Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015149.1 Corchorus olitorius cultivar O-4 contig15182, 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: 262315
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:15264 original size:18 final size:18
Alignment explanation
Indices: 15241--15279 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
15231 AAATATCGGA
15241 CGGGCTTACGGGCTTGGG
1 CGGGCTTACGGGCTTGGG
15259 CGGGCTTACGGGCTTGGG
1 CGGGCTTACGGGCTTGGG
15277 CGG
1 CGG
15280 ATAGCCCGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.05, C:0.23, G:0.51, T:0.21
Consensus pattern (18 bp):
CGGGCTTACGGGCTTGGG
Found at i:17071 original size:130 final size:130
Alignment explanation
Indices: 16926--17188 Score: 404
Period size: 130 Copynumber: 2.0 Consensus size: 130
16916 TTGTTTAAAC
* * *
16926 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATCAAATCTAATATCCTTATAACTA
* **
16991 TTTTATTTTTACCATTTTACTATTTTAATTAAAAAAAACTT-ATATATTAGAATT-TTTTAATAT
66 TTTTATTTTTACCATTTTACTAATTTAATT--AAAAAACTTAATATATTAGAATTGTTAGAATAT
17054 AT
129 AT
* *
17056 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATCAAATCTAATATCTTTATACCTA
1 TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATCAAATCTAATATCCTTATAACTA
*
17121 TTTTATTTTTACTATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTGTTAGAATATA
66 TTTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTA-ATATATTAGAATTGTTAGAATATA
17186 T
130 T
17187 TT
1 TT
17189 CTTAAATAAC
Statistics
Matches: 121, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
128 9 0.07
130 101 0.83
131 11 0.09
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (130 bp):
TTTTATAATTTTACTCAACTAAAAACTCTATTTCTATTTAATCAAATCTAATATCCTTATAACTA
TTTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTAATATATTAGAATTGTTAGAATATAT
Found at i:19493 original size:5 final size:5
Alignment explanation
Indices: 19483--19512 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
19473 AATAATAGTT
19483 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
19513 ACCAAGGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:27276 original size:1 final size:1
Alignment explanation
Indices: 27270--27302 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
27260 CTTATGAATT
27270 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
27303 CTCTAATTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:30198 original size:69 final size:70
Alignment explanation
Indices: 30069--30209 Score: 230
Period size: 69 Copynumber: 2.0 Consensus size: 70
30059 AAATATATAT
* *
30069 ATGTTTGATTTGAGAAGCAAAATTTCTAATAATTGGTATAAGCCTTTTAGTATCTAACAGTTACG
1 ATGTTTGATTTGAGAAGCAAAATTTC--ATAATTGATATAAGCCCTTTAGTATCTAACAGTTACG
*
30134 TTGAATC
64 TAGAATC
30141 ATGTTTGATTTGAGAAGCAAAATTTC-TAATTGATATAAGCCCTTTAGTATCTAACAGTTACGTA
1 ATGTTTGATTTGAGAAGCAAAATTTCATAATTGATATAAGCCCTTTAGTATCTAACAGTTACGTA
30205 GAATC
66 GAATC
30210 CCGATTAATT
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
69 40 0.61
72 26 0.39
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (70 bp):
ATGTTTGATTTGAGAAGCAAAATTTCATAATTGATATAAGCCCTTTAGTATCTAACAGTTACGTA
GAATC
Found at i:39530 original size:30 final size:30
Alignment explanation
Indices: 39494--39572 Score: 106
Period size: 30 Copynumber: 2.6 Consensus size: 30
39484 ATCGTTTGAG
* *
39494 AGGGGGCAAAACATCCAAAATTGAGAGTTT-
1 AGGGGGCAAAACGTCCAAAATTGA-AATTTC
*
39524 AGGGGGCAAAATGTCCAAAATTGAAATTTC
1 AGGGGGCAAAACGTCCAAAATTGAAATTTC
*
39554 AGAGGGCAAAACGTCCAAA
1 AGGGGGCAAAACGTCCAAA
39573 CGATACAAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 4 0.09
30 39 0.91
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.18
Consensus pattern (30 bp):
AGGGGGCAAAACGTCCAAAATTGAAATTTC
Found at i:57405 original size:35 final size:35
Alignment explanation
Indices: 57354--57421 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
57344 CTATAATAAT
* *
57354 GTGGTTTGTTGGTAGAGTGCTCGATTATGAGTTGC
1 GTGGTTTGTTGATAGAGTGCTCGATTACGAGTTGC
57389 GTGGTTTGTTGATAGAGTGCTCGATTACGAGTT
1 GTGGTTTGTTGATAGAGTGCTCGATTACGAGTT
57422 CAAGTGATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.16, C:0.09, G:0.35, T:0.40
Consensus pattern (35 bp):
GTGGTTTGTTGATAGAGTGCTCGATTACGAGTTGC
Found at i:57994 original size:60 final size:60
Alignment explanation
Indices: 57924--58081 Score: 253
Period size: 60 Copynumber: 2.6 Consensus size: 60
57914 GCTAATTGCT
* * *
57924 CAAATAAGGGTCTAATATTTACCAAAATGTTCAAATAAGGGCATGATCTTTTAATTTGGC
1 CAAATAAGGGTCTAATATTTGCCAAAATGCTCAAATAAGGACATGATCTTTTAATTTGGC
*
57984 CAAATAAGGGTCTAATATTTGTCAAAATGCTCAAATAAGGACATGATCTTTTAATTTGGC
1 CAAATAAGGGTCTAATATTTGCCAAAATGCTCAAATAAGGACATGATCTTTTAATTTGGC
* **
58044 CAAATAAGGATCTAACGTTTGCCAAAATGCTCAAATAA
1 CAAATAAGGGTCTAATATTTGCCAAAATGCTCAAATAA
58082 AGGCCTGGCG
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 90 1.00
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (60 bp):
CAAATAAGGGTCTAATATTTGCCAAAATGCTCAAATAAGGACATGATCTTTTAATTTGGC
Found at i:58022 original size:31 final size:30
Alignment explanation
Indices: 57920--58023 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 30
57910 TTTGGCTAAT
*
57920 TGCTCAAATAAGGGTCTAATATTTACCAAAA
1 TGCTCAAATAAGGGTCTAATATTT-TCAAAA
* * * **
57951 TGTTCAAATAAGGG-CATGATCTTTT-AATT
1 TGCTCAAATAAGGGTC-TAATATTTTCAAAA
57980 TGGC-CAAATAAGGGTCTAATATTTGTCAAAA
1 T-GCTCAAATAAGGGTCTAATATTT-TCAAAA
58011 TGCTCAAATAAGG
1 TGCTCAAATAAGG
58024 ACATGATCTT
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
29 19 0.34
30 6 0.11
31 31 0.55
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (30 bp):
TGCTCAAATAAGGGTCTAATATTTTCAAAA
Found at i:58052 original size:29 final size:29
Alignment explanation
Indices: 57955--58053 Score: 94
Period size: 29 Copynumber: 3.3 Consensus size: 29
57945 CCAAAATGTT
*
57955 CAAATAAGGGCATGATCTTTTAATTTGGC
1 CAAATAAGGACATGATCTTTTAATTTGGC
* * * **
57984 CAAATAAGGGTC-TAATATTTGTCAAAAT-GC
1 CAAATAA-GGACATGATCTTT-T-AATTTGGC
58014 TCAAATAAGGACATGATCTTTTAATTTGGC
1 -CAAATAAGGACATGATCTTTTAATTTGGC
58044 CAAATAAGGA
1 CAAATAAGGA
58054 TCTAACGTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
29 26 0.48
30 12 0.22
31 16 0.30
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.31
Consensus pattern (29 bp):
CAAATAAGGACATGATCTTTTAATTTGGC
Found at i:58204 original size:60 final size:60
Alignment explanation
Indices: 58130--58285 Score: 224
Period size: 60 Copynumber: 2.6 Consensus size: 60
58120 AATGTCAGAT
* *
58130 CCTTATTTGAGCATTTTTTATAACGTTAGGCCCTTATTTGGCCAAATTAAAAAATTGGAC
1 CCTTATTTGAGCATTTTTTATAACATTAGGCCCTTATTTGGCCAAATTAAAAAATCGGAC
* ** * *
58190 TCTTATTTGAGCATTTTCGATAACATTAGGTCCTTATTTGGCCAAATTAAAAGATCGGAC
1 CCTTATTTGAGCATTTTTTATAACATTAGGCCCTTATTTGGCCAAATTAAAAAATCGGAC
*
58250 CCTTATTTGAGCATTTTGTTA-AATATTAGGCCCTTA
1 CCTTATTTGAGCATTTT-TTATAACATTAGGCCCTTA
58286 CTTGAACAAT
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
60 82 0.99
61 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (60 bp):
CCTTATTTGAGCATTTTTTATAACATTAGGCCCTTATTTGGCCAAATTAAAAAATCGGAC
Found at i:65984 original size:60 final size:60
Alignment explanation
Indices: 65902--66038 Score: 204
Period size: 60 Copynumber: 2.3 Consensus size: 60
65892 GGCTAATTGC
* * *
65902 CCAAATAAGGGTCTAACGTTTGCCAAAATGT-TCAAATAAGGGTCTGATCTTTTAATTTGG
1 CCAAATAAGGGCCTAACATTTGCCAAAAT-TCTCAAATAAGGGCCTGATCTTTTAATTTGG
* *
65962 CCAAATAAGAGCCTAATATTTGCCAAAATTCTCAAATAAGGGCCTGATCTTTTAATTTGG
1 CCAAATAAGGGCCTAACATTTGCCAAAATTCTCAAATAAGGGCCTGATCTTTTAATTTGG
*
66022 CCAATTAAGGGCCTAAC
1 CCAAATAAGGGCCTAAC
66039 GTAGGGCCCG
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 1 0.01
60 67 0.99
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (60 bp):
CCAAATAAGGGCCTAACATTTGCCAAAATTCTCAAATAAGGGCCTGATCTTTTAATTTGG
Found at i:66045 original size:41 final size:41
Alignment explanation
Indices: 66000--66079 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
65990 TTCTCAAATA
* * *
66000 AGGGCCTGATCTTTTAATTTGGCCAATTAAGGGCCTAACGT
1 AGGGCCCGATCTTTTAATTTAGCCAAATAAGGGCCTAACGT
*
66041 AGGGCCCGATCTTTTAATTTAGCCAAATAAGGGTCTAAC
1 AGGGCCCGATCTTTTAATTTAGCCAAATAAGGGCCTAAC
66080 ATTTGCCAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (41 bp):
AGGGCCCGATCTTTTAATTTAGCCAAATAAGGGCCTAACGT
Found at i:66189 original size:31 final size:31
Alignment explanation
Indices: 66154--66258 Score: 99
Period size: 31 Copynumber: 3.5 Consensus size: 31
66144 AACTGATACC
66154 AGGCCCTTATTTGAACATTTTCGATAACATT
1 AGGCCCTTATTTGAACATTTTCGATAACATT
** ** * *
66185 AGGCCCTTATTTGGCCAAATT--AAAAGA-T
1 AGGCCCTTATTTGAACATTTTCGATAACATT
* **
66213 CGGACCCTTATTTGAGTATTTTCGATAACATT
1 AGG-CCCTTATTTGAACATTTTCGATAACATT
66245 AGGCCCTTATTTGA
1 AGGCCCTTATTTGA
66259 CCAAATTAAA
Statistics
Matches: 55, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
28 3 0.05
29 17 0.31
31 32 0.58
32 3 0.05
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (31 bp):
AGGCCCTTATTTGAACATTTTCGATAACATT
Found at i:66234 original size:60 final size:60
Alignment explanation
Indices: 66157--66326 Score: 252
Period size: 60 Copynumber: 2.9 Consensus size: 60
66147 TGATACCAGG
* *
66157 CCCTTATTTGAACATTTTCGATAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA
1 CCCTTATTTGAACATTTTCGATAACATTAGGCCCTTATTTGACCAAATTAAAAGATCGAA
**
66217 CCCTTATTTGAGTATTTTCGATAACATTAGGCCCTTATTTGACCAAATTAAAAGATCGAA
1 CCCTTATTTGAACATTTTCGATAACATTAGGCCCTTATTTGACCAAATTAAAAGATCGAA
* ** * *
66277 CCCTTATTTGAACATTTTCAATAATGTTAGACCCTTATTTGAAC-AATTAA
1 CCCTTATTTGAACATTTTCGATAACATTAGGCCCTTATTTGACCAAATTAA
66327 CCTAAATTGT
Statistics
Matches: 99, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
59 6 0.06
60 93 0.94
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (60 bp):
CCCTTATTTGAACATTTTCGATAACATTAGGCCCTTATTTGACCAAATTAAAAGATCGAA
Found at i:67669 original size:33 final size:33
Alignment explanation
Indices: 67632--67700 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
67622 GAAAAGAATT
*
67632 TTAAAACAAACA-AATCCAATATTTTAGTGGAAC
1 TTAAAACAAACATAAT-CAATATTTTAATGGAAC
** *
67665 TTAAAATTAACATAATCTATATTTTAATGGAAC
1 TTAAAACAAACATAATCAATATTTTAATGGAAC
67698 TTA
1 TTA
67701 TAAAACTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 28 0.90
34 3 0.10
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (33 bp):
TTAAAACAAACATAATCAATATTTTAATGGAAC
Found at i:74899 original size:21 final size:21
Alignment explanation
Indices: 74862--74917 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
74852 AGGCTAGGAT
*
74862 GCACCAGCAGCAACAGCAGCA
1 GCACCATCAGCAACAGCAGCA
* *
74883 GCATCATCAGCACCAGCAGCA
1 GCACCATCAGCAACAGCAGCA
*
74904 GCACCATCAACAAC
1 GCACCATCAGCAAC
74918 CTCCTGTTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.38, C:0.39, G:0.18, T:0.05
Consensus pattern (21 bp):
GCACCATCAGCAACAGCAGCA
Found at i:79554 original size:31 final size:31
Alignment explanation
Indices: 79516--79577 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
79506 GAGTTTTGTA
** *
79516 AAACTTTTGAATCGTTTATTATACCCTTATT
1 AAACTTTTGAATCGCCTATCATACCCTTATT
79547 AAACTTTTGAATCGCCTATCATACCCTTATT
1 AAACTTTTGAATCGCCTATCATACCCTTATT
79578 TTTTGAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (31 bp):
AAACTTTTGAATCGCCTATCATACCCTTATT
Found at i:85908 original size:28 final size:28
Alignment explanation
Indices: 85877--85952 Score: 75
Period size: 30 Copynumber: 2.7 Consensus size: 28
85867 AGTAATATTT
*
85877 ATAATTAAATATATATTATATATATAAA
1 ATAATTAAATATATATTATACATATAAA
* *
85905 ATAATATTAAATATATATAATTACATATATA
1 AT-A-ATTAAATATATATTA-TACATATAAA
*
85936 ATAA-TATATATA-ATTAT
1 ATAATTAAATATATATTAT
85953 TAAACGGTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
26 1 0.03
27 3 0.08
28 9 0.22
29 2 0.05
30 15 0.38
31 10 0.25
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (28 bp):
ATAATTAAATATATATTATACATATAAA
Found at i:85911 original size:21 final size:20
Alignment explanation
Indices: 85871--85952 Score: 68
Period size: 19 Copynumber: 4.3 Consensus size: 20
85861 CCGTTTAGTA
*
85871 ATATT-TATA-ATTAAATAT
1 ATATTATATATATAAAATAT
85889 ATATTATATATATAAAATA-
1 ATATTATATATATAAAATAT
* *
85908 ATATTAAATATATATAAT-T
1 ATATTATATATATAAAATAT
* *
85927 ACA-TATATA-ATAATATAT
1 ATATTATATATATAAAATAT
85945 ATAATTAT
1 AT-ATTAT
85953 TAAACGGTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
17 5 0.10
18 12 0.24
19 23 0.46
20 10 0.20
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATTATATATATAAAATAT
Found at i:85927 original size:14 final size:14
Alignment explanation
Indices: 85870--85951 Score: 59
Period size: 12 Copynumber: 6.0 Consensus size: 14
85860 ACCGTTTAGT
*
85870 AATATTTATAATTA
1 AATATATATAATTA
85884 AATATATATTATATATA
1 AATATATA-TA-AT-TA
*
85901 TAAAATA-AT-ATTA
1 -AATATATATAATTA
85914 AATATATATAATT-
1 AATATATATAATTA
*
85927 -ACATATATAA-T-
1 AATATATATAATTA
85938 AATATATATAATTA
1 AATATATATAATTA
85952 TTAAACGGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 18
0.70 0.06 0.23
Matches are distributed among these distances:
11 1 0.02
12 23 0.43
13 5 0.09
14 12 0.22
15 2 0.04
16 3 0.06
17 3 0.06
18 5 0.09
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (14 bp):
AATATATATAATTA
Found at i:100898 original size:4 final size:4
Alignment explanation
Indices: 100891--100929 Score: 62
Period size: 4 Copynumber: 9.8 Consensus size: 4
100881 GAAGAAGAAG
100891 AAGA AAGA AAGA AAGA AAGA AAGAA AAGA AA-A AAGA AAG
1 AAGA AAGA AAGA AAGA AAGA AAG-A AAGA AAGA AAGA AAG
100930 GTTTTGACAG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 3 0.09
4 26 0.79
5 4 0.12
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:102548 original size:30 final size:30
Alignment explanation
Indices: 102512--102689 Score: 311
Period size: 30 Copynumber: 5.9 Consensus size: 30
102502 TTGTGACGAA
*
102512 GCTGCTGCTGCTGTCGCTGAAGTTCCAACT
1 GCTGCTGCTGTTGTCGCTGAAGTTCCAACT
102542 GCTGCTGCTGTTGTCGCTGAAGTTCCAACT
1 GCTGCTGCTGTTGTCGCTGAAGTTCCAACT
102572 GCTGCTGCTGTTGTCGCTGAAGTTCCAACT
1 GCTGCTGCTGTTGTCGCTGAAGTTCCAACT
102602 GCTGCTGCTGTTGTCGCTGAAGTTCCAACT
1 GCTGCTGCTGTTGTCGCTGAAGTTCCAACT
102632 GCTGCTGCTGTTGTCGCTGAAGTTCCAACT
1 GCTGCTGCTGTTGTCGCTGAAGTTCCAACT
* ***
102662 GCCGCTGCTGTTGAAACTGAAGTTCCAA
1 GCTGCTGCTGTTGTCGCTGAAGTTCCAA
102690 AAGATGTTCC
Statistics
Matches: 143, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 143 1.00
ACGTcount: A:0.15, C:0.27, G:0.26, T:0.31
Consensus pattern (30 bp):
GCTGCTGCTGTTGTCGCTGAAGTTCCAACT
Found at i:104458 original size:5 final size:5
Alignment explanation
Indices: 104450--104483 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
104440 CAGAAAGGAA
104450 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
104484 AACAACAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:107615 original size:34 final size:34
Alignment explanation
Indices: 107567--107632 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
107557 GATGGGTCTA
107567 TTTTCACCACATTGGGTTATGATAATTTGCCTGT
1 TTTTCACCACATTGGGTTATGATAATTTGCCTGT
*
107601 TTTTCACCATATTGGGTTATGATAATTTGCCT
1 TTTTCACCACATTGGGTTATGATAATTTGCCT
107633 TGACCATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.45
Consensus pattern (34 bp):
TTTTCACCACATTGGGTTATGATAATTTGCCTGT
Found at i:107781 original size:21 final size:19
Alignment explanation
Indices: 107756--107813 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
107746 GCTGCTCTAA
107756 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
107777 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
107796 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
107814 TGCTAAACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:108025 original size:36 final size:36
Alignment explanation
Indices: 107978--108049 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
107968 CCATAAATTG
107978 TGATAATCCATTTTAGCCAATTTTAATCACAATCCA
1 TGATAATCCATTTTAGCCAATTTTAATCACAATCCA
108014 TGATAATCCATTTTAGCCAATTTTAATCACAATCCA
1 TGATAATCCATTTTAGCCAATTTTAATCACAATCCA
108050 ATCACCATGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (36 bp):
TGATAATCCATTTTAGCCAATTTTAATCACAATCCA
Found at i:111308 original size:30 final size:27
Alignment explanation
Indices: 111200--111291 Score: 175
Period size: 27 Copynumber: 3.4 Consensus size: 27
111190 TGGTGACGAA
111200 GCTGCTGCTGTCGCTGAAGTTCCAACT
1 GCTGCTGCTGTCGCTGAAGTTCCAACT
111227 GCTGCTGCTGTCGCTGAAGTTCCAACT
1 GCTGCTGCTGTCGCTGAAGTTCCAACT
*
111254 GCTGCTGCTGTCGCTGAAGTTCCAATT
1 GCTGCTGCTGTCGCTGAAGTTCCAACT
111281 GCTGCTGCTGT
1 GCTGCTGCTGT
111292 TGAAACTGAA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.13, C:0.28, G:0.27, T:0.32
Consensus pattern (27 bp):
GCTGCTGCTGTCGCTGAAGTTCCAACT
Found at i:128421 original size:67 final size:69
Alignment explanation
Indices: 128329--128556 Score: 336
Period size: 67 Copynumber: 3.3 Consensus size: 69
128319 ATTTCCCGCA
*
128329 ACAACTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTAATTTGCGTTCCTC-A
1 ACAAGTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTAATTTGCGTTCCTCAA
128393 -AGC
66 CAGC
* * * *
128396 ACAAGTCCAGGACAGGACTTGGGTAACTCCCGCCCAGGTCTTGTCCTGTAATTTGCGCTCTTCAA
1 ACAAGTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTAATTTGCGTTCCTCAA
128461 CAGC
66 CAGC
* **
128465 ACAAGTCC-GAGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTTTGTATTCCTC
1 ACAAGTCCTG-GACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTA-ATTTGCGTTCCTC
128529 AACAGC
64 AACAGC
*
128535 CCAAGTCCTGGACAGGACTTGG
1 ACAAGTCCTGGACAGGACTTGG
128557 CCAAGATCTG
Statistics
Matches: 144, Mismatches: 12, Indels: 7
0.88 0.07 0.04
Matches are distributed among these distances:
67 58 0.40
68 2 0.01
69 50 0.35
70 33 0.23
71 1 0.01
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (69 bp):
ACAAGTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTAATTTGCGTTCCTCAA
CAGC
Found at i:132547 original size:75 final size:75
Alignment explanation
Indices: 132424--132568 Score: 254
Period size: 75 Copynumber: 1.9 Consensus size: 75
132414 AGTTAGACCT
* * *
132424 CAAATGAAGAAACTCTTCCAATACCTATTTTCTCTATTCACAAGACTCGAACTTGAGACCTTGTT
1 CAAATGAAGAAACTCTTCCAATACCTATTTTCTATATTAACAAGACTCGAACTTGAGACCTTGCT
132489 TAAGATAACC
66 TAAGATAACC
*
132499 CAAATGAAGAAACTCTTCCAATACCTATTTTCTATATTAACAAGACTCGAACTTGAGACTTTGCT
1 CAAATGAAGAAACTCTTCCAATACCTATTTTCTATATTAACAAGACTCGAACTTGAGACCTTGCT
132564 TAAGA
66 TAAGA
132569 GACATTGAAC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 66 1.00
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (75 bp):
CAAATGAAGAAACTCTTCCAATACCTATTTTCTATATTAACAAGACTCGAACTTGAGACCTTGCT
TAAGATAACC
Found at i:133799 original size:29 final size:30
Alignment explanation
Indices: 133765--133823 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
133755 CATAAATAAT
*
133765 ATAATATAATTAAATAA-TTATATCTATAC
1 ATAATAAAATTAAATAATTTATATCTATAC
* *
133794 ATAATAAAATTGAATAATTTATATGTATAC
1 ATAATAAAATTAAATAATTTATATCTATAC
133824 TAAAACTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (30 bp):
ATAATAAAATTAAATAATTTATATCTATAC
Found at i:134892 original size:106 final size:103
Alignment explanation
Indices: 134638--134894 Score: 287
Period size: 101 Copynumber: 2.5 Consensus size: 103
134628 AGTTTTTCTA
** ** *
134638 ACCCTTAAAATAAAATTTTAATTTTAATTTAAG-CTAAACTTACTG-AATTATTTATATATTTTA
1 ACCCTTAAAATAAAA--AAAATTTTAATTTGGGACTAAACTTAGTGAAATTATTTATATATTTTA
*
134701 TTTCTAAAACCCTATAACAATATTATTAATCATGGAATTT
64 TTTCTAAAACCCTATAACAATATTATTAATCATGAAATTT
* *
134741 ACCCTTAAAATAAAAAAAA--TGAATTTGGGACTAAACTT-GATGAAATTAGTTT-TGTATTTTA
1 ACCCTTAAAATAAAAAAAATTTTAATTTGGGACTAAACTTAG-TGAAATTA-TTTATATATTTTA
*
134802 TTTCTAAAACCCTATAACAATTAATTATTAA-CTTTGAAATTT
64 TTTCTAAAACCCTATAACAA-T-ATTATTAATC-ATGAAATTT
*
134844 A-CCTTTAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTA
1 ACCCTTAAAAT-AAAA-AAAATTTTAATTTGGGACTAAACTTAGTGAAATTA
134895 AGGCTAAACT
Statistics
Matches: 131, Mismatches: 11, Indels: 21
0.80 0.07 0.13
Matches are distributed among these distances:
99 7 0.05
100 10 0.08
101 35 0.27
102 13 0.10
103 35 0.27
104 4 0.03
106 26 0.20
107 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (103 bp):
ACCCTTAAAATAAAAAAAATTTTAATTTGGGACTAAACTTAGTGAAATTATTTATATATTTTATT
TCTAAAACCCTATAACAATATTATTAATCATGAAATTT
Found at i:148471 original size:6 final size:6
Alignment explanation
Indices: 148462--148491 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
148452 TATGACTATG
*
148462 AGATTA AGATTA AGGTTA AGATTA AGATTA
1 AGATTA AGATTA AGATTA AGATTA AGATTA
148492 TTTATTGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (6 bp):
AGATTA
Found at i:159293 original size:82 final size:83
Alignment explanation
Indices: 159156--159314 Score: 241
Period size: 82 Copynumber: 1.9 Consensus size: 83
159146 TAAAGTCTCT
* * * *
159156 AGATCAACTTTCGTGGATGTCAAAAATCACCTCTTAAGAGAGTTTTAACTCATAATGGTTCCATT
1 AGATCAACTCTCATGGATGTCAAAAATCACCTCGTAAGAGAGTTTTAACGCATAATGGTTCCATT
159221 AAGCAAAGTCCCAAGACA
66 AAGCAAAGTCCCAAGACA
* *
159239 AGATCAACTCTCATGGATGT-AAAAAGTCACCTCGT-GGAGAGTTTTAACGCATAATGGTTCCTT
1 AGATCAACTCTCATGGATGTCAAAAA-TCACCTCGTAAGAGAGTTTTAACGCATAATGGTTCCAT
159302 TAAGCAAAGTCCC
65 TAAGCAAAGTCCC
159315 TCTTAGATGT
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
82 43 0.62
83 26 0.38
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Consensus pattern (83 bp):
AGATCAACTCTCATGGATGTCAAAAATCACCTCGTAAGAGAGTTTTAACGCATAATGGTTCCATT
AAGCAAAGTCCCAAGACA
Found at i:165311 original size:112 final size:112
Alignment explanation
Indices: 165114--165339 Score: 434
Period size: 112 Copynumber: 2.0 Consensus size: 112
165104 TATACTTAGA
165114 GAAATTATTAGGTGGACCGGGTCCACCACGTCATCCGTAGTCCTGACCAATAAGATTTTGACAAG
1 GAAATTATTAGGTGGACCGGGTCCACCACGTCATCCGTAGTCCTGACCAATAAGATTTTGACAAG
165179 TAAGATTTTTCTAATTAGTCAAAATCTTATTGGTCGGGACCACAGAT
66 TAAGATTTTTCTAATTAGTCAAAATCTTATTGGTCGGGACCACAGAT
*
165226 GAAATTATTAGGTGGACCGGGTCCACCACGTCATCCGTGGTCCTGACCAATAAGATTTTGACAAG
1 GAAATTATTAGGTGGACCGGGTCCACCACGTCATCCGTAGTCCTGACCAATAAGATTTTGACAAG
*
165291 TAAGATTTTTCTAATTAGTCAAAATCTTATTGGTCTGGACCACAGAT
66 TAAGATTTTTCTAATTAGTCAAAATCTTATTGGTCGGGACCACAGAT
165338 GA
1 GA
165340 TGTGGTGGAC
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 112 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (112 bp):
GAAATTATTAGGTGGACCGGGTCCACCACGTCATCCGTAGTCCTGACCAATAAGATTTTGACAAG
TAAGATTTTTCTAATTAGTCAAAATCTTATTGGTCGGGACCACAGAT
Found at i:171989 original size:20 final size:20
Alignment explanation
Indices: 171957--172002 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
171947 TTTATATTTT
171957 TATAAATACTAAACA-TAATA
1 TATAAATACTAAACACTAA-A
*
171977 TATAAATTA-TAAATACTAAA
1 TATAAA-TACTAAACACTAAA
171997 TATAAA
1 TATAAA
172003 AAATATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (20 bp):
TATAAATACTAAACACTAAA
Found at i:180011 original size:29 final size:29
Alignment explanation
Indices: 179978--180039 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
179968 AGATCCATAA
179978 TTCACTCTTAAAGATGAATTGATTTTCTT
1 TTCACTCTTAAAGATGAATTGATTTTCTT
180007 TTCACTCTTAAAGATGAATTGATTTTCTT
1 TTCACTCTTAAAGATGAATTGATTTTCTT
180036 TTCA
1 TTCA
180040 TAATACTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (29 bp):
TTCACTCTTAAAGATGAATTGATTTTCTT
Found at i:186525 original size:2 final size:2
Alignment explanation
Indices: 186518--186557 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
186508 TCTTCATCTC
*
186518 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
186558 CGGACCAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:202728 original size:24 final size:24
Alignment explanation
Indices: 202701--202770 Score: 122
Period size: 24 Copynumber: 2.9 Consensus size: 24
202691 GTAAGATTTA
*
202701 AGCAAAACCTTGTGCAGATAATCG
1 AGCAAAACCATGTGCAGATAATCG
*
202725 AGCAAAACCATGTGCAGAAAATCG
1 AGCAAAACCATGTGCAGATAATCG
202749 AGCAAAACCATGTGCAGATAAT
1 AGCAAAACCATGTGCAGATAAT
202771 GGATTTTGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (24 bp):
AGCAAAACCATGTGCAGATAATCG
Found at i:206233 original size:2 final size:2
Alignment explanation
Indices: 206226--206252 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
206216 TTTGATTGTA
206226 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 A
206253 GGCAAATTAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:207734 original size:17 final size:17
Alignment explanation
Indices: 207692--207738 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
207682 AATGAGAATG
* *
207692 AAACATTAATAAACGTTT
1 AAACATTAAT-AACATTA
*
207710 AGACATTAATAACATTA
1 AAACATTAATAACATTA
207727 AAACATTAATAA
1 AAACATTAATAA
207739 GTACTTAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 16 0.64
18 9 0.36
ACGTcount: A:0.55, C:0.11, G:0.04, T:0.30
Consensus pattern (17 bp):
AAACATTAATAACATTA
Found at i:207774 original size:38 final size:38
Alignment explanation
Indices: 207727--207814 Score: 167
Period size: 38 Copynumber: 2.3 Consensus size: 38
207717 AATAACATTA
207727 AAACATTAATAAGTACTTAATGGTTTAATGTTATTAAT
1 AAACATTAATAAGTACTTAATGGTTTAATGTTATTAAT
*
207765 AAACATTAATAAGTACTTAATGTTTTAATGTTATTAAT
1 AAACATTAATAAGTACTTAATGGTTTAATGTTATTAAT
207803 AAACATTAATAA
1 AAACATTAATAA
207815 CATTAAAACA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (38 bp):
AAACATTAATAAGTACTTAATGGTTTAATGTTATTAAT
Found at i:208531 original size:32 final size:32
Alignment explanation
Indices: 208490--208550 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
208480 TAATATTATG
208490 ATTTCTACTCTCACCCAACCAAACTTTTTAAT
1 ATTTCTACTCTCACCCAACCAAACTTTTTAAT
*
208522 ATTTCTACTCTCACTCAACCAAACTTTTT
1 ATTTCTACTCTCACCCAACCAAACTTTTT
208551 TATCTACCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.30, C:0.31, G:0.00, T:0.39
Consensus pattern (32 bp):
ATTTCTACTCTCACCCAACCAAACTTTTTAAT
Found at i:209690 original size:32 final size:30
Alignment explanation
Indices: 209654--209725 Score: 99
Period size: 32 Copynumber: 2.3 Consensus size: 30
209644 TTTCTTTATG
*
209654 CATTATAATGGTTATGTATGATTGTTATTTAC
1 CATTATAATAGTTA--TATGATTGTTATTTAC
209686 CATTATAAAATAGTTATATGATTGTTATTTAC
1 CATTAT--AATAGTTATATGATTGTTATTTAC
209718 CATTATAA
1 CATTATAA
209726 ATTAGTTAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
30 2 0.05
32 28 0.76
34 7 0.19
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.47
Consensus pattern (30 bp):
CATTATAATAGTTATATGATTGTTATTTAC
Found at i:209726 original size:32 final size:32
Alignment explanation
Indices: 209670--209733 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
209660 AATGGTTATG
209670 TATGATTGTTATTTACCATTATAAAATAGTTA
1 TATGATTGTTATTTACCATTATAAAATAGTTA
*
209702 TATGATTGTTATTTACCATTATAAATTAGTTA
1 TATGATTGTTATTTACCATTATAAAATAGTTA
209734 ATACGGTGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (32 bp):
TATGATTGTTATTTACCATTATAAAATAGTTA
Found at i:210080 original size:29 final size:29
Alignment explanation
Indices: 210046--210146 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 29
210036 ACAAAATGCT
210046 CAAATAAGGGCCCGATTTTTTAATTTGGC
1 CAAATAAGGGCCCGATTTTTTAATTTGGC
** ** **
210075 CAAATAAGGGCCTAATATTTGCCAAAAT-GC
1 CAAATAAGGGCCCGAT-TTT-TTAATTTGGC
* *
210105 TCAAATAAGGGTCCGATCTTTTAATTTGGC
1 -CAAATAAGGGCCCGATTTTTTAATTTGGC
*
210135 CGAATAAGGGCC
1 CAAATAAGGGCC
210147 TAATGTTTGC
Statistics
Matches: 52, Mismatches: 16, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
29 27 0.52
30 9 0.17
31 16 0.31
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.29
Consensus pattern (29 bp):
CAAATAAGGGCCCGATTTTTTAATTTGGC
Found at i:210109 original size:60 final size:60
Alignment explanation
Indices: 210016--210175 Score: 257
Period size: 60 Copynumber: 2.7 Consensus size: 60
210006 CTAATTGCTT
* * * *
210016 AAATAAAGGCCTAACGTTTGACAAAATGCTCAAATAAGGGCCCGATTTTTTAATTTGGCC
1 AAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCC
* *
210076 AAATAAGGGCCTAATATTTGCCAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGCC
1 AAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCC
*
210136 GAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGG
1 AAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGG
210176 ACTGACATCA
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 92 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (60 bp):
AAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCC
Found at i:210113 original size:31 final size:31
Alignment explanation
Indices: 210075--210175 Score: 93
Period size: 31 Copynumber: 3.3 Consensus size: 31
210065 TTAATTTGGC
210075 CAAATAAGGGCCTAATATTTGCCAAAATGCT
1 CAAATAAGGGCCTAATATTTGCCAAAATGCT
* * * **
210106 CAAATAAGGGTCC-GATCTTT--TAATTTGGC-
1 CAAATAAGGG-CCTAATATTTGCCAAAAT-GCT
* *
210135 CGAATAAGGGCCTAATGTTTGCCAAAATGCT
1 CAAATAAGGGCCTAATATTTGCCAAAATGCT
210166 CAAATAAGGG
1 CAAATAAGGG
210176 ACTGACATCA
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
28 2 0.04
29 17 0.33
30 4 0.08
31 27 0.52
32 2 0.04
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (31 bp):
CAAATAAGGGCCTAATATTTGCCAAAATGCT
Found at i:210259 original size:31 final size:31
Alignment explanation
Indices: 210214--210320 Score: 96
Period size: 31 Copynumber: 3.5 Consensus size: 31
210204 CCAAACGGAT
*
210214 GTCAGGTCCTTATTTGAGCATTTTCGATAAC
1 GTCAGGCCCTTATTTGAGCATTTTCGATAAC
* ** *
210245 GTTAGGCCCTTATTTG-GTCAAATT--A-AAA
1 GTCAGGCCCTTATTTGAG-CATTTTCGATAAC
*
210273 GATCGGGCCCTTATTTGAGCATTTTCGATAAC
1 G-TCAGGCCCTTATTTGAGCATTTTCGATAAC
* *
210305 ATCAAGCCCTTATTTG
1 GTCAGGCCCTTATTTG
210321 GCCAAATTAA
Statistics
Matches: 57, Mismatches: 13, Indels: 12
0.70 0.16 0.15
Matches are distributed among these distances:
28 3 0.05
29 18 0.32
30 2 0.04
31 32 0.56
32 2 0.04
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (31 bp):
GTCAGGCCCTTATTTGAGCATTTTCGATAAC
Found at i:210378 original size:60 final size:60
Alignment explanation
Indices: 210220--210380 Score: 216
Period size: 60 Copynumber: 2.7 Consensus size: 60
210210 GGATGTCAGG
* *
210220 TCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGTCAAATTAAAAGATCGGG
1 TCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA
* * * * *
210280 CCCTTATTTGAGCATTTTCGATAACATCAAGCCCTTATTTGGCCAAATTAAAGGATCGGA
1 TCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA
* * *
210340 TCCTTATTTGAGCATTTTTGCA-AATGTTAGGCCTTTATTTG
1 TCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTG
210381 AGCAATTAGC
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
60 85 0.99
61 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (60 bp):
TCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGA
Found at i:211253 original size:159 final size:159
Alignment explanation
Indices: 210964--211278 Score: 576
Period size: 159 Copynumber: 2.0 Consensus size: 159
210954 ACACTTTCAG
*
210964 AATCCACACAAACCATCGACTTAGAGATGTTGAGAGAGCTAGCAAACAACAAACCATCTCTAATA
1 AATCCACACAAACCATCAACTTAGAGATGTTGAGAGAGCTAGCAAACAACAAACCATCTCTAATA
* * *
211029 TCCCCAAAACTCAGCCTGTATACTATTAGTAATGGGAATCCTTCTTGCATAACCACCAAGCCACT
66 CCCCCAAAACTCAGCCTGTACACTATTAGCAATGGGAATCCTTCTTGCATAACCACCAAGCCACT
211094 TTCCATAATGATCTCTAATAACAGCAGGA
131 TTCCATAATGATCTCTAATAACAGCAGGA
*
211123 AATCCACACAAACCATCAACTTAGAGATGTTGAGAGAGCTAGCTAACAACAAACCATCTCTAATA
1 AATCCACACAAACCATCAACTTAGAGATGTTGAGAGAGCTAGCAAACAACAAACCATCTCTAATA
*
211188 CCCCCAAATCTCAGCCTGTACACTATTAGCAATGGGAATCCTTCTTGCATAACCACCAAGCCACT
66 CCCCCAAAACTCAGCCTGTACACTATTAGCAATGGGAATCCTTCTTGCATAACCACCAAGCCACT
211253 TTCCATAATGATCTCTAATAACAGCA
131 TTCCATAATGATCTCTAATAACAGCA
211279 CCTGCTCCAC
Statistics
Matches: 150, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
159 150 1.00
ACGTcount: A:0.37, C:0.28, G:0.12, T:0.23
Consensus pattern (159 bp):
AATCCACACAAACCATCAACTTAGAGATGTTGAGAGAGCTAGCAAACAACAAACCATCTCTAATA
CCCCCAAAACTCAGCCTGTACACTATTAGCAATGGGAATCCTTCTTGCATAACCACCAAGCCACT
TTCCATAATGATCTCTAATAACAGCAGGA
Found at i:218609 original size:26 final size:26
Alignment explanation
Indices: 218571--218626 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
218561 ATAACCTATT
*
218571 TTCTTCTTAACCAAAATTTTTGTCTA
1 TTCTTCCTAACCAAAATTTTTGTCTA
*
218597 TTCTTCCTGACCAAAATTTTTGTCTA
1 TTCTTCCTAACCAAAATTTTTGTCTA
218623 TTCT
1 TTCT
218627 AATGGAGTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.50
Consensus pattern (26 bp):
TTCTTCCTAACCAAAATTTTTGTCTA
Found at i:218820 original size:28 final size:28
Alignment explanation
Indices: 218780--218838 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
218770 CTAAGTTGAA
* *
218780 AGGGAGGTCCAAATGGCAGAAGATAGCG
1 AGGGAGGTCCAAATGCCAGAAGATAACG
218808 AGGGAGGTCCAAATGCCAGAAGATAACG
1 AGGGAGGTCCAAATGCCAGAAGATAACG
218836 AGG
1 AGG
218839 CAAAGACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.37, T:0.10
Consensus pattern (28 bp):
AGGGAGGTCCAAATGCCAGAAGATAACG
Found at i:219189 original size:17 final size:17
Alignment explanation
Indices: 219167--219201 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
219157 CTTAGCTTAG
219167 TGTCGATGTTTGAAACT
1 TGTCGATGTTTGAAACT
219184 TGTCGATGTTTGAAACT
1 TGTCGATGTTTGAAACT
219201 T
1 T
219202 ATAAGCACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (17 bp):
TGTCGATGTTTGAAACT
Found at i:221286 original size:21 final size:19
Alignment explanation
Indices: 221243--221298 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 19
221233 GTTTAGCAAT
221243 TGTACAGATGAGATTACAC
1 TGTACAGATGAGATTACAC
* *
221262 TGTACAGATTAGATTAGGTAC
1 TGTACAGATGAGATTA--CAC
221283 TGTACAGATGAGATTA
1 TGTACAGATGAGATTA
221299 TTAGAGCAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 15 0.47
21 17 0.53
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (19 bp):
TGTACAGATGAGATTACAC
Found at i:229708 original size:15 final size:15
Alignment explanation
Indices: 229688--229719 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
229678 ATCTCCTTCG
*
229688 GATGATGATAACAGT
1 GATGATCATAACAGT
229703 GATGATCATAACAGT
1 GATGATCATAACAGT
229718 GA
1 GA
229720 AGGTAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.09, G:0.25, T:0.25
Consensus pattern (15 bp):
GATGATCATAACAGT
Found at i:229964 original size:27 final size:27
Alignment explanation
Indices: 229888--229965 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 27
229878 TCCCTCCAAA
*
229888 AAAAAGAAGAGCATTGTCAAATCACAC
1 AAAAGGAAGAGCATTGTCAAATCACAC
* * *
229915 AAAACGTTCAAGAGCATTGTCAATTCCCAC
1 AAAA-G--GAAGAGCATTGTCAAATCACAC
*
229945 AAAAGGAAGAGCATTCTCAAA
1 AAAAGGAAGAGCATTGTCAAA
229966 GGGTCAAGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
27 17 0.41
29 1 0.02
30 23 0.56
ACGTcount: A:0.46, C:0.21, G:0.15, T:0.18
Consensus pattern (27 bp):
AAAAGGAAGAGCATTGTCAAATCACAC
Found at i:230439 original size:28 final size:29
Alignment explanation
Indices: 230385--230439 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
230375 GGGGTGAAAT
*
230385 GTCTTGAATTTGGGAAATTTAAAGGGCTA
1 GTCTTGAATTTGGAAAATTTAAAGGGCTA
*
230414 GTCTTGAATTT-GAAAATTTATAGGGC
1 GTCTTGAATTTGGAAAATTTAAAGGGC
230440 AAGTTTAGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.31, C:0.07, G:0.25, T:0.36
Consensus pattern (29 bp):
GTCTTGAATTTGGAAAATTTAAAGGGCTA
Found at i:241981 original size:21 final size:22
Alignment explanation
Indices: 241957--242001 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
241947 ACAAAAACCC
*
241957 AAAAAAGAAAAGG-AAAATAAA
1 AAAAAACAAAAGGAAAAATAAA
*
241978 AAAAATCAAAAGGAAAAATAAA
1 AAAAAACAAAAGGAAAAATAAA
242000 AA
1 AA
242002 CGCTTCACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.80, C:0.02, G:0.11, T:0.07
Consensus pattern (22 bp):
AAAAAACAAAAGGAAAAATAAA
Found at i:252081 original size:17 final size:17
Alignment explanation
Indices: 252059--252093 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
252049 ATTATTATGA
252059 ACTAAACTTTCATACGG
1 ACTAAACTTTCATACGG
252076 ACTAAACTTTCATACGG
1 ACTAAACTTTCATACGG
252093 A
1 A
252094 GAAAATCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (17 bp):
ACTAAACTTTCATACGG
Found at i:258202 original size:21 final size:21
Alignment explanation
Indices: 258178--258237 Score: 79
Period size: 19 Copynumber: 3.0 Consensus size: 21
258168 GCTGCTCTAA
258178 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGTACC
* * *
258199 TAATTTGATCTGTACAGT--G
1 TAATCTCATCTGTACAGTACC
258218 TAATCTCATCTGTACAGTAC
1 TAATCTCATCTGTACAGTAC
258238 ATAAACAGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (21 bp):
TAATCTCATCTGTACAGTACC
Found at i:261188 original size:3 final size:3
Alignment explanation
Indices: 261180--261228 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
261170 GTTTACACAT
261180 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
261228 T
1 T
261229 GTTTCATTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:262084 original size:2 final size:2
Alignment explanation
Indices: 262077--262105 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
262067 TAATATAGTG
262077 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 T
262106 GGCAAGGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.