Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004132.1 Hibiscus syriacus cultivar Beakdansim tig00009038_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: 72596
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:15667 original size:51 final size:51
Alignment explanation
Indices: 15591--15687 Score: 194
Period size: 51 Copynumber: 1.9 Consensus size: 51
15581 ACTCGTAAGG
15591 GGTGGGTTAGTCAGGGGTATGATGTTCAATGTAGAATTCCTGAGGCTACGA
1 GGTGGGTTAGTCAGGGGTATGATGTTCAATGTAGAATTCCTGAGGCTACGA
15642 GGTGGGTTAGTCAGGGGTATGATGTTCAATGTAGAATTCCTGAGGC
1 GGTGGGTTAGTCAGGGGTATGATGTTCAATGTAGAATTCCTGAGGC
15688 CATATCTCAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.23, C:0.11, G:0.36, T:0.30
Consensus pattern (51 bp):
GGTGGGTTAGTCAGGGGTATGATGTTCAATGTAGAATTCCTGAGGCTACGA
Found at i:20076 original size:19 final size:19
Alignment explanation
Indices: 20052--20122 Score: 133
Period size: 19 Copynumber: 3.7 Consensus size: 19
20042 GAATGCATTT
20052 CATGCATCGATGCACATAC
1 CATGCATCGATGCACATAC
*
20071 CATGCATCGATGTACATAC
1 CATGCATCGATGCACATAC
20090 CATGCATCGATGCACATAC
1 CATGCATCGATGCACATAC
20109 CATGCATCGATGCA
1 CATGCATCGATGCA
20123 ATGAGGTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.23
Consensus pattern (19 bp):
CATGCATCGATGCACATAC
Found at i:20169 original size:57 final size:56
Alignment explanation
Indices: 20108--20214 Score: 144
Period size: 56 Copynumber: 1.9 Consensus size: 56
20098 GATGCACATA
* * *
20108 CCATGCATCGATGCAATGAGG-TTTTTATGAAAACATCGAATGCATTTGATGTACCAG
1 CCATGCATCGATGCAATCAGGCTATTT-TG-AAACATCGAATGCACTTGATGTACCAG
* *
20165 CCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATG
1 CCATGCATCGATGCAATCAGGCTATTTTGAAACATCGAATGCACTTGATG
20215 CATCGATGCA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
56 20 0.45
57 20 0.45
58 4 0.09
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30
Consensus pattern (56 bp):
CCATGCATCGATGCAATCAGGCTATTTTGAAACATCGAATGCACTTGATGTACCAG
Found at i:25272 original size:2 final size:2
Alignment explanation
Indices: 25260--25315 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
25250 TTCTTCTTTT
25260 TA TA T- 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
25301 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
25316 GCATGCAAGG
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25649 original size:52 final size:52
Alignment explanation
Indices: 25571--25689 Score: 175
Period size: 52 Copynumber: 2.3 Consensus size: 52
25561 TCGAGATTGA
* * * **
25571 ATGCCCTACATGGATTACTTCTGTCTTTTTTATGCTGATGTGAGCCTTCAAG
1 ATGCCCAACATGGATTACTTCAGTCTTTTTCATGCTGACATGAGCCTTCAAG
*
25623 ATGCCCAACATGGATTACTTCAGTCTTTTTCATGCTGACATGAGCCTTCAGG
1 ATGCCCAACATGGATTACTTCAGTCTTTTTCATGCTGACATGAGCCTTCAAG
*
25675 ATGCCCCACATGGAT
1 ATGCCCAACATGGAT
25690 AATATGGACC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 60 1.00
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.34
Consensus pattern (52 bp):
ATGCCCAACATGGATTACTTCAGTCTTTTTCATGCTGACATGAGCCTTCAAG
Found at i:27194 original size:10 final size:10
Alignment explanation
Indices: 27175--27224 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
27165 CTTGATTCAA
27175 TTTC-TTTTT
1 TTTCTTTTTT
27184 TTTCTTTTTT
1 TTTCTTTTTT
27194 TTTCTTTTTT
1 TTTCTTTTTT
*
27204 TTTATTTTTT
1 TTTCTTTTTT
*
27214 TCTTATTTTTT
1 T-TTCTTTTTT
27225 CTCTTTCTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
9 4 0.11
10 25 0.66
11 9 0.24
ACGTcount: A:0.04, C:0.08, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:27222 original size:28 final size:29
Alignment explanation
Indices: 27176--27240 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 29
27166 TTGATTCAAT
* *
27176 TTCT-TTTTTTTCTTTTTTTTTCT-TTTT
1 TTCTATTTTTTTCTTATTTTTTCTCTTTC
*
27203 TTTTATTTTTTTCTTATTTTTTCTCTTTC
1 TTCTATTTTTTTCTTATTTTTTCTCTTTC
27232 TTCTATTTT
1 TTCTATTTT
27241 CTCTTTTCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 3 0.09
28 18 0.56
29 11 0.34
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (29 bp):
TTCTATTTTTTTCTTATTTTTTCTCTTTC
Found at i:27225 original size:10 final size:9
Alignment explanation
Indices: 27175--27255 Score: 83
Period size: 9 Copynumber: 8.7 Consensus size: 9
27165 CTTGATTCAA
27175 TTTCTTTTT
1 TTTCTTTTT
27184 TTTCTTTTTT
1 TTTC-TTTTT
27194 TTTCTTTTT
1 TTTCTTTTT
27203 TTT-TATTTT
1 TTTCT-TTTT
27212 TTTCTTATTT
1 TTTCTT-TTT
*
27222 TTTCTCTTT
1 TTTCTTTTT
* *
27231 CTTCTATTT
1 TTTCTTTTT
*
27240 TCTCTTTTCT
1 TTTCTTTT-T
27250 TTTCTT
1 TTTCTT
27256 CTGATAGATG
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
8 1 0.02
9 35 0.58
10 24 0.40
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:27231 original size:16 final size:14
Alignment explanation
Indices: 27179--27255 Score: 63
Period size: 13 Copynumber: 5.6 Consensus size: 14
27169 ATTCAATTTC
27179 TTTTT-TTTCTTTT
1 TTTTTCTTTCTTTT
27192 TTTTTCTTT-TTTT
1 TTTTTCTTTCTTTT
*
27205 TTATTTTTTTCTTATT
1 TT-TTTCTTTCTT-TT
*
27221 TTTTCTCTTTCTTCT
1 TTTT-TCTTTCTTTT
*
27236 ATTTTC--TCTTTT
1 TTTTTCTTTCTTTT
*
27248 CTTTTCTT
1 TTTTTCTT
27256 CTGATAGATG
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
12 10 0.20
13 11 0.22
14 11 0.22
15 8 0.16
16 11 0.22
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTCTTTCTTTT
Found at i:27245 original size:28 final size:26
Alignment explanation
Indices: 27176--27255 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 26
27166 TTGATTCAAT
* *
27176 TTCTTTTTTTTCTTTTTTTTTCTTTTT
1 TTCTATTTTTTC-TTTTTTTTCTTTTC
*
27203 TTTTATTTTTTTCTTATTTTTTCTCTTTC
1 TTCTA-TTTTTTCTT-TTTTTTCT-TTTC
*
27232 TTCTATTTTCTCTTTTCTTTTCTT
1 TTCTATTTTTTCTTTT-TTTTCTT
27256 CTGATAGATG
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
27 8 0.18
28 29 0.66
29 7 0.16
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (26 bp):
TTCTATTTTTTCTTTTTTTTCTTTTC
Found at i:27771 original size:8 final size:8
Alignment explanation
Indices: 27758--27800 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
27748 TAAATCAATC
27758 TCTTTTTT
1 TCTTTTTT
27766 TCTTTTTT
1 TCTTTTTT
*
27774 TCTTTTCT
1 TCTTTTTT
*
27782 T-TTCTTT
1 TCTTTTTT
*
27789 TCTCTTTT
1 TCTTTTTT
27797 TCTT
1 TCTT
27801 ACTTCGATCA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
7 5 0.18
8 23 0.82
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (8 bp):
TCTTTTTT
Found at i:30316 original size:58 final size:57
Alignment explanation
Indices: 30243--30405 Score: 166
Period size: 58 Copynumber: 2.8 Consensus size: 57
30233 AATTGTTGTT
* * *
30243 AGGTGATATTTTGGGAAATATTTCGATAAAGGTGACATTTTGGGAATTATTTTG-AAA
1 AGGTGACATTATGGGAAATATTTCGA-AAAGGTGACATTTTGGGAATTATTTCGTAAA
* * * *
30300 AGGGTGACATTATGGGAAATATTTGGAAAAAGTAACATATTGGGAATTATTTCGTAAA
1 A-GGTGACATTATGGGAAATATTTCGAAAAGGTGACATTTTGGGAATTATTTCGTAAA
* * * * ** *
30358 AGGTGACACTCTAGGAATTATTTTTAAAAAGGTGACATTATGGGAATT
1 AGGTGACATTATGGGAAATA-TTTCGAAAAGGTGACATTTTGGGAATT
30406 TTCAAATGTT
Statistics
Matches: 86, Mismatches: 17, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
57 39 0.45
58 47 0.55
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.34
Consensus pattern (57 bp):
AGGTGACATTATGGGAAATATTTCGAAAAGGTGACATTTTGGGAATTATTTCGTAAA
Found at i:30364 original size:57 final size:57
Alignment explanation
Indices: 30243--30365 Score: 158
Period size: 57 Copynumber: 2.1 Consensus size: 57
30233 AATTGTTGTT
* * * * * *
30243 AGGTGATATTTTGGGAAATATTTCGATAAAGGTGACATTTTGGGAATTATTTTGAAA
1 AGGTGACATTATGGGAAATATTTCGATAAAAGTAACATATTGGGAATTATTTCGAAA
*
30300 AGGGTGACATTATGGGAAATATTTGGA-AAAAGTAACATATTGGGAATTATTTCGTAAA
1 A-GGTGACATTATGGGAAATATTTCGATAAAAGTAACATATTGGGAATTATTTCG-AAA
30358 AGGTGACA
1 AGGTGACA
30366 CTCTAGGAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
57 31 0.54
58 26 0.46
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (57 bp):
AGGTGACATTATGGGAAATATTTCGATAAAAGTAACATATTGGGAATTATTTCGAAA
Found at i:30387 original size:57 final size:57
Alignment explanation
Indices: 30256--30405 Score: 151
Period size: 57 Copynumber: 2.6 Consensus size: 57
30246 TGATATTTTG
* * * * * *
30256 GGAAATATTTCGATAAAGGTGACATTTTGGGAATTATTTTGAAAAGGGTGACATTATG
1 GGAAATATTTGGAAAAAGGTAACA-TTTGGGAATTATTTCGAAAAGGGTGACACTATA
*
30314 GGAAATATTTGGAAAAA-GTAACATATTGGGAATTATTTCGTAAAA-GGTGACACTCTA
1 GGAAATATTTGGAAAAAGGTAACAT-TTGGGAATTATTTCG-AAAAGGGTGACACTATA
* ** *
30371 GGAATTATTTTTAAAAAGGTGACATTATGGGAATT
1 GGAAATATTTGGAAAAAGGTAACATT-TGGGAATT
30406 TTCAAATGTT
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
56 1 0.01
57 43 0.56
58 33 0.43
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.33
Consensus pattern (57 bp):
GGAAATATTTGGAAAAAGGTAACATTTGGGAATTATTTCGAAAAGGGTGACACTATA
Found at i:30404 original size:29 final size:29
Alignment explanation
Indices: 30243--30405 Score: 150
Period size: 29 Copynumber: 5.7 Consensus size: 29
30233 AATTGTTGTT
* * * * *
30243 AGGTGATATTTTGGGAAATATTTCGATAA
1 AGGTGACATTATGGGAATTATTTGGAAAA
* *
30272 AGGTGACATTTTGGGAATTATTTTGAAAA
1 AGGTGACATTATGGGAATTATTTGGAAAA
* *
30301 GGGTGACATTATGGGAAATATTTGGAAAA
1 AGGTGACATTATGGGAATTATTTGGAAAA
* * *
30330 A-GTAACA-TATTGGGAATTATTTCGTAAA
1 AGGTGACATTA-TGGGAATTATTTGGAAAA
* * * **
30358 AGGTGACACTCTAGGAATTATTTTTAAAA
1 AGGTGACATTATGGGAATTATTTGGAAAA
30387 AGGTGACATTATGGGAATT
1 AGGTGACATTATGGGAATT
30406 TTCAAATGTT
Statistics
Matches: 109, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 2 0.02
28 21 0.19
29 85 0.78
30 1 0.01
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.34
Consensus pattern (29 bp):
AGGTGACATTATGGGAATTATTTGGAAAA
Found at i:35506 original size:13 final size:13
Alignment explanation
Indices: 35488--35514 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35478 TTTTTGCCTT
35488 TGGCTGAATTTGC
1 TGGCTGAATTTGC
35501 TGGCTGAATTTGC
1 TGGCTGAATTTGC
35514 T
1 T
35515 TACAATAACA
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:0.15, C:0.15, G:0.30, T:0.41
Consensus pattern (13 bp):
TGGCTGAATTTGC
Found at i:37094 original size:29 final size:29
Alignment explanation
Indices: 37062--37127 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
37052 GGTAACATAT
**
37062 TGGGAATTATTTCGTAAAAGGTGACACTC
1 TGGGAATTATTTCAAAAAAGGTGACACTC
* * *
37091 TGGGAATTATTTTAAAAAAGGTGACATTT
1 TGGGAATTATTTCAAAAAAGGTGACACTC
37120 TGGGAATT
1 TGGGAATT
37128 TTCAAATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35
Consensus pattern (29 bp):
TGGGAATTATTTCAAAAAAGGTGACACTC
Found at i:41005 original size:2 final size:2
Alignment explanation
Indices: 40998--41029 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
40988 ATAAAAGTTA
*
40998 AT AT AT AT AT AT AC 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
41030 CATACACGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:41280 original size:21 final size:22
Alignment explanation
Indices: 41239--41289 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
41229 TGACTATCGT
41239 ATTGCGA-TTTCCCAAATTCGC
1 ATTGCGATTTTCCCAAATTCGC
* *
41260 GTTGCGATTTTCCTAAA-TCGC
1 ATTGCGATTTTCCCAAATTCGC
*
41281 AATGCGATT
1 ATTGCGATT
41290 ACGTAAATCG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (22 bp):
ATTGCGATTTTCCCAAATTCGC
Found at i:41307 original size:41 final size:41
Alignment explanation
Indices: 41262--41390 Score: 147
Period size: 41 Copynumber: 3.2 Consensus size: 41
41252 AAATTCGCGT
*
41262 TGCGATTTTCCTAAATCGCAATGCGATTACGTAAATCGCAA
1 TGCGATTTACCTAAATCGCAATGCGATTACGTAAATCGCAA
* ***
41303 TGCGAATTAGGAAAATCGCAATGCGATTACGTAAATCGCAA
1 TGCGATTTACCTAAATCGCAATGCGATTACGTAAATCGCAA
* * * *
41344 TGCGA-TTACGT-ATTCGCATTGCGATTTACGT-AATCGCAT
1 TGCGATTTACCTAAATCGCAATGCGA-TTACGTAAATCGCAA
41383 TGCGATTT
1 TGCGATTT
41391 TTCTAATTCG
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
39 23 0.30
40 12 0.16
41 41 0.54
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (41 bp):
TGCGATTTACCTAAATCGCAATGCGATTACGTAAATCGCAA
Found at i:41318 original size:21 final size:20
Alignment explanation
Indices: 41273--41389 Score: 157
Period size: 20 Copynumber: 5.8 Consensus size: 20
41263 GCGATTTTCC
41273 TAAATCGCAATGCGATTACG
1 TAAATCGCAATGCGATTACG
*
41293 TAAATCGCAATGCGAATTAGG
1 TAAATCGCAATGCG-ATTACG
*
41314 AAAATCGCAATGCGATTACG
1 TAAATCGCAATGCGATTACG
41334 TAAATCGCAATGCGATTACG
1 TAAATCGCAATGCGATTACG
* *
41354 T-ATTCGCATTGCGATTTACG
1 TAAATCGCAATGCGA-TTACG
*
41374 T-AATCGCATTGCGATT
1 TAAATCGCAATGCGATT
41390 TTTCTAATTC
Statistics
Matches: 88, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
19 13 0.15
20 57 0.65
21 18 0.20
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (20 bp):
TAAATCGCAATGCGATTACG
Found at i:41351 original size:61 final size:59
Alignment explanation
Indices: 41273--41389 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 59
41263 GCGATTTTCC
*
41273 TAAATCGCAATGCGATTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGATTACG
1 TAAATCGCAATGCGATTACGT-AATCGCAATGCGAATTACG-AAATCGCAATGCGATTACG
* * * * *
41334 TAAATCGCAATGCGATTACGTATTCGCATTGCGATTTACGTAATCGCATTGCGATT
1 TAAATCGCAATGCGATTACGTAATCGCAATGCGAATTACGAAATCGCAATGCGATT
41390 TTTCTAATTC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
59 14 0.28
60 15 0.30
61 21 0.42
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (59 bp):
TAAATCGCAATGCGATTACGTAATCGCAATGCGAATTACGAAATCGCAATGCGATTACG
Found at i:41403 original size:21 final size:22
Alignment explanation
Indices: 41253--41411 Score: 99
Period size: 20 Copynumber: 7.8 Consensus size: 22
41243 CGATTTCCCA
* *
41253 AATTCGCGTTGCGATTTT-CCT
1 AATTCGCATTGCGATTTTACGT
* *
41274 AAATCGCAATGCGA--TTACGT
1 AATTCGCATTGCGATTTTACGT
* * * * *
41294 AAATCGCAATGCGA-ATTAGGA
1 AATTCGCATTGCGATTTTACGT
* *
41315 AAATCGCAATGCGA--TTACGT
1 AATTCGCATTGCGATTTTACGT
* *
41335 AAATCGCAATGCGA--TTACGT
1 AATTCGCATTGCGATTTTACGT
41355 -ATTCGCATTGCGA-TTTACGT
1 AATTCGCATTGCGATTTTACGT
*
41375 AA-TCGCATTGCGATTTTTC-T
1 AATTCGCATTGCGATTTTACGT
*
41395 AATTCGCATTGTGATTT
1 AATTCGCATTGCGATTT
41412 ACATAGCGCC
Statistics
Matches: 120, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.11
20 60 0.50
21 47 0.39
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (22 bp):
AATTCGCATTGCGATTTTACGT
Found at i:41971 original size:20 final size:19
Alignment explanation
Indices: 41946--42009 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
41936 AAACTTAAAC
41946 TCGCAACATGAAAATGAAAA
1 TCGCAACA-GAAAATGAAAA
**
41966 TCGCAACACGAAAATGACTA
1 TCGCAACA-GAAAATGAAAA
*
41986 TCGCAATGAGAGAAATGAAAA
1 TCGCAA-CAGA-AAATGAAAA
42007 TCG
1 TCG
42010 TAACGAGAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 25 0.69
21 11 0.31
ACGTcount: A:0.48, C:0.17, G:0.19, T:0.16
Consensus pattern (19 bp):
TCGCAACAGAAAATGAAAA
Found at i:42009 original size:21 final size:20
Alignment explanation
Indices: 41957--42020 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
41947 CGCAACATGA
*
41957 AAATGAAAATCGCAACACGA-
1 AAATGAAAATCGCAAGA-GAG
**
41977 AAATGACTATCGCAATGAGAG
1 AAATGAAAATCGCAA-GAGAG
*
41998 AAATGAAAATCGTAACGAGAG
1 AAATGAAAATCGCAA-GAGAG
42019 AA
1 AA
42021 TCGCAACGCG
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
20 15 0.43
21 20 0.57
ACGTcount: A:0.52, C:0.14, G:0.20, T:0.14
Consensus pattern (20 bp):
AAATGAAAATCGCAAGAGAG
Found at i:42062 original size:19 final size:19
Alignment explanation
Indices: 42040--42146 Score: 81
Period size: 19 Copynumber: 6.1 Consensus size: 19
42030 GAAACCAAAA
*
42040 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
42059 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
42073 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
42092 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
42106 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
42125 TCCGCGTTGGGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
42145 TC
1 TC
42147 AACCAAAAGA
Statistics
Matches: 68, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
14 20 0.29
16 5 0.07
17 6 0.09
19 22 0.32
20 15 0.22
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:42081 original size:14 final size:14
Alignment explanation
Indices: 42062--42117 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
42052 TTTCATTTCG
42062 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
42076 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
42095 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
42109 CGTTGCGAT
1 CGTTGCGAT
42118 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:42087 original size:33 final size:33
Alignment explanation
Indices: 42045--42138 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
42035 CAAAATCGCA
42045 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
42078 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
** *
42111 TTGCGATAGTCATTTCCGCGTTGGGATT
1 TTGCGATTTTCATTT-CGCGTTGCGATT
42139 TTCATTTCAA
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 46 0.81
34 11 0.19
ACGTcount: A:0.11, C:0.22, G:0.23, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:44052 original size:94 final size:94
Alignment explanation
Indices: 43830--44297 Score: 716
Period size: 94 Copynumber: 5.1 Consensus size: 94
43820 TAGATTGCTT
* * * * *
43830 AGTAAATTTATTTGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAAT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* *
43891 ATTTGTCTTT-TGTTGTCGTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
43918 AGTAAATTTATTCGATTGCCGCTAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
43983 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
44012 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
44077 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
44106 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTTTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* *
44171 ATTTGTCTTTGTTTCGTCCTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * * *
44200 AGTAAATTTGTTCGTTTGCTACCAATCCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
44265 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
44293 AGTAA
1 AGTAA
44298 TGCAATCCAT
Statistics
Matches: 350, Mismatches: 24, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
88 31 0.09
90 3 0.01
91 2 0.01
92 28 0.08
93 20 0.06
94 266 0.76
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (94 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:44436 original size:39 final size:38
Alignment explanation
Indices: 44388--44462 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 38
44378 TCTTTTGGTT
*
44388 GAAATGAAAATCGCAACGAGAGAATGAAAATCACAACGC
1 GAAACGAAAATCGCAACGAGA-AATGAAAATCACAACGC
* *
44427 GAAACGAAAATCGCAACGCGAAATGAAAATCGCAAC
1 GAAACGAAAATCGCAACGAGAAATGAAAATCACAAC
44463 AAGAGAATCG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 14 0.42
39 19 0.58
ACGTcount: A:0.51, C:0.20, G:0.20, T:0.09
Consensus pattern (38 bp):
GAAACGAAAATCGCAACGAGAAATGAAAATCACAACGC
Found at i:44437 original size:19 final size:19
Alignment explanation
Indices: 44388--44503 Score: 116
Period size: 19 Copynumber: 6.3 Consensus size: 19
44378 TCTTTTGGTT
* *
44388 GAAATGAAAATCGCAACGA
1 GAAACGAAAATCGCAACGC
* *
44407 GAGAATGAAAATCACAACGC
1 GA-AACGAAAATCGCAACGC
44427 GAAACGAAAATCGCAACGC
1 GAAACGAAAATCGCAACGC
*
44446 GAAATGAAAATCGCAA--C
1 GAAACGAAAATCGCAACGC
*
44463 --AA-GAGAATCGCAACGC
1 GAAACGAAAATCGCAACGC
*
44479 GAAACCAAAAATCGCAACGC
1 GAAA-CGAAAATCGCAACGC
44499 GAAAC
1 GAAAC
44504 TATAATCGCG
Statistics
Matches: 82, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
14 10 0.12
15 2 0.02
16 1 0.01
17 1 0.01
18 2 0.02
19 33 0.40
20 33 0.40
ACGTcount: A:0.50, C:0.22, G:0.20, T:0.08
Consensus pattern (19 bp):
GAAACGAAAATCGCAACGC
Found at i:44455 original size:58 final size:53
Alignment explanation
Indices: 44388--44502 Score: 151
Period size: 53 Copynumber: 2.1 Consensus size: 53
44378 TCTTTTGGTT
*
44388 GAAATGAAAATCGCAACGAGAGAATGAAAATCACAACGCGAAA-CGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC-A-AG-A-G--AATCACAACGCGAAACCAAAAATCGCAACGC
*
44446 GAAATGAAAATCGCAACAAGAGAATCGCAACGCGAAACCAAAAATCGCAACGC
1 GAAATGAAAATCGCAACAAGAGAATCACAACGCGAAACCAAAAATCGCAACGC
44499 GAAA
1 GAAA
44503 CTATAATCGC
Statistics
Matches: 54, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
52 14 0.26
53 18 0.33
54 1 0.02
55 1 0.02
56 2 0.04
57 1 0.02
58 17 0.31
ACGTcount: A:0.50, C:0.22, G:0.20, T:0.08
Consensus pattern (53 bp):
GAAATGAAAATCGCAACAAGAGAATCACAACGCGAAACCAAAAATCGCAACGC
Found at i:44536 original size:19 final size:19
Alignment explanation
Indices: 44509--44615 Score: 98
Period size: 19 Copynumber: 5.8 Consensus size: 19
44499 GAAACTATAA
44509 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
44528 CCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
44542 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
44561 TCGCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTCATT
**
44580 TCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
44601 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
44616 ATGTTCCAGA
Statistics
Matches: 68, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
14 8 0.12
16 3 0.04
17 3 0.04
19 40 0.59
21 14 0.21
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:45086 original size:21 final size:21
Alignment explanation
Indices: 45062--45128 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
45052 TCATTCCTCG
45062 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
45083 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
45104 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
45125 AGAG
1 AGAG
45129 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:45086 original size:42 final size:42
Alignment explanation
Indices: 45040--45128 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
45030 CCTATTGTTG
* *
45040 AAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTC
1 AAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCACCATTC
* * *
45082 AAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCACCATTC
1 AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
45124 AAGAG
1 AAGAG
45129 CCCGATTCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 4 0.10
42 34 0.85
43 2 0.05
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.20
Consensus pattern (42 bp):
AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
Found at i:46498 original size:14 final size:14
Alignment explanation
Indices: 46479--46515 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
46469 ATTGTTTAAT
46479 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
46493 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
46507 TGATTTGTA
1 TGATTTGTA
46516 TAATTGATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:46636 original size:19 final size:17
Alignment explanation
Indices: 46620--46703 Score: 72
Period size: 14 Copynumber: 5.1 Consensus size: 17
46610 AAAAATGACT
46620 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
46639 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
46653 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
46672 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
46686 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
46703 A
1 A
46704 AATCGCAACG
Statistics
Matches: 53, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
14 16 0.30
16 10 0.19
17 12 0.23
19 15 0.28
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:46662 original size:33 final size:33
Alignment explanation
Indices: 46620--46746 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
46610 AAAAATGACT
46620 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
46653 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
46686 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
46719 ATCGCAACGCGAAACT-AAAATTGCAACG
1 ATCGCAATGCGAAA-TGAAAATCGCAACG
46747 CGAAACTAAA
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
33 88 0.99
34 1 0.01
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:46709 original size:19 final size:18
Alignment explanation
Indices: 46620--46763 Score: 91
Period size: 19 Copynumber: 8.4 Consensus size: 18
46610 AAAAATGACT
46620 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
46639 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
46653 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
46672 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
46686 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
46705 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
46719 ATCGCAACGCGAAACT-AAA
1 ATCGCAA-GCGAAA-TGAAA
*
46738 ATTGCAACGCGAAACT-AAA
1 ATCGCAA-GCGAAA-TGAAA
46757 ATCGCAA
1 ATCGCAA
46764 CACGAAACTA
Statistics
Matches: 102, Mismatches: 7, Indels: 32
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.29
15 3 0.03
16 6 0.06
17 6 0.06
18 3 0.03
19 54 0.53
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:46764 original size:19 final size:19
Alignment explanation
Indices: 46685--46781 Score: 107
Period size: 19 Copynumber: 5.4 Consensus size: 19
46675 GCAACGAGAG
*
46685 AATCGCAATGCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
46704 AATCGCAA--CG--AC-AA
1 AATCGCAACGCGAAACTAA
46718 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
46737 AATTGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
46756 AATCGCAACACGAAACTAA
1 AATCGCAACGCGAAACTAA
*
46775 ATTCGCA
1 AATCGCA
46782 TTGCGATTCT
Statistics
Matches: 68, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
14 10 0.15
15 1 0.01
16 2 0.03
17 2 0.03
18 2 0.03
19 51 0.75
ACGTcount: A:0.47, C:0.24, G:0.15, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:46813 original size:33 final size:33
Alignment explanation
Indices: 46776--46887 Score: 197
Period size: 33 Copynumber: 3.4 Consensus size: 33
46766 CGAAACTAAA
*
46776 TTCGCATTGCGATTCTCTCGTTGCAATTTTCAT
1 TTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
* *
46809 TTCGCATTGCGATTCTCTCGTTGTGATTTTTAT
1 TTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
46842 TTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
46875 TTCGCATTGCGAT
1 TTCGCATTGCGAT
46888 AGTCATTTCC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 74 1.00
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
Found at i:46886 original size:19 final size:19
Alignment explanation
Indices: 46796--46907 Score: 73
Period size: 19 Copynumber: 6.4 Consensus size: 19
46786 GATTCTCTCG
*
46796 TTGCAATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
46815 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
* *
46829 TTGTGATTTTTATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
46848 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
46862 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
46881 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
46901 TTGCGAT
1 TTGCGAT
46908 AGACATTAAG
Statistics
Matches: 70, Mismatches: 12, Indels: 21
0.68 0.12 0.20
Matches are distributed among these distances:
14 11 0.16
16 13 0.19
17 13 0.19
19 23 0.33
20 10 0.14
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:46906 original size:20 final size:19
Alignment explanation
Indices: 46860--46914 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
46850 GCGATTCTCT
**
46860 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
46879 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
46899 CGTTGCGATAGACATT
1 CGTTGCGATAGTCATT
46915 AAGATGATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:46953 original size:20 final size:20
Alignment explanation
Indices: 46881--46953 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
46871 TCATTTCGCA
**
46881 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCATG
* ***
46901 TTGCGATAGACATTAAGATG
1 TTGCGATAGTCATTTCCATG
46921 ATTGCGA-ACGTCATTTCCATG
1 -TTGCGATA-GTCATTTCCATG
46942 TTGCGATAGTCA
1 TTGCGATAGTCA
46954 AATGAATGCC
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
20 25 0.62
21 15 0.38
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCATG
Found at i:49440 original size:22 final size:22
Alignment explanation
Indices: 49415--49458 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
49405 CACCACAGCT
*
49415 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
* *
49437 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
49459 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.20
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:49707 original size:149 final size:149
Alignment explanation
Indices: 49437--49740 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
49427 CCGAAGTGCC
*
49437 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
49502 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
*
49567 CATATGTCCCGAAGAACCG
131 CATATGTCCCAAAGAACCG
49586 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
49651 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
*
49716 CATATGTCCTAAAGAACCG
131 CATATGTCCCAAAGAACCG
49735 CGTAGA
1 CGTAGA
49741 CCCTCGACTC
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCAAAGAACCG
Found at i:51269 original size:21 final size:21
Alignment explanation
Indices: 51239--51283 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
51229 ATTCTTTCGT
* *
51239 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
51260 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
51281 TTG
1 TTG
51284 CCCAGAAATC
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:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:54379 original size:147 final size:147
Alignment explanation
Indices: 54122--54421 Score: 516
Period size: 147 Copynumber: 2.0 Consensus size: 147
54112 CGAAGTGCCC
* *
54122 CGTAGAATTGCACCGTATTGCCATATAATGATGTCCATAGGACCACATAGAATTCTTTAAGAATC
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAGGACCACATAGAATTCTTTAAGAATC
54187 ATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATG-TTCCAAAGAATATA
66 A-ATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTTCC-AAGAATATA
*
54251 CATATGTCCCGAAGAACCG
129 CATATGTCCCAAAGAACCG
54270 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCAT-AGGACCACATAGAATTCTTTAAGAAT
54335 C-ATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTTCCAAGAATATAC
65 CAATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTTCCAAGAATATAC
*
54399 ATATGTCCTAAAGAACCG
130 ATATGTCCCAAAGAACCG
54417 C-TAGA
1 CGTAGA
54422 CCCTCGACTC
Statistics
Matches: 146, Mismatches: 4, Indels: 6
0.94 0.03 0.04
Matches are distributed among these distances:
146 4 0.03
147 75 0.51
148 40 0.27
149 27 0.18
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (147 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAGGACCACATAGAATTCTTTAAGAATC
AATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTTCCAAGAATATACA
TATGTCCCAAAGAACCG
Found at i:55938 original size:21 final size:21
Alignment explanation
Indices: 55908--55952 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
55898 ATTCTTTCGT
* *
55908 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
55929 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
55950 TTG
1 TTG
55953 CCCAGAAATC
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:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:58333 original size:21 final size:20
Alignment explanation
Indices: 58248--58365 Score: 164
Period size: 20 Copynumber: 5.8 Consensus size: 20
58238 TGCGATTTTC
58248 TAAATCGCAATGCGATTACG
1 TAAATCGCAATGCGATTACG
58268 TAAATCGCAATGCGATTACG
1 TAAATCGCAATGCGATTACG
58288 TAAATCGCAATGCGATTACG
1 TAAATCGCAATGCGATTACG
*
58308 TAAATCGCAATGCGAATTAGG
1 TAAATCGCAATGCG-ATTACG
* * **
58329 GAAATCGCAACGCGAATTTGG
1 TAAATCGCAATGCG-ATTACG
*
58350 GAAATCGCAATGCGAT
1 TAAATCGCAATGCGAT
58366 AGTCAGAATT
Statistics
Matches: 92, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
20 56 0.61
21 36 0.39
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.23
Consensus pattern (20 bp):
TAAATCGCAATGCGATTACG
Found at i:59447 original size:2 final size:2
Alignment explanation
Indices: 59440--59532 Score: 186
Period size: 2 Copynumber: 46.5 Consensus size: 2
59430 ACATCTTCTT
59440 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
59482 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
59524 TA TA TA TA T
1 TA TA TA TA T
59533 GCATGCAAGG
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 91 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:66877 original size:13 final size:13
Alignment explanation
Indices: 66859--66883 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
66849 TTGAAAAAAT
66859 AAAAAATTAACAA
1 AAAAAATTAACAA
66872 AAAAAATTAACA
1 AAAAAATTAACA
66884 CATCAATGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAAATTAACAA
Found at i:71127 original size:21 final size:19
Alignment explanation
Indices: 71084--71145 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 19
71074 ATGGTACTAG
71084 TACTCCTCATTGGGTATAC-A
1 TACTCCTC-TTGGGTAT-CGA
71104 TACTCCTCTTTGTGGTATCGA
1 TACTCCTC-TTG-GGTATCGA
*
71125 TACTCC-CTTGAGTATCGA
1 TACTCCTCTTGGGTATCGA
71143 TAC
1 TAC
71146 CAATTTTCCT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 10 0.26
19 3 0.08
20 13 0.34
21 12 0.32
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (19 bp):
TACTCCTCTTGGGTATCGA
Found at i:71333 original size:20 final size:20
Alignment explanation
Indices: 71289--71343 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
71279 CCAAGTCCCT
*
71289 GAGTATCGATACT-ATATGA
1 GAGTATCGATACTCCTATGA
71308 GTAGTATCGATACTCCTGATG-
1 G-AGTATCGATACTCCT-ATGA
*
71329 GAGTATAGATACTCC
1 GAGTATCGATACTCC
71344 CCTCATATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 1 0.03
20 25 0.81
21 2 0.06
22 3 0.10
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (20 bp):
GAGTATCGATACTCCTATGA
Done.