Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 7 of 199
Found at i:2095833 original size:8 final size:8
Alignment explanation
Indices: 2095820--2095847 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
2095810 CATTCAGAAA
2095820 AAAAAAAG
1 AAAAAAAG
2095828 AAAAAAAG
1 AAAAAAAG
2095836 AAAAAAAG
1 AAAAAAAG
2095844 AAAA
1 AAAA
2095848 GCAGAGTGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:2107958 original size:30 final size:30
Alignment explanation
Indices: 2107924--2108013 Score: 180
Period size: 30 Copynumber: 3.0 Consensus size: 30
2107914 TGAATGCATA
2107924 GAGGAAAGGAGTTAAATGGGGTATTGATAT
1 GAGGAAAGGAGTTAAATGGGGTATTGATAT
2107954 GAGGAAAGGAGTTAAATGGGGTATTGATAT
1 GAGGAAAGGAGTTAAATGGGGTATTGATAT
2107984 GAGGAAAGGAGTTAAATGGGGTATTGATAT
1 GAGGAAAGGAGTTAAATGGGGTATTGATAT
2108014 ATGGAAGCAG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.27
Consensus pattern (30 bp):
GAGGAAAGGAGTTAAATGGGGTATTGATAT
Found at i:2127727 original size:58 final size:58
Alignment explanation
Indices: 2127658--2127771 Score: 160
Period size: 58 Copynumber: 1.9 Consensus size: 58
2127648 TCACTTTTCA
* *
2127658 TTTTCATTTTGGAGAAAACCA-CATCCATTTCCAAATGATTT-CATTTCTCCATTTTCGT
1 TTTTCATTTTGGAGAAAACCATAAT-CATTTCCAAATG-TTTCCATTTATCCATTTTCGT
*
2127716 TTTTCATTTTGGAGAAACCCATAATCATTTCCAAATGTTTCCCATTTATCCATTTT
1 TTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTT-CCATTTATCCATTTT
2127772 TCACCATTTC
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
57 3 0.06
58 32 0.64
59 15 0.30
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.44
Consensus pattern (58 bp):
TTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTCCATTTATCCATTTTCGT
Found at i:2139757 original size:27 final size:27
Alignment explanation
Indices: 2139727--2139782 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
2139717 TATTGCATTA
2139727 ATTTATATAGAATTCCAAATTTTTTTT
1 ATTTATATAGAATTCCAAATTTTTTTT
2139754 ATTTATATAGAATTCCAAATTTTTTTT
1 ATTTATATAGAATTCCAAATTTTTTTT
2139781 AT
1 AT
2139783 AGAAAAACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.55
Consensus pattern (27 bp):
ATTTATATAGAATTCCAAATTTTTTTT
Found at i:2140308 original size:113 final size:114
Alignment explanation
Indices: 2140110--2140330 Score: 282
Period size: 113 Copynumber: 1.9 Consensus size: 114
2140100 TTGATCATAG
* * * * ** *
2140110 TGATGGTAATAGATTTGAGGTGATGAAGAGGAGGATAGACCATTTGAGATTTGGCCTTTTATGCA
1 TGATGGTAATAGATCTAAGGTGATGAAGAGGAGAATAGACCATTTGAAACGTGGCCTTTTACGCA
* *
2140175 TCATTGATGTGGTGGGTCTCTT-GGGGCTTTTGACAGTTTTTTCAACCA
66 TCACTGATGCGGTGGGTCTCTTGGGGGCTTTTGACAGTTTTTTCAACCA
* * * * *
2140223 TGATGGTGATAGATCTAAGGTGATGAAGAGGAGAATGGGCCATTTGAAACGTGGCTTTTTGCGCA
1 TGATGGTAATAGATCTAAGGTGATGAAGAGGAGAATAGACCATTTGAAACGTGGCCTTTTACGCA
* * *
2140288 TTACTGATGCGGTGGGTCTCTTGGGGGTTTTTGATAGTTTTTT
66 TCACTGATGCGGTGGGTCTCTTGGGGGCTTTTGACAGTTTTTT
2140331 TTTGTTAATC
Statistics
Matches: 90, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
113 72 0.80
114 18 0.20
ACGTcount: A:0.22, C:0.11, G:0.31, T:0.36
Consensus pattern (114 bp):
TGATGGTAATAGATCTAAGGTGATGAAGAGGAGAATAGACCATTTGAAACGTGGCCTTTTACGCA
TCACTGATGCGGTGGGTCTCTTGGGGGCTTTTGACAGTTTTTTCAACCA
Found at i:2145706 original size:17 final size:18
Alignment explanation
Indices: 2145673--2145713 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
2145663 GCCGGCCCAC
*
2145673 TAAACAAAATAATAT-AA
1 TAAACAAAACAATATAAA
2145690 TAAACAAAACCAA-ATAAA
1 TAAACAAAA-CAATATAAA
2145708 TAAACA
1 TAAACA
2145714 GTGCAGTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.71, C:0.12, G:0.00, T:0.17
Consensus pattern (18 bp):
TAAACAAAACAATATAAA
Found at i:2152450 original size:11 final size:11
Alignment explanation
Indices: 2152436--2152461 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2152426 TTTTTTTAAA
2152436 TTTTAAAATAC
1 TTTTAAAATAC
2152447 TTTTAAAATAC
1 TTTTAAAATAC
2152458 TTTT
1 TTTT
2152462 TTTTTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:2152485 original size:42 final size:41
Alignment explanation
Indices: 2152424--2152528 Score: 149
Period size: 42 Copynumber: 2.5 Consensus size: 41
2152414 AATAATAAAT
2152424 ATTTTTTTTAAATTTTAAAATACTTTTAAAATACTTTTTTTTTA
1 ATTTTTTTT-AATTTTAAAATACTTTTAAAATAC--TTTTTTTA
*
2152468 A-TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTTA
2152508 ATTTTAATTTTAATTTTAAAA
1 ATTTT--TTTTAATTTTAAAA
2152529 ATAAATTTTT
Statistics
Matches: 57, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
40 9 0.16
41 3 0.05
42 23 0.40
43 21 0.37
44 1 0.02
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (41 bp):
ATTTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTTA
Found at i:2156846 original size:12 final size:12
Alignment explanation
Indices: 2156829--2156855 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2156819 CAAAAGCATC
2156829 AGCTTTGTAGCA
1 AGCTTTGTAGCA
2156841 AGCTTTGTAGCA
1 AGCTTTGTAGCA
2156853 AGC
1 AGC
2156856 CTAATAACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (12 bp):
AGCTTTGTAGCA
Found at i:2156870 original size:2 final size:2
Alignment explanation
Indices: 2156863--2156906 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2156853 AGCCTAATAA
2156863 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2156905 CT
1 CT
2156907 ATGCATGCAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2185032 original size:13 final size:14
Alignment explanation
Indices: 2185001--2185033 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2184991 GTCAAATATT
*
2185001 AATATTTTATGTCA
1 AATATTTTATGTAA
2185015 AATATTTTAT-TAA
1 AATATTTTATGTAA
2185028 AATATT
1 AATATT
2185034 CTTAAAATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (14 bp):
AATATTTTATGTAA
Found at i:2187122 original size:18 final size:19
Alignment explanation
Indices: 2187084--2187122 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
2187074 TTAATAATGA
2187084 TTGAAACTAGACGTTCAAT
1 TTGAAACTAGACGTTCAAT
2187103 TTGAAACT-GA-GTTACAAT
1 TTGAAACTAGACGTT-CAAT
2187121 TT
1 TT
2187123 ATTTTTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.16
18 8 0.42
19 8 0.42
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (19 bp):
TTGAAACTAGACGTTCAAT
Found at i:2187527 original size:2 final size:2
Alignment explanation
Indices: 2187522--2187556 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
2187512 ATATAGTTCA
2187522 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
2187557 GGATAATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2194460 original size:25 final size:25
Alignment explanation
Indices: 2194426--2194502 Score: 127
Period size: 25 Copynumber: 3.1 Consensus size: 25
2194416 CGAGTGATTC
2194426 AAAGTGCATTTCGAAGCTAAGGGAT
1 AAAGTGCATTTCGAAGCTAAGGGAT
*
2194451 AAAGTGCATTTCAAAGCTAAGGGAT
1 AAAGTGCATTTCGAAGCTAAGGGAT
* *
2194476 AAAGTGCATTTCGAAGTTAAGAGAT
1 AAAGTGCATTTCGAAGCTAAGGGAT
2194501 AA
1 AA
2194503 CTCTTCAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.25
Consensus pattern (25 bp):
AAAGTGCATTTCGAAGCTAAGGGAT
Found at i:2197236 original size:27 final size:27
Alignment explanation
Indices: 2197178--2197237 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
2197168 ATAAATATTT
**
2197178 ATTTTTTATTTTTTAATTTTAAAATGC
1 ATTTTTTATTTTTTAATTTTAAAATAA
* *
2197205 TTTTTTTATTTTTTATTTTTAAAATAA
1 ATTTTTTATTTTTTAATTTTAAAATAA
2197232 ATTTTT
1 ATTTTT
2197238 GGTGTTTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (27 bp):
ATTTTTTATTTTTTAATTTTAAAATAA
Found at i:2197702 original size:17 final size:17
Alignment explanation
Indices: 2197680--2197718 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2197670 TTTTAAAAAT
* *
2197680 AATTTTTATAATTTTAA
1 AATTTTTAAAATTTAAA
2197697 AATTTTTAAAATTTAAA
1 AATTTTTAAAATTTAAA
2197714 AATTT
1 AATTT
2197719 AAAACAAAGT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATTTTTAAAATTTAAA
Found at i:2199878 original size:21 final size:21
Alignment explanation
Indices: 2199836--2199879 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2199826 ACTATATTTC
*
2199836 AAATATTTAAATATAGCCATT
1 AAATATTTAAATATAGACATT
*
2199857 AAATATTTATAAT-TAGATATT
1 AAATATTTA-AATATAGACATT
2199878 AA
1 AA
2199880 CACATTTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (21 bp):
AAATATTTAAATATAGACATT
Found at i:2199922 original size:18 final size:18
Alignment explanation
Indices: 2199890--2199928 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2199880 CACATTTGTA
*
2199890 TTATTTTAAAAAATATTT
1 TTATTTTAAAAAATAATT
**
2199908 TTATTTTAATTAATAATT
1 TTATTTTAAAAAATAATT
2199926 TTA
1 TTA
2199929 ACATATTTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATTTTAAAAAATAATT
Found at i:2206907 original size:68 final size:69
Alignment explanation
Indices: 2206797--2206939 Score: 252
Period size: 68 Copynumber: 2.1 Consensus size: 69
2206787 GTTAAATCTA
*
2206797 AAGGGGAAGAAGAAAAGGAAAATAAAGAAATAAAAAGGAAAAATTAAATTGTTCG-AAAAAATAA
1 AAGGGGAAGAAGAAAAGGAAAATAAAGAAATAAAAAGAAAAAATTAAATTGTTCGAAAAAAATAA
2206861 AAGT
66 AAGT
*
2206865 AAGGGGAAGAAGAAAAGGAAAATAAAGAAATAAAAAGAAAAAATTAAATTTTTCGAAAAAAATAA
1 AAGGGGAAGAAGAAAAGGAAAATAAAGAAATAAAAAGAAAAAATTAAATTGTTCGAAAAAAATAA
2206930 AAGT
66 AAGT
2206934 ATAGGG
1 A-AGGG
2206940 ACTAGTTTTA
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
68 53 0.75
69 14 0.20
70 4 0.06
ACGTcount: A:0.63, C:0.01, G:0.20, T:0.15
Consensus pattern (69 bp):
AAGGGGAAGAAGAAAAGGAAAATAAAGAAATAAAAAGAAAAAATTAAATTGTTCGAAAAAAATAA
AAGT
Found at i:2207724 original size:23 final size:22
Alignment explanation
Indices: 2207695--2207741 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
2207685 CAAAGAAAAC
* *
2207695 AATATGAATATACAAATATATAT
1 AATATGAATAAAAAAATATA-AT
2207718 AATATGAATAAAAAAATATAAT
1 AATATGAATAAAAAAATATAAT
2207740 AA
1 AA
2207742 AATAAATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (22 bp):
AATATGAATAAAAAAATATAAT
Found at i:2207742 original size:13 final size:15
Alignment explanation
Indices: 2207718--2207749 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2207708 AAATATATAT
2207718 AATATGAATAAAA-A
1 AATATGAATAAAATA
2207732 AATAT-AATAAAATA
1 AATATGAATAAAATA
2207746 AATA
1 AATA
2207750 CATGATTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (15 bp):
AATATGAATAAAATA
Found at i:2209607 original size:18 final size:18
Alignment explanation
Indices: 2209586--2209623 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2209576 GTAATTTTAT
2209586 TTTTATATAAAAATTAAA
1 TTTTATATAAAAATTAAA
*
2209604 TTTTATATATAAATTAAA
1 TTTTATATAAAAATTAAA
2209622 TT
1 TT
2209624 AAATCAAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTATATAAAAATTAAA
Found at i:2209775 original size:16 final size:17
Alignment explanation
Indices: 2209739--2209775 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
2209729 AATTTTATTT
2209739 TAATAATAAATTTTAAA
1 TAATAATAAATTTTAAA
2209756 -AATAATAAA-TTTAAA
1 TAATAATAAATTTTAAA
2209771 TAATA
1 TAATA
2209776 TTCAATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAATAAATTTTAAA
Found at i:2211484 original size:28 final size:28
Alignment explanation
Indices: 2211453--2211518 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
2211443 ATAAAAAAAT
2211453 TAAAATATATAAAATCCTATA-ATATATA
1 TAAAATATATAAAA-CCTATAGATATATA
* *
2211481 TAAACATATA-AAAACGTATAGATTTATA
1 TAAA-ATATATAAAACCTATAGATATATA
2211509 -AAAATATATA
1 TAAAATATATA
2211519 TTGATAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
26 5 0.15
27 9 0.27
28 14 0.42
29 5 0.15
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (28 bp):
TAAAATATATAAAACCTATAGATATATA
Found at i:2211556 original size:21 final size:23
Alignment explanation
Indices: 2211511--2211560 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
2211501 GATTTATAAA
2211511 AATATATATTGATAAATATTGAT
1 AATATATATTGATAAATATTGAT
*
2211534 AATATATATTTATAAAT-TT-AT
1 AATATATATTGATAAATATTGAT
2211555 AATATA
1 AATATA
2211561 AAAATTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 8 0.31
22 2 0.08
23 16 0.62
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (23 bp):
AATATATATTGATAAATATTGAT
Found at i:2211611 original size:14 final size:14
Alignment explanation
Indices: 2211592--2211632 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
2211582 GTAAGCCATT
2211592 ATAATATTTTTATA
1 ATAATATTTTTATA
*
2211606 ATAATA--TATATA
1 ATAATATTTTTATA
*
2211618 ATATTATTTTTATA
1 ATAATATTTTTATA
2211632 A
1 A
2211633 ATGTACTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
12 10 0.45
14 12 0.55
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATAATATTTTTATA
Found at i:2211715 original size:15 final size:16
Alignment explanation
Indices: 2211671--2211722 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
2211661 ATTATAGGTT
* *
2211671 TTTATATATTTAGATA
1 TTTATAAATTTATATA
2211687 TTTTAATAAATTTATA-A
1 -TTT-ATAAATTTATATA
*
2211704 TTTATAATTTTATATA
1 TTTATAAATTTATATA
2211720 TTT
1 TTT
2211723 TCAAAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 10 0.33
16 7 0.23
17 4 0.13
18 9 0.30
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TTTATAAATTTATATA
Found at i:2219306 original size:20 final size:21
Alignment explanation
Indices: 2219281--2219324 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
2219271 ATTTTTCACC
*
2219281 ATCTAGGA-AAAAGTATCGAT
1 ATCTAGGACAAAAATATCGAT
2219301 ATCTAGGACCAAAAATATCGAT
1 ATCTAGGA-CAAAAATATCGAT
2219323 AT
1 AT
2219325 TTTTACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
22 13 0.62
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (21 bp):
ATCTAGGACAAAAATATCGAT
Found at i:2248009 original size:2 final size:2
Alignment explanation
Indices: 2248002--2248053 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
2247992 ACCCTTTATT
2248002 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
2248044 TA TA TA TA TA
1 TA TA TA TA TA
2248054 CTCTCACAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2248291 original size:16 final size:18
Alignment explanation
Indices: 2248262--2248298 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2248252 AGTTCTATTT
*
2248262 AATTATTATTAATT-TAA
1 AATTATTATAAATTATAA
2248279 AATT-TTATAAATTATAA
1 AATTATTATAAATTATAA
2248296 AAT
1 AAT
2248299 GCCTAAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATTATTATAAATTATAA
Found at i:2255906 original size:14 final size:15
Alignment explanation
Indices: 2255862--2255912 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
2255852 TTACCTTAGG
2255862 TTACGTTTTAGTCAC
1 TTACGTTTTAGTCAC
* * **
2255877 TTATGTTTGAAACA-
1 TTACGTTTTAGTCAC
*
2255891 TTACGTTTTAGTCAT
1 TTACGTTTTAGTCAC
2255906 TTACGTT
1 TTACGTT
2255913 ATCATGTTGT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 10 0.37
15 17 0.63
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (15 bp):
TTACGTTTTAGTCAC
Found at i:2256255 original size:14 final size:14
Alignment explanation
Indices: 2256219--2256252 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
2256209 TCATCATTTG
2256219 CCTATAACCAAAAC
1 CCTATAACCAAAAC
2256233 CCTATAACCAAAAC
1 CCTATAACCAAAAC
2256247 CC-ATAA
1 CCTATAA
2256253 ACCCATACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:2256369 original size:10 final size:11
Alignment explanation
Indices: 2256352--2256377 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2256342 GCAGAGAATG
2256352 GAAAAAAAAAA
1 GAAAAAAAAAA
2256363 GAAAAAAAAAA
1 GAAAAAAAAAA
2256374 GAAA
1 GAAA
2256378 GTTAACAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:2257605 original size:3 final size:3
Alignment explanation
Indices: 2257597--2257622 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2257587 CTTTGTCTAC
2257597 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
2257623 CCACGCTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2261925 original size:2 final size:2
Alignment explanation
Indices: 2261912--2261943 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2261902 ATAAATCTGA
*
2261912 GT GT GT GA GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
2261944 ATACAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.50, T:0.47
Consensus pattern (2 bp):
GT
Found at i:2265922 original size:30 final size:30
Alignment explanation
Indices: 2265877--2265941 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
2265867 AATCAAGATG
*
2265877 TCATTTATAAAATTGCACGA-AAATCAAAGT
1 TCATGTATAAAATTGCAC-ATAAATCAAAGT
* *
2265907 TCATGTATAACATTGCACATTAAATCGAAGT
1 TCATGTATAAAATTGCACA-TAAATCAAAGT
2265938 TCAT
1 TCAT
2265942 ATGTAATCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 1 0.03
30 16 0.53
31 13 0.43
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (30 bp):
TCATGTATAAAATTGCACATAAATCAAAGT
Found at i:2283922 original size:30 final size:30
Alignment explanation
Indices: 2283865--2283923 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
2283855 TTATAAACTT
* * * *
2283865 ATAAATTGATTATTTGAATTCAGTAACTCG
1 ATAAATTAATTAATTAAATTCAATAACTCG
*
2283895 ATAAATTAATTAATTAAATTTAATAACTC
1 ATAAATTAATTAATTAAATTCAATAACTC
2283924 ATACTGATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (30 bp):
ATAAATTAATTAATTAAATTCAATAACTCG
Found at i:2302207 original size:21 final size:21
Alignment explanation
Indices: 2302183--2302222 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2302173 AATAAATTTT
2302183 AATTAATTAATATAA-AATTAA
1 AATTAATTAA-ATAATAATTAA
*
2302204 AATTTATTAAATAATAATT
1 AATTAATTAAATAATAATT
2302223 TATTTAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTAATTAAATAATAATTAA
Found at i:2302510 original size:22 final size:24
Alignment explanation
Indices: 2302479--2302523 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
2302469 ATTTTAAATA
2302479 ATTTAATAAATTTA-ATCCTTCAC
1 ATTTAATAAATTTATATCCTTCAC
*
2302502 ATTT-ATAAATTTATTTCCTTCA
1 ATTTAATAAATTTATATCCTTCA
2302524 AGGTACATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTTAATAAATTTATATCCTTCAC
Found at i:2304112 original size:5 final size:5
Alignment explanation
Indices: 2304102--2304136 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
2304092 CATGACATAG
2304102 AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT
2304137 TTAGATTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:2312058 original size:20 final size:20
Alignment explanation
Indices: 2312035--2312093 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
2312025 TATTTTTAAG
*
2312035 TTGTAAAAATTCTAAAAAAT
1 TTGTAAAAATTATAAAAAAT
* *
2312055 TTGTAAAAATTATAATAATT
1 TTGTAAAAATTATAAAAAAT
*
2312075 TTTTAAAAA-TA-AAAAAAT
1 TTGTAAAAATTATAAAAAAT
2312093 T
1 T
2312094 AAAACTATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 6 0.18
19 2 0.06
20 25 0.76
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (20 bp):
TTGTAAAAATTATAAAAAAT
Found at i:2312448 original size:2 final size:2
Alignment explanation
Indices: 2312441--2312488 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
2312431 TAAAATATTA
2312441 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
2312483 -T AT AT A
1 AT AT AT A
2312489 ANNNNNNNNN
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2319781 original size:21 final size:20
Alignment explanation
Indices: 2319744--2319786 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
2319734 TATATATTTT
2319744 AAATTTAAAATTAATAAATAA
1 AAATTTAAAATTAATAAA-AA
2319765 AAATTTAAAA-TATATAAAAA
1 AAATTTAAAATTA-ATAAAAA
2319785 AA
1 AA
2319787 CTTAAAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AAATTTAAAATTAATAAAAA
Found at i:2321768 original size:20 final size:20
Alignment explanation
Indices: 2321745--2321804 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
2321735 TATTTTGAAG
2321745 TTGTAAAAATTCTAAAAAAT
1 TTGTAAAAATTCTAAAAAAT
* * *
2321765 TTGTAAAAATTATAATAATT
1 TTGTAAAAATTCTAAAAAAT
*
2321785 TTTTAAAAATTAC-AAAAAAT
1 TTGTAAAAATT-CTAAAAAAT
2321805 ATTAAAACTA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
TTGTAAAAATTCTAAAAAAT
Found at i:2322085 original size:20 final size:20
Alignment explanation
Indices: 2322057--2322099 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
2322047 GTTGTTTTGA
2322057 TTTTCAAAAAATTTTAAT-AT
1 TTTTC-AAAAATTTTAATGAT
*
2322077 TTTTTAAAAATTTTAATGAT
1 TTTTCAAAAATTTTAATGAT
2322097 TTT
1 TTT
2322100 CACATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTCAAAAATTTTAATGAT
Found at i:2322366 original size:21 final size:22
Alignment explanation
Indices: 2322342--2322384 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2322332 TATTTTTCAT
*
2322342 ATTTT-TAAATTAAATTTTAAA
1 ATTTTCTAAATAAAATTTTAAA
2322363 ATTTTCTAAATAAAATTTTAAA
1 ATTTTCTAAATAAAATTTTAAA
2322385 CTAATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTTTCTAAATAAAATTTTAAA
Found at i:2322400 original size:33 final size:32
Alignment explanation
Indices: 2322344--2322412 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 32
2322334 TTTTTCATAT
*
2322344 TTTTAAATTAAATTTTAAAATTTTCTAAATAAAA
1 TTTTAAACTAAATTTTAAAATTTT-TAAA-AAAA
* * *
2322378 TTTTAAACT-AATTTTTATATTTTTAAAATAA
1 TTTTAAACTAAATTTTAAAATTTTTAAAAAAA
2322409 TTTT
1 TTTT
2322413 GCAAGTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
31 7 0.23
32 4 0.13
33 12 0.39
34 8 0.26
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (32 bp):
TTTTAAACTAAATTTTAAAATTTTTAAAAAAA
Found at i:2324870 original size:97 final size:97
Alignment explanation
Indices: 2324668--2324859 Score: 336
Period size: 97 Copynumber: 2.0 Consensus size: 97
2324658 GTACAATAAA
*
2324668 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTGGGCACGATTC
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGCACGATTC
* *
2324733 CTCTAGAATCCCAAACTCGGAATATTTCCTTT
66 ATCTAAAATCCCAAACTCGGAATATTTCCTTT
2324765 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGCAC-ATTC
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGCACGATTC
2324829 AT-TAAAATCCCAAACTCGG-ATATTTCCTTT
66 ATCTAAAATCCCAAACTCGGAATATTTCCTTT
2324859 A
1 A
2324860 TTATTTTAAA
Statistics
Matches: 92, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
94 12 0.13
95 16 0.17
96 5 0.05
97 59 0.64
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (97 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGCACGATTC
ATCTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:2326216 original size:19 final size:19
Alignment explanation
Indices: 2326178--2326291 Score: 129
Period size: 19 Copynumber: 5.8 Consensus size: 19
2326168 AAATTAAATC
*
2326178 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
* *
2326198 TCTAATATTATATATCATA
1 TCTAAGATTACATATCATA
*
2326217 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
2326236 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
* *
2326257 TCTAGGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
2326276 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
2326292 CTCAAAAATT
Statistics
Matches: 80, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
19 55 0.69
20 9 0.11
21 16 0.20
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.38
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:2326257 original size:40 final size:40
Alignment explanation
Indices: 2326178--2326290 Score: 167
Period size: 40 Copynumber: 2.9 Consensus size: 40
2326168 AAATTAAATC
* * *
2326178 TCTAAGATTACAAAATCATATCTAATATT--ATATATCATA
1 TCTAAGATTGC-ATATCATATCTAAGATTGCATATATCATA
2326217 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
*
2326257 TCTAGGATTGCATATCATATCTAAGATTGCATAT
1 TCTAAGATTGCATATCATATCTAAGATTGCATAT
2326291 CCTCAAAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
38 15 0.22
39 10 0.15
40 43 0.63
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (40 bp):
TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
Found at i:2326274 original size:59 final size:58
Alignment explanation
Indices: 2326178--2326291 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 58
2326168 AAATTAAATC
* *
2326178 TCTAAGATTACAAAATCATATCTAATATTATATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACAAAATCATATCTAAGATTACATATCATATCTAAGATTGCATATCATA
* * * *
2326236 TCTAAGATTGCATATATCATATCTAGGATTGCATATCATATCTAAGATTGCATATC
1 TCTAAGATTACA-AAATCATATCTAAGATTACATATCATATCTAAGATTGCATATC
2326292 CTCAAAAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
58 11 0.22
59 38 0.78
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.38
Consensus pattern (58 bp):
TCTAAGATTACAAAATCATATCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:2330135 original size:29 final size:31
Alignment explanation
Indices: 2330103--2330160 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
2330093 ATAAAATTAT
2330103 AATTTAAT-TC-TTATACTTTT-AATTTTAGG
1 AATTTAATCTCATTATA-TTTTAAATTTTAGG
2330132 AATTTAATCTCATTATATTTTAAATTTTA
1 AATTTAATCTCATTATATTTTAAATTTTA
2330161 AAATTCAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 8 0.31
30 6 0.23
31 12 0.46
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.55
Consensus pattern (31 bp):
AATTTAATCTCATTATATTTTAAATTTTAGG
Found at i:2331761 original size:25 final size:25
Alignment explanation
Indices: 2331731--2331780 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2331721 TTCTAGTATC
2331731 AAATTAT-ATTTCTAATATTTTTATA
1 AAATTATAATTTCTAAT-TTTTTATA
* *
2331756 AAATTATAATTTTTTATTTTTTATA
1 AAATTATAATTTCTAATTTTTTATA
2331781 TTTTAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (25 bp):
AAATTATAATTTCTAATTTTTTATA
Found at i:2337301 original size:19 final size:19
Alignment explanation
Indices: 2337271--2337316 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2337261 TAATAAGATG
2337271 GTTAGCTCATAACCGTTTTA
1 GTTAG-TCATAACCGTTTTA
*
2337291 GTTAGTCATAACTGTTTTA
1 GTTAGTCATAACCGTTTTA
2337310 GTTAGTC
1 GTTAGTC
2337317 GGTTGAAGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.43
Consensus pattern (19 bp):
GTTAGTCATAACCGTTTTA
Found at i:2339563 original size:43 final size:42
Alignment explanation
Indices: 2339514--2339734 Score: 264
Period size: 43 Copynumber: 5.2 Consensus size: 42
2339504 AGAAATAAAT
*
2339514 GCCGCTATAGATCATGACCTTTAGCGGCGTCTTTTCCACAAAC
1 GCCGCTATAGATCAAGACCTTTAGCGGCG-CTTTTCCACAAAC
* * ** *
2339557 GCCGCTATAAATCAGGACCTTTAGCAACGCTTTTACACAAAC
1 GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCACAAAC
* * *
2339599 GCCACTATAGCTCAAGATCTTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTT-CCACAAAC
*
2339642 GCCGCTATAGATCAAGGCCTTTAGCGGCGCTTTTTCCACAAAC
1 GCCGCTATAGATCAAGACCTTTAGCGGCGC-TTTTCCACAAAC
* * *
2339685 GCTGCTATAGCTCAAGACCTTTAGCGACGCTTTGAT-CACAAAC
1 GCCGCTATAGATCAAGACCTTTAGCGGCGCTTT--TCCACAAAC
*
2339728 GCTGCTA
1 GCCGCTA
2339735 AAAATATCAT
Statistics
Matches: 153, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
42 42 0.27
43 106 0.69
44 5 0.03
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (42 bp):
GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCACAAAC
Found at i:2339787 original size:16 final size:16
Alignment explanation
Indices: 2339766--2339799 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2339756 GTTTATTAAA
*
2339766 TATTAAAATCAAACAT
1 TATTAAAATCAAAAAT
2339782 TATTAAAATCAAAAAT
1 TATTAAAATCAAAAAT
2339798 TA
1 TA
2339800 ATTAGTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (16 bp):
TATTAAAATCAAAAAT
Found at i:2341617 original size:2 final size:2
Alignment explanation
Indices: 2341610--2341636 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2341600 ACAATTTTCT
2341610 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 T
2341637 CAGTCAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2349844 original size:4 final size:4
Alignment explanation
Indices: 2349837--2349863 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2349827 TATATATATA
2349837 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
2349864 ATGTTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:2349870 original size:12 final size:12
Alignment explanation
Indices: 2349833--2349875 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
2349823 AATATATATA
2349833 TATATATTTATT
1 TATATATTTATT
*
2349845 TATTTATTTATT
1 TATATATTTATT
* * *
2349857 TATTTATATGTT
1 TATATATTTATT
2349869 TATATAT
1 TATATAT
2349876 GATTTTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (12 bp):
TATATATTTATT
Found at i:2351102 original size:2 final size:2
Alignment explanation
Indices: 2351095--2351131 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2351085 ATCAAACTAG
2351095 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2351132 CTTGTGCAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2356575 original size:7 final size:7
Alignment explanation
Indices: 2356563--2356587 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2356553 GGTTGTCTAT
2356563 GTTTTGG
1 GTTTTGG
2356570 GTTTTGG
1 GTTTTGG
2356577 GTTTTGG
1 GTTTTGG
2356584 GTTT
1 GTTT
2356588 ATTTGTCTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.40, T:0.60
Consensus pattern (7 bp):
GTTTTGG
Found at i:2362435 original size:22 final size:21
Alignment explanation
Indices: 2362401--2362451 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
2362391 TAAAAACAGT
*
2362401 AAAGAAAAAGAAA-AAATTGAAA
1 AAAGAAATAGAAAGAAA--GAAA
*
2362423 AAAGAAATCGAAAGAAAGAAA
1 AAAGAAATAGAAAGAAAGAAA
2362444 AAA-AAATA
1 AAAGAAATA
2362452 AAGGACCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 4 0.16
21 7 0.28
22 11 0.44
23 3 0.12
ACGTcount: A:0.76, C:0.02, G:0.14, T:0.08
Consensus pattern (21 bp):
AAAGAAATAGAAAGAAAGAAA
Found at i:2362440 original size:14 final size:14
Alignment explanation
Indices: 2362407--2362443 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
2362397 CAGTAAAGAA
*
2362407 AAAGAAA-AAATTG
1 AAAGAAAGAAATCG
2362420 AAA-AAAGAAATCG
1 AAAGAAAGAAATCG
2362433 AAAGAAAGAAA
1 AAAGAAAGAAA
2362444 AAAAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 3 0.14
13 11 0.52
14 7 0.33
ACGTcount: A:0.73, C:0.03, G:0.16, T:0.08
Consensus pattern (14 bp):
AAAGAAAGAAATCG
Found at i:2364059 original size:19 final size:18
Alignment explanation
Indices: 2364024--2364073 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
2364014 ATTTTAGAAA
2364024 AATTTTAATTTTTTTTAG
1 AATTTTAATTTTTTTTAG
*
2364042 AATTTTTATATTTTTTTA-
1 AATTTTAAT-TTTTTTTAG
*
2364060 AA-TATAATTTTTTT
1 AATTTTAATTTTTTT
2364074 AATATTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 6 0.21
17 4 0.14
18 10 0.36
19 8 0.29
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
AATTTTAATTTTTTTTAG
Found at i:2364083 original size:18 final size:18
Alignment explanation
Indices: 2364046--2364094 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
2364036 TTTTAGAATT
2364046 TTTAT-ATTTTTTTAA-A
1 TTTATAATTTTTTTAATA
2364062 --TATAATTTTTTTAATA
1 TTTATAATTTTTTTAATA
* *
2364078 TTTATAAATATTTTAAT
1 TTTATAATTTTTTTAAT
2364095 TTTTTTTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 3 0.11
15 10 0.37
16 1 0.04
18 13 0.48
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATAATTTTTTTAATA
Found at i:2364979 original size:25 final size:26
Alignment explanation
Indices: 2364931--2364984 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
2364921 GGTTGCTACC
*
2364931 ATTGTTCAATTTATAATTAGAAAG-A
1 ATTGTTCAATTTAGAATTAGAAAGTA
*
2364956 ATTGTTCCATATTAGAATTA-AAAGTA
1 ATTGTTCAAT-TTAGAATTAGAAAGTA
2364982 ATT
1 ATT
2364985 CAAAATTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.41
Consensus pattern (26 bp):
ATTGTTCAATTTAGAATTAGAAAGTA
Found at i:2374470 original size:31 final size:32
Alignment explanation
Indices: 2374435--2374517 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 32
2374425 CCATTGAGTC
*
2374435 AGGACTAAAATTTCA-AAATTCGAAAAGTATA
1 AGGACTAAAATTTCACAAATTCGAAAAATATA
* *
2374466 AGGACTAAAA-TTGACCAATTCGAAAAATATA
1 AGGACTAAAATTTCACAAATTCGAAAAATATA
* *
2374497 AAGATTAAAA-TTCATCAAATT
1 AGGACTAAAATTTCA-CAAATT
2374518 AAAGTACAGG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 3 0.07
31 35 0.81
32 5 0.12
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.27
Consensus pattern (32 bp):
AGGACTAAAATTTCACAAATTCGAAAAATATA
Found at i:2375559 original size:16 final size:18
Alignment explanation
Indices: 2375525--2375567 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
2375515 TTTAGACGAA
*
2375525 TTTTTAATTAATTTGATT
1 TTTTTATTTAATTTGATT
2375543 TTTTTATTTAA-TT-ATT
1 TTTTTATTTAATTTGATT
*
2375559 TTTTGATTT
1 TTTTTATTT
2375568 TATAATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 11 0.48
17 2 0.09
18 10 0.43
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (18 bp):
TTTTTATTTAATTTGATT
Found at i:2377077 original size:17 final size:18
Alignment explanation
Indices: 2377051--2377086 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2377041 AAAAAAATTG
*
2377051 AAAATAAAATTGTTTTAT
1 AAAATAAAATTATTTTAT
2377069 AAAAT-AAATTATTTTAT
1 AAAATAAAATTATTTTAT
2377086 A
1 A
2377087 TAAAAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
AAAATAAAATTATTTTAT
Found at i:2386584 original size:38 final size:38
Alignment explanation
Indices: 2386542--2386624 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 38
2386532 GTACTGGTTG
* * * * *
2386542 CATGCTTACCGTTATTGTTAAACTGAATACATGTTAAA
1 CATGCCTACCGTTACTATTAAACTAAATACATGATAAA
* * *
2386580 CATGCCTACTGTTACTATTGAACTAAATACATGATAAT
1 CATGCCTACCGTTACTATTAAACTAAATACATGATAAA
2386618 CATGCCT
1 CATGCCT
2386625 TTTGTTAATG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (38 bp):
CATGCCTACCGTTACTATTAAACTAAATACATGATAAA
Found at i:2388404 original size:42 final size:42
Alignment explanation
Indices: 2388357--2388440 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
2388347 AGGCTGCACA
* * *
2388357 GAAGCACATA-AGTGCTAAACGAAAACCCGTAAGGGTTTAACG
1 GAAGCACATAGA-AGCTAAACGAAAACCCATAAGGGTTAAACG
*
2388399 GAAGCACATAGAAGCTAAACGAAAACCCATTAGGGTTAAACG
1 GAAGCACATAGAAGCTAAACGAAAACCCATAAGGGTTAAACG
2388441 AAAACATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 36 0.97
43 1 0.03
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (42 bp):
GAAGCACATAGAAGCTAAACGAAAACCCATAAGGGTTAAACG
Found at i:2390419 original size:17 final size:18
Alignment explanation
Indices: 2390394--2390427 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2390384 ATTTTACTAA
*
2390394 AAATATTTTTTTTAAATG
1 AAATATTTTTATTAAATG
2390412 AAAT-TTTTTATTAAAT
1 AAATATTTTTATTAAAT
2390428 AACACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
AAATATTTTTATTAAATG
Found at i:2395114 original size:15 final size:16
Alignment explanation
Indices: 2395094--2395126 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2395084 TACTTCATGC
*
2395094 TAAATTCTTTT-TTTT
1 TAAATTATTTTCTTTT
2395109 TAAATTATTTTCTTTT
1 TAAATTATTTTCTTTT
2395125 TA
1 TA
2395127 TTTTTTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (16 bp):
TAAATTATTTTCTTTT
Found at i:2397860 original size:18 final size:18
Alignment explanation
Indices: 2397839--2397878 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2397829 TTAAAATTAA
2397839 AAATATATAAAAAAATAG
1 AAATATATAAAAAAATAG
* * *
2397857 AAATTTATAAAATATTAG
1 AAATATATAAAAAAATAG
2397875 AAAT
1 AAAT
2397879 GTTGTTTCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (18 bp):
AAATATATAAAAAAATAG
Found at i:2403122 original size:27 final size:28
Alignment explanation
Indices: 2403094--2403146 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
2403084 AGCCGTAACT
2403094 TTTTATAA-ATAAATA-TATTATAATAC
1 TTTTATAACATAAATATTATTATAATAC
* *
2403120 TTTTATAACATATATATTTTTATAATA
1 TTTTATAACATAAATATTATTATAATA
2403147 AGCTTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 8 0.35
27 6 0.26
28 9 0.39
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTTATAACATAAATATTATTATAATAC
Found at i:2403167 original size:15 final size:16
Alignment explanation
Indices: 2403136--2403168 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2403126 AACATATATA
2403136 TTTTTATAATAAGCTT
1 TTTTTATAATAAGCTT
*
2403152 TTTTTATCATAA-CTT
1 TTTTTATAATAAGCTT
2403167 TT
1 TT
2403169 AAAAAGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.27, C:0.09, G:0.03, T:0.61
Consensus pattern (16 bp):
TTTTTATAATAAGCTT
Found at i:2403183 original size:36 final size:39
Alignment explanation
Indices: 2403138--2403210 Score: 89
Period size: 37 Copynumber: 1.9 Consensus size: 39
2403128 CATATATATT
*
2403138 TTTATAATAAGCT-TTTTTTATCATAACTTT-TAAAAAG
1 TTTATAATAAGATATTTTTTATCATAACTTTATAAAAAG
* * *
2403175 TTTA-AATAATATATTTTTTGTTATAACTTTATAAAA
1 TTTATAATAAGATATTTTTTATCATAACTTTATAAAA
2403211 TATACATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
36 6 0.20
37 19 0.63
38 5 0.17
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (39 bp):
TTTATAATAAGATATTTTTTATCATAACTTTATAAAAAG
Found at i:2406089 original size:18 final size:18
Alignment explanation
Indices: 2406066--2406103 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2406056 AAAAGACTAA
2406066 AATTTATTTGAATAATAT
1 AATTTATTTGAATAATAT
* *
2406084 AATTTATTTTAATTATAT
1 AATTTATTTGAATAATAT
2406102 AA
1 AA
2406104 GTACATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
AATTTATTTGAATAATAT
Found at i:2417560 original size:19 final size:20
Alignment explanation
Indices: 2417533--2417583 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
2417523 CAACTAATTT
* **
2417533 AAAATTTATAAAAATAT-CC
1 AAAAATTATAAAAATATAAA
*
2417552 AAAAATTATAAAATTATAAA
1 AAAAATTATAAAAATATAAA
2417572 AAAAATTATAAA
1 AAAAATTATAAA
2417584 CATCCGCATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAATTATAAAAATATAAA
Found at i:2421454 original size:22 final size:23
Alignment explanation
Indices: 2421427--2421469 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2421417 AAACATATGA
**
2421427 AATAACTTTAAAT-TTTAAAAAT
1 AATAACTACAAATATTTAAAAAT
2421449 AATAACTACAAATATTTAAAA
1 AATAACTACAAATATTTAAAA
2421470 TTTTATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (23 bp):
AATAACTACAAATATTTAAAAAT
Found at i:2426424 original size:139 final size:137
Alignment explanation
Indices: 2426237--2426623 Score: 458
Period size: 139 Copynumber: 2.8 Consensus size: 137
2426227 TCTTCTACTG
* *
2426237 ACATTTGTATTTTTTATTTCACGTTGCTTCAAGCTTTTTAAATCTTTAATTAATTTTTTTAACAT
1 ACATTTGTATTTTTTATTTCATGTTGCTTCAAGC-TTTTAAAT-TTTAATTAATATTTTTAACAT
* * * **
2426302 ATTAGTTCTTTGGTTAGATGGTTAAATAGTTACAATTACATCCTTGAGTCTCAAGTTTAATTCAT
64 ATTAGTTCTTTCGTTAGATGGTTAGATAGTTGCAATTACATCCTTGAGTCTCAAGTCCAATTCAT
*
2426367 CTCCGACTC
129 CTACGACTC
* * *
2426376 ATATTTGTATTTTCTATTTCATGTTACTTCAAGCATTTTAAAATTTTAATTAATATTTTTAACAT
1 ACATTTGTATTTTTTATTTCATGTTGCTTCAAGC-TTTT-AAATTTTAATTAATATTTTTAACAT
* * * * * * * * * *
2426441 TTTAATTCTTTCGTTAGATAGTTAGATAGTCGTAAGTACATTCTTGAGTCTCGAGTCCGATTCCT
64 ATTAGTTCTTTCGTTAGATGGTTAGATAGTTGCAATTACATCCTTGAGTCTCAAGTCCAATTCAT
*
2426506 CTACTACTC
129 CTACGACTC
* *
2426515 ACATTTGTATTTTTTATTTCATGTTGCTTCAAG-TTTT---TTCTAATTAATATTTCTAACATAT
1 ACATTTGTATTTTTTATTTCATGTTGCTTCAAGCTTTTAAATTTTAATTAATATTTTTAACATAT
* * *
2426576 TAGCTTTTTTCGTTAGATGGTTAGATAATTGCTATTACATCCTTGAGT
66 TAG-TTCTTTCGTTAGATGGTTAGATAGTTGCAATTACATCCTTGAGT
2426624 ATGAGATTCC
Statistics
Matches: 208, Mismatches: 38, Indels: 9
0.82 0.15 0.04
Matches are distributed among these distances:
133 23 0.11
134 36 0.17
137 4 0.02
139 141 0.68
140 4 0.02
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.48
Consensus pattern (137 bp):
ACATTTGTATTTTTTATTTCATGTTGCTTCAAGCTTTTAAATTTTAATTAATATTTTTAACATAT
TAGTTCTTTCGTTAGATGGTTAGATAGTTGCAATTACATCCTTGAGTCTCAAGTCCAATTCATCT
ACGACTC
Found at i:2444377 original size:2 final size:2
Alignment explanation
Indices: 2444370--2444403 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2444360 AACAAGTATC
2444370 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2444404 GAATGCCGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2457534 original size:28 final size:28
Alignment explanation
Indices: 2457442--2457535 Score: 71
Period size: 28 Copynumber: 3.2 Consensus size: 28
2457432 AATTGAACCT
*
2457442 AAAAAAAACTTAGGTACCAAATTAGGAA
1 AAAAAAAATTTAGGTACCAAATTAGGAA
** * * * **
2457470 AAAAATGCCAGGTTCAGGTGCCAAATTGGGCC
1 AAAAA----AAATTTAGGTACCAAATTAGGAA
*
2457502 CAAAAAAATTTAGGTACCAAATTAGGAA
1 AAAAAAAATTTAGGTACCAAATTAGGAA
2457530 AAAAAA
1 AAAAAA
2457536 TGTAAAGTTT
Statistics
Matches: 45, Mismatches: 17, Indels: 8
0.64 0.24 0.11
Matches are distributed among these distances:
28 26 0.58
32 19 0.42
ACGTcount: A:0.50, C:0.14, G:0.18, T:0.18
Consensus pattern (28 bp):
AAAAAAAATTTAGGTACCAAATTAGGAA
Found at i:2457555 original size:61 final size:60
Alignment explanation
Indices: 2457443--2457556 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
2457433 ATTGAACCTA
* *
2457443 AAAAAAACTTAGGTACCAAATTAGGAAAAAAATGCCAGGTTCAGGTGCCAAATTGGGCCC
1 AAAAAAACTTAGGTACCAAATTAGGAAAAAAATGCAAAGTTCAGGTGCCAAATTGGGCCC
* * * *
2457503 AAAAAAATTTAGGTACCAAATTAGGAAAAAAAATGTAAAGTTTAGGTTCCAAAT
1 AAAAAAACTTAGGTACCAAATTAGG-AAAAAAATGCAAAGTTCAGGTGCCAAAT
2457557 GTTATATTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
60 24 0.51
61 23 0.49
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.22
Consensus pattern (60 bp):
AAAAAAACTTAGGTACCAAATTAGGAAAAAAATGCAAAGTTCAGGTGCCAAATTGGGCCC
Found at i:2467250 original size:9 final size:9
Alignment explanation
Indices: 2467236--2467281 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
2467226 TTTCATTTTC
2467236 TTATAATTT
1 TTATAATTT
2467245 TTATAATGTT
1 TTATAAT-TT
*
2467255 TTACAATTT
1 TTATAATTT
* *
2467264 TTAAAAGTT
1 TTATAATTT
2467273 TTATAATTT
1 TTATAATTT
2467282 AAAAATTACA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
9 23 0.74
10 8 0.26
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (9 bp):
TTATAATTT
Found at i:2467870 original size:51 final size:51
Alignment explanation
Indices: 2467807--2467904 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 51
2467797 ATTTTTTGAT
* * * **
2467807 TTTTTTAGAATTAGGATTAAATTGATATCATTTGTAAATTTTGAGGGTTAA
1 TTTTTTAAAATTAGGATTAAATTGATATAATATGTAAAAGTTGAGGGTTAA
* *
2467858 TTTTTTAAAATTATGATTCAATTGATATAATATGTAAAAGTTGAGGG
1 TTTTTTAAAATTAGGATTAAATTGATATAATATGTAAAAGTTGAGGG
2467905 CTAAATTTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.45
Consensus pattern (51 bp):
TTTTTTAAAATTAGGATTAAATTGATATAATATGTAAAAGTTGAGGGTTAA
Found at i:2484446 original size:22 final size:22
Alignment explanation
Indices: 2484421--2484466 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
2484411 CCAACTATTC
2484421 CAACATGAACCTCCAATATCAT
1 CAACATGAACCTCCAATATCAT
*
2484443 CAACATGGACCTCCAATATCAT
1 CAACATGAACCTCCAATATCAT
2484465 CA
1 CA
2484467 TTCTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.33, G:0.07, T:0.22
Consensus pattern (22 bp):
CAACATGAACCTCCAATATCAT
Found at i:2492918 original size:11 final size:11
Alignment explanation
Indices: 2492894--2492942 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
2492884 TTAAAAAATA
*
2492894 AAAAAATTTC-
1 AAAAAATATCT
2492904 AAAAAATATCT
1 AAAAAATATCT
*
2492915 AAAAAATATAT
1 AAAAAATATCT
2492926 AAAGAAA-AT-T
1 AAA-AAATATCT
2492936 AAAAAAT
1 AAAAAAT
2492943 TAAAAATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 3 0.09
10 13 0.38
11 15 0.44
12 3 0.09
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.24
Consensus pattern (11 bp):
AAAAAATATCT
Found at i:2493115 original size:15 final size:16
Alignment explanation
Indices: 2493088--2493117 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2493078 TTATATTGTA
2493088 ACAATATTTTAATTTG
1 ACAATATTTTAATTTG
2493104 ACAATA-TTTAATTT
1 ACAATATTTTAATTT
2493118 TTTTAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (16 bp):
ACAATATTTTAATTTG
Found at i:2501975 original size:22 final size:23
Alignment explanation
Indices: 2501940--2501989 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
2501930 AAATACTTTA
* *
2501940 AAAATATTTTTTTTTTATTTTTT
1 AAAATATTTTTTTTGTATTTATT
*
2501963 AAAATA-TTTTTTTGTGTTTATT
1 AAAATATTTTTTTTGTATTTATT
2501985 AAAAT
1 AAAAT
2501990 TCGGGCCGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (23 bp):
AAAATATTTTTTTTGTATTTATT
Found at i:2509252 original size:20 final size:20
Alignment explanation
Indices: 2509216--2509253 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2509206 ACAACACACG
*
2509216 GCCATGAAGAAGGAAAAGAA
1 GCCATGAAGAAGAAAAAGAA
2509236 GCCAT-AAGAGAGAAAAAG
1 GCCATGAAGA-AGAAAAAG
2509254 GAATATGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.55, C:0.11, G:0.29, T:0.05
Consensus pattern (20 bp):
GCCATGAAGAAGAAAAAGAA
Found at i:2515988 original size:9 final size:9
Alignment explanation
Indices: 2515976--2516016 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
2515966 TCAATTTGGT
2515976 TAATTCGGG
1 TAATTCGGG
*
2515985 TAATTCGGT
1 TAATTCGGG
2515994 TAATTCGGG
1 TAATTCGGG
*
2516003 TAATTCGGT
1 TAATTCGGG
2516012 TAATT
1 TAATT
2516017 TTTAACCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.41
Consensus pattern (9 bp):
TAATTCGGG
Found at i:2515994 original size:18 final size:18
Alignment explanation
Indices: 2515968--2516016 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
2515958 GTAGTGATTC
*
2515968 AATTTGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
2515986 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
2516004 AATTCGGTTAATT
1 AATTCGGTTAATT
2516017 TTTAACCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.43
Consensus pattern (18 bp):
AATTCGGTTAATTCGGGT
Found at i:2517462 original size:14 final size:14
Alignment explanation
Indices: 2517443--2517475 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2517433 TCAAAAGCAA
2517443 AGAGAAAAAGAGAG
1 AGAGAAAAAGAGAG
*
2517457 AGAGAAAGAGAGAG
1 AGAGAAAAAGAGAG
2517471 AGAGA
1 AGAGA
2517476 GGTGACAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (14 bp):
AGAGAAAAAGAGAG
Found at i:2517472 original size:12 final size:12
Alignment explanation
Indices: 2517443--2517473 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2517433 TCAAAAGCAA
*
2517443 AGAGAAAAAGAG
1 AGAGAGAAAGAG
2517455 AGAGAGAAAGAG
1 AGAGAGAAAGAG
2517467 AGAGAGA
1 AGAGAGA
2517474 GAGGTGACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (12 bp):
AGAGAGAAAGAG
Found at i:2517850 original size:15 final size:16
Alignment explanation
Indices: 2517827--2517859 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2517817 CTTTATTTTT
*
2517827 TTTTTATTT-TGTTCA
1 TTTTGATTTATGTTCA
2517842 TTTTGATTTATGTTCA
1 TTTTGATTTATGTTCA
2517858 TT
1 TT
2517860 AAAATTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.15, C:0.06, G:0.09, T:0.70
Consensus pattern (16 bp):
TTTTGATTTATGTTCA
Found at i:2519833 original size:3 final size:3
Alignment explanation
Indices: 2519825--2519867 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
2519815 TAACGTCAGC
2519825 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2519868 CGTCCTCGTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2529920 original size:13 final size:13
Alignment explanation
Indices: 2529904--2529934 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2529894 TTTATTTTTC
2529904 TAATTTTGATATG
1 TAATTTTGATATG
2529917 TAATTTTGATATG
1 TAATTTTGATATG
*
2529930 CAATT
1 TAATT
2529935 ATATCATCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.13, T:0.52
Consensus pattern (13 bp):
TAATTTTGATATG
Found at i:2537672 original size:2 final size:2
Alignment explanation
Indices: 2537665--2537699 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2537655 TTTACTTTAT
2537665 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2537700 TAGCAATTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2539850 original size:18 final size:18
Alignment explanation
Indices: 2539811--2539870 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
2539801 AAAATTACAA
*
2539811 AAAATTCAAAATAATTTTT
1 AAAATTCAAAAT-ATTTAT
2539830 AAAATTCAAAATATTTAT
1 AAAATTCAAAATATTTAT
* *
2539848 AAAAATTCTAAAACATATAT
1 -AAAATTC-AAAATATTTAT
2539868 AAA
1 AAA
2539871 GAAAGTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 5 0.14
19 22 0.61
20 9 0.25
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAATTCAAAATATTTAT
Found at i:2539868 original size:20 final size:19
Alignment explanation
Indices: 2539830--2539870 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
2539820 AATAATTTTT
* *
2539830 AAAATTCAAAATATTTATA
1 AAAATTCAAAACATATATA
2539849 AAAATTCTAAAACATATATA
1 AAAATTC-AAAACATATATA
2539869 AA
1 AA
2539871 GAAAGTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAATTCAAAACATATATA
Found at i:2545801 original size:22 final size:22
Alignment explanation
Indices: 2545776--2545824 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2545766 TGGTGTAAAA
*
2545776 TATATAAACAAATTAATGAAAT
1 TATATAAACAAATAAATGAAAT
* * *
2545798 TATAAAAATAAATAAATTAAAT
1 TATATAAACAAATAAATGAAAT
2545820 TATAT
1 TATAT
2545825 CAAAATTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (22 bp):
TATATAAACAAATAAATGAAAT
Found at i:2547015 original size:274 final size:274
Alignment explanation
Indices: 2546521--2547348 Score: 1647
Period size: 274 Copynumber: 3.0 Consensus size: 274
2546511 GGTAGACTTG
*
2546521 TAGGCCGGATTAGTTTACATGTTGATAATGTTCTGCTTTGGTGTTGTGGTATTATCTTAACTATT
1 TAGGTCGGATTAGTTTACATGTTGATAATGTTCTGCTTTGGTGTTGTGGTATTATCTTAACTATT
2546586 GTTGTAATATTACGAGTATTAATTTAAAAGTTGACAAATTTGAGTTATATGTTTTATTATTTGTT
66 GTTGTAATATTACGAGTATTAATTTAAAAGTTGACAAATTTGAGTTATATGTTTTATTATTTGTT
2546651 ATTTATTTTGAGATTATGAAATGAATATTAGGATTTGGTTTTCAATCAAATTTCATCATTACTTG
131 ATTTATTTTGAGATTATGAAATGAATATTAGGATTTGGTTTTCAATCAAATTTCATCATTACTTG
2546716 GAGGACTTATCCTGAAATAAGGGCAAATTTAAAGGGGTGAGTAAGCCTCCGATGCCCTTAAACTT
196 GAGGACTTATCCTGAAATAAGGGCAAATTTAAAGGGGTGAGTAAGCCTCCGATGCCCTTAAACTT
2546781 TTCAGATTATATTT
261 TTCAGATTATATTT
2546795 TAGGTCGGATTAGTTTACATGTTGATAATGTTCTGCTTTGGTGTTGTGGTATTATCTTAACTATT
1 TAGGTCGGATTAGTTTACATGTTGATAATGTTCTGCTTTGGTGTTGTGGTATTATCTTAACTATT
2546860 GTTGTAATATTACGAGTATTAATTTAAAAGTTGACAAATTTGAGTTATATGTTTTATTATTTGTT
66 GTTGTAATATTACGAGTATTAATTTAAAAGTTGACAAATTTGAGTTATATGTTTTATTATTTGTT
2546925 ATTTATTTTGAGATTATGAAATGAATATTAGGATTTGGTTTTCAATCAAATTTCATCATTACTTG
131 ATTTATTTTGAGATTATGAAATGAATATTAGGATTTGGTTTTCAATCAAATTTCATCATTACTTG
2546990 GAGGACTTATCCTGAAATAAGGGCAAATTTAAAGGGGTGAGTAAGCCTCCGATGCCCTTAAACTT
196 GAGGACTTATCCTGAAATAAGGGCAAATTTAAAGGGGTGAGTAAGCCTCCGATGCCCTTAAACTT
2547055 TTCAGATTATATTT
261 TTCAGATTATATTT
2547069 TAGGTCGGATTAGTTTACATGTTGATAATGTTCTGCTTTGGTGTTGTGGTATTATCTTAACTATT
1 TAGGTCGGATTAGTTTACATGTTGATAATGTTCTGCTTTGGTGTTGTGGTATTATCTTAACTATT
2547134 GTTGTAATATTACGAGTATTAATTTAAAAGTTGACAAATTTGAGTTATATGTTTTATTATTTGTT
66 GTTGTAATATTACGAGTATTAATTTAAAAGTTGACAAATTTGAGTTATATGTTTTATTATTTGTT
2547199 ATTTATTTTGAGATTATGAAATGAATATTAGGATTTGGTTTTCAATCAAATTTCATCATTACTTG
131 ATTTATTTTGAGATTATGAAATGAATATTAGGATTTGGTTTTCAATCAAATTTCATCATTACTTG
2547264 GAGGACTTATCCTGAAATAAGGGCAAATTTAAAGGGGTGAGTAAGCCTCCGATGCCCTTAAACTT
196 GAGGACTTATCCTGAAATAAGGGCAAATTTAAAGGGGTGAGTAAGCCTCCGATGCCCTTAAACTT
2547329 TTCAGATTATATTT
261 TTCAGATTATATTT
2547343 TAGGTC
1 TAGGTC
2547349 TTATGAATTT
Statistics
Matches: 553, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
274 553 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.43
Consensus pattern (274 bp):
TAGGTCGGATTAGTTTACATGTTGATAATGTTCTGCTTTGGTGTTGTGGTATTATCTTAACTATT
GTTGTAATATTACGAGTATTAATTTAAAAGTTGACAAATTTGAGTTATATGTTTTATTATTTGTT
ATTTATTTTGAGATTATGAAATGAATATTAGGATTTGGTTTTCAATCAAATTTCATCATTACTTG
GAGGACTTATCCTGAAATAAGGGCAAATTTAAAGGGGTGAGTAAGCCTCCGATGCCCTTAAACTT
TTCAGATTATATTT
Found at i:2547582 original size:21 final size:23
Alignment explanation
Indices: 2547556--2547598 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
2547546 TATTTAGATT
2547556 ATATTTTCAATTA-AT-TAAAAA
1 ATATTTTCAATTATATGTAAAAA
*
2547577 ATATTTTTAATTATATGTAAAA
1 ATATTTTCAATTATATGTAAAA
2547599 GTTAAAAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 2 0.11
23 5 0.26
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATATTTTCAATTATATGTAAAAA
Found at i:2549746 original size:52 final size:52
Alignment explanation
Indices: 2549668--2549768 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
2549658 GGAGTTAAGG
* *
2549668 GGGAGCATGTATATGAATGAGATTGTATGATATGCTTCTGAATCTGAATTAT
1 GGGAGCATGTATATGAATGAGATTGTATGACAAGCTTCTGAATCTGAATTAT
*
2549720 GGGAGTATGTATATGAATGAGATTGTATGACAAGCTTCTGAATCTGAAT
1 GGGAGCATGTATATGAATGAGATTGTATGACAAGCTTCTGAATCTGAAT
2549769 GAGCTATTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.35
Consensus pattern (52 bp):
GGGAGCATGTATATGAATGAGATTGTATGACAAGCTTCTGAATCTGAATTAT
Found at i:2551439 original size:14 final size:14
Alignment explanation
Indices: 2551420--2551448 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2551410 ATAGATAAGT
2551420 GTATGGGTATTCTA
1 GTATGGGTATTCTA
2551434 GTATGGGTATTCTA
1 GTATGGGTATTCTA
2551448 G
1 G
2551449 CTCAGTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.31, T:0.41
Consensus pattern (14 bp):
GTATGGGTATTCTA
Found at i:2551488 original size:2 final size:2
Alignment explanation
Indices: 2551481--2551516 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2551471 CTTTCGGATA
2551481 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
2551517 CAACAATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2556068 original size:40 final size:40
Alignment explanation
Indices: 2556019--2556158 Score: 142
Period size: 40 Copynumber: 3.5 Consensus size: 40
2556009 AACATACCAG
* * * *
2556019 TTTGGCACCCAGTGCCTCATCGGATAATTTGAAATAATAA
1 TTTGACACCCAATGCCTCATCGGATAATCTGAAGTAATAA
* * *
2556059 TTTGACACCCAATGTCTCATCGGCTAAACTGAAGT-A-AA
1 TTTGACACCCAATGCCTCATCGGATAATCTGAAGTAATAA
* * *
2556097 -TTGGCACCCAATGCCTCATCGAATATATCCGAAGTAATAA
1 TTTGACACCCAATGCCTCATCGGATA-ATCTGAAGTAATAA
* *
2556137 TTTGACACCCAGTGTCTCATCG
1 TTTGACACCCAATGCCTCATCG
2556159 ACTCGAAGTC
Statistics
Matches: 80, Mismatches: 16, Indels: 7
0.78 0.16 0.07
Matches are distributed among these distances:
37 21 0.26
38 9 0.11
39 2 0.03
40 30 0.38
41 18 0.22
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.28
Consensus pattern (40 bp):
TTTGACACCCAATGCCTCATCGGATAATCTGAAGTAATAA
Found at i:2557115 original size:5 final size:5
Alignment explanation
Indices: 2557105--2557194 Score: 102
Period size: 5 Copynumber: 19.0 Consensus size: 5
2557095 TCTTTATTAT
2557105 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATAT-
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* * *
2557154 ATATA CT-TA ATA-A TTA-A GATATA ATAT- -TATA TTATA ATATA
1 ATATA ATATA ATATA ATATA -ATATA ATATA ATATA ATATA ATATA
2557195 TATTTTAACT
Statistics
Matches: 74, Mismatches: 5, Indels: 12
0.81 0.05 0.13
Matches are distributed among these distances:
3 3 0.04
4 11 0.15
5 59 0.80
6 1 0.01
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:2565972 original size:40 final size:41
Alignment explanation
Indices: 2565923--2566021 Score: 128
Period size: 41 Copynumber: 2.4 Consensus size: 41
2565913 ACCAGTTTGG
* * *
2565923 CACCTAGTGCCTCATCGGA-TAATTCAAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGAATTAATCCAAAGTAATAAATTGA
* * *
2565963 CACTCAGTGCCTCATTGAATTAATCCAAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAATTAATCCAAAGTAATAAATTGA
*
2566004 CACCCAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
2566022 CTCGAAGTTG
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 15 0.31
41 34 0.69
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.27
Consensus pattern (41 bp):
CACCCAGTGCCTCATCGAATTAATCCAAAGTAATAAATTGA
Found at i:2566898 original size:27 final size:28
Alignment explanation
Indices: 2566858--2566925 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
2566848 CTTTCTCCAT
* *
2566858 TTTCTTTTTCTTTCTTTC-TTCTTTCTG
1 TTTCGTTTTCTTTCTATCTTTCTTTCTG
* *
2566885 TTTCGTTTTGTTTCTATCTTTCTTTCTT
1 TTTCGTTTTCTTTCTATCTTTCTTTCTG
2566913 TTTC-TATTTCTTT
1 TTTCGT-TTTCTTT
2566926 TTATTACTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 16 0.47
28 18 0.53
ACGTcount: A:0.03, C:0.19, G:0.04, T:0.74
Consensus pattern (28 bp):
TTTCGTTTTCTTTCTATCTTTCTTTCTG
Found at i:2567203 original size:23 final size:23
Alignment explanation
Indices: 2567177--2567224 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
2567167 TCACTTAACC
*
2567177 AAAACTTAATTAACTATACAACT
1 AAAACCTAATTAACTATACAACT
2567200 AAAACCTAATTAACTATACAACT
1 AAAACCTAATTAACTATACAACT
2567223 AA
1 AA
2567225 CTTCGTCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (23 bp):
AAAACCTAATTAACTATACAACT
Found at i:2567696 original size:22 final size:23
Alignment explanation
Indices: 2567668--2567713 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
2567658 TATAAAATTA
2567668 ATAAATATAAATT-AAAAATAAT
1 ATAAATATAAATTAAAAAATAAT
**
2567690 ATAAATATATTTTAAAAAATAAT
1 ATAAATATAAATTAAAAAATAAT
2567713 A
1 A
2567714 CGGATGGGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
ATAAATATAAATTAAAAAATAAT
Found at i:2568260 original size:16 final size:15
Alignment explanation
Indices: 2568220--2568260 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
2568210 TTTTAATTTT
2568220 ATTTT-AATAATAAA
1 ATTTTAAATAATAAA
2568234 A-TTTAAA-AATAATA
1 ATTTTAAATAATAA-A
2568248 ATTTTAAATAATA
1 ATTTTAAATAATA
2568261 TTCTTCGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 8 0.35
14 5 0.22
15 6 0.26
16 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTTTAAATAATAAA
Found at i:2568649 original size:32 final size:34
Alignment explanation
Indices: 2568613--2568684 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
2568603 AGCTTTTATG
*
2568613 AAATATTTTTA-AAAAATTTGT-CAAACAACAGA
1 AAATATTTTTACAAAAATTTATCCAAACAACAGA
* *
2568645 AAATA-TTTTACACAAATTTATCCAAACACCAGA
1 AAATATTTTTACAAAAATTTATCCAAACAACAGA
2568678 AAATATT
1 AAATATT
2568685 AACTTTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 5 0.15
32 13 0.38
33 15 0.44
34 1 0.03
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.31
Consensus pattern (34 bp):
AAATATTTTTACAAAAATTTATCCAAACAACAGA
Found at i:2584577 original size:32 final size:31
Alignment explanation
Indices: 2584522--2584596 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 31
2584512 TCTGAACTTG
*
2584522 AAATTGACCCAAACCTGAATGACCCGGAGTCA
1 AAATTGACCCAAACCTGAATGACCCAGA-TCA
*
2584554 AAATTGACCCAAA-CTGGAGTGACCCAGATCA
1 AAATTGACCCAAACCT-GAATGACCCAGATCA
*
2584585 AAACTTAACCCA
1 AAA-TTGACCCA
2584597 TCCTGCTCGA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 8 0.21
32 30 0.79
ACGTcount: A:0.40, C:0.28, G:0.16, T:0.16
Consensus pattern (31 bp):
AAATTGACCCAAACCTGAATGACCCAGATCA
Found at i:2589108 original size:18 final size:20
Alignment explanation
Indices: 2589085--2589129 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
2589075 TTTCAAATTT
**
2589085 TAAAAAT-ATTTTTAAAG-A
1 TAAAAATAATTTAAAAAGTA
2589103 TAAAAATAATTTAAAAAGTA
1 TAAAAATAATTTAAAAAGTA
2589123 TAAAAAT
1 TAAAAAT
2589130 TGTAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 8 0.35
20 8 0.35
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (20 bp):
TAAAAATAATTTAAAAAGTA
Found at i:2592786 original size:26 final size:27
Alignment explanation
Indices: 2592757--2592807 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
2592747 GGTTTGGGAT
*
2592757 TTTGGATTTGAG-TTCATGTTTCAAGG
1 TTTGGATTTGAGACTCATGTTTCAAGG
* *
2592783 TTTGGGTTTGGGACTCATGTTTCAA
1 TTTGGATTTGAGACTCATGTTTCAA
2592808 AGTTCAGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 10 0.48
27 11 0.52
ACGTcount: A:0.18, C:0.10, G:0.27, T:0.45
Consensus pattern (27 bp):
TTTGGATTTGAGACTCATGTTTCAAGG
Found at i:2593276 original size:43 final size:43
Alignment explanation
Indices: 2593223--2593451 Score: 306
Period size: 43 Copynumber: 5.3 Consensus size: 43
2593213 ACGTCGCTAA
* *
2593223 CTTTTGCGGCGCTTACAGAAAAAAACG-CGCTAAAGAACATGTT
1 CTTTAGCGGCGCTTA-AGAAAAAAACGCCGCTAAAGATCATGTT
2593266 CTTTAGCGGCGC-TAAGAAAATAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAAGAAAA-AAACGCCGCTAAAGATCATGTT
* *
2593309 CTTTAGCGGCGCTT-AGGAAAAAACGCCGCTAAAGATCATATT
1 CTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATGTT
* *
2593351 CTTTAGCGGCGCTTAGGAAGAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATGTT
** *
2593394 CTTTAGCGGCGCTTGGGAAGAAAACGCCGCTAAA-AGT-AGTGTT
1 CTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGA-TCA-TGTT
2593437 CTTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTA
2593452 TTTCACAAAC
Statistics
Matches: 170, Mismatches: 10, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
41 6 0.04
42 44 0.26
43 119 0.70
44 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (43 bp):
CTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATGTT
Found at i:2593342 original size:85 final size:84
Alignment explanation
Indices: 2593223--2593449 Score: 305
Period size: 85 Copynumber: 2.7 Consensus size: 84
2593213 ACGTCGCTAA
* *
2593223 CTTTTGCGGCGCTTACAGAAAAAAACG-CGCTAAAGAACATGTTCTTTAGCGGCGCTAAGAAAAT
1 CTTTAGCGGCGCTT--AGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTAAGAAAA-
2593287 AAACGCCGCTAAAGATCATGTT
63 AAACGCCGCTAAAGATCATGTT
* * * *
2593309 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATATTCTTTAGCGGCGCTTAGGAAGAAA
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGC-TAAGAAAAAA
2593374 ACGCCGCTAAAGATCATGTT
65 ACGCCGCTAAAGATCATGTT
* * *
2593394 CTTTAGCGGCGCTTGGGAAGAAAACGCCGCTAAAAGTA-GTGTTCTTTAGCGGCGCT
1 CTTTAGCGGCGCTTAGGAA-AAAACGCCGCT-AAAGAACATGTTCTTTAGCGGCGCT
2593450 TATTTCACAA
Statistics
Matches: 126, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
84 10 0.08
85 67 0.53
86 45 0.36
87 4 0.03
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (84 bp):
CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTAAGAAAAAAA
CGCCGCTAAAGATCATGTT
Done.