Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002776.1 Hibiscus syriacus cultivar Beakdansim tig00005718_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: 99201
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8899 original size:131 final size:130
Alignment explanation
Indices: 8664--9030 Score: 520
Period size: 131 Copynumber: 2.8 Consensus size: 130
8654 TATTGAGAAT
8664 AATAATATCTTTTCATTTCGGTTGGAGTAATAAATGATTGCTTTAAGGCAATGAGAGGTCATTTA
1 AATAATATCTTTTCATTTCGGTTGGAGTAATAAATGATTGCTTTAAGGC-ATGAGAGGTCATTTA
* * * *
8729 TTCTCGATTGGAAATAATTTGATATTACTGTTTTCTCTCGAATCAATATTGATTTTTAATACGAA
65 TTCTC-AATGGAAATAATTAGATATTACTGTTTTCTCTCGAATCAATATTGAATTTTAAGACGAA
8794 AC
129 AC
* * *
8796 AATAATATCTTTTCATTTCGGTTGAAGTAATAAATGATTGTTTTAAGGCATGAGAAGTCATTTAT
1 AATAATATCTTTTCATTTCGGTTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTAT
* *
8861 TCTCAAATGGAAATAATTCGATATTACTGTTTTCTCTCGAATCGATATTGAATTTTAAGACGAAA
66 TCTC-AATGGAAATAATTAGATATTACTGTTTTCTCTCGAATCAATATTGAATTTTAAGACGAAA
*
8926 T
130 C
* * * * *
8927 AGTGATATCTCTTCATTTCGATTGGTGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTAT
1 AATAATATCTTTTCATTTCGGTTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTAT
* * *
8992 TCTCGATCAGAAATAATTAGATATTA-TCATTTTCTCTCG
66 TCTCAAT-GGAAATAATTAGATATTACT-GTTTTCTCTCG
9031 TAGAATTATT
Statistics
Matches: 211, Mismatches: 22, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
130 3 0.01
131 161 0.76
132 47 0.22
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (130 bp):
AATAATATCTTTTCATTTCGGTTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTAT
TCTCAATGGAAATAATTAGATATTACTGTTTTCTCTCGAATCAATATTGAATTTTAAGACGAAAC
Found at i:12296 original size:17 final size:19
Alignment explanation
Indices: 12256--12298 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
12246 ACTTCATACA
12256 ATTTTATTTTCTACATATT
1 ATTTTATTTTCTACATATT
*
12275 TTTTTATTTTCTA-A-ATT
1 ATTTTATTTTCTACATATT
12292 ATTTTAT
1 ATTTTAT
12299 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 9 0.41
18 1 0.05
19 12 0.55
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTTATTTTCTACATATT
Found at i:12487 original size:6 final size:6
Alignment explanation
Indices: 12476--12501 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12466 GCTTTGCTCA
12476 TGGTCG TGGTCG TGGTCG TGGTCG TG
1 TGGTCG TGGTCG TGGTCG TGGTCG TG
12502 ATCATACGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.50, T:0.35
Consensus pattern (6 bp):
TGGTCG
Found at i:17611 original size:3 final size:3
Alignment explanation
Indices: 17603--17654 Score: 95
Period size: 3 Copynumber: 17.0 Consensus size: 3
17593 AATCAAATAT
17603 AGA AGA AGA AGAA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
17649 AGA AGA
1 AGA AGA
17655 GAAAAGGGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:25455 original size:21 final size:21
Alignment explanation
Indices: 25401--25451 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
25391 ACACGCAGCG
25401 AAGGGATCGATCCGTTTTGAA
1 AAGGGATCGATCCGTTTTGAA
*
25422 AAGGGATCGATCCGTTTTG-T
1 AAGGGATCGATCCGTTTTGAA
25442 AAGGGATCGA
1 AAGGGATCGA
25452 ATCCTGTGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 10 0.34
21 19 0.66
ACGTcount: A:0.27, C:0.14, G:0.31, T:0.27
Consensus pattern (21 bp):
AAGGGATCGATCCGTTTTGAA
Found at i:31584 original size:32 final size:32
Alignment explanation
Indices: 31512--31584 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 32
31502 TTATAAATGT
* * *
31512 TAATATTATTGGTACTACACTAGTATCGACAC
1 TAATAATATTGATACTACAATAGTATCGACAC
* * * **
31544 TGACAATATTGATACTACAATAGTATTGGTAC
1 TAATAATATTGATACTACAATAGTATCGACAC
31576 TAATAATAT
1 TAATAATAT
31585 CAGTATCACA
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (32 bp):
TAATAATATTGATACTACAATAGTATCGACAC
Found at i:31678 original size:20 final size:20
Alignment explanation
Indices: 31644--31696 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
31634 TATTGATACT
** *
31644 AATATCAATGTTACAGGAAC
1 AATATCAATACTACAAGAAC
*
31664 AATATCAATACTACAAGAAT
1 AATATCAATACTACAAGAAC
*
31684 AATATCGATACTA
1 AATATCAATACTA
31697 TAATCTAGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.26
Consensus pattern (20 bp):
AATATCAATACTACAAGAAC
Found at i:33067 original size:15 final size:15
Alignment explanation
Indices: 33047--33077 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
33037 TTCATTTTTC
33047 TTGTAATTCAAAGCA
1 TTGTAATTCAAAGCA
*
33062 TTGTAATTTAAAGCA
1 TTGTAATTCAAAGCA
33077 T
1 T
33078 GCCAATCTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (15 bp):
TTGTAATTCAAAGCA
Found at i:41205 original size:19 final size:21
Alignment explanation
Indices: 41164--41205 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
41154 AAATATATTA
*
41164 ATTTATATATATTAATAAGAT
1 ATTTATATATATTAATAAAAT
*
41185 ATTTATTTAT-TTAA-AAAAT
1 ATTTATATATATTAATAAAAT
41204 AT
1 AT
41206 CAGAAAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 6 0.32
20 4 0.21
21 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
ATTTATATATATTAATAAAAT
Found at i:42985 original size:7 final size:7
Alignment explanation
Indices: 42975--43043 Score: 51
Period size: 6 Copynumber: 10.4 Consensus size: 7
42965 TTGGGCTTTT
*
42975 TAATATT
1 TAATATA
*
42982 TAATAAA
1 TAATATA
42989 TAATATA
1 TAATATA
42996 TAATA-A
1 TAATATA
43002 TAATA-A
1 TAATATA
43008 TAATAATTA
1 TAAT-A-TA
43017 TAATA-A
1 TAATATA
*
43023 TAAT-TT
1 TAATATA
43029 TAATA-A
1 TAATATA
43035 TAATA-A
1 TAATATA
43041 TAA
1 TAA
43044 ATTTAAATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
6 29 0.56
7 17 0.33
8 1 0.02
9 5 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TAATATA
Found at i:42994 original size:14 final size:13
Alignment explanation
Indices: 42975--43042 Score: 70
Period size: 12 Copynumber: 5.4 Consensus size: 13
42965 TTGGGCTTTT
*
42975 TAATATTTAATAAA
1 TAATATATAAT-AA
42989 TAATATATAATAA
1 TAATATATAATAA
43002 TAATA-ATAATAA
1 TAATATATAATAA
*
43014 TTATA-ATAATAA
1 TAATATATAATAA
**
43026 TTTTA-ATAATAA
1 TAATATATAATAA
43038 TAATA
1 TAATA
43043 AATTTAAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
12 32 0.65
13 7 0.14
14 10 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TAATATATAATAA
Found at i:43001 original size:3 final size:3
Alignment explanation
Indices: 42982--43043 Score: 79
Period size: 3 Copynumber: 20.0 Consensus size: 3
42972 TTTTAATATT
* **
42982 TAA TAAA TAA TATA TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA TTT
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
43029 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
43044 ATTTAAATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
3 45 0.88
4 6 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:59751 original size:17 final size:17
Alignment explanation
Indices: 59726--59761 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
59716 ATGAACTAAA
*
59726 TTTATTCAAATCAAATT
1 TTTAATCAAATCAAATT
*
59743 TTTAATCAAATCTAATT
1 TTTAATCAAATCAAATT
59760 TT
1 TT
59762 ACTCGCCACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTAATCAAATCAAATT
Found at i:68158 original size:31 final size:28
Alignment explanation
Indices: 68115--68171 Score: 78
Period size: 31 Copynumber: 1.9 Consensus size: 28
68105 TACTTTTAAT
*
68115 AAATTAAAATAAATTATATGTTTTTAAATGA
1 AAATGAAAATAAA--ATAT-TTTTTAAATGA
68146 AAATGAAAATAAAATATTTTTTAAAT
1 AAATGAAAATAAAATATTTTTTAAAT
68172 TAAGTTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 9 0.36
29 4 0.16
31 12 0.48
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.40
Consensus pattern (28 bp):
AAATGAAAATAAAATATTTTTTAAATGA
Found at i:68587 original size:39 final size:39
Alignment explanation
Indices: 68482--68587 Score: 92
Period size: 39 Copynumber: 2.7 Consensus size: 39
68472 TTTAAAAAAA
*
68482 AATTTAGAATGTTA-ATGTGAAATAATTTAAGAAATTAAT
1 AATTTAGAATGTTAGA-GTGAAATAATTTAAGAAATTAAG
* * ** * *
68521 AATTTAGAACGTCATG-GTG-TCTAAATTTAAGACATTAGG
1 AATTTAGAATGTTA-GAGTGAAAT-AATTTAAGAAATTAAG
*
68560 ATTTTAGAATGTTAGAGTGAAATAATTT
1 AATTTAGAATGTTAGAGTGAAATAATTT
68588 GAGGATTATG
Statistics
Matches: 50, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
38 2 0.04
39 47 0.94
40 1 0.02
ACGTcount: A:0.42, C:0.04, G:0.17, T:0.38
Consensus pattern (39 bp):
AATTTAGAATGTTAGAGTGAAATAATTTAAGAAATTAAG
Found at i:68626 original size:20 final size:20
Alignment explanation
Indices: 68601--68642 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
68591 GATTATGAAT
68601 AAAAATGAAAATATAAAATA
1 AAAAATGAAAATATAAAATA
*
68621 AAAAATGAAAATATATAATA
1 AAAAATGAAAATATAAAATA
68641 AA
1 AA
68643 TCGGGTATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (20 bp):
AAAAATGAAAATATAAAATA
Found at i:69282 original size:20 final size:19
Alignment explanation
Indices: 69257--69310 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
69247 GCGAAATAAA
69257 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
69277 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
69297 AATCGCAACGCGAT
1 AATCGCAACGCGAT
69311 TATGAATAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:69323 original size:21 final size:21
Alignment explanation
Indices: 69297--69429 Score: 82
Period size: 20 Copynumber: 6.5 Consensus size: 21
69287 CAGTTCCCAG
69297 AATCGCAACGCGATTATGAAT
1 AATCGCAACGCGATTATGAAT
*
69318 AATCGCAATGCGA-TA-GTACA-
1 AATCGCAACGCGATTATG-A-AT
** * **
69338 AATTCGCATTGCGATTTTCCAT
1 AA-TCGCAACGCGATTATGAAT
*
69360 AATCGCAACGCGAATATGAA-
1 AATCGCAACGCGATTATGAAT
**
69380 AATCGCAACGCGAACAT--AT
1 AATCGCAACGCGATTATGAAT
* *
69399 AAATCGCAACGCGATTCTGACT
1 -AATCGCAACGCGATTATGAAT
69421 -ATCGCAACG
1 AATCGCAACG
69430 AGTATCCGTA
Statistics
Matches: 86, Mismatches: 16, Indels: 21
0.70 0.13 0.17
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 44 0.51
21 36 0.42
22 4 0.05
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (21 bp):
AATCGCAACGCGATTATGAAT
Found at i:69385 original size:20 final size:20
Alignment explanation
Indices: 69360--69557 Score: 112
Period size: 20 Copynumber: 9.8 Consensus size: 20
69350 GATTTTCCAT
69360 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATATGAA
*
69380 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGAATATGA-A
* * *
69400 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGAATATGAA
* * * **
69420 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATATG-AA
* * * * *
69441 AATCGTAACACGTATTTGTA
1 AATCGCAACGCGAATATGAA
*
69461 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATATG-AA
* ** *
69482 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATATGAA
* * *
69502 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATATGAA
* * *
69522 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATATGAA
*
69542 AATCGCAACGAGAATA
1 AATCGCAACGCGAATA
69558 CGTAAATCGT
Statistics
Matches: 135, Mismatches: 37, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
19 1 0.01
20 104 0.77
21 30 0.22
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATATGAA
Found at i:69409 original size:40 final size:40
Alignment explanation
Indices: 69360--69632 Score: 232
Period size: 40 Copynumber: 6.8 Consensus size: 40
69350 GATTTTCCAT
* * * *
69360 AATCGCAACGCGAATATGAAAATCGCAACGCGA-ACATATA
1 AATCGCAACGCGTATCTGTAAATCGCAACGAGATACATA-A
* * *
69400 AATCGCAACGCG-ATTCTG-ACTATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGTA-TCTGTA-AATCGCAACGAG-ATACATAA
* * * * *
69441 AATCGTAACACGTATTTGTAAATCGCAACGACAATACGTAA
1 AATCGCAACGCGTATCTGTAAATCGCAACGA-GATACATAA
* *
69482 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT-A
1 AATCGCAACGCGTATCTGTAAATCGCAACGAG-ATACATAA
*
69522 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGT-A
1 AATCGCAACGCGTATCTGTAAATCGCAACGAG-ATACATAA
* * * * * *
69562 AATCGTAATGCGTATCCGTAAATCACAACGACAATACGTAA
1 AATCGCAACGCGTATCTGTAAATCGCAACGA-GATACATAA
* *
69603 AATCGTAACGCGTATCCGTAAATCGCAACG
1 AATCGCAACGCGTATCTGTAAATCGCAACG
69633 CGATTTTTAA
Statistics
Matches: 199, Mismatches: 24, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
39 2 0.01
40 98 0.49
41 94 0.47
42 5 0.03
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (40 bp):
AATCGCAACGCGTATCTGTAAATCGCAACGAGATACATAA
Found at i:69466 original size:41 final size:41
Alignment explanation
Indices: 69421--69632 Score: 302
Period size: 41 Copynumber: 5.2 Consensus size: 41
69411 GATTCTGACT
* * * **
69421 ATCGCAACGAGTATCCGTAAAATCGTAACACGTATTTGTAA
1 ATCGCAACGAGAATACGTAAAATCGTAACGCGTATCCGTAA
* *
69462 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGTAACGCGTATCCGTAA
* *
69503 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGTAACGCGTATCCGTAA
*
69543 ATCGCAACGAGAATACGT-AAATCGTAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGTAACGCGTATCCGTAA
* *
69583 ATCACAACGACAATACGTAAAATCGTAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGTAACGCGTATCCGTAA
69624 ATCGCAACG
1 ATCGCAACG
69633 CGATTTTTAA
Statistics
Matches: 154, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 74 0.48
41 80 0.52
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGTAACGCGTATCCGTAA
Found at i:69633 original size:20 final size:20
Alignment explanation
Indices: 69421--69634 Score: 189
Period size: 20 Copynumber: 10.6 Consensus size: 20
69411 GATTCTGACT
*
69421 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
* * **
69442 ATCGTAACACGTATTTGTAA
1 ATCGCAACGCGTATCCGTAA
* *
69462 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
69483 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
69503 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
69523 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
69543 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
* *
69563 ATCGTAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
69583 ATCACAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
*
69604 ATCGTAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
69624 ATCGCAACGCG
1 ATCGCAACGCG
69635 ATTTTTAAAG
Statistics
Matches: 149, Mismatches: 38, Indels: 13
0.75 0.19 0.06
Matches are distributed among these distances:
20 104 0.70
21 45 0.30
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:70220 original size:20 final size:20
Alignment explanation
Indices: 70195--70291 Score: 108
Period size: 20 Copynumber: 4.8 Consensus size: 20
70185 TTCTAAACTT
* *
70195 AAAATCACAACATGAAAATG
1 AAAATCGCAACACGAAAATG
70215 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
70235 ACTATCGCAACGA-GAGAAATG
1 AAAATCGCAAC-ACGA-AAATG
*
70256 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
*
70275 AAAATCGCAACGCGAAA
1 AAAATCGCAACACGAAA
70292 CCAAAATCGC
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
19 19 0.29
20 31 0.47
21 16 0.24
ACGTcount: A:0.52, C:0.20, G:0.18, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:70272 original size:41 final size:40
Alignment explanation
Indices: 70210--70286 Score: 118
Period size: 41 Copynumber: 1.9 Consensus size: 40
70200 CACAACATGA
**
70210 AAATGAAAATCGCAACACGAAAATGACTATCGCAACGAGAG
1 AAATGAAAATCGCAACACG-AAATGAAAATCGCAACGAGAG
*
70251 AAATGAAAATCGCAACGCGAAATGAAAATCGCAACG
1 AAATGAAAATCGCAACACGAAATGAAAATCGCAACG
70287 CGAAACCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 15 0.45
41 18 0.55
ACGTcount: A:0.49, C:0.19, G:0.19, T:0.12
Consensus pattern (40 bp):
AAATGAAAATCGCAACACGAAATGAAAATCGCAACGAGAG
Found at i:70274 original size:19 final size:19
Alignment explanation
Indices: 70210--70302 Score: 105
Period size: 19 Copynumber: 4.7 Consensus size: 19
70200 CACAACATGA
*
70210 AAATGAAAATCGCAACACG
1 AAATGAAAATCGCAACGCG
** *
70229 AAAATGACTATCGCAACGAGAG
1 -AAATGAAAATCGCAAC--GCG
70251 AAATGAAAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
70270 AAATGAAAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
**
70289 AAACCAAAATCGCA
1 AAATGAAAATCGCA
70303 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
19 33 0.53
20 14 0.23
21 14 0.23
22 1 0.02
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.11
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:70368 original size:20 final size:20
Alignment explanation
Indices: 70303--70391 Score: 77
Period size: 20 Copynumber: 4.8 Consensus size: 20
70293 CAAAATCGCA
70303 TTGCGATTTTCATTT-CGCG
1 TTGCGATTTTCATTTCCGCG
*
70322 TTGCGA--TTC---T-CTCG
1 TTGCGATTTTCATTTCCGCG
**
70336 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTTCCGCG
*
70356 TTGCGATTTTCA-TTCTCTCG
1 TTGCGATTTTCATTTC-CGCG
70376 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
70392 AAGCAAAAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 3 0.05
19 10 0.18
20 28 0.50
21 3 0.05
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (20 bp):
TTGCGATTTTCATTTCCGCG
Found at i:73344 original size:14 final size:14
Alignment explanation
Indices: 73325--73360 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
73315 ATTGTTTAAT
73325 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
73339 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
73353 TGATTTGT
1 TGATTTGT
73361 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:73497 original size:19 final size:19
Alignment explanation
Indices: 73462--73516 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
73452 AAAACAGACT
*
73462 ATCGCAACGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
73482 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
73501 ATCGTAATGCGAAATG
1 ATCGCAATGCGAAATG
73517 TTTCGCGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 24 0.73
20 9 0.27
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:73575 original size:53 final size:53
Alignment explanation
Indices: 73517--73656 Score: 165
Period size: 53 Copynumber: 2.6 Consensus size: 53
73507 ATGCGAAATG
* **
73517 TTTCGCGTTGCGATTTTCATTTTTGCATTGCGATTCACTCTTTGCGATTTTCA-
1 TTTCGCGTTGCGATTTTCA-TTTTGCATTGCGATTCACTCGTTGCGATAGTCAT
* * *
73570 TTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATTTTCATTTTGCATTGCGATTCACTCGTTGCGATAGTCAT
* ** *
73623 TTTCGCGTTGCAATAGTCAATTCTGCATTGCGAT
1 TTTCGCGTTGCGATTTTC-ATTTTGCATTGCGAT
73657 AGTCAAATGA
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
52 28 0.38
53 32 0.44
54 13 0.18
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (53 bp):
TTTCGCGTTGCGATTTTCATTTTGCATTGCGATTCACTCGTTGCGATAGTCAT
Found at i:73580 original size:19 final size:19
Alignment explanation
Indices: 73517--73603 Score: 94
Period size: 19 Copynumber: 4.8 Consensus size: 19
73507 ATGCGAAATG
*
73517 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
*
73536 TTTTTGCATTGCGA--TTCA
1 -TTTCGCATTGCGATTTTCA
* *
73554 ---CTCTTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
73570 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
73589 TTTCGCATTGCGATT
1 TTTCGCATTGCGATT
73604 CTCTCGTTGC
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
14 7 0.13
16 4 0.07
18 4 0.07
19 29 0.53
20 11 0.20
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:73633 original size:20 final size:20
Alignment explanation
Indices: 73608--73662 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
73598 GCGATTCTCT
*
73608 CGTTGCGATAGTC-ATTTTCG
1 CGTTGCGATAGTCAATTCT-G
*
73628 CGTTGCAATAGTCAATTCTG
1 CGTTGCGATAGTCAATTCTG
*
73648 CATTGCGATAGTCAA
1 CGTTGCGATAGTCAA
73663 ATGAATGTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 26 0.87
21 4 0.13
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTCTG
Found at i:74004 original size:19 final size:19
Alignment explanation
Indices: 73977--74022 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
73967 GATTCACTCG
*
73977 TTGCAATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
73996 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
74015 TTGCGATT
1 TTGCGATT
74023 CTCTCGTTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.17, C:0.20, G:0.15, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:74012 original size:52 final size:54
Alignment explanation
Indices: 73954--74075 Score: 158
Period size: 52 Copynumber: 2.3 Consensus size: 54
73944 ACGCGAAACT
** **
73954 AATTTCGCATTGCGATTCACTCGTTGCAATTTTCATTT-CGCATTGCGATTTTC
1 AATTTCGCATTGCGATTCACTCGTTGCAATAGTCATTTCCGCATTGCGATAGTC
* * *
74007 -ATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGATAGTC
1 AATTTCGCATTGCGATTCACTCGTTGCAATAGTCATTTCCGCATTGCGATAGTC
*
74060 AATTCCGCATTGCGAT
1 AATTTCGCATTGCGAT
74076 AGTCAAATGA
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
52 33 0.56
53 12 0.20
54 14 0.24
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (54 bp):
AATTTCGCATTGCGATTCACTCGTTGCAATAGTCATTTCCGCATTGCGATAGTC
Found at i:74052 original size:20 final size:20
Alignment explanation
Indices: 74027--74081 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
74017 GCGATTCTCT
*
74027 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCAATTCCG
74047 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
*
74067 CATTGCGATAGTCAA
1 CGTTGCGATAGTCAA
74082 ATGAATGTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTCCG
Found at i:77451 original size:20 final size:20
Alignment explanation
Indices: 77408--77639 Score: 182
Period size: 20 Copynumber: 11.4 Consensus size: 20
77398 GTCAGAATCT
* *
77408 CGTTGCGATTTACAGATTA-A
1 CGTTGCGATTTACGGA-TACG
77428 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* * *
77448 CGTTGTGATTTTACGTAT-TG
1 CGTTGCGA-TTTACGGATACG
77468 TCGTTGCGATTTACGGATACG
1 -CGTTGCGATTTACGGATACG
* * * * *
77489 CATTACGATTTACGTATTCT
1 CGTTGCGATTTACGGATACG
* **
77509 TGTTGCGATTTAAAGATACG
1 CGTTGCGATTTACGGATACG
* * * *
77529 TGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACG
* *
77549 CGTTACGATTTATGGATACG
1 CGTTGCGATTTACGGATACG
* *
77569 CGTTGCGATTGTACGTAT-TG
1 CGTTGCGATT-TACGGATACG
77589 TCGTTGCGATTTACGGATACG
1 -CGTTGCGATTTACGGATACG
* *
77610 CGTTACGATTTTACGGATACT
1 CGTTGCGA-TTTACGGATACG
77631 CGTTGCGAT
1 CGTTGCGAT
77640 AGTCAGAATC
Statistics
Matches: 163, Mismatches: 41, Indels: 16
0.74 0.19 0.07
Matches are distributed among these distances:
19 2 0.01
20 111 0.68
21 50 0.31
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:77452 original size:40 final size:40
Alignment explanation
Indices: 77408--77639 Score: 277
Period size: 41 Copynumber: 5.7 Consensus size: 40
77398 GTCAGAATCT
**
77408 CGTTGCGATTTACAG-ATTAACGTTGCGATTTACGGATACG
1 CGTTGCGATTTAC-GTATTCTCGTTGCGATTTACGGATACG
* *
77448 CGTTGTGATTTTACGTATTGTCGTTGCGATTTACGGATACG
1 CGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACG
* * * **
77489 CATTACGATTTACGTATTCTTGTTGCGATTTAAAGATACG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
* * *
77529 TGTTGCGATTTACGTATTCTCGTTACGATTTATGGATACG
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
*
77569 CGTTGCGATTGTACGTATTGTCGTTGCGATTTACGGATACG
1 CGTTGCGATT-TACGTATTCTCGTTGCGATTTACGGATACG
* * *
77610 CGTTACGATTTTACGGATACTCGTTGCGAT
1 CGTTGCGA-TTTACGTATTCTCGTTGCGAT
77640 AGTCAGAATC
Statistics
Matches: 163, Mismatches: 25, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
40 78 0.48
41 83 0.51
42 2 0.01
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
Found at i:77604 original size:121 final size:122
Alignment explanation
Indices: 77409--77639 Score: 349
Period size: 121 Copynumber: 1.9 Consensus size: 122
77399 TCAGAATCTC
* * *
77409 GTTGCGATTTACAGATTAACGTTGCGATTTACGGATACGCGTTGTGATTTTACGTATTGTCGTTG
1 GTTGCGATTTACAGATTAACGTTACGATTTACGGATACGCGTTGCGATTGTACGTATTGTCGTTG
* * *
77474 CGATTTACGGATACGCATTACGA-TTTACGTATTCTTGTTGCGATTTAAAGATACGT
66 CGATTTACGGATACGCATTACGATTTTACGGATACTCGTTGCGATTTAAAGATACGT
** *
77530 GTTGCGATTTAC-GTATTCTCGTTACGATTTATGGATACGCGTTGCGATTGTACGTATTGTCGTT
1 GTTGCGATTTACAG-ATTAACGTTACGATTTACGGATACGCGTTGCGATTGTACGTATTGTCGTT
*
77594 GCGATTTACGGATACGCGTTACGATTTTACGGATACTCGTTGCGAT
65 GCGATTTACGGATACGCATTACGATTTTACGGATACTCGTTGCGAT
77640 AGTCAGAATC
Statistics
Matches: 98, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
120 1 0.01
121 79 0.81
122 18 0.18
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (122 bp):
GTTGCGATTTACAGATTAACGTTACGATTTACGGATACGCGTTGCGATTGTACGTATTGTCGTTG
CGATTTACGGATACGCATTACGATTTTACGGATACTCGTTGCGATTTAAAGATACGT
Found at i:77681 original size:20 final size:20
Alignment explanation
Indices: 77648--77695 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
77638 ATAGTCAGAA
*
77648 TCGCGTTGTGATTTAT-ATGT
1 TCGCGTTGTGATTT-TCATAT
77668 TCGCGTTGAT-ATTTTCATAT
1 TCGCGTTG-TGATTTTCATAT
77688 TCGCGTTG
1 TCGCGTTG
77696 CGATAATGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 1 0.04
20 23 0.92
21 1 0.04
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.48
Consensus pattern (20 bp):
TCGCGTTGTGATTTTCATAT
Found at i:77799 original size:20 final size:19
Alignment explanation
Indices: 77750--77803 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
77740 ATTCTTCATA
77750 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
77769 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
77790 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
77804 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:78821 original size:17 final size:17
Alignment explanation
Indices: 78795--78832 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
78785 CGTAAACCAA
78795 TTTTTATCTTTAAAA-TG
1 TTTTTATC-TTAAAATTG
*
78812 TTTTTTTCTTAAAATTG
1 TTTTTATCTTAAAATTG
78829 TTTT
1 TTTT
78833 AAAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (17 bp):
TTTTTATCTTAAAATTG
Found at i:83728 original size:184 final size:184
Alignment explanation
Indices: 83408--83777 Score: 634
Period size: 184 Copynumber: 2.0 Consensus size: 184
83398 ATTAAATTTT
* *
83408 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
83473 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTG
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTG
*
83538 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAA
* *
83592 AAATATTAAATATATTATATATAACATTTGGGCTAAGCCCAAACAATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
* * *
83657 TTTAAGATCCAATAACTTTTAAATCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATAT-AAATTT
* *
83722 -TTATTTTATAATTATATATTATTTAAATTAATTATACACTTTTTTTTAATTAAA
130 GTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAA
83776 AA
1 AA
83778 CATTTAATTT
Statistics
Matches: 175, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
184 169 0.97
185 6 0.03
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (184 bp):
AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTG
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAA
Found at i:92620 original size:27 final size:27
Alignment explanation
Indices: 92568--92620 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
92558 AAATACTTTA
* *
92568 GGTCATTTTACACTTTAGGGATATTTT
1 GGTCATTTTAAACTTTAGGGACATTTT
92595 GGTCATTTTAAACTTTAAGGG-CATTT
1 GGTCATTTTAAACTTT-AGGGACATTT
92621 CTATAAATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45
Consensus pattern (27 bp):
GGTCATTTTAAACTTTAGGGACATTTT
Found at i:97612 original size:14 final size:15
Alignment explanation
Indices: 97593--97632 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
97583 CAAAAGTCGG
97593 GTTGACTCAGA-CGA
1 GTTGACTCAGACCGA
* *
97607 GTTGACTTAGACCTA
1 GTTGACTCAGACCGA
97622 GTTGACTCAGA
1 GTTGACTCAGA
97633 TGGGTTAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (15 bp):
GTTGACTCAGACCGA
Done.