Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold72
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: 5928628
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 261288 characters in sequence are not A, C, G, or T
File 34 of 39
Found at i:4925683 original size:99 final size:99
Alignment explanation
Indices: 4925448--4925711 Score: 343
Period size: 99 Copynumber: 2.6 Consensus size: 99
4925438 GGCCACCTTT
* * * * *
4925448 TCTATTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATAACCACCTCTCTATATTGTC-AAAGA
1 TCTATTGTCAAAGATTGGTGAAGAATCGTCAACAATTATGATCA-CTCTCTCTATTATCAAAAG-
* * * *
4925512 TTGGTGAAGAATCGTCAACAATTACGGTCATCTCTT
64 TTGGTGAAGAATCATCAACAATTACGATCACCTCTC
* *
4925548 TCTATTGTCAAAGTTTGGTGAAGAATCGTCAACAATTACGATCATCTCTCTCTATTATCAAAAGT
1 TCTATTGTCAAAGATTGGTGAAGAATCGTCAACAATTATGATCA-CTCTCTCTATTATCAAAAGT
4925613 TGGTGAA-AATCATCAACAATTACGATCACCTCTC
65 TGGTGAAGAATCATCAACAATTACGATCACCTCTC
** * *
4925647 TCTATTGTCAAAGATTAATGAAGAATCATCAACAATTATGATCACTTTCTTCTATTATCAAAAGT
1 TCTATTGTCAAAGATTGGTGAAGAATCGTCAACAATTATGATCACTCTC-TCTATTATCAAAAGT
4925712 ACTTTCCACC
Statistics
Matches: 145, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
98 4 0.03
99 77 0.53
100 60 0.41
101 4 0.03
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (99 bp):
TCTATTGTCAAAGATTGGTGAAGAATCGTCAACAATTATGATCACTCTCTCTATTATCAAAAGTT
GGTGAAGAATCATCAACAATTACGATCACCTCTC
Found at i:4925998 original size:21 final size:22
Alignment explanation
Indices: 4925969--4926017 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
4925959 TAAATAAAAT
* *
4925969 TTAATTTAATATATTAAGATAA
1 TTAAATTAAAATATTAAGATAA
*
4925991 -TAAATTAAAATATTAATATAA
1 TTAAATTAAAATATTAAGATAA
4926012 TTAAAT
1 TTAAAT
4926018 CTTATTTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TTAAATTAAAATATTAAGATAA
Found at i:4926677 original size:6 final size:6
Alignment explanation
Indices: 4926668--4926707 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
4926658 TTATATTTAT
*
4926668 ATATAA ATATTA AT-TAA ATATAA ATATTAA ATATAA ATAT
1 ATATAA ATATAA ATATAA ATATAA ATA-TAA ATATAA ATAT
4926708 TTTAAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 4 0.13
6 20 0.67
7 6 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (6 bp):
ATATAA
Found at i:4926690 original size:17 final size:19
Alignment explanation
Indices: 4926668--4926707 Score: 66
Period size: 17 Copynumber: 2.2 Consensus size: 19
4926658 TTATATTTAT
4926668 ATATAAATATT-AAT-TAA
1 ATATAAATATTAAATATAA
4926685 ATATAAATATTAAATATAA
1 ATATAAATATTAAATATAA
4926704 ATAT
1 ATAT
4926708 TTTAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 11 0.52
18 3 0.14
19 7 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATATAAATATTAAATATAA
Found at i:4926698 original size:13 final size:13
Alignment explanation
Indices: 4926680--4926708 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
4926670 ATAAATATTA
4926680 ATTAAATATAAAT
1 ATTAAATATAAAT
4926693 ATTAAATATAAAT
1 ATTAAATATAAAT
4926706 ATT
1 ATT
4926709 TTAAATAAAA
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATTAAATATAAAT
Found at i:4927519 original size:19 final size:18
Alignment explanation
Indices: 4927482--4927520 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
4927472 TCGATGAAAA
* *
4927482 AAATATTTTAAAATTAAT
1 AAATATTTAAAAATAAAT
4927500 AAATATTATAAAAATAAAT
1 AAATATT-TAAAAATAAAT
4927519 AA
1 AA
4927521 TTATATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATATTTAAAAATAAAT
Found at i:4927540 original size:27 final size:24
Alignment explanation
Indices: 4927493--4927565 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 24
4927483 AATATTTTAA
*
4927493 AATTAATAAATAT-TATAAAAATAAAT
1 AATTAATAATTATATAT-AAAAT--AT
4927519 AATTATATAATTATATATAAAATAT
1 AATTA-ATAATTATATATAAAATAT
* *
4927544 AATTAAAAATAATTATATAAAA
1 AATTAATAATTA-TATATAAAA
4927566 ATGGATCTAG
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 5 0.12
25 16 0.39
26 5 0.12
27 12 0.29
28 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
AATTAATAATTATATATAAAATAT
Found at i:4933596 original size:2 final size:2
Alignment explanation
Indices: 4933589--4933614 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4933579 GGTATTTCCC
4933589 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
4933615 AAAATTGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4934373 original size:18 final size:17
Alignment explanation
Indices: 4934348--4934393 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
4934338 TTTTTAATTC
4934348 AATAAAATAATTTATTT
1 AATAAAATAATTTATTT
*
4934365 AATACAAATAATTTTTTT
1 AATA-AAATAATTTATTT
*
4934383 AA-ATAATAATT
1 AATAAAATAATT
4934394 AAATAACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 7 0.27
17 5 0.19
18 14 0.54
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
AATAAAATAATTTATTT
Found at i:4934872 original size:20 final size:20
Alignment explanation
Indices: 4934809--4934872 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
4934799 ATAGATTTTA
* *
4934809 AAAAAAATTTATAATTA-AT
1 AAAAATATTTAAAATTATAT
*
4934828 ATATAATATTTTAAAACTT-TA-
1 A-AAAATA-TTTAAAA-TTATAT
4934849 AAAAATATTTAAAATTATAT
1 AAAAATATTTAAAATTATAT
4934869 AAAA
1 AAAA
4934873 TTTAATTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 11
0.70 0.08 0.22
Matches are distributed among these distances:
18 2 0.06
19 10 0.29
20 13 0.37
21 7 0.20
22 3 0.09
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAATATTTAAAATTATAT
Found at i:4934928 original size:23 final size:23
Alignment explanation
Indices: 4934886--4934938 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
4934876 AATTAATTTG
4934886 AATTAAATTTTATTAATTTAAATA
1 AATTAAATTTTATTAATTTAAA-A
* *
4934910 AGTTAAA-TTTATTATTTTAAAA
1 AATTAAATTTTATTAATTTAAAA
4934932 AATTAAA
1 AATTAAA
4934939 AAAATTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 7 0.27
23 13 0.50
24 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AATTAAATTTTATTAATTTAAAA
Found at i:4935003 original size:34 final size:35
Alignment explanation
Indices: 4934965--4935045 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 35
4934955 TTTAAATTTT
* *
4934965 TTATATTAATTTAAAAAT-AAATATATATTTTATA
1 TTATATTAATTTAAAAATAAAATAAATATTTAATA
**
4934999 TTATAAAAATTT-AAAATAAAATAAATATTTAATA
1 TTATATTAATTTAAAAATAAAATAAATATTTAATA
*
4935033 TAAT-TTAATTTAA
1 TTATATTAATTTAA
4935046 TTTAATTTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
33 10 0.26
34 28 0.74
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (35 bp):
TTATATTAATTTAAAAATAAAATAAATATTTAATA
Found at i:4935028 original size:18 final size:18
Alignment explanation
Indices: 4935001--4935035 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4934991 ATTTTATATT
4935001 ATAAAAATTTAAAATAAA
1 ATAAAAATTTAAAATAAA
* *
4935019 ATAAATATTTAATATAA
1 ATAAAAATTTAAAATAA
4935036 TTTAATTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAAAAATTTAAAATAAA
Found at i:4935036 original size:5 final size:5
Alignment explanation
Indices: 4935025--4935055 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
4935015 TAAAATAAAT
*
4935025 ATTTA ATATA ATTTA ATTTA ATTTA ATTTA A
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA A
4935056 ATAATAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (5 bp):
ATTTA
Found at i:4938562 original size:22 final size:22
Alignment explanation
Indices: 4938537--4938578 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
4938527 ATATTCATTG
*
4938537 AATAATTTTAATTAATGAGTTC
1 AATAATTTTAATGAATGAGTTC
4938559 AATAATTTTAATGAATGAGT
1 AATAATTTTAATGAATGAGT
4938579 GTAGGCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (22 bp):
AATAATTTTAATGAATGAGTTC
Found at i:4944183 original size:19 final size:17
Alignment explanation
Indices: 4944155--4944204 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 17
4944145 TAAATTAAAA
*
4944155 AAATTATATTTTTATTTT
1 AAATTATATTTATA-TTT
4944173 AAATATATATTTATATTT
1 AAAT-TATATTTATATTT
4944191 AATATTTATATTTA
1 AA-A-TTATATTTA
4944205 ATCTAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 9 0.32
19 18 0.64
20 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AAATTATATTTATATTT
Found at i:4944195 original size:13 final size:13
Alignment explanation
Indices: 4944179--4944206 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4944169 TTTTAAATAT
4944179 ATATTTATATTTA
1 ATATTTATATTTA
4944192 ATATTTATATTTA
1 ATATTTATATTTA
4944205 AT
1 AT
4944207 CTAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
ATATTTATATTTA
Found at i:4944235 original size:13 final size:13
Alignment explanation
Indices: 4944210--4944244 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
4944200 ATTTAATCTA
4944210 AAAAATATAAATT
1 AAAAATATAAATT
4944223 ATAAAAT-TAAATT
1 A-AAAATATAAATT
4944236 AAAAATATA
1 AAAAATATA
4944245 TTACTTTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 5 0.25
13 10 0.50
14 5 0.25
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAATATAAATT
Found at i:4944685 original size:16 final size:16
Alignment explanation
Indices: 4944664--4944724 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
4944654 TATTATTCAA
4944664 ATAAAAATATTAATAT
1 ATAAAAATATTAATAT
*
4944680 ATAAAAAAATTAAAATTAT
1 ATAAAAATATT--AA-TAT
** *
4944699 ATATTAATATTTATAT
1 ATAAAAATATTAATAT
*
4944715 TTAAAAATAT
1 ATAAAAATAT
4944725 ATATTAAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
16 20 0.59
17 1 0.03
18 2 0.06
19 11 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATAAAAATATTAATAT
Found at i:4944715 original size:12 final size:13
Alignment explanation
Indices: 4944688--4944732 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
4944678 ATATAAAAAA
4944688 ATTAAAATTATAT
1 ATTAAAATTATAT
*
4944701 ATTAATATT-TAT
1 ATTAAAATTATAT
*
4944713 ATTTAAAAATATAT
1 A-TTAAAATTATAT
4944727 ATTAAA
1 ATTAAA
4944733 TATAAATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 4 0.15
13 19 0.70
14 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTAAAATTATAT
Found at i:4944731 original size:13 final size:13
Alignment explanation
Indices: 4944688--4944748 Score: 52
Period size: 13 Copynumber: 4.6 Consensus size: 13
4944678 ATATAAAAAA
*
4944688 ATTAAAATTATAT
1 ATTAAAAATATAT
* *
4944701 ATT-AATATTTAT
1 ATTAAAAATATAT
4944713 ATTTAAAAATATAT
1 A-TTAAAAATATAT
* *
4944727 ATTAAATATAAAT
1 ATTAAAAATATAT
4944740 ATTGAAAAA
1 ATT-AAAAA
4944749 AAATCTGATC
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
12 7 0.19
13 18 0.49
14 12 0.32
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (13 bp):
ATTAAAAATATAT
Found at i:4944741 original size:27 final size:27
Alignment explanation
Indices: 4944670--4944748 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
4944660 TCAAATAAAA
* * *
4944670 ATATTAATATATAAAAAAATTAAAATTAT
1 ATATTAA-ATAT-AAATATTTAAAAATAT
**
4944699 ATATT-AATATTTATATTTAAAAATAT
1 ATATTAAATATAAATATTTAAAAATAT
*
4944725 ATATTAAATATAAATATTGAAAAA
1 ATATTAAATATAAATATTTAAAAA
4944749 AAATCTGATC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
26 16 0.39
27 19 0.46
28 1 0.02
29 5 0.12
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (27 bp):
ATATTAAATATAAATATTTAAAAATAT
Found at i:4944741 original size:33 final size:33
Alignment explanation
Indices: 4944652--4944742 Score: 83
Period size: 35 Copynumber: 2.6 Consensus size: 33
4944642 TACAGTATCT
*
4944652 TATATTATTCAAATAAAAATATTAATATATAAAAA
1 TATA-TATT-AAATATAAATATTAATATATAAAAA
* * * * * *
4944687 AATTAAAATTATATATTAATATTTATATTTAAAAA
1 TA-T-ATATTAAATATAAATATTAATATATAAAAA
4944722 TATATATTAAATATAAATATT
1 TATATATTAAATATAAATATT
4944743 GAAAAAAAAT
Statistics
Matches: 43, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
33 15 0.35
34 1 0.02
35 22 0.51
36 4 0.09
37 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (33 bp):
TATATATTAAATATAAATATTAATATATAAAAA
Found at i:4948043 original size:18 final size:18
Alignment explanation
Indices: 4948009--4948043 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4947999 TATATCTTTT
* *
4948009 AAAATTTTTAAATATATA
1 AAAATTTTGAAACATATA
4948027 AAAATTTTGAAACATAT
1 AAAATTTTGAAACATAT
4948044 TTAATATATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (18 bp):
AAAATTTTGAAACATATA
Found at i:4952658 original size:20 final size:20
Alignment explanation
Indices: 4952597--4952667 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
4952587 ATGATTAAAA
*
4952597 AATTTAAA-AAATTTATCTTT
1 AATTTAAATAAATTTA-ATTT
** *
4952617 AATTTAAAATTTTATCTAATTT
1 AATTT-AAA-TAAATTTAATTT
4952639 AATTTAAATAAATTTAATTT
1 AATTTAAATAAATTTAATTT
*
4952659 AATCTAAAT
1 AATTTAAAT
4952668 TAATCAATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
20 22 0.55
21 6 0.15
22 8 0.20
23 4 0.10
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTTAAATAAATTTAATTT
Found at i:4952670 original size:15 final size:15
Alignment explanation
Indices: 4952624--4952671 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
4952614 TTTAATTTAA
* *
4952624 AATTTTATCTAATTT
1 AATTTAATCTAAATT
*
4952639 AATTTAA-ATAAATTT
1 AATTTAATCTAAA-TT
4952654 AATTTAATCTAAATT
1 AATTTAATCTAAATT
4952669 AAT
1 AAT
4952672 CAATTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
14 3 0.11
15 20 0.74
16 4 0.15
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTTAATCTAAATT
Found at i:4954221 original size:29 final size:28
Alignment explanation
Indices: 4954184--4954248 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
4954174 GATTTATATT
*
4954184 AATTGAATATATTAAT-ATAAATAAAATA
1 AATTAAATAT-TTAATGATAAATAAAATA
* *
4954212 AATTTAAATATTTAATGATAATTAAATTA
1 AA-TTAAATATTTAATGATAAATAAAATA
4954241 AATTAAAT
1 AATTAAAT
4954249 TAATTTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 13 0.41
29 19 0.59
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (28 bp):
AATTAAATATTTAATGATAAATAAAATA
Found at i:4954268 original size:21 final size:20
Alignment explanation
Indices: 4954195--4954274 Score: 60
Period size: 20 Copynumber: 4.0 Consensus size: 20
4954185 ATTGAATATA
*
4954195 TTAATATAAA-TAAAATAAAT
1 TTAAAATAAATTAAAAT-AAT
* *
4954215 TT-AAAT-ATTTAATGATAA-
1 TTAAAATAAATTAA-AATAAT
* *
4954233 TTAAATTAAATTAAATTAAT
1 TTAAAATAAATTAAAATAAT
4954253 TTAAAATAAATATAAAATAAT
1 TTAAAATAAAT-TAAAATAAT
4954274 T
1 T
4954275 CATACCTAAT
Statistics
Matches: 45, Mismatches: 9, Indels: 11
0.69 0.14 0.17
Matches are distributed among these distances:
18 3 0.07
19 14 0.31
20 19 0.42
21 9 0.20
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (20 bp):
TTAAAATAAATTAAAATAAT
Found at i:4956265 original size:13 final size:13
Alignment explanation
Indices: 4956247--4956273 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4956237 AAATTTAATT
4956247 ATATTTATATTTA
1 ATATTTATATTTA
4956260 ATATTTATATTTA
1 ATATTTATATTTA
4956273 A
1 A
4956274 ATTCAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATATTTATATTTA
Found at i:4957322 original size:17 final size:17
Alignment explanation
Indices: 4957300--4957337 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
4957290 TCCGATACCC
4957300 ATATCAGATATTTTTGG
1 ATATCAGATATTTTTGG
4957317 ATATCAGATATTTTTGG
1 ATATCAGATATTTTTGG
4957334 ATAT
1 ATAT
4957338 GAGTATAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (17 bp):
ATATCAGATATTTTTGG
Found at i:4959057 original size:25 final size:25
Alignment explanation
Indices: 4959020--4959078 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
4959010 TATTTGTATT
4959020 AAATATATATTAATTATAA-ATATAA
1 AAATATATATTAATTA-AATATATAA
4959045 AAATATA-ATTTAATTAAATATATAA
1 AAATATATA-TTAATTAAATATATAA
**
4959070 TTATATATA
1 AAATATATA
4959079 ATATCTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 3 0.10
25 25 0.86
26 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
AAATATATATTAATTAAATATATAA
Found at i:4959879 original size:2 final size:2
Alignment explanation
Indices: 4959872--4959902 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4959862 AATGTGAATC
4959872 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4959903 CACACACAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4961567 original size:17 final size:17
Alignment explanation
Indices: 4961542--4961582 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
4961532 TTAAACTCGA
* *
4961542 AATAAATATTAAATATT
1 AATATATATTAAATATG
*
4961559 AATATATATTTAATATG
1 AATATATATTAAATATG
4961576 AATATAT
1 AATATAT
4961583 TTATTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
AATATATATTAAATATG
Found at i:4962188 original size:19 final size:20
Alignment explanation
Indices: 4962155--4962199 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
4962145 TCGAAAAGCT
**
4962155 ATTTTATTATTTAAA-AATA
1 ATTTTATTAAATAAATAATA
*
4962174 TTTTTATTAAATAAATAATA
1 ATTTTATTAAATAAATAATA
4962194 ATTTTA
1 ATTTTA
4962200 AAATAATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTTATTAAATAAATAATA
Found at i:4962427 original size:2 final size:2
Alignment explanation
Indices: 4962420--4962449 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4962410 ACGAACGGAA
4962420 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
4962450 TGTACAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4963707 original size:28 final size:26
Alignment explanation
Indices: 4963675--4963738 Score: 78
Period size: 25 Copynumber: 2.4 Consensus size: 26
4963665 TAGTTAAAAA
4963675 TTAATTAATTATTATTTAAT-ATATTATT
1 TTAATTAA-TATT-TTTAATGATATT-TT
4963703 TTAATTAA-ATTTTTAATGATATTTT
1 TTAATTAATATTTTTAATGATATTTT
*
4963728 TTTATTAATAT
1 TTAATTAATAT
4963739 ATAACTTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 15 0.45
26 10 0.30
28 8 0.24
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (26 bp):
TTAATTAATATTTTTAATGATATTTT
Found at i:4964407 original size:14 final size:14
Alignment explanation
Indices: 4964390--4964433 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
4964380 TAAATTTAAT
*
4964390 TATAATATATAAAA
1 TATAATATTTAAAA
4964404 TATAA-ATTTAAAAA
1 TATAATATTT-AAAA
4964418 TATATATATTTAAAA
1 TATA-ATATTTAAAA
4964433 T
1 T
4964434 TTTATAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 3 0.12
14 13 0.50
15 6 0.23
16 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TATAATATTTAAAA
Found at i:4965678 original size:44 final size:43
Alignment explanation
Indices: 4965610--4965706 Score: 105
Period size: 42 Copynumber: 2.3 Consensus size: 43
4965600 GAATTAATTC
*
4965610 ATATTATT--ATTTAAAATAATATTTAAAATTAAAAAT-ATTTTT
1 ATATTATTAAATTTAAAATAATATTT--AATTAAAAATAAATTTT
*
4965652 ATATTATTAAATTTATAATTAA-ATTTAATTAAAAATAAATTTT
1 ATATTATTAAATTTA-AAATAATATTTAATTAAAAATAAATTTT
4965695 -TATTATATAAAT
1 ATATTAT-TAAAT
4965707 AACAATTCTA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
42 24 0.50
43 10 0.21
44 9 0.19
45 5 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (43 bp):
ATATTATTAAATTTAAAATAATATTTAATTAAAAATAAATTTT
Found at i:4966045 original size:14 final size:14
Alignment explanation
Indices: 4966003--4966057 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
4965993 TTTAAAAGTG
*
4966003 ATATATTTTATTTAT
1 ATATATTTTA-TTAA
*
4966018 TTATTATTTT-TTAA
1 ATA-TATTTTATTAA
4966032 ATATATTTTATTAA
1 ATATATTTTATTAA
*
4966046 ATATATATTATT
1 ATATATTTTATT
4966058 TTATAAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
13 6 0.18
14 20 0.59
15 2 0.06
16 6 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATATATTTTATTAA
Found at i:4966054 original size:29 final size:30
Alignment explanation
Indices: 4966003--4966060 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
4965993 TTTAAAAGTG
* *
4966003 ATATATTTTATTTATTTATTATT-TTTTAA
1 ATATATTTTATTAATATATTATTATTTTAA
4966032 ATATATTTTATTAA-ATATATATTATTTTA
1 ATATATTTTATTAATATAT-TATTATTTTA
4966061 TAAATTTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 17 0.68
30 5 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (30 bp):
ATATATTTTATTAATATATTATTATTTTAA
Found at i:4966055 original size:32 final size:29
Alignment explanation
Indices: 4966003--4966065 Score: 81
Period size: 32 Copynumber: 2.1 Consensus size: 29
4965993 TTTAAAAGTG
* *
4966003 ATATATTTTATTTATTTATTATTTTTTAA
1 ATATATTTTATTTATATATTATTTTATAA
4966032 ATATATTTTATTAAATATATATTATTTTATAA
1 ATATATTTTATT---TATATATTATTTTATAA
4966064 AT
1 AT
4966066 TTTACTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 12 0.41
32 17 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
ATATATTTTATTTATATATTATTTTATAA
Found at i:4966379 original size:31 final size:31
Alignment explanation
Indices: 4966344--4966416 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
4966334 TCGTGTTTTT
* * * *
4966344 TATATTAATTTTATAAATATAAGT-TATTAAA
1 TATATTAAATTT-TAAATATAAATAAAATAAA
4966375 TATATTAAAATTTTAAATATAAATAAAATAAA
1 TATATT-AAATTTTAAATATAAATAAAATAAA
4966407 TATATTAAAT
1 TATATTAAAT
4966417 ATATTTTATG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
31 20 0.56
32 16 0.44
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (31 bp):
TATATTAAATTTTAAATATAAATAAAATAAA
Found at i:4966382 original size:9 final size:9
Alignment explanation
Indices: 4966368--4966421 Score: 53
Period size: 9 Copynumber: 6.4 Consensus size: 9
4966358 AAATATAAGT
4966368 TATTAAATA
1 TATTAAATA
4966377 TATTAAA-A
1 TATTAAATA
*
4966385 T-TTTAA-A
1 TATTAAATA
4966392 TA-TAAATA
1 TATTAAATA
* *
4966400 AAATAAATA
1 TATTAAATA
4966409 TATTAAATA
1 TATTAAATA
4966418 TATT
1 TATT
4966422 TTATGTATCA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
7 9 0.24
8 4 0.11
9 24 0.65
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
TATTAAATA
Found at i:4966392 original size:17 final size:15
Alignment explanation
Indices: 4966369--4966415 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
4966359 AATATAAGTT
4966369 ATTAAATATATTAAA
1 ATTAAATATATTAAA
*
4966384 ATTTTAAATATAAATAAA
1 A--TTAAATAT-ATTAAA
4966402 A-TAAATATATTAAA
1 ATTAAATATATTAAA
4966416 TATATTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
14 5 0.19
15 8 0.30
17 8 0.30
18 6 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTAAATATATTAAA
Found at i:4966927 original size:14 final size:14
Alignment explanation
Indices: 4966886--4966933 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
4966876 TATATGTTAT
*
4966886 ATTTATTATAATAA
1 ATTTATTATATTAA
4966900 ATTT-TTAAATATTAA
1 ATTTATT--ATATTAA
4966915 ATTTATTATATT-A
1 ATTTATTATATTAA
4966928 ATTTAT
1 ATTTAT
4966934 ATTTTTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 9 0.30
14 9 0.30
15 10 0.33
16 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTTATTATATTAA
Found at i:4968094 original size:28 final size:26
Alignment explanation
Indices: 4968026--4968122 Score: 97
Period size: 28 Copynumber: 3.7 Consensus size: 26
4968016 TAAAAATTAG
* *
4968026 CCACAAATTTTGACAAATA-AAAAAG
1 CCACAATTTTTGACAAATACAAAAAA
* * *
4968051 CCTCCATATTTGACAAATACAAAGGAAA
1 CCACAATTTTTGACAAATACAAA--AAA
*
4968079 CCACAATTTTTGACAAACACAAAATAA
1 CCACAATTTTTGACAAATACAAAA-AA
*
4968106 CTACAATTTTTGACAAA
1 CCACAATTTTTGACAAA
4968123 CAAATGGGTG
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
25 15 0.26
26 4 0.07
27 18 0.31
28 21 0.36
ACGTcount: A:0.49, C:0.20, G:0.07, T:0.24
Consensus pattern (26 bp):
CCACAATTTTTGACAAATACAAAAAA
Found at i:4968119 original size:27 final size:27
Alignment explanation
Indices: 4968059--4968124 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
4968049 AGCCTCCATA
*
4968059 TTTGACAAATACAAAGGAAACCACAATT
1 TTTGACAAACACAAA-GAAACCACAATT
*
4968087 TTTGACAAACACAAA-ATAACTACAATT
1 TTTGACAAACACAAAGA-AACCACAATT
4968114 TTTGACAAACA
1 TTTGACAAACA
4968125 AATGGGTGGC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
26 1 0.03
27 20 0.57
28 14 0.40
ACGTcount: A:0.50, C:0.18, G:0.08, T:0.24
Consensus pattern (27 bp):
TTTGACAAACACAAAGAAACCACAATT
Found at i:4970039 original size:21 final size:22
Alignment explanation
Indices: 4970001--4970046 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
4969991 ATCTGTTGAA
* **
4970001 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
4970022 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
4970044 ACT
1 ACT
4970047 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:4972679 original size:27 final size:28
Alignment explanation
Indices: 4972619--4972689 Score: 108
Period size: 27 Copynumber: 2.6 Consensus size: 28
4972609 AAACAAGTCT
*
4972619 CCATATTTGACAAATACAAAGAAAACCA
1 CCATTTTTGACAAATACAAAGAAAACCA
* *
4972647 CCATTTTTAACAAATACAAA-ATAACCA
1 CCATTTTTGACAAATACAAAGAAAACCA
4972674 CCATTTTTGACAAATA
1 CCATTTTTGACAAATA
4972690 AATGGGTGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.49, C:0.21, G:0.04, T:0.25
Consensus pattern (28 bp):
CCATTTTTGACAAATACAAAGAAAACCA
Found at i:4975948 original size:30 final size:30
Alignment explanation
Indices: 4975857--4975948 Score: 91
Period size: 30 Copynumber: 3.1 Consensus size: 30
4975847 GTTTAGTTAC
4975857 AAATTAAAG-TTAATGG-TTTATTTTGAGTAA
1 AAATTAAAGATTAA-GGATTTA-TTTGAGTAA
* * * *
4975887 AAAGTAAAAATTAAAGACTTATTTG-GATAA
1 AAATTAAAGATTAAGGATTTATTTGAG-TAA
*
4975917 AAATTAAAGATTAAGGATTTAATTGAGTAA
1 AAATTAAAGATTAAGGATTTATTTGAGTAA
4975947 AA
1 AA
4975949 TAAAAAGATT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
29 1 0.02
30 40 0.82
31 8 0.16
ACGTcount: A:0.49, C:0.01, G:0.15, T:0.35
Consensus pattern (30 bp):
AAATTAAAGATTAAGGATTTATTTGAGTAA
Found at i:4979541 original size:17 final size:19
Alignment explanation
Indices: 4979504--4979543 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
4979494 TATTGATATA
*
4979504 AAATTTATCATAATTTTTT
1 AAATTTATCATAATTTATT
4979523 AAATTTA-CA-AATTTATT
1 AAATTTATCATAATTTATT
4979540 AAAT
1 AAAT
4979544 ATTCATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 11 0.55
18 2 0.10
19 7 0.35
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (19 bp):
AAATTTATCATAATTTATT
Found at i:4981972 original size:2 final size:2
Alignment explanation
Indices: 4981965--4981992 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4981955 TCAGAGCATT
4981965 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
4981993 AATTAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4983652 original size:11 final size:11
Alignment explanation
Indices: 4983636--4983670 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
4983626 TAAATCAATA
4983636 TAATTTTTAAT
1 TAATTTTTAAT
4983647 TAATTTTT-AT
1 TAATTTTTAAT
*
4983657 TAATATTTAAT
1 TAATTTTTAAT
4983668 TAA
1 TAA
4983671 ATTGATTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TAATTTTTAAT
Found at i:4983699 original size:16 final size:17
Alignment explanation
Indices: 4983675--4983708 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4983665 AATTAAATTG
4983675 ATTAGTTTAAAT-TAAA
1 ATTAGTTTAAATGTAAA
*
4983691 ATTATTTTAAATGTAAA
1 ATTAGTTTAAATGTAAA
4983708 A
1 A
4983709 AATTTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATTAGTTTAAATGTAAA
Found at i:4983713 original size:16 final size:17
Alignment explanation
Indices: 4983680--4983720 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
4983670 AATTGATTAG
*
4983680 TTTAAAT-TAAAATTAT
1 TTTAAATGTAAAATAAT
4983696 TTTAAATGTAAAA-AAT
1 TTTAAATGTAAAATAAT
*
4983712 TTTTAATGT
1 TTTAAATGT
4983721 TCTATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (17 bp):
TTTAAATGTAAAATAAT
Found at i:4986226 original size:32 final size:32
Alignment explanation
Indices: 4986150--4986269 Score: 92
Period size: 32 Copynumber: 3.8 Consensus size: 32
4986140 ATATGAGATG
*
4986150 ATATAAATATATATTTAAATATTTTATAATATAA
1 ATATAAA-ATATA-TTAAATATTATATAATATAA
*
4986184 AT-TATTAATATATTAAAT-TTATATAAATATAA
1 ATATA-AAATATATTAAATATTATAT-AATATAA
* *
4986216 ATATAAAATATCTTAAACA-TA-AT--TATAA
1 ATATAAAATATATTAAATATTATATAATATAA
*
4986244 CATAATAAAATATA-TAAATATAATAT
1 -AT-ATAAAATATATTAAATATTATAT
4986270 GAATGCATAA
Statistics
Matches: 70, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
28 5 0.07
29 7 0.10
30 10 0.14
31 9 0.13
32 27 0.39
33 9 0.13
34 3 0.04
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (32 bp):
ATATAAAATATATTAAATATTATATAATATAA
Found at i:4986829 original size:39 final size:39
Alignment explanation
Indices: 4986735--4986834 Score: 106
Period size: 39 Copynumber: 2.7 Consensus size: 39
4986725 AATCGAATTA
*
4986735 ATTTA-AAATAATATTTAAATTT--A-AAAATATTTTAT
1 ATTTATAAATAATAATTAAATTTAAATAAAATATTTTAT
* *
4986770 ATTAATAAATTTATAA-TAAATTTAAATAAAATATTTTAT
1 ATTTATAAA-TAATAATTAAATTTAAATAAAATATTTTAT
4986809 -TTTATAAATAATAATGTAAA-TTAAAT
1 ATTTATAAATAATAAT-TAAATTTAAAT
4986835 TAATTTAAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
35 4 0.08
36 10 0.19
37 9 0.17
38 14 0.26
39 16 0.30
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (39 bp):
ATTTATAAATAATAATTAAATTTAAATAAAATATTTTAT
Found at i:4987115 original size:14 final size:14
Alignment explanation
Indices: 4987098--4987160 Score: 63
Period size: 14 Copynumber: 4.4 Consensus size: 14
4987088 TAATTATTTA
4987098 TTATTAAATATATT
1 TTATTAAATATATT
*
4987112 TTATTAAATATGTT
1 TTATTAAATATATT
** *
4987126 TTATTTTATAAATT
1 TTATTAAATATATT
*
4987140 TTATTTATAAAATATT
1 TTA-TTA-AATATATT
4987156 TTATT
1 TTATT
4987161 TTTATTATTG
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
14 26 0.68
15 4 0.11
16 8 0.21
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
TTATTAAATATATT
Found at i:4987148 original size:13 final size:14
Alignment explanation
Indices: 4987124--4987162 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
4987114 ATTAAATATG
4987124 TTTTATTTTATAAA
1 TTTTATTTTATAAA
*
4987138 TTTTATTTATAAAATA
1 TTTTATTT-TATAA-A
4987154 TTTTATTTT
1 TTTTATTTT
4987163 TATTATTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 8 0.36
15 5 0.23
16 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTATTTTATAAA
Found at i:4987427 original size:15 final size:16
Alignment explanation
Indices: 4987406--4987444 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
4987396 TTGTGTTTTT
4987406 TATATTAATT-TTATAA
1 TATATTAATTATT-TAA
4987422 -ATATTAATTATTTAA
1 TATATTAATTATTTAA
4987437 TATATTAA
1 TATATTAA
4987445 AATTTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATTAATTATTTAA
Found at i:4987575 original size:37 final size:41
Alignment explanation
Indices: 4987515--4987590 Score: 97
Period size: 38 Copynumber: 2.0 Consensus size: 41
4987505 ATATTGTATT
* *
4987515 TATTATATTATTTTTATAAATG-TTAAACTTATCATATTAA
1 TATTATATTATTTTTATAAATGTTTAAAATGATCATATTAA
*
4987555 TATTATA-T-TTTTTAT-TATGTTTAAAATGATCATATT
1 TATTATATTATTTTTATAAATGTTTAAAATGATCATATT
4987591 TACATGCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 3 0.09
38 21 0.66
39 1 0.03
40 7 0.22
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (41 bp):
TATTATATTATTTTTATAAATGTTTAAAATGATCATATTAA
Found at i:4987706 original size:6 final size:6
Alignment explanation
Indices: 4987695--4987756 Score: 67
Period size: 6 Copynumber: 10.3 Consensus size: 6
4987685 GGATTCTTAA
4987695 ATAAAT ATAAAT ATAAAT ATAAA- ATAAAT AATTAAAT AT--AT ATAAATT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT -A-TAAAT ATAAAT ATAAA-T
*
4987743 TTAAAT ATAAAT AT
1 ATAAAT ATAAAT AT
4987757 GATAAATATA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
4 4 0.08
5 5 0.10
6 27 0.56
7 7 0.15
8 5 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
ATAAAT
Found at i:4987721 original size:23 final size:21
Alignment explanation
Indices: 4987693--4987756 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 21
4987683 TTGGATTCTT
4987693 AAATAAATATAAATATAAATATA
1 AAATAAATATAAATAT--ATATA
4987716 AAATAAATAATTAAATATATATA
1 AAATAAAT-A-TAAATATATATA
*
4987739 AATTTTAAATATAAATAT
1 AA--ATAAATATAAATAT
4987757 GATAAATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
23 22 0.61
24 2 0.06
25 12 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATAAATATAAATATATATA
Found at i:4987723 original size:17 final size:18
Alignment explanation
Indices: 4987695--4987756 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 18
4987685 GGATTCTTAA
4987695 ATAAATATAAATATAAAT
1 ATAAATATAAATATAAAT
4987713 ATAAA-ATAAATAATTAAAT
1 ATAAATATAAAT-A-TAAAT
*
4987732 AT--ATATAAATTTTAAAT
1 ATAAATATAAA-TATAAAT
4987749 ATAAATAT
1 ATAAATAT
4987757 GATAAATATA
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
17 14 0.38
18 11 0.30
19 12 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAAATATAAATATAAAT
Found at i:4987733 original size:31 final size:31
Alignment explanation
Indices: 4987696--4987755 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
4987686 GATTCTTAAA
4987696 TAAATATAAATATAAA-TATAAA-ATAAATAAT
1 TAAATAT--ATATAAATTATAAATATAAATAAT
*
4987727 TAAATATATATAAATTTTAAATATAAATA
1 TAAATATATATAAATTATAAATATAAATA
4987756 TGATAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 7 0.27
30 5 0.19
31 14 0.54
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (31 bp):
TAAATATATATAAATTATAAATATAAATAAT
Found at i:4988989 original size:24 final size:26
Alignment explanation
Indices: 4988962--4989011 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
4988952 TAATAAATAT
*
4988962 ATTAAATATATTATATT-T-TTTATA
1 ATTAAATATATCATATTATATTTATA
4988986 ATTAAATATATCATATTATATTTATA
1 ATTAAATATATCATATTATATTTATA
4989012 TTATTTTCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.70
25 1 0.04
26 6 0.26
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (26 bp):
ATTAAATATATCATATTATATTTATA
Found at i:4997001 original size:13 final size:13
Alignment explanation
Indices: 4996983--4997007 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4996973 ATCTTGCAAG
4996983 TCCAAGATCGAGT
1 TCCAAGATCGAGT
4996996 TCCAAGATCGAG
1 TCCAAGATCGAG
4997008 GAAAGAACCT
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:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (13 bp):
TCCAAGATCGAGT
Found at i:4998641 original size:2 final size:2
Alignment explanation
Indices: 4998598--4998626 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4998588 AGGAGAATAC
4998598 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4998627 ATTCTTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4998760 original size:3 final size:3
Alignment explanation
Indices: 4998752--4998798 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
4998742 AAAGAGGATC
4998752 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
4998799 GACAATCTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4999142 original size:18 final size:18
Alignment explanation
Indices: 4999100--4999143 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
4999090 AAACTTATTT
*
4999100 AAATGTAATAAAATATAA
1 AAATTTAATAAAATATAA
*
4999118 AATTTTAATAAAATA-AA
1 AAATTTAATAAAATATAA
4999135 ATAATTTAA
1 A-AATTTAA
4999144 CTTTTTATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
AAATTTAATAAAATATAA
Found at i:4999315 original size:23 final size:24
Alignment explanation
Indices: 4999289--4999334 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
4999279 TATTTTATTT
4999289 ATTAATAATATA-TAAATATAAAA
1 ATTAATAATATATTAAATATAAAA
*
4999312 ATTATTAATATATTAAATATAAA
1 ATTAATAATATATTAAATATAAA
4999335 TACAACAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
ATTAATAATATATTAAATATAAAA
Found at i:4999882 original size:2 final size:2
Alignment explanation
Indices: 4999875--4999899 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4999865 AATTAATTAC
4999875 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 T
4999900 CATTGGGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5000288 original size:89 final size:91
Alignment explanation
Indices: 5000133--5000310 Score: 308
Period size: 90 Copynumber: 2.0 Consensus size: 91
5000123 ATATTAATAT
5000133 TTTATTTATTCATAATATAATTAAAAAAAGTCATCAATTATTTTAAAATTCATTATCCTGTCCTT
1 TTTATTTATTCATAATATAATTAAAAAAAGTCATCAATTATTTTAAAATTCATTATCCTGTCCTT
*
5000198 TG-TCGTCTCGATAGGTTCACATTGA
66 TGTTCGTCTCGATAGATTCACATTGA
5000223 TTTATTTATTCATAATATAATTAAAAAAA-TCTATCAA-TATTTTAAAATTCATTATCCTGTCCT
1 TTTATTTATTCATAATATAATTAAAAAAAGTC-ATCAATTATTTTAAAATTCATTATCCTGTCCT
*
5000286 TTGTTCGTCTTGATAGATTCACATT
65 TTGTTCGTCTCGATAGATTCACATT
5000311 TACTTTTAAA
Statistics
Matches: 84, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
89 31 0.37
90 53 0.63
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (91 bp):
TTTATTTATTCATAATATAATTAAAAAAAGTCATCAATTATTTTAAAATTCATTATCCTGTCCTT
TGTTCGTCTCGATAGATTCACATTGA
Found at i:5000370 original size:6 final size:6
Alignment explanation
Indices: 5000354--5000513 Score: 61
Period size: 6 Copynumber: 26.2 Consensus size: 6
5000344 TAAATAAATA
*
5000354 ATTTAAT ATTTAT ATTTAA ATTTAAT AATTTAT A-TTAT ATTTAT ATTTAAAAT
1 ATTT-AT ATTTAT ATTTAT ATTT-AT -ATTTAT ATTTAT ATTTAT ATTT---AT
** * * *
5000407 ATTATAT ATTTAT ATAAAT -TTTA- ATATAT -TTATAT ATTTAC A-TAAT
1 ATT-TAT ATTTAT ATTTAT ATTTAT ATTTAT ATT-TAT ATTTAT ATTTAT
* *
5000453 ATTTAT A-TTAT ATTTTAAT ATTT-T A-TTAT TTTTAAT ATTATTAA ATTTAT
1 ATTTAT ATTTAT A-TTT-AT ATTTAT ATTTAT ATTT-AT A-T-TTAT ATTTAT
5000503 A--TAT ATTTAT A
1 ATTTAT ATTTAT A
5000514 AACTATTTCA
Statistics
Matches: 115, Mismatches: 16, Indels: 45
0.65 0.09 0.26
Matches are distributed among these distances:
4 6 0.05
5 22 0.19
6 47 0.41
7 22 0.19
8 10 0.09
9 7 0.06
10 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (6 bp):
ATTTAT
Found at i:5000372 original size:26 final size:26
Alignment explanation
Indices: 5000335--5000421 Score: 83
Period size: 26 Copynumber: 3.3 Consensus size: 26
5000325 ACTTACAACA
5000335 ATTTA-ATCTTAAA-TAAATAATTTAAT
1 ATTTATAT-TTAAATTAAATAATTT-AT
*
5000361 ATTTATATTTAAATTTAATAATTTAT
1 ATTTATATTTAAATTAAATAATTTAT
*
5000387 A-TTATATTTATATTTAAA-ATATTATAT
1 ATTTATATTTA-AATTAAATA-ATT-TAT
5000414 ATTTATAT
1 ATTTATAT
5000422 AAATTTTAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
25 10 0.19
26 21 0.40
27 15 0.29
28 6 0.12
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (26 bp):
ATTTATATTTAAATTAAATAATTTAT
Found at i:5000375 original size:19 final size:18
Alignment explanation
Indices: 5000353--5000491 Score: 76
Period size: 19 Copynumber: 7.6 Consensus size: 18
5000343 TTAAATAAAT
5000353 AATTTAATATTTATATTTA
1 AATTTAATATTTATA-TTA
5000372 AATTTAATAATTTATATTA
1 AATTTAAT-ATTTATATTA
*
5000391 TATTT-ATA-TT-TA--A
1 AATTTAATATTTATATTA
5000404 AATATTATATATTTATA-TA
1 AAT-TTA-ATATTTATATTA
*
5000423 AATTTTAATATATTTATATATT
1 AA-TTT-A-ATATTTATAT-TA
* **
5000445 TACATAATATTTATATTA
1 AATTTAATATTTATATTA
*
5000463 TATTTTAATATTT-TATTA
1 -AATTTAATATTTATATTA
**
5000481 TTTTTAATATT
1 AATTTAATATT
5000492 ATTAAATTTA
Statistics
Matches: 96, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
13 3 0.03
14 2 0.02
15 2 0.02
16 5 0.05
17 13 0.14
18 10 0.10
19 38 0.40
20 20 0.21
21 1 0.01
22 2 0.02
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (18 bp):
AATTTAATATTTATATTA
Found at i:5000408 original size:20 final size:20
Alignment explanation
Indices: 5000385--5000504 Score: 59
Period size: 20 Copynumber: 5.8 Consensus size: 20
5000375 TTAATAATTT
5000385 ATATTATATTTATATTTAAA
1 ATATTATATTTATATTTAAA
*
5000405 ATATTATATATT-TATATAAA
1 ATATTATAT-TTATATTTAAA
* *
5000425 TTTTAATATATTTATATATTTACATA
1 --ATATTATA-TT-TATATTTA-A-A
*
5000451 ATATT-TATATTATATTT-TA
1 ATATTATAT-TTATATTTAAA
* *
5000470 ATATTTTA-TTATTTTTAATA
1 ATATTATATTTATATTTAA-A
* *
5000490 TTATTAAATTTATAT
1 ATATTATATTTATAT
5000505 ATATTTATAA
Statistics
Matches: 74, Mismatches: 13, Indels: 25
0.66 0.12 0.22
Matches are distributed among these distances:
18 7 0.09
19 6 0.08
20 24 0.32
21 7 0.09
22 15 0.20
23 5 0.07
24 8 0.11
25 1 0.01
26 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATTATATTTATATTTAAA
Found at i:5000470 original size:67 final size:67
Alignment explanation
Indices: 5000364--5000511 Score: 152
Period size: 67 Copynumber: 2.2 Consensus size: 67
5000354 ATTTAATATT
5000364 TATATTTA-A-ATTTAATAATTTATATTATATTTATATTTAAAATATTATATATTTATATAA-AT
1 TATATTTATATATTTAATAA-TTATATTATATTTATATTTAAAATATTAT-TATTT-T-TAATAT
5000426 T-TTAA
62 TATTAA
* *
5000431 TATATTTATATATTTACATAA-TAT-TTATA-TTATATTTTAATATTTTATTATTTTTAATATTA
1 TATATTTATATATTTA-ATAATTATATTATATTTATA-TTTAAAATATTATTATTTTTAATATTA
5000493 TTAA
64 TTAA
5000497 -AT-TTATATATATTTA
1 TATATT-TATATATTTA
5000512 TAAACTATTT
Statistics
Matches: 72, Mismatches: 2, Indels: 16
0.80 0.02 0.18
Matches are distributed among these distances:
64 5 0.07
65 16 0.22
66 14 0.19
67 24 0.33
68 4 0.06
69 5 0.07
70 4 0.06
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (67 bp):
TATATTTATATATTTAATAATTATATTATATTTATATTTAAAATATTATTATTTTTAATATTATT
AA
Found at i:5000482 original size:27 final size:29
Alignment explanation
Indices: 5000395--5000513 Score: 80
Period size: 26 Copynumber: 4.3 Consensus size: 29
5000385 ATATTATATT
*
5000395 TATATTTA-A-AATATTA-TATATTTATA
1 TATATTTATATAATATTATTAAATTTATA
* * *
5000421 TAAATTT-TA-ATATATT-TATATATTTACA
1 TATATTTATATA-ATATTAT-TAAATTTATA
*
5000449 TAATATTTATATTATATT-TTAATATTT-TA
1 T-ATATTTATATAATATTATTAA-ATTTATA
5000478 T-TATTT-T-TAATATTATTAAATTTATA
1 TATATTTATATAATATTATTAAATTTATA
5000504 TATATTTATA
1 TATATTTATA
5000514 AACTATTTCA
Statistics
Matches: 73, Mismatches: 7, Indels: 23
0.71 0.07 0.22
Matches are distributed among these distances:
25 10 0.14
26 16 0.22
27 15 0.21
28 11 0.15
29 9 0.12
30 12 0.16
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (29 bp):
TATATTTATATAATATTATTAAATTTATA
Found at i:5000493 original size:15 final size:17
Alignment explanation
Indices: 5000386--5000512 Score: 68
Period size: 18 Copynumber: 7.2 Consensus size: 17
5000376 TAATAATTTA
5000386 TATTATA-TTT-ATATT
1 TATTATATTTTAATATT
** *
5000401 TAAAATATTAT-ATATT
1 TATTATATTTTAATATT
*
5000417 TATATAAATTTTAATATAT
1 TAT-TATATTTTAATAT-T
5000436 T-TATATATTTACATAATATTT
1 TAT-TATATTT---TAATA-TT
5000457 ATATTATATTTTAATATTT
1 -TATTATATTTTAATA-TT
5000476 TATTAT-TTTTAATA-T
1 TATTATATTTTAATATT
*
5000491 TATTAAATTTATATATATT
1 TATTATATTT-TA-ATATT
5000510 TAT
1 TAT
5000513 AAACTATTTC
Statistics
Matches: 89, Mismatches: 9, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
15 11 0.12
16 12 0.13
17 15 0.17
18 21 0.24
19 14 0.16
21 6 0.07
22 9 0.10
23 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTATATTTTAATATT
Found at i:5000500 original size:17 final size:17
Alignment explanation
Indices: 5000412--5000514 Score: 66
Period size: 17 Copynumber: 5.6 Consensus size: 17
5000402 AAAATATTAT
*
5000412 ATATTTATATAAATTTTA
1 ATATTT-TATAATTTTTA
*
5000430 ATATATTTATATATTTACATA
1 ATAT-TTTATA-ATTT--TTA
*
5000451 ATATTTATATTATATTTTA
1 ATATTT-TATAAT-TTTTA
*
5000470 ATATTTTATTATTTTTA
1 ATATTTTATAATTTTTA
*
5000487 ATATTATTA-AATTTAT-
1 ATATT-TTATAATTTTTA
5000503 ATATATTTATAA
1 ATAT-TTTATAA
5000515 ACTATTTCAT
Statistics
Matches: 70, Mismatches: 6, Indels: 19
0.74 0.06 0.20
Matches are distributed among these distances:
16 7 0.10
17 18 0.26
18 17 0.24
19 13 0.19
20 4 0.06
21 11 0.16
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATTTTATAATTTTTA
Found at i:5000537 original size:91 final size:92
Alignment explanation
Indices: 5000357--5000538 Score: 216
Period size: 91 Copynumber: 2.0 Consensus size: 92
5000347 ATAAATAATT
5000357 TAATATTTATATTTAAATTTAATAATTTATATTATATTTATATTTAAAATATTATATATTTATAT
1 TAATATTTATATTTAAATTTAATAATTTATATTATATTTATATTTAAAATATTATATATTTATAT
*
5000422 AAATTTTAATATATTTATATATTTACA
66 AAATTTTAATATAATTATATATTTACA
* * *
5000449 TAATATTTATA-TTATATTTTAAT-ATTT-TATTATTTTTAATATTATTAAAT-TTATATATATT
1 TAATATTTATATTTA-AATTTAATAATTTATATTATATTT-ATATT-TAAAATATTATATAT-TT
*
5000510 -TATAAACTATTTCATATAATT-T-TATTTAC
62 ATATAAA-T-TTTAATATAATTATATATTTAC
5000539 TTGGTAGATA
Statistics
Matches: 79, Mismatches: 5, Indels: 13
0.81 0.05 0.13
Matches are distributed among these distances:
90 9 0.11
91 33 0.42
92 27 0.34
93 10 0.13
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (92 bp):
TAATATTTATATTTAAATTTAATAATTTATATTATATTTATATTTAAAATATTATATATTTATAT
AAATTTTAATATAATTATATATTTACA
Found at i:5000710 original size:2 final size:2
Alignment explanation
Indices: 5000703--5000732 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5000693 TAAACAAATA
5000703 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
5000733 GTATGTCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5006585 original size:2 final size:2
Alignment explanation
Indices: 5006578--5006617 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5006568 CATCTGCTGA
5006578 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5006618 GTATTATAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5015565 original size:21 final size:21
Alignment explanation
Indices: 5015527--5015587 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 21
5015517 AAAATTTATT
5015527 TTATTATTTATGATATTAATAAA
1 TTATTATTT-T-ATATTAATAAA
*
5015550 TTATTATTTTATATTAATATA
1 TTATTATTTTATATTAATAAA
*
5015571 TATATTGTTTTA-ATTAA
1 T-TATTATTTTATATTAA
5015588 ATTAAATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.46
22 10 0.29
23 9 0.26
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.57
Consensus pattern (21 bp):
TTATTATTTTATATTAATAAA
Found at i:5023640 original size:15 final size:15
Alignment explanation
Indices: 5023617--5023667 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
5023607 TCTTTTCAAA
5023617 TATAATATAAATATT
1 TATAATATAAATATT
* **
5023632 TATATTATATTTATT
1 TATAATATAAATATT
*
5023647 TTTAATATAATATATT
1 TATAATATAA-ATATT
5023663 TATAA
1 TATAA
5023668 CTATTTTAAC
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
15 19 0.70
16 8 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATAATATAAATATT
Found at i:5023675 original size:11 final size:11
Alignment explanation
Indices: 5023622--5023866 Score: 86
Period size: 10 Copynumber: 23.8 Consensus size: 11
5023612 TCAAATATAA
5023622 TATAA-ATATT
1 TATAATATATT
*
5023632 TATATTATATT
1 TATAATATATT
* * *
5023643 TAT-TTTTA-A
1 TATAATATATT
5023652 TATAATATATT
1 TATAATATATT
*
5023663 TATAA-CTATT
1 TATAATATATT
* *
5023673 T-TAACATA-A
1 TATAATATATT
5023682 TATAATA-A-T
1 TATAATATATT
*
5023691 AATAATATA-T
1 TATAATATATT
*
5023701 TAT-ATAAATT
1 TATAATATATT
5023711 T-T-ATATATT
1 TATAATATATT
5023720 TAT-ATCATATT
1 TATAAT-ATATT
* * *
5023731 TATTATTTTTAT
1 TATAATATAT-T
*
5023743 TATATTATATT
1 TATAATATATT
* *
5023754 TATATTTTTATAT
1 TATA-ATATAT-T
5023767 TATAATTATATT
1 TATAA-TATATT
5023779 TATAATA-ATT
1 TATAATATATT
5023789 T-TAATATATT
1 TATAATATATT
*
5023799 AATAATAT-TAT
1 TATAATATAT-T
*
5023810 TAT-ATAAATT
1 TATAATATATT
*
5023820 T-TAATA-AAT
1 TATAATATATT
*
5023829 T-T-ACATATT
1 TATAATATATT
5023838 TAT-ATATATT
1 TATAATATATT
*
5023848 TATAAT-TTTT
1 TATAATATATT
*
5023858 TATTATATA
1 TATAATATA
5023867 ATATTTTATG
Statistics
Matches: 178, Mismatches: 34, Indels: 45
0.69 0.13 0.18
Matches are distributed among these distances:
8 2 0.01
9 39 0.22
10 65 0.37
11 43 0.24
12 20 0.11
13 9 0.05
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (11 bp):
TATAATATATT
Found at i:5023741 original size:28 final size:23
Alignment explanation
Indices: 5023720--5023872 Score: 84
Period size: 25 Copynumber: 6.5 Consensus size: 23
5023710 TTTATATATT
*
5023720 TATATCATATTTATTATTTTTAT-
1 TATATTATATTTA-TATTTTTATA
5023743 TATATTATATTTATATTTTTATA
1 TATATTATATTTATATTTTTATA
5023766 TTATAATTATATTTATAATAATTTTA-A
1 -TAT-ATTATATTTAT-AT--TTTTATA
* *
5023793 TATATTA-A-TAATATTATTATA
1 TATATTATATTTATATTTTTATA
* * * * **
5023814 TAAATTTTA-ATAAATTTACATA
1 TATATTATATTTATATTTTTATA
*
5023836 TTTATATATATTTATAATTTTT-TA
1 TATAT-TATATTTAT-ATTTTTATA
*
5023860 TTATATAATATTT
1 -TATATTATATTT
5023873 TATGTATTTT
Statistics
Matches: 98, Mismatches: 20, Indels: 23
0.70 0.14 0.16
Matches are distributed among these distances:
20 4 0.04
21 6 0.06
22 22 0.22
23 18 0.18
24 14 0.14
25 23 0.23
26 5 0.05
27 1 0.01
28 5 0.05
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (23 bp):
TATATTATATTTATATTTTTATA
Found at i:5023748 original size:14 final size:13
Alignment explanation
Indices: 5023727--5023781 Score: 51
Period size: 14 Copynumber: 4.2 Consensus size: 13
5023717 ATTTATATCA
*
5023727 TATTTATTATTTT
1 TATTTATTATATT
5023740 TATTATATTATATT
1 TATT-TATTATATT
*
5023754 TATATTTTTATA-T
1 TAT-TTATTATATT
*
5023767 TA-TAATTATATT
1 TATTTATTATATT
5023779 TAT
1 TAT
5023782 AATAATTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
11 6 0.18
12 3 0.09
13 7 0.21
14 17 0.50
15 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTTATTATATT
Found at i:5023752 original size:23 final size:23
Alignment explanation
Indices: 5023719--5023799 Score: 83
Period size: 23 Copynumber: 3.3 Consensus size: 23
5023709 TTTTATATAT
*
5023719 TTATATCATATTTATTATTTTTA
1 TTATATTATATTTATTATTTTTA
5023742 TTATATTATATTTA-TATTTTTATA
1 TTATATTATATTTATTA-TTTT-TA
*
5023766 TTATAATTATATTTATAATAATTTTA
1 TTAT-ATTATATTTAT--TATTTTTA
*
5023792 ATATATTA
1 TTATATTA
5023800 ATAATATTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
22 2 0.04
23 17 0.35
24 6 0.12
25 14 0.29
26 5 0.10
27 3 0.06
28 2 0.04
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATATTATATTTATTATTTTTA
Found at i:5023801 original size:17 final size:16
Alignment explanation
Indices: 5023762--5023856 Score: 63
Period size: 17 Copynumber: 5.9 Consensus size: 16
5023752 TTTATATTTT
*
5023762 TATATTATAATTAT-A
1 TATATTATAATTTTAA
* *
5023777 TTTATAATAATTTTAA
1 TATATTATAATTTTAA
* *
5023793 TATATTAATAATATTAT
1 TATATT-ATAATTTTAA
5023810 TATA-TA-AATTTTAA
1 TATATTATAATTTTAA
*
5023824 TAAATT-TACATATTTATA
1 TATATTATA-AT-TTTA-A
5023842 TATATTTATAATTTT
1 TATA-TTATAATTTT
5023857 TTATTATATA
Statistics
Matches: 60, Mismatches: 11, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
14 9 0.15
15 14 0.23
16 8 0.13
17 16 0.27
18 7 0.12
19 4 0.07
20 2 0.03
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (16 bp):
TATATTATAATTTTAA
Found at i:5023872 original size:118 final size:115
Alignment explanation
Indices: 5023631--5023893 Score: 308
Period size: 118 Copynumber: 2.3 Consensus size: 115
5023621 ATATAAATAT
5023631 TTATATTATA-TTTATTTTTA-A-TATAA-TATATTTATAACTATTTTAACATAATATAATAATA
1 TTATATTATATTTTATTTTTATATTATAATTATATTTATAACTATTTTAACATAATATAATAATA
* * *
5023692 ATAATATATTATATAAATTTTATATATTTATATCATATTTATTATTTTTA
66 ATAATAAATTATATAAATTTTACATATTTATATCATATTTATAATTTTTA
* *
5023742 TTATATTATATTTATATTTTTATATTATAATTATATTTATAA-TAATTTTAATATATTAATAATA
1 TTATATTATATTT-TATTTTTATATTATAATTATATTTATAACT-ATTTTAACATAAT-ATAATA
* * *
5023806 TTATTATATAAATTTTAATAAA-TTTACATATTTATAT-ATATTTATAATTTTTTA
63 ATAATA-ATAAATTAT-ATAAATTTTACATATTTATATCATATTTATAA-TTTTTA
* *
5023860 TTATATAATATTTTATGTATTT-TATTTTAATTAT
1 TTATATTATATTTTAT-T-TTTATATTATAATTAT
5023894 GTTATTGATT
Statistics
Matches: 130, Mismatches: 10, Indels: 17
0.83 0.06 0.11
Matches are distributed among these distances:
111 10 0.08
112 2 0.02
113 8 0.06
114 1 0.01
115 6 0.05
116 22 0.17
117 22 0.17
118 51 0.39
119 8 0.06
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (115 bp):
TTATATTATATTTTATTTTTATATTATAATTATATTTATAACTATTTTAACATAATATAATAATA
ATAATAAATTATATAAATTTTACATATTTATATCATATTTATAATTTTTA
Found at i:5024747 original size:12 final size:11
Alignment explanation
Indices: 5024719--5024779 Score: 56
Period size: 12 Copynumber: 5.5 Consensus size: 11
5024709 ATTTGTTACA
5024719 AATAATTTATT
1 AATAATTTATT
5024730 --TAATTTATTT
1 AATAATTTA-TT
5024740 AATAATTTATT
1 AATAATTTATT
*
5024751 AATTAATTTAAT
1 AA-TAATTTATT
*
5024763 -ATAATTTTACT
1 AATAA-TTTATT
5024774 AATAAT
1 AATAAT
5024780 ATTAAACTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
9 7 0.17
10 5 0.12
11 11 0.26
12 19 0.45
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (11 bp):
AATAATTTATT
Found at i:5024779 original size:22 final size:23
Alignment explanation
Indices: 5024741--5024784 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5024731 AATTTATTTA
*
5024741 ATAATTTATTAATTAAT-TTAAT
1 ATAATTTACTAATTAATATTAAT
5024763 ATAATTTTACTAA-TAATATTAA
1 ATAA-TTTACTAATTAATATTAA
5024785 ACTCAATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
ATAATTTACTAATTAATATTAAT
Found at i:5025178 original size:2 final size:2
Alignment explanation
Indices: 5025171--5025222 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
5025161 CATACACATC
5025171 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5025213 AT AT AT AT AT
1 AT AT AT AT AT
5025223 CTTCTCTATG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5025987 original size:20 final size:18
Alignment explanation
Indices: 5025954--5025996 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
5025944 TATTTATGTT
*
5025954 TAAATCTTTCAATTATTAAA
1 TAAATCTTT-AAAT-TTAAA
*
5025974 TAAATTTTTAAATTTAAA
1 TAAATCTTTAAATTTAAA
5025992 TAAAT
1 TAAAT
5025997 AATTTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 10 0.48
19 3 0.14
20 8 0.38
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAATCTTTAAATTTAAA
Found at i:5027587 original size:16 final size:16
Alignment explanation
Indices: 5027566--5027640 Score: 71
Period size: 17 Copynumber: 4.6 Consensus size: 16
5027556 ATTAATCTAA
5027566 ATTTAAATATAAAATG
1 ATTTAAATATAAAATG
*
5027582 ATTTAAATTTAAAATTG
1 ATTTAAATATAAAA-TG
*
5027599 ACTTAAACT-TAAAATG
1 ATTTAAA-TATAAAATG
* *
5027615 ATTCAAAATTTAAAATG
1 ATT-TAAATATAAAATG
*
5027632 ATTCAAATA
1 ATTTAAATA
5027641 ATTAACTCGA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
16 22 0.45
17 26 0.53
18 1 0.02
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.37
Consensus pattern (16 bp):
ATTTAAATATAAAATG
Found at i:5027803 original size:18 final size:18
Alignment explanation
Indices: 5027775--5027811 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
5027765 ACTCAAAATT
5027775 AAAATAATTT-AAATTTA
1 AAAATAATTTAAAATTTA
5027792 AAAATAAATTTAAAATTTA
1 AAAAT-AATTTAAAATTTA
5027811 A
1 A
5027812 TTCAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 5 0.28
19 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATAATTTAAAATTTA
Found at i:5028471 original size:2 final size:2
Alignment explanation
Indices: 5028461--5028492 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5028451 TATCAATGCA
5028461 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5028493 AAGGTTTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5028869 original size:31 final size:31
Alignment explanation
Indices: 5028834--5028899 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
5028824 TATTTAAATA
* *
5028834 ATAAAAT-TTAATTTTTTATTTAAAT-ATAAT
1 ATAAAATATTAATATTAT-TTTAAATAATAAT
5028864 -TATAAATATTAATATTATTTTAAATAATAAT
1 ATA-AAATATTAATATTATTTTAAATAATAAT
5028895 ATAAA
1 ATAAA
5028900 TTTTTAAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
29 2 0.07
30 11 0.37
31 15 0.50
32 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
ATAAAATATTAATATTATTTTAAATAATAAT
Found at i:5028877 original size:18 final size:18
Alignment explanation
Indices: 5028856--5028898 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
5028846 TTTTTATTTA
*
5028856 AATATAATTATAAATATT
1 AATATAATTATAAATAAT
* *
5028874 AATATTATTTTAAATAAT
1 AATATAATTATAAATAAT
5028892 AATATAA
1 AATATAA
5028899 ATTTTTAAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATATAATTATAAATAAT
Found at i:5029011 original size:2 final size:2
Alignment explanation
Indices: 5029006--5029032 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5028996 AAAATTATTT
5029006 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 T
5029033 GTATGCATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5029494 original size:21 final size:21
Alignment explanation
Indices: 5029468--5029543 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 21
5029458 AAATTATTTC
5029468 AATTATTTAATTAATAATTAA
1 AATTATTTAATTAATAATTAA
**
5029489 AATTATTTTAATTGATTATAAAAAA
1 AATTA-TTTAATT-A--ATAATTAA
* * *
5029514 AATTTAATTAATCAGTAATTAA
1 AA-TTATTTAATTAATAATTAA
5029536 AATTATTT
1 AATTATTT
5029544 TGATTTATTA
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
21 10 0.24
22 14 0.33
23 1 0.02
24 1 0.02
25 13 0.31
26 3 0.07
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (21 bp):
AATTATTTAATTAATAATTAA
Found at i:5030138 original size:28 final size:28
Alignment explanation
Indices: 5030106--5030163 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
5030096 TAATATATAA
*
5030106 TTAAATAAAAATTT-AAATTAA-TTTAAAT
1 TTAAA-AAAAATTTCAAA-AAATTTTAAAT
*
5030134 TTAAAAAATATTTCAAAAAATTTTAAAT
1 TTAAAAAAAATTTCAAAAAATTTTAAAT
5030162 TT
1 TT
5030164 TGATCCAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 9 0.35
28 17 0.65
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (28 bp):
TTAAAAAAAATTTCAAAAAATTTTAAAT
Found at i:5030525 original size:15 final size:16
Alignment explanation
Indices: 5030489--5030528 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
5030479 TTTAATATTT
*
5030489 ATAAAATTTTTCATTAA
1 ATAAAA-TTATCATTAA
5030506 ATAAAATTATCATT-A
1 ATAAAATTATCATTAA
5030521 ATAAAATT
1 ATAAAATT
5030529 TATTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTATCATTAA
Found at i:5030531 original size:16 final size:17
Alignment explanation
Indices: 5030489--5030531 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
5030479 TTTAATATTT
*
5030489 ATAAAATTTTTCATTAA
1 ATAAAATTTATCATTAA
5030506 ATAAAA-TTATCATT-A
1 ATAAAATTTATCATTAA
5030521 ATAAAATTTAT
1 ATAAAATTTAT
5030532 TTAAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATTTATCATTAA
Found at i:5030586 original size:37 final size:34
Alignment explanation
Indices: 5030489--5030587 Score: 87
Period size: 37 Copynumber: 2.8 Consensus size: 34
5030479 TTTAATATTT
*
5030489 ATAAAATTTTTCATTAAA-TAAAAT-TATCATTA
1 ATAAAATTTTTTATTAAATTAAAATATATCATTA
* *
5030521 ATAAAATTTATTTA-AAAATAATACAAATATATTATTA
1 ATAAAATTT-TTTATTAAAT--TA-AAATATATCATTA
5030558 ATACATAAATTTTTTATTAAATTAAAATAT
1 AT--A-AAATTTTTTATTAAATTAAAATAT
5030588 TATGATAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
32 12 0.23
33 3 0.06
35 2 0.04
36 4 0.08
37 15 0.28
38 2 0.04
39 5 0.09
40 10 0.19
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (34 bp):
ATAAAATTTTTTATTAAATTAAAATATATCATTA
Found at i:5031045 original size:8 final size:8
Alignment explanation
Indices: 5031032--5031061 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
5031022 AATACATATA
5031032 TTTTTTCT
1 TTTTTTCT
5031040 TTTTTTCT
1 TTTTTTCT
*
5031048 TTCTTTCT
1 TTTTTTCT
5031056 TTTTTT
1 TTTTTT
5031062 TTATAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTCT
Found at i:5031957 original size:12 final size:12
Alignment explanation
Indices: 5031937--5032002 Score: 64
Period size: 12 Copynumber: 5.4 Consensus size: 12
5031927 TATGAATATC
*
5031937 ATATGTATAAAA
1 ATATATATAAAA
5031949 ATATATAT-AAA
1 ATATATATAAAA
*
5031960 ATA-AAATAAATA
1 ATATATATAAA-A
5031972 ATTAATATATAAAA
1 A-T-ATATATAAAA
*
5031986 ATTTATATAAAA
1 ATATATATAAAA
5031998 ATATA
1 ATATA
5032003 ATATTTTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
10 3 0.07
11 8 0.18
12 22 0.50
13 2 0.05
14 3 0.07
15 6 0.14
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (12 bp):
ATATATATAAAA
Found at i:5031995 original size:27 final size:27
Alignment explanation
Indices: 5031948--5032034 Score: 74
Period size: 27 Copynumber: 3.3 Consensus size: 27
5031938 TATGTATAAA
5031948 AATATATATAAAATAAAATAAATAAT-T
1 AATATATATAAAATAAAATAAA-AATAT
* *
5031975 AATATATA-AAAATTTATATAAAAATAT
1 AATATATATAAAA-TAAAATAAAAATAT
* * *
5032002 AATAT-TTTAAATATAGAATAATAATAT
1 AATATATATAAA-ATAAAATAAAAATAT
5032029 AA-ATAT
1 AATATAT
5032035 CAACATATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
26 10 0.21
27 37 0.77
28 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (27 bp):
AATATATATAAAATAAAATAAAAATAT
Found at i:5032075 original size:4 final size:4
Alignment explanation
Indices: 5032066--5032106 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
5032056 TGTTTTTCTC
* *
5032066 CTTT CTTT CTTT CTTT CTTTT TTTT CTTT CTTT CTTC CTTT
1 CTTT CTTT CTTT CTTT C-TTT CTTT CTTT CTTT CTTT CTTT
5032107 TTCACGATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
4 29 0.91
5 3 0.09
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
CTTT
Found at i:5032093 original size:13 final size:13
Alignment explanation
Indices: 5032045--5032098 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
5032035 CAACATATAA
5032045 TTTTTTTCTTT-T
1 TTTTTTTCTTTCT
*
5032057 GTTTTTCTCCTTTC-
1 -TTTTT-TTCTTTCT
*
5032071 TTTCTTTCTTTCT
1 TTTTTTTCTTTCT
5032084 TTTTTTTCTTTCT
1 TTTTTTTCTTTCT
5032097 TT
1 TT
5032099 CTTCCTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 6 0.18
13 23 0.68
14 5 0.15
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.80
Consensus pattern (13 bp):
TTTTTTTCTTTCT
Found at i:5032093 original size:21 final size:21
Alignment explanation
Indices: 5032067--5032108 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
5032057 GTTTTTCTCC
*
5032067 TTTCTTTCTTTCTTTCTTTTT
1 TTTCTTTCTTTCTTCCTTTTT
5032088 TTTCTTTCTTTCTTCCTTTTT
1 TTTCTTTCTTTCTTCCTTTTT
5032109 CACGATAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTCTTTCTTTCTTCCTTTTT
Found at i:5032107 original size:17 final size:17
Alignment explanation
Indices: 5032071--5032107 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5032061 TTCTCCTTTC
**
5032071 TTTCTTTCTTTCTTTTT
1 TTTCTTTCTTTCTTCCT
5032088 TTTCTTTCTTTCTTCCT
1 TTTCTTTCTTTCTTCCT
5032105 TTT
1 TTT
5032108 TCACGATAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTCTTTCTTTCTTCCT
Found at i:5032197 original size:13 final size:13
Alignment explanation
Indices: 5032179--5032230 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
5032169 CAAAATAGAT
*
5032179 TAATATATAGATA
1 TAATATATAAATA
*
5032192 TAATATATAAAAA
1 TAATATATAAATA
5032205 TAAT-TA-AAATA
1 TAATATATAAATA
*
5032216 TAATATAAAAATA
1 TAATATATAAATA
5032229 TA
1 TA
5032231 CGATTATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
11 8 0.24
12 4 0.12
13 22 0.65
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (13 bp):
TAATATATAAATA
Found at i:5032230 original size:30 final size:31
Alignment explanation
Indices: 5032170--5032230 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
5032160 TAGGTAGTTC
* *
5032170 AAAATAGATTAATATATAGATATAATATATA
1 AAAATAGATTAAAATATAGATATAAAATATA
5032201 AAAATA-ATTAAAATATA-ATATAAAAATATA
1 AAAATAGATTAAAATATAGATAT-AAAATATA
5032231 CGATTATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 4 0.15
30 17 0.63
31 6 0.22
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (31 bp):
AAAATAGATTAAAATATAGATATAAAATATA
Found at i:5035559 original size:24 final size:23
Alignment explanation
Indices: 5035532--5035583 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
5035522 ATATCACTTG
*
5035532 ATAAATTCAAAATAAATAATAAAT
1 ATAAATTCAAAATAAA-AATAAAA
* *
5035556 ATAAATTTAATATAAAAATAAAA
1 ATAAATTCAAAATAAAAATAAAA
5035579 ATAAA
1 ATAAA
5035584 AATTTTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (23 bp):
ATAAATTCAAAATAAAAATAAAA
Found at i:5035658 original size:12 final size:11
Alignment explanation
Indices: 5035632--5035674 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
5035622 AAATTAATAA
*
5035632 AAAAATTAAATT
1 AAAAA-TAAAGT
5035644 AAAAATAAAGAT
1 AAAAATAAAG-T
*
5035656 AAAAATAATGT
1 AAAAATAAAGT
5035667 AAAAATAA
1 AAAAATAA
5035675 TACCATTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 13 0.46
12 15 0.54
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (11 bp):
AAAAATAAAGT
Found at i:5035669 original size:11 final size:12
Alignment explanation
Indices: 5035643--5035675 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
5035633 AAAATTAAAT
*
5035643 TAAAAATAAAGA
1 TAAAAATAATGA
5035655 TAAAAATAATG-
1 TAAAAATAATGA
5035666 TAAAAATAAT
1 TAAAAATAAT
5035676 ACCATTGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (12 bp):
TAAAAATAATGA
Found at i:5035752 original size:14 final size:15
Alignment explanation
Indices: 5035733--5035761 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5035723 TTTTAAAAAA
5035733 ATAAAAAT-AATTTT
1 ATAAAAATAAATTTT
5035747 ATAAAAATAAATTTT
1 ATAAAAATAAATTTT
5035762 TGATTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAAAAATAAATTTT
Done.