Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004106.1 Hibiscus syriacus cultivar Beakdansim tig00008980_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: 56349
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1664 original size:12 final size:12
Alignment explanation
Indices: 1647--1671 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1637 TCTTCGGGGA
1647 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1659 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1671 C
1 C
1672 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:1877 original size:24 final size:24
Alignment explanation
Indices: 1845--1898 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1835 TCTGAACATC
* *
1845 ATCAAAATCTGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
*
1869 ATCAAAATCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1893 ATCAAA
1 ATCAAA
1899 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2665 original size:20 final size:20
Alignment explanation
Indices: 2640--2690 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
2630 TGTATTATCT
*
2640 CGTTGCAAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
2660 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
2680 CGTTGCGAAAG
1 CGTTGCGAAAG
2691 GCAATCATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.20, G:0.29, T:0.20
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:2941 original size:19 final size:20
Alignment explanation
Indices: 2903--2952 Score: 93
Period size: 19 Copynumber: 2.5 Consensus size: 20
2893 ATTCATTTGA
2903 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
2923 CTATCGCAACGCG-AAATGG
1 CTATCGCAACGCGAAAATGG
2942 CTATCGCAACG
1 CTATCGCAACG
2953 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.32, C:0.28, G:0.24, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:3019 original size:19 final size:19
Alignment explanation
Indices: 2978--3042 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
2968 GAAATGAAAA
2978 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
2994 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3011 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3030 TCGCATTGCGATT
1 TCGCATTGCGATT
3043 CTCTCGTTGC
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.25
16 3 0.07
17 3 0.07
19 27 0.61
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:5074 original size:20 final size:20
Alignment explanation
Indices: 5032--5117 Score: 61
Period size: 20 Copynumber: 4.3 Consensus size: 20
5022 TAGTTTACTT
* *
5032 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAAATGAAAA
**
5052 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGAAAA
***
5072 TCGC-A-ACGTAGAAATGGCTA
1 TCGCAACACG-A-AAATGAAAA
*
5092 TCGCAATACG-AAATGAAAA
1 TCGCAACACGAAAATGAAAA
5111 TCGCAAC
1 TCGCAAC
5118 GACAAAATCG
Statistics
Matches: 53, Mismatches: 9, Indels: 9
0.75 0.13 0.13
Matches are distributed among these distances:
18 3 0.06
19 14 0.26
20 32 0.60
21 1 0.02
22 3 0.06
ACGTcount: A:0.44, C:0.23, G:0.16, T:0.16
Consensus pattern (20 bp):
TCGCAACACGAAAATGAAAA
Found at i:5126 original size:14 final size:14
Alignment explanation
Indices: 5107--5164 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
5097 ATACGAAATG
5107 AAAATCGCAACGAC
1 AAAATCGCAACGAC
5121 AAAATCGCAATGCGA-
1 AAAATCGCAA--CGAC
5136 AATGAGATCGCAACGAC
1 AA--A-ATCGCAACGAC
5153 AAAATCGCAACG
1 AAAATCGCAACG
5165 CGAAACACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
14 19 0.50
15 3 0.08
16 6 0.16
17 3 0.08
18 7 0.18
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:5151 original size:32 final size:33
Alignment explanation
Indices: 5091--5169 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
5081 AGAAATGGCT
*
5091 ATCGCAATACGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
5124 ATCGCAATGCGAAATG-AGATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
5156 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
5170 CACAAATCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 28 0.65
33 15 0.35
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:5198 original size:19 final size:18
Alignment explanation
Indices: 5176--5269 Score: 80
Period size: 14 Copynumber: 5.7 Consensus size: 18
5166 GAAACACAAA
5176 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
* *
5195 TCGCGTTGCGATTT--TG
1 TCGCATTGCGATTTCATT
5211 TCG--TTGCGA-TTCATT
1 TCGCATTGCGATTTCATT
* *
5226 TTGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
5242 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
5258 TCGCATTGCGAT
1 TCGCATTGCGAT
5270 AGCCATTTCC
Statistics
Matches: 59, Mismatches: 7, Indels: 19
0.69 0.08 0.22
Matches are distributed among these distances:
13 2 0.03
14 15 0.25
15 3 0.05
16 11 0.19
17 6 0.10
18 12 0.20
19 10 0.17
ACGTcount: A:0.13, C:0.19, G:0.22, T:0.46
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:5264 original size:32 final size:32
Alignment explanation
Indices: 5181--5269 Score: 144
Period size: 31 Copynumber: 2.8 Consensus size: 32
5171 ACAAATCGCA
*
5181 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
*
5214 TTGCGA-TTCATTTTGCATTGCGATTTTGTCG
1 TTGCGATTTCATTTCGCATTGCGATTTTGTCG
5245 TTGCGATTTCATTTCGCATTGCGAT
1 TTGCGATTTCATTTCGCATTGCGAT
5270 AGCCATTTCC
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
31 29 0.56
32 17 0.33
33 6 0.12
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.47
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCATTGCGATTTTGTCG
Found at i:5288 original size:20 final size:19
Alignment explanation
Indices: 5254--5308 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
5244 GTTGCGATTT
*
5254 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
5273 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
5293 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
5309 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:5811 original size:18 final size:18
Alignment explanation
Indices: 5785--5829 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
5775 GTCGATCAGA
*
5785 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
5803 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
5821 TGATGGCTC
1 TGATGGCTC
5830 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:7173 original size:20 final size:20
Alignment explanation
Indices: 7148--7189 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
7138 ATAGTTTCTA
7148 AAAATGAAAATCGCAACACG
1 AAAATGAAAATCGCAACACG
** *
7168 AAAATGACTATCGCAACGCG
1 AAAATGAAAATCGCAACACG
7188 AA
1 AA
7190 TTTGACTATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.21, G:0.17, T:0.12
Consensus pattern (20 bp):
AAAATGAAAATCGCAACACG
Found at i:7195 original size:20 final size:20
Alignment explanation
Indices: 7157--7205 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
7147 AAAAATGAAA
*
7157 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
7177 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
7197 ATCGCAACG
1 ATCGCAACG
7206 AGAGAATCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:7496 original size:22 final size:22
Alignment explanation
Indices: 7469--7512 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
7459 ATGGGAGATA
7469 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
7491 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
7513 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:7719 original size:20 final size:20
Alignment explanation
Indices: 7694--7745 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
7684 ATTATGTATT
7694 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
* *
7714 ATCGCGTTGCGAAAGTCGGT
1 ATCGCGTTGCGAAAGTCAGA
*
7734 ATCTCGTTGCGA
1 ATCGCGTTGCGA
7746 TTTTGTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.23, C:0.21, G:0.31, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:7779 original size:20 final size:20
Alignment explanation
Indices: 7754--7807 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
7744 GATTTTGTAT
7754 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
7774 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
7794 TATCGCATTGCGAT
1 TATCGCATTGCGAT
7808 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:7779 original size:61 final size:61
Alignment explanation
Indices: 7673--7810 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
7663 CGCTTTGAAA
* * * * *
7673 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCGGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
7734 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
7795 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
7811 CCCAATTCGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:7826 original size:61 final size:61
Alignment explanation
Indices: 7673--7828 Score: 152
Period size: 61 Copynumber: 2.6 Consensus size: 61
7663 CGCTTTGAAA
* ** * * * * *
7673 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCGGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * ** * * * *
7734 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
7795 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
7829 TTACTTATTC
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
61 76 0.97
62 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:11911 original size:31 final size:31
Alignment explanation
Indices: 11876--11937 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
11866 TTCGCCTAAT
11876 TTTATCGATCTAGCACCCTTTCTAACAAGGC
1 TTTATCGATCTAGCACCCTTTCTAACAAGGC
11907 TTTATCGATCTAGCACCCTTTCTAACAAGGC
1 TTTATCGATCTAGCACCCTTTCTAACAAGGC
11938 GCAGATCGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (31 bp):
TTTATCGATCTAGCACCCTTTCTAACAAGGC
Found at i:13361 original size:37 final size:38
Alignment explanation
Indices: 13316--13396 Score: 146
Period size: 38 Copynumber: 2.2 Consensus size: 38
13306 ATTCATATAT
13316 TCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGTCGAG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGAG
*
13353 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGAG
13391 TCGGGT
1 TCGGGT
13397 TCGAGTTTAG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 10 0.24
38 32 0.76
ACGTcount: A:0.11, C:0.11, G:0.40, T:0.38
Consensus pattern (38 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGAG
Found at i:13431 original size:222 final size:218
Alignment explanation
Indices: 13130--13544 Score: 670
Period size: 222 Copynumber: 1.9 Consensus size: 218
13120 TTTTGGTAGG
* *
13130 GTCGGATCGAGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTTAAAAAA
1 GTCGGATCGAGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGAGTTTAGGGTGAAAAAA
* *
13195 ACCGGACCGACCCGAAAATATATATAATTCAGGTCGGGT-TGGATTAAGTCACTGTTTTCATTAA
66 ACCAGACCGACCCGAAAATATATATAATTCAGGTCGGGTCT-GATTAAGTCACTATTTTCATTAA
13259 ATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGTTGGATTTCTAATTCATATATTCGGGTCG
130 ATAAAAATAATTTTTTATTATTTCGGGTCGGGTC----GGATTTCTAATTCATATATTCGGGTCG
13324 GGTTTTTTAAGTGTGATATTCGGGTCGA
191 GGTTTTTTAAGTGTGATATTCGGGTCGA
* * *
13352 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGAGTTTAGGGTGAAAAGA
1 GTCGGATCGAGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGAGTTTAGGGTGAAAAAA
* * * *
13417 ACCAGACTGACCCGAAAATATATATAATTCGGGTCGGGTCTGATTAAGTCATTATTTTTATTAAA
66 ACCAGACCGACCCGAAAATATATATAATTCAGGTCGGGTCTGATTAAGTCACTATTTTCATTAAA
*
13482 TAAAAATAATTTTTTATTATTTCGGGTTGGGTCGGATTTCTAATTCATATATTCGGGTCGGGT
131 TAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGT
13545 CGGATAAAAC
Statistics
Matches: 180, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
218 30 0.17
222 149 0.83
223 1 0.01
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.37
Consensus pattern (218 bp):
GTCGGATCGAGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGAGTTTAGGGTGAAAAAA
ACCAGACCGACCCGAAAATATATATAATTCAGGTCGGGTCTGATTAAGTCACTATTTTCATTAAA
TAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTTT
TTTAAGTGTGATATTCGGGTCGA
Found at i:13570 original size:222 final size:219
Alignment explanation
Indices: 13026--13599 Score: 652
Period size: 222 Copynumber: 2.6 Consensus size: 219
13016 ACTTATCATA
* * * *
13026 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGATCGGGTTTTTAATTTATATATT
1 TATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGA-----TTTCTAATTCATATATT
* * * *
13091 CGGGTTGGGTCGGGTCGGGTGAAACTTTATTTT--GGTAGGGTCGGATCGAGTTTTTTTAAGTGT
61 C-----GGGTCGGGTCGGATAAAACTTTATTTTCGGGTCGAGTCGGATCGAGTTTTTTTAAGTGT
* * *
13154 GATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTTAAAAAAACCGGACCGACCCGAAAATATATA
121 GATATTCGGGTCGGGTCGGGTTCGAGTTTAGGGTGAAAAAAACCAGACCGACCCGAAAATATATA
*
13219 TAATTCAGGTCGGGTTGGATTAAGTCACTGTTTT
186 TAATTCAGGTCGGGTTGGATTAAGTCACTATTTT
*
13253 CATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGTTGGATTTCTAATTCATATATTC
1 TATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTC----GGATTTCTAATTCATATATTC
** ** * * * * *
13318 GGGTCGGGT--TTTTTAAGTGTGATATTCGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATAT
62 GGGTCGGGTCGGATAAAACT-TTATTTTCGGGTCGAGTCGGATCGAGTTTTTTTAAGTGTGATAT
* *
13381 TCGGGTCGGGTCGGGTTCGAGTTTAGGGTGAAAAGAACCAGACTGACCCGAAAATATATATAATT
126 TCGGGTCGGGTCGGGTTCGAGTTTAGGGTGAAAAAAACCAGACCGACCCGAAAATATATATAATT
* *
13446 CGGGTCGGGTCT-GATTAAGTCATTATTTT
191 CAGGTCGGGT-TGGATTAAGTCACTATTTT
*
13475 TATTAAATAAAAATAATTTTTTATTATTTCGGGTTGGGTCGGATTTCTAATTCATATATTCGGGT
1 TATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGT
* *
13540 CGGGTCGGATAAAACTTTATTTT---GT----TCGGGTCG-GGTTTTTTAAGTGTGATATTCGGG
66 CGGGTCGGATAAAACTTTATTTTCGGGTCGAGTCGGATCGAGTTTTTTTAAGTGTGATATTCGGG
13597 TCG
131 TCG
13600 AGTTGGGTCG
Statistics
Matches: 303, Mismatches: 34, Indels: 36
0.81 0.09 0.10
Matches are distributed among these distances:
211 26 0.09
212 8 0.03
216 2 0.01
218 30 0.10
219 9 0.03
220 9 0.03
221 9 0.03
222 153 0.50
223 1 0.00
226 16 0.05
227 37 0.12
231 3 0.01
ACGTcount: A:0.23, C:0.11, G:0.27, T:0.39
Consensus pattern (219 bp):
TATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGT
CGGGTCGGATAAAACTTTATTTTCGGGTCGAGTCGGATCGAGTTTTTTTAAGTGTGATATTCGGG
TCGGGTCGGGTTCGAGTTTAGGGTGAAAAAAACCAGACCGACCCGAAAATATATATAATTCAGGT
CGGGTTGGATTAAGTCACTATTTT
Found at i:14263 original size:18 final size:16
Alignment explanation
Indices: 14220--14265 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 16
14210 TATGAAATTG
14220 GATTCCAATTCCTACA
1 GATTCCAATTCCTACA
*
14236 TATTCCAATTCCTTCACA
1 GATTCCAATTCC-T-ACA
*
14254 GATTCTAATTCC
1 GATTCCAATTCC
14266 CTTATAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 11 0.44
17 1 0.04
18 13 0.52
ACGTcount: A:0.28, C:0.30, G:0.04, T:0.37
Consensus pattern (16 bp):
GATTCCAATTCCTACA
Found at i:14957 original size:26 final size:28
Alignment explanation
Indices: 14896--14958 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
14886 ATATAATAAA
14896 ATTTAATAAAATAATAAATTATTAATTT
1 ATTTAATAAAATAATAAATTATTAATTT
* *
14924 ATTATAATACAATAA-AATATT-TTACTTT
1 ATT-TAATAAAATAATAA-ATTATTAATTT
14952 -TTTAATA
1 ATTTAATA
14959 GAATTTGAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
26 5 0.16
27 2 0.06
28 11 0.35
29 13 0.42
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (28 bp):
ATTTAATAAAATAATAAATTATTAATTT
Found at i:15038 original size:9 final size:11
Alignment explanation
Indices: 15016--15045 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
15006 TTTGGATGTT
15016 TGTGTTTGGTG
1 TGTGTTTGGTG
15027 TGTGTTTGGTG
1 TGTGTTTGGTG
15038 TGTGTTTG
1 TGTGTTTG
15046 AATGAATAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.43, T:0.57
Consensus pattern (11 bp):
TGTGTTTGGTG
Found at i:17453 original size:23 final size:22
Alignment explanation
Indices: 17422--17490 Score: 65
Period size: 21 Copynumber: 3.2 Consensus size: 22
17412 TCATTTGAGA
17422 CAAA-TATGTGGCATTTCGGTG
1 CAAACTATGTGGCATTTCGGTG
17443 CAAACCTATGTGGTCATTT-GG-G
1 CAAA-CTATGTGG-CATTTCGGTG
* *
17465 -ATAATTATGTGGCACTTCGGTG
1 CA-AACTATGTGGCATTTCGGTG
17487 CAAA
1 CAAA
17491 TTACGAGCTG
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
20 4 0.10
21 14 0.36
22 6 0.15
23 10 0.26
24 5 0.13
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (22 bp):
CAAACTATGTGGCATTTCGGTG
Found at i:18345 original size:46 final size:46
Alignment explanation
Indices: 18292--18386 Score: 154
Period size: 46 Copynumber: 2.1 Consensus size: 46
18282 CCATTCTTTG
* * *
18292 AGTTGTAAAAATATTATTGACACGACTTTCTCTGAGTTATTTAATC
1 AGTTGTAAAAATATCATTGACACAACTTTCTCCGAGTTATTTAATC
*
18338 AGTTGTAAAAATATCATTGACATAACTTTCTCCGAGTTATTTAATC
1 AGTTGTAAAAATATCATTGACACAACTTTCTCCGAGTTATTTAATC
18384 AGT
1 AGT
18387 CTCTTTGTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.40
Consensus pattern (46 bp):
AGTTGTAAAAATATCATTGACACAACTTTCTCCGAGTTATTTAATC
Found at i:20688 original size:21 final size:21
Alignment explanation
Indices: 20664--20714 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
20654 TTAAGGGTAA
20664 TATCGATACCTGTTGAAGAGG
1 TATCGATACCTGTTGAAGAGG
20685 TATCGATACCTGTTGAAGAGG
1 TATCGATACCTGTTGAAGAGG
20706 TATCGATAC
1 TATCGATAC
20715 TGTAAGGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (21 bp):
TATCGATACCTGTTGAAGAGG
Found at i:21387 original size:21 final size:21
Alignment explanation
Indices: 21342--21387 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
21332 GGGTTTAATG
* * * *
21342 TGGTCTTTCGGGATAATTATG
1 TGGTCATTCGGGACAAATATA
21363 TGGTCATTCGGGACAAATATA
1 TGGTCATTCGGGACAAATATA
21384 TGGT
1 TGGT
21388 ACTTCGGTGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.11, G:0.28, T:0.37
Consensus pattern (21 bp):
TGGTCATTCGGGACAAATATA
Found at i:21400 original size:21 final size:22
Alignment explanation
Indices: 21376--21465 Score: 69
Period size: 23 Copynumber: 4.1 Consensus size: 22
21366 TCATTCGGGA
*
21376 CAAA-TATATGGTACTTCGGTG
1 CAAACTATATGGCACTTCGGTG
*
21397 CAAACCTATTTGGCACTTCGGTG
1 CAAA-CTATATGGCACTTCGGTG
* * *
21420 CAAGCCTATGTGGTCA-TTCGGGG
1 CAA-ACTATATGG-CACTTCGGTG
* *
21443 C-AATTATGTGGCACTTCGGTG
1 CAAACTATATGGCACTTCGGTG
21464 CA
1 CA
21466 GATTACGAGC
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
20 2 0.04
21 18 0.33
22 1 0.02
23 32 0.58
24 2 0.04
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (22 bp):
CAAACTATATGGCACTTCGGTG
Found at i:21415 original size:23 final size:23
Alignment explanation
Indices: 21388--21465 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
21378 AATATATGGT
*
21388 ACTTCGGTGCAAACCTATTTGGC
1 ACTTCGGTGCAAACCTATGTGGC
*
21411 ACTTCGGTGCAAGCCTATGTGGTC
1 ACTTCGGTGCAAACCTATGTGG-C
* *
21435 A-TTCGGGGC-AA-TTATGTGGC
1 ACTTCGGTGCAAACCTATGTGGC
21455 ACTTCGGTGCA
1 ACTTCGGTGCA
21466 GATTACGAGC
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 2 0.04
21 14 0.30
22 1 0.02
23 27 0.59
24 2 0.04
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.29
Consensus pattern (23 bp):
ACTTCGGTGCAAACCTATGTGGC
Found at i:27278 original size:20 final size:22
Alignment explanation
Indices: 27224--27283 Score: 74
Period size: 20 Copynumber: 2.9 Consensus size: 22
27214 TATGAAATTA
27224 TTAAGGGTAGTATCGATACTTG
1 TTAAGGGTAGTATCGATACTTG
*
27246 TTGAA--GAAGTATCGATAC-TG
1 TT-AAGGGTAGTATCGATACTTG
27266 -TAAGGGTAGTATCGATAC
1 TTAAGGGTAGTATCGATAC
27284 CTAAAGGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
18 2 0.06
19 1 0.03
20 14 0.42
21 12 0.36
22 2 0.06
23 2 0.06
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.32
Consensus pattern (22 bp):
TTAAGGGTAGTATCGATACTTG
Found at i:27290 original size:20 final size:20
Alignment explanation
Indices: 27253--27302 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
27243 TTGTTGAAGA
* *
27253 AGTATCGATACTGTAAGGGT
1 AGTATCGATACTGAAAGGAT
27273 AGTATCGATACCT-AAAGGAT
1 AGTATCGATA-CTGAAAGGAT
*
27293 GGTATCGATA
1 AGTATCGATA
27303 GCATCTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (20 bp):
AGTATCGATACTGAAAGGAT
Found at i:28007 original size:21 final size:21
Alignment explanation
Indices: 27906--28007 Score: 50
Period size: 21 Copynumber: 4.8 Consensus size: 21
27896 GTCGAGGGTT
*
27906 TTATGTGGTCA-TTCGGGATAA
1 TTATGTGG-CACTTCGGGACAA
*
27927 TTATGTAGTCA-TTCGGGACAA
1 TTATGT-GGCACTTCGGGACAA
* * * *
27948 ATATTTAGCACTTTGGTG-CAAA
1 TTATGTGGCACTTCGG-GAC-AA
* *
27970 CCTATGTGGTC-CATCGGGACAA
1 -TTATGTGG-CACTTCGGGACAA
27992 TTATGTGGCACTTCGG
1 TTATGTGGCACTTCGG
28008 TGGAAATTAC
Statistics
Matches: 59, Mismatches: 14, Indels: 16
0.66 0.16 0.18
Matches are distributed among these distances:
20 3 0.05
21 38 0.64
22 7 0.12
23 10 0.17
24 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (21 bp):
TTATGTGGCACTTCGGGACAA
Found at i:28871 original size:20 final size:20
Alignment explanation
Indices: 28846--28886 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
28836 ACAGCGGTGA
28846 ACGACGGAGAGCTCGATTTC
1 ACGACGGAGAGCTCGATTTC
28866 ACGACGGAGAGCTCGATTTC
1 ACGACGGAGAGCTCGATTTC
28886 A
1 A
28887 GAACGTCGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (20 bp):
ACGACGGAGAGCTCGATTTC
Found at i:35443 original size:20 final size:22
Alignment explanation
Indices: 35389--35448 Score: 74
Period size: 20 Copynumber: 2.9 Consensus size: 22
35379 TATGAAATTA
35389 TTAAGGGTAGTATCGATACTTG
1 TTAAGGGTAGTATCGATACTTG
*
35411 TTGAA--GAAGTATCGATAC-TG
1 TT-AAGGGTAGTATCGATACTTG
35431 -TAAGGGTAGTATCGATAC
1 TTAAGGGTAGTATCGATAC
35449 CTAAAGGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
18 2 0.06
19 1 0.03
20 14 0.42
21 12 0.36
22 2 0.06
23 2 0.06
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.32
Consensus pattern (22 bp):
TTAAGGGTAGTATCGATACTTG
Found at i:35455 original size:20 final size:20
Alignment explanation
Indices: 35418--35467 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
35408 TTGTTGAAGA
* *
35418 AGTATCGATACTGTAAGGGT
1 AGTATCGATACTGAAAGGAT
35438 AGTATCGATACCT-AAAGGAT
1 AGTATCGATA-CTGAAAGGAT
*
35458 GGTATCGATA
1 AGTATCGATA
35468 GCATCTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (20 bp):
AGTATCGATACTGAAAGGAT
Found at i:39758 original size:45 final size:44
Alignment explanation
Indices: 39661--39761 Score: 116
Period size: 45 Copynumber: 2.3 Consensus size: 44
39651 AAACCCAACG
* ** * *
39661 GATGTATCGATGCACATTCAAGGAGTGCATCGGTGCATCTTTAT
1 GATGTATCGATGCACATTCAAGGAGTACATCGACGCAGCTTCAT
39705 GATGTATCGATGCACATTCAAAGG-GATACATCGACGCAGCTTCAT
1 GATGTATCGATGCACATTC-AAGGAG-TACATCGACGCAGCTTCAT
39750 -AGTGTATCGATG
1 GA-TGTATCGATG
39762 AATTATGCAC
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
44 21 0.43
45 28 0.57
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29
Consensus pattern (44 bp):
GATGTATCGATGCACATTCAAGGAGTACATCGACGCAGCTTCAT
Found at i:45564 original size:20 final size:20
Alignment explanation
Indices: 45539--45580 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
45529 TGTATCGGTA
45539 CACTGGGGTGTGCATAGGTG
1 CACTGGGGTGTGCATAGGTG
*
45559 CACTGGGGTGTGCATCGGTG
1 CACTGGGGTGTGCATAGGTG
45579 CA
1 CA
45581 TAAATCTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.19, G:0.43, T:0.24
Consensus pattern (20 bp):
CACTGGGGTGTGCATAGGTG
Found at i:45645 original size:64 final size:65
Alignment explanation
Indices: 45567--45755 Score: 192
Period size: 65 Copynumber: 2.9 Consensus size: 65
45557 TGCACTGGGG
* * *
45567 TGTGCATCGGTGCAT-AAATCTACTTCGATATTTTGA-AATAGC-TGGGGTGCATCGATGCATGG
1 TGTGCATCGGTGCATAAAATC-AATTCGATATTTTAATAATA-CATGGAGTGCATCGATGCATGG
45629 CT
64 CT
*
45631 TGTGCATCGGTGCATAAAATCAATTCGATATTTTAATAATACATGGAGTGCATCGATGCATAG-T
1 TGTGCATCGGTGCATAAAATCAATTCGATATTTTAATAATACATGGAGTGCATCGATGCATGGCT
* * * * * * * *
45695 ATGTGTATCGGTACAAAAAATCTATTCGAT-GTTCAATTAAAACAAGG-GTGCATCGATGCAT
1 -TGTGCATCGGTGCATAAAATCAATTCGATATTTTAA-TAATACATGGAGTGCATCGATGCAT
45756 TGATTTATGC
Statistics
Matches: 108, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
64 48 0.44
65 60 0.56
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (65 bp):
TGTGCATCGGTGCATAAAATCAATTCGATATTTTAATAATACATGGAGTGCATCGATGCATGGCT
Found at i:45770 original size:65 final size:64
Alignment explanation
Indices: 45611--45774 Score: 177
Period size: 65 Copynumber: 2.5 Consensus size: 64
45601 GAAATAGCTG
* * * * * * * *
45611 GGGTGCATCGATGCATGGCTTGTGCATCGGTGCATAAAATCAATTCGATATTTTAATAATACAT
1 GGGTGCATCGATGCATTGTTTGTGCATCGGTACAAAAAATCAATTCGATAGTTCAATAAAACAA
* * * *
45675 GGAGTGCATCGATGCATAGTATGTGTATCGGTACAAAAAATCTATTCGAT-GTTCAATTAAAACA
1 GG-GTGCATCGATGCATTGTTTGTGCATCGGTACAAAAAATCAATTCGATAGTTCAA-TAAAACA
45739 A
64 A
*
45740 GGGTGCATCGATGCATTGATTTATGCATCGGTACA
1 GGGTGCATCGATGCATTG-TTTGTGCATCGGTACA
45775 CTTACCTAAA
Statistics
Matches: 82, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
64 21 0.26
65 61 0.74
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (64 bp):
GGGTGCATCGATGCATTGTTTGTGCATCGGTACAAAAAATCAATTCGATAGTTCAATAAAACAA
Found at i:47365 original size:16 final size:16
Alignment explanation
Indices: 47318--47368 Score: 93
Period size: 16 Copynumber: 3.2 Consensus size: 16
47308 TCTGTGGGTG
*
47318 TCGTCGGCTTAATGCG
1 TCGTCGGCTTAATGCA
47334 TCGTCGGCTTAATGCA
1 TCGTCGGCTTAATGCA
47350 TCGTCGGCTTAATGCA
1 TCGTCGGCTTAATGCA
47366 TCG
1 TCG
47369 ACCTTTGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.31
Consensus pattern (16 bp):
TCGTCGGCTTAATGCA
Found at i:49707 original size:54 final size:54
Alignment explanation
Indices: 49625--50044 Score: 578
Period size: 54 Copynumber: 7.8 Consensus size: 54
49615 GTACTATAGA
* * *
49625 CACTATGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTTCATG
1 CACTAAGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTCAGG
* **
49679 CACTAAGTGTGCAACCCACAGAATTCATCATAAGTTGATGAAAAATTGTTCAGG
1 CACTAAGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTCAGG
* * * *
49733 CACTAGGTGTGCAACCCACAAAATTCATCATAAATTAATGAACAACCGTTCAGG
1 CACTAAGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTCAGG
*
49787 CACTAAGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAATCGTTCAGG
1 CACTAAGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTCAGG
* *
49841 CTCTAAGTGTGCAACCTACTA-AATTCATCATAAGTTGATGAACAACCGTTCAGG
1 CACTAAGTGTGCAACCCAC-AGAATTCATCATAAGTTGATGAACAACCGTTCAGG
* *
49895 CACTAAGTGTGCTACCCACAGAATTCATCATAAGTTGATAAACAACCGTTCAGG
1 CACTAAGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTCAGG
* **
49949 CACTAAGTGTGCAACCCAGAGAATTCATCATGTGTTGATGAACAACCGTAT-AGG
1 CACTAAGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGT-TCAGG
** * *
50003 CACTCTGTGTGCGAA-CCA-AGAAATTCATAATAAGTTTATGAA
1 CACTAAGTGTGC-AACCCACAG-AATTCATCATAAGTTGATGAA
50045 TTTCCGCATG
Statistics
Matches: 325, Mismatches: 36, Indels: 10
0.88 0.10 0.03
Matches are distributed among these distances:
53 3 0.01
54 318 0.98
55 4 0.01
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (54 bp):
CACTAAGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTTCAGG
Found at i:49712 original size:27 final size:27
Alignment explanation
Indices: 49631--49713 Score: 75
Period size: 27 Copynumber: 3.1 Consensus size: 27
49621 TAGACACTAT
*
49631 GTGTGCAACCCACGGAATTCATCATAA
1 GTGTGCAACCCACAGAATTCATCATAA
* *
49658 GTTGATG-AA-CAACCG--TTCATGCACTAA
1 G-TG-TGCAACCCACAGAATTCAT-CA-TAA
49685 GTGTGCAACCCACAGAATTCATCATAA
1 GTGTGCAACCCACAGAATTCATCATAA
49712 GT
1 GT
49714 TGATGAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
25 7 0.16
26 6 0.14
27 18 0.41
28 6 0.14
29 7 0.16
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (27 bp):
GTGTGCAACCCACAGAATTCATCATAA
Found at i:49901 original size:27 final size:26
Alignment explanation
Indices: 49871--49956 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 26
49861 AAATTCATCA
49871 TAAGTTGATGAACAACCGTTCAGGCAC
1 TAAGTTGAT-AACAACCGTTCAGGCAC
* * * * *
49898 TAAGTGTGCTACCCACAGAATTCA-TCA-
1 TAAGT-TGATAACAACCG--TTCAGGCAC
49925 TAAGTTGATAAACAACCGTTCAGGCAC
1 TAAGTTGAT-AACAACCGTTCAGGCAC
49952 TAAGT
1 TAAGT
49957 GTGCAACCCA
Statistics
Matches: 43, Mismatches: 10, Indels: 12
0.66 0.15 0.18
Matches are distributed among these distances:
25 4 0.09
26 5 0.12
27 25 0.58
28 5 0.12
29 4 0.09
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (26 bp):
TAAGTTGATAACAACCGTTCAGGCAC
Found at i:50085 original size:56 final size:56
Alignment explanation
Indices: 50020--50127 Score: 198
Period size: 56 Copynumber: 1.9 Consensus size: 56
50010 TGTGCGAACC
50020 AAGAAATTCATAATAAGTTTATGAATTTCCGCATGGACACTATGTGTACAAAAACT
1 AAGAAATTCATAATAAGTTTATGAATTTCCGCATGGACACTATGTGTACAAAAACT
* *
50076 AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTATGTGTACAAA
1 AAGAAATTCATAATAAGTTTATGAATTTCCGCATGGACACTATGTGTACAAA
50128 CTATAGAGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (56 bp):
AAGAAATTCATAATAAGTTTATGAATTTCCGCATGGACACTATGTGTACAAAAACT
Found at i:50323 original size:45 final size:45
Alignment explanation
Indices: 50238--50323 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
50228 TTAAATACAC
* * * *
50238 GAAAGGATGCCATAAATGAAATTCATAACAGTTCATTAAAGGCAT
1 GAAAGGATGCCATAAATGAAAATAATAACAATTCACTAAAGGCAT
* *
50283 GAAAGGATGCCCTAAATGAAAATAATGAATAATT-ACTAAAG
1 GAAAGGATGCCATAAATGAAAATAAT-AACAATTCACTAAAG
50324 AATAATGGGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
45 29 0.85
46 5 0.15
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.23
Consensus pattern (45 bp):
GAAAGGATGCCATAAATGAAAATAATAACAATTCACTAAAGGCAT
Found at i:54780 original size:30 final size:30
Alignment explanation
Indices: 54745--54802 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
54735 AACTTAAAAG
* *
54745 AGTTTTGCAATACTGAGATTTAAATAATTT
1 AGTTTTACAATACTGAAATTTAAATAATTT
54775 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
54803 CATACAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (30 bp):
AGTTTTACAATACTGAAATTTAAATAATTT
Found at i:55290 original size:20 final size:19
Alignment explanation
Indices: 55242--55290 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
55232 AACTTAAATC
*
55242 AAAATAATTAAAATAAATAT
1 AAAATAATT-TAATAAATAT
55262 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAA-ATAT
55280 AAAATAATTTA
1 AAAATAATTTA
55291 TATGATATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 5 0.20
18 11 0.44
20 9 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATAATTTAATAAATAT
Found at i:55377 original size:61 final size:61
Alignment explanation
Indices: 55311--55428 Score: 193
Period size: 61 Copynumber: 1.9 Consensus size: 61
55301 ATTAAATATC
* * *
55311 TATAATATAATAT-TAAAATTAATATTTAATTTATTTAAAAAATCATATTAAAATTAATTTT
1 TATAATATAATATAAAAAAATAATATTTAATTTATTT-AAAAATAATATTAAAATTAATTTT
55372 TATAATATAATATAAAAAAATAATATTTAATTTATTTAAAAATAATATTAAAATTAA
1 TATAATATAATATAAAAAAATAATATTTAATTTATTTAAAAATAATATTAAAATTAA
55429 AATCAAATAT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
61 32 0.60
62 21 0.40
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (61 bp):
TATAATATAATATAAAAAAATAATATTTAATTTATTTAAAAATAATATTAAAATTAATTTT
Found at i:55454 original size:61 final size:64
Alignment explanation
Indices: 55311--55454 Score: 190
Period size: 61 Copynumber: 2.3 Consensus size: 64
55301 ATTAAATATC
* * ** *
55311 TATAATATAATATTAAAATTAATATTTAATTTATTTAAAAAATCATATTAAAATTAATTTTTATA
1 TATAATATAAAATT-AAA-TAATATTTAATTTATTTAAAAAATAATATTAAAATTAATAATCATA
55376 A
64 A
55377 TATAATATAAAA--AAATAATATTTAATTTATTT-AAAAATAATATTAAAATTAA-AATCA-AA
1 TATAATATAAAATTAAATAATATTTAATTTATTTAAAAAATAATATTAAAATTAATAATCATAA
55436 TATAATATAAAATTAAATA
1 TATAATATAAAATTAAATA
55455 TAAAAAACCT
Statistics
Matches: 71, Mismatches: 5, Indels: 9
0.84 0.06 0.11
Matches are distributed among these distances:
59 14 0.20
60 2 0.03
61 24 0.34
62 17 0.24
63 3 0.04
66 11 0.15
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (64 bp):
TATAATATAAAATTAAATAATATTTAATTTATTTAAAAAATAATATTAAAATTAATAATCATAA
Done.