Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004341.1 Hibiscus syriacus cultivar Beakdansim tig00009513_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: 119465
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.34
Found at i:2281 original size:70 final size:69
Alignment explanation
Indices: 2200--2337 Score: 222
Period size: 70 Copynumber: 2.0 Consensus size: 69
2190 ATCCATAGCA
*
2200 ATAAAATAAAAAGTAATAAATTTGAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAATA
1 ATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAA-AAAGCTCCTAAATCATCCAAATAATA
2265 CACTT
65 CACTT
*** *
2270 ATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAAGGGGCTCCTAAATCATCCAAATAATGC
1 ATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAAAAAGCTCCTAAATCATCCAAATAATAC
2335 ACT
66 ACT
2338 GAGTTTAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
69 26 0.41
70 37 0.59
ACGTcount: A:0.50, C:0.15, G:0.08, T:0.27
Consensus pattern (69 bp):
ATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAAAAAGCTCCTAAATCATCCAAATAATAC
ACTT
Found at i:3054 original size:20 final size:20
Alignment explanation
Indices: 3003--3054 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
2993 ACTGTTCATA
3003 GGTATCGATACTAAGCCCTC
1 GGTATCGATACTAAGCCCTC
* * * *
3023 AGTATTGGTACTAA-CCTCTG
1 GGTATCGATACTAAGCC-CTC
3043 GGTATCGATACT
1 GGTATCGATACT
3055 TGTAACAACC
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (20 bp):
GGTATCGATACTAAGCCCTC
Found at i:3858 original size:2 final size:2
Alignment explanation
Indices: 3813--3840 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3803 ATTTTTGAAC
3813 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3841 CCTCATATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4014 original size:81 final size:81
Alignment explanation
Indices: 3970--4529 Score: 760
Period size: 81 Copynumber: 7.0 Consensus size: 81
3960 ACTAATCCCC
* * *
3970 TATTCTTTTACTCAACAGTGTTTAACCGTACATCTAACTGGCATAATTAACACCTTTCTGTCAAT
1 TATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAT
4035 TGCACAGTTAGGCCAT
66 TGCACAGTTAGGCCAT
*
4051 TATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGAATAATTGACACCTTTCTGTCAAT
1 TATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAT
4116 TGCACAGTTAGGCCAT
66 TGCACAGTTAGGCCAT
* **
4132 TATTCTTTTACTCAAC-GATATTCAACAATTCATCTAACTGGCATAATTGACACCTTTCT-TCCA
1 TATTCTTTTACTCAACAG-TATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGT-CA
4195 ATTGCACAGTTAGGCCAT
64 ATTGCACAGTTAGGCCAT
* * *
4213 TATTCTTTTACTCAACGGTATTTAA-CGTTCATCTAACTGGC---ATTGACACTTTTCTGCCAAA
1 TATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTC-AA
**
4274 TTGCACAGTTAGGTTAT
65 TTGCACAGTTAGGCCAT
* * * * *
4291 TATTCTTTTACTCAA-AGGTAATTAACTGTTCATCTAACTAGCATAATTGGCACTTTTCT-TCCA
1 TATTCTTTTACTCAACA-GTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGT-CA
*
4354 ATTGCACAATTAGGCCAT
64 ATTGCACAGTTAGGCCAT
* * *
4372 TATTCTTTTACTCAACGGTATTTAACCATTCATCTAACT-GCATAATTGACACCTTTCTGCCAAT
1 TATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAT
*
4436 TGCATAGTTAGGCCAT
66 TGCACAGTTAGGCCAT
* * * * * *
4452 TATTCTTTTACTCAACGGTATTCAATCGTTCATCTAACTAGCATAATTGACACATTTCTGTCATT
1 TATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAT
4517 TGCACAGTTAGGC
66 TGCACAGTTAGGC
4530 TTCAAAGGCA
Statistics
Matches: 425, Mismatches: 40, Indels: 28
0.86 0.08 0.06
Matches are distributed among these distances:
77 14 0.03
78 39 0.09
79 14 0.03
80 87 0.20
81 256 0.60
82 15 0.04
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.38
Consensus pattern (81 bp):
TATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAT
TGCACAGTTAGGCCAT
Found at i:4361 original size:240 final size:240
Alignment explanation
Indices: 3970--4529 Score: 795
Period size: 240 Copynumber: 2.3 Consensus size: 240
3960 ACTAATCCCC
* * * * *
3970 TATTCTTTTACTCAACAGTGTTTAACCGTACATCTAACTGGCATAATTAACACCTTTCTGTCAAT
1 TATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGC--AATTGACACATTTCTGTCAAT
* *
4035 TGCACAGTTAGGCCATTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGAATAATTG
64 TGCACAGTTAGGCCATTATTCTTTTACTCAACAGTAATTAACCGTTCATCTAACTAGAATAATTG
*
4100 ACACCTTTCTGTCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGATATTCAACAATTCAT
129 ACACCTTTCTGTCAATTGCACAATTAGGCCATTATTCTTTTACTCAACGATATTCAACAATTCAT
*
4165 CTAACTGGCATAATTGACACCTTTCTTCCAATTGCACAGTTAGGCCAT
194 CTAACT-GCATAATTGACACCTTTCTGCCAATTGCACAGTTAGGCCAT
* *
4213 TATTCTTTTACTCAACGGTATTTAA-CGTTCATCTAACTGGC-ATTGACACTTTTCTGCCAAATT
1 TATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCAATTGACACATTTCTGTC-AATT
** * *
4276 GCACAGTTAGGTTATTATTCTTTTACTCAA-AGGTAATTAACTGTTCATCTAACTAGCATAATTG
65 GCACAGTTAGGCCATTATTCTTTTACTCAACA-GTAATTAACCGTTCATCTAACTAGAATAATTG
* * * * *
4340 GCACTTTTCT-TCCAATTGCACAATTAGGCCATTATTCTTTTACTCAACGGTATTTAACCATTCA
129 ACACCTTTCTGT-CAATTGCACAATTAGGCCATTATTCTTTTACTCAACGATATTCAACAATTCA
*
4404 TCTAACTGCATAATTGACACCTTTCTGCCAATTGCATAGTTAGGCCAT
193 TCTAACTGCATAATTGACACCTTTCTGCCAATTGCACAGTTAGGCCAT
* * * *
4452 TATTCTTTTACTCAACGGTATTCAATCGTTCATCTAACTAGCATAATTGACACATTTCTGTCATT
1 TATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGC--AATTGACACATTTCTGTCAAT
4517 TGCACAGTTAGGC
64 TGCACAGTTAGGC
4530 TTCAAAGGCA
Statistics
Matches: 284, Mismatches: 26, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
239 79 0.28
240 138 0.49
242 29 0.10
243 38 0.13
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.38
Consensus pattern (240 bp):
TATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCAATTGACACATTTCTGTCAATTG
CACAGTTAGGCCATTATTCTTTTACTCAACAGTAATTAACCGTTCATCTAACTAGAATAATTGAC
ACCTTTCTGTCAATTGCACAATTAGGCCATTATTCTTTTACTCAACGATATTCAACAATTCATCT
AACTGCATAATTGACACCTTTCTGCCAATTGCACAGTTAGGCCAT
Found at i:4589 original size:68 final size:68
Alignment explanation
Indices: 4480--4735 Score: 413
Period size: 68 Copynumber: 3.8 Consensus size: 68
4470 TATTCAATCG
* * *
4480 TTCATCTAACTAGCATAATTGACACATTTCTGTCATTTGCACAGTTAGGCTTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
*
4545 TCT
66 CCT
* *
4548 TTCATCTAACTGGCATAAATGGCACATTTCTGTCATTTGCACAGTTAGGCCCCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
4613 CCT
66 CCT
* * *
4616 TTCATCTAACTGGCATAAATGATATATTTCTGTCATTTGCACAGTTAGGCCTCAAAGACACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
4681 CCT
66 CCT
* *
4684 TTCATCTAACTGACATAAATGACACATTTCTGTCATTTGCACAGTTATGCCT
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCT
4736 ATAATCGTTT
Statistics
Matches: 173, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 173 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:5059 original size:55 final size:55
Alignment explanation
Indices: 4937--5094 Score: 192
Period size: 55 Copynumber: 2.9 Consensus size: 55
4927 ACATCTATTT
* * * * ** *
4937 CCCATACGGAAATTCATACACTTAGTATGAATTTCTCA-GTTCGCACCCATGGTG
1 CCCATACAGAAATTCATACACTTAGTATGAATTTTTCATTTTTGCACCCAAAGTC
* *
4991 CCCATACTGAAATTCCTACACTTAGTATGAATTTTTCATTTTTGCACCCAAAGTC
1 CCCATACAGAAATTCATACACTTAGTATGAATTTTTCATTTTTGCACCCAAAGTC
* *
5046 CCCATACAAAAATTCATACACTTAGTATGAATTTGTTAAATTTTTGCAC
1 CCCATACAGAAATTCATACACTTAGTATGAATTT-TT-CATTTTTGCAC
5095 ACCTAGTGCC
Statistics
Matches: 89, Mismatches: 12, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
54 35 0.39
55 42 0.47
56 2 0.02
57 10 0.11
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (55 bp):
CCCATACAGAAATTCATACACTTAGTATGAATTTTTCATTTTTGCACCCAAAGTC
Found at i:5608 original size:95 final size:95
Alignment explanation
Indices: 5422--5646 Score: 224
Period size: 95 Copynumber: 2.4 Consensus size: 95
5412 TCTGACTTTA
* * * * * * *
5422 TAGTATCGATACTAC-TACCCTAGTACCGATACTTCTATACTATGGTATCGATACCCCCTTCTGG
1 TAGTATCGATAC-ACTTATCATGGTATCGATACTACTATACTATGGTACCGATACCCCCTTCTGA
* * **
5486 TATCGATACTGATTTTAGGTTTGATGTTCCC
65 TATCGATACAGATTTTAGATTCAATGTTCCC
***
5517 TAGTATCGATATTGTTA-CTATGGTATCGATACTACTATACTATGGTACCGATACCCCCTTAC-G
1 TAGTATCGATACACTTATC-ATGGTATCGATACTACTATACTATGGTACCGATACCCCCTT-CTG
* * *
5580 ATATCGATACCAG-TTTTTGATTCAATGTTGCT
64 ATATCGATA-CAGATTTTAGATTCAATGTTCCC
*
5612 TGGTATCGATACACTTATCATGGTATCGATACTAC
1 TAGTATCGATACACTTATCATGGTATCGATACTAC
5647 CTCTTCGGTA
Statistics
Matches: 105, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
94 1 0.01
95 100 0.95
96 4 0.04
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (95 bp):
TAGTATCGATACACTTATCATGGTATCGATACTACTATACTATGGTACCGATACCCCCTTCTGAT
ATCGATACAGATTTTAGATTCAATGTTCCC
Found at i:16944 original size:31 final size:31
Alignment explanation
Indices: 16907--16980 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
16897 AAAAATTAAA
*
16907 TGTTTAGGTACTAAAATGGATCAAAACTTAT
1 TGTTTAGGTACTAAAACGGATCAAAACTTAT
* *
16938 TGTTTAGATACTAAAACGGTTCAAAACTTAT
1 TGTTTAGGTACTAAAACGGATCAAAACTTAT
**
16969 AATTTAGGTACT
1 TGTTTAGGTACT
16981 TAATGCATAG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (31 bp):
TGTTTAGGTACTAAAACGGATCAAAACTTAT
Found at i:17243 original size:2 final size:2
Alignment explanation
Indices: 17238--17268 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17228 CAGAAACGTT
17238 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17269 GGGTTACGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18039 original size:70 final size:70
Alignment explanation
Indices: 17957--18096 Score: 208
Period size: 70 Copynumber: 2.0 Consensus size: 70
17947 TCCATATCAA
* *
17957 TATAAAATAAAAAGTAATAAATTTGAGTTTACAATACAACAAAGCTCCTAAATCAACCAAATAAT
1 TATAAAATAAAAAGTAATAAATTTAAGTTTAAAATACAACAAAGCTCCTAAATCAACCAAATAAT
18022 ACACT
66 ACACT
* *** *
18027 TATAAGATAAAAAGTAATAAATTTAAGTTTAAAATACAAGGGAGCTCCTAAATCATCCAAATAAT
1 TATAAAATAAAAAGTAATAAATTTAAGTTTAAAATACAACAAAGCTCCTAAATCAACCAAATAAT
*
18092 GCACT
66 ACACT
18097 GAGTTTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (70 bp):
TATAAAATAAAAAGTAATAAATTTAAGTTTAAAATACAACAAAGCTCCTAAATCAACCAAATAAT
ACACT
Found at i:18832 original size:20 final size:20
Alignment explanation
Indices: 18809--18853 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
18799 TCAGTATTGG
* *
18809 TACTAACCTCTGGGTATCGA
1 TACTAACCCCTGGATATCGA
*
18829 TACTAACCCCTGGATATGGA
1 TACTAACCCCTGGATATCGA
18849 TACTA
1 TACTA
18854 CTAACTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (20 bp):
TACTAACCCCTGGATATCGA
Found at i:26846 original size:31 final size:31
Alignment explanation
Indices: 26809--26882 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
26799 AAAAATTAAA
*
26809 TGTTTAGGTACTAAAATGGATCAAAACTTAT
1 TGTTTAGGTACTAAAACGGATCAAAACTTAT
* *
26840 TGTTTAGATACTAAAACGGTTCAAAACTTAT
1 TGTTTAGGTACTAAAACGGATCAAAACTTAT
**
26871 AATTTAGGTACT
1 TGTTTAGGTACT
26883 TAATGCATAG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (31 bp):
TGTTTAGGTACTAAAACGGATCAAAACTTAT
Found at i:27933 original size:70 final size:70
Alignment explanation
Indices: 27859--27991 Score: 230
Period size: 70 Copynumber: 1.9 Consensus size: 70
27849 CAATATAAAA
*
27859 TAAAAAGTAATAAATTTGAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAATACACTTA
1 TAAAAAGTAATAAATTTAAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAATACACTTA
27924 TAAGT
66 TAAGT
* * *
27929 TAAAAAGTAATAAATTTAAGTTTACAATACAAGAGAGCTCCTAAATCATCCAAATAATGCACT
1 TAAAAAGTAATAAATTTAAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAATACACT
27992 GAGTTTAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 59 1.00
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (70 bp):
TAAAAAGTAATAAATTTAAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAATACACTTA
TAAGT
Found at i:28726 original size:20 final size:20
Alignment explanation
Indices: 28703--28747 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
28693 TCAGTATTGG
* *
28703 TACTAACCTCTGGGTATCGA
1 TACTAACCCCTGGATATCGA
28723 TACTAACCCCTGGATATCGA
1 TACTAACCCCTGGATATCGA
28743 TACTA
1 TACTA
28748 CTAACTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (20 bp):
TACTAACCCCTGGATATCGA
Found at i:36732 original size:31 final size:31
Alignment explanation
Indices: 36695--36768 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
36685 AAAAATTAAA
*
36695 TGTTTAGGTACTAAAATGGATCAAAACTTAT
1 TGTTTAGGTACTAAAACGGATCAAAACTTAT
* *
36726 TGTTTAGATACTAAAACGGTTCAAAACTTAT
1 TGTTTAGGTACTAAAACGGATCAAAACTTAT
**
36757 AATTTAGGTACT
1 TGTTTAGGTACT
36769 TAATGCATAG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (31 bp):
TGTTTAGGTACTAAAACGGATCAAAACTTAT
Found at i:37819 original size:70 final size:70
Alignment explanation
Indices: 37738--37877 Score: 235
Period size: 70 Copynumber: 2.0 Consensus size: 70
37728 TCCATAGCAA
*
37738 TATAAAATAAAAAGTAATAAATTTGAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAAT
1 TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAAT
37803 ACACT
66 ACACT
* * *
37808 TATAAGATAAAAAGTAATAAATTTAAGTTTACAATACAAGAGAGCTCCTAAATCATCCAAATAAT
1 TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAAT
*
37873 GCACT
66 ACACT
37878 GAGTTTAAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.50, C:0.15, G:0.08, T:0.27
Consensus pattern (70 bp):
TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAAT
ACACT
Found at i:38613 original size:20 final size:20
Alignment explanation
Indices: 38564--38632 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
38554 TCATTGGTAC
38564 CGATACTAAGCCCCTCA-ATAT
1 CGATACTAA-CCCCT-AGATAT
* * * * *
38585 TGGTACTAACCTCTGGGTAT
1 CGATACTAACCCCTAGATAT
38605 CGATACTAACCCCTAGATAT
1 CGATACTAACCCCTAGATAT
38625 CGATACTA
1 CGATACTA
38633 CTAACTTATT
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
20 30 0.81
21 7 0.19
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (20 bp):
CGATACTAACCCCTAGATAT
Found at i:48830 original size:26 final size:25
Alignment explanation
Indices: 48794--48848 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 25
48784 AAGTGCTAAG
* *
48794 ACACATAAGGTTGTGCCCACCATAAT
1 ACACACAAGGTCGTGCCCACCAT-AT
*
48820 ACACACAAGGTCGTGCCTACCATAT
1 ACACACAAGGTCGTGCCCACCATAT
48845 ACAC
1 ACAC
48849 TAAGTTTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 6 0.23
26 20 0.77
ACGTcount: A:0.35, C:0.31, G:0.15, T:0.20
Consensus pattern (25 bp):
ACACACAAGGTCGTGCCCACCATAT
Found at i:50178 original size:7 final size:7
Alignment explanation
Indices: 50158--50216 Score: 50
Period size: 7 Copynumber: 8.0 Consensus size: 7
50148 TACTCTCTAA
50158 TTAAA-T
1 TTAAATT
*
50164 TTATATT
1 TTAAATT
50171 TTAAATT
1 TTAAATT
50178 TTAATTAATT
1 TT-A--AATT
50188 TTAAATT
1 TTAAATT
50195 TATAAATT
1 T-TAAATT
50203 ATTAAA-T
1 -TTAAATT
50210 TTAAATT
1 TTAAATT
50217 ACATAATCTC
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
6 9 0.20
7 16 0.36
8 11 0.25
9 2 0.05
10 6 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTAAATT
Found at i:50275 original size:20 final size:20
Alignment explanation
Indices: 50233--50276 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
50223 TCTCTAATTA
*
50233 ATTTATAATTTAAATAGTGT
1 ATTTATAATTTAAATACTGT
*
50253 ATTTA-AATTTAAAATACTTT
1 ATTTATAATTT-AAATACTGT
50273 ATTT
1 ATTT
50277 TCTGTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (20 bp):
ATTTATAATTTAAATACTGT
Found at i:50854 original size:24 final size:24
Alignment explanation
Indices: 50822--50873 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
50812 TAATCCATCC
50822 TTCCTTCTTAATTTAATAAAACAA
1 TTCCTTCTTAATTTAATAAAACAA
50846 TTCCTTCTTAATTTAATAAAACAA
1 TTCCTTCTTAATTTAATAAAACAA
50870 TTCC
1 TTCC
50874 ATGACCGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.42
Consensus pattern (24 bp):
TTCCTTCTTAATTTAATAAAACAA
Found at i:50919 original size:20 final size:20
Alignment explanation
Indices: 50894--50933 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
50884 GGCTTGAAAT
50894 TACTGTAGCA-GTATCGATAC
1 TACTGTAG-AGGTATCGATAC
50914 TACTGTAGAGGTATCGATAC
1 TACTGTAGAGGTATCGATAC
50934 CCATTTTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (20 bp):
TACTGTAGAGGTATCGATAC
Found at i:51004 original size:20 final size:19
Alignment explanation
Indices: 50976--51044 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 19
50966 TACTGCTCAT
* *
50976 TACTGTTCACACAGTATCGA
1 TACTATTCATACAGTA-CGA
50996 TACTATTCATACAGTAACGA
1 TACTATTCATACAGT-ACGA
* * *
51016 CACTATTCATACAATACAA
1 TACTATTCATACAGTACGA
51035 TACTATTCAT
1 TACTATTCAT
51045 GAAAACATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 12 0.29
20 29 0.69
21 1 0.02
ACGTcount: A:0.38, C:0.23, G:0.07, T:0.32
Consensus pattern (19 bp):
TACTATTCATACAGTACGA
Found at i:52353 original size:23 final size:23
Alignment explanation
Indices: 52325--52383 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
52315 TTCAAATCAA
*
52325 AATTTTCTTTTTTTAAAACTTTC
1 AATTTTCATTTTTTAAAACTTTC
52348 AATTTTCATTTTTTAAAACTTTC
1 AATTTTCATTTTTTAAAACTTTC
52371 AATTTTCATTTTT
1 AATTTTCATTTTT
52384 GAAAGCTCTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (23 bp):
AATTTTCATTTTTTAAAACTTTC
Found at i:52425 original size:19 final size:19
Alignment explanation
Indices: 52401--52446 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
52391 CTAAATCCCT
*
52401 TTTCAAAAT-TTATTTTGGC
1 TTTCAAAATCTAATTTT-GC
*
52420 TTTCAAAATCTAATTTTGT
1 TTTCAAAATCTAATTTTGC
52439 TTTCAAAA
1 TTTCAAAA
52447 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.50
Consensus pattern (19 bp):
TTTCAAAATCTAATTTTGC
Found at i:53348 original size:33 final size:33
Alignment explanation
Indices: 53303--53374 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
53293 CTTTAAAAAC
* * *
53303 TCCCTAGTTTTTCATGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTCACGGGATAAACTAGAACCTT
* *
53336 TCCCTAGCTTTTCACGGGATCAACTAGAACTTT
1 TCCCTAGCTTTTCACGGGATAAACTAGAACCTT
53369 TACCCT
1 T-CCCT
53375 TTACAATGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
33 29 0.88
34 4 0.12
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.35
Consensus pattern (33 bp):
TCCCTAGCTTTTCACGGGATAAACTAGAACCTT
Found at i:53842 original size:20 final size:20
Alignment explanation
Indices: 53814--53861 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
53804 TTCATTATTG
* *
53814 TTCACACAATATCGGTACTA
1 TTCATACAATATCGGTAATA
53834 TTCATACAATATCGGTAATA
1 TTCATACAATATCGGTAATA
53854 TTCATACA
1 TTCATACA
53862 GTACAGTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (20 bp):
TTCATACAATATCGGTAATA
Found at i:63421 original size:16 final size:17
Alignment explanation
Indices: 63396--63429 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
63386 ATTACCCTAA
*
63396 GATGTTAGACTT-TGTT
1 GATGTGAGACTTATGTT
63412 GATGTGAGACTTATGTT
1 GATGTGAGACTTATGTT
63429 G
1 G
63430 CCCATTGTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.21, C:0.06, G:0.29, T:0.44
Consensus pattern (17 bp):
GATGTGAGACTTATGTT
Found at i:65073 original size:17 final size:17
Alignment explanation
Indices: 65028--65073 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
65018 TAAAAAAAAT
* *
65028 AAAAATTATT-TAGATT
1 AAAAATTATTAAAGATA
*
65044 AAAAA-TATAAAAGATA
1 AAAAATTATTAAAGATA
65060 AAAAATTATTAAAG
1 AAAAATTATTAAAG
65074 TACTCAATAC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 3 0.12
16 14 0.58
17 7 0.29
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (17 bp):
AAAAATTATTAAAGATA
Found at i:65101 original size:24 final size:25
Alignment explanation
Indices: 65062--65122 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 25
65052 AAAAGATAAA
*
65062 AAATTATT-AAAGTACT-CAATACATT
1 AAATTATTAAAAATACTACAA-A-ATT
65087 AAA-TA-TAAAAATACTACAAAATT
1 AAATTATTAAAAATACTACAAAATT
65110 AAATTATTAAAAA
1 AAATTATTAAAAA
65123 AATTAATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
23 7 0.23
24 12 0.39
25 12 0.39
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (25 bp):
AAATTATTAAAAATACTACAAAATT
Found at i:66356 original size:30 final size:30
Alignment explanation
Indices: 66315--66376 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
66305 GGCACTACCA
*
66315 AGGCGCAGGCACTTATCACAGCGCAGGCGC
1 AGGCACAGGCACTTATCACAGCGCAGGCGC
66345 AGGCACAGGCACTTATCACAGCGCAGGCGC
1 AGGCACAGGCACTTATCACAGCGCAGGCGC
66375 AG
1 AG
66377 CCACCGGTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.32, G:0.32, T:0.10
Consensus pattern (30 bp):
AGGCACAGGCACTTATCACAGCGCAGGCGC
Found at i:72746 original size:2 final size:2
Alignment explanation
Indices: 72739--72770 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
72729 CTCATGACTG
72739 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
72771 TTCTAACATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82522 original size:5 final size:5
Alignment explanation
Indices: 82490--82576 Score: 99
Period size: 5 Copynumber: 17.4 Consensus size: 5
82480 TAAAATGTGT
* * *
82490 TAATT TAATA AAATAA TAATA TTTATA TAATA T-ATA TATATA TAATA
1 TAATA TAATA TAAT-A TAATA -TAATA TAATA TAATA TA-ATA TAATA
82537 TAATA TAATA TAATA TAATA TAATA TAATA T-ATA -AATA TA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TA
82577 TATGGTCATG
Statistics
Matches: 71, Mismatches: 5, Indels: 12
0.81 0.06 0.14
Matches are distributed among these distances:
4 10 0.14
5 48 0.68
6 13 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TAATA
Found at i:83198 original size:106 final size:106
Alignment explanation
Indices: 83053--83696 Score: 887
Period size: 106 Copynumber: 6.0 Consensus size: 106
83043 GTATTGTTCT
* * * * * *
83053 GAGTCCAATATCCTCCGCCGTGAAGTTTAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGGGAAATGGTTTGTTGACAA
83118 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC-C
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
* * * *
83158 TGAGTCCAATACCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAGTTGTTTGTTGACA
1 -GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGGGAAATGGTTTGTTGACA
* *
83223 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTCGTCTC
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
* * * * * *
83265 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTAGGAAATTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGGGAAATGGTTTGTTGACAA
* * * * *
83330 CCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTC
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
* * *
83371 GAGTCTAATATCCTTCGATGTGAAGTTGAAATTGACACTGAAACTGGGAAATGGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGGGAAATGGTTTGTTGACAA
**
83436 CCATACGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
* * * *
83477 GAGTCCAATATTCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGTAATGGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGGGAAATGGTTTGTTGACAA
* *
83542 CCAACCGTCCCTTCCTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
*
83583 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACT-GAAAAGTGGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTC----TGAAACTGGGAAA-TGGTTTGTT
* *
83647 GACAACCAGCCGTCCCTTCATTGTGAAGTTGAATTTGTGTTGTCTC
61 GACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
83693 GAGT
1 GAGT
83697 GGCGTGATAT
Statistics
Matches: 476, Mismatches: 56, Indels: 8
0.88 0.10 0.01
Matches are distributed among these distances:
106 410 0.86
107 1 0.00
109 3 0.01
110 62 0.13
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGGGAAATGGTTTGTTGACAA
CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
Found at i:84725 original size:10 final size:11
Alignment explanation
Indices: 84703--84727 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
84693 ACCCACCTTA
84703 TTTTGTTCTTT
1 TTTTGTTCTTT
84714 TTTTGTTCTTT
1 TTTTGTTCTTT
84725 TTT
1 TTT
84728 CTCTTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (11 bp):
TTTTGTTCTTT
Found at i:84840 original size:78 final size:77
Alignment explanation
Indices: 84713--84856 Score: 218
Period size: 78 Copynumber: 1.9 Consensus size: 77
84703 TTTTGTTCTT
*
84713 TTTTTGTTCTTTTTTCTCTTTTTCATTTTTTTCAATTTAGGGCGCCCTTTCGGGTTTTCACCCTA
1 TTTTTGTTCTTTTTTCTCTTTTTCATTTTTTTCAATTTAGGACGCCCTTTCGGGTTTTCACCCTA
84778 AATGTTTTTCAC
66 AATGTTTTTCAC
* ** *
84790 TTTTTGTTCTTTTTTCTGTTTTGTTTTTTTTTTCGAA-TTAGGACGCCCTTTCGGGTTTTCATCC
1 TTTTTGTTCTTTTTTCTCTTTT-TCATTTTTTTC-AATTTAGGACGCCCTTTCGGGTTTTCACCC
84854 TAA
64 TAA
84857 GCGAAGTATT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
77 21 0.35
78 37 0.62
79 2 0.03
ACGTcount: A:0.11, C:0.19, G:0.13, T:0.57
Consensus pattern (77 bp):
TTTTTGTTCTTTTTTCTCTTTTTCATTTTTTTCAATTTAGGACGCCCTTTCGGGTTTTCACCCTA
AATGTTTTTCAC
Found at i:96145 original size:11 final size:11
Alignment explanation
Indices: 96131--96176 Score: 67
Period size: 11 Copynumber: 4.2 Consensus size: 11
96121 TAATAAAATA
*
96131 ATAATATTTAT
1 ATAATATATAT
96142 ATAATATATAT
1 ATAATATATAT
96153 ATAATATAATAT
1 ATAATAT-ATAT
96165 ATAA-ATATAT
1 ATAATATATAT
96175 AT
1 AT
96177 GGTCATGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
10 6 0.18
11 19 0.58
12 8 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATAATATATAT
Found at i:98608 original size:31 final size:31
Alignment explanation
Indices: 98571--98632 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
98561 AAAAATTAAA
* **
98571 TGTTTAGGTACTAAAATGGATCAAAACTTAT
1 TGTTTAGATACTAAAACAGATCAAAACTTAT
*
98602 TGTTTAGATACTAAAACAGTTCAAAACTTAT
1 TGTTTAGATACTAAAACAGATCAAAACTTAT
98633 AATTTACGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (31 bp):
TGTTTAGATACTAAAACAGATCAAAACTTAT
Found at i:98911 original size:2 final size:2
Alignment explanation
Indices: 98906--98932 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
98896 CAGAAACGTT
98906 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
98933 TATGCGTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:99705 original size:70 final size:70
Alignment explanation
Indices: 99623--99762 Score: 235
Period size: 70 Copynumber: 2.0 Consensus size: 70
99613 TCCATAGCAA
*
99623 TATAAAATAAAAAGTAATAAATTTGAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAAT
1 TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAAT
99688 ACACT
66 ACACT
***
99693 TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAAGGGAGCTCCTAAATCATCCAAATAAT
1 TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAAT
*
99758 GCACT
66 ACACT
99763 GAGTTTAAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.50, C:0.15, G:0.08, T:0.27
Consensus pattern (70 bp):
TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAAT
ACACT
Found at i:100495 original size:20 final size:21
Alignment explanation
Indices: 100443--100495 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
100433 ACTGTTCATA
100443 GGTATCGATACTAAGCCCCTC
1 GGTATCGATACTAAGCCCCTC
* * * * *
100464 AGTATTGGTACTAA-CCTCTG
1 GGTATCGATACTAAGCCCCTC
100484 GGTATCGATACT
1 GGTATCGATACT
100496 TGTAACAACC
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (21 bp):
GGTATCGATACTAAGCCCCTC
Found at i:101268 original size:2 final size:2
Alignment explanation
Indices: 101261--101293 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
101251 TTTTAAACAT
101261 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
101294 CCCTTCATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:101320 original size:20 final size:21
Alignment explanation
Indices: 101287--101326 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
101277 TATATATATA
*
101287 TATATATCCCTTCATATCACT
1 TATATATCCATTCATATCACT
101308 TATATA-CCATTCATATCAC
1 TATATATCCATTCATATCAC
101327 ATTACATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (21 bp):
TATATATCCATTCATATCACT
Found at i:101464 original size:81 final size:80
Alignment explanation
Indices: 101425--101989 Score: 738
Period size: 81 Copynumber: 7.0 Consensus size: 80
101415 AACTAATCCC
* * *
101425 TTATTCTTTTACTCAACAGTGTTTAACCGTACATCTAACTGGCATAATTAACACCTTTCTTTCAA
1 TTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTC-TTCAA
101490 TTGCACAGTTAGGCCA
65 TTGCACAGTTAGGCCA
* * *
101506 TTATTCTTTTACTCAACAATATTTAACTGTTCATCTAACTGGAATAATTGACACCTTTCTGTCAA
1 TTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCT-TCAA
101571 TTGCACAGTTAGGCCA
65 TTGCACAGTTAGGCCA
* * **
101587 TTATTCTTTTACTCAACGGTATTCAACAATTCATCTAACTGGCATAATTGACACCTTTCTTCCAA
1 TTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTT-CAA
101652 TTGCACAGTTAGGCCA
65 TTGCACAGTTAGGCCA
* * * *
101668 TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCAAAATTGACACTTTTCTGCCAA
1 TTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCT-TC-A
*
101733 ATTGCACAGTTAGGTCA
64 ATTGCACAGTTAGGCCA
* * * *
101750 TTATTCTTTTACTCAA-AGGTAATTAACCGTTCATCTAACTAGCATAATTGGCACTTTTCTTCCA
1 TTATTCTTTTACTCAACA-GTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTT-CA
*
101814 ATTGCACAATTAGGCCA
64 ATTGCACAGTTAGGCCA
* * * * * *
101831 TTATTCTTTTACTCAACGGTATTTAACCATTTATCTAACT-GTATAATTAACACCTTTCTGCCAA
1 TTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCT-TCAA
*
101895 TTGCATAGTTAGGCCA
65 TTGCACAGTTAGGCCA
* * * * * *
101911 TTATTCTTTTACTCAACGGTATTCAATCGTTCATCTAACTAGCATAATTGACACATTTCTGTCAT
1 TTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCT-TCAA
101976 TTGCACAGTTAGGC
65 TTGCACAGTTAGGC
101990 TTCAAAGGCA
Statistics
Matches: 427, Mismatches: 48, Indels: 18
0.87 0.10 0.04
Matches are distributed among these distances:
80 70 0.16
81 285 0.67
82 72 0.17
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (80 bp):
TTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTTCAAT
TGCACAGTTAGGCCA
Found at i:101624 original size:162 final size:162
Alignment explanation
Indices: 101425--101989 Score: 814
Period size: 162 Copynumber: 3.5 Consensus size: 162
101415 AACTAATCCC
* * * * * * *
101425 TTATTCTTTTACTCAACAGTGTTTAACCGTACATCTAACTGGCATAATTAACACCTTTCTTTCAA
1 TTATTCTTTTACTCAACGGTATTCAACCGTTCATCTAACTAGCATAATTGACACCTTTCTTCCAA
** *
101490 TTGCACAGTTAGGCCATTATTCTTTTACTCAACAATATTTAACTGTTCATCTAACTGGAATAATT
66 TTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGAATAATT
*
101555 GACACCTTTCTGTCAATTGCACAGTTAGGCCA
131 GACACCTTTCTGCCAATTGCACAGTTAGGCCA
** *
101587 TTATTCTTTTACTCAACGGTATTCAACAATTCATCTAACTGGCATAATTGACACCTTTCTTCCAA
1 TTATTCTTTTACTCAACGGTATTCAACCGTTCATCTAACTAGCATAATTGACACCTTTCTTCCAA
101652 TTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCAA-AAT
66 TTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGG-AATAAT
* *
101716 TGACACTTTTCTGCCAAATTGCACAGTTAGGTCA
130 TGACACCTTTCTGCC-AATTGCACAGTTAGGCCA
* * *
101750 TTATTCTTTTACTCAAAGGTAATT-AACCGTTCATCTAACTAGCATAATTGGCACTTTTCTTCCA
1 TTATTCTTTTACTCAACGGT-ATTCAACCGTTCATCTAACTAGCATAATTGACACCTTTCTTCCA
* * * *
101814 ATTGCACAATTAGGCCATTATTCTTTTACTCAACGGTATTTAACCATTTATCTAACT-GTATAAT
65 ATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGAATAAT
* *
101878 TAACACCTTTCTGCCAATTGCATAGTTAGGCCA
130 TGACACCTTTCTGCCAATTGCACAGTTAGGCCA
* *
101911 TTATTCTTTTACTCAACGGTATTCAATCGTTCATCTAACTAGCATAATTGACACATTTCTGT-CA
1 TTATTCTTTTACTCAACGGTATTCAACCGTTCATCTAACTAGCATAATTGACACCTTTCT-TCCA
*
101975 TTTGCACAGTTAGGC
65 ATTGCACAGTTAGGC
101990 TTCAAAGGCA
Statistics
Matches: 363, Mismatches: 34, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
160 3 0.01
161 84 0.23
162 146 0.40
163 127 0.35
164 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (162 bp):
TTATTCTTTTACTCAACGGTATTCAACCGTTCATCTAACTAGCATAATTGACACCTTTCTTCCAA
TTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGAATAATT
GACACCTTTCTGCCAATTGCACAGTTAGGCCA
Found at i:101916 original size:243 final size:243
Alignment explanation
Indices: 101425--101989 Score: 821
Period size: 243 Copynumber: 2.3 Consensus size: 243
101415 AACTAATCCC
* * * * * *
101425 TTATTCTTTTACTCAACAGTGTTTAACCGTACATCTAACTGGCATAATTAACACCTTTCTTTCAA
1 TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGTCAA
* * *
101490 TTGCACAGTTAGGCCATTATTCTTTTACTCAACAATATTTAACTGTTCATCTAACTGGAATAATT
66 TTGCACAGTTAGGCCATTATTCTTTTACTCAACAATAATTAACCGTTCATCTAACTAGAATAATT
*
101555 GACACCTTTCTGTCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTCAACAATTCA
131 GACACCTTTCTGTCAATTGCACAATTAGGCCATTATTCTTTTACTCAACGGTATTCAACAATTCA
* *
101620 TCTAACTGGCATAATTGACACCTTTCTTCCAATTGCACAGTTAGGCCA
196 TCTAACTGGCATAATTAACACCTTTCTGCCAATTGCACAGTTAGGCCA
* * *
101668 TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCAAAATTGACACTTTTCTGCCAA
1 TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGTC-A
* * *
101733 ATTGCACAGTTAGGTCATTATTCTTTTACTCAA-AGGTAATTAACCGTTCATCTAACTAGCATAA
65 ATTGCACAGTTAGGCCATTATTCTTTTACTCAACA-ATAATTAACCGTTCATCTAACTAGAATAA
* * * *
101797 TTGGCACTTTTCT-TCCAATTGCACAATTAGGCCATTATTCTTTTACTCAACGGTATTTAACCAT
129 TTGACACCTTTCTGT-CAATTGCACAATTAGGCCATTATTCTTTTACTCAACGGTATTCAACAAT
* * *
101861 TTATCTAACT-GTATAATTAACACCTTTCTGCCAATTGCATAGTTAGGCCA
193 TCATCTAACTGGCATAATTAACACCTTTCTGCCAATTGCACAGTTAGGCCA
* * * *
101911 TTATTCTTTTACTCAACGGTATTCAATCGTTCATCTAACTAGCATAATTGACACATTTCTGTCAT
1 TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGTCAA
101976 TTGCACAGTTAGGC
66 TTGCACAGTTAGGC
101990 TTCAAAGGCA
Statistics
Matches: 287, Mismatches: 32, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
242 14 0.05
243 150 0.52
244 123 0.43
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (243 bp):
TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGTCAA
TTGCACAGTTAGGCCATTATTCTTTTACTCAACAATAATTAACCGTTCATCTAACTAGAATAATT
GACACCTTTCTGTCAATTGCACAATTAGGCCATTATTCTTTTACTCAACGGTATTCAACAATTCA
TCTAACTGGCATAATTAACACCTTTCTGCCAATTGCACAGTTAGGCCA
Found at i:102123 original size:68 final size:68
Alignment explanation
Indices: 101940--102194 Score: 422
Period size: 68 Copynumber: 3.8 Consensus size: 68
101930 TATTCAATCG
* * *
101940 TTCATCTAACTAGCATAATTGACACATTTCTGTCATTTGCACAGTTAGGCTTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
102005 CCT
66 CCT
* *
102008 TTCATCTAACT-GCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCCCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
102072 CCT
66 CCT
* *
102075 TTCATCTAACTGGCATAAATGATATATTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
102140 CCT
66 CCT
* *
102143 TTCATCTAACTGACATAAATGACACATTTCTGTCATTTGCACAGTTATGCCT
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCT
102195 ATAATCATTT
Statistics
Matches: 174, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
67 63 0.36
68 111 0.64
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:102470 original size:54 final size:54
Alignment explanation
Indices: 102404--102544 Score: 171
Period size: 54 Copynumber: 2.6 Consensus size: 54
102394 ACATCTATTT
*
102404 CCCATACGGAAATTCATACACTTAGTATGAATTTCTT-A-GTTCGCACCCAAGGTG
1 CCCATAC-GAAATTCATACACTTAGTATGAATTT-TTCATGTTCGCACCCAAAGTG
* * * * *
102458 CCCATACTGAAATTCCTACACTTAGTATGAATTTTTCATTTTTGCAGCCAAAGTT
1 CCCATAC-GAAATTCATACACTTAGTATGAATTTTTCATGTTCGCACCCAAAGTG
*
102513 CCCATA-AAAATTCATACACTTAGTATGAATTT
1 CCCATACGAAATTCATACACTTAGTATGAATTT
102545 GTTAAATTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
53 26 0.34
54 33 0.43
55 17 0.22
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (54 bp):
CCCATACGAAATTCATACACTTAGTATGAATTTTTCATGTTCGCACCCAAAGTG
Found at i:103011 original size:20 final size:22
Alignment explanation
Indices: 102986--103037 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
102976 ATGTTCCCTA
*
102986 GTATCGATACT-GT-TACTATG
1 GTATCGATACTACTATACTATG
*
103006 GTATCGTTACTACTATACTATG
1 GTATCGATACTACTATACTATG
*
103028 GTACCGATAC
1 GTATCGATAC
103038 CCCCTTACGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 10 0.38
21 1 0.04
22 15 0.58
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (22 bp):
GTATCGATACTACTATACTATG
Found at i:103102 original size:95 final size:95
Alignment explanation
Indices: 102889--103113 Score: 240
Period size: 95 Copynumber: 2.4 Consensus size: 95
102879 TCCGACTTTA
** * * * * *
102889 TAGTATCGATACTAC-TACCCTAGTACCGATACTTCTATACTATGGTATCGATACCCCCTTCTGG
1 TAGTATCGATAC-ACTTACTATGGTATCGATACTACTATACTATGGTACCGATACCCCCTTCTGA
* * *
102953 TATCGATACTGATTTTAGGTTTGATGTTCCC
65 TATCGATACCGATTTTAGATTCGATGTTCCC
** *
102984 TAGTATCGATACTGTTACTATGGTATCGTTACTACTATACTATGGTACCGATACCCCCTTAC-GA
1 TAGTATCGATACACTTACTATGGTATCGATACTACTATACTATGGTACCGATACCCCCTT-CTGA
* * *
103048 TATCGATACCGATTTTTGATTCGATGTTGCT
65 TATCGATACCGATTTTAGATTCGATGTTCCC
* *
103079 TGGTATCGATACACTTA-TCATGGTATTGATACTAC
1 TAGTATCGATACACTTACT-ATGGTATCGATACTAC
103114 CTCTTCGGTA
Statistics
Matches: 106, Mismatches: 21, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
94 1 0.01
95 104 0.98
96 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.37
Consensus pattern (95 bp):
TAGTATCGATACACTTACTATGGTATCGATACTACTATACTATGGTACCGATACCCCCTTCTGAT
ATCGATACCGATTTTAGATTCGATGTTCCC
Found at i:114362 original size:31 final size:31
Alignment explanation
Indices: 114296--114367 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
114286 AAATTAAATG
* **
114296 TTTAGGTACTAAAATGGATCAAAACTTATTG
1 TTTAGGTACTAAAACGGATCAAAACTTATAA
* *
114327 TTTAGATACTAAAACGGTTCAAAACTTATAA
1 TTTAGGTACTAAAACGGATCAAAACTTATAA
114358 TTTAGGTACT
1 TTTAGGTACT
114368 TAATGCATAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (31 bp):
TTTAGGTACTAAAACGGATCAAAACTTATAA
Found at i:115404 original size:70 final size:70
Alignment explanation
Indices: 115323--115455 Score: 221
Period size: 70 Copynumber: 1.9 Consensus size: 70
115313 TCCATAGCAA
*
115323 TATAAAATAAAAAGTAATAAATTTGAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAAT
1 TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAAT
115388 ACACT
66 ACACT
* ***
115393 TATAAGATAAAAAGTAATAAATTTAAGTTTACAATACAAGGGAGCTCCTAAATCATCCAAATA
1 TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATA
115456 GTGCACTGAG
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 58 1.00
ACGTcount: A:0.50, C:0.14, G:0.08, T:0.27
Consensus pattern (70 bp):
TATAAAATAAAAAGTAATAAATTTAAGTTTACAATACAACAAAGCTCCTAAATCATCCAAATAAT
ACACT
Done.