Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 117 of 120
Found at i:35691732 original size:19 final size:19
Alignment explanation
Indices: 35691689--35691749 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
35691679 CACTCTCGAG
* *
35691689 AAAATTATAAAAAATTTAATA
1 AAAATTATATAAAA-TT-CTA
35691710 AAAATTA-ATTAAAATTCTA
1 AAAATTATA-TAAAATTCTA
*
35691729 AAAATTATATAAAATTTTA
1 AAAATTATATAAAATTCTA
35691748 AA
1 AA
35691750 TTTAAAATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 20 0.57
20 4 0.11
21 11 0.31
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATTATATAAAATTCTA
Found at i:35691734 original size:9 final size:9
Alignment explanation
Indices: 35691689--35691749 Score: 50
Period size: 10 Copynumber: 6.2 Consensus size: 9
35691679 CACTCTCGAG
35691689 AAAATTATAA
1 AAAATTAT-A
35691699 AAAATTTAATA
1 AAAA-TT-ATA
*
35691710 AAAATTAATT
1 AAAATT-ATA
*
35691720 AAAATTCTA
1 AAAATTATA
35691729 AAAATTATA
1 AAAATTATA
*
35691738 TAAAATTTTA
1 -AAAATTATA
35691748 AA
1 AA
35691750 TTTAAAATGA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
9 11 0.26
10 23 0.53
11 7 0.16
12 2 0.05
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (9 bp):
AAAATTATA
Found at i:35695571 original size:15 final size:15
Alignment explanation
Indices: 35695553--35695582 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35695543 TCGATTTTTC
35695553 CTTTTTTCTTTTTGA
1 CTTTTTTCTTTTTGA
*
35695568 CTTTTTTTTTTTTGA
1 CTTTTTTCTTTTTGA
35695583 AAATAAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.10, G:0.07, T:0.77
Consensus pattern (15 bp):
CTTTTTTCTTTTTGA
Found at i:35709678 original size:18 final size:17
Alignment explanation
Indices: 35709621--35709682 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 17
35709611 AACATCTCTT
*
35709621 TTAAAAAATTATATAAAA
1 TTAAAAAA-TAAATAAAA
* *
35709639 TGAAAATATAAATTAAACA
1 TTAAAAAATAAA-TAAA-A
35709658 TTAAATAAATAAATAAAA
1 TTAAA-AAATAAATAAAA
35709676 TTAAAAA
1 TTAAAAA
35709683 GAAAATTGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
17 5 0.14
18 16 0.44
19 9 0.25
20 6 0.17
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (17 bp):
TTAAAAAATAAATAAAA
Found at i:35710022 original size:26 final size:27
Alignment explanation
Indices: 35709970--35710027 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 27
35709960 TATTTTTTTA
* * **
35709970 TTTTTAATATTCAATTTTAATTTAATT
1 TTTTTAAAATTCAATTTAAATCAAATT
35709997 TTTTTAAAATT-AATTTAAATCAAATT
1 TTTTTAAAATTCAATTTAAATCAAATT
*
35710023 GTTTT
1 TTTTT
35710028 GATCATATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (27 bp):
TTTTTAAAATTCAATTTAAATCAAATT
Found at i:35726495 original size:20 final size:20
Alignment explanation
Indices: 35726470--35726531 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
35726460 ACATTCATTT
35726470 AAACCAAACCCATTTAAACC
1 AAACCAAACCCATTTAAACC
35726490 AAACCAAACCCATTTAAACC
1 AAACCAAACCCATTTAAACC
* *
35726510 TAACCAAACCCATTTGAACC
1 AAACCAAACCCATTTAAACC
35726530 AA
1 AA
35726532 GTCCAACCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.48, C:0.34, G:0.02, T:0.16
Consensus pattern (20 bp):
AAACCAAACCCATTTAAACC
Found at i:35726514 original size:15 final size:15
Alignment explanation
Indices: 35726465--35726494 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
35726455 AACCCACATT
35726465 CATTTAAACCAAACC
1 CATTTAAACCAAACC
35726480 CATTTAAACCAAACC
1 CATTTAAACCAAACC
35726495 AAACCCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (15 bp):
CATTTAAACCAAACC
Found at i:35726591 original size:11 final size:11
Alignment explanation
Indices: 35726565--35726603 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
35726555 CATTGACCGG
*
35726565 CGTTGACCG-G
1 CGTTGACCGAC
*
35726575 CGTTGATCGAC
1 CGTTGACCGAC
35726586 CGTTGACCGAC
1 CGTTGACCGAC
35726597 CGTTGAC
1 CGTTGAC
35726604 TTTGATTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (11 bp):
CGTTGACCGAC
Found at i:35726628 original size:14 final size:14
Alignment explanation
Indices: 35726594--35726665 Score: 83
Period size: 14 Copynumber: 5.2 Consensus size: 14
35726584 ACCGTTGACC
35726594 GACCGTTGACT-TT
1 GACCGTTGACTGTT
**
35726607 GATTGTTGACTGTT
1 GACCGTTGACTGTT
***
35726621 GACCGTTGACAACT
1 GACCGTTGACTGTT
35726635 GACCGTTGACTGTT
1 GACCGTTGACTGTT
*
35726649 GACCGTTGACCGTT
1 GACCGTTGACTGTT
35726663 GAC
1 GAC
35726666 TTTGACCTTT
Statistics
Matches: 47, Mismatches: 11, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
13 9 0.19
14 38 0.81
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.33
Consensus pattern (14 bp):
GACCGTTGACTGTT
Found at i:35726658 original size:21 final size:20
Alignment explanation
Indices: 35726594--35726678 Score: 80
Period size: 21 Copynumber: 4.2 Consensus size: 20
35726584 ACCGTTGACC
**
35726594 GACCGTTGACTTTGATTGTT
1 GACCGTTGACTTTGACCGTT
* * ***
35726614 GACTGTTGACCGTTGACAACT
1 GACCGTTGA-CTTTGACCGTT
35726635 GACCGTTGACTGTTGACCGTT
1 GACCGTTGACT-TTGACCGTT
*
35726656 GACCGTTGACTTTGACCTTT
1 GACCGTTGACTTTGACCGTT
35726676 GAC
1 GAC
35726679 TTTTTTCGAA
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
20 20 0.39
21 31 0.61
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (20 bp):
GACCGTTGACTTTGACCGTT
Found at i:35726675 original size:7 final size:7
Alignment explanation
Indices: 35726583--35726678 Score: 67
Period size: 7 Copynumber: 14.4 Consensus size: 7
35726573 GGCGTTGATC
35726583 GACCGTT
1 GACCGTT
35726590 GACC---
1 GACCGTT
35726594 GACCGTT
1 GACCGTT
*
35726601 GA-CTTT
1 GACCGTT
**
35726607 GATTGTT
1 GACCGTT
*
35726614 GACTGTT
1 GACCGTT
35726621 GACCGTT
1 GACCGTT
***
35726628 GACAACT
1 GACCGTT
35726635 GACCGTT
1 GACCGTT
*
35726642 GACTGTT
1 GACCGTT
35726649 GACCGTT
1 GACCGTT
35726656 GACCGTT
1 GACCGTT
*
35726663 GA-CTTT
1 GACCGTT
*
35726669 GACCTTT
1 GACCGTT
35726676 GAC
1 GAC
35726679 TTTTTTCGAA
Statistics
Matches: 70, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
4 4 0.06
6 10 0.14
7 56 0.80
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.33
Consensus pattern (7 bp):
GACCGTT
Found at i:35727740 original size:3 final size:3
Alignment explanation
Indices: 35727728--35727760 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
35727718 TATTCTATTC
35727728 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
35727761 TTGGGATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:35733256 original size:15 final size:15
Alignment explanation
Indices: 35733211--35733250 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
35733201 ACCCACATTC
*
35733211 ATTTAAACCAAACCA
1 ATTTGAACCAAACCA
35733226 ATTTGAACCAAACCA
1 ATTTGAACCAAACCA
35733241 A-TTGAACCAA
1 ATTTGAACCAA
35733251 GTCCAACCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 9 0.38
15 15 0.62
ACGTcount: A:0.50, C:0.25, G:0.05, T:0.20
Consensus pattern (15 bp):
ATTTGAACCAAACCA
Found at i:35733310 original size:11 final size:11
Alignment explanation
Indices: 35733294--35733332 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
35733284 CGTTGACCGG
35733294 CGTTGATCGAC
1 CGTTGATCGAC
*
35733305 CGTTGATTGAC
1 CGTTGATCGAC
*
35733316 CGTTGACCGAC
1 CGTTGATCGAC
35733327 CGTTGA
1 CGTTGA
35733333 CTTTGACCGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.28
Consensus pattern (11 bp):
CGTTGATCGAC
Found at i:35733326 original size:22 final size:23
Alignment explanation
Indices: 35733294--35733346 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
35733284 CGTTGACCGG
*
35733294 CGTTGATCGACCGTTGA-TTGAC
1 CGTTGACCGACCGTTGACTTGAC
35733316 CGTTGACCGACCGTTGACTTTGAC
1 CGTTGACCGACCGTTGAC-TTGAC
35733340 CGTTGAC
1 CGTTGAC
35733347 TTTTTTCGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 16 0.57
24 12 0.43
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.30
Consensus pattern (23 bp):
CGTTGACCGACCGTTGACTTGAC
Found at i:35733333 original size:11 final size:11
Alignment explanation
Indices: 35733284--35733333 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
35733274 CATTGACCGG
*
35733284 CGTTGACCG-G
1 CGTTGACCGAC
*
35733294 CGTTGATCGAC
1 CGTTGACCGAC
**
35733305 CGTTGATTGAC
1 CGTTGACCGAC
35733316 CGTTGACCGAC
1 CGTTGACCGAC
35733327 CGTTGAC
1 CGTTGAC
35733334 TTTGACCGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 8 0.24
11 26 0.76
ACGTcount: A:0.16, C:0.28, G:0.30, T:0.26
Consensus pattern (11 bp):
CGTTGACCGAC
Found at i:35734404 original size:3 final size:3
Alignment explanation
Indices: 35734396--35734426 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
35734386 TATTCTATTC
35734396 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
35734427 TTGGGATGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:35737066 original size:16 final size:16
Alignment explanation
Indices: 35737029--35737067 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
35737019 AAAAATATTT
*
35737029 TAATATAAATTTTAAA
1 TAATATAAATTTGAAA
35737045 -ACATATAAATTTGAAA
1 TA-ATATAAATTTGAAA
35737061 TAATATA
1 TAATATA
35737068 TATTCAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
15 1 0.05
16 18 0.90
17 1 0.05
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (16 bp):
TAATATAAATTTGAAA
Found at i:35737086 original size:20 final size:21
Alignment explanation
Indices: 35737063--35737104 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
35737053 ATTTGAAATA
*
35737063 ATATA-TATTCAAAATTTTAT
1 ATATATTATTAAAAATTTTAT
*
35737083 ATATATTTTTAAAAATTTTAT
1 ATATATTATTAAAAATTTTAT
35737104 A
1 A
35737105 ATTTTTTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
ATATATTATTAAAAATTTTAT
Found at i:35737099 original size:21 final size:20
Alignment explanation
Indices: 35737073--35737113 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
35737063 ATATATATTC
35737073 AAAATTTTATATATATTTTTA
1 AAAATTTTATA-ATATTTTTA
*
35737094 AAAATTTTATAATTTTTTTA
1 AAAATTTTATAATATTTTTA
35737114 GAACTACAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
AAAATTTTATAATATTTTTA
Found at i:35737150 original size:20 final size:19
Alignment explanation
Indices: 35737125--35737177 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
35737115 AACTACAAAA
35737125 TTTAGAATTTTTATAAATAT
1 TTTAGAATTTTTA-AAATAT
35737145 TTTAG-A-TTTTAAAATTAT
1 TTTAGAATTTTTAAAA-TAT
*
35737163 TTT-CAATTTTTAAAA
1 TTTAGAATTTTTAAAA
35737178 ATTACTTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 3 0.10
18 12 0.41
19 9 0.31
20 5 0.17
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (19 bp):
TTTAGAATTTTTAAAATAT
Found at i:35737163 original size:18 final size:18
Alignment explanation
Indices: 35737133--35737192 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 18
35737123 AATTTAGAAT
35737133 TTTTATAAA-TATTTTAGA
1 TTTTA-AAATTATTTTAGA
35737151 TTTTAAAATTATTTTCA-A
1 TTTTAAAATTATTTT-AGA
35737169 TTTTTAAAAATTACTTTT-GA
1 -TTTT-AAAATTA-TTTTAGA
35737189 TTTT
1 TTTT
35737193 TTTAAATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
17 3 0.08
18 12 0.33
19 9 0.25
20 8 0.22
21 4 0.11
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.58
Consensus pattern (18 bp):
TTTTAAAATTATTTTAGA
Found at i:35737191 original size:20 final size:20
Alignment explanation
Indices: 35737125--35737193 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
35737115 AACTACAAAA
*
35737125 TTTAGAATTTTTATAAA-TAT
1 TTTAG-ATTTTTAAAAATTAT
35737145 TTTAGA-TTTT-AAAATTAT
1 TTTAGATTTTTAAAAATTAT
35737163 TTTCA-ATTTTTAAAAATTACT
1 TTT-AGATTTTTAAAAATTA-T
35737184 TTT-GATTTTT
1 TTTAGATTTTT
35737194 TTAAATTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
17 3 0.07
18 11 0.26
19 6 0.14
20 18 0.43
21 4 0.10
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTAGATTTTTAAAAATTAT
Found at i:35738341 original size:33 final size:34
Alignment explanation
Indices: 35738293--35738358 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 34
35738283 TAATTTAACC
*
35738293 ATCTATTTATATTAAT-TTATAAAT-TATTTTTTT
1 ATCTATTTAAATTAATATT-TAAATATATTTTTTT
* *
35738326 ATCTTTTTAAATTAATATTTTAATATATTTTTT
1 ATCTATTTAAATTAATATTTAAATATATTTTTT
35738359 ATTCAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 18 0.64
34 10 0.36
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (34 bp):
ATCTATTTAAATTAATATTTAAATATATTTTTTT
Found at i:35741449 original size:33 final size:36
Alignment explanation
Indices: 35741374--35741449 Score: 83
Period size: 33 Copynumber: 2.3 Consensus size: 36
35741364 GAAGATATAG
* *
35741374 AATGAAAG-AAAATAAAGAGGAAAATGGAAATAGAA
1 AATGAAAGAAAAATAAAGAGGAAAAAGGAAAGAGAA
*
35741409 AA-G-AAGAAAAAT-AAG-GTAAAAAGG-AAGAGAA
1 AATGAAAGAAAAATAAAGAGGAAAAAGGAAAGAGAA
35741440 AATGAAAGAA
1 AATGAAAGAA
35741450 TTAAAAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
31 8 0.23
32 8 0.23
33 11 0.31
34 6 0.17
35 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (36 bp):
AATGAAAGAAAAATAAAGAGGAAAAAGGAAAGAGAA
Found at i:35752612 original size:22 final size:22
Alignment explanation
Indices: 35752584--35752626 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
35752574 ATATATTAAT
*
35752584 AATCATACCTAGTTAGCTGATG
1 AATCATACCTAATTAGCTGATG
35752606 AATCATACCTAATTAGCTGAT
1 AATCATACCTAATTAGCTGAT
35752627 ATTTAGTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (22 bp):
AATCATACCTAATTAGCTGATG
Found at i:35754907 original size:7 final size:7
Alignment explanation
Indices: 35754850--35755008 Score: 106
Period size: 7 Copynumber: 24.1 Consensus size: 7
35754840 AATTGAAAAC
35754850 GAGAAAG
1 GAGAAAG
*
35754857 G-GAAAA
1 GAGAAAG
35754863 GAGAAAG
1 GAGAAAG
*
35754870 G-GGAAG
1 GAGAAAG
*
35754876 G-GGAAG
1 GAGAAAG
*
35754882 G-GGAAG
1 GAGAAAG
35754888 G-GAAAG
1 GAGAAAG
35754894 G-GAAAG
1 GAGAAAG
35754900 GAGAAAG
1 GAGAAAG
35754907 GAGAAAG
1 GAGAAAG
35754914 GAGAAAG
1 GAGAAAG
35754921 GAGAAAG
1 GAGAAAG
* *
35754928 GGGGAAG
1 GAGAAAG
* *
35754935 GGGGAAG
1 GAGAAAG
*
35754942 GGGAAAG
1 GAGAAAG
35754949 G-G-AAG
1 GAGAAAG
35754954 GAGAAAG
1 GAGAAAG
*
35754961 GAGGAAG
1 GAGAAAG
* *
35754968 GGGGAAG
1 GAGAAAG
35754975 G-GAAATG
1 GAGAAA-G
*
35754982 GGGAAAG
1 GAGAAAG
35754989 G-G-AAG
1 GAGAAAG
35754994 GAGAAAG
1 GAGAAAG
*
35755001 GAGGAAG
1 GAGAAAG
35755008 G
1 G
35755009 GGGAAGGGAA
Statistics
Matches: 133, Mismatches: 11, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
5 8 0.06
6 40 0.30
7 81 0.61
8 4 0.03
ACGTcount: A:0.46, C:0.00, G:0.53, T:0.01
Consensus pattern (7 bp):
GAGAAAG
Found at i:35754927 original size:14 final size:13
Alignment explanation
Indices: 35754850--35755001 Score: 123
Period size: 12 Copynumber: 11.6 Consensus size: 13
35754840 AATTGAAAAC
*
35754850 GAGAAAGGGAAAA
1 GAGAAAGGGAAAG
*
35754863 GAGAAAGGGGAAG
1 GAGAAAGGGAAAG
* *
35754876 G-GGAAGGGGAAG
1 GAGAAAGGGAAAG
35754888 G-GAAAGGGAAAG
1 GAGAAAGGGAAAG
35754900 GAGAAAGGAGAAAG
1 GAGAAAGG-GAAAG
35754914 GAGAAAGGAGAAAGG
1 GAGAAAGG-GAAA-G
* * *
35754929 GGGAAGGGGGAAG
1 GAGAAAGGGAAAG
*
35754942 GGGAAAGGG-AAG
1 GAGAAAGGGAAAG
*
35754954 GAGAAAGGAGGAAG
1 GAGAAAGG-GAAAG
* *
35754968 GGGGAAGGGAAATG
1 GAGAAAGGGAAA-G
*
35754982 GGGAAAGGG-AAG
1 GAGAAAGGGAAAG
35754994 GAGAAAGG
1 GAGAAAGG
35755002 AGGAAGGGGG
Statistics
Matches: 118, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
12 39 0.33
13 33 0.28
14 39 0.33
15 7 0.06
ACGTcount: A:0.46, C:0.00, G:0.53, T:0.01
Consensus pattern (13 bp):
GAGAAAGGGAAAG
Found at i:35755006 original size:14 final size:13
Alignment explanation
Indices: 35754850--35755008 Score: 119
Period size: 14 Copynumber: 12.1 Consensus size: 13
35754840 AATTGAAAAC
* *
35754850 GAGAAAGGGAAAA
1 GAGAAAGGGGAAG
35754863 GAGAAAGGGGAAG
1 GAGAAAGGGGAAG
*
35754876 G-GGAAGGGGAAG
1 GAGAAAGGGGAAG
*
35754888 G-GAAAGGGAAAG
1 GAGAAAGGGGAAG
*
35754900 GAGAAAGGAGAAAG
1 GAGAAAGG-GGAAG
*
35754914 GAGAAAGGAGAAAGG
1 GAGAAAGG-GGAA-G
* *
35754929 GGGAAGGGGGAAG
1 GAGAAAGGGGAAG
*
35754942 GGGAAA-GGGAAG
1 GAGAAAGGGGAAG
35754954 GAGAAAGGAGGAAG
1 GAGAAAGG-GGAAG
* * *
35754968 GGGGAAGGGAAATG
1 GAGAAAGGGGAA-G
*
35754982 GGGAAA-GGGAAG
1 GAGAAAGGGGAAG
35754994 GAGAAAGGAGGAAG
1 GAGAAAGG-GGAAG
35755008 G
1 G
35755009 GGGAAGGGAA
Statistics
Matches: 122, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
12 38 0.31
13 33 0.27
14 44 0.36
15 7 0.06
ACGTcount: A:0.46, C:0.00, G:0.53, T:0.01
Consensus pattern (13 bp):
GAGAAAGGGGAAG
Found at i:35755014 original size:21 final size:21
Alignment explanation
Indices: 35754887--35755016 Score: 117
Period size: 21 Copynumber: 6.4 Consensus size: 21
35754877 GGAAGGGGAA
*
35754887 GGGAAAGGGAAAGGAGAAAGG
1 GGGAAGGGGAAAGGAGAAAGG
* * *
35754908 AGAAAGGAGAAAGGAGAAAGG
1 GGGAAGGGGAAAGGAGAAAGG
* *
35754929 GGGAAGGGGGAAGGGGAAA--
1 GGGAAGGGGAAAGGAGAAAGG
* *
35754948 GGGAAGGAGAAAGGAGGAAGG
1 GGGAAGGGGAAAGGAGAAAGG
*
35754969 GGGAA-GGGAAATGGGGAAA--
1 GGGAAGGGGAAA-GGAGAAAGG
* *
35754988 GGGAAGGAGAAAGGAGGAAGG
1 GGGAAGGGGAAAGGAGAAAGG
35755009 GGGAAGGG
1 GGGAAGGG
35755017 AAATGTCTTA
Statistics
Matches: 83, Mismatches: 20, Indels: 12
0.72 0.17 0.10
Matches are distributed among these distances:
19 25 0.30
20 10 0.12
21 48 0.58
ACGTcount: A:0.44, C:0.00, G:0.55, T:0.01
Consensus pattern (21 bp):
GGGAAGGGGAAAGGAGAAAGG
Found at i:35755021 original size:40 final size:39
Alignment explanation
Indices: 35754854--35755019 Score: 203
Period size: 40 Copynumber: 4.2 Consensus size: 39
35754844 GAAAACGAGA
* * * *
35754854 AAGGGAAAAGAGAAAGGGGAAGG-GGAAGG-GGAA-GGGA
1 AAGGGAAAGGGGAAA-GGGAAGGAGAAAGGAGGAAGGGGG
* *
35754891 AAGGGAAAGGAGAAAGGAGAAAGGAGAAAGGAGAAAGGGGG
1 AAGGGAAAGGGGAAAGG-G-AAGGAGAAAGGAGGAAGGGGG
*
35754932 AAGGGGGAAGGGGAAAGGGAAGGAGAAAGGAGGAAGGGGG
1 AA-GGGAAAGGGGAAAGGGAAGGAGAAAGGAGGAAGGGGG
35754972 AAGGGAAATGGGGAAAGGGAAGGAGAAAGGAGGAAGGGGG
1 AAGGGAAA-GGGGAAAGGGAAGGAGAAAGGAGGAAGGGGG
35755012 AAGGGAAA
1 AAGGGAAA
35755020 TGTCTTACCG
Statistics
Matches: 114, Mismatches: 8, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
36 2 0.02
37 15 0.13
38 4 0.04
39 10 0.09
40 64 0.56
41 6 0.05
42 13 0.11
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.01
Consensus pattern (39 bp):
AAGGGAAAGGGGAAAGGGAAGGAGAAAGGAGGAAGGGGG
Found at i:35758555 original size:17 final size:17
Alignment explanation
Indices: 35758533--35758565 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
35758523 ATCTTTCATC
35758533 TATTTACTTTTT-CATTA
1 TATTTA-TTTTTGCATTA
35758550 TATTTATTTTTGCATT
1 TATTTATTTTTGCATT
35758566 TCTTCAGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.21, C:0.09, G:0.03, T:0.67
Consensus pattern (17 bp):
TATTTATTTTTGCATTA
Found at i:35770206 original size:12 final size:11
Alignment explanation
Indices: 35770182--35770218 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
35770172 TACTCTTATT
35770182 AAAAATTAGAA
1 AAAAATTAGAA
*
35770193 AAAAAGTTAAAA
1 AAAAA-TTAGAA
35770205 AAAAATTAGAA
1 AAAAATTAGAA
35770216 AAA
1 AAA
35770219 TTATTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (11 bp):
AAAAATTAGAA
Found at i:35770339 original size:21 final size:21
Alignment explanation
Indices: 35770315--35770355 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
35770305 TTGTAAGAAT
35770315 TTATAGAAAT-CATAAAAAAAA
1 TTATA-AAATGCATAAAAAAAA
*
35770336 TTATAAAATGCATCAAAAAA
1 TTATAAAATGCATAAAAAAA
35770356 TTCTTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.63, C:0.07, G:0.05, T:0.24
Consensus pattern (21 bp):
TTATAAAATGCATAAAAAAAA
Found at i:35770533 original size:9 final size:9
Alignment explanation
Indices: 35770521--35770678 Score: 74
Period size: 9 Copynumber: 17.1 Consensus size: 9
35770511 TTTTGGTACG
35770521 ATAATTTTT
1 ATAATTTTT
35770530 ATAATTTTT
1 ATAATTTTT
* *
35770539 TTACGAATTTT
1 ATA--ATTTTT
35770550 AT-ATTTTGT
1 ATAATTTT-T
35770559 ATAATTTTTT
1 ATAA-TTTTT
* * *
35770569 TTCA-CTTT
1 ATAATTTTT
*
35770577 ATAAAATTTT
1 AT-AATTTTT
*
35770587 ACAATTTTTT
1 ATAA-TTTTT
*
35770597 ATATTTTTT
1 ATAATTTTT
*
35770606 ATGATTTTT
1 ATAATTTTT
*
35770615 A-ATTTTTT
1 ATAATTTTT
* *
35770623 ATCAAATTTA
1 AT-AATTTTT
35770633 ATAATTTTT
1 ATAATTTTT
35770642 ATAATTTTT
1 ATAATTTTT
*
35770651 ATTGA-TTTT
1 A-TAATTTTT
35770660 A-AATTTTTT
1 ATAA-TTTTT
*
35770669 ATATTTTTT
1 ATAATTTTT
35770678 A
1 A
35770679 ATAAAAGCAA
Statistics
Matches: 109, Mismatches: 26, Indels: 28
0.67 0.16 0.17
Matches are distributed among these distances:
7 1 0.01
8 14 0.13
9 61 0.56
10 23 0.21
11 10 0.09
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (9 bp):
ATAATTTTT
Found at i:35770624 original size:46 final size:46
Alignment explanation
Indices: 35770574--35770671 Score: 135
Period size: 46 Copynumber: 2.1 Consensus size: 46
35770564 TTTTTTTCAC
* * *
35770574 TTTATAAAATTTTACAATTTTTTATATTTTTTA-TGATTTTTAATTT
1 TTTATAAAATTTAACAA-TTTTTATAATTTTTATTGATTTTAAATTT
* *
35770620 TTTATCAAATTTAATAATTTTTATAATTTTTATTGATTTTAAATTT
1 TTTATAAAATTTAACAATTTTTATAATTTTTATTGATTTTAAATTT
35770666 TTTATA
1 TTTATA
35770672 TTTTTTAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 14 0.31
46 31 0.69
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (46 bp):
TTTATAAAATTTAACAATTTTTATAATTTTTATTGATTTTAAATTT
Found at i:35770647 original size:29 final size:29
Alignment explanation
Indices: 35770521--35770678 Score: 104
Period size: 27 Copynumber: 5.7 Consensus size: 29
35770511 TTTTGGTACG
*
35770521 ATAATTTTTATAATTTTTT-TACGAATTTT
1 ATAATTTTTATAATTTTTTAT-CAAATTTT
* *
35770550 AT-ATTTTGTATAATTTTTTTTC--ACTTT
1 ATAATTTT-TATAATTTTTTATCAAATTTT
* * **
35770577 ATAAAATTTTACAATTTTTTAT-ATTTTTT
1 AT-AATTTTTATAATTTTTTATCAAATTTT
* *
35770606 ATGA-TTTT-TAATTTTTTATCAAATTTA
1 ATAATTTTTATAATTTTTTATCAAATTTT
**
35770633 ATAATTTTTATAA-TTTTTAT-TGATTTT
1 ATAATTTTTATAATTTTTTATCAAATTTT
35770660 A-AATTTTT-TATATTTTTTA
1 ATAATTTTTATA-ATTTTTTA
35770679 ATAAAAGCAA
Statistics
Matches: 103, Mismatches: 15, Indels: 24
0.73 0.11 0.17
Matches are distributed among these distances:
25 2 0.02
26 18 0.17
27 28 0.27
28 28 0.27
29 26 0.25
30 1 0.01
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (29 bp):
ATAATTTTTATAATTTTTTATCAAATTTT
Found at i:35770676 original size:17 final size:18
Alignment explanation
Indices: 35770583--35770680 Score: 64
Period size: 17 Copynumber: 5.5 Consensus size: 18
35770573 CTTTATAAAA
*
35770583 TTTTACAATTTTTTATATT
1 TTTTATAATTTTTTATA-T
* *
35770602 TTTTATGATTTTTAAT-T
1 TTTTATAATTTTTTATAT
* *
35770619 TTTTATCAA-ATTTAATAAT
1 TTTTAT-AATTTTTTAT-AT
35770638 TTTTATAA-TTTTTAT-T
1 TTTTATAATTTTTTATAT
35770654 GATTTTA-AATTTTTTATAT
1 --TTTTATAATTTTTTATAT
35770673 TTTT-TAAT
1 TTTTATAAT
35770681 AAAAGCAAGA
Statistics
Matches: 64, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
16 1 0.02
17 22 0.34
18 20 0.31
19 21 0.33
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTTATAATTTTTTATAT
Found at i:35772906 original size:4 final size:4
Alignment explanation
Indices: 35772897--35772944 Score: 60
Period size: 4 Copynumber: 11.5 Consensus size: 4
35772887 CAGCATACCA
* *
35772897 GAGG GAGG GAGG GAGG GAGG GAGG GAGGG GAGG GGGG GTGCG GAGG GA
1 GAGG GAGG GAGG GAGG GAGG GAGG GA-GG GAGG GAGG GAG-G GAGG GA
35772945 TAAGATGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
4 32 0.82
5 7 0.18
ACGTcount: A:0.21, C:0.02, G:0.75, T:0.02
Consensus pattern (4 bp):
GAGG
Found at i:35772914 original size:12 final size:12
Alignment explanation
Indices: 35772897--35772944 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
35772887 CAGCATACCA
35772897 GAGGGAGGGAGG
1 GAGGGAGGGAGG
35772909 GAGGGAGGGAGG
1 GAGGGAGGGAGG
*
35772921 GAGGGGAGGGGGG
1 GA-GGGAGGGAGG
*
35772934 GTGCGGAGGGA
1 GAG-GGAGGGA
35772945 TAAGATGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 15 0.48
13 16 0.52
ACGTcount: A:0.21, C:0.02, G:0.75, T:0.02
Consensus pattern (12 bp):
GAGGGAGGGAGG
Found at i:35780677 original size:138 final size:138
Alignment explanation
Indices: 35780496--35780779 Score: 442
Period size: 138 Copynumber: 2.1 Consensus size: 138
35780486 TAGAAAAAAA
* * *
35780496 AATTATATTCTTTTCAAAAGAATATTAATTTTCATATCTTTTATATTTTAACCGAAATTAATTAA
1 AATTATATTATTTTCAAAAGAATATTAATTTTCAGATCTTTTATATTTTAACCAAAATTAATTAA
* * * *
35780561 TATAACTATTTATATTAATAAATTTAGTAAATTATATACAATTAATATTTTGTGTGAATCAAATT
66 TATAACGATTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
35780626 CATATATT
131 CATATATT
* * * **
35780634 GATTATATTATTTTCAAAAGAATATTAATTTTCAGGTCTTTTATATTTTGATTAAAATTAATTAA
1 AATTATATTATTTTCAAAAGAATATTAATTTTCAGATCTTTTATATTTTAACCAAAATTAATTAA
* *
35780699 TATAACGGTTTATATTAATAAATTCAGTAAAATATATATAATTAATATTTTGTATGAATCAAATT
66 TATAACGATTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
35780764 CATATATT
131 CATATATT
35780772 AATTATAT
1 AATTATAT
35780780 CTATGTTCTT
Statistics
Matches: 131, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
138 131 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.47
Consensus pattern (138 bp):
AATTATATTATTTTCAAAAGAATATTAATTTTCAGATCTTTTATATTTTAACCAAAATTAATTAA
TATAACGATTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:35781508 original size:13 final size:13
Alignment explanation
Indices: 35781490--35781516 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35781480 TGACTATTAC
35781490 ATAGTAATCTAAG
1 ATAGTAATCTAAG
35781503 ATAGTAATCTAAG
1 ATAGTAATCTAAG
35781516 A
1 A
35781517 AACATACTCA
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:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (13 bp):
ATAGTAATCTAAG
Found at i:35785489 original size:45 final size:45
Alignment explanation
Indices: 35785405--35785494 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 45
35785395 ATATGTTGGG
* ** *
35785405 ATTTGAATTTAGACTGGTGATACCTCATCTTATTTATGAACAAGT
1 ATTTGAATTTAGACTGGTGACACCTCATCTTATGAATGAAAAAGT
* *
35785450 ATTTGAATTTAGGCAT-GTGACATCTCATCTTATGAATGAAAAAGT
1 ATTTGAATTTAGAC-TGGTGACACCTCATCTTATGAATGAAAAAGT
35785495 GAAGACATGA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 37 0.97
46 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (45 bp):
ATTTGAATTTAGACTGGTGACACCTCATCTTATGAATGAAAAAGT
Found at i:35796621 original size:22 final size:23
Alignment explanation
Indices: 35796596--35796642 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
35796586 CCAAATCTAC
35796596 TTAAACCT-AAATGGGC-TAAAAA
1 TTAAACCTGAAAT-GGCTTAAAAA
*
35796618 TTAAACTTGAAATGGCTTAAAAA
1 TTAAACCTGAAATGGCTTAAAAA
35796641 TT
1 TT
35796643 TAACAACCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.30
Consensus pattern (23 bp):
TTAAACCTGAAATGGCTTAAAAA
Found at i:35801173 original size:14 final size:14
Alignment explanation
Indices: 35801156--35801190 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
35801146 GCACCAATTG
35801156 AAAGCTCTCAATCT
1 AAAGCTCTCAATCT
* *
35801170 AAAGTTTTCAATCT
1 AAAGCTCTCAATCT
35801184 AAAGCTC
1 AAAGCTC
35801191 ACTTTCCTTT
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.37, C:0.23, G:0.09, T:0.31
Consensus pattern (14 bp):
AAAGCTCTCAATCT
Found at i:35803408 original size:6 final size:6
Alignment explanation
Indices: 35803397--35803429 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
35803387 AATATTGTTT
35803397 AAATAA AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAA
35803430 CATAATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:35805348 original size:17 final size:16
Alignment explanation
Indices: 35805302--35805352 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
35805292 ATCATAAAAT
35805302 ATTTATTATTAATAT-
1 ATTTATTATTAATATA
*
35805317 ATTTATAATTGTAATATA
1 ATTTATTA-T-TAATATA
35805335 CATTTATTATTAATATA
1 -ATTTATTATTAATATA
35805352 A
1 A
35805353 ATATTTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
15 7 0.23
16 2 0.07
17 13 0.43
18 1 0.03
19 7 0.23
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (16 bp):
ATTTATTATTAATATA
Found at i:35806071 original size:6 final size:6
Alignment explanation
Indices: 35806060--35806087 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
35806050 AATATTGTTT
35806060 AAAATA AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAA
35806088 CATAATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:35806099 original size:18 final size:18
Alignment explanation
Indices: 35806057--35806099 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
35806047 TCAAATATTG
*
35806057 TTTAAAATAAAAATAAAA
1 TTTAAAATAAAAACAAAA
* * *
35806075 ATAAAAATAAAAACATAA
1 TTTAAAATAAAAACAAAA
35806093 TTTAAAA
1 TTTAAAA
35806100 CTTGATATAC
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (18 bp):
TTTAAAATAAAAACAAAA
Found at i:35806460 original size:21 final size:21
Alignment explanation
Indices: 35806436--35806478 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
35806426 ATTTTCTATG
*
35806436 TTTATAATATATTATATTATT
1 TTTATAATATATTATATAATT
35806457 TTTATAATATATTATATAATT
1 TTTATAATATATTATATAATT
35806478 T
1 T
35806479 ATAAAACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTATAATATATTATATAATT
Found at i:35807954 original size:17 final size:16
Alignment explanation
Indices: 35807908--35807958 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
35807898 ATCATAAAAT
35807908 ATTTATTATTAATAT-
1 ATTTATTATTAATATA
*
35807923 ATTTATAATTGTAATATA
1 ATTTATTA-T-TAATATA
35807941 CATTTATTATTAATATA
1 -ATTTATTATTAATATA
35807958 A
1 A
35807959 ATATTTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
15 7 0.23
16 2 0.07
17 13 0.43
18 1 0.03
19 7 0.23
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (16 bp):
ATTTATTATTAATATA
Found at i:35812189 original size:13 final size:13
Alignment explanation
Indices: 35812171--35812200 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
35812161 ATTTGATATT
*
35812171 ATAAAAAATTAGA
1 ATAAAAAATTAAA
35812184 ATAAAAAATTAAA
1 ATAAAAAATTAAA
35812197 ATAA
1 ATAA
35812201 TTTTAAATTT
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:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (13 bp):
ATAAAAAATTAAA
Found at i:35812434 original size:33 final size:34
Alignment explanation
Indices: 35812356--35812437 Score: 98
Period size: 36 Copynumber: 2.4 Consensus size: 34
35812346 AATGTTAACT
35812356 ATATTTAAATAATTCAATATAATTATATTTTATATA
1 ATATTTAAATAATTCAATATAATTATA--TTATATA
*
35812392 ATATTTAAATAATTTAATATAA-TA-A-TATATGA
1 ATATTTAAATAATTCAATATAATTATATTATAT-A
35812424 CATATTTAAATAAT
1 -ATATTTAAATAAT
35812438 ATATAAAATA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
31 5 0.12
32 1 0.02
33 13 0.30
34 1 0.02
35 2 0.05
36 21 0.49
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.46
Consensus pattern (34 bp):
ATATTTAAATAATTCAATATAATTATATTATATA
Found at i:35812847 original size:18 final size:17
Alignment explanation
Indices: 35812814--35812847 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
35812804 AGTTGAATTT
35812814 ATTTATATTTTTTATTA
1 ATTTATATTTTTTATTA
*
35812831 ATTTTTATTTATTTATT
1 ATTTATATTT-TTTATT
35812848 TATTGTTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
ATTTATATTTTTTATTA
Found at i:35814529 original size:7 final size:7
Alignment explanation
Indices: 35814512--35814555 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
35814502 TCAATTTTAG
35814512 TTTCT-C
1 TTTCTGC
35814518 TTTCTGC
1 TTTCTGC
35814525 TTTCTGC
1 TTTCTGC
*
35814532 TTTTTGC
1 TTTCTGC
*
35814539 TTTTTGC
1 TTTCTGC
*
35814546 TTTTTGC
1 TTTCTGC
35814553 TTT
1 TTT
35814556 TTGGTCCACC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
6 5 0.14
7 31 0.86
ACGTcount: A:0.00, C:0.20, G:0.11, T:0.68
Consensus pattern (7 bp):
TTTCTGC
Found at i:35814539 original size:14 final size:14
Alignment explanation
Indices: 35814512--35814555 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
35814502 TCAATTTTAG
*
35814512 TTTCT-CTTTCTGC
1 TTTCTGCTTTTTGC
35814525 TTTCTGCTTTTTGC
1 TTTCTGCTTTTTGC
*
35814539 TTTTTGCTTTTTGC
1 TTTCTGCTTTTTGC
35814553 TTT
1 TTT
35814556 TTGGTCCACC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
13 5 0.18
14 23 0.82
ACGTcount: A:0.00, C:0.20, G:0.11, T:0.68
Consensus pattern (14 bp):
TTTCTGCTTTTTGC
Found at i:35814556 original size:7 final size:7
Alignment explanation
Indices: 35814517--35814558 Score: 66
Period size: 7 Copynumber: 6.0 Consensus size: 7
35814507 TTTAGTTTCT
*
35814517 CTTTCTG
1 CTTTTTG
*
35814524 CTTTCTG
1 CTTTTTG
35814531 CTTTTTG
1 CTTTTTG
35814538 CTTTTTG
1 CTTTTTG
35814545 CTTTTTG
1 CTTTTTG
35814552 CTTTTTG
1 CTTTTTG
35814559 GTCCACCATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.00, C:0.19, G:0.14, T:0.67
Consensus pattern (7 bp):
CTTTTTG
Found at i:35825244 original size:27 final size:27
Alignment explanation
Indices: 35825201--35825267 Score: 116
Period size: 27 Copynumber: 2.4 Consensus size: 27
35825191 AGATTATGTA
35825201 AAAATAACACTGGTTCGTGTAAATAAGC
1 AAAA-AACACTGGTTCGTGTAAATAAGC
*
35825229 AAAGAACACTGGTTCGTGTAAATAAGC
1 AAAAAACACTGGTTCGTGTAAATAAGC
35825256 AAAAAACACTGG
1 AAAAAACACTGG
35825268 CTGTGTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
27 34 0.92
28 3 0.08
ACGTcount: A:0.45, C:0.15, G:0.19, T:0.21
Consensus pattern (27 bp):
AAAAAACACTGGTTCGTGTAAATAAGC
Found at i:35827098 original size:5 final size:5
Alignment explanation
Indices: 35827088--35827112 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
35827078 ATGGTATTAC
35827088 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
35827113 TTCTTACAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:35829782 original size:65 final size:56
Alignment explanation
Indices: 35829698--35829851 Score: 191
Period size: 57 Copynumber: 2.6 Consensus size: 56
35829688 CAACTCAAAT
35829698 TTGGCCATTGCATGGCTGACACCCCTATTTCAAAAAAAAATTGCATTGCATTGTATTTTTGGGTG
1 TTGGCCATTGCATGGCTGACACCCCTATTTCAAAAAAAAATTG---T--A---T-TTTTTGGGTG
*
35829763 TTGGCCATTGCATGACTGACACCCCTTATTTCAAAAAAAAATTGTATTTTTTGGGTG
1 TTGGCCATTGCATGGCTGACACCCC-TATTTCAAAAAAAAATTGTATTTTTTGGGTG
*
35829820 TTGGCCATTGCATGGCCGACATCCCCTATTTC
1 TTGGCCATTGCATGGCTGACA-CCCCTATTTC
35829852 TCGAGAAAAA
Statistics
Matches: 84, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
57 35 0.42
58 5 0.06
61 1 0.01
63 1 0.01
65 24 0.29
66 18 0.21
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (56 bp):
TTGGCCATTGCATGGCTGACACCCCTATTTCAAAAAAAAATTGTATTTTTTGGGTG
Found at i:35829915 original size:61 final size:63
Alignment explanation
Indices: 35829809--35829938 Score: 183
Period size: 62 Copynumber: 2.1 Consensus size: 63
35829799 AAAAATTGTA
*** * *
35829809 TTTTTTGGGTGTTGGCCATTGCATGGCCGACATCCCCTATTTCTCGAGAAAAAAA-TTCAAAT
1 TTTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCTAGTTCTCGAGAAAAAAATTTCAAAT
*
35829871 TTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCT-GTTCTCGAGAAAAAAATTTCAAAT
1 TTTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCTAGTTCTCGAGAAAAAAATTTCAAAT
*
35829933 ATTTTT
1 TTTTTT
35829939 CCCCTGTTCT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
61 15 0.25
62 45 0.75
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (63 bp):
TTTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCTAGTTCTCGAGAAAAAAATTTCAAAT
Found at i:35829944 original size:35 final size:35
Alignment explanation
Indices: 35829904--35829973 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
35829894 TGGCCGACAC
35829904 CCCCTGTTCTCGAGAAAAAAATTTCAAATATTTTT
1 CCCCTGTTCTCGAGAAAAAAATTTCAAATATTTTT
35829939 CCCCTGTTCTCGAGAAAAAAATTTCAAATATTTTT
1 CCCCTGTTCTCGAGAAAAAAATTTCAAATATTTTT
35829974 GGTATTGGCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (35 bp):
CCCCTGTTCTCGAGAAAAAAATTTCAAATATTTTT
Found at i:35829959 original size:96 final size:96
Alignment explanation
Indices: 35829849--35830022 Score: 305
Period size: 96 Copynumber: 1.8 Consensus size: 96
35829839 CATCCCCTAT
* *
35829849 TTCTCGAGAAAAAAA-TTCAAATTTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTGTTC
1 TTCTCGAGAAAAAAATTTCAAA-TATTTTTGGTATTGGCCATCAAATGGCCGACACCCCCTGTTC
*
35829913 TCGAGAAAAAAATTTCAAATATTTTTCCCCTG
65 TAGAGAAAAAAATTTCAAATATTTTTCCCCTG
35829945 TTCTCGAGAAAAAAATTTCAAATATTTTTGGTATTGGCCATCAAATGGCCGACACCCCCTGTTCT
1 TTCTCGAGAAAAAAATTTCAAATATTTTTGGTATTGGCCATCAAATGGCCGACACCCCCTGTTCT
35830010 AGAGAAAAAAATT
66 AGAGAAAAAAATT
35830023 CAATTTTTTT
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
96 68 0.92
97 6 0.08
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.32
Consensus pattern (96 bp):
TTCTCGAGAAAAAAATTTCAAATATTTTTGGTATTGGCCATCAAATGGCCGACACCCCCTGTTCT
AGAGAAAAAAATTTCAAATATTTTTCCCCTG
Found at i:35830019 original size:61 final size:60
Alignment explanation
Indices: 35829939--35830122 Score: 246
Period size: 61 Copynumber: 3.0 Consensus size: 60
35829929 AAATATTTTT
*
35829939 CCCCTGTTCTCGAGAAAAAAATTTCAAATATTTTTGGTATTGGCCATCAAATGGCCGACAC
1 CCCCTGTTCTCGAGAAAAAAATTTCAAAT-TTTTTGGTGTTGGCCATCAAATGGCCGACAC
* *
35830000 CCCCTGTTCTAGAGAAAAAAA-TTCAATTTTTTTTGGGTGTTGGCCATCAAATGGCCGACA-
1 CCCCTGTTCTCGAGAAAAAAATTTCAA-ATTTTTT-GGTGTTGGCCATCAAATGGCCGACAC
* * * *
35830060 CCCCTTTTCTCGAATAAAAAAATTCCAAATTTTTCTGATGTTGGCCATCAAATGGCCGACAC
1 CCCCTGTTCTCG-AGAAAAAAATTTCAAATTTTT-TGGTGTTGGCCATCAAATGGCCGACAC
35830122 C
1 C
35830123 AACTTCTCAT
Statistics
Matches: 108, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
60 20 0.19
61 82 0.76
62 6 0.06
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (60 bp):
CCCCTGTTCTCGAGAAAAAAATTTCAAATTTTTTGGTGTTGGCCATCAAATGGCCGACAC
Found at i:35834899 original size:30 final size:30
Alignment explanation
Indices: 35834865--35834962 Score: 101
Period size: 30 Copynumber: 3.3 Consensus size: 30
35834855 TCCCTTTACT
*
35834865 TTTTAAATTTAATTT-GTAATTTCGTT-TTTA
1 TTTTAAATTTAATTTCG-AATTTC-TTGTATA
35834895 TTTTAAATTTAATTTCGAATTTCTTGTATA
1 TTTTAAATTTAATTTCGAATTTCTTGTATA
* ** * *
35834925 TTTTAATTTTTCTTTCTAATTTCATGTATA
1 TTTTAAATTTAATTTCGAATTTCTTGTATA
*
35834955 TTCTAAAT
1 TTTTAAAT
35834963 ATTATTTTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
29 2 0.03
30 55 0.95
31 1 0.02
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (30 bp):
TTTTAAATTTAATTTCGAATTTCTTGTATA
Found at i:35835956 original size:60 final size:59
Alignment explanation
Indices: 35835845--35836232 Score: 315
Period size: 61 Copynumber: 6.5 Consensus size: 59
35835835 ATTAGAGGAA
* * * *
35835845 AATGGCTAACACCCAAAAAATTTGAATTTTTTTTCTCGGGAACAGGGGGTGTCGCCCATTT
1 AATGGCCAACA-CCAAAAAATTTGAA-TTTTTTTCTCGAGAACAGGAGGTGTCGGCCATTT
* *
35835906 AATGGCCAACACAAAAAAAATTTGAATTTTTTTCTCGAGAACAGGAGGTGTCGACCATTT
1 AATGGCCAACAC-CAAAAAATTTGAATTTTTTTCTCGAGAACAGGAGGTGTCGGCCATTT
* * * * * **
35835966 GATGGCCAACATCAAAAAAATTTGAATTTTTTTCTCGAGAAAAAAGAGTTGTCAACCATTT
1 AATGGCCAACA-CCAAAAAATTTGAATTTTTTTCTCGAG-AACAGGAGGTGTCGGCCATTT
* * * * **
35836027 GATGGCCAACACCAAAAAAATTTAAAATTTGTTTCTCGAGAA-AAGAGGGTGTCGGCCATGC
1 AATGGCCAACACC-AAAAAATTT-GAATTTTTTTCTCGAGAACAGGA-GGTGTCGGCCATTT
** * * * * **
35836088 AATGGCTGACACCCAAAAAATAT-AATTTTTTT-T-GA-AATAGGGGGTGTCGGTCATGC
1 AATGGCCAACA-CCAAAAAATTTGAATTTTTTTCTCGAGAACAGGAGGTGTCGGCCATTT
* * * * *
35836144 AATGGCCAACACCAAAAAATGT-AATTTTTTT-TTGA-AATAGGGGGTGTCGGACATTT
1 AATGGCCAACACCAAAAAATTTGAATTTTTTTCTCGAGAACAGGAGGTGTCGGCCATTT
* * *
35836200 GATGGCCAACATCCCAAAATTTTGAATTTTTTT
1 AATGGCCAACA-CCAAAAAATTTGAATTTTTTT
35836233 TCTAACAAAA
Statistics
Matches: 280, Mismatches: 36, Indels: 25
0.82 0.11 0.07
Matches are distributed among these distances:
55 20 0.07
56 54 0.19
57 12 0.04
58 10 0.04
59 8 0.03
60 73 0.26
61 87 0.31
62 16 0.06
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (59 bp):
AATGGCCAACACCAAAAAATTTGAATTTTTTTCTCGAGAACAGGAGGTGTCGGCCATTT
Found at i:35835982 original size:61 final size:59
Alignment explanation
Indices: 35835859--35836085 Score: 276
Period size: 60 Copynumber: 3.7 Consensus size: 59
35835849 GCTAACACCC
* * * * *
35835859 AAAAAATTTGAATTTTTTTTCTCGGGAACAGGGGGTGTCGCCCATTTAATGGCCAACACAA
1 AAAAAATTTGAA-TTTTTTTCTCGAGAACAAGAGGTGTCGACCATTTGATGGCCAACAC-A
*
35835920 AAAAAATTTGAATTTTTTTCTCGAGAACAGGAGGTGTCGACCATTTGATGGCCAACATCA
1 AAAAAATTTGAATTTTTTTCTCGAGAACAAGAGGTGTCGACCATTTGATGGCCAACA-CA
* * *
35835980 AAAAAATTTGAATTTTTTTCTCGAGAAAAAAGAGTTGTCAACCATTTGATGGCCAACACCA
1 AAAAAATTTGAATTTTTTTCTCGAG-AACAAGAGGTGTCGACCATTTGATGGCCAACA-CA
* * *
35836041 AAAAAATTTAAAATTTGTTTCTCGAGAA-AAGAGGGTGTCGGCCAT
1 AAAAAATTT-GAATTTTTTTCTCGAGAACAAGA-GGTGTCGACCAT
35836086 GCAATGGCTG
Statistics
Matches: 148, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
60 71 0.48
61 63 0.43
62 14 0.09
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (59 bp):
AAAAAATTTGAATTTTTTTCTCGAGAACAAGAGGTGTCGACCATTTGATGGCCAACACA
Found at i:35836106 original size:121 final size:120
Alignment explanation
Indices: 35835845--35836119 Score: 311
Period size: 121 Copynumber: 2.3 Consensus size: 120
35835835 ATTAGAGGAA
* * * * **
35835845 AATGGCTAACACCCAAAAAATTTGAATTTTTTTTCTCGGGAACAGGGGGTGTCGCCCATTTAATG
1 AATGGCTAACACCCAAAAAATTTGAA-TTTTTTTCTCGGAAAAAAGAGGTGTCAACCATTTAATG
* * * **
35835910 GCCAACACAAAAAAAATTTGAATTTTTTTCTCGAGAACAGGAGGTGTCGACCATTT
65 GCCAACACAAAAAAAATTTAAATTTGTTTCTCGAGAAAAGGAGGTGTCGACCATGC
* * * * * *
35835966 GATGGCCAACATCAAAAAAATTTGAATTTTTTTCTCGAGAAAAAAGAGTTGTCAACCATTTGATG
1 AATGGCTAACACCCAAAAAATTTGAATTTTTTTCTCG-GAAAAAAGAGGTGTCAACCATTTAATG
* *
35836031 GCCAACACCAAAAAAATTTAAAATTTGTTTCTCGAGAAAA-GAGGGTGTCGGCCATGC
65 GCCAACACAAAAAAAATTT-AAATTTGTTTCTCGAGAAAAGGA-GGTGTCGACCATGC
* *
35836088 AATGGCTGACACCCAAAAAATAT-AATTTTTTT
1 AATGGCTAACACCCAAAAAATTTGAATTTTTTT
35836120 TGAAATAGGG
Statistics
Matches: 126, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
120 11 0.09
121 70 0.56
122 45 0.36
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (120 bp):
AATGGCTAACACCCAAAAAATTTGAATTTTTTTCTCGGAAAAAAGAGGTGTCAACCATTTAATGG
CCAACACAAAAAAAATTTAAATTTGTTTCTCGAGAAAAGGAGGTGTCGACCATGC
Found at i:35836146 original size:56 final size:56
Alignment explanation
Indices: 35836028--35836262 Score: 202
Period size: 56 Copynumber: 4.0 Consensus size: 56
35836018 CAACCATTTG
* * * * *
35836028 ATGGCCAACACCAAAAAAATTTAAAATTTGTTTCTCGAGAAAAGAGGGTGTCGGCCATGCA
1 ATGGCCAACACC-AAAAAA--TATAATTT-TTTTTTGA-AATAGGGGGTGTCGGCCATGCA
** *
35836089 ATGGCTGACACCCAAAAAATATAA-TTTTTTTTGAAATAGGGGGTGTCGGTCATGCA
1 ATGGCCAACA-CCAAAAAATATAATTTTTTTTTGAAATAGGGGGTGTCGGCCATGCA
* * ***
35836145 ATGGCCAACACCAAAAAATGTAATTTTTTTTTGAAATAGGGGGTGTCGGACATTTG
1 ATGGCCAACACCAAAAAATATAATTTTTTTTTGAAATAGGGGGTGTCGGCCATGCA
* * * * *
35836201 ATGGCCAACATCCCAAAATTTTGAATTTTTTTTCTAACAAAAAGGGGGTGTCGGCCATGCA
1 ATGGCCAACA-CCAAAAAATAT-AATTTTTTTT-T--GAAATAGGGGGTGTCGGCCATGCA
35836262 A
1 A
35836263 ATTTTTTTTT
Statistics
Matches: 143, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
55 12 0.08
56 65 0.45
57 14 0.10
58 12 0.08
59 5 0.03
61 33 0.23
62 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.29
Consensus pattern (56 bp):
ATGGCCAACACCAAAAAATATAATTTTTTTTTGAAATAGGGGGTGTCGGCCATGCA
Found at i:35836488 original size:61 final size:61
Alignment explanation
Indices: 35836377--35836531 Score: 233
Period size: 59 Copynumber: 2.5 Consensus size: 61
35836367 TTTATGTCTG
*
35836377 ACACCAAAAAAAAATTGAATTTTTTTCTCGAG-AACAGGGGTGTCGACCATTGCATGGCC-A
1 ACACC-AAAAAAAATTGAATTTTTTTCTCGAGAAAAAGGGGTGTCGACCATTGCATGGCCAA
* *
35836437 ACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAAGGGAGTGTCGGCCATTGCATGGCCAA
1 ACACCAAAAAAAATTGAATTTTTTTCTCGAGAAAAAGGG-GTGTCGACCATTGCATGGCCAA
*
35836499 ACACAAAAAAAAATTGAAATTTTTTTCTCGAGA
1 ACACCAAAAAAAATTG-AATTTTTTTCTCGAGA
35836532 TGCCGACACC
Statistics
Matches: 86, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
59 25 0.29
60 11 0.13
61 19 0.22
62 15 0.17
63 16 0.19
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.26
Consensus pattern (61 bp):
ACACCAAAAAAAATTGAATTTTTTTCTCGAGAAAAAGGGGTGTCGACCATTGCATGGCCAA
Found at i:35848383 original size:2 final size:2
Alignment explanation
Indices: 35848376--35848403 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35848366 GACAATAAGC
35848376 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
35848404 ACATGAAGCA
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:35868039 original size:36 final size:35
Alignment explanation
Indices: 35867998--35868073 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 35
35867988 ATTACATTAA
35867998 AATAACGGGTGACTTATAAATTAATGACCAATAAC
1 AATAACGGGTGACTTATAAATTAATGACCAATAAC
35868033 GAATAACGGGTGACTTATAAATTAATGACCAATAAC
1 -AATAACGGGTGACTTATAAATTAATGACCAATAAC
35868069 AATAA
1 AATAA
35868074 GTTGGGGGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 5 0.12
36 35 0.88
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.25
Consensus pattern (35 bp):
AATAACGGGTGACTTATAAATTAATGACCAATAAC
Found at i:35874967 original size:29 final size:28
Alignment explanation
Indices: 35874933--35875005 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
35874923 GTAAAATTGA
* *
35874933 ATAATTGAGTGATCATTTTGTAACT-TTT
1 ATAATTG-GTGACCATTTTATAACTCTTT
35874961 AGTAATTGGATGACCATTTTATAACTCTTT
1 A-TAATTGG-TGACCATTTTATAACTCTTT
35874991 ATAATTGGGTGACCA
1 ATAATT-GGTGACCA
35875006 AAAAAAGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
28 2 0.05
29 31 0.79
30 6 0.15
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.42
Consensus pattern (28 bp):
ATAATTGGTGACCATTTTATAACTCTTT
Found at i:35887692 original size:2 final size:2
Alignment explanation
Indices: 35887687--35887712 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35887677 CGCTTTTTTC
35887687 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
35887713 TTGCTATCAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35894224 original size:6 final size:6
Alignment explanation
Indices: 35894209--35894238 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
35894199 TGAGTTGTTG
*
35894209 GAGTTT GAGTTC GAGTTT GAGTTT GAGTTT
1 GAGTTT GAGTTT GAGTTT GAGTTT GAGTTT
35894239 AAAATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.03, G:0.33, T:0.47
Consensus pattern (6 bp):
GAGTTT
Found at i:35900166 original size:31 final size:30
Alignment explanation
Indices: 35900128--35900198 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 30
35900118 GGTCACAAAA
35900128 TAGTCACTAAGCTATTCT-AAAGTTTTCATTT
1 TAGTCACTAA-CTATT-TGAAAGTTTTCATTT
*
35900159 TAGTCACTGAACTATTTGAAAGTTTTTATTT
1 TAGTCACT-AACTATTTGAAAGTTTTCATTT
*
35900190 AAGTCACTA
1 TAGTCACTA
35900199 GATTATTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
30 2 0.06
31 32 0.89
32 2 0.06
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (30 bp):
TAGTCACTAACTATTTGAAAGTTTTCATTT
Found at i:35904346 original size:7 final size:7
Alignment explanation
Indices: 35904330--35904364 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
35904320 TTGAACCATC
35904330 TAATAAT
1 TAATAAT
*
35904337 TAACAAT
1 TAATAAT
35904344 TAATAAT
1 TAATAAT
35904351 TAATAAT
1 TAATAAT
35904358 TAATAAT
1 TAATAAT
35904365 GTTATATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (7 bp):
TAATAAT
Found at i:35906343 original size:48 final size:49
Alignment explanation
Indices: 35906272--35906365 Score: 147
Period size: 48 Copynumber: 1.9 Consensus size: 49
35906262 CAAGTCCCCG
35906272 ATACTCCGTTTGGCAACTAAGAAAATA-TTCATTTTC-TTTTGTCATCCA
1 ATACTCCGTTTGGCAACTAAGAAAATATTTCATTTTCATTTT-TCATCCA
* *
35906320 ATACTCTGTTTGGCAACTAAGAAAATATTTCTTTTTCATTTTTCAT
1 ATACTCCGTTTGGCAACTAAGAAAATATTTCATTTTCATTTTTCAT
35906366 AGGTATGGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
48 26 0.62
49 12 0.29
50 4 0.10
ACGTcount: A:0.29, C:0.18, G:0.10, T:0.44
Consensus pattern (49 bp):
ATACTCCGTTTGGCAACTAAGAAAATATTTCATTTTCATTTTTCATCCA
Found at i:35913084 original size:20 final size:20
Alignment explanation
Indices: 35913048--35913087 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
35913038 GAAAAATAAT
*
35913048 GTAACTAAAATATAATTAAA
1 GTAACTAAAATAAAATTAAA
35913068 GTAA-TAAAATTAAAATTAAA
1 GTAACTAAAA-TAAAATTAAA
35913088 ATTTTGCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (20 bp):
GTAACTAAAATAAAATTAAA
Found at i:35917688 original size:15 final size:16
Alignment explanation
Indices: 35917654--35917700 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 16
35917644 AAAATAAAAA
35917654 TAAAAACACCATAAAACAT
1 TAAAAACA-CAT--AACAT
35917673 TAAAAACA-ATAACAT
1 TAAAAACACATAACAT
*
35917688 TAAGAACACATAA
1 TAAAAACACATAA
35917701 TAATGTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 12 0.46
16 4 0.15
17 2 0.08
19 8 0.31
ACGTcount: A:0.64, C:0.17, G:0.02, T:0.17
Consensus pattern (16 bp):
TAAAAACACATAACAT
Found at i:35919421 original size:16 final size:15
Alignment explanation
Indices: 35919400--35919437 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
35919390 TTTTTAATAT
35919400 AAATTCAATAATTATA
1 AAATTCAATAATTA-A
*
35919416 AAATTC-ATTATTAA
1 AAATTCAATAATTAA
35919430 AAATTCAA
1 AAATTCAA
35919438 AACTTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 7 0.35
15 7 0.35
16 6 0.30
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATTCAATAATTAA
Found at i:35920864 original size:4 final size:4
Alignment explanation
Indices: 35920857--35920929 Score: 74
Period size: 4 Copynumber: 17.2 Consensus size: 4
35920847 AAAAAAACGG
* * * *
35920857 GAAA GAAA GAGAG GAAA GAAA GAAA GAAA AAAA GAAA GAAA GAAG GAGA
1 GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
35920906 GAAAA GAAA GAAGA GGAAA GAAA G
1 G-AAA GAAA GAA-A -GAAA GAAA G
35920930 GTAATGTGTT
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
4 46 0.81
5 8 0.14
6 3 0.05
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:35920883 original size:21 final size:20
Alignment explanation
Indices: 35920857--35920917 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
35920847 AAAAAAACGG
35920857 GAAAGAAAGAGAGGAAAGAAA
1 GAAAGAAAGAGA-GAAAGAAA
35920878 GAAAG-AA-A-A-AAAGAAA
1 GAAAGAAAGAGAGAAAGAAA
*
35920894 GAAAGAAGGAGAGAAAAGAAA
1 GAAAGAAAGAGAG-AAAGAAA
35920915 GAA
1 GAA
35920918 GAGGAAAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
16 12 0.35
17 1 0.03
18 2 0.06
19 2 0.06
20 2 0.06
21 15 0.44
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (20 bp):
GAAAGAAAGAGAGAAAGAAA
Found at i:35921596 original size:20 final size:21
Alignment explanation
Indices: 35921571--35921613 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
35921561 TACTTACTAC
35921571 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
*
35921591 TACTAACTAACAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
35921612 TA
1 TA
35921614 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:35921737 original size:22 final size:21
Alignment explanation
Indices: 35921707--35921748 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
35921697 CAAATCAATT
* *
35921707 AAAAATTAAATTAAAGAAATA
1 AAAAATTAAAATAAACAAATA
35921728 AAAAACTTAAAATAAACAAAT
1 AAAAA-TTAAAATAAACAAAT
35921749 TAATTAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.21
Consensus pattern (21 bp):
AAAAATTAAAATAAACAAATA
Found at i:35922324 original size:18 final size:19
Alignment explanation
Indices: 35922292--35922327 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
35922282 TTTTATTTTT
35922292 AAATATATAAAAAAAATAA
1 AAATATATAAAAAAAATAA
*
35922311 AAATA-ATAATAAAAATA
1 AAATATATAAAAAAAATA
35922328 CGTGTCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (19 bp):
AAATATATAAAAAAAATAA
Found at i:35922671 original size:15 final size:15
Alignment explanation
Indices: 35922651--35922682 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
35922641 AGTAACGGTT
35922651 TATATTTTGTACATA
1 TATATTTTGTACATA
35922666 TATATTTTGTACATA
1 TATATTTTGTACATA
35922681 TA
1 TA
35922683 AACATTCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.53
Consensus pattern (15 bp):
TATATTTTGTACATA
Found at i:35922911 original size:20 final size:20
Alignment explanation
Indices: 35922886--35922925 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
35922876 CACAGATACT
35922886 CTTATA-TTTTAAAACCCTAG
1 CTTATACTTTT-AAACCCTAG
35922906 CTTATACCTTTTAAACCCTA
1 CTTATA-CTTTTAAACCCTA
35922926 ATTTATCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 8 0.44
22 4 0.22
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.40
Consensus pattern (20 bp):
CTTATACTTTTAAACCCTAG
Found at i:35922931 original size:21 final size:21
Alignment explanation
Indices: 35922892--35922935 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
35922882 TACTCTTATA
*
35922892 TTTTAAAACCCTAGCTTATACC
1 TTTTAAAACCCTAACTTAT-CC
*
35922914 TTTT-AAACCCTAATTTATCC
1 TTTTAAAACCCTAACTTATCC
35922934 TT
1 TT
35922936 ATTCGACGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.30, C:0.25, G:0.02, T:0.43
Consensus pattern (21 bp):
TTTTAAAACCCTAACTTATCC
Found at i:35930742 original size:35 final size:35
Alignment explanation
Indices: 35930703--35930790 Score: 90
Period size: 36 Copynumber: 2.5 Consensus size: 35
35930693 TAAAAATTAT
* *
35930703 TTCAT-TACAAGTTTATATATACTTTT-TAATTTTTA
1 TTCATATA-AAGTTTAAATATA-TTTTCAAATTTTTA
*
35930738 TTCATGATAAATTTTAAATATATTTTCAAATTTTTA
1 TTCAT-ATAAAGTTTAAATATATTTTCAAATTTTTA
*
35930774 TTCATAATAAATTTTAA
1 TTCAT-ATAAAGTTTAA
35930791 GGATAAAGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
35 9 0.20
36 35 0.76
37 2 0.04
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (35 bp):
TTCATATAAAGTTTAAATATATTTTCAAATTTTTA
Found at i:35936782 original size:5 final size:5
Alignment explanation
Indices: 35936772--35936806 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
35936762 ACTCCCCTTT
35936772 CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC
1 CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC
35936807 ACTTACGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (5 bp):
CTTCC
Found at i:35941989 original size:26 final size:25
Alignment explanation
Indices: 35941954--35942002 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 25
35941944 GGATAATAAT
35941954 AATAATAATT-ATTATTATTATTTAC
1 AATAATAATTAATTATT-TTATTTAC
35941979 AATATATAATTAATTATTTTATTT
1 AATA-ATAATTAATTATTTTATTT
35942003 CGAAAAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 4 0.18
26 12 0.55
27 6 0.27
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
AATAATAATTAATTATTTTATTTAC
Found at i:35942555 original size:2 final size:2
Alignment explanation
Indices: 35942548--35942573 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35942538 TTTTATTAAG
35942548 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
35942574 TGCATGTATA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35943183 original size:15 final size:15
Alignment explanation
Indices: 35943163--35943195 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
35943153 AATCTTTTAA
35943163 AAATTA-TAAAAATAT
1 AAATTATTAAAAAT-T
35943178 AAATTATTAAAAATT
1 AAATTATTAAAAATT
35943193 AAA
1 AAA
35943196 ATTTAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTATTAAAAATT
Found at i:35945701 original size:4 final size:4
Alignment explanation
Indices: 35945692--35945725 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
35945682 CATTAATTTA
*
35945692 TATG TATG TATG TAAG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TA
35945726 ATACTTTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:35947382 original size:21 final size:22
Alignment explanation
Indices: 35947357--35947402 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
35947347 ATAAAATAAT
*
35947357 AAAATTCCAATTT-TTTTTTAA
1 AAAATACCAATTTATTTTTTAA
*
35947378 AAAATACCAGTTTAATTTTTTAA
1 AAAATACCAATTT-ATTTTTTAA
35947401 AA
1 AA
35947403 TTCTTTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
23 10 0.48
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (22 bp):
AAAATACCAATTTATTTTTTAA
Found at i:35955293 original size:73 final size:72
Alignment explanation
Indices: 35955154--35955294 Score: 192
Period size: 73 Copynumber: 1.9 Consensus size: 72
35955144 GAGAATGGCG
** * *
35955154 CACGCGCGCATATCCCAAAATCGGTGCCAATTTTAACTTTCCGCCAATTGCATTACACCAATCGT
1 CACGCGCGCATATCCCAAAATCGGTGCCAAAATTAACTTTCCGCCAATGGCATTACACCAAGCGT
35955219 GAAGTCT
66 GAAGTCT
* * * * *
35955226 CACGCGCGCATCTCCCAAAATTTGGTGCCAAAATTAACTTTCCGCTAATGGCATTACGCCACGCG
1 CACGCGCGCATATCCCAAAA-TCGGTGCCAAAATTAACTTTCCGCCAATGGCATTACACCAAGCG
35955291 TGAA
65 TGAA
35955295 ATAGCACGCG
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
72 19 0.32
73 40 0.68
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (72 bp):
CACGCGCGCATATCCCAAAATCGGTGCCAAAATTAACTTTCCGCCAATGGCATTACACCAAGCGT
GAAGTCT
Found at i:35963805 original size:14 final size:15
Alignment explanation
Indices: 35963773--35963808 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
35963763 TTAACATGAA
35963773 CAAAAAACTAATTCT
1 CAAAAAACTAATTCT
*
35963788 CAAAAAACTAGTTC-
1 CAAAAAACTAATTCT
35963802 CAAAAAA
1 CAAAAAA
35963809 GCTTTAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.58, C:0.19, G:0.03, T:0.19
Consensus pattern (15 bp):
CAAAAAACTAATTCT
Found at i:35964568 original size:15 final size:14
Alignment explanation
Indices: 35964548--35964584 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
35964538 AATATTTTTA
35964548 TTAATTAATTTGAAT
1 TTAATTAATTT-AAT
35964563 TTAATTAATTTAAT
1 TTAATTAATTTAAT
35964577 TT-ATTAAT
1 TTAATTAAT
35964585 AATAGGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 6 0.27
14 5 0.23
15 11 0.50
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (14 bp):
TTAATTAATTTAAT
Found at i:35965692 original size:31 final size:32
Alignment explanation
Indices: 35965628--35965693 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
35965618 ACAATCTAAA
*
35965628 GATTTAAATTAAAAAATTTCAAATAGTTTAAT
1 GATTTAAATTAAAAAATTTCAAATAATTTAAT
* * *
35965660 GATTTAAA-TGAAAACTTTCGAATAATTTAAT
1 GATTTAAATTAAAAAATTTCAAATAATTTAAT
35965691 GAT
1 GAT
35965694 CCTTTTTGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 22 0.73
32 8 0.27
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.39
Consensus pattern (32 bp):
GATTTAAATTAAAAAATTTCAAATAATTTAAT
Found at i:35971877 original size:31 final size:31
Alignment explanation
Indices: 35971832--35971892 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
35971822 AAAGGATTAC
*
35971832 TGAACTATTCAAAAG-TTTTCATTTAAGTCAT
1 TGAACCATTCAAAAGTTTTTC-TTTAAGTCAT
*
35971863 TGAACCATTTAAAAGTTTTTCTTTAAGTCA
1 TGAACCATTCAAAAGTTTTTCTTTAAGTCA
35971893 CTAAGCTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (31 bp):
TGAACCATTCAAAAGTTTTTCTTTAAGTCAT
Found at i:35972572 original size:22 final size:22
Alignment explanation
Indices: 35972546--35972591 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
35972536 GATTGAAACC
*
35972546 TTGAATTTATTCATTAAATCTA
1 TTGAATTTATCCATTAAATCTA
35972568 TTGAATTTATCCATTAAATCTA
1 TTGAATTTATCCATTAAATCTA
35972590 TT
1 TT
35972592 AAAAAATGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.50
Consensus pattern (22 bp):
TTGAATTTATCCATTAAATCTA
Found at i:35976429 original size:6 final size:6
Alignment explanation
Indices: 35976418--35976443 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
35976408 AATAATTTAA
35976418 AAAATT AAAATT AAAATT AAAATT AA
1 AAAATT AAAATT AAAATT AAAATT AA
35976444 CATAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:35980653 original size:26 final size:27
Alignment explanation
Indices: 35980600--35980654 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
35980590 TTGCACCAAA
*
35980600 TAAAAAATCATATATCAAATTACGTAT
1 TAAAAAATCATATATCAAATTACATAT
*
35980627 TAAAAAATCATGTAT-AAATTTA-ATAT
1 TAAAAAATCATATATCAAA-TTACATAT
35980653 TA
1 TA
35980655 TCACTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (27 bp):
TAAAAAATCATATATCAAATTACATAT
Found at i:35986811 original size:7 final size:6
Alignment explanation
Indices: 35986793--35986831 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
35986783 GGATTTTTTT
* *
35986793 AGAAAA GGAAAA AGAAAA AGAAAA AGAAAC AGAAAA AGA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGA
35986832 TGGGCGAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.77, C:0.03, G:0.21, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:35990667 original size:174 final size:174
Alignment explanation
Indices: 35990176--35990832 Score: 646
Period size: 174 Copynumber: 3.7 Consensus size: 174
35990166 AGTTTCACAT
* * * * * * *
35990176 GGTTTCACCTGTTACTACAAGACACTCAACTCTGTCAACCTGATAGGATTCTCGGTAGAGTTAGG
1 GGTTTCACCTGTTACTACAAAACACTCAACTTTCTCAACCTAACAGGAGTCTCGGTAGAG-T-CG
* * * *
35990241 AAACAAAACCTCGA-CAGGGACACGGTTT-ACCTGTTACTACAAAACACTCAACTCTGTCAACCT
64 AGACAAAACCTCGACCAAGGACACAGTTTCACCTGTTACTACAAGACACTCAACTCTGTCAACCT
* * * * * * *
35990304 AATATGAGTCTCAGTAAAGTAGGGAAACAAAACCTTGACAGGAGACAT
129 AATAGGAGTCTCAATAGAGTCGGGAGACAAAACC-TAACAGG-GACAC
* * * *
35990352 GGTTTCACTTGTTACTACAAGAA-ACTCAACTCTAC-CAACCTAATAAGAGTCTCGGTAGAGTCA
1 GGTTTCACCTGTTACTACAA-AACACTCAACT-TTCTCAACCTAACAGGAGTCTCGGTAGAGTC-
* * * *
35990415 GGAGACAAAACCTCAACCTAGGACACGGTTTCATCTGTTACTACAAGACACTCAACTCTGTCAAC
63 -GAGACAAAACCTCGACCAAGGACACAGTTTCACCTGTTACTACAAGACACTCAACTCTGTCAAC
* * * *
35990480 TTAATAGGAGTCTCAATAGAGTCGAGAGACAAAAGCTCAACAGGGATAC
127 CTAATAGGAGTCTCAATAGAGTCGGGAGACAAAACCT-AACAGGGACAC
* * * *
35990529 GGTTTCACTTGTTACTACAAAACACTCAACTTTCTCCACCTAACAGGAGTCTCTGTGGAGTC-AG
1 GGTTTCACCTGTTACTACAAAACACTCAACTTTCTCAACCTAACAGGAGTCTCGGTAGAGTCGAG
** * * * * *
35990593 ACAAAACCTCGACCGGGGATATAGTTTCACCTATTACTACATGACACACAACTCTGTCAACCT-A
66 ACAAAACCTCGACCAAGGACACAGTTTCACCTGTTACTACAAGACACTCAACTCTGTCAACCTAA
* *
35990657 TCAGGAGTCTCGATAGAGTCGGGAGACAAAACCTAGACAGCGACAC
131 T-AGGAGTCTCAATAGAGTCGGGAGACAAAACCTA-ACAGGGACAC
* * * * *
35990703 GGTTTCACCTGTTACTACAAGACACTCAA-TTCTATCAACCTGACAGGATTCTCGGCAGAGTCGG
1 GGTTTCACCTGTTACTACAAAACACTCAACTT-TCTCAACCTAACAGGAGTCTCGGTAGAGTC--
* * * * *
35990767 GAGACAAAACCTCCACCAAGGATATAGATTCAACTGTTACTACAAGACACTCAACTCTAG-CAAC
63 GAGACAAAACCTCGACCAAGGACACAGTTTCACCTGTTACTACAAGACACTCAACTCT-GTCAAC
35990831 CT
127 CT
35990833 GACAGGATTC
Statistics
Matches: 400, Mismatches: 65, Indels: 31
0.81 0.13 0.06
Matches are distributed among these distances:
173 5 0.01
174 141 0.35
175 1 0.00
176 66 0.17
177 122 0.31
178 65 0.16
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (174 bp):
GGTTTCACCTGTTACTACAAAACACTCAACTTTCTCAACCTAACAGGAGTCTCGGTAGAGTCGAG
ACAAAACCTCGACCAAGGACACAGTTTCACCTGTTACTACAAGACACTCAACTCTGTCAACCTAA
TAGGAGTCTCAATAGAGTCGGGAGACAAAACCTAACAGGGACAC
Found at i:35990835 original size:89 final size:88
Alignment explanation
Indices: 35990176--35990845 Score: 668
Period size: 89 Copynumber: 7.6 Consensus size: 88
35990166 AGTTTCACAT
* * * **
35990176 GGTTTCACCTGTTACTACAAGACACTCAACTCTGTCAACCTGATAGGATTCTCGGTAGAGTTAGG
1 GGTTTCACCTGTTACTACAAGACACTCAACTCTGTCAACCTAACAGGAGTCTCGGTAGAGTCGGG
*
35990241 AAACAAAACCTCGACAGGGACAC
66 AGACAAAACCTCGACAGGGACAC
* * * * * *
35990264 GGTTT-ACCTGTTACTACAAAACACTCAACTCTGTCAACCTAATATGAGTCTCAGTAAAGTAGGG
1 GGTTTCACCTGTTACTACAAGACACTCAACTCTGTCAACCTAACAGGAGTCTCGGTAGAGTCGGG
* * *
35990328 AAACAAAACCTTGACAGGAGACAT
66 AGACAAAACCTCGACAGG-GACAC
* * ** * * *
35990352 GGTTTCACTTGTTACTACAAGAAACTCAACTCTACCAACCTAATAAGAGTCTCGGTAGAGTCAGG
1 GGTTTCACCTGTTACTACAAGACACTCAACTCTGTCAACCTAACAGGAGTCTCGGTAGAGTCGGG
*
35990417 AGACAAAACCTCAACCTA-GGACAC
66 AGACAAAACCTCGA-C-AGGGACAC
* * * ** *
35990441 GGTTTCATCTGTTACTACAAGACACTCAACTCTGTCAACTTAATAGGAGTCTCAATAGAGTCGAG
1 GGTTTCACCTGTTACTACAAGACACTCAACTCTGTCAACCTAACAGGAGTCTCGGTAGAGTCGGG
* * *
35990506 AGACAAAAGCTCAACAGGGATAC
66 AGACAAAACCTCGACAGGGACAC
* * * * * * *
35990529 GGTTTCACTTGTTACTACAAAACACTCAACTTTCTCCACCTAACAGGAGTCTCTGTGGAGTC---
1 GGTTTCACCTGTTACTACAAGACACTCAACTCTGTCAACCTAACAGGAGTCTCGGTAGAGTCGGG
* * *
35990591 AGACAAAACCTCGACCGGGGATAT
66 AGACAAAACCTCGA-CAGGGACAC
* * * * * *
35990615 AGTTTCACCTATTACTACATGACACACAACTCTGTCAACCTATCAGGAGTCTCGATAGAGTCGGG
1 GGTTTCACCTGTTACTACAAGACACTCAACTCTGTCAACCTAACAGGAGTCTCGGTAGAGTCGGG
* *
35990680 AGACAAAACCTAGACAGCGACAC
66 AGACAAAACCTCGACAGGGACAC
* * * * *
35990703 GGTTTCACCTGTTACTACAAGACACTCAATTCTATCAACCTGACAGGATTCTCGGCAGAGTCGGG
1 GGTTTCACCTGTTACTACAAGACACTCAACTCTGTCAACCTAACAGGAGTCTCGGTAGAGTCGGG
* * * *
35990768 AGACAAAACCTCCACCAAGGATAT
66 AGACAAAACCTCGA-CAGGGACAC
* * * * *
35990792 AGATTCAACTGTTACTACAAGACACTCAACTCTAG-CAACCTGACAGGATTCTCG
1 GGTTTCACCTGTTACTACAAGACACTCAACTCT-GTCAACCTAACAGGAGTCTCG
35990846 ACAGAGGCGG
Statistics
Matches: 479, Mismatches: 92, Indels: 21
0.81 0.16 0.04
Matches are distributed among these distances:
85 12 0.03
86 56 0.12
87 69 0.14
88 142 0.30
89 197 0.41
90 2 0.00
91 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (88 bp):
GGTTTCACCTGTTACTACAAGACACTCAACTCTGTCAACCTAACAGGAGTCTCGGTAGAGTCGGG
AGACAAAACCTCGACAGGGACAC
Found at i:35991636 original size:20 final size:20
Alignment explanation
Indices: 35991611--35991669 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
35991601 TCTTGAGTGA
35991611 AATTATCATTGTAGCTGGTG
1 AATTATCATTGTAGCTGGTG
35991631 AATTATCATTGTA-----T-
1 AATTATCATTGTAGCTGGTG
*
35991645 AATTATCATTGTTGCTGGTG
1 AATTATCATTGTAGCTGGTG
35991665 AATTA
1 AATTA
35991670 CGTTAATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
14 12 0.38
15 1 0.03
19 1 0.03
20 18 0.56
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.44
Consensus pattern (20 bp):
AATTATCATTGTAGCTGGTG
Found at i:35992514 original size:31 final size:31
Alignment explanation
Indices: 35992454--35992522 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
35992444 TTATAATTCG
35992454 GTCACTGAACTATCCAGAACTTTTCATTTAA
1 GTCACTGAACTATCCAGAACTTTTCATTTAA
* * *
35992485 GTCATTGAATTATTCAGAAGCTTTT-ATTTAA
1 GTCACTGAACTATCCAGAA-CTTTTCATTTAA
35992516 GTCACTG
1 GTCACTG
35992523 GAATGCTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 28 0.85
32 5 0.15
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.39
Consensus pattern (31 bp):
GTCACTGAACTATCCAGAACTTTTCATTTAA
Found at i:36012752 original size:60 final size:60
Alignment explanation
Indices: 36012601--36013111 Score: 351
Period size: 60 Copynumber: 8.5 Consensus size: 60
36012591 AAAAAATTGA
* * * * * * *
36012601 TGTTGGCTATTGCAAGGCCGACATCC-C-TTTTTGTCAGATAAAAAATTTAAATTTTTTGT
1 TGTTGGCCATTGCATGGCCGACA-CCACTTTTTTATCTGATAAAAAATTCAACTTTTTTGG
* * * * * * * *
36012660 TGTTGGCCATTACTTAGTCAACACC-TTTTTTTATCAGATAAAAAAGTCAACTTTTTT-G
1 TGTTGGCCATTGCATGGCCGACACCACTTTTTTATCTGATAAAAAATTCAACTTTTTTGG
* * * *
36012718 TGTTGCCCATTGCATGACCGACACCTCTTTTTTTATCTGATAAAAAA-TCAATTTTTTTGG
1 TGTTGGCCATTGCATGGCCGACACCAC-TTTTTTATCTGATAAAAAATTCAACTTTTTTGG
* ** * * * * *
36012778 TGTTGGCCATTGCATGACTAATACC-CCTTTTTGTCAT-ATAAAAAATTCAAATTTTTTCG
1 TGTTGGCCATTGCATGGCCGACACCACTTTTTTATC-TGATAAAAAATTCAACTTTTTTGG
* * ** * *
36012837 TGTTGGTCATTGTATGGCCGACACCACCTTTTAAATTTGATAAAAATTTTCAACTTTTTTGG
1 TGTTGGCCATTGCATGGCCGACACCA-CTTTTTTATCTGATAAAAA-ATTCAACTTTTTTGG
** * * * * *
36012899 TGTTGGCCATTGCATGGCTAACACCAC-CTATTATCTGATTAAAAAAATCAAATTTTTTTG
1 TGTTGGCCATTGCATGGCCGACACCACTTTTTTATCTGA-TAAAAAATTCAACTTTTTTGG
* * * * *
36012959 TGTTGGCCATTGCATGGCCGACACCACCTTTCTGTCTGATAAAAAAATTCAAATATTTTTTG
1 TGTTGGCCATTGCATGGCCGACACCACTTTTTTATCTGAT-AAAAAATTCAACT-TTTTTGG
* * * * * *
36013021 TGTTGGCCA-TGTATTGACTGACACCACATTTTTATCT-A-AAAAGAAATCAAATTTTTTGG
1 TGTTGGCCATTGCA-TGGCCGACACCACTTTTTTATCTGATAAAA-AATTCAACTTTTTTGG
* * *
36013080 TGTTAGGTCATTGCTTGGCCAACACCAACTTT
1 TGTT-GGCCATTGCATGGCCGACACC-ACTTT
36013112 CTCTCGTTTT
Statistics
Matches: 353, Mismatches: 80, Indels: 36
0.75 0.17 0.08
Matches are distributed among these distances:
58 35 0.10
59 98 0.28
60 104 0.29
61 48 0.14
62 68 0.19
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (60 bp):
TGTTGGCCATTGCATGGCCGACACCACTTTTTTATCTGATAAAAAATTCAACTTTTTTGG
Found at i:36013112 original size:122 final size:120
Alignment explanation
Indices: 36012640--36013113 Score: 403
Period size: 122 Copynumber: 3.9 Consensus size: 120
36012630 TTTGTCAGAT
* * * * ** *
36012640 AAAAAATTTAAA-TTTTTTGTTGTTGGCCATTAC-TTAGTCAACACCTTTTTTTATCAGATAAAA
1 AAAAAATTCAAATTTTTTTG-TGTTGGCCATTGCATGACT-AACACCACTTTTTATC-TATAAAA
* * ** * * * * * *
36012703 AAGTCAACTTTTTT-GTGTTGCCCATTGCATGACCGACACCTCTTTTTTTATCTGAT-
63 AAATCAAATTTTTTCGTGTTGGTCATTGCTTGGCCGACACCACCTTTCTAATCTGATA
* * *
36012759 AAAAAA-TC-AATTTTTTTGGTGTTGGCCATTGCATGACTAATACCCCTTTTTGTCATATAAAAA
1 AAAAAATTCAAATTTTTTT-GTGTTGGCCATTGCATGACTAACACCACTTTTTATC-TATAAAAA
* *
36012822 ATTCAAATTTTTTCGTGTTGGTCATTG-TATGGCCGACACCACCTTT-TAAATTTGATA
64 AATCAAATTTTTTCGTGTTGGTCATTGCT-TGGCCGACACCACCTTTCT-AATCTGATA
** * * * * *
36012879 AAAATTTTCAACTTTTTTGGTGTTGGCCATTGCATGGCTAACACCACCTATTATCTGATTAAAAA
1 AAAAAATTCAAATTTTTTTGTGTTGGCCATTGCATGACTAACACCACTTTTTATCT-A-TAAAAA
* * * *
36012944 AATCAAATTTTTTTGTGTTGGCCATTGCATGGCCGACACCACCTTTCT-GTCTGATA
64 AATCAAATTTTTTCGTGTTGGTCATTGCTTGGCCGACACCACCTTTCTAATCTGATA
* *
36013000 AAAAAATTCAAATATTTTTTGTGTTGGCCA-TGTATTGACTGACACCACATTTTTATCTA-AAAA
1 AAAAAATTCAAAT-TTTTTTGTGTTGGCCATTGCA-TGACTAACACCAC-TTTTTATCTATAAAA
* * *
36013063 GAAATCAAATTTTTTGGTGTTAGGTCATTGCTTGGCCAACACCAACTTTCT
63 -AAATCAAATTTTTTCGTGTT-GGTCATTGCTTGGCCGACACCACCTTTCT
36013114 CTCGTTTTTC
Statistics
Matches: 288, Mismatches: 49, Indels: 33
0.78 0.13 0.09
Matches are distributed among these distances:
117 2 0.01
118 51 0.18
119 41 0.14
120 9 0.03
121 71 0.25
122 106 0.37
123 8 0.03
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (120 bp):
AAAAAATTCAAATTTTTTTGTGTTGGCCATTGCATGACTAACACCACTTTTTATCTATAAAAAAA
TCAAATTTTTTCGTGTTGGTCATTGCTTGGCCGACACCACCTTTCTAATCTGATA
Found at i:36020901 original size:19 final size:20
Alignment explanation
Indices: 36020865--36020902 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
36020855 TTTTTGATTG
**
36020865 AAGAATGAAGGAGGGAGAAT
1 AAGAATGAAGGAAAGAGAAT
36020885 AAGAAT-AAGGAAAGAGAA
1 AAGAATGAAGGAAAGAGAA
36020903 AACTAACTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.58, C:0.00, G:0.34, T:0.08
Consensus pattern (20 bp):
AAGAATGAAGGAAAGAGAAT
Found at i:36027968 original size:6 final size:6
Alignment explanation
Indices: 36027943--36027990 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
36027933 ACAATTCATA
* * * *
36027943 TCACTT TCAATT CCAATT TCGCTT TCACTT TCACTT TCACTT TCACTT
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT
36027991 CCAATTTTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.19, C:0.31, G:0.02, T:0.48
Consensus pattern (6 bp):
TCACTT
Found at i:36027969 original size:18 final size:18
Alignment explanation
Indices: 36027943--36027997 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
36027933 ACAATTCATA
*
36027943 TCACTTTCAATTCCAATT
1 TCACTTTCACTTCCAATT
* * *
36027961 TCGCTTTCACTTTCACTT
1 TCACTTTCACTTCCAATT
36027979 TCACTTTCACTTCCAATT
1 TCACTTTCACTTCCAATT
36027997 T
1 T
36027998 TGATCATAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.20, C:0.31, G:0.02, T:0.47
Consensus pattern (18 bp):
TCACTTTCACTTCCAATT
Found at i:36035077 original size:11 final size:11
Alignment explanation
Indices: 36035057--36035089 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
36035047 AATTTAAATT
36035057 ATTTTTTATAA
1 ATTTTTTATAA
*
36035068 ATTTTATATAA
1 ATTTTTTATAA
36035079 ATTTTTTATAA
1 ATTTTTTATAA
36035090 TAATATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
ATTTTTTATAA
Found at i:36035104 original size:22 final size:19
Alignment explanation
Indices: 36035054--36035106 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 19
36035044 TGTAATTTAA
36035054 ATTATTTTTTATAAATTTT
1 ATTATTTTTTATAAATTTT
36035073 ATATAAATTTTTTATAATAATATTT
1 AT-T--ATTTTTTAT-A-AAT-TTT
36035098 ATTATTTTT
1 ATTATTTTT
36035107 AAATATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
19 2 0.07
20 1 0.04
22 15 0.54
23 1 0.04
24 4 0.14
25 5 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTATTTTTTATAAATTTT
Found at i:36035158 original size:20 final size:20
Alignment explanation
Indices: 36035133--36035172 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
36035123 AAATACTTAC
36035133 AATTTTATTTTAAATAATTT
1 AATTTTATTTTAAATAATTT
36035153 AATTTTATTTTAAATAATTT
1 AATTTTATTTTAAATAATTT
36035173 CATTATAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
AATTTTATTTTAAATAATTT
Found at i:36061286 original size:19 final size:20
Alignment explanation
Indices: 36061243--36061292 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
36061233 ATTAGTATAA
36061243 ATAAATTAT-TTTTAAAAAT
1 ATAAATTATATTTTAAAAAT
* *
36061262 ACAAATTATATTTTAAACAT
1 ATAAATTATATTTTAAAAAT
36061282 -TAAATTCATAT
1 ATAAATT-ATAT
36061293 AATTGACAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAAATTATATTTTAAAAAT
Found at i:36061503 original size:29 final size:30
Alignment explanation
Indices: 36061469--36061527 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
36061459 TATAGTTTAA
*
36061469 TGTATAATTGTATATATG-AATTTTAATTT
1 TGTATAATTGTATACATGAAATTTTAATTT
* *
36061498 TGTATAATTTTATACATGAAATTTTGATTT
1 TGTATAATTGTATACATGAAATTTTAATTT
36061528 AATCCAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (30 bp):
TGTATAATTGTATACATGAAATTTTAATTT
Found at i:36062293 original size:16 final size:17
Alignment explanation
Indices: 36062263--36062294 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
36062253 ATAAATGATA
36062263 TTTATTTTTATTATAAT
1 TTTATTTTTATTATAAT
36062280 TTTATTTTTA-TATAA
1 TTTATTTTTATTATAA
36062295 AAATTAACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTATTTTTATTATAAT
Done.