Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003981.1 Hibiscus syriacus cultivar Beakdansim tig00008652_pilon, 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: 94547
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:483 original size:34 final size:35
Alignment explanation
Indices: 445--521 Score: 120
Period size: 34 Copynumber: 2.2 Consensus size: 35
435 GGGGTCGAAT
*
445 ATGTAATTGAAGTATTTTGAATTTGA-GGTTTATA
1 ATGTAATTGAAGTATTTTGAATTTGAGGGTTTAGA
* *
479 ATGTAATTGAAGTATTTTGGATTTTAGGGTTTAGA
1 ATGTAATTGAAGTATTTTGAATTTGAGGGTTTAGA
514 ATGTAATT
1 ATGTAATT
522 ATGACTATGT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 24 0.62
35 15 0.38
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (35 bp):
ATGTAATTGAAGTATTTTGAATTTGAGGGTTTAGA
Found at i:12479 original size:185 final size:186
Alignment explanation
Indices: 12154--12543 Score: 653
Period size: 185 Copynumber: 2.1 Consensus size: 186
12144 ATTTCGAATT
* * * *
12154 TATATAA-AAATTAAATA-TTTTTAATTCAAAAAAATAGTTTATAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
12217 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTA
66 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTA
* * *
12282 TTAAATCTTAAATTATTAATT-AGGTTTTAAATGGTTTGGACTTAGCCCATATGTTA
131 TTAAATCTTAAATTATTAATTGA-ATTTTAAATGGTTTGGACTAAGCCCATATGTCA
12338 TATATAATATATTTAATATTTTTTAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
*
12403 ATTATAAAATAAAAATTTTATAT-AATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
66 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTA
* *
12467 TTGAATCTTAAATTATTAATTGAATTTTAAATGGTTTGGGCTAAGCCCATATGTCA
131 TTAAATCTTAAATTATTAATTGAATTTTAAATGGTTTGGACTAAGCCCATATGTCA
12523 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
12544 AAAATTTAAT
Statistics
Matches: 193, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
184 7 0.04
185 118 0.61
186 68 0.35
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (186 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAACAGTTTACAATTAATTTAAATAATATATA
ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTA
TTAAATCTTAAATTATTAATTGAATTTTAAATGGTTTGGACTAAGCCCATATGTCA
Found at i:12572 original size:9 final size:9
Alignment explanation
Indices: 12549--12582 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
12539 TATTTAAAAT
12549 TTAATTTCGG
1 TTAA-TTCGG
*
12559 TTAATTCTG
1 TTAATTCGG
12568 TTAATTCGG
1 TTAATTCGG
12577 TTAATT
1 TTAATT
12583 AACCGATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 18 0.82
10 4 0.18
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.53
Consensus pattern (9 bp):
TTAATTCGG
Found at i:19592 original size:21 final size:21
Alignment explanation
Indices: 19567--19606 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
19557 GTTAATTAGT
19567 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
19588 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
19607 CATATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:19852 original size:15 final size:15
Alignment explanation
Indices: 19834--19883 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
19824 GTTTAAATTG
19834 TATTAAAGAATAGTT
1 TATTAAAGAATAGTT
**
19849 TATTAGTTG-A-AGTT
1 TATTA-AAGAATAGTT
19863 ATATTAAAGAATAGTT
1 -TATTAAAGAATAGTT
19879 TATTA
1 TATTA
19884 GTTGTTTAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
14 5 0.19
15 17 0.63
16 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (15 bp):
TATTAAAGAATAGTT
Found at i:19868 original size:30 final size:30
Alignment explanation
Indices: 19797--19887 Score: 121
Period size: 30 Copynumber: 3.0 Consensus size: 30
19787 TTTTAGTATT
* *
19797 AAATTATAATTTAAA-AATCGTTTATTAGTTT
1 AAATTAT-A-TTAAAGAATAGTTTATTAGTTG
*
19828 AAATTGTATTAAAGAATAGTTTATTAGTTG
1 AAATTATATTAAAGAATAGTTTATTAGTTG
*
19858 AAGTTATATTAAAGAATAGTTTATTAGTTG
1 AAATTATATTAAAGAATAGTTTATTAGTTG
19888 TTTAAGGAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
29 5 0.09
30 43 0.80
31 6 0.11
ACGTcount: A:0.41, C:0.01, G:0.13, T:0.45
Consensus pattern (30 bp):
AAATTATATTAAAGAATAGTTTATTAGTTG
Found at i:20497 original size:20 final size:20
Alignment explanation
Indices: 20472--20527 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
20462 TTTCAAAGTG
20472 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
20492 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
* *
20512 TTGCATCGATGCACCA
1 ATGCACCGATGCACCA
20528 TGGAATAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.29, C:0.38, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:20568 original size:65 final size:64
Alignment explanation
Indices: 20491--20699 Score: 176
Period size: 65 Copynumber: 3.2 Consensus size: 64
20481 TGCACCAATC
* *
20491 CATGCACCGATGCACCAATCCTTGCATCGATGCACCAT-GGAATAAATTG-AACATCGAATGCAT
1 CATGCATCGATGCACC-ATCCATGCATCGATGCA-CATAGGAATAAA-TGAAACATCGAATGCAT
20554 TT
63 TT
* ** **
20556 CATGCATCGATGCA-CATACCATGCATCGATGCACTTAGGGTTTTATGAAAACATCGAATGCATT
1 CATGCATCGATGCACCAT-CCATGCATCGATGCACATAGGAATAAATG-AAACATCGAATGCATT
20620 T
64 T
* * * * *** *
20621 GATGCATCGATGCACCAGCCATGCATCGATACAC-TCAGG-CTTTTTCAAAGCATCGAATGCATT
1 CATGCATCGATGCACCATCCATGCATCGATGCACAT-AGGAATAAATGAAA-CATCGAATGCATT
20684 T
64 T
*
20685 TATGCATCGATGCAC
1 CATGCATCGATGCAC
20700 ACTTAGTGCA
Statistics
Matches: 123, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
63 9 0.07
64 52 0.42
65 60 0.49
66 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACCATCCATGCATCGATGCACATAGGAATAAATGAAACATCGAATGCATTT
Found at i:20697 original size:64 final size:66
Alignment explanation
Indices: 20540--20699 Score: 227
Period size: 65 Copynumber: 2.5 Consensus size: 66
20530 GAATAAATTG
* * * *
20540 AACATCGAATGCATTTCATGCATCGATGCA-CATACCATGCATCGATGCACTTAGGGTTTTATGA
1 AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATACACTCAGGCTTTTATCA
20604 A
66 A
* *
20605 AACATCGAATGCATTTGATGCATCGATGCACCA-GCCATGCATCGATACACTCAGGCTTTT-TCA
1 AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATACACTCAGGCTTTTATCA
20668 A
66 A
* *
20669 AGCATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
20700 ACTTAGTGCA
Statistics
Matches: 86, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
64 32 0.37
65 52 0.60
66 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (66 bp):
AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATACACTCAGGCTTTTATCA
A
Found at i:21895 original size:11 final size:11
Alignment explanation
Indices: 21875--21988 Score: 102
Period size: 11 Copynumber: 10.2 Consensus size: 11
21865 AATTTTGATT
*
21875 ATTATCAAATC
1 ATTATTAAATC
*
21886 ATTACTAAATC
1 ATTATTAAATC
*
21897 ATTGTTAAATC
1 ATTATTAAATC
* *
21908 ATTATTATCATT
1 ATTATTA-AATC
*
21920 ATTATCAAATC
1 ATTATTAAATC
*
21931 ATTACTAAATC
1 ATTATTAAATC
*
21942 ATTGTTAAATC
1 ATTATTAAATC
* *
21953 ATTATTATCATT
1 ATTATTA-AATC
*
21965 ATTATCAAATC
1 ATTATTAAATC
*
21976 ATTACTAAATC
1 ATTATTAAATC
21987 AT
1 AT
21989 CAAATCATTA
Statistics
Matches: 79, Mismatches: 22, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
11 63 0.80
12 16 0.20
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (11 bp):
ATTATTAAATC
Found at i:21919 original size:9 final size:9
Alignment explanation
Indices: 21905--21971 Score: 52
Period size: 9 Copynumber: 7.4 Consensus size: 9
21895 TCATTGTTAA
21905 ATCATTATT
1 ATCATTATT
21914 ATCATTATT
1 ATCATTATT
21923 ATCA--A--
1 ATCATTATT
*
21928 ATCATTACTAA
1 ATCATTA-T-T
*
21939 ATCATTGTT
1 ATCATTATT
21948 AAATCATTATT
1 --ATCATTATT
21959 ATCATTATT
1 ATCATTATT
21968 ATCA
1 ATCA
21972 AATCATTACT
Statistics
Matches: 47, Mismatches: 3, Indels: 16
0.71 0.05 0.24
Matches are distributed among these distances:
5 4 0.09
7 2 0.04
9 26 0.55
10 1 0.02
11 14 0.30
ACGTcount: A:0.39, C:0.13, G:0.01, T:0.46
Consensus pattern (9 bp):
ATCATTATT
Found at i:21933 original size:14 final size:14
Alignment explanation
Indices: 21914--22028 Score: 54
Period size: 14 Copynumber: 8.5 Consensus size: 14
21904 AATCATTATT
21914 ATCATTATTATCAA
1 ATCATTATTATCAA
*
21928 ATCATTA--CT-AA
1 ATCATTATTATCAA
*
21939 ATCATT-GT-T-AA
1 ATCATTATTATCAA
21950 ATCATTATTATC--
1 ATCATTATTATCAA
21962 ---ATTATTATCAA
1 ATCATTATTATCAA
21973 ATCATTACTAAATCATCAA
1 ATCATTA-T---T-ATCAA
* *
21992 ATCATTAAATATTAAA
1 ATCATT-ATTA-TCAA
22008 ATCATTATTATCAA
1 ATCATTATTATCAA
22022 ATCATTA
1 ATCATTA
22029 CTAAATCATA
Statistics
Matches: 78, Mismatches: 6, Indels: 34
0.66 0.05 0.29
Matches are distributed among these distances:
9 9 0.12
11 17 0.22
12 2 0.03
13 1 0.01
14 21 0.27
15 5 0.06
16 10 0.13
18 1 0.01
19 11 0.14
20 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.41
Consensus pattern (14 bp):
ATCATTATTATCAA
Found at i:21936 original size:45 final size:45
Alignment explanation
Indices: 21872--22037 Score: 253
Period size: 45 Copynumber: 3.6 Consensus size: 45
21862 GGGAATTTTG
21872 ATTATTATCAAATCATTACTAAATCATTGTTAAATCATTATTATC
1 ATTATTATCAAATCATTACTAAATCATTGTTAAATCATTATTATC
21917 ATTATTATCAAATCATTACTAAATCATTGTTAAATCATTATTATC
1 ATTATTATCAAATCATTACTAAATCATTGTTAAATCATTATTATC
* **
21962 ATTATTATCAAATCATTACTAAATCATCAAATCATTAAAT-ATTAAAATC
1 ATTATTATCAAATCATTACTAAATCAT----T-GTTAAATCATTATTATC
22011 ATTATTATCAAATCATTACTAAATCAT
1 ATTATTATCAAATCATTACTAAATCAT
22038 ATAATTATTA
Statistics
Matches: 113, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
45 72 0.64
49 35 0.31
50 6 0.05
ACGTcount: A:0.43, C:0.14, G:0.01, T:0.42
Consensus pattern (45 bp):
ATTATTATCAAATCATTACTAAATCATTGTTAAATCATTATTATC
Found at i:22000 original size:16 final size:15
Alignment explanation
Indices: 21967--22028 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 15
21957 TTATCATTAT
21967 TATCAAATCATTACTAAA
1 TATCAAATCA-T--TAAA
21985 TCATCAAATCATTAAA
1 T-ATCAAATCATTAAA
* *
22001 TATTAAAATCATT-AT
1 TA-TCAAATCATTAAA
22016 TATCAAATCATTA
1 TATCAAATCATTA
22029 CTAAATCATA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 9 0.24
15 4 0.11
16 14 0.37
18 2 0.05
19 9 0.24
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (15 bp):
TATCAAATCATTAAA
Found at i:22292 original size:11 final size:12
Alignment explanation
Indices: 22278--22327 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 12
22268 ATTATTAATG
22278 ATTA-AATCATT
1 ATTACAATCATT
22289 ATTACAATTTCATT
1 ATTACAA--TCATT
22303 ATTACTAATCATT
1 ATTAC-AATCATT
*
22316 ATT-TAATCATT
1 ATTACAATCATT
22327 A
1 A
22328 ATATCAAATC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
11 12 0.35
12 2 0.06
13 8 0.24
14 10 0.29
15 2 0.06
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTACAATCATT
Found at i:22363 original size:14 final size:14
Alignment explanation
Indices: 22280--22396 Score: 56
Period size: 13 Copynumber: 8.7 Consensus size: 14
22270 TATTAATGAT
22280 TAAATCATTATTACA
1 TAAATCATTATTA-A
** *
22295 -ATTTCATTATTAC
1 TAAATCATTATTAA
22308 T-AATCATTATT--
1 TAAATCATTATTAA
*
22319 T-AATCATTAAT-A
1 TAAATCATTATTAA
22331 TCAAATC-TTAATATAA
1 T-AAATCATT-AT-TAA
22347 TAAATCATTATTAA
1 TAAATCATTATTAA
*
22361 T-AATCATTACTAA
1 TAAATCATTATTAA
* *
22374 -ATGAT-ATTATTAG
1 TA-AATCATTATTAA
22387 TAAATCATTA
1 TAAATCATTA
22397 AATAATTATT
Statistics
Matches: 78, Mismatches: 12, Indels: 25
0.68 0.10 0.22
Matches are distributed among these distances:
11 10 0.13
12 1 0.01
13 29 0.37
14 26 0.33
15 8 0.10
16 4 0.05
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (14 bp):
TAAATCATTATTAA
Found at i:22405 original size:22 final size:22
Alignment explanation
Indices: 22379--22422 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
22369 ACTAAATGAT
*
22379 ATTATTAGTAAATCATTAAATA
1 ATTATTACTAAATCATTAAATA
*
22401 ATTATTACTAAGTCATTAAATA
1 ATTATTACTAAATCATTAAATA
22423 CAAAATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (22 bp):
ATTATTACTAAATCATTAAATA
Found at i:25674 original size:17 final size:17
Alignment explanation
Indices: 25652--25715 Score: 83
Period size: 17 Copynumber: 3.7 Consensus size: 17
25642 ATCTAATAAA
25652 TTAAACAAAATATTTTT
1 TTAAACAAAATATTTTT
*
25669 TTAAACAACAATATATTT
1 TTAAACAA-AATATTTTT
*
25687 TTAAACAGAATATTTTT
1 TTAAACAAAATATTTTT
* *
25704 TAAAACAGAATA
1 TTAAACAAAATA
25716 AATTAAACTA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
17 27 0.64
18 15 0.36
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (17 bp):
TTAAACAAAATATTTTT
Found at i:26603 original size:46 final size:53
Alignment explanation
Indices: 26528--26632 Score: 134
Period size: 51 Copynumber: 2.1 Consensus size: 53
26518 GTTTAATCAC
*
26528 ACTAAGAAACAACTAATTAAATAA-TTTTTTA-A-CATAT-A-ATATAACTTAA
1 ACTAAGAAAC-ACTAATTAAATAATTTTTTTATATAATATAATATATAACTTAA
*
26577 ACTAAGAAAC-C-AATTAACTAATTTTTTTATATAATATAATATATAACTTAA
1 ACTAAGAAACACTAATTAAATAATTTTTTTATATAATATAATATATAACTTAA
26628 ACTAA
1 ACTAA
26633 TAATTTAAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
46 9 0.18
47 8 0.16
48 1 0.02
49 14 0.29
50 1 0.02
51 16 0.33
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.36
Consensus pattern (53 bp):
ACTAAGAAACACTAATTAAATAATTTTTTTATATAATATAATATATAACTTAA
Found at i:26797 original size:20 final size:19
Alignment explanation
Indices: 26767--26806 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
26757 CTTTTCTGCC
*
26767 TTTCTTCTGCTTCCTTTCT
1 TTTCTTCTGCTTCCGTTCT
26786 TTTCTCTCTGCTTCCGTTCT
1 TTTCT-TCTGCTTCCGTTCT
26806 T
1 T
26807 GCTTTGTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.00, C:0.33, G:0.07, T:0.60
Consensus pattern (19 bp):
TTTCTTCTGCTTCCGTTCT
Found at i:27115 original size:30 final size:30
Alignment explanation
Indices: 27079--27151 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
27069 ACGCTGGGAC
*
27079 TGCATGGCAACCTCCGACCGTGCATGGGCG
1 TGCATGGCGACCTCCGACCGTGCATGGGCG
*
27109 TGCATGGCGACCTCCGACCGTGCATTGGCG
1 TGCATGGCGACCTCCGACCGTGCATGGGCG
27139 TGCATGGCGACCT
1 TGCATGGCGACCT
27152 TCAACAGTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.15, C:0.33, G:0.33, T:0.19
Consensus pattern (30 bp):
TGCATGGCGACCTCCGACCGTGCATGGGCG
Found at i:29660 original size:29 final size:29
Alignment explanation
Indices: 29626--29684 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
29616 CCTAAATTAA
29626 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
29655 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
29684 T
1 T
29685 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:32187 original size:29 final size:29
Alignment explanation
Indices: 32153--32211 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
32143 CCTAAATTAA
32153 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
32182 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
32211 T
1 T
32212 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:32599 original size:30 final size:30
Alignment explanation
Indices: 32531--32626 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
32521 GAAGGACCTA
* * * *
32531 TCCAAAGGTCACAAAG-ACCCCGGTAACTA
1 TCCATAGGTCACAAAGAACCTCGGAAACTG
* * *
32560 TCCAGAGGTCATAAAGAACCTCGGCAACTG
1 TCCATAGGTCACAAAGAACCTCGGAAACTG
* *
32590 TCCATAGGTCCCAAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGAACCTCGG-AAACTG
32621 TCCATA
1 TCCATA
32627 TGTTCTTTAG
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 14 0.25
30 30 0.55
31 11 0.20
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.18
Consensus pattern (30 bp):
TCCATAGGTCACAAAGAACCTCGGAAACTG
Found at i:32639 original size:31 final size:31
Alignment explanation
Indices: 32604--32712 Score: 114
Period size: 31 Copynumber: 3.5 Consensus size: 31
32594 TAGGTCCCAA
* *
32604 AGAACCTAGGTAAACTGTCCATATGTTCTTT
1 AGAACATAGGTAAACTGTCCATATGTTCTCT
* * * *
32635 AGAACATAGGTATACTGTCTATATG-CCTCG
1 AGAACATAGGTAAACTGTCCATATGTTCTCT
*
32665 AAAGACATAGGTAAAACTGTCCATATGTTC-CGT
1 AGA-ACATAGGT-AAACTGTCCATATGTTCTC-T
32698 AGAACATAGGTAAAC
1 AGAACATAGGTAAAC
32713 CCTCGACTCT
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
30 4 0.06
31 34 0.55
32 21 0.34
33 3 0.05
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (31 bp):
AGAACATAGGTAAACTGTCCATATGTTCTCT
Found at i:33513 original size:63 final size:63
Alignment explanation
Indices: 33443--33604 Score: 193
Period size: 63 Copynumber: 2.6 Consensus size: 63
33433 ATCCCTAGAT
* * * * **
33443 GGGTGCATCGATGCACT-ATCTATGCATCGGTGCATAAATCCCATTCGATGTTTGTATTTT-AG
1 GGGTGCATCGATGCACTCCT-TATGCATCGATGCACAAATCACATTCGATGTTTCCATTTTAAG
* *
33505 GGGATGCATCGATGCACTCCTTATGCATCGATGCACCAATCACATTCGATGTTTCCATTTTAAT
1 GGG-TGCATCGATGCACTCCTTATGCATCGATGCACAAATCACATTCGATGTTTCCATTTTAAG
* * *
33569 GGGTGCATCGATGCACTCCCTGTGCATCGATACACA
1 GGGTGCATCGATGCACTCCTTATGCATCGATGCACA
33605 CTGAACAATT
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
62 3 0.04
63 77 0.91
64 5 0.06
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.31
Consensus pattern (63 bp):
GGGTGCATCGATGCACTCCTTATGCATCGATGCACAAATCACATTCGATGTTTCCATTTTAAG
Found at i:35692 original size:19 final size:20
Alignment explanation
Indices: 35663--35700 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
35653 AGAAATTTGT
35663 TGAAGGTGCATCGATGCATA
1 TGAAGGTGCATCGATGCATA
35683 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
35701 TAATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:35753 original size:63 final size:63
Alignment explanation
Indices: 35668--35826 Score: 212
Period size: 63 Copynumber: 2.5 Consensus size: 63
35658 TTTGTTGAAG
* * * *
35668 GTGCATCGATGCATATGAAGTGCATCGATGCATTAAT-TTAAATACAAACATCGAATGTCATCA
1 GTGCATCGATGCATAAGGAGTGCATCGATGCATTAATAATAAA-ACAAACATCGAATGCCATCA
** ** *
35731 GTGCATCGATGCATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCATAAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCATCA
*
35794 GTGCATCGATGCATCAGGAGTGCATCGATGCAT
1 GTGCATCGATGCATAAGGAGTGCATCGATGCAT
35827 GCCTCCATTA
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
63 81 0.95
64 4 0.05
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCATAAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCATCA
Found at i:37160 original size:18 final size:17
Alignment explanation
Indices: 37133--37169 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
37123 CTTAAGGAAT
37133 GATATGTGGTCCTTCGG
1 GATATGTGGTCCTTCGG
37150 GATATTGTGGTCCTTCGG
1 GATA-TGTGGTCCTTCGG
37168 GA
1 GA
37170 CATATATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.14, C:0.16, G:0.35, T:0.35
Consensus pattern (17 bp):
GATATGTGGTCCTTCGG
Found at i:37192 original size:121 final size:121
Alignment explanation
Indices: 37034--37397 Score: 674
Period size: 121 Copynumber: 3.0 Consensus size: 121
37024 CGAGGGTCTA
37034 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
37099 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGATAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
37155 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
37220 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
* *
37276 TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* **
37341 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
37397 T
1 T
37398 ATTATATGGC
Statistics
Matches: 237, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
121 237 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.36
Consensus pattern (121 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:37281 original size:18 final size:18
Alignment explanation
Indices: 37258--37293 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
37248 AGGAATGATA
37258 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
*
37276 TGTGGTCCTTTGGGACAT
1 TGTGGTCCTTCGGGACAT
37294 ATATGTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.33, T:0.36
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:37295 original size:62 final size:62
Alignment explanation
Indices: 37108--37295 Score: 137
Period size: 62 Copynumber: 3.1 Consensus size: 62
37098 TGATCCCTAG
* *
37108 CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGATATTGTGGTCCTTCGGGA
1 CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTTGGGA
* * * * * * *
37170 CATA--TATGT-ATTCTT-TGGAA-CATGTGTGAAGT-CTGGT-GAGACACATACT-TGATCC-C
1 CATATGTATATGATTCTTAAGGAATGATATGTG--GTCCT--TCG-G-GACAT--TGTGGTCCTT
*
37226 T-AG-
58 TGGGA
37229 CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTTGGGA
1 CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTTGGGA
37291 CATAT
1 CATAT
37296 ATGTATTCTT
Statistics
Matches: 89, Mismatches: 18, Indels: 38
0.61 0.12 0.26
Matches are distributed among these distances:
57 6 0.07
58 7 0.08
59 18 0.20
60 12 0.13
61 10 0.11
62 23 0.26
63 7 0.08
64 6 0.07
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.36
Consensus pattern (62 bp):
CATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTTGGGA
Found at i:37461 original size:23 final size:23
Alignment explanation
Indices: 37404--37464 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
37394 CATTATTATA
*
37404 TGGCACTACAGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
37427 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTACG
*
37450 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
37465 TTTATATGAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:37472 original size:23 final size:23
Alignment explanation
Indices: 37395--37472 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
37385 CCTTATGGAC
* *
37395 ATTATTATATGGCACTACAGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * *
37419 ATTCTACGCGGCACTACGGTGCA
1 ATTATATGTGGCACTACGGTGCA
* *
37442 ATTCTATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
37465 TTTATATG
1 ATTATATG
37473 AGCTGTGGTG
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 41 0.93
24 3 0.07
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:44692 original size:23 final size:23
Alignment explanation
Indices: 44666--44710 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
44656 CACCACAGCT
*
44666 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
44689 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
44711 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:45245 original size:149 final size:149
Alignment explanation
Indices: 44678--45291 Score: 1142
Period size: 149 Copynumber: 4.1 Consensus size: 149
44668 TATAATTGCA
*
44678 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
44742 TTCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTCACCAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTCACCAGACTTCACACATGTT
44807 CCAAAGAATATATATATATATC
130 CCAAAG-A-ATATATATATATC
44829 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
44894 TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTCACCAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTCACCAGACTTCACACATGTTC
*
44959 TAAAGAATATATATATATC
131 CAAAGAATATATATATATC
*
44978 CCGAA-GACCGCGTAGAATTGCACCGTAGTGCCATAAAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
45042 TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTCACCAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTCACCAGACTTCACACATGTTC
45107 CAAAGAATATATATATATC
131 CAAAGAATATATATATATC
*
45126 CTGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
*
45191 TCCTTAAGAATCATATACATATACTAGGGATCATATATGTGTCTCACCAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTCACCAGACTTCACACATGTTC
45256 CAAAGAATATATATATATC
131 CAAAGAATATATATATATC
45275 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
45292 CCCTCGACTC
Statistics
Matches: 453, Mismatches: 8, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
148 145 0.32
149 175 0.39
150 2 0.00
151 131 0.29
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTCACCAGACTTCACACATGTTC
CAAAGAATATATATATATC
Found at i:45249 original size:297 final size:300
Alignment explanation
Indices: 44678--45291 Score: 1146
Period size: 297 Copynumber: 2.1 Consensus size: 300
44668 TATAATTGCA
*
44678 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATAAAATAATGTCCATAAGGACCACATAGAA
44742 TTCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTCACCAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTCACCAGACTTCACACATGTT
44807 CCAAAGAATATATATATATATCCCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGAT
130 CCAAAGAATATATATATATATCCCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGAT
*
44872 GTCCATAAGGACCACATAGAATTCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTC
195 GTCCATAAGGACCACATAGAATTCCTTAAGAATCATATACATATACTAGGGATCATATATGTGTC
*
44937 TCACCAGACTTCACACATGTTCTAAAGAATATATATATATC
260 TCACCAGACTTCACACATGTTCCAAAGAATATATATATATC
*
44978 CCGAA-GACCGCGTAGAATTGCACCGTAGTGCCATAAAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATAAAATAATGTCCATAAGGACCACATAGAAT
45042 TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTCACCAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTCACCAGACTTCACACATGTTC
*
45107 CAAAG-A-ATATATATATATCCTGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATG
131 CAAAGAATATATATATATATCCCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATG
45170 TCCATAAGGACCACATAGAATTCCTTAAGAATCATATACATATACTAGGGATCATATATGTGTCT
196 TCCATAAGGACCACATAGAATTCCTTAAGAATCATATACATATACTAGGGATCATATATGTGTCT
45235 CACCAGACTTCACACATGTTCCAAAGAATATATATATATC
261 CACCAGACTTCACACATGTTCCAAAGAATATATATATATC
45275 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
45292 CCCTCGACTC
Statistics
Matches: 307, Mismatches: 5, Indels: 6
0.97 0.02 0.02
Matches are distributed among these distances:
297 164 0.53
298 13 0.04
299 125 0.41
300 5 0.02
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (300 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATAAAATAATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTCACCAGACTTCACACATGTTC
CAAAGAATATATATATATATCCCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATG
TCCATAAGGACCACATAGAATTCCTTAAGAATCATATACATATACTAGGGATCATATATGTGTCT
CACCAGACTTCACACATGTTCCAAAGAATATATATATATC
Found at i:46211 original size:18 final size:18
Alignment explanation
Indices: 46190--46224 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
46180 TCCCATCTAG
46190 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
46208 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
46225 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:46814 original size:64 final size:63
Alignment explanation
Indices: 46716--46876 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 63
46706 TAATGAAGGT
* *
46716 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT--
46779 GA
62 GA
**
46781 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGA
* *
46845 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
46877 CCTTACACAA
Statistics
Matches: 86, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
63 1 0.01
64 58 0.67
65 24 0.28
66 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATGA
Found at i:50830 original size:29 final size:30
Alignment explanation
Indices: 50769--50841 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 30
50759 GAAAATCAAA
50769 TTAAATGGGGACGGGAAAAAACTGTTTAAG
1 TTAAATGGGGACGGGAAAAAACTGTTTAAG
* * *
50799 TTAAACGGGGACGGGAAAAATC-GTTTATG
1 TTAAATGGGGACGGGAAAAAACTGTTTAAG
50828 TTAAATGGGGACGG
1 TTAAATGGGGACGG
50842 AGACGGGGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 19 0.49
30 20 0.51
ACGTcount: A:0.36, C:0.08, G:0.33, T:0.23
Consensus pattern (30 bp):
TTAAATGGGGACGGGAAAAAACTGTTTAAG
Found at i:50957 original size:38 final size:38
Alignment explanation
Indices: 50915--51110 Score: 129
Period size: 38 Copynumber: 5.2 Consensus size: 38
50905 AATAATTATT
50915 ATATATATATAATATTAATAAATTTAATTTAAATTAAC
1 ATATATATATAATATTAATAAATTTAATTTAAATTAAC
* *
50953 ATATATATATAATATTTATATATTTAATTTAAA-TAACC
1 ATATATATATAATATTAATAAATTTAATTTAAATTAA-C
** ** ****** ** **
50991 CGAT-TACCT-GGCCCGATAAATATTAA-AAATAATTATT
1 ATATATATATAATATTAATAAAT-TTAATTTA-AATTAAC
51028 ATATATATATAATATTAATAAATTTAATTTAAATTAAC
1 ATATATATATAATATTAATAAATTTAATTTAAATTAAC
* *
51066 ATATATATAT-ATA-TAAT-ATTTATATATTTAATTTAA-
1 ATATATATATAATATTAATAAATT-TA-ATTTAAATTAAC
51102 ATATATATA
1 ATATATATA
51111 CTCGGCCCGA
Statistics
Matches: 116, Mismatches: 33, Indels: 20
0.69 0.20 0.12
Matches are distributed among these distances:
35 3 0.03
36 21 0.18
37 27 0.23
38 58 0.50
39 7 0.06
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.44
Consensus pattern (38 bp):
ATATATATATAATATTAATAAATTTAATTTAAATTAAC
Found at i:51038 original size:113 final size:114
Alignment explanation
Indices: 50876--51104 Score: 399
Period size: 113 Copynumber: 2.0 Consensus size: 114
50866 TAATCTCTGT
50876 CCCGATTACTCGACCCGATAAATATTAAAAATAATTATTATATATATATAATATTAATAAATTTA
1 CCCGATTACTCGACCCGATAAATATTAAAAATAATTATTATATATATATAATATTAATAAATTTA
50941 ATTTAAATTAAC-ATATATATATAATATTTATATATTTAATTTAAATAA
66 ATTTAAATTAACAATATATATATAATATTTATATATTTAATTTAAATAA
*
50989 CCCGATTAC-CTGGCCCGATAAATATTAAAAATAATTATTATATATATATAATATTAATAAATTT
1 CCCGATTACTC-GACCCGATAAATATTAAAAATAATTATTATATATATATAATATTAATAAATTT
51053 AATTTAAATTAACATATATATATATATAATATTTATATATTTAATTTAAATA
65 AATTTAAATTAAC--A-ATATATATATAATATTTATATATTTAATTTAAATA
51105 TATATACTCG
Statistics
Matches: 110, Mismatches: 1, Indels: 6
0.94 0.01 0.05
Matches are distributed among these distances:
112 1 0.01
113 74 0.67
117 35 0.32
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (114 bp):
CCCGATTACTCGACCCGATAAATATTAAAAATAATTATTATATATATATAATATTAATAAATTTA
ATTTAAATTAACAATATATATATAATATTTATATATTTAATTTAAATAA
Found at i:51083 original size:36 final size:38
Alignment explanation
Indices: 51028--51110 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 38
51018 AATAATTATT
51028 ATATATATATAATATTAATAAATT-TA-ATTTAAATTAA
1 ATATATATATAATATTAAT-AATTATATATTTAAATTAA
* *
51065 CATATATATAT-ATA-TAATATTTATATATTTAATTTAA
1 -ATATATATATAATATTAATAATTATATATTTAAATTAA
51102 ATATATATA
1 ATATATATA
51111 CTCGGCCCGA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
35 3 0.07
36 15 0.37
37 13 0.32
38 10 0.24
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (38 bp):
ATATATATATAATATTAATAATTATATATTTAAATTAA
Found at i:53434 original size:2 final size:2
Alignment explanation
Indices: 53427--53514 Score: 56
Period size: 2 Copynumber: 50.0 Consensus size: 2
53417 GAAAATATTT
* *
53427 TA TA TA TA -A T- TA -A TA TA -A AA TA TA TA -A AA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
53463 TA TA TA -A T- TA -A TA TA -A AA AA TA T- TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53499 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
53515 ATCGAGGCGG
Statistics
Matches: 71, Mismatches: 3, Indels: 24
0.72 0.03 0.24
Matches are distributed among these distances:
1 12 0.17
2 59 0.83
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:53458 original size:34 final size:34
Alignment explanation
Indices: 53418--53502 Score: 134
Period size: 34 Copynumber: 2.5 Consensus size: 34
53408 CTCGAATCCG
* *
53418 AAAATATTTTATATATAATTAATATAAAATATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
53452 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
* *
53486 TATATATTATATATATA
1 AAAATATTATATATATA
53503 TATATATATA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:53475 original size:27 final size:30
Alignment explanation
Indices: 53447--53510 Score: 89
Period size: 27 Copynumber: 2.2 Consensus size: 30
53437 TAATATAAAA
53447 TATATAAAATATTATATA-TATA-AT-TAA
1 TATATAAAATATTATATATTATATATATAA
*
53474 TATAAAAAATATTATATATTATATATATATA
1 TATATAAAATATTATATATTATATATATA-A
53505 TATATA
1 TATATA
53511 TATAATCGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 17 0.55
28 4 0.13
29 2 0.06
30 2 0.06
31 6 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
TATATAAAATATTATATATTATATATATAA
Found at i:53514 original size:25 final size:24
Alignment explanation
Indices: 53421--53514 Score: 74
Period size: 23 Copynumber: 4.1 Consensus size: 24
53411 GAATCCGAAA
*
53421 ATATTTTATATATA-ATTA-ATAT
1 ATATTATATATATATATTATATAT
* * *
53443 AAAATATATA-AAATATTATATAT
1 ATATTATATATATATATTATATAT
* * *
53466 ATAATTA-ATATAAAAAATAT-TAT
1 AT-ATTATATATATATATTATATAT
53489 ATATTATATATATATA-TATATAT
1 ATATTATATATATATATTATATAT
53512 ATA
1 ATA
53515 ATCGAGGCGG
Statistics
Matches: 56, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
21 2 0.04
22 18 0.32
23 26 0.46
24 10 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATATTATATATATATATTATATAT
Found at i:53904 original size:23 final size:25
Alignment explanation
Indices: 53878--53937 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 25
53868 TGTTATTAAC
*
53878 TTTTAAAAATTATTTTTTTAAA-A-
1 TTTTAAAAATTATTATTTTAAATAT
** *
53901 TTTTAACCATCATTATTTTAAATAT
1 TTTTAAAAATTATTATTTTAAATAT
53926 TTTTAAAAATTA
1 TTTTAAAAATTA
53938 AATTTTATAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
23 18 0.64
24 1 0.04
25 9 0.32
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (25 bp):
TTTTAAAAATTATTATTTTAAATAT
Found at i:57128 original size:14 final size:14
Alignment explanation
Indices: 57109--57137 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
57099 TGAATCTATA
57109 AAAAAAATTAAATT
1 AAAAAAATTAAATT
57123 AAAAAAATTAAATT
1 AAAAAAATTAAATT
57137 A
1 A
57138 TATATTGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAAAAATTAAATT
Found at i:58118 original size:11 final size:11
Alignment explanation
Indices: 58102--58142 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
58092 TATATTTTAA
58102 AAAATATTTTT
1 AAAATATTTTT
* *
58113 AAAATATATAT
1 AAAATATTTTT
58124 AAAATATTTTT
1 AAAATATTTTT
58135 AAAATATT
1 AAAATATT
58143 GTGTCATTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:62215 original size:87 final size:87
Alignment explanation
Indices: 62067--62241 Score: 278
Period size: 87 Copynumber: 2.0 Consensus size: 87
62057 TTTCTCATTC
* *
62067 TACAATCGTTTAAATTAATTAGAGTGAATCTTAAAGAAGCATAACTTTAGATAATTGCTTACAAC
1 TACAATCGTTTAAATTAATTAGAGTCAATCTTAAAGAAGCATAACTTTAAATAATTGCTTACAAC
*
62132 ATTTATTTAATGTTAAGAGATT
66 ATTTATTTAATGTTAAAAGATT
* * * * *
62154 TACAATCTTTTAAATTAATTAGAGTCAATCTTTAGGAAGCATAACTTTAAATAATTTCTTACAAT
1 TACAATCGTTTAAATTAATTAGAGTCAATCTTAAAGAAGCATAACTTTAAATAATTGCTTACAAC
62219 ATTTATTTAATGTTAAAAGATT
66 ATTTATTTAATGTTAAAAGATT
62241 T
1 T
62242 TGTATTTGTC
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 80 1.00
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (87 bp):
TACAATCGTTTAAATTAATTAGAGTCAATCTTAAAGAAGCATAACTTTAAATAATTGCTTACAAC
ATTTATTTAATGTTAAAAGATT
Found at i:62610 original size:26 final size:26
Alignment explanation
Indices: 62574--62640 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
62564 TTTATTTCCT
62574 AAATTTTATAA-TT-TCTTCCCTACTGA
1 AAATTTTATAAGTTCTCTT--CTACTGA
*
62600 AAATTTTATAAGTTCTCTTCTACTTA
1 AAATTTTATAAGTTCTCTTCTACTGA
62626 AAATTTTATAAGTTC
1 AAATTTTATAAGTTC
62641 ACTCCAACAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
26 32 0.84
27 2 0.05
28 4 0.11
ACGTcount: A:0.33, C:0.15, G:0.04, T:0.48
Consensus pattern (26 bp):
AAATTTTATAAGTTCTCTTCTACTGA
Found at i:64023 original size:16 final size:17
Alignment explanation
Indices: 63996--64030 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
63986 TAATTAAGTA
63996 AAAAATACATTTATTTT
1 AAAAATACATTTATTTT
64013 AAAAATA-ATTTATTTT
1 AAAAATACATTTATTTT
64029 AA
1 AA
64031 GGATTTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
AAAAATACATTTATTTT
Found at i:66806 original size:19 final size:20
Alignment explanation
Indices: 66779--66828 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
66769 GCTCACTAAC
*
66779 TATTAATTATTA-ATAAAAA
1 TATTTATTATTAGATAAAAA
*
66798 TATTTATTATTAGATAAATA
1 TATTTATTATTAGATAAAAA
66818 TATTTAATTAT
1 TATTT-ATTAT
66829 CACATCAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 11 0.41
20 11 0.41
21 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TATTTATTATTAGATAAAAA
Found at i:66838 original size:21 final size:20
Alignment explanation
Indices: 66791--66842 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
66781 TTAATTATTA
* * *
66791 ATAAAAATATTTATTATTAG
1 ATAAATATATTTATTATCAC
66811 ATAAATATATTTAATTATCAC
1 ATAAATATATTT-ATTATCAC
*
66832 ATCAATA-ATTT
1 ATAAATATATTT
66843 TTAACAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (20 bp):
ATAAATATATTTATTATCAC
Found at i:68944 original size:38 final size:38
Alignment explanation
Indices: 68900--68979 Score: 101
Period size: 37 Copynumber: 2.1 Consensus size: 38
68890 TTTTACTAAA
* *
68900 TATTATTTATCTATATTTA-TCTGTTTGATTTA-TTTTAT
1 TATTA-TTAT-TATATTAATTCTGTTTCATTTATTTTTAT
*
68938 TATTATTATTATATTAATTCTTTTTCATTTATTTTTAT
1 TATTATTATTATATTAATTCTGTTTCATTTATTTTTAT
68976 TATT
1 TATT
68980 TTCCCCTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 7 0.19
37 15 0.41
38 15 0.41
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (38 bp):
TATTATTATTATATTAATTCTGTTTCATTTATTTTTAT
Found at i:72786 original size:17 final size:16
Alignment explanation
Indices: 72764--72805 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
72754 AATCGCAGTA
72764 AATTCATACATACACAT
1 AATTCAT-CATACACAT
*
72781 AATTCATCATTCACAT
1 AATTCATCATACACAT
72797 -ATT-ATCATA
1 AATTCATCATA
72806 TAATCACATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 5 0.22
15 3 0.13
16 8 0.35
17 7 0.30
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (16 bp):
AATTCATCATACACAT
Found at i:73005 original size:22 final size:22
Alignment explanation
Indices: 72988--73054 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
72978 CTCGTATAAA
72988 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
73010 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
73032 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
73054 T
1 T
73055 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:74671 original size:22 final size:22
Alignment explanation
Indices: 74631--74692 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
74621 TTTTCCTTTA
*
74631 GGGGGAATCGGTTCGCCCCCCAT
1 GGGGGTATCGGTTC-CCCCCCAT
74654 GGGGGTATCGGTTCCCCCCCAT
1 GGGGGTATCGGTTCCCCCCCAT
74676 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
74693 TATGACATAC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 25 0.66
23 13 0.34
ACGTcount: A:0.10, C:0.34, G:0.35, T:0.21
Consensus pattern (22 bp):
GGGGGTATCGGTTCCCCCCCAT
Found at i:74744 original size:21 final size:21
Alignment explanation
Indices: 74720--74764 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
74710 TCTTGTTCGT
* *
74720 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
74741 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
74762 TTG
1 TTG
74765 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:76054 original size:7 final size:7
Alignment explanation
Indices: 76042--76066 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
76032 TTTCATTTCT
76042 TTATTCC
1 TTATTCC
76049 TTATTCC
1 TTATTCC
76056 TTATTCC
1 TTATTCC
76063 TTAT
1 TTAT
76067 ACATTAATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (7 bp):
TTATTCC
Found at i:77839 original size:17 final size:16
Alignment explanation
Indices: 77817--77858 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
77807 AATCGCAGTA
77817 AATTCATACATACACAT
1 AATTCAT-CATACACAT
*
77834 AATTCATCATTCACAT
1 AATTCATCATACACAT
77850 -ATT-ATCATA
1 AATTCATCATA
77859 TAATCACATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 5 0.22
15 3 0.13
16 8 0.35
17 7 0.30
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (16 bp):
AATTCATCATACACAT
Found at i:78058 original size:22 final size:22
Alignment explanation
Indices: 78041--78107 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
78031 CTCGTATAAA
78041 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
78063 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
78085 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
78107 T
1 T
78108 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:79706 original size:23 final size:23
Alignment explanation
Indices: 79674--79736 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
79664 TTTTCCTTTA
*
79674 GGGGGAATCGGTTCCCCCCCCAT
1 GGGGGTATCGGTTCCCCCCCCAT
79697 GGGGGTATCGGTTCCCCCCCCAT
1 GGGGGTATCGGTTCCCCCCCCAT
79720 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
79737 TATGACATAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.10, C:0.37, G:0.33, T:0.21
Consensus pattern (23 bp):
GGGGGTATCGGTTCCCCCCCCAT
Found at i:79788 original size:21 final size:21
Alignment explanation
Indices: 79764--79807 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
79754 TCTTGTTCGT
* *
79764 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
79785 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
79806 TT
1 TT
79808 ACCCAGAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:81544 original size:40 final size:40
Alignment explanation
Indices: 81493--81594 Score: 120
Period size: 40 Copynumber: 2.6 Consensus size: 40
81483 TTTAAAGAAT
* *
81493 ATTTTGTCTCGCTTGAGATGGTTTCCCTCGAAAAAAAAAG
1 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAAAAAAAG
* *
81533 ATTTTATCTCGCTTGAGATAGTTTCCCTTG--AAACAAA-
1 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAAAAAAAG
* * *
81570 ATTATATCTCTCTTGAGACAGTTTC
1 ATTTTATCTCGCTTGAGATAGTTTC
81595 TCTTGAGACA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
37 22 0.40
38 6 0.11
40 27 0.49
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (40 bp):
ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAAAAAAAG
Found at i:81587 original size:37 final size:38
Alignment explanation
Indices: 81499--81600 Score: 116
Period size: 37 Copynumber: 2.7 Consensus size: 38
81489 GAATATTTTG
* * *
81499 TCTCGCTTGAGATGGTTTCCCTCGAAAAAAAAAGATTTTA
1 TCTCGCTTGAGATAGTTTCCCTTG--AAAAAAAGATTATA
*
81539 TCTCGCTTGAGATAGTTTCCCTTGAAACAAA-ATTATA
1 TCTCGCTTGAGATAGTTTCCCTTGAAAAAAAGATTATA
* * *
81576 TCTCTCTTGAGACAGTTTCTCTTGA
1 TCTCGCTTGAGATAGTTTCCCTTGA
81601 GACAGTTTCT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
37 27 0.49
38 6 0.11
40 22 0.40
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (38 bp):
TCTCGCTTGAGATAGTTTCCCTTGAAAAAAAGATTATA
Found at i:81598 original size:15 final size:15
Alignment explanation
Indices: 81578--81615 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
81568 AAATTATATC
81578 TCTCTTGAGACAGTT
1 TCTCTTGAGACAGTT
81593 TCTCTTGAGACAGTT
1 TCTCTTGAGACAGTT
81608 TCTCTTGA
1 TCTCTTGA
81616 AACATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.42
Consensus pattern (15 bp):
TCTCTTGAGACAGTT
Found at i:81742 original size:65 final size:68
Alignment explanation
Indices: 81593--81753 Score: 204
Period size: 65 Copynumber: 2.4 Consensus size: 68
81583 TGAGACAGTT
* *
81593 TCTCTTGAGACAGTTTCTCTTGAAACATAAAAATTTGAAAACATTTCCCTCGAAACAGAAAACTT
1 TCTCTTGAGATAGTTTCTCTTGAAACATAAAAATTTGAAAACATTTCACTCGAAACAG-AAACTT
81658 TGTC
65 TGTC
* * * * *
81662 TC-CATTGAGATAGTTTCTCTTGAAACATAAACA-TTGAAAACATTTCATTTGAAA-TG-AATTT
1 TCTC-TTGAGATAGTTTCTCTTGAAACATAAAAATTTGAAAACATTTCACTCGAAACAGAAACTT
81723 TGTC
65 TGTC
*
81727 TCTCTTGAGATAGTTTCCCTTGAAACA
1 TCTCTTGAGATAGTTTCTCTTGAAACA
81754 AATTTTGTCT
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
65 32 0.39
66 1 0.01
67 1 0.01
68 19 0.23
69 29 0.35
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (68 bp):
TCTCTTGAGATAGTTTCTCTTGAAACATAAAAATTTGAAAACATTTCACTCGAAACAGAAACTTT
GTC
Found at i:81758 original size:36 final size:36
Alignment explanation
Indices: 81718--81789 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
81708 ATTTGAAATG
* *
81718 AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
*
81754 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
81790 TAAACTGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (36 bp):
AATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
Found at i:81923 original size:128 final size:130
Alignment explanation
Indices: 81756--82050 Score: 452
Period size: 128 Copynumber: 2.3 Consensus size: 130
81746 TTGAAACAAA
* *
81756 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTGTGAAAATAGTTTCCCTTGAAACAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTATGAAAACAGTTTCCCTTGAAACAA
* *
81821 AATCTTTGAATATGTTTTACATTAAACAAATTTCATCTCCCTTGAGACAGTTTC-TTTTG-GAAG
66 AATATTTGAATATGTTTTACATTAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTTGAAAAG
*
81884 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTATGAAGACAGTTTCCCTTGAAACAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTATGAAAACAGTTTCCCTTGAAACAA
* **
81949 AATATTTGAATATGTTTTACATTAAACTAATTTTGTCTCCCTTGAGACAGTTTCTTTTTGAAACA
66 AATATTTGAATATGTTTTACATTAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTTG--A-A
82014 AAG
128 AAG
*
82017 TTTTGTCTCCTTTGAG-CATGTTTCTCTTGAAACA
1 TTTTGTCTCCCTTGAGACA-GTTTCTCTTGAAACA
82051 CCAAACCTTT
Statistics
Matches: 152, Mismatches: 9, Indels: 7
0.90 0.05 0.04
Matches are distributed among these distances:
128 112 0.74
129 5 0.03
132 2 0.01
133 33 0.22
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (130 bp):
TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACTATGAAAACAGTTTCCCTTGAAACAA
AATATTTGAATATGTTTTACATTAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTTGAAAAG
Found at i:82032 original size:38 final size:37
Alignment explanation
Indices: 81979--82050 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 37
81969 ATTAAACTAA
*
81979 TTTTGTCTCCCTTGAGACA-GTTTCTTTTTGAAACAAAG
1 TTTTGTCTCCCTTGAG-CATGTTTC-TCTTGAAACAAAG
*
82017 TTTTGTCTCCTTTGAGCATGTTTCTCTTGAAACA
1 TTTTGTCTCCCTTGAGCATGTTTCTCTTGAAACA
82051 CCAAACCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
37 11 0.35
38 20 0.65
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.44
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGCATGTTTCTCTTGAAACAAAG
Found at i:83571 original size:38 final size:38
Alignment explanation
Indices: 83529--83608 Score: 101
Period size: 37 Copynumber: 2.1 Consensus size: 38
83519 TTTAACTAAA
* *
83529 TATTATTTATCTATATTTA-TCTGTTTGATTTA-TTTTAT
1 TATTA-TTAT-TATATTAATTCTGTTTCATTTATTTTTAT
*
83567 TATTATTATTATATTAATTCTTTTTCATTTATTTTTAT
1 TATTATTATTATATTAATTCTGTTTCATTTATTTTTAT
83605 TATT
1 TATT
83609 TTCCCCTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 7 0.19
37 15 0.41
38 15 0.41
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (38 bp):
TATTATTATTATATTAATTCTGTTTCATTTATTTTTAT
Found at i:84190 original size:98 final size:98
Alignment explanation
Indices: 84021--84213 Score: 314
Period size: 98 Copynumber: 2.0 Consensus size: 98
84011 ATATATAAAG
* * *
84021 ATATCTATTAGAAGGAGCTCCATCATTATTCTGAAGGTGAAGATAGAACCCTCCATCATTGGTTA
1 ATATCAATTAGAAGGAGCTCAATCATTAATCTGAAGGTGAAGATAGAACCCTCCATCATTGGTTA
*
84086 AGTGATATATTTTCTGTTAAACAATATGTGTGT
66 AGTGATAAATTTTCTGTTAAACAATATGTGTGT
* *
84119 ATATCAATTAGAAGGAGCTCAATGATTAATCTGAAGGTGAAGATTGAACCCTCCATCATTGGTTA
1 ATATCAATTAGAAGGAGCTCAATCATTAATCTGAAGGTGAAGATAGAACCCTCCATCATTGGTTA
* *
84184 AGTGATAAATTTTCTGTTAAATAATGTGTG
66 AGTGATAAATTTTCTGTTAAACAATATGTG
84214 CGCGTGTGTG
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 87 1.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (98 bp):
ATATCAATTAGAAGGAGCTCAATCATTAATCTGAAGGTGAAGATAGAACCCTCCATCATTGGTTA
AGTGATAAATTTTCTGTTAAACAATATGTGTGT
Found at i:84222 original size:2 final size:2
Alignment explanation
Indices: 84217--84257 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
84207 ATGTGTGCGC
* * *
84217 GT GT GT GT GT GC AT GT GT GT GT GT GG GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
84258 GGTGCGCGTG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.02, C:0.02, G:0.51, T:0.44
Consensus pattern (2 bp):
GT
Found at i:84223 original size:12 final size:12
Alignment explanation
Indices: 84208--84268 Score: 59
Period size: 12 Copynumber: 5.1 Consensus size: 12
84198 TGTTAAATAA
*
84208 TGTGTGCGCGTG
1 TGTGTGTGCGTG
*
84220 TGTGTGTGCATG
1 TGTGTGTGCGTG
* *
84232 TGTGTGTGTGGG
1 TGTGTGTGCGTG
*
84244 TGTGTGTGTGTG
1 TGTGTGTGCGTG
* *
84256 TGGGTGCGCGTG
1 TGTGTGTGCGTG
84268 T
1 T
84269 AATACCCCAA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.02, C:0.08, G:0.51, T:0.39
Consensus pattern (12 bp):
TGTGTGTGCGTG
Found at i:84227 original size:14 final size:13
Alignment explanation
Indices: 84208--84253 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
84198 TGTTAAATAA
84208 TGTGTGCGCGTGTG
1 TGTGTGCG-GTGTG
*
84222 TGTGTGCATGTGTG
1 TGTGTGC-GGTGTG
84236 TGTGTG-GGTGTG
1 TGTGTGCGGTGTG
84248 TGTGTG
1 TGTGTG
84254 TGTGGGTGCG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 11 0.38
14 18 0.62
ACGTcount: A:0.02, C:0.07, G:0.50, T:0.41
Consensus pattern (13 bp):
TGTGTGCGGTGTG
Found at i:84916 original size:2 final size:2
Alignment explanation
Indices: 84909--85013 Score: 71
Period size: 2 Copynumber: 56.0 Consensus size: 2
84899 TCGAGCTGGG
* * * *
84909 TA TA TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
84949 TA TA TT TT TA -A TT TA -A TT TA AA TT TA T- TA -A TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
84986 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
85014 ATTATATTTT
Statistics
Matches: 78, Mismatches: 18, Indels: 14
0.71 0.16 0.13
Matches are distributed among these distances:
1 7 0.09
2 71 0.91
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:84970 original size:37 final size:36
Alignment explanation
Indices: 84909--85014 Score: 122
Period size: 37 Copynumber: 2.9 Consensus size: 36
84899 TCGAGCTGGG
84909 TATATATATATATATTTAAATTAAATATATAAATAT
1 TATATATATATATATTTAAATTAAATATATAAATAT
* * * * *
84945 TATATATATTTTTAATTTAATTTAAATTTATTAATAT
1 TATATATATATAT-ATTTAAATTAAATATATAAATAT
* * *
84982 TATATATATATATATATATATATATATATATAA
1 TATATATATATATATTTAAAT-TAAATATATAA
85015 TTATATTTTA
Statistics
Matches: 55, Mismatches: 13, Indels: 3
0.77 0.18 0.04
Matches are distributed among these distances:
36 16 0.29
37 39 0.71
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (36 bp):
TATATATATATATATTTAAATTAAATATATAAATAT
Found at i:85019 original size:8 final size:9
Alignment explanation
Indices: 84978--85020 Score: 56
Period size: 8 Copynumber: 5.0 Consensus size: 9
84968 AAATTTATTA
84978 ATATTATAT
1 ATATTATAT
84987 ATA-TATAT
1 ATATTATAT
84995 ATA-TATAT
1 ATATTATAT
85003 ATA-TATAT
1 ATATTATAT
85011 ATAATTATAT
1 AT-ATTATAT
85021 TTTAATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 23 0.72
9 4 0.12
10 5 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
ATATTATAT
Found at i:85119 original size:35 final size:35
Alignment explanation
Indices: 85080--85151 Score: 101
Period size: 35 Copynumber: 2.0 Consensus size: 35
85070 CCCGCCCCTG
*
85080 TCCCCGTTTAGCATAAACA-ATTTTCCCCGTCCCCA
1 TCCCCGTTTAACATAAA-AGATTTTCCCCGTCCCCA
*
85115 TCCCCGTTTAACATAAAAGGTTTTTCCCCGTCCCCA
1 TCCCCGTTTAACATAAAA-GATTTTCCCCGTCCCCA
85151 T
1 T
85152 TTAATTCAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 1 0.03
35 16 0.48
36 16 0.48
ACGTcount: A:0.22, C:0.38, G:0.10, T:0.31
Consensus pattern (35 bp):
TCCCCGTTTAACATAAAAGATTTTCCCCGTCCCCA
Found at i:92825 original size:27 final size:27
Alignment explanation
Indices: 92794--92861 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
92784 TCTATTTACA
92794 AAATCACATCTCTATAGGAATGGTAAC
1 AAATCACATCTCTATAGGAATGGTAAC
*
92821 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCACATCTCTATAGGAATGGTAAC
92848 AAAT--CATCTCTATA
1 AAATCACATCTCTATA
92862 ATTCCTACAC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
25 9 0.23
27 30 0.77
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (27 bp):
AAATCACATCTCTATAGGAATGGTAAC
Done.