Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 125 of 235
Found at i:42606584 original size:13 final size:13
Alignment explanation
Indices: 42606566--42606591 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42606556 AAATTTTCAT
42606566 AAATATTTATGAA
1 AAATATTTATGAA
42606579 AAATATTTATGAA
1 AAATATTTATGAA
42606592 GCTAGTTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
AAATATTTATGAA
Found at i:42606756 original size:42 final size:42
Alignment explanation
Indices: 42606683--42606763 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 42
42606673 AGGAAAATCT
** *
42606683 AAGATTTTTATGTTTAATATATTATTATATTATTTTATAATA
1 AAGATTTTTATGTTTAATATATTAAAATATTATATTATAATA
42606725 AAGATATTTTATGTTTTAAT-TA-TAAAATATTATATTATA
1 AAGAT-TTTTATG-TTTAATATATTAAAATATTATATTATA
42606764 TTATATTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 19 0.56
43 9 0.26
44 6 0.18
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (42 bp):
AAGATTTTTATGTTTAATATATTAAAATATTATATTATAATA
Found at i:42606761 original size:5 final size:5
Alignment explanation
Indices: 42606751--42606786 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
42606741 TAATTATAAA
42606751 ATATT ATATT ATATT ATA-T -TATT ATATT ATA-T ATAT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATAT
42606787 AAACTAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
3 2 0.07
4 6 0.21
5 20 0.71
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:42606775 original size:13 final size:13
Alignment explanation
Indices: 42606757--42606782 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42606747 TAAAATATTA
42606757 TATTATATTATAT
1 TATTATATTATAT
42606770 TATTATATTATAT
1 TATTATATTATAT
42606783 ATATAAACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTATATTATAT
Found at i:42606775 original size:18 final size:17
Alignment explanation
Indices: 42606752--42606786 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
42606742 AATTATAAAA
42606752 TATTATATTATATTATAT
1 TATTATATTATA-TATAT
42606770 TATTATATTATATATAT
1 TATTATATTATATATAT
42606787 AAACTAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTATATTATATATAT
Found at i:42607997 original size:18 final size:18
Alignment explanation
Indices: 42607945--42608002 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
42607935 ATTACTGGAC
42607945 TGAATAACTGATTGTTAT
1 TGAATAACTGATTGTTAT
* *
42607963 TG-AT---TGTTTGATAT
1 TGAATAACTGATTGTTAT
42607977 TGAATAACTGATTGTTAT
1 TGAATAACTGATTGTTAT
42607995 TGAATAAC
1 TGAATAAC
42608003 AATAAACAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 10 0.31
15 2 0.06
17 2 0.06
18 18 0.56
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (18 bp):
TGAATAACTGATTGTTAT
Found at i:42612569 original size:42 final size:43
Alignment explanation
Indices: 42612426--42612570 Score: 147
Period size: 42 Copynumber: 3.4 Consensus size: 43
42612416 CCATATTTCG
* * *
42612426 GATATGGTCTTACATGTAA-A-CTTATATCGATGCCAATAGCCCA
1 GATATGGTCTTACACGTAATATCATA-ATCGATGCC-ATATCCCA
* * * * *
42612469 -ACTATGGTCTTACACGAAATTTCGT-ATCGATGCCATGTCTCA
1 GA-TATGGTCTTACACGTAATATCATAATCGATGCCATATCCCA
*
42612511 GACATGGTCTTACACGTAATATCATAAT-GATGCCATATCCCA
1 GATATGGTCTTACACGTAATATCATAATCGATGCCATATCCCA
42612553 GATATGGTCTTACACGTA
1 GATATGGTCTTACACGTA
42612571 TTCTCATTTC
Statistics
Matches: 83, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
42 54 0.65
43 27 0.33
45 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (43 bp):
GATATGGTCTTACACGTAATATCATAATCGATGCCATATCCCA
Found at i:42615541 original size:23 final size:22
Alignment explanation
Indices: 42615502--42615616 Score: 106
Period size: 23 Copynumber: 4.8 Consensus size: 22
42615492 GTTGATGGAT
*
42615502 AGTAAGCTCTATTGAGCTGAAAC
1 AGTAAGCTCTA-CGAGCTGAAAC
*
42615525 GGTAAGCTCTGACGAGCT-AAATC
1 AGTAAGCTCT-ACGAGCTGAAA-C
*
42615548 AGTAAGCTCATACGAGCTAAGAAC
1 AGTAAGCTC-TACGAGCTGA-AAC
42615572 AGTAAGCTCTTACGAGCTGATATATC
1 AGTAAGCTC-TACGAGCTGA-A-A-C
42615598 AGTAAGCTCATACGAGCTG
1 AGTAAGCTC-TACGAGCTG
42615617 CGGTGAGTCC
Statistics
Matches: 78, Mismatches: 7, Indels: 11
0.81 0.07 0.11
Matches are distributed among these distances:
22 3 0.04
23 30 0.38
24 23 0.29
25 3 0.04
26 19 0.24
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (22 bp):
AGTAAGCTCTACGAGCTGAAAC
Found at i:42615616 original size:26 final size:23
Alignment explanation
Indices: 42615526--42615615 Score: 110
Period size: 24 Copynumber: 3.7 Consensus size: 23
42615516 AGCTGAAACG
42615526 GTAAGCTC-TGACGAGCTAAATCA
1 GTAAGCTCAT-ACGAGCTAAATCA
*
42615549 GTAAGCTCATACGAGCTAAGAACA
1 GTAAGCTCATACGAGCTAA-ATCA
*
42615573 GTAAGCTCTTACGAGCTGATATATCA
1 GTAAGCTCATACGAGCT-A-A-ATCA
42615599 GTAAGCTCATACGAGCT
1 GTAAGCTCATACGAGCT
42615616 GCGGTGAGTC
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.29
24 20 0.34
25 1 0.02
26 20 0.34
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (23 bp):
GTAAGCTCATACGAGCTAAATCA
Found at i:42616182 original size:13 final size:13
Alignment explanation
Indices: 42616164--42616190 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42616154 TTTTCTCAAT
42616164 TTAATAAAATAAA
1 TTAATAAAATAAA
42616177 TTAATAAAATAAA
1 TTAATAAAATAAA
42616190 T
1 T
42616191 ATTTTTACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TTAATAAAATAAA
Found at i:42624108 original size:24 final size:26
Alignment explanation
Indices: 42624071--42624138 Score: 95
Period size: 24 Copynumber: 2.7 Consensus size: 26
42624061 GAGCTAAATT
42624071 AGTAAGCTCATACGAGCTGAGA-A-C
1 AGTAAGCTCATACGAGCTGAGATATC
* * *
42624095 AGTAAGATCTTACGAGCTGATATATC
1 AGTAAGCTCATACGAGCTGAGATATC
42624121 AGTAAGCTCATACGAGCT
1 AGTAAGCTCATACGAGCT
42624139 ACGGTGAGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 19 0.51
25 1 0.03
26 17 0.46
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (26 bp):
AGTAAGCTCATACGAGCTGAGATATC
Found at i:42626055 original size:28 final size:28
Alignment explanation
Indices: 42626012--42626117 Score: 78
Period size: 28 Copynumber: 3.7 Consensus size: 28
42626002 GAATTTAGTG
*
42626012 TTAA-CTGGGCCTTAGCCCATATCAATA
1 TTAATCTGGGCCATAGCCCATATCAATA
42626039 TTAATCTGGGCCATAGCCCCTTACAGTATCAGAGTA
1 TTAATCTGGGCCATAG--CC---CA-TATCA-A-TA
*
42626075 -T-AT-TGGGCC-TAGCCCATATCAGTA
1 TTAATCTGGGCCATAGCCCATATCAATA
*
42626099 TCAATCTGGGCCATAGCCC
1 TTAATCTGGGCCATAGCCC
42626118 TACTACAAGT
Statistics
Matches: 63, Mismatches: 3, Indels: 25
0.69 0.03 0.27
Matches are distributed among these distances:
24 2 0.03
26 7 0.11
27 12 0.19
28 16 0.25
30 4 0.06
32 3 0.05
33 8 0.13
34 7 0.11
35 2 0.03
36 2 0.03
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.27
Consensus pattern (28 bp):
TTAATCTGGGCCATAGCCCATATCAATA
Found at i:42626095 original size:60 final size:59
Alignment explanation
Indices: 42626017--42626156 Score: 178
Period size: 60 Copynumber: 2.3 Consensus size: 59
42626007 TAGTGTTAAC
*
42626017 TGGGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCCT-TAC-AGTATC-AGAGTATAT
1 TGGGCC-TAGCCCATATCAATATCAATCTGGGCCATAG-CCCTATACAAG--TCGAGA-TATAT
*
42626078 TGGGCCTAGCCCATATCAGTATCAATCTGGGCCATAGCCCTACTACAAGTCGAGATATAT
1 TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTA-TACAAGTCGAGATATAT
*
42626138 TGGGCCTTGCCCATATCAA
1 TGGGCCTAGCCCATATCAA
42626157 CACAGTTGGG
Statistics
Matches: 71, Mismatches: 4, Indels: 9
0.85 0.05 0.11
Matches are distributed among these distances:
59 4 0.06
60 53 0.75
61 12 0.17
62 2 0.03
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.27
Consensus pattern (59 bp):
TGGGCCTAGCCCATATCAATATCAATCTGGGCCATAGCCCTATACAAGTCGAGATATAT
Found at i:42632217 original size:7 final size:7
Alignment explanation
Indices: 42632205--42632274 Score: 89
Period size: 6 Copynumber: 10.9 Consensus size: 7
42632195 TGCAAATGAA
42632205 TCATTTC
1 TCATTTC
42632212 TCATTTC
1 TCATTTC
42632219 TCATTTC
1 TCATTTC
42632226 TCATTTC
1 TCATTTC
42632233 TCATTT-
1 TCATTTC
42632239 TCATTT-
1 TCATTTC
42632245 TCATTTC
1 TCATTTC
*
42632252 -CACTTC
1 TCATTTC
42632258 -CATTTC
1 TCATTTC
42632264 -CATTTC
1 TCATTTC
42632270 -CATTT
1 TCATTT
42632275 TGAGAAAACC
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
6 33 0.55
7 27 0.45
ACGTcount: A:0.16, C:0.29, G:0.00, T:0.56
Consensus pattern (7 bp):
TCATTTC
Found at i:42632923 original size:7 final size:7
Alignment explanation
Indices: 42632911--42632944 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
42632901 TAAATAAAAC
42632911 CATAAAT
1 CATAAAT
42632918 CATAAAT
1 CATAAAT
*
42632925 CATAGAT
1 CATAAAT
42632932 CATAAAT
1 CATAAAT
*
42632939 CGTAAA
1 CATAAA
42632945 AGTCCAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.53, C:0.15, G:0.06, T:0.26
Consensus pattern (7 bp):
CATAAAT
Found at i:42638749 original size:3 final size:3
Alignment explanation
Indices: 42638741--42638772 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
42638731 TCTAATTGTT
42638741 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
42638773 GCAGTCTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:42639349 original size:9 final size:8
Alignment explanation
Indices: 42639337--42639400 Score: 60
Period size: 9 Copynumber: 7.6 Consensus size: 8
42639327 TTTTATATTT
42639337 TTTTTATGA
1 TTTTTAT-A
42639346 TTTTTATAA
1 TTTTTAT-A
42639355 TTTTTA-A
1 TTTTTATA
*
42639362 TATTTTATT
1 T-TTTTATA
42639371 TTTTTATAA
1 TTTTTAT-A
42639380 TTTTTAT-
1 TTTTTATA
42639387 TTTTTATAA
1 TTTTTAT-A
42639396 TTTTT
1 TTTTT
42639401 TTGTAACATG
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
7 9 0.19
8 11 0.23
9 27 0.57
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (8 bp):
TTTTTATA
Found at i:42639366 original size:38 final size:37
Alignment explanation
Indices: 42639245--42639375 Score: 104
Period size: 38 Copynumber: 3.4 Consensus size: 37
42639235 TGGTATGATA
* *
42639245 ATTTTTATATTTTTTTTTTACGAATTTTATATTTCTTTGAAT
1 ATTTTTATA--TTTTTTTTATG-ATTTTATAATT-TTT-AAT
* * * * * * *
42639287 TTTTTTATAATTTTCTTATGACTTTATAAAATTTCACT
1 ATTTTTATATTTTTTTTATGATTTTAT-AATTTTTAAT
42639325 ATTTTTATATTTTTTTTATGATTTTTATAATTTTTAAT
1 ATTTTTATATTTTTTTTATGA-TTTTATAATTTTTAAT
42639363 A-TTTTAT-TTTTTT
1 ATTTTTATATTTTTT
42639376 ATAATTTTTA
Statistics
Matches: 71, Mismatches: 16, Indels: 10
0.73 0.16 0.10
Matches are distributed among these distances:
36 6 0.08
37 6 0.08
38 28 0.39
39 13 0.18
40 10 0.14
42 8 0.11
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.67
Consensus pattern (37 bp):
ATTTTTATATTTTTTTTATGATTTTATAATTTTTAAT
Found at i:42639376 original size:16 final size:18
Alignment explanation
Indices: 42639327--42639400 Score: 68
Period size: 16 Copynumber: 4.3 Consensus size: 18
42639317 ATTTCACTAT
* *
42639327 TTTTATATTTTTTTTATGA
1 TTTT-TATTTTTTTAATAA
*
42639346 TTTTTATAATTTTTAAT-A
1 TTTTTAT-TTTTTTAATAA
42639364 -TTTTATTTTTTT-ATAA
1 TTTTTATTTTTTTAATAA
42639380 TTTTTA-TTTTTT-ATAA
1 TTTTTATTTTTTTAATAA
42639396 TTTTT
1 TTTTT
42639401 TTGTAACATG
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
15 2 0.04
16 21 0.43
17 11 0.22
18 4 0.08
19 11 0.22
ACGTcount: A:0.24, C:0.00, G:0.01, T:0.74
Consensus pattern (18 bp):
TTTTTATTTTTTTAATAA
Found at i:42639380 original size:25 final size:24
Alignment explanation
Indices: 42639346--42639393 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
42639336 TTTTTTATGA
42639346 TTTTTATAATTTTTAATATTTTATT
1 TTTTTATAATTTTT-ATATTTTATT
*
42639371 TTTTTATAATTTTTATTTTTTAT
1 TTTTTATAATTTTTATATTTTAT
42639394 AATTTTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTTATAATTTTTATATTTTATT
Found at i:42639641 original size:20 final size:23
Alignment explanation
Indices: 42639605--42639647 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
42639595 ATAAAATTTC
42639605 AAATATATAAGAATTTA-TAAAA
1 AAATATATAAGAATTTATTAAAA
42639627 AAAT-TATAA-AATTTATTAAAA
1 AAATATATAAGAATTTATTAAAA
42639648 TATAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 10 0.50
22 4 0.20
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
AAATATATAAGAATTTATTAAAA
Found at i:42639660 original size:9 final size:9
Alignment explanation
Indices: 42639625--42639666 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
42639615 GAATTTATAA
42639625 AAAAATTAT
1 AAAAATTAT
*
42639634 AAAATTTAT
1 AAAAATTAT
*
42639643 TAAAA-TAT
1 AAAAATTAT
42639651 AAAAATTAT
1 AAAAATTAT
42639660 AGAAAAT
1 A-AAAAT
42639667 AAATAAAAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
8 7 0.26
9 15 0.56
10 5 0.19
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:42642324 original size:25 final size:25
Alignment explanation
Indices: 42642296--42642438 Score: 107
Period size: 25 Copynumber: 5.8 Consensus size: 25
42642286 TGATAATATT
*
42642296 AAAAATATGTACATAATATAGTGTA
1 AAAAATATATACATAATATAGTGTA
* *
42642321 AAAAATACATACATAATATAAT-T-
1 AAAAATATATACATAATATAGTGTA
* *
42642344 -AAAATATATACATAAGATAACATGTA
1 AAAAATATATACATAATAT-A-GTGTA
* * * *
42642370 AAATATATATAAATAATATAGTATT
1 AAAAATATATACATAATATAGTGTA
* *
42642395 AAAGATATATACATAAAATA--GTA
1 AAAAATATATACATAATATAGTGTA
* * *
42642418 TAATATATATACGTAATATAG
1 AAAAATATATACATAATATAG
42642439 AATTTAGAAT
Statistics
Matches: 92, Mismatches: 20, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
22 16 0.17
23 18 0.20
24 3 0.03
25 39 0.42
26 1 0.01
27 15 0.16
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (25 bp):
AAAAATATATACATAATATAGTGTA
Found at i:42642377 original size:27 final size:25
Alignment explanation
Indices: 42642329--42642410 Score: 71
Period size: 27 Copynumber: 3.3 Consensus size: 25
42642319 TAAAAAATAC
*
42642329 ATACATAATAT-A-ATTAAA-ATAT
1 ATACATAAGATAACATTAAAGATAT
*
42642351 ATACATAAGATAACATGTAAAATATAT
1 ATACATAAGATAACAT-T-AAAGATAT
* * **
42642378 ATAAATAATATAGTATTAAAGATAT
1 ATACATAAGATAACATTAAAGATAT
42642403 ATACATAA
1 ATACATAA
42642411 AATAGTATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
22 10 0.21
23 1 0.02
24 2 0.04
25 15 0.31
26 4 0.08
27 16 0.33
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (25 bp):
ATACATAAGATAACATTAAAGATAT
Found at i:42642409 original size:74 final size:73
Alignment explanation
Indices: 42642287--42642429 Score: 171
Period size: 74 Copynumber: 1.9 Consensus size: 73
42642277 ATAAATATGT
* * * * *
42642287 GATAATATTAAAAATATGTACATAATATAGTGTAAAAAATACATACATAATATAAT-TAAAATAT
1 GATAACATTAAAAATATATAAATAATATAGTATAAAAAATACATACATAAAATAATATAAAATAT
42642351 ATACATAA
66 ATACATAA
* * * * *
42642359 GATAACATGTAAAATATATATAAATAATATAGTATTAAAGATATATACATAAAATAGTATAATAT
1 GATAACAT-TAAAA-ATATATAAATAATATAGTATAAAAAATACATACATAAAATAATATAAAAT
42642424 ATATAC
64 ATATAC
42642430 GTAATATAGA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
72 7 0.12
73 5 0.09
74 35 0.60
75 11 0.19
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.33
Consensus pattern (73 bp):
GATAACATTAAAAATATATAAATAATATAGTATAAAAAATACATACATAAAATAATATAAAATAT
ATACATAA
Found at i:42642481 original size:24 final size:23
Alignment explanation
Indices: 42642454--42642505 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
42642444 AGAATATACC
*
42642454 TAATATATTA-AAAGAATATATATA
1 TAATATAATATAAAGAA-ATATA-A
*
42642478 TAATATAATATTAAGAAATATAA
1 TAATATAATATAAAGAAATATAA
42642501 TAATA
1 TAATA
42642506 ACAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.24
24 14 0.56
25 5 0.20
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (23 bp):
TAATATAATATAAAGAAATATAA
Found at i:42644944 original size:3 final size:3
Alignment explanation
Indices: 42644930--42644964 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
42644920 GAGAGAAAGG
*
42644930 AGA AGG AGA AGA AGA AGGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA A
42644965 AAAAAAAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:42644952 original size:19 final size:18
Alignment explanation
Indices: 42644926--42644964 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
42644916 AAATGAGAGA
*
42644926 AAGGAGAAGGAGAAGAAG
1 AAGGAGAAGAAGAAGAAG
42644944 AAGGAAGAAGAAGAAGAAG
1 AAGG-AGAAGAAGAAGAAG
42644963 AA
1 AA
42644965 AAAAAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (18 bp):
AAGGAGAAGAAGAAGAAG
Found at i:42644962 original size:16 final size:16
Alignment explanation
Indices: 42644931--42644962 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42644921 AGAGAAAGGA
*
42644931 GAAGGAGAAGAAGAAG
1 GAAGAAGAAGAAGAAG
42644947 GAAGAAGAAGAAGAAG
1 GAAGAAGAAGAAGAAG
42644963 AAAAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (16 bp):
GAAGAAGAAGAAGAAG
Found at i:42645397 original size:54 final size:54
Alignment explanation
Indices: 42645338--42645511 Score: 122
Period size: 54 Copynumber: 3.1 Consensus size: 54
42645328 ATAGCTATTT
42645338 TATTAGTAATTTAAGATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTA
1 TATTAGTAATTTAAGATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTA
* ** **** * * * * *
42645392 TATTAGCGAATTGTAATTTTTTTA-GTAATATATTTAAAAAAAATA-TTTTTA-TAG-CTATTT
1 TATTAG-TAATT-TAA---GATTAGGT--TATA--T-AAATTGTTAGTGTTTAGTGGTTTAGTA
42645452 TATTAGTAATTTAAGATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTA
1 TATTAGTAATTTAAGATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTA
42645506 TATTAG
1 TATTAG
42645512 CGAATTGTAA
Statistics
Matches: 82, Mismatches: 24, Indels: 28
0.61 0.18 0.21
Matches are distributed among these distances:
51 5 0.06
52 6 0.07
53 2 0.02
54 19 0.23
55 7 0.09
56 5 0.06
58 5 0.06
59 7 0.09
60 13 0.16
61 2 0.02
62 6 0.07
63 5 0.06
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.49
Consensus pattern (54 bp):
TATTAGTAATTTAAGATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTA
Found at i:42645491 original size:114 final size:115
Alignment explanation
Indices: 42645237--42645567 Score: 556
Period size: 114 Copynumber: 2.9 Consensus size: 115
42645227 TTTTATAGTT
* ** * * * *
42645237 GATTTGGTTATATAAATTGTTAGTGTTTAGTAATTTAGTGTATTAGTGTATTGTGATTTTTTTAG
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTATATTAGCGAATTGTAATTTTTTTAG
42645302 TAATATATTTTTTAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAA
66 TAATATATTTTTTAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAA
42645352 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTATATTAGCGAATTGTAATTTTTTTAG
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTATATTAGCGAATTGTAATTTTTTTAG
** *
42645417 TAATATA-TTTAAAAAAAATATTTTTATAGCTATTTTATTAGTAATTTAA
66 TAATATATTTTTTAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAA
42645466 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTATATTAGCGAATTGTAATTTTTTTAG
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTATATTAGCGAATTGTAATTTTTTTAG
*
42645531 TAATATATTTTTTAAAAAATAATTTTATAGTTATTTT
66 TAATATATTTTTTAAAAAATAATTTTATAGCTATTTT
42645568 GTGTTAGTAT
Statistics
Matches: 201, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
114 111 0.55
115 90 0.45
ACGTcount: A:0.33, C:0.01, G:0.14, T:0.51
Consensus pattern (115 bp):
GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTATATTAGCGAATTGTAATTTTTTTAG
TAATATATTTTTTAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAA
Found at i:42647746 original size:33 final size:33
Alignment explanation
Indices: 42647709--42647804 Score: 99
Period size: 33 Copynumber: 2.9 Consensus size: 33
42647699 ATTTATCTCA
42647709 GTACTCTACTCCTTCCGGCCCGTATCCACC-CAT
1 GTACTCTACTCCTTCCGGCCCGTATCCACCGC-T
* *
42647742 GTACTCAACTCC-TCCAAAG-CCGTATCCACCGCT
1 GTACTCTACTCCTTCC--GGCCCGTATCCACCGCT
* * *
42647775 GTACTCTACTCCTCCCGACCCATATCCACC
1 GTACTCTACTCCTTCCGGCCCGTATCCACC
42647805 ACCATATTCT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
32 3 0.06
33 44 0.86
34 4 0.08
ACGTcount: A:0.20, C:0.46, G:0.10, T:0.24
Consensus pattern (33 bp):
GTACTCTACTCCTTCCGGCCCGTATCCACCGCT
Found at i:42651474 original size:27 final size:27
Alignment explanation
Indices: 42651436--42651495 Score: 120
Period size: 27 Copynumber: 2.2 Consensus size: 27
42651426 CCCATCAGTT
42651436 GTGCCTACCAAGAAGGCACAACTAGTC
1 GTGCCTACCAAGAAGGCACAACTAGTC
42651463 GTGCCTACCAAGAAGGCACAACTAGTC
1 GTGCCTACCAAGAAGGCACAACTAGTC
42651490 GTGCCT
1 GTGCCT
42651496 GTCAGATAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.17
Consensus pattern (27 bp):
GTGCCTACCAAGAAGGCACAACTAGTC
Found at i:42651506 original size:27 final size:27
Alignment explanation
Indices: 42651449--42651538 Score: 101
Period size: 27 Copynumber: 3.3 Consensus size: 27
42651439 CCTACCAAGA
**
42651449 AGGCACAACTAGTCGTGCCTACCAAGA-
1 AGGCACAACTAGTCGTGCCTGTC-AGAT
42651476 AGGCACAACTAGTCGTGCCTGTCAGAT
1 AGGCACAACTAGTCGTGCCTGTCAGAT
* * * * *
42651503 AGGCTCAACTAGTTGAGCTTGTCAGGT
1 AGGCACAACTAGTCGTGCCTGTCAGAT
42651530 AGGCACAAC
1 AGGCACAAC
42651539 ATGTATGTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
26 3 0.06
27 51 0.94
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.20
Consensus pattern (27 bp):
AGGCACAACTAGTCGTGCCTGTCAGAT
Found at i:42654590 original size:21 final size:22
Alignment explanation
Indices: 42654561--42654607 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
42654551 CAGAAGGAGT
*
42654561 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
42654583 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
42654604 GAGT
1 GAGT
42654608 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:42658063 original size:26 final size:26
Alignment explanation
Indices: 42657955--42658088 Score: 80
Period size: 26 Copynumber: 4.9 Consensus size: 26
42657945 ATAAATAATC
42657955 TAAATA-ATATAATAT-TGAAAAATA-
1 TAAATACATATAATATAT-AAAAATAT
*
42657979 TATATACATAATAATATATAAAATATAATGT
1 TAAATACAT-ATAATATATAAAA-AT-A--T
*
42658010 TAAA-AGCGTATATAACATATAAAAATAT
1 TAAATA-C--ATATAATATATAAAAATAT
* **
42658038 ATATATA-ATATAATATATAAGTATAT
1 -TAAATACATATAATATATAAAAATAT
42658064 TAAATACATATACATATATATAAAA
1 TAAATACATATA-ATATATA-AAAA
42658089 GATCATACAC
Statistics
Matches: 84, Mismatches: 10, Indels: 28
0.69 0.08 0.23
Matches are distributed among these distances:
24 5 0.06
25 7 0.08
26 32 0.38
27 10 0.12
28 4 0.05
29 3 0.04
30 3 0.04
31 6 0.07
32 12 0.14
33 2 0.02
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (26 bp):
TAAATACATATAATATATAAAAATAT
Found at i:42659872 original size:12 final size:12
Alignment explanation
Indices: 42659851--42659884 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
42659841 TATATATTTT
*
42659851 AAAATTATATAA
1 AAAATAATATAA
42659863 AAAATAATATAA
1 AAAATAATATAA
*
42659875 AAATTAATAT
1 AAAATAATAT
42659885 GGGCAGGCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:42668800 original size:35 final size:35
Alignment explanation
Indices: 42668754--42668954 Score: 280
Period size: 35 Copynumber: 5.8 Consensus size: 35
42668744 GGTTTTCCTC
42668754 ATGGAAAATACCATACCTACGTTTCACAACTCAGT
1 ATGGAAAATACCATACCTACGTTTCACAACTCAGT
*
42668789 ATGGAAAATACCATACCTACGTTTCACAACTCGGT
1 ATGGAAAATACCATACCTACGTTTCACAACTCAGT
* * * * *
42668824 ATGGAAAATACCATACCTATGTATCATAGCTCGGT
1 ATGGAAAATACCATACCTACGTTTCACAACTCAGT
* *
42668859 ATGG-AAATACCATACCTACATTTCATAACTCAGT
1 ATGGAAAATACCATACCTACGTTTCACAACTCAGT
* * * *
42668893 ATAGAAAATACCATGCCTACGTATCATAACTCAGT
1 ATGGAAAATACCATACCTACGTTTCACAACTCAGT
42668928 ATGG-AAATACCATACCTACGTTTCACA
1 ATGGAAAATACCATACCTACGTTTCACA
42668955 TTTTTCCATG
Statistics
Matches: 147, Mismatches: 18, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
34 48 0.33
35 99 0.67
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (35 bp):
ATGGAAAATACCATACCTACGTTTCACAACTCAGT
Found at i:42668900 original size:69 final size:69
Alignment explanation
Indices: 42668757--42668954 Score: 297
Period size: 69 Copynumber: 2.9 Consensus size: 69
42668747 TTTCCTCATG
* * *
42668757 GAAAATACCATACCTACGTTTCACAACTCAGTATGGAAAATACCATACCTACGTTTCACAACTCG
1 GAAAATACCATACCTACGTATCATAACTCAGTATGG-AAATACCATACCTACGTTTCACAACTCA
*
42668822 GTATG
65 GTATA
* * * * *
42668827 GAAAATACCATACCTATGTATCATAGCTCGGTATGGAAATACCATACCTACATTTCATAACTCAG
1 GAAAATACCATACCTACGTATCATAACTCAGTATGGAAATACCATACCTACGTTTCACAACTCAG
42668892 TATA
66 TATA
*
42668896 GAAAATACCATGCCTACGTATCATAACTCAGTATGGAAATACCATACCTACGTTTCACA
1 GAAAATACCATACCTACGTATCATAACTCAGTATGGAAATACCATACCTACGTTTCACA
42668955 TTTTTCCATG
Statistics
Matches: 113, Mismatches: 15, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
69 82 0.73
70 31 0.27
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (69 bp):
GAAAATACCATACCTACGTATCATAACTCAGTATGGAAATACCATACCTACGTTTCACAACTCAG
TATA
Found at i:42670104 original size:12 final size:12
Alignment explanation
Indices: 42670087--42670137 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 12
42670077 AACACTCCAT
42670087 AAATATTTATAA
1 AAATATTTATAA
42670099 AAATATTTATACTCCA
1 AAATATTTATA----A
42670115 TAAATATTTATAA
1 -AAATATTTATAA
42670128 AAATATTTAT
1 AAATATTTAT
42670138 GATTCGGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
12 21 0.62
13 1 0.03
16 1 0.03
17 11 0.32
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (12 bp):
AAATATTTATAA
Found at i:42670113 original size:29 final size:29
Alignment explanation
Indices: 42670080--42670137 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
42670070 ACTTAATAAC
42670080 ACTCCATAAATATTTATAAAAATATTTAT
1 ACTCCATAAATATTTATAAAAATATTTAT
42670109 ACTCCATAAATATTTATAAAAATATTTAT
1 ACTCCATAAATATTTATAAAAATATTTAT
42670138 GATTCGGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (29 bp):
ACTCCATAAATATTTATAAAAATATTTAT
Found at i:42670121 original size:17 final size:17
Alignment explanation
Indices: 42670080--42670126 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
42670070 ACTTAATAAC
42670080 ACTCCATAAATATTTAT
1 ACTCCATAAATATTTAT
42670097 A----A-AAATATTTAT
1 ACTCCATAAATATTTAT
42670109 ACTCCATAAATATTTAT
1 ACTCCATAAATATTTAT
42670126 A
1 A
42670127 AAAATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
12 11 0.44
13 1 0.04
16 1 0.04
17 12 0.48
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (17 bp):
ACTCCATAAATATTTAT
Found at i:42671580 original size:15 final size:15
Alignment explanation
Indices: 42671560--42671611 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
42671550 ACTACAAAAA
42671560 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
42671575 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
42671594 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
42671609 ATT
1 ATT
42671612 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:42671732 original size:22 final size:22
Alignment explanation
Indices: 42671692--42671747 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
42671682 AATAAAATTG
*
42671692 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
42671712 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* * *
42671734 TATTAATAATTTAT
1 AAATAATAAATTAT
42671748 TATATGACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.30
21 2 0.07
22 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:42673453 original size:15 final size:15
Alignment explanation
Indices: 42673429--42673477 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
42673419 CTTGTACGAC
*
42673429 CCCTAGGTGTGTGAA
1 CCCTAGGTGTGCGAA
* *
42673444 CCCTAAGTGTGCAAA
1 CCCTAGGTGTGCGAA
*
42673459 CCCTAGGTATGCGAA
1 CCCTAGGTGTGCGAA
42673474 CCCT
1 CCCT
42673478 TGTACAAACT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.22
Consensus pattern (15 bp):
CCCTAGGTGTGCGAA
Found at i:42673496 original size:57 final size:57
Alignment explanation
Indices: 42673394--42673504 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 57
42673384 CAAACCCATC
* * * * * *
42673394 TGTGCGAACCCTAGGTATACGAAAGCTTGTACGACCCCTAGGTGTGTGAACCCTAAG
1 TGTGCAAACCCTAGGTATACGAAACCTTGTACAAACCCTAAGTGTGCGAACCCTAAG
* * *
42673451 TGTGCAAACCCTAGGTATGCGAACCCTTGTACAAACTCTAAGTGTGCGAACCCT
1 TGTGCAAACCCTAGGTATACGAAACCTTGTACAAACCCTAAGTGTGCGAACCCT
42673505 GATGTGGCAC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
57 45 1.00
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.23
Consensus pattern (57 bp):
TGTGCAAACCCTAGGTATACGAAACCTTGTACAAACCCTAAGTGTGCGAACCCTAAG
Found at i:42674256 original size:40 final size:40
Alignment explanation
Indices: 42674201--42674280 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
42674191 GTGTCTCCCC
42674201 TACCTTAACAATTACTTAAAATTCAAAATCAACAAGGTTT
1 TACCTTAACAATTACTTAAAATTCAAAATCAACAAGGTTT
* *
42674241 TACCTTAATAATTACTTAAAATTCAAACTCAACAAGGTTT
1 TACCTTAACAATTACTTAAAATTCAAAATCAACAAGGTTT
42674281 AACATCCTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (40 bp):
TACCTTAACAATTACTTAAAATTCAAAATCAACAAGGTTT
Found at i:42675872 original size:30 final size:29
Alignment explanation
Indices: 42675836--42675903 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
42675826 ACATCCAATA
42675836 TTCACATGACAGTGTCTTAAACCCGTGTGG
1 TTCACATGAC-GTGTCTTAAACCCGTGTGG
* * **
42675866 TTCACATAGTCGTGTCTTCAGGCCGTGTGG
1 TTCACAT-GACGTGTCTTAAACCCGTGTGG
42675896 TTCACATG
1 TTCACATG
42675904 GTTGTGTCCG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 1 0.03
30 30 0.91
31 2 0.06
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (29 bp):
TTCACATGACGTGTCTTAAACCCGTGTGG
Found at i:42676120 original size:16 final size:16
Alignment explanation
Indices: 42676099--42676149 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
42676089 AAAATTTAAT
* *
42676099 ATAAAAAATAGTTTTA
1 ATAAAAAATAATATTA
**
42676115 ATAAAATTTAATATTA
1 ATAAAAAATAATATTA
42676131 ATAAAAAATAAATATTA
1 ATAAAAAAT-AATATTA
42676148 AT
1 AT
42676150 GAATAAAACA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 19 0.68
17 9 0.32
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
ATAAAAAATAATATTA
Found at i:42678015 original size:60 final size:60
Alignment explanation
Indices: 42677921--42678111 Score: 162
Period size: 57 Copynumber: 3.3 Consensus size: 60
42677911 GGATTTAAAT
* * * * * *
42677921 TTTTTTGT-CTAAGTTGGTCCCTGAAATTGATAATTGTTCCTATATTAGGGCTTGAATTA
1 TTTTTTGTCCCAAGTTAGTCCTTGAACTTGGTAATTGTTCCTACATTAGGGCTTGAATTA
** * * * *
42677980 TTTTTTGTTTCAAGTTAGTCCTTGAACTTGGTAATTATT-TTCACATTAGGGCCTGAA--C
1 TTTTTTGTCCCAAGTTAGTCCTTGAACTTGGTAATTGTTCCT-ACATTAGGGCTTGAATTA
* * * * * *
42678038 TTTTTT-TCCCAAATTAGTCCTTAAACTTGGCAATTGTTCCTACCTTCGGGCTTG-ATTT
1 TTTTTTGTCCCAAGTTAGTCCTTGAACTTGGTAATTGTTCCTACATTAGGGCTTGAATTA
42678096 TTTTTTGT-CCAAGTTA
1 TTTTTTGTCCCAAGTTA
42678112 ATCCCTGACA
Statistics
Matches: 103, Mismatches: 23, Indels: 13
0.74 0.17 0.09
Matches are distributed among these distances:
56 1 0.01
57 36 0.35
58 20 0.19
59 10 0.10
60 36 0.35
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.46
Consensus pattern (60 bp):
TTTTTTGTCCCAAGTTAGTCCTTGAACTTGGTAATTGTTCCTACATTAGGGCTTGAATTA
Found at i:42678728 original size:17 final size:16
Alignment explanation
Indices: 42678708--42678741 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
42678698 AAAATTAATT
*
42678708 TTTTTATTTTTTTCACA
1 TTTTAATTTTTTT-ACA
42678725 TTTTAATTTTTTTACA
1 TTTTAATTTTTTTACA
42678741 T
1 T
42678742 AATATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTAATTTTTTTACA
Found at i:42680990 original size:13 final size:15
Alignment explanation
Indices: 42680966--42680999 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
42680956 TTTAATTTTC
42680966 AAAATTTCAAAAA-A
1 AAAATTTCAAAAATA
42680980 AAAATTT-AAAAATA
1 AAAATTTCAAAAATA
42680994 AAAATT
1 AAAATT
42681000 GTATTTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATTTCAAAAATA
Found at i:42681029 original size:30 final size:30
Alignment explanation
Indices: 42680995--42681096 Score: 86
Period size: 30 Copynumber: 3.4 Consensus size: 30
42680985 TTAAAAATAA
42680995 AAATTGTATTTTGACCCCTAAACTTTTC-CT
1 AAATT-TATTTTGACCCCTAAACTTTTCTCT
** *
42681025 AAATTTTATTTTGACCTTTAAAC-TTTCTTT
1 AAA-TTTATTTTGACCCCTAAACTTTTCTCT
* *
42681055 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTT-ATTTTGACCCCTAAACTTTTC-TCT
42681085 AAATTTCATTTT
1 AAATTT-ATTTT
42681097 AATCCTAAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
29 7 0.12
30 49 0.83
31 3 0.05
ACGTcount: A:0.29, C:0.20, G:0.04, T:0.47
Consensus pattern (30 bp):
AAATTTATTTTGACCCCTAAACTTTTCTCT
Found at i:42681491 original size:3 final size:3
Alignment explanation
Indices: 42681483--42681544 Score: 51
Period size: 3 Copynumber: 21.0 Consensus size: 3
42681473 GCTAGACTTT
*
42681483 GAA GAA GAA GAA GGAA GAA GAA -AA GAG GAA GAA GAAA GAAA GAA -AA
1 GAA GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA G-AA G-AA GAA GAA
*
42681529 -AA GAA AAA GAA -AA GAA
1 GAA GAA GAA GAA GAA GAA
42681545 ATAATAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
2 8 0.16
3 32 0.64
4 10 0.20
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:42681513 original size:14 final size:13
Alignment explanation
Indices: 42681483--42681545 Score: 58
Period size: 13 Copynumber: 4.8 Consensus size: 13
42681473 GCTAGACTTT
*
42681483 GAAGAAGAAGAAG
1 GAAGAAGAAAAAG
42681496 GAAGAAGAAAAGAG
1 GAAGAAGAAAA-AG
42681510 GAAGAAGAAAGAAAG
1 GAAGAAG-AA-AAAG
* *
42681525 AAAAAAGAAAAA-
1 GAAGAAGAAAAAG
42681537 GAA-AAGAAA
1 GAAGAAGAAA
42681546 TAATAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
11 6 0.14
12 2 0.05
13 13 0.30
14 11 0.26
15 9 0.21
16 2 0.05
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAAAAG
Found at i:42681513 original size:21 final size:22
Alignment explanation
Indices: 42681484--42681545 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
42681474 CTAGACTTTG
*
42681484 AAGAAGAAGAAGGAAG-AAGAA
1 AAGAAGAAGAAGAAAGAAAGAA
*
42681505 AAGAGGAAGAAGAAAGAAAGAA
1 AAGAAGAAGAAGAAAGAAAGAA
*
42681527 AA-AAGAAAAAGAAAAGAAA
1 AAGAAGAAGAAG-AAAGAAA
42681546 TAATAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 21 0.60
22 14 0.40
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (22 bp):
AAGAAGAAGAAGAAAGAAAGAA
Found at i:42681518 original size:24 final size:24
Alignment explanation
Indices: 42681486--42681532 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
42681476 AGACTTTGAA
*
42681486 GAAGAAG-AAGGAAGAAGAAAAGAG
1 GAAGAAGAAAGAAAGAA-AAAAGAG
42681510 GAAGAAGAAAGAAAGAAAAAAGA
1 GAAGAAGAAAGAAAGAAAAAAGA
42681533 AAAAGAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (24 bp):
GAAGAAGAAAGAAAGAAAAAAGAG
Found at i:42681538 original size:24 final size:24
Alignment explanation
Indices: 42681487--42681545 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
42681477 GACTTTGAAG
* **
42681487 AAGAAGAAGGAAGAAGAAAAGAGG
1 AAGAAGAAGAAAGAAGAAAAGAAA
42681511 AAGAAGAAAGAAAGAA-AAAAGAAA
1 AAGAAG-AAGAAAGAAGAAAAGAAA
42681535 AAGAA-AAGAAA
1 AAGAAGAAGAAA
42681546 TAATAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 6 0.19
24 17 0.55
25 8 0.26
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (24 bp):
AAGAAGAAGAAAGAAGAAAAGAAA
Found at i:42682320 original size:18 final size:17
Alignment explanation
Indices: 42682246--42682408 Score: 159
Period size: 17 Copynumber: 9.4 Consensus size: 17
42682236 ATCAATTTTC
* *
42682246 CAAAATTTTTAGTGTCTT
1 CAAAAATTTTCGTGT-TT
*
42682264 CTAAAAATTTTTGTGTTT
1 C-AAAAATTTTCGTGTTT
42682282 CAAAAATTTTCGT-TTT
1 CAAAAATTTTCGTGTTT
*
42682298 CAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTT
42682315 CAAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
* *
42682333 CAAAATTTTTCGTATTT
1 CAAAAATTTTCGTGTTT
** *
42682350 CAAAAATCCTCTTGTTTT
1 CAAAAATTTTCGTG-TTT
42682368 CAAAAA-TTTCGGTGTTT
1 CAAAAATTTTC-GTGTTT
**
42682385 TGAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
42682403 CAAAAA
1 CAAAAA
42682409 AAAAATCTCG
Statistics
Matches: 119, Mismatches: 19, Indels: 14
0.78 0.12 0.09
Matches are distributed among these distances:
16 15 0.13
17 51 0.43
18 41 0.34
19 12 0.10
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (17 bp):
CAAAAATTTTCGTGTTT
Found at i:42682408 original size:35 final size:34
Alignment explanation
Indices: 42682246--42682408 Score: 168
Period size: 35 Copynumber: 4.7 Consensus size: 34
42682236 ATCAATTTTC
* * * *
42682246 CAAAATTTTTAGTGTCTTCTAAAAATTTTTGTGTTT
1 CAAAAATTTTCGTGTTTTC-AAAAA-TTTCGTGTTT
42682282 CAAAAATTTTC--GTTTTCAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTT-CGTGTTT
* *
42682315 CAAAAATTTTCGTGTTTTCAAAATTTTTCGTATTT
1 CAAAAATTTTCGTGTTTTCAAAA-ATTTCGTGTTT
** *
42682350 CAAAAATCCTCTTGTTTTCAAAAATTTCGGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTC-GTGTTT
**
42682385 TGAAAATTTTCGTGTTTTCAAAAA
1 CAAAAATTTTCGTGTTTTCAAAAA
42682409 AAAAATCTCG
Statistics
Matches: 106, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
32 3 0.03
33 22 0.21
34 9 0.08
35 60 0.57
36 12 0.11
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (34 bp):
CAAAAATTTTCGTGTTTTCAAAAATTTCGTGTTT
Found at i:42682423 original size:39 final size:38
Alignment explanation
Indices: 42682369--42682497 Score: 115
Period size: 36 Copynumber: 3.4 Consensus size: 38
42682359 TCTTGTTTTC
*
42682369 AAAAATTTCGGTGTTTTGAAAATTTTCGTGTTTTCAAAAA
1 AAAAATCTC-GTGTTTT-AAAATTTTCGTGTTTTCAAAAA
*
42682409 AAAAATCTCGTGTTTCATAAATTTT-G-GTTTT-AAAAA
1 AAAAATCTCGTGTTTTA-AAATTTTCGTGTTTTCAAAAA
** * * *
42682445 AATTAT-T-ATGTCTTAAAATTCTCGTGTTTTCAAAAA
1 AAAAATCTCGTGTTTTAAAATTTTCGTGTTTTCAAAAA
42682481 AAGAAATTCTCGTGTTT
1 AA-AAA-TCTCGTGTTT
42682498 CAATCGGATC
Statistics
Matches: 69, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
33 6 0.09
34 6 0.09
35 6 0.09
36 16 0.23
37 6 0.09
38 3 0.04
39 14 0.20
40 12 0.17
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (38 bp):
AAAAATCTCGTGTTTTAAAATTTTCGTGTTTTCAAAAA
Found at i:42683116 original size:18 final size:19
Alignment explanation
Indices: 42683073--42683117 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
42683063 TTTAAATTAT
42683073 TTTATTT-TAATTTTTAAA
1 TTTATTTATAATTTTTAAA
42683091 TATT-TTTATAA-TTTTAAA
1 T-TTATTTATAATTTTTAAA
42683109 TTTATTTAT
1 TTTATTTAT
42683118 TGATCTGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 2 0.08
18 17 0.71
19 5 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTATTTATAATTTTTAAA
Found at i:42684362 original size:11 final size:11
Alignment explanation
Indices: 42684348--42684393 Score: 67
Period size: 11 Copynumber: 4.1 Consensus size: 11
42684338 AGATACATAT
42684348 TATTTTATTAA
1 TATTTTATTAA
42684359 TATTTTAATT-A
1 TATTTT-ATTAA
42684370 TATATTTATTAA
1 TAT-TTTATTAA
42684382 TATTTTATTAA
1 TATTTTATTAA
42684393 T
1 T
42684394 TTAAGGTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 22 0.69
12 10 0.31
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:42688002 original size:45 final size:46
Alignment explanation
Indices: 42687935--42688058 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
42687925 CATATGACCT
*
42687935 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
42687978 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
42688024 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
42688059 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.28
46 41 0.55
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:42688041 original size:46 final size:45
Alignment explanation
Indices: 42687935--42688169 Score: 207
Period size: 37 Copynumber: 5.8 Consensus size: 45
42687925 CATATGACCT
*
42687935 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
42687978 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
42688024 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
42688061 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
42688098 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
42688135 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
42688170 CACTTATCAC
Statistics
Matches: 177, Mismatches: 7, Indels: 18
0.88 0.03 0.09
Matches are distributed among these distances:
37 101 0.57
39 2 0.01
40 3 0.02
42 1 0.01
43 9 0.05
44 6 0.03
45 21 0.12
46 34 0.19
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:42688062 original size:37 final size:37
Alignment explanation
Indices: 42688020--42688196 Score: 300
Period size: 37 Copynumber: 4.8 Consensus size: 37
42688010 AGCTGAAGCT
* **
42688020 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
* *
42688057 GCCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
42688094 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
42688131 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
*
42688168 GCCACTTATCACTTTGTTTCTTGATCAGA
1 ACCACTTATCACTTTGTTTCTTGATCAGA
42688197 AGTACTCAAA
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (37 bp):
ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
Found at i:42695701 original size:45 final size:46
Alignment explanation
Indices: 42695634--42695757 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
42695624 CATATGACCT
*
42695634 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
42695677 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
42695723 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
42695758 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.28
46 41 0.55
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:42695740 original size:46 final size:45
Alignment explanation
Indices: 42695634--42695868 Score: 207
Period size: 37 Copynumber: 5.8 Consensus size: 45
42695624 CATATGACCT
*
42695634 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
42695677 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
42695723 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
42695760 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
42695797 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
42695834 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
42695869 CACTTATCAC
Statistics
Matches: 177, Mismatches: 7, Indels: 18
0.88 0.03 0.09
Matches are distributed among these distances:
37 101 0.57
39 2 0.01
40 3 0.02
42 1 0.01
43 9 0.05
44 6 0.03
45 21 0.12
46 34 0.19
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:42695761 original size:37 final size:37
Alignment explanation
Indices: 42695719--42695895 Score: 300
Period size: 37 Copynumber: 4.8 Consensus size: 37
42695709 AGCTGAAGCT
* **
42695719 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
* *
42695756 GCCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
42695793 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
42695830 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
*
42695867 GCCACTTATCACTTTGTTTCTTGATCAGA
1 ACCACTTATCACTTTGTTTCTTGATCAGA
42695896 AGTACTCAAA
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (37 bp):
ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
Found at i:42700600 original size:11 final size:11
Alignment explanation
Indices: 42700586--42700618 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
42700576 TTTTTTTTAA
*
42700586 TGTTATTTTCT
1 TGTTGTTTTCT
42700597 TGTTGTTTTCT
1 TGTTGTTTTCT
42700608 TGTTGTTTTCT
1 TGTTGTTTTCT
42700619 CTATATTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.03, C:0.09, G:0.15, T:0.73
Consensus pattern (11 bp):
TGTTGTTTTCT
Found at i:42700636 original size:11 final size:11
Alignment explanation
Indices: 42700622--42700660 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
42700612 GTTTTCTCTA
42700622 TATTTTGCTAC
1 TATTTTGCTAC
* *
42700633 TATTTTACTAT
1 TATTTTGCTAC
*
42700644 TATGTTGCTAC
1 TATTTTGCTAC
42700655 TATTTT
1 TATTTT
42700661 ATTATTATTA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.59
Consensus pattern (11 bp):
TATTTTGCTAC
Found at i:42700638 original size:22 final size:22
Alignment explanation
Indices: 42700626--42700668 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
42700616 TCTCTATATT
42700626 TTGCTACTATTTTACTATTATG
1 TTGCTACTATTTTACTATTATG
*
42700648 TTGCTACTATTTTATTATTAT
1 TTGCTACTATTTTACTATTAT
42700669 TATTTGGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.12, G:0.07, T:0.58
Consensus pattern (22 bp):
TTGCTACTATTTTACTATTATG
Found at i:42700760 original size:30 final size:30
Alignment explanation
Indices: 42700698--42700760 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
42700688 ACTTATTTTA
* **
42700698 TTGTTAATTTTGTTATTATTTTAAAGTTAT
1 TTGTTAATTTTATTATTATTTTAAAGGCAT
* *
42700728 TTGTTGATTTTATTATTATTTTAGAGGCAT
1 TTGTTAATTTTATTATTATTTTAAAGGCAT
42700758 TTG
1 TTG
42700761 CTTGTTAAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGGCAT
Found at i:42706080 original size:9 final size:9
Alignment explanation
Indices: 42706066--42706095 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
42706056 AGTGATCAGC
42706066 TTTTTTTTA
1 TTTTTTTTA
42706075 TTTTTTTTA
1 TTTTTTTTA
42706084 TTTTTTTTA
1 TTTTTTTTA
42706093 TTT
1 TTT
42706096 AGTTATTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:42707878 original size:132 final size:132
Alignment explanation
Indices: 42707665--42708002 Score: 448
Period size: 132 Copynumber: 2.6 Consensus size: 132
42707655 TAGGAGAATC
* * * * * ** *
42707665 GCAACCCAGCACGATAGGGCACGATTCC-CAAATTTCCAAACATCAAGTATTTCCTTTGTTTTAA
1 GCAACCCAGCACGTTAGGGCACGATTCCGCGAATTGCCAAATATCAAATATCGCCTTCGTTTTAA
*
42707729 A-GAGTTTTTAGAAGACATGAAC-AAGATTCTAAAGGGACATTCGATTACTTTGAGCAAATGAGA
66 AGGA-TTTTTAGAAGACATGAACGAA-ATTCTAAAGGGACATTCGATTACTTTGAGCAAACGAGA
42707792 AATT
129 AATT
* *
42707796 GCAACCCAGCACGTTAGGGCACGATTCCGCGAATTGCCAAATGTCAAACATCGCCTTCGTTTTAA
1 GCAACCCAGCACGTTAGGGCACGATTCCGCGAATTGCCAAATATCAAATATCGCCTTCGTTTTAA
* ** * * *
42707861 AGGATTTTTAGAAGACATGAACGAAATTTTGGAGGGATATTCGATTATTTTGAGCAAACGCGAAA
66 AGGATTTTTAGAAGACATGAACGAAATTCTAAAGGGACATTCGATTACTTTGAGCAAACGAGAAA
42707926 TT
131 TT
* * *
42707928 GCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAATATCAAATATCGTCTCCGTTTTAA
1 GCAACCCAGCACGTTAGGGCACGATTCCGCGAATTGCCAAATATCAAATATCGCCTTCGTTTTAA
*
42707993 AGAATTTTTA
66 AGGATTTTTA
42708003 AATGAATATG
Statistics
Matches: 181, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
131 27 0.15
132 150 0.83
133 4 0.02
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (132 bp):
GCAACCCAGCACGTTAGGGCACGATTCCGCGAATTGCCAAATATCAAATATCGCCTTCGTTTTAA
AGGATTTTTAGAAGACATGAACGAAATTCTAAAGGGACATTCGATTACTTTGAGCAAACGAGAAA
TT
Found at i:42708909 original size:39 final size:39
Alignment explanation
Indices: 42708851--42709007 Score: 142
Period size: 39 Copynumber: 4.0 Consensus size: 39
42708841 TTCAGTGATG
**
42708851 TATATCCGGACTTAGGGT-CCGCAGGCTATGTGCTGGAAT
1 TATATCCGGACTTAAAGTCCCGCAGGCT-TGTGCTGGAAT
* * *
42708890 TATATCCGGACTTAAGGT-CCGCAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAAAGTCCCGCAGGCT-TGTGCTGGAAT
* * * *
42708929 TATGTCCGGGC-TAAAGTCCCGCAGGCTTCGAGCTGGTAT
1 TATATCCGGACTTAAAGTCCCGCAGGCTT-GTGCTGGAAT
** *
42708968 TATA-CCGGGTTTAAATTCCCGCAGGCTTGTGCTGGTAAT
1 TATATCCGGACTTAAAGTCCCGCAGGCTTGTGCTGG-AAT
42709007 T
1 T
42709008 GGTTTCAAGT
Statistics
Matches: 99, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
38 16 0.16
39 83 0.84
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (39 bp):
TATATCCGGACTTAAAGTCCCGCAGGCTTGTGCTGGAAT
Found at i:42717794 original size:17 final size:16
Alignment explanation
Indices: 42717766--42717797 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
42717756 TTCTTTCAAT
42717766 TAGTTTAATTAATTAC
1 TAGTTTAATTAATTAC
42717782 TAGTTTCAATTAATTA
1 TAGTTT-AATTAATTA
42717798 TAACTGAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (16 bp):
TAGTTTAATTAATTAC
Found at i:42718079 original size:3 final size:3
Alignment explanation
Indices: 42718073--42718120 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
42718063 TTTTTATTAC
* * * *
42718073 TAA TAA TAA TAA TAA TAA CAA CAA CAA TAA TAA TAA TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42718121 CTATTCTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (3 bp):
TAA
Found at i:42718101 original size:21 final size:21
Alignment explanation
Indices: 42718077--42718117 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
42718067 TATTACTAAT
42718077 AATAATAATAATAACAACAAC
1 AATAATAATAATAACAACAAC
*
42718098 AATAATAATAATAATAACAA
1 AATAATAATAATAACAACAA
42718118 TAACTATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.22
Consensus pattern (21 bp):
AATAATAATAATAACAACAAC
Found at i:42723989 original size:22 final size:21
Alignment explanation
Indices: 42723964--42724009 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
42723954 TAAAAAGTTA
42723964 AAAAATAATCA-TTAAATTAATT
1 AAAAA-AATCATTTAAATT-ATT
*
42723986 AAAAAAATTATTTAAATTATT
1 AAAAAAATCATTTAAATTATT
42724007 AAA
1 AAA
42724010 TTAAATCACC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAAAAATCATTTAAATTATT
Found at i:42730318 original size:28 final size:25
Alignment explanation
Indices: 42730156--42730356 Score: 92
Period size: 24 Copynumber: 7.8 Consensus size: 25
42730146 AAATGGAATA
* * *
42730156 ATATATAAAACAATTTGAAGTAAAT
1 ATATAGAAAACAATTTAAAATAAAT
42730181 AGTAT--AAAACAATTTAAAATAAACGAT
1 A-TATAGAAAACAATTTAAAAT-AA--AT
* * *
42730208 GTGTAGAGAAAC---TTAAAACAAAT
1 ATATAGA-AAACAATTTAAAATAAAT
* * *
42730231 AATATACAAAACGATTTAAACTAAAT
1 -ATATAGAAAACAATTTAAAATAAAT
** * *
42730257 A-ATTTAAGACAATTTTAAATGAATAAT
1 ATATAGAAAACAATTTAAAAT--A-AAT
*
42730284 ATATAGAAAAACATGTTTAAAATAAAT
1 ATATAG-AAAACA-ATTTAAAATAAAT
*
42730311 ACTATAGAAAGCAATTTAAAATAAAT
1 A-TATAGAAAACAATTTAAAATAAAT
* *
42730337 AGA-ATAAAACAATTTAAAAT
1 ATATAGAAAACAATTTAAAAT
42730357 CATTTAATAT
Statistics
Matches: 132, Mismatches: 26, Indels: 37
0.68 0.13 0.19
Matches are distributed among these distances:
23 6 0.05
24 45 0.34
25 7 0.05
26 34 0.26
27 15 0.11
28 9 0.07
29 9 0.07
30 7 0.05
ACGTcount: A:0.57, C:0.06, G:0.08, T:0.28
Consensus pattern (25 bp):
ATATAGAAAACAATTTAAAATAAAT
Found at i:42730328 original size:26 final size:24
Alignment explanation
Indices: 42730299--42730356 Score: 80
Period size: 26 Copynumber: 2.3 Consensus size: 24
42730289 GAAAAACATG
*
42730299 TTTAAAATAAATACTATAGAAAGCAA
1 TTTAAAATAAATACAATA-AAA-CAA
*
42730325 TTTAAAATAAATAGAATAAAACAA
1 TTTAAAATAAATACAATAAAACAA
42730349 TTTAAAAT
1 TTTAAAAT
42730357 CATTTAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 11 0.37
25 3 0.10
26 16 0.53
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.29
Consensus pattern (24 bp):
TTTAAAATAAATACAATAAAACAA
Found at i:42732224 original size:29 final size:29
Alignment explanation
Indices: 42732180--42732241 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
42732170 CTTGGGATTC
*
42732180 AAAAGTATAATAATTTATTTG-AATATAAT
1 AAAAGTATAATAATTTA-TTGAAATAAAAT
*
42732209 AAAAGTATAATGATTTATTGAAATAAAAT
1 AAAAGTATAATAATTTATTGAAATAAAAT
42732238 AAAA
1 AAAA
42732242 AAAGTTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 3 0.10
29 27 0.90
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (29 bp):
AAAAGTATAATAATTTATTGAAATAAAAT
Found at i:42735508 original size:8 final size:9
Alignment explanation
Indices: 42735486--42735603 Score: 67
Period size: 9 Copynumber: 12.7 Consensus size: 9
42735476 TAAAATTATT
42735486 ATTTTTAAA
1 ATTTTTAAA
42735495 ATTTTTAAA
1 ATTTTTAAA
*
42735504 A-TTTTAAC
1 ATTTTTAAA
* *
42735512 TTTCTTTATAT
1 ATT-TTTA-AA
*
42735523 ATTCTTTAGA
1 ATT-TTTAAA
42735533 ATTTTTAAA
1 ATTTTTAAA
*
42735542 AATTTTAAA
1 ATTTTTAAA
** *
42735551 ACATATAAA
1 ATTTTTAAA
**
42735560 ATTTTTGGA
1 ATTTTTAAA
42735569 ATTTTTATAA
1 ATTTTTA-AA
* *
42735579 ATATTTTGAT
1 AT-TTTTAAA
*
42735589 TTTTTTAAA
1 ATTTTTAAA
42735598 ATTTTT
1 ATTTTT
42735604 TGTTGAGAAA
Statistics
Matches: 80, Mismatches: 24, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
8 6 0.08
9 50 0.62
10 12 0.15
11 12 0.15
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.56
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:42735604 original size:19 final size:18
Alignment explanation
Indices: 42735556--42735605 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
42735546 TTAAAACATA
*
42735556 TAAAATTTTTGGAATTTT
1 TAAAATTTTTTGAATTTT
* *
42735574 TATAAATATTTTGATTTTTT
1 TA-AAATTTTTTGA-ATTTT
42735594 TAAAATTTTTTG
1 TAAAATTTTTTG
42735606 TTGAGAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 2 0.08
19 18 0.69
20 6 0.23
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (18 bp):
TAAAATTTTTTGAATTTT
Found at i:42737072 original size:55 final size:54
Alignment explanation
Indices: 42736990--42737210 Score: 216
Period size: 55 Copynumber: 4.0 Consensus size: 54
42736980 GTCAGGCTTT
* ** * *
42736990 AAAAAATT-ATTTTTTTTGGTTTTGGCCTATCAATGGCCGGCACCAGTATTAAA
1 AAAAAATTGAATTTTTTTGGTGCTGGCCTGTCAATGGCCGGCACCAATATTAAA
* * **
42737043 AAAAAAGTTGAATTTTTTTTGTGCTGGCCTGTCAATGGCCGACACCAAAATACGAGTTTTCA
1 AAAAAA-TTGAATTTTTTTGGTGCTGGCCTGTCAATGGCCGGCACC--AAT---A--TTAAA
*
42737105 AAAAAA---AATTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCAATATTAAA
1 AAAAAATTGAATTTTTTTGGTGCTGGCCTGTCAATGGCCGGCACCAATATTAAA
* * *
42737156 AAAAATTTGAAATTTTTTTGGTGCTGGCCTGTCAATGGCTGGCACCAGTATTAAA
1 AAAAAATTG-AATTTTTTTGGTGCTGGCCTGTCAATGGCCGGCACCAATATTAAA
42737211 TTTTTTTTGT
Statistics
Matches: 137, Mismatches: 18, Indels: 24
0.77 0.10 0.13
Matches are distributed among these distances:
51 8 0.06
53 7 0.05
54 2 0.01
55 72 0.53
56 3 0.02
57 2 0.01
58 33 0.24
60 1 0.01
62 9 0.07
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (54 bp):
AAAAAATTGAATTTTTTTGGTGCTGGCCTGTCAATGGCCGGCACCAATATTAAA
Found at i:42737239 original size:16 final size:16
Alignment explanation
Indices: 42737220--42737253 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
42737210 ATTTTTTTTG
42737220 TATGCATTATTAAAAT
1 TATGCATTATTAAAAT
*
42737236 TATGCATTCTTAAAAT
1 TATGCATTATTAAAAT
42737252 TA
1 TA
42737254 AATTAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (16 bp):
TATGCATTATTAAAAT
Found at i:42737571 original size:62 final size:63
Alignment explanation
Indices: 42737474--42737604 Score: 210
Period size: 62 Copynumber: 2.1 Consensus size: 63
42737464 ATCATATTAG
* * *
42737474 TGAATCTGCTAATGCGTACTTCATACGGATAAAGTATGCATTATTAAAATTAAATT-AAATAT
1 TGAATATGCTAATACATACTTCATACGGATAAAGTATGCATTATTAAAATTAAATTAAAATAT
*
42737536 TGAATATGCTAATACATACTTCATCCGGATAAAGTATGCATTATTAAAATTAAATTAAAATAT
1 TGAATATGCTAATACATACTTCATACGGATAAAGTATGCATTATTAAAATTAAATTAAAATAT
*
42737599 TAAATA
1 TGAATA
42737605 AGAAATAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
62 52 0.83
63 11 0.17
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.35
Consensus pattern (63 bp):
TGAATATGCTAATACATACTTCATACGGATAAAGTATGCATTATTAAAATTAAATTAAAATAT
Found at i:42737726 original size:272 final size:275
Alignment explanation
Indices: 42737230--42737818 Score: 997
Period size: 272 Copynumber: 2.1 Consensus size: 275
42737220 TATGCATTAT
*
42737230 TAAAATTATGCATTCTTAAAATTAAATTAAATATTGAATATGCTAATACATACTTCATCCGGATA
1 TAAAA-TATGCATTATTAAAATTAAATTAAATATTGAATATGCTAATACATACTTCATCCGGATA
*
42737295 AAGTATGCATTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAATTATAAAACAATATGTT
65 AAGTATGCATTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAATTACAAAACAATATGTT
* *
42737360 ATTTGGAAAATAACAATTATTGTAATGAGATACATGTTTTATTAAGTATAAGTATTTAAAATTTT
130 ATTTGGAAAATAACAATTATTATAATGAGATACATGTTTTATTAAGTATAAATATTTAAAATTTT
* *
42737425 GTTTTTGTAATGTGATACATGCGT-A-A-ATATATATATATAATCATATTAGTGAATCTGCTAAT
195 GTTTTTGTAATGTGATACATGCATAATATATATATATATATAATCATATTACTGAATCTGCTAAT
* * *
42737487 GCGTACTTCATAC-GGA
260 ACATACTTCAT-CTAGA
*
42737503 TAAAGTATGCATTATTAAAATTAAATTAAATATTGAATATGCTAATACATACTTCATCCGGATAA
1 TAAAATATGCATTATTAAAATTAAATTAAATATTGAATATGCTAATACATACTTCATCCGGATAA
42737568 AGTATGCATTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAATTACAAAACAATATGTTA
66 AGTATGCATTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAATTACAAAACAATATGTTA
* *
42737633 TTTGGGAAATAACAATTATTATAATGAGATACATGTTTTATTAGGTATAAATATTTAAAATTTTG
131 TTTGGAAAATAACAATTATTATAATGAGATACATGTTTTATTAAGTATAAATATTTAAAATTTTG
42737698 TTTTTGTAATGTGATACATGCATAAATATATATATATATATAATCATATTACTGAATCTGCTAAT
196 TTTTTGTAATGTGATACATGCAT-AATATATATATATATATAATCATATTACTGAATCTGCTAAT
42737763 ACATACTTCATCTAGA
260 ACATACTTCATCTAGA
*
42737779 TAAAATATGCATTATTAAAATTAAATTAAAATATTAAATA
1 TAAAATATGCATTATTAAAATTAAATT-AAATATTGAATA
42737819 AGAAATAAAA
Statistics
Matches: 296, Mismatches: 14, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
272 206 0.70
273 4 0.01
274 1 0.00
275 2 0.01
276 72 0.24
277 11 0.04
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (275 bp):
TAAAATATGCATTATTAAAATTAAATTAAATATTGAATATGCTAATACATACTTCATCCGGATAA
AGTATGCATTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAATTACAAAACAATATGTTA
TTTGGAAAATAACAATTATTATAATGAGATACATGTTTTATTAAGTATAAATATTTAAAATTTTG
TTTTTGTAATGTGATACATGCATAATATATATATATATATAATCATATTACTGAATCTGCTAATA
CATACTTCATCTAGA
Found at i:42737911 original size:214 final size:214
Alignment explanation
Indices: 42737536--42737932 Score: 704
Period size: 214 Copynumber: 1.9 Consensus size: 214
42737526 AATTAAATAT
* *
42737536 TGAATATGCTAATACATACTTCATCCGGATAAAGTATGCATTATTAAAATTAAATTAAAATATTA
1 TGAATATGCTAATACATACTTCATCCAGATAAAATATGCATTATTAAAATTAAATTAAAATATTA
*
42737601 AATAAGAAATAAAATTACAAAACAATATGTTATTTGGGAAATAACAATTATTATAATGAGATACA
66 AATAAGAAATAAAATTACAAAACAATATGTTATTTGGAAAATAACAATTATTATAATGAGATACA
*
42737666 TGTTTTATTAGGTATAAATATTTAAAATTTTGTTTTTGTAATGTGATACATGCATAAATATATAT
131 TGTTTTATTAAGTATAAATATTTAAAATTTTGTTTTTGTAATGTGATACATGCATAAATATATAT
42737731 ATATATATAATCATATTAC
196 ATATATATAATCATATTAC
* *
42737750 TGAATCTGCTAATACATACTTCATCTAGATAAAATATGCATTATTAAAATTAAATTAAAATATTA
1 TGAATATGCTAATACATACTTCATCCAGATAAAATATGCATTATTAAAATTAAATTAAAATATTA
* * *
42737815 AATAAGAAATAAAATTATAAAACAATATGTTATTTGGAAAATAACTATTATTGTAATGAGATACA
66 AATAAGAAATAAAATTACAAAACAATATGTTATTTGGAAAATAACAATTATTATAATGAGATACA
*
42737880 TGTTTTATTAAGTATAACTATTTAAAATTTTGTTTTTGTAATGTGATACATGC
131 TGTTTTATTAAGTATAAATATTTAAAATTTTGTTTTTGTAATGTGATACATGC
42737933 GCAAAAAAAA
Statistics
Matches: 173, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
214 173 1.00
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (214 bp):
TGAATATGCTAATACATACTTCATCCAGATAAAATATGCATTATTAAAATTAAATTAAAATATTA
AATAAGAAATAAAATTACAAAACAATATGTTATTTGGAAAATAACAATTATTATAATGAGATACA
TGTTTTATTAAGTATAAATATTTAAAATTTTGTTTTTGTAATGTGATACATGCATAAATATATAT
ATATATATAATCATATTAC
Found at i:42745441 original size:23 final size:23
Alignment explanation
Indices: 42745401--42745449 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
42745391 TAATTACAAT
* * *
42745401 TTAATTAATATTATAATTATAT-A
1 TTAATTAAAAATAAAATT-TATCA
42745424 TTAATTAAAAATAAAATTTATCA
1 TTAATTAAAAATAAAATTTATCA
42745447 TTA
1 TTA
42745450 TAAATAACCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TTAATTAAAAATAAAATTTATCA
Found at i:42747441 original size:4 final size:4
Alignment explanation
Indices: 42747432--42747459 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
42747422 AAGTTTTATT
42747432 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
42747460 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:42749562 original size:30 final size:30
Alignment explanation
Indices: 42749526--42749586 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
42749516 AAATTTAACA
* *
42749526 AGCAAATGCCTCTAAAATAATAATAAAATT
1 AGCAAATACCTCTAAAATAATAAAAAAATT
* *
42749556 AGCAAATATCTTTAAAATAATAAAAAAATT
1 AGCAAATACCTCTAAAATAATAAAAAAATT
42749586 A
1 A
42749587 ACAATAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (30 bp):
AGCAAATACCTCTAAAATAATAAAAAAATT
Found at i:42749645 original size:22 final size:22
Alignment explanation
Indices: 42749620--42749662 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
42749610 TATCCAAACA
42749620 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
42749642 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
42749663 AATAGGGAGA
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:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:42749666 original size:11 final size:11
Alignment explanation
Indices: 42749627--42749667 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
42749617 ACAATAACAA
42749627 CAAAATAGTAG
1 CAAAATAGTAG
* *
42749638 CAACATAATAG
1 CAAAATAGTAG
*
42749649 TAAAATAGTAG
1 CAAAATAGTAG
42749660 CAAAATAG
1 CAAAATAG
42749668 GGAGAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:42749684 original size:103 final size:103
Alignment explanation
Indices: 42749569--42749790 Score: 444
Period size: 103 Copynumber: 2.2 Consensus size: 103
42749559 AAATATCTTT
42749569 AAAATAATAAAAAAATTAACAATAAAATAAGTTTTATATAATATCCAAACAATAACAACAAAATA
1 AAAATAATAAAAAAATTAACAATAAAATAAGTTTTATATAATATCCAAACAATAACAACAAAATA
42749634 GTAGCAACATAATAGTAAAATAGTAGCAAAATAGGGAG
66 GTAGCAACATAATAGTAAAATAGTAGCAAAATAGGGAG
42749672 AAAATAATAAAAAAATTAACAATAAAATAAGTTTTATATAATATCCAAACAATAACAACAAAATA
1 AAAATAATAAAAAAATTAACAATAAAATAAGTTTTATATAATATCCAAACAATAACAACAAAATA
42749737 GTAGCAACATAATAGTAAAATAGTAGCAAAATAGGGAG
66 GTAGCAACATAATAGTAAAATAGTAGCAAAATAGGGAG
42749775 AAAATAATAAAAAAAT
1 AAAATAATAAAAAAAT
42749791 AATATTAAAA
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 119 1.00
ACGTcount: A:0.61, C:0.08, G:0.09, T:0.22
Consensus pattern (103 bp):
AAAATAATAAAAAAATTAACAATAAAATAAGTTTTATATAATATCCAAACAATAACAACAAAATA
GTAGCAACATAATAGTAAAATAGTAGCAAAATAGGGAG
Found at i:42749748 original size:22 final size:22
Alignment explanation
Indices: 42749723--42749765 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
42749713 TATCCAAACA
42749723 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
42749745 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
42749766 AATAGGGAGA
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:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:42749769 original size:11 final size:11
Alignment explanation
Indices: 42749730--42749770 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
42749720 ACAATAACAA
42749730 CAAAATAGTAG
1 CAAAATAGTAG
* *
42749741 CAACATAATAG
1 CAAAATAGTAG
*
42749752 TAAAATAGTAG
1 CAAAATAGTAG
42749763 CAAAATAG
1 CAAAATAG
42749771 GGAGAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:42757602 original size:3 final size:3
Alignment explanation
Indices: 42757594--42757662 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
42757584 AACCAAGTTT
42757594 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42757642 ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA
42757663 GGCTTATATT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:42764144 original size:30 final size:29
Alignment explanation
Indices: 42764110--42764168 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
42764100 AAACTAAATC
42764110 AAATCAAAATTTAATGTATAGA-ATTGCACA
1 AAATCAAAATTT-ATGTAT-GATATTGCACA
*
42764140 AAATCAAAGTTTATGTATGATATTGCACA
1 AAATCAAAATTTATGTATGATATTGCACA
42764169 TTATATCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 2 0.07
29 14 0.52
30 11 0.41
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (29 bp):
AAATCAAAATTTATGTATGATATTGCACA
Found at i:42764155 original size:29 final size:31
Alignment explanation
Indices: 42764110--42764190 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 31
42764100 AAACTAAATC
*
42764110 AAATCAAAATTTAATGTATAGA-ATTGCACA-
1 AAATCAAAGTTT-ATGTATAGATATTGCACAT
42764140 AAATCAAAGTTTATGTAT-GATATTGCACATT
1 AAATCAAAGTTTATGTATAGATATTGCACA-T
* *
42764171 ATATCAAAGTTCATGTATAG
1 AAATCAAAGTTTATGTATAG
42764191 TTTTTGTATT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
28 2 0.05
29 14 0.32
30 11 0.25
31 16 0.36
32 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (31 bp):
AAATCAAAGTTTATGTATAGATATTGCACAT
Found at i:42766783 original size:25 final size:25
Alignment explanation
Indices: 42766754--42766805 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
42766744 ATATCTTCTG
42766754 ATATTTAGCTTTGGATTAAAATCTA
1 ATATTTAGCTTTGGATTAAAATCTA
42766779 ATATTTAGCTTTGGATTAAAATCTA
1 ATATTTAGCTTTGGATTAAAATCTA
42766804 AT
1 AT
42766806 TTCACATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.44
Consensus pattern (25 bp):
ATATTTAGCTTTGGATTAAAATCTA
Found at i:42767638 original size:25 final size:26
Alignment explanation
Indices: 42767609--42767683 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
42767599 TTTCACATCC
*
42767609 CAATTTTA-CCCCAATAAAGTTTTGA
1 CAATTTTACCCCCAATAAAATTTTGA
* * *
42767634 CAATTTTATCCCTAGTAAAATTTTGA
1 CAATTTTACCCCCAATAAAATTTTGA
* *
42767660 CTATTTTACCCCCAATAAATTTTT
1 CAATTTTACCCCCAATAAAATTTT
42767684 AAGAAAATTC
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
25 8 0.20
26 33 0.80
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.41
Consensus pattern (26 bp):
CAATTTTACCCCCAATAAAATTTTGA
Found at i:42773544 original size:17 final size:18
Alignment explanation
Indices: 42773519--42773552 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
42773509 ATAAAATAAC
42773519 AAAACCCCTAAACCCATT
1 AAAACCCCTAAACCCATT
*
42773537 AAAA-CCCTTAACCCAT
1 AAAACCCCTAAACCCAT
42773553 CAGACCCACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.18
Consensus pattern (18 bp):
AAAACCCCTAAACCCATT
Found at i:42775179 original size:19 final size:19
Alignment explanation
Indices: 42775112--42775191 Score: 62
Period size: 19 Copynumber: 4.3 Consensus size: 19
42775102 GTATCACTTT
42775112 TTTTA-TATTATTATGTATA
1 TTTTAGTATTATTAT-TATA
*
42775131 TATTT-GTATATAGTATT-T-
1 T-TTTAGTAT-TATTATTATA
* *
42775149 TATTATTATTATTACTT-TA
1 TTTTAGTATTATTA-TTATA
42775168 TTTTAGTATTATTATTATA
1 TTTTAGTATTATTATTATA
42775187 TTTTA
1 TTTTA
42775192 TCTACTTATG
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
17 6 0.12
18 9 0.19
19 21 0.44
20 7 0.15
21 5 0.10
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTTAGTATTATTATTATA
Found at i:42778276 original size:31 final size:31
Alignment explanation
Indices: 42778215--42778284 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
42778205 TTTCTTATAC
* *
42778215 TTTAATTTGATCAATTTTAATCTTTGTACTT
1 TTTAAATTGATCAATTTTAATCTTTATACTT
* *
42778246 TTTGAATTGATCAATTTT-AGCTCTTATACTT
1 TTTAAATTGATCAATTTTAATCT-TTATACTT
42778277 TTTAAATT
1 TTTAAATT
42778285 TTAAAAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 3 0.09
31 30 0.91
ACGTcount: A:0.27, C:0.10, G:0.07, T:0.56
Consensus pattern (31 bp):
TTTAAATTGATCAATTTTAATCTTTATACTT
Found at i:42779204 original size:22 final size:20
Alignment explanation
Indices: 42779188--42779227 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
42779178 AAATGAAATT
* *
42779188 TTTAGGATAAATCAATGTAA
1 TTTAGGAGAAATCAATGAAA
*
42779208 TTTAGGAGGAATCAATGAAA
1 TTTAGGAGAAATCAATGAAA
42779228 GGACATTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (20 bp):
TTTAGGAGAAATCAATGAAA
Found at i:42783098 original size:18 final size:18
Alignment explanation
Indices: 42783077--42783112 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
42783067 TATTTGATTG
42783077 AATTTTGTTATTAAATTT
1 AATTTTGTTATTAAATTT
*
42783095 AATTTTTTTATTAAATTT
1 AATTTTGTTATTAAATTT
42783113 TGCTATTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
AATTTTGTTATTAAATTT
Found at i:42783113 original size:31 final size:33
Alignment explanation
Indices: 42783059--42783125 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 33
42783049 ATTTTGTGGC
* * *
42783059 TTTACTTTTATTTGATTGAATTTTGTTATTAAA
1 TTTAATTTTATTTGATTAAATTTTGCTATTAAA
*
42783092 TTTAATTTT-TTT-ATTAAATTTTGCTATTCAA
1 TTTAATTTTATTTGATTAAATTTTGCTATTAAA
42783123 TTT
1 TTT
42783126 TTATTTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 19 0.63
32 3 0.10
33 8 0.27
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (33 bp):
TTTAATTTTATTTGATTAAATTTTGCTATTAAA
Found at i:42795351 original size:27 final size:27
Alignment explanation
Indices: 42795321--42795464 Score: 200
Period size: 27 Copynumber: 5.3 Consensus size: 27
42795311 TACTGAAATG
* *
42795321 CCCTCGATTTGTAGAATTACCATTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
42795348 CCCTCGATTTATAAAATTACCATTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
* * *
42795375 CCATCGATTTATAGAATTACCGTTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
*
42795402 CCCTCGATTTACAAAATTACCATTTTA
1 CCCTCGATTTATAAAATTACCATTTTA
* *
42795429 CCCTC-AGTTTACAAAATTACCGTTTTA
1 CCCTCGA-TTTATAAAATTACCATTTTA
42795456 CCCTCGATT
1 CCCTCGATT
42795465 GTGAAAATAC
Statistics
Matches: 105, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
26 1 0.01
27 103 0.98
28 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (27 bp):
CCCTCGATTTATAAAATTACCATTTTA
Found at i:42795506 original size:27 final size:27
Alignment explanation
Indices: 42795468--42795659 Score: 113
Period size: 27 Copynumber: 7.1 Consensus size: 27
42795458 CTCGATTGTG
*
42795468 AAAA-TACTAAAATACCCCT-GTAGGAT
1 AAAATTACCAAAATACCCCTAGTAGG-T
* * **
42795494 AGAATTACCAAAATACTCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAGTAGGT
* **
42795521 AAAATTACCAAAATACCCTTAGTTTGT
1 AAAATTACCAAAATACCCCTAGTAGGT
* * * **
42795548 AAAATTACCGAAATACCACTGGTTTGT
1 AAAATTACCAAAATACCCCTAGTAGGT
* * * **
42795575 GAAATTACCGAAATA-CCCTCAATTTGT
1 AAAATTACCAAAATACCCCT-AGTAGGT
* *
42795602 AAAATTACCAAAATA-ACCTTGTAGGAT
1 AAAATTACCAAAATACCCCTAGTAGG-T
* * * *
42795629 GAAATGACTAAAATACCCCTAATAGGT
1 AAAATTACCAAAATACCCCTAGTAGGT
42795656 AAAA
1 AAAA
42795660 AGACCGTAAA
Statistics
Matches: 131, Mismatches: 30, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
26 8 0.06
27 113 0.86
28 10 0.08
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.28
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTAGTAGGT
Found at i:42795554 original size:54 final size:54
Alignment explanation
Indices: 42795496--42795616 Score: 172
Period size: 54 Copynumber: 2.2 Consensus size: 54
42795486 TGTAGGATAG
* *
42795496 AATTACCAAAATACTC-CTAGTTTGTAAAATTACCAAAATACCCTTAGTTTGTAA
1 AATTACCAAAATAC-CACTAGTTTGTAAAATTACCAAAATACCCTCAATTTGTAA
* * * *
42795550 AATTACCGAAATACCACTGGTTTGTGAAATTACCGAAATACCCTCAATTTGTAA
1 AATTACCAAAATACCACTAGTTTGTAAAATTACCAAAATACCCTCAATTTGTAA
42795604 AATTACCAAAATA
1 AATTACCAAAATA
42795617 ACCTTGTAGG
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
53 1 0.02
54 58 0.98
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (54 bp):
AATTACCAAAATACCACTAGTTTGTAAAATTACCAAAATACCCTCAATTTGTAA
Found at i:42795632 original size:54 final size:54
Alignment explanation
Indices: 42795522--42795646 Score: 144
Period size: 54 Copynumber: 2.3 Consensus size: 54
42795512 CTAGTTTGTA
* * * * **
42795522 AAATTACCAAAATACCCTTAGTTTGTAAAATTACCGAAATACCACTGGTTTGTG
1 AAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATAACACTGGTAGGTG
* *
42795576 AAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATAAC-CTTGTAGGATG
1 AAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATAACACTGGTAGG-TG
* *
42795630 AAATGACTAAAATACCC
1 AAATTACCAAAATACCC
42795647 CTAATAGGTA
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
53 5 0.08
54 54 0.92
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (54 bp):
AAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATAACACTGGTAGGTG
Found at i:42795643 original size:81 final size:81
Alignment explanation
Indices: 42795496--42795645 Score: 187
Period size: 81 Copynumber: 1.9 Consensus size: 81
42795486 TGTAGGATAG
* * ** * *
42795496 AATTACCAAAATACTCCTAGTTTGTAAAATTACCAAAATACCCTTAGTTTGTAAAATTACCGAAA
1 AATTACCAAAATACTCCTAATTTGTAAAATTACCAAAATAACCTTAGTAGGTAAAATGACCAAAA
42795561 TACCACTGGTTTGTGA
66 TACCACTGGTTTGTGA
* * *
42795577 AATTACCGAAATAC-CCTCAATTTGTAAAATTACCAAAATAACCTT-GTAGGATGAAATGACTAA
1 AATTACCAAAATACTCCT-AATTTGTAAAATTACCAAAATAACCTTAGTAGG-TAAAATGACCAA
42795640 AATACC
64 AATACC
42795646 CCTAATAGGT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
80 6 0.10
81 52 0.90
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (81 bp):
AATTACCAAAATACTCCTAATTTGTAAAATTACCAAAATAACCTTAGTAGGTAAAATGACCAAAA
TACCACTGGTTTGTGA
Found at i:42795683 original size:27 final size:27
Alignment explanation
Indices: 42795640--42795713 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
42795630 AAATGACTAA
*
42795640 AATACCCCTAATA-GGTAAAAAGACCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
**
42795667 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAAAGACCGT
* *
42795694 AATACCCTTGTATGGTAAAA
1 AATACCCCTGTAGGGTAAAA
42795714 TGACGAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.08
27 34 0.89
28 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:42795717 original size:27 final size:27
Alignment explanation
Indices: 42795653--42795717 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
42795643 ACCCCTAATA
*
42795653 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* * *
42795680 GGTAAAGTGACCGTAATA-CCCTTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
42795707 GGTAAAATGAC
1 GGTAAAATGAC
42795718 GAATATGCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:42796626 original size:42 final size:42
Alignment explanation
Indices: 42796567--42796700 Score: 259
Period size: 42 Copynumber: 3.2 Consensus size: 42
42796557 NNNNNNNNNN
42796567 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
42796609 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
*
42796651 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
42796693 AAATGGGC
1 AAATGGGC
42796701 CTAAGGGCCA
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (42 bp):
AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
Found at i:42796759 original size:31 final size:31
Alignment explanation
Indices: 42796724--42796807 Score: 152
Period size: 31 Copynumber: 2.7 Consensus size: 31
42796714 CGTTTACAGT
42796724 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
42796755 AAAGGCTTCGGCCCAGTGATATGATTTATGG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
42796786 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
42796808 TCAAGACTAA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 5 0.10
31 47 0.90
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:42800076 original size:39 final size:40
Alignment explanation
Indices: 42799992--42800076 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
42799982 ACTTAATTCA
* * *
42799992 CCAGCATTAAGCCTGCGGGACTTTAAACCCGGATACAATC
1 CCAGCATGAAGCCAGCGGGACTCTAAACCCGGATACAATC
* *
42800032 CCAGCATGAAGCCAGCGGGTCTCT-AACCCGGATGCAATC
1 CCAGCATGAAGCCAGCGGGACTCTAAACCCGGATACAATC
*
42800071 TCAGCA
1 CCAGCA
42800077 CAATTCATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 19 0.49
40 20 0.51
ACGTcount: A:0.28, C:0.32, G:0.22, T:0.18
Consensus pattern (40 bp):
CCAGCATGAAGCCAGCGGGACTCTAAACCCGGATACAATC
Found at i:42800246 original size:47 final size:46
Alignment explanation
Indices: 42800147--42800302 Score: 199
Period size: 47 Copynumber: 3.3 Consensus size: 46
42800137 TGCACACTTT
* * *
42800147 TCACAATTGGTCATTCGGCCTTATCACA-TATTCACTTACACATAT-A
1 TCAC-ATTGGCCATTCGGCCTTATCACATTATACACTTTCACAT-TCA
** *
42800193 TCACATTAACCATTCGGCCTTATCACATGTATGCACTTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACAT-TATACACTTTCACATTCA
*
42800240 TCACATTGGCCATTCGGCCTTATCACATATACACACTTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACAT-TATACACTTTCACATTCA
42800287 TCACATTGGCCATTCG
1 TCACATTGGCCATTCG
42800303 ATCTTAAGCT
Statistics
Matches: 97, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
45 20 0.21
46 5 0.05
47 72 0.74
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.33
Consensus pattern (46 bp):
TCACATTGGCCATTCGGCCTTATCACATTATACACTTTCACATTCA
Done.