Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006550.1 Hibiscus syriacus cultivar Beakdansim tig00016004_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1576944
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 8
Found at i:564714 original size:38 final size:37
Alignment explanation
Indices: 564617--564719 Score: 111
Period size: 38 Copynumber: 2.7 Consensus size: 37
564607 GGAGCCGTTT
*
564617 GAGCCGAGCCGTTTGAGCCGAGCCGTTTGAGCTGAGCC
1 GAGCCGAGCCG-CTGAGCCGAGCCGTTTGAGCTGAGCC
* * *
564655 GAGCCGTTTG-AGCTGAGCCGAGCCGTTTTAGCTGAGCC
1 GAGCCG--AGCCGCTGAGCCGAGCCGTTTGAGCTGAGCC
564693 GAGCCGAGCCGCCT-AGACCGAGCCGTT
1 GAGCCGAGCCG-CTGAG-CCGAGCCGTT
564720 ACTGTTGACC
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
36 1 0.02
37 3 0.06
38 48 0.89
39 1 0.02
40 1 0.02
ACGTcount: A:0.17, C:0.30, G:0.35, T:0.18
Consensus pattern (37 bp):
GAGCCGAGCCGCTGAGCCGAGCCGTTTGAGCTGAGCC
Found at i:566049 original size:18 final size:18
Alignment explanation
Indices: 566023--566057 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
566013 TCGAAAGGAC
*
566023 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
566041 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
566058 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:568661 original size:16 final size:17
Alignment explanation
Indices: 568626--568663 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
568616 GAAAATATTG
*
568626 AAAAAGAGAACAAAAGA
1 AAAAAGAGAACAAAACA
*
568643 AAAAAGAGAA-AGAACA
1 AAAAAGAGAACAAAACA
568659 AAAAA
1 AAAAA
568664 TAAGGTGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAGAGAACAAAACA
Found at i:569700 original size:106 final size:106
Alignment explanation
Indices: 569512--569723 Score: 268
Period size: 106 Copynumber: 2.0 Consensus size: 106
569502 TCAACACTTA
*
569512 AGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAACTTCCCAATTT
1 AGACAACACAAGCTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAACTTCCCAATTT
*
569577 AAGAGTCAATTTCAACTTCAC-AGCGAAGGATATTAGACTCG
66 AAGAGCCAATTTCAACTTCACGA-CGAAGGATATTAGACTCG
* * * * * * *
569618 AGACAGCACAAGCTCAACTTCACAGCGAAGGGGCG-GTTGTCTGTCAACAAACAATTTCCCAGTT
1 AGACAACACAAGCTCAACTTCACAACGAAGGGACGACTGGT-TGTCAACAAACAACTTCCCAATT
* * *
569682 CT-AGAGCCAATTTTAACTTCACGACGGAGGATATTGGACTCG
65 -TAAGAGCCAATTTCAACTTCACGACGAAGGATATTAGACTCG
569724 GAGCAATACA
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
105 3 0.03
106 86 0.95
107 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (106 bp):
AGACAACACAAGCTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAACTTCCCAATTT
AAGAGCCAATTTCAACTTCACGACGAAGGATATTAGACTCG
Found at i:571003 original size:19 final size:20
Alignment explanation
Indices: 570979--571017 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
570969 TATTTTTGTC
570979 TTTTTTATTAC-TATTATTA
1 TTTTTTATTACTTATTATTA
570998 TTTTTTATTACTTATTATTA
1 TTTTTTATTACTTATTATTA
571018 CTATTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTTTATTACTTATTATTA
Found at i:571313 original size:20 final size:21
Alignment explanation
Indices: 571284--571322 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
571274 TTACTTCATT
*
571284 CTTTTTCTTA-TTTATTTTTA
1 CTTTTACTTATTTTATTTTTA
571304 CTTTTACTTATTTTATTTT
1 CTTTTACTTATTTTATTTT
571323 CTTAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.74
Consensus pattern (21 bp):
CTTTTACTTATTTTATTTTTA
Found at i:582907 original size:26 final size:26
Alignment explanation
Indices: 582877--582936 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
582867 CCTTTATTAA
582877 CACTTTTTGCTTTCAACTTGCTTTCT
1 CACTTTTTGCTTTCAACTTGCTTTCT
582903 CACTTTTTGCTTTCAACTTGCTTTCT
1 CACTTTTTGCTTTCAACTTGCTTTCT
582929 CACTTTTT
1 CACTTTTT
582937 TCATCGACCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.12, C:0.27, G:0.07, T:0.55
Consensus pattern (26 bp):
CACTTTTTGCTTTCAACTTGCTTTCT
Found at i:583077 original size:41 final size:41
Alignment explanation
Indices: 583030--583220 Score: 152
Period size: 41 Copynumber: 4.7 Consensus size: 41
583020 TTGTAAATAC
* * *
583030 AAACGCCACTAATGTACTTA-TAAATT-GCGGTGTTTGTATAA
1 AAACGCCACTAAAGTA-TGAGT-AATTAGCGGTGTTCGTATAA
*
583071 AAACGCCACTAAAGTATGAGTATTTAGCGGTGTTCGTATAA
1 AAACGCCACTAAAGTATGAGTAATTAGCGGTGTTCGTATAA
* * * ** * **
583112 AAATGCCACTAAATTACGAGTCTTTAGCTGTGTTTATATAA
1 AAACGCCACTAAAGTATGAGTAATTAGCGGTGTTCGTATAA
* * ** * * * *
583153 AAATGCCACTAAAGTACGAGTCTTTAGCAGCGTTTGAATAA
1 AAACGCCACTAAAGTATGAGTAATTAGCGGTGTTCGTATAA
* *
583194 AAACGACACTAAAGTATGAGTATTTAG
1 AAACGCCACTAAAGTATGAGTAATTAG
583221 TGGCGTTTGT
Statistics
Matches: 128, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
40 5 0.04
41 123 0.96
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (41 bp):
AAACGCCACTAAAGTATGAGTAATTAGCGGTGTTCGTATAA
Found at i:583227 original size:41 final size:41
Alignment explanation
Indices: 583061--583369 Score: 290
Period size: 41 Copynumber: 7.6 Consensus size: 41
583051 AAATTGCGGT
* * * * *
583061 GTTTGTATAAAAACGCCACTAAAGTATGAGTATTTAGCGGT
1 GTTTGAATAAAAATGCCACTAAAGTACGAGTATTTAGTGGC
* * * * *
583102 GTTCGTATAAAAATGCCACTAAATTACGAGTCTTTAGCT-GT
1 GTTTGAATAAAAATGCCACTAAAGTACGAGTATTTAG-TGGC
* **
583143 GTTT-ATATAAAAATGCCACTAAAGTACGAGTCTTTAGCAGC
1 GTTTGA-ATAAAAATGCCACTAAAGTACGAGTATTTAGTGGC
* * *
583184 GTTTGAATAAAAACGACACTAAAGTATGAGTATTTAGTGGC
1 GTTTGAATAAAAATGCCACTAAAGTACGAGTATTTAGTGGC
** * * *
583225 GTTTGTTCTTAAAATGCCTCTAAAGTAC-AGTATTTAGTGTC
1 GTTTG-AATAAAAATGCCACTAAAGTACGAGTATTTAGTGGC
*
583266 GTTT-ATATAAAAATGCCTCTAAAGTAC-AGTATTTAGTGGC
1 GTTTGA-ATAAAAATGCCACTAAAGTACGAGTATTTAGTGGC
*
583306 GTTT-ATATAAAAATGCCACTAAAGTACGAGTATTTACTGGC
1 GTTTGA-ATAAAAATGCCACTAAAGTACGAGTATTTAGTGGC
* *
583347 GTTTG-TTCAAAAATGCCGCTAAA
1 GTTTGAAT-AAAAATGCCACTAAA
583370 AACTCATTTT
Statistics
Matches: 226, Mismatches: 33, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
40 58 0.26
41 152 0.67
42 16 0.07
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33
Consensus pattern (41 bp):
GTTTGAATAAAAATGCCACTAAAGTACGAGTATTTAGTGGC
Found at i:583261 original size:123 final size:123
Alignment explanation
Indices: 583061--583369 Score: 394
Period size: 123 Copynumber: 2.5 Consensus size: 123
583051 AAATTGCGGT
* * * * *
583061 GTTTGTATAAAAACGCCACTAAAGTATGAGTATTTAGCGGTGTTCG-TATAAAAATGCCACTAAA
1 GTTTGAATAAAAACGCCACTAAAGTATGAGTATTTAGTGGCGTTTGTTCTAAAAATGCCACTAAA
* * *
583125 TTACGAGTCTTTAGCTGT-GTTTATATAAAAATGCCACTAAAGTACGAGTCTTTAGCAGC
66 GTACGAGTATTTAG-TGTCGTTTATATAAAAATGCCACTAAAGTAC-AGTATTTAGCAGC
* * *
583184 GTTTGAATAAAAACGACACTAAAGTATGAGTATTTAGTGGCGTTTGTTCTTAAAATGCCTCTAAA
1 GTTTGAATAAAAACGCCACTAAAGTATGAGTATTTAGTGGCGTTTGTTCTAAAAATGCCACTAAA
* **
583249 GTAC-AGTATTTAGTGTCGTTTATATAAAAATGCCTCTAAAGTACAGTATTTAGTGGC
66 GTACGAGTATTTAGTGTCGTTTATATAAAAATGCCACTAAAGTACAGTATTTAGCAGC
* * * *
583306 GTTT-ATATAAAAATGCCACTAAAGTACGAGTATTTACTGGCGTTTGTTC-AAAAATGCCGCTAA
1 GTTTGA-ATAAAAACGCCACTAAAGTATGAGTATTTAGTGGCGTTTGTTCTAAAAATGCCACTAA
583369 A
65 A
583370 AACTCATTTT
Statistics
Matches: 163, Mismatches: 20, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
121 14 0.09
122 56 0.34
123 75 0.46
124 18 0.11
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33
Consensus pattern (123 bp):
GTTTGAATAAAAACGCCACTAAAGTATGAGTATTTAGTGGCGTTTGTTCTAAAAATGCCACTAAA
GTACGAGTATTTAGTGTCGTTTATATAAAAATGCCACTAAAGTACAGTATTTAGCAGC
Found at i:584975 original size:14 final size:14
Alignment explanation
Indices: 584958--584990 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
584948 TTGTTTCACT
584958 GAAAACGTTTTCCG
1 GAAAACGTTTTCCG
584972 GAAAACGTTTTCCG
1 GAAAACGTTTTCCG
*
584986 TAAAA
1 GAAAA
584991 TGAATTATAT
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:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (14 bp):
GAAAACGTTTTCCG
Found at i:585164 original size:29 final size:28
Alignment explanation
Indices: 585132--585189 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
585122 TTATTTATCA
585132 TAAAACATAATATTATTATT-TTAAAATAT
1 TAAAA-ATAAT-TTATTATTGTTAAAATAT
585161 T-AAAATAATTTATTATTGTTAAAATAT
1 TAAAAATAATTTATTATTGTTAAAATAT
585188 TA
1 TA
585190 TTTTTATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.30
27 15 0.56
28 3 0.11
29 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (28 bp):
TAAAAATAATTTATTATTGTTAAAATAT
Found at i:585182 original size:27 final size:27
Alignment explanation
Indices: 585138--585189 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
585128 ATCATAAAAC
585138 ATAATATTATTATTTTAAAATATTAAA
1 ATAATATTATTATTTTAAAATATTAAA
585165 ATAAT-TTATTATTGTTAAAATATTA
1 ATAATATTATTATT-TTAAAATATTA
585190 TTTTTATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
ATAATATTATTATTTTAAAATATTAAA
Found at i:585247 original size:33 final size:30
Alignment explanation
Indices: 585181--585251 Score: 90
Period size: 33 Copynumber: 2.3 Consensus size: 30
585171 TATTATTGTT
* *
585181 AAAATATT-ATTTTTATAATTTTATTAATA
1 AAAATATTAATATTGATAATTTTATTAATA
585210 AAAATATTAATATTGATATATTTTATTGAAATA
1 AAAATATTAATATTGATA-ATTTTATT--AATA
585243 AAAATATTA
1 AAAATATTA
585252 TAAATTATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 8 0.22
30 7 0.19
31 8 0.22
33 13 0.36
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (30 bp):
AAAATATTAATATTGATAATTTTATTAATA
Found at i:585261 original size:31 final size:29
Alignment explanation
Indices: 585193--585262 Score: 70
Period size: 31 Copynumber: 2.2 Consensus size: 29
585183 AATATTATTT
*
585193 TTATAATTTTATTAATAAAAATATTAATAT
1 TTAT-ATTTTATTAATAAAAATATTAATAA
585223 TGATATATTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTATT--AATAAAAATATTAAT-AA
585256 TTATATT
1 TTATATT
585263 AATTATTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
30 1 0.03
31 14 0.41
32 5 0.15
33 14 0.41
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (29 bp):
TTATATTTTATTAATAAAAATATTAATAA
Found at i:585269 original size:33 final size:33
Alignment explanation
Indices: 585206--585269 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
585196 TAATTTTATT
* *
585206 AATAAAAATATTAATATTGATATATTTTATTGA
1 AATAAAAATATTAAAATTGATATATATTATTGA
585239 AATAAAAATATTATAAATT-ATAT-TAATTATT
1 AATAAAAATATTA-AAATTGATATAT-ATTATT
585270 TATTAAAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 1 0.04
33 22 0.81
34 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (33 bp):
AATAAAAATATTAAAATTGATATATATTATTGA
Found at i:585341 original size:23 final size:22
Alignment explanation
Indices: 585293--585342 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
585283 GTTTTATATT
* **
585293 ATATTTTAAAATGTTAATTAGT
1 ATATTTTAAAATCTTAATTAAA
*
585315 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAA-ATCTTAATTAAA
585338 ATATT
1 ATATT
585343 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (22 bp):
ATATTTTAAAATCTTAATTAAA
Found at i:585376 original size:18 final size:17
Alignment explanation
Indices: 585332--585379 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
585322 AAATATCTTT
* *
585332 ATTA-AAATATTATTAG
1 ATTATAAATAATATTAA
*
585348 ATTATATATAATATTAA
1 ATTATAAATAATATTAA
585365 ATATATAAATAATAT
1 AT-TATAAATAATAT
585380 ATTCACTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 4 0.15
17 11 0.42
18 11 0.42
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
ATTATAAATAATATTAA
Found at i:585503 original size:23 final size:22
Alignment explanation
Indices: 585463--585515 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
585453 ATTATTAAAA
**
585463 TAAAATATAATATCTTATATTAT
1 TAAAATATAATAGATTAT-TTAT
*
585486 TAAAATATAATGGATTATTTAT
1 TAAAATATAATAGATTATTTAT
*
585508 TATAATAT
1 TAAAATAT
585516 TAAAATATAA
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:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (22 bp):
TAAAATATAATAGATTATTTAT
Found at i:585511 original size:30 final size:28
Alignment explanation
Indices: 585438--585537 Score: 98
Period size: 28 Copynumber: 3.5 Consensus size: 28
585428 TATAATTTAT
585438 TAATAATTA-TTA-TATATTATTAAAATA
1 TAAT-ATTATTTATTATATTATTAAAATA
* * * *
585465 AAATATAATATCTTATATTATTAAAATA
1 TAATATTATTTATTATATTATTAAAATA
*
585493 TAATGGATTATTTATTATAATATTAAAATA
1 TAAT--ATTATTTATTATATTATTAAAATA
585523 TAAT-TTATATTATTA
1 TAATATTAT-TTATTA
585538 GAAATATTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
26 3 0.05
27 8 0.14
28 24 0.41
30 24 0.41
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (28 bp):
TAATATTATTTATTATATTATTAAAATA
Found at i:585544 original size:29 final size:28
Alignment explanation
Indices: 585483--585547 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 28
585473 TATCTTATAT
*
585483 TATTAAAATATAATGGATTATTTATTATAA
1 TATTAAAATATAAT-G-TTATTTATTAAAA
585513 TATTAAAATATAAT-TTATATTATTAGAAA
1 TATTAAAATATAATGTTAT-TTATTA-AAA
585542 TATTAA
1 TATTAA
585548 TAAATATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 4 0.12
28 6 0.19
29 8 0.25
30 14 0.44
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (28 bp):
TATTAAAATATAATGTTATTTATTAAAA
Found at i:585554 original size:22 final size:20
Alignment explanation
Indices: 585513--585564 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
585503 TTTATTATAA
**
585513 TATTAAAATATAATTTATAT
1 TATTAAAATATAATAAATAT
585533 TATTAGAAATATTAATAAATA-
1 TATTA-AAATA-TAATAAATAT
*
585554 TATTTAAATAT
1 TATTAAAATAT
585565 TTTAATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 1 0.04
20 10 0.37
21 9 0.33
22 7 0.26
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
TATTAAAATATAATAAATAT
Found at i:585558 original size:53 final size:55
Alignment explanation
Indices: 585435--585559 Score: 136
Period size: 53 Copynumber: 2.3 Consensus size: 55
585425 ATATATAATT
* *
585435 TATTAATAATTATTATATATTATTAAAATAAAATATAATATCTTATATTATTAAAA
1 TATTAATAAATA-TATTTATTATTAAAATAAAATATAATATCTTATATTATTAAAA
** *
585491 TA-TAATGGAT-TATTTATTA-TAATATTAAAATAT-A-AT-TTATATTATTAGAAA
1 TATTAATAAATATATTTATTATTAA-AATAAAATATAATATCTTATATTATTA-AAA
585542 TATTAATAAATATATTTA
1 TATTAATAAATATATTTA
585560 AATATTTTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
50 11 0.19
51 7 0.12
52 10 0.17
53 23 0.40
55 5 0.09
56 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (55 bp):
TATTAATAAATATATTTATTATTAAAATAAAATATAATATCTTATATTATTAAAA
Found at i:586052 original size:2 final size:2
Alignment explanation
Indices: 586045--586074 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
586035 GCAAAAATTC
586045 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
586075 TGAAAATAAG
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:590892 original size:29 final size:28
Alignment explanation
Indices: 590860--591007 Score: 124
Period size: 28 Copynumber: 5.2 Consensus size: 28
590850 AGGCAAGGAT
*
590860 AAAAACAAAGAGAAAAAGCAAAGAAATA
1 AAAAACAAAGAGAAAAAACAAAGAAATA
590888 AAAAACAAAGAGAAAAAACAAAGAAATAA
1 AAAAACAAAGAGAAAAAACAAAGAAAT-A
* *
590917 AAAAACAAAGAGCAAAGAGAA-AAAAAAACA
1 AAAAACAAAGAG-AAA-A-AACAAAGAAATA
* * * **
590947 AAGAGCAAAGA-AAAAACACAAATAAAGC
1 AAAAACAAAGAGAAAAA-ACAAAGAAATA
* *
590975 AAAGAGAAAGA-AAAAAACAAAGAAA-A
1 AAAAACAAAGAGAAAAAACAAAGAAATA
591001 AACAAAC
1 AA-AAAC
591008 GAAAATGCAA
Statistics
Matches: 97, Mismatches: 16, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.03
27 12 0.12
28 47 0.48
29 13 0.13
30 13 0.13
31 7 0.07
32 2 0.02
ACGTcount: A:0.76, C:0.09, G:0.13, T:0.02
Consensus pattern (28 bp):
AAAAACAAAGAGAAAAAACAAAGAAATA
Found at i:590921 original size:16 final size:15
Alignment explanation
Indices: 590860--590927 Score: 72
Period size: 13 Copynumber: 4.7 Consensus size: 15
590850 AGGCAAGGAT
*
590860 AAAAACAAAG--AGA
1 AAAAACAAAGAAATA
*
590873 AAAAGCAAAGAAATA
1 AAAAACAAAGAAATA
*
590888 AAAAACAAAG--AGA
1 AAAAACAAAGAAATA
590901 AAAAACAAAGAAATAA
1 AAAAACAAAGAAAT-A
590917 AAAAACAAAGA
1 AAAAACAAAGA
590928 GCAAAGAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
13 21 0.47
15 12 0.27
16 12 0.27
ACGTcount: A:0.78, C:0.07, G:0.12, T:0.03
Consensus pattern (15 bp):
AAAAACAAAGAAATA
Found at i:590932 original size:23 final size:22
Alignment explanation
Indices: 590906--591033 Score: 99
Period size: 23 Copynumber: 5.9 Consensus size: 22
590896 AGAGAAAAAA
590906 CAAAGAAATAAAAAAACAAAGAG
1 CAAAGAAA-AAAAAAACAAAGAG
590929 CAAAGAGAAAAAAAAACAAAGAG
1 CAAAGA-AAAAAAAAACAAAGAG
*
590952 CAAAGAAAAAACACAAA-TAA-AG
1 CAAAGAAAAAA-A-AAACAAAGAG
* *
590974 CAAAG-AGAAAGAAA-AAA-A-
1 CAAAGAAAAAAAAAACAAAGAG
*
590992 CAAAGAAAAAACAAACGAAA-ATG
1 CAAAGAAAAAAAAAAC-AAAGA-G
* *
591015 CAAAGAAAAAGAAGACAAA
1 CAAAGAAAAAAAAAACAAA
591034 AAGAACATGC
Statistics
Matches: 88, Mismatches: 9, Indels: 17
0.77 0.08 0.15
Matches are distributed among these distances:
18 5 0.06
19 13 0.15
21 8 0.09
22 15 0.17
23 42 0.48
24 5 0.06
ACGTcount: A:0.73, C:0.10, G:0.14, T:0.02
Consensus pattern (22 bp):
CAAAGAAAAAAAAAACAAAGAG
Found at i:591011 original size:28 final size:28
Alignment explanation
Indices: 590862--591007 Score: 113
Period size: 29 Copynumber: 5.1 Consensus size: 28
590852 GCAAGGATAA
*
590862 AAACAAAGAGAAAAAGCAAAGAAATAAA-
1 AAACAAAGAGAAAAAACAAAGAAA-AAAC
*
590890 AAACAAAGAGAAAAAACAAAGAAATAAAA
1 AAACAAAGAGAAAAAACAAAGAAA-AAAC
* * *
590919 AAACAAAGAGCAAAGAGAAA-AAAAAAC
1 AAACAAAGAGAAAAAACAAAGAAAAAAC
* * *
590946 AAAGAGCAA-AGAAAAAACACAA-ATAAAGC
1 AAACA--AAGAGAAAAAACA-AAGAAAAAAC
*
590975 AAAGAGAA-AGAAAAAAACAAAGAAAAAAC
1 AAACA-AAGAG-AAAAAACAAAGAAAAAAC
591004 AAAC
1 AAAC
591008 GAAAATGCAA
Statistics
Matches: 97, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
27 7 0.07
28 43 0.44
29 47 0.48
ACGTcount: A:0.75, C:0.10, G:0.13, T:0.02
Consensus pattern (28 bp):
AAACAAAGAGAAAAAACAAAGAAAAAAC
Found at i:591024 original size:12 final size:11
Alignment explanation
Indices: 590887--591024 Score: 61
Period size: 11 Copynumber: 12.5 Consensus size: 11
590877 GCAAAGAAAT
590887 AAAAAACAAAGAG
1 AAAAAAC-AA-AG
590900 AAAAAACAAAG
1 AAAAAACAAAG
* *
590911 AAATAAAAAAAC
1 AAA-AAACAAAG
* *
590923 AAAGAGCAAAG
1 AAAAAACAAAG
* *
590934 AGAAAAAAAAAC
1 A-AAAAACAAAG
* *
590946 AAAGAGCAAAG
1 AAAAAACAAAG
590957 AAAAAACACAA-
1 AAAAAACA-AAG
* *
590968 ATAAAGCAAAG
1 AAAAAACAAAG
* *
590979 --AGAA-AGA-
1 AAAAAACAAAG
590986 AAAAAACAAAG
1 AAAAAACAAAG
590997 AAAAAACAAACG
1 AAAAAACAAA-G
**
591009 AAAATGCAAAG
1 AAAAAACAAAG
591020 AAAAA
1 AAAAA
591025 GAAGACAAAA
Statistics
Matches: 90, Mismatches: 26, Indels: 20
0.66 0.19 0.15
Matches are distributed among these distances:
8 2 0.02
9 5 0.06
10 4 0.04
11 43 0.48
12 29 0.32
13 7 0.08
ACGTcount: A:0.75, C:0.09, G:0.13, T:0.02
Consensus pattern (11 bp):
AAAAAACAAAG
Found at i:591038 original size:40 final size:40
Alignment explanation
Indices: 590860--591027 Score: 105
Period size: 41 Copynumber: 4.0 Consensus size: 40
590850 AGGCAAGGAT
* * * *
590860 AAAAACAAAGAGAAAAA-GCAAAGAAA-TAAAAAACAAAGAGA
1 AAAAACAAAGA-AAAAACACAAATAAAGCAAAGAA-AAAGA-A
* *
590901 AAAAACAAAGAAATAAA-A-AAACAAAGAGCAAAGAGAAAAAAAA
1 AAAAACAAAGAAA-AAACACAAA-TAA-AGC-AA-AGAAAAAGAA
*
590944 ACAAAGAGCAAAGAAAAAACACAAATAAAGCAAAGAGAAAGAA
1 A-AAA-A-CAAAGAAAAAACACAAATAAAGCAAAGAAAAAGAA
590987 AAAAACAAAGAAAAAACA-AACGA-AAATGCAAAGAAAAAGAA
1 AAAAACAAAGAAAAAACACAA--ATAAA-GCAAAGAAAAAGAA
591028 GACAAAAAGA
Statistics
Matches: 104, Mismatches: 9, Indels: 28
0.74 0.06 0.20
Matches are distributed among these distances:
39 2 0.02
40 21 0.20
41 31 0.30
42 4 0.04
43 11 0.11
44 11 0.11
45 10 0.10
46 11 0.11
47 3 0.03
ACGTcount: A:0.75, C:0.09, G:0.14, T:0.02
Consensus pattern (40 bp):
AAAAACAAAGAAAAAACACAAATAAAGCAAAGAAAAAGAA
Found at i:593512 original size:35 final size:36
Alignment explanation
Indices: 593467--593565 Score: 103
Period size: 36 Copynumber: 2.8 Consensus size: 36
593457 TGTTTTTCTT
593467 AAAACAAAATTTTGTCTCGCTTGAGACAGA-TT-TATA
1 AAAAC-AAATTTTGTCTCGCTTGAGACA-ACTTCTATA
* * * * *
593503 AAAACAAATTTTGTCTCACTTAAGATAACTTCTCTT
1 AAAACAAATTTTGTCTCGCTTGAGACAACTTCTATA
* *
593539 AAAACAAACTTCGTCTCGCTTGAGACA
1 AAAACAAATTTTGTCTCGCTTGAGACA
593566 TTTTTCCTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
34 1 0.02
35 21 0.41
36 29 0.57
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCGCTTGAGACAACTTCTATA
Found at i:593663 original size:105 final size:105
Alignment explanation
Indices: 593539--593839 Score: 426
Period size: 105 Copynumber: 2.9 Consensus size: 105
593529 AACTTCTCTT
*
593539 AAAACAAACTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTCGAATTTGCTTCACT
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTCGAATTTGCTTCACT
* * *
593604 TGAAACAAAATTAATCTCACTTGAGATTGTTGTTTCTTTC
66 TGAAACAAAATTAATCTCACTTGAGATTGTTATTTATTCC
* *
593644 AAAACAAATTTCATCTCGCTTAAGACATTTTTCCTTTGAGATACAAATTTCGAATTTGCTTCACT
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTCGAATTTGCTTCACT
* *
593709 TGGAACAAAATTAATCTCACTTGCGATTGTTATTTATTCC
66 TGAAACAAAATTAATCTCACTTGAGATTGTTATTTATTCC
* * * * ** * * * *
593749 AAAACAAATTTTGTCTCACTTGAGATATTTTCCCTCAGA-ATACAAATTTCAAAGTTG-TTTAAT
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTCGAATTTGCTTCACT
593812 TGAAACAAAATTAATCTCACTTGAGATT
66 TGAAACAAAATTAATCTCACTTGAGATT
593840 TTCAAAATCG
Statistics
Matches: 174, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
103 30 0.17
104 16 0.09
105 128 0.74
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (105 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTCGAATTTGCTTCACT
TGAAACAAAATTAATCTCACTTGAGATTGTTATTTATTCC
Found at i:593978 original size:27 final size:25
Alignment explanation
Indices: 593922--594003 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 25
593912 CTCTCGAAAC
*
593922 AAATCTTTGAGTCTGTTCCTTTTGAAA
1 AAATCTTTGAGTCTGTTTC-TTT-AAA
593949 AAATCTTTGAGTCTGTTTCTCTTAACA
1 AAATCTTTGAGTCTGTTTCT-TTAA-A
*
593976 AAATCATATGTGAGTCTATTTCTTTAAA
1 AAATC-T-T-TGAGTCTGTTTCTTTAAA
594004 CACAAATATT
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
26 3 0.06
27 26 0.54
28 2 0.04
29 5 0.10
30 12 0.25
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (25 bp):
AAATCTTTGAGTCTGTTTCTTTAAA
Found at i:594279 original size:27 final size:27
Alignment explanation
Indices: 594235--594319 Score: 89
Period size: 28 Copynumber: 3.0 Consensus size: 27
594225 AGACAGTTGC
* *
594235 TTTTGAAACACAACATCTTTGAGTTTGTT
1 TTTTTAAA-ACAA-ATCTTTGAGTCTGTT
594264 TTTTTAAAACAAATCTTTGAGTCTGTT
1 TTTTTAAAACAAATCTTTGAGTCTGTT
* * * *
594291 TCTTTTGAACCATATCTTTGAGTCAGTT
1 T-TTTTAAAACAAATCTTTGAGTCTGTT
594319 T
1 T
594320 CTCTTGAAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
27 15 0.31
28 27 0.55
29 7 0.14
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.47
Consensus pattern (27 bp):
TTTTTAAAACAAATCTTTGAGTCTGTT
Found at i:594320 original size:28 final size:28
Alignment explanation
Indices: 594249--594333 Score: 100
Period size: 28 Copynumber: 3.0 Consensus size: 28
594239 GAAACACAAC
* * * *
594249 ATCTTTGAGTTTGTTT-TTTTAAAACAA
1 ATCTTTGAGTCTGTTTCTTTTGAACCAT
594276 ATCTTTGAGTCTGTTTCTTTTGAACCAT
1 ATCTTTGAGTCTGTTTCTTTTGAACCAT
* *
594304 ATCTTTGAGTCAGTTTCTCTTGAAACCAT
1 ATCTTTGAGTCTGTTTCTTTTG-AACCAT
594333 A
1 A
594334 ATCCCTAAGG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
27 15 0.30
28 28 0.56
29 7 0.14
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.47
Consensus pattern (28 bp):
ATCTTTGAGTCTGTTTCTTTTGAACCAT
Found at i:594418 original size:40 final size:40
Alignment explanation
Indices: 594352--594453 Score: 102
Period size: 43 Copynumber: 2.5 Consensus size: 40
594342 GGATGGCCAA
* *
594352 CCATCCTCATCACGTAGAAACTGTGTCATACC-T-TGACCAG
1 CCATCCTCATCACGTAG-GACTGTGTCA-ACCATATAACCAG
*
594392 ACC-TCCTCATCACGTAGGAGTAGTGTCAACCATAGATAACCAG
1 -CCATCCTCATCACGTAGGACT-GTGTCAACCAT--ATAACCAG
594435 CCATCCTCATCACGTAGGA
1 CCATCCTCATCACGTAGGA
594454 ACCAAGTTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
39 5 0.10
40 21 0.40
41 2 0.04
42 2 0.04
43 22 0.42
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (40 bp):
CCATCCTCATCACGTAGGACTGTGTCAACCATATAACCAG
Found at i:594662 original size:130 final size:132
Alignment explanation
Indices: 594338--594686 Score: 346
Period size: 134 Copynumber: 2.6 Consensus size: 132
594328 ACCATAATCC
* * * * * * *** * *
594338 CTAAGGATGGCCAACCATCCTCATCACGTAGAAACTGTGTCATACCTTGACCAGACCTCCTCATC
1 CTAAAGATGGCCAGCCCTCCTCATCACGTAGGAACAGTGTCATTCCCCAACCACACCTTCTCATC
*
594403 ACGTAGGAGTAGTGTCAACCATAGATAACCAGCCATCCTCATCACGTAGGAACCAAGTTATCACC
66 ACGTAGGAGTAGTGTCACCCATAGATAACCAGCCATCCTCATCACGTAGGAACCAAGTTAT--CC
594468 ACTT
129 ACTT
* * *
594472 CTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACAGTGTCATTCCCCGACCAGACCTTCTCATC
1 CTAAAGATGGCCAGCCCTCCTCATCACGTAGGAACAGTGTCATTCCCCAACCACACCTTCTCATC
** * * * * ***
594537 ACGTAGGAGCCGTGTCACCCCT-GATAACCAGTCGTCCTCATCATGTAGGAACTGTGTTAT-CA-
66 ACGTAGGAGTAGTGTCACCCATAGATAACCAGCCATCCTCATCACGTAGGAACCAAGTTATCCAC
594599 TT
131 TT
* * * * * *
594601 CCTAAAGATGG-CATGCCCTCTTCATCACGTATGAGCAGTGTTATTCCTCAACCACATCTTCTCA
1 -CTAAAGATGGCCA-GCCCTCCTCATCACGTAGGAACAGTGTCATTCCCCAACCACACCTTCTCA
* *
594665 TCACGTAGAAGTTGTGTCACCC
64 TCACGTAGGAGTAGTGTCACCC
594687 TTCGACGACC
Statistics
Matches: 182, Mismatches: 31, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
129 4 0.02
130 72 0.40
133 32 0.18
134 74 0.41
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.25
Consensus pattern (132 bp):
CTAAAGATGGCCAGCCCTCCTCATCACGTAGGAACAGTGTCATTCCCCAACCACACCTTCTCATC
ACGTAGGAGTAGTGTCACCCATAGATAACCAGCCATCCTCATCACGTAGGAACCAAGTTATCCAC
TT
Found at i:594885 original size:3 final size:3
Alignment explanation
Indices: 594879--594923 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
594869 AGTCTTCTTT
*
594879 TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
594924 CATTTTATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:595822 original size:19 final size:19
Alignment explanation
Indices: 595784--595822 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
595774 TCACTGTAAA
*
595784 TTATTTTTTTAATTATTTT
1 TTATTTTTTTAATTAATTT
595803 TTATTTTTTT-ATGTAATTT
1 TTATTTTTTTAAT-TAATTT
595822 T
1 T
595823 GCATAGTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (19 bp):
TTATTTTTTTAATTAATTT
Found at i:596095 original size:30 final size:30
Alignment explanation
Indices: 595946--596080 Score: 84
Period size: 29 Copynumber: 4.6 Consensus size: 30
595936 TTTAGTTTTC
* * *
595946 TATTTTTT-TATTTTAGTCATTTAAAGGTT
1 TATTTTTTCTATTTTGGTCCTTTAAAGTTT
* * * * **
595975 TGTATTTTCTA-TTTAGCCCCCTAAA-TTT
1 TATTTTTTCTATTTTGGTCCTTTAAAGTTT
* * *
596003 CTATTTTTACTGTTTTAGTCC-TT-AAGTTT
1 -TATTTTTTCTATTTTGGTCCTTTAAAGTTT
**
596032 CTA-TTTTTCTATTTTGGTCCTTTAGGGTTT
1 -TATTTTTTCTATTTTGGTCCTTTAAAGTTT
596062 TATTTTTTCTATTTTGGTC
1 TATTTTTTCTATTTTGGTC
596081 TTACAAGTTA
Statistics
Matches: 81, Mismatches: 18, Indels: 13
0.72 0.16 0.12
Matches are distributed among these distances:
28 18 0.22
29 34 0.42
30 29 0.36
ACGTcount: A:0.17, C:0.13, G:0.11, T:0.59
Consensus pattern (30 bp):
TATTTTTTCTATTTTGGTCCTTTAAAGTTT
Found at i:598114 original size:9 final size:9
Alignment explanation
Indices: 598047--598115 Score: 68
Period size: 9 Copynumber: 7.4 Consensus size: 9
598037 AATACTAAAC
*
598047 AATAAAATA
1 AATAAAAAA
*
598056 AATAAAGAA
1 AATAAAAAA
*
598065 AAT-GAAAA
1 AATAAAAAA
*
598073 AATGAAAAA
1 AATAAAAAA
598082 AATAAAATAA
1 AATAAAA-AA
598092 CAATAAAGAAA
1 -AATAAA-AAA
598103 AATAAAAAA
1 AATAAAAAA
598112 AATA
1 AATA
598116 TTATTTTAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
8 6 0.12
9 27 0.54
10 8 0.16
11 8 0.16
12 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.14
Consensus pattern (9 bp):
AATAAAAAA
Found at i:599178 original size:26 final size:26
Alignment explanation
Indices: 599119--599178 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
599109 GATTTTGGAC
599119 CTAATAAATAAAAAAAGAAAAAAGAA
1 CTAATAAATAAAAAAAGAAAAAAGAA
* * * *
599145 CGAGTAAATAATAAAATAAAAAATGAA
1 CTAATAAATAAAAAAAGAAAAAA-GAA
599172 -TAATAAA
1 CTAATAAA
599179 AATTATATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
26 24 0.89
27 3 0.11
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.17
Consensus pattern (26 bp):
CTAATAAATAAAAAAAGAAAAAAGAA
Found at i:599193 original size:2 final size:2
Alignment explanation
Indices: 599182--599226 Score: 58
Period size: 2 Copynumber: 22.5 Consensus size: 2
599172 TAATAAAAAT
599182 TA TA TA -A TA TA TA TA TA TA TA TA TA TA GTA TA CTA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA
599224 TA T
1 TA T
599227 TTTAAAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 2 0.05
2 33 0.85
3 4 0.10
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:599313 original size:35 final size:34
Alignment explanation
Indices: 599215--599679 Score: 224
Period size: 37 Copynumber: 12.4 Consensus size: 34
599205 TATAGTATAC
*
599215 TATATAATATAT-TTTAAAAAAATTGTTTT-AAAAC-
1 TATATTATATATATTT--AAAAA-TGTTTTCAAAACA
* *
599249 TATATAATATATATTTCAAAAATATTTTCAAAATCA
1 TATATTATATATATTT-AAAAATGTTTTCAAAA-CA
599285 TATATTATATATATATT-AAAATGTTTTCAAAACTA
1 TATATTATATATAT-TTAAAAATGTTTTCAAAAC-A
* *
599320 TATATTATATATAATTTTTGAAATGTCAAAAGGATTTTTAAAA-A
1 TATATTATATAT-A--TTT---A----AAAATG-TTTTCAAAACA
* *
599364 CTATATAATATATAAATGTTTTCAAAATGTTTTCAAAACTA
1 -TATATTATATAT--A---TTTAAAAATGTTTTCAAAAC-A
599405 TATATTATATATATTTTAAAAATGTTTTCAAAAACTA
1 TATATTATATATA-TTTAAAAATGTTTTC-AAAAC-A
* *
599442 TATATTATATATAATTTTCAAAATGTTTTAAAAACTA
1 TATATTATATAT-A-TTTAAAAATGTTTTCAAAAC-A
* * *
599479 TATATTATATATATTTTTCACAATGATTTTTAAAAACTA
1 TATATTATATATA--TTTAAAAATG--TTTTCAAAAC-A
* * *
599518 TATAATATATAAATGTCTTCAAAATGTTTTCAAAACTA
1 TAT-AT-TATATATAT-TTAAAAATGTTTTCAAAAC-A
*
599556 TATATTATATATATTTTAAAAATGTTTTTAAAAACTA
1 TATATTATATATA-TTTAAAAATG-TTTTCAAAAC-A
* * * *
599593 TATAATATATATTTTTGAAAAACGTTTTCTGAAAATTA
1 TATATTATATATATTT-AAAAATGTTTTC--AAAA-CA
* *
599631 TATATTATAT-T-TTGTCAAAAACGTTTTCAAAAACC
1 TATATTATATATATT-T-AAAAATGTTTTC-AAAACA
599666 TATATTACTATATA
1 TATATTA-TATATA
599680 CATATATATA
Statistics
Matches: 356, Mismatches: 34, Indels: 78
0.76 0.07 0.17
Matches are distributed among these distances:
33 5 0.01
34 22 0.06
35 38 0.11
36 60 0.17
37 98 0.28
38 45 0.13
39 24 0.07
40 26 0.07
41 7 0.02
44 1 0.00
45 16 0.04
46 10 0.03
47 4 0.01
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (34 bp):
TATATTATATATATTTAAAAATGTTTTCAAAACA
Found at i:599344 original size:37 final size:36
Alignment explanation
Indices: 599233--599640 Score: 344
Period size: 38 Copynumber: 10.8 Consensus size: 36
599223 ATATTTTAAA
**
599233 AAAATTGTTTT-AAAACTATATA--ATATATATTTCA
1 AAAA-TGTTTTCAAAACTATATATTATATATATTTTT
* *
599267 AAAATATTTTCAAAA-TCATATATTATATATA-TATT
1 AAAATGTTTTCAAAACT-ATATATTATATATATTTTT
599302 AAAATGTTTTCAAAACTATATATTATATATAATTTTTGAAATGT
1 AAAATGTTTTCAAAACTATATATTATATAT-A--TTT----T-T
* * * *
599346 CAAAAGGATTTTTAAAAACTATATAATATATAAATGTTTT
1 -AAAATG--TTTTCAAAACTATATATTATATATAT-TTTT
*
599386 CAAAATGTTTTCAAAACTATATATTATATATATTTTA
1 -AAAATGTTTTCAAAACTATATATTATATATATTTTT
*
599423 AAAATGTTTTCAAAAACTATATATTATATATAATTTTC
1 AAAATGTTTTC-AAAACTATATATTATATAT-ATTTTT
*
599461 AAAATGTTTTAAAAACTATATATTATATATATTTTT
1 AAAATGTTTTCAAAACTATATATTATATATATTTTT
* * * * *
599497 CACAATGATTTTTAAAAACTATATAATATATAAATGTCTTC
1 -AAAATG--TTTTCAAAACTATATATTATATATAT-T-TTT
*
599538 AAAATGTTTTCAAAACTATATATTATATATATTTTA
1 AAAATGTTTTCAAAACTATATATTATATATATTTTT
*
599574 AAAATGTTTTTAAAAACTATATA--ATATATATTTTT
1 AAAATG-TTTTCAAAACTATATATTATATATATTTTT
* *
599609 GAAAAACGTTTTCTGAAAATTATATATTATAT
1 --AAAATGTTTTC--AAAACTATATATTATAT
599641 TTTGTCAAAA
Statistics
Matches: 310, Mismatches: 32, Indels: 58
0.77 0.08 0.14
Matches are distributed among these distances:
33 6 0.02
34 13 0.04
35 39 0.13
36 37 0.12
37 67 0.22
38 71 0.23
39 25 0.08
40 17 0.05
41 3 0.01
43 1 0.00
44 2 0.01
45 7 0.02
46 1 0.00
47 21 0.07
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
AAAATGTTTTCAAAACTATATATTATATATATTTTT
Found at i:599393 original size:11 final size:11
Alignment explanation
Indices: 599377--599401 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
599367 TATAATATAT
599377 AAATGTTTTCA
1 AAATGTTTTCA
599388 AAATGTTTTCA
1 AAATGTTTTCA
599399 AAA
1 AAA
599402 CTATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:599533 original size:151 final size:153
Alignment explanation
Indices: 599233--599604 Score: 535
Period size: 151 Copynumber: 2.4 Consensus size: 153
599223 ATATTTTAAA
* * *
599233 AAAATTGTTTT-AAAACTATATA--ATATATATTTCAAAAATATTTTCAAAATC-ATATATTATA
1 AAAA-TGTTTTCAAAACTATATATTATATATATTTTAAAAATGTTTTCAAAAACTATATATTATA
*
599294 TATATATTAAAATGTTTTCAAAACTATATATTATATATAATTTTTGAAATGTCAAAAGGATTTTT
65 TATATATTAAAATGTTTTAAAAACTATATATTATATATAA-TTTT---ATGTCAAAAGGATTTTT
*
599359 AAAAACTATATAATATATAAATGTTTTC
126 AAAAACTATATAATATATAAATGTCTTC
599387 AAAATGTTTTCAAAACTATATATTATATATATTTTAAAAATGTTTTCAAAAACTATATATTATAT
1 AAAATGTTTTCAAAACTATATATTATATATATTTTAAAAATGTTTTCAAAAACTATATATTATAT
* * *
599452 ATAATTTTCAAAATGTTTTAAAAACTATATATTATATAT-A-TTT-T-TCACAATGATTTTTAAA
66 AT-ATATT-AAAATGTTTTAAAAACTATATATTATATATAATTTTATGTCAAAAGGATTTTTAAA
599513 AACTATATAATATATAAATGTCTTC
129 AACTATATAATATATAAATGTCTTC
* *
599538 AAAATGTTTTCAAAACTATATATTATATATATTTTAAAAATGTTTTTAAAAACTATATAATATAT
1 AAAATGTTTTCAAAACTATATATTATATATATTTTAAAAATGTTTTCAAAAACTATATATTATAT
599603 AT
66 AT
599605 TTTTGAAAAA
Statistics
Matches: 202, Mismatches: 10, Indels: 15
0.89 0.04 0.07
Matches are distributed among these distances:
151 104 0.51
152 1 0.00
153 6 0.03
154 15 0.07
156 29 0.14
157 13 0.06
158 5 0.02
159 29 0.14
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (153 bp):
AAAATGTTTTCAAAACTATATATTATATATATTTTAAAAATGTTTTCAAAAACTATATATTATAT
ATATATTAAAATGTTTTAAAAACTATATATTATATATAATTTTATGTCAAAAGGATTTTTAAAAA
CTATATAATATATAAATGTCTTC
Found at i:600410 original size:84 final size:84
Alignment explanation
Indices: 600302--601688 Score: 1406
Period size: 84 Copynumber: 16.6 Consensus size: 84
600292 GCAGTAAACT
** * * * *
600302 TGATATGCCTTTGAGCTGAATGTAATCGAACTTGAAGGTCTTTTGTTGACAGATAACCCTTCTCG
1 TGATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
* ** *
600367 TCACGAGTTATGTTGTAAA
66 CCTTGAGTTATGTTGCAAA
* * * * * * *
600386 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTTGAAGGTC-TTGGTTGGCAGATAGCCCTTCTTG
1 TGATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
** **
600450 CCTTGAGTTATACTATAAA
66 CCTTGAGTTATGTTGCAAA
* * * *
600469 TG--ATGCGCTCTTGAGCTGAGTGTAATTGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCT
1 TGATATGC-CT-TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCT
* **
600531 AGCCTTGATTTATACTGCAAA
64 AGCCTTGAGTTATGTTGCAAA
* * * * * * * * * *
600552 TAATGTGCCTTGGAGCCGAGTGTAATCGAACTCGAAGGTC-TTGGTTGGAAAATAACCCTTCTTG
1 TGATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
* *
600616 CCTTGAGCTATGATGCAAA
66 CCTTGAGTTATGTTGCAAA
* * * * * * *
600635 TGATGTGCATTGGAGCTGAGCATAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCATTCTAG
1 TGATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
*
600700 CCTTGAGTTATGCTGCAAA
66 CCTTGAGTTATGTTGCAAA
* * * * * *
600719 TGAAATGCCTTTGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGTTGGCAAATAACCATGCTTG
1 TGATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
* *
600784 CCTTTG-GCTATGTTGTAAA
66 CC-TTGAGTTATGTTGCAAA
* * * * * *
600803 TGATGTGCCTTGGAGCTGAGCATAGTCAAACTCGAAGGTCTTTAGTTGGCAGATAACTCTTCTAG
1 TGATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
600868 CCTTGAGTTATGTTGCAAA
66 CCTTGAGTTATGTTGCAAA
* * * * * * * **
600887 TGATATGCCTTTGAGCTGAGCATAGTCAAACTTGAAGGTCTTTTGTTGGAAAATATCCGTTCTTT
1 TGATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
*
600952 CCTTGAGCTAT-TTGCAAA
66 CCTTGAGTTATGTTGCAAA
* * * *
600970 TGATATGCCTTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGTAGATAACCCTTCTAA
1 TGATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
* * *
601035 CCTTGAGTTAAGCTACAAA
66 CCTTGAGTTATGTTGCAAA
* * * * * *
601054 TGATAAGCCTTTGAGCTTAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTATTG
1 TGATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
* *
601119 CCTTGAGCTATGTTACAAA
66 CCTTGAGTTATGTTGCAAA
* * * *
601138 TGATGTGCCTTCGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTGTAG
1 TGATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
*
601203 CCTTGAGTTATGCTGCAAA
66 CCTTGAGTTATGTTGCAAA
* * * * * * *
601222 TAATATTCCTTTGAGCTGAGCGTAGTCAAACTCGAAGGTATTTTGTTGGCAAATAGCCCTTCTTG
1 TGATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
* *
601287 CCTTGAGCTATTTTGCAAA
66 CCTTGAGTTATGTTGCAAA
* * * * * * *
601306 TGATATGCCTTGGAACTTAGCGTAGTCAAACTCGAATGTCTTTGGTTGGTAGATAACCCTTCTAG
1 TGATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
**
601371 CCTTGAGTTATACTGCAAA
66 CCTTGAGTTATGTTGCAAA
* * * * * * *
601390 TTATATGCCTTTGAGCTGAGTGTAGTCGAAATTGAAAGTCTTTTGTTGGCAAATAGCCCTTCTTA
1 TGATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTC-TA
* *
601455 -CCTTGAGCTATATTGCAAA
65 GCCTTGAGTTATGTTGCAAA
* * ** * *
601474 TGATGTGCCTTGGAGCTGAGCGTAGTCGAACAAGAAGGTCTTTGGTTGGTAGATAACCCTTCTAG
1 TGATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
** *
601539 CCTTGAGTTATACTGTAAA
66 CCTTGAGTTATGTTGCAAA
* * * * * * * * *
601558 TAATATGCCTTTGAACTGAGAGTAGTCAAACTTGAAGGTCTTTTGTTGGCAAATAGCTCTTCT-T
1 TGATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
*
601622 CCTTGAGCTATGTTGCAAA
66 CCTTGAGTTATGTTGCAAA
* * *
601641 TGATATGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTG
1 TGATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTG
601689 AAGGTGCTTA
Statistics
Matches: 1080, Mismatches: 213, Indels: 21
0.82 0.16 0.02
Matches are distributed among these distances:
81 3 0.00
82 2 0.00
83 325 0.30
84 742 0.69
85 8 0.01
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.34
Consensus pattern (84 bp):
TGATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAG
CCTTGAGTTATGTTGCAAA
Found at i:600829 original size:168 final size:168
Alignment explanation
Indices: 600271--601688 Score: 1679
Period size: 168 Copynumber: 8.5 Consensus size: 168
600261 GTTGACCGAT
* ** * * * ** * *
600271 GCCCTTCTTACCTTGAGCTATGCAGTAAACTTGATATGCCTTTGAGCTGAATGTAATCGAACTTG
1 GCCCTTCTTGCCTTGAGCTATGTTGCAAA--TGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCG
* * * * ** * * **
600336 AAGGTCTTTTGTTGACAGATAACCCTTCTCGTCACGAGTTATGTTGTAAATGATGTGCCTTTGAG
64 AAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAAATGCCTTTGAG
* * *
600401 CTGAGTGTAATCGAACTTGAAGGTC-TTGGTTGGCAGATA
129 CTGAGTGTAGTCGAACTTGAAGGTCTTTTGTTGGCAAATA
* ** ** * * * *
600440 GCCCTTCTTGCCTTGAGTTATACTATAAATGATGCGCTCTT-GAGCTGAGTGTAATTGAACTCGA
1 GCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGC-CTTGGAGCTGAGCGTAGTCGAACTCGA
* * * * *
600504 AGGTCTTT-GTTGACAGATAACCCTTCTAGCCTTGATTTATACTGCAAAT-AATGTGCCTTGGAG
65 AGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAA-ATGCCTTTGAG
* * * * *
600567 CCGAGTGTAATCGAACTCGAAGGTC-TTGGTTGGAAAATA
129 CTGAGTGTAGTCGAACTTGAAGGTCTTTTGTTGGCAAATA
* * * * *
600606 ACCCTTCTTGCCTTGAGCTATGATGCAAATGATGTGCATTGGAGCTGAGCATAGTCGAACTCAAA
1 GCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
*
600671 GGTCTTTGGTTGGCAGATAACCATTCTAGCCTTGAGTTATGCTGCAAATGAAATGCCTTTGAGCT
66 GGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAAATGCCTTTGAGCT
*
600736 GAGCGTAGTCGAACTTGAAGGTCTTTTGTTGGCAAATA
131 GAGTGTAGTCGAACTTGAAGGTCTTTTGTTGGCAAATA
* * * * * *
600774 ACCATGCTTGCCTTTG-GCTATGTTGTAAATGATGTGCCTTGGAGCTGAGCATAGTCAAACTCGA
1 GCCCTTCTTGCC-TTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGA
* * * *
600838 AGGTCTTTAGTTGGCAGATAACTCTTCTAGCCTTGAGTTATGTTGCAAATGATATGCCTTTGAGC
65 AGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAAATGCCTTTGAGC
** * *
600903 TGAGCATAGTCAAACTTGAAGGTCTTTTGTTGGAAAATA
130 TGAGTGTAGTCGAACTTGAAGGTCTTTTGTTGGCAAATA
* * * * * *
600942 TCCGTTCTTTCCTTGAGCTAT-TTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGAACTCAAA
1 GCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
* * * *
601006 GGTCTTTGGTTGGTAGATAACCCTTCTAACCTTGAGTTAAGCTACAAATGATAA-GCCTTTGAGC
66 GGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGA-AATGCCTTTGAGC
* *
601070 TTAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATA
130 TGAGTGTAGTCGAACTTGAAGGTCTTTTGTTGGCAAATA
* * * *
601109 ACCCTTATTGCCTTGAGCTATGTTACAAATGATGTGCCTTCGAGCTGAGCGTAGTCGAACTCGAA
1 GCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
* *
601174 GGTCTTTGGTTGGCAGATAACCCTTGTAGCCTTGAGTTATGCTGCAAAT-AATATTCCTTTGAGC
66 GGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAA-ATGCCTTTGAGC
* * * *
601238 TGAGCGTAGTCAAACTCGAAGGTATTTTGTTGGCAAATA
130 TGAGTGTAGTCGAACTTGAAGGTCTTTTGTTGGCAAATA
* * * * *
601277 GCCCTTCTTGCCTTGAGCTATTTTGCAAATGATATGCCTTGGAACTTAGCGTAGTCAAACTCGAA
1 GCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
* * * * *
601342 TGTCTTTGGTTGGTAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATTATATGCCTTTGAGCT
66 GGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAAATGCCTTTGAGCT
* *
601407 GAGTGTAGTCGAAATTGAAAGTCTTTTGTTGGCAAATA
131 GAGTGTAGTCGAACTTGAAGGTCTTTTGTTGGCAAATA
* * **
601445 GCCCTTCTTACCTTGAGCTATATTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACAAGAA
1 GCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
* * * *
601510 GGTCTTTGGTTGGTAGATAACCCTTCTAGCCTTGAGTTATACTGTAAAT-AATATGCCTTTGAAC
66 GGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAA-ATGCCTTTGAGC
* *
601574 TGAGAGTAGTCAAACTTGAAGGTCTTTTGTTGGCAAATA
130 TGAGTGTAGTCGAACTTGAAGGTCTTTTGTTGGCAAATA
* * * *
601613 GCTCTTCTT-CCTTGAGCTATGTTGCAAATGATATGCCTTGGAGCTGAGTGTAATCGAACTCGAA
1 GCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
*
601677 GGTCTTTTGTTG
66 GGTCTTTGGTTG
601689 AAGGTGCTTA
Statistics
Matches: 1084, Mismatches: 151, Indels: 30
0.86 0.12 0.02
Matches are distributed among these distances:
165 3 0.00
166 135 0.12
167 308 0.28
168 610 0.56
169 28 0.03
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.33
Consensus pattern (168 bp):
GCCCTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
GGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAAATGCCTTTGAGCT
GAGTGTAGTCGAACTTGAAGGTCTTTTGTTGGCAAATA
Found at i:600999 original size:335 final size:336
Alignment explanation
Indices: 600271--601688 Score: 1765
Period size: 335 Copynumber: 4.2 Consensus size: 336
600261 GTTGACCGAT
* ** * * ** * *
600271 GCCCTTCTTACCTTGAGCTATGCAGTAAACTTGATATGCCTTTGAGCTGAATGTAATCGAACTTG
1 GCCCTTCTTGCCTTGAGCTATGTTGCAAA--TGATATGCCTTGGAGCTGAGCGTAGTCGAACTCG
* * * * ** * * **
600336 AAGGTCTTTTGTTGACAGATAACCCTTCTCGTCACGAGTTATGTTGTAAATGATGTGCCTTTGAG
64 AAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAAATGCCTTTGAG
* * * * * *
600401 CTGAGTGTAATCGAACTTGAAGGTC-TTGGTTGGCAGATAGCCCTTCTTGCCTTGAGTTATACTA
129 CTGAGTGTAGTCGAACTTGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATATTA
* * * * * *
600465 TAAATGATGCGCTCTT-GAGCTGAGTGTAATTGAACTCGAAGGTCTTT-GTTGACAGATAACCCT
194 CAAATGATGTGC-CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCT
* * * * ** * *
600528 TCTAGCCTTGATTTATACTGCAAATAATGTGCCTTGGAGCCGAGTGTAATCGAACTCGAAGGTC-
258 TCTAGCCTTGAGTTATACTGCAAATAATATGCCTTTGAGCTGAGCATAGTCAAACTCGAAGGTCT
*
600592 TTGGTTGGAAAATA
323 TTTGTTGGAAAATA
* * * * * *
600606 ACCCTTCTTGCCTTGAGCTATGATGCAAATGATGTGCATTGGAGCTGAGCATAGTCGAACTCAAA
1 GCCCTTCTTGCCTTGAGCTATGTTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
*
600671 GGTCTTTGGTTGGCAGATAACCATTCTAGCCTTGAGTTATGCTGCAAATGAAATGCCTTTGAGCT
66 GGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAAATGCCTTTGAGCT
* * * * **
600736 GAGCGTAGTCGAACTTGAAGGTCTTTTGTTGGCAAATAACCATGCTTGCCTTTG-GCTATGTTGT
131 GAGTGTAGTCGAACTTGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCC-TTGAGCTATATTAC
* * * *
600800 AAATGATGTGCCTTGGAGCTGAGCATAGTCAAACTCGAAGGTCTTTAGTTGGCAGATAACTCTTC
195 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
** * *
600865 TAGCCTTGAGTTATGTTGCAAATGATATGCCTTTGAGCTGAGCATAGTCAAACTTGAAGGTCTTT
260 TAGCCTTGAGTTATACTGCAAATAATATGCCTTTGAGCTGAGCATAGTCAAACTCGAAGGTCTTT
600930 TGTTGGAAAATA
325 TGTTGGAAAATA
* * * * *
600942 TCCGTTCTTTCCTTGAGCTAT-TTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGAACTCAAA
1 GCCCTTCTTGCCTTGAGCTATGTTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
* * * *
601006 GGTCTTTGGTTGGTAGATAACCCTTCTAACCTTGAGTTAAGCTACAAATGATAA-GCCTTTGAGC
66 GGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGA-AATGCCTTTGAGC
* * * *
601070 TTAGTGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTATTGCCTTGAGCTATGTTAC
130 TGAGTGTAGTCGAACTTGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATATTAC
* *
601135 AAATGATGTGCCTTCGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTG
195 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
* * * *
601200 TAGCCTTGAGTTATGCTGCAAATAATATTCCTTTGAGCTGAGCGTAGTCAAACTCGAAGGTATTT
260 TAGCCTTGAGTTATACTGCAAATAATATGCCTTTGAGCTGAGCATAGTCAAACTCGAAGGTCTTT
*
601265 TGTTGGCAAATA
325 TGTTGGAAAATA
* * * *
601277 GCCCTTCTTGCCTTGAGCTATTTTGCAAATGATATGCCTTGGAACTTAGCGTAGTCAAACTCGAA
1 GCCCTTCTTGCCTTGAGCTATGTTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
* * * * *
601342 TGTCTTTGGTTGGTAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATTATATGCCTTTGAGCT
66 GGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAAATGCCTTTGAGCT
* * * * *
601407 GAGTGTAGTCGAAATTGAAAGTCTTTTGTTGGCAAATAGCCCTTCTTACCTTGAGCTATATTGCA
131 GAGTGTAGTCGAACTTGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATATTACA
** *
601472 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACAAGAAGGTCTTTGGTTGGTAGATAACCCTTCT
196 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
* * *
601537 AGCCTTGAGTTATACTGTAAATAATATGCCTTTGAACTGAG-AGTAGTCAAACTTGAAGGTCTTT
261 AGCCTTGAGTTATACTGCAAATAATATGCCTTTGAGCTGAGCA-TAGTCAAACTCGAAGGTCTTT
*
601601 TGTTGGCAAATA
325 TGTTGGAAAATA
* * *
601613 GCTCTTCTT-CCTTGAGCTATGTTGCAAATGATATGCCTTGGAGCTGAGTGTAATCGAACTCGAA
1 GCCCTTCTTGCCTTGAGCTATGTTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
*
601677 GGTCTTTTGTTG
66 GGTCTTTGGTTG
601689 AAGGTGCTTA
Statistics
Matches: 937, Mismatches: 136, Indels: 20
0.86 0.12 0.02
Matches are distributed among these distances:
333 105 0.11
334 66 0.07
335 447 0.48
336 319 0.34
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.33
Consensus pattern (336 bp):
GCCCTTCTTGCCTTGAGCTATGTTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
GGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAAATGCCTTTGAGCT
GAGTGTAGTCGAACTTGAAGGTCTTTTGTTGGCAAATAACCCTTCTTGCCTTGAGCTATATTACA
AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
AGCCTTGAGTTATACTGCAAATAATATGCCTTTGAGCTGAGCATAGTCAAACTCGAAGGTCTTTT
GTTGGAAAATA
Found at i:602974 original size:111 final size:111
Alignment explanation
Indices: 602780--603002 Score: 446
Period size: 111 Copynumber: 2.0 Consensus size: 111
602770 TTACGCATCT
602780 TCTGCACGATTCTCTTGAATGCGTAACAGTTCTCAATGGTGTGCCTTGGGACACCACCGTGATAT
1 TCTGCACGATTCTCTTGAATGCGTAACAGTTCTCAATGGTGTGCCTTGGGACACCACCGTGATAT
602845 TCACAATGAGCATTATCATCATACCACTTGGAGTATGGGGGCTTCA
66 TCACAATGAGCATTATCATCATACCACTTGGAGTATGGGGGCTTCA
602891 TCTGCACGATTCTCTTGAATGCGTAACAGTTCTCAATGGTGTGCCTTGGGACACCACCGTGATAT
1 TCTGCACGATTCTCTTGAATGCGTAACAGTTCTCAATGGTGTGCCTTGGGACACCACCGTGATAT
602956 TCACAATGAGCATTATCATCATACCACTTGGAGTATGGGGGCTTCA
66 TCACAATGAGCATTATCATCATACCACTTGGAGTATGGGGGCTTCA
603002 T
1 T
603003 GGGTTCCACC
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 112 1.00
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.30
Consensus pattern (111 bp):
TCTGCACGATTCTCTTGAATGCGTAACAGTTCTCAATGGTGTGCCTTGGGACACCACCGTGATAT
TCACAATGAGCATTATCATCATACCACTTGGAGTATGGGGGCTTCA
Found at i:605622 original size:21 final size:21
Alignment explanation
Indices: 605596--605643 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
605586 ATTAGATAGA
* *
605596 AAAATAAAAAGGAAAAAACAT
1 AAAATAAAAAGAAAAAAAAAT
605617 AAAATAAAAAGAAAAAAAAAT
1 AAAATAAAAAGAAAAAAAAAT
*
605638 ATAATA
1 AAAATA
605644 TATAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.12
Consensus pattern (21 bp):
AAAATAAAAAGAAAAAAAAAT
Found at i:606832 original size:2 final size:2
Alignment explanation
Indices: 606827--606857 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
606817 ATGAATAATA
606827 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
606858 TTAAAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:606944 original size:35 final size:37
Alignment explanation
Indices: 606880--607061 Score: 187
Period size: 35 Copynumber: 4.9 Consensus size: 37
606870 GTTTTAAAGC
* * *
606880 TATATAATATATATTTCAAAAATATTTTCAAAATC-A
1 TATATTATATATATTTTAAAAATGTTTTCAAAATCTA
606916 TATATTATATATATTTT-AAAATGTTTTCAAAA-CTA
1 TATATTATATATATTTTAAAAATGTTTTCAAAATCTA
* *
606951 TATATTATATATATTTTAAAAATGTTTTTAAAAACTA
1 TATATTATATATATTTTAAAAATGTTTTCAAAATCTA
* *
606988 TATAATATATATATTTTTTTCGAAAATCGTTTTCAAAAAT-TA
1 TAT-AT-TATATA-TATTTT-AAAAAT-GTTTTC-AAAATCTA
*
607030 TATATTATAT-T-TTTTCAAAAACGTTTTCAAAA
1 TATATTATATATATTTT-AAAAATGTTTTCAAAA
607062 AACTATATTA
Statistics
Matches: 127, Mismatches: 10, Indels: 19
0.81 0.06 0.12
Matches are distributed among these distances:
34 1 0.01
35 36 0.28
36 35 0.28
37 15 0.12
38 3 0.02
39 6 0.05
40 10 0.08
41 7 0.06
42 10 0.08
43 4 0.03
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.47
Consensus pattern (37 bp):
TATATTATATATATTTTAAAAATGTTTTCAAAATCTA
Found at i:606985 original size:37 final size:37
Alignment explanation
Indices: 606840--607069 Score: 179
Period size: 37 Copynumber: 6.1 Consensus size: 37
606830 TATATATATA
* * *
606840 TATATATATATATAATATTTAAAAAAAT-TTGTTTTAAAGC
1 TATATAT-TATAT-ATATTT-TAAAAATGTT-TTTAAAAAC
* * * *
606880 TATATA--ATATATATTTCAAAAATATTTTCAAAATC
1 TATATATTATATATATTTTAAAAATGTTTTTAAAAAC
*
606915 -ATATATTATATATATTTT-AAAATG-TTTTCAAAAC
1 TATATATTATATATATTTTAAAAATGTTTTTAAAAAC
606949 TATATATTATATATATTTTAAAAATGTTTTTAAAAAC
1 TATATATTATATATATTTTAAAAATGTTTTTAAAAAC
* * * *
606986 TATATAATATATATATTTTTTTCGAAAATCGTTTTCAAAAAT
1 TATAT-AT-TATATA-TATTTT-AAAAAT-GTTTTTAAAAAC
* *
607028 TATATATTATAT-T-TTTTCAAAAACGTTTTCAAAAAAC
1 TATATATTATATATATTTT-AAAAATGTTTT-TAAAAAC
607065 TATAT
1 TATAT
607070 TACTAGATAC
Statistics
Matches: 160, Mismatches: 18, Indels: 27
0.78 0.09 0.13
Matches are distributed among these distances:
34 12 0.08
35 35 0.22
36 29 0.18
37 37 0.23
38 3 0.02
39 6 0.04
40 16 0.10
41 7 0.04
42 15 0.09
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (37 bp):
TATATATTATATATATTTTAAAAATGTTTTTAAAAAC
Found at i:612696 original size:64 final size:63
Alignment explanation
Indices: 612628--612806 Score: 218
Period size: 64 Copynumber: 2.8 Consensus size: 63
612618 TGGAACACTT
* * * **
612628 AGTGCATCGATGCACCAAGTGTGCATCGATGCATAAAATGCATTCGATGTTTGAA-AATAGCCTG
1 AGTGCATCGATGCA-TAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAA-AACCCA
* * *
612692 AGTGCATCGGTGCAT-TGCTTGTGCATCGATGCATGAAATGCATTCGATGTTTTAATAAAACCCA
1 AGTGCATCGATGCATAAG--TGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA
*
612756 AGTGCATCGATGCATAGAGAGTGCATCGATGCATGAAATGCATTCGATGTT
1 AGTGCATCGATGCATA-AGTGTGCATCGATGCATGAAATGCATTCGATGTT
612807 CAATTTATTT
Statistics
Matches: 99, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
62 1 0.01
64 95 0.96
65 2 0.02
66 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (63 bp):
AGTGCATCGATGCATAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA
Found at i:616054 original size:22 final size:21
Alignment explanation
Indices: 616024--616065 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
616014 AATTAATCCT
616024 TTAAATTTCATTAAACATAAAA
1 TTAAATTTCA-TAAACATAAAA
* *
616046 TTAATTTTCATCAACATAAA
1 TTAAATTTCATAAACATAAA
616066 CCCCCTAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (21 bp):
TTAAATTTCATAAACATAAAA
Found at i:621694 original size:19 final size:19
Alignment explanation
Indices: 621670--621721 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
621660 AATAGCCTGA
621670 GTGCATCGGTGCATTGCTT
1 GTGCATCGGTGCATTGCTT
621689 GTGCATCGGTGCATTGCTT
1 GTGCATCGGTGCATTGCTT
*
621708 GTGCATCGATGCAT
1 GTGCATCGGTGCAT
621722 GAAATGCATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.13, C:0.21, G:0.31, T:0.35
Consensus pattern (19 bp):
GTGCATCGGTGCATTGCTT
Found at i:621776 original size:83 final size:83
Alignment explanation
Indices: 621624--621778 Score: 186
Period size: 83 Copynumber: 1.9 Consensus size: 83
621614 GTGCACCAAG
* ** * * *****
621624 TGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGGTGCATTGCTT
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAACCCAAATGCATCGATGCATAAAGA
621689 GTGCATCGGTGCATTGCT
66 GTGCATCGGTGCATTGCT
* *
621707 TGTGCATCGATGCATGAAATGCATTCGATGTTTTAATAA-AACCCAAATGCATCGATGCATAAAG
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTGAA-AATAACCCAAATGCATCGATGCATAAAG
621771 AGTGCATC
65 AGTGCATC
621779 AATGCATGAA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
83 57 0.97
84 2 0.03
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (83 bp):
TGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAACCCAAATGCATCGATGCATAAAGA
GTGCATCGGTGCATTGCT
Found at i:623981 original size:22 final size:22
Alignment explanation
Indices: 623951--624009 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 22
623941 TGGTGCAAGA
* *
623951 GGAATCGATACCCCTTTGAAGG
1 GGAACCGATTCCCCTTTGAAGG
*
623973 GGAACCGATTCCACCTTTGAATG
1 GGAACCGATTCC-CCTTTGAAGG
623996 GGAACCGATTCCCC
1 GGAACCGATTCCCC
624010 ATGGGAATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 12 0.36
23 21 0.64
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (22 bp):
GGAACCGATTCCCCTTTGAAGG
Found at i:624015 original size:17 final size:18
Alignment explanation
Indices: 623993--624032 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
623983 CCACCTTTGA
*
623993 ATGGGAACCGATT-CCCC
1 ATGGGAACCAATTCCCCC
*
624010 ATGGGAATCAATTCCCCC
1 ATGGGAACCAATTCCCCC
624028 ATGGG
1 ATGGG
624033 GTCTGTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.20
Consensus pattern (18 bp):
ATGGGAACCAATTCCCCC
Found at i:624017 original size:23 final size:23
Alignment explanation
Indices: 623972--624017 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
623962 CCCTTTGAAG
**
623972 GGGAACCGATTCCACCTTTGAAT
1 GGGAACCGATTCCACCTGGGAAT
623995 GGGAACCGATTCC-CCATGGGAAT
1 GGGAACCGATTCCACC-TGGGAAT
624018 CAATTCCCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (23 bp):
GGGAACCGATTCCACCTGGGAAT
Found at i:626555 original size:19 final size:20
Alignment explanation
Indices: 626517--626557 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
626507 GGGCAGATTG
*
626517 CCCAGAGGGAACCGATTCCC
1 CCCAGAGGGAACCAATTCCC
*
626537 CCCAG-GGGTACCAATTCCC
1 CCCAGAGGGAACCAATTCCC
626556 CC
1 CC
626558 TGAATGGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.22, C:0.44, G:0.22, T:0.12
Consensus pattern (20 bp):
CCCAGAGGGAACCAATTCCC
Found at i:627715 original size:65 final size:65
Alignment explanation
Indices: 627643--627795 Score: 218
Period size: 65 Copynumber: 2.4 Consensus size: 65
627633 CTAAGGGTGA
* * *
627643 ATCGGTACACTAATTACATTCGATGTTTCAAAAGAGTCAGGAGTGCATCGATGCATGG-TCTGTG
1 ATCGGTACACAAAATACATTCGATGTTTCAAAAGAGTCAAGAGTGCATCGATGCATGGCT-TGTG
627707 C
65 C
* ***
627708 ATCGGTACACAAAATGCATTCGATGTTTCAAAATTTTCAAGAGTGCATCGATGCATGGCTTGTGC
1 ATCGGTACACAAAATACATTCGATGTTTCAAAAGAGTCAAGAGTGCATCGATGCATGGCTTGTGC
*
627773 ATCGGTACACAAAATGCATTCGA
1 ATCGGTACACAAAATACATTCGA
627796 AATGGGTGTG
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
65 79 0.99
66 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (65 bp):
ATCGGTACACAAAATACATTCGATGTTTCAAAAGAGTCAAGAGTGCATCGATGCATGGCTTGTGC
Found at i:628327 original size:6 final size:6
Alignment explanation
Indices: 628316--628420 Score: 61
Period size: 6 Copynumber: 16.8 Consensus size: 6
628306 TTGTCCGGGA
* *
628316 TATTTT TATTTT TATTCT TACTTTT ATATTTT ATATTTT TATTTT TA-TCT
1 TATTTT TATTTT TATTTT TA-TTTT -TATTTT -TATTTT TATTTT TATTTT
* * * * * *
628366 TATCTT CATTTC TATTCTT TCTTAGTT TA-TTT TATTTT CATTTT CATTTT
1 TATTTT TATTTT TATT-TT TATT--TT TATTTT TATTTT TATTTT TATTTT
*
628416 CATTT
1 TATTT
628421 GCATTTGCAT
Statistics
Matches: 79, Mismatches: 14, Indels: 12
0.75 0.13 0.11
Matches are distributed among these distances:
5 8 0.10
6 47 0.59
7 19 0.24
8 5 0.06
ACGTcount: A:0.18, C:0.10, G:0.01, T:0.70
Consensus pattern (6 bp):
TATTTT
Found at i:628425 original size:6 final size:6
Alignment explanation
Indices: 628394--628438 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
628384 TTCTTAGTTT
* *
628394 ATTTT- ATTTTC ATTTTC ATTTTC ATTTGC ATTTGC ATTTTC ATTT
1 ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTT
628439 CTATTCTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
5 5 0.14
6 32 0.86
ACGTcount: A:0.18, C:0.13, G:0.04, T:0.64
Consensus pattern (6 bp):
ATTTTC
Found at i:636379 original size:16 final size:16
Alignment explanation
Indices: 636343--636381 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
636333 CAACGTGATT
*
636343 GGTTAAATAAATGATC
1 GGTTAAATAAATGACC
* *
636359 AGTTAAATAAGTGACC
1 GGTTAAATAAATGACC
636375 GGTTAAA
1 GGTTAAA
636382 ATTGATACCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.28
Consensus pattern (16 bp):
GGTTAAATAAATGACC
Found at i:636894 original size:226 final size:226
Alignment explanation
Indices: 636499--637253 Score: 1064
Period size: 226 Copynumber: 3.3 Consensus size: 226
636489 AATATTGACG
* **
636499 ATAACCGATTAATTATCGGAAATGTTATCAAGCATAATAACATATTAGGTAGCGCTTATGTAACG
1 ATAACCGATTAATTATTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTATGTAACG
* * *
636564 AAATAGGTAGCGCATTTTTAAAGCTGACGGGGCCTTATAAATCCGGCGATAACAAAATAGGTTAA
66 AAATAGGTAGCGCATTTTTAAAGCTGATGGGGCCTTAGAAATCCGACGATAACAAAATAGGTTAA
* *
636629 TTACTTAATTTGTTATCAGTATTATCAACATACTAGGTAACACCTCAAATGTTACCAAAGTTTAA
131 TTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAACACCTAAAATGTTACCAAAGTTTAA
*
636694 GCTGATAGAGCCTTAGAAATCCGACGATAAC
196 GCTGATGGAGCCTTAGAAATCCGACGATAAC
* ** *
636725 ATAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAAATAGCGCTTATTTAACG
1 ATAACCGATTAATTATTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTATGTAACG
* * **
636790 AAATAGGTAGCGCCTTTTTAAAACTGATGGGGCCTTAGAAATTTGACGATAACAAAATAGGTTAA
66 AAATAGGTAGCGCATTTTTAAAGCTGATGGGGCCTTAGAAATCCGACGATAACAAAATAGGTTAA
* * *
636855 TTACTTAATTTGTTATTAGTGTTATCAACATATTAGGTAACACTTAAAATGTTACCAAAGTTTAA
131 TTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAACACCTAAAATGTTACCAAAGTTTAA
*
636920 GCTGATGGAGCCTTAGAAATCTGACGATAAC
196 GCTGATGGAGCCTTAGAAATCCGACGATAAC
* * *
636951 ATAACTGATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGCAGCGCTTATGTAACG
1 ATAACCGATTAATTATTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTATGTAACG
* * * * *
637016 TAATAAGTAGCGCGTTTTTAAAGCCGATGGGGCCTTAGAAATCCGACGATAACAAAATTGGTTAA
66 AAATAGGTAGCGCATTTTTAAAGCTGATGGGGCCTTAGAAATCCGACGATAACAAAATAGGTTAA
* **
637081 TTACTTAATTTGTTATCAGTATTATCATCATATTAGGTAACGTCTAAAATGTTACCAAAGTTTAA
131 TTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAACACCTAAAATGTTACCAAAGTTTAA
* *
637146 GATGATGGAGCCTTAGAAATCCGACGATAGC
196 GCTGATGGAGCCTTAGAAATCCGACGATAAC
* **** * * * * *
637177 ATAA-CAAGTTAATTACTT-GATTTGTTATCAACCTTTATGAACATATTAGGTAGCGTTTATATA
1 ATAACCGA-TTAATTA-TTGGAAACATTATCAAGCATAAT-AACATATTAGGTAGCGCTTATGTA
*
637240 ACGTAATAGGTAGC
63 ACGAAATAGGTAGC
637254 AGCTTAACGC
Statistics
Matches: 467, Mismatches: 59, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
225 1 0.00
226 431 0.92
227 35 0.07
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (226 bp):
ATAACCGATTAATTATTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTATGTAACG
AAATAGGTAGCGCATTTTTAAAGCTGATGGGGCCTTAGAAATCCGACGATAACAAAATAGGTTAA
TTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAACACCTAAAATGTTACCAAAGTTTAA
GCTGATGGAGCCTTAGAAATCCGACGATAAC
Found at i:637487 original size:2 final size:2
Alignment explanation
Indices: 637474--637507 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
637464 AGTATGGAAA
*
637474 AT AT AT AC 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
637508 GTATGTATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:641365 original size:6 final size:6
Alignment explanation
Indices: 641354--641445 Score: 78
Period size: 6 Copynumber: 15.2 Consensus size: 6
641344 TAGTGGAGCC
* * * * * * *
641354 GAAATT GAAATT CAAACT CAAATT AAAATT GAAATT GAAAAT CAAACT
1 GAAATT GAAATT GAAATT GAAATT GAAATT GAAATT GAAATT GAAATT
* *
641402 CAAATT GAAATT GAAATT -CAATAT GAAATT GAAATT GGAAATT G
1 GAAATT GAAATT GAAATT GAAAT-T GAAATT GAAATT -GAAATT G
641446 CATAAATGAT
Statistics
Matches: 71, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
5 3 0.04
6 59 0.83
7 9 0.13
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (6 bp):
GAAATT
Found at i:641387 original size:24 final size:24
Alignment explanation
Indices: 641355--641443 Score: 99
Period size: 24 Copynumber: 3.7 Consensus size: 24
641345 AGTGGAGCCG
* *
641355 AAATTGAAATTCAAACTCAAATTA
1 AAATTGAAATTGAAAATCAAATTA
* *
641379 AAATTGAAATTGAAAATCAAACTC
1 AAATTGAAATTGAAAATCAAATTA
* *
641403 AAATTGAAATTGAAATTC-AATATG
1 AAATTGAAATTGAAAATCAAAT-TA
*
641427 AAATTGAAATTGGAAAT
1 AAATTGAAATTGAAAAT
641444 TGCATAAATG
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 2 0.04
24 53 0.96
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (24 bp):
AAATTGAAATTGAAAATCAAATTA
Found at i:641390 original size:30 final size:30
Alignment explanation
Indices: 641354--641419 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
641344 TAGTGGAGCC
*
641354 GAAATTGAAATTCAAACTCAAATTAAAATT
1 GAAATTGAAAATCAAACTCAAATTAAAATT
*
641384 GAAATTGAAAATCAAACTCAAATTGAAATT
1 GAAATTGAAAATCAAACTCAAATTAAAATT
641414 GAAATT
1 GAAATT
641420 CAATATGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (30 bp):
GAAATTGAAAATCAAACTCAAATTAAAATT
Found at i:644676 original size:200 final size:201
Alignment explanation
Indices: 644441--644898 Score: 666
Period size: 200 Copynumber: 2.3 Consensus size: 201
644431 ATGCTAGAAC
*
644441 AAAAGTATCGAAACTTTATGTTTACATATTTTGTCATTAAACCGGTATATTTTTACCACTTACAT
1 AAAAGTATCGAAACTTTATGTTTACGTATTTTGTCATTAAACCGGTATATTTTTACCACTTACAT
* * ** *
644506 TTTAAATTTACCTATTAATTTAAAGTAATCGGTTTTGAAATTGTAAGAATCGATACTTTTGATAC
66 TGTAAATTTACATATTAATTTAAAGTAATCAATTTCGAAATTGTAAGAATCGATACTTTTGATAC
* ** *
644571 GTGTATCGATACTTTCTGTGTGTATCTCGTTTGGGAAGCATACTGAACC-AAAACTATCAATACA
131 ATGTATCGATACTTTCTGCATGCATCTCGTTTGGGAAGCATACTGAACCAAAAACTATCAATACA
644635 TATACA
196 TATACA
* * * *
644641 AAAAGTATCAAAACTTTATGTTTACGTATTTTGTCATTAAACTGGTGTATTTTTACTACTTACAT
1 AAAAGTATCGAAACTTTATGTTTACGTATTTTGTCATTAAACCGGTATATTTTTACCACTTACAT
* * * *
644706 TGTAAATTTACATATTACTTTAAAGTAATCAATTTCGAAGTTGTAAGAATTGATACTTTTGATAT
66 TGTAAATTTACATATTAATTTAAAGTAATCAATTTCGAAATTGTAAGAATCGATACTTTTGATAC
* * * *
644771 ATGTATCGATACTTTCTGCATGCATCTCGTTTGGGAAGCATACTGGACCAAAAAGTGTCGATACA
131 ATGTATCGATACTTTCTGCATGCATCTCGTTTGGGAAGCATACTGAACCAAAAACTATCAATACA
644836 TATACA
196 TATACA
* * * * *
644842 AAAAGCATCGAAACTTTATATTTACGCATTTAGTCATTAAACCAGTATATTTTTACC
1 AAAAGTATCGAAACTTTATGTTTACGTATTTTGTCATTAAACCGGTATATTTTTACC
644899 TTGGGATTTA
Statistics
Matches: 226, Mismatches: 31, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
200 160 0.71
201 66 0.29
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (201 bp):
AAAAGTATCGAAACTTTATGTTTACGTATTTTGTCATTAAACCGGTATATTTTTACCACTTACAT
TGTAAATTTACATATTAATTTAAAGTAATCAATTTCGAAATTGTAAGAATCGATACTTTTGATAC
ATGTATCGATACTTTCTGCATGCATCTCGTTTGGGAAGCATACTGAACCAAAAACTATCAATACA
TATACA
Found at i:646216 original size:230 final size:230
Alignment explanation
Indices: 645808--646271 Score: 673
Period size: 230 Copynumber: 2.0 Consensus size: 230
645798 TAGTAAAACA
* *
645808 GTTTCCTTCAAATGAATGGGAATACTCTCTACTACAAGTATCAGTACCTTTATACAACATACAAT
1 GTTTCCTTCAAAGGAATGAGAATACTCTCTACTACAAGTATCAGTACCTTTATACAACATACAAT
* * * *
645873 ATCATTTTCTACCTATAATCTTATATAAAAGTATCGATATTTATTTTCTACCTATAATATCACTT
66 AGCATTTTCTACCTATAATATTATATAAAAGTATCAATATTTATTTTCTACCTACAATATCACTT
*
645938 TCTAACTGTAATCGGTCGAAAATCCTTCTTTACTTTAAAAAACCCAAACCCATAAACCTTAATCC
131 TCTAACTGTAATCGGTCGAAAATCCTTCTTTACTTTAAAAAACCCAAACCCATAAACC-TAACCC
*
646003 CTA-TTTTTAAATATTATAATACT-AAAAAATCTAGG
195 CTATTTTTTAAATACTATAATACTGAAAAAA-CTAGG
* * * *
646038 GTTTCCTTGAAAGGAATGAGAATACTCTCTACTGCAAGTATCTGTACCTTTATACAACCTACAAT
1 GTTTCCTTCAAAGGAATGAGAATACTCTCTACTACAAGTATCAGTACCTTTATACAACATACAAT
*
646103 AGCATTTTCTACCTATAATATTATATAAAAGTATCAATATTTATTTTTTACCTACAATATCACTT
66 AGCATTTTCTACCTATAATATTATATAAAAGTATCAATATTTATTTTCTACCTACAATATCACTT
* * * * * * *
646168 TCTACCTGTAATTGGTAC-CAAATGCTTCTTTACTTTAAAAACCCCAAACCCATACATCTAACCC
131 TCTAACTGTAATCGGT-CGAAAATCCTTCTTTACTTTAAAAAACCCAAACCCATAAACCTAACCC
* * *
646232 CTATTTTTTTATTACTGTAATACTGAAAAAACTAGG
195 CTATTTTTTAAATACTATAATACTGAAAAAACTAGG
646268 GTTT
1 GTTT
646272 TGACAATGTA
Statistics
Matches: 208, Mismatches: 23, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
229 8 0.04
230 193 0.93
231 7 0.03
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (230 bp):
GTTTCCTTCAAAGGAATGAGAATACTCTCTACTACAAGTATCAGTACCTTTATACAACATACAAT
AGCATTTTCTACCTATAATATTATATAAAAGTATCAATATTTATTTTCTACCTACAATATCACTT
TCTAACTGTAATCGGTCGAAAATCCTTCTTTACTTTAAAAAACCCAAACCCATAAACCTAACCCC
TATTTTTTAAATACTATAATACTGAAAAAACTAGG
Found at i:649079 original size:131 final size:131
Alignment explanation
Indices: 648900--649269 Score: 462
Period size: 131 Copynumber: 2.8 Consensus size: 131
648890 AATAATTTTA
* * ** * *
648900 AGAGAGAAAACAATATTATCTAATTATTTTTAAATCGAGAATAAATGACCTTTCATGACTTAAAG
1 AGAGAGAAAACAATAATATATAATTA-TTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAG
*
648965 CTA-TCATTTATTACTCCGACTGAAATGAAGAGATATCACTATTCCATCTTAAAATTCAATATTG
65 CTAGTCATTTATTACTCC-ACTGAAATGAAGAGATATCACTATTCCATCTTAAAAATCAATATTG
649029 ATT
129 ATT
* * *
649032 TGGGAGGAAACAATAATATATAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
1 AGAGAGAAAACAATAATATATAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
* * * * ***
649097 -ATTCATTTATTACTCCAATCGAAATGAAGATATATCACCATTTTGTCTTAAAAATCAATATTGA
66 TAGTCATTTATTACTCCACT-GAAATGAAGAGATATCACTATTCCATCTTAAAAATCAATATTGA
649161 TT
130 TT
** *
649163 AGAGAGAAAATTATAATATATTATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAA--
1 AGAGAGAAAACAATAATATATAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
*
649226 TGAGTCATTTATTACTCCAACTGAAATG-AGAAGATATTACTATT
66 T-AGTCATTTATTACTCC-ACTGAAATGAAG-AGATATCACTATT
649270 TTCAATATTA
Statistics
Matches: 205, Mismatches: 27, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
130 5 0.02
131 177 0.86
132 23 0.11
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (131 bp):
AGAGAGAAAACAATAATATATAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGC
TAGTCATTTATTACTCCACTGAAATGAAGAGATATCACTATTCCATCTTAAAAATCAATATTGAT
T
Found at i:651268 original size:3 final size:3
Alignment explanation
Indices: 651253--651370 Score: 173
Period size: 3 Copynumber: 39.3 Consensus size: 3
651243 TTGCAAAATT
* * * * * * *
651253 TAA TAA AAA TAA TAA TAT TAA TAA TTA TGA TGA TGA TAC TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
651301 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
651349 TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
651371 GGTGTCGAGA
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 106 1.00
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:651874 original size:133 final size:132
Alignment explanation
Indices: 651667--652037 Score: 501
Period size: 133 Copynumber: 2.8 Consensus size: 132
651657 CTACTACTCA
* *
651667 GGAAAGAGGGGATATGTTCCGCTGCTTATTTAGGGAAAAACAAAGTTGGAGACATTGATTCATTC
1 GGAAAGAGGGGATATGTTCCGCTGCTTCTTTAGGGAAAATCAAA-TTGGAGACATTGATTCATTC
** *
651732 CGTTGTTCTTCAGGGAAGATTGAATCAAGGAAGACTTGTTCCACT-ACTATTCAGGGAAGATCAA
65 CACTGTTCTTCAGGGAAGATTGAATCAAGGAAGACTTGTTCCACTGA-TACTCAGGGAAGATCAA
651796 ATAT
129 ATAT
* * * **
651800 GTAAAGAGGGGATCTGTTTCGCTGCTTCTTTAGGGAAAATCAAATCTGGAGATGTTGATTCATTC
1 GGAAAGAGGGGATATGTTCCGCTGCTTCTTTAGGGAAAATCAAAT-TGGAGACATTGATTCATTC
* * * *
651865 CACTATTCTTTAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTGATACTCAGGGAAGATCAAA
65 CACTGTTCTTCAGGGAAGATTGAATCAAGGAAGACTTGTTCCACTGATACTCAGGGAAGATCAAA
*
651930 TCT
130 TAT
* * * *
651933 GGAAAGAGGGGTTATATTCCGCTGCTTCTTTAGGGAAAATCATATATGGAGACATTGATTTATTC
1 GGAAAGAGGGGATATGTTCCGCTGCTTCTTTAGGGAAAATCAAAT-TGGAGACATTGATTCATTC
* * *
651998 CACTGTTCTACAGGGAAGATTGAATCAAGGTAGATTTGTT
65 CACTGTTCTTCAGGGAAGATTGAATCAAGGAAGACTTGTT
652038 ACTCTTGTCT
Statistics
Matches: 205, Mismatches: 31, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
132 1 0.00
133 203 0.99
134 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (132 bp):
GGAAAGAGGGGATATGTTCCGCTGCTTCTTTAGGGAAAATCAAATTGGAGACATTGATTCATTCC
ACTGTTCTTCAGGGAAGATTGAATCAAGGAAGACTTGTTCCACTGATACTCAGGGAAGATCAAAT
AT
Found at i:653139 original size:8 final size:8
Alignment explanation
Indices: 653126--653175 Score: 63
Period size: 8 Copynumber: 6.8 Consensus size: 8
653116 TTTATTCTAT
653126 TTTTTTCC
1 TTTTTTCC
653134 TTTTTTCC
1 TTTTTTCC
653142 TTTTTT--
1 TTTTTTCC
*
653148 TCTTTTCC
1 TTTTTTCC
653156 TTTTTTCC
1 TTTTTTCC
653164 --TTTTCC
1 TTTTTTCC
653170 TTTTTT
1 TTTTTT
653176 ACATTTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
6 11 0.31
8 25 0.69
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTTCC
Found at i:653145 original size:14 final size:14
Alignment explanation
Indices: 653126--653175 Score: 73
Period size: 14 Copynumber: 3.4 Consensus size: 14
653116 TTTATTCTAT
653126 TTTTTTCCTTTTTTCC
1 TTTTTTCC--TTTTCC
*
653142 TTTTTTTCTTTTCC
1 TTTTTTCCTTTTCC
653156 TTTTTTCCTTTTCC
1 TTTTTTCCTTTTCC
653170 TTTTTT
1 TTTTTT
653176 ACATTTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 25 0.78
16 7 0.22
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTTCCTTTTCC
Found at i:653175 original size:22 final size:21
Alignment explanation
Indices: 653126--653175 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
653116 TTTATTCTAT
*
653126 TTTTTTCCTTTTTTCCTTTTT
1 TTTTTTCCTTTTTTCCTTTTC
653147 TTCTTTTCCTTTTTTCCTTTTCC
1 TT-TTTTCCTTTTTTCCTTTT-C
653170 TTTTTT
1 TTTTTT
653176 ACATTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 2 0.08
22 22 0.85
23 2 0.08
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTTCCTTTTTTCCTTTTC
Found at i:653217 original size:14 final size:14
Alignment explanation
Indices: 653182--653208 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
653172 TTTTACATTT
653182 ATTTTTCATTTTTA
1 ATTTTTCATTTTTA
653196 ATTTTTCATTTTT
1 ATTTTTCATTTTT
653209 CTTTCTTCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (14 bp):
ATTTTTCATTTTTA
Found at i:663067 original size:111 final size:111
Alignment explanation
Indices: 662858--663079 Score: 331
Period size: 111 Copynumber: 2.0 Consensus size: 111
662848 ATATATTCTC
* *
662858 ATTTCGATTGGAGTAATAAATGATTGCTTTAAGCCATGAGAGGTCATTTATTCTCGATTGGAAAT
1 ATTTCGATTGGAGTAATAAATGATTGCTTTAAGCCATGAGAGGTCATTTATTCTCGATCGAAAAT
* * *
662923 AATTAGATATCATCATTTTCTCTTCAATTAATATTGATTTTTAAGA
66 AATTAGATATCATCATTTCCTCTTCAATCAATATTGAATTTTAAGA
* *
662969 ATTTCGATTGGAGTAATAAATGACTT-CTTTAAGGCATGAGAGGTCATTTATTCTTGATCGAAAA
1 ATTTCGATTGGAGTAATAAATGA-TTGCTTTAAGCCATGAGAGGTCATTTATTCTCGATCGAAAA
* *
663033 TAGTTAGATATTATCATTTCCTC-TCGAATCAATATTGAATTTTAAGA
65 TAATTAGATATCATCATTTCCTCTTC-AATCAATATTGAATTTTAAGA
663080 CAGAATAATG
Statistics
Matches: 100, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
110 2 0.02
111 96 0.96
112 2 0.02
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (111 bp):
ATTTCGATTGGAGTAATAAATGATTGCTTTAAGCCATGAGAGGTCATTTATTCTCGATCGAAAAT
AATTAGATATCATCATTTCCTCTTCAATCAATATTGAATTTTAAGA
Found at i:666042 original size:3 final size:3
Alignment explanation
Indices: 665997--666027 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
665987 CTGCAAAATT
665997 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
666028 CTAGGTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:666322 original size:32 final size:33
Alignment explanation
Indices: 666285--666355 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 33
666275 TTAGTACTTG
*
666285 TTATTAAAGGTCTAATTTTCTCTC-AATATTTA
1 TTATTAAAGGTCTAATTTTCTCTCTAATATTCA
* * * *
666317 TTATTAAGGGTTTAATTTTTTTTCTAATATTCA
1 TTATTAAAGGTCTAATTTTCTCTCTAATATTCA
666350 TTATTA
1 TTATTA
666356 GAGGCATACT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
32 20 0.61
33 13 0.39
ACGTcount: A:0.30, C:0.08, G:0.07, T:0.55
Consensus pattern (33 bp):
TTATTAAAGGTCTAATTTTCTCTCTAATATTCA
Found at i:666421 original size:29 final size:31
Alignment explanation
Indices: 666378--666444 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
666368 TATAATTTAT
* * *
666378 ATTTTTT-TAATATTT-GTA-TAAGTGTCCA
1 ATTTTTTCTAACATTTAGTATTAAGGGACCA
*
666406 ATTTTTTCTAACATTTATTATTAAGGGACCA
1 ATTTTTTCTAACATTTAGTATTAAGGGACCA
666437 ATTTTTTC
1 ATTTTTTC
666445 AATACTGTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 7 0.22
29 7 0.22
30 2 0.06
31 16 0.50
ACGTcount: A:0.28, C:0.10, G:0.09, T:0.52
Consensus pattern (31 bp):
ATTTTTTCTAACATTTAGTATTAAGGGACCA
Found at i:666582 original size:166 final size:165
Alignment explanation
Indices: 666307--666653 Score: 660
Period size: 166 Copynumber: 2.1 Consensus size: 165
666297 TAATTTTCTC
666307 TCAATATTTATTATTAAGGGTTTAATTTTTTTTCTAATATTCATTATTAGAGGCATACTCTTATA
1 TCAATATTTATTATTAAGGGTTTAATTTTTTTTCTAATATTCATTATTAGAGGCATACTCTTATA
666372 ATTTATATTTTTTTAATATTTGTATAAGTGTCCAATTTTTTCTAACATTTATTATTAAGGGACCA
66 ATTTATATTTTTTTAATATTTGTATAAGTGTCCAATTTTTTCTAACATTTATTATTAAGGGACCA
666437 ATTTTTTCAATAC-TGTTATAAGGGACTTAGTTTT
131 ATTTTTTCAATACTTGTTATAAGGGACTTAGTTTT
666471 TCACAATATTTATTATTAAGGGTTTAATTTTTTTTCTAATATTCATTATTAGAGGCATACTCTTA
1 T--CAATATTTATTATTAAGGGTTTAATTTTTTTTCTAATATTCATTATTAGAGGCATACTCTTA
666536 TAATTTATATTTTTTTAATATTTGTATAAGTGTCCAATTTTTTCTAACATTTATTATTAAGGGAC
64 TAATTTATATTTTTTTAATATTTGTATAAGTGTCCAATTTTTTCTAACATTTATTATTAAGGGAC
666601 CAATTTTTTCAATACTTGTTATAAGGGACTTAGTTTT
129 CAATTTTTTCAATACTTGTTATAAGGGACTTAGTTTT
*
666638 TCAATATTTGTTATTA
1 TCAATATTTATTATTA
666654 GGTACTTACT
Statistics
Matches: 179, Mismatches: 1, Indels: 5
0.97 0.01 0.03
Matches are distributed among these distances:
164 1 0.01
165 14 0.08
166 142 0.79
167 22 0.12
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.51
Consensus pattern (165 bp):
TCAATATTTATTATTAAGGGTTTAATTTTTTTTCTAATATTCATTATTAGAGGCATACTCTTATA
ATTTATATTTTTTTAATATTTGTATAAGTGTCCAATTTTTTCTAACATTTATTATTAAGGGACCA
ATTTTTTCAATACTTGTTATAAGGGACTTAGTTTT
Found at i:666587 original size:29 final size:31
Alignment explanation
Indices: 666544--666610 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
666534 TATAATTTAT
* * *
666544 ATTTTTT-TAATATTT-GTA-TAAGTGTCCA
1 ATTTTTTCTAACATTTAGTATTAAGGGACCA
*
666572 ATTTTTTCTAACATTTATTATTAAGGGACCA
1 ATTTTTTCTAACATTTAGTATTAAGGGACCA
666603 ATTTTTTC
1 ATTTTTTC
666611 AATACTTGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 7 0.22
29 7 0.22
30 2 0.06
31 16 0.50
ACGTcount: A:0.28, C:0.10, G:0.09, T:0.52
Consensus pattern (31 bp):
ATTTTTTCTAACATTTAGTATTAAGGGACCA
Found at i:666626 original size:29 final size:29
Alignment explanation
Indices: 666544--666651 Score: 110
Period size: 29 Copynumber: 3.7 Consensus size: 29
666534 TATAATTTAT
* * *
666544 ATTTTTTTAATATTTG-TATAAGTGTCCA
1 ATTTTTTCAATATTTGTTATAAGGGACCA
* *
666572 ATTTTTTCTAACATTTATTATTAAGGGACCA
1 ATTTTTTC-AATATTTGTTA-TAAGGGACCA
* **
666603 ATTTTTTCAATACTTGTTATAAGGGACTT
1 ATTTTTTCAATATTTGTTATAAGGGACCA
*
666632 AGTTTTTCAATATTTGTTAT
1 ATTTTTTCAATATTTGTTAT
666652 TAGGTACTTA
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
28 7 0.11
29 32 0.49
30 10 0.15
31 16 0.25
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (29 bp):
ATTTTTTCAATATTTGTTATAAGGGACCA
Found at i:666660 original size:29 final size:29
Alignment explanation
Indices: 666605--666661 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
666595 AGGGACCAAT
666605 TTTTTCAATACTTGTTATAAGGGACTTAG
1 TTTTTCAATACTTGTTATAAGGGACTTAG
* * *
666634 TTTTTCAATATTTGTTATTAGGTACTTA
1 TTTTTCAATACTTGTTATAAGGGACTTA
666662 CTCTTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.51
Consensus pattern (29 bp):
TTTTTCAATACTTGTTATAAGGGACTTAG
Found at i:671608 original size:13 final size:13
Alignment explanation
Indices: 671590--671626 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
671580 TTATGGATGT
671590 AGCATGGTCTTGC
1 AGCATGGTCTTGC
*
671603 AGCATGGTCTTGT
1 AGCATGGTCTTGC
*
671616 AACATGGTCTT
1 AGCATGGTCTT
671627 CATGGTTGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (13 bp):
AGCATGGTCTTGC
Found at i:673355 original size:93 final size:95
Alignment explanation
Indices: 673192--673414 Score: 256
Period size: 95 Copynumber: 2.4 Consensus size: 95
673182 ATACCTACGG
* * * * * *
673192 GGTAGTATCGATACCATGATCAGGGGTATCGATACCAAGAAACATCGAATCTAATTTCGGTATTG
1 GGTAGTATCGATACCAGGGT-AGTGGTATCGATACCAAGAAACATCGAACCTAAATTCGGTATCG
* * *
673257 GTACCATAAGGGG-TATC-ATACCATATTAT
65 ATACCAAAAGGGGTTATCAATACCATAATAT
* * *
673286 GGTAGTATCGATACCAGGGTAGTGGTATCGATATCAGGCAAA-ATCGAACCTAAAATT-GTTATC
1 GGTAGTATCGATACCAGGGTAGTGGTATCGATACCAAG-AAACATCGAACCT-AAATTCGGTATC
673349 GATACCAAAAGGGGTTATCAATACCATAATAT
64 GATACCAAAAGGGGTTATCAATACCATAATAT
* * *
673381 AGAAGTATCGATACCAGGGTAGTGATATCGATAC
1 GGTAGTATCGATACCAGGGTAGTGGTATCGATAC
673415 TATTGAGCTT
Statistics
Matches: 109, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
93 39 0.36
94 29 0.27
95 41 0.38
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (95 bp):
GGTAGTATCGATACCAGGGTAGTGGTATCGATACCAAGAAACATCGAACCTAAATTCGGTATCGA
TACCAAAAGGGGTTATCAATACCATAATAT
Found at i:673986 original size:80 final size:80
Alignment explanation
Indices: 673853--674228 Score: 465
Period size: 80 Copynumber: 4.9 Consensus size: 80
673843 GGCACTGTGT
* * * *
673853 GTGCATTACTGGCATGAAATGATGCCTTAGCTGAAATGTATATGGGTATATTATCAGCATAAAAA
1 GTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATATATATGGGTACATTATCAGCATAAAAA
*
673918 TAATAATGCATATGG
66 GAATAATGCATATGG
*
673933 GTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATATATATGGGTACATTATTAGCATAAAAA
1 GTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATATATATGGGTACATTATCAGCATAAAAA
*
673998 GAATAATGTATATGG
66 GAATAATGCATATGG
* * *
674013 GTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATTTATGTGGGTACATTATCGGCAT-AAAA
1 GTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATATATATGGGTACATTATCAGCATAAAAA
674077 GAATAATGCATATGG
66 GAATAATGCATATGG
* *
674092 GTACATTATTGGCATGAAATGATGCCTTAGCTG--A-A-ATATGGGTACATTATC-GTCAT---A
1 GTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATATATATGGGTACATTATCAG-CATAAAA
674149 A-AATAAT--A-ATGG
65 AGAATAATGCATATGG
* ** * * * * *
674161 GTGAATTATTGGCATGAAAGGATGCCAAAGTTGAAATGTATATGGGTGCATTTTCAACAT-AAAA
1 GTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATATATATGGGTACATTATCAGCATAAAAA
674225 GAAT
66 GAAT
674229 GCTATAATTA
Statistics
Matches: 261, Mismatches: 26, Indels: 22
0.84 0.08 0.07
Matches are distributed among these distances:
69 31 0.12
70 1 0.00
71 1 0.00
72 6 0.02
73 19 0.07
74 1 0.00
75 20 0.08
76 3 0.01
77 1 0.00
79 49 0.19
80 129 0.49
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (80 bp):
GTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATATATATGGGTACATTATCAGCATAAAAA
GAATAATGCATATGG
Found at i:675319 original size:52 final size:52
Alignment explanation
Indices: 675241--675363 Score: 219
Period size: 52 Copynumber: 2.4 Consensus size: 52
675231 GCCTTAACAC
* *
675241 TGTAAGAGCATCGAGAGATCGCCTGGGGTTTCGGTAAAACATGTCTGGGCAT
1 TGTAAGAGCATCGAGAGATCACCTGGGGTTTCGGTAAAACATGTATGGGCAT
*
675293 TGTAAGAGCATCGAGAGATCACCTGGGGTTTTGGTAAAACATGTATGGGCAT
1 TGTAAGAGCATCGAGAGATCACCTGGGGTTTCGGTAAAACATGTATGGGCAT
675345 TGTAAGAGCATCGAGAGAT
1 TGTAAGAGCATCGAGAGAT
675364 AGCCTTTTGT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.28, C:0.15, G:0.32, T:0.25
Consensus pattern (52 bp):
TGTAAGAGCATCGAGAGATCACCTGGGGTTTCGGTAAAACATGTATGGGCAT
Found at i:675829 original size:19 final size:20
Alignment explanation
Indices: 675790--675835 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
675780 TCATTGAATC
675790 ATTA-TTTTTAGCTCCTTAAT
1 ATTAGTTTTTAGCT-CTTAAT
675810 ATTAGTTTTTAGCT-TTAAT
1 ATTAGTTTTTAGCTCTTAAT
675829 ACTTAGT
1 A-TTAGT
675836 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.54
Consensus pattern (20 bp):
ATTAGTTTTTAGCTCTTAAT
Found at i:689082 original size:19 final size:19
Alignment explanation
Indices: 689050--689093 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
689040 TTTGTTTGTA
*
689050 TCTTCTTTTCACTTTTACTT
1 TCTT-TTTTCACTTTAACTT
*
689070 TCTTTTTTTACTTTAACTT
1 TCTTTTTTCACTTTAACTT
689089 TCTTT
1 TCTTT
689094 CATCTTCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.68
Consensus pattern (19 bp):
TCTTTTTTCACTTTAACTT
Found at i:689145 original size:241 final size:228
Alignment explanation
Indices: 688705--689175 Score: 793
Period size: 241 Copynumber: 2.0 Consensus size: 228
688695 GAGGGAAATT
688705 TTTACCTTTTTGACTTTTGACTTGGGGATTAGTTTTTTTACTTCATTTGTTTCTTCCGCCAGGCC
1 TTTACCTTTTTGACTTTTGACTTGGGGATTAGTTTTTTTACTTCATTTGTTTCTTCCGCCAGGCC
688770 ACCTTTTATTTAACATTCCGCACAAAAATCTTTATTTTGTTTGTATCTTCTTCACTTTTTTTCTT
66 ACCTTTTATTTAACATTCCGCACAAAAATCTTTATTTTGTTTGTATCTTCTTCACTTTTTTTCTT
688835 TTTTTACTTAACTTTTTTCATCTTCTCTTCTCCCTTTCACTTTAAACTGAACCTCCATAGCCGAC
131 TTTTTACTTAACTTTTTTCATCTTCTCTTCTCCCTTTCACTTTAAACTGAACCTCCATAGCCGAC
688900 CAAGCCAAGCTTTCTTCTTCTTCC-TTTTCGTG
196 CAAGCCAAGCTTTCTTCTTCTTCCTTTTTCGTG
688932 TTTACCTTTTTGACTTTTGACTTGGGGATTAGTTTTTTTACTTCATTTTGTTTCTTTCCCGCCCA
1 TTTACCTTTTTGACTTTTGACTTGGGGATTAGTTTTTTTACTTCA-TTTGTTTC-TT-CCG-CCA
688997 GGCCCCACCTTTTTATTTAACATTTCCGCACAAAAATCTTTATTTTGTTTGTATCTTCTTTTCAC
62 GG--CCACC-TTTTATTTAACA-TTCCGCACAAAAATCTTTATTTTGTTTGTATCTTC--TTCAC
689062 TTTTACTTTCTTTTTTTACTTTAACTTTCTTTCATCTTCTTCTTCTCCCTTTCACTTT-AACTGA
121 TTTT--TTTCTTTTTTTAC-TTAACTTT-TTTCATCTTC-TCTTCTCCCTTTCACTTTAAACTGA
689126 ACCTCCATAGCCGACCAAGCCAAGCTTTCTTCTTCTTCCTTTTTCGTG
181 ACCTCCATAGCCGACCAAGCCAAGCTTTCTTCTTCTTCCTTTTTCGTG
689174 TT
1 TT
689176 CTCATCATGG
Statistics
Matches: 228, Mismatches: 0, Indels: 17
0.93 0.00 0.07
Matches are distributed among these distances:
227 45 0.20
228 8 0.04
229 2 0.01
230 3 0.01
231 5 0.02
233 5 0.02
234 12 0.05
235 35 0.15
237 9 0.04
239 13 0.06
240 8 0.04
241 55 0.24
242 28 0.12
ACGTcount: A:0.17, C:0.25, G:0.09, T:0.49
Consensus pattern (228 bp):
TTTACCTTTTTGACTTTTGACTTGGGGATTAGTTTTTTTACTTCATTTGTTTCTTCCGCCAGGCC
ACCTTTTATTTAACATTCCGCACAAAAATCTTTATTTTGTTTGTATCTTCTTCACTTTTTTTCTT
TTTTTACTTAACTTTTTTCATCTTCTCTTCTCCCTTTCACTTTAAACTGAACCTCCATAGCCGAC
CAAGCCAAGCTTTCTTCTTCTTCCTTTTTCGTG
Found at i:695832 original size:16 final size:15
Alignment explanation
Indices: 695811--695853 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
695801 GGCACTCATT
695811 TTTCTTACATTTTACA
1 TTTCTTA-ATTTTACA
*
695827 TTTCTTTATTTTTACA
1 TTTC-TTAATTTTACA
695843 TTTCTTTAATT
1 TTTC-TTAATT
695854 CGTTTCGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 21 0.88
17 3 0.12
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTCTTAATTTTACA
Found at i:702640 original size:90 final size:89
Alignment explanation
Indices: 702488--702660 Score: 278
Period size: 90 Copynumber: 1.9 Consensus size: 89
702478 CCACACCCTT
702488 TTATATCCAAGATACTCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATATCCAAGATACTCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
* *
702553 ATTAATTGGAATTTAATAATTCTC
66 ATTAATTGAAATTAAATAATTCTC
*
702577 TTATATCCAAG-TCAC-CTTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATGTATAT
1 TTATATCCAAGAT-ACTC-TAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATAT
702640 TTAATTAATTGAAATTAAATA
63 TTAATTAATTGAAATTAAATA
702661 TTCAGGATTA
Statistics
Matches: 78, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
88 2 0.03
89 27 0.35
90 49 0.63
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (89 bp):
TTATATCCAAGATACTCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAAATAATTCTC
Found at i:710014 original size:13 final size:12
Alignment explanation
Indices: 709999--710037 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
709989 TTTTATTAGT
709999 TTTTTTCTTTAA
1 TTTTTTCTTTAA
710011 TTTTTTCTTT-A
1 TTTTTTCTTTAA
*
710022 TTATTTCTTTACA
1 TTTTTTCTTTA-A
710035 TTT
1 TTT
710038 ATGATCTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 10 0.43
12 10 0.43
13 3 0.13
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTTCTTTAA
Found at i:715822 original size:22 final size:22
Alignment explanation
Indices: 715797--715839 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
715787 TAATAAATTA
715797 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
715819 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
715840 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:715848 original size:22 final size:22
Alignment explanation
Indices: 715799--715847 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
715789 ATAAATTATT
**
715799 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
715821 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
715844 TAAA
1 TAAA
715848 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:715857 original size:32 final size:32
Alignment explanation
Indices: 715819--715974 Score: 166
Period size: 32 Copynumber: 5.4 Consensus size: 32
715809 CAATCCATAT
715819 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
715851 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
*
715881 --T--AACAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
715899 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
715931 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
715963 TTTAAAATAAAT
1 TTTAAAATAAAT
715975 TATTTTAAAA
Statistics
Matches: 105, Mismatches: 3, Indels: 32
0.75 0.02 0.23
Matches are distributed among these distances:
20 1 0.01
22 13 0.12
23 1 0.01
24 2 0.02
25 1 0.01
26 14 0.13
28 1 0.01
30 1 0.01
31 2 0.02
32 69 0.66
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:715895 original size:80 final size:80
Alignment explanation
Indices: 715805--715952 Score: 296
Period size: 80 Copynumber: 1.9 Consensus size: 80
715795 TATTTAAAAT
715805 AAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
1 AAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
715870 TACAACTACAATAAC
66 TACAACTACAATAAC
715885 AAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
1 AAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
715950 TAC
66 TAC
715953 TAATAAATTA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (80 bp):
AAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
TACAACTACAATAAC
Found at i:715925 original size:18 final size:18
Alignment explanation
Indices: 715904--715960 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
715894 CATATTTTAA
715904 AATAAATCAATCCATACT
1 AATAAATCAATCCATACT
* * *
715922 AATAAAT-TAT--TTA-A
1 AATAAATCAATCCATACT
715936 AATAAATCAATCCATACT
1 AATAAATCAATCCATACT
715954 AATAAAT
1 AATAAAT
715961 TATTTAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
14 7 0.24
15 4 0.14
17 4 0.14
18 14 0.48
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAATCAATCCATACT
Found at i:715928 original size:22 final size:22
Alignment explanation
Indices: 715855--715928 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 22
715845 AAATTATTTA
715855 AAATAAATCAATCCATAC-AACT
1 AAATAAATCAATCCATACTAA-T
**
715877 ACAATAACAAATCAATCCATA-TTTT
1 A-AAT---AAATCAATCCATACTAAT
715902 AAAATAAATCAATCCATACTAAT
1 -AAATAAATCAATCCATACTAAT
715925 AAAT
1 AAAT
715929 TATTTAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
22 18 0.44
23 5 0.12
25 4 0.10
26 14 0.34
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (22 bp):
AAATAAATCAATCCATACTAAT
Found at i:715983 original size:15 final size:15
Alignment explanation
Indices: 715954--716041 Score: 97
Period size: 15 Copynumber: 5.5 Consensus size: 15
715944 AATCCATACT
715954 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
715968 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
715983 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
716005 AATAAATTATTTTAA
1 AATAAATTATTTTAA
716020 AATAAATTATTTTAA
1 AATAAATTATTTTAA
716035 AATAAAT
1 AATAAAT
716042 AGTCTTATTA
Statistics
Matches: 64, Mismatches: 2, Indels: 15
0.79 0.02 0.19
Matches are distributed among these distances:
14 9 0.14
15 37 0.58
17 1 0.02
18 3 0.05
19 3 0.05
20 1 0.02
22 10 0.16
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:715989 original size:47 final size:49
Alignment explanation
Indices: 715922--716041 Score: 183
Period size: 52 Copynumber: 2.4 Consensus size: 49
715912 AATCCATACT
*
715922 AATAAATTA-TTTAAAATAAATCAATCCATA-CTAATAAATTA-TTTAA
1 AATAAATTATTTTAAAATAAATCAATCCATATATAATAAATTATTTTAA
715968 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAA
1 AATAAATTATTTTAAAATAAATCAATCCATA---TATAATAAATTATTTTAA
716020 AATAAATTATTTTAAAATAAAT
1 AATAAATTATTTTAAAATAAAT
716042 AGTCTTATTA
Statistics
Matches: 67, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
46 9 0.13
47 21 0.31
51 10 0.15
52 27 0.40
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (49 bp):
AATAAATTATTTTAAAATAAATCAATCCATATATAATAAATTATTTTAA
Found at i:719302 original size:15 final size:16
Alignment explanation
Indices: 719282--719314 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
719272 AACAGAAAGT
719282 AAGATGTAG-AAATTA
1 AAGATGTAGAAAATTA
719297 AAGATGTAGAAAATTA
1 AAGATGTAGAAAATTA
719313 AA
1 AA
719315 TGCTAGAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.24
Consensus pattern (16 bp):
AAGATGTAGAAAATTA
Found at i:719445 original size:15 final size:15
Alignment explanation
Indices: 719408--719478 Score: 61
Period size: 15 Copynumber: 4.7 Consensus size: 15
719398 CAAAAGGACC
* *
719408 AAATTAAAATTGCAG
1 AAATTTAAAGTGCAG
* *
719423 AAAATTAAAGTGCTG
1 AAATTTAAAGTGCAG
719438 AAATTTAAATGTGCAG
1 AAATTTAAA-GTGCAG
* * * *
719454 AAAATTAAATTTCTG
1 AAATTTAAAGTGCAG
719469 AAATTTAAAG
1 AAATTTAAAG
719479 AATAAAAAAT
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
15 30 0.70
16 13 0.30
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (15 bp):
AAATTTAAAGTGCAG
Found at i:719446 original size:31 final size:32
Alignment explanation
Indices: 719411--719477 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 32
719401 AAGGACCAAA
719411 TTAAAAT-TGCAGAAAATTAAAGTGCTGAAAT
1 TTAAAATGTGCAGAAAATTAAAGTGCTGAAAT
* *
719442 TT-AAATGTGCAGAAAATTAAATTTCTGAAAT
1 TTAAAATGTGCAGAAAATTAAAGTGCTGAAAT
719473 TTAAA
1 TTAAA
719478 GAATAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 4 0.12
31 26 0.81
32 2 0.06
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.33
Consensus pattern (32 bp):
TTAAAATGTGCAGAAAATTAAAGTGCTGAAAT
Found at i:719463 original size:16 final size:16
Alignment explanation
Indices: 719408--719463 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
719398 CAAAAGGACC
719408 AAATTAAAAT-TGCAGA
1 AAATT-AAATGTGCAGA
*
719424 AAATTAAA-GTGCTGA
1 AAATTAAATGTGCAGA
*
719439 AATTTAAATGTGCAGA
1 AAATTAAATGTGCAGA
719455 AAATTAAAT
1 AAATTAAAT
719464 TTCTGAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 15 0.44
16 19 0.56
ACGTcount: A:0.52, C:0.05, G:0.14, T:0.29
Consensus pattern (16 bp):
AAATTAAATGTGCAGA
Found at i:720583 original size:10 final size:10
Alignment explanation
Indices: 720544--720593 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
720534 TTCATCACAC
720544 CAAATTCTCT
1 CAAATTCTCT
*
720554 CAATTTCTCT
1 CAAATTCTCT
*
720564 CAACTTCTCT
1 CAAATTCTCT
*
720574 CAAATACTCT
1 CAAATTCTCT
* *
720584 TATATTCTCT
1 CAAATTCTCT
720594 GTTTAAGGTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.44
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:726739 original size:53 final size:49
Alignment explanation
Indices: 726635--726740 Score: 140
Period size: 53 Copynumber: 2.1 Consensus size: 49
726625 AAAGGCACGG
* * * *
726635 TATATATAATTATGTCAGTTAAAGGTATGACGTAGCCCCTGCCCCGCGC
1 TATATATAATTATGTCAGTTAAAGGTAAGACGCAGCCCCTGACCCGAGC
726684 TATATATAATTATGTCAGAGAATTAAAGGTAAGACGCAGCCCCTGACCCGAGC
1 TATATATAATTATGTC--AG--TTAAAGGTAAGACGCAGCCCCTGACCCGAGC
726737 TATA
1 TATA
726741 CCCTACGTGG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
49 16 0.33
51 2 0.04
53 31 0.63
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (49 bp):
TATATATAATTATGTCAGTTAAAGGTAAGACGCAGCCCCTGACCCGAGC
Found at i:726953 original size:30 final size:29
Alignment explanation
Indices: 726893--726953 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
726883 CTACAAAGGA
*
726893 TGTTAGATCGAAAAATATAGTCTGACCGG
1 TGTTAGATCGAAAAATATAGTCTCACCGG
*
726922 TGTTAGATCGATAAATATA-TCGGTCACCGG
1 TGTTAGATCGAAAAATATAGTC--TCACCGG
726952 TG
1 TG
726954 ATTTTTCGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 2 0.07
29 18 0.64
30 8 0.29
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.30
Consensus pattern (29 bp):
TGTTAGATCGAAAAATATAGTCTCACCGG
Found at i:727546 original size:6 final size:6
Alignment explanation
Indices: 727535--727563 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
727525 CAATTAAAAG
727535 ATTTGA ATTTGA ATTTGA ATTTGA ATTTG
1 ATTTGA ATTTGA ATTTGA ATTTGA ATTTG
727564 GACCCTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (6 bp):
ATTTGA
Found at i:743600 original size:15 final size:13
Alignment explanation
Indices: 743567--743604 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
743557 GGAGGGTATT
743567 AAAAT-TATTTTA
1 AAAATATATTTTA
743579 AAAATATATTTTA
1 AAAATATATTTTA
743592 AGGAAATATATTT
1 A--AAATATATTT
743605 CTACTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.22
13 8 0.35
15 10 0.43
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (13 bp):
AAAATATATTTTA
Found at i:745497 original size:22 final size:22
Alignment explanation
Indices: 745472--745514 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
745462 ATCATTGAGT
* *
745472 TTGACTAGAGTTGACTTTGATG
1 TTGACCAGAGTTAACTTTGATG
*
745494 TTGACCAGTGTTAACTTTGAT
1 TTGACCAGAGTTAACTTTGAT
745515 CAAAAAGTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.23, T:0.42
Consensus pattern (22 bp):
TTGACCAGAGTTAACTTTGATG
Found at i:753421 original size:15 final size:15
Alignment explanation
Indices: 753397--753440 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
753387 TGAGTAAACC
753397 CGAACTAAGTCAACT
1 CGAACTAAGTCAACT
**
753412 CGCTCTAAGTCAACT
1 CGAACTAAGTCAACT
753427 CGAACTAAGTCAAC
1 CGAACTAAGTCAAC
753441 CTATTGACCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.36, C:0.30, G:0.14, T:0.20
Consensus pattern (15 bp):
CGAACTAAGTCAACT
Found at i:758554 original size:18 final size:18
Alignment explanation
Indices: 758531--758575 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
758521 TTAACCGAAC
*
758531 TAATTCGGTCTTATTGGT
1 TAATTCGGTCTGATTGGT
758549 TAATTCGGTCTGATTGGT
1 TAATTCGGTCTGATTGGT
758567 TAATTCGGT
1 TAATTCGGT
758576 TAAAATTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.18, C:0.11, G:0.24, T:0.47
Consensus pattern (18 bp):
TAATTCGGTCTGATTGGT
Found at i:760030 original size:24 final size:24
Alignment explanation
Indices: 759998--760046 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
759988 AACCCCTTTC
759998 AACCAATCATGAAATCTTGTATTT
1 AACCAATCATGAAATCTTGTATTT
760022 AACCAATCATGAAATCTTGTATTT
1 AACCAATCATGAAATCTTGTATTT
760046 A
1 A
760047 CATGACCGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (24 bp):
AACCAATCATGAAATCTTGTATTT
Done.