Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003971.1 Hibiscus syriacus cultivar Beakdansim tig00008610_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: 80224
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:2335 original size:15 final size:16
Alignment explanation
Indices: 2309--2338 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2299 AAGTAGAAAA
2309 CTTTTTATTAAAGTAG
1 CTTTTTATTAAAGTAG
2325 CTTTTTA-TAAAGTA
1 CTTTTTATTAAAGTA
2339 TATTTTCACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (16 bp):
CTTTTTATTAAAGTAG
Found at i:7796 original size:46 final size:46
Alignment explanation
Indices: 7696--7924 Score: 345
Period size: 46 Copynumber: 5.0 Consensus size: 46
7686 AAATAAATGA
* * * *
7696 ACAAATGAAAATGCATAATGGTGTATTAT-GACATGAAAAGATGCC
1 ACAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
7741 ACAAGTGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
1 ACAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
7787 ACAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
1 ACAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
7833 ACAAATGAAAATGCATAACGGTGCATTCTCGGCATGAAAGGATGCC
1 ACAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * * * *
7879 ACAAATGAATATGCATAACGGTGTATTAACGACATAAAAGG-TGCC
1 ACAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
7924 A
1 A
7925 GTCATGGTAT
Statistics
Matches: 170, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 31 0.18
46 139 0.82
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (46 bp):
ACAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
Found at i:14809 original size:46 final size:46
Alignment explanation
Indices: 14676--14840 Score: 251
Period size: 46 Copynumber: 3.6 Consensus size: 46
14666 AAATGAATGA
* * * *
14676 ACAAATGAAAATGCATCATAATGCATTATCGACATGAAAGGATGCC
1 ACAAATGAAAATGCATAACAGTGCATTATCGGCATGAAAGGATGCC
*
14722 ACAAATAAAAATGCATAACA-TGCATTATCGGCATGAAAGGATGCC
1 ACAAATGAAAATGCATAACAGTGCATTATCGGCATGAAAGGATGCC
*
14767 ACAAATGAAAATGTATAACAGTGCATTATCGGCATGAAAGGATGCC
1 ACAAATGAAAATGCATAACAGTGCATTATCGGCATGAAAGGATGCC
**
14813 ACAAATGAAAATGCATAATGGTGCATTA
1 ACAAATGAAAATGCATAACAGTGCATTA
14841 ACGACATAAA
Statistics
Matches: 109, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
45 42 0.39
46 67 0.61
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.22
Consensus pattern (46 bp):
ACAAATGAAAATGCATAACAGTGCATTATCGGCATGAAAGGATGCC
Found at i:17753 original size:17 final size:17
Alignment explanation
Indices: 17716--17753 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
17706 TTCTAGGTGG
* *
17716 CAGTGGTCCCCAGCAGG
1 CAGTGGTCCCCAACAGA
17733 CAGTGGTCCCCAACAGA
1 CAGTGGTCCCCAACAGA
17750 CAGT
1 CAGT
17754 TACAACCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.34, G:0.29, T:0.13
Consensus pattern (17 bp):
CAGTGGTCCCCAACAGA
Found at i:21013 original size:129 final size:130
Alignment explanation
Indices: 20777--21035 Score: 457
Period size: 129 Copynumber: 2.0 Consensus size: 130
20767 CTTGCAATGT
*
20777 ATCTTTGACTTCAGCTCTGTAGGAGTGTGTCGAACCTAATATTTTTTATCTTGTGAAAAAAATGG
1 ATCTTTGACTTCAGCTCTGTAGGAGTGTGTCGAACCTAATATTTTTTATCTTGTGAAAAAAATGA
* * * * *
20842 TGTTGAGAGCTTGGCTTTACCTTGGTTGGCACTAATTTGTATTTAACAAAAGATTCAAGTTAAAA
66 TGTCGACAGCTTGACTTTACCTTGGATGGAACTAATTTGTATTTAACAAAAGATTCAAGTTAAAA
20907 ATCTTTGACTTCAGCTCTGTAGGAGTGTGTCGAACCTAATA-TTTTTATCTTGTGAAAAAAATGA
1 ATCTTTGACTTCAGCTCTGTAGGAGTGTGTCGAACCTAATATTTTTTATCTTGTGAAAAAAATGA
20971 TGTCGACAGCTTGACTTTACCTTGGATGGAACTAATTTGTATTTAACAAAAGATTCAAGTTAAAA
66 TGTCGACAGCTTGACTTTACCTTGGATGGAACTAATTTGTATTTAACAAAAGATTCAAGTTAAAA
21036 TTTATTCTAG
Statistics
Matches: 123, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
129 82 0.67
130 41 0.33
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.37
Consensus pattern (130 bp):
ATCTTTGACTTCAGCTCTGTAGGAGTGTGTCGAACCTAATATTTTTTATCTTGTGAAAAAAATGA
TGTCGACAGCTTGACTTTACCTTGGATGGAACTAATTTGTATTTAACAAAAGATTCAAGTTAAAA
Found at i:25737 original size:21 final size:21
Alignment explanation
Indices: 25676--25737 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
25666 AAAAAACAAT
*
25676 TAATAAT-AAAC-TTAATTAA
1 TAATAATAAAACATTAAATAA
** *
25695 -AATAACTAAAACAACAAGTAA
1 TAATAA-TAAAACATTAAATAA
25716 TAATAATAAAACATTAAATAA
1 TAATAATAAAACATTAAATAA
25737 T
1 T
25738 CAACAACATA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
18 5 0.15
19 1 0.03
20 4 0.12
21 18 0.55
22 5 0.15
ACGTcount: A:0.63, C:0.08, G:0.02, T:0.27
Consensus pattern (21 bp):
TAATAATAAAACATTAAATAA
Found at i:28033 original size:64 final size:65
Alignment explanation
Indices: 27948--28092 Score: 188
Period size: 64 Copynumber: 2.3 Consensus size: 65
27938 GCACCATCTA
* ** * *
27948 ATGCATCGATGCAC-CCTTGAATAAATTGTATTTCGAATGCATTTTGTGTACCGATGCACA-AGG
1 ATGCATCGATGCACTCCTTGAATAAATTGAACATCAAATGCATTTTGTGTACCGATGCACAGA-C
28011 C
65 C
** *
28012 ATGCATCGATGCACTCC-TGAATATTTTGAACATCAAATGCATTTTGTGTACTGATGCACAGACC
1 ATGCATCGATGCACTCCTTGAATAAATTGAACATCAAATGCATTTTGTGTACCGATGCACAGACC
28076 ATGCATCGATGCACTCC
1 ATGCATCGATGCACTCC
28093 AGGCTCATTT
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
64 68 0.96
65 3 0.04
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (65 bp):
ATGCATCGATGCACTCCTTGAATAAATTGAACATCAAATGCATTTTGTGTACCGATGCACAGACC
Found at i:29093 original size:19 final size:20
Alignment explanation
Indices: 29055--29095 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
29045 ACTTAAATTT
*
29055 GCAACGCGAAAATGAAAATC
1 GCAACACGAAAATGAAAATC
*
29075 GCAACACGAAACT-AAAATC
1 GCAACACGAAAATGAAAATC
29094 GC
1 GC
29096 GTTGCGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (20 bp):
GCAACACGAAAATGAAAATC
Found at i:29149 original size:13 final size:13
Alignment explanation
Indices: 29131--29162 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
29121 GAGTTTCTTC
29131 AACAAAAAGACAA
1 AACAAAAAGACAA
29144 AACAAAAAGACAA
1 AACAAAAAGACAA
29157 AACAAA
1 AACAAA
29163 GACAAATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.78, C:0.16, G:0.06, T:0.00
Consensus pattern (13 bp):
AACAAAAAGACAA
Found at i:29165 original size:11 final size:12
Alignment explanation
Indices: 29135--29168 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
29125 TTCTTCAACA
29135 AAAAGACAAAAC
1 AAAAGACAAAAC
29147 AAAAAGACAAAAC
1 -AAAAGACAAAAC
29160 -AAAGACAAA
1 AAAAGACAAA
29169 TACTAATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
13 12 0.57
ACGTcount: A:0.76, C:0.15, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAGACAAAAC
Found at i:29626 original size:20 final size:20
Alignment explanation
Indices: 29603--29760 Score: 180
Period size: 20 Copynumber: 8.0 Consensus size: 20
29593 CATTTGGCAT
29603 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
29623 TCGCGTTGCGAATTTGACTTA
1 TCGCGTTGCGAATTTGAC-TA
* *
29644 T-GTGTTGCG-ATTT-ACAAA
1 TCGCGTTGCGAATTTGAC-TA
* *
29662 TTCGCGTTGCAAATTTGACTT
1 -TCGCGTTGCGAATTTGACTA
* *
29683 TTGTGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
*
29703 TCGCGTTACGAATTTGACT-
1 TCGCGTTGCGAATTTGACTA
* *
29722 TTGCGTTGTGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
29742 TCGCGTTGCGAATTTGACT
1 TCGCGTTGCGAATTTGACT
29761 TCTGTGTTAC
Statistics
Matches: 113, Mismatches: 19, Indels: 12
0.78 0.13 0.08
Matches are distributed among these distances:
18 3 0.03
19 21 0.19
20 80 0.71
21 7 0.06
22 2 0.02
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:29651 original size:40 final size:39
Alignment explanation
Indices: 29607--29768 Score: 220
Period size: 40 Copynumber: 4.1 Consensus size: 39
29597 TGGCATTCGC
29607 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTT-TGT
* *
29647 GTTGCG-ATTT-ACAAATTCGCGTTGCAAATTTGACTTTTGT
1 GTTGCGAATTTGAC-TA-TCGCGTTGCGAATTTGAC-TTTGT
* *
29687 GTTGCGAATTTGACTATCGCGTTACGAATTTGACTTTGC
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTGT
*
29726 GTTGTGAATTTGACTATCGCGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTT-TGT
29766 GTT
1 GTT
29769 ACGATTTACA
Statistics
Matches: 107, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
38 2 0.02
39 43 0.40
40 53 0.50
41 7 0.07
42 2 0.02
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.41
Consensus pattern (39 bp):
GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTGT
Found at i:29789 original size:20 final size:20
Alignment explanation
Indices: 29764--29803 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
29754 TTTGACTTCT
29764 GTGTTACGATTTACAAATTC
1 GTGTTACGATTTACAAATTC
*
29784 GTGTTACGATTTACAGATTC
1 GTGTTACGATTTACAAATTC
29804 ACGTTGCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (20 bp):
GTGTTACGATTTACAAATTC
Found at i:29920 original size:19 final size:20
Alignment explanation
Indices: 29879--29928 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
29869 TGGAAATTGG
* * *
29879 GTTGCGAAATTGAAGTTCGC
1 GTTGCGAATTTGAAGATCAC
29899 GTTGCGAATTTG-AGATCAC
1 GTTGCGAATTTGAAGATCAC
*
29918 GTTACGAATTT
1 GTTGCGAATTT
29929 ATTGGTCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (20 bp):
GTTGCGAATTTGAAGATCAC
Found at i:40178 original size:13 final size:13
Alignment explanation
Indices: 40160--40214 Score: 83
Period size: 13 Copynumber: 4.2 Consensus size: 13
40150 TGCGTCATAA
40160 ATTTATGACGCGC
1 ATTTATGACGCGC
*
40173 ATTTATGACACGC
1 ATTTATGACGCGC
*
40186 ATTTATGACGCAC
1 ATTTATGACGCGC
*
40199 ATTTATGACGCTC
1 ATTTATGACGCGC
40212 ATT
1 ATT
40215 GCACGTCATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:44219 original size:21 final size:21
Alignment explanation
Indices: 44195--44240 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
44185 TTTCAAAGAG
44195 GGGACGACCAGCCCTTGCTTT
1 GGGACGACCAGCCCTTGCTTT
44216 GGGACGACCAGCCCTTGCTTT
1 GGGACGACCAGCCCTTGCTTT
44237 GGGA
1 GGGA
44241 AGAATCTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.15, C:0.30, G:0.33, T:0.22
Consensus pattern (21 bp):
GGGACGACCAGCCCTTGCTTT
Found at i:51818 original size:36 final size:36
Alignment explanation
Indices: 51692--51850 Score: 178
Period size: 36 Copynumber: 4.4 Consensus size: 36
51682 GGAGAAAAGT
* * *
51692 CCATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAT
1 CCATCTTAAGCCTTCACCAGAGAATAGTGAAGCAAA
* * *
51728 CAATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAA
1 CCATCTTAAGCCTTCACCAGAGAATAGTGAAGCAAA
* * *
51764 CCATCATAAGTCTTCACCAGAGAGTAGTGAAGCAAA
1 CCATCTTAAGCCTTCACCAGAGAATAGTGAAGCAAA
* *
51800 CCATCTTAAGTCTTCACCA-A-AAGTAGTGAAGCAGAT
1 CCATCTTAAGCCTTCACCAGAGAA-TAGTGAAGCA-AA
*
51836 CCATTTTAAGCCTTC
1 CCATCTTAAGCCTTC
51851 TCAGAAGAGT
Statistics
Matches: 108, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
34 1 0.01
35 11 0.10
36 96 0.89
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (36 bp):
CCATCTTAAGCCTTCACCAGAGAATAGTGAAGCAAA
Found at i:52228 original size:54 final size:54
Alignment explanation
Indices: 52046--53304 Score: 1135
Period size: 54 Copynumber: 23.7 Consensus size: 54
52036 AAGATTATTT
* *
52046 GAGTTCCATACTCCCTAGAGAGAGAGGGAGCGAACCCGTTTGAAG-AGATG-TC
1 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
* *
52098 TGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAA-AA-TTGTTC
1 -GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
* * * *
52151 GAGTTCTATACTCCCTAGAGAAAGAGAGAGCGAACTCGTTTGCAGAAGATATTC
1 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
* * * * ** *
52205 GAGTTCCATAATCCCTAGAGAAAGAGGGAACGAACCCGATTGTTGAAGTTTGTTC
1 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAG-ATGTTC
* * * * * ** *
52260 GAG-TCTTATACTCTCT-GAAAGAATAGGGAGC-AGACACGATTGTTGAAGATTATTC
1 GAGTTC-TATACTCCCTAGAGA-AAGAGGGAGCGA-ACCCGTTTGAAGAAGA-TGTTC
* * * * * * **
52315 GAG-TCTCATACTCTCT-GAAAGAATAGGGAG-TAGACACGATTGTCGAAGATTGTTC
1 GAGTTCT-ATACTCCCTAGAGA-AAGAGGGAGCGA-ACCCGTTTGAAGAAGA-TGTTC
* * * ** *
52370 GAG-TCTCATACTCTCT-GAAGGAATAGGGAGC-ATACACATTTTCAA-AAGATGTTC
1 GAGTTCT-ATACTCCCTAG-AGAAAGAGGGAGCGA-AC-CCGTTTGAAGAAGATGTTC
* * * * *
52424 GAGTTCCATACTCCTTAAAGGAAGAAGGAGCGAACCCGTTT---GAAGATGTTC
1 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
** * * * ** * *
52475 GAGTTCTATACTCTTTAAAGAGAGAAGGAGCGAACCCGTAAGAAGAAGATTTTT
1 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
52529 GAGTTCTATACTCCCT-GAAGAAAGAGGGAGCGAACCCAG-TT---GAAGATGTTC
1 GAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCC-GTTTGAAGAAGATGTTC
*
52580 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG-A-TTGTTC
1 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
* * ** *
52632 GAGTTCTATACTTCCT-GAAGAAAGATGGAGCGAACTTGTTTGAAAAAGATGTTC
1 GAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
* * *
52686 GAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCGTTTGAAGAATATGTCC
1 GAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
* * * *
52740 AAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCTGTTTGAAGAAGATGTCC
1 GAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
* *
52794 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAGGAATATGTTC
1 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
* * *
52848 GAGTTCTATACTCCCTA-A-AGAGAGGGAGCGAACCCGTTTGAAG-A-TTGTTT
1 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
* * ** *
52898 GAGTTATATACTCCCTAGAGAAAGAGGGAGCAAACCCGTAAGAAGAAGATGTTT
1 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
* * * * *
52952 TAGTTCCATACTCCCT-GAAGAAAGAGGGAGCGAACCCATTTGAAGAATATGTCC
1 GAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
* * * **
53006 GAGTTCTATACTCCCTAGAGAAAGTGGGAGTGAACCCATAAGAAGAAGATGTTC
1 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
* * *
53060 GAGTTCCATACTCCCTA-A-AGAGAGGGAGCGAACCCGTTTGAAG-A-TTGTTC
1 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
* *
53110 GAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCC
1 GAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
* * * * *
53164 GAGTTCTATACTCCCTAGAGAAAGAGGGAACAAATCCGTTT---GAAGATTTTT
1 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
* * * * *
53215 GAGTTGTATACTCCCTA-ATAAAGAGGGAGCAAACCCGTTTGCAGAAGAAGTTC
1 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
*
53268 GAGTTCTATACTCCCTA-AAAAAGAGGGAGCGAACCCG
1 GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCG
53305 ATGGTTGAAG
Statistics
Matches: 1015, Mismatches: 144, Indels: 94
0.81 0.11 0.08
Matches are distributed among these distances:
50 60 0.06
51 117 0.12
52 173 0.17
53 100 0.10
54 432 0.43
55 130 0.13
56 3 0.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (54 bp):
GAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
Found at i:52399 original size:55 final size:55
Alignment explanation
Indices: 52241--52406 Score: 269
Period size: 55 Copynumber: 3.0 Consensus size: 55
52231 GGAACGAACC
* *
52241 CGATTGTTGAAGTTTGTTCGAGTCTTATACTCTCTGAAAGAATAGGGAGCAGACA
1 CGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAGCAGACA
* *
52296 CGATTGTTGAAGATTATTCGAGTCTCATACTCTCTGAAAGAATAGGGAGTAGACA
1 CGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAGCAGACA
* * *
52351 CGATTGTCGAAGATTGTTCGAGTCTCATACTCTCTGAAGGAATAGGGAGCATACA
1 CGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAGCAGACA
52406 C
1 C
52407 ATTTTCAAAA
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 102 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (55 bp):
CGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAGCAGACA
Found at i:52419 original size:55 final size:55
Alignment explanation
Indices: 52241--52436 Score: 249
Period size: 55 Copynumber: 3.6 Consensus size: 55
52231 GGAACGAACC
* *
52241 CGATTGTT-GAAGTTTGTTCGAGTCTTATACTCTCTGAAAGAATAGGGAGCAGACA
1 CGATT-TTCGAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAGCAGACA
* *
52296 CGATTGTT-GAAGATTATTCGAGTCTCATACTCTCTGAAAGAATAGGGAGTAGACA
1 CGATT-TTCGAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAGCAGACA
* * *
52351 CGATTGTCGAAGATTGTTCGAGTCTCATACTCTCTGAAGGAATAGGGAGCATACA
1 CGATTTTCGAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAGCAGACA
*
52406 C-ATTTTCAAAAGA-TGTTCGAGT-TCCATACTC
1 CGATTTTC-GAAGATTGTTCGAGTCT-CATACTC
52437 CTTAAAGGAA
Statistics
Matches: 127, Mismatches: 11, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
53 1 0.01
54 22 0.17
55 104 0.82
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (55 bp):
CGATTTTCGAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAGCAGACA
Found at i:52964 original size:158 final size:159
Alignment explanation
Indices: 52046--53304 Score: 1156
Period size: 158 Copynumber: 7.9 Consensus size: 159
52036 AAGATTATTT
* * * *
52046 GAGTTCCATACTCCCTAGAGAGAGAGGGAGCGAACCCGTTTGAAGAGATG-TCTGAGTTCCATAC
1 GAGTTCTATACTCCCTA-AGAAAGAGGGAGCGAACCCGTTTGAAGA-TTGTTC-GAGTTCTATAC
*
52110 TCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAA-AA-TTGTTCGAGTTCTATACTCCCT-AGAGA
63 TCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCTATACTCCCTGA-AGA
* * * *
52172 AAGAGAGAGCGAACTCGTTTGCAGAAGATATTC
127 AAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
* * * *
52205 GAGTTCCATAATCCCTAGAGAAAGAGGGAACGAACCCGATTGTTGAAGTTTGTTCGAG-TCTTAT
1 GAGTTCTATACTCCCTA-AGAAAGAGGGAGCGAACCCG--T-TTGAAGATTGTTCGAGTTC-TAT
* * * * * ** * *
52269 ACTCTCT-GAAAGAATAGGGAGC-AGACACGATTGTTGAAGATTATTCGAG-TCTCATACTCTCT
61 ACTCCCTAGAGA-AAGAGGGAGCGA-ACCCGTTTGAAGAAGA-TGTTCGAGTTCT-ATACTCCCT
* * * * **
52331 GAA-AGAATAGGGAG-TAGACACGATTGTCGAAGATTGTTC
122 GAAGA-AAGAGGGAGCGA-ACCCGTTTGAAGAAGA-TGTTC
* * * ** * *
52370 GAG-TCTCATACTCTCTGAAGGAATAGGGAGC-ATACACATTTTCAAAAGA-TGTTCGAGTTCCA
1 GAGTTCT-ATACTCCCT-AAGAAAGAGGGAGCGA-AC-CCGTTT--GAAGATTGTTCGAGTTCTA
* * * * ** *
52432 TACTCCTTAAAGGAAGAAGGAGCGAACCCGTTT---GAAGATGTTCGAGTTCTATACTCTTTAAA
60 TACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCTATACTCCCTGAA
* * ** * *
52494 GAGAGAAGGAGCGAACCCGTAAGAAGAAGATTTTT
125 GAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
52529 GAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCAG-TTGAAGA-TGTTCGAGTTCTATACT
1 GAGTTCTATACTCCCT-AAGAAAGAGGGAGCGAACCC-GTTTGAAGATTGTTCGAGTTCTATACT
* *
52592 CCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG-A-TTGTTCGAGTTCTATACTTCCTGAAGAAA
64 CCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCTATACTCCCTGAAGAAA
* ** *
52655 GATGGAGCGAACTTGTTTGAAAAAGATGTTC
129 GAGGGAGCGAACCCGTTTGAAGAAGATGTTC
* * *
52686 GAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAATATGTCCAAGTTCTATAC
1 GAGTTCTATACTCCCT-AAGAAAGAGGGAGCGAACCCGTTTGAAG-AT-TGTTCGAGTTCTATAC
* * *
52751 TTCCT-GAAGAAAGAGGGAGCGAACCTGTTTGAAGAAGATGTCCGAGTTCTATACTCCCT-AGAG
63 TCCCTAG-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCTATACTCCCTGA-AG
* *
52814 AAAGAGGGAGCGAACCCGTTTGAGGAATATGTTC
126 AAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
* * *
52848 GAGTTCTATACTCCCTAA-AGAGAGGGAGCGAACCCGTTTGAAGATTGTTTGAGTTATATACTCC
1 GAGTTCTATACTCCCTAAGAAAGAGGGAGCGAACCCGTTTGAAGATTGTTCGAGTTCTATACTCC
* ** ** *
52912 CTAGAGAAAGAGGGAGCAAACCCGTAAGAAGAAGATGTTTTAGTTCCATACTCCCTGAAGAAAGA
66 CTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCTATACTCCCTGAAGAAAGA
* * *
52977 GGGAGCGAACCCATTTGAAGAATATGTCC
131 GGGAGCGAACCCGTTTGAAGAAGATGTTC
* * * ** * *
53006 GAGTTCTATACTCCCTAGAGAAAGTGGGAGTGAACCCATAAGAAGAAGATGTTCGAGTTCCATAC
1 GAGTTCTATACTCCCTA-AGAAAGAGGGAGCGAACCCGTTTGAAG-A-TTGTTCGAGTTCTATAC
* * *
53071 TCCCTA-A-AGAGAGGGAGCGAACCCGTTTGAAG-A-TTGTTCGAGTTCTATACTTCCTGAAGAA
63 TCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCTATACTCCCTGAAGAA
*
53132 AGAGGGAGCGAACCCGTTTGAAGAAGATGTCC
128 AGAGGGAGCGAACCCGTTTGAAGAAGATGTTC
* * * * *
53164 GAGTTCTATACTCCCTAGAGAAAGAGGGAACAAATCCGTTTGAAGATT-TTTGAGTTGTATACTC
1 GAGTTCTATACTCCCTA-AGAAAGAGGGAGCGAACCCGTTTGAAGATTGTTCGAGTTCTATACTC
* * * * *
53228 CCTA-ATAAAGAGGGAGCAAACCCGTTTGCAGAAGAAGTTCGAGTTCTATACTCCCT-AAAAAAG
65 CCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCTATACTCCCTGAAGAAAG
53291 AGGGAGCGAACCCG
130 AGGGAGCGAACCCG
53305 ATGGTTGAAG
Statistics
Matches: 894, Mismatches: 156, Indels: 102
0.78 0.14 0.09
Matches are distributed among these distances:
155 18 0.02
156 69 0.08
157 110 0.12
158 224 0.25
159 72 0.08
160 151 0.17
161 46 0.05
162 93 0.10
163 7 0.01
164 68 0.08
165 34 0.04
166 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (159 bp):
GAGTTCTATACTCCCTAAGAAAGAGGGAGCGAACCCGTTTGAAGATTGTTCGAGTTCTATACTCC
CTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCTATACTCCCTGAAGAAAGA
GGGAGCGAACCCGTTTGAAGAAGATGTTC
Found at i:53007 original size:212 final size:208
Alignment explanation
Indices: 52034--53351 Score: 1211
Period size: 212 Copynumber: 6.2 Consensus size: 208
52024 GTGAAGCAAA
* * * * *
52034 TGAAGATTATTTGAGTTCCATACTCCCTAGAGAGAGAGGGAGCGAACCCGTTTGAAG-AGATGTC
1 TGAAGATTGTTCGAGTTCTATACTCCCT-GAGAAAGAGGGAGCGAACCCGTATGAAGAAGATGTC
* *
52098 TGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTGAAAATTGTTCGAGTTCTATAC
65 TGAGTTCCATACTCCCTGA-AGAAAGAGGGAGCGAACCCATTTGAAGATTGTTCGAGTTCTATAC
* * * *
52162 TCCCTAGAGAAAGAGAGAGCGAACTCGTTTGCAGAAGATATTCGAGTTCCATAATCCCTAGAGAA
129 TCCCTAGAGAAAGAGGGAGCGAACCCGTTTG-AGAAGATGTTCGAGTTCCATACTCCCTA-A-AA
*
52227 AGAGGGAACGAACCCGATTGT
191 AGAGGGAGCGAACCCG--T-T
* * * * * **
52248 TGAAGTTTGTTCGAG-TCTTATACTCTCTGAAAGAATAGGGAGC-AGACACG-ATTGTTGAAGAT
1 TGAAGATTGTTCGAGTTC-TATACTCCCTGAGA-AAGAGGGAGCGA-ACCCGTA-TGAAGAAGAT
* * * * *
52310 -TATTCGAG-TCTCATACTCTCTGAA-AGAATAGGGAG-TAGACACGATTGTCGAAGATTGTTCG
62 GT-CT-GAGTTC-CATACTCCCTGAAGA-AAGAGGGAGCGA-AC-CCATT-T-GAAGATTGTTCG
* * * ** * *
52371 AG-TCTCATACTCTCT-GAAGGAATAGGGAGC-ATACACATTTTCAAAAGATGTTCGAGTTCCAT
119 AGTTCT-ATACTCCCTAG-AGAAAGAGGGAGCGA-AC-CCGTTTGAGAAGATGTTCGAGTTCCAT
* *
52433 ACTCCTTAAAGGAAGAAGGAGCGAACCCGTT
180 ACTCCCTAAA--AAGAGGGAGCGAACCCGTT
** * * * * * *
52464 TGAAGA-TGTTCGAGTTCTATACTCTTTAAAGAGAGAAGGAGCGAACCCGTAAGAAGAAGATTTT
1 TGAAGATTGTTCGAGTTCTATACTCCCT-GAGAAAGAGGGAGCGAACCCGTATGAAGAAGATGTC
* *
52528 TGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCAGTTGAAGA-TGTTCGAGTTCTATACT
65 TGAGTTCCATACTCCCTGAAGAAAGAGGGAGCGAACCCATTTGAAGATTGTTCGAGTTCTATACT
* *
52592 CCCTAGAGAAAGAGGGAGCGAACCCGTTT--GAAGATTGTTCGAGTTCTATACTTCCTGAAGAAA
130 CCCTAGAGAAAGAGGGAGCGAACCCGTTTGAGAAGA-TGTTCGAGTTCCATACTCCCT-AA-AAA
* **
52655 GATGGAGCGAACTTGTT
192 GAGGGAGCGAACCCGTT
* * *
52672 TGAAAAAGA-TGTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAATAT
1 TG---AAGATTGTTCGAGTTCTATACTCCCTG-AGAAAGAGGGAGCGAACCCGTATGAAGAAGAT
** * * ** * *
52736 GTCCAAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCTGTTTGAAGAAGATGTCCGAGTTCT
62 GTCTGAGTTCCATACTCCCTGAAGAAAGAGGGAGCGAACCCATTTGAAG-A-TTGTTCGAGTTCT
* *
52801 ATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAGGAATATGTTCGAGTTCTATACTCCCTAA
125 ATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGA-GAAGATGTTCGAGTTCCATACTCCCTAA
*
52866 AGAGAGGGAGCGAACCCGTT
189 AAAGAGGGAGCGAACCCGTT
* * * * *
52886 TGAAGATTGTTTGAGTTATATACTCCCTAGAGAAAGAGGGAGCAAACCCGTAAGAAGAAGATGTT
1 TGAAGATTGTTCGAGTTCTATACTCCCT-GAGAAAGAGGGAGCGAACCCGTATGAAGAAGATGTC
* *
52951 TTAGTTCCATACTCCCTGAAGAAAGAGGGAGCGAACCCATTTGAAGAATATGTCCGAGTTCTATA
65 TGAGTTCCATACTCCCTGAAGAAAGAGGGAGCGAACCCATTTGAAG-AT-TGTTCGAGTTCTATA
* * * ** *
53016 CTCCCTAGAGAAAGTGGGAGTGAACCCATAAGAAGAAGATGTTCGAGTTCCATACTCCCTAAAGA
128 CTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG-AGAAGATGTTCGAGTTCCATACTCCCTAAAAA
53081 GAGGGAGCGAACCCGTT
192 GAGGGAGCGAACCCGTT
* *
53098 TGAAGATTGTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTC
1 TGAAGATTGTTCGAGTTCTATACTCCCTG-AGAAAGAGGGAGCGAACCCGTATGAAGAAGATGTC
* * * * * * * *
53163 CGAGTTCTATACTCCCT-AGAGAAAGAGGGAACAAATCCGTTTGAAGATT-TTTGAGTTGTATAC
65 TGAGTTCCATACTCCCTGA-AGAAAGAGGGAGCGAACCCATTTGAAGATTGTTCGAGTTCTATAC
* * * *
53226 TCCCTA-ATAAAGAGGGAGCAAACCCGTTTGCAGAAGAAGTTCGAGTTCTATACTCCCTAAAAAA
129 TCCCTAGAGAAAGAGGGAGCGAACCCGTTTG-AGAAGATGTTCGAGTTCCATACTCCCT-AAAAA
53290 GAGGGAGCGAACCCGATGGT
192 GAGGGAGCGAACCCG-T--T
* * *
53310 TGAAGATTGTTCGA-ATCTTATACTCTCTGAAGAAATAGGGAG
1 TGAAGATTGTTCGAGTTC-TATACTCCCTG-AGAAAGAGGGAG
53352 TAGACACGAT
Statistics
Matches: 909, Mismatches: 140, Indels: 112
0.78 0.12 0.10
Matches are distributed among these distances:
207 4 0.00
208 78 0.09
209 42 0.05
210 32 0.04
211 110 0.12
212 309 0.34
213 11 0.01
214 123 0.14
215 52 0.06
216 56 0.06
217 10 0.01
218 7 0.01
219 72 0.08
220 3 0.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (208 bp):
TGAAGATTGTTCGAGTTCTATACTCCCTGAGAAAGAGGGAGCGAACCCGTATGAAGAAGATGTCT
GAGTTCCATACTCCCTGAAGAAAGAGGGAGCGAACCCATTTGAAGATTGTTCGAGTTCTATACTC
CCTAGAGAAAGAGGGAGCGAACCCGTTTGAGAAGATGTTCGAGTTCCATACTCCCTAAAAAGAGG
GAGCGAACCCGTT
Found at i:53373 original size:55 final size:55
Alignment explanation
Indices: 53309--53681 Score: 400
Period size: 55 Copynumber: 6.8 Consensus size: 55
53299 AACCCGATGG
*
53309 TTGAAGATTGTTCGAATCTTATACTCTCTGAAGAAATAGGGAGTAGACACGATTA
1 TTGAAGATTGTTCGAATCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTA
* * *
53364 TTAAAGATTGTTCAAATCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
1 TTGAAGATTGTTCGAATCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATT-A
* * *
53420 TTGAAGATTGTTC-AAGTCTTATACTCTCTGAAGGAATAGGGAGCATACACGATTG
1 TTGAAGATTGTTCGAA-TCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTA
* * * * * **
53475 TTGAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATCG
1 TTGAAGATTGTTCGAATCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTA
* *
53530 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGG-GACAGACGCGATTGA
1 TTGAAGATTGTTCGAATCTTATACTCTCTGAAGAAATAGGGAG-CAGACACGATT-A
* ** * *
53586 -TGAAGACTG-T-GGGTCTTATACTCTCTTAAGAAATAGGGAGCAGACCCGATTA
1 TTGAAGATTGTTCGAATCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTA
** * * * *
53638 CAGAAGATTATTTGAGT-TCTATACT-TCCTGAAGAAAGAGGGAGC
1 TTGAAGATTGTTCGAATCT-TATACTCT-CTGAAGAAATAGGGAGC
53682 GAACCCATAG
Statistics
Matches: 279, Mismatches: 28, Indels: 22
0.85 0.09 0.07
Matches are distributed among these distances:
52 1 0.00
53 42 0.15
54 6 0.02
55 181 0.65
56 49 0.18
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (55 bp):
TTGAAGATTGTTCGAATCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTA
Found at i:53440 original size:111 final size:110
Alignment explanation
Indices: 53264--53636 Score: 429
Period size: 111 Copynumber: 3.4 Consensus size: 110
53254 TGCAGAAGAA
* * * * *
53264 GTTCGAGT-TCTATACTCCCT-AAAAAAGAGGGAGC-GAACCCGATGGTTGAAGATTGTTCGAA-
1 GTTCGAGTCT-TATACTCTCTGAAGAAATAGGGAGCAG-ACACGATTGTTGAAGATTGTTC-AAG
* *
53325 TCTTATACTCTCTGAAGAAATAGGGAGTAGACACGATTATTAAAGATT
63 TCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAGATT
* *
53373 GTTCAAATCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTTGAAGATTGTTCAAGTC
1 GTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG-TTGAAGATTGTTCAAGTC
* * *
53438 TTATACTCTCTGAAGGAATAGGGAGCATACACGATTGTTGAAGATT
65 TTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAGATT
* * * * * *
53484 ATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATCGTTGAAGATTGTTCGAGTCT
1 GTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCAAGTCT
* *
53549 TATACTCTCTGAAGAAATAGGG-GACAGACGCGATTGA-TGAAGACT
66 TATACTCTCTGAAGAAATAGGGAG-CAGACACGATT-ATTGAAGATT
* * *
53594 G-T-GGGTCTTATACTCTCTTAAGAAATAGGGAGCAGACCCGATT
1 GTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATT
53637 ACAGAAGATT
Statistics
Matches: 225, Mismatches: 32, Indels: 15
0.83 0.12 0.06
Matches are distributed among these distances:
108 35 0.16
109 17 0.08
110 77 0.34
111 96 0.43
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (110 bp):
GTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCAAGTCT
TATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAGATT
Found at i:53483 original size:166 final size:163
Alignment explanation
Indices: 53303--53681 Score: 440
Period size: 166 Copynumber: 2.3 Consensus size: 163
53293 GGAGCGAACC
* * * *
53303 CGATGGTTGAAGATTGTTCGAATCTTATACTCTCTGAAGAAATAGGGAGTAGACACGATTATTAA
1 CGATTGTTGAAGATTATTCGAATCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCATTAA
* *
53368 AGATTGTTCAAATCTTATACTCTCTGAAGAAATA-GGGAGCAGACACGATTGTTTGAAGATTGTT
66 AGATTGTTCAAATCTTATACTCTCTGAAGAAATAGGGGA-CAGACACGATTG-ATGAAGACTG-T
* *
53432 CAAGTCTTATACTCTCTGAAGGAATAGGGAGCATACA
128 -AAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACA
* * * * * *
53469 CGATTGTTGAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATCGTTGA
1 CGATTGTTGAAGATTATTCGAATCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCATTAA
* * * **
53534 AGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGACAGACGCGATTGATGAAGACTGTGGG
66 AGATTGTTCAAATCTTATACTCTCTGAAGAAATAGGGGACAGACACGATTGATGAAGACTGTAAG
* *
53599 TCTTATACTCTCTTAAGAAATAGGGAGCAGACC
131 TCTTATACTCTCTGAAGAAATAGGGAGCAGACA
*** * * *
53632 CGATTACAGAAGATTATTTGAGT-TCTATACT-TCCTGAAGAAAGAGGGAGC
1 CGATTGTTGAAGATTATTCGAATCT-TATACTCT-CTGAAGAAATAGGGAGC
53682 GAACCCATAG
Statistics
Matches: 183, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
162 2 0.01
163 70 0.38
164 1 0.01
165 8 0.04
166 98 0.54
167 4 0.02
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (163 bp):
CGATTGTTGAAGATTATTCGAATCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCATTAA
AGATTGTTCAAATCTTATACTCTCTGAAGAAATAGGGGACAGACACGATTGATGAAGACTGTAAG
TCTTATACTCTCTGAAGAAATAGGGAGCAGACA
Found at i:53662 original size:108 final size:111
Alignment explanation
Indices: 53309--53678 Score: 389
Period size: 111 Copynumber: 3.4 Consensus size: 111
53299 AACCCGATGG
* * *
53309 TTGAAGATTGTTCGAATCTTATACTCTCTGAAGAAATA-GGGAGTAGACACGATT-ATTAAAGA-
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGAGCAGACACGATTGA-TGAAGAC
* * * *
53371 TTGTTCAAATCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGT
65 TAG-TCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATT-A
* * * * *
53420 TTGAAGATTGTTCAAGTCTTATACTCTCTGAAGGAATA-GGGAGCATACACGATTGTTGAAGATT
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGAGCAGACACGATTGATGAAGACT
* * * * **
53484 ATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATCG
66 AGTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTA
*
53530 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGA-CAGACGCGATTGATGAAGACT
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGAGCAGACACGATTGATGAAGACT
* * *
53594 -GT-GGGTCTTATACTCTCTTAAGAAATAGGGAGCAGACCCGATTA
66 AGTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTA
** * * *
53638 CAGAAGATTATTTGAGT-TCTATACT-TCCTGAAGAAAGAGGG
1 TTGAAGATTGTTCGAGTCT-TATACTCT-CTGAAGAAATAGGG
53679 AGCGAACCCA
Statistics
Matches: 219, Mismatches: 35, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
107 2 0.01
108 67 0.31
109 1 0.00
110 53 0.24
111 95 0.43
112 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (111 bp):
TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGAGCAGACACGATTGATGAAGACT
AGTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTA
Found at i:54984 original size:21 final size:21
Alignment explanation
Indices: 54960--55005 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
54950 TTTCAAAGAG
54960 GGGACGACCAGCCCTTGCTTT
1 GGGACGACCAGCCCTTGCTTT
54981 GGGACGACCAGCCCTTGCTTT
1 GGGACGACCAGCCCTTGCTTT
55002 GGGA
1 GGGA
55006 AGAATCTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.15, C:0.30, G:0.33, T:0.22
Consensus pattern (21 bp):
GGGACGACCAGCCCTTGCTTT
Found at i:56867 original size:13 final size:13
Alignment explanation
Indices: 56849--56880 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
56839 TTTTTTGGAT
56849 TATGACTATTAAA
1 TATGACTATTAAA
56862 TATGACTATTAAA
1 TATGACTATTAAA
56875 TATGAC
1 TATGAC
56881 ACATTATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (13 bp):
TATGACTATTAAA
Found at i:59031 original size:54 final size:54
Alignment explanation
Indices: 58930--59346 Score: 274
Period size: 54 Copynumber: 7.7 Consensus size: 54
58920 AAGATTAAAC
* * * * **
58930 AAGCTCTAGCGTTCCTTTGTAATGGATGAGTAGATAAAAATTT-TAAGATCGAGT
1 AAGCTCTAGCATTCATTTGTTATGGAGGAGTAGA-GCAAATTTCTAAGATCGAGT
* * * * *
58984 AAACTCTGGCATTCATTTGTTACGGAGGAGT-GAAGTAAATTTCTAAGATCAAGT
1 AAGCTCTAGCATTCATTTGTTATGGAGGAGTAG-AGCAAATTTCTAAGATCGAGT
* * * * * * * * *
59038 AAGCTCTAGCGTTCCTTTTTTATGGAGGGGTATAGTAAACTTT-TAAGACCAACT
1 AAGCTCTAGCATTCATTTGTTATGGAGGAGTAGAGCAAA-TTTCTAAGATCGAGT
* *
59092 AAGCTCT-G-ATGTTAATTTGTTACGGAGGAGTAGAGCAAATTTCTAAGA-CTGAGT
1 AAGCTCTAGCA--TTCATTTGTTATGGAGGAGTAGAGCAAATTTCTAAGATC-GAGT
* * * * * *
59146 AAAG-TCTAGTATTCCTTTGTCATGGAAGAGTAGAGCAGATTTCTATGATCGAGT
1 -AAGCTCTAGCATTCATTTGTTATGGAGGAGTAGAGCAAATTTCTAAGATCGAGT
* * * *
59200 AAGCTCTAGCATTCTTTTGTTATGGAGTAGTAGAGCAAATTTTTAAGATAGAGT
1 AAGCTCTAGCATTCATTTGTTATGGAGGAGTAGAGCAAATTTCTAAGATCGAGT
** * *** * * * * *
59254 AAGAACCATTGTTCCTTTGTTATGGAGGAGTAAAGCACATTCCTAAGA-CTAAGT
1 AAGCTCTAGCATTCATTTGTTATGGAGGAGTAGAGCAAATTTCTAAGATC-GAGT
*** * *
59308 AAGCTCTAGTGCTCCTTTGTTATAGAGGAGTAGAGCAAA
1 AAGCTCTAGCATTCATTTGTTATGGAGGAGTAGAGCAAA
59347 ATTTTCAATA
Statistics
Matches: 281, Mismatches: 68, Indels: 28
0.75 0.18 0.07
Matches are distributed among these distances:
53 15 0.05
54 257 0.91
55 8 0.03
56 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (54 bp):
AAGCTCTAGCATTCATTTGTTATGGAGGAGTAGAGCAAATTTCTAAGATCGAGT
Found at i:60869 original size:19 final size:20
Alignment explanation
Indices: 60842--60879 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
60832 TATTGGAAAA
60842 TTTTAATTTAATT-ATTAAT
1 TTTTAATTTAATTAATTAAT
* *
60861 TTTTGATTTTATTAATTAA
1 TTTTAATTTAATTAATTAA
60880 ATCATTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTAATTTAATTAATTAAT
Found at i:61454 original size:3 final size:3
Alignment explanation
Indices: 61446--61536 Score: 173
Period size: 3 Copynumber: 30.3 Consensus size: 3
61436 CTCTTTTCTG
61446 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
61494 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TCT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
61537 TTGAAATTTT
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:63280 original size:29 final size:29
Alignment explanation
Indices: 63247--63305 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
63237 TTTCGTCACT
*
63247 TAAAATTTTATAAATTTAAGTTCATTCTC
1 TAAAATTTTATAAATTTAAATTCATTCTC
*
63276 TAAAATTTTATAAATTTAAATTTATTCTC
1 TAAAATTTTATAAATTTAAATTCATTCTC
63305 T
1 T
63306 GACTTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (29 bp):
TAAAATTTTATAAATTTAAATTCATTCTC
Found at i:64614 original size:16 final size:18
Alignment explanation
Indices: 64593--64631 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
64583 ATATATTTTT
64593 AAAAAT-AATTTTAAGA-
1 AAAAATCAATTTTAAGAC
*
64609 AAAAATCATTTTTAAGAC
1 AAAAATCAATTTTAAGAC
64627 AAAAA
1 AAAAA
64632 GCTGGTCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 9 0.45
18 5 0.25
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (18 bp):
AAAAATCAATTTTAAGAC
Found at i:65060 original size:2 final size:2
Alignment explanation
Indices: 65053--65115 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
65043 GGGTAAATTA
65053 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65095 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
65116 AAACAGTAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:67318 original size:91 final size:91
Alignment explanation
Indices: 67147--67478 Score: 528
Period size: 91 Copynumber: 3.7 Consensus size: 91
67137 AATGAAAATG
* * * * * *
67147 TTGAAAGCATTTTGC-CCGAAGGTCTTATGG-TTGCCTGAAGGACTTAAAAAATCAAGAAACCCC
1 TTGAAAACATTCTGCACTGAAGGTCTTACGGATGGCCCGAAGGACTTAAAAAATCAAGAAACCCC
* *
67210 TGAAGGCTTAGTTTCTTAAATCTCAT
66 CGAAGGCTCAGTTTCTTAAATCTCAT
67236 TTGAAAACATTCTGCACTGAAGGTCTTACGGATGGCCCGAAGGACTTAAAAAATCAAGAAACCCC
1 TTGAAAACATTCTGCACTGAAGGTCTTACGGATGGCCCGAAGGACTTAAAAAATCAAGAAACCCC
67301 CGAAGGCTCAGTTTCTTAAATCTCAT
66 CGAAGGCTCAGTTTCTTAAATCTCAT
*
67327 TTGAAAACATCCTGCACTGAAGGTCTTACGGATGGCCCGAAGGACTTAAAAAATCAAGAAACCCC
1 TTGAAAACATTCTGCACTGAAGGTCTTACGGATGGCCCGAAGGACTTAAAAAATCAAGAAACCCC
*
67392 CGAAGGCTCAGTTTCTTAAATCTTAT
66 CGAAGGCTCAGTTTCTTAAATCTCAT
*
67418 TTGAAAACA-TCATGCACTGAAGGTCTTACGGATGGTCCGAAGGACTT-AAAAATCAAGAAAC
1 TTGAAAACATTC-TGCACTGAAGGTCTTACGGATGGCCCGAAGGACTTAAAAAATCAAGAAAC
67479 TCTTGAAAAT
Statistics
Matches: 228, Mismatches: 12, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
89 13 0.06
90 28 0.12
91 187 0.82
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.25
Consensus pattern (91 bp):
TTGAAAACATTCTGCACTGAAGGTCTTACGGATGGCCCGAAGGACTTAAAAAATCAAGAAACCCC
CGAAGGCTCAGTTTCTTAAATCTCAT
Found at i:67620 original size:43 final size:43
Alignment explanation
Indices: 67567--68033 Score: 443
Period size: 43 Copynumber: 10.3 Consensus size: 43
67557 AAATTTGTCT
* *
67567 TCAAGGAACCCCTACATATCACGATGGTCCCTCAAACTTTTCA
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
** *
67610 TCAAGAAACCCCTACATATCACGATGGTTTCTCAAGCTTGTCA
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
* *
67653 TCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTTTTA
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
** * * *
67696 TCAAGAAACCCCTACATATCACGATGGTTTCTCAAGATTGTCC
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
*
67739 TCAA-AGAACCCCTACATATCACGATGGTCCTTCAAGCTTGTCATCAAA
1 TCAAGA-AACCCCTACATATCACGATGGTCCCTCAAGCTT-T--TC--A
* *
67787 TTTGTCGTCAAGGAACCCCTACATATCACGACGGTCCCTCAAGCTTTTCA
1 -------TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
** * ** *
67837 TCAAGAAACCCCTACATATCGTGATGATTTCTCAAGCTTTTCC
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
*
67880 TCAA-AGAACCCCTACATATCACGATGGTCCTTCAAGCTTGTCATCAAATTTGTCA
1 TCAAGA-AACCCCTACATATCACGATGGTCCCTCAA----G----C---TTT-TCA
* *
67935 TCAAGGAACCCCTACATATCACGACGGTCCCTCAAGCTTTTCA
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
** *
67978 TCAAGAAACCCCTACATATCACGATGGTTTCTCAAGCTTTTCT
1 TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
68021 TCAAGAAACCCCT
1 TCAAGAAACCCCT
68034 GAAAATCAGG
Statistics
Matches: 347, Mismatches: 49, Indels: 56
0.77 0.11 0.12
Matches are distributed among these distances:
42 2 0.01
43 261 0.75
44 3 0.01
46 2 0.01
47 2 0.01
50 1 0.00
51 2 0.01
52 2 0.01
54 4 0.01
55 68 0.20
ACGTcount: A:0.29, C:0.30, G:0.13, T:0.28
Consensus pattern (43 bp):
TCAAGAAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCA
Found at i:67706 original size:86 final size:86
Alignment explanation
Indices: 67561--68033 Score: 489
Period size: 86 Copynumber: 5.2 Consensus size: 86
67551 CTCATCAAAT
* *
67561 TTGTCTTCAAGGAACCCCTACATATCACGATGGTCCCTCAAACTTTTCATCAAGAAACCCCTACA
1 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCATCAAGAAACCCCTACA
67626 TATCACGATGGTTTCTCAAGC
66 TATCACGATGGTTTCTCAAGC
*
67647 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTTTTATCAAGAAACCCCTACA
1 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCATCAAGAAACCCCTACA
*
67712 TATCACGATGGTTTCTCAAGA
66 TATCACGATGGTTTCTCAAGC
* * *
67733 TTGTCCTCAAAGAACCCCTACATATCACGATGGTCCTTCAAGCTTGTCATCAAATTTGTCGTCAA
1 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTT-T--TC--A-------TCAA
* * **
67798 GGAACCCCTACATATCACGACGGTCCCTCAAGC
54 GAAACCCCTACATATCACGATGGTTTCTCAAGC
* * ** * ** *
67831 TTTTCATCAAGAAACCCCTACATATCGTGATGATTTCTCAAGCTTTTCCTCAA-AGAACCCCTAC
1 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCATCAAGA-AACCCCTAC
**
67895 ATATCACGATGGTCCTTCAAGCTTGTCATCAAAT
65 ATATCACGAT-G--------G-TT-TC-TCAAGC
*
67929 TTGTCATCAAGGAACCCCTACATATCACGACGGTCCCTCAAGCTTTTCATCAAGAAACCCCTACA
1 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCATCAAGAAACCCCTACA
67994 TATCACGATGGTTTCTCAAGC
66 TATCACGATGGTTTCTCAAGC
* * *
68015 TTTTCTTCAAGAAACCCCT
1 TTGTCATCAAGGAACCCCT
68034 GAAAATCAGG
Statistics
Matches: 317, Mismatches: 44, Indels: 52
0.77 0.11 0.13
Matches are distributed among these distances:
86 166 0.52
87 4 0.01
88 2 0.01
89 2 0.01
91 1 0.00
95 3 0.01
96 1 0.00
97 3 0.01
98 134 0.42
99 1 0.00
ACGTcount: A:0.29, C:0.30, G:0.13, T:0.28
Consensus pattern (86 bp):
TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCATCAAGAAACCCCTACA
TATCACGATGGTTTCTCAAGC
Found at i:67817 original size:55 final size:52
Alignment explanation
Indices: 67723--67981 Score: 189
Period size: 55 Copynumber: 5.2 Consensus size: 52
67713 ATCACGATGG
*
67723 TTTC-TCAAGATTGTCCTCAAAGAACCCCTACATATCACGATGGTCCTTCAAGC
1 TTTCATCAA-ATTGT-CTCAAGGAACCCCTACATATCACGATGGTCCTTCAAGC
* *
67776 TTGTCATCAAATTTGTCGTCAAGGAACCCCTACATATCACGACGGTCCCTCAAGC
1 TT-TCATCAAA-TTGTC-TCAAGGAACCCCTACATATCACGATGGTCCTTCAAGC
* ** * *
67831 TTT--TC--A-----TCAAGAAACCCCTACATATCGTGATGAT-TTCTCAAGC
1 TTTCATCAAATTGTCTCAAGGAACCCCTACATATCACGATGGTCCT-TCAAGC
*
67874 TTT--TC-------CTCAAAGAACCCCTACATATCACGATGGTCCTTCAAGC
1 TTTCATCAAATTGTCTCAAGGAACCCCTACATATCACGATGGTCCTTCAAGC
* *
67917 TTGTCATCAAATTTGTCATCAAGGAACCCCTACATATCACGACGGTCCCTCAAGC
1 TT-TCATCAAA-TTGTC-TCAAGGAACCCCTACATATCACGATGGTCCTTCAAGC
67972 TTTTCATCAA
1 -TTTCATCAA
67982 GAAACCCCTA
Statistics
Matches: 167, Mismatches: 19, Indels: 38
0.75 0.08 0.17
Matches are distributed among these distances:
43 65 0.39
44 2 0.01
46 2 0.01
50 1 0.01
52 2 0.01
53 2 0.01
54 6 0.04
55 85 0.51
56 2 0.01
ACGTcount: A:0.29, C:0.30, G:0.13, T:0.29
Consensus pattern (52 bp):
TTTCATCAAATTGTCTCAAGGAACCCCTACATATCACGATGGTCCTTCAAGC
Found at i:68014 original size:141 final size:141
Alignment explanation
Indices: 67647--68033 Score: 677
Period size: 141 Copynumber: 2.7 Consensus size: 141
67637 TTTCTCAAGC
* *
67647 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTTTTATCAAGAAACCCCTACA
1 TTGTCATCAAGGAACCCCTACATATCACGACGGTCCCTCAAGCTTTTCATCAAGAAACCCCTACA
* *
67712 TATCACGATGGTTTCTCAAGATTGTCCTCAAAGAACCCCTACATATCACGATGGTCCTTCAAGCT
66 TATCACGATGGTTTCTCAAGCTTTTCCTCAAAGAACCCCTACATATCACGATGGTCCTTCAAGCT
67777 TGTCATCAAAT
131 TGTCATCAAAT
*
67788 TTGTCGTCAAGGAACCCCTACATATCACGACGGTCCCTCAAGCTTTTCATCAAGAAACCCCTACA
1 TTGTCATCAAGGAACCCCTACATATCACGACGGTCCCTCAAGCTTTTCATCAAGAAACCCCTACA
** *
67853 TATCGTGATGATTTCTCAAGCTTTTCCTCAAAGAACCCCTACATATCACGATGGTCCTTCAAGCT
66 TATCACGATGGTTTCTCAAGCTTTTCCTCAAAGAACCCCTACATATCACGATGGTCCTTCAAGCT
67918 TGTCATCAAAT
131 TGTCATCAAAT
67929 TTGTCATCAAGGAACCCCTACATATCACGACGGTCCCTCAAGCTTTTCATCAAGAAACCCCTACA
1 TTGTCATCAAGGAACCCCTACATATCACGACGGTCCCTCAAGCTTTTCATCAAGAAACCCCTACA
*
67994 TATCACGATGGTTTCTCAAGCTTTTCTTC-AAGAAACCCCT
66 TATCACGATGGTTTCTCAAGCTTTTCCTCAAAG-AACCCCT
68034 GAAAATCAGG
Statistics
Matches: 232, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
140 3 0.01
141 229 0.99
ACGTcount: A:0.29, C:0.30, G:0.13, T:0.28
Consensus pattern (141 bp):
TTGTCATCAAGGAACCCCTACATATCACGACGGTCCCTCAAGCTTTTCATCAAGAAACCCCTACA
TATCACGATGGTTTCTCAAGCTTTTCCTCAAAGAACCCCTACATATCACGATGGTCCTTCAAGCT
TGTCATCAAAT
Found at i:68159 original size:36 final size:36
Alignment explanation
Indices: 68064--68391 Score: 221
Period size: 36 Copynumber: 9.0 Consensus size: 36
68054 AAAACTATTG
* * * * *
68064 TGTTTCGAGCGAAACTATCTCAAGCGAGATAAAATCTTT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA---TT
* *
68103 TGTTTCAAGTGAAATTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
* * *
68139 TGTTTCAAGGGAAACCGTCTCAAGAGAGGCAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
* *
68175 TGTTTCAATGGAAACTGTCTCAAGGGAGACAAAATA
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
* * *
68211 TGTTTCAAGGGAGACAAAACTTGTTTC----GAGA-GAAA-C
1 TGTTTCAA-GG-G---AAAC-TGTCTCAAGGGAGACAAAATT
* * *
68247 TGTCTCAAGGGAGACAAAATTTGTTTCAA-GG-G---AAA-T
1 TGTTTCAA-GG-G---AAA-CTGTCTCAAGGGAGACAAAATT
* * *
68283 TGTCTCAAGGGAGATTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
* * *
68319 TATTTCAAGGGAAACCGTCTCAAGGGAGACAATATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
68355 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
68391 T
1 T
68392 TTCTGTTTCG
Statistics
Matches: 239, Mismatches: 34, Indels: 35
0.78 0.11 0.11
Matches are distributed among these distances:
30 8 0.03
31 4 0.02
32 1 0.00
34 1 0.00
35 5 0.02
36 172 0.72
37 4 0.02
38 6 0.03
39 29 0.12
41 4 0.02
42 5 0.02
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATT
Found at i:68220 original size:21 final size:20
Alignment explanation
Indices: 68194--68279 Score: 83
Period size: 21 Copynumber: 4.4 Consensus size: 20
68184 GGAAACTGTC
68194 TCAAGGGAGACAAAATATGTT
1 TCAAGGGAGACAAAAT-TGTT
68215 TCAAGGGAGACAAAACTTGTT
1 TCAAGGGAGACAAAA-TTGTT
* * *
68236 TC----GAGA-GAAACTGTC
1 TCAAGGGAGACAAAATTGTT
68251 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAA-TTGTT
68272 TCAAGGGA
1 TCAAGGGA
68280 AATTGTCTCA
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
15 5 0.10
16 3 0.06
17 4 0.08
19 4 0.08
20 3 0.06
21 32 0.62
22 1 0.02
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (20 bp):
TCAAGGGAGACAAAATTGTT
Found at i:68246 original size:57 final size:57
Alignment explanation
Indices: 68158--68330 Score: 189
Period size: 57 Copynumber: 3.1 Consensus size: 57
68148 GGAAACCGTC
* * *
68158 TCAAGAGAGGCAAAATTTGTTTCAATGGAAACTGTCTCAAGGGAGACAAAATATGTT
1 TCAAGGGAGACAAAACTTGTTTCAATGGAAACTGTCTCAAGGGAGACAAAATATGTT
* *
68215 TCAAGGGAGACAAAACTTGTTTCGA-GAGAAACTGTCTCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAACTTGTTTCAATG-GAAACTGTCTCAAGGGAGACAAAATATGTT
* * * * * *
68272 TCAA-GG-G---AAA-TTGTCTCAAGGGAGATTGTCTCAAGGGAGACAAAATTTATT
1 TCAAGGGAGACAAAACTTGTTTCAATGGAAACTGTCTCAAGGGAGACAAAATATGTT
68323 TCAAGGGA
1 TCAAGGGA
68331 AACCGTCTCA
Statistics
Matches: 102, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
51 38 0.37
52 6 0.06
55 1 0.01
56 3 0.03
57 54 0.53
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (57 bp):
TCAAGGGAGACAAAACTTGTTTCAATGGAAACTGTCTCAAGGGAGACAAAATATGTT
Found at i:68310 original size:15 final size:15
Alignment explanation
Indices: 68267--68311 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
68257 GAGACAAAAT
* *
68267 TTGTTTCAAGGGAAA
1 TTGTCTCAAGGGAGA
68282 TTGTCTCAAGGGAGA
1 TTGTCTCAAGGGAGA
68297 TTGTCTCAAGGGAGA
1 TTGTCTCAAGGGAGA
68312 CAAAATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.29, C:0.11, G:0.31, T:0.29
Consensus pattern (15 bp):
TTGTCTCAAGGGAGA
Found at i:68325 original size:51 final size:51
Alignment explanation
Indices: 68247--68347 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 51
68237 CGAGAGAAAC
* **
68247 TGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATTGTCTCAAGGGAGAT
1 TGTCTCAAGGGAGACAAAATTTATTTCAAGGGAAACCGTCTCAAGGGAGAT
68298 TGTCTCAAGGGAGACAAAATTTATTTCAAGGGAAACCGTCTCAAGGGAGA
1 TGTCTCAAGGGAGACAAAATTTATTTCAAGGGAAACCGTCTCAAGGGAGA
68348 CAATATTTGT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.25
Consensus pattern (51 bp):
TGTCTCAAGGGAGACAAAATTTATTTCAAGGGAAACCGTCTCAAGGGAGAT
Found at i:68755 original size:34 final size:34
Alignment explanation
Indices: 68715--68803 Score: 142
Period size: 34 Copynumber: 2.6 Consensus size: 34
68705 TCTCAGAGAA
* **
68715 AAATTGTCTCAAGCGAGACGGAATTTGTTTTGAG
1 AAATTGTCTCAAGTGAGACAAAATTTGTTTTGAG
68749 AAATTGTCTCAAGTGAGACAAAATTTGTTTTGAG
1 AAATTGTCTCAAGTGAGACAAAATTTGTTTTGAG
*
68783 AAATTATCTCAAGTGAGACAA
1 AAATTGTCTCAAGTGAGACAA
68804 TTTTTTTAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Consensus pattern (34 bp):
AAATTGTCTCAAGTGAGACAAAATTTGTTTTGAG
Found at i:68972 original size:33 final size:32
Alignment explanation
Indices: 68907--69043 Score: 177
Period size: 33 Copynumber: 4.2 Consensus size: 32
68897 AGGATATTGA
* * * *
68907 ATGCCCC-AATATTCGATATTGAATCACAAAAG
1 ATGCCCCAAAT-TTTGATGTTGAATCTCCAAAG
68939 ATGCCCCAACATTTTGATGTTGAATCTCCAAAG
1 ATGCCCCAA-ATTTTGATGTTGAATCTCCAAAG
*
68972 ATGCCCCCAATATTTGATGTTGAATCTCCAAAG
1 ATGCCCCAAAT-TTTGATGTTGAATCTCCAAAG
*
69005 ATGCCCCAAACTTTTGATGTTGAATCTTCAAAG
1 ATGCCCCAAA-TTTTGATGTTGAATCTCCAAAG
69038 ATGCCC
1 ATGCCC
69044 TCTATTGCTT
Statistics
Matches: 94, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
32 9 0.10
33 82 0.87
34 3 0.03
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (32 bp):
ATGCCCCAAATTTTGATGTTGAATCTCCAAAG
Found at i:69012 original size:66 final size:66
Alignment explanation
Indices: 68910--69043 Score: 207
Period size: 66 Copynumber: 2.0 Consensus size: 66
68900 ATATTGAATG
68910 CCCCAATATTCGATATTGAATCACAAAAGATGCCCC-AACATTTTGATGTTGAATCTCCAAAGAT
1 CCCCAATATTCGATATTGAATCACAAAAGATGCCCCAAAC-TTTTGATGTTGAATCTCCAAAGAT
68974 GC
65 GC
* * * * *
68976 CCCCAATATTTGATGTTGAATCTCCAAAGATGCCCCAAACTTTTGATGTTGAATCTTCAAAGATG
1 CCCCAATATTCGATATTGAATCACAAAAGATGCCCCAAACTTTTGATGTTGAATCTCCAAAGATG
69041 C
66 C
69042 CC
1 CC
69044 TCTATTGCTT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
66 59 0.95
67 3 0.05
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (66 bp):
CCCCAATATTCGATATTGAATCACAAAAGATGCCCCAAACTTTTGATGTTGAATCTCCAAAGATG
C
Found at i:74515 original size:16 final size:18
Alignment explanation
Indices: 74494--74532 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
74484 ATATCTTTTT
74494 AAAAAT-AATTTTAAGA-
1 AAAAATCAATTTTAAGAC
*
74510 AAAAATCATTTTTAAGAC
1 AAAAATCAATTTTAAGAC
74528 AAAAA
1 AAAAA
74533 GCTAGTCTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 9 0.45
18 5 0.25
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (18 bp):
AAAAATCAATTTTAAGAC
Found at i:74960 original size:2 final size:2
Alignment explanation
Indices: 74953--74982 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
74943 CAAGGGTAAT
74953 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
74983 ATTTACCCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:75089 original size:2 final size:2
Alignment explanation
Indices: 75082--75118 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
75072 GGGTAAATTA
75082 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
75119 AACAGTAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:75514 original size:16 final size:15
Alignment explanation
Indices: 75463--75506 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
75453 ATTAAATCGG
75463 AATAAAATCAAAAATCA
1 AATAAAA-C-AAAATCA
*
75480 AATCAAAACAAAACCA
1 AAT-AAAACAAAATCA
75496 AATAAAACAAA
1 AATAAAACAAA
75507 CATTAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 8 0.32
16 9 0.36
17 4 0.16
18 4 0.16
ACGTcount: A:0.73, C:0.16, G:0.00, T:0.11
Consensus pattern (15 bp):
AATAAAACAAAATCA
Done.