Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003473.1 Hibiscus syriacus cultivar Beakdansim tig00007344_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: 111669
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Found at i:2892 original size:7 final size:6
Alignment explanation
Indices: 2885--2909 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2875 TTAAATTTTA
2885 AAAATT AAAATT AAAATT AAAATT A
1 AAAATT AAAATT AAAATT AAAATT A
2910 TTATTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:2912 original size:21 final size:22
Alignment explanation
Indices: 2864--2912 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
2854 ACTACTAACG
* *
2864 AATTATTAAATTTAAATTTTAA
1 AATTATTAAAATTAAATATTAA
2886 AA--ATTAAAATTAAA-ATTAA
1 AATTATTAAAATTAAATATTAA
2905 AATTATTA
1 AATTATTA
2913 TTATATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 6 0.26
20 11 0.48
21 4 0.17
22 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTATTAAAATTAAATATTAA
Found at i:3358 original size:35 final size:35
Alignment explanation
Indices: 3312--3384 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
3302 AACAGTCCTC
* **
3312 ATTTCATTCTAAACCCCAATTTCCAAAGTAATTCA
1 ATTTCATTCTAAACCCCAAATTCCAAAACAATTCA
*
3347 ATTTCATTCTAAACCCTAAATTCCAAAACAATTCA
1 ATTTCATTCTAAACCCCAAATTCCAAAACAATTCA
3382 ATT
1 ATT
3385 CAATTCAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.40, C:0.25, G:0.01, T:0.34
Consensus pattern (35 bp):
ATTTCATTCTAAACCCCAAATTCCAAAACAATTCA
Found at i:4365 original size:28 final size:27
Alignment explanation
Indices: 4334--4396 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
4324 AGTTGATACA
*
4334 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** *
4362 ATATATTTTTAAAATAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
4390 ATATTTT
1 ATATTTT
4397 CATATTTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 3 0.10
28 22 0.73
29 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:4492 original size:15 final size:16
Alignment explanation
Indices: 4468--4504 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
4458 TTTAATTTCT
4468 TATT-AAAAATA-AAA
1 TATTCAAAAATATAAA
4482 TATTCAAAAATATAAA
1 TATTCAAAAATATAAA
4498 TGATTCA
1 T-ATTCA
4505 TACATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
TATTCAAAAATATAAA
Found at i:5184 original size:14 final size:15
Alignment explanation
Indices: 5159--5188 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5149 AATTTAAATC
5159 TTTTATTTAATTATA
1 TTTTATTTAATTATA
5174 TTTTA-TTAATTATA
1 TTTTATTTAATTATA
5188 T
1 T
5189 CTTTTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTATTTAATTATA
Found at i:5199 original size:16 final size:15
Alignment explanation
Indices: 5164--5205 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
5154 AAATCTTTTA
5164 TTTAATTATAT-TTT
1 TTTAATTATATCTTT
*
5178 ATTAATTATATCTTT
1 TTTAATTATATCTTT
*
5193 TTATAATTTTATC
1 TT-TAATTATATC
5206 AATATTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 10 0.43
15 4 0.17
16 9 0.39
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTAATTATATCTTT
Found at i:5850 original size:30 final size:32
Alignment explanation
Indices: 5783--5850 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 32
5773 TGAACCTGTG
*
5783 TTATAAAAACATTAATAAAATACATCACAACA
1 TTATAAAAACATTAATAAAATACATCAAAACA
*
5815 -T-TAAAAATATTAAT-AAA-A-ATCAAAACGA
1 TTATAAAAACATTAATAAAATACATCAAAAC-A
5843 TTATAAAA
1 TTATAAAA
5851 TGAAATTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
27 7 0.23
28 2 0.06
29 4 0.13
30 17 0.55
31 1 0.03
ACGTcount: A:0.62, C:0.10, G:0.01, T:0.26
Consensus pattern (32 bp):
TTATAAAAACATTAATAAAATACATCAAAACA
Found at i:5956 original size:3 final size:3
Alignment explanation
Indices: 5948--5974 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5938 TAGTTTAACC
5948 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
5975 ACTTAGTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:8198 original size:49 final size:49
Alignment explanation
Indices: 8126--8263 Score: 240
Period size: 49 Copynumber: 2.8 Consensus size: 49
8116 TGAAGCAACA
*
8126 CTGCAGTTGTCAAAGGCTCGGGCTGTCGAAAACAGGGATGGACCGAAGG
1 CTGCAGTTGTCAAAGGCTTGGGCTGTCGAAAACAGGGATGGACCGAAGG
8175 CTGCAGTTGTCAAAGGCTTGGGCTGTCGAAAACAGGGATGGACCGAAGG
1 CTGCAGTTGTCAAAGGCTTGGGCTGTCGAAAACAGGGATGGACCGAAGG
* * *
8224 CTGCAGTTGTCAAAGGCTTGGGCTGTTGAAGATAGGGATG
1 CTGCAGTTGTCAAAGGCTTGGGCTGTCGAAAACAGGGATG
8264 ACCTGAATTT
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 85 1.00
ACGTcount: A:0.25, C:0.17, G:0.37, T:0.20
Consensus pattern (49 bp):
CTGCAGTTGTCAAAGGCTTGGGCTGTCGAAAACAGGGATGGACCGAAGG
Found at i:13134 original size:16 final size:16
Alignment explanation
Indices: 13113--13146 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
13103 CGCATACACA
13113 TTATAGATGAAACTGT
1 TTATAGATGAAACTGT
13129 TTATAGATGAAACTGT
1 TTATAGATGAAACTGT
13145 TT
1 TT
13147 GAATTCAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (16 bp):
TTATAGATGAAACTGT
Found at i:14376 original size:2 final size:2
Alignment explanation
Indices: 14371--14408 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
14361 ATGTAATTAA
*
14371 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14409 AATAATAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:14392 original size:17 final size:17
Alignment explanation
Indices: 14370--14402 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
14360 AATGTAATTA
14370 AATATATATATATATAT
1 AATATATATATATATAT
14387 AATATATATATATATA
1 AATATATATATATATA
14403 CATATAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATATATATATATATAT
Found at i:15885 original size:106 final size:106
Alignment explanation
Indices: 15701--16973 Score: 1942
Period size: 106 Copynumber: 12.0 Consensus size: 106
15691 GCATTGTTCC
* * * * * *
15701 GAGTCCAATATCCTCCATCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * * * *
15766 CCAACCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
15807 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
15872 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
15913 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
15978 CTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
16019 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
16084 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
16125 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
16190 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTACATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
16231 GAGT-CAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
16295 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
16336 GAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
16400 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
16441 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTAGCTCTGAAATTGAGAAGTTTTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
16506 CCAGTGGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
16547 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
16612 CCAGCGGTCCCTTCGTCATAAAGTTGAACTTGAGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
16653 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATT-TGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
16717 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTATG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
16758 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
** *
16823 CCAGCGGTCTTTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
16864 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTTTGAATTTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
16929 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
16970 GAGT
1 GAGT
16974 GGCACGTTAT
Statistics
Matches: 1074, Mismatches: 89, Indels: 8
0.92 0.08 0.01
Matches are distributed among these distances:
105 295 0.27
106 778 0.72
107 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:16338 original size:211 final size:212
Alignment explanation
Indices: 15701--16973 Score: 1946
Period size: 211 Copynumber: 6.0 Consensus size: 212
15691 GCATTGTTCC
* * *
15701 GAGTCCAATATCC-TC-CATCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGAC
1 GAGTCCAATATCCTTCGC-T-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGAC
* * * * * * *
15764 AACCAACCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTTGTTGTG
64 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
*
15829 AAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
129 AAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
* *
15894 GTTGAACTTGTGTTGTCTC
194 GTTGAACTTGCGTTGTCTG
* *
15913 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
15978 CTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* * *
16043 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCATGAAGT
131 GTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
16108 TGAACTTGCGTTGTCTG
196 TGAACTTGCGTTGTCTG
* * * *
16125 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
16190 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTACATTGTCTGGAGT-CAATATCTTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
16254 GTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*
16319 TGAACTTACGTTGTCTG
196 TGAACTTGCGTTGTCTG
*
16336 GAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
16400 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* * * * * *
16465 GTTGAAATTAGCTCTGAAATTGAGAAGTTTTTTGTTGACAACCAGTGGTCCCTTCATCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*
16530 TGAACTTGTGTTGTCTG
196 TGAACTTGCGTTGTCTG
*
16547 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * * *
16612 CCAGCGGTCCCTTCGTCATAAAGTTGAACTTGAGTTGTCTTGAGTCCAATATCCTTCGCTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* * *
16677 GTTGAAATTGGCTCTAAAATT-TGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*
16741 TGAACTTGCGTTGTATG
196 TGAACTTGCGTTGTCTG
* * *
16758 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
** * *
16823 CCAGCGGTCTTTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGATGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* * * *
16888 GTTGAAATTGGCTTTGAATTTGGGAAGTTGTTTGTTGACAACCAGTC-GTCCCTTCGTTGTGAAG
131 GTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAG-CGGTCCCTTCGTCGTGAAG
* *
16952 TTGAACTTGTGTTGTCTC
195 TTGAACTTGCGTTGTCTG
16970 GAGT
1 GAGT
16974 GGCACGTTAT
Statistics
Matches: 967, Mismatches: 88, Indels: 12
0.91 0.08 0.01
Matches are distributed among these distances:
210 53 0.05
211 477 0.49
212 432 0.45
213 4 0.00
214 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (212 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
GTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
TGAACTTGCGTTGTCTG
Found at i:16558 original size:317 final size:318
Alignment explanation
Indices: 15701--16973 Score: 1957
Period size: 317 Copynumber: 4.0 Consensus size: 318
15691 GCATTGTTCC
* *
15701 GAGTCCAATATCC-TC-CATCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGAC
1 GAGTCCAATATCCTTCGC-T-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
* * * * * * *
15764 AACCAACCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTTGTTGTG
64 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
*
15829 AAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
129 AAGTTGAAATTGGCTCCGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
* * *
15894 GTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTAAAATTG
194 GTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG
* *
15959 GGAAGTTGTTTGTTGACAACTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
259 GGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
* * *
16019 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
16084 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* * *
16149 GTTGAAATTGACTCCGAAATTGGGAAATTGTTTGTTGACAACCAACGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCCGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
*** * *
16214 TGAACTTACATTGTCTGGAGT-CAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGG
196 TGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
*
16278 AAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
261 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
* *
16336 GAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
16400 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* * * * * *
16465 GTTGAAATTAGCTCTGAAATTGAGAAGTTTTTTGTTGACAACCAGTGGTCCCTTCATCGTGAAGT
131 GTTGAAATTGGCTCCGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
16530 TGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
196 TGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
* * * *
16595 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCATAAAGTTGAACTTGA-GTTGTCTT
261 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT-ACGTTGTCTG
* * *
16653 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATT-TGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
16717 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTATGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* * * **
16782 GTTGAAATTGGTTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCTTTTCGTCGTGAAGT
131 GTTGAAATTGGCTCCGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
* * *
16847 TGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTTTGAATTTGGG
196 TGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
* ** *
16912 AAGTTGTTTGTTGACAACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
261 AAGTTGTTTGTTGACAACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
16970 GAGT
1 GAGT
16974 GGCACGTTAT
Statistics
Matches: 877, Mismatches: 71, Indels: 15
0.91 0.07 0.02
Matches are distributed among these distances:
316 154 0.18
317 526 0.60
318 194 0.22
319 3 0.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (318 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
GTTGAAATTGGCTCCGAAATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
TGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
Found at i:18571 original size:19 final size:17
Alignment explanation
Indices: 18547--18609 Score: 67
Period size: 19 Copynumber: 3.6 Consensus size: 17
18537 TTTATCCCTT
18547 TTTCTTTTGATTTTTGTTC
1 TTTCTTTT--TTTTTGTTC
18566 TTTCTTTTTTTTTG-T-
1 TTTCTTTTTTTTTGTTC
*
18581 TTTCTTCTTTTTTTCTTC
1 TTTCTT-TTTTTTTGTTC
18599 TTTGCTTTTTT
1 TTT-CTTTTTT
18610 ATTTTTGCCC
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
15 6 0.15
16 8 0.21
17 7 0.18
18 7 0.18
19 11 0.28
ACGTcount: A:0.02, C:0.13, G:0.06, T:0.79
Consensus pattern (17 bp):
TTTCTTTTTTTTTGTTC
Found at i:18575 original size:15 final size:15
Alignment explanation
Indices: 18557--18609 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
18547 TTTCTTTTGA
18557 TTTTTGTTCTTTCTTTT
1 TTTTTGTTCTTTC--TT
*
18574 TTTTTGTTTTCTTCTT
1 TTTTTGTTCT-TTCTT
*
18590 TTTTTCTTCTTTGCTT
1 TTTTTGTTCTTT-CTT
18606 TTTT
1 TTTT
18610 ATTTTTGCCC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 2 0.06
16 17 0.55
17 9 0.29
18 3 0.10
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (15 bp):
TTTTTGTTCTTTCTT
Found at i:18596 original size:11 final size:12
Alignment explanation
Indices: 18558--18607 Score: 52
Period size: 11 Copynumber: 4.3 Consensus size: 12
18548 TTCTTTTGAT
*
18558 TTTTGTTCTTTC
1 TTTTCTTCTTTC
*
18570 TTTT-TT-TTTG
1 TTTTCTTCTTTC
18580 TTTTCTTCTTT-
1 TTTTCTTCTTTC
18591 TTTTCTTCTTTGC
1 TTTTCTTCTTT-C
18604 TTTT
1 TTTT
18608 TTATTTTTGC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
10 7 0.21
11 15 0.45
12 7 0.21
13 4 0.12
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (12 bp):
TTTTCTTCTTTC
Found at i:23041 original size:18 final size:18
Alignment explanation
Indices: 23006--23115 Score: 52
Period size: 18 Copynumber: 5.9 Consensus size: 18
22996 AATATAATGA
23006 AAAT-AAATAA-ATAGTAT
1 AAATAAAATAATATA-TAT
23023 AAATAAAATAATATATAT
1 AAATAAAATAATATATAT
* * *
23041 ATAT-ATATATATGTATAAT
1 AAATAAAATA-ATATAT-AT
* *
23060 ATAATAAAATACTAAATAGT
1 A-AATAAAATAATATATA-T
23080 -AATAATAATAATA-ATAAT
1 AAATAA-AATAATATAT-AT
23098 AAATGAAAAATAA-ATATA
1 AAAT--AAAATAATATATA
23116 CATATAATAT
Statistics
Matches: 71, Mismatches: 9, Indels: 24
0.68 0.09 0.23
Matches are distributed among these distances:
17 8 0.11
18 25 0.35
19 19 0.27
20 13 0.18
21 6 0.08
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.33
Consensus pattern (18 bp):
AAATAAAATAATATATAT
Found at i:23045 original size:22 final size:22
Alignment explanation
Indices: 22992--23045 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
22982 ACAAAGAAAC
*
22992 TAAAAATAT-AATGAAAATAAA
1 TAAATATATAAATGAAAATAAA
23013 TAAATAGTATAAAT-AAAATAATA
1 TAAATA-TATAAATGAAAATAA-A
*
23036 TATATATATA
1 TAAATATATA
23046 TATATATGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 5 0.18
22 14 0.50
23 9 0.32
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (22 bp):
TAAATATATAAATGAAAATAAA
Found at i:23218 original size:2 final size:2
Alignment explanation
Indices: 23173--23201 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23163 TGAAGTAAGA
23173 AT AT 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 AT AT A
23202 GAAAAATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23794 original size:37 final size:37
Alignment explanation
Indices: 23753--23837 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 37
23743 TGGATCTCTC
* * *
23753 TTTAGGAGTTTAAATAATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCATATT
* ** *
23790 TTTAGGAGTTTGAATCCTAGCAAAATTCTATCATATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCATATT
23827 TTTAGGAGTTT
1 TTTAGGAGTTT
23838 GAATCCTAGT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (37 bp):
TTTAGGAGTTTAAATAATAGCAAAACTCTATCATATT
Found at i:24457 original size:60 final size:60
Alignment explanation
Indices: 24393--24601 Score: 210
Period size: 60 Copynumber: 3.5 Consensus size: 60
24383 AAATAATAAA
* * * **
24393 TCTCATTTTAAATT-GATCCTTAAACTTTTGAATATT-TCAAATTCAT-ATTCAAACTATGAC
1 TCTCATTCTAAATTAG-TCCTTAAACTTTTAAACATTAT-AAATTCATCCCT-AAACTATGAC
**
24453 TCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTATACTTTCATCCCTAAACTATGAC
1 TCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTATAAATTCATCCCTAAACTATGAC
** ** *
24513 TCTCATTCTAAATTAGTCCTTAAACTTTTAAATGTTATACTTTCATACCTAAACTATGAGC
1 TCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTATAAATTCATCCCTAAACTATGA-C
* * * *
24574 -CTCTTTATAAATTAGTTCTCAAACTTTT
1 TCTCATTCTAAATTAGTCCTTAAACTTTT
24602 GAATGTGCCG
Statistics
Matches: 131, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
60 127 0.97
61 4 0.03
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.43
Consensus pattern (60 bp):
TCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTATAAATTCATCCCTAAACTATGAC
Found at i:24478 original size:31 final size:31
Alignment explanation
Indices: 24443--24538 Score: 90
Period size: 31 Copynumber: 3.2 Consensus size: 31
24433 ATTCATATTC
24443 AAACTATGACTCTCATTCTAAATTAGTCCTT
1 AAACTATGACTCTCATTCTAAATTAGTCCTT
* * ** * ** *
24474 AAACTTTTA--AACATTATACTTTCA-TCCCT
1 AAACTATGACTCTCATTCTAAATT-AGTCCTT
24503 AAACTATGACTCTCATTCTAAATTAGTCCTT
1 AAACTATGACTCTCATTCTAAATTAGTCCTT
24534 AAACT
1 AAACT
24539 TTTAAATGTT
Statistics
Matches: 45, Mismatches: 16, Indels: 8
0.65 0.23 0.12
Matches are distributed among these distances:
29 19 0.42
30 2 0.04
31 24 0.53
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (31 bp):
AAACTATGACTCTCATTCTAAATTAGTCCTT
Found at i:24607 original size:60 final size:60
Alignment explanation
Indices: 24443--24607 Score: 242
Period size: 60 Copynumber: 2.8 Consensus size: 60
24433 ATTCATATTC
** *
24443 AAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTATACTTTCATCCCT
1 AAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAATGTTATACTTTCATACCT
24503 AAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAATGTTATACTTTCATACCT
1 AAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAATGTTATACTTTCATACCT
* * * * *
24563 AAACTATGAGC-CTCTTTATAAATTAGTTCTCAAACTTTTGAATGT
1 AAACTATGA-CTCTCATTCTAAATTAGTCCTTAAACTTTTAAATGT
24608 GCCGATTTCA
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
60 95 0.99
61 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (60 bp):
AAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAATGTTATACTTTCATACCT
Found at i:36593 original size:32 final size:31
Alignment explanation
Indices: 36534--36594 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
36524 GATTTTAAAA
36534 AAGAATAGTAGAATGACCAAAATATAATTGC
1 AAGAATAGTAGAATGACCAAAATATAATTGC
* *
36565 AAGAATAAGT-GAGTGACTAAATATATAATT
1 AAGAAT-AGTAGAATGACCAAA-ATATAATT
36595 TATATTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 15 0.58
32 11 0.42
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.26
Consensus pattern (31 bp):
AAGAATAGTAGAATGACCAAAATATAATTGC
Found at i:36853 original size:15 final size:16
Alignment explanation
Indices: 36819--36852 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
36809 ACAAACTTTG
36819 TTTAGTCAAATGTTTT
1 TTTAGTCAAATGTTTT
*
36835 TTTAGTTAAATGTTTT
1 TTTAGTCAAATGTTTT
36851 TT
1 TT
36853 AATTATAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.03, G:0.12, T:0.62
Consensus pattern (16 bp):
TTTAGTCAAATGTTTT
Found at i:42914 original size:20 final size:21
Alignment explanation
Indices: 42875--42923 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
42865 ACACCATCAC
42875 TTAATTATGATGAAATTTTAAT
1 TTAATTAT-ATGAAATTTTAAT
*
42897 TTAATTAT-TGATATTTTAAT
1 TTAATTATATGAAATTTTAAT
*
42917 TTTATTA
1 TTAATTA
42924 ATTTTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 17 0.68
22 8 0.32
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (21 bp):
TTAATTATATGAAATTTTAAT
Found at i:52820 original size:48 final size:50
Alignment explanation
Indices: 52761--52865 Score: 160
Period size: 48 Copynumber: 2.1 Consensus size: 50
52751 TCAGACAAGA
*
52761 AAATTGTCATATTAGATGTATCCGACACTCA-T-TGGTGTGTTGAACCTC
1 AAATTGCCATATTAGATGTATCCGACACTCATTATGGTGTGTTGAACCTC
*
52809 AAATTGCCATATTAGATGTCTCCGACACTCATTGAATGGTGTGTTGAACCTC
1 AAATTGCCATATTAGATGTATCCGACACTCATT--ATGGTGTGTTGAACCTC
52861 AAATT
1 AAATT
52866 ATCATGAAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
48 29 0.57
49 1 0.02
52 21 0.41
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (50 bp):
AAATTGCCATATTAGATGTATCCGACACTCATTATGGTGTGTTGAACCTC
Found at i:57251 original size:97 final size:97
Alignment explanation
Indices: 57083--57281 Score: 380
Period size: 97 Copynumber: 2.1 Consensus size: 97
57073 GACATGCACA
57083 CTGTTGCCAAGGAAAGAAACAAACCGTTGCGAGTAGAGATATATGGAGAAAGAATAGAACAGCTC
1 CTGTTGCCAAGGAAAGAAACAAACCGTTGCGAGTAGAGATATATGGAGAAAGAATAGAACAGCTC
*
57148 AGATACAACTTAAACAGATAGCTATATGTTTT
66 AAATACAACTTAAACAGATAGCTATATGTTTT
*
57180 CTGTTGCCAAGGAAAGAAACAAACCGTTGCGAGTAGAGATATATGGAGAAAGGATAGAACAGCTC
1 CTGTTGCCAAGGAAAGAAACAAACCGTTGCGAGTAGAGATATATGGAGAAAGAATAGAACAGCTC
57245 AAATACAACTTAAACAGATAGCTATATGTTTT
66 AAATACAACTTAAACAGATAGCTATATGTTTT
57277 CTGTT
1 CTGTT
57282 TCTCTTTGAC
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 100 1.00
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.24
Consensus pattern (97 bp):
CTGTTGCCAAGGAAAGAAACAAACCGTTGCGAGTAGAGATATATGGAGAAAGAATAGAACAGCTC
AAATACAACTTAAACAGATAGCTATATGTTTT
Found at i:74432 original size:61 final size:61
Alignment explanation
Indices: 74365--74497 Score: 248
Period size: 61 Copynumber: 2.2 Consensus size: 61
74355 TCTATTTTTA
74365 TCAAACACTCTCAAATTTCATTTTCTTTCATAATTATCTAACCTTTTGGATTTCTAACCTC
1 TCAAACACTCTCAAATTTCATTTTCTTTCATAATTATCTAACCTTTTGGATTTCTAACCTC
* *
74426 TCAAACACTGTCAAATTTCATTTTCTTTCATAATTATCTAATCTTTTGGATTTCTAACCTC
1 TCAAACACTCTCAAATTTCATTTTCTTTCATAATTATCTAACCTTTTGGATTTCTAACCTC
74487 TCAAACACTCT
1 TCAAACACTCT
74498 TTATCCTCCC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 69 1.00
ACGTcount: A:0.29, C:0.24, G:0.04, T:0.44
Consensus pattern (61 bp):
TCAAACACTCTCAAATTTCATTTTCTTTCATAATTATCTAACCTTTTGGATTTCTAACCTC
Found at i:75535 original size:19 final size:19
Alignment explanation
Indices: 75507--75575 Score: 129
Period size: 19 Copynumber: 3.6 Consensus size: 19
75497 ATGCAATTAA
75507 TGCATCGATGCATAAGGAG
1 TGCATCGATGCATAAGGAG
*
75526 TGCATTGATGCATAAGGAG
1 TGCATCGATGCATAAGGAG
75545 TGCATCGATGCATAAGGAG
1 TGCATCGATGCATAAGGAG
75564 TGCATCGATGCA
1 TGCATCGATGCA
75576 CATGTTAAGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.23
Consensus pattern (19 bp):
TGCATCGATGCATAAGGAG
Found at i:75584 original size:24 final size:23
Alignment explanation
Indices: 75519--75620 Score: 75
Period size: 19 Copynumber: 4.9 Consensus size: 23
75509 CATCGATGCA
*
75519 TAAGGAGTGCATTGATG--CA--
1 TAAGGAGTGCATCGATGCACATT
75538 TAAGGAGTGCATCGATG--CA--
1 TAAGGAGTGCATCGATGCACATT
75557 TAAGGAGTGCATCGATGCACATGT
1 TAAGGAGTGCATCGATGCACAT-T
*
75581 TAAGG-GATGCATCGATACAC-TT
1 TAAGGAG-TGCATCGATGCACATT
*
75603 T-A-GAATGCATCGATGCAC
1 TAAGGAGTGCATCGATGCAC
75621 TTCAAGGGAA
Statistics
Matches: 72, Mismatches: 4, Indels: 13
0.81 0.04 0.15
Matches are distributed among these distances:
19 35 0.49
20 13 0.18
21 3 0.04
22 2 0.03
23 2 0.03
24 17 0.24
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (23 bp):
TAAGGAGTGCATCGATGCACATT
Found at i:76524 original size:29 final size:31
Alignment explanation
Indices: 76467--76537 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
76457 CAATTTAAGG
*
76467 CAAAATGGTTTTTGGACTTGAATTGAATTTA-
1 CAAAAT-GTATTTGGACTTGAATTGAATTTAT
76498 CAAAATGTATTTGGACTT-AATTGAATTTATT
1 CAAAATGTATTTGGACTTGAATTGAATTTA-T
76529 CAAAATGTA
1 CAAAATGTA
76538 CAAAAATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 11 0.30
30 11 0.30
31 15 0.41
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (31 bp):
CAAAATGTATTTGGACTTGAATTGAATTTAT
Found at i:77146 original size:29 final size:31
Alignment explanation
Indices: 77089--77159 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
77079 CAATTTAAGG
*
77089 CAAAATGGTTTTTGGACTTGAATTGAATTTA-
1 CAAAAT-GTATTTGGACTTGAATTGAATTTAT
77120 CAAAATGTATTTGGACTT-AATTGAATTTATT
1 CAAAATGTATTTGGACTTGAATTGAATTTA-T
77151 CAAAATGTA
1 CAAAATGTA
77160 CAAAAATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 11 0.30
30 11 0.30
31 15 0.41
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (31 bp):
CAAAATGTATTTGGACTTGAATTGAATTTAT
Found at i:77252 original size:19 final size:19
Alignment explanation
Indices: 77230--77279 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
77220 TAATTTACAA
77230 TTTGAACAGTAAATCACTG
1 TTTGAACAGTAAATCACTG
77249 TTTGAACAGTAAATCACTG
1 TTTGAACAGTAAATCACTG
77268 TTTGAACAGTAA
1 TTTGAACAGTAA
77280 CCCGAGGCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (19 bp):
TTTGAACAGTAAATCACTG
Found at i:77410 original size:20 final size:21
Alignment explanation
Indices: 77385--77425 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
77375 ATTTGAATAT
*
77385 TATGAA-GGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
77405 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
77426 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:77487 original size:21 final size:21
Alignment explanation
Indices: 77454--77493 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
77444 TTTTTGCAGA
*
77454 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
77476 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
77494 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:79412 original size:21 final size:21
Alignment explanation
Indices: 79370--79412 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
79360 TTTATGGGCT
*
79370 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
79391 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
79412 A
1 A
79413 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:80287 original size:103 final size:103
Alignment explanation
Indices: 79959--80276 Score: 575
Period size: 103 Copynumber: 3.1 Consensus size: 103
79949 GTAGAGGGTC
*
79959 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
80024 TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
80062 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
80127 TTGATCCTTGGTATATGTATAT-AGTTATTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGA-TTCTTAAGGAATGA
80165 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
80230 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
80268 TATGTGGTC
1 TATGTGGTC
80277 CTTATGGACA
Statistics
Matches: 205, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
102 1 0.00
103 203 0.99
104 1 0.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36
Consensus pattern (103 bp):
TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:80329 original size:23 final size:23
Alignment explanation
Indices: 80296--80358 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
80286 ATTATTATAT
80296 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
80319 GGCACTCCGGTGCAATTTTACGT
1 GGCACTACGGTGCAATTCTACGC
80342 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
80359 ATATGAGCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 34 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:81081 original size:23 final size:23
Alignment explanation
Indices: 81032--81081 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
81022 GGCACTTCGG
*
81032 TACGCGGCACTACGGTGCAATTC
1 TACGCGGCACTACGGTGCAATTA
* * *
81055 TACGTGGCACTTCGGTGCATTTA
1 TACGCGGCACTACGGTGCAATTA
81078 TACG
1 TACG
81082 AGCTGTGGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (23 bp):
TACGCGGCACTACGGTGCAATTA
Found at i:88945 original size:24 final size:26
Alignment explanation
Indices: 88917--88968 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
88907 TTTTAGGAAG
**
88917 ATAAAAAT-ATATTTTTAATAAA-AA
1 ATAAAAATAATATTTAAAATAAATAA
88941 AT-AAAATAATATTTAAAATAAATAA
1 ATAAAAATAATATTTAAAATAAATAA
88966 ATA
1 ATA
88969 TGAATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
23 5 0.22
24 14 0.61
25 4 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
ATAAAAATAATATTTAAAATAAATAA
Found at i:88965 original size:21 final size:21
Alignment explanation
Indices: 88920--88980 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
88910 TAGGAAGATA
* *
88920 AAAATATATTTTTAATAAAAAAT
1 AAAATA-ATATTTAA-AATAAAT
88943 AAAATAATATTTAAAATAAAT
1 AAAATAATATTTAAAATAAAT
*
88964 AAATATGA-ATTTAAAAT
1 AAA-ATAATATTTAAAAT
88981 TTTCAGAACG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 18 0.53
22 10 0.29
23 6 0.18
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
AAAATAATATTTAAAATAAAT
Found at i:90168 original size:27 final size:27
Alignment explanation
Indices: 90136--90190 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
90126 TCACTTTTTA
90136 TAAAAATAAATAAAAATGCAATAAAAAT
1 TAAAAATAAAT-AAAATGCAATAAAAAT
* *
90164 TAAAAATGAATAAAATTCAATAAAAAT
1 TAAAAATAAATAAAATGCAATAAAAAT
90191 ATAATGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.24
Consensus pattern (27 bp):
TAAAAATAAATAAAATGCAATAAAAAT
Found at i:91457 original size:21 final size:22
Alignment explanation
Indices: 91428--91471 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
91418 AAGAATTACA
* *
91428 TTATATTTTTATTGAATTTTAT
1 TTATATTTTAATTCAATTTTAT
*
91450 TTAT-TTTTAATTCATTTTTAT
1 TTATATTTTAATTCAATTTTAT
91471 T
1 T
91472 GCATTTATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (22 bp):
TTATATTTTAATTCAATTTTAT
Found at i:91476 original size:11 final size:10
Alignment explanation
Indices: 91432--91489 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
91422 ATTACATTAT
*
91432 ATTTTTATTG
1 ATTTTTATTC
* *
91442 AATTTTATTT
1 ATTTTTATTC
91452 ATTTTTAATTC
1 ATTTTT-ATTC
91463 ATTTTTATTGC
1 ATTTTTATT-C
* *
91474 ATTTATATTT
1 ATTTTTATTC
91484 ATTTTT
1 ATTTTT
91490 TTTTAAAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
10 21 0.54
11 18 0.46
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.69
Consensus pattern (10 bp):
ATTTTTATTC
Found at i:93291 original size:21 final size:21
Alignment explanation
Indices: 93249--93291 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
93239 TTTCTGGGCT
* * *
93249 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
93270 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
93291 A
1 A
93292 ACGAACCATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:93863 original size:2 final size:2
Alignment explanation
Indices: 93856--93883 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
93846 TGAATCATTG
93856 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
93884 GAATATAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:95459 original size:21 final size:21
Alignment explanation
Indices: 95430--95474 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
95420 GATTTATGGG
* *
95430 CAAGGGGAATCGATACCCATT
1 CAAGAGGAACCGATACCCATT
*
95451 CAAGAGGAACCGATACCCCTT
1 CAAGAGGAACCGATACCCATT
95472 CAA
1 CAA
95475 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.29, G:0.20, T:0.16
Consensus pattern (21 bp):
CAAGAGGAACCGATACCCATT
Found at i:96878 original size:103 final size:103
Alignment explanation
Indices: 96653--96870 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
96643 GTCGAGGGTC
96653 TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATAC
* *
96718 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
96756 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATAC
*
96821 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
96859 TATGTGGTCCTT
1 TATGTGGTCCTT
96871 ATGGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:97000 original size:23 final size:23
Alignment explanation
Indices: 96886--96992 Score: 169
Period size: 23 Copynumber: 4.7 Consensus size: 23
96876 CATTATTATA
*
96886 TGGCACTACGGTGCAATTCTACA
1 TGGCACTACGGTGCAATTCTACG
96909 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
96932 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * *
96955 CGGCACTATGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTACG
*
96978 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
96993 TTTATATGAG
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 77 1.00
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.27
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Done.