Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 52 of 91
Found at i:18253426 original size:37 final size:37
Alignment explanation
Indices: 18253379--18253460 Score: 130
Period size: 37 Copynumber: 2.2 Consensus size: 37
18253369 AATGCAATAT
* *
18253379 CATCATCATGTGTGCACTCCCTACTTGCACAC-TCTAA
1 CATCATCATGTGTGAACTCCCTACTCGCACACTTC-AA
18253416 CATCATCATGTGTGAACTCCCTACTCGCACACTTCAA
1 CATCATCATGTGTGAACTCCCTACTCGCACACTTCAA
18253453 CATCATCA
1 CATCATCA
18253461 AACAACATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
37 40 0.95
38 2 0.05
ACGTcount: A:0.27, C:0.35, G:0.10, T:0.28
Consensus pattern (37 bp):
CATCATCATGTGTGAACTCCCTACTCGCACACTTCAA
Found at i:18256244 original size:2 final size:2
Alignment explanation
Indices: 18256228--18256270 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
18256218 CCTATAACAC
* *
18256228 AT AT AT TT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18256270 A
1 A
18256271 CACACANNNN
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:18269973 original size:36 final size:35
Alignment explanation
Indices: 18269905--18269989 Score: 98
Period size: 37 Copynumber: 2.4 Consensus size: 35
18269895 AAACCAAGAT
* *
18269905 CTCTCTCTCTTTTTCCGTTAGCAACCACAACCCAG
1 CTCTCTCTCTTTTTCCGTCAACAACCACAACCCAG
* * *
18269940 CTCTTTCTCTTTTTCTCGTCAACCACCACAACCCCAA
1 CTCTCTCTCTTTTTC-CGTCAACAACCACAA-CCCAG
*
18269977 CTTTCTCTCTTTT
1 CTCTCTCTCTTTT
18269990 CCTTTCTTTC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
35 14 0.34
36 12 0.29
37 15 0.37
ACGTcount: A:0.18, C:0.40, G:0.05, T:0.38
Consensus pattern (35 bp):
CTCTCTCTCTTTTTCCGTCAACAACCACAACCCAG
Found at i:18274751 original size:2 final size:2
Alignment explanation
Indices: 18274746--18274778 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18274736 ACACACACAA
18274746 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18274779 CATACATCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18278574 original size:85 final size:85
Alignment explanation
Indices: 18278431--18278600 Score: 324
Period size: 85 Copynumber: 2.0 Consensus size: 85
18278421 GAAAAGCTTG
18278431 CAAAAATAGTTTATATTTCTTCTTTGACTTTTTCCTTTTTCATTTGGCTGGCCAAATAAGGCCAA
1 CAAAAATAGTTTATATTTCTTCTTTGACTTTTTCCTTTTTCATTTGGCTGGCCAAATAAGGCCAA
18278496 CCTTTCCTAC-TTTTCTTTC
66 CCTTTCCTACTTTTTCTTTC
18278515 NCAAAAATAGTTTATATTTCTTCTTTGACTTTTTCCTTTTTCATTTGGCTGGCCAAATAAGGCCA
1 -CAAAAATAGTTTATATTTCTTCTTTGACTTTTTCCTTTTTCATTTGGCTGGCCAAATAAGGCCA
18278580 ACCTTTCCTACTTTTTCTTTC
65 ACCTTTCCTACTTTTTCTTTC
18278601 TTGGCCTAAT
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 75 0.89
86 9 0.11
ACGTcount: A:0.21, C:0.22, G:0.09, T:0.46
Consensus pattern (85 bp):
CAAAAATAGTTTATATTTCTTCTTTGACTTTTTCCTTTTTCATTTGGCTGGCCAAATAAGGCCAA
CCTTTCCTACTTTTTCTTTC
Found at i:18282948 original size:22 final size:21
Alignment explanation
Indices: 18282909--18282949 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
18282899 TCTAGGTGGA
*
18282909 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGAAAAAGTGTG
*
18282930 AAAATTCAATGAAACAAGTG
1 AAAATTCAAGGAAA-AAGTG
18282950 AAAAAGGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.51, C:0.07, G:0.22, T:0.20
Consensus pattern (21 bp):
AAAATTCAAGGAAAAAGTGTG
Found at i:18282954 original size:21 final size:20
Alignment explanation
Indices: 18282907--18282954 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
18282897 ACTCTAGGTG
*
18282907 GAAAAATTCAAGGGAAAAGT
1 GAAAAATTCAAGGAAAAAGT
* *
18282927 GTGAAAATTCAATGAAACAAGT
1 G-AAAAATTCAAGGAAA-AAGT
18282949 GAAAAA
1 GAAAAA
18282955 GGTAAGATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.05
21 16 0.73
22 5 0.23
ACGTcount: A:0.56, C:0.06, G:0.21, T:0.17
Consensus pattern (20 bp):
GAAAAATTCAAGGAAAAAGT
Found at i:18289028 original size:17 final size:18
Alignment explanation
Indices: 18288992--18289031 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
18288982 GTTTTGCCAA
*
18288992 CTCCATTTTTGTCTTATT
1 CTCCATCTTTGTCTTATT
*
18289010 CTCCATCTTT-TCTTTTT
1 CTCCATCTTTGTCTTATT
18289027 CTCCA
1 CTCCA
18289032 AGTGTCTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.10, C:0.30, G:0.03, T:0.57
Consensus pattern (18 bp):
CTCCATCTTTGTCTTATT
Found at i:18292808 original size:43 final size:43
Alignment explanation
Indices: 18292747--18292833 Score: 133
Period size: 43 Copynumber: 2.0 Consensus size: 43
18292737 CTCTCCACAC
*
18292747 TCAGCTCATGTGCACTCCCTC-CTCGCACATAG-TCGGGTCATCA
1 TCAGCTCATGTGCACTCCCACAC-CGCACATAGCT-GGGTCATCA
18292790 TCAGCTCATGTGCACTCCCACACCGCACATAGCTGGGTCATCA
1 TCAGCTCATGTGCACTCCCACACCGCACATAGCTGGGTCATCA
18292833 T
1 T
18292834 TATCACACAA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
43 39 0.95
44 2 0.05
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.24
Consensus pattern (43 bp):
TCAGCTCATGTGCACTCCCACACCGCACATAGCTGGGTCATCA
Found at i:18298117 original size:15 final size:15
Alignment explanation
Indices: 18298085--18298114 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
18298075 AGTAATTGGG
18298085 ATTATGAGTTGTTTT
1 ATTATGAGTTGTTTT
18298100 ATTATTGAGTTGTTT
1 ATTA-TGAGTTGTTT
18298115 ATTCATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (15 bp):
ATTATGAGTTGTTTT
Found at i:18298656 original size:43 final size:42
Alignment explanation
Indices: 18298553--18298725 Score: 134
Period size: 42 Copynumber: 4.1 Consensus size: 42
18298543 GTAATGATAT
* * **
18298553 TGACCCGGCTATATGCTAGTAGGAGTGCGCATGTG-TCGATGA
1 TGACCCGGCTATATGCGAGTAGGAGTGTGCATAAGCT-GATGA
* * * *
18298595 TGACCTGCCTATGTGCGAGTAGGAGTGTGCATACGCTGATGA
1 TGACCCGGCTATATGCGAGTAGGAGTGTGCATAAGCTGATGA
* * *
18298637 TTGACCCGGCTATCTGCGAGT-GGAAGTATGCATAAGCCGATGA
1 -TGACCCGGCTATATGCGAGTAGG-AGTGTGCATAAGCTGATGA
* * * * ** *
18298680 TGACCCGGCCATGTGCTAGTGGGGAGTGCACATGAGCTGATGA
1 TGACCCGGCTATATGCGAGT-AGGAGTGTGCATAAGCTGATGA
18298723 TGA
1 TGA
18298726 TGGGAGTGTG
Statistics
Matches: 105, Mismatches: 21, Indels: 9
0.78 0.16 0.07
Matches are distributed among these distances:
42 52 0.50
43 51 0.49
44 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.24
Consensus pattern (42 bp):
TGACCCGGCTATATGCGAGTAGGAGTGTGCATAAGCTGATGA
Found at i:18298739 original size:26 final size:24
Alignment explanation
Indices: 18298701--18298748 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
18298691 TGTGCTAGTG
18298701 GGGAGTGCACATGAGCTGATGATGAT
1 GGGAGTGCACATGA--TGATGATGAT
**
18298727 GGGAGTGTGCATGATGATGATG
1 GGGAGTGCACATGATGATGATG
18298749 GATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
26 12 0.60
ACGTcount: A:0.25, C:0.08, G:0.42, T:0.25
Consensus pattern (24 bp):
GGGAGTGCACATGATGATGATGAT
Found at i:18298757 original size:2 final size:2
Alignment explanation
Indices: 18298750--18298837 Score: 90
Period size: 2 Copynumber: 45.0 Consensus size: 2
18298740 ATGATGATGG
* *
18298750 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT A- AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * ** *
18298791 GT -T AN GG AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
18298832 AA AT AT
1 AT AT AT
18298838 GTGTTATAGG
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
1 2 0.03
2 70 0.97
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:18315321 original size:2 final size:2
Alignment explanation
Indices: 18315316--18315352 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
18315306 TTGTGTTATC
18315316 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18315353 GGTTTGAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18316278 original size:12 final size:12
Alignment explanation
Indices: 18316261--18316285 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18316251 AAGAAAATGA
18316261 AATATTTTATTT
1 AATATTTTATTT
18316273 AATATTTTATTT
1 AATATTTTATTT
18316285 A
1 A
18316286 GTTTGATTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
AATATTTTATTT
Found at i:18319945 original size:2 final size:2
Alignment explanation
Indices: 18319938--18320017 Score: 144
Period size: 2 Copynumber: 40.5 Consensus size: 2
18319928 ACACTATCAG
*
18319938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18319979 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18320018 NNNNNNNNNN
Statistics
Matches: 76, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
1 1 0.01
2 75 0.99
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:18321264 original size:16 final size:16
Alignment explanation
Indices: 18321243--18321279 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
18321233 TTTCTGTTGC
*
18321243 ATAAATATATATATAT
1 ATAAATATATACATAT
*
18321259 ATAAATGTATACATAT
1 ATAAATATATACATAT
18321275 ATAAA
1 ATAAA
18321280 CACCAATACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (16 bp):
ATAAATATATACATAT
Found at i:18332134 original size:2 final size:2
Alignment explanation
Indices: 18332127--18332166 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
18332117 TATNATGATG
*
18332127 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18332167 GGTATATGGT
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:18332405 original size:21 final size:21
Alignment explanation
Indices: 18332361--18332447 Score: 93
Period size: 21 Copynumber: 4.1 Consensus size: 21
18332351 TAGCCGAAAA
*
18332361 CTCGCTGCAACGAGAATCCATT
1 CTCGCTGCAACGAG-ATTCATT
*
18332383 CTCGCTGTAACGAGATTCATT
1 CTCGCTGCAACGAGATTCATT
* * *
18332404 CTTGTTGCAGCGAGATTCATT
1 CTCGCTGCAACGAGATTCATT
* * *
18332425 CTTGTTGCAGCGAGATTCATT
1 CTCGCTGCAACGAGATTCATT
18332446 CT
1 CT
18332448 TGTTGAAACC
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 46 0.78
22 13 0.22
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (21 bp):
CTCGCTGCAACGAGATTCATT
Found at i:18332448 original size:21 final size:21
Alignment explanation
Indices: 18332393--18332452 Score: 120
Period size: 21 Copynumber: 2.9 Consensus size: 21
18332383 CTCGCTGTAA
18332393 CGAGATTCATTCTTGTTGCAG
1 CGAGATTCATTCTTGTTGCAG
18332414 CGAGATTCATTCTTGTTGCAG
1 CGAGATTCATTCTTGTTGCAG
18332435 CGAGATTCATTCTTGTTG
1 CGAGATTCATTCTTGTTG
18332453 AAACCTAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.40
Consensus pattern (21 bp):
CGAGATTCATTCTTGTTGCAG
Found at i:18354027 original size:15 final size:16
Alignment explanation
Indices: 18354003--18354035 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
18353993 TTGATATTAG
*
18354003 AGCTTTTGG-TTTAAA
1 AGCTTATGGTTTTAAA
18354018 AGCTTATGGTTTTAAA
1 AGCTTATGGTTTTAAA
18354034 AG
1 AG
18354036 AAGTTTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.42
Consensus pattern (16 bp):
AGCTTATGGTTTTAAA
Found at i:18364462 original size:67 final size:67
Alignment explanation
Indices: 18364379--18364508 Score: 251
Period size: 67 Copynumber: 1.9 Consensus size: 67
18364369 TTCATTTTAC
18364379 TATTCTTTGTCTTCATTCAAGATTAGAATCTTCAACCTTTGTCGAGACGTAACTCTTGATAAAGG
1 TATTCTTTGTCTTCATTCAAGATTAGAATCTTCAACCTTTGTCGAGACGTAACTCTTGATAAAGG
18364444 CA
66 CA
*
18364446 TATTCTTTGTCTTCATTCAAGATTAGAATCTTCAACCTTTGTTGAGACGTAACTCTTGATAAA
1 TATTCTTTGTCTTCATTCAAGATTAGAATCTTCAACCTTTGTCGAGACGTAACTCTTGATAAA
18364509 TTCACATAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.39
Consensus pattern (67 bp):
TATTCTTTGTCTTCATTCAAGATTAGAATCTTCAACCTTTGTCGAGACGTAACTCTTGATAAAGG
CA
Found at i:18366848 original size:36 final size:35
Alignment explanation
Indices: 18366807--18366899 Score: 96
Period size: 36 Copynumber: 2.6 Consensus size: 35
18366797 AAGGTTGCAC
*
18366807 TTGATCTTATAAAAGGCAAGTTGTGAAGGTTACGCT
1 TTGATCTTATAAAAGGCAAGTTGTGAAGATTACG-T
* ** * *
18366843 TTGATCCTGCAAAAGGCATGTTGTGAAGATTATGT
1 TTGATCTTATAAAAGGCAAGTTGTGAAGATTACGT
*
18366878 TTGATCTTGTTGAAAAGGCAAG
1 TTGATCTT-AT-AAAAGGCAAG
18366900 CTGATAGTGG
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
35 8 0.18
36 28 0.62
37 9 0.20
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.33
Consensus pattern (35 bp):
TTGATCTTATAAAAGGCAAGTTGTGAAGATTACGT
Found at i:18373142 original size:22 final size:21
Alignment explanation
Indices: 18373107--18373151 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
18373097 CACTAAATAT
* *
18373107 TTATTCTTTTCTATATTTTTTA
1 TTATTCTTTCCTAT-TTTTATA
*
18373129 TTATTGTTTCCTATTTTTATA
1 TTATTCTTTCCTATTTTTATA
18373150 TT
1 TT
18373152 TTTGCCTCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.18, C:0.09, G:0.02, T:0.71
Consensus pattern (21 bp):
TTATTCTTTCCTATTTTTATA
Found at i:18378469 original size:28 final size:28
Alignment explanation
Indices: 18378429--18378486 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
18378419 AGATGCAAAG
18378429 TATGTTTAAATGTCTATCTTATATATGT
1 TATGTTTAAATGTCTATCTTATATATGT
*
18378457 TATGTTTCAATGTCTATCTTATATATGT
1 TATGTTTAAATGTCTATCTTATATATGT
18378485 TA
1 TA
18378487 GCTCTTCAAA
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:0.28, C:0.09, G:0.10, T:0.53
Consensus pattern (28 bp):
TATGTTTAAATGTCTATCTTATATATGT
Found at i:18381034 original size:39 final size:41
Alignment explanation
Indices: 18380985--18381062 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 41
18380975 ACGGGTATAC
18380985 GTTTAATAAACGTG-TA-ACACGACACGACACGATTAACAT
1 GTTTAATAAACGTGCTATACACGACACGACACGATTAACAT
* * *
18381024 GTTTATTAAACGTGTCTATATATGACACGACACGATTAA
1 GTTTAATAAACGTG-CTATACACGACACGACACGATTAA
18381063 TAACACGTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 13 0.39
41 2 0.06
42 18 0.55
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (41 bp):
GTTTAATAAACGTGCTATACACGACACGACACGATTAACAT
Found at i:18381100 original size:18 final size:18
Alignment explanation
Indices: 18381063--18381101 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
18381053 ACACGATTAA
*
18381063 TAACACGTTTAATACGAT
1 TAACACGTTTAACACGAT
* *
18381081 TAACATGTTTAACACTAT
1 TAACACGTTTAACACGAT
18381099 TAA
1 TAA
18381102 ATAAAAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (18 bp):
TAACACGTTTAACACGAT
Found at i:18381482 original size:18 final size:18
Alignment explanation
Indices: 18381455--18381489 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18381445 TCATGTATAC
18381455 ACGTTCAAACACAATAAT
1 ACGTTCAAACACAATAAT
* *
18381473 ACGTTTAAACACGATAA
1 ACGTTCAAACACAATAA
18381490 CACGATTAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.20, G:0.09, T:0.23
Consensus pattern (18 bp):
ACGTTCAAACACAATAAT
Found at i:18381907 original size:41 final size:41
Alignment explanation
Indices: 18381849--18381927 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
18381839 GACAATTTTC
* ***
18381849 AAATATATTGTTATGAAAAATTCCTAAAAAATTAAAAATGG
1 AAATATATTGTTATGAAAAAGTAAAAAAAAATTAAAAATGG
*
18381890 AAATA-ATTGTTTTTGAAAAAGTAAAAAAAAATTAAAAA
1 AAATATATTG-TTATGAAAAAGTAAAAAAAAATTAAAAA
18381928 GAGATTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 4 0.12
41 28 0.88
ACGTcount: A:0.58, C:0.03, G:0.09, T:0.30
Consensus pattern (41 bp):
AAATATATTGTTATGAAAAAGTAAAAAAAAATTAAAAATGG
Found at i:18391077 original size:21 final size:21
Alignment explanation
Indices: 18391051--18391113 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
18391041 TGTTCATTCA
18391051 ATTCATGACAAAGACTGATGC
1 ATTCATGACAAAGACTGATGC
*
18391072 ATTCATGACAAAGATTGATGC
1 ATTCATGACAAAGACTGATGC
*
18391093 ATTCATAACAAAGACTGATGC
1 ATTCATGACAAAGACTGATGC
18391114 TTTTATGATA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.25
Consensus pattern (21 bp):
ATTCATGACAAAGACTGATGC
Found at i:18392622 original size:18 final size:17
Alignment explanation
Indices: 18392601--18392659 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
18392591 TTCAAAAAAA
18392601 ATTTCAAGAAAAAAATAT
1 ATTTCAA-AAAAAAATAT
*
18392619 ATTTCAAAAAAAAATTT
1 ATTTCAAAAAAAAATAT
*
18392636 CATGT--AAAAAAAATAT
1 -ATTTCAAAAAAAAATAT
18392652 ATTTCAAA
1 ATTTCAAA
18392660 TTTTTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
15 3 0.09
16 10 0.29
17 11 0.32
18 10 0.29
ACGTcount: A:0.59, C:0.07, G:0.03, T:0.31
Consensus pattern (17 bp):
ATTTCAAAAAAAAATAT
Found at i:18392632 original size:31 final size:32
Alignment explanation
Indices: 18392594--18392659 Score: 107
Period size: 33 Copynumber: 2.1 Consensus size: 32
18392584 TTTAAAATTC
18392594 AAAAAAAATTTCAAG-AAAAAAATATATTTCA
1 AAAAAAAATTTCAAGAAAAAAAATATATTTCA
*
18392625 AAAAAAAATTTCATGTAAAAAAAATATATTTCA
1 AAAAAAAATTTCAAG-AAAAAAAATATATTTCA
18392658 AA
1 AA
18392660 TTTTTTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 14 0.44
33 18 0.56
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (32 bp):
AAAAAAAATTTCAAGAAAAAAAATATATTTCA
Found at i:18392985 original size:8 final size:8
Alignment explanation
Indices: 18392950--18393030 Score: 67
Period size: 8 Copynumber: 10.4 Consensus size: 8
18392940 TTATTTGGAC
18392950 TACCCA-T
1 TACCCACT
* *
18392957 TATCCATT
1 TACCCACT
*
18392965 TACCTAC-
1 TACCCACT
18392972 TACCCACT
1 TACCCACT
*
18392980 TACCCAAT
1 TACCCACT
* *
18392988 AACCCATT
1 TACCCACT
18392996 TACCCACT
1 TACCCACT
18393004 TACCCACT
1 TACCCACT
* *
18393012 AACCCATT
1 TACCCACT
*
18393020 TACCCATT
1 TACCCACT
18393028 TAC
1 TAC
18393031 TTATTACCCA
Statistics
Matches: 59, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
7 11 0.19
8 48 0.81
ACGTcount: A:0.30, C:0.41, G:0.00, T:0.30
Consensus pattern (8 bp):
TACCCACT
Found at i:18392998 original size:16 final size:16
Alignment explanation
Indices: 18392950--18393030 Score: 76
Period size: 16 Copynumber: 5.2 Consensus size: 16
18392940 TTATTTGGAC
*
18392950 TACCCA-TTATCCATT
1 TACCCACTTACCCATT
* *
18392965 TACCTAC-TACCCACT
1 TACCCACTTACCCATT
* *
18392980 TACCCAATAACCCATT
1 TACCCACTTACCCATT
*
18392996 TACCCACTTACCCACT
1 TACCCACTTACCCATT
* *
18393012 AACCCATTTACCCATT
1 TACCCACTTACCCATT
18393028 TAC
1 TAC
18393031 TTATTACCCA
Statistics
Matches: 50, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
15 16 0.32
16 34 0.68
ACGTcount: A:0.30, C:0.41, G:0.00, T:0.30
Consensus pattern (16 bp):
TACCCACTTACCCATT
Found at i:18393004 original size:24 final size:24
Alignment explanation
Indices: 18392972--18393030 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
18392962 ATTTACCTAC
18392972 TACCCACTTACCCAATAACCCATT
1 TACCCACTTACCCAATAACCCATT
*
18392996 TACCCACTTACCCACTAACCCATT
1 TACCCACTTACCCAATAACCCATT
*
18393020 TACCCATTTAC
1 TACCCACTTAC
18393031 TTATTACCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.31, C:0.42, G:0.00, T:0.27
Consensus pattern (24 bp):
TACCCACTTACCCAATAACCCATT
Found at i:18393063 original size:10 final size:10
Alignment explanation
Indices: 18393048--18393090 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
18393038 CCAACAAAAA
18393048 TTTTTTTATT
1 TTTTTTTATT
*
18393058 TTTTTTTAGT
1 TTTTTTTATT
*
18393068 TATTTTTATT
1 TTTTTTTATT
*
18393078 TATTATTTATT
1 T-TTTTTTATT
18393089 TT
1 TT
18393091 ATTTCTCTAC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
10 19 0.70
11 8 0.30
ACGTcount: A:0.16, C:0.00, G:0.02, T:0.81
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:18393073 original size:13 final size:12
Alignment explanation
Indices: 18393048--18393093 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
18393038 CCAACAAAAA
18393048 TTTTTTTA-T-T
1 TTTTTTTATTAT
18393058 TTTTTTTAGTTAT
1 TTTTTTTA-TTAT
18393071 TTTTATTTATTAT
1 TTTT-TTTATTAT
*
18393084 TTATTTTATT
1 TTTTTTTATT
18393094 TCTCTACATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
10 8 0.26
12 7 0.23
13 12 0.39
14 4 0.13
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.80
Consensus pattern (12 bp):
TTTTTTTATTAT
Found at i:18394693 original size:22 final size:23
Alignment explanation
Indices: 18394661--18394707 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
18394651 ATATAGAGTT
18394661 ATTTGAGCTTA-ATTTTGATAATA
1 ATTTGAGCTTAGATTTTG-TAATA
*
18394684 ATTTG-GCTTAGTTTTTGTAATA
1 ATTTGAGCTTAGATTTTGTAATA
18394706 AT
1 AT
18394708 GCATAGAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.30, C:0.04, G:0.15, T:0.51
Consensus pattern (23 bp):
ATTTGAGCTTAGATTTTGTAATA
Found at i:18402511 original size:2 final size:2
Alignment explanation
Indices: 18402504--18402540 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
18402494 CCAGGCAATC
18402504 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T CAT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT A
18402541 CACATAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 31 0.94
3 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18402546 original size:10 final size:10
Alignment explanation
Indices: 18402503--18402546 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
18402493 TCCAGGCAAT
18402503 CATATATATA
1 CATATATATA
*
18402513 TATATATATA
1 CATATATATA
* *
18402523 TATATATATT
1 CATATATATA
*
18402533 CATATATACA
1 CATATATATA
18402543 CATA
1 CATA
18402547 AACATAAATC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (10 bp):
CATATATATA
Found at i:18404946 original size:42 final size:42
Alignment explanation
Indices: 18404827--18404939 Score: 172
Period size: 42 Copynumber: 2.7 Consensus size: 42
18404817 CATATGCAAT
* * *
18404827 GGCTTATGCGCACTCCCACTCACACATAGCCGGGTCAGCAAC
1 GGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCAACAAC
*
18404869 GGCTTATGTGCACTCCCACTAGCACATAGCCGGGTCAACAAC
1 GGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCAACAAC
* *
18404911 GGCTTATGTGTACTCCTACTCGCACATAG
1 GGCTTATGTGCACTCCCACTCGCACATAG
18404940 TTGGGTCCAC
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (42 bp):
GGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCAACAAC
Found at i:18405711 original size:3 final size:3
Alignment explanation
Indices: 18405703--18405728 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
18405693 AATTGAAAGG
18405703 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
18405729 CTGCTGGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:18409814 original size:42 final size:43
Alignment explanation
Indices: 18409767--18409849 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 43
18409757 TTGTGTGATA
18409767 ATGATGACCCAGCTATATGCGAGT-GGGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATATGCGAGTAGGGAGTGCACATGAGCTG
*
18409809 ATGATGACCCAGCTATGTGCGAGTAGGGAGTGCACATGAGC
1 ATGATGACCCAGCTATATGCGAGTAGGGAGTGCACATGAGC
18409850 GGAGTGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
42 23 0.59
43 16 0.41
ACGTcount: A:0.27, C:0.19, G:0.34, T:0.20
Consensus pattern (43 bp):
ATGATGACCCAGCTATATGCGAGTAGGGAGTGCACATGAGCTG
Found at i:18416414 original size:2 final size:2
Alignment explanation
Indices: 18416407--18416457 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
18416397 NNNNNNNNNN
18416407 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
18416449 TA TA TA TA T
1 TA TA TA TA T
18416458 CAACAGTATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18422152 original size:36 final size:36
Alignment explanation
Indices: 18422121--18422260 Score: 192
Period size: 36 Copynumber: 3.9 Consensus size: 36
18422111 GAATCATGCA
* *
18422121 TGTGCCAAAGCAATGGGTGGAGAGTTAAATCA-AGCG
1 TGTGCCAAAGCAACGGGTGGAGAGTCAAATCACA-CG
* * *
18422157 CGTGCTAAAACAACGGGTGGAGAGTCAAATCACACG
1 TGTGCCAAAGCAACGGGTGGAGAGTCAAATCACACG
*
18422193 TGTGCCAAAGCAAAGGGTGGAGAGTCAAATCACACG
1 TGTGCCAAAGCAACGGGTGGAGAGTCAAATCACACG
* *
18422229 TGTGCTAAAGCAACGGGTGGAGAATCAAATCA
1 TGTGCCAAAGCAACGGGTGGAGAGTCAAATCA
18422261 TCATCTGGAG
Statistics
Matches: 91, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
36 90 0.99
37 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.30, T:0.16
Consensus pattern (36 bp):
TGTGCCAAAGCAACGGGTGGAGAGTCAAATCACACG
Found at i:18422197 original size:72 final size:72
Alignment explanation
Indices: 18422121--18422260 Score: 219
Period size: 72 Copynumber: 1.9 Consensus size: 72
18422111 GAATCATGCA
* * *
18422121 TGTGCCAAAGCAATGGGTGGAGAGTTAAATCA-AGCGCGTGCTAAAACAACGGGTGGAGAGTCAA
1 TGTGCCAAAGCAAAGGGTGGAGAGTCAAATCACA-CGCGTGCTAAAACAACGGGTGGAGAATCAA
18422185 ATCACACG
65 ATCACACG
* *
18422193 TGTGCCAAAGCAAAGGGTGGAGAGTCAAATCACACGTGTGCTAAAGCAACGGGTGGAGAATCAAA
1 TGTGCCAAAGCAAAGGGTGGAGAGTCAAATCACACGCGTGCTAAAACAACGGGTGGAGAATCAAA
18422258 TCA
66 TCA
18422261 TCATCTGGAG
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
72 61 0.98
73 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.30, T:0.16
Consensus pattern (72 bp):
TGTGCCAAAGCAAAGGGTGGAGAGTCAAATCACACGCGTGCTAAAACAACGGGTGGAGAATCAAA
TCACACG
Found at i:18422631 original size:19 final size:19
Alignment explanation
Indices: 18422607--18422643 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
18422597 CCATTTGACT
18422607 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
*
18422626 TATTGGAGTTTGATTTGA
1 TATTGGAGTATGATTTGA
18422644 AGTTTAGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:18425872 original size:2 final size:2
Alignment explanation
Indices: 18425865--18425897 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18425855 ACTTATACAA
18425865 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
18425898 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:18436858 original size:2 final size:2
Alignment explanation
Indices: 18436851--18436891 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
18436841 AGAACCAAAC
18436851 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18436892 AAGTTCCCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18438509 original size:41 final size:40
Alignment explanation
Indices: 18438442--18438551 Score: 166
Period size: 41 Copynumber: 2.7 Consensus size: 40
18438432 CCTCCCCAGC
*
18438442 TCATGTGCATCCCCCCACATTGTGCACATAGCTGGAGTCA
1 TCATGTGCATCCCCCCACATCGTGCACATAGCTGGAGTCA
* * *
18438482 TCATGTGTATCCCCCCCACATCATGCACATAGTTGGAGTCA
1 TCATGTGCAT-CCCCCCACATCGTGCACATAGCTGGAGTCA
*
18438523 TCATGTGCATTCCCCCACATCGTGCACAT
1 TCATGTGCATCCCCCCACATCGTGCACAT
18438552 CTAATGCCGT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 26 0.42
41 36 0.58
ACGTcount: A:0.23, C:0.34, G:0.17, T:0.26
Consensus pattern (40 bp):
TCATGTGCATCCCCCCACATCGTGCACATAGCTGGAGTCA
Found at i:18441215 original size:15 final size:14
Alignment explanation
Indices: 18441195--18441228 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
18441185 GAATAAGTAA
18441195 GAAAAGAAAGGAAAG
1 GAAAAGAAA-GAAAG
18441210 GAAAAGAAAGAAAG
1 GAAAAGAAAGAAAG
18441224 GAAAA
1 GAAAA
18441229 CAAATGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (14 bp):
GAAAAGAAAGAAAG
Found at i:18441237 original size:19 final size:19
Alignment explanation
Indices: 18441197--18441237 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
18441187 ATAAGTAAGA
**
18441197 AAAGAAAGGAAAGGAAAAG
1 AAAGAAAGGAAAACAAAAG
*
18441216 AAAGAAAGGAAAACAAATG
1 AAAGAAAGGAAAACAAAAG
18441235 AAA
1 AAA
18441238 AAAATTTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.71, C:0.02, G:0.24, T:0.02
Consensus pattern (19 bp):
AAAGAAAGGAAAACAAAAG
Found at i:18449136 original size:43 final size:43
Alignment explanation
Indices: 18449071--18449180 Score: 139
Period size: 43 Copynumber: 2.6 Consensus size: 43
18449061 ACACCAGATC
* ** * *
18449071 ATGCGCACTCCCTACTCACACATGGTTGGGTCATCACCGGTTT
1 ATGCGCACTCCCTACTCGCACATAATCGGGTCATCACCGGCTT
* **
18449114 ATGCGCACTCCTTACTCGCACATAATCGGGTCATCATTGGCTT
1 ATGCGCACTCCCTACTCGCACATAATCGGGTCATCACCGGCTT
*
18449157 ATGTGCACTCCCTACTCGCACATA
1 ATGCGCACTCCCTACTCGCACATA
18449181 GCCGAGTCCA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.21, C:0.33, G:0.18, T:0.28
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAATCGGGTCATCACCGGCTT
Found at i:18453962 original size:21 final size:20
Alignment explanation
Indices: 18453937--18453996 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
18453927 AGATGTCTAA
*
18453937 AATAATTATTTGAAATGAAAT
1 AATAATTATTTG-AATAAAAT
* *
18453958 TATAATTGTTTGAATAAAAT
1 AATAATTATTTGAATAAAAT
18453978 AATAA-TATTT-AATAAAAT
1 AATAATTATTTGAATAAAAT
18453996 A
1 A
18453997 TTTTATTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 9 0.26
19 4 0.12
20 11 0.32
21 10 0.29
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (20 bp):
AATAATTATTTGAATAAAAT
Found at i:18458733 original size:46 final size:46
Alignment explanation
Indices: 18458628--18458734 Score: 166
Period size: 43 Copynumber: 2.4 Consensus size: 46
18458618 ATTCATCGTC
*
18458628 ATAGTCGGGTCATCATCATCTGCTTATGCACACTCCGTACTCGCAT
1 ATAGTCGGGTCATCATCATCGGCTTATGCACACTCCGTACTCGCAT
*
18458674 ATAGTCGGG---TCATCATCGGCTTATGCGCACTCCGTACTCGCAT
1 ATAGTCGGGTCATCATCATCGGCTTATGCACACTCCGTACTCGCAT
*
18458717 ATAGCCGGGTCATCATCA
1 ATAGTCGGGTCATCATCA
18458735 ACTCATGTGC
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
43 40 0.73
46 15 0.27
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.28
Consensus pattern (46 bp):
ATAGTCGGGTCATCATCATCGGCTTATGCACACTCCGTACTCGCAT
Found at i:18458747 original size:43 final size:43
Alignment explanation
Indices: 18458628--18458749 Score: 145
Period size: 43 Copynumber: 2.8 Consensus size: 43
18458618 ATTCATCGTC
* * *
18458628 ATAGTCGGGTCATCATCATCTGCTTATGCACACTCCGTACTCGCAT
1 ATAGCCGGGTCATCATCAACT-C--ATGCGCACTCCGTACTCGCAT
* ** *
18458674 ATAGTCGGGTCATCATCGGCTTATGCGCACTCCGTACTCGCAT
1 ATAGCCGGGTCATCATCAACTCATGCGCACTCCGTACTCGCAT
*
18458717 ATAGCCGGGTCATCATCAACTCATGTGCACTCC
1 ATAGCCGGGTCATCATCAACTCATGCGCACTCC
18458750 CACATCACAC
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
43 48 0.72
46 19 0.28
ACGTcount: A:0.21, C:0.31, G:0.20, T:0.28
Consensus pattern (43 bp):
ATAGCCGGGTCATCATCAACTCATGCGCACTCCGTACTCGCAT
Found at i:18459493 original size:2 final size:2
Alignment explanation
Indices: 18459486--18459518 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
18459476 TACTCACTCA
18459486 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
18459519 ACATGTCCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:18463869 original size:28 final size:29
Alignment explanation
Indices: 18463828--18463887 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
18463818 GTCTATGGGC
*
18463828 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
18463856 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
18463886 AA
1 AA
18463888 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:18480075 original size:27 final size:26
Alignment explanation
Indices: 18480031--18480102 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 26
18480021 TGTCTGGAAG
*
18480031 ATATATA-TA-ATTATTAATATAAT-
1 ATATATATTATATTAATAATATAATA
* *
18480054 ATATCCATATTATATTAATAATTCTAGTA
1 ATAT--ATATTATATTAATAA-TATAATA
18480083 ATATATATTATATTAATAAT
1 ATATATATTATATTAATAAT
18480103 TTTAACAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
23 4 0.10
25 3 0.08
26 3 0.08
27 22 0.55
28 4 0.10
29 4 0.10
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (26 bp):
ATATATATTATATTAATAATATAATA
Found at i:18485909 original size:18 final size:18
Alignment explanation
Indices: 18485886--18485922 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
18485876 ATTCTAATAT
18485886 CATGCTTCTAGGTCGTAG
1 CATGCTTCTAGGTCGTAG
18485904 CATGCTTCTAGGTCGTAG
1 CATGCTTCTAGGTCGTAG
18485922 C
1 C
18485923 TCATTACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.32
Consensus pattern (18 bp):
CATGCTTCTAGGTCGTAG
Found at i:18492496 original size:38 final size:37
Alignment explanation
Indices: 18492454--18492584 Score: 127
Period size: 38 Copynumber: 3.5 Consensus size: 37
18492444 GTTGCTTCAG
* *
18492454 CACTAAGTGTGATTTGATTTCTTTGTCAATGACTTCGA
1 CACTAAGCGTGATTTGATTT-TTTGCCAATGACTTCGA
* *
18492492 CACTAAGCGTGATTTGATTTTTGTGCCAATGGCTTTGA
1 CACTAAGCGTGATTTGATTTTT-TGCCAATGACTTCGA
* * * * *
18492530 CACTGAGCATGAATTGATCTTTCTGCCAGTGACTTCGA
1 CACTAAGCGTGATTTGAT-TTTTTGCCAATGACTTCGA
* * *
18492568 CATTGAGTGTGATTTGA
1 CACTAAGCGTGATTTGA
18492585 CTTTCTATCG
Statistics
Matches: 76, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
37 2 0.03
38 71 0.93
39 3 0.04
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (37 bp):
CACTAAGCGTGATTTGATTTTTTGCCAATGACTTCGA
Found at i:18493684 original size:20 final size:21
Alignment explanation
Indices: 18493643--18493687 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
18493633 CCTAGGTGGA
*
18493643 AAAATTCAACGGAAAAGTGTG
1 AAAATTCAACGGAAAAGAGTG
18493664 AAAATTCAA-GGAAACA-AGTG
1 AAAATTCAACGGAAA-AGAGTG
18493684 AAAA
1 AAAA
18493688 AAGGTAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.56, C:0.09, G:0.20, T:0.16
Consensus pattern (21 bp):
AAAATTCAACGGAAAAGAGTG
Found at i:18493689 original size:22 final size:21
Alignment explanation
Indices: 18493642--18493689 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
18493632 CCCTAGGTGG
*
18493642 AAAAATTCAACGGAAAAGTGT
1 AAAAATTCAACGGAAAAGTGA
*
18493663 GAAAATTCAA-GGAAACAAGTGA
1 AAAAATTCAACGG-AA-AAGTGA
18493685 AAAAA
1 AAAAA
18493690 GGTAAGATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 2 0.09
21 11 0.50
22 9 0.41
ACGTcount: A:0.58, C:0.08, G:0.19, T:0.15
Consensus pattern (21 bp):
AAAAATTCAACGGAAAAGTGA
Found at i:18513559 original size:24 final size:24
Alignment explanation
Indices: 18513532--18513590 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
18513522 ATGGGCTTTT
18513532 CCCATTTCTTCCTATTGGGCCACG
1 CCCATTTCTTCCTATTGGGCCACG
* * * *
18513556 CCCATTCTTTTCTTATTGGGCTATG
1 CCCATT-TCTTCCTATTGGGCCACG
18513581 CCCACTTTCT
1 CCCA-TTTCT
18513591 CTTCTTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 6 0.21
25 20 0.71
26 2 0.07
ACGTcount: A:0.12, C:0.34, G:0.14, T:0.41
Consensus pattern (24 bp):
CCCATTTCTTCCTATTGGGCCACG
Found at i:18513642 original size:12 final size:12
Alignment explanation
Indices: 18513586--18513650 Score: 66
Period size: 12 Copynumber: 5.7 Consensus size: 12
18513576 CTATGCCCAC
18513586 TTTCTC-TTCTT
1 TTTCTCTTTCTT
*
18513597 TTT-TTTTTCTT
1 TTTCTCTTTCTT
* *
18513608 TTTTTC-TTC-A
1 TTTCTCTTTCTT
18513618 TTTCTCGTTTCTT
1 TTTCTC-TTTCTT
18513631 TTTCTCTTTCTT
1 TTTCTCTTTCTT
18513643 TTTCTCTT
1 TTTCTCTT
18513651 CTCTCCTACT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
10 6 0.14
11 14 0.32
12 18 0.41
13 6 0.14
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (12 bp):
TTTCTCTTTCTT
Found at i:18513652 original size:11 final size:11
Alignment explanation
Indices: 18513586--18513652 Score: 64
Period size: 11 Copynumber: 5.9 Consensus size: 11
18513576 CTATGCCCAC
18513586 TTTCTCTTCTT
1 TTTCTCTTCTT
* *
18513597 TTTTTTTTCTT
1 TTTCTCTTCTT
* *
18513608 TTTTTCTTC-A
1 TTTCTCTTCTT
18513618 TTTCTCGTTTCTT
1 TTTCTC--TTCTT
18513631 TTTCTCTTTCTT
1 TTTCTC-TTCTT
18513643 TTTCTCTTCT
1 TTTCTCTTCT
18513653 CTCCTACTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
10 5 0.11
11 21 0.45
12 15 0.32
13 6 0.13
ACGTcount: A:0.01, C:0.22, G:0.01, T:0.75
Consensus pattern (11 bp):
TTTCTCTTCTT
Found at i:18513652 original size:23 final size:22
Alignment explanation
Indices: 18513586--18513652 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
18513576 CTATGCCCAC
* *
18513586 TTTCTCTTCTTTTTTTTTTCTT
1 TTTCTCTTCTTTTTCTCTTCTT
* *
18513608 TTTTTCTTC-ATTTCTCGTTTCTT
1 TTTCTCTTCTTTTTCTC--TTCTT
18513631 TTTCTCTTTCTTTTTCTCTTCT
1 TTTCTC-TTCTTTTTCTCTTCT
18513653 CTCCTACTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
21 4 0.11
22 8 0.23
23 14 0.40
24 3 0.09
25 6 0.17
ACGTcount: A:0.01, C:0.22, G:0.01, T:0.75
Consensus pattern (22 bp):
TTTCTCTTCTTTTTCTCTTCTT
Found at i:18513805 original size:34 final size:34
Alignment explanation
Indices: 18513763--18513955 Score: 212
Period size: 35 Copynumber: 5.6 Consensus size: 34
18513753 ACACTAGCTC
*
18513763 TTCT-TTTCTCTCTC-AAATTTGCTGCAAAACTCT
1 TTCTATTTC-CTCTCAAAATTTGCAGCAAAACTCT
* * *
18513796 TTCTATTTCTTCTCAAAATTTGTAGCAAAACTAT
1 TTCTATTTCCTCTCAAAATTTGCAGCAAAACTCT
* *
18513830 ATCTTTTTCCCTCTCAAAATTTGCAGCAAAACTCT
1 TTCTATTT-CCTCTCAAAATTTGCAGCAAAACTCT
* * *
18513865 TTCTATTTCCTTCTAAAAATTTGAAACAAAACTCT
1 TTCTATTTCC-TCTCAAAATTTGCAGCAAAACTCT
18513900 TAT-TATTTCCCTCTCAAAATTTGCAGCAAAACTCT
1 T-TCTATTT-CCTCTCAAAATTTGCAGCAAAACTCT
** *
18513935 GCCTTTTTCCTCTCAAAATTT
1 TTCTATTTCCTCTCAAAATTT
18513956 TGTAGCACAA
Statistics
Matches: 133, Mismatches: 20, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
33 8 0.06
34 41 0.31
35 81 0.61
36 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.41
Consensus pattern (34 bp):
TTCTATTTCCTCTCAAAATTTGCAGCAAAACTCT
Found at i:18513944 original size:70 final size:70
Alignment explanation
Indices: 18513767--18513955 Score: 251
Period size: 70 Copynumber: 2.7 Consensus size: 70
18513757 TAGCTCTTCT
* * * *
18513767 TTTCTCTCTC-AAATTTGCTGCAAAACTCTTTCTATTT-CTTCTCAAAATTTGTAGCAAAACTAT
1 TTTCCCTCTCAAAATTTGCAGCAAAACTCTTTCTATTTCCTTCTCAAAATTTGAAACAAAACTAT
*
18513830 ATCTT
66 ATCTA
* *
18513835 TTTCCCTCTCAAAATTTGCAGCAAAACTCTTTCTATTTCCTTCTAAAAATTTGAAACAAAACTCT
1 TTTCCCTCTCAAAATTTGCAGCAAAACTCTTTCTATTTCCTTCTCAAAATTTGAAACAAAACT-A
18513900 TAT-TA
65 TATCTA
** *
18513905 TTTCCCTCTCAAAATTTGCAGCAAAACTCTGCCTTTTTCC-TCTCAAAATTT
1 TTTCCCTCTCAAAATTTGCAGCAAAACTCTTTCTATTTCCTTCTCAAAATTT
18513956 TGTAGCACAA
Statistics
Matches: 107, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
68 9 0.08
69 36 0.34
70 59 0.55
71 3 0.03
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.41
Consensus pattern (70 bp):
TTTCCCTCTCAAAATTTGCAGCAAAACTCTTTCTATTTCCTTCTCAAAATTTGAAACAAAACTAT
ATCTA
Found at i:18514097 original size:43 final size:44
Alignment explanation
Indices: 18514008--18514094 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 44
18513998 TTCCCTTTTT
*
18514008 CTCTCTCACACCAACTTCTCTCTTTCTACTTCAGCTTTCTCTTTG
1 CTCTCTCACACCAACTTCTCTCTTTCTACTTCA-CTCTCTCTTTG
*
18514053 CTCTCTCACACCAACTTCTCTCTTTCTTCTTCA-TCTCATCTT
1 CTCTCTCACACCAACTTCTCTCTTTCTACTTCACTCTC-TCTT
18514095 GCTTACCAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
43 3 0.08
44 4 0.10
45 32 0.82
ACGTcount: A:0.14, C:0.39, G:0.02, T:0.45
Consensus pattern (44 bp):
CTCTCTCACACCAACTTCTCTCTTTCTACTTCACTCTCTCTTTG
Found at i:18519613 original size:21 final size:21
Alignment explanation
Indices: 18519571--18519613 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
18519561 GGTAACAATT
* **
18519571 TCGCTGTAGCGAAATTCATTC
1 TCGCTGCAGCGAAAAACATTC
*
18519592 TCGCTGCAGCGAAAAACTTTC
1 TCGCTGCAGCGAAAAACATTC
18519613 T
1 T
18519614 GTTTTGTCTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (21 bp):
TCGCTGCAGCGAAAAACATTC
Found at i:18522625 original size:19 final size:18
Alignment explanation
Indices: 18522592--18522630 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
18522582 ATACTCTATT
* *
18522592 TTTTAAAATCATTATTAA
1 TTTTAAAATAATTATAAA
18522610 TTTTAAAATAATTTATAAA
1 TTTTAAAATAA-TTATAAA
18522629 TT
1 TT
18522631 AATTTCATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTAAAATAATTATAAA
Found at i:18527548 original size:34 final size:34
Alignment explanation
Indices: 18527503--18527694 Score: 199
Period size: 35 Copynumber: 5.5 Consensus size: 34
18527493 CTTGTTTTGT
*
18527503 CTCTC-AAATTTGCAGCAAAACTCTTTCTATTTC
1 CTCTCAAAATTTGTAGCAAAACTCTTTCTATTTC
* * *
18527536 TTCTCAAAATTTGTAGCAAAACTCTCTCTTTTTTAC
1 CTCTCAAAATTTGTAGCAAAACTCTTTC-TATTT-C
*
18527572 CTCTCAAAATTTGTAGCAAAACTTTTTCTATTTC
1 CTCTCAAAATTTGTAGCAAAACTCTTTCTATTTC
* * *
18527606 TTTCTAAAAATCTGTAGCAAAACTCTTAT-TATTTTC
1 -CTCTCAAAATTTGTAGCAAAACTCTT-TCTA-TTTC
* * ** *
18527642 CTCTTAAAATTTGCAGCAAAACTCTGCCTTTTTC
1 CTCTCAAAATTTGTAGCAAAACTCTTTCTATTTC
18527676 CTCTCAAAATTTTGTAGCA
1 CTCTCAAAA-TTTGTAGCA
18527695 CAAAGCCTCT
Statistics
Matches: 130, Mismatches: 21, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
33 4 0.03
34 33 0.25
35 62 0.48
36 31 0.24
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (34 bp):
CTCTCAAAATTTGTAGCAAAACTCTTTCTATTTC
Found at i:18527583 original size:70 final size:70
Alignment explanation
Indices: 18527503--18527709 Score: 249
Period size: 70 Copynumber: 2.9 Consensus size: 70
18527493 CTTGTTTTGT
18527503 CTCTC-AAATTTGCAGCAAAACTCTTTCTATTTCTTCTCAAAATTTGTAGCAAAACTCTCTCTT-
1 CTCTCAAAATTTGCAGCAAAACTCTTTCTATTTCTTCTCAAAATTTGTAGCAAAACTCTCTCTTA
18527566 TTTTAC
66 TTTT-C
* * * * *
18527572 CTCTCAAAATTTGTAGCAAAACTTTTTCTATTTCTTTCTAAAAATCTGTAGCAAAACTCT-TATT
1 CTCTCAAAATTTGCAGCAAAACTCTTTCTATTTC-TTCTCAAAATTTGTAGCAAAACTCTCTCTT
18527636 ATTTTC
65 ATTTTC
* ** * *
18527642 CTCTTAAAATTTGCAGCAAAACTCTGCCTTTTTCCTCTCAAAATTTTGTAGCACAAAGCCTCTCT
1 CTCTCAAAATTTGCAGCAAAACTCTTTCTATTTCTTCTCAAAA-TTTGTAGCA-AAA--CTCTCT
18527707 CTT
62 CTT
18527710 CACTCCCCTA
Statistics
Matches: 115, Mismatches: 15, Indels: 11
0.82 0.11 0.08
Matches are distributed among these distances:
69 12 0.10
70 66 0.57
71 30 0.26
73 4 0.03
74 3 0.03
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.41
Consensus pattern (70 bp):
CTCTCAAAATTTGCAGCAAAACTCTTTCTATTTCTTCTCAAAATTTGTAGCAAAACTCTCTCTTA
TTTTC
Found at i:18528322 original size:13 final size:14
Alignment explanation
Indices: 18528297--18528325 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
18528287 TACTCCATAT
18528297 TTATTTAATTATTA
1 TTATTTAATTATTA
18528311 TTATTT-ATTATTA
1 TTATTTAATTATTA
18528324 TT
1 TT
18528326 TTTGACCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATTTAATTATTA
Found at i:18531368 original size:20 final size:20
Alignment explanation
Indices: 18531337--18531384 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
18531327 ATGGGAGGAA
*
18531337 GAAAAA-GAAGAAGCTGTTG
1 GAAAAATGAAGAAGCTGCTG
*
18531356 GAGAAATGAAGAAGCTGCTG
1 GAAAAATGAAGAAGCTGCTG
18531376 GAAAAATGA
1 GAAAAATGA
18531385 TATTTATAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.48, C:0.06, G:0.31, T:0.15
Consensus pattern (20 bp):
GAAAAATGAAGAAGCTGCTG
Found at i:18536379 original size:21 final size:19
Alignment explanation
Indices: 18536353--18536393 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
18536343 AATTTAAAAC
18536353 AAAATAACATAAAATTTAACT
1 AAAATAAC-TAAAA-TTAACT
*
18536374 AAAATAACTTAAATTAACT
1 AAAATAACTAAAATTAACT
18536393 A
1 A
18536394 CTCAACATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAACTAAAATTAACT
Found at i:18537166 original size:29 final size:28
Alignment explanation
Indices: 18537134--18537201 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
18537124 TCATCGATAG
*
18537134 GAGTAATCTCTCTACGTTAG-CATCACCCA
1 GAGTAATCTCCCTACG-TAGACATCA-CCA
* *
18537163 GAGTAACCTCCCTACGTCGACATCACCA
1 GAGTAATCTCCCTACGTAGACATCACCA
18537191 GAAGTAATCTC
1 G-AGTAATCTC
18537202 AACGGATGGC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 6 0.18
29 27 0.82
ACGTcount: A:0.29, C:0.32, G:0.15, T:0.24
Consensus pattern (28 bp):
GAGTAATCTCCCTACGTAGACATCACCA
Found at i:18543116 original size:2 final size:2
Alignment explanation
Indices: 18543109--18543142 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
18543099 ATAATATTCA
18543109 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18543143 TACATATCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18548473 original size:21 final size:22
Alignment explanation
Indices: 18548448--18548488 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
18548438 CATAGGTGGA
*
18548448 AAAATTCAAGGGAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
18548469 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
18548489 AAAAAAGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:18548489 original size:20 final size:21
Alignment explanation
Indices: 18548448--18548492 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
18548438 CATAGGTGGA
*
18548448 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGGAAAAGAGTG
18548469 AAAATTCAA-GGAAACA-AGTG
1 AAAATTCAAGGGAAA-AGAGTG
18548489 AAAA
1 AAAA
18548493 AAGGTAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.16
Consensus pattern (21 bp):
AAAATTCAAGGGAAAAGAGTG
Found at i:18548493 original size:21 final size:20
Alignment explanation
Indices: 18548446--18548493 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
18548436 ACCATAGGTG
*
18548446 GAAAAATTCAAGGGAAAAGT
1 GAAAAATTCAAGGAAAAAGT
*
18548466 GTGAAAATTCAAGGAAACAAGT
1 G-AAAAATTCAAGGAAA-AAGT
18548488 GAAAAA
1 GAAAAA
18548494 AGGTAAGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.56, C:0.06, G:0.23, T:0.15
Consensus pattern (20 bp):
GAAAAATTCAAGGAAAAAGT
Found at i:18556764 original size:10 final size:10
Alignment explanation
Indices: 18556745--18556777 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
18556735 TTTTTTCTTC
18556745 TTAATTTGTT
1 TTAATTTGTT
*
18556755 TTAGTTTGTT
1 TTAATTTGTT
18556765 TTAATTTGTT
1 TTAATTTGTT
18556775 TTA
1 TTA
18556778 TGGGATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.70
Consensus pattern (10 bp):
TTAATTTGTT
Found at i:18558444 original size:21 final size:21
Alignment explanation
Indices: 18558418--18558507 Score: 137
Period size: 21 Copynumber: 4.3 Consensus size: 21
18558408 GCCATATGTC
* *
18558418 GCTCAAATTGGTGCCTAAGTT
1 GCTCAACTAGGTGCCTAAGTT
18558439 GCTCAACTAGGTGCCTAAGTT
1 GCTCAACTAGGTGCCTAAGTT
18558460 GCTCAACTAGGTGCCTAAGTT
1 GCTCAACTAGGTGCCTAAGTT
*
18558481 GCTCAACTAGTTG-CTCAAGTT
1 GCTCAACTAGGTGCCT-AAGTT
18558502 GCTCAA
1 GCTCAA
18558508 TCCTCTAAGT
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
20 2 0.03
21 63 0.97
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.30
Consensus pattern (21 bp):
GCTCAACTAGGTGCCTAAGTT
Found at i:18558494 original size:12 final size:12
Alignment explanation
Indices: 18558435--18558498 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 12
18558425 TTGGTGCCTA
18558435 AGTTGCTCAACT
1 AGTTGCTCAACT
* *
18558447 AGGTGC-CTA--
1 AGTTGCTCAACT
18558456 AGTTGCTCAACT
1 AGTTGCTCAACT
* *
18558468 AGGTGC-CTA--
1 AGTTGCTCAACT
18558477 AGTTGCTCAACT
1 AGTTGCTCAACT
18558489 AGTTGCTCAA
1 AGTTGCTCAA
18558499 GTTGCTCAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 12
0.66 0.14 0.21
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 20 0.53
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (12 bp):
AGTTGCTCAACT
Found at i:18559344 original size:6 final size:6
Alignment explanation
Indices: 18559333--18559359 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
18559323 GCCATTAGAA
18559333 CTTGCT CTTGCT CTTGCT CTTGCT CTT
1 CTTGCT CTTGCT CTTGCT CTTGCT CTT
18559360 TTGGGTGCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.15, T:0.52
Consensus pattern (6 bp):
CTTGCT
Found at i:18563021 original size:17 final size:17
Alignment explanation
Indices: 18562991--18563023 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
18562981 TTCTTCATAA
18562991 AATAAAACTCCTTATTG
1 AATAAAACTCCTTATTG
18563008 AATAATAACT-CTTATT
1 AATAA-AACTCCTTATT
18563024 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAAAACTCCTTATTG
Found at i:18563312 original size:29 final size:28
Alignment explanation
Indices: 18563186--18563338 Score: 166
Period size: 28 Copynumber: 5.3 Consensus size: 28
18563176 ATTAAAACAA
*
18563186 AAATAT-TTTATCTTGTCTAAATTGAGAC
1 AAATATGTTT-TCTTGTCTAAATTAAGAC
*
18563214 AAATATGTTTTCTTGTCTAGATTAAGAC
1 AAATATGTTTTCTTGTCTAAATTAAGAC
* * *
18563242 AAAAAATACTTTGCTTGTCTTAAATTAAGAC
1 -AAATAT-GTTTTCTTGTC-TAAATTAAGAC
*
18563273 -AATCATATTTTCTTGTCTAAATTAAGACC
1 AAAT-ATGTTTTCTTGTCTAAATTAAGA-C
*
18563302 AAATATGTTTTCTTGTATAAATTAAGAC
1 AAATATGTTTTCTTGTCTAAATTAAGAC
*
18563330 AAACATGTT
1 AAATATGTT
18563339 AAAGCTGCCA
Statistics
Matches: 106, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
28 41 0.39
29 41 0.39
30 14 0.13
31 10 0.09
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (28 bp):
AAATATGTTTTCTTGTCTAAATTAAGAC
Found at i:18575460 original size:28 final size:29
Alignment explanation
Indices: 18575413--18575467 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
18575403 ACAAGTGTTT
* *
18575413 GGTGTGTAAAATTACCATTTTTCCCCTGG
1 GGTGTGTAAAATAACCATTTTGCCCCTGG
*
18575442 GGTG-GTAAAATAACTATTTTGCCCCT
1 GGTGTGTAAAATAACCATTTTGCCCCT
18575468 ATCCTCGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (29 bp):
GGTGTGTAAAATAACCATTTTGCCCCTGG
Found at i:18581057 original size:38 final size:39
Alignment explanation
Indices: 18580967--18581069 Score: 140
Period size: 38 Copynumber: 2.6 Consensus size: 39
18580957 ACCCGGCTCA
18580967 TGTACATCCCCCCACATCGTGCAC-ATAGTCGGCACCATCG
1 TGTACATCCCCCCACATCGTGCACAATAGTC-G-ACCATCG
* *
18581007 TGTGCATTCCCCCACATCGTGCACAATTAGT-G-CCATCG
1 TGTACATCCCCCCACATCGTGCACAA-TAGTCGACCATCG
18581045 TGTACATCCCCCCACATCGTGCACA
1 TGTACATCCCCCCACATCGTGCACA
18581070 CGTGCACTAT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
38 29 0.51
40 23 0.40
41 1 0.02
42 4 0.07
ACGTcount: A:0.22, C:0.39, G:0.17, T:0.22
Consensus pattern (39 bp):
TGTACATCCCCCCACATCGTGCACAATAGTCGACCATCG
Found at i:18587686 original size:16 final size:16
Alignment explanation
Indices: 18587665--18587698 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
18587655 TAGACAACAA
18587665 TCCATTTAAAATCTCG
1 TCCATTTAAAATCTCG
18587681 TCCATTTAAAATCTCG
1 TCCATTTAAAATCTCG
18587697 TC
1 TC
18587699 TGATCATGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.38
Consensus pattern (16 bp):
TCCATTTAAAATCTCG
Found at i:18593933 original size:64 final size:64
Alignment explanation
Indices: 18593853--18593979 Score: 202
Period size: 64 Copynumber: 2.0 Consensus size: 64
18593843 CCACGTCACC
*
18593853 TAGTCTTAAGCAACACTAATAGGCACACCACA-TAATTGCAATCTATAACAGCGACCTTGCCACA
1 TAGTCTTAAACAACACTAATAGGCACACCA-AGTAATTGCAATCTATAACAGCGACCTTGCCACA
* * *
18593917 TAGTCTTAAACAACACTAATAGGCACACCAAGTACTTGCAATCTATAACAGTGGCCTTGCCAC
1 TAGTCTTAAACAACACTAATAGGCACACCAAGTAATTGCAATCTATAACAGCGACCTTGCCAC
18593980 GTACCCATCA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
63 1 0.02
64 57 0.98
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (64 bp):
TAGTCTTAAACAACACTAATAGGCACACCAAGTAATTGCAATCTATAACAGCGACCTTGCCACA
Found at i:18594107 original size:32 final size:32
Alignment explanation
Indices: 18594049--18594115 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
18594039 ACCACGTACA
*
18594049 CATAATCAACATTAGTGGCAACGCCACATGAT
1 CATAATCAACATTAGTGGCAACGCCACATAAT
* ***
18594081 CATAATCAACGTTAGTGGCCGTGCCACATAAT
1 CATAATCAACATTAGTGGCAACGCCACATAAT
18594113 CAT
1 CAT
18594116 CGACCTTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.24
Consensus pattern (32 bp):
CATAATCAACATTAGTGGCAACGCCACATAAT
Found at i:18595734 original size:46 final size:45
Alignment explanation
Indices: 18595670--18595759 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 45
18595660 CATGCACAAC
* *
18595670 ATATATATATATATCAACATAATGTAGTAGTGCATGAATCCANTAT
1 ATATATATATATACCAACATAATGTAGTAGTGCACGAATCCA-TAT
18595716 ATATATATATATACCAACATAATGTAGTAGTGCACGAATCCATA
1 ATATATATATATACCAACATAATGTAGTAGTGCACGAATCCATA
18595760 ACAACCACAT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 2 0.05
46 40 0.95
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.32
Consensus pattern (45 bp):
ATATATATATATACCAACATAATGTAGTAGTGCACGAATCCATAT
Found at i:18600699 original size:22 final size:22
Alignment explanation
Indices: 18600671--18600718 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
18600661 GAGAGGAAAA
*
18600671 GAAGAGACGAAGCCACGGTGGT
1 GAAGAGACGAAGCCACGATGGT
*
18600693 GAAGAGAGGAAGCCACGATGGT
1 GAAGAGACGAAGCCACGATGGT
18600715 GAAG
1 GAAG
18600719 GGAGTGACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.15, G:0.42, T:0.08
Consensus pattern (22 bp):
GAAGAGACGAAGCCACGATGGT
Found at i:18600874 original size:26 final size:25
Alignment explanation
Indices: 18600818--18600874 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
18600808 AGTAGAAAAT
* *
18600818 AAAAATGGGCATTGCTCAATAGGAG
1 AAAAATGGGCATTGCCCAATAGGAA
*
18600843 ATAAATGGGC-TTAGCCCAAATAGGAA
1 AAAAATGGGCATT-GCCC-AATAGGAA
18600869 AAAAAT
1 AAAAAT
18600875 TGGAAAAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 2 0.08
25 12 0.46
26 12 0.46
ACGTcount: A:0.46, C:0.12, G:0.23, T:0.19
Consensus pattern (25 bp):
AAAAATGGGCATTGCCCAATAGGAA
Found at i:18621743 original size:19 final size:19
Alignment explanation
Indices: 18621719--18621817 Score: 74
Period size: 19 Copynumber: 5.1 Consensus size: 19
18621709 TGCCCGTGTG
18621719 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
**** *
18621738 CACGATG-GCACTGATTGTG
1 CACGATGTGGGGGGA-TGTA
*
18621757 CACGATGTGGGGGGATGCA
1 CACGATGTGGGGGGATGTA
* ** *
18621776 CACGATGGTGCCGGCTATGTG
1 CACGAT-GTG-GGGGGATGTA
18621797 CACGATGTGGGGGGATGTA
1 CACGATGTGGGGGGATGTA
18621816 CA
1 CA
18621818 TGAGCCGGGT
Statistics
Matches: 56, Mismatches: 20, Indels: 8
0.67 0.24 0.10
Matches are distributed among these distances:
18 3 0.05
19 33 0.59
20 9 0.16
21 11 0.20
ACGTcount: A:0.20, C:0.17, G:0.41, T:0.21
Consensus pattern (19 bp):
CACGATGTGGGGGGATGTA
Found at i:18621757 original size:38 final size:40
Alignment explanation
Indices: 18621715--18621817 Score: 149
Period size: 38 Copynumber: 2.6 Consensus size: 40
18621705 ATAGTGCCCG
*
18621715 TGTGCACGATGTGGGGGGATGTACACGAT-G-GCACTGAT-
1 TGTGCACGATGTGGGGGGATGTACACGATGGTGC-CGGATA
* *
18621753 TGTGCACGATGTGGGGGGATGCACACGATGGTGCCGGCTA
1 TGTGCACGATGTGGGGGGATGTACACGATGGTGCCGGATA
18621793 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
18621818 TGAGCCGGGT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
38 28 0.48
39 4 0.07
40 26 0.45
ACGTcount: A:0.19, C:0.17, G:0.42, T:0.22
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACACGATGGTGCCGGATA
Found at i:18627714 original size:73 final size:73
Alignment explanation
Indices: 18627607--18627787 Score: 190
Period size: 73 Copynumber: 2.5 Consensus size: 73
18627597 GCAGAATGCT
* * ** *
18627607 CTTAGTCGACTAACTGATATCTAAGTCGACTAAGTT-GTCTCTATCTTCT-AA-TCCCAATTTCT
1 CTTAGTCGACTAACTCATTTCTTGGTCGACTAAGTTGGT-TCTAT-TT-TGAAGTCCAAATTTCT
*
18627669 GGCAGTGAG-TA
63 GGCAAT-AGCTA
* * * *
18627680 CTTAGTCAACTAACTCATTTCTTGGTCAACTAAGTTGGTTCTGTTTTGAAGTCCAAATTTTTGGC
1 CTTAGTCGACTAACTCATTTCTTGGTCGACTAAGTTGGTTCTATTTTGAAGTCCAAATTTCTGGC
*
18627745 AATAGCTT
66 AATAGCTA
*
18627753 CTTAGTCGACTAACCCATTTCTTGGTCGACTAAGT
1 CTTAGTCGACTAACTCATTTCTTGGTCGACTAAGT
18627788 CTTTTTTGTC
Statistics
Matches: 90, Mismatches: 14, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
71 1 0.01
72 6 0.07
73 81 0.90
74 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (73 bp):
CTTAGTCGACTAACTCATTTCTTGGTCGACTAAGTTGGTTCTATTTTGAAGTCCAAATTTCTGGC
AATAGCTA
Found at i:18633640 original size:23 final size:24
Alignment explanation
Indices: 18633597--18633645 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
18633587 GCCCATAACC
18633597 AAGAAGAAAAGAGAAAGGAAAGGA
1 AAGAAGAAAAGAGAAAGGAAAGGA
18633621 AAGAA-AAAAGA-AAAGAGAAAGGA
1 AAGAAGAAAAGAGAAAG-GAAAGGA
18633644 AA
1 AA
18633646 ATAAAGAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 4 0.17
23 15 0.62
24 5 0.21
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (24 bp):
AAGAAGAAAAGAGAAAGGAAAGGA
Found at i:18633640 original size:28 final size:29
Alignment explanation
Indices: 18633600--18633659 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 29
18633590 CATAACCAAG
*
18633600 AAGAAAAGAGAAAGGAAAGGAAAGAAA-A
1 AAGAAAAGAGAAAGGAAAAGAAAGAAAGA
*
18633628 AAGAAAAGAGAAAGGAAAATAAAGAAAGA
1 AAGAAAAGAGAAAGGAAAAGAAAGAAAGA
18633657 AAG
1 AAG
18633660 GAAGAAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.02
Consensus pattern (29 bp):
AAGAAAAGAGAAAGGAAAAGAAAGAAAGA
Found at i:18633646 original size:18 final size:17
Alignment explanation
Indices: 18633615--18633680 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 17
18633605 AAGAGAAAGG
*
18633615 AAAG-GAAAGAAAAAAGA
1 AAAGAGAAAGGAAAAA-A
18633632 AAAGAGAAAGGAAAATAA
1 AAAGAGAAAGGAAAA-AA
18633650 AGAA-AGAAAGGAAGAAAA
1 A-AAGAGAAAGGAA-AAAA
*
18633668 AGAGAGAAAGGAA
1 AAAGAGAAAGGAA
18633681 GGTAAGGGTC
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
17 5 0.12
18 32 0.76
19 5 0.12
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (17 bp):
AAAGAGAAAGGAAAAAA
Found at i:18633681 original size:18 final size:19
Alignment explanation
Indices: 18633634--18633681 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
18633624 AAAAAAGAAA
18633634 AGAGAAAGGAA-AATAAAG
1 AGAGAAAGGAAGAATAAAG
*
18633652 AAAGAAAGGAAGAA-AAAG
1 AGAGAAAGGAAGAATAAAG
18633670 AGAGAAAGGAAG
1 AGAGAAAGGAAG
18633682 GTAAGGGTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 25 0.93
19 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (19 bp):
AGAGAAAGGAAGAATAAAG
Found at i:18635022 original size:2 final size:2
Alignment explanation
Indices: 18635015--18635050 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
18635005 TTCCCATAAT
18635015 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
18635051 CGTGATGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18651967 original size:21 final size:20
Alignment explanation
Indices: 18651933--18651976 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
18651923 CAATCAATTT
**
18651933 TAAGAAGCCATAGTTGACTA
1 TAAGAAGCCATAGTCAACTA
*
18651953 TAAGAAAGGCATAGTCAACTA
1 TAAG-AAGCCATAGTCAACTA
18651974 TAA
1 TAA
18651977 AGGTCAAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.23
Consensus pattern (20 bp):
TAAGAAGCCATAGTCAACTA
Found at i:18655948 original size:43 final size:42
Alignment explanation
Indices: 18655887--18656052 Score: 162
Period size: 43 Copynumber: 4.0 Consensus size: 42
18655877 CAACACTCTC
* *
18655887 TCAGCTTATATGCACTCCCACACCGCACATAGCTGGGTCATCA
1 TCAGCTCATGTGCACTCCCACACC-CACATAGCTGGGTCATCA
* *
18655930 TCAGCTCATGTGCACTCCCTAC-TCAATCATAGCTGGGTCATCA
1 TCAGCTCATGTGCACTCCC-ACACCCA-CATAGCTGGGTCATCA
* * *
18655973 TCAGCTCATGTGTACTCCTC-CA--CACATGGCTGGGTCAGCA
1 TCAGCTCATGTGCACTCC-CACACCCACATAGCTGGGTCATCA
* * *
18656013 -CAACTCATGTGCACTCCTACACCGCACATGGCTGGGTCAT
1 TCAGCTCATGTGCACTCCCACACC-CACATAGCTGGGTCAT
18656053 AATTATCACG
Statistics
Matches: 103, Mismatches: 12, Indels: 17
0.78 0.09 0.13
Matches are distributed among these distances:
39 17 0.17
40 14 0.14
41 1 0.01
42 17 0.17
43 51 0.50
44 3 0.03
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.25
Consensus pattern (42 bp):
TCAGCTCATGTGCACTCCCACACCCACATAGCTGGGTCATCA
Found at i:18658117 original size:40 final size:43
Alignment explanation
Indices: 18658007--18658170 Score: 228
Period size: 43 Copynumber: 3.9 Consensus size: 43
18657997 CAACTCTCTC
* * *
18658007 TCAGCTTATGTGCACTCCC-ACACCGCACATAGCTGGGTCATCA
1 TCAGCTCATGTGCACTCCCTAC-TCACACATAGCTGGGTCATCA
18658050 TCAGCTCATGTGCACTCCCTACTCACACATAGCTGGGTCATCA
1 TCAGCTCATGTGCACTCCCTACTCACACATAGCTGGGTCATCA
* * *
18658093 TCAACTCATGTGTACT-CCT-C-CACACATGGCTGGGTCATCA
1 TCAGCTCATGTGCACTCCCTACTCACACATAGCTGGGTCATCA
*
18658133 TCAGCTCATGTGCACTCCCTACTCGCACATAGCTGGGT
1 TCAGCTCATGTGCACTCCCTACTCACACATAGCTGGGT
18658171 GCGGAATATT
Statistics
Matches: 107, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
40 33 0.31
41 4 0.04
42 4 0.04
43 64 0.60
44 2 0.02
ACGTcount: A:0.22, C:0.34, G:0.18, T:0.26
Consensus pattern (43 bp):
TCAGCTCATGTGCACTCCCTACTCACACATAGCTGGGTCATCA
Found at i:18678202 original size:2 final size:2
Alignment explanation
Indices: 18678195--18678221 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18678185 GACCCCTCCC
18678195 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
18678222 GCCCCCCTTC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:18681443 original size:77 final size:73
Alignment explanation
Indices: 18681320--18681461 Score: 221
Period size: 77 Copynumber: 1.9 Consensus size: 73
18681310 TAACAAGCAA
18681320 GAGCCATAAGCAGCTCTCCCTACACACCCTACCATCTGAGCAGAAGAAGCTACATTTATGCAAGC
1 GAGCCATAAGCAGCTCTCCCTACACACCCTACCATCTGAGCAGAAGAAGCTACATTTATGCAAGC
18681385 TTGTGCAT
66 TTGTGCAT
* * *
18681393 GAGCCATAAGCAGCTCCTCCCCCCTGCCCACCCTATCATCTGAGCAGAAGAAGCTACATTTATGC
1 GAGCCATAAGCAGCT-CT---CCCTACACACCCTACCATCTGAGCAGAAGAAGCTACATTTATGC
18681458 AAGC
62 AAGC
18681462 CAACTATCAA
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
73 15 0.24
74 2 0.03
77 45 0.73
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (73 bp):
GAGCCATAAGCAGCTCTCCCTACACACCCTACCATCTGAGCAGAAGAAGCTACATTTATGCAAGC
TTGTGCAT
Found at i:18685211 original size:15 final size:15
Alignment explanation
Indices: 18685191--18685230 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
18685181 ATGTTTAAGA
*
18685191 GATTTGATTTCATTT
1 GATTTGATTTAATTT
18685206 GATTTGATTTAATTT
1 GATTTGATTTAATTT
* *
18685221 TATTTAATTT
1 GATTTGATTT
18685231 TTTTCCCTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.25, C:0.03, G:0.10, T:0.62
Consensus pattern (15 bp):
GATTTGATTTAATTT
Found at i:18694050 original size:28 final size:27
Alignment explanation
Indices: 18694011--18694063 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
18694001 ATATCCTAGT
*
18694011 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTACCCCTGA
*
18694038 GGTGGCAAAATTACCATTTTACCCCT
1 GGTGG-AAAATTACAATTTTACCCCT
18694064 AGTTAGTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCCTGA
Found at i:18699847 original size:29 final size:29
Alignment explanation
Indices: 18699805--18699861 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
18699795 AGATATTCAA
*
18699805 TATATTTTGCTTAGCTACTGTGGATATTG
1 TATATCTTGCTTAGCTACTGTGGATATTG
* *
18699834 TATATCTTGTTTAGCTATTGTGGATATT
1 TATATCTTGCTTAGCTACTGTGGATATT
18699862 ATAAATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.21, C:0.09, G:0.19, T:0.51
Consensus pattern (29 bp):
TATATCTTGCTTAGCTACTGTGGATATTG
Found at i:18703479 original size:35 final size:33
Alignment explanation
Indices: 18703405--18703493 Score: 99
Period size: 35 Copynumber: 2.7 Consensus size: 33
18703395 GTTTTTACCG
* *
18703405 GGATCAACCAAAATCCAA-AGTGGTTTTTCAAA
1 GGATCAACCAAAACCCAACAATGGTTTTTCAAA
* * **
18703437 GGCTCAACCACAACCTACAACAATGGTTTTTCACG
1 GGATCAACCAAAACC--CAACAATGGTTTTTCAAA
18703472 GGATCAACCAAAACCCAACAAT
1 GGATCAACCAAAACCCAACAAT
18703494 TAACTTTTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
32 12 0.26
33 7 0.15
34 3 0.07
35 24 0.52
ACGTcount: A:0.39, C:0.27, G:0.13, T:0.20
Consensus pattern (33 bp):
GGATCAACCAAAACCCAACAATGGTTTTTCAAA
Found at i:18703680 original size:32 final size:32
Alignment explanation
Indices: 18703598--18703735 Score: 125
Period size: 35 Copynumber: 4.1 Consensus size: 32
18703588 AAGAAATGAA
*
18703598 CCAAAGTGGTTTTTCAAAGGCTCAACCACAAC
1 CCAAAGTGGTTTTTCAAAGGCTCAACCAAAAC
**
18703630 CTTTCACAA-TGGTTTTTCACGGGCTCAACCAAAAC
1 C---CA-AAGTGGTTTTTCAAAGGCTCAACCAAAAC
*
18703665 CCAAAGTGGTTTTTCAAAGGCTCAACCACAAC
1 CCAAAGTGGTTTTTCAAAGGCTCAACCAAAAC
* * ** *
18703697 CTAAAATAATGGTTTTTCACGGGATCAACCAAAAC
1 C--CAA-AGTGGTTTTTCAAAGGCTCAACCAAAAC
18703732 CCAA
1 CCAA
18703736 CAACTAACTT
Statistics
Matches: 85, Mismatches: 13, Indels: 15
0.75 0.12 0.13
Matches are distributed among these distances:
31 2 0.02
32 27 0.32
33 2 0.02
34 2 0.02
35 50 0.59
36 2 0.02
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (32 bp):
CCAAAGTGGTTTTTCAAAGGCTCAACCAAAAC
Found at i:18703708 original size:67 final size:67
Alignment explanation
Indices: 18703598--18703735 Score: 231
Period size: 67 Copynumber: 2.1 Consensus size: 67
18703588 AAGAAATGAA
*** *
18703598 CCAAAGTGGTTTTTCAAAGGCTCAACCACAACCTTTCACAATGGTTTTTCACGGGCTCAACCAAA
1 CCAAAGTGGTTTTTCAAAGGCTCAACCACAACCTAAAACAATGGTTTTTCACGGGATCAACCAAA
18703663 AC
66 AC
*
18703665 CCAAAGTGGTTTTTCAAAGGCTCAACCACAACCTAAAATAATGGTTTTTCACGGGATCAACCAAA
1 CCAAAGTGGTTTTTCAAAGGCTCAACCACAACCTAAAACAATGGTTTTTCACGGGATCAACCAAA
18703730 AC
66 AC
18703732 CCAA
1 CCAA
18703736 CAACTAACTT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (67 bp):
CCAAAGTGGTTTTTCAAAGGCTCAACCACAACCTAAAACAATGGTTTTTCACGGGATCAACCAAA
AC
Found at i:18703815 original size:246 final size:246
Alignment explanation
Indices: 18703381--18703843 Score: 820
Period size: 246 Copynumber: 1.9 Consensus size: 246
18703371 GCTTAGAAAA
* *
18703381 AACCTTTCACCATAGTTTTTACCGGGATCAACCAAAATCCAAAGTGGTTTTTCAAAGGCTCAACC
1 AACCTTTCACAATAGTTTTTACCGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
* * *
18703446 ACAACCTACAACAATGGTTTTTCACGGGATCAACCAAAACCCAACAATTAACTTTTTAAGGCTAA
66 ACAACCTAAAACAATGGTTTTTCACGGGATCAACCAAAACCCAACAACTAACTTTTCAAGGCTAA
* *
18703511 GTTAGAACCTATACACTCAATCAAGCAATTCAAGCTTGAATTAATCCTTTAGAGTGTCTTGCACA
131 GTTAGAACCTATACACTCAATCAAGCAATCCAAGCTTGAATTAATCCCTTAGAGTGTCTTGCACA
18703576 CTCTAAGTAATCAAGAAATGAACCAAAGTGGTTTTTCAAAGGCTCAACCAC
196 CTCTAAGTAATCAAGAAATGAACCAAAGTGGTTTTTCAAAGGCTCAACCAC
* *
18703627 AACCTTTCACAATGGTTTTT-CACGGGCTCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
1 AACCTTTCACAATAGTTTTTAC-CGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
*
18703691 CACAACCTAAAATAATGGTTTTTCACGGGATCAACCAAAACCCAACAACTAACTTTTCAAGGCTA
65 CACAACCTAAAACAATGGTTTTTCACGGGATCAACCAAAACCCAACAACTAACTTTTCAAGGCTA
18703756 AGTTAGAACCTATACACTCAATCAAGCAATCCAAGCTTGAATTAATCCCTTAGAGTGTCTTGCAC
130 AGTTAGAACCTATACACTCAATCAAGCAATCCAAGCTTGAATTAATCCCTTAGAGTGTCTTGCAC
18703821 ACTCTAAGTAATCAAGAAATGAA
195 ACTCTAAGTAATCAAGAAATGAA
18703844 GAAAAGATGA
Statistics
Matches: 206, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
245 1 0.00
246 205 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (246 bp):
AACCTTTCACAATAGTTTTTACCGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
ACAACCTAAAACAATGGTTTTTCACGGGATCAACCAAAACCCAACAACTAACTTTTCAAGGCTAA
GTTAGAACCTATACACTCAATCAAGCAATCCAAGCTTGAATTAATCCCTTAGAGTGTCTTGCACA
CTCTAAGTAATCAAGAAATGAACCAAAGTGGTTTTTCAAAGGCTCAACCAC
Found at i:18706170 original size:80 final size:79
Alignment explanation
Indices: 18706037--18706300 Score: 325
Period size: 80 Copynumber: 3.3 Consensus size: 79
18706027 GGACCAACAA
* * *
18706037 ATGTACGTGTTGGGATAGTCATATACACTATGAGCTAAGTATGTGAATTATTTATGAAGTTATGA
1 ATGTATGTGTTGAGATAGTCATATACACTATG-GCTAAGTATGTGAGTTATTTATGAAGTTATGA
18706102 AATGCATGCCATGAG
65 AATGCATGCCATGAG
* * *
18706117 ATGTATGTGTTGGGATAGTCATATACACTCTAGGCTAAGCATGTGAGTTATTTATG-AGATTATG
1 ATGTATGTGTTGAGATAGTCATATACACTAT-GGCTAAGTATGTGAGTTATTTATGAAG-TTATG
18706181 AAATGCATGCCATGAG
64 AAATGCATGCCATGAG
* * * * * * * *
18706197 ATATATGTGCTGAGATAGTCATATACACTATGGGTTAAGTATATAAGTGATTTATGAGGTCATGA
1 ATGTATGTGTTGAGATAGTCATATACACTAT-GGCTAAGTATGTGAGTTATTTATGAAGTTATGA
*
18706262 AATGTATGCCATGAG
65 AATGCATGCCATGAG
* *
18706277 -TGTATGTATTGAGATAATCATATA
1 ATGTATGTGTTGAGATAGTCATATA
18706301 AATTATAGAC
Statistics
Matches: 160, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
79 22 0.14
80 136 0.85
81 2 0.01
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.34
Consensus pattern (79 bp):
ATGTATGTGTTGAGATAGTCATATACACTATGGCTAAGTATGTGAGTTATTTATGAAGTTATGAA
ATGCATGCCATGAG
Found at i:18707729 original size:21 final size:21
Alignment explanation
Indices: 18707703--18707744 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
18707693 AAACAGAAGG
* *
18707703 TTTCTCGCTGTAGCGAAATTC
1 TTTCTCGCTGCAGCAAAATTC
18707724 TTTCTCGCTGCAGCAAAATTC
1 TTTCTCGCTGCAGCAAAATTC
18707745 AACTGATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (21 bp):
TTTCTCGCTGCAGCAAAATTC
Found at i:18707759 original size:60 final size:61
Alignment explanation
Indices: 18707666--18707797 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 61
18707656 TTTCGCTGAA
* *
18707666 TCTCGCTGCAGCGAAATTGAAACCCAGAAACAGA-AGGTTTCTCGCTGTAGCGAAATT-CTT
1 TCTCGCTGCAGCAAAATTGAAACCCAGAAACAGAGA-GTTTCTCGCTGCAGCGAAATTCCTT
* ** * * *
18707726 TCTCGCTGCAGCAAAATT-CAACTGATGAAACAGAGAGTTTTTTGCTGCAGCGAGATTCCTT
1 TCTCGCTGCAGCAAAATTGAAACCCA-GAAACAGAGAGTTTCTCGCTGCAGCGAAATTCCTT
18707787 T-TCGCTGCAGC
1 TCTCGCTGCAGC
18707798 GAGAAGCTAC
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
59 4 0.07
60 52 0.85
61 5 0.08
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.27
Consensus pattern (61 bp):
TCTCGCTGCAGCAAAATTGAAACCCAGAAACAGAGAGTTTCTCGCTGCAGCGAAATTCCTT
Found at i:18709744 original size:18 final size:19
Alignment explanation
Indices: 18709721--18709756 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
18709711 GCGAAGAAAA
18709721 TATTTTA-AAATAAAATAT
1 TATTTTATAAATAAAATAT
18709739 TATTTTATAAATAAAATA
1 TATTTTATAAATAAAATA
18709757 ATGTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TATTTTATAAATAAAATAT
Done.