Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000447.1 Hibiscus syriacus cultivar Beakdansim tig00000817_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: 62438
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:5938 original size:4 final size:4
Alignment explanation
Indices: 5929--5954 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5919 AAAAACATAA
5929 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
5955 TGTACAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:6668 original size:13 final size:14
Alignment explanation
Indices: 6650--6681 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
6640 TAAATAATTC
6650 TAAAAATATTA-TT
1 TAAAAATATTATTT
6663 TAAAAATATTATTT
1 TAAAAATATTATTT
6677 TAAAA
1 TAAAA
6682 CTAAAGGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAAAAATATTATTT
Found at i:7964 original size:3 final size:3
Alignment explanation
Indices: 7954--7999 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
7944 GTATTATTTG
* *
7954 TAA T-A TAA TAA TAT TAA T-A TAA TAA TAA TAA TATA TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
7998 TA
1 TA
8000 CGATACGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 4 0.11
3 29 0.81
4 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:7971 original size:14 final size:14
Alignment explanation
Indices: 7954--7999 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
7944 GTATTATTTG
*
7954 TAATATAATAATAT
1 TAATATAATAATAA
7968 TAATATAATAATAA
1 TAATATAATAATAA
7982 TAATAT-ATAATAA
1 TAATATAATAATAA
*
7995 AAATA
1 TAATA
8000 CGATACGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 11 0.37
14 19 0.63
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TAATATAATAATAA
Found at i:9623 original size:23 final size:22
Alignment explanation
Indices: 9597--9640 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
9587 CAAAATATTA
9597 TGTACTGTAACTATGTATTTTTT
1 TGTACTGTAACTATGT-TTTTTT
9620 TGTACTGTAACTATGTTTTTT
1 TGTACTGTAACTATGTTTTTT
9641 AACTTGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.20, C:0.09, G:0.14, T:0.57
Consensus pattern (22 bp):
TGTACTGTAACTATGTTTTTTT
Found at i:10166 original size:16 final size:17
Alignment explanation
Indices: 10144--10190 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
10134 ATGAATGAAA
10144 TTTTTAATTAAA-TT-T
1 TTTTTAATTAAAGTTAT
10159 TATTTTAATTAAAAGTTAT
1 T-TTTTAATT-AAAGTTAT
10178 TTTTTAATTAAAG
1 TTTTTAATTAAAG
10191 ATTTTCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 8 0.29
17 7 0.25
18 10 0.36
19 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (17 bp):
TTTTTAATTAAAGTTAT
Found at i:10222 original size:17 final size:17
Alignment explanation
Indices: 10200--10232 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
10190 GATTTTCATT
10200 TTTGTTTACATATTTTA
1 TTTGTTTACATATTTTA
10217 TTTGTTTACATATTTT
1 TTTGTTTACATATTTT
10233 TCAAATTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTGTTTACATATTTTA
Found at i:13931 original size:21 final size:20
Alignment explanation
Indices: 13907--13955 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
13897 CAGAAATATT
*
13907 TATTTTAAATAATAAAATTAA
1 TATTTTAAATAA-AAAAATAA
* *
13928 TATTTTCATTAAAAAAATAA
1 TATTTTAAATAAAAAAATAA
*
13948 CATTTTAA
1 TATTTTAA
13956 GTAGCCAACG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (20 bp):
TATTTTAAATAAAAAAATAA
Found at i:14887 original size:27 final size:27
Alignment explanation
Indices: 14831--14888 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
14821 TAAATTAAGA
* *
14831 TCTAATAAATAATATTAGATTCTTTAT
1 TCTAATAAATAATATTAGATACTATAT
* *
14858 TCTAATTAATAATAGTTTGATACTAT-T
1 TCTAATAAATAATA-TTAGATACTATAT
14885 TCTA
1 TCTA
14889 TAATTATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 18 0.69
28 8 0.31
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.48
Consensus pattern (27 bp):
TCTAATAAATAATATTAGATACTATAT
Found at i:23392 original size:20 final size:20
Alignment explanation
Indices: 23369--23425 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
23359 TGTTGGCCCT
23369 TTAGTATCGATACTGACCCC
1 TTAGTATCGATACTGACCCC
* * *
23389 TTAGTATCAATACTCACCTC
1 TTAGTATCGATACTGACCCC
*
23409 TTGGTATCGATACTGAC
1 TTAGTATCGATACTGAC
23426 TGATTGAGCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.33
Consensus pattern (20 bp):
TTAGTATCGATACTGACCCC
Found at i:27000 original size:19 final size:20
Alignment explanation
Indices: 26958--27013 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
26948 CTCTTTCCTT
*
26958 TCTCTTTTTTTTTGTTTCGAA
1 TCTCTCTTTTTTT-TTTCGAA
*
26979 TCTCTCTTTTTTTTTTC-TA
1 TCTCTCTTTTTTTTTTCGAA
26998 TCT-TCTGTTTTTTTTT
1 TCTCTCT-TTTTTTTTT
27014 TGTTTTCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 3 0.09
19 13 0.41
20 4 0.12
21 12 0.38
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.73
Consensus pattern (20 bp):
TCTCTCTTTTTTTTTTCGAA
Found at i:27021 original size:18 final size:19
Alignment explanation
Indices: 26963--27026 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 19
26953 TCCTTTCTCT
*
26963 TTTTTTTTGTTTCGAATC-TC
1 TTTTTTTT-TTTC-TATCTTC
26983 TCTTTTTTTTTTCTATCTTC
1 T-TTTTTTTTTTCTATCTTC
*
27003 TGTTTTTTTTTTGT-T-TTC
1 T-TTTTTTTTTTCTATCTTC
27021 TTTTTT
1 TTTTTT
27027 CCTTTTTCTC
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
17 5 0.13
18 4 0.10
19 4 0.10
20 19 0.49
21 7 0.18
ACGTcount: A:0.05, C:0.12, G:0.06, T:0.77
Consensus pattern (19 bp):
TTTTTTTTTTTCTATCTTC
Found at i:27567 original size:25 final size:25
Alignment explanation
Indices: 27533--27605 Score: 128
Period size: 26 Copynumber: 2.9 Consensus size: 25
27523 ATTTAGGGGA
27533 TTAGGGTTTGAAACCCTAATCTAAT
1 TTAGGGTTTGAAACCCTAATCTAAT
*
27558 TTAGGGTTTGAAACCCTAAATCTGAT
1 TTAGGGTTTGAAACCCT-AATCTAAT
27584 TTAGGGTTTGAAACCCTAATCT
1 TTAGGGTTTGAAACCCTAATCT
27606 GATGGGTTGA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
25 22 0.48
26 24 0.52
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTAAT
Found at i:27586 original size:26 final size:25
Alignment explanation
Indices: 27533--27608 Score: 134
Period size: 25 Copynumber: 3.0 Consensus size: 25
27523 ATTTAGGGGA
*
27533 TTAGGGTTTGAAACCCTAATCTAAT
1 TTAGGGTTTGAAACCCTAATCTGAT
27558 TTAGGGTTTGAAACCCTAAATCTGAT
1 TTAGGGTTTGAAACCCT-AATCTGAT
27584 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
27609 GGGTTGATTG
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
25 25 0.51
26 24 0.49
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:27684 original size:3 final size:3
Alignment explanation
Indices: 27676--27734 Score: 100
Period size: 3 Copynumber: 19.3 Consensus size: 3
27666 ATTAATAAAC
*
27676 ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA AAA ATA ATA ATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
27722 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
27735 AAAAAAAACC
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:28031 original size:40 final size:40
Alignment explanation
Indices: 27976--28216 Score: 216
Period size: 40 Copynumber: 5.8 Consensus size: 40
27966 TTATCTAGGG
**
27976 TGACACGGCTCATACGTGATGAAGAGATCTGGTC-GGAGAA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCAGCTG-A
* * *
28016 AGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGG---TC---AGCTGA
* * * * * * * * *
28062 TAATACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTAAGGG
1 TGACACGGCTCATACGTGATGAAGA-GATCTGGTCAGCT---GA
* *
28105 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGCTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCAGCTGA
28145 TGACACGGCTCATACGTGATGAAGAGATCTGGTCAGCTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCAGCTGA
*
28185 TGACACGGCTCATACGTGATGAAGAGTTCTGG
1 TGACACGGCTCATACGTGATGAAGAGATCTGG
28217 CCATCTAAAG
Statistics
Matches: 165, Mismatches: 24, Indels: 24
0.77 0.11 0.11
Matches are distributed among these distances:
40 102 0.62
42 1 0.01
43 34 0.21
46 24 0.15
47 4 0.02
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (40 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGTCAGCTGA
Found at i:28224 original size:169 final size:169
Alignment explanation
Indices: 27976--28304 Score: 570
Period size: 169 Copynumber: 1.9 Consensus size: 169
27966 TTATCTAGGG
*
27976 TGACACGGCTCATACGTGATGAAGAGATCTGGTCGGAGAAAGACACGGCTCATACGTGATGAAGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCGCAGAAAGACACGGCTCATACGTGATGAAGA
*
28041 GTTCTGGCCATCTAAAGGTGATAATACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGGT
66 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGGT
*
28106 GACACGGCTCCTACGTGATGAGGAGATCTGGTCAGCTGA
131 GACACGGCTCCTACGTGATGAAGAGATCTGGTCAGCTGA
* *
28145 TGACACGGCTCATACGTGATGAAGAGATCTGGTCAGCTG-ATGACACGGCTCATACGTGATGAAG
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTC-GCAGAAAGACACGGCTCATACGTGATGAAG
* *
28209 AGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
65 AGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGG
*
28274 TGACACGGCTCCTACGTGATGAAGAGCTCTG
130 TGACACGGCTCCTACGTGATGAAGAGATCTG
28305 ATCTGGGGAT
Statistics
Matches: 151, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
169 149 0.99
170 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (169 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGTCGCAGAAAGACACGGCTCATACGTGATGAAGA
GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGGT
GACACGGCTCCTACGTGATGAAGAGATCTGGTCAGCTGA
Found at i:28413 original size:28 final size:28
Alignment explanation
Indices: 28363--28416 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
28353 AGGATTTATG
* *
28363 GTTTCAAGAGAAACCAAATCAAAGATTT
1 GTTTCAAAAGAAACCAAACCAAAGATTT
28391 GTTTCAAAAGAAA-CAAACCCAAAGAT
1 GTTTCAAAAGAAACCAAA-CCAAAGAT
28417 AATATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (28 bp):
GTTTCAAAAGAAACCAAACCAAAGATTT
Found at i:28608 original size:66 final size:65
Alignment explanation
Indices: 28432--28614 Score: 210
Period size: 66 Copynumber: 2.8 Consensus size: 65
28422 TTTTAAAAGC
* * *
28432 AACTGTCTCAAAAGAGACCAAATTCGTTTTAAGGGAAACGA-CTCAAAGATGACATTTAAAGGGA
1 AACTGTCTCAAATGAGACAAAATTCATTTTAAGGGAAACGATCTCAAAGATGACATTTAAAGGGA
* * * * * *
28496 AACTGTCTC--GTGCAAGACAAAATTCGTTTTTAAGGGAAACGTTCTCAAAGATCGACGTTTCAT
1 AACTGTCTCAAATG--AGACAAAATTC-ATTTTAAGGGAAACGATCTCAAAGAT-GACATTTAAA
28559 GGGA
62 GGGA
* *
28563 AATTGTCTCAAATGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
1 AACTGTCTCAAATGAGACAAAATTCATTTTAAGGGAAACGATCTCAAAGATG
28615 TTTGTTTTGT
Statistics
Matches: 99, Mismatches: 13, Indels: 13
0.79 0.10 0.10
Matches are distributed among these distances:
62 1 0.01
64 19 0.19
65 15 0.15
66 32 0.32
67 30 0.30
69 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.25
Consensus pattern (65 bp):
AACTGTCTCAAATGAGACAAAATTCATTTTAAGGGAAACGATCTCAAAGATGACATTTAAAGGGA
Found at i:28734 original size:66 final size:63
Alignment explanation
Indices: 28655--28811 Score: 165
Period size: 66 Copynumber: 2.5 Consensus size: 63
28645 AGATGGTAAA
* *
28655 TTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTTTCTCAAAGAAACTGTCTCGAGAGATACAAA
1 TTTTGTTTCCAAAGAAACAAACTCAAAGA-TTTTTTC-AAAAGAAACTGTCTCAAGAGATA-AAA
28720 C
63 C
* * * * * * * *
28721 TTTTGTTTCCAAAGAAAGAGATTCAATGA-TTTTTCAAAAGAAATTGTTTTAAGGGATAAAAC
1 TTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTTCAAAAGAAACTGTCTCAAGAGATAAAAC
* *
28783 -ATTGTTTCCAGAGAAACAAACTCAAAGAT
1 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
28812 GATCTTGTTT
Statistics
Matches: 74, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
61 22 0.30
62 4 0.05
63 17 0.23
64 6 0.08
66 25 0.34
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (63 bp):
TTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTTCAAAAGAAACTGTCTCAAGAGATAAAAC
Found at i:28841 original size:15 final size:15
Alignment explanation
Indices: 28817--28860 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
28807 AAGATGATCT
*
28817 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
28832 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
28847 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
28861 CGACTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:29405 original size:67 final size:64
Alignment explanation
Indices: 29316--29580 Score: 275
Period size: 67 Copynumber: 4.0 Consensus size: 64
29306 AAAGATTTAC
* * * * * *
29316 TTCAAGAGAAACTGTCTCAAGAGATACAAAATTCATTTTAAGAGAAACAGATTCAAAGATTTTTT
1 TTCAAAAGAAATTATCTTAAGAGAGACAAAATT-ATTTTAA-AGAAACAGACTCAAAGA-TTTTT
*
29381 TT
63 GT
*
29383 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTT
1 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTAT-TTT--AAAGAAACAGACTCAAAGATTTTT
29448 GT
63 GT
*
29450 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTATTTCCAAAGAAACCA-ACTCAAAGATTTT
1 TTCAAAAGAAATTATCTTAAGAGAGACAAAA--TTATTT-TAAAGAAA-CAGACTCAAAGATTTT
29514 TGT
62 TGT
** *
29517 TTCAAAAG-AAGCATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACCA-ACTCAAAGATTTT
1 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTAT-TTT--AAAGAAA-CAGACTCAAAGATTTT
29580 T
62 T
29581 TCAAAAGAAA
Statistics
Matches: 174, Mismatches: 14, Indels: 21
0.83 0.07 0.10
Matches are distributed among these distances:
64 3 0.02
65 2 0.01
66 45 0.26
67 99 0.57
68 20 0.11
69 5 0.03
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.31
Consensus pattern (64 bp):
TTCAAAAGAAATTATCTTAAGAGAGACAAAATTATTTTAAAGAAACAGACTCAAAGATTTTTGT
Found at i:29581 original size:67 final size:67
Alignment explanation
Indices: 29368--29580 Score: 358
Period size: 67 Copynumber: 3.2 Consensus size: 67
29358 AGAAACAGAT
*
29368 TCAAAGATTTTTTTTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAA-C
1 TCAAAGA-TTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACC
29432 AGAC
65 A-AC
*
29436 TCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTATTTCCAAAGAAACCA
1 TCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACCA
29501 AC
66 AC
**
29503 TCAAAGATTTTTGTTTCAAAAG-AAGCATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACCA
1 TCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACCA
29567 AC
66 AC
29569 TCAAAGATTTTT
1 TCAAAGATTTTT
29581 TCAAAAGAAA
Statistics
Matches: 139, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
66 53 0.38
67 77 0.55
68 9 0.06
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (67 bp):
TCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACCA
AC
Found at i:29606 original size:26 final size:27
Alignment explanation
Indices: 29552--29608 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
29542 CAAAATTTTG
*
29552 TTTCCAAAGAAACCAACTCAAAGATTT
1 TTTCAAAAGAAACCAACTCAAAGATTT
29579 TTTCAAAAGAAA-CAATCTCAAAGATTT
1 TTTCAAAAGAAACCAA-CTCAAAGATTT
29606 TTT
1 TTT
29609 TCACAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.32
Consensus pattern (27 bp):
TTTCAAAAGAAACCAACTCAAAGATTT
Found at i:29670 original size:52 final size:53
Alignment explanation
Indices: 29595--29698 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 53
29585 AAGAAACAAT
29595 CTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
1 CTCAAAGA-TTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
*
29649 CTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
29699 AAATAAATAG
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 41 0.84
54 8 0.16
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (53 bp):
CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
Found at i:29725 original size:28 final size:27
Alignment explanation
Indices: 29694--29836 Score: 126
Period size: 29 Copynumber: 5.1 Consensus size: 27
29684 CAAAACTTTG
* *
29694 TTTCAAAATAAATAGACTCAAAGATATT
1 TTTCAAAAGAAACA-ACTCAAAGATATT
*
29722 TTTCAAAAGAAACAACTCAAAGATTTT
1 TTTCAAAAGAAACAACTCAAAGATATT
* * *
29749 TATTCAAAAGGAACAAACTCCAAGATTTT
1 T-TTCAAAAGAAAC-AACTCAAAGATATT
* *
29778 TATTCAAAAGGAGCAAACTCAAAGAT-TT
1 T-TTCAAAAGAAAC-AACTCAAAGATATT
* * *
29806 TTTCAAGAGGAACAAACTCAAAGATTTT
1 TTTCAAAAGAAAC-AACTCAAAGATATT
29834 TTT
1 TTT
29837 TTTCAAGAGA
Statistics
Matches: 103, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
27 35 0.34
28 31 0.30
29 37 0.36
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.30
Consensus pattern (27 bp):
TTTCAAAAGAAACAACTCAAAGATATT
Found at i:29774 original size:56 final size:56
Alignment explanation
Indices: 29709--29867 Score: 196
Period size: 56 Copynumber: 2.8 Consensus size: 56
29699 AAATAAATAG
*
29709 ACTCAAAGATATTTTTCAAAAGAAAC-AACTCAAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTTTCAAAAGAAACAAACTCAAAGATTTTT-TTCAAAAGGAACAA
* * * *
29765 ACTCCAAGATTTTTATTCAAAAGGAGCAAACTCAAAGA-TTTTTTCAAGAGGAACAA
1 ACTCAAAGATTTTT-TTCAAAAGAAACAAACTCAAAGATTTTTTTCAAAAGGAACAA
* *
29821 ACTCAAAGATTTTTTTTTTCAAGAGAAACAAACCCAAAGATTTTTTT
1 ACTCAAAGA---TTTTTTTCAAAAGAAACAAACTCAAAGATTTTTTT
29868 TTTCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
56 33 0.38
57 14 0.16
58 29 0.33
59 11 0.13
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (56 bp):
ACTCAAAGATTTTTTTCAAAAGAAACAAACTCAAAGATTTTTTTCAAAAGGAACAA
Found at i:29777 original size:29 final size:28
Alignment explanation
Indices: 29709--29867 Score: 187
Period size: 29 Copynumber: 5.6 Consensus size: 28
29699 AAATAAATAG
* *
29709 ACTCAAAGATATTTTTCAAAAGAAAC-A
1 ACTCAAAGATTTTTTTCAAAAGGAACAA
29736 ACTCAAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTT-TTCAAAAGGAACAA
* *
29765 ACTCCAAGATTTTTATTCAAAAGGAGCAA
1 ACTCAAAGATTTTT-TTCAAAAGGAACAA
*
29794 ACTCAAAGA-TTTTTTCAAGAGGAACAA
1 ACTCAAAGATTTTTTTCAAAAGGAACAA
* *
29821 ACTCAAAGATTTTTTTTTTCAAGAGAAACAA
1 ACTCAAAGA---TTTTTTTCAAAAGGAACAA
*
29852 ACCCAAAGATTTTTTT
1 ACTCAAAGATTTTTTT
29868 TTTCAAAAGA
Statistics
Matches: 117, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
27 34 0.29
28 22 0.19
29 36 0.31
31 25 0.21
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (28 bp):
ACTCAAAGATTTTTTTCAAAAGGAACAA
Found at i:29869 original size:31 final size:31
Alignment explanation
Indices: 29803--29879 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
29793 AACTCAAAGA
* *
29803 TTTTTTCAAGAGGAACAAACTCAAAGATTTT
1 TTTTTTCAAGAGAAACAAACCCAAAGATTTT
29834 TTTTTTCAAGAGAAACAAACCCAAAGATTTT
1 TTTTTTCAAGAGAAACAAACCCAAAGATTTT
*
29865 TTTTTTCAAAAGAAA
1 TTTTTTCAAGAGAAA
29880 TTGTCTTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (31 bp):
TTTTTTCAAGAGAAACAAACCCAAAGATTTT
Found at i:30196 original size:36 final size:36
Alignment explanation
Indices: 30112--30215 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
30102 GAGAAAATGA
* * *
30112 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
30146 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
30182 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
30216 CGATTTCAAG
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 19 0.33
35 10 0.17
36 29 0.50
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:30369 original size:105 final size:100
Alignment explanation
Indices: 30183--30414 Score: 259
Period size: 105 Copynumber: 2.3 Consensus size: 100
30173 TAGAGAAATT
* * **
30183 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAACGATTTCAAGTGAGATCAACTTTGTTTAATGT
1 GTCTCAAGCGAGACAAAATTTG-TTTTGAGAAACAAAATCAAGTGAGATCAACTTTGTTTAATGT
* *
30248 GAAACAAATCCGAAATTTGGATCTCAAAGGGAAAAG
65 GAAACAAATCCAAAATTTGGATCTCAAAGGAAAAAG
* *
30284 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCTAAGGTGAGATTAATTTTGTTT-
1 GTCTCAAGCGAGACAAAATTTGTTTTG--AGAAACAA-AATC-AA-GTGAGATCAACTTTGTTTA
* * * * *
30348 TTAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
61 AT-GTGAAACAAATCCAAAATTTGGATCTCAAAGGAAAAAG
**
30389 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTT
30415 AAAATTCTCA
Statistics
Matches: 110, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
100 5 0.05
101 21 0.19
102 7 0.06
103 2 0.02
104 3 0.03
105 72 0.65
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.31
Consensus pattern (100 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAGAAACAAAATCAAGTGAGATCAACTTTGTTTAATGTG
AAACAAATCCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:30501 original size:21 final size:21
Alignment explanation
Indices: 30440--30501 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
30430 TGTGGAAAAA
*
30440 TGTCTCAAGCGAGACATAATT
1 TGTCTCAAGCGAGACAAAATT
* * * *
30461 TGTTTTAA---AGA-GAAAGT
1 TGTCTCAAGCGAGACAAAATT
30478 TGTCTCAAGCGAGACAAAATT
1 TGTCTCAAGCGAGACAAAATT
30499 TGT
1 TGT
30502 TTTTAAGAAA
Statistics
Matches: 28, Mismatches: 9, Indels: 8
0.62 0.20 0.18
Matches are distributed among these distances:
17 9 0.32
18 3 0.11
20 3 0.11
21 13 0.46
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (21 bp):
TGTCTCAAGCGAGACAAAATT
Found at i:30520 original size:36 final size:38
Alignment explanation
Indices: 30442--30528 Score: 115
Period size: 38 Copynumber: 2.3 Consensus size: 38
30432 TGGAAAAATG
* * *
30442 TCTCAAGCGAGACATAATTTGTTTTAAAGAGAAAGTTG
1 TCTCAAGCGAGACAAAATTTGTTTTAAAGAGAAAGCTA
*
30480 TCTCAAGCGAGACAAAATTTGTTTTTAAGA-AAA-CTA
1 TCTCAAGCGAGACAAAATTTGTTTTAAAGAGAAAGCTA
*
30516 TCTCAAGTGAGAC
1 TCTCAAGCGAGAC
30529 GACACTTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
36 13 0.30
37 3 0.07
38 28 0.64
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (38 bp):
TCTCAAGCGAGACAAAATTTGTTTTAAAGAGAAAGCTA
Found at i:30910 original size:28 final size:28
Alignment explanation
Indices: 30878--30981 Score: 199
Period size: 28 Copynumber: 3.7 Consensus size: 28
30868 TGTAACATGC
*
30878 ATGTATGTGTTGATGTATGTATATATGT
1 ATGTATGAGTTGATGTATGTATATATGT
30906 ATGTATGAGTTGATGTATGTATATATGT
1 ATGTATGAGTTGATGTATGTATATATGT
30934 ATGTATGAGTTGATGTATGTATATATGT
1 ATGTATGAGTTGATGTATGTATATATGT
30962 ATGTATGAGTTGATGTATGT
1 ATGTATGAGTTGATGTATGT
30982 TTCTCAATCT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
28 75 1.00
ACGTcount: A:0.27, C:0.00, G:0.26, T:0.47
Consensus pattern (28 bp):
ATGTATGAGTTGATGTATGTATATATGT
Found at i:30981 original size:4 final size:4
Alignment explanation
Indices: 30890--30968 Score: 75
Period size: 4 Copynumber: 21.8 Consensus size: 4
30880 GTATGTGTTG
* *
30890 ATGT ATGT ATAT ATGT ATGT ATG- A-GT -TG- ATGT ATGT ATAT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
30934 ATGT ATG- A-GT -TG- ATGT ATGT ATAT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
30969 AGTTGATGTA
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
2 2 0.03
3 8 0.13
4 51 0.84
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:32857 original size:26 final size:24
Alignment explanation
Indices: 32827--32897 Score: 87
Period size: 20 Copynumber: 3.0 Consensus size: 24
32817 CAAGGTGGAA
32827 AGAATATTTCAAGGTCTCAAAGAG
1 AGAATATTTCAAGGTCTCAAAGAG
*
32851 AGGGAATGTTTCAAGGTCT--AA-A-
1 A--GAATATTTCAAGGTCTCAAAGAG
32873 AGAATATTTCAAGGTCTCAAAGAG
1 AGAATATTTCAAGGTCTCAAAGAG
32897 A
1 A
32898 TAGAATGTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
20 15 0.38
22 3 0.08
23 2 0.05
24 4 0.10
26 15 0.38
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.25
Consensus pattern (24 bp):
AGAATATTTCAAGGTCTCAAAGAG
Found at i:32902 original size:26 final size:25
Alignment explanation
Indices: 32826--32903 Score: 85
Period size: 26 Copynumber: 3.2 Consensus size: 25
32816 TCAAGGTGGA
32826 AAGAATATTTCAAGGTCTCAAAGAG
1 AAGAATATTTCAAGGTCTCAAAGAG
* *
32851 AGGGAATGTTTCAAGGTCT---A-A-
1 A-AGAATATTTCAAGGTCTCAAAGAG
32872 AAGAATATTTCAAGGTCTCAAAGAG
1 AAGAATATTTCAAGGTCTCAAAGAG
32897 ATAGAAT
1 A-AGAAT
32904 GTCAAAAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
20 15 0.36
21 1 0.02
22 1 0.02
23 2 0.05
24 1 0.02
25 2 0.05
26 20 0.48
ACGTcount: A:0.42, C:0.10, G:0.22, T:0.26
Consensus pattern (25 bp):
AAGAATATTTCAAGGTCTCAAAGAG
Found at i:32904 original size:46 final size:45
Alignment explanation
Indices: 32812--32905 Score: 143
Period size: 46 Copynumber: 2.1 Consensus size: 45
32802 ATAAATACAG
* *
32812 TGTTTCAAGGTGGAAAGAATATTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
* *
32857 TGTTTCAAGGTCTAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
32903 TGT
1 TGT
32906 CAAAAATTGG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 11 0.25
46 33 0.75
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.28
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
Found at i:35105 original size:210 final size:210
Alignment explanation
Indices: 34743--35158 Score: 564
Period size: 210 Copynumber: 2.0 Consensus size: 210
34733 AAATAGATCG
* * * *
34743 CTGCTTCGTCTCAGATCTTCGTCCTTGAAAATAATGCCCCTCAATGATCTGTAATCTGACACCAT
1 CTGCTTCGTCTCAGATCTTCGTACTTGAAAACAATGCCCCTCAATGATCTGTAAACTAACACCAT
* * * * *
34808 TAATGCCCCGGCGGTGCTGAAGTCAGTGCGTCGCTCCTTGATGGATAGCGATGAAATAATTGTAG
66 TAATACCCCGGCGATGCTGAAGTCAGTGCGTCACTCCCTGATGGATAACGATGAAATAATTGTAG
* *
34873 ATGAGAATCTACTGTTGGATTACT-CTTCGGATCAATGGATTATCATATCAGTCTCGAATGATGC
131 ATGAGAATCTACTGCTGGATTACTCCTT-AGATCAATGGATTATCATATCAGTCTCGAATGATGC
34937 ACGATCTTCGAGCTCA
195 ACGATCTTCGAGCTCA
* * * * * * * *
34953 CTGCTTCGTCTCGGATCTTTGTACTTGGAACCGATGCCCCTCTATGCTCTGTAAACTAACTCCAT
1 CTGCTTCGTCTCAGATCTTCGTACTTGAAAACAATGCCCCTCAATGATCTGTAAACTAACACCAT
* * ** * * * *
35018 TAATACCTCGGCTATGCTGAAGTTTGTGCTTCACTCCCTGATGGTTAACGATGGAATAATTGTGG
66 TAATACCCCGGCGATGCTGAAGTCAGTGCGTCACTCCCTGATGGATAACGATGAAATAATTGTAG
*
35083 ATGAGAATCTACTGCTGGATTACTCCTTAGATCAGTGGATTATCATATCAGTCTCGAATGATGCA
131 ATGAGAATCTACTGCTGGATTACTCCTTAGATCAATGGATTATCATATCAGTCTCGAATGATGCA
35148 CGATCTTCGAG
196 CGATCTTCGAG
35159 AAAATCTCAT
Statistics
Matches: 177, Mismatches: 28, Indels: 2
0.86 0.14 0.01
Matches are distributed among these distances:
210 174 0.98
211 3 0.02
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (210 bp):
CTGCTTCGTCTCAGATCTTCGTACTTGAAAACAATGCCCCTCAATGATCTGTAAACTAACACCAT
TAATACCCCGGCGATGCTGAAGTCAGTGCGTCACTCCCTGATGGATAACGATGAAATAATTGTAG
ATGAGAATCTACTGCTGGATTACTCCTTAGATCAATGGATTATCATATCAGTCTCGAATGATGCA
CGATCTTCGAGCTCA
Found at i:35394 original size:31 final size:31
Alignment explanation
Indices: 35337--35430 Score: 170
Period size: 31 Copynumber: 3.0 Consensus size: 31
35327 TGACAAAATG
35337 ACACAAACAAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAAC-AAAAGAGAA-AAATAAGTTAGTAT
35370 ACACAAACAAAAGAGAAAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAAAATAAGTTAGTAT
35401 ACACAAACAAAAGAGAAAAATAAGTTAGTA
1 ACACAAACAAAAGAGAAAAATAAGTTAGTA
35431 CATGTAAAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
31 44 0.72
32 9 0.15
33 8 0.13
ACGTcount: A:0.62, C:0.10, G:0.14, T:0.15
Consensus pattern (31 bp):
ACACAAACAAAAGAGAAAAATAAGTTAGTAT
Found at i:38519 original size:24 final size:24
Alignment explanation
Indices: 38486--38550 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 24
38476 CCTCTTTCCT
38486 TTCTCTTTTTTTTTTGTTTCGAATC
1 TTCTCTTTTTTTTTTGTTTC-AATC
*
38511 -TCTC-TTTTTTTTT-TTTCTATC
1 TTCTCTTTTTTTTTTGTTTCAATC
*
38532 TTCTGTTTTTTTTTTGTTT
1 TTCTCTTTTTTTTTTGTTT
38551 TCTTTTTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
21 3 0.09
22 7 0.20
23 18 0.51
24 7 0.20
ACGTcount: A:0.05, C:0.14, G:0.06, T:0.75
Consensus pattern (24 bp):
TTCTCTTTTTTTTTTGTTTCAATC
Found at i:38553 original size:18 final size:19
Alignment explanation
Indices: 38489--38558 Score: 56
Period size: 20 Copynumber: 3.6 Consensus size: 19
38479 CTTTCCTTTC
*
38489 TCTT-TTTTTTTTGTTTCGAA
1 TCTTCTTTTTTTT-TTTC-TA
38509 TCTCTCTTTTTTTTTTTTCTA
1 TCT-TC-TTTTTTTTTTTCTA
*
38530 TCTTCTGTTTTTTTTTTGT-
1 TCTTCT-TTTTTTTTTTCTA
38549 T-TTCTTTTTT
1 TCTTCTTTTTT
38559 CCTTTTTCTC
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
17 5 0.11
18 4 0.09
19 2 0.05
20 16 0.36
21 5 0.11
22 4 0.09
23 8 0.18
ACGTcount: A:0.04, C:0.13, G:0.06, T:0.77
Consensus pattern (19 bp):
TCTTCTTTTTTTTTTTCTA
Found at i:39101 original size:25 final size:25
Alignment explanation
Indices: 39067--39139 Score: 128
Period size: 26 Copynumber: 2.9 Consensus size: 25
39057 ATTTAGGGGA
39067 TTAGGGTTTGAAACCCTAATCTAAT
1 TTAGGGTTTGAAACCCTAATCTAAT
*
39092 TTAGGGTTTGAAACCCTAAATCTGAT
1 TTAGGGTTTGAAACCCT-AATCTAAT
39118 TTAGGGTTTGAAACCCTAATCT
1 TTAGGGTTTGAAACCCTAATCT
39140 GATGGGTTGA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
25 22 0.48
26 24 0.52
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTAAT
Found at i:39120 original size:26 final size:25
Alignment explanation
Indices: 39067--39142 Score: 134
Period size: 25 Copynumber: 3.0 Consensus size: 25
39057 ATTTAGGGGA
*
39067 TTAGGGTTTGAAACCCTAATCTAAT
1 TTAGGGTTTGAAACCCTAATCTGAT
39092 TTAGGGTTTGAAACCCTAAATCTGAT
1 TTAGGGTTTGAAACCCT-AATCTGAT
39118 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
39143 GGGTTGATTG
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
25 25 0.51
26 24 0.49
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:39218 original size:3 final size:3
Alignment explanation
Indices: 39210--39258 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
39200 ATTAATAAAC
39210 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
39258 A
1 A
39259 AAAAAAACCC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:51861 original size:20 final size:20
Alignment explanation
Indices: 51778--51864 Score: 77
Period size: 20 Copynumber: 4.2 Consensus size: 20
51768 GTACATTTAC
* * *
51778 TATCAATATTGTTCATACAG
1 TATCGATATTATTCTTACAG
* *
51798 TATCGATACTATTCTTTATTAG
1 TATCGATATTATTC-TTA-CAG
* *
51820 TATCGATATTGTTCGT-CAAG
1 TATCGATATTATTCTTAC-AG
51840 TATCGATATTATTCTTACAG
1 TATCGATATTATTCTTACAG
51860 TATCG
1 TATCG
51865 TTAGTAGTAT
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
20 34 0.65
21 4 0.08
22 14 0.27
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.44
Consensus pattern (20 bp):
TATCGATATTATTCTTACAG
Found at i:52497 original size:33 final size:31
Alignment explanation
Indices: 52447--52507 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
52437 TTTTGTTTAC
*
52447 ATTTTTTTCCTTCTATATAC-TTATATATACA
1 ATTTTTTTACTTCTATATACATT-TATATACA
52478 ATTTTTTTACTTCTATATATACATTTATAT
1 ATTTTTTTACTTC--TATATACATTTATAT
52508 TTATACTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 12 0.46
33 12 0.46
34 2 0.08
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (31 bp):
ATTTTTTTACTTCTATATACATTTATATACA
Found at i:52772 original size:12 final size:12
Alignment explanation
Indices: 52755--52784 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
52745 TCTCCTACTT
52755 CAAATCCACCTC
1 CAAATCCACCTC
52767 CAAATCCACCTC
1 CAAATCCACCTC
52779 CAAATC
1 CAAATC
52785 ATATTCCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.37, C:0.47, G:0.00, T:0.17
Consensus pattern (12 bp):
CAAATCCACCTC
Found at i:57319 original size:2 final size:2
Alignment explanation
Indices: 57312--57367 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
57302 CAAATATAAC
57312 TA TA TA TA TA TA TA TA 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
57354 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
57368 ACATGGAATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58531 original size:3 final size:3
Alignment explanation
Indices: 58511--58564 Score: 65
Period size: 3 Copynumber: 17.7 Consensus size: 3
58501 ATTTTTATAT
* *
58511 TAA TAA TAT TAA TAAA TAA TAA TAA TAA TAA TAA -AA CAAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA
58557 TAA TAA TA
1 TAA TAA TA
58565 TTGAAATGAC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
2 2 0.04
3 38 0.84
4 5 0.11
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Done.