Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009630.1 Hibiscus syriacus cultivar Beakdansim tig00117026_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1249403
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 6
Found at i:5600 original size:25 final size:25
Alignment explanation
Indices: 5539--5593 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
5529 ATACATCATC
5539 AACAAGAAGGGAATCAATCACTAGT
1 AACAAGAAGGGAATCAATCACTAGT
5564 AACAAGAAGGGAATCAATCACTAGT
1 AACAAGAAGGGAATCAATCACTAGT
5589 AACAA
1 AACAA
5594 TTAGGGATCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.51, C:0.16, G:0.18, T:0.15
Consensus pattern (25 bp):
AACAAGAAGGGAATCAATCACTAGT
Found at i:14488 original size:2 final size:2
Alignment explanation
Indices: 14481--14507 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
14471 TTTATACACC
14481 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
14508 TTTGTGTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25878 original size:25 final size:25
Alignment explanation
Indices: 25849--25897 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
25839 ATAAGATTCT
25849 CATGAGAATGAAATCCATATTTTTC
1 CATGAGAATGAAATCCATATTTTTC
**
25874 CATGAGAATGAAATTTATATTTTT
1 CATGAGAATGAAATCCATATTTTT
25898 TTCCGTTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (25 bp):
CATGAGAATGAAATCCATATTTTTC
Found at i:30023 original size:30 final size:29
Alignment explanation
Indices: 29989--30162 Score: 78
Period size: 30 Copynumber: 5.6 Consensus size: 29
29979 GATGGAGATA
29989 TAATCTCATGCAAATGTCAGAACGAGGAAC
1 TAATCTCATGCAAATGTCAGAAC-AGGAAC
** ** *
30019 TAATCTCATATAGTTGTCAGAACAAGAAAC
1 TAATCTCATGCAAATGTCAGAAC-AGGAAC
* * * *
30049 TAATCTCGTTACCCGTACAAAGGTTAGAACAGGGAAT
1 TAATCTC---A----TGCAAATGTCAGAACA-GGAAC
* * *
30086 TAATCCCATGCAGATGTTAGAACAGTGAAC
1 TAATCTCATGCAAATGTCAGAACAG-GAAC
* * *
30116 AAATCTCATGCAATTGTCAGAACGGGGAAC
1 TAATCTCATGCAAATGTCAGAAC-AGGAAC
* * *
30146 CAATCCCATGCAGATGT
1 TAATCTCATGCAAATGT
30163 TCAAACGGGA
Statistics
Matches: 106, Mismatches: 28, Indels: 20
0.69 0.18 0.13
Matches are distributed among these distances:
29 1 0.01
30 82 0.77
31 1 0.01
33 1 0.01
34 1 0.01
36 1 0.01
37 19 0.18
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (29 bp):
TAATCTCATGCAAATGTCAGAACAGGAAC
Found at i:30170 original size:30 final size:31
Alignment explanation
Indices: 30087--30171 Score: 97
Period size: 30 Copynumber: 2.8 Consensus size: 31
30077 ACAGGGAATT
* *
30087 AATCCCATGCAGATGTT-AGAACAGTGAACA
1 AATCCCATGCAGATGTTCAGAACGGGGAACA
* *
30117 AATCTCATGCA-AT-TGTCAGAACGGGGAACC
1 AATCCCATGCAGATGT-TCAGAACGGGGAACA
30147 AATCCCATGCAGATGTTCA-AACGGG
1 AATCCCATGCAGATGTTCAGAACGGG
30172 AAACTATGCT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
28 1 0.02
29 3 0.07
30 36 0.78
31 5 0.11
32 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.20
Consensus pattern (31 bp):
AATCCCATGCAGATGTTCAGAACGGGGAACA
Found at i:32666 original size:20 final size:21
Alignment explanation
Indices: 32641--32692 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
32631 TTTTCCCAAT
*
32641 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
32661 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
32682 TCGCAATGCGA
1 TCGCAATGCGA
32693 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:32706 original size:20 final size:20
Alignment explanation
Indices: 32681--32794 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
32671 AATTGGGAAA
*
32681 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
32701 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
32721 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
32742 ATTGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
32762 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
32782 TTCGCAACGCGAT
1 ATCGCAACGCGAT
32795 TTACATAGCG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.80
21 12 0.15
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:32725 original size:61 final size:61
Alignment explanation
Indices: 32678--32794 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
32668 GCGAATTGGG
* * * * *
32678 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
32739 AAAATTGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
32795 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:33382 original size:19 final size:19
Alignment explanation
Indices: 33335--33376 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
33325 AATTAACTAT
*
33335 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
*
33354 CGCAACGCGAAACAAAAAT
1 CGCAACGCGAAACAAAAAA
33373 CGCA
1 CGCA
33377 TTGCGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.26, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:33468 original size:34 final size:33
Alignment explanation
Indices: 33388--33473 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
33378 TGCGATTTTT
* *
33388 ATTTCGCGTTGCGATTGTCTGGTCGCGATAGTC
1 ATTTCGCGTTGCGATTCTCTCGTCGCGATAGTC
*
33421 ATTTCGCGTTGCGATTCTCTCGTTGCGATAGTC
1 ATTTCGCGTTGCGATTCTCTCGTCGCGATAGTC
33454 ATTTCCGCGTTGCGATTCTC
1 ATTT-CGCGTTGCGATTCTC
33474 ATTATCTCGT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 34 0.69
34 15 0.31
ACGTcount: A:0.12, C:0.24, G:0.26, T:0.38
Consensus pattern (33 bp):
ATTTCGCGTTGCGATTCTCTCGTCGCGATAGTC
Found at i:33475 original size:20 final size:20
Alignment explanation
Indices: 33441--33498 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
33431 GCGATTCTCT
**
33441 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
33461 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
33481 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
33499 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:35561 original size:42 final size:42
Alignment explanation
Indices: 35501--35623 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
35491 GCCTGACTCG
* * *
35501 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
35543 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
35585 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
35624 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:35581 original size:21 final size:21
Alignment explanation
Indices: 35557--35623 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
35547 TCATTCCTCG
35557 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
35578 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
35599 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
35620 AGAG
1 AGAG
35624 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:36558 original size:17 final size:17
Alignment explanation
Indices: 36536--36571 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
36526 GACCGCACCA
36536 CAACAAACGAAAGGACC
1 CAACAAACGAAAGGACC
36553 CAACAAACGAAAGGACC
1 CAACAAACGAAAGGACC
36570 CA
1 CA
36572 GTGGGGATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.31, G:0.17, T:0.00
Consensus pattern (17 bp):
CAACAAACGAAAGGACC
Found at i:37011 original size:14 final size:14
Alignment explanation
Indices: 36992--37027 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
36982 ATTGTTTAAT
36992 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
37006 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
37020 TGATTTGT
1 TGATTTGT
37028 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:37234 original size:19 final size:19
Alignment explanation
Indices: 37212--37342 Score: 129
Period size: 19 Copynumber: 7.4 Consensus size: 19
37202 TAAATCCGCG
37212 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
**
37231 TTGCGA--TTC-CCTCG--
1 TTGCGATTTTCATTTCGCA
*
37245 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
37264 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
37283 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
37297 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
37316 TTGCGATAGTAATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
37336 TTGCGAT
1 TTGCGAT
37343 AGACATTAAG
Statistics
Matches: 93, Mismatches: 8, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
14 12 0.13
16 14 0.15
17 14 0.15
19 42 0.45
20 11 0.12
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:37286 original size:52 final size:52
Alignment explanation
Indices: 37208--37342 Score: 207
Period size: 52 Copynumber: 2.6 Consensus size: 52
37198 AAATTAAATC
37208 CGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTT
1 CGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTT
**
37260 CGCGTTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTT
1 CGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTT
* ** *
37312 CGCATTGCGATAGTAATTTCCGCATTGCGAT
1 CGCGTTGCGATTTTCATTT-CGCATTGCGAT
37343 AGACATTAAG
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
52 65 0.86
53 11 0.14
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (52 bp):
CGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTT
Found at i:39846 original size:24 final size:24
Alignment explanation
Indices: 39812--39865 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
39802 CTGAAACATC
* *
39812 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
39836 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
39860 ATCAAA
1 ATCAAA
39866 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:40954 original size:20 final size:20
Alignment explanation
Indices: 40929--40973 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
40919 ATTCATTTGA
*
40929 CTATCGTAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
40949 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
40969 CTATC
1 CTATC
40974 TGCGATTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.20
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:40993 original size:14 final size:16
Alignment explanation
Indices: 40974--41045 Score: 62
Period size: 19 Copynumber: 4.4 Consensus size: 16
40964 AATGGCTATC
40974 TGCGATTTTC-TCG-T
1 TGCGATTTTCTTCGAT
40988 TGCGATTTTCATTTCGCAT
1 TGCGATTTTC--TTCG-AT
41007 TGCGATTTTCATTTCGCAT
1 TGCGATTTTC--TTCG-AT
41026 TGCGATTTTC-TCG-T
1 TGCGATTTTCTTCGAT
41040 TGCGAT
1 TGCGAT
41046 AGTCTGTTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
14 17 0.32
16 3 0.06
17 3 0.06
19 30 0.57
ACGTcount: A:0.12, C:0.21, G:0.19, T:0.47
Consensus pattern (16 bp):
TGCGATTTTCTTCGAT
Found at i:41009 original size:19 final size:19
Alignment explanation
Indices: 40987--41035 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
40977 GATTTTCTCG
40987 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
41006 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
41025 TTGCGATTTTC
1 TTGCGATTTTC
41036 TCGTTGCGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.14, C:0.20, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:41153 original size:14 final size:14
Alignment explanation
Indices: 41134--41170 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
41124 CATCAATTAA
41134 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
41148 ACAAATCATCTTTT
1 ACAAATCAACATTT
41162 ACAAATCAA
1 ACAAATCAA
41171 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:43058 original size:19 final size:19
Alignment explanation
Indices: 43015--43118 Score: 102
Period size: 19 Copynumber: 5.4 Consensus size: 19
43005 TAGTTTACTT
* * *
43015 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAATA
*
43035 TCGCAACGCGAAATGATTA
1 TCGCAACGCGAAATGAATA
**
43054 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAATA
* *
43074 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAATA
43093 TCGCAACGCGAAATGAA-A
1 TCGCAACGCGAAATGAATA
*
43111 TCACAACG
1 TCGCAACG
43119 ACAAAATCGC
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
18 8 0.11
19 35 0.49
20 28 0.39
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.15
Consensus pattern (19 bp):
TCGCAACGCGAAATGAATA
Found at i:43077 original size:39 final size:38
Alignment explanation
Indices: 43034--43107 Score: 112
Period size: 39 Copynumber: 1.9 Consensus size: 38
43024 GAAACTTAAA
**
43034 ATCGCAACGCGAAATGATTATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAATGAAAATCGCAACGC-GAAATGGCT
*
43073 ATCGCAATGCGAAATGAAAATCGCAACGCGAAATG
1 ATCGCAACGCGAAATGAAAATCGCAACGCGAAATG
43108 AAATCACAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 6 0.19
39 26 0.81
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (38 bp):
ATCGCAACGCGAAATGAAAATCGCAACGCGAAATGGCT
Found at i:43125 original size:19 final size:19
Alignment explanation
Indices: 43084--43125 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
43074 TCGCAATGCG
* *
43084 AAATGAAAATCGCAACGCG
1 AAATGAAAATCACAACGCA
43103 AAATG-AAATCACAACGACA
1 AAATGAAAATCACAACG-CA
43122 AAAT
1 AAAT
43126 CGCAACGCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.55, C:0.19, G:0.14, T:0.12
Consensus pattern (19 bp):
AAATGAAAATCACAACGCA
Found at i:43166 original size:19 final size:18
Alignment explanation
Indices: 43144--43208 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 18
43134 GAAACACAAA
43144 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
* *
43163 TCGCGTTGCGATTT--TG
1 TCGCATTGCGATTTCATT
43179 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
*
43195 TCGCATTACGATTT
1 TCGCATTGCGATTT
43209 TGTCGTTGCG
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
14 9 0.24
16 8 0.21
18 11 0.29
19 10 0.26
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:43185 original size:14 final size:14
Alignment explanation
Indices: 43166--43223 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
43156 TTTCATTTCG
43166 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
43180 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
43196 CGCATTACGATTTTGT
1 CG--TTGCGATTTTGT
*
43212 CGTTGCGCTTTT
1 CGTTGCGATTTT
43224 TATTTCACAT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
14 19 0.54
16 8 0.23
18 8 0.23
ACGTcount: A:0.10, C:0.19, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:43196 original size:32 final size:33
Alignment explanation
Indices: 43149--43239 Score: 121
Period size: 32 Copynumber: 2.8 Consensus size: 33
43139 ACAAATCGCA
* *
43149 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTACGATTTTGTCG
43182 TTGCGA-TTTCATTTCGCATTACGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTACGATTTTGTCG
* * * *
43214 TTGCGCTTTTTATTTCACATTGCGAT
1 TTGCGATTTTCATTTCGCATTACGAT
43240 AGCCATTTCC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
32 29 0.57
33 22 0.43
ACGTcount: A:0.13, C:0.19, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTACGATTTTGTCG
Found at i:43247 original size:19 final size:20
Alignment explanation
Indices: 43225--43267 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
43215 TGCGCTTTTT
43225 ATTT-CACATTGCGATAGCC
1 ATTTCCACATTGCGATAGCC
* * *
43244 ATTTCCGCGTTGCGATAGTC
1 ATTTCCACATTGCGATAGCC
43264 ATTT
1 ATTT
43268 TCGTGTTGCG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (20 bp):
ATTTCCACATTGCGATAGCC
Found at i:43258 original size:20 final size:20
Alignment explanation
Indices: 43233--43278 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
43223 TTATTTCACA
43233 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
43253 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
43273 TTGCGA
1 TTGCGA
43279 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:43786 original size:18 final size:18
Alignment explanation
Indices: 43760--43804 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
43750 GTCGATCAGA
*
43760 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
43778 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
43796 TGATGGCTC
1 TGATGGCTC
43805 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:45145 original size:20 final size:20
Alignment explanation
Indices: 45120--45162 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
45110 AATAGTTTCT
45120 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
45140 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
45160 GAA
1 GAA
45163 TTCGACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:45733 original size:20 final size:20
Alignment explanation
Indices: 45672--45741 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
45662 GATTATGTAT
45672 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
45692 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
45712 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
45732 TATCTCGTTG
1 TATCGCGTTG
45742 TGATTTTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.27
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:45788 original size:41 final size:41
Alignment explanation
Indices: 45712--45789 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 41
45702 CGAAAGTCAG
* * *
45712 TATCGCGTTGCGAAAGTAAGTATCTCGTTGTGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCTCATTGCGATTTTTTAT
* *
45753 TATCGCATTGCGATAGTCAGTAT-TGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCT-CATTGCGATTTT
45790 CCCAATTCGC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 1 0.03
41 30 0.97
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.42
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCTCATTGCGATTTTTTAT
Found at i:45805 original size:41 final size:41
Alignment explanation
Indices: 45755--45863 Score: 132
Period size: 41 Copynumber: 2.7 Consensus size: 41
45745 TTTTTTATTA
* *
45755 TCGCATTGCGATAGTCA-GTATT-GCATTGCGATTTTCCCAAT
1 TCGCGTTGCGAT--TCACGTATTCGCATTACGATTTTCCCAAT
* *
45796 TCGCGTTGCGATTTACTTATTCGCATTACGATTTTCCCAAT
1 TCGCGTTGCGATTCACGTATTCGCATTACGATTTTCCCAAT
* *
45837 TCGCGTTGCGATTTACTTATTCGCATT
1 TCGCGTTGCGATTCACGTATTCGCATT
45864 GCGAATTGGG
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
39 2 0.03
40 4 0.06
41 56 0.90
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.40
Consensus pattern (41 bp):
TCGCGTTGCGATTCACGTATTCGCATTACGATTTTCCCAAT
Found at i:45806 original size:21 final size:21
Alignment explanation
Indices: 45780--45850 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
45770 CAGTATTGCA
45780 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
* ** *
45801 TTGCGA-TTTACTTATTCGCA
1 TTGCGATTTTCCCAATTCGCG
*
45821 TTACGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
45842 TTGCGATTT
1 TTGCGATTT
45851 ACTTATTCGC
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 15 0.38
21 24 0.62
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.42
Consensus pattern (21 bp):
TTGCGATTTTCCCAATTCGCG
Found at i:45819 original size:20 final size:20
Alignment explanation
Indices: 45794--45867 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
45784 GATTTTCCCA
*
45794 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
* * **
45814 ATTCGCATTACGATTTTCCCA
1 ATTCGCATTGCGA-TTTACTT
*
45835 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
45855 ATTCGCATTGCGA
1 ATTCGCATTGCGA
45868 ATTGGGAAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTT
Found at i:48082 original size:18 final size:18
Alignment explanation
Indices: 48061--48100 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
48051 CGTTATACAC
48061 TTTGACTGCTTTATTGTT
1 TTTGACTGCTTTATTGTT
**
48079 TTTGTTTGCTTTATTGTT
1 TTTGACTGCTTTATTGTT
48097 TTTG
1 TTTG
48101 TTTGCTTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.07, C:0.07, G:0.17, T:0.68
Consensus pattern (18 bp):
TTTGACTGCTTTATTGTT
Found at i:48101 original size:18 final size:18
Alignment explanation
Indices: 48067--48107 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
48057 ACACTTTGAC
48067 TGCTTTATTGTTTTTGTT
1 TGCTTTATTGTTTTTGTT
48085 TGCTTTATTGTTTTTGTT
1 TGCTTTATTGTTTTTGTT
48103 TGCTT
1 TGCTT
48108 GCATTACAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.05, C:0.07, G:0.17, T:0.71
Consensus pattern (18 bp):
TGCTTTATTGTTTTTGTT
Found at i:50043 original size:11 final size:11
Alignment explanation
Indices: 50027--50052 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
50017 TGAATCAAAA
50027 CTATACATGAC
1 CTATACATGAC
50038 CTATACATGAC
1 CTATACATGAC
50049 CTAT
1 CTAT
50053 CTAACCCGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.31
Consensus pattern (11 bp):
CTATACATGAC
Found at i:52640 original size:150 final size:155
Alignment explanation
Indices: 52354--52666 Score: 449
Period size: 156 Copynumber: 2.0 Consensus size: 155
52344 TTTAGAACAT
* * * *
52354 TTAATTTTGACTATAGTTTATATATATATATGTAAACAAGTATGTAGAATGAGAATCAAGTTCAT
1 TTAATTTCGACTATAGTTTATATATATATATGCAAACAAATATGTAGAATGAGAATCAAATTCAT
*
52419 AAATTATTATTAGGATTATTTTTAAATAAATTACACCCGTTACCATTTAATTATGAGTAGAATCT
66 AAATTATTATT--GATTATTTTTAAATAAATTACACCCGTTACCATTTAATTATGAGGAGAATCT
*
52484 AGTTTGATC-TCCTTCTTTTGATTTTG
129 AATTTGATCATCCTTCTTTTGATTTTG
* * *
52510 TTAATTTCGATTATAGTTTAT-TAATATTTATGCAAACAAATATGTAGAATTAGAATCAAATTCA
1 TTAATTTCGACTATAGTTTATAT-ATATATATGCAAACAAATATGTAGAATGAGAATCAAATTCA
* * *
52574 TGAATTATTATT-A-T-TTTTT-GATAAATTACATCCGTTACCATTTAATTATGAGGAGAATCTA
65 TAAATTATTATTGATTATTTTTAAATAAATTACACCCGTTACCATTTAATTATGAGGAGAATCTA
52635 ATTTGATCATCCTTCTTTTGATTTTG
130 ATTTGATCATCCTTCTTTTGATTTTG
52661 TTAATT
1 TTAATT
52667 AGATCACATA
Statistics
Matches: 143, Mismatches: 12, Indels: 9
0.87 0.07 0.05
Matches are distributed among these distances:
150 46 0.32
151 28 0.20
152 1 0.01
153 1 0.01
155 1 0.01
156 66 0.46
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.45
Consensus pattern (155 bp):
TTAATTTCGACTATAGTTTATATATATATATGCAAACAAATATGTAGAATGAGAATCAAATTCAT
AAATTATTATTGATTATTTTTAAATAAATTACACCCGTTACCATTTAATTATGAGGAGAATCTAA
TTTGATCATCCTTCTTTTGATTTTG
Found at i:65762 original size:9 final size:9
Alignment explanation
Indices: 65745--65789 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
65735 GAGCTTTATA
*
65745 AATAATAAT
1 AATATTAAT
65754 AATATTAAT
1 AATATTAAT
65763 AATATTAAT
1 AATATTAAT
*
65772 ATTATATAAT
1 AATAT-TAAT
65782 ATATATTA
1 A-ATATTA
65790 TAAAAACGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 21 0.68
10 7 0.23
11 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AATATTAAT
Found at i:70287 original size:13 final size:13
Alignment explanation
Indices: 70269--70333 Score: 62
Period size: 13 Copynumber: 5.2 Consensus size: 13
70259 GGAAGATAAC
70269 TTTTTTAACTTTA
1 TTTTTTAACTTTA
**
70282 TTTTTT-ACTAAA
1 TTTTTTAACTTTA
*
70294 TTTTTGAA-TTTA
1 TTTTTTAACTTTA
* *
70306 TATTTTATCTTTA
1 TTTTTTAACTTTA
*
70319 TTTTTTAATTTTA
1 TTTTTTAACTTTA
70332 TT
1 TT
70334 AATTATATTA
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
12 16 0.41
13 23 0.59
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.69
Consensus pattern (13 bp):
TTTTTTAACTTTA
Found at i:72837 original size:24 final size:22
Alignment explanation
Indices: 72810--72867 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 22
72800 AGTAAAAAAG
72810 ATAATAGAAAATAATAAAATAATA
1 ATAATA-AAAA-AATAAAATAATA
* *
72834 ATAA-AATAAAGTAAAATAATA
1 ATAATAAAAAAATAAAATAATA
72855 ATAATATAAAAAA
1 ATAATA-AAAAAA
72868 AGGTTAGCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
21 15 0.54
22 4 0.14
23 5 0.18
24 4 0.14
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.24
Consensus pattern (22 bp):
ATAATAAAAAAATAAAATAATA
Found at i:72848 original size:21 final size:20
Alignment explanation
Indices: 72817--72868 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
72807 AAGATAATAG
72817 AAAAT-AATAAAATAATAAT
1 AAAATAAATAAAATAATAAT
72836 AAAATAAAGTAAAATAATAAT
1 AAAATAAA-TAAAATAATAAT
*
72857 AATATAAA-AAAA
1 AAAATAAATAAAA
72869 GGTTAGCTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 9 0.30
20 2 0.07
21 19 0.63
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAATAAATAAAATAATAAT
Found at i:73125 original size:14 final size:15
Alignment explanation
Indices: 73087--73125 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
73077 TTATTATTAT
*
73087 AATAATAAATAAAAC
1 AATACTAAATAAAAC
73102 AATACTAAATAAAAC
1 AATACTAAATAAAAC
73117 AAT-CTAAAT
1 AATACTAAAT
73126 TAGGACTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (15 bp):
AATACTAAATAAAAC
Found at i:74886 original size:106 final size:106
Alignment explanation
Indices: 74686--75609 Score: 1438
Period size: 106 Copynumber: 8.7 Consensus size: 106
74676 TCCTCCGTCG
*
74686 TGAAATT-GAAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
74750 CTTGAGTCCAATATCCTTCGCTATGAAGTTGAAATTGACTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTC
* * * *
74791 TGAAATTGGGAAATTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCATTGT
1 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
74856 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTC
* * * * *
74897 TGATATTGAGAAGTTATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
1 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
74962 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTC
*
75003 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAATTTGCGTTGT
1 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
75068 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTC
* * * *
75109 TAAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
1 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
75174 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTC
* * * * *
75215 TGAAATTGAGAAGTTGTTTGTTGACAACCATCGATCCCTTCGTCGTGAAGTTGAACATGCGTTGT
1 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
75280 CTGGAGTCCAATATTCTTCGTTGTGAAGTTGAAATTGACTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTC
* ** *
75321 TGAAATTGGGAAGTTGTTTATTAACAACCAGCAATCCCTTCGTCGTGAAGTTGAACTTGTGTTGT
1 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
75386 CTGGAGTCTACTATCCTTCGCTGTGAAGTTGAAATTGACTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTC
*
75427 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGT
1 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* * *
75492 CTGGAGTCCACTATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTC
* ** * *
75533 T-AGTATTGCAAAATTGTTTATTAACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
1 TGA-AATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
75597 TCTGGAGTCCAAT
65 TCTGGAGTCCAAT
75610 TTTCTTCGTG
Statistics
Matches: 759, Mismatches: 58, Indels: 3
0.93 0.07 0.00
Matches are distributed among these distances:
105 8 0.01
106 751 0.99
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTC
Found at i:78627 original size:149 final size:149
Alignment explanation
Indices: 78357--78671 Score: 576
Period size: 149 Copynumber: 2.1 Consensus size: 149
78347 GGGTAGAGGG
* *
78357 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACTTGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
* *
78422 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
78487 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
78506 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
78571 ACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
78636 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
78655 TCTACGCGGTACTTCGG
1 TCTACGCGGTCCTTCGG
78672 TGCATTTATA
Statistics
Matches: 160, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 160 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:81767 original size:3 final size:3
Alignment explanation
Indices: 81752--81799 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
81742 GATAATAGAA
* *
81752 AAT AAT AAA AAT AAT AAT AA- AAT AA- AAT AA- AGT AA- AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
81796 AAT A
1 AAT A
81800 TAAAAAAGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 7 0.19
3 30 0.81
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:81770 original size:6 final size:5
Alignment explanation
Indices: 81750--81804 Score: 58
Period size: 5 Copynumber: 10.8 Consensus size: 5
81740 AAGATAATAG
* * *
81750 AAAAT AATA- AAAAT AATAAT AAAAT AAAAT AAAGT AAAAT AATAAT AATAT
1 AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT
81801 AAAA
1 AAAA
81805 AAGGTTAGCT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
4 3 0.07
5 28 0.68
6 10 0.24
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (5 bp):
AAAAT
Found at i:81778 original size:16 final size:16
Alignment explanation
Indices: 81759--81804 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
81749 GAAAATAATA
81759 AAAATAATAATAAAAT
1 AAAATAATAATAAAAT
*
81775 AAAATAA-AGTAAAAT
1 AAAATAATAATAAAAT
81790 AATAATAAT-ATAAAA
1 AA-AATAATAATAAAA
81805 AAGGTTAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 9 0.35
16 17 0.65
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (16 bp):
AAAATAATAATAAAAT
Found at i:82061 original size:14 final size:15
Alignment explanation
Indices: 82023--82061 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
82013 TTATTATTAT
*
82023 AATAATAAATAAAAC
1 AATACTAAATAAAAC
82038 AATACTAAATAAAAC
1 AATACTAAATAAAAC
82053 AAT-CTAAAT
1 AATACTAAAT
82062 TAGGACTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (15 bp):
AATACTAAATAAAAC
Found at i:84001 original size:21 final size:21
Alignment explanation
Indices: 83977--84037 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 21
83967 GCATTTCGTT
83977 TTGCGATAGTTGAAAATCGCG
1 TTGCGATAGTTGAAAATCGCG
* * ** **
83998 TTGCGGT-TTTTCATTTCGCG
1 TTGCGATAGTTGAAAATCGCG
84018 TTGCGATAGTTGAAAATCGC
1 TTGCGATAGTTGAAAATCGC
84038 AACATTTCGC
Statistics
Matches: 27, Mismatches: 12, Indels: 2
0.66 0.29 0.05
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.36
Consensus pattern (21 bp):
TTGCGATAGTTGAAAATCGCG
Found at i:84071 original size:21 final size:20
Alignment explanation
Indices: 84047--84117 Score: 56
Period size: 21 Copynumber: 3.5 Consensus size: 20
84037 CAACATTTCG
84047 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATA-TCTACAGTGT
* * * *
84068 CGTTTCGAT-TTTCCA-TTT
1 CGTTGCGATATCTACAGTGT
84086 CGCGTTGCGATAATCTACAGTGT
1 --CGTTGCGAT-ATCTACAGTGT
84109 CGTTGCGAT
1 CGTTGCGAT
84118 TTTCCATTTC
Statistics
Matches: 37, Mismatches: 8, Indels: 10
0.67 0.15 0.18
Matches are distributed among these distances:
18 2 0.05
19 4 0.11
20 8 0.22
21 17 0.46
22 4 0.11
23 2 0.05
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (20 bp):
CGTTGCGATATCTACAGTGT
Found at i:84096 original size:20 final size:20
Alignment explanation
Indices: 84068--84137 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
84058 TCTACAGTGT
*
84068 CGTTTCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
* * *
84088 CGTTGCGATAATCTACA-GT-G
1 CGTTGCGAT--TTTCCATTTCG
84108 TCGTTGCGATTTTCCATTTCG
1 -CGTTGCGATTTTCCATTTCG
84129 CGTTGCGAT
1 CGTTGCGAT
84138 AGTTTTAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
19 4 0.11
20 19 0.50
21 11 0.29
22 4 0.11
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.41
Consensus pattern (20 bp):
CGTTGCGATTTTCCATTTCG
Found at i:84097 original size:41 final size:41
Alignment explanation
Indices: 84040--84140 Score: 184
Period size: 41 Copynumber: 2.5 Consensus size: 41
84030 AAAATCGCAA
*
84040 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTTCGATTTTC
1 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
*
84081 CATTTCGCGTTGCGATAATCTACAGTGTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
84122 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
84141 TTTAAAAATG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.40
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
Found at i:84981 original size:6 final size:6
Alignment explanation
Indices: 84965--85010 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
84955 TCTCGTCTAG
* *
84965 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGG GGTCGG GGTCG
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCG
85011 GGGGTAATAC
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
5 5 0.13
6 34 0.87
ACGTcount: A:0.00, C:0.17, G:0.57, T:0.26
Consensus pattern (6 bp):
GGTCGT
Found at i:87972 original size:15 final size:16
Alignment explanation
Indices: 87952--87984 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
87942 TAGTAGAATC
87952 AAATTTAACT-TTTTT
1 AAATTTAACTATTTTT
*
87967 AAATTTAATTATTTTT
1 AAATTTAACTATTTTT
87983 AA
1 AA
87985 TATAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
AAATTTAACTATTTTT
Found at i:97236 original size:22 final size:23
Alignment explanation
Indices: 97188--97230 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
97178 TCTGATATTT
*
97188 TTTTTTATATTTGTATTACATAA
1 TTTTTTATATTTGTATGACATAA
*
97211 TTTTTTATATTT-TCTGACAT
1 TTTTTTATATTTGTATGACAT
97231 GCTTTTAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.26, C:0.07, G:0.05, T:0.63
Consensus pattern (23 bp):
TTTTTTATATTTGTATGACATAA
Found at i:98650 original size:20 final size:20
Alignment explanation
Indices: 98588--98817 Score: 223
Period size: 20 Copynumber: 11.5 Consensus size: 20
98578 TCAGTTTCCA
* ** *
98588 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
98608 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
98628 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
98648 AAACCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
98668 AAATAGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
98688 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
98708 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
98728 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
98748 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
* *
98768 AAATCACAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
98788 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
98808 AAATCACAAC
1 AAATCGCAAC
98818 ACTGAAATTT
Statistics
Matches: 174, Mismatches: 30, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 170 0.98
21 2 0.01
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:99549 original size:24 final size:24
Alignment explanation
Indices: 99510--99556 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
99500 AAATTTGGTC
99510 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
99534 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
99557 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:99748 original size:12 final size:12
Alignment explanation
Indices: 99731--99755 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
99721 ATATAATCCT
99731 GAAGAAGAAAAA
1 GAAGAAGAAAAA
99743 GAAGAAGAAAAA
1 GAAGAAGAAAAA
99755 G
1 G
99756 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:101687 original size:72 final size:72
Alignment explanation
Indices: 101594--101827 Score: 297
Period size: 72 Copynumber: 3.3 Consensus size: 72
101584 GCAACGAGAG
101594 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
101659 AAATGAA
66 AAATGAA
* *
101666 AATCGCAATGCGAAATGAAAATCGCAACGAT-AGAATCGCAATGCGGAAATGAAAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAAAATCGCAATGC
101730 GAAATGAA
65 GAAATGAA
* * * * *
101738 AATCGCAACGAGAGAATCG-CAATGCGAA-ATGAAAATCGCAATGC-GAAATGAAAATCGCAA--
1 AATCGCAATGCGA-AAT-GAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATG
*
101798 CG--A-GAG
64 CGAAATGAA
101804 AATCGCAATGCGGAAATGAAAATC
1 AATCGCAATGC-GAAATGAAAATC
101828 GCAATGCGAA
Statistics
Matches: 142, Mismatches: 14, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
65 1 0.01
66 17 0.12
67 3 0.02
69 2 0.01
71 18 0.13
72 90 0.63
73 10 0.07
74 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAA
Found at i:101709 original size:105 final size:102
Alignment explanation
Indices: 101580--101849 Score: 375
Period size: 105 Copynumber: 2.6 Consensus size: 102
101570 CGGAAATTAC
101580 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA-C-ATGAAAATCGCAATGCGGAA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCCCAAGCAATGAAAATCGCAA--C-G--
101642 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
61 A-GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* *
101685 AATCGCAACGATAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAG
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCCCAA-GC--AATGAAAATCGCAACGAG
*
101750 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
63 AAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
101790 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCCCAA-GC--AATGAAAATCGCA
101850 TTGCGATTCT
Statistics
Matches: 155, Mismatches: 4, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
105 123 0.79
106 16 0.10
108 2 0.01
109 1 0.01
111 13 0.08
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (102 bp):
AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCCCAAGCAATGAAAATCGCAACGAGAAA
ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:101715 original size:53 final size:52
Alignment explanation
Indices: 101580--101849 Score: 406
Period size: 53 Copynumber: 5.1 Consensus size: 52
101570 CGGAAATTAC
*
101580 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
101627 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
101685 AATCGCAACGATAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
101738 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
101790 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
101843 AATCGCA
1 AATCGCA
101850 TTGCGATTCT
Statistics
Matches: 205, Mismatches: 5, Indels: 20
0.89 0.02 0.09
Matches are distributed among these distances:
47 8 0.04
49 1 0.00
50 1 0.00
52 65 0.32
53 114 0.56
55 2 0.01
56 1 0.00
58 13 0.06
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:101855 original size:72 final size:68
Alignment explanation
Indices: 101561--101854 Score: 276
Period size: 72 Copynumber: 4.2 Consensus size: 68
101551 GCATTTGACT
** * * *
101561 ATCGCAACACGGAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAC-ATG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGATG
101625 AAA
66 AAA
*
101628 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAA
*
101693 CGAT-AGA
61 CGATGAAA
* * * * *
101700 ATCGCAATGCGGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-AATCGCAA--
101762 CGAAATGAAA
61 CG--ATGAAA
101772 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAA--CG
101836 AAATGAAA
63 --ATGAAA
*
101844 ATCGCATTGCG
1 ATCGCAATGCG
101855 ATTCTTTCGT
Statistics
Matches: 189, Mismatches: 19, Indels: 32
0.79 0.08 0.13
Matches are distributed among these distances:
65 7 0.04
66 7 0.04
67 33 0.17
69 4 0.02
70 1 0.01
71 22 0.12
72 105 0.56
73 5 0.03
74 5 0.03
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (68 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGATG
AAA
Found at i:101892 original size:20 final size:19
Alignment explanation
Indices: 101845--101943 Score: 92
Period size: 20 Copynumber: 5.6 Consensus size: 19
101835 GAAATGAAAA
101845 TCGCATTGCGA--TTC-TT
1 TCGCATTGCGATTTTCATT
*
101861 TCG--TTGCAATTTTCATT
1 TCGCATTGCGATTTTCATT
101878 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
*
101898 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
101915 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
101932 TCGCATTGCGAT
1 TCGCATTGCGAT
101944 AGTCATTTTT
Statistics
Matches: 68, Mismatches: 4, Indels: 19
0.75 0.04 0.21
Matches are distributed among these distances:
14 11 0.16
16 11 0.16
17 9 0.13
18 5 0.07
19 7 0.10
20 25 0.37
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:102069 original size:14 final size:14
Alignment explanation
Indices: 102050--102083 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
102040 CATCAATTAC
102050 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
102064 ACAAATCATCTTTT
1 ACAAATCAACTTTT
102078 ACAAAT
1 ACAAAT
102084 TAATTAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:102797 original size:20 final size:20
Alignment explanation
Indices: 102766--102829 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
102756 TTTTGGTTGA
102766 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
102786 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
102806 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
102827 AAT
1 AAT
102830 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:102818 original size:21 final size:21
Alignment explanation
Indices: 102764--102828 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
102754 TCTTTTGGTT
102764 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
102785 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
102805 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
102826 GAA
1 GAA
102829 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:102889 original size:14 final size:14
Alignment explanation
Indices: 102870--102926 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
102860 TTTGGTTTCG
102870 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
102884 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
102903 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
102917 CGTTGCGATT
1 CGTTGCGATT
102927 TTTATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:102902 original size:33 final size:33
Alignment explanation
Indices: 102854--102933 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
102844 AAAATCGCAA
**
102854 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
102887 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
102920 TGCGATTTTTATTT
1 TGCGATTTTCATTT
102934 TTCTCGTTGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.09, C:0.20, G:0.23, T:0.49
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:102939 original size:21 final size:21
Alignment explanation
Indices: 102914--102987 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
102904 GTTGCGATTC
*
102914 TCTCGTTGCGATTTTTATTTT
1 TCTCGTTGCGATTTTCATTTT
**
102935 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
102956 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
102977 TCTCGTTGCGA
1 TCTCGTTGCGA
102988 CTCTTCTGCA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.74
22 5 0.12
ACGTcount: A:0.15, C:0.19, G:0.18, T:0.49
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:103109 original size:33 final size:33
Alignment explanation
Indices: 103067--103137 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
103057 AATACTAACT
103067 TGAAAATCGCAACGAGAGAATA-GCAACGCGAAA
1 TGAAAATCGCAACGAGAGAA-ACGCAACGCGAAA
103100 TGAAAATCGCAACGAGAGAAACGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAAACGCAACGCGAAA
103133 TGAAA
1 TGAAA
103138 TCTAAGTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 1 0.03
33 36 0.97
ACGTcount: A:0.49, C:0.18, G:0.24, T:0.08
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAAACGCAACGCGAAA
Found at i:103542 original size:20 final size:20
Alignment explanation
Indices: 103517--103610 Score: 161
Period size: 20 Copynumber: 4.7 Consensus size: 20
103507 CTTTAAAAAT
103517 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
103537 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
103557 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
** *
103577 CATGTTGCGGTTTACGGATA
1 CGCGTTGCGATTTACGGATA
103597 CGCGTTGCGATTTA
1 CGCGTTGCGATTTA
103611 TGTGTTCGCG
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:103620 original size:20 final size:20
Alignment explanation
Indices: 103597--103648 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
103587 TTTACGGATA
* *
103597 CGCGTTGCGATTTAT-GTGTT
1 CGCGTTGCGATTT-TCATATT
*
103617 CGCGTTGTGATTTTCATATT
1 CGCGTTGCGATTTTCATATT
103637 CGCGTTGCGATT
1 CGCGTTGCGATT
103649 CTGGAAAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.12, C:0.17, G:0.27, T:0.44
Consensus pattern (20 bp):
CGCGTTGCGATTTTCATATT
Found at i:103644 original size:60 final size:60
Alignment explanation
Indices: 103516--103648 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 60
103506 GCTTTAAAAA
*
103516 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTACAGAT
* ** * * * * * *
103576 ACATGTTGCGGTTTACGGATACGCGTTGCGATTTATGTG-TTCGCGTTGTGATTTTCATAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACG-GATACGCGTTGCGATTTACAGAT
103636 TCGCGTTGCGATT
1 TCGCGTTGCGATT
103649 CTGGAAAATC
Statistics
Matches: 58, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
60 57 0.98
61 1 0.02
ACGTcount: A:0.17, C:0.18, G:0.29, T:0.37
Consensus pattern (60 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTACAGAT
Found at i:104704 original size:20 final size:22
Alignment explanation
Indices: 104659--104705 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
104649 CTTAAATATC
104659 TAAATTCAATTTACATATTTAA
1 TAAATTCAATTTACATATTTAA
104681 -AAATT-AATTTA-AGTA-TTAA
1 TAAATTCAATTTACA-TATTTAA
104700 TAAATT
1 TAAATT
104706 TTAAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
19 5 0.22
20 13 0.57
21 5 0.22
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (22 bp):
TAAATTCAATTTACATATTTAA
Found at i:104717 original size:7 final size:7
Alignment explanation
Indices: 104707--104731 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
104697 TAATAAATTT
104707 TAAAAAA
1 TAAAAAA
104714 TAAAAAA
1 TAAAAAA
104721 TAAAAAA
1 TAAAAAA
104728 TAAA
1 TAAA
104732 TAAAAATTAT
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAAAAA
Found at i:113703 original size:2 final size:2
Alignment explanation
Indices: 113696--113721 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
113686 TGAGTTTCAG
113696 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
113722 GTTTCTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:121455 original size:22 final size:22
Alignment explanation
Indices: 121412--121455 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
121402 AAATTTACAT
*
121412 TCACATAAAATAAAATAAATTG
1 TCACATAAAATAAAACAAATTG
* * *
121434 TCACTTAAAATAACACACATTG
1 TCACATAAAATAAAACAAATTG
121456 CATCGTTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (22 bp):
TCACATAAAATAAAACAAATTG
Found at i:123927 original size:3 final size:3
Alignment explanation
Indices: 123921--123976 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
123911 AAAAAATATG
* * **
123921 TAA TAA TAAA TAA TAA AAA TAA TAA -GA TAA CGA TAA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
123966 TAA TAA -AA TAA
1 TAA TAA TAA TAA
123977 CGGAAAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
2 3 0.07
3 36 0.86
4 3 0.07
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:123958 original size:26 final size:26
Alignment explanation
Indices: 123929--123978 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
123919 TGTAATAATA
*
123929 AATAATAAAAATAATAAGATAACGAT
1 AATAATAAAAATAATAAAATAACGAT
*
123955 AATAATAATAATAATAAAATAACG
1 AATAATAAAAATAATAAAATAACG
123979 GAAAAAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.24
Consensus pattern (26 bp):
AATAATAAAAATAATAAAATAACGAT
Found at i:124313 original size:43 final size:42
Alignment explanation
Indices: 124265--124641 Score: 250
Period size: 43 Copynumber: 8.8 Consensus size: 42
124255 TAAGGTGATA
* *
124265 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGA-GGCTGGTCATCTATGGTTG
* ** *
124308 ACACGGCTCCTACGTGATGAGGAGATCT-G--ATCTGGGGAATG
1 ACACGGCTCCTACGTGATGAGGAG-GCTGGTCATCTATGG-TTG
* * * * * *
124349 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGAG-GCTGGTCATCT-ATGGT--TG
* *
124395 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGA-GGCTGGTCATCTATGGTTG
* * *
124438 ACACGGCTCCTACGTGATGAGGAGATCTGGTCAGC--T-GATG
1 ACACGGCTCCTACGTGATGAGGAG-GCTGGTCATCTATGGTTG
* * * * * *
124478 ACACGGCTCATACGTGATGAAGAGTTCCGGCCATCTAAAGG-TG
1 ACACGGCTCCTACGTGATGAGGAG-GCTGGTCATCT-ATGGTTG
* *
124521 ATACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
1 --ACACGGCTCCTACGTGATGAGGA-GGCTGGTCATCTATGGTTG
* * * ** *
124566 ACACGGCTCCTACGTGATGAAGA-GCT-CTGATCTGGGGATG
1 ACACGGCTCCTACGTGATGAGGAGGCTGGTCATCTATGGTTG
* * *
124606 ACACGGTTCCTACATGATGAGGACGGCTGGCCATCT
1 ACACGGCTCCTACGTGATGAGGA-GGCTGGTCATCT
124642 TTAGGATTTA
Statistics
Matches: 260, Mismatches: 53, Indels: 42
0.73 0.15 0.12
Matches are distributed among these distances:
40 67 0.26
41 31 0.12
42 7 0.03
43 81 0.31
44 8 0.03
45 35 0.13
46 30 0.12
47 1 0.00
ACGTcount: A:0.23, C:0.21, G:0.31, T:0.25
Consensus pattern (42 bp):
ACACGGCTCCTACGTGATGAGGAGGCTGGTCATCTATGGTTG
Found at i:124641 original size:128 final size:129
Alignment explanation
Indices: 124176--124625 Score: 679
Period size: 130 Copynumber: 3.5 Consensus size: 129
124166 CGTCTAAGGG
* * * * * * ** *
124176 TGACATGGTTCCTACGTGATGAAGACATCTGGTC-GAAGGATGACACTACTCATACATGATGAAG
1 TGACACGGCTCCTACGTGATGAGGAGATCTGATCTG-GGGATGACACGGCTCATACGTGATGAAG
*
124240 AGTTCTTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGG
65 AGTTC-TGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGG
124305 T
129 T
124306 TGACACGGCTCCTACGTGATGAGGAGATCTGATCTGGGGAATGACACGGCTCATACGTGATGAAG
1 TGACACGGCTCCTACGTGATGAGGAGATCTGATCTGGGG-ATGACACGGCTCATACGTGATGAAG
124371 AGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
65 AGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
* * **
124436 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGCTGATGACACGGCTCATACGTGATGAAGA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGATCTGGGGATGACACGGCTCATACGTGATGAAGA
*
124501 GTTCCGGCCATCTAAAGGTGAT-ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
66 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
* * * * *
124564 TGACACGGCTCCTACGTGATGAAGAGCTCTGATCTGGGGATGACACGGTTCCTACATGATGA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGATCTGGGGATGACACGGCTCATACGTGATGA
124626 GGACGGCTGG
Statistics
Matches: 294, Mismatches: 24, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
128 94 0.32
129 47 0.16
130 125 0.43
131 28 0.10
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (129 bp):
TGACACGGCTCCTACGTGATGAGGAGATCTGATCTGGGGATGACACGGCTCATACGTGATGAAGA
GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
Found at i:124704 original size:28 final size:28
Alignment explanation
Indices: 124654--124707 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
124644 AGGATTTATG
* *
124654 GTTTCAAGAGAAACCAAATCAAAGATTT
1 GTTTCAAAAGAAACCAAACCAAAGATTT
124682 GTTTCAAAAGAAA-CAAACCCAAAGAT
1 GTTTCAAAAGAAACCAAA-CCAAAGAT
124708 GATATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (28 bp):
GTTTCAAAAGAAACCAAACCAAAGATTT
Found at i:124824 original size:65 final size:63
Alignment explanation
Indices: 124723--124904 Score: 179
Period size: 66 Copynumber: 2.8 Consensus size: 63
124713 TTTTAAAAGC
* *
124723 AACTGTCTCAAAAGAGACCAAATTCGTTTTAAGGGAAACGACTCAAAGATGACATTTAAAGGGA
1 AACTGTCTC-AATGAGACAAAATTCGTTTTAAGGGAAACGACTCAAAGATGACATTTAAAGGGA
* * * * *
124787 AACTGTCTC-GTGCAAGACAAAATTCGTTTTTAAGGGAAACGTTCTC-AAGATCGACGTTTCATG
1 AACTGTCTCAATG--AGACAAAATTCG-TTTTAAGGGAAACG-ACTCAAAGAT-GACATTTAAAG
124850 GGA
61 GGA
* * * *
124853 AATTGTCTCAAATGAGACAAAATTCATTTCAAGGGAAACGATCTCACAGATG
1 AACTGTCTC-AATGAGACAAAATTCGTTTTAAGGGAAACGA-CTCAAAGATG
124905 TTTGTTTGTT
Statistics
Matches: 96, Mismatches: 13, Indels: 17
0.76 0.10 0.13
Matches are distributed among these distances:
62 1 0.01
64 20 0.21
65 36 0.38
66 37 0.39
68 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.25
Consensus pattern (63 bp):
AACTGTCTCAATGAGACAAAATTCGTTTTAAGGGAAACGACTCAAAGATGACATTTAAAGGGA
Found at i:124871 original size:66 final size:63
Alignment explanation
Indices: 124723--124904 Score: 188
Period size: 65 Copynumber: 2.8 Consensus size: 63
124713 TTTTAAAAGC
* * *
124723 AACTGTCTCAAAAGAGACCAAATTCGTTTTAAGGGAAACGACTCAAAGATGACATTTAAAGGGA
1 AACTGTCTCAAATGAGACAAAATTCGTTTTAAGGGAAACGTCTC-AAGATGACATTTAAAGGGA
* * * *
124787 AACTGTCTC--GTGCAAGACAAAATTCGTTTTTAAGGGAAACGTTCTCAAGATCGACGTTTCATG
1 AACTGTCTCAAATG--AGACAAAATTCG-TTTTAAGGGAAACG-TCTCAAGAT-GACATTTAAAG
124850 GGA
61 GGA
* * *
124853 AATTGTCTCAAATGAGACAAAATTCATTTCAAGGGAAACGATCTCACAGATG
1 AACTGTCTCAAATGAGACAAAATTCGTTTTAAGGGAAACG-TCTCA-AGATG
124905 TTTGTTTGTT
Statistics
Matches: 98, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
62 1 0.01
64 20 0.20
65 38 0.39
66 37 0.38
68 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.25
Consensus pattern (63 bp):
AACTGTCTCAAATGAGACAAAATTCGTTTTAAGGGAAACGTCTCAAGATGACATTTAAAGGGA
Found at i:125028 original size:28 final size:25
Alignment explanation
Indices: 124996--125049 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 25
124986 AACTGTCTCG
*
124996 AGAGATACAAACTTTTGTTTCCAAAGAA
1 AGAGATAC-AA-TTTT-TTTCAAAAGAA
*
125024 AGAGATTCAATTTTTTTCAAAAGAA
1 AGAGATACAATTTTTTTCAAAAGAA
125049 A
1 A
125050 TTGTTTTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 11 0.46
26 4 0.17
27 2 0.08
28 7 0.29
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (25 bp):
AGAGATACAATTTTTTTCAAAAGAA
Found at i:125126 original size:15 final size:15
Alignment explanation
Indices: 125103--125145 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
125093 AAGATGATCT
125103 TGTTT-AAGAGAAAA
1 TGTTTCAAGAGAAAA
125117 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
125132 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
125146 CGACTCAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
14 5 0.19
15 22 0.81
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:125196 original size:30 final size:30
Alignment explanation
Indices: 125134--125207 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
125124 AGAGAAAATG
*
125134 TTTCAAGTGAAACGACTCAAAAATGGTTTTA
1 TTTCAAGTGAAACAACTCAAAAAT-GTTTTA
* *
125165 TTTCAATTGAAACAAACTCAAAGAT-TTTTA
1 TTTCAAGTGAAAC-AACTCAAAAATGTTTTA
* *
125195 TTTCTAGAGAAAC
1 TTTCAAGTGAAAC
125208 TGCTCACGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 15 0.42
31 12 0.33
32 9 0.25
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.34
Consensus pattern (30 bp):
TTTCAAGTGAAACAACTCAAAAATGTTTTA
Found at i:125514 original size:1 final size:1
Alignment explanation
Indices: 125508--125533 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
125498 AGACACATTG
125508 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
125534 AGAATAGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:125677 original size:65 final size:62
Alignment explanation
Indices: 125605--125812 Score: 199
Period size: 65 Copynumber: 3.3 Consensus size: 62
125595 TCAAGATTAC
* * * * *
125605 TTCAAAAGAGACTGTCTCAAGAGATACAAAATTCATTTTAAGAGAAACAGATTCAAAGATTTTTT
1 TTCAAAAGAAACTATCTTAAGAGA-ACAAAATT-ATTTTAA-AGAAACAAACTCAAAGATTTTTT
* * **
125670 TTTAAAAGAAATTATCTTAAGAG-ACAAAATTTATTCCAAAGAAACAAACTC-AA-ATTTTTGT
1 TTCAAAAGAAACTATCTTAAGAGAACAAAA-TTATTTTAAAGAAACAAACTCAAAGATTTTT-T
*
125731 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGA-TTTT
1 TTCAAAAGAAACTATCTTAAGAGA-ACAAAATTAT-TTT--AAAGAAACAAACTCAAAGATTTTT
125795 T
62 T
* *
125796 TTGAAAAGAAACAATCT
1 TTCAAAAGAAACTATCT
125813 CAAAGATTTT
Statistics
Matches: 118, Mismatches: 16, Indels: 18
0.78 0.11 0.12
Matches are distributed among these distances:
60 6 0.05
61 24 0.20
62 13 0.11
63 18 0.15
64 2 0.02
65 48 0.41
66 6 0.05
67 1 0.01
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.30
Consensus pattern (62 bp):
TTCAAAAGAAACTATCTTAAGAGAACAAAATTATTTTAAAGAAACAAACTCAAAGATTTTTT
Found at i:125747 original size:61 final size:64
Alignment explanation
Indices: 125663--125812 Score: 200
Period size: 65 Copynumber: 2.4 Consensus size: 64
125653 AGATTCAAAG
* *
125663 ATTTTTTTTTAAAAGAAATTATCTT-A-AGAGACAAAA-TTT-ATTCCAAAGAAACAAACTCAA
1 ATTTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGATTCCAAAGAAACAAACTCAA
*
125723 ATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAA
1 ATTTTT-TTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGATTCCAAAGAAACAAACTCAA
* * *
125788 AGATTTTTTTGAAAAGAAACAATCT
1 A-TTTTTTTTCAAAAGAAACTATCT
125813 CAAAGATTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
60 6 0.08
61 17 0.22
62 1 0.01
63 10 0.13
64 3 0.04
65 37 0.47
66 4 0.05
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (64 bp):
ATTTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGATTCCAAAGAAACAAACTCAA
Found at i:125803 original size:28 final size:28
Alignment explanation
Indices: 125772--125825 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
125762 TTTTGTTTCC
125772 AAAGAAACAAACTCAAAGATTTTTTTGA
1 AAAGAAACAAACTCAAAGATTTTTTTGA
*
125800 AAAGAAACAATCTCAAAGATTTTTTT
1 AAAGAAACAAACTCAAAGATTTTTTT
125826 CACAAAATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.31
Consensus pattern (28 bp):
AAAGAAACAAACTCAAAGATTTTTTTGA
Found at i:125875 original size:54 final size:52
Alignment explanation
Indices: 125811--125914 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 52
125801 AAGAAACAAT
125811 CTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
1 CTCAAAGA--TTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
* *
125865 CTCAAGGATTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
125915 AAATAAATAG
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 41 0.85
54 7 0.15
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (52 bp):
CTCAAAGATTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
Found at i:125957 original size:25 final size:27
Alignment explanation
Indices: 125911--126004 Score: 111
Period size: 28 Copynumber: 3.4 Consensus size: 27
125901 AAAACTTTGT
* *
125911 TTCAAAATAAATAGACTCAAAGATTT-
1 TTCAAAAGAAACAGACTCAAAGATTTA
125937 TTCAAAAGAAACA-ACTCAAAGATTTTTA
1 TTCAAAAGAAACAGACTCAAAGA--TTTA
*
125965 TTCAAAAGGAACAGACTCAAAGATTTA
1 TTCAAAAGAAACAGACTCAAAGATTTA
*
125992 TCTCAAGAGAAAC
1 T-TCAAAAGAAAC
126005 TGTCTCCAGA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
25 9 0.16
26 11 0.19
27 8 0.14
28 21 0.36
29 9 0.16
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.26
Consensus pattern (27 bp):
TTCAAAAGAAACAGACTCAAAGATTTA
Found at i:126333 original size:36 final size:36
Alignment explanation
Indices: 126249--126352 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
126239 GAGAAAATGA
* * *
126249 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
126283 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
126319 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
126353 CGATTTCAAG
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 19 0.33
35 10 0.17
36 29 0.50
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:126506 original size:105 final size:100
Alignment explanation
Indices: 126320--126551 Score: 259
Period size: 105 Copynumber: 2.3 Consensus size: 100
126310 TAGAGAAATT
* * **
126320 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAACGATTTCAAGTGAGATCAACTTTGTTTAATGT
1 GTCTCAAGCGAGACAAAATTTG-TTTTGAGAAACAAAATCAAGTGAGATCAACTTTGTTTAATGT
* *
126385 GAAACAAATCCGAAATTTGGATCTCAAAGGGAAAAG
65 GAAACAAATCCAAAATTTGGATCTCAAAGGAAAAAG
* *
126421 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCTAAGGTGAGATTAATTTTGTTT-
1 GTCTCAAGCGAGACAAAATTTGTTTTG--AGAAACAA-AATC-AA-GTGAGATCAACTTTGTTTA
* * * * *
126485 TTAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
61 AT-GTGAAACAAATCCAAAATTTGGATCTCAAAGGAAAAAG
**
126526 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTT
126552 AAAATTCTCA
Statistics
Matches: 110, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
100 5 0.05
101 21 0.19
102 7 0.06
103 2 0.02
104 3 0.03
105 72 0.65
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.31
Consensus pattern (100 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAGAAACAAAATCAAGTGAGATCAACTTTGTTTAATGTG
AAACAAATCCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:126625 original size:66 final size:67
Alignment explanation
Indices: 126554--126686 Score: 241
Period size: 67 Copynumber: 2.0 Consensus size: 67
126544 TTTGTTTTAA
126554 AATTCTCAAAATTTGTGG-AAAAATGTCTCAAGCGAGACATAATATGTTTTAAAGAGAAAGTTGT
1 AATTCTCAAAATTTGTGGAAAAAATGTCTCAAGCGAGACATAATATGTTTTAAAGAGAAAGTTGT
126618 CT
66 CT
* *
126620 AATTCTCAAAATTTGTGGAAAAAATGTCTCAAGCGAGACATAATTTGTTTTAAAGAGAGAGTTGT
1 AATTCTCAAAATTTGTGGAAAAAATGTCTCAAGCGAGACATAATATGTTTTAAAGAGAAAGTTGT
126685 CT
66 CT
126687 CAAGCGAGAC
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
66 18 0.28
67 46 0.72
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (67 bp):
AATTCTCAAAATTTGTGGAAAAAATGTCTCAAGCGAGACATAATATGTTTTAAAGAGAAAGTTGT
CT
Found at i:126732 original size:36 final size:38
Alignment explanation
Indices: 126646--126732 Score: 106
Period size: 38 Copynumber: 2.3 Consensus size: 38
126636 GGAAAAAATG
* ** *
126646 TCTCAAGCGAGACATAATTTGTTTTAAAGAGAGAGTTG
1 TCTCAAGCGAGACAAAATTTGTTTTAAAGAGAGAACTA
*
126684 TCTCAAGCGAGACAAAATTTGTTTTTAAGA-A-AACTA
1 TCTCAAGCGAGACAAAATTTGTTTTAAAGAGAGAACTA
*
126720 TCTCAAGTGAGAC
1 TCTCAAGCGAGAC
126733 GACACTTTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 14 0.33
37 1 0.02
38 28 0.65
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.30
Consensus pattern (38 bp):
TCTCAAGCGAGACAAAATTTGTTTTAAAGAGAGAACTA
Found at i:127101 original size:12 final size:12
Alignment explanation
Indices: 127084--127151 Score: 68
Period size: 12 Copynumber: 5.7 Consensus size: 12
127074 TGTAACATGC
127084 ATGTATGTGTTG
1 ATGTATGTGTTG
*
127096 ATGTATGTATAT-
1 ATGTATGTGT-TG
*
127108 ATGTATGAGTTG
1 ATGTATGTGTTG
*
127120 ATGTATGTATAT-
1 ATGTATGTGT-TG
*
127132 ATGTATGAGTTG
1 ATGTATGTGTTG
127144 ATGTATGT
1 ATGTATGT
127152 TTCTCAATCT
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
11 2 0.05
12 40 0.91
13 2 0.05
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (12 bp):
ATGTATGTGTTG
Found at i:127112 original size:24 final size:24
Alignment explanation
Indices: 127084--127151 Score: 127
Period size: 24 Copynumber: 2.8 Consensus size: 24
127074 TGTAACATGC
*
127084 ATGTATGTGTTGATGTATGTATAT
1 ATGTATGAGTTGATGTATGTATAT
127108 ATGTATGAGTTGATGTATGTATAT
1 ATGTATGAGTTGATGTATGTATAT
127132 ATGTATGAGTTGATGTATGT
1 ATGTATGAGTTGATGTATGT
127152 TTCTCAATCT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (24 bp):
ATGTATGAGTTGATGTATGTATAT
Found at i:128349 original size:12 final size:11
Alignment explanation
Indices: 128321--128358 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
128311 TCCTCTTTTG
*
128321 TTCTTTGCTTT
1 TTCTTTGATTT
128332 TTCTTTGATTT
1 TTCTTTGATTT
128343 TTGCTTTGATTT
1 TT-CTTTGATTT
128355 TTCT
1 TTCT
128359 CTTTGCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.05, C:0.13, G:0.11, T:0.71
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:129058 original size:46 final size:45
Alignment explanation
Indices: 128966--129059 Score: 125
Period size: 46 Copynumber: 2.1 Consensus size: 45
128956 ATAAATGCAG
* * * *
128966 TGTTTCAAGGTGGAAAGAATGTTTCAAGGCCTTAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGCCTCAAAGAGAGAGAA
* *
129011 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGCCTCAAAGAGAGAGAA
129057 TGT
1 TGT
129060 CAAAAATTGG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 11 0.26
46 31 0.74
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.27
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGCCTCAAAGAGAGAGAA
Found at i:131521 original size:31 final size:31
Alignment explanation
Indices: 131483--131543 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
131473 TGACAAAATG
131483 ACACAAAC-AAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAA-AAATAAGTTAGTAT
131514 ACACAAACAAAAGAGAAAAATAAGTTAGTA
1 ACACAAACAAAAGAGAAAAATAAGTTAGTA
131544 CATGTAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 21 0.72
32 8 0.28
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (31 bp):
ACACAAACAAAAGAGAAAAATAAGTTAGTAT
Found at i:133080 original size:22 final size:22
Alignment explanation
Indices: 133037--133080 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
133027 AAATTTACAT
*
133037 TCACATAAAATAAAATAAATTG
1 TCACATAAAATAAAACAAATTG
* * *
133059 TCACTTAAAATAACACACATTG
1 TCACATAAAATAAAACAAATTG
133081 CATCGTTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (22 bp):
TCACATAAAATAAAACAAATTG
Found at i:135576 original size:3 final size:3
Alignment explanation
Indices: 135570--135630 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
135560 AAAAAATATG
* **
135570 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
135614 TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
135631 CGGAAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:139628 original size:18 final size:18
Alignment explanation
Indices: 139588--139629 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
139578 AATATTCTCA
*
139588 GTAATCTTATTCTCCCTG
1 GTAATCATATTCTCCCTG
*
139606 ATAATCATATTC-CCACTG
1 GTAATCATATTCTCC-CTG
139624 GTAATC
1 GTAATC
139630 TTACATTCTG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.38
Consensus pattern (18 bp):
GTAATCATATTCTCCCTG
Found at i:140739 original size:12 final size:12
Alignment explanation
Indices: 140718--140751 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
140708 ACCACATTTC
*
140718 CAATACCAAACA
1 CAATATCAAACA
140730 CAATATCAAACA
1 CAATATCAAACA
*
140742 CAATCTCAAA
1 CAATATCAAA
140752 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:140904 original size:24 final size:24
Alignment explanation
Indices: 140877--140930 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
140867 TTATTCGAAA
140877 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
140901 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
140925 TTTGAT
1 TTTGAT
140931 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:143218 original size:18 final size:18
Alignment explanation
Indices: 143195--143230 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
143185 AAGCAAAAGG
143195 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
143213 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
143231 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:143526 original size:49 final size:49
Alignment explanation
Indices: 143467--143574 Score: 137
Period size: 49 Copynumber: 2.2 Consensus size: 49
143457 AAATTCGCAA
** * *
143467 CGCAAAAATCGCAATGCGAATTTGACTTTCGTGTTGTA-AATTTGACTTT
1 CGCAAAAATCGCAACACGAATTTGACTTTCGCGTTG-AGAATTTGACTAT
* *
143516 CGCAATAATCGCAACACGAATTTTACTTTCGCGTTGAGAATTTGACTAT
1 CGCAAAAATCGCAACACGAATTTGACTTTCGCGTTGAGAATTTGACTAT
*
143565 CGCAACAATC
1 CGCAAAAATC
143575 AAAACGAGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
48 1 0.02
49 50 0.98
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (49 bp):
CGCAAAAATCGCAACACGAATTTGACTTTCGCGTTGAGAATTTGACTAT
Found at i:143729 original size:25 final size:25
Alignment explanation
Indices: 143689--143738 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
143679 AAATGAATTA
* *
143689 AACATTGTTGTTGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
143714 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
143739 GAAAATAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.26, C:0.08, G:0.20, T:0.46
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:145364 original size:20 final size:20
Alignment explanation
Indices: 145339--145440 Score: 125
Period size: 20 Copynumber: 5.1 Consensus size: 20
145329 TTGCAACGCC
145339 AATTTGACTTTCGCGTTGCG
1 AATTTGACTTTCGCGTTGCG
*
145359 AATTTGACTTTCACGTTGCG
1 AATTTGACTTTCGCGTTGCG
* *
145379 AATTTGACTTTCGCGTTACA
1 AATTTGACTTTCGCGTTGCG
* **
145399 AATTTGACTATCGCAACT-CG
1 AATTTGACTTTCGC-GTTGCG
*
145419 AATTTGACTTTCGCATTGCG
1 AATTTGACTTTCGCGTTGCG
145439 AA
1 AA
145441 AGTGTACCTT
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.03
20 67 0.96
21 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.37
Consensus pattern (20 bp):
AATTTGACTTTCGCGTTGCG
Found at i:145472 original size:20 final size:20
Alignment explanation
Indices: 145447--145495 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
145437 CGAAAGTGTA
145447 CCTTCAACAGGTCTTTTTTG
1 CCTTCAACAGGTCTTTTTTG
145467 CCTTCAACAGGTCTTTTTTG
1 CCTTCAACAGGTCTTTTTTG
145487 CCTTCAACA
1 CCTTCAACA
145496 TAATGCAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.18, C:0.29, G:0.12, T:0.41
Consensus pattern (20 bp):
CCTTCAACAGGTCTTTTTTG
Found at i:146988 original size:21 final size:21
Alignment explanation
Indices: 146961--147052 Score: 112
Period size: 21 Copynumber: 4.4 Consensus size: 21
146951 GTGAATCGGG
* *
146961 CTCTTGAACGGTGGGAGTGAC
1 CTCTTGAACGGTGGGAGGGGC
* * **
146982 ATCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
147003 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
* *
147024 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
147045 CTCTTGAA
1 CTCTTGAA
147053 TGATAGGATG
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.22, C:0.20, G:0.37, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:147008 original size:42 final size:42
Alignment explanation
Indices: 146961--147052 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
146951 GTGAATCGGG
*
146961 CTCTTGAACGGTGGGAGTGACATCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGACATCTTGAACGATGACAGGGGC
* * *
147003 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGGTGGGAGGGACATCTTGAACGATGACAGGGGC
147045 CTCTTGAA
1 CTCTTGAA
147053 TGATAGGATG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.22, C:0.20, G:0.37, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACATCTTGAACGATGACAGGGGC
Found at i:147069 original size:42 final size:42
Alignment explanation
Indices: 146983--147083 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
146973 GGGAGTGACA
* * *
146983 TCTTGAACGATGACAGGGGCCTCTTGAACGGTGGGAGGGGCC
1 TCTTGAACGATGACAGGGGCCTCTTGAACGATAGGAGGCGCC
* * * *
147025 TCTTGAACGATGAGAGGGGCCTCTTGAATGATAGGATGCTCC
1 TCTTGAACGATGACAGGGGCCTCTTGAACGATAGGAGGCGCC
*
147067 TCTTGAATGATGACAGG
1 TCTTGAACGATGACAGG
147084 TGAATCGGGC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.24
Consensus pattern (42 bp):
TCTTGAACGATGACAGGGGCCTCTTGAACGATAGGAGGCGCC
Found at i:147244 original size:4 final size:4
Alignment explanation
Indices: 147223--147256 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
147213 GGGCCGCTGA
* *
147223 AAAT AAAT TAAT ACAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
147257 TGCCGAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Done.