Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008910.1 Hibiscus syriacus cultivar Beakdansim tig00112207_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: 73231
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1028 original size:12 final size:12
Alignment explanation
Indices: 990--1028 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
980 TCAAATATGT
990 TTCTTC-TCCTC
1 TTCTTCTTCCTC
*
1001 TTCCTCTTCCTC
1 TTCTTCTTCCTC
*
1013 TTCTTCTTCTTC
1 TTCTTCTTCCTC
1025 TTCT
1 TTCT
1029 GTCGTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 5 0.21
12 19 0.79
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (12 bp):
TTCTTCTTCCTC
Found at i:2773 original size:27 final size:27
Alignment explanation
Indices: 2735--2786 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
2725 AATATTATTA
2735 AAAATA-TTTTTTAAAATATATAAATTT
1 AAAATATTTTTTTAAAAT-TATAAATTT
2762 AAAAT-TTATTTTTAAAATTATAAAT
1 AAAATATT-TTTTTAAAATTATAAAT
2787 AATTTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
AAAATATTTTTTTAAAATTATAAATTT
Found at i:6028 original size:27 final size:29
Alignment explanation
Indices: 5998--6062 Score: 100
Period size: 27 Copynumber: 2.3 Consensus size: 29
5988 CCTAAACCCG
*
5998 AACCCGACCCA-AATATCACACTT-AAAA
1 AACCCGACCCAGAATATCAAACTTAAAAA
6025 AACCCGA-CCAGAATATCAAACTTAAAAA
1 AACCCGACCCAGAATATCAAACTTAAAAA
6053 AACCCGACCC
1 AACCCGACCC
6063 GACCGACCCC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
26 3 0.09
27 18 0.53
28 11 0.32
29 2 0.06
ACGTcount: A:0.48, C:0.34, G:0.06, T:0.12
Consensus pattern (29 bp):
AACCCGACCCAGAATATCAAACTTAAAAA
Found at i:9689 original size:2 final size:2
Alignment explanation
Indices: 9684--9731 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
9674 CCTTATAACT
9684 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9725 -A TA TA TA
1 TA TA TA TA
9732 ATGTACGAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10619 original size:145 final size:143
Alignment explanation
Indices: 10484--10770 Score: 380
Period size: 145 Copynumber: 2.0 Consensus size: 143
10474 TGTTTACATT
* * * * * *
10484 ACACAACTTTTCACTGTT-TGAAGTATTGATCGG-AGATCCCGATCGCCGGCAAAAGGCTAAAAA
1 ACACAACTTTTCACCGTTCGGAA-TATTAATCGGCA-ATCCCGATCGCAGGCAAAAGACCAAAAA
*
10547 CCTTTCGACTTATTTTCTCCGATCTGCCATCGTCCACCGTCTGATCGTTCTGAATTTTCAGTATG
64 CCGTTCGACTTATTTTCTCCGATC--CCATCGTCCACCGTCTGATCGTTCTGAATTTTCAGTATG
10612 TTGTTCGTGATGGTCTC
127 TTGTTCGTGATGGTCTC
* * * * * *
10629 GCGCAACTTTTGACCGTTCGGAATGTTAATCGGCACTCCCGATCGCAGGCAAGAGACCAAAAACC
1 ACACAACTTTTCACCGTTCGGAATATTAATCGGCAATCCCGATCGCAGGCAAAAGACCAAAAACC
* * *
10694 GTTCGGCTTATTTTCTCCGATCCCCTCGTCCACCGTCTGATCGTCCTGAATTTTCAGTATGTTGT
66 GTTCGACTTATTTTCTCCGATCCCATCGTCCACCGTCTGATCGTTCTGAATTTTCAGTATGTTGT
10759 TCGTGATGGTCT
131 TCGTGATGGTCT
10771 TGCGCAACTT
Statistics
Matches: 124, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
143 53 0.43
145 67 0.54
146 4 0.03
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (143 bp):
ACACAACTTTTCACCGTTCGGAATATTAATCGGCAATCCCGATCGCAGGCAAAAGACCAAAAACC
GTTCGACTTATTTTCTCCGATCCCATCGTCCACCGTCTGATCGTTCTGAATTTTCAGTATGTTGT
TCGTGATGGTCTC
Found at i:10770 original size:143 final size:143
Alignment explanation
Indices: 10520--10795 Score: 437
Period size: 143 Copynumber: 1.9 Consensus size: 143
10510 TGATCGGAGA
* * * *
10520 TCCCGATCGCCGGCAAAAGGCTAAAAACCTTTCGACTTATTTTCTCCGATCTGCCATCGTCCACC
1 TCCCGATCGCAGGCAAAAGACCAAAAACCGTTCGACTTATTTTCTCCGATC-GCCATCGTCCACC
* *
10585 GTCTGATCGTTCTGAATTTTCAGTATGTTGTTCGTGATGGTCTCGCGCAACTTTTGACCGTTCGG
65 GTCTGATCGTCCTGAATTTTCAGTATGTTGTTCGTGATGGTCTCGCGCAACTTTTGA-CATTCGG
10650 AATGTTAATCGGCAC
129 AATGTTAATCGGCAC
* * *
10665 TCCCGATCGCAGGCAAGAGACCAAAAACCGTTCGGCTTATTTTCTCCGATC-CCCTCGTCCACCG
1 TCCCGATCGCAGGCAAAAGACCAAAAACCGTTCGACTTATTTTCTCCGATCGCCATCGTCCACCG
*
10729 TCTGATCGTCCTGAATTTTCAGTATGTTGTTCGTGATGGTCTTGCGCAACTTTTGACATTCGGAA
66 TCTGATCGTCCTGAATTTTCAGTATGTTGTTCGTGATGGTCTCGCGCAACTTTTGACATTCGGAA
10794 TG
131 TG
10796 GTGATCGGAG
Statistics
Matches: 121, Mismatches: 10, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
142 10 0.08
143 66 0.55
145 45 0.37
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.32
Consensus pattern (143 bp):
TCCCGATCGCAGGCAAAAGACCAAAAACCGTTCGACTTATTTTCTCCGATCGCCATCGTCCACCG
TCTGATCGTCCTGAATTTTCAGTATGTTGTTCGTGATGGTCTCGCGCAACTTTTGACATTCGGAA
TGTTAATCGGCAC
Found at i:11904 original size:15 final size:15
Alignment explanation
Indices: 11856--11904 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
11846 TTTGACCGGT
11856 CCTTCTTCAACCCAA
1 CCTTCTTCAACCCAA
* **
11871 TCCCTCCTTCAACTAAA
1 --CCTTCTTCAACCCAA
11888 CCTTCTTCAACCCAA
1 CCTTCTTCAACCCAA
11903 CC
1 CC
11905 CTTTCTTCTC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 14 0.54
17 12 0.46
ACGTcount: A:0.27, C:0.47, G:0.00, T:0.27
Consensus pattern (15 bp):
CCTTCTTCAACCCAA
Found at i:11912 original size:17 final size:16
Alignment explanation
Indices: 11856--11912 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 16
11846 TTTGACCGGT
11856 CCTTCTTCAACCCAATC
1 CCTTCTTCAACCCAA-C
* * *
11873 CCTCCTTCAA-CTAAA
1 CCTTCTTCAACCCAAC
11888 CCTTCTTCAACCCAAC
1 CCTTCTTCAACCCAAC
11904 CCTTTCTTC
1 CC-TTCTTC
11913 TCCTTTTTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
15 9 0.28
16 8 0.25
17 15 0.47
ACGTcount: A:0.23, C:0.46, G:0.00, T:0.32
Consensus pattern (16 bp):
CCTTCTTCAACCCAAC
Found at i:14203 original size:20 final size:20
Alignment explanation
Indices: 14175--14224 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
14165 ACATTTTCTA
*
14175 TAATTATTTATACAAGAAAC
1 TAATCATTTATACAAGAAAC
* *
14195 TAATCATTTATACAATAAAT
1 TAATCATTTATACAAGAAAC
*
14215 TAACCATTTA
1 TAATCATTTA
14225 AGATCATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (20 bp):
TAATCATTTATACAAGAAAC
Found at i:17777 original size:20 final size:20
Alignment explanation
Indices: 17752--17814 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
17742 AGTAAAAGGT
17752 TGAACAAGTTCTTCTTATTA
1 TGAACAAGTTCTTCTTATTA
* *
17772 TGAACATA-TTCTTCCTCTT-
1 TGAACA-AGTTCTTCTTATTA
* * *
17791 CGAACGAGTTCTTCTCATTA
1 TGAACAAGTTCTTCTTATTA
17811 TGAA
1 TGAA
17815 TTCTTCCATT
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 1 0.03
19 12 0.38
20 18 0.56
21 1 0.03
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (20 bp):
TGAACAAGTTCTTCTTATTA
Found at i:18360 original size:28 final size:29
Alignment explanation
Indices: 18320--18384 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
18310 ATTATTTTAA
* *
18320 ATTTATTACTATAATTTTAAT-AA-AATAT
1 ATTTATTTCTAT-ATTTTAATAAATAAGAT
* *
18348 ATTTATTTTTATATTTTTATAAATAAGAT
1 ATTTATTTCTATATTTTAATAAATAAGAT
18377 ATTTATTT
1 ATTTATTT
18385 ATTTAGAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 7 0.23
28 12 0.39
29 12 0.39
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (29 bp):
ATTTATTTCTATATTTTAATAAATAAGAT
Found at i:18704 original size:3 final size:3
Alignment explanation
Indices: 18696--18727 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
18686 AATATGACTA
18696 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
18728 ATATATTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:20046 original size:3 final size:3
Alignment explanation
Indices: 20038--20154 Score: 121
Period size: 3 Copynumber: 39.0 Consensus size: 3
20028 CGGTAATATG
* * *
20038 TAA TAA TAA TATC TAT TAT TAA TAA T-A TAA -ATA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
* * *
20083 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA CAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
20131 TTA TAA TAA TAG TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
20155 AACGGGAAAA
Statistics
Matches: 95, Mismatches: 15, Indels: 8
0.81 0.13 0.07
Matches are distributed among these distances:
2 3 0.03
3 89 0.94
4 3 0.03
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:20544 original size:139 final size:139
Alignment explanation
Indices: 20240--20627 Score: 560
Period size: 139 Copynumber: 2.8 Consensus size: 139
20230 AGTCGAGCAA
* * * ** *
20240 AAGGTTGAACAAGCTCTTCTCATTATGAACGTCTTCTCCCTCAACGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* *
20305 GAACTCTTCTACTGAAAATGTTGATCCCTCGAGTGAGGGAGGGGTCGCTGATTCAACTCCATATA
66 GAACTC-TCCACTGGAAATGTTGATCCCTCGAGTGAGGGA----TCGCTGATTCAACTCCATATA
*
20370 CGATGAATCGAGCT
126 CAATGAATCGAGCT
*
20384 AAGGTTGTACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * * *
20449 GAACTCTCCACTGGAAATGCTGATCCCTCTAGTGATGGATCGCTGATTCAACTCTATATGCAATG
66 GAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGGATCGCTGATTCAACTCCATATACAATG
20514 AATCGAGCT
131 AATCGAGCT
* * *
20523 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTTTTCAGATTAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
*
20588 GAACTCTCCACTGGAAATGTTGATCTCTCGAGTGAGGGAT
66 GAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGGAT
20628 TCAAATTTTT
Statistics
Matches: 221, Mismatches: 23, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
139 129 0.58
143 28 0.13
144 64 0.29
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (139 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
GAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGGATCGCTGATTCAACTCCATATACAATG
AATCGAGCT
Found at i:29525 original size:3 final size:3
Alignment explanation
Indices: 29517--29576 Score: 88
Period size: 3 Copynumber: 20.3 Consensus size: 3
29507 GAGGCATGTG
29517 ATA ATA AT- ATA ATTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
29562 ATA ATA TTA A-A ATA A
1 ATA ATA ATA ATA ATA A
29577 AATGGGACAA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 4 0.08
3 45 0.87
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:30661 original size:21 final size:21
Alignment explanation
Indices: 30637--30688 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
30627 GGGCTTGACC
30637 AGTATCGATACTATGCTTCCT
1 AGTATCGATACTATGCTTCCT
30658 AGTATCGATACTATGCTTCCT
1 AGTATCGATACTATGCTTCCT
30679 AGTATCGATA
1 AGTATCGATA
30689 TCACTTGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (21 bp):
AGTATCGATACTATGCTTCCT
Found at i:34025 original size:29 final size:29
Alignment explanation
Indices: 33968--34034 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
33958 AGGGATCCCA
* * *
33968 ATTTTTTCGTCTTTATAATTAGTGTCTCT-
1 ATTTTTT-ATCTTTATAATTAGGGCCTCTG
33997 AGTTTTTTATCTTTATAATTAGGGCCTCTG
1 A-TTTTTTATCTTTATAATTAGGGCCTCTG
34027 ATTTTTTA
1 ATTTTTTA
34035 AATTTTATCT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 26 0.79
30 7 0.21
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.57
Consensus pattern (29 bp):
ATTTTTTATCTTTATAATTAGGGCCTCTG
Found at i:34147 original size:40 final size:41
Alignment explanation
Indices: 34100--34181 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
34090 ATCTTGATAG
* *
34100 TTGAAGTATCTAA-TTTTCCAATCCCATTTTTTAAACTTTA
1 TTGAAGTACCTAATTTTTCCAATCCCACTTTTTAAACTTTA
** *
34140 TTGAAGTACCTAATTTTTTTAATCCCACTTTTTAAATTTTA
1 TTGAAGTACCTAATTTTTCCAATCCCACTTTTTAAACTTTA
34181 T
1 T
34182 AATTGAGGCC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 12 0.33
41 24 0.67
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.50
Consensus pattern (41 bp):
TTGAAGTACCTAATTTTTCCAATCCCACTTTTTAAACTTTA
Found at i:35408 original size:2 final size:2
Alignment explanation
Indices: 35401--35446 Score: 58
Period size: 2 Copynumber: 23.0 Consensus size: 2
35391 TAAATTAATT
* *
35401 TA TA TA TA TA TA TA TA CA TA TA TA TA AA TA -A TA TGA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
35443 TA TA
1 TA TA
35447 ACAACATAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (2 bp):
TA
Found at i:38056 original size:105 final size:108
Alignment explanation
Indices: 37824--38068 Score: 282
Period size: 105 Copynumber: 2.3 Consensus size: 108
37814 AGCCAAGGTT
* *
37824 GAACAAATTCTTCTCATTATGAACTCCTTCTCCCTTATTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACT-CTTCTCCCTTA-TGGACGAGTTCTTCTCATTATGAACTC
* * *
37889 TCAACTGGAAATCTTGAACCAAATCCTTTTGCGGTGGACTTAGAAG
64 T-AACTGGAAATCTTGAACCAAATCCATCTGCGGTGAACTTAGAAG
* *
37935 GAACATGTTTTTCTCATTATGAACT-TTCTCCCTTA-GGACGAGTTCTTCTCATTATGAACTCT-
1 GAACAAGTTCTTCTCATTATGAACTCTTCTCCCTTATGGACGAGTTCTTCTCATTATGAACTCTA
* * *** ** * *
37997 TCTGGAAATGTTGGTTCACCTCCATCTGTGGTGAA-TTTGAAAG
66 ACTGGAAATCTTGAACCAAATCCATCTGCGGTGAACTTAG-AAG
38040 GAACAAGTTCTTCTCATTATGAACTCTTC
1 GAACAAGTTCTTCTCATTATGAACTCTTC
38069 ATTGGAAATG
Statistics
Matches: 114, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
104 3 0.03
105 50 0.44
106 3 0.03
107 26 0.23
109 10 0.09
111 22 0.19
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (108 bp):
GAACAAGTTCTTCTCATTATGAACTCTTCTCCCTTATGGACGAGTTCTTCTCATTATGAACTCTA
ACTGGAAATCTTGAACCAAATCCATCTGCGGTGAACTTAGAAG
Found at i:39340 original size:20 final size:18
Alignment explanation
Indices: 39317--39406 Score: 89
Period size: 17 Copynumber: 4.9 Consensus size: 18
39307 CCTTTTTCTC
39317 TTTTCATTTTTTCATTTCTTT
1 TTTTCA-TTTTTCA-TT-TTT
39338 TTTTCATTTTTCA-TTTT
1 TTTTCATTTTTCATTTTT
39355 TTTTCATTTTTTTTCATTTTT
1 TTTTCA---TTTTTCATTTTT
39376 TTTTC-TTTTTCATTTTT
1 TTTTCATTTTTCATTTTT
*
39393 TTATC-TTTTT-ATTT
1 TTTTCATTTTTCATTT
39407 GTTCCCTTTT
Statistics
Matches: 64, Mismatches: 1, Indels: 13
0.82 0.01 0.17
Matches are distributed among these distances:
16 4 0.06
17 30 0.47
18 1 0.02
20 14 0.22
21 15 0.23
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTCATTTTTCATTTTT
Found at i:39348 original size:10 final size:10
Alignment explanation
Indices: 39344--39394 Score: 72
Period size: 10 Copynumber: 5.4 Consensus size: 10
39334 CTTTTTTTCA
39344 TTTTTCATTT
1 TTTTTCATTT
39354 TTTTTCATTT
1 TTTTTCATTT
39364 TTTTTCA-TT
1 TTTTTCATTT
*
39373 TTTTT--TTC
1 TTTTTCATTT
39381 TTTTTCATTT
1 TTTTTCATTT
39391 TTTT
1 TTTT
39395 ATCTTTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
8 6 0.17
9 7 0.19
10 23 0.64
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTCATTT
Found at i:39365 original size:27 final size:27
Alignment explanation
Indices: 39335--39406 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
39325 TTTTCATTTC
39335 TTTTTTTCATTTTTCATTT-TTTTTCAT
1 TTTTTTTCATTTTT-ATTTCTTTTTCAT
*
39362 TTTTTTTCATTTTTTTTTCTTTTTCAT
1 TTTTTTTCATTTTTATTTCTTTTTCAT
39389 TTTTTTATC-TTTTTATTT
1 TTTTTT-TCATTTTTATTT
39407 GTTCCCTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
26 3 0.07
27 36 0.88
28 2 0.05
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (27 bp):
TTTTTTTCATTTTTATTTCTTTTTCAT
Found at i:39401 original size:10 final size:9
Alignment explanation
Indices: 39344--39406 Score: 51
Period size: 8 Copynumber: 7.1 Consensus size: 9
39334 CTTTTTTTCA
*
39344 TTTTTCATT
1 TTTTTTATT
39353 TTTTTTCATT
1 TTTTTT-ATT
39363 TTTTTTCATT
1 TTTTTT-ATT
*
39373 TTTTTT-TC
1 TTTTTTATT
*
39381 TTTTTCA-T
1 TTTTTTATT
39389 TTTTTTA-T
1 TTTTTTATT
*
39397 CTTTTTATT
1 TTTTTTATT
39406 T
1 T
39407 GTTCCCTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
8 19 0.43
9 6 0.14
10 19 0.43
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTATT
Found at i:50950 original size:2 final size:2
Alignment explanation
Indices: 50943--50995 Score: 65
Period size: 2 Copynumber: 27.0 Consensus size: 2
50933 TAAATTAATT
* *
50943 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA AA TA -A TA TGA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
50985 TA -A TA TA TA TA
1 TA TA TA TA TA TA
50996 AACAACATAG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
1 2 0.05
2 40 0.91
3 2 0.05
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (2 bp):
TA
Found at i:53879 original size:2 final size:2
Alignment explanation
Indices: 53872--53913 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
53862 ACATACATAC
53872 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
53914 TGTCAACTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54923 original size:20 final size:20
Alignment explanation
Indices: 54898--54936 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
54888 CCACTTAGTC
*
54898 TTGTAAGTATAGCTAAAGAG
1 TTGTAAGTATAACTAAAGAG
54918 TTGTAAGTATAACTAAAGA
1 TTGTAAGTATAACTAAAGA
54937 TTTTTTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.31
Consensus pattern (20 bp):
TTGTAAGTATAACTAAAGAG
Found at i:55968 original size:20 final size:21
Alignment explanation
Indices: 55929--55968 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
55919 TATTTTGTTA
55929 TAATGAAAACATGATAATAAT
1 TAATGAAAACATGATAATAAT
* *
55950 TAATGTAAA-ATGATCATAA
1 TAATGAAAACATGATAATAA
55969 ATAAAGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.30
Consensus pattern (21 bp):
TAATGAAAACATGATAATAAT
Found at i:60867 original size:12 final size:12
Alignment explanation
Indices: 60846--60881 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
60836 TAAAATTACC
60846 TTTT-AAAATAA
1 TTTTAAAAATAA
60857 TTTTAAAAATAA
1 TTTTAAAAATAA
60869 TTTTAAAAGATAA
1 TTTTAAAA-ATAA
60882 AAAATGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 4 0.17
12 15 0.65
13 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (12 bp):
TTTTAAAAATAA
Found at i:62863 original size:3 final size:3
Alignment explanation
Indices: 62857--62899 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
62847 AAATTATTAT
*
62857 TAA TAA TAA T-A TAAA TAA TAA TAA TAA TAA TAT TAAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
62900 CCTAGACAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 29 0.83
4 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:62875 original size:12 final size:12
Alignment explanation
Indices: 62858--62899 Score: 54
Period size: 13 Copynumber: 3.7 Consensus size: 12
62848 AATTATTATT
62858 AATAATAATATA
1 AATAATAATATA
62870 AATAAT-A-AT-
1 AATAATAATATA
62879 AATAATAATATTA
1 AATAATAATA-TA
62892 AATAATAA
1 AATAATAA
62900 CCTAGACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
9 6 0.23
10 3 0.12
11 2 0.08
12 7 0.27
13 8 0.31
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AATAATAATATA
Found at i:63600 original size:254 final size:256
Alignment explanation
Indices: 63044--64227 Score: 1593
Period size: 254 Copynumber: 4.6 Consensus size: 256
63034 AACCCGAAAA
** * * * * *
63044 CATCATGCTCGAAAGACTTACTGATGGCTTGAAGGACTTACTAAATTTTGTAAATAATTTACTAG
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAC-CAATTTGGGAAATAGTTTACTGG
* * * * * *
63109 GTAAGAAACTTTGAAAATCACTTTTTTACTTTTCAAAATTTTCATTTTTTAGAAAATATTTAAAT
65 GTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCT-GAAAATA-CTAAAT
* * * *
63174 GAGAAACTTTGAAAATAGTTTTCTCATTTTTCAAAAT-ATTGTGAAAACATCCTACCCCGAAGGT
128 GAGAAACTTTGGAAATCGCTTTCTCA-TTTTCAAATTCA-TGTGAAAACATCCTA-CCCGAAGGT
* * * * *
63238 CTTATGGATTG-TCGAAGGACTTATCATCTTGCTCGAAAGACTTATAGATGACCCGATGGATTTA
190 CTTACGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTA
63302 AT
255 AT
*
63304 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTGGGAAATAATTTACTGGG
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTGGGAAATAGTTTACTGGG
*
63369 TAAGAAACTTTGGAAATTGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATACTAAATGAG
66 TAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATACTAAATGAG
* * *
63434 AAACTTTAGAAATCGCTTTCTCATATTTCAATTTCATGTG-AAACATCCTACCCAAAGGTCTTAC
131 AAACTTTGGAAATCGCTTTCTCAT-TTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTAC
* * * *
63498 GGATGGCCCGAGGGACTTATAATCTTGCTCGAAAGACTTACTG-TGACCTGAAGGA-TTAAT
195 GGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAT
63558 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTT-GGAGAATAGTTTACTGG
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTGGGA-AATAGTTTACTGG
* * * *
63622 GAAAGAAACTTTGGAAATCGTTTTCTTACTCTTCAAAAATTTCATTTTCTGAAATTACTAAATGA
65 GTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATACTAAATGA
*
63687 GAAACTTTGGAAATCGCTTTCTTACTTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTA
130 GAAACTTTGGAAATCGCTTTCTCA-TTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTA
* * *
63752 CGGATGGCCCGAATGACTTATCATCTTGCTCAAAAGACTTACAGATGACCCGAAGGATTTAGT
194 CGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAT
** * * * ** **
63815 CATCATGCTTAAAAGACTTA--AATGG-CAGAAGAACTTACCAATTTAAGAAATAGTTTACTTAG
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTGGGAAATAGTTTACTGGG
*
63877 TAAGAAACTTTGGAAATCTCTTT-TTACTTTTCAAAAATTTCATTTTCTGAAAATACTAAATGAG
66 TAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATACTAAATGAG
* *
63941 AAACTTTGGAAATCGCTTTCTCACTTTTCAAATTCATGTGAAAACATCCTACCTGAAGGTTTTAC
131 AAACTTTGGAAATCGCTTTCTCA-TTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTAC
* ** * *
64006 GGATGGCCTGAAGGACTTATCATCTTATTCGAAAGACTTACAGATGACCCAAATGATTTAAT
195 GGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAT
* * *
64068 CATCATGTTCGAAATACTTACTGATGGGCCGAAGGACTTACCAATTTGGGAAATAGTTTACTGGG
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTGGGAAATAGTTTACTGGG
* * * *
64133 TAAGAAACTTTGGAAATCG-TTTCCTTACTTTTCAAAAATTTCATTTTCAGAAAAGATTTAAT--
66 TAAGAAACTTTGGAAATCGCTTT-CTTACTTTTCAAAAATTTCATTTTCTGAAAATACTAAATGA
*
64195 GAAACTTTGGAAATCACTTTCTCATTTTTCAAA
130 GAAACTTTGGAAATCGCTTTCTCA-TTTTCAAA
64228 ATAACTTAAT
Statistics
Matches: 822, Mismatches: 88, Indels: 33
0.87 0.09 0.03
Matches are distributed among these distances:
253 174 0.21
254 209 0.25
255 133 0.16
256 102 0.12
257 94 0.11
258 8 0.01
259 63 0.08
260 39 0.05
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Consensus pattern (256 bp):
CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTGGGAAATAGTTTACTGGG
TAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATACTAAATGAG
AAACTTTGGAAATCGCTTTCTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTACG
GATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAT
Found at i:63805 original size:41 final size:42
Alignment explanation
Indices: 63748--63834 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 42
63738 ACCCGAAGGT
* * * *
63748 CTTACGGATGGCCCGAATGACTTA-TCATCTTGCTCAAAAGA
1 CTTACAGATGACCCGAAGGACTTAGTCATCATGCTCAAAAGA
* *
63789 CTTACAGATGACCCGAAGGATTTAGTCATCATGCTTAAAAGA
1 CTTACAGATGACCCGAAGGACTTAGTCATCATGCTCAAAAGA
63831 CTTA
1 CTTA
63835 AATGGCAGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 20 0.51
42 19 0.49
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (42 bp):
CTTACAGATGACCCGAAGGACTTAGTCATCATGCTCAAAAGA
Found at i:66377 original size:17 final size:16
Alignment explanation
Indices: 66336--66377 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
66326 AAATATATTT
66336 TAAAATAATTTTAAGA
1 TAAAATAATTTTAAGA
66352 -AAAATAATTTTAAAAGA
1 TAAAATAATTTT--AAGA
66369 TAAAA-AATT
1 TAAAATAATT
66378 GATTTGCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 11 0.48
17 8 0.35
18 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (16 bp):
TAAAATAATTTTAAGA
Found at i:66961 original size:14 final size:15
Alignment explanation
Indices: 66935--66963 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
66925 AATATTATTA
66935 AAAATATTTAAAATT
1 AAAATATTTAAAATT
66950 AAAATA-TTAAAATT
1 AAAATATTTAAAATT
66964 TGGAGATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATATTTAAAATT
Found at i:68246 original size:3 final size:3
Alignment explanation
Indices: 68240--68308 Score: 77
Period size: 3 Copynumber: 22.7 Consensus size: 3
68230 TTAATTATTA
* * *
68240 AAT AAT AAT AAT AAT AAT CAT AAT AAT AAG AATT AA- AAT AAT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
*
68285 AACT AAT AAT AAT AAC AAT AAT AA
1 AA-T AAT AAT AAT AAT AAT AAT AA
68309 AATGGGACAA
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
2 2 0.04
3 48 0.87
4 5 0.09
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:68578 original size:82 final size:82
Alignment explanation
Indices: 68454--68712 Score: 351
Period size: 82 Copynumber: 3.1 Consensus size: 82
68444 TCTTTCAGGA
* * * * * *
68454 AAGATCAGACTTGATTTGCT-CCATTTTTTTTGGCTATTCAGATCAATTTTGGAAGACATGTCTT
1 AAGATCAGACTTGATATG-TGCCA-CTTTTTCGGGTAGTCAGATCAATTTTGGAAGACGTGTCTT
68518 CTCCACTATTCATTCATGG
64 CTCCACTATTCATTCATGG
* * *
68537 AAAATCAGATTTGATCTGTGCCACTTTTTCGGGTAGTCAGATCAATTTTGGAAGACGTGTCTTCT
1 AAGATCAGACTTGATATGTGCCACTTTTTCGGGTAGTCAGATCAATTTTGGAAGACGTGTCTTCT
68602 CCACTATTCATTCA-GG
66 CCACTATTCATTCATGG
* * * *
68618 AGAGATCAGACTTGATATGTGCCTCTTTTTTGGGTAGTCAGATCAAATTTGGAAGACGTGTCTGC
1 A-AGATCAGACTTGATATGTGCCACTTTTTCGGGTAGTCAGATCAATTTTGGAAGACGTGTCTTC
68683 TCCACTATTCATTCATGG
65 TCCACTATTCATTCATGG
*
68701 GAGATCAGACTT
1 AAGATCAGACTT
68713 AAAATTGATT
Statistics
Matches: 157, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
81 3 0.02
82 134 0.85
83 20 0.13
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.37
Consensus pattern (82 bp):
AAGATCAGACTTGATATGTGCCACTTTTTCGGGTAGTCAGATCAATTTTGGAAGACGTGTCTTCT
CCACTATTCATTCATGG
Found at i:69108 original size:42 final size:41
Alignment explanation
Indices: 69034--69134 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 41
69024 AGATCTTACG
* * *
69034 GATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTAAA
1 GATGACCCGAAGGACTTAGCATCATGCTCGAAAGACTTAAA
* **
69075 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGACTT-AGCATCATGCTCGAAAGACTTAAA
69117 GAATGA-CCGAAGGACTTA
1 G-ATGACCCGAAGGACTTA
69135 AAAATTCTAG
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
41 16 0.31
42 31 0.61
43 4 0.08
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.23
Consensus pattern (41 bp):
GATGACCCGAAGGACTTAGCATCATGCTCGAAAGACTTAAA
Found at i:69216 original size:249 final size:248
Alignment explanation
Indices: 68772--69237 Score: 722
Period size: 249 Copynumber: 1.9 Consensus size: 248
68762 GGTGAATATG
* * * *
68772 CCGAAGGTCTTACGGATGGCCGGAAGGACTTATCATCTTGCTTGAAAGACTAACTGATGACCCAA
1 CCGAAGATCTTACGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTAACAGATGACCCAA
* * * * *
68837 AAGATTAATCATCATGCTCAAAGACTTACTGATGGCCCGAAGGACTTACAAATTTTGGAAATAAT
66 AAGATTAAGCATCATGCTCAAAGACTTACTGATGGACCGAAGGACTTAAAAATTCTAGAAATAAT
* * * *
68902 TTACTGGGTAAGAAACTTTGGTAATCGCTTTCTTACTTTTCAAGAATTTCATTTTTTCAAAACAT
131 TTAATGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAGAATTTCATTTTCTAAAAACAT
68967 TAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATGTGAAAACATCCTAC
196 TAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATGTGAAAACATCCTAC
*
69020 CCGAAGATCTTACGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTAA-AGATGACCCG
1 CCGAAGATCTTACGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGAC-TAACAGATGACCCA
*
69084 AAGGATTTAAGCATCATGCTCGAAAGACTTACTGAAT-GACCGAAGGACTTAAAAATTCTAGAAA
65 AAAGA-TTAAGCATCATGCTC-AAAGACTTACTG-ATGGACCGAAGGACTTAAAAATTCTAGAAA
*
69148 TAATTTAAT-GGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAATAATTTCATTTTCTAAAA
127 TAATTTAATGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAGAATTTCATTTTCTAAAA
*
69212 ACATTAAATTAGAAACTTTGGTAATC
192 ACATTAAATGAGAAACTTTGGTAATC
69238 AATTTTCATT
Statistics
Matches: 197, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
248 59 0.30
249 93 0.47
250 43 0.22
251 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (248 bp):
CCGAAGATCTTACGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTAACAGATGACCCAA
AAGATTAAGCATCATGCTCAAAGACTTACTGATGGACCGAAGGACTTAAAAATTCTAGAAATAAT
TTAATGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAGAATTTCATTTTCTAAAAACAT
TAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATGTGAAAACATCCTAC
Found at i:71555 original size:2 final size:2
Alignment explanation
Indices: 71548--71601 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
71538 CTTTATTGTG
71548 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
71589 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
71602 CACCTTTATC
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:71758 original size:105 final size:106
Alignment explanation
Indices: 71574--71809 Score: 354
Period size: 105 Copynumber: 2.2 Consensus size: 106
71564 TATATATATA
* *
71574 TATTATATATATATATATATATATATATCACCTTTATCTGGCTAGCTGAATCTTATCCATAAAGC
1 TATTATATATATATATATAT-TATATATCACCTTTACCAGGCTAGCTGAATCTTATCCATAAAGC
71639 TAGGGCATTTAACCAATTACTCTATAGGGACAACTT-AAGCTT
65 TAGGGCATTTAACCAATTACTCTATAGGGA-AACTTCAAGCTT
71681 TATTATATATATATATATATTATA-ATCACCTTTACCAGGCTAGCTGAATCTTATCCATAAAGCT
1 TATTATATATATATATATATTATATATCACCTTTACCAGGCTAGCTGAATCTTATCCATAAAGCT
* * *
71745 -GGGTCATTTAACCAATTGCTCTATAGGGATAGTTCAAGCTT
66 AGGG-CATTTAACCAATTACTCTATAGGGAAACTTCAAGCTT
* *
71786 TATTGTATACATATA-ATATTATAT
1 TATTATATATATATATATATTATAT
71810 TCTGGGTATA
Statistics
Matches: 119, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
104 14 0.12
105 81 0.68
106 4 0.03
107 20 0.17
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (106 bp):
TATTATATATATATATATATTATATATCACCTTTACCAGGCTAGCTGAATCTTATCCATAAAGCT
AGGGCATTTAACCAATTACTCTATAGGGAAACTTCAAGCTT
Done.