Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009796.1 Kokia drynarioides strain JFW-HI SEQ_124517, 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: 76799
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 120 characters in sequence are not A, C, G, or T
Found at i:305 original size:29 final size:29
Alignment explanation
Indices: 272--334 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
262 ATTATTTACG
*
272 AACTCGATTTACTAAGACGGAGGTTCTAT
1 AACTCGATTTACTAAGACGGAGGCTCTAT
*
301 AACTCGGTTTACTAAGACGGAGGCTCTAT
1 AACTCGATTTACTAAGACGGAGGCTCTAT
330 AACTC
1 AACTC
335 ACTTTTCCGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (29 bp):
AACTCGATTTACTAAGACGGAGGCTCTAT
Found at i:5862 original size:21 final size:19
Alignment explanation
Indices: 5838--5878 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
5828 ATATCCTAAG
5838 ATGATCTTTTGTAATTGTAGT
1 ATGATCTTTTG-AATTG-AGT
*
5859 ATGATGTTTTGAATTGAGT
1 ATGATCTTTTGAATTGAGT
5878 A
1 A
5879 AATCTTGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 5 0.26
21 10 0.53
ACGTcount: A:0.27, C:0.02, G:0.22, T:0.49
Consensus pattern (19 bp):
ATGATCTTTTGAATTGAGT
Found at i:7094 original size:23 final size:22
Alignment explanation
Indices: 7067--7112 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
7057 AAAATTAACC
*
7067 ATTAACCGAATTTCTAAAAAATT
1 ATTAACCG-ACTTCTAAAAAATT
* *
7090 ATTAATCGACTTCTAATAAATT
1 ATTAACCGACTTCTAAAAAATT
7112 A
1 A
7113 ACCAAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (22 bp):
ATTAACCGACTTCTAAAAAATT
Found at i:12126 original size:17 final size:17
Alignment explanation
Indices: 12104--12142 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
12094 AGGTGGAGAA
* *
12104 CTTGTTCATTGAGAGTT
1 CTTGTTCATAGAGAATT
*
12121 CTTGTTCGTAGAGAATT
1 CTTGTTCATAGAGAATT
12138 CTTGT
1 CTTGT
12143 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (17 bp):
CTTGTTCATAGAGAATT
Found at i:13570 original size:28 final size:28
Alignment explanation
Indices: 13549--13742 Score: 92
Period size: 29 Copynumber: 6.8 Consensus size: 28
13539 TTTTGGATTC
13549 CCGAGGGTAAAATGGTAATTTTGGGACGT
1 CCGA-GGTAAAATGGTAATTTTGGGACGT
* * *
13578 CTGAGGTAAAATGGTAATTTTTGGAAAGT
1 CCGAGGTAAAATGGTAA-TTTTGGGACGT
** * *
13607 -TTAGGGTCAAAAAT-GTAATTTTTGGACAT
1 CCGA-GGT--AAAATGGTAATTTTGGGACGT
* * *
13636 TCGAGGATAAAATGGTAATTTTTGGATGT
1 CCGAGG-TAAAATGGTAATTTTGGGACGT
** * * *
13665 TTGAGGGAAAATAGTAAATTTT-GGAAGT
1 CCGAGGTAAAATGGT-AATTTTGGGACGT
* * *
13693 TC-AGGGTAAAAAT-GTAATTTTTGGACAT
1 CCGA-GGT-AAAATGGTAATTTTGGGACGT
*
13721 CTGAGGGTAAAATGGTAATTTT
1 CCGA-GGTAAAATGGTAATTTT
13743 TGGATGTTTA
Statistics
Matches: 130, Mismatches: 22, Indels: 26
0.73 0.12 0.15
Matches are distributed among these distances:
27 7 0.05
28 46 0.35
29 66 0.51
30 6 0.05
31 5 0.04
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.35
Consensus pattern (28 bp):
CCGAGGTAAAATGGTAATTTTGGGACGT
Found at i:13626 original size:30 final size:28
Alignment explanation
Indices: 13552--14033 Score: 325
Period size: 28 Copynumber: 17.0 Consensus size: 28
13542 TGGATTCCCG
* * *
13552 AGGGT-AAAATGGTAATTTTGGGACGTCT
1 AGGGTAAAAAT-GTAATTTTTGGAAGTTT
13580 -GAGGT-AAAATGGTAATTTTTGGAAAGTTT
1 AG-GGTAAAAAT-GTAATTTTTGG-AAGTTT
*
13609 AGGGTCAAAAATGTAATTTTTGGACA-TTCG
1 AGGGT-AAAAATGTAATTTTTGGA-AGTT-T
* *
13639 AGGAT-AAAATGGTAATTTTTGGATGTTT
1 AGGGTAAAAAT-GTAATTTTTGGAAGTTT
* *
13667 GAGGG--AAAATAGTAAATTTTGGAAGTTC
1 -AGGGTAAAAAT-GTAATTTTTGGAAGTTT
*
13695 AGGGTAAAAATGTAATTTTTGGACA-TCTG
1 AGGGTAAAAATGTAATTTTTGGA-AGT-TT
*
13724 AGGGT-AAAATGGTAATTTTTGGATGTTT
1 AGGGTAAAAAT-GTAATTTTTGGAAGTTT
*
13752 AGGGGTAAAAATGTAATTTTTAGAAAGTTT
1 A-GGGTAAAAATGTAATTTTT-GGAAGTTT
* **
13782 GGGGTTAAAAATGTAATTTTTGGAAGCTCA
1 AGGG-TAAAAATGTAATTTTTGGAAG-TTT
* * *
13812 AGGGTAAAATTGTAATTTTTAGAAGTTC
1 AGGGTAAAAATGTAATTTTTGGAAGTTT
* * * * *
13840 GGGGGAAAAATGTGATTTTTGCAAGTTCG
1 AGGGTAAAAATGTAATTTTTGGAAGTT-T
13869 AGGGT-AAAATGTAATTTTT----G---
1 AGGGTAAAAATGTAATTTTTGGAAGTTT
* * *
13889 AGGCTAAAAATGTGATTTTTGAAAAGTTT
1 AGGGTAAAAATGTAATTTTTG-GAAGTTT
*
13918 AGGGTTAAAAATGTAATTTTTGAAAAGTTT
1 AGGG-TAAAAATGTAATTTTTG-GAAGTTT
13948 AGGGTAAAAAATGTAATTTTTGGAAGTTT
1 AGGGT-AAAAATGTAATTTTTGGAAGTTT
* * * *
13977 AAGGG-AAAAATATGATTTTTGAAAGTTC
1 -AGGGTAAAAATGTAATTTTTGGAAGTTT
* *
14005 AGGGGTAAAAATATAATATTTGAGAAGTT
1 A-GGGTAAAAATGTAATTTTTG-GAAGTT
14034 CGAGGTTGAA
Statistics
Matches: 368, Mismatches: 49, Indels: 72
0.75 0.10 0.15
Matches are distributed among these distances:
20 4 0.01
21 13 0.04
24 1 0.00
26 1 0.00
27 6 0.02
28 119 0.32
29 118 0.32
30 101 0.27
31 5 0.01
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (28 bp):
AGGGTAAAAATGTAATTTTTGGAAGTTT
Found at i:13922 original size:49 final size:51
Alignment explanation
Indices: 13845--13940 Score: 144
Period size: 49 Copynumber: 1.9 Consensus size: 51
13835 AGTTCGGGGG
*
13845 AAAAATGTGATTTTTGCAAGTTCGAGGG-T-AAAATGTAATTTTTGAGGCT
1 AAAAATGTGATTTTTGAAAGTTCGAGGGTTAAAAATGTAATTTTTGAGGCT
*
13894 AAAAATGTGATTTTTGAAAAGTT-TAGGGTTAAAAATGTAATTTTTGA
1 AAAAATGTGATTTTTG-AAAGTTCGAGGGTTAAAAATGTAATTTTTGA
13941 AAAGTTTAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
49 20 0.48
50 6 0.14
51 16 0.38
ACGTcount: A:0.36, C:0.03, G:0.22, T:0.39
Consensus pattern (51 bp):
AAAAATGTGATTTTTGAAAGTTCGAGGGTTAAAAATGTAATTTTTGAGGCT
Found at i:13955 original size:29 final size:29
Alignment explanation
Indices: 13893--14085 Score: 153
Period size: 30 Copynumber: 6.6 Consensus size: 29
13883 TTTTTGAGGC
*
13893 TAAAAATGTGATTTTTGAAAAGTTTAGGG
1 TAAAAATGTAATTTTTGAAAAGTTTAGGG
13922 TTAAAAATGTAATTTTTGAAAAGTTTAGGG
1 -TAAAAATGTAATTTTTGAAAAGTTTAGGG
*
13952 TAAAAAATGTAATTTTTG-GAAGTTTAAGGG
1 T-AAAAATGTAATTTTTGAAAAGTTT-AGGG
* * *
13982 -AAAAATATGATTTTTG-AAAGTTCAGGGG
1 TAAAAATGTAATTTTTGAAAAGTTTA-GGG
* * * *
14010 TAAAAATATAATATTTGAGAAG-TTCGAGG
1 TAAAAATGTAATTTTTGAAAAGTTTAG-GG
** *
14039 TTGAAATGCAA-TTTTGAAATAGTTTGAGGG
1 TAAAAATGTAATTTTTGAAA-AGTTT-AGGG
* * *
14069 TCAAAATATGATTTTTG
1 TAAAAATGTAATTTTTG
14086 GACAGTTCAG
Statistics
Matches: 130, Mismatches: 23, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
27 1 0.01
28 29 0.22
29 33 0.25
30 61 0.47
31 6 0.05
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.37
Consensus pattern (29 bp):
TAAAAATGTAATTTTTGAAAAGTTTAGGG
Found at i:15155 original size:15 final size:15
Alignment explanation
Indices: 15116--15161 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
15106 CTACTTCTTG
15116 ATTT-TATTTATTAA
1 ATTTATATTTATTAA
15130 ATATGTATATTTATTAA
1 AT-T-TATATTTATTAA
*
15147 ATTTATATTTGTTAA
1 ATTTATATTTATTAA
15162 TTATTATTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 2 0.07
15 12 0.43
16 2 0.07
17 12 0.43
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (15 bp):
ATTTATATTTATTAA
Found at i:15356 original size:121 final size:121
Alignment explanation
Indices: 15142--15383 Score: 394
Period size: 121 Copynumber: 2.0 Consensus size: 121
15132 ATGTATATTT
* * * **
15142 ATTAAATTTATATTTGTTAATTATTATTTCTTAAAAAACGTTTCATAATAAGTGGTCATAAAAAG
1 ATTAAATTTATATTTATTAATTATTATTTCCTAAAAAACATTTCATAATAAAAGGTCATAAAAAG
*
15207 TTATAATAATGGAATAAATTAATGCATTAATGTACATTAAAACGTTTTTAAATTCA
66 TTATAATAATGGAATAAATTAATGCATTAATGTACATTAAAACGTTTTGAAATTCA
* *
15263 ATTAAATTTATATTTATTAATTATTATTTCCTAAAAAGCATTTCATAATAAAAGGTCATAAAAGG
1 ATTAAATTTATATTTATTAATTATTATTTCCTAAAAAACATTTCATAATAAAAGGTCATAAAAAG
**
15328 TTATAATAATGGAATAAATTAATGCATTAATGTTTATTAAAACGTTTTGAAATTCA
66 TTATAATAATGGAATAAATTAATGCATTAATGTACATTAAAACGTTTTGAAATTCA
15384 TATAATAAAC
Statistics
Matches: 111, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
121 111 1.00
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (121 bp):
ATTAAATTTATATTTATTAATTATTATTTCCTAAAAAACATTTCATAATAAAAGGTCATAAAAAG
TTATAATAATGGAATAAATTAATGCATTAATGTACATTAAAACGTTTTGAAATTCA
Found at i:15949 original size:19 final size:19
Alignment explanation
Indices: 15906--15951 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
15896 GGGCCTCTTG
15906 TAAA-TTTGGACATTAATC
1 TAAATTTTGGACATTAATC
*
15924 TATAATTTTGGACTTTTAAT-
1 TA-AATTTTGGAC-ATTAATC
15944 TAAATTTT
1 TAAATTTT
15952 AAATTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 2 0.08
19 8 0.33
20 9 0.38
21 5 0.21
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.50
Consensus pattern (19 bp):
TAAATTTTGGACATTAATC
Found at i:15960 original size:6 final size:6
Alignment explanation
Indices: 15943--16026 Score: 73
Period size: 6 Copynumber: 14.0 Consensus size: 6
15933 GGACTTTTAA
* * * * *
15943 TTAAATT TTAAAT TTAAAT TTAAA- ATAAAT TTAAAC TTAAAA ATAAGT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
15991 TTAAAT TTAAA- ATAAAT TAAAAT TTAAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TT-AAAT TTAAAT
16027 GTTGGGTCCG
Statistics
Matches: 61, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
5 8 0.13
6 42 0.69
7 11 0.18
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (6 bp):
TTAAAT
Found at i:15971 original size:17 final size:17
Alignment explanation
Indices: 15951--16020 Score: 104
Period size: 17 Copynumber: 4.1 Consensus size: 17
15941 AATTAAATTT
15951 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
15968 TAAATTTAAACTTAAAAA
1 TAAATTTAAA-TTTAAAA
*
15986 TAAGTTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
16003 TAAATTAAAATTTAAAA
1 TAAATTTAAATTTAAAA
16020 T
1 T
16021 TTAAATGTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
17 32 0.68
18 15 0.32
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:17001 original size:209 final size:209
Alignment explanation
Indices: 16382--17590 Score: 1732
Period size: 209 Copynumber: 5.8 Consensus size: 209
16372 TCTTGATCTT
* **
16382 CTTCTCTGTATCTCATCAGGAAGACAACCATTTTATTACTTCGATTTGCTTCTCAGTATCTCATC
1 CTTCTCTGTATCTCATCAGGAAGACGACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATC
* * * * *
16447 AGAAAGATGGTGTTTGAAGTTTCGCTCACATTGAGCATTGTTTCATTGATTTGGTATACTTCTCT
66 AGGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTGATTTGGTATACTTCTCT
*
16512 GTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAAGAAG
131 GTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAGGAAG
**
16577 ATTGATTTGGTCCA
196 ACGGATTTGGTCCA
* * * * * *
16591 CTCCTCTGTATATCATTAGGAAGACGACCATTTTATTGCTTCGATCTTCTTCTCAGTATCTCAT-
1 CTTCTCTGTATCTCATCAGGAAGACGACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATC
* *
16655 ATGGAAGCTGAGGTTCGAAGTTTCACTCACATTGAGCTTTGTTTCATTGA-TTGGTATACTTCTC
66 A-GGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTGATTTGGTATACTTCTC
* * * *
16719 TGTATCTCATCAAGAAGATGATCGCCTCACTTGTTTTAATCTGCTTCTCTGTATCTCATCAGGAA
130 TGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAGGAA
16784 GACGGATTTGGTCCA
195 GACGGATTTGGTCCA
* * * *
16799 CTTCTCTATATCTCATCTGGAAGACGACCTTTTTATTACTTCGACCTGCTTCTCAGTACCTCATC
1 CTTCTCTGTATCTCATCAGGAAGACGACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATC
*
16864 AGGAAGCTGGGGTTCGAATTTTCGCTCACATTGAGCTTTGTTTCATTGATTTGGTATACTTCTCT
66 AGGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTGATTTGGTATACTTCTCT
* *
16929 GTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAATCCGCTTCTCTGTATCTTATCAGGAAG
131 GTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAGGAAG
16994 ACGGATTTGGTCCA
196 ACGGATTTGGTCCA
* * **
17008 CTTCTCTATATCTCATCAGGAAG-CTGA-CATTTTATTGCTTCGACCTATTTCTCAGTATCTCAT
1 CTTCTCTGTATCTCATCAGGAAGAC-GACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCAT
* * * *
17071 TAGGAAG-TCGGGGTTCGAAGTTTCGATCACATTGAACTTTTGTCTCATTGATTTGGTATACTTC
65 CAGGAAGCT-GGGGTTCGAAGTTTCGCTCACATTGAGC-TTTGTTTCATTGATTTGGTATACTTC
* * * *
17135 TCAGTATCTCATCAGGAAGATAACCGCATCACTTGTTTTGATCCGCTTCTCTGTATCTTATCAGG
128 TCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAGG
*
17200 AAGAAGGATTTGGTCCA
193 AAGACGGATTTGGTCCA
* * * *
17217 CTTCTCTGTATCTCATCAGTAAGACGACCGTTTTATTGCTTCGACCTGTTTCTCAGTATCTCATC
1 CTTCTCTGTATCTCATCAGGAAGACGACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATC
* * *
17282 AGGAAGCTGGGGTTCGAAGTTTCGCTCACATCGAGCTTTGGTCTCATTGATTTGG--T-CTACTC
66 AGGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTT-GTTTCATTGATTTGGTATACTTCTC
* * * * * *
17344 AGTATCTTATCAAGAAGATGATCGCATCACTTGTTTTAATCCGTTTCTCTGTATCTCATAAGGAA
130 TGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAGGAA
17409 GACGGATTTGGTCCA
195 GACGGATTTGGTCCA
* * ** *
17424 CTTCTCTGTATCTCATAAGGAAGACGATCGCTTTATTACTTCAACCTGCTTCTCAGTATCTCATC
1 CTTCTCTGTATCTCATCAGGAAGACGACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATC
* * *
17489 AGGAAGCTGGGGTTTGAAGTTTTGCTCACATTGAGCTTTGTTTAATTGATTTGGTATACTTCTCT
66 AGGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTGATTTGGTATACTTCTCT
*
17554 GTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTA
131 GTATCTCATCAGGAAGATGACCGCATCACTTGTTTTA
17591 GATAACTGCA
Statistics
Matches: 897, Mismatches: 90, Indels: 26
0.89 0.09 0.03
Matches are distributed among these distances:
206 13 0.01
207 171 0.19
208 252 0.28
209 379 0.42
210 81 0.09
211 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (209 bp):
CTTCTCTGTATCTCATCAGGAAGACGACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATC
AGGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTGATTTGGTATACTTCTCT
GTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAGGAAG
ACGGATTTGGTCCA
Found at i:17572 original size:625 final size:625
Alignment explanation
Indices: 16382--17590 Score: 1840
Period size: 625 Copynumber: 1.9 Consensus size: 625
16372 TCTTGATCTT
* ** *
16382 CTTCTCTGTATCTCATCAGGAAGACAACCATTTTATTACTTCGATTTGCTTCTCAGTATCTCATC
1 CTTCTCTATATCTCATCAGGAAGACAACCATTTTATTACTTCGACCTACTTCTCAGTATCTCATC
* * * * * *
16447 AGAAAGATGGTGTTTGAAGTTTCGCTCACATTGAGCATTGTTTCATTGATTTGGTATACTTCTCT
66 AGAAAGATGGGGTTCGAAGTTTCGATCACATTGAACATTGTCTCATTGATTTGGTATACTTCTCA
*
16512 GTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAAGAAG
131 GTATCTCATCAGGAAGATAACCGCATCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAAGAAG
** * *
16577 ATTGATTTGGTCCACTCCTCTGTATATCATTAGGAAGACGACCATTTTATTGCTTCGATCTTCTT
196 AAGGATTTGGTCCACTCCTCTGTATATCATCAGGAAGACGACCATTTTATTGCTTCGACCTTCTT
* *
16642 CTCAGTATCTCATATGGAAGCTGAGGTTCGAAGTTTCACTCACATTGAGCTTTGTTTCATTGATT
261 CTCAGTATCTCATATGGAAGCTGAGGTTCGAAGTTTCACTCACATCGAGCTTTGTCTCATTGATT
* * * *
16707 GGTATACTTCTCTGTATCTCATCAAGAAGATGATCGCCTCACTTGTTTTAATCTGCTTCTCTGTA
326 GG-ATACTACTCAGTATCTCATCAAGAAGATGATCGCATCACTTGTTTTAATCCGCTTCTCTGTA
* ** **
16772 TCTCATCAGGAAGACGGATTTGGTCCACTTCTCTATATCTCATCTGGAAGACGACCTTTTTATTA
390 TCTCATAAGGAAGACGGATTTGGTCCACTTCTCTATATCTCATAAGGAAGACGACCGCTTTATTA
*
16837 CTTCGACCTGCTTCTCAGTACCTCATCAGGAAGCTGGGGTTCGAATTTTCGCTCACATTGAGCTT
455 CTTCAACCTGCTTCTCAGTACCTCATCAGGAAGCTGGGGTTCGAATTTTCGCTCACATTGAGCTT
*
16902 TGTTTCATTGATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAA
520 TGTTTAATTGATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAA
16967 TCCGCTTCTCTGTATCTTATCAGGAAGACGGATTTGGTCCA
585 TCCGCTTCTCTGTATCTTATCAGGAAGACGGATTTGGTCCA
* * *
17008 CTTCTCTATATCTCATCAGGAAG-CTGA-CATTTTATTGCTTCGACCTATTTCTCAGTATCTCAT
1 CTTCTCTATATCTCATCAGGAAGAC-AACCATTTTATTACTTCGACCTACTTCTCAGTATCTCAT
* * *
17071 TAGGAAG-TCGGGGTTCGAAGTTTCGATCACATTGAACTTTTGTCTCATTGATTTGGTATACTTC
65 CAGAAAGAT-GGGGTTCGAAGTTTCGATCACATTGAAC-ATTGTCTCATTGATTTGGTATACTTC
* * *
17135 TCAGTATCTCATCAGGAAGATAACCGCATCACTTGTTTTGATCCGCTTCTCTGTATCTTATCAGG
128 TCAGTATCTCATCAGGAAGATAACCGCATCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAAG
* * * *
17200 AAGAAGGATTTGGTCCACTTCTCTGTATCTCATCAGTAAGACGACCGTTTTATTGCTTCGACCTG
193 AAGAAGGATTTGGTCCACTCCTCTGTATATCATCAGGAAGACGACCATTTTATTGCTTCGACCT-
* *
17265 T-TTCTCAGTATCTCATCA-GGAAGCTGGGGTTCGAAGTTTCGCTCACATCGAGCTTTGGTCTCA
257 TCTTCTCAGTATCTCAT-ATGGAAGCTGAGGTTCGAAGTTTCACTCACATCGAGCTTT-GTCTCA
* *
17328 TTGATTTGG-T-CTACTCAGTATCTTATCAAGAAGATGATCGCATCACTTGTTTTAATCCGTTTC
320 TTGA-TTGGATACTACTCAGTATCTCATCAAGAAGATGATCGCATCACTTGTTTTAATCCGCTTC
* *
17391 TCTGTATCTCATAAGGAAGACGGATTTGGTCCACTTCTCTGTATCTCATAAGGAAGACGATCGCT
384 TCTGTATCTCATAAGGAAGACGGATTTGGTCCACTTCTCTATATCTCATAAGGAAGACGACCGCT
* *
17456 TTATTACTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTTGAAGTTTT-GCTCACAT
449 TTATTACTTCAACCTGCTTCTCAGTACCTCATCAGGAAGCTGGGGTTCGAA-TTTTCGCTCACAT
17520 TGAGCTTTGTTTAATTGATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTT
513 TGAGCTTTGTTTAATTGATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTT
17585 GTTTTA
578 GTTTTA
17591 GATAACTGCA
Statistics
Matches: 526, Mismatches: 49, Indels: 17
0.89 0.08 0.03
Matches are distributed among these distances:
624 1 0.00
625 292 0.56
626 218 0.41
627 11 0.02
628 4 0.01
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (625 bp):
CTTCTCTATATCTCATCAGGAAGACAACCATTTTATTACTTCGACCTACTTCTCAGTATCTCATC
AGAAAGATGGGGTTCGAAGTTTCGATCACATTGAACATTGTCTCATTGATTTGGTATACTTCTCA
GTATCTCATCAGGAAGATAACCGCATCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAAGAAG
AAGGATTTGGTCCACTCCTCTGTATATCATCAGGAAGACGACCATTTTATTGCTTCGACCTTCTT
CTCAGTATCTCATATGGAAGCTGAGGTTCGAAGTTTCACTCACATCGAGCTTTGTCTCATTGATT
GGATACTACTCAGTATCTCATCAAGAAGATGATCGCATCACTTGTTTTAATCCGCTTCTCTGTAT
CTCATAAGGAAGACGGATTTGGTCCACTTCTCTATATCTCATAAGGAAGACGACCGCTTTATTAC
TTCAACCTGCTTCTCAGTACCTCATCAGGAAGCTGGGGTTCGAATTTTCGCTCACATTGAGCTTT
GTTTAATTGATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAAT
CCGCTTCTCTGTATCTTATCAGGAAGACGGATTTGGTCCA
Found at i:17759 original size:78 final size:75
Alignment explanation
Indices: 17670--17901 Score: 209
Period size: 78 Copynumber: 3.0 Consensus size: 75
17660 TAAGGTATTG
17670 GCTGATGGTGATTTGCCCTAGGCTCGAGGTAAAAGATCGAATGACTACAATCTACCCTAGGCTCG
1 GCTGATGGTGATTT-CCC-AGGCTCGAGGTAAAAGATCGAATGACTACAATCTACCCTAGGCTCG
17735 GAGTAAGAGATTA
64 G-GTAAGAGATTA
* ** * * * *
17748 GCTGATAGTGATCCACCCCAAGCTCGAGGTAAAAGATCGGATG-GTAGCAATCT-TCCTCAGGCT
1 GCTGATGGTGAT--TTCCCAGGCTCGAGGTAAAAGATCGAATGACTA-CAATCTACCCT-AGGCT
*
17811 CGGGATAAGAGATTG
62 CGGG-TAAGAGATTA
* * * * **
17826 GCTGATGGTGATCTATCCCAGGCTCGGGGTAAGAGATTGACTGACTATGATCTACCC-AGGCTCG
1 GCTGATGGTGAT-T-TCCCAGGCTCGAGGTAAAAGATCGAATGACTACAATCTACCCTAGGCTC-
*
17890 GGGTAAAAGATT
63 GGGTAAGAGATT
17902 GAAATCTTCA
Statistics
Matches: 123, Mismatches: 22, Indels: 19
0.75 0.13 0.12
Matches are distributed among these distances:
77 21 0.17
78 95 0.77
79 7 0.06
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (75 bp):
GCTGATGGTGATTTCCCAGGCTCGAGGTAAAAGATCGAATGACTACAATCTACCCTAGGCTCGGG
TAAGAGATTA
Found at i:17848 original size:39 final size:38
Alignment explanation
Indices: 17719--17902 Score: 149
Period size: 39 Copynumber: 4.7 Consensus size: 38
17709 AATGACTACA
*
17719 ATCTACCCTAGGCTC-GGAGTAAGAGATTAGCTGATAGTG
1 ATCTACCC-AGGCTCGGGA-TAAGAGATTGGCTGATAGTG
* * * * * * **
17758 ATCCACCCCAAGCTCGAGG-TAAAAGATCGGATGGTAGCA
1 ATCTA-CCCAGGCTCG-GGATAAGAGATTGGCTGATAGTG
* *
17797 ATCTTCCTCAGGCTCGGGATAAGAGATTGGCTGATGGTG
1 ATCTACC-CAGGCTCGGGATAAGAGATTGGCTGATAGTG
* *
17836 ATCTATCCCAGGCTCGGGGTAAGAGATTGACTGACTA-TG
1 ATCTA-CCCAGGCTCGGGATAAGAGATTGGCTGA-TAGTG
* *
17875 ATCTACCCAGGCTCGGGGTAAAAGATTG
1 ATCTACCCAGGCTCGGGATAAGAGATTG
17903 AAATCTTCAC
Statistics
Matches: 114, Mismatches: 24, Indels: 15
0.75 0.16 0.10
Matches are distributed among these distances:
38 26 0.23
39 80 0.70
40 6 0.05
41 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (38 bp):
ATCTACCCAGGCTCGGGATAAGAGATTGGCTGATAGTG
Found at i:17937 original size:41 final size:41
Alignment explanation
Indices: 17890--17986 Score: 142
Period size: 41 Copynumber: 2.4 Consensus size: 41
17880 CCCAGGCTCG
*
17890 GGGTAAAAGATTGAAATCTTCACTCTGCCCTTCTTGATTAA
1 GGGTAAAAGATTGAAATCTTCAATCTGCCCTTCTTGATTAA
* * *
17931 GGGTAAAAAACT-AGAATCTTCAATCTGCCTTTCTTGATTAA
1 GGGTAAAAGATTGA-AATCTTCAATCTGCCCTTCTTGATTAA
17972 GGGTAAAAGATTGAA
1 GGGTAAAAGATTGAA
17987 TGATGATGTG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
40 1 0.02
41 46 0.96
42 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (41 bp):
GGGTAAAAGATTGAAATCTTCAATCTGCCCTTCTTGATTAA
Found at i:18304 original size:50 final size:50
Alignment explanation
Indices: 18250--18567 Score: 262
Period size: 50 Copynumber: 6.4 Consensus size: 50
18240 CTAGATTTTT
* * *
18250 CGTTGTGACCTCAATCTTTCCCATCACATCTTTTGAGGTACCGAGTTCAC
1 CGTTGCGACCTCAACCTTTCCCATCACATCTTTTCAGGTACCGAGTTCAC
* *
18300 CGTTGC-AGCCTTAACCTTTCCCATCACATCTTCTT-AGGTACTGAGTT-AGC
1 CGTTGCGA-CCTCAACCTTTCCCATCACATCTT-TTCAGGTACCGAGTTCA-C
* * *
18350 CGTTACGACCTCAACCTTTCCCTTTACATC--TTCATGGTACC-AGGTTCAC
1 CGTTGCGACCTCAACCTTTCCCATCACATCTTTTCA-GGTACCGA-GTTCAC
* * * *
18399 TGTTGCGACCTCAACCTTTCCCATAACATCTTTTAAGGTATC-AGATTCAC
1 CGTTGCGACCTCAACCTTTCCCATCACATCTTTTCAGGTACCGAG-TTCAC
* * * * * * * *
18449 CATCGCGGCCTCAATCC-TTCAC-T-TCATCTCTTCATGGTATCG-GTTCGC
1 CGTTGCGACCTCAA-CCTTTCCCATCACATCTTTTCA-GGTACCGAGTTCAC
* * *
18497 CGTTGCGACCTCATCCTTTCCCATCACATCTTTTTAGGTACCGGGTTCAC
1 CGTTGCGACCTCAACCTTTCCCATCACATCTTTTCAGGTACCGAGTTCAC
* *
18547 CGTTGTGGCCTCAACCTTTCC
1 CGTTGCGACCTCAACCTTTCC
18568 TTGTCAAACC
Statistics
Matches: 213, Mismatches: 37, Indels: 36
0.74 0.13 0.13
Matches are distributed among these distances:
47 4 0.02
48 28 0.13
49 53 0.25
50 120 0.56
51 8 0.04
ACGTcount: A:0.19, C:0.32, G:0.15, T:0.34
Consensus pattern (50 bp):
CGTTGCGACCTCAACCTTTCCCATCACATCTTTTCAGGTACCGAGTTCAC
Found at i:18421 original size:99 final size:98
Alignment explanation
Indices: 18286--18537 Score: 264
Period size: 99 Copynumber: 2.5 Consensus size: 98
18276 CATCTTTTGA
* *
18286 GGTACCGAGTTCACCGTTGC-AGCCTTAACCTTTCCCATCACATCTTCTTAGGTACTGAG-TT-A
1 GGTACCG-GTTCACCGTTGCGA-CCTCAACCTTTCCCATCACATCTT-TTAGGTACTCAGATTCA
* * * *
18348 GCCGTTACGACCTCAA-CCTTTCCCTTTA-CATCTTCAT
63 -CCATCACGACCTCAATCC-TTCACTTCATC-TCTTCAT
* *
18385 GGTACCAGGTTCACTGTTGCGACCTCAACCTTTCCCATAACATCTTTTAAGGTA-TCAGATTCAC
1 GGTACC-GGTTCACCGTTGCGACCTCAACCTTTCCCATCACATCTTTT-AGGTACTCAGATTCAC
* *
18449 CATCGCGGCCTCAATCCTTCACTTCATCTCTTCAT
64 CATCACGACCTCAATCCTTCACTTCATCTCTTCAT
* * *
18484 GGTATCGGTTCGCCGTTGCGACCTCATCCTTTCCCATCACATCTTTTTAGGTAC
1 GGTACCGGTTCACCGTTGCGACCTCAACCTTTCCCATCACATC-TTTTAGGTAC
18538 CGGGTTCACC
Statistics
Matches: 129, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
98 43 0.33
99 80 0.62
100 6 0.05
ACGTcount: A:0.20, C:0.32, G:0.15, T:0.33
Consensus pattern (98 bp):
GGTACCGGTTCACCGTTGCGACCTCAACCTTTCCCATCACATCTTTTAGGTACTCAGATTCACCA
TCACGACCTCAATCCTTCACTTCATCTCTTCAT
Found at i:18546 original size:98 final size:98
Alignment explanation
Indices: 18378--18564 Score: 250
Period size: 98 Copynumber: 1.9 Consensus size: 98
18368 TCCCTTTACA
* *
18378 TCTTCATGGTACCAGGTTCACTGTTGCGACCTCAACCTTTCCCATAACATCTTTTAAGGTATCAG
1 TCTTCATGGTACCAGGTTCACCGTTGCGACCTCAACCTTTCCCATAACATCTTTTAAGGTACCAG
18443 ATTCACCATCGCGGCCTCAATCCTTCACTTCATC
66 ATTCACCATCGCGGCCTCAA-CCTTCACTTCATC
* * * * * *
18477 TCTTCATGGTATC-GGTTCGCCGTTGCGACCTCATCCTTTCCCATCACATCTTTTTAGGTACCGG
1 TCTTCATGGTACCAGGTTCACCGTTGCGACCTCAACCTTTCCCATAACATCTTTTAAGGTACCAG
* * * *
18541 GTTCACCGTTGTGGCCTCAACCTT
66 ATTCACCATCGCGGCCTCAACCTT
18565 TCCTTGTCAA
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
97 4 0.05
98 60 0.79
99 12 0.16
ACGTcount: A:0.18, C:0.32, G:0.16, T:0.34
Consensus pattern (98 bp):
TCTTCATGGTACCAGGTTCACCGTTGCGACCTCAACCTTTCCCATAACATCTTTTAAGGTACCAG
ATTCACCATCGCGGCCTCAACCTTCACTTCATC
Found at i:19470 original size:9 final size:9
Alignment explanation
Indices: 19456--19530 Score: 53
Period size: 10 Copynumber: 7.9 Consensus size: 9
19446 CATCTCGACC
19456 TCTTTTTTT
1 TCTTTTTTT
19465 TC-TTTTTT
1 TCTTTTTTT
19473 TCGTTTTTTCT
1 TC-TTTTTT-T
**
19484 AATTTCTTTT
1 TCTTT-TTTT
19494 TCATTTTTTCT
1 TC-TTTTTT-T
*
19505 TCTTTTTCT
1 TCTTTTTTT
*
19514 TCTTTTATT
1 TCTTTTTTT
*
19523 TATTTTTT
1 TCTTTTTT
19531 CTTAATTGAA
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
8 8 0.16
9 16 0.31
10 17 0.33
11 10 0.20
ACGTcount: A:0.07, C:0.13, G:0.01, T:0.79
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:24945 original size:59 final size:57
Alignment explanation
Indices: 24739--24960 Score: 198
Period size: 58 Copynumber: 3.8 Consensus size: 57
24729 GCTTGGGGGC
** ** * *
24739 AAAATGGTAATTTTGGGACATTCGGGGGTAAAACGGTAA-TTTTGGAAAGTCCAAGGTCA
1 AAAAT-GTAATTTTTAGACATTC-GGGGTAAAATAGTAATTTTTGGAAAGTTC-GGGTCA
* * * * *
24798 AAAATGTAATTTATAGACATTCGGGGATAAAATGGTAATTTTT-GAATGTTTGGG-GA
1 AAAATGTAATTTTTAGACATTCGGGG-TAAAATAGTAATTTTTGGAAAGTTCGGGTCA
* ** *
24854 TAAAATGATAATTTTTGGATGTTCGAGGGTAAAATAGTATTTTTTGGAAAGTTCGGTGTCA
1 -AAAATG-TAATTTTTAGACATTCG-GGGTAAAATAGTAATTTTTGGAAAGTTCGG-GTCA
*
24915 AAAATGTAATTTTTAGACATCCGGGAGTAAAATAGTAATTTTTGGA
1 AAAATGTAATTTTTAGACATTCGGG-GTAAAATAGTAATTTTTGGA
24961 TGTTTAGGGG
Statistics
Matches: 131, Mismatches: 23, Indels: 18
0.76 0.13 0.10
Matches are distributed among these distances:
56 1 0.01
57 12 0.09
58 58 0.44
59 52 0.40
60 7 0.05
61 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.25, T:0.34
Consensus pattern (57 bp):
AAAATGTAATTTTTAGACATTCGGGGTAAAATAGTAATTTTTGGAAAGTTCGGGTCA
Found at i:25091 original size:28 final size:28
Alignment explanation
Indices: 24798--25336 Score: 264
Period size: 29 Copynumber: 18.6 Consensus size: 28
24788 TCCAAGGTCA
* *
24798 AAAATGTAATTTATAGACA-TTCG-GGGAT
1 AAAATGTAATTTTTGGA-AGTTCGAGGG-T
*
24826 AAAATGGTAATTTTT-GAATGTTTG-GGGAT
1 AAAAT-GTAATTTTTGGAA-GTTCGAGGG-T
*
24855 AAAATGATAATTTTTGGATGTTCGAGGGT
1 AAAATG-TAATTTTTGGAAGTTCGAGGGT
* *
24884 AAAATAGTATTTTTTGGAAAGTTCG-GTGT
1 AAAAT-GTAATTTTTGG-AAGTTCGAGGGT
* *
24913 CAAAAATGTAATTTTTAGACA-TCCG-GGAGT
1 --AAAATGTAATTTTTGGA-AGTTCGAGG-GT
* *
24943 AAAATAGTAATTTTTGGATGTT-TAGGGGT
1 AAAAT-GTAATTTTTGGAAGTTCGA-GGGT
** * *
24972 AAAAACATAATTTTTGTAAAAGTTCG-GAGT
1 -AAAATGTAATTTTTG--GAAGTTCGAGGGT
*
25002 ACTAAATGCAATTTTTGGAAG--CGAAAGGGT
1 A--AAATGTAATTTTTGGAAGTTCG--AGGGT
* ** *
25032 AAAATGGTAATTTTTAGAAGGGCGA-GGC
1 AAAAT-GTAATTTTTGGAAGTTCGAGGGT
*
25060 AAAATGTGATTTTTGGAAGTTCGAGGGT
1 AAAATGTAATTTTTGGAAGTTCGAGGGT
* **
25088 AAAATGCAATTTTTGGAAGTTTAAGGGT
1 AAAATGTAATTTTTGGAAGTTCGAGGGT
* * *
25116 AAAAATGTGATTTTTGGAAGTTTGAGGGCA
1 -AAAATGTAATTTTTGGAAGTTCGAGGG-T
* * * *
25146 AAAATGTGATTTTTGTATGTT-TAGGGT
1 AAAATGTAATTTTTGGAAGTTCGAGGGT
** * *
25173 CAAAAATGTAATTTTTAAAAGTTTAGGGGGT
1 --AAAATGTAATTTTTGGAAG-TTCGAGGGT
* *
25204 AAAATGGTTATTTTTGGAAGTT-TAGGGGT
1 AAAAT-GTAATTTTTGGAAGTTCGA-GGGT
** *
25233 AAAATGGTAATTTTTGGAAGTTAAAGGGC
1 AAAAT-GTAATTTTTGGAAGTTCGAGGGT
* * *
25262 AAAATATGATTTTTTGAAGTTCGAGGGT
1 AAAATGTAATTTTTGGAAGTTCGAGGGT
* *
25290 AAAAATGTAATTTTTAAGAAGTTCG-GGCTT
1 -AAAATGTAATTTTT-GGAAGTTCGAGG-GT
*
25320 AAAATGT-AGTTTTGGAA
1 AAAATGTAATTTTTGGAA
25337 CTTTTTGAGG
Statistics
Matches: 398, Mismatches: 72, Indels: 83
0.72 0.13 0.15
Matches are distributed among these distances:
27 21 0.05
28 76 0.19
29 215 0.54
30 60 0.15
31 26 0.07
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (28 bp):
AAAATGTAATTTTTGGAAGTTCGAGGGT
Found at i:25106 original size:84 final size:86
Alignment explanation
Indices: 25005--25160 Score: 210
Period size: 84 Copynumber: 1.8 Consensus size: 86
24995 TCGGAGTACT
25005 AAATGCAATTTTTGGAAGCGAAAGGGT-AAAATGGTAATTTTTAGAAGGGCGA-GGC-AAAATGT
1 AAATGCAATTTTTGGAAGCGAAAGGGTAAAAAT-GTAATTTTTAGAAGGGCGAGGGCAAAAATGT
25067 GATTTTTGGAAGTTCGAGGGTA
65 GATTTTTGGAAGTTCGAGGGTA
*** * * ***
25089 AAATGCAATTTTTGGAAGTTTAAGGGTAAAAATGTGATTTTTGGAAGTTTGAGGGCAAAAATGTG
1 AAATGCAATTTTTGGAAGCGAAAGGGTAAAAATGTAATTTTTAGAAGGGCGAGGGCAAAAATGTG
25154 ATTTTTG
66 ATTTTTG
25161 TATGTTTAGG
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
84 38 0.62
85 8 0.13
86 15 0.25
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (86 bp):
AAATGCAATTTTTGGAAGCGAAAGGGTAAAAATGTAATTTTTAGAAGGGCGAGGGCAAAAATGTG
ATTTTTGGAAGTTCGAGGGTA
Found at i:25235 original size:117 final size:117
Alignment explanation
Indices: 25096--25312 Score: 307
Period size: 117 Copynumber: 1.9 Consensus size: 117
25086 GTAAAATGCA
* ** *
25096 ATTTTTGGAAGTTTAAGGGTAAAAAT-GTGATTTTTGGAAGTTTGAGGGCAAAAATGTGA-TTTT
1 ATTTTTGGAAGTTTAAGGGT-AAAATGGTAATTTTTGGAAGTTAAAGGGC-AAAATATGATTTTT
* *
25159 TGTATGTT-TAGGGTCAAAAATGTAATTTTTAA-AAGTTTAGGGGGTAAAATGGTT
64 TG-AAGTTCGAGGGT-AAAAATGTAATTTTTAAGAAGTTTAGGGGGTAAAATGGTT
*
25213 ATTTTTGGAAGTTTAGGGGTAAAATGGTAATTTTTGGAAGTTAAAGGGCAAAATATGATTTTTTG
1 ATTTTTGGAAGTTTAAGGGTAAAATGGTAATTTTTGGAAGTTAAAGGGCAAAATATGATTTTTTG
25278 AAGTTCGAGGGTAAAAATGTAATTTTTAAGAAGTT
66 AAGTTCGAGGGTAAAAATGTAATTTTTAAGAAGTT
25313 CGGGCTTAAA
Statistics
Matches: 89, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
116 34 0.38
117 55 0.62
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.39
Consensus pattern (117 bp):
ATTTTTGGAAGTTTAAGGGTAAAATGGTAATTTTTGGAAGTTAAAGGGCAAAATATGATTTTTTG
AAGTTCGAGGGTAAAAATGTAATTTTTAAGAAGTTTAGGGGGTAAAATGGTT
Found at i:26552 original size:121 final size:121
Alignment explanation
Indices: 26408--26649 Score: 421
Period size: 121 Copynumber: 2.0 Consensus size: 121
26398 GATTTTTTTT
* *
26408 ATTAAATTTATATTTATTAATTATTATTTCCTAAAAAACGTTTCATAATAAATGGTTATAAAAGG
1 ATTAAATTTATATTTATTAATTATTATTTCCTAAAAAACATTTCATAATAAATGGTCATAAAAGG
* *
26473 TTATAATAATGGAATAAATTAATGCATTAATGTACATTAAAACGTTCTGAAATTCA
66 CTATAATAATGGAATAAATTAATGCATTAATATACATTAAAACGTTCTGAAATTCA
*
26529 ATTAAATTTATATTTATTAATTATTATTTCCTAAAAAGCATTTCATAATAAATGGTCATAAAAGG
1 ATTAAATTTATATTTATTAATTATTATTTCCTAAAAAACATTTCATAATAAATGGTCATAAAAGG
* *
26594 CTATAATAATGGAATAAATTAATGCATTAATATATATTAAAACGTTTTGAAATTCA
66 CTATAATAATGGAATAAATTAATGCATTAATATACATTAAAACGTTCTGAAATTCA
26650 TATAATAAAC
Statistics
Matches: 114, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
121 114 1.00
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (121 bp):
ATTAAATTTATATTTATTAATTATTATTTCCTAAAAAACATTTCATAATAAATGGTCATAAAAGG
CTATAATAATGGAATAAATTAATGCATTAATATACATTAAAACGTTCTGAAATTCA
Found at i:26686 original size:121 final size:121
Alignment explanation
Indices: 26436--26678 Score: 301
Period size: 121 Copynumber: 2.0 Consensus size: 121
26426 AATTATTATT
* * * *
26436 TCCTAAAAAACGTTTCATAATAAATGGTTATAAAAGGTTATAATAATGGAATAAATTAATGCATT
1 TCCTAAAAAGCATTTCATAATAAATGGTCATAAAAGGCTATAATAATGGAATAAATTAATGCATT
* ** * *** * * * *
26501 AATGTACATTAAAACGTTCTGAAATTCAATTAAATTTATATTTATTAATTATTATT
66 AATATACATTAAAACGTTCTGAAATTCAATTAAATAAACAAGCAGTAATAAATATA
26557 TCCTAAAAAGCATTTCATAATAAATGGTCATAAAAGGCTATAATAATGGAATAAATTAATGCATT
1 TCCTAAAAAGCATTTCATAATAAATGGTCATAAAAGGCTATAATAATGGAATAAATTAATGCATT
* * *
26622 AATATATATTAAAACGTTTTGAAATTC-A-TATAATAAACAAGCAGTAATAAATGTA
66 AATATACATTAAAACGTTCTGAAATTCAATTA-AATAAACAAGCAGTAATAAATATA
26677 TC
1 TC
26679 TTGAAAAAAC
Statistics
Matches: 103, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
119 2 0.02
120 16 0.16
121 85 0.83
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.36
Consensus pattern (121 bp):
TCCTAAAAAGCATTTCATAATAAATGGTCATAAAAGGCTATAATAATGGAATAAATTAATGCATT
AATATACATTAAAACGTTCTGAAATTCAATTAAATAAACAAGCAGTAATAAATATA
Found at i:27226 original size:6 final size:6
Alignment explanation
Indices: 27209--27309 Score: 64
Period size: 6 Copynumber: 17.0 Consensus size: 6
27199 GGACTTTTAA
* * * * * *
27209 TTAAATT TTAAAT TTAAAT TCAAA- ATAAAT TTAAAT TCAAAA ATAAGT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * * * *
27257 TTAAAT TTAAA- ATAAAT TTAAAC TTAAA- ATAGAT TAAAAT TTAAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT-AAAT
27304 TTAAAT
1 TTAAAT
27310 GTTGGGCCCG
Statistics
Matches: 69, Mismatches: 21, Indels: 9
0.70 0.21 0.09
Matches are distributed among these distances:
5 10 0.14
6 48 0.70
7 11 0.16
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (6 bp):
TTAAAT
Found at i:27237 original size:17 final size:17
Alignment explanation
Indices: 27217--27303 Score: 104
Period size: 17 Copynumber: 5.1 Consensus size: 17
27207 AATTAAATTT
27217 TAAATTTAAATTCAAAA
1 TAAATTTAAATTCAAAA
27234 TAAATTTAAATTCAAAAA
1 TAAATTTAAATTC-AAAA
* *
27252 TAAGTTTAAATTTAAAA
1 TAAATTTAAATTCAAAA
27269 TAAATTTAAACTT-AAAA
1 TAAATTTAAA-TTCAAAA
* * *
27286 TAGATTAAAATTTAAAA
1 TAAATTTAAATTCAAAA
27303 T
1 T
27304 TTAAATGTTG
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
16 2 0.03
17 43 0.69
18 17 0.27
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.37
Consensus pattern (17 bp):
TAAATTTAAATTCAAAA
Found at i:33808 original size:9 final size:9
Alignment explanation
Indices: 33790--33820 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
33780 AAACATGTTA
*
33790 TTCCTGCTG
1 TTCCTACTG
33799 TTCCTACTG
1 TTCCTACTG
33808 TTCCTACTG
1 TTCCTACTG
33817 TTCC
1 TTCC
33821 ATAGGAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.06, C:0.35, G:0.13, T:0.45
Consensus pattern (9 bp):
TTCCTACTG
Found at i:36039 original size:46 final size:44
Alignment explanation
Indices: 35978--36072 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
35968 GGTTCGCTAT
* *
35978 AATGAAATAGGGCTGTAATCAGTATTTCAGTTATTTGGTTGAATGG
1 AATGAAATAGAGCTGTAAT-AGTA-TTCAGTTACTTGGTTGAATGG
* ** *
36024 AATGGAATAGAGCTGTAATAGTATTCTTTTGCTTGGTTGAATGG
1 AATGAAATAGAGCTGTAATAGTATTCAGTTACTTGGTTGAATGG
36068 AATGA
1 AATGA
36073 TGTTGTAATA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 21 0.50
45 4 0.10
46 17 0.40
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (44 bp):
AATGAAATAGAGCTGTAATAGTATTCAGTTACTTGGTTGAATGG
Found at i:36204 original size:37 final size:37
Alignment explanation
Indices: 36163--36233 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
36153 TTGTTATTAA
* * *
36163 ATTTTAATAAGATTGTTATTAAATATAATTTAATCAT
1 ATTTTAACAAGATTATTATTAAATACAATTTAATCAT
**
36200 ATTTTAACGTGATTATTATTAAATACAATTTAAT
1 ATTTTAACAAGATTATTATTAAATACAATTTAAT
36234 AAAATAGTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (37 bp):
ATTTTAACAAGATTATTATTAAATACAATTTAATCAT
Found at i:43415 original size:32 final size:32
Alignment explanation
Indices: 43378--43448 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
43368 TTTGTTTAAA
43378 AAGCAACTTGACCAAGAAGGCCATGAAAGTTT
1 AAGCAACTTGACCAAGAAGGCCATGAAAGTTT
43410 AAGCAACTTGACCAAGAAGGCCATGAAAGTTT
1 AAGCAACTTGACCAAGAAGGCCATGAAAGTTT
43442 AAGCAAC
1 AAGCAAC
43449 ACAATATGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.42, C:0.20, G:0.21, T:0.17
Consensus pattern (32 bp):
AAGCAACTTGACCAAGAAGGCCATGAAAGTTT
Found at i:52068 original size:15 final size:15
Alignment explanation
Indices: 52050--52101 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
52040 CTTTCTTTTC
52050 TTATATTTTATAATA
1 TTATATTTTATAATA
** *
52065 TTATATAATAAAATA
1 TTATATTTTATAATA
52080 TTATTATTTATTATAATA
1 TTA-TA-TT-TTATAATA
52098 TTAT
1 TTAT
52102 TATTAATTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 15 0.54
16 2 0.07
17 2 0.07
18 9 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTATATTTTATAATA
Found at i:52110 original size:18 final size:18
Alignment explanation
Indices: 52057--52110 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
52047 TTCTTATATT
52057 TTATAATATTA-TA-TAA
1 TTATAATATTATTATTAA
* *
52073 -TAAAATATTATTATTTA
1 TTATAATATTATTATTAA
52090 TTATAATATTATTATTAA
1 TTATAATATTATTATTAA
52108 TTA
1 TTA
52111 ATATATCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 9 0.29
16 2 0.06
17 2 0.06
18 18 0.58
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATAATATTATTATTAA
Found at i:52116 original size:18 final size:18
Alignment explanation
Indices: 52058--52116 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
52048 TCTTATATTT
*
52058 TATAATATTATATAA-TAA
1 TATATTATTAT-TAATTAA
* *
52076 AATATTATTATTTATT-A
1 TATATTATTATTAATTAA
52093 TAATATTATTATTAATTAA
1 T-ATATTATTATTAATTAA
52112 TATAT
1 TATAT
52117 CTTTTAATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
17 3 0.09
18 28 0.85
19 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATATTATTATTAATTAA
Found at i:59450 original size:10 final size:10
Alignment explanation
Indices: 59435--59480 Score: 58
Period size: 10 Copynumber: 4.4 Consensus size: 10
59425 ATTTGTTAAT
59435 AAAAGAAAAA
1 AAAAGAAAAA
59445 AAAAG-AAAA
1 AAAAGAAAAA
59454 AAAAGAAAAA
1 AAAAGAAAAA
59464 ACAAAGGAAAAGA
1 A-AAA-GAAAA-A
59477 AAAA
1 AAAA
59481 AAATAAGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.28
10 10 0.31
11 3 0.09
12 8 0.25
13 2 0.06
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:62599 original size:26 final size:25
Alignment explanation
Indices: 62569--62625 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
62559 ATTAAATTCT
62569 ATTTTTTAG--TTTTTATATTAAAA
1 ATTTTTTAGTATTTTTATATTAAAA
*
62592 ATATTTTTAGTATTTTTATATTTAAA
1 AT-TTTTTAGTATTTTTATATTAAAA
62618 ATTTTTTA
1 ATTTTTTA
62626 ATTTAAAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 2 0.07
24 7 0.23
25 6 0.20
26 15 0.50
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (25 bp):
ATTTTTTAGTATTTTTATATTAAAA
Found at i:62625 original size:16 final size:15
Alignment explanation
Indices: 62604--62633 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
62594 ATTTTTAGTA
62604 TTTTTATATTTAAAAT
1 TTTTTA-ATTTAAAAT
62620 TTTTTAATTTAAAA
1 TTTTTAATTTAAAA
62634 CTAAATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTTAATTTAAAAT
Found at i:63076 original size:20 final size:20
Alignment explanation
Indices: 63034--63081 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
63024 TTTAGAGTTG
*
63034 TAAATTATATAAAACAATTA
1 TAAATTATATAAAACAATAA
*
63054 TAAATTATAATAATA-AATAA
1 TAAATTAT-ATAAAACAATAA
*
63074 TAATTTAT
1 TAAATTAT
63082 TTTTGTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATTATATAAAACAATAA
Found at i:63711 original size:6 final size:6
Alignment explanation
Indices: 63700--63729 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
63690 ATATATTGAA
63700 TTCAAC TTCAAC TTCAAC TTCAA- TTCAAC T
1 TTCAAC TTCAAC TTCAAC TTCAAC TTCAAC T
63730 ATCTAGTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (6 bp):
TTCAAC
Found at i:64494 original size:12 final size:12
Alignment explanation
Indices: 64473--64573 Score: 53
Period size: 12 Copynumber: 8.2 Consensus size: 12
64463 AAAAATTAAG
64473 ATTA-TTTTATT
1 ATTATTTTTATT
64484 ATTATTTTTATT
1 ATTATTTTTATT
**
64496 AAAAATTTTATATT
1 -ATTATTTT-TATT
* *
64510 -TTAAGTTTCTCTT
1 ATT-A-TTTTTATT
* **
64523 TTTATTTTTAGG
1 ATTATTTTTATT
*
64535 ATTTATTATTATT
1 A-TTATTTTTATT
*
64548 ATTATTATTATT
1 ATTATTTTTATT
*
64560 ATTATTATTATT
1 ATTATTTTTATT
64572 AT
1 AT
64574 ATATAAACTT
Statistics
Matches: 69, Mismatches: 14, Indels: 13
0.72 0.15 0.14
Matches are distributed among these distances:
11 4 0.06
12 36 0.52
13 20 0.29
14 9 0.13
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (12 bp):
ATTATTTTTATT
Found at i:64545 original size:3 final size:3
Alignment explanation
Indices: 64537--64573 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
64527 TTTTTAGGAT
64537 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
64574 ATATAAACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:71546 original size:21 final size:21
Alignment explanation
Indices: 71520--71577 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
71510 TAAAAGCAAG
*
71520 ACTTGTTTCGGTAGAAGTGAC
1 ACTTGTATCGGTAGAAGTGAC
* *
71541 ATTTGTATCGGTAAAAGTGAC
1 ACTTGTATCGGTAGAAGTGAC
71562 ACTTGTATCGGTAGAA
1 ACTTGTATCGGTAGAA
71578 CTATCACAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (21 bp):
ACTTGTATCGGTAGAAGTGAC
Done.