Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002344.1 Hibiscus syriacus cultivar Beakdansim tig00004785_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: 91325
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3555 original size:148 final size:146
Alignment explanation
Indices: 3254--3555 Score: 452
Period size: 147 Copynumber: 2.0 Consensus size: 146
3244 TCCTCATACG
3254 GTTAGGGATGTTTTGTAACGAGGTCCTTTAGGTGGTGTACTTTGTAATATATTTTTAAGACAAAT
1 GTTAGGGATGTTTTGTAACGAGGTCCTTTAGGTGGTGTACTTTGTAATATATTTTTAAGACAAAT
3319 ACCCTCTTTAAAAAATATATATATTTGTTGGGGGGGGGTTTAAGCCAACATGTAAGAGATTTATT
66 ACCCTCTTTAAAAAATATATATATTTGTTGGGGGGGGGTTTAAGCCAACATGTAAGAGATTTATT
** *
3384 TTAATTTTTCCTCATA
131 TTAATTTTGACTAATA
3400 CGGTTAGGGATGTTTTGTAACGAGGTCCTTTAGGT-GTGTACTTTGTAATATA-TTTTAAGACAA
1 --GTTAGGGATGTTTTGTAACGAGGTCCTTTAGGTGGTGTACTTTGTAATATATTTTTAAGAC-A
*
3463 AATACCCTCTTTAAAAAA-ATATATATTTTTTTGGGGGGGGGGGGGTTTAAGCCAACATGTAAGA
63 AATACCCTCTTTAAAAAATATATATA-TTTGTT----GGGGGGGGGTTTAAGCCAACATGTAAGA
3527 GATTTATTTTTAATTTTGAC-AATA
123 GATTTA-TTTTAATTTTGACTAATA
3551 -TTAGG
1 GTTAGG
3556 TTGAAATTGG
Statistics
Matches: 143, Mismatches: 4, Indels: 14
0.89 0.02 0.09
Matches are distributed among these distances:
146 16 0.11
147 41 0.29
148 38 0.27
151 37 0.26
152 11 0.08
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (146 bp):
GTTAGGGATGTTTTGTAACGAGGTCCTTTAGGTGGTGTACTTTGTAATATATTTTTAAGACAAAT
ACCCTCTTTAAAAAATATATATATTTGTTGGGGGGGGGTTTAAGCCAACATGTAAGAGATTTATT
TTAATTTTGACTAATA
Found at i:6845 original size:2 final size:2
Alignment explanation
Indices: 6801--6834 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6791 GCATGTAGTC
6801 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
6835 TGATGTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17507 original size:30 final size:29
Alignment explanation
Indices: 17471--17567 Score: 110
Period size: 30 Copynumber: 3.3 Consensus size: 29
17461 CGTTGAACTC
*
17471 CCTCCAGTTGTAAAACCTCCAATTACACTT
1 CCTCCAGTTGT-AAACCACCAATTACACTT
* * *
17501 CCTCCAG-TG-AAGCCACCAGTTGA-ACTC
1 CCTCCAGTTGTAAACCACCAATT-ACACTT
17528 CCTCCAGTTGTTAAACCACCAATTACACTT
1 CCTCCAGTTG-TAAACCACCAATTACACTT
17558 CCTCCAGTTG
1 CCTCCAGTTG
17568 AACTTCCTCC
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
27 19 0.35
28 3 0.05
29 3 0.05
30 30 0.55
ACGTcount: A:0.27, C:0.35, G:0.11, T:0.27
Consensus pattern (29 bp):
CCTCCAGTTGTAAACCACCAATTACACTT
Found at i:17523 original size:57 final size:57
Alignment explanation
Indices: 17450--17682 Score: 215
Period size: 57 Copynumber: 4.0 Consensus size: 57
17440 TCCTCCGGTG
* *
17450 GTGAAGCCACCCGTTGAACTCCCTCCAGTTGTAAAACCTCCAATTACACTTCCTCCA
1 GTGAAGCCACCAGTTGAACTCCCTCCAGTTGTAAAACCACCAATTACACTTCCTCCA
*
17507 GTGAAGCCACCAGTTGAACTCCCTCCAGTTGTTAAACCACCAATTACACTTCCTCCA
1 GTGAAGCCACCAGTTGAACTCCCTCCAGTTGTAAAACCACCAATTACACTTCCTCCA
* * * * ** * ** * ***
17564 GTTGAACTTCCTCCAGCAGTGAAAC-CAC-CC--TT-TACACTTCCTCCGGTGAGTGTTCCTCCA
1 G-TGAA--GCCACCAG--TTG-AACTCCCTCCAGTTGTA-A-AACCACCAATTACACTTCCTCCA
17624 GTGAAGCCACCAGTTGAACTCCCTCCAGTTGTAAAACCACCAATTACACTTCCTCCA
1 GTGAAGCCACCAGTTGAACTCCCTCCAGTTGTAAAACCACCAATTACACTTCCTCCA
17681 GT
1 GT
17683 TGAACTACCT
Statistics
Matches: 133, Mismatches: 30, Indels: 26
0.70 0.16 0.14
Matches are distributed among these distances:
54 3 0.02
55 4 0.03
56 2 0.02
57 77 0.58
58 8 0.06
59 9 0.07
60 21 0.16
61 2 0.02
62 4 0.03
63 3 0.02
ACGTcount: A:0.26, C:0.35, G:0.14, T:0.25
Consensus pattern (57 bp):
GTGAAGCCACCAGTTGAACTCCCTCCAGTTGTAAAACCACCAATTACACTTCCTCCA
Found at i:17535 original size:27 final size:27
Alignment explanation
Indices: 17450--17535 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 27
17440 TCCTCCGGTG
*
17450 GTGAAGCCACCCGTTGAACTCCCTCCA
1 GTGAAGCCACCAGTTGAACTCCCTCCA
* * * *
17477 GTTGTAAAACCTCCAATT-ACACTTCCTCCA
1 G-TG--AAGCCACCAGTTGA-ACTCCCTCCA
17507 GTGAAGCCACCAGTTGAACTCCCTCCA
1 GTGAAGCCACCAGTTGAACTCCCTCCA
17534 GT
1 GT
17536 TGTTAAACCA
Statistics
Matches: 45, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
27 21 0.47
28 3 0.07
29 3 0.07
30 18 0.40
ACGTcount: A:0.26, C:0.36, G:0.15, T:0.23
Consensus pattern (27 bp):
GTGAAGCCACCAGTTGAACTCCCTCCA
Found at i:17566 original size:45 final size:45
Alignment explanation
Indices: 17516--17607 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 45
17506 AGTGAAGCCA
** *
17516 CCAGTTGAACTCCCTCCAGTTGTTAAACCACCAATTACACTTCCT
1 CCAGTTGAACTCCCTCCAGCAGTGAAACCACCAATTACACTTCCT
* **
17561 CCAGTTGAACTTCCTCCAGCAGTGAAACCACCCTTTACACTTCCT
1 CCAGTTGAACTCCCTCCAGCAGTGAAACCACCAATTACACTTCCT
17606 CC
1 CC
17608 GGTGAGTGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.25, C:0.38, G:0.10, T:0.27
Consensus pattern (45 bp):
CCAGTTGAACTCCCTCCAGCAGTGAAACCACCAATTACACTTCCT
Found at i:17622 original size:132 final size:131
Alignment explanation
Indices: 17481--17943 Score: 657
Period size: 132 Copynumber: 3.6 Consensus size: 131
17471 CCTCCAGTTG
* *
17481 TAAAACCTCCAATTACACTTCCTCCAGTGAAGCCACCAGTTGAACTCCCTCCAGTTGTTAAACCA
1 TAAAACCACCAATTACACTTCCTCCAGTGAAGCCACCAGTTGAACTCCCTCCAGTTGTAAAACCA
* **
17546 CCAATTACACTTCCTCCAGTTGAACTTCCTCCAGCAGTGAAACCACCCTTTACACTTCCTCCGG-
66 CCAATTACACTTCCTCCAGTTGAACTTCCTCCAGCAGTAAAACCACCAATTACACTTCCTCCGGT
17610 -
131 C
* * *
17610 T---------GAGT---GTTCCTCCAGTGAAGCCACCAGTTGAACTCCCTCCAGTTGTAAAACCA
1 TAAAACCACCAATTACACTTCCTCCAGTGAAGCCACCAGTTGAACTCCCTCCAGTTGTAAAACCA
* *
17663 CCAATTACACTTCCTCCAGTTGAACTACCTCCAGCAGTAAAACCACCAATTACACTTCCTCCAGC
66 CCAATTACACTTCCTCCAGTTGAACTTCCTCCAGCAGTAAAACCACCAATTACACTTCCTCC-GG
17728 TC
130 TC
* * *
17730 TAAAACCACCAATTACACTCCCCCCAGTGAAGCCACCAGTTGAACTCCCTCCAGTTTTAAAACCA
1 TAAAACCACCAATTACACTTCCTCCAGTGAAGCCACCAGTTGAACTCCCTCCAGTTGTAAAACCA
**
17795 CCAATTACACTTCCTCCAGTTGAACTTCCTCCAGCTCTAAAACCACCAATTACACTTCCTCCGGC
66 CCAATTACACTTCCTCCAGTTGAACTTCCTCCAGCAGTAAAACCACCAATTACACTTCCTCCGG-
17860 TC
130 TC
* *
17862 TAAAACCACCAATTACACTTCCTCCAGTGAAGTCACCAGTTGAACTTCCTCCAGTTGTAAAACCA
1 TAAAACCACCAATTACACTTCCTCCAGTGAAGCCACCAGTTGAACTCCCTCCAGTTGTAAAACCA
17927 CCAATTACACTTCCTCC
66 CCAATTACACTTCCTCC
17944 GGTTACTGTT
Statistics
Matches: 294, Mismatches: 24, Indels: 29
0.85 0.07 0.08
Matches are distributed among these distances:
117 104 0.35
118 1 0.00
120 3 0.01
129 3 0.01
131 1 0.00
132 182 0.62
ACGTcount: A:0.29, C:0.36, G:0.10, T:0.25
Consensus pattern (131 bp):
TAAAACCACCAATTACACTTCCTCCAGTGAAGCCACCAGTTGAACTCCCTCCAGTTGTAAAACCA
CCAATTACACTTCCTCCAGTTGAACTTCCTCCAGCAGTAAAACCACCAATTACACTTCCTCCGGT
C
Found at i:17650 original size:117 final size:117
Alignment explanation
Indices: 17499--17724 Score: 407
Period size: 117 Copynumber: 1.9 Consensus size: 117
17489 CCAATTACAC
*
17499 TTCCTCCAGTGAAGCCACCAGTTGAACTCCCTCCAGTTGTTAAACCACCAATTACACTTCCTCCA
1 TTCCTCCAGTGAAGCCACCAGTTGAACTCCCTCCAGTTGTAAAACCACCAATTACACTTCCTCCA
* * **
17564 GTTGAACTTCCTCCAGCAGTGAAACCACCCTTTACACTTCCTCCGGTGAGTG
66 GTTGAACTACCTCCAGCAGTAAAACCACCAATTACACTTCCTCCGGTGAGTG
17616 TTCCTCCAGTGAAGCCACCAGTTGAACTCCCTCCAGTTGTAAAACCACCAATTACACTTCCTCCA
1 TTCCTCCAGTGAAGCCACCAGTTGAACTCCCTCCAGTTGTAAAACCACCAATTACACTTCCTCCA
17681 GTTGAACTACCTCCAGCAGTAAAACCACCAATTACACTTCCTCC
66 GTTGAACTACCTCCAGCAGTAAAACCACCAATTACACTTCCTCC
17725 AGCTCTAAAA
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
117 104 1.00
ACGTcount: A:0.27, C:0.36, G:0.12, T:0.25
Consensus pattern (117 bp):
TTCCTCCAGTGAAGCCACCAGTTGAACTCCCTCCAGTTGTAAAACCACCAATTACACTTCCTCCA
GTTGAACTACCTCCAGCAGTAAAACCACCAATTACACTTCCTCCGGTGAGTG
Found at i:17684 original size:45 final size:45
Alignment explanation
Indices: 17633--17856 Score: 206
Period size: 45 Copynumber: 5.0 Consensus size: 45
17623 AGTGAAGCCA
*
17633 CCAGTTGAACTCCCTCCAGTTGTAAAACCACCAATTACACTTCCT
1 CCAGTTGAACTACCTCCAGTTGTAAAACCACCAATTACACTTCCT
**
17678 CCAGTTGAACTACCTCCAGCAGTAAAACCACCAATTACACTTCCT
1 CCAGTTGAACTACCTCCAGTTGTAAAACCACCAATTACACTTCCT
* * * ** *** * * * * *
17723 CCAGCTCT-AA-AACCACCAATTACACTCCCCCCAGTGA-A--GCCA
1 CCAG-T-TGAACTACCTCCAGTTGTAAAACCACCAATTACACTTCCT
* *
17765 CCAGTTGAACTCCCTCCAGTTTTAAAACCACCAATTACACTTCCT
1 CCAGTTGAACTACCTCCAGTTGTAAAACCACCAATTACACTTCCT
* * *
17810 CCAGTTGAACTTCCTCCAGCTCTAAAACCACCAATTACACTTCCT
1 CCAGTTGAACTACCTCCAGTTGTAAAACCACCAATTACACTTCCT
17855 CC
1 CC
17857 GGCTCTAAAA
Statistics
Matches: 137, Mismatches: 35, Indels: 14
0.74 0.19 0.08
Matches are distributed among these distances:
40 1 0.01
41 3 0.02
42 21 0.15
43 1 0.01
44 1 0.01
45 106 0.77
46 3 0.02
47 1 0.01
ACGTcount: A:0.30, C:0.38, G:0.08, T:0.24
Consensus pattern (45 bp):
CCAGTTGAACTACCTCCAGTTGTAAAACCACCAATTACACTTCCT
Found at i:17694 original size:72 final size:75
Alignment explanation
Indices: 17561--17757 Score: 197
Period size: 75 Copynumber: 2.7 Consensus size: 75
17551 TACACTTCCT
* * ** * ** *
17561 CCAGTTGAACTTCCTCCAGCAGTGAAACCACCCTTTACACTTCCTCC-GGTGAGTGTTCCT-C-C
1 CCAGTTGAACTTCCTCCAGCTGTAAAACCACCAATTACACTTCCTCCAGTTGAGACTACCTCCAC
* *
17623 AGTGAAGCCA
66 AGTAAAACCA
* *
17633 CCAGTTGAACTCCCTCCAGTTGTAAAACCACCAATTACACTTCCTCCAGTTGA-ACTACCTCCAG
1 CCAGTTGAACTTCCTCCAGCTGTAAAACCACCAATTACACTTCCTCCAGTTGAGACTACCTCCA-
17697 CAGTAAAACCA
65 CAGTAAAACCA
* * * *
17708 CCAATT-ACACTTCCTCCAGCTCTAAAACCACCAATTACACTCCCCCCAGT
1 CCAGTTGA-ACTTCCTCCAGCTGTAAAACCACCAATTACACTTCCTCCAGT
17758 GAAGCCACCA
Statistics
Matches: 102, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
72 45 0.44
73 5 0.05
74 1 0.01
75 51 0.50
ACGTcount: A:0.28, C:0.37, G:0.12, T:0.23
Consensus pattern (75 bp):
CCAGTTGAACTTCCTCCAGCTGTAAAACCACCAATTACACTTCCTCCAGTTGAGACTACCTCCAC
AGTAAAACCA
Found at i:17695 original size:15 final size:15
Alignment explanation
Indices: 17633--17696 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
17623 AGTGAAGCCA
*
17633 CCAGTTGAACTCCCT
1 CCAGTTGAACTACCT
* *
17648 CCAGTTGTAA-AACCA
1 CCAGTTG-AACTACCT
* *
17663 CCAATT-ACACTTCCT
1 CCAGTTGA-ACTACCT
17678 CCAGTTGAACTACCT
1 CCAGTTGAACTACCT
17693 CCAG
1 CCAG
17697 CAGTAAAACC
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
13 1 0.03
14 1 0.03
15 31 0.86
16 3 0.08
ACGTcount: A:0.28, C:0.36, G:0.11, T:0.25
Consensus pattern (15 bp):
CCAGTTGAACTACCT
Found at i:17814 original size:30 final size:29
Alignment explanation
Indices: 17700--17815 Score: 121
Period size: 30 Copynumber: 4.0 Consensus size: 29
17690 CCTCCAGCAG
* *
17700 TAAAACCACCAATTACACTTCCTCCAGCTC
1 TAAAACCACCAATTACACTCCCTCCAG-TT
*
17730 TAAAACCACCAATTACACTCCCCCCAG--
1 TAAAACCACCAATTACACTCCCTCCAGTT
* * *
17757 TGAAGCCACCAGTTGA-ACTCCCTCCAGTTT
1 TAAAACCACCAATT-ACACTCCCTCCAG-TT
*
17787 TAAAACCACCAATTACACTTCCTCCAGTT
1 TAAAACCACCAATTACACTCCCTCCAGTT
17816 GAACTTCCTC
Statistics
Matches: 71, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
27 21 0.30
28 1 0.01
29 3 0.04
30 46 0.65
ACGTcount: A:0.32, C:0.38, G:0.07, T:0.23
Consensus pattern (29 bp):
TAAAACCACCAATTACACTCCCTCCAGTT
Found at i:17854 original size:30 final size:30
Alignment explanation
Indices: 17818--17943 Score: 152
Period size: 30 Copynumber: 4.3 Consensus size: 30
17808 CTCCAGTTGA
17818 ACTTCCTCCAGCTCTAAAACCACCAATTAC
1 ACTTCCTCCAGCTCTAAAACCACCAATTAC
*
17848 ACTTCCTCCGGCTCTAAAACCACCAATTAC
1 ACTTCCTCCAGCTCTAAAACCACCAATTAC
* ** *
17878 ACTTCCTCCAG---TGAAGTCACCAGTTGA-
1 ACTTCCTCCAGCTCTAAAACCACCAATT-AC
* *
17905 ACTTCCTCCAGTTGTAAAACCACCAATTAC
1 ACTTCCTCCAGCTCTAAAACCACCAATTAC
17935 ACTTCCTCC
1 ACTTCCTCC
17944 GGTTACTGTT
Statistics
Matches: 81, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
27 21 0.26
28 1 0.01
29 1 0.01
30 58 0.72
ACGTcount: A:0.29, C:0.37, G:0.08, T:0.25
Consensus pattern (30 bp):
ACTTCCTCCAGCTCTAAAACCACCAATTAC
Found at i:17899 original size:102 final size:100
Alignment explanation
Indices: 17716--17918 Score: 223
Period size: 102 Copynumber: 2.0 Consensus size: 100
17706 CACCAATTAC
* * * *
17716 ACTTCCTCCAGCTCTAAAACCACCAATTACACTCCCCCCAGTGAAGCCACCAGTTGAACTCCCTC
1 ACTTCCTCCAGCTCTAAAACCACCAATTACACTCCCCCCACTAAAACCACCAATTGAACTCCCTC
17781 CAGTTTTAAAACCACCAATT-ACACTTCCTCCAGTTGA
66 CAG--TTAAAACCACCAATTGA-ACTTCCTCCAGTTGA
* * *
17818 ACTTCCTCCAGCTCTAAAACCACCAATTACACTTCCTCCGGCTCTAAAACCACCAATT-ACACTT
1 ACTTCCTCCAGCTCTAAAACCACCAATTACAC-TCC-CC-CCACTAAAACCACCAATTGA-ACTC
* ** *
17882 CCTCCAG-TGAAGTCACCAGTTGAACTTCCTCCAGTTG
62 CCTCCAGTTAAAACCACCAATTGAACTTCCTCCAGTTG
17919 TAAAACCACC
Statistics
Matches: 85, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
102 56 0.66
103 4 0.05
104 3 0.04
105 22 0.26
ACGTcount: A:0.29, C:0.37, G:0.09, T:0.25
Consensus pattern (100 bp):
ACTTCCTCCAGCTCTAAAACCACCAATTACACTCCCCCCACTAAAACCACCAATTGAACTCCCTC
CAGTTAAAACCACCAATTGAACTTCCTCCAGTTGA
Found at i:17955 original size:15 final size:15
Alignment explanation
Indices: 17937--18018 Score: 74
Period size: 15 Copynumber: 5.5 Consensus size: 15
17927 CCAATTACAC
* *
17937 TTCCTCCGGTTACTG
1 TTCCTCCGGTCACCG
* *
17952 TTCCTCCAGTCACGG
1 TTCCTCCGGTCACCG
* *
17967 TCCCTCCGGTGACCG
1 TTCCTCCGGTCACCG
* *
17982 TTCCTCCAGTCACGG
1 TTCCTCCGGTCACCG
* *
17997 TCCCTCCGGTGACCG
1 TTCCTCCGGTCACCG
18012 TTCCTCC
1 TTCCTCC
18019 TGTACTGAAG
Statistics
Matches: 51, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 51 1.00
ACGTcount: A:0.09, C:0.43, G:0.21, T:0.28
Consensus pattern (15 bp):
TTCCTCCGGTCACCG
Found at i:17975 original size:30 final size:30
Alignment explanation
Indices: 17939--18018 Score: 142
Period size: 30 Copynumber: 2.7 Consensus size: 30
17929 AATTACACTT
* *
17939 CCTCCGGTTACTGTTCCTCCAGTCACGGTC
1 CCTCCGGTGACCGTTCCTCCAGTCACGGTC
17969 CCTCCGGTGACCGTTCCTCCAGTCACGGTC
1 CCTCCGGTGACCGTTCCTCCAGTCACGGTC
17999 CCTCCGGTGACCGTTCCTCC
1 CCTCCGGTGACCGTTCCTCC
18019 TGTACTGAAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.09, C:0.44, G:0.21, T:0.26
Consensus pattern (30 bp):
CCTCCGGTGACCGTTCCTCCAGTCACGGTC
Found at i:23566 original size:22 final size:22
Alignment explanation
Indices: 23517--23595 Score: 97
Period size: 22 Copynumber: 3.6 Consensus size: 22
23507 TATGGGCTAA
* *
23517 GGGAATCGGTACCCATTC-AAT
1 GGGAATCGATACCCATTCAAAG
* * *
23538 GGGAATCGATACCTATTTAAGG
1 GGGAATCGATACCCATTCAAAG
*
23560 GGGAATCGGTACCCATTCAAAG
1 GGGAATCGATACCCATTCAAAG
23582 GGGAATCGATACCC
1 GGGAATCGATACCC
23596 CCTCAACCGA
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
21 15 0.32
22 32 0.68
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.22
Consensus pattern (22 bp):
GGGAATCGATACCCATTCAAAG
Found at i:25252 original size:105 final size:104
Alignment explanation
Indices: 25062--25284 Score: 259
Period size: 105 Copynumber: 2.1 Consensus size: 104
25052 GAGTCGAGGG
*
25062 TCTACGCGGTCCTTCGGGACATATAGGTATCCTATGGAACATCTATGAGGTCCTTTGAGACACGT
1 TCTACGTGGTCCTTCGGGACATATAGGTATCCTATGGAACATCTATGAGGTCCTTTGAGACACGT
* * * *
25127 ATTTGGTCTTTAGCATATGTATATGATTCTTAAAGAATTT
66 ACTTGATCCTTAGCACATGTATATGATTCTTAAAGAA-TT
* * * * * * *
25167 TCTACGTGGTCCTTCGGGACGTATATGTATTCTTTGGAGCATAC-ATGAGGTCTTTTGAGACACT
1 TCTACGTGGTCCTTCGGGACATATAGGTATCCTATGGAACAT-CTATGAGGTCCTTTGAGACACG
* * * *
25231 TACTTGATCCTTGGTACATGTATATGGTTCTTAAGGAATT
65 TACTTGATCCTTAGCACATGTATATGATTCTTAAAGAATT
* *
25271 TATATGTGGTCCTT
1 TCTACGTGGTCCTT
25285 ATGGACAATC
Statistics
Matches: 99, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
104 14 0.14
105 84 0.85
106 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (104 bp):
TCTACGTGGTCCTTCGGGACATATAGGTATCCTATGGAACATCTATGAGGTCCTTTGAGACACGT
ACTTGATCCTTAGCACATGTATATGATTCTTAAAGAATT
Found at i:25346 original size:23 final size:24
Alignment explanation
Indices: 25301--25346 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
25291 AATCTTATAT
*
25301 GGCACTACGGTGCAAATTCTACGC
1 GGCACTACGGTGCAAATTATACGC
*
25325 GGCACTTCGGTGC-AATTATACG
1 GGCACTACGGTGCAAATTATACG
25347 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (24 bp):
GGCACTACGGTGCAAATTATACGC
Found at i:29897 original size:2 final size:2
Alignment explanation
Indices: 29890--29922 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29880 TAAAATCACC
29890 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 A
29923 CTCAATGATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:37586 original size:2 final size:2
Alignment explanation
Indices: 37579--37616 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
37569 ATTTCTATTA
37579 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
37617 TCACTCTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39120 original size:29 final size:29
Alignment explanation
Indices: 39073--39155 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
39063 CTCACCTAAC
*
39073 TAAATTGATGTAAGTAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
39103 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
39132 TAAATGATGTAAGCAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
39156 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:43879 original size:29 final size:29
Alignment explanation
Indices: 43836--43918 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
43826 CTCACCTAAC
43836 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTACT
*
43866 TAAATGATGTAAGCAATGACATCTTTACT
1 TAAATGATGTAAGCAATGACATCATTACT
*
43895 TAAATGATGTAAGCAATGGCATCA
1 TAAATGATGTAAGCAATGACATCA
43919 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTACT
Found at i:45483 original size:31 final size:31
Alignment explanation
Indices: 45448--45522 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
45438 ATTGAGCTTG
45448 ACTCAACTCGAAAAGTTTAAAAT-TGAGTTCA
1 ACTCAACTCGAAAAGTTT-AAATGTGAGTTCA
* *
45479 ACTCAACTTGAAAAGTTTAAATGTGAGTTCG
1 ACTCAACTCGAAAAGTTTAAATGTGAGTTCA
45510 ACTCAACTC-AAAA
1 ACTCAACTCGAAAA
45523 TTGTCAAGCT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 8 0.20
31 32 0.80
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.28
Consensus pattern (31 bp):
ACTCAACTCGAAAAGTTTAAATGTGAGTTCA
Found at i:49404 original size:113 final size:112
Alignment explanation
Indices: 48986--49448 Score: 730
Period size: 112 Copynumber: 4.1 Consensus size: 112
48976 TTGTCGATTT
* * * *
48986 GTGTCGATAATTTATAAAATTATATTGATCCATAACAATATAACATGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
49051 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
49098 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGT-AAAAAATGACAAAACT
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * **
49162 GGTCTATAAATGACAAAACATGTAAATCGTTATAGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
49209 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
49274 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
49321 GTGTCGATATTTTATAAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATAACAAAAC
1 GTGTCGATACTTTAT-AAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAAC
* * * *
49386 CGATCTATAAATGACAAAACAGGTAAAGCGCTATCGGATATGTTGATA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
49434 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
49449 TATAAGTATC
Statistics
Matches: 323, Mismatches: 26, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
111 103 0.32
112 115 0.36
113 105 0.33
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:49626 original size:182 final size:181
Alignment explanation
Indices: 49318--49767 Score: 648
Period size: 182 Copynumber: 2.5 Consensus size: 181
49308 GGATATATTG
* * *
49318 AAAGTGTCGATATTTTATAAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATAACAA
1 AAAGTGTCGATACTTTAT-AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAA
* ** * * *
49383 AACCGATCTATAAATGACAAAACAGGTAAAGCGCTATCGGATATGTTGATAGTGTCGATACTTTA
65 AACCGGTCTCGAAATGA-AAAACAGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTA
* * * *
49448 TTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGATCTAAT
129 TTATAAGTATCGACACTTTTGAAATTTAAAAGAAAAGAAGTTATAGAGCCAAT
*
49501 AAAGTGTTGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* *
49566 ACCGGTCTCGAAATGAAAATACCGGTAAAGAGCTACCGGATATTTTGAAAGTGTCGATACTTTAT
66 ACCGGTCTCGAAATGAAAA-ACAGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTAT
* *
49631 TATAAGTATCGATACTTTTGAAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
130 TATAAGTATCGACACTTTTGAAATTTAAAAGAAAAGAAGTTATAGAGCCAAT
* * * *
49683 AAAATGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACATGTAAAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* * *
49748 ATCAGTCTCGAAATAAAAAA
66 ACCGGTCTCGAAATGAAAAA
49768 AACCGATAGT
Statistics
Matches: 240, Mismatches: 26, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
181 4 0.02
182 220 0.92
183 16 0.07
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.29
Consensus pattern (181 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ACCGGTCTCGAAATGAAAAACAGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTATT
ATAAGTATCGACACTTTTGAAATTTAAAAGAAAAGAAGTTATAGAGCCAAT
Found at i:50438 original size:23 final size:23
Alignment explanation
Indices: 50392--50439 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
50382 AAATATGTCA
* *
50392 ATATAAACGCTACTTATTACATT
1 ATATAAACGCTACCTAATACATT
*
50415 ATATAAACGCTACCTAATATATT
1 ATATAAACGCTACCTAATACATT
50438 AT
1 AT
50440 TATACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.38
Consensus pattern (23 bp):
ATATAAACGCTACCTAATACATT
Found at i:57121 original size:56 final size:56
Alignment explanation
Indices: 57054--57166 Score: 165
Period size: 56 Copynumber: 2.0 Consensus size: 56
57044 TTGTAGAAAT
* * *
57054 GCAAGTACACATCTTTCAATAG-ATTCTGATGATGTTCATGGGCCCACTGGAACCTG
1 GCAAGTACACATCTTTCAATAGAATT-TGATGATATTCACGGGCCAACTGGAACCTG
* *
57110 GCAAGTACACATCTTTCTATAGAATTTGATGATATTCACGGGCCAACTGGAATCTG
1 GCAAGTACACATCTTTCAATAGAATTTGATGATATTCACGGGCCAACTGGAACCTG
57166 G
1 G
57167 TATAGTCATC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
56 48 0.94
57 3 0.06
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (56 bp):
GCAAGTACACATCTTTCAATAGAATTTGATGATATTCACGGGCCAACTGGAACCTG
Found at i:58381 original size:58 final size:56
Alignment explanation
Indices: 58266--58388 Score: 142
Period size: 58 Copynumber: 2.2 Consensus size: 56
58256 TACTCCCTGA
* *
58266 CAACTTTTCCCAACTTGGTTTCTGATTTTTTTGTCCAAATTAGTTCCTAAACTTGG
1 CAACTTTTCCCAACTTGGTTTATGATTTTTTTGTCCAAATTAGTGCCTAAACTTGG
* * *
58322 CAACTTTTTCCAACTTGGTCCTTAT-ATTTTTTTGCTCCACATTAG-GCCTCGAACTTGG
1 CAACTTTTCCCAACTTGGT--TTATGATTTTTTTG-TCCAAATTAGTGCCT-AAACTTGG
*
58380 CATCTTTTC
1 CAACTTTTC
58389 TGGTCCTTGA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
56 18 0.32
57 12 0.21
58 26 0.46
ACGTcount: A:0.20, C:0.24, G:0.12, T:0.44
Consensus pattern (56 bp):
CAACTTTTCCCAACTTGGTTTATGATTTTTTTGTCCAAATTAGTGCCTAAACTTGG
Found at i:62727 original size:7 final size:7
Alignment explanation
Indices: 62717--62768 Score: 70
Period size: 7 Copynumber: 7.4 Consensus size: 7
62707 CGGAGTGTGG
62717 CGGCGGA
1 CGGCGGA
62724 CGGCGGA
1 CGGCGGA
62731 CGGCAGG-
1 CGGC-GGA
62738 CGGCGGA
1 CGGCGGA
*
62745 CGGCGGT
1 CGGCGGA
*
62752 CGACGGA
1 CGGCGGA
62759 CGGCGGA
1 CGGCGGA
62766 CGG
1 CGG
62769 TGATGATTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
6 2 0.05
7 35 0.90
8 2 0.05
ACGTcount: A:0.13, C:0.29, G:0.56, T:0.02
Consensus pattern (7 bp):
CGGCGGA
Found at i:63891 original size:20 final size:19
Alignment explanation
Indices: 63866--63919 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
63856 GCGAAATAAA
63866 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
63886 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
63906 AATCGCAACGCGAT
1 AATCGCAACGCGAT
63920 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:63930 original size:21 final size:20
Alignment explanation
Indices: 63906--64038 Score: 74
Period size: 20 Copynumber: 6.5 Consensus size: 20
63896 CAGTTCCCAG
63906 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
* *
63926 GAATCGAAATGCGA-TA-GTACA
1 -AATCGCAACGCGATTATG-A-A
** * * *
63947 AATTCGCATTGCGATTTTCTAG
1 AA-TCGCAACGCGATTAT-GAA
*
63969 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGATTATGAA
**
63989 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGATTATGA-A
* *
64009 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGATTATGAA
*
64029 TATCGCAACG
1 AATCGCAACG
64039 AGCATCCGTA
Statistics
Matches: 85, Mismatches: 19, Indels: 17
0.70 0.16 0.14
Matches are distributed among these distances:
19 2 0.02
20 46 0.54
21 33 0.39
22 3 0.04
23 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:63994 original size:20 final size:20
Alignment explanation
Indices: 63969--64243 Score: 168
Period size: 20 Copynumber: 13.7 Consensus size: 20
63959 GATTTTCTAG
*
63969 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
63989 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* *
64009 AATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * *
64029 TATCGCAACGAGCATCCGTAA
1 AATCGCAACGCGAATACG-AA
64050 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
64071 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* *
64091 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* *
64111 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GAA
** *
64131 AATCGCAACAAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * *
64151 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
*
64171 AATTGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
64192 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
64212 AATCGCAACGCG-AT-CGATA
1 AATCGCAACGCGAATACGA-A
*
64231 ATTCGCAACGCGA
1 AATCGCAACGCGA
64244 TCTCCGGTAT
Statistics
Matches: 200, Mismatches: 41, Indels: 28
0.74 0.15 0.10
Matches are distributed among these distances:
18 2 0.01
19 17 0.09
20 130 0.65
21 51 0.25
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:64015 original size:40 final size:40
Alignment explanation
Indices: 63969--64246 Score: 221
Period size: 40 Copynumber: 6.9 Consensus size: 40
63959 GATTTTCTAG
* *
63969 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACATATA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGTATC-TATA
* ** * *
64009 AATCGCAACGCG-ATTCTGACTATCGCAACGAGCATCCGTA-A
1 AATCGCAACGCGAATAC-GAAAATCGCAACGCGTAT-C-TATA
**
64050 AATCGCAACGAC-AATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACG-CGAATACG-AAAATCGCAACGCGTATCTATA
* * *
64091 AATCGCAACGAGAATACGTAAATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGTATCTATA
** * * **
64131 AATCGCAACAAGAATACGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAAAATCGCAACGCGTATCTATA
* **
64171 AATTGCAACGAC-AATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACG-CGAATACG-AAAATCGCAACGCGTATCTATA
*
64212 AATCGCAACGCG-AT-CGATAATTCGCAACGCG-ATCT
1 AATCGCAACGCGAATACGA-AAATCGCAACGCGTATCT
64247 CCGGTATCGC
Statistics
Matches: 198, Mismatches: 28, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
38 4 0.02
39 16 0.08
40 98 0.49
41 60 0.30
42 20 0.10
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (40 bp):
AATCGCAACGCGAATACGAAAATCGCAACGCGTATCTATA
Found at i:64335 original size:22 final size:21
Alignment explanation
Indices: 64293--64345 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
64283 ATTCTGACTA
64293 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* *
64314 TCGCGTTGCGATTTTCCTAAA-
1 TCGCATTGCGA-TTTCCCAAAT
*
64335 TCGCAATGCGA
1 TCGCATTGCGA
64346 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:65246 original size:24 final size:24
Alignment explanation
Indices: 65219--65272 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
65209 GTATTCGAAA
65219 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
65243 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
65267 TTTGAT
1 TTTGAT
65273 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:65929 original size:20 final size:20
Alignment explanation
Indices: 65904--66117 Score: 216
Period size: 20 Copynumber: 10.6 Consensus size: 20
65894 AATTATCGAT
65904 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
65924 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
65944 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * * *
65965 CGCATTGCGATTTATGTATT
1 CGCGTTGCGATTTACGGATA
* * *
65985 CTCGTTGTGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
66005 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
66025 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
66045 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
66065 TGTCATTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
66086 CACGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
* *
66107 CTCGTTACGAT
1 CGCGTTGCGAT
66118 AGTCAGAATC
Statistics
Matches: 156, Mismatches: 31, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
20 106 0.68
21 50 0.32
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:65953 original size:41 final size:41
Alignment explanation
Indices: 65906--66102 Score: 301
Period size: 40 Copynumber: 4.9 Consensus size: 41
65896 TTATCGATCG
65906 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
* * *
65947 CGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
* *
65987 CGTTGTGATTTACAGATACGCGTTGCGA-TTTACGTATTCG-
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATT-GT
66027 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
* *
66068 CATTGCGATTTACGGATACACGTTGCGATTTTACG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACG
66103 GATACTCGTT
Statistics
Matches: 141, Mismatches: 12, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
40 71 0.50
41 70 0.50
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
Found at i:65997 original size:40 final size:40
Alignment explanation
Indices: 65906--66117 Score: 289
Period size: 41 Copynumber: 5.2 Consensus size: 40
65896 TTATCGATCG
*
65906 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
* *
65947 CGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
* * *
65987 CGTTGTGATTTACAGATACGCGTTGCGATTTACGTATTCG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
*
66027 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
* * * *
66068 CATTGCGATTTACGGATACACGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
*
66109 CGTTACGAT
1 CGTTGCGAT
66118 AGTCAGAATC
Statistics
Matches: 151, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
40 71 0.47
41 80 0.53
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
Found at i:66149 original size:20 final size:20
Alignment explanation
Indices: 66126--66178 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
66116 ATAGTCAGAA
*
66126 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
* *
66146 TCGCATTGTGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
*
66166 TCGCGATGCGATT
1 TCGCGTTGCGATT
66179 CTGGAAAATC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:66277 original size:20 final size:19
Alignment explanation
Indices: 66228--66281 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
66218 ATTCTTCATA
66228 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
66247 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
66268 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
66282 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:72828 original size:19 final size:20
Alignment explanation
Indices: 72793--72830 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
72783 AATGGATTTG
72793 GATGATGAAAAGAAGAAGAC
1 GATGATGAAAAGAAGAAGAC
*
72813 GATGATG-AAGGAAGAAGA
1 GATGATGAAAAGAAGAAGA
72831 TATCGTCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.53, C:0.03, G:0.34, T:0.11
Consensus pattern (20 bp):
GATGATGAAAAGAAGAAGAC
Found at i:84228 original size:23 final size:23
Alignment explanation
Indices: 84202--84250 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
84192 TCATACTTAA
*
84202 CTCGATTGAAGCTCAAACTCAAG
1 CTCGATTGAAGCTCAAACGCAAG
* * *
84225 CTCGATTTAAGTTCTAACGCAAG
1 CTCGATTGAAGCTCAAACGCAAG
84248 CTC
1 CTC
84251 AAATTTGCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.27
Consensus pattern (23 bp):
CTCGATTGAAGCTCAAACGCAAG
Found at i:84302 original size:21 final size:22
Alignment explanation
Indices: 84278--84318 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
84268 GACAACGCCG
*
84278 TAATTGTCAA-ATAAATAAACC
1 TAATTCTCAATATAAATAAACC
*
84299 TAATTCTCAATTTAAATAAA
1 TAATTCTCAATATAAATAAA
84319 TAAAGTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.34
Consensus pattern (22 bp):
TAATTCTCAATATAAATAAACC
Found at i:85117 original size:20 final size:20
Alignment explanation
Indices: 85088--85130 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
85078 TTAGCATTGT
85088 AAAAAGAAAATA-ATGAAAGA
1 AAAAAGAAAA-AGATGAAAGA
* *
85108 AAAAATAAAAAGATGAAATA
1 AAAAAGAAAAAGATGAAAGA
85128 AAA
1 AAA
85131 GTATAACTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (20 bp):
AAAAAGAAAAAGATGAAAGA
Done.