Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007752.1 Hibiscus syriacus cultivar Beakdansim tig00110018_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: 61922
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2505 original size:21 final size:21
Alignment explanation
Indices: 2481--2543 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2471 TTTCTTCTTT
2481 ATTTTCATTTTTCAATCATTC
1 ATTTTCATTTTTCAATCATTC
* *
2502 A-TTT--TTTTTC-TTC-TTT
1 ATTTTCATTTTTCAATCATTC
*
2518 TTTTTCATTTTTCAATCATTC
1 ATTTTCATTTTTCAATCATTC
*
2539 TTTTT
1 ATTTT
2544 AGTAGAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 10
0.68 0.11 0.21
Matches are distributed among these distances:
16 2 0.06
17 5 0.16
18 6 0.19
19 6 0.19
20 5 0.16
21 8 0.25
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (21 bp):
ATTTTCATTTTTCAATCATTC
Found at i:2516 original size:37 final size:36
Alignment explanation
Indices: 2464--2543 Score: 142
Period size: 37 Copynumber: 2.2 Consensus size: 36
2454 AATGGTAAGA
2464 TCTTTTTTTTCTTCTTTATTTTCATTTTTCAATCAT
1 TCTTTTTTTTCTTCTTTATTTTCATTTTTCAATCAT
*
2500 TCATTTTTTTTCTTCTTTTTTTTCATTTTTCAATCAT
1 TC-TTTTTTTTCTTCTTTATTTTCATTTTTCAATCAT
2537 TCTTTTT
1 TCTTTTT
2544 AGTAGAATTA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
36 7 0.17
37 35 0.83
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.71
Consensus pattern (36 bp):
TCTTTTTTTTCTTCTTTATTTTCATTTTTCAATCAT
Found at i:7188 original size:312 final size:314
Alignment explanation
Indices: 6604--7244 Score: 1182
Period size: 312 Copynumber: 2.0 Consensus size: 314
6594 GAGTGGAGAA
* * *
6604 TACATA-TTTTCAGATTAGATCGAATTGGGTTGATAAAAAATTTAATCTTAACCCGACATGTGCA
1 TACATATTTTTCGGATTAGATCGAATTGAGTTGATAAAAAATTTAATCCTAACCCGACATGTGCA
6668 ATCCCCCATCTACTAATGTATTCTCACCACTTTCGTCAAAGCTAACCATTCATATTCTATCCTCC
66 ATCCCCCATCTACTAATGTATTCTCACCACTTTCGTCAAAGCTAACCATTCATATTCTATCCTCC
6733 CTGATCTTTTTCTGAGTGGTTTCTACAAACTATGCTTCTAAGGTGAGCTTGTTTTAAACTAGAGT
131 CTGATCTTTTTCTGAGTGGTTTCTACAAACTATGCTTCTAAGGTGAGCTTGTTTTAAACTAGAGT
6798 TAATTCATCAAAACAGCCAATGGACCTTGCATGGAGTGTTAGATGCCAGTTCCAAGTATGTTTTT
196 TAATTCATCAAAACAGCCAATGGACCTTGCATGGAGTGTTAGATGCCAGTTCCAAGTATGTTTTT
*
6863 TTT--AATTTTTTTTTCGTTACAGGGTATTAGATACACTTTTTTGTACACGGCG
261 TTTAAAATTTTTTTATCGTTACAGGGTATTAGATACACTTTTTTGTACACGGCG
6915 TACATATTTTTCGGATTAGATCGAATTGAGTTGATAAAAAATTTAATCCTAACCCGACATGTTGC
1 TACATATTTTTCGGATTAGATCGAATTGAGTTGATAAAAAATTTAATCCTAACCCGACATG-TGC
6980 AATCCCCCATCTACTAATGTATTCTCACCACTTTCGTCAAAGCTAACCATTCATATTCTATCCTC
65 AATCCCCCATCTACTAATGTATTCTCACCACTTTCGTCAAAGCTAACCATTCATATTCTATCCTC
7045 CCTGATCTTTTTC-GAGTGGTTTCTACAAACTATGCTTCTAAGGTGAGCTTGTTTTAAACTAGAG
130 CCTGATCTTTTTCTGAGTGGTTTCTACAAACTATGCTTCTAAGGTGAGCTTGTTTTAAACTAGAG
*
7109 TTAATTCATCAAAACAGCCCATGGACCTTGCATGGAGTGTTAGATGCCAGTTCCAAGTATGTTTT
195 TTAATTCATCAAAACAGCCAATGGACCTTGCATGGAGTGTTAGATGCCAGTTCCAAGTATGTTTT
7174 TTTTAAAATTTTTTTTTATCGTTACAGGGTATTAGATACACTTTTTTGTACACGGCG
260 TTTTAAAA--TTTTTTTATCGTTACAGGGTATTAGATACACTTTTTTGTACACGGCG
7231 TACATATTTTTCGG
1 TACATATTTTTCGG
7245 CTATTGTTCT
Statistics
Matches: 319, Mismatches: 5, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
311 6 0.02
312 170 0.53
313 81 0.25
314 2 0.01
316 60 0.19
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (314 bp):
TACATATTTTTCGGATTAGATCGAATTGAGTTGATAAAAAATTTAATCCTAACCCGACATGTGCA
ATCCCCCATCTACTAATGTATTCTCACCACTTTCGTCAAAGCTAACCATTCATATTCTATCCTCC
CTGATCTTTTTCTGAGTGGTTTCTACAAACTATGCTTCTAAGGTGAGCTTGTTTTAAACTAGAGT
TAATTCATCAAAACAGCCAATGGACCTTGCATGGAGTGTTAGATGCCAGTTCCAAGTATGTTTTT
TTTAAAATTTTTTTATCGTTACAGGGTATTAGATACACTTTTTTGTACACGGCG
Found at i:12396 original size:5 final size:5
Alignment explanation
Indices: 12386--12573 Score: 284
Period size: 5 Copynumber: 38.4 Consensus size: 5
12376 GGTACACTAC
12386 TAATA TAATA TAATA TAATA TAATA TAATA TAATA T-ATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
12435 T-ATA T-ATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA T-A-ATA
12485 TAATA TAATA TAATA T-ATA TAATA TAATA TAATA TAATA T-ATA T-ATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
12532 TAATA TAATA TAATA T-ATA TATATA TAATAA TAATA -AATA TA
1 TAATA TAATA TAATA TAATA TA-ATA TAAT-A TAATA TAATA TA
12574 TAGTCTAAGA
Statistics
Matches: 173, Mismatches: 0, Indels: 20
0.90 0.00 0.10
Matches are distributed among these distances:
4 32 0.18
5 125 0.72
6 12 0.07
7 4 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:12535 original size:89 final size:90
Alignment explanation
Indices: 12386--12575 Score: 320
Period size: 89 Copynumber: 2.2 Consensus size: 90
12376 GGTACACTAC
12386 TAATAT-A-ATATAATATAATATAATATAATATAATATATATAATATAATATATATATATAATAT
1 TAATATAATATATAATATAATATAATATAATATAATATATATAATATAATATATATATATAATAT
12449 AATATAATATA-ATATAATATAAT-A
66 AATATAATATATATAT-ATATAATAA
12473 TAATATAATATATAATATAATATAATAT-ATATAATATAATATAATATAATATATATATATAATA
1 TAATATAATATATAATATAATATAATATAATATAATAT-ATATAATATAATATATATATATAATA
12537 TAATATAATATATATATATATAATAA
65 TAATATAATATATATATATATAATAA
12563 TAATA-AATATATA
1 TAATATAATATATA
12576 GTCTAAGATC
Statistics
Matches: 98, Mismatches: 0, Indels: 8
0.92 0.00 0.08
Matches are distributed among these distances:
87 6 0.06
88 10 0.10
89 72 0.73
90 10 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (90 bp):
TAATATAATATATAATATAATATAATATAATATAATATATATAATATAATATATATATATAATAT
AATATAATATATATATATATAATAA
Found at i:17898 original size:20 final size:20
Alignment explanation
Indices: 17873--17965 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
17863 TTTTCCCAAT
17873 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
17893 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
17913 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
17934 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
17955 TCGCAATGCGA
1 TCGCAATGCGA
17966 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:17915 original size:41 final size:41
Alignment explanation
Indices: 17870--17965 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
17860 CGATTTTCCC
17870 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
17911 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
17952 AAATCGCAATGCGA
1 AATTCGCAATGCGA
17966 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:17919 original size:21 final size:20
Alignment explanation
Indices: 17873--17965 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
17863 TTTTCCCAAT
*
17873 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
17893 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
17913 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
17934 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
17955 TCGCAATGCGA
1 TCGCAATGCGA
17966 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:17978 original size:41 final size:41
Alignment explanation
Indices: 17892--18026 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
17882 GAATAAGTAA
* * *
17892 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
17933 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
17974 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
18015 TTCGCAACGCGA
1 ATCGCAACGCGA
18027 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:17979 original size:20 final size:20
Alignment explanation
Indices: 17954--18047 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
17944 AATTGGGAAA
*
17954 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
17974 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
17995 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
18015 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
18035 TTCGCAACGCGAT
1 ATCGCAACGCGAT
18048 TTACTTAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:18665 original size:19 final size:19
Alignment explanation
Indices: 18643--18884 Score: 270
Period size: 19 Copynumber: 13.1 Consensus size: 19
18633 GAAACCAAAA
*
18643 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
18662 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
18681 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
18700 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
18719 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
18738 TCGCGTTGTGATTTTAATT
1 TCGCGTTGCGATTTTCATT
18757 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
18777 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
18793 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
18810 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
18824 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
18843 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
18863 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
18883 TC
1 TC
18885 AACCAAAAGA
Statistics
Matches: 193, Mismatches: 17, Indels: 26
0.82 0.07 0.11
Matches are distributed among these distances:
14 20 0.10
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 116 0.60
20 48 0.25
21 1 0.01
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:18809 original size:33 final size:33
Alignment explanation
Indices: 18772--18859 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
18762 GTTGCGATTT
* *
18772 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
18805 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
18838 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
18860 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:18861 original size:20 final size:20
Alignment explanation
Indices: 18827--18884 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
18817 GCGATTCTCT
**
18827 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
18847 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
18867 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
18885 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:20942 original size:42 final size:42
Alignment explanation
Indices: 20881--20964 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
20871 GCCCGACTCG
* * * *
20881 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATAATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
20923 CCTATAATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATAATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
20965 ACTGTCATCG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTATAATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:20961 original size:21 final size:21
Alignment explanation
Indices: 20937--21003 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
20927 TAATTCCTCG
20937 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
20958 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
20979 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
21000 AGAG
1 AGAG
21004 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:22379 original size:14 final size:14
Alignment explanation
Indices: 22360--22395 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
22350 ATTGTTTAAT
*
22360 TGATTTGTAAAAGG
1 TGATTTGTAAAAAG
*
22374 TGATTTGTAAAAAT
1 TGATTTGTAAAAAG
22388 TGATTTGT
1 TGATTTGT
22396 TTAATTGATG
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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAAG
Found at i:22596 original size:19 final size:19
Alignment explanation
Indices: 22574--22691 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
22564 CGAAATTAAA
22574 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
22593 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
22608 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
22626 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
22641 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
22659 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
22678 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
22692 GGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:22620 original size:33 final size:33
Alignment explanation
Indices: 22578--22671 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
22568 ATTAAATTCG
22578 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
22611 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
22644 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
22672 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:24975 original size:12 final size:12
Alignment explanation
Indices: 24958--24982 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24948 TCTTCGGGGA
24958 CTTTTTCTTCTT
1 CTTTTTCTTCTT
24970 CTTTTTCTTCTT
1 CTTTTTCTTCTT
24982 C
1 C
24983 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:26472 original size:14 final size:14
Alignment explanation
Indices: 26453--26489 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
26443 CATCAATTAA
26453 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
26467 ACAAATCATCTTTT
1 ACAAATCAACATTT
26481 ACAAATCAA
1 ACAAATCAA
26490 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:27059 original size:14 final size:14
Alignment explanation
Indices: 27040--27076 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
27030 CATCAATTAA
27040 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
27054 ACAAATCATCTTTT
1 ACAAATCAACATTT
27068 ACAAATCAA
1 ACAAATCAA
27077 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:28970 original size:19 final size:18
Alignment explanation
Indices: 28944--29095 Score: 121
Period size: 14 Copynumber: 8.9 Consensus size: 18
28934 ACGAAACTTA
28944 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
28962 ACTATCGCAACGCGGAAATGG
1 A-AATCGCAACGC-GAAAT-G
** *
28983 CTATCGCAATGCGAAATG
1 AAATCGCAACGCGAAATG
*
29001 AAAATCGCAACG-G-CA--
1 -AAATCGCAACGCGAAATG
29016 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
29034 AAATCGCAA--CGACA--
1 AAATCGCAACGCGAAATG
29048 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
29066 AAATCGCAA--CGACA--
1 AAATCGCAACGCGAAATG
29080 AAATCGCAACGCGAAA
1 AAATCGCAACGCGAAA
29096 CACAAATCGC
Statistics
Matches: 108, Mismatches: 12, Indels: 30
0.72 0.08 0.20
Matches are distributed among these distances:
14 29 0.27
15 1 0.01
16 17 0.16
17 1 0.01
18 21 0.19
19 23 0.21
20 15 0.14
21 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.11
Consensus pattern (18 bp):
AAATCGCAACGCGAAATG
Found at i:28981 original size:20 final size:19
Alignment explanation
Indices: 28946--29044 Score: 93
Period size: 19 Copynumber: 5.5 Consensus size: 19
28936 GAAACTTAAA
28946 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
28965 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
28985 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
*
29004 ATCGCAACG-GCAA--A--
1 ATCGCAACGCGAAATGACT
*
29018 ATCGCAACGCGAAATGA-A
1 ATCGCAACGCGAAATGACT
29036 ATCGCAACG
1 ATCGCAACG
29045 ACAAAATCGC
Statistics
Matches: 67, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
14 9 0.13
15 3 0.04
16 1 0.01
17 1 0.01
18 12 0.18
19 24 0.36
20 17 0.25
ACGTcount: A:0.39, C:0.24, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:29043 original size:32 final size:32
Alignment explanation
Indices: 28985--29095 Score: 195
Period size: 32 Copynumber: 3.4 Consensus size: 32
28975 GGAAATGGCT
* *
28985 ATCGCAATGCGAAATGAAAATCGCAACGGCAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
29018 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
29050 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
29082 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
29096 CACAAATCGC
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 61 0.80
33 15 0.20
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:29124 original size:19 final size:16
Alignment explanation
Indices: 29102--29197 Score: 65
Period size: 19 Copynumber: 5.7 Consensus size: 16
29092 GAAACACAAA
29102 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTT-ATT
*
29121 TCGCGTTGCGATTT-TG
1 TCGC-TTGCGATTTATT
29137 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTT-ATT
*
29153 TCGCGTTGCGATTT-TG
1 TCGC-TTGCGATTTATT
29169 TCG-TTGCGATTTTTATT
1 TCGCTTGCGA--TTTATT
29186 TCGCATTGCGAT
1 TCGC-TTGCGAT
29198 AGCCATTTCT
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 15 0.24
16 15 0.24
17 5 0.08
18 12 0.19
19 16 0.25
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (16 bp):
TCGCTTGCGATTTATT
Found at i:29143 original size:14 final size:14
Alignment explanation
Indices: 29124--29181 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
29114 TTTCATTTCG
29124 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
29138 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
29154 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
29170 CGTTGCGATTTT
1 CGTTGCGATTTT
29182 TATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:29154 original size:32 final size:33
Alignment explanation
Indices: 29107--29197 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
29097 ACAAATCGCA
29107 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
29140 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
* *
29172 TTGCGATTTTTATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
29198 AGCCATTTCT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 32 0.58
33 23 0.42
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:29205 original size:19 final size:20
Alignment explanation
Indices: 29183--29225 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
29173 TGCGATTTTT
29183 ATTTC-GCATTGCGATAGCC
1 ATTTCTGCATTGCGATAGCC
* *
29202 ATTTCTGCGTTGCGATAGTC
1 ATTTCTGCATTGCGATAGCC
29222 ATTT
1 ATTT
29226 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40
Consensus pattern (20 bp):
ATTTCTGCATTGCGATAGCC
Found at i:29735 original size:18 final size:18
Alignment explanation
Indices: 29709--29753 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
29699 GTCGATCAGA
*
29709 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
29727 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
29745 TGATGGCTC
1 TGATGGCTC
29754 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:31096 original size:20 final size:20
Alignment explanation
Indices: 31071--31108 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31061 AATAGTTTCT
31071 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
31091 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
31109 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:31397 original size:22 final size:22
Alignment explanation
Indices: 31372--31415 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
31362 GATTTAGATA
31372 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
31394 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
31416 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:31668 original size:41 final size:42
Alignment explanation
Indices: 31623--31758 Score: 118
Period size: 41 Copynumber: 3.3 Consensus size: 42
31613 CGAAAGTCAG
* * * *
31623 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTAT
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
* * *
31664 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAA
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
** ** * *
31706 T-TCGCGTTGCG-ATTTACTTATTCGCATTGCGAATTTCCCAA
1 TATCGCGTTGCGAAAGTAAGTA-TCGCATTGCGATTTTCTCAA
31747 T-TCGCGTTGCGA
1 TATCGCGTTGCGA
31759 TTTACTTATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
40 3 0.04
41 70 0.92
42 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (42 bp):
TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
Found at i:31674 original size:21 final size:21
Alignment explanation
Indices: 31641--31720 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
31631 TGCGAAAGTA
* * *
31641 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
31662 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
31682 AGTATCGCATTGCGATTTTCTC
1 AGTATCGCATTGCGATTTT-TC
* *
31704 AAT-TCGCGTTGCGATTT
1 AGTATCGCATTGCGATTT
31721 ACTTATTCGC
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 16 0.35
21 26 0.57
22 4 0.09
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:31697 original size:20 final size:20
Alignment explanation
Indices: 31603--31697 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
31593 GATTATGTAT
*
31603 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
31623 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGATAGTCAG
* ** * *
31643 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-TAGTCAG
*
31664 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
31684 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
31698 TTTCTCAATT
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 48 0.79
21 13 0.21
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:31730 original size:20 final size:20
Alignment explanation
Indices: 31686--31778 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
31676 ATAGTCAGTA
*
31686 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
31707 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
31727 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
31748 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
31768 TCGCATTGCGA
1 TCGCATTGCGA
31779 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:31759 original size:41 final size:41
Alignment explanation
Indices: 31686--31781 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
31676 ATAGTCAGTA
* *
31686 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
31727 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
31768 TCGCATTGCGAATT
1 TCGCATTGCGAATT
31782 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:32962 original size:15 final size:15
Alignment explanation
Indices: 32938--32967 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
32928 TAATTCGATA
32938 GCTATCTGGTCTACT
1 GCTATCTGGTCTACT
*
32953 GCTATTTGGTCTACT
1 GCTATCTGGTCTACT
32968 AGTCTATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.43
Consensus pattern (15 bp):
GCTATCTGGTCTACT
Found at i:39409 original size:25 final size:23
Alignment explanation
Indices: 39363--39418 Score: 85
Period size: 25 Copynumber: 2.3 Consensus size: 23
39353 CGAAAATTCG
*
39363 ATTTGATTTAAAAAATTGATTTA
1 ATTTGATTAAAAAAATTGATTTA
39386 ATTTGATGTAAAAGAAATTGATTTA
1 ATTTGAT-TAAAA-AAATTGATTTA
39411 ATTTGATT
1 ATTTGATT
39419 TAATCTGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 7 0.23
24 5 0.17
25 18 0.60
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (23 bp):
ATTTGATTAAAAAAATTGATTTA
Found at i:40114 original size:174 final size:174
Alignment explanation
Indices: 39824--40171 Score: 660
Period size: 174 Copynumber: 2.0 Consensus size: 174
39814 CAAAATGATC
*
39824 ATTAGACTATTCATTACGTTCCAAGTTTGTCCTTTTCCGTTAAAAATTTAACATTCAACTAAGTT
1 ATTAGACTATTCATTACGTTCCAAGTTTGTCCTTTTCCGTTAAAAAATTAACATTCAACTAAGTT
*
39889 GGAAGTTAACATGTTGACTGAGATGTGATAGTCGTTTGAGATTATGATATCAAATTTTATCATAT
66 GGAAGTTAACATGTTGACTGAGATATGATAGTCGTTTGAGATTATGATATCAAATTTTATCATAT
* *
39954 CTCGGTCAGCAAGTTAACGTACAGCTCATACTATTGTCAAATTT
131 CTCGGTCAGCAAGTTAAAGTACAGCTCATACTATCGTCAAATTT
39998 ATTAGACTATTCATTACGTTCCAAGTTTGTCCTTTTCCGTTAAAAAATTAACATTCAACTAAGTT
1 ATTAGACTATTCATTACGTTCCAAGTTTGTCCTTTTCCGTTAAAAAATTAACATTCAACTAAGTT
40063 GGAAGTTAACATGTTGACTGAGATATGATAGTCGTTTGAGATTATGATATCAAATTTTATCATAT
66 GGAAGTTAACATGTTGACTGAGATATGATAGTCGTTTGAGATTATGATATCAAATTTTATCATAT
40128 CTCGGTCAGCAAGTTAAAGTACAGCTCATACTATCGTCAAATTT
131 CTCGGTCAGCAAGTTAAAGTACAGCTCATACTATCGTCAAATTT
40172 TAATGGAAAA
Statistics
Matches: 170, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 170 1.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (174 bp):
ATTAGACTATTCATTACGTTCCAAGTTTGTCCTTTTCCGTTAAAAAATTAACATTCAACTAAGTT
GGAAGTTAACATGTTGACTGAGATATGATAGTCGTTTGAGATTATGATATCAAATTTTATCATAT
CTCGGTCAGCAAGTTAAAGTACAGCTCATACTATCGTCAAATTT
Found at i:43006 original size:8 final size:8
Alignment explanation
Indices: 42993--43055 Score: 126
Period size: 8 Copynumber: 7.9 Consensus size: 8
42983 GATGCTTGCT
42993 TGAATGCA
1 TGAATGCA
43001 TGAATGCA
1 TGAATGCA
43009 TGAATGCA
1 TGAATGCA
43017 TGAATGCA
1 TGAATGCA
43025 TGAATGCA
1 TGAATGCA
43033 TGAATGCA
1 TGAATGCA
43041 TGAATGCA
1 TGAATGCA
43049 TGAATGC
1 TGAATGC
43056 CTGCCAACTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 55 1.00
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (8 bp):
TGAATGCA
Found at i:47955 original size:230 final size:223
Alignment explanation
Indices: 47608--48046 Score: 576
Period size: 230 Copynumber: 1.9 Consensus size: 223
47598 TATCGGATCT
* * * * *
47608 ATCCTAACCCATATAGGGACATGATTTGTTTAAACACAGTGTAAAACTAAAAGTCTTACATCTTT
1 ATCCTAACCCACACAAGGACATGATCTGTTTAAACACAATGTAAAACTAAAAGTCTTACATCTTT
** * *
47673 TTAGGATTATTCAATGAGAGAAATCAATGGTTGAGATTAATAGTAAGAAATGAGAAGATATTCAT
66 TTAGGACCACTCAATGAGAGAAATCAATGGTTGAGATTAACAGTAAGAAATGAGAAGATATTCAT
*
47738 TGGGAAAACAAACAAAGACTTAATCTCAGCCTTTGATTTCCCCCAATCCAATGGTCCTAAAAAGG
131 T--G--AAC-AA-AAAGACTTAATCTCAGCCATTGATTTCCCCCAATCCAATGGTCC-AAAAAGG
47803 TGTAAAACTCTTAATTTTACATTGGGTCTATCTGG
189 TGTAAAACTCTTAATTTTACATTGGGTCTATCTGG
* * * * *
47838 ATCCTAACCCACACAAGGACATGATCTGTTTACACCCAATGTAAAATTAAGAGTTTTACATCTTT
1 ATCCTAACCCACACAAGGACATGATCTGTTTAAACACAATGTAAAACTAAAAGTCTTACATCTTT
** *
47903 TTAGGACCACT-AGATGAGAGAAATCAAAT-GTTGAGATTAACAGTTGGAAATGAGAATATATTC
66 TTAGGACCACTCA-ATGAGAGAAATC-AATGGTTGAGATTAACAGTAAGAAATGAGAAGATATTC
* * * * *
47966 ATTGAACAAGATGAGTTAATCTCAGTCATTGATTTCCCTCAATCCAATGGTCCAAAAAGGTGTAA
129 ATTGAACAAAAAGACTTAATCTCAGCCATTGATTTCCCCCAATCCAATGGTCCAAAAAGGTGTAA
48031 AACTCTTAATTTTACA
194 AACTCTTAATTTTACA
48047 CTGATGTAAG
Statistics
Matches: 184, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
223 28 0.15
224 38 0.21
225 2 0.01
226 3 0.02
228 1 0.01
229 1 0.01
230 108 0.59
231 3 0.02
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (223 bp):
ATCCTAACCCACACAAGGACATGATCTGTTTAAACACAATGTAAAACTAAAAGTCTTACATCTTT
TTAGGACCACTCAATGAGAGAAATCAATGGTTGAGATTAACAGTAAGAAATGAGAAGATATTCAT
TGAACAAAAAGACTTAATCTCAGCCATTGATTTCCCCCAATCCAATGGTCCAAAAAGGTGTAAAA
CTCTTAATTTTACATTGGGTCTATCTGG
Found at i:49042 original size:332 final size:330
Alignment explanation
Indices: 48448--49056 Score: 841
Period size: 332 Copynumber: 1.8 Consensus size: 330
48438 AAAACTAAGA
** *
48448 GTTTTACATTTTTTTAGGACCACATGATGAGAGAAATCAAATGTTGAGATTAACAATAGGAAATG
1 GTTTTACACCTTTTTAGGACCACATGATGAGAGAAATCAAAGGTTGAGATTAACAATAGGAAATG
* * * * *
48513 AGAAGATATTCACTGAACAAAATGAGTTAATCTCAGCCTTTGATTTCCCTCAATCCAATGGTCCA
66 AGAAGATATTCACTAAAAAAAAGGAGTTAATCTCAACCTTTAATTTCCCTCAATCCAATGGTCCA
* * * * * * *
48578 AAAAAGGTGTAAAACCCTTAATTTTATATTGTGTTAGTGGATTCTAACCCATATAGGGGCATGAT
131 AAAAAGGTATAAAACCCTTAATTTTACACTGGGTTACTGGATCCTAACCCACATAGGGGCATGAT
* *
48643 CCATTTACACCTAGTGTAAAACTAAGAGTTTTACATCTTTTTAAGACCATTGGATTCAGGAAAAT
196 CCATTTACACCCAATGTAAAACTAAGAGTTTTACATCTTTTTAAGACCATTGGATTCAGGAAAAT
* *
48708 CAAATGTTGAGATTAACTCATTGTTTTTTTATACATGGATATATCCATTTACATCCAGTGTAAAA
261 CAAAGGTTGAGACTAACTCATTGTTTTTTTATACATGGATATATCCATTTACATCCAGTGTAAAA
48773 CTCTT
326 CTCTT
* * * *
48778 GTTTTACACCTTTTTAGGACCA-TTGGATTGAGGGAAATCAAAGGTTGTGATTAACAATTGGAAA
1 GTTTTACACCTTTTTAGGACCACAT-GA-TGAGAGAAATCAAAGGTTGAGATTAACAATAGGAAA
*
48842 TGAGAATATATTCACTAAAAAACAAGGAGTTAATCTCAACCTTTAATTTCCCTCAATCCAATGGT
64 TGAGAAGATATTCACTAAAAAA-AAGGAGTTAATCTCAACCTTTAATTTCCCTCAATCCAATGGT
* * * *
48907 CCTAAAAAGGTATAAAACTCTTAATTTTACACTGGGTCTAACTGGATCCTAATCCACATGGGGGC
128 CCAAAAAAGGTATAAAACCCTTAATTTTACACTGGGT-T-ACTGGATCCTAACCCACATAGGGGC
* * *
48972 ATGATCTATTTACACCCAATGTAAAACTAAGAGTTTTACATC-TTTTAGGACCACTT-GA-TGA-
191 ATGATCCATTTACACCCAATGTAAAACTAAGAGTTTTACATCTTTTTAAGACCA-TTGGATTCAG
49033 GAGAAATCAAAGGTTGAGACTAAC
255 GA-AAATCAAAGGTTGAGACTAAC
49057 AGTAGGAAAT
Statistics
Matches: 241, Mismatches: 31, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
329 1 0.00
330 22 0.09
331 53 0.22
332 91 0.38
333 13 0.05
334 61 0.25
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (330 bp):
GTTTTACACCTTTTTAGGACCACATGATGAGAGAAATCAAAGGTTGAGATTAACAATAGGAAATG
AGAAGATATTCACTAAAAAAAAGGAGTTAATCTCAACCTTTAATTTCCCTCAATCCAATGGTCCA
AAAAAGGTATAAAACCCTTAATTTTACACTGGGTTACTGGATCCTAACCCACATAGGGGCATGAT
CCATTTACACCCAATGTAAAACTAAGAGTTTTACATCTTTTTAAGACCATTGGATTCAGGAAAAT
CAAAGGTTGAGACTAACTCATTGTTTTTTTATACATGGATATATCCATTTACATCCAGTGTAAAA
CTCTT
Found at i:49148 original size:223 final size:224
Alignment explanation
Indices: 48778--49276 Score: 673
Period size: 223 Copynumber: 2.2 Consensus size: 224
48768 TAAAACTCTT
* * * * *
48778 GTTTTACACCTTTTTAGGACCATTGGATTGAGGGAAATCAAAGGTTGTGATTAACAATTGGAAAT
1 GTTTTACATC-TTTTAGGACCATTGGATTGAGAGAAATCAAAGGTTGAGACTAACAATAGGAAAT
*
48843 GAGAATATATTCACTAAAAAACAAGGAGTTAATCTCAACCTTTAATTTCCCTCAATCCAATGGTC
65 GAGAAGATATTCACTAAAAAACAAGGAGTTAATCTCAACCTTTAATTTCCCTCAATCCAATGGTC
* * * **
48908 CTAAAAAGGTATAAAACTCTTAATTTTACACTGGGTCTAACTGGATCCTAATCCACATGGGGGCA
130 CAAAAAAGGTATAAAACTCTTAATTTTACACT-GGTCTAACTGGATCCTAACCCACATAGCAGCA
*
48973 TGAT-CTATTTACACCCAATGTAAAACTAAGA
194 TGATAC-ATATACACCCAATGTAAAACTAAGA
*
49004 GTTTTACATCTTTTAGGACCACTT-GA-TGAGAGAAATCAAAGGTTGAGACTAACAGTAGGAAAT
1 GTTTTACATCTTTTAGGACCA-TTGGATTGAGAGAAATCAAAGGTTGAGACTAACAATAGGAAAT
* * * *
49067 GAGAAGATATTCACTGAACAA-AATGAGTTAATCTCAACCTTTGATTTCCCTCAATCCAATGGTC
65 GAGAAGATATTCACTAAAAAACAAGGAGTTAATCTCAACCTTTAATTTCCCTCAATCCAATGGTC
* * * * *
49131 CAAAAAAGGTGTAAAACTCTTAATTTTACACTGGTGTAAGTGGATCCTAACCCATATAGCAGTAT
130 CAAAAAAGGTATAAAACTCTTAATTTTACACTGGTCTAACTGGATCCTAACCCACATAGCAGCAT
* *
49196 GATACATATACACCTAGTGTAAAACTAAGA
195 GATACATATACACCCAATGTAAAACTAAGA
* * *
49226 GTTTTACATCTTCTTAGGACCATTGGATTAAGGAAAAATCAAATGTTGAGA
1 GTTTTACATCTT-TTAGGACCATTGGATTGA-GAGAAATCAAAGGTTGAGA
49277 TTAAATCCTT
Statistics
Matches: 240, Mismatches: 27, Indels: 13
0.86 0.10 0.05
Matches are distributed among these distances:
222 64 0.27
223 83 0.35
224 52 0.22
225 30 0.12
226 11 0.05
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (224 bp):
GTTTTACATCTTTTAGGACCATTGGATTGAGAGAAATCAAAGGTTGAGACTAACAATAGGAAATG
AGAAGATATTCACTAAAAAACAAGGAGTTAATCTCAACCTTTAATTTCCCTCAATCCAATGGTCC
AAAAAAGGTATAAAACTCTTAATTTTACACTGGTCTAACTGGATCCTAACCCACATAGCAGCATG
ATACATATACACCCAATGTAAAACTAAGA
Found at i:49175 original size:556 final size:558
Alignment explanation
Indices: 47719--49280 Score: 2304
Period size: 558 Copynumber: 2.8 Consensus size: 558
47709 TTAATAGTAA
* * * * *
47719 GAAATGAGAAGATATTCATTGGGAAAACAAACAAAGACTTAATCTCAGCCTTTGATTTCCCCCAA
1 GAAATGAGAAGATATTCACT---AAAA-AAACAAGGAGTTAATCTCAACCTTTGATTTCCCTCAA
* *
47784 TCCAATGGTCCTAAAAAGGTGTAAAACTCTTAATTTTACATTGGGTCTATCTGGATCCTAACCCA
62 TCCAATGGTCCTAAAAAGGTATAAAACTCTTAATTTTACATTGGGTCTAACTGGATCCTAACCCA
*** *
47849 CACAAGGACATGATCTGTTTACACCCAATGTAAAATTAAGAGTTTTACATCTTTTTAGGACCACT
127 CATGGGGACATGATCTGTTTACACCCAATGTAAAACTAAGAGTTTTACATC-TTTTAGGACCACT
* * * * *
47914 AGATGAGAGAAATCAAATGTTGAGATTAACAGTTGGAAATGAGAATATATTCATTGAACAAGATG
191 TGATGAGAGAAATCAAATGTTGAGATTAACAGTAGGAAATGAGAAGATATTCACTGAACAAAATG
* *
47979 AGTTAATCTCAGTCATTGATTTCCCTCAATCCAATGGTCC-AAAAAGGTGTAAAACTCTTAATTT
256 AGTTAATCTCAGCCTTTGATTTCCCTCAATCCAATGGTCCAAAAAAGGTGTAAAACTCTTAATTT
* * * *
48043 TACACTGATGTAAGTGGAATCTAACCTATATAGGGGTAGGATCCATTTACACCTAGTGTAAAACT
321 TACACTGGTGTAAGTGGATTCTAACCCATATAGGGGTATGATCCATTTACACCTAGTGTAAAACT
** * * * * * *
48108 AAGAGTTTTACATCTTTTTAGGATAATTGGATTGAGAAAAATCAAATATTAAAATTAACTCTTTG
386 AAGAGTTTTACATCTTTTTAGGACCATTGGATTAAGGAAAATCAAATGTTGAGATTAACTCATTG
* *
48173 TTTTTTTATATAGGGAGAGGATCCGTTTACACCCAATGTAAAACTCTTGTTATACACCTTTTTAG
451 TTTTTTTATACAGGGAGAGGATCCATTTACACCCAATGTAAAACTCTTGTTATACACCTTTTTAG
* * *
48238 GACAATTAGATTTAGGAAAATCAAAGGCTAAGATTAATAGTAG
516 GACAATTAGATTGAGGAAAATCAAAGGCTAAGATTAACAATAG
* * *
48281 GAAATGAGAAGGTATTCACTAAAAAAACATGGAGTTAATATCAACCTTTGATTTCCCTCAATCCA
1 GAAATGAGAAGATATTCACTAAAAAAACAAGGAGTTAATCTCAACCTTTGATTTCCCTCAATCCA
* * * *
48346 ATGGTTCTAAAAATGTATAAAACTCTTAATTTTACATTGGGTCTAAATGAATCCTAACCCACATG
66 ATGGTCCTAAAAAGGTATAAAACTCTTAATTTTACATTGGGTCTAACTGGATCCTAACCCACATG
* * *
48411 GGGATATGATCTGTTTACACCCAATGTAAAACTAAGAGTTTTACATTTTTTTAGGACCACATGAT
131 GGGACATGATCTGTTTACACCCAATGTAAAACTAAGAGTTTTACA-TCTTTTAGGACCACTTGAT
*
48476 GAGAGAAATCAAATGTTGAGATTAACAATAGGAAATGAGAAGATATTCACTGAACAAAATGAGTT
195 GAGAGAAATCAAATGTTGAGATTAACAGTAGGAAATGAGAAGATATTCACTGAACAAAATGAGTT
* *
48541 AATCTCAGCCTTTGATTTCCCTCAATCCAATGGTCCAAAAAAGGTGTAAAACCCTTAATTTTATA
260 AATCTCAGCCTTTGATTTCCCTCAATCCAATGGTCCAAAAAAGGTGTAAAACTCTTAATTTTACA
* * *
48606 -TTGTGTTAGTGGATTCTAACCCATATAGGGGCATGATCCATTTACACCTAGTGTAAAACTAAGA
325 CTGGTGTAAGTGGATTCTAACCCATATAGGGGTATGATCCATTTACACCTAGTGTAAAACTAAGA
* *
48670 GTTTTACATCTTTTTAAGACCATTGGATTCAGGAAAATCAAATGTTGAGATTAACTCATTGTTTT
390 GTTTTACATCTTTTTAGGACCATTGGATTAAGGAAAATCAAATGTTGAGATTAACTCATTGTTTT
* * * * * * *
48735 TTTATACATGGATA-TATCCATTTACATCCAGTGTAAAACTCTTGTTTTACACCTTTTTAGGACC
455 TTTATACAGGGAGAGGATCCATTTACACCCAATGTAAAACTCTTGTTATACACCTTTTTAGGACA
* * * ** *
48799 ATTGGATTGAGGGAAATCAAAGGTTGTGATTAACAATTG
520 ATTAGATTGAGGAAAATCAAAGGCTAAGATTAACAATAG
* *
48838 GAAATGAGAATATATTCACT-AAAAAACAAGGAGTTAATCTCAACCTTTAATTTCCCTCAATCCA
1 GAAATGAGAAGATATTCACTAAAAAAACAAGGAGTTAATCTCAACCTTTGATTTCCCTCAATCCA
* *
48902 ATGGTCCTAAAAAGGTATAAAACTCTTAATTTTACACTGGGTCTAACTGGATCCTAATCCACATG
66 ATGGTCCTAAAAAGGTATAAAACTCTTAATTTTACATTGGGTCTAACTGGATCCTAACCCACATG
* *
48967 GGGGCATGATCTATTTACACCCAATGTAAAACTAAGAGTTTTACATCTTTTAGGACCACTTGATG
131 GGGACATGATCTGTTTACACCCAATGTAAAACTAAGAGTTTTACATCTTTTAGGACCACTTGATG
* *
49032 AGAGAAATCAAAGGTTGAGACTAACAGTAGGAAATGAGAAGATATTCACTGAACAAAATGAGTTA
196 AGAGAAATCAAATGTTGAGATTAACAGTAGGAAATGAGAAGATATTCACTGAACAAAATGAGTTA
*
49097 ATCTCAACCTTTGATTTCCCTCAATCCAATGGTCCAAAAAAGGTGTAAAACTCTTAATTTTACAC
261 ATCTCAGCCTTTGATTTCCCTCAATCCAATGGTCCAAAAAAGGTGTAAAACTCTTAATTTTACAC
* ** * *
49162 TGGTGTAAGTGGATCCTAACCCATATAGCAGTATGATACATATACACCTAGTGTAAAACTAAGAG
326 TGGTGTAAGTGGATTCTAACCCATATAGGGGTATGATCCATTTACACCTAGTGTAAAACTAAGAG
*
49227 TTTTACATCTTCTTAGGACCATTGGATTAAGGAAAAATCAAATGTTGAGATTAA
391 TTTTACATCTTTTTAGGACCATTGGATTAAGG-AAAATCAAATGTTGAGATTAA
49281 ATCCTTTTTC
Statistics
Matches: 898, Mismatches: 98, Indels: 13
0.89 0.10 0.01
Matches are distributed among these distances:
555 141 0.16
556 228 0.25
557 113 0.13
558 367 0.41
559 31 0.03
562 18 0.02
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (558 bp):
GAAATGAGAAGATATTCACTAAAAAAACAAGGAGTTAATCTCAACCTTTGATTTCCCTCAATCCA
ATGGTCCTAAAAAGGTATAAAACTCTTAATTTTACATTGGGTCTAACTGGATCCTAACCCACATG
GGGACATGATCTGTTTACACCCAATGTAAAACTAAGAGTTTTACATCTTTTAGGACCACTTGATG
AGAGAAATCAAATGTTGAGATTAACAGTAGGAAATGAGAAGATATTCACTGAACAAAATGAGTTA
ATCTCAGCCTTTGATTTCCCTCAATCCAATGGTCCAAAAAAGGTGTAAAACTCTTAATTTTACAC
TGGTGTAAGTGGATTCTAACCCATATAGGGGTATGATCCATTTACACCTAGTGTAAAACTAAGAG
TTTTACATCTTTTTAGGACCATTGGATTAAGGAAAATCAAATGTTGAGATTAACTCATTGTTTTT
TTATACAGGGAGAGGATCCATTTACACCCAATGTAAAACTCTTGTTATACACCTTTTTAGGACAA
TTAGATTGAGGAAAATCAAAGGCTAAGATTAACAATAG
Found at i:55287 original size:11 final size:13
Alignment explanation
Indices: 55262--55299 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
55252 AAGTTATGAT
55262 AATTTGTGAATAAA
1 AATTTGTGAA-AAA
55276 AATTT-TGAAAAA
1 AATTTGTGAAAAA
55288 AATTTGTGAAAA
1 AATTTGTGAAAA
55300 CAAAAGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 8 0.35
13 10 0.43
14 5 0.22
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.34
Consensus pattern (13 bp):
AATTTGTGAAAAA
Found at i:55289 original size:13 final size:14
Alignment explanation
Indices: 55262--55304 Score: 54
Period size: 12 Copynumber: 3.1 Consensus size: 14
55252 AAGTTATGAT
*
55262 AATTTGTGAATAAA
1 AATTTGTGAAAAAA
55276 AATTT-TG-AAAAA
1 AATTTGTGAAAAAA
55288 AATTTGTGAAAACAA
1 AATTTGTGAAAA-AA
55303 AA
1 AA
55305 GATTATAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 9 0.36
13 4 0.16
14 8 0.32
15 4 0.16
ACGTcount: A:0.56, C:0.02, G:0.12, T:0.30
Consensus pattern (14 bp):
AATTTGTGAAAAAA
Found at i:56049 original size:20 final size:20
Alignment explanation
Indices: 56013--56050 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
56003 ATCCTATTCC
**
56013 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
56033 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
56051 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:57837 original size:2 final size:2
Alignment explanation
Indices: 57830--57870 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
57820 TTAGACAGGT
57830 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
57871 AGTCAAATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Done.