810 TTACTTTTTA
20820 TATTTAATTTTAATTT
1 TATTTAATTTTAATTT
20836 TATTT-ATTTTACTCATTGTT
1 TATTTAATTTTA---A-T-TT
20856 TATTTATATTTTAATTT
1 TATTTA-ATTTTAATTT
20873 TAT
1 TAT
20876 ATGTTTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
15 6 0.18
16 5 0.15
17 5 0.15
18 2 0.06
19 2 0.06
20 7 0.21
22 6 0.18
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.68
Consensus pattern (16 bp):
TATTTAATTTTAATTT
Found at i:21858 original size:16 final size:17
Alignment explanation
Indices: 21839--21878 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
21829 TCTTTCAAAT
21839 TTTTTATTA-CTTATTA
1 TTTTTATTATCTTATTA
*
21855 TTTTTA-TATGTTATTA
1 TTTTTATTATCTTATTA
21871 TTTTTATT
1 TTTTTATT
21879 TATTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 18 0.86
17 1 0.05
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (17 bp):
TTTTTATTATCTTATTA
Found at i:21881 original size:13 final size:15
Alignment explanation
Indices: 21849--21890 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
21839 TTTTTATTAC
21849 TTATTATTTTTATATG
1 TTATTA-TTTTATATG
21865 TTATTATTTT-TAT-
1 TTATTATTTTATATG
21878 TTATTTATTTTAT
1 TTA-TTATTTTAT
21891 TCAAGTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.12
14 10 0.42
15 5 0.21
16 6 0.25
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (15 bp):
TTATTATTTTATATG
Found at i:23344 original size:15 final size:15
Alignment explanation
Indices: 23324--23359 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
23314 CATGCATTTG
23324 CATTTTGCATCTTTA
1 CATTTTGCATCTTTA
*
23339 CATTTTGCATCTTTG
1 CATTTTGCATCTTTA
23354 CATTTT
1 CATTTT
23360 TTATTTTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.17, C:0.19, G:0.08, T:0.56
Consensus pattern (15 bp):
CATTTTGCATCTTTA
Found at i:23348 original size:22 final size:22
Alignment explanation
Indices: 23320--23369 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
23310 CATACATGCA
23320 TTTGCAT-TTTGCATCTTTACAT
1 TTTGCATCTTTGCAT-TTTACAT
**
23342 TTTGCATCTTTGCATTTTTTAT
1 TTTGCATCTTTGCATTTTACAT
23364 TTTGCA
1 TTTGCA
23370 ATTATACTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.16, C:0.16, G:0.10, T:0.58
Consensus pattern (22 bp):
TTTGCATCTTTGCATTTTACAT
Found at i:23355 original size:8 final size:7
Alignment explanation
Indices: 23316--23369 Score: 56
Period size: 7 Copynumber: 7.6 Consensus size: 7
23306 TTTTCATACA
23316 TGCA-TT
1 TGCATTT
23322 TGCATTT
1 TGCATTT
23329 TGCATCTT
1 TGCAT-TT
*
23337 TACATTT
1 TGCATTT
23344 TGCATCTT
1 TGCAT-TT
23352 TGCATTT
1 TGCATTT
**
23359 TTTATTT
1 TGCATTT
23366 TGCA
1 TGCA
23370 ATTATACTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
6 4 0.10
7 22 0.56
8 13 0.33
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.56
Consensus pattern (7 bp):
TGCATTT
Found at i:29005 original size:76 final size:76
Alignment explanation
Indices: 28880--29027 Score: 172
Period size: 76 Copynumber: 1.9 Consensus size: 76
28870 GAAAACTTTT
* * * *
28880 TTTTTCCAATCAGAATCAGGAATGTTGATGTATCCTGAATGTTTATATCAGCAAAATGCTGGGGC
1 TTTTTCCAATCAGAATCAAGAATGTTGATGTATCCTGAACGTTCATATCAAC-AAATGCTGGGGC
28945 ATGCTGAAAGCC
65 ATGCTGAAAGCC
* * ** * * **
28957 TTTTT-CAATCAGAATGAAGAATGTTGATTTATTTTGAACGTTCGTATCAACAATTTTTGGGGCA
1 TTTTTCCAATCAGAATCAAGAATGTTGATGTATCCTGAACGTTCATATCAACAAATGCTGGGGCA
29021 TGCTGAA
66 TGCTGAA
29028 GGCCCATATC
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
75 17 0.29
76 37 0.63
77 5 0.08
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (76 bp):
TTTTTCCAATCAGAATCAAGAATGTTGATGTATCCTGAACGTTCATATCAACAAATGCTGGGGCA
TGCTGAAAGCC
Found at i:30363 original size:22 final size:22
Alignment explanation
Indices: 30338--30416 Score: 113
Period size: 22 Copynumber: 3.6 Consensus size: 22
30328 ACATCTACAT
*
30338 TCTTCAAAGATGATAGATTTTC
1 TCTTCAAAGATGATAGATTCTC
*
30360 TCTTCAAAGATGATAGATTCTA
1 TCTTCAAAGATGATAGATTCTC
* *
30382 TTTTTAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
30404 TTTTCAAAGATGA
1 TCTTCAAAGATGA
30417 AAGCTTTATG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:31205 original size:164 final size:165
Alignment explanation
Indices: 30934--31419 Score: 773
Period size: 164 Copynumber: 3.0 Consensus size: 165
30924 AGAATGAGTA
*
30934 TTATCTTGAGATTGGGGCATGTTACCCAATCAACGTGTTATTTTGAAACATAATGAGAAAACAAT
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACGTGTTATTTTGAAACATAATGAGAAAACGAT
30999 TTCCATAGTTTCTCATTTTATC-TTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTCT
66 TTCCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTCT
*
31063 TAGTTTTTTTACTTAGTAAACTATTTCCAGCAGCC
131 TAGTTTTTTTACTTAGTAAACTATTTCCAACAGCC
**
31098 TTATCTTGAGATTACGGCATGTTACCCAATCAACGTGTTATTTTGAAACATAATGAGAAAACGAT
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACGTGTTATTTTGAAACATAATGAGAAAACGAT
31163 TTCCATAGTTTCTCATTTTATCTTTTCT-AAATGAAATTGTTGAAAAGTAAGAAAACGATTTTCT
66 TTCCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTCT
*
31227 TAGTTTTTTTACTTCA-TAAACTATTTCCAACATCC
131 TAGTTTTTTTACTT-AGTAAACTATTTCCAACAGCC
* * * *
31262 TTATCTTGAGATTGGGGTATATTACCCAATCAACATGTTATCTTGAAACATAATGAGAAAACGAT
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACGTGTTATTTTGAAACATAATGAGAAAACGAT
** * * *
31327 TTCCATAGTTTCTCATTCAATATTTTCTGAAAATGAAACTGTTGAAAAGTAAGAAAACGATTTCC
66 TTCCATAGTTTCTCATTTTATCTTTTCT-AAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTC
* * *
31392 ATAG-TATCTTACTTAGTAAACTATTTCC
130 TTAGTTTTTTTACTTAGTAAACTATTTCC
31420 CACATCCATA
Statistics
Matches: 298, Mismatches: 19, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
164 236 0.79
165 26 0.09
166 36 0.12
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (165 bp):
TTATCTTGAGATTGGGGCATGTTACCCAATCAACGTGTTATTTTGAAACATAATGAGAAAACGAT
TTCCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTCT
TAGTTTTTTTACTTAGTAAACTATTTCCAACAGCC
Found at i:31512 original size:36 final size:36
Alignment explanation
Indices: 31459--31567 Score: 121
Period size: 36 Copynumber: 3.0 Consensus size: 36
31449 TTTCAAATAG
31459 CAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1 CAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
* * ** ** **
31495 -AATTGTTTCTCGCTTGAGAAAGTTTCCCTCGAAACAA
1 CAATT-TATCTCACTTGAGATTGTTTTTCTTAAAAC-A
31532 CAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1 CAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
31568 GAACTTTGTC
Statistics
Matches: 54, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
35 4 0.07
36 23 0.43
37 23 0.43
38 4 0.07
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.40
Consensus pattern (36 bp):
CAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
Found at i:31567 original size:37 final size:37
Alignment explanation
Indices: 31459--31567 Score: 123
Period size: 37 Copynumber: 3.0 Consensus size: 37
31449 TTTCAAATAG
31459 CAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC-A
1 CAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
* * ** ** **
31495 -AATTGTTTCTCGCTTGAGAAAGTTTCCCTCGAAACAA
1 CAATT-TATCTCACTTGAGATTGTTTTTCTTAAAACAA
31532 CAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1 CAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
31568 GAACTTTGTC
Statistics
Matches: 54, Mismatches: 16, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
35 4 0.07
36 22 0.41
37 24 0.44
38 4 0.07
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.40
Consensus pattern (37 bp):
CAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
Found at i:31807 original size:37 final size:37
Alignment explanation
Indices: 31563--31792 Score: 361
Period size: 37 Copynumber: 6.2 Consensus size: 37
31553 GTTTTTCTTA
*
31563 AAACAGAACTTTGTCTCGCTCGAGACAGTTTCACTCG
1 AAACATAACTTTGTCTCGCTCGAGACAGTTTCACTCG
*
31600 AAACATAACTTTGTCTCGCTCGAGAAAGTTTCACTCG
1 AAACATAACTTTGTCTCGCTCGAGACAGTTTCACTCG
* * *
31637 AAACATAACTTTGTCTCGCTCGAGACAGTATCATTAG
1 AAACATAACTTTGTCTCGCTCGAGACAGTTTCACTCG
* * *
31674 AAACAGAACTTTGTCTCTCTTGAGACAGTTTCACTCG
1 AAACATAACTTTGTCTCGCTCGAGACAGTTTCACTCG
31711 AAACATAACTTTGTCTCGCTCGAGACAGTTTCACTCG
1 AAACATAACTTTGTCTCGCTCGAGACAGTTTCACTCG
* *
31748 AAACAGAACTTTGTCTCGCTCGAGGCAGTTTCACTCG
1 AAACATAACTTTGTCTCGCTCGAGACAGTTTCACTCG
*
31785 AAATATAA
1 AAACATAA
31793 ATTTCCATCT
Statistics
Matches: 174, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 174 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (37 bp):
AAACATAACTTTGTCTCGCTCGAGACAGTTTCACTCG
Found at i:31962 original size:3 final size:3
Alignment explanation
Indices: 31954--32009 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
31944 TTTGTTTTAT
* *
31954 TTA TTA TTA TTA TT- TTG TT- TTA ATA TTA TTA TTA TTA -TA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31998 TTA TTA TTA TTA
1 TTA TTA TTA TTA
32010 AATAAATAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 8 0.17
3 39 0.83
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:31980 original size:19 final size:20
Alignment explanation
Indices: 31953--32009 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
31943 ATTTGTTTTA
* *
31953 TTTATTATTATTATT-TTGT
1 TTTAATATTATTATTATTAT
31972 TTTAATATTATTATTATTAT
1 TTTAATATTATTATTATTAT
*
31992 ATT-ATATTATTATTATTA
1 TTTAATATTATTATTATTA
32010 AATAAATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 29 0.85
20 5 0.15
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTAATATTATTATTATTAT
Found at i:31980 original size:22 final size:22
Alignment explanation
Indices: 31944--32009 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
31934 TTTTATTTCA
31944 TTTGTTTTATTTATTATTATTAT
1 TTTGTTTTA-TTATTATTATTAT
*
31967 TTTGTTTTAATATTATTATTAT
1 TTTGTTTTATTATTATTATTAT
* * *
31989 TATATTATATTATTATTATTA
1 TTTGTTTTATTATTATTATTA
32010 AATAAATAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
22 29 0.76
23 9 0.24
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (22 bp):
TTTGTTTTATTATTATTATTAT
Found at i:33203 original size:16 final size:16
Alignment explanation
Indices: 33184--33239 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 16
33174 TTACTTTTTA
33184 TATTTAATTTTAATTT
1 TATTTAATTTTAATTT
33200 TATTT-ATTTTACTCATTGTT
1 TATTTAATTTTA---A-T-TT
33220 TATTTATATTTTAATTT
1 TATTTA-ATTTTAATTT
33237 TAT
1 TAT
33240 ATGTTTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
15 6 0.18
16 5 0.15
17 5 0.15
18 2 0.06
19 2 0.06
20 7 0.21
22 6 0.18
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.68
Consensus pattern (16 bp):
TATTTAATTTTAATTT
Found at i:35052 original size:24 final size:20
Alignment explanation
Indices: 34995--35052 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
34985 TTCCCCTTGA
*
34995 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATCCTAC
*
35015 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CC-T-AC
35038 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
35053 CTACCTATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 14 0.45
21 1 0.03
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTAC
Found at i:35163 original size:64 final size:63
Alignment explanation
Indices: 35040--35176 Score: 170
Period size: 64 Copynumber: 2.2 Consensus size: 63
35030 CCCTTAACAT
* * *
35040 GTGCATCGATGCACTACCTATGCATCGATACACCAATCACCTTCGATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCACTACCTATGCATCGATACACCAATCACATTCGATGTTTTCATTTTAA-AGA
* * * *
35104 GTGCATCGATGCACT-CCTTATGCATCGATGCACTAATTACATTCGATG-TTTCTTCTTTAAAGA
1 GTGCATCGATGCACTACC-TATGCATCGATACACCAATCACATTCGATGTTTTCAT-TTTAAAGA
35167 GTGCATCGAT
1 GTGCATCGAT
35177 ACACATTAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
63 18 0.28
64 46 0.72
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (63 bp):
GTGCATCGATGCACTACCTATGCATCGATACACCAATCACATTCGATGTTTTCATTTTAAAGA
Found at i:37269 original size:11 final size:11
Alignment explanation
Indices: 37253--37287 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
37243 ATTTATCATT
37253 TTAAAACACAC
1 TTAAAACACAC
37264 TTAAAACACACAC
1 TT-AAA-ACACAC
37277 TTAAAACACAC
1 TTAAAACACAC
37288 ACTTCTCCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 8 0.36
12 6 0.27
13 8 0.36
ACGTcount: A:0.54, C:0.29, G:0.00, T:0.17
Consensus pattern (11 bp):
TTAAAACACAC
Found at i:37276 original size:13 final size:13
Alignment explanation
Indices: 37258--37291 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
37248 TCATTTTAAA
37258 ACACACTTAAAAC
1 ACACACTTAAAAC
37271 ACACACTTAAAAC
1 ACACACTTAAAAC
37284 ACACACTT
1 ACACACTT
37292 CTCCCCCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (13 bp):
ACACACTTAAAAC
Found at i:39137 original size:12 final size:11
Alignment explanation
Indices: 39118--39145 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
39108 GAAAAACAAC
39118 AATTTTTTTTT
1 AATTTTTTTTT
39129 AATTTTTTTTT
1 AATTTTTTTTT
39140 AATTTT
1 AATTTT
39146 GAAAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
AATTTTTTTTT
Found at i:39583 original size:20 final size:21
Alignment explanation
Indices: 39529--39591 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
39519 GATTCCCCTG
39529 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
39553 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
39573 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
39592 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:43674 original size:117 final size:117
Alignment explanation
Indices: 43454--43675 Score: 279
Period size: 117 Copynumber: 1.9 Consensus size: 117
43444 CTTTCAAATC
* *
43454 GAAATTTTCTTTTTCAATACTTTCAAATTTCATTCTTGAAAGCTCTAAATCCTTCTTCAATATTT
1 GAAAATTTCTTTTTCAATACTTTCAAATTTCATTCTTGAAAGCTCTAAATCCTTCTTCAACATTT
* *
43519 CATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGATTAATTT
66 CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGATTAATTT
* * * * *
43571 GAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTCCTT-TCTCAACAT
1 GAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTCTTGAAAGCTCTAAATCCTTCT-TCAACAT
* * **
43634 TTCATTTTGATTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAAG
64 TTCATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAAG
43676 ATCATTTTTA
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
116 2 0.02
117 83 0.93
118 4 0.04
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.47
Consensus pattern (117 bp):
GAAAATTTCTTTTTCAATACTTTCAAATTTCATTCTTGAAAGCTCTAAATCCTTCTTCAACATTT
CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGATTAATTT
Found at i:48132 original size:2 final size:2
Alignment explanation
Indices: 48125--48215 Score: 182
Period size: 2 Copynumber: 45.5 Consensus size: 2
48115 CAATGTATGT
48125 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
48167 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
48209 TA TA TA T
1 TA TA TA T
48216 GTTTTGTGAT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49342 original size:22 final size:23
Alignment explanation
Indices: 49298--49343 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
49288 TTGGTGCTGG
49298 AAACAAGATAATAAATAAGATTA
1 AAACAAGATAATAAATAAGATTA
49321 AAACAAGATAA-AGAA-AAGATTA
1 AAACAAGATAATA-AATAAGATTA
49343 A
1 A
49344 GGAATTGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.67, C:0.04, G:0.11, T:0.17
Consensus pattern (23 bp):
AAACAAGATAATAAATAAGATTA
Found at i:53654 original size:10 final size:11
Alignment explanation
Indices: 53634--53658 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
53624 AAATTTTAGC
53634 TTTTTGTTTTT
1 TTTTTGTTTTT
53645 TTTTTGTTTTT
1 TTTTTGTTTTT
53656 TTT
1 TTT
53659 GGAAAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTGTTTTT
Found at i:54032 original size:22 final size:23
Alignment explanation
Indices: 53987--54033 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
53977 TTTTGTGCTG
53987 AAAACAAGATAAGAAATAAGATT
1 AAAACAAGATAAGAAATAAGATT
54010 AAAACAAGATAA-AGAA-AAGATT
1 AAAACAAGATAAGA-AATAAGATT
54032 AA
1 AA
54034 GGAATTGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.68, C:0.04, G:0.13, T:0.15
Consensus pattern (23 bp):
AAAACAAGATAAGAAATAAGATT
Found at i:55540 original size:23 final size:23
Alignment explanation
Indices: 55514--55579 Score: 105
Period size: 23 Copynumber: 2.9 Consensus size: 23
55504 CACCACAGCT
*
55514 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
55537 CGTAGAATTGTACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
55560 CGTAGAATTGCACCGTAGTG
1 CGTAGAATTGCACCGAAGTG
55580 TCATATAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.23
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:58600 original size:3 final size:3
Alignment explanation
Indices: 58587--58646 Score: 61
Period size: 3 Copynumber: 20.3 Consensus size: 3
58577 GTAATATGTA
**
58587 AAT AA- AAT AAT AAT AAT AAT GCT AAT AAT AAT AAT AATT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT
* *
58631 AAC GAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
58647 TAAAAAAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
2 4 0.09
3 39 0.85
4 3 0.07
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:58827 original size:103 final size:103
Alignment explanation
Indices: 58687--58886 Score: 339
Period size: 103 Copynumber: 1.9 Consensus size: 103
58677 TCTACAATTC
*
58687 CTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
1 CTTAAGAATCATATACATATACTAGGGATCAAGTATGTATCTCACCAGACTTCACACATGTTCCA
*
58752 AAGAATGCATATATGTCCCAAAGGACCACATATCATTT
66 AAGAATACATATATGTCCCAAAGGACCACATATCATTT
* *
58790 CTTAAGAATCATATACATAT-GTCATGGATCAAGTATGTATCTCACCAGACTTCACACATGTTCC
1 CTTAAGAATCATATACATATACT-AGGGATCAAGTATGTATCTCACCAGACTTCACACATGTTCC
*
58854 AAAGAATACATATATGTCCCGAAGGACCACATA
65 AAAGAATACATATATGTCCCAAAGGACCACATA
58887 GACCCTCGAC
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
102 1 0.01
103 90 0.99
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.28
Consensus pattern (103 bp):
CTTAAGAATCATATACATATACTAGGGATCAAGTATGTATCTCACCAGACTTCACACATGTTCCA
AAGAATACATATATGTCCCAAAGGACCACATATCATTT
Found at i:63866 original size:23 final size:23
Alignment explanation
Indices: 63840--63903 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
63830 CAGCTCGTAT
63840 AATTGCACCGAAGTGCCACATAG
1 AATTGCACCGAAGTGCCACATAG
* * *
63863 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACATAG
*
63886 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
63904 TATAATAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACATAG
Found at i:64090 original size:103 final size:103
Alignment explanation
Indices: 63919--64136 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
63909 TAATGTCCAT
* *
63919 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
63984 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
64022 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* *
64087 GACTTCACACATGTTCTAAAGAATACATATATGTTCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
64125 AAGGACCACATA
1 AAGGACCACATA
64137 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:70490 original size:20 final size:20
Alignment explanation
Indices: 70465--70512 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
70455 AATAATTTTA
*
70465 TGATTTATATTTTTTTTATT
1 TGATTTAGATTTTTTTTATT
* *
70485 TGATTTGGGTTTTTTTTATT
1 TGATTTAGATTTTTTTTATT
70505 TGAGTTTA
1 TGA-TTTA
70513 AAATTAATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.69
Consensus pattern (20 bp):
TGATTTAGATTTTTTTTATT
Found at i:70622 original size:14 final size:14
Alignment explanation
Indices: 70603--70636 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
70593 TGGACTAAAT
70603 ATAAACAAATGAAC
1 ATAAACAAATGAAC
70617 ATAAACAAATGAAC
1 ATAAACAAATGAAC
70631 ATAAAC
1 ATAAAC
70637 GATCGATCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.65, C:0.15, G:0.06, T:0.15
Consensus pattern (14 bp):
ATAAACAAATGAAC
Found at i:80169 original size:24 final size:24
Alignment explanation
Indices: 80130--80187 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
80120 AGAACATGAT
*
80130 GATGGTAGAAGAGAAGATGA-GGAA
1 GATGGTAGATGAGAAGATGATGG-A
* *
80154 GATGGTAGATGTGAAGTTGATGGA
1 GATGGTAGATGAGAAGATGATGGA
80178 GATGG-AGATG
1 GATGGTAGATG
80188 GAGATGGTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.17
24 23 0.77
25 2 0.07
ACGTcount: A:0.36, C:0.00, G:0.43, T:0.21
Consensus pattern (24 bp):
GATGGTAGATGAGAAGATGATGGA
Found at i:80246 original size:24 final size:25
Alignment explanation
Indices: 80183--80249 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 25
80173 ATGGAGATGG
80183 AGATGGAGATGGTAGAAGTGAATGT
1 AGATGGAGATGGTAGAAGTGAATGT
** * *
80208 -GATAAATATGGTAGATGTGAA-GT
1 AGATGGAGATGGTAGAAGTGAATGT
*
80231 AGATGGAGATGATAGAAGT
1 AGATGGAGATGGTAGAAGT
80250 TGAGATAATG
Statistics
Matches: 32, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
23 2 0.06
24 30 0.94
ACGTcount: A:0.39, C:0.00, G:0.36, T:0.25
Consensus pattern (25 bp):
AGATGGAGATGGTAGAAGTGAATGT
Found at i:81525 original size:40 final size:39
Alignment explanation
Indices: 81469--81601 Score: 140
Period size: 41 Copynumber: 3.3 Consensus size: 39
81459 TAAATATTTG
* *
81469 TACTTTAATGGCGTTTTAATATAAACACCGCTAAAGACTA
1 TACTTTAGTGGTGTTTT-ATATAAACACCGCTAAAGACTA
* * * * *
81509 TACTTTAGTGTTGTTTTTCTACAAACGCCGCTAAAGACTTG
1 TACTTTAGTGGTG-TTTTATATAAACACCGCTAAAGAC-TA
* *
81550 TACTTTAGTGGTGTTTCTACATAAACACCGCAAAAGACTAA
1 TACTTTAGTGGTGTTT-TATATAAACACCGCTAAAGACT-A
81591 TACTTTAGTGG
1 TACTTTAGTGG
81602 CATTTTTTGA
Statistics
Matches: 75, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
40 31 0.41
41 44 0.59
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (39 bp):
TACTTTAGTGGTGTTTTATATAAACACCGCTAAAGACTA
Found at i:81574 original size:81 final size:82
Alignment explanation
Indices: 81448--81600 Score: 220
Period size: 81 Copynumber: 1.9 Consensus size: 82
81438 CGTTTTTTGA
* * * * *
81448 ACAAATGCCGCTAAATATTTGTACTTTAATGGCGTTTTAATATAAACACCGCTAAAGACT-ATAC
1 ACAAACGCCGCTAAAGACTTGTACTTTAATGGCGTTTTAACATAAACACCGCAAAAGACTAATAC
81512 TTTAGTGTTGTTTTTCT
66 TTTAGTGTTGTTTTTCT
* *
81529 ACAAACGCCGCTAAAGACTTGTACTTTAGTGGTGTTTCT-ACATAAACACCGCAAAAGACTAATA
1 ACAAACGCCGCTAAAGACTTGTACTTTAATGGCGTTT-TAACATAAACACCGCAAAAGACTAATA
81593 CTTTAGTG
65 CTTTAGTG
81601 GCATTTTTTG
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 51 0.81
82 12 0.19
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (82 bp):
ACAAACGCCGCTAAAGACTTGTACTTTAATGGCGTTTTAACATAAACACCGCAAAAGACTAATAC
TTTAGTGTTGTTTTTCT
Found at i:82280 original size:5 final size:5
Alignment explanation
Indices: 82263--82301 Score: 60
Period size: 5 Copynumber: 7.6 Consensus size: 5
82253 AAAAAAGATA
*
82263 ATTTT ATTCT ATTTT ATTTT ATTTT GATTTT ATTTT ATT
1 ATTTT ATTTT ATTTT ATTTT ATTTT -ATTTT ATTTT ATT
82302 ATTAATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 26 0.84
6 5 0.16
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (5 bp):
ATTTT
Found at i:82294 original size:16 final size:15
Alignment explanation
Indices: 82263--82301 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
82253 AAAAAAGATA
82263 ATTTTATTCTATTTT
1 ATTTTATTCTATTTT
*
82278 ATTTTATTTTGATTTT
1 ATTTTATTCT-ATTTT
82294 ATTTTATT
1 ATTTTATT
82302 ATTAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (15 bp):
ATTTTATTCTATTTT
Found at i:83892 original size:31 final size:31
Alignment explanation
Indices: 83844--83907 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
83834 GTTTGCAAGG
*
83844 TTATCACATATCGACTTATTTTCAACAGAAA
1 TTATCACATATCAACTTATTTTCAACAGAAA
*
83875 TTATCACGTATCAACTTATTTTCAACAGAAA
1 TTATCACATATCAACTTATTTTCAACAGAAA
83906 TT
1 TT
83908 CTCTCATACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (31 bp):
TTATCACATATCAACTTATTTTCAACAGAAA
Found at i:84551 original size:35 final size:35
Alignment explanation
Indices: 84477--84588 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 35
84467 CTATTATCAT
* * **
84477 TTTTC-AACAAATATCTACCAAACTTTGAAAACTGT
1 TTTTCAAAGAAATATTTACCAAACTTTGAAAAC-AA
*
84512 TTTTCAAAGAAATATTTACCAAACTTTGAAAACCA
1 TTTTCAAAGAAATATTTACCAAACTTTGAAAACAA
* *
84547 TTTTCAAAGAAACATTTACCAAACTTTGAATACAA
1 TTTTCAAAGAAATATTTACCAAACTTTGAAAACAA
84582 TTTTCAA
1 TTTTCAA
84589 CACTAGTCTG
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
35 44 0.64
36 25 0.36
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.34
Consensus pattern (35 bp):
TTTTCAAAGAAATATTTACCAAACTTTGAAAACAA
Found at i:95370 original size:3 final size:3
Alignment explanation
Indices: 95356--95398 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
95346 TGTATCTGCT
* * *
95356 ATG ATA ATG ATG ATG ATG GTG GTG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
95399 GAGTGAGGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:101057 original size:20 final size:19
Alignment explanation
Indices: 101010--101057 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
101000 AAGGATTTTC
* * *
101010 TTTTGAAAGCTAAAATGGA
1 TTTTGAAAACCAAAATGAA
*
101029 TTTTCAAAACCAAAATGAAA
1 TTTTGAAAACCAAAATG-AA
101049 TTTTGAAAA
1 TTTTGAAAA
101058 AGGATTTAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.31
Consensus pattern (19 bp):
TTTTGAAAACCAAAATGAA
Found at i:103543 original size:160 final size:163
Alignment explanation
Indices: 103302--103626 Score: 629
Period size: 160 Copynumber: 2.0 Consensus size: 163
103292 TATACCTCAT
103302 AATACACTAGTTGAGCATATATGTCACTATTTAAAAGTGTGAGGATCTAATTGAATAAATTGAAA
1 AATACACTAGTTGAGCATATATGTCACTATTTAAAAGTGTGAGGATCTAATTGAATAAATTGAAA
103367 ATTGAAGGTTAACAATAGT-AATAATTTTG-ATTTAAGCACTAAATTAAATAACCTTCAAAATGA
66 ATTGAAGGTTAACAATAGTAAATAATTTTGAATTTAAGCACTAAATTAAATAACCTTCAAAATGA
103430 GAATAGCA-AATCATAATTTTATCTTTGATTCC
131 GAATAGCATAATCATAATTTTATCTTTGATTCC
103462 AATACACTAGTTGAGCATATATGTCACTATTTAAAAGTGTGAGGATCTAATTGAATAAATTGAAA
1 AATACACTAGTTGAGCATATATGTCACTATTTAAAAGTGTGAGGATCTAATTGAATAAATTGAAA
103527 ATTGAAGGTTAACAATAGTAAATAATTTTGAATTTAAGCACTAAATTAAATAACCTTCAAAATGA
66 ATTGAAGGTTAACAATAGTAAATAATTTTGAATTTAAGCACTAAATTAAATAACCTTCAAAATGA
103592 GAATAGCATAATCATAATTTTATCTTTGATTCC
131 GAATAGCATAATCATAATTTTATCTTTGATTCC
103625 AA
1 AA
103627 AACATGTGGA
Statistics
Matches: 162, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
160 84 0.52
161 10 0.06
162 42 0.26
163 26 0.16
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (163 bp):
AATACACTAGTTGAGCATATATGTCACTATTTAAAAGTGTGAGGATCTAATTGAATAAATTGAAA
ATTGAAGGTTAACAATAGTAAATAATTTTGAATTTAAGCACTAAATTAAATAACCTTCAAAATGA
GAATAGCATAATCATAATTTTATCTTTGATTCC
Found at i:105559 original size:18 final size:18
Alignment explanation
Indices: 105524--105568 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
105514 CAACCCAAGA
* *
105524 AAAATAAAATAGTGAAAT
1 AAAATAAAATAATCAAAT
*
105542 AAAATTAAATAATCAAAT
1 AAAATAAAATAATCAAAT
*
105560 CAAATAAAA
1 AAAATAAAA
105569 GAAAAAGATG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.22
Consensus pattern (18 bp):
AAAATAAAATAATCAAAT
Found at i:111524 original size:19 final size:19
Alignment explanation
Indices: 111500--111569 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
111490 GTCTACAATG
111500 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * * **
111519 TCGTTGCGAAAGTCTACAGTT
1 TCGTTGCG--ATTTTCCAAAT
111540 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
111560 TCGTTGCGAT
1 TCGTTGCGAT
111570 AGTTAAAAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 18 0.47
20 6 0.16
21 6 0.16
22 8 0.21
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:111533 original size:40 final size:41
Alignment explanation
Indices: 111480--111568 Score: 153
Period size: 41 Copynumber: 2.2 Consensus size: 41
111470 TTCCATTTCG
*
111480 CGTTGCGATAGTCTACA-ATGTCGTTGCGATTTTCCAAATT
1 CGTTGCGAAAGTCTACAGATGTCGTTGCGATTTTCCAAATT
*
111520 CGTTGCGAAAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGAAAGTCTACAGATGTCGTTGCGATTTTCCAAATT
111561 CGTTGCGA
1 CGTTGCGA
111569 TAGTTAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
40 16 0.35
41 30 0.65
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.36
Consensus pattern (41 bp):
CGTTGCGAAAGTCTACAGATGTCGTTGCGATTTTCCAAATT
Found at i:111661 original size:6 final size:6
Alignment explanation
Indices: 111650--111715 Score: 102
Period size: 6 Copynumber: 11.5 Consensus size: 6
111640 GACACGTATT
111650 ACCACG ACCACG ACCACG ACCACG ACC-CG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
111697 ACCCCG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACC
111716 CGAGACGAGA
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
5 15 0.26
6 43 0.74
ACGTcount: A:0.29, C:0.55, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:111680 original size:23 final size:24
Alignment explanation
Indices: 111654--111715 Score: 103
Period size: 23 Copynumber: 2.7 Consensus size: 24
111644 CGTATTACCA
111654 CGACCACGACCACGACCACGA-CC
1 CGACCACGACCACGACCACGACCC
111677 CGACCACGACCACGACCACGACCC
1 CGACCACGACCACGACCACGACCC
111701 CGACC-CGACC-CGACC
1 CGACCACGACCACGACC
111716 CGAGACGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
22 5 0.13
23 26 0.68
24 7 0.18
ACGTcount: A:0.27, C:0.55, G:0.18, T:0.00
Consensus pattern (24 bp):
CGACCACGACCACGACCACGACCC
Found at i:111683 original size:29 final size:29
Alignment explanation
Indices: 111650--111715 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
111640 GACACGTATT
111650 ACCACGACCACGACCACGACCACGACCCG
1 ACCACGACCACGACCACGACCACGACCCG
*
111679 ACCACGACCACGACCACGACCCCGACCCG
1 ACCACGACCACGACCACGACCACGACCCG
111708 ACC-CGACC
1 ACCACGACC
111716 CGAGACGAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
28 5 0.14
29 31 0.86
ACGTcount: A:0.29, C:0.55, G:0.17, T:0.00
Consensus pattern (29 bp):
ACCACGACCACGACCACGACCACGACCCG
Found at i:112222 original size:6 final size:6
Alignment explanation
Indices: 112211--112282 Score: 123
Period size: 6 Copynumber: 12.5 Consensus size: 6
112201 TCTCGTCTCA
112211 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT -G--GT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
112256 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
112283 AATACGTGTC
Statistics
Matches: 63, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
3 2 0.03
4 1 0.02
5 1 0.02
6 59 0.94
ACGTcount: A:0.00, C:0.15, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:112259 original size:27 final size:27
Alignment explanation
Indices: 112221--112276 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
112211 GGTCGTGGTC
112221 GTGGTCGTGGTCGTGGTCGTGGTCGTG
1 GTGGTCGTGGTCGTGGTCGTGGTCGTG
112248 GTGGTCGTGGTCGTGGTCGTGGTCGTG
1 GTGGTCGTGGTCGTGGTCGTGGTCGTG
112275 GT
1 GT
112277 CGTGGTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.00, C:0.14, G:0.52, T:0.34
Consensus pattern (27 bp):
GTGGTCGTGGTCGTGGTCGTGGTCGTG
Found at i:112428 original size:20 final size:20
Alignment explanation
Indices: 112375--112454 Score: 99
Period size: 20 Copynumber: 3.9 Consensus size: 20
112365 ACAACGAATT
112375 TGGAAAATCGCAACGAC-AAC
1 TGGAAAATCGCAACG-CGAAC
**
112395 TGTAGACTATCGCAACGCGAAC
1 TG--GAAAATCGCAACGCGAAC
*
112417 TGGAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGAAC
112437 TGGAAAATCGCAACGCGA
1 TGGAAAATCGCAACGCGA
112455 TTTTCAACTA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
20 35 0.67
21 1 0.02
22 16 0.31
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.12
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAC
Found at i:112473 original size:21 final size:21
Alignment explanation
Indices: 112447--112496 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
112437 TGGAAAATCG
112447 CAACGCGATTTTCAACTATCA
1 CAACGCGATTTTCAACTATCA
* *
112468 CAACGCGATTTTCAATTATCG
1 CAACGCGATTTTCAACTATCA
112489 CAACGCGA
1 CAACGCGA
112497 ATTTGCGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (21 bp):
CAACGCGATTTTCAACTATCA
Done.