Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013584.1 Kokia drynarioides strain JFW-HI SEQ_128611, 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: 119834
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 66 characters in sequence are not A, C, G, or T
Found at i:1487 original size:23 final size:22
Alignment explanation
Indices: 1438--1484 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1428 ATATGTTGTC
* * *
1438 AATAGTAAAAAAAAAAATTCAGA
1 AATA-TAAAATAAAAAATCCAAA
1461 AATATAAAATAAAAAATCCAAA
1 AATATAAAATAAAAAATCCAAA
1483 AA
1 AA
1485 ATAGATAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.72, C:0.06, G:0.04, T:0.17
Consensus pattern (22 bp):
AATATAAAATAAAAAATCCAAA
Found at i:1535 original size:32 final size:34
Alignment explanation
Indices: 1489--1560 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 34
1479 CAAAAAATAG
* *
1489 ATAAAATATTTAAG-AATTATTGAAACTTCAAAA
1 ATAAAATAATTAAGAAATTATTAAAACTTCAAAA
* *
1522 ATAAAA-AATTAAGAAATTTTTAAAATTTCAAAA
1 ATAAAATAATTAAGAAATTATTAAAACTTCAAAA
1555 ATAAAA
1 ATAAAA
1561 CGTTACAGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (34 bp):
ATAAAATAATTAAGAAATTATTAAAACTTCAAAA
Found at i:9069 original size:19 final size:19
Alignment explanation
Indices: 9040--9088 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 19
9030 TGTTACCTAG
* *
9040 AAATCATAAAATATTTTTTA
1 AAAT-ATAAAATATTATTAA
9060 AAATAT-AAA-ATTATTAA
1 AAATATAAAATATTATTAA
9077 AAATATAAAATA
1 AAATATAAAATA
9089 ATCATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 12 0.48
18 6 0.24
19 3 0.12
20 4 0.16
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATATAAAATATTATTAA
Found at i:9209 original size:17 final size:18
Alignment explanation
Indices: 9187--9220 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
9177 TATAAAAATC
9187 ATAA-TTTCTTTTAAAAG
1 ATAATTTTCTTTTAAAAG
*
9204 ATAATTTTTTTTTAAAA
1 ATAATTTTCTTTTAAAA
9221 ATTCTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
ATAATTTTCTTTTAAAAG
Found at i:10574 original size:19 final size:19
Alignment explanation
Indices: 10532--10601 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
10522 TAAAACAATT
* **
10532 TTTTATAAATTTTAAATATG
1 TTTTAT-AATTTTTAATAAC
10552 TTTTATAATTTTTAATAAC
1 TTTTATAATTTTTAATAAC
10571 TTTTA-ATATTTTT-ATAAC
1 TTTTATA-ATTTTTAATAAC
*
10589 ATTTAATAATTTT
1 -TTTTATAATTTT
10602 ATTTTAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
18 6 0.14
19 30 0.70
20 7 0.16
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (19 bp):
TTTTATAATTTTTAATAAC
Found at i:10587 original size:18 final size:18
Alignment explanation
Indices: 10559--10603 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
10549 ATGTTTTATA
*
10559 ATTTTTAATAACTTTTAAT
1 ATTTTT-ATAACATTTAAT
10578 ATTTTTATAACATTTAAT
1 ATTTTTATAACATTTAAT
*
10596 AATTTTAT
1 ATTTTTAT
10604 TTTAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTTTATAACATTTAAT
Found at i:11175 original size:17 final size:16
Alignment explanation
Indices: 11145--11187 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
11135 ATATTTTATT
*
11145 TAATATAAAAATAATTAA
1 TAAT-TAAATATAATT-A
11163 TAATTAAATATAATTA
1 TAATTAAATATAATTA
*
11179 TAAATAAAT
1 TAATTAAAT
11188 TTTAATGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 10 0.43
18 4 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAATTAAATATAATTA
Found at i:12928 original size:24 final size:23
Alignment explanation
Indices: 12877--12922 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
12867 ATTTTGAATT
* *
12877 TTTTTATATTTAATTTATTTTTA
1 TTTTTATATGTAAGTTATTTTTA
12900 TTTTTATAATGTAAGTTATTTTT
1 TTTTTAT-ATGTAAGTTATTTTT
12923 TGTTTTTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (23 bp):
TTTTTATATGTAAGTTATTTTTA
Found at i:13834 original size:43 final size:42
Alignment explanation
Indices: 13761--13893 Score: 158
Period size: 43 Copynumber: 3.1 Consensus size: 42
13751 TTTTGAGGAA
* * *
13761 AAACGCCGCTATAGAACATGGTCTTTAGCGGCGCTTTTCCAAC
1 AAACACCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCC-AC
* * *
13804 AAACACCGCTAAAGATCATGTTCTTCAGCGGCGCTTTTCTCAC
1 AAACACCGCTAAAGAACATGATCTTTAGCGGCGCTTTTC-CAC
* * *
13847 AAACATCGCTAAAGAACATGATCTTTAACGGTGCTTTTCCCAC
1 AAACACCGCTAAAGAACATGATCTTTAGCGGCGCTTTT-CCAC
13890 AAAC
1 AAAC
13894 GCCGATAACA
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
43 75 0.97
44 2 0.03
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (42 bp):
AAACACCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCAC
Found at i:17673 original size:41 final size:41
Alignment explanation
Indices: 17616--17698 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
17606 AAAATCCACT
17616 TTTAGCGGCACTTTTCCATAAGCGCCACTAATGCTATGACC
1 TTTAGCGGCACTTTTCCATAAGCGCCACTAATGCTATGACC
** *
17657 TTTAGCGGTGCTTTTCCATATGCGCCACTAATGCTATGACC
1 TTTAGCGGCACTTTTCCATAAGCGCCACTAATGCTATGACC
17698 T
1 T
17699 AATGCTCTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.22, C:0.28, G:0.18, T:0.33
Consensus pattern (41 bp):
TTTAGCGGCACTTTTCCATAAGCGCCACTAATGCTATGACC
Found at i:17751 original size:54 final size:54
Alignment explanation
Indices: 17643--17752 Score: 139
Period size: 54 Copynumber: 2.0 Consensus size: 54
17633 ATAAGCGCCA
** * *
17643 CTAATGCTATGACCTTTAGCGGTGCTTTTCCATATGCGCCACTAATGCTATGAC
1 CTAATGCTATGACCTTTAGCGGCACTTTTCCATAAGCGCCACTAATACTATGAC
* * ** *
17697 CTAATGCTCTGACCTTTAGCGGCACTTTTTCATAAGCGCCGTTAATACTCTGAC
1 CTAATGCTATGACCTTTAGCGGCACTTTTCCATAAGCGCCACTAATACTATGAC
17751 CT
1 CT
17753 TTAGGGGCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.34
Consensus pattern (54 bp):
CTAATGCTATGACCTTTAGCGGCACTTTTCCATAAGCGCCACTAATACTATGAC
Found at i:17771 original size:41 final size:41
Alignment explanation
Indices: 17697--17842 Score: 168
Period size: 41 Copynumber: 3.6 Consensus size: 41
17687 ATGCTATGAC
* *
17697 CTAATGCTCTGACCTTTAGCGGCACTTTTTCATAAGCGCCG
1 CTAATACTCTGACCTTTAGCGGCGCTTTTTCATAAGCGCCG
* * *
17738 TTAATACTCTGACCTTTAGGGGCGCTTTCTCATAAGCGCCG
1 CTAATACTCTGACCTTTAGCGGCGCTTTTTCATAAGCGCCG
* * * * *
17779 CTAATTCTCTGACATTTAACGGTGTTTTTTCATAAGCGCCG
1 CTAATACTCTGACCTTTAGCGGCGCTTTTTCATAAGCGCCG
* * *
17820 CTAATGCT-TTACCTTTTGCGGCG
1 CTAATACTCTGACCTTTAGCGGCG
17843 TTTATGGAAA
Statistics
Matches: 86, Mismatches: 19, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
40 10 0.12
41 76 0.88
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.35
Consensus pattern (41 bp):
CTAATACTCTGACCTTTAGCGGCGCTTTTTCATAAGCGCCG
Found at i:26804 original size:16 final size:15
Alignment explanation
Indices: 26793--26845 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
26783 AAAATAATTT
26793 TTTTTTAAAATATAA
1 TTTTTTAAAATATAA
26808 TTTTTTAAAA-AT-A
1 TTTTTTAAAATATAA
26821 --TTTTAAAAT-TAA
1 TTTTTTAAAATATAA
26833 -TTTTT-AAATATAA
1 TTTTTTAAAATATAA
26846 AATTATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
11 9 0.26
12 5 0.15
13 8 0.24
14 2 0.06
15 10 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTTTAAAATATAA
Found at i:26837 original size:13 final size:13
Alignment explanation
Indices: 26794--26840 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
26784 AAATAATTTT
26794 TTTTTAAAATATAA
1 TTTTTAAAAT-TAA
*
26808 TTTTTTAAA--AA
1 TTTTTAAAATTAA
26819 TATTTTAAAATTAA
1 T-TTTTAAAATTAA
26833 TTTTTAAA
1 TTTTTAAA
26841 TATAAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
11 3 0.11
12 7 0.25
13 7 0.25
14 11 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTTTTAAAATTAA
Found at i:26902 original size:6 final size:6
Alignment explanation
Indices: 26894--26932 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
26884 TTTCTGCTCT
* *
26894 CCTTCT CCTTCCC CCTTCC CCTTCC CCTTCG CCTTCC CC
1 CCTTCC CCTT-CC CCTTCC CCTTCC CCTTCC CCTTCC CC
26933 ACCACTTGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.00, C:0.64, G:0.03, T:0.33
Consensus pattern (6 bp):
CCTTCC
Found at i:26916 original size:13 final size:13
Alignment explanation
Indices: 26894--26932 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
26884 TTTCTGCTCT
*
26894 CCTTCTCCTTCCC
1 CCTTCCCCTTCCC
26907 CCTTCCCCTT-CC
1 CCTTCCCCTTCCC
*
26919 CCTTCGCCTTCCC
1 CCTTCCCCTTCCC
26932 C
1 C
26933 ACCACTTGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.00, C:0.64, G:0.03, T:0.33
Consensus pattern (13 bp):
CCTTCCCCTTCCC
Found at i:27994 original size:11 final size:11
Alignment explanation
Indices: 27953--27993 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
27943 ATAATTTTAT
*
27953 ATTTAAAAATA
1 ATTTTAAAATA
*
27964 ATTTTAAACTA
1 ATTTTAAAATA
27975 ATTTTAAAAT-
1 ATTTTAAAATA
27985 ATTTTAAAA
1 ATTTTAAAA
27994 AATAATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (11 bp):
ATTTTAAAATA
Found at i:28719 original size:9 final size:9
Alignment explanation
Indices: 28692--28736 Score: 56
Period size: 10 Copynumber: 4.8 Consensus size: 9
28682 AATAATATAT
28692 ATTTTAAAAA
1 ATTTT-AAAA
28702 ATTTCTAAAA
1 ATTT-TAAAA
28712 ATTTT-AAA
1 ATTTTAAAA
28720 ATTTTAAAA
1 ATTTTAAAA
28729 ATATTTAA
1 AT-TTTAA
28737 CAACTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.25
9 6 0.19
10 17 0.53
11 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:28722 original size:18 final size:18
Alignment explanation
Indices: 28699--28736 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
28689 TATATTTTAA
28699 AAAATTTCTAAAAAT-TTT
1 AAAATTT-TAAAAATATTT
28717 AAAATTTTAAAAATATTT
1 AAAATTTTAAAAATATTT
28735 AA
1 AA
28737 CAACTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAATTTTAAAAATATTT
Found at i:29266 original size:61 final size:61
Alignment explanation
Indices: 29181--29307 Score: 155
Period size: 61 Copynumber: 2.1 Consensus size: 61
29171 CCTAAATACA
* ** * * * *
29181 AAAAAATTCAACAAATCTAACCCTCAATGTTTACAAAATTTGTCATTTTAGTTCTAATTCT
1 AAAAAATTCAACAAATCTAACCCTCAATATTTACAAAATCAGTCAATTAAGTCCTAACTCT
* * **
29242 AAAAAATTCAATAAATTTGGCCCTCAATATTTACAAAATCAGTCAATTAAGTCCTAACTCT
1 AAAAAATTCAACAAATCTAACCCTCAATATTTACAAAATCAGTCAATTAAGTCCTAACTCT
29303 AAAAA
1 AAAAA
29308 TTTTAAAATA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.43, C:0.18, G:0.06, T:0.33
Consensus pattern (61 bp):
AAAAAATTCAACAAATCTAACCCTCAATATTTACAAAATCAGTCAATTAAGTCCTAACTCT
Found at i:29832 original size:14 final size:14
Alignment explanation
Indices: 29801--29829 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29791 TTATAAAGGG
29801 TTAAAAATGATTTT
1 TTAAAAATGATTTT
29815 TTAAAAAT-ATTTT
1 TTAAAAATGATTTT
29828 TT
1 TT
29830 TAATTTTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (14 bp):
TTAAAAATGATTTT
Found at i:30753 original size:31 final size:31
Alignment explanation
Indices: 30717--30775 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
30707 TTTTAGTCTT
* *
30717 AAATAATTAAA-ATATTCATTAAATCCTCATA
1 AAATAATTAAAGA-ATTAATTAAAACCTCATA
30748 AAATAATTAAAGAATTAATTAAAACCTC
1 AAATAATTAAAGAATTAATTAAAACCTC
30776 CATGTCAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (31 bp):
AAATAATTAAAGAATTAATTAAAACCTCATA
Found at i:31295 original size:3 final size:3
Alignment explanation
Indices: 31287--31327 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
31277 TCAACATTAA
31287 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
31328 AGACCCATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:33133 original size:29 final size:29
Alignment explanation
Indices: 33101--33161 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
33091 AAAATGAGAC
33101 TTTTTGAATACCCGAGGGCAAAATGGTAA
1 TTTTTGAATACCCGAGGGCAAAATGGTAA
* * * *
33130 -TTTTGGATTCTCGAGGGTAAAATGGTAA
1 TTTTTGAATACCCGAGGGCAAAATGGTAA
33158 TTTT
1 TTTT
33162 GGGAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.36
Consensus pattern (29 bp):
TTTTTGAATACCCGAGGGCAAAATGGTAA
Found at i:33301 original size:59 final size:58
Alignment explanation
Indices: 33237--33431 Score: 223
Period size: 59 Copynumber: 3.3 Consensus size: 58
33227 AAATCGGGAT
* *
33237 AAAAATGGAATTTTTGGACATTTTAGGGTAAAATGATAATTATTGAGAGTTTCGAGGTC
1 AAAAATAGAATTTTTGGACATTTTAGGGTAAAATG-TAATTTTTGAGAGTTTCGAGGTC
* * * * * *
33296 AAAAATGGAGTTTTGGGACATCTGAGGGTAAAATGGTAATTTTTGAAAGTTTCGAGGTC
1 AAAAATAGAATTTTTGGACATTTTAGGGTAAAAT-GTAATTTTTGAGAGTTTCGAGGTC
** *
33355 AAAAATAGAATTTTTGGATGTTCGT-GGGTAAAAATGTAATTTTTTGAG-GTTTCGAGGTC
1 AAAAATAGAATTTTTGGACATT-TTAGGGT-AAAATGTAA-TTTTTGAGAGTTTCGAGGTC
*
33414 AAAAATACAATTTTTGGA
1 AAAAATAGAATTTTTGGA
33432 AGTTCGAGGA
Statistics
Matches: 116, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
59 103 0.89
60 13 0.11
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.35
Consensus pattern (58 bp):
AAAAATAGAATTTTTGGACATTTTAGGGTAAAATGTAATTTTTGAGAGTTTCGAGGTC
Found at i:33378 original size:29 final size:28
Alignment explanation
Indices: 33325--33460 Score: 123
Period size: 29 Copynumber: 4.6 Consensus size: 28
33315 ATCTGAGGGT
*
33325 AAAATGGTAATTTTTGAAAGTTTCGAGGTCA
1 AAAAT-GTAATTTTTGGAAG-TTCGAGGT-A
* *
33356 AAAATAG-AATTTTTGGATGTTCGTGGGTA
1 AAAAT-GTAATTTTTGGAAGTTCG-AGGTA
* *
33385 AAAATGTAATTTTTTGAGGTTTCGAGGTCA
1 AAAATGTAATTTTTGGAAG-TTCGAGGT-A
**
33415 AAAATACAATTTTTGGAAGTTCGAGGATA
1 AAAATGTAATTTTTGGAAGTTCGAGG-TA
33444 AAAATGTAA-TTTTGGAA
1 AAAATGTAATTTTTGGAA
33461 AAGTTTAAGG
Statistics
Matches: 87, Mismatches: 13, Indels: 13
0.77 0.12 0.12
Matches are distributed among these distances:
28 9 0.10
29 38 0.44
30 34 0.39
31 6 0.07
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (28 bp):
AAAATGTAATTTTTGGAAGTTCGAGGTA
Found at i:33437 original size:59 final size:57
Alignment explanation
Indices: 33237--33456 Score: 221
Period size: 59 Copynumber: 3.7 Consensus size: 57
33227 AAATCGGGAT
* ** *
33237 AAAAATGGAATTTTTGGACA-TTTTAGGGTAAAATGATAATTATTGAGAGTTTCGAGGTC
1 AAAAATAGAATTTTTGGA-AGTTCGAGGGTAAAATG-TAATTTTTGAG-GTTTCGAGGTC
* * * *
33296 AAAAATGGAGTTTTGGGACA--TCTGAGGGTAAAATGGTAATTTTTGAAAGTTTCGAGGTC
1 AAAAATAGAATTTTTGGA-AGTTC-GAGGGTAAAAT-GTAATTTTTG-AGGTTTCGAGGTC
* *
33355 AAAAATAGAATTTTTGGATGTTCGTGGGTAAAAATGTAATTTTTTGAGGTTTCGAGGTC
1 AAAAATAGAATTTTTGGAAGTTCGAGGGT-AAAATGTAA-TTTTTGAGGTTTCGAGGTC
* *
33414 AAAAATACAATTTTTGGAAGTTCGAGGATAAAAATGTAATTTT
1 AAAAATAGAATTTTTGGAAGTTCGAGGGT-AAAATGTAATTTT
33457 GGAAAAGTTT
Statistics
Matches: 138, Mismatches: 16, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
58 5 0.04
59 118 0.86
60 15 0.11
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.35
Consensus pattern (57 bp):
AAAAATAGAATTTTTGGAAGTTCGAGGGTAAAATGTAATTTTTGAGGTTTCGAGGTC
Found at i:34537 original size:3 final size:3
Alignment explanation
Indices: 34529--34600 Score: 101
Period size: 3 Copynumber: 24.0 Consensus size: 3
34519 TTTTCCTTTT
* * *
34529 TTA TTA TTA TTA ATG TTA TTA TTA ATA TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
34575 TTA TTA -TA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
34601 ATGACATTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.03
3 56 0.92
4 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:35368 original size:17 final size:16
Alignment explanation
Indices: 35342--35405 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 16
35332 CTTTTTAATT
*
35342 AATTTTAATTTACAATG
1 AATTTAAATTTA-AATG
*
35359 AATTTAAATTTAAAGTA
1 AATTTAAATTTAAA-TG
**
35376 AATTTAAACTCAAAAATG
1 AATTTAAA-T-TTAAATG
35394 AATTTAAATTTA
1 AATTTAAATTTA
35406 GAACAAATTC
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
16 3 0.08
17 21 0.57
18 10 0.27
19 3 0.08
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (16 bp):
AATTTAAATTTAAATG
Found at i:36075 original size:121 final size:121
Alignment explanation
Indices: 35870--36124 Score: 384
Period size: 121 Copynumber: 2.1 Consensus size: 121
35860 CTTCTCCGTG
** * * *
35870 TCTCATCAAAAAGTTGGGGTTCGAAGATTTGCTCGCATTGAGCGTGGGTTTGATTTGGTCTTCTT
1 TCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTT
* * * *
35935 CTCAATATCTCATCAGGAAGGTGACTGCATCGCTTGTTTCAATCTGGTTCTCTATA
66 CTCAATATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTATA
* *
35991 TCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATATCGAGTGTGGGTTTGATTTGGTCTTCTT
1 TCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTT
* * *
36056 CTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTTCTCTGTA
66 CTCAATATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTATA
36112 TCTCATCAGGAAG
1 TCTCATCAGGAAG
36125 ACGAATTTGA
Statistics
Matches: 120, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
121 120 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (121 bp):
TCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTT
CTCAATATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTATA
Found at i:36450 original size:78 final size:78
Alignment explanation
Indices: 36339--36612 Score: 329
Period size: 78 Copynumber: 3.5 Consensus size: 78
36329 GGGTAGGAGT
* * * * * * * *
36339 TTGGTTGACGATGATTTGCCCCAAGCTCAGGGTAAGAGATCGAATGACTGT-AATTTACCTCTA-
1 TTGGTTGATGATGATCTGCCCTAGGCTCGGGGTAAAAGATCAAATGGCT-TCAATTTACCTC-AG
*
36402 GCTCGAGGTAAAAGA
64 GCTTGAGGTAAAAGA
36417 TTGGTTGATGATGATCTGCCCTAGGCTCGGGGTAAAAGATCAAATGGCTTCAATTTACCTCAGGC
1 TTGGTTGATGATGATCTGCCCTAGGCTCGGGGTAAAAGATCAAATGGCTTCAATTTACCTCAGGC
*
36482 TTGGGGTAAAAGA
66 TTGAGGTAAAAGA
* * * * *
36495 TTGGTTGATAATGATCTG-CCTCAGGCTCGGGGTAAAAGATTAAATGGCTTCAATCTGCCCCAGG
1 TTGGTTGATGATGATCTGCCCT-AGGCTCGGGGTAAAAGATCAAATGGCTTCAATTTACCTCAGG
*
36559 CTTGAGGTAAGAGA
65 CTTGAGGTAAAAGA
* * *
36573 TTGGTTAATGATTATCTGCCCTAGGCTCGGGGTAAGAGAT
1 TTGGTTGATGATGATCTGCCCTAGGCTCGGGGTAAAAGAT
36613 TGGTTAACGA
Statistics
Matches: 171, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
77 5 0.03
78 163 0.95
79 3 0.02
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (78 bp):
TTGGTTGATGATGATCTGCCCTAGGCTCGGGGTAAAAGATCAAATGGCTTCAATTTACCTCAGGC
TTGAGGTAAAAGA
Found at i:36618 original size:39 final size:39
Alignment explanation
Indices: 36402--36619 Score: 141
Period size: 39 Copynumber: 5.6 Consensus size: 39
36392 TTTACCTCTA
* * *
36402 GCTCGAGGTAAAAGATTGGTTGATGATGATCTGCCCTAG
1 GCTCGGGGTAAAAGATTGGTTAATGATTATCTGCCCTAG
*
36441 GCTCGGGGTAAAAGATCAAATGGCTTCAAT--TTA-C--CTC-AG
1 GCTCGGGGTAAAAGAT----TGG-TT-AATGATTATCTGCCCTAG
* * * *
36480 GCTTGGGGTAAAAGATTGGTTGATAATGATCTG-CCTCAG
1 GCTCGGGGTAAAAGATTGGTTAATGATTATCTGCCCT-AG
* * *
36519 GCTCGGGGTAAAAGA-T--TAAATGGCTTCAATCTGCCCCAG
1 GCTCGGGGTAAAAGATTGGTTAAT-GATT--ATCTGCCCTAG
* * *
36558 GCTTGAGGTAAGAGATTGGTTAATGATTATCTGCCCTAG
1 GCTCGGGGTAAAAGATTGGTTAATGATTATCTGCCCTAG
*
36597 GCTCGGGGTAAGAGATTGGTTAA
1 GCTCGGGGTAAAAGATTGGTTAA
36620 CGATGTAGCT
Statistics
Matches: 136, Mismatches: 23, Indels: 40
0.68 0.12 0.20
Matches are distributed among these distances:
33 2 0.01
34 2 0.01
35 5 0.04
36 4 0.03
37 2 0.01
38 1 0.01
39 98 0.72
40 5 0.04
41 3 0.02
42 5 0.04
43 5 0.04
44 2 0.01
45 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (39 bp):
GCTCGGGGTAAAAGATTGGTTAATGATTATCTGCCCTAG
Found at i:36880 original size:101 final size:101
Alignment explanation
Indices: 36679--36872 Score: 262
Period size: 101 Copynumber: 1.9 Consensus size: 101
36669 GATGCTGTAG
* * * * *
36679 TTTTATTCCAACTTCGCTGTAACTTCAAGAAGATAGGATTTGATGTTGAGGCTTCATCTTGCTCT
1 TTTTAATCCAACTTCGCTGCAACTTCAAGAAGATAGGAATTGATGTTAAAGCTTCATCTTGCTCT
*
36744 TACTACAACTTCAGAGAGATAAAGACTTACTATTGT
66 TACTACAACTTCAAAGAGATAAAGACTTACTATTGT
* * * * *
36780 TTTTAATCCGACTTTGCTGCAACTTCAAGAGGATGGGAATTGATGTTAAAGCTTCATTTTGCTCT
1 TTTTAATCCAACTTCGCTGCAACTTCAAGAAGATAGGAATTGATGTTAAAGCTTCATCTTGCTCT
** *
36845 TGTTGCAACTTCAAAGAGATAAAGACTT
66 TACTACAACTTCAAAGAGATAAAGACTT
36873 GTCATTGTAG
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
101 79 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (101 bp):
TTTTAATCCAACTTCGCTGCAACTTCAAGAAGATAGGAATTGATGTTAAAGCTTCATCTTGCTCT
TACTACAACTTCAAAGAGATAAAGACTTACTATTGT
Found at i:37191 original size:49 final size:49
Alignment explanation
Indices: 37075--37474 Score: 197
Period size: 49 Copynumber: 8.1 Consensus size: 49
37065 CGGTCCATCG
* * *
37075 TTGCGACTTAAACTTTTCCCTTT-TGTATCTTTGTGGTATTGGATCCGCCA
1 TTGCGACTTAAACCTTTCCCTTTATG--TCTTTGAGGTACTGGATCCGCCA
* * * *
37125 TTGCG-GTCT-AGCTCTTTCCCTTTATGTCTCTGAGGTACTGGGTCCGCCA
1 TTGCGACT-TAAAC-CTTTCCCTTTATGTCTTTGAGGTACTGGATCCGCCA
* * * * *
37174 TTGCGACTTAAACCTTTCCC-TTGTGTCTTCGTGGTACTGGATCCGTCG
1 TTGCGACTTAAACCTTTCCCTTTATGTCTTTGAGGTACTGGATCCGCCA
* * * * * * * * * **
37222 TCGCGACTTAGATCTTTCCCTTCATGTCTTCGCGGCACTAGATCTGCTG
1 TTGCGACTTAAACCTTTCCCTTTATGTCTTTGAGGTACTGGATCCGCCA
* * * * * * *
37271 TTGCGGCTTAGATCTTTCCCGTTATGTCTCTGAGGTA-TAAGG-TTCGCCG
1 TTGCGACTTAAACCTTTCCCTTTATGTCTTTGAGGTACT--GGATCCGCCA
* * * * * *
37320 TTGCAACTTAAACCCTTTCCTTTTGTATCTTTGCGGTACTGGATCCACCA
1 TTGCGACTTAAA-CCTTTCCCTTTATGTCTTTGAGGTACTGGATCCGCCA
* * * * * *
37370 TTGCGGTCTTAAATCTTTCCCATCATGTCTTTAAGGTA-TAAGG-TTCGCCA
1 TTGC-GACTTAAACCTTTCCCTTTATGTCTTTGAGGTACT--GGATCCGCCA
* * * * * *
37420 TTGCGACTTAAACCCTTCTCTTT-TGTATCTTTGCGGTAATGGATCTGCCG
1 TTGCGACTTAAACCTTTCCCTTTATG--TCTTTGAGGTACTGGATCCGCCA
37470 TTGCG
1 TTGCG
37475 GTCTTAGATC
Statistics
Matches: 257, Mismatches: 75, Indels: 36
0.70 0.20 0.10
Matches are distributed among these distances:
48 41 0.16
49 115 0.45
50 89 0.35
51 12 0.05
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (49 bp):
TTGCGACTTAAACCTTTCCCTTTATGTCTTTGAGGTACTGGATCCGCCA
Found at i:37407 original size:100 final size:100
Alignment explanation
Indices: 37271--37497 Score: 332
Period size: 100 Copynumber: 2.3 Consensus size: 100
37261 AGATCTGCTG
* * *
37271 TTGCGG-CTTAGATCTTTCCCGTTATGTCTCTGAGGTATAAGGTTCGCCGTTGCAACTTAAACCC
1 TTGCGGTCTTAGATCTTTCCCGTCATGTCTCTAAGGTATAAGGTTCGCCATTGCAACTTAAACCC
*
37335 TT-TCCTTTTGTATCTTTGCGGTACTGGATCCACCA
66 TTCT-CTTTTGTATCTTTGCGGTAATGGATCCACCA
* * * *
37370 TTGCGGTCTTAAATCTTTCCCATCATGTCTTTAAGGTATAAGGTTCGCCATTGCGACTTAAACCC
1 TTGCGGTCTTAGATCTTTCCCGTCATGTCTCTAAGGTATAAGGTTCGCCATTGCAACTTAAACCC
** *
37435 TTCTCTTTTGTATCTTTGCGGTAATGGATCTGCCG
66 TTCTCTTTTGTATCTTTGCGGTAATGGATCCACCA
37470 TTGCGGTCTTAGATCTTTCCCGTCATGT
1 TTGCGGTCTTAGATCTTTCCCGTCATGT
37498 TTCGTGGTGT
Statistics
Matches: 113, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
99 6 0.05
100 106 0.94
101 1 0.01
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (100 bp):
TTGCGGTCTTAGATCTTTCCCGTCATGTCTCTAAGGTATAAGGTTCGCCATTGCAACTTAAACCC
TTCTCTTTTGTATCTTTGCGGTAATGGATCCACCA
Found at i:37474 original size:50 final size:49
Alignment explanation
Indices: 37314--37474 Score: 112
Period size: 50 Copynumber: 3.2 Consensus size: 49
37304 GGTATAAGGT
* * *
37314 TCGCCGTTGCAACTTAAACCCTT-TCCTTTTGTATCTTTGCGGTACTGGA
1 TCGCCATTGCGACTTAAACCCTTCT-CTTTTGTATCTTTGCGGTAATGGA
* * * * * ** ** * *
37363 TCCACCATTGCGGTCTTAAATCTTTCCCATCATG--TCTTTAAGGTATAAGGT
1 T-CGCCATTGC-GACTTAAACCCTTCTC-TTTTGTATCTTTGCGGTA-ATGGA
37414 TCGCCATTGCGACTTAAACCCTTCTCTTTTGTATCTTTGCGGTAATGGA
1 TCGCCATTGCGACTTAAACCCTTCTCTTTTGTATCTTTGCGGTAATGGA
*
37463 TCTGCCGTTGCG
1 TC-GCCATTGCG
37475 GTCTTAGATC
Statistics
Matches: 78, Mismatches: 26, Indels: 15
0.66 0.22 0.13
Matches are distributed among these distances:
48 3 0.04
49 18 0.23
50 41 0.53
51 13 0.17
52 3 0.04
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (49 bp):
TCGCCATTGCGACTTAAACCCTTCTCTTTTGTATCTTTGCGGTAATGGA
Found at i:43279 original size:96 final size:96
Alignment explanation
Indices: 43098--43289 Score: 255
Period size: 96 Copynumber: 2.0 Consensus size: 96
43088 AATTTTGGAA
* * ** *
43098 AAAGATATTTGATTATCTCGATTTGAAGAAAAGTTGCACCTAGTAAGTTAAGACGTAAATTTTCA
1 AAAGATATTCGATTATCTCGATTTGAAGAAAACTTGCACCTAGTAAGTTAAGACACAAAATTTCA
43163 GAATCGAAGATAAGAAAATATTGCCTCGATT
66 GAATCGAAGATAAGAAAATATTGCCTCGATT
* * *
43194 AAAGGTATTCGATTATTTCGATTTGAAGAAAACTTGCACCTAGTAAGTTAAGGCACAAAATTTC-
1 AAAGATATTCGATTATCTCGATTTGAAGAAAACTTGCACCTAGTAAGTTAAGACACAAAATTTCA
*
43258 GAAACTCGAA-ATGAA-AGAATATTGCCTCGATT
66 G-AA-TCGAAGAT-AAGAAAATATTGCCTCGATT
43290 TTAAAGTTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
95 1 0.01
96 76 0.90
97 7 0.08
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (96 bp):
AAAGATATTCGATTATCTCGATTTGAAGAAAACTTGCACCTAGTAAGTTAAGACACAAAATTTCA
GAATCGAAGATAAGAAAATATTGCCTCGATT
Found at i:43755 original size:30 final size:30
Alignment explanation
Indices: 43641--43863 Score: 171
Period size: 29 Copynumber: 7.7 Consensus size: 30
43631 AAAATCGGGA
* *
43641 TAAAAATGGAATTTTTGGA--TATTCAAGGG
1 TAAAAATGTAATTTTTGGAGGT-TTCGAGGG
* *
43670 T-AAAATAGT-ATTTTTTGAGAATTTCG-GGG
1 TAAAAAT-GTAATTTTTGGAG-GTTTCGAGGG
* *
43699 T-CAAATGAAATTTTTGGAGG-TTCGAGGG
1 TAAAAATGTAATTTTTGGAGGTTTCGAGGG
43727 TAAAAATGTAATTTTTGGAGGTTTCGA-GG
1 TAAAAATGTAATTTTTGGAGGTTTCGAGGG
* * *
43756 TAAAAAATGAAATTTTTGGAAG-TTCAAGGG
1 T-AAAAATGTAATTTTTGGAGGTTTCGAGGG
* * * * *
43786 TAAAAATGTAATTTTCGAAAGTTTCGAAGT
1 TAAAAATGTAATTTTTGGAGGTTTCGAGGG
* *
43816 TAAAAATGAAATTTTTGGA-ATTTCGAGGG
1 TAAAAATGTAATTTTTGGAGGTTTCGAGGG
* *
43845 TAAGAATATAA-TTTTGGAG
1 TAAAAATGTAATTTTTGGAG
43864 AAGTTTGGGG
Statistics
Matches: 155, Mismatches: 27, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
27 4 0.03
28 25 0.16
29 75 0.48
30 50 0.32
31 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.35
Consensus pattern (30 bp):
TAAAAATGTAATTTTTGGAGGTTTCGAGGG
Found at i:43881 original size:59 final size:59
Alignment explanation
Indices: 43641--43869 Score: 238
Period size: 59 Copynumber: 3.9 Consensus size: 59
43631 AAAATCGGGA
* * * *
43641 TAAAAATGGAATTTTTGGATA-TTCAAGGGT-AAAATAGTATTTTTTGAGAA-TTTCGGGG
1 TAAAAATGAAATTTTTGGA-AGTTCAAGGGTAAAAATA-TAATTTTGGAGAAGTTTCGAGG
* * * *
43699 T-CAAATGAAATTTTTGGAGGTTCGAGGGTAAAAATGTAATTTTTGGAG--GTTTCGAGG
1 TAAAAATGAAATTTTTGGAAGTTCAAGGGTAAAAATATAA-TTTTGGAGAAGTTTCGAGG
* * *
43756 TAAAAAATGAAATTTTTGGAAGTTCAAGGGTAAAAATGTAATTTTCGA-AAGTTTCGAAGT
1 T-AAAAATGAAATTTTTGGAAGTTCAAGGGTAAAAATATAATTTTGGAGAAGTTTCG-AGG
* * *
43816 TAAAAATGAAATTTTTGGAATTTCGAGGGTAAGAATATAATTTTGGAGAAGTTT
1 TAAAAATGAAATTTTTGGAAGTTCAAGGGTAAAAATATAATTTTGGAGAAGTTT
43870 GGGGGTCAAA
Statistics
Matches: 143, Mismatches: 18, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
57 33 0.23
58 19 0.13
59 82 0.57
60 9 0.06
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (59 bp):
TAAAAATGAAATTTTTGGAAGTTCAAGGGTAAAAATATAATTTTGGAGAAGTTTCGAGG
Found at i:44944 original size:3 final size:3
Alignment explanation
Indices: 44936--44986 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
44926 TTCCTTTTCC
44936 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
44984 TTA
1 TTA
44987 ATGACATTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:47629 original size:3 final size:3
Alignment explanation
Indices: 47621--47650 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
47611 ATTCTAAACA
47621 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
47651 ATTATTATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:52682 original size:21 final size:22
Alignment explanation
Indices: 52658--52701 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
52648 CATGAAGTTT
*
52658 CAAAGAACATTT-CGAGGGCAC
1 CAAAGAACATTTACAAGGGCAC
**
52679 CAAAGTGCATTTACAAGGGCAC
1 CAAAGAACATTTACAAGGGCAC
52701 C
1 C
52702 GTAGTGCAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.36, C:0.25, G:0.23, T:0.16
Consensus pattern (22 bp):
CAAAGAACATTTACAAGGGCAC
Found at i:52717 original size:21 final size:21
Alignment explanation
Indices: 52691--52760 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
52681 AAGTGCATTT
52691 ACAAGGGCACCGTAGTGCAAG
1 ACAAGGGCACCGTAGTGCAAG
* * *
52712 ACAAGGGCATAC-TGGTGCAAT
1 ACAAGGGCA-CCGTAGTGCAAG
** *
52733 TTAGGGGCACCGTAGTGCAAG
1 ACAAGGGCACCGTAGTGCAAG
52754 AC-AGGGC
1 ACAAGGGC
52761 GTCACATAAC
Statistics
Matches: 35, Mismatches: 12, Indels: 5
0.67 0.23 0.10
Matches are distributed among these distances:
20 5 0.14
21 29 0.83
22 1 0.03
ACGTcount: A:0.30, C:0.21, G:0.34, T:0.14
Consensus pattern (21 bp):
ACAAGGGCACCGTAGTGCAAG
Found at i:53538 original size:9 final size:8
Alignment explanation
Indices: 53515--53539 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
53505 AGAAAATCCC
53515 CCCTTTTT
1 CCCTTTTT
53523 CCCTTTTT
1 CCCTTTTT
53531 CCCTTTTT
1 CCCTTTTT
53539 C
1 C
53540 ATTTCATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (8 bp):
CCCTTTTT
Found at i:60731 original size:100 final size:100
Alignment explanation
Indices: 60558--60758 Score: 366
Period size: 100 Copynumber: 2.0 Consensus size: 100
60548 CGGATGAGGT
*
60558 AGCTAGTAGCGAGGGAGACTGGGCAGCAGCTGCTGGCGTGTTACGTGACTCAAGCAAAGGATGGA
1 AGCTAGTAGCGAGGGAGACTGGGCAGCAGCTGCTGGCGTGTTACGCGACTCAAGCAAAGGATGGA
60623 TCGTGGGCTATCAATGGTTTCTAGGCAGTGGTCTG
66 TCGTGGGCTATCAATGGTTTCTAGGCAGTGGTCTG
* **
60658 AGCTAGTAGCGAGGGAGATTGGGCAGCAGCTGCTGGCGTGTTACGCGACTCAAGCGGAGGATGGA
1 AGCTAGTAGCGAGGGAGACTGGGCAGCAGCTGCTGGCGTGTTACGCGACTCAAGCAAAGGATGGA
60723 TCGTGGGCTATCAATGGTTTCTAGGCAGTGGTCTG
66 TCGTGGGCTATCAATGGTTTCTAGGCAGTGGTCTG
60758 A
1 A
60759 CTTTATCTTC
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 97 1.00
ACGTcount: A:0.21, C:0.18, G:0.38, T:0.23
Consensus pattern (100 bp):
AGCTAGTAGCGAGGGAGACTGGGCAGCAGCTGCTGGCGTGTTACGCGACTCAAGCAAAGGATGGA
TCGTGGGCTATCAATGGTTTCTAGGCAGTGGTCTG
Found at i:69672 original size:50 final size:51
Alignment explanation
Indices: 69597--69729 Score: 187
Period size: 51 Copynumber: 2.6 Consensus size: 51
69587 GAAATTTCTA
**
69597 GAAAGCCTTTGTGATGAATTCTCTGGAAAGTC-TTTATGGCATATCATCTG
1 GAAAGCCTTTGTGGCGAATTCTCTGGAAAGTCTTTTATGGCATATCATCTG
* * * *
69647 GAAAGCCTTTGTGGCGAATTCTCTGGAAAGCCTTTTGTGGCGTATCATTTG
1 GAAAGCCTTTGTGGCGAATTCTCTGGAAAGTCTTTTATGGCATATCATCTG
* *
69698 GAAAGCCTTTGTGGCGAATTATTTGGAAAGTC
1 GAAAGCCTTTGTGGCGAATTCTCTGGAAAGTC
69730 GTTGTGGTGA
Statistics
Matches: 73, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
50 29 0.40
51 44 0.60
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.35
Consensus pattern (51 bp):
GAAAGCCTTTGTGGCGAATTCTCTGGAAAGTCTTTTATGGCATATCATCTG
Found at i:69721 original size:25 final size:25
Alignment explanation
Indices: 69589--69736 Score: 138
Period size: 25 Copynumber: 5.9 Consensus size: 25
69579 AAACTCGAGA
* **
69589 AATT-TCTAGAAAGCCTTTGTGATG
1 AATTATCTGGAAAGCCTTTGTGGCG
* * *
69613 AATTCTCTGGAAAGTCTTTATGGC-
1 AATTATCTGGAAAGCCTTTGTGGCG
*
69637 ATATCATCTGGAAAGCCTTTGTGGCG
1 A-ATTATCTGGAAAGCCTTTGTGGCG
*
69663 AATTCTCTGGAAAGCCTTTTGTGGCG
1 AATTATCTGGAAAGCC-TTTGTGGCG
* * *
69689 TATCATTTGGAAAGCCTTTGTGGCG
1 AATTATCTGGAAAGCCTTTGTGGCG
* * *
69714 AATTATTTGGAAAGTCGTTGTGG
1 AATTATCTGGAAAGCCTTTGTGG
69737 TGATTGTTAT
Statistics
Matches: 101, Mismatches: 19, Indels: 7
0.80 0.15 0.06
Matches are distributed among these distances:
24 5 0.05
25 74 0.73
26 22 0.22
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.36
Consensus pattern (25 bp):
AATTATCTGGAAAGCCTTTGTGGCG
Found at i:76747 original size:29 final size:29
Alignment explanation
Indices: 76713--76789 Score: 118
Period size: 29 Copynumber: 2.7 Consensus size: 29
76703 TAATGAAATT
* * *
76713 AAACTTTAGGTACCACATTGAATATTTTA
1 AAACTTCAAGTACCACATTGAACATTTTA
76742 AAACTTCAAGTACCACATTGAACATTTTA
1 AAACTTCAAGTACCACATTGAACATTTTA
*
76771 AAACTTCAAATACCACATT
1 AAACTTCAAGTACCACATT
76790 CAAATAAGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (29 bp):
AAACTTCAAGTACCACATTGAACATTTTA
Found at i:78801 original size:20 final size:20
Alignment explanation
Indices: 78776--78850 Score: 91
Period size: 20 Copynumber: 3.8 Consensus size: 20
78766 AAAAACGCAT
78776 AAAAATAACAGCAAAACAAC
1 AAAAATAACAGCAAAACAAC
*
78796 AAAAATAACA--AACAATAAC
1 AAAAATAACAGCAA-AACAAC
*
78815 AAAAATAATAGCAAAACAAC
1 AAAAATAACAGCAAAACAAC
* *
78835 AAAAACAACAACAAAA
1 AAAAATAACAGCAAAA
78851 ATAACAGAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
18 2 0.04
19 14 0.30
20 28 0.61
21 2 0.04
ACGTcount: A:0.73, C:0.17, G:0.03, T:0.07
Consensus pattern (20 bp):
AAAAATAACAGCAAAACAAC
Found at i:78814 original size:10 final size:9
Alignment explanation
Indices: 78776--78845 Score: 59
Period size: 9 Copynumber: 7.2 Consensus size: 9
78766 AAAAACGCAT
78776 AAAAATAAC
1 AAAAATAAC
*
78785 AGCAAAACAAC
1 A--AAAATAAC
78796 AAAAATAAC
1 AAAAATAAC
78805 AAACAATAAC
1 AAA-AATAAC
*
78815 AAAAATAAT
1 AAAAATAAC
*
78824 AGCAAAACAAC
1 A--AAAATAAC
*
78835 AAAAACAAC
1 AAAAATAAC
78844 AA
1 AA
78846 CAAAAATAAC
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
9 27 0.53
10 9 0.18
11 15 0.29
ACGTcount: A:0.73, C:0.17, G:0.03, T:0.07
Consensus pattern (9 bp):
AAAAATAAC
Found at i:81379 original size:74 final size:75
Alignment explanation
Indices: 81247--81396 Score: 216
Period size: 74 Copynumber: 2.0 Consensus size: 75
81237 ATAATTGTTT
* * *
81247 ATCACATTGCCGAAAATTTATTTATTTTTTTAATATTAAAAATTTTAATTTCAAAACATAAAAAT
1 ATCACATTGCCGAAAAATTATTAATTTTTTTAATACTAAAAATTTTAATTTCAAAACATAAAAAT
81312 CAATTAAATA
66 CAATTAAATA
*
81322 ATCACATTGCC-AAAAATT-TTAATTTTTTTCAATACTGAAAATTTTAACTTT-AAAACATAAAA
1 ATCACATTGCCGAAAAATTATTAATTTTTTT-AATACTAAAAATTTTAA-TTTCAAAACATAAAA
*
81384 ATCAGTTAAATA
64 ATCAATTAAATA
81396 A
1 A
81397 ATTATTAAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
73 10 0.15
74 44 0.65
75 14 0.21
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (75 bp):
ATCACATTGCCGAAAAATTATTAATTTTTTTAATACTAAAAATTTTAATTTCAAAACATAAAAAT
CAATTAAATA
Found at i:87402 original size:18 final size:19
Alignment explanation
Indices: 87361--87409 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
87351 CGTTTTTGTC
87361 CAACGGTTAAAAAAATATA
1 CAACGGTTAAAAAAATATA
* * *
87380 AAACGGTCAAAAAAAT-TT
1 CAACGGTTAAAAAAATATA
87398 CAACGGTTAAAA
1 CAACGGTTAAAA
87410 TTTCAAATGG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.20
Consensus pattern (19 bp):
CAACGGTTAAAAAAATATA
Found at i:90131 original size:15 final size:16
Alignment explanation
Indices: 90111--90140 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
90101 ACCTATTACA
90111 ACTAATTACA-TAATC
1 ACTAATTACACTAATC
90126 ACTAATTACACTAAT
1 ACTAATTACACTAAT
90141 TAGTCTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (16 bp):
ACTAATTACACTAATC
Found at i:93477 original size:14 final size:13
Alignment explanation
Indices: 93450--93487 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
93440 GGATAAATAG
*
93450 TTAATTAAATTAT
1 TTAATTATATTAT
93463 TTAATTTATATTAT
1 TTAA-TTATATTAT
93477 TTAATTATATT
1 TTAATTATATT
93488 GTACATTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TTAATTATATTAT
Found at i:95786 original size:58 final size:58
Alignment explanation
Indices: 95716--95912 Score: 224
Period size: 58 Copynumber: 3.4 Consensus size: 58
95706 AATAAAGGTC
* *
95716 AAAATGGAATTTTGGAAAGTTTCAGAGGTAAAAA-GTAATTTTTGAAAGTTTATGGGTA
1 AAAATGTAATTTTGGAAAGTTTCAGAGGTAAAAATGTAATTTTTGGAAGTTTA-GGGTA
* * * *
95774 AAAATGTAATTTTTAGAAAGTTTC-GGGGTCAAAAATGGAA-TTTTGGAATTTTAGGGTA
1 AAAATGTAA-TTTTGGAAAGTTTCAGAGGT-AAAAATGTAATTTTTGGAAGTTTAGGGTA
* *
95832 AAAATATAATTTTTGAAAG-TT-AGAGGTAAAAATGTAATTTTTAGGAAGTTTGAGGGTA
1 AAAATGTAATTTTGGAAAGTTTCAGAGGTAAAAATGTAATTTTT-GGAAGTTT-AGGGTA
*
95890 AAAATGTAATTTTAGGGAAGTTT
1 AAAATGTAATTTT-GGAAAGTTT
95913 GGGGACTTCT
Statistics
Matches: 116, Mismatches: 14, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
55 9 0.08
56 10 0.09
57 16 0.14
58 43 0.37
59 33 0.28
60 5 0.04
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (58 bp):
AAAATGTAATTTTGGAAAGTTTCAGAGGTAAAAATGTAATTTTTGGAAGTTTAGGGTA
Found at i:95795 original size:30 final size:28
Alignment explanation
Indices: 95716--95902 Score: 200
Period size: 30 Copynumber: 6.5 Consensus size: 28
95706 AATAAAGGTC
* *
95716 AAAATGGAATTTTGGAAAGTTTCAGAGGTA
1 AAAATGTAATTTTTGAAAGTTT-AG-GGTA
95746 AAAA-GTAATTTTTGAAAGTTTATGGGTA
1 AAAATGTAATTTTTGAAAGTTTA-GGGTA
*
95774 AAAATGTAATTTTTAGAAAGTTTCGGGGTCA
1 AAAATGTAATTTTT-GAAAGTTT-AGGGT-A
* * *
95805 AAAATGGAA-TTTTGGAATTTTAGGGTA
1 AAAATGTAATTTTTGAAAGTTTAGGGTA
*
95832 AAAATATAATTTTTGAAAG-TTAGAGGTA
1 AAAATGTAATTTTTGAAAGTTTAG-GGTA
*
95860 AAAATGTAATTTTTAGGAAGTTTGAGGGTA
1 AAAATGTAATTTTT-GAAAGTTT-AGGGTA
95890 AAAATGTAATTTT
1 AAAATGTAATTTT
95903 AGGGAAGTTT
Statistics
Matches: 134, Mismatches: 13, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
27 12 0.09
28 37 0.28
29 35 0.26
30 39 0.29
31 11 0.08
ACGTcount: A:0.40, C:0.02, G:0.22, T:0.36
Consensus pattern (28 bp):
AAAATGTAATTTTTGAAAGTTTAGGGTA
Found at i:95913 original size:30 final size:28
Alignment explanation
Indices: 95716--95902 Score: 168
Period size: 28 Copynumber: 6.5 Consensus size: 28
95706 AATAAAGGTC
* *
95716 AAAATGGAATTTTGGAAAGTTTCAGAGGTA
1 AAAATGTAATTTT-GAAAGTTTGAG-GGTA
95746 AAAA-GTAATTTTTGAAAGTTT-ATGGGTA
1 AAAATGTAA-TTTTGAAAGTTTGA-GGGTA
95774 AAAATGTAATTTTTAGAAAGTTTCG-GGGTCA
1 AAAATGTAA-TTTT-GAAAGTTT-GAGGGT-A
* * *
95805 AAAATGGAATTTTGGAA-TTTTAGGGTA
1 AAAATGTAATTTTGAAAGTTTGAGGGTA
* *
95832 AAAATATAATTTTTGAAAGTTAGA-GGTA
1 AAAATGTAA-TTTTGAAAGTTTGAGGGTA
*
95860 AAAATGTAATTTTTAGGAAGTTTGAGGGTA
1 AAAATGTAA-TTTT-GAAAGTTTGAGGGTA
95890 AAAATGTAATTTT
1 AAAATGTAATTTT
95903 AGGGAAGTTT
Statistics
Matches: 133, Mismatches: 12, Indels: 25
0.78 0.07 0.15
Matches are distributed among these distances:
27 8 0.06
28 40 0.30
29 39 0.29
30 37 0.28
31 9 0.07
ACGTcount: A:0.40, C:0.02, G:0.22, T:0.36
Consensus pattern (28 bp):
AAAATGTAATTTTGAAAGTTTGAGGGTA
Found at i:96938 original size:16 final size:18
Alignment explanation
Indices: 96917--96964 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 18
96907 CGTCCTTTTG
96917 TTTAATATTTTTTA-TT-
1 TTTAATATTTTTTATTTA
***
96933 TTTAATATTAAATATTTA
1 TTTAATATTTTTTATTTA
96951 TTTAATATTTTTTA
1 TTTAATATTTTTTA
96965 ATAAGTTCAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 11 0.46
17 2 0.08
18 11 0.46
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTAATATTTTTTATTTA
Found at i:97033 original size:24 final size:25
Alignment explanation
Indices: 96979--97033 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
96969 GTTCATTATT
* * *
96979 ACTGTTATTATTAATAATATTTATT
1 ACTGTTATAATTAATAATATTAATG
*
97004 A-GGTTATAATTAAT-ATATTAATG
1 ACTGTTATAATTAATAATATTAATG
97027 ACTGTTA
1 ACTGTTA
97034 ATGCCTTTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
23 8 0.33
24 15 0.62
25 1 0.04
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (25 bp):
ACTGTTATAATTAATAATATTAATG
Found at i:97757 original size:6 final size:6
Alignment explanation
Indices: 97737--97814 Score: 65
Period size: 6 Copynumber: 13.3 Consensus size: 6
97727 TTTTTAATTC
* *
97737 AATTTA AA-TTC AATTTA AATTTA AACTT- AATTTA AATTTA AACTTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AA-TTTA
** *
97784 AA-AGA AAGTTCA AATTTA AA-TTA AATTTA AA
1 AATTTA AA-TTTA AATTTA AATTTA AATTTA AA
97815 CCCAAAATGA
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
5 16 0.28
6 32 0.56
7 9 0.16
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (6 bp):
AATTTA
Found at i:97759 original size:17 final size:17
Alignment explanation
Indices: 97737--97781 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 17
97727 TTTTTAATTC
97737 AATTTAAA-TTCAATTTA
1 AATTTAAACTT-AATTTA
97754 AATTTAAACTTAATTTA
1 AATTTAAACTTAATTTA
97771 AATTTAAACTT
1 AATTTAAACTT
97782 TAAAAGAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 25 0.93
18 2 0.07
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTTAAACTTAATTTA
Found at i:97811 original size:11 final size:11
Alignment explanation
Indices: 97732--97814 Score: 60
Period size: 11 Copynumber: 7.2 Consensus size: 11
97722 GGACTTTTTT
*
97732 AATTCAATTTA
1 AATTAAATTTA
*
97743 AATTCAATTTA
1 AATTAAATTTA
*
97754 AATTTAAACTTA
1 AA-TTAAATTTA
*
97766 ATTTAAATTTA
1 AATTAAATTTA
**
97777 AACTTTAAA-AGA
1 AA--TTAAATTTA
97789 AAGTTCAAATTTA
1 AA-TT-AAATTTA
97802 AATTAAATTTA
1 AATTAAATTTA
97813 AA
1 AA
97815 CCCAAAATGA
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
11 33 0.58
12 16 0.28
13 8 0.14
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (11 bp):
AATTAAATTTA
Found at i:98609 original size:202 final size:201
Alignment explanation
Indices: 98190--98788 Score: 979
Period size: 202 Copynumber: 3.0 Consensus size: 201
98180 ACCAAATTGC
* * *
98190 TTGTTTCAATCCGCTTCTCTATACCTCATCAAGAAGACGAATTTGTTCCACTTCTCAGTGTCTCA
1 TTGTTTCAATCCGCTTCTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCA
*
98255 TCAGGAAGCTAACCTTTTTATTGCTTC-ACCTTACTTCTTAGTATCTCATCAGGGAGCTGGGATT
66 TCAGGAAGCTAACCTTTTTATTGCTTCGACC-TGCTTCTTAGTATCTCATCAGGGAGCTGGGATT
* *
98319 CGAAGATTTGCTCACAAT-GAGCCCTGAGTTGATATACTTCTCTGTATTTCATCAGGAAGATAAC
130 CGAAGATTTGCTCAC-ATCGAGCCCTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATAAC
98383 CGCCCCAT
194 CGCCCCAT
* * *
98391 TTGTTTCAATCCGCTTCTTTGTACCTCATCAGGAAGACAAATTTGGTCCACTTCTCAGTATCTCA
1 TTGTTTCAATCCGCTTCTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCA
* *
98456 TCAGGAAGCTAACCTTTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGATTGGGATT
66 TCAGGAAGCTAACCTTTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGGAG-CTGGGATT
* *
98521 CGAAGATTTGCTCACATCGAGCCCTGAGTTGGTATACTTCTCTGTATCTCATCTGGAAGATAATC
130 CGAAGATTTGCTCACATCGAGCCCTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATAACC
*
98586 GCCCCGT
195 GCCCCAT
*
98593 TTGTTTCAATCCGCTTCTCTGTACCTCACCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCA
1 TTGTTTCAATCCGCTTCTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCA
*
98658 TCAGAAAGCTAACCTTTTTATTGCTTCGACCTGCTT-TTCAGTATCTCATCAGGGAGCTGGGATT
66 TCAGGAAGCTAACCTTTTTATTGCTTCGACCTGCTTCTT-AGTATCTCATCAGGGAGCTGGGATT
* *
98722 CGAAGATTTGCTCACATCGAGCCCTGAGTTGGTATACTTCTCTGTATCTCATCAAGAAGATGACC
130 CGAAGATTTGCTCACATCGAGCCCTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATAACC
98787 GC
195 GC
98789 ATCACTGTTT
Statistics
Matches: 369, Mismatches: 25, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
201 183 0.50
202 186 0.50
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (201 bp):
TTGTTTCAATCCGCTTCTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCA
TCAGGAAGCTAACCTTTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGGAGCTGGGATTC
GAAGATTTGCTCACATCGAGCCCTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATAACCG
CCCCAT
Found at i:110869 original size:29 final size:29
Alignment explanation
Indices: 110827--111160 Score: 148
Period size: 29 Copynumber: 11.4 Consensus size: 29
110817 ATCGAGGTCA
*
110827 AAAATGGAA-TTTTGGAAAGTTCAGAGGT
1 AAAATGTAATTTTTGGAAAGTTCAGAGGT
* *
110855 AAAATGTAATTTTT-GAAAGTTCGGGGGT
1 AAAATGTAATTTTTGGAAAGTTCAGAGGT
*
110883 AAAATGGTAATTTTTGGTTAAA--TC-GAGAT
1 AAAAT-GTAATTTTTGG--AAAGTTCAGAGGT
* * * *
110912 AAAAAATG-AAATTTTAGAAAGCTT-GGGGGT
1 --AAAATGTAATTTTTGGAAAG-TTCAGAGGT
*
110942 AGAAATGTAATTTTT-TAAAGTTC-GAGGGT
1 A-AAATGTAATTTTTGGAAAGTTCAGA-GGT
*
110971 AAAATTGTAATTTTAGGTGAAA-TT-A-AGGTT
1 AAAA-TGTAATTTT-TG-GAAAGTTCAGAGG-T
* *
111001 AAAAATGGAA-TTTTGGAAAGTTTAGAGGGT
1 -AAAATGTAATTTTTGGAAAGTTCAGA-GGT
** * *
111031 GCAATGTAA-TTTTAGAAAGTT-TGAGGGT
1 AAAATGTAATTTTTGGAAAGTTCAGA-GGT
*
111059 AAAAATGTAATTTTTGAAAAGTTTC-GAGGT
1 -AAAATGTAATTTTTGGAAAG-TTCAGAGGT
* **
111089 CAAAAATGGAA-TTTTGGAAA-TTTTGAGGGT
1 --AAAATGTAATTTTTGGAAAGTTCAGA-GGT
* *
111119 AAAATGTAATTTTT-GAAAGTTTAGGGGT
1 AAAATGTAATTTTTGGAAAGTTCAGAGGT
111147 AAAAATGTAATTTT
1 -AAAATGTAATTTT
111161 CAATAAGTTC
Statistics
Matches: 239, Mismatches: 31, Indels: 71
0.70 0.09 0.21
Matches are distributed among these distances:
27 7 0.03
28 58 0.24
29 98 0.41
30 44 0.18
31 26 0.11
32 6 0.03
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAAGTTCAGAGGT
Found at i:110971 original size:88 final size:88
Alignment explanation
Indices: 110814--111160 Score: 393
Period size: 88 Copynumber: 4.0 Consensus size: 88
110804 TTTTGGAAAA
*
110814 AAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCAGA-GGTAAAATGTAATTTTTGAAAGTTCG
1 AAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTAGAGGGTAAAATGTAATTTTTGAAAGTTCG
*
110878 GGGGT-AAAATGGTAATTTTTGGT
66 AGGGTAAAAAT-GTAATTTTTGGT
* * * * * * * *
110901 TAAATCGAGATAAAAAATGAAATTTTAGAAAGCTT-GGGGGTAGAAATGTAATTTTTTAAAGTTC
1 AAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTAGAGGGTA-AAATGTAATTTTTGAAAGTTC
* *
110965 GAGGGTAAAATTGTAATTTTAGGT
65 GAGGGTAAAAATGTAATTTTTGGT
* ** * ** * *
110989 GAAATTAAGGTTAAAAATGGAATTTTGGAAAGTTTAGAGGGTGCAATGTAATTTTAGAAAGTTTG
1 AAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTAGAGGGTAAAATGTAATTTTTGAAAGTTCG
111054 AGGGTAAAAATGTAATTTTT-G-
66 AGGGTAAAAATGTAATTTTTGGT
*
111075 AAAAGTTTCGAGGTCAAAAATGGAATTTTGGAAA-TTTTGAGGGTAAAATGTAATTTTTGAAAGT
1 AAAA---TCGAGGTCAAAAATGGAATTTTGGAAAGTTTAGAGGGTAAAATGTAATTTTTGAAAGT
*
111139 T-TAGGGGTAAAAATGTAATTTT
63 TCGA-GGGTAAAAATGTAATTTT
111161 CAATAAGTTC
Statistics
Matches: 215, Mismatches: 37, Indels: 15
0.81 0.14 0.06
Matches are distributed among these distances:
86 4 0.02
87 34 0.16
88 144 0.67
89 33 0.15
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.34
Consensus pattern (88 bp):
AAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTAGAGGGTAAAATGTAATTTTTGAAAGTTCG
AGGGTAAAAATGTAATTTTTGGT
Found at i:110974 original size:59 final size:56
Alignment explanation
Indices: 110827--111160 Score: 236
Period size: 59 Copynumber: 5.8 Consensus size: 56
110817 ATCGAGGTCA
* * * *
110827 AAAATGGAATTTTGGAAAGTTC-AGAGGT-AAAATGTAATTTTTGAAAGTTCGGGGGT
1 AAAATGTAATTTTTGAAAGTTCGAG-GGTAAAAATGTAATTTTAGAAAGTT-GAGGGT
* * *
110883 AAAATGGTAATTTTTGGTTAAA--TCGA-GATAAAAAATGAAATTTTAGAAAGCTTGGGGGT
1 AAAAT-GTAATTTTT-G--AAAGTTCGAGGGT-AAAAATGTAATTTTAGAAAG-TTGAGGGT
* * * *
110942 AGAAATGTAATTTTTTAAAGTTCGAGGGTAAAATTGTAATTTTAGGTGAAA-TTAAGGTT
1 A-AAATGTAATTTTTGAAAGTTCGAGGGTAAAAATGTAATTTTA---GAAAGTTGAGGGT
* * * **
111001 AAAAATGGAATTTTGGAAAGTTTAGAGGGT-GCAATGTAATTTTAGAAAGTTTGAGGGT
1 -AAAATGTAATTTTTGAAAG-TTCGAGGGTAAAAATGTAATTTTAGAAAG-TTGAGGGT
* * *
111059 AAAAATGTAATTTTTGAAAAGTTTCGA-GGTCAAAAATGGAATTTTGGAAATTTTGAGGGT
1 -AAAATGTAATTTTTG-AAAG-TTCGAGGGT-AAAAATGTAATTTTAGAAA-GTTGAGGGT
*
111119 AAAATGTAATTTTTGAAAGTT-TAGGGGTAAAAATGTAATTTT
1 AAAATGTAATTTTTGAAAGTTCGA-GGGTAAAAATGTAATTTT
111161 CAATAAGTTC
Statistics
Matches: 222, Mismatches: 31, Indels: 49
0.74 0.10 0.16
Matches are distributed among these distances:
56 13 0.06
57 24 0.11
58 50 0.23
59 91 0.41
60 40 0.18
61 4 0.02
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (56 bp):
AAAATGTAATTTTTGAAAGTTCGAGGGTAAAAATGTAATTTTAGAAAGTTGAGGGT
Found at i:111123 original size:117 final size:116
Alignment explanation
Indices: 110913--111189 Score: 289
Period size: 117 Copynumber: 2.4 Consensus size: 116
110903 AATCGAGATA
* * * * * *
110913 AAAAATGAAATTTTAGAAAGCTTGGGGGTAGAAATGTAATTTTTTAAAGTTCGAGGGTAAAATTG
1 AAAAATGTAATTTTAGAAAGTTTGAGGGTAAAAATGTAATTTTTAAAAGTTCGAGGGTAAAAATG
* *
110978 TAATTTTAGGTGAAATTAAGGTTAAAAATGGAATTTTGGAAAGTTTAGAGGGT
66 GAATTTTA-GTGAAATTAAGGGTAAAAATGGAATTTTGGAAAGTTTAG-GGGT
**
111031 -GCAATGTAATTTTAGAAAGTTTGAGGGTAAAAATGTAATTTTTGAAAAGTTTCGA-GGTCAAAA
1 AAAAATGTAATTTTAGAAAGTTTGAGGGTAAAAATGTAATTTTT-AAAAG-TTCGAGGGT-AAAA
* * *
111094 ATGGAATTTT-G-GAAATTTTGAGGGT-AAAATGTAATTTTTGAAAGTTTAGGGGT
63 ATGGAATTTTAGTGAAA--TTAAGGGTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* *
111147 AAAAATGTAATTTTCA-ATAAGTTCGA-TGTAAAAATGTAATTTT
1 AAAAATGTAATTTT-AGA-AAGTTTGAGGGTAAAAATGTAATTTT
111190 GGGGAAGTTT
Statistics
Matches: 134, Mismatches: 17, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
116 8 0.06
117 88 0.66
118 21 0.16
119 17 0.13
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.36
Consensus pattern (116 bp):
AAAAATGTAATTTTAGAAAGTTTGAGGGTAAAAATGTAATTTTTAAAAGTTCGAGGGTAAAAATG
GAATTTTAGTGAAATTAAGGGTAAAAATGGAATTTTGGAAAGTTTAGGGGT
Found at i:111187 original size:58 final size:57
Alignment explanation
Indices: 110913--111189 Score: 215
Period size: 58 Copynumber: 4.7 Consensus size: 57
110903 AATCGAGATA
* * * * * *
110913 AAAAATGAAATTTTAGAAAGCTTGGGGGTAGAAATGTAATTTTTTAAAG-TTCGAGGGT
1 AAAAATGTAATTTTA-AAAGTTTGAGGGTAAAAATGTAATTTTTGAAAGTTTAG-GGGT
* * * * *
110971 AAAATTGTAATTTTAGGTGAAA--TTAAGGTTAAAAATGGAATTTTGGAAAGTTTAGAGGGT
1 AAAAATGTAATTTTA----AAAGTTTGAGGGTAAAAATGTAATTTTTGAAAGTTTAG-GGGT
** * *
111031 -GCAATGTAATTTTAGAAAGTTTGAGGGTAAAAATGTAATTTTTGAAAAGTTTCGAGGT
1 AAAAATGTAATTTTA-AAAGTTTGAGGGTAAAAATGTAATTTTTG-AAAGTTTAGGGGT
* * *
111089 CAAAAATGGAATTTTGGAAATTTTGAGGGT-AAAATGTAATTTTTGAAAGTTTAGGGGT
1 -AAAAATGTAATTTT-AAAAGTTTGAGGGTAAAAATGTAATTTTTGAAAGTTTAGGGGT
* *
111147 AAAAATGTAATTTTCAATAAGTTCGA-TGTAAAAATGTAATTTT
1 AAAAATGTAATTTT-AA-AAGTTTGAGGGTAAAAATGTAATTTT
111190 GGGGAAGTTT
Statistics
Matches: 175, Mismatches: 32, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
56 4 0.02
57 16 0.09
58 66 0.38
59 55 0.31
60 30 0.17
61 4 0.02
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.36
Consensus pattern (57 bp):
AAAAATGTAATTTTAAAAGTTTGAGGGTAAAAATGTAATTTTTGAAAGTTTAGGGGT
Found at i:112251 original size:3 final size:3
Alignment explanation
Indices: 112243--112306 Score: 56
Period size: 3 Copynumber: 20.0 Consensus size: 3
112233 AAATATTTAT
* * * *
112243 TTA TTA TTA TTAA TAA GTTCA TTA TTA CTG TTA TTA TTA ATA TTA TTA
1 TTA TTA TTA TT-A TTA -TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
112291 TTA TTA TTA TTTA TTA
1 TTA TTA TTA -TTA TTA
112307 GGTTATAACT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
3 40 0.82
4 8 0.16
5 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:113068 original size:6 final size:6
Alignment explanation
Indices: 113048--113102 Score: 78
Period size: 6 Copynumber: 9.3 Consensus size: 6
113038 TTTTTAATTC
*
113048 AATTTA AA-TTC AATTTA AATTTA AATTTA AATTT- AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
113094 AACTTTA AA
1 AA-TTTA AA
113103 AGAAAAGTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
5 9 0.20
6 29 0.66
7 6 0.14
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (6 bp):
AATTTA
Found at i:113070 original size:17 final size:17
Alignment explanation
Indices: 113043--113095 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
113033 TGGACTTTTT
* *
113043 AATTCAATTTAAATTCA
1 AATTAAATTTAAATTTA
*
113060 ATTTAAATTTAAATTTA
1 AATTAAATTTAAATTTA
*
113077 AATTTAATTTAAATTTA
1 AATTAAATTTAAATTTA
113094 AA
1 AA
113096 CTTTAAAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTAAATTTAAATTTA
Found at i:113075 original size:23 final size:23
Alignment explanation
Indices: 113048--113102 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 23
113038 TTTTTAATTC
113048 AATTTAAATTCAATTTAAATTTA
1 AATTTAAATTCAATTTAAATTTA
*
113071 AATTTAAATTTAATTTAAATTTA
1 AATTTAAATTCAATTTAAATTTA
113094 AACTTTAAA
1 AA-TTTAAA
113103 AGAAAAGTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 24 0.80
24 6 0.20
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTTAAATTCAATTTAAATTTA
Found at i:113092 original size:11 final size:11
Alignment explanation
Indices: 113043--113094 Score: 77
Period size: 11 Copynumber: 4.6 Consensus size: 11
113033 TGGACTTTTT
*
113043 AATTCAATTTA
1 AATTTAATTTA
*
113054 AATTCAATTTA
1 AATTTAATTTA
113065 AATTTAAATTTA
1 AATTT-AATTTA
113077 AATTTAATTTA
1 AATTTAATTTA
113088 AATTTAA
1 AATTTAA
113095 ACTTTAAAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
11 28 0.72
12 11 0.28
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:115264 original size:96 final size:96
Alignment explanation
Indices: 115090--115271 Score: 235
Period size: 96 Copynumber: 1.9 Consensus size: 96
115080 AAGGATGTTC
* * * *
115090 GATTATTTTGATTTAAAGAAAGATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAGA
1 GATTATTTCGATTTAAAGAAAAATTGCACATAGTAAGTTAAGGCACAAATTTTCAGAATCGAAGA
*
115155 TAAGGAAACATTGCCTCGATTAGGGGTATTT
66 TAAAGAAACATTGCCTCGATTAGGGGTATTT
* * *
115186 GATTATTTCGATTTGAAGAAAAATTGCACATAGTAAGTTAAGGTACAAATTTT-TGAAACTCGAA
1 GATTATTTCGATTTAAAGAAAAATTGCACATAGTAAGTTAAGGCACAAATTTTCAG-AA-TCGAA
*
115250 -ATAAA-AGAATATTGCCTCGATT
64 GATAAAGA-AACATTGCCTCGATT
115272 TTAAAGTTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
95 2 0.03
96 67 0.91
97 5 0.07
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (96 bp):
GATTATTTCGATTTAAAGAAAAATTGCACATAGTAAGTTAAGGCACAAATTTTCAGAATCGAAGA
TAAAGAAACATTGCCTCGATTAGGGGTATTT
Found at i:115660 original size:29 final size:28
Alignment explanation
Indices: 115628--115761 Score: 128
Period size: 30 Copynumber: 4.6 Consensus size: 28
115618 AAAAATGGAT
*
115628 TTTTTGGAAGTTTAGGGGTAAAATGTAA
1 TTTTTGGAAGTTTAGGGGTAAAATATAA
* * *
115656 TTTTTGGAAGTTTTGAGGTTAAAAATGTAA
1 TTTTTGGAAGTTTAG-GGGT-AAAATATAA
115686 -TTTTGGAAAGTTTAGGGGTTAAAATATAA
1 TTTTTGG-AAGTTTAGGGG-TAAAATATAA
* * *
115715 TTTTGGAGAAGTTTGAGGGTTAAAATATGA
1 TTTTTG-GAAGTTT-AGGGGTAAAATATAA
115745 -TTTTGGATAGTTTAGGG
1 TTTTTGGA-AGTTTAGGG
115762 ACTTTTAAGG
Statistics
Matches: 89, Mismatches: 9, Indels: 16
0.78 0.08 0.14
Matches are distributed among these distances:
28 20 0.22
29 28 0.31
30 36 0.40
31 5 0.06
ACGTcount: A:0.32, C:0.00, G:0.28, T:0.40
Consensus pattern (28 bp):
TTTTTGGAAGTTTAGGGGTAAAATATAA
Found at i:115683 original size:30 final size:30
Alignment explanation
Indices: 115612--115759 Score: 123
Period size: 30 Copynumber: 5.0 Consensus size: 30
115602 TGAAAAAATC
* * *
115612 GAGGTCAAAAATGGATTTTTTGGAAGTTTA
1 GAGGTTAAAAATGTAATTTTTGGAAGTTTA
* *
115642 G-GGGT-AAAATGTAATTTTTGGAAGTTTT
1 GAGGTTAAAAATGTAATTTTTGGAAGTTTA
115670 GAGGTTAAAAATGTAA-TTTTGGAAAGTTTA
1 GAGGTTAAAAATGTAATTTTTGG-AAGTTTA
* * *
115700 GGGGTT-AAAATATAATTTTGGAGAAGTTT-
1 GAGGTTAAAAATGTAATTTTTG-GAAGTTTA
115729 GAGGGTTAAAATATG--A-TTTTGGATAGTTTA
1 GA-GGTTAAAA-ATGTAATTTTTGGA-AGTTTA
115759 G
1 G
115760 GGACTTTTAA
Statistics
Matches: 95, Mismatches: 13, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
28 23 0.24
29 29 0.31
30 37 0.39
31 4 0.04
32 2 0.02
ACGTcount: A:0.34, C:0.01, G:0.27, T:0.39
Consensus pattern (30 bp):
GAGGTTAAAAATGTAATTTTTGGAAGTTTA
Found at i:115740 original size:59 final size:58
Alignment explanation
Indices: 115629--115761 Score: 173
Period size: 59 Copynumber: 2.3 Consensus size: 58
115619 AAAATGGATT
* * *
115629 TTTTGG-AAGTTTAGGGGTAAAATGTAATTTTTGGAAGTTTTGAGGTTAAAAATGTAA
1 TTTTGGAAAGTTTAGGGGTAAAATATAATTTTGGGAAGTTTTGAGGTTAAAAATATAA
*
115686 TTTTGGAAAGTTTAGGGGTTAAAATATAATTTTGGAGAAG-TTTGAGGGTT-AAAATATGA
1 TTTTGGAAAGTTTAGGGG-TAAAATATAATTTTGG-GAAGTTTTGA-GGTTAAAAATATAA
*
115745 TTTTGGATAGTTTAGGG
1 TTTTGGAAAGTTTAGGG
115762 ACTTTTAAGG
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
57 6 0.09
58 11 0.16
59 42 0.63
60 8 0.12
ACGTcount: A:0.32, C:0.00, G:0.28, T:0.40
Consensus pattern (58 bp):
TTTTGGAAAGTTTAGGGGTAAAATATAATTTTGGGAAGTTTTGAGGTTAAAAATATAA
Found at i:116783 original size:3 final size:3
Alignment explanation
Indices: 116777--116863 Score: 50
Period size: 3 Copynumber: 28.0 Consensus size: 3
116767 TTCTCTTTTT
* * * *
116777 TTA TTA TTA ATA TTA TTA TTA TTAA TTA CTGTA GTA TTA TTTA ATG TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA -T-TA TTA TTA -TTA TTA TTA
* * * * *
116826 -TA GTA TTA TTA TTA ATG TTA TTA TGA CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
116864 CTAATGACAT
Statistics
Matches: 62, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
2 2 0.03
3 51 0.82
4 7 0.11
5 2 0.03
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:116797 original size:15 final size:15
Alignment explanation
Indices: 116777--116868 Score: 58
Period size: 15 Copynumber: 5.7 Consensus size: 15
116767 TTCTCTTTTT
116777 TTATTATTAATATTA
1 TTATTATTAATATTA
116792 TTATTATTAATTACTGTA
1 TTATTATTAA-TA-T-TA
* *
116810 GTATTATTTAATGTTA
1 TTATTA-TTAATATTA
* * *
116826 TAGTATTATTATTAATG
1 T--TATTATTAATATTA
* *
116843 TTATTATGACTATTA
1 TTATTATTAATATTA
*
116858 TTATTACTAAT
1 TTATTATTAAT
116869 GACATTTATT
Statistics
Matches: 57, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
15 28 0.49
16 4 0.07
17 8 0.14
18 13 0.23
19 4 0.07
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (15 bp):
TTATTATTAATATTA
Found at i:116816 original size:21 final size:20
Alignment explanation
Indices: 116790--116846 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
116780 TTATTAATAT
116790 TATTATTATTAA--TTACT-G
1 TATTATTATTAATGTTA-TAG
*
116808 TAGTATTATTTAATGTTATAG
1 TATTATTA-TTAATGTTATAG
116829 TATTATTATTAATGTTAT
1 TATTATTATTAATGTTAT
116847 TATGACTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 7 0.21
19 4 0.12
20 11 0.33
21 11 0.33
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (20 bp):
TATTATTATTAATGTTATAG
Found at i:116856 original size:21 final size:20
Alignment explanation
Indices: 116811--116860 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
116801 ATTACTGTAG
*
116811 TATTATTTAATGTTATAGTAT
1 TATTA-TTAATGTTATAGTAC
116832 TATTATTAATGTTATTA-TGAC
1 TATTATTAATGTTA-TAGT-AC
116853 TATTATTA
1 TATTATTA
116861 TTACTAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.56
Consensus pattern (20 bp):
TATTATTAATGTTATAGTAC
Found at i:117553 original size:6 final size:6
Alignment explanation
Indices: 117544--117619 Score: 52
Period size: 6 Copynumber: 13.2 Consensus size: 6
117534 TTTGGACATT
* * *
117544 AATTTA AATTTA AATTTA AACTTA AATTTA TAA--TA GATTTA AATTTT
1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATTTA
** * *
117591 AA-GAA AATTTA AACTTA AA-ATA AATTTA A
1 AATTTA AATTTA AATTTA AATTTA AATTTA A
117620 CTTCTGTTGG
Statistics
Matches: 52, Mismatches: 13, Indels: 10
0.69 0.17 0.13
Matches are distributed among these distances:
4 1 0.02
5 8 0.15
6 41 0.79
7 2 0.04
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (6 bp):
AATTTA
Found at i:117615 original size:17 final size:17
Alignment explanation
Indices: 117544--117619 Score: 73
Period size: 17 Copynumber: 4.4 Consensus size: 17
117534 TTTGGACATT
*
117544 AATTTAAATTTAAATTTA
1 AATTTAAATTTAAA-ATA
* *
117562 AACTTAAATTTATAATA
1 AATTTAAATTTAAAATA
* *
117579 GATTTAAATTTTAAGA-A
1 AATTTAAA-TTTAAAATA
*
117596 AATTTAAACTTAAAATA
1 AATTTAAATTTAAAATA
117613 AATTTAA
1 AATTTAA
117620 CTTCTGTTGG
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
16 5 0.11
17 24 0.52
18 17 0.37
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:118412 original size:206 final size:205
Alignment explanation
Indices: 117951--118420 Score: 613
Period size: 206 Copynumber: 2.3 Consensus size: 205
117941 TTTCATTGAC
* * * ** *
117951 TTGGCCTTCTTCTCAGTATCTCATCAAGAAGATGACCACATCACTTGTTTTGATCCACTTCTCTA
1 TTGGTCTTCTTCTCAG-ATCTCATCAAGAAGATGACCACGTCATTTGTTTCAATCCGCTTCTCTA
* * * * * *
118016 TGTTTCATTAGGAAGACGGATTTGGTTCACTTCTCCGTATCTCATCAAGAAGCTAACCATTTTAT
65 TATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTAT
*
118081 TACTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTTACATCGAAC
130 TACTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAAC
*
118146 ATGAGTTTGAT
195 ATGAGTTTAAT
* * * *
118157 TTGGTCTTCTTCTCTATG-TCTTATCAAGAAGATGACCGCG-CTGTTTGTTTCAATCCGCTTCTG
1 TTGGTCTTCTTCTC-A-GATCTCATCAAGAAGATGACCACGTC-ATTTGTTTCAATCCGCTTCTC
* * *
118220 TGTATCTCATCAGGAAGATC-AATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAATCATTT
63 TATATCTCATCAGGAAGA-CGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTT
** *
118284 TATTACTTTGACCTGTTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCG
127 TATTACTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCG
* *
118349 AGCGTGAGTTTAAT
192 AACATGAGTTTAAT
* *
118363 TTGGTCTTCTTCTCAGCATCTCATCAGGAAGATGACCATGTCATTTGTTTCAATCCGC
1 TTGGTCTTCTTCTCAG-ATCTCATCAAGAAGATGACCACGTCATTTGTTTCAATCCGC
118421 GAATTTGGTC
Statistics
Matches: 226, Mismatches: 31, Indels: 14
0.83 0.11 0.05
Matches are distributed among these distances:
204 1 0.00
205 2 0.01
206 219 0.97
207 3 0.01
208 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (205 bp):
TTGGTCTTCTTCTCAGATCTCATCAAGAAGATGACCACGTCATTTGTTTCAATCCGCTTCTCTAT
ATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATT
ACTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAACA
TGAGTTTAAT
Found at i:118549 original size:182 final size:182
Alignment explanation
Indices: 118240--118601 Score: 634
Period size: 182 Copynumber: 2.0 Consensus size: 182
118230 CAGGAAGATC
* * **
118240 AATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAATCATTTTATTACTTTGACCTGTTTCTC
1 AATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAGCATTTTATTACTTCGACCTACTTCTC
118305 AGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGAGTTTAATTTGGTCT
66 AGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGAGTTTAATTTGGTCT
118370 TCTTCTCAGCATCTCATCAGGAAGATGACCATGTCATTTGTTTCAATCCGCG
131 TCTTCTCAGCATCTCATCAGGAAGATGACCATGTCATTTGTTTCAATCCGCG
*
118422 AATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAGCATTTTATTGCTTCGACCTACTTCTC
1 AATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAGCATTTTATTACTTCGACCTACTTCTC
* * * *
118487 AGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGTGTGGGTTTGATTTGGTCT
66 AGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGAGTTTAATTTGGTCT
*
118552 TCTTCTCAGCATCTCATCAGGAAGATGACCGTGTCATTTGTTTCAATCCG
131 TCTTCTCAGCATCTCATCAGGAAGATGACCATGTCATTTGTTTCAATCCG
118602 TTTCTCTGTT
Statistics
Matches: 170, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
182 170 1.00
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.35
Consensus pattern (182 bp):
AATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAGCATTTTATTACTTCGACCTACTTCTC
AGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGAGTTTAATTTGGTCT
TCTTCTCAGCATCTCATCAGGAAGATGACCATGTCATTTGTTTCAATCCGCG
Found at i:118775 original size:207 final size:206
Alignment explanation
Indices: 118420--118874 Score: 784
Period size: 207 Copynumber: 2.2 Consensus size: 206
118410 TTTCAATCCG
*
118420 CGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAGCATTTTATTGCTTCGACCTACTTC
1 CGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTACTTC
* * * *
118485 TCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGTGTGGGTTTGATTTGGT
66 TCAATGTCTCATCAGGAAGCTGAGGTTCGAAGATTTGCGCACATCGAGCGTGGGTTTGATTTGGT
*
118550 CTTCTTCTCAGCATCTCATCAGGAAGATGACCGTGTCATTTGTTTCAATCCGTTTCTCTGTTATC
131 CTTCTTCTCAGCATCTCATCAGGAAGATGACCGTGTCATTTGTTTCAATCCGCTTCTCTG-TATC
118615 TCATCAGGAAGA
195 TCATCAGGAAGA
* *
118627 CGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGATCTGCTTC
1 CGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTACTTC
118692 TCAATGTCTCATCAGGAAGCTGAGGTTCGAAGATTTGCGCACATCGAGCGTGGGTTTGATTTGGT
66 TCAATGTCTCATCAGGAAGCTGAGGTTCGAAGATTTGCGCACATCGAGCGTGGGTTTGATTTGGT
**
118757 CTTCTTCTCAGCATCTCATCAGGAAGATGACCGTGTTGTTTGTTTCAATCCGCTTCTCTGTATCT
131 CTTCTTCTCAGCATCTCATCAGGAAGATGACCGTGTCATTTGTTTCAATCCGCTTCTCTGTATCT
118822 CATCAGGAAGA
196 CATCAGGAAGA
* * *
118833 CGAATTTGGTCCACTTCTCAATATCTCATCAAGAAGATAACC
1 CGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACC
118875 GCATCGCAGT
Statistics
Matches: 235, Mismatches: 13, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
206 55 0.23
207 180 0.77
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.34
Consensus pattern (206 bp):
CGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTACTTC
TCAATGTCTCATCAGGAAGCTGAGGTTCGAAGATTTGCGCACATCGAGCGTGGGTTTGATTTGGT
CTTCTTCTCAGCATCTCATCAGGAAGATGACCGTGTCATTTGTTTCAATCCGCTTCTCTGTATCT
CATCAGGAAGA
Found at i:118780 original size:389 final size:388
Alignment explanation
Indices: 118035--118809 Score: 1180
Period size: 389 Copynumber: 2.0 Consensus size: 388
118025 AGGAAGACGG
* * *
118035 ATTTGGTTCACTTCTCCGTATCTCATCAAGAAGCTAACCATTTTATTACTTCAACCTGCTTCTCA
1 ATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTACTTCAACCTACTTCTCA
*
118100 GTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTTACATCGAACATGAGTTTGATTTGGTCTT
66 GTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAACATGAGTTTGATTTGGTCTT
* * *
118165 CTTCTCTATGTCTTATCAAGAAGATGACCGCGCTGTTTGTTTCAATCCGCTTCTGTGTATCTCAT
131 CTTCTCTATGTCTCATCAAGAAGATGACCGCGCTATTTGTTTCAATCCGCTTCTCTGTATCTCAT
* *
118230 CAGGAAGATCAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAATCATTTTATTACTTTGA
196 CAGGAAGATCAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGA
* * * *
118295 CCTGTTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGAGTTT
261 CCTGCTTCTCAATATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCGCACATCGAGCGTGAGTTT
118360 AATTTGGTCTTCTTCTCAGCATCTCATCAGGAAGATGACCATGTCATTTGTTTCAATCCGCGA
326 AATTTGGTCTTCTTCTCAGCATCTCATCAGGAAGATGACCATGTCATTTGTTTCAATCCGCGA
* * * *
118423 ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAAGCATTTTATTGCTTCGACCTACTTCTCA
1 ATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTACTTCAACCTACTTCTCA
* *** *
118488 GTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGTGTGGGTTTGATTTGGTCTT
66 GTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAACATGAGTTTGATTTGGTCTT
* * *
118553 CTTCTC-A-GCATCTCATCAGGAAGATGACCGTG-TCATTTGTTTCAATCCGTTTCTCTGTTATC
131 CTTCTCTATG--TCTCATCAAGAAGATGACCGCGCT-ATTTGTTTCAATCCGCTTCTCTG-TATC
*
118615 TCATCAGGAAGA-CGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGC
192 TCATCAGGAAGATC-AATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTAC
* *
118679 TTCGATCTGCTTCTCAATGTCTCATCAGGAAGCTGAGGTTCGAAGATTTGCGCACATCGAGCGTG
256 TTCGACCTGCTTCTCAATATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCGCACATCGAGCGTG
* * * **
118744 GGTTTGATTTGGTCTTCTTCTCAGCATCTCATCAGGAAGATGACCGTGTTGTTTGTTTCAATCCG
321 AGTTTAATTTGGTCTTCTTCTCAGCATCTCATCAGGAAGATGACCATGTCATTTGTTTCAATCCG
118809 C
386 C
118810 TTCTCTGTAT
Statistics
Matches: 349, Mismatches: 33, Indels: 9
0.89 0.08 0.02
Matches are distributed among these distances:
386 1 0.00
387 2 0.01
388 163 0.47
389 183 0.52
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (388 bp):
ATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTACTTCAACCTACTTCTCA
GTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAACATGAGTTTGATTTGGTCTT
CTTCTCTATGTCTCATCAAGAAGATGACCGCGCTATTTGTTTCAATCCGCTTCTCTGTATCTCAT
CAGGAAGATCAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGA
CCTGCTTCTCAATATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCGCACATCGAGCGTGAGTTT
AATTTGGTCTTCTTCTCAGCATCTCATCAGGAAGATGACCATGTCATTTGTTTCAATCCGCGA
Done.