Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 94 of 316
Found at i:28750049 original size:6 final size:6
Alignment explanation
Indices: 28750038--28750076 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
28750028 AGTTCATTTG
* *
28750038 TTTTAT TTTTAT TTTTAT GTTTAT GTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
28750077 GTTAGACTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.15, C:0.00, G:0.05, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:28751902 original size:19 final size:19
Alignment explanation
Indices: 28751880--28751923 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
28751870 CCATACAGCT
* *
28751880 TGGGCATTTCCATATGGGC
1 TGGGCATTTCCACAAGGGC
*
28751899 TGGGTATTTCCACAAGGGC
1 TGGGCATTTCCACAAGGGC
28751918 TGGGCA
1 TGGGCA
28751924 CACGCCCGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.18, C:0.20, G:0.34, T:0.27
Consensus pattern (19 bp):
TGGGCATTTCCACAAGGGC
Found at i:28769293 original size:22 final size:24
Alignment explanation
Indices: 28769246--28769294 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
28769236 TATTTGAAAT
*
28769246 ATTTTATAATATATGTTTTTTAAA
1 ATTTTATAATATATGATTTTTAAA
*
28769270 ATTTTA-AATATAT-ATTTTTGAA
1 ATTTTATAATATATGATTTTTAAA
28769292 ATT
1 ATT
28769295 AATTTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 10 0.43
23 7 0.30
24 6 0.26
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
ATTTTATAATATATGATTTTTAAA
Found at i:28769465 original size:13 final size:13
Alignment explanation
Indices: 28769435--28769464 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
28769425 TTTAAATATT
28769435 TAAAATTTTTAAA
1 TAAAATTTTTAAA
28769448 TAAAATTTTT-AA
1 TAAAATTTTTAAA
28769460 TAAAA
1 TAAAA
28769465 ACTTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TAAAATTTTTAAA
Found at i:28769503 original size:10 final size:11
Alignment explanation
Indices: 28769479--28769508 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
28769469 TAAAATGGCT
28769479 AAATATATTTAA
1 AAATA-ATTTAA
28769491 AAATAATTTAA
1 AAATAATTTAA
28769502 AAATAAT
1 AAATAAT
28769509 AATTTAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AAATAATTTAA
Found at i:28769511 original size:14 final size:15
Alignment explanation
Indices: 28769488--28769520 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
28769478 TAAATATATT
28769488 TAAA-AATAATTTAA
1 TAAATAATAATTTAA
28769502 -AAATAATAATTTAA
1 TAAATAATAATTTAA
28769516 TAAAT
1 TAAAT
28769521 TCTATGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.18
14 10 0.59
15 4 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAATAATAATTTAA
Found at i:28769590 original size:13 final size:14
Alignment explanation
Indices: 28769563--28769595 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
28769553 TAAATTTTTT
*
28769563 AAATTTTTTTATAA
1 AAATTTTATTATAA
28769577 AAATTTTATT-TAA
1 AAATTTTATTATAA
28769590 AAATTT
1 AAATTT
28769596 CAATGTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AAATTTTATTATAA
Found at i:28769637 original size:20 final size:21
Alignment explanation
Indices: 28769601--28769769 Score: 87
Period size: 22 Copynumber: 8.3 Consensus size: 21
28769591 AATTTCAATG
28769601 TTTAAATATTATTAAAAAATATA
1 TTTAAA-ATT-TTAAAAAATATA
*
28769624 TTTAATA-TTTAAAAAATAATA
1 TTTAAAATTTTAAAAAAT-ATA
28769645 TTTAAAATTTTAAAAAATA-A
1 TTTAAAATTTTAAAAAATATA
* * *
28769665 TTTCAAA----AATATA-ATA
1 TTTAAAATTTTAAAAAATATA
* *
28769681 TTCAAAATTTAAAAAAAATA-A
1 TTTAAAATTT-TAAAAAATATA
* *
28769702 TTTC--A----AAAATATATA
1 TTTAAAATTTTAAAAAATATA
*
28769717 TTTAAAATTTTAGAAAATAATA
1 TTTAAAATTTTAAAAAAT-ATA
28769739 TTTAAAATTTTAAAAATTATATA
1 TTTAAAATTTTAAAAA--ATATA
28769762 TTATAAAA
1 TT-TAAAA
28769770 CATTTCAAAT
Statistics
Matches: 110, Mismatches: 16, Indels: 39
0.67 0.10 0.24
Matches are distributed among these distances:
14 7 0.06
15 5 0.05
16 10 0.09
17 1 0.01
19 1 0.01
20 16 0.15
21 23 0.21
22 30 0.27
23 10 0.09
24 7 0.06
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (21 bp):
TTTAAAATTTTAAAAAATATA
Found at i:28769645 original size:21 final size:22
Alignment explanation
Indices: 28769601--28769665 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
28769591 AATTTCAATG
28769601 TTTAAATATTATTAAAAAAT-ATA
1 TTTAAA-ATT-TTAAAAAATAATA
*
28769624 TTTAATA-TTTAAAAAATAATA
1 TTTAAAATTTTAAAAAATAATA
28769645 TTTAAAATTTTAAAAAATAAT
1 TTTAAAATTTTAAAAAATAAT
28769666 TTCAAAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
20 9 0.24
21 10 0.26
22 14 0.37
23 5 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTAAAATTTTAAAAAATAATA
Found at i:28769678 original size:14 final size:14
Alignment explanation
Indices: 28769650--28769723 Score: 56
Period size: 14 Copynumber: 5.7 Consensus size: 14
28769640 TAATATTTAA
*
28769650 AATTTTAAAAA-AT
1 AATTTCAAAAATAT
28769663 AATTTCAAAAATAT
1 AATTTCAAAAATAT
*
28769677 AATATTC-AAAATTT
1 AAT-TTCAAAAATAT
28769691 AA----AAAAA-AT
1 AATTTCAAAAATAT
28769700 AATTTCAAAAATAT
1 AATTTCAAAAATAT
28769714 ATATTT-AAAA
1 A-ATTTCAAAA
28769724 TTTTAGAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 17
0.71 0.04 0.25
Matches are distributed among these distances:
9 3 0.06
10 4 0.08
13 15 0.31
14 20 0.41
15 7 0.14
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (14 bp):
AATTTCAAAAATAT
Found at i:28769679 original size:36 final size:36
Alignment explanation
Indices: 28769630--28769737 Score: 159
Period size: 36 Copynumber: 3.1 Consensus size: 36
28769620 TATATTTAAT
28769630 ATTT-AAAAA-ATAATATTTAAAATTTTAAAAAATA
1 ATTTCAAAAATATAATATTTAAAATTTTAAAAAATA
* *
28769664 ATTTCAAAAATATAATATTCAAAATTTAAAAAAAATA
1 ATTTCAAAAATATAATATTTAAAATTT-TAAAAAATA
*
28769701 ATTTCAAAAATAT-ATATTTAAAATTTTAGAAAATA
1 ATTTCAAAAATATAATATTTAAAATTTTAAAAAATA
28769736 AT
1 AT
28769738 ATTTAAAATT
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
34 4 0.06
35 14 0.21
36 27 0.41
37 21 0.32
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (36 bp):
ATTTCAAAAATATAATATTTAAAATTTTAAAAAATA
Found at i:28769686 original size:15 final size:13
Alignment explanation
Indices: 28769650--28769723 Score: 50
Period size: 13 Copynumber: 5.8 Consensus size: 13
28769640 TAATATTTAA
*
28769650 AATTTTAAAAAAT
1 AATTTCAAAAAAT
28769663 AATTTCAAAAATAT
1 AATTTCAAAAA-AT
28769677 AATATTC--AAAAT
1 AAT-TTCAAAAAAT
**
28769689 --TTAAAAAAAAT
1 AATTTCAAAAAAT
28769700 AATTTCAAAAATAT
1 AATTTCAAAAA-AT
28769714 ATATTT-AAAA
1 A-ATTTCAAAA
28769724 TTTTAGAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
9 1 0.02
10 1 0.02
11 5 0.10
12 2 0.04
13 20 0.42
14 12 0.25
15 7 0.15
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (13 bp):
AATTTCAAAAAAT
Found at i:28769711 original size:23 final size:23
Alignment explanation
Indices: 28769663--28769709 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
28769653 TTTAAAAAAT
* *
28769663 AATTTCAAAAATATAATATTCAA
1 AATTTAAAAAAAATAATATTCAA
28769686 AATTTAAAAAAAATAAT-TTCAA
1 AATTTAAAAAAAATAATATTCAA
28769708 AA
1 AA
28769710 ATATATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (23 bp):
AATTTAAAAAAAATAATATTCAA
Found at i:28769733 original size:23 final size:22
Alignment explanation
Indices: 28769700--28769795 Score: 97
Period size: 22 Copynumber: 4.3 Consensus size: 22
28769690 TAAAAAAAAT
*
28769700 AATTTCAAAAATATATATTTAA
1 AATTTTAAAAATATATATTTAA
28769722 AATTTTAGAAAATA-ATATTTAA
1 AATTTTA-AAAATATATATTTAA
28769744 AATTTTAAAAATTATATATTATAA
1 AATTTTAAAAA-TATATATT-TAA
* * * *
28769768 AACATTT-CAAATATACATTTTA
1 AA-TTTTAAAAATATATATTTAA
28769790 AATTTT
1 AATTTT
28769796 TTAAAATTAA
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
21 7 0.11
22 27 0.43
23 18 0.29
24 8 0.13
25 3 0.05
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (22 bp):
AATTTTAAAAATATATATTTAA
Found at i:28769859 original size:17 final size:17
Alignment explanation
Indices: 28769846--28769897 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
28769836 AATAAAACAA
28769846 AAAGAAAAAGAAAAAACT
1 AAAGAAAAAGAAAAAA-T
*
28769864 TAA-AAAAAGAAAAAAATT
1 AAAGAAAAAG-AAAAAA-T
28769882 AAAGAAAAAGAAAAAA
1 AAAGAAAAAGAAAAAA
28769898 GTTAAAAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 6 0.21
18 17 0.59
19 6 0.21
ACGTcount: A:0.81, C:0.02, G:0.10, T:0.08
Consensus pattern (17 bp):
AAAGAAAAAGAAAAAAT
Found at i:28769878 original size:19 final size:18
Alignment explanation
Indices: 28769850--28769921 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 18
28769840 AAACAAAAAG
*
28769850 AAAAAG-AAAAAACTTAA
1 AAAAAGAAAAAAAATTAA
28769867 AAAAAG-AAAAAAATTAA
1 AAAAAGAAAAAAAATTAA
*
28769884 AGAAAA-AGAAAAAAGTTAA
1 A-AAAAGA-AAAAAAATTAA
28769903 AAAGAAGTAAAAAAAATTA
1 AAA-AAG-AAAAAAAATTA
28769922 GAATTAGCGT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
17 17 0.37
18 6 0.13
19 13 0.28
20 9 0.20
21 1 0.02
ACGTcount: A:0.76, C:0.01, G:0.10, T:0.12
Consensus pattern (18 bp):
AAAAAGAAAAAAAATTAA
Found at i:28769886 original size:36 final size:38
Alignment explanation
Indices: 28769846--28769917 Score: 121
Period size: 36 Copynumber: 1.9 Consensus size: 38
28769836 AATAAAACAA
28769846 AAAGAAAAAGAAAAAACTTAAAAA-AAG-AAAAAAATT
1 AAAGAAAAAGAAAAAACTTAAAAAGAAGTAAAAAAATT
*
28769882 AAAGAAAAAGAAAAAAGTTAAAAAGAAGTAAAAAAA
1 AAAGAAAAAGAAAAAACTTAAAAAGAAGTAAAAAAA
28769918 ATTAGAATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
36 23 0.70
37 3 0.09
38 7 0.21
ACGTcount: A:0.78, C:0.01, G:0.11, T:0.10
Consensus pattern (38 bp):
AAAGAAAAAGAAAAAACTTAAAAAGAAGTAAAAAAATT
Found at i:28773211 original size:16 final size:15
Alignment explanation
Indices: 28773192--28773238 Score: 60
Period size: 14 Copynumber: 3.1 Consensus size: 15
28773182 TAAGTAAGTG
*
28773192 ATATTTTATTTTAATT
1 ATATTTTATTAT-ATT
28773208 ATATTATTATTATATT
1 ATATT-TTATTATATT
28773224 ATA-TTTATTATATT
1 ATATTTTATTATATT
28773238 A
1 A
28773239 GTTATAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 11 0.38
15 1 0.03
16 11 0.38
17 6 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATATTTTATTATATT
Found at i:28773219 original size:11 final size:10
Alignment explanation
Indices: 28773205--28773238 Score: 52
Period size: 9 Copynumber: 3.4 Consensus size: 10
28773195 TTTTATTTTA
28773205 ATTATATTATT
1 ATTATATTA-T
28773216 ATTATATTAT
1 ATTATATTAT
28773226 ATT-TATTAT
1 ATTATATTAT
28773235 ATTA
1 ATTA
28773239 GTTATAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.41
10 4 0.18
11 9 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTATATTAT
Found at i:28773237 original size:5 final size:5
Alignment explanation
Indices: 28773205--28773238 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
28773195 TTTTATTTTA
28773205 ATTAT ATTATT ATTAT ATTAT ATT-T ATTAT ATTA
1 ATTAT ATTA-T ATTAT ATTAT ATTAT ATTAT ATTA
28773239 GTTATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 18 0.67
6 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
ATTAT
Found at i:28782362 original size:16 final size:17
Alignment explanation
Indices: 28782321--28782362 Score: 61
Period size: 15 Copynumber: 2.5 Consensus size: 17
28782311 ACGATTTTCA
28782321 TTTATTTATATTAAATTT
1 TTTATTT-TATTAAATTT
28782339 TTTA-TTTATT-AATTT
1 TTTATTTTATTAAATTT
28782354 TTTATTTTA
1 TTTATTTTA
28782363 AATAGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 9 0.39
16 8 0.35
17 2 0.09
18 4 0.17
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATTTTATTAAATTT
Found at i:28785033 original size:20 final size:22
Alignment explanation
Indices: 28784991--28785033 Score: 54
Period size: 20 Copynumber: 2.0 Consensus size: 22
28784981 AAAATTAATT
28784991 AAGAATCCATAGACATTCATTA
1 AAGAATCCATAGACATTCATTA
* *
28785013 AAGAA-CCA-AGAGATTCTTTA
1 AAGAATCCATAGACATTCATTA
28785033 A
1 A
28785034 TTTAAAGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.58
21 3 0.16
22 5 0.26
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.26
Consensus pattern (22 bp):
AAGAATCCATAGACATTCATTA
Found at i:28789266 original size:40 final size:40
Alignment explanation
Indices: 28789220--28789295 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
28789210 GCACACCATG
*
28789220 TGGGGATAAAATCGACCCACCCATCCCTACACACCAAATA
1 TGGGGATAAAATCGACCCACCCAACCCTACACACCAAATA
* *
28789260 TGGGGATAATATCGACCCATCCAACCCTACACACCA
1 TGGGGATAAAATCGACCCACCCAACCCTACACACCA
28789296 TAAGGTACCG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.36, C:0.36, G:0.13, T:0.16
Consensus pattern (40 bp):
TGGGGATAAAATCGACCCACCCAACCCTACACACCAAATA
Found at i:28789672 original size:18 final size:18
Alignment explanation
Indices: 28789649--28789683 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28789639 TGCCTATGTG
28789649 ACATGCCTGTATGGCCCT
1 ACATGCCTGTATGGCCCT
*
28789667 ACATGCCTGTGTGGCCC
1 ACATGCCTGTATGGCCC
28789684 ACACAGCCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.34, G:0.26, T:0.26
Consensus pattern (18 bp):
ACATGCCTGTATGGCCCT
Found at i:28796235 original size:30 final size:26
Alignment explanation
Indices: 28796175--28796227 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
28796165 ACAGTGAGTC
*
28796175 ACTTATTAGACCGAAATCAATTTTTA
1 ACTTATGAGACCGAAATCAATTTTTA
28796201 ACTTATGAGACCGAAATCAATTTTTA
1 ACTTATGAGACCGAAATCAATTTTTA
28796227 A
1 A
28796228 GTTACTTACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (26 bp):
ACTTATGAGACCGAAATCAATTTTTA
Found at i:28797596 original size:27 final size:27
Alignment explanation
Indices: 28797549--28797607 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 27
28797539 AATTATATTT
* *
28797549 AAAATAAGATATATTATTTAATTTTTAA
1 AAAATAAGATATATTAATTAA-ATTTAA
*
28797577 AAAATAATATATA-TAATTAAATTTAA
1 AAAATAAGATATATTAATTAAATTTAA
28797603 AAAAT
1 AAAAT
28797608 TAATTTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 10 0.36
27 6 0.21
28 12 0.43
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (27 bp):
AAAATAAGATATATTAATTAAATTTAA
Found at i:28800806 original size:13 final size:13
Alignment explanation
Indices: 28800754--28800806 Score: 70
Period size: 13 Copynumber: 4.1 Consensus size: 13
28800744 AGTTTGGCAA
28800754 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
28800767 TGCTGTAGAAAAG
1 TGCTTTTGAAAAG
**
28800780 TGCTTTTGGGAAG
1 TGCTTTTGAAAAG
28800793 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
28800806 T
1 T
28800807 TTGGTTTAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:28801816 original size:20 final size:20
Alignment explanation
Indices: 28801791--28801833 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
28801781 ATTTAATGTT
28801791 TATCTACAAGATAAACATTC
1 TATCTACAAGATAAACATTC
28801811 TATCTACAAGATAAACATTC
1 TATCTACAAGATAAACATTC
28801831 TAT
1 TAT
28801834 TAATTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.33
Consensus pattern (20 bp):
TATCTACAAGATAAACATTC
Found at i:28803371 original size:46 final size:46
Alignment explanation
Indices: 28803318--28803417 Score: 130
Period size: 46 Copynumber: 2.2 Consensus size: 46
28803308 CTTAAGGGTG
* *
28803318 TTACAGAATACGCCACACAGTCATCA-CAGAATACTCCACAAAGGCT
1 TTACAGAATACACCACACAGGCATCACCA-AATACTCCACAAAGGCT
* * *
28803364 TTACAGAATACACCACACAGGCTTTACCAAATACTCCACCAAGGCT
1 TTACAGAATACACCACACAGGCATCACCAAATACTCCACAAAGGCT
*
28803410 TTATAGAA
1 TTACAGAA
28803418 AATTACGTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
46 45 0.96
47 2 0.04
ACGTcount: A:0.39, C:0.29, G:0.12, T:0.20
Consensus pattern (46 bp):
TTACAGAATACACCACACAGGCATCACCAAATACTCCACAAAGGCT
Found at i:28803386 original size:23 final size:23
Alignment explanation
Indices: 28803318--28803417 Score: 105
Period size: 23 Copynumber: 4.3 Consensus size: 23
28803308 CTTAAGGGTG
* * *
28803318 TTACAGAATACGCCACACAGTCA
1 TTACAGAATACTCCACACAGGCT
* *
28803341 TCACAGAATACTCCACAAAGGCT
1 TTACAGAATACTCCACACAGGCT
*
28803364 TTACAGAATACACCACACAGGCT
1 TTACAGAATACTCCACACAGGCT
28803387 TTACCA-AATACTCCAC-CAAGGCT
1 TTA-CAGAATACTCCACAC-AGGCT
*
28803410 TTATAGAA
1 TTACAGAA
28803418 AATTACGTGT
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
22 2 0.03
23 60 0.94
24 2 0.03
ACGTcount: A:0.39, C:0.29, G:0.12, T:0.20
Consensus pattern (23 bp):
TTACAGAATACTCCACACAGGCT
Found at i:28805434 original size:21 final size:21
Alignment explanation
Indices: 28805408--28805457 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
28805398 ATTACTCCAA
*
28805408 AGAAGCCGATTGACCTATCTC
1 AGAAGCCGATTGACCCATCTC
*
28805429 AGAAGCCGATTGACCCATCTT
1 AGAAGCCGATTGACCCATCTC
28805450 AGAAGCCG
1 AGAAGCCG
28805458 GATTCATCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (21 bp):
AGAAGCCGATTGACCCATCTC
Found at i:28812974 original size:41 final size:41
Alignment explanation
Indices: 28812917--28812997 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
28812907 TTAGCATGCC
* *
28812917 TACTATTACTTTTGAACCAG-ATACATGTTAAGCATGTCTAT
1 TACTACTACTATTGAA-CAGAATACATGTTAAGCATGTCTAT
*
28812958 TACTACTACTATTGAACTGAATACATGTTAAGCATGTCTA
1 TACTACTACTATTGAACAGAATACATGTTAAGCATGTCTA
28812998 CTGTTTTCAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 2 0.06
41 34 0.94
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.37
Consensus pattern (41 bp):
TACTACTACTATTGAACAGAATACATGTTAAGCATGTCTAT
Found at i:28814679 original size:40 final size:40
Alignment explanation
Indices: 28814616--28814695 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
28814606 GTTCATATTA
* *
28814616 TGACAAGAACCATGTGAGTGAGAGCTAGAAAGCGTTAGGT
1 TGACAAGAACCATATGAGCGAGAGCTAGAAAGCGTTAGGT
*
28814656 TGACAAGGACCATATGAGCGAGAGCTAGAAAGCGTTAGGT
1 TGACAAGAACCATATGAGCGAGAGCTAGAAAGCGTTAGGT
28814696 ACTTTTTTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.35, C:0.14, G:0.33, T:0.19
Consensus pattern (40 bp):
TGACAAGAACCATATGAGCGAGAGCTAGAAAGCGTTAGGT
Found at i:28817632 original size:35 final size:35
Alignment explanation
Indices: 28817593--28817682 Score: 119
Period size: 35 Copynumber: 2.6 Consensus size: 35
28817583 GATATTTTGT
*
28817593 TTCGCATGTTGAGCATGAT-ATTATTCTAATTATGA
1 TTCGCATGTTAAGCATG-TCATTATTCTAATTATGA
* *
28817628 TTCGCATGTTAAGCATGTCATTATTCTGATTCTGA
1 TTCGCATGTTAAGCATGTCATTATTCTAATTATGA
* *
28817663 TTTGCATGTTAAACATGTCA
1 TTCGCATGTTAAGCATGTCA
28817683 CTGTGATAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
34 1 0.02
35 48 0.98
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (35 bp):
TTCGCATGTTAAGCATGTCATTATTCTAATTATGA
Found at i:28817892 original size:30 final size:30
Alignment explanation
Indices: 28817858--28817922 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 30
28817848 ATCTAGTAGT
*
28817858 ATATTTACA-TTATCTGGTGGCTCAACCACA
1 ATATTTACAGTT-TCTGGTAGCTCAACCACA
* *
28817888 ATA-TT-CAGTTTCTGGTAGCTCGACTACA
1 ATATTTACAGTTTCTGGTAGCTCAACCACA
28817916 ATATTTA
1 ATATTTA
28817923 GTGGCTTGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
28 20 0.69
29 6 0.21
30 3 0.10
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (30 bp):
ATATTTACAGTTTCTGGTAGCTCAACCACA
Found at i:28819058 original size:16 final size:16
Alignment explanation
Indices: 28819021--28819072 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
28819011 AATATAGATT
*
28819021 ACTATAGATTGTG--A
1 ACTATAGATTCTGAAA
*
28819035 ACTCTAGATTCTGAAA
1 ACTATAGATTCTGAAA
28819051 ACTATAGATTCT-AAA
1 ACTATAGATTCTGAAA
28819066 ACTATAG
1 ACTATAG
28819073 TGACAACTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
14 11 0.33
15 10 0.30
16 12 0.36
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (16 bp):
ACTATAGATTCTGAAA
Found at i:28825167 original size:35 final size:35
Alignment explanation
Indices: 28825128--28825227 Score: 182
Period size: 35 Copynumber: 2.9 Consensus size: 35
28825118 ATTGACATTC
28825128 TGATTCGCATGTTGAGCATGCCATTATTCTGATTA
1 TGATTCGCATGTTGAGCATGCCATTATTCTGATTA
*
28825163 TGATTCGCAGGTTGAGCATGCCATTATTCTGATTA
1 TGATTCGCATGTTGAGCATGCCATTATTCTGATTA
*
28825198 TGATTCGCATGTTAAGCATGCCATTATTCT
1 TGATTCGCATGTTGAGCATGCCATTATTCT
28825228 AATTCTAATT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 62 1.00
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (35 bp):
TGATTCGCATGTTGAGCATGCCATTATTCTGATTA
Found at i:28828683 original size:48 final size:49
Alignment explanation
Indices: 28828607--28828736 Score: 147
Period size: 48 Copynumber: 2.7 Consensus size: 49
28828597 ACATCAAAGT
** * *
28828607 CGATGCCATGTCTTAGATAGGTCTTACACTGACTTTCATATATCGATGC
1 CGATGCCATGTCCCAAATAGGTCTTACACTGACTCTCATATATCGATGC
* * * * *
28828656 CGATGCCGTGTCCC-AGTAGGTCTTACACT-AGCTCTCATCTATCGGTGT
1 CGATGCCATGTCCCAAATAGGTCTTACACTGA-CTCTCATATATCGATGC
*
28828704 CGATGCCATGTCCCAAACAGGTCTTACACTGAC
1 CGATGCCATGTCCCAAATAGGTCTTACACTGAC
28828737 ACGCAACAAG
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
47 1 0.02
48 39 0.59
49 25 0.38
50 1 0.02
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (49 bp):
CGATGCCATGTCCCAAATAGGTCTTACACTGACTCTCATATATCGATGC
Found at i:28828821 original size:141 final size:142
Alignment explanation
Indices: 28828554--28828871 Score: 348
Period size: 141 Copynumber: 2.2 Consensus size: 142
28828544 CATGGGATAA
* * * *
28828554 GATGCCGAAGCCATGTCCAAAACATGGTCTTACACTGGCTAGCACATCAAAGTCGATGCCATGTC
1 GATGCCGATGCCATGTCCCAAACA-GGTCTTACACTGACTAGCACATCAAAGTCGACGCCATGTC
* * * * * *
28828619 TTAGATAGGTCTTACACTGACTTTCATATATCGATGCCGATGCCGTGTCCCAGTAGGTCTTACAC
65 TCAGACAGGTCTTACACTGACTTTCATATATCGAGGCCGATGACATGTCCCAGCAGGTCTTACAC
28828684 TAGCTCTCATCTAT
130 TAGCTCTCATCT-T
* *
28828698 CGGTGTCGATGCCATGTCCCAAACAGGTCTTACACTGAC-ACGCA-A-C-AAG-CTGACGCCATG
1 -GATGCCGATGCCATGTCCCAAACAGGTCTTACACTGACTA-GCACATCAAAGTC-GACGCCATG
* *
28828758 TCTCAGACAGGTCTTACACT-AGCTTGT-ATATCTCGAGGCCGAT-ACATGTCCCAGACATGTCT
63 TCTCAGACAGGTCTTACACTGA-CTT-TCATATATCGAGGCCGATGACATGTCCCAG-CAGGTCT
28828820 TACACTAGCTCTCATCTT
125 TACACTAGCTCTCATCTT
* * *
28828838 TATGCCGATG-CATGTCCCAGACATGTCTTACACT
1 GATGCCGATGCCATGTCCCAAACAGGTCTTACACT
28828872 AGCTCTCATC
Statistics
Matches: 149, Mismatches: 19, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
138 22 0.15
139 7 0.05
140 12 0.08
141 68 0.46
142 2 0.01
143 2 0.01
144 16 0.11
145 20 0.13
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.27
Consensus pattern (142 bp):
GATGCCGATGCCATGTCCCAAACAGGTCTTACACTGACTAGCACATCAAAGTCGACGCCATGTCT
CAGACAGGTCTTACACTGACTTTCATATATCGAGGCCGATGACATGTCCCAGCAGGTCTTACACT
AGCTCTCATCTT
Found at i:28828861 original size:46 final size:46
Alignment explanation
Indices: 28828754--28828966 Score: 291
Period size: 46 Copynumber: 4.6 Consensus size: 46
28828744 AAGCTGACGC
* * * * ** * *
28828754 CATGTCTCAGACAGGTCTTACACTAGCTTGTATATCTCGAGGCCGATA
1 CATGTCCCAGACATGTCTTACACTAGC-TCT-CATCTTTATGCCGATG
28828802 CATGTCCCAGACATGTCTTACACTAGCTCTCATCTTTATGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTCATCTTTATGCCGATG
*
28828848 CATGTCCCAGACATGTCTTACACTAGCTCTCATCTTTATGCCTATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTCATCTTTATGCCGATG
* *
28828894 CATATCCCAGACATGTCTTACACTAGCTCTCGTCTTTATGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTCATCTTTATGCCGATG
* *
28828940 CATGTGCCAGACATGTCTTACTCTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
28828967 ATACATATCA
Statistics
Matches: 150, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
46 123 0.82
47 2 0.01
48 25 0.17
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTCATCTTTATGCCGATG
Found at i:28834920 original size:22 final size:23
Alignment explanation
Indices: 28834895--28834946 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
28834885 TATAAAACCT
28834895 AATAAAAA-TACG-CTTAAAGAAA
1 AATAAAAAGTA-GTCTTAAAGAAA
* *
28834917 AATAAAAAGTAGTCTTAAAGTAG
1 AATAAAAAGTAGTCTTAAAGAAA
28834940 AATAAAA
1 AATAAAA
28834947 GTGAAAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.21
Consensus pattern (23 bp):
AATAAAAAGTAGTCTTAAAGAAA
Found at i:28838392 original size:47 final size:47
Alignment explanation
Indices: 28838322--28838440 Score: 202
Period size: 47 Copynumber: 2.5 Consensus size: 47
28838312 TGGATGCGAA
*
28838322 CATCTGAACTCGTTGAGTTGAGTCCGACTTCGTGAAATGTAACTAGG
1 CATCCGAACTCGTTGAGTTGAGTCCGACTTCGTGAAATGTAACTAGG
* * *
28838369 CATCCGAACTTGTTAAGTTGAGTCCGAGTTCGTGAAATGTAACTAGG
1 CATCCGAACTCGTTGAGTTGAGTCCGACTTCGTGAAATGTAACTAGG
28838416 CATCCGAACTCGTTGAGTTGAGTCC
1 CATCCGAACTCGTTGAGTTGAGTCC
28838441 AAGTTCACTT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 66 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (47 bp):
CATCCGAACTCGTTGAGTTGAGTCCGACTTCGTGAAATGTAACTAGG
Found at i:28838446 original size:47 final size:47
Alignment explanation
Indices: 28838274--28838446 Score: 199
Period size: 47 Copynumber: 3.7 Consensus size: 47
28838264 CGGATATTTG
* * * * *
28838274 GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTCACT--TATGGATGCGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTC-GTGAAATGTA-ACTA
* * * *
28838321 -ACATCTGAACTCGTTGAGTTGAGTCCGACTTCGTGAAATGTAACTA
1 GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTCGTGAAATGTAACTA
* * *
28838367 GGCATCCGAACTTGTTAAGTTGAGTCCGAGTTCGTGAAATGTAACTA
1 GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTCGTGAAATGTAACTA
28838414 GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTC
1 GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTC
28838447 ACTTATGGAT
Statistics
Matches: 106, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
45 1 0.01
46 30 0.28
47 75 0.71
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (47 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCAAGTTCGTGAAATGTAACTA
Found at i:28843929 original size:46 final size:46
Alignment explanation
Indices: 28843841--28843932 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
28843831 CACTATTCAC
* * *
28843841 TGATCAGGTAGCCGGAGCTACCATTTTTCACTAATTAAGTAGCCGA
1 TGATCAGGTAGCCGAAGCTACCACTTTTCACTAATCAAGTAGCCGA
* * *
28843887 TGATCAGGTAGCCGAAGCTACCACTTTTCATTGATCAGGTAGCCGA
1 TGATCAGGTAGCCGAAGCTACCACTTTTCACTAATCAAGTAGCCGA
28843933 AGCTATCACT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (46 bp):
TGATCAGGTAGCCGAAGCTACCACTTTTCACTAATCAAGTAGCCGA
Found at i:28844000 original size:50 final size:50
Alignment explanation
Indices: 28843925--28844150 Score: 391
Period size: 50 Copynumber: 4.5 Consensus size: 50
28843915 CATTGATCAG
* *
28843925 GTAGCCGAAGCTATCACTTATCACTTTCACTTATCCTTGATCAAATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
*
28843975 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
*
28844025 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
28844075 GTAGCCGAAGCTATCACTTATCACTTTCACTTG-CCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCC-TTGATCAGATAAGT
*
28844125 GTAGCCAAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
28844151 GTTGCCATGG
Statistics
Matches: 170, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
49 2 0.01
50 168 0.99
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
Found at i:28847798 original size:42 final size:46
Alignment explanation
Indices: 28847751--28847894 Score: 140
Period size: 49 Copynumber: 3.2 Consensus size: 46
28847741 ACGTCTTCAA
28847751 CTATGGTCTTACAC-AT-C-T-TCACATAAT-GATGCCATAGCCCAG
1 CTATGGTCTTACACAATACATATCACAT-ATCGATGCCATAGCCCAG
*
28847793 CTATGGTCTTAAACGTAATCACATATCACATATCGATGCCATAGCCCAG
1 CTATGGTCTTACAC--AAT-ACATATCACATATCGATGCCATAGCCCAG
* * *
28847842 CTATGGTCTTACACGAATCACATATCTC--ACCGATGCCATATCCCAG
1 CTATGGTCTTACAC-AAT-ACATATCACATATCGATGCCATAGCCCAG
*
28847888 ATATGGT
1 CTATGGT
28847895 TTTATACGGA
Statistics
Matches: 87, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
42 13 0.15
45 2 0.02
46 22 0.25
47 1 0.01
48 15 0.17
49 34 0.39
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (46 bp):
CTATGGTCTTACACAATACATATCACATATCGATGCCATAGCCCAG
Found at i:28847835 original size:49 final size:48
Alignment explanation
Indices: 28847769--28847894 Score: 168
Period size: 49 Copynumber: 2.6 Consensus size: 48
28847759 TTACACATCT
28847769 TCACATAAT-GATGCCATAGCCCAGCTATGGTCTTAAACGTAATCACATA
1 TCACAT-ATCGATGCCATAGCCCAGCTATGGTCTTAAACG-AATCACATA
*
28847818 TCACATATCGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATA
1 TCACATATCGATGCCATAGCCCAGCTATGGTCTTAAACGAATCACATA
* * * *
28847866 TCTC--ACCGATGCCATATCCCAGATATGGT
1 TCACATATCGATGCCATAGCCCAGCTATGGT
28847895 TTTATACGGA
Statistics
Matches: 71, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
46 22 0.31
48 14 0.20
49 35 0.49
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (48 bp):
TCACATATCGATGCCATAGCCCAGCTATGGTCTTAAACGAATCACATA
Found at i:28847962 original size:31 final size:31
Alignment explanation
Indices: 28847927--28848075 Score: 217
Period size: 31 Copynumber: 4.8 Consensus size: 31
28847917 CTTGTCACTT
*
28847927 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
28847958 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
28847989 GTAGCCGGAGCTACTACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
28848020 GTAGCAGAAGCTACCACTTTTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
28848051 GGAGCTGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
28848076 TGTCATTTGT
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 107 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:28848150 original size:50 final size:50
Alignment explanation
Indices: 28848057--28848227 Score: 279
Period size: 50 Copynumber: 3.4 Consensus size: 50
28848047 TTAGGGAGCT
* * *
28848057 GAAGCTACCACTTTTCACTTGTCATTTGTCATTGATCAGATAAGTGTAGCC
1 GAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGTGTAGCC
*
28848108 GAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGTGTAGCC
1 GAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGTGTAGCC
* *
28848158 GAAGCTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGTGTAGTC
1 GAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGTGTAGCC
28848208 GAAGCTATCACTTATCACTT
1 GAAGCTATCACTTATCACTT
28848228 GTTGCCATGG
Statistics
Matches: 112, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
50 94 0.84
51 18 0.16
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (50 bp):
GAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGTGTAGCC
Found at i:28851497 original size:25 final size:25
Alignment explanation
Indices: 28851464--28851523 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
28851454 GAGTTGTAAA
*
28851464 CGGTAAGCTTATACGAGCTAAATAT
1 CGGTAAGCTCATACGAGCTAAATAT
** *
28851489 CGGTAAGCTCATGTGAGCTGAATAT
1 CGGTAAGCTCATACGAGCTAAATAT
28851514 CGGTAAGCTC
1 CGGTAAGCTC
28851524 TCTCGAGTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (25 bp):
CGGTAAGCTCATACGAGCTAAATAT
Found at i:28851540 original size:25 final size:25
Alignment explanation
Indices: 28851464--28851544 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
28851454 GAGTTGTAAA
* *
28851464 CGGTAAGCTTATAC-GAGCTAAATAT
1 CGGTAAGCTCAT-CTGAGCTGAATAT
*
28851489 CGGTAAGCTCATGTGAGCTGAATAT
1 CGGTAAGCTCATCTGAGCTGAATAT
*
28851514 CGGTAAGCTC-TCTCGAGTTGAGA-AT
1 CGGTAAGCTCATCT-GAGCTGA-ATAT
28851539 CGGTAA
1 CGGTAA
28851545 CCCTAATGAC
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
24 2 0.04
25 45 0.94
26 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (25 bp):
CGGTAAGCTCATCTGAGCTGAATAT
Found at i:28853826 original size:38 final size:38
Alignment explanation
Indices: 28853714--28853826 Score: 138
Period size: 38 Copynumber: 3.0 Consensus size: 38
28853704 ACACGGTCAT
* * * * *
28853714 GTAACCCTTTCACACAGCCTATAGCTTCGCACA-CCCGT
1 GTAACCCTTCCACACAACCTATAGCTTCACA-AGGCCGC
* *
28853752 GTAACCCTTCCATACAACCTATAGCTTCACATGGCCGC
1 GTAACCCTTCCACACAACCTATAGCTTCACAAGGCCGC
*
28853790 GTAACCCTTCCACACAATCTATAGCTTCACAAGGCCG
1 GTAACCCTTCCACACAACCTATAGCTTCACAAGGCCG
28853827 TGTGCCCCCT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.27, C:0.37, G:0.13, T:0.23
Consensus pattern (38 bp):
GTAACCCTTCCACACAACCTATAGCTTCACAAGGCCGC
Found at i:28857210 original size:21 final size:21
Alignment explanation
Indices: 28857186--28857225 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28857176 CTACCTTTTT
28857186 TCGA-ATTAATATATTTATATG
1 TCGATATTAA-ATATTTATATG
*
28857207 TCGATTTTAAATATTTATA
1 TCGATATTAAATATTTATA
28857226 ATATTGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (21 bp):
TCGATATTAAATATTTATATG
Found at i:28858585 original size:26 final size:26
Alignment explanation
Indices: 28858556--28858621 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
28858546 ATAGTTACCC
28858556 ATTTTTTAAATTTAT-TTTTATTTAAT
1 ATTTTTTAAATTTATATTTTA-TTAAT
**
28858582 ATTTAGT-AATTATATATTTTATTAAT
1 ATTTTTTAAATT-TATATTTTATTAAT
*
28858608 A-TTTTTAATTTTAT
1 ATTTTTTAAATTTAT
28858622 GATATTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
25 10 0.31
26 17 0.53
27 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
ATTTTTTAAATTTATATTTTATTAAT
Found at i:28858620 original size:18 final size:17
Alignment explanation
Indices: 28858597--28858632 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
28858587 GTAATTATAT
28858597 ATTTTATTAATATTTTTA
1 ATTTTA-TAATATTTTTA
*
28858615 ATTTTATGATATTTTTA
1 ATTTTATAATATTTTTA
28858632 A
1 A
28858633 ACATAAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
ATTTTATAATATTTTTA
Found at i:28859872 original size:30 final size:32
Alignment explanation
Indices: 28859836--28859901 Score: 91
Period size: 34 Copynumber: 2.1 Consensus size: 32
28859826 AATTCAACTA
*
28859836 TTTTTT-A-AAAGATTAATTGTCGAATTTGAT
1 TTTTTTAATAAAGATTAATTGTCGAATTGGAT
28859866 TTTTTTAAAATAAAGATTAATTGTCGAATTGGAT
1 TTTTTT--AATAAAGATTAATTGTCGAATTGGAT
28859900 TT
1 TT
28859902 AGGCAGGAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 6 0.19
33 1 0.03
34 24 0.77
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.48
Consensus pattern (32 bp):
TTTTTTAATAAAGATTAATTGTCGAATTGGAT
Found at i:28862830 original size:20 final size:20
Alignment explanation
Indices: 28862788--28862836 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
28862778 AGAACATAAT
**
28862788 AGAAAACGG-GAAAGAAAGGA
1 AGAAAA-GGAGAAAGAAAAAA
28862808 AGAAAAGGAGAAAGAAAAAA
1 AGAAAAGGAGAAAGAAAAAA
28862828 AGAAAAGGA
1 AGAAAAGGA
28862837 AAAACTAGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (20 bp):
AGAAAAGGAGAAAGAAAAAA
Found at i:28864025 original size:18 final size:17
Alignment explanation
Indices: 28864002--28864113 Score: 80
Period size: 18 Copynumber: 6.2 Consensus size: 17
28863992 TAAATAAATG
*
28864002 TACTGAATGACTGACTGT
1 TACTGAATAACTGA-TGT
*
28864020 TACTGAATAATTGATCGT
1 TACTGAATAACTGAT-GT
*
28864038 TACTGAATAACTGATTGC
1 TACTGAATAACTGA-TGT
** * *
28864056 TACTGAGCAAATAATTGT
1 TACTGAATAACTGA-TGT
* *
28864074 TACTGAATAACTAATTGC
1 TACTGAATAACTGA-TGT
*
28864092 TACTGAATAATTGAATGT
1 TACTGAATAACTG-ATGT
28864110 TACT
1 TACT
28864114 AAGTGAAACT
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
17 1 0.01
18 72 0.96
19 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (17 bp):
TACTGAATAACTGATGT
Found at i:28864051 original size:36 final size:35
Alignment explanation
Indices: 28864002--28864113 Score: 125
Period size: 36 Copynumber: 3.1 Consensus size: 35
28863992 TAAATAAATG
* * *
28864002 TACTGAATGACTGACTGTTACTGAATAATTGATCGT
1 TACTGAATAACTGATTGCTACTGAATAATTGAT-GT
** * *
28864038 TACTGAATAACTGATTGCTACTGAGCAAATAATTGT
1 TACTGAATAACTGATTGCTACTGAATAATTGA-TGT
*
28864074 TACTGAATAACTAATTGCTACTGAATAATTGAATGT
1 TACTGAATAACTGATTGCTACTGAATAATTG-ATGT
28864110 TACT
1 TACT
28864114 AAGTGAAACT
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
36 60 0.97
37 2 0.03
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (35 bp):
TACTGAATAACTGATTGCTACTGAATAATTGATGT
Found at i:28869965 original size:17 final size:17
Alignment explanation
Indices: 28869943--28869985 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
28869933 AATTTAGGCT
28869943 GTGTAGGCCACATGGGC
1 GTGTAGGCCACATGGGC
28869960 GTGTAGGCCACATGGGC
1 GTGTAGGCCACATGGGC
28869977 GTGTAGGCC
1 GTGTAGGCC
28869986 CACACGGGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.16, C:0.23, G:0.42, T:0.19
Consensus pattern (17 bp):
GTGTAGGCCACATGGGC
Found at i:28870941 original size:13 final size:13
Alignment explanation
Indices: 28870923--28870948 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28870913 CACTTGATAA
28870923 GGTTTCCTAAAAG
1 GGTTTCCTAAAAG
28870936 GGTTTCCTAAAAG
1 GGTTTCCTAAAAG
28870949 TACTTTCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GGTTTCCTAAAAG
Found at i:28872895 original size:18 final size:17
Alignment explanation
Indices: 28872872--28872983 Score: 89
Period size: 18 Copynumber: 6.2 Consensus size: 17
28872862 CAAATAAAGG
*
28872872 TACTGAATGACTGACTGT
1 TACTGAATAACTGA-TGT
*
28872890 TACTGAATAATTGATCGT
1 TACTGAATAACTGAT-GT
*
28872908 TACTGAATAACTGATTGC
1 TACTGAATAACTGA-TGT
** *
28872926 TACTGAGCAAATGATTGT
1 TACTGAATAACTGA-TGT
* *
28872944 TACTGAATAACTAATTGC
1 TACTGAATAACTGA-TGT
*
28872962 TACTGAATAATTGAATGT
1 TACTGAATAACTG-ATGT
28872980 TACT
1 TACT
28872984 AAGTGAAACT
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
17 1 0.01
18 72 0.96
19 2 0.03
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (17 bp):
TACTGAATAACTGATGT
Found at i:28872912 original size:36 final size:35
Alignment explanation
Indices: 28872872--28872983 Score: 134
Period size: 36 Copynumber: 3.1 Consensus size: 35
28872862 CAAATAAAGG
* * *
28872872 TACTGAATGACTGACTGTTACTGAATAATTGATCGT
1 TACTGAATAACTGATTGCTACTGAATAATTGAT-GT
** *
28872908 TACTGAATAACTGATTGCTACTGAGCAAATGATTGT
1 TACTGAATAACTGATTGCTACTGAATAATTGA-TGT
*
28872944 TACTGAATAACTAATTGCTACTGAATAATTGAATGT
1 TACTGAATAACTGATTGCTACTGAATAATTG-ATGT
28872980 TACT
1 TACT
28872984 AAGTGAAACT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
36 62 0.97
37 2 0.03
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (35 bp):
TACTGAATAACTGATTGCTACTGAATAATTGATGT
Found at i:28874409 original size:339 final size:339
Alignment explanation
Indices: 28873789--28874465 Score: 1196
Period size: 339 Copynumber: 2.0 Consensus size: 339
28873779 GCACACGGGA
* *
28873789 GTGTGTCTTGGCTGTATGAAACTATTTTGTTCATAAGTAATTAGTCAGAGAGTTACACGGATAAA
1 GTGTGTCTTGGCAGTATGAAACTATTTTGTTCATAAGTAATAAGTCAGAGAGTTACACGGATAAA
*
28873854 GGACACGGGCATGTCCCCTAGACCACACGAGCGTGTGGGCACTGTTCAATAGGAAAATTTTGAAA
66 GGACACGGGCATGTCCCCTAGACCACACGAGCGTGTGGGCACTATTCAATAGGAAAATTTTGAAA
*
28873919 TTTTGAGAAAAATTCGTAGTGATTTTAAATTAGTCTCGAATTGATTTTACTATTCATATTGGACT
131 TTTTGAGAAAAATTCATAGTGATTTTAAATTAGTCTCGAATTGATTTTACTATTCATATTGGACT
28873984 TCGAGGGACCATTAAAGGGACGATACATTAAATTTAGGATAAGTGTAAACAATTATATTAATTAA
196 TCGAGGGACCATTAAAGGGACGATACATTAAATTTAGGATAAGTGTAAACAATTATATTAATTAA
*
28874049 TGTCCGTAATTGAACTGTATTGACTGGTAATGCCCCGCAATACTATT-TCGGGGATGAATAAGGG
261 TGTCCGTAATTGAACTGTATTGACTGGTAATGCCCCGCAATACTGTTCT-GGGGATGAATAAGGG
28874113 TTAGGGGATGTTACC
325 TTAGGGGATGTTACC
28874128 GTGTGTCTTGGCAGTATGAAACTATTTTGTTCATAAGTAATAAGTCAGAGAGTTACACGGATAAA
1 GTGTGTCTTGGCAGTATGAAACTATTTTGTTCATAAGTAATAAGTCAGAGAGTTACACGGATAAA
* * * *
28874193 GGACATGGGCGTGTCCCCTAGACCATACGAGCGTGTGGGTACTATTCAATAGGAAAATTTTGAAA
66 GGACACGGGCATGTCCCCTAGACCACACGAGCGTGTGGGCACTATTCAATAGGAAAATTTTGAAA
*
28874258 TTTTGAGAAAAATTCATAGTGATTTTAAATTAGT-TCCGAATTGATTTTACTGTTCATATTGGAC
131 TTTTGAGAAAAATTCATAGTGATTTTAAATTAGTCT-CGAATTGATTTTACTATTCATATTGGAC
*
28874322 TTCGAGGGCCCATTAAAGGGACGATACATTAAATTTAGGATAAGTGTAAACAATTATATTAATTA
195 TTCGAGGGACCATTAAAGGGACGATACATTAAATTTAGGATAAGTGTAAACAATTATATTAATTA
* * *
28874387 ATGTCCGTAGTTGAACTGTATTGACTGGTAATGCCCCGCAATCCTGTTCTGGGGATGGATAAGGG
260 ATGTCCGTAATTGAACTGTATTGACTGGTAATGCCCCGCAATACTGTTCTGGGGATGAATAAGGG
28874452 TTAGGGGATGTTAC
325 TTAGGGGATGTTAC
28874466 AGTAGGACTA
Statistics
Matches: 322, Mismatches: 14, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
338 1 0.00
339 320 0.99
340 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (339 bp):
GTGTGTCTTGGCAGTATGAAACTATTTTGTTCATAAGTAATAAGTCAGAGAGTTACACGGATAAA
GGACACGGGCATGTCCCCTAGACCACACGAGCGTGTGGGCACTATTCAATAGGAAAATTTTGAAA
TTTTGAGAAAAATTCATAGTGATTTTAAATTAGTCTCGAATTGATTTTACTATTCATATTGGACT
TCGAGGGACCATTAAAGGGACGATACATTAAATTTAGGATAAGTGTAAACAATTATATTAATTAA
TGTCCGTAATTGAACTGTATTGACTGGTAATGCCCCGCAATACTGTTCTGGGGATGAATAAGGGT
TAGGGGATGTTACC
Found at i:28887296 original size:39 final size:40
Alignment explanation
Indices: 28887243--28887377 Score: 245
Period size: 40 Copynumber: 3.4 Consensus size: 40
28887233 GACTTATAGT
* *
28887243 CCGCAGACTTTGTGCTGGTAATAGATATCTGGGTTAAATC
1 CCGCAGGCTTTGTGCTGGTAATAGATATCCGGGTTAAATC
28887283 CCGCAGGC-TTGTGCTGGTAATAGATATCCGGGTTAAATC
1 CCGCAGGCTTTGTGCTGGTAATAGATATCCGGGTTAAATC
28887322 CCGCAGGCTTTGTGCTGGTAATAGATATCCGGGTTAAATC
1 CCGCAGGCTTTGTGCTGGTAATAGATATCCGGGTTAAATC
28887362 CCGCAGGCTTTGTGCT
1 CCGCAGGCTTTGTGCT
28887378 AGAAATTGGA
Statistics
Matches: 92, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
39 38 0.41
40 54 0.59
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (40 bp):
CCGCAGGCTTTGTGCTGGTAATAGATATCCGGGTTAAATC
Found at i:28894541 original size:39 final size:39
Alignment explanation
Indices: 28894488--28894618 Score: 212
Period size: 39 Copynumber: 3.4 Consensus size: 39
28894478 CTTATAGTCT
28894488 GCAGGCTTTGTGCTGGCAATAGATATCCGGGTTAAATCCC
1 GCAGGCTTTGTGCTGG-AATAGATATCCGGGTTAAATCCC
28894528 GCAGGC-TTGTGCTGGTAATAGATATCCGGGTTAAATCCC
1 GCAGGCTTTGTGCTGG-AATAGATATCCGGGTTAAATCCC
*
28894567 GCAGGCTTTGTGCTGGTATAGATATCCGGGTTAAAT-CC
1 GCAGGCTTTGTGCTGGAATAGATATCCGGGTTAAATCCC
*
28894605 GTAGGCTTTGTGCT
1 GCAGGCTTTGTGCT
28894619 AGAAATTGGA
Statistics
Matches: 87, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
38 15 0.17
39 57 0.66
40 15 0.17
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.31
Consensus pattern (39 bp):
GCAGGCTTTGTGCTGGAATAGATATCCGGGTTAAATCCC
Found at i:28896438 original size:42 final size:41
Alignment explanation
Indices: 28896329--28896449 Score: 111
Period size: 42 Copynumber: 2.9 Consensus size: 41
28896319 ATTTATATGC
*
28896329 CACACGGCCTGGACACACACCCATGTCCTTGCCCATGTAACT
1 CACAC-GCCTGGAGACACACCCATGTCCTTGCCCATGTAACT
* * * *
28896371 TACACGCCCT--AGACACATGCCCATGTCCTTGCTCGTGTGACT
1 CACACG-CCTGGAGACACA--CCCATGTCCTTGCCCATGTAACT
* *
28896413 CACACAGCCTGGAGACACACTCATGTCATCTGCCCAT
1 CACAC-GCCTGGAGACACACCCATGTCCT-TGCCCAT
28896450 ATGGTTCTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
40 6 0.10
41 1 0.02
42 42 0.68
43 6 0.10
44 7 0.11
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.21
Consensus pattern (41 bp):
CACACGCCTGGAGACACACCCATGTCCTTGCCCATGTAACT
Found at i:28899857 original size:19 final size:19
Alignment explanation
Indices: 28899820--28899858 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
28899810 GTCATTTAAT
*
28899820 ACATATCCCCTTTCCACAA
1 ACATATCCCCTTTACACAA
* *
28899839 ACATTTCCCCTTTAGACAA
1 ACATATCCCCTTTACACAA
28899858 A
1 A
28899859 ATTAGCTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.33, C:0.36, G:0.03, T:0.28
Consensus pattern (19 bp):
ACATATCCCCTTTACACAA
Found at i:28901400 original size:78 final size:79
Alignment explanation
Indices: 28901309--28901463 Score: 204
Period size: 79 Copynumber: 2.0 Consensus size: 79
28901299 TTAACAATAG
* * * * *
28901309 AAATCGAATAAATTCTATTGAATGACA-TAATAGAATCCTGAAACAGAATTGTTTAATTGATTTC
1 AAATCGAAAAAATTCTATTGAACGACAGGAATAAAATCCTGAAACAGAATTGTTCAATTGATTTC
28901373 TATTTAAAAACAAA
66 TATTTAAAAACAAA
* * * *
28901387 AAATCGAAAAAATTCTGTTGAACGATAGGAATAAAATCTTGAAATAGAATTGTTCAATTGATTTC
1 AAATCGAAAAAATTCTATTGAACGACAGGAATAAAATCCTGAAACAGAATTGTTCAATTGATTTC
* *
28901452 TGTTTACAAACA
66 TATTTAAAAACA
28901464 TAATACAATT
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
78 23 0.35
79 42 0.65
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (79 bp):
AAATCGAAAAAATTCTATTGAACGACAGGAATAAAATCCTGAAACAGAATTGTTCAATTGATTTC
TATTTAAAAACAAA
Found at i:28902004 original size:203 final size:203
Alignment explanation
Indices: 28901655--28902056 Score: 579
Period size: 203 Copynumber: 2.0 Consensus size: 203
28901645 AATTGGATGA
* * *
28901655 AAATTGTGTACTCGTAGGTAAGAAAAAATCCAACTGGTAATTGAGGCCTGTTTGCACAGTTTCCT
1 AAATTGTGTACTCATAGGTAAGAAAAAATCCAACTGGTAATTGAAGCCTATTTGCACAGTTTCCT
* * *
28901720 TAAGAAAGATTTAGTAGCTCCTTTGGTGCTAGAGAAATGTTGGTCAACTGTCTCCTAGGATATAA
66 TAAGAAAGATTCAGTAGCTCCTTTGGTGCTAGAGAAACGTTGGTCAACTGTCTCCTAGGATACAA
*
28901785 CAAAAAGATGAGCACGGCTGCAGTAATCAATGAACTATAGCCTAGCTTTCTTCTATCACCGAAAA
131 CAAAAAGATGAGCACGGCTGCAGTAATCAACGAACTATAGCCTAGCTTTCTTCTATCACCGAAAA
28901850 CAGGATCG
196 CAGGATCG
* * * * * *
28901858 AAATTGTGTACTCATAGGTAGGCAGAAGTCCGACTGGTAATTGAAGCCTATTTTCACAGTTTCCT
1 AAATTGTGTACTCATAGGTAAGAAAAAATCCAACTGGTAATTGAAGCCTATTTGCACAGTTTCCT
* * * * * *
28901923 TAAGACAGATTCAGTCGTTCCTTTGGTGCTGGAGAAACGTTGGTCGATTGTCTCCTAGGATACAA
66 TAAGAAAGATTCAGTAGCTCCTTTGGTGCTAGAGAAACGTTGGTCAACTGTCTCCTAGGATACAA
** * ** *
28901988 CAACGAGATGAGCACGGCTGCAGTGATCAACGAACTATAGTGTAGCTTTCTTCTATCACTGAAAA
131 CAAAAAGATGAGCACGGCTGCAGTAATCAACGAACTATAGCCTAGCTTTCTTCTATCACCGAAAA
28902053 CAGG
196 CAGG
28902057 TTCGGAATAT
Statistics
Matches: 174, Mismatches: 25, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
203 174 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (203 bp):
AAATTGTGTACTCATAGGTAAGAAAAAATCCAACTGGTAATTGAAGCCTATTTGCACAGTTTCCT
TAAGAAAGATTCAGTAGCTCCTTTGGTGCTAGAGAAACGTTGGTCAACTGTCTCCTAGGATACAA
CAAAAAGATGAGCACGGCTGCAGTAATCAACGAACTATAGCCTAGCTTTCTTCTATCACCGAAAA
CAGGATCG
Found at i:28910856 original size:12 final size:12
Alignment explanation
Indices: 28910839--28910871 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
28910829 TGGCCCGCCC
28910839 ATATTAATTTTT
1 ATATTAATTTTT
28910851 ATATT-ATTTTT
1 ATATTAATTTTT
28910862 ATA-TAATTTT
1 ATATTAATTTT
28910872 AAAAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:28911035 original size:29 final size:30
Alignment explanation
Indices: 28910993--28911052 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 30
28910983 ACTTAACAAG
28910993 CAAATGCTTCTAAAATAATAA-AAAATTAA
1 CAAATGCTTCTAAAATAATAACAAAATTAA
28911022 CAAATGTCTT-TAAAATAATAACAAAATTAA
1 CAAATG-CTTCTAAAATAATAACAAAATTAA
28911052 C
1 C
28911053 GATAAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.57, C:0.12, G:0.03, T:0.28
Consensus pattern (30 bp):
CAAATGCTTCTAAAATAATAACAAAATTAA
Found at i:28911179 original size:11 final size:11
Alignment explanation
Indices: 28911140--28911180 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
28911130 AAGTTTTATA
28911140 CAAAATAGTAG
1 CAAAATAGTAG
* *
28911151 CAACATAATAG
1 CAAAATAGTAG
*
28911162 TAAAATAGTAG
1 CAAAATAGTAG
28911173 CAAAATAG
1 CAAAATAG
28911181 GAAGAAAACA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:28914118 original size:43 final size:43
Alignment explanation
Indices: 28914056--28914214 Score: 239
Period size: 43 Copynumber: 3.7 Consensus size: 43
28914046 CAGATATAAG
*
28914056 TTCGGTTTAATGTAA-TGGCACTAAGTGTGCGATATAATTATAGC
1 TTCGG-TTAAT-TAATTGGCACTAAGTGTGCGATACAATTATAGC
*
28914100 TTCGGCTAATTAATTGGCACTAAGTGTGCGATACAATTATAGC
1 TTCGGTTAATTAATTGGCACTAAGTGTGCGATACAATTATAGC
* * *
28914143 TTCGGTTAATTAATTGGCACTAAGTGTGCGAAACCATTATAAC
1 TTCGGTTAATTAATTGGCACTAAGTGTGCGATACAATTATAGC
*
28914186 TTCGGTTAATTAATTAGCACTAAGTGTGC
1 TTCGGTTAATTAATTGGCACTAAGTGTGC
28914215 AATTTTGTTG
Statistics
Matches: 107, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
42 3 0.03
43 99 0.93
44 5 0.05
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (43 bp):
TTCGGTTAATTAATTGGCACTAAGTGTGCGATACAATTATAGC
Found at i:28919819 original size:91 final size:91
Alignment explanation
Indices: 28919664--28919842 Score: 340
Period size: 91 Copynumber: 2.0 Consensus size: 91
28919654 AATTATAGAG
28919664 AATTGAATGACATGTATAAGTTAGATTTAATTCCTATTTTTAATAATAATATTGAAAAATGCAAT
1 AATTGAATGACATGTATAAGTTAGATTTAATTCCTATTTTTAATAATAATATTGAAAAATGCAAT
28919729 ACATGTATGTTGACTAAAATTACGAA
66 ACATGTATGTTGACTAAAATTACGAA
* *
28919755 AATTGAATGACATGTATAAGTTAGATTTAATTCTTGTTTTTAATAATAATATTGAAAAATGCAAT
1 AATTGAATGACATGTATAAGTTAGATTTAATTCCTATTTTTAATAATAATATTGAAAAATGCAAT
28919820 ACATGTATGTTGACTAAAATTAC
66 ACATGTATGTTGACTAAAATTAC
28919843 AAGAAACCCT
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 86 1.00
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (91 bp):
AATTGAATGACATGTATAAGTTAGATTTAATTCCTATTTTTAATAATAATATTGAAAAATGCAAT
ACATGTATGTTGACTAAAATTACGAA
Found at i:28925217 original size:27 final size:27
Alignment explanation
Indices: 28925187--28925656 Score: 353
Period size: 27 Copynumber: 17.1 Consensus size: 27
28925177 GTTGTTAAGA
***
28925187 CCCTAGTTTGTAAAATTATTAAAATAC
1 CCCTAGTTTGTAAAATTACCGAAATAC
* *
28925214 CCCTAGTTTGTAAAATTATCGAAATTTC
1 CCCTAGTTTGTAAAATTACCGAAA-TAC
28925242 CCC-AGTTTGTAAAATTACCGAAATAC
1 CCCTAGTTTGTAAAATTACCGAAATAC
** **
28925268 CCCCGGTTTGTAAAATTATTGAAATAC
1 CCCTAGTTTGTAAAATTACCGAAATAC
*
28925295 CTCTAGTTTGTAAAATTACCGAAATA-
1 CCCTAGTTTGTAAAATTACCGAAATAC
* * *
28925321 CCTTCAGATTGTAAAATTATCGAAATAC
1 CCCT-AGTTTGTAAAATTACCGAAATAC
* * *
28925349 CTCTAGTTTTTAGAATTACCGAAATA-
1 CCCTAGTTTGTAAAATTACCGAAATAC
* * * *
28925375 CCATCGGATTGTAAAATTACCAAAATAC
1 CCCT-AGTTTGTAAAATTACCGAAATAC
* * *
28925403 CCTCGAATTGTCGATTTGTAAAATTACCAAAATAA
1 CC-C------TAG-TTTGTAAAATTACCGAAATAC
* *
28925438 CCCTAATTTTTAAAATTACCGAAATAC
1 CCCTAGTTTGTAAAATTACCGAAATAC
**
28925465 CCC-AAATTGTAAAATTACCGAAATA-
1 CCCTAGTTTGTAAAATTACCGAAATAC
* *
28925490 CCCTCAGATTGTAAAATTATCGAAATA-
1 CCCT-AGTTTGTAAAATTACCGAAATAC
* * * *
28925517 CCCTCGGATTGAAAAATTACCAAAATA-
1 CCCT-AGTTTGTAAAATTACCGAAATAC
* * *
28925544 CCCTCAGATTGTAAAATTATCAAAATAC
1 CCCT-AGTTTGTAAAATTACCGAAATAC
* * *
28925572 CCCTGGTTTGTGAAATTACTGAAATAC
1 CCCTAGTTTGTAAAATTACCGAAATAC
** * *
28925599 CTTTAGATTGTAAAATTACTGAAATA-
1 CCCTAGTTTGTAAAATTACCGAAATAC
*
28925625 CCCTCAGTTTGTAAAATTACTGAAATAC
1 CCCT-AGTTTGTAAAATTACCGAAATAC
28925653 CCCT
1 CCCT
28925657 GTAGGGTAAA
Statistics
Matches: 360, Mismatches: 64, Indels: 37
0.78 0.14 0.08
Matches are distributed among these distances:
25 3 0.01
26 31 0.09
27 284 0.79
28 18 0.05
34 2 0.01
35 22 0.06
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.32
Consensus pattern (27 bp):
CCCTAGTTTGTAAAATTACCGAAATAC
Found at i:28925277 original size:54 final size:53
Alignment explanation
Indices: 28925186--28925654 Score: 424
Period size: 54 Copynumber: 8.6 Consensus size: 53
28925176 GGTTGTTAAG
* *** *
28925186 ACCCTAGTTTGTAAAATTATTAAAATACCC-CTAGTTTGTAAAATTATCGAAATT
1 ACCCCAGTTTGTAAAATTACCGAAATACCCTC-AGATTGTAAAATTATCGAAA-T
* * * * *
28925240 TCCCCAGTTTGTAAAATTACCGAAATACCCCCGGTTTGTAAAATTATTGAAAT
1 ACCCCAGTTTGTAAAATTACCGAAATACCCTCAGATTGTAAAATTATCGAAAT
* *
28925293 ACCTCTAGTTTGTAAAATTACCGAAATACCTTCAGATTGTAAAATTATCGAAAT
1 ACC-CCAGTTTGTAAAATTACCGAAATACCCTCAGATTGTAAAATTATCGAAAT
* * * * * * *
28925347 ACCTCTAGTTTTTAGAATTACCGAAATACCATCGGATTGTAAAATTACCAAAAT
1 ACC-CCAGTTTGTAAAATTACCGAAATACCCTCAGATTGTAAAATTATCGAAAT
* * *
28925401 ACCCTCGAATTGTCGATTTGTAAAATTACCAAAATAACCCT-A-ATTTTTAAAATTACCGAAAT
1 ACCC-C--A-----G-TTTGTAAAATTACCGAAAT-ACCCTCAGA-TTGTAAAATTATCGAAAT
**
28925463 ACCCCAAATTGTAAAATTACCGAAATACCCTCAGATTGTAAAATTATCGAAAT
1 ACCCCAGTTTGTAAAATTACCGAAATACCCTCAGATTGTAAAATTATCGAAAT
* * * * *
28925516 ACCCTCGGATTGAAAAATTACCAAAATACCCTCAGATTGTAAAATTATCAAAAT
1 ACCC-CAGTTTGTAAAATTACCGAAATACCCTCAGATTGTAAAATTATCGAAAT
* * * * *
28925570 ACCCCTGGTTTGTGAAATTACTGAAATACCTTTAGATTGTAAAATTA-CTGAAAT
1 ACCCC-AGTTTGTAAAATTACCGAAATACCCTCAGATTGTAAAATTATC-GAAAT
*
28925624 ACCCTCAGTTTGTAAAATTACTGAAATACCC
1 ACCC-CAGTTTGTAAAATTACCGAAATACCC
28925655 CTGTAGGGTA
Statistics
Matches: 347, Mismatches: 49, Indels: 38
0.80 0.11 0.09
Matches are distributed among these distances:
52 5 0.01
53 44 0.13
54 251 0.72
55 2 0.01
56 1 0.00
59 1 0.00
61 3 0.01
62 36 0.10
63 4 0.01
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.32
Consensus pattern (53 bp):
ACCCCAGTTTGTAAAATTACCGAAATACCCTCAGATTGTAAAATTATCGAAAT
Found at i:28927218 original size:15 final size:15
Alignment explanation
Indices: 28927198--28927227 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28927188 TTTGGCCGAA
28927198 TAGGCACTCTTATTT
1 TAGGCACTCTTATTT
*
28927213 TAGGCATTCTTATTT
1 TAGGCACTCTTATTT
28927228 CTTTCTTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (15 bp):
TAGGCACTCTTATTT
Found at i:28929168 original size:46 final size:47
Alignment explanation
Indices: 28929118--28929239 Score: 149
Period size: 46 Copynumber: 2.6 Consensus size: 47
28929108 ACTGATACAT
* * *
28929118 GTCCCAGACATGTCTTACACTGGCT-TACGTTTCGAGGCCGATG-CAA
1 GTCCCAGACATGTCTTACACTGGCTCT-CGTCTCAAGACCGATGCCAA
* * * *
28929164 GTCCCAAACATGTCTTACACTAGCTCTCGTCTCAATACCGATGCCAT
1 GTCCCAGACATGTCTTACACTGGCTCTCGTCTCAAGACCGATGCCAA
28929211 GTCCCAGACATGGTCTTACACTGGCTCTC
1 GTCCCAGACAT-GTCTTACACTGGCTCTC
28929240 ATAATGTGGC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
46 35 0.55
47 13 0.20
48 16 0.25
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.27
Consensus pattern (47 bp):
GTCCCAGACATGTCTTACACTGGCTCTCGTCTCAAGACCGATGCCAA
Found at i:28930664 original size:54 final size:53
Alignment explanation
Indices: 28930572--28931034 Score: 411
Period size: 54 Copynumber: 8.6 Consensus size: 53
28930562 GGTTGTTAAG
* * * *
28930572 ACCCTAGTTTGTAAAATTATTAAAATACCTCT-AGTTTGTAAAATTATCGAAAT
1 ACCCCAGTTTGTAAAATTACTGAAATACCCCTGA-TTTGTAAAATTATCGAAAT
* *
28930625 ACCACCAGTTTGTAAAATTACCGAAATACCCCTGATTTGTAAAATTACCGAAAT
1 ACC-CCAGTTTGTAAAATTACTGAAATACCCCTGATTTGTAAAATTATCGAAAT
* * * * ** * *
28930679 ACCCCCAATTTATGAAATTACCGAAATAGCTTCGGA-TTGTAAAATTATTGAAAT
1 A-CCCCAGTTTGTAAAATTACTGAAATA-CCCCTGATTTGTAAAATTATCGAAAT
* * * * *
28930733 ACCTCGGATTTGTAAAATTAGTGAAATACCCCCGATTTGTAAAATTAACGAAAT
1 ACCCCAG-TTTGTAAAATTACTGAAATACCCCTGATTTGTAAAATTATCGAAAT
* * * * * * *
28930787 ACCCTC-GAATTATAAAATTACTAAAATACCCTCAGA-TTGTAAAGTTACCAAAAT
1 ACCC-CAG-TTTGTAAAATTACTGAAATACCC-CTGATTTGTAAAATTATCGAAAT
* * * *
28930841 ACCCTCGGTTTGTAAAATTACCGAAATACCCTTGACTTGTAAAATTATCGAAAT
1 ACCC-CAGTTTGTAAAATTACTGAAATACCCCTGATTTGTAAAATTATCGAAAT
* * * *
28930895 ACCCCTGATTTATAAAATTACTGAAATACCCTTGAATTGTAAAATTATCGAAAT
1 ACCCCAG-TTTGTAAAATTACTGAAATACCCCTGATTTGTAAAATTATCGAAAT
*
28930949 ACCCCTAGTTTTTAAAATTA-TCGAAATACCCCTG-TTT-TAAAATTA-CTGAAAT
1 ACCCC-AGTTTGTAAAATTACT-GAAATACCCCTGATTTGTAAAATTATC-GAAAT
* *
28931001 ACCCCTAATTTGTAAAATTACTAAAATACCCCTG
1 ACCCC-AGTTTGTAAAATTACTGAAATACCCCTG
28931035 TAGGGTAAAA
Statistics
Matches: 340, Mismatches: 55, Indels: 31
0.80 0.13 0.07
Matches are distributed among these distances:
51 1 0.00
52 42 0.12
53 18 0.05
54 266 0.78
55 13 0.04
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (53 bp):
ACCCCAGTTTGTAAAATTACTGAAATACCCCTGATTTGTAAAATTATCGAAAT
Found at i:28930719 original size:81 final size:81
Alignment explanation
Indices: 28930579--28931031 Score: 427
Period size: 81 Copynumber: 5.6 Consensus size: 81
28930569 AAGACCCTAG
* * * * * * * *
28930579 TTTGTAAAATTATTAAAATACCTCTAGTTTGTAAAATTATCGAAATACCAC-CAGTTTGTAAAAT
1 TTTGTAAAATTACTGAAATACCCCCAATTTGTAAAATTACCGAAATACC-CTCGGATTGTAAAAT
*
28930643 TACCGAAATACCCCTGA
65 TATCGAAATACCCCTGA
* * * * *
28930660 TTTGTAAAATTACCGAAATACCCCCAATTTATGAAATTACCGAAATAGCTTCGGATTGTAAAATT
1 TTTGTAAAATTACTGAAATACCCCCAATTTGTAAAATTACCGAAATACCCTCGGATTGTAAAATT
* * *
28930725 ATTGAAATACCTCGGA
66 ATCGAAATACCCCTGA
* * * * *
28930741 TTTGTAAAATTAGTGAAATACCCCCGATTTGTAAAATTAACGAAATACCCTCGAATTATAAAATT
1 TTTGTAAAATTACTGAAATACCCCCAATTTGTAAAATTACCGAAATACCCTCGGATTGTAAAATT
* *
28930806 A-CTAAAATACCCTCAGA
66 ATC-GAAATACCC-CTGA
* ** * ** *
28930823 -TTGTAAAGTTACCAAAATACCCTCGGTTTGTAAAATTACCGAAATACCCT-TGACTTGTAAAAT
1 TTTGTAAAATTACTGAAATACCCCCAATTTGTAAAATTACCGAAATACCCTCGGA-TTGTAAAAT
28930886 TATCGAAATACCCCTGA
65 TATCGAAATACCCCTGA
* ** * * * *
28930903 TTTATAAAATTACTGAAATACCCTTGAA-TTGTAAAATTATCGAAATACCC-CTAGTTTTTAAAA
1 TTTGTAAAATTACTGAAATACCC-CCAATTTGTAAAATTACCGAAATACCCTC-GGATTGTAAAA
28930966 TTATCGAAATACCCCTG-
64 TTATCGAAATACCCCTGA
* **
28930983 TTT-TAAAATTACTGAAATACCCCTAATTTGTAAAATTACTAAAATACCC
1 TTTGTAAAATTACTGAAATACCCCCAATTTGTAAAATTACCGAAATACCC
28931032 CTGTAGGGTA
Statistics
Matches: 303, Mismatches: 59, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
78 2 0.01
79 38 0.13
80 7 0.02
81 250 0.83
82 6 0.02
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (81 bp):
TTTGTAAAATTACTGAAATACCCCCAATTTGTAAAATTACCGAAATACCCTCGGATTGTAAAATT
ATCGAAATACCCCTGA
Found at i:28931032 original size:27 final size:27
Alignment explanation
Indices: 28930573--28931033 Score: 329
Period size: 27 Copynumber: 17.1 Consensus size: 27
28930563 GTTGTTAAGA
* * *
28930573 CCCTAGTTTGTAAAATTATTAAAATAC
1 CCCTAATTTGTAAAATTACTGAAATAC
* *
28930600 CTCTAGTTTGTAAAATTA-TCGAAATAC
1 CCCTAATTTGTAAAATTACT-GAAATAC
* *
28930627 CACC-AGTTTGTAAAATTACCGAAATAC
1 C-CCTAATTTGTAAAATTACTGAAATAC
* *
28930654 CCCTGATTTGTAAAATTACCGAAATAC
1 CCCTAATTTGTAAAATTACTGAAATAC
* * * *
28930681 CCCCAATTTATGAAATTACCGAAATAGC
1 CCCTAATTTGTAAAATTACTGAAATA-C
** ** *
28930709 TTCGGA-TTGTAAAATTATTGAAATAC
1 CCCTAATTTGTAAAATTACTGAAATAC
* ** *
28930735 CTCGGATTTGTAAAATTAGTGAAATAC
1 CCCTAATTTGTAAAATTACTGAAATAC
**
28930762 CCCCGATTTGTAAAATTAAC-GAAATAC
1 CCCTAATTTGTAAAATT-ACTGAAATAC
* * *
28930789 CCTCGAA-TTATAAAATTACTAAAATA-
1 CC-CTAATTTGTAAAATTACTGAAATAC
* **
28930815 CCCTCAGA-TTGTAAAGTTACCAAAATA-
1 CCCT-A-ATTTGTAAAATTACTGAAATAC
** *
28930842 CCCTCGGTTTGTAAAATTACCGAAATAC
1 CCCT-AATTTGTAAAATTACTGAAATAC
* * *
28930870 CCTTGACTTGTAAAATTA-TCGAAATAC
1 CCCTAATTTGTAAAATTACT-GAAATAC
* *
28930897 CCCTGATTTATAAAATTACTGAAATAC
1 CCCTAATTTGTAAAATTACTGAAATAC
*
28930924 CCTTGAA-TTGTAAAATTA-TCGAAATAC
1 CCCT-AATTTGTAAAATTACT-GAAATAC
* *
28930951 CCCTAGTTTTTAAAATTA-TCGAAATAC
1 CCCTAATTTGTAAAATTACT-GAAATAC
*
28930978 CCCT-GTTT-TAAAATTACTGAAATAC
1 CCCTAATTTGTAAAATTACTGAAATAC
*
28931003 CCCTAATTTGTAAAATTACTAAAATAC
1 CCCTAATTTGTAAAATTACTGAAATAC
28931030 CCCT
1 CCCT
28931034 GTAGGGTAAA
Statistics
Matches: 363, Mismatches: 50, Indels: 42
0.80 0.11 0.09
Matches are distributed among these distances:
25 20 0.06
26 24 0.07
27 307 0.85
28 12 0.03
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (27 bp):
CCCTAATTTGTAAAATTACTGAAATAC
Found at i:28931042 original size:27 final size:27
Alignment explanation
Indices: 28930986--28931050 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
28930976 ACCCCTGTTT
* **
28930986 TAAAATTACTGAAATACCCCTAATTTG
1 TAAAATTACTAAAATACCCCTAATGGG
*
28931013 TAAAATTACTAAAATACCCCT-GTAGGG
1 TAAAATTACTAAAATACCCCTAAT-GGG
*
28931040 TAAAATGACTA
1 TAAAATTACTA
28931051 TTTTGCCCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 1 0.03
27 31 0.97
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (27 bp):
TAAAATTACTAAAATACCCCTAATGGG
Found at i:28954828 original size:9 final size:8
Alignment explanation
Indices: 28954803--28954838 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
28954793 TCAAAACTAC
28954803 AAAATTTA
1 AAAATTTA
28954811 AAAATTTA
1 AAAATTTA
28954819 AAAATATTA
1 AAAAT-TTA
28954828 ATAAATTTA
1 A-AAATTTA
28954837 AA
1 AA
28954839 TACGCTTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 14 0.54
9 8 0.31
10 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AAAATTTA
Found at i:28954835 original size:18 final size:16
Alignment explanation
Indices: 28954803--28954838 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
28954793 TCAAAACTAC
28954803 AAAATTTAAAAATTTA
1 AAAATTTAAAAATTTA
28954819 AAAATATTAATAAATTTA
1 AAAAT-TTAA-AAATTTA
28954837 AA
1 AA
28954839 TACGCTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 4 0.22
18 9 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATTTAAAAATTTA
Found at i:28956849 original size:40 final size:40
Alignment explanation
Indices: 28956812--28957037 Score: 271
Period size: 40 Copynumber: 5.7 Consensus size: 40
28956802 GCTACTCGTT
* *
28956812 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
28956852 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28956892 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** *
28956932 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCGCA
** * * * * *
28956972 CAAATGCCTTC-GGATCTTAGTCCAGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
28957013 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
28957038 CATCATTCAA
Statistics
Matches: 169, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
39 3 0.02
40 154 0.91
41 12 0.07
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:28964858 original size:40 final size:40
Alignment explanation
Indices: 28964821--28965046 Score: 271
Period size: 40 Copynumber: 5.7 Consensus size: 40
28964811 GCTACTCGTT
* *
28964821 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
28964861 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
28964901 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** *
28964941 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCGCA
** * * * * *
28964981 CAAATGCCTTC-GGATCTTAGTCCGTATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
28965022 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
28965047 CATCATTCAA
Statistics
Matches: 169, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
39 3 0.02
40 154 0.91
41 12 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:28969046 original size:34 final size:34
Alignment explanation
Indices: 28969007--28969077 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
28968997 AAATGCATTA
*
28969007 GTAATAGTATTACATAATCCCTCCAAATTAGTGT
1 GTAATAGTAGTACATAATCCCTCCAAATTAGTGT
28969041 GTAATAGTAGTACATAATCCCTCCAAATTAGTGT
1 GTAATAGTAGTACATAATCCCTCCAAATTAGTGT
28969075 GTA
1 GTA
28969078 CCATGACTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (34 bp):
GTAATAGTAGTACATAATCCCTCCAAATTAGTGT
Found at i:28974885 original size:46 final size:46
Alignment explanation
Indices: 28974835--28975010 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
28974825 TGGTTGAGCA
28974835 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
28974881 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
28974926 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * **
28974974 CCCGAGCTCGTTGAGTTGAGTCCGAGTTTGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28975011 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.56
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:28974991 original size:93 final size:93
Alignment explanation
Indices: 28974832--28975001 Score: 313
Period size: 93 Copynumber: 1.8 Consensus size: 93
28974822 GGATGGTTGA
* *
28974832 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28974897 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
28974925 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28974990 TGAGTCCGAGTT
66 TGAGTCCGAGTT
28975002 TGCTTATGGG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:28976545 original size:22 final size:22
Alignment explanation
Indices: 28976520--28976563 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
28976510 ATAGGTTCTG
28976520 TACATACCTGTATCGCCTCGTA
1 TACATACCTGTATCGCCTCGTA
*
28976542 TACATACCTGTATTGCCTCGTA
1 TACATACCTGTATCGCCTCGTA
28976564 CTAACCTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.34
Consensus pattern (22 bp):
TACATACCTGTATCGCCTCGTA
Found at i:28980390 original size:27 final size:26
Alignment explanation
Indices: 28980325--28980455 Score: 104
Period size: 27 Copynumber: 4.9 Consensus size: 26
28980315 AATACTTTAG
* *
28980325 TTTACTAAAATTACTGAAATACCC-CCA
1 TTTA-TAAAATTAC-CAAATACCCTCGA
* *
28980352 GTTGTAAAATTACCAAAGTACCCTCGA
1 TTTATAAAATTACCAAA-TACCCTCGA
**
28980379 TTTATAAAATTACCCAAATATTCTCGA
1 TTTATAAAATTA-CCAAATACCCTCGA
* *
28980406 TTTGTAAAATTACCGAAATACCGTCGA
1 TTTATAAAATTACC-AAATACCCTCGA
* *
28980433 TTGA-AAAATTACTAAAATACCCT
1 TTTATAAAATTAC-CAAATACCCT
28980456 TGTAAGGTAG
Statistics
Matches: 83, Mismatches: 16, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
25 3 0.04
26 32 0.39
27 43 0.52
28 5 0.06
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (26 bp):
TTTATAAAATTACCAAATACCCTCGA
Found at i:28980479 original size:27 final size:27
Alignment explanation
Indices: 28980439--28980645 Score: 244
Period size: 27 Copynumber: 7.7 Consensus size: 27
28980429 TCGATTGAAA
* *
28980439 AATTACTA-AAATACCCTTGTAAGGTAG
1 AATTAC-AGAAATACCCCTGTAGGGTAG
*
28980466 AAATATC-GAAATACCCCTGTAGGGTAG
1 AATTA-CAGAAATACCCCTGTAGGGTAG
*
28980493 AATTACAGAAATACCCCTGTAGAGTAG
1 AATTACAGAAATACCCCTGTAGGGTAG
*
28980520 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACAGAAATACCCCTGTAGGGTAG
*
28980547 AATTATC-GAAATACCCTTGTAGGGTAG
1 AATTA-CAGAAATACCCCTGTAGGGTAG
* **
28980574 AAATACTA-AAATATTCCTGTAGGGTAG
1 AATTAC-AGAAATACCCCTGTAGGGTAG
28980601 AATTACTA-AAATACCCCTGTAGGGTAG
1 AATTAC-AGAAATACCCCTGTAGGGTAG
*
28980628 AATTACTGAAATACCCCT
1 AATTACAGAAATACCCCT
28980646 AGGGTGTTAA
Statistics
Matches: 157, Mismatches: 16, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
26 2 0.01
27 153 0.97
28 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (27 bp):
AATTACAGAAATACCCCTGTAGGGTAG
Found at i:28980546 original size:81 final size:81
Alignment explanation
Indices: 28980439--28980645 Score: 301
Period size: 81 Copynumber: 2.6 Consensus size: 81
28980429 TCGATTGAAA
* * * *
28980439 AATTACTAAAATACCCTTGTAAGGTAGAAATATCGAAATACCCCTGTAGGGTAGAATTAC-AGAA
1 AATTACTAAAATACCCCTGTAGGGTAGAATTATCGAAATACCCCTGTAGGGTAGAAATACTA-AA
28980503 ATACCCCTGTAGAGTAG
65 ATACCCCTGTAGAGTAG
* *
28980520 AATTACTGAAATACCCCTGTAGGGTAGAATTATCGAAATACCCTTGTAGGGTAGAAATACTAAAA
1 AATTACTAAAATACCCCTGTAGGGTAGAATTATCGAAATACCCCTGTAGGGTAGAAATACTAAAA
** *
28980585 TATTCCTGTAGGGTAG
66 TACCCCTGTAGAGTAG
28980601 AATTACTAAAATACCCCTGTAGGGTAGAATTA-CTGAAATACCCCT
1 AATTACTAAAATACCCCTGTAGGGTAGAATTATC-GAAATACCCCT
28980646 AGGGTGTTAA
Statistics
Matches: 113, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
80 1 0.01
81 111 0.98
82 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (81 bp):
AATTACTAAAATACCCCTGTAGGGTAGAATTATCGAAATACCCCTGTAGGGTAGAAATACTAAAA
TACCCCTGTAGAGTAG
Found at i:28980889 original size:27 final size:26
Alignment explanation
Indices: 28980859--28980940 Score: 101
Period size: 27 Copynumber: 3.1 Consensus size: 26
28980849 GGATGAAGCA
28980859 TTCTGGTGGCTATGCCACAAATATCTG
1 TTCTGGTGGCTATGCCAC-AATATCTG
*
28980886 TTCTGGTGGCTCTGCCACAATATCTG
1 TTCTGGTGGCTATGCCACAATATCTG
* * * *
28980912 TATTTGGTGACTTTGTCACAATATCTG
1 T-TCTGGTGGCTATGCCACAATATCTG
28980939 TT
1 TT
28980941 GACCGATCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
26 10 0.20
27 39 0.80
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.39
Consensus pattern (26 bp):
TTCTGGTGGCTATGCCACAATATCTG
Found at i:28981076 original size:22 final size:22
Alignment explanation
Indices: 28981048--28981106 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
28981038 CCCATTATCG
28981048 ATGGCTTTGTGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
* * * *
28981070 ATGGCTTTGTGCCATCTTGACT
1 ATGGCTTTGTGCCAACCTAAAT
*
28981092 ATGGCTTCGTGCCAA
1 ATGGCTTTGTGCCAA
28981107 ACGTATTTAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Found at i:28981346 original size:27 final size:26
Alignment explanation
Indices: 28981273--28981347 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 26
28981263 AGTGGATTTG
* * *
28981273 CCACATTATCTGTTTCTAGTGGCTATG
1 CCACAATATCTG-TTCTGGTGGCTATA
* * *
28981300 CCACAAATATCTATTTTGGTGGCTCTA
1 CCAC-AATATCTGTTCTGGTGGCTATA
28981327 CCACAATATCTGTATCTGGTG
1 CCACAATATCTGT-TCTGGTG
28981348 ACTTTGTCAC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
26 8 0.21
27 24 0.63
28 6 0.16
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (26 bp):
CCACAATATCTGTTCTGGTGGCTATA
Found at i:28985735 original size:25 final size:24
Alignment explanation
Indices: 28985707--28985753 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
28985697 AAGGGAATAG
28985707 GGGAAGGAA-ATGAGGAAAAATGAAA
1 GGGAAGGAAGA-GA-GAAAAATGAAA
*
28985732 GGGAATGAAGAGAGAAAAATGA
1 GGGAAGGAAGAGAGAAAAATGA
28985754 GAGAGAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 9 0.45
25 10 0.50
26 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.36, T:0.09
Consensus pattern (24 bp):
GGGAAGGAAGAGAGAAAAATGAAA
Found at i:28985749 original size:24 final size:25
Alignment explanation
Indices: 28985721--28985769 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
28985711 AGGAAATGAG
*
28985721 GAAAAATGAAAG-GGAATGAAGAGA
1 GAAAAATGAAAGAGAAATGAAGAGA
*
28985745 GAAAAATGAGAGAGAAATGAAGAGA
1 GAAAAATGAAAGAGAAATGAAGAGA
28985770 TGACAAGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.59, C:0.00, G:0.33, T:0.08
Consensus pattern (25 bp):
GAAAAATGAAAGAGAAATGAAGAGA
Found at i:29010724 original size:44 final size:45
Alignment explanation
Indices: 29010634--29010762 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
29010624 ACAGAATAGA
*
29010634 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
29010680 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
29010724 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
29010763 CAGGGTATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:29030437 original size:46 final size:44
Alignment explanation
Indices: 29030333--29030440 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
29030323 TGTCTTTGAC
** * * *
29030333 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
29030377 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
29030423 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
29030441 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:29039745 original size:39 final size:39
Alignment explanation
Indices: 29039692--29039815 Score: 158
Period size: 39 Copynumber: 3.2 Consensus size: 39
29039682 GGATTTTAGC
* * ** *
29039692 CCGGACATATTTCCAGCATGTAGCCTGCAGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
* * *
29039731 CCGGTTATAATTCCAGCACATAGCCTACGGACTTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
* *
29039770 CCAGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
29039809 CCGGATA
1 CCGGATA
29039816 AATATCACTG
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 71 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.24
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGT
Found at i:29047540 original size:22 final size:22
Alignment explanation
Indices: 29047510--29047552 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
29047500 AACTTACTAT
* *
29047510 TTTCTGCTCACTAGAGCTTACC
1 TTTCAGCTCAATAGAGCTTACC
29047532 TTTCAGCTCAATAGAGCTTAC
1 TTTCAGCTCAATAGAGCTTAC
29047553 TGTCTATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.35
Consensus pattern (22 bp):
TTTCAGCTCAATAGAGCTTACC
Found at i:29053907 original size:34 final size:34
Alignment explanation
Indices: 29053869--29053936 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
29053859 ATCCCATATG
* *
29053869 TCCATCGAAATTCATCATTCAAACGGAACTTAAC
1 TCCATCGAAATTCACCATTCAAACAGAACTTAAC
* *
29053903 TCCATTGAAATTCACCATTCAAATAGAACTTAAC
1 TCCATCGAAATTCACCATTCAAACAGAACTTAAC
29053937 ATTTTCCAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.40, C:0.25, G:0.07, T:0.28
Consensus pattern (34 bp):
TCCATCGAAATTCACCATTCAAACAGAACTTAAC
Found at i:29055882 original size:46 final size:45
Alignment explanation
Indices: 29055832--29055973 Score: 132
Period size: 43 Copynumber: 3.1 Consensus size: 45
29055822 ACATGTCTAA
*
29055832 GACATGCATCGGCCTCGAGACGTAAGCCACTGTAAGA-CATGTTTGG
1 GACATGCATCGGCCTCGAGATGTAAG-CA-TGTAAGACCATGTTTGG
* **
29055878 GACATCCATCGGCGACGAGATG-ATAG--TGTAAGACCATGTTTGG
1 GACATGCATCGGCCTCGAGATGTA-AGCATGTAAGACCATGTTTGG
* * *
29055921 GACATGGCATC-GACTTGAGATGTAAGCTAGTGTAAGACCATGTATGG
1 GACAT-GCATCGGCCTCGAGATGTAAGC-A-TGTAAGACCATGTTTGG
29055968 GACATG
1 GACATG
29055974 GCGTTGGTAC
Statistics
Matches: 78, Mismatches: 10, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
42 7 0.09
43 23 0.29
44 5 0.06
45 1 0.01
46 21 0.27
47 21 0.27
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (45 bp):
GACATGCATCGGCCTCGAGATGTAAGCATGTAAGACCATGTTTGG
Found at i:29055969 original size:47 final size:46
Alignment explanation
Indices: 29055717--29055975 Score: 166
Period size: 47 Copynumber: 5.7 Consensus size: 46
29055707 GTTGTTGTTG
*
29055717 GCTAGTGTAAGA-CATGCCTGGGACAT-GCATCAGCCACATT-ATGA-G-A
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-G--AC-TTGA-GACGAA
* *
29055763 GCTATTGTAAGACCATGTCTGGGACATGGCATC-AGCATTGTGACGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGA-C-TTGAGACGA-A
** * *
29055811 GCTAGTGTAAGA-CATGTCTAAGACAT-GCATCGGCCTCGAGACGTAA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-GACTTGAGACG-AA
* * * * * *
29055857 GCCACTGTAAGA-CATGTTTGGGACAT-CCATCGGC--GACGA-GAT
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGA-GACGAA
* * *
29055899 GATAGTGTAAGACCATGTTTGGGACATGGCATCGACTTGAGATGTAA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGACG-AA
*
29055946 GCTAGTGTAAGACCATGTATGGGACATGGC
1 GCTAGTGTAAGACCATGTCTGGGACATGGC
29055976 GTTGGTACGT
Statistics
Matches: 171, Mismatches: 25, Indels: 33
0.75 0.11 0.14
Matches are distributed among these distances:
42 10 0.06
43 17 0.10
44 9 0.05
45 10 0.06
46 52 0.30
47 56 0.33
48 17 0.10
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.24
Consensus pattern (46 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGACGAA
Found at i:29063429 original size:46 final size:46
Alignment explanation
Indices: 29063286--29063453 Score: 153
Period size: 46 Copynumber: 3.6 Consensus size: 46
29063276 GTTGTTGTTG
* * **
29063286 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCAC-A-TTATGAGA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCAGCCTCGAGACAT-A-A
* * * * * *
29063332 GCCAATGTAAGACCATGTCTAGGACGTGGCATCAGCATTGAGACGA-GA
1 GCTAGTGTAAGA-CATGTCTAGGACAT-GCATCAGCCTCGAGAC-ATAA
*
29063380 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGACATAA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCAGCCTCGAGACATAA
* *
29063426 GCTAGTGTAAGACATGTTTGGGACATGC
1 GCTAGTGTAAGACATGTCTAGGACATGC
29063454 GCCTGCTATG
Statistics
Matches: 97, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
45 1 0.01
46 50 0.52
47 25 0.26
48 19 0.20
49 1 0.01
51 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.23
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTAGGACATGCATCAGCCTCGAGACATAA
Found at i:29063499 original size:47 final size:47
Alignment explanation
Indices: 29063330--29063552 Score: 172
Period size: 47 Copynumber: 4.8 Consensus size: 47
29063320 CACATTATGA
* * * * * *
29063330 GAGCCAATGTAAGACCATGTCTAGGACGTGGCATC-AGCATTGAGACGA
1 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGA-C-TTGAGATGT
* * * * * **
29063378 GAGCTAGTGTAAGA-CATGTCTAGGACAT-GCATCGGCCTCGAGACAT
1 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATC-GACTTGAGATGT
* * *
29063424 AAGCTAGTGTAAGA-CATGTTTGGGACATGCGCCT-G-CTATGAGATGAT
1 GAGCCAGTGTAAGACCATGTTTGGGACATG-GCATCGACT-TGAGATG-T
*
29063471 -AGTCAGTGTAAGACCATGTTTGGGACATGGCATCGACTTGAGATGT
1 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGACTTGAGATGT
* *
29063517 GAGCCAATGTAAGACCATGTCTGGGACATGGCATCG
1 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCG
29063553 GCACCTTACC
Statistics
Matches: 145, Mismatches: 20, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
45 2 0.01
46 56 0.39
47 70 0.48
48 17 0.12
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (47 bp):
GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGACTTGAGATGT
Found at i:29065218 original size:60 final size:60
Alignment explanation
Indices: 29065125--29065245 Score: 206
Period size: 60 Copynumber: 2.0 Consensus size: 60
29065115 TGATATAAAA
* *
29065125 TGATAATATTAAACATTTGTTTAATGTATCATCTTTTAAATTTTCCACTTTCCAATTTAG
1 TGATAATATTAAACATTTATTTAATGTATCATCTTTTAAACTTTCCACTTTCCAATTTAG
* *
29065185 TGATAATATTAAACATTTATTTAATTTATCATCTTTTAAGCTTTCCACTTTCCAATTTAG
1 TGATAATATTAAACATTTATTTAATGTATCATCTTTTAAACTTTCCACTTTCCAATTTAG
29065245 T
1 T
29065246 CATTGTCCTT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (60 bp):
TGATAATATTAAACATTTATTTAATGTATCATCTTTTAAACTTTCCACTTTCCAATTTAG
Found at i:29067919 original size:31 final size:31
Alignment explanation
Indices: 29067883--29067946 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
29067873 TTAAGTTCCG
*
29067883 TTAATTTTCCTTGAAACTGGAATCATACACC
1 TTAATTTTCCTTGAAACTAGAATCATACACC
29067914 TTAATTTTCCTTGAAACTAGAATCATACACC
1 TTAATTTTCCTTGAAACTAGAATCATACACC
29067945 TT
1 TT
29067947 TATCCCATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.38
Consensus pattern (31 bp):
TTAATTTTCCTTGAAACTAGAATCATACACC
Found at i:29068893 original size:46 final size:47
Alignment explanation
Indices: 29068799--29068931 Score: 128
Period size: 46 Copynumber: 2.9 Consensus size: 47
29068789 ATAATCTCAC
* * *
29068799 CCATAATGAACTCGAAACGCAACTCAACGAGCTCAGG-TG-TTCGTAT
1 CCATAATGAACTCGGAACGCAACTCAACGAG-TTAGGATGCTTCGCAT
* *
29068845 CCATAATGAACTCGGAACACAACTCAACGAGTTTGGATGCTT-GCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTAGGATGCTTCGCAT
* ** * * *
29068891 CCATAGGTGAACTTAGAATGCAACTCAACAAGTTCGGATGC
1 CCATA-ATGAACTCGGAACGCAACTCAACGAGTTAGGATGC
29068932 CTCATAATTC
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
45 3 0.04
46 39 0.54
47 30 0.42
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (47 bp):
CCATAATGAACTCGGAACGCAACTCAACGAGTTAGGATGCTTCGCAT
Found at i:29071350 original size:19 final size:19
Alignment explanation
Indices: 29071326--29071366 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
29071316 TCACTTTTTT
29071326 ACTTAAATTCATTGTTAAA
1 ACTTAAATTCATTGTTAAA
29071345 ACTTAAATTCATTGTTAAA
1 ACTTAAATTCATTGTTAAA
29071364 ACT
1 ACT
29071367 AAGTAATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.41
Consensus pattern (19 bp):
ACTTAAATTCATTGTTAAA
Found at i:29071377 original size:17 final size:19
Alignment explanation
Indices: 29071326--29071377 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
29071316 TCACTTTTTT
* *
29071326 ACTTAAATTCATTGTTAAA
1 ACTTAAAGTAATTGTTAAA
* *
29071345 ACTTAAATTCATTGTTAAA
1 ACTTAAAGTAATTGTTAAA
29071364 AC-T-AAGTAATTGTT
1 ACTTAAAGTAATTGTT
29071378 TAATAAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.29
18 1 0.03
19 21 0.68
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (19 bp):
ACTTAAAGTAATTGTTAAA
Found at i:29073673 original size:68 final size:66
Alignment explanation
Indices: 29073601--29073772 Score: 165
Period size: 67 Copynumber: 2.6 Consensus size: 66
29073591 CATCATGTGT
* * * *
29073601 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCACATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC-AG-CA-TAT-ATGTAGCTAGGTCACATGCGTGATACCAGTGAAGGACACCA
29073664 TGTAG
62 TGTAG
* * * *
29073669 ACAAGAGAGCTACAGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACAGCATATATGTAGCTAGGTCACATGCGTGATACCA-GTGAAGGACACCATGT
29073734 AG
65 AG
*
29073736 ACAAGAGAGCTACGAG-ATAAACTG--GCTAGGTCACATG
1 ACAAGAGAGCTAC-AGCATATA-TGTAGCTAGGTCACATG
29073773 GGTGGTACTA
Statistics
Matches: 89, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
64 23 0.26
65 3 0.03
66 15 0.17
67 31 0.35
68 17 0.19
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (66 bp):
ACAAGAGAGCTACAGCATATATGTAGCTAGGTCACATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:29086003 original size:39 final size:39
Alignment explanation
Indices: 29085940--29086236 Score: 303
Period size: 39 Copynumber: 7.5 Consensus size: 39
29085930 CAAAGCATGT
* *
29085940 GGGACTTTAAGCCCGAATATAATACCAGCAC-AAAGCCTGC
1 GGGAC-TT-AGCCCGGATATAATACCAGCACGAAAGCCTTC
* *
29085980 GGGACTTTAGCCCGGATATAATACCAGTACGAATGCCTTC
1 GGGAC-TTAGCCCGGATATAATACCAGCACGAAAGCCTTC
* * *
29086020 GGGACGTAGCCCGGATATAACACCAGCGC-AAATGCCTTTC
1 GGGACTTAGCCCGGATATAATACCAGCACGAAA-GCC-TTC
* **
29086060 GGGACTTAGCCCGGATATAATACCAGTACGAATTCCTTC
1 GGGACTTAGCCCGGATATAATACCAGCACGAAAGCCTTC
* **
29086099 GGGACTTAGCCCAGATATAATACCAGCACGAATTCCTTC
1 GGGACTTAGCCCGGATATAATACCAGCACGAAAGCCTTC
* * * * * **
29086138 GGGATTTATCCTGAACATAATACCAGCACGAATTCCTTC
1 GGGACTTAGCCCGGATATAATACCAGCACGAAAGCCTTC
* *
29086177 GGGACTTAGCTCGGATATAACACCAGCAC-AAATGCCTTC
1 GGGACTTAGCCCGGATATAATACCAGCACGAAA-GCCTTC
* *
29086216 GGGACTTAACTCGGATATAAT
1 GGGACTTAGCCCGGATATAAT
29086237 TCTCCATTAT
Statistics
Matches: 218, Mismatches: 34, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
38 4 0.02
39 162 0.74
40 50 0.23
41 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (39 bp):
GGGACTTAGCCCGGATATAATACCAGCACGAAAGCCTTC
Found at i:29086176 original size:78 final size:78
Alignment explanation
Indices: 29085940--29086236 Score: 371
Period size: 78 Copynumber: 3.8 Consensus size: 78
29085930 CAAAGCATGT
* * *
29085940 GGGACTTTAAGCCCGAATATAATACCAGCACAAA-GCCTGCGGGACTTTAGCCCGGATATAATAC
1 GGGAC-TT-AGCCCGGATATAACACCAGCACAAATGCCTTCGGGA-TTTAGCCCGGATATAATAC
*
29086004 CAGTACGAATGCCTTC
63 CAGTACGAATTCCTTC
* * *
29086020 GGGACGTAGCCCGGATATAACACCAGCGCAAATGCCTTTCGGGACTTAGCCCGGATATAATACCA
1 GGGACTTAGCCCGGATATAACACCAGCACAAATGCC-TTCGGGATTTAGCCCGGATATAATACCA
29086085 GTACGAATTCCTTC
65 GTACGAATTCCTTC
* * * * * * * *
29086099 GGGACTTAGCCCAGATATAATACCAGCACGAATTCCTTCGGGATTTATCCTGAACATAATACCAG
1 GGGACTTAGCCCGGATATAACACCAGCACAAATGCCTTCGGGATTTAGCCCGGATATAATACCAG
*
29086164 CACGAATTCCTTC
66 TACGAATTCCTTC
* * * *
29086177 GGGACTTAGCTCGGATATAACACCAGCACAAATGCCTTCGGGACTTAACTCGGATATAAT
1 GGGACTTAGCCCGGATATAACACCAGCACAAATGCCTTCGGGATTTAGCCCGGATATAAT
29086237 TCTCCATTAT
Statistics
Matches: 185, Mismatches: 30, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
78 107 0.58
79 67 0.36
80 11 0.06
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (78 bp):
GGGACTTAGCCCGGATATAACACCAGCACAAATGCCTTCGGGATTTAGCCCGGATATAATACCAG
TACGAATTCCTTC
Found at i:29100554 original size:17 final size:17
Alignment explanation
Indices: 29100532--29100565 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
29100522 AATCATTATG
29100532 TAGGTTCATGGAACCCC
1 TAGGTTCATGGAACCCC
29100549 TAGGTTCATGGAACCCC
1 TAGGTTCATGGAACCCC
29100566 CAAACTTGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (17 bp):
TAGGTTCATGGAACCCC
Found at i:29103828 original size:9 final size:10
Alignment explanation
Indices: 29103801--29103827 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
29103791 TGAGTTAAAG
29103801 AAGAAAAATA
1 AAGAAAAATA
29103811 AAGAAAAATA
1 AAGAAAAATA
29103821 AAGAAAA
1 AAGAAAA
29103828 TGGAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.07
Consensus pattern (10 bp):
AAGAAAAATA
Found at i:29113313 original size:8 final size:7
Alignment explanation
Indices: 29113292--29113316 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29113282 TTGGAACATT
29113292 ATTAAAA
1 ATTAAAA
29113299 ATTAAAA
1 ATTAAAA
29113306 ATTAAAA
1 ATTAAAA
29113313 ATTA
1 ATTA
29113317 TAAAGACTAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
ATTAAAA
Found at i:29113990 original size:20 final size:20
Alignment explanation
Indices: 29113973--29114012 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29113963 ATAACTAATT
*
29113973 TCACCATTATCAAACTAAGC
1 TCACCATAATCAAACTAAGC
*
29113993 TCACCCTAATCAAACTAAGC
1 TCACCATAATCAAACTAAGC
29114013 CTAAATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.33, G:0.05, T:0.23
Consensus pattern (20 bp):
TCACCATAATCAAACTAAGC
Done.