Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 14 of 325
Found at i:3144419 original size:14 final size:15
Alignment explanation
Indices: 3144402--3144454 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
3144392 ACAAGGACAA
3144402 TAATAAATAAT-AAT
1 TAATAAATAATAAAT
**
3144416 TAAT-AATGCTAAAT
1 TAATAAATAATAAAT
*
3144430 TAATTAATAATAAAT
1 TAATAAATAATAAAT
*
3144445 AAATAAATAA
1 TAATAAATAA
3144455 ACACAAAAGG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 4 0.13
14 11 0.35
15 16 0.52
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (15 bp):
TAATAAATAATAAAT
Found at i:3144521 original size:2 final size:2
Alignment explanation
Indices: 3144514--3144543 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3144504 AAAATAATAC
*
3144514 TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3144544 AAACATACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3144524 original size:14 final size:13
Alignment explanation
Indices: 3144507--3144543 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
3144497 AGTAATTAAA
3144507 ATAATACTATATAT
1 ATAATA-TATATAT
3144521 ATAA-ATATATAT
1 ATAATATATATAT
3144533 AT-ATATATATA
1 ATAATATATATA
3144544 AAACATACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 1 0.05
12 16 0.73
13 1 0.05
14 4 0.18
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (13 bp):
ATAATATATATAT
Found at i:3144568 original size:3 final size:3
Alignment explanation
Indices: 3144554--3144722 Score: 62
Period size: 3 Copynumber: 57.0 Consensus size: 3
3144544 AAACATACAC
* * * **
3144554 TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA TATG TAT TAAA TGG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA
* * * * ** * * *
3144601 -AA GAA TAA TAG TAA CAA T-G TTT TAA -AA TGA TAA TAG TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
3144646 TAA AAA TAA TAG TGA TAA TAA TAG TAA TAA TAA TAAA TAG TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
* *
3144692 TAA TAA -AA GTAA -AA -AA TAA TAG TAG TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
3144723 CAGTAAATAC
Statistics
Matches: 119, Mismatches: 38, Indels: 18
0.68 0.22 0.10
Matches are distributed among these distances:
2 11 0.09
3 99 0.83
4 9 0.08
ACGTcount: A:0.59, C:0.01, G:0.09, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:3144692 original size:22 final size:23
Alignment explanation
Indices: 3144625--3144744 Score: 57
Period size: 25 Copynumber: 4.8 Consensus size: 23
3144615 CAATGTTTTA
* *
3144625 AAATGATAATAGTAATAA-AAAT
1 AAATAATAATAGTAATAATAAGT
*
3144647 AAA-AATAATAGTGATAATAATAGT
1 AAATAATAATAGTAATAAT-A-AGT
3144671 AATAATAATAAATAGTAATAGTAATAAAAGT
1 -A-AATAAT-AATAGTAA---TAAT--AAGT
* *
3144702 AAAAAATAATAGTAGTAATAACAGT
1 AAATAATAATAGTAATAAT-A-AGT
3144727 AAATACA-AATAGTAATAA
1 AAATA-ATAATAGTAATAA
3144745 CAATAAGACA
Statistics
Matches: 77, Mismatches: 8, Indels: 23
0.71 0.07 0.21
Matches are distributed among these distances:
21 12 0.16
22 3 0.04
23 1 0.01
24 4 0.05
25 22 0.29
26 3 0.04
27 3 0.04
28 14 0.18
29 5 0.06
30 1 0.01
31 7 0.09
32 2 0.03
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.27
Consensus pattern (23 bp):
AAATAATAATAGTAATAATAAGT
Found at i:3144745 original size:22 final size:22
Alignment explanation
Indices: 3144665--3144746 Score: 74
Period size: 22 Copynumber: 3.6 Consensus size: 22
3144655 TAGTGATAAT
* * **
3144665 AATAGTAATAATAATAAATAGT
1 AATAGTAATAACAGTAAATACA
* * *
3144687 AATAGTAATAAAAGTAAAAAATA
1 AATAGTAATAACAGT-AAATACA
3144710 ATAGTAGTAATAACAGTAAATACA
1 A-A-TAGTAATAACAGTAAATACA
3144734 AATAGTAATAACA
1 AATAGTAATAACA
3144747 ATAAGACAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
22 24 0.49
23 6 0.12
24 7 0.14
25 12 0.24
ACGTcount: A:0.61, C:0.04, G:0.10, T:0.26
Consensus pattern (22 bp):
AATAGTAATAACAGTAAATACA
Found at i:3144749 original size:12 final size:12
Alignment explanation
Indices: 3144630--3144749 Score: 87
Period size: 12 Copynumber: 10.5 Consensus size: 12
3144620 TTTTAAAATG
3144630 ATAATAGTAATA
1 ATAATAGTAATA
*
3144642 A-AA-A-TAAAA
1 ATAATAGTAATA
*
3144651 ATAATAGTGATA
1 ATAATAGTAATA
3144663 ATAATAGTAATA
1 ATAATAGTAATA
3144675 ATAATA--AATA
1 ATAATAGTAATA
*
3144685 GTAATAGTAAT-
1 ATAATAGTAATA
*
3144696 A-AA-AGTAAAAA
1 ATAATAGT-AATA
*
3144707 ATAATAGTAGTA
1 ATAATAGTAATA
*
3144719 ATAACAGTAAATA
1 ATAATAGT-AATA
3144732 CA-AATAGTAATA
1 -ATAATAGTAATA
*
3144744 ACAATA
1 ATAATA
3144750 AGACAAATAA
Statistics
Matches: 84, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
9 8 0.10
10 16 0.19
11 5 0.06
12 43 0.51
13 11 0.13
14 1 0.01
ACGTcount: A:0.62, C:0.03, G:0.09, T:0.27
Consensus pattern (12 bp):
ATAATAGTAATA
Found at i:3144932 original size:3 final size:3
Alignment explanation
Indices: 3144924--3145035 Score: 129
Period size: 3 Copynumber: 36.3 Consensus size: 3
3144914 AAGGAAAATT
* * *
3144924 TAA TAA TAA TAG CAA TAA T-A CAA 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
*
3144971 TAA TAA TAA TAA GGT-A TAA TAA TACA TTAGA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA --TAA TAA TAA TA-A -TA-A TAA TAA TAA TAA TAA
3145017 TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
3145036 GATGATGATG
Statistics
Matches: 94, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
2 2 0.02
3 84 0.89
4 4 0.04
5 4 0.04
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:3145040 original size:3 final size:3
Alignment explanation
Indices: 3145034--3145188 Score: 310
Period size: 3 Copynumber: 51.7 Consensus size: 3
3145024 AATAATAATA
3145034 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
3145082 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
3145130 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
3145178 ATG ATG ATG AT
1 ATG ATG ATG AT
3145189 AGTGATATTA
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 152 1.00
ACGTcount: A:0.34, C:0.00, G:0.33, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:3145234 original size:15 final size:15
Alignment explanation
Indices: 3145197--3145235 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
3145187 ATAGTGATAT
*
3145197 TAGTAATAATAATAA
1 TAGTAATAAAAATAA
*
3145212 TAGAAATAAAAATAA
1 TAGTAATAAAAATAA
*
3145227 TATTAATAA
1 TAGTAATAA
3145236 TATTAATAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (15 bp):
TAGTAATAAAAATAA
Found at i:3147675 original size:17 final size:18
Alignment explanation
Indices: 3147641--3147935 Score: 193
Period size: 18 Copynumber: 16.1 Consensus size: 18
3147631 TCATTAACAA
* *
3147641 TCAG-AACAATTATTTAT
1 TCAGTAACAATCAATTAT
*
3147658 TCAGTAACAGTCAA-TAT
1 TCAGTAACAATCAATTAT
*
3147675 TCGGTAACAATCAATTAT
1 TCAGTAACAATCAATTAT
* * * *
3147693 TCAATAATAACCAGTTAT
1 TCAGTAACAATCAATTAT
*
3147711 TCAGTATCGATCAATTGATCGATTAT
1 TCAGTA---A-C-A---ATCAATTAT
* *
3147737 CCAGTAACAGTCAATTAT
1 TCAGTAACAATCAATTAT
*
3147755 TTAGTAA-AATCAGA-TAT
1 TCAGTAACAATCA-ATTAT
* *
3147772 TCAGTAGCAATTAAGTTAT
1 TCAGTAACAATCAA-TTAT
*
3147791 TCAGTAACAATCATTTAT
1 TCAGTAACAATCAATTAT
* *
3147809 TCAGTGACAATCAGTTAT
1 TCAGTAACAATCAATTAT
** *
3147827 TCAGTAATGATCATTTAT
1 TCAGTAACAATCAATTAT
* *
3147845 TCAGTAATATTCAATTAT
1 TCAGTAACAATCAATTAT
* *
3147863 TCAGTAACAGTCTATTAT
1 TCAGTAACAATCAATTAT
* * *
3147881 CCAGTAACAATCAGTTAC
1 TCAGTAACAATCAATTAT
*
3147899 TCGGTAACAATCAATTAT
1 TCAGTAACAATCAATTAT
* * *
3147917 TCAGAAATAATCAGTTAT
1 TCAGTAACAATCAATTAT
3147935 T
1 T
3147936 TTATACCTTT
Statistics
Matches: 212, Mismatches: 52, Indels: 27
0.73 0.18 0.09
Matches are distributed among these distances:
17 32 0.15
18 150 0.71
19 14 0.07
21 2 0.01
22 1 0.00
23 2 0.01
26 11 0.05
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (18 bp):
TCAGTAACAATCAATTAT
Found at i:3148165 original size:45 final size:45
Alignment explanation
Indices: 3148108--3148213 Score: 158
Period size: 45 Copynumber: 2.4 Consensus size: 45
3148098 GAACAGTAAT
* *
3148108 AGTAAAAGTAACAGTATTCAACACACAAAGTGCTGAATCGATAAC
1 AGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCGATAAC
* * *
3148153 GGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGGTAAC
1 AGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCGATAAC
*
3148198 AGTAACGGTAACAGTA
1 AGTAACAGTAACAGTA
3148214 ATAGTAGTCG
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.42, C:0.19, G:0.20, T:0.19
Consensus pattern (45 bp):
AGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCGATAAC
Found at i:3148204 original size:51 final size:49
Alignment explanation
Indices: 3148098--3148236 Score: 144
Period size: 45 Copynumber: 2.9 Consensus size: 49
3148088 AACAAATCCG
** * * *
3148098 GAACAGTAATAGTAAAAGTAACAGTATTCAACACACAAAGTGCTGAATC
1 GAACAGTAACGGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC
3148147 G---A-TAACGGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC
1 GAACAGTAACGGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC
* * * *
3148192 GGTAACAGTAACGGTAACAGTAATAGTAGTCGGCACA-TAAGTGCC
1 -G-AACAGTAACGGTAACAGTAACAGTATTCGACACACAAAGTGCC
3148237 TGATCAGTAA
Statistics
Matches: 75, Mismatches: 9, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
45 38 0.51
46 2 0.03
49 1 0.01
50 8 0.11
51 26 0.35
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.19
Consensus pattern (49 bp):
GAACAGTAACGGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC
Found at i:3149001 original size:23 final size:23
Alignment explanation
Indices: 3148974--3149018 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
3148964 TAATTTTTCC
3148974 TGAAACTAGACTCACAAATCTTT
1 TGAAACTAGACTCACAAATCTTT
3148997 TGAAACTAGACTCACAAATCTT
1 TGAAACTAGACTCACAAATCTT
3149019 CTTACCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (23 bp):
TGAAACTAGACTCACAAATCTTT
Found at i:3149988 original size:5 final size:5
Alignment explanation
Indices: 3149978--3150022 Score: 63
Period size: 5 Copynumber: 8.6 Consensus size: 5
3149968 TTACTTATTT
*
3149978 ATATA ATATAA TATATA ATATA AAATA ATATA ATATA ATATA ATA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA ATATA ATA
3150023 ACAATTTCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
5 30 0.83
6 2 0.06
7 4 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:3150086 original size:24 final size:25
Alignment explanation
Indices: 3150047--3150094 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
3150037 TTTAAGTAAT
*
3150047 TATTTAGTTGTATTACAAATGTATG
1 TATTTAATTGTATTACAAATGTATG
*
3150072 TATTTAATT-TATTACACATGTAT
1 TATTTAATTGTATTACAAATGTAT
3150095 TTATAATTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.50
Consensus pattern (25 bp):
TATTTAATTGTATTACAAATGTATG
Found at i:3154463 original size:2 final size:2
Alignment explanation
Indices: 3154456--3154484 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3154446 TATTATTGCA
3154456 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3154485 TGACTAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3155768 original size:19 final size:18
Alignment explanation
Indices: 3155734--3155798 Score: 55
Period size: 18 Copynumber: 3.5 Consensus size: 18
3155724 TCTAAAATGC
3155734 AACTA-TTTTAATTTTAT
1 AACTATTTTTAATTTTAT
3155751 AACTATTTTTATATTTTA-
1 AACTATTTTTA-ATTTTAT
*
3155769 AATTATAATTTTTAAATTTTAT
1 AA--CT-ATTTTT-AATTTTAT
3155791 AA-TATTTT
1 AACTATTTT
3155799 ATAACACATA
Statistics
Matches: 40, Mismatches: 1, Indels: 13
0.74 0.02 0.24
Matches are distributed among these distances:
17 5 0.12
18 12 0.30
19 7 0.17
20 1 0.03
21 12 0.30
22 3 0.08
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
AACTATTTTTAATTTTAT
Found at i:3155866 original size:67 final size:69
Alignment explanation
Indices: 3155737--3155879 Score: 159
Period size: 67 Copynumber: 2.1 Consensus size: 69
3155727 AAAATGCAAC
* * * * *
3155737 TATTTTAATTTTATAACTATTTTTATATTTTAAATTATAATTTTTAAATTTTATAATATTTTATA
1 TATTTTAATATTATAAATATTTATATATTTTAAATTACAATTTTTAAATTTTATAAGATTTTATA
3155802 ACACA
66 A-ACA
* * *
3155807 TATTTTAATATTA-AAATA-TTATATATTTT-TATTACAATTTCTT-AATTTTATAGGGTTTTAT
1 TATTTTAATATTATAAATATTTATATATTTTAAATTACAATTT-TTAAATTTTATAAGATTTTAT
*
3155868 AAATA
65 AAACA
3155873 TATTTTA
1 TATTTTA
3155880 TTGAATCTTA
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
66 9 0.14
67 26 0.41
68 12 0.19
69 4 0.06
70 12 0.19
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (69 bp):
TATTTTAATATTATAAATATTTATATATTTTAAATTACAATTTTTAAATTTTATAAGATTTTATA
AACA
Found at i:3157381 original size:18 final size:17
Alignment explanation
Indices: 3157360--3157393 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3157350 AACTTTTATG
3157360 ATTTTTTAAATAATTTTC
1 ATTTTTTAAA-AATTTTC
*
3157378 ATTTTTTTAAAATTTT
1 ATTTTTTAAAAATTTT
3157394 ATAAAGTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTTTAAAAATTTTC
Found at i:3158951 original size:3 final size:3
Alignment explanation
Indices: 3158943--3158970 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3158933 GGTAATGAAT
3158943 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3158971 GAAGTGATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3159395 original size:107 final size:107
Alignment explanation
Indices: 3159209--3159423 Score: 385
Period size: 107 Copynumber: 2.0 Consensus size: 107
3159199 GTATTTAAAA
*
3159209 ACTCATTTAGTAATTAGATTTATAGTCTAATAATTTATAATTACTTATGCATGGTTATTATGATT
1 ACTCATTTAGTAATTAGATTTATAGCCTAATAATTTATAATTACTTATGCATGGTTATTATGATT
**
3159274 AAATTTTAGCTTGAATTGTATCGACATTGTTGTCAATATAGG
66 AAATTTTAGCTTGAATTACATCGACATTGTTGTCAATATAGG
*
3159316 ACTCATTTAGTAATTAGATTTGTAGCCTAATAATTTATAATTACTTATGCATGGTTATTATGATT
1 ACTCATTTAGTAATTAGATTTATAGCCTAATAATTTATAATTACTTATGCATGGTTATTATGATT
*
3159381 AAATTTTAGCTTGAATTACATCGACATTGTTGTCAATGTAGG
66 AAATTTTAGCTTGAATTACATCGACATTGTTGTCAATATAGG
3159423 A
1 A
3159424 AGTTGTGAGT
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
107 103 1.00
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (107 bp):
ACTCATTTAGTAATTAGATTTATAGCCTAATAATTTATAATTACTTATGCATGGTTATTATGATT
AAATTTTAGCTTGAATTACATCGACATTGTTGTCAATATAGG
Found at i:3164416 original size:13 final size:13
Alignment explanation
Indices: 3164400--3164454 Score: 51
Period size: 13 Copynumber: 4.1 Consensus size: 13
3164390 AAATTTAAAA
3164400 TTTAGATTTAGGG
1 TTTAGATTTAGGG
*
3164413 TTTA-AGTTT-GAGA
1 TTTAGA-TTTAG-GG
3164426 TTTAAGATTTAGGG
1 TTT-AGATTTAGGG
3164440 TTTAGATTTAAGGG
1 TTTAGATTT-AGGG
3164454 T
1 T
3164455 CAGAGTTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
12 2 0.06
13 17 0.50
14 13 0.38
15 2 0.06
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (13 bp):
TTTAGATTTAGGG
Found at i:3164436 original size:20 final size:20
Alignment explanation
Indices: 3164400--3164451 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
3164390 AAATTTAAAA
* *
3164400 TTTAGATTTAGGGTTTA-AG
1 TTTAGATTTAAGATTTAGAG
*
3164419 TTTGAGATTTAAGATTTAGGG
1 TTT-AGATTTAAGATTTAGAG
3164440 TTTAGATTTAAG
1 TTTAGATTTAAG
3164452 GGTCAGAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.11
20 21 0.75
21 4 0.14
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (20 bp):
TTTAGATTTAAGATTTAGAG
Found at i:3164462 original size:20 final size:20
Alignment explanation
Indices: 3164400--3164462 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
3164390 AAATTTAAAA
3164400 TTTAGATTT-AGGGTTTA-AG
1 TTTAGATTTAAGGG-TTAGAG
** *
3164419 TTTGAGATTTAAGATTTAGGG
1 TTT-AGATTTAAGGGTTAGAG
*
3164440 TTTAGATTTAAGGGTCAGAG
1 TTTAGATTTAAGGGTTAGAG
3164460 TTT
1 TTT
3164463 GAGGATCTGG
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
19 3 0.09
20 25 0.74
21 6 0.18
ACGTcount: A:0.27, C:0.02, G:0.27, T:0.44
Consensus pattern (20 bp):
TTTAGATTTAAGGGTTAGAG
Found at i:3168238 original size:16 final size:15
Alignment explanation
Indices: 3168219--3168249 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
3168209 GTTTATAATA
3168219 TTTTATATTATGTTAT
1 TTTTATA-TATGTTAT
3168235 TTTTATATATGTTAT
1 TTTTATATATGTTAT
3168250 GTAATTTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATATATGTTAT
Found at i:3168362 original size:26 final size:27
Alignment explanation
Indices: 3168304--3168367 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
3168294 TAACACAAAC
*
3168304 ATTAAAATAATGTTAAAATTTTCAATA
1 ATTAAAATAATGTTAAAATTTTAAATA
*
3168331 AATAAAA-AATGTATAAAATTTTAAAT-
1 ATTAAAATAATGT-TAAAATTTTAAATA
3168357 ATTAAAATAAT
1 ATTAAAATAAT
3168368 ATGGGCTGGC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 11 0.34
27 21 0.66
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (27 bp):
ATTAAAATAATGTTAAAATTTTAAATA
Found at i:3172309 original size:17 final size:18
Alignment explanation
Indices: 3172287--3172323 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3172277 AAATTGATAG
3172287 AAATGA-TAAAGTTAAAA
1 AAATGAGTAAAGTTAAAA
*
3172304 AAATGAGTTAAGTTAAAA
1 AAATGAGTAAAGTTAAAA
3172322 AA
1 AA
3172324 TGAACGCGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (18 bp):
AAATGAGTAAAGTTAAAA
Found at i:3175987 original size:24 final size:24
Alignment explanation
Indices: 3175950--3175997 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3175940 CCTGATGAAA
* *
3175950 ACAATGCAATTGTTGAAACTAAAG
1 ACAATGCAAATGTTGAAAATAAAG
*
3175974 ACAATGGAAATGTTGAAAATAAAG
1 ACAATGCAAATGTTGAAAATAAAG
3175998 TCTCATTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.50, C:0.08, G:0.19, T:0.23
Consensus pattern (24 bp):
ACAATGCAAATGTTGAAAATAAAG
Found at i:3180883 original size:2 final size:2
Alignment explanation
Indices: 3180876--3180904 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3180866 ATCCAAAATT
3180876 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3180905 TGTTAAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3181264 original size:60 final size:59
Alignment explanation
Indices: 3181192--3181309 Score: 209
Period size: 60 Copynumber: 2.0 Consensus size: 59
3181182 TAGGTGTTAG
3181192 ATTACAAAAAGGATCAAAGAGTAAACTATCTAAGAGTAGATTGATTTTTTTAAAATTAAT
1 ATTACAAAAAGGATCAAAGAGTAAACTATCTAAGAGTAGATTGATTTTTTT-AAATTAAT
* *
3181252 ATTACAAAAAGGATCAAAGAGTAAATTATCTAAGAGTATATTGATTTTTTTAAATTAA
1 ATTACAAAAAGGATCAAAGAGTAAACTATCTAAGAGTAGATTGATTTTTTTAAATTAA
3181310 AAAAATCATT
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
59 7 0.12
60 49 0.88
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.35
Consensus pattern (59 bp):
ATTACAAAAAGGATCAAAGAGTAAACTATCTAAGAGTAGATTGATTTTTTTAAATTAAT
Found at i:3182689 original size:15 final size:16
Alignment explanation
Indices: 3182662--3182694 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
3182652 AATTAAACTA
3182662 AATATATAAAGTAATT
1 AATATATAAAGTAATT
3182678 AATATA-AAAGTAATT
1 AATATATAAAGTAATT
3182693 AA
1 AA
3182695 AATCTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
AATATATAAAGTAATT
Found at i:3187149 original size:15 final size:15
Alignment explanation
Indices: 3187129--3187163 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3187119 ATGAATAAAG
3187129 AATAATTATAAAAAA
1 AATAATTATAAAAAA
**
3187144 AATAATTATATTAAA
1 AATAATTATAAAAAA
3187159 AATAA
1 AATAA
3187164 ATAATAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATAATTATAAAAAA
Found at i:3187456 original size:24 final size:24
Alignment explanation
Indices: 3187429--3187482 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
3187419 GAATTTGTTC
*
3187429 AATTTAATTAAATAAATAATTAAA
1 AATTTAATTAAAAAAATAATTAAA
* *
3187453 AATTT-CTTAAAAAAATATTTAAA
1 AATTTAATTAAAAAAATAATTAAA
*
3187476 AAATTAA
1 AATTTAA
3187483 AAAAATTCAG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
AATTTAATTAAAAAAATAATTAAA
Found at i:3202189 original size:27 final size:28
Alignment explanation
Indices: 3202135--3202189 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
3202125 ATTAAACTTA
* *
3202135 AAAAAAAAAAGTTAATATTTTATCTTAT
1 AAAAAAAAAAGTTAATATTTGATATTAT
3202163 AAAAAAAAAAGTTAA-A-TTGATGATTAT
1 AAAAAAAAAAGTTAATATTTGAT-ATTAT
3202190 GCAATTTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 4 0.17
27 5 0.21
28 15 0.62
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (28 bp):
AAAAAAAAAAGTTAATATTTGATATTAT
Found at i:3203736 original size:3 final size:3
Alignment explanation
Indices: 3203728--3203784 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
3203718 TTTATGTTTT
3203728 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
3203776 ATA ATA ATA
1 ATA ATA ATA
3203785 TAAAAGGTGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3203844 original size:18 final size:17
Alignment explanation
Indices: 3203820--3203862 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
3203810 TAAAAAATAT
*
3203820 AATTTAATATTAATTAC
1 AATTTAATAATAATTAC
* *
3203837 ACATTTAAAAATAATTAT
1 A-ATTTAATAATAATTAC
3203855 AATTTAAT
1 AATTTAAT
3203863 TCACAATTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTTAATAATAATTAC
Found at i:3207372 original size:47 final size:49
Alignment explanation
Indices: 3207321--3207424 Score: 140
Period size: 47 Copynumber: 2.1 Consensus size: 49
3207311 TTTTCGTGAC
*
3207321 CCTAATTCAATTCTAGCTAAGATATA-TAT-AAATATAAATTCCGTAAT
1 CCTAATTCAATTCTAACTAAGATATATTATAAAATATAAATTCCGTAAT
* * * *
3207368 CCTAATTCAATTCTAACTAATATATATTTATAAAATATAATTTTCTTAAT
1 CCTAATTCAATTCTAACTAAGATATA-TTATAAAATATAAATTCCGTAAT
3207418 CCTAATT
1 CCTAATT
3207425 AAGTTATAAG
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
47 24 0.49
49 3 0.06
50 22 0.45
ACGTcount: A:0.41, C:0.14, G:0.03, T:0.41
Consensus pattern (49 bp):
CCTAATTCAATTCTAACTAAGATATATTATAAAATATAAATTCCGTAAT
Found at i:3207641 original size:3 final size:3
Alignment explanation
Indices: 3207633--3207681 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
3207623 ATGTTTTATC
3207633 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3207681 A
1 A
3207682 TAAAAGGTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3214035 original size:23 final size:23
Alignment explanation
Indices: 3213991--3214037 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
3213981 CATTTTACAT
**
3213991 TTTTATAAATTTTATATGTTTTA
1 TTTTATAAATTTTATAAATTTTA
3214014 TTTTATAAA-TTTATACAATTTTA
1 TTTTATAAATTTTATA-AATTTTA
3214037 T
1 T
3214038 ATTTGTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTTATAAATTTTATAAATTTTA
Found at i:3215904 original size:13 final size:13
Alignment explanation
Indices: 3215886--3215911 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3215876 TAGAAGGAAG
3215886 AAAAAAATAAAAA
1 AAAAAAATAAAAA
3215899 AAAAAAATAAAAA
1 AAAAAAATAAAAA
3215912 GGAGAAATGG
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:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAAAAATAAAAA
Found at i:3216493 original size:9 final size:9
Alignment explanation
Indices: 3216479--3216503 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3216469 AATATAATAC
3216479 ATTAAAAAT
1 ATTAAAAAT
3216488 ATTAAAAAT
1 ATTAAAAAT
3216497 ATTAAAA
1 ATTAAAA
3216504 TAAATGTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
ATTAAAAAT
Found at i:3225278 original size:48 final size:48
Alignment explanation
Indices: 3225207--3225303 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
3225197 TGCAAAAAAG
**
3225207 TATGAAAAATCTTGAGTTAAGTATGTGTTTGGTACGGATATGTTTGAT
1 TATGAAAAATCTTGAGTTAAGTATGTGTTTAATACGGATATGTTTGAT
*
3225255 TATGAAAAATCTTGAGTTCAGTATGTGTTTAATACGGATATGTTTGAT
1 TATGAAAAATCTTGAGTTAAGTATGTGTTTAATACGGATATGTTTGAT
3225303 T
1 T
3225304 TTCTTTTAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.42
Consensus pattern (48 bp):
TATGAAAAATCTTGAGTTAAGTATGTGTTTAATACGGATATGTTTGAT
Found at i:3225963 original size:14 final size:16
Alignment explanation
Indices: 3225944--3225982 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
3225934 TAAATAAAAA
3225944 AATATTAAATT-AT-T
1 AATATTAAATTAATAT
3225958 AATATTAAATTAATAT
1 AATATTAAATTAATAT
3225974 AATA-TAAAT
1 AATATTAAAT
3225983 ATTTTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 11 0.48
15 7 0.30
16 5 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATATTAAATTAATAT
Found at i:3230932 original size:31 final size:31
Alignment explanation
Indices: 3230903--3230960 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
3230893 TTTTATATTC
3230903 TTTTTATAA-TTTTT-A-ATTTTTAAAAATA
1 TTTTTATAATTTTTTAATATTTTTAAAAATA
3230931 TTTTTATAATTTTTTAATATTTTTAAAAAT
1 TTTTTATAATTTTTTAATATTTTTAAAAAT
3230961 TTTAAAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 9 0.33
29 5 0.19
30 1 0.04
31 12 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
TTTTTATAATTTTTTAATATTTTTAAAAATA
Found at i:3230949 original size:19 final size:19
Alignment explanation
Indices: 3230887--3230955 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 19
3230877 AATATTAAAA
3230887 AATATATTTTAT-ATTCTTTT
1 AATAT-TTTTATAATT-TTTT
* * *
3230907 TATAATTTT-TAATTTTTAAA
1 AATATTTTTATAATTTTT--T
3230927 AATATTTTTATAATTTTTT
1 AATATTTTTATAATTTTTT
3230946 AATATTTTTA
1 AATATTTTTA
3230956 AAAATTTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 4 0.10
19 17 0.44
20 10 0.26
21 8 0.21
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (19 bp):
AATATTTTTATAATTTTTT
Found at i:3230962 original size:10 final size:10
Alignment explanation
Indices: 3230917--3230967 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
3230907 TATAATTTTT
3230917 AATTTTTAAA
1 AATTTTTAAA
* *
3230927 AATATTTTTAT
1 AAT-TTTTAAA
*
3230938 AATTTTTTAA
1 AATTTTTAAA
*
3230948 TATTTTTAAA
1 AATTTTTAAA
3230958 AA-TTTTAAA
1 AATTTTTAAA
3230967 A
1 A
3230968 GAAATAATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
9 8 0.24
10 18 0.53
11 8 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
AATTTTTAAA
Found at i:3230963 original size:19 final size:19
Alignment explanation
Indices: 3230927--3230963 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3230917 AATTTTTAAA
* *
3230927 AATATTTTTATAATTTTTT
1 AATATTTTTAAAAATTTTT
3230946 AATATTTTTAAAAATTTT
1 AATATTTTTAAAAATTTT
3230964 AAAAGAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
AATATTTTTAAAAATTTTT
Found at i:3233603 original size:19 final size:20
Alignment explanation
Indices: 3233563--3233605 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
3233553 ACAAAAAAGT
*
3233563 ATTCAAAATAATTTTCATAA
1 ATTCAAAATAATTTTCAAAA
3233583 ATTCAAAAT-ATTTAT-AAAA
1 ATTCAAAATAATTT-TCAAAA
3233602 ATTC
1 ATTC
3233606 TCAATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTCAAAATAATTTTCAAAA
Found at i:3234947 original size:15 final size:14
Alignment explanation
Indices: 3234916--3234966 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
3234906 CCATATTGAA
*
3234916 ATTTTTATATTATTT
1 ATTTTTATA-TAATT
3234931 ATTTTTAATATAATT
1 ATTTTT-ATATAATT
*
3234946 ATTCTTTTTATAATT
1 ATT-TTTATATAATT
3234961 ATTTTT
1 ATTTTT
3234967 TAATTTGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 3 0.09
15 23 0.72
16 6 0.19
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTTTTATATAATT
Found at i:3240331 original size:4 final size:4
Alignment explanation
Indices: 3240322--3240366 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
3240312 GCTAAAAGGG
3240322 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA T
3240367 TCATTCGCAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:3241614 original size:6 final size:6
Alignment explanation
Indices: 3241603--3241629 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3241593 CAATGAAAGA
3241603 GGGTGG GGGTGG GGGTGG GGGTGG GGG
1 GGGTGG GGGTGG GGGTGG GGGTGG GGG
3241630 GATCAAGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.85, T:0.15
Consensus pattern (6 bp):
GGGTGG
Found at i:3245866 original size:25 final size:26
Alignment explanation
Indices: 3245809--3245859 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
3245799 TAAGTAATTA
* **
3245809 ATATAAATTATTTGTAAAATTAATGAT
1 ATATAAAATATTTAAAAAATTAAT-AT
3245836 ATATAAAATATTTAAAAAATTAAT
1 ATATAAAATATTTAAAAAATTAAT
3245860 TTTATAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (26 bp):
ATATAAAATATTTAAAAAATTAATAT
Found at i:3247715 original size:14 final size:14
Alignment explanation
Indices: 3247698--3247739 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
3247688 TATATTTGAT
*
3247698 ATTTTATAATAAAA
1 ATTTTTTAATAAAA
3247712 ATTTTTTAAT--AA
1 ATTTTTTAATAAAA
3247724 ATTTTTTAATAAAA
1 ATTTTTTAATAAAA
3247738 AT
1 AT
3247740 ATATTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 12 0.48
14 13 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTTTTAATAAAA
Found at i:3247727 original size:12 final size:12
Alignment explanation
Indices: 3247710--3247736 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3247700 TTTATAATAA
3247710 AAATTTTTTAAT
1 AAATTTTTTAAT
3247722 AAATTTTTTAAT
1 AAATTTTTTAAT
3247734 AAA
1 AAA
3247737 AATATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
AAATTTTTTAAT
Found at i:3247762 original size:27 final size:27
Alignment explanation
Indices: 3247732--3247784 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
3247722 AAATTTTTTA
3247732 ATAAAAATATA-TTAAAATAATAAATAG
1 ATAAAAAT-TACTTAAAATAATAAATAG
**
3247759 ATAAAAATTACTTATCATAATAAATA
1 ATAAAAATTACTTAAAATAATAAATA
3247785 ATAGGTTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (27 bp):
ATAAAAATTACTTAAAATAATAAATAG
Found at i:3252636 original size:19 final size:20
Alignment explanation
Indices: 3252612--3252652 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
3252602 TTAGATATAA
*
3252612 AATTTTTAAA-AAATAATAT
1 AATTTTTAAATAAATAAAAT
3252631 AATTTTTAAATAAATAAAAT
1 AATTTTTAAATAAATAAAAT
3252651 AA
1 AA
3252653 AAATAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTTTTAAATAAATAAAAT
Found at i:3252678 original size:22 final size:21
Alignment explanation
Indices: 3252638--3252679 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3252628 TATAATTTTT
3252638 AAATAAATAAAATAAAAATAA
1 AAATAAATAAAATAAAAATAA
3252659 AAATAAA-AACAATTAAAAATA
1 AAATAAATAA-AA-TAAAAATA
3252680 TTATACATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.11
21 9 0.47
22 8 0.42
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (21 bp):
AAATAAATAAAATAAAAATAA
Found at i:3257303 original size:31 final size:31
Alignment explanation
Indices: 3257268--3257328 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
3257258 ATGATTACTA
3257268 AATTAATAGAAAATTTTCATTTAAGTCACTG
1 AATTAATAGAAAATTTTCATTTAAGTCACTG
* * * *
3257299 AATTATTTGAAAGTTTTTATTTAAGTCACT
1 AATTAATAGAAAATTTTCATTTAAGTCACT
3257329 CGAGTGTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (31 bp):
AATTAATAGAAAATTTTCATTTAAGTCACTG
Found at i:3258440 original size:30 final size:30
Alignment explanation
Indices: 3258404--3258480 Score: 118
Period size: 30 Copynumber: 2.6 Consensus size: 30
3258394 TGATTTGAGA
*
3258404 GACGAACACGGCAACCCTATTCAACTCACC
1 GACGAACACGGCAACCCGATTCAACTCACC
* *
3258434 GACGAACACGGCAACCCGGTTCAACTCACT
1 GACGAACACGGCAACCCGATTCAACTCACC
*
3258464 GACGAACACGGTAACCC
1 GACGAACACGGCAACCC
3258481 CATTTATGTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.32, C:0.38, G:0.18, T:0.12
Consensus pattern (30 bp):
GACGAACACGGCAACCCGATTCAACTCACC
Found at i:3258681 original size:6 final size:6
Alignment explanation
Indices: 3258670--3258705 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
3258660 AACGCTCCAG
*
3258670 CAGCTC CAGCTC CAGCTC CAGCTC CAGCTC TAGCTC
1 CAGCTC CAGCTC CAGCTC CAGCTC CAGCTC CAGCTC
3258706 GGTAATGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.47, G:0.17, T:0.19
Consensus pattern (6 bp):
CAGCTC
Found at i:3258905 original size:8 final size:8
Alignment explanation
Indices: 3258888--3258929 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
3258878 TCATTTGAAA
3258888 TTTA-ATT
1 TTTATATT
3258895 TTTATATT
1 TTTATATT
3258903 TTTATTTATT
1 TTTA--TATT
3258913 TTTATATT
1 TTTATATT
3258921 TTTAT-TT
1 TTTATATT
3258928 TT
1 TT
3258930 AGAAATTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 8 0.25
8 16 0.50
10 8 0.25
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTATATT
Found at i:3258913 original size:18 final size:19
Alignment explanation
Indices: 3258887--3258927 Score: 75
Period size: 18 Copynumber: 2.2 Consensus size: 19
3258877 TTCATTTGAA
3258887 ATTTAATTTTTATATTTTT
1 ATTTAATTTTTATATTTTT
3258906 ATTT-ATTTTTATATTTTT
1 ATTTAATTTTTATATTTTT
3258924 ATTT
1 ATTT
3258928 TTAGAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (19 bp):
ATTTAATTTTTATATTTTT
Found at i:3268072 original size:12 final size:12
Alignment explanation
Indices: 3268055--3268082 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3268045 CAGTAGAGTG
3268055 ACAATCTTCGTA
1 ACAATCTTCGTA
3268067 ACAATCTTCGTA
1 ACAATCTTCGTA
3268079 ACAA
1 ACAA
3268083 AATAATAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.25, G:0.07, T:0.29
Consensus pattern (12 bp):
ACAATCTTCGTA
Found at i:3269408 original size:141 final size:140
Alignment explanation
Indices: 3269159--3269412 Score: 325
Period size: 141 Copynumber: 1.8 Consensus size: 140
3269149 GGGATGAACT
* * * *
3269159 TTTTCACCTCCGTTAGAGGAGGAAAAGGGAAAGGCATACCGTACACTAAGTTTCTTCTCGATACT
1 TTTTCACCACCGTTAAAGGAGGAAAAGGGAAAGGCATACCGAACACTAAGTTTCTTCTCGATAAT
** * *
3269224 TCATCACGATGAAACGATGCATCGTCATGTGATGGATCATGATCATCATTATCATGATCATGCAT
66 TCATCACGATGAAACGATGCATCAACA-GTCATGCATCATGATCATCATTATCATGATCATGCAT
3269289 CAGGTTAAGCC
130 CAGGTTAAGCC
* *
3269300 TTTTCACCACCGTTAAATGG-GGGAAAGGGAAAGGCATACCGAACGCTAAGTTTCTTCTTCTCGA
1 TTTTCACCACCGTTAAA-GGAGGAAAAGGGAAAGGCATACCGAACACTAAG--T-TTCTTCTCGA
* * *
3269364 TAATTCGTCACGATGAAATGATGCATCAACA-TCAT-CATCTTGATCATCA
62 TAATTCATCACGATGAAACGATGCATCAACAGTCATGCATCATGATCATCA
3269413 GATCCATCAA
Statistics
Matches: 96, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
141 54 0.56
142 5 0.05
143 1 0.01
144 36 0.38
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (140 bp):
TTTTCACCACCGTTAAAGGAGGAAAAGGGAAAGGCATACCGAACACTAAGTTTCTTCTCGATAAT
TCATCACGATGAAACGATGCATCAACAGTCATGCATCATGATCATCATTATCATGATCATGCATC
AGGTTAAGCC
Found at i:3275579 original size:16 final size:16
Alignment explanation
Indices: 3275558--3275593 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
3275548 AAATTATGAA
3275558 CTCAATAGCATCCCTT
1 CTCAATAGCATCCCTT
3275574 CTCAATAGCATCCCTT
1 CTCAATAGCATCCCTT
3275590 CTCA
1 CTCA
3275594 GCAATAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.39, G:0.06, T:0.31
Consensus pattern (16 bp):
CTCAATAGCATCCCTT
Found at i:3281866 original size:37 final size:37
Alignment explanation
Indices: 3281824--3281894 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
3281814 TTTCTAATTA
3281824 ACATGTATAACCGTGGCATATCCACTTAGCACCACTT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACTT
* *
3281861 ACATGTTTAACCGTGGTATATCCACTTAGCACCA
1 ACATGTATAACCGTGGCATATCCACTTAGCACCA
3281895 TGTTAATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (37 bp):
ACATGTATAACCGTGGCATATCCACTTAGCACCACTT
Found at i:3285650 original size:3 final size:3
Alignment explanation
Indices: 3285642--3285671 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3285632 GAAGCATTGA
3285642 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3285672 TCAAAAGTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3287298 original size:51 final size:51
Alignment explanation
Indices: 3287217--3287333 Score: 162
Period size: 51 Copynumber: 2.3 Consensus size: 51
3287207 ACTTCTAATC
* * * *
3287217 AGTGACAAGTGAAAAGTGGTAGCCTCAGCTACACTTATCTGATTAGTGACA
1 AGTGACAAGCGATAAGTGGTAGCCTCAGCTACACTTATCCGATCAGTGACA
* * *
3287268 AGTGATAAGCGATAAGTGGTAGCTTTAGCTACACTTATCCGATCAGTGACA
1 AGTGACAAGCGATAAGTGGTAGCCTCAGCTACACTTATCCGATCAGTGACA
*
3287319 AGTGACAAGTGATAA
1 AGTGACAAGCGATAA
3287334 ATGTGATCCG
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (51 bp):
AGTGACAAGCGATAAGTGGTAGCCTCAGCTACACTTATCCGATCAGTGACA
Found at i:3289352 original size:14 final size:14
Alignment explanation
Indices: 3289333--3289361 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3289323 TCAATTATAA
3289333 ATATATTAATTAAT
1 ATATATTAATTAAT
3289347 ATATATTAATTAAT
1 ATATATTAATTAAT
3289361 A
1 A
3289362 ATAAGATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATATTAATTAAT
Found at i:3289676 original size:24 final size:25
Alignment explanation
Indices: 3289632--3289679 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
3289622 AGTTTCTTAT
3289632 AAAGACATAATAAAATATTTTTAAA
1 AAAGACATAATAAAATATTTTTAAA
*
3289657 AAAGAGAT-ATAATAAT-TTTTTAA
1 AAAGACATAATAA-AATATTTTTAA
3289680 TACTGCTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.35
Consensus pattern (25 bp):
AAAGACATAATAAAATATTTTTAAA
Found at i:3290913 original size:2 final size:2
Alignment explanation
Indices: 3290908--3290940 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3290898 ATGTGTTGTG
*
3290908 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3290941 GAATGAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3309237 original size:29 final size:28
Alignment explanation
Indices: 3309205--3309282 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 28
3309195 TTAATTTTAT
3309205 TAAAAATTAGAAAAATATTATAAAAATC-G
1 TAAAAATTA-AAAAATATTATAAAAA-CGG
* *
3309234 TAAAAAATTATAAAATTTTATAAAAACGG
1 T-AAAAATTAAAAAATATTATAAAAACGG
3309263 TAAAAAAATATAAAAAATAT
1 T--AAAAAT-TAAAAAATAT
3309283 AAAATTTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 1 0.02
29 17 0.41
30 15 0.37
31 8 0.20
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (28 bp):
TAAAAATTAAAAAATATTATAAAAACGG
Found at i:3309258 original size:19 final size:19
Alignment explanation
Indices: 3309234--3309295 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
3309224 ATAAAAATCG
3309234 TAAAAAATTATAAAATTTTA
1 TAAAAAA-TATAAAATTTTA
*** ***
3309254 TAAAAACGGTAAAAAAATA
1 TAAAAAATATAAAATTTTA
3309273 TAAAAAATATAAAATTTTA
1 TAAAAAATATAAAATTTTA
3309292 TAAA
1 TAAA
3309296 GTCGTAAAAA
Statistics
Matches: 30, Mismatches: 12, Indels: 1
0.70 0.28 0.02
Matches are distributed among these distances:
19 24 0.80
20 6 0.20
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.31
Consensus pattern (19 bp):
TAAAAAATATAAAATTTTA
Found at i:3309306 original size:38 final size:40
Alignment explanation
Indices: 3309226--3309317 Score: 129
Period size: 38 Copynumber: 2.4 Consensus size: 40
3309216 AAAATATTAT
3309226 AAAAATCG-TAAAAAATTATAAAATTTTATAAAAACGGTAA
1 AAAAAT-GATAAAAAATTATAAAATTTTATAAAAACGGTAA
**
3309266 AAAAAT-ATAAAAAA-TATAAAATTTTATAAAGTC-GTAA
1 AAAAATGATAAAAAATTATAAAATTTTATAAAAACGGTAA
3309303 AAAAATGATAAAAAA
1 AAAAATGATAAAAAA
3309318 GTAGAGAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
37 10 0.21
38 25 0.52
39 7 0.15
40 6 0.12
ACGTcount: A:0.64, C:0.03, G:0.07, T:0.26
Consensus pattern (40 bp):
AAAAATGATAAAAAATTATAAAATTTTATAAAAACGGTAA
Found at i:3309558 original size:8 final size:9
Alignment explanation
Indices: 3309537--3309561 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3309527 TTATAAATTT
3309537 TTTTTATGA
1 TTTTTATGA
3309546 TTTTTATGA
1 TTTTTATGA
3309555 TTTTTAT
1 TTTTTAT
3309562 AAAATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (9 bp):
TTTTTATGA
Found at i:3309587 original size:19 final size:20
Alignment explanation
Indices: 3309565--3309607 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
3309555 TTTTTATAAA
*
3309565 ATTTTATAAAATT-TATATT
1 ATTTTACAAAATTCTATATT
*
3309584 ATTTTACAACATTCTATATT
1 ATTTTACAAAATTCTATATT
3309604 ATTT
1 ATTT
3309608 ATATTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTACAAAATTCTATATT
Found at i:3309589 original size:29 final size:29
Alignment explanation
Indices: 3309556--3309612 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
3309546 TTTTTATGAT
* *
3309556 TTTTATAAAATTTTATAAAATTTATATTA
1 TTTTACAAAATTCTATAAAATTTATATTA
* **
3309585 TTTTACAACATTCTATATTATTTATATT
1 TTTTACAAAATTCTATAAAATTTATATT
3309613 TTTATTAAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (29 bp):
TTTTACAAAATTCTATAAAATTTATATTA
Found at i:3316171 original size:29 final size:30
Alignment explanation
Indices: 3316128--3316192 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
3316118 TTGAACTTAT
* * *
3316128 TTAATTATTTTTAATACTATAAAAATTAAA
1 TTAATTATATTTAATAATAAAAAAATTAAA
*
3316158 TTAATT-TATTTAATAATAAAAAAATTAAT
1 TTAATTATATTTAATAATAAAAAAATTAAA
3316187 TTAATT
1 TTAATT
3316193 CGGTTCTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 25 0.81
30 6 0.19
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (30 bp):
TTAATTATATTTAATAATAAAAAAATTAAA
Found at i:3323995 original size:14 final size:14
Alignment explanation
Indices: 3323976--3324006 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3323966 CAACCCCGAT
3323976 TAACCGATTTGAGA
1 TAACCGATTTGAGA
3323990 TAACCGATTTGAGA
1 TAACCGATTTGAGA
3324004 TAA
1 TAA
3324007 GGCATGTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (14 bp):
TAACCGATTTGAGA
Found at i:3328692 original size:16 final size:17
Alignment explanation
Indices: 3328671--3328714 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
3328661 TATTAAATTT
*
3328671 AAAATTAAAATAAGA-A
1 AAAATTAAAATAAAATA
*
3328687 AAAATT-AATTAAAATA
1 AAAATTAAAATAAAATA
3328703 AAAATTAAAATA
1 AAAATTAAAATA
3328715 TATTGTGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 6 0.26
16 13 0.57
17 4 0.17
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (17 bp):
AAAATTAAAATAAAATA
Found at i:3329387 original size:258 final size:258
Alignment explanation
Indices: 3328930--3329442 Score: 947
Period size: 258 Copynumber: 2.0 Consensus size: 258
3328920 TCATTAATTT
*
3328930 ATTCAATGAATGAGACCATTCAATTCGGAGGAGGGGAATAACAAATAGCCTTTGTAGGCGGTAAA
1 ATTCAATGAATGAGACCATTCAATTCGGAGGAGGGGAATAACAAATACCCTTTGTAGGCGGTAAA
*
3328995 GGACAAGCTCCATCAACATAACAAATATTTCATCTTCAACATTAATAGAATGACAGTTGCCTATG
66 GGACAAGCTCCATCAACACAACAAATATTTCATCTTCAACATTAATAGAATGACAGTTGCCTATG
*
3329060 TCACAACTCAAACACAATATTTCATTTCACCCTTAAATGGAACGACCAAATGTTTTCGGTCTAAT
131 TCACAACTCAAACACAATATTTCATTTCACCCTTAAATGGAACGACCAAATATTTTCGGTCTAAT
3329125 TATATCCTCAGTCCCTAAACTCTTTGTATTCT-AAAATTTATTCGCTATACTCTTAGTGAGACC
196 TATATCCTCAGTCCCTAAACTCTTTGTATT-TAAAAATTTATTCGCTATACTCTTAGTGAGACC
* *
3329188 ATTCAATGAATGAGACCATTCAATTCGGGGGAGGGGAATAACAAATACCCTTTGTAGGCGGTGAA
1 ATTCAATGAATGAGACCATTCAATTCGGAGGAGGGGAATAACAAATACCCTTTGTAGGCGGTAAA
*
3329253 TGACAAGCTCCATCAACACAACAAATATTTCATCTTCAACATTAATAGAATGACAGTTGCCTATG
66 GGACAAGCTCCATCAACACAACAAATATTTCATCTTCAACATTAATAGAATGACAGTTGCCTATG
*
3329318 TCACAACTCAAGCACAATATTTCATTTCACCCTTAAATGGAACGACCAAATATTTTCGGTCTAAT
131 TCACAACTCAAACACAATATTTCATTTCACCCTTAAATGGAACGACCAAATATTTTCGGTCTAAT
3329383 TATATCCTCAGTCCCTAAACTCTTTGTATTTAAAAATTTATTCGCTATACTCTTAGTGAG
196 TATATCCTCAGTCCCTAAACTCTTTGTATTTAAAAATTTATTCGCTATACTCTTAGTGAG
3329443 CTATCTAAAA
Statistics
Matches: 247, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
257 1 0.00
258 246 1.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.30
Consensus pattern (258 bp):
ATTCAATGAATGAGACCATTCAATTCGGAGGAGGGGAATAACAAATACCCTTTGTAGGCGGTAAA
GGACAAGCTCCATCAACACAACAAATATTTCATCTTCAACATTAATAGAATGACAGTTGCCTATG
TCACAACTCAAACACAATATTTCATTTCACCCTTAAATGGAACGACCAAATATTTTCGGTCTAAT
TATATCCTCAGTCCCTAAACTCTTTGTATTTAAAAATTTATTCGCTATACTCTTAGTGAGACC
Found at i:3335083 original size:18 final size:18
Alignment explanation
Indices: 3335060--3335113 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
3335050 ACAAGTGGTG
3335060 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
*
3335078 GT-G-G--AGT-AGG-TA
1 GTGGAGCAAGTGTGGCTA
3335090 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
3335108 GTGGAG
1 GTGGAG
3335114 TTAATGGTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 4 0.14
13 3 0.11
14 4 0.14
16 4 0.14
17 3 0.11
18 10 0.36
ACGTcount: A:0.22, C:0.07, G:0.48, T:0.22
Consensus pattern (18 bp):
GTGGAGCAAGTGTGGCTA
Found at i:3335096 original size:30 final size:30
Alignment explanation
Indices: 3335056--3335153 Score: 144
Period size: 30 Copynumber: 3.3 Consensus size: 30
3335046 AGGTACAAGT
3335056 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
1 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
*
3335086 GGTAGTGGAGCAAGTGTGGCTAGTGGAGTTA
1 GGTGGTGGAGCAAGTGTGGCTAGTGGAG-TA
* * *
3335117 -ATGGTGGAGCAAGTGTGGTTAGTGGAGTT
1 GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
3335146 GGTGGTGG
1 GGTGGTGG
3335154 CAAAGGCTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
29 1 0.02
30 57 0.95
31 2 0.03
ACGTcount: A:0.19, C:0.05, G:0.49, T:0.27
Consensus pattern (30 bp):
GGTGGTGGAGCAAGTGTGGCTAGTGGAGTA
Found at i:3341393 original size:10 final size:10
Alignment explanation
Indices: 3341378--3341408 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
3341368 AAATATCTAG
3341378 ATTTCTCTTC
1 ATTTCTCTTC
3341388 ATTTCTCTTC
1 ATTTCTCTTC
3341398 ATTTCTCTTC
1 ATTTCTCTTC
3341408 A
1 A
3341409 ATTCCAGCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.13, C:0.29, G:0.00, T:0.58
Consensus pattern (10 bp):
ATTTCTCTTC
Found at i:3347101 original size:23 final size:22
Alignment explanation
Indices: 3347075--3347120 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
3347065 TGTGATGACG
3347075 TTATATT-ATAAATATGTATGAAT
1 TTATATTGA-AAATATGT-TGAAT
*
3347098 TTATCTTGAAAATATGTTGAAT
1 TTATATTGAAAATATGTTGAAT
3347120 T
1 T
3347121 GATTTGGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (22 bp):
TTATATTGAAAATATGTTGAAT
Found at i:3347336 original size:2 final size:2
Alignment explanation
Indices: 3347331--3347363 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3347321 AAAAAAGTAA
3347331 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3347364 ATGAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3350682 original size:6 final size:6
Alignment explanation
Indices: 3350671--3350697 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3350661 AGCAAAACCC
3350671 GCCGAG GCCGAG GCCGAG GCCGAG GCC
1 GCCGAG GCCGAG GCCGAG GCCGAG GCC
3350698 CCGGCCACCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.37, G:0.48, T:0.00
Consensus pattern (6 bp):
GCCGAG
Found at i:3351605 original size:2 final size:2
Alignment explanation
Indices: 3351598--3351631 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3351588 GGAATTTAAA
3351598 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3351632 GAAATTTGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3352387 original size:18 final size:18
Alignment explanation
Indices: 3352364--3352402 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3352354 TGTATTTCAT
* * *
3352364 AAAATATAATAAAAAGTA
1 AAAATAAAACAAAAAATA
3352382 AAAATAAAACAAAAAATA
1 AAAATAAAACAAAAAATA
3352400 AAA
1 AAA
3352403 CAGTTGTCAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (18 bp):
AAAATAAAACAAAAAATA
Found at i:3353294 original size:4 final size:4
Alignment explanation
Indices: 3353285--3353311 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3353275 ATATTAAAAA
3353285 TAAT TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAA
3353312 ATTTTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:3361277 original size:2 final size:2
Alignment explanation
Indices: 3361270--3361307 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3361260 TGAATTCCAT
3361270 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3361308 AGGTTTTGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3368706 original size:22 final size:21
Alignment explanation
Indices: 3368658--3368708 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
3368648 ATTACATGAG
* *
3368658 AATATTTTTGGAAAATCCTCT
1 AATATTTTTGGAAAATACACT
* *
3368679 ACTATTTTTGGAAATTGACACT
1 AATATTTTTGGAAAAT-ACACT
3368701 AATATTTT
1 AATATTTT
3368709 ATCATTTTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (21 bp):
AATATTTTTGGAAAATACACT
Found at i:3370547 original size:18 final size:19
Alignment explanation
Indices: 3370510--3370549 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
3370500 TTCAATTTAT
3370510 TTTATTATATATATAAATA
1 TTTATTATATATATAAATA
* *
3370529 TTTATT-TATTTATATATA
1 TTTATTATATATATAAATA
3370547 TTT
1 TTT
3370550 GTTCGCTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATTATATATATAAATA
Found at i:3372137 original size:46 final size:46
Alignment explanation
Indices: 3372084--3372175 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
3372074 AGAAAATTGA
*
3372084 GGGAAGTGGGACGACTAAAAGGAGAAATCTTAGAGGTATTTTTTTT
1 GGGAAGTGAGACGACTAAAAGGAGAAATCTTAGAGGTATTTTTTTT
3372130 GGGAAGTGAGACGACTAAAAGGAGAAATCTTAGAGGTATTTTTTTT
1 GGGAAGTGAGACGACTAAAAGGAGAAATCTTAGAGGTATTTTTTTT
3372176 TCTTCTTAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.30
Consensus pattern (46 bp):
GGGAAGTGAGACGACTAAAAGGAGAAATCTTAGAGGTATTTTTTTT
Found at i:3374669 original size:13 final size:13
Alignment explanation
Indices: 3374651--3374679 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3374641 TATACTGTAA
3374651 TAATATTTTTATT
1 TAATATTTTTATT
3374664 TAATATTTTTATT
1 TAATATTTTTATT
3374677 TAA
1 TAA
3374680 AATGTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TAATATTTTTATT
Found at i:3375732 original size:34 final size:34
Alignment explanation
Indices: 3375689--3375757 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
3375679 GTCATCGTCA
3375689 CCTTAAATACAACATACTTAATTCATTTTATTTT
1 CCTTAAATACAACATACTTAATTCATTTTATTTT
*
3375723 CCTTAAATACAACATACTTAGTTCATTTTATTTT
1 CCTTAAATACAACATACTTAATTCATTTTATTTT
3375757 C
1 C
3375758 GTTTTTAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.33, C:0.19, G:0.01, T:0.46
Consensus pattern (34 bp):
CCTTAAATACAACATACTTAATTCATTTTATTTT
Found at i:3380991 original size:115 final size:115
Alignment explanation
Indices: 3380789--3381016 Score: 402
Period size: 115 Copynumber: 2.0 Consensus size: 115
3380779 GGGTAGATCT
* **
3380789 ATTAAGGCTAACACAAGGCAGCATGAGTAGACACTGTCCGTATGATCGGGCCCTGGACCATCAAA
1 ATTAAGGCTAACACAAGGAAGCATGAGTAGACACTGTCCCCATGATCGGGCCCTGGACCATCAAA
* *
3380854 TCATTGTTTCTTCTCCTCTTTTCCATCACCACCATGATCAACTTCCATCA
66 TCATTGTTTCCTCTCCTCTTTTCCATCACCACCAAGATCAACTTCCATCA
3380904 ATTAAGGCTAACACAAGGAAGCATGAGTAGACACTGTCCCCATGATCGGGCCCTGGACCATCAAA
1 ATTAAGGCTAACACAAGGAAGCATGAGTAGACACTGTCCCCATGATCGGGCCCTGGACCATCAAA
*
3380969 TCATTGTTTCCTCTCCTCTTTTCCATCACCACCAAGATCAATTTCCAT
66 TCATTGTTTCCTCTCCTCTTTTCCATCACCACCAAGATCAACTTCCAT
3381017 GGTATCACAT
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
115 107 1.00
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.27
Consensus pattern (115 bp):
ATTAAGGCTAACACAAGGAAGCATGAGTAGACACTGTCCCCATGATCGGGCCCTGGACCATCAAA
TCATTGTTTCCTCTCCTCTTTTCCATCACCACCAAGATCAACTTCCATCA
Found at i:3384904 original size:28 final size:28
Alignment explanation
Indices: 3384869--3384927 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
3384859 TAAAAATTGG
*
3384869 CATTGCTGACTGAATAACCAAACAATTA
1 CATTGCTGACAGAATAACCAAACAATTA
3384897 CATTGCTGACAGAATAACCAAACAATTA
1 CATTGCTGACAGAATAACCAAACAATTA
3384925 CAT
1 CAT
3384928 GCGGCATGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.44, C:0.22, G:0.10, T:0.24
Consensus pattern (28 bp):
CATTGCTGACAGAATAACCAAACAATTA
Found at i:3389133 original size:31 final size:31
Alignment explanation
Indices: 3389098--3389160 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
3389088 TTAACAGTAA
* * *
3389098 AGTGACTTGAATAAGAACTTTTGAATAGTTC
1 AGTGACTTAAATAAAAACTTTTAAATAGTTC
3389129 AGTGACTTAAATAAAAACTTTTAAATAGTTC
1 AGTGACTTAAATAAAAACTTTTAAATAGTTC
3389160 A
1 A
3389161 ATAACCAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (31 bp):
AGTGACTTAAATAAAAACTTTTAAATAGTTC
Found at i:3390062 original size:7 final size:7
Alignment explanation
Indices: 3390050--3390083 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
3390040 GCGAAATTCC
3390050 TTTAGGG
1 TTTAGGG
3390057 TTTAGGG
1 TTTAGGG
3390064 TTTAGGG
1 TTTAGGG
3390071 TTTAGGG
1 TTTAGGG
3390078 TTTAGG
1 TTTAGG
3390084 ATCATAATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.44
Consensus pattern (7 bp):
TTTAGGG
Found at i:3393458 original size:516 final size:520
Alignment explanation
Indices: 3392479--3393513 Score: 1523
Period size: 516 Copynumber: 2.0 Consensus size: 520
3392469 TCTTATAATT
* *
3392479 ATTTATTATGCTTTAAATGTTTCTATAAAAATATAAAATACTATATTATATTTCCATAATCTATA
1 ATTTATTATGCTTTAAATGTTTCCATAAAAATATAAAATAATATATTATATTTCCATAATCTATA
* * * * *
3392544 ATCGACTAAATTTTTTTTTGAACAATTTCACTATAAATTCTGATCATTTCAGTTATTTTTGACAT
66 ATCGACCAAATTTTTTTTTGAACAATTTCACTACAAATTCTGATCATATCAGCTATTTTTGACAC
** * *
3392609 AATGTCTAAAATTACCCATAACCCCTTCTCAATCAACAAATACTATATATCTTAATTAACATAAA
131 AATACCTAAAACTACCCATAA-CCC-TCTCAACCAACAAATACTATATATCTTAATTAACATAAA
* * *
3392674 ATATTAAGTTCAAAATCAATTTGTTTTTATTATTATATATAGCTAAAATCAAATTATGAAATTTT
194 ACATTAAGTTCAAAATCAATTTG-TTTTATTATTATACATAGCTAAAATCAAATTACGAAATTTT
* *
3392739 TAGGTAAACAAAATAAATGTTTTACTAATTTTTTTAAAATCGAAAAAATGAAAGGGAAGGGTAGG
258 TAGGGAAACAAAATAAATGTTTTACTAATTTTTTTAAAATCAAAAAAATGAAAGGGAAGGGTAGG
* * * * * *
3392804 TCCATACCAACCATTGATGGGTTGGGTTGTCTGTTTAGACCTGAATTTTGAGAGGATTTTGACAA
323 TCCATACCAACCATTGATGGGTTGAGTTATCCGATCAGACCTAAATTTTGAGAGGATTTTGACAA
*
3392869 AAATATTAGGTCAGAAAAATGAGCTTAGATAAAAAAATTAGGTCTATTTAAAATAAGGGTTGGGC
388 AAATATTAGGTCAGAAAAATGAGCTTAGACAAAAAAATTAGGTCTATTTAAAATAAGGGTTGGGC
* *
3392934 TTGGGCTTGAACATTCAAGTCTCAAGCTCGGCCCA-GCTCGATCC-TTTTTTAAAATTTCTAATG
453 TCGGGCTTGAACATTCAAGTCCCAAGCTCGG-CCAGGCTCGATCCATTTTTT-AAATTTCTAATG
3392997 CAGAA
516 CAGAA
*
3393002 ATTTATTATGCTTTAAATGTTTCCATAAAAATTTAAAATAATATATTATATTTCCATAATCTATA
1 ATTTATTATGCTTTAAATGTTTCCATAAAAATATAAAATAATATATTATATTTCCATAATCTATA
** * ** *
3393067 ATCGACCAGTTTATTTTTTTGAACAATTTCATTACAGGTTCTGATCATATCAGCTCTTTTTGACA
66 ATCGACCAAATT-TTTTTTTGAACAATTTCACTACAAATTCTGATCATATCAGCTATTTTTGACA
* * * *
3393132 CAATACCTATAACTGCTCAT-A-GC-C-CAACCAACAAATACTATATATCTTAATTAACATAAAA
130 CAATACCTAAAACTACCCATAACCCTCTCAACCAACAAATACTATATATCTTAATTAACATAAAA
* *
3393193 CATTAAGTTCAAAATTAATTTG-TTT-TTATTAT-CGTAGCTAAAATCAAATTACGAAATTTTTA
195 CATTAAGTTCAAAATCAATTTGTTTTATTATTATACATAGCTAAAATCAAATTACGAAATTTTTA
3393255 GGGAAACAAAATAAATGTTTTACTAATTTTTTTAAAATCAAAAAAAATTGAAAGGGAAGGGTAGG
260 GGGAAACAAAATAAATGTTTTACTAATTTTTTTAAAATC-AAAAAAA-TGAAAGGGAAGGGTAGG
* * * *
3393320 TCCATACCAACCGTTGATGGGTTGAGTTATCCGATCATACCTAAATTTTTATAGGATTTTGACAA
323 TCCATACCAACCATTGATGGGTTGAGTTATCCGATCAGACCTAAATTTTGAGAGGATTTTGACAA
*
3393385 AAATATTAGGTCGGAAAAATGAGCTTA-AGCAAAAAAATTAGGTCTATTTAAAATAAGGGTTGGG
388 AAATATTAGGTCAGAAAAATGAGCTTAGA-CAAAAAAATTAGGTCTATTTAAAATAAGGGTTGGG
*
3393449 CTCGGGCTTGAACATTCAAGTCCCAAGCTTGGCCAGGCTCGATCCATTTTTTAAATTTCTAATGC
452 CTCGGGCTTGAACATTCAAGTCCCAAGCTCGGCCAGGCTCGATCCATTTTTTAAATTTCTAATGC
3393514 TTTATATTAT
Statistics
Matches: 462, Mismatches: 44, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
514 65 0.14
515 17 0.04
516 186 0.40
517 6 0.01
518 56 0.12
519 1 0.00
521 1 0.00
523 72 0.16
524 58 0.13
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (520 bp):
ATTTATTATGCTTTAAATGTTTCCATAAAAATATAAAATAATATATTATATTTCCATAATCTATA
ATCGACCAAATTTTTTTTTGAACAATTTCACTACAAATTCTGATCATATCAGCTATTTTTGACAC
AATACCTAAAACTACCCATAACCCTCTCAACCAACAAATACTATATATCTTAATTAACATAAAAC
ATTAAGTTCAAAATCAATTTGTTTTATTATTATACATAGCTAAAATCAAATTACGAAATTTTTAG
GGAAACAAAATAAATGTTTTACTAATTTTTTTAAAATCAAAAAAATGAAAGGGAAGGGTAGGTCC
ATACCAACCATTGATGGGTTGAGTTATCCGATCAGACCTAAATTTTGAGAGGATTTTGACAAAAA
TATTAGGTCAGAAAAATGAGCTTAGACAAAAAAATTAGGTCTATTTAAAATAAGGGTTGGGCTCG
GGCTTGAACATTCAAGTCCCAAGCTCGGCCAGGCTCGATCCATTTTTTAAATTTCTAATGCAGAA
Found at i:3393669 original size:15 final size:17
Alignment explanation
Indices: 3393630--3393662 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3393620 GACTATATGT
3393630 AAAAT-TATAATAAATA
1 AAAATATATAATAAATA
3393646 AAAATATATAA-AAATA
1 AAAATATATAATAAATA
3393662 A
1 A
3393663 TATATATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATATATAATAAATA
Found at i:3395355 original size:12 final size:12
Alignment explanation
Indices: 3395338--3395362 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3395328 TTAACAAGTT
3395338 GGATTTAAAAAG
1 GGATTTAAAAAG
3395350 GGATTTAAAAAG
1 GGATTTAAAAAG
3395362 G
1 G
3395363 ACCCTATGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (12 bp):
GGATTTAAAAAG
Found at i:3397797 original size:21 final size:20
Alignment explanation
Indices: 3397752--3397797 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
3397742 AAACCTCTCA
*
3397752 AATT-TTAAAAATTCTCATT
1 AATTCTTAAAAATTCTAATT
*
3397771 AA-TCTTATAAAATTTTAATT
1 AATTCTTA-AAAATTCTAATT
3397791 AATTCTT
1 AATTCTT
3397798 TAATCTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 1 0.05
19 5 0.23
20 12 0.55
21 4 0.18
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTCTTAAAAATTCTAATT
Found at i:3397805 original size:28 final size:28
Alignment explanation
Indices: 3397751--3397825 Score: 77
Period size: 26 Copynumber: 2.8 Consensus size: 28
3397741 TAAACCTCTC
3397751 AAATTTTAAAAATTCTCATTAATCTTATA
1 AAATTTTAAAAATTCT-ATTAATCTTATA
*
3397780 AAATTTTAATTAATTCT-TTAATC-T-TA
1 AAATTTTAA-AAATTCTATTAATCTTATA
**
3397806 ATTTTTTAAAAATT-TATTAA
1 AAATTTTAAAAATTCTATTAA
3397826 ATTTTACTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
24 1 0.03
25 8 0.20
26 9 0.22
27 1 0.03
28 6 0.15
29 9 0.22
30 6 0.15
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.51
Consensus pattern (28 bp):
AAATTTTAAAAATTCTATTAATCTTATA
Found at i:3403841 original size:104 final size:101
Alignment explanation
Indices: 3403646--3403894 Score: 331
Period size: 104 Copynumber: 2.4 Consensus size: 101
3403636 ATCAAATTCT
** *
3403646 TTTGGTGCTGGCCTGTCAATGGCTAGCACAAAGTACGAGATTTTAATTTTTTTTTTGGCCTTCTA
1 TTTGGTGCTGGCCTGTCAATGGCCGGCACAAGGTACGAGATTTTAATTTTTTTTTTGGCCTTCTA
3403711 ATGGTCGACACCAACATAAGTATTTAAAAAAAAAAA
66 ATGGTCGACACCAACATAAGTATTTAAAAAAAAAAA
* **
3403747 -TTGGTGCTGGCCTATCAATGGCCGGCATTAGGTACGAGATTTTAATTTTTTTTTGTTTTGGCCT
1 TTTGGTGCTGGCCTGTCAATGGCCGGCACAAGGTACGAGATTTTAA---TTTTTT-TTTTGGCCT
* * *
3403811 TCTAATGG-CTGGCACCAGCATGAGTATTTAAAAAAAAAAA
62 TCTAATGGTC-GACACCAACATAAGTATTTAAAAAAAAAAA
* *
3403851 TTTTGGTGCTGGCCTGTCAATGGTCGGCACCAGGTACGAGATTT
1 -TTTGGTGCTGGCCTGTCAATGGCCGGCACAAGGTACGAGATTT
3403895 AAAAAAAAAT
Statistics
Matches: 128, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
100 39 0.30
103 7 0.05
104 44 0.34
106 38 0.30
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.34
Consensus pattern (101 bp):
TTTGGTGCTGGCCTGTCAATGGCCGGCACAAGGTACGAGATTTTAATTTTTTTTTTGGCCTTCTA
ATGGTCGACACCAACATAAGTATTTAAAAAAAAAAA
Found at i:3404490 original size:31 final size:31
Alignment explanation
Indices: 3404452--3404520 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
3404442 ATGGTCACTA
* **
3404452 AACTATTCGTAAGTTTTCATTTAAGTTGTTG
1 AACTATTCGGAAGTTTTCATTTAAGTCATTG
*
3404483 AACTATTCGGAAGTTTTTATTTAAGTCATTG
1 AACTATTCGGAAGTTTTCATTTAAGTCATTG
3404514 AACTATT
1 AACTATT
3404521 GAACCCCAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.46
Consensus pattern (31 bp):
AACTATTCGGAAGTTTTCATTTAAGTCATTG
Found at i:3407904 original size:19 final size:19
Alignment explanation
Indices: 3407880--3407917 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3407870 TGCAAGAGTA
3407880 TGTGGCTTCGAGACTGTTG
1 TGTGGCTTCGAGACTGTTG
3407899 TGTGGCTTCGAGACTGTTG
1 TGTGGCTTCGAGACTGTTG
3407918 AAACGCATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.16, G:0.37, T:0.37
Consensus pattern (19 bp):
TGTGGCTTCGAGACTGTTG
Found at i:3408170 original size:14 final size:14
Alignment explanation
Indices: 3408136--3408173 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3408126 AGTTTATTTC
3408136 ATTAAATA-AAAAA
1 ATTAAATATAAAAA
*
3408149 ATTAAAATATAATAA
1 ATT-AAATATAAAAA
3408164 ATTAAATATA
1 ATTAAATATA
3408174 TTTAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 3 0.14
14 12 0.55
15 7 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATTAAATATAAAAA
Found at i:3415533 original size:24 final size:22
Alignment explanation
Indices: 3415487--3415534 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
3415477 TCTAAATTCC
* *
3415487 AAATATATTATTTTTTTTTTTG
1 AAATATATTATTTTTTGTATTG
3415509 AAATATATTGATTTATTTGTATTG
1 AAATATATT-ATTT-TTTGTATTG
3415533 AA
1 AA
3415535 TTAGACAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 9 0.41
23 4 0.18
24 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (22 bp):
AAATATATTATTTTTTGTATTG
Found at i:3418582 original size:17 final size:17
Alignment explanation
Indices: 3418560--3418606 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
3418550 AGTTCATGTT
* *
3418560 AATTTTGGGTTTGAATC
1 AATTTTAGGTTCGAATC
3418577 AATTTTAGGTTCGAAT-
1 AATTTTAGGTTCGAATC
* *
3418593 AACTTTAAGTTCGA
1 AATTTTAGGTTCGA
3418607 GCCATTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.43
Consensus pattern (17 bp):
AATTTTAGGTTCGAATC
Found at i:3420051 original size:18 final size:18
Alignment explanation
Indices: 3420030--3420079 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
3420020 TAAAAATATT
*
3420030 TATTTTATATTATTTTAC
1 TATTTTATATTATTATAC
*
3420048 TATTTAATAATT-TTATAC
1 TATTTTAT-ATTATTATAC
*
3420066 TTTTTTAT-TTATTA
1 TATTTTATATTATTA
3420080 AAATTTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
16 2 0.08
17 3 0.12
18 18 0.69
19 3 0.12
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTTATATTATTATAC
Found at i:3421540 original size:72 final size:72
Alignment explanation
Indices: 3421443--3421661 Score: 339
Period size: 72 Copynumber: 3.0 Consensus size: 72
3421433 AACCTCTTCC
* * * * * * *
3421443 ACCACCGGTTTATAAGCCTCATCCGGTGCCGGTCTACAAGAAACCACTCCCTCCACCGGTTCCTG
1 ACCACCGGTTTATAAGCCTCATCCGGTGCCGGTTTATAAGAAGCCGCTTCCACCGCCGGTTCCTG
3421508 TCTACAA
66 TCTACAA
* *
3421515 ACCACCGGTTTATAAGCCTCCTCCGGTGCCAGTTTATAAGAAGCCGCTTCCACCGCCGGTTCCTG
1 ACCACCGGTTTATAAGCCTCATCCGGTGCCGGTTTATAAGAAGCCGCTTCCACCGCCGGTTCCTG
3421580 TCTACAA
66 TCTACAA
*
3421587 ACCACCGGTTTATAAGCCTCATCCGGTGCCGGTTTATAAGAAGCCGCTTCCACCGCCGGTTCCTA
1 ACCACCGGTTTATAAGCCTCATCCGGTGCCGGTTTATAAGAAGCCGCTTCCACCGCCGGTTCCTG
*
3421652 TTTACAA
66 TCTACAA
3421659 ACC
1 ACC
3421662 GAAACCCTTC
Statistics
Matches: 134, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 134 1.00
ACGTcount: A:0.22, C:0.35, G:0.18, T:0.24
Consensus pattern (72 bp):
ACCACCGGTTTATAAGCCTCATCCGGTGCCGGTTTATAAGAAGCCGCTTCCACCGCCGGTTCCTG
TCTACAA
Found at i:3422882 original size:19 final size:19
Alignment explanation
Indices: 3422835--3422886 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
3422825 ATACAAGTTT
*
3422835 AAAGGCTAAAAA-AAAATA
1 AAAGACTAAAAATAAAATA
*
3422853 AAA-AGTAAAAAATAAAATA
1 AAAGACT-AAAAATAAAATA
3422872 AAAGACT-AAAATAAA
1 AAAGACTAAAAATAAA
3422887 TTTTTTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 1 0.04
18 16 0.57
19 9 0.32
20 2 0.07
ACGTcount: A:0.75, C:0.04, G:0.08, T:0.13
Consensus pattern (19 bp):
AAAGACTAAAAATAAAATA
Found at i:3423585 original size:16 final size:18
Alignment explanation
Indices: 3423550--3423587 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
3423540 TAAACATGTA
*
3423550 TTTTAATGCTTTTAATAT
1 TTTTAATGCTATTAATAT
3423568 TTTTAATG-TATT-ATAT
1 TTTTAATGCTATTAATAT
3423584 TTTT
1 TTTT
3423588 TAAAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 3 0.16
18 8 0.42
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTTAATGCTATTAATAT
Found at i:3427416 original size:3 final size:3
Alignment explanation
Indices: 3427357--3427534 Score: 205
Period size: 3 Copynumber: 58.0 Consensus size: 3
3427347 TTTTCATTGT
* * * * *
3427357 TTA TTC TTA TT- TTC TTA TTAA ATA TTC TTA TTA TTCA TATA ATA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TT-A T-TA TTA TTA
* * * * * *
3427404 GTA CTA TTA TTA TTA CTA TTG TTC TTA TTA TTA TTA TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3427452 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
3427498 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TGTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
3427535 GTTTATGTTT
Statistics
Matches: 150, Mismatches: 19, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.01
3 136 0.91
4 11 0.07
5 1 0.01
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3427757 original size:15 final size:15
Alignment explanation
Indices: 3427724--3427762 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3427714 TTTAATGTCG
*
3427724 TATTATTATGTTTTAA
1 TATTA-TATATTTTAA
*
3427740 TATTATATATTTTCA
1 TATTATATATTTTAA
3427755 TATTATAT
1 TATTATAT
3427763 TATATACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (15 bp):
TATTATATATTTTAA
Found at i:3434453 original size:46 final size:44
Alignment explanation
Indices: 3434401--3434486 Score: 136
Period size: 46 Copynumber: 1.9 Consensus size: 44
3434391 CAGAACGAAA
*
3434401 TGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGGAT
1 TGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAGACAGGAT
*
3434447 TGAGCCATGTAAGTCCATATTATATATGGCATTGGAGACA
1 TGAGCCATGTAAGTCCATATTAAATATGGCATTGGAGACA
3434487 AGAATAATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 17 0.45
46 21 0.55
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (44 bp):
TGAGCCATGTAAGTCCATATTAAATATGGCATTGGAGACAGGAT
Found at i:3434500 original size:44 final size:45
Alignment explanation
Indices: 3434403--3434527 Score: 135
Period size: 44 Copynumber: 2.8 Consensus size: 45
3434393 GAACGAAATG
* * * *
3434403 AGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGGATTG
1 AGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAAGAATA
*
3434449 AGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAAGAATA
1 AGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAAGAATA
** * * *
3434493 ATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
3434528 CAGGATATTG
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
44 35 0.53
45 1 0.02
46 30 0.45
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (45 bp):
AGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAAGAATA
Done.