Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003266.1 Hibiscus syriacus cultivar Beakdansim tig00006863_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: 94277
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:2097 original size:20 final size:20
Alignment explanation
Indices: 2072--2281 Score: 122
Period size: 20 Copynumber: 10.4 Consensus size: 20
2062 GATTTTCCAT
2072 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATATGAA
*
2092 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGAATATGA-A
* * *
2112 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGAATATGAA
* * * **
2132 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATATG-AA
*
2153 AATCGCAACGCG--TATCCATA
1 AATCGCAACGCGAATAT-GA-A
*
2173 AATCGCAACGAC-AATATATAA
1 AATCGCAACG-CGAATAT-GAA
* ** *
2194 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATATGAA
* * *
2214 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATATGAA
* * *
2234 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATATGAA
* * *
2254 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATATGAA
2274 AATCGCAA
1 AATCGCAA
2282 TGCGTATCCG
Statistics
Matches: 147, Mismatches: 34, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
19 3 0.02
20 114 0.78
21 26 0.18
22 4 0.03
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATATGAA
Found at i:2293 original size:20 final size:20
Alignment explanation
Indices: 2133--2303 Score: 184
Period size: 20 Copynumber: 8.4 Consensus size: 20
2123 GATTCTGACT
*
2133 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
*
2154 ATCGCAACGCGTATCCATAA
1 ATCGCAACGCGTATCCGTAA
* *
2174 ATCGCAACGACAATAT--ATAAA
1 ATCGCAACG-C-GTATCCGT-AA
2195 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
2215 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
2235 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
2255 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
2275 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
2295 ATCGCAACG
1 ATCGCAACG
2304 ACAATACGTA
Statistics
Matches: 124, Mismatches: 21, Indels: 11
0.79 0.13 0.07
Matches are distributed among these distances:
19 3 0.02
20 89 0.72
21 29 0.23
22 3 0.02
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:2310 original size:40 final size:40
Alignment explanation
Indices: 2072--2313 Score: 263
Period size: 40 Copynumber: 6.0 Consensus size: 40
2062 GATTTTCCAT
* ** * * * **
2072 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* * * *
2112 AATCGCAACGCG-ATTC-TGACTATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGTATCCGT-A-AATCGCAACGAGAATACGT-A
* * **
2153 AATCGCAACGCGTATCCATAAATCGCAACGACAATATATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT-A
2194 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
*
2234 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* *
2274 AATCGCAATGCGTATCCGTAAATCGCAACGACAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
2314 CGCGTATCCG
Statistics
Matches: 172, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
39 3 0.02
40 101 0.59
41 63 0.37
42 4 0.02
43 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
Found at i:2573 original size:25 final size:28
Alignment explanation
Indices: 2545--2601 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 28
2535 ATTTCCGTCC
*
2545 CCATTTC-CGG-CA-AAATCTCTCACAA
1 CCATTTCACGGTCAGAAATCCCTCACAA
2570 CCA-TTCACGGTCAGAAATCCCTCACAA
1 CCATTTCACGGTCAGAAATCCCTCACAA
*
2597 TCATT
1 CCATT
2602 CAGAAATGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 3 0.12
25 6 0.23
26 2 0.08
27 14 0.54
28 1 0.04
ACGTcount: A:0.32, C:0.35, G:0.09, T:0.25
Consensus pattern (28 bp):
CCATTTCACGGTCAGAAATCCCTCACAA
Found at i:2939 original size:21 final size:20
Alignment explanation
Indices: 2899--2971 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 20
2889 TTTTAAACTT
*
2899 AAAATCGTAACATG-AAAATG
1 AAAATCGCAACA-GAAAAATG
2919 AAAATCGCAACACGAAAAATG
1 AAAATCGCAACA-GAAAAATG
** *
2940 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC-AGAAAAATG
2961 AAAATCGCAAC
1 AAAATCGCAAC
2972 GAGAGAATCG
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 12 0.27
21 31 0.70
22 1 0.02
ACGTcount: A:0.52, C:0.18, G:0.16, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACAGAAAAATG
Found at i:2972 original size:21 final size:21
Alignment explanation
Indices: 2914--2978 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
2904 CGTAACATGA
*
2914 AAATGAAAATCGCAAC-ACGAA
1 AAATGAAAATCGCAACGA-GAG
**
2935 AAATGACTATCGCAACGAGAG
1 AAATGAAAATCGCAACGAGAG
2956 AAATGAAAATCGCAACGAGAG
1 AAATGAAAATCGCAACGAGAG
2977 AA
1 AA
2979 TCGCAACGCG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
21 37 0.97
22 1 0.03
ACGTcount: A:0.52, C:0.17, G:0.20, T:0.11
Consensus pattern (21 bp):
AAATGAAAATCGCAACGAGAG
Found at i:2982 original size:14 final size:14
Alignment explanation
Indices: 2960--3024 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 14
2950 CGAGAGAAAT
2960 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
2974 GAGAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
2992 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
3007 GATAATCGCAACGC
1 GAAAATCGCAACGA
3021 GAAA
1 GAAA
3025 CCAAAATCGC
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 25 0.61
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.24
ACGTcount: A:0.46, C:0.22, G:0.23, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:2996 original size:33 final size:33
Alignment explanation
Indices: 2955--3035 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
2945 CGCAACGAGA
2955 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
2988 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
3021 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
3036 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3102 original size:20 final size:19
Alignment explanation
Indices: 3031--3110 Score: 106
Period size: 20 Copynumber: 4.1 Consensus size: 19
3021 GAAACCAAAA
*
3031 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
3050 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
3069 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
3089 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
3109 TC
1 TC
3111 AACCAAAAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
19 19 0.36
20 33 0.62
21 1 0.02
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5160 original size:21 final size:21
Alignment explanation
Indices: 5136--5202 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
5126 TCATTCCTCG
5136 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
5157 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
5178 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
5199 AGAG
1 AGAG
5203 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:5160 original size:42 final size:42
Alignment explanation
Indices: 5084--5202 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
5074 GACTCGCCTG
* * * * * * *
5084 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
5126 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
5168 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
5203 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:6571 original size:14 final size:14
Alignment explanation
Indices: 6552--6587 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
6542 ATTGTTTAAT
6552 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
6566 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
6580 TGATTTGT
1 TGATTTGT
6588 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:6753 original size:19 final size:19
Alignment explanation
Indices: 6729--6774 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
6719 GATTCTCTCG
6729 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
6748 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
6767 TTGCGATT
1 TTGCGATT
6775 CTCTCGTTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.50
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:6806 original size:20 final size:20
Alignment explanation
Indices: 6781--6833 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
6771 GATTCTCTCG
*
6781 TTGCGATAGTCATTTCCGCA
1 TTGCGATAGTCAATTCCGCA
6801 TTGCGATAGTCAATTCCGCA
1 TTGCGATAGTCAATTCCGCA
6821 TTGCGATAGTCAA
1 TTGCGATAGTCAA
6834 ATGAATTTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAATTCCGCA
Found at i:8345 original size:24 final size:24
Alignment explanation
Indices: 8311--8364 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
8301 CTGAAAAATC
8311 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
8335 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
8359 ATCAAA
1 ATCAAA
8365 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:8378 original size:24 final size:24
Alignment explanation
Indices: 8311--8378 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
8301 CTGAAAAATC
* * *
8311 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
8335 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
8359 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
8379 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:9250 original size:20 final size:20
Alignment explanation
Indices: 9227--9380 Score: 157
Period size: 20 Copynumber: 7.6 Consensus size: 20
9217 ATAGTCAGAA
*
9227 TCTCGTTGCGATTTACGTAT
1 TCTCGTTGCGATTTACGGAT
* *
9247 TCTCGTTGCAATTTACAGAT
1 TCTCGTTGCGATTTACGGAT
* *
9267 AT-GCGTTGCGATTTACGTAT
1 -TCTCGTTGCGATTTACGGAT
9287 TCTCGTTGCGATTTACGGAT
1 TCTCGTTGCGATTTACGGAT
* * *
9307 ACGCGTTGCGATTTTACGTAT
1 TCTCGTTGCGA-TTTACGGAT
*
9328 TGTCGTTGCGATTTACGGAT
1 TCTCGTTGCGATTTACGGAT
* *
9348 ACGCGTTGCGATTTTACGGAT
1 TCTCGTTGCGA-TTTACGGAT
* *
9369 ACTCATTGCGAT
1 TCTCGTTGCGAT
9381 AGTCAGAATC
Statistics
Matches: 109, Mismatches: 21, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
19 1 0.01
20 73 0.67
21 35 0.32
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (20 bp):
TCTCGTTGCGATTTACGGAT
Found at i:9335 original size:41 final size:40
Alignment explanation
Indices: 9230--9380 Score: 221
Period size: 41 Copynumber: 3.7 Consensus size: 40
9220 GTCAGAATCT
* * *
9230 CGTTGCGATTTACGTATTCTCGTTGCAATTTACAGATATG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
9270 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
*
9310 CGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACG
1 CGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACG
* * *
9351 CGTTGCGATTTTACGGATACTCATTGCGAT
1 CGTTGCGA-TTTACGTATTCTCGTTGCGAT
9381 AGTCAGAATC
Statistics
Matches: 102, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
40 45 0.44
41 57 0.56
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
Found at i:9394 original size:41 final size:39
Alignment explanation
Indices: 9212--9402 Score: 172
Period size: 41 Copynumber: 4.7 Consensus size: 39
9202 AAATTCAGTA
*
9212 TTGCGATAGTCAGAATCTCGTTGCGA-TTTACGTATTCTCG
1 TTGCGAT--TCAGAATCGCGTTGCGATTTTACGTATTCTCG
*
9252 TTGCAATTTACAGATAT-GCGTTGCGA-TTTACGTATTCTCG
1 TTGCGA-TT-CAGA-ATCGCGTTGCGATTTTACGTATTCTCG
* * *
9292 TTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCG
1 TTGCGATTCA-GAAT-CGCGTTGCGATTTTACGTATTCTCG
* * * * *
9333 TTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCA
1 TTGCGATTCA-GAAT-CGCGTTGCGATTTTACGTATTCTCG
9374 TTGCGATAGTCAGAATCGCGTTGCGATTT
1 TTGCGAT--TCAGAATCGCGTTGCGATTT
9403 ATATGTTCGC
Statistics
Matches: 130, Mismatches: 12, Indels: 17
0.82 0.08 0.11
Matches are distributed among these distances:
38 3 0.02
39 4 0.03
40 45 0.35
41 73 0.56
42 3 0.02
43 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (39 bp):
TTGCGATTCAGAATCGCGTTGCGATTTTACGTATTCTCG
Found at i:9396 original size:61 final size:60
Alignment explanation
Indices: 9269--9403 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 60
9259 TTACAGATAT
* * * * * * * *
9269 GCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATT
1 GCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCATTGCGATGTCACGAATC
*
9329 GTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCATTGCGATAGTCA-GAATC
1 G-CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGGATACGCATTGCGAT-GTCACGAATC
9391 GCGTTGCGATTTA
1 GCGTTGCGATTTA
9404 TATGTTCGCG
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
60 1 0.02
61 37 0.59
62 23 0.37
63 2 0.03
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (60 bp):
GCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCATTGCGATGTCACGAATC
Found at i:9412 original size:20 final size:20
Alignment explanation
Indices: 9389--9441 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
9379 ATAGTCAGAA
*
9389 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
9409 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
*
9429 TCGCGTTGTGATT
1 TCGCGTTGCGATT
9442 ATGGAAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.13, C:0.17, G:0.25, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:9540 original size:20 final size:20
Alignment explanation
Indices: 9494--9544 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
9484 CTTCATAATC
9494 GCGTTGCGATTCTGGGAACT
1 GCGTTGCGATTCTGGGAACT
** *
9514 GATTTGCGATTCT-GGAGATT
1 GCGTTGCGATTCTGGGA-ACT
9534 GCGTTGCGATT
1 GCGTTGCGATT
9545 TTTATTTCGT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.16, C:0.16, G:0.33, T:0.35
Consensus pattern (20 bp):
GCGTTGCGATTCTGGGAACT
Found at i:25235 original size:15 final size:15
Alignment explanation
Indices: 25199--25237 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
25189 TACAAAATAT
*
25199 AATACTTAATTTTAAA
1 AATA-TTAAATTTAAA
25215 ATATATTAAATTTAAA
1 A-ATATTAAATTTAAA
25231 AATATTA
1 AATATTA
25238 TTCTCATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 6 0.29
16 12 0.57
17 3 0.14
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
AATATTAAATTTAAA
Found at i:34106 original size:12 final size:12
Alignment explanation
Indices: 34081--34150 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
34071 ACGAAGATAT
* *
34081 CAGAAATCAAAA
1 CAGAATTCAGAA
34093 CAGAATTCAGAA
1 CAGAATTCAGAA
34105 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
34117 CAGAATCCAGAT
1 CAGAATTCAGAA
*
34129 CAGAAATCAGAA
1 CAGAATTCAGAA
34141 CAGAATTCAG
1 CAGAATTCAG
34151 GTCATTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:34150 original size:48 final size:47
Alignment explanation
Indices: 34079--34187 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 47
34069 AAACGAAGAT
*
34079 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
** ** *
34126 GATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
*
34174 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
34188 TAAAATATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 52 0.98
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
Found at i:34185 original size:24 final size:25
Alignment explanation
Indices: 34079--34187 Score: 109
Period size: 24 Copynumber: 4.5 Consensus size: 25
34069 AAACGAAGAT
*
34079 ATCAGAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
34103 AACAGATATCAGAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
34127 ATCAGAAATCAGAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* ***
34151 GTCATTTATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
34176 -TCGGAAATCAGA
1 ATCAGAAATCAGA
34188 TAAAATATTT
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.03
24 63 0.91
25 4 0.06
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:35814 original size:17 final size:18
Alignment explanation
Indices: 35782--35818 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
35772 TAAAACTAAC
35782 ATTTTTATGCACATCAAT
1 ATTTTTATGCACATCAAT
*
35800 ATTTTTAT-CAGATCAAT
1 ATTTTTATGCACATCAAT
35817 AT
1 AT
35819 ATCTGTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.46
Consensus pattern (18 bp):
ATTTTTATGCACATCAAT
Found at i:36669 original size:7 final size:7
Alignment explanation
Indices: 36657--36704 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
36647 GGTCAACGTG
36657 GGTCAAC
1 GGTCAAC
36664 GGTCAAC
1 GGTCAAC
36671 GGGTCAAC
1 -GGTCAAC
36679 GGTCAAC
1 GGTCAAC
*
36686 GG--GAC
1 GGTCAAC
36691 GGTTCAAC
1 GG-TCAAC
36699 GGTCAA
1 GGTCAA
36705 TGGGTCGGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
5 4 0.11
7 20 0.57
8 11 0.31
ACGTcount: A:0.27, C:0.25, G:0.33, T:0.15
Consensus pattern (7 bp):
GGTCAAC
Found at i:36676 original size:15 final size:15
Alignment explanation
Indices: 36656--36688 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
36646 TGGTCAACGT
36656 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
36671 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
36686 GGG
1 GGG
36689 ACGGTTCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.39, T:0.12
Consensus pattern (15 bp):
GGGTCAACGGTCAAC
Found at i:36722 original size:18 final size:18
Alignment explanation
Indices: 36699--36768 Score: 78
Period size: 18 Copynumber: 4.2 Consensus size: 18
36689 ACGGTTCAAC
36699 GGTCAATGGGTCGGGTCG
1 GGTCAATGGGTCGGGTCG
36717 GGTCAA-----CGGGTCG
1 GGTCAATGGGTCGGGTCG
* *
36730 AGTAAATGGGTCGGGTCG
1 GGTCAATGGGTCGGGTCG
*
36748 GGTCAACGGGTCGGGTCG
1 GGTCAATGGGTCGGGTCG
36766 GGT
1 GGT
36769 TGTGACCGGT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
13 11 0.26
18 31 0.74
ACGTcount: A:0.14, C:0.17, G:0.49, T:0.20
Consensus pattern (18 bp):
GGTCAATGGGTCGGGTCG
Found at i:38276 original size:2 final size:2
Alignment explanation
Indices: 38269--38317 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
38259 CATCGTTGCT
38269 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
38311 TA TA TA T
1 TA TA TA T
38318 GAAATGGTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40237 original size:17 final size:19
Alignment explanation
Indices: 40217--40262 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
40207 TATATTAATT
*
40217 AAAAAAA-TCTTATTTT-A
1 AAAAAAATTCCTATTTTCA
40234 AAAAAAATTCCTATTTTCA
1 AAAAAAATTCCTATTTTCA
40253 AAAAATAATT
1 AAAAA-AATT
40263 AAAATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 7 0.28
18 8 0.32
19 6 0.24
20 4 0.16
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAAAATTCCTATTTTCA
Found at i:40677 original size:23 final size:23
Alignment explanation
Indices: 40645--40699 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
40635 AGGTCAAATC
* * *
40645 TTTTTTTTTATTTAGTTAATTAA
1 TTTTTATTTAGTTACTTAATTAA
* *
40668 TTTTTATTTAGTTACTTAGTTAT
1 TTTTTATTTAGTTACTTAATTAA
40691 TTTTTATTT
1 TTTTTATTT
40700 TTAAATTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (23 bp):
TTTTTATTTAGTTACTTAATTAA
Found at i:41344 original size:10 final size:10
Alignment explanation
Indices: 41329--41353 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41319 GCTCATCTAC
41329 GCAATTTTTA
1 GCAATTTTTA
41339 GCAATTTTTA
1 GCAATTTTTA
41349 GCAAT
1 GCAAT
41354 CTAGAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (10 bp):
GCAATTTTTA
Found at i:52325 original size:17 final size:18
Alignment explanation
Indices: 52299--52338 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
52289 TTTAAATATT
*
52299 TAAAATATAAATT-TTCA
1 TAAAAAATAAATTATTCA
*
52316 TAAAAAATAAATTATTTA
1 TAAAAAATAAATTATTCA
52334 TAAAA
1 TAAAA
52339 TTTCATGCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAAAATAAATTATTCA
Found at i:52694 original size:2 final size:2
Alignment explanation
Indices: 52687--52757 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
52677 ATTTACATAC
52687 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
52729 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
52758 AATTTACGCA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60338 original size:23 final size:23
Alignment explanation
Indices: 60312--60356 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
60302 CACCACAGCT
*
60312 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
60335 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
60357 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:60605 original size:149 final size:149
Alignment explanation
Indices: 60335--60638 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
60325 CGAAGTGCCC
* *
60335 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCATATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
*
60400 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
60465 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCG
60484 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
60549 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
60614 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCG
60633 CGTAGA
1 CGTAGA
60639 CCCTCTACCC
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:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCAAAGAACCG
Found at i:61221 original size:18 final size:20
Alignment explanation
Indices: 61184--61221 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
61174 TATTCGTTGA
*
61184 GGGGGTATCGGTTCTCCCCT
1 GGGGGTATCGGATCTCCCCT
61204 GGGGGTATC-GAT-TCCCCT
1 GGGGGTATCGGATCTCCCCT
61222 CTAGCATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.08, C:0.29, G:0.34, T:0.29
Consensus pattern (20 bp):
GGGGGTATCGGATCTCCCCT
Found at i:61225 original size:67 final size:67
Alignment explanation
Indices: 61116--61267 Score: 277
Period size: 67 Copynumber: 2.3 Consensus size: 67
61106 TTTTTCTCAT
*
61116 GGGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATTCGT
1 GGGGGTATCGGTT-CCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATTCGT
61181 TGA
65 TGA
*
61184 GGGGGTATCGGTTCTCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATTCGTT
1 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATTCGTT
61249 GA
66 GA
61251 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
61268 TTGAATGGGT
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
67 69 0.85
68 12 0.15
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATTCGTT
GA
Found at i:66038 original size:17 final size:16
Alignment explanation
Indices: 65985--66040 Score: 51
Period size: 17 Copynumber: 3.5 Consensus size: 16
65975 ATTAAAAATA
* *
65985 ATTTAATAAATTTAAC
1 ATTTAATCATTTTAAC
* * *
66001 ATTTGAT-ATTTGAAA
1 ATTTAATCATTTTAAC
66016 ATTTAATCATTTTTAAC
1 ATTTAATCA-TTTTAAC
66033 ATTTAATC
1 ATTTAATC
66041 TTCTTCCAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
15 11 0.35
16 7 0.23
17 13 0.42
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (16 bp):
ATTTAATCATTTTAAC
Found at i:70489 original size:31 final size:31
Alignment explanation
Indices: 70454--70512 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
70444 AATAAATTGG
70454 TCACTAATATTATTGATTTATAACAAAATGA
1 TCACTAATATTATTGATTTATAACAAAATGA
* * *
70485 TCACTATTGTTATTGATTTGTAACAAAA
1 TCACTAATATTATTGATTTATAACAAAA
70513 ATAGTCACTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (31 bp):
TCACTAATATTATTGATTTATAACAAAATGA
Found at i:70521 original size:32 final size:30
Alignment explanation
Indices: 70453--70521 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
70443 TAATAAATTG
70453 GTCACTAATATTATTGATTTATAACAAAAT
1 GTCACTAATATTATTGATTTATAACAAAAT
* * *
70483 GATCACTATTGTTATTGATTTGTAACAAAAAT
1 G-TCACTAATATTATTGATTTATAAC-AAAAT
70515 AGTCACT
1 -GTCACT
70522 CCACTGTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 1 0.03
31 21 0.64
32 10 0.30
33 1 0.03
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (30 bp):
GTCACTAATATTATTGATTTATAACAAAAT
Found at i:71149 original size:31 final size:29
Alignment explanation
Indices: 71112--71170 Score: 100
Period size: 31 Copynumber: 2.0 Consensus size: 29
71102 ATAACGATGG
71112 AGTGACCATTTTGTTATAAATCGATAACGTT
1 AGTGACCATTTTGTTAT-AA-CGATAACGTT
71143 AGTGACCATTTTGTTATAACGATAACGT
1 AGTGACCATTTTGTTATAACGATAACGT
71171 GGGTGACTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 9 0.32
30 2 0.07
31 17 0.61
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (29 bp):
AGTGACCATTTTGTTATAACGATAACGTT
Found at i:71176 original size:29 final size:31
Alignment explanation
Indices: 71101--71187 Score: 106
Period size: 29 Copynumber: 2.8 Consensus size: 31
71091 ATTTAACAGG
71101 GATAACGATGGAGTGACCATTTTGTTATAAATC
1 GATAACG-TGG-GTGACCATTTTGTTATAAATC
**
71134 GATAACGTTAGTGACCATTTTGTTAT-AA-C
1 GATAACGTGGGTGACCATTTTGTTATAAATC
* *
71163 GATAACGTGGGTGACTAATTTGTTA
1 GATAACGTGGGTGACCATTTTGTTA
71188 CTTTTGAAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
29 22 0.46
30 2 0.04
31 16 0.33
32 1 0.02
33 7 0.15
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (31 bp):
GATAACGTGGGTGACCATTTTGTTATAAATC
Found at i:71950 original size:35 final size:35
Alignment explanation
Indices: 71903--71998 Score: 138
Period size: 35 Copynumber: 2.7 Consensus size: 35
71893 AACACATTCA
* *
71903 TCAATTATATTCTAAACCCCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAACACT
*
71938 TCAATTACATTCTAAACCTCAAATTCCAAAACACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAACACT
* **
71973 TCAATTACATGCCCAACCCCAAATTC
1 TCAATTACATTCTAAACCCCAAATTC
71999 ATAATTCATT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.41, C:0.30, G:0.01, T:0.28
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAACACT
Found at i:72768 original size:143 final size:140
Alignment explanation
Indices: 72480--72770 Score: 426
Period size: 143 Copynumber: 2.0 Consensus size: 140
72470 AAACTATTTA
* * * *
72480 AATTAGAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACAGAAACTTGAA
1 AATTGGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCGAA
*
72545 AAATTCAATTCAACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTCGAGTCAGCTATTTT
66 AAATTCAATTCAACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTCGAGTCAACTATTTT
72610 ATAAACTAAACTG
131 ATAAACT--A-TG
72623 AATTGGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCG-A
1 AATTGGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCGAA
*
72687 AAATTCAATTCAATTTGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAAT
66 AAATTCAATTC-A----ACTTGATTTAAATTTTATAAACTCAAATCGAAAAAA-TTCGAGTCAAC
72752 TATTTTATAAA-T-TG
125 TATTTTATAAACTATG
72766 AATTG
1 AATTG
72771 AGTATTTAGG
Statistics
Matches: 136, Mismatches: 6, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
142 12 0.09
143 67 0.49
147 37 0.27
148 20 0.15
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.37
Consensus pattern (140 bp):
AATTGGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCGAA
AAATTCAATTCAACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTCGAGTCAACTATTTT
ATAAACTATG
Found at i:72983 original size:35 final size:35
Alignment explanation
Indices: 72941--73017 Score: 111
Period size: 35 Copynumber: 2.2 Consensus size: 35
72931 ATTGGGCATG
* *
72941 TAATTGAAGTATTTTTGAATTT-GAGGTTTAGAATA
1 TAATTGAAATATTTTGGAATTTAG-GGTTTAGAATA
*
72976 TATTTGAAATATTTTGGAATTTAGGGTTTAGAATA
1 TAATTGAAATATTTTGGAATTTAGGGTTTAGAATA
73011 TAATTGA
1 TAATTGA
73018 TGACTGTGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
35 36 0.97
36 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.45
Consensus pattern (35 bp):
TAATTGAAATATTTTGGAATTTAGGGTTTAGAATA
Found at i:79373 original size:2 final size:2
Alignment explanation
Indices: 79368--79393 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
79358 TTATTTTTTA
79368 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
79394 TGTTCATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:79539 original size:30 final size:31
Alignment explanation
Indices: 79488--79554 Score: 102
Period size: 30 Copynumber: 2.2 Consensus size: 31
79478 GGTTATTTTA
*
79488 TAATTTAAATCTTGAAATTTAGATAAAGTAT
1 TAATTTAAATCTTGAAATTTAGATAAAATAT
79519 TAATTT-AATCTT-AAATTTTAGATAAAATAT
1 TAATTTAAATCTTGAAA-TTTAGATAAAATAT
79549 TAATTT
1 TAATTT
79555 GACCAGAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 3 0.09
30 25 0.74
31 6 0.18
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (31 bp):
TAATTTAAATCTTGAAATTTAGATAAAATAT
Found at i:79565 original size:30 final size:30
Alignment explanation
Indices: 79501--79565 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
79491 TTTAAATCTT
* * *
79501 GAAA-TTTAGATAAAGTATTAATTTAATCT
1 GAAATTTTAGATAAAATATTAATTTAACCA
* *
79530 TAAATTTTAGATAAAATATTAATTTGACCA
1 GAAATTTTAGATAAAATATTAATTTAACCA
79560 GAAATT
1 GAAATT
79566 AACCAAAGTC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
29 3 0.10
30 26 0.90
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.40
Consensus pattern (30 bp):
GAAATTTTAGATAAAATATTAATTTAACCA
Found at i:90760 original size:20 final size:20
Alignment explanation
Indices: 90735--90776 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
90725 CTCTATTGTC
90735 ACCCCTTCAAACTTTCTGTG
1 ACCCCTTCAAACTTTCTGTG
90755 ACCCCTTCAAACTTTCTGTG
1 ACCCCTTCAAACTTTCTGTG
90775 AC
1 AC
90777 TGTAACTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.21, C:0.36, G:0.10, T:0.33
Consensus pattern (20 bp):
ACCCCTTCAAACTTTCTGTG
Found at i:92679 original size:21 final size:21
Alignment explanation
Indices: 92653--92704 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
92643 ATCTAAGGTT
92653 TCTGGTTCAC-GTAAATCAAAA
1 TCTGGTTCACAG-AAATCAAAA
*
92674 TCTGGTACACAGAAATCAAAA
1 TCTGGTTCACAGAAATCAAAA
*
92695 CCTGGCTTCA
1 TCTGG-TTCA
92705 ATGAAACAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (21 bp):
TCTGGTTCACAGAAATCAAAA
Done.