Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011016.1 Kokia drynarioides strain JFW-HI SEQ_125987, 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: 82005
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Warning! 265 characters in sequence are not A, C, G, or T
Found at i:10175 original size:78 final size:79
Alignment explanation
Indices: 10045--10205 Score: 306
Period size: 78 Copynumber: 2.1 Consensus size: 79
10035 TTAATGAATT
*
10045 AATATTAAATAAAAAACAAGAGTTTTAAAACCCTAAATAAAATAAATTCATTATTTTAAATTATA
1 AATATTAAATAAAAAACAAGAGTTTTAAAACCCAAAATAAAATAAATTCATTATTTTAAATTATA
10110 AAATGAAATAAATA
66 AAATGAAATAAATA
10124 AATATTAAATAAAAAACAAGAG-TTTAAAACCCAAAATAAAATAAATTCATTATTTTAAATTATA
1 AATATTAAATAAAAAACAAGAGTTTTAAAACCCAAAATAAAATAAATTCATTATTTTAAATTATA
10188 AAATGAAATAAATA
66 AAATGAAATAAATA
10202 AATA
1 AATA
10206 AAACTAAAGG
Statistics
Matches: 81, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
78 59 0.73
79 22 0.27
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (79 bp):
AATATTAAATAAAAAACAAGAGTTTTAAAACCCAAAATAAAATAAATTCATTATTTTAAATTATA
AAATGAAATAAATA
Found at i:12455 original size:58 final size:59
Alignment explanation
Indices: 12393--12698 Score: 273
Period size: 58 Copynumber: 5.3 Consensus size: 59
12383 GACATCTGAT
* * *
12393 GGTAAAATGGTGATTTTTGGAAAAATCAGGGT-AAAAATGGAGTTTTTGGAAGTGCGGA
1 GGTAAAATGGTAATTTTTGGAAAAATCAGGGTCAAAAATGGAATTTTTGGAAGTTCGGA
** * * *
12451 GGTAAAATGGTAATTTTTAAAAAAATCGGGGTCAACAAT-GAATTTTTTGGAAGCTTAGG-
1 GGTAAAATGGTAATTTTTGGAAAAATCAGGGTCAAAAATGGAA-TTTTTGGAAG-TTCGGA
* *
12510 GGTAAAGTGGTAATTTTTGG-AAAATC-GGTGTCAAAAATGGAATTTTTGGAAGTTC-AA
1 GGTAAAATGGTAATTTTTGGAAAAATCAGG-GTCAAAAATGGAATTTTTGGAAGTTCGGA
* *
12567 GGGTAAAATAGTAA-TTTTGGAAAAATTAGGGTC---AATGGAA-TTTTGGAAAGTTC-GA
1 -GGTAAAATGGTAATTTTTGGAAAAATCAGGGTCAAAAATGGAATTTTTGG-AAGTTCGGA
* ** **
12622 GGGTAAAAAT-GTAATTTTTGGGAAAATTGGGGTCAAAAATGGAATTTGGGGAAGTTC-GA
1 -GGT-AAAATGGTAATTTTTGGAAAAATCAGGGTCAAAAATGGAATTTTTGGAAGTTCGGA
12681 GGGTAAAAAT-GTAATTTT
1 -GGT-AAAATGGTAATTTT
12699 AAAAAGTTTA
Statistics
Matches: 210, Mismatches: 22, Indels: 31
0.80 0.08 0.12
Matches are distributed among these distances:
54 6 0.03
55 22 0.10
56 22 0.10
57 10 0.05
58 73 0.35
59 70 0.33
60 7 0.03
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.31
Consensus pattern (59 bp):
GGTAAAATGGTAATTTTTGGAAAAATCAGGGTCAAAAATGGAATTTTTGGAAGTTCGGA
Found at i:12574 original size:29 final size:27
Alignment explanation
Indices: 12494--12748 Score: 108
Period size: 29 Copynumber: 8.9 Consensus size: 27
12484 AACAATGAAT
*
12494 TTTTTGGAAGCTTAGGGGT-AAAGTGGTAA
1 TTTTTGGAAG-TTA-GGGTAAAAATGG-AA
** *
12523 TTTTTGGAAAATCGGTGTCAAAAATGGAA
1 TTTTTGGAAGTTAGG-GT-AAAAATGGAA
*
12552 TTTTTGGAAGTTCAAGGGT-AAAATAGTAA
1 TTTTTGGAAGTT--AGGGTAAAAAT-GGAA
* *
12581 -TTTTGGAAAAATTAGGGT--CAATGGAA
1 TTTTTGG--AAGTTAGGGTAAAAATGGAA
*
12607 -TTTTGGAAAGTTCGAGGGTAAAAATGTAA
1 TTTTTGG-AAGTT--AGGGTAAAAATGGAA
* *
12636 TTTTTGGGAAAATTGGGGTCAAAAATGGAA
1 TTTTT-GG-AAGTTAGGGT-AAAAATGGAA
** *
12666 TTTGGGGAAGTTCGAGGGTAAAAATGTAA
1 TTTTTGGAAGTT--AGGGTAAAAATGGAA
*** * *
12695 TTTTAAAAAGTTTAGGGTTAAAATGAAA
1 TTTTTGGAAG-TTAGGGTAAAAATGGAA
*
12723 TTTTTGAAAGTTTAAGGGTAAAAATG
1 TTTTTGGAAG-TT-AGGGTAAAAATG
12749 TATTTTTTTG
Statistics
Matches: 176, Mismatches: 31, Indels: 38
0.72 0.13 0.16
Matches are distributed among these distances:
25 5 0.03
26 9 0.05
27 10 0.06
28 47 0.27
29 62 0.35
30 34 0.19
31 9 0.05
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.33
Consensus pattern (27 bp):
TTTTTGGAAGTTAGGGTAAAAATGGAA
Found at i:12675 original size:114 final size:114
Alignment explanation
Indices: 12519--12777 Score: 310
Period size: 114 Copynumber: 2.2 Consensus size: 114
12509 GGGTAAAGTG
* **
12519 GTAATTTTTGGAAAATCGGTGTCAAAAATGGAATTTTTGGAAGTTCAAGGGT-AAAATAGTAATT
1 GTAATTTTTGGAAAATCGGGGTCAAAAATGGAATTTGGGGAAGTTCAAGGGTAAAAAT-GTAATT
* * *
12583 TTGGAAAAA-TTAGGG-T-CAATGGAATTTTGGAAAGTTCGAGGGTAAAAAT
65 TT--AAAAAGTTAGGGTTAAAATGAAATTTTGGAAAGTTCAAGGGTAAAAAT
* *
12632 GTAATTTTTGGGAAAATTGGGGTCAAAAATGGAATTTGGGGAAGTTCGAGGGTAAAAATGTAATT
1 GTAATTTTT-GGAAAATCGGGGTCAAAAATGGAATTTGGGGAAGTTCAAGGGTAAAAATGTAATT
* *
12697 TTAAAAAGTTTAGGGTTAAAATGAAATTTTTGAAAGTTTAAGGGTAAAAAT
65 TTAAAAAG-TTAGGGTTAAAATGAAATTTTGGAAAGTTCAAGGGTAAAAAT
* *
12748 GTATTTTTTTGGAAAGTCCAGGGGTCAAAA
1 GTA-ATTTTTGGAAAAT-C-GGGGTCAAAA
12778 TATAATTTTG
Statistics
Matches: 124, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
112 5 0.04
113 9 0.07
114 52 0.42
115 6 0.05
116 37 0.30
117 5 0.04
118 10 0.08
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (114 bp):
GTAATTTTTGGAAAATCGGGGTCAAAAATGGAATTTGGGGAAGTTCAAGGGTAAAAATGTAATTT
TAAAAAGTTAGGGTTAAAATGAAATTTTGGAAAGTTCAAGGGTAAAAAT
Found at i:12755 original size:29 final size:28
Alignment explanation
Indices: 12680--12756 Score: 100
Period size: 28 Copynumber: 2.7 Consensus size: 28
12670 GGGAAGTTCG
*
12680 AGGGTAAAAATGTAATTTTAAAAAGTTT
1 AGGGTAAAAATGTAATTTTTAAAAGTTT
* * *
12708 AGGGTTAAAATGAAATTTTTGAAAGTTT
1 AGGGTAAAAATGTAATTTTTAAAAGTTT
*
12736 AAGGGTAAAAATGTATTTTTT
1 -AGGGTAAAAATGTAATTTTT
12757 TGGAAAGTCC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
28 24 0.59
29 17 0.41
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (28 bp):
AGGGTAAAAATGTAATTTTTAAAAGTTT
Found at i:13813 original size:16 final size:17
Alignment explanation
Indices: 13792--13823 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
13782 CTTCTTTTTG
13792 TTATTAATA-TTATTAA
1 TTATTAATATTTATTAA
13808 TTATTAATATTTATTA
1 TTATTAATATTTATTA
13824 CTGTTGTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATTAATATTTATTAA
Found at i:13844 original size:21 final size:21
Alignment explanation
Indices: 13818--13859 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
13808 TTATTAATAT
13818 TTATTACTGTTGTTACTATTA
1 TTATTACTGTTGTTACTATTA
*
13839 TTATTACTGTTGTTATTATTA
1 TTATTACTGTTGTTACTATTA
13860 ATAATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.07, G:0.10, T:0.60
Consensus pattern (21 bp):
TTATTACTGTTGTTACTATTA
Found at i:14648 original size:6 final size:6
Alignment explanation
Indices: 14637--14708 Score: 62
Period size: 6 Copynumber: 12.7 Consensus size: 6
14627 TATAATAACT
* * *
14637 TTTAAA TTTAAA TATAAA TCTAAA TTT-AT TTTAAA TTTAAA -TTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** *
14683 -ACAAA TTTAAA TTTAAA -ATAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA
14709 TATTCAAAAC
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
5 16 0.31
6 36 0.69
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:14681 original size:11 final size:11
Alignment explanation
Indices: 14637--14708 Score: 56
Period size: 11 Copynumber: 6.4 Consensus size: 11
14627 TATAATAACT
14637 TTTAAATTTAAA
1 TTTAAA-TTAAA
*
14649 TATAAATCTAAA
1 TTTAAAT-TAAA
**
14661 TTTATTTTAAA
1 TTTAAATTAAA
14672 TTTAAATTAAA
1 TTTAAATTAAA
**
14683 -ACAAATTTAAA
1 TTTAAA-TTAAA
*
14694 TTTAAAATAAA
1 TTTAAATTAAA
14705 TTTA
1 TTTA
14709 TATTCAAAAC
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
10 3 0.07
11 27 0.59
12 16 0.35
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:14696 original size:29 final size:29
Alignment explanation
Indices: 14636--14691 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
14626 TTATAATAAC
*
14636 TTTTAAATTTAAATATAAATCTAAATTTA
1 TTTTAAATTTAAATATAAAACTAAATTTA
14665 TTTTAAATTTAAAT-TAAAAC-AAATTTA
1 TTTTAAATTTAAATATAAAACTAAATTTA
14692 AATTTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 7 0.27
28 5 0.19
29 14 0.54
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (29 bp):
TTTTAAATTTAAATATAAAACTAAATTTA
Found at i:14698 original size:17 final size:17
Alignment explanation
Indices: 14637--14737 Score: 87
Period size: 17 Copynumber: 5.8 Consensus size: 17
14627 TATAATAACT
14637 TTTAAATTTAAATATAAA
1 TTTAAATTTAAA-ATAAA
* ***
14655 TCTAAATTTATTTTAAA
1 TTTAAATTTAAAATAAA
*
14672 TTTAAA-TTAAAACAAA
1 TTTAAATTTAAAATAAA
14688 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
14705 TTTATATTCAAAACTTAAA
1 TTTAAATTTAAAA--TAAA
* *
14724 ATAAAATTTAAAAT
1 TTTAAATTTAAAAT
14738 GAGTTTAGTT
Statistics
Matches: 64, Mismatches: 16, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
16 12 0.19
17 30 0.47
18 9 0.14
19 13 0.20
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:14734 original size:12 final size:12
Alignment explanation
Indices: 14691--14737 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
14681 AAACAAATTT
14691 AAATTTAAAAT-
1 AAATTTAAAATA
* *
14702 AAATTTATATTCA
1 AAATTTAAAAT-A
*
14715 AAACTTAAAATA
1 AAATTTAAAATA
14727 AAATTTAAAAT
1 AAATTTAAAAT
14738 GAGTTTAGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
11 9 0.32
12 11 0.39
13 8 0.29
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (12 bp):
AAATTTAAAATA
Found at i:15524 original size:108 final size:108
Alignment explanation
Indices: 15348--15556 Score: 355
Period size: 108 Copynumber: 1.9 Consensus size: 108
15338 CTTCTCAGTG
*
15348 TCTCATCAGGAAGCTAACCTTTTTATTGCTTCGCCCTACTTCTCAATATCTCATCAGGAAGCTGG
1 TCTCATCAGGAAGCTAACCTTTTTATTGCTTCGCCCTACTTCTCAATATCTCATCAGGAAGCTAG
**
15413 GGTTTGAAGATTTGTTCGCATTGAGTTGGTATACTTCTCTATA
66 GGTTCAAAGATTTGTTCGCATTGAGTTGGTATACTTCTCTATA
* * * *
15456 TCTCATCAGGAAGCTAACTTTTTTATTGCTTCGCCCTGCTTCTCAGTATCTCATCGGGAAGCTAG
1 TCTCATCAGGAAGCTAACCTTTTTATTGCTTCGCCCTACTTCTCAATATCTCATCAGGAAGCTAG
15521 GGTTCAAAGATTTGTTCGCATTGAGTTGGTATACTT
66 GGTTCAAAGATTTGTTCGCATTGAGTTGGTATACTT
15557 TTATGTATCT
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
108 94 1.00
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.38
Consensus pattern (108 bp):
TCTCATCAGGAAGCTAACCTTTTTATTGCTTCGCCCTACTTCTCAATATCTCATCAGGAAGCTAG
GGTTCAAAGATTTGTTCGCATTGAGTTGGTATACTTCTCTATA
Found at i:15702 original size:302 final size:305
Alignment explanation
Indices: 15135--15770 Score: 899
Period size: 302 Copynumber: 2.1 Consensus size: 305
15125 GAATTTGATC
*
15135 TACTTCTC-AGTATTTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTC
1 TACTTCTCTA-TATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTC
* * *
15199 ATCAGGAAACTGGGATTCGAAGATTTGCTCACATCGAGCCCTGAGTTGGTATACTTCTCTGTATC
65 ATCAGGAAACTGGGATTCAAAGATTTGCT---ATC-AGCACTGAGTTGGTATACTTCTATGTATC
* ** *
15264 TCATCAAGAAGATAACCGCCCCGTTTGTTTCAATTCGCTTCTCTATACCTCATCAGAAAGACGAA
126 TAATCAAGAAGATAACCGCCCCACTTGTTTCAATTCGCTTCTCTATACCTCATCAGAAAGACAAA
* *
15329 TTTGGTCCACTTCTCAGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTTCGCCCTACTTCTCAA
191 TTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTTATTGCTTCGCCCTACTTCTCAA
* **
15394 TATCTCATCAGGAAGCTGGGGTTTGAAGATTTGTTCGCA-TTGAGTTGGTA
256 TATCTCATCAGG-AGCTGGGGTTCGAAGATTTGTTCGCATTTGAGTTGACA
** *
15444 TACTTCTCTATATCTCATCAGGAAGCTAACTTTTTTATTGCTTCGCCCTGCTTCTCAGTATCTCA
1 TACTTCTCTATATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCA
* * * *
15509 TCGGGAAGCTAGGG-TTCAAAGATTTG-T-TC-GCATTGAGTTGGTATACTTTTATGTATCTAAT
66 TCAGGAAACT-GGGATTCAAAGATTTGCTATCAGCACTGAGTTGGTATACTTCTATGTATCTAAT
* * * * *
15570 CAAGAAGATGATCGCCTCACTTGTTTCAATTCGCTTCTCTGTACCTCATCAGGAAGACAAATTTG
130 CAAGAAGATAACCGCCCCACTTGTTTCAATTCGCTTCTCTATACCTCATCAGAAAGACAAATTTG
* *
15635 GTCCACTTCTCAGTATCTTATCAAGAAGCTAACCTTTTTATTGCTTCGCCCTTCTTCT-AAGTAT
195 GTCCACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTTATTGCTTCGCCCTACTTCTCAA-TAT
15699 CTCATCAGGAGCTGGGGTTCGAAGATTTGTTCGCATTTGAGTTGACA
259 CTCATCAGGAGCTGGGGTTCGAAGATTTGTTCGCATTTGAGTTGACA
*
15746 TACTTCTCTGTATCTCATCAGGAAG
1 TACTTCTCTATATCTCATCAGGAAG
15771 ATGACCGCCT
Statistics
Matches: 295, Mismatches: 28, Indels: 15
0.87 0.08 0.04
Matches are distributed among these distances:
301 27 0.09
302 183 0.62
304 2 0.01
308 1 0.00
309 78 0.26
310 4 0.01
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (305 bp):
TACTTCTCTATATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCA
TCAGGAAACTGGGATTCAAAGATTTGCTATCAGCACTGAGTTGGTATACTTCTATGTATCTAATC
AAGAAGATAACCGCCCCACTTGTTTCAATTCGCTTCTCTATACCTCATCAGAAAGACAAATTTGG
TCCACTTCTCAGTATCTCATCAAGAAGCTAACCTTTTTATTGCTTCGCCCTACTTCTCAATATCT
CATCAGGAGCTGGGGTTCGAAGATTTGTTCGCATTTGAGTTGACA
Found at i:15774 original size:194 final size:193
Alignment explanation
Indices: 15445--15990 Score: 722
Period size: 194 Copynumber: 2.8 Consensus size: 193
15435 GAGTTGGTAT
* *
15445 ACTTCTCTA-TATCTCATCAGGAAGCTAACTTTTTTATTGCTTCGCCCTGCTTCTCAGTATCTCA
1 ACTTCTC-AGTATCTCATCAGGAAGCTAACATTTTTATTGCTTCGCCCTTCTTCTCAGTATCTCA
* * * * * * *
15509 TCGGGAAGCTAGGGTTCAAAGATTTGTTCGCATTGAGTTGGTATACTTTTATGTATCTAATCAAG
65 TCAGG-AGCTGGGGTTCGAAGATTTGTTCGCATTGAGTTGGTATACTTCTCTGTATCTCATCAGG
* *
15574 AAGATGATCGCCTCACTTGTTTCAATTCGCTTCTCTGTACCTCATCAGGAAGACAAATTTGGTCC
129 AAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTGTACCTCATCAGGAAGACAAATTTGGTCC
* * * *
15639 ACTTCTCAGTATCTTATCAAGAAGCTAACCTTTTTATTGCTTCGCCCTTCTTCTAAGTATCTCAT
1 ACTTCTCAGTATCTCATCAGGAAGCTAACATTTTTATTGCTTCGCCCTTCTTCTCAGTATCTCAT
**
15704 CAGGAGCTGGGGTTCGAAGATTTGTTCGCATTTGAGTTGACATACTTCTCTGTATCTCATCAGGA
66 CAGGAGCTGGGGTTCGAAGATTTGTTCGCA-TTGAGTTGGTATACTTCTCTGTATCTCATCAGGA
* *
15769 AGATGACCGCCTCACTTGTTTCAATCCGCTTCTTTGTACCTCATCAGGAAGACGAATTTGGTCC
130 AGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTGTACCTCATCAGGAAGACAAATTTGGTCC
*
15833 ACTTCTCCGTATCTCATCAGGAAGCTAACATTTTTATTGCTTCG-CCTTGCTTCTCAGTATCTCA
1 ACTTCTCAGTATCTCATCAGGAAGCTAACATTTTTATTGCTTCGCCCTT-CTTCTCAGTATCTCA
* * *
15897 TCAAGAAGCTGGGGGTTCGAAGATTTGCTCATATTGAACCTTGAGTTGGTATACTTCTCTGTATC
65 TC-AGGAGCT-GGGGTTCGAAGATTTG----T-TCG--CATTGAGTTGGTATACTTCTCTGTATC
*
15962 TCATCAGGAAGACT-ACCGCTTCAC-TGTTT
121 TCATCAGGAAGA-TGACCGCCTCACTTGTTT
15991 GTGGATAATC
Statistics
Matches: 310, Mismatches: 29, Indels: 19
0.87 0.08 0.05
Matches are distributed among these distances:
193 29 0.09
194 205 0.66
195 6 0.02
196 16 0.05
200 1 0.00
201 7 0.02
202 44 0.14
203 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (193 bp):
ACTTCTCAGTATCTCATCAGGAAGCTAACATTTTTATTGCTTCGCCCTTCTTCTCAGTATCTCAT
CAGGAGCTGGGGTTCGAAGATTTGTTCGCATTGAGTTGGTATACTTCTCTGTATCTCATCAGGAA
GATGACCGCCTCACTTGTTTCAATCCGCTTCTCTGTACCTCATCAGGAAGACAAATTTGGTCC
Found at i:16163 original size:38 final size:39
Alignment explanation
Indices: 16121--16263 Score: 148
Period size: 39 Copynumber: 3.7 Consensus size: 39
16111 GTTGACGATG
*
16121 ATCTGTCCCA-GCTCAGGGTAAAAGATCAAATGGCTACA
1 ATCTGCCCCAGGCTCAGGGTAAAAGATCAAATGGCTACA
* *** * * *
16159 ATCTGCCCCAAGCTCAGGGTAAAAGAT-TGGTTGATGATA
1 ATCTGCCCCAGGCTCAGGGTAAAAGATCAAATGGCT-ACA
*
16198 ATCTGCCCCAGGCTC-GAGGTAAAAGATCAAATGGCTTCA
1 ATCTGCCCCAGGCTCAG-GGTAAAAGATCAAATGGCTACA
* *
16237 ATTTGCCCCAGGCTCAGGGTAAGAGAT
1 ATCTGCCCCAGGCTCAGGGTAAAAGAT
16264 TGGTTGACAA
Statistics
Matches: 83, Mismatches: 17, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
38 13 0.16
39 66 0.80
40 4 0.05
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.22
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCAGGGTAAAAGATCAAATGGCTACA
Found at i:16244 original size:78 final size:77
Alignment explanation
Indices: 16027--16271 Score: 266
Period size: 78 Copynumber: 3.2 Consensus size: 77
16017 TCGGGGTAGG
* * * *
16027 AGATTGGTTGACGGTGATCTGCCCCAAGCTCGGGGTAAGATATTC-AATGGCTGT-AATCTGCCC
1 AGATTGGTTGACGATGATCTGCCCC-AGCTCGAGGTAAAAGA-TCAAATGGCT-TCAATCTGCCC
**
16090 CTTGCTC-GAGGTAAGA
63 CAAGCTCAG-GGTAA-A
* * *
16106 A-ATTAGTTGACGATGATCTGTCCCAGCTC-AGGGTAAAAGATCAAATGGCTACAATCTGCCCCA
1 AGATTGGTTGACGATGATCTGCCCCAGCTCGA-GGTAAAAGATCAAATGGCTTCAATCTGCCCCA
16169 AGCTCAGGGTAAA
65 AGCTCAGGGTAAA
* * *
16182 AGATTGGTTGATGATAATCTGCCCCAGGCTCGAGGTAAAAGATCAAATGGCTTCAATTTGCCCCA
1 AGATTGGTTGACGATGATCTGCCCCA-GCTCGAGGTAAAAGATCAAATGGCTTCAATCTGCCCCA
* *
16247 GGCTCAGGGTAAG
65 AGCTCAGGGTAAA
16260 AGATTGGTTGAC
1 AGATTGGTTGAC
16272 AATGTAACTT
Statistics
Matches: 141, Mismatches: 18, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
76 4 0.03
77 58 0.41
78 77 0.55
79 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.25
Consensus pattern (77 bp):
AGATTGGTTGACGATGATCTGCCCCAGCTCGAGGTAAAAGATCAAATGGCTTCAATCTGCCCCAA
GCTCAGGGTAAA
Found at i:16803 original size:100 final size:100
Alignment explanation
Indices: 16620--17106 Score: 302
Period size: 100 Copynumber: 4.9 Consensus size: 100
16610 GTATCGGTTT
* * * *** * * ** *
16620 CGCCATTGCGACTTAAATCTTTCCCCTTCAAATCTTCGGGGTACTGGATTAGCCGTTAC-AACTT
1 CGCCGTTGCGACTTAAATATTTCCCTTTTGTATCTTTGTGGTACTGGATCCGCCGTTACGGA-TT
* * * *
16684 AAAACTTTCCCTTCCTGTCTTCTGA-GGTACACGG-TC
65 AGATCTTTCCCTTCATGTCTTCT-ATGGTA-ATGGATC
*
16720 CGCCGTTGCGAC-TAAACT-TTTCCCTTTTGTATCTTTGTGATACTGGATCCGCCGTTACGGTAT
1 CGCCGTTGCGACTTAAA-TATTTCCCTTTTGTATCTTTGTGGTACTGGATCCGCCGTTACGG-AT
* *
16783 TAGATCTTTCCCTTCATGTCTTC-ATGGTATTGGATT
64 TAGATCTTTCCCTTCATGTCTTCTATGGTAATGGATC
* * * * * *
16819 CGCCATTGCGGCTTAAATATTTCCCTTTT-TGTCTTCTGAGGTACATGG-TCCGCCATTGC-GAC
1 CGCCGTTGCGACTTAAATATTTCCCTTTTGTATCTT-TGTGGTAC-TGGATCCGCCGTTACGGA-
* *
16881 TTAGACCTTTCCCTT-TTGTATCTT-TATGGTAATGGATC
63 TTAGATCTTTCCCTTCATG--TCTTCTATGGTAATGGATC
* * * * * ** ** * * *
16919 TGCCGTTGCGGTCTTAGATCTTTCCCTTCATG--TCTTCATGGTACTGGATTGGCCGTTGCAGCT
1 CGCCGTTGC-GACTTAAATATTTCCCTT-TTGTATCTTTGTGGTACTGGATCCGCCGTTACGGAT
* * *
16982 TAAATCTGTCCCTTCGTGTCTTCTGA-GGTACATGG-TC
64 TAGATCTTTCCCTTCATGTCTTCT-ATGGTA-ATGGATC
* * ** *
17019 CTACCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTGTGGTACTGGATCCGCCGTTACGGTCT
1 C-GCCGTTGCGACTTAAATATTTCCCTTTTGTATCTTTGTGGTACTGGATCCGCCGTTACGG-AT
*
17084 TAGATCTTTCCCTTCATATCTTC
64 TAGATCTTTCCCTTCATGTCTTC
17107 ATGTTACTGA
Statistics
Matches: 301, Mismatches: 60, Indels: 50
0.73 0.15 0.12
Matches are distributed among these distances:
98 6 0.02
99 80 0.27
100 132 0.44
101 61 0.20
102 22 0.07
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.39
Consensus pattern (100 bp):
CGCCGTTGCGACTTAAATATTTCCCTTTTGTATCTTTGTGGTACTGGATCCGCCGTTACGGATTA
GATCTTTCCCTTCATGTCTTCTATGGTAATGGATC
Found at i:16892 original size:50 final size:51
Alignment explanation
Indices: 16620--17098 Score: 261
Period size: 50 Copynumber: 9.5 Consensus size: 51
16610 GTATCGGTTT
* * *** * *
16620 CGCCATTGCGACTTAAATCTTTCCCCTTCAAATCTTC-GGGGTAC-TGGATT
1 CGCCGTTGCGACTTAGATCTTT-CCCTTCTTGTCTTCTGAGGTACATGGATC
* * * * * * *
16670 AGCCGTTACAACTTAAAACTTTCCCTTCCTGTCTTCTGAGGTACACGG-TC
1 CGCCGTTGCGACTTAGATCTTTCCCTTCTTGTCTTCTGAGGTACATGGATC
* * *
16720 CGCCGTTGCGAC-TA-AACTTTTCCCTT-TTGTATCTT-TGTGATAC-TGGATC
1 CGCCGTTGCGACTTAGATC-TTTCCCTTCTTG--TCTTCTGAGGTACATGGATC
* * * *
16769 CGCCGTTACGGTA-TTAGATCTTTCCCTTCATGTCTTC--ATGGTA-TTGGATT
1 CGCCGTTGC-G-ACTTAGATCTTTCCCTTCTTGTCTTCTGA-GGTACATGGATC
* * * * *
16819 CGCCATTGCGGCTTAAATATTTCCCTTTTTGTCTTCTGAGGTACATGG-TC
1 CGCCGTTGCGACTTAGATCTTTCCCTTCTTGTCTTCTGAGGTACATGGATC
* *
16869 CGCCATTGCGACTTAGACCTTTCCCTT-TTGTATCTT-T-ATGGTA-ATGGATC
1 CGCCGTTGCGACTTAGATCTTTCCCTTCTTG--TCTTCTGA-GGTACATGGATC
* * * *
16919 TGCCGTTGCGGTCTTAGATCTTTCCCTTCATGTCTTC--ATGGTAC-TGGATT
1 CGCCGTTGC-GACTTAGATCTTTCCCTTCTTGTCTTCTGA-GGTACATGGATC
* * * *
16969 GGCCGTTGC-AGCTTAAATCTGTCCCTTCGTGTCTTCTGAGGTACATGG-TC
1 CGCCGTTGCGA-CTTAGATCTTTCCCTTCTTGTCTTCTGAGGTACATGGATC
* * *
17019 CTACCGTTGCGACTTAGACCTTTCCCTT-TTGTATCTT-TGTGGTAC-TGGATC
1 C-GCCGTTGCGACTTAGATCTTTCCCTTCTTG--TCTTCTGAGGTACATGGATC
* *
17070 CGCCGTTACGGTCTTAGATCTTTCCCTTC
1 CGCCGTTGC-GACTTAGATCTTTCCCTTC
17099 ATATCTTCAT
Statistics
Matches: 332, Mismatches: 60, Indels: 72
0.72 0.13 0.16
Matches are distributed among these distances:
48 7 0.02
49 88 0.27
50 139 0.42
51 87 0.26
52 11 0.03
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.38
Consensus pattern (51 bp):
CGCCGTTGCGACTTAGATCTTTCCCTTCTTGTCTTCTGAGGTACATGGATC
Found at i:16954 original size:150 final size:150
Alignment explanation
Indices: 16631--17115 Score: 650
Period size: 150 Copynumber: 3.2 Consensus size: 150
16621 GCCATTGCGA
* ** ** * * * *
16631 CTTAAATCTTTCCCCTTCAAATCTTCGGGGTACTGGATTAGCCGTTACAACTTAAA-ACTTTCCC
1 CTTAGATCTTT-CCCTTCATGTCTTCATGGTACTGGATTCGCCATTGCAGCTTAAATA-TTTCCC
* * *
16695 TTCCTGTCTTCTGAGGTACACGGTCCGCCGTTGCGAC-TAAACTTTTCCCTTTTGTATCTTTGTG
64 TTCCTGTCTTCTGAGGTACATGGTCCGCCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTGTG
*
16759 ATACTGGATCCGCCGTTACGGT
129 GTACTGGATCCGCCGTTACGGT
* * *
16781 ATTAGATCTTTCCCTTCATGTCTTCATGGTATTGGATTCGCCATTGCGGCTTAAATATTTCCCTT
1 CTTAGATCTTTCCCTTCATGTCTTCATGGTACTGGATTCGCCATTGCAGCTTAAATATTTCCCTT
** * *
16846 TTTGTCTTCTGAGGTACATGGTCCGCCATTGCGACTTAGACCTTTCCCTTTTGTATCTTTATGGT
66 CCTGTCTTCTGAGGTACATGGTCCGCCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTGTGGT
* * *
16911 AATGGATCTGCCGTTGCGGT
131 ACTGGATCCGCCGTTACGGT
* * * *
16931 CTTAGATCTTTCCCTTCATGTCTTCATGGTACTGGATTGGCCGTTGCAGCTTAAATCTGTCCCTT
1 CTTAGATCTTTCCCTTCATGTCTTCATGGTACTGGATTCGCCATTGCAGCTTAAATATTTCCCTT
* *
16996 CGTGTCTTCTGAGGTACATGGTCCTACCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTGTGG
66 CCTGTCTTCTGAGGTACATGGTCC-GCCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTGTGG
17061 TACTGGATCCGCCGTTACGGT
130 TACTGGATCCGCCGTTACGGT
* *
17082 CTTAGATCTTTCCCTTCATATCTTCATGTTACTG
1 CTTAGATCTTTCCCTTCATGTCTTCATGGTACTG
17116 AGACCTGTAA
Statistics
Matches: 292, Mismatches: 40, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
149 73 0.25
150 132 0.45
151 87 0.30
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.39
Consensus pattern (150 bp):
CTTAGATCTTTCCCTTCATGTCTTCATGGTACTGGATTCGCCATTGCAGCTTAAATATTTCCCTT
CCTGTCTTCTGAGGTACATGGTCCGCCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTGTGGT
ACTGGATCCGCCGTTACGGT
Found at i:17115 original size:50 final size:50
Alignment explanation
Indices: 16760--17115 Score: 264
Period size: 50 Copynumber: 7.1 Consensus size: 50
16750 ATCTTTGTGA
* *
16760 TACTGGATCCGCCGTTACGGTATTAGATCTTTCCCTTCATGTCTTCATGG
1 TACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCATGTCTTCATGG
* * * * * **
16810 TATTGGATTCGCCATTGCGG-CTTAAATATTTCCCTTTTTGTCTTC-TGAGG
1 TACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCATGTCTTCAT--GG
* * * * *
16860 TACATGG-TCCGCCATTGC-GACTTAGACCTTTCCCTT-TTGTATCTTTATGG
1 TAC-TGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCATG--TCTTCATGG
* *
16910 TAATGGATCTGCCGTTGCGGTCTTAGATCTTTCCCTTCATGTCTTCATGG
1 TACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCATGTCTTCATGG
** * * * *
16960 TACTGGATTGGCCGTTGCAG-CTTAAATCTGTCCCTTCGTGTCTTC-TGAGG
1 TACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCATGTCTTCAT--GG
* * * * **
17010 TACATGG-TCCTACCGTTGC-GACTTAGACCTTTCCCTT-TTGTATCTTTGTGG
1 TAC-TGGATCC-GCCGTTGCGGTCTTAGATCTTTCCCTTCATG--TCTTCATGG
* * *
17061 TACTGGATCCGCCGTTACGGTCTTAGATCTTTCCCTTCATATCTTCATGT
1 TACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCATGTCTTCATGG
17111 TACTG
1 TACTG
17116 AGACCTGTAA
Statistics
Matches: 239, Mismatches: 46, Indels: 42
0.73 0.14 0.13
Matches are distributed among these distances:
48 2 0.01
49 49 0.21
50 109 0.46
51 70 0.29
52 8 0.03
53 1 0.00
ACGTcount: A:0.15, C:0.25, G:0.20, T:0.40
Consensus pattern (50 bp):
TACTGGATCCGCCGTTGCGGTCTTAGATCTTTCCCTTCATGTCTTCATGG
Found at i:23890 original size:29 final size:30
Alignment explanation
Indices: 23858--24110 Score: 111
Period size: 29 Copynumber: 8.6 Consensus size: 30
23848 AGAAGTGCGG
*
23858 GGGT-AAAATGGTAATTTTTGGAAAAATCT
1 GGGTAAAAATGGTAATTTTTGGAAAAATCA
* * ** *
23887 GGGTCAAAAAT-GAAATTTTTTG-AAGTTTA
1 GGGT-AAAAATGGTAATTTTTGGAAAAATCA
* * *
23916 GGGGT-AAAGTTGTAATTTTTGGAAGAATCA
1 -GGGTAAAAATGGTAATTTTTGGAAAAATCA
* **
23946 AGGTAAAAAATGG-AATTTTTGG-AAGTTCGA
1 GGGT-AAAAATGGTAATTTTTGGAAAAATC-A
*
23976 GGGT-AAAATGGTAATTTTTGGAAAAAT-T
1 GGGTAAAAATGGTAATTTTTGGAAAAATCA
* * ** *
24004 GAGGTCAAAATGG-AA-TTTTGCAAAGTTTGA
1 G-GGTAAAAATGGTAATTTTTGGAAA-AATCA
* * *
24034 GGGTAAGAAT-GTAATTTTTGGGAAAATTA
1 GGGTAAAAATGGTAATTTTTGGAAAAATCA
* * **
24063 GGGTCAAAAATGG-AA-TTTAGGGAAGTTCGA
1 GGGT-AAAAATGGTAATTTTTGGAAAAATC-A
24093 GGGTAAAAAT-GTAATTTT
1 GGGTAAAAATGGTAATTTT
24111 AAAAAAGTTT
Statistics
Matches: 164, Mismatches: 39, Indels: 41
0.67 0.16 0.17
Matches are distributed among these distances:
28 22 0.13
29 69 0.42
30 62 0.38
31 11 0.07
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (30 bp):
GGGTAAAAATGGTAATTTTTGGAAAAATCA
Found at i:23965 original size:30 final size:28
Alignment explanation
Indices: 23929--24022 Score: 91
Period size: 30 Copynumber: 3.2 Consensus size: 28
23919 GTAAAGTTGT
23929 AATTTTTGGAAGAATCAAGGTAAAAAATGG
1 AATTTTTGGAAGAATCAAGGT--AAAATGG
* *
23959 AATTTTTGGAAG-TTCGAGGGTAAAATGG
1 AATTTTTGGAAGAATC-AAGGTAAAATGG
* **
23987 TAATTTTTGGAAAAATTGAGGTCAAAATGG
1 -AATTTTTGGAAGAATCAAGGT-AAAATGG
24017 AATTTT
1 AATTTT
24023 GCAAAGTTTG
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
28 7 0.13
29 22 0.42
30 24 0.45
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.33
Consensus pattern (28 bp):
AATTTTTGGAAGAATCAAGGTAAAATGG
Found at i:24087 original size:117 final size:115
Alignment explanation
Indices: 23798--24188 Score: 362
Period size: 117 Copynumber: 3.3 Consensus size: 115
23788 TAGACATCAG
* * * * * *** * *
23798 GGGTAAAATGGTGATTTTTGGAAAAAATCGAGGTCAAAAATAGAGTTTTTAGAAGTGCGGGGGTA
1 GGGTAAAAT-GTAATTTTTGG-AAAATTAG-GGTCAAAAATGGAATTTAGGGAAGTTCGAGGGTA
* ***
23863 AAATGGTAATTTTTGGAAAAATCTGGGTCAAAAATGAAATTTTTTGAAGTTT-A
63 AAATGGTAATTTTTGGAAAAAT-TGGGTCAAAAATGGAATTTTGCAAAGTTTGA
* * * * **
23916 GGGGTAAAGTTGTAATTTTTGGAAGAATCAAGGTAAAAAATGGAATTTTTGGAAGTTCGAGGGTA
1 -GGGTAAA-ATGTAATTTTTGGAA-AATTAGGGTCAAAAATGGAATTTAGGGAAGTTCGAGGGTA
23981 AAATGGTAATTTTTGGAAAAATTGAGGTC-AAAATGGAATTTTGCAAAGTTTGA
63 AAATGGTAATTTTTGGAAAAATTG-GGTCAAAAATGGAATTTTGCAAAGTTTGA
24034 GGGTAAGAATGTAATTTTTGGGAAAATTAGGGTCAAAAATGGAATTTAGGGAAGTTCGAGGGTAA
1 GGGTAA-AATGTAATTTTT-GGAAAATTAGGGTCAAAAATGGAATTTAGGGAAGTTCGAGGGT-A
* * * *
24099 AAAT-GTAA-TTTT-AAAAAAGTTTGGGGTCAAAAATGGAATTTTGGAATGTTTGT
63 AAATGGTAATTTTTGGAAAAA--TT-GGGTCAAAAATGGAATTTTGCAAAGTTTGA
* *
24152 GGGTAAAAATGT-ATTTTTAGAAAGTTTAGGGTCAAAA
1 GGGT-AAAATGTAATTTTTGGAAA-ATTAGGGTCAAAA
24189 TATAATTTTA
Statistics
Matches: 231, Mismatches: 28, Indels: 28
0.80 0.10 0.10
Matches are distributed among these distances:
115 5 0.02
116 8 0.03
117 98 0.42
118 98 0.42
119 21 0.09
120 1 0.00
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.32
Consensus pattern (115 bp):
GGGTAAAATGTAATTTTTGGAAAATTAGGGTCAAAAATGGAATTTAGGGAAGTTCGAGGGTAAAA
TGGTAATTTTTGGAAAAATTGGGTCAAAAATGGAATTTTGCAAAGTTTGA
Found at i:24125 original size:29 final size:29
Alignment explanation
Indices: 24093--24200 Score: 103
Period size: 29 Copynumber: 3.7 Consensus size: 29
24083 GGAAGTTCGA
24093 GGGTAAAAATGTAATTTTAAAAAAGTTTG
1 GGGTAAAAATGTAATTTTAAAAAAGTTTG
* ** *
24122 GGGTCAAAAATGGAATTTT-GGAATGTTTG
1 GGGT-AAAAATGTAATTTTAAAAAAGTTTG
* * *
24151 TGGGTAAAAATGT-ATTTTTAGAAAGTTTA
1 -GGGTAAAAATGTAATTTTAAAAAAGTTTG
* *
24180 GGGTCAAAATATAATTTTAAA
1 GGGTAAAAATGTAATTTTAAA
24201 GAGTTTAGGG
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
28 15 0.24
29 31 0.49
30 17 0.27
ACGTcount: A:0.40, C:0.02, G:0.22, T:0.36
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTAAAAAAGTTTG
Found at i:24140 original size:30 final size:31
Alignment explanation
Indices: 23951--24188 Score: 132
Period size: 29 Copynumber: 8.1 Consensus size: 31
23941 AATCAAGGTA
* * *
23951 AAAAATGGAATTTT-TGGAAGTTCGAGGGT-
1 AAAAATGGAATTTTAAGAAAGTTTGAGGGTC
** **
23980 -AAAATGGTAATTTTTGGAAAAATTGA-GGTC
1 AAAAATGG-AATTTTAAGAAAGTTTGAGGGTC
24010 -AAAATGGAATTTT--GCAAAGTTTGAGGGT-
1 AAAAATGGAATTTTAAG-AAAGTTTGAGGGTC
* * ** *
24038 AAGAATGTAATTTTTGGGAAA-ATT-AGGGTC
1 AAAAATGGAA-TTTTAAGAAAGTTTGAGGGTC
* * *
24068 AAAAATGGAA-TTTAGGGAAGTTCGAGGGT-
1 AAAAATGGAATTTTAAGAAAGTTTGAGGGTC
* *
24097 AAAAATGTAATTTTAAAAAAGTTTG-GGGTC
1 AAAAATGGAATTTTAAGAAAGTTTGAGGGTC
* * *
24127 AAAAATGGAATTTT-GGAATGTTTGTGGGT-
1 AAAAATGGAATTTTAAGAAAGTTTGAGGGTC
* *
24156 AAAAAT-GTATTTTTAGAAAGTTT-AGGGTC
1 AAAAATGGAATTTTAAGAAAGTTTGAGGGTC
24185 AAAA
1 AAAA
24189 TATAATTTTA
Statistics
Matches: 163, Mismatches: 29, Indels: 34
0.72 0.13 0.15
Matches are distributed among these distances:
27 1 0.01
28 31 0.19
29 68 0.42
30 59 0.36
31 3 0.02
32 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.32
Consensus pattern (31 bp):
AAAAATGGAATTTTAAGAAAGTTTGAGGGTC
Found at i:24156 original size:59 final size:58
Alignment explanation
Indices: 23798--24188 Score: 316
Period size: 59 Copynumber: 6.7 Consensus size: 58
23788 TAGACATCAG
* * * * * * * *
23798 GGGT-AAAATGGTGATTTTTGGAAAAAATCGAGGTCAAAAATAGAGTTTTTAGAAGTGCGG
1 GGGTAAAAAT-GTAATTTTTGGAAAAATTAG-GGTCAAAAATGGA-ATTTTGGAAGTTCGA
* * *
23858 GGGT-AAAATGGTAATTTTTGGAAAAATCT-GGGTCAAAAATGAAATTTTTTGAAGTT-TA
1 GGGTAAAAAT-GTAATTTTTGGAAAAAT-TAGGGTCAAAAATGGAA-TTTTGGAAGTTCGA
** * * * *
23916 GGGGTAAAGTTGTAATTTTTGGAAGAATCAAGGTAAAAAATGGAATTTTTGGAAGTTCGA
1 -GGGTAAAAATGTAATTTTTGGAAAAATTAGGGTCAAAAATGGAA-TTTTGGAAGTTCGA
* *
23976 GGGT-AAAATGGTAATTTTTGGAAAAATT-GAGGTC-AAAATGGAATTTTGCAAAGTTTGA
1 GGGTAAAAAT-GTAATTTTTGGAAAAATTAG-GGTCAAAAATGGAATTTTG-GAAGTTCGA
* * *
24034 GGGTAAGAATGTAATTTTTGGGAAAATTAGGGTCAAAAATGGAATTTAGGGAAGTTCGA
1 GGGTAAAAATGTAATTTTTGGAAAAATTAGGGTCAAAAATGGAATTT-TGGAAGTTCGA
* * * *
24093 GGGTAAAAATGTAA-TTTT-AAAAAAGTTTGGGGTCAAAAATGGAATTTTGGAATGTTTGT
1 GGGTAAAAATGTAATTTTTGGAAAAA--TTAGGGTCAAAAATGGAATTTTGGAA-GTTCGA
* **
24152 GGGTAAAAATGT-ATTTTTAGAAAGTTTAGGGTCAAAA
1 GGGTAAAAATGTAATTTTTGGAAAAATTAGGGTCAAAA
24189 TATAATTTTA
Statistics
Matches: 271, Mismatches: 42, Indels: 38
0.77 0.12 0.11
Matches are distributed among these distances:
57 9 0.03
58 64 0.24
59 163 0.60
60 34 0.13
61 1 0.00
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.32
Consensus pattern (58 bp):
GGGTAAAAATGTAATTTTTGGAAAAATTAGGGTCAAAAATGGAATTTTGGAAGTTCGA
Found at i:25228 original size:16 final size:16
Alignment explanation
Indices: 25193--25231 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
25183 CTTCTTTTTG
**
25193 TTATTAATATTAATGT
1 TTATTAATATTAATAA
*
25209 TTATTAATATTATTAA
1 TTATTAATATTAATAA
25225 TTATTAA
1 TTATTAA
25232 AATTTATTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
TTATTAATATTAATAA
Found at i:25261 original size:21 final size:21
Alignment explanation
Indices: 25235--25276 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
25225 TTATTAAAAT
25235 TTATTACTGCTGTTACTATTA
1 TTATTACTGCTGTTACTATTA
* *
25256 TTATTACTGTTGTTATTATTA
1 TTATTACTGCTGTTACTATTA
25277 ATAATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.57
Consensus pattern (21 bp):
TTATTACTGCTGTTACTATTA
Found at i:26109 original size:7 final size:6
Alignment explanation
Indices: 26062--26153 Score: 66
Period size: 6 Copynumber: 15.8 Consensus size: 6
26052 ATAATAAGAT
* * *
26062 TTTAAA TTTAAA TATAAA TCTAAA TTTATA -TTAAA TTTAAA TTTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA
** * * * *
26110 -ACAAA TTTAAA TTTAAA -ATAAA TTTATA TTCAAA -ATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
26154 CCTTAAAATA
Statistics
Matches: 64, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
5 14 0.22
6 44 0.69
7 6 0.09
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:26115 original size:29 final size:29
Alignment explanation
Indices: 26063--26118 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
26053 TAATAAGATT
*
26063 TTAAATTTAAATATAAATCTAAATTTATA
1 TTAAATTTAAATATAAAACTAAATTTATA
*
26092 TTAAATTTAAATTTTAAAAC-AAATTTA
1 TTAAATTTAAA-TATAAAACTAAATTTA
26119 AATTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (29 bp):
TTAAATTTAAATATAAAACTAAATTTATA
Found at i:26144 original size:17 final size:17
Alignment explanation
Indices: 26048--26168 Score: 116
Period size: 17 Copynumber: 6.9 Consensus size: 17
26038 GACTTTCAAT
*
26048 ATTTATAATAAGATTTTAA
1 ATTTAAAATAA-A-TTTAA
*
26067 ATTTAAATATAAATCTAA
1 ATTTAAA-ATAAATTTAA
* *
26085 ATTTATATTAAATTTAA
1 ATTTAAAATAAATTTAA
*
26102 ATTTTAAAACAAATTTAA
1 A-TTTAAAATAAATTTAA
*
26120 ATTTAAAATAAATTTAT
1 ATTTAAAATAAATTTAA
*
26137 ATTCAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
** *
26154 CCTTAAAATATATTT
1 ATTTAAAATAAATTT
26169 TAAAATGAGT
Statistics
Matches: 84, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
17 49 0.58
18 24 0.29
19 7 0.08
20 4 0.05
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:26160 original size:34 final size:35
Alignment explanation
Indices: 26062--26168 Score: 92
Period size: 35 Copynumber: 3.1 Consensus size: 35
26052 ATAATAAGAT
* * * * *
26062 TTTAAATTT-AAATATAAATCTAAATTTATATTAAA
1 TTTAAATTTCAAA-ACAAATTTAAACTTAAAATAAA
* *
26097 TTTAAATTTTAAAACAAATTTAAATTTAAAATAAA
1 TTTAAATTTCAAAACAAATTTAAACTTAAAATAAA
* * * *
26132 TTTATA-TTCAAAATAAATTTAACCTTAAAATATA
1 TTTAAATTTCAAAACAAATTTAAACTTAAAATAAA
26166 TTT
1 TTT
26169 TAAAATGAGT
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 26 0.43
35 32 0.52
36 3 0.05
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (35 bp):
TTTAAATTTCAAAACAAATTTAAACTTAAAATAAA
Found at i:30535 original size:29 final size:30
Alignment explanation
Indices: 30486--30557 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 30
30476 TAACCAAAAA
30486 ATAATTAAAAAATAATAAAAAT-TATT-AAATT
1 ATAATT-AAAAAT-ATAAAAATGT-TTAAAATT
30517 ATAATTAAAAATATAAAAATGTTTAAAATT
1 ATAATTAAAAATATAAAAATGTTTAAAATT
30547 -T-ATTAAAAATA
1 ATAATTAAAAATA
30558 ATTAAAAAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
28 10 0.26
29 11 0.28
30 12 0.31
31 6 0.15
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (30 bp):
ATAATTAAAAATATAAAAATGTTTAAAATT
Found at i:30565 original size:10 final size:10
Alignment explanation
Indices: 30482--30565 Score: 75
Period size: 10 Copynumber: 8.5 Consensus size: 10
30472 CATGTAACCA
30482 AAAAATAATT
1 AAAAATAATT
30492 AAAAAATAA-T
1 -AAAAATAATT
*
30502 AAAAATTATT
1 AAAAATAATT
*
30512 AAATTATAATT
1 AAA-AATAATT
30523 AAAAAT-A-T
1 AAAAATAATT
**
30531 AAAAATGTTT
1 AAAAATAATT
* *
30541 AAAATTTATT
1 AAAAATAATT
30551 AAAAATAATT
1 AAAAATAATT
30561 AAAAA
1 AAAAA
30566 ACCAAAAGAA
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
8 7 0.12
9 8 0.14
10 28 0.47
11 16 0.27
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (10 bp):
AAAAATAATT
Found at i:30566 original size:11 final size:11
Alignment explanation
Indices: 30481--30532 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
30471 ACATGTAACC
30481 AAAAAATAATT
1 AAAAAATAATT
30492 AAAAAATAA-T
1 AAAAAATAATT
*
30502 -AAAAATTATT
1 AAAAAATAATT
**
30512 AAATTATAATT
1 AAAAAATAATT
30523 AAAAATATAA
1 AAAAA-ATAA
30533 AAATGTTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
9 7 0.22
10 2 0.06
11 19 0.59
12 4 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAAAATAATT
Found at i:30754 original size:19 final size:19
Alignment explanation
Indices: 30730--30794 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
30720 ATTAAAGGTT
*
30730 TTTTTTATGAATTTTATAA
1 TTTTTTATGAATTTTTTAA
*
30749 TTTTTTTATGATTTTTTTTAA
1 -TTTTTTATGA-ATTTTTTAA
*
30770 -ATTTTAT-AATTTTTTAAA
1 TTTTTTATGAATTTTTT-AA
30788 TTTTTTA
1 TTTTTTA
30795 AAAAAATTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
17 6 0.16
18 3 0.08
19 11 0.30
20 10 0.27
21 7 0.19
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (19 bp):
TTTTTTATGAATTTTTTAA
Found at i:30793 original size:9 final size:9
Alignment explanation
Indices: 30762--30796 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
30752 TTTTATGATT
30762 TTTTTTAAA
1 TTTTTTAAA
*
30771 TTTTAT-AA
1 TTTTTTAAA
30779 TTTTTTAAA
1 TTTTTTAAA
30788 TTTTTTAAA
1 TTTTTTAAA
30797 AAAATTGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:38704 original size:23 final size:25
Alignment explanation
Indices: 38678--38723 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
38668 CCAATTAAGG
38678 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
38701 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
38724 TGGATCCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:42386 original size:22 final size:22
Alignment explanation
Indices: 42354--42411 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
42344 TAATATATTT
42354 ATTTTCATATTTATTTTTATTGTT-A
1 ATTTT-AT-TTTA-TTTTATT-TTAA
*
42379 GTTTTATTTTATTTTATTTTAA
1 ATTTTATTTTATTTTATTTTAA
42401 ATTTTATTTTA
1 ATTTTATTTTA
42412 ATTATGCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 2 0.07
22 18 0.60
23 4 0.13
24 2 0.07
25 4 0.13
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (22 bp):
ATTTTATTTTATTTTATTTTAA
Found at i:42390 original size:5 final size:5
Alignment explanation
Indices: 42351--42411 Score: 59
Period size: 5 Copynumber: 10.8 Consensus size: 5
42341 AATTAATATA
42351 TTTAT TTTCAT ATTTATT TTTAT TGTTAGT TTTAT TTTAT TTTAT TTTAAAT
1 TTTAT TTT-AT -TTTA-T TTTAT T-TTA-T TTTAT TTTAT TTTAT TTT--AT
42403 TTTAT TTTA
1 TTTAT TTTA
42412 ATTATGCAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
5 25 0.51
6 13 0.27
7 11 0.22
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.72
Consensus pattern (5 bp):
TTTAT
Found at i:42404 original size:12 final size:12
Alignment explanation
Indices: 42380--42412 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
42370 TTATTGTTAG
42380 TTTTATTTT--A
1 TTTTATTTTAAA
42390 TTTTATTTTAAA
1 TTTTATTTTAAA
42402 TTTTATTTTAA
1 TTTTATTTTAA
42413 TTATGCAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 9 0.43
12 12 0.57
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTATTTTAAA
Found at i:52576 original size:28 final size:27
Alignment explanation
Indices: 52506--52576 Score: 67
Period size: 28 Copynumber: 2.6 Consensus size: 27
52496 TCACTCGTAT
52506 TATTTTTTAAATTT-TTTAAAAATATTTA
1 TATTTTTT--ATTTATTTAAAAATATTTA
*
52534 TATTATTTTA-ATATTTAATAAAT-TTATA
1 TATT-TTTTATTTATTTAA-AAATATT-TA
52562 TATTTTTTATTTATT
1 TATTTTTTATTTATT
52577 GAATTTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
26 1 0.03
27 13 0.36
28 18 0.50
29 4 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
TATTTTTTATTTATTTAAAAATATTTA
Found at i:55359 original size:27 final size:27
Alignment explanation
Indices: 55329--55405 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 27
55319 CCTATCGATA
*
55329 TATTCTTTTAATTTATTAAAATATATT
1 TATTATTTTAATTTATTAAAATATATT
** *
55356 TATTATTTTAATTTAATATTTAATATTTT
1 TATTATTTTAATTT-AT-TAAAATATATT
*
55385 TA-TATTTTCATTTATTAAAAT
1 TATTATTTTAATTTATTAAAAT
55406 TTTATATAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
26 4 0.10
27 15 0.37
28 12 0.29
29 10 0.24
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (27 bp):
TATTATTTTAATTTATTAAAATATATT
Found at i:55679 original size:22 final size:23
Alignment explanation
Indices: 55653--55695 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
55643 TTGAATTTTT
55653 AATTTATTTGAAA-TTAAATTTG
1 AATTTATTTGAAATTTAAATTTG
*
55675 AATTTATTTTAAATTTAAATT
1 AATTTATTTGAAATTTAAATT
55696 CATTTTGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (23 bp):
AATTTATTTGAAATTTAAATTTG
Found at i:55688 original size:17 final size:17
Alignment explanation
Indices: 55666--55750 Score: 98
Period size: 17 Copynumber: 5.0 Consensus size: 17
55656 TTATTTGAAA
*
55666 TTAAATTTGAATTTATT
1 TTAAATTTAAATTTATT
*
55683 TTAAATTTAAATTCATT
1 TTAAATTTAAATTTATT
* **
55700 TTGAGGTTAAATTTATT
1 TTAAATTTAAATTTATT
*
55717 TTAAATTTGAATTTATT
1 TTAAATTTAAATTTATT
* *
55734 TTAAATTAAAAATTATT
1 TTAAATTTAAATTTATT
55751 AATTAAAAGA
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 55 1.00
ACGTcount: A:0.39, C:0.01, G:0.06, T:0.54
Consensus pattern (17 bp):
TTAAATTTAAATTTATT
Found at i:56490 original size:3 final size:3
Alignment explanation
Indices: 56482--56536 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
56472 ACAATGAATT
* * * *
56482 TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAG TAT TAA TAT TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
56528 TAA TAA TAA
1 TAA TAA TAA
56537 AAAAGAAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 42 0.95
4 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:57732 original size:31 final size:30
Alignment explanation
Indices: 57696--57826 Score: 101
Period size: 29 Copynumber: 4.4 Consensus size: 30
57686 AAATTTTCTA
**
57696 AAAATTACATTTTTTACACCCAAACTTCTTG
1 AAAATTACATTTTTTACACCCAAACTT-TCC
* *
57727 AAAATTACA-TATTTACCCCCAAACTTTCC
1 AAAATTACATTTTTTACACCCAAACTTTCC
* *
57756 AAAATTACCATTTTAT-C-CCTAAACTTTCC
1 AAAATTA-CATTTTTTACACCCAAACTTTCC
** * *
57785 AAAATTA-AAATTTTAC-CTTCGAACTTTCC
1 AAAATTACATTTTTTACAC-CCAAACTTTCC
*
57814 AAAATTTCATTTT
1 AAAATTACATTTT
57827 AACCCTTATT
Statistics
Matches: 79, Mismatches: 16, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
27 4 0.05
28 2 0.03
29 40 0.51
30 21 0.27
31 12 0.15
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.38
Consensus pattern (30 bp):
AAAATTACATTTTTTACACCCAAACTTTCC
Found at i:57966 original size:117 final size:117
Alignment explanation
Indices: 57806--58094 Score: 420
Period size: 117 Copynumber: 2.5 Consensus size: 117
57796 TTTACCTTCG
* ** * *
57806 AACTTTCCAAAATTTCATTTTAACCCTTATTTCACCAAAAATTACCGTTTTACCCTCAAACTTTC
1 AACTTTCCAAAATTCCATTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCCAAACTTTC
*
57871 CAAAATTCCATTTTT-AGCCTCGATTTCACCAAAAAATA-CATTTTTACCCCTA
66 CAAAATTCCATTTTTGA-CCTCGATTTCACCAAAAAATACCA-TTTTACCCCAA
* *
57923 AACTTTCGAAAATTCCATTTTGACCCCAATTTCACCAAAAATTACCATTTTACCCCCAAACTTTC
1 AACTTTCCAAAATTCCATTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCCAAACTTTC
*
57988 CAAAATTCCATTTTTGACCTCGATTTCACCAAAAATTACCATTTTACCCCAA
66 CAAAATTCCATTTTTGACCTCGATTTCACCAAAAAATACCATTTTACCCCAA
* * * *
58040 AATTTTCCCAAATTCCATTTTTTACCCCAATTTCACCAAAAATTATCATTTTACC
1 AACTTTCCAAAATTCCA-TTTTAACCCCAATTTCACCAAAAATTACCATTTTACC
58095 ATTGGATGTC
Statistics
Matches: 155, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
117 117 0.75
118 38 0.25
ACGTcount: A:0.34, C:0.28, G:0.02, T:0.36
Consensus pattern (117 bp):
AACTTTCCAAAATTCCATTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCCAAACTTTC
CAAAATTCCATTTTTGACCTCGATTTCACCAAAAAATACCATTTTACCCCAA
Found at i:58092 original size:59 final size:57
Alignment explanation
Indices: 57727--58094 Score: 370
Period size: 59 Copynumber: 6.3 Consensus size: 57
57717 AAACTTCTTG
*
57727 AAAATTA-CATATTTACCCCCAAACTTTCCAAAATTACCATTTT-ATCCCTAAACTTT--CC-
1 AAAATTACCAT-TTTA-CCCCAAACTTTCCAAAATT-CCATTTTGA-CCC-CAA-TTTCACCA
** * * * * **
57785 AAAATTAAAATTTTACCTTCGAACTTTCCAAAATTTCATTTTAACCCTTATTTCACCA
1 AAAATTACCATTTTACC-CCAAACTTTCCAAAATTCCATTTTGACCCCAATTTCACCA
* * * *
57843 AAAATTACCGTTTTACCCTCAAACTTTCCAAAATTCCATTTTTAGCCTCGATTTCACCA
1 AAAATTACCATTTTACCC-CAAACTTTCCAAAATTCCATTTTGA-CCCCAATTTCACCA
* *
57902 AAAAATA-CATTTTTACCCCTAAACTTTCGAAAATTCCATTTTGACCCCAATTTCACCA
1 AAAATTACCA-TTTTACCCC-AAACTTTCCAAAATTCCATTTTGACCCCAATTTCACCA
* *
57960 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCTCGATTTCACCA
1 AAAATTACCATTTTA-CCCCAAACTTTCCAAAATTCCA-TTTTGACCCCAATTTCACCA
* * *
58019 AAAATTACCATTTTACCCCAAAATTTTCCCAAATTCCATTTTTTACCCCAATTTCACCA
1 AAAATTACCATTTTACCCC-AAACTTTCCAAAATTCCA-TTTTGACCCCAATTTCACCA
*
58078 AAAATTATCATTTTACC
1 AAAATTACCATTTTACC
58095 ATTGGATGTC
Statistics
Matches: 264, Mismatches: 32, Indels: 27
0.82 0.10 0.08
Matches are distributed among these distances:
55 3 0.01
56 1 0.00
57 13 0.05
58 109 0.41
59 138 0.52
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.36
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCAAACTTTCCAAAATTCCATTTTGACCCCAATTTCACCA
Found at i:58195 original size:27 final size:28
Alignment explanation
Indices: 58134--58195 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
58124 TCGGTTTTTT
* *
58134 TCCAAAATTACCATTTTGCCCTAGAGTG
1 TCCAAAATTACCATTTTGACCTAGAGTA
* *
58162 TCTAAAATTACCATTTT-ACCTCGAGTA
1 TCCAAAATTACCATTTTGACCTAGAGTA
58189 TCCAAAA
1 TCCAAAA
58196 AATCACATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 13 0.45
28 16 0.55
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.32
Consensus pattern (28 bp):
TCCAAAATTACCATTTTGACCTAGAGTA
Found at i:66537 original size:30 final size:31
Alignment explanation
Indices: 66503--66565 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 31
66493 AAAATTACAT
*
66503 TTTAATCAGTTAAAAATAATAA-AATTTTAA
1 TTTAATCAGTTAAAAATAATAACAATATTAA
*** *
66533 TTTAATTTTTTAAAAATTATAACAATATTAA
1 TTTAATCAGTTAAAAATAATAACAATATTAA
66564 TT
1 TT
66566 AATATTACAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (31 bp):
TTTAATCAGTTAAAAATAATAACAATATTAA
Found at i:73735 original size:14 final size:14
Alignment explanation
Indices: 73718--73759 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
73708 AAACTGTACA
73718 TATATGTATGTATG
1 TATATGTATGTATG
* *
73732 TATATATATATATG
1 TATATGTATGTATG
73746 TATATGTATG-ATG
1 TATATGTATGTATG
73759 T
1 T
73760 GTTTCAGTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (14 bp):
TATATGTATGTATG
Found at i:73738 original size:18 final size:18
Alignment explanation
Indices: 73712--73748 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
73702 ATGAAAAAAC
*
73712 TGTACATATATGTATGTA
1 TGTACATATATATATGTA
*
73730 TGTATATATATATATGTA
1 TGTACATATATATATGTA
73748 T
1 T
73749 ATGTATGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.49
Consensus pattern (18 bp):
TGTACATATATATATGTA
Done.