Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008283.1 Hibiscus syriacus cultivar Beakdansim tig00110945_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: 2862730
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 14
Found at i:2325162 original size:2 final size:2
Alignment explanation
Indices: 2325155--2325180 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2325145 AGATGCAGTC
2325155 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
2325181 GACGTACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2325374 original size:164 final size:165
Alignment explanation
Indices: 2325167--2325499 Score: 545
Period size: 164 Copynumber: 2.0 Consensus size: 165
2325157 ATATATATAT
2325167 ATATATATATATATGACGTACACATGCAACATGTATAGCTTTGTATTTAAAGTGAG-AA-AAT-A
1 ATATATATATATATGACGTACACATGCAACATGTATAGCTTTGTATTTAAAGTGAGAAATAATGA
*
2325229 A-T-AATTAT-AGTTTTATATATATATATATGATACTGCATCTTATAATTTACATTTATTATTTC
66 AGTAAATTATAAGTTATATATATATATATATG--ACTGCATCTTATAA-TTACA-TTATTA-TTC
2325291 TCACTTTAAATAC-AAGCTATACATGTTGCATGTGTACGTC
126 TCACTTTAAATACAAAGCTATA-ATGTTGCATGTGTACGTC
2325331 ATATATATATATATGACGTACACATGCAACATGTATAGCTTTGTATTTAAAGTGAGAAATAATGA
1 ATATATATATATATGACGTACACATGCAACATGTATAGCTTTGTATTTAAAGTGAGAAATAATGA
2325396 ATGTAAATTATAAGTTATATATATATATATATGACTGCATCTTATAATTACATTATTATTCTCAC
66 A-GTAAATTATAAGTTATATATATATATATATGACTGCATCTTATAATTACATTATTATTCTCAC
2325461 TTTAAATACAAAGCTATAATGTTGCATGTGTACGTC
130 TTTAAATACAAAGCTATAATGTTGCATGTGTACGTC
2325497 ATA
1 ATA
2325500 GCTTGTATTT
Statistics
Matches: 160, Mismatches: 1, Indels: 14
0.91 0.01 0.08
Matches are distributed among these distances:
164 56 0.35
165 2 0.01
166 40 0.25
167 16 0.10
168 5 0.03
169 15 0.09
170 6 0.04
171 20 0.12
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (165 bp):
ATATATATATATATGACGTACACATGCAACATGTATAGCTTTGTATTTAAAGTGAGAAATAATGA
AGTAAATTATAAGTTATATATATATATATATGACTGCATCTTATAATTACATTATTATTCTCACT
TTAAATACAAAGCTATAATGTTGCATGTGTACGTC
Found at i:2325549 original size:2 final size:2
Alignment explanation
Indices: 2325542--2325616 Score: 122
Period size: 2 Copynumber: 39.5 Consensus size: 2
2325532 AATTATAAAT
2325542 TA TA TA TA TA TA TA TA TA TA TA TA -A T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2325582 TA TA TA TA TA TA TA TA TA -A TA TA TA TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2325617 GACTGCATCT
Statistics
Matches: 69, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
1 4 0.06
2 65 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2325746 original size:14 final size:15
Alignment explanation
Indices: 2325727--2325773 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
2325717 AATAAATGAA
*
2325727 ATTATAAAT-TATAT
1 ATTATATATATATAT
2325741 ATTATATATATATAT
1 ATTATATATATATAT
2325756 ATATATATATATATAT
1 AT-TATATATATATAT
2325772 AT
1 AT
2325774 AACACATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 8 0.27
15 7 0.23
16 15 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTATATATATATAT
Found at i:2325748 original size:2 final size:2
Alignment explanation
Indices: 2325736--2325774 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2325726 AATTATAAAT
2325736 TA TA TA T- TA 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 TA TA TA TA TA
2325775 ACACATTAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2327392 original size:150 final size:146
Alignment explanation
Indices: 2327155--2327452 Score: 560
Period size: 150 Copynumber: 2.0 Consensus size: 146
2327145 AATGTAATGC
2327155 TTTTCCTTCACCTAATCCCTTTGTTTTTTCCTTTTTTTTCTTCTTGCTTTATTTGGTGATTATGG
1 TTTTCCTTCACCTAATCCCTTTGTTTTTTCCTTTTTTTTCTTCTTGCTTTATTTGGTGATTATGG
2327220 TTGGAGCAGGTCAGGATTAGGTTGGCGGTTTGTCTCGAAATTTGCTTGAACTTTCGGTGGATTAT
66 TTGGAGCAGGTCAGGATTAGGTTGGCGGTTTGTCTCGAAATTTGCTTGAACTTTCGGTGGATTAT
2327285 TAATTCTTTGTTAACT
131 TAATTCTTTGTTAACT
2327301 TTTTCCTTCACCTAATCCCTTTGTTTTTTTCCTTTTTTTTTCTTCATTGCTTTATTTGGTGAATT
1 TTTTCCTTCACCTAATCCCTTTG-TTTTTTCC-TTTTTTTTCTTC-TTGCTTTATTTGGTG-ATT
2327366 ATGGTTGGAGCAGGTCAGGATTAGGTTGGCGGTTTGTCTCGAAATTTGCTTGAACTTTCGGTGGA
62 ATGGTTGGAGCAGGTCAGGATTAGGTTGGCGGTTTGTCTCGAAATTTGCTTGAACTTTCGGTGGA
2327431 TTATTAATTCTTTGTTAACT
127 TTATTAATTCTTTGTTAACT
2327451 TT
1 TT
2327453 GTTTGCAGGT
Statistics
Matches: 148, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
146 23 0.16
147 8 0.05
148 12 0.08
149 15 0.10
150 90 0.61
ACGTcount: A:0.15, C:0.15, G:0.19, T:0.50
Consensus pattern (146 bp):
TTTTCCTTCACCTAATCCCTTTGTTTTTTCCTTTTTTTTCTTCTTGCTTTATTTGGTGATTATGG
TTGGAGCAGGTCAGGATTAGGTTGGCGGTTTGTCTCGAAATTTGCTTGAACTTTCGGTGGATTAT
TAATTCTTTGTTAACT
Found at i:2332938 original size:3 final size:3
Alignment explanation
Indices: 2332930--2332956 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2332920 CTCTAACCAT
2332930 CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA
2332957 AACCCAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:2334637 original size:20 final size:20
Alignment explanation
Indices: 2334612--2334669 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
2334602 CAATTTATTC
2334612 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
2334632 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
2334652 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
2334670 ACCTTTGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.19, C:0.16, G:0.34, T:0.31
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:2334640 original size:65 final size:64
Alignment explanation
Indices: 2334505--2334649 Score: 170
Period size: 65 Copynumber: 2.2 Consensus size: 64
2334495 TGGAACACTT
*
2334505 AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAATCCTGAGTGTATCGATGCATGGAG
1 AGTGCATCGATGCATAAAATGCATTCGATG-TTTCATAAAATCCTGAGTGCATCGATGCATGGAG
* ** * *
2334570 AGTGCATCGATGCATAAAATGTATTCGATG-TTCAATTTATTCATTG-GTGCATCGATGCATGGA
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTC-ATAAAATC-CTGAGTGCATCGATGCATGGA
2334633 TTG
64 --G
2334636 -GTGCATCGATGCAT
1 AGTGCATCGATGCAT
2334650 GGATTGGTGC
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
63 3 0.04
64 21 0.30
65 45 0.64
66 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.33
Consensus pattern (64 bp):
AGTGCATCGATGCATAAAATGCATTCGATGTTTCATAAAATCCTGAGTGCATCGATGCATGGAG
Found at i:2343056 original size:64 final size:65
Alignment explanation
Indices: 2342984--2343126 Score: 198
Period size: 64 Copynumber: 2.2 Consensus size: 65
2342974 TGGAACACTT
* * *
2342984 AGTGCATCGCTGCACCAAGTGTGCATCGATGCATAAAATGCATTCGATGTTTTGA-AAAAGCCTG
1 AGTGCATCGATGCACCAACTGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAGCCTG
**** *
2343048 AGTGCATCGATGCATGGTCTGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAATCCTG
1 AGTGCATCGATGCACCAACTGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAGCCTG
*
2343113 AGTGTATCGATGCA
1 AGTGCATCGATGCA
2343127 TAAAATGCAT
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
64 48 0.70
65 21 0.30
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (65 bp):
AGTGCATCGATGCACCAACTGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAGCCTG
Found at i:2343141 original size:64 final size:63
Alignment explanation
Indices: 2343005--2343142 Score: 179
Period size: 64 Copynumber: 2.2 Consensus size: 63
2342995 GCACCAAGTG
* ****
2343005 TGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAGCCTGAGTGCATCGATGCATGGTCTG
1 TGCATCGATGCATAAAATGCATTCGATGTTTTCAAAAAGCCTGAGTGCATCGATGCAT-GAAAA
* *
2343069 TGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAATCCTGAGTGTATCGATGCAT-AAAA
1 TGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAAAGCCTGAGTGCATCGATGCATGAAAA
2343132 TGCATTCGATG
1 TGCA-TCGATG
2343143 TTCAATTTAT
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
63 4 0.06
64 39 0.60
65 22 0.34
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (63 bp):
TGCATCGATGCATAAAATGCATTCGATGTTTTCAAAAAGCCTGAGTGCATCGATGCATGAAAA
Found at i:2343180 original size:20 final size:20
Alignment explanation
Indices: 2343155--2343192 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2343145 CAATTTATTC
2343155 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
2343175 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
2343193 ACCTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:2346949 original size:14 final size:15
Alignment explanation
Indices: 2346930--2346963 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
2346920 TTTTTCTTAT
2346930 AAAATAAATGAAT-A
1 AAAATAAATGAATGA
2346944 AAAATAAATGAATGA
1 AAAATAAATGAATGA
2346959 AAAAT
1 AAAAT
2346964 TTTTTCTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (15 bp):
AAAATAAATGAATGA
Found at i:2347009 original size:21 final size:22
Alignment explanation
Indices: 2346983--2347023 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2346973 AATCTCTCTC
2346983 TCCTTCT-AAAATCTCATTTCT
1 TCCTTCTAAAAATCTCATTTCT
2347004 TCCTTCTAAAAATCTCATTT
1 TCCTTCTAAAAATCTCATTT
2347024 TTCTTCGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.46
Consensus pattern (22 bp):
TCCTTCTAAAAATCTCATTTCT
Found at i:2348056 original size:75 final size:75
Alignment explanation
Indices: 2347933--2348083 Score: 275
Period size: 75 Copynumber: 2.0 Consensus size: 75
2347923 TTTCCCTTAC
* *
2347933 TTGCTTTTGTCCCTCTTTGATCTTCTCTTGTTCCTTCCTTAGCCTTTTCATCTCCGATCTCTGGT
1 TTGCTTTTGACCCTCTTTGATCTTCTCTTGTTCCTTCCTTAGCCTTTTCATCTCCGATCTCTGCT
2347998 TTCTGATGCG
66 TTCTGATGCG
*
2348008 TTGCTTTTGACCCTCTTTGATCTTCTCTTGTTCCTTCCTTAGCCTTTTCGTCTCCGATCTCTGCT
1 TTGCTTTTGACCCTCTTTGATCTTCTCTTGTTCCTTCCTTAGCCTTTTCATCTCCGATCTCTGCT
2348073 TTCTGATGCG
66 TTCTGATGCG
2348083 T
1 T
2348084 CCGATTATTT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.07, C:0.30, G:0.15, T:0.49
Consensus pattern (75 bp):
TTGCTTTTGACCCTCTTTGATCTTCTCTTGTTCCTTCCTTAGCCTTTTCATCTCCGATCTCTGCT
TTCTGATGCG
Found at i:2349571 original size:17 final size:17
Alignment explanation
Indices: 2349537--2349584 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
2349527 GTCTTTAAAA
*
2349537 TTTTAAAATTATAATATT-
1 TTTTAAAATT-T-TTATTC
2349555 TTTTAAATATTTTTATTC
1 TTTTAAA-ATTTTTATTC
2349573 TTTTAAAATTTT
1 TTTTAAAATTTT
2349585 ATAAATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 9 0.33
18 15 0.56
19 3 0.11
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAAAATTTTTATTC
Found at i:2350276 original size:35 final size:35
Alignment explanation
Indices: 2350234--2350320 Score: 92
Period size: 34 Copynumber: 2.5 Consensus size: 35
2350224 AAATTATCAC
2350234 ATTTTTATATTTTTAAATATTTTTATTAAA-AT-TTT
1 ATTTTTATATTTTTAAA-ATTTTTA-TAAATATATTT
*
2350269 ATTTTTAT-TCTTTTAAAA-TTTTATAAATTTATTT
1 ATTTTTATAT-TTTTAAAATTTTTATAAATATATTT
* *
2350303 ATTTTTAAAATTTTAAAA
1 ATTTTTATATTTTTAAAA
2350321 ATTTATTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
32 4 0.09
33 6 0.13
34 20 0.44
35 15 0.33
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (35 bp):
ATTTTTATATTTTTAAAATTTTTATAAATATATTT
Found at i:2350298 original size:26 final size:26
Alignment explanation
Indices: 2350279--2350328 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
2350269 ATTTTTATTC
*
2350279 TTTTAAAATTTTATAAATTTATTTAT
1 TTTTAAAATTTTAAAAATTTATTTAT
2350305 TTTTAAAATTTTAAAAATTTATTT
1 TTTTAAAATTTTAAAAATTTATTT
2350329 TTATTCTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
TTTTAAAATTTTAAAAATTTATTTAT
Found at i:2351282 original size:21 final size:23
Alignment explanation
Indices: 2351258--2351301 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
2351248 TTGGTGTTCG
2351258 GAGTTTGGCCGG-T-GGTGGCCT
1 GAGTTTGGCCGGTTGGGTGGCCT
*
2351279 GAGTTTGGTCGGTTGGGTGGCCT
1 GAGTTTGGCCGGTTGGGTGGCCT
2351302 CGGTTAGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 1 0.05
23 8 0.40
ACGTcount: A:0.05, C:0.16, G:0.48, T:0.32
Consensus pattern (23 bp):
GAGTTTGGCCGGTTGGGTGGCCT
Found at i:2371614 original size:29 final size:29
Alignment explanation
Indices: 2371571--2371678 Score: 137
Period size: 29 Copynumber: 3.7 Consensus size: 29
2371561 AATTCGTATA
* *
2371571 TCAATTTGATCATTAAACTTTAAAGCACT
1 TCAATTTTAGCATTAAACTTTAAAGCACT
*
2371600 TCAATTTTAGTATTAAACTTT-AAGACACT
1 TCAATTTTAGCATTAAACTTTAAAG-CACT
* *
2371629 TCTATTTTAGCATTAAACTTTAAAACACT
1 TCAATTTTAGCATTAAACTTTAAAGCACT
* *
2371658 TCAATCTTAGGATTAAACTTT
1 TCAATTTTAGCATTAAACTTT
2371679 CAATATTGGT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
28 3 0.04
29 63 0.93
30 2 0.03
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (29 bp):
TCAATTTTAGCATTAAACTTTAAAGCACT
Found at i:2378647 original size:81 final size:81
Alignment explanation
Indices: 2378548--2379267 Score: 1005
Period size: 81 Copynumber: 9.0 Consensus size: 81
2378538 TCCTTTCATG
* * *
2378548 TCAAAGGCATTTAACCTTTCATCTAACTTGG-ATTATTGACACCTTTCTGCCAAATGCACAG-TC
1 TCAAAGGTATTTAACCTTTCATCTAAC-TGGCATGATTGACACCTTTCTGTCAAATGCACAGCT-
*
2378611 AGGCAATTAATCTTTTAC
64 AGGCAATTAGTCTTTTAC
2378629 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
* *
2378694 G-AATTAATTTTTTTAC
66 GCAATT-AGTCTTTTAC
* *
2378710 TCAAAGGTATTTAACC-TT--TC--A-T--CATGATTGACACATTTCTGTCAAATGCACAACTAG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
2378767 GCAATTAGTCTTTTAC
66 GCAATTAGTCTTTTAC
* * *
2378783 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGATACATTTCTGTTAAATGCACAGCTAG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
*
2378848 ACAATTAGTCTTTTAC
66 GCAATTAGTCTTTTAC
* * * *
2378864 TCAAAGGTATTTAACTTTTCATCTAACTGGCATGATTGACACCTTTTTGTCAAATGCATAGTTAG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
** * *
2378929 ATAATTAATTTTTTAC
66 GCAATTAGTCTTTTAC
* *
2378945 TCAAAGGTATTTAACCTTTCATCTAACTGGCAAGATTGACACCTTTCTGTCAAATGCACATCTAG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
2379010 GCAATTAGTCTTTTAC
66 GCAATTAGTCTTTTAC
* * *
2379026 TCAAAGGTATTTAACCTTTCATCTAGCTGGCATGATTGACACCTTTATGTCAAATGCACATCTAG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
*
2379091 GCAATTAGTATTTTAC
66 GCAATTAGTCTTTTAC
* **
2379107 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTAACACCTTTCTGTCAAATGTGCAGCTAG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
2379172 GCAATTAGTCTTTTAC
66 GCAATTAGTCTTTTAC
* * * * *
2379188 TCAAAGGTATTTAACATTTCATCTAATTGGCATGATTAACACATTTCTTTCAAATGCACAGCTAG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
*
2379253 ACAATT-GATCTTTTA
66 GCAATTAG-TCTTTTA
2379268 TTTTAGAATA
Statistics
Matches: 575, Mismatches: 51, Indels: 26
0.88 0.08 0.04
Matches are distributed among these distances:
73 58 0.10
74 6 0.01
75 1 0.00
76 3 0.01
78 3 0.01
79 1 0.00
80 10 0.02
81 492 0.86
82 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (81 bp):
TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
GCAATTAGTCTTTTAC
Found at i:2380056 original size:22 final size:23
Alignment explanation
Indices: 2380013--2380056 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
2380003 ACAAAATTAA
*
2380013 AAAAAAAGTATAAGAACGAAAAC
1 AAAAAAAGTATAAGAAAGAAAAC
* *
2380036 AAAATAAG-ATAAGAAATAAAA
1 AAAAAAAGTATAAGAAAGAAAA
2380057 AGAAAATTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.73, C:0.05, G:0.11, T:0.11
Consensus pattern (23 bp):
AAAAAAAGTATAAGAAAGAAAAC
Found at i:2380281 original size:49 final size:50
Alignment explanation
Indices: 2380167--2380308 Score: 207
Period size: 49 Copynumber: 2.8 Consensus size: 50
2380157 CTTTTTATAA
2380167 ATTTTCAAAATGGTTTTTAAAAACTATATAGTATATATATGTTTTTTTAAAATG
1 ATTTTCAAAAT-GTTTTTAAAAACTATATAGTATA-ATA--TTTTTTTAAAATG
*
2380221 GTTTTCAAAATGTTTTTAAAAACTATATAGTATAATATTTTTTT-AAATG
1 ATTTTCAAAATGTTTTTAAAAACTATATAGTATAATATTTTTTTAAAATG
* *
2380270 ATTTTCAAAATGGTTTCAAAAACTATATA-TATAATATTT
1 ATTTTCAAAATGTTTTTAAAAACTATATAGTATAATATTT
2380309 CTATACCATT
Statistics
Matches: 84, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
48 10 0.12
49 31 0.37
50 7 0.08
52 3 0.04
53 23 0.27
54 10 0.12
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (50 bp):
ATTTTCAAAATGTTTTTAAAAACTATATAGTATAATATTTTTTTAAAATG
Found at i:2380759 original size:113 final size:118
Alignment explanation
Indices: 2380509--2380782 Score: 398
Period size: 113 Copynumber: 2.3 Consensus size: 118
2380499 TATTTAAGCC
*
2380509 TTTTAAGAATTATACCATAAATGACAAAATTTTAAATTATTTATTCTTTATATTTCCACATAACA
1 TTTTAAGAATTATACCATAAATGAC-AAATTTTAAATTAATTATTCTTTATATTTCCACAT---A
*
2380574 TAAAGTATGTTTTCTTAAGGACAATTCCACGCACAAAAACATGATACATGGAACTAA
62 TAAAGTATGTTTTCTCAAGGACAATTCCACGCACAAAAACATGATACATGGAACTAA
*
2380631 TTTTAAGAATTATACCATAAACGAC-AATTTTAAATTAATTATTCTTTAT-TTTACCACAT-T-A
1 TTTTAAGAATTATACCATAAATGACAAATTTTAAATTAATTATTCTTTATATTT-CCACATATAA
* *
2380692 AGTGTGTTTTCTCAAGGACAATTCCAC-CA-AAAAAGATGATACATGGAACTAA
65 AGTATGTTTTCTCAAGGACAATTCCACGCACAAAAACATGATACATGGAACTAA
*
2380744 TTTTAAGAATCATACCATAAATGACAAAGTTTTAAATTA
1 TTTTAAGAATTATACCATAAATGACAAA-TTTTAAATTA
2380783 CGTATTACTG
Statistics
Matches: 142, Mismatches: 7, Indels: 13
0.88 0.04 0.08
Matches are distributed among these distances:
113 45 0.32
114 4 0.03
115 36 0.25
116 1 0.01
119 3 0.02
120 29 0.20
122 24 0.17
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (118 bp):
TTTTAAGAATTATACCATAAATGACAAATTTTAAATTAATTATTCTTTATATTTCCACATATAAA
GTATGTTTTCTCAAGGACAATTCCACGCACAAAAACATGATACATGGAACTAA
Found at i:2381266 original size:20 final size:21
Alignment explanation
Indices: 2381233--2381271 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2381223 ATAACAAGTA
*
2381233 AAAATATGATAAAACCGGTCT
1 AAAATATGACAAAACCGGTCT
2381254 AAAA-ATGACAAAACCGGT
1 AAAATATGACAAAACCGGT
2381272 AAAGAGCCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.18
Consensus pattern (21 bp):
AAAATATGACAAAACCGGTCT
Found at i:2381390 original size:181 final size:182
Alignment explanation
Indices: 2381019--2381574 Score: 850
Period size: 181 Copynumber: 3.1 Consensus size: 182
2381009 GATACAAATA
** *
2381019 AAAAATGTATCGATCCATAGTAATATAAC-AGATAAAAATATGATAAAACCGGTCTCAAAATGAC
1 AAAAATGTATCGATCCATAACAATATAACAAG-TAAAAATATGATAAAACCGGTCTAAAAATGAC
* * * *
2381083 CAAACCGGTAAAGCGCTACCGGATATGTT--GAGTGTCGATACTTTATTATAAGTATCGACACTT
65 AAAACCGGTAAAGAGCCACCGGATATGTTAAAAGTGTCGATACTTTATTATAAGTATCGACACTT
* * ** *
2381146 TTAGAATTTAAAAGACAAGCAGTAATAGCGTTTATAAAGTGTCGATACTTTAA
130 TTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
*
2381199 AAAAATGTATCGGTCCATAACAATATAACAAGTAAAAATATGATAAAACCGGTCTAAAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGATAAAACCGGTCTAAAAATGACA
* *
2381264 AAACCGGTAAAGAGCCACCGGATATGTTAAAAATGTCGATAC-TTATTATAAATATCGACACTTT
66 AAACCGGTAAAGAGCCACCGGATATGTTAAAAGTGTCGATACTTTATTATAAGTATCGACACTTT
* *
2381328 TGGAATTTAAAAGAGAAGCAGTAATAACGCCTATAAAGTGTCTATACTTTAT
131 TGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
* * *
2381380 AAAAATGTATCGATCCATAACAATATAACATGTAAAAAAATGATAAAATCGGTCTAAAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGATAAAACCGGTCTAAAAATGACA
* * *
2381445 AAACCGGTAAAGAGTCACCAGATATGTTAAAAGTGTCGATACTTTATCATAAGTATCGACACTTT
66 AAACCGGTAAAGAGCCACCGGATATGTTAAAAGTGTCGATACTTTATTATAAGTATCGACACTTT
*
2381510 TGGAATTTAAAAAAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
131 TGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
*
2381562 AAAAATGCATCGA
1 AAAAATGTATCGA
2381575 CACTTGGGTT
Statistics
Matches: 342, Mismatches: 30, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
180 83 0.24
181 168 0.49
182 91 0.27
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGATAAAACCGGTCTAAAAATGACA
AAACCGGTAAAGAGCCACCGGATATGTTAAAAGTGTCGATACTTTATTATAAGTATCGACACTTT
TGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
Found at i:2381440 original size:20 final size:20
Alignment explanation
Indices: 2381415--2381452 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2381405 TAACATGTAA
* *
2381415 AAAAATGATAAAATCGGTCT
1 AAAAATGACAAAACCGGTCT
2381435 AAAAATGACAAAACCGGT
1 AAAAATGACAAAACCGGT
2381453 AAAGAGTCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.13, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAATGACAAAACCGGTCT
Found at i:2389019 original size:22 final size:21
Alignment explanation
Indices: 2388977--2389016 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2388967 GAGTTTATTT
*
2388977 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2388998 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2389017 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:2394010 original size:17 final size:17
Alignment explanation
Indices: 2393983--2394024 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
2393973 TGGATAACTA
2393983 TGTGA-AATTCACCGAC
1 TGTGAGAATTCACCGAC
2393999 TGTGAGAATTCACCGAC
1 TGTGAGAATTCACCGAC
2394016 TGTGAGAAT
1 TGTGAGAAT
2394025 GTAAGACACC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (17 bp):
TGTGAGAATTCACCGAC
Found at i:2394847 original size:19 final size:19
Alignment explanation
Indices: 2394823--2394871 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
2394813 AATGTAGGGT
2394823 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
2394842 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
2394861 TAATTTTGTAT
1 TAATTTTGTAT
2394872 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:2395670 original size:201 final size:201
Alignment explanation
Indices: 2395320--2396287 Score: 1445
Period size: 201 Copynumber: 4.8 Consensus size: 201
2395310 GTAAACATAT
*
2395320 GTGTCGATACATTTATAAGAAGCGTCGATCCCAAGAACATCGAAACCCATAATTACAATGTAATA
1 GTGTCGATACATTTATAAGAAGTGTCGATCCCAAGAACATCGAAACCCATAATTACAATGTAATA
*
2395385 TGTAATTTTTCAATGTAACCGGTATAAATAGACCGGTTTTATGAGAGAATAGGTCTACATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATAGACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* *
2395450 ATCGATACTTGTGGAATTTGTGTTGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGGTGCA-A
131 ATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGGTGCACA
2395514 GCATAAA
196 -CATAAA
* * *
2395521 GTGTTGATACATTTATAATAAGTGTCGATCCCAAGAACATCGAAACCCATAATTACAATGTAAGA
1 GTGTCGATACATTTATAAGAAGTGTCGATCCCAAGAACATCGAAACCCATAATTACAATGTAATA
* * *
2395586 GGTAATTTTTCAATGTAACTGGTATAAATAGACTGGTTTTATGAGAGAATATGTCTACATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATAGACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* * * * ** * * *
2395651 ATCAACACTTATGGAATTTGTGTCGATATTTTTTTTCCTTAATAAATGCCCTAAAGGGGTGCACG
131 ATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGGTGCACA
2395716 CATAAA
196 CATAAA
* * * * *
2395722 TTGTCGATACATTTATAAGAAGTGTCGATCCCAAGAACATTGAAACCTATAATTACAATATAAGA
1 GTGTCGATACATTTATAAGAAGTGTCGATCCCAAGAACATCGAAACCCATAATTACAATGTAATA
* * *
2395787 GGTAATTTTTCAATGTAACCAGTATAAATAGACCAGTTTTATGAGAGAATAGGTCTACATAATAT
66 GGTAATTTTTCAATGTAACCGGTATAAATAGACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* * *
2395852 ATCGACACTTGTGGGATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGGTACATA
131 ATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGGTGCACA
2395917 CATAAA
196 CATAAA
* * * *
2395923 GTGTCGATACATTTATAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAGTTACAATATAATA
1 GTGTCGATACATTTATAAGAAGTGTCGATCCCAAGAACATCGAAACCCATAATTACAATGTAATA
* *
2395988 GGTAATTTTCCAATGTAACCGGTATAAATAGACCGGTTTTATGATAGAATAGGTCTACATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATAGACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* *
2396053 ATCGACACTTGTGGAATTTATGTCGATACTTTTTGTCCAGAATGAATACCCAAAAGGGGTGCACA
131 ATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGGTGCACA
2396118 CATAAA
196 CATAAA
* * * * *
2396124 GTGTCGATACATTTATAATAAGTGTCGATCGCAAAAACATCGAAACTCATAATTACAATGCAATA
1 GTGTCGATACATTTATAAGAAGTGTCGATCCCAAGAACATCGAAACCCATAATTACAATGTAATA
* * **
2396189 GGTAATTTTTCAATGTAACTGATATAAATA-AATGGTTTTATGAGAGAATAGGTCTACATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATAGACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* * **
2396253 ATCGATACTTTTTAAATTTGTGTCGATACATTTTT
131 ATCGACACTTGTGGAATTTGTGTCGATAC-TTTTT
2396288 AAATTTCACG
Statistics
Matches: 688, Mismatches: 77, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
200 55 0.08
201 633 0.92
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (201 bp):
GTGTCGATACATTTATAAGAAGTGTCGATCCCAAGAACATCGAAACCCATAATTACAATGTAATA
GGTAATTTTTCAATGTAACCGGTATAAATAGACCGGTTTTATGAGAGAATAGGTCTACATAATGT
ATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGGTGCACA
CATAAA
Found at i:2396597 original size:15 final size:15
Alignment explanation
Indices: 2396577--2396620 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
2396567 GTCTTTCTCA
2396577 AAGCTCTTCTCAACC
1 AAGCTCTTCTCAACC
*
2396592 AAGCTCTTCTCAATC
1 AAGCTCTTCTCAACC
2396607 AAGCTCTTCTCAAC
1 AAGCTCTTCTCAAC
2396621 GACAACCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.27, C:0.36, G:0.07, T:0.30
Consensus pattern (15 bp):
AAGCTCTTCTCAACC
Found at i:2398470 original size:19 final size:19
Alignment explanation
Indices: 2398446--2398493 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
2398436 ATGTAGGGGA
2398446 AATTTTGTATACGATTCAT
1 AATTTTGTATACGATTCAT
*
2398465 AATTTTGTATACGATTTAT
1 AATTTTGTATACGATTCAT
2398484 AATTTTGTAT
1 AATTTTGTAT
2398494 GTCAATGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.52
Consensus pattern (19 bp):
AATTTTGTATACGATTCAT
Found at i:2400876 original size:13 final size:13
Alignment explanation
Indices: 2400858--2400900 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
2400848 ATTTTTTTTC
2400858 AAAAAAAAGGCAA
1 AAAAAAAAGGCAA
*
2400871 AAAAAAGAGGCAA
1 AAAAAAAAGGCAA
*
2400884 AAAAAAAAGCCAA
1 AAAAAAAAGGCAA
2400897 AAAA
1 AAAA
2400901 GCCAAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.77, C:0.09, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGGCAA
Found at i:2407212 original size:191 final size:191
Alignment explanation
Indices: 2406750--2407417 Score: 830
Period size: 199 Copynumber: 3.4 Consensus size: 191
2406740 ACCTAAATAT
*
2406750 GTGTCGATACATTTATAAAAAATATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAATATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
*
2406815 GGTAAATTTACAATGTAACCGATATAAATTTACCGGTTTTATGAGAAAATAGGTCTACATAATGT
66 GGTAAATTTACAATGTAACCGATAGAAATTTACC-GTTTTATGAGAAAATAGGTCTACATAATGT
* * * * *
2406880 AT-GACACTTGTGGAACTTGTGTCGATACTTGTTGTCTAAAATGAATGCCTAAAAGGGTGCACAC
130 ATCGACAC-T-T--AA--T-TGTCGATACTTTTTGTCCAGAATGAATGCC-AAACGGGTGCACTC
2406944 ATAAA
187 ATAAA
2406949 GTGTCGATACATTTATAAAAAATATCGATCCCAAAAACATCGAAACTC-ATAATTATAATGTAAT
1 GTGTCGATACATTTATAAAAAATATCGATCCCAAAAACATCGAAAC-CGATAATTATAATGTAAT
* * *
2407013 ATGTAAATTTACAATGTAACCGGTAGAAATTTACCAGTTTTATGAAAAAATAGGTCTACATAATG
65 AGGTAAATTTACAATGTAACCGATAGAAATTTACC-GTTTTATGAGAAAATAGGTCTACATAATG
2407078 TATCGACACTT-A-TGTCGATACTTTTTGTCCAGAATGAATGCCAAACGGGATGCACTCATAAA
129 TATCGACACTTAATTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGGG-TGCACTCATAAA
* * * * * * *
2407140 GTGTCGATACATTTATTAAAAGTATAGGTCCCAAAAATATCGAAACCGATAATTACAATATAATA
1 GTGTCGATACATTTATAAAAAATATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* *
2407205 GGTAAATTTACAATGT-ACCAGATAGAAATATACCGTTTTATGAGAAAATAGTTCTACATAATGT
66 GGTAAATTTACAATGTAACC-GATAGAAATTTACCGTTTTATGAGAAAATAGGTCTACATAATGT
* *
2407269 ATCGACATTTTTTAAGTTTGTGTCGATACTTTTT-TCCAGAATGAATGCCCAACGAGGTGCA-TG
130 ATCGACA---CTTAA---T-TGTCGATACTTTTTGTCCAGAATGAATGCCAAACG-GGTGCACT-
*
2407332 TATAAA
186 CATAAA
*** * *
2407338 GTGTCGATACATTTA-AAATTGTATCGATCCCAAAAATATTGAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAATATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
*
2407402 GGTCAATTTACAATGT
66 GGTAAATTTACAATGT
2407418 TACTTGTATA
Statistics
Matches: 419, Mismatches: 34, Indels: 34
0.86 0.07 0.07
Matches are distributed among these distances:
190 45 0.11
191 121 0.29
193 2 0.00
194 1 0.00
195 1 0.00
197 57 0.14
198 44 0.11
199 142 0.34
200 6 0.01
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (191 bp):
GTGTCGATACATTTATAAAAAATATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGATAGAAATTTACCGTTTTATGAGAAAATAGGTCTACATAATGTA
TCGACACTTAATTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGGGTGCACTCATAAA
Found at i:2407560 original size:23 final size:23
Alignment explanation
Indices: 2407534--2407614 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
2407524 AGTTAAATGT
* *
2407534 CTATTTTATTATGTAAGCGCTAC
1 CTATTATATTATATAAGCGCTAC
* *
2407557 CTATTACATTATATAAGTGCTAC
1 CTATTATATTATATAAGCGCTAC
2407580 CTATTATATTATATAAGCGCTAC
1 CTATTATATTATATAAGCGCTAC
* *
2407603 CTAATATGTTAT
1 CTATTATATTAT
2407615 TGTACTTGAT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (23 bp):
CTATTATATTATATAAGCGCTAC
Found at i:2408026 original size:23 final size:23
Alignment explanation
Indices: 2408000--2408048 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2407990 TAATATAAAT
2408000 ATTAATTAAAATTAAAAAACAAA
1 ATTAATTAAAATTAAAAAACAAA
* * * *
2408023 ATTAATTACATTTAATAAATAAA
1 ATTAATTAAAATTAAAAAACAAA
2408046 ATT
1 ATT
2408049 TTAAACTAAA
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:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (23 bp):
ATTAATTAAAATTAAAAAACAAA
Found at i:2408975 original size:89 final size:89
Alignment explanation
Indices: 2408862--2409035 Score: 348
Period size: 89 Copynumber: 2.0 Consensus size: 89
2408852 AAGTAGCAAT
2408862 CTGCCGACAGATCTAAAAACTTTTTTTTAGGATGAATACATGTATATTAATAATATAAAATTTTT
1 CTGCCGACAGATCTAAAAACTTTTTTTTAGGATGAATACATGTATATTAATAATATAAAATTTTT
2408927 ATATTTAAATAGATACGATACTAC
66 ATATTTAAATAGATACGATACTAC
2408951 CTGCCGACAGATCTAAAAACTTTTTTTTAGGATGAATACATGTATATTAATAATATAAAATTTTT
1 CTGCCGACAGATCTAAAAACTTTTTTTTAGGATGAATACATGTATATTAATAATATAAAATTTTT
2409016 ATATTTAAATAGATACGATA
66 ATATTTAAATAGATACGATA
2409036 AAATTTTAGG
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 85 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (89 bp):
CTGCCGACAGATCTAAAAACTTTTTTTTAGGATGAATACATGTATATTAATAATATAAAATTTTT
ATATTTAAATAGATACGATACTAC
Found at i:2409611 original size:3 final size:3
Alignment explanation
Indices: 2409603--2409629 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2409593 AAGATAAAAA
2409603 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
2409630 ATAATCGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2410077 original size:21 final size:21
Alignment explanation
Indices: 2410045--2410105 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
2410035 AAGACCTGTC
*
2410045 GATGAAATGACTTAACCTTTT
1 GATGAAAAGACTTAACCTTTT
* **
2410066 GATTAAAAGACTTCTCCTTTT
1 GATGAAAAGACTTAACCTTTT
* * *
2410087 TATGAAAGGGCTTAACCTT
1 GATGAAAAGACTTAACCTT
2410106 CTCATAAAAT
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (21 bp):
GATGAAAAGACTTAACCTTTT
Found at i:2413138 original size:21 final size:21
Alignment explanation
Indices: 2413099--2413155 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
2413089 AATACTTCTC
* * *
2413099 CTTTTTATAAAAGGGTTTAA-
1 CTTTTCATAAAAAGATTTAAT
2413119 CATTTTCATAAAAAGATTTAAT
1 C-TTTTCATAAAAAGATTTAAT
*
2413141 CTTTTCACAAAAAGA
1 CTTTTCATAAAAAGA
2413156 ATTGTTGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.39
Consensus pattern (21 bp):
CTTTTCATAAAAAGATTTAAT
Found at i:2414017 original size:32 final size:32
Alignment explanation
Indices: 2413981--2414045 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
2413971 GGTCGGATCG
* *
2413981 GAGTCGGGTGGAGGATATATATTTTTCGGGTC
1 GAGTCGGATGGAGGATATATATTTTTCGAGTC
* **
2414013 GAGTCGGATGTATTATATATATTTTTCGAGTC
1 GAGTCGGATGGAGGATATATATTTTTCGAGTC
2414045 G
1 G
2414046 GGTTGGGATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.22, C:0.09, G:0.31, T:0.38
Consensus pattern (32 bp):
GAGTCGGATGGAGGATATATATTTTTCGAGTC
Found at i:2417185 original size:7 final size:7
Alignment explanation
Indices: 2417173--2417213 Score: 75
Period size: 7 Copynumber: 6.0 Consensus size: 7
2417163 TAATTGTTGC
2417173 ATGCAAA
1 ATGCAAA
2417180 ATGCAAA
1 ATGCAAA
2417187 ATGCAAA
1 ATGCAAA
2417194 ATGCAAA
1 ATGCAAA
2417201 ATGCAAA
1 ATGCAAA
2417208 A-GCAAA
1 ATGCAAA
2417214 GAGTAGGGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 5 0.15
7 29 0.85
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.12
Consensus pattern (7 bp):
ATGCAAA
Found at i:2419456 original size:22 final size:23
Alignment explanation
Indices: 2419409--2419460 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
2419399 ATATTCTCAC
*
2419409 AAAACAATGAATTATGATAATGAT
1 AAAA-AATGAATTATGATAATAAT
2419433 AAAAAATGAATTAT-ATAATAAT
1 AAAAAATGAATTATGATAATAAT
2419455 AAAAAA
1 AAAAAA
2419461 GTTATCATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 13 0.48
23 10 0.37
24 4 0.15
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (23 bp):
AAAAAATGAATTATGATAATAAT
Found at i:2423073 original size:23 final size:23
Alignment explanation
Indices: 2423043--2423086 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2423033 TGTTCGTTTC
2423043 TTCATGTTCACGAACATGTTCGT
1 TTCATGTTCACGAACATGTTCGT
* *
2423066 TTCATGTTCATGAATATGTTC
1 TTCATGTTCACGAACATGTTC
2423087 ATTTAACGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.43
Consensus pattern (23 bp):
TTCATGTTCACGAACATGTTCGT
Found at i:2423102 original size:23 final size:23
Alignment explanation
Indices: 2423071--2423116 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2423061 TTCGTTTCAT
* * *
2423071 GTTCATGAATATGTTCATTTAAC
1 GTTCATGAAAATATGCATTTAAC
*
2423094 GTTCTTGAAAATATGCATTTAAC
1 GTTCATGAAAATATGCATTTAAC
2423117 ATTTGCGAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (23 bp):
GTTCATGAAAATATGCATTTAAC
Found at i:2425543 original size:15 final size:15
Alignment explanation
Indices: 2425523--2425551 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2425513 ACGATGCTTC
2425523 GTCTACTGTTGTTTA
1 GTCTACTGTTGTTTA
2425538 GTCTACTGTTGTTT
1 GTCTACTGTTGTTT
2425552 GTGCAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.14, G:0.21, T:0.55
Consensus pattern (15 bp):
GTCTACTGTTGTTTA
Found at i:2428928 original size:32 final size:32
Alignment explanation
Indices: 2428887--2428950 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
2428877 AGTGGACCTA
2428887 ATGTGTTTTGTTTGATTCATGTCATATTTCTT
1 ATGTGTTTTGTTTGATTCATGTCATATTTCTT
2428919 ATGTGTTTTGTTTGATTCATGTCATATTTCTT
1 ATGTGTTTTGTTTGATTCATGTCATATTTCTT
2428951 CTATTTAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.16, C:0.09, G:0.16, T:0.59
Consensus pattern (32 bp):
ATGTGTTTTGTTTGATTCATGTCATATTTCTT
Found at i:2435091 original size:9 final size:9
Alignment explanation
Indices: 2435079--2435109 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
2435069 ATAAAAAAAT
2435079 GAAAATAAA
1 GAAAATAAA
2435088 GAAAATAAA
1 GAAAATAAA
2435097 GAAAATAAA
1 GAAAATAAA
2435106 -AAAA
1 GAAAA
2435110 CAACCGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.18
9 18 0.82
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (9 bp):
GAAAATAAA
Found at i:2435186 original size:23 final size:23
Alignment explanation
Indices: 2435146--2435193 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
2435136 AGTAAAGATA
* * *
2435146 AAAATGAATACAATAAGAAAAAT
1 AAAATGAAGAAAAAAAGAAAAAT
*
2435169 AAAATGAAGAAAAAAAGAATAAT
1 AAAATGAAGAAAAAAAGAAAAAT
2435192 AA
1 AA
2435194 TGATAATAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (23 bp):
AAAATGAAGAAAAAAAGAAAAAT
Found at i:2435509 original size:2 final size:2
Alignment explanation
Indices: 2435504--2435551 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2435494 GGAAAAAATG
2435504 TA TA TA TA TA TA 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 TA TA TA TA TA TA
2435546 TA TA TA
1 TA TA TA
2435552 ATAATAGAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2436142 original size:37 final size:37
Alignment explanation
Indices: 2436092--2436166 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
2436082 ATGTTTGTGG
2436092 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
*
2436129 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
2436166 A
1 A
2436167 ACGTTATGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:2436947 original size:35 final size:36
Alignment explanation
Indices: 2436903--2436996 Score: 154
Period size: 35 Copynumber: 2.6 Consensus size: 36
2436893 CGGAAAACAG
2436903 TTTTTTTGTGTTTCAAGAGAAACAATTTCAAAGG-T
1 TTTTTTTGTGTTTCAAGAGAAACAATTTCAAAGGTT
**
2436938 TTTTTTTGTGTTTCAAGAGAAATGATTTCAAAGGTT
1 TTTTTTTGTGTTTCAAGAGAAACAATTTCAAAGGTT
*
2436974 TTTTTTTGTGTTTTAAGAGAAAC
1 TTTTTTTGTGTTTCAAGAGAAAC
2436997 TGTCTCAAGA
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
35 32 0.59
36 22 0.41
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (36 bp):
TTTTTTTGTGTTTCAAGAGAAACAATTTCAAAGGTT
Found at i:2437060 original size:74 final size:73
Alignment explanation
Indices: 2436982--2437315 Score: 250
Period size: 73 Copynumber: 4.7 Consensus size: 73
2436972 TTTTTTTTTG
* *
2436982 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTTCAAAGGAAACTGTCTCAAGAGA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTG-TTTCAAAGGAAACTGTCTCAAGAGA
2437047 GACAAAATT
65 GACAAAATT
* * * * *
2437056 TGTTTCAAGAGAAACTGA-CTCAAGAGATACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGA
1 TGTTTCAAGAGAAACT-ATCTCAAGAGAGACAAAACTTTGTTTCAAAGGAAACTGTCTCAAGAGA
** *
2437120 GATGAATTT
65 GACAAAATT
* * *
2437129 TGTTTCAAG-GAAAACATAT-TC-A-A-AG-----ATTTTGTTTCAAGGGAAACTGCCTCAAGAG
1 TGTTTCAAGAG-AAAC-TATCTCAAGAGAGACAAAACTTTGTTTCAAAGGAAACTGTCTCAAGAG
2437184 AGACAAAATT
64 AGACAAAATT
* * **** * * *
2437194 TGTTTCAAGGGAAACTATCTCAAGAGTGACAAAA-AAAATTTC-AAGAAAAATTGTCTCAAGAAA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAAG-GAAACTGTCTCAAGAGA
2437257 GACAAAACTT
65 GACAAAA-TT
* * * * *
2437267 AGTTCCAAAAGAAACTGTCTCAAG-GAAGACGAAA-TTTGTTTC-AAGGAAA
1 TGTTTCAAGAGAAACTATCTCAAGAG-AGACAAAACTTTGTTTCAAAGGAAA
2437316 ACATATTTAA
Statistics
Matches: 200, Mismatches: 43, Indels: 36
0.72 0.15 0.13
Matches are distributed among these distances:
64 3 0.01
65 45 0.22
66 2 0.01
67 1 0.00
68 1 0.00
70 1 0.00
71 3 0.01
72 30 0.15
73 79 0.40
74 35 0.17
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (73 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAAGGAAACTGTCTCAAGAGAG
ACAAAATT
Found at i:2437062 original size:36 final size:36
Alignment explanation
Indices: 2436992--2437380 Score: 237
Period size: 36 Copynumber: 11.1 Consensus size: 36
2436982 TGTTTTAAGA
2436992 GAAACTGTCTCAAGAGAGACAAAACTTTGTTTTCAAAG
1 GAAACTGTCTCAAGAGAGACAAAA-TTTG-TTTCAAAG
2437030 GAAACTGTCTCAAGAGAGACAAAATTTGTTTC-AAG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAG
* * * * *
2437065 AGAAACTGACTCAAGAGATACAAAACTTAGTTCCAAAA
1 -GAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAAG
* ** *
2437103 GAAACTGTCTCAAGGGAGATGAATTTTGTTTC-AAG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAG
* * *
2437138 GAAAACATAT-TC-A-A-AG----ATTTTGTTTCAAGG
1 G-AAAC-TGTCTCAAGAGAGACAAAATTTGTTTCAAAG
* *
2437168 GAAACTGCCTCAAGAGAGACAAAATTTGTTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAG
* * ****
2437204 GAAACTATCTCAAGAGTGACAAAAAAAATTTC-AAG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAG
* * * * * *
2437239 AAAAATTGTCTCAAGAAAGACAAAACTTAGTTCCAAAA
1 -GAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAAG
*
2437277 GAAACTGTCTCAAG-GAAGACGAAATTTGTTTC-AAG
1 GAAACTGTCTCAAGAG-AGACAAAATTTGTTTCAAAG
* * * *
2437312 GAAAACATAT-T-TA-A-AG----ATTTTGTTTCAAGG
1 G-AAAC-TGTCTCAAGAGAGACAAAATTTGTTTCAAAG
*
2437342 GAAACTGTCTCAAGAGAGGCAAAATTTGTTTC-AAG
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAG
2437377 GAAA
1 GAAA
2437381 ACATATTCAA
Statistics
Matches: 268, Mismatches: 53, Indels: 63
0.70 0.14 0.16
Matches are distributed among these distances:
28 3 0.01
29 30 0.11
30 8 0.03
31 2 0.01
32 4 0.01
33 4 0.01
35 19 0.07
36 115 0.43
37 55 0.21
38 28 0.10
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAG
Found at i:2437254 original size:174 final size:174
Alignment explanation
Indices: 2436982--2437390 Score: 595
Period size: 174 Copynumber: 2.3 Consensus size: 174
2436972 TTTTTTTTTG
* * * *
2436982 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTTCAAAGGAAACTGTCTCAAGAGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTG-TTTCAAGGGAAACTATCTCAAGAGA
**** * * *
2437047 GACAAAATTTGTTTCAAGAGAAACTGACTCAAGAGATACAAAACTTAGTTCCAAAAGAAACTGTC
64 GACAAAAAAAATTTCAAGAAAAACTGACTCAAGAAAGACAAAACTTAGTTCCAAAAGAAACTGTC
* * *
2437112 TCAAGGGAGATGAATTTTGTTTCAAGGAAAACATATTCAAAGATTT
129 TCAAGGAAGACGAAATTTGTTTCAAGGAAAACATATTCAAAGATTT
* *
2437158 TGTTTCAAGGGAAACTGCCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGTGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGA
* *
2437223 CAAAAAAAATTTCAAGAAAAATTGTCTCAAGAAAGACAAAACTTAGTTCCAAAAGAAACTGTCTC
66 CAAAAAAAATTTCAAGAAAAACTGACTCAAGAAAGACAAAACTTAGTTCCAAAAGAAACTGTCTC
*
2437288 AAGGAAGACGAAATTTGTTTCAAGGAAAACATATTTAAAGATTT
131 AAGGAAGACGAAATTTGTTTCAAGGAAAACATATTCAAAGATTT
* *
2437332 TGTTTCAAGGGAAACTGTCTCAAGAGAGGCAAAATTTGTTTCAAGGAAAACATAT-TCAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC-TATCTCAA
2437391 AGATTTTGTT
Statistics
Matches: 210, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
174 172 0.82
175 7 0.03
176 31 0.15
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (174 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGA
CAAAAAAAATTTCAAGAAAAACTGACTCAAGAAAGACAAAACTTAGTTCCAAAAGAAACTGTCTC
AAGGAAGACGAAATTTGTTTCAAGGAAAACATATTCAAAGATTT
Found at i:2437341 original size:29 final size:29
Alignment explanation
Indices: 2437301--2437411 Score: 89
Period size: 29 Copynumber: 3.6 Consensus size: 29
2437291 GAAGACGAAA
*
2437301 TTTGTTTCAAGGAAAACATATTTAAAGAT
1 TTTGTTTCAAGGAAAACATATTAAAAGAT
* * *
2437330 TTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGGCAAAA
1 TTTGTTTCAAGGAAAACATAT-T-AA-A-A-G---AT
*
2437366 TTTGTTTCAAGGAAAACATATTCAAAGAT
1 TTTGTTTCAAGGAAAACATATTAAAAGAT
*
2437395 TTTGTTTCAAGGGAAAC
1 TTTGTTTCAAGGAAAAC
2437412 TGTCTCAAGA
Statistics
Matches: 64, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
28 2 0.03
29 34 0.53
30 1 0.02
31 1 0.02
32 2 0.03
33 2 0.03
34 1 0.02
35 1 0.02
36 18 0.28
37 2 0.03
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (29 bp):
TTTGTTTCAAGGAAAACATATTAAAAGAT
Found at i:2437352 original size:65 final size:66
Alignment explanation
Indices: 2437277--2437433 Score: 257
Period size: 65 Copynumber: 2.4 Consensus size: 66
2437267 AGTTCCAAAA
* *
2437277 GAAACTGTCTCAAGGA-AGACGAAATTTGTTTCAAGGAAAACATATTTAAAGATTTTGTTTCAAG
1 GAAACTGTCTCAAGGAGAGACAAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAG
2437341 G
66 G
*
2437342 GAAACTGTCTCAA-GAGAGGCAAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAG
1 GAAACTGTCTCAAGGAGAGACAAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAG
2437406 G
66 G
*
2437407 GAAACTGTCTCAA-GAGAGAGAAAATTT
1 GAAACTGTCTCAAGGAGAGACAAAATTT
2437434 TATTCTGAGT
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
64 2 0.02
65 84 0.98
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.29
Consensus pattern (66 bp):
GAAACTGTCTCAAGGAGAGACAAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAG
G
Found at i:2444744 original size:22 final size:20
Alignment explanation
Indices: 2444718--2444780 Score: 56
Period size: 19 Copynumber: 3.1 Consensus size: 20
2444708 TTAGTGCAGA
2444718 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCC-T-AAG
* * * *
2444740 GGGAACCGATTCCCCC-CAT
1 GGGAATCGATACCCCCTAAG
*
2444759 GGGAATCGATACCCCCTGAG
1 GGGAATCGATACCCCCTAAG
2444779 GG
1 GG
2444781 TTCTGGTTTT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 15 0.47
20 3 0.09
22 14 0.44
ACGTcount: A:0.24, C:0.32, G:0.29, T:0.16
Consensus pattern (20 bp):
GGGAATCGATACCCCCTAAG
Found at i:2445531 original size:155 final size:154
Alignment explanation
Indices: 2445224--2445532 Score: 577
Period size: 155 Copynumber: 2.0 Consensus size: 154
2445214 TGTTATGAAA
2445224 ACTATACATATTGATTTTCAAAACTTTATTTTTCATAAGTTTTTCAAAAACTTTGCCCATTAGGA
1 ACTATACATATTGATTTTCAAAACTTTATTTTTCATAAGTTTTTCAAAAACTTTGCCCATTAGGA
2445289 TTGGTTTAGAGAACCTTGAAATATTGAGGACTCAATTGAGTTTTGGGATTGATTATTTTGAATAC
66 TTGGTTTAGAGAACCTTGAAATATTGAGGACTCAATTGAGTTTTGGGATTGATTATTTTGAATAC
2445354 ATATGTTTTTAAAAATGCGGTTAT
131 ATATGTTTTTAAAAATGCGGTTAT
2445378 ACTATACATATATTGATTTTCAAAACTTTATTTTTCATAAG-TTTTCAAAAACTTTGCCCATTAG
1 ACTATAC--ATATTGATTTTCAAAACTTTATTTTTCATAAGTTTTTCAAAAACTTTGCCCATTAG
2445442 GATTGGTTTAGAGAACCTTGAAATATTGAGGACTCAATTGAG-TTTGGGATTGATTATTTTGAAT
64 GATTGGTTTAGAGAACCTTGAAATATTGAGGACTCAATTGAGTTTTGGGATTGATTATTTTGAAT
2445506 ACATATGTTTTTAAAAATGCAGGTTAT
129 ACATATGTTTTTAAAAATGC-GGTTAT
2445533 CTTTCCATTC
Statistics
Matches: 152, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
154 49 0.32
155 71 0.47
156 32 0.21
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (154 bp):
ACTATACATATTGATTTTCAAAACTTTATTTTTCATAAGTTTTTCAAAAACTTTGCCCATTAGGA
TTGGTTTAGAGAACCTTGAAATATTGAGGACTCAATTGAGTTTTGGGATTGATTATTTTGAATAC
ATATGTTTTTAAAAATGCGGTTAT
Found at i:2446502 original size:18 final size:18
Alignment explanation
Indices: 2446464--2446509 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
2446454 TTGACGACAC
*
2446464 GAGGAACAAACACGAGCA
1 GAGGAACAAACACGAACA
2446482 GAGGAACAAACAC-AACTA
1 GAGGAACAAACACGAAC-A
*
2446500 GAGGATCAAA
1 GAGGAACAAA
2446510 TGCCTCCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 2 0.08
18 23 0.92
ACGTcount: A:0.52, C:0.20, G:0.24, T:0.04
Consensus pattern (18 bp):
GAGGAACAAACACGAACA
Found at i:2447168 original size:35 final size:38
Alignment explanation
Indices: 2447138--2447208 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
2447128 CATTTTTAAA
2447138 GAGTAGTGTTAGAGTAAGGGGGAGTAATTTTCAAAGAG
1 GAGTAGTGTTAGAGTAAGGGGGAGTAATTTTCAAAGAG
2447176 GAGTAGTGTTAGAGTAAGGGGGAGT-A-TTTCAAA
1 GAGTAGTGTTAGAGTAAGGGGGAGTAATTTTCAAA
2447209 CTTGAAACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
36 7 0.21
37 1 0.03
38 25 0.76
ACGTcount: A:0.34, C:0.03, G:0.37, T:0.27
Consensus pattern (38 bp):
GAGTAGTGTTAGAGTAAGGGGGAGTAATTTTCAAAGAG
Found at i:2447201 original size:21 final size:21
Alignment explanation
Indices: 2447138--2447201 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
2447128 CATTTTTAAA
2447138 GAGTAGTGTTAGAGTAAGGGG
1 GAGTAGTGTTAGAGTAAGGGG
* ** *
2447159 GAGTAAT-TTTCA--AA-GAG
1 GAGTAGTGTTAGAGTAAGGGG
2447176 GAGTAGTGTTAGAGTAAGGGG
1 GAGTAGTGTTAGAGTAAGGGG
2447197 GAGTA
1 GAGTA
2447202 TTTCAAACTT
Statistics
Matches: 31, Mismatches: 8, Indels: 8
0.66 0.17 0.17
Matches are distributed among these distances:
17 8 0.26
18 5 0.16
20 5 0.16
21 13 0.42
ACGTcount: A:0.33, C:0.02, G:0.41, T:0.25
Consensus pattern (21 bp):
GAGTAGTGTTAGAGTAAGGGG
Found at i:2449110 original size:23 final size:23
Alignment explanation
Indices: 2449080--2449126 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
2449070 GTCCGAAGCT
*
2449080 TGTGGAGGTATGTCCAGTGTTTG
1 TGTGGAGGTACGTCCAGTGTTTG
*
2449103 TGTGGAGGTACGTCTAGTGTTTG
1 TGTGGAGGTACGTCCAGTGTTTG
2449126 T
1 T
2449127 ACCCTTTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.13, C:0.09, G:0.38, T:0.40
Consensus pattern (23 bp):
TGTGGAGGTACGTCCAGTGTTTG
Found at i:2450861 original size:6 final size:6
Alignment explanation
Indices: 2450850--2450884 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
2450840 TAATCCGCAA
2450850 AAATTT AAATTT AAATTT AAATTT AAATTT AAATT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATT
2450885 ATTCGATCCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
AAATTT
Found at i:2451464 original size:3 final size:3
Alignment explanation
Indices: 2451403--2451447 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
2451393 GTATATATAT
2451403 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2451448 CATATAGATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2452196 original size:20 final size:20
Alignment explanation
Indices: 2452162--2452226 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
2452152 AAATAAATAC
*
2452162 TTAAA-ATATAATTTTTTAT
1 TTAAATATATATTTTTTTAT
2452181 TTAAATATATATTTTTTTAT
1 TTAAATATATATTTTTTTAT
* *
2452201 TTAAATATAT-TATTTTCAT
1 TTAAATATATATTTTTTTAT
2452220 TTAAATA
1 TTAAATA
2452227 GTTTAACTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
19 19 0.45
20 23 0.55
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TTAAATATATATTTTTTTAT
Found at i:2452270 original size:27 final size:30
Alignment explanation
Indices: 2452204--2452272 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
2452194 TTTTTATTTA
*
2452204 AATATATTATTTTCATTTAAATAGTTTAACTT
1 AATATA-T-TTTTCATTTAAATAGTCTAACTT
2452236 AAATATATTTTTCATTTAAATA-TCTAA-TT
1 -AATATATTTTTCATTTAAATAGTCTAACTT
2452265 -ATATATTT
1 AATATATTT
2452273 AGTACCTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
27 8 0.23
29 2 0.06
30 4 0.11
31 14 0.40
32 1 0.03
33 6 0.17
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (30 bp):
AATATATTTTTCATTTAAATAGTCTAACTT
Found at i:2453902 original size:3 final size:3
Alignment explanation
Indices: 2453894--2453920 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2453884 CCAAGCACAC
2453894 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
2453921 GTACCTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2455913 original size:16 final size:16
Alignment explanation
Indices: 2455889--2455932 Score: 65
Period size: 14 Copynumber: 2.9 Consensus size: 16
2455879 TGGATGAAAC
2455889 TGTAGAAAACAGACTG
1 TGTAGAAAACAGACTG
*
2455905 TGTATAAAACAGAC--
1 TGTAGAAAACAGACTG
2455919 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
2455933 AAGTCTGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 13 0.50
16 13 0.50
ACGTcount: A:0.48, C:0.14, G:0.20, T:0.18
Consensus pattern (16 bp):
TGTAGAAAACAGACTG
Found at i:2459291 original size:16 final size:14
Alignment explanation
Indices: 2459270--2459313 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 14
2459260 CCTGATACCA
2459270 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
*
2459284 TGTGTAGAAAACAAAC
1 --TGTAGAAAACAGAC
2459300 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
2459314 AAGTCTGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 13 0.50
16 13 0.50
ACGTcount: A:0.50, C:0.14, G:0.20, T:0.16
Consensus pattern (14 bp):
TGTAGAAAACAGAC
Found at i:2459305 original size:14 final size:15
Alignment explanation
Indices: 2459270--2459310 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
2459260 CCTGATACCA
*
2459270 TGTAGAAAACAGACTG
1 TGTAGAAAACAAAC-G
2459286 TGTAGAAAACAAAC-
1 TGTAGAAAACAAACG
2459300 TGTAGAAAACA
1 TGTAGAAAACA
2459311 GACAAGTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 11 0.46
16 13 0.54
ACGTcount: A:0.51, C:0.12, G:0.20, T:0.17
Consensus pattern (15 bp):
TGTAGAAAACAAACG
Found at i:2464495 original size:28 final size:28
Alignment explanation
Indices: 2464455--2464512 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
2464445 AAGTCATAAG
*
2464455 AAGCATGAGCATTCCTTCCAGGGAAAAA
1 AAGCATGAGCATTCCTTCAAGGGAAAAA
2464483 AAGCATGAGCATTCCTTCAAGGGAAAAA
1 AAGCATGAGCATTCCTTCAAGGGAAAAA
2464511 AA
1 AA
2464513 CCAACAAGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (28 bp):
AAGCATGAGCATTCCTTCAAGGGAAAAA
Found at i:2468293 original size:41 final size:40
Alignment explanation
Indices: 2468185--2468340 Score: 253
Period size: 41 Copynumber: 3.9 Consensus size: 40
2468175 TAATTACTGA
* *
2468185 AACTATACGATAAGTATTAATTTGAATCACATGAATGTCTG
1 AACTATATGAT-ACTATTAATTTGAATCACATGAATGTCTG
2468226 AACTATAT-AT-CTATTAATTTGAATCACATGAATGTCTG
1 AACTATATGATACTATTAATTTGAATCACATGAATGTCTG
2468264 AACTATATGATACCTATTAATTTGAATCACATGAATGTCTG
1 AACTATATGATA-CTATTAATTTGAATCACATGAATGTCTG
2468305 AACTATATGATATCTATTAATTTGAATCACATGAAT
1 AACTATATGATA-CTATTAATTTGAATCACATGAAT
2468341 ACAATTAAAA
Statistics
Matches: 109, Mismatches: 3, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
38 35 0.32
39 2 0.02
40 2 0.02
41 70 0.64
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (40 bp):
AACTATATGATACTATTAATTTGAATCACATGAATGTCTG
Found at i:2469102 original size:21 final size:21
Alignment explanation
Indices: 2469078--2469130 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2469068 ATTCTGACTA
2469078 TCGCATTGCGA-TTTCTCAAAT
1 TCGCATTGCGATTTTC-CAAAT
* *
2469099 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
2469120 TCGCAATGCGA
1 TCGCATTGCGA
2469131 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:2469145 original size:20 final size:20
Alignment explanation
Indices: 2469120--2469213 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
2469110 TTTTCCTAAT
2469120 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
2469140 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
2469161 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
2469181 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
2469201 TCGCAATGCGAAT
1 TCGCAATGCGAAT
2469214 CTGACTATCG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 48 0.76
21 15 0.24
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:2469166 original size:41 final size:40
Alignment explanation
Indices: 2469120--2469213 Score: 134
Period size: 41 Copynumber: 2.3 Consensus size: 40
2469110 TTTTCCTAAT
**
2469120 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAA-TACGAAAA
* * *
2469161 TCGCAATGCGATTACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATACGAAAA
2469201 TCGCAATGCGAAT
1 TCGCAATGCGAAT
2469214 CTGACTATCG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 17 0.36
41 30 0.64
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.21
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATACGAAAA
Found at i:2469193 original size:61 final size:60
Alignment explanation
Indices: 2469120--2469233 Score: 183
Period size: 61 Copynumber: 1.9 Consensus size: 60
2469110 TTTTCCTAAT
*
2469120 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAATCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATCT-GAAAATCGCAATGCGATTACGTAAA
* **
2469181 TCGCAATGCGAATACGTAAATCGCAATGCGAATCTGACTATCGCAATGCGATT
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATCTGAAAATCGCAATGCGATT
2469234 TACATAGCGC
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
60 16 0.33
61 33 0.67
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (60 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATCTGAAAATCGCAATGCGATTACGTAAA
Found at i:2469426 original size:22 final size:22
Alignment explanation
Indices: 2469401--2469476 Score: 98
Period size: 22 Copynumber: 3.5 Consensus size: 22
2469391 CACTCTCTAA
* *
2469401 GACGACATCCGTCCCCATCTCC
1 GACGAAATCAGTCCCCATCTCC
*
2469423 GACGAAATCAGTCCCCATCGCC
1 GACGAAATCAGTCCCCATCTCC
* *
2469445 GACGATATCAGTCTCCATCTCC
1 GACGAAATCAGTCCCCATCTCC
*
2469467 GGCGAAATCA
1 GACGAAATCA
2469477 TTCACGGTCA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.25, C:0.39, G:0.17, T:0.18
Consensus pattern (22 bp):
GACGAAATCAGTCCCCATCTCC
Found at i:2469839 original size:33 final size:32
Alignment explanation
Indices: 2469802--2469915 Score: 93
Period size: 40 Copynumber: 3.2 Consensus size: 32
2469792 ACTATCGCAA
2469802 TGCGATTCTATCGTTGCGATTTTCATTTCGCGT
1 TGCGATTCT-TCGTTGCGATTTTCATTTCGCGT
** *
2469835 TGCGATTCTTGCGTTGCGATAGTCAAATTCGCGT
1 TGCGATTCTT-CGTTGCGATTTTC-ATTTCGCGT
*
2469869 TGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCGTGT
1 TGCGAT--TC---TTC--GTTGCGATTTTCA-TTTCGCGT
2469909 TGCGATT
1 TGCGATT
2469916 TAAAGTTTCA
Statistics
Matches: 64, Mismatches: 7, Indels: 15
0.74 0.08 0.17
Matches are distributed among these distances:
32 1 0.02
33 20 0.31
34 14 0.22
36 2 0.03
38 2 0.03
39 3 0.05
40 22 0.34
ACGTcount: A:0.14, C:0.18, G:0.24, T:0.44
Consensus pattern (32 bp):
TGCGATTCTTCGTTGCGATTTTCATTTCGCGT
Found at i:2469870 original size:20 final size:20
Alignment explanation
Indices: 2469845--2469894 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
2469835 TGCGATTCTT
2469845 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
**
2469865 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCAAATTC
*
2469885 GTGTTGCGAT
1 GCGTTGCGAT
2469895 TTTCATTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:2469871 original size:34 final size:33
Alignment explanation
Indices: 2469802--2469874 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
2469792 ACTATCGCAA
** *
2469802 TGCGATTCTATCGTTGCGATTTTCATTTCGCGT
1 TGCGATTCTATCGTTGCGATAGTCAATTCGCGT
2469835 TGCGATTCT-TGCGTTGCGATAGTCAAATTCGCGT
1 TGCGATTCTAT-CGTTGCGATAGTC-AATTCGCGT
2469869 TGCGAT
1 TGCGAT
2469875 AGTCATTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 20 0.57
34 14 0.40
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (33 bp):
TGCGATTCTATCGTTGCGATAGTCAATTCGCGT
Found at i:2469900 original size:20 final size:20
Alignment explanation
Indices: 2469862--2469916 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
2469852 GATAGTCAAA
* **
2469862 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
2469882 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
2469902 TTCGTGTTGCGATTT
1 TTCGTGTTGCGATTT
2469917 AAAGTTTCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:2469924 original size:20 final size:20
Alignment explanation
Indices: 2469881--2469924 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2469871 CGATAGTCAT
** *
2469881 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
2469901 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
2469921 TTTC
1 TTTC
2469925 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:2471820 original size:20 final size:20
Alignment explanation
Indices: 2471795--2471951 Score: 153
Period size: 20 Copynumber: 8.5 Consensus size: 20
2471785 AGAATAGTTT
2471795 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
2471815 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
2471835 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
2471855 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
2471871 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
2471888 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
2471904 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
2471922 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
2471942 ACTATCGCAA
1 ACTATCGCAA
2471952 CGAGAGAATC
Statistics
Matches: 118, Mismatches: 5, Indels: 28
0.78 0.03 0.19
Matches are distributed among these distances:
14 14 0.12
16 10 0.08
17 8 0.07
18 5 0.04
19 7 0.06
20 74 0.63
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:2471895 original size:33 final size:33
Alignment explanation
Indices: 2471838--2471918 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
2471828 GAAAATGACT
* ** * * *
2471838 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCG-AAATGAAAATCGCAACAACAAA
2471872 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
2471905 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
2471919 ATGACTATCG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
33 31 0.76
34 10 0.24
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACAACAAA
Found at i:2471992 original size:20 final size:20
Alignment explanation
Indices: 2471967--2472117 Score: 190
Period size: 20 Copynumber: 7.9 Consensus size: 20
2471957 GAATCGCAAT
2471967 TCATTTTCGCATTGCGATAG
1 TCATTTTCGCATTGCGATAG
2471987 TCATTTTCGCATTGCGATAG
1 TCATTTTCGCATTGCGATAG
*
2472007 TCATTTTCGCATTGTGATAG
1 TCATTTTCGCATTGCGATAG
* **
2472027 TCATTTTCGCGTTGCGATTT
1 TCATTTTCGCATTGCGATAG
2472047 TCA-TTTCGCATTGCGAT--
1 TCATTTTCGCATTGCGATAG
*
2472064 TC--TCTCG--TTGCGATAG
1 TCATTTTCGCATTGCGATAG
*
2472080 TCATTTTCGCGTTGCGATAG
1 TCATTTTCGCATTGCGATAG
*
2472100 TCATTTTCGCGTTGCGAT
1 TCATTTTCGCATTGCGAT
2472118 TTTAAGTTTC
Statistics
Matches: 117, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
14 7 0.06
16 6 0.05
17 2 0.02
18 4 0.03
19 13 0.11
20 85 0.73
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.42
Consensus pattern (20 bp):
TCATTTTCGCATTGCGATAG
Found at i:2472692 original size:21 final size:21
Alignment explanation
Indices: 2472624--2472692 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
2472614 GGCCTCCCCT
*
2472624 ATCGTTCAAGAGGCCTCTATC
1 ATCGTTCAAGAGGCCACTATC
** * * **
2472645 ATCCCTCAAGAGTCCCCTCCC
1 ATCGTTCAAGAGGCCACTATC
* *
2472666 ACCGTTCAAGAGGCCACTGTC
1 ATCGTTCAAGAGGCCACTATC
2472687 ATCGTT
1 ATCGTT
2472693 GAAAGAGGTC
Statistics
Matches: 34, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCACTATC
Found at i:2474108 original size:14 final size:14
Alignment explanation
Indices: 2474089--2474124 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2474079 ATTGTTTAAT
2474089 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2474103 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2474117 TGATTTGT
1 TGATTTGT
2474125 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2474379 original size:20 final size:20
Alignment explanation
Indices: 2474295--2474369 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
2474285 GCGATTCTCT
*
2474295 CGTTGAGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
2474315 CGTTGTGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
2474335 CGTTGCAATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
2474355 TGTTGCGATAGTCAT
1 CGTTGCGATAGTCAT
2474370 ATTCACGTTG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:2474379 original size:40 final size:40
Alignment explanation
Indices: 2474302--2474403 Score: 119
Period size: 40 Copynumber: 2.7 Consensus size: 40
2474292 TCTCGTTGAG
* *
2474302 ATAGTCATTTCCGCGTTGTGATAGTCAATTCCGCGTTGCA
1 ATAGTCATTTCCGCGTTGCGATAGTCAATTCCACGTTGCA
*
2474342 ATAGTCATTTCCGTGTTGCGATAGTCATATT-CACGTTG--
1 ATAGTCATTTCCGCGTTGCGATAGTCA-ATTCCACGTTGCA
2474380 -T-G--ATTTCCGCGTTGCGATAGTCAA
1 ATAGTCATTTCCGCGTTGCGATAGTCAA
2474404 ATGAATGTCT
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
33 1 0.02
34 20 0.35
36 1 0.02
37 1 0.02
40 31 0.54
41 3 0.05
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (40 bp):
ATAGTCATTTCCGCGTTGCGATAGTCAATTCCACGTTGCA
Found at i:2476847 original size:24 final size:24
Alignment explanation
Indices: 2476820--2476866 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
2476810 CAAAATCCGA
2476820 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
2476844 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
2476867 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:2476875 original size:24 final size:24
Alignment explanation
Indices: 2476824--2476875 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2476814 ATCCGAGTAT
** *
2476824 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
2476848 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
2476872 TGAC
1 TGAC
2476876 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:2477552 original size:22 final size:21
Alignment explanation
Indices: 2477513--2477553 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2477503 TGCCGGATGG
**
2477513 GGAAGGATGTCGTTGGATATA
1 GGAAGGATGTCGCCGGATATA
2477534 GGAACGGATGTCGCCGGATA
1 GGAA-GGATGTCGCCGGATA
2477554 GAGTGATAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.27, C:0.12, G:0.39, T:0.22
Consensus pattern (21 bp):
GGAAGGATGTCGCCGGATATA
Found at i:2477729 original size:20 final size:20
Alignment explanation
Indices: 2477704--2477750 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
2477694 AAATTCAGTA
*
2477704 TTGCGATAGTTAGAATCTCG
1 TTGCGATAGTTAGAATCACG
*
2477724 TTGCGATAGTTAGATTCACG
1 TTGCGATAGTTAGAATCACG
2477744 TTGCGAT
1 TTGCGAT
2477751 TTACATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTTAGAATCACG
Found at i:2477760 original size:20 final size:20
Alignment explanation
Indices: 2477744--2477890 Score: 222
Period size: 20 Copynumber: 7.3 Consensus size: 20
2477734 TAGATTCACG
*
2477744 TTGCGATTTACATATTCGCA
1 TTGCGATTTACGTATTCGCA
2477764 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
2477784 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
2477804 TTGCGCTTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
2477824 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
* ** *
2477844 TTGCGATTTTCCAAATTCGCG
1 TTGCGA-TTTACGTATTCGCA
2477865 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
2477885 TTGCGA
1 TTGCGA
2477891 ATTAGGAAAA
Statistics
Matches: 113, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
20 98 0.87
21 15 0.13
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:2477789 original size:60 final size:58
Alignment explanation
Indices: 2477724--2477890 Score: 217
Period size: 60 Copynumber: 2.8 Consensus size: 58
2477714 TAGAATCTCG
* * *
2477724 TTGCGATAGTTAGATTCACGTTGCGATTTACATATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGAT--TTAGATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCA
* *
2477784 TTGCGATTTACGTATTCGCATTGCGCTTTACGTATTCGCATTGCGATTTACGTAATCGCA
1 TTGCGATTTA-G-ATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCA
*
2477844 TTGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCATTGCGA
1 TTGCGA-TTT--AGATTCGCGTTGCGATTTACGTATTCGCATTGCGA
2477891 ATTAGGAAAA
Statistics
Matches: 94, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
58 3 0.03
59 1 0.01
60 55 0.59
61 34 0.36
63 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.38
Consensus pattern (58 bp):
TTGCGATTTAGATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCA
Found at i:2477913 original size:21 final size:21
Alignment explanation
Indices: 2477887--2477932 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2477877 TATTCGCATT
*
2477887 GCGAATTAGGAAAATTGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
2477908 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
2477929 GCGA
1 GCGA
2477933 TAGTCAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.20
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:2486301 original size:30 final size:30
Alignment explanation
Indices: 2486265--2486337 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
2486255 CCCGAAGGAC
*
2486265 CTATCCAGAGGTCATAAAGATCCTTGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
2486295 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
2486325 CTGTCCATAGGTC
1 CTATCCAGAGGTC
2486338 CCGAAGAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:2486354 original size:30 final size:30
Alignment explanation
Indices: 2486311--2486395 Score: 89
Period size: 31 Copynumber: 2.8 Consensus size: 30
2486301 AGAGGTCATA
* *
2486311 AAGATCCTCGGTAACTGTCCATAGGTCCCG
1 AAGAACCTAGGTAACTGTCCATAGGTCCCG
* * *
2486341 AAGAACCTAGGTAAACTGTCCATATGTTCCT
1 AAGAACCTAGGT-AACTGTCCATAGGTCCCG
* *
2486372 TAGAACATAGGTATACTGTCCATA
1 AAGAACCTAGGTA-ACTGTCCATA
2486396 TGTTCCTTAG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
30 11 0.24
31 35 0.76
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (30 bp):
AAGAACCTAGGTAACTGTCCATAGGTCCCG
Found at i:2486361 original size:31 final size:31
Alignment explanation
Indices: 2486323--2486448 Score: 128
Period size: 31 Copynumber: 4.1 Consensus size: 31
2486313 GATCCTCGGT
* *
2486323 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* **
2486354 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* * **
2486385 TACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* * *
2486416 TACCGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGTA
2486447 AA
1 AA
2486449 ACCCTCGACT
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
30 1 0.01
31 81 0.99
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:2487931 original size:21 final size:21
Alignment explanation
Indices: 2487907--2487951 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2487897 TTTTGTTCGT
* *
2487907 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2487928 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2487949 TTG
1 TTG
2487952 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2491096 original size:30 final size:30
Alignment explanation
Indices: 2491060--2491132 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
2491050 CTCGAAGGAC
2491060 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
2491090 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
2491120 CTGTCCATAGGTC
1 CTATCCAGAGGTC
2491133 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:2491149 original size:30 final size:30
Alignment explanation
Indices: 2491106--2491190 Score: 89
Period size: 31 Copynumber: 2.8 Consensus size: 30
2491096 AGAGGTCATA
* *
2491106 AAGATCCTCGGTAACTGTCCATAGGTCCCG
1 AAGAACCTAGGTAACTGTCCATAGGTCCCG
* * *
2491136 AAGAACCTAGGTAAACTGTCCATATGTTCCT
1 AAGAACCTAGGT-AACTGTCCATAGGTCCCG
* *
2491167 TAGAACATAGGTATACTGTCCATA
1 AAGAACCTAGGTA-ACTGTCCATA
2491191 TGTTCCTTAG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
30 11 0.24
31 35 0.76
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (30 bp):
AAGAACCTAGGTAACTGTCCATAGGTCCCG
Found at i:2491156 original size:31 final size:31
Alignment explanation
Indices: 2491118--2491243 Score: 101
Period size: 31 Copynumber: 4.1 Consensus size: 31
2491108 GATCCTCGGT
*
2491118 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
* * **
2491149 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
* * * **
2491180 TACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
* * * * *
2491211 TACCGTCTATATGTCTCGAA-AGACATAGGTA
1 AACTGTCCATAGGTCCCGAAGA-ACATAGGTA
2491242 AA
1 AA
2491244 ACCCTCGACT
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
30 1 0.01
31 80 0.99
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.29
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACATAGGTA
Found at i:2492737 original size:21 final size:21
Alignment explanation
Indices: 2492713--2492757 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2492703 TTTTGTTCGT
* *
2492713 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2492734 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2492755 TTG
1 TTG
2492758 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2497930 original size:32 final size:32
Alignment explanation
Indices: 2497894--2497989 Score: 129
Period size: 32 Copynumber: 2.8 Consensus size: 32
2497884 AAAAGTTATG
2497894 TATTCTATTAATTACAATTTAATATATATATA
1 TATTCTATTAATTACAATTTAATATATATATA
*
2497926 TATTCTATTAATTATAATTTAATATATATATA
1 TATTCTATTAATTACAATTTAATATATATATA
*
2497958 TATATATATTCTATTATTACAATTTAATATAT
1 TAT-TCTA-T-TA--ATTACAATTTAATATAT
2497990 GTGTGTGCGC
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
32 34 0.61
33 3 0.05
34 1 0.02
35 2 0.04
37 16 0.29
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (32 bp):
TATTCTATTAATTACAATTTAATATATATATA
Found at i:2497957 original size:38 final size:37
Alignment explanation
Indices: 2497915--2497989 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 37
2497905 TTACAATTTA
*
2497915 ATATATATATATATTCTATTAATTATAATTTAATATAT
1 ATATATATATATATTCTATT-ATTACAATTTAATATAT
2497953 ATATATATATATATTCTATTATTACAATTTAATATAT
1 ATATATATATATATTCTATTATTACAATTTAATATAT
2497990 GTGTGTGCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 16 0.44
38 20 0.56
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (37 bp):
ATATATATATATATTCTATTATTACAATTTAATATAT
Found at i:2498013 original size:20 final size:20
Alignment explanation
Indices: 2497988--2498026 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2497978 AATTTAATAT
2497988 ATGTGTGTGCGCGTGTGTGC
1 ATGTGTGTGCGCGTGTGTGC
**
2498008 ATGTGTGTTTGCGTGTGTG
1 ATGTGTGTGCGCGTGTGTG
2498027 TGTCTATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.05, C:0.10, G:0.44, T:0.41
Consensus pattern (20 bp):
ATGTGTGTGCGCGTGTGTGC
Found at i:2498066 original size:29 final size:27
Alignment explanation
Indices: 2498021--2498077 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 27
2498011 TGTGTTTGCG
2498021 TGTGTGTGTCTATTAATTACAATTTAA
1 TGTGTGTGTCTATTAATTACAATTTAA
2498048 TGTGTGTGTACTATATAATTACAATTTAA
1 TGTGTGTGT-CTAT-TAATTACAATTTAA
2498077 T
1 T
2498078 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 9 0.32
28 4 0.14
29 15 0.54
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (27 bp):
TGTGTGTGTCTATTAATTACAATTTAA
Found at i:2499383 original size:2 final size:2
Alignment explanation
Indices: 2499376--2499400 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2499366 TTAACTTTTA
2499376 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 A
2499401 GGGTTAGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2501146 original size:22 final size:22
Alignment explanation
Indices: 2501121--2501163 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2501111 GCCTAGCTGT
* *
2501121 TACTATCTCTAGCTTTTACTGA
1 TACTATCTCTAACTGTTACTGA
*
2501143 TACTATTTCTAACTGTTACTG
1 TACTATCTCTAACTGTTACTG
2501164 TTATTGTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (22 bp):
TACTATCTCTAACTGTTACTGA
Found at i:2505148 original size:20 final size:20
Alignment explanation
Indices: 2505123--2505168 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
2505113 GCTTGAAATT
*
2505123 ACTGTAGCAGTATCGATACC
1 ACTGTAGCAGTATCAATACC
2505143 ACTGTAGCAGTATCAATACC
1 ACTGTAGCAGTATCAATACC
*
2505163 CCTGTA
1 ACTGTA
2505169 ACATTCTGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (20 bp):
ACTGTAGCAGTATCAATACC
Found at i:2508588 original size:20 final size:20
Alignment explanation
Indices: 2508559--2508606 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2508549 CTTGAAATTA
* *
2508559 CTGTAACAGTATCGATACCC
1 CTGTAGCAGTATCAATACCC
2508579 CTGTAGCAGTATCAATACCC
1 CTGTAGCAGTATCAATACCC
2508599 CTGTAGCA
1 CTGTAGCA
2508607 TTCTGGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (20 bp):
CTGTAGCAGTATCAATACCC
Found at i:2508673 original size:20 final size:20
Alignment explanation
Indices: 2508650--2508688 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2508640 CTGTTAACAC
*
2508650 AGTATCGGTACTATTCATAT
1 AGTATCAGTACTATTCATAT
*
2508670 AGTATCAGTATTATTCATA
1 AGTATCAGTACTATTCATA
2508689 CAACATAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (20 bp):
AGTATCAGTACTATTCATAT
Found at i:2511318 original size:13 final size:12
Alignment explanation
Indices: 2511294--2511388 Score: 63
Period size: 12 Copynumber: 7.5 Consensus size: 12
2511284 ATATTTGTAA
2511294 ATATAATAATAT
1 ATATAATAATAT
2511306 ATATAATTAATAT
1 ATATAA-TAATAT
*
2511319 ATTATATATAATAA
1 A-TATA-ATAATAT
*
2511333 ATATGCAA-GATA-
1 ATAT--AATAATAT
2511345 ATAATAATAATA-
1 AT-ATAATAATAT
2511357 ATAATAATAATA-
1 AT-ATAATAATAT
2511369 ATAATAATAATAT
1 AT-ATAATAATAT
2511382 ATTATAA
1 A-TATAA
2511389 AAACTCAAAC
Statistics
Matches: 71, Mismatches: 3, Indels: 17
0.78 0.03 0.19
Matches are distributed among these distances:
11 2 0.03
12 35 0.49
13 20 0.28
14 12 0.17
15 2 0.03
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (12 bp):
ATATAATAATAT
Found at i:2511348 original size:3 final size:3
Alignment explanation
Indices: 2511342--2511380 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2511332 AATATGCAAG
2511342 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2511381 TATTATAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2520224 original size:3 final size:3
Alignment explanation
Indices: 2520216--2520261 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
2520206 TATGTAAGAC
2520216 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2520262 TATTATAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2521247 original size:21 final size:21
Alignment explanation
Indices: 2521223--2521277 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
2521213 ACCAGACCCT
*
2521223 AGTATCGATACTCTATAAATG
1 AGTATCAATACTCTATAAATG
*
2521244 AGTATCAACACTCTATAAATG
1 AGTATCAATACTCTATAAATG
2521265 AGTATCAATACTC
1 AGTATCAATACTC
2521278 CCCTTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (21 bp):
AGTATCAATACTCTATAAATG
Found at i:2521358 original size:27 final size:27
Alignment explanation
Indices: 2521319--2521381 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
2521309 TGAAGAACAA
* *
2521319 TATCGGTATTGTTTTGGCTCAAAAGAG
1 TATCGATACTGTTTTGGCTCAAAAGAG
2521346 TATCGATACTGTTTTGGCTCAAAAGAG
1 TATCGATACTGTTTTGGCTCAAAAGAG
2521373 TATCGATAC
1 TATCGATAC
2521382 CTCTACTACG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (27 bp):
TATCGATACTGTTTTGGCTCAAAAGAG
Done.