Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009630.1 Hibiscus syriacus cultivar Beakdansim tig00117026_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: 1249403
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:149655 original size:22 final size:22
Alignment explanation
Indices: 149600--149657 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
149590 GATGGAGATA
*
149600 GACGGATTTCGCCGGAGATTGG
1 GACGGATTTCGCCGGAGATGGG
* *
149622 GAAGTATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
149644 GACGGATGTCGCCG
1 GACGGATTTCGCCG
149658 TAGAGAGTGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.19, C:0.19, G:0.41, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:149830 original size:20 final size:20
Alignment explanation
Indices: 149805--149846 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
149795 TAAACGCGCT
149805 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
149825 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
149845 TT
1 TT
149847 ACGATTTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.24, T:0.48
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTG
Found at i:151346 original size:12 final size:11
Alignment explanation
Indices: 151314--151349 Score: 56
Period size: 10 Copynumber: 3.3 Consensus size: 11
151304 GTCCGTCTCG
151314 GGTCGGGTCG-
1 GGTCGGGTCGT
151324 GGTCGGGTCGT
1 GGTCGGGTCGT
151335 GGTCGTGGTCGT
1 GGTCG-GGTCGT
151347 GGT
1 GGT
151350 AATACGTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.42
11 5 0.21
12 9 0.38
ACGTcount: A:0.00, C:0.17, G:0.56, T:0.28
Consensus pattern (11 bp):
GGTCGGGTCGT
Found at i:151349 original size:6 final size:5
Alignment explanation
Indices: 151311--151345 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
151301 GTCGTCCGTC
151311 TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG
151346 TGGTAATACG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.26
Consensus pattern (5 bp):
TCGGG
Found at i:151472 original size:20 final size:20
Alignment explanation
Indices: 151447--151719 Score: 168
Period size: 20 Copynumber: 13.4 Consensus size: 20
151437 TTTTGGACTA
*
151447 TCGCATGGCAATTTACATAT
1 TCGCATTGCAATTTACATAT
*
151467 TCGCATTGCAATAGT-CGACTA-
1 TCGCATTGCAAT-TTAC-A-TAT
*
151488 TCGCATTGCGATTTACATAT
1 TCGCATTGCAATTTACATAT
*
151508 TCGCATTGCAATAGT-CGACTA-
1 TCGCATTGCAAT-TTAC-A-TAT
*
151529 TCGCATTGCGATTTACATAT
1 TCGCATTGCAATTTACATAT
* * *
151549 TCGCATTGCGATAGTCCA-AGT
1 TCGCATTGCAAT-TTACATA-T
* *
151570 TCGCATTGCGATAGT-CGACTA-
1 TCGCATTGCAAT-TTAC-A-TAT
* *
151591 TCGCATTGCGATAGT-CGACTA-
1 TCGCATTGCAAT-TTAC-A-TAT
*
151612 TCGCATTGCGATTTACATAT
1 TCGCATTGCAATTTACATAT
* *
151632 TCGTATTGCGATTTACATAT
1 TCGCATTGCAATTTACATAT
*
151652 TCGCATTGCGATTTACATAT
1 TCGCATTGCAATTTACATAT
* *
151672 TCGCATTGCGATTTATATAT
1 TCGCATTGCAATTTACATAT
* *
151692 TCGCATTGCGATTTATATAT
1 TCGCATTGCAATTTACATAT
*
151712 TCGTATTG
1 TCGCATTG
151720 TGATAGTCCA
Statistics
Matches: 221, Mismatches: 15, Indels: 34
0.82 0.06 0.13
Matches are distributed among these distances:
19 6 0.03
20 128 0.58
21 82 0.37
22 4 0.02
23 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (20 bp):
TCGCATTGCAATTTACATAT
Found at i:151492 original size:21 final size:21
Alignment explanation
Indices: 151467--151623 Score: 166
Period size: 21 Copynumber: 7.6 Consensus size: 21
151457 ATTTACATAT
*
151467 TCGCATTGCAATAGTCGACTA
1 TCGCATTGCGATAGTCGACTA
*
151488 TCGCATTGCGAT--T-TACATA
1 TCGCATTGCGATAGTCGAC-TA
*
151507 TTCGCATTGCAATAGTCGACTA
1 -TCGCATTGCGATAGTCGACTA
*
151529 TCGCATTGCGAT--T-TACATA
1 TCGCATTGCGATAGTCGAC-TA
* *
151548 TTCGCATTGCGATAGTCCAAGT-
1 -TCGCATTGCGATAGT-CGACTA
151570 TCGCATTGCGATAGTCGACTA
1 TCGCATTGCGATAGTCGACTA
151591 TCGCATTGCGATAGTCGACTA
1 TCGCATTGCGATAGTCGACTA
151612 TCGCATTGCGAT
1 TCGCATTGCGAT
151624 TTACATATTC
Statistics
Matches: 114, Mismatches: 10, Indels: 24
0.77 0.07 0.16
Matches are distributed among these distances:
18 4 0.04
19 6 0.05
20 26 0.23
21 70 0.61
22 4 0.04
23 3 0.03
24 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGACTA
Found at i:151502 original size:41 final size:41
Alignment explanation
Indices: 151442--151771 Score: 329
Period size: 41 Copynumber: 8.0 Consensus size: 41
151432 TGCGATTTTG
* * *
151442 GACTATCGCATGGCAATTTACATATTCGCATTGCAATAGTC
1 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTC
*
151483 GACTATCGCATTGCGATTTACATATTCGCATTGCAATAGTC
1 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTC
151524 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCC
1 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGT-C
* * *
151566 AAGT-TCGCATTGCGATAGT-CGACTA-TCGCATTGCGATAGTC
1 GACTATCGCATTGCGAT-TTAC-A-TATTCGCATTGCGATAGTC
*
151607 GACTATCGCATTGCGATTTACATATTCGTATTGCGAT--T-
1 GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTC
* * *
151645 TACATATTCGCATTGCGATTTACATATTCGCATTGCGAT-TTA
1 GAC-TA-TCGCATTGCGATTTACATATTCGCATTGCGATAGTC
* * * *
151687 TA-TATTCGCATTGCGATTTATATATTCGTATTGTGATAGTCC
1 GACTA-TCGCATTGCGATTTACATATTCGCATTGCGATAGT-C
* * * *
151729 AAGT-TCGCATTGCGATAGTCCA-AGTTCGCATTGCGATAGTC
1 GACTATCGCATTGCGAT-TTACATA-TTCGCATTGCGATAGTC
151770 GA
1 GA
151772 AGTTCGCGTT
Statistics
Matches: 249, Mismatches: 24, Indels: 32
0.82 0.08 0.10
Matches are distributed among these distances:
38 2 0.01
39 3 0.01
40 65 0.26
41 124 0.50
42 52 0.21
43 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.35
Consensus pattern (41 bp):
GACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTC
Found at i:151640 original size:103 final size:103
Alignment explanation
Indices: 151466--151783 Score: 271
Period size: 103 Copynumber: 3.1 Consensus size: 103
151456 AATTTACATA
*
151466 TTCGCATTGCAATAGTCGACTATCGCATTGCGATTTACATATTCGCATTGCAATAGTCGACTATC
1 TTCGCATTGCAATAGTCGACTATCGCATTGCGATTGACATATTCGCATTGCAATAGTCGACTATC
151531 GCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
66 GCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
* * *
151569 TTCGCATTGCGATAGTCGACTATCGCATTGCGATAGTCGAC-TA-TCGCATTGCGAT--T-TACA
1 TTCGCATTGCAATAGTCGACTATCGCATTGCGAT--T-GACATATTCGCATTGCAATAGTCGAC-
* * *
151629 TATTCGTATTGCGATTTACATATTCGCATTGCGAT-TTACATA-
62 TA-TCGCATTGCGATTTACATATTCGCATTGCGATAGTCCA-AG
* * ** * * * ** * *
151671 TTCGCATTGCGAT-TTATA-TATTCGCATTGCGATTTATATATTCGTATTGTGATAGTCCAAGT-
1 TTCGCATTGCAATAGTCGACTA-TCGCATTGCGATTGACATATTCGCATTGCAATAGT-CGACTA
* * *
151733 TCGCATTGCGATAGTCCA-AGTTCGCATTGCGATAGTCGAAG
64 TCGCATTGCGAT-TTACATA-TTCGCATTGCGATAGTCCAAG
*
151774 TTCGCGTTGC
1 TTCGCATTGC
151784 GAATCTGGAA
Statistics
Matches: 175, Mismatches: 23, Indels: 34
0.75 0.10 0.15
Matches are distributed among these distances:
98 1 0.01
99 3 0.02
100 12 0.07
101 28 0.16
102 37 0.21
103 77 0.44
104 12 0.07
105 3 0.02
106 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (103 bp):
TTCGCATTGCAATAGTCGACTATCGCATTGCGATTGACATATTCGCATTGCAATAGTCGACTATC
GCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
Found at i:151735 original size:21 final size:21
Alignment explanation
Indices: 151711--151785 Score: 114
Period size: 21 Copynumber: 3.6 Consensus size: 21
151701 GATTTATATA
* *
151711 TTCGTATTGTGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
151732 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
151753 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
151774 TTCGCGTTGCGA
1 TTCGCATTGCGA
151786 ATCTGGAAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:158595 original size:51 final size:51
Alignment explanation
Indices: 158535--158636 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
158525 ATTACATAAC
158535 ATACATTTAAAGGCTTTACAATTTACTCCCGTCGCGTTTATTCGCTGCTAT
1 ATACATTTAAAGGCTTTACAATTTACTCCCGTCGCGTTTATTCGCTGCTAT
** *
158586 ATACATTTAAAGGCTTTACAATTTACTCCCGTCTTGTTTCTTCGCTGCTAT
1 ATACATTTAAAGGCTTTACAATTTACTCCCGTCGCGTTTATTCGCTGCTAT
158637 TGTATTCATA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.41
Consensus pattern (51 bp):
ATACATTTAAAGGCTTTACAATTTACTCCCGTCGCGTTTATTCGCTGCTAT
Found at i:160591 original size:3 final size:3
Alignment explanation
Indices: 160578--160642 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
160568 GATCTACAAA
* * *
160578 ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT GTT ATA ATT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
160625 -TT ATAT ATT ATA ATT ATT
1 ATT AT-T ATT ATT ATT ATT
160643 TTTTTTACAG
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
2 4 0.08
3 44 0.86
4 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:161964 original size:21 final size:21
Alignment explanation
Indices: 161935--161987 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
161925 ATTCTGACTA
161935 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
161956 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
161977 TCGCAATGCGA
1 TCGCATTGCGA
161988 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:162002 original size:20 final size:20
Alignment explanation
Indices: 161977--162029 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
161967 TTTTCCTAAT
161977 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
161997 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
162017 TCGCAATGCGAAT
1 TCGCAATGCGAAT
162030 CTGACTATCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:162065 original size:20 final size:20
Alignment explanation
Indices: 162016--162067 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
162006 GAATACGTAA
*
162016 ATCGCAATGCGAATCTGACT
1 ATCGCAATGTGAATCTGACT
162036 ATCGCAATGTGAATCTGACT
1 ATCGCAATGTGAATCTGACT
162056 ATCGCAATGTGA
1 ATCGCAATGTGA
162068 TTTACATAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (20 bp):
ATCGCAATGTGAATCTGACT
Found at i:162271 original size:22 final size:22
Alignment explanation
Indices: 162246--162302 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
162236 GGCGATATCC
162246 GTCCCCATCTCCGACAAAATCA
1 GTCCCCATCTCCGACAAAATCA
* * *
162268 GTCCCCATCGCCGACGATATCA
1 GTCCCCATCTCCGACAAAATCA
*
162290 GTCTCCATCTCCG
1 GTCCCCATCTCCG
162303 GCGAAACCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.23, C:0.42, G:0.14, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACAAAATCA
Found at i:162705 original size:20 final size:20
Alignment explanation
Indices: 162680--162729 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
162670 TGCGATTCTT
162680 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
**
162700 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCAAATTC
*
162720 GTGTTGCGAT
1 GCGTTGCGAT
162730 TTTCATTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:162735 original size:20 final size:20
Alignment explanation
Indices: 162697--162751 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
162687 GATAGTCAAA
* **
162697 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
162717 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
*
162737 TTCGTGTTACGATTT
1 TTCGTGTTGCGATTT
162752 AAAGTTTCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.13, C:0.16, G:0.22, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:162759 original size:20 final size:20
Alignment explanation
Indices: 162716--162759 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
162706 CGATAGTCAT
* ** *
162716 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTACGATTTAAAG
162736 TTTCGTGTTACGATTTAAAG
1 TTTCGTGTTACGATTTAAAG
162756 TTTC
1 TTTC
162760 AGAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.14, G:0.18, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTACGATTTAAAG
Found at i:164654 original size:20 final size:20
Alignment explanation
Indices: 164629--164785 Score: 126
Period size: 20 Copynumber: 8.5 Consensus size: 20
164619 AGAATAGTTT
164629 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
164649 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
164669 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
164685 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
164702 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
164718 A--ATCGCAATACGAAAATG
1 ACTATCGCAATGCGAAAATG
*
164736 ACTATCGCAATGTGAAAATG
1 ACTATCGCAATGCGAAAATG
* **
164756 ACTATCACAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
164776 ACTATCGCAA
1 ACTATCGCAA
164786 CGAAAGAATC
Statistics
Matches: 113, Mismatches: 10, Indels: 28
0.75 0.07 0.19
Matches are distributed among these distances:
14 14 0.12
16 10 0.09
17 8 0.07
18 5 0.04
19 7 0.06
20 69 0.61
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:164698 original size:34 final size:34
Alignment explanation
Indices: 164652--164806 Score: 143
Period size: 34 Copynumber: 4.4 Consensus size: 34
164642 GAAAATGACT
* *
164652 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
** *
164686 ATCGCAATGCG-AAATGAAAATCGCAAC-AACAAA
1 ATCGCAATGCGAAAATGACTATCGCAACGAA-AGA
* *
164719 ATCGCAATACGAAAATGACTATCGCAATGTGAAAATGA
1 ATCGCAATGCGAAAATGACTATCGCAA--CG-AAA-GA
* **
164757 CTATCACAATGCGAATTTGACTATCGCAACGAAAGA
1 --ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
164793 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
164807 TGAAAATCGC
Statistics
Matches: 95, Mismatches: 17, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
32 1 0.01
33 26 0.27
34 35 0.37
36 2 0.02
37 4 0.04
38 4 0.04
40 23 0.24
ACGTcount: A:0.44, C:0.21, G:0.19, T:0.17
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
Found at i:164838 original size:20 final size:20
Alignment explanation
Indices: 164813--164864 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
164803 GAAATGAAAA
164813 TCGCATTGCGATAGTCAAAT
1 TCGCATTGCGATAGTCAAAT
**
164833 TCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCAAAT
*
164853 TCGCGTTGCGAT
1 TCGCATTGCGAT
164865 TTTAAGTTTC
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:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (20 bp):
TCGCATTGCGATAGTCAAAT
Found at i:167087 original size:33 final size:34
Alignment explanation
Indices: 167030--167105 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 34
167020 ACTAATTTCG
167030 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
167064 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
167097 CGTTGCGAT
1 CGTTGCGAT
167106 AGTCAATTCC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 27 0.66
34 14 0.34
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:167126 original size:20 final size:20
Alignment explanation
Indices: 167097--167165 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
167087 GCGATTCTCT
167097 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
* *
167117 CGTTGTGATAGTCATTTCCG
1 CGTTGCGATAGTCAATTCCG
*
167137 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCA-ATTCCG
167157 CGTTGCGAT
1 CGTTGCGAT
167166 TTCCGCGTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 40 0.95
21 2 0.05
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTCCG
Found at i:169540 original size:24 final size:24
Alignment explanation
Indices: 169513--169559 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
169503 CAAAATCCGA
*
169513 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACAAAGATCAAAGTTCGG
*
169537 GTATTGACAAAGATCAAATTTCG
1 GTATTGACAAAGATCAAAGTTCG
169560 AATACTGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACAAAGATCAAAGTTCGG
Found at i:169568 original size:24 final size:24
Alignment explanation
Indices: 169517--169568 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
169507 ATCCGAGTAT
* ** *
169517 TGACCAAGATCAAAGTTCGGGTAT
1 TGACAAAGATCAAAGTTCGAATAC
*
169541 TGACAAAGATCAAATTTCGAATAC
1 TGACAAAGATCAAAGTTCGAATAC
169565 TGAC
1 TGAC
169569 TAGTACTCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACAAAGATCAAAGTTCGAATAC
Found at i:170433 original size:20 final size:20
Alignment explanation
Indices: 170392--170434 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
170382 AAATTCAGTA
*
170392 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
170412 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
170432 TTG
1 TTG
170435 TGATTTACGT
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:0.21, C:0.19, G:0.28, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:170448 original size:20 final size:20
Alignment explanation
Indices: 170425--170538 Score: 138
Period size: 20 Copynumber: 5.7 Consensus size: 20
170415 CGATAGTCAG
* *
170425 ATTCGCGTTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
170445 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
170465 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
170485 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
* * *
170506 ATTCGCGTTGTGATTTATGT
1 ATTCGCATTGCGATTTACGT
170526 ATTCGCATTGCGA
1 ATTCGCATTGCGA
170539 ATTAGGAAAA
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
20 64 0.82
21 14 0.18
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:170469 original size:40 final size:41
Alignment explanation
Indices: 170425--170538 Score: 158
Period size: 41 Copynumber: 2.8 Consensus size: 41
170415 CGATAGTCAG
**
170425 ATTCGCGTTGTGATTTACGTATTCGCATTGCGA-TTTACGT
1 ATTCGCGTTGTGATTTACGTATTCGCATTGCGATTTTACAA
* * * *
170465 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCAA
1 ATTCGCGTTGTGATTTACGTATTCGCATTGCGATTTTACAA
*
170506 ATTCGCGTTGTGATTTATGTATTCGCATTGCGA
1 ATTCGCGTTGTGATTTACGTATTCGCATTGCGA
170539 ATTAGGAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
40 30 0.48
41 33 0.52
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.40
Consensus pattern (41 bp):
ATTCGCGTTGTGATTTACGTATTCGCATTGCGATTTTACAA
Found at i:170570 original size:21 final size:21
Alignment explanation
Indices: 170535--170601 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
170525 TATTCGCATT
* *
170535 GCGAATTAGGAAAATCGCAAC
1 GCGAATTTGGGAAATCGCAAC
*
170556 GCGGATTTGGGAAATCGCAAC
1 GCGAATTTGGGAAATCGCAAC
*
170577 GCGAATTTGGGAAATCGCAAT
1 GCGAATTTGGGAAATCGCAAC
170598 GCGA
1 GCGA
170602 TAGTCAGAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.34, C:0.18, G:0.30, T:0.18
Consensus pattern (21 bp):
GCGAATTTGGGAAATCGCAAC
Found at i:174878 original size:110 final size:110
Alignment explanation
Indices: 174686--175123 Score: 625
Period size: 110 Copynumber: 4.0 Consensus size: 110
174676 GATGGTGGTT
* *
174686 GCTCAACTTCACAGTGAA-GGG-G-C-GACTGTCAATAAACAACTTTTCAGGTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGGTTCATTCAGAGTC
*
174747 AATTTCAACTTCACAGAGAAGGATATTAGACTCGAAACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTAGACTCGAAACAACACAA
* * *
174792 GCTCAAATTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGCC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGGTTCATTCAGAGTC
* *
174857 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTAGACTCGAAACAACACAA
* * * * ** * *
174902 GCTCAACTTCACAACGAATGGGTGACTGAATGGAAACAAACAACTTTTCAGTTTCATTAAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGGTTCATTCAGAGTC
* * *
174967 AATTTCAACTTCACAACGAATGATATTGGACTC-AAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTAGACTCGAA-ACAACACAA
* * *
175012 GCTCGACTTCACAGCGAAGGGGCGGCTGACTGTCAAAAAACAACTTTTCAGGTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGGTTCATTCAGAGTC
*
175077 AATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTAGACTCGAAACAACACAA
175122 GC
1 GC
175124 CCAATTCCGA
Statistics
Matches: 291, Mismatches: 35, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
106 16 0.05
107 3 0.01
108 1 0.00
109 2 0.01
110 268 0.92
111 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (110 bp):
GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGGTTCATTCAGAGTC
AATTTCAACTTCACAGCGAAGGATATTAGACTCGAAACAACACAA
Found at i:179544 original size:36 final size:36
Alignment explanation
Indices: 179475--179544 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
179465 TCTGACCGGA
* * *
179475 CAGGGACTAGTTACAAGCCCAACTTTTCTGACCAGG
1 CAGGGACTAGTCACAAGCCCAACGTTTCCGACCAGG
*
179511 CAGGGATTAGTCACAAGCCTC-ACGTTTCCGACCA
1 CAGGGACTAGTCACAAGCC-CAACGTTTCCGACCA
179545 CCAACCGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 28 0.97
37 1 0.03
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.21
Consensus pattern (36 bp):
CAGGGACTAGTCACAAGCCCAACGTTTCCGACCAGG
Found at i:181734 original size:37 final size:37
Alignment explanation
Indices: 181658--181734 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
181648 TTTTTATATT
*
181658 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* *
181695 TTTAATTTT-TGAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGT-AAAAAAAATTATATAAATATTAT-CAA
181732 TTT
1 TTT
181735 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 14 0.40
37 21 0.60
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.45
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:183385 original size:2 final size:2
Alignment explanation
Indices: 183339--183367 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
183329 GATGTTAGTT
183339 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 T
183368 TACATTCAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:203393 original size:18 final size:18
Alignment explanation
Indices: 203370--203436 Score: 134
Period size: 18 Copynumber: 3.7 Consensus size: 18
203360 CTTTGTGGTC
203370 GAAGCGTGAGATTCGTCT
1 GAAGCGTGAGATTCGTCT
203388 GAAGCGTGAGATTCGTCT
1 GAAGCGTGAGATTCGTCT
203406 GAAGCGTGAGATTCGTCT
1 GAAGCGTGAGATTCGTCT
203424 GAAGCGTGAGATT
1 GAAGCGTGAGATT
203437 TGTTGTATGC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.24, C:0.15, G:0.34, T:0.27
Consensus pattern (18 bp):
GAAGCGTGAGATTCGTCT
Found at i:205651 original size:172 final size:173
Alignment explanation
Indices: 205357--205715 Score: 569
Period size: 172 Copynumber: 2.1 Consensus size: 173
205347 CATCAAATAT
* **
205357 AAAATGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTTGCAATTTAATCACTAAATT
1 AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAACAATTTAATCACTAAATT
* *
205422 TATAAATTCTTTCAAATTTAACCAATTAAGCATATTAATACTAAATTCAAGCATAGTATACCAAC
66 TATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATAACAAC
* *
205487 TTTTTATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTGC
131 TTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
* *
205530 AAAACGATCCCTAATTACTATTTGGTTCTCAACATTTTCAAAGTTAACAATTTAATC-CATAAAT
1 AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAACAATTTAATCAC-TAAAT
* *
205594 TT-TAAATTCTTTCTAATTTAACCAATTAAGCATACTAATACTAAATTCCAGCATAGTATAACAA
65 TTATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATAACAA
* *
205658 CTTTTAATAATTTACTCTTATTCCTTAAATTCCTTAAATTTTAC
130 CTTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
*
205702 AAAACGGTCCCTAA
1 AAAACGATCCCTAA
205716 AACTTTACAA
Statistics
Matches: 171, Mismatches: 14, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
172 112 0.65
173 59 0.35
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.39
Consensus pattern (173 bp):
AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAACAATTTAATCACTAAATT
TATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATAACAAC
TTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
Found at i:206199 original size:22 final size:22
Alignment explanation
Indices: 206174--206215 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
206164 GTTGCATGCC
206174 CCCCACATGCAGACGTGCAGGA
1 CCCCACATGCAGACGTGCAGGA
206196 CCCCACATGCAGACGTGCAG
1 CCCCACATGCAGACGTGCAG
206216 CCCTGCAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.38, G:0.26, T:0.10
Consensus pattern (22 bp):
CCCCACATGCAGACGTGCAGGA
Found at i:206273 original size:22 final size:22
Alignment explanation
Indices: 206245--206298 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
206235 CGTGATTTCT
206245 GTGCTTTCTCCTTGCAGAACCC
1 GTGCTTTCTCCTTGCAGAACCC
206267 GTGCTTTCTCCTTGCAGAACCC
1 GTGCTTTCTCCTTGCAGAACCC
*
206289 GTGATTTCTC
1 GTGCTTTCTC
206299 ACGTCCAGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.13, C:0.33, G:0.19, T:0.35
Consensus pattern (22 bp):
GTGCTTTCTCCTTGCAGAACCC
Found at i:206363 original size:34 final size:34
Alignment explanation
Indices: 206320--206438 Score: 220
Period size: 34 Copynumber: 3.5 Consensus size: 34
206310 CATGCACAGC
* *
206320 ACTGAAGACGCCGAGATTTCCTACGAAGAATCCA
1 ACTGAAGACGCCGAGAGTTCCTATGAAGAATCCA
206354 ACTGAAGACGCCGAGAGTTCCTATGAAGAATCCA
1 ACTGAAGACGCCGAGAGTTCCTATGAAGAATCCA
206388 ACTGAAGACGCCGAGAGTTCCTATGAAGAATCCA
1 ACTGAAGACGCCGAGAGTTCCTATGAAGAATCCA
206422 ACTGAAGACGCCGAGAG
1 ACTGAAGACGCCGAGAG
206439 ATCAATCATA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 83 1.00
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.16
Consensus pattern (34 bp):
ACTGAAGACGCCGAGAGTTCCTATGAAGAATCCA
Found at i:209332 original size:4 final size:4
Alignment explanation
Indices: 209288--209312 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
209278 TACCATATCT
209288 TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T
209313 CTTTTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:212482 original size:2 final size:2
Alignment explanation
Indices: 212475--212509 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
212465 TCTTAAAACC
212475 TA TA 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 TA TA T
212510 TCTTTGCATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:214397 original size:31 final size:30
Alignment explanation
Indices: 214357--214439 Score: 89
Period size: 31 Copynumber: 2.8 Consensus size: 30
214347 TAAAATCATA
* *
214357 ATAA-ATTTGATAAATTTATTAATTATTTT
1 ATAATATTTGATAAATTTATTAATCATTGT
* *
214386 ATAATAGTTTGATAAACTTAATAATCATTGT
1 ATAATA-TTTGATAAATTTATTAATCATTGT
* *
214417 ATAATATTTCA-AAGTTTATTAAT
1 ATAATATTTGATAAATTTATTAAT
214440 AAAAAATATC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
29 13 0.30
30 5 0.11
31 26 0.59
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (30 bp):
ATAATATTTGATAAATTTATTAATCATTGT
Found at i:215622 original size:14 final size:14
Alignment explanation
Indices: 215603--215636 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
215593 AAATATAATT
215603 TATTTTATGAAAAA
1 TATTTTATGAAAAA
*
215617 TATTTTTTGAAAAA
1 TATTTTATGAAAAA
*
215631 TGTTTT
1 TATTTT
215637 CAGTAAACAA
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:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (14 bp):
TATTTTATGAAAAA
Found at i:216952 original size:2 final size:2
Alignment explanation
Indices: 216945--216974 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
216935 CCCCAAAACA
216945 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
216975 ATCAAATCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:219409 original size:2 final size:2
Alignment explanation
Indices: 219402--219435 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
219392 AATGTAATTA
219402 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
219436 AACTAATACG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:225363 original size:17 final size:18
Alignment explanation
Indices: 225332--225365 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
225322 ATTGTTGGAT
225332 TTAATATTTACATTTATA
1 TTAATATTTACATTTATA
*
225350 TTAA-ATTTATATTTAT
1 TTAATATTTACATTTAT
225366 TTTGATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAATATTTACATTTATA
Found at i:236148 original size:87 final size:87
Alignment explanation
Indices: 236002--236170 Score: 313
Period size: 87 Copynumber: 1.9 Consensus size: 87
235992 TGATCTTGTC
*
236002 TTACACTGAGTGCATGTCCAATCTCTGAAGGTTATAGTTTGTTATTTTATCATTTGACGAAACTT
1 TTACACTGAGTGCATGTCCAATCTCTGAAGGTTATAGTTTGTTATATTATCATTTGACGAAACTT
236067 GTTTGATTGGCAGTATAGTTTG
66 GTTTGATTGGCAGTATAGTTTG
236089 TTACACTGAGTGCATGTCCAATCTCTGAAGGTGTATAG-TTGTTATATTATCATTTGACGAAACT
1 TTACACTGAGTGCATGTCCAATCTCTGAAGGT-TATAGTTTGTTATATTATCATTTGACGAAACT
236153 TGTTTGATTGGCAGTATA
65 TGTTTGATTGGCAGTATA
236171 TTCTAAAAGA
Statistics
Matches: 80, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
87 75 0.94
88 5 0.06
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (87 bp):
TTACACTGAGTGCATGTCCAATCTCTGAAGGTTATAGTTTGTTATATTATCATTTGACGAAACTT
GTTTGATTGGCAGTATAGTTTG
Found at i:246963 original size:10 final size:10
Alignment explanation
Indices: 246950--246982 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
246940 TTTATGTTCA
246950 TTCATTTATG
1 TTCATTTATG
246960 TTCATTTATG
1 TTCATTTATG
*
246970 TTCGTTTATG
1 TTCATTTATG
246980 TTC
1 TTC
246983 GTTCGTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.15, C:0.12, G:0.12, T:0.61
Consensus pattern (10 bp):
TTCATTTATG
Found at i:247017 original size:34 final size:33
Alignment explanation
Indices: 246932--247018 Score: 95
Period size: 34 Copynumber: 2.5 Consensus size: 33
246922 TGAACGATAA
*
246932 TATGTTTGTTTATGTTCATTCATTTATGTTCATT
1 TATG-TTGTTTATGTTCGTTCATTTATGTTCATT
* **
246966 TATGTTCGTTTATGTTCGTTCGTTT-TCGTTTGTT
1 TATGTT-GTTTATGTTCGTTCATTTAT-GTTCATT
247000 TATGCTTGTTTATGTTCGT
1 TATG-TTGTTTATGTTCGT
247019 GTACTTTCGT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
33 3 0.07
34 41 0.89
35 2 0.04
ACGTcount: A:0.11, C:0.10, G:0.17, T:0.61
Consensus pattern (33 bp):
TATGTTGTTTATGTTCGTTCATTTATGTTCATT
Found at i:247268 original size:23 final size:23
Alignment explanation
Indices: 247237--247292 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
247227 TGTTGTTGCA
247237 GTTTATGTTCATTTACGTTCGTTT
1 GTTT-TGTTCATTTACGTTCGTTT
* *
247261 GTTTTGTTCATTTATGTTCTTTT
1 GTTTTGTTCATTTACGTTCGTTT
247284 GTGTTTGTT
1 GT-TTTGTT
247293 TACGTCCGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 19 0.66
24 10 0.34
ACGTcount: A:0.09, C:0.09, G:0.18, T:0.64
Consensus pattern (23 bp):
GTTTTGTTCATTTACGTTCGTTT
Found at i:248216 original size:470 final size:470
Alignment explanation
Indices: 247336--248226 Score: 1480
Period size: 470 Copynumber: 1.9 Consensus size: 470
247326 TACATCAGTT
* *
247336 AGTTTATGTTTGTTCATTTGTGTTTGTTTATCATTTAAATGAACAAACACGAACGAACACGAACA
1 AGTTTATGTTTGTTAATTTGTGTTCGTTTATCATTTAAATGAACAAACACGAACGAACACGAACA
*
247401 AGCTACATTCTTTAAGGAATAATAATTTTTTTATTCGTTTATGTTCGTATTCATTTATTTGTTCG
66 AGCTACATTCTTTAAGGAACAATAATTTTTTTATTCGTTTATGTTCGTATTCATTTATTTGTTCG
* * * *
247466 ATTAAAGTTAAACGAACGAACATGAACATGTTGGAAAAGTCAAAGTTGGGGGCGTTAAAAATCAA
131 ATTAAAGTTAAACGAACGAACATGAACATGTAGAAAAAGTCAAAATTGAGGGCGTTAAAAATCAA
* *
247531 GAATGGGGGCGTCAAATTTGGTGAATTGGGCACCGAATTCGGTGCAATTAAATTATTGAAAATGG
196 GAATGGGGGCGTCAAATTCGGTGAATTGGGCACCGAATTCGGTACAATTAAATTATTGAAAATGG
** * * *
247596 TAATGGAGAAATTGCATATTAGTCCATGCACACTTTAGGGTATTTACAAGTTTAGTCCTTAAGCT
261 TAATGGAGAAATTAAATATTAATCCATACACACTTTAGGGTATTTACAAATTTAGTCCTTAAGCT
* *
247661 TCAACTATAAATACTCGAACCCATTTAGCTTCAAAATCATCCAAAATTATTTATTTCTCCCAATA
326 TCAACTATAAATACTCGAACCCATTTAACTTCAAAATCATCCAAAATCATTTATTTCTCCCAATA
247726 CTAAAGAGTTTAGAGAGTATTCTTGTGAGTTGTAAGTGTTTTGTAAACATCTGTAAATTTTCTCA
391 CTAAAGAGTTTAGAGAGTATTCTTGTGAGTTGTAAGTGTTTTGTAAACATCTGTAAATTTTCTCA
247791 TTTGTGAGTTTAAAG
456 TTTGTGAGTTTAAAG
* *
247806 AGTTTATGTTTGTTAATTTGTGTTCGTTTATCATTTAAATGAACAAACACGAACGAACATGAATA
1 AGTTTATGTTTGTTAATTTGTGTTCGTTTATCATTTAAATGAACAAACACGAACGAACACGAACA
* *
247871 AGCTACATTCTTTAATGAACAATAATTTTTTTATTCGTTTATGTTCGTATTCGTTTATTTGTTCG
66 AGCTACATTCTTTAAGGAACAATAATTTTTTTATTCGTTTATGTTCGTATTCATTTATTTGTTCG
*
247936 ATTAAAGTTAAACGAACGAACATGAACATGTAGAAAAAGTCAAAATTTAGGGCGTTAAAAATCAA
131 ATTAAAGTTAAACGAACGAACATGAACATGTAGAAAAAGTCAAAATTGAGGGCGTTAAAAATCAA
* * * *
248001 GAATGGGGGCG-CAAATTCGGTGAATTGGGCATCGAATTTGGTACAATTAATTTTGTTGAAAATG
196 GAATGGGGGCGTCAAATTCGGTGAATTGGGCACCGAATTCGGTACAATTAA-ATTATTGAAAATG
* * *
248065 GTAATGGAGAAATTAAATTTTAATCCCTACATACTTTAGGGTATTTACAAATTTAGTCCTTAAGC
260 GTAATGGAGAAATTAAATATTAATCCATACACACTTTAGGGTATTTACAAATTTAGTCCTTAAGC
* *
248130 TTCAACTATAAATA-TCCTAACCCATTTAACTTCAAAATCATTCAAAATCATTTATTTCTCCCAA
325 TTCAACTATAAATACT-CGAACCCATTTAACTTCAAAATCATCCAAAATCATTTATTTCTCCCAA
248194 TACTAAAGAGTTTAGAGAGTATTCTTGTGAGTT
389 TACTAAAGAGTTTAGAGAGTATTCTTGTGAGTT
248227 TAGAGAGTAT
Statistics
Matches: 389, Mismatches: 30, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
469 36 0.09
470 353 0.91
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (470 bp):
AGTTTATGTTTGTTAATTTGTGTTCGTTTATCATTTAAATGAACAAACACGAACGAACACGAACA
AGCTACATTCTTTAAGGAACAATAATTTTTTTATTCGTTTATGTTCGTATTCATTTATTTGTTCG
ATTAAAGTTAAACGAACGAACATGAACATGTAGAAAAAGTCAAAATTGAGGGCGTTAAAAATCAA
GAATGGGGGCGTCAAATTCGGTGAATTGGGCACCGAATTCGGTACAATTAAATTATTGAAAATGG
TAATGGAGAAATTAAATATTAATCCATACACACTTTAGGGTATTTACAAATTTAGTCCTTAAGCT
TCAACTATAAATACTCGAACCCATTTAACTTCAAAATCATCCAAAATCATTTATTTCTCCCAATA
CTAAAGAGTTTAGAGAGTATTCTTGTGAGTTGTAAGTGTTTTGTAAACATCTGTAAATTTTCTCA
TTTGTGAGTTTAAAG
Found at i:248258 original size:7 final size:7
Alignment explanation
Indices: 248248--248329 Score: 103
Period size: 7 Copynumber: 11.7 Consensus size: 7
248238 TAGTTTATAG
*
248248 AAACCCT
1 AAACCAT
*
248255 AAACCCT
1 AAACCAT
248262 AAACCAT
1 AAACCAT
248269 AAACCAT
1 AAACCAT
248276 AAACCAT
1 AAACCAT
248283 AAACCAT
1 AAACCAT
248290 AAACCAT
1 AAACCAT
**
248297 AAACTTT
1 AAACCAT
248304 AAACCAT
1 AAACCAT
248311 AAA-CACT
1 AAACCA-T
*
248318 AAGCCAT
1 AAACCAT
248325 AAACC
1 AAACC
248330 CTAATATAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
6 2 0.03
7 62 0.94
8 2 0.03
ACGTcount: A:0.52, C:0.30, G:0.01, T:0.16
Consensus pattern (7 bp):
AAACCAT
Found at i:248436 original size:20 final size:20
Alignment explanation
Indices: 248413--248457 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
248403 AAACTAATGT
248413 AAATGGACTATCACTATTGC
1 AAATGGACTATCACTATTGC
248433 AAATGGACTATCACTATTGC
1 AAATGGACTATCACTATTGC
248453 AAATG
1 AAATG
248458 AACTTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.29
Consensus pattern (20 bp):
AAATGGACTATCACTATTGC
Found at i:248733 original size:20 final size:21
Alignment explanation
Indices: 248696--248750 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
248686 AAATATTTTT
*
248696 ATATAATATGTATGTATAAACC
1 ATAT-ATATGTATATATAAACC
* *
248718 ATGTATA-GTATATATAAACT
1 ATATATATGTATATATAAACC
248738 ATATATATGTATA
1 ATATATATGTATA
248751 GTGTATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 17 0.61
21 8 0.29
22 3 0.11
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.40
Consensus pattern (21 bp):
ATATATATGTATATATAAACC
Found at i:248776 original size:17 final size:17
Alignment explanation
Indices: 248721--248778 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
248711 ATAAACCATG
248721 TATAGTATATATAAACTA
1 TATA-TATATATAAACTA
**
248739 TATATATGTATAGTGTA-TA
1 TATATA--TATA-TAAACTA
248758 TATATATATATAAACTA
1 TATATATATATAAACTA
248775 TATA
1 TATA
248779 AAATAAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
16 2 0.06
17 12 0.38
18 4 0.12
19 12 0.38
20 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (17 bp):
TATATATATATAAACTA
Found at i:248870 original size:49 final size:48
Alignment explanation
Indices: 248767--248883 Score: 110
Period size: 49 Copynumber: 2.4 Consensus size: 48
248757 ATATATATAT
* ** * * ***
248767 ATAAACTATATAAAATAAATTACTTATATAGTTTATAGAAATACTATGT
1 ATAAACTATATAAAAT-AATAAAATATATAGTTTATAAAAACACTAAAC
*
248816 ATAAACTATATAAAATAATAAAATATATAGTTTATAAAAACCCTAAAC
1 ATAAACTATATAAAATAATAAAATATATAGTTTATAAAAACACTAAAC
*
248864 ACTAAACCATA-AAACATAAT
1 A-TAAACTATATAAA-ATAAT
248884 GCAAATGGAC
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
48 27 0.48
49 29 0.52
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.32
Consensus pattern (48 bp):
ATAAACTATATAAAATAATAAAATATATAGTTTATAAAAACACTAAAC
Found at i:249067 original size:14 final size:14
Alignment explanation
Indices: 249048--249094 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
249038 ATTTTTTATT
249048 TATATAAATTAAAC
1 TATATAAATTAAAC
249062 TATAT-AATT----
1 TATATAAATTAAAC
249071 TATATAAATTAAAC
1 TATATAAATTAAAC
*
249085 TATATTAATT
1 TATATAAATT
249095 TTCCTTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:249072 original size:23 final size:24
Alignment explanation
Indices: 249045--249095 Score: 95
Period size: 23 Copynumber: 2.2 Consensus size: 24
249035 ATTATTTTTT
249045 ATTTATATAAATTAAACTATA-TA
1 ATTTATATAAATTAAACTATATTA
249068 ATTTATATAAATTAAACTATATTA
1 ATTTATATAAATTAAACTATATTA
249092 ATTT
1 ATTT
249096 TCCTTTGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.78
24 6 0.22
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTTATATAAATTAAACTATATTA
Found at i:249386 original size:16 final size:16
Alignment explanation
Indices: 249365--249435 Score: 106
Period size: 16 Copynumber: 4.4 Consensus size: 16
249355 CGGATCATTT
249365 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
*
249381 ACAGGTCAAGTTAAAA
1 ACAGGTCAGGTTAAAA
*
249397 ACATGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
* *
249413 TCAGGTCAGGTTGAAA
1 ACAGGTCAGGTTAAAA
249429 ACAGGTC
1 ACAGGTC
249436 GGGTAATACC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:249583 original size:64 final size:63
Alignment explanation
Indices: 249460--249607 Score: 158
Period size: 64 Copynumber: 2.3 Consensus size: 63
249450 ATTTACCAGG
* * *
249460 TCAATCTCGGGTTCAGGTTCATATCAGTCGGATGCAGTTCGGGTTCGGGTATCATATTTTC-GAT
1 TCAAT-TCGGGTTCAGG-TCATATCAGTCGGATGCAGGTCGGGTTCGAGTATCAAATTTTCAGAT
*
249524 TCAATTCGGGTTCAGGTCATTCTCAGGTCGGATGCAGGTCGGGTTC-AG-ATCCACAATTTTCAG
1 TCAATTCGGGTTCAGGTCA-TATCA-GTCGGATGCAGGTCGGGTTCGAGTAT-CA-AATTTTCAG
*
249587 GT
62 AT
* *
249589 CCAAATCGGGTTCAGGTCA
1 TCAATTCGGGTTCAGGTCA
249608 ACACCAGTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
62 5 0.07
63 18 0.25
64 30 0.42
65 19 0.26
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (63 bp):
TCAATTCGGGTTCAGGTCATATCAGTCGGATGCAGGTCGGGTTCGAGTATCAAATTTTCAGAT
Found at i:255614 original size:18 final size:18
Alignment explanation
Indices: 255591--255630 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
255581 CACTAATATA
255591 GTTTTAGGAAAATTACTC
1 GTTTTAGGAAAATTACTC
255609 GTTTTAGGAAAATTACTC
1 GTTTTAGGAAAATTACTC
255627 GTTT
1 GTTT
255631 ATTTCCTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.42
Consensus pattern (18 bp):
GTTTTAGGAAAATTACTC
Found at i:261886 original size:30 final size:31
Alignment explanation
Indices: 261801--261892 Score: 150
Period size: 31 Copynumber: 3.0 Consensus size: 31
261791 CAATTTAAGG
**
261801 CAAAATGGTTTTTGGACTTGAATTGAATGCA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
261832 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
*
261863 CAAAATGTTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
261893 TTCAAAATTT
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
30 11 0.19
31 47 0.81
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:261992 original size:19 final size:19
Alignment explanation
Indices: 261970--262023 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
261960 ATAGTAATTT
261970 ACTATTTGAACAGTAAATA
1 ACTATTTGAACAGTAAATA
*
261989 ACTATTTGAACAGTAAATC
1 ACTATTTGAACAGTAAATA
*
262008 ACTGTTTGAACAGTAA
1 ACTATTTGAACAGTAA
262024 CCCGAGGCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (19 bp):
ACTATTTGAACAGTAAATA
Found at i:262155 original size:21 final size:21
Alignment explanation
Indices: 262129--262170 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
262119 ATTTGAATAT
*
262129 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
262150 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
262171 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:262492 original size:34 final size:32
Alignment explanation
Indices: 262453--262522 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
262443 TTTTGTAAAG
*
262453 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
262487 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
262519 GGGA
1 GGGA
262523 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:263499 original size:3 final size:3
Alignment explanation
Indices: 263493--263547 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
263483 ATGATGGTGA
* * * *
263493 AAG AAG ATG AAG AA- AGG GAAG -AG AAG AAA AAC AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG
263537 AAG AAG AAG AA
1 AAG AAG AAG AA
263548 TGAGGATGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
2 3 0.07
3 37 0.88
4 2 0.05
ACGTcount: A:0.65, C:0.02, G:0.31, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:265421 original size:31 final size:31
Alignment explanation
Indices: 265323--265413 Score: 150
Period size: 31 Copynumber: 3.0 Consensus size: 31
265313 CAATTTAAGG
**
265323 CAAAATGGTTTTTGGACTTGAATTGAATGCA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
265354 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
265385 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
265414 TTCAAAATTT
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
29 11 0.19
30 12 0.21
31 35 0.60
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.41
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:265619 original size:21 final size:21
Alignment explanation
Indices: 265593--265634 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
265583 ATTTGAATAT
*
265593 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTAACGATTCCC
265614 TATGAAGGGGTAACGATTCCC
1 TATGAAGGGGTAACGATTCCC
265635 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTAACGATTCCC
Found at i:265955 original size:34 final size:32
Alignment explanation
Indices: 265916--265985 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
265906 TTTTGTAAAG
*
265916 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
265950 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
265982 GGGA
1 GGGA
265986 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:266481 original size:13 final size:13
Alignment explanation
Indices: 266435--266478 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
266425 GTGGGATAAG
266435 GCGCCCCCCTGAA
1 GCGCCCCCCTGAA
*
266448 GCGCTCCCCCTAAA
1 GCGC-CCCCCTGAA
* *
266462 GCACGCCCCTGAA
1 GCGCCCCCCTGAA
266475 GCGC
1 GCGC
266479 GCCTTATGCT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.18, C:0.50, G:0.23, T:0.09
Consensus pattern (13 bp):
GCGCCCCCCTGAA
Found at i:269416 original size:9 final size:9
Alignment explanation
Indices: 269386--269437 Score: 56
Period size: 8 Copynumber: 6.1 Consensus size: 9
269376 ATGTGCAAAA
269386 AAATTAAAT
1 AAATTAAAT
*
269395 -AAGTAAA-
1 AAATTAAAT
*
269402 ATATTAAAT
1 AAATTAAAT
269411 AAATTAAAT
1 AAATTAAAT
*
269420 -ACTTAAAT
1 AAATTAAAT
269428 AAATTAAAT
1 AAATTAAAT
269437 A
1 A
269438 CAAAATATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
8 18 0.53
9 16 0.47
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (9 bp):
AAATTAAAT
Found at i:269418 original size:17 final size:17
Alignment explanation
Indices: 269383--269435 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
269373 TATATGTGCA
* *
269383 AAAAAATTAAAT-AAGT
1 AAAATATTAAATAAATT
269399 AAAATATTAAATAAATT
1 AAAATATTAAATAAATT
269416 -AAATACTTAAATAAATT
1 AAAATA-TTAAATAAATT
269433 AAA
1 AAA
269436 TACAAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 16 0.50
17 14 0.44
18 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (17 bp):
AAAATATTAAATAAATT
Found at i:269436 original size:17 final size:17
Alignment explanation
Indices: 269389--269438 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
269379 TGCAAAAAAA
* *
269389 TTAAATAAGTAAAATA-
1 TTAAATAAATTAAATAC
269405 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
269422 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
269439 AAAATATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (17 bp):
TTAAATAAATTAAATAC
Found at i:273316 original size:14 final size:14
Alignment explanation
Indices: 273297--273335 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
273287 AATTTGTTCG
*
273297 TTATGTTCGTTCAT
1 TTATGTTCATTCAT
*
273311 TTATGTTTATTCAT
1 TTATGTTCATTCAT
*
273325 TTATGGTCATT
1 TTATGTTCATT
273336 TATGTACGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.18, C:0.10, G:0.13, T:0.59
Consensus pattern (14 bp):
TTATGTTCATTCAT
Found at i:274060 original size:5 final size:5
Alignment explanation
Indices: 274050--274089 Score: 73
Period size: 5 Copynumber: 8.2 Consensus size: 5
274040 CAAAATGAGA
274050 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
274090 GTATTAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.12
5 30 0.88
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:274098 original size:15 final size:14
Alignment explanation
Indices: 274051--274089 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
274041 AAAATGAGAA
*
274051 AAATAAAATAAAATA
1 AAATAAAAT-AAATT
*
274066 AAATAAAATAAAAT
1 AAATAAAATAAATT
274080 AAATAAAATA
1 AAATAAAATA
274090 GTATTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAAATAAATT
Found at i:275579 original size:20 final size:20
Alignment explanation
Indices: 275554--275620 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
275544 TTTTCCCAAT
275554 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
275574 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
275594 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
275615 TCGCAA
1 TCGCAA
275621 CGTGAATTGG
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:275596 original size:41 final size:41
Alignment explanation
Indices: 275551--275646 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
275541 CGATTTTCCC
275551 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
275592 AATTCGCAATGCGAATAAGTAAATCGCAACGTGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
275633 AAATCGCAATGCGA
1 AATTCGCAATGCGA
275647 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.20
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:275600 original size:21 final size:20
Alignment explanation
Indices: 275554--275646 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
275544 TTTTCCCAAT
*
275554 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
275574 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
275594 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* * **
275615 TCGCAACGTGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
275636 TCGCAATGCGA
1 TCGCAATGCGA
275647 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 28 0.50
21 28 0.50
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:275660 original size:20 final size:20
Alignment explanation
Indices: 275635--275729 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
275625 AATTGGGAAA
*
275635 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
275655 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
275676 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
275696 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
275716 TTCGCAACGCGATA
1 ATCGCAACGCGATA
275730 ATACATAATC
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
20 45 0.76
21 14 0.24
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:275709 original size:41 final size:41
Alignment explanation
Indices: 275632--275709 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
275622 GTGAATTGGG
* * **
275632 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
* *
275673 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
275710 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
Found at i:277577 original size:18 final size:18
Alignment explanation
Indices: 277556--277600 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
277546 TCCACTTCGG
*
277556 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
277574 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
277592 GAGCCATCA
1 GAGCCATCA
277601 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:278127 original size:19 final size:20
Alignment explanation
Indices: 278073--278139 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
278063 TAGTTTACTT
* *
278073 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
278093 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
278113 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
278132 TCGCAACG
1 TCGCAACG
278140 ACAAAAGCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:278150 original size:14 final size:14
Alignment explanation
Indices: 278128--278217 Score: 81
Period size: 14 Copynumber: 5.9 Consensus size: 14
278118 ATGCGAAATG
278128 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
278142 AAAAGCGCAACGCGAA
1 AAAATCGCAA--CGAC
278158 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
278174 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
278190 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
278206 AAAATCGCAACG
1 AAAATCGCAACG
278218 CGAAACACAA
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
14 29 0.47
16 16 0.26
18 17 0.27
ACGTcount: A:0.48, C:0.26, G:0.19, T:0.08
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:278170 original size:32 final size:32
Alignment explanation
Indices: 278112--278222 Score: 195
Period size: 32 Copynumber: 3.4 Consensus size: 32
278102 GGAAATGGCT
*
278112 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
*
278145 AGCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
278177 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
278209 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
278223 CACAAATCGC
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 61 0.81
33 14 0.19
ACGTcount: A:0.47, C:0.24, G:0.20, T:0.09
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:278251 original size:19 final size:19
Alignment explanation
Indices: 278229--278382 Score: 114
Period size: 19 Copynumber: 8.6 Consensus size: 19
278219 GAAACACAAA
*
278229 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
278248 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
278264 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
*
278280 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
278296 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* ***
278313 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATTTTCATT
**
278332 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
278352 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
278372 TCGTGTTGCGA
1 TCGCGTTGCGA
278383 AAGTAAACTA
Statistics
Matches: 109, Mismatches: 15, Indels: 21
0.75 0.10 0.14
Matches are distributed among these distances:
14 19 0.17
15 3 0.03
16 6 0.06
17 2 0.02
18 14 0.13
19 36 0.33
20 29 0.27
ACGTcount: A:0.13, C:0.20, G:0.24, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:278270 original size:14 final size:14
Alignment explanation
Indices: 278251--278308 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
278241 TTTCATTTCG
278251 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
278265 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
278281 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
278297 CGTTGCGATTTT
1 CGTTGCGATTTT
278309 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:278315 original size:33 final size:33
Alignment explanation
Indices: 278234--278324 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
278224 ACAAATCGCA
278234 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
278267 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
278299 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
278325 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:278343 original size:20 final size:19
Alignment explanation
Indices: 278309--278363 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
278299 TTGCGATTTT
*
278309 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
278328 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
278348 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
278364 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:279556 original size:14 final size:14
Alignment explanation
Indices: 279537--279572 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
279527 ATTGTTTAAT
279537 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
279551 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
279565 TGATTTGT
1 TGATTTGT
279573 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:279696 original size:14 final size:15
Alignment explanation
Indices: 279677--279753 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 15
279667 CGAAATGGCT
279677 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
279691 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
279709 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
279728 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
279742 ATCGCAATGCGA
1 ATCGCAA-GCGA
279754 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.13
17 2 0.04
18 13 0.25
19 9 0.17
20 1 0.02
21 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:279709 original size:19 final size:19
Alignment explanation
Indices: 279687--279753 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
279677 ATCGCAACGA
279687 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
279706 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
279724 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
279738 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
279754 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:280188 original size:14 final size:14
Alignment explanation
Indices: 280169--280204 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
280159 ATTGTTTAAT
280169 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
280183 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
280197 TGATTTGT
1 TGATTTGT
280205 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:280330 original size:14 final size:15
Alignment explanation
Indices: 280311--280387 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 15
280301 CGAAATGGCT
280311 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
280325 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
280343 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
280362 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
280376 ATCGCAATGCGA
1 ATCGCAA-GCGA
280388 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.13
17 2 0.04
18 13 0.25
19 9 0.17
20 1 0.02
21 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:280343 original size:19 final size:19
Alignment explanation
Indices: 280321--280387 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
280311 ATCGCAACGA
280321 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
280340 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
280358 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
280372 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
280388 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:280913 original size:33 final size:33
Alignment explanation
Indices: 280871--280964 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
280861 GGAAATTACT
*
280871 ATCGCAATGCAAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
280904 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
280937 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
280965 CGAATTTAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:280967 original size:19 final size:19
Alignment explanation
Indices: 280871--280968 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
280861 GGAAATTACT
*
280871 ATCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
280890 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
280904 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
280923 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
280937 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
280956 ATCGCAACGCGAA
1 ATCGCAATGCGAA
280969 TTTAATTTCG
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.07
17 3 0.05
18 2 0.03
19 31 0.51
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:280986 original size:19 final size:20
Alignment explanation
Indices: 280964--281006 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
280954 AAATCGCAAC
280964 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
280983 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
281003 GCGA
1 GCGA
281007 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:280991 original size:14 final size:14
Alignment explanation
Indices: 280992--281025 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
280982 TGCGATTTTC
280992 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
281006 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
281020 ATTTTC
1 ATTTTC
281026 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:281166 original size:14 final size:14
Alignment explanation
Indices: 281147--281183 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
281137 CATCAATTAA
281147 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
281161 ACAAATCACCTTTT
1 ACAAATCAACTTTT
281175 ACAAATCAA
1 ACAAATCAA
281184 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:282607 original size:21 final size:21
Alignment explanation
Indices: 282541--282607 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
282531 GTGAATCGGG
*
282541 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
282561 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
282583 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
282604 CTCT
1 CTCT
282608 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:282626 original size:42 final size:41
Alignment explanation
Indices: 282541--282663 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
282531 GTGAATCGGG
* * * * *
282541 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
282583 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
282625 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
282664 CGAGTCGAGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:284779 original size:19 final size:19
Alignment explanation
Indices: 284662--284846 Score: 156
Period size: 19 Copynumber: 10.1 Consensus size: 19
284652 TCTTTTGGTT
*
284662 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* *
284681 GATAATGAGAATCGTAACGC
1 GA-AATGAAAATCGCAACGC
**
284701 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
284719 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
284735 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
284753 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
284768 GAAATGAAAATCGCAACCAC
1 GAAATGAAAATCGCAA-CGC
*
284788 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
284807 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
284826 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
284845 GA
1 GA
284847 TTTTGGTTTC
Statistics
Matches: 134, Mismatches: 19, Indels: 26
0.75 0.11 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 61 0.46
20 42 0.31
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:284811 original size:39 final size:38
Alignment explanation
Indices: 284662--284846 Score: 149
Period size: 33 Copynumber: 5.1 Consensus size: 38
284652 TCTTTTGGTT
* *
284662 GAAATGAAAATCGCAACGA-GATAATGAGAATCGTAACGC
1 GAAATGAAAATCGCAAC-ACGA-AATGAAAATCGCAACGC
** *
284701 GGAAATGACTATCGC-A-ACG--A-GAGAATCGCAACGC
1 -GAAATGAAAATCGCAACACGAAATGAAAATCGCAACGC
** * *
284735 GAAATGACTATCGCGAC-C---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACACGAAATGAAAATCGCAACGC
*
284768 GAAATGAAAATCGCAACCACGAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAA-CACGAAATGAAAATCGCAACGC
* *
284807 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACACGAAATGAAAATCGCAACGC
284845 GA
1 GA
284847 TTTTGGTTTC
Statistics
Matches: 124, Mismatches: 12, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
33 41 0.33
34 16 0.13
35 2 0.02
37 1 0.01
38 23 0.19
39 29 0.23
40 12 0.10
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.13
Consensus pattern (38 bp):
GAAATGAAAATCGCAACACGAAATGAAAATCGCAACGC
Found at i:284875 original size:19 final size:19
Alignment explanation
Indices: 284842--284886 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
284832 AAAATCGCAA
*
284842 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
284861 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
284880 TGCGATT
1 TGCGATT
284887 ATCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:285526 original size:20 final size:20
Alignment explanation
Indices: 285441--285534 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
285431 CGCTAAGTAA
*
285441 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* * *
285461 ATCGTGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
285481 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
285502 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
285522 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
285535 TTTCCCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:285553 original size:41 final size:41
Alignment explanation
Indices: 285523--285618 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
285513 ATAGTCAGTA
* * *
285523 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
* *
285564 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
285605 TCGCATTGCGAATT
1 TCGCATTGCGAATT
285619 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:285567 original size:20 final size:20
Alignment explanation
Indices: 285523--285615 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
285513 ATAGTCAGTA
* **
285523 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
285544 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
285564 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
285585 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
285605 TCGCATTGCGA
1 TCGCATTGCGA
285616 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:290632 original size:18 final size:19
Alignment explanation
Indices: 290596--290633 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
290586 CTCTTATCAA
*
290596 AGTATATTTTATTATATTT
1 AGTATATTTTAGTATATTT
*
290615 AGTATTTTTTAGTA-ATTT
1 AGTATATTTTAGTATATTT
290633 A
1 A
290634 TTTAATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.61
Consensus pattern (19 bp):
AGTATATTTTAGTATATTT
Found at i:297736 original size:19 final size:19
Alignment explanation
Indices: 297699--297790 Score: 114
Period size: 19 Copynumber: 4.7 Consensus size: 19
297689 AACACATAAG
297699 TCAAATTCGCAACACTGAATT
1 TCAAATTCGC-A-ACTGAATT
297720 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
297739 TCAAATTCGCAACTCGATTT
1 TCAAATTCGCAACT-GAATT
*
297759 TCAAATTCGCAACACGAATT
1 TCAAATTCGCAAC-TGAATT
*
297779 T-AATTTCGCAAC
1 TCAAATTCGCAAC
297791 AGGTTTTAGT
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
19 32 0.49
20 23 0.35
21 10 0.15
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.30
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:297791 original size:19 final size:20
Alignment explanation
Indices: 297620--297791 Score: 129
Period size: 20 Copynumber: 8.7 Consensus size: 20
297610 AAATGACCAA
* * * *
297620 CAAATTCGTAACGCGAACTC
1 CAAATTCGCAACACGAATTT
* * *
297640 CAATTTCGCAAC-CCAGTTT
1 CAAATTCGCAACACGAATTT
**
297659 CCAAATTCGCAACGTGAATTT
1 -CAAATTCGCAACACGAATTT
* **
297680 GTAAA-TCGCAACAC-ATAAGT
1 -CAAATTCGCAACACGA-ATTT
297700 CAAATTCGCAACACTGAATTT
1 CAAATTCGCAACAC-GAATTT
*
297721 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACACGAATTT
* *
297740 CAAATTCGCAACTCGATTTT
1 CAAATTCGCAACACGAATTT
297760 CAAATTCGCAACACGAATTT
1 CAAATTCGCAACACGAATTT
*
297780 -AATTTCGCAACA
1 CAAATTCGCAACA
297792 GGTTTTAGTT
Statistics
Matches: 120, Mismatches: 25, Indels: 15
0.75 0.16 0.09
Matches are distributed among these distances:
19 36 0.30
20 62 0.52
21 21 0.17
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (20 bp):
CAAATTCGCAACACGAATTT
Found at i:297981 original size:16 final size:15
Alignment explanation
Indices: 297946--297984 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
297936 TCCCCATCTC
*
297946 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
297961 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
297977 TAATTTTT
1 TAATTTTT
297985 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:298600 original size:12 final size:12
Alignment explanation
Indices: 298579--298612 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
298569 ACCACATTTT
*
298579 CAATACCAAACA
1 CAATATCAAACA
298591 CAATATCAAACA
1 CAATATCAAACA
*
298603 CAATCTCAAA
1 CAATATCAAA
298613 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:301082 original size:18 final size:18
Alignment explanation
Indices: 301067--301101 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
301057 TCAAAATCGC
*
301067 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
301085 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
301102 GAACCGACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:301094 original size:12 final size:12
Alignment explanation
Indices: 301053--301094 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
301043 CAAGCAAAAG
301053 GAAATCAAAATC
1 GAAATCAAAATC
*
301065 GCAATCAAAATC
1 GAAATCAAAATC
*
301077 GCAATCAAAATC
1 GAAATCAAAATC
*
301089 AAAATC
1 GAAATC
301095 CCAATCAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.55, C:0.21, G:0.07, T:0.17
Consensus pattern (12 bp):
GAAATCAAAATC
Found at i:301101 original size:12 final size:12
Alignment explanation
Indices: 301055--301088 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
301045 AGCAAAAGGA
301055 AATCAAAATCGC
1 AATCAAAATCGC
301067 AATCAAAATCGC
1 AATCAAAATCGC
301079 AATCAAAATC
1 AATCAAAATC
301089 AAAATCCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.53, C:0.24, G:0.06, T:0.18
Consensus pattern (12 bp):
AATCAAAATCGC
Found at i:301521 original size:34 final size:34
Alignment explanation
Indices: 301469--301546 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
301459 AATCACAAAC
*
301469 CGAAAATCGCAACACGAATTTGACTTTCGCAACG
1 CGAAAATCGCAACACGAATTTGACTATCGCAACG
* ** *
301503 CGAAAATTGCAATGCGAATTTGACTATCGCAGCG
1 CGAAAATCGCAACACGAATTTGACTATCGCAACG
*
301537 AGAAAATCGC
1 CGAAAATCGC
301547 GTTGTGAAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (34 bp):
CGAAAATCGCAACACGAATTTGACTATCGCAACG
Found at i:301682 original size:64 final size:64
Alignment explanation
Indices: 301609--301766 Score: 271
Period size: 64 Copynumber: 2.5 Consensus size: 64
301599 TTAATTTAAC
301609 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTATTATTTACACATCAATTA
* * * *
301673 AACAAATCAACTTTTACAAATAAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTATTATTTACACATCAATTA
301737 AACAAATCAACTTTTACAAATCAATGTAAA
1 AACAAATCAACTTTTACAAATCAAT-TAAA
301767 ATTCAATTAA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
64 84 0.95
65 4 0.05
ACGTcount: A:0.52, C:0.16, G:0.02, T:0.30
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTATTATTTACACATCAATTA
Found at i:303388 original size:45 final size:45
Alignment explanation
Indices: 303290--303393 Score: 122
Period size: 45 Copynumber: 2.3 Consensus size: 45
303280 GCACATTGAA
* *
303290 TGTGCATCGATGCA-CTCTTTAAAAAAGAAACATCGAATGCAAAT
1 TGTGCATCGATGCATCCCTTTAAAAAAGAAACATCGAAGGCAAAT
* * * *
303334 GGTGCATCGATGCATCCCTTT-AAAATGAAAACATCGAAGGTAATT
1 TGTGCATCGATGCATCCCTTTAAAAAAG-AAACATCGAAGGCAAAT
*
303379 TGTGTATCGATGCAT
1 TGTGCATCGATGCAT
303394 GGGTAGTGCA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
44 18 0.36
45 32 0.64
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (45 bp):
TGTGCATCGATGCATCCCTTTAAAAAAGAAACATCGAAGGCAAAT
Found at i:303448 original size:20 final size:22
Alignment explanation
Indices: 303400--303457 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
303390 GCATGGGTAG
303400 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
*
303424 TGCATCGATGCACTG-T-AGCA
1 TGCATCGATGCACTGTTAAGAA
303444 TGCATCGATGCACT
1 TGCATCGATGCACT
303458 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:305776 original size:21 final size:20
Alignment explanation
Indices: 305762--305866 Score: 113
Period size: 21 Copynumber: 5.0 Consensus size: 20
305752 TGAACAGTGG
305762 GAGGGACCTCTTGAACGATGA
1 GAGGG-CCTCTTGAACGATGA
* * *
305783 CACGGGCCTCTTGAACGGTGT
1 GA-GGGCCTCTTGAACGATGA
*
305804 GAGGGGCCTCTTGAATGATGA
1 GA-GGGCCTCTTGAACGATGA
305825 GAGGGGCCTCTTGAACGAT-A
1 GA-GGGCCTCTTGAACGATGA
305845 GGAGGCGCCTCTTGAACGATGA
1 -GAGG-GCCTCTTGAACGATGA
305867 CAGGTGAATC
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
20 3 0.04
21 64 0.90
22 4 0.06
ACGTcount: A:0.23, C:0.21, G:0.35, T:0.21
Consensus pattern (20 bp):
GAGGGCCTCTTGAACGATGA
Done.