Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002677.1 Hibiscus syriacus cultivar Beakdansim tig00005534_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: 108784
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4370 original size:10 final size:10
Alignment explanation
Indices: 4355--4384 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
4345 TGTAAATTAA
*
4355 TAATAATAGT
1 TAATAATAAT
4365 TAATAATAAT
1 TAATAATAAT
4375 TAATAATAAT
1 TAATAATAAT
4385 AAAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (10 bp):
TAATAATAAT
Found at i:4386 original size:13 final size:14
Alignment explanation
Indices: 4349--4386 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
4339 GTAATATGTA
4349 AATTAATAATAA-T
1 AATTAATAATAATT
*
4362 AGTTAATAATAATT
1 AATTAATAATAATT
4376 AA-TAATAATAA
1 AATTAATAATAA
4387 AAAAATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 20 0.91
14 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (14 bp):
AATTAATAATAATT
Found at i:8890 original size:21 final size:21
Alignment explanation
Indices: 8864--9119 Score: 209
Period size: 21 Copynumber: 12.6 Consensus size: 21
8854 CTATTTTAAA
8864 ATTTATTTTAAATATAGATTG
1 ATTTATTTTAAATATAGATTG
8885 ATTTATTTTAAA-ATA-ATT-
1 ATTTATTTTAAATATAGATTG
***
8903 ATTTA----AAATAT-GAAAA
1 ATTTATTTTAAATATAGATTG
* *
8919 AATTATTTTAAAATATGGATTG
1 ATTTATTTT-AAATATAGATTG
*
8941 ATTTATTTAAAATATAGATTG
1 ATTTATTTTAAATATAGATTG
***
8962 ATTTATTTTAAA-ATATGAAAA
1 ATTTATTTTAAATATA-GATTG
* *
8983 AATTATTTAAAATATA-ATTG
1 ATTTATTTTAAATATAGATTG
9003 ATTT-TTTTAAAATATAGATTG
1 ATTTATTTT-AAATATAGATTG
* **
9024 ATTTATTTTAAAATATGGA-AA
1 ATTTATTTT-AAATATAGATTG
9045 ATTTATTTTAAA-ATATG-TTG
1 ATTTATTTTAAATATA-GATTG
9065 ATTTATTTTAAA-ATATGATTG
1 ATTTATTTTAAATATA-GATTG
*
9086 ATTTATTTTAAAATATGGATTG
1 ATTTATTTT-AAATATAGATTG
9108 ATTTATTTTAAA
1 ATTTATTTTAAA
9120 AAATTTATTG
Statistics
Matches: 189, Mismatches: 27, Indels: 38
0.74 0.11 0.15
Matches are distributed among these distances:
14 3 0.02
15 3 0.02
16 4 0.02
18 5 0.03
19 8 0.04
20 38 0.20
21 84 0.44
22 42 0.22
23 2 0.01
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.48
Consensus pattern (21 bp):
ATTTATTTTAAATATAGATTG
Found at i:9049 original size:83 final size:84
Alignment explanation
Indices: 8894--9120 Score: 280
Period size: 83 Copynumber: 2.7 Consensus size: 84
8884 GATTTATTTT
*** *
8894 AAAATAATTATTTAAAATATGAAAAAATTATTTTAAAATATGGATTGATTTA-TTTAAAATATAG
1 AAAA-AATTATTTAAAATAT-AATTGATTTTTTTAAAATATGGATTGATTTATTTTAAAATATAG
**
8958 ATTGATTTATTTTAAAATATG
64 ATAAATTTATTTTAAAATATG
* *
8979 AAAAAATTATTTAAAATATAATTGATTTTTTTAAAATATAGATTGATTTATTTTAAAATATGGA-
1 AAAAAATTATTTAAAATATAATTGATTTTTTTAAAATATGGATTGATTTATTTTAAAATATAGAT
9043 AAATTTATTTTAAAATATG
66 AAATTTATTTTAAAATATG
*** * *
9062 -TTGATTTATTTTAAAATATGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAA
1 AAAAAATTA-TTTAAAATATAATTGATTT-TTTTAAAATATGGATTGATTTATTTTAAAA
9121 AATTTATTGT
Statistics
Matches: 125, Mismatches: 14, Indels: 7
0.86 0.10 0.05
Matches are distributed among these distances:
82 4 0.03
83 61 0.49
84 56 0.45
85 4 0.03
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (84 bp):
AAAAAATTATTTAAAATATAATTGATTTTTTTAAAATATGGATTGATTTATTTTAAAATATAGAT
AAATTTATTTTAAAATATG
Found at i:9104 original size:62 final size:64
Alignment explanation
Indices: 8904--9102 Score: 318
Period size: 62 Copynumber: 3.2 Consensus size: 64
8894 AAAATAATTA
*
8904 TTTAAAATATGAAAAAATTATTTTAAAATATGGATTGATTTA-TTTAAAATATAGATTGATTTAT
1 TTTAAAATATGAAAAAATTATTTTAAAATATAG-TTGATTTATTTTAAAATATAGATTGATTTAT
*
8968 TTTAAAATATGAAAAAATTA-TTTAAAATATAATTGATTT-TTTTAAAATATAGATTGATTTAT
1 TTTAAAATATGAAAAAATTATTTTAAAATATAGTTGATTTATTTTAAAATATAGATTGATTTAT
* *
9030 TTTAAAATATGGAAAATTTATTTTAAAATAT-GTTGATTTATTTTAAAATAT-GATTGATTTAT
1 TTTAAAATATGAAAAAATTATTTTAAAATATAGTTGATTTATTTTAAAATATAGATTGATTTAT
9092 TTTAAAATATG
1 TTTAAAATATG
9103 GATTGATTTA
Statistics
Matches: 127, Mismatches: 5, Indels: 8
0.91 0.04 0.06
Matches are distributed among these distances:
62 76 0.60
63 31 0.24
64 20 0.16
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (64 bp):
TTTAAAATATGAAAAAATTATTTTAAAATATAGTTGATTTATTTTAAAATATAGATTGATTTAT
Found at i:21026 original size:29 final size:29
Alignment explanation
Indices: 20991--21056 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
20981 AACATAATGA
20991 ATAGTCGGATGACAATTTTGTAACTTTTG
1 ATAGTCGGATGACAATTTTGTAACTTTTG
*
21020 ATAGTCGGATGACCATTTTGTAACTTTTG
1 ATAGTCGGATGACAATTTTGTAACTTTTG
21049 ATAGTCGG
1 ATAGTCGG
21057 TAGACTTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (29 bp):
ATAGTCGGATGACAATTTTGTAACTTTTG
Found at i:21846 original size:5 final size:5
Alignment explanation
Indices: 21836--21862 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
21826 TGGATGGTAT
21836 GAGTC GAGTC GAGTC GAGTC GAGTC GA
1 GAGTC GAGTC GAGTC GAGTC GAGTC GA
21863 ATTAAGTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.19, G:0.41, T:0.19
Consensus pattern (5 bp):
GAGTC
Found at i:23201 original size:42 final size:40
Alignment explanation
Indices: 23135--23232 Score: 137
Period size: 42 Copynumber: 2.4 Consensus size: 40
23125 TGTTTATTAT
* *
23135 AATATATTTATAATTATTTATTATATTTTAAATTATTAAAAG
1 AATATATTTATAATAATTTATTATATTTT-AATAATT-AAAG
23177 AATATATTATATAATAATTT-TTATATTTTAATAATTAAAG
1 AATATATT-TATAATAATTTATTATATTTTAATAATTAAAG
23217 AATATATTT-TAATAAT
1 AATATATTTATAATAAT
23233 ATAAAAACAA
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
38 7 0.13
39 1 0.02
40 12 0.23
41 6 0.11
42 17 0.32
43 10 0.19
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (40 bp):
AATATATTTATAATAATTTATTATATTTTAATAATTAAAG
Found at i:29141 original size:33 final size:32
Alignment explanation
Indices: 29088--29158 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
29078 TTGGTATTCA
29088 GGTC-GATTTTTTTTAAAAAAAAAATCGGGATCG
1 GGTCGGATTTTTTTT--AAAAAAAATCGGGATCG
* *
29121 GGTCGGATTTGTTTTT-AAAAAAATCGGGTTTG
1 GGTCGGATTT-TTTTTAAAAAAAATCGGGATCG
29153 GGTCGG
1 GGTCGG
29159 GTTTAGGGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 20 0.59
33 4 0.12
34 5 0.15
35 5 0.15
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.35
Consensus pattern (32 bp):
GGTCGGATTTTTTTTAAAAAAAATCGGGATCG
Found at i:31936 original size:18 final size:18
Alignment explanation
Indices: 31915--31954 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31905 CTAGTGATTT
*
31915 CTCCCGGCCTAGCGACTA
1 CTCCCGACCTAGCGACTA
* *
31933 CTCCCGACCTAGTGATTA
1 CTCCCGACCTAGCGACTA
31951 CTCC
1 CTCC
31955 AGAATAGGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.42, G:0.17, T:0.23
Consensus pattern (18 bp):
CTCCCGACCTAGCGACTA
Found at i:34804 original size:3 final size:3
Alignment explanation
Indices: 34798--34846 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
34788 TTTTTTTGTA
**
34798 TAT TAT TAT TAT CGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
34846 T
1 T
34847 TAATTTACAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:38520 original size:31 final size:33
Alignment explanation
Indices: 38484--38546 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
38474 ATTTTACATG
38484 TACTAACTT-ATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTAATTTCTTCTCTTTTGTTTGTGTA
38515 TACTAACTTAATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTAATTTCTTCTCTTTTGTTTGTGT
38547 CATTTTGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 9 0.30
32 4 0.13
33 17 0.57
ACGTcount: A:0.16, C:0.14, G:0.10, T:0.60
Consensus pattern (33 bp):
TACTAACTTAATTTCTTCTCTTTTGTTTGTGTA
Found at i:41001 original size:26 final size:25
Alignment explanation
Indices: 40970--41049 Score: 80
Period size: 26 Copynumber: 3.3 Consensus size: 25
40960 CCAATTTTTG
40970 ACATTCTATCTCTTTGAGACCTTG-A
1 ACATTCT-TCTCTTTGAGACCTTGAA
* *
40995 A-A-TATTCT-TTT-CGACCTTGAA
1 ACATTCTTCTCTTTGAGACCTTGAA
*
41016 ACATTCCCTCTCTTTGAGACCTTGAA
1 ACATT-CTTCTCTTTGAGACCTTGAA
41042 ACATTCTT
1 ACATTCTT
41050 TCCACCTTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
20 7 0.16
21 5 0.12
22 4 0.09
23 3 0.07
24 4 0.09
25 6 0.14
26 14 0.33
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (25 bp):
ACATTCTTCTCTTTGAGACCTTGAA
Found at i:41677 original size:22 final size:22
Alignment explanation
Indices: 41650--41758 Score: 96
Period size: 22 Copynumber: 4.7 Consensus size: 22
41640 AAGATCCAAT
41650 CAAAAACAAAGAAAAATCAAAG
1 CAAAAACAAAGAAAAATCAAAG
* *
41672 AGAAAAGAGCAAAGAAAAAAACAAAGAG
1 -CAAAA-A-CAAAG-AAAAATC-AA-AG
* * *
41700 CAGAGA-GAA-AAAAATCAAAG
1 CAAAAACAAAGAAAAATCAAAG
41720 CAAAAACAAAGAAAAATCAAAG
1 CAAAAACAAAGAAAAATCAAAG
41742 CAAAAATCAAAGAAAAA
1 CAAAAA-CAAAGAAAAA
41759 AACAAAGAAC
Statistics
Matches: 68, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
20 6 0.09
21 4 0.06
22 23 0.34
23 14 0.21
24 3 0.04
25 5 0.07
26 7 0.10
27 4 0.06
28 2 0.03
ACGTcount: A:0.72, C:0.11, G:0.14, T:0.04
Consensus pattern (22 bp):
CAAAAACAAAGAAAAATCAAAG
Found at i:41696 original size:12 final size:12
Alignment explanation
Indices: 41651--41773 Score: 78
Period size: 12 Copynumber: 10.4 Consensus size: 12
41641 AGATCCAATC
41651 AAAAACAAAG-A
1 AAAAACAAAGAA
*
41662 AAAATCAAAGAGA
1 AAAAACAAAGA-A
*
41675 AAAGAGCAAAGAA
1 AAA-AACAAAGAA
41688 AAAAACAAAG--
1 AAAAACAAAGAA
** * *
41698 -AGCAGAGAGAA
1 AAAAACAAAGAA
*
41709 AAAAATCAAAG-C
1 AAAAA-CAAAGAA
41721 AAAAACAAAG-A
1 AAAAACAAAGAA
* *
41732 AAAATCAAAGCA
1 AAAAACAAAGAA
*
41744 AAAATCAAAGAA
1 AAAAACAAAGAA
41756 AAAAACAAAGAA
1 AAAAACAAAGAA
41768 CAAAAA
1 -AAAAA
41774 GAGGACAAAG
Statistics
Matches: 87, Mismatches: 16, Indels: 16
0.73 0.13 0.13
Matches are distributed among these distances:
9 5 0.06
11 23 0.26
12 36 0.41
13 16 0.18
14 7 0.08
ACGTcount: A:0.73, C:0.11, G:0.13, T:0.03
Consensus pattern (12 bp):
AAAAACAAAGAA
Found at i:41699 original size:19 final size:22
Alignment explanation
Indices: 41675--41719 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
41665 ATCAAAGAGA
41675 AAAGAGCA-A-AGAAAAAAA-C
1 AAAGAGCAGAGAGAAAAAAATC
41694 AAAGAGCAGAGAGAAAAAAATC
1 AAAGAGCAGAGAGAAAAAAATC
41716 AAAG
1 AAAG
41720 CAAAAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.35
20 1 0.04
21 9 0.39
22 5 0.22
ACGTcount: A:0.69, C:0.09, G:0.20, T:0.02
Consensus pattern (22 bp):
AAAGAGCAGAGAGAAAAAAATC
Found at i:42882 original size:4 final size:4
Alignment explanation
Indices: 42873--42982 Score: 152
Period size: 4 Copynumber: 28.0 Consensus size: 4
42863 AAGAGTATAC
* * * *
42873 ACAT ACAT ACAT ACGT ATAC ACAT ACAT ACAT ATAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
42921 ACAT ACAT ACAT ACAT ACAT ACAT ATAT ACAT ACAT ATAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
42969 ACAT --AT ACAT ACAT
1 ACAT ACAT ACAT ACAT
42983 GATACATAAA
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
2 2 0.02
4 90 0.98
ACGTcount: A:0.49, C:0.22, G:0.01, T:0.28
Consensus pattern (4 bp):
ACAT
Found at i:43378 original size:36 final size:36
Alignment explanation
Indices: 43338--43436 Score: 180
Period size: 36 Copynumber: 2.8 Consensus size: 36
43328 GATTTTTCTA
43338 AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
43374 AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
**
43410 AAAACAAATTTTGTCTCATTTGAGACA
1 AAAACAAATTTTGTCTCGCTTGAGACA
43437 TTTTCCCTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.37
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCGCTTGAGACAATTTATTTC
Found at i:43765 original size:101 final size:98
Alignment explanation
Indices: 43559--43792 Score: 251
Period size: 101 Copynumber: 2.3 Consensus size: 98
43549 TGAGAATTTT
** * *
43559 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACT
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
*
43624 AAAAACAAAATCTCACCTTAGATTGTTGTTTCTTTC
66 AAAAACAAAATCTCACCTTAGA-T-TCGTTTC-TTC
* * *
43660 AAAACAAATTTTGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCAC-
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
*
43724 ATTAAACAAAGTTGATCTCA-CTTGAGA-TCGTTTC-TC
66 A-AAAACAAA----ATCTCACCTT-AGATTCGTTTCTTC
* *
43760 AAAAACAAACTTTGTCTCGCTTGAGACAATTTC
1 -AAAACAAATTTTGTCTCGCTTGAGACATTTTC
43793 TCTAAAAACA
Statistics
Matches: 114, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
100 3 0.03
101 93 0.82
102 6 0.05
104 3 0.03
105 9 0.08
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (98 bp):
AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
AAAAACAAAATCTCACCTTAGATTCGTTTCTTC
Found at i:43766 original size:35 final size:36
Alignment explanation
Indices: 43739--43857 Score: 113
Period size: 36 Copynumber: 3.4 Consensus size: 36
43729 ACAAAGTTGA
*
43739 TCTCACTTGAGATC-GTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTTCTCTAAAAACAAACTTTG
* *
43774 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
* * * *
43810 TCTCATTTGAGACTATATCT-T-AAAGCAAA-TTTCG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTT-G
*
43844 TCTCGCTTGAGACA
1 TCTCACTTGAGACA
43858 TCATTTTCTC
Statistics
Matches: 70, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
33 3 0.04
34 20 0.29
35 18 0.26
36 29 0.41
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
Found at i:43810 original size:36 final size:36
Alignment explanation
Indices: 43754--43857 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
43744 CTTGAGATCG
*
43754 TTTCTC-AAAAACAAACTTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
** *
43789 TTTCTCTAAAAACAAATTTTGTCTCATTTGAGACTA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
* * *
43825 TATCT-T-AAAGCAAATTTCGTCTCGCTTGAGACA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACA
43858 TCATTTTCTC
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 22 0.38
35 7 0.12
36 29 0.50
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.36
Consensus pattern (36 bp):
TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
Found at i:44148 original size:29 final size:28
Alignment explanation
Indices: 44106--44370 Score: 182
Period size: 29 Copynumber: 9.2 Consensus size: 28
44096 ACAGTTTCTC
44106 TTGAAAAAAATCTTTGAGTTTGTTCCTT
1 TTGAAAAAAATCTTTGAGTTTGTTCCTT
* *
44134 TAGAATAAAAATCTTGGAGTTTGTTCCTT
1 TTGAA-AAAAATCTTTGAGTTTGTTCCTT
* *
44163 TTGAATAAATATCTTTGAG-TTGTTTCTT
1 TTGAA-AAAAATCTTTGAGTTTGTTCCTT
* * **
44191 TTG--AAAAATCTTTGAGTCTATTTATT
1 TTGAAAAAAATCTTTGAGTTTGTTCCTT
* *** * *
44217 TTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTC
1 TTGAAA-AAA-------ATCT-TTGAGTTTGTTCCTT
44254 TTGAAAAAAATCTTTGAGTTTGTTCCTT
1 TTGAAAAAAATCTTTGAGTTTGTTCCTT
* *
44282 TAGAATAAAAATCTTGGAGTTTGTTCCTT
1 TTGAA-AAAAATCTTTGAGTTTGTTCCTT
* *
44311 TTGAATAAATATCTTTGAG-TTGTTTCTT
1 TTGAA-AAAAATCTTTGAGTTTGTTCCTT
* * *
44339 TTG--AAAAATCTTTGAGTCTATTCATT
1 TTGAAAAAAATCTTTGAGTTTGTTCCTT
44365 TTGAAA
1 TTGAAA
44371 CAAAGTTTTG
Statistics
Matches: 187, Mismatches: 33, Indels: 34
0.74 0.13 0.13
Matches are distributed among these distances:
25 24 0.13
26 17 0.09
28 42 0.22
29 82 0.44
36 6 0.03
37 16 0.09
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.46
Consensus pattern (28 bp):
TTGAAAAAAATCTTTGAGTTTGTTCCTT
Found at i:44255 original size:148 final size:148
Alignment explanation
Indices: 44080--44399 Score: 622
Period size: 148 Copynumber: 2.2 Consensus size: 148
44070 AAACGATTTT
44080 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTTTAGAATAAAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTTTAGAATAAAAA
44145 TCTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCT
66 TCTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCT
*
44210 ATTTATTTTGAAACAAAG
131 ATTCATTTTGAAACAAAG
44228 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTTTAGAATAAAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTTTAGAATAAAAA
44293 TCTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCT
66 TCTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCT
44358 ATTCATTTTGAAACAAAG
131 ATTCATTTTGAAACAAAG
*
44376 TTTTGTCTCTCTTGAGACAATTTC
1 TTTTGTCTCTCTTGAGACAGTTTC
44400 GTGAAAAATC
Statistics
Matches: 170, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
148 170 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (148 bp):
TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTCCTTTAGAATAAAAA
TCTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCT
ATTCATTTTGAAACAAAG
Found at i:44444 original size:52 final size:53
Alignment explanation
Indices: 44366--44469 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 53
44356 CTATTCATTT
*
44366 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCCTGAGACAATTTCGTGAAAAAATCTTTGAGTC
*
44418 TGAAACAAAGTTTTGTCTCTCCTGAGACAATTTTGTGAAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCCTGAGACAATTTCGTG-AAAAAATCTTTGAG
44470 ATTGTTTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 35 0.73
54 13 0.27
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (53 bp):
TGAAACAAAGTTTTGTCTCTCCTGAGACAATTTCGTGAAAAAATCTTTGAGTC
Found at i:44491 original size:30 final size:30
Alignment explanation
Indices: 44457--44520 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
44447 ATTTTGTGAA
*
44457 AAAAATCTTTGAGATTGTTTCTTTTGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
*
44487 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
44517 AAAA
1 AAAA
44521 TTTTGTCTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (30 bp):
AAAAATCTTTGAGATTGTTTCTTTGGAAAC
Found at i:44521 original size:29 final size:29
Alignment explanation
Indices: 44449--44525 Score: 104
Period size: 30 Copynumber: 2.7 Consensus size: 29
44439 CTGAGACAAT
44449 TTTGTGAAA-AAAATCTTTGAGATTGTTTC
1 TTTG-GAAACAAAATCTTTGAGATTGTTTC
* *
44478 TTTTGAAACAAAAATCTTTGAGTTTGTTTC
1 TTTGGAAAC-AAAATCTTTGAGATTGTTTC
44508 TTTGGAAACAAAAT-TTTG
1 TTTGGAAACAAAATCTTTG
44526 TCTCTCTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 8 0.19
29 8 0.19
30 27 0.63
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (29 bp):
TTTGGAAACAAAATCTTTGAGATTGTTTC
Found at i:44812 original size:120 final size:119
Alignment explanation
Indices: 44674--44897 Score: 276
Period size: 120 Copynumber: 1.9 Consensus size: 119
44664 TTAACAAAAT
* * *
44674 CATCTTTGAGTCTATTTCTTTAAAAAC-AAATGTTGTCTCTCTT-GAGACAGTTTCTAATGAAAA
1 CATCTTTGAGTCTATTTCTTTAAAAACAAAAT-TT-TATCTCTTAAAGACAATTTCTAATGAAAA
44737 ACTAA-CTTTTGAGATTGTTTCATTTGAAAC-AAATTTGGTCTCACTTAAGATGGGATC
64 A--AATC-TTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGGGATC
* ** **
44794 CATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAA
1 CATCTTTGAGTCTATTTCTTTAAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAAA
* * *
44859 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC
66 ATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTC
44898 TCGAGACAAC
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
118 23 0.26
119 19 0.21
120 43 0.48
121 4 0.04
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (119 bp):
CATCTTTGAGTCTATTTCTTTAAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAAA
ATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGGGATC
Found at i:44874 original size:64 final size:63
Alignment explanation
Indices: 44795--44919 Score: 187
Period size: 64 Copynumber: 2.0 Consensus size: 63
44785 GATGGGATCC
* *
44795 ATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTC-TAAAGACAACTTCTTTTGAAAAAA
* * **
44859 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAA
44920 TACCCACATT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
63 19 0.35
64 36 0.65
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (63 bp):
ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAAAA
Found at i:44964 original size:40 final size:40
Alignment explanation
Indices: 44901--44980 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
44891 TTGTCTCTCG
44901 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
* * *
44941 AGACAATTTCTTTT-AAAACTACCCACCTTTGAGATTGTTT
1 AGACAACTTCTTTTGAAAA-TACCCACATTTGAGATCGTTT
44981 TTATTAAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (40 bp):
AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
Found at i:45099 original size:15 final size:15
Alignment explanation
Indices: 45076--45119 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
45066 TTTTGAGTCG
*
45076 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
45091 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
*
45106 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
45120 AGATCATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:45447 original size:38 final size:36
Alignment explanation
Indices: 45405--45494 Score: 110
Period size: 36 Copynumber: 2.4 Consensus size: 36
45395 CATTTGAATC
45405 TGTTTTTCTTGAAACAAAACAAACAA-AGTCTTTGAGTA
1 TGTTTTTCTTGAAACAAAA-AAA-AACA-TCTTTGAGTA
* *
45443 TGTTTTTCTTAAAACAAAAAAAAACATCTTTGAGTT
1 TGTTTTTCTTGAAACAAAAAAAAACATCTTTGAGTA
* *
45479 TGTTTCTCTCGAAACA
1 TGTTTTTCTTGAAACA
45495 CTAATCTTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
36 24 0.52
37 4 0.09
38 18 0.39
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (36 bp):
TGTTTTTCTTGAAACAAAAAAAAACATCTTTGAGTA
Found at i:45483 original size:36 final size:38
Alignment explanation
Indices: 45405--45483 Score: 110
Period size: 38 Copynumber: 2.1 Consensus size: 38
45395 CATTTGAATC
*
45405 TGTTTTTCTTGAAACAAAACAAACAAAGTCTTTGAGTA
1 TGTTTTTCTTAAAACAAAACAAACAAAGTCTTTGAGTA
*
45443 TGTTTTTCTTAAAACAAAA-AAA-AACA-TCTTTGAGTT
1 TGTTTTTCTTAAAACAAAACAAACAA-AGTCTTTGAGTA
45479 TGTTT
1 TGTTT
45484 CTCTCGAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
36 16 0.42
37 4 0.11
38 18 0.47
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.39
Consensus pattern (38 bp):
TGTTTTTCTTAAAACAAAACAAACAAAGTCTTTGAGTA
Found at i:45494 original size:36 final size:35
Alignment explanation
Indices: 45353--45494 Score: 106
Period size: 36 Copynumber: 3.9 Consensus size: 35
45343 TTTCTTTGAG
**
45353 AAAAATCTTTGAGTTTGTTTCT-TTGGAAACAAATTT
1 AAAAATCTTTGAGTTTGTTTCTCTT-GAAACAAA-AA
* ** * * *
45389 TACCATCATTTGAATCTGTTTTTCTTGAAACAAAACA
1 AAAAATC-TTTGAGTTTGTTTCTCTTGAAACAAAA-A
* * *
45426 AACAAAGTCTTTGAGTATGTTTTTCTTAAAACAAAAA
1 AA-AAA-TCTTTGAGTTTGTTTCTCTTGAAACAAAAA
*
45463 AAAACATCTTTGAGTTTGTTTCTCTCGAAACA
1 AAAA-ATCTTTGAGTTTGTTTCTCTTGAAACA
45495 CTAATCTTTG
Statistics
Matches: 82, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
36 28 0.34
37 25 0.30
38 27 0.33
39 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (35 bp):
AAAAATCTTTGAGTTTGTTTCTCTTGAAACAAAAA
Found at i:45552 original size:36 final size:34
Alignment explanation
Indices: 45499--45612 Score: 98
Period size: 36 Copynumber: 3.4 Consensus size: 34
45489 GAAACACTAA
*
45499 TCTTTGAGATCA-ATTCCCTTTAAACGAACTTTGTC
1 TCTTTGAGA-CAGTTTCCCTTTAAACGAA-TTTGTC
*
45534 TCATTTGAGACAGTTTCCCTTTAAACG---TCG--
1 TC-TTTGAGACAGTTTCCCTTTAAACGAATTTGTC
* *
45564 TCTTTGAGTC-GTTTCCCTTAAAACGAATTTTGTC
1 TCTTTGAGACAGTTTCCCTTTAAACGAA-TTTGTC
45598 TCTTTTGAGACAGTT
1 TC-TTTGAGACAGTT
45613 GCTTTTAAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 19
0.72 0.07 0.22
Matches are distributed among these distances:
28 14 0.22
29 7 0.11
30 2 0.03
32 4 0.06
34 2 0.03
35 11 0.17
36 23 0.37
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (34 bp):
TCTTTGAGACAGTTTCCCTTTAAACGAATTTGTC
Found at i:45830 original size:43 final size:44
Alignment explanation
Indices: 45739--45967 Score: 185
Period size: 43 Copynumber: 5.4 Consensus size: 44
45729 TGGCCAGCCG
* *
45739 TCCTCATCATGTAGGAACCGTGTCATCACC--AG---ACCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCAT-ACCATAGATAACCAGATC
* *
45779 TCCTCATCACGTAGGAGCCGTGTCA-ACCATATATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGATC
* * * ** *
45821 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAGCCGTGTCAT-ACC-ATAGATAACCAGATC
* * * **
45868 TCTTCATCACGTATGAGCCGTGTCATTCCCCAGAT---CAGATC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGATC
45909 TCCTCATCACGTAGGAGCCGTGTCA-ACCATAGATAACCAG-TC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGATC
*
45951 GTCCCCATCACGTAGGA
1 -TCCTCATCACGTAGGA
45968 ACCGAGTTAT
Statistics
Matches: 150, Mismatches: 25, Indels: 25
0.75 0.12 0.12
Matches are distributed among these distances:
38 3 0.02
40 30 0.20
41 28 0.19
42 3 0.02
43 46 0.31
44 4 0.03
45 5 0.03
46 30 0.20
47 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (44 bp):
TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGATC
Found at i:45960 original size:130 final size:132
Alignment explanation
Indices: 45742--46068 Score: 448
Period size: 130 Copynumber: 2.5 Consensus size: 132
45732 CCAGCCGTCC
* * *
45742 TCATCATGTAGGAACCGTGTCATCACCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
1 TCATCATGTATGAGCCGTGTCATCCCCAGA-CAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
* * *
45807 ATATATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA-CCTT-T-AGATGGCC-AGAAC
65 ATAGATAACCAGCCGTCCCCATCACGTAGGAACCGAGTTATCACCCTTCTAAGATGGCCAAGAAC
45868 TCT
130 TCT
*
45871 TCATCACGTATGAGCCGTGTCATTCCCCAGATCAGATCTCCTCATCACGTAGGAGCCGTGTCAAC
1 TCATCATGTATGAGCCGTGTCA-TCCCCAGA-CAGATCTCCTCATCACGTAGGAGCCGTGTCAAC
*
45936 CATAGATAACCAGTCGTCCCCATCACGTAGGAACCGAGTTATCACCCTTCCTAAAGATGGCCAAG
64 CATAGATAACCAGCCGTCCCCATCACGTAGGAACCGAGTTATCACCCTT-CT-AAGATGGCCAAG
46001 AACTCT
127 AACTCT
* * * *
46007 TCATCATGTATGAGCAGTGTCATCCCTC-GACTAGATTTCCTCATCACGTAGGAACCATGTCA
1 TCATCATGTATGAGCCGTGTCATCCC-CAGAC-AGATCTCCTCATCACGTAGGAGCCGTGTCA
46069 CCCTTAGACG
Statistics
Matches: 175, Mismatches: 14, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
129 19 0.11
130 80 0.46
131 4 0.02
133 1 0.01
134 1 0.01
135 41 0.23
136 29 0.17
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.24
Consensus pattern (132 bp):
TCATCATGTATGAGCCGTGTCATCCCCAGACAGATCTCCTCATCACGTAGGAGCCGTGTCAACCA
TAGATAACCAGCCGTCCCCATCACGTAGGAACCGAGTTATCACCCTTCTAAGATGGCCAAGAACT
CT
Found at i:46273 original size:3 final size:3
Alignment explanation
Indices: 46267--46312 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
46257 TTTTTTTGTA
**
46267 TAT TAT TAT TAT CGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
46313 TAATTTACAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:49222 original size:53 final size:53
Alignment explanation
Indices: 49142--49247 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
49132 ATATATATAC
49142 ATCTCAAATTGTTCATATCCCCTGCAACTCATCATCATGCACAGCAACATGCG
1 ATCTCAAATTGTTCATATCCCCTGCAACTCATCATCATGCACAGCAACATGCG
*
49195 ATCTCAACTTGTTCATATCCCCTGCAACTCATCATCATGCACAGCAACATGCG
1 ATCTCAAATTGTTCATATCCCCTGCAACTCATCATCATGCACAGCAACATGCG
49248 TACACCTGAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.29, C:0.33, G:0.11, T:0.26
Consensus pattern (53 bp):
ATCTCAAATTGTTCATATCCCCTGCAACTCATCATCATGCACAGCAACATGCG
Found at i:51637 original size:16 final size:16
Alignment explanation
Indices: 51616--51648 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
51606 TAATAAATAA
51616 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
51632 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
51648 A
1 A
51649 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:51738 original size:16 final size:16
Alignment explanation
Indices: 51717--51777 Score: 86
Period size: 16 Copynumber: 3.8 Consensus size: 16
51707 TAATAAATAA
51717 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
51733 ACGAACATAAACAAAA
1 ACGAACATAAACGAAC
* *
51749 ACGAATATAAATGAAC
1 ACGAACATAAACGAAC
51765 ACGAACATAAACG
1 ACGAACATAAACG
51778 TTAGAGACCC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.59, C:0.20, G:0.11, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:51751 original size:32 final size:32
Alignment explanation
Indices: 51715--51776 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
51705 TTTAATAAAT
51715 AAACGAACATAAACGAACACGAACATAAACAA
1 AAACGAACATAAACGAACACGAACATAAACAA
* *
51747 AAACGAATATAAATGAACACGAACATAAAC
1 AAACGAACATAAACGAACACGAACATAAAC
51777 GTTAGAGACC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.61, C:0.19, G:0.10, T:0.10
Consensus pattern (32 bp):
AAACGAACATAAACGAACACGAACATAAACAA
Found at i:52695 original size:14 final size:14
Alignment explanation
Indices: 52678--52713 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
52668 GATTGAGTTA
52678 AACATAAATGAACG
1 AACATAAATGAACG
*
52692 AACATAACTGAACG
1 AACATAAATGAACG
52706 AACATAAA
1 AACATAAA
52714 CAAACATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.58, C:0.17, G:0.11, T:0.14
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:52934 original size:29 final size:29
Alignment explanation
Indices: 52882--52953 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
52872 TTTTTTTAAA
* * * *
52882 TTTTTAAACTTGACACCTTTAAAAGTGTAT
1 TTTTTAAATTTGACACCATCAAAA-TATAT
52912 TTTTTAAATTTGACA-CATCAAAATATAT
1 TTTTTAAATTTGACACCATCAAAATATAT
52940 TTTTTAAAATTTGA
1 TTTTT-AAATTTGA
52954 TGCCTAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 9 0.24
29 14 0.38
30 14 0.38
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.46
Consensus pattern (29 bp):
TTTTTAAATTTGACACCATCAAAATATAT
Found at i:53397 original size:29 final size:29
Alignment explanation
Indices: 53354--53436 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
53344 CTCACCTAAC
53354 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
53384 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
53413 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
53437 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:58167 original size:29 final size:29
Alignment explanation
Indices: 58124--58206 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
58114 CTCACCTAAC
58124 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
58154 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
58183 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
58207 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:59251 original size:111 final size:111
Alignment explanation
Indices: 59070--59290 Score: 379
Period size: 111 Copynumber: 2.0 Consensus size: 111
59060 AACAGTGCTG
* *
59070 GAGAGAATTCGAGGATCAGAGAGAGCAACAAGAAGGGAGAGGCCGCGTCCGCCATGAATCGAGCC
1 GAGAGAATTCGAGGATCAGAGAGAACAACAAGAAGGGAGAGGCCGCGGCCGCCATGAATCGAGCC
*
59135 CCGAAGATCCTCAGAGGAGGTTCAAGGAATGCCAACAACAATGCCA
66 CCGAAGATCCCCAGAGGAGGTTCAAGGAATGCCAACAACAATGCCA
*
59181 GAGAGAATTCGGGGATCAGAGAGAACAACAAGAAGGGAGAGGCCGCGGCCGCCATGAATCGAGCC
1 GAGAGAATTCGAGGATCAGAGAGAACAACAAGAAGGGAGAGGCCGCGGCCGCCATGAATCGAGCC
* * *
59246 CCGAAGATCCCCAGAGGAGGTTCGAGGATTGCCAACAACGATGCC
66 CCGAAGATCCCCAGAGGAGGTTCAAGGAATGCCAACAACAATGCC
59291 GACAATAAGG
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 103 1.00
ACGTcount: A:0.33, C:0.24, G:0.32, T:0.10
Consensus pattern (111 bp):
GAGAGAATTCGAGGATCAGAGAGAACAACAAGAAGGGAGAGGCCGCGGCCGCCATGAATCGAGCC
CCGAAGATCCCCAGAGGAGGTTCAAGGAATGCCAACAACAATGCCA
Found at i:61226 original size:35 final size:34
Alignment explanation
Indices: 61185--61270 Score: 93
Period size: 35 Copynumber: 2.5 Consensus size: 34
61175 AATATTCAAT
61185 TTTTTATTTTTTTTAAAATTATACTTAAAATTTAA
1 TTTTTATTTTTTTTAAAATTATA-TTAAAATTTAA
* ** *
61220 TTTTTATTTCATTTTAGTATTTTATTAAAATTTAA
1 TTTTTATTT-TTTTTAAAATTATATTAAAATTTAA
* *
61255 -TGTTAGTTTTTTTAAA
1 TTTTTATTTTTTTTAAA
61271 TTTTAATTTA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
33 5 0.12
34 6 0.15
35 20 0.49
36 10 0.24
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (34 bp):
TTTTTATTTTTTTTAAAATTATATTAAAATTTAA
Found at i:61269 original size:22 final size:24
Alignment explanation
Indices: 61233--61277 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
61223 TTATTTCATT
61233 TTAGTATTTTATTAAAATTTAATG
1 TTAGTATTTTATTAAAATTTAATG
*
61257 TTAGT-TTTT-TTAAATTTTAAT
1 TTAGTATTTTATTAAAATTTAAT
61278 TTAAAGTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 4 0.20
24 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (24 bp):
TTAGTATTTTATTAAAATTTAATG
Found at i:61783 original size:23 final size:23
Alignment explanation
Indices: 61753--61800 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
61743 CGAGCTGTAT
*
61753 ATTTTCAACTGGTAAAATGATTA
1 ATTTTCAACTGATAAAATGATTA
*
61776 ATTTTCAACTGATAGAATGATTA
1 ATTTTCAACTGATAAAATGATTA
61799 AT
1 AT
61801 ATTATAGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (23 bp):
ATTTTCAACTGATAAAATGATTA
Found at i:68873 original size:21 final size:21
Alignment explanation
Indices: 68838--68909 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
68828 CGGTTAAATT
* *
68838 ATCAATCACCATGGACTGCCAC
1 ATCAA-CACCGTGGACCGCCAC
*
68860 ATTAACACCGTGGACCGCCAC
1 ATCAACACCGTGGACCGCCAC
*
68881 ATCAACATCGTGGACCGCCAC
1 ATCAACACCGTGGACCGCCAC
68902 ATCAACAC
1 ATCAACAC
68910 TATTGACTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 40 0.91
22 4 0.09
ACGTcount: A:0.32, C:0.38, G:0.15, T:0.15
Consensus pattern (21 bp):
ATCAACACCGTGGACCGCCAC
Found at i:71490 original size:31 final size:31
Alignment explanation
Indices: 71455--71521 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
71445 CCAAGTACGG
*
71455 AATTTGGACACCCAAACAAAACAAAAAGT-AT
1 AATTTGGACACCAAAACAAAACAAAAA-TAAT
* * *
71486 AATTTGGGCATCAAAACGAAACAAAAATAAT
1 AATTTGGACACCAAAACAAAACAAAAATAAT
71517 AATTT
1 AATTT
71522 AAATACTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.54, C:0.15, G:0.10, T:0.21
Consensus pattern (31 bp):
AATTTGGACACCAAAACAAAACAAAAATAAT
Found at i:79972 original size:18 final size:18
Alignment explanation
Indices: 79947--80042 Score: 120
Period size: 18 Copynumber: 5.3 Consensus size: 18
79937 AGTTTGTCGC
79947 TTAGGTTTGGCTGATCCT
1 TTAGGTTTGGCTGATCCT
* * *
79965 TCAGGTTTTGTTGATCCT
1 TTAGGTTTGGCTGATCCT
* *
79983 TTAGATTTGTCTGATCCT
1 TTAGGTTTGGCTGATCCT
* *
80001 TCAGGTTTGGTTGATCCT
1 TTAGGTTTGGCTGATCCT
*
80019 TTAGATTTGGCTGATCCT
1 TTAGGTTTGGCTGATCCT
80037 TTAGGT
1 TTAGGT
80043 GTCTTCTGCT
Statistics
Matches: 62, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.14, C:0.16, G:0.24, T:0.47
Consensus pattern (18 bp):
TTAGGTTTGGCTGATCCT
Found at i:79997 original size:36 final size:36
Alignment explanation
Indices: 79947--80042 Score: 156
Period size: 36 Copynumber: 2.7 Consensus size: 36
79937 AGTTTGTCGC
* *
79947 TTAGGTTTGGCTGATCCTTCAGGTTTTGTTGATCCT
1 TTAGATTTGGCTGATCCTTCAGGTTTGGTTGATCCT
*
79983 TTAGATTTGTCTGATCCTTCAGGTTTGGTTGATCCT
1 TTAGATTTGGCTGATCCTTCAGGTTTGGTTGATCCT
*
80019 TTAGATTTGGCTGATCCTTTAGGT
1 TTAGATTTGGCTGATCCTTCAGGT
80043 GTCTTCTGCT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.14, C:0.16, G:0.24, T:0.47
Consensus pattern (36 bp):
TTAGATTTGGCTGATCCTTCAGGTTTGGTTGATCCT
Found at i:82197 original size:42 final size:42
Alignment explanation
Indices: 82151--82247 Score: 119
Period size: 39 Copynumber: 2.4 Consensus size: 42
82141 ATATCAGTTA
* *
82151 CCGGAAATTCGTCTTTGTTACTTCCATTATCAACATCATTCC
1 CCGGAAATTCATCTTTGTCACTTCCATTATCAACATCATTCC
* * *
82193 CCGG-AA-T-ATCTTTGTCACTTCCATTATCGATATCATTTC
1 CCGGAAATTCATCTTTGTCACTTCCATTATCAACATCATTCC
*
82232 CCAGAAATTCATCTTT
1 CCGGAAATTCATCTTT
82248 TGGTGCAGAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
39 30 0.65
40 3 0.07
41 3 0.07
42 10 0.22
ACGTcount: A:0.25, C:0.27, G:0.09, T:0.39
Consensus pattern (42 bp):
CCGGAAATTCATCTTTGTCACTTCCATTATCAACATCATTCC
Found at i:95904 original size:2 final size:2
Alignment explanation
Indices: 95897--95921 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
95887 CTGCCAATGA
95897 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
95922 ATTACTTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:103280 original size:13 final size:13
Alignment explanation
Indices: 103262--103288 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
103252 TTACAGAATC
103262 GCATATGAAGACT
1 GCATATGAAGACT
103275 GCATATGAAGACT
1 GCATATGAAGACT
103288 G
1 G
103289 TTTAACTATG
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:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Done.