Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006627.1 Hibiscus syriacus cultivar Beakdansim tig00016284_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: 218705
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2336 original size:3 final size:3
Alignment explanation
Indices: 2328--2394 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
2318 TCCCAACATC
2328 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2376 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
2395 TTATTATTAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2399 original size:3 final size:3
Alignment explanation
Indices: 2393--2429 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2383 ATAATAATAA
2393 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2430 TACAGGCTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:10685 original size:16 final size:15
Alignment explanation
Indices: 10651--10703 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
10641 TCAACTAGCC
*
10651 CAATAAAGGCAACTA
1 CAATAAAGGCAATTA
10666 CAATAAAGTTG-AATTA
1 CAATAAAG--GCAATTA
10682 CAATAAAGGCAATTA
1 CAATAAAGGCAATTA
10697 CAATAAA
1 CAATAAA
10704 TTAAATCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
14 1 0.03
15 20 0.59
16 12 0.35
17 1 0.03
ACGTcount: A:0.55, C:0.13, G:0.11, T:0.21
Consensus pattern (15 bp):
CAATAAAGGCAATTA
Found at i:11404 original size:43 final size:44
Alignment explanation
Indices: 11343--11481 Score: 156
Period size: 43 Copynumber: 3.2 Consensus size: 44
11333 AGAAATGATG
*
11343 AATGTTGGGGCACTTTTGAAGAACCATATCATCCAGAAGTAATG
1 AATGTTGGGGCACTTTTGAAGAACCATATCATCCAGAAGTAATA
* * **
11387 AATGTT-GGGCACTTTTGAATATCTGTATCATCCAGAAGTAATA
1 AATGTTGGGGCACTTTTGAAGAACCATATCATCCAGAAGTAATA
* ** * * * *
11430 AATATTGGGGCA-TTTTGAAGGCCCATATTAGCAAGAAATAATA
1 AATGTTGGGGCACTTTTGAAGAACCATATCATCCAGAAGTAATA
11473 AATGTTGGG
1 AATGTTGGG
11482 ACATTTTTTT
Statistics
Matches: 78, Mismatches: 16, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
43 67 0.86
44 11 0.14
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (44 bp):
AATGTTGGGGCACTTTTGAAGAACCATATCATCCAGAAGTAATA
Found at i:12752 original size:38 final size:38
Alignment explanation
Indices: 12698--13010 Score: 338
Period size: 38 Copynumber: 8.1 Consensus size: 38
12688 AGTCGATTTT
* *
12698 TCTTTGTTATTATTGACTTCCTCTTGAAGAGAAGTCAA
1 TCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAA
* * ** * *
12736 TCTTTTTTACTCTTGACTTCCAAGTGAATAGAAGTAAA
1 TCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAA
* * * *
12774 TCTTTGTTACTCTTGACTTCCTCATAAAGAGAAGTCAG
1 TCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAA
* * * *
12812 TCTTTGTTATTTTTGATTTCTTCGTGAAGAAAAGTCAA
1 TCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAA
* * * *
12850 TCCTTGTTATTCTTGAATTCCTCATGAAGAGAAGCCAA
1 TCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAA
* *
12888 TCTTTTTTATTCTTGACTTTCTCGTGAAGAGAAGTCAA
1 TCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAA
* *
12926 TCTTTGTTATTCTTAACTTCCTCGTGAAGAAAAGTCAA
1 TCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAA
* * * *
12964 TCTTTCAATGTCATTCTTGACTTTCTCATAAAGAGAAGTCAA
1 TC-TT---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAA
13006 TCTTT
1 TCTTT
13011 TAGTGTTGGC
Statistics
Matches: 224, Mismatches: 47, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
38 190 0.85
39 2 0.01
41 2 0.01
42 30 0.13
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.41
Consensus pattern (38 bp):
TCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAA
Found at i:13034 original size:45 final size:45
Alignment explanation
Indices: 12935--13145 Score: 203
Period size: 45 Copynumber: 4.8 Consensus size: 45
12925 ATCTTTGTTA
* * * * * *
12935 TTCTTAACTTCCTCGTGAAGAAAAGTCAATCTTTCA---ATGTCA
1 TTCTTAACTTTCTCATAAAGAGAAGTCAATCTTTCAGTGTTGTCC
* * *
12977 TTCTTGACTTTCTCATAAAGAGAAGTCAATCTTTTAGTGTTGGCC
1 TTCTTAACTTTCTCATAAAGAGAAGTCAATCTTTCAGTGTTGTCC
* ** * * *
13022 TTCTTAACTTTCTTACGAAGAGGAGTCAATCTTCCAGTGTCGTCC
1 TTCTTAACTTTCTCATAAAGAGAAGTCAATCTTTCAGTGTTGTCC
* *
13067 TTCTTAACTTTCTCATAAAGGGAAGTCAATCTTTCAGTGTTGTCT
1 TTCTTAACTTTCTCATAAAGAGAAGTCAATCTTTCAGTGTTGTCC
* *** *
13112 TTCTTGACTTTCTTGCAAAGAGGAGTCAATCTTT
1 TTCTTAACTTTCTCATAAAGAGAAGTCAATCTTT
13146 TAGATTTGGT
Statistics
Matches: 134, Mismatches: 32, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
42 30 0.22
45 104 0.78
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (45 bp):
TTCTTAACTTTCTCATAAAGAGAAGTCAATCTTTCAGTGTTGTCC
Found at i:13093 original size:90 final size:90
Alignment explanation
Indices: 12977--13144 Score: 264
Period size: 90 Copynumber: 1.9 Consensus size: 90
12967 TTCAATGTCA
* * *
12977 TTCTTGACTTTCTCATAAAGAGAAGTCAATCTTTTAGTGTTGGCCTTCTTAACTTTCTTACGAAG
1 TTCTTAACTTTCTCATAAAGAGAAGTCAATCTTTCAGTGTTGGCCTTCTTAACTTTCTTACAAAG
13042 AGGAGTCAATCTTCCAGTGTCGTCC
66 AGGAGTCAATCTTCCAGTGTCGTCC
* * * * *
13067 TTCTTAACTTTCTCATAAAGGGAAGTCAATCTTTCAGTGTTGTCTTTCTTGACTTTCTTGCAAAG
1 TTCTTAACTTTCTCATAAAGAGAAGTCAATCTTTCAGTGTTGGCCTTCTTAACTTTCTTACAAAG
13132 AGGAGTCAATCTT
66 AGGAGTCAATCTT
13145 TTAGATTTGG
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 70 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (90 bp):
TTCTTAACTTTCTCATAAAGAGAAGTCAATCTTTCAGTGTTGGCCTTCTTAACTTTCTTACAAAG
AGGAGTCAATCTTCCAGTGTCGTCC
Found at i:13388 original size:136 final size:134
Alignment explanation
Indices: 13141--13749 Score: 668
Period size: 135 Copynumber: 4.5 Consensus size: 134
13131 GAGGAGTCAA
* * * * *
13141 TCTTTTAGATTTGGTCTTCATGAAGAGCAACGAAGCAAATCAAGTTCGATTCAATCTTTCCTGAT
1 TCTTTCAGATTTGGTCTTCCTGAAGAGCATCGAAGCAAATCAAGTTCGATTCAATCTTCCCTGAA
* * * *
13206 GTGCAGCGAAGTGGATCAAAATTTTTCTCGAGTCTGATCTCCCCTAAATAGTAGCAGAGCAGATT
66 GAGCAACGAAGTGGATCAAAATTTTTCTCAAGTCTGATCT-CCCTAAAGAGTAGCAGAGCAGATT
13271 CTTCT
130 CTTCT
* * * *
13276 TCTTTCAGATTTGGTATTCCTGAAGAGCATCAAAAGAAAATCAAGTTCGATTCAATCTTTCCTGA
1 TCTTTCAGATTTGGTCTTCCTGAAGAGCATC-GAAGCAAATCAAGTTCGATTCAATCTTCCCTGA
* * * * * * *
13341 TGAGCAACAAAGTGGATGAAAATTTTTCTCGAGTCTGATCTCACCTAAAGAGTAGCAAAACATAT
65 AGAGCAACGAAGTGGATCAAAATTTTTCTCAAGTCTGATCTC-CCTAAAGAGTAGCAGAGCAGAT
*
13406 TCTTGT
129 TCTTCT
* * * * *
13412 TCTTTTAGATTTGGTCCTCCTGAAGAGAAGT-GAAGCAAATCAAGTTTGATTTAATCTTCCCTGA
1 TCTTTCAGATTTGGTCTTCCTGAAGAGCA-TCGAAGCAAATCAAGTTCGATTCAATCTTCCCTGA
* *
13476 AGAGCAACGAAGTGGATCAAAATTTTTCTCAAGTCTGATCTCGCCTAAAGAGTAGCGGACCAGAT
65 AGAGCAACGAAGTGGATCAAAATTTTTCTCAAGTCTGATCTC-CCTAAAGAGTAGCAGAGCAGAT
13541 TCTTCT
129 TCTTCT
* * * *
13547 TCTTTCAGATTTGGTCTTCCTAAAGAGCAGCGGAGCAAATCAAGTTCGATTCAATCTTCCCAGAA
1 TCTTTCAGATTTGGTCTTCCTGAAGAGCATCGAAGCAAATCAAGTTCGATTCAATCTTCCCTGAA
* * * * * *
13612 GAGTAGCGAAGTGGATCAAAA-TTTTATCAAGTCTGATCTCCGTTAAAGAGTAGCGGAGTAGATT
66 GAGCAACGAAGTGGATCAAAATTTTTCTCAAGTCTGATCTCC-CTAAAGAGTAGCAGAGCAGA--
*
13676 TTCTTTT
128 TTCTTCT
* ** * * * * **
13683 TCTTTAAGATTTTATCTCCCTGAAGAGTAGT-AAAGCAAATCGA-TTATTATTCAATCTTCCCTG
1 TCTTTCAGATTTGGTCTTCCTGAAGAGCA-TCGAAGCAAATCAAGTT-CGATTCAATCTTCCCTG
13746 AAGA
64 AAGA
13750 ACAGTGAAAT
Statistics
Matches: 402, Mismatches: 63, Indels: 17
0.83 0.13 0.04
Matches are distributed among these distances:
133 1 0.00
134 35 0.09
135 193 0.48
136 172 0.43
137 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (134 bp):
TCTTTCAGATTTGGTCTTCCTGAAGAGCATCGAAGCAAATCAAGTTCGATTCAATCTTCCCTGAA
GAGCAACGAAGTGGATCAAAATTTTTCTCAAGTCTGATCTCCCTAAAGAGTAGCAGAGCAGATTC
TTCT
Found at i:13707 original size:271 final size:271
Alignment explanation
Indices: 13141--13749 Score: 726
Period size: 271 Copynumber: 2.2 Consensus size: 271
13131 GAGGAGTCAA
* * * * * * *
13141 TCTTTTAGATTTGGTCTTCATGAAGAGCAA-CGAAGCAAATCAAGTTCGATTCAATCTTTCCTGA
1 TCTTTAAGATTTGATCCTCCTGAAGAG-AAGTGAAGCAAATCAAGTTTGATTCAATCTTCCCTGA
* * * * * *
13205 TGTGCAGCGAAGTGGATCAAAATTTTTCTCGAGTCTGATCTCCCCTAAATAGTAGCAGAGCAGAT
65 AGAGCAACGAAGTGGATCAAAATTTTTCTCAAGTCTGATCTCCCCTAAAGAGTAGCAGACCAGAT
* *
13270 TCTTCTTCTTTCAGATTTGGTATTCCTGAAGAGCATCAAAAGAAAATCAAGTTCGATTCAATCTT
130 TCTTCTTCTTTCAGATTTGGTATTCCTAAAGAGCAGCAAAAGAAAATCAAGTTCGATTCAATCTT
* * * * * *
13335 TCCTGATGAGCAACAAAGTGGATGAAAATTTTTCTCGAGTCTGATCTCACCTAAAGAGTAGCAAA
195 CCCAGAAGAGCAACAAAGTGGATCAAAATTTTTATCAAGTCTGATCTCACCTAAAGAGTAGCAAA
13400 ACATATTCTTGT
260 ACATATTCTTGT
* * *
13412 TCTTTTAGATTTGGTCCTCCTGAAGAGAAGTGAAGCAAATCAAGTTTGATTTAATCTTCCCTGAA
1 TCTTTAAGATTTGATCCTCCTGAAGAGAAGTGAAGCAAATCAAGTTTGATTCAATCTTCCCTGAA
* *
13477 GAGCAACGAAGTGGATCAAAATTTTTCTCAAGTCTGATCTCGCCTAAAGAGTAGCGGACCAGATT
66 GAGCAACGAAGTGGATCAAAATTTTTCTCAAGTCTGATCTCCCCTAAAGAGTAGCAGACCAGATT
* ** *
13542 CTTCTTCTTTCAGATTTGGTCTTCCTAAAGAGCAGC-GGAGCAAATCAAGTTCGATTCAATCTTC
131 CTTCTTCTTTCAGATTTGGTATTCCTAAAGAGCAGCAAAAGAAAATCAAGTTCGATTCAATCTTC
* * * *
13606 CCAGAAGAGTAGCGAAGTGGATCAAAA-TTTTATCAAGTCTGATCTC-CGTTAAAGAGTAGCGGA
196 CCAGAAGAGCAACAAAGTGGATCAAAATTTTTATCAAGTCTGATCTCAC-CTAAAGAGTAGC--A
** * * *
13669 GTAGATTTTCTTTT
258 AAACATATTCTTGT
* * * * *
13683 TCTTTAAGATTTTAT-CTCCCTGAAGAGTAGTAAAGCAAATCGA-TTATTATTCAATCTTCCCTG
1 TCTTTAAGATTTGATCCT-CCTGAAGAGAAGTGAAGCAAATCAAGTT-TGATTCAATCTTCCCTG
13746 AAGA
64 AAGA
13750 ACAGTGAAAT
Statistics
Matches: 289, Mismatches: 43, Indels: 12
0.84 0.12 0.03
Matches are distributed among these distances:
268 1 0.00
269 28 0.10
270 51 0.18
271 209 0.72
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (271 bp):
TCTTTAAGATTTGATCCTCCTGAAGAGAAGTGAAGCAAATCAAGTTTGATTCAATCTTCCCTGAA
GAGCAACGAAGTGGATCAAAATTTTTCTCAAGTCTGATCTCCCCTAAAGAGTAGCAGACCAGATT
CTTCTTCTTTCAGATTTGGTATTCCTAAAGAGCAGCAAAAGAAAATCAAGTTCGATTCAATCTTC
CCAGAAGAGCAACAAAGTGGATCAAAATTTTTATCAAGTCTGATCTCACCTAAAGAGTAGCAAAA
CATATTCTTGT
Found at i:13966 original size:3 final size:3
Alignment explanation
Indices: 13960--13997 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
13950 CATCATCATC
13960 ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
13998 TATAGGCTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:14669 original size:17 final size:19
Alignment explanation
Indices: 14639--14679 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
14629 TTTAAATGAT
14639 TTTTTATCCTTTTT-T-TA
1 TTTTTATCCTTTTTATATA
14656 TTTTTAT-CTATTTTATATA
1 TTTTTATCCT-TTTTATATA
14675 TTTTT
1 TTTTT
14680 TGAATCTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 2 0.10
17 11 0.52
18 1 0.05
19 7 0.33
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTATCCTTTTTATATA
Found at i:17103 original size:22 final size:22
Alignment explanation
Indices: 17078--17120 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
17068 TGAAAGCTTC
17078 TATACACATTATTTGCAACTTA
1 TATACACATTATTTGCAACTTA
17100 TATACACATTATTTGCAACTT
1 TATACACATTATTTGCAACTT
17121 CTACTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.42
Consensus pattern (22 bp):
TATACACATTATTTGCAACTTA
Found at i:24611 original size:21 final size:21
Alignment explanation
Indices: 24550--24611 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
24540 GATACTTAAG
**
24550 GGAGTATCGATACTAGGGGTA
1 GGAGTATCGATACTAGGAATA
* ***
24571 -GTGTATCGATACTCTCAATA
1 GGAGTATCGATACTAGGAATA
24591 GGAGTATCGATACTAGGAATA
1 GGAGTATCGATACTAGGAATA
24612 ATTTTGAAAT
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.27
Consensus pattern (21 bp):
GGAGTATCGATACTAGGAATA
Found at i:27761 original size:21 final size:20
Alignment explanation
Indices: 27735--27788 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
27725 ATTGATACCT
* *
27735 TGGTATCCATACAGGATGAAG
1 TGGTATCTATAC-GGATGAAC
*
27756 TGGTATTTATATCGGATGAAC
1 TGGTATCTATA-CGGATGAAC
27777 TGGTATCTATAC
1 TGGTATCTATAC
27789 CAGATAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (20 bp):
TGGTATCTATACGGATGAAC
Found at i:29596 original size:45 final size:45
Alignment explanation
Indices: 29545--29771 Score: 278
Period size: 45 Copynumber: 5.0 Consensus size: 45
29535 CATTAAGCAC
*
29545 TTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCATATGCA
1 TTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCA
*
29590 TTTCAACTATAGTATACTTTTCTGTTGATAATGCATCCATATGCA
1 TTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCA
* * * * * *
29635 TTTCAACTATAATATAGTCTTCTGTTGATTATGTACCCATATACA
1 TTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCA
* * * *
29680 TTTCAACTATAGTATACTTTTATGTTGATAATGTACCTATATACA
1 TTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCA
* * * *
29725 TTTCAACTAT-G-ACATCCTTTCATATCGATAATGCACCCATATGCA
1 TTTCAACTATAGTATA-CTTTTC-TGTTGATAATGCACCCATATGCA
29770 TT
1 TT
29772 ATTATTTTCA
Statistics
Matches: 157, Mismatches: 23, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
43 2 0.01
44 5 0.03
45 150 0.96
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (45 bp):
TTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCA
Found at i:37986 original size:21 final size:20
Alignment explanation
Indices: 37960--38013 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
37950 ATTGATACCT
* *
37960 TGGTATCCATACAGGATGAAG
1 TGGTATCTATAC-GGATGAAC
*
37981 TGGTATTTATATCGGATGAAC
1 TGGTATCTATA-CGGATGAAC
38002 TGGTATCTATAC
1 TGGTATCTATAC
38014 CAGAGAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (20 bp):
TGGTATCTATACGGATGAAC
Found at i:39822 original size:45 final size:45
Alignment explanation
Indices: 39771--39997 Score: 278
Period size: 45 Copynumber: 5.0 Consensus size: 45
39761 CATTAAGCAC
*
39771 TTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCATATGCA
1 TTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCA
*
39816 TTTCAACTATAGTATACTTTTCTGTTGATAATGCATCCATATGCA
1 TTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCA
* * * * * *
39861 TTTCAACTATAATATAGTCTTCTGTTGATTATGTACCCATATACA
1 TTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCA
* * * * *
39906 TTTCAACTATAGTATAATTTTATGTTGATAATGTACCTATATACA
1 TTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCA
* * *
39951 TTTCAACTAT-G-ACATCCTTTCATGTCGATAATGCACCCATATGCA
1 TTTCAACTATAGTATA-CTTTTC-TGTTGATAATGCACCCATATGCA
39996 TT
1 TT
39998 ATTATTTTCA
Statistics
Matches: 157, Mismatches: 23, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
43 2 0.01
44 4 0.03
45 151 0.96
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (45 bp):
TTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCA
Found at i:46307 original size:45 final size:45
Alignment explanation
Indices: 46251--46477 Score: 285
Period size: 45 Copynumber: 5.0 Consensus size: 45
46241 CATTAAGCAC
* * *
46251 TTTCAACTATAGCATATTTTTCTGTTGATAATGCATCCATATGCA
1 TTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCA
*
46296 TTTCAATTATAGTATACTTTTCTGTTGATAATGCACCCATATGCA
1 TTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCA
* * * * *
46341 TTTCAACTATATTATACTCTTCTTTTGATAATGTACCCATATACA
1 TTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCA
* * * *
46386 TTTCAACTATAGTTTACTTTTCTGTTGATAATGTACCCATTTACA
1 TTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCA
* * * *
46431 TTTCAACTATAGCAT-CCTTTCATGCTGATAATGAACCCATATGCA
1 TTTCAACTATAGTATACTTTTC-TGTTGATAATGCACCCATATGCA
46476 TT
1 TT
46478 ATTATTTTCA
Statistics
Matches: 159, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
44 5 0.03
45 154 0.97
ACGTcount: A:0.29, C:0.19, G:0.09, T:0.42
Consensus pattern (45 bp):
TTTCAACTATAGTATACTTTTCTGTTGATAATGCACCCATATGCA
Found at i:49433 original size:12 final size:12
Alignment explanation
Indices: 49416--49440 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49406 AAGAGATACC
49416 AACAAAATCTAT
1 AACAAAATCTAT
49428 AACAAAATCTAT
1 AACAAAATCTAT
49440 A
1 A
49441 TCCATTGTCC
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:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (12 bp):
AACAAAATCTAT
Found at i:59819 original size:30 final size:29
Alignment explanation
Indices: 59744--59819 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
59734 TTTTTTTGTC
* * *
59744 ATATTTAGAGTTTTTCTTTTTTTTTTTACA
1 ATATTCAGAGTTTTT-TTCTTTTTGTTACA
*
59774 ATATTCAGAGTTTTTTCCTTTTTGTTACA
1 ATATTCAGAGTTTTTTTCTTTTTGTTACA
59803 ATATTCAGAGTTTTTTT
1 ATATTCAGAGTTTTTTT
59820 TTCTCTAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 27 0.66
30 14 0.34
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.61
Consensus pattern (29 bp):
ATATTCAGAGTTTTTTTCTTTTTGTTACA
Found at i:60732 original size:31 final size:31
Alignment explanation
Indices: 60695--60758 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
60685 AATTAAAAAA
**
60695 AATATTTGGCCACTTTTGTTTTTATGTAATT
1 AATATTTGGCCACTTTCATTTTTATGTAATT
* *
60726 AATATTTGGTCACTTTCATTTTTATTTAATT
1 AATATTTGGCCACTTTCATTTTTATGTAATT
60757 AA
1 AA
60759 GATATGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.55
Consensus pattern (31 bp):
AATATTTGGCCACTTTCATTTTTATGTAATT
Found at i:63499 original size:75 final size:76
Alignment explanation
Indices: 63373--63526 Score: 292
Period size: 75 Copynumber: 2.0 Consensus size: 76
63363 AATGTCATTT
63373 AATAATAACTAAGGAGAAGATGTATTTTAACACACAGAGAGAGAGAGGGCCTAAATATGCCCAAA
1 AATAATAACTAAGGAGAAGATGTATTTTAACACACAGAGAGAGAGAGGGCCTAAATATGCCCAAA
63438 AGAGAAAAGGC
66 AGAGAAAAGGC
*
63449 AATAATAACTAAGGAGAAGATGTA-TTTAACACACAGAGAGAGAGAGGGCCTTAATATGCCCAAA
1 AATAATAACTAAGGAGAAGATGTATTTTAACACACAGAGAGAGAGAGGGCCTAAATATGCCCAAA
63513 AGAGAAAAGGC
66 AGAGAAAAGGC
63524 AAT
1 AAT
63527 GTTGTATAAT
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
75 53 0.69
76 24 0.31
ACGTcount: A:0.47, C:0.13, G:0.23, T:0.16
Consensus pattern (76 bp):
AATAATAACTAAGGAGAAGATGTATTTTAACACACAGAGAGAGAGAGGGCCTAAATATGCCCAAA
AGAGAAAAGGC
Found at i:64987 original size:30 final size:29
Alignment explanation
Indices: 64928--64992 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 29
64918 ATTATTATTA
* *
64928 TTATTTTGCCCATTAGGGCATTCCCGTTTT
1 TTATTTAGCCCATTAGGGCATTCCAG-TTT
64958 TTATTTAGCCCATTAGGGCA-TCCGAGTTT
1 TTATTTAGCCCATTAGGGCATTCC-AGTTT
64987 TTATTT
1 TTATTT
64993 TGAGAATACA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 12 0.38
30 20 0.62
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (29 bp):
TTATTTAGCCCATTAGGGCATTCCAGTTT
Found at i:70988 original size:19 final size:20
Alignment explanation
Indices: 70952--70989 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
70942 TTTTAAATGG
*
70952 ACTTTGAATTATTTTTGAAA
1 ACTTTGAATTAATTTTGAAA
70972 ACTTTGAA-TAATTTTGAA
1 ACTTTGAATTAATTTTGAA
70990 TAAATTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (20 bp):
ACTTTGAATTAATTTTGAAA
Found at i:71731 original size:16 final size:16
Alignment explanation
Indices: 71707--71747 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
71697 TAATAAAATT
71707 ATTAATTTAATTTTTA
1 ATTAATTTAATTTTTA
* *
71723 ATTATTTTATTTTTTA
1 ATTAATTTAATTTTTA
71739 A--AATTTAAT
1 ATTAATTTAAT
71748 CCAGTCGAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
14 6 0.29
16 15 0.71
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTAATTTAATTTTTA
Found at i:71992 original size:30 final size:30
Alignment explanation
Indices: 71927--72009 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 30
71917 ACCCTAGTGT
** * **
71927 CCTAATGGATTAAATAAAAAATCTGCGTGC
1 CCTAATGGGCTAAATAAAAAATTTGAATGC
*
71957 ACTAATGGGCTAAATAAAAAATTTGAATGC
1 CCTAATGGGCTAAATAAAAAATTTGAATGC
*
71987 CCTAATGGGC-AAAAAAACAAATT
1 CCTAATGGGCTAAATAAA-AAATT
72010 ATTTTTTTAG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 6 0.14
30 38 0.86
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (30 bp):
CCTAATGGGCTAAATAAAAAATTTGAATGC
Found at i:72864 original size:20 final size:20
Alignment explanation
Indices: 72839--72879 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
72829 AATGTTCACC
72839 TATAAACGAG-TGAATGTTAT
1 TATAAACGAGATGAAT-TTAT
*
72859 TATAAATGAGATGAATTTAT
1 TATAAACGAGATGAATTTAT
72879 T
1 T
72880 TTATGATAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.41, C:0.02, G:0.17, T:0.39
Consensus pattern (20 bp):
TATAAACGAGATGAATTTAT
Found at i:74280 original size:41 final size:41
Alignment explanation
Indices: 74230--74349 Score: 134
Period size: 41 Copynumber: 2.9 Consensus size: 41
74220 CCAATTTTTA
* * *
74230 ATATCGATACCAGTTCATCTGGTATGGATA-CAAATCCTTCG
1 ATATGGATACCAGTTCATCTGGTATGGATAGC-AACCCTACG
* ***
74271 ATATGGATACTAGTTCATCCCTTATGGATAGCAACCCTACG
1 ATATGGATACCAGTTCATCTGGTATGGATAGCAACCCTACG
* * *
74312 ATATGGATACCAATTCATCTGGTATGGAAACCAACCCT
1 ATATGGATACCAGTTCATCTGGTATGGATAGCAACCCT
74350 CCAGTATTGG
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
41 63 0.98
42 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (41 bp):
ATATGGATACCAGTTCATCTGGTATGGATAGCAACCCTACG
Found at i:74339 original size:21 final size:20
Alignment explanation
Indices: 74230--74345 Score: 54
Period size: 21 Copynumber: 5.7 Consensus size: 20
74220 CCAATTTTTA
* *
74230 ATATCGATACCAGTTCATCTG
1 ATATGGATACCAATTCATC-G
* * * *
74251 GTATGGATACAAATCCTTCG
1 ATATGGATACCAATTCATCG
* * *
74271 ATATGGATACTAGTTCATCCC
1 ATATGGATACCAATTCAT-CG
* * * *
74292 TTATGGATAGCAA-CCCTACG
1 ATATGGATACCAATTCAT-CG
74312 ATATGGATACCAATTCATCTG
1 ATATGGATACCAATTCATC-G
* *
74333 GTATGGAAACCAA
1 ATATGGATACCAA
74346 CCCTCCAGTA
Statistics
Matches: 66, Mismatches: 26, Indels: 6
0.67 0.27 0.06
Matches are distributed among these distances:
20 29 0.44
21 37 0.56
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (20 bp):
ATATGGATACCAATTCATCG
Found at i:76589 original size:20 final size:20
Alignment explanation
Indices: 76566--76605 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
76556 TCTAGGGTTC
*
76566 CAATATCGATACTAGATGAA
1 CAATATCAATACTAGATGAA
*
76586 CAATATCAATATTAGATGAA
1 CAATATCAATACTAGATGAA
76606 TGGGGGCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (20 bp):
CAATATCAATACTAGATGAA
Found at i:77945 original size:32 final size:32
Alignment explanation
Indices: 77869--77945 Score: 118
Period size: 32 Copynumber: 2.4 Consensus size: 32
77859 GTTACCATGA
* * *
77869 AATTCAGATAATACATAATAGAGTTAGTATTG
1 AATTTAGATAATGCAAAATAGAGTTAGTATTG
*
77901 AATTTAGATAATGCAAAATATAGTTAGTATTG
1 AATTTAGATAATGCAAAATAGAGTTAGTATTG
77933 AATTTAGATAATG
1 AATTTAGATAATG
77946 TACAAGAGCG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (32 bp):
AATTTAGATAATGCAAAATAGAGTTAGTATTG
Found at i:77959 original size:32 final size:32
Alignment explanation
Indices: 77869--77960 Score: 103
Period size: 32 Copynumber: 2.9 Consensus size: 32
77859 GTTACCATGA
* * * *
77869 AATTCAGATAATACATAATAGAGTTAGTATTG
1 AATTTAGATAATGCAAAAGAGAGTTAGTATTG
* *
77901 AATTTAGATAATGCAAAATATAGTTAGTATTG
1 AATTTAGATAATGCAAAAGAGAGTTAGTATTG
* * *
77933 AATTTAGATAATGTACAAGAGCGTTAGT
1 AATTTAGATAATGCAAAAGAGAGTTAGT
77961 GTCACATTTA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.35
Consensus pattern (32 bp):
AATTTAGATAATGCAAAAGAGAGTTAGTATTG
Found at i:87575 original size:20 final size:20
Alignment explanation
Indices: 87546--87658 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
87536 CAAGAGTATA
87546 CATACTTTGGTAAAAGTTTC
1 CATACTTTGGTAAAAGTTTC
* * *
87566 CATGCTTTGGTAAGAGTATC
1 CATACTTTGGTAAAAGTTTC
** *
87586 CATACTTTCATCAAAA-TTTT
1 CATACTTTGGT-AAAAGTTTC
* *
87606 CGTACTTTGGTAAGAGTATT-
1 CATACTTTGGTAAAAGT-TTC
* *
87626 CATAATTTGGTAAAAGTTTT
1 CATACTTTGGTAAAAGTTTC
87646 CATACTTTGGTAA
1 CATACTTTGGTAA
87659 GAGTATCAAT
Statistics
Matches: 72, Mismatches: 17, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
19 5 0.07
20 62 0.86
21 5 0.07
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (20 bp):
CATACTTTGGTAAAAGTTTC
Found at i:87592 original size:40 final size:40
Alignment explanation
Indices: 87537--87675 Score: 172
Period size: 40 Copynumber: 3.5 Consensus size: 40
87527 ATACTAGTGC
* * *
87537 AAGAGTATACATACTTTGGTAAAAGTTTCCATGCTTTGGT
1 AAGAGTATCCATACTTTGGTAAAAGTTTTCATACTTTGGT
** *
87577 AAGAGTATCCATACTTTCATCAAAA-TTTTCGTACTTTGGT
1 AAGAGTATCCATACTTTGGT-AAAAGTTTTCATACTTTGGT
* *
87617 AAGAGTATTCATAATTTGGTAAAAGTTTTCATACTTTGGT
1 AAGAGTATCCATACTTTGGTAAAAGTTTTCATACTTTGGT
* *
87657 AAGAGTATCAATAGTTTGG
1 AAGAGTATCCATACTTTGG
87676 CAATAGTATC
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
39 4 0.05
40 75 0.90
41 4 0.05
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.39
Consensus pattern (40 bp):
AAGAGTATCCATACTTTGGTAAAAGTTTTCATACTTTGGT
Found at i:87674 original size:20 final size:19
Alignment explanation
Indices: 87611--87686 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 19
87601 ATTTTCGTAC
87611 TTTGGTAAGAGTATTCATAA
1 TTTGGTAAGAGTA-TCATAA
* * *
87631 TTTGGTAAAAGTTTTCATAC
1 TTTGGTAAGAG-TATCATAA
*
87651 TTTGGTAAGAGTATCAATAG
1 TTTGGTAAGAGTATC-ATAA
* *
87671 TTTGGCAATAGTATCA
1 TTTGGTAAGAGTATCA
87687 ATACATTTTC
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
19 4 0.09
20 41 0.89
21 1 0.02
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (19 bp):
TTTGGTAAGAGTATCATAA
Found at i:93551 original size:17 final size:17
Alignment explanation
Indices: 93518--93551 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
93508 TTTGTTTTAA
* *
93518 TAAAATTTAATATAATT
1 TAAAATTTAAAAAAATT
93535 TAAAATTTAAAAAAATT
1 TAAAATTTAAAAAAATT
93552 AAATAAATGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAATTTAAAAAAATT
Found at i:99356 original size:21 final size:20
Alignment explanation
Indices: 99332--99405 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 20
99322 CCCAGAGGGT
99332 ATCGATTCCCCTGTGGGGGGA
1 ATCGATTCCCCT-TGGGGGGA
* *
99353 ATCGGTTCCCCTTAAAAGGGGGA
1 ATCGATTCCCCTT---GGGGGGA
*
99376 ATCGATTCCCTCATGGGGGG-
1 ATCGATTCCC-CTTGGGGGGA
99396 ATCGATTCCC
1 ATCGATTCCC
99406 TCTGCACCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
20 11 0.25
21 16 0.36
23 15 0.34
24 2 0.05
ACGTcount: A:0.19, C:0.26, G:0.31, T:0.24
Consensus pattern (20 bp):
ATCGATTCCCCTTGGGGGGA
Found at i:99399 original size:20 final size:20
Alignment explanation
Indices: 99370--99407 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
99360 CCCCTTAAAA
99370 GGGGGAATCGATTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
99390 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
99408 TGCACCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.26, G:0.34, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:108139 original size:82 final size:82
Alignment explanation
Indices: 108003--108440 Score: 465
Period size: 82 Copynumber: 5.4 Consensus size: 82
107993 CAAATTAGAA
* * * *
108003 GGAAGACGAGTCTGCTCCACTATTCTTTTA-GGGAGACCAGACTTGATATGTTCCTCTTTCTT-G
1 GGAAGACGGGTCTGCTCCACTATTCTTTCAGGGGAGATCAAACTTGATATGTTCCTCTTT-TTCG
*
108066 GGTAGTCAGATCAATTTC
65 GGTAGTCAGATCAATTTT
* * * * * * *
108084 GGAAAACGGGTCTGTTCCATTATTCTTTCGGGGGAGATCATACTTGA-ATTATTCCTCTTTTTCA
1 GGAAGACGGGTCTGCTCCACTATTCTTTCAGGGGAGATCAAACTTGATA-TGTTCCTCTTTTTCG
*
108148 GGTACTCAGATCAATTTT
65 GGTAGTCAGATCAATTTT
* ** * * * * *
108166 TGAAGATAGATCTGCTCCACTAATCTTTCAAGGGAGATCAGACTTGATATGTTCCTATTTTTCGG
1 GGAAGACGGGTCTGCTCCACTATTCTTTCAGGGGAGATCAAACTTGATATGTTCCTCTTTTTCGG
*
108231 GTAGTTAGATCAATTTT
66 GTAGTCAGATCAATTTT
* * * * * *
108248 AGAAGACGGGTATGCTCCACTATTCTTTTAGGGGAGATCAAAATTGATTTGTTCTTCTTTTTCGG
1 GGAAGACGGGTCTGCTCCACTATTCTTTCAGGGGAGATCAAACTTGATATGTTCCTCTTTTTCGG
*
108313 GTAGTCAGATCAATTTC
66 GTAGTCAGATCAATTTT
* * * *
108330 GGAAGACGGGT-TGCTCTATTATTCTTTCAGGGGAGATCAAATTTGATCT-TTGCCTCTTTTTCG
1 GGAAGACGGGTCTGCTCCACTATTCTTTCAGGGGAGATCAAACTTGATATGTT-CCTCTTTTTCG
*
108393 AGTAGTCAGAAT-AATTTT
65 GGTAGTCAG-ATCAATTTT
* * *
108411 GGAAAACGAGTCTGCTCCACTCTTCTTTCA
1 GGAAGACGGGTCTGCTCCACTATTCTTTCA
108441 TGGAGATAAG
Statistics
Matches: 293, Mismatches: 57, Indels: 13
0.81 0.16 0.04
Matches are distributed among these distances:
80 2 0.01
81 92 0.31
82 198 0.68
83 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (82 bp):
GGAAGACGGGTCTGCTCCACTATTCTTTCAGGGGAGATCAAACTTGATATGTTCCTCTTTTTCGG
GTAGTCAGATCAATTTT
Found at i:108691 original size:89 final size:89
Alignment explanation
Indices: 108479--108821 Score: 305
Period size: 89 Copynumber: 3.8 Consensus size: 89
108469 AATGGGTATG
* * * * ** * * *
108479 CTCCACTACTATTCCGGGGAGATCAGACTCAAGATTGATTTTCTTTGCTGCTTCTTTTGGGAAGA
1 CTCCACTACTCTTCCAGGGAGATCAGACTCGAGATTGATTTGCTTCACTAC-TATTTCGGGAAGA
* * * * *
108544 CCAAATCTGAAATAATAAAAAAAATATG
65 CCAAATCT--CA-AAGAAAAAGAATCTA
* * * * *
108572 TTCCACTACTATTCC-GAGGAGATCTGACTCGAGATTGATTTGCTTCACTACTCTTTTGGGAAGA
1 CTCCACTACTCTTCCAG-GGAGATCAGACTCGAGATTGATTTGCTTCACTACTATTTCGGGAAGA
* *
108636 CCAAATTTCAAATAAAAAGAATCTA
65 CCAAATCTCAAAGAAAAAGAATCTA
*** * * *
108661 CTCCACTACT-TTTTTGGGAAGATCATACTCGAGATTGATTTACTTCTCTACTATTTCGGGAAGA
1 CTCCACTACTCTTCCAGGG-AGATCAGACTCGAGATTGATTTGCTTCACTACTATTTCGGGAAGA
* *
108725 CCAAATCTGAAAGAAAAAGAATCTG
65 CCAAATCTCAAAGAAAAAGAATCTA
* * * *
108750 CTCCACTTCTCTTCCAGGGAGATCAGACTCGAGATTGATTTGCTTCGCTGCT-TCTTCAGGAAGA
1 CTCCACTACTCTTCCAGGGAGATCAGACTCGAGATTGATTTGCTTCACTACTAT-TTCGGGAAGA
108814 CCAAATCT
65 CCAAATCT
108822 AACCTAATTT
Statistics
Matches: 211, Mismatches: 34, Indels: 14
0.81 0.13 0.05
Matches are distributed among these distances:
88 5 0.02
89 137 0.65
90 6 0.03
92 21 0.10
93 42 0.20
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (89 bp):
CTCCACTACTCTTCCAGGGAGATCAGACTCGAGATTGATTTGCTTCACTACTATTTCGGGAAGAC
CAAATCTCAAAGAAAAAGAATCTA
Found at i:108814 original size:178 final size:181
Alignment explanation
Indices: 108479--108819 Score: 417
Period size: 178 Copynumber: 1.9 Consensus size: 181
108469 AATGGGTATG
* * *
108479 CTCCACTACTATTCCGGGGAGATCAGACTCAAGATTGATTTTCTTTGCTGCTTCTTTTGGGAAGA
1 CTCCACTACTATTCCGGGAAGATCAGACTCAAGATTGATTTACTTTGCTGCTACTTTTGGGAAGA
* * *
108544 CCAAATCTGAAATAATAAAAAAAATATGTTCCACTACTATTCCGAGGAGATCTGACTCGAGATTG
66 CCAAATCTG-AATAAGAAAAAAAATATGCTCCACTACTATTCCGAGGAGATCAGACTCGAGATTG
**
108609 ATTTGCTTCACTACTCTTTTGGGAAGACCAAATTTCAAATAAAAAGAATCTA
130 ATTTGCTTCACTACTCTTTCAGGAAGACCAAATTTCAAATAAAAAGAATCTA
* ** * *
108661 CTCCACTACTTTTTTGGGAAGATCATACTCGAGATTGATTTAC-TT-CT-CTACTATTTCGGGAA
1 CTCCACTACTATTCCGGGAAGATCAGACTCAAGATTGATTTACTTTGCTGCTACT-TTT-GGGAA
* * * *
108723 GACCAAATCTG-A-AAGAAAAAGAATCTGCTCCACTTCTCTTCC-AGGGAGATCAGACTCGAGAT
64 GACCAAATCTGAATAAGAAAAAAAATATGCTCCACTACTATTCCGA-GGAGATCAGACTCGAGAT
* *
108785 TGATTTGCTTCGCTGCT-TCTTCAGGAAGACCAAAT
128 TGATTTGCTTCACTACTCT-TTCAGGAAGACCAAAT
108820 CTAACCTAAT
Statistics
Matches: 136, Mismatches: 19, Indels: 12
0.81 0.11 0.07
Matches are distributed among these distances:
177 2 0.01
178 70 0.51
179 5 0.04
180 5 0.04
181 18 0.13
182 36 0.26
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (181 bp):
CTCCACTACTATTCCGGGAAGATCAGACTCAAGATTGATTTACTTTGCTGCTACTTTTGGGAAGA
CCAAATCTGAATAAGAAAAAAAATATGCTCCACTACTATTCCGAGGAGATCAGACTCGAGATTGA
TTTGCTTCACTACTCTTTCAGGAAGACCAAATTTCAAATAAAAAGAATCTA
Found at i:108895 original size:29 final size:29
Alignment explanation
Indices: 108862--108931 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
108852 TATCAAATCA
108862 CAAAGATTGACTTATATTCA-CAAGGAAGT
1 CAAAGATTGACTTAT-TTCATCAAGGAAGT
* * * **
108891 CAAAGGTTGAATTATTTTATTGAGGAAGT
1 CAAAGATTGACTTATTTCATCAAGGAAGT
*
108920 CAAGGATTGACT
1 CAAAGATTGACT
108932 CTTCTTCGCG
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
28 3 0.09
29 29 0.91
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.31
Consensus pattern (29 bp):
CAAAGATTGACTTATTTCATCAAGGAAGT
Found at i:109168 original size:38 final size:37
Alignment explanation
Indices: 109060--109193 Score: 160
Period size: 38 Copynumber: 3.5 Consensus size: 37
109050 AAATGTTTAC
* * * * *
109060 TTCTCTTTACGAGGAATTCGAGAATAACAAAGATTTAT
1 TTCTCTTCACGAGGAAGTCAAG-ATAACAAAGGTTGAT
109098 TTCTCTTCACGAGGAAGTCAAGGATAACAAAGGTTGAT
1 TTCTCTTCACGAGGAAGTCAA-GATAACAAAGGTTGAT
* *
109136 TTCTCTTTACGAGGAAGTCAATGATAACAAAGGTTGAC
1 TTCTCTTCACGAGGAAGTCAA-GATAACAAAGGTTGAT
* *
109174 TTATCTTCAAGAGGAAGTCA
1 TTCTCTTCACGAGGAAGTCA
109194 TGGATTGACT
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
38 83 0.99
39 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (37 bp):
TTCTCTTCACGAGGAAGTCAAGATAACAAAGGTTGAT
Found at i:109294 original size:167 final size:167
Alignment explanation
Indices: 109109--109423 Score: 506
Period size: 167 Copynumber: 1.9 Consensus size: 167
109099 TCTCTTCACG
* * *
109109 AGGAAGTCAAGGATAACAAAGGTTGATTTCTCTTTACGAGGAAGTCAATGATAACAAAGGTTGAC
1 AGGAAGTCAAGAATAACAAAGGTTGACTTCTCTTTACGAGGAAGTCAAGGATAACAAAGGTTGAC
* * *
109174 TTATCTTCAAGAGGAAGTCATGGATTGACTTTGCTGGGGAGTCAGA-AATAACAAAGATTGACTT
66 TTATCTTCAAGAGGAAGTCAAGGATTGACTCTGCTAGGGAGTCA-ACAATAACAAAGATTGACTT
109238 CTCTTAACGAGAAAGTCAAAGGCTGAATTTTCCTTATT
130 CTCTTAACGAGAAAGTCAAAGGCTGAATTTTCCTTATT
109276 AGGAAGTCAAGAATAACAAAGGTTGACTTCTCTTTACGAGGAAGTCAAGGATAACAAAGGTTGAC
1 AGGAAGTCAAGAATAACAAAGGTTGACTTCTCTTTACGAGGAAGTCAAGGATAACAAAGGTTGAC
* * * *
109341 TTGTCTTCACGAGGAAGTCAAGGATTGACTCTGCTAGGGAGTCAACGATAACAAAGGTTGACTTC
66 TTATCTTCAAGAGGAAGTCAAGGATTGACTCTGCTAGGGAGTCAACAATAACAAAGATTGACTTC
* *
109406 TCTTTACGAGGAAGTCAA
131 TCTTAACGAGAAAGTCAA
109424 GGATAACAAA
Statistics
Matches: 135, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
166 1 0.01
167 134 0.99
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.27
Consensus pattern (167 bp):
AGGAAGTCAAGAATAACAAAGGTTGACTTCTCTTTACGAGGAAGTCAAGGATAACAAAGGTTGAC
TTATCTTCAAGAGGAAGTCAAGGATTGACTCTGCTAGGGAGTCAACAATAACAAAGATTGACTTC
TCTTAACGAGAAAGTCAAAGGCTGAATTTTCCTTATT
Found at i:109363 original size:38 final size:38
Alignment explanation
Indices: 109276--109365 Score: 153
Period size: 38 Copynumber: 2.4 Consensus size: 38
109266 TTTCCTTATT
* *
109276 AGGAAGTCAAGAATAACAAAGGTTGACTTCTCTTTACG
1 AGGAAGTCAAGGATAACAAAGGTTGACTTCTCTTCACG
*
109314 AGGAAGTCAAGGATAACAAAGGTTGACTTGTCTTCACG
1 AGGAAGTCAAGGATAACAAAGGTTGACTTCTCTTCACG
109352 AGGAAGTCAAGGAT
1 AGGAAGTCAAGGAT
109366 TGACTCTGCT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (38 bp):
AGGAAGTCAAGGATAACAAAGGTTGACTTCTCTTCACG
Found at i:109414 original size:100 final size:100
Alignment explanation
Indices: 109275--109471 Score: 297
Period size: 100 Copynumber: 2.0 Consensus size: 100
109265 TTTTCCTTAT
* *
109275 TAGGAAGTCAAGAATAACAAAGGTTGACTTCTCTTTACGAGGAAGTCAAGGATAACAAAGGTTGA
1 TAGGAAGTCAAGAATAACAAAGGTTGACTTCTCTTTACGAGGAAGTCAAGGATAACAAAGATAGA
* * *
109340 CTTGTCTTCACGAGGAAGTCAAGGATTGACTCTGC
66 CTTCTCTTAACGAGGAAGTCAAGAATTGACTCTGC
* *
109375 TAGGGAGTCAACG-ATAACAAAGGTTGACTTCTCTTTACGAGGAAGTCAAGGATAACAAATATAG
1 TAGGAAGTCAA-GAATAACAAAGGTTGACTTCTCTTTACGAGGAAGTCAAGGATAACAAAGATAG
* *
109439 ACTTCTCTTAATGAGGAAGTCAATAATTGACTC
65 ACTTCTCTTAACGAGGAAGTCAAGAATTGACTC
109472 CTCTGGGAGG
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
100 86 0.99
101 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.26
Consensus pattern (100 bp):
TAGGAAGTCAAGAATAACAAAGGTTGACTTCTCTTTACGAGGAAGTCAAGGATAACAAAGATAGA
CTTCTCTTAACGAGGAAGTCAAGAATTGACTCTGC
Found at i:109431 original size:38 final size:38
Alignment explanation
Indices: 109380--109461 Score: 110
Period size: 38 Copynumber: 2.2 Consensus size: 38
109370 TCTGCTAGGG
* * *
109380 AGTCAACGATAACAAAGGTTGACTTCTCTTTACGAGGA
1 AGTCAACGATAACAAAGATAGACTTCTCTTAACGAGGA
* * *
109418 AGTCAAGGATAACAAATATAGACTTCTCTTAATGAGGA
1 AGTCAACGATAACAAAGATAGACTTCTCTTAACGAGGA
109456 AGTCAA
1 AGTCAA
109462 TAATTGACTC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.26
Consensus pattern (38 bp):
AGTCAACGATAACAAAGATAGACTTCTCTTAACGAGGA
Found at i:123373 original size:2 final size:2
Alignment explanation
Indices: 123366--123415 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
123356 AGCTTTATTG
* *
123366 TA TA TA TA TG TA TA TG TA TA TA TA TA TA TA 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
123408 TA TA TA TA
1 TA TA TA TA
123416 ATCGCCTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:127776 original size:48 final size:45
Alignment explanation
Indices: 127722--127821 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 45
127712 ATTTTACCCC
* * *
127722 CATGCTTTGTTATAAAAAAATAATCCTAACCTCATGATATCTAATTCG
1 CATGCTTTATT-TAAAAAAA-AAT-CTAACCGCATGATATCTAATTCA
* * *
127770 CATGC-TTATTTGAAAAAAAATCTAACCGCATGATTTCTAGTTCA
1 CATGCTTTATTTAAAAAAAAATCTAACCGCATGATATCTAATTCA
127814 CATGCTTT
1 CATGCTTT
127822 TGAAAAACAC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
44 24 0.53
45 5 0.11
46 7 0.16
47 4 0.09
48 5 0.11
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (45 bp):
CATGCTTTATTTAAAAAAAAATCTAACCGCATGATATCTAATTCA
Found at i:127818 original size:44 final size:44
Alignment explanation
Indices: 127736--127828 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
127726 CTTTGTTATA
* *
127736 AAAAAATAATCCTAACCTCATGATATCTAATTCGCATGCTTATTTG
1 AAAAAATAATCCTAACCGCATGATATCTAATTCACATGC-T-TTTG
* *
127782 AAAAAA-AAT-CTAACCGCATGATTTCTAGTTCACATGCTTTTG
1 AAAAAATAATCCTAACCGCATGATATCTAATTCACATGCTTTTG
127824 AAAAA
1 AAAAA
127829 CACATAAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
42 9 0.21
43 1 0.02
44 24 0.56
45 3 0.07
46 6 0.14
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (44 bp):
AAAAAATAATCCTAACCGCATGATATCTAATTCACATGCTTTTG
Found at i:133010 original size:30 final size:31
Alignment explanation
Indices: 132976--133046 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
132966 TTTCGGAAAA
*
132976 ACATAGGTAAA-TATCCATATGTC-CCAAAGG
1 ACATAGGTAAACTATCAATATGTCTCCAAA-G
*
133006 ACATAGGTAAACTATCAATATGTCTCGAAAG
1 ACATAGGTAAACTATCAATATGTCTCCAAAG
133037 ACATAGGTAA
1 ACATAGGTAA
133047 CACTTGACTC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 11 0.30
31 22 0.59
32 4 0.11
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (31 bp):
ACATAGGTAAACTATCAATATGTCTCCAAAG
Found at i:133828 original size:24 final size:20
Alignment explanation
Indices: 133772--133868 Score: 67
Period size: 19 Copynumber: 4.8 Consensus size: 20
133762 TTCCTTTTGA
133772 AGTGTATCGATACACACTAT
1 AGTGTATCGATACACACTAT
* * *
133792 AGTGCATCAATACATCCCTTCACT
1 AGTGTATCGATACA-CAC-T-A-T
*
133816 AGTGTATCGATACACTAC-CT
1 AGTGTATCGATACAC-ACTAT
*
133836 -GTGTATCGATACACTAC-CT
1 AGTGTATCGATACAC-ACTAT
133855 -GTGTATCGATACAC
1 AGTGTATCGATACAC
133869 TTATTGCATT
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
19 33 0.51
20 13 0.20
21 2 0.03
22 1 0.02
23 2 0.03
24 14 0.22
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (20 bp):
AGTGTATCGATACACACTAT
Found at i:133841 original size:19 final size:19
Alignment explanation
Indices: 133817--133869 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
133807 CCCTTCACTA
133817 GTGTATCGATACACTACCT
1 GTGTATCGATACACTACCT
133836 GTGTATCGATACACTACCT
1 GTGTATCGATACACTACCT
133855 GTGTATCGATACACT
1 GTGTATCGATACACT
133870 TATTGCATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (19 bp):
GTGTATCGATACACTACCT
Found at i:135288 original size:3 final size:3
Alignment explanation
Indices: 135282--135314 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
135272 AATTATTATT
135282 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
135315 TTACTAGGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:139552 original size:30 final size:30
Alignment explanation
Indices: 139516--139638 Score: 142
Period size: 30 Copynumber: 4.0 Consensus size: 30
139506 TGAAGGACAT
*
139516 GTCCATATGTTCCAAAGAGCATAGGTAA-CA
1 GTCCATATGTCCCAAAGA-CATAGGTAACCA
*
139546 GTCCATATGTCCCAAATGACATAGGTAATCCT
1 GTCCATATGTCCCAAA-GACATAGGTAA-CCA
*
139578 GTCCATATGTCCCAAAGGACATAGGGAAACCA
1 GTCCATATGTCCCAAA-GACATA-GGTAACCA
*
139610 -TCCATATGTCTCGAAAGACATAGGTAACC
1 GTCCATATGTC-CCAAAGACATAGGTAACC
139639 CTCGACTCTT
Statistics
Matches: 81, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
30 30 0.37
31 18 0.22
32 29 0.36
33 4 0.05
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.23
Consensus pattern (30 bp):
GTCCATATGTCCCAAAGACATAGGTAACCA
Found at i:145643 original size:134 final size:134
Alignment explanation
Indices: 145471--145967 Score: 488
Period size: 134 Copynumber: 3.7 Consensus size: 134
145461 ATTTTAATTT
* * * ** * * * *
145471 ACTTCACTGCTATTCAGGGAAGGTTGAATCAAATTTGATTTTCTTTAATGCTCTTCAGGAACACC
1 ACTTCACTGATCTTCAGGGAAGATTGAATTGAATTTGATTTGCTTCACTGCTCTTCAGGAAGACC
*
145536 AAATATGAAAGGAGAAGAATTTGTTCCACTACTCTTTAGGAGAGATTAAAATCAAGGAAATTTTG
66 AAATATGAAAGGAGAAGAATTTGTTCCACTACTCTTTAGGAGAGATTAAACTCAAGGAAATTTTG
145601 ATCC
131 ATCC
* * *
145605 ACTTCACTGATCTTCATGGAAGATTGAATTGAATTTGATTTGCTTCGCTGCTCTTCAGGAATACC
1 ACTTCACTGATCTTCAGGGAAGATTGAATTGAATTTGATTTGCTTCACTGCTCTTCAGGAAGACC
* * * * *
145670 AAATCTGAAAGGAGAAGAATCTAG-TCCATTACTCTTTA-GAG-GATATCAGACTCGAGGAAATT
66 AAATATGAAAGGAGAAGAAT-TTGTTCCACTACTCTTTAGGAGAGAT-T-AAACTCAAGGAAATT
*
145732 TTGTTCC
128 TTGATCC
* * *
145739 ACTTCACT-ACTCTTCATGGAAGATTGAATTGAATTTGATTTGGTT-AGCTGCTCTTTAGGAAGA
1 ACTTCACTGA-TCTTCAGGGAAGATTGAATTGAATTTGATTTGCTTCA-CTGCTCTTCAGGAAGA
* * * * * * * * * * *
145802 CCAATTCTGAAA-GATAAAGAATCTGCTCCACTATTATTTAGGGGAGACTACACTCAAGAAAATT
64 CCAAATATGAAAGGA-GAAGAATTTGTTCCACTACTCTTTAGGAGAGATTAAACTCAAGGAAATT
*
145866 TTGAACC
128 TTGATCC
* * * * *
145873 ACTTCATTGTTCTTCAGGGAAGATTCAATAT-AATTTGATTTGCTTCGCTGCTATTCAGGAAGAC
1 ACTTCACTGATCTTCAGGGAAGATTGAAT-TGAATTTGATTTGCTTCACTGCTCTTCAGGAAGAC
* * *
145937 AAAATATGAAAGAAG-AGAAATATGTTCCACT
65 CAAATATGAAAGGAGAAG-AATTTGTTCCACT
145968 TTTTTGGGTA
Statistics
Matches: 298, Mismatches: 51, Indels: 28
0.79 0.14 0.07
Matches are distributed among these distances:
132 3 0.01
133 10 0.03
134 276 0.93
135 7 0.02
136 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Consensus pattern (134 bp):
ACTTCACTGATCTTCAGGGAAGATTGAATTGAATTTGATTTGCTTCACTGCTCTTCAGGAAGACC
AAATATGAAAGGAGAAGAATTTGTTCCACTACTCTTTAGGAGAGATTAAACTCAAGGAAATTTTG
ATCC
Found at i:147468 original size:22 final size:22
Alignment explanation
Indices: 147442--147487 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
147432 CTCCCTTTAA
*
147442 TTTCTTTTCCTTTT-TTCTTATT
1 TTTCTTTT-ATTTTCTTCTTATT
147464 TTTCTTTTATTTTCTTCTTATT
1 TTTCTTTTATTTTCTTCTTATT
147486 TT
1 TT
147488 CTTCTTCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTCTTTTATTTTCTTCTTATT
Found at i:147473 original size:11 final size:12
Alignment explanation
Indices: 147452--147493 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
147442 TTTCTTTTCC
147452 TTTT-TTCTTAT
1 TTTTCTTCTTAT
147463 TTTTCTT-TTA-
1 TTTTCTTCTTAT
147473 TTTTCTTCTTA-
1 TTTTCTTCTTAT
147484 TTTTCTTCTT
1 TTTTCTTCTT
147494 CTTCAAGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 7 0.24
11 20 0.69
12 2 0.07
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTCTTCTTAT
Found at i:153401 original size:57 final size:57
Alignment explanation
Indices: 153307--153462 Score: 228
Period size: 57 Copynumber: 2.8 Consensus size: 57
153297 ACATATCACA
* *
153307 AGAAGGA-TTTATCCTAATT-CTATTCATGACT-TAATATCTAATCAGATCTCTTTACT
1 AGAAGGATTTTATCCTAATTCCT-TTCATGTCTCT-ATATCTAATCAGATCTCTTTACC
153363 AGAAGGATTTTATCCTAATTCCTTTCATGTCTCTATATCTAATCAGATCTCTTTACC
1 AGAAGGATTTTATCCTAATTCCTTTCATGTCTCTATATCTAATCAGATCTCTTTACC
* * *
153420 AGAAGGATTTTATCCTAATTCCTTTCATATCTCCACATCTAAT
1 AGAAGGATTTTATCCTAATTCCTTTCATGTCTCTATATCTAAT
153463 TTGATCTCGA
Statistics
Matches: 92, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
56 7 0.08
57 82 0.89
58 3 0.03
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.41
Consensus pattern (57 bp):
AGAAGGATTTTATCCTAATTCCTTTCATGTCTCTATATCTAATCAGATCTCTTTACC
Found at i:161321 original size:10 final size:10
Alignment explanation
Indices: 161302--161331 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
161292 TTCTCAGAGT
*
161302 AATTCAATCA
1 AATTCCATCA
161312 AATTCCATCA
1 AATTCCATCA
161322 AATTCCATCA
1 AATTCCATCA
161332 TCCTTCAGTA
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:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (10 bp):
AATTCCATCA
Found at i:184291 original size:44 final size:46
Alignment explanation
Indices: 184256--184353 Score: 137
Period size: 47 Copynumber: 2.2 Consensus size: 46
184246 ATAAGTTTTT
184256 GAGCTTACGGAA-T-AATGGCAAGTATATTGGAAAAATAAGCTTAC
1 GAGCTTACGGAATTAAATGGCAAGTATATTGGAAAAATAAGCTTAC
* * * *
184300 GAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAAAATAAGCTTAC
1 GAGCTTACGGAA-TTAAATGGCAAGTATATTGGAAAAATAAGCTTAC
184347 GAGCTTA
1 GAGCTTA
184354 TGGGATAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
44 11 0.23
46 1 0.02
47 35 0.74
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (46 bp):
GAGCTTACGGAATTAAATGGCAAGTATATTGGAAAAATAAGCTTAC
Found at i:191449 original size:47 final size:45
Alignment explanation
Indices: 191367--191480 Score: 149
Period size: 47 Copynumber: 2.5 Consensus size: 45
191357 ATAATTTTAT
* *
191367 GAGCTTACGGAAT-AATGGCAAGTATACTGGAAAAATAAGCTTAC
1 GAGCTTATGGAATAAATGGTAAGTATACTGGAAAAATAAGCTTAC
** *
191411 GAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAAAATAAGCTTAC
1 GAGCTTATGGAA--TAAATGGTAAGTATACTGGAAAAATAAGCTTAC
*
191458 GAGCTTATGGGATAAATGGTAAG
1 GAGCTTATGGAATAAATGGTAAG
191481 AGATTTTATA
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
44 11 0.18
45 11 0.18
46 1 0.02
47 38 0.62
ACGTcount: A:0.38, C:0.09, G:0.25, T:0.29
Consensus pattern (45 bp):
GAGCTTATGGAATAAATGGTAAGTATACTGGAAAAATAAGCTTAC
Found at i:194831 original size:18 final size:18
Alignment explanation
Indices: 194808--194848 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
194798 CTTCATCTTC
* *
194808 TTATTTTTTTAATTGCTT
1 TTATTTATTTAATCGCTT
194826 TTATTTATTTAATCGCTT
1 TTATTTATTTAATCGCTT
194844 TTATT
1 TTATT
194849 ATCTTTTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (18 bp):
TTATTTATTTAATCGCTT
Found at i:203388 original size:13 final size:12
Alignment explanation
Indices: 203367--203401 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
203357 ATCTGTTCGA
203367 AAAAGAAAAAAG
1 AAAAGAAAAAAG
203379 AAAAGAAAAAAG
1 AAAAGAAAAAAG
* *
203391 ACATGAAAAAA
1 AAAAGAAAAAA
203402 ATGGAAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.80, C:0.03, G:0.14, T:0.03
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:205085 original size:18 final size:18
Alignment explanation
Indices: 205059--205097 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
205049 TCATCTTCTA
* *
205059 ATTTTTTTAATTACTTTT
1 ATTTATTTAATCACTTTT
*
205077 ATTTATTTAATCATTTTT
1 ATTTATTTAATCACTTTT
205095 ATT
1 ATT
205098 ATCTTTTACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTATTTAATCACTTTT
Found at i:215420 original size:16 final size:16
Alignment explanation
Indices: 215395--215430 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
215385 TTATTGATTT
215395 TATTAATATTAATTAG
1 TATTAATATTAATTAG
* *
215411 TATTATTATTAATTAT
1 TATTAATATTAATTAG
215427 TATT
1 TATT
215431 GTTTTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
TATTAATATTAATTAG
Found at i:216066 original size:16 final size:16
Alignment explanation
Indices: 216047--216083 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
216037 AGTTACTTAG
216047 AGAGGGGAGCCAAACC
1 AGAGGGGAGCCAAACC
216063 AGAGGGGAGCCAAACC
1 AGAGGGGAGCCAAACC
216079 AGAGG
1 AGAGG
216084 TTGTTTCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.22, G:0.41, T:0.00
Consensus pattern (16 bp):
AGAGGGGAGCCAAACC
Done.