Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004307.1 Hibiscus syriacus cultivar Beakdansim tig00009444_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: 76284
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:1389 original size:43 final size:42
Alignment explanation
Indices: 1324--1435 Score: 134
Period size: 43 Copynumber: 2.6 Consensus size: 42
1314 CTGGAATGGT
* ** * *
1324 GGGGGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGGTGG
1 GGGGGGGA-CTCTTGAGGGATGACAGGGGCCTCTTGAACGAT-G
* *
1368 GGGGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGATT
1 GGGGGGGACTCTTGAGGGATGACAGGGGCCTCTTGAACGATG
*
1410 GGAGGGGACTCTTGAGGGATGACAGG
1 GGGGGGGACTCTTGAGGGATGACAGG
1436 TGAGTCGGAC
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 24 0.41
43 27 0.46
44 8 0.14
ACGTcount: A:0.20, C:0.17, G:0.43, T:0.21
Consensus pattern (42 bp):
GGGGGGGACTCTTGAGGGATGACAGGGGCCTCTTGAACGATG
Found at i:1400 original size:21 final size:21
Alignment explanation
Indices: 1371--1431 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
1361 ACGGTGGGGG
*
1371 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
1392 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
1413 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
1432 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:1430 original size:42 final size:43
Alignment explanation
Indices: 1342--1435 Score: 136
Period size: 42 Copynumber: 2.2 Consensus size: 43
1332 CCTCTTCAAC
* * *
1342 GATGACAGTGGCCTCTTGAACGGTGGGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGGAGGGGACTCTTGAGG
* *
1385 GATGATAGGGGCCTCTTGAACGAT-TGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGGAGGGGACTCTTGAGG
1427 GATGACAGG
1 GATGACAGG
1436 TGAGTCGGAC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
42 24 0.53
43 21 0.47
ACGTcount: A:0.20, C:0.15, G:0.44, T:0.21
Consensus pattern (43 bp):
GATGACAGGGGCCTCTTGAACGATGGGGAGGGGACTCTTGAGG
Found at i:1798 original size:20 final size:19
Alignment explanation
Indices: 1762--1833 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 19
1752 AAGAATAGTT
1762 TACTTTCGCAACACGAAACA
1 TACTTTCGCAACACGAAA-A
**
1782 TACTTTCGCAATGCGAAAA
1 TACTTTCGCAACACGAAAA
* * *
1801 TGACTATCGCAACGCGGAAA
1 T-ACTTTCGCAACACGAAAA
*
1821 TGACTATCGCAAC
1 T-ACTTTCGCAAC
1834 GCGGAAATGG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 2 0.04
20 44 0.96
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (19 bp):
TACTTTCGCAACACGAAAA
Found at i:1812 original size:40 final size:40
Alignment explanation
Indices: 1767--1852 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
1757 TAGTTTACTT
* *
1767 TCGCAACACGAAACAT-ACTTTCGCAATGCGAAAATGACTA
1 TCGCAACACGAAA-ATGACTATCGCAACGCGAAAATGACTA
* * * *
1807 TCGCAACGCGGAAATGACTATCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTATCGCAACGCGAAAATGACTA
1847 TCGCAA
1 TCGCAA
1853 TGCGAAATGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 2 0.05
40 37 0.95
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (40 bp):
TCGCAACACGAAAATGACTATCGCAACGCGAAAATGACTA
Found at i:1834 original size:20 final size:20
Alignment explanation
Indices: 1787--1862 Score: 109
Period size: 20 Copynumber: 3.9 Consensus size: 20
1777 AAACATACTT
* *
1787 TCGCAATGCGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
1807 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1827 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
1847 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
1863 AAATCACAAC
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 6 0.12
20 45 0.88
ACGTcount: A:0.36, C:0.22, G:0.25, T:0.17
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1873 original size:39 final size:40
Alignment explanation
Indices: 1798--1873 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
1788 CGCAATGCGA
** *
1798 AAATGACTATCGCAACGCGGAAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGGAAATGAAAATCACAACGCGG
* *
1838 AAATGGCTATCGCAATGC-GAAATGAAAATCACAACG
1 AAATGACTATCGCAACGCGGAAATGAAAATCACAACG
1874 ACAAAATCGC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
39 15 0.48
40 16 0.52
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.16
Consensus pattern (40 bp):
AAATGACTATCGCAACGCGGAAATGAAAATCACAACGCGG
Found at i:1888 original size:33 final size:33
Alignment explanation
Indices: 1846--1934 Score: 151
Period size: 33 Copynumber: 2.7 Consensus size: 33
1836 GGAAATGGCT
1846 ATCGCAATGCGAAATGAAAATCACAACGACAAA
1 ATCGCAATGCGAAATGAAAATCACAACGACAAA
*
1879 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCACAACGACAAA
* *
1912 ATCGCAACGCAAAATGAAAATCA
1 ATCGCAATGCGAAATGAAAATCA
1935 AAAATTCGTG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.51, C:0.21, G:0.16, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCACAACGACAAA
Found at i:1926 original size:13 final size:14
Alignment explanation
Indices: 1862--1926 Score: 60
Period size: 14 Copynumber: 4.4 Consensus size: 14
1852 ATGCGAAATG
*
1862 AAAATCACAACGAC
1 AAAATCGCAACGAC
*
1876 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
1895 AAAATCGCAACGAC
1 AAAATCGCAACGAC
1909 AAAATCGCAACG-C
1 AAAATCGCAACGAC
1922 AAAAT
1 AAAAT
1927 GAAAATCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
13 6 0.14
14 21 0.49
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.23
ACGTcount: A:0.52, C:0.23, G:0.14, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1931 original size:19 final size:18
Alignment explanation
Indices: 1876--1933 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 18
1866 TCACAACGAC
*
1876 AAAATCGCAATGCGAAATG
1 AAAATCGCAACGC-AAATG
*
1895 AAAATCGCAACG---A-C
1 AAAATCGCAACGCAAATG
1909 AAAATCGCAACGCAAAATG
1 AAAATCGCAACGC-AAATG
1928 AAAATC
1 AAAATC
1934 AAAAATTCGT
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
14 12 0.39
15 1 0.03
18 1 0.03
19 17 0.55
ACGTcount: A:0.52, C:0.21, G:0.16, T:0.12
Consensus pattern (18 bp):
AAAATCGCAACGCAAATG
Found at i:2530 original size:17 final size:18
Alignment explanation
Indices: 2484--2530 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
2474 CGGGTCGATC
2484 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
2502 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
2520 A-GTGATGGCTC
1 AGGTGATGGCTC
2531 CCGAAGTGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.15, C:0.13, G:0.45, T:0.28
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:3865 original size:20 final size:20
Alignment explanation
Indices: 3823--3881 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
3813 AATAGTTTCT
* * *
3823 GAAAATGAAAATCGTAACAC
1 GAAAATGACAATCGCAACGC
3843 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
3863 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
3882 AGAGAATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.44, C:0.20, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:4438 original size:20 final size:20
Alignment explanation
Indices: 4374--4487 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
4364 GATTATGTAT
*
4374 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
**
4394 TATCTAGTTGCGAAAGT-ATG
1 TATCGCGTTGCGAAAGTCA-G
4414 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
4434 TATCGCATTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
4455 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
4475 TATCGCATTGCGA
1 TATCGCGTTGCGA
4488 TTTTCCAAAT
Statistics
Matches: 78, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
19 4 0.05
20 58 0.74
21 14 0.18
22 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:4488 original size:20 final size:19
Alignment explanation
Indices: 4354--4488 Score: 83
Period size: 20 Copynumber: 6.7 Consensus size: 19
4344 CGCTTTGAAA
*
4354 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGA-TA-GTAGT
* * *
4375 ATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGT-AGT
* *
4395 ATC-TAGTTGCGAAAGTATGT
1 ATCGCA-TTGCGATAGTA-GT
* *
4415 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGT-AGT
* *
4435 ATCGCATTGCGATTTTGTATT
1 ATCGCATTGCGA--TAGTAGT
*
4456 ATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATAGT-AGT
4476 ATCGCATTGCGAT
1 ATCGCATTGCGAT
4489 TTTCCAAATT
Statistics
Matches: 90, Mismatches: 16, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
19 6 0.07
20 58 0.64
21 24 0.27
22 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (19 bp):
ATCGCATTGCGATAGTAGT
Found at i:4491 original size:41 final size:41
Alignment explanation
Indices: 4354--4489 Score: 188
Period size: 41 Copynumber: 3.3 Consensus size: 41
4344 CGCTTTGAAA
*
4354 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* *
4395 ATC-TAGTTGCGA--AAGTATGTATCGCGTTGCGAAAGTCAGT
1 ATCGCA-TTGCGATTATGTAT-TATCGCGTTGCGAAAGTCAGT
* *
4435 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
4476 ATCGCATTGCGATT
1 ATCGCATTGCGATT
4490 TTCCAAATTT
Statistics
Matches: 83, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
39 5 0.06
40 30 0.36
41 44 0.53
42 4 0.05
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:4507 original size:41 final size:41
Alignment explanation
Indices: 4414--4509 Score: 115
Period size: 41 Copynumber: 2.3 Consensus size: 41
4404 CGAAAGTATG
* * **
4414 TATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTGTAT
1 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTAAAT
*
4455 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT--AAAT
4498 T-T-GCATTGCGAT
1 TATCGCATTGCGAT
4510 TTACTTATTC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
41 45 0.92
42 1 0.02
43 3 0.06
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (41 bp):
TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTAAAT
Found at i:4535 original size:15 final size:15
Alignment explanation
Indices: 4515--4545 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4505 GCGATTTACT
*
4515 TATTCGCGTTGCGAA
1 TATTCGCATTGCGAA
4530 TATTCGCATTGCGAA
1 TATTCGCATTGCGAA
4545 T
1 T
4546 TGGGAAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (15 bp):
TATTCGCATTGCGAA
Found at i:4585 original size:21 final size:22
Alignment explanation
Indices: 4533--4585 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
4523 TTGCGAATAT
4533 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
4554 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
4575 TCGCATTGCGA
1 TCGCATTGCGA
4586 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:21597 original size:42 final size:42
Alignment explanation
Indices: 21544--21646 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 42
21534 CACATAAAAC
* *
21544 TGTCCCTAAGGACCACATATATGTTCCAAAGAACCAAATATA
1 TGTCCCGAAGGACCGCATATATGTTCCAAAGAACCAAATATA
* * * * *
21586 TGTCCCGAAGGACTGCGTATATGTTCCAAAGGATCACATATA
1 TGTCCCGAAGGACCGCATATATGTTCCAAAGAACCAAATATA
* *
21628 TGTCTCGAATGACCGCATA
1 TGTCCCGAAGGACCGCATA
21647 GAACCCTCGA
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.25
Consensus pattern (42 bp):
TGTCCCGAAGGACCGCATATATGTTCCAAAGAACCAAATATA
Found at i:21627 original size:21 final size:21
Alignment explanation
Indices: 21551--21630 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 21
21541 AACTGTCCCT
21551 AAGGACCACATATATGTTCCA
1 AAGGACCACATATATGTTCCA
* * * *
21572 AAGAACCAAATATATGTCCCG
1 AAGGACCACATATATGTTCCA
** *
21593 AAGGACTGCGTATATGTTCCA
1 AAGGACCACATATATGTTCCA
*
21614 AAGGATCACATATATGT
1 AAGGACCACATATATGT
21631 CTCGAATGAC
Statistics
Matches: 44, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (21 bp):
AAGGACCACATATATGTTCCA
Found at i:22406 original size:36 final size:35
Alignment explanation
Indices: 22343--22413 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 35
22333 CATTGTAAAA
22343 ATGGTACCGATACTTCCACATTAGTATCGATTACCC
1 ATGGTACCGATACTTCCACATTAGTATCGA-TACCC
*
22379 ATGGTACCGATA-TTACCA-ATTCGGTATCGATACCC
1 ATGGTACCGATACTT-CCACATT-AGTATCGATACCC
22414 TATGAAGAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
35 10 0.31
36 22 0.69
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (35 bp):
ATGGTACCGATACTTCCACATTAGTATCGATACCC
Found at i:39101 original size:12 final size:13
Alignment explanation
Indices: 39076--39117 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
39066 ATTGGTCAAC
39076 GGTCAACGGGTCG
1 GGTCAACGGGTCG
39089 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
*
39101 GGTAAACGGGTCG
1 GGTCAACGGGTCG
39114 GGTC
1 GGTC
39118 GGGTAAACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.17, C:0.21, G:0.45, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:39119 original size:18 final size:18
Alignment explanation
Indices: 39096--39149 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
39086 TCGGGTCAAC
39096 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
*
39114 GGTCGGGTAAACTGGTCG
1 GGTCGGGTAAACGGGTCG
39132 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
39150 TGACCGGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.17, C:0.17, G:0.48, T:0.19
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCG
Found at i:39149 original size:13 final size:13
Alignment explanation
Indices: 39080--39116 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
39070 GTCAACGGTC
*
39080 AACGGGTCGGGTC
1 AACGGGTCGGGTA
39093 AAC-GGTCGGGTA
1 AACGGGTCGGGTA
39105 AACGGGTCGGGT
1 AACGGGTCGGGT
39117 CGGGTAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.19, C:0.19, G:0.46, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:39182 original size:11 final size:11
Alignment explanation
Indices: 39166--39207 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
39156 GTCAAACAGG
39166 TCAAAACCGGT
1 TCAAAACCGGT
39177 TCAAAACCGGT
1 TCAAAACCGGT
39188 T--AAACCGG-
1 TCAAAACCGGT
39196 TCAAAACCGGT
1 TCAAAACCGGT
39207 T
1 T
39208 TCCAGCGTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 1 0.04
9 7 0.25
10 7 0.25
11 13 0.46
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (11 bp):
TCAAAACCGGT
Found at i:39201 original size:19 final size:20
Alignment explanation
Indices: 39169--39207 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
39159 AAACAGGTCA
39169 AAACCGGTTCAAAACCGGTT
1 AAACCGGTTCAAAACCGGTT
39189 AAACCGG-TCAAAACCGGTT
1 AAACCGGTTCAAAACCGGTT
39208 TCCAGCGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.18
Consensus pattern (20 bp):
AAACCGGTTCAAAACCGGTT
Found at i:46371 original size:7 final size:7
Alignment explanation
Indices: 46359--46389 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
46349 AGAATAGCAC
46359 CGGTCAA
1 CGGTCAA
46366 CGGTCAA
1 CGGTCAA
46373 CGGTCAA
1 CGGTCAA
46380 CGGTCAA
1 CGGTCAA
46387 CGG
1 CGG
46390 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.32, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:46399 original size:13 final size:13
Alignment explanation
Indices: 46381--46422 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
46371 AACGGTCAAC
46381 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
46394 GGTCAAC-GTTCG
1 GGTCAACGGGTCG
*
46406 GGTAAACGGGTCG
1 GGTCAACGGGTCG
46419 GGTC
1 GGTC
46423 GGGTAAACTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.17, C:0.21, G:0.43, T:0.19
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:46426 original size:18 final size:18
Alignment explanation
Indices: 46403--46454 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
46393 GGGTCAACGT
46403 TCGGGTAAACGGGTCGGG
1 TCGGGTAAACGGGTCGGG
*
46421 TCGGGTAAACTGGTCGGG
1 TCGGGTAAACGGGTCGGG
46439 TCGGGTAAACGGGTCG
1 TCGGGTAAACGGGTCG
46455 TGACCGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.17, C:0.17, G:0.46, T:0.19
Consensus pattern (18 bp):
TCGGGTAAACGGGTCGGG
Found at i:46477 original size:10 final size:10
Alignment explanation
Indices: 46457--46511 Score: 69
Period size: 10 Copynumber: 5.6 Consensus size: 10
46447 ACGGGTCGTG
46457 ACCGGTC-AA
1 ACCGGTCAAA
46466 ACCGGTCAAA
1 ACCGGTCAAA
46476 ACCGGTTCAAA
1 ACCGG-TCAAA
* *
46487 ATCGGT-TAA
1 ACCGGTCAAA
46496 ACCGGTCAAA
1 ACCGGTCAAA
46506 ACCGGT
1 ACCGGT
46512 TTCCAGCGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
9 14 0.36
10 16 0.41
11 9 0.23
ACGTcount: A:0.35, C:0.27, G:0.22, T:0.16
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:46497 original size:20 final size:19
Alignment explanation
Indices: 46457--46512 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
46447 ACGGGTCGTG
*
46457 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
*
46476 ACCGGTTCAAAATCGGTTAA
1 ACCGG-TCAAAACCGGTTAA
46496 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
46513 TCCAGCGTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 16 0.50
20 9 0.28
21 7 0.22
ACGTcount: A:0.34, C:0.27, G:0.21, T:0.18
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:51549 original size:22 final size:21
Alignment explanation
Indices: 51524--51581 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
51514 AGTTTATTAA
*
51524 ATTTATTATTTTTTAATTCTTT
1 ATTTAATATTTTTTAATT-TTT
*
51546 ATTTACATATTTGTTAATTTTT
1 ATTTA-ATATTTTTTAATTTTT
51568 ATTATAATATTTTT
1 ATT-TAATATTTTT
51582 AAATATTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 18 0.58
23 13 0.42
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTTAATATTTTTTAATTTTT
Found at i:51590 original size:21 final size:22
Alignment explanation
Indices: 51544--51592 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
51534 TTTTAATTCT
* *
51544 TTATTTACATATTTGTTAATTT
1 TTATTTACATATTTGTTAAATA
51566 TTATTATA-ATATTT-TTAAATA
1 TTATT-TACATATTTGTTAAATA
51587 TTATTT
1 TTATTT
51593 TACTCAAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.04
21 10 0.42
22 11 0.46
23 2 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (22 bp):
TTATTTACATATTTGTTAAATA
Found at i:56623 original size:99 final size:99
Alignment explanation
Indices: 56447--56635 Score: 281
Period size: 99 Copynumber: 1.9 Consensus size: 99
56437 ATATTATATT
* * * *
56447 ATATGTATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACACCCTGACTTTATGG
1 ATATATATACAATAAAGCTTGAGCTATCCCTCTAGAGCAATTGGTTAAACACCCAGACTTTATGG
* **
56512 ATAAGGTTCAGCTAGCTTAATAAAGGTGATTATA
66 ATAAGATTCAGCTAGCCCAATAAAGGTGATTATA
*
56546 ATATATATACAATAAAGCTTGAGCTATCCCTCTAGTGCAATTGGTTAAACACCCCAG-CTTTATG
1 ATATATATACAATAAAGCTTGAGCTATCCCTCTAGAGCAATTGGTTAAACA-CCCAGACTTTATG
*
56610 GATTAGATTCAGCTAGCCCAATAAAG
65 GATAAGATTCAGCTAGCCCAATAAAG
56636 TCAAATTACA
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
99 76 0.95
100 4 0.05
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (99 bp):
ATATATATACAATAAAGCTTGAGCTATCCCTCTAGAGCAATTGGTTAAACACCCAGACTTTATGG
ATAAGATTCAGCTAGCCCAATAAAGGTGATTATA
Found at i:57696 original size:13 final size:13
Alignment explanation
Indices: 57678--57726 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
57668 TGCGTCATAA
57678 ATTTATGACGCGT
1 ATTTATGACGCGT
* **
57691 ATTTATGACACAC
1 ATTTATGACGCGT
57704 ATTTATGACGCGT
1 ATTTATGACGCGT
57717 ATTTATGACG
1 ATTTATGACG
57727 TTCATTGAGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (13 bp):
ATTTATGACGCGT
Found at i:62401 original size:33 final size:33
Alignment explanation
Indices: 62339--62401 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
62329 AGTATGAAAT
* ***
62339 AATGTTGGGGCATTTTGAACGCTTGTATCAGTA
1 AATGTTGGGGCATTTTAAACGCCCATATCAGTA
*
62372 AATGTTGGGGCATTTTAAAGGCCCATATCA
1 AATGTTGGGGCATTTTAAACGCCCATATCA
62402 TACAAGAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.33
Consensus pattern (33 bp):
AATGTTGGGGCATTTTAAACGCCCATATCAGTA
Found at i:63576 original size:62 final size:62
Alignment explanation
Indices: 63478--64269 Score: 882
Period size: 62 Copynumber: 13.0 Consensus size: 62
63468 TCTTGTTTCC
** * *
63478 TAGAGTCAATTCTTGACTTCCTCATGAAGA-AGAGTCAACCTTTGTTATTCCTGACTCCCTAG
1 TAGAGTCAACCCTTGACTTCCTCGTGAAGAGA-AGTCAACCTTTGTTATTTCTGACTCCCTAG
*** * *
63540 TAGAGTCAATTTTTGACTTCCTCATAAAGAGAAGTCAACCTTTGTTA-TTCATGA-----T--
1 TAGAGTCAACCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTC-TGACTCCCTAG
* * * * *
63595 T----TCAACCATTGACTTTCTCATGAAGAGAAGTCAACCTTTGTTATTCCTGA-TCCCCAG
1 TAGAGTCAACCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCTAG
* ** * * * * * *
63652 TAGAGTCAACCCTTAACTTCCTTATAAAGAAAAGTCAACATATGTTA-TCCTTGAATCCCTAG
1 TAGAGTCAACCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTC-TGACTCCCTAG
* * *
63714 TAGAGTCAACCCTTGACTTCATCATGAAGAGAAGTCAGCCTTTGTTATTTCTGACTCCCTAG
1 TAGAGTCAACCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCTAG
* *
63776 TAGAATCAACCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTT-TTCATTTATGACTCACC-AG
1 TAGAGTCAACCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTT-ATTTCTGACTC-CCTAG
* ** * *
63838 TAGAGTTAACCCTTGACTTCCTCGTGAAGAGAAGTCAAGTTTTGTTATTTGTGACTCCCCCAG
1 TAGAGTCAACCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACT-CCCTAG
* *
63901 TAGAGTCAACCCTTGACTTCCTCGTGAAGAGAAGTCAAACTTTGTTATTTCTGACTCCCCAG
1 TAGAGTCAACCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCTAG
** * *
63963 TAGAGTCAACCCTTGACTTCCTTATGAAGAGAAGTCAACCTTTGTTATTTCTAACTCCCGAG
1 TAGAGTCAACCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCTAG
* * * *
64025 TAGAGTCAACCCTTGACTTCCTCGTGAATAAAAGTCAACGTTTGTTATTTCTAACTACCC-AG
1 TAGAGTCAACCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACT-CCCTAG
* * * *
64087 TAAAGTCAATCCTTGACTTCCTCGTGAAGAGAAGTCAACTTTTATTATTTCTGACTCCCTAG
1 TAGAGTCAACCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCTAG
* * * *
64149 TAGAGTCAACCCTTGACTTCCTCGTGAAGAGAAGTCGATCTTTGTTATTTATGACTCCCCAG
1 TAGAGTCAACCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCTAG
* * *** *
64211 TAGAGTCAACCCTTGACTTCGTCGTGAATAGAAGTCGGTCTTTGTTATTCCTGACTCCC
1 TAGAGTCAACCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCC
64270 CAGCACGGGT
Statistics
Matches: 634, Mismatches: 73, Indels: 46
0.84 0.10 0.06
Matches are distributed among these distances:
51 40 0.06
52 2 0.00
55 1 0.00
57 2 0.00
60 3 0.00
61 44 0.07
62 477 0.75
63 65 0.10
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (62 bp):
TAGAGTCAACCCTTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCCTAG
Found at i:64436 original size:89 final size:89
Alignment explanation
Indices: 64278--65078 Score: 847
Period size: 89 Copynumber: 9.0 Consensus size: 89
64268 CCCAGCACGG
* * * * * * *
64278 GTCTGATCACCACGGAAAAGTAGTGGAGCAGATTC-TCTTTATGTCAGATTTGCTCTCCACGGAA
1 GTCTGATCTCCACGGAAGAGTAGTGGAACATATTCTTC-TTATTTCAGATTTGGTCTCCACGAAA
*
64342 GAGTAGTGAAGCAAATTAATCTCGA
65 GAGTAGTGAAGCAAATCAATCTCGA
* * * * * ** *
64367 GTCTGATCACCATGGAAGAGTAGTGGATCATATTCTCCTTATGTCAGATTTGGTCTCCATAAAAA
1 GTCTGATCTCCACGGAAGAGTAGTGGAACATATTCTTCTTATTTCAGATTTGGTCTCCACGAAAG
* * *
64432 AGTAGTGAAGCAACTCATTTTCGA
66 AGTAGTGAAGCAAATCAATCTCGA
*** * * * * *
64456 GTCTGAAAACCACAGAAGTGTAGTGGAGCAAATTCTTCTTATATCAGATTTGGTCTCCACGAAAG
1 GTCTGATCTCCACGGAAGAGTAGTGGAACATATTCTTCTTATTTCAGATTTGGTCTCCACGAAAG
*
64521 AGTAGTGAAGCAAATTAATCTCGA
66 AGTAGTGAAGCAAATCAATCTCGA
* * * * * * *
64545 GTATGAACTCCAC-GAATGAGTAGTGGAAAATATTTTTCTTATTTTAGTTTTGGTCTCCACGGAA
1 GTCTGATCTCCACGGAA-GAGTAGTGGAACATATTCTTCTTATTTCAGATTTGGTCTCCACGAAA
* *
64609 GAGTTGTGAGGCAAATCAATCTCGA
65 GAGTAGTGAAGCAAATCAATCTCGA
* * ** * ** * * *
64634 GTCTGATATCCCCGGAAGAGTAAAGGAACAAATTCACCATATTTCAGATTTAGTCTCCACAAAAG
1 GTCTGATCTCCACGGAAGAGTAGTGGAACATATTCTTCTTATTTCAGATTTGGTCTCCACGAAAG
*
64699 AGTAGTGAAGCAAATCAATTTCGA
66 AGTAGTGAAGCAAATCAATCTCGA
* * * *
64723 GTCTGATCTCCATGGAAGAGTAGTGGAACATATTCTTTTTTATTTCAAATGTTGGTCTTCACGAA
1 GTCTGATCTCCACGGAAGAGTAGTGGAACATATTC-TTCTTATTTCAGAT-TTGGTCTCCACGAA
* *
64788 AGAGTAGTGAAACAAATCAATCTTGA
64 AGAGTAGTGAAGCAAATCAATCTCGA
* * * * *
64814 GTATGATCTCCACGGAAGAGTAGTGGAATAGATTCTTCTTATTTCAGATTTGATCTCCACGGAAG
1 GTCTGATCTCCACGGAAGAGTAGTGGAACATATTCTTCTTATTTCAGATTTGGTCTCCACGAAAG
64879 AGTAGTGAAGCAAATCAA--T-GA
66 AGTAGTGAAGCAAATCAATCTCGA
* * * * * * * *
64900 GTCTGATTTCCCCGGAATAGTAGAGGAACATATTGTTCTTATTTCAGATTTGATCTCCATGGAAG
1 GTCTGATCTCCACGGAAGAGTAGTGGAACATATTCTTCTTATTTCAGATTTGGTCTCCACGAAAG
*
64965 AGTAGTGAAGCAAATCAATCCCGA
66 AGTAGTGAAGCAAATCAATCTCGA
* * * * * *
64989 GTCTGATCTCCATGGAAGAGTAGTGCAACAAATTCTTCTTATTTCAGATTTGATCTCTAAGAAAG
1 GTCTGATCTCCACGGAAGAGTAGTGGAACATATTCTTCTTATTTCAGATTTGGTCTCCACGAAAG
* *
65054 AGTAGTGAAGAAAATCAGTCTCGA
66 AGTAGTGAAGCAAATCAATCTCGA
65078 G
1 G
65079 CCCCGTCTCC
Statistics
Matches: 588, Mismatches: 116, Indels: 16
0.82 0.16 0.02
Matches are distributed among these distances:
86 76 0.13
87 1 0.00
88 3 0.01
89 418 0.71
90 25 0.04
91 65 0.11
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (89 bp):
GTCTGATCTCCACGGAAGAGTAGTGGAACATATTCTTCTTATTTCAGATTTGGTCTCCACGAAAG
AGTAGTGAAGCAAATCAATCTCGA
Found at i:64742 original size:42 final size:42
Alignment explanation
Indices: 64598--65021 Score: 149
Period size: 42 Copynumber: 9.6 Consensus size: 42
64588 TTAGTTTTGG
* * *
64598 TCTCCACGGAAGAGTTGTGAGGCAAATCAATCTCGAGTCTGA
1 TCTCCACGGAAGAGTAGTGAAGCAAATCAATTTCGAGTCTGA
* * *
64640 TATCCCCGGAAGAGTAAAG-GAA-CAAATTCACCATATTTC-AGAT-TTA
1 TCTCCACGGAAGAGT--AGTGAAGCAAA-T---CA-ATTTCGAG-TCTGA
**
64686 GTCTCCACAAAAGAGTAGTGAAGCAAATCAATTTCGAGTCTGA
1 -TCTCCACGGAAGAGTAGTGAAGCAAATCAATTTCGAGTCTGA
* * * * *
64729 TCTCCATGGAAGAGTAGTGGAA-CATATTCTTTTTTATTTCAAATGT-TGG
1 TCTCCACGGAAGAGTAGT-GAAGCA-AATC-----AATTTC-GA-GTCTGA
* * * *
64778 TCTTCACGAAAGAGTAGTGAAACAAATCAATCTT-GAGTATGA
1 TCTCCACGGAAGAGTAGTGAAGCAAATCAAT-TTCGAGTCTGA
** * *
64820 TCTCCACGGAAGAGTAGTGGAATAG-ATTCTTCTTATTTC-AGATTTGA
1 TCTCCACGGAAGAGTAGT-G-A-AGCA--AATC-AATTTCGAG-TCTGA
64867 TCTCCACGGAAGAGTAGTGAAGCAAATCAA--T-GAGTCTGA
1 TCTCCACGGAAGAGTAGTGAAGCAAATCAATTTCGAGTCTGA
* * * * * * *
64906 TTTCCCCGGAATAGTAGAGGAA-CATATTGTTCTTATTTC-AGATTTGA
1 TCTCCACGGAAGAGTAG-TGAAGCA-A---ATC-AATTTCGAG-TCTGA
* **
64953 TCTCCATGGAAGAGTAGTGAAGCAAATCAATCCCGAGTCTGA
1 TCTCCACGGAAGAGTAGTGAAGCAAATCAATTTCGAGTCTGA
*
64995 TCTCCATGGAAGAGTAGTGCAA-CAAAT
1 TCTCCACGGAAGAGTAGTG-AAGCAAAT
65022 TCTTCTTATT
Statistics
Matches: 281, Mismatches: 53, Indels: 96
0.65 0.12 0.22
Matches are distributed among these distances:
39 20 0.07
40 7 0.02
41 2 0.01
42 91 0.32
43 28 0.10
44 8 0.03
45 5 0.02
46 24 0.09
47 63 0.22
48 11 0.04
49 20 0.07
50 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (42 bp):
TCTCCACGGAAGAGTAGTGAAGCAAATCAATTTCGAGTCTGA
Found at i:65277 original size:82 final size:82
Alignment explanation
Indices: 65084--65434 Score: 330
Period size: 82 Copynumber: 4.3 Consensus size: 82
65074 TCGAGCCCCG
* * * * * * * * *
65084 TCTCCCCTGAATGAATAATGGAGCAAACACGTTTTCCAAAATTGATCTGACTACCCG-AAAATAT
1 TCTCCCTTAAATGAATAGTAGAGCAGACACGTCTTCCAAAATTGATCTAACTACCCGAAAAAGAG
* *
65148 ACATATATTAAGTCTGA
66 ACACATATCAAGTCTGA
* *
65165 TCTCCCCTGAATGAATAGTAGAGCAGACACGTCTTCCAAAATTGATCTAACTACCCGAAAAAGAG
1 TCTCCCTTAAATGAATAGTAGAGCAGACACGTCTTCCAAAATTGATCTAACTACCCGAAAAAGAG
* * *
65230 ACACAGATCAAGACTAA
66 ACACATATCAAGTCTGA
* * * *
65247 TCTCCCTTAAATGAATAGTAGAGTAGACACGTCTTCCAAAATTAATCTAAATACCTGAAAAAGAG
1 TCTCCCTTAAATGAATAGTAGAGCAGACACGTCTTCCAAAATTGATCTAACTACCCGAAAAAGAG
* * * *
65312 GCACAAATCATGTCTTA
66 ACACATATCAAGTCTGA
* * * * * * * *
65329 TCTGCCCTGAAA-GAATAGTGGAGCATACCCATCTTCCAAAATTGATATGACTACCCAAAAAAGA
1 TCT-CCCTTAAATGAATAGTAGAGCAGACACGTCTTCCAAAATTGATCTAACTACCCGAAAAAGA
*
65393 GGA-ACATATCAAGGCTGA
65 -GACACATATCAAGTCTGA
* * * *
65411 TCTCCCCTGAATAAATAGTTGAGC
1 TCTCCCTTAAATGAATAGTAGAGC
65435 GAATTTCCCA
Statistics
Matches: 221, Mismatches: 45, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
81 57 0.26
82 156 0.71
83 8 0.04
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.24
Consensus pattern (82 bp):
TCTCCCTTAAATGAATAGTAGAGCAGACACGTCTTCCAAAATTGATCTAACTACCCGAAAAAGAG
ACACATATCAAGTCTGA
Found at i:65572 original size:3 final size:3
Alignment explanation
Indices: 65564--65592 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
65554 CTACATTGTA
65564 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
65593 AATAATGAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:66744 original size:15 final size:15
Alignment explanation
Indices: 66724--66754 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
66714 AATCCTAGAA
*
66724 TTTTAATATTTTTAT
1 TTTTAATATTATTAT
66739 TTTTAATATTATTAT
1 TTTTAATATTATTAT
66754 T
1 T
66755 GGTTTATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTAATATTATTAT
Found at i:69097 original size:8 final size:9
Alignment explanation
Indices: 69073--69105 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
69063 TTACAAATTT
69073 ATTATTAAA
1 ATTATTAAA
*
69082 TTTATTAAA
1 ATTATTAAA
69091 A-TATTAAA
1 ATTATTAAA
69099 ATTATTA
1 ATTATTA
69106 TAGTTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
ATTATTAAA
Found at i:69418 original size:18 final size:19
Alignment explanation
Indices: 69397--69432 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
69387 AAAAAATAGA
*
69397 AAACACAAAA-TTTGAAAT
1 AAACAAAAAACTTTGAAAT
69415 AAACAAAAAACTTTGAAA
1 AAACAAAAAACTTTGAAA
69433 ACCATCATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.64, C:0.11, G:0.06, T:0.19
Consensus pattern (19 bp):
AAACAAAAAACTTTGAAAT
Found at i:73427 original size:2 final size:2
Alignment explanation
Indices: 73420--73455 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
73410 ATAAGCTATC
73420 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
73456 TGTTGAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.