Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 8 of 199
Found at i:2595450 original size:41 final size:41
Alignment explanation
Indices: 2595405--2595486 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
2595395 TTAAAGTGAT
* *
2595405 ATTTTCAAAAGTATTTTGATGTTATAAGCGAATTTTTTTAA
1 ATTTTCAAAAGTATTATGATGTTATAAGCCAATTTTTTTAA
2595446 ATTTTCAAAAGTATTATGATGTTATAAGCCAATTTTTTTAA
1 ATTTTCAAAAGTATTATGATGTTATAAGCCAATTTTTTTAA
2595487 CTCACAAACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.48
Consensus pattern (41 bp):
ATTTTCAAAAGTATTATGATGTTATAAGCCAATTTTTTTAA
Found at i:2596573 original size:49 final size:50
Alignment explanation
Indices: 2596516--2596633 Score: 143
Period size: 49 Copynumber: 2.4 Consensus size: 50
2596506 AACCCGTTAT
* * * *
2596516 CGTATAACCACTGTCAACTAGGG-G-CCTGAGTTATACTTGAATCCGTGAC
1 CGTATAACCACCGTCAACTAGGGAGCCCT-AGTTATACTTCAACCCATGAC
* *
2596565 TGTATAACCACCGTTAACT-GGGAGCCCTAGTTATACTTCAACCCATGAC
1 CGTATAACCACCGTCAACTAGGGAGCCCTAGTTATACTTCAACCCATGAC
*
2596614 CGTATAACCACCGTGAACTA
1 CGTATAACCACCGTCAACTA
2596634 AGAGCTTGAG
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
48 3 0.05
49 52 0.90
50 3 0.05
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (50 bp):
CGTATAACCACCGTCAACTAGGGAGCCCTAGTTATACTTCAACCCATGAC
Found at i:2604306 original size:59 final size:59
Alignment explanation
Indices: 2604233--2604378 Score: 152
Period size: 59 Copynumber: 2.5 Consensus size: 59
2604223 AGTTGTCAAA
* * *
2604233 TTCAAGTTCTAATGTGGGAATAGTTGT-TAAATTTAAGGCCTAACTTAAACC-ATAAAACT
1 TTCAAGCTCTAATGTGGGAATAGTTGTCT-AATTCAA-GCCTAACTTAAACCAAAAAAACT
** * *
2604292 TTCAAGCTCTAATGTGAAAATGGTTGTCTAATTCAAGCCTAACTTAGACCAAAAAAACT
1 TTCAAGCTCTAATGTGGGAATAGTTGTCTAATTCAAGCCTAACTTAAACCAAAAAAACT
* * * * *
2604351 TTGAAGCCCTAATATAGGTATAGTTGTC
1 TTCAAGCTCTAATGTGGGAATAGTTGTC
2604379 AAGTTCATGT
Statistics
Matches: 70, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
58 13 0.19
59 56 0.80
60 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (59 bp):
TTCAAGCTCTAATGTGGGAATAGTTGTCTAATTCAAGCCTAACTTAAACCAAAAAAACT
Found at i:2612819 original size:18 final size:17
Alignment explanation
Indices: 2612791--2612825 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2612781 ATTTTTAAGA
*
2612791 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
2612808 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
2612826 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:2613079 original size:16 final size:16
Alignment explanation
Indices: 2613058--2613096 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2613048 TTGATTTGCT
*
2613058 ATTACACAGCTTTTCC
1 ATTACACAGCTATTCC
**
2613074 ATTACACCTCTATTCC
1 ATTACACAGCTATTCC
2613090 ATTACAC
1 ATTACAC
2613097 CTCTAATCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACAGCTATTCC
Found at i:2613097 original size:16 final size:16
Alignment explanation
Indices: 2613071--2613127 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
2613061 ACACAGCTTT
* *
2613071 TCCATTACACCTCTAT
1 TCCAATACACCTCTAA
*
2613087 TCCATTACACCTCTAA
1 TCCAATACACCTCTAA
2613103 TCCAATACACCTCTAA
1 TCCAATACACCTCTAA
2613119 TCCAATACA
1 TCCAATACA
2613128 GCGAACCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (16 bp):
TCCAATACACCTCTAA
Found at i:2628773 original size:29 final size:29
Alignment explanation
Indices: 2628741--2628796 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
2628731 AAAGGCCGAT
2628741 TTTTTTCAA-AATTTACCGAAATGGGCCGG
1 TTTTTT-AATAATTTACCGAAATGGGCCGG
* *
2628770 TTTTTTAATTATTTACCGGAATGGGCC
1 TTTTTTAATAATTTACCGAAATGGGCC
2628797 ATTTTCCGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (29 bp):
TTTTTTAATAATTTACCGAAATGGGCCGG
Found at i:2628774 original size:30 final size:29
Alignment explanation
Indices: 2628734--2628801 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
2628724 AACCAAAAAA
2628734 GGCCGATTTTTTTCAA-AATTTACCGAAATG
1 GGCCGA-TTTTTT-AATAATTTACCGAAATG
* * *
2628764 GGCCGGTTTTTTAATTATTTACCGGAATG
1 GGCCGATTTTTTAATAATTTACCGAAATG
2628793 GGCC-ATTTT
1 GGCCGATTTT
2628802 CCGCGAAACC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 6 0.18
29 22 0.67
30 5 0.15
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (29 bp):
GGCCGATTTTTTAATAATTTACCGAAATG
Found at i:2630172 original size:22 final size:24
Alignment explanation
Indices: 2630146--2630189 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2630136 GAAAAATATT
2630146 AAATAT-ATA-TTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
2630168 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
2630190 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:2630319 original size:59 final size:59
Alignment explanation
Indices: 2630256--2630425 Score: 304
Period size: 59 Copynumber: 2.9 Consensus size: 59
2630246 TCAAGTTTGT
* *
2630256 TTTACTAATTAAATGTTAGATTTTGTTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
*
2630315 TTTACTAATCAAATGTTAGATTTTATTACAACAATCAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
*
2630374 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATT
2630426 AATAATTTGA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 106 1.00
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (59 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
Found at i:2630457 original size:16 final size:16
Alignment explanation
Indices: 2630436--2630477 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
2630426 AATAATTTGA
2630436 TAATTTTACA-AACAAT
1 TAATTTTA-ATAACAAT
2630452 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
2630468 TAGTTTTAAT
1 TAATTTTAAT
2630478 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 1 0.04
16 23 0.96
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:2630476 original size:22 final size:22
Alignment explanation
Indices: 2630451--2630512 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
2630441 TTACAAACAA
* * *
2630451 TTAATTTTAATAACAATTAGTT
1 TTAATTTTAATAAAAAATAATT
*
2630473 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
*
2630495 TTAATTTTAATTAAAAAT
1 TTAATTTTAATAAAAAAT
2630513 GGGCCGGGCC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:2632780 original size:31 final size:31
Alignment explanation
Indices: 2632739--2632808 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
2632729 CAAGTTAGTC
* *
2632739 CCTAAACTTGGTAATT-TGTCCCATATTGGGA
1 CCTAAACTTGGCAATTAT-TCCCACATTGGGA
* *
2632770 CCTGAACTTGGCAATTATTCCCACATTGGGG
1 CCTAAACTTGGCAATTATTCCCACATTGGGA
2632801 CCTAAACT
1 CCTAAACT
2632809 CTAGGGTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (31 bp):
CCTAAACTTGGCAATTATTCCCACATTGGGA
Found at i:2635441 original size:28 final size:28
Alignment explanation
Indices: 2635366--2635441 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 28
2635356 GTTATAAAAA
* *
2635366 AATTATATTAATTATATATATTAAATAAT
1 AATTATATTAATAATTTA-ATTAAATAAT
* * *
2635395 ATTTATATTAAATCA-TTAATTCAATAAT
1 AATTATATT-AATAATTTAATTAAATAAT
*
2635423 AATTAAATTAATAATTTAA
1 AATTATATTAATAATTTAA
2635442 AACCTAAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
27 4 0.11
28 20 0.53
29 10 0.26
30 4 0.11
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
AATTATATTAATAATTTAATTAAATAAT
Found at i:2638570 original size:13 final size:13
Alignment explanation
Indices: 2638548--2638577 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2638538 AAACTTAAAG
*
2638548 TAGGTGATCAAAA
1 TAGGTAATCAAAA
2638561 TAGGTAATCAAAA
1 TAGGTAATCAAAA
2638574 TAGG
1 TAGG
2638578 AACACGAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.07, G:0.23, T:0.23
Consensus pattern (13 bp):
TAGGTAATCAAAA
Found at i:2651393 original size:23 final size:23
Alignment explanation
Indices: 2651367--2651419 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
2651357 AGTATTAGTG
*
2651367 TTATATATAATTAT-ATTGGTTTA
1 TTATATATAATTATAATT-ATTTA
* *
2651390 TTATATATCATTTTAATTATTTA
1 TTATATATAATTATAATTATTTA
2651413 TTATATA
1 TTATATA
2651420 CCCATCTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (23 bp):
TTATATATAATTATAATTATTTA
Found at i:2657561 original size:52 final size:51
Alignment explanation
Indices: 2657490--2657936 Score: 599
Period size: 52 Copynumber: 9.0 Consensus size: 51
2657480 ATCAAGTGAC
* *
2657490 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-G
** * *
2657542 AAAGTGATAAGCAATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
2657588 AAAGTGATAAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGAT-AAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-G
*
2657641 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
*
2657692 AAAAGTGATAAGTGATAG----AGCTATACTTATCTGATCAAGTGAC-----
1 -AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
2657735 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* *
2657786 AAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 -AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
2657833 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-G
* *
2657885 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGATAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
2657936 A
1 A
2657937 TAGCTTCGGC
Statistics
Matches: 351, Mismatches: 20, Indels: 49
0.84 0.05 0.12
Matches are distributed among these distances:
42 17 0.05
46 76 0.22
47 34 0.10
48 23 0.07
51 3 0.01
52 190 0.54
53 8 0.02
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
Found at i:2657596 original size:98 final size:97
Alignment explanation
Indices: 2657476--2657936 Score: 541
Period size: 98 Copynumber: 4.7 Consensus size: 97
2657466 TTTGAGTACT
* *
2657476 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-
** * *
2657541 GAAAGTGATAAGCAATAGCTTCGGCTATACTTA
65 GAAAGTGATAAGTGATAGCTTCAGCTACACTTA
2657574 TCTGATCAAGTGACAAAGTGATAAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT
1 TCTGATCAAGTGACAAAGTGAT-AAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT
*
2657639 GGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
65 -GAAAGTGATAAGTGATAGCTTCAGCTACACTTA
* * *
2657673 TCTGATCAAGTGAC-AAGTGAAAAGTGATAAG-TGATAGAGCTATACTTATCTGATCAAGTGAC-
1 TCTGATCAAGTGACAAAGTGATAAGTGAT-AGCT--T-CAGCTACACTTATCTGATCAAGTGACA
2657735 ----AAAGTGATAAGTGATAGCTTCAGCTACACTTA
62 AGTGAAAGTGATAAGTGATAGCTTCAGCTACACTTA
* *
2657767 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
2657832 C-----AAAGTGATAAGTGATAGCTTCAGCTACACTTA
60 CAAGTGAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
2657865 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
*
2657930 TAAGTGA
60 CAAGTGA
2657937 TAGCTTCGGC
Statistics
Matches: 330, Mismatches: 15, Indels: 31
0.88 0.04 0.08
Matches are distributed among these distances:
94 45 0.14
97 8 0.02
98 149 0.45
99 87 0.26
100 26 0.08
101 14 0.04
103 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (97 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
AAAGTGATAAGTGATAGCTTCAGCTACACTTA
Found at i:2657977 original size:46 final size:46
Alignment explanation
Indices: 2657787--2658018 Score: 237
Period size: 46 Copynumber: 5.3 Consensus size: 46
2657777 TGACAAGTGA
* **
2657787 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAAAC
* *
2657833 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAA--GA-AA---C
2657885 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT-------C
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAAAC
*
2657924 -AAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAAAC
2657969 AAAGTG---A-T-A-AG--T-GGCTACACTTATCTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAAAC
2658006 AAAGTGATAAGTG
1 AAAGTGATAAGTG
2658019 GCTACACTTA
Statistics
Matches: 158, Mismatches: 9, Indels: 42
0.76 0.04 0.20
Matches are distributed among these distances:
37 30 0.19
38 37 0.23
40 3 0.02
41 2 0.01
42 1 0.01
43 1 0.01
45 1 0.01
46 44 0.28
48 1 0.01
49 1 0.01
52 37 0.23
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAAAC
Found at i:2657994 original size:37 final size:37
Alignment explanation
Indices: 2657906--2658053 Score: 187
Period size: 37 Copynumber: 4.0 Consensus size: 37
2657896 TGATAGCTTC
** *
2657906 GGCTACACTTATCTGATCAAGTGA-TAAGTGAT-AGCTT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAG--T
*
2657943 CGGCTATACTTATCTGATCAAGAAACAAAGTGATAAGT
1 -GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
2657981 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
**
2658018 GGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
2658053 G
1 G
2658054 ATCATACGTA
Statistics
Matches: 101, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
35 12 0.12
36 4 0.04
37 54 0.53
38 22 0.22
39 7 0.07
40 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
Found at i:2659660 original size:39 final size:38
Alignment explanation
Indices: 2659579--2659705 Score: 123
Period size: 45 Copynumber: 3.2 Consensus size: 38
2659569 ATTTTCCGGC
* * *
2659579 TTACTGATCAGGCAC-TTATGTGCCGACTAC-GTTACTG
1 TTACTGATC-GGCACTTTGTGTGTCGAATACTGTTACTG
2659616 TTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
1 TTACTGA-TCGGCACTTTGTGTGTCGAATACTGTTACTG
*
2659655 TTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGTTACCG
1 TTAC---T---GA-TCGGCACTTTGTGTGTCGAATACTGTTACTG
2659700 TTACTG
1 TTACTG
2659706 TTACAGATTC
Statistics
Matches: 76, Mismatches: 5, Indels: 16
0.78 0.05 0.16
Matches are distributed among these distances:
37 12 0.16
38 14 0.18
39 12 0.16
42 2 0.03
45 36 0.47
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (38 bp):
TTACTGATCGGCACTTTGTGTGTCGAATACTGTTACTG
Found at i:2659673 original size:45 final size:45
Alignment explanation
Indices: 2659609--2659757 Score: 203
Period size: 45 Copynumber: 3.4 Consensus size: 45
2659599 TGCCGACTAC
*
2659609 GTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGTTACT
1 GTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGTTACT
* * *
2659654 GTTACTGTTACCGACTCGGCACTTTGTGTGTCGAATACTGTTACC
1 GTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGTTACT
* *
2659699 GTTACTGTTACAGATTCAGCAC--TGTGTGTTGAATACTGTTACT
1 GTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGTTACT
* * *
2659742 GCTACCGTTACTGATT
1 GTTACTGTTACAGATT
2659758 ACTGTTTACT
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
43 32 0.34
45 61 0.66
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.39
Consensus pattern (45 bp):
GTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGTTACT
Found at i:2660273 original size:13 final size:15
Alignment explanation
Indices: 2660255--2660286 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2660245 TATAGGAAAT
2660255 AATGATT-TT-ATGA
1 AATGATTATTGATGA
2660268 AATGATTATTGATGA
1 AATGATTATTGATGA
2660283 AATG
1 AATG
2660287 CATGAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 2 0.12
15 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (15 bp):
AATGATTATTGATGA
Found at i:2665900 original size:18 final size:18
Alignment explanation
Indices: 2665879--2665915 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2665869 ATATGAAAAA
2665879 TTATACAAATGATATACT
1 TTATACAAATGATATACT
* *
2665897 TTATTCAAATTATATACT
1 TTATACAAATGATATACT
2665915 T
1 T
2665916 GATTAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.46
Consensus pattern (18 bp):
TTATACAAATGATATACT
Found at i:2665930 original size:17 final size:18
Alignment explanation
Indices: 2665884--2665923 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2665874 AAAAATTATA
* *
2665884 CAAATGATATACTTTATT
1 CAAATTATATACTTGATT
2665902 CAAATTATATACTTGATT
1 CAAATTATATACTTGATT
2665920 -AAAT
1 CAAAT
2665924 ATAATACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (18 bp):
CAAATTATATACTTGATT
Found at i:2666040 original size:27 final size:27
Alignment explanation
Indices: 2666010--2666339 Score: 192
Period size: 26 Copynumber: 13.4 Consensus size: 27
2666000 GAAAAAAATG
*
2666010 TAAATTAAAATGGAAAGAAAGATAATT
1 TAAATTGAAATGGAAAGAAAGATAATT
** *
2666037 TAAATAAAAATAGAAA-AAAG-TAAATT
1 TAAATTGAAATGGAAAGAAAGAT-AATT
*
2666063 TAAA-TGAAAT-G--AGAAA-A-AA-A
1 TAAATTGAAATGGAAAGAAAGATAATT
*
2666083 TAAATTAAAATGGAAAGAAAGATAATT
1 TAAATTGAAATGGAAAGAAAGATAATT
*
2666110 TAAA-TGAAAT-G--AGAAA-A-AAAT
1 TAAATTGAAATGGAAAGAAAGATAATT
*
2666131 TAAATTAAAATGGAAAGAAAGATAATT
1 TAAATTGAAATGGAAAGAAAGATAATT
*
2666158 TAAA-TGAAA--G-AAGAAA-A-AAAT
1 TAAATTGAAATGGAAAGAAAGATAATT
* * *
2666179 TAAATTTAAATGGGAAGATAGATAATT
1 TAAATTGAAATGGAAAGAAAGATAATT
2666206 TAAA-TGAAAT--AATA-AAA-A-AA-T
1 TAAATTGAAATGGAA-AGAAAGATAATT
* * *
2666227 TAAATTAAAATGGGAAGATAGATAATT
1 TAAATTGAAATGGAAAGAAAGATAATT
* * *
2666254 TAAA-TGAAAT-GAGAGAAA-AAAAAT
1 TAAATTGAAATGGAAAGAAAGATAATT
* * *
2666278 TAAATTTAAATGGGAAGATAGATAATT
1 TAAATTGAAATGGAAAGAAAGATAATT
2666305 TAAA-TGAAATGAGAAA-AAA-A-AATT
1 TAAATTGAAATG-GAAAGAAAGATAATT
2666329 TAAA-TGAAATG
1 TAAATTGAAATG
2666340 AAACTGAAAT
Statistics
Matches: 232, Mismatches: 37, Indels: 71
0.68 0.11 0.21
Matches are distributed among these distances:
20 4 0.02
21 26 0.11
22 20 0.09
23 17 0.07
24 37 0.16
25 30 0.13
26 50 0.22
27 48 0.21
ACGTcount: A:0.61, C:0.00, G:0.15, T:0.24
Consensus pattern (27 bp):
TAAATTGAAATGGAAAGAAAGATAATT
Found at i:2666094 original size:21 final size:21
Alignment explanation
Indices: 2666069--2666182 Score: 74
Period size: 21 Copynumber: 5.1 Consensus size: 21
2666059 AATTTAAATG
2666069 AAATGAGAAAAAAATAAATTA
1 AAATGAGAAAAAAATAAATTA
*
2666090 AAATG-GAAAGAAAGATAATTTAAA
1 AAATGAGAAA-AAA-ATAAATT--A
2666114 TGAAATGAGAAAAAAATTAAATTA
1 --AAATGAGAAAAAAA-TAAATTA
*
2666138 AAATG-GAAAGAAAGAT-AATTT
1 AAATGAGAAA-AAA-ATAAATTA
*
2666159 AAATGA-AAGAAGAAAAAAATTA
1 AAATGAGAA-AA-AAATAAATTA
2666181 AA
1 AA
2666183 TTTAAATGGG
Statistics
Matches: 74, Mismatches: 5, Indels: 27
0.70 0.05 0.25
Matches are distributed among these distances:
20 4 0.05
21 25 0.34
22 24 0.32
23 1 0.01
24 2 0.03
25 1 0.01
26 13 0.18
27 4 0.05
ACGTcount: A:0.66, C:0.00, G:0.14, T:0.20
Consensus pattern (21 bp):
AAATGAGAAAAAAATAAATTA
Found at i:2666147 original size:48 final size:48
Alignment explanation
Indices: 2666036--2666324 Score: 397
Period size: 48 Copynumber: 6.0 Consensus size: 48
2666026 GAAAGATAAT
* *
2666036 TTAAATAAAAATAGAAA-AAAG-TAAATTTAAATGAAATGAGAAAAAAA
1 TTAAATTAAAATGGAAAGAAAGAT-AATTTAAATGAAATGAGAAAAAAA
2666083 -TAAATTAAAATGGAAAGAAAGATAATTTAAATGAAATGAGAAAAAAA
1 TTAAATTAAAATGGAAAGAAAGATAATTTAAATGAAATGAGAAAAAAA
2666130 TTAAATTAAAATGGAAAGAAAGATAATTTAAATGAAA-GAAGAAAAAAA
1 TTAAATTAAAATGGAAAGAAAGATAATTTAAATGAAATG-AGAAAAAAA
* * * * *
2666178 TTAAATTTAAATGGGAAGATAGATAATTTAAATGAAATAATAAAAAAA
1 TTAAATTAAAATGGAAAGAAAGATAATTTAAATGAAATGAGAAAAAAA
* *
2666226 TTAAATTAAAATGGGAAGATAGATAATTTAAATGAAATGAGAGAAAAAAAA
1 TTAAATTAAAATGGAAAGAAAGATAATTTAAATGAAAT--GAG-AAAAAAA
* * *
2666277 TTAAATTTAAATGGGAAGATAGATAATTTAAATGAAATGAGAAAAAAA
1 TTAAATTAAAATGGAAAGAAAGATAATTTAAATGAAATGAGAAAAAAA
2666325 AATTTAAATG
Statistics
Matches: 223, Mismatches: 11, Indels: 15
0.90 0.04 0.06
Matches are distributed among these distances:
46 14 0.06
47 29 0.13
48 132 0.59
49 3 0.01
50 1 0.00
51 44 0.20
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.24
Consensus pattern (48 bp):
TTAAATTAAAATGGAAAGAAAGATAATTTAAATGAAATGAGAAAAAAA
Found at i:2666328 original size:96 final size:96
Alignment explanation
Indices: 2666037--2666377 Score: 398
Period size: 96 Copynumber: 3.6 Consensus size: 96
2666027 AAAGATAATT
* * * *
2666037 TAAATAAAAATAGAAA-AAAG-TAAATTTAAATGAAAT--GAGAAAAAAA-TAAATTAAAATGGA
1 TAAATTAAAATGGAAAGAAAGAT-AATTTAAATGAAATGAGAGAAAAAAATTAAATTTAAATGGG
*
2666097 AAGAAAGATAATTTAAATGAAATGAGAAAAAAA
65 AAGATAGATAATTTAAATGAAATGAG-AAAAAA
2666130 TTAAATTAAAATGGAAAGAAAGATAATTTAAATGAAA-GA-AGAAAAAAATTAAATTTAAATGGG
1 -TAAATTAAAATGGAAAGAAAGATAATTTAAATGAAATGAGAGAAAAAAATTAAATTTAAATGGG
* *
2666193 AAGATAGATAATTTAAATGAAATAATAAAAAAA
65 AAGATAGATAATTTAAATGAAATGA-GAAAAAA
* *
2666226 TTAAATTAAAATGGGAAGATAGATAATTTAAATGAAATGAGAGAAAAAAAATTAAATTTAAATGG
1 -TAAATTAAAATGGAAAGAAAGATAATTTAAATGAAATGAGAG-AAAAAAATTAAATTTAAATGG
2666291 GAAGATAGATAATTTAAATGAAATGAGAAAAAA
64 GAAGATAGATAATTTAAATGAAATGAGAAAAAA
* ** * *
2666324 -AAATTTAAAT-GAAATGAAACTGA-AATAGAAATGAAATGA-AAAAAAAAATGAAAT
1 TAAATTAAAATGGAAA-GAAA--GATAATTTAAATGAAATGAGAGAAAAAAATTAAAT
2666378 GACATCTTAG
Statistics
Matches: 217, Mismatches: 18, Indels: 23
0.84 0.07 0.09
Matches are distributed among these distances:
94 14 0.06
95 41 0.19
96 90 0.41
97 16 0.07
98 10 0.05
99 46 0.21
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.23
Consensus pattern (96 bp):
TAAATTAAAATGGAAAGAAAGATAATTTAAATGAAATGAGAGAAAAAAATTAAATTTAAATGGGA
AGATAGATAATTTAAATGAAATGAGAAAAAA
Found at i:2666347 original size:11 final size:10
Alignment explanation
Indices: 2666330--2666364 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 10
2666320 AAAAAAATTT
2666330 AAATGAAATG
1 AAATGAAATG
2666340 AAACTGAAATAG
1 AAA-TGAAAT-G
2666352 AAATGAAATG
1 AAATGAAATG
2666362 AAA
1 AAA
2666365 AAAAAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 7 0.30
11 12 0.52
12 4 0.17
ACGTcount: A:0.63, C:0.03, G:0.17, T:0.17
Consensus pattern (10 bp):
AAATGAAATG
Found at i:2666349 original size:22 final size:22
Alignment explanation
Indices: 2666001--2666379 Score: 133
Period size: 22 Copynumber: 15.7 Consensus size: 22
2665991 AATTAATATG
* *
2666001 AAAAAAATGTAAATTAAAATGGAA
1 AAAAAAATTTAAA-TGAAAT-GAA
*
2666025 AGAAAGATAATTTAAATAAAAATAGAA
1 A-AAA-A-AATTTAAAT-GAAAT-GAA
*
2666052 AAAAGTAAATTTAAATGAAATGAG
1 AAAA--AAATTTAAATGAAATGAA
*
2666076 AAAAAAA--TAAATTAAAATGGAA
1 AAAAAAATTTAAA-TGAAAT-GAA
*
2666098 AGAAAGATAATTTAAATGAAATGAG
1 A-AAA-A-AATTTAAATGAAATGAA
*
2666123 AAAAAAA-TTAAATTAAAATGGAA
1 AAAAAAATTTAAA-TGAAAT-GAA
2666146 AGAAAGATAATTTAAATGAAA-GAA
1 A-AAA-A-AATTTAAATGAAATGAA
*
2666170 GAAAAAAA-TTAAATTTAAATGGGAA
1 -AAAAAAATTTAAA-TGAAAT--GAA
* *
2666195 GATAGATAATTTAAATGAAAT-AA
1 -A-AAAAAATTTAAATGAAATGAA
*
2666218 TAAAAAAA-TTAAATTAAAATGGGAA
1 -AAAAAAATTTAAA-TGAAAT--GAA
* *
2666243 GATAGATAATTTAAATGAAATGAGA
1 -A-AAAAAATTTAAATGAAATGA-A
* *
2666268 GAAAAAAAATTAAATTTAAATGGGAA
1 -AAAAAAATTTAAA-TGAAAT--GAA
* *
2666294 GATAGATAATTTAAATGAAATGAGAA
1 -A-AAAAAATTTAAATGAAAT--GAA
2666320 AAAAAAATTTAAATGAAATGAA
1 AAAAAAATTTAAATGAAATGAA
*** **
2666342 ACTGAAATAGAAATGAAATGAA
1 AAAAAAATTTAAATGAAATGAA
* *
2666364 AAAAAAAATGAAATGA
1 AAAAAAATTTAAATGA
2666380 CATCTTAGAC
Statistics
Matches: 274, Mismatches: 45, Indels: 74
0.70 0.11 0.19
Matches are distributed among these distances:
20 4 0.01
21 20 0.07
22 59 0.22
23 11 0.04
24 47 0.17
25 31 0.11
26 55 0.20
27 47 0.17
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (22 bp):
AAAAAAATTTAAATGAAATGAA
Found at i:2666367 original size:144 final size:142
Alignment explanation
Indices: 2666064--2666370 Score: 390
Period size: 147 Copynumber: 2.1 Consensus size: 142
2666054 AAGTAAATTT
2666064 AAATGAAATGAGAAAAAAATAAATTAAAATGGAAAGAAAGATAATTTAAATGAAATGAGAAAAAA
1 AAATGAAATGAGAAAAAAATAAATTAAAATGGAAAGAAAGATAATTTAAATGAAATGAGAAAAAA
* *
2666129 ATTAAATTAAAATGGAAAGAAAGATAATTTAAATGAAAGAAGAAAAAAATTAAATTTAAATGGGA
66 ATTAAATTAAAATGGAAAGAAAGATAATTTAAATGAAAGAAAAAAAAAATTAAATTGAAAT-GGA
**
2666194 AGATAGATAATTT
130 AGATAGATAATAG
* * * *
2666207 AAATGAAATAATAAAAAAATTAAATTAAAATGGGAAGATAGATAATTTAAATGAAATGAGAGAAA
1 AAATGAAATGAGAAAAAAA-TAAATTAAAATGGAAAGAAAGATAATTTAAATGAAAT--GAG-AA
* * *
2666272 AAAAATTAAATTTAAATGGGAAGATAGATAATTTAAATGAAATGAGAAAAAAAAATTTAAA-TGA
62 AAAAATTAAATTAAAATGGAAAGAAAGATAATTTAAATGAAA-GA-AAAAAAAAA-TTAAATTGA
2666336 AAT-GAA-ACT-GA-AATAG
124 AATGGAAGA-TAGATAATAG
*
2666352 AAATGAAATGAAAAAAAAA
1 AAATGAAATGAGAAAAAAA
2666371 ATGAAATGAC
Statistics
Matches: 143, Mismatches: 13, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
143 17 0.12
144 35 0.24
145 20 0.14
146 6 0.04
147 45 0.31
148 2 0.01
149 13 0.09
150 5 0.03
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (142 bp):
AAATGAAATGAGAAAAAAATAAATTAAAATGGAAAGAAAGATAATTTAAATGAAATGAGAAAAAA
ATTAAATTAAAATGGAAAGAAAGATAATTTAAATGAAAGAAAAAAAAAATTAAATTGAAATGGAA
GATAGATAATAG
Found at i:2666379 original size:5 final size:5
Alignment explanation
Indices: 2666330--2666364 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
2666320 AAAAAAATTT
2666330 AAATG AAATG AAACTG AAATAG AAATG AAATG AAA
1 AAATG AAATG AAA-TG AAAT-G AAATG AAATG AAA
2666365 AAAAAAATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 18 0.64
6 10 0.36
ACGTcount: A:0.63, C:0.03, G:0.17, T:0.17
Consensus pattern (5 bp):
AAATG
Found at i:2666653 original size:5 final size:5
Alignment explanation
Indices: 2666645--2666766 Score: 59
Period size: 5 Copynumber: 22.4 Consensus size: 5
2666635 AAAAAAGATT
* *
2666645 AATGA AATGA AATGTTA AATGAA ATATGA ATATGA AATGA AATGTA ATTTGT
1 AATGA AATGA AATG--A AATG-A A-ATGA A-ATGA AATGA AATG-A A-ATGA
* * *
2666697 AATGA ATATAA AATGA AATGA GATGTTA AATGA ATATAA AATGA AATG-
1 AATGA A-ATGA AATGA AATGA AATG--A AATGA A-ATGA AATGA AATGA
* *
2666745 -ATGA TTATGA AATGG AATGA AA
1 AATGA -AATGA AATGA AATGA AA
2666767 GTTTAAATGA
Statistics
Matches: 91, Mismatches: 14, Indels: 24
0.71 0.11 0.19
Matches are distributed among these distances:
3 3 0.03
5 49 0.54
6 25 0.27
7 14 0.15
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (5 bp):
AATGA
Found at i:2666701 original size:35 final size:33
Alignment explanation
Indices: 2666645--2666745 Score: 106
Period size: 28 Copynumber: 3.2 Consensus size: 33
2666635 AAAAAAGATT
* *
2666645 AATGAAATGAAATGTTAAATGAAATATGAATATGA
1 AATGAAATGTAATGTTAAATG-AATAT-AAAATGA
*
2666680 AATGAAATGTAAT-TTGTAATGAATATAAAATGA
1 AATGAAATGTAATGTT-AAATGAATATAAAATGA
2666713 AATG--A-G--ATGTTAAATGAATATAAAATGA
1 AATGAAATGTAATGTTAAATGAATATAAAATGA
2666741 AATGA
1 AATGA
2666746 TGATTATGAA
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
28 22 0.37
29 2 0.03
30 1 0.02
31 1 0.02
33 10 0.17
34 7 0.12
35 16 0.27
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.30
Consensus pattern (33 bp):
AATGAAATGTAATGTTAAATGAATATAAAATGA
Found at i:2666882 original size:5 final size:5
Alignment explanation
Indices: 2666872--2666948 Score: 50
Period size: 5 Copynumber: 14.6 Consensus size: 5
2666862 AAATAAATTT
*
2666872 AAATG AAATG AAAATG AAAATAC AAATG AAATG AAAATG AAA-- AAATG
1 AAATG AAATG -AAATG -AAAT-G AAATG AAATG -AAATG AAATG AAATG
* * *
2666919 AAATG AATTGG AAATAT AAATA AAATG AAA
1 AAATG AAAT-G AAAT-G AAATG AAATG AAA
2666949 AAAAAAAGTT
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
3 3 0.05
5 28 0.48
6 27 0.47
ACGTcount: A:0.65, C:0.01, G:0.14, T:0.19
Consensus pattern (5 bp):
AAATG
Found at i:2666884 original size:23 final size:23
Alignment explanation
Indices: 2666872--2666948 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
2666862 AAATAAATTT
*
2666872 AAATGAAATGAAAATGAAAATAC
1 AAATGAAATGAAAATAAAAATAC
*
2666895 AAATGAAATGAAAATGAAAAA-ATG
1 AAATGAAATGAAAAT-AAAAATA-C
* * *
2666919 AAATGAATTGGAAATATAAATA-
1 AAATGAAATGAAAATAAAAATAC
2666941 AAATGAAA
1 AAATGAAA
2666949 AAAAAAAGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
22 7 0.16
23 20 0.44
24 18 0.40
ACGTcount: A:0.65, C:0.01, G:0.14, T:0.19
Consensus pattern (23 bp):
AAATGAAATGAAAATAAAAATAC
Found at i:2666949 original size:6 final size:6
Alignment explanation
Indices: 2666872--2666914 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
2666862 AAATAAATTT
2666872 AAATG- AAATGA AAATGA AAAT-A CAAATG- AAATGA AAATGA AAA
1 AAATGA AAATGA AAATGA AAATGA -AAATGA AAATGA AAATGA AAA
2666915 AATGAAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
5 11 0.32
6 23 0.68
ACGTcount: A:0.67, C:0.02, G:0.14, T:0.16
Consensus pattern (6 bp):
AAATGA
Found at i:2666962 original size:41 final size:41
Alignment explanation
Indices: 2666872--2666955 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 41
2666862 AAATAAATTT
*
2666872 AAATGAAATGAAAATGAAAATACAAATGAAATGAAAATGAAA
1 AAATGAAATGAAAATGAAAATACAAATAAAATGAAAA-GAAA
* * *
2666914 AAATGAAATG-AATTGGAAATATAAATAAAATGAAAA-AAA
1 AAATGAAATGAAAATGAAAATACAAATAAAATGAAAAGAAA
2666953 AAA
1 AAA
2666956 GTTGAAAGGA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 6 0.16
41 22 0.58
42 10 0.26
ACGTcount: A:0.68, C:0.01, G:0.13, T:0.18
Consensus pattern (41 bp):
AAATGAAATGAAAATGAAAATACAAATAAAATGAAAAGAAA
Found at i:2667340 original size:21 final size:19
Alignment explanation
Indices: 2667298--2667349 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 19
2667288 TTTATATTTA
2667298 AATATTTTTTAAAAATAAT
1 AATATTTTTTAAAAATAAT
2667317 AATATTTTATTCAAAAA-AATT
1 AATATTTT-TT-AAAAATAA-T
2667338 AATATTTTTTAA
1 AATATTTTTTAA
2667350 TTCATTGGCG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 10 0.33
20 6 0.20
21 14 0.47
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
AATATTTTTTAAAAATAAT
Found at i:2667347 original size:23 final size:24
Alignment explanation
Indices: 2667308--2667353 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
2667298 AATATTTTTT
2667308 AAAAATAATAATATTTT-ATTCAA
1 AAAAATAATAATATTTTAATTCAA
*
2667331 AAAAATTAAT-ATTTTTTAATTCA
1 AAAAA-TAATAATATTTTAATTCA
2667354 TTGGCGCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAAATAATAATATTTTAATTCAA
Found at i:2668552 original size:17 final size:17
Alignment explanation
Indices: 2668530--2668564 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2668520 GGGGAATATT
*
2668530 AATATTTCTTATAGATA
1 AATATTTATTATAGATA
*
2668547 AATATTTATTATGGATA
1 AATATTTATTATAGATA
2668564 A
1 A
2668565 TTTGTATTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.46
Consensus pattern (17 bp):
AATATTTATTATAGATA
Found at i:2672041 original size:15 final size:15
Alignment explanation
Indices: 2672010--2672046 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2672000 ATTTTATTTT
2672010 AAATAA-ATAATATA
1 AAATAATATAATATA
2672024 AAATAATATAAT-TCA
1 AAATAATATAATAT-A
2672039 AAATAATA
1 AAATAATA
2672047 ACTATAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATAATATAATATA
Found at i:2682007 original size:22 final size:22
Alignment explanation
Indices: 2681982--2682042 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
2681972 TATTAAACAG
2681982 AGAGCACTAAAGTGCTATACAA
1 AGAGCACTAAAGTGCTATACAA
*
2682004 AGAGCAC-AAATGTGCTATACAG
1 AGAGCACTAAA-GTGCTATACAA
*
2682026 AGAGCACTAATGTGCTA
1 AGAGCACTAAAGTGCTA
2682043 ATAATCGGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 3 0.09
22 30 0.86
23 2 0.06
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.20
Consensus pattern (22 bp):
AGAGCACTAAAGTGCTATACAA
Found at i:2682058 original size:25 final size:25
Alignment explanation
Indices: 2681979--2682152 Score: 122
Period size: 25 Copynumber: 7.4 Consensus size: 25
2681969 CACTATTAAA
*
2681979 CAGAGAGCACTAAAGTGCT-AT-A-
1 CAGAGAGCACTAATGTGCTAATAAT
* *
2682001 CAAAGAGCACAAATGTGCT-AT-A-
1 CAGAGAGCACTAATGTGCTAATAAT
2682023 CAGAGAGCACTAATGTGCTAATAAT
1 CAGAGAGCACTAATGTGCTAATAAT
* *
2682048 CGGAGAGCACTAACGTGCTAGA-AAT
1 CAGAGAGCACTAATGTGCTA-ATAAT
* *
2682073 CAGAGAG--C-GA-GT--TAGTAAT
1 CAGAGAGCACTAATGTGCTAATAAT
* * * *
2682092 CAGAGAGCACTGACGTGCTAATGAC
1 CAGAGAGCACTAATGTGCTAATAAT
* *
2682117 CAGAGAGCATTGATGTGCTAATAAT
1 CAGAGAGCACTAATGTGCTAATAAT
*
2682142 TAGAGAGCACT
1 CAGAGAGCACT
2682153 CTAAACTCCC
Statistics
Matches: 122, Mismatches: 19, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
19 12 0.10
21 3 0.02
22 39 0.32
23 5 0.04
24 1 0.01
25 61 0.50
26 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (25 bp):
CAGAGAGCACTAATGTGCTAATAAT
Found at i:2688064 original size:180 final size:180
Alignment explanation
Indices: 2687762--2688122 Score: 713
Period size: 180 Copynumber: 2.0 Consensus size: 180
2687752 CTCTCTTCGA
2687762 TCATCATTCTCCCCCATCTTGTTGAATCAAATCTTTATTTTAAAAAAATGGGAATTCTGTCAGAA
1 TCATCATTCTCCCCCATCTTGTTGAATCAAATCTTTATTTTAAAAAAATGGGAATTCTGTCAGAA
2687827 ATGAGGGATGTTTGGGTACAGAGAAGAGCAAAGTTCTTCATAATTCCTTCTCCCGCTGAAGACCA
66 ATGAGGGATGTTTGGGTACAGAGAAGAGCAAAGTTCTTCATAATTCCTTCTCCCGCTGAAGACCA
2687892 GAAGAAATTGAGAGCCCAGCAATCCTCCCAAGGTTTTTTTTTTTTTTGGC
131 GAAGAAATTGAGAGCCCAGCAATCCTCCCAAGGTTTTTTTTTTTTTTGGC
*
2687942 TCATCATTCTCCCCCATCTTGTTGAATCAAATCTTTATTTTAAAAAAGTGGGAATTCTGTCAGAA
1 TCATCATTCTCCCCCATCTTGTTGAATCAAATCTTTATTTTAAAAAAATGGGAATTCTGTCAGAA
2688007 ATGAGGGATGTTTGGGTACAGAGAAGAGCAAAGTTCTTCATAATTCCTTCTCCCGCTGAAGACCA
66 ATGAGGGATGTTTGGGTACAGAGAAGAGCAAAGTTCTTCATAATTCCTTCTCCCGCTGAAGACCA
2688072 GAAGAAATTGAGAGCCCAGCAATCCTCCCAAGGTTTTTTTTTTTTTTGGC
131 GAAGAAATTGAGAGCCCAGCAATCCTCCCAAGGTTTTTTTTTTTTTTGGC
2688122 T
1 T
2688123 TTGAATCTTT
Statistics
Matches: 180, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
180 180 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (180 bp):
TCATCATTCTCCCCCATCTTGTTGAATCAAATCTTTATTTTAAAAAAATGGGAATTCTGTCAGAA
ATGAGGGATGTTTGGGTACAGAGAAGAGCAAAGTTCTTCATAATTCCTTCTCCCGCTGAAGACCA
GAAGAAATTGAGAGCCCAGCAATCCTCCCAAGGTTTTTTTTTTTTTTGGC
Found at i:2708964 original size:7 final size:7
Alignment explanation
Indices: 2708954--2708987 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
2708944 TTTTACCATT
2708954 TATTTTA
1 TATTTTA
2708961 TATTTTA
1 TATTTTA
2708968 TATTTTA
1 TATTTTA
2708975 TATTTTA
1 TATTTTA
2708982 TATTTT
1 TATTTT
2708988 TCTTTTTTTC
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TATTTTA
Found at i:2711855 original size:46 final size:45
Alignment explanation
Indices: 2711788--2712113 Score: 359
Period size: 46 Copynumber: 7.6 Consensus size: 45
2711778 TTTGAGTACT
* * *
2711788 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGTTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
2711834 TCTGATCAAGTGAAAAAGTGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
2711870 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
2711916 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
2711952 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
*
2711998 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* * *
2712044 TCTGATCAAGTGACAAAGTGATAAGTGATAGCCTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
2712089 TCTGATC-AG-GGACAAGTGATAAGTG
1 TCTGATCAAGTGAAAAAGTGATAAGTG
2712114 ATCATACGTA
Statistics
Matches: 243, Mismatches: 17, Indels: 43
0.80 0.06 0.14
Matches are distributed among these distances:
36 57 0.23
37 2 0.01
38 1 0.00
39 1 0.00
40 5 0.02
41 1 0.00
42 6 0.02
43 15 0.06
44 3 0.01
45 22 0.09
46 130 0.53
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:2711867 original size:36 final size:36
Alignment explanation
Indices: 2711826--2711978 Score: 180
Period size: 36 Copynumber: 4.0 Consensus size: 36
2711816 TAGCTTTAGT
2711826 TACACTTATCTGATCAAGTGAAAAAGTGATAAGTGC
1 TACACTTATCTGATCAAGTGAAAAAGTGATAAGTGC
* *
2711862 TACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGC
1 TACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T-GC
2711908 TACACTTATCTGATCAAGTGAAAAAGTGATAAGTGC
1 TACACTTATCTGATCAAGTGAAAAAGTGATAAGTGC
* *
2711944 TATACTTATCTGATCAAGTGACAAAGTGATAAGTG
1 TACACTTATCTGATCAAGTGAAAAAGTGATAAGTG
2711979 TTAGCCTTAG
Statistics
Matches: 101, Mismatches: 6, Indels: 20
0.80 0.05 0.16
Matches are distributed among these distances:
36 63 0.62
37 2 0.02
40 2 0.02
42 2 0.02
45 2 0.02
46 30 0.30
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (36 bp):
TACACTTATCTGATCAAGTGAAAAAGTGATAAGTGC
Found at i:2711925 original size:82 final size:82
Alignment explanation
Indices: 2711788--2712113 Score: 433
Period size: 82 Copynumber: 3.9 Consensus size: 82
2711778 TTTGAGTACT
* *
2711788 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGTTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
2711853 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
2711870 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
2711935 GATAAGTGCTATACTTA
66 GATAAGTGCTACACTTA
* * * *
2711952 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTGATCAAGTGAGAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
2712017 GATAAGTGGTAGCCTTAGCTACACTTA
66 GAT-A-----AG---T-GCTACACTTA
* * * * *
2712044 TCTGATCAAGTGACAAAGTGATAAGTGATAGC-CTAGCTACACTTATCTGATC-AG-GGACAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
2712106 GATAAGTG
66 GATAAGTG
2712114 ATCATACGTA
Statistics
Matches: 221, Mismatches: 13, Indels: 23
0.86 0.05 0.09
Matches are distributed among these distances:
79 1 0.00
80 1 0.00
82 143 0.65
83 3 0.01
88 3 0.01
89 8 0.04
90 2 0.01
91 20 0.09
92 40 0.18
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (82 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTACACTTA
Found at i:2712106 original size:128 final size:126
Alignment explanation
Indices: 2711788--2712113 Score: 358
Period size: 128 Copynumber: 2.6 Consensus size: 126
2711778 TTTGAGTACT
* * * * *
2711788 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGTTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGAAAAAGTGATAAGTGATAGC-TTAGCTACACTTATCTGATCAAG-GGAAAAGT
*
2711853 GATAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
64 GATAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
* * * ** * *
2711916 TCTGATCAAGTGAAAAAGTGATAAGTGCTATA-CTTATCT-GA-TCAAGTGA-CAAAGTGATAAG
1 TCTGATCAAGTGAAAAAGTGATAAGTG--ATAGCTTAGCTACACTTATCTGATC-AAGGGAAAAG
* * *
2711977 TG-TTAGCCTTAGCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACAC
63 TGATAAG---T-GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACAC
2712041 TTA
124 TTA
* * *
2712044 TCTGATCAAGTGACAAAGTGATAAGTGATAGCCTAGCTACACTTATCTGATC-AGGGACAAGTGA
1 TCTGATCAAGTGAAAAAGTGATAAGTGATAGCTTAGCTACACTTATCTGATCAAGGGAAAAGTGA
2712108 TAAGTG
66 TAAGTG
2712114 ATCATACGTA
Statistics
Matches: 160, Mismatches: 26, Indels: 27
0.75 0.12 0.13
Matches are distributed among these distances:
124 3 0.02
125 8 0.05
126 12 0.08
127 7 0.04
128 118 0.74
129 9 0.06
130 3 0.02
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (126 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGATAGCTTAGCTACACTTATCTGATCAAGGGAAAAGTGA
TAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
Found at i:2713815 original size:15 final size:17
Alignment explanation
Indices: 2713795--2713829 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
2713785 ACATTGTGTG
2713795 AAAAATAAA-T-AAAAC
1 AAAAATAAATTAAAAAC
2713810 AAAAATAAATTAAAAAC
1 AAAAATAAATTAAAAAC
2713827 AAA
1 AAA
2713830 TTAACTAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 1 0.06
17 8 0.44
ACGTcount: A:0.80, C:0.06, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAAATAAATTAAAAAC
Found at i:2722277 original size:29 final size:31
Alignment explanation
Indices: 2722240--2722304 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
2722230 ATAGTTCATA
*
2722240 TACCACATTAGATA-TTT-TCAAAGTATATG
1 TACCACATTAGATACTTTATCAAAGTATAGG
* *
2722269 TACCACATTGGATACTTTATGAAAGTATAGG
1 TACCACATTAGATACTTTATCAAAGTATAGG
2722300 TACCA
1 TACCA
2722305 TAATAAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 13 0.42
30 3 0.10
31 15 0.48
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (31 bp):
TACCACATTAGATACTTTATCAAAGTATAGG
Found at i:2722369 original size:92 final size:92
Alignment explanation
Indices: 2722212--2722390 Score: 270
Period size: 92 Copynumber: 1.9 Consensus size: 92
2722202 ATCAAATACT
* *
2722212 ATAATAAAACACATATTGATAGTTCATATACCACATTAGATATTTTCAAAGTATATGTACCACAT
1 ATAATAAAACACATATTGATAGTTCAAATACCACATTAGATATTTTCAAAGTACATGTACCACAT
* *
2722277 TGGATACTTTATGAAAGTATAGGTACC
66 TGAACACTTTATGAAAGTATAGGTACC
* *
2722304 ATAATAAAATACATATTGATAGTTCAAATATCACATT-GAATATTTTCAAAGTACATGTACCACA
1 ATAATAAAACACATATTGATAGTTCAAATACCACATTAG-ATATTTTCAAAGTACATGTACCACA
* *
2722368 TTGAACATTTTATGAATGTATAG
65 TTGAACACTTTATGAAAGTATAG
2722391 ATACTAAATG
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
91 1 0.01
92 77 0.99
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (92 bp):
ATAATAAAACACATATTGATAGTTCAAATACCACATTAGATATTTTCAAAGTACATGTACCACAT
TGAACACTTTATGAAAGTATAGGTACC
Found at i:2723281 original size:29 final size:31
Alignment explanation
Indices: 2723211--2723282 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 31
2723201 TTTTTGAAAC
* *
2723211 TGTGTATAGTTGAACCAAAATCAAAATTTTA
1 TGTGTATAATTGAACCAAAATCAAAATTTCA
** * *
2723242 TGTGTGCAATT-AACC-AAATTAAAGTTTCA
1 TGTGTATAATTGAACCAAAATCAAAATTTCA
2723271 TGTGTATAATTG
1 TGTGTATAATTG
2723283 CATCAAATTG
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
29 20 0.62
30 4 0.12
31 8 0.25
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (31 bp):
TGTGTATAATTGAACCAAAATCAAAATTTCA
Found at i:2723808 original size:18 final size:17
Alignment explanation
Indices: 2723777--2723814 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
2723767 TCACATGTCC
2723777 TATTTTCTTATATATAT
1 TATTTTCTTATATATAT
*
2723794 TATTTTTTTACTATATAT
1 TATTTTCTTA-TATATAT
2723812 TAT
1 TAT
2723815 ATACACTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTTCTTATATATAT
Found at i:2733890 original size:16 final size:14
Alignment explanation
Indices: 2733869--2733902 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 14
2733859 TATAATTTTT
2733869 TTATAAATATTATATA
1 TTATAAA-ATT-TATA
2733885 TTATAAAATTTATA
1 TTATAAAATTTATA
2733899 TTAT
1 TTAT
2733903 TTTTGATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 3 0.17
16 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTATAAAATTTATA
Found at i:2733894 original size:36 final size:37
Alignment explanation
Indices: 2733853--2733929 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
2733843 AAAGTTTTGG
*
2733853 AAAATTTATAATT-TTTTT-A-TAAATATTATATATTAT
1 AAAATTTAT-ATTATTTTTGATTAAAT-TTACATATTAT
*
2733889 AAAATTTATATTATTTTTGATTTAATTTACATATTAT
1 AAAATTTATATTATTTTTGATTAAATTTACATATTAT
2733926 AAAA
1 AAAA
2733930 AGGAATTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
35 3 0.08
36 14 0.39
37 15 0.42
38 4 0.11
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (37 bp):
AAAATTTATATTATTTTTGATTAAATTTACATATTAT
Found at i:2738766 original size:25 final size:23
Alignment explanation
Indices: 2738722--2738776 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
2738712 AATATATTAA
*
2738722 ATTAAAAAATAATTAATTATTCT
1 ATTAAAAAATAATTAATTATACT
* *
2738745 ATTAAAAAATTCATTTATTTATACT
1 ATTAAAAAA-T-AATTAATTATACT
2738770 ATTAAAA
1 ATTAAAA
2738777 GCTGATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 9 0.33
24 1 0.04
25 17 0.63
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTAAAAAATAATTAATTATACT
Found at i:2750724 original size:27 final size:28
Alignment explanation
Indices: 2750694--2750752 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
2750684 ACACACCCGG
2750694 AATAATAT-AAATCCT-CCATAACACACC
1 AATAATATCAAATCCTCCCA-AACACACC
*
2750721 AAT-ATATCATATCCTCCCAAACACACC
1 AATAATATCAAATCCTCCCAAACACACC
2750748 AATAA
1 AATAA
2750753 GGCATTAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 4 0.14
27 20 0.71
28 4 0.14
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (28 bp):
AATAATATCAAATCCTCCCAAACACACC
Found at i:2751044 original size:24 final size:23
Alignment explanation
Indices: 2751000--2751046 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
2750990 TATTCACACA
2751000 TATTATTACTTAATTTCAAATGT
1 TATTATTACTTAATTTCAAATGT
*
2751023 TATTACTTACCTTACTTT-AAATGT
1 TATTA-TTA-CTTAATTTCAAATGT
2751047 CCCATGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 9 0.43
25 7 0.33
ACGTcount: A:0.32, C:0.13, G:0.04, T:0.51
Consensus pattern (23 bp):
TATTATTACTTAATTTCAAATGT
Found at i:2751321 original size:22 final size:24
Alignment explanation
Indices: 2751279--2751322 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
2751269 TAACCAAGCT
2751279 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTCTAACTTAATTCA
2751303 TACTT-CTTTTCT-ACTTAATT
1 TACTTACTTTTCTAACTTAATT
2751323 TCTTGCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTCTAACTTAATTCA
Found at i:2751700 original size:22 final size:20
Alignment explanation
Indices: 2751675--2751729 Score: 51
Period size: 22 Copynumber: 2.6 Consensus size: 20
2751665 TCTTCCGCTG
2751675 TTTTCGTCTTTTTCTCTGTTTC
1 TTTTCGTCTTTTT-T-TGTTTC
*
2751697 TTTTCTGTTCTTCTTTTGTTTC
1 TTTTC-G-TCTTTTTTTGTTTC
2751719 -TTT-GTCTTTTT
1 TTTTCGTCTTTTT
2751730 ATTTTACTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 6 0.21
19 1 0.03
21 3 0.10
22 11 0.38
23 2 0.07
24 6 0.21
ACGTcount: A:0.00, C:0.18, G:0.09, T:0.73
Consensus pattern (20 bp):
TTTTCGTCTTTTTTTGTTTC
Found at i:2753771 original size:59 final size:59
Alignment explanation
Indices: 2753699--2753817 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
2753689 TGAAAGAATC
2753699 AAATGAACAAGATCACCATGTAAAATGGAAGATATTTCTACAAACTATTTATAATTCCT
1 AAATGAACAAGATCACCATGTAAAATGGAAGATATTTCTACAAACTATTTATAATTCCT
2753758 AAATGAACAAGATCACCATGTAAAATGGAAGATATTTCTACAAACTATTTATAATTCCT
1 AAATGAACAAGATCACCATGTAAAATGGAAGATATTTCTACAAACTATTTATAATTCCT
2753817 A
1 A
2753818 TACATGGTTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (59 bp):
AAATGAACAAGATCACCATGTAAAATGGAAGATATTTCTACAAACTATTTATAATTCCT
Found at i:2755109 original size:32 final size:32
Alignment explanation
Indices: 2755068--2755135 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
2755058 AAAAACCCGA
2755068 TCAAACATTTTAAAAAAGAACACCAGAATGGT
1 TCAAACATTTTAAAAAAGAACACCAGAATGGT
2755100 TCAAACATTTTAAAAAAGAACACCAGAATGGT
1 TCAAACATTTTAAAAAAGAACACCAGAATGGT
2755132 TCAA
1 TCAA
2755136 TCTCAAGGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.22
Consensus pattern (32 bp):
TCAAACATTTTAAAAAAGAACACCAGAATGGT
Found at i:2759546 original size:13 final size:13
Alignment explanation
Indices: 2759530--2759554 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2759520 ATTTTATTTA
2759530 AAGAATTTAATTG
1 AAGAATTTAATTG
2759543 AAGAATTTAATT
1 AAGAATTTAATT
2759555 TATTAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (13 bp):
AAGAATTTAATTG
Found at i:2759932 original size:25 final size:23
Alignment explanation
Indices: 2759904--2759959 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
2759894 AAAATAAGTA
*
2759904 AAATAATTATAAATTTATAAAATAG
1 AAATAATTA-AAA-ATATAAAATAG
* *
2759929 AAATTATTAAAAATATAAAATAT
1 AAATAATTAAAAATATAAAATAG
*
2759952 AAAAAATT
1 AAATAATT
2759960 GTATTAAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 15 0.58
24 3 0.12
25 8 0.31
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (23 bp):
AAATAATTAAAAATATAAAATAG
Found at i:2759939 original size:23 final size:22
Alignment explanation
Indices: 2759908--2759950 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2759898 TAAGTAAAAT
**
2759908 AATTATAAATTTATAAAATAGA
1 AATTATAAAAATATAAAATAGA
2759930 AATTATTAAAAATATAAAATA
1 AATTA-TAAAAATATAAAATA
2759951 TAAAAAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
AATTATAAAAATATAAAATAGA
Found at i:2760309 original size:18 final size:18
Alignment explanation
Indices: 2760271--2760354 Score: 68
Period size: 18 Copynumber: 4.7 Consensus size: 18
2760261 ATTTTTTAAT
2760271 ATTTTATAA-ATATT-AATA
1 ATTTTATAATAT-TTCAA-A
*
2760289 ATTTTATAATCTTTCAAA
1 ATTTTATAATATTTCAAA
**
2760307 ATTTTATGTTATTTCAAA
1 ATTTTATAATATTTCAAA
*
2760325 ATTTTTATAATGTTT-AATA
1 A-TTTTATAATATTTCAA-A
2760344 A-TTTATAATAT
1 ATTTTATAATAT
2760355 ATTTTTAATG
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
17 9 0.17
18 30 0.56
19 15 0.28
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTTTATAATATTTCAAA
Found at i:2779081 original size:89 final size:89
Alignment explanation
Indices: 2778930--2779109 Score: 360
Period size: 89 Copynumber: 2.0 Consensus size: 89
2778920 CCTTTATTGT
2778930 CATTTCAAGTTTTTTCTTGCTAAAAAGGCTTCTCCAATCCCTCTAAAAAAATTCGGAGTAATTTA
1 CATTTCAAGTTTTTTCTTGCTAAAAAGGCTTCTCCAATCCCTCTAAAAAAATTCGGAGTAATTTA
2778995 ATTTCTATCAATTTCGAAAGTGAG
66 ATTTCTATCAATTTCGAAAGTGAG
2779019 CATTTCAAGTTTTTTCTTGCTAAAAAGGCTTCTCCAATCCCTCTAAAAAAATTCGGAGTAATTTA
1 CATTTCAAGTTTTTTCTTGCTAAAAAGGCTTCTCCAATCCCTCTAAAAAAATTCGGAGTAATTTA
2779084 ATTTCTATCAATTTCGAAAGTGAG
66 ATTTCTATCAATTTCGAAAGTGAG
2779108 CA
1 CA
2779110 GTTAAGGATA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 91 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (89 bp):
CATTTCAAGTTTTTTCTTGCTAAAAAGGCTTCTCCAATCCCTCTAAAAAAATTCGGAGTAATTTA
ATTTCTATCAATTTCGAAAGTGAG
Found at i:2782384 original size:21 final size:21
Alignment explanation
Indices: 2782358--2782399 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2782348 AGAAAGAAAG
2782358 AACATTCTTGAGTTTTCTTAT
1 AACATTCTTGAGTTTTCTTAT
2782379 AACATTCTTGAGTTTTCTTAT
1 AACATTCTTGAGTTTTCTTAT
2782400 CCTTCATAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.10, T:0.52
Consensus pattern (21 bp):
AACATTCTTGAGTTTTCTTAT
Found at i:2784112 original size:120 final size:121
Alignment explanation
Indices: 2783860--2784117 Score: 475
Period size: 121 Copynumber: 2.1 Consensus size: 121
2783850 TAAGAGAAAA
2783860 TTACACTCTTTTTTTTTAATAATTTCGAAAGCCTTCCTTTTCCTTGAATTATTTAGTTTTTATTT
1 TTACACTC-TTTTTTTTAATAATTTCGAAAGCCTTCCTTTTCCTTGAATTATTTAGTTTTTATTT
2783925 ACCGGAGAAGCTATGGACAAAAAAGTAGGGTTTATTTTAAAATGTAAATTAACATTT
65 ACCGGAGAAGCTATGGACAAAAAAGTAGGGTTTATTTTAAAATGTAAATTAACATTT
2783982 TTACACTCTTTTTTTTAATAATTTCGAAAGCCTTCCTTTTCCTTGAATTATTTAGTTTTTATTTA
1 TTACACTCTTTTTTTTAATAATTTCGAAAGCCTTCCTTTTCCTTGAATTATTTAGTTTTTATTTA
2784047 CCGGAGAAGCTATGGACAAAAAAGTA-GGTTTATTTTAAAATGTAAATTAACATTT
66 CCGGAGAAGCTATGGACAAAAAAGTAGGGTTTATTTTAAAATGTAAATTAACATTT
*
2784102 TTATC-TTCTTTTTTTT
1 TTA-CACTCTTTTTTTT
2784118 TTTTTGTAAG
Statistics
Matches: 134, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
120 42 0.31
121 84 0.63
122 8 0.06
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (121 bp):
TTACACTCTTTTTTTTAATAATTTCGAAAGCCTTCCTTTTCCTTGAATTATTTAGTTTTTATTTA
CCGGAGAAGCTATGGACAAAAAAGTAGGGTTTATTTTAAAATGTAAATTAACATTT
Found at i:2784632 original size:29 final size:30
Alignment explanation
Indices: 2784595--2784688 Score: 77
Period size: 29 Copynumber: 3.1 Consensus size: 30
2784585 TGTCTTTATA
*
2784595 TTTATTTTTATAAAAAT-TTTATTGAATTT
1 TTTAATTTTATAAAAATATTTATTGAATTT
* *
2784624 TTTAATTTTTTAAAAATATTT-TT-AATAGTA
1 TTTAATTTTATAAAAATATTTATTGAAT--TT
* * *
2784654 TATAATTTTTATAAAAATGTTTAGTTGATTTT
1 TTTAA-TTTTATAAAAATATTTA-TTGAATTT
2784686 TTT
1 TTT
2784689 TTTGAATTTG
Statistics
Matches: 49, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
28 3 0.06
29 17 0.35
30 8 0.16
31 14 0.29
32 3 0.06
33 2 0.04
34 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (30 bp):
TTTAATTTTATAAAAATATTTATTGAATTT
Found at i:2788594 original size:19 final size:19
Alignment explanation
Indices: 2788571--2788622 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
2788561 AAATTACAAA
2788571 AAAAATTCAAAATAGTTT-T
1 AAAAATTCAAAATA-TTTAT
* *
2788590 TAAAATTAAAAATATTTAT
1 AAAAATTCAAAATATTTAT
2788609 AAAAATTTCAAAAT
1 AAAAA-TTCAAAAT
2788623 TTATATATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 3 0.11
19 17 0.63
20 7 0.26
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:2788666 original size:19 final size:19
Alignment explanation
Indices: 2788630--2788666 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2788620 AATTTATATA
*
2788630 TTTTAAAAAATATATAAAT
1 TTTTAAAAAAAATATAAAT
*
2788649 TTTTAAAAAAAATCTAAA
1 TTTTAAAAAAAATATAAA
2788667 GAATATATAA
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:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
TTTTAAAAAAAATATAAAT
Found at i:2799540 original size:28 final size:28
Alignment explanation
Indices: 2799493--2799609 Score: 91
Period size: 28 Copynumber: 4.2 Consensus size: 28
2799483 TTAAAATTCT
* *
2799493 AATT-TAAAAAAAGT-ATAAATTATAAA
1 AATTATAAAAAAATTAAAAAATTATAAA
2799519 AATTATAAAAAAATTAAAAAATTATAAA
1 AATTATAAAAAAATTAAAAAATTATAAA
* *
2799547 TTATTAT-AAAAAATTAAAAGA-TATATAA
1 -AATTATAAAAAAATTAAAAAATTATA-AA
* ** * *
2799575 ATTTATTAAAATTATTTAAATATTAT-AA
1 AATTA-TAAAAAAATTAAAAAATTATAAA
2799603 AATTATA
1 AATTATA
2799610 GATATGTAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 13
0.75 0.11 0.13
Matches are distributed among these distances:
26 4 0.05
27 18 0.25
28 33 0.45
29 15 0.21
30 3 0.04
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (28 bp):
AATTATAAAAAAATTAAAAAATTATAAA
Found at i:2799556 original size:20 final size:20
Alignment explanation
Indices: 2799509--2799562 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
2799499 AAAAAAGTAT
2799509 AAATTAT-AAAAATTATAAA
1 AAATTATAAAAAATTATAAA
*
2799528 AAAAT-TAAAAAATTATAAA
1 AAATTATAAAAAATTATAAA
**
2799547 TTATTATAAAAAATTA
1 AAATTATAAAAAATTA
2799563 AAAGATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 1 0.03
19 18 0.62
20 10 0.34
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATTATAAAAAATTATAAA
Found at i:2799558 original size:19 final size:20
Alignment explanation
Indices: 2799509--2799546 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
2799499 AAAAAAGTAT
2799509 AAATTATAAAAATTATAAAA
1 AAATTATAAAAATTATAAAA
2799529 AAATTA-AAAAATTATAAA
1 AAATTATAAAAATTATAAA
2799547 TTATTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATTATAAAAATTATAAAA
Found at i:2799573 original size:29 final size:30
Alignment explanation
Indices: 2799477--2799582 Score: 66
Period size: 29 Copynumber: 3.7 Consensus size: 30
2799467 TATTTAAGTA
*
2799477 AAAAAATTA-AAATTCTAATT-TAAAAAAAGT
1 AAAAAATTATAAATT-T-ATTATAAAAAAATT
* * * *
2799507 -ATAAATTATAAAAATTA-TA-AAAAAATTA
1 AAAAAATTAT-AAATTTATTATAAAAAAATT
2799535 AAAAA-TTATAAAT-TATTAT-AAAAAATT
1 AAAAAATTATAAATTTATTATAAAAAAATT
*
2799562 AAAAGATATATAAATTTATTA
1 AAAAAAT-TATAAATTTATTA
2799583 AAATTATTTA
Statistics
Matches: 57, Mismatches: 10, Indels: 18
0.67 0.12 0.21
Matches are distributed among these distances:
26 2 0.04
27 15 0.26
28 12 0.21
29 18 0.32
30 6 0.11
31 4 0.07
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (30 bp):
AAAAAATTATAAATTTATTATAAAAAAATT
Found at i:2799594 original size:19 final size:19
Alignment explanation
Indices: 2799515--2799652 Score: 79
Period size: 19 Copynumber: 6.9 Consensus size: 19
2799505 GTATAAATTA
* **
2799515 TAAAAATTATAAAAAAATT
1 TAAATATTATAAAATTATT
* *
2799534 AAAAAATTAT-AAATTATT
1 TAAATATTATAAAATTATT
* *
2799552 ATAAAAAATTA-AAAGA-TATA
1 -T-AAATATTATAAA-ATTATT
2799572 TAAAT-TTATTAAAATTATT
1 TAAATATTA-TAAAATTATT
2799591 TAAATATTATAAAATTATAGATAT
1 TAAATATTATAAAA-T-T--AT-T
2799615 GTAAAT-TTATTAAAATTATT
1 -TAAATATTA-TAAAATTATT
2799635 TAAATATTATAAAATTAT
1 TAAATATTATAAAATTAT
2799653 AAAATTTAAA
Statistics
Matches: 96, Mismatches: 7, Indels: 32
0.71 0.05 0.24
Matches are distributed among these distances:
17 3 0.03
18 10 0.10
19 40 0.42
20 21 0.22
21 4 0.04
23 3 0.03
24 5 0.05
25 10 0.10
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
TAAATATTATAAAATTATT
Found at i:2799607 original size:25 final size:25
Alignment explanation
Indices: 2799579--2799651 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
2799569 ATATAAATTT
2799579 ATTAAAATTATTTAAATATTATAAA
1 ATTAAAATTATTTAAATATTATAAA
* *
2799604 ATTATAGA-TATGT-AA-ATT-T---
1 ATTA-AAATTATTTAAATATTATAAA
2799623 ATTAAAATTATTTAAATATTATAAA
1 ATTAAAATTATTTAAATATTATAAA
2799648 ATTA
1 ATTA
2799652 TAAAATTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
18 2 0.06
19 8 0.22
20 2 0.06
21 3 0.08
22 2 0.06
23 3 0.08
24 2 0.06
25 12 0.33
26 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (25 bp):
ATTAAAATTATTTAAATATTATAAA
Found at i:2799620 original size:44 final size:44
Alignment explanation
Indices: 2799556--2799653 Score: 169
Period size: 44 Copynumber: 2.2 Consensus size: 44
2799546 ATTATTATAA
*
2799556 AAAATTAAAAGATATATAAATTTATTAAAATTATTTAAATATTAT
1 AAAATT-ATAGATATATAAATTTATTAAAATTATTTAAATATTAT
*
2799601 AAAATTATAGATATGTAAATTTATTAAAATTATTTAAATATTAT
1 AAAATTATAGATATATAAATTTATTAAAATTATTTAAATATTAT
2799645 AAAATTATA
1 AAAATTATA
2799654 AAATTTAAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 45 0.88
45 6 0.12
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (44 bp):
AAAATTATAGATATATAAATTTATTAAAATTATTTAAATATTAT
Found at i:2801518 original size:5 final size:6
Alignment explanation
Indices: 2801501--2801525 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2801491 TTATATATAG
2801501 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
2801526 AGACTTCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:2809656 original size:26 final size:25
Alignment explanation
Indices: 2809627--2809686 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 25
2809617 CCATTTTTTT
* *
2809627 AATAAACACCAAAAAGTTATTTTAAA
1 AATAAAAACAAAAAAG-TATTTTAAA
*
2809653 AATAAAAAATAAAAAAGTATTTTAAA
1 AAT-AAAAACAAAAAAGTATTTTAAA
2809679 AATAAAAA
1 AATAAAAA
2809687 ATAAAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 5 0.17
26 15 0.50
27 10 0.33
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.25
Consensus pattern (25 bp):
AATAAAAACAAAAAAGTATTTTAAA
Found at i:2809684 original size:6 final size:7
Alignment explanation
Indices: 2809650--2809698 Score: 53
Period size: 7 Copynumber: 6.3 Consensus size: 7
2809640 AAGTTATTTT
2809650 AAAAATA
1 AAAAATA
2809657 AAAAATA
1 AAAAATA
2809664 AAAAAGTA
1 AAAAA-TA
2809672 TTTTAAAAATA
1 ----AAAAATA
2809683 AAAAATA
1 AAAAATA
2809690 AAAAATA
1 AAAAATA
2809697 AA
1 AA
2809699 TATTTATTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
7 28 0.76
8 2 0.05
11 2 0.05
12 5 0.14
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (7 bp):
AAAAATA
Found at i:2809687 original size:26 final size:27
Alignment explanation
Indices: 2809637--2809694 Score: 109
Period size: 26 Copynumber: 2.2 Consensus size: 27
2809627 AATAAACACC
2809637 AAAAAGTTATTTTAAAAATAAAAAATA
1 AAAAAGTTATTTTAAAAATAAAAAATA
2809664 AAAAAG-TATTTTAAAAATAAAAAATA
1 AAAAAGTTATTTTAAAAATAAAAAATA
2809690 AAAAA
1 AAAAA
2809695 TAAATATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 25 0.81
27 6 0.19
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (27 bp):
AAAAAGTTATTTTAAAAATAAAAAATA
Found at i:2813194 original size:23 final size:23
Alignment explanation
Indices: 2813168--2813265 Score: 133
Period size: 23 Copynumber: 4.3 Consensus size: 23
2813158 GTGTTATTGA
*
2813168 TCAGTGGTAGCTTTGACTACATT
1 TCAGTGGTAGCTTCGACTACATT
* *
2813191 TCAGCGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTTCGACTACATT
*
2813214 TCAGTGGTAGCTACGACTACATT
1 TCAGTGGTAGCTTCGACTACATT
* * *
2813237 TCAGTGGTAGCTTTGGCTACATA
1 TCAGTGGTAGCTTCGACTACATT
2813260 TCAGTG
1 TCAGTG
2813266 TGACACTTAT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 65 1.00
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.34
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGACTACATT
Found at i:2813221 original size:46 final size:46
Alignment explanation
Indices: 2813167--2813265 Score: 153
Period size: 46 Copynumber: 2.2 Consensus size: 46
2813157 AGTGTTATTG
**
2813167 ATCAGTGGTAGCTTTGACTACATTTCAGCGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTACGACTACATTTCAGCGGTAGCTTCGGCTACAT
* * *
2813213 TTCAGTGGTAGCTACGACTACATTTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTACGACTACATTTCAGCGGTAGCTTCGGCTACAT
2813259 ATCAGTG
1 ATCAGTG
2813266 TGACACTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.33
Consensus pattern (46 bp):
ATCAGTGGTAGCTACGACTACATTTCAGCGGTAGCTTCGGCTACAT
Found at i:2815836 original size:9 final size:9
Alignment explanation
Indices: 2815822--2815865 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
2815812 ATATTTATTC
*
2815822 AATTAATTT
1 AATTAATTA
2815831 AATTAATTA
1 AATTAATTA
*
2815840 AACTAATTA
1 AATTAATTA
*
2815849 AATTAACTA
1 AATTAATTA
2815858 AATTAATT
1 AATTAATT
2815866 TCTCAATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (9 bp):
AATTAATTA
Found at i:2825956 original size:15 final size:16
Alignment explanation
Indices: 2825936--2825970 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2825926 AATAATTTAT
*
2825936 TAAAAATATT-TAAAA
1 TAAAAATATTAGAAAA
2825951 TAAAAATATTAGAAAA
1 TAAAAATATTAGAAAA
2825967 TAAA
1 TAAA
2825971 GAAAACCAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAATATTAGAAAA
Found at i:2830378 original size:16 final size:18
Alignment explanation
Indices: 2830346--2830378 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
2830336 CAATAAACAC
2830346 TATTTTATTACTTTAAAT
1 TATTTTATTACTTTAAAT
2830364 TATTTT-TTA-TTTAAA
1 TATTTTATTACTTTAAA
2830379 ACCAATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
TATTTTATTACTTTAAAT
Found at i:2830403 original size:23 final size:22
Alignment explanation
Indices: 2830362--2830407 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
2830352 ATTACTTTAA
2830362 ATTATTTTTTATTTAAAACCAAT
1 ATTATTTTTTATTTAAAA-CAAT
*
2830385 ATTA-TTTTTATTATGAAACAAT
1 ATTATTTTTTATT-TAAAACAAT
2830407 A
1 A
2830408 AAAACACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTATTTTTTATTTAAAACAAT
Found at i:2831840 original size:13 final size:13
Alignment explanation
Indices: 2831822--2831847 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2831812 ATATATCATC
2831822 ATATTATTTTTAT
1 ATATTATTTTTAT
2831835 ATATTATTTTTAT
1 ATATTATTTTTAT
2831848 TATAATTGTA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATATTATTTTTAT
Found at i:2832775 original size:15 final size:17
Alignment explanation
Indices: 2832745--2832777 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
2832735 TGTATTTATT
2832745 ATTTTATTTATAATTTA
1 ATTTTATTTATAATTTA
2832762 ATTTT-TTT-TAATTTA
1 ATTTTATTTATAATTTA
2832777 A
1 A
2832778 GAAAAAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 3 0.19
17 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTATTTATAATTTA
Found at i:2834570 original size:3 final size:3
Alignment explanation
Indices: 2834562--2834591 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2834552 GAAACATAAA
2834562 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
2834592 AATACAAGCT
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:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:2838028 original size:21 final size:21
Alignment explanation
Indices: 2838004--2838047 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2837994 TACAGACCTG
* *
2838004 AAGTTGAGTGCACGTTTGAGC
1 AAGTGGAGTGCAAGTTTGAGC
*
2838025 AAGTGGAGTGTAAGTTTGAGC
1 AAGTGGAGTGCAAGTTTGAGC
2838046 AA
1 AA
2838048 CACGTGTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.34, T:0.27
Consensus pattern (21 bp):
AAGTGGAGTGCAAGTTTGAGC
Found at i:2846361 original size:119 final size:118
Alignment explanation
Indices: 2846161--2846393 Score: 378
Period size: 119 Copynumber: 2.0 Consensus size: 118
2846151 TATTCATTAT
* *
2846161 GCTGGGCATTGGAAATGAAAAGAAGAATTTAATGGTATCCAGCTATTCTTGATTTGACTGGATAA
1 GCTGGGCATTGGAAATGAAAAGAAGAATATAATGGTATCCAGCTATTCTTGATTTGACTAGATAA
*
2846226 GGTAAGATTAGTTGCATTTATTTTTATTTTATTCTTTTGAACGGGATGGATATG
66 GGTAAGATTAGATGCATTTA-TTTTATTTTATTCTTTTGAACGGGATGGATATG
2846280 GCTGGGCATTGGAAATGAAAAGAAGAA-ATAGATGGTATCCAGCTATTCTTGATTTGACTAGATA
1 GCTGGGCATTGGAAATGAAAAGAAGAATATA-ATGGTATCCAGCTATTCTTGATTTGACTAGATA
* * * *
2846344 GGGTAGGATTTGATGCATTTATTTTATTTTTTTCTTTTGAACGGGATGGA
65 AGGTAAGATTAGATGCATTTATTTTATTTTATTCTTTTGAACGGGATGGA
2846394 CTATCTAGGC
Statistics
Matches: 106, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
118 30 0.28
119 76 0.72
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (118 bp):
GCTGGGCATTGGAAATGAAAAGAAGAATATAATGGTATCCAGCTATTCTTGATTTGACTAGATAA
GGTAAGATTAGATGCATTTATTTTATTTTATTCTTTTGAACGGGATGGATATG
Found at i:2848326 original size:18 final size:17
Alignment explanation
Indices: 2848293--2848331 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
2848283 TTGTATAAAT
2848293 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
2848311 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
2848328 TGTG
1 TGTG
2848332 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:2848426 original size:75 final size:75
Alignment explanation
Indices: 2848336--2848482 Score: 294
Period size: 75 Copynumber: 2.0 Consensus size: 75
2848326 AATGTGGAAG
2848336 GAAAGTTGTTCATGAATTATTCAAGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCC
1 GAAAGTTGTTCATGAATTATTCAAGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCC
2848401 GGTTGAAAAT
66 GGTTGAAAAT
2848411 GAAAGTTGTTCATGAATTATTCAAGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCC
1 GAAAGTTGTTCATGAATTATTCAAGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCC
2848476 GGTTGAA
66 GGTTGAA
2848483 CTTAGGAATA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (75 bp):
GAAAGTTGTTCATGAATTATTCAAGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCC
GGTTGAAAAT
Found at i:2848659 original size:23 final size:23
Alignment explanation
Indices: 2848632--2848706 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
2848622 AGTGTTATTG
*
2848632 ATCAGTGGTAGGTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
2848655 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
2848678 CT-AGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2848700 ATCAGTG
1 ATCAGTG
2848707 TGGCACTTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 20 0.44
23 25 0.56
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:2850558 original size:4 final size:4
Alignment explanation
Indices: 2850549--2850581 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
2850539 TCCATGCATC
2850549 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
2850582 TTGTTACTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:2851184 original size:14 final size:13
Alignment explanation
Indices: 2851167--2851204 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
2851157 TTATAAATAA
2851167 AAAGAAGAAGAAAG
1 AAAGAAGAA-AAAG
2851181 AAAGAACGAAAAAG
1 AAAGAA-GAAAAAG
2851195 AAA-AAGAAAA
1 AAAGAAGAAAA
2851205 TTTATACGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.22
13 2 0.09
14 13 0.57
15 3 0.13
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAGAAGAAAAAG
Found at i:2860577 original size:24 final size:23
Alignment explanation
Indices: 2860550--2860600 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
2860540 TTAGTAAGTC
*
2860550 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAAT-AATACT
* *
2860574 AAATATATTATACTAATAATACT
1 AAATAAACTATACTAATAATACT
2860597 AAAT
1 AAAT
2860601 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (23 bp):
AAATAAACTATACTAATAATACT
Found at i:2862553 original size:24 final size:24
Alignment explanation
Indices: 2862526--2862577 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2862516 TTAGTAAGTC
*
2862526 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
2862550 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
2862574 AAAT
1 AAAT
2862578 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:2879481 original size:17 final size:18
Alignment explanation
Indices: 2879459--2879495 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
2879449 ATTAAATCGC
2879459 ATTACATTGT-TTAAAAT
1 ATTACATTGTATTAAAAT
*
2879476 ATTACATTTTATTAAAAT
1 ATTACATTGTATTAAAAT
2879494 AT
1 AT
2879496 CGAAATAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (18 bp):
ATTACATTGTATTAAAAT
Found at i:2879778 original size:21 final size:21
Alignment explanation
Indices: 2879752--2879795 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
2879742 CTATGTTTGG
2879752 AATTTTGAGAAATTGTGCCCT
1 AATTTTGAGAAATTGTGCCCT
*
2879773 AATTTTGAGAAATTGTGCTCT
1 AATTTTGAGAAATTGTGCCCT
2879794 AA
1 AA
2879796 CAATTGAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (21 bp):
AATTTTGAGAAATTGTGCCCT
Found at i:2880488 original size:34 final size:35
Alignment explanation
Indices: 2880450--2880517 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 35
2880440 CCAGTAAAAT
*
2880450 ATTTTCCGTAAAATGATTT-CGGGAAAATGTTTTA
1 ATTTTCCGTAAAATGATTTACGGGAAAATATTTTA
* *
2880484 ATTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 ATTTTCCGTAAAATGATTTACGGGAAAATATTTT
2880518 CTGATGTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 18 0.60
35 12 0.40
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (35 bp):
ATTTTCCGTAAAATGATTTACGGGAAAATATTTTA
Found at i:2887556 original size:53 final size:53
Alignment explanation
Indices: 2887493--2887652 Score: 284
Period size: 53 Copynumber: 3.0 Consensus size: 53
2887483 CAATTAGATA
2887493 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
1 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
2887546 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
1 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
* * * *
2887599 TGCCATGAGCATTGATAACAATACATGGTAACAGTGTGACCATGTCCATAAGC
1 TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
2887652 T
1 T
2887653 ATGTAATCAA
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 103 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (53 bp):
TGCCATGAGCATTGATAACAATACATAGTAACAGTGTAACTATATCCATAAGC
Found at i:2889937 original size:8 final size:8
Alignment explanation
Indices: 2889924--2889959 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
2889914 ATAACATACT
2889924 TTTTTATA
1 TTTTTATA
2889932 TTTTTATA
1 TTTTTATA
2889940 TTTTTTATA
1 -TTTTTATA
2889949 TTTTTA-A
1 TTTTTATA
2889956 TTTT
1 TTTT
2889960 ATTAAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 5 0.19
8 14 0.52
9 8 0.30
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTATA
Found at i:2889944 original size:9 final size:9
Alignment explanation
Indices: 2889923--2889953 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
2889913 AATAACATAC
2889923 TTTTTTATA
1 TTTTTTATA
2889932 -TTTTTATA
1 TTTTTTATA
2889940 TTTTTTATA
1 TTTTTTATA
2889949 TTTTT
1 TTTTT
2889954 AATTTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTATA
Found at i:2889945 original size:17 final size:16
Alignment explanation
Indices: 2889923--2889959 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 16
2889913 AATAACATAC
2889923 TTTTTTATATTTTTATA
1 TTTTTTATATTTTTA-A
2889940 TTTTTTATATTTTTAA
1 TTTTTTATATTTTTAA
2889956 TTTT
1 TTTT
2889960 ATTAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTTATATTTTTAA
Found at i:2893905 original size:19 final size:19
Alignment explanation
Indices: 2893878--2893915 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2893868 TTAAGGTCCG
* *
2893878 TAATTTTTAATTTTCTTCT
1 TAATCTTTAATTTTATTCT
2893897 TAATCTTTAATTTTATTCT
1 TAATCTTTAATTTTATTCT
2893916 CAAATAATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.66
Consensus pattern (19 bp):
TAATCTTTAATTTTATTCT
Found at i:2895304 original size:109 final size:108
Alignment explanation
Indices: 2895114--2895328 Score: 358
Period size: 109 Copynumber: 2.0 Consensus size: 108
2895104 ATTACAATTG
* * *
2895114 TTTCGGTAGCTAAAAGCTAATAACGTTAAAAATAAAAGGAGTTAACTAATGAGAAAGTGTCACGT
1 TTTCGGTAGCTAAAAACTAATAACGTTAAAAATAAAAGGAGTTAACCAATGAGAAAGCGTCACGT
2895179 CATCAATGACATGGCATATTGACCAACGACATGGTATGTTATA
66 CATCAATGACATGGCATATTGACCAACGACATGGTATGTTATA
* * *
2895222 TTTCGGTAGCTAAAAAATTAATTACGTTAAAAATAAAAGGAGTTAACCAATGAGAACGCGTCACG
1 TTTCGGTAGCT-AAAAACTAATAACGTTAAAAATAAAAGGAGTTAACCAATGAGAAAGCGTCACG
*
2895287 TCATCAATGACATGGCATATTGACCAACGGCATGGTATGTTA
65 TCATCAATGACATGGCATATTGACCAACGACATGGTATGTTA
2895329 ACGATCATTG
Statistics
Matches: 99, Mismatches: 7, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
108 11 0.11
109 88 0.89
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (108 bp):
TTTCGGTAGCTAAAAACTAATAACGTTAAAAATAAAAGGAGTTAACCAATGAGAAAGCGTCACGT
CATCAATGACATGGCATATTGACCAACGACATGGTATGTTATA
Found at i:2895434 original size:10 final size:10
Alignment explanation
Indices: 2895419--2895487 Score: 52
Period size: 10 Copynumber: 7.0 Consensus size: 10
2895409 AAAAGTTATC
*
2895419 TAAAAAATTG
1 TAAAAAATTA
2895429 T-AAAAATTA
1 TAAAAAATTA
**
2895438 TTGAAAATTA
1 TAAAAAATTA
2895448 T-AAAAATTA
1 TAAAAAATTA
*
2895457 AAAAAAATGTA
1 TAAAAAAT-TA
* *
2895468 AAAAAAAGTA
1 TAAAAAATTA
*
2895478 TTAAAAATTA
1 TAAAAAATTA
2895488 CTTCGGTTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
9 15 0.31
10 24 0.50
11 9 0.19
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:2895463 original size:19 final size:19
Alignment explanation
Indices: 2895420--2895464 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
2895410 AAAGTTATCT
* *
2895420 AAAAAATTGTAAAAATTAT
1 AAAAAATTATAAAAATTAA
**
2895439 TGAAAATTATAAAAATTAA
1 AAAAAATTATAAAAATTAA
2895458 AAAAAAT
1 AAAAAAT
2895465 GTAAAAAAAA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (19 bp):
AAAAAATTATAAAAATTAA
Found at i:2896234 original size:20 final size:20
Alignment explanation
Indices: 2896209--2896247 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2896199 TTGTTTAATA
*
2896209 TTTTAAATAATTTTTACAAT
1 TTTTAAATAAATTTTACAAT
2896229 TTTTAAATAAATTTTACAA
1 TTTTAAATAAATTTTACAA
2896248 GTTCTTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTAAATAAATTTTACAAT
Found at i:2896787 original size:125 final size:124
Alignment explanation
Indices: 2896564--2896831 Score: 412
Period size: 125 Copynumber: 2.2 Consensus size: 124
2896554 CAATTTCTAG
* * *
2896564 GACCTACTGTAGCAAAAGCGCGTCCACGAGAGCGCGATTTCACAAATTCTTCTCAAATAGCATCC
1 GACCTACTGTAGCAAAAGCGCGTCCACGAGAGCGCGATTTCACAAATTCTTATCAAACAACATCC
*
2896629 TGCTAGAAGCGATTTTATACTATTTCCTTAGAAACGTCAACTCGAAATTATTTCTTCCAA
66 TGCTAGAAGCGATTTTATACTATTTCCTCAGAAACGTCAACTCGAAATTATTT-TTCCAA
* * *
2896689 GACCTACTATAGCAAAATCGCGTCCACGA-AGCCTCGATTTCACAAATTCTTATCAAACAACATC
1 GACCTACTGTAGCAAAAGCGCGTCCACGAGAG-CGCGATTTCACAAATTCTTATCAAACAACATC
* * * *
2896753 CTGCTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTTGAAATTATTTTTTCAG
65 CTGCTAGAAGCGATTTTATACTATTTCCTCAGAAACGTCAACTCGAAATTATTTTTCCAA
2896813 GACCTACTGTAGCAAAAGC
1 GACCTACTGTAGCAAAAGC
2896832 ACGTAAACGT
Statistics
Matches: 129, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
124 23 0.18
125 106 0.82
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (124 bp):
GACCTACTGTAGCAAAAGCGCGTCCACGAGAGCGCGATTTCACAAATTCTTATCAAACAACATCC
TGCTAGAAGCGATTTTATACTATTTCCTCAGAAACGTCAACTCGAAATTATTTTTCCAA
Found at i:2897310 original size:20 final size:20
Alignment explanation
Indices: 2897287--2897324 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2897277 GTCAATCTAG
2897287 CACGTCATCAGTCAACATTT
1 CACGTCATCAGTCAACATTT
**
2897307 CACGTCATTGGTCAACAT
1 CACGTCATCAGTCAACAT
2897325 GCCTATTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (20 bp):
CACGTCATCAGTCAACATTT
Found at i:2897874 original size:60 final size:59
Alignment explanation
Indices: 2897800--2897913 Score: 185
Period size: 60 Copynumber: 1.9 Consensus size: 59
2897790 AAGACAATTG
*
2897800 AATAGTTGAGTGACCATTTTGTAACTTTTCATAGTTGAGTGACCAAAAAAGAAAATTACT
1 AATAGTTGAGTGACCATTTTGTAACATTTCATA-TTGAGTGACCAAAAAAGAAAATTACT
*
2897860 AATAGTTGTA-TGACCATTTTGTAACATTTCATATTGGGTGACCAAAAAAGAAAA
1 AATAGTTG-AGTGACCATTTTGTAACATTTCATATTGAGTGACCAAAAAAGAAAA
2897914 GAAAAAACCA
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
59 20 0.39
60 30 0.59
61 1 0.02
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.32
Consensus pattern (59 bp):
AATAGTTGAGTGACCATTTTGTAACATTTCATATTGAGTGACCAAAAAAGAAAATTACT
Found at i:2909663 original size:18 final size:18
Alignment explanation
Indices: 2909635--2909673 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2909625 GGCTAATTGG
*
2909635 ATTTTTTTTATCT-TAAA
1 ATTTTTTTTATATGTAAA
2909652 ATTTTTTATTATATGTAAA
1 ATTTTTT-TTATATGTAAA
2909671 ATT
1 ATT
2909674 GAATTAGGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 5 0.26
19 7 0.37
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (18 bp):
ATTTTTTTTATATGTAAA
Done.