Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005706.1 Hibiscus syriacus cultivar Beakdansim tig00013341_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 142956
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:4800 original size:3 final size:3
Alignment explanation
Indices: 4792--4819 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4782 CGGGCAACGG
4792 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
4820 AATACTTAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:6919 original size:20 final size:22
Alignment explanation
Indices: 6871--6919 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
6861 GTCCATCCAT
* *
6871 TACCGATATTGTTCTTTGTAAG
1 TACCGATATTGTTCTATGAAAG
*
6893 TATCGATATTGTTC-AT-AAAG
1 TACCGATATTGTTCTATGAAAG
6913 TACCGAT
1 TACCGAT
6920 TTTATTCTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 9 0.39
21 1 0.04
22 13 0.57
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (22 bp):
TACCGATATTGTTCTATGAAAG
Found at i:9830 original size:20 final size:20
Alignment explanation
Indices: 9791--9900 Score: 150
Period size: 20 Copynumber: 5.5 Consensus size: 20
9781 CAAATTTTTT
**
9791 TATGAATAGTATTG-TACTG
1 TATGAATAGTACCGATACTG
9810 TATGAATAGTACCGATACTG
1 TATGAATAGTACCGATACTG
*
9830 TATGAATAGTACCGATATTG
1 TATGAATAGTACCGATACTG
*
9850 TATGAATAGTACCAATACTG
1 TATGAATAGTACCGATACTG
*
9870 TATGAATAGTATCGATACTG
1 TATGAATAGTACCGATACTG
* *
9890 TGTGAACAGTA
1 TATGAATAGTA
9901 ATGAACAATG
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
19 12 0.15
20 69 0.85
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (20 bp):
TATGAATAGTACCGATACTG
Found at i:10342 original size:33 final size:33
Alignment explanation
Indices: 10300--10365 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
10290 TAAAGGGGTT
* * *
10300 TTGGTTCTAGCTGAGCCTGTTAAAAGCTAGGGA
1 TTGGTTCTAGCTGAGCCCGTGAAAAACTAGGGA
* *
10333 TTGGTTCTAGTTTAGCCCGTGAAAAACTAGGGA
1 TTGGTTCTAGCTGAGCCCGTGAAAAACTAGGGA
10366 GTTGTAAAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (33 bp):
TTGGTTCTAGCTGAGCCCGTGAAAAACTAGGGA
Found at i:13273 original size:20 final size:20
Alignment explanation
Indices: 13234--13290 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 20
13224 AAATTTTTTT
* *
13234 TATGAATAATACTG-TACTG
1 TATGAATAGTACCGATACTG
13253 TATGAATAGTACCGATACTG
1 TATGAATAGTACCGATACTG
* *
13273 TGTGAACAGTA-CGATACT
1 TATGAATAGTACCGATACT
13291 AAAAAATTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
TATGAATAGTACCGATACTG
Found at i:13289 original size:19 final size:20
Alignment explanation
Indices: 13248--13290 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
13238 AATAATACTG
*
13248 TACTGTATGAATAGTACCGA
1 TACTGTATGAACAGTACCGA
*
13268 TACTGTGTGAACAGTA-CGA
1 TACTGTATGAACAGTACCGA
13287 TACT
1 TACT
13291 AAAAAATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (20 bp):
TACTGTATGAACAGTACCGA
Found at i:13750 original size:33 final size:32
Alignment explanation
Indices: 13711--13775 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
13701 CAAAGGGATT
* *
13711 TTGGTTCTAGCTGAGCCTGTTAAAAGCTAGGGA
1 TTGGTTCTAGCTGAGCCCGTGAAAA-CTAGGGA
* *
13744 TTGGTTCTAGTTTAGCCCGTGAAAACTAGGGA
1 TTGGTTCTAGCTGAGCCCGTGAAAACTAGGGA
13776 GTTATAAAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 7 0.25
33 21 0.75
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (32 bp):
TTGGTTCTAGCTGAGCCCGTGAAAACTAGGGA
Found at i:15647 original size:5 final size:6
Alignment explanation
Indices: 15630--15654 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
15620 GTGATTGATC
15630 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
15655 AGAATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:18150 original size:17 final size:17
Alignment explanation
Indices: 18124--18156 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
18114 TTTTGTTTTT
18124 AATTTATTTAAGTATTTA
1 AATTTATTTAA-TATTTA
18142 AATTT-TTTAATATTT
1 AATTTATTTAATATTT
18157 CATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
AATTTATTTAATATTTA
Found at i:26229 original size:24 final size:23
Alignment explanation
Indices: 26167--26267 Score: 94
Period size: 24 Copynumber: 4.3 Consensus size: 23
26157 GAGTCGAGGG
*
26167 TTCTACGCGGTCTTTCAGGACAA
1 TTCTACGCGGTCCTTCAGGACAA
* * *
26190 TTCTATGTGGTCCTTCGGGACAAA
1 TTCTACGCGGTCCTTCAGGAC-AA
* *
26214 TTCTACGCGGTTCTTCAAGACAA
1 TTCTACGCGGTCCTTCAGGACAA
** * *
26237 TTTCTACATGGTCCTTCGGGACAT
1 -TTCTACGCGGTCCTTCAGGACAA
26261 TTCTACG
1 TTCTACG
26268 TGTCACTTTG
Statistics
Matches: 60, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
23 25 0.42
24 35 0.58
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCAGGACAA
Found at i:26236 original size:47 final size:47
Alignment explanation
Indices: 26167--26267 Score: 134
Period size: 47 Copynumber: 2.1 Consensus size: 47
26157 GAGTCGAGGG
* **
26167 TTCTACGCGGTCTTTCAGGACAA-TTCTATGTGGTCCTTCGGGACAAA
1 TTCTACGCGGTCTTTCAAGACAATTTCTACATGGTCCTTCGGGAC-AA
*
26214 TTCTACGCGGT-TCTTCAAGACAATTTCTACATGGTCCTTCGGGACAT
1 TTCTACGCGGTCT-TTCAAGACAATTTCTACATGGTCCTTCGGGACAA
26261 TTCTACG
1 TTCTACG
26268 TGTCACTTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
46 1 0.02
47 28 0.58
48 19 0.40
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (47 bp):
TTCTACGCGGTCTTTCAAGACAATTTCTACATGGTCCTTCGGGACAA
Found at i:37900 original size:23 final size:20
Alignment explanation
Indices: 37849--37908 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 20
37839 TTTTGGTGCA
*
37849 GAGGGAATCGA-TCCCCCTT
1 GAGGGAACCGATTCCCCCTT
37868 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC-TT
37889 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
37909 CCACAGGGGA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 10 0.28
20 6 0.17
21 3 0.08
22 1 0.03
23 16 0.44
ACGTcount: A:0.22, C:0.33, G:0.27, T:0.18
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCTT
Found at i:42856 original size:24 final size:24
Alignment explanation
Indices: 42770--42881 Score: 99
Period size: 23 Copynumber: 4.8 Consensus size: 24
42760 GAGTCGAGGG
* * *
42770 TTCTACGCGGTCTTTCAGGATAA-
1 TTCTACGTGGTCCTTCGGGATAAT
* *
42793 TTCTATGTGGTCCTTCGGGATAAA
1 TTCTACGTGGTCCTTCGGGATAAT
*
42817 TTCTACACT-GTCCTTCGGGATAAT
1 TTCTAC-GTGGTCCTTCGGGATAAT
*
42841 TTCTACGTGGTTCTTCGGGACT--T
1 TTCTACGTGGTCCTTCGGGA-TAAT
42864 TTCTACGTGG-CACTTCGG
1 TTCTACGTGGTC-CTTCGG
42882 TGCAATTCTA
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
23 37 0.50
24 35 0.47
25 2 0.03
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (24 bp):
TTCTACGTGGTCCTTCGGGATAAT
Found at i:43585 original size:16 final size:16
Alignment explanation
Indices: 43560--43608 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
43550 TTTGTTATTC
43560 TTTGTTAAAT-TCAAT
1 TTTGTTAAATGTCAAT
*
43575 TTTGTTTAAATGTCAAG
1 TTTG-TTAAATGTCAAT
*
43592 CTT-TTAAA-GTCAAT
1 TTTGTTAAATGTCAAT
43606 TTT
1 TTT
43609 TTGTTTGGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
14 7 0.25
15 9 0.32
16 6 0.21
17 6 0.21
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (16 bp):
TTTGTTAAATGTCAAT
Found at i:43786 original size:23 final size:23
Alignment explanation
Indices: 43756--43805 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
43746 TATGGGTTTG
* *
43756 AAAAAAATTCAATTTCTCAATGA
1 AAAAAAATTAAATTTATCAATGA
43779 AAAAAAATTAAATTTATCAATGA
1 AAAAAAATTAAATTTATCAATGA
43802 AAAA
1 AAAA
43806 GGGGGAGCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.28
Consensus pattern (23 bp):
AAAAAAATTAAATTTATCAATGA
Found at i:46032 original size:143 final size:143
Alignment explanation
Indices: 45774--46059 Score: 493
Period size: 143 Copynumber: 2.0 Consensus size: 143
45764 CTTCTACGTT
*
45774 ACTTCAGACACTTTTGTGATAATTACTTCATTTATGATATGTAAGTATAACTTGAAGATTATTTA
1 ACTTCAGACACTTTTGTGATAATTACTTCATTTATGATATGTAAGTATAACATGAAGATTATTTA
* *
45839 TATCTTATGCATGATGTATATATATGATATCAATCTCGAGCATGATTATTCATACATTGTAATAA
66 TATCTTATGCATGATGCATATATATGATATCAATCTCGAGCATGATTATTCATACACTGTAATAA
45904 AAATATGATTTAC
131 AAATATGATTTAC
* *
45917 ACTTCA-ATCACTTTTGTGATAATTACTTCATTTATGATATGTAAGTATGACATGACGATTATTT
1 ACTTCAGA-CACTTTTGTGATAATTACTTCATTTATGATATGTAAGTATAACATGAAGATTATTT
*
45981 ATATCTTTTGCATGATGCATATATATGATATCAATCTCGAGCATGATTATTCATACACTGTAATA
65 ATATCTTATGCATGATGCATATATATGATATCAATCTCGAGCATGATTATTCATACACTGTAATA
*
46046 AAAATATGGTTTAC
130 AAAATATGATTTAC
46060 TTGTCCCCTG
Statistics
Matches: 135, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
142 1 0.01
143 134 0.99
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (143 bp):
ACTTCAGACACTTTTGTGATAATTACTTCATTTATGATATGTAAGTATAACATGAAGATTATTTA
TATCTTATGCATGATGCATATATATGATATCAATCTCGAGCATGATTATTCATACACTGTAATAA
AAATATGATTTAC
Found at i:46473 original size:19 final size:19
Alignment explanation
Indices: 46436--46474 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
46426 TCAGGTGAGG
46436 TCAATGATCAATGATGGTT
1 TCAATGATCAATGATGGTT
*
46455 TCAAGTGATCGATGA-GGTT
1 TCAA-TGATCAATGATGGTT
46474 T
1 T
46475 TGAGAGTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.28, C:0.10, G:0.26, T:0.36
Consensus pattern (19 bp):
TCAATGATCAATGATGGTT
Found at i:50333 original size:26 final size:27
Alignment explanation
Indices: 50245--50341 Score: 98
Period size: 24 Copynumber: 3.7 Consensus size: 27
50235 GTGTTTAAAT
50245 ACTTAAATTTATAATATTTTATATATATTA
1 ACTT-AATTTA-AATATTTT-TATATATTA
*
50275 ACTTAA--CAAATATTTTT-TATATTA
1 ACTTAATTTAAATATTTTTATATATTA
50299 ACTT-A-TTAAATATTTTTAT-TATTA
1 ACTTAATTTAAATATTTTTATATATTA
*
50323 ATTTAATTTAAAATATTTT
1 ACTTAATTT-AAATATTTT
50342 ATTTTTATTT
Statistics
Matches: 59, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
23 1 0.02
24 29 0.49
25 3 0.05
26 10 0.17
27 10 0.17
29 2 0.03
30 4 0.07
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (27 bp):
ACTTAATTTAAATATTTTTATATATTA
Found at i:50365 original size:27 final size:26
Alignment explanation
Indices: 50282--50361 Score: 76
Period size: 26 Copynumber: 3.1 Consensus size: 26
50272 TTAACTTAAC
* *
50282 AAATATTTTTTATATTAACTT-A-TT-
1 AAATATTTTAT-TATTAATTTAATTTA
50306 AAATATTTTTATTATTAATTTAATTTA
1 AAATA-TTTTATTATTAATTTAATTTA
* * *
50333 AAATATTTTATTTTTATTTTCATTTA
1 AAATATTTTATTATTAATTTAATTTA
50359 AAA
1 AAA
50362 ATATATATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
24 13 0.28
25 6 0.13
26 23 0.49
27 5 0.11
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (26 bp):
AAATATTTTATTATTAATTTAATTTA
Found at i:50551 original size:30 final size:31
Alignment explanation
Indices: 50500--50567 Score: 102
Period size: 30 Copynumber: 2.2 Consensus size: 31
50490 AACTGTGATT
* *
50500 ACCACATCTTAATTAAATAAAAATGAAAGTG
1 ACCATATCTTAATTAAATAAAAACGAAAGTG
*
50531 ATCATATCTTAATT-AATAAAAACGAAAGTG
1 ACCATATCTTAATTAAATAAAAACGAAAGTG
50561 ACCATAT
1 ACCATAT
50568 TTTTTTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 21 0.64
31 12 0.36
ACGTcount: A:0.50, C:0.13, G:0.09, T:0.28
Consensus pattern (31 bp):
ACCATATCTTAATTAAATAAAAACGAAAGTG
Found at i:51698 original size:23 final size:23
Alignment explanation
Indices: 51668--51716 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
51658 ATATAATGTT
*
51668 AACCTAAAACAAATAAATATCAA
1 AACCTAAAACAAATAAACATCAA
51691 AACCTAAAACAAATAAACATCAA
1 AACCTAAAACAAATAAACATCAA
51714 AAC
1 AAC
51717 AATTAAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.65, C:0.20, G:0.00, T:0.14
Consensus pattern (23 bp):
AACCTAAAACAAATAAACATCAA
Found at i:51809 original size:20 final size:21
Alignment explanation
Indices: 51775--51829 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
51765 ATAAGATAAC
* * *
51775 TAAAATAGTTGTAAAACAAT-
1 TAAAATATTTTTAAAAAAATA
51795 TAAAATATTTTTAAAAAAAATA
1 TAAAATATTTTT-AAAAAAATA
51817 TAAAATATTTTTA
1 TAAAATATTTTTA
51830 TTTTTATACT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 10 0.33
21 8 0.27
22 12 0.40
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (21 bp):
TAAAATATTTTTAAAAAAATA
Found at i:51827 original size:21 final size:21
Alignment explanation
Indices: 51787--51829 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
51777 AAATAGTTGT
*
51787 AAAACAATTAAAATATTTTTA
1 AAAAAAATTAAAATATTTTTA
51808 AAAAAAATATAAAATATTTTTA
1 AAAAAAAT-TAAAATATTTTTA
51830 TTTTTATACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAAAAATTAAAATATTTTTA
Found at i:51888 original size:28 final size:28
Alignment explanation
Indices: 51856--51910 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
51846 TTTATTCCAT
51856 AAATTTCA-TTTAAAAATATAAAAATATA
1 AAATTT-AGTTTAAAAATATAAAAATATA
* *
51884 AAATTTAGTTTAAAATTATAGAAATAT
1 AAATTTAGTTTAAAAATATAAAAATAT
51911 TAAACTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (28 bp):
AAATTTAGTTTAAAAATATAAAAATATA
Found at i:53551 original size:23 final size:23
Alignment explanation
Indices: 53525--53582 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
53515 TCAATTCTGA
**
53525 TTCGATTCAAGTATGAAATCAAC
1 TTCGATTCAACCATGAAATCAAC
53548 TTCGATTCAACCATGAAATCAAC
1 TTCGATTCAACCATGAAATCAAC
*
53571 TTTGATTCAACC
1 TTCGATTCAACC
53583 TTATAAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.31
Consensus pattern (23 bp):
TTCGATTCAACCATGAAATCAAC
Found at i:67683 original size:20 final size:20
Alignment explanation
Indices: 67658--67748 Score: 64
Period size: 20 Copynumber: 4.5 Consensus size: 20
67648 TAGTATAGTA
67658 GTATCGATACTGAGAGAAGG
1 GTATCGATACTGAGAGAAGG
67678 GTATCGATACT-A-A-AAGGG
1 GTATCGATACTGAGAGAA-GG
* * * * *
67696 AGTATTGGTA-TTATAGTATAGTA
1 -GTATCGATACTGAGAG-A-AG-G
67719 GTATCGATACTGAGAGAAGG
1 GTATCGATACTGAGAGAAGG
67739 GTATCGATAC
1 GTATCGATAC
67749 CATGCAACAC
Statistics
Matches: 54, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
17 2 0.04
18 4 0.07
19 9 0.17
20 22 0.41
21 2 0.04
22 10 0.19
23 5 0.09
ACGTcount: A:0.35, C:0.09, G:0.29, T:0.27
Consensus pattern (20 bp):
GTATCGATACTGAGAGAAGG
Found at i:67691 original size:61 final size:61
Alignment explanation
Indices: 67616--67748 Score: 266
Period size: 61 Copynumber: 2.2 Consensus size: 61
67606 ATGTCAAAAT
67616 GGTATCGATACTAAAAGGGAGTATTGGTATTATAGTATAGTAGTATCGATACTGAGAGAAG
1 GGTATCGATACTAAAAGGGAGTATTGGTATTATAGTATAGTAGTATCGATACTGAGAGAAG
67677 GGTATCGATACTAAAAGGGAGTATTGGTATTATAGTATAGTAGTATCGATACTGAGAGAAG
1 GGTATCGATACTAAAAGGGAGTATTGGTATTATAGTATAGTAGTATCGATACTGAGAGAAG
67738 GGTATCGATAC
1 GGTATCGATAC
67749 CATGCAACAC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 72 1.00
ACGTcount: A:0.35, C:0.08, G:0.28, T:0.29
Consensus pattern (61 bp):
GGTATCGATACTAAAAGGGAGTATTGGTATTATAGTATAGTAGTATCGATACTGAGAGAAG
Found at i:68305 original size:72 final size:72
Alignment explanation
Indices: 68188--68343 Score: 186
Period size: 72 Copynumber: 2.2 Consensus size: 72
68178 TCGCTAAGGA
** * * * *
68188 ATGAAAGGATGCCATAATTAAAATGCATGTCCGGATGCATTAAGGCATGAAATAATGCCATAATT
1 ATGAAAGGATGCCATAATTAAAATGCATGAACAGATCCAATAAGGCATGAAAGAATGCCATAATT
* *
68253 CACGTGT
66 AACGTGC
* * * *
68260 ATGAAAGGATGCCATAATTAACATGCATGAATAGTTCCAATAAGGCATGAAAGGATGCCATAATT
1 ATGAAAGGATGCCATAATTAAAATGCATGAACAGATCCAATAAGGCATGAAAGAATGCCATAATT
*
68325 AATGTGC
66 AACGTGC
*
68332 ATGAACGGATGC
1 ATGAAAGGATGC
68344 ACTAAGGCAT
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (72 bp):
ATGAAAGGATGCCATAATTAAAATGCATGAACAGATCCAATAAGGCATGAAAGAATGCCATAATT
AACGTGC
Found at i:68310 original size:46 final size:46
Alignment explanation
Indices: 68260--68649 Score: 487
Period size: 46 Copynumber: 8.5 Consensus size: 46
68250 ATTCACGTGT
** * * *
68260 ATGAAAGGATGCCATAATTAACATGCATGAATAGTTCCAATAAGGC
1 ATGAAAGGATGCCATAATTAACATGCATGAACGGATGCACTAAGGC
**
68306 ATGAAAGGATGCCATAATTAATGTGCATGAACGGATGCACTAAGGC
1 ATGAAAGGATGCCATAATTAACATGCATGAACGGATGCACTAAGGC
* *
68352 ATGAAAGGATGCCATAATTAAAATGCATGAACGGATGCATTAAGGC
1 ATGAAAGGATGCCATAATTAACATGCATGAACGGATGCACTAAGGC
* *
68398 ATGAAAGGATGACAT-ATTCAACGTGCATGAACGGATGCACTAAGGC
1 ATGAAAGGATGCCATAATT-AACATGCATGAACGGATGCACTAAGGC
* * *
68444 ATGAAAGGATCCCATAATTAAAATGCATGAACGGATGCA-TCAAGGA
1 ATGAAAGGATGCCATAATTAACATGCATGAACGGATGCACT-AAGGC
* * * * *
68490 AAGAAAGGATTCCATAATTAACGTGCATGAACAGATGCACTAAGTC
1 ATGAAAGGATGCCATAATTAACATGCATGAACGGATGCACTAAGGC
* *
68536 ATGAAAGGATGCCATAAATAACATGCATGAACGGATGCACTAAGGA
1 ATGAAAGGATGCCATAATTAACATGCATGAACGGATGCACTAAGGC
* * * * * * *
68582 ACGAAAGGATTCCATAATTAAAATGCATGAACGCATACATTAAGGT
1 ATGAAAGGATGCCATAATTAACATGCATGAACGGATGCACTAAGGC
*
68628 ATGAAAGGATGCCATCATTAAC
1 ATGAAAGGATGCCATAATTAAC
68650 GTGTATAAAC
Statistics
Matches: 295, Mismatches: 45, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
45 4 0.01
46 287 0.97
47 4 0.01
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (46 bp):
ATGAAAGGATGCCATAATTAACATGCATGAACGGATGCACTAAGGC
Found at i:68322 original size:20 final size:21
Alignment explanation
Indices: 68300--68453 Score: 71
Period size: 26 Copynumber: 6.8 Consensus size: 21
68290 ATAGTTCCAA
*
68300 TAAGGCATGAAAGGATGCCATAAT
1 TAAGGCATGAAAGGATGCC---AC
*
68324 TAATGTGCATGAACGGATG-CAC
1 TAA-G-GCATGAAAGGATGCCAC
*
68346 TAAGGCATGAAAGGATGCCATAAT
1 TAAGGCATGAAAGGATGCC---AC
* * *
68370 TAAAATGCATGAACGGATG-CAT
1 T--AAGGCATGAAAGGATGCCAC
* *
68392 TAAGGCATGAAAGGATGACATAT
1 TAAGGCATGAAAGGATG-C-CAC
*
68415 TCAACGTGCATGAACGGATG-CAC
1 T-AA-G-GCATGAAAGGATGCCAC
68438 TAAGGCATGAAAGGAT
1 TAAGGCATGAAAGGAT
68454 CCCATAATTA
Statistics
Matches: 103, Mismatches: 13, Indels: 32
0.70 0.09 0.22
Matches are distributed among these distances:
20 37 0.36
21 3 0.03
22 9 0.09
23 5 0.05
24 7 0.07
25 4 0.04
26 38 0.37
ACGTcount: A:0.39, C:0.14, G:0.26, T:0.21
Consensus pattern (21 bp):
TAAGGCATGAAAGGATGCCAC
Found at i:71951 original size:8 final size:8
Alignment explanation
Indices: 71934--71979 Score: 58
Period size: 8 Copynumber: 5.6 Consensus size: 8
71924 GTAATATTTG
71934 TAATATAA
1 TAATATAA
71942 T-ATAATAA
1 TAAT-ATAA
71950 TAATATAA
1 TAATATAA
71958 TAATATACA
1 TAATATA-A
*
71967 TTATATAA
1 TAATATAA
71975 TAATA
1 TAATA
71980 AGACTCAGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
7 2 0.06
8 22 0.67
9 9 0.27
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (8 bp):
TAATATAA
Found at i:71954 original size:11 final size:11
Alignment explanation
Indices: 71934--71962 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
71924 GTAATATTTG
71934 TAAT-ATAATA
1 TAATAATAATA
71944 TAATAATAATA
1 TAATAATAATA
71955 TAATAATA
1 TAATAATA
71963 TACATTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TAATAATAATA
Found at i:76804 original size:95 final size:95
Alignment explanation
Indices: 76634--76806 Score: 208
Period size: 95 Copynumber: 1.8 Consensus size: 95
76624 CAGAATGTCA
* * * *
76634 AAATGGTATCGATACTGGAAGGGAGTATCGGTACCATAGTATAGTAGTATCGATACTGAGAGAAG
1 AAATGGTATCAATACTGGAAGGGAGTATCAGTACCATAGTATAGAAGTATCGATACTCAGAGAAG
*
76699 GGTATCGATACTATGCAACACATAATATGG
66 AGTATCGATACTATGCAACACATAATATGG
* * * *
76729 AAATGGTATCAATA-TGGAAAGAGG-GTATCAGTGCCATATTATAGAAGTATCGATAC-CAGGGT
1 AAATGGTATCAATACTGG-AAG-GGAGTATCAGTACCATAGTATAGAAGTATCGATACTCAGAGA
*
76791 AGTAGTATTGATACTA
64 AG-AGTATCGATACTA
76807 ACGAGATTGG
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
94 8 0.12
95 55 0.85
96 2 0.03
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (95 bp):
AAATGGTATCAATACTGGAAGGGAGTATCAGTACCATAGTATAGAAGTATCGATACTCAGAGAAG
AGTATCGATACTATGCAACACATAATATGG
Found at i:77183 original size:26 final size:26
Alignment explanation
Indices: 77147--77205 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
77137 TATCACTAAG
77147 GCATGAAAGAATGCCATAATTAAAAT
1 GCATGAAAGAATGCCATAATTAAAAT
*
77173 GCATTAAAGAATGCCATAATTAAAAT
1 GCATGAAAGAATGCCATAATTAAAAT
77199 GCATGAA
1 GCATGAA
77206 CGGATGCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.24
Consensus pattern (26 bp):
GCATGAAAGAATGCCATAATTAAAAT
Found at i:77236 original size:46 final size:46
Alignment explanation
Indices: 77173--77573 Score: 561
Period size: 46 Copynumber: 8.7 Consensus size: 46
77163 TAATTAAAAT
* * ** *
77173 GCATTAAAGAATGCCATAATTAAAATGCATGAACGGATGCATTAAG
1 GCATGAAAGGATGCCATAATTAACGTGCATGAACGGATGCACTAAG
* * *
77219 GCATGAAATGATGCCATAATTCATGTGCATGAACGGATGCACTAAG
1 GCATGAAAGGATGCCATAATTAACGTGCATGAACGGATGCACTAAG
* *
77265 GAATGAAAGGATGCCATAATTAACGTGCATGAACAGATGCACTAAG
1 GCATGAAAGGATGCCATAATTAACGTGCATGAACGGATGCACTAAG
* *
77311 GCATGAAAGGATACCATAATTAACGTGCATGAACGGATTCACTAAG
1 GCATGAAAGGATGCCATAATTAACGTGCATGAACGGATGCACTAAG
* ** * *
77357 GCATGAAAGGATGCCAAAATTAAAATGCATGAACAGATGCATTAAG
1 GCATGAAAGGATGCCATAATTAACGTGCATGAACGGATGCACTAAG
* *
77403 GCATGAAAGGATGCCATATTTAACGTGCATGAACGGATGCACTAAT
1 GCATGAAAGGATGCCATAATTAACGTGCATGAACGGATGCACTAAG
77449 GCATGAAAGGATGCCATAATTAACGTGCATGAACGGATGCACTAAG
1 GCATGAAAGGATGCCATAATTAACGTGCATGAACGGATGCACTAAG
* ** * *
77495 GCACGAAAGGATGCCATAATTAAAATGCATGAAC-GAGTTCATTAAG
1 GCATGAAAGGATGCCATAATTAACGTGCATGAACGGA-TGCACTAAG
*
77541 GCATGAAAGGATGCCATCATTAACGTGCATGAA
1 GCATGAAAGGATGCCATAATTAACGTGCATGAA
77574 TGACATAACT
Statistics
Matches: 313, Mismatches: 41, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
45 2 0.01
46 311 0.99
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.22
Consensus pattern (46 bp):
GCATGAAAGGATGCCATAATTAACGTGCATGAACGGATGCACTAAG
Found at i:91924 original size:14 final size:15
Alignment explanation
Indices: 91905--91941 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
91895 GAGCTAGTTC
*
91905 GGAGGTGAATTAG-T
1 GGAGGTGAATGAGCT
91919 GGAGGTGAATGAGCT
1 GGAGGTGAATGAGCT
91934 GGAGGTGA
1 GGAGGTGA
91942 CTTGTATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.27, C:0.03, G:0.49, T:0.22
Consensus pattern (15 bp):
GGAGGTGAATGAGCT
Found at i:99330 original size:13 final size:13
Alignment explanation
Indices: 99296--99322 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
99286 CATGGTGTGG
99296 CAAAAGTATCATC
1 CAAAAGTATCATC
99309 CAAAAGTATCATC
1 CAAAAGTATCATC
99322 C
1 C
99323 TTAAGTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.26, G:0.07, T:0.22
Consensus pattern (13 bp):
CAAAAGTATCATC
Found at i:103501 original size:2 final size:2
Alignment explanation
Indices: 103494--103537 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
103484 GTGGTTCGGC
103494 AT 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 AT
103536 AT
1 AT
103538 CATGGTTTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:104797 original size:16 final size:16
Alignment explanation
Indices: 104776--104809 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
104766 CCAATGAAAG
104776 AATTTAATAATAGGGT
1 AATTTAATAATAGGGT
104792 AATTTAATAATAGGGT
1 AATTTAATAATAGGGT
104808 AA
1 AA
104810 ACTATAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (16 bp):
AATTTAATAATAGGGT
Found at i:116935 original size:39 final size:39
Alignment explanation
Indices: 116891--116970 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
116881 AACAGCAGCC
116891 TTTGAAGAATCAGTTGCAACATTAACCTCTCCCTCAGAT
1 TTTGAAGAATCAGTTGCAACATTAACCTCTCCCTCAGAT
** *
116930 TTTGAAGAATTGGTTGCAGCATTAACCTCTCCCTCAGAT
1 TTTGAAGAATCAGTTGCAACATTAACCTCTCCCTCAGAT
116969 TT
1 TT
116971 AGACACAGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.34
Consensus pattern (39 bp):
TTTGAAGAATCAGTTGCAACATTAACCTCTCCCTCAGAT
Found at i:131346 original size:46 final size:46
Alignment explanation
Indices: 131271--131505 Score: 344
Period size: 46 Copynumber: 5.1 Consensus size: 46
131261 AAATGAATTT
* *
131271 ATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTC
1 ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
** *
131317 ATAATTAAAATGCATGAAAGGATATATTAAGGCATGAAAGGATACC
1 ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
* *
131363 GTAATTAAAATGCATAAAAGGATGCATTAAGGCATGAAAGGATGCC
1 ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
* * *
131409 ATAACTAAAAATGCAAGAAAGGATGCATTAAGGCATGAAAGAATGCC
1 ATAA-TTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
* * *
131456 ATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTC
1 ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
131502 ATAA
1 ATAA
131506 ATGAAATTAA
Statistics
Matches: 167, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
46 125 0.75
47 42 0.25
ACGTcount: A:0.46, C:0.10, G:0.23, T:0.21
Consensus pattern (46 bp):
ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCC
Found at i:131469 original size:93 final size:92
Alignment explanation
Indices: 131271--131505 Score: 353
Period size: 93 Copynumber: 2.5 Consensus size: 92
131261 AAATGAATTT
* * *
131271 ATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAATTAAAATGCATGAAA
1 ATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAATAAAAATGCAAGAAA
* *
131336 GGATATATTAAGGCATGAAAGGATACC
66 GGATACATTAAGGCATGAAAGAATACC
* * * *
131363 GTAATTAAAATGCATAAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCAAGAA
1 ATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAA-TAAAAATGCAAGAA
* *
131428 AGGATGCATTAAGGCATGAAAGAATGCC
65 AGGATACATTAAGGCATGAAAGAATACC
*
131456 ATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAA
1 ATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAA
131506 ATGAAATTAA
Statistics
Matches: 127, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
92 46 0.36
93 81 0.64
ACGTcount: A:0.46, C:0.10, G:0.23, T:0.21
Consensus pattern (92 bp):
ATAAATAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAATAAAAATGCAAGAAA
GGATACATTAAGGCATGAAAGAATACC
Found at i:137792 original size:96 final size:94
Alignment explanation
Indices: 137673--137852 Score: 254
Period size: 96 Copynumber: 1.9 Consensus size: 94
137663 TCAAAGGGAA
* * *
137673 GTATCGATACCATGGATCCAGAATGTCA-AAATGGCATCGATACTGAAAGGGGGTATCGATACCA
1 GTATCGATACCATGAAACCAGAATAT-AGAAATGGCATCGATACTGAAAGGGGGTATCGATACCA
**
137737 TAGTATAGTAGTATCGATACTGAGAGAAAG
65 TAGTATAAAAGTATCGATACTGAGAGAAAG
* * *
137767 GTATCGATACCATGCAAACACAGAATATAGAAATGGTATTGATACTGAAAGGGGGTATCGGTACC
1 GTATCGATACCATG-AAAC-CAGAATATAGAAATGGCATCGATACTGAAAGGGGGTATCGATACC
137832 ATAGTATAAAAGTATCGATAC
64 ATAGTATAAAAGTATCGATAC
137853 CAGGGTTGTA
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
94 14 0.19
95 3 0.04
96 58 0.77
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (94 bp):
GTATCGATACCATGAAACCAGAATATAGAAATGGCATCGATACTGAAAGGGGGTATCGATACCAT
AGTATAAAAGTATCGATACTGAGAGAAAG
Found at i:138307 original size:20 final size:20
Alignment explanation
Indices: 138282--138498 Score: 110
Period size: 20 Copynumber: 9.7 Consensus size: 20
138272 TAACTAAAAT
*
138282 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
138302 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
*
138328 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
138348 GCATGAAAGGATGTCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
*
138374 GCATGAAAGGATGTATTAAG
1 GCATGAAAGGATGCATTAAG
*
138394 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
**
138420 GCATGAAAGGAAACATTAAG
1 GCATGAAAGGATGCATTAAG
* *
138440 GCATGAAAGGATTCCATAATTAAAT
1 GCATGAAAGGA-TGC---ATT-AAG
**
138465 GCATGAAAAAATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
138485 GTATGAAAGGATGC
1 GCATGAAAGGATGC
138499 CATAACTAAA
Statistics
Matches: 151, Mismatches: 23, Indels: 46
0.69 0.10 0.21
Matches are distributed among these distances:
20 67 0.44
21 6 0.04
22 9 0.06
24 14 0.09
25 13 0.09
26 42 0.28
ACGTcount: A:0.44, C:0.10, G:0.23, T:0.24
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:138329 original size:46 final size:46
Alignment explanation
Indices: 138271--138648 Score: 488
Period size: 46 Copynumber: 8.4 Consensus size: 46
138261 AAACAAATTA
*
138271 ATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCC
1 ATAATTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCC
*
138317 ATAATTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGTC
1 ATAATTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCC
* *
138363 ATAATTAAAATGCATGAAAGGATGTATTAAGGCATGAAAGGATGCC
1 ATAATTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCC
* ** *
138409 ATAATTAAAATGCATGAAAGGAAACATTAAGGCATGAAAGGATTCC
1 ATAATTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCC
** *
138455 ATAATT-AAATGCATGAAAAAATGCATTAAGGTATGAAAGGATGCC
1 ATAATTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCC
*
138500 ATAACTAAAATGCATGAAATGATGCA-T------T--AAGGATGCC
1 ATAATTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCC
* * * * *
138537 ATAATTTAAATGCATGAAAGGATACATTGACGCATGAAAGGATGCC
1 ATAATTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCC
* *
138583 ATAACTAAAAATGCATGAAATGATGCATTAAGGCATGAAAGAATGCC
1 ATAA-TTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCC
* *
138630 ATAAATGAAATGCATGAAA
1 ATAATTAAAATGCATGAAA
138649 GAATGCCATA
Statistics
Matches: 289, Mismatches: 32, Indels: 22
0.84 0.09 0.06
Matches are distributed among these distances:
37 31 0.11
38 1 0.00
39 1 0.00
44 1 0.00
45 39 0.13
46 177 0.61
47 39 0.13
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (46 bp):
ATAATTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCC
Found at i:138536 original size:37 final size:37
Alignment explanation
Indices: 138491--138615 Score: 124
Period size: 37 Copynumber: 3.1 Consensus size: 37
138481 TAAGGTATGA
138491 AAGGATGCCATAACTAAAATGCATGAAATGATGCATT
1 AAGGATGCCATAACTAAAATGCATGAAATGATGCATT
* * * *
138528 AAGGATGCCATAATTTAAATGCATGAAAGGATACATTGACGCATGA
1 AAGGATGCCATAACTAAAATGCAT-----GA-A-A-TGATGCAT-T
138574 AAGGATGCCATAACTAAAAATGCATGAAATGATGCATT
1 AAGGATGCCATAACT-AAAATGCATGAAATGATGCATT
138612 AAGG
1 AAGG
138616 CATGAAAGAA
Statistics
Matches: 70, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
37 22 0.31
38 4 0.06
39 7 0.10
40 1 0.01
41 1 0.01
42 4 0.06
43 1 0.01
44 1 0.01
45 7 0.10
46 14 0.20
47 8 0.11
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (37 bp):
AAGGATGCCATAACTAAAATGCATGAAATGATGCATT
Found at i:138559 original size:26 final size:25
Alignment explanation
Indices: 138528--138680 Score: 101
Period size: 26 Copynumber: 6.3 Consensus size: 25
138518 ATGATGCATT
138528 AAGGATGCCATAATTTAAATGCATGA
1 AAGGATGCCATAA-TTAAATGCATGA
* * *
138554 AAGGAT---A-CATT-GACGCATGA
1 AAGGATGCCATAATTAAATGCATGA
*
138574 AAGGATGCCATAACTAAAAATGCATGA
1 AAGGATGCCATAA-T-TAAATGCATGA
* *
138601 AATGATG-C---ATT-AAGGCATGA
1 AAGGATGCCATAATTAAATGCATGA
* *
138621 AAGAATGCCATAAATGAAATGCATGA
1 AAGGATGCCAT-AATTAAATGCATGA
* *
138647 AAGAATGCCATAAATGAAATGCATGA
1 AAGGATGCCAT-AATTAAATGCATGA
138673 AAGGATGC
1 AAGGATGC
138681 ATTAAGGTAT
Statistics
Matches: 99, Mismatches: 15, Indels: 26
0.71 0.11 0.19
Matches are distributed among these distances:
20 26 0.26
21 3 0.03
22 2 0.02
23 3 0.03
24 1 0.01
25 3 0.03
26 48 0.48
27 13 0.13
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.21
Consensus pattern (25 bp):
AAGGATGCCATAATTAAATGCATGA
Found at i:138572 original size:128 final size:130
Alignment explanation
Indices: 138400--138648 Score: 376
Period size: 128 Copynumber: 1.9 Consensus size: 130
138390 TAAGGCATGA
* * *
138400 AAGGATGCCATAATTAAAATGCATGAAAGGAAACATTAAGGCATGAAAGGATTCCATAA-T-TAA
1 AAGGATGCCATAATTAAAATGCATGAAAGGAAACATTAACGCATGAAAGGATGCCATAACTAAAA
* * *
138463 ATGCATGAAAAAATGCATTAAGGTATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCATT
66 ATGCATGAAAAAATGCATTAAGGCATGAAAGAATGCCATAAATAAAATGCATGAAATGATGCATT
* * *
138528 AAGGATGCCATAATTTAAATGCATGAAAGGATACATTGACGCATGAAAGGATGCCATAACTAAAA
1 AAGGATGCCATAATTAAAATGCATGAAAGGAAACATTAACGCATGAAAGGATGCCATAACTAAAA
** *
138593 ATGCATGAAATGATGCATTAAGGCATGAAAGAATGCCATAAATGAAATGCATGAAA
66 ATGCATGAAAAAATGCATTAAGGCATGAAAGAATGCCATAAATAAAATGCATGAAA
138649 GAATGCCATA
Statistics
Matches: 107, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
128 54 0.50
129 1 0.01
130 52 0.49
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.22
Consensus pattern (130 bp):
AAGGATGCCATAATTAAAATGCATGAAAGGAAACATTAACGCATGAAAGGATGCCATAACTAAAA
ATGCATGAAAAAATGCATTAAGGCATGAAAGAATGCCATAAATAAAATGCATGAAATGATGCATT
Found at i:138584 original size:83 final size:83
Alignment explanation
Indices: 138446--138615 Score: 261
Period size: 83 Copynumber: 2.0 Consensus size: 83
138436 TAAGGCATGA
* * * *
138446 AAGGATTCCATAATTAAATGCATGAAAAAATGCATTAAGGTATGAAAGGATGCCATAACT-AAAA
1 AAGGATGCCATAATTAAATGCATGAAAAAATACATTAACGCATGAAAGGATGCCATAACTAAAAA
138510 TGCATGAAATGATGCATT
66 TGCATGAAATGATGCATT
** *
138528 AAGGATGCCATAATTTAAATGCATGAAAGGATACATTGACGCATGAAAGGATGCCATAACTAAAA
1 AAGGATGCCATAA-TTAAATGCATGAAAAAATACATTAACGCATGAAAGGATGCCATAACTAAAA
138593 ATGCATGAAATGATGCATT
65 ATGCATGAAATGATGCATT
138612 AAGG
1 AAGG
138616 CATGAAAGAA
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
82 12 0.15
83 41 0.52
84 26 0.33
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (83 bp):
AAGGATGCCATAATTAAATGCATGAAAAAATACATTAACGCATGAAAGGATGCCATAACTAAAAA
TGCATGAAATGATGCATT
Found at i:138619 original size:47 final size:45
Alignment explanation
Indices: 138528--138649 Score: 145
Period size: 47 Copynumber: 2.6 Consensus size: 45
138518 ATGATGCATT
* *
138528 AAGGATGCCATAATTTAAATGCATGAAAGGATACATTGACGCATGA
1 AAGGATGCCATAA-TAAAATGCATGAAAGGATACATTAACGCATGA
* * *
138574 AAGGATGCCATAACTAAAAATGCATGAAATGATGCATTAAGGCATGA
1 AAGGATGCCATAA-T-AAAATGCATGAAAGGATACATTAACGCATGA
* *
138621 AAGAATGCCATAAATGAAATGCATGAAAG
1 AAGGATGCCAT-AATAAAATGCATGAAAG
138650 AATGCCATAA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
46 26 0.40
47 37 0.57
48 2 0.03
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.21
Consensus pattern (45 bp):
AAGGATGCCATAATAAAATGCATGAAAGGATACATTAACGCATGA
Found at i:138681 original size:72 final size:73
Alignment explanation
Indices: 138568--138710 Score: 209
Period size: 72 Copynumber: 2.0 Consensus size: 73
138558 ATACATTGAC
* * *
138568 GCATGAAAGGATGCCATAACTAAAAATGCATGAAATGATGCATTAAGGCATGAAA-GAATGCCAT
1 GCATGAAAGAATGCCATAAATAAAAATGCATGAAAGGATGCATTAAGGCATGAAATG-ATGCCAT
138632 AAATGAAAT
65 AAATGAAAT
* * *
138641 GCATGAAAGAATGCCATAAAT-GAAATGCATGAAAGGATGCATTAAGGTATGAAATGATGTCATA
1 GCATGAAAGAATGCCATAAATAAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGCCATA
138705 AATGAA
66 AATGAA
138711 TTTAATGAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
72 43 0.68
73 20 0.32
ACGTcount: A:0.46, C:0.10, G:0.22, T:0.22
Consensus pattern (73 bp):
GCATGAAAGAATGCCATAAATAAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGCCATA
AATGAAAT
Done.