Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, whole genome shotgun sequence
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: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 30 of 113
Found at i:9727240 original size:83 final size:83
Alignment explanation
Indices: 9727103--9727401 Score: 298
Period size: 83 Copynumber: 3.5 Consensus size: 83
9727093 GATTGTCAAT
* ** * * * **
9727103 GAGCAATTTATTTTTCAAATTTGTGATGCCTCTGTTTAGAGAAGCAACCTATTTTTC-AAAGTTG
1 GAGCAATTTATTTTTCAAAGTCATTAAGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAAGTTG
9727167 -TGATGCCTCTAATTAGAG
66 TTGA-GCCTCTAATTAGAG
* * *
9727185 GAGCAATTTACTTTTCAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAAGTT
1 GAGCAATTTATTTTTC-AAAGTCATTAAGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAAGTT
* *
9727250 GTTGAGCCTTTGATTAGAG
65 GTTGAGCCTCTAATTAGAG
** * * * *
9727269 GAGCCTTTTATTTTTAAAAGTTATTAAGCCTTTGTTTAGAGGAGC-TTTACTATCTTTTCAAAAG
1 GAGCAATTTATTTTTCAAAGTCATTAAGCCTCTGTTTAGAGGAGCAATT--TAT-TTTTCAAAAG
* *
9727333 TCGTTGAGCCTCTATTTAGAG
63 TTGTTGAGCCTCTAATTAGAG
* *
9727354 GAGCTTTATTTATTTTTTCAAAGTCATTAAGCCTCTGCTTAGAGGAGC
1 GAGC--AATTTA-TTTTTCAAAGTCATTAAGCCTCTGTTTAGAGGAGC
9727402 CTTCGTTTAT
Statistics
Matches: 178, Mismatches: 30, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
82 17 0.10
83 58 0.33
84 34 0.19
85 34 0.19
87 4 0.02
88 31 0.17
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (83 bp):
GAGCAATTTATTTTTCAAAGTCATTAAGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAAGTTG
TTGAGCCTCTAATTAGAG
Found at i:9727662 original size:12 final size:12
Alignment explanation
Indices: 9727645--9727686 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
9727635 TTTCATTCTA
9727645 TTTTATTTTATT
1 TTTTATTTTATT
* *
9727657 TTTTATTTTGTA
1 TTTTATTTTATT
9727669 TTTTA-TTTATT
1 TTTTATTTTATT
*
9727680 TATTATT
1 TTTTATT
9727687 ACTATTTATT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:9727768 original size:27 final size:28
Alignment explanation
Indices: 9727667--9727795 Score: 99
Period size: 31 Copynumber: 4.5 Consensus size: 28
9727657 TTTTATTTTG
9727667 TATT-TTATTTATTTATTA-TTA-CTATT
1 TATTATTATTTATTTATTATTTATCTA-T
* * *
9727693 TATTAATATATATTTATTATTTATCTGT
1 TATTATTATTTATTTATTATTTATCTAT
9727721 TAATATATATACTTTA-TTATTATTTATCTAT
1 T-AT-TAT-TA-TTTATTTATTATTTATCTAT
* *
9727752 TATTATTATTATCTATTAATATATTATCT-T
1 TATTATTATT-TAT-TTATTAT-TTATCTAT
9727782 TATT-TTATTTATTT
1 TATTATTATTTATTT
9727796 TTTTCTTTCT
Statistics
Matches: 83, Mismatches: 9, Indels: 21
0.73 0.08 0.19
Matches are distributed among these distances:
26 4 0.05
27 16 0.19
28 10 0.12
29 12 0.14
30 15 0.18
31 23 0.28
32 3 0.04
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.64
Consensus pattern (28 bp):
TATTATTATTTATTTATTATTTATCTAT
Found at i:9728677 original size:4 final size:4
Alignment explanation
Indices: 9728663--9728706 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
9728653 TTTTTTTTTC
9728663 ATTT ATATT ATTT ATTT ATTT A-TT A-TT A-TT A-TT ATTT ATTT ATT
1 ATTT AT-TT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATT
9728707 AGGTTAGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 12 0.32
4 22 0.58
5 4 0.11
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:9728749 original size:6 final size:6
Alignment explanation
Indices: 9728724--9728764 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
9728714 AATTATTTAG
*
9728724 TATTTCT TA-TTT TA-TTT TATTTT TATCTT TATTTT TATTTT
1 TATTT-T TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT
9728765 CTTTAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
5 8 0.26
6 21 0.68
7 2 0.06
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (6 bp):
TATTTT
Found at i:9728754 original size:17 final size:17
Alignment explanation
Indices: 9728724--9728764 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
9728714 AATTATTTAG
9728724 TATTTCTTATTTTA-TTT
1 TATTT-TTATTTTATTTT
9728741 TATTTTTATCTTTATTTT
1 TATTTTTAT-TTTATTTT
9728759 TATTTT
1 TATTTT
9728765 CTTTAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.18
17 9 0.41
18 9 0.41
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (17 bp):
TATTTTTATTTTATTTT
Found at i:9728900 original size:57 final size:58
Alignment explanation
Indices: 9728784--9728916 Score: 250
Period size: 57 Copynumber: 2.3 Consensus size: 58
9728774 AAATTCCAAA
9728784 AAAGTATCAATTTTTCTTAAAAATAAGTTTTTCTAAAAAATATTTTTGAGGAAAGTTG
1 AAAGTATCAATTTTTCTTAAAAATAAGTTTTTCTAAAAAATATTTTTGAGGAAAGTTG
*
9728842 AAAGTATCAATTTTTCTTAAAAATAAG-TTTTCTAAAAGATATTTTTGAGGAAAGTTG
1 AAAGTATCAATTTTTCTTAAAAATAAGTTTTTCTAAAAAATATTTTTGAGGAAAGTTG
9728899 AAAGTATCAATTTTTCTT
1 AAAGTATCAATTTTTCTT
9728917 GTACGAAAGC
Statistics
Matches: 74, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
57 47 0.64
58 27 0.36
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (58 bp):
AAAGTATCAATTTTTCTTAAAAATAAGTTTTTCTAAAAAATATTTTTGAGGAAAGTTG
Found at i:9729736 original size:15 final size:15
Alignment explanation
Indices: 9729716--9729751 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
9729706 AAATTTATAG
9729716 AATTTTCAAATGGTA
1 AATTTTCAAATGGTA
9729731 AATTTTCAAATGGTA
1 AATTTTCAAATGGTA
9729746 AATTTT
1 AATTTT
9729752 TATGAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (15 bp):
AATTTTCAAATGGTA
Found at i:9729934 original size:21 final size:21
Alignment explanation
Indices: 9729909--9729949 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
9729899 ATTATTTAAT
*
9729909 GATGAAATTCATAGAAATTTA
1 GATGAAATTCATAAAAATTTA
* *
9729930 GATGAGATTCTTAAAAATTT
1 GATGAAATTCATAAAAATTT
9729950 CAAATGATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.37
Consensus pattern (21 bp):
GATGAAATTCATAAAAATTTA
Found at i:9731446 original size:14 final size:14
Alignment explanation
Indices: 9731415--9731479 Score: 55
Period size: 14 Copynumber: 4.7 Consensus size: 14
9731405 CTTCTTTCAT
*
9731415 TTTATTTTTATT-TT
1 TTTATTTTT-TTATA
9731429 TTTATTTTTTTATA
1 TTTATTTTTTTATA
**
9731443 TTTA-ACTTTTATA
1 TTTATTTTTTTATA
*
9731456 TTTAGTTTTTTA-A
1 TTTATTTTTTTATA
9731469 CTTTATTTTTT
1 -TTTATTTTTT
9731480 ATTAGATGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
13 14 0.33
14 28 0.67
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (14 bp):
TTTATTTTTTTATA
Found at i:9731452 original size:21 final size:19
Alignment explanation
Indices: 9731428--9731479 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
9731418 ATTTTTATTT
9731428 TTTTATTTTTTTATATTTAAC
1 TTTTATTTTTTT-T-TTTAAC
*
9731449 TTTTATATTTAGTTTTTTAAC
1 TTTTAT-TTT-TTTTTTTAAC
9731470 -TTTATTTTTT
1 TTTTATTTTTT
9731480 ATTAGATGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
18 1 0.04
19 3 0.11
20 5 0.19
21 12 0.44
22 4 0.15
23 2 0.07
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTATTTTTTTTTTTAAC
Found at i:9731716 original size:18 final size:18
Alignment explanation
Indices: 9731681--9731714 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9731671 CCTCATTCTT
*
9731681 TTTGTTTTTATCATTTTA
1 TTTGTTTTTATAATTTTA
9731699 TTTGTTTTT-TAATTTT
1 TTTGTTTTTATAATTTT
9731715 TACATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (18 bp):
TTTGTTTTTATAATTTTA
Found at i:9731735 original size:25 final size:26
Alignment explanation
Indices: 9731685--9731732 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
9731675 ATTCTTTTTG
9731685 TTTTTATCATTTTATTTGTTTTTTAA
1 TTTTTATCATTTTATTTGTTTTTTAA
*
9731711 TTTTTA-CATTTT-TTTCTTTTTT
1 TTTTTATCATTTTATTTGTTTTTT
9731733 TAAAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
25 6 0.29
26 6 0.29
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (26 bp):
TTTTTATCATTTTATTTGTTTTTTAA
Found at i:9732070 original size:27 final size:23
Alignment explanation
Indices: 9732040--9732098 Score: 57
Period size: 23 Copynumber: 2.4 Consensus size: 23
9732030 ATTTTATAAA
9732040 AATTATATTTATAAATAATTAAATTAT
1 AATTATATTT-TAAA-AA-TAAA-TAT
*
9732067 AATT-TATATTAAAAATAAATAT
1 AATTATATTTTAAAAATAAATAT
*
9732089 ACTTATATTT
1 AATTATATTT
9732099 GTTTATACGT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 6 0.21
23 8 0.29
24 2 0.07
25 4 0.14
26 4 0.14
27 4 0.14
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTATATTTTAAAAATAAATAT
Found at i:9733898 original size:6 final size:6
Alignment explanation
Indices: 9733877--9733949 Score: 53
Period size: 6 Copynumber: 12.3 Consensus size: 6
9733867 TTTAATATTC
* * * * *
9733877 TTTTTA TCTTTA TTTTATT TTTTTA CTTTTC TTTATTT TTTTTA -TTTTA
1 TTTTTA TTTTTA TTTT-TA TTTTTA TTTTTA TTT-TTA TTTTTA TTTTTA
*
9733926 TTTTTA --TTTA TTTTTA TTATTA TT
1 TTTTTA TTTTTA TTTTTA TTTTTA TT
9733950 CTCTTTTCTT
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
4 4 0.08
5 5 0.10
6 33 0.63
7 10 0.19
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:9733898 original size:18 final size:18
Alignment explanation
Indices: 9733872--9733918 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 18
9733862 GTTTATTTAA
9733872 TATTCTTTTTATCTTTAT-TT
1 TATT-TTTTTA-CTTT-TCTT
9733892 TATTTTTTTACTTTTCTT
1 TATTTTTTTACTTTTCTT
9733910 TATTTTTTT
1 TATTTTTTT
9733919 TATTTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 1 0.04
18 15 0.58
19 6 0.23
20 4 0.15
ACGTcount: A:0.13, C:0.09, G:0.00, T:0.79
Consensus pattern (18 bp):
TATTTTTTTACTTTTCTT
Found at i:9733915 original size:9 final size:8
Alignment explanation
Indices: 9733889--9733946 Score: 55
Period size: 8 Copynumber: 6.9 Consensus size: 8
9733879 TTTATCTTTA
9733889 TTTTATTT
1 TTTTATTT
9733897 TTTTACTTT
1 TTTTA-TTT
9733906 TCTTTATTTT
1 T-TTTA-TTT
9733916 TTTTATTT
1 TTTTATTT
*
9733924 TATT-TTT
1 TTTTATTT
*
9733931 ATTTATTT
1 TTTTATTT
9733939 TTATTATT
1 TT-TTATT
9733947 ATTCTCTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
7 5 0.12
8 15 0.37
9 13 0.32
10 8 0.20
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTATTT
Found at i:9733916 original size:10 final size:9
Alignment explanation
Indices: 9733872--9733943 Score: 65
Period size: 10 Copynumber: 7.4 Consensus size: 9
9733862 GTTTATTTAA
*
9733872 TATTCTTTT
1 TATTTTTTT
9733881 TATCTTTATTT
1 TAT-TTT-TTT
9733892 TA-TTTTTT
1 TATTTTTTT
*
9733900 TACTTTTCTT
1 TA-TTTTTTT
9733910 TATTTTTTT
1 TATTTTTTT
9733919 TATTTTATTTT
1 TA-TTT-TTTT
9733930 TATTTATTTT
1 TATTT-TTTT
9733940 TATT
1 TATT
9733944 ATTATTCTCT
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
8 5 0.09
9 14 0.26
10 24 0.44
11 11 0.20
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (9 bp):
TATTTTTTT
Found at i:9734190 original size:61 final size:59
Alignment explanation
Indices: 9733982--9734265 Score: 382
Period size: 59 Copynumber: 4.7 Consensus size: 59
9733972 AAAAATTCCA
*
9733982 AAAAAAAATATTTTTAGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAA-GAAAAATAAATTTC
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAATG--AAAT---TTTC
* *
9734045 -CAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAA-GTAAATTTTC
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAATG-AAATTTTC
*
9734103 AAAAAAAAGATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCGAAATTTTC
1 AAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTT-AAAAT-GAAATTTTC
*
9734164 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTCTCCTTAAAAAT-AAATTTTC
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAATGAAATTTTC
9734223 AAAAAAAGA-ATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
9734266 CTACACAAGA
Statistics
Matches: 204, Mismatches: 10, Indels: 18
0.88 0.04 0.08
Matches are distributed among these distances:
58 5 0.02
59 88 0.43
60 5 0.02
61 58 0.28
62 48 0.24
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (59 bp):
AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAATGAAATTTTC
Found at i:9734209 original size:120 final size:118
Alignment explanation
Indices: 9733982--9734265 Score: 410
Period size: 120 Copynumber: 2.4 Consensus size: 118
9733972 AAAAATTCCA
* *
9733982 AAAAAAAATATTTTTAGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCCA
1 AAAAAAAAGATTTTTAG-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAAT--ATTTCAA
* * *
9734047 AAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGTAAATTTTC
63 AAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTCTCCTTAAAAATAAATTTTC
***
9734103 AAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCGAAAT-TTTCAAA
1 AAAAAAAAGATTTTT-AGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAAGAAAAATATTTC-AA
9734167 AAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTCTCCTTAAAAATAAATTTTC
63 AAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTCTCCTTAAAAATAAATTTTC
9734223 -AAAAAAAGAATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAAAG-ATTTTTA-GGAAAAGTTGAAAGTATCAATTTTCC
9734266 CTACACAAGA
Statistics
Matches: 150, Mismatches: 8, Indels: 11
0.89 0.05 0.07
Matches are distributed among these distances:
119 13 0.09
120 86 0.57
121 41 0.27
122 10 0.07
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (118 bp):
AAAAAAAAGATTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATATTTCAAAAA
AATATTTTTAGGGAAAAGTTGAAAGTATCAATTCTCCTTAAAAATAAATTTTC
Found at i:9743213 original size:59 final size:59
Alignment explanation
Indices: 9743026--9743455 Score: 568
Period size: 59 Copynumber: 7.3 Consensus size: 59
9743016 CTGATTTCTC
*
9743026 TGAAAGTATCAATTTTCCTTAAAAATAAA-TTTC--AAAAAGGGTTTTT-GAGGAAAAGT
1 TGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGGATTTTTAG-GGAAAAGT
* * * *
9743082 TGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCCAAAAAA-TATTTTTAGGAAAAAGT
1 TGAAAGTATCAATTTTCCTTAAAA-ATAAAT---TTTCAAAAAAAGGATTTTTAGGGAAAAGT
* * *
9743144 TGAAAGTATCAATTTTTCTTAAAAGTAAATTTTCAAAAAAAGGATTTTTAAGGAAAAGT
1 TGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGGATTTTTAGGGAAAAGT
* **
9743203 TGAAAGTATCAATTTTCCTTGAAAATCGAAATTTTCAAAAAAAATATTTTTAGGGAAAAGT
1 TGAAAGTATCAATTTTCCTTAAAAAT--AAATTTTCAAAAAAAGGATTTTTAGGGAAAAGT
* * * * *
9743264 TAAAAATATCAATTCTCCTTAAAAATAAATTTCCAAAAAATA-TATTTTTAGGGAAAAGT
1 TGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAA-AGGATTTTTAGGGAAAAGT
9743323 TGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGGATTTTTAGGGAAAAGT
1 TGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGGATTTTTAGGGAAAAGT
** *
9743382 TGAAAGTATCAATTTTCCTTAAAAATAAA-TTTCAAAAAAATAATTTTTGGGGAAAAGT
1 TGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGGATTTTTAGGGAAAAGT
9743440 TGAAAGTATCAATTTT
1 TGAAAGTATCAATTTT
9743456 TCCTACACAA
Statistics
Matches: 331, Mismatches: 30, Indels: 24
0.86 0.08 0.06
Matches are distributed among these distances:
56 24 0.07
57 4 0.01
58 53 0.16
59 148 0.45
60 1 0.00
61 60 0.18
62 35 0.11
63 6 0.02
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.34
Consensus pattern (59 bp):
TGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGGATTTTTAGGGAAAAGT
Found at i:9743242 original size:118 final size:116
Alignment explanation
Indices: 9743026--9743455 Score: 571
Period size: 120 Copynumber: 3.6 Consensus size: 116
9743016 CTGATTTCTC
* *
9743026 TGAAAGTATCAATTTTCCTTAAAAATAAATTTC--AAAAAGGGTTTTTGAGGAAAAGTTGAAAGT
1 TGAAAGTATCAATTTTCCTTAAAAATAAATTTCAAAAAAAGGATTTTTAAGGAAAAGTTGAAAGT
* *
9743089 ATCAATTTTCCTTAAAAGAAAAATAAA-TTTCCAAAAAATATTTTTAGGAAAAAGT
66 ATCAATTTTCCTT----G-AAAATAAATTTTCAAAAAAATATTTTTAGGGAAAAGT
* *
9743144 TGAAAGTATCAATTTTTCTTAAAAGTAAATTTTCAAAAAAAGGATTTTTAAGGAAAAGTTGAAAG
1 TGAAAGTATCAATTTTCCTTAAAAATAAA-TTTCAAAAAAAGGATTTTTAAGGAAAAGTTGAAAG
9743209 TATCAATTTTCCTTGAAAATCGAAATTTTCAAAAAAAATATTTTTAGGGAAAAGT
65 TATCAATTTTCCTTGAAAAT--AAATTTTC-AAAAAAATATTTTTAGGGAAAAGT
* * * * *
9743264 TAAAAATATCAATTCTCCTTAAAAATAAATTTCCAAAAAATA-TATTTTTAGGGAAAAGTTGAAA
1 TGAAAGTATCAATTTTCCTTAAAAATAAATTT-CAAAAAA-AGGATTTTTAAGGAAAAGTTGAAA
* *
9743328 GTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGGATTTTTAGGGAAAAGT
64 GTATCAATTTTCCTTGAAAATAAATTTTCAAAAAAA-TATTTTTAGGGAAAAGT
** **
9743382 TGAAAGTATCAATTTTCCTTAAAAATAAATTTCAAAAAAATAATTTTTGGGGAAAAGTTGAAAGT
1 TGAAAGTATCAATTTTCCTTAAAAATAAATTTCAAAAAAAGGATTTTTAAGGAAAAGTTGAAAGT
9743447 ATCAATTTT
66 ATCAATTTT
9743456 TCCTACACAA
Statistics
Matches: 281, Mismatches: 20, Indels: 23
0.87 0.06 0.07
Matches are distributed among these distances:
116 6 0.02
117 46 0.16
118 83 0.30
119 11 0.04
120 93 0.33
121 42 0.15
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.34
Consensus pattern (116 bp):
TGAAAGTATCAATTTTCCTTAAAAATAAATTTCAAAAAAAGGATTTTTAAGGAAAAGTTGAAAGT
ATCAATTTTCCTTGAAAATAAATTTTCAAAAAAATATTTTTAGGGAAAAGT
Found at i:9743354 original size:179 final size:175
Alignment explanation
Indices: 9743026--9743453 Score: 621
Period size: 179 Copynumber: 2.4 Consensus size: 175
9743016 CTGATTTCTC
*** *
9743026 TGAAAGTATCAATTTTCCTTAAAAATAAATTTCAAAAAGGGT-TTTTGA-GGAAAAGTTGAAAGT
1 TGAAAGTATCAATTTTCCTTAAAAATAAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGT
*
9743089 ATCAATTTTCCTTAAAAGAAAAATAAATTTCCAAAAAATATTTTTAGGAAAAAGTTGAAAGTATC
66 ATCAATTCTCCTT---A-AAAAATAAATTTCCAAAAAATATTTTTAGGAAAAAGTTGAAAGTATC
* *
9743154 AATTTTTCTTAAAAGTAAATTTTCAAAAAAAGGATTTTTAAGGAAAAGT
127 AATTTTCCTTAAAAATAAATTTTCAAAAAAAGGATTTTTAAGGAAAAGT
* *
9743203 TGAAAGTATCAATTTTCCTTGAAAATCGAAATTTTCAAAAAAAATATTTTTAGGGAAAAGTTAAA
1 TGAAAGTATCAATTTTCCTTAAAAAT--AAA-TTTCAAAAAAAATATTTTTAGGGAAAAGTTGAA
* *
9743268 AATATCAATTCTCCTT-AAAAATAAATTTCCAAAAAATATATTTTTAGGGAAAAGTTGAAAGTAT
63 AGTATCAATTCTCCTTAAAAAATAAATTTCC-AAAAA-ATATTTTTAGGAAAAAGTTGAAAGTAT
*
9743332 CAATTTTCCTTAAAAATAAATTTTCAAAAAAAGGATTTTTAGGGAAAAGT
126 CAATTTTCCTTAAAAATAAATTTTCAAAAAAAGGATTTTTAAGGAAAAGT
*
9743382 TGAAAGTATCAATTTTCCTTAAAAATAAATTTC-AAAAAAATAATTTTTGGGGAAAAGTTGAAAG
1 TGAAAGTATCAATTTTCCTTAAAAATAAATTTCAAAAAAAAT-ATTTTTAGGGAAAAGTTGAAAG
9743446 TATCAATT
65 TATCAATT
9743454 TTTCCTACAC
Statistics
Matches: 227, Mismatches: 16, Indels: 17
0.87 0.06 0.07
Matches are distributed among these distances:
175 8 0.04
176 31 0.14
177 42 0.19
178 5 0.02
179 101 0.44
180 10 0.04
181 5 0.02
182 25 0.11
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.34
Consensus pattern (175 bp):
TGAAAGTATCAATTTTCCTTAAAAATAAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGT
ATCAATTCTCCTTAAAAAATAAATTTCCAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATT
TTCCTTAAAAATAAATTTTCAAAAAAAGGATTTTTAAGGAAAAGT
Found at i:9746914 original size:98 final size:98
Alignment explanation
Indices: 9746745--9746930 Score: 336
Period size: 98 Copynumber: 1.9 Consensus size: 98
9746735 TAATAAATAC
* *
9746745 ATAAATTATTTCTTAATTAAATACAAAAATCATAGTCATTAAATGGCCAATGCTTTCAAAGCATA
1 ATAAATTATTTCTTAATTAAATAAAAAAATCATAGTCATTAAATAGCCAATGCTTTCAAAGCATA
9746810 TTTCTTATTTATAGTATACGTGTTTGATGTTTA
66 TTTCTTATTTATAGTATACGTGTTTGATGTTTA
* *
9746843 ATAAATTATTTCTTAATTAAATAAAAAAATCATGGTCATTAAATAGTCAATGCTTTCAAAGCATA
1 ATAAATTATTTCTTAATTAAATAAAAAAATCATAGTCATTAAATAGCCAATGCTTTCAAAGCATA
9746908 TTTCTTATTTATAGTATACGTGT
66 TTTCTTATTTATAGTATACGTGT
9746931 CGATATTTAA
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 84 1.00
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (98 bp):
ATAAATTATTTCTTAATTAAATAAAAAAATCATAGTCATTAAATAGCCAATGCTTTCAAAGCATA
TTTCTTATTTATAGTATACGTGTTTGATGTTTA
Found at i:9748886 original size:12 final size:13
Alignment explanation
Indices: 9748861--9748925 Score: 63
Period size: 12 Copynumber: 5.4 Consensus size: 13
9748851 TATGTATAAA
9748861 AATTATT-T-TTT
1 AATTATTATATTT
9748872 AATTATT-TATTT
1 AATTATTATATTT
9748884 AATT-TTATATTT
1 AATTATTATATTT
9748896 --TTATATATATTT
1 AATTAT-TATATTT
9748908 AATT-TTATATTT
1 AATTATTATATTT
9748920 ATATTA
1 A-ATTA
9748926 AAAAATATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
10 2 0.04
11 11 0.24
12 27 0.59
13 4 0.09
14 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
AATTATTATATTT
Found at i:9748922 original size:18 final size:17
Alignment explanation
Indices: 9748869--9748924 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 17
9748859 AAAATTATTT
9748869 TTTAATTATTTATTTA-A
1 TTTAATT-TTTATTTATA
*
9748886 TTTTATATTTTTATATATA
1 -TTTA-ATTTTTATTTATA
9748905 TTTAATTTTATATTTATA
1 TTTAATTTT-TATTTATA
9748923 TT
1 TT
9748925 AAAAAATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 5 0.15
18 24 0.73
19 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTAATTTTTATTTATA
Found at i:9748941 original size:19 final size:19
Alignment explanation
Indices: 9748913--9748960 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
9748903 TATTTAATTT
9748913 TATA-TTTATATTAAAAAA
1 TATATTTTATATTAAAAAA
*
9748931 TATATTTTATATTTAAAAA
1 TATATTTTATATTAAAAAA
9748950 TAGTATTTTAT
1 TA-TATTTTAT
9748961 TAATTTTGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 4 0.15
19 15 0.56
20 8 0.30
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TATATTTTATATTAAAAAA
Found at i:9750214 original size:17 final size:17
Alignment explanation
Indices: 9750192--9750227 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
9750182 TATGTTTTTT
* *
9750192 AAAGGGAAACAAATGAA
1 AAAGGGAAAAAAAGGAA
9750209 AAAGGGAAAAAAAGGAA
1 AAAGGGAAAAAAAGGAA
9750226 AA
1 AA
9750228 CTGAAAGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.03, G:0.25, T:0.03
Consensus pattern (17 bp):
AAAGGGAAAAAAAGGAA
Found at i:9753455 original size:23 final size:23
Alignment explanation
Indices: 9753413--9753468 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
9753403 TTGATATTTT
9753413 TATTAAAATTT-A--ATTTTTAA
1 TATTAAAATTTAATGATTTTTAA
9753433 TACTT-AAATTTAATGATTTTTAA
1 TA-TTAAAATTTAATGATTTTTAA
9753456 TATTAAAATTTAA
1 TATTAAAATTTAA
9753469 AAAATCATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
20 8 0.26
21 3 0.10
22 2 0.06
23 18 0.58
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TATTAAAATTTAATGATTTTTAA
Found at i:9754574 original size:25 final size:25
Alignment explanation
Indices: 9754543--9754593 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
9754533 TATCAATTTA
9754543 TTTTAT-TTTAT-TTTCTTTTTCTT
1 TTTTATATTTATATTTCTTTTTCTT
9754566 TTTTATATTTATATTTCTTTTTCTT
1 TTTTATATTTATATTTCTTTTTCTT
9754591 TTT
1 TTT
9754594 CATTTATCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 6 0.23
24 5 0.19
25 15 0.58
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (25 bp):
TTTTATATTTATATTTCTTTTTCTT
Found at i:9754713 original size:16 final size:17
Alignment explanation
Indices: 9754677--9754714 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
9754667 CATATTTTTT
*
9754677 AATAAATTTTTAAATAA
1 AATAAATTTGTAAATAA
9754694 AATAAATTTGTAAA-AA
1 AATAAATTTGTAAATAA
9754710 AATAA
1 AATAA
9754715 TATTAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AATAAATTTGTAAATAA
Found at i:9754976 original size:20 final size:21
Alignment explanation
Indices: 9754950--9754990 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
9754940 ATCTCAAAAA
9754950 ATATATTCA-TTATTCTTTTTCT
1 ATAT-TTCATTTATT-TTTTTCT
9754972 ATATTTCATTTATTTTTTT
1 ATATTTCATTTATTTTTTT
9754991 TTAATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.68
Consensus pattern (21 bp):
ATATTTCATTTATTTTTTTCT
Found at i:9754979 original size:21 final size:23
Alignment explanation
Indices: 9754950--9754991 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
9754940 ATCTCAAAAA
9754950 ATATATTCA-TTATTCTTTTTCT
1 ATATATTCATTTATTCTTTTTCT
*
9754972 ATAT-TTCATTTATTTTTTTT
1 ATATATTCATTTATTCTTTTT
9754992 TAATAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (23 bp):
ATATATTCATTTATTCTTTTTCT
Found at i:9758086 original size:199 final size:199
Alignment explanation
Indices: 9757733--9758125 Score: 519
Period size: 199 Copynumber: 2.0 Consensus size: 199
9757723 TAACTCTCAT
* * * *
9757733 TATAATTTTAAATACCAGTCTTGTAATCATCTTGACGAAGAAAGAAGTATACTCAAATTTTAAAA
1 TATAATTTTAAATACCAATCGTGTAATCATCTTGACGAAGAAAGAAGCATACTCAAAATTTAAAA
* * *
9757798 TTTAATTTAATTGATTTATATAATTATTTTTAAAAAATTATATTCAATAAATTTAAAATTTAAAT
66 TTTAATTTAATTGATTTATATAATTATTTTTAAAAAATAACATTCAATAAATATAAAATTTAAAT
* * *
9757863 TTAAATACTTATAATCTTTTTTATTATTTTCAAATTACAACTTATTTTGTAAAAA-ATATAAAAT
131 TTAAATACCTACAATCTTTTTTATTATTTTCAAATTACAACCTATTTTGTAAAAATATATAAAAT
9757927 TATA
196 TATA
* * * *
9757931 TATAATTTTAAATTCCAATCGTGTAATCATCTTTAGCGGTA-AAAGAAGCATATTCATAAAATTT
1 TATAATTTTAAATACCAATCGTGTAATCATCTTGA-C-GAAGAAAGAAGCATACTC--AAAATTT
* * *
9757995 AAAATTTAATTTAATTGATTTTTATAA-TATTTTT-AAAAATAACATTTAATAAATATATAATTT
62 AAAATTTAATTTAATTGATTTATATAATTATTTTTAAAAAATAACATTCAATAAATATAAAATTT
* *
9758058 AAAATTT-AATACCTACAAT-TTCTTTTATTATTTTCAAGTTACAACCTATTTTGTAAAAATATG
127 -AAATTTAAATACCTACAATCTT-TTTTATTATTTTCAAATTACAACCTATTTTGTAAAAATATA
9758121 TAAAA
190 TAAAA
9758126 AAAAAAAAAA
Statistics
Matches: 169, Mismatches: 19, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
198 33 0.20
199 82 0.49
200 22 0.13
201 32 0.19
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (199 bp):
TATAATTTTAAATACCAATCGTGTAATCATCTTGACGAAGAAAGAAGCATACTCAAAATTTAAAA
TTTAATTTAATTGATTTATATAATTATTTTTAAAAAATAACATTCAATAAATATAAAATTTAAAT
TTAAATACCTACAATCTTTTTTATTATTTTCAAATTACAACCTATTTTGTAAAAATATATAAAAT
TATA
Found at i:9758447 original size:14 final size:14
Alignment explanation
Indices: 9758428--9758485 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 14
9758418 CCTTCTTTCA
*
9758428 TTTTATTTTTATTT
1 TTTTATATTTATTT
**
9758442 TTTTATATTTA-AC
1 TTTTATATTTATTT
*
9758455 TTTTATATTTAGTT
1 TTTTATATTTATTT
9758469 TTTTA-ACTTTATTT
1 TTTTATA-TTTATTT
9758483 TTT
1 TTT
9758486 ATTAGATGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
13 12 0.33
14 24 0.67
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTTATATTTATTT
Found at i:9758458 original size:21 final size:19
Alignment explanation
Indices: 9758434--9758485 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
9758424 TTCATTTTAT
9758434 TTTTATTTTTTTATATTTAAC
1 TTTTATTTTTTT-T-TTTAAC
*
9758455 TTTTATATTTAGTTTTTTAAC
1 TTTTAT-TTT-TTTTTTTAAC
9758476 -TTTATTTTTT
1 TTTTATTTTTT
9758486 ATTAGATGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
18 1 0.04
19 3 0.11
20 5 0.19
21 12 0.44
22 4 0.15
23 2 0.07
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTATTTTTTTTTTTAAC
Found at i:9758724 original size:18 final size:18
Alignment explanation
Indices: 9758689--9758722 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9758679 CCTCATTCTT
*
9758689 TTTGTTTTTATCATTTTA
1 TTTGTTTTTATAATTTTA
9758707 TTTGTTTTT-TAATTTT
1 TTTGTTTTTATAATTTT
9758723 TACATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (18 bp):
TTTGTTTTTATAATTTTA
Found at i:9758743 original size:25 final size:26
Alignment explanation
Indices: 9758693--9758740 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
9758683 ATTCTTTTTG
9758693 TTTTTATCATTTTATTTGTTTTTTAA
1 TTTTTATCATTTTATTTGTTTTTTAA
*
9758719 TTTTTA-CATTTT-TTTCTTTTTT
1 TTTTTATCATTTTATTTGTTTTTT
9758741 TAAAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
25 6 0.29
26 6 0.29
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (26 bp):
TTTTTATCATTTTATTTGTTTTTTAA
Found at i:9761746 original size:59 final size:58
Alignment explanation
Indices: 9761683--9761977 Score: 355
Period size: 59 Copynumber: 4.8 Consensus size: 58
9761673 AAAAATAAAA
9761683 AAATTCTAAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT-AGAAAT-
1 AAATT-TAAAAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGA-AAATC
*
9761742 AAATTTCCAAAAAAATATTTTT-GGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAAT-
1 AAATTT-AAAAAAAATATTTTTAGG-GAAAAGTTGAAAGTATCAATTTTCCTT----G-AAAATC
*
9761805 AAATTTCCAAAAAAAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC
1 AAATTT----AAAAAAAA-TATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC
*
9761868 AAATTTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC
1 AAA-TTT-AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC
**
9761928 GAAATTTCCAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
1 -AAATTTAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
9761978 CTAAAAAAAA
Statistics
Matches: 213, Mismatches: 7, Indels: 32
0.85 0.03 0.13
Matches are distributed among these distances:
57 2 0.01
58 36 0.17
59 51 0.24
60 47 0.22
61 11 0.05
62 5 0.02
63 14 0.07
64 4 0.02
66 7 0.03
67 34 0.16
68 2 0.01
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (58 bp):
AAATTTAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC
Found at i:9761890 original size:60 final size:58
Alignment explanation
Indices: 9761690--9761977 Score: 382
Period size: 60 Copynumber: 4.7 Consensus size: 58
9761680 AAAAAATTCT
*
9761690 AAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT-AGAAATAAATTTC
1 AAAAAAA-ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGA-AAATAAATTTC
* *
9761749 CAAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCC
1 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT----G-AAAATAAATTT-C
9761813 AAAAAAAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAATTTTC
1 --AAAAAAAA-TATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAA-TTTC
9761876 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCGAAATTTC
1 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT--AAATTTC
* *
9761936 -CAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
9761978 CTAAAAAAAA
Statistics
Matches: 208, Mismatches: 8, Indels: 26
0.86 0.03 0.11
Matches are distributed among these distances:
58 36 0.17
59 46 0.22
60 47 0.23
61 11 0.05
62 5 0.02
63 15 0.07
64 5 0.02
66 7 0.03
67 36 0.17
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.33
Consensus pattern (58 bp):
AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTC
Found at i:9765888 original size:23 final size:24
Alignment explanation
Indices: 9765847--9765902 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
9765837 ACACTAGATG
*
9765847 AAAAATGAGAAAAAAAAAAGA-GA
1 AAAAATGAGAAAAAAAAAAAATGA
**
9765870 AAAAATGAGAAAATGAAAAAATGA
1 AAAAATGAGAAAAAAAAAAAATGA
9765894 AAAAA-GAGA
1 AAAAATGAGA
9765903 TCCAAATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 22 0.76
24 7 0.24
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (24 bp):
AAAAATGAGAAAAAAAAAAAATGA
Found at i:9765889 original size:16 final size:15
Alignment explanation
Indices: 9765844--9765897 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
9765834 TCAACACTAG
9765844 ATGAAAAATGAGAAAA
1 ATGAAAAATGA-AAAA
*
9765860 A--AAAAAGAGAAAAA
1 ATGAAAAA-TGAAAAA
9765874 ATGAGAAAATGAAAAA
1 ATGA-AAAATGAAAAA
9765890 ATGAAAAA
1 ATGAAAAA
9765898 AGAGATCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 10 0.31
15 6 0.19
16 12 0.38
17 4 0.12
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (15 bp):
ATGAAAAATGAAAAA
Found at i:9767176 original size:41 final size:40
Alignment explanation
Indices: 9767131--9767828 Score: 897
Period size: 41 Copynumber: 16.9 Consensus size: 40
9767121 GTCTAGGAGT
9767131 ATTTACTTTTTCAAAGTTCGT-TGCCTCTGTTTAGAGGAGCA
1 ATTTA-TTTTTCAAAG-TCGTGTGCCTCTGTTTAGAGGAGCA
9767172 ATTTATTTTTCAAAGTTTCGT-TGCCTCTGTTTAGAGGAGCA
1 ATTTATTTTTCAAAG--TCGTGTGCCTCTGTTTAGAGGAGCA
9767213 ATTTATTTTTCAAAGTTTCGT-TGCCTCTGTTTAGAGGAGCA
1 ATTTATTTTTCAAAG--TCGTGTGCCTCTGTTTAGAGGAGCA
* *
9767254 ATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
1 ATTTATTTTT-CAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
* *
9767296 ATTTACTTTCCAAAGTCGTGTTGCCTCTGTTTAGAGGAGCA
1 ATTTATTTTTCAAAGTCGTG-TGCCTCTGTTTAGAGGAGCA
* *
9767337 ATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
1 ATTTATTTTT-CAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
*
9767379 ATTTA-CTTTCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTATTTTTC-AAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
9767420 ATTTACTTTTTCAAAGTTCGT-TGCCTCTGTTTAGAGGAGCA
1 ATTTA-TTTTTCAAAG-TCGTGTGCCTCTGTTTAGAGGAGCA
*
9767461 ATTTACTTTTCCAAAGTCGTGTTGCCTCTGTTTAGAGGAGCA
1 ATTTA-TTTTTCAAAGTCGTG-TGCCTCTGTTTAGAGGAGCA
9767503 ATTTATTTTTCAAAGTTCGT-TGCCTCTGTTTAGAGGAGCA
1 ATTTATTTTTCAAAG-TCGTGTGCCTCTGTTTAGAGGAGCA
*
9767543 ATTTATTTTTCAAAGTTCCGT-TGCCTTTGTTTAGAGGAGCA
1 ATTTATTTTTCAAAG-T-CGTGTGCCTCTGTTTAGAGGAGCA
* * *
9767584 ATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAAAGGAGCA
1 ATTTATTTTT-CAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
* * * *
9767626 ATTTACTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
1 ATTTATTTTTCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
* *
9767667 ATTTATTTTTCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
1 ATTTATTTTTCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
* *
9767708 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTATTTTTCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
* *
9767749 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCA
1 ATTTATTTTTCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
9767790 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGA
1 ATTTATTTTT-CAAAGTCGT-GTGCCTCTGTTTAGAGGA
9767829 ACTTCGACAA
Statistics
Matches: 604, Mismatches: 34, Indels: 37
0.89 0.05 0.05
Matches are distributed among these distances:
40 60 0.10
41 383 0.63
42 152 0.25
43 9 0.01
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (40 bp):
ATTTATTTTTCAAAGTCGTGTGCCTCTGTTTAGAGGAGCA
Found at i:9767295 original size:124 final size:121
Alignment explanation
Indices: 9767131--9767828 Score: 910
Period size: 124 Copynumber: 5.6 Consensus size: 121
9767121 GTCTAGGAGT
* *
9767131 ATTTACTTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTTTCGTT
1 ATTTA-TTTTCCAAAG-TCGTGGTGCCTCTGTTGAGAGGAGCAATTTATTTTTCAAAG-TTCGTT
9767194 GCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTTTCGT-TGCCTCTGTTTAGAGGAGCA
63 GCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAG--TCGTGTGCCTCTGTTTAGAGGAGCA
* * *
9767254 ATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTTACTTTCCAAAG-TCGTGTT
1 ATTTA-TTTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTATTTTTCAAAGTTC--GTT
* *
9767318 GCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
63 GCCTCTGTTTAGAGGAGCAATTTATTTTT-CAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
* * *
9767379 ATTTACTTTCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTTCAAAGTTCGTTGC
1 ATTTATTTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTA-TTTTTCAAAGTTCGTTGC
*
9767444 CTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGTTGCCTCTGTTTAGAGGAGCA
65 CTCTGTTTAGAGGAGCAATTTA-TTTTTCAAAGTCGTG-TGCCTCTGTTTAGAGGAGCA
* *
9767503 ATTTATTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTTCCGTTG
1 ATTTATTTTCCAAAG-TCGTGGTGCCTCTGTTGAGAGGAGCAATTTATTTTTCAAAGTT-CGTTG
* * * *
9767566 CCTTTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAAAGGAGCA
64 CCTCTGTTTAGAGGAGCAATTTATTTTT-CAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
* * *
9767626 ATTTACTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTTATTTTTCAAAG-TCGTGGTA
1 ATTTATTTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTATTTTTCAAAGTTCGT--TG
* * *
9767690 CCTCTGTTGAGAGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
64 CCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
9767749 ATTTACTTTT-CAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTATTTTTCCAAAG-TCGTGG
1 ATTTA-TTTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTATTTTT-CAAAGTTCGT--
9767812 TGCCTCTGTTTAGAGGA
62 TGCCTCTGTTTAGAGGA
9767829 ACTTCGACAA
Statistics
Matches: 513, Mismatches: 41, Indels: 41
0.86 0.07 0.07
Matches are distributed among these distances:
122 29 0.06
123 184 0.36
124 254 0.50
125 44 0.09
126 2 0.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (121 bp):
ATTTATTTTCCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAATTTATTTTTCAAAGTTCGTTGCC
TCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGTGCCTCTGTTTAGAGGAGCA
Found at i:9767319 original size:83 final size:82
Alignment explanation
Indices: 9767150--9767828 Score: 978
Period size: 83 Copynumber: 8.2 Consensus size: 82
9767140 TTCAAAGTTC
* *
9767150 GTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTTTCGT--TGCCTCTGTTTAGAGGAGCA
1 GTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAG--TCGTGGTACCTCTGTTGAGAGGAGCA
* * *
9767213 ATTTATTTTTCAAAGT-TT
64 ATTTACTTTCCAAAGTCGT
9767231 CGTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
1 -GTTGCCTCTGTTTAGAGGAGCAATTTATTTTT-CAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
9767296 ATTTACTTTCCAAAGTCGT
64 ATTTACTTTCCAAAGTCGT
9767315 GTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAA
1 GTTGCCTCTGTTTAGAGGAGCAATTTATTTTT-CAAAGTCGTGGTACCTCTGTTGAGAGGAGCAA
*
9767380 TTTACTTTCAAAAGTCGT
65 TTTACTTTCCAAAGTCGT
* * *
9767398 GGTGCCTCTGTTTAGAGGAGCAATTTACTTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
1 GTTGCCTCTGTTTAGAGGAGCAATTTA-TTTTTCAAAG-TCGTGGTACCTCTGTTGAGAGGAGCA
9767461 ATTTACTTTTCCAAAGTCGT
64 ATTTAC-TTTCCAAAGTCGT
* *
9767481 GTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAA
1 GTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAG-TCGTGGTACCTCTGTTGAGAGGAGCAA
* * *
9767544 TTTATTTTTCAAAGTTC-C
65 TTTACTTTCCAAAG-TCGT
* *
9767562 GTTGCCTTTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAAAGGAGCAA
1 GTTGCCTCTGTTTAGAGGAGCAATTTATTTTT-CAAAGTCGTGGTACCTCTGTTGAGAGGAGCAA
9767627 TTTACTTTCCAAAGTCGT
65 TTTACTTTCCAAAGTCGT
* * *
9767645 GGTACCTCTGTTGAGAGGAGCAATTTATTTTTCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAAT
1 GTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAAT
9767710 TTACTTTCCAAAGTCGT
66 TTACTTTCCAAAGTCGT
* * *
9767727 GGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTGCCTCTGTTGAGAGGAGCAAT
1 GTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAAT
*
9767792 TTATTTTTCCAAAGTCGT
66 TTA-CTTTCCAAAGTCGT
*
9767810 GGTGCCTCTGTTTAGAGGA
1 GTTGCCTCTGTTTAGAGGA
9767829 ACTTCGACAA
Statistics
Matches: 553, Mismatches: 31, Indels: 25
0.91 0.05 0.04
Matches are distributed among these distances:
81 47 0.08
82 218 0.39
83 278 0.50
84 10 0.02
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.38
Consensus pattern (82 bp):
GTTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAAT
TTACTTTCCAAAGTCGT
Found at i:9767855 original size:7 final size:7
Alignment explanation
Indices: 9767837--9767909 Score: 105
Period size: 7 Copynumber: 10.6 Consensus size: 7
9767827 GAACTTCGAC
9767837 AAAAACA
1 AAAAACA
9767844 AAAAA-A
1 AAAAACA
*
9767850 ACAAA-A
1 AAAAACA
9767856 AAAAACAA
1 AAAAAC-A
9767864 AAAAACA
1 AAAAACA
9767871 AAAAACA
1 AAAAACA
*
9767878 AAAAATA
1 AAAAACA
9767885 AAAAACA
1 AAAAACA
9767892 AAAAACA
1 AAAAACA
9767899 AAAAACA
1 AAAAACA
9767906 AAAA
1 AAAA
9767910 TTTTAAAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
6 10 0.17
7 43 0.72
8 7 0.12
ACGTcount: A:0.88, C:0.11, G:0.00, T:0.01
Consensus pattern (7 bp):
AAAAACA
Found at i:9767887 original size:28 final size:27
Alignment explanation
Indices: 9767837--9767937 Score: 114
Period size: 28 Copynumber: 3.7 Consensus size: 27
9767827 GAACTTCGAC
* *
9767837 AAAAACAAAAAA-AACAAAAAAAAACAA
1 AAAAACAAAAAACAA-AAAATAAAAAAA
9767864 AAAAACAAAAAACAAAAAATAAAAAACA
1 AAAAACAAAAAACAAAAAATAAAAAA-A
* *
9767892 AAAAACAAAAAACAAAAATTTTAAAAAA
1 AAAAACAAAAAACAAAAA-ATAAAAAAA
* *
9767920 AAAATCAAAAAATAAAAA
1 AAAAACAAAAAACAAAAA
9767938 TGTTGAGTTG
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
27 21 0.32
28 38 0.58
29 6 0.09
ACGTcount: A:0.84, C:0.09, G:0.00, T:0.07
Consensus pattern (27 bp):
AAAAACAAAAAACAAAAAATAAAAAAA
Found at i:9767923 original size:1 final size:1
Alignment explanation
Indices: 9767837--9767909 Score: 65
Period size: 1 Copynumber: 73.0 Consensus size: 1
9767827 GAACTTCGAC
* * * * * * * *
9767837 AAAAACAAAAAAAACAAAAAAAAACAAAAAAACAAAAAACAAAAAATAAAAAACAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
9767902 AACAAAAA
1 AAAAAAAA
9767910 TTTTAAAAAA
Statistics
Matches: 54, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.88, C:0.11, G:0.00, T:0.01
Consensus pattern (1 bp):
A
Found at i:9767938 original size:14 final size:14
Alignment explanation
Indices: 9767835--9767938 Score: 85
Period size: 14 Copynumber: 7.6 Consensus size: 14
9767825 AGGAACTTCG
9767835 ACAAAAA-CAAAAA
1 ACAAAAATCAAAAA
9767848 A-AACAAA--AAAAA
1 ACAA-AAATCAAAAA
*
9767860 ACAAAAAAACAAAAA
1 AC-AAAAATCAAAAA
9767875 ACAAAAAAT-AAAAA
1 AC-AAAAATCAAAAA
*
9767889 ACAAAAAACAAAAA
1 ACAAAAATCAAAAA
**
9767903 ACAAAAATTTTAAAA
1 ACAAAAA-TCAAAAA
9767918 A-AAAAATCAAAAA
1 ACAAAAATCAAAAA
*
9767931 ATAAAAAT
1 ACAAAAAT
9767939 GTTGAGTTGA
Statistics
Matches: 76, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
12 8 0.11
13 18 0.24
14 32 0.42
15 18 0.24
ACGTcount: A:0.83, C:0.10, G:0.00, T:0.08
Consensus pattern (14 bp):
ACAAAAATCAAAAA
Found at i:9768763 original size:31 final size:32
Alignment explanation
Indices: 9768728--9768797 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
9768718 ATTTCCAGAA
** *
9768728 TCCGGCGAA-AATTCCGGCGAATTTTGAATTT
1 TCCGGCGAACAATTCCGGCGAACATTGAAGTT
*
9768759 TCCGGC-AACAATTCCGGCTAACATTGAAGTT
1 TCCGGCGAACAATTCCGGCGAACATTGAAGTT
9768790 TCCGGCGA
1 TCCGGCGA
9768798 CCAGTCCAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 2 0.06
31 30 0.91
32 1 0.03
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (32 bp):
TCCGGCGAACAATTCCGGCGAACATTGAAGTT
Found at i:9768878 original size:19 final size:19
Alignment explanation
Indices: 9768850--9768899 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 19
9768840 TCCGGCCAAC
*
9768850 TTCCGACGAAATTTCCAGA
1 TTCCGGCGAAATTTCCAGA
9768869 TTCCGGCGAAAATTTCCAGA
1 TTCCGGCG-AAATTTCCAGA
*
9768889 ATCCGGCGAAA
1 TTCCGGCGAAA
9768900 ATTTTTAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (19 bp):
TTCCGGCGAAATTTCCAGA
Found at i:9768883 original size:20 final size:20
Alignment explanation
Indices: 9768858--9768915 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
9768848 ACTTCCGACG
*
9768858 AAATTTCCAGATTCCGGCGA
1 AAATTTCCAGAATCCGGCGA
9768878 AAATTTCCAGAATCCGGCGA
1 AAATTTCCAGAATCCGGCGA
**
9768898 AAATTTTTAGAATCCGGC
1 AAATTTCCAGAATCCGGC
9768916 ACCGGTGTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (20 bp):
AAATTTCCAGAATCCGGCGA
Found at i:9769558 original size:60 final size:59
Alignment explanation
Indices: 9769354--9769639 Score: 402
Period size: 60 Copynumber: 4.7 Consensus size: 59
9769344 AAAAAATTCT
9769354 AAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT-AGAAATAAATTTTC
1 AAAAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGA-AAATAAATTTTC
*
9769414 -AAAAAAATATTTTT-GGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCC
1 AAAAAAAATATTTTTAGG-GAAAAGTTGAAAGTATCAATTTTCCTT----G-AAAATAAATTTTC
9769477 AAAATAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAATTTTC
1 AAAA-AAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAATTTTC
*
9769538 AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCGAAA-TTTC
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT--AAATTTTC
*
9769598 -CAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
9769640 CTAAAAAAAA
Statistics
Matches: 208, Mismatches: 6, Indels: 25
0.87 0.03 0.10
Matches are distributed among these distances:
57 2 0.01
58 35 0.17
59 46 0.22
60 55 0.26
61 15 0.07
63 11 0.05
64 4 0.02
65 38 0.18
66 2 0.01
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (59 bp):
AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTC
Found at i:9772001 original size:3 final size:3
Alignment explanation
Indices: 9771993--9772039 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
9771983 GCGTAAAGTC
9771993 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9772040 TCATAATATA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:9777272 original size:98 final size:98
Alignment explanation
Indices: 9777146--9777329 Score: 323
Period size: 98 Copynumber: 1.9 Consensus size: 98
9777136 TAATAAATAC
* **
9777146 ATAAATTATTTCTTAATTAAATACAAAAATCATAGTCATTAAATGGTCAATGCTTTCAAAGCATA
1 ATAAATTATTTCTTAATTAAATAAAAAAATCATAGTCATTAAATAATCAATGCTTTCAAAGCATA
9777211 TTTCTTATTTATAATATATGTATTTGATGTTTA
66 TTTCTTATTTATAATATATGTATTTGATGTTTA
*
9777244 ATAAATTATTTCTTAATTAAATAAAAAAATCATGGTCATTAAATAATCAATGCTTTCAAAGCATA
1 ATAAATTATTTCTTAATTAAATAAAAAAATCATAGTCATTAAATAATCAATGCTTTCAAAGCATA
*
9777309 TTTCTTATTTATAGTATATGT
66 TTTCTTATTTATAATATATGT
9777330 GTTGATATTT
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 81 1.00
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (98 bp):
ATAAATTATTTCTTAATTAAATAAAAAAATCATAGTCATTAAATAATCAATGCTTTCAAAGCATA
TTTCTTATTTATAATATATGTATTTGATGTTTA
Found at i:9779294 original size:12 final size:13
Alignment explanation
Indices: 9779269--9779333 Score: 63
Period size: 12 Copynumber: 5.4 Consensus size: 13
9779259 TATAATATAA
9779269 AATTATT-T-TTT
1 AATTATTATATTT
9779280 AATTATT-TATTT
1 AATTATTATATTT
9779292 AATT-TTATATTT
1 AATTATTATATTT
9779304 --TTATATATATTT
1 AATTAT-TATATTT
9779316 AATT-TTATATTT
1 AATTATTATATTT
9779328 ATATTA
1 A-ATTA
9779334 AAAAATTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
10 2 0.04
11 11 0.24
12 27 0.59
13 4 0.09
14 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
AATTATTATATTT
Found at i:9779330 original size:18 final size:17
Alignment explanation
Indices: 9779277--9779332 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 17
9779267 AAAATTATTT
9779277 TTTAATTATTTATTTA-A
1 TTTAATT-TTTATTTATA
*
9779294 TTTTATATTTTTATATATA
1 -TTTA-ATTTTTATTTATA
9779313 TTTAATTTTATATTTATA
1 TTTAATTTT-TATTTATA
9779331 TT
1 TT
9779333 AAAAAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 5 0.15
18 24 0.73
19 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTAATTTTTATTTATA
Found at i:9779345 original size:15 final size:16
Alignment explanation
Indices: 9779325--9779355 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9779315 TAATTTTATA
9779325 TTTATA-TTAAAAAAT
1 TTTATATTTAAAAAAT
9779340 TTTATATTTAAAAAAT
1 TTTATATTTAAAAAAT
9779356 AATATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTATATTTAAAAAAT
Found at i:9779362 original size:21 final size:21
Alignment explanation
Indices: 9779316--9779365 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
9779306 ATATATATTT
*
9779316 AATTTTATATTTATATTAAAA
1 AATTTTATATTTATATAAAAA
9779337 AATTTTATATTTA-A-AAAATA
1 AATTTTATATTTATATAAAA-A
9779357 ATATTTTAT
1 A-ATTTTAT
9779366 TAATTTTGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 3 0.12
20 3 0.12
21 20 0.77
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTTTATATTTATATAAAAA
Found at i:9781989 original size:42 final size:41
Alignment explanation
Indices: 9781942--9782027 Score: 102
Period size: 42 Copynumber: 2.1 Consensus size: 41
9781932 TAAATAATTA
9781942 TATTTGAACACAAATA-ATTATCATATGAAAAATGGTCATAAC
1 TATTTGAACACAAATAGATTATCAT-TGAAAAA-GGTCATAAC
* * * * *
9781984 TATTTGAATATAAATAGATTATTATTTATAAAGGTCATAAC
1 TATTTGAACACAAATAGATTATCATTGAAAAAGGTCATAAC
9782025 TAT
1 TAT
9782028 ATAAAAGGTC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
41 12 0.32
42 19 0.50
43 7 0.18
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.37
Consensus pattern (41 bp):
TATTTGAACACAAATAGATTATCATTGAAAAAGGTCATAAC
Found at i:9788161 original size:5 final size:5
Alignment explanation
Indices: 9788148--9788238 Score: 53
Period size: 5 Copynumber: 17.6 Consensus size: 5
9788138 TTATTTAAAG
* *
9788148 AAAAT AAAAC AAAAT AAAAGT GAAAAT AAAA- AAAAT AAAGA- AAAGT
1 AAAAT AAAAT AAAAT AAAA-T -AAAAT AAAAT AAAAT AAA-AT AAAAT
* * * *
9788194 AAAACA AAAAT AAAAAT AAGAT AAAGAT AAAA- AATAT TAAAT AAA
1 AAAA-T AAAAT -AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAA
9788239 TCTAATCTAA
Statistics
Matches: 65, Mismatches: 12, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
4 7 0.11
5 37 0.57
6 17 0.26
7 4 0.06
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:9788197 original size:31 final size:31
Alignment explanation
Indices: 9788143--9788225 Score: 80
Period size: 31 Copynumber: 2.6 Consensus size: 31
9788133 GATTTTTATT
* **
9788143 TAAAGAAAATAAA-ACAAAATAAAAGTGAAAA
1 TAAAAAAAATAAAGACAAAATAAAA-CAAAAA
*
9788174 TAAAAAAAATAAAGA-AAAGTAAAACAAAAA
1 TAAAAAAAATAAAGACAAAATAAAACAAAAA
*
9788204 TAAAAATAAGATAAAGATAAAA
1 TAAAAA-AA-ATAAAGACAAAA
9788226 AATATTAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
30 10 0.23
31 22 0.51
32 8 0.19
33 3 0.07
ACGTcount: A:0.76, C:0.02, G:0.08, T:0.13
Consensus pattern (31 bp):
TAAAAAAAATAAAGACAAAATAAAACAAAAA
Found at i:9788234 original size:27 final size:27
Alignment explanation
Indices: 9788148--9788225 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 27
9788138 TTATTTAAAG
* *
9788148 AAAATAAAACA-AAATAAAAGTGAAA-A
1 AAAATAAAA-ATAAAGAAAAGTAAAACA
*
9788174 TAAA-AAAAATAAAGAAAAGTAAAACA
1 AAAATAAAAATAAAGAAAAGTAAAACA
9788200 AAAATAAAAAT-AAGATAAAGATAAAA
1 AAAATAAAAATAAAGA-AAAG-TAAAA
9788226 AATATTAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
24 1 0.02
25 16 0.37
26 11 0.26
27 10 0.23
28 5 0.12
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.13
Consensus pattern (27 bp):
AAAATAAAAATAAAGAAAAGTAAAACA
Found at i:9788254 original size:4 final size:4
Alignment explanation
Indices: 9788247--9788293 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
9788237 AATCTAATCT
* * *
9788247 AATA AATA AA-A AATA AATA AATA AACAA AACA AATA AACA AATA AAT
1 AATA AATA AATA AATA AATA AATA AA-TA AATA AATA AATA AATA AAT
9788294 TAAAAAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
3 3 0.08
4 30 0.83
5 3 0.08
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (4 bp):
AATA
Found at i:9788283 original size:32 final size:32
Alignment explanation
Indices: 9788220--9788293 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 32
9788210 TAAGATAAAG
* * * *
9788220 ATAAAAAATATTAAATAAATCTAATCTAATAA
1 ATAAAAAATAATAAATAAATCAAAACAAATAA
9788252 ATAAAAAATAAATAAATAAA-CAAAACAAATAA
1 ATAAAAAAT-AATAAATAAATCAAAACAAATAA
*
9788284 ACAAATAAAT
1 ATAAA-AAAT
9788294 TAAAAAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
32 22 0.63
33 13 0.37
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (32 bp):
ATAAAAAATAATAAATAAATCAAAACAAATAA
Found at i:9788297 original size:13 final size:12
Alignment explanation
Indices: 9788250--9788293 Score: 54
Period size: 13 Copynumber: 3.7 Consensus size: 12
9788240 CTAATCTAAT
*
9788250 AAATAAA-AAAT
1 AAATAAATAAAC
9788261 AAATAAATAAAC
1 AAATAAATAAAC
*
9788273 AAAACAAATAAAC
1 -AAATAAATAAAC
9788286 AAATAAAT
1 AAATAAAT
9788294 TAAAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 7 0.25
12 10 0.36
13 11 0.39
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (12 bp):
AAATAAATAAAC
Found at i:9789206 original size:6 final size:6
Alignment explanation
Indices: 9789195--9789335 Score: 59
Period size: 6 Copynumber: 22.7 Consensus size: 6
9789185 AGATAAAAAA
9789195 AATAAT AATAAT -ATAAT AATAAT AA-ATAT AACTATAT AAATAA- AATACAT
1 AATAAT AATAAT AATAAT AATAAT AATA-AT AA-TA-AT -AATAAT AATA-AT
*
9789245 -ATAAAT ATTAA- AATAAAT AAATAAAT AAATAA- AGAT-AT ACAT-AT
1 AAT-AAT AATAAT AAT-AAT -AAT-AAT -AATAAT A-ATAAT A-ATAAT
*
9789289 ATTAAT ACATAAT AATAAT AATAAT AAATAAT AA-AAT ACATAA- AATA
1 AATAAT A-ATAAT AATAAT AATAAT -AATAAT AATAAT A-ATAAT AATA
9789336 CAAAAGAAGA
Statistics
Matches: 111, Mismatches: 5, Indels: 39
0.72 0.03 0.25
Matches are distributed among these distances:
5 22 0.20
6 52 0.47
7 18 0.16
8 17 0.15
9 2 0.02
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.30
Consensus pattern (6 bp):
AATAAT
Found at i:9789241 original size:23 final size:22
Alignment explanation
Indices: 9789187--9789335 Score: 82
Period size: 24 Copynumber: 6.8 Consensus size: 22
9789177 ATATTACAAG
*
9789187 ATAAAAAAAATAATAATA-ATATA
1 ATAAAATAAAT-ATAATATATA-A
9789210 ATAATAATAAATATAACTATATAA
1 ATAA-AATAAATATAA-TATATAA
*
9789234 ATAAAATACATATAA-ATAT--
1 ATAAAATAAATATAATATATAA
*
9789253 -TAAAATAAATA-AATAAATAA
1 ATAAAATAAATATAATATATAA
* *
9789273 ATAAAGATATACATATATTA-ATAC
1 ATAAA-ATA-A-ATATAATATATAA
*
9789297 ATAATAAT-AATAATAATAAAT-A
1 ATAA-AATAAAT-ATAATATATAA
* *
9789319 ATAAAATACATAAAATA
1 ATAAAATAAATATAATA
9789336 CAAAAGAAGA
Statistics
Matches: 101, Mismatches: 10, Indels: 32
0.71 0.07 0.22
Matches are distributed among these distances:
17 2 0.02
18 13 0.13
21 18 0.18
22 15 0.15
23 21 0.21
24 25 0.25
25 7 0.07
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (22 bp):
ATAAAATAAATATAATATATAA
Found at i:9789539 original size:1 final size:1
Alignment explanation
Indices: 9789528--9789582 Score: 56
Period size: 1 Copynumber: 55.0 Consensus size: 1
9789518 AACATTGTCA
* * * * * *
9789528 TTTTTTATTTTTTTTATGTTTTTTTTGTTTTTTTTATTTTTTTATTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
9789583 ACCAAAGCTC
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.07, C:0.00, G:0.04, T:0.89
Consensus pattern (1 bp):
T
Found at i:9789542 original size:9 final size:9
Alignment explanation
Indices: 9789528--9789579 Score: 70
Period size: 9 Copynumber: 5.7 Consensus size: 9
9789518 AACATTGTCA
9789528 TTTTTTATT
1 TTTTTTATT
9789537 TTTTTTATGTT
1 TTTTTTA--TT
*
9789548 TTTTTTGTT
1 TTTTTTATT
9789557 TTTTTTA-T
1 TTTTTTATT
9789565 TTTTTTATT
1 TTTTTTATT
9789574 TTTTTT
1 TTTTTT
9789580 TTTACCAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
8 8 0.21
9 22 0.58
11 8 0.21
ACGTcount: A:0.08, C:0.00, G:0.04, T:0.88
Consensus pattern (9 bp):
TTTTTTATT
Found at i:9789553 original size:20 final size:19
Alignment explanation
Indices: 9789528--9789583 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
9789518 AACATTGTCA
9789528 TTTTTTATTTTTTTTATGTT
1 TTTTTTATTTTTTTTAT-TT
*
9789548 TTTTTTGTTTTTTTTATTT
1 TTTTTTATTTTTTTTATTT
*
9789567 TTTTATTTTTTTTTTTA
1 TTTT-TTATTTTTTTTA
9789584 CCAAAGCTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.18
20 27 0.82
ACGTcount: A:0.09, C:0.00, G:0.04, T:0.88
Consensus pattern (19 bp):
TTTTTTATTTTTTTTATTT
Found at i:9789683 original size:41 final size:41
Alignment explanation
Indices: 9789589--9789884 Score: 387
Period size: 43 Copynumber: 7.0 Consensus size: 41
9789579 TTTTACCAAA
* * * * *
9789589 GCTCCTCTAAATAGAGGCTCAACGACTTTGAGAAACATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-TGAAA-GTAAATT
9789632 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAGTAAATT
*
9789673 GCTCCTCTAAACAGAGGCACCATGACTTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTT-GAAAGTAAATT
* * *
9789715 GCTCATCTAAATAGAGGCACCACAAC-TTTGAAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTTG--AAAGTAAATT
9789757 GCTCCTCTAAACAGAGGCACCACGACTTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTT-G-AAAGTAAATT
* *
9789800 GCTCCTCTAAACAGAGGCACTACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAGTAAATT
* *
9789841 GCTCCTCTAAACAGAGGCACCATGACTTTGGAAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTTG--AAAGTAAATT
9789884 G
1 G
9789885 TTCCCTGACA
Statistics
Matches: 229, Mismatches: 17, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.00
41 77 0.34
42 71 0.31
43 79 0.34
44 1 0.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAGTAAATT
Found at i:9789724 original size:42 final size:41
Alignment explanation
Indices: 9789589--9789884 Score: 412
Period size: 42 Copynumber: 7.0 Consensus size: 41
9789579 TTTTACCAAA
* * * *
9789589 GCTCCTCTAAATAGAGGCTCAACGACTTTGAGAAACATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-GAAA-GTAAATT
*
9789632 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
*
9789673 GCTCCTCTAAACAGAGGCACCATGACTTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGGAAAGTAAATT
* * * *
9789715 GCTCATCTAAATAGAGGCACCACAACTTTGAAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-GAAAGTAAATT
9789757 GCTCCTCTAAACAGAGGCACCACGACTTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGG-AAAGTAAATT
*
9789800 GCTCCTCTAAACAGAGGCACTACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
*
9789841 GCTCCTCTAAACAGAGGCACCATGACTTTGGAAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGG--AAAGTAAATT
9789884 G
1 G
9789885 TTCCCTGACA
Statistics
Matches: 228, Mismatches: 19, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
41 74 0.32
42 78 0.34
43 76 0.33
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
Found at i:9790468 original size:22 final size:22
Alignment explanation
Indices: 9790420--9790478 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
9790410 GGTTTCACTC
9790420 CTCAAAGATTCTCATTTTGAAAT
1 CTCAAAGATTCTCA-TTTGAAAT
**
9790443 -TCAAAGATTCTCATTTGAGTT
1 CTCAAAGATTCTCATTTGAAAT
* *
9790464 CTCAAAAATTATCAT
1 CTCAAAGATTCTCAT
9790479 CAAAACATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 6 0.19
22 25 0.81
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (22 bp):
CTCAAAGATTCTCATTTGAAAT
Found at i:9791583 original size:20 final size:19
Alignment explanation
Indices: 9791555--9791594 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
9791545 CTTTTTTCCA
9791555 TTTTTTCAT-TTTTTCTTTT
1 TTTTTTCATCTTTTT-TTTT
9791574 TTTTTATCATCTTTTTTTTT
1 TTTTT-TCATCTTTTTTTTT
9791594 T
1 T
9791595 CTCATTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 9 0.47
21 5 0.26
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTTCATCTTTTTTTTT
Found at i:9791589 original size:16 final size:15
Alignment explanation
Indices: 9791570--9791603 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
9791560 TCATTTTTTC
9791570 TTTTTTTTTATCATCT
1 TTTTTTTTTATCAT-T
*
9791586 TTTTTTTTTCTCATT
1 TTTTTTTTTATCATT
9791601 TTT
1 TTT
9791604 CATCTATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTTTTTATCATT
Found at i:9791944 original size:11 final size:11
Alignment explanation
Indices: 9791928--9791963 Score: 72
Period size: 11 Copynumber: 3.3 Consensus size: 11
9791918 GTGGCATTTA
9791928 TTTTTTTCTTT
1 TTTTTTTCTTT
9791939 TTTTTTTCTTT
1 TTTTTTTCTTT
9791950 TTTTTTTCTTT
1 TTTTTTTCTTT
9791961 TTT
1 TTT
9791964 GAGACCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:9795635 original size:9 final size:9
Alignment explanation
Indices: 9795623--9795707 Score: 55
Period size: 9 Copynumber: 8.8 Consensus size: 9
9795613 GATTTTTATT
*
9795623 TAAAGAAAA
1 TAAAAAAAA
9795632 TAAAAAAAA
1 TAAAAAAAA
9795641 TAAAAGTGAAAA
1 TAAAA---AAAA
*
9795653 TAAAAAAAT
1 TAAAAAAAA
9795662 TAAAAAAAAA
1 T-AAAAAAAA
*
9795672 GTAAAACAAA
1 -TAAAAAAAA
*
9795682 -AATAAAAA
1 TAAAAAAAA
*
9795690 TAAGATAAAGA
1 TAA-A-AAAAA
9795701 TAAAAAA
1 TAAAAAA
9795708 TATTAAATAA
Statistics
Matches: 60, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
8 6 0.10
9 22 0.37
10 15 0.25
11 8 0.13
12 9 0.15
ACGTcount: A:0.78, C:0.01, G:0.07, T:0.14
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:9795651 original size:21 final size:21
Alignment explanation
Indices: 9795627--9795666 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
9795617 TTTATTTAAA
9795627 GAAAATAAAAAAAATAAAAGT
1 GAAAATAAAAAAAATAAAAGT
*
9795648 GAAAATAAAAAAATTAAAA
1 GAAAATAAAAAAAATAAAA
9795667 AAAAAGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (21 bp):
GAAAATAAAAAAAATAAAAGT
Found at i:9795669 original size:12 final size:11
Alignment explanation
Indices: 9795633--9795709 Score: 50
Period size: 11 Copynumber: 6.9 Consensus size: 11
9795623 TAAAGAAAAT
9795633 AAAAAAAATAA
1 AAAAAAAATAA
**
9795644 AAGTGAAAAT--
1 AA-AAAAAATAA
*
9795654 AAAAAAATTAA
1 AAAAAAAATAA
*
9795665 AAAAAAAGTAA
1 AAAAAAAATAA
*
9795676 AACAAAAATAA
1 AAAAAAAATAA
* *
9795687 AAATAAGATAA
1 AAAAAAAATAA
9795698 AGATAAAAAATA
1 A-A-AAAAAATA
9795710 TTAAATAAAT
Statistics
Matches: 48, Mismatches: 13, Indels: 8
0.70 0.19 0.12
Matches are distributed among these distances:
9 4 0.08
10 2 0.04
11 30 0.62
12 6 0.12
13 6 0.12
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.14
Consensus pattern (11 bp):
AAAAAAAATAA
Found at i:9795670 original size:11 final size:10
Alignment explanation
Indices: 9795628--9795689 Score: 56
Period size: 11 Copynumber: 6.0 Consensus size: 10
9795618 TTATTTAAAG
9795628 AAAAT-AAAA
1 AAAATAAAAA
*
9795637 AAAATAAAAGTG
1 AAAATAAAA--A
9795649 AAAAT-AAAA
1 AAAATAAAAA
*
9795658 AAATTAAAAA
1 AAAATAAAAA
9795668 AAAAGTAAAACA
1 AAAA-TAAAA-A
9795680 AAAATAAAAA
1 AAAATAAAAA
9795690 TAAGATAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
9 9 0.21
10 11 0.26
11 13 0.30
12 10 0.23
ACGTcount: A:0.81, C:0.02, G:0.05, T:0.13
Consensus pattern (10 bp):
AAAATAAAAA
Found at i:9795734 original size:4 final size:4
Alignment explanation
Indices: 9795727--9795769 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
9795717 AATCTAATCT
* *
9795727 AATA AAT- AATA AATA AATA AATAA AACA AATA AACA AATA AAT
1 AATA AATA AATA AATA AATA AAT-A AATA AATA AATA AATA AAT
9795770 TAAAAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 3 0.09
4 27 0.82
5 3 0.09
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:9795758 original size:21 final size:22
Alignment explanation
Indices: 9795734--9795781 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
9795724 TCTAATAAAT
*
9795734 AATAAATAAATAAA-TAAAACA
1 AATAAACAAATAAATTAAAACA
9795755 AATAAACAAATAAATTAAAA-A
1 AATAAACAAATAAATTAAAACA
9795776 AA-AAAC
1 AATAAAC
9795782 TGGAGCGGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 4 0.16
21 16 0.64
22 5 0.20
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (22 bp):
AATAAACAAATAAATTAAAACA
Found at i:9796646 original size:20 final size:21
Alignment explanation
Indices: 9796621--9796661 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
9796611 AAATCATAAT
*
9796621 AATCAGATAATTGAA-AAAAA
1 AATCAGATAAATGAATAAAAA
9796641 AATCAGATAAATGAATAAAAA
1 AATCAGATAAATGAATAAAAA
9796662 TAAAATTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.66, C:0.05, G:0.10, T:0.20
Consensus pattern (21 bp):
AATCAGATAAATGAATAAAAA
Found at i:9796737 original size:3 final size:3
Alignment explanation
Indices: 9796731--9796859 Score: 53
Period size: 3 Copynumber: 42.3 Consensus size: 3
9796721 AAGATAAAAA
9796731 AAT AAT AAT AAT -AT AAT AAT AAT AA- ATAT AACT ATAT AAAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA-T A-AT -AAT AAT AAT
* *
9796777 ACAT -AT AAAT ATT AAT AGA- AA- AAA AAT AAAT AA- AGAT -AT ACAT
1 A-AT AAT -AAT AAT AAT A-AT AAT AAT AAT -AAT AAT A-AT AAT A-AT
*
9796820 -AT ATT AAT ACAT AAT AAT AAT AAT AAT AAAT AAT AA- AAT A
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT -AAT AAT AAT AAT A
9796860 CAAAAAATAC
Statistics
Matches: 100, Mismatches: 5, Indels: 42
0.68 0.03 0.29
Matches are distributed among these distances:
2 17 0.17
3 59 0.59
4 22 0.22
5 2 0.02
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:9796767 original size:23 final size:22
Alignment explanation
Indices: 9796724--9796808 Score: 70
Period size: 23 Copynumber: 3.8 Consensus size: 22
9796714 ATATTACAAG
9796724 ATAAAA-AAATA-ATAATAATATA
1 ATAAAATAAATATA-AAT-ATATA
*
9796746 ATAATAATAAATATAACTATATAA
1 ATAA-AATAAATATAAATATAT-A
*
9796770 ATAAAATACATATAAATAT-TA
1 ATAAAATAAATATAAATATATA
*
9796791 ATAGAAA-AAAAATAAATA
1 ATA-AAATAAATATAAATA
9796809 AAGATATACA
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
21 13 0.25
22 8 0.15
23 19 0.36
24 12 0.23
25 1 0.02
ACGTcount: A:0.68, C:0.02, G:0.01, T:0.28
Consensus pattern (22 bp):
ATAAAATAAATATAAATATATA
Found at i:9797402 original size:3 final size:3
Alignment explanation
Indices: 9797394--9797429 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
9797384 CATAAAGTCC
9797394 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9797430 ATATACAGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:9799186 original size:13 final size:12
Alignment explanation
Indices: 9799163--9799187 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9799153 ATTCAAAACT
9799163 GAAATAAAAAAA
1 GAAATAAAAAAA
9799175 GAAATAAAAAAA
1 GAAATAAAAAAA
9799187 G
1 G
9799188 GGCAACAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (12 bp):
GAAATAAAAAAA
Found at i:9805607 original size:3 final size:3
Alignment explanation
Indices: 9805601--9805634 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
9805591 TTCGATATCA
9805601 ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
9805635 ATTTTTCCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:9805983 original size:19 final size:17
Alignment explanation
Indices: 9805961--9806008 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
9805951 AACAAAAAAA
*
9805961 AAAAGAAAAGAAAACCTTG
1 AAAA-AAAA-AAAACCTAG
*
9805980 AAAAAAAAAACACCTAG
1 AAAAAAAAAAAACCTAG
9805997 AAAAAAAAAAAA
1 AAAAAAAAAAAA
9806009 GCTCTACTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 18 0.69
18 4 0.15
19 4 0.15
ACGTcount: A:0.75, C:0.10, G:0.08, T:0.06
Consensus pattern (17 bp):
AAAAAAAAAAAACCTAG
Found at i:9806001 original size:38 final size:38
Alignment explanation
Indices: 9805928--9806009 Score: 94
Period size: 37 Copynumber: 2.1 Consensus size: 38
9805918 AAGGATCCAT
* * *
9805928 AAAAGAAAAACTTTGCAAAAAAAAACAAAAAAAAAAAG
1 AAAAGAAAAACCTTGAAAAAAAAAACAAAAAAAAAAAA
* *
9805966 AAAAG-AAAACCTTGAAAAAAAAAACACCTAGAAAAAAAA
1 AAAAGAAAAACCTTGAAAAAAAAAACA--AAAAAAAAAAA
9806005 AAAAG
1 AAAAG
9806010 CTCTACTAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
37 19 0.51
38 5 0.14
39 13 0.35
ACGTcount: A:0.74, C:0.10, G:0.09, T:0.07
Consensus pattern (38 bp):
AAAAGAAAAACCTTGAAAAAAAAAACAAAAAAAAAAAA
Found at i:9806812 original size:16 final size:15
Alignment explanation
Indices: 9806779--9806815 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
9806769 TGATAATTAG
9806779 TAAAA-AAATAAAAA
1 TAAAATAAATAAAAA
9806793 TAAAATAAATAAATAA
1 TAAAATAAATAAA-AA
9806809 TAAAATA
1 TAAAATA
9806816 CATAGTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 5 0.24
15 7 0.33
16 9 0.43
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (15 bp):
TAAAATAAATAAAAA
Found at i:9807039 original size:13 final size:12
Alignment explanation
Indices: 9807010--9807038 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
9807000 AAAAATTAGT
9807010 AAAAATGTAAGA
1 AAAAATGTAAGA
9807022 AAAAATGTAAGA
1 AAAAATGTAAGA
9807034 AAAAA
1 AAAAA
9807039 AATTTTATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (12 bp):
AAAAATGTAAGA
Found at i:9807218 original size:31 final size:31
Alignment explanation
Indices: 9807161--9807219 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
9807151 TTTTCAATAC
**
9807161 AATAAAAAAAATTTTTTGCTATAAAATAGTA
1 AATAAAAAAAATAATTTGCTATAAAATAGTA
*
9807192 AATAAAAATAAATAATTTGTTA-AAAATA
1 AATAAAAA-AAATAATTTGCTATAAAATA
9807220 AGAAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 14 0.58
32 10 0.42
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (31 bp):
AATAAAAAAAATAATTTGCTATAAAATAGTA
Found at i:9808854 original size:133 final size:135
Alignment explanation
Indices: 9808675--9808948 Score: 383
Period size: 144 Copynumber: 2.0 Consensus size: 135
9808665 TTAAATTAGT
*
9808675 AAGCCTTTTCTTTGCATAGTGACAATTTTAGCATAATTGATTGG-T-T-TACGTCAACTTGACTC
1 AAGCCTTTTCTTTGCATAGAGACAATTTTAGCATAATTGATTGGTTATCTACGTCAACTTGACTC
*
9808737 AGTCATTTACTTTTAAATTAGTGATACATAATTTGAACAAATAGCCACGTGCTTCACAATTCAGC
66 AGTCATTTACTCTTAAATTAGTGATACATAATTTGAACAAATAGCCACGTGCTTCACAATTCAGC
9808802 TAACC
131 TAACC
* *
9808807 AAGCCTTTTCTTTTTCATAGAGACAATTTTAGCATAGTTGATTGGTTTCATTGACTCCTACGTCA
1 AAGCCTTTTC-TTTGCATAGAGACAATTTTAGCATAATTGATTGG-----TT-A-T-CTACGTCA
* *
9808872 ACTTGACTCAGTCATTTACTCTTAAATTAGTGATATATAATTTGATCAAATAGCCACGTGCTTCA
57 ACTTGACTCAGTCATTTACTCTTAAATTAGTGATACATAATTTGAACAAATAGCCACGTGCTTCA
*
9808937 TAATTCAGCTAA
122 CAATTCAGCTAA
9808949 TCAAAATTGG
Statistics
Matches: 123, Mismatches: 7, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
132 10 0.08
133 31 0.25
139 1 0.01
142 1 0.01
144 80 0.65
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (135 bp):
AAGCCTTTTCTTTGCATAGAGACAATTTTAGCATAATTGATTGGTTATCTACGTCAACTTGACTC
AGTCATTTACTCTTAAATTAGTGATACATAATTTGAACAAATAGCCACGTGCTTCACAATTCAGC
TAACC
Found at i:9809232 original size:2 final size:2
Alignment explanation
Indices: 9809225--9809258 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9809215 ACAAGTTCTT
9809225 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9809259 AAATTTAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9810018 original size:22 final size:22
Alignment explanation
Indices: 9809982--9810023 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
9809972 TTATAGTTTA
* *
9809982 TAATTAAATATTAAATAAAACT
1 TAATTAAATAGTAAACAAAACT
*
9810004 TAATTAATTAGTAAACAAAA
1 TAATTAAATAGTAAACAAAA
9810024 AAGGAAAGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (22 bp):
TAATTAAATAGTAAACAAAACT
Found at i:9810557 original size:6 final size:6
Alignment explanation
Indices: 9810546--9810622 Score: 73
Period size: 6 Copynumber: 12.2 Consensus size: 6
9810536 TTTTTGAATT
* *
9810546 TTTTTA TTTTTA TTTTTA TCATTTTAA GTTTTA TTTTTA TTTTTA TTATTA
1 TTTTTA TTTTTA TTTTTA T--TTTT-A TTTTTA TTTTTA TTTTTA TTTTTA
* * *
9810597 TTATTA TTATTA TTATTA TTATTTA T
1 TTTTTA TTTTTA TTTTTA TT-TTTA T
9810623 GCATGTTTAA
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
6 50 0.79
7 8 0.13
8 4 0.06
9 1 0.02
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.73
Consensus pattern (6 bp):
TTTTTA
Found at i:9810562 original size:15 final size:15
Alignment explanation
Indices: 9810543--9810622 Score: 69
Period size: 15 Copynumber: 5.5 Consensus size: 15
9810533 AATTTTTTGA
9810543 ATTTTT-TTATTTTT
1 ATTTTTATTATTTTT
*
9810557 ATTTTTATCA-TTTT
1 ATTTTTATTATTTTT
**
9810571 A-AGTT-TTATTTTT
1 ATTTTTATTATTTTT
*
9810584 ATTTTTATTATTATT
1 ATTTTTATTATTTTT
* *
9810599 ATTATTATTATTATT
1 ATTTTTATTATTTTT
9810614 ATTATTTAT
1 ATT-TTTAT
9810623 GCATGTTTAA
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
12 2 0.04
13 7 0.13
14 13 0.25
15 26 0.50
16 4 0.08
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.72
Consensus pattern (15 bp):
ATTTTTATTATTTTT
Found at i:9810596 original size:3 final size:3
Alignment explanation
Indices: 9810576--9810619 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
9810566 ATTTTAAGTT
* *
9810576 TTA TTT TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9810620 TATGCATGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:9812312 original size:14 final size:15
Alignment explanation
Indices: 9812287--9812316 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
9812277 TTTTATTTAA
9812287 ATTTATTAATTATCT
1 ATTTATTAATTATCT
9812302 ATTTA-TAATTATCT
1 ATTTATTAATTATCT
9812316 A
1 A
9812317 AATCTAATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTATTAATTATCT
Found at i:9813401 original size:3 final size:3
Alignment explanation
Indices: 9813393--9813417 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
9813383 AAAGTCCTAC
9813393 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
9813418 CTTTCATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:9814621 original size:21 final size:21
Alignment explanation
Indices: 9814566--9814625 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
9814556 CATTTATGCT
* *
9814566 TTTTAATAA-AAT-TTTAAAT
1 TTTTAACAATAATATTTAAAA
**
9814585 TTTTAACAATTTTATTTAAAA
1 TTTTAACAATAATATTTAAAA
*
9814606 TTTTAAGAATAATA-TTAAAA
1 TTTTAACAATAATATTTAAAA
9814626 GAAGACATTA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
19 8 0.25
20 7 0.22
21 17 0.53
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
TTTTAACAATAATATTTAAAA
Found at i:9817667 original size:14 final size:16
Alignment explanation
Indices: 9817644--9817680 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
9817634 ATAATTATTT
9817644 TTTAAAAAATA-AT-A
1 TTTAAAAAATATATAA
*
9817658 TTTAATAAATATATAA
1 TTTAAAAAATATATAA
9817674 TTTAAAA
1 TTTAAAA
9817681 TTTAACACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
14 10 0.53
15 2 0.11
16 7 0.37
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTAAAAAATATATAA
Found at i:9818121 original size:43 final size:43
Alignment explanation
Indices: 9818063--9818293 Score: 157
Period size: 43 Copynumber: 5.3 Consensus size: 43
9818053 TTTAGGGAAG
* * *
9818063 CTTTTTAAATCTTTTAAAATTATTGAGCCTCTTCTTAGATGAGC
1 CTTTTT-AATTTTTTAAAATTATTAAGCCTCTACTTAGATGAGC
* *
9818107 CTTTTTAATTTTTTAAAATTTATAAAGCCTCTACTTGGA-GAAGC
1 CTTTTTAATTTTTTAAAA-TTATTAAGCCTCTACTTAGATG-AGC
* * * * *
9818151 C-TTTTAA-TTTTTAAAAGTTATCAAGACTCTGCTTAAATGAGT
1 CTTTTTAATTTTTTAAAA-TTATTAAGCCTCTACTTAGATGAGC
* ** * *
9818193 CTTTTAAAATTTTCAAAAATTATTAAGTCTCTACTTAGATGTG-
1 CTTTT-TAATTTTTTAAAATTATTAAGCCTCTACTTAGATGAGC
** * ** *
9818236 CTTTTTAAATTTTAAAAAATTATCGAA-TATCTACTTAGAGGAGC
1 CTTTTT-AATTTTTTAAAATTAT-TAAGCCTCTACTTAGATGAGC
**
9818280 CTTTCAAATTTTTT
1 CTTTTTAATTTTTT
9818294 TTAAAAAAGA
Statistics
Matches: 148, Mismatches: 30, Indels: 19
0.75 0.15 0.10
Matches are distributed among these distances:
42 27 0.18
43 61 0.41
44 53 0.36
45 7 0.05
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.44
Consensus pattern (43 bp):
CTTTTTAATTTTTTAAAATTATTAAGCCTCTACTTAGATGAGC
Found at i:9818136 original size:44 final size:44
Alignment explanation
Indices: 9818063--9818292 Score: 186
Period size: 44 Copynumber: 5.3 Consensus size: 44
9818053 TTTAGGGAAG
* *
9818063 CTTTTTAAATCTTTT-AAAATTATTGAGCCTCTTCTTAGATGAGC
1 CTTTTTAAAT-TTTTAAAAATTATTAAGCCTCTACTTAGATGAGC
* * * *
9818107 CTTTTTAATTTTTTAAAATTTATAAAGCCTCTACTTGGA-GAAGC
1 CTTTTTAAATTTTTAAAAATTATTAAGCCTCTACTTAGATG-AGC
* * * * * *
9818151 C-TTTT-AATTTTTAAAAGTTATCAAGACTCTGCTTAAATGAGT
1 CTTTTTAAATTTTTAAAAATTATTAAGCCTCTACTTAGATGAGC
* * * *
9818193 CTTTTAAAATTTTCAAAAATTATTAAGTCTCTACTTAGATGTG-
1 CTTTTTAAATTTTTAAAAATTATTAAGCCTCTACTTAGATGAGC
* * ** *
9818236 CTTTTTAAATTTTAAAAAATTATCGAA-TATCTACTTAGAGGAGC
1 CTTTTTAAATTTTTAAAAATTAT-TAAGCCTCTACTTAGATGAGC
*
9818280 C-TTTCAAATTTTT
1 CTTTTTAAATTTTT
9818293 TTTAAAAAAG
Statistics
Matches: 149, Mismatches: 30, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
42 28 0.19
43 57 0.38
44 64 0.43
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (44 bp):
CTTTTTAAATTTTTAAAAATTATTAAGCCTCTACTTAGATGAGC
Found at i:9818242 original size:86 final size:85
Alignment explanation
Indices: 9818045--9818252 Score: 202
Period size: 86 Copynumber: 2.4 Consensus size: 85
9818035 AAAGTTGTTG
* * * ** * * *
9818045 AGCCTTTATTTAGGGAAGCTTTTTAAATCTTTTAAAATTATTGAGCCTCTTCTTAGATGAGCCTT
1 AGCCTCTACTTAGAGAAGCTTTTT-AAT-TTTTAAAATTATCAAGACTCTGCTTAAATGAGCCTT
* * * *
9818110 TTTAATTTTTTAAAATTTATAA
64 TTAAAATTTTCAAAAATTATAA
* * *
9818132 AGCCTCTACTTGGAGAAGCCTTTTAATTTTTAAAAGTTATCAAGACTCTGCTTAAATGAGTCTTT
1 AGCCTCTACTTAGAGAAGCTTTTTAATTTTTAAAA-TTATCAAGACTCTGCTTAAATGAGCCTTT
*
9818197 TAAAATTTTCAAAAATTATTA
65 TAAAATTTTCAAAAATTATAA
* * *
9818218 AGTCTCTACTTAGATG-TGCTTTTTAAATTTTAAAA
1 AGCCTCTACTTAGA-GAAGCTTTTTAATTTTTAAAA
9818253 AATTATCGAA
Statistics
Matches: 98, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
85 8 0.08
86 70 0.71
87 20 0.20
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (85 bp):
AGCCTCTACTTAGAGAAGCTTTTTAATTTTTAAAATTATCAAGACTCTGCTTAAATGAGCCTTTT
AAAATTTTCAAAAATTATAA
Found at i:9818616 original size:22 final size:22
Alignment explanation
Indices: 9818579--9818620 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
9818569 TTATTATTAT
9818579 TATTTCTTTTCTTTTCTTTCCC
1 TATTTCTTTTCTTTTCTTTCCC
9818601 TATTATCTTTTC-TTTCTTTC
1 TATT-TCTTTTCTTTTCTTTC
9818621 TTTTCTGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.69
Consensus pattern (22 bp):
TATTTCTTTTCTTTTCTTTCCC
Found at i:9818880 original size:27 final size:27
Alignment explanation
Indices: 9818847--9818898 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
9818837 ATCTGAATAG
*
9818847 ATGTTTAATACATTTAATATGTTTAAT
1 ATGTTTAACACATTTAATATGTTTAAT
**
9818874 ATGTTTAACACATTTTTTATGTTTA
1 ATGTTTAACACATTTAATATGTTTA
9818899 TTTTAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.54
Consensus pattern (27 bp):
ATGTTTAACACATTTAATATGTTTAAT
Found at i:9818962 original size:31 final size:30
Alignment explanation
Indices: 9818868--9818971 Score: 88
Period size: 30 Copynumber: 3.5 Consensus size: 30
9818858 ATTTAATATG
*
9818868 TTTAATATGTTTAACACATTTTTTATGTTTAT
1 TTTAATATGTTTAA-A-AATTTTTATGTTTAT
* * ** **
9818900 TTT-A-AT-TTAAAAAATTATTAAATACAT
1 TTTAATATGTTTAAAAATTTTTATGTTTAT
*
9818927 TTTAACATGTTTAAAAATTTTTATGTTTAT
1 TTTAATATGTTTAAAAATTTTTATGTTTAT
9818957 GTTTAATATGTTTAA
1 -TTTAATATGTTTAA
9818972 CATATAAAAA
Statistics
Matches: 54, Mismatches: 14, Indels: 9
0.70 0.18 0.12
Matches are distributed among these distances:
27 12 0.22
28 2 0.04
29 6 0.11
30 17 0.31
31 14 0.26
32 3 0.06
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.54
Consensus pattern (30 bp):
TTTAATATGTTTAAAAATTTTTATGTTTAT
Found at i:9819428 original size:10 final size:10
Alignment explanation
Indices: 9819413--9819482 Score: 74
Period size: 10 Copynumber: 7.2 Consensus size: 10
9819403 CGTGTTAATA
9819413 ATGTCTATTC
1 ATGTCTATTC
9819423 ATGTCTATTC
1 ATGTCTATTC
* *
9819433 ATTTATATTC
1 ATGTCTATTC
9819443 ATGT-TAGTT-
1 ATGTCTA-TTC
9819452 ATGTCTATTC
1 ATGTCTATTC
*
9819462 ATGTATATTC
1 ATGTCTATTC
*
9819472 ATAT-TATTC
1 ATGTCTATTC
9819481 AT
1 AT
9819483 ATTTATTTGT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
9 15 0.29
10 37 0.71
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.53
Consensus pattern (10 bp):
ATGTCTATTC
Found at i:9819456 original size:39 final size:39
Alignment explanation
Indices: 9819395--9819482 Score: 124
Period size: 39 Copynumber: 2.3 Consensus size: 39
9819385 GTAATCTTTT
* *
9819395 TATATATTCGTGTTAATAATGTCTATTCATGTCTATTCA
1 TATATATTCATGTTAATAATGTCTATTCATGTATATTCA
* * *
9819434 TTTATATTCATGTTAGTTATGTCTATTCATGTATATTCA
1 TATATATTCATGTTAATAATGTCTATTCATGTATATTCA
9819473 TAT-TATTCAT
1 TATATATTCAT
9819483 ATTTATTTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
38 7 0.16
39 36 0.84
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.52
Consensus pattern (39 bp):
TATATATTCATGTTAATAATGTCTATTCATGTATATTCA
Found at i:9819479 original size:19 final size:19
Alignment explanation
Indices: 9819395--9819482 Score: 63
Period size: 19 Copynumber: 4.6 Consensus size: 19
9819385 GTAATCTTTT
* * *
9819395 TATATATTCGTGTTAATAA
1 TATATATTCATGTTATTCA
* *
9819414 TGTCTATTCATGTCTATTCA
1 TATATATTCATGT-TATTCA
*
9819434 TTTATATTCATGTTAGTT-A
1 TATATATTCATGTTA-TTCA
* *
9819453 TGTCTATTCATGTATATTCA
1 TATATATTCATGT-TATTCA
9819473 TAT-TATTCAT
1 TATATATTCAT
9819483 ATTTATTTGT
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
19 33 0.60
20 22 0.40
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.52
Consensus pattern (19 bp):
TATATATTCATGTTATTCA
Found at i:9819489 original size:29 final size:29
Alignment explanation
Indices: 9819418--9819482 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 29
9819408 TAATAATGTC
* *
9819418 TATTCATGTCTATTCATTTATATTCATGT
1 TATTCATGTCTATTCATGTATATTCATAT
9819447 TAGTT-ATGTCTATTCATGTATATTCATAT
1 TA-TTCATGTCTATTCATGTATATTCATAT
9819476 TATTCAT
1 TATTCAT
9819483 ATTTATTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 2 0.06
29 28 0.88
30 2 0.06
ACGTcount: A:0.26, C:0.12, G:0.08, T:0.54
Consensus pattern (29 bp):
TATTCATGTCTATTCATGTATATTCATAT
Found at i:9820863 original size:19 final size:21
Alignment explanation
Indices: 9820820--9820863 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 21
9820810 TGTTTCATTC
9820820 TCTTTTTTATTATTTATTCTA
1 TCTTTTTTATTATTTATTCTA
*
9820841 --TTTTTTATT-TTT-TTGTA
1 TCTTTTTTATTATTTATTCTA
9820858 TCTTTT
1 TCTTTT
9820864 GAGTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 6
0.74 0.04 0.22
Matches are distributed among these distances:
17 4 0.20
18 3 0.15
19 13 0.65
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.77
Consensus pattern (21 bp):
TCTTTTTTATTATTTATTCTA
Found at i:9821278 original size:236 final size:242
Alignment explanation
Indices: 9820994--9821496 Score: 627
Period size: 236 Copynumber: 2.1 Consensus size: 242
9820984 AAATAACTAC
* * *
9820994 AAAGTCACAAGTGGTGGTTTTATGAAAAATATTCACACAAATAAATTTTTTAAAATATTCTAAAA
1 AAAGTCACAAGTGGTGATTTTATGAAAAATATTCACACAAAAAAATTTTCTAAAATATTCTAAAA
* * *
9821059 GTGTTTA-AATTATTTTAAAATCTTTT-AAGC-ATAAAAAAT-AT-T-ATTAAT-AAAAA-AAA-
66 GTG-TCAGAAATATTTTAAAAT-TTTTCAAGCAAAAAAAAATAATATCATTAATAAAAAATAAAG
* * *
9821115 TCACAAGTGGTGATTTTATTAAAAATATTTAC-GCAA-AATTTTTTTAAAAATT-TTCCAAAAAT
129 CCACAAGTGGTGATTTTATTAAAAATATTTACAGAAAGAAATTTTTT--AAATTATTCCAAAAAT
*
9821177 GTTAGAAATA-TTAAAAATTTTTCAAGCATAAAAAAACATTATTAATAAAAAAT
192 GTTAAAAATATTTAAAAA-TTTTCAAG--TAAAAAAACATTATTAATAAAAAAT
* * *
9821230 AAAGTCACAAGTGGTGATTTTATTAAAAATATTTATACAAAAAAATTTTCTAAAATATTCTAAAA
1 AAAGTCACAAGTGGTGATTTTATGAAAAATATTCACACAAAAAAATTTTCTAAAATATTCTAAAA
* *
9821295 TTGTCAGAAATATTTTAGAATTTTTCAAGCAGAAAAAAAATAAAATATCATTAATAAAAAAATAA
66 GTGTCAGAAATATTTTAAAATTTTTCAAGCA-AAAAAAAAT--AATATCATTAAT-AAAAAATAA
* * *
9821360 AGCCACAAGTGGTGATTTTATTAAAAATATTTACATAAAGAAATTTTTTAAATTATTCTAAAAGT
127 AGCCACAAGTGGTGATTTTATTAAAAATATTTACAGAAAGAAATTTTTTAAATTATTCCAAAAAT
* *
9821425 GTTAAAAATATTTTAAAATTTTCAAGTAAAAAAACATTATTAATAAAGAAT
192 GTTAAAAATATTTAAAAATTTTCAAGTAAAAAAACATTATTAATAAAAAAT
*
9821476 AAAATCACAAGTGGTGATTTT
1 AAAGTCACAAGTGGTGATTTT
9821497 CATACAAAGA
Statistics
Matches: 229, Mismatches: 21, Indels: 24
0.84 0.08 0.09
Matches are distributed among these distances:
235 6 0.03
236 77 0.34
238 8 0.03
241 2 0.01
242 1 0.00
243 6 0.03
245 5 0.02
246 47 0.21
247 36 0.16
248 27 0.12
249 14 0.06
ACGTcount: A:0.49, C:0.07, G:0.08, T:0.36
Consensus pattern (242 bp):
AAAGTCACAAGTGGTGATTTTATGAAAAATATTCACACAAAAAAATTTTCTAAAATATTCTAAAA
GTGTCAGAAATATTTTAAAATTTTTCAAGCAAAAAAAAATAATATCATTAATAAAAAATAAAGCC
ACAAGTGGTGATTTTATTAAAAATATTTACAGAAAGAAATTTTTTAAATTATTCCAAAAATGTTA
AAAATATTTAAAAATTTTCAAGTAAAAAAACATTATTAATAAAAAAT
Found at i:9821296 original size:20 final size:20
Alignment explanation
Indices: 9821271--9821318 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
9821261 TTTATACAAA
9821271 AAAATTTTCTA-AAATATTCT
1 AAAATTTTC-AGAAATATTCT
* *
9821291 AAAATTGTCAGAAATATTTT
1 AAAATTTTCAGAAATATTCT
*
9821311 AGAATTTT
1 AAAATTTT
9821319 TCAAGCAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (20 bp):
AAAATTTTCAGAAATATTCT
Found at i:9823729 original size:27 final size:27
Alignment explanation
Indices: 9823699--9823758 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
9823689 AAGCCCACTC
9823699 ACAAGAATTTTCTTCATGCCCCATAAA
1 ACAAGAATTTTCTTCATGCCCCATAAA
*
9823726 ACAAGAATTTTCTTCATGCCCCGTAAA
1 ACAAGAATTTTCTTCATGCCCCATAAA
*
9823753 ATAAGA
1 ACAAGA
9823759 TCTTGACTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.28
Consensus pattern (27 bp):
ACAAGAATTTTCTTCATGCCCCATAAA
Found at i:9828067 original size:5 final size:5
Alignment explanation
Indices: 9828054--9828136 Score: 55
Period size: 5 Copynumber: 16.2 Consensus size: 5
9828044 AATAATCAGC
* *
9828054 ATAAG ATAAA AT-AA A-AAA ATAAA ATAAA ATAAA AAATAA ATAAA ACCTAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATA-AA ATAAA A--TAAA
* * *
9828105 A-AATA ATATA ATATA ATATAA ATAAT ATAAA A
1 ATAA-A ATAAA ATAAA ATA-AA ATAAA ATAAA A
9828137 AAAGATAATT
Statistics
Matches: 63, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
4 8 0.13
5 41 0.65
6 9 0.14
7 5 0.08
ACGTcount: A:0.73, C:0.02, G:0.01, T:0.23
Consensus pattern (5 bp):
ATAAA
Found at i:9828080 original size:18 final size:17
Alignment explanation
Indices: 9828054--9828136 Score: 78
Period size: 18 Copynumber: 4.6 Consensus size: 17
9828044 AATAATCAGC
*
9828054 ATAAGATAAAATAAAAAA
1 ATAAAATAAAAT-AAAAA
9828072 ATAAAATAAAATAAAAA
1 ATAAAATAAAATAAAAA
9828089 AT-AAATAAAACCTAAAAA
1 ATAAAATAAAA--TAAAAA
* *
9828107 ATAATATAATATAATATAA
1 ATAAAATAAAATAA-A-AA
*
9828126 ATAATATAAAA
1 ATAAAATAAAA
9828137 AAAGATAATT
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
16 8 0.14
17 10 0.18
18 20 0.36
19 18 0.32
ACGTcount: A:0.73, C:0.02, G:0.01, T:0.23
Consensus pattern (17 bp):
ATAAAATAAAATAAAAA
Done.