Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015028.1 Kokia drynarioides strain JFW-HI SEQ_130072, 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: 198098
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 733 characters in sequence are not A, C, G, or T
Found at i:11343 original size:11 final size:11
Alignment explanation
Indices: 11327--11352 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
11317 ATTGCGCCAG
11327 TTTTTTTTTCT
1 TTTTTTTTTCT
11338 TTTTTTTTTCT
1 TTTTTTTTTCT
11349 TTTT
1 TTTT
11353 CTTGAAGGAA
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:19412 original size:20 final size:18
Alignment explanation
Indices: 19367--19414 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
19357 CTTAAATCTA
*
19367 AATATATAAATAAAATTT
1 AATATTTAAATAAAATTT
19385 AATTTATTTAAATAAAATTATT
1 AA--TATTTAAATAAAA-T-TT
19407 AATATTTA
1 AATATTTA
19415 GTAACAAGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 2 0.08
20 18 0.72
21 1 0.04
22 4 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATATTTAAATAAAATTT
Found at i:21680 original size:29 final size:28
Alignment explanation
Indices: 21648--21805 Score: 97
Period size: 29 Copynumber: 5.4 Consensus size: 28
21638 TCAAAAATAG
21648 AATTTTTGGACATCCGGGGGTAAAATGGT
1 AATTTTTGGACAT-CGGGGGTAAAATGGT
* * ** *
21677 AATTTTTAGGAAAATTGAGATGAAAAATGG-
1 AATTTTT-GG-ACATCG-GGGGTAAAATGGT
* * *
21707 AATTTTTGGACATTTGAGGGTAAAATGTT
1 AATTTTTGGACA-TCGGGGGTAAAATGGT
* *
21736 AATTTTTAGGAAAATC-GGGATCAAAAATGG-
1 AATTTTT-GG-ACATCGGGGGT--AAAATGGT
*
21766 AATTTTTTGGACATCCGGGGGCAAAATGGT
1 AA-TTTTTGGACAT-CGGGGGTAAAATGGT
21796 AATTTTTGGA
1 AATTTTTGGA
21806 AATTTTGGGG
Statistics
Matches: 97, Mismatches: 19, Indels: 26
0.68 0.13 0.18
Matches are distributed among these distances:
28 9 0.09
29 40 0.41
30 20 0.21
31 28 0.29
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.33
Consensus pattern (28 bp):
AATTTTTGGACATCGGGGGTAAAATGGT
Found at i:21802 original size:60 final size:59
Alignment explanation
Indices: 21607--21835 Score: 300
Period size: 59 Copynumber: 3.9 Consensus size: 59
21597 AGACACTCGA
* * *
21607 GGGTAAAACGGTAATTTTTA-AAAAATCGGGATCAAAAATAGAATTTTTGGACATCCGG
1 GGGTAAAATGGTAATTTTTAGGAAAATCGGGATCAAAAATGGAATTTTTGGACATCCGG
* * * ** *
21665 GGGTAAAATGGTAATTTTTAGGAAAATTGAGATGAAAAATGGAATTTTTGGACATTTGA
1 GGGTAAAATGGTAATTTTTAGGAAAATCGGGATCAAAAATGGAATTTTTGGACATCCGG
*
21724 GGGTAAAATGTTAATTTTTAGGAAAATCGGGATCAAAAATGGAATTTTTTGGACATCCGG
1 GGGTAAAATGGTAATTTTTAGGAAAATCGGGATCAAAAATGGAA-TTTTTGGACATCCGG
* * * *
21784 GGGCAAAATGGTAATTTTT-GGAAATTTTGGGGTCAAAAATGGAATTTTTGGA
1 GGGTAAAATGGTAATTTTTAGGAAA-ATCGGGATCAAAAATGGAATTTTTGGA
21836 TGTTTGGGGT
Statistics
Matches: 147, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
58 19 0.13
59 83 0.56
60 45 0.31
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTAGGAAAATCGGGATCAAAAATGGAATTTTTGGACATCCGG
Found at i:21815 original size:29 final size:29
Alignment explanation
Indices: 21664--21880 Score: 99
Period size: 29 Copynumber: 7.3 Consensus size: 29
21654 TGGACATCCG
* *
21664 GGGGTAAAATGGTAATTTTTAGGAAA-ATT
1 GGGGCAAAATGGTAATTTTT-GGAAATTTT
* * *
21693 GAGATGAAAAATGG-AATTTTTGGACA-TTT
1 G-G-GGCAAAATGGTAATTTTTGGAAATTTT
* * * *
21722 GAGGGTAAAATGTTAATTTTTAGGAAA-ATC
1 G-GGGCAAAATGGTAATTTTT-GGAAATTTT
* * ***
21752 GGGATCAAAAATGG-AATTTTTTGGACATCCG
1 GGG-GC-AAAATGGTAA-TTTTTGGAAATTTT
21783 GGGGCAAAATGGTAATTTTTGGAAATTTT
1 GGGGCAAAATGGTAATTTTTGGAAATTTT
21812 GGGGTCAAAAATGG-AATTTTTGG--ATGTTT
1 GGGG-C-AAAATGGTAATTTTTGGAAAT-TTT
* * * * *
21841 GGGGTAAAATGATTATTTTTGGGAGTTTT
1 GGGGCAAAATGGTAATTTTTGGAAATTTT
21870 GGGGTCAAAAT
1 GGGG-CAAAAT
21881 CGGGATTTTT
Statistics
Matches: 145, Mismatches: 27, Indels: 31
0.71 0.13 0.15
Matches are distributed among these distances:
27 6 0.04
28 17 0.12
29 54 0.37
30 39 0.27
31 29 0.20
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (29 bp):
GGGGCAAAATGGTAATTTTTGGAAATTTT
Found at i:21822 original size:119 final size:117
Alignment explanation
Indices: 21605--21860 Score: 356
Period size: 119 Copynumber: 2.2 Consensus size: 117
21595 TTAGACACTC
* * *
21605 GAGGGTAAAACGGTAATTTTTAAAAAATCGGGATCAAAAATAGAATTTTTGGACATCCGGGGGTA
1 GAGGGTAAAATGTTAATTTTTAAAAAATCGGGATCAAAAATAGAATTTTTGGACATCCGGGGGCA
*
21670 AAATGGTAATTTTTAGGAAAATTGAGATGAAAAATGGAATTTTTGGACATTT
66 AAATGGTAATTTTTAGGAAAATTGAGATCAAAAATGGAATTTTTGGACATTT
* *
21722 GAGGGTAAAATGTTAATTTTTAGGAAAATCGGGATCAAAAATGGAATTTTTTGGACATCCGGGGG
1 GAGGGTAAAATGTTAATTTTTA-AAAAATCGGGATCAAAAATAGAA-TTTTTGGACATCCGGGGG
* * * **
21787 CAAAATGGTAATTTTT-GGAAATTTTGGGGTCAAAAATGGAATTTTTGGATGTTT
64 CAAAATGGTAATTTTTAGGAAA-ATTGAGATCAAAAATGGAATTTTTGGACATTT
21841 G-GGGTAAAATGATT-ATTTTT
1 GAGGGTAAAATG-TTAATTTTT
21861 GGGAGTTTTG
Statistics
Matches: 124, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
117 20 0.16
118 42 0.34
119 62 0.50
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (117 bp):
GAGGGTAAAATGTTAATTTTTAAAAAATCGGGATCAAAAATAGAATTTTTGGACATCCGGGGGCA
AAATGGTAATTTTTAGGAAAATTGAGATCAAAAATGGAATTTTTGGACATTT
Found at i:21833 original size:30 final size:30
Alignment explanation
Indices: 21638--21997 Score: 155
Period size: 30 Copynumber: 12.2 Consensus size: 30
21628 AAAATCGGGA
* * ***
21638 TCAAAAATAGAATTTTTGGACATCCGGGGG
1 TCAAAAATGGAATTTTTGGAAATTTTGGGG
* * *
21668 T--AAAATGGTAATTTTTAGGAAA-ATTGAGA
1 TCAAAAATGG-AATTTTT-GGAAATTTTGGGG
* *
21697 TGAAAAATGGAATTTTTGGACA-TTTGAGGG
1 TCAAAAATGGAATTTTTGGAAATTTTG-GGG
* * * *
21727 T--AAAATGTTAATTTTTAGGAAA-ATCGGGA
1 TCAAAAATG-GAATTTTT-GGAAATTTTGGGG
* **
21756 TCAAAAATGGAATTTTTTGGACA-TCCGGGG
1 TCAAAAATGGAA-TTTTTGGAAATTTTGGGG
*
21786 GC-AAAATGGTAATTTTTGGAAATTTTGGGG
1 TCAAAAATGG-AATTTTTGGAAATTTTGGGG
21816 TCAAAAATGGAATTTTTGG--ATGTTTGGGG
1 TCAAAAATGGAATTTTTGGAAAT-TTTGGGG
* *
21845 T--AAAAT-GATTATTTTTGGGAGTTTTGGGG
1 TCAAAAATGGA--ATTTTTGGAAATTTTGGGG
* ****
21874 TC-AAAATCGGGATTTTT-GAAAGTTCAAAGG
1 TCAAAAAT-GGAATTTTTGGAAA-TTTTGGGG
* * *
21904 T-AAAAATGTAATTTTTGGAAGTTTTAGGG
1 TCAAAAATGGAATTTTTGGAAATTTTGGGG
* * *
21933 TTAAAAATGGAATTTTTAG-AAGTTTGTGGG
1 TCAAAAATGGAATTTTTGGAAATTTTG-GGG
** * *
21963 T-AAAAATATAATTTTTGGAAGTTTCGGGG
1 TCAAAAATGGAATTTTTGGAAATTTTGGGG
21992 TCAAAA
1 TCAAAA
21998 TATAATTTTG
Statistics
Matches: 251, Mismatches: 51, Indels: 56
0.70 0.14 0.16
Matches are distributed among these distances:
26 2 0.01
27 5 0.02
28 22 0.09
29 96 0.38
30 100 0.40
31 25 0.10
32 1 0.00
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (30 bp):
TCAAAAATGGAATTTTTGGAAATTTTGGGG
Found at i:21917 original size:29 final size:29
Alignment explanation
Indices: 21788--22016 Score: 106
Period size: 29 Copynumber: 7.8 Consensus size: 29
21778 ATCCGGGGGC
**
21788 AAAATGGTAATTTTTGGAAA-TTTTGGGGTCA
1 AAAAT-GTAATTTTT-GAAAGTTTAAGGGT-A
* * * *
21819 AAAATGGAATTTTTGGATGTTT-GGGGT-
1 AAAATGTAATTTTTGAAAGTTTAAGGGTA
* ** ** *
21846 AAAATGATTATTTTTGGGAGTTTTGGGGTC
1 AAAATG-TAATTTTTGAAAGTTTAAGGGTA
** * *
21876 AAAATCGGGATTTTTGAAAGTTCAAAGGTA
1 AAAAT-GTAATTTTTGAAAGTTTAAGGGTA
* *
21906 AAAATGTAATTTTTGGAAGTTTTAGGGTTA
1 AAAATGTAATTTTTGAAAGTTTAAGGG-TA
* **
21936 AAAATGGAATTTTT-AGAAGTTTGTGGGTA
1 AAAATGTAATTTTTGA-AAGTTTAAGGGTA
* * ** *
21965 AAAATATAATTTTTGGAAGTTTCGGGGTC
1 AAAATGTAATTTTTGAAAGTTTAAGGGTA
* *
21994 AAAATATAATTTTGGAGAAGTTT
1 AAAATGTAATTTTTGA-AAGTTT
22017 GGGGACCTCC
Statistics
Matches: 155, Mismatches: 34, Indels: 19
0.75 0.16 0.09
Matches are distributed among these distances:
27 6 0.04
28 12 0.08
29 66 0.43
30 65 0.42
31 6 0.04
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.39
Consensus pattern (29 bp):
AAAATGTAATTTTTGAAAGTTTAAGGGTA
Found at i:22013 original size:59 final size:58
Alignment explanation
Indices: 21795--22020 Score: 221
Period size: 59 Copynumber: 3.9 Consensus size: 58
21785 GGCAAAATGG
* *
21795 TAATTTTTGGAAATTTTGGGGTCAAAAATGGAATTTTTG-GATGTTTGGGGT-AAAATGA
1 TAATTTTTGGAAGTTTTGGGGTCAAAAAT-GAATTTTTGAGAAGTTTGGGGTAAAAAT-A
* * * *** *
21853 TTATTTTTGGGAGTTTTGGGGTC-AAAATCGGGATTTTTGA-AAGTTCAAAGGTAAAAATG
1 TAATTTTTGGAAGTTTTGGGGTCAAAAAT--GAATTTTTGAGAAGTT-TGGGGTAAAAATA
* *
21912 TAATTTTTGGAAGTTTTAGGGTTAAAAATGGAATTTTT-AGAAGTTTGTGGGTAAAAATA
1 TAATTTTTGGAAGTTTTGGGGTCAAAAAT-GAATTTTTGAGAAGTTTG-GGGTAAAAATA
* *
21971 TAATTTTTGGAAGTTTCGGGGTCAAAATAT-AATTTTGGAGAAGTTTGGGG
1 TAATTTTTGGAAGTTTTGGGGTCAAAA-ATGAATTTTTGAGAAGTTTGGGG
22021 ACCTCCAAGA
Statistics
Matches: 137, Mismatches: 22, Indels: 18
0.77 0.12 0.10
Matches are distributed among these distances:
57 5 0.04
58 43 0.31
59 77 0.56
60 12 0.09
ACGTcount: A:0.31, C:0.03, G:0.27, T:0.39
Consensus pattern (58 bp):
TAATTTTTGGAAGTTTTGGGGTCAAAAATGAATTTTTGAGAAGTTTGGGGTAAAAATA
Found at i:22020 original size:29 final size:29
Alignment explanation
Indices: 21902--22020 Score: 109
Period size: 29 Copynumber: 4.1 Consensus size: 29
21892 AAAGTTCAAA
* *
21902 GGTAAAAATGTAATTTTTG-GAAGTTTTAGG
1 GGTAAAAATATAATTTTGGAGAAG-TTT-GG
* ** *
21932 GTTAAAAATGGAATTTT-TAGAAGTTTGTG
1 GGTAAAAATATAATTTTGGAGAAGTTTG-G
*
21961 GGTAAAAATATAATTTTTG-GAAGTTTCGG
1 GGTAAAAATATAATTTTGGAGAAGTTT-GG
*
21990 GGTCAAAATATAATTTTGGAGAAGTTTGG
1 GGTAAAAATATAATTTTGGAGAAGTTTGG
22019 GG
1 GG
22021 ACCTCCAAGA
Statistics
Matches: 75, Mismatches: 9, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
28 1 0.01
29 47 0.63
30 27 0.36
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.38
Consensus pattern (29 bp):
GGTAAAAATATAATTTTGGAGAAGTTTGG
Found at i:22544 original size:35 final size:35
Alignment explanation
Indices: 22467--22535 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
22457 CCCTTTTACT
*
22467 AAAAAAAAAAAATAATCATTTTTCCTTAGTTTTNA
1 AAAAAAAAAAAATAATCATTTTTCCTTAGTTTTTA
22502 AAAAAAAAAAAATAATCATTTTTCCTTAGTTTTT
1 AAAAAAAAAAAATAATCATTTTTCCTTAGTTTTT
22536 TTTAAAAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.39
Consensus pattern (35 bp):
AAAAAAAAAAAATAATCATTTTTCCTTAGTTTTTA
Found at i:23877 original size:17 final size:16
Alignment explanation
Indices: 23851--23914 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 16
23841 CTTTTTAATT
*
23851 AATTTTAATTTACAATG
1 AATTTAAATTTA-AATG
*
23868 AATTTAAATTTAAAGTA
1 AATTTAAATTTAAA-TG
**
23885 AATTTAAACTAAAAAATG
1 AATTTAAA-T-TTAAATG
23903 AATTTAAATTTA
1 AATTTAAATTTA
23915 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:0.52, C:0.03, G:0.05, T:0.41
Consensus pattern (16 bp):
AATTTAAATTTAAATG
Found at i:23913 original size:52 final size:52
Alignment explanation
Indices: 23851--23953 Score: 134
Period size: 52 Copynumber: 2.0 Consensus size: 52
23841 CTTTTTAATT
* ** * * *
23851 AATTTTAATTTACAATGAATTTAAATTTAAAGTAAATTTAAACTAAAAAATG
1 AATTTAAATTTACAACAAATTCAAACTTAAAGTAAATTAAAACTAAAAAATG
* *
23903 AATTTAAATTTAGAACAAATTCAAACTTAAAGTAAATTAAAATTAAAAAAT
1 AATTTAAATTTACAACAAATTCAAACTTAAAGTAAATTAAAACTAAAAAAT
23954 TGGACTCAGT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (52 bp):
AATTTAAATTTACAACAAATTCAAACTTAAAGTAAATTAAAACTAAAAAATG
Found at i:24661 original size:206 final size:206
Alignment explanation
Indices: 24284--25160 Score: 1135
Period size: 206 Copynumber: 4.3 Consensus size: 206
24274 TCTAGTTCTA
* * * * * * *
24284 TTGACTTGGCCTTTTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATCCGCTT
* * * *
24349 CTCTATGT-T-TCATCAGGAAGACGAATTTGGTTCACTTTTCTGTATCTCATCAAGAAGCTAACC
66 CT-T-TGTATCTCATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACC
* * * * * *
24412 TTTTTATTGCTACGCCCTGCTTCTTAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCGC
129 ATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCTAGAAGCTGGGGTTCGAAGATTTGCTCAC
*
24477 ATTGAGCGTGGGT
194 ATCGAGCGTGGGT
* ** * *
24490 TTGATTTGGTCTTCTTCTTAGTATCTCATCAGGAAGATGATAGCGTCGTTTGTTTCAATTCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATCCGCTT
* *
24555 CTTTGTATCTCATTAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
66 CTTTGTATCTCATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCAT
* * * *
24620 TTTATTGTTTCGACCTGCTTCTAAGTATCTCATCTAGAAGCTGGCGTTCGAAGATTTGCTCAAAT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCTAGAAGCTGGGGTTCGAAGATTTGCTCACAT
**
24685 CGAGCGCAGGT
196 CGAGCGTGGGT
24696 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATCCGCTT
* * * * * *
24761 CTCTGTATCTCATCAGGAATACGTATTTGGTCCACTTTTTAGTATCTCATCAAGAAGCTAACCAT
66 CTTTGTATCTCATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCAT
*
24826 TTTATTGCTTCGACCTGCTTCTCAGTGTCTCAT-TAGAAAGCTGGGGTTCGAAGATTTGCTCACA
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCTAG-AAGCTGGGGTTCGAAGATTTGCTCACA
24890 TCGAGCGTGGGT
195 TCGAGCGTGGGT
*
24902 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGA---C--C--TTG------T-CGTTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATCCGCTT
* * * * *
24953 GTTTGTATCTTATCA-AGAAGACGAATTTGGTTCACTTCTTAGTATCTCATCAGGAAGCTAACCA
66 CTTTGTATCTCATCAGA-AAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCA
* *
25017 TTTTATCGCTTCGACCTGCTTCTCAGTATCTCATC-AGGAAGTTGGGGTTCGAAGATTTGCTCAC
130 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCTA-GAAGCTGGGGTTCGAAGATTTGCTCAC
25081 ATCGAGCGTGGGT
194 ATCGAGCGTGGGT
* * *
25094 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGTGTCGTTTGTTTTAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATCCGCTT
25159 CT
66 CT
25161 CTCGAGCGTA
Statistics
Matches: 585, Mismatches: 66, Indels: 40
0.85 0.10 0.06
Matches are distributed among these distances:
192 169 0.29
193 2 0.00
197 1 0.00
199 6 0.01
201 1 0.00
203 1 0.00
204 3 0.01
205 6 0.01
206 396 0.68
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (206 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATCCGCTT
CTTTGTATCTCATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCAT
TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCTAGAAGCTGGGGTTCGAAGATTTGCTCACAT
CGAGCGTGGGT
Found at i:25091 original size:192 final size:192
Alignment explanation
Indices: 24764--25148 Score: 653
Period size: 192 Copynumber: 2.0 Consensus size: 192
24754 TCCGCTTCTC
* * * *
24764 TGTATCTCATCAGGAATACGTATTTGGTCCACTTTTTAGTATCTCATCAAGAAGCTAACCATTTT
1 TGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTTAGTATCTCATCAAGAAGCTAACCATTTT
* * *
24829 ATTGCTTCGACCTGCTTCTCAGTGTCTCATTAGAAAGCTGGGGTTCGAAGATTTGCTCACATCGA
66 ATCGCTTCGACCTGCTTCTCAGTATCTCATCAGAAAGCTGGGGTTCGAAGATTTGCTCACATCGA
*
24894 GCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCTTGTCGTTTGTT
131 GCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGTGTCGTTTGTT
* * *
24956 TGTATCTTATCAAGAAGACGAATTTGGTTCACTTCTTAGTATCTCATCAGGAAGCTAACCATTTT
1 TGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTTAGTATCTCATCAAGAAGCTAACCATTTT
* *
25021 ATCGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTCACATCGA
66 ATCGCTTCGACCTGCTTCTCAGTATCTCATCAGAAAGCTGGGGTTCGAAGATTTGCTCACATCGA
25086 GCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGTGTCGTTTGTT
131 GCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGTGTCGTTTGTT
25148 T
1 T
25149 TAATCCGCTT
Statistics
Matches: 180, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
192 180 1.00
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (192 bp):
TGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTTAGTATCTCATCAAGAAGCTAACCATTTT
ATCGCTTCGACCTGCTTCTCAGTATCTCATCAGAAAGCTGGGGTTCGAAGATTTGCTCACATCGA
GCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGTGTCGTTTGTT
Found at i:25186 original size:80 final size:80
Alignment explanation
Indices: 25082--25240 Score: 255
Period size: 80 Copynumber: 2.0 Consensus size: 80
25072 TTTGCTCACA
* * ** *
25082 TCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGTGTCGTTTGT
1 TCGAGCGTAGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCACGTCATTTGT
*
25147 TTTAATCCGCTTCTC
66 TTCAATCCGCTTCTC
25162 TCGAGCGTAGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCACGTCATTTGT
1 TCGAGCGTAGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCACGTCATTTGT
*
25227 TTCAATCTGCTTCT
66 TTCAATCCGCTTCT
25241 TTCTATCTCA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 72 1.00
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (80 bp):
TCGAGCGTAGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCACGTCATTTGT
TTCAATCCGCTTCTC
Found at i:25492 original size:39 final size:39
Alignment explanation
Indices: 25436--25574 Score: 122
Period size: 39 Copynumber: 3.6 Consensus size: 39
25426 GATAATCGCA
* *
25436 ATCTGCCCC-GTGATCGGGGTAGGAGTTTGGTTGACGATG
1 ATCTGCCCCAG-GCTCGGGGTAAGAGTTTGGTTGACGATG
* * * ** * *
25475 ATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCTG-TA
1 ATCTGCCCCAGGCTCGGGGTAAGAGTTTGGTTGAC-GATG
* * *
25514 ATCTGCCTCTGGCTCGGGGTAAGAGATTT-GTTGATGATG
1 ATCTGCCCCAGGCTCGGGGTAAGAG-TTTGGTTGACGATG
25553 ATCTGCCCCAGGCTCGGGGTAA
1 ATCTGCCCCAGGCTCGGGGTAA
25575 AAGATCAAAT
Statistics
Matches: 75, Mismatches: 21, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
38 1 0.01
39 71 0.95
40 3 0.04
ACGTcount: A:0.19, C:0.21, G:0.34, T:0.26
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCGGGGTAAGAGTTTGGTTGACGATG
Found at i:25700 original size:39 final size:39
Alignment explanation
Indices: 25646--25793 Score: 147
Period size: 39 Copynumber: 3.8 Consensus size: 39
25636 NNNNNNNNNA
* *
25646 ATCTGCCTCTGGCTCGGGGTAAGAGATTGGTTGATGATG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGATG
* **** *
25685 ATCTGCCCCAGGCTCGGGGTAAAAGATCAAATGACT--TCA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGA-TGAT-G
* * *
25724 ATCTGCCCTAGGCTTGGGGTAAGTGATTGGTTGATGATG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGATG
* *
25763 ATCTGCCCTAGGCTCAGGGTAAGAGATTGGT
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGT
25794 AACGATGTAG
Statistics
Matches: 85, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
38 2 0.02
39 81 0.95
40 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGATG
Found at i:25776 original size:78 final size:78
Alignment explanation
Indices: 25645--25789 Score: 229
Period size: 78 Copynumber: 1.9 Consensus size: 78
25635 NNNNNNNNNN
*
25645 AATCTGCCTCTGGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAGGCTCGGGGTAAAAG
1 AATCTGCCTCTGGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAGGCTCAGGGTAAAAG
25710 ATCAAATGACTTC
66 ATCAAATGACTTC
* * * *
25723 AATCTGCC-CTAGGCTTGGGGTAAGTGATTGGTTGATGATGATCTGCCCTAGGCTCAGGGTAAGA
1 AATCTGCCTCT-GGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAGGCTCAGGGTAAAA
25787 GAT
65 GAT
25790 TGGTAACGAT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
77 2 0.03
78 59 0.97
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (78 bp):
AATCTGCCTCTGGCTCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAGGCTCAGGGTAAAAG
ATCAAATGACTTC
Found at i:26370 original size:99 final size:99
Alignment explanation
Indices: 26146--26432 Score: 311
Period size: 100 Copynumber: 2.9 Consensus size: 99
26136 GTATCGGGTT
* *** * *
26146 CGCCATTGCGACTTAAACCTTTCCCCTTCAAAT-TTTCGTGGTACTGGATTCGCCGTTGCGGCTT
1 CGCCATTACGACTTAAACCTTT-CCCTTTGTATCTTT-GTGGTATTGGATCCGCCGTTGCGGCTT
*
26210 AAATCTTTCCCTTCTTGTCTTCTGAGGTTCACGGTC
64 AAATCTTTCCCTTCTTGTCTTCTGAGGTACACGGTC
* *
26246 CGCCGTTACGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTATTGGATCCGCTGTTGCGG-TCT
1 CGCCATTACGACTTAAACCTTTCCC-TTTGTATCTTTGTGGTATTGGATCCGCCGTTGCGGCT-T
*
26310 AGATCTTTCCCTT-TATGTC-TCTGAGGTACTA-GGTC
64 AAATCTTTCCCTTCT-TGTCTTCTGAGGTAC-ACGGTC
* * * **
26345 TGCCATTACGACTTAAACCTTTCCC-TTGTGTCTTCGTGGTATTGGATCCGCCGTTGCAACTTAA
1 CGCCATTACGACTTAAACCTTTCCCTTTGTATCTTTGTGGTATTGGATCCGCCGTTGCGGCTTAA
*
26409 AT-TCTTCCCTTCATGTCTTC-GAGG
66 ATCT-TTCCCTTCTTGTCTTCTGAGG
26433 CACTGGATCC
Statistics
Matches: 159, Mismatches: 19, Indels: 21
0.80 0.10 0.11
Matches are distributed among these distances:
96 1 0.01
97 48 0.30
98 3 0.02
99 41 0.26
100 63 0.40
101 3 0.02
ACGTcount: A:0.15, C:0.27, G:0.20, T:0.38
Consensus pattern (99 bp):
CGCCATTACGACTTAAACCTTTCCCTTTGTATCTTTGTGGTATTGGATCCGCCGTTGCGGCTTAA
ATCTTTCCCTTCTTGTCTTCTGAGGTACACGGTC
Found at i:26466 original size:49 final size:49
Alignment explanation
Indices: 26146--26666 Score: 264
Period size: 49 Copynumber: 10.5 Consensus size: 49
26136 GTATCGGGTT
* * *** * * *
26146 CGCCATTGCGACTTAAACCTTTCCCCTTCAAATTTTCGTGGTACTGGATT
1 CGCCGTTGCGACTTAAATCTTT-CCCTTCTTGTCTTCGAGGTACTGGATC
*
26196 CGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTGAGGTTCAC-GG-TC
1 CGCCGTTGCGACTTAAATCTTTCCCTTCTTGTCTTC-GAGG-T-ACTGGATC
* * * * *
26246 CGCCGTTACGACTTAAACCTTTCCCTT-TTGTATCTTTGTGGTATTGGATC
1 CGCCGTTGCGACTTAAATCTTTCCCTTCTTG--TCTTCGAGGTACTGGATC
* * *
26296 CGCTGTTGCG-GTCTAGATCTTTCCCTT-TATGTC-TCTGAGGTACTAGG-TC
1 CGCCGTTGCGACT-TAAATCTTTCCCTTCT-TGTCTTC-GAGGTACT-GGATC
* * * * * * *
26345 TGCCATTACGACTTAAACCTTTCCCTT-GTGTCTTCGTGGTATTGGATC
1 CGCCGTTGCGACTTAAATCTTTCCCTTCTTGTCTTCGAGGTACTGGATC
* * *
26393 CGCCGTTGCAACTTAAAT-TCTTCCCTTCATGTCTTCGAGGCACTGGATC
1 CGCCGTTGCGACTTAAATCT-TTCCCTTCTTGTCTTCGAGGTACTGGATC
* * * * *
26442 CGCCGTTGCGACTTAGATATTTCCCATCTTGTC-TCTGAGGTACAAGG-TT
1 CGCCGTTGCGACTTAAATCTTTCCCTTCTTGTCTTC-GAGGTAC-TGGATC
* * * * * *
26491 CGCTGATGCGACTTAAA-CTCTTCCCTTTCGTATCTTTGCGGTACTGGATC
1 CGCCGTTGCGACTTAAATCT-TTCCC-TTCTTGTCTTCGAGGTACTGGATC
* * * * * *
26541 TGCCATTGCGGTCTTAAATCTTTCCCGTCATGTC-TCTGAGGTA-TAAGG-TT
1 CGCCGTTGC-GACTTAAATCTTTCCCTTCTTGTCTTC-GAGGTACT--GGATC
* * * * * *
26591 CGCCGTTGCGACTTAAACCCTTCCCTT-TTGTATTTTTGCGGTATTGGATC
1 CGCCGTTGCGACTTAAATCTTTCCCTTCTTG--TCTTCGAGGTACTGGATC
* *
26641 CGCCGTTGCAATCTTAGATCTTTCCC
1 CGCCGTTGCGA-CTTAAATCTTTCCC
26667 GTCATGTTTC
Statistics
Matches: 351, Mismatches: 86, Indels: 67
0.70 0.17 0.13
Matches are distributed among these distances:
47 3 0.01
48 39 0.11
49 137 0.39
50 131 0.37
51 37 0.11
52 4 0.01
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.37
Consensus pattern (49 bp):
CGCCGTTGCGACTTAAATCTTTCCCTTCTTGTCTTCGAGGTACTGGATC
Found at i:26466 original size:97 final size:97
Alignment explanation
Indices: 26154--26456 Score: 319
Period size: 97 Copynumber: 3.1 Consensus size: 97
26144 TTCGCCATTG
*** * * *
26154 CGACTTAAACCTTTCCCCTTCAAATTTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTC
1 CGACTTAAACCTTT-CCCTTTGTATCTTCGTGGTATTGGATCCGCCGTTGC-GCTTAAATCTTTC
*
26219 CCTTCTTGTCTTCTGAGGTTCAC-GGTCCGCCGTTA
64 CCTTCATGTCTTCTGAGG--CACTGGTCCGCCGTTA
* * * *
26254 CGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTATTGGATCCGCTGTTGCGGTCTAGATCTTTC
1 CGACTTAAACCTTTCCC-TTTGTATCTTCGTGGTATTGGATCCGCCGTTGCGCT-TAAATCTTTC
* * * *
26319 CCTTTATGTC-TCTGAGGTACTAGGTCTGCCATTA
64 CCTTCATGTCTTCTGAGGCACT-GGTCCGCCGTTA
* *
26353 CGACTTAAACCTTTCCC-TTGTGTCTTCGTGGTATTGGATCCGCCGTTGCAACTTAAAT-TCTTC
1 CGACTTAAACCTTTCCCTTTGTATCTTCGTGGTATTGGATCCGCCGTTGC-GCTTAAATCT-TTC
*
26416 CCTTCATGTCTTC-GAGGCACTGGATCCGCCGTTG
64 CCTTCATGTCTTCTGAGGCACTGG-TCCGCCGTTA
26450 CGACTTA
1 CGACTTA
26457 GATATTTCCC
Statistics
Matches: 169, Mismatches: 26, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
96 3 0.02
97 68 0.40
98 3 0.02
99 39 0.23
100 56 0.33
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.38
Consensus pattern (97 bp):
CGACTTAAACCTTTCCCTTTGTATCTTCGTGGTATTGGATCCGCCGTTGCGCTTAAATCTTTCCC
TTCATGTCTTCTGAGGCACTGGTCCGCCGTTA
Found at i:26580 original size:100 final size:99
Alignment explanation
Indices: 26393--26673 Score: 330
Period size: 100 Copynumber: 2.8 Consensus size: 99
26383 GTATTGGATC
* * * * * * * * *
26393 CGCCGTTGCAACTTAAATTCTTCCC-TTCATGTCTTCGAGGCACTGGATCCGCCGTTGCGACTTA
1 CGCCGATGCGACTTAAACTCTTCCCTTTCGTATCTTTGCGGTACTGGATCCGCCGTTGCGTCTTA
* * *
26457 GATATTTCCCATCTTGTCTCTGAGGTACAAGGTT
66 GATCTTTCCCGTCATGTCTCTGAGGTACAAGGTT
* * *
26491 CGCTGATGCGACTTAAACTCTTCCCTTTCGTATCTTTGCGGTACTGGATCTGCCATTGCGGTCTT
1 CGCCGATGCGACTTAAACTCTTCCCTTTCGTATCTTTGCGGTACTGGATCCGCCGTTGC-GTCTT
* *
26556 AAATCTTTCCCGTCATGTCTCTGAGGTATAAGGTT
65 AGATCTTTCCCGTCATGTCTCTGAGGTACAAGGTT
* * * * * *
26591 CGCCGTTGCGACTTAAACCCTTCCCTTTTGTATTTTTGCGGTATTGGATCCGCCGTTGCAATCTT
1 CGCCGATGCGACTTAAACTCTTCCCTTTCGTATCTTTGCGGTACTGGATCCGCCGTTGC-GTCTT
26656 AGATCTTTCCCGTCATGT
65 AGATCTTTCCCGTCATGT
26674 TTCATGGTGC
Statistics
Matches: 153, Mismatches: 28, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
98 21 0.14
99 26 0.17
100 106 0.69
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.36
Consensus pattern (99 bp):
CGCCGATGCGACTTAAACTCTTCCCTTTCGTATCTTTGCGGTACTGGATCCGCCGTTGCGTCTTA
GATCTTTCCCGTCATGTCTCTGAGGTACAAGGTT
Found at i:26605 original size:246 final size:248
Alignment explanation
Indices: 26188--26673 Score: 608
Period size: 246 Copynumber: 2.0 Consensus size: 248
26178 TTTTCGTGGT
* * * * * * *
26188 ACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTGAGGTTCACGGTCCGCCGTT
1 ACTGGATCCGCCGTTGCGACTTAAATATTTCCCATCTTGTCTTCTGAGGTACAAGGTCCGCCGAT
* * * ** *
26253 ACGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTATTGGATCCGCTGTTGCGGTCTAGATCTTT
66 ACGACTTAAACCTTTCCCTTTCGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTAAATCTTT
* * * * *
26318 CCCTTTATGTCTCTGAGGTACTAGGTCTGCCATTACGACTTAAACCTTTCCC-TTGTGTCTTCGT
131 CCCGTCATGTCTCTGAGGTACTAGGTCTGCCATTACGACTTAAACCCTTCCCTTTGTATCTTCGC
*
26382 GGTATTGGATCCGCCGTTGCAA-CTTAAAT-TCTTCCCTTCATGTCTTCGAGGC
196 GGTATTGGATCCGCCGTTGCAATCTTAAATCT-TTCCCGTCATGTCTTCGAGGC
* * *
26434 ACTGGATCCGCCGTTGCGACTTAGATATTTCCCATCTTGTC-TCTGAGGTACAAGGTTCGCTGAT
1 ACTGGATCCGCCGTTGCGACTTAAATATTTCCCATCTTGTCTTCTGAGGTACAAGGTCCGCCGAT
* *
26498 GCGACTTAAA-CTCTTCCCTTTCGTATCTTTGCGGTACTGGATCTGCCATTGCGGTCTTAAATCT
66 ACGACTTAAACCT-TTCCCTTTCGTATCTTTGCGGTACTGGATCCGCCATTGCGGTC-TAAATCT
* * *
26562 TTCCCGTCATGTCTCTGAGGTA-TAAGGT-TCGCCGTTGCGACTTAAACCCTTCCCTTTTGTATT
129 TTCCCGTCATGTCTCTGAGGTACT-AGGTCT-GCCATTACGACTTAAACCCTTCCC-TTTGTATC
* *
26625 TTTGCGGTATTGGATCCGCCGTTGCAATCTTAGATCTTTCCCGTCATGT
191 TTCGCGGTATTGGATCCGCCGTTGCAATCTTAAATCTTTCCCGTCATGT
26674 TTCATGGTGC
Statistics
Matches: 203, Mismatches: 29, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
244 2 0.01
245 66 0.33
246 87 0.43
248 30 0.15
249 17 0.08
250 1 0.00
ACGTcount: A:0.16, C:0.26, G:0.21, T:0.38
Consensus pattern (248 bp):
ACTGGATCCGCCGTTGCGACTTAAATATTTCCCATCTTGTCTTCTGAGGTACAAGGTCCGCCGAT
ACGACTTAAACCTTTCCCTTTCGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTAAATCTTT
CCCGTCATGTCTCTGAGGTACTAGGTCTGCCATTACGACTTAAACCCTTCCCTTTGTATCTTCGC
GGTATTGGATCCGCCGTTGCAATCTTAAATCTTTCCCGTCATGTCTTCGAGGC
Found at i:27914 original size:3 final size:3
Alignment explanation
Indices: 27908--27945 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
27898 TCTTTTTTTA
*
27908 ATT ATT ATT -CT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
27946 TCATTGAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 1 0.03
3 31 0.97
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:30523 original size:30 final size:30
Alignment explanation
Indices: 30487--30546 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
30477 TCATCAAGTA
*
30487 AGTCAACATGTTCATGATTGGATATTTGCC
1 AGTCAACATATTCATGATTGGATATTTGCC
30517 AGTCAACATATTCATGATTGGATATTTGCC
1 AGTCAACATATTCATGATTGGATATTTGCC
30547 TCATTTTGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (30 bp):
AGTCAACATATTCATGATTGGATATTTGCC
Found at i:32621 original size:86 final size:85
Alignment explanation
Indices: 32529--33007 Score: 429
Period size: 85 Copynumber: 5.5 Consensus size: 85
32519 AATTTAATAT
* * * *
32529 TATTTAAATAAAAAAGATTATTATTATATTACAATTTATATCAAATATTGTGTTAATTTGACAAT
1 TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAT
*
32594 ACATTATTTATCAAATTTTCA
66 ACATTATTTAT-AAATTTTAA
* * *** *
32615 TATTTAAAGT--ACAA-ATTATTATTATATTATAATTTTTATCAAATAATGTGTTG-TCAAATAA
1 TATTTAAA-TAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAA
** * *
32676 TGTATTGATTTGACAATATATTATTTAT
65 TACATT-ATTT----ATA-AAT-TTTAA
32704 TAATTTTAAATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTGTTG
1 T-A-TTTAAA----T--A-AAAAA-TATTATTATTATATTACAATTTTTATCAAATAATGTGTTG
* *
32769 ATTTGACAATATATTATTTATTAATTTTATA
56 ATTTGACAATACATTATTTATAAATTTTA-A
* * * * *
32800 TATTTAAATTAAAATTATTATTATTATGTTACAA-CTTTATCAAATAATGTGTTGATTTGATAAT
1 TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAT
*
32864 ACATTA-TT-T--ATTTAAA
66 ACATTATTTATAAATTTTAA
* * *
32880 TATTTAAATAAAATTATTATTATTATTATATTACATTTTTTATCAAATAATATGTTGATTTGACA
1 TATTTAAATAAAA--AATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACA
*
32945 ATACATTATTTATTAATTTTAAA
64 ATACATTATTTATAAATTTT-AA
*
32968 TATTTAAATAAAAATTATTATTA-TATATTACAATTTTTAT
1 TATTTAAATAAAAAATATTATTATTATATTACAATTTTTAT
33008 TATATTTTAA
Statistics
Matches: 323, Mismatches: 40, Indels: 61
0.76 0.09 0.14
Matches are distributed among these distances:
80 13 0.04
81 5 0.02
82 19 0.06
83 42 0.13
84 43 0.13
85 53 0.16
86 36 0.11
87 10 0.03
88 19 0.06
89 4 0.01
90 2 0.01
91 6 0.02
94 7 0.02
95 5 0.02
96 3 0.01
97 2 0.01
99 3 0.01
101 42 0.13
102 9 0.03
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (85 bp):
TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAAT
ACATTATTTATAAATTTTAA
Found at i:32687 original size:99 final size:100
Alignment explanation
Indices: 32569--32768 Score: 280
Period size: 99 Copynumber: 2.0 Consensus size: 100
32559 ACAATTTATA
* * * *
32569 TCAAATATTGTGTTAATTTGACAATACATTATTTATCAAATTTT-CATATTTAAAGT-ACAA-AT
1 TCAAATAATGTATTAATTTGACAATACATTATTTAT-AAATTTTAAATATTTAAA-TAAAAATAT
*
32631 TATTATTATATTATAATTTTTATCAAATAATGTGTTG
64 TATTATTATATTACAATTTTTATCAAATAATGTGTTG
* * *
32668 TCAAATAATGTATTGATTTGACAATATATTATTTATTAATTTTAAATATTTAAATAAAAATTATT
1 TCAAATAATGTATTAATTTGACAATACATTATTTATAAATTTTAAATATTTAAATAAAAA-TATT
32733 ATTATTATATTACAATTTTTATCAAATAATGTGTTG
65 ATTATTATATTACAATTTTTATCAAATAATGTGTTG
32769 ATTTGACAAT
Statistics
Matches: 89, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
98 7 0.08
99 44 0.49
101 38 0.43
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.48
Consensus pattern (100 bp):
TCAAATAATGTATTAATTTGACAATACATTATTTATAAATTTTAAATATTTAAATAAAAATATTA
TTATTATATTACAATTTTTATCAAATAATGTGTTG
Found at i:32938 original size:168 final size:169
Alignment explanation
Indices: 32668--33000 Score: 521
Period size: 168 Copynumber: 2.0 Consensus size: 169
32658 TAATGTGTTG
*
32668 TCAAATAATGTATTGATTTGACAATATATTATTTATTAATTTTAAATATTTAAATAAAAATTATT
1 TCAAATAATGTATTGATTTGACAATACATTA-TTATTAATTTTAAATATTTAAATAAAAATTATT
* *
32733 ATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATATATTATTTATTAATTTTA
65 ATTATTATATTACAATTTTTATCAAATAATATGTTGATTTGACAATACATTATTTATTAATTTTA
* * *
32798 TATATTTAAATTAAAATTATTATTATTATGTTACAACTTTA
130 AATATTTAAATAAAAATTATTATTA-TATATTACAACTTTA
* *
32839 TCAAATAATGTGTTGATTTGATAATACATTA-T-TT-A-TTTAAATATTTAAATAAAATTATTAT
1 TCAAATAATGTATTGATTTGACAATACATTATTATTAATTTTAAATATTTAAATAAAA--ATTAT
*
32900 TATTATTATATTACATTTTTTATCAAATAATATGTTGATTTGACAATACATTATTTATTAATTTT
64 TATTATTATATTACAATTTTTATCAAATAATATGTTGATTTGACAATACATTATTTATTAATTTT
32965 AAATATTTAAATAAAAATTATTATTATATATTACAA
129 AAATATTTAAATAAAAATTATTATTATATATTACAA
33001 TTTTTATTAT
Statistics
Matches: 151, Mismatches: 9, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
166 19 0.13
167 10 0.07
168 93 0.62
169 1 0.01
171 28 0.19
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.50
Consensus pattern (169 bp):
TCAAATAATGTATTGATTTGACAATACATTATTATTAATTTTAAATATTTAAATAAAAATTATTA
TTATTATATTACAATTTTTATCAAATAATATGTTGATTTGACAATACATTATTTATTAATTTTAA
ATATTTAAATAAAAATTATTATTATATATTACAACTTTA
Found at i:33007 original size:19 final size:18
Alignment explanation
Indices: 32979--33021 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
32969 ATTTAAATAA
*
32979 AAATTATTATTATATATT
1 AAATTTTTATTATATATT
*
32997 ACAATTTTTATTATATTTT
1 A-AATTTTTATTATATATT
33016 AAATTT
1 AAATTT
33022 ATTAACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
AAATTTTTATTATATATT
Found at i:33199 original size:20 final size:20
Alignment explanation
Indices: 33171--33221 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
33161 CCCCCTCGAA
33171 ACCGCCGTTGACC-ACTGTTG
1 ACCGCCGTTGACCGACT-TTG
* *
33191 ACCGTCGTTAACCGACTTTG
1 ACCGCCGTTGACCGACTTTG
*
33211 TCCGCCGTTGA
1 ACCGCCGTTGA
33222 TCGAGTTTCG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 22 0.88
21 3 0.12
ACGTcount: A:0.16, C:0.33, G:0.24, T:0.27
Consensus pattern (20 bp):
ACCGCCGTTGACCGACTTTG
Found at i:36447 original size:61 final size:61
Alignment explanation
Indices: 36380--36523 Score: 182
Period size: 62 Copynumber: 2.3 Consensus size: 61
36370 GGAAGTTGGT
* * *
36380 AAAAAAAATTGAAATTTTTTTAT-GTGAAAAAGGGGGTGTCGACCATTGTATGATCAACACC
1 AAAAAAAATTGAAATTTTTTTATCGAGAAAAA-GGGGTGTCGACCATTGCATGACCAACACC
* * *
36441 AAAAAAAATTGTAATTTTTTTATCCGAGAAAAAGGGGTGTCGGCCATTGCATGGCCAACACC
1 AAAAAAAATTGAAATTTTTTTAT-CGAGAAAAAGGGGTGTCGACCATTGCATGACCAACACC
** *
36503 AAAAAATTTTGAATTTTTTTT
1 AAAAAAAATTGAAATTTTTTT
36524 TTCTAAAAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
61 22 0.31
62 42 0.59
63 7 0.10
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (61 bp):
AAAAAAAATTGAAATTTTTTTATCGAGAAAAAGGGGTGTCGACCATTGCATGACCAACACC
Found at i:36567 original size:62 final size:62
Alignment explanation
Indices: 36380--36569 Score: 163
Period size: 61 Copynumber: 3.1 Consensus size: 62
36370 GGAAGTTGGT
* ** * * * * *
36380 AAAAAAAATTGAAATTTTTTTATGTG-AAAAAGGGGGTGTC-GACCATTGTATGATCAACACC
1 AAAAAAAATTGTAATTTTTTTATCCGAAAAAAAGAGCTGTCAG-CCATTGCATGGTCAACACC
* * * * *
36441 AAAAAAAATTGTAATTTTTTTATCCGAGAAAAAGGGGTGTCGGCCATTGCATGGCCAACACC
1 AAAAAAAATTGTAATTTTTTTATCCGAAAAAAAGAGCTGTCAGCCATTGCATGGTCAACACC
** * * *
36503 AAAAAATTTTG-AATTTTTTTTTTCTAAAAAAAGAGCTGTCAGCCATTGCAAT-GTCAACACC
1 AAAAAAAATTGTAATTTTTTTATCCGAAAAAAAGAGCTGTCAGCCATTGC-ATGGTCAACACC
*
36564 CAAAAA
1 AAAAAA
36570 TAAAAAAAAA
Statistics
Matches: 107, Mismatches: 19, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
61 67 0.63
62 39 0.36
63 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (62 bp):
AAAAAAAATTGTAATTTTTTTATCCGAAAAAAAGAGCTGTCAGCCATTGCATGGTCAACACC
Found at i:36682 original size:56 final size:55
Alignment explanation
Indices: 36413--36683 Score: 159
Period size: 56 Copynumber: 4.6 Consensus size: 55
36403 GTGAAAAAGG
* * ** * *
36413 GGGTGTCGACCATTGTATGATCAACACCAAAAAAAATTGTAATTTTTTTATCCGAGAAAAAG
1 GGGTGTCGGCCATTGCATGGCCAACACC--AAAAAA-TG-AATTTTTTTCT-C-A-AAAAAA
*
36475 GGGTGTCGGCCATTGCATGGCCAACACCAAAAAATTTTGAATTTTTTTTTTCTAAAAAAA
1 GGGTGTCGGCCATTGCATGGCCAACACCAAAAAA---TGAA-TTTTTTTCTC-AAAAAAA
* * * ** ***** **
36535 GAGCTGTCAGCCATTGCAAT-GTCAACACCCAAAAATAAAAAAAAAATTCTCAAAAAGG
1 G-GGTGTCGGCCATTGC-ATGGCCAACA-CCAAAAA-ATGAATTTTTTTCTCAAAAAAA
* * *
36593 GGGTGTTGACTATTGCATGGCCAACACTC-AAAAATGCAATTTTTTTCTCAAAAAAA
1 GGGTGTCGGCCATTGCATGGCCAACAC-CAAAAAATG-AATTTTTTTCTCAAAAAAA
*
36649 GGGTGTCGGCCATTGCATGGCCAACATCAAAAAAT
1 GGGTGTCGGCCATTGCATGGCCAACACCAAAAAAT
36684 TTTACAATTT
Statistics
Matches: 159, Mismatches: 39, Indels: 28
0.70 0.17 0.12
Matches are distributed among these distances:
55 2 0.01
56 48 0.30
57 17 0.11
58 6 0.04
59 4 0.03
60 14 0.09
61 23 0.14
62 44 0.28
63 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (55 bp):
GGGTGTCGGCCATTGCATGGCCAACACCAAAAAATGAATTTTTTTCTCAAAAAAA
Found at i:36840 original size:52 final size:52
Alignment explanation
Indices: 36744--36842 Score: 126
Period size: 52 Copynumber: 1.9 Consensus size: 52
36734 TCTTAAAAAG
* *** *
36744 GGGTGTCAGTCATTGCATAGCCAACACAAAAAAATTGTATTTTTTATTTGAC
1 GGGTGTCAGCCATTGCATAGCCAACACAAAAAAATACAAATTTTTATTTGAC
* * *
36796 GGGTGTCGGCCATTGCATGGCCAACACCAAAAAATACAAATTTTTAT
1 GGGTGTCAGCCATTGCATAGCCAACACAAAAAAATACAAATTTTTAT
36843 GTTTGACACC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 39 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
GGGTGTCAGCCATTGCATAGCCAACACAAAAAAATACAAATTTTTATTTGAC
Found at i:37923 original size:289 final size:289
Alignment explanation
Indices: 37404--37982 Score: 1158
Period size: 289 Copynumber: 2.0 Consensus size: 289
37394 GATGCGAAAG
37404 TACATTGCACTTTGCACCAATAACAAGAAGTGTAAGAAGGCAACTATCGATTTGTTGGTGGCTAG
1 TACATTGCACTTTGCACCAATAACAAGAAGTGTAAGAAGGCAACTATCGATTTGTTGGTGGCTAG
37469 TAAATGAATGAATGAAGTTTTATAAACTTGGGTGAAGAAGCATCCATCAACTTAAATGCATTGGG
66 TAAATGAATGAATGAAGTTTTATAAACTTGGGTGAAGAAGCATCCATCAACTTAAATGCATTGGG
37534 AGACAGTGTGGGTGGTAAATAGCACAAGCGACGCAGAAGAGAAGGGAGACCACATGTTTTTATTA
131 AGACAGTGTGGGTGGTAAATAGCACAAGCGACGCAGAAGAGAAGGGAGACCACATGTTTTTATTA
37599 GACTCAGAGGCCAGGGCAAGCTGGCAATAGCATTATCATTTATCAAGGTCGCAAAAAGGTCGATT
196 GACTCAGAGGCCAGGGCAAGCTGGCAATAGCATTATCATTTATCAAGGTCGCAAAAAGGTCGATT
37664 AATGAAGTTTTCTGACGGTCGAAAAACTT
261 AATGAAGTTTTCTGACGGTCGAAAAACTT
37693 TACATTGCACTTTGCACCAATAACAAGAAGTGTAAGAAGGCAACTATCGATTTGTTGGTGGCTAG
1 TACATTGCACTTTGCACCAATAACAAGAAGTGTAAGAAGGCAACTATCGATTTGTTGGTGGCTAG
37758 TAAATGAATGAATGAAGTTTTATAAACTTGGGTGAAGAAGCATCCATCAACTTAAATGCATTGGG
66 TAAATGAATGAATGAAGTTTTATAAACTTGGGTGAAGAAGCATCCATCAACTTAAATGCATTGGG
37823 AGACAGTGTGGGTGGTAAATAGCACAAGCGACGCAGAAGAGAAGGGAGACCACATGTTTTTATTA
131 AGACAGTGTGGGTGGTAAATAGCACAAGCGACGCAGAAGAGAAGGGAGACCACATGTTTTTATTA
37888 GACTCAGAGGCCAGGGCAAGCTGGCAATAGCATTATCATTTATCAAGGTCGCAAAAAGGTCGATT
196 GACTCAGAGGCCAGGGCAAGCTGGCAATAGCATTATCATTTATCAAGGTCGCAAAAAGGTCGATT
37953 AATGAAGTTTTCTGACGGTCGAAAAACTT
261 AATGAAGTTTTCTGACGGTCGAAAAACTT
37982 T
1 T
37983 TAATTAATTG
Statistics
Matches: 290, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
289 290 1.00
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (289 bp):
TACATTGCACTTTGCACCAATAACAAGAAGTGTAAGAAGGCAACTATCGATTTGTTGGTGGCTAG
TAAATGAATGAATGAAGTTTTATAAACTTGGGTGAAGAAGCATCCATCAACTTAAATGCATTGGG
AGACAGTGTGGGTGGTAAATAGCACAAGCGACGCAGAAGAGAAGGGAGACCACATGTTTTTATTA
GACTCAGAGGCCAGGGCAAGCTGGCAATAGCATTATCATTTATCAAGGTCGCAAAAAGGTCGATT
AATGAAGTTTTCTGACGGTCGAAAAACTT
Found at i:39577 original size:10 final size:10
Alignment explanation
Indices: 39562--39596 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
39552 ATTTATGCTT
*
39562 TAATATAATA
1 TAATATAATG
39572 TAATATAATG
1 TAATATAATG
*
39582 TAATGTAATG
1 TAATATAATG
39592 TAATA
1 TAATA
39597 GTAGATAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (10 bp):
TAATATAATG
Found at i:41925 original size:20 final size:20
Alignment explanation
Indices: 41882--41925 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
41872 GATCATACCC
* *
41882 AAAAAATATTAAAAATTGTA
1 AAAAAAAATTAAAAATTATA
41902 AAAAAAAATTAAAAATATATA
1 AAAAAAAATTAAAAAT-TATA
41923 AAA
1 AAA
41926 TTATAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAAAAAATTAAAAATTATA
Found at i:41945 original size:29 final size:29
Alignment explanation
Indices: 41902--41968 Score: 66
Period size: 29 Copynumber: 2.3 Consensus size: 29
41892 AAAAATTGTA
*
41902 AAAAAAAATTAAAAATATAT-AAAATTAT
1 AAAAAATATTAAAAATATATAAAAATTAT
* * *
41930 AAAATAATATTTAAAAT-TATCAGAAATCAT
1 AAAA-AATATTAAAAATATAT-AAAAATTAT
41960 AAAAAATAT
1 AAAAAATAT
41969 AAACTACACT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
28 7 0.22
29 15 0.47
30 10 0.31
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (29 bp):
AAAAAATATTAAAAATATATAAAAATTAT
Found at i:43886 original size:21 final size:21
Alignment explanation
Indices: 43862--43912 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
43852 TTTTTAATCA
*
43862 TTAATCGAATCGAATTAACAG
1 TTAATCGAACCGAATTAACAG
43883 TTAATCGAACCGAATTAACAG
1 TTAATCGAACCGAATTAACAG
43904 TTAATCGAA
1 TTAATCGAA
43913 ATTTTAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (21 bp):
TTAATCGAACCGAATTAACAG
Found at i:45758 original size:2 final size:2
Alignment explanation
Indices: 45751--45775 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45741 TTTATTGTAT
45751 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 T
45776 TTAATATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:51170 original size:3 final size:3
Alignment explanation
Indices: 51162--51219 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
51152 TACTGTTTAC
51162 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
51210 CTG CTG CTG C
1 CTG CTG CTG C
51220 CGCCTCTTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.00, C:0.34, G:0.33, T:0.33
Consensus pattern (3 bp):
CTG
Found at i:51527 original size:3 final size:3
Alignment explanation
Indices: 51519--51549 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
51509 TGTCGTGGAC
51519 TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
51550 ATGCAAACGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:61918 original size:19 final size:19
Alignment explanation
Indices: 61896--61937 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
61886 AATTTTTTAA
*
61896 ATTTATAAAAATATAATT-T
1 ATTTA-AAAAATAAAATTAT
*
61915 ATTTAAATAATAAAATTAT
1 ATTTAAAAAATAAAATTAT
61934 ATTT
1 ATTT
61938 TTATTATCAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTTAAAAAATAAAATTAT
Found at i:61940 original size:21 final size:24
Alignment explanation
Indices: 61886--61939 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
61876 ATTTAATTCA
*
61886 AATTTTTTAAATTTATAAAAATAT
1 AATTTTTTAAATTAATAAAAATAT
*
61910 AATTTATTTAAA-TAATAAAATTAT
1 AATTT-TTTAAATTAATAAAAATAT
61934 -ATTTTT
1 AATTTTT
61940 ATTATCATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 2 0.07
23 4 0.15
24 15 0.56
25 6 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
AATTTTTTAAATTAATAAAAATAT
Found at i:62461 original size:36 final size:35
Alignment explanation
Indices: 62421--62531 Score: 94
Period size: 36 Copynumber: 3.3 Consensus size: 35
62411 ACATAATGTT
62421 TATAAAAAAATAAAATAAATAATAAATTAGGTACAC
1 TATAAAAAAAT-AAATAAATAATAAATTAGGTACAC
* * * * *
62457 TATAAAAAAAT---T-TAT-GTAACATAATGT---T
1 TATAAAAAAATAAATAAATAATAA-ATTAGGTACAC
62485 TATAAAAAAATAATATAAATAATAAATTAGGTACAC
1 TATAAAAAAATAA-ATAAATAATAAATTAGGTACAC
62521 TATAAAAAAAT
1 TATAAAAAAAT
62532 TATGTAACAC
Statistics
Matches: 55, Mismatches: 10, Indels: 20
0.65 0.12 0.24
Matches are distributed among these distances:
28 11 0.20
30 3 0.05
31 7 0.13
32 2 0.04
33 7 0.13
34 3 0.05
36 22 0.40
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (35 bp):
TATAAAAAAATAAATAAATAATAAATTAGGTACAC
Found at i:62539 original size:63 final size:64
Alignment explanation
Indices: 62394--62579 Score: 338
Period size: 64 Copynumber: 2.9 Consensus size: 64
62384 TATAGTGTAG
*
62394 ATAAAAAAATTTATGTAACATAATGTTTATAAAAAAATAAAATAAATAATAAATTAGGTACACT
1 ATAAAAAAATTTATGTAACATAATGTTTATAAAAAAATAATATAAATAATAAATTAGGTACACT
62458 ATAAAAAAATTTATGTAACATAATGTTTATAAAAAAATAATATAAATAATAAATTAGGTACACT
1 ATAAAAAAATTTATGTAACATAATGTTTATAAAAAAATAATATAAATAATAAATTAGGTACACT
* *
62522 ATAAAAAAA-TTATGTAACACAGTGTTTATAAAAAAATAATATAAATAATAAATTAGGT
1 ATAAAAAAATTTATGTAACATAATGTTTATAAAAAAATAATATAAATAATAAATTAGGT
62580 TTGGGTTGAA
Statistics
Matches: 119, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
63 47 0.39
64 72 0.61
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.32
Consensus pattern (64 bp):
ATAAAAAAATTTATGTAACATAATGTTTATAAAAAAATAATATAAATAATAAATTAGGTACACT
Found at i:63738 original size:61 final size:61
Alignment explanation
Indices: 63673--63851 Score: 189
Period size: 64 Copynumber: 2.9 Consensus size: 61
63663 TTAATCTAAC
* * * ** **
63673 ATTTGGTACTTGAATTTTACATTTTTTTTTCTAATTTGGTATTTAATTTTTTTTTG-ACTCA
1 ATTTGGTACCTGAACTTGACATTTTTTTTTCTAATTTGGTACCTAA-ACTTTTTTGAACTCA
* *
63734 ATTTGATACCTGAACTTGACATTTTTTTTTTTTCTAATTTGGTACCTAAACTTTTTTGAATTCA
1 ATTTGGTACCTGAACTTGACA---TTTTTTTTTCTAATTTGGTACCTAAACTTTTTTGAACTCA
** ** *
63798 ATTTGGTACCTGAACTTGACATTTTTTTCCCTAATTTGACACCTAAGCTTTTTT
1 ATTTGGTACCTGAACTTGACATTTTTTTTTCTAATTTGGTACCTAAACTTTTTT
63852 ATTTAGATTC
Statistics
Matches: 99, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
61 45 0.45
63 7 0.07
64 47 0.47
ACGTcount: A:0.23, C:0.14, G:0.10, T:0.53
Consensus pattern (61 bp):
ATTTGGTACCTGAACTTGACATTTTTTTTTCTAATTTGGTACCTAAACTTTTTTGAACTCA
Found at i:63777 original size:64 final size:64
Alignment explanation
Indices: 63694--63825 Score: 194
Period size: 64 Copynumber: 2.1 Consensus size: 64
63684 GAATTTTACA
** **
63694 TTTTTTTTTCTAATTTGGTATTTAATTTTTTTTTG-ACTCAATTTGATACCTGAACTTGACATTT
1 TTTTTTTTTCTAATTTGGTACCTAA-ACTTTTTTGAACTCAATTTGATACCTGAACTTGACATTT
* *
63758 TTTTTTTTTCTAATTTGGTACCTAAACTTTTTTGAATTCAATTTGGTACCTGAACTTGACATTT
1 TTTTTTTTTCTAATTTGGTACCTAAACTTTTTTGAACTCAATTTGATACCTGAACTTGACATTT
63822 TTTT
1 TTTT
63826 CCCTAATTTG
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
63 7 0.11
64 54 0.89
ACGTcount: A:0.22, C:0.12, G:0.10, T:0.56
Consensus pattern (64 bp):
TTTTTTTTTCTAATTTGGTACCTAAACTTTTTTGAACTCAATTTGATACCTGAACTTGACATTT
Found at i:64116 original size:32 final size:31
Alignment explanation
Indices: 64079--64218 Score: 94
Period size: 32 Copynumber: 4.5 Consensus size: 31
64069 GGATCCCAAA
* *
64079 AAGTTTAAGTATCAACTTTAATAAAA-AGTGTC
1 AAGTTTAAGTATCAA-ATTAAGAAAATA-TGTC
* *
64111 AAGTTTAAGTACCAAATTAGGAAAATATGTC
1 AAGTTTAAGTATCAAATTAAGAAAATATGTC
* * *
64142 AAGTTTGAGTATCAAA-TGAGACCAAA-A---A
1 AAGTTTAAGTATCAAATTAAGA--AAATATGTC
* *
64170 AAGTTTAAGTATCAAATTAAGGAAAAAATATC
1 AAGTTTAAGTATCAAATTAA-GAAAATATGTC
* *
64202 AAGTTCAAATATCAAAT
1 AAGTTTAAGTATCAAAT
64219 GTTATATTAA
Statistics
Matches: 85, Mismatches: 14, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
28 18 0.21
29 3 0.04
30 5 0.06
31 26 0.31
32 33 0.39
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.29
Consensus pattern (31 bp):
AAGTTTAAGTATCAAATTAAGAAAATATGTC
Found at i:74495 original size:12 final size:12
Alignment explanation
Indices: 74478--74509 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
74468 AACAATATTA
74478 ACAATTAAACTT
1 ACAATTAAACTT
74490 ACAATTAAACTT
1 ACAATTAAACTT
74502 A-AATTAAA
1 ACAATTAAA
74510 AACTTTGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (12 bp):
ACAATTAAACTT
Found at i:78304 original size:22 final size:20
Alignment explanation
Indices: 78272--78337 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
78262 AGTTCTAAAT
*
78272 TTTTTTTTATATATTTTTAA
1 TTTTTTATATATATTTTTAA
* *
78292 TTTTTTAAATATAAATTTTGAA
1 TTTTTT--ATATATATTTTTAA
*
78314 TTTTTTATAAATATTTTTAA
1 TTTTTTATATATATTTTTAA
78334 TTTT
1 TTTT
78338 AAAATTTACT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
20 21 0.55
22 17 0.45
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTTTATATATATTTTTAA
Found at i:78327 original size:24 final size:22
Alignment explanation
Indices: 78279--78320 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
78269 AATTTTTTTT
* *
78279 TATATATTTTTAATTTTTTAAA
1 TATAAATTTTGAATTTTTTAAA
78301 TATAAATTTTGAATTTTTTA
1 TATAAATTTTGAATTTTTTA
78321 TAAATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TATAAATTTTGAATTTTTTAAA
Found at i:91285 original size:13 final size:12
Alignment explanation
Indices: 91261--91293 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 12
91251 AAAAACACCC
91261 TTTGTTTTGTTT
1 TTTGTTTTGTTT
91273 TTTGTTCTTGTTT
1 TTTGTT-TTGTTT
91286 TTTGTTTT
1 TTTGTTTT
91294 TTTAAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (12 bp):
TTTGTTTTGTTT
Found at i:92143 original size:9 final size:10
Alignment explanation
Indices: 92116--92140 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
92106 AAAAGTACAA
92116 AAAAAATTTT
1 AAAAAATTTT
92126 AAAAAATTTT
1 AAAAAATTTT
92136 AAAAA
1 AAAAA
92141 TTTATATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAAAATTTT
Found at i:93856 original size:43 final size:43
Alignment explanation
Indices: 93795--93879 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
93785 TTCAAATCTG
93795 CATATAGAAACCGACATTAATTTAATTGTTCAAATGGAATAGA
1 CATATAGAAACCGACATTAATTTAATTGTTCAAATGGAATAGA
93838 CATATAGAAACCGACATTAATTTAATTGTTCAAATGGAATAG
1 CATATAGAAACCGACATTAATTTAATTGTTCAAATGGAATAG
93880 GAGGAGGAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.31
Consensus pattern (43 bp):
CATATAGAAACCGACATTAATTTAATTGTTCAAATGGAATAGA
Found at i:96936 original size:28 final size:29
Alignment explanation
Indices: 96905--96959 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
96895 AAAATAGTGC
96905 AAATTTA-TAAAAA-AAAATAAAAATGATA
1 AAATTTACTAAAAATAAAA-AAAAATGATA
*
96933 AAATTTACTAAAAATATAAAAAAATGA
1 AAATTTACTAAAAATAAAAAAAAATGA
96960 AAATATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 7 0.29
29 14 0.58
30 3 0.12
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (29 bp):
AAATTTACTAAAAATAAAAAAAAATGATA
Found at i:96962 original size:27 final size:27
Alignment explanation
Indices: 96905--96971 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 27
96895 AAAATAGTGC
96905 AAATTTATAAAAAAAAATAAAAATGATA
1 AAATTTATAAAAAAAAATAAAAATGA-A
*
96933 AAATTTACTAAAAATATAA-AAAAATGAA
1 AAATTTA-TAAAAA-AAAATAAAAATGAA
*
96961 AATATTAATAA
1 AA-ATTTATAA
96972 TATATATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 13 0.38
29 18 0.53
30 3 0.09
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (27 bp):
AAATTTATAAAAAAAAATAAAAATGAA
Found at i:103068 original size:24 final size:24
Alignment explanation
Indices: 103041--103090 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
103031 GCATCAAGAC
103041 TAAAAATTCAAAATTCAAAAAATA
1 TAAAAATTCAAAATTCAAAAAATA
*
103065 TAAAAATTCAAAATTCGAAAAATA
1 TAAAAATTCAAAATTCAAAAAATA
103089 TA
1 TA
103091 GGGACTTAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.64, C:0.08, G:0.02, T:0.26
Consensus pattern (24 bp):
TAAAAATTCAAAATTCAAAAAATA
Found at i:103258 original size:31 final size:32
Alignment explanation
Indices: 103218--103284 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
103208 AAAATTTCAG
* * **
103218 AATTTGAAAAGTGCAGGGACTAAAATTGA-CA
1 AATTCGAAAAGTACAGAAACTAAAATTGATCA
*
103249 AATTCGAAAAGTATAGAAACTAAAATTGATCA
1 AATTCGAAAAGTACAGAAACTAAAATTGATCA
103281 AATT
1 AATT
103285 AAAGTATAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 24 0.80
32 6 0.20
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.25
Consensus pattern (32 bp):
AATTCGAAAAGTACAGAAACTAAAATTGATCA
Found at i:103299 original size:29 final size:29
Alignment explanation
Indices: 103235--103301 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 29
103225 AAAGTGCAGG
103235 GACTAAAATTGACAAATTCGAAAAGTATAGA
1 GACTAAAATTGACAAATT--AAAAGTATAGA
*
103266 AACTAAAATTGATCAAATT-AAAGTATAGA
1 GACTAAAATTGA-CAAATTAAAAGTATAGA
103295 GACTAAA
1 GACTAAA
103302 TCTACAACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 16 0.48
31 11 0.33
32 6 0.18
ACGTcount: A:0.54, C:0.09, G:0.13, T:0.24
Consensus pattern (29 bp):
GACTAAAATTGACAAATTAAAAGTATAGA
Found at i:106942 original size:25 final size:23
Alignment explanation
Indices: 106914--106964 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
106904 GTGTTCCCAC
106914 AAATATTGAGTACCTTTTTCCAATT
1 AAATATTGA-TA-CTTTTTCCAATT
* * *
106939 AAATTTTGATATTTTTTTCAATT
1 AAATATTGATACTTTTTCCAATT
106962 AAA
1 AAA
106965 CTTTAACTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 13 0.57
24 2 0.09
25 8 0.35
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.49
Consensus pattern (23 bp):
AAATATTGATACTTTTTCCAATT
Found at i:113526 original size:41 final size:41
Alignment explanation
Indices: 113469--113559 Score: 182
Period size: 41 Copynumber: 2.2 Consensus size: 41
113459 TTTGTAGCAG
113469 GTTTTATTCTTATCACAATTTTCAATAGTAACCGAGTCTTT
1 GTTTTATTCTTATCACAATTTTCAATAGTAACCGAGTCTTT
113510 GTTTTATTCTTATCACAATTTTCAATAGTAACCGAGTCTTT
1 GTTTTATTCTTATCACAATTTTCAATAGTAACCGAGTCTTT
113551 GTTTTATTC
1 GTTTTATTC
113560 CATGGCGTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.25, C:0.16, G:0.10, T:0.48
Consensus pattern (41 bp):
GTTTTATTCTTATCACAATTTTCAATAGTAACCGAGTCTTT
Found at i:113704 original size:2 final size:2
Alignment explanation
Indices: 113697--113736 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
113687 TCATTTATTC
113697 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
113737 TGAGGCTTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:114327 original size:24 final size:23
Alignment explanation
Indices: 114294--114341 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
114284 TTTTAGAAGA
*
114294 ATTAAAATATAATTTTATTATTTT
1 ATTAAAATATAATTTT-TAATTTT
*
114318 ATTAATATATAATTTTTAATTTT
1 ATTAAAATATAATTTTTAATTTT
114341 A
1 A
114342 AAATGACTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTAAAATATAATTTTTAATTTT
Found at i:115717 original size:4 final size:4
Alignment explanation
Indices: 115710--115764 Score: 74
Period size: 4 Copynumber: 13.5 Consensus size: 4
115700 CGGGCAGAAG
* *
115710 AAGA AAGA AAGA AAGAA AACA AAGA AAGA AAGA AAGA AAGG AAGA AAGA
1 AAGA AAGA AAGA AAG-A AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
*
115759 GAGA AA
1 AAGA AA
115765 AGTAGTGTGC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
4 41 0.93
5 3 0.07
ACGTcount: A:0.73, C:0.02, G:0.25, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:116242 original size:24 final size:24
Alignment explanation
Indices: 116210--116256 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
116200 TGTGGAACCT
*
116210 GTAGAAAATGAAGATCCAACTCCA
1 GTAGAAAATAAAGATCCAACTCCA
116234 GTAGAAAATAAAGATCCAACTCC
1 GTAGAAAATAAAGATCCAACTCC
116257 GTGTATGGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (24 bp):
GTAGAAAATAAAGATCCAACTCCA
Found at i:120202 original size:31 final size:31
Alignment explanation
Indices: 120164--120225 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
120154 ATTGGATGCA
120164 CATCGTTGCCGGCTCTTGGAAAAAACTAACG
1 CATCGTTGCCGGCTCTTGGAAAAAACTAACG
*
120195 CATCGTTGTCGGCTCTTGGAAAAAACTAACG
1 CATCGTTGCCGGCTCTTGGAAAAAACTAACG
120226 TCGGTGACCG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (31 bp):
CATCGTTGCCGGCTCTTGGAAAAAACTAACG
Found at i:121187 original size:16 final size:16
Alignment explanation
Indices: 121166--121197 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
121156 ACTTACTACT
121166 AATAACAAAGTAAAAA
1 AATAACAAAGTAAAAA
121182 AATAACAAAGTAAAAA
1 AATAACAAAGTAAAAA
121198 TTACTTACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.12
Consensus pattern (16 bp):
AATAACAAAGTAAAAA
Found at i:121520 original size:13 final size:13
Alignment explanation
Indices: 121502--121530 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
121492 ATAAATTAAA
121502 AAATTTTAAAAAT
1 AAATTTTAAAAAT
121515 AAA-TTTAAAAAT
1 AAATTTTAAAAAT
121527 AAAT
1 AAAT
121531 ACATTACCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.80
13 3 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AAATTTTAAAAAT
Found at i:121553 original size:6 final size:6
Alignment explanation
Indices: 121542--121595 Score: 72
Period size: 6 Copynumber: 8.7 Consensus size: 6
121532 CATTACCTTT
* *
121542 TTCTCC TTCTCC TTCTCC TTCTCC TTTTCC TTCTCC TTTCTTTC TTCTCC
1 TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC -TTC-TCC TTCTCC
121592 TTCT
1 TTCT
121596 TCTTTCTTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
6 34 0.81
7 6 0.14
8 2 0.05
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (6 bp):
TTCTCC
Found at i:121565 original size:18 final size:19
Alignment explanation
Indices: 121541--121602 Score: 81
Period size: 18 Copynumber: 3.3 Consensus size: 19
121531 ACATTACCTT
121541 TTTCTCCTTCTCCTTCTCC
1 TTTCTCCTTCTCCTTCTCC
*
121560 -TTCTCCTTTTCCTTCTCC
1 TTTCTCCTTCTCCTTCTCC
* *
121578 TTTCTTTCTTCTCCTTCTTC
1 TTTC-TCCTTCTCCTTCTCC
121598 TTTCT
1 TTTCT
121603 TTCTTTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 17 0.46
19 4 0.11
20 16 0.43
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTCTCCTTCTCCTTCTCC
Found at i:121586 original size:4 final size:4
Alignment explanation
Indices: 121577--121629 Score: 56
Period size: 4 Copynumber: 13.2 Consensus size: 4
121567 TTTCCTTCTC
* *
121577 CTTT CTTT CTTCT CCTT C-TT CTTT CTTT CTTT -TTT CTAT CTTTT CTTT
1 CTTT CTTT CTT-T CTTT CTTT CTTT CTTT CTTT CTTT CTTT C-TTT CTTT
121625 CTTT C
1 CTTT C
121630 GATACCCGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
3 6 0.14
4 30 0.71
5 6 0.14
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (4 bp):
CTTT
Found at i:121594 original size:20 final size:20
Alignment explanation
Indices: 121547--121607 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
121537 CCTTTTTCTC
*
121547 CTTCTCCTTCTCC-TTC-TC
1 CTTCTCCTTCTCCTTTCTTT
*
121565 CTTTTCCTTCTCCTTTCTTT
1 CTTCTCCTTCTCCTTTCTTT
*
121585 CTTCTCCTTCTTCTTTCTTT
1 CTTCTCCTTCTCCTTTCTTT
121605 CTT
1 CTT
121608 TTTTCTATCT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.32
19 3 0.08
20 22 0.59
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (20 bp):
CTTCTCCTTCTCCTTTCTTT
Found at i:121613 original size:24 final size:23
Alignment explanation
Indices: 121559--121629 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 23
121549 TCTCCTTCTC
121559 CTTCTCCTTTTCCTTCTCCTTTCTTT
1 CTTCTCCTTTT-CTT-T-CTTTCTTT
121585 CTTCTCCTTCTTCTTTCTTTCTTT
1 CTTCTCCTT-TTCTTTCTTTCTTT
* *
121609 TTTCTATCTTTTCTTTCTTTC
1 CTTCT-CCTTTTCTTTCTTTC
121630 GATACCCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
24 23 0.56
25 4 0.10
26 12 0.29
27 2 0.05
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.66
Consensus pattern (23 bp):
CTTCTCCTTTTCTTTCTTTCTTT
Found at i:131578 original size:14 final size:14
Alignment explanation
Indices: 131549--131577 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
131539 AATAAATAAG
131549 TTCTTTTCTTTCTT
1 TTCTTTTCTTTCTT
131563 TTCTTTTCTTT-TT
1 TTCTTTTCTTTCTT
131576 TT
1 TT
131578 TGTTAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTCTTTTCTTTCTT
Found at i:171821 original size:79 final size:79
Alignment explanation
Indices: 171727--171880 Score: 281
Period size: 79 Copynumber: 1.9 Consensus size: 79
171717 GGAATAGGCC
* *
171727 ATGTTTAAAATGATTGAGTTGAAACTTTTAAAAAATATATTTTGAATTTAAATTTATAATATTTT
1 ATGTTTAAAATGATTGAGTTAAAACTTTTAAAAAATATATTTCGAATTTAAATTTATAATATTTT
171792 ATTTTAAAATGACG
66 ATTTTAAAATGACG
*
171806 ATGTTTAAAATGATTGAGTTAAAACTTTTAAAAAATATATTTCGAGTTTAAATTTATAATATTTT
1 ATGTTTAAAATGATTGAGTTAAAACTTTTAAAAAATATATTTCGAATTTAAATTTATAATATTTT
171871 ATTTTAAAAT
66 ATTTTAAAAT
171881 TTATATAAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 72 1.00
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (79 bp):
ATGTTTAAAATGATTGAGTTAAAACTTTTAAAAAATATATTTCGAATTTAAATTTATAATATTTT
ATTTTAAAATGACG
Found at i:172409 original size:32 final size:32
Alignment explanation
Indices: 172337--172429 Score: 98
Period size: 32 Copynumber: 2.9 Consensus size: 32
172327 GATATTTAGT
* * *
172337 TTTTTTTTTTCAATTTGATACTTAAATTTGACA
1 TTTTTTTTTT-AATTTGGTACTTAAACTTGAAA
* * *
172370 CTCTTTTTTTAATTTGGTACATAAACTTGAAA
1 TTTTTTTTTTAATTTGGTACTTAAACTTGAAA
*
172402 TTTTTTTTTT-ATGTTGGTGCTTAAACTT
1 TTTTTTTTTTAAT-TTGGTACTTAAACTT
172430 TTGGGATCTA
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
31 2 0.04
32 39 0.80
33 8 0.16
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.56
Consensus pattern (32 bp):
TTTTTTTTTTAATTTGGTACTTAAACTTGAAA
Found at i:172773 original size:12 final size:13
Alignment explanation
Indices: 172748--172794 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
172738 AAAAAAAAGT
172748 TATCAAATTTAAA
1 TATCAAATTTAAA
172761 TATCAAA-TTAAA
1 TATCAAATTTAAA
**
172773 TAAAAAATTTAAA
1 TATCAAATTTAAA
*
172786 TACCAAATT
1 TATCAAATT
172795 AAAAAAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (13 bp):
TATCAAATTTAAA
Found at i:172780 original size:25 final size:24
Alignment explanation
Indices: 172752--172802 Score: 84
Period size: 25 Copynumber: 2.1 Consensus size: 24
172742 AAAAGTTATC
*
172752 AAATTTAAATATCAAATTAAATAAA
1 AAATTTAAATACCAAATTAAA-AAA
172777 AAATTTAAATACCAAATTAAAAAA
1 AAATTTAAATACCAAATTAAAAAA
172801 AA
1 AA
172803 TGTGAAGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (24 bp):
AAATTTAAATACCAAATTAAAAAA
Found at i:173198 original size:24 final size:24
Alignment explanation
Indices: 173171--173217 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
173161 AAAATATAAT
* * *
173171 TTTATTATTTTAATAATTTATATA
1 TTTATAATTTTAAGAATTCATATA
173195 TTTATAATTTTAAGAATTCATAT
1 TTTATAATTTTAAGAATTCATAT
173218 CAGTTATCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTATAATTTTAAGAATTCATATA
Found at i:176314 original size:30 final size:30
Alignment explanation
Indices: 176273--176329 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
176263 GGTCCCAAAT
*
176273 TATTATTTTAGAAAATTTTTATTTTTTTTTA
1 TATTATTTTAG-AAATTTTTAATTTTTTTTA
*
176304 TATT-TTTTAGAATTTTTTAATTTTTT
1 TATTATTTTAGAAATTTTTAATTTTTT
176330 AAAAATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 14 0.58
30 6 0.25
31 4 0.17
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (30 bp):
TATTATTTTAGAAATTTTTAATTTTTTTTA
Found at i:176380 original size:27 final size:27
Alignment explanation
Indices: 176322--176376 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
176312 AGAATTTTTT
*
176322 AATTTTTTAAAAATAAATATAAATTTT
1 AATTTTTTAAAAATAAATATAAATTTA
* * *
176349 AATTTTTTATAAAT-ATTTTAAATTTA
1 AATTTTTTAAAAATAAATATAAATTTA
176375 AA
1 AA
176377 ATTTATTTCG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
AATTTTTTAAAAATAAATATAAATTTA
Found at i:176396 original size:20 final size:21
Alignment explanation
Indices: 176371--176414 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
176361 ATATTTTAAA
176371 TTTAAAATTTATTTCG-AATT
1 TTTAAAATTTATTTCGTAATT
* *
176391 TTT-AAATTTTTTTTGTAATT
1 TTTAAAATTTATTTCGTAATT
176411 TTTA
1 TTTA
176415 TTGAAAGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (21 bp):
TTTAAAATTTATTTCGTAATT
Found at i:179832 original size:147 final size:147
Alignment explanation
Indices: 179565--179860 Score: 592
Period size: 147 Copynumber: 2.0 Consensus size: 147
179555 GCATTATAAA
179565 AGAGAACCATGTTTTCTACCTTTTATTCTAGTGAAGGACAACAAAGATTTTGGTTACAACACAAT
1 AGAGAACCATGTTTTCTACCTTTTATTCTAGTGAAGGACAACAAAGATTTTGGTTACAACACAAT
179630 TGAATAAATGCCTCCTAGTTGTACTACCAGTCAAAAAGTTTGGGGAAAACAATAATGTTCAATTT
66 TGAATAAATGCCTCCTAGTTGTACTACCAGTCAAAAAGTTTGGGGAAAACAATAATGTTCAATTT
179695 CCATAGCAGGAAAGGAG
131 CCATAGCAGGAAAGGAG
179712 AGAGAACCATGTTTTCTACCTTTTATTCTAGTGAAGGACAACAAAGATTTTGGTTACAACACAAT
1 AGAGAACCATGTTTTCTACCTTTTATTCTAGTGAAGGACAACAAAGATTTTGGTTACAACACAAT
179777 TGAATAAATGCCTCCTAGTTGTACTACCAGTCAAAAAGTTTGGGGAAAACAATAATGTTCAATTT
66 TGAATAAATGCCTCCTAGTTGTACTACCAGTCAAAAAGTTTGGGGAAAACAATAATGTTCAATTT
179842 CCATAGCAGGAAAGGAG
131 CCATAGCAGGAAAGGAG
179859 AG
1 AG
179861 GAAGGGATCA
Statistics
Matches: 149, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 149 1.00
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (147 bp):
AGAGAACCATGTTTTCTACCTTTTATTCTAGTGAAGGACAACAAAGATTTTGGTTACAACACAAT
TGAATAAATGCCTCCTAGTTGTACTACCAGTCAAAAAGTTTGGGGAAAACAATAATGTTCAATTT
CCATAGCAGGAAAGGAG
Found at i:180320 original size:19 final size:21
Alignment explanation
Indices: 180298--180351 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 21
180288 TAAAAAAAAC
180298 AAATATATTAAAAATA-TTA-
1 AAATATATTAAAAATATTTAT
*
180317 AAAT-TA-TAAAAAAATTTAT
1 AAATATATTAAAAATATTTAT
180336 AAATAT-TATAAAAATA
1 AAATATAT-TAAAAATA
180352 CAAAAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 7 0.25
18 5 0.18
19 8 0.29
20 1 0.04
21 7 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATATATTAAAAATATTTAT
Found at i:180337 original size:12 final size:11
Alignment explanation
Indices: 180316--180387 Score: 57
Period size: 10 Copynumber: 7.1 Consensus size: 11
180306 TAAAAATATT
180316 AAAATTATAAA
1 AAAATTATAAA
*
180327 AAAATT-TATA
1 AAAATTATAAA
*
180337 AATATTAT--A
1 AAAATTATAAA
*
180346 AAAA-TACAAA
1 AAAATTATAAA
*
180356 AAAATTAT-AC
1 AAAATTATAAA
*
180366 TAAATTATAAA
1 AAAATTATAAA
180377 AAAA-TATAAA
1 AAAATTATAAA
180387 A
1 A
180388 TTAATAAAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 11
0.70 0.13 0.16
Matches are distributed among these distances:
8 2 0.04
9 4 0.09
10 28 0.60
11 13 0.28
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (11 bp):
AAAATTATAAA
Found at i:180338 original size:29 final size:29
Alignment explanation
Indices: 180306--180378 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
180296 ACAAATATAT
* *
180306 TAAAAA-TATTAAAATTATAAAAAAATTTA
1 TAAAAATTA-TAAAAATACAAAAAAATTTA
*
180335 TAAATATTATAAAAATACAAAAAAA-TTA
1 TAAAAATTATAAAAATACAAAAAAATTTA
*
180363 TACTAAATTATAAAAA
1 TA-AAAATTATAAAAA
180379 AATATAAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 5 0.14
29 30 0.81
30 2 0.05
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (29 bp):
TAAAAATTATAAAAATACAAAAAAATTTA
Found at i:180345 original size:21 final size:19
Alignment explanation
Indices: 180307--180447 Score: 63
Period size: 18 Copynumber: 7.8 Consensus size: 19
180297 CAAATATATT
180307 AAAAATATTAAAATTATAA
1 AAAAATATTAAAATTATAA
*
180326 AAAAAT-TTATAAA-TATTA
1 AAAAATATTA-AAATTATAA
* *
180344 TAAAA-A-TACAA--A-AA
1 AAAAATATTAAAATTATAA
** *
180358 AATTATACT-AAATTATAA
1 AAAAATATTAAAATTATAA
180376 AAAAATA-TAAAATTA-ATA
1 AAAAATATTAAAATTATA-A
**
180394 AAACTTATTTAAAATTA-AA
1 AAAAATA-TTAAAATTATAA
* * *
180413 AAAACATATTAGAATTCT-T
1 AAAA-ATATTAAAATTATAA
180432 AAAAATATTAAAATTA
1 AAAAATATTAAAATTA
180448 ATATAAACTT
Statistics
Matches: 90, Mismatches: 19, Indels: 27
0.66 0.14 0.20
Matches are distributed among these distances:
14 3 0.03
15 4 0.04
16 3 0.03
17 5 0.06
18 40 0.44
19 24 0.27
20 11 0.12
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.33
Consensus pattern (19 bp):
AAAAATATTAAAATTATAA
Found at i:180377 original size:20 final size:19
Alignment explanation
Indices: 180353--180473 Score: 61
Period size: 19 Copynumber: 6.3 Consensus size: 19
180343 ATAAAAATAC
180353 AAAAAAATTATACTAAATT-AT
1 AAAAAAA-TATA--AAATTAAT
180374 AAAAAAATATAAAATTAAT
1 AAAAAAATATAAAATTAAT
** *
180393 AAAACTTATTTAAAATTAA-
1 AAAA-AAATATAAAATTAAT
* * **
180412 AAAAACATATTAGAATTCTT
1 AAAAAAATA-TAAAATTAAT
*
180432 AAAAATAT-TAAAATTAAT
1 AAAAAAATATAAAATTAAT
* ** *
180450 ATAAACTTATAAAAATAA-
1 AAAAAAATATAAAATTAAT
180468 AAAAAA
1 AAAAAA
180474 TCATAAAAAC
Statistics
Matches: 76, Mismatches: 19, Indels: 13
0.70 0.18 0.12
Matches are distributed among these distances:
18 23 0.30
19 24 0.32
20 22 0.29
21 7 0.09
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.31
Consensus pattern (19 bp):
AAAAAAATATAAAATTAAT
Found at i:180380 original size:31 final size:29
Alignment explanation
Indices: 180281--180387 Score: 80
Period size: 31 Copynumber: 3.7 Consensus size: 29
180271 AAAACCAGAA
* * *
180281 AAATATATAAAAAAA-ACAAATATA-TTAA
1 AAATAT-TAAAAAAATACAAAAAAATTTAT
* *
180309 AAATATT--AAAATTATAAAAAAATTTAT
1 AAATATTAAAAAAATACAAAAAAATTTAT
*
180336 AAATATTATAAAAATACAAAAAAATTATACT
1 AAATATTAAAAAAATACAAAAAAATT-TA-T
*
180367 AAAT-TATAAAAAAATATAAAA
1 AAATAT-TAAAAAAATACAAAA
180388 TTAATAAAAC
Statistics
Matches: 63, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
25 4 0.06
26 6 0.10
27 11 0.17
28 6 0.10
29 15 0.24
30 3 0.05
31 18 0.29
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (29 bp):
AAATATTAAAAAAATACAAAAAAATTTAT
Found at i:180414 original size:57 final size:58
Alignment explanation
Indices: 180341--180478 Score: 167
Period size: 57 Copynumber: 2.4 Consensus size: 58
180331 TTTATAAATA
*
180341 TTATAAAAATACAAAAAAATTATACTA-AATTATAAAAAA-ATATAAAATTAATA-AAAC
1 TTATAAAAATA-AAAAAAATCATACTAGAATTATAAAAAATAT-TAAAATTAATATAAAC
* * * * *
180398 TTATTTAAAATTAAAAAAA-CATATTAGAATTCTTAAAAATATTAAAATTAATATAAAC
1 TTA-TAAAAATAAAAAAAATCATACTAGAATTATAAAAAATATTAAAATTAATATAAAC
180456 TTATAAAAATAAAAAAAATCATA
1 TTATAAAAATAAAAAAAATCATA
180479 AAAACTTGAG
Statistics
Matches: 68, Mismatches: 8, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
56 5 0.07
57 44 0.65
58 19 0.28
ACGTcount: A:0.63, C:0.05, G:0.01, T:0.31
Consensus pattern (58 bp):
TTATAAAAATAAAAAAAATCATACTAGAATTATAAAAAATATTAAAATTAATATAAAC
Found at i:180485 original size:28 final size:27
Alignment explanation
Indices: 180279--180482 Score: 96
Period size: 28 Copynumber: 7.2 Consensus size: 27
180269 TAAAAACCAG
180279 AAAAATATATAAAAA-AAACAAATATATTA-
1 AAAAAT-TATAAAAATAAA-AAA-A-ATTAT
* *
180308 AAAATATTA-AAATTATAAAAAAATTTAT
1 AAAA-ATTATAAA-AATAAAAAAAATTAT
*
180336 AAATATTATAAAAATACAAAAAAATTAT
1 AAAAATTATAAAAATA-AAAAAAATTAT
* *
180364 ACTAAATTATAAAAA-AATATAAAATTAAT
1 A-AAAATTATAAAAATAA-AAAAAATT-AT
* *
180393 AAAACTTATTTAAAATTAAAAAAACA-TAT
1 AAAAATTA--TAAAAATAAAAAAA-ATTAT
* * * **
180422 TAGAATTCTTAAAAAT-ATTAAAATTAAT
1 AAAAATT-ATAAAAATAAAAAAAATT-AT
* *
180450 ATAAACTTATAAAAATAAAAAAAATCAT
1 A-AAAATTATAAAAATAAAAAAAATTAT
180478 AAAAA
1 AAAAA
180483 CTTGAGTTGG
Statistics
Matches: 130, Mismatches: 27, Indels: 38
0.67 0.14 0.19
Matches are distributed among these distances:
26 1 0.01
27 19 0.15
28 52 0.40
29 40 0.31
30 15 0.12
31 3 0.02
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (27 bp):
AAAAATTATAAAAATAAAAAAAATTAT
Found at i:181025 original size:9 final size:9
Alignment explanation
Indices: 180983--181121 Score: 56
Period size: 9 Copynumber: 15.0 Consensus size: 9
180973 ATTTTATAAA
*
180983 AATTATTAT
1 AATTTTTAT
180992 AATTTATTA-
1 AATTT-TTAT
*
181001 GATTTATTAT
1 AATTT-TTAT
181011 AA-TTTTAT
1 AATTTTTAT
*
181019 AATTTTTGTT
1 AATTTTT-AT
* *
181029 AGTTTATAT
1 AATTTTTAT
*
181038 CAATTTTCAT
1 -AATTTTTAT
181048 -ATTATTTAT
1 AATT-TTTAT
*
181057 AATATTTAAT
1 AAT-TTTTAT
* *
181067 AAATTTTCT
1 AATTTTTAT
181076 --TTTTTATTT
1 AATTTTTA--T
181085 AATATTTTAT
1 AAT-TTTTAT
181095 AATTTTTAT
1 AATTTTTAT
*
181104 GATTTTTA-
1 AATTTTTAT
181112 AATATTTTAT
1 AAT-TTTTAT
181122 GAAAAAAATA
Statistics
Matches: 96, Mismatches: 19, Indels: 29
0.67 0.13 0.20
Matches are distributed among these distances:
7 4 0.04
8 11 0.11
9 46 0.48
10 28 0.29
11 2 0.02
12 5 0.05
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (9 bp):
AATTTTTAT
Found at i:181831 original size:30 final size:31
Alignment explanation
Indices: 181774--181846 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
181764 ATTAGTAAAG
*
181774 ATAAAAATATATTTTAATATCTTTAAAAATA
1 ATAAAAATATAATTTAATATCTTTAAAAATA
* * *
181805 ATAAAAATTTAATTTAAT-TTTTTAAAAATT
1 ATAAAAATATAATTTAATATCTTTAAAAATA
*
181835 ATAAATATATAA
1 ATAAAAATATAA
181847 ATTATTAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 20 0.56
31 16 0.44
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (31 bp):
ATAAAAATATAATTTAATATCTTTAAAAATA
Found at i:181857 original size:17 final size:18
Alignment explanation
Indices: 181832--181868 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
181822 TTTTTTAAAA
181832 ATTATAAAT-ATATAAATT
1 ATTATAAATGATA-AAATT
181850 ATTA-AAATGATAAAATT
1 ATTATAAATGATAAAATT
181867 AT
1 AT
181869 GTTTTTACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
ATTATAAATGATAAAATT
Found at i:194880 original size:30 final size:30
Alignment explanation
Indices: 194844--194902 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
194834 ATTAGTAAAG
* *
194844 ATAAAATTATACTTTGACCCTTTAAAAATA
1 ATAAAATTATAATTTAACCCTTTAAAAATA
* *
194874 ATAAAATTTTAATTTAATCCTTTAAAAAT
1 ATAAAATTATAATTTAACCCTTTAAAAAT
194903 TGTACTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.41
Consensus pattern (30 bp):
ATAAAATTATAATTTAACCCTTTAAAAATA
Found at i:198045 original size:11 final size:11
Alignment explanation
Indices: 198029--198085 Score: 60
Period size: 12 Copynumber: 4.9 Consensus size: 11
198019 GGGGACCAAC
* *
198029 GAAAAATGAAG
1 GAAAAAAGAAA
198040 GAAAAAAGAAA
1 GAAAAAAGAAA
198051 GAAAAAAGAGAAA
1 G-AAAAA-AGAAA
198064 GAAAGAAAGAAA
1 GAAA-AAAGAAA
*
198076 GAAAGAAGAA
1 GAAAAAAGAA
198086 GGAAGAAGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 15 0.38
12 17 0.43
13 8 0.20
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.02
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:198053 original size:4 final size:4
Alignment explanation
Indices: 198040--198082 Score: 61
Period size: 4 Copynumber: 10.8 Consensus size: 4
198030 AAAAATGAAG
*
198040 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAA
198083 GAAGGAAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 29 0.83
5 3 0.09
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Done.