Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, 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: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 15 of 125
Found at i:2441728 original size:6 final size:6
Alignment explanation
Indices: 2441712--2441740 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2441702 TATGAATTAA
2441712 TTAAA- TTAAAT TTAAAT TTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
2441741 ATGATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TTAAAT
Found at i:2444750 original size:24 final size:24
Alignment explanation
Indices: 2444723--2444770 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2444713 TTACCTTCTC
2444723 GATCTGATCATTGCTACCGTTGTT
1 GATCTGATCATTGCTACCGTTGTT
2444747 GATCTGATCATTGCTACCGTTGTT
1 GATCTGATCATTGCTACCGTTGTT
2444771 CTCGCCATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.42
Consensus pattern (24 bp):
GATCTGATCATTGCTACCGTTGTT
Found at i:2445365 original size:12 final size:12
Alignment explanation
Indices: 2445347--2445395 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
2445337 AAGGGTTTGG
2445347 GGAGGAAGAGAT
1 GGAGGAAGAGAT
* *
2445359 AGAGGAAGGGAT
1 GGAGGAAGAGAT
2445371 GGAGGAA-AGGAT
1 GGAGGAAGA-GAT
2445383 GGAGGAAAGAGAT
1 GGAGG-AAGAGAT
2445396 TGGATGGATG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
12 24 0.80
13 5 0.17
14 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.49, T:0.08
Consensus pattern (12 bp):
GGAGGAAGAGAT
Found at i:2451523 original size:94 final size:99
Alignment explanation
Indices: 2451377--2451558 Score: 257
Period size: 96 Copynumber: 1.9 Consensus size: 99
2451367 CTTTTTGAGT
* * * *
2451377 ATTTTTCAATACAACTGAGTTTTTGGAAAACAATTAAAAAAAGACAACAATTCTTAAAC-AAGTA
1 ATTTTCCAATACAACTGAGCTTTCGGAAAACAATTAAAAAAAGACAACAATTCTCAAACAAAGTA
2451441 ACCTGCTATA-AATTGAGTCTGGTAACGTCGAGA
66 ACCTGCTATAGAATTGAGTCTGGTAACGTCGAGA
* *
2451474 ATTTTCCAATACAA-TGAGCTTTCGGAAAACAA-T-GAAAAAGACTACAATTCTCAAACAAAAGT
1 ATTTTCCAATACAACTGAGCTTTCGGAAAACAATTAAAAAAAGACAACAATTCTCAAAC-AAAGT
*
2451536 AACCTGCTATAGATTTGAGTCTG
65 AACCTGCTATAGAATTGAGTCTG
2451559 TCGCTATCGT
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
94 20 0.27
95 1 0.01
96 31 0.41
97 23 0.31
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (99 bp):
ATTTTCCAATACAACTGAGCTTTCGGAAAACAATTAAAAAAAGACAACAATTCTCAAACAAAGTA
ACCTGCTATAGAATTGAGTCTGGTAACGTCGAGA
Found at i:2453869 original size:6 final size:6
Alignment explanation
Indices: 2453858--2453885 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2453848 AGTTCTTGAC
2453858 AAAATA AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAA
2453886 ATTTGGTGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:2454952 original size:23 final size:21
Alignment explanation
Indices: 2454900--2454966 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 21
2454890 CTAAAGCGAA
2454900 TGTAAATGGAAATGATTGTCTGT
1 TGTAAATGGAAATGATTG-CT-T
* *
2454923 TGCAAATGGCAATGATTGCTT
1 TGTAAATGGAAATGATTGCTT
*
2454944 ACTGTAAATGAAAATGATTGCTT
1 --TGTAAATGGAAATGATTGCTT
2454967 GAATCTTTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 2 0.05
23 34 0.92
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.36
Consensus pattern (21 bp):
TGTAAATGGAAATGATTGCTT
Found at i:2464275 original size:59 final size:59
Alignment explanation
Indices: 2464195--2464311 Score: 171
Period size: 59 Copynumber: 2.0 Consensus size: 59
2464185 ATATTGTTTG
* * * *
2464195 GAATATTAACCATCAACTGCCTCACATAACAGCAATTTCAGGTCGTATGATCAATTTTA
1 GAATATTAACAATCAAATGCCTCACATAACACCAATTTCAAGTCGTATGATCAATTTTA
* * *
2464254 GAATATTGACAATCAAATGCCTCACATAACACCAATTTCAAGTCTTATGATCTATTTT
1 GAATATTAACAATCAAATGCCTCACATAACACCAATTTCAAGTCGTATGATCAATTTT
2464312 TCTTTCTTTG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.32
Consensus pattern (59 bp):
GAATATTAACAATCAAATGCCTCACATAACACCAATTTCAAGTCGTATGATCAATTTTA
Found at i:2479243 original size:15 final size:15
Alignment explanation
Indices: 2479223--2479267 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
2479213 TTTGATTCTC
2479223 ATTTGATTCTAATTA
1 ATTTGATTCTAATTA
* *
2479238 ATTTGATTATACTTA
1 ATTTGATTCTAATTA
2479253 ATTTGATTCTAATTA
1 ATTTGATTCTAATTA
2479268 CTTCTCCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (15 bp):
ATTTGATTCTAATTA
Found at i:2480190 original size:142 final size:140
Alignment explanation
Indices: 2480035--2480292 Score: 401
Period size: 142 Copynumber: 1.8 Consensus size: 140
2480025 TATTTGATTT
* * * * *
2480035 ATTTATATTTGATTAAATATAATATTCATTTGAGTAATTGACT-TATTTCATGTGTGAATATAGA
1 ATTTATATTTGATTAAATAGAACATCCATTTGAGTAATTGA-TGTATTTCATGTGTAAATATAAA
2480099 AAGTAAATATATCAAATGAATTCTCCATAATTAAATTAATAGAATAAAATATTTTATTAATTTAT
65 AAGTAAATATATCAAATGAATTCTCCATAATTAAATTAAT-GAA-AAAATATTTTATTAATTTAT
2480164 ATTTGATTGACAC
128 ATTTGATTGACAC
* *
2480177 ATTTATATTTGATTAGATAGAGCATCCATTTGAGTAATTGATGTATTTCATGTGTAAATATAAAA
1 ATTTATATTTGATTAAATAGAACATCCATTTGAGTAATTGATGTATTTCATGTGTAAATATAAAA
* *
2480242 AGTAATTATATCAAATTAATTCTCCATAATTAAATTAATGAAAAAATATTT
66 AGTAAATATATCAAATGAATTCTCCATAATTAAATTAATGAAAAAATATTT
2480293 AATTGACAGA
Statistics
Matches: 106, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
140 9 0.08
141 4 0.04
142 93 0.88
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.42
Consensus pattern (140 bp):
ATTTATATTTGATTAAATAGAACATCCATTTGAGTAATTGATGTATTTCATGTGTAAATATAAAA
AGTAAATATATCAAATGAATTCTCCATAATTAAATTAATGAAAAAATATTTTATTAATTTATATT
TGATTGACAC
Found at i:2480807 original size:142 final size:142
Alignment explanation
Indices: 2480517--2480778 Score: 337
Period size: 142 Copynumber: 1.9 Consensus size: 142
2480507 TCTCAATTAA
* * * * **
2480517 ATTTTTTTTCATTAATTTAATTATAAAGAATTAATTTGATATAGTTACTTTTTATATTTACACAC
1 ATTTTATTCCATTAATTTAACTATAAAGAATTAATTTAATATAGTTACTTTCAATATTTACACAC
* ** * * *
2480582 GAGATATGTCAATTGCTCAAATGGATACTATATTTAATCAAATATAAATTTATCAATCAAATATA
66 GAAATACATCAATTACTCAAATGGATACTACATTTAATCAAATATAAATGTATCAATCAAATATA
*
2480647 AATTAACAAAAT
131 AATGAACAAAAT
* * * *
2480659 ATTTTATTCCATTAATTTAACTATAGAGAATTAATTTAATATATTTGCTTTCAATATTTACACAT
1 ATTTTATTCCATTAATTTAACTATAAAGAATTAATTTAATATAGTTACTTTCAATATTTACACAC
* * *
2480724 TAAATACATCAATTACTCAAAT-GATGCTGCATTTAATCAAATATAAATGTATCAA
66 GAAATACATCAATTACTCAAATGGATACTACATTTAATCAAATATAAATGTATCAA
2480779 ATAATTGATT
Statistics
Matches: 101, Mismatches: 19, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
141 29 0.29
142 72 0.71
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.42
Consensus pattern (142 bp):
ATTTTATTCCATTAATTTAACTATAAAGAATTAATTTAATATAGTTACTTTCAATATTTACACAC
GAAATACATCAATTACTCAAATGGATACTACATTTAATCAAATATAAATGTATCAATCAAATATA
AATGAACAAAAT
Found at i:2481076 original size:22 final size:22
Alignment explanation
Indices: 2481050--2481092 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2481040 ATAAATACCC
2481050 TATATTTCTATGTATAATTATA
1 TATATTTCTATGTATAATTATA
* *
2481072 TATATTTTTGTGTATAATTAT
1 TATATTTCTATGTATAATTAT
2481093 TAAAATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (22 bp):
TATATTTCTATGTATAATTATA
Found at i:2483584 original size:2 final size:2
Alignment explanation
Indices: 2483577--2483622 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
2483567 CCAAACATAC
* *
2483577 AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AC 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
2483619 AT AT
1 AT AT
2483623 GTTGATAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2493544 original size:16 final size:16
Alignment explanation
Indices: 2493525--2493555 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2493515 TTTCTTATAT
*
2493525 TATTATTTTTTAAAAC
1 TATTATTTATTAAAAC
2493541 TATTATTTATTAAAA
1 TATTATTTATTAAAA
2493556 TTTATTATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTATTTATTAAAAC
Found at i:2494144 original size:165 final size:166
Alignment explanation
Indices: 2493923--2494230 Score: 406
Period size: 165 Copynumber: 1.9 Consensus size: 166
2493913 TTACATTAAA
** * *
2493923 CACAATAGACTTTTAGTTACCTATTTTTTTAATAAATTTCTGACTTTTGGTTTTCTTTTATTTAT
1 CACAATAGACTTTTAGTTACCTAACTTTTTAATAAATTTCTGACTTTTGATTTTCTTCTATTTAT
* *
2493988 G-TTCTTTAAA-ATCGTTATTTGTTAAAATTTATAG-AAATTTTTATTTTTCTAATATTAATATT
66 GTTTC-TTAAATATCATTATTTGTTAAAATTTATAGTAAATTTTT-GTTTTCTAATATTAATATT
*
2494050 TTTTATTATTAATTTTCTTATGATTTATAATTTTTCAT
129 TTTTACTATTAATTTTCTTATGATTTATAATTTTTCAT
* * ** **
2494088 CACAATAGACTTTTTGTTATCTAACTTTTTAATGGATTTCTGGTTTTTGATTTTCTTCTATTTAT
1 CACAATAGACTTTTAGTTACCTAACTTTTTAATAAATTTCTGACTTTTGATTTTCTTCTATTTAT
* * * * *
2494153 GTTTCTTAAATTTTATTATTTGTTAAAATTTATTGTAACTTTTTGTTTTCTAATATTAATGTTTT
66 GTTTCTTAAATATCATTATTTGTTAAAATTTATAGTAAATTTTTGTTTTCTAATATTAATATTTT
*
2494218 TTACTATTGATTT
131 TTACTATTAATTT
2494231 GTTAAAATTT
Statistics
Matches: 121, Mismatches: 19, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
165 61 0.50
166 53 0.44
167 7 0.06
ACGTcount: A:0.26, C:0.08, G:0.07, T:0.58
Consensus pattern (166 bp):
CACAATAGACTTTTAGTTACCTAACTTTTTAATAAATTTCTGACTTTTGATTTTCTTCTATTTAT
GTTTCTTAAATATCATTATTTGTTAAAATTTATAGTAAATTTTTGTTTTCTAATATTAATATTTT
TTACTATTAATTTTCTTATGATTTATAATTTTTCAT
Found at i:2494666 original size:23 final size:23
Alignment explanation
Indices: 2494640--2494700 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
2494630 AAAGAAAAAA
*
2494640 TAAAAACAAATAGTTAAGTCTGT
1 TAAAAATAAATAGTTAAGTCTGT
* * *
2494663 TAAAAATAGAGAGCTAAGTCTGT
1 TAAAAATAAATAGTTAAGTCTGT
*
2494686 TCAAAATAAATAGTT
1 TAAAAATAAATAGTT
2494701 TCAACTGTTC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.30
Consensus pattern (23 bp):
TAAAAATAAATAGTTAAGTCTGT
Found at i:2506126 original size:8 final size:8
Alignment explanation
Indices: 2506113--2506143 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
2506103 ATATAAGCAA
2506113 ACACACAG
1 ACACACAG
2506121 ACACACAG
1 ACACACAG
*
2506129 ACACACAA
1 ACACACAG
2506137 ACACACA
1 ACACACA
2506144 CACAACTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.55, C:0.39, G:0.06, T:0.00
Consensus pattern (8 bp):
ACACACAG
Found at i:2507777 original size:2 final size:2
Alignment explanation
Indices: 2507770--2507805 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2507760 ATCCATAAGA
2507770 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
2507806 TAAGAGATCT
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:2516414 original size:2 final size:2
Alignment explanation
Indices: 2516407--2516435 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2516397 GTAAGGTCAA
2516407 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2516436 AATACGGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2516688 original size:25 final size:28
Alignment explanation
Indices: 2516660--2516712 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
2516650 TTATTAACTA
2516660 AATTAT-A-ATTTTAAT-ATAATAAAAT
1 AATTATAATATTTTAATAATAATAAAAT
* *
2516685 AATTTTAATATTTTTATAATAATAAAAT
1 AATTATAATATTTTAATAATAATAAAAT
2516713 TGAAATAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 5 0.22
26 1 0.04
27 7 0.30
28 10 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
AATTATAATATTTTAATAATAATAAAAT
Found at i:2518816 original size:22 final size:22
Alignment explanation
Indices: 2518788--2518962 Score: 88
Period size: 22 Copynumber: 8.0 Consensus size: 22
2518778 GATTGAAAAT
* *
2518788 TAAGTTATCATTGATTTATTAC
1 TAAGTTATCAATGATTTACTAC
* * * ** *
2518810 TATGTTATTAGTGATTTGTTAT
1 TAAGTTATCAATGATTTACTAC
* *
2518832 TAAATTATCAATGATTTACTAT
1 TAAGTTATCAATGATTTACTAC
*
2518854 TAAGTTATGAATGATTTACTAC
1 TAAGTTATCAATGATTTACTAC
* ** * *
2518876 TAAATTATTGATAATTTATTA-
1 TAAGTTATCAATGATTTACTAC
* *
2518897 TAAAGTTAT-AACTAATTTTCTA-
1 T-AAGTTATCAA-TGATTTACTAC
*
2518919 TGAAGTTATTAATGATTTACTA-
1 T-AAGTTATCAATGATTTACTAC
* * *
2518941 TAAAATTATTAATGATTAACTA
1 T-AAGTTATCAATGATTTACTA
2518963 ATTTACTACT
Statistics
Matches: 121, Mismatches: 29, Indels: 6
0.78 0.19 0.04
Matches are distributed among these distances:
21 2 0.02
22 117 0.97
23 2 0.02
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (22 bp):
TAAGTTATCAATGATTTACTAC
Found at i:2518861 original size:44 final size:43
Alignment explanation
Indices: 2518786--2518957 Score: 123
Period size: 44 Copynumber: 3.9 Consensus size: 43
2518776 TTGATTGAAA
* * * * *
2518786 ATTAAGTTATCATTGATTTATTACT-ATGTTATTAGTGATTTGTT
1 ATTAAATTATCAATGATTTACTA-TAAAGTTATTAATGATTT-TT
* * *
2518830 ATTAAATTATCAATGATTTACTATTAAGTTATGAATGATTTACT
1 ATTAAATTATCAATGATTTACTATAAAGTTATTAATGATTT-TT
* ** * * *
2518874 ACTAAATTATTGATAATTTATTATAAAGTTA-TAACTAATTTTCT
1 ATTAAATTATCAATGATTTACTATAAAGTTATTAA-TGATTTT-T
* * * *
2518918 ATGAAGTTATTAATGATTTACTATAAAATTATTAATGATT
1 ATTAAATTATCAATGATTTACTATAAAGTTATTAATGATT
2518958 AACTAATTTA
Statistics
Matches: 99, Mismatches: 25, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
43 3 0.03
44 93 0.94
45 3 0.03
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.48
Consensus pattern (43 bp):
ATTAAATTATCAATGATTTACTATAAAGTTATTAATGATTTTT
Found at i:2518877 original size:66 final size:66
Alignment explanation
Indices: 2518786--2518950 Score: 167
Period size: 66 Copynumber: 2.5 Consensus size: 66
2518776 TTGATTGAAA
* * ** * * *
2518786 ATTAAGTTATCATTGATTTATTACTATGTTATT-AGTGATTTGTTATTAAA-TTATCAA-TGATT
1 ATTAAGTTATCAATGATTTACTACTAAATTATTGA-TAATTTATTA-TAAAGTTAT-AACTAATT
2518848 TACT
63 TACT
* *
2518852 ATTAAGTTATGAATGATTTACTACTAAATTATTGATAATTTATTATAAAGTTATAACTAATTTTC
1 ATTAAGTTATCAATGATTTACTACTAAATTATTGATAATTTATTATAAAGTTATAACTAATTTAC
2518917 T
66 T
* *
2518918 ATGAAGTTATTAATGATTTACTA-TAAAATTATT
1 ATTAAGTTATCAATGATTTACTACT-AAATTATT
2518951 AATGATTAAC
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
65 7 0.08
66 76 0.90
67 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.48
Consensus pattern (66 bp):
ATTAAGTTATCAATGATTTACTACTAAATTATTGATAATTTATTATAAAGTTATAACTAATTTAC
T
Found at i:2519140 original size:22 final size:22
Alignment explanation
Indices: 2519112--2519194 Score: 85
Period size: 22 Copynumber: 3.7 Consensus size: 22
2519102 TAATAATTAG
*
2519112 CTATTAAGTTATCAATTATTTA
1 CTATTAAGTTATCAATGATTTA
*
2519134 CTATTAAGTTATCAACTGAATTA
1 CTATTAAGTTATCAA-TGATTTA
* * **
2519157 CAACTAAGTTATTTATGATTTA
1 CTATTAAGTTATCAATGATTTA
* *
2519179 TTATTAATTTATCAAT
1 CTATTAAGTTATCAAT
2519195 AAATTACCAT
Statistics
Matches: 47, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
22 31 0.66
23 16 0.34
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (22 bp):
CTATTAAGTTATCAATGATTTA
Found at i:2519164 original size:23 final size:22
Alignment explanation
Indices: 2519116--2519168 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
2519106 AATTAGCTAT
* * * *
2519116 TAAGTTATCAATTATTTACTAT
1 TAAGTTATCAATGAATTACAAC
2519138 TAAGTTATCAACTGAATTACAAC
1 TAAGTTATCAA-TGAATTACAAC
2519161 TAAGTTAT
1 TAAGTTAT
2519169 TTATGATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.42
Consensus pattern (22 bp):
TAAGTTATCAATGAATTACAAC
Found at i:2519167 original size:45 final size:44
Alignment explanation
Indices: 2519116--2519201 Score: 109
Period size: 45 Copynumber: 1.9 Consensus size: 44
2519106 AATTAGCTAT
* *
2519116 TAAGTTATCAATTATTTACTATTAAGTTATCAACTGAATTACAAC
1 TAAGTTATCAATGATTTACTATTAAGTTATCAA-TAAATTACAAC
** * *
2519161 TAAGTTATTTATGATTTATTATTAATTTATCAATAAATTAC
1 TAAGTTATCAATGATTTACTATTAAGTTATCAATAAATTAC
2519202 CATATATGAG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
44 7 0.20
45 28 0.80
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (44 bp):
TAAGTTATCAATGATTTACTATTAAGTTATCAATAAATTACAAC
Found at i:2519470 original size:22 final size:21
Alignment explanation
Indices: 2519445--2519584 Score: 97
Period size: 22 Copynumber: 6.4 Consensus size: 21
2519435 CCTATCATTT
*
2519445 ATTTACTACTAAATTATCATCA
1 ATTTACTACTAAATTATGAT-A
* *
2519467 ATTTA-TCACTAAGTTATAGATG
1 ATTTACT-ACTAAATTAT-GATA
*
2519489 ATTTACTACTGAATTATTGATA
1 ATTTACTACTAAATTA-TGATA
* *
2519511 ATTTACTATTAAGTTATAGATA
1 ATTTACTACTAAATTAT-GATA
* * *
2519533 ATATATTA-TAAAGTTATTATTA
1 ATTTACTACTAAA-TTATGA-TA
2519555 ATTTACTA-TGAAATTATTGATA
1 ATTTACTACT-AAATTA-TGATA
2519577 ATTTACTA
1 ATTTACTA
2519585 TGAAATTTTT
Statistics
Matches: 93, Mismatches: 16, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
21 6 0.06
22 78 0.84
23 9 0.10
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (21 bp):
ATTTACTACTAAATTATGATA
Found at i:2519493 original size:44 final size:44
Alignment explanation
Indices: 2519445--2519601 Score: 119
Period size: 44 Copynumber: 3.6 Consensus size: 44
2519435 CCTATCATTT
2519445 ATTTACTACTAAATTA-TCATCAATTTA-TCACTAAGTTATAGATG
1 ATTTACTACTAAATTATTCAT-AATTTACT-ACTAAGTTATAGATG
* * * *
2519489 ATTTACTACTGAATTATTGATAATTTACTATTAAGTTATAGATA
1 ATTTACTACTAAATTATTCATAATTTACTACTAAGTTATAGATG
* * * * *
2519533 ATATATTA-TAAAGTTATT-ATTAATTTACTA-TGAAATTATTGATA
1 ATTTACTACTAAA-TTATTCA-TAATTTACTACT-AAGTTATAGATG
* *
2519577 ATTTACTA-TGAAATTTTTAATAATT
1 ATTTACTACT-AAATTATTCATAATT
2519602 AATTAATTTA
Statistics
Matches: 94, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
43 5 0.05
44 81 0.86
45 8 0.09
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (44 bp):
ATTTACTACTAAATTATTCATAATTTACTACTAAGTTATAGATG
Found at i:2519515 original size:66 final size:66
Alignment explanation
Indices: 2519445--2519584 Score: 153
Period size: 66 Copynumber: 2.1 Consensus size: 66
2519435 CCTATCATTT
* *
2519445 ATTTACTACTAAATTAT-CATCAATTTATCACT-AAGTTA-TAGATGATTTACTACTG-AATTAT
1 ATTTACTACTAAATTATACAT-AATATATCA-TAAAGTTATTA-ATAATTTACTA-TGAAATTAT
2519506 TGATA
62 TGATA
* * * * *
2519511 ATTTACTATTAAGTTATAGATAATATATTATAAAGTTATTATTAATTTACTATGAAATTATTGAT
1 ATTTACTACTAAATTATACATAATATATCATAAAGTTATTAATAATTTACTATGAAATTATTGAT
2519576 A
66 A
2519577 ATTTACTA
1 ATTTACTA
2519585 TGAAATTTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
65 3 0.05
66 56 0.89
67 4 0.06
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (66 bp):
ATTTACTACTAAATTATACATAATATATCATAAAGTTATTAATAATTTACTATGAAATTATTGAT
A
Found at i:2519585 original size:22 final size:22
Alignment explanation
Indices: 2519480--2519601 Score: 115
Period size: 22 Copynumber: 5.5 Consensus size: 22
2519470 TATCACTAAG
* *
2519480 TTATAGATGATTTACTACTG-AA
1 TTATTGATAATTTACTA-TGAAA
* *
2519502 TTATTGATAATTTACTATTAAG
1 TTATTGATAATTTACTATGAAA
* * *
2519524 TTATAGATAATATATTAT-AAA
1 TTATTGATAATTTACTATGAAA
2519545 GTTATT-ATTAATTTACTATGAAA
1 -TTATTGA-TAATTTACTATGAAA
2519568 TTATTGATAATTTACTATGAAA
1 TTATTGATAATTTACTATGAAA
* *
2519590 TTTTTAATAATT
1 TTATTGATAATT
2519602 AATTAATTTA
Statistics
Matches: 82, Mismatches: 13, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
21 4 0.05
22 74 0.90
23 4 0.05
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (22 bp):
TTATTGATAATTTACTATGAAA
Found at i:2519641 original size:22 final size:22
Alignment explanation
Indices: 2519607--2519743 Score: 75
Period size: 22 Copynumber: 6.2 Consensus size: 22
2519597 TAATTAATTA
* *
2519607 ATTTACAACTAAATTATCA-TT
1 ATTTATAACTAAATTATCACTG
* *
2519628 ATATTATAATTAAATCATCACTG
1 AT-TTATAACTAAATTATCACTG
* *
2519651 ATTTATAACTAAGTTATCAATG
1 ATTTATAACTAAATTATCACTG
* ** *
2519673 ATTTATTA-TGACGTTAGT-AGTG
1 ATTTATAACT-AAATTA-TCACTG
* * *
2519695 ATTTATTACTAAATTATCAATA
1 ATTTATAACTAAATTATCACTG
* *
2519717 ATTTACT-ATTAAATTATCAATG
1 ATTTA-TAACTAAATTATCACTG
2519739 ATTTA
1 ATTTA
2519744 CTATATAACG
Statistics
Matches: 92, Mismatches: 17, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
21 4 0.04
22 82 0.89
23 6 0.07
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (22 bp):
ATTTATAACTAAATTATCACTG
Found at i:2519741 original size:44 final size:43
Alignment explanation
Indices: 2519607--2519743 Score: 116
Period size: 44 Copynumber: 3.1 Consensus size: 43
2519597 TAATTAATTA
* * * *
2519607 ATTTACAACTAAATTATC-ATTATATTATAATTAAATCATCACTG
1 ATTTATAACTAAATTATCAATAAT-TTAT-ATTAAATTATCAATG
* * * ** *
2519651 ATTTATAACTAAGTTATCAATGATTTATTATGACGTTAGT-AGTG
1 ATTTATAACTAAATTATCAATAATTTA-TATTAAATTA-TCAATG
*
2519695 ATTTATTACTAAATTATCAATAATTTACTATTAAATTATCAATG
1 ATTTATAACTAAATTATCAATAATTTA-TATTAAATTATCAATG
2519739 ATTTA
1 ATTTA
2519744 CTATATAACG
Statistics
Matches: 73, Mismatches: 16, Indels: 8
0.75 0.16 0.08
Matches are distributed among these distances:
43 1 0.01
44 66 0.90
45 6 0.08
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (43 bp):
ATTTATAACTAAATTATCAATAATTTATATTAAATTATCAATG
Found at i:2519744 original size:22 final size:22
Alignment explanation
Indices: 2519636--2519747 Score: 84
Period size: 22 Copynumber: 5.1 Consensus size: 22
2519626 TTATATTATA
* *
2519636 ATTAAATCATCACTGATTTA-T
1 ATTAAATTATCAATGATTTACT
* * *
2519657 AACTAAGTTATCAATGATTTATT
1 -ATTAAATTATCAATGATTTACT
* ** * *
2519680 ATGACGTTAGT-AGTGATTTATT
1 ATTAAATTA-TCAATGATTTACT
* *
2519702 ACTAAATTATCAATAATTTACT
1 ATTAAATTATCAATGATTTACT
2519724 ATTAAATTATCAATGATTTACT
1 ATTAAATTATCAATGATTTACT
2519746 AT
1 AT
2519748 ATAACGTTAT
Statistics
Matches: 70, Mismatches: 17, Indels: 6
0.75 0.18 0.06
Matches are distributed among these distances:
21 1 0.01
22 67 0.96
23 2 0.03
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (22 bp):
ATTAAATTATCAATGATTTACT
Found at i:2520620 original size:152 final size:153
Alignment explanation
Indices: 2520419--2520708 Score: 417
Period size: 152 Copynumber: 1.9 Consensus size: 153
2520409 ATTTTTAATT
* *
2520419 GATTTAAATTTAAATAACTAACGAATAAAAAGTTATATATTTAATGACAAATAAT-TTTATTAAA
1 GATTTAAATTTAAATAACTAACCAATAAAAAGCTATATATTTAATGACAAATAATCTTTATTAAA
* * * **
2520483 TAAATAAAAA-ATGCT-TGAAATTGAAATATAAATTTGTTATTTTTTAAAATTTATAAAGGTATT
66 TAAATAAAAATAT--TAT-AAATTGAAAGATAAATTTGTTATTTCTTAAAATTCATAAAAATATT
*
2520546 TATGTTATTCATTTCTAACACTTTTA
128 TATGTCATTCATTTCTAACACTTTTA
* * *
2520572 GATTTAAATTTAAATAACTAACCAAT-GAGAGCTATATATTTAATGACAAGTAATCTTTATTAAA
1 GATTTAAATTTAAATAACTAACCAATAAAAAGCTATATATTTAATGACAAATAATCTTTATTAAA
*
2520636 TAAATAAAAATATTATAAATTTAAAGATAAATTTGTTATTTCTTAAAATTCATAAAAATATTTAT
66 TAAATAAAAATATTATAAATTGAAAGATAAATTTGTTATTTCTTAAAATTCATAAAAATATTTAT
2520701 GTCATTCA
131 GTCATTCA
2520709 CTTTTAATAT
Statistics
Matches: 122, Mismatches: 12, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
152 75 0.61
153 45 0.37
154 2 0.02
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (153 bp):
GATTTAAATTTAAATAACTAACCAATAAAAAGCTATATATTTAATGACAAATAATCTTTATTAAA
TAAATAAAAATATTATAAATTGAAAGATAAATTTGTTATTTCTTAAAATTCATAAAAATATTTAT
GTCATTCATTTCTAACACTTTTA
Found at i:2520748 original size:2 final size:2
Alignment explanation
Indices: 2520741--2520784 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2520731 AACTTTTAGA
2520741 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
2520783 AT
1 AT
2520785 TCAAGTTTTT
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:2524192 original size:32 final size:32
Alignment explanation
Indices: 2524142--2524202 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
2524132 TTCACGTAGT
2524142 GTCTATAACAACAGTCTCATGTGATGGTTAAA
1 GTCTATAACAACAGTCTCATGTGATGGTTAAA
* * *
2524174 GTCTATAGCCACATTCTCATGTGATGGTT
1 GTCTATAACAACAGTCTCATGTGATGGTT
2524203 GTATAAGTGA
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:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (32 bp):
GTCTATAACAACAGTCTCATGTGATGGTTAAA
Found at i:2535641 original size:22 final size:22
Alignment explanation
Indices: 2535616--2535659 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2535606 TGTATATTTA
*
2535616 TATTTGTATATCTAGAATTAAG
1 TATTTGTATACCTAGAATTAAG
*
2535638 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATACCTAGAATTAAG
2535660 GACAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATACCTAGAATTAAG
Found at i:2539638 original size:22 final size:22
Alignment explanation
Indices: 2539599--2539642 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2539589 TGTATATTTA
* *
2539599 TATTTGTATATCTGAAATTAAG
1 TATTTGTATACCTAAAATTAAG
*
2539621 TATTTGTATCCCTAAAATTAAG
1 TATTTGTATACCTAAAATTAAG
2539643 GACAAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.43
Consensus pattern (22 bp):
TATTTGTATACCTAAAATTAAG
Found at i:2540025 original size:16 final size:16
Alignment explanation
Indices: 2540004--2540035 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2539994 TTGTTCACCA
*
2540004 TTTTATGCAGAAAATG
1 TTTTATACAGAAAATG
2540020 TTTTATACAGAAAATG
1 TTTTATACAGAAAATG
2540036 GTTGATTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.38
Consensus pattern (16 bp):
TTTTATACAGAAAATG
Found at i:2542636 original size:15 final size:13
Alignment explanation
Indices: 2542612--2542646 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
2542602 TACTTTGATT
2542612 AAAAAAATTAAATA
1 AAAAAAATTAAA-A
2542626 AAAAGAAATTAAAA
1 AAAA-AAATTAAAA
2542640 AAAAAAA
1 AAAAAAA
2542647 AACTCGTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 3 0.15
14 9 0.45
15 8 0.40
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (13 bp):
AAAAAAATTAAAA
Found at i:2542866 original size:6 final size:6
Alignment explanation
Indices: 2542850--2542882 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
2542840 AGATGTTTTC
*
2542850 TCAAAA ACAAAA TCAAAA TCAAAA TCAAAA TCA
1 TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA TCA
2542883 TGAGGGCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.67, C:0.18, G:0.00, T:0.15
Consensus pattern (6 bp):
TCAAAA
Found at i:2543439 original size:13 final size:13
Alignment explanation
Indices: 2543423--2543465 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2543413 TTCTAACACC
*
2543423 AAAAAATAACATA
1 AAAAAATAAAATA
*
2543436 AAAATATAAAATA
1 AAAAAATAAAATA
2543449 ATAAAAATAAAAATA
1 A-AAAAAT-AAAATA
2543464 AA
1 AA
2543466 TAATCATCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 12 0.48
14 6 0.24
15 7 0.28
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (13 bp):
AAAAAATAAAATA
Found at i:2543467 original size:16 final size:16
Alignment explanation
Indices: 2543424--2543468 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
2543414 TCTAACACCA
2543424 AAAAATAACATAAAAAT
1 AAAAATAA-ATAAAAAT
2543441 ATAAAAT-AATAAAAAT
1 A-AAAATAAATAAAAAT
2543457 AAAAATAAATAA
1 AAAAATAAATAA
2543469 TCATCTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 5 0.19
16 14 0.54
17 2 0.08
18 5 0.19
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (16 bp):
AAAAATAAATAAAAAT
Found at i:2544546 original size:19 final size:19
Alignment explanation
Indices: 2544522--2544560 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2544512 TATTTTATTA
* *
2544522 TTTTTTGGTTTAATCTCTT
1 TTTTTTAGTCTAATCTCTT
2544541 TTTTTTAGTCTAATCTCTT
1 TTTTTTAGTCTAATCTCTT
2544560 T
1 T
2544561 CATTATTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (19 bp):
TTTTTTAGTCTAATCTCTT
Found at i:2546289 original size:5 final size:5
Alignment explanation
Indices: 2546279--2546303 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2546269 TCATGCTATC
2546279 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
2546304 TTGCTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:2551139 original size:28 final size:28
Alignment explanation
Indices: 2551099--2551153 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
2551089 ACTTTAAAAC
*
2551099 TAATACCTGCATATATTCCGATATAGGT
1 TAATACCTCCATATATTCCGATATAGGT
*
2551127 TAATGCCTCCATATATTCCGATATAGG
1 TAATACCTCCATATATTCCGATATAGG
2551154 CTTTTGGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.35
Consensus pattern (28 bp):
TAATACCTCCATATATTCCGATATAGGT
Found at i:2554602 original size:21 final size:23
Alignment explanation
Indices: 2554577--2554626 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
2554567 TATAAATTTT
*
2554577 TAATTTTATTTATA-AAATTAAA
1 TAATTTTATTAATATAAATTAAA
*
2554599 -AATTTTATTAATATATATTAAA
1 TAATTTTATTAATATAAATTAAA
2554621 TAATTT
1 TAATTT
2554627 CTCGTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 12 0.50
22 7 0.29
23 5 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAATTTTATTAATATAAATTAAA
Found at i:2557173 original size:20 final size:20
Alignment explanation
Indices: 2557148--2557187 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2557138 TTTCTTACCC
*
2557148 AAAACCTCTTA-TTTATTGTT
1 AAAACCCCTTACTTT-TTGTT
2557168 AAAACCCCTTACTTTTTGTT
1 AAAACCCCTTACTTTTTGTT
2557188 TATTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.47
Consensus pattern (20 bp):
AAAACCCCTTACTTTTTGTT
Found at i:2558342 original size:27 final size:26
Alignment explanation
Indices: 2558304--2558363 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
2558294 ATAAAATAAG
* *
2558304 ATAATATTATTTAATC-TAATTTTATTC
1 ATAATATCATTTAATCAT-ATTCTA-TC
*
2558331 ATAATATCATTTTATCATATTCTATC
1 ATAATATCATTTAATCATATTCTATC
2558357 ATAATAT
1 ATAATAT
2558364 TTTGTATCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 9 0.31
27 19 0.66
28 1 0.03
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (26 bp):
ATAATATCATTTAATCATATTCTATC
Found at i:2560477 original size:29 final size:29
Alignment explanation
Indices: 2560405--2560490 Score: 122
Period size: 29 Copynumber: 3.0 Consensus size: 29
2560395 GAATAATAAC
* *
2560405 ATCAGAATATTTTTCTCCATGCTCTGATG
1 ATCAGAATATTTTTCTTCTTGCTCTGATG
2560434 ATCAGAA-ATTTTTTCTTCTTGCTCTGATG
1 ATCAGAATA-TTTTTCTTCTTGCTCTGATG
*
2560463 ATCAGAATATTTTTCTTCTTACTC-GATG
1 ATCAGAATATTTTTCTTCTTGCTCTGATG
2560491 CCGTTCACAC
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
28 5 0.10
29 46 0.88
30 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (29 bp):
ATCAGAATATTTTTCTTCTTGCTCTGATG
Found at i:2571325 original size:27 final size:27
Alignment explanation
Indices: 2571286--2571347 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
2571276 GGGTGTGCAC
2571286 CAAGCAAAGAGATCTAGCGAGCAACTGA
1 CAAGC-AAGAGATCTAGCGAGCAACTGA
2571314 CAAGCAAGAGATCTAGCGAGCAACTGA
1 CAAGCAAGAGATCTAGCGAGCAACTGA
2571341 CAAGCAA
1 CAAGCAA
2571348 ACATGAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 29 0.85
28 5 0.15
ACGTcount: A:0.44, C:0.23, G:0.24, T:0.10
Consensus pattern (27 bp):
CAAGCAAGAGATCTAGCGAGCAACTGA
Found at i:2580903 original size:22 final size:23
Alignment explanation
Indices: 2580871--2580914 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
2580861 ATATATTTTT
2580871 TAATTTTATT-AAA-TTTAAATA
1 TAATTTTATTAAAATTTTAAATA
2580892 TAATTATTATTAAAATTTTAAAT
1 TAATT-TTATTAAAATTTTAAAT
2580915 TACGTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 5 0.25
23 3 0.15
24 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAATTTTATTAAAATTTTAAATA
Found at i:2580911 original size:70 final size:78
Alignment explanation
Indices: 2580773--2580911 Score: 168
Period size: 78 Copynumber: 1.9 Consensus size: 78
2580763 ATATTTATAT
* * *
2580773 AATATAAAATATAAAATTTTATATATTTATATTATATTTTATATAAAAATTATGTATTATAATTT
1 AATATAAAATATAAAATTTTATATATTTATATTATAATTTAAATAAAAATTATGTATTATAATAT
2580838 TTTATGATATAAA
66 TTTATGATATAAA
* * *
2580851 AATATAAAATAT-ATATTTTTTA-ATTT-TATTA-AATTTAAAT-ATAATTAT-TATTA-AA-AT
1 AATATAAAATATAAAATTTTATATATTTATATTATAATTTAAATAAAAATTATGTATTATAATAT
2580908 TTTA
66 TTTA
2580912 AATTACGTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
70 5 0.09
71 2 0.04
72 5 0.09
73 7 0.13
74 7 0.13
75 5 0.09
76 4 0.07
77 8 0.15
78 12 0.22
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (78 bp):
AATATAAAATATAAAATTTTATATATTTATATTATAATTTAAATAAAAATTATGTATTATAATAT
TTTATGATATAAA
Found at i:2583559 original size:17 final size:17
Alignment explanation
Indices: 2583515--2583551 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
2583505 TATACAAAAT
*
2583515 TAAAATAA-AATA-AAA
1 TAAAATAATATTATAAA
2583530 TAAAATAATATTATAAA
1 TAAAATAATATTATAAA
2583547 TAAAA
1 TAAAA
2583552 ATATATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 3 0.16
17 8 0.42
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAAATAATATTATAAA
Found at i:2587509 original size:2 final size:2
Alignment explanation
Indices: 2587502--2587538 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2587492 TTGTGTTGGA
2587502 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2587539 ATGCTACAAT
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:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:2588827 original size:2 final size:2
Alignment explanation
Indices: 2588820--2588848 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2588810 TGCTCATTAA
2588820 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2588849 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2588853 original size:2 final size:2
Alignment explanation
Indices: 2588848--2588885 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
2588838 ATATATATAT
2588848 AG AG AG AG AG AG AG AG AG AG AG AG AG ATG AG AG A- AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A-G AG AG AG AG AG
2588886 CATACAAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 31 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
AG
Found at i:2591512 original size:22 final size:22
Alignment explanation
Indices: 2591486--2591527 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2591476 TGTATATTTA
* *
2591486 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
2591508 TATTTGTATCCCTAAAATTA
1 TATTTGTATCCCTAAAATTA
2591528 GGATAGACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:2595466 original size:22 final size:22
Alignment explanation
Indices: 2595440--2595481 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2595430 TGTATATTTA
* *
2595440 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
2595462 TATTTGTATCCCTAAAATTA
1 TATTTGTATCCCTAAAATTA
2595482 GGATAAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:2597464 original size:21 final size:21
Alignment explanation
Indices: 2597431--2597476 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2597421 GTCCAAGGCG
* *
2597431 GCTGTTGTTGTTGCTGCGGCT
1 GCTGCTGTAGTTGCTGCGGCT
*
2597452 GCTGCTGTAGTTGCTGCGGTT
1 GCTGCTGTAGTTGCTGCGGCT
2597473 GCTG
1 GCTG
2597477 AGACACAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.02, C:0.20, G:0.39, T:0.39
Consensus pattern (21 bp):
GCTGCTGTAGTTGCTGCGGCT
Found at i:2597926 original size:35 final size:35
Alignment explanation
Indices: 2597887--2597954 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
2597877 ACAACTCAGG
* *
2597887 ATTTGTATGAACAA-CATGGGGCACTAGTTGTGGGT
1 ATTTGGATGAA-AAGCATGAGGCACTAGTTGTGGGT
* *
2597922 ATTTGGATGAAAAGCATGATGCACTGGTTGTGG
1 ATTTGGATGAAAAGCATGAGGCACTAGTTGTGG
2597955 AATTGTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 2 0.07
35 26 0.93
ACGTcount: A:0.26, C:0.10, G:0.32, T:0.31
Consensus pattern (35 bp):
ATTTGGATGAAAAGCATGAGGCACTAGTTGTGGGT
Found at i:2598498 original size:126 final size:124
Alignment explanation
Indices: 2598341--2598597 Score: 309
Period size: 126 Copynumber: 2.1 Consensus size: 124
2598331 TATCATTAAT
* * * * * *
2598341 AAAAAATATAAAAAATTATTTAAGGTGTTTTT-ATTGAGAAACACCTTAAATAATTTCATTTATT
1 AAAAAATAAAAAAAATTATTTAAGGTATTTTTGAATAAAAAACACCTTAAAT-AGTTCATTTATT
* * *
2598405 ATTTTAAAAGAGATTATTTAAAAAATTTTTCAAACAAAAAATACATTAAATAATATCTTTTA
65 ATTTTAAAAGACATTATTTAAAAAATTTTT-AAAC-AAAAACACATTAAATAATACCTTTTA
* * * *
2598467 AAAAAATAAAAAAAATTATTTAAGGTATTTTTGAATAAAAAATACTTTAAATAGTTCTTTTATTT
1 AAAAAATAAAAAAAATTATTTAAGGTATTTTTGAATAAAAAACACCTTAAATAGTTCATTTATTA
* *** * *
2598532 TTTTAAACGACATTATTTAAAGTGTTTTTGAACAAAAACACATTAAATAATGCCTTTTA
66 TTTTAAAAGACATTATTTAAAAAATTTTTAAACAAAAACACATTAAATAATACCTTTTA
2598591 AAAAAAT
1 AAAAAAT
2598598 GAATTATTTA
Statistics
Matches: 111, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
124 30 0.27
125 3 0.03
126 64 0.58
127 14 0.13
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.39
Consensus pattern (124 bp):
AAAAAATAAAAAAAATTATTTAAGGTATTTTTGAATAAAAAACACCTTAAATAGTTCATTTATTA
TTTTAAAAGACATTATTTAAAAAATTTTTAAACAAAAACACATTAAATAATACCTTTTA
Found at i:2599076 original size:63 final size:64
Alignment explanation
Indices: 2599006--2599179 Score: 198
Period size: 63 Copynumber: 2.8 Consensus size: 64
2598996 TAAACCCTAT
* * * * * *
2599006 AATATAAAATGATTATTTAAGGTCTTTTT-TTTA-TAGAATCGTCTTAAATAATCCATTTATAAA
1 AATATAAAAAGATTATTTAAGGACTTTTTCTATACAAAAAT-GCCTTAAATAATCCATTTATAAA
* **
2599069 AATATAAAAAAATTATTTAA-GACTTTTTCTATACAAAAATGCCTTAAATAATTTATTTATAAA
1 AATATAAAAAGATTATTTAAGGACTTTTTCTATACAAAAATGCCTTAAATAATCCATTTATAAA
* *
2599132 AATATAAAAAGATTATTTAA-GACCTTTTCTCTACAAAAA--CCTTAAATA
1 AATATAAAAAGATTATTTAAGGACTTTTTCTATACAAAAATGCCTTAAATA
2599180 TAAAAATATT
Statistics
Matches: 97, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
61 9 0.09
62 7 0.07
63 77 0.79
64 4 0.04
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (64 bp):
AATATAAAAAGATTATTTAAGGACTTTTTCTATACAAAAATGCCTTAAATAATCCATTTATAAA
Found at i:2602131 original size:20 final size:22
Alignment explanation
Indices: 2602103--2602151 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2602093 TTGTAGGACA
* *
2602103 AATGGTATT-AAC-TGTGTTGG
1 AATGATATTGAACTTGTATTGG
*
2602123 AATGATATTGTACTTGTATTGG
1 AATGATATTGAACTTGTATTGG
2602145 AATGATA
1 AATGATA
2602152 ATTATTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.33
21 2 0.08
22 14 0.58
ACGTcount: A:0.31, C:0.04, G:0.24, T:0.41
Consensus pattern (22 bp):
AATGATATTGAACTTGTATTGG
Found at i:2602657 original size:21 final size:19
Alignment explanation
Indices: 2602619--2602669 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 19
2602609 TTTATGGATG
2602619 TGGATGTTATGGATTTTT-
1 TGGATGTTATGGATTTTTA
2602637 TGGAATGTTATGGATATTTTTA
1 TGG-ATGTTATGG--ATTTTTA
2602659 TGGATGTTATG
1 TGGATGTTATG
2602670 AATTGACTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.10
19 9 0.31
21 14 0.48
22 3 0.10
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (19 bp):
TGGATGTTATGGATTTTTA
Found at i:2603058 original size:13 final size:13
Alignment explanation
Indices: 2603040--2603064 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2603030 ATAGATTATT
2603040 GATGGAATTTTTC
1 GATGGAATTTTTC
2603053 GATGGAATTTTT
1 GATGGAATTTTT
2603065 ATTGATGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.48
Consensus pattern (13 bp):
GATGGAATTTTTC
Found at i:2603609 original size:22 final size:22
Alignment explanation
Indices: 2603581--2603628 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
2603571 TTTTTTAAAT
2603581 TATGAACTTTACGTGTATATAA
1 TATGAACTTTACGTGTATATAA
2603603 TATGAACTTTACGTGTATATAA
1 TATGAACTTTACGTGTATATAA
2603625 -ATGA
1 TATGA
2603629 TAATTAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.40
Consensus pattern (22 bp):
TATGAACTTTACGTGTATATAA
Found at i:2605268 original size:23 final size:22
Alignment explanation
Indices: 2605238--2605286 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
2605228 AAAATATAAA
2605238 AAAATACAAAAAAAGAAAAATAC
1 AAAATACAAAAAAAGAAAAA-AC
* *
2605261 AAAATACAAATATAGAAAAAAC
1 AAAATACAAAAAAAGAAAAAAC
2605283 AAAA
1 AAAA
2605287 AAAGAGGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.78, C:0.08, G:0.04, T:0.10
Consensus pattern (22 bp):
AAAATACAAAAAAAGAAAAAAC
Found at i:2605280 original size:16 final size:16
Alignment explanation
Indices: 2605225--2605264 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
2605215 ATTAAATTAA
2605225 ACAAAAATATAAAAAAAT
1 ACAAAAA-A-AAAAAAAT
*
2605243 ACAAAAAAAGAAAAAT
1 ACAAAAAAAAAAAAAT
2605259 ACAAAA
1 ACAAAA
2605265 TACAAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 13 0.62
17 1 0.05
18 7 0.33
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (16 bp):
ACAAAAAAAAAAAAAT
Found at i:2605287 original size:23 final size:24
Alignment explanation
Indices: 2605228--2605287 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
2605218 AAATTAAACA
*
2605228 AAAATATAAAAAAATACAAAAAAAG
1 AAAA-ATACAAAAATACAAAAAAAG
* *
2605253 AAAAATAC-AAAATACAAATATAG
1 AAAAATACAAAAATACAAAAAAAG
2605276 AAAAA-ACAAAAA
1 AAAAATACAAAAA
2605288 AAGAGGTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 2 0.06
23 22 0.71
24 3 0.10
25 4 0.13
ACGTcount: A:0.78, C:0.07, G:0.03, T:0.12
Consensus pattern (24 bp):
AAAAATACAAAAATACAAAAAAAG
Found at i:2605818 original size:5 final size:6
Alignment explanation
Indices: 2605799--2605833 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
2605789 AAGAGGTTAG
2605799 AATACAA AATAAA AATAAA AATAAAA AATAAA AAT
1 AATA-AA AATAAA AATAAA AAT-AAA AATAAA AAT
2605834 TTTCGTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 17 0.63
7 10 0.37
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:2605825 original size:13 final size:12
Alignment explanation
Indices: 2605799--2605833 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
2605789 AAGAGGTTAG
2605799 AATACAAAATAAA
1 AATA-AAAATAAA
2605812 AATAAAAATAAAA
1 AATAAAAAT-AAA
2605825 AATAAAAAT
1 AATAAAAAT
2605834 TTTCGTCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.24
13 16 0.76
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (12 bp):
AATAAAAATAAA
Found at i:2606531 original size:7 final size:7
Alignment explanation
Indices: 2606519--2606557 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
2606509 AAACTTTAAT
2606519 AATAAAA
1 AATAAAA
*
2606526 AATAAAT
1 AATAAAA
2606533 AATGAAAA
1 AAT-AAAA
2606541 AATAAAAA
1 AAT-AAAA
2606549 AATAAAA
1 AATAAAA
2606556 AA
1 AA
2606558 AAACTTTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
7 15 0.54
8 13 0.46
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (7 bp):
AATAAAA
Found at i:2606542 original size:15 final size:14
Alignment explanation
Indices: 2606516--2606557 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
2606506 GATAAACTTT
2606516 AATAATAAAAAATA
1 AATAATAAAAAATA
2606530 AATAATGAAAAAATAA
1 AATAAT-AAAAAAT-A
*
2606546 AAAAATAAAAAA
1 AATAATAAAAAA
2606558 AAACTTTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 6 0.24
15 13 0.52
16 6 0.24
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (14 bp):
AATAATAAAAAATA
Found at i:2607787 original size:21 final size:21
Alignment explanation
Indices: 2607758--2607797 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2607748 AAAAAGGTCA
2607758 AAAGAAAAAA-AAAACAAATCG
1 AAAGAAAAAAGAAAA-AAATCG
*
2607779 AAAGCAAAAAGAAAAAAAT
1 AAAGAAAAAAGAAAAAAAT
2607798 TTCCTTCACA
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:0.78, C:0.07, G:0.10, T:0.05
Consensus pattern (21 bp):
AAAGAAAAAAGAAAAAAATCG
Found at i:2618855 original size:49 final size:49
Alignment explanation
Indices: 2618801--2619102 Score: 272
Period size: 48 Copynumber: 6.1 Consensus size: 49
2618791 GATGAAATTT
* * *
2618801 TTTTTAAAATTGTTGAGTCTCTACTGAGATGAGCCTTTTTCAAGATG-GA
1 TTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAG-CTTTTTCAAGATGAGA
* * * * *
2618850 GTTTTAAAGTTATTGAGCCTTTGCTGAGATGAGCTTTTTCAAGATGAGAA
1 TTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGATGAG-A
* ** *
2618900 TTTTTTTAAAGTTGTTGAGCCTTCTGCTGAGAAAAGCTTTTTTAAGATGAGAA
1 --TTTTTAAAGTTGTTGAGCC-TCTACTGAGAGGAGCTTTTTCAAGATGAG-A
*
2618953 TTTCTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTTAAGAT-A-A
1 -TT-TTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGATGAGA
* * * * * * *
2619002 ATTTTAAAGTTGTT-ATACCTCTGCTTAGAGGACCTTTTT-TAGATGATA
1 TTTTTAAAGTTGTTGA-GCCTCTACTGAGAGGAGCTTTTTCAAGATGAGA
* * * *
2619050 TTTTTAAAATTGTTGAGTCTCTACTGAGAGAAGCTTTTTCAAGATAAGA
1 TTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGATGAGA
2619099 TTTT
1 TTTT
2619103 AGCAGATGAG
Statistics
Matches: 210, Mismatches: 32, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
46 5 0.02
47 32 0.15
48 44 0.21
49 40 0.19
50 1 0.00
51 1 0.00
52 43 0.20
53 44 0.21
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (49 bp):
TTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGATGAGA
Found at i:2618918 original size:52 final size:52
Alignment explanation
Indices: 2618790--2619102 Score: 255
Period size: 53 Copynumber: 6.2 Consensus size: 52
2618780 TTTGGAAAAC
* *
2618790 AGATGA-AATTTTTTTTAAAATTGTTGAGTCTCTACTGAGATGAGCCTTTTTCA
1 AGATGAGAA-TTTTTTTAAAGTTGTTGAGCCTCTACTGAGATGAG-CTTTTTCA
* * * *
2618843 AGATG-G-A--GTTTTAAAGTTATTGAGCCTTTGCTGAGATGAGCTTTTTCA
1 AGATGAGAATTTTTTTAAAGTTGTTGAGCCTCTACTGAGATGAGCTTTTTCA
* ** *
2618891 AGATGAGAATTTTTTTAAAGTTGTTGAGCCTTCTGCTGAGAAAAGCTTTTTTA
1 AGATGAGAATTTTTTTAAAGTTGTTGAGCC-TCTACTGAGATGAGCTTTTTCA
* * *
2618944 AGATGAGAATTTCTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTTA
1 AGATGAGAATTTTTTTAAAGTTGTTGAGCCTCTACTGAGATGAGCTTTTTCA
* * * * * *
2618996 AGAT-A-AA---TTTTAAAGTTGTT-ATACCTCTGCTTAGAGGACCTTTTT-T
1 AGATGAGAATTTTTTTAAAGTTGTTGA-GCCTCTACTGAGATGAGCTTTTTCA
* * *
2619042 AGAT--G-ATATTTTTAAAATTGTTGAGTCTCTACTGAGA-GAAGCTTTTTCA
1 AGATGAGAATTTTTTTAAAGTTGTTGAGCCTCTACTGAGATG-AGCTTTTTCA
*
2619091 AGATAAG-ATTTT
1 AGATGAGAATTTT
2619103 AGCAGATGAG
Statistics
Matches: 214, Mismatches: 30, Indels: 34
0.77 0.11 0.12
Matches are distributed among these distances:
45 1 0.00
46 5 0.02
47 32 0.15
48 41 0.19
49 33 0.15
50 3 0.01
51 6 0.03
52 41 0.19
53 52 0.24
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (52 bp):
AGATGAGAATTTTTTTAAAGTTGTTGAGCCTCTACTGAGATGAGCTTTTTCA
Found at i:2619215 original size:130 final size:125
Alignment explanation
Indices: 2618985--2619218 Score: 294
Period size: 130 Copynumber: 1.8 Consensus size: 125
2618975 CTACTGAGAG
* * * * *
2618985 GAGCTTTTTTAAGATAAATTTTAAAGTTGTTATACCTCTGCTTAGAGGACCTTTTTTAGATGATA
1 GAGCTTTTTTAAGAAAAATTTTAAAGTTATTATACCTCTGCTGAGAGGACCTTTTTAAGATGAAA
2619050 TTTTTAAAATTGTTGAGTCTCTACTGAGAGAAGCTTTTTCAAGATAAGATTTTAGCAGAT
66 TTTTTAAAATTGTTGAGTCTCTACTGAGAGAAGCTTTTTCAAGATAAGATTTTAGCAGAT
* * * *
2619110 GAGCTTTTTTCAGAAAAATTTTTAAAGTTATT-TAGCCTTTGCTGATAGGAGCTTTTTCAAGATG
1 GAGCTTTTTTAAGAAAAA-TTTTAAAGTTATTATA-CCTCTGCTGAGAGGACCTTTTT-AAGATG
2619174 AAAATTTCTTTAAAATTGTTGAG-CTTCTACTGAGATG-AGCTTTTT
63 -AAA-TT-TTTAAAATTGTTGAGTC-TCTACTGAGA-GAAGCTTTTT
2619219 TCATATTTCA
Statistics
Matches: 92, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
125 18 0.20
126 30 0.33
127 5 0.05
128 2 0.02
129 3 0.03
130 33 0.36
131 1 0.01
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (125 bp):
GAGCTTTTTTAAGAAAAATTTTAAAGTTATTATACCTCTGCTGAGAGGACCTTTTTAAGATGAAA
TTTTTAAAATTGTTGAGTCTCTACTGAGAGAAGCTTTTTCAAGATAAGATTTTAGCAGAT
Found at i:2619619 original size:9 final size:8
Alignment explanation
Indices: 2619599--2619640 Score: 57
Period size: 8 Copynumber: 5.0 Consensus size: 8
2619589 TAAATTAAAC
*
2619599 AAAAATAT
1 AAAAATAA
2619607 AAAAATACA
1 AAAAATA-A
2619616 AAAAATAA
1 AAAAATAA
2619624 AAAAATAGA
1 AAAAATA-A
2619633 AAAAATAA
1 AAAAATAA
2619641 GAAAGGGGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 16 0.52
9 15 0.48
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (8 bp):
AAAAATAA
Found at i:2619619 original size:17 final size:17
Alignment explanation
Indices: 2619599--2619640 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
2619589 TAAATTAAAC
*
2619599 AAAAATATAAAAATACA
1 AAAAATAAAAAAATACA
*
2619616 AAAAATAAAAAAATAGA
1 AAAAATAAAAAAATACA
2619633 AAAAATAA
1 AAAAATAA
2619641 GAAAGGGGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (17 bp):
AAAAATAAAAAAATACA
Found at i:2620834 original size:14 final size:14
Alignment explanation
Indices: 2620815--2620859 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
2620805 GATAAACTTT
2620815 AATAATAATAAATA
1 AATAATAATAAATA
2620829 AATAATGAA-AAAT-
1 AATAAT-AATAAATA
*
2620842 AATAA-AATAAAAA
1 AATAATAATAAATA
2620855 AATAA
1 AATAA
2620860 AAATGAACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
11 2 0.07
12 3 0.11
13 10 0.37
14 10 0.37
15 2 0.07
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (14 bp):
AATAATAATAAATA
Found at i:2630084 original size:2 final size:2
Alignment explanation
Indices: 2630079--2630132 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
2630069 TATATATATA
*
2630079 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2630121 TG TG TG TG TG TG
1 TG TG TG TG TG TG
2630133 CCGTGCTGGG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.02, C:0.00, G:0.48, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2645723 original size:63 final size:63
Alignment explanation
Indices: 2645595--2645812 Score: 190
Period size: 63 Copynumber: 3.5 Consensus size: 63
2645585 TGTAGAAAAT
* * * * ** *
2645595 TCAATTACTGCGTTTCGTT-AAAGATAAACATAGTAATTGAT-CATTGT-AGTTTAAAAAAGAAA
1 TCAATTATTGCGTTTCTTTGAAA-ATAAACACAGTAATT-ATACATTGTAATTTTATTAAA-ATA
2645657 A
63 A
* * * * * *
2645658 TCAAATATTGCGTTTCTTTGAAAATAAATACATTAATTATTCATTGTAATTTTTTTTAAATAA
1 TCAATTATTGCGTTTCTTTGAAAATAAACACAGTAATTATACATTGTAATTTTATTAAAATAA
* * ** *** *
2645721 TCAATTACTGCATTGATTTGGTTATAAACGCAGTAATTATACATTGTAATTTTATTAAAATAA
1 TCAATTATTGCGTTTCTTTGAAAATAAACACAGTAATTATACATTGTAATTTTATTAAAATAA
*
2645784 TCAATTATTGTGTTTCTTTGAAAATAAAC
1 TCAATTATTGCGTTTCTTTGAAAATAAAC
2645813 GCATTATTTT
Statistics
Matches: 118, Mismatches: 34, Indels: 6
0.75 0.22 0.04
Matches are distributed among these distances:
62 2 0.02
63 107 0.91
64 9 0.08
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (63 bp):
TCAATTATTGCGTTTCTTTGAAAATAAACACAGTAATTATACATTGTAATTTTATTAAAATAA
Found at i:2655063 original size:13 final size:13
Alignment explanation
Indices: 2655045--2655069 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2655035 CAAAGATTGC
2655045 TTCCTGATCACTA
1 TTCCTGATCACTA
2655058 TTCCTGATCACT
1 TTCCTGATCACT
2655070 GTTATGGTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.32, G:0.08, T:0.40
Consensus pattern (13 bp):
TTCCTGATCACTA
Found at i:2657186 original size:29 final size:29
Alignment explanation
Indices: 2657141--2657202 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 29
2657131 TAGAGGTTTG
*
2657141 TTTAAAAATT-TTAAAAAATACAAAGACTT
1 TTTAAAAATTATAAAAAAATACAAAGA-TT
2657170 TTTAAAAATTATGAAAAAAATACAAAGATT
1 TTTAAAAATTAT-AAAAAAATACAAAGATT
2657200 TTT
1 TTT
2657203 GCAAAAATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 10 0.33
30 6 0.20
31 14 0.47
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (29 bp):
TTTAAAAATTATAAAAAAATACAAAGATT
Found at i:2673945 original size:2 final size:2
Alignment explanation
Indices: 2673938--2673967 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2673928 TGTAATATTA
2673938 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
2673968 TTCTCATAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2677197 original size:14 final size:13
Alignment explanation
Indices: 2677171--2677204 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
2677161 GGGTTTCTTA
2677171 TTTTTTATTTTAT
1 TTTTTTATTTTAT
2677184 TTTTTTATTATTAT
1 TTTTTTATT-TTAT
2677198 TATTTTT
1 T-TTTTT
2677205 CTTTATTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.47
14 5 0.26
15 5 0.26
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTATTTTAT
Found at i:2677211 original size:19 final size:16
Alignment explanation
Indices: 2677171--2677204 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2677161 GGGTTTCTTA
2677171 TTTT-TTATTTTATTT
1 TTTTATTATTTTATTT
2677186 TTTTATTATTATTATTT
1 TTTTATTATT-TTATTT
2677203 TT
1 TT
2677205 CTTTATTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 5 0.29
17 8 0.47
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTATTATTTTATTT
Found at i:2677242 original size:2 final size:2
Alignment explanation
Indices: 2677235--2677283 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2677225 ATATCGATCT
2677235 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2677277 GA GA GA G
1 GA GA GA G
2677284 GAAACGAAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2678128 original size:21 final size:21
Alignment explanation
Indices: 2678104--2678143 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2678094 TTCATCACAA
*
2678104 AAATTTGTCAATATATAATAT
1 AAATCTGTCAATATATAATAT
* *
2678125 AAATCTGTCACTATCTAAT
1 AAATCTGTCAATATATAAT
2678144 TTTAATAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.40
Consensus pattern (21 bp):
AAATCTGTCAATATATAATAT
Found at i:2679150 original size:144 final size:144
Alignment explanation
Indices: 2678889--2679150 Score: 330
Period size: 144 Copynumber: 1.8 Consensus size: 144
2678879 AAAAAGATTC
* *
2678889 AGATCATGTTTTTATATTATTTCATGAATTTTGTTGCAATAAAAATATTAATTACACCTCAAAAA
1 AGATCATGTTTTGATATTATTTCATGAATTTTGATGCAATAAAAATATTAATTACACCTCAAAAA
* * **
2678954 GGTTGAAATTACCAAAACACCTATTAAGGGTATTTTCGTAATTTGATTTTCTCCATGTTGGCTTT
66 GGTTGAAATTACCAAAACACCTATTAAGGGTATTTTCATAACTTGACCTTCTCCATGTTGGCTTT
2679019 TAGTGAAATGCTCT
131 TAGTGAAATGCTCT
* * * * ** *
2679033 AGATCATGTTTTGATATTATTTCATGAATTTTGATGTATTGAAAACT-TTGATTGTACCTCAGAA
1 AGATCATGTTTTGATATTATTTCATGAATTTTGATGCAAT-AAAAATATTAATTACACCTCAAAA
* ** * *
2679097 AGGTTGAAGTTACCAAAATGCTCT-TTATGGGTATTTTCATTACTTGACCTTCTC
65 AGGTTGAAATTACCAAAACAC-CTATTAAGGGTATTTTCATAACTTGACCTTCTC
2679151 AAGATTGATT
Statistics
Matches: 98, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
144 91 0.93
145 7 0.07
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.42
Consensus pattern (144 bp):
AGATCATGTTTTGATATTATTTCATGAATTTTGATGCAATAAAAATATTAATTACACCTCAAAAA
GGTTGAAATTACCAAAACACCTATTAAGGGTATTTTCATAACTTGACCTTCTCCATGTTGGCTTT
TAGTGAAATGCTCT
Found at i:2681608 original size:18 final size:18
Alignment explanation
Indices: 2681568--2681609 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
2681558 AAAGCCCAAA
2681568 ATTTTTAATTATAATATG
1 ATTTTTAATTATAATATG
*
2681586 A-TTTTAATT-TAGATTTG
1 ATTTTTAATTATA-ATATG
2681603 ATTTTTA
1 ATTTTTA
2681610 TAATTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.10
17 13 0.62
18 6 0.29
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (18 bp):
ATTTTTAATTATAATATG
Found at i:2683066 original size:4 final size:4
Alignment explanation
Indices: 2683021--2683047 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2683011 TGTTTGTATT
2683021 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
2683048 TCATATTTAT
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:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:2686948 original size:198 final size:198
Alignment explanation
Indices: 2686597--2686996 Score: 631
Period size: 198 Copynumber: 2.0 Consensus size: 198
2686587 AAAATAAAAT
*
2686597 AAAAAACCTTGTAATTCGGGTTAGGTCAAAACGGATTAGCGCACGAATCTAACTTGGGTTCACAC
1 AAAAAACCTTGTAATTCGGGTTAGGTCAAAACGGATTAGCGCACGAATCTAACTTAGGTTCACAC
* * * *
2686662 GAATTTTAAGTCACCTAGAACAACGTCGTACAGAAGTAGTATAAAAGTCAGGTTTAGTGCTTTTT
66 AAATTTTAAGTCAACTAGAACAACGTCGTACAAAAGTAGTATAAAAGTCAAGTTTAGTGCTTTTT
* * *
2686727 GCTCAGAAACTTTCTTTTCTTTCTCTCTCTAGTCGGATTCTCTCTGCCTTCTCTCTAAAACCCAA
131 GCTCAGAAACTTTCTTCTCTTTCTCTCTCTAGTCGAATTCTCTCTGCCTTCTCTCTAAAACCAAA
2686792 CAA
196 CAA
* * *
2686795 AAAAAATCTTGTAATTCGGGTTAGGTCGAAATGGATT-GACGCACGAATCTAACTTAGGTTCACA
1 AAAAAACCTTGTAATTCGGGTTAGGTCAAAACGGATTAG-CGCACGAATCTAACTTAGGTTCACA
* * *
2686859 CAAATTTTAAGTCAACTAGAACGACGTCGTATAAAAGTAGTGTAAAAGTCAAGTTTAGTGCTTTT
65 CAAATTTTAAGTCAACTAGAACAACGTCGTACAAAAGTAGTATAAAAGTCAAGTTTAGTGCTTTT
* *
2686924 TGCTCATAAGCTTTCTTCTCTTTCTCTCTCTAGTCGAATTCTCTCTGCCTTCTCTCTAAAACCAA
130 TGCTCAGAAACTTTCTTCTCTTTCTCTCTCTAGTCGAATTCTCTCTGCCTTCTCTCTAAAACCAA
*
2686989 ACCA
195 ACAA
2686993 AAAA
1 AAAA
2686997 CACCATCGAA
Statistics
Matches: 184, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
197 1 0.01
198 183 0.99
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.32
Consensus pattern (198 bp):
AAAAAACCTTGTAATTCGGGTTAGGTCAAAACGGATTAGCGCACGAATCTAACTTAGGTTCACAC
AAATTTTAAGTCAACTAGAACAACGTCGTACAAAAGTAGTATAAAAGTCAAGTTTAGTGCTTTTT
GCTCAGAAACTTTCTTCTCTTTCTCTCTCTAGTCGAATTCTCTCTGCCTTCTCTCTAAAACCAAA
CAA
Found at i:2687647 original size:21 final size:21
Alignment explanation
Indices: 2687623--2687668 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2687613 AATTGGAGCA
2687623 AAAAGA-AAAAACAAAAGAAAG
1 AAAAGAGAAAAACAAAA-AAAG
*
2687644 AAAAGAGAAAAACAAAAAAAT
1 AAAAGAGAAAAACAAAAAAAG
2687665 AAAA
1 AAAA
2687669 ATAAAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.83, C:0.04, G:0.11, T:0.02
Consensus pattern (21 bp):
AAAAGAGAAAAACAAAAAAAG
Found at i:2687647 original size:22 final size:21
Alignment explanation
Indices: 2687622--2687675 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
2687612 AAATTGGAGC
2687622 AAAAAGAAAAAACAAAAGAAAG
1 AAAAAGAAAAAACAAAA-AAAG
*
2687644 -AAAAGAGAAAAACAAAAAAAT
1 AAAAAGA-AAAAACAAAAAAAG
*
2687665 AAAAATAAAAA
1 AAAAAGAAAAA
2687676 TAATATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.83, C:0.04, G:0.09, T:0.04
Consensus pattern (21 bp):
AAAAAGAAAAAACAAAAAAAG
Found at i:2687680 original size:3 final size:3
Alignment explanation
Indices: 2687662--2687742 Score: 101
Period size: 3 Copynumber: 27.3 Consensus size: 3
2687652 AAAACAAAAA
* * * * *
2687662 AAT AAA AAT AAA AAT AAT -AT ATT AGT AAT AAT AAT AAT GAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
2687709 AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2687743 CGGTACAATA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
2 2 0.03
3 64 0.97
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2690312 original size:45 final size:46
Alignment explanation
Indices: 2690242--2690362 Score: 154
Period size: 45 Copynumber: 2.6 Consensus size: 46
2690232 TTTAAAGGAG
* * *
2690242 TTTTTCGACTGAGAATCTTTGAAATTTTGGATGCAAAACTCTAAAGT
1 TTTTTAGA-TGAGAATCTTTGAAATTTTGGATGCAAAACCCTAAAAT
* * **
2690289 TTTTTA-ATGAGAAGCTTTAAAATTTTGGATGTGAAACCCTAAAAT
1 TTTTTAGATGAGAATCTTTGAAATTTTGGATGCAAAACCCTAAAAT
*
2690334 TTTTTAGATGAGAATTTTTGAAATTTTGG
1 TTTTTAGATGAGAATCTTTGAAATTTTGG
2690363 TTGTAAAAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
45 38 0.60
46 20 0.32
47 5 0.08
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.41
Consensus pattern (46 bp):
TTTTTAGATGAGAATCTTTGAAATTTTGGATGCAAAACCCTAAAAT
Found at i:2690689 original size:35 final size:34
Alignment explanation
Indices: 2690650--2690729 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 34
2690640 ATGACAAAGT
* *
2690650 TAAAAGTTCTTGC-AAACTTGAAGTTTTTGCGAATC
1 TAAAAG-TCTTGCGAAACTTCAA-TTTTTGCAAATC
* * *
2690685 TAAAAATCTTGCGAATCTTCAATTTTTGTAAATC
1 TAAAAGTCTTGCGAAACTTCAATTTTTGCAAATC
2690719 TAAAAGTCTTG
1 TAAAAGTCTTG
2690730 TGAATCTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
34 26 0.68
35 12 0.32
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (34 bp):
TAAAAGTCTTGCGAAACTTCAATTTTTGCAAATC
Found at i:2690823 original size:18 final size:17
Alignment explanation
Indices: 2690800--2690838 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2690790 TAATTCTTGC
2690800 GAATCTAAAAATCTTTGT
1 GAATCTAAAAAT-TTTGT
* *
2690818 GAATCTGAAACTTTTGT
1 GAATCTAAAAATTTTGT
2690835 GAAT
1 GAAT
2690839 TTGGAACCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (17 bp):
GAATCTAAAAATTTTGT
Found at i:2690850 original size:17 final size:17
Alignment explanation
Indices: 2690812--2690851 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2690802 ATCTAAAAAT
2690812 CTTTGTGAATCTGAAAC
1 CTTTGTGAATCTGAAAC
* * *
2690829 TTTTGTGAATTTGGAAC
1 CTTTGTGAATCTGAAAC
2690846 CTTTGT
1 CTTTGT
2690852 AAAACTTGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.23, C:0.12, G:0.20, T:0.45
Consensus pattern (17 bp):
CTTTGTGAATCTGAAAC
Found at i:2691564 original size:30 final size:28
Alignment explanation
Indices: 2691495--2691566 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
2691485 TAATTTATTA
* *
2691495 AATATATTTTGTATGATTGCATGATAATT
1 AATATA-TTTGCATTATTGCATGATAATT
2691524 AATATATTTGCATTATTGCATGAT-ATT
1 AATATATTTGCATTATTGCATGATAATT
2691551 ATATTATTATTTGCAT
1 A-A-TA-TATTTGCAT
2691567 AATATTATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
27 4 0.11
28 17 0.45
29 8 0.21
30 9 0.24
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (28 bp):
AATATATTTGCATTATTGCATGATAATT
Found at i:2692548 original size:31 final size:31
Alignment explanation
Indices: 2692483--2692558 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
2692473 TTAAAGGGAT
* * **
2692483 TAAATTTTAAATTTCATGTAAGTATAGAGGC
1 TAAATTTCAAATTTCATGTAAGTATAAAAAC
*
2692514 TAAATTTCAAATTTCATGTAGGTATAAAAAC
1 TAAATTTCAAATTTCATGTAAGTATAAAAAC
*
2692545 TAAATTTCTAATTT
1 TAAATTTCAAATTT
2692559 TGTGTGAGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.41
Consensus pattern (31 bp):
TAAATTTCAAATTTCATGTAAGTATAAAAAC
Found at i:2696859 original size:27 final size:26
Alignment explanation
Indices: 2696827--2696883 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 26
2696817 CAAAAAGTAA
2696827 AAAAAATACCAAAAGTAAAAAAAACATGG
1 AAAAAA-A-CAAAA-TAAAAAAAACATGG
*
2696856 AAAAAAATAAAATAAAAAAAACATGG
1 AAAAAAACAAAATAAAAAAAACATGG
2696882 AA
1 AA
2696884 TTGTTGTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 16 0.59
27 4 0.15
28 1 0.04
29 6 0.22
ACGTcount: A:0.74, C:0.07, G:0.09, T:0.11
Consensus pattern (26 bp):
AAAAAAACAAAATAAAAAAAACATGG
Found at i:2698660 original size:26 final size:26
Alignment explanation
Indices: 2698613--2698662 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2698603 TAAAAAAGAT
*
2698613 TAATGATAACTCCTAAAGTTTATATC
1 TAATGATAACTCATAAAGTTTATATC
*
2698639 TAATGATAAATTCATAAA-TTTATA
1 TAATGAT-AACTCATAAAGTTTATA
2698663 CGTTATGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (26 bp):
TAATGATAACTCATAAAGTTTATATC
Found at i:2700626 original size:16 final size:17
Alignment explanation
Indices: 2700602--2700635 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2700592 ACGTAGTTAT
2700602 AATTCAATTATT-ATTA
1 AATTCAATTATTAATTA
*
2700618 AATTTAATTATTAATTA
1 AATTCAATTATTAATTA
2700635 A
1 A
2700636 TTAGGTCTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTCAATTATTAATTA
Found at i:2702299 original size:4 final size:4
Alignment explanation
Indices: 2702290--2702355 Score: 78
Period size: 4 Copynumber: 16.5 Consensus size: 4
2702280 CGTTCTTGAA
* * * * * *
2702290 ATAT ATAT ATAA ATAA ATAA ATAT AAAT ATAA ATAT AAAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
2702338 ATAT ATAT ATAT ATAT AT
1 ATAT ATAT ATAT ATAT AT
2702356 TGAGAATACC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (4 bp):
ATAT
Found at i:2702315 original size:6 final size:6
Alignment explanation
Indices: 2702288--2702355 Score: 73
Period size: 6 Copynumber: 11.0 Consensus size: 6
2702278 ACCGTTCTTG
* *
2702288 AAATAT ATATAT AAATAAAT AAATAT AAATAT AAATAT AAATAT ATATAT
1 AAATAT AAATAT AAAT--AT AAATAT AAATAT AAATAT AAATAT AAATAT
* * *
2702338 ATATAT ATATAT ATATAT
1 AAATAT AAATAT AAATAT
2702356 TGAGAATACC
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
6 51 0.89
8 6 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (6 bp):
AAATAT
Found at i:2703577 original size:2 final size:2
Alignment explanation
Indices: 2703570--2703613 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2703560 ATGTTTAATT
2703570 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
2703612 TA
1 TA
2703614 CAACATACCA
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):
TA
Found at i:2704487 original size:5 final size:5
Alignment explanation
Indices: 2704477--2704527 Score: 61
Period size: 5 Copynumber: 10.2 Consensus size: 5
2704467 TTTGAAAAGT
*
2704477 TATAA TATAA TATAA TATAA TTATAT TATAA TTATAA TATAA T-TAA -ATAA
1 TATAA TATAA TATAA TATAA -TATAA TATAA -TATAA TATAA TATAA TATAA
2704527 T
1 T
2704528 TTTAGTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 6 0.15
5 25 0.62
6 9 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (5 bp):
TATAA
Found at i:2704506 original size:11 final size:11
Alignment explanation
Indices: 2704476--2704525 Score: 77
Period size: 11 Copynumber: 4.7 Consensus size: 11
2704466 GTTTGAAAAG
2704476 TTATAATATAA
1 TTATAATATAA
2704487 -TATAATATAA
1 TTATAATATAA
*
2704497 TTATATTATAA
1 TTATAATATAA
2704508 TTATAATATAA
1 TTATAATATAA
2704519 TTA-AATA
1 TTATAATA
2704526 ATTTTAGTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
10 14 0.39
11 22 0.61
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TTATAATATAA
Found at i:2705334 original size:22 final size:21
Alignment explanation
Indices: 2705279--2705417 Score: 81
Period size: 22 Copynumber: 6.4 Consensus size: 21
2705269 GAAATAGAAC
*
2705279 AATTTACTACTAAGTTATACATT
1 AATTTACTATTAAGTTATA-A-T
* *
2705302 TATTTATTATTAAGTTATGAAT
1 AATTTACTATTAAGTTAT-AAT
*
2705324 GATTTACTATTAAGTTATCAAT
1 AATTTACTATTAAGTTAT-AAT
2705346 AATTTA-TCA--AA-TTATCAA-
1 AATTTACT-ATTAAGTTAT-AAT
* **
2705364 AGATTTATTACAAAGTTATTAAT
1 A-ATTTACTATTAAGTTA-TAAT
* *
2705387 AATTTACTATTAAATTAATATT
1 AATTTACTATTAAGTT-ATAAT
2705409 AATTTACTA
1 AATTTACTA
2705418 CTAAACAATT
Statistics
Matches: 94, Mismatches: 12, Indels: 21
0.74 0.09 0.17
Matches are distributed among these distances:
18 1 0.01
19 13 0.14
20 3 0.03
21 3 0.03
22 54 0.57
23 19 0.20
24 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (21 bp):
AATTTACTATTAAGTTATAAT
Found at i:2705422 original size:22 final size:22
Alignment explanation
Indices: 2705381--2705439 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
2705371 TTACAAAGTT
* * *
2705381 ATTAATAATTTACTATTAAATTA
1 ATTATTAATTTACTACTAAA-CA
2705404 A-TATTAATTTACTACTAAACA
1 ATTATTAATTTACTACTAAACA
*
2705425 ATTATCAATTTACTA
1 ATTATTAATTTACTA
2705440 TTATAACTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 2 0.06
22 28 0.90
23 1 0.03
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTATTAATTTACTACTAAACA
Found at i:2705542 original size:22 final size:22
Alignment explanation
Indices: 2705517--2705618 Score: 98
Period size: 22 Copynumber: 4.6 Consensus size: 22
2705507 AAGTTAACAC
*
2705517 TTATCATTAATTTAATATTAAA
1 TTATCATTAATTTACTATTAAA
* * *
2705539 TTATAATTTATTTATTATTAAA
1 TTATCATTAATTTACTATTAAA
*
2705561 TTATCATTAA-TTAGCTATTAAG
1 TTATCATTAATTTA-CTATTAAA
* * *
2705583 TTACCAATAATTTACTACTAAA
1 TTATCATTAATTTACTATTAAA
* *
2705605 TTAACAATAATTTA
1 TTATCATTAATTTA
2705619 TCACTAAGTT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
21 3 0.05
22 60 0.91
23 3 0.05
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (22 bp):
TTATCATTAATTTACTATTAAA
Found at i:2705630 original size:22 final size:22
Alignment explanation
Indices: 2705579--2705630 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
2705569 AATTAGCTAT
*
2705579 TAAGTTACCAATAATTTACTAC
1 TAAGTTAACAATAATTTACTAC
*
2705601 TAAATTAACAATAATTTA-TCAC
1 TAAGTTAACAATAATTTACT-AC
2705623 TAAGTTAA
1 TAAGTTAA
2705631 TACTGATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 1 0.04
22 25 0.96
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (22 bp):
TAAGTTAACAATAATTTACTAC
Found at i:2706343 original size:10 final size:10
Alignment explanation
Indices: 2706320--2706368 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
2706310 ATAAGTTACT
* *
2706320 AAAATTTGTT
1 AAAATTTATC
2706330 AAAATTTATC
1 AAAATTTATC
2706340 AAAATTATATC
1 AAAATT-TATC
*
2706351 AACATATTATC
1 AAAAT-TTATC
2706362 AAAATTT
1 AAAATTT
2706369 TGTCTAAGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 16 0.48
11 16 0.48
12 1 0.03
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (10 bp):
AAAATTTATC
Found at i:2706490 original size:20 final size:20
Alignment explanation
Indices: 2706440--2706492 Score: 79
Period size: 21 Copynumber: 2.6 Consensus size: 20
2706430 AATATCAAAG
2706440 GTTACCAAAATTTTATTCAA
1 GTTACCAAAATTTTATTCAA
*
2706460 GATTACCAAAATTTTATTGAA
1 G-TTACCAAAATTTTATTCAA
*
2706481 GTTACTAAAATT
1 GTTACCAAAATT
2706493 ATTTTAACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 11 0.37
21 19 0.63
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.40
Consensus pattern (20 bp):
GTTACCAAAATTTTATTCAA
Found at i:2706721 original size:47 final size:48
Alignment explanation
Indices: 2706603--2706721 Score: 168
Period size: 47 Copynumber: 2.5 Consensus size: 48
2706593 AACTTTTAAC
*
2706603 AAAAGATTATCAAATTATATCAAAGTTTTATCAAAATCAAAATTATAT
1 AAAAAATTATCAAATTATATCAAAGTTTTATCAAAATCAAAATTATAT
* ** *
2706651 GAAATGTTATCAACTTATATCAAAG-TTTATCAAAATCAAAATTATAT
1 AAAAAATTATCAAATTATATCAAAGTTTTATCAAAATCAAAATTATAT
* *
2706698 AAAAAATTATAAAATTATGTCAAA
1 AAAAAATTATCAAATTATATCAAA
2706722 AGTTACTAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
47 40 0.66
48 21 0.34
ACGTcount: A:0.52, C:0.08, G:0.05, T:0.34
Consensus pattern (48 bp):
AAAAAATTATCAAATTATATCAAAGTTTTATCAAAATCAAAATTATAT
Found at i:2706731 original size:21 final size:20
Alignment explanation
Indices: 2706688--2706752 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
2706678 TATCAAAATC
* *
2706688 AAAATTATATAAAAAATTAT
1 AAAATTATATCAAAAGTTAT
*
2706708 AAAATTATGTCAAAAGTTACT
1 AAAATTATATCAAAAGTTA-T
2706729 AAAATTATATC-AAAGTTAT
1 AAAATTATATCAAAAGTTAT
2706748 CAAAA
1 -AAAA
2706753 CAATTTCTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 27 0.69
21 11 0.28
ACGTcount: A:0.57, C:0.06, G:0.05, T:0.32
Consensus pattern (20 bp):
AAAATTATATCAAAAGTTAT
Found at i:2709050 original size:41 final size:41
Alignment explanation
Indices: 2709002--2709752 Score: 571
Period size: 41 Copynumber: 18.1 Consensus size: 41
2708992 AATAAACAAA
*
2709002 GCTCCTCTAAATAGAGGTTCAACAACTTTAAAAAATAAAAG
1 GCTCCTCTAAATAGAGGCTCAACAACTTTAAAAAATAAAAG
* * * * *
2709043 GCCCCTCTAAACAGAGGTTCAACAACTTTTAAAAAAAAAAAAAAAAA
1 GCTCCTCTAAATAGAGGCTCAACAAC-TTT-----AAAAAATAAAAG
* * * *
2709090 ACTCCTCTAAATAGAGG-TATAACAACTTTAGAACATAAAAG
1 GCTCCTCTAAATAGAGGCT-CAACAACTTTAAAAAATAAAAG
* * *
2709131 GCTCCTCT-AATCAGAGGCACAATAACTTTTAAAAAATAAAAA
1 GCTCCTCTAAAT-AGAGGCTCAACAAC-TTTAAAAAATAAAAG
* * *
2709173 GCTCCTCTAAACAGAGGCACAACAACTTTTAAAAA-AAAAG
1 GCTCCTCTAAATAGAGGCTCAACAACTTTAAAAAATAAAAG
* * * * *
2709213 GCTCCTCTAAACAGAAGCACAACAACTTTGAAAAATAAAAA
1 GCTCCTCTAAATAGAGGCTCAACAACTTTAAAAAATAAAAG
* * * ** * ** * *
2709254 GTTACTCTAAGTAGAGATTCAATGATTTTTGAAAAATAAAAA
1 GCTCCTCTAAATAGAGGCTCAA-CAACTTTAAAAAATAAAAG
* * *
2709296 GCTCCTCTAAATAGAGGCACTACAACTTTAAAAAATAAAAA
1 GCTCCTCTAAATAGAGGCTCAACAACTTTAAAAAATAAAAG
* * *
2709337 GCTCCTCTAAATATAGGCACAACAACTTTGAAAAATAAAAG
1 GCTCCTCTAAATAGAGGCTCAACAACTTTAAAAAATAAAAG
* ** * * **
2709378 GTTCCTCTAAGCAGATGCTCAATAACTTTTGAAAATAAAAG
1 GCTCCTCTAAATAGAGGCTCAACAACTTTAAAAAATAAAAG
* *
2709419 GCTCCTCTAAACAGAGGCAT-AATAACTTTTAAAAAATAAAAG
1 GCTCCTCTAAATAGAGGC-TCAACAAC-TTTAAAAAATAAAAG
** *
2709461 GCTCCTCTAAGCAGAGGCAT-AACAACTTTGAAAAATAAAAG
1 GCTCCTCTAAATAGAGGC-TCAACAACTTTAAAAAATAAAAG
* *
2709502 GCTCCTCTAAATAGAGGCTCAACGACTTTTAAAAATAAAAG
1 GCTCCTCTAAATAGAGGCTCAACAACTTTAAAAAATAAAAG
* * * * *
2709543 GCTCCTATAAATAGAGACACAACAAATTTTGAAAAATAAAAG
1 GCTCCTCTAAATAGAGGCTCAAC-AACTTTAAAAAATAAAAG
* * * * * * *
2709585 ACTCCTCTAAACAGAGACACAATAACTTTAGAAAATAAAAT
1 GCTCCTCTAAATAGAGGCTCAACAACTTTAAAAAATAAAAG
* * * * **
2709626 GCTCTTC-AAGTATAGGCTCAATAACTTTTGAAAATAAAAG
1 GCTCCTCTAAATAGAGGCTCAACAACTTTAAAAAATAAAAG
** * ** * ** ***
2709666 GCTTTTTTAAGCAGAAGCTCAATGACTTTTGTAAATAAAA-
1 GCTCCTCTAAATAGAGGCTCAACAACTTTAAAAAATAAAAG
* * * *
2709706 GCTCCTCTAAATAGAGACACAATAACTTTGAAAAATAAAAG
1 GCTCCTCTAAATAGAGGCTCAACAACTTTAAAAAATAAAAG
2709747 GCTCCT
1 GCTCCT
2709753 TGACAATCAT
Statistics
Matches: 576, Mismatches: 115, Indels: 38
0.79 0.16 0.05
Matches are distributed among these distances:
40 100 0.17
41 301 0.52
42 139 0.24
43 2 0.00
46 4 0.01
47 30 0.05
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAAATAGAGGCTCAACAACTTTAAAAAATAAAAG
Found at i:2709158 original size:88 final size:86
Alignment explanation
Indices: 2709003--2709253 Score: 280
Period size: 88 Copynumber: 2.9 Consensus size: 86
2708993 ATAAACAAAG
* **
2709003 CTCCTCTAAATAGAGGT-TCAACAACTTTAAAAAATAAAAGGCCCCTCTAAACAGAGGTTCAACA
1 CTCCTCTAAATAGAGGTAT-AACAACTTT--AAAATAAAAGGCTCCTCTAAACAGAGGCACAACA
2709067 ACTTTTAAAAAAAAAAAAAAAAAA
63 ACTTTTAAAAAAAAAAAAAAAAAA
* *
2709091 CTCCTCTAAATAGAGGTATAACAACTTTAGAACATAAAAGGCTCCTCTAATCAGAGGCACAATAA
1 CTCCTCTAAATAGAGGTATAACAACTTTA-AA-ATAAAAGGCTCCTCTAAACAGAGGCACAACAA
* *
2709156 CTTTT-----AAAAAATAAAAAG
64 CTTTTAAAAAAAAAAAAAAAAAA
* * * * *
2709174 CTCCTCTAAACAGAGGCACAACAACTTTTAAAAAAAAAGGCTCCTCTAAACAGAAGCACAACAAC
1 CTCCTCTAAATAGAGGTATAACAAC-TTTAAAATAAAAGGCTCCTCTAAACAGAGGCACAACAAC
* *
2709239 TTTGAAAAATAAAAA
65 TTTTAAAAAAAAAAA
2709254 GTTACTCTAA
Statistics
Matches: 138, Mismatches: 16, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
82 32 0.23
83 35 0.25
84 4 0.03
86 1 0.01
87 7 0.05
88 58 0.42
89 1 0.01
ACGTcount: A:0.49, C:0.20, G:0.10, T:0.21
Consensus pattern (86 bp):
CTCCTCTAAATAGAGGTATAACAACTTTAAAATAAAAGGCTCCTCTAAACAGAGGCACAACAACT
TTTAAAAAAAAAAAAAAAAAA
Done.