Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000052.1 Hibiscus syriacus cultivar Beakdansim tig00000079_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: 83736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1131 original size:15 final size:15
Alignment explanation
Indices: 1092--1139 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
1082 TAGCTTCTGA
1092 ATTAA-AAATT-ATT
1 ATTAATAAATTAATT
*
1105 ATTTAT-AATTAATT
1 ATTAATAAATTAATT
1119 ATTAATAAATTAATT
1 ATTAATAAATTAATT
1134 ATTAAT
1 ATTAAT
1140 TGATCTTTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 8 0.27
14 8 0.27
15 14 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTAATAAATTAATT
Found at i:1532 original size:14 final size:14
Alignment explanation
Indices: 1513--1546 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1503 GATCCAACAA
*
1513 AAAAAAAGTGAAAG
1 AAAAAAAGGGAAAG
*
1527 AAAAAATGGGAAAG
1 AAAAAAAGGGAAAG
1541 AAAAAA
1 AAAAAA
1547 TTGTGATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.06
Consensus pattern (14 bp):
AAAAAAAGGGAAAG
Found at i:2052 original size:22 final size:22
Alignment explanation
Indices: 2025--2068 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2015 TAATAAATTT
2025 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
2047 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
2069 CTGAATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:2199 original size:31 final size:31
Alignment explanation
Indices: 2163--2221 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2153 AACTTAAAAG
* *
2163 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
2194 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
2222 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:2522 original size:11 final size:11
Alignment explanation
Indices: 2506--2544 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
2496 AAGAGGCCAC
2506 TAAATTATTAA
1 TAAATTATTAA
*
2517 TAAATTATTAT
1 TAAATTATTAA
*
2528 TAACTTATT-A
1 TAAATTATTAA
2538 TAAATTA
1 TAAATTA
2545 AAAAAAAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 6 0.25
11 18 0.75
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (11 bp):
TAAATTATTAA
Found at i:9178 original size:2 final size:2
Alignment explanation
Indices: 9171--9204 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9161 GGATCCTAAC
9171 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
9205 TGCCACATCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10215 original size:20 final size:20
Alignment explanation
Indices: 10190--10283 Score: 111
Period size: 20 Copynumber: 4.7 Consensus size: 20
10180 AATTTGGAAA
10190 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
10210 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
10231 ATCGCAACGCAATACTGACT
1 ATCGCAACGCGATACTGACT
10251 -TCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
10270 TTCGCAACGAGATA
1 ATCGCAACGCGATA
10284 ATACATAATC
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
19 20 0.32
20 27 0.43
21 14 0.22
22 2 0.03
ACGTcount: A:0.35, C:0.28, G:0.18, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:10236 original size:21 final size:22
Alignment explanation
Indices: 10187--10303 Score: 72
Period size: 20 Copynumber: 5.7 Consensus size: 22
10177 GCGAATTTGG
*
10187 AAAATCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATAATGAC
*
10209 --TATCGCAACGCGATAAT-AC
1 AAAATCGCAACGCGATAATGAC
* *
10228 AAAATCGCAACGCAATACTGAC
1 AAAATCGCAACGCGATAATGAC
* *
10250 ---TTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATAATGAC
** *
10269 --TTTCGCAACGAGATAAT-AC
1 AAAATCGCAACGCGATAATGAC
* *
10288 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
10304 TTTCAAAGCG
Statistics
Matches: 76, Mismatches: 13, Indels: 13
0.75 0.13 0.13
Matches are distributed among these distances:
19 21 0.28
20 29 0.38
21 24 0.32
22 2 0.03
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.20
Consensus pattern (22 bp):
AAAATCGCAACGCGATAATGAC
Found at i:10256 original size:19 final size:19
Alignment explanation
Indices: 10191--10278 Score: 79
Period size: 19 Copynumber: 4.4 Consensus size: 19
10181 ATTTGGAAAA
*
10191 TCGCAACGCGATACTGACT
1 TCGCAACGCAATACTGACT
* **
10210 ATCGCAACGCGATAATAC-AAAA
1 -TCGCAACGC---AATACTGACT
10232 TCGCAACGCAATACTGACT
1 TCGCAACGCAATACTGACT
*
10251 TCGCAACGCGATACTGACTT
1 TCGCAACGCAATACTGAC-T
10271 TCGCAACG
1 TCGCAACG
10279 AGATAATACA
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
18 5 0.09
19 18 0.33
20 18 0.33
21 9 0.16
22 1 0.02
23 4 0.07
ACGTcount: A:0.33, C:0.30, G:0.18, T:0.19
Consensus pattern (19 bp):
TCGCAACGCAATACTGACT
Found at i:10499 original size:22 final size:22
Alignment explanation
Indices: 10471--10514 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
10461 ACTCTCTCAC
10471 CCATCTCCGACGAAATCCGTCT
1 CCATCTCCGACGAAATCCGTCT
*
10493 CCATCTCCGGCGAAATCCGTCT
1 CCATCTCCGACGAAATCCGTCT
10515 ATCTCCATCT
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:0.20, C:0.41, G:0.16, T:0.23
Consensus pattern (22 bp):
CCATCTCCGACGAAATCCGTCT
Found at i:10809 original size:20 final size:20
Alignment explanation
Indices: 10776--10825 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
10766 TTTATTCTCT
* *
10776 CGTTGTGATAGTCAAATTCG
1 CGTTGCGATTGTCAAATTCG
**
10796 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCAAATTCG
*
10816 TGTTGCGATT
1 CGTTGCGATT
10826 TTCATTTTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.26, T:0.42
Consensus pattern (20 bp):
CGTTGCGATTGTCAAATTCG
Found at i:10830 original size:20 final size:20
Alignment explanation
Indices: 10792--10834 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
10782 GATAGTCAAA
10792 TTCGCGTTGCGATTGTCATT
1 TTCGCGTTGCGATTGTCATT
* *
10812 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTGTCATT
10832 TTC
1 TTC
10835 AGAAACTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.09, C:0.19, G:0.21, T:0.51
Consensus pattern (20 bp):
TTCGCGTTGCGATTGTCATT
Found at i:11025 original size:25 final size:24
Alignment explanation
Indices: 10971--11025 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
10961 TGTTTATTAT
* *
10971 TGTTTTTGGTATATCTTCACAATG
1 TGTTTTTGGTATATCTTAACAATA
10995 TAGTTTTTGGTATATC-TAACTTAATA
1 T-GTTTTTGGTATATCTTAAC--AATA
11021 TGTTT
1 TGTTT
11026 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAATA
Found at i:12175 original size:18 final size:18
Alignment explanation
Indices: 12154--12201 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
12144 TCCACTTCGG
12154 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
12172 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
12190 GAGCCATCACCT
1 GAGCCATCACCT
12202 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:12761 original size:20 final size:20
Alignment explanation
Indices: 12736--12781 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
12726 TAGTTTACTT
12736 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
** * *
12756 TCGCAATGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
12776 TCGCAA
1 TCGCAA
12782 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:12790 original size:19 final size:20
Alignment explanation
Indices: 12747--12791 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
12737 CGCAACACGA
12747 AAATGACTATCGCAATGCGG
1 AAATGACTATCGCAATGCGG
*
12767 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAATGCGG
12786 AAATGA
1 AAATGA
12792 AAATCGCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (20 bp):
AAATGACTATCGCAATGCGG
Found at i:12797 original size:19 final size:19
Alignment explanation
Indices: 12755--12839 Score: 72
Period size: 19 Copynumber: 4.6 Consensus size: 19
12745 GAAAATGACT
***
12755 ATCGCAATGCGGAAATGGCT
1 ATCGCAATGC-GAAATGAAA
12775 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
12794 ATCGCAA--C--TA-CAAA
1 ATCGCAATGCGAAATGAAA
12808 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
12827 ATCGCAACTGCGA
1 ATCGCAA-TGCGA
12840 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 23 0.44
20 15 0.29
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:12882 original size:20 final size:20
Alignment explanation
Indices: 12844--12918 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
12834 CTGCGATTTT
*
12844 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
12863 CATTTCCGCGTTGTGATAGC
1 CATTTCCGCGTTGCGATAGC
*
12883 CATTTTCGCGTTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
12903 CATTTCCGCGTTGCGA
1 CATTTCCGCGTTGCGA
12919 AAGTAAGTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 5 0.10
20 45 0.90
ACGTcount: A:0.16, C:0.27, G:0.24, T:0.33
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:12930 original size:40 final size:40
Alignment explanation
Indices: 12846--12938 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 40
12836 GCGATTTTCA
* * * * *
12846 TTTCGCATTGCGATAGCCATTTCCGCGTTGTGATAGCCAT
1 TTTCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGCAAG
*
12886 TTTCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTAAG
1 TTTCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGCAAG
*
12926 TTTCGTGTTGCGA
1 TTTCGCGTTGCGA
12939 AAGTAAACTA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34
Consensus pattern (40 bp):
TTTCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGCAAG
Found at i:13337 original size:21 final size:20
Alignment explanation
Indices: 13285--13345 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
13275 GACTCACCTG
13285 TCATCCCTCAAGAGTCCCCT
1 TCATCCCTCAAGAGTCCCCT
* ** *
13305 CCAGTCATTCAAGAGACCCCT
1 TCA-TCCCTCAAGAGTCCCCT
13326 ATCATCCCTCAAGAGTCCCC
1 -TCATCCCTCAAGAGTCCCC
13346 CCCACCGTTC
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.25, C:0.43, G:0.11, T:0.21
Consensus pattern (20 bp):
TCATCCCTCAAGAGTCCCCT
Found at i:13372 original size:41 final size:42
Alignment explanation
Indices: 13282--13372 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
13272 CCCGACTCAC
* * *
13282 CTGTCATCCCTCAAGAGTCCCCTCCAGTCATTCAAGAGACCC
1 CTGTCATCCCTCAAGAGTCCCCCCCAGCCATTCAAGAGACCA
* * *
13324 CTATCATCCCTCAAGAGTCCCCCCCA-CCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCCCCAGCCATTCAAGAGACCA
13365 CTGTCATC
1 CTGTCATC
13373 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 18 0.43
42 24 0.57
ACGTcount: A:0.23, C:0.42, G:0.14, T:0.21
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCCCCAGCCATTCAAGAGACCA
Found at i:13904 original size:20 final size:20
Alignment explanation
Indices: 13881--13984 Score: 103
Period size: 20 Copynumber: 5.5 Consensus size: 20
13871 GCAAAACAGC
*
13881 CTATCGCAACACGAAACTGA
1 CTATCGCAACACGAAAATGA
*
13901 CTATCGC-A-ACG-AGA-GA
1 CTATCGCAACACGAAAATGA
* *
13917 --ATCGCAACGCGAAAATGG
1 CTATCGCAACACGAAAATGA
13935 CTATCGCAACACGAAAATGA
1 CTATCGCAACACGAAAATGA
* * *
13955 CTATTGCAACGCGAAAATGG
1 CTATCGCAACACGAAAATGA
13975 CTATCGCAAC
1 CTATCGCAAC
13985 GAGAAAATCG
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
14 5 0.07
15 1 0.01
16 4 0.06
17 3 0.04
18 4 0.06
19 1 0.01
20 49 0.73
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
CTATCGCAACACGAAAATGA
Found at i:13985 original size:20 final size:20
Alignment explanation
Indices: 13917--13992 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
13907 CAACGAGAGA
13917 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
* *
13937 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGGCT
*
13957 ATTGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
13977 ATCGCAACGAGAAAAT
1 ATCGCAACGCGAAAAT
13993 CGCAATGCGA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:14046 original size:20 final size:20
Alignment explanation
Indices: 14021--14078 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
14011 TCGCATTGCG
14021 ATTTTCTCGTTGCGATAGCC
1 ATTTTCTCGTTGCGATAGCC
* * *
14041 ATTTTCGCGTTGCAATATCC
1 ATTTTCTCGTTGCGATAGCC
14061 ATTTTCGT-GTTGCGATAG
1 ATTTTC-TCGTTGCGATAG
14079 TCAAATGAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41
Consensus pattern (20 bp):
ATTTTCTCGTTGCGATAGCC
Found at i:14301 original size:20 final size:20
Alignment explanation
Indices: 14285--14361 Score: 127
Period size: 20 Copynumber: 3.9 Consensus size: 20
14275 ATTGCGATTT
*
14285 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
14305 TCAGAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
*
14325 TCAGAATCGCATTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
*
14345 TCAGTATCGCGTTGCGA
1 TCAGAATCGCGTTGCGA
14362 TTTTGTATTA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (20 bp):
TCAGAATCGCGTTGCGAAAG
Found at i:14403 original size:20 final size:20
Alignment explanation
Indices: 14294--14402 Score: 121
Period size: 20 Copynumber: 5.4 Consensus size: 20
14284 TTCAGAATCT
*
14294 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGTATCG
*
14314 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGTATCG
*
14334 CATTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGTATCG
** *
14354 CGTTGCGATTTTGT-ATTATCG
1 CGTTGCGA--AAGTCAGTATCG
*
14375 CGTTGCGATAGTCAGTATCG
1 CGTTGCGAAAGTCAGTATCG
*
14395 CATTGCGA
1 CGTTGCGA
14403 TTTTCCAAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
19 3 0.04
20 58 0.75
21 14 0.18
22 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGTATCG
Found at i:14485 original size:21 final size:22
Alignment explanation
Indices: 14433--14485 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
14423 ATTTACTTAT
14433 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
* ** *
14454 TCGTAACGCGAAATT-GTAAAA
1 TCGCATTGCGAAATTGGGAAAA
14475 TCGCATTGCGA
1 TCGCATTGCGA
14486 TAGTCATAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:14801 original size:2 final size:2
Alignment explanation
Indices: 14796--14859 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
14786 CTCTCGACTC
14796 TA TA TA -A 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
14837 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
14860 TTTATATGGT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19638 original size:108 final size:108
Alignment explanation
Indices: 19440--19655 Score: 378
Period size: 108 Copynumber: 2.0 Consensus size: 108
19430 TGCATGGATT
* *
19440 GTCTATTTTCTTCCTTAATAGTACACTATAGAACCAAACTAGGCTAAAATCGAGAACTTTGCTCC
1 GTCTATTTTCTTCCTTAATAGTAAACTATAGAACCAAACTAGGCTAAAATCAAGAACTTTGCTCC
* *
19505 GGGTTAACTTTTTTTAATTTCCTTAAATGCATCCTCCTTAATA
66 GGGTTAACTTCTTTTAATTTACTTAAATGCATCCTCCTTAATA
*
19548 GTCTATTTTCTTCCTTAATAGTAAACTATAGAACCAAACTAGGCTGAAATCAAGAACTTTGCTCC
1 GTCTATTTTCTTCCTTAATAGTAAACTATAGAACCAAACTAGGCTAAAATCAAGAACTTTGCTCC
*
19613 GGGTTAACTTCTTTTAGTTTACTTAAATGCATCCTCCTTAATA
66 GGGTTAACTTCTTTTAATTTACTTAAATGCATCCTCCTTAATA
19656 CTCTTCATAC
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
108 102 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.38
Consensus pattern (108 bp):
GTCTATTTTCTTCCTTAATAGTAAACTATAGAACCAAACTAGGCTAAAATCAAGAACTTTGCTCC
GGGTTAACTTCTTTTAATTTACTTAAATGCATCCTCCTTAATA
Found at i:24117 original size:65 final size:65
Alignment explanation
Indices: 24013--24154 Score: 257
Period size: 65 Copynumber: 2.2 Consensus size: 65
24003 ACCGATATAC
*
24013 GATCAATCAATGTTTTGTACATCGTGAACTCTAGGACGAAAATCGAGATCCCACGCGATTTCGAT
1 GATCAATCGATGTTTTGTACATCGTGAACTCTAGGACGAAAATCGAGATCCCACGCGATTTCGAT
* *
24078 GATCAAACGATGTTTTGTACATCGTGAACTCTAGGACGAAAATCGAGATCCCACGCGATTTTGAT
1 GATCAATCGATGTTTTGTACATCGTGAACTCTAGGACGAAAATCGAGATCCCACGCGATTTCGAT
24143 GATCAATCGATG
1 GATCAATCGATG
24155 ACAACTGCGG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 73 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (65 bp):
GATCAATCGATGTTTTGTACATCGTGAACTCTAGGACGAAAATCGAGATCCCACGCGATTTCGAT
Found at i:24306 original size:2 final size:2
Alignment explanation
Indices: 24299--24329 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
24289 AACTTAGGAT
24299 TA TA 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 TA TA T
24330 TAATTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24599 original size:10 final size:10
Alignment explanation
Indices: 24575--24610 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
24565 TTGTTAAATA
24575 TAAAA-TAAT
1 TAAAATTAAT
24584 TAAAAATTAAT
1 T-AAAATTAAT
24595 TAAAATTAAT
1 TAAAATTAAT
24605 TAAAAT
1 TAAAAT
24611 AAACATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 1 0.04
10 19 0.76
11 5 0.20
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
TAAAATTAAT
Found at i:24619 original size:21 final size:20
Alignment explanation
Indices: 24569--24619 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
24559 TCTTAATTGT
24569 TAAATATAAAATAATTAAAAA
1 TAAA-ATAAAATAATTAAAAA
* *
24590 TTAATTAAAATTAATT-AAAA
1 TAAAATAAAA-TAATTAAAAA
24610 TAAACATAAA
1 TAAA-ATAAA
24620 TATATTTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAAATAAAATAATTAAAAA
Found at i:24821 original size:9 final size:9
Alignment explanation
Indices: 24807--24831 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
24797 ATTGAATTTA
24807 TTCAAAATT
1 TTCAAAATT
24816 TTCAAAATT
1 TTCAAAATT
24825 TTCAAAA
1 TTCAAAA
24832 ATAATTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (9 bp):
TTCAAAATT
Found at i:31004 original size:27 final size:27
Alignment explanation
Indices: 30974--31027 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
30964 TGTAAGGTAC
*
30974 CAATAAACTCTACCCAAATAGGTGTTT
1 CAATAAAATCTACCCAAATAGGTGTTT
31001 CAATAAAATCTACCCAAATAGGTGTTT
1 CAATAAAATCTACCCAAATAGGTGTTT
31028 AAAAAAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (27 bp):
CAATAAAATCTACCCAAATAGGTGTTT
Found at i:38693 original size:246 final size:246
Alignment explanation
Indices: 38259--38752 Score: 979
Period size: 246 Copynumber: 2.0 Consensus size: 246
38249 AATCAAAACC
*
38259 ATAATATACGAACACTGTTCATACCCAAATCTAGATCTCTTCCTTAAGCTTTAAATTGCAAGACT
1 ATAATATACAAACACTGTTCATACCCAAATCTAGATCTCTTCCTTAAGCTTTAAATTGCAAGACT
38324 CATGGAGATGATTAAATTACAATCCAGCATGAGAGAGATTCCTAGTTGGAGTTCAATGCATAATT
66 CATGGAGATGATTAAATTACAATCCAGCATGAGAGAGATTCCTAGTTGGAGTTCAATGCATAATT
38389 TCAAGCACTTCTAAGCCTGCAAAACTTTGGCATAAAGCAGAAACTGCAAAACATATCGCGACTGA
131 TCAAGCACTTCTAAGCCTGCAAAACTTTGGCATAAAGCAGAAACTGCAAAACATATCGCGACTGA
38454 AATCTCCTTTAATAAGTGATTTCCTATGTAGACACTCATTTTCGTTCATAT
196 AATCTCCTTTAATAAGTGATTTCCTATGTAGACACTCATTTTCGTTCATAT
38505 ATAATATACAAACACTGTTCATACCCAAATCTAGATCTCTTCCTTAAGCTTTAAATTGCAAGACT
1 ATAATATACAAACACTGTTCATACCCAAATCTAGATCTCTTCCTTAAGCTTTAAATTGCAAGACT
38570 CATGGAGATGATTAAATTACAATCCAGCATGAGAGAGATTCCTAGTTGGAGTTCAATGCATAATT
66 CATGGAGATGATTAAATTACAATCCAGCATGAGAGAGATTCCTAGTTGGAGTTCAATGCATAATT
38635 TCAAGCACTTCTAAGCCTGCAAAACTTTGGCATAAAGCAGAAACTGCAAAACATATCGCGACTGA
131 TCAAGCACTTCTAAGCCTGCAAAACTTTGGCATAAAGCAGAAACTGCAAAACATATCGCGACTGA
38700 AATCTCCTTTAATAAGTGATTTCCTATGTAGACACTCATTTTCGTTCATAT
196 AATCTCCTTTAATAAGTGATTTCCTATGTAGACACTCATTTTCGTTCATAT
38751 AT
1 AT
38753 CTTTTTTTTA
Statistics
Matches: 247, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
246 247 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (246 bp):
ATAATATACAAACACTGTTCATACCCAAATCTAGATCTCTTCCTTAAGCTTTAAATTGCAAGACT
CATGGAGATGATTAAATTACAATCCAGCATGAGAGAGATTCCTAGTTGGAGTTCAATGCATAATT
TCAAGCACTTCTAAGCCTGCAAAACTTTGGCATAAAGCAGAAACTGCAAAACATATCGCGACTGA
AATCTCCTTTAATAAGTGATTTCCTATGTAGACACTCATTTTCGTTCATAT
Found at i:38839 original size:39 final size:38
Alignment explanation
Indices: 38775--39063 Score: 168
Period size: 38 Copynumber: 7.5 Consensus size: 38
38765 GATATATATG
* ** *
38775 TATATTATATAG-TTTACAAATTATTTTTGAAAACAAGTA
1 TATAATATATAGTTTTA-AAACCATTTTTGAAAACTA-TA
* *
38814 TATAATATATAGTCTTTAAAA-TATTTTTGGAAACTATA
1 TATAATATATAGT-TTTAAAACCATTTTTGAAAACTATA
*
38852 TA-ATATATATAGTTTTGAAAA-CATTTTAGAAAA-TATA
1 TATA-ATATATAGTTTT-AAAACCATTTTTGAAAACTATA
*
38889 TATATTATATAGTTTTTAAAACCATTTTTGAAAACT-TA
1 TATAATATATAG-TTTTAAAACCATTTTTGAAAACTATA
* * * * *
38927 TAAAATATAAAGTTTTTTAAAAAAACGTTTTGGAAAA-TATA
1 TATAATATATAG--TTTT--AAAACCATTTTTGAAAACTATA
* * * *
38968 TATAATATGTAATTTTAAAA-TATCTTTTGAAAA-TATGT
1 TATAATATATAGTTTTAAAACCAT-TTTTGAAAACTAT-A
* * * *
39006 TATATTATAT-GATTTTAAAAAACATTTTTTAAATC-ATA
1 TATAATATATAG-TTTT-AAAACCATTTTTGAAAACTATA
* *
39044 TATAAAATATAATTTTAAAA
1 TATAATATATAGTTTTAAAA
39064 AATATTTTTT
Statistics
Matches: 199, Mismatches: 32, Indels: 40
0.73 0.12 0.15
Matches are distributed among these distances:
36 1 0.01
37 40 0.20
38 77 0.39
39 47 0.24
40 6 0.03
41 28 0.14
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.44
Consensus pattern (38 bp):
TATAATATATAGTTTTAAAACCATTTTTGAAAACTATA
Found at i:38878 original size:38 final size:37
Alignment explanation
Indices: 38818--38942 Score: 130
Period size: 37 Copynumber: 3.3 Consensus size: 37
38808 CAAGTATATA
*
38818 ATATATAGTCTTTAAAATATTTTTGGAAACTATATAAT
1 ATATATAGT-TTTAAAACATTTTTGGAAACTATATAAT
* *
38856 ATATATAGTTTTGAAAACA-TTTTAGAAAATATAT-AT
1 ATATATAGTTTT-AAAACATTTTTGGAAACTATATAAT
* *
38892 ATTATATAGTTTTTAAAACCATTTTTGAAAACT-TATAAA
1 A-TATATAG-TTTTAAAA-CATTTTTGGAAACTATATAAT
*
38931 ATATAAAGTTTT
1 ATATATAGTTTT
38943 TTAAAAAAAC
Statistics
Matches: 73, Mismatches: 8, Indels: 13
0.78 0.09 0.14
Matches are distributed among these distances:
36 3 0.04
37 31 0.42
38 29 0.40
39 10 0.14
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (37 bp):
ATATATAGTTTTAAAACATTTTTGGAAACTATATAAT
Found at i:38908 original size:75 final size:76
Alignment explanation
Indices: 38812--39000 Score: 213
Period size: 75 Copynumber: 2.5 Consensus size: 76
38802 TGAAAACAAG
* * * * *
38812 TATATAATATATAGTCTTTAAAATATTTTTGGAAACTATATAATATATATAG-TTTT-GAAAACA
1 TATATAATATATAGTTTTTAAAATATTTTTGAAAACT-TATAAAATATAAAGTTTTTAAAAAACA
38875 TTTTAGAAAATA
65 TTTTAGAAAATA
* *
38887 TATATATTATATAGTTTTTAAAACCATTTTTGAAAACTTATAAAATATAAAGTTTTTTAAAAAAA
1 TATATAATATATAGTTTTTAAAA-TATTTTTGAAAACTTATAAAATATAAAG-TTTTT-AAAAAA
* *
38952 CGTTTTGGAAAATA
63 CATTTTAGAAAATA
* *
38966 TATATAATATGTA-ATTTTAAAATATCTTTTGAAAA
1 TATATAATATATAGTTTTTAAAATAT-TTTTGAAAA
39001 TATGTTATAT
Statistics
Matches: 95, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
75 33 0.35
76 12 0.13
77 6 0.06
78 17 0.18
79 27 0.28
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (76 bp):
TATATAATATATAGTTTTTAAAATATTTTTGAAAACTTATAAAATATAAAGTTTTTAAAAAACAT
TTTAGAAAATA
Found at i:39123 original size:25 final size:24
Alignment explanation
Indices: 39072--39119 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
39062 AAAATATTTT
*
39072 TTTCTTTTATTTATTTATTTGTTA
1 TTTCTTTTATTTATTTATTTATTA
39096 TTTCATTTTATTTA-TTATTTATTA
1 TTTC-TTTTATTTATTTATTTATTA
39120 ATTTTCCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (24 bp):
TTTCTTTTATTTATTTATTTATTA
Found at i:41433 original size:732 final size:732
Alignment explanation
Indices: 40028--41493 Score: 2534
Period size: 732 Copynumber: 2.0 Consensus size: 732
40018 TTTGGAGACC
40028 TCGGGGGCACTTTTCGCGTGGGTAAATCAAGCACTAGGGGCTCACATGTTTTGCATATTCATGCT
1 TCGGGGGCACTTTTCGCGTGGGTAAATCAAGCACTAGGGGCTCACATGTTTTGCATATTCATGCT
*
40093 TTGATTACCTATTGTGTTTTAATTAAATTGAAGTTCATGCCTTGTATTTATTAACCTTATATTTT
66 TTGATTACCTATTGTGTTTTAATTAAATTGAAGTTCATGCCTCGTATTTATTAACCTTATATTTT
*
40158 GGTCCTTATTTTTAATTAAATCTTGAATTTGGCCCATATATTTATTTTGATTTTGCTTTGGTCCT
131 AGTCCTTATTTTTAATTAAATCTTGAATTTGGCCCATATATTTATTTTGATTTTGCTTTGGTCCT
40223 CTAACCTCTTTGTTACATTTACATTTATTTATTTATTTATTATATATATATATATTATTCTCTTT
196 CTAACCTCTTTGTTACATTTACATTTATTTATTTATTTATTATATATATATATATTATTCTCTTT
40288 TAATTTTTTTCTTTTTTCTACACATGTATACATATATATTTCATTTTTTATTTCATTTTTAAGGC
261 TAATTTTTTTCTTTTTTCTA-ACATGTATACATATATATTTCATTTTTTATTTCATTTTTAAGGC
**
40353 CGAATATTTCTTTTTTTCATTTTTTTCTTAACATTATTATTTTTATTTTCCCATTTCTTTATTAT
325 CGAATATTTCTTTTTTTCATTTTTTTCTTAACATTATTATTTTTATTTT-CCATTTCCATATTAT
40418 ATATATATATATATATATGTTTCAATCTAACAATATTTATGACTTTGTAGAGAAATTTCAACTAA
389 ATATATATATATATATATGTTTCAATCTAACAATATTTATGACTTTGTAGAGAAATTTCAACTAA
*
40483 TCAAAGGTAAGCAATTTGAATCGGATTCTTAAATTTTTATTTAAATTCTTAATTTTCGTAATTAA
454 TCAAAGGTAAGCAATTTGAATCGGATTCTTAAATTTTTATTTAAATTCTTAATTTTCGCAATTAA
* * *
40548 AGACAACCGATAAATTAATTGGTACCGAAAGAGCAGTTCAAGGGTGTTAATCCTTCTTTGACCGT
519 AGACAACCGATAAATTAATTGGTACCGAAAGAGCAGTTCAAGGGTGCTAATCCTTCCTTGACCGA
* * *
40613 AACCGACTCCCGAACCCGATACGTTTCTGGTACAACGCATATCGTGTAAGAAATAGGATATCCGA
584 AACCGACTCCCGAACACGATACGTTTCTGGTACAACGCAGATCATGTAAGAAATAGGATATCCGA
*
40678 TCAACCCATTTGTTTTAAAATAAATGATCGGTGGCGACTCTAATTCATTTAATCCAAGTCGAAAC
649 TCAACCCATTTGTTTTAAAATAAATGATCGGTGGCGACTCCAATTCATTTAATCCAAGTCGAAAC
40743 CCAATTTTGGGCCCAACCG
714 CCAATTTTGGGCCCAACCG
*
40762 TCGGGGGCATTTTTCGCGTGGGTAAATCAAGCACTAGGGGCTCACATGTTTTGCATATTCATGCT
1 TCGGGGGCACTTTTCGCGTGGGTAAATCAAGCACTAGGGGCTCACATGTTTTGCATATTCATGCT
*
40827 TTGATTACCTATTGTGTTTTAATTAAATTGAAGTTCATGCCTCGTATTTATTAATCTTATATTTT
66 TTGATTACCTATTGTGTTTTAATTAAATTGAAGTTCATGCCTCGTATTTATTAACCTTATATTTT
40892 AGTCCTTATTTTTAATTAAATCTTGAATTTGGCCCATATATTTATTTTGATTTTGCTTTGGTCCT
131 AGTCCTTATTTTTAATTAAATCTTGAATTTGGCCCATATATTTATTTTGATTTTGCTTTGGTCCT
*
40957 CTAACCTCTTTGTTTTTACCTTTACATTTATTTATTTATTTATT-TAT-TATATATATTATTCTC
196 CTAACCTCTTTG---TTACATTTACATTTATTTATTTATTTATTATATATATATATATTATTCTC
*** *
41020 TTTTAATTTTTTTCTTTTTTCT-TTTTGTATATATATATATATT-ATTTTTTATTTCATTTTTTA
258 TTTTAATTTTTTTCTTTTTTCTAACATGTATACATATATAT-TTCATTTTTTATTTCA-TTTTTA
*
41083 AGGCCGAATATTTCTTTTTTTCA-TTTTTTCTTAACATTATTATTTTTATTTT-TATTTTCCCAT
321 AGGCCGAATATTTCTTTTTTTCATTTTTTTCTTAACATTATTATTTTTATTTTCCA-TTT-CCAT
* *
41146 -TTCTTTAT-TATATATATATATGCTTTCAATCTAACAATATTTATGACTTTGTAGAGAAATTTC
384 ATTATATATATATATATATATATG-TTTCAATCTAACAATATTTATGACTTTGTAGAGAAATTTC
*
41209 AACTAATCAAAGGTAATCAATTTGAATCGGATTCTTAAATTTTTATTTAAATTCTTAATTTTCGC
448 AACTAATCAAAGGTAAGCAATTTGAATCGGATTCTTAAATTTTTATTTAAATTCTTAATTTTCGC
* *
41274 AATTAAAGACAACCGATAAATTAATTGGTACCGAAAGGGCAGTTCAAGTGTGCTAATCCTTCCTT
513 AATTAAAGACAACCGATAAATTAATTGGTACCGAAAGAGCAGTTCAAGGGTGCTAATCCTTCCTT
*
41339 GACCGAAACCGACTCCCGAACACGATACGTTTCTGGTACAACGTAGATCATGTAAGAAATAGGAT
578 GACCGAAACCGACTCCCGAACACGATACGTTTCTGGTACAACGCAGATCATGTAAGAAATAGGAT
41404 ATCCGATCAACCCATTTGTTTTAAAATAAATGATCGGTGGCGACTCCAATTCATTTAATCCAAGT
643 ATCCGATCAACCCATTTGTTTTAAAATAAATGATCGGTGGCGACTCCAATTCATTTAATCCAAGT
* *
41469 CGAAACCTAATTTTGGGTCCAACCG
708 CGAAACCCAATTTTGGGCCCAACCG
41494 AAAGACGGTT
Statistics
Matches: 696, Mismatches: 28, Indels: 18
0.94 0.04 0.02
Matches are distributed among these distances:
731 15 0.02
732 320 0.46
733 58 0.08
734 234 0.34
735 38 0.05
736 3 0.00
737 28 0.04
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (732 bp):
TCGGGGGCACTTTTCGCGTGGGTAAATCAAGCACTAGGGGCTCACATGTTTTGCATATTCATGCT
TTGATTACCTATTGTGTTTTAATTAAATTGAAGTTCATGCCTCGTATTTATTAACCTTATATTTT
AGTCCTTATTTTTAATTAAATCTTGAATTTGGCCCATATATTTATTTTGATTTTGCTTTGGTCCT
CTAACCTCTTTGTTACATTTACATTTATTTATTTATTTATTATATATATATATATTATTCTCTTT
TAATTTTTTTCTTTTTTCTAACATGTATACATATATATTTCATTTTTTATTTCATTTTTAAGGCC
GAATATTTCTTTTTTTCATTTTTTTCTTAACATTATTATTTTTATTTTCCATTTCCATATTATAT
ATATATATATATATATGTTTCAATCTAACAATATTTATGACTTTGTAGAGAAATTTCAACTAATC
AAAGGTAAGCAATTTGAATCGGATTCTTAAATTTTTATTTAAATTCTTAATTTTCGCAATTAAAG
ACAACCGATAAATTAATTGGTACCGAAAGAGCAGTTCAAGGGTGCTAATCCTTCCTTGACCGAAA
CCGACTCCCGAACACGATACGTTTCTGGTACAACGCAGATCATGTAAGAAATAGGATATCCGATC
AACCCATTTGTTTTAAAATAAATGATCGGTGGCGACTCCAATTCATTTAATCCAAGTCGAAACCC
AATTTTGGGCCCAACCG
Found at i:44641 original size:2 final size:2
Alignment explanation
Indices: 44634--44665 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
44624 TTATTTAATA
*
44634 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44666 TTATGTCGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:47758 original size:22 final size:22
Alignment explanation
Indices: 47719--47769 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
47709 CTGAGTGGCA
* *
47719 TATGAGATTTGTCTCGAAGGACC
1 TATGA-ATATGTCCCGAAGGACC
47742 TATGAATATGTCCCGAAGGACC
1 TATGAATATGTCCCGAAGGACC
47764 TATGAA
1 TATGAA
47770 ACCCTCGACT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (22 bp):
TATGAATATGTCCCGAAGGACC
Found at i:49009 original size:27 final size:27
Alignment explanation
Indices: 48978--49033 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
48968 GCGATTGTGA
* *
48978 TTTA-GAATTTATGATTTTTTTGAGATT
1 TTTAGGAATTTAGGATTTTTTGGA-ATT
*
49005 TTTAGGAATTTAGGGTTTTTTGGAATT
1 TTTAGGAATTTAGGATTTTTTGGAATT
49032 TT
1 TT
49034 ATGAAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 9 0.36
28 16 0.64
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (27 bp):
TTTAGGAATTTAGGATTTTTTGGAATT
Found at i:49041 original size:27 final size:29
Alignment explanation
Indices: 48993--49055 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 29
48983 AATTTATGAT
* *
48993 TTTTTTGAGATTTTTAGGAATTT-AGG-G
1 TTTTTTGAGAATTTTAGAAATTTAAGGTG
49020 TTTTTTG-GAATTTTATGAAATTTAAGGTG
1 TTTTTTGAGAATTTTA-GAAATTTAAGGTG
49049 TTTTTTG
1 TTTTTTG
49056 TTGTTGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 7 0.23
27 13 0.42
28 3 0.10
29 8 0.26
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (29 bp):
TTTTTTGAGAATTTTAGAAATTTAAGGTG
Found at i:73679 original size:2 final size:2
Alignment explanation
Indices: 73672--73719 Score: 87
Period size: 2 Copynumber: 23.5 Consensus size: 2
73662 AAAGTTGACC
73672 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
73715 AT AT A
1 AT AT A
73720 AACAAATTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 43 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:78342 original size:22 final size:22
Alignment explanation
Indices: 78314--78367 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
78304 TAAGGAAGCA
78314 ATAAAATAAAGATAAACAGTGT
1 ATAAAATAAAGATAAACAGTGT
*
78336 ATAAAATGAAGATAAACAGTGT
1 ATAAAATAAAGATAAACAGTGT
78358 ATAAAATAAA
1 ATAAAATAAA
78368 CAAAATGACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.61, C:0.04, G:0.13, T:0.22
Consensus pattern (22 bp):
ATAAAATAAAGATAAACAGTGT
Found at i:78496 original size:2 final size:2
Alignment explanation
Indices: 78489--78519 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
78479 ATAGTAAATA
78489 AT 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 AT A
78520 CGAAATAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:80408 original size:105 final size:105
Alignment explanation
Indices: 80227--81012 Score: 1457
Period size: 105 Copynumber: 7.5 Consensus size: 105
80217 CCCATACAAG
* * * ** *
80227 TTGCGTTGTTTCGAGGCCAATATCCTTCG-TGTGAAGCAGTAATTGGCTCTGAAATTGAGAAATG
1 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
80291 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
80331 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
1 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
80396 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
*
80436 TTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
1 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
*
80501 TTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAAC
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
* *
80541 TTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGAGAAATG
1 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
80606 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
80646 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
1 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
80711 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
80751 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
1 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
80816 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
*
80856 TTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
1 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
80921 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
*
80961 TTGCGTTGTCTGGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTG
1 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
81013 GGTAAAACCT
Statistics
Matches: 666, Mismatches: 15, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
104 26 0.04
105 640 0.96
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (105 bp):
TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
Found at i:81812 original size:53 final size:52
Alignment explanation
Indices: 81732--81834 Score: 152
Period size: 53 Copynumber: 2.0 Consensus size: 52
81722 ACCCACCTTA
* * *
81732 TTTTCTTTTTTTTCAATTTAGGGCGCCCTTTCGGGTTTTCACCCTAAGCGTT
1 TTTTCTTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAGCGTT
* *
81784 TTTTTTTTTTTTTCCAACTTAGGACGCCCTCTCGGGTTTTCATCCTAAGCG
1 TTTTCTTTTTTTT-CAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAGCG
81835 AAGTATTTCT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 12 0.27
53 33 0.73
ACGTcount: A:0.13, C:0.24, G:0.17, T:0.47
Consensus pattern (52 bp):
TTTTCTTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAGCGTT
Done.