Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008104.1 Hibiscus syriacus cultivar Beakdansim tig00110634_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: 639954
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:1802 original size:33 final size:33
Alignment explanation
Indices: 1760--1825 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1750 AAATAGATGG
*
1760 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
1793 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1826 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:3623 original size:18 final size:18
Alignment explanation
Indices: 3600--3634 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3590 TCGAGTTAAT
3600 TTTGTATAAGATTTATAA
1 TTTGTATAAGATTTATAA
*
3618 TTTGTATACGATTTATA
1 TTTGTATAAGATTTATA
3635 TTTTTTTATG
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:0.34, C:0.03, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGTATAAGATTTATAA
Found at i:4440 original size:197 final size:198
Alignment explanation
Indices: 3721--5112 Score: 2356
Period size: 198 Copynumber: 7.1 Consensus size: 198
3711 TTAAGGGTCA
*
3721 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTTTCCAGAATGAATTAAAAACAAGGTGCA
1 TGTCGACACTAATATAGTTTGTGTCGATA--TTTTTTTTCCAGAATGAATTAAAAACAAGGTGCA
3786 -CAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAATCATCGAACCCAAAAGTATAAT
64 CCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAATCATCGAACCCAAAAGTATAAT
* *
3850 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGG-TTTATGAGAGAATAAGTCTAAA
129 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAA
3914 TAATG
194 TAATG
*
3919 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
3984 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACCCAAAAGTATAATG
* *
4049 TAATCTGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
130 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
4114 AATG
195 AATG
*
4118 TGTCGACACTAATATAG-TTGTGTCGATATTTTTTTTACAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
*
4182 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAATCATCGAACCCAAAAGTATAATG
*
4247 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATA-GTCTAAAT
130 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
4311 AATG
195 AATG
4315 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
4380 AAT-AAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACCCAAAAGTATAATG
4444 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
130 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
4509 AATG
195 AATG
*
4513 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
* *
4578 CATAACGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAATCATCGAACCCAAAAGTATAATGT
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAATCATCGAACCCAAAAGTATAATGT
4642 AATATGTAATTTTTCAATCTAACC-GTACAATTATACCGGTTTTAT--GAGAATATGTCTAAATA
131 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATA
4704 ATG
196 ATG
*
4707 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
* *
4772 CATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACCCAAAAGTATAATG
*
4837 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
130 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
4902 AATG
195 AATG
* *
4906 TGTCGACACTAATATAGTTTGTTTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
4971 AATAAAGTGTCGATCC---------------C-A----AAATCATCGAACCCAAAAGTATAATGT
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAATCATCGAACCCAAAAGTATAATGT
5016 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATA
131 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATA
5081 ATG
196 ATG
*
5084 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
5113 CTAATTTAAA
Statistics
Matches: 1159, Mismatches: 22, Indels: 46
0.94 0.02 0.04
Matches are distributed among these distances:
178 121 0.10
183 1 0.00
184 1 0.00
194 106 0.09
195 14 0.01
196 122 0.11
197 238 0.21
198 380 0.33
199 176 0.15
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (198 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAATCATCGAACCCAAAAGTATAATGT
AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATA
ATG
Found at i:6588 original size:18 final size:18
Alignment explanation
Indices: 6565--6632 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
6555 ATCGGTCGCA
6565 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
6583 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
6604 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
6625 GAAGATGA
1 GAAGATGA
6633 TGACGATGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 1 0.03
21 17 0.44
22 1 0.03
23 1 0.03
24 5 0.13
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:6589 original size:6 final size:6
Alignment explanation
Indices: 6565--6656 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
6555 ATCGGTCGCA
* * * * * *
6565 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** * * * *
6613 GAAGCT GGCGAT GAAGAT GATGAC GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
6657 TGATCCAAAC
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:6600 original size:3 final size:3
Alignment explanation
Indices: 6580--6660 Score: 72
Period size: 3 Copynumber: 27.0 Consensus size: 3
6570 TGAAGCTGAC
* * * * * ** *
6580 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
6628 GAT GAT GAC GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
6661 CCAAACAAGT
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.36, C:0.06, G:0.35, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:6615 original size:42 final size:42
Alignment explanation
Indices: 6565--6656 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
6555 ATCGGTCGCA
*
6565 GAAGATGAAGCTGACGATGAAGATGACGATGATGATGATGAT
1 GAAGATGAAGCTGACGATGAAGATGACGACGATGATGATGAT
* * *
6607 GACGATGAAGCTGGCGATGAAGATGATGACGATGATGATGAT
1 GAAGATGAAGCTGACGATGAAGATGACGACGATGATGATGAT
6649 GAAGATGA
1 GAAGATGA
6657 TGATCCAAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.21
Consensus pattern (42 bp):
GAAGATGAAGCTGACGATGAAGATGACGACGATGATGATGAT
Found at i:6643 original size:12 final size:12
Alignment explanation
Indices: 6565--6660 Score: 84
Period size: 12 Copynumber: 8.0 Consensus size: 12
6555 ATCGGTCGCA
* *
6565 GAAGATGAAGCT
1 GAAGATGATGAT
* *
6577 GACGATGAAGAT
1 GAAGATGATGAT
*
6589 GACGATGATGAT
1 GAAGATGATGAT
* *
6601 GATGATGACGAT
1 GAAGATGATGAT
* **
6613 GAAGCTGGCGAT
1 GAAGATGATGAT
*
6625 GAAGATGATGAC
1 GAAGATGATGAT
*
6637 GATGATGATGAT
1 GAAGATGATGAT
6649 GAAGATGATGAT
1 GAAGATGATGAT
6661 CCAAACAAGT
Statistics
Matches: 69, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 69 1.00
ACGTcount: A:0.36, C:0.07, G:0.34, T:0.22
Consensus pattern (12 bp):
GAAGATGATGAT
Found at i:6660 original size:18 final size:18
Alignment explanation
Indices: 6568--6660 Score: 78
Period size: 18 Copynumber: 5.2 Consensus size: 18
6558 GGTCGCAGAA
* * *
6568 GATGAAGCTGACGATGAA
1 GATGAAGATGAAGATGAT
* *
6586 GATGACGATGATGATGAT
1 GATGAAGATGAAGATGAT
* * **
6604 GATGACGATGAAGCTGGC
1 GATGAAGATGAAGATGAT
* *
6622 GATGAAGATGATGACGAT
1 GATGAAGATGAAGATGAT
*
6640 GATGATGATGAAGATGAT
1 GATGAAGATGAAGATGAT
6658 GAT
1 GAT
6661 CCAAACAAGT
Statistics
Matches: 58, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 58 1.00
ACGTcount: A:0.35, C:0.08, G:0.34, T:0.23
Consensus pattern (18 bp):
GATGAAGATGAAGATGAT
Found at i:8558 original size:184 final size:184
Alignment explanation
Indices: 8125--8793 Score: 1236
Period size: 184 Copynumber: 3.7 Consensus size: 184
8115 CTTTCAACAT
** *
8125 ATTATAATAAAATAGATAA-TTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
8189 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
8254 AATGTGTCGATACGATTT-AAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
8307 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCCAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
8372 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
8437 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
*
8491 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
8556 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
8621 AATGTGTCGATACGATTTAAAAAAGTGTCGAAATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
8675 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGT-TTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
*
8739 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
8794 CCATTTAAAA
Statistics
Matches: 472, Mismatches: 13, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
182 17 0.04
183 190 0.40
184 265 0.56
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:11379 original size:23 final size:23
Alignment explanation
Indices: 11348--11411 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
11338 ATAGGTAAAC
*
11348 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
11371 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
11394 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
11412 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:11418 original size:23 final size:23
Alignment explanation
Indices: 11348--11420 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
11338 ATAGGTAAAC
* **
11348 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
11371 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
11394 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
11417 ATAT
1 ATAT
11421 TGTAAGTGTC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:11832 original size:23 final size:23
Alignment explanation
Indices: 11769--11833 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
11759 ATAGGTAAAC
* *
11769 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCCCTT
**
11792 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCCCTT
11815 ATATAATGTAATAGGTATC
1 ATATAATGTAATAGGTATC
11834 TATCTCGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCCCTT
Found at i:12058 original size:18 final size:18
Alignment explanation
Indices: 12037--12073 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12027 GTAATTGGAG
12037 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
12055 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
12073 T
1 T
12074 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:12081 original size:24 final size:24
Alignment explanation
Indices: 12029--12075 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
12019 TTTCATATGT
* *
12029 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
12053 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
12076 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:13415 original size:21 final size:21
Alignment explanation
Indices: 13391--13523 Score: 101
Period size: 21 Copynumber: 6.5 Consensus size: 21
13381 ACTTCGACTA
*
13391 TCGCATTGCGATTTTCCAAAT
1 TCGCGTTGCGATTTTCCAAAT
* *
13412 TCGCGTTGCGA-TTTACATAT
1 TCGCGTTGCGATTTTCCAAAT
* ** *
13432 TTGCGTTGCGATAGTCCAAGT
1 TCGCGTTGCGATTTTCCAAAT
*
13453 TCGCGTTGCGATTTTCTAAAT
1 TCGCGTTGCGATTTTCCAAAT
**
13474 T--CGTTGCGATAGTCCAAAT
1 TCGCGTTGCGATTTTCCAAAT
** ** *
13493 TCATGTTGCGATAGTCCAAGT
1 TCGCGTTGCGATTTTCCAAAT
*
13514 TCACGTTGCG
1 TCGCGTTGCG
13524 TCACGTTGCG
Statistics
Matches: 89, Mismatches: 20, Indels: 6
0.77 0.17 0.05
Matches are distributed among these distances:
19 16 0.18
20 17 0.19
21 56 0.63
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCAAAT
Found at i:13490 original size:40 final size:41
Alignment explanation
Indices: 13396--13504 Score: 132
Period size: 41 Copynumber: 2.7 Consensus size: 41
13386 GACTATCGCA
** *
13396 TTGCGATTTTCCAAATTCGCGTTGCGATTTACATATTTGCG
1 TTGCGATAGTCCAAATTCGCGTTGCGATTTACATAATTGCG
* *
13437 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTC-TAAATT-CG
1 TTGCGATAGTCCAAATTCGCGTTGCGATTTACAT-AATTGCG
**
13477 TTGCGATAGTCCAAATTCATGTTGCGAT
1 TTGCGATAGTCCAAATTCGCGTTGCGAT
13505 AGTCCAAGTT
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
40 28 0.47
41 31 0.53
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (41 bp):
TTGCGATAGTCCAAATTCGCGTTGCGATTTACATAATTGCG
Found at i:14507 original size:21 final size:21
Alignment explanation
Indices: 14477--14522 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
14467 GCGATTTTGG
14477 GCAACATGAACTTCGACTATC
1 GCAACATGAACTTCGACTATC
* *
14498 GCAACGTGAACTTGGACTATC
1 GCAACATGAACTTCGACTATC
14519 GCAA
1 GCAA
14523 TGCGAATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.22
Consensus pattern (21 bp):
GCAACATGAACTTCGACTATC
Found at i:20369 original size:19 final size:19
Alignment explanation
Indices: 20345--20392 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
20335 TTGAAGGTGT
*
20345 ATCGATGCATAGGTAGTGC
1 ATCGATGCACAGGTAGTGC
20364 ATCGATGCACAGGTAGTGC
1 ATCGATGCACAGGTAGTGC
20383 ATCGATGCAC
1 ATCGATGCAC
20393 TCTTTTAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (19 bp):
ATCGATGCACAGGTAGTGC
Found at i:20430 original size:64 final size:65
Alignment explanation
Indices: 20360--20520 Score: 168
Period size: 64 Copynumber: 2.5 Consensus size: 65
20350 TGCATAGGTA
*** *
20360 GTGCATCGATGCACAGGTAGTGCATCGATGCACT-CTTTTAATCTAA-AAACATCGAATGCAATT
1 GTGCATCGATGCACAGGTAGTGCATCGATGCACTCCCAGTAAT-AAACAAACATCGAATGCAATT
20423 G
65 G
* * * * *
20424 GTGCATCTATGCATAAGGCA-TGCATCGATGCA-TCCCAGTAATAAACAAACATCGAATGTATTT
1 GTGCATCGATGCA-CAGGTAGTGCATCGATGCACTCCCAGTAATAAACAAACATCGAATGCAATT
*
20487 T
65 G
* *
20488 ATGCACCGATGCACAGGTAGTGCATCGATGCAC
1 GTGCATCGATGCACAGGTAGTGCATCGATGCAC
20521 CGATAGGGAA
Statistics
Matches: 77, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
63 7 0.09
64 66 0.86
65 4 0.05
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (65 bp):
GTGCATCGATGCACAGGTAGTGCATCGATGCACTCCCAGTAATAAACAAACATCGAATGCAATTG
Found at i:21470 original size:103 final size:103
Alignment explanation
Indices: 21291--21608 Score: 564
Period size: 103 Copynumber: 3.1 Consensus size: 103
21281 GTCGAGGGTC
* *
21291 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTTTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
21356 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
21394 TATGTGGTCTTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
21459 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
21497 TATGTGGTCATTCGGGACATATACGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
21562 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
21600 TATGTGGTC
1 TATGTGGTC
21609 CTTATGGACA
Statistics
Matches: 206, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 206 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:21655 original size:23 final size:23
Alignment explanation
Indices: 21629--21695 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
21619 TTATTATATG
21629 GCACTACGGTGCAATTCTATGCA
1 GCACTACGGTGCAATTCTATGCA
* * **
21652 GCACTCCGGTGCAATTCTACGTG
1 GCACTACGGTGCAATTCTATGCA
* *
21675 GCACTTCGGTGCAATTATATG
1 GCACTACGGTGCAATTCTATG
21696 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.28
Consensus pattern (23 bp):
GCACTACGGTGCAATTCTATGCA
Found at i:27202 original size:103 final size:103
Alignment explanation
Indices: 27018--27243 Score: 355
Period size: 103 Copynumber: 2.2 Consensus size: 103
27008 GTCGAGGGTC
* * * *
27018 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTATGAAGTCTCGTGAGACACATAC
* * *
27083 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATTA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
27121 TATGTGGTCCTTTGGGACATATATGTATTCTTTGGAACTTGTATGAAGTCTCGTGAGACACATAC
1 TATGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTATGAAGTCTCGTGAGACACATAC
*
27186 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
27224 TATGTGGTCCTTAT-GGACAT
1 TATGTGGTCCTT-TGGGACAT
27244 TATTATATGG
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
103 112 0.99
104 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTATGAAGTCTCGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:27285 original size:23 final size:23
Alignment explanation
Indices: 27252--27314 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
27242 ATTATTATAT
27252 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
27275 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
27298 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
27315 ATATGAGCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:32694 original size:241 final size:240
Alignment explanation
Indices: 32216--32706 Score: 921
Period size: 241 Copynumber: 2.0 Consensus size: 240
32206 TACAAAGAAT
*
32216 ATAATAATAATATTTTTTTATAATTATGTGGTAAATATAAAATAATATCTGTTCAAATACTCCCA
1 ATAATAATAATATTTTTTTATAATTATGTGGTAAATATAAAATAATATATGTTCAAATACTCCCA
32281 ACCATTTAAAAATGGACGTTCATACCTCTAATATATGTGGTACTATAATAATCACATTAAATCAA
66 ACCATTTAAAAATGGACGTTCATACCTCTAATATATGTGGTACTATAATAATCACATTAAATCAA
*
32346 CATGTTTTCACGTAATAGTCATGACACGTATTTCTCGTAACCATGCAACGAATATATATATACAA
131 CATGTTTTCACGTAATAGTCATGACACATATTTCTCGTAACCATGCAACGAATATATATATACAA
*
32411 TGATTGAAGTACATTATCTAGGTAATCGTACATGATTTACAAATA
196 AGATTGAAGTACATTATCTAGGTAATCGTACATGATTTACAAATA
32456 ATAATAATAATA-TTTTTTATAATTATGTGGTAAATATAAAATAATATATGTTCAAATACTCCCA
1 ATAATAATAATATTTTTTTATAATTATGTGGTAAATATAAAATAATATATGTTCAAATACTCCCA
*
32520 ACTATTTAAAAATGGACGTTCATACCTCTAATATATGTGGTACTATAATAATCACATATTAAATC
66 ACCATTTAAAAATGGACGTTCATACCTCTAATATATGTGGTACTATAATAATCAC--ATTAAATC
32585 AACATGTTTTCACGTAATAGTCATGACACATATTTCTCGTAACCATGCAACGAATATATATATAC
129 AACATGTTTTCACGTAATAGTCATGACACATATTTCTCGTAACCATGCAACGAATATATATATAC
32650 AAAGATTGAAGTACATTATCTAGGTAATCGTACATGATTTACAAATA
194 AAAGATTGAAGTACATTATCTAGGTAATCGTACATGATTTACAAATA
32697 ATAATAATAA
1 ATAATAATAA
32707 ACAATCATAG
Statistics
Matches: 245, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
239 105 0.43
240 12 0.05
241 128 0.52
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (240 bp):
ATAATAATAATATTTTTTTATAATTATGTGGTAAATATAAAATAATATATGTTCAAATACTCCCA
ACCATTTAAAAATGGACGTTCATACCTCTAATATATGTGGTACTATAATAATCACATTAAATCAA
CATGTTTTCACGTAATAGTCATGACACATATTTCTCGTAACCATGCAACGAATATATATATACAA
AGATTGAAGTACATTATCTAGGTAATCGTACATGATTTACAAATA
Found at i:33702 original size:25 final size:25
Alignment explanation
Indices: 33674--33723 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
33664 TTTTTTATAT
33674 ATGGTCCTTATATGATCTAAACTAA
1 ATGGTCCTTATATGATCTAAACTAA
*
33699 ATGGTCCTTATATGATCTGAACTAA
1 ATGGTCCTTATATGATCTAAACTAA
33724 CTAGTTTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (25 bp):
ATGGTCCTTATATGATCTAAACTAA
Found at i:35593 original size:22 final size:21
Alignment explanation
Indices: 35557--35601 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
35547 TAATCACTAA
35557 AATTATAATAAAATTAAACTT
1 AATTATAATAAAATTAAACTT
* *
35578 AATTATAAATATAATTTAACTT
1 AATTAT-AATAAAATTAAACTT
35600 AA
1 AA
35602 CATATAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
AATTATAATAAAATTAAACTT
Found at i:36296 original size:21 final size:20
Alignment explanation
Indices: 36256--36297 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
36246 TCAACTTACA
*
36256 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
36276 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
36297 A
1 A
36298 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:45374 original size:12 final size:12
Alignment explanation
Indices: 45357--45389 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
45347 ACTATATGGT
45357 ATGAACAGTACC
1 ATGAACAGTACC
45369 ATGAACAGTACC
1 ATGAACAGTACC
45381 ATGAACAGT
1 ATGAACAGT
45390 GAACATTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.18
Consensus pattern (12 bp):
ATGAACAGTACC
Found at i:46352 original size:24 final size:23
Alignment explanation
Indices: 46309--46353 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
46299 TATGTCATTT
46309 CATATAACATGTAATACATATTG
1 CATATAACATGTAATACATATTG
46332 CATATAATCATGT-ATATCATAT
1 CATATAA-CATGTAATA-CATAT
46354 CCTATATCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (23 bp):
CATATAACATGTAATACATATTG
Found at i:52430 original size:72 final size:72
Alignment explanation
Indices: 52345--52489 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
52335 TCCCTTTGAA
52345 ACCTTGATTTTGAACGATAATGTACATATATAAATGGACATTCCTTTTATGATGTTTTACTCTAT
1 ACCTTGATTTTGAACGATAATGTACATATATAAATGGACATTCCTTTTATGATGTTTTACTCTAT
52410 GCAGTTG
66 GCAGTTG
52417 ACCTTGATTTTGAACGATAATGTACATATATAAATGGACATTCCTTTTATGATGTTTTACTCTAT
1 ACCTTGATTTTGAACGATAATGTACATATATAAATGGACATTCCTTTTATGATGTTTTACTCTAT
52482 GCAGTTG
66 GCAGTTG
52489 A
1 A
52490 TAAACTCGAA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (72 bp):
ACCTTGATTTTGAACGATAATGTACATATATAAATGGACATTCCTTTTATGATGTTTTACTCTAT
GCAGTTG
Found at i:54943 original size:14 final size:14
Alignment explanation
Indices: 54924--54958 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
54914 CATTTAAATG
*
54924 ACAAACGAACACAA
1 ACAAACAAACACAA
*
54938 ACAAACAAACATAA
1 ACAAACAAACACAA
54952 ACAAACA
1 ACAAACA
54959 CAATAAATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.69, C:0.26, G:0.03, T:0.03
Consensus pattern (14 bp):
ACAAACAAACACAA
Found at i:59230 original size:26 final size:26
Alignment explanation
Indices: 59165--59241 Score: 109
Period size: 26 Copynumber: 3.0 Consensus size: 26
59155 AAAATAAAGA
*
59165 TAAAAGAGATTTAATTCCTCTTTTAT
1 TAAAAGAGATTTATTTCCTCTTTTAT
59191 TAAAAGAGATTTATTTCCTCTTTTAT
1 TAAAAGAGATTTATTTCCTCTTTTAT
* * **
59217 TAGAAGATATTTATTAGCTCTTTTA
1 TAAAAGAGATTTATTTCCTCTTTTA
59242 ATCCAATTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.32, C:0.10, G:0.09, T:0.48
Consensus pattern (26 bp):
TAAAAGAGATTTATTTCCTCTTTTAT
Found at i:68372 original size:3 final size:3
Alignment explanation
Indices: 68364--68390 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
68354 TAAAAATATA
68364 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
68391 TGAGATTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:69334 original size:32 final size:30
Alignment explanation
Indices: 69263--69372 Score: 123
Period size: 30 Copynumber: 3.6 Consensus size: 30
69253 TGGAAAATAA
*
69263 TTTACGTAAAATGAATTATCTCAAAACTGT
1 TTTACGTAAAATGAATTACCTCAAAACTGT
* *
69293 TTTACGTAAAATGAATTACCTCAAAAGTTTTT
1 TTTACGTAAAATGAATTACCTCAAAA--CTGT
* * * *
69325 TTTATGTAAATTGAATTACCTAAAAAATG-
1 TTTACGTAAAATGAATTACCTCAAAACTGT
*
69354 TTTACGTAAAATAAATTAC
1 TTTACGTAAAATGAATTAC
69373 ATTTTCTGGA
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
29 16 0.24
30 26 0.39
32 25 0.37
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (30 bp):
TTTACGTAAAATGAATTACCTCAAAACTGT
Found at i:70010 original size:23 final size:22
Alignment explanation
Indices: 69984--70027 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
69974 TTTATGACGC
69984 GTTTATCTATGCCTTTGTGGTAT
1 GTTTATCTATGCCTTT-TGGTAT
* *
70007 GTTTTTCTCTGCCTTTTGGTA
1 GTTTATCTATGCCTTTTGGTA
70028 GTTAATGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.09, C:0.16, G:0.20, T:0.55
Consensus pattern (22 bp):
GTTTATCTATGCCTTTTGGTAT
Found at i:72406 original size:12 final size:12
Alignment explanation
Indices: 72389--72413 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
72379 GATTATCTAC
72389 TTTTTATTTATT
1 TTTTTATTTATT
72401 TTTTTATTTATT
1 TTTTTATTTATT
72413 T
1 T
72414 ACTCTTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTATTTATT
Found at i:80009 original size:14 final size:15
Alignment explanation
Indices: 79990--80018 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
79980 AATTATATTT
79990 TTTTAAAAAC-AAAA
1 TTTTAAAAACTAAAA
80004 TTTTAAAAACTAAAA
1 TTTTAAAAACTAAAA
80019 ATCAAATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (15 bp):
TTTTAAAAACTAAAA
Found at i:80143 original size:19 final size:19
Alignment explanation
Indices: 80119--80156 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
80109 AATTACATAC
*
80119 TTTGATTAATACCATTTAA
1 TTTGATCAATACCATTTAA
*
80138 TTTGATCGATACCATTTAA
1 TTTGATCAATACCATTTAA
80157 AATAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (19 bp):
TTTGATCAATACCATTTAA
Found at i:81970 original size:23 final size:23
Alignment explanation
Indices: 81944--81989 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
81934 CTATGATGAC
81944 TGATATGCCATATATTATGTGTA
1 TGATATGCCATATATTATGTGTA
81967 TGATATGCCATATATTATGTGTA
1 TGATATGCCATATATTATGTGTA
81990 ATACTTAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.43
Consensus pattern (23 bp):
TGATATGCCATATATTATGTGTA
Found at i:95104 original size:8 final size:8
Alignment explanation
Indices: 95073--95150 Score: 56
Period size: 8 Copynumber: 10.1 Consensus size: 8
95063 TCATTAAAAT
95073 TTTTATTA
1 TTTTATTA
* *
95081 TTTAAATA
1 TTTTATTA
* *
95089 ATTAATTA
1 TTTTATTA
95097 TTTTATTA
1 TTTTATTA
95105 TTATT-TTA
1 TT-TTATTA
*
95113 TTTTAGTA
1 TTTTATTA
95121 TTTT-TTA
1 TTTTATTA
95128 TTTT-TTA
1 TTTTATTA
*
95135 -TTGATTA
1 TTTTATTA
*
95142 TTTAATTA
1 TTTTATTA
95150 T
1 T
95151 AAACCTATTT
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
6 2 0.04
7 14 0.25
8 38 0.68
9 2 0.04
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (8 bp):
TTTTATTA
Found at i:95109 original size:11 final size:11
Alignment explanation
Indices: 95093--95150 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
95083 TAAATAATTA
95093 ATTATTTTATT
1 ATTATTTTATT
95104 ATTATTTTATT
1 ATTATTTTATT
*
95115 -TTAGTATTTTTT
1 ATTA-T-TTTATT
95127 ATT-TTTTATT
1 ATTATTTTATT
*
95137 GATTATTTAATT
1 -ATTATTTTATT
95149 AT
1 AT
95151 AAACCTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
10 8 0.21
11 18 0.46
12 11 0.28
13 2 0.05
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:95113 original size:16 final size:15
Alignment explanation
Indices: 95094--95150 Score: 62
Period size: 15 Copynumber: 3.8 Consensus size: 15
95084 AAATAATTAA
95094 TTATTTTATTATTATT
1 TTATTTTATTATT-TT
*
95110 TTATTTTAGTATTTT
1 TTATTTTATTATTTT
**
95125 TTATTTT-TTATTGA
1 TTATTTTATTATTTT
*
95139 TTATTTAATTAT
1 TTATTTTATTAT
95151 AAACCTATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 10 0.29
15 13 0.37
16 12 0.34
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.72
Consensus pattern (15 bp):
TTATTTTATTATTTT
Found at i:98257 original size:32 final size:32
Alignment explanation
Indices: 98221--98281 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
98211 GAAAAGTCTG
*
98221 TTTTAGGTGTGTGTGCATGCTTTTATTTACTA
1 TTTTAGGTGTATGTGCATGCTTTTATTTACTA
* *
98253 TTTTAGGTGTATGTGTATGTTTTTATTTA
1 TTTTAGGTGTATGTGCATGCTTTTATTTA
98282 TTGTTTAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.16, C:0.05, G:0.21, T:0.57
Consensus pattern (32 bp):
TTTTAGGTGTATGTGCATGCTTTTATTTACTA
Found at i:99364 original size:83 final size:83
Alignment explanation
Indices: 99268--99749 Score: 572
Period size: 83 Copynumber: 5.8 Consensus size: 83
99258 ATGTCATAGT
* * *
99268 ATTTTCCATTATTATTCAGAGAATCTCTGCCATATAATAGTGTTTCATCCCATCCGAAATGAAAG
1 ATTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
* *
99333 ACACATTCCAGATGAAAC
66 ACGCATTCCAGAGGAAAC
* * * *
99351 GTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAATGTTTCATCCCATCCAAAATGAAAG
1 ATTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
* * *
99416 GCGCGTTCCATAGGAAAC
66 ACGCATTCCAGAGGAAAC
* *
99434 GTTTTTCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
1 ATTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
** * *
99499 GTGCGTTCCA-AGGGAATC
66 ACGCATTCCAGA-GGAAAC
*** * * * *
99517 ATTTTCCATTATTATTCAGAGAATCTCTATGATGTCATAGTATTTCATCCTATCCTAAATGAAAG
1 ATTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
* * * *
99582 ACGCGTTCTAGGGGAATC
66 ACGCATTCCAGAGGAAAC
* * * *
99600 ATTTTTCATTATTATTCAGAGAATCTCTACCATGTCATTGTGTTCCATCTCATCCGAAATGAAAT
1 ATTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAA-
* * * *
99665 G-CGCATTCTACAAGAAGC
65 GACGCATTCCAGAGGAAAC
* * *
99683 ATTTTCTATTATTATTCAAAGAATCTTTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
1 ATTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
99748 AC
66 AC
99750 ACATGTTCCA
Statistics
Matches: 345, Mismatches: 50, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
82 2 0.01
83 342 0.99
84 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (83 bp):
ATTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
ACGCATTCCAGAGGAAAC
Found at i:99708 original size:249 final size:249
Alignment explanation
Indices: 99268--99747 Score: 665
Period size: 249 Copynumber: 1.9 Consensus size: 249
99258 ATGTCATAGT
* *
99268 ATTTTCCATTATTATTCAGAGAATCTCTGCCATATAATAGTGTTTCATCCCATCCGAAATGAAAG
1 ATTTTCCATTATTATTCAGAGAATCTCTACCATATAATAGTATTTCATCCCATCCGAAATGAAAG
* * * *
99333 ACACATTCCAGATGAAACGTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCATAATGTTTCA
66 ACACATTCCAGAGGAAACATTTTCCATTATTATTCAGAGAATCTCTACCATGTCATAATGTTCCA
* * * * *
99398 TCCCATCCAAAATGAAAGGCGCGTTCCATAGGAAACGTTTTTCATTATTATTCAGAGAATCTCTG
131 TCCCATCCAAAATGAAAGGCGCATTCCACAAGAAACATTTTTCATTATTATTCAAAGAATCTCTG
99463 CCATGTCATAGTGTTCCATCCCATCCGAAATGAAAGGTGCGTTCCAAGGGAATC
196 CCATGTCATAGTGTTCCATCCCATCCGAAATGAAAGGTGCGTTCCAAGGGAATC
** * * * *
99517 ATTTTCCATTATTATTCAGAGAATCTCTATGATGTCATAGTATTTCATCCTATCCTAAATGAAAG
1 ATTTTCCATTATTATTCAGAGAATCTCTACCATATAATAGTATTTCATCCCATCCGAAATGAAAG
* * * * * * **
99582 ACGCGTTCTAGGGGAATCATTTTTCATTATTATTCAGAGAATCTCTACCATGTCATTGTGTTCCA
66 ACACATTCCAGAGGAAACATTTTCCATTATTATTCAGAGAATCTCTACCATGTCATAATGTTCCA
* * * * * *
99647 TCTCATCCGAAATGAAATGCGCATTCTACAAGAAGCA-TTTTCTATTATTATTCAAAGAATCTTT
131 TCCCATCCAAAATGAAAGGCGCATTCCACAAGAAACATTTTTC-ATTATTATTCAAAGAATCTCT
99711 GCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
195 GCCATGTCATAGTGTTCCATCCCATCCGAAATGAAAG
99748 ACACATGTTC
Statistics
Matches: 199, Mismatches: 31, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
248 5 0.03
249 194 0.97
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (249 bp):
ATTTTCCATTATTATTCAGAGAATCTCTACCATATAATAGTATTTCATCCCATCCGAAATGAAAG
ACACATTCCAGAGGAAACATTTTCCATTATTATTCAGAGAATCTCTACCATGTCATAATGTTCCA
TCCCATCCAAAATGAAAGGCGCATTCCACAAGAAACATTTTTCATTATTATTCAAAGAATCTCTG
CCATGTCATAGTGTTCCATCCCATCCGAAATGAAAGGTGCGTTCCAAGGGAATC
Found at i:110969 original size:278 final size:279
Alignment explanation
Indices: 110172--111166 Score: 1201
Period size: 279 Copynumber: 3.6 Consensus size: 279
110162 CAAGCACACA
* * *
110172 ATCATTTTCCGTCTCGACATTGGAGGAACTCCCTCCATGTTCCATGCTATTCCTCCCTTTCTCAT
1 ATCATTTTCCGTCTCGATATTGGAGGAACTCCCTCCATGTTCCATGCTATTCCTCCCTTCCTCGT
** * * *
110237 CGAAGACTTC--CTTCGGGCTTTCATCCAAGAAATTAGGATTACTAAACAAACTAGAAAGACCAT
66 CGAAGA--TCGACTTCGGATTTTCATCCAAGAAATTACGATCACTAAACAAACTAGCAAGACCAT
* * * *
110300 AAGGACTTCTAGGAGAAAATAATTTCATTTCCTCGCGAAACAAATTAGCAATACCATAAGGTGTT
129 AAGGACTTCTAGGAGAAAACATTTTCATTTCCTCACGAAACAAATTAGCAATACCATAAGGAGTT
* * * *
110365 CTAGGAGAAAACCTGTCCATTTCCTCCCTTTCCGA-CTGTTCTTGAAA-TCTATCACTCGATAGA
194 CTAGGAGAAAACCTGTCCATTTCCTCCC-TTCCTATCTGTTCTTGAAAGT-TATCACTCAATCGT
* * * * *
110428 CAATTCGTATT-ATCAAGCGCACG
257 GAATTCAT-TTCAGCAAGTGCTCG
* *
110451 GTCATTTTCCGACTCGATATTGGAGGAACTCCCTCCATGTTCCATG-TCATTCCTCCCTTCCTCG
1 ATCATTTTCCGTCTCGATATTGGAGGAACTCCCTCCATGTTCCATGCT-ATTCCTCCCTTCCTCG
* * * *
110515 TCAAAGATCGACTTCGGATTTTCATCAAAGAAATTACGATCACTAAACAATCTAGCAAGACCGTA
65 TCGAAGATCGACTTCGGATTTTCATCCAAGAAATTACGATCACTAAACAAACTAGCAAGACCATA
*
110580 AGGACTTCTTGGAGAAAACATTTTCATTTCCTCACGAAACAAATTAGCAATACCATAAGGAGTTC
130 AGGACTTCTAGGAGAAAACATTTTCATTTCCTCACGAAACAAATTAGCAATACCATAAGGAGTTC
* * * * *
110645 TAGGTGAGAACTTGTCCATTTCCTCCCATCCTGTCTGTTCTTGAAAGTTATCACTCAATCGTGAA
195 TAGGAGAAAACCTGTCCATTTCCTCCCTTCCTATCTGTTCTTGAAAGTTATCACTCAATCGTGAA
110710 TTCATTTCAGCAAGTGCTCG
260 TTCATTTCAGCAAGTGCTCG
* *
110730 ATCATTTGCAGTCTCGATATTGGAGGAACTCCCTCCATGTTCCATG-TCATTCCTCCCTTCCTCG
1 ATCATTTTCCGTCTCGATATTGGAGGAACTCCCTCCATGTTCCATGCT-ATTCCTCCCTTCCTCG
* * * * * *
110794 TCGAAGATTGACTTTGAATTTTCATCCGAGAAATTACTATCACT-AACAAACGAGCAAGACCATA
65 TCGAAGATCGACTTCGGATTTTCATCCAAGAAATTACGATCACTAAACAAACTAGCAAGACCATA
*
110858 AGGACTTCTGGGAGAAAACATTTTCATTTCCTCACGAAACAAATTAGCAATACCATAAGGAGTTC
130 AGGACTTCTAGGAGAAAACATTTTCATTTCCTCACGAAACAAATTAGCAATACCATAAGGAGTTC
* * * * * * *
110923 TAGGAGAAAACCTGTTCGTTTCCTCCCTTCCTATCTGTTGTTGAAAGCTATCACTAAACCGTGAC
195 TAGGAGAAAACCTGTCCATTTCCTCCCTTCCTATCTGTTCTTGAAAGTTATCACTCAATCGTGAA
**
110988 TTCCTACCTC-G-AAGTGCTCG
260 TT-C-ATTTCAGCAAGTGCTCG
** ** ** * *
111008 ATCATTTTTTGTCTTAATATTAAAGGAACTCCCTCCATGTTCCATGCTATTCCTTCCTTTCTCGT
1 ATCATTTTCCGTCTCGATATTGGAGGAACTCCCTCCATGTTCCATGCTATTCCTCCCTTCCTCGT
* * * *
111073 CGAATACCGAC-TCTGGATTTTCATCCAAG---TTAGGATCACTAAACAAACTAGCAAGTCCATA
66 CGAAGATCGACTTC-GGATTTTCATCCAAGAAATTACGATCACTAAACAAACTAGCAAGACCATA
* *
111134 GGGACTTCTAGGAGAAAATC-TGTTCATTTCCTC
130 AGGACTTCTAGGAGAAAA-CATTTTCATTTCCTC
111167 CCTTCCTGAC
Statistics
Matches: 620, Mismatches: 84, Indels: 27
0.85 0.11 0.04
Matches are distributed among these distances:
275 9 0.01
276 46 0.07
277 4 0.01
278 226 0.36
279 331 0.53
280 4 0.01
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (279 bp):
ATCATTTTCCGTCTCGATATTGGAGGAACTCCCTCCATGTTCCATGCTATTCCTCCCTTCCTCGT
CGAAGATCGACTTCGGATTTTCATCCAAGAAATTACGATCACTAAACAAACTAGCAAGACCATAA
GGACTTCTAGGAGAAAACATTTTCATTTCCTCACGAAACAAATTAGCAATACCATAAGGAGTTCT
AGGAGAAAACCTGTCCATTTCCTCCCTTCCTATCTGTTCTTGAAAGTTATCACTCAATCGTGAAT
TCATTTCAGCAAGTGCTCG
Found at i:111430 original size:222 final size:221
Alignment explanation
Indices: 110889--111607 Score: 917
Period size: 219 Copynumber: 3.3 Consensus size: 221
110879 TTTCATTTCC
* * * * * * *
110889 TCACGAAACAAATTAGCAATACCATAAGGAGTTCTAGGAGAAAACCTGTTCGTTTCCTCCCTTCC
1 TCACTAAACAAACTAGCAAGACCATAGGGACTTCTAGGAGAAAATCTGTTCATTTCCTCCCTTCC
*
110954 T-ATCTGTTGTTGAAAGCTATCACTAAACCGTGACTTCCTACC-TCGAAGTGCTCGATCATTTTT
66 TGA-CTGTTGTTGAAAGCTATCACTAAACCGCGACTT-CTACCAT-GAAGTGCTCGATCATTTTT
* *
111017 TGTCTTAATATTAAAGGAACTCCCTCC-ATGTTCCATGCTATTCCTTCCTTTCTCGTCGAATACC
128 TGTCTTAATATTGAAGGAACTCCCTCCTATGTTCCATGCTATTCCTCCCTTTCTCGTCGAATACC
* * *
111081 GACTCTGGATTTTCATCC--AAGTTAGGA
193 GACTCCGGATTTTCGTCCAGAAATTAGGA
*
111108 TCACTAAACAAACTAGCAAGTCCATAGGGACTTCTAGGAGAAAATCTGTTCATTTCCTCCCTTCC
1 TCACTAAACAAACTAGCAAGACCATAGGGACTTCTAGGAGAAAATCTGTTCATTTCCTCCCTTCC
* *
111173 TGACTGTTGTTGAAAGCTATTACTAAACCGCGACTTCGTACCATGAAGTGCTTGATCATTTTTT-
66 TGACTGTTGTTGAAAGCTATCACTAAACCGCGACTTC-TACCATGAAGTGCTCGATCATTTTTTG
* * *
111237 TCCTTAATATTGAAGGAACTCCC-CCTATGTTCCATGCTATTACTCCCTTTCTCGGCAAATACCG
130 T-CTTAATATTGAAGGAACTCCCTCCTATGTTCCATGCTATTCCTCCCTTTCTCGTCGAATACCG
*
111301 ACTCCGAATTTTCGTCCGAGAAATTAGGA
194 ACTCCGGATTTTCGTCC-AGAAATTAGGA
* * *
111330 ACACTAAACAAACTA-CGATGACCGTAGGGACTTCTAGGAGAAAATCTGTTCATTTCCTCCCTTC
1 TCACTAAACAAACTAGC-AAGACCATAGGGACTTCTAGGAGAAAATCTGTTCATTTCCTCCCTTC
* * * ** * *
111394 CTGACTGTCGTTGGAAGCTATCACTCAATTGCGAC-T-T---AGGAAGTGCCCGATCATTTTTTG
65 CTGACTGTTGTTGAAAGCTATCACTAAACCGCGACTTCTACCATGAAGTGCTCGATCATTTTTTG
* *
111454 TCTTAATATTGAAGGAACTCCCTCCTCCATGTTCCATGCTATTCCTCCCTTTGTCGTCGAAGACC
130 TCTTAATATTGAAGGAACTCCCTCCT--ATGTTCCATGCTATTCCTCCCTTTCTCGTCGAATACC
111519 GACTCCGGATTTTCGTCCAAGAAATTAGGA
193 GACTCCGGATTTTCGTCC-AGAAATTAGGA
* * * *
111549 TCATTAAACAAACTAGCAGGACCATAAGGACTTCTAGGAGAAAA-CATTTTCATTTCCTC
1 TCACTAAACAAACTAGCAAGACCATAGGGACTTCTAGGAGAAAATC-TGTTCATTTCCTC
111608 ATGAAACAAG
Statistics
Matches: 439, Mismatches: 46, Indels: 30
0.85 0.09 0.06
Matches are distributed among these distances:
216 40 0.09
217 4 0.01
218 5 0.01
219 290 0.66
220 3 0.01
221 2 0.00
222 95 0.22
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (221 bp):
TCACTAAACAAACTAGCAAGACCATAGGGACTTCTAGGAGAAAATCTGTTCATTTCCTCCCTTCC
TGACTGTTGTTGAAAGCTATCACTAAACCGCGACTTCTACCATGAAGTGCTCGATCATTTTTTGT
CTTAATATTGAAGGAACTCCCTCCTATGTTCCATGCTATTCCTCCCTTTCTCGTCGAATACCGAC
TCCGGATTTTCGTCCAGAAATTAGGA
Found at i:111663 original size:57 final size:57
Alignment explanation
Indices: 111549--111665 Score: 139
Period size: 57 Copynumber: 2.1 Consensus size: 57
111539 GAAATTAGGA
* * * *
111549 TCATTAAACAAACTAGCAGGACCATAAGGACTTCTAGGAGAAAACATTTTCATTTCC
1 TCATGAAACAAACTAGCAAGACCATAAGGACTTCTAGGAGAAAACATGTTCAATTCC
* * *
111606 TCATGAAACAAGCTAGCAATACCATAAGGACTTGC-AGGAGAAATGC-TGTTCAATTCC
1 TCATGAAACAAACTAGCAAGACCATAAGGACTT-CTAGGAGAAA-ACATGTTCAATTCC
111663 TCA
1 TCA
111666 CTATCTTTTC
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
57 49 0.96
58 2 0.04
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (57 bp):
TCATGAAACAAACTAGCAAGACCATAAGGACTTCTAGGAGAAAACATGTTCAATTCC
Found at i:112793 original size:21 final size:21
Alignment explanation
Indices: 112754--112794 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
112744 GTTGCAACAC
112754 TTTCCTTCTTCTCATCCTCCCT
1 TTTCCTTCTTCTCA-CCTCCCT
112776 TTTCCTCTCTTCTC-CCTCC
1 TTTCCT-TCTTCTCACCTCC
112795 GCAAAGCTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.02, C:0.49, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTCCTTCTTCTCACCTCCCT
Found at i:113528 original size:3 final size:3
Alignment explanation
Indices: 113520--113544 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
113510 AACCGAGGAT
113520 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
113545 GTGCTGAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:123175 original size:2 final size:2
Alignment explanation
Indices: 123168--123214 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
123158 ATCTATCTAC
123168 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
123210 TA TA T
1 TA TA T
123215 GATTTCGTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:139703 original size:3 final size:3
Alignment explanation
Indices: 139692--139747 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
139682 TTTATTTTTT
139692 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
139739 TTA TTA TTA
1 TTA TTA TTA
139748 AATAAATATT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:142888 original size:20 final size:21
Alignment explanation
Indices: 142848--142904 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
142838 ACCAGAACCC
142848 CATGGGGGTATCGATTCCCCT
1 CATGGGGGTATCGATTCCCCT
* *
142869 ACA-GGGGGAATCGGTT-CCCT
1 -CATGGGGGTATCGATTCCCCT
142889 CATGGGGGTATCGATT
1 CATGGGGGTATCGATT
142905 ACCTATGCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 15 0.50
21 11 0.37
22 2 0.07
ACGTcount: A:0.18, C:0.23, G:0.33, T:0.26
Consensus pattern (21 bp):
CATGGGGGTATCGATTCCCCT
Found at i:151439 original size:19 final size:19
Alignment explanation
Indices: 151415--151452 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
151405 TTTTAAAAGA
151415 TTTGGAGTAATATTTTGAT
1 TTTGGAGTAATATTTTGAT
151434 TTTGGAGTAATATTTTGAT
1 TTTGGAGTAATATTTTGAT
151453 ATTCAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (19 bp):
TTTGGAGTAATATTTTGAT
Found at i:151717 original size:26 final size:25
Alignment explanation
Indices: 151660--151718 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
151650 ACAGGGGGGA
* * * *
151660 GACAGCAACGAGAAAAAGTAAAACC
1 GACAGCAACCACAAAAAGAAAAAAC
*
151685 GAGAGCAACCACAGAAAAGAAAAAAC
1 GACAGCAACCACA-AAAAGAAAAAAC
151711 GACAGCAA
1 GACAGCAA
151719 GAAAAATAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.58, C:0.20, G:0.20, T:0.02
Consensus pattern (25 bp):
GACAGCAACCACAAAAAGAAAAAAC
Found at i:152204 original size:21 final size:21
Alignment explanation
Indices: 152167--152206 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
152157 ATTTTTTAAT
*
152167 TTTTAATCTTTATATTTTATA
1 TTTTAATCTATATATTTTATA
152188 TTTTAATCCTATA-ATTTTA
1 TTTTAAT-CTATATATTTTA
152207 GTTTTCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTAATCTATATATTTTATA
Found at i:152336 original size:19 final size:17
Alignment explanation
Indices: 152312--152360 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
152302 ATCAATACTT
152312 TAAATATTATTTTAACGTA
1 TAAATATTATTTTAA--TA
*
152331 TAAATA-TATATTTAATT
1 TAAATATTAT-TTTAATA
152348 TAAATATTATTTT
1 TAAATATTATTTT
152361 TTAAGGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 10 0.37
18 6 0.22
19 11 0.41
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
TAAATATTATTTTAATA
Found at i:152700 original size:18 final size:18
Alignment explanation
Indices: 152679--152714 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
152669 TAGGAAAATT
152679 ATTATTT-TATTATTAATA
1 ATTATTTAT-TTATTAATA
152697 ATTATTTATTTATTAATA
1 ATTATTTATTTATTAATA
152715 TTAAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 16 0.94
19 1 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTATTTATTTATTAATA
Found at i:152741 original size:158 final size:157
Alignment explanation
Indices: 152389--152780 Score: 405
Period size: 158 Copynumber: 2.5 Consensus size: 157
152379 ATTTTCAATA
* * * *
152389 CTTATTTTTAATATCAAATAAAAGGACAGTCTTAATA-TAACTAGATGTCCTATTCTGGTATTTT
1 CTTATTTTTAATATTAAAGAAAA-GACAGTCTTAA-AGCAACTAGATGTCCTATTCTAGTATTTT
*
152453 -AA-AAATAAATATCCTACTTATAAAAACCAGAAAATACATGTTTTATTTAAATTATTTTCTTAG
64 AAATAAATAAATATCATACTTATAAAAACCAGAAAATACATGTTTTATTTAAATTATTTTCTTAG
*
152516 GAAAATTATTATTTTTAATATTTATTTAT
129 GAAAATTATTATTTTTAATATTTAATTAT
* * *
152545 CTT-TTTTCAAATATT-AAGAAATGACAGTCTTAAGGCAACTAGATGTCCTATTCTAGTATTTTA
1 CTTATTTT-TAATATTAAAGAAAAGACAGTCTTAAAGCAACTAGATGTCCTATTCTAGTATTTT-
*** * * * *
152608 AAAATAAATAAATATCATACTTAT-AAATGTA-TATATATAT-TTACTTAGTTT-TATTATTTT-
64 -AAATAAATAAATATCATACTTATAAAAACCAGAAAATACATGTT--TTA-TTTAAATTATTTTC
*
152668 TTAGGAAAATTATTA-TTTTATTATTAATAATTAT
125 TTAGGAAAATTATTATTTTTAATATT--TAATTAT
* *
152702 -TTATTTATTAATATTAAAGAAAAGACAGTCTTAAAGCAACTAGATGTCCT-TTTTTGATATTTT
1 CTTATTT-TTAATATTAAAGAAAAGACAGTCTTAAAGCAACTAGATGTCCTATTCTAG-TA-TTT
152765 TAAATAAATAAATATC
63 TAAATAAATAAATATC
152781 CTATTTACAA
Statistics
Matches: 198, Mismatches: 22, Indels: 31
0.79 0.09 0.12
Matches are distributed among these distances:
154 36 0.18
155 20 0.10
156 31 0.16
157 51 0.26
158 56 0.28
159 4 0.02
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.44
Consensus pattern (157 bp):
CTTATTTTTAATATTAAAGAAAAGACAGTCTTAAAGCAACTAGATGTCCTATTCTAGTATTTTAA
ATAAATAAATATCATACTTATAAAAACCAGAAAATACATGTTTTATTTAAATTATTTTCTTAGGA
AAATTATTATTTTTAATATTTAATTAT
Found at i:152823 original size:157 final size:154
Alignment explanation
Indices: 152389--152826 Score: 414
Period size: 157 Copynumber: 2.8 Consensus size: 154
152379 ATTTTCAATA
* * * *
152389 CTTATTTTTAATATCAAATAAAAGGACAGTCTTAATA-TAACTAGATGTCCTATTCTGGTA-TTT
1 CTTATTTTTAATATTAAAGAAAA-GACAGTCTTAA-AGCAACTAGATGTCCTATTCTGATATTTT
* *
152452 T-AA-AAATAAATATCCTACTTATAAAAACCAGAAAATACATGT-TT-TATTTAAATTATTTTCT
64 TAAATAAATAAATATCCTA-TT-TAAAAACCA-TAAATATATGTATTATATTT-AA-TATTTT-T
*
152513 TAGGAAAATTATTATTTTTAATATTTATTTAT
123 TAGGAAAATTATTATTTTTAATATTTAATTAT
* * *
152545 CTT-TTTTCAAATATT-AAGAAATGACAGTCTTAAGGCAACTAGATGTCCTATTCT-AGTATTTT
1 CTTATTTT-TAATATTAAAGAAAAGACAGTCTTAAAGCAACTAGATGTCCTATTCTGA-TATTTT
* * * *** * * *
152607 AAAAATAAATAAATATCATACTTATAAATGTATATATATATTTACTTAGT-TTTATTATTTTTTA
64 -TAAATAAATAAATATCCTATTTA-AAAACCATAAATATATGTA-TTA-TATTTAATATTTTTTA
*
152671 GGAAAATTATTA-TTTTATTATTAATAATTAT
125 GGAAAATTATTATTTTTAATATT--TAATTAT
* *
152702 -TTATTTATTAATATTAAAGAAAAGACAGTCTTAAAGCAACTAGATGTCCTTTTTTGATATTTTT
1 CTTATTT-TTAATATTAAAGAAAAGACAGTCTTAAAGCAACTAGATGTCCTATTCTGATATTTTT
*
152766 AAATAAATAAATATCCTATTTACAAAACCCTAAATATATGTATATATATTTAATATTTTTT
65 AAATAAATAAATATCCTATTTA-AAAACCATAAATATATGTAT-TATATTTAATATTTTTT
152827 CCTTAGAAAT
Statistics
Matches: 226, Mismatches: 36, Indels: 39
0.75 0.12 0.13
Matches are distributed among these distances:
154 31 0.14
155 21 0.09
156 36 0.16
157 75 0.33
158 58 0.26
159 4 0.02
160 1 0.00
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (154 bp):
CTTATTTTTAATATTAAAGAAAAGACAGTCTTAAAGCAACTAGATGTCCTATTCTGATATTTTTA
AATAAATAAATATCCTATTTAAAAACCATAAATATATGTATTATATTTAATATTTTTTAGGAAAA
TTATTATTTTTAATATTTAATTAT
Found at i:158384 original size:9 final size:9
Alignment explanation
Indices: 158305--158399 Score: 51
Period size: 9 Copynumber: 10.7 Consensus size: 9
158295 ATTTGCTTGT
*
158305 TTTATCTTA
1 TTTATTTTA
158314 TTTACTTTT-
1 TTTA-TTTTA
158323 TTTATTTTA
1 TTTATTTTA
158332 TTT-TTTTA
1 TTTATTTTA
158340 GTTT-TTTTA
1 -TTTATTTTA
** *
158349 CTCAATCTTA
1 -TTTATTTTA
158359 -TTATCTTTA
1 TTTAT-TTTA
158368 TTTA--TTA
1 TTTATTTTA
158375 TTTATTTTA
1 TTTATTTTA
158384 -TTATTGTTA
1 TTTATT-TTA
158393 TTATATT
1 TT-TATT
158400 AATATTTTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
7 7 0.10
8 16 0.24
9 29 0.43
10 11 0.16
11 4 0.06
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTATTTTA
Found at i:158385 original size:25 final size:25
Alignment explanation
Indices: 158356--158424 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 25
158346 TTACTCAATC
*
158356 TTATTATCTTTATT-TATTATTTATT
1 TTATTATCTTTATTATATTA-ATATT
158381 TTATTAT-TGTTATTATATTAATATT
1 TTATTATCT-TTATTATATTAATATT
158406 TT-TTATCATTTATATATAT
1 TTATTATC-TTTAT-TATAT
158425 ATATATATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
24 5 0.13
25 22 0.58
26 11 0.29
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (25 bp):
TTATTATCTTTATTATATTAATATT
Found at i:159490 original size:13 final size:14
Alignment explanation
Indices: 159472--159500 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
159462 TCTGAATATG
159472 TTCCTCTGAAC-GT
1 TTCCTCTGAACTGT
159485 TTCCTCTGAACTGT
1 TTCCTCTGAACTGT
159499 TT
1 TT
159501 TGTCATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.14, C:0.28, G:0.14, T:0.45
Consensus pattern (14 bp):
TTCCTCTGAACTGT
Found at i:161747 original size:35 final size:35
Alignment explanation
Indices: 161708--161778 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
161698 AAAAAATAAG
* *
161708 TTTATGGGCCCTGCTTCTAATTTAGTTTATTAATA
1 TTTATGGGCCCTGCTTCTAATTTAATATATTAATA
* *
161743 TTTATGGGTCCTGCTTTTAATTTAATATATTAATA
1 TTTATGGGCCCTGCTTCTAATTTAATATATTAATA
161778 T
1 T
161779 AATTTTTAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.25, C:0.11, G:0.13, T:0.51
Consensus pattern (35 bp):
TTTATGGGCCCTGCTTCTAATTTAATATATTAATA
Found at i:170224 original size:16 final size:16
Alignment explanation
Indices: 170203--170238 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
170193 ATGTTACAGA
170203 TTCATA-TTCTAATTCC
1 TTCATATTTC-AATTCC
170219 TTCATATTTCAATTCC
1 TTCATATTTCAATTCC
170235 TTCA
1 TTCA
170239 CAGATTCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.84
17 3 0.16
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (16 bp):
TTCATATTTCAATTCC
Found at i:172495 original size:21 final size:21
Alignment explanation
Indices: 172466--172521 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
172456 ACCGTGATTG
* *
172466 CGGCTGTCGCGGGCTCTATTA
1 CGGCCGTCGCGGGCGCTATTA
* * *
172487 CGGTCGTCGCGGACGCTATTG
1 CGGCCGTCGCGGGCGCTATTA
172508 CGGCCGTCGCGGGC
1 CGGCCGTCGCGGGC
172522 AACTCGGACG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.07, C:0.32, G:0.39, T:0.21
Consensus pattern (21 bp):
CGGCCGTCGCGGGCGCTATTA
Found at i:189833 original size:43 final size:44
Alignment explanation
Indices: 189638--189954 Score: 196
Period size: 42 Copynumber: 7.4 Consensus size: 44
189628 TAATTTTATT
* **
189638 TTTTTA-TCTTTATAATTGAGG-CCCTTAA--TTTTTCAATCCCAC
1 TTTTTACT-TTTATAATTTAGGTCCC-TAATTTTTTTCAATCTTAC
* * * * *
189680 TTTGTACTTTTATAATTGAGCT-CCTAA-GTTTTTCAACCTTAC
1 TTTTTACTTTTATAATTTAGGTCCCTAATTTTTTTCAATCTTAC
* * * * * *
189722 TTTCTACCTTTATAATTGAGG-CCCCAAATTTTTT-AATCTCAC
1 TTTTTACTTTTATAATTTAGGTCCCTAATTTTTTTCAATCTTAC
* * ** **
189764 TTTTTACCTTTAT-AGTT-GCCCCCCTAATTTTTTTCAATCCCA-
1 TTTTTACTTTTATAATTTAG-GTCCCTAATTTTTTTCAATCTTAC
* * *
189806 TTTTTACTTATATAATTTAGGTCCCTAATTTTTTTTATTCTTAC
1 TTTTTACTTTTATAATTTAGGTCCCTAATTTTTTTCAATCTTAC
* * * *
189850 TTTTTAGC-TTTAAAATTAAGGCCCCT-ATTTTTTTTAAT-TTGAC
1 TTTTTA-CTTTTATAATTTAGGTCCCTAATTTTTTTCAATCTT-AC
* * * *
189893 TTTTTAATTTTATAATTGAGGTCCTTAA-TTTTTTCAATCATAC
1 TTTTTACTTTTATAATTTAGGTCCCTAATTTTTTTCAATCTTAC
*
189936 TTTTTACTTTTATAGTTTA
1 TTTTTACTTTTATAATTTA
189955 AGCCTCTAAT
Statistics
Matches: 216, Mismatches: 43, Indels: 31
0.74 0.15 0.11
Matches are distributed among these distances:
40 1 0.00
41 5 0.02
42 94 0.44
43 92 0.43
44 23 0.11
45 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.51
Consensus pattern (44 bp):
TTTTTACTTTTATAATTTAGGTCCCTAATTTTTTTCAATCTTAC
Found at i:189965 original size:43 final size:43
Alignment explanation
Indices: 189638--189966 Score: 190
Period size: 43 Copynumber: 7.7 Consensus size: 43
189628 TAATTTTATT
* * * **
189638 TTTTTA-TCTTTATAATTGAGGCCCTTAA-TTTTTCAATCCCAC
1 TTTTTACT-TTTATAATTTAAGCCCCTAATTTTTTCAATCTTAC
* * * * *
189680 TTTGTACTTTTATAA-TTGAGCTCCTAAGTTTTTCAACCTTAC
1 TTTTTACTTTTATAATTTAAGCCCCTAATTTTTTCAATCTTAC
* * * * * *
189722 TTTCTACCTTTATAATTGAGGCCCCAAATTTTTT-AATCTCAC
1 TTTTTACTTTTATAATTTAAGCCCCTAATTTTTTCAATCTTAC
* * *** **
189764 TTTTTACCTTTAT-AGTTGCCCCCCTAATTTTTTTCAATCCCA-
1 TTTTTACTTTTATAATTTAAGCCCCTAA-TTTTTTCAATCTTAC
* * * * *
189806 TTTTTACTTATATAATTTAGGTCCCTAATTTTTTTTATTCTTAC
1 TTTTTACTTTTATAATTTAAGCCCCTAA-TTTTTTCAATCTTAC
* * *
189850 TTTTTAGC-TTTA-AAATTAAGGCCCCTATTTTTTTTAAT-TTGAC
1 TTTTTA-CTTTTATAATTTAA-GCCCCTAATTTTTTCAATCTT-AC
* * * * * *
189893 TTTTTAATTTTATAATTGAGGTCCTTAATTTTTTCAATCATAC
1 TTTTTACTTTTATAATTTAAGCCCCTAATTTTTTCAATCTTAC
* *
189936 TTTTTACTTTTATAGTTTAAGCCTCTAATTT
1 TTTTTACTTTTATAATTTAAGCCCCTAATTT
189967 AATCACATTT
Statistics
Matches: 214, Mismatches: 60, Indels: 25
0.72 0.20 0.08
Matches are distributed among these distances:
41 15 0.07
42 73 0.34
43 105 0.49
44 20 0.09
45 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.51
Consensus pattern (43 bp):
TTTTTACTTTTATAATTTAAGCCCCTAATTTTTTCAATCTTAC
Found at i:195702 original size:25 final size:26
Alignment explanation
Indices: 195674--195723 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
195664 AACAATTTTA
* *
195674 ATAT-ATTTTTAAGTACTTTTAATTG
1 ATATAATTTATAAGTAATTTTAATTG
*
195699 ATATAATTTATAATTAATTTTAATT
1 ATATAATTTATAAGTAATTTTAATT
195724 ATAGTAGTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (26 bp):
ATATAATTTATAAGTAATTTTAATTG
Found at i:196169 original size:3 final size:3
Alignment explanation
Indices: 196161--196294 Score: 268
Period size: 3 Copynumber: 44.7 Consensus size: 3
196151 ATACATTGAT
196161 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
196209 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
196257 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
196295 GTTGTAATGC
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 131 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:198214 original size:12 final size:13
Alignment explanation
Indices: 198177--198217 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
198167 TAGATAATAC
*
198177 TTTATAAACA-AT
1 TTTAAAAACATAT
198189 TTTAAAAACTATAT
1 TTTAAAAAC-ATAT
198203 TTTAAAAA-ATAT
1 TTTAAAAACATAT
198215 TTT
1 TTT
198218 TCTATTCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 15 0.58
13 1 0.04
14 10 0.38
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTAAAAACATAT
Found at i:211037 original size:15 final size:15
Alignment explanation
Indices: 211017--211073 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
211007 CCGGATATTA
211017 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
**
211032 CGGGTACCCGGATTTT
1 CGGGTACCCGG-TAAT
*
211048 GTGGGTACCCGGTAAT
1 -CGGGTACCCGGTAAT
211064 CGGGTACCCG
1 CGGGTACCCG
211074 ATACCCGGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.59
16 4 0.12
17 10 0.29
ACGTcount: A:0.16, C:0.26, G:0.35, T:0.23
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:211041 original size:32 final size:32
Alignment explanation
Indices: 211005--211073 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
210995 CCGTGTCCCG
211005 ACCCGGATATTACGGGTACCCGGTAATCGGGT
1 ACCCGGATATTACGGGTACCCGGTAATCGGGT
* **
211037 ACCCGGATTTTGTGGGTACCCGGTAATCGGGT
1 ACCCGGATATTACGGGTACCCGGTAATCGGGT
211069 ACCCG
1 ACCCG
211074 ATACCCGGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.19, C:0.26, G:0.32, T:0.23
Consensus pattern (32 bp):
ACCCGGATATTACGGGTACCCGGTAATCGGGT
Found at i:216058 original size:23 final size:23
Alignment explanation
Indices: 216027--216078 Score: 95
Period size: 23 Copynumber: 2.2 Consensus size: 23
216017 CAATTCTGCC
216027 TAAACTAGACATAACTAGCTTTAA
1 TAAA-TAGACATAACTAGCTTTAA
216051 TAAATAGACATAACTAGCTTTAA
1 TAAATAGACATAACTAGCTTTAA
216074 TAAAT
1 TAAAT
216079 GTGAAATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 24 0.86
24 4 0.14
ACGTcount: A:0.48, C:0.13, G:0.08, T:0.31
Consensus pattern (23 bp):
TAAATAGACATAACTAGCTTTAA
Found at i:220417 original size:41 final size:41
Alignment explanation
Indices: 220369--220450 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
220359 ACTTTTGACA
*
220369 GTTGAAAATCAATTTTCAACCAATGACTTACTTTTGCCTCC
1 GTTGAAAATCAATTTCCAACCAATGACTTACTTTTGCCTCC
*
220410 GTTGAAAATCAATTTCCAACCAATGACTTACTTTTTCCTCC
1 GTTGAAAATCAATTTCCAACCAATGACTTACTTTTGCCTCC
220451 ATTCTCATCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.37
Consensus pattern (41 bp):
GTTGAAAATCAATTTCCAACCAATGACTTACTTTTGCCTCC
Found at i:238677 original size:17 final size:17
Alignment explanation
Indices: 238651--238693 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
238641 TAAGGTTAGT
*
238651 ATTTGAGGATTTTATAG
1 ATTTGGGGATTTTATAG
*
238668 ATTTGGGGATTTTATGG
1 ATTTGGGGATTTTATAG
238685 ATTTAGGGG
1 ATTT-GGGG
238694 GCTACTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.44
Consensus pattern (17 bp):
ATTTGGGGATTTTATAG
Found at i:243194 original size:2 final size:2
Alignment explanation
Indices: 243187--243230 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
243177 AAATACATAC
243187 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
243229 AT
1 AT
243231 GGGCCATGCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:243337 original size:2 final size:2
Alignment explanation
Indices: 243330--243405 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
243320 AAAGTAAGAA
243330 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
243372 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
243406 TTTCCCTAAT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:243527 original size:2 final size:2
Alignment explanation
Indices: 243520--243576 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
243510 ATTCAAAGCG
243520 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
243562 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
243577 TTTGAATTTG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:246179 original size:21 final size:21
Alignment explanation
Indices: 246153--246217 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
246143 TTGATAACAC
246153 CTAATTTGTCTAATATTTAAA
1 CTAATTTGTCTAATATTTAAA
* *
246174 CTAATTTATAC-AAGA--TAATA
1 CTAATTTGT-CTAATATTTAA-A
246194 CATAATTTGTCTAATATTTAAA
1 C-TAATTTGTCTAATATTTAAA
246216 CT
1 CT
246218 TACAATGACC
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
19 3 0.09
20 3 0.09
21 22 0.65
22 3 0.09
23 3 0.09
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.43
Consensus pattern (21 bp):
CTAATTTGTCTAATATTTAAA
Found at i:246472 original size:17 final size:17
Alignment explanation
Indices: 246450--246482 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
246440 ATCACTGATG
246450 ATAACATAATAATACAC
1 ATAACATAATAATACAC
*
246467 ATAACATACTAATACA
1 ATAACATAATAATACA
246483 TTGGTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (17 bp):
ATAACATAATAATACAC
Found at i:261126 original size:49 final size:49
Alignment explanation
Indices: 261054--261152 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
261044 ATTTTGTTTT
261054 CACTCTACTTACATACATGTATTATACACAAAAATTAAAGAAATTAGCC
1 CACTCTACTTACATACATGTATTATACACAAAAATTAAAGAAATTAGCC
261103 CACTCTACTTACATACATGTATTATACACAAAAATTAAAGAAATTAGCC
1 CACTCTACTTACATACATGTATTATACACAAAAATTAAAGAAATTAGCC
261152 C
1 C
261153 GCGCATATAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.28
Consensus pattern (49 bp):
CACTCTACTTACATACATGTATTATACACAAAAATTAAAGAAATTAGCC
Found at i:261164 original size:2 final size:2
Alignment explanation
Indices: 261157--261181 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
261147 TAGCCCGCGC
261157 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
261182 ATGTAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:261603 original size:21 final size:21
Alignment explanation
Indices: 261579--261639 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
261569 TTCAAAGAAA
261579 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
261600 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
261614 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
261635 CATTT
1 CATTT
261640 TTTTCAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:261613 original size:35 final size:35
Alignment explanation
Indices: 261531--261640 Score: 168
Period size: 35 Copynumber: 3.1 Consensus size: 35
261521 CCATTATCAT
* * *
261531 TTTTC-AACAAACATCTACCAAACTTTGAAAAACTA
1 TTTTCAAAGAAACATTTACCAAACTTTG-AAAACCA
261566 TTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
261602 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
261637 TTTT
1 TTTT
261641 TTTCAAAATT
Statistics
Matches: 70, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
35 39 0.56
36 11 0.16
37 20 0.29
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.32
Consensus pattern (35 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
Found at i:261666 original size:35 final size:35
Alignment explanation
Indices: 261617--261709 Score: 161
Period size: 34 Copynumber: 2.7 Consensus size: 35
261607 AAAGAAACAT
261617 TTACCAAACTTTGAAAACCATTTTTTTCAAAATTGG
1 TTACCAAAC-TTGAAAACCATTTTTTTCAAAATTGG
*
261653 TTACCAAACTTGAAAACCA-TTTTTTCAAAGTTGG
1 TTACCAAACTTGAAAACCATTTTTTTCAAAATTGG
261687 TTACCAAACTTGAAAACCATTTT
1 TTACCAAACTTGAAAACCATTTT
261710 AATACTTTCA
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
34 33 0.60
35 13 0.24
36 9 0.16
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.37
Consensus pattern (35 bp):
TTACCAAACTTGAAAACCATTTTTTTCAAAATTGG
Found at i:261678 original size:72 final size:73
Alignment explanation
Indices: 261528--261682 Score: 185
Period size: 72 Copynumber: 2.2 Consensus size: 73
261518 ATCCCATTAT
* *
261528 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAGAAACATTTACCAAACT
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAGAAACAGTTACCAAACT
261592 TTGAAAAC
66 TTGAAAAC
* * * ***
261600 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAACCATTTTTTTC-AA-AATTGGTTACCAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC-TATTTTTCAAAGAAACAGTTACCAAAC
261662 -TTGAAAAC
65 TTTGAAAAC
261670 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
261683 TTGGTTACCA
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
70 10 0.14
71 16 0.23
72 38 0.54
73 7 0.10
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (73 bp):
CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAACTATTTTTCAAAGAAACAGTTACCAAACT
TTGAAAAC
Found at i:266262 original size:21 final size:21
Alignment explanation
Indices: 266238--266298 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
266228 TTCAAAGAAA
266238 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
266259 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
266273 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
266294 CATTT
1 CATTT
266299 TTCAAAGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:266272 original size:35 final size:36
Alignment explanation
Indices: 266187--266305 Score: 188
Period size: 35 Copynumber: 3.3 Consensus size: 36
266177 ATCCCATTAT
* *
266187 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
266223 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
266259 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
266294 CATTTTTCAAAG
1 CATTTTTCAAAG
266306 TTTTGCTAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
35 35 0.45
36 22 0.29
37 20 0.26
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.31
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:266398 original size:2 final size:2
Alignment explanation
Indices: 266391--266447 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
266381 TAGCCCGCGC
266391 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
266433 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
266448 ATAATTAACC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:272291 original size:18 final size:17
Alignment explanation
Indices: 272265--272303 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
272255 TTTTTTTTCT
*
272265 TTTATGTAGAATGTCTAC
1 TTTAAGTAG-ATGTCTAC
*
272283 TTTAAGTAGATTTCTAC
1 TTTAAGTAGATGTCTAC
272300 TTTA
1 TTTA
272304 TAAATTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (17 bp):
TTTAAGTAGATGTCTAC
Found at i:278550 original size:12 final size:11
Alignment explanation
Indices: 278510--278552 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
278500 ATTAATTGTG
278510 ATTATAATTAT
1 ATTATAATTAT
*
278521 -TTAAATATTAT
1 ATTATA-ATTAT
278532 ATTATAATTAT
1 ATTATAATTAT
278543 ATTTATAATT
1 A-TTATAATT
278553 TACAAATACT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 4 0.15
11 11 0.41
12 12 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTATAATTAT
Found at i:291248 original size:17 final size:17
Alignment explanation
Indices: 291211--291249 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
291201 TATTGTGAAA
*
291211 CAGGCTTTTAAACAGAT
1 CAGGCTTTTAAACAGAC
*
291228 CAGGCTTTTAAACAGGC
1 CAGGCTTTTAAACAGAC
291245 CAGGC
1 CAGGC
291250 CGAGCCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (17 bp):
CAGGCTTTTAAACAGAC
Found at i:297589 original size:2 final size:2
Alignment explanation
Indices: 297582--297609 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
297572 ATTCGATCTG
297582 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
297610 TAGTCAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:298536 original size:15 final size:15
Alignment explanation
Indices: 298516--298560 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
298506 TTCTGACAAT
298516 TTTAAAATATATATA
1 TTTAAAATATATATA
*
298531 TTTAAAAT-TATAAA
1 TTTAAAATATATATA
* *
298545 ATTAAAAAATATATA
1 TTTAAAATATATATA
298560 T
1 T
298561 ATAATTAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TTTAAAATATATATA
Found at i:298577 original size:31 final size:30
Alignment explanation
Indices: 298519--298578 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 30
298509 TGACAATTTT
*
298519 AAAATATATATATTTAAAATTATAAAATTAA
1 AAAATATATATATTTAAAA-TACAAAATTAA
298550 AAAATATATATATAATTAAAA-ACAAAATT
1 AAAATATATATAT--TTAAAATACAAAATT
298579 TTGAAAATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 20 0.77
33 6 0.23
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (30 bp):
AAAATATATATATTTAAAATACAAAATTAA
Found at i:302303 original size:145 final size:142
Alignment explanation
Indices: 301853--302380 Score: 579
Period size: 145 Copynumber: 3.7 Consensus size: 142
301843 ATCTTATCAT
* * *
301853 GTTGGAACTGCCAAGAATGCTGGAACTGTATTCAAGAATAAGCTTCCTTTCGGTAGATCGGCTGA
1 GTTGGACCTGCCAAGAATGCTGGAACTGTATTCATGAATAAGCTT-CTTTCGGTAGATCGGCTGG
** * * * * * * *
301918 CC-AACACCAGCCCTGGTGCCGGAGGCTGGT-TTCTCCCTTCTCTTACTAGGCCGTATTT-ATT-
65 CCGAA-ACCAGCATTGGTGCCGGAGGCCGGTCTCCCCCCCTCTCATACTAGGTCGTATTTCTTTA
*
301979 TGTGTCTTTATGAA
129 TGTATCTTTATGAA
* * * * *
301993 GTTGGACCTGCCGAGAATGCTGAAACTGT-TTCATGAATAAGCTTCATTCCGGTAGATTGGATGG
1 GTTGGACCTGCCAAGAATGCTGGAACTGTATTCATGAATAAGCTTC-TTTCGGTAGATCGGCTGG
* * * * * *
302057 CTGAAACCAG-ACTTGGTGTCGGAGGCCGG-CTCCCCTCCTCTCATAATAGGTTGTATTTATTTA
65 CCGAAACCAGCA-TTGGTGCCGGAGGCCGGTCTCCCCCCCTCTCATACTAGGTCGTATTTCTTTA
* *
302120 TGTATATTTACGAA
129 TGTATCTTTATGAA
*
302134 GTTGGACCTGCCAAGAATGCTGGAACTGTATTCATGAATAAGCTTCTTTCCGGTAGATTGGCTGG
1 GTTGGACCTGCCAAGAATGCTGGAACTGTATTCATGAATAAGCTTCTTT-CGGTAGATCGGCTGG
** * *
302199 CCGAAACTGGCATTGGTGTCGGAGGCCGGCTCCTCCCCCCCTCTCGTACTAGGTCGTATTTCTTT
65 CCGAAACCAGCATTGGTGCCGGAGGCCGG-T-CTCCCCCCCTCTCATACTAGGTCGTATTTCTTT
*
302264 ATTTATCTTTATGAA
128 ATGTATCTTTATGAA
* *
302279 GTTGGACCTGCCAAGAATGCTGGAATTTTATTCATGAATAAGCTT-TGCTTCGGTAGATCGGCTG
1 GTTGGACCTGCCAAGAATGCTGGAACTGTATTCATGAATAAGCTTCT--TTCGGTAGATCGGCTG
* * *
302343 GCCGACACCAGCCTTGGTGCCGGAGGCCCG-CTCCCCCC
64 GCCGAAACCAGCATTGGTGCCGGAGGCCGGTCTCCCCCC
302381 TCCCCTCCCC
Statistics
Matches: 325, Mismatches: 49, Indels: 26
0.81 0.12 0.06
Matches are distributed among these distances:
138 1 0.00
139 68 0.21
140 30 0.09
141 40 0.12
142 62 0.19
143 1 0.00
144 1 0.00
145 120 0.37
146 2 0.01
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.30
Consensus pattern (142 bp):
GTTGGACCTGCCAAGAATGCTGGAACTGTATTCATGAATAAGCTTCTTTCGGTAGATCGGCTGGC
CGAAACCAGCATTGGTGCCGGAGGCCGGTCTCCCCCCCTCTCATACTAGGTCGTATTTCTTTATG
TATCTTTATGAA
Found at i:312937 original size:31 final size:32
Alignment explanation
Indices: 312896--312955 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
312886 AAGGATAAAT
* *
312896 TATGTGTTTAGTACTTAAATTATCAATTTCAG
1 TATGTGTTTAGTACCTAAACTATCAATTTCAG
312928 TATGT-TTTAGTACCTAAACTATCAATTT
1 TATGTGTTTAGTACCTAAACTATCAATTT
312956 TTTCAAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.47
Consensus pattern (32 bp):
TATGTGTTTAGTACCTAAACTATCAATTTCAG
Found at i:313175 original size:22 final size:21
Alignment explanation
Indices: 313150--313195 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
313140 ATGATTTTAA
*
313150 AAAATTTAAAAGTTTAGGTACT
1 AAAATTGAAAA-TTTAGGTACT
*
313172 AAAATTGATAATTTAGGTACT
1 AAAATTGAAAATTTAGGTACT
313193 AAA
1 AAA
313196 CTATCAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (21 bp):
AAAATTGAAAATTTAGGTACT
Found at i:321576 original size:2 final size:2
Alignment explanation
Indices: 321569--321644 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
321559 TTTTGACCTC
321569 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
321611 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
321645 ATGAGTATAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:328668 original size:2 final size:2
Alignment explanation
Indices: 328661--328735 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
328651 CTCTATCCTG
328661 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
328703 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 T
328736 GTTTCCGGCA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:329502 original size:21 final size:21
Alignment explanation
Indices: 329458--329502 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
329448 ATCCCACAAC
*
329458 TTTAATAATTAAATTATCAGT
1 TTTAATAATTAAATTATCAAT
* * *
329479 TTTAATATTTAAATTTTTAAT
1 TTTAATAATTAAATTATCAAT
329500 TTT
1 TTT
329503 TTAAAATCAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTAATAATTAAATTATCAAT
Found at i:331196 original size:2 final size:2
Alignment explanation
Indices: 331185--331213 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
331175 CGATTTATTA
331185 AT AT -T 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
331214 TTTTATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:338997 original size:87 final size:87
Alignment explanation
Indices: 338862--339100 Score: 442
Period size: 87 Copynumber: 2.7 Consensus size: 87
338852 ATTTAATTGA
*
338862 AAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGATAGCGCTTATAT
1 AAATATTATCAAATACAATAACATATTAGGTAACGCTTATATAATGTAATAGATAGCGCTTATAT
338927 AATAAAATAGGTATTTAACGGG
66 AATAAAATAGGTATTTAACGGG
*
338949 AAATATTATCAAATACAATAACATATTAGGTAACGCTTATATAATGTAATAGATAGCGGTTATAT
1 AAATATTATCAAATACAATAACATATTAGGTAACGCTTATATAATGTAATAGATAGCGCTTATAT
339014 AATAAAATAGGTATTTAACGGG
66 AATAAAATAGGTATTTAACGGG
* *
339036 AAATATTATCAAATACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATAT
1 AAATATTATCAAATACAATAACATATTAGGTAACGCTTATATAATGTAATAGATAGCGCTTATAT
339101 TGACCTATTT
Statistics
Matches: 147, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 147 1.00
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.33
Consensus pattern (87 bp):
AAATATTATCAAATACAATAACATATTAGGTAACGCTTATATAATGTAATAGATAGCGCTTATAT
AATAAAATAGGTATTTAACGGG
Found at i:341521 original size:120 final size:120
Alignment explanation
Indices: 341308--341554 Score: 404
Period size: 120 Copynumber: 2.1 Consensus size: 120
341298 TTTTTCTTCC
* *
341308 ATTCTTGACATAAAATACCGACACAATATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAATACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
341373 AATAAAACCGGTATACTTATACCAGTTATATTACAAAATTATCTAGTACATTATA
66 AATAAAACCGGTATACTTATACCAGTTATATTACAAAATTATCTAGTACATTATA
* *
341428 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAATACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
* * * * * *
341493 CATAAAATCGGTATATTTATACCGGTTATATTATAAAATTATCTATTACATTATA
66 AATAAAACCGGTATACTTATACCAGTTATATTACAAAATTATCTAGTACATTATA
341548 ATTCTGG
1 ATTCTGG
341555 GTTCCGATGT
Statistics
Matches: 117, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
120 117 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (120 bp):
ATTCTGGACATAAAATACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
AATAAAACCGGTATACTTATACCAGTTATATTACAAAATTATCTAGTACATTATA
Found at i:341690 original size:303 final size:303
Alignment explanation
Indices: 341143--341737 Score: 1068
Period size: 303 Copynumber: 2.0 Consensus size: 303
341133 TTAAAATTAG
* *
341143 CGACACAATATTAAAAAGTGTTGATATAGGTTGTAGACCTATTCGCTCATAAAACTGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACTGGTATATTT
*
341208 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGCTGTGTAAATGTCGA
66 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
*
341273 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTTGACATAAAATACCGACACAATATT
131 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAATACCGACACAATATT
341338 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACC-AGTTAT
196 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGA-TTAT
341402 ATTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
260 ATTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
341446 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAA-TCGGTATATT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACT-GGTATATT
*
341510 TATACCGGTTATATTATAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCG
65 TATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCG
*
341575 ACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATAT
130 ACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAATACCGACACAATAT
* * *
341640 TAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGATTAT
195 TAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGATTAT
*
341705 ATTACAAAATTATCTATTACATTATAATTCTGG
260 ATTACAAAATTATCTAGTACATTATAATTCTGG
341738 GTTCCGATGT
Statistics
Matches: 280, Mismatches: 10, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
302 1 0.00
303 278 0.99
304 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (303 bp):
CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACTGGTATATTT
ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAATACCGACACAATATT
AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGATTATA
TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
Found at i:341883 original size:184 final size:183
Alignment explanation
Indices: 341428--342200 Score: 1330
Period size: 183 Copynumber: 4.2 Consensus size: 183
341418 GTACATTATA
*
341428 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* * *
341493 CATAAAATCGGTATATTTATACCGGTTATATTATAAAATTATCTATTACATTATAATTCTGGGTT
66 CATAAAACCGGTATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
341558 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
131 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
341611 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
341676 CATAAAACCGGTATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
66 CATAAAACCGGTATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
** *
341741 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTAATGTCA
131 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCT-TCC
* *
341795 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATATGTTGTAGACCTATTCACT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* *
341860 CATAAAACCGGAATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
66 CATAAAACCGGTATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
341925 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
131 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
*
341978 ATTTTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* *
342043 CATAAAACCGGTATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGAGTT
66 CATAAAACCGGTATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
* *** * * *
342108 CCGATGTTTTTTTAATCGACACTTCTTGAAAAGGTATCGACACATTTTTCTTCC
131 CCGATGTGTAAAT-GTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
*
342162 ATTCTGGACATAAAGTATCGACACAATATTAAAAAGTGT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGT
342201 GAAAACTTTG
Statistics
Matches: 558, Mismatches: 30, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
183 308 0.55
184 250 0.45
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (183 bp):
ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
CATAAAACCGGTATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
Found at i:342100 original size:367 final size:367
Alignment explanation
Indices: 341427--342200 Score: 1352
Period size: 367 Copynumber: 2.1 Consensus size: 367
341417 AGTACATTAT
* *
341427 AATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGC
1 AATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCAC
* * *
341492 TCATAAAATCGGTATATTTATACCGGTTATATTATAAAATTATCTATTACATTATAATTCTGGGT
66 TCATAAAACCGGAATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGT
341557 TCCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACAT
131 TCCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACAT
341622 AAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGG
196 AAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGG
* *
341687 TATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAA
261 TATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGAGTTCCGATGTGTAA
* * *
341752 AT-GTCGACACTTTTTGACAAGGTATCGACACATTTTAATGTC
326 ATAATCGACACTTCTTGAAAAGGTATCGACACATTTTAAT-TC
*
341794 AATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATATGTTGTAGACCTATTCAC
1 AATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCAC
341859 TCATAAAACCGGAATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGT
66 TCATAAAACCGGAATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGT
*
341924 TCCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTTTGGACAT
131 TCCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACAT
341989 AAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGG
196 AAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGG
* **
342054 TATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGAGTTCCGATGTTTTT
261 TATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGAGTTCCGATGTGTAA
* **
342119 TTAATCGACACTTCTTGAAAAGGTATCGACACATTTTTCTTC
326 ATAATCGACACTTCTTGAAAAGGTATCGACACATTTTAATTC
* *
342161 CATTCTGGACATAAAGTATCGACACAATATTAAAAAGTGT
1 AATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGT
342201 GAAAACTTTG
Statistics
Matches: 386, Mismatches: 20, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
367 354 0.92
368 32 0.08
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (367 bp):
AATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCAC
TCATAAAACCGGAATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGT
TCCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACAT
AAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGG
TATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGAGTTCCGATGTGTAA
ATAATCGACACTTCTTGAAAAGGTATCGACACATTTTAATTC
Found at i:343062 original size:33 final size:33
Alignment explanation
Indices: 343025--343087 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
343015 CATCTTAATA
343025 TCACCCCTTAACACCCCAACTTCTTTCACCGCT
1 TCACCCCTTAACACCCCAACTTCTTTCACCGCT
* *
343058 TCACCCCTTAACACCTCTACTTCTTTCACC
1 TCACCCCTTAACACCCCAACTTCTTTCACC
343088 ACTCCATCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.21, C:0.48, G:0.02, T:0.30
Consensus pattern (33 bp):
TCACCCCTTAACACCCCAACTTCTTTCACCGCT
Found at i:343149 original size:21 final size:21
Alignment explanation
Indices: 343124--343167 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
343114 CCCCTTATGC
343124 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
343145 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
343166 CT
1 CT
343168 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:345254 original size:23 final size:23
Alignment explanation
Indices: 345228--345272 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
345218 CACCACAGCT
*
345228 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
345251 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
345273 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:345524 original size:149 final size:149
Alignment explanation
Indices: 345254--345550 Score: 567
Period size: 149 Copynumber: 2.0 Consensus size: 149
345244 AGTGCCCCGT
* *
345254 AGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCCTTAAGAATCAT
1 AGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATCAT
*
345319 ATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGAATATACAT
66 ATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGAATATACAT
345384 ATGTCCTAAAGAACCGAAG
131 ATGTCCTAAAGAACCGAAG
345403 AGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATCAT
1 AGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATCAT
345468 ATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGAATATACAT
66 ATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGAATATACAT
345533 ATGTCCTAAAGAACCGAA
131 ATGTCCTAAAGAACCGAA
345551 TAGACCCTCT
Statistics
Matches: 145, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 145 1.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.27
Consensus pattern (149 bp):
AGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATCAT
ATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGAATATACAT
ATGTCCTAAAGAACCGAAG
Found at i:345666 original size:30 final size:30
Alignment explanation
Indices: 345632--345701 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
345622 CCGTAGTTCA
* *
345632 TATCACGTAGACATAGT-ATTTTCATACCTT
1 TATCACATAGACATA-TCATTTACATACCTT
*
345662 TATCACATAGGCATATCATTTACATACCTT
1 TATCACATAGACATATCATTTACATACCTT
*
345692 CATCACATAG
1 TATCACATAG
345702 CTCATATAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 1 0.03
30 34 0.97
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.36
Consensus pattern (30 bp):
TATCACATAGACATATCATTTACATACCTT
Found at i:345802 original size:34 final size:29
Alignment explanation
Indices: 345723--345794 Score: 126
Period size: 29 Copynumber: 2.5 Consensus size: 29
345713 TTTTCTGCAT
*
345723 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATATAA
*
345752 ATTCATGTCATGTAATACATTTAATATAA
1 ATTCATGTCATGTAATACATATAATATAA
345781 ATTCATGTCATGTA
1 ATTCATGTCATGTA
345795 TCATAATATG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATATAA
Found at i:346195 original size:66 final size:67
Alignment explanation
Indices: 346096--346246 Score: 223
Period size: 66 Copynumber: 2.3 Consensus size: 67
346086 TTTTTCTTAT
* * *
346096 GGGGGAATCGGTTCCCCTCCTGGGGGTATCGATTCCCCACTAGCCTTCTGGAATTCATATGCGTT
1 GGGGGTATCGGTTCCCCTCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATCATATGCGTT
346161 GA
66 GA
* * * *
346163 GGGGGTATCGGTTCCCC-CCTGGGGGTATCGATTCCCCTCTATCATTCTGGAAATCATGTTCGTT
1 GGGGGTATCGGTTCCCCTCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATCATATGCGTT
346227 GA
66 GA
*
346229 AGGGGTATCGGTTCCCCT
1 GGGGGTATCGGTTCCCCT
346247 TGAATGGGTA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
66 59 0.79
67 16 0.21
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.30
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCTCCTGGGGGTATCGATTCCCCACTAGCATTCTGGAAATCATATGCGTT
GA
Found at i:346249 original size:21 final size:21
Alignment explanation
Indices: 346225--346267 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
346215 ATCATGTTCG
* *
346225 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
346246 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
346267 T
1 T
346268 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:348016 original size:180 final size:180
Alignment explanation
Indices: 347712--348129 Score: 577
Period size: 181 Copynumber: 2.3 Consensus size: 180
347702 GGTATCGTTT
* * * *
347712 TACCGGTTTTATTATATTTTTATCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCG
1 TACCGGTTTTATCATATTTTTA-CTGTTATATCGTTTTGGATCGATACA-TTTTTAAAAGTATCG
* * *
347777 ACACATTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATTCTTATA-TAAAG
64 ACACATTATAAGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAG
* * * * **
347841 TATCAACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGA
129 TACCAACACTTTAAATATATCCGGTAACGCTTTACCGATTTTATCATTTCAA
*
347893 TACCGGTTTTATCATATTTTTACATGGTATATCGTTTTGGATCGATACATTTTTAAAAGTATCGA
1 TACCGGTTTTATCATATTTTTAC-TGTTATATCGTTTTGGATCGATACATTTTTAAAAGTATCGA
* ** *
347958 CACTTTATAAGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATTAAAGT
65 CACATTATAAGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAGT
* * * *
348023 GCCGACACTTTAAATGTATCCGGTAGCGCTTTACCGATTTTATCATTTCAA
130 ACCAACACTTTAAATATATCCGGTAACGCTTTACCGATTTTATCATTTCAA
* *
348074 TACCGGTTTTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAA
1 TACCGGTTTTATCATATTTTTA-CTGTTATATCGTTTTGGATCGATACATTTTTAA
348130 TTTGGATCGA
Statistics
Matches: 209, Mismatches: 25, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
180 67 0.32
181 141 0.67
182 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.43
Consensus pattern (180 bp):
TACCGGTTTTATCATATTTTTACTGTTATATCGTTTTGGATCGATACATTTTTAAAAGTATCGAC
ACATTATAAGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAGTA
CCAACACTTTAAATATATCCGGTAACGCTTTACCGATTTTATCATTTCAA
Found at i:349993 original size:23 final size:23
Alignment explanation
Indices: 349949--349996 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
349939 GATTAAGAAG
*
349949 AGAAAAGGAAAAAAAGCGAAAAA
1 AGAAAAGGAAAAAAAGCAAAAAA
**
349972 AGAAAAGGAAGAAAAATAAAAAAA
1 AGAAAAGGAA-AAAAAGCAAAAAA
349996 A
1 A
349997 ACTTTTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (23 bp):
AGAAAAGGAAAAAAAGCAAAAAA
Found at i:352679 original size:25 final size:25
Alignment explanation
Indices: 352634--352681 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
352624 TTGAATTCAA
*
352634 ATTTTAATTATTTATTCTTTTAAAC
1 ATTTTAATTATTTATTATTTTAAAC
352659 ATTTTAA-TATTTATTTATTTTAA
1 ATTTTAATTATTTA-TTATTTTAA
352682 TTTTTTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (25 bp):
ATTTTAATTATTTATTATTTTAAAC
Done.