Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008513.1 Hibiscus syriacus cultivar Beakdansim tig00111373_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: 128947
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:2694 original size:2 final size:2
Alignment explanation
Indices: 2687--2732 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2677 AATTTACCAA
2687 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2729 AT AT
1 AT AT
2733 TGACTCCGCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3071 original size:9 final size:9
Alignment explanation
Indices: 3052--3088 Score: 65
Period size: 9 Copynumber: 4.0 Consensus size: 9
3042 GTTTAATGTC
3052 AAATGATTTA
1 AAAT-ATTTA
3062 AAATATTTA
1 AAATATTTA
3071 AAATATTTA
1 AAATATTTA
3080 AAATATTTA
1 AAATATTTA
3089 GAACAAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 23 0.85
10 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (9 bp):
AAATATTTA
Found at i:3292 original size:20 final size:20
Alignment explanation
Indices: 3267--3379 Score: 102
Period size: 20 Copynumber: 5.5 Consensus size: 20
3257 TTTTCCCAAT
3267 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
3287 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
3308 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
3328 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
**
3349 TCGCAATGCG-ATACTTAATA
1 TCGCAATGCGAATAAGTAA-A
3369 TCGCAATGCGA
1 TCGCAATGCGA
3380 TAATACAAAA
Statistics
Matches: 72, Mismatches: 17, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
19 3 0.04
20 39 0.54
21 30 0.42
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:3310 original size:21 final size:21
Alignment explanation
Indices: 3284--3359 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
3274 GCGAATAAGT
3284 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
3305 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
3325 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
3346 AAATCGCAATGCGA
1 AAATCGCAACGCGA
3360 TACTTAATAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:3374 original size:41 final size:41
Alignment explanation
Indices: 3267--3359 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
3257 TTTTCCCAAT
3267 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
3308 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
3349 TCGCAATGCGA
1 TCGCAATGCGA
3360 TACTTAATAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:3390 original size:41 final size:41
Alignment explanation
Indices: 3345--3422 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
3335 GCGAATTGGG
* * *
3345 AAAATCGCAATGCGATACTTAATATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTTAATATCGCAACGCGATAATAC
* * *
3386 AAAATCGTAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTTAATATCGCAACGCGATA
3423 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTTAATATCGCAACGCGATAATAC
Found at i:3422 original size:20 final size:20
Alignment explanation
Indices: 3394--3437 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
3384 ACAAAATCGT
*
3394 AACGAGATACTTACTTTCGC
1 AACGAGATACTGACTTTCGC
*
3414 AACGCGATACTGACTTTCGC
1 AACGAGATACTGACTTTCGC
3434 AACG
1 AACG
3438 TGATTTACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (20 bp):
AACGAGATACTGACTTTCGC
Found at i:3997 original size:18 final size:18
Alignment explanation
Indices: 3948--4005 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 18
3938 ATAGTTTCGA
*
3948 GAATGAAAATCGCAACGC
1 GAATAAAAATCGCAACGC
**
3966 GGAAATAACTATCGCAACGC
1 -G-AATAAAAATCGCAACGC
3986 GAATAAAAATCGC-ACGC
1 GAATAAAAATCGCAACGC
4003 GAA
1 GAA
4006 ACCAAATCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
17 7 0.21
18 10 0.30
19 2 0.06
20 14 0.42
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (18 bp):
GAATAAAAATCGCAACGC
Found at i:4039 original size:19 final size:19
Alignment explanation
Indices: 4012--4201 Score: 171
Period size: 19 Copynumber: 10.1 Consensus size: 19
4002 CGAAACCAAA
*
4012 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
4031 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
4050 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
4069 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
4088 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
4104 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
4121 TCGCGTTGCGATTCTCTC-GT
1 TCGCGTTGCGATT-T-TCATT
* *
4141 T-GCGATAGTC-ATTTCCATT
1 TCGCG-TTG-CGATTTTCATT
*
4160 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
4180 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
4200 TC
1 TC
4202 AACCAAAAGA
Statistics
Matches: 139, Mismatches: 18, Indels: 28
0.75 0.10 0.15
Matches are distributed among these distances:
14 10 0.07
15 1 0.01
16 1 0.01
17 1 0.01
18 2 0.01
19 85 0.61
20 32 0.23
21 7 0.05
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:4120 original size:33 final size:33
Alignment explanation
Indices: 4083--4155 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
4073 GTTGCGATTT
* *
4083 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
4116 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
4149 TCATTTC
1 TCATTTC
4156 CATTTCCGCG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.12, C:0.23, G:0.25, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:6228 original size:43 final size:43
Alignment explanation
Indices: 6167--6290 Score: 117
Period size: 43 Copynumber: 2.9 Consensus size: 43
6157 AAGCCCGACG
* * *
6167 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGGCC
* * *
6210 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGA-GGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGGCC
* * ** * *
6252 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
6291 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
42 29 0.45
43 36 0.55
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.23
Consensus pattern (43 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGGCC
Found at i:6248 original size:21 final size:21
Alignment explanation
Indices: 6224--6290 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
6214 TCATTCCTCG
6224 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
6245 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
6266 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
6287 AGAG
1 AGAG
6291 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:7305 original size:14 final size:14
Alignment explanation
Indices: 7286--7321 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
7276 ATTGTTTAAT
7286 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
7300 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
7314 TGATTTGT
1 TGATTTGT
7322 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:7523 original size:19 final size:19
Alignment explanation
Indices: 7501--7651 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
7491 CGAAATTAAA
7501 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
7520 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
7535 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
7553 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
7567 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
7586 TTCGCATTACGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
7601 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
7619 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
7638 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
7652 GGACATTAAG
Statistics
Matches: 93, Mismatches: 23, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 27 0.29
16 6 0.06
17 6 0.06
19 44 0.47
20 10 0.11
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:7547 original size:33 final size:32
Alignment explanation
Indices: 7505--7631 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
7495 ATTAAATTCG
7505 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
7538 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
7571 CGTTGCGATTTTCATTTCGCATTACGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
7604 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
7632 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:7599 original size:66 final size:66
Alignment explanation
Indices: 7498--7630 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
7488 ACGCGAAATT
* *
7498 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTACGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
7563 G
66 G
*
7564 AAATTAGCGTTGCGATTTTCATTTCGCATTACGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTACGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
7629 G
66 G
7630 A
1 A
7631 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTACGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:9628 original size:12 final size:12
Alignment explanation
Indices: 9611--9635 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9601 TCTTCGGGGA
9611 CTTTTTCTTCTT
1 CTTTTTCTTCTT
9623 CTTTTTCTTCTT
1 CTTTTTCTTCTT
9635 C
1 C
9636 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:10948 original size:20 final size:20
Alignment explanation
Indices: 10923--11014 Score: 106
Period size: 20 Copynumber: 4.9 Consensus size: 20
10913 ATTCATTTGA
10923 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
10943 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
10963 TTATCGCAACGAG-AAA---
1 CTATCGCAACGCGAAAATGG
10979 --ATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
10997 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
11015 CGCAATGCGA
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
14 10 0.16
15 3 0.05
19 3 0.05
20 46 0.74
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:10988 original size:34 final size:34
Alignment explanation
Indices: 10945--11026 Score: 155
Period size: 34 Copynumber: 2.4 Consensus size: 34
10935 GAAAATGGCT
10945 ATCGCAACGCGAAAATGGTTATCGCAACGAGAAA
1 ATCGCAACGCGAAAATGGTTATCGCAACGAGAAA
10979 ATCGCAACGCGAAAATGGTTATCGCAACGAGAAA
1 ATCGCAACGCGAAAATGGTTATCGCAACGAGAAA
*
11013 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
11027 TGAAAATCGC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.15
Consensus pattern (34 bp):
ATCGCAACGCGAAAATGGTTATCGCAACGAGAAA
Found at i:11026 original size:14 final size:14
Alignment explanation
Indices: 10965--10994 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
10955 GAAAATGGTT
10965 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
*
10979 ATCGCAACGCGAAA
1 ATCGCAACGAGAAA
10993 AT
1 AT
10995 GGTTATCGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:11074 original size:19 final size:19
Alignment explanation
Indices: 11033--11153 Score: 171
Period size: 19 Copynumber: 6.6 Consensus size: 19
11023 GAAATGAAAA
11033 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
11049 TCG--TTGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
11066 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
11085 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
11104 TCGCATTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
*
11123 TCGCATTGCGATTTCCATT
1 TCGCATTGCGATTTTCATT
*
11142 TCGCGTTGCGAT
1 TCGCATTGCGAT
11154 AGTCTGTTTC
Statistics
Matches: 94, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
14 10 0.11
16 3 0.03
17 3 0.03
19 78 0.83
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:11165 original size:20 final size:20
Alignment explanation
Indices: 11140--11182 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
11130 GCGATTTCCA
11140 TTTCGCGTTGCGATAGTCTG
1 TTTCGCGTTGCGATAGTCTG
11160 TTTCGCGTTGCGATAGTCTG
1 TTTCGCGTTGCGATAGTCTG
11180 TTT
1 TTT
11183 TGCCTTCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.09, C:0.19, G:0.28, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCTG
Found at i:13157 original size:31 final size:31
Alignment explanation
Indices: 13119--13274 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
13109 CCCGAAGGAC
* *
13119 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
13150 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
13181 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
13212 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
13243 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
13274 C
1 C
13275 CCTCGACCCT
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:13478 original size:23 final size:24
Alignment explanation
Indices: 13452--13498 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
13442 ATATACTTGT
*
13452 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
13475 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
13499 CAGGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:14039 original size:21 final size:21
Alignment explanation
Indices: 14009--14052 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
13999 ATTCTGTCAT
* *
14009 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
14030 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
14051 TT
1 TT
14053 ACCCAGAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:17079 original size:31 final size:31
Alignment explanation
Indices: 17041--17195 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
17031 CCCGAAGGAC
* *
17041 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
17072 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
17103 CAGTCCATATGTTCCGAAGAACATAGGT-AA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
17133 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
17164 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
17195 C
1 C
17196 CCTCGACCCT
Statistics
Matches: 114, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
30 29 0.25
31 84 0.74
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:17160 original size:61 final size:62
Alignment explanation
Indices: 17041--17193 Score: 265
Period size: 61 Copynumber: 2.5 Consensus size: 62
17031 CCCGAAGGAC
* *
17041 CAGTCCATA-GATTCCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATG-TTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
17103 CAGTCCATATGTTCCGAAGAACATAGGTAA-CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
17164 CAGTCCATATGTTCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
17194 ACCCTCGACC
Statistics
Matches: 88, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
61 60 0.68
62 27 0.31
63 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (62 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:17399 original size:23 final size:24
Alignment explanation
Indices: 17373--17419 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
17363 ATATACTTGT
*
17373 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
17396 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
17420 CAGGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:17962 original size:21 final size:21
Alignment explanation
Indices: 17932--17975 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
17922 ATTCTGTCGT
* *
17932 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
17953 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
17974 TT
1 TT
17976 ACCCAGAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:19469 original size:20 final size:19
Alignment explanation
Indices: 19434--19500 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
19424 GAAACTTAAA
19434 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
19453 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
19473 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
19492 ATCGCAACG
1 ATCGCAACG
19501 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:19508 original size:14 final size:14
Alignment explanation
Indices: 19489--19546 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
19479 ATGCGAAATG
19489 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
19503 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
19519 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
19535 AAAATCGCAACG
1 AAAATCGCAACG
19547 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:19531 original size:32 final size:33
Alignment explanation
Indices: 19473--19551 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
19463 GGAAATGGCT
*
19473 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
19506 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
19538 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
19552 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:19580 original size:19 final size:19
Alignment explanation
Indices: 19558--19691 Score: 101
Period size: 19 Copynumber: 7.6 Consensus size: 19
19548 GAAACACAAA
*
19558 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
19577 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
19593 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
*
19609 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
19625 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* ***
19642 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATTTTCATT
**
19661 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
19681 TCGCGTTGCGA
1 TCGCGTTGCGA
19692 AAGTAAACTA
Statistics
Matches: 94, Mismatches: 11, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
14 19 0.20
15 3 0.03
16 6 0.06
17 2 0.02
18 14 0.15
19 33 0.35
20 17 0.18
ACGTcount: A:0.13, C:0.22, G:0.24, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:19599 original size:14 final size:14
Alignment explanation
Indices: 19580--19637 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
19570 TTTCATTTCG
19580 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
19594 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
19610 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
19626 CGTTGCGATTTT
1 CGTTGCGATTTT
19638 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:19644 original size:33 final size:33
Alignment explanation
Indices: 19563--19653 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
19553 ACAAATCGCA
19563 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
19596 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
19628 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
19654 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:19672 original size:20 final size:19
Alignment explanation
Indices: 19638--19691 Score: 81
Period size: 20 Copynumber: 2.8 Consensus size: 19
19628 TTGCGATTTT
*
19638 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
19657 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
19677 CATTTCGCGTTGCGA
1 CATTTCGCGTTGCGA
19692 AAGTAAACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:20184 original size:18 final size:18
Alignment explanation
Indices: 20158--20202 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
20148 GTCGATTAGA
* *
20158 TGATGGCTCTGGGTGGGG
1 TGATGGCTCTGGGCGAGG
*
20176 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
20194 TGATGGCTC
1 TGATGGCTC
20203 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.47, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:21541 original size:20 final size:20
Alignment explanation
Indices: 21516--21569 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
21506 AATAGTTTCT
21516 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
21536 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
*
21556 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
21570 GTTGCGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:21828 original size:22 final size:22
Alignment explanation
Indices: 21803--21845 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
21793 GATTTAGATA
*
21803 GACGGATTTCGCCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
*
21825 GACGAATTTCGTCGGAGATGG
1 GACGAATTTCGCCGGAGATGG
21846 ATGAGAGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.42, T:0.21
Consensus pattern (22 bp):
GACGAATTTCGCCGGAGATGGG
Found at i:22057 original size:20 final size:20
Alignment explanation
Indices: 22034--22085 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
22024 GATTATGTAA
*
22034 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTAAGT
22054 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
22074 ATCGCGTTGCGA
1 ATCGCGTTGCGA
22086 TTTTCCCAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTAAGT
Found at i:22101 original size:21 final size:21
Alignment explanation
Indices: 22075--22150 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
22065 AAAGTAAGTA
22075 TCGCGTTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
* **
22096 TCGCGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTCCCAAT
* *
22116 TCACATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
22137 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
22151 ACTTATTCGC
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.41
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:22124 original size:20 final size:20
Alignment explanation
Indices: 22094--22167 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
22084 GATTTTCCCA
*
22094 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
* * **
22114 ATTCACATTGCGATTTTCCCA
1 ATTCGCATTGCGA-TTTACTT
*
22135 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
22155 ATTCGCATTGCGA
1 ATTCGCATTGCGA
22168 ATTGGGAAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTT
Found at i:22125 original size:41 final size:41
Alignment explanation
Indices: 22080--22167 Score: 167
Period size: 41 Copynumber: 2.1 Consensus size: 41
22070 AAGTATCGCG
22080 TTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCACA
1 TTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCACA
*
22121 TTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCGCA
1 TTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCACA
22162 TTGCGA
1 TTGCGA
22168 ATTGGGAAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.18, C:0.24, G:0.17, T:0.41
Consensus pattern (41 bp):
TTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCACA
Found at i:26698 original size:21 final size:22
Alignment explanation
Indices: 26672--26722 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
26662 AGACAGACAA
26672 AGGCACCCCC-CCTAATGCCTC
1 AGGCACCCCCGCCTAATGCCTC
26693 AGGCACCCCCGCCTAATGCCTC
1 AGGCACCCCCGCCTAATGCCTC
*
26715 TGGCACCC
1 AGGCACCC
26723 TTGATACCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 10 0.36
22 18 0.64
ACGTcount: A:0.18, C:0.51, G:0.18, T:0.14
Consensus pattern (22 bp):
AGGCACCCCCGCCTAATGCCTC
Found at i:32354 original size:52 final size:52
Alignment explanation
Indices: 32292--32394 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
32282 TTATAATATT
32292 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATGC
* *
32344 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATG
32395 TGTCCAATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATGC
Found at i:36950 original size:52 final size:52
Alignment explanation
Indices: 36888--36990 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
36878 TTATAATATT
36888 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATGC
* *
36940 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATG
36991 TGTCCAATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAATCTCCTATTTCTATGC
Found at i:46354 original size:10 final size:10
Alignment explanation
Indices: 46338--46377 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
46328 AAATTGATAC
*
46338 ATAAATTATA
1 ATAAATTTTA
*
46348 TTAAATTTTA
1 ATAAATTTTA
46358 ATAAATTTTA
1 ATAAATTTTA
46368 ATAAATTTTA
1 ATAAATTTTA
46378 TAATCTTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
ATAAATTTTA
Found at i:49238 original size:43 final size:43
Alignment explanation
Indices: 49172--49255 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
49162 TTAAGAATGA
*
49172 TTGTAATATATTAGTTTGATGTATTTTTGGATTGTTACTTTAG
1 TTGTAATATATTAGTTTGATGTATTTGTGGATTGTTACTTTAG
* *
49215 TTGTAATATGTTAGTTTGGTGTATTTGTGGATTGTTACTTT
1 TTGTAATATATTAGTTTGATGTATTTGTGGATTGTTACTTT
49256 GGAGTTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.20, C:0.02, G:0.21, T:0.56
Consensus pattern (43 bp):
TTGTAATATATTAGTTTGATGTATTTGTGGATTGTTACTTTAG
Found at i:73854 original size:2 final size:2
Alignment explanation
Indices: 73847--73871 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
73837 AACAATTTCT
73847 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
73872 TTATTTAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:74581 original size:160 final size:160
Alignment explanation
Indices: 74372--74760 Score: 689
Period size: 160 Copynumber: 2.5 Consensus size: 160
74362 ATGTTAGTCT
*
74372 TAATTTAAAATAAGATTTAAG--A-TT-TTTTTTTAATATTTATAAATTATATCAATTTAATATT
1 TAATTTAAAATATGATTTAAGAAATTTATTTTTTTAATATTTATAAATTATATCAATTTAATATT
74433 ATTTTAATTCTAGATAATGAGATTGATATGATATTTTAAAATTTATACAATAACATATTTAGTTT
66 ATTTTAATTCTAGATAATGAGATTGATATGATATTTTAAAATTTATACAATAACATATTTAGTTT
74498 TCATATTTATATATTTAATCAAGCTAATCC
131 TCATATTTATATATTTAATCAAGCTAATCC
74528 TAATTTAAAATATGATTTAAGAAATTTATTTTTTTAATATTTATAAATTATATCAATTTAATATT
1 TAATTTAAAATATGATTTAAGAAATTTATTTTTTTAATATTTATAAATTATATCAATTTAATATT
* *
74593 ATTTTACTTCTAGATAATGAGATTTATATGATATTTTAAAATTTATACAATAACATATTTAGTTT
66 ATTTTAATTCTAGATAATGAGATTGATATGATATTTTAAAATTTATACAATAACATATTTAGTTT
*
74658 TCATATTTATATATTTAATCAAGCTAGTCC
131 TCATATTTATATATTTAATCAAGCTAATCC
* *
74688 TAATTTAAAATATGATTTAATAAATTTA-TTTTTTAATATTTATAAATTATATCGATTTAATATT
1 TAATTTAAAATATGATTTAAGAAATTTATTTTTTTAATATTTATAAATTATATCAATTTAATATT
74752 ATTTTAATT
66 ATTTTAATT
74761 ATAATTAGTT
Statistics
Matches: 222, Mismatches: 7, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
156 20 0.09
158 1 0.00
159 45 0.20
160 156 0.70
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (160 bp):
TAATTTAAAATATGATTTAAGAAATTTATTTTTTTAATATTTATAAATTATATCAATTTAATATT
ATTTTAATTCTAGATAATGAGATTGATATGATATTTTAAAATTTATACAATAACATATTTAGTTT
TCATATTTATATATTTAATCAAGCTAATCC
Found at i:77233 original size:5 final size:5
Alignment explanation
Indices: 77225--77254 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
77215 TTCAGAGTTT
77225 TCGAG TCGAG TCGAG TCGAG TCGAG TCGAG
1 TCGAG TCGAG TCGAG TCGAG TCGAG TCGAG
77255 CTCAGCAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.40, T:0.20
Consensus pattern (5 bp):
TCGAG
Found at i:80191 original size:63 final size:62
Alignment explanation
Indices: 80071--80192 Score: 149
Period size: 63 Copynumber: 2.0 Consensus size: 62
80061 CCTCGGCAAC
* * * *
80071 TGTCCATAGGTCTCGAAGAACCTAGGTAAATTATCCATATGTTCCTTAGAACATAGGTATAT
1 TGTCCATAGGTCTCGAAGAACATAGGTAAATTATCCATAAGTTCCGTAAAACATAGGTATAT
* *
80133 TGTCCGTATGTCTCGAA-AGACATAGGT-AATTATGTCCATAAGTTCCGTAAAACATAGGTA
1 TGTCCATAGGTCTCGAAGA-ACATAGGTAAATTA--TCCATAAGTTCCGTAAAACATAGGTA
80193 AACCCTCGAC
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
61 6 0.12
62 22 0.43
63 23 0.45
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (62 bp):
TGTCCATAGGTCTCGAAGAACATAGGTAAATTATCCATAAGTTCCGTAAAACATAGGTATAT
Found at i:80716 original size:2 final size:2
Alignment explanation
Indices: 80709--80735 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
80699 TTATCACATT
80709 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
80736 TTACACAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:83446 original size:27 final size:29
Alignment explanation
Indices: 83391--83447 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
83381 GATGATTACG
83391 TCTTAATTAAATAAAAACGAAAGTGAATATA
1 TCTTAATTAAATAAAAACGAAA--GAATATA
*
83422 TCTTAATTGAATAAAAAC-AAA-AATAT
1 TCTTAATTAAATAAAAACGAAAGAATAT
83448 CATGTATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 5 0.20
30 3 0.12
31 17 0.68
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (29 bp):
TCTTAATTAAATAAAAACGAAAGAATATA
Found at i:85892 original size:31 final size:31
Alignment explanation
Indices: 85854--85978 Score: 180
Period size: 31 Copynumber: 4.0 Consensus size: 31
85844 TCCGAAGGAC
* * * *
85854 CAGTCCATA-GATTCCGATGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
85885 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
85916 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
85947 CAGTCCATATGACCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
85978 C
1 C
85979 CCTCGACCTT
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 85 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:90021 original size:33 final size:31
Alignment explanation
Indices: 89956--90059 Score: 163
Period size: 31 Copynumber: 3.3 Consensus size: 31
89946 TTCCAAAACC
* *
89956 TAGGTAATCAGTCCATATGTCCCGAAGGACA
1 TAGGTAAACAGTCCATATGTCCCGAAGAACA
89987 TAGGTAAACAGTCCATATGTCCCCCGAAGAACA
1 TAGGTAAACAGTCCATATGT--CCCGAAGAACA
*
90020 TAGGTAAACAGTCCATATGACCCGAAGAACA
1 TAGGTAAACAGTCCATATGTCCCGAAGAACA
90051 TAGGTAAAC
1 TAGGTAAAC
90060 CCTCGACCCT
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
31 39 0.57
33 29 0.43
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (31 bp):
TAGGTAAACAGTCCATATGTCCCGAAGAACA
Found at i:90288 original size:58 final size:58
Alignment explanation
Indices: 90178--90288 Score: 134
Period size: 58 Copynumber: 1.9 Consensus size: 58
90168 ACATATCTTT
* * * *
90178 TTTTCAGTCACGTATCACATGTACGTGTAATCATGATCTCATAATCACATGTTCCTTC
1 TTTTCAGTCACATACCACATGTACGTGTAAACATGATCTAATAATCACATGTTCCTTC
* * * *
90236 TTTTCTGTCACATACCACATGTATGTGTAAACATATATCTAAT-ATCATATGTT
1 TTTTCAGTCACATACCACATGTACGTGTAAACAT-GATCTAATAATCACATGTT
90289 GCAGTATCAC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
58 38 0.86
59 6 0.14
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.40
Consensus pattern (58 bp):
TTTTCAGTCACATACCACATGTACGTGTAAACATGATCTAATAATCACATGTTCCTTC
Found at i:90875 original size:21 final size:20
Alignment explanation
Indices: 90851--90894 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
90841 TGTTGTTCGT
* *
90851 TTGAAGGGGTATCGGTTCCCC
1 TTGAA-GGGTACCGATTCCCC
*
90872 TTGAATGGTACCGATTCCCC
1 TTGAAGGGTACCGATTCCCC
90892 TTG
1 TTG
90895 CCCAGAATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (20 bp):
TTGAAGGGTACCGATTCCCC
Found at i:95082 original size:17 final size:17
Alignment explanation
Indices: 95060--95107 Score: 96
Period size: 17 Copynumber: 2.8 Consensus size: 17
95050 GCTTAATTCC
95060 GAGGATTAAAATGAATG
1 GAGGATTAAAATGAATG
95077 GAGGATTAAAATGAATG
1 GAGGATTAAAATGAATG
95094 GAGGATTAAAATGA
1 GAGGATTAAAATGA
95108 TAGTTTTACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.23
Consensus pattern (17 bp):
GAGGATTAAAATGAATG
Found at i:97989 original size:20 final size:21
Alignment explanation
Indices: 97954--97992 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
97944 AACATAACGT
*
97954 TAGTTATGATTTTTAAAAAAA
1 TAGTTATGATTATTAAAAAAA
97975 TAGTTA-GATTATTAAAAA
1 TAGTTATGATTATTAAAAA
97993 TGAAATCGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (21 bp):
TAGTTATGATTATTAAAAAAA
Found at i:102272 original size:3 final size:3
Alignment explanation
Indices: 102266--102290 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
102256 CTTGGTTTTC
102266 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
102291 TTTTTTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:112184 original size:2 final size:2
Alignment explanation
Indices: 112146--112172 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
112136 AAGCCAAGAA
112146 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 A
112173 ATGTGCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:112636 original size:42 final size:42
Alignment explanation
Indices: 112570--112676 Score: 178
Period size: 42 Copynumber: 2.5 Consensus size: 42
112560 GTATAATTAC
* * *
112570 TTAAAAACTCTTTAAAATAATAATTATTAATTTATCGATAAA
1 TTAATAACTCTCTAAATTAATAATTATTAATTTATCGATAAA
*
112612 TTAATAACTCTCTAAATTATTAATTATTAATTTATCGATAAA
1 TTAATAACTCTCTAAATTAATAATTATTAATTTATCGATAAA
112654 TTAATAACTCTCTAAATTAATAA
1 TTAATAACTCTCTAAATTAATAA
112677 ATTTCTTCGG
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (42 bp):
TTAATAACTCTCTAAATTAATAATTATTAATTTATCGATAAA
Found at i:118823 original size:16 final size:17
Alignment explanation
Indices: 118790--118827 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
118780 ACAGATCACT
118790 ATTTT-AGATATCTAAA
1 ATTTTCAGATATCTAAA
*
118806 ATTTTCAGATATC-CAA
1 ATTTTCAGATATCTAAA
118822 ATTTTC
1 ATTTTC
118828 CGCTCGGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (17 bp):
ATTTTCAGATATCTAAA
Found at i:119019 original size:19 final size:19
Alignment explanation
Indices: 118972--119025 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
118962 GAGTATAATA
* **
118972 AATTAAAATAAACCTATTG
1 AATTAAAATGAATTTATTG
118991 AATTAAAATGAATTTATTG
1 AATTAAAATGAATTTATTG
119010 AATTAAAATGAATTTA
1 AATTAAAATGAATTTA
119026 GGGTCCGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.37
Consensus pattern (19 bp):
AATTAAAATGAATTTATTG
Found at i:119654 original size:14 final size:14
Alignment explanation
Indices: 119635--119665 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
119625 GTTTTAATTC
119635 AATAAATTAATTTT
1 AATAAATTAATTTT
*
119649 AATAAATTTATTTT
1 AATAAATTAATTTT
119663 AAT
1 AAT
119666 CCAATAGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AATAAATTAATTTT
Found at i:120315 original size:2 final size:2
Alignment explanation
Indices: 120308--120337 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
120298 CACCAAATCA
120308 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
120338 TTTTTTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:127311 original size:72 final size:72
Alignment explanation
Indices: 127227--127361 Score: 252
Period size: 72 Copynumber: 1.9 Consensus size: 72
127217 TTTTATTTTA
*
127227 TTTTTAATATTTAAATTATTTGTTGACATAGAACATGAAATAAAATATCACGTGTGCAAAATTTA
1 TTTTTAATATTTAAATTATTTGTTGACATAGAACATAAAATAAAATATCACGTGTGCAAAATTTA
127292 GTTTATT
66 GTTTATT
*
127299 TTTTTTATATTTAAATTATTTGTTGACATAGAACATAAAATAAAATATCACGTGTGCAAAATT
1 TTTTTAATATTTAAATTATTTGTTGACATAGAACATAAAATAAAATATCACGTGTGCAAAATT
127362 ATTCATATAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.42
Consensus pattern (72 bp):
TTTTTAATATTTAAATTATTTGTTGACATAGAACATAAAATAAAATATCACGTGTGCAAAATTTA
GTTTATT
Found at i:127514 original size:31 final size:31
Alignment explanation
Indices: 127470--127552 Score: 157
Period size: 31 Copynumber: 2.6 Consensus size: 31
127460 TAGGGTAAAT
127470 TATATATTTAGTACTTAAACTATCAATTTTGA
1 TATAT-TTTAGTACTTAAACTATCAATTTTGA
127502 TATATTTTAGTACTTAAACTATCAATTTTGA
1 TATATTTTAGTACTTAAACTATCAATTTTGA
127533 TATATTTTAGTACTTAAACT
1 TATATTTTAGTACTTAAACT
127553 TTAAAAAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 46 0.90
32 5 0.10
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (31 bp):
TATATTTTAGTACTTAAACTATCAATTTTGA
Done.