Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 4 of 295
Found at i:1165105 original size:47 final size:47
Alignment explanation
Indices: 1165052--1165172 Score: 115
Period size: 47 Copynumber: 2.6 Consensus size: 47
1165042 CATCTTGATT
* *
1165052 CATGTCCCAGACATGTCTTACACTAGCACTCGTCTTAA-T-GCCGATGC
1 CATGTCCCAGACATGTCTTACACTAGCACTC-TCATAAGTGGCCGAT-A
* * * *
1165099 CATGTCCTAGACGTGGTCTTACA-TTG-GCTCTCATAATGTGGCCGATA
1 CATGTCCCAGACAT-GTCTTACACTAGCACTCTCATAA-GTGGCCGATA
*
1165146 AATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
1165173 TCACTTACAT
Statistics
Matches: 58, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
45 5 0.09
46 11 0.19
47 28 0.48
48 14 0.24
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (47 bp):
CATGTCCCAGACATGTCTTACACTAGCACTCTCATAAGTGGCCGATA
Found at i:1165492 original size:19 final size:19
Alignment explanation
Indices: 1165456--1165492 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1165446 TAACTAGGCT
* *
1165456 TTAATTAAGTGAATTTAGC
1 TTAATTAAGAGAAATTAGC
1165475 TTAATTAAGAGAAATTAG
1 TTAATTAAGAGAAATTAG
1165493 GAAAAATGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (19 bp):
TTAATTAAGAGAAATTAGC
Found at i:1165649 original size:23 final size:24
Alignment explanation
Indices: 1165617--1165669 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
1165607 AAAATCCTAG
*
1165617 ATTTT-TTGTAGATTATATT-ATT
1 ATTTTATTGTAAATTATATTAATT
*
1165639 ATTTTATTGTAAATTATGTTAATT
1 ATTTTATTGTAAATTATATTAATT
*
1165663 ATATTAT
1 ATTTTAT
1165670 AATATTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 5 0.19
23 12 0.46
24 9 0.35
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (24 bp):
ATTTTATTGTAAATTATATTAATT
Found at i:1165852 original size:19 final size:20
Alignment explanation
Indices: 1165802--1165845 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
1165792 AAATAGATAT
*
1165802 TTATT-TAAATATTAAATTA
1 TTATTATAATTATTAAATTA
*
1165821 TTGTTATAATTATT-AATTA
1 TTATTATAATTATTAAATTA
1165840 TTATTA
1 TTATTA
1165846 ATATTATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TTATTATAATTATTAAATTA
Found at i:1166995 original size:12 final size:12
Alignment explanation
Indices: 1166921--1167008 Score: 58
Period size: 12 Copynumber: 7.7 Consensus size: 12
1166911 AAAAAGATAG
1166921 TAATAATAGTAA
1 TAATAATAGTAA
*
1166933 CAATAATAGTAA
1 TAATAATAGTAA
* * * *
1166945 T-GTAAAAGGAT
1 TAATAATAGTAA
1166956 TAATAATAGTAA
1 TAATAATAGTAA
* * ***
1166968 CAATAAGAGCGT
1 TAATAATAGTAA
1166980 TAATAATAGTAA
1 TAATAATAGTAA
1166992 TAAT-ATA--AA
1 TAATAATAGTAA
1167001 TAATAATA
1 TAATAATA
1167009 TATATGTATG
Statistics
Matches: 54, Mismatches: 20, Indels: 6
0.68 0.25 0.08
Matches are distributed among these distances:
9 6 0.11
10 3 0.06
11 10 0.19
12 35 0.65
ACGTcount: A:0.56, C:0.03, G:0.11, T:0.30
Consensus pattern (12 bp):
TAATAATAGTAA
Found at i:1167646 original size:13 final size:13
Alignment explanation
Indices: 1167628--1167653 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1167618 GTGACATCGC
1167628 CGCCGGCCACCGT
1 CGCCGGCCACCGT
1167641 CGCCGGCCACCGT
1 CGCCGGCCACCGT
1167654 GGAATTCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.54, G:0.31, T:0.08
Consensus pattern (13 bp):
CGCCGGCCACCGT
Found at i:1167701 original size:16 final size:17
Alignment explanation
Indices: 1167671--1167704 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1167661 CAAAATGTAC
*
1167671 TTTTTTCTTTCTTTTTA
1 TTTTTTCTTTATTTTTA
1167688 TTTTTT-TTTATTTTTA
1 TTTTTTCTTTATTTTTA
1167704 T
1 T
1167705 ATGTTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTCTTTATTTTTA
Found at i:1177187 original size:18 final size:20
Alignment explanation
Indices: 1177166--1177203 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
1177156 TTTTTGAACA
1177166 ATTTATTT-TTT-TCTTTTT
1 ATTTATTTATTTCTCTTTTT
*
1177184 ATTTCTTTATTTCTCTTTTT
1 ATTTATTTATTTCTCTTTTT
1177204 TTCTTCCCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 3 0.18
20 7 0.41
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (20 bp):
ATTTATTTATTTCTCTTTTT
Found at i:1179002 original size:9 final size:9
Alignment explanation
Indices: 1178985--1179021 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
1178975 TGAGTTTTCG
1178985 AATTCGAAT
1 AATTCGAAT
*
1178994 AACTCGAAT
1 AATTCGAAT
1179003 AATTCGAAT
1 AATTCGAAT
1179012 AATTCGAAT
1 AATTCGAAT
1179021 A
1 A
1179022 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:1179943 original size:5 final size:5
Alignment explanation
Indices: 1179933--1179963 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
1179923 GAACAAATAT
1179933 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
1179964 ATTCCATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (5 bp):
ATTCG
Found at i:1193320 original size:2 final size:2
Alignment explanation
Indices: 1193313--1193342 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1193303 TCATGAACAA
1193313 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
1193343 GAAGAAGGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1197004 original size:67 final size:67
Alignment explanation
Indices: 1196924--1197060 Score: 274
Period size: 67 Copynumber: 2.0 Consensus size: 67
1196914 TTAAGATTTC
1196924 AATTATAATTTATTTTAATGTTAGAATTCATACTAGAAATAAAAAATTAAACTTTTTATATATTA
1 AATTATAATTTATTTTAATGTTAGAATTCATACTAGAAATAAAAAATTAAACTTTTTATATATTA
1196989 AA
66 AA
1196991 AATTATAATTTATTTTAATGTTAGAATTCATACTAGAAATAAAAAATTAAACTTTTTATATATTA
1 AATTATAATTTATTTTAATGTTAGAATTCATACTAGAAATAAAAAATTAAACTTTTTATATATTA
1197056 AA
66 AA
1197058 AAT
1 AAT
1197061 GTAAAGAACT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 70 1.00
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (67 bp):
AATTATAATTTATTTTAATGTTAGAATTCATACTAGAAATAAAAAATTAAACTTTTTATATATTA
AA
Found at i:1200936 original size:15 final size:16
Alignment explanation
Indices: 1200916--1200948 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1200906 TCATTTCTCA
1200916 TAAATAGAAA-ACATT
1 TAAATAGAAATACATT
*
1200931 TAAATATAAATACATT
1 TAAATAGAAATACATT
1200947 TA
1 TA
1200949 GTTATTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (16 bp):
TAAATAGAAATACATT
Found at i:1223162 original size:32 final size:32
Alignment explanation
Indices: 1223121--1223186 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
1223111 ACAATATCAC
1223121 TATCCAAAGTAAAATAATATTGCCAAAAAGGT
1 TATCCAAAGTAAAATAATATTGCCAAAAAGGT
*
1223153 TATCCAAAGTAAAATAATGTTGCCAAAAAGGT
1 TATCCAAAGTAAAATAATATTGCCAAAAAGGT
1223185 TA
1 TA
1223187 AATTACATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (32 bp):
TATCCAAAGTAAAATAATATTGCCAAAAAGGT
Found at i:1230013 original size:40 final size:37
Alignment explanation
Indices: 1229944--1230424 Score: 175
Period size: 35 Copynumber: 12.8 Consensus size: 37
1229934 ATGAGTTTAC
* * * *
1229944 GCCCAGCGCTAGTCGGATTAATCGACGATAGTGAATGTGA
1 GCCCAGCTCTAGTTGGA-TAAACCACGATA-T-AATGTGA
*
1229984 GCCCAGCTCTAGTTGGATAAACCATCGATAT--T-TGT
1 GCCCAGCTCTAGTTGGATAAACCA-CGATATAATGTGA
* * *
1230019 GCCCAGCACTAGTTGGATATACTGACGATAATAATTGTGA
1 GCCCAGCTCTAGTTGGATAAAC-CACGAT-ATAA-TGTGA
*
1230059 GCCCAACTCTAGTTGGATAAACCAACGATAT--T-TGCA
1 GCCCAGCTCTAGTTGGATAAACC-ACGATATAATGTG-A
* * * * *
1230095 -CCTA-CTGCTAGTCGGATATACTAACGATAATAATTTTGA
1 GCCCAGCT-CTAGTTGGATAAAC-CACGAT-ATAA-TGTGA
* * *
1230134 GCCCAGCTCTAGTCGGATATACCAACTG-TAATAATTTTGA
1 GCCCAGCTCTAGTTGGATAAACC-AC-GAT-ATAA-TGTGA
1230174 GCCCAGCTCTAGTTGGATAAACCAACGATAT--T-TGCA
1 GCCCAGCTCTAGTTGGATAAACC-ACGATATAATGTG-A
* * *
1230210 -CCCAG-TGCTAGTCGGATATACCGAAGATAATAATTGTGA
1 GCCCAGCT-CTAGTTGGATAAACC-ACGAT-ATAA-TGTGA
* * * *
1230249 ACCTAACACTAGTTGGATAAACCAACGATAT--T-TGCA
1 GCCCAGCTCTAGTTGGATAAACC-ACGATATAATGTG-A
* * * * *
1230285 -CCTAG-TGCTAGTCGGATATATCAACAATAATAATTGTGA
1 GCCCAGCT-CTAGTTGGATA-AACCACGAT-ATAA-TGTGA
* *
1230324 ACCCAGCTCTAGTTGGATAAACCAAC-A-ATAAT-TGT
1 GCCCAGCTCTAGTTGGATAAACC-ACGATATAATGTGA
* * *
1230359 GCCCAACTCTAGTTGGATAAACTAAC-A-ATAAT-TGC
1 GCCCAGCTCTAGTTGGATAAAC-CACGATATAATGTGA
* *
1230394 GCCCAGCACTAGTCGGATAAACCGACGATAT
1 GCCCAGCTCTAGTTGGATAAACC-ACGATAT
1230425 TGATTATTCA
Statistics
Matches: 345, Mismatches: 51, Indels: 93
0.71 0.10 0.19
Matches are distributed among these distances:
34 3 0.01
35 145 0.42
36 20 0.06
37 6 0.02
39 23 0.07
40 144 0.42
41 4 0.01
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (37 bp):
GCCCAGCTCTAGTTGGATAAACCACGATATAATGTGA
Found at i:1230069 original size:75 final size:75
Alignment explanation
Indices: 1229943--1230159 Score: 269
Period size: 75 Copynumber: 2.9 Consensus size: 75
1229933 GATGAGTTTA
* *
1229943 CGCCCAGCGCTAGTCGGAT-TAATCGACGATAGTGAA-TGTGAGCCCAGCTCTAGTTGGATAAAC
1 CGCCCAGCGCTAGTCGGATATACT-GACGATAAT-AATTGTGAGCCCAGCTCTAGTTGGATAAAC
*
1230006 CATCGATATTTG
64 CAACGATATTTG
* * * *
1230018 TGCCCAGCACTAGTTGGATATACTGACGATAATAATTGTGAGCCCAACTCTAGTTGGATAAACCA
1 CGCCCAGCGCTAGTCGGATATACTGACGATAATAATTGTGAGCCCAGCTCTAGTTGGATAAACCA
1230083 ACGATATTTG
66 ACGATATTTG
* * * * * *
1230093 CACCTA-CTGCTAGTCGGATATACTAACGATAATAATTTTGAGCCCAGCTCTAGTCGGATATACC
1 CGCCCAGC-GCTAGTCGGATATACTGACGATAATAATTGTGAGCCCAGCTCTAGTTGGATAAACC
1230157 AAC
65 AAC
1230160 TGTAATAATT
Statistics
Matches: 122, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
74 3 0.02
75 116 0.95
76 3 0.02
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.27
Consensus pattern (75 bp):
CGCCCAGCGCTAGTCGGATATACTGACGATAATAATTGTGAGCCCAGCTCTAGTTGGATAAACCA
ACGATATTTG
Found at i:1230152 original size:115 final size:115
Alignment explanation
Indices: 1230014--1230274 Score: 346
Period size: 115 Copynumber: 2.3 Consensus size: 115
1230004 ACCATCGATA
* * **
1230014 TTTGTGCCCAGCACTAGTTGGATATACTGAC-GATAATAATTGTGAGCCCAACTCTAGTTGGATA
1 TTTGAGCCCAGCACTAGTCGGATATACCAACTG-TAATAATTGTGAGCCCAACTCTAGTTGGATA
* *
1230078 AACCAACGATATTTGCACCTACTGCTAGTCGGATATA-CTAACGATAATAAT
65 AACCAACGATATTTGCACCCACTGCTAGTCGGATATACCGAA-GATAATAAT
* * *
1230129 TTTGAGCCCAGCTCTAGTCGGATATACCAACTGTAATAATTTTGAGCCCAGCTCTAGTTGGATAA
1 TTTGAGCCCAGCACTAGTCGGATATACCAACTGTAATAATTGTGAGCCCAACTCTAGTTGGATAA
*
1230194 ACCAACGATATTTGCACCCAGTGCTAGTCGGATATACCGAAGATAATAAT
66 ACCAACGATATTTGCACCCACTGCTAGTCGGATATACCGAAGATAATAAT
* * * * * *
1230244 TGTGAACCTAACACTAGTTGGATAAACCAAC
1 TTTGAGCCCAGCACTAGTCGGATATACCAAC
1230275 GATATTTGCA
Statistics
Matches: 127, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
115 123 0.97
116 4 0.03
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (115 bp):
TTTGAGCCCAGCACTAGTCGGATATACCAACTGTAATAATTGTGAGCCCAACTCTAGTTGGATAA
ACCAACGATATTTGCACCCACTGCTAGTCGGATATACCGAAGATAATAAT
Found at i:1230214 original size:75 final size:74
Alignment explanation
Indices: 1230142--1230425 Score: 303
Period size: 75 Copynumber: 3.9 Consensus size: 74
1230132 GAGCCCAGCT
* * *
1230142 CTAGTCGGATATACCAACTGTAATAATTTTGAGCCCAGCTCTAGTTGGATAAACCAACGATATTT
1 CTAGTCGGATATACCAAC-GTAATAATTGTGAACCCAGCACTAGTTGGATAAACCAACGATATTT
1230207 GCACCCAGTG
65 GCACCCAGTG
* *
1230217 CTAGTCGGATATACCGAA-GATAATAATTGTGAACCTAACACTAGTTGGATAAACCAACGATATT
1 CTAGTCGGATATACC-AACG-TAATAATTGTGAACCCAGCACTAGTTGGATAAACCAACGATATT
*
1230281 TGCACCTAGTG
64 TGCACCCAGTG
* * * *
1230292 CTAGTCGGATATATCAACAATAATAATTGTGAACCCAGCTCTAGTTGGATAAACCAACAATAATT
1 CTAGTCGGATATACCAAC-GTAATAATTGTGAACCCAGCACTAGTTGGATAAACCAACGAT-ATT
* *
1230357 GTGC-CCAACT-
64 -TGCACCCAGTG
* * * * * *
1230367 CTAGTTGGATAAACTAAC--AATAATTGCG--CCCAGCACTAGTCGGATAAACCGACGATATT
1 CTAGTCGGATATACCAACGTAATAATTGTGAACCCAGCACTAGTTGGATAAACCAACGATATT
1230426 GATTATTCAC
Statistics
Matches: 180, Mismatches: 23, Indels: 18
0.81 0.10 0.08
Matches are distributed among these distances:
69 3 0.02
70 24 0.13
72 9 0.05
74 3 0.02
75 129 0.72
76 9 0.05
77 3 0.02
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (74 bp):
CTAGTCGGATATACCAACGTAATAATTGTGAACCCAGCACTAGTTGGATAAACCAACGATATTTG
CACCCAGTG
Found at i:1230267 original size:190 final size:185
Alignment explanation
Indices: 1229981--1230423 Score: 618
Period size: 190 Copynumber: 2.4 Consensus size: 185
1229971 ATAGTGAATG
* * * *
1229981 TGAGCCCAGCTCTAGTTGGATAAACCATCGATATTTGTGCCCAGCACTAGTTGGATATACTGACG
1 TGAGCCCAGCTCTAGTTGGATAAACCAACGATATTTGCGCCCAGCACTAGTCGGATATACCGACG
* *
1230046 ATAATAATTGTGAGCCCAACTCTAGTTGGATAAACCAACGATATTTGCACCTACTGCTAGTCGGA
66 ATAATAATTGTGAACCCAACACTAGTTGGATAAACCAACGATATTTGCACCTACTGCTAGTCGGA
* * * *
1230111 TATA-CTAACGATAATAATTTTGAGCCCAGCTCTAGTCGGATATACCAACTGTAATAATTT
131 TATATC-AACAATAATAATTGTGAACCCAGCTCTAGTCGGATAAACCAAC---AATAA--T
* ** *
1230171 TGAGCCCAGCTCTAGTTGGATAAACCAACGATATTTGCACCCAGTGCTAGTCGGATATACCGAAG
1 TGAGCCCAGCTCTAGTTGGATAAACCAACGATATTTGCGCCCAGCACTAGTCGGATATACCGACG
* *
1230236 ATAATAATTGTGAACCTAACACTAGTTGGATAAACCAACGATATTTGCACCTAGTGCTAGTCGGA
66 ATAATAATTGTGAACCCAACACTAGTTGGATAAACCAACGATATTTGCACCTACTGCTAGTCGGA
*
1230301 TATATCAACAATAATAATTGTGAACCCAGCTCTAGTTGGATAAACCAACAATAAT
131 TATATCAACAATAATAATTGTGAACCCAGCTCTAGTCGGATAAACCAACAATAAT
* * * * * *
1230356 TGTGCCCAACTCTAGTTGGATAAACTAACAATAATTGCGCCCAGCACTAGTCGGATAAACCGACG
1 TGAGCCCAGCTCTAGTTGGATAAACCAACGATATTTGCGCCCAGCACTAGTCGGATATACCGACG
1230421 ATA
66 ATA
1230424 TTGATTATTC
Statistics
Matches: 225, Mismatches: 27, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
185 59 0.26
187 5 0.02
190 160 0.71
191 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (185 bp):
TGAGCCCAGCTCTAGTTGGATAAACCAACGATATTTGCGCCCAGCACTAGTCGGATATACCGACG
ATAATAATTGTGAACCCAACACTAGTTGGATAAACCAACGATATTTGCACCTACTGCTAGTCGGA
TATATCAACAATAATAATTGTGAACCCAGCTCTAGTCGGATAAACCAACAATAAT
Found at i:1232176 original size:6 final size:6
Alignment explanation
Indices: 1232165--1232194 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1232155 GTTTTCTCTA
1232165 AAAATG AAAATG AAAATG AAAATG AAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG
1232195 GAGAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:1232231 original size:70 final size:69
Alignment explanation
Indices: 1232119--1232252 Score: 189
Period size: 70 Copynumber: 1.9 Consensus size: 69
1232109 AAACGAATAG
* * *
1232119 AAATGAAGAAATATGAAACATTTGGAAGTGATTATGGTTTTCTCTAAAAATGAAAATGAAAATGA
1 AAATGAAGAAATA-GAAACATTTGGAAATGAATATGGCTTTCTCT-AAAATGAAAATGAAAATGA
1232184 AAATGA
64 AAATGA
* *
1232190 AAATGGAGAAATA-AAATCATTTGGAAATGAATGTGGCTTTCTCTAAAATGAAAATGAAAATGA
1 AAATGAAGAAATAGAAA-CATTTGGAAATGAATATGGCTTTCTCTAAAATGAAAATGAAAATGA
1232253 CTTGAAAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
69 22 0.39
70 23 0.40
71 12 0.21
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.28
Consensus pattern (69 bp):
AAATGAAGAAATAGAAACATTTGGAAATGAATATGGCTTTCTCTAAAATGAAAATGAAAATGAAA
ATGA
Found at i:1233773 original size:25 final size:23
Alignment explanation
Indices: 1233713--1233774 Score: 61
Period size: 25 Copynumber: 2.6 Consensus size: 23
1233703 TATTTATTTT
*
1233713 TATTAAATATAAATTAAAAAATA
1 TATTAAATATAAAGTAAAAAATA
* * *
1233736 TATAAAAAAATAAAGTAATATAATA
1 TAT-TAAATATAAAGTAA-AAAATA
1233761 TATTACAATATAAA
1 TATTA-AATATAAA
1233775 AAAAAGTCAG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
23 3 0.10
24 12 0.40
25 15 0.50
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (23 bp):
TATTAAATATAAAGTAAAAAATA
Found at i:1242121 original size:2 final size:2
Alignment explanation
Indices: 1242114--1242138 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1242104 CCAAACTCAT
1242114 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 T
1242139 TAAAGTAGAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1245713 original size:24 final size:24
Alignment explanation
Indices: 1245686--1245742 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
1245676 ATAAATAAAA
1245686 AATAGATATGAAATAATAATATAT
1 AATAGATATGAAATAATAATATAT
* *** *
1245710 AATATATATGTTTTAATTATATAT
1 AATAGATATGAAATAATAATATAT
1245734 ATATAGATA
1 A-ATAGATA
1245743 GATATGTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 20 0.77
25 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (24 bp):
AATAGATATGAAATAATAATATAT
Found at i:1245821 original size:3 final size:3
Alignment explanation
Indices: 1245813--1245858 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
1245803 AAAAACAATT
*
1245813 ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1245859 AATTGCTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:1250095 original size:14 final size:14
Alignment explanation
Indices: 1250076--1250108 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1250066 AGAGGAAGGC
1250076 AAGAAAA-AGAAAGA
1 AAGAAAATAGAAA-A
1250090 AAGAAAATAGAAAA
1 AAGAAAATAGAAAA
1250104 AAGAA
1 AAGAA
1250109 GAAAAAGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (14 bp):
AAGAAAATAGAAAA
Found at i:1250892 original size:20 final size:20
Alignment explanation
Indices: 1250855--1250894 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1250845 CATTTTGATT
*
1250855 GAAATTGAATTTAGAATTGA
1 GAAATTGAATTGAGAATTGA
1250875 GAAATTGAAATTGA-AATTGA
1 GAAATTG-AATTGAGAATTGA
1250895 AAACCCTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (20 bp):
GAAATTGAATTGAGAATTGA
Found at i:1251438 original size:52 final size:52
Alignment explanation
Indices: 1251381--1251548 Score: 121
Period size: 52 Copynumber: 3.1 Consensus size: 52
1251371 GGATTTGGAA
1251381 ATTATATGAATTAAATGTGCATGTTTAATTATTTTGTTTTAAAAGTATTCGG
1 ATTATATGAATTAAATGTGCATGTTTAATTATTTTGTTTTAAAAGTATTCGG
* ** * * * *
1251433 ATTATA-GAAAT-ACCGCTG-AGTATTTATATGTGA-ATTGATTAATTGAATAG-ATTTGG
1 ATTATATGAATTAAATG-TGCA-TGTTTA-AT-T-ATTTTG-TT--TT-AAAAGTATTCGG
* *
1251489 AAATTATATGAATTAAATTTGCATGTTTAATTATTTTGTTTTAAAAGTATTCAG
1 --ATTATATGAATTAAATGTGCATGTTTAATTATTTTGTTTTAAAAGTATTCGG
1251543 ATTATA
1 ATTATA
1251549 GAAATACCGC
Statistics
Matches: 84, Mismatches: 16, Indels: 32
0.64 0.12 0.24
Matches are distributed among these distances:
50 3 0.04
51 11 0.13
52 14 0.17
53 8 0.10
54 9 0.11
56 10 0.12
57 8 0.10
58 8 0.10
59 11 0.13
60 2 0.02
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (52 bp):
ATTATATGAATTAAATGTGCATGTTTAATTATTTTGTTTTAAAAGTATTCGG
Found at i:1251475 original size:110 final size:110
Alignment explanation
Indices: 1251344--1251563 Score: 413
Period size: 110 Copynumber: 2.0 Consensus size: 110
1251334 GTGATAAATG
*
1251344 ATTTATATGTGAATTGATTAATTGAATGGATTTGGAAATTATATGAATTAAATGTGCATGTTTAA
1 ATTTATATGTGAATTGATTAATTGAATAGATTTGGAAATTATATGAATTAAATGTGCATGTTTAA
*
1251409 TTATTTTGTTTTAAAAGTATTCGGATTATAGAAATACCGCTGAGT
66 TTATTTTGTTTTAAAAGTATTCAGATTATAGAAATACCGCTGAGT
*
1251454 ATTTATATGTGAATTGATTAATTGAATAGATTTGGAAATTATATGAATTAAATTTGCATGTTTAA
1 ATTTATATGTGAATTGATTAATTGAATAGATTTGGAAATTATATGAATTAAATGTGCATGTTTAA
1251519 TTATTTTGTTTTAAAAGTATTCAGATTATAGAAATACCGCTGAGT
66 TTATTTTGTTTTAAAAGTATTCAGATTATAGAAATACCGCTGAGT
1251564 TTATACTTAG
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 107 1.00
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (110 bp):
ATTTATATGTGAATTGATTAATTGAATAGATTTGGAAATTATATGAATTAAATGTGCATGTTTAA
TTATTTTGTTTTAAAAGTATTCAGATTATAGAAATACCGCTGAGT
Found at i:1261766 original size:12 final size:12
Alignment explanation
Indices: 1261751--1261790 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
1261741 GAAAAATTTT
1261751 AAAATTTTACGA
1 AAAATTTTACGA
1261763 AAAATTTT----
1 AAAATTTTACGA
1261771 AAAATTTTACGA
1 AAAATTTTACGA
1261783 AAAATTTT
1 AAAATTTT
1261791 CTAGACTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
8 8 0.33
12 16 0.67
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (12 bp):
AAAATTTTACGA
Found at i:1261786 original size:21 final size:20
Alignment explanation
Indices: 1261741--1261790 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1261731 CTGTACTTAA
1261741 GAAAAATTTTAAAATTTTAC
1 GAAAAATTTTAAAATTTTAC
1261761 GAAAAATTTTAAAATTTTAC
1 GAAAAATTTTAAAATTTTAC
1261781 GAAAAATTTT
1 GAAAAATTTT
1261791 CTAGACTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (20 bp):
GAAAAATTTTAAAATTTTAC
Found at i:1262128 original size:2 final size:2
Alignment explanation
Indices: 1262121--1262156 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1262111 TGTAATTTGG
1262121 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1262157 GTAACATCGA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1265486 original size:29 final size:31
Alignment explanation
Indices: 1265428--1265500 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 31
1265418 AAAATTTTAA
*
1265428 AAAAATTACATCTTAGACCCCTAAACTTTCCT
1 AAAAATTACATTTTAGACCCCTAAACTTT-CT
* *
1265460 -TAAATTACATTTTA-A-CCCTAAATTTTCT
1 AAAAATTACATTTTAGACCCCTAAACTTTCT
1265488 AAAAATTACATTT
1 AAAAATTACATTT
1265501 AGCCCTAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 2 0.06
29 21 0.58
30 1 0.03
31 12 0.33
ACGTcount: A:0.40, C:0.21, G:0.01, T:0.38
Consensus pattern (31 bp):
AAAAATTACATTTTAGACCCCTAAACTTTCT
Found at i:1265996 original size:19 final size:19
Alignment explanation
Indices: 1265959--1265999 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1265949 TGTTTTCATA
* *
1265959 TTTTCTTTCCTTGGTTTTT
1 TTTTCTTTCCTTAGATTTT
*
1265978 TTTTCTTTCTTTAGATTTT
1 TTTTCTTTCCTTAGATTTT
1265997 TTT
1 TTT
1266000 ATTTTCTGTG
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:0.05, C:0.12, G:0.07, T:0.76
Consensus pattern (19 bp):
TTTTCTTTCCTTAGATTTT
Found at i:1267815 original size:6 final size:6
Alignment explanation
Indices: 1267804--1267831 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1267794 GTTTCGACAC
1267804 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1267832 TAAAATCCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAA
Found at i:1281188 original size:65 final size:65
Alignment explanation
Indices: 1281084--1281215 Score: 264
Period size: 65 Copynumber: 2.0 Consensus size: 65
1281074 GACAGATACA
1281084 CATAACCGCAATCAAGAGCTCTGATTGATCTTTAGCATGGCACCATGGACGAAGACAAAGAGGGG
1 CATAACCGCAATCAAGAGCTCTGATTGATCTTTAGCATGGCACCATGGACGAAGACAAAGAGGGG
1281149 CATAACCGCAATCAAGAGCTCTGATTGATCTTTAGCATGGCACCATGGACGAAGACAAAGAGGGG
1 CATAACCGCAATCAAGAGCTCTGATTGATCTTTAGCATGGCACCATGGACGAAGACAAAGAGGGG
1281214 CA
1 CA
1281216 GGCGATGGCC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.34, C:0.22, G:0.26, T:0.18
Consensus pattern (65 bp):
CATAACCGCAATCAAGAGCTCTGATTGATCTTTAGCATGGCACCATGGACGAAGACAAAGAGGGG
Found at i:1286847 original size:28 final size:28
Alignment explanation
Indices: 1286815--1286884 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
1286805 AATGAGATTG
1286815 GCACTAAGTGTGCGAGTTT-AAT-TGTATA
1 GCACTAAGTGTGCGAGTTTGAATAT-TA-A
*
1286843 GCACTAAGTGTGCGAGTTTGACTATTAA
1 GCACTAAGTGTGCGAGTTTGAATATTAA
1286871 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
1286885 GACTTACTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 34 0.87
29 4 0.10
30 1 0.03
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.31
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGAATATTAA
Found at i:1288972 original size:20 final size:22
Alignment explanation
Indices: 1288943--1288985 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
1288933 GAGTCAACAC
*
1288943 GCCCATGTGG-AGG-GGCACAT
1 GCCCACGTGGAAGGAGGCACAT
1288963 GCCCACGTGGAAGGAGGCACAT
1 GCCCACGTGGAAGGAGGCACAT
1288985 G
1 G
1288986 GCCGTGTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 3 0.15
22 8 0.40
ACGTcount: A:0.23, C:0.26, G:0.40, T:0.12
Consensus pattern (22 bp):
GCCCACGTGGAAGGAGGCACAT
Found at i:1291337 original size:15 final size:15
Alignment explanation
Indices: 1291286--1291337 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
1291276 ATTCAATATT
*
1291286 AATATCTTAATAATA
1 AATATATTAATAATA
*
1291301 AATATTCATTACAATTATA
1 AATA-T-ATT--AATAATA
1291320 AATATATTAATAATA
1 AATATATTAATAATA
1291335 AAT
1 AAT
1291338 GCTTTGTAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 13 0.43
16 1 0.03
17 5 0.17
18 1 0.03
19 10 0.33
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (15 bp):
AATATATTAATAATA
Found at i:1293132 original size:14 final size:14
Alignment explanation
Indices: 1293115--1293142 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1293105 AAATATTAAA
1293115 AATATTTTTATATT
1 AATATTTTTATATT
1293129 AATATTTTTATATT
1 AATATTTTTATATT
1293143 TTATAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
AATATTTTTATATT
Found at i:1293549 original size:35 final size:34
Alignment explanation
Indices: 1293510--1293583 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 34
1293500 AAATAAAAAC
* *
1293510 ATATATATA-ATTTTATTAAATA-TTAAAATAACATA
1 ATATAAATATATTTT-TTAAAAATTTAAAA-AA-ATA
1293545 ATATAAATATATTTTTTAAAAATTTAAAAAAATA
1 ATATAAATATATTTTTTAAAAATTTAAAAAAATA
1293579 ATATA
1 ATATA
1293584 GGTGGGTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
34 8 0.23
35 16 0.46
36 11 0.31
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (34 bp):
ATATAAATATATTTTTTAAAAATTTAAAAAAATA
Found at i:1293555 original size:39 final size:34
Alignment explanation
Indices: 1293512--1293583 Score: 81
Period size: 34 Copynumber: 2.0 Consensus size: 34
1293502 ATAAAAACAT
*
1293512 ATATATAATTTTATTAAATATTAAAATAACATAATATAA
1 ATATAT-ATTTTA-AAAAT-TTAAAA-AA-ATAATATAA
*
1293551 ATATATTTTTTAAAAATTTAAAAAAATAATATA
1 ATATATATTTTAAAAATTTAAAAAAATAATATA
1293584 GGTGGGTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
34 8 0.26
35 2 0.06
36 6 0.19
37 4 0.13
38 5 0.16
39 6 0.19
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (34 bp):
ATATATATTTTAAAAATTTAAAAAAATAATATAA
Found at i:1301897 original size:263 final size:263
Alignment explanation
Indices: 1301423--1301920 Score: 723
Period size: 263 Copynumber: 1.9 Consensus size: 263
1301413 ATCGAAAATA
* * * *
1301423 TTTTTGGGTAAACTATATTTACGGTTATTAAATTACTAATAAGTTTACGTTTTAGTCACTCAATT
1 TTTTTGGGTAAACTACATTTAAGGTTACTAAATTACTAATAAGTTTACGTTTTAGTCACTCAACT
* * * *
1301488 TCAGAAGGTTACAAAATGGTTACTGAACTATTCGAAAGTTTTCATTTAAGTCATTGATTGTTAAA
66 TCAAAAGGTTACAAAATAGTTACTGAACTATTCGAAAATTTTCATTTAAGTCATTGATCGTTAAA
* * * * * * *
1301553 TTTTTTTTAATTGACTAGCTTGCAGCTCCAAGCTATAAATTGAAGATTGGTATGGTGGATTAATA
131 GTTTTTTTAATTGACTAGCTAGCAGCTCCAAGATACAAATTGAAGATTGGTACGATAGATTAATA
* * *
1301618 CCTATTGACAAGTAGAAAAATATACCTTAGGGCTTAGATCAATACCCATTGACGAGTAGAAAATA
196 CCCATTGACAAGTAGAAAAACATACCTTAGAGCTTAGATCAATACCCATTGACGAGTAGAAAATA
1301683 GTT
261 GTT
* *
1301686 TTTTTGGGTAAACTACATTTAAGGTTACTAAATTATTAGTAAGTTTACGTTTTAGTCACTCAACT
1 TTTTTGGGTAAACTACATTTAAGGTTACTAAATTACTAATAAGTTTACGTTTTAGTCACTCAACT
*
1301751 TCAAAAGGTTACAAAATAGTTGCTGAACTATTCGAAAATTTTCATTTAAGTCATTGAATCGTT-A
66 TCAAAAGGTTACAAAATAGTTACTGAACTATTCGAAAATTTTCATTTAAGTCATTG-ATCGTTAA
* * *
1301815 AGTTTTTTTAATTG-TTCAGCTAGCAGTTCCAA-ATGACAAATTGATGATTGGTACGATAGATTA
130 AGTTTTTTTAATTGACT-AGCTAGCAGCTCCAAGAT-ACAAATTGAAGATTGGTACGATAGATTA
*
1301878 ATACCCATTGACGAGTAGAAAAACATACCTTAGAGCTTAGATC
193 ATACCCATTGACAAGTAGAAAAACATACCTTAGAGCTTAGATC
1301921 CAAATCGAAG
Statistics
Matches: 207, Mismatches: 25, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
262 2 0.01
263 200 0.97
264 5 0.02
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (263 bp):
TTTTTGGGTAAACTACATTTAAGGTTACTAAATTACTAATAAGTTTACGTTTTAGTCACTCAACT
TCAAAAGGTTACAAAATAGTTACTGAACTATTCGAAAATTTTCATTTAAGTCATTGATCGTTAAA
GTTTTTTTAATTGACTAGCTAGCAGCTCCAAGATACAAATTGAAGATTGGTACGATAGATTAATA
CCCATTGACAAGTAGAAAAACATACCTTAGAGCTTAGATCAATACCCATTGACGAGTAGAAAATA
GTT
Found at i:1304340 original size:22 final size:25
Alignment explanation
Indices: 1304291--1304340 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
1304281 TTGAAACTCC
*
1304291 ATGACATGAAAAAAATTATATGTCA
1 ATGACATGAAAAAAATTATATGTAA
1304316 ATGACATG-AAAAAATTAT-TG-AA
1 ATGACATGAAAAAAATTATATGTAA
1304338 ATG
1 ATG
1304341 TCATTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 2 0.08
24 10 0.42
25 8 0.33
ACGTcount: A:0.52, C:0.06, G:0.14, T:0.28
Consensus pattern (25 bp):
ATGACATGAAAAAAATTATATGTAA
Found at i:1312109 original size:48 final size:48
Alignment explanation
Indices: 1312036--1312163 Score: 175
Period size: 48 Copynumber: 2.7 Consensus size: 48
1312026 ATCACCTCCT
* * * *
1312036 CCGCCTTATGAGTATAAGTCACCACCACCGCCTTCTCCTTCTCCACCA
1 CCGCCTTATGTGTATAAGTCTCCACCACCACCTTCACCTTCTCCACCA
* *
1312084 CCGCCTTATGTGTATAAATCTCCACCACCACCTTCACCTTCTCCTCCA
1 CCGCCTTATGTGTATAAGTCTCCACCACCACCTTCACCTTCTCCACCA
* * *
1312132 CCTCCGTATGTGTACAAGTCTCCACCACCACC
1 CCGCCTTATGTGTATAAGTCTCCACCACCACC
1312164 ACCTAAACAT
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 70 1.00
ACGTcount: A:0.21, C:0.44, G:0.09, T:0.26
Consensus pattern (48 bp):
CCGCCTTATGTGTATAAGTCTCCACCACCACCTTCACCTTCTCCACCA
Found at i:1312196 original size:48 final size:44
Alignment explanation
Indices: 1312138--1312478 Score: 235
Period size: 48 Copynumber: 7.5 Consensus size: 44
1312128 TCCACCTCCG
*
1312138 TATGTGTACAAGTCTCCACCACCACCACCTAAACATGAGGAGAAGCCT
1 TATGAGTACAAGTCTCCACCACCACCACC---ACAT-AGGAGAAGCCT
*
1312186 TATGAATACAAGTCTCCACCACCACCACCA-A-AGGAGAAGCCT
1 TATGAGTACAAGTCTCCACCACCACCACCACATAGGAGAAGCCT
* * * ***** **
1312228 TATGAGTACAAGTCTCCACCCCCACCATCACCTTCTCCTCCACCTCCT
1 TATGAGTACAAGTCTCCACCACCACCACCA-C--ATAGGAGA-AGCCT
* * * * *** * **
1312276 TATGAGTACAAATCTCCACCACCTCCATCACCTTCTCCACCACCTCCT
1 TATGAGTACAAGTCTCCACCACCACCACCA-CAT-AGGA-GA-AGCCT
* * *
1312324 TACGTGTACAAGTCTCCACCACCTCCACCAAAGCATGAGGAGAAGCCT
1 TATGAGTACAAGTCTCCACCACCACCACC--A-CAT-AGGAGAAGCCT
* *
1312372 TATGAATACAAGTCTCCACCACCACCACC-GA-AGGAGAAGCCT
1 TATGAGTACAAGTCTCCACCACCACCACCACATAGGAGAAGCCT
*
1312414 TATGAGTACAAGTCTCCACCACCACCACC-GA-AGGAGAAGCCT
1 TATGAGTACAAGTCTCCACCACCACCACCACATAGGAGAAGCCT
*
1312456 TATGAATACAAGTCTCCACCACC
1 TATGAGTACAAGTCTCCACCACC
1312479 TCCATCGCCT
Statistics
Matches: 243, Mismatches: 40, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
42 112 0.46
44 2 0.01
45 1 0.00
46 1 0.00
47 2 0.01
48 120 0.49
49 1 0.00
50 4 0.02
ACGTcount: A:0.31, C:0.37, G:0.13, T:0.19
Consensus pattern (44 bp):
TATGAGTACAAGTCTCCACCACCACCACCACATAGGAGAAGCCT
Found at i:1312299 original size:27 final size:26
Alignment explanation
Indices: 1312261--1312349 Score: 71
Period size: 27 Copynumber: 3.5 Consensus size: 26
1312251 ACCATCACCT
*
1312261 TCTCCTCCACCTCCTTATGAGTACAAA
1 TCTCCACCACCTCCTTATG-GTACAAA
* **
1312288 TCTCCACCACCTCC--AT--CAC-CT
1 TCTCCACCACCTCCTTATGGTACAAA
* *
1312309 TCTCCACCACCTCCTTACGTGTACAAG
1 TCTCCACCACCTCCTTATG-GTACAAA
1312336 TCTCCACCACCTCC
1 TCTCCACCACCTCC
1312350 ACCAAAGCAT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
21 14 0.29
22 2 0.04
23 1 0.02
25 2 0.04
26 2 0.04
27 27 0.56
ACGTcount: A:0.21, C:0.47, G:0.06, T:0.26
Consensus pattern (26 bp):
TCTCCACCACCTCCTTATGGTACAAA
Found at i:1312363 original size:186 final size:186
Alignment explanation
Indices: 1312038--1312440 Score: 637
Period size: 186 Copynumber: 2.2 Consensus size: 186
1312028 CACCTCCTCC
* * * * * * *
1312038 GCCTTATGAGTATAAGTCACCACCACCGCCTTCTCCTTCTCCACCACCGCCTTATGTGTATAAAT
1 GCCTTATGAGTACAAGTCTCCACCACCACCATCACCTTCTCCACCACCGCCTTATGAGTACAAAT
* * *
1312103 CTCCACCACCACCTTCACCTTCTCCTCCACCTCCGTATGTGTACAAGTCTCCACCACCACCACCT
66 CTCCACCACCACCATCACCTTCTCCACCACCTCCGTACGTGTACAAGTCTCCACCACCACCACCT
1312168 AAACATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAA
131 AAACATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAA
* * *
1312224 GCCTTATGAGTACAAGTCTCCACCCCCACCATCACCTTCTCCTCCACCTCCTTATGAGTACAAAT
1 GCCTTATGAGTACAAGTCTCCACCACCACCATCACCTTCTCCACCACCGCCTTATGAGTACAAAT
* * *
1312289 CTCCACCACCTCCATCACCTTCTCCACCACCTCCTTACGTGTACAAGTCTCCACCACCTCCACC-
66 CTCCACCACCACCATCACCTTCTCCACCACCTCCGTACGTGTACAAGTCTCCACCACCACCACCT
*
1312353 AAAGCATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCGAAGGAGAA
131 AAA-CATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAA
1312410 GCCTTATGAGTACAAGTCTCCACCACCACCA
1 GCCTTATGAGTACAAGTCTCCACCACCACCA
1312441 CCGAAGGAGA
Statistics
Matches: 198, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
185 3 0.02
186 195 0.98
ACGTcount: A:0.28, C:0.39, G:0.12, T:0.21
Consensus pattern (186 bp):
GCCTTATGAGTACAAGTCTCCACCACCACCATCACCTTCTCCACCACCGCCTTATGAGTACAAAT
CTCCACCACCACCATCACCTTCTCCACCACCTCCGTACGTGTACAAGTCTCCACCACCACCACCT
AAACATGAGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAA
Found at i:1312456 original size:228 final size:228
Alignment explanation
Indices: 1312175--1312589 Score: 697
Period size: 228 Copynumber: 1.8 Consensus size: 228
1312165 CCTAAACATG
*
1312175 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAAGCCTTATGAGTACAAG
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAAGCCTTATGAATACAAG
*
1312240 TCTCCACCCCCACCATCACCTTCTCCTCCACCTCCTTATGAGTACAAATCTCCACCACCTCCATC
66 TCTCCACCACCACCATCACCTTCTCCTCCACCTCCTTATGAGTACAAATCTCCACCACCTCCATC
* * * * * *
1312305 ACCTTCTCCACCACCTCCTTACGT-GTACAAGTCTCCACCACCTCCACCAAAGCATGAGGAGAAG
131 ACCATCACCACCACCTCCATAC-TACTACAAGTCCCCACCACCACCACCAAAGCATGAGGAGAAG
1312369 CCTTATGAATACAAGTCTCCACCACCACCACCGA
195 CCTTATGAATACAAGTCTCCACCACCACCACCGA
* *
1312403 AGGAGAAGCCTTATGAGTACAAGTCTCCACCACCACCACCGAAGGAGAAGCCTTATGAATACAAG
1 AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAAGCCTTATGAATACAAG
* * *
1312468 TCTCCACCACCTCCATCGCCTTCTCCTCCACCTCCTTATGAGTATAAATCTCCACCACCTCCATC
66 TCTCCACCACCACCATCACCTTCTCCTCCACCTCCTTATGAGTACAAATCTCCACCACCTCCATC
1312533 ACCATCACCACCACCTCCATACTACTACAAGTCCCCACCACCACCACCAAAGCATGA
131 ACCATCACCACCACCTCCATACTACTACAAGTCCCCACCACCACCACCAAAGCATGA
1312590 AGAACAACCA
Statistics
Matches: 173, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
227 1 0.01
228 172 0.99
ACGTcount: A:0.30, C:0.40, G:0.11, T:0.19
Consensus pattern (228 bp):
AGGAGAAGCCTTATGAATACAAGTCTCCACCACCACCACCAAAGGAGAAGCCTTATGAATACAAG
TCTCCACCACCACCATCACCTTCTCCTCCACCTCCTTATGAGTACAAATCTCCACCACCTCCATC
ACCATCACCACCACCTCCATACTACTACAAGTCCCCACCACCACCACCAAAGCATGAGGAGAAGC
CTTATGAATACAAGTCTCCACCACCACCACCGA
Found at i:1312575 original size:99 final size:98
Alignment explanation
Indices: 1312471--1313066 Score: 409
Period size: 99 Copynumber: 6.1 Consensus size: 98
1312461 ATACAAGTCT
* * * * * * *
1312471 CCACCACCTCCATCGCCTTCTCCTCCACCTCCTTA-TGAGTATAAATCTCCACCACCTCCATCAC
1 CCACCACCTCCATCGCCTTCACCACCACCACCATACT-ACTACAAATCTCCACCACCACCATCAC
1312535 CATCACCACCACCTCCATACTACTACAAGTCCCCA
65 CATCACCACCACCTCCATACTACTACAAGT-CCCA
* ** * ** ** * * * * * * *
1312570 CCACCACCACCAAAGCATGAAGAACAACCACCATACTACTACAAGTCACCTCCTCCTCCATCTCC
1 CCACCACCTCCATCGCCTTCACCACCACCACCATACTACTACAAATCTCCACCACCACCATCACC
* *
1312635 ATCACCACCTCCTCCTTACTACTACAAGT-CC-
66 ATCACCACCACCTCCATACTACTACAAGTCCCA
* * * * * *
1312666 CCACCACCTCCGTCTCCATCACCACCTCCTCCATACTACTACAAATCTCCACCACCACCACCAAA
1 CCACCACCTCCATCGCCTTCACCACCACCACCATACTACTACAAATCTCCACCACCACCATC--A
* * ** * * *
1312731 GCATGAAGAACAACCCCCATACTACTACAAGT--CT
64 CCAT-CACCACCACCTCCATACTACTACAAGTCCCA
* * * * *
1312765 CCACCACCTCCATCACCCTCACCACCACCACCTTACTACTATAAATCTCCACCACCACCTTCACC
1 CCACCACCTCCATCGCCTTCACCACCACCACCATACTACTACAAATCTCCACCACCACCATCACC
* *
1312830 ATCTCCACCACCTCCTTACTACTACAAGTCCCCA
66 ATCACCACCACCTCCATACTACTACAAGT-CCCA
* ** * ** ** * * * *
1312864 CCACCACCACCAAAGCATGAAGAACAACCCCCATACTACTACAAGTCTCCACCACCTCCATCACC
1 CCACCACCTCCATCGCCTTCACCACCACCACCATACTACTACAAATCTCCACCACCACCATCACC
* * *
1312929 CTCACCACCACCACCTTACTACTACAAGTCTCCA
66 ATCACCACCACCTCCATACTACTACAAGTC-CCA
* * * * * **
1312963 CCACCACCT---TCACCATCTCCTCCACCACCTTACTACTACAAATCTCCACCACCACCCCCA-C
1 CCACCACCTCCATCGCCTTCACCACCACCACCATACTACTACAAATCTCCACCACCACCATCACC
* ** * *
1313024 ATTACGTCTCACCACCATACTACTACAAATCTCCA
66 ATCACCAC-CACCTCCATACTACTACAAGTC-CCA
1313059 CCACCACC
1 CCACCACC
1313067 AATGAAGTCT
Statistics
Matches: 373, Mismatches: 114, Indels: 23
0.73 0.22 0.05
Matches are distributed among these distances:
95 5 0.01
96 127 0.34
97 6 0.02
98 5 0.01
99 229 0.61
100 1 0.00
ACGTcount: A:0.30, C:0.48, G:0.04, T:0.19
Consensus pattern (98 bp):
CCACCACCTCCATCGCCTTCACCACCACCACCATACTACTACAAATCTCCACCACCACCATCACC
ATCACCACCACCTCCATACTACTACAAGTCCCA
Found at i:1312816 original size:27 final size:26
Alignment explanation
Indices: 1312786--1312871 Score: 83
Period size: 27 Copynumber: 3.4 Consensus size: 26
1312776 ATCACCCTCA
1312786 CCACCACCACCTTACTACTATAAATCT
1 CCACCACCACCTTACTACTA-AAATCT
*
1312813 CCACCACCACCTT-C-AC---CATCT
1 CCACCACCACCTTACTACTAAAATCT
* * *
1312834 CCACCACCTCCTTACTACTACAAGTCC
1 CCACCACCACCTTACTACTA-AAATCT
1312861 CCACCACCACC
1 CCACCACCACC
1312872 ACCAAAGCAT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
21 16 0.34
22 1 0.02
23 2 0.04
25 2 0.04
26 1 0.02
27 25 0.53
ACGTcount: A:0.28, C:0.51, G:0.01, T:0.20
Consensus pattern (26 bp):
CCACCACCACCTTACTACTAAAATCT
Found at i:1312963 original size:24 final size:23
Alignment explanation
Indices: 1312936--1313063 Score: 75
Period size: 24 Copynumber: 5.3 Consensus size: 23
1312926 ACCCTCACCA
*
1312936 CCACCACCTTACTACTACAAGTCT
1 CCACCACC-TACTACTACAAATCT
* **
1312960 CCACCACC-ACCTTC-ACCATCTCCT
1 CCACCACCTA-CTACTA-CAAAT-CT
1312984 CCACCACCTTACTACTACAAATCT
1 CCACCACC-TACTACTACAAATCT
** * *
1313008 CCACCACC-ACCCCCAC-ATTACGT
1 CCACCACCTACTACTACAAAT-C-T
1313031 CTCACCACCATACTACTACAAATCT
1 C-CACCACC-TACTACTACAAATCT
1313056 CCACCACC
1 CCACCACC
1313064 ACCAATGAAG
Statistics
Matches: 78, Mismatches: 14, Indels: 24
0.67 0.12 0.21
Matches are distributed among these distances:
21 2 0.03
22 8 0.10
23 8 0.10
24 42 0.54
25 8 0.10
26 8 0.10
27 2 0.03
ACGTcount: A:0.29, C:0.49, G:0.02, T:0.20
Consensus pattern (23 bp):
CCACCACCTACTACTACAAATCT
Found at i:1312963 original size:27 final size:27
Alignment explanation
Indices: 1312933--1313066 Score: 114
Period size: 27 Copynumber: 5.4 Consensus size: 27
1312923 ATCACCCTCA
*
1312933 CCACCACCACCTTACTACTACAAGTCT
1 CCACCACCACCTTACTACTACAAATCT
1312960 CCACCACCACCTT-C-AC--C--ATCT
1 CCACCACCACCTTACTACTACAAATCT
*
1312981 CCTCCACCACCTTACTACTACAAATCT
1 CCACCACCACCTTACTACTACAAATCT
** * *
1313008 CCACCACCACCCCCAC-ATTAC--GTCT
1 CCACCACCA-CCTTACTACTACAAATCT
1313033 -CACCACCA---TACTACTACAAATCT
1 CCACCACCACCTTACTACTACAAATCT
1313056 CCACCACCACC
1 CCACCACCACC
1313067 AATGAAGTCT
Statistics
Matches: 84, Mismatches: 10, Indels: 27
0.69 0.08 0.22
Matches are distributed among these distances:
20 2 0.02
21 19 0.23
22 1 0.01
23 6 0.07
24 16 0.19
25 6 0.07
26 1 0.01
27 29 0.35
28 4 0.05
ACGTcount: A:0.29, C:0.50, G:0.01, T:0.19
Consensus pattern (27 bp):
CCACCACCACCTTACTACTACAAATCT
Found at i:1312981 original size:21 final size:21
Alignment explanation
Indices: 1312909--1312993 Score: 71
Period size: 21 Copynumber: 3.8 Consensus size: 21
1312899 CTACTACAAG
* * *
1312909 TCTCCACCACCTCCATCACCC
1 TCTCCACCACCACCTTCACCA
*
1312930 TCACCACCACCACCTTACTACTACAA
1 TCTCCACCACCACCTT-C-AC--C-A
1312956 GTCTCCACCACCACCTTCACCA
1 -TCTCCACCACCACCTTCACCA
*
1312978 TCTCCTCCACCACCTT
1 TCTCCACCACCACCTT
1312994 ACTACTACAA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
21 28 0.54
22 2 0.04
23 3 0.06
25 3 0.06
26 1 0.02
27 15 0.29
ACGTcount: A:0.24, C:0.54, G:0.01, T:0.21
Consensus pattern (21 bp):
TCTCCACCACCACCTTCACCA
Found at i:1313016 original size:48 final size:48
Alignment explanation
Indices: 1312462--1313067 Score: 451
Period size: 48 Copynumber: 12.4 Consensus size: 48
1312452 GCCTTATGAA
* * * * * * *
1312462 TACAAGTCTCCACCACCTCCATCGCCTTCTCCTCCACCTCCTTA-TGAG
1 TACAAGTCTCCACCACCACCATCACCATCACCACCACCACCTTACT-AC
* * * * *
1312510 TATAAATCTCCACCACCTCCATCACCATCACCACCACCTCCATACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCACCACCACCTTACTAC
* * * * ** * *
1312558 TACAAGTCCCCACCACCACCACCAAAGCATGAAGAACAACCACCATACTAC
1 TACAAGTCTCCACCACCACCATC--ACCAT-CACCACCACCACCTTACTAC
* * * * * * *
1312609 TACAAGTCACCTCCTCCTCCATCTCCATCACCACCTCCTCCTTACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCACCACCACCTTACTAC
* * * * * * *
1312657 TACAAGTCCCCACCACCTCCGTCTCCATCACCACCTCCTCCATACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCACCACCACCTTACTAC
* * * * ** * * *
1312705 TACAAATCTCCACCACCACCACCAAAGCATGAAGAACAACCCCCATACTAC
1 TACAAGTCTCCACCACCACCATC--ACCAT-CACCACCACCACCTTACTAC
* *
1312756 TACAAGTCTCCACCACCTCCATCACCCTCACCACCACCACCTTACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCACCACCACCTTACTAC
* * * * *
1312804 TATAAATCTCCACCACCACCTTCACCATCTCCACCACCTCCTTACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCACCACCACCTTACTAC
* * * * ** * * *
1312852 TACAAGTCCCCACCACCACCACCAAAGCATGAAGAACAACCCCCATACTAC
1 TACAAGTCTCCACCACCACCATC--ACCAT-CACCACCACCACCTTACTAC
* *
1312903 TACAAGTCTCCACCACCTCCATCACCCTCACCACCACCACCTTACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCACCACCACCTTACTAC
* * *
1312951 TACAAGTCTCCACCACCACCTTCACCATCTCCTCCACCACCTTACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCACCACCACCTTACTAC
* ** * ** *
1312999 TACAAATCTCCACCACCACCCCCA-CATTACGTCTCACCACCATACTAC
1 TACAAGTCTCCACCACCACCATCACCATCACCAC-CACCACCTTACTAC
*
1313047 TACAAATCTCCACCACCACCA
1 TACAAGTCTCCACCACCACCA
1313068 ATGAAGTCTC
Statistics
Matches: 441, Mismatches: 106, Indels: 22
0.78 0.19 0.04
Matches are distributed among these distances:
47 6 0.01
48 314 0.71
49 10 0.02
50 11 0.02
51 100 0.23
ACGTcount: A:0.30, C:0.48, G:0.04, T:0.19
Consensus pattern (48 bp):
TACAAGTCTCCACCACCACCATCACCATCACCACCACCACCTTACTAC
Found at i:1313049 original size:147 final size:147
Alignment explanation
Indices: 1312462--1313018 Score: 783
Period size: 147 Copynumber: 3.8 Consensus size: 147
1312452 GCCTTATGAA
* * * * * * *
1312462 TACAAGTCTCCACCACCTCCATCGCCTTCTCCTCCACCTCCTTA-TGAGTATAAATCTCCACCAC
1 TACAAGTCTCCACCACCTCCATCACCCTCACCACCACCACCTTACT-ACTACAAATCTCCACCAC
* * *
1312526 CTCCATCACCATCACCACCACCTCCATACTACTACAAGTCCCCACCACCACCACCAAAGCATGAA
65 CACCTTCACCATCACCACCACCTCCATACTACTACAAATCCCCACCACCACCACCAAAGCATGAA
*
1312591 GAACAACCACCATACTAC
130 GAACAACCCCCATACTAC
* * * * * * * * *
1312609 TACAAGTCACCTCCTCCTCCATCTCCATCACCACCTCCTCCTTACTACTACAAGTCCCCACCACC
1 TACAAGTCTCCACCACCTCCATCACCCTCACCACCACCACCTTACTACTACAAATCTCCACCACC
* * * * *
1312674 TCCGTCTCCATCACCACCTCCTCCATACTACTACAAATCTCCACCACCACCACCAAAGCATGAAG
66 ACCTTCACCATCACCACCACCTCCATACTACTACAAATCCCCACCACCACCACCAAAGCATGAAG
1312739 AACAACCCCCATACTAC
131 AACAACCCCCATACTAC
*
1312756 TACAAGTCTCCACCACCTCCATCACCCTCACCACCACCACCTTACTACTATAAATCTCCACCACC
1 TACAAGTCTCCACCACCTCCATCACCCTCACCACCACCACCTTACTACTACAAATCTCCACCACC
* * *
1312821 ACCTTCACCATCTCCACCACCTCCTTACTACTACAAGTCCCCACCACCACCACCAAAGCATGAAG
66 ACCTTCACCATCACCACCACCTCCATACTACTACAAATCCCCACCACCACCACCAAAGCATGAAG
1312886 AACAACCCCCATACTAC
131 AACAACCCCCATACTAC
*
1312903 TACAAGTCTCCACCACCTCCATCACCCTCACCACCACCACCTTACTACTACAAGTCTCCACCACC
1 TACAAGTCTCCACCACCTCCATCACCCTCACCACCACCACCTTACTACTACAAATCTCCACCACC
* * * * *
1312968 ACCTTCACCATCTCCTCCACCACCTTACTACTACAAATCTCCACCACCACC
66 ACCTTCACCATCACCACCACCTCCATACTACTACAAATCCCCACCACCACC
1313019 CCCACATTAC
Statistics
Matches: 367, Mismatches: 42, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
147 366 1.00
148 1 0.00
ACGTcount: A:0.30, C:0.48, G:0.04, T:0.19
Consensus pattern (147 bp):
TACAAGTCTCCACCACCTCCATCACCCTCACCACCACCACCTTACTACTACAAATCTCCACCACC
ACCTTCACCATCACCACCACCTCCATACTACTACAAATCCCCACCACCACCACCAAAGCATGAAG
AACAACCCCCATACTAC
Found at i:1313087 original size:42 final size:44
Alignment explanation
Indices: 1312985--1313110 Score: 132
Period size: 48 Copynumber: 2.8 Consensus size: 44
1312975 CCATCTCCTC
* * *
1312985 CACCACCTTACTACTACAAATCTCCACCACCACCCCCACATTACGTCT
1 CACCACCATACTACTACAAATCTCCACCACCA---CCA-ATGAAGTCT
1313033 CACCACCATACTACTACAAATCTCCACCACCACCAATGAAGTCT
1 CACCACCATACTACTACAAATCTCCACCACCACCAATGAAGTCT
* * *
1313077 C-CTC-CC-TACTACTACCATTCTCCTCCACCACCAA
1 CAC-CACCATACTACTACAAATCTCCACCACCACCAA
1313111 CTCCTTACTA
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
42 25 0.35
43 3 0.04
44 9 0.13
45 3 0.04
48 31 0.44
ACGTcount: A:0.30, C:0.47, G:0.02, T:0.21
Consensus pattern (44 bp):
CACCACCATACTACTACAAATCTCCACCACCACCAATGAAGTCT
Found at i:1313131 original size:6 final size:6
Alignment explanation
Indices: 1313120--1313165 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
1313110 ACTCCTTACT
* *
1313120 ACCCCC ACCCCC ACCCTC ACCCCC ACCCCC ACCCCC ACCCAC ACCC
1 ACCCCC ACCCCC ACCCCC ACCCCC ACCCCC ACCCCC ACCCCC ACCC
1313166 GCTCATAGTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.20, C:0.78, G:0.00, T:0.02
Consensus pattern (6 bp):
ACCCCC
Found at i:1314271 original size:36 final size:36
Alignment explanation
Indices: 1314224--1314303 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
1314214 GTACTATTAT
* * * *
1314224 AAGTCTCCACCTCCACCGGCTCCCACTTATGTTTAC
1 AAGTCACCACCTCCACCAGCACCAACTTATGTTTAC
*
1314260 AAGTCACCACCTCCACCATCACCAACTTATGTTTAC
1 AAGTCACCACCTCCACCAGCACCAACTTATGTTTAC
1314296 AAGTCACC
1 AAGTCACC
1314304 TCCACCTCCT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.26, C:0.40, G:0.09, T:0.25
Consensus pattern (36 bp):
AAGTCACCACCTCCACCAGCACCAACTTATGTTTAC
Found at i:1314412 original size:114 final size:114
Alignment explanation
Indices: 1314260--1314531 Score: 472
Period size: 114 Copynumber: 2.4 Consensus size: 114
1314250 TTATGTTTAC
* ** * *
1314260 AAGTCACCACCTCCACCATCACCAACTTATGTTTACAAGTCACCTCCACCTCCTGCGTACTACTA
1 AAGTCTCCACCTCCACCGGCTCCCACTTATGTTTACAAGTCACCTCCACCTCCTGCGTACTACTA
* *
1314325 CAAGTCTCCACCACCACCAAAGCATGTGGAACAGCCTCCATACTACTAT
66 CAAGTCTCCACCACCACCAAAACATGTGGAACAACCTCCATACTACTAT
*
1314374 AAGTCTCCACCTCCACCGGCTCCCACTTATGTTTACAAGTCACCTCCACCTCCTGTGTACTACTA
1 AAGTCTCCACCTCCACCGGCTCCCACTTATGTTTACAAGTCACCTCCACCTCCTGCGTACTACTA
1314439 CAAGTCTCCACCACCACCAAAACATGTGGAACAACCTCCATACTACTAT
66 CAAGTCTCCACCACCACCAAAACATGTGGAACAACCTCCATACTACTAT
1314488 AAGTCTCCACCTCCACCGGCTCCCACTTATGTTTACAAGTCACC
1 AAGTCTCCACCTCCACCGGCTCCCACTTATGTTTACAAGTCACC
1314532 ACCTCCACCA
Statistics
Matches: 150, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 150 1.00
ACGTcount: A:0.28, C:0.39, G:0.10, T:0.23
Consensus pattern (114 bp):
AAGTCTCCACCTCCACCGGCTCCCACTTATGTTTACAAGTCACCTCCACCTCCTGCGTACTACTA
CAAGTCTCCACCACCACCAAAACATGTGGAACAACCTCCATACTACTAT
Found at i:1314535 original size:36 final size:36
Alignment explanation
Indices: 1314488--1314576 Score: 115
Period size: 36 Copynumber: 2.5 Consensus size: 36
1314478 ATACTACTAT
* * *
1314488 AAGTCTCCACCTCCACCGGCTCCCACTTATGTTTAC
1 AAGTCACCACCTCCACCAGCGCCCACTTATGTTTAC
* *
1314524 AAGTCACCACCTCCACCATCGCCGACTTATGTTTAC
1 AAGTCACCACCTCCACCAGCGCCCACTTATGTTTAC
* *
1314560 AAGTCACCTCCACCACC
1 AAGTCACCACCTCCACC
1314577 TGTGTACTAC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.24, C:0.43, G:0.10, T:0.24
Consensus pattern (36 bp):
AAGTCACCACCTCCACCAGCGCCCACTTATGTTTAC
Found at i:1314711 original size:48 final size:48
Alignment explanation
Indices: 1314659--1315642 Score: 689
Period size: 48 Copynumber: 20.6 Consensus size: 48
1314649 GCAGCCCCCG
* * *
1314659 TACTACTACAAGTCTCCTCCACCACCATCACCATCTCCTCCTCCACCA
1 TACTACTACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCA
* *
1314707 TACTATTACAAGTCCCCACCACCACCAGTTCA-C-TCTCCACCACCACCA
1 TACTACTACAAGTCTCCACCACCACCA--TCACCATCTCCACCACCACCA
* * * **** * *
1314755 TACTACTACAAGTCCCCACCACCACCA-AAACATGAGGAGCAACCTCCA
1 TACTACTACAAGTCTCCACCACCACCATCACCATCTCCA-CCACCACCA
* * * * *
1314803 TACTACTACAAATCTCCTCCTCCACCATCGCCATCTCCTCCACCACCA
1 TACTACTACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCA
* * * * * * ** ** *
1314851 TATTACTACAAATCCCCACCACCACCA-AAACATGTAGAAGAGCCCCCA
1 TACTACTACAAGTCTCCACCACCACCATCACCATCTCCACCA-CCACCA
* * * *
1314899 TACTACTACAAATCTCCTCCACCACCATCACCATCTCCTCCTCCACCA
1 TACTACTACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCA
* * * *
1314947 TACTACTACAAGTCCCCACCACCACCATCTCCATCACCACCCCCACCA
1 TACTACTACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCA
* * * * * *
1314995 TACTATTACAAATCACCCCCACCACCATCGCCATCTCC-TCATCCACCA
1 TACTACTACAAGTCTCCACCACCACCATCACCATCTCCACCA-CCACCA
* * * * ** ** *
1315043 TACTACTACAAGTCCCCACCACCGCCGA--AACATGTAGAGGAGCCCCCA
1 TACTACTACAAGTCTCCACCACCACC-ATCACCATCTCCACCA-CCACCA
* * * *
1315091 TACTACTACAAGTCTCCCCCACCACCATCGCCATCTCCTCCTCCACCA
1 TACTACTACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCA
* * * *
1315139 TACTATTACAAATCTCCTCCACCACCATCACCATCT---CCTCCACCA
1 TACTACTACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCA
* * * ** ** *
1315184 TACTACTACAAGTCCCCACCACCACCGA--AACATGTAGAGGAGCCCCCA
1 TACTACTACAAGTCTCCACCACCACC-ATCACCATCTCCACCA-CCACCA
* * * *
1315232 TAC-ATCTACAAATCTCCTCCACCACCATCGCCATCTCCTCCACCACCA
1 TACTA-CTACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCA
* * *
1315280 TACTATTACAAGTCCCCACCACCACCAGTTCA--TTCTCCACCACCACCA
1 TACTACTACAAGTCTCCACCACCACCA--TCACCATCTCCACCACCACCA
* *
1315328 TACTACTACAAGTCTCCACCACCACCAGT--CCACTCCCCACCCCCACCA
1 TACTACTACAAGTCTCCACCACCACCA-TCACCA-TCTCCACCACCACCA
* * * * *
1315376 TACTACTACAAGTCTCCACCACCACCTTCTCCCTCACCACCTCCACCA
1 TACTACTACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCA
* * * ** ** *
1315424 TACTATTACAAGTCTCCACCACCACCA-AAACA-CGTAGAGAAGCCCCCA
1 TACTACTACAAGTCTCCACCACCACCATCACCATC-TCCACCA-CCACCA
* * * *
1315472 TAC-ATCTACAAATCTCCTCCACCACCATCGCCATCTCCTCCACCACCA
1 TACTA-CTACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCA
* * * *
1315520 TACTATTACAAGTCCCCACCACCACCAGTTCA--TTCCCCACCACCACCA
1 TACTACTACAAGTCTCCACCACCACCA--TCACCATCTCCACCACCACCA
* * * * *
1315568 TACTACTACAAGTCTCCACCACCACCTTCTCCCTCACCACCTCCACCA
1 TACTACTACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCA
* *
1315616 TACTATTACAAGTCCCCACCACCACCA
1 TACTACTACAAGTCTCCACCACCACCA
1315643 AAACACGTAG
Statistics
Matches: 715, Mismatches: 182, Indels: 78
0.73 0.19 0.08
Matches are distributed among these distances:
44 5 0.01
45 32 0.04
46 5 0.01
47 20 0.03
48 618 0.86
49 27 0.04
50 8 0.01
ACGTcount: A:0.29, C:0.47, G:0.05, T:0.19
Consensus pattern (48 bp):
TACTACTACAAGTCTCCACCACCACCATCACCATCTCCACCACCACCA
Found at i:1315174 original size:21 final size:21
Alignment explanation
Indices: 1315103--1315183 Score: 72
Period size: 21 Copynumber: 3.6 Consensus size: 21
1315093 CTACTACAAG
* *
1315103 TCTCCCCCACCACCATCGCCA
1 TCTCCTCCACCACCATCACCA
* *
1315124 TCTCCTCCTCCACCATACTATTACAAA
1 TCTCCTCCACCACCAT-C----AC-CA
1315151 TCTCCTCCACCACCATCACCA
1 TCTCCTCCACCACCATCACCA
1315172 TCTCCTCCACCA
1 TCTCCTCCACCA
1315184 TACTACTACA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
21 27 0.56
22 3 0.06
26 2 0.04
27 16 0.33
ACGTcount: A:0.23, C:0.53, G:0.01, T:0.22
Consensus pattern (21 bp):
TCTCCTCCACCACCATCACCA
Found at i:1315496 original size:192 final size:189
Alignment explanation
Indices: 1314725--1315732 Score: 878
Period size: 192 Copynumber: 5.3 Consensus size: 189
1314715 CAAGTCCCCA
* *** *
1314725 CCACCACCAGTTCACTCTCCACCACCACCATACTACTACAAGTCCCCACCACCACCAAAACATGA
1 CCACCACCA-TTCA-TCTCCTCCACCACCATACTACTACAAGTCCCCACCACCACCAGTCCATCA
** * * * * * * * * *
1314790 GGAGCAACCTCCATACTACTACAAATCTCCTCCTCCACCATCGCCATCTCCTCCACCACCATATT
64 CCA-CCACCACCATACTACTACAAGTCTCCACCACCACCATCGCCATCACCACCTCCACCATACT
* * *
1314855 ACTACAAATCCCCACCACCACCAAAACATGTAGA-AGAGCCCCCATAC-TACTACAAATCTCCT
128 ATTACAAGTCCCCACCACCACCAAAACACGTAGAGA-AGCCCCCATACAT-CTACAAATCTCCT
* * *
1314917 CCACCACCATCACCATCTCCTCCTCCACCATACTACTACAAGTCCCCACCACCACCATCTCCATC
1 CCACCACCAT--TCATCTCCTCCACCACCATACTACTACAAGTCCCCACCACCACCA-GTCCATC
* * * * * * * *
1314982 ACCACCCCCACCATACTATTACAAATCACCCCCACCACCATCGCCATCTCCTCATCCACCATACT
63 ACCACCACCACCATACTACTACAAGTCTCCACCACCACCATCGCCATCACCACCTCCACCATACT
* * * * * * *
1315047 ACTACAAGTCCCCACCACCGCCGAAACATGTAGAGGAGCCCCCATAC-TACTACAAGTCTCCC
128 ATTACAAGTCCCCACCACCACCAAAACACGTAGAGAAGCCCCCATACAT-CTACAAATCTCCT
* * * * * * *
1315109 CCACCACCATCGCCATCTCCTCCTCCACCATACTATTACAAATCTCCTCCACCACCA-T-CACCA
1 CCACCACCAT--TCATCTCCTCCACCACCATACTACTACAAGTCCCCACCACCACCAGTCCATCA
* * * * ** * ** *
1315172 TCTCCTCCACCATACTACTACAAGTCCCCACCACCACCGA--AACATGTAGAGGAGC-CC-CCAT
64 CCACCACCACCATACTACTACAAGTCTCCACCACCACC-ATCGCCA--T-CACCACCTCCACCAT
* * * *** ***** * *
1315233 AC-ATCTACAAATCTCCTCCACCACCATCGCCATC-TCCTCCA-CCACCATACTAT-TACAAGTC
125 ACTAT-TACAAGTCCCCACCACCACCA-AAACA-CGTAGAGAAGCCCCCATAC-ATCTACAAATC
* *
1315294 CCCA
186 TCCT
* *
1315298 CCACCACCAGTTCATTCTCCACCACCACCATACTACTACAAGTCTCCACCACCACCAGTCCACTC
1 CCACCACCA-TTCA-TCTCCTCCACCACCATACTACTACAAGTCCCCACCACCACCAGTCCA-TC
* * * * *
1315363 CCCACCCCCACCATACTACTACAAGTCTCCACCACCACCTTCTCCCTCACCACCTCCACCATACT
63 ACCACCACCACCATACTACTACAAGTCTCCACCACCACCATCGCCATCACCACCTCCACCATACT
*
1315428 ATTACAAGTCTCCACCACCACCAAAACACGTAGAGAAGCCCCCATACATCTACAAATCTCCT
128 ATTACAAGTCCCCACCACCACCAAAACACGTAGAGAAGCCCCCATACATCTACAAATCTCCT
* * *
1315490 CCACCACCATCGCCATCTCCTCCACCACCATACTATTACAAGTCCCCACCACCACCAGTTCATTC
1 CCACCACCAT--TCATCTCCTCCACCACCATACTACTACAAGTCCCCACCACCACCAGTCCA-TC
* * * *
1315555 CCCACCACCACCATACTACTACAAGTCTCCACCACCACCTTCTCCCTCACCACCTCCACCATACT
63 ACCACCACCACCATACTACTACAAGTCTCCACCACCACCATCGCCATCACCACCTCCACCATACT
*
1315620 ATTACAAGTCCCCACCACCACCAAAACACGTAGAGGAGCCCCCATACATCTACAAATCTCCT
128 ATTACAAGTCCCCACCACCACCAAAACACGTAGAGAAGCCCCCATACATCTACAAATCTCCT
* *
1315682 CCACCACCATCGCCATCTCCT---CCACCATACTATTACAAGTCCCCACCACCA
1 CCACCACCAT--TCATCTCCTCCACCACCATACTACTACAAGTCCCCACCACCA
1315733 TACTACTACA
Statistics
Matches: 680, Mismatches: 108, Indels: 59
0.80 0.13 0.07
Matches are distributed among these distances:
188 5 0.01
189 151 0.22
190 15 0.02
191 14 0.02
192 483 0.71
193 12 0.02
ACGTcount: A:0.30, C:0.47, G:0.05, T:0.18
Consensus pattern (189 bp):
CCACCACCATTCATCTCCTCCACCACCATACTACTACAAGTCCCCACCACCACCAGTCCATCACC
ACCACCACCATACTACTACAAGTCTCCACCACCACCATCGCCATCACCACCTCCACCATACTATT
ACAAGTCCCCACCACCACCAAAACACGTAGAGAAGCCCCCATACATCTACAAATCTCCT
Found at i:1315546 original size:27 final size:27
Alignment explanation
Indices: 1315511--1315642 Score: 99
Period size: 27 Copynumber: 5.3 Consensus size: 27
1315501 GCCATCTCCT
1315511 CCACCACCATACTATTACAAGTCCCCA
1 CCACCACCATACTATTACAAGTCCCCA
* *
1315538 CCACCACC--A--GTT-C-ATTCCCCA
1 CCACCACCATACTATTACAAGTCCCCA
* *
1315559 CCACCACCATACTACTACAAGTCTCCA
1 CCACCACCATACTATTACAAGTCCCCA
* ** *
1315586 CCACCACC-T--T-CT-C-CCTCACCA
1 CCACCACCATACTATTACAAGTCCCCA
*
1315607 CCTCCACCATACTATTACAAGTCCCCA
1 CCACCACCATACTATTACAAGTCCCCA
1315634 CCACCACCA
1 CCACCACCA
1315643 AAACACGTAG
Statistics
Matches: 78, Mismatches: 15, Indels: 24
0.67 0.13 0.21
Matches are distributed among these distances:
21 27 0.35
22 3 0.04
23 5 0.06
24 2 0.03
25 3 0.04
26 3 0.04
27 35 0.45
ACGTcount: A:0.29, C:0.50, G:0.03, T:0.18
Consensus pattern (27 bp):
CCACCACCATACTATTACAAGTCCCCA
Found at i:1315732 original size:24 final size:24
Alignment explanation
Indices: 1315703--1315804 Score: 91
Period size: 24 Copynumber: 4.2 Consensus size: 24
1315693 GCCATCTCCT
1315703 CCACCATACTATTACAAGTCCCCA
1 CCACCATACTATTACAAGTCCCCA
* *
1315727 CCACCATACTACTACAAGTCTCCA
1 CCACCATACTATTACAAGTCCCCA
* * **** *
1315751 CCACCA-CCT-TCTCCCTCACCACCT
1 CCACCATACTAT-TACAAGTCC-CCA
1315775 CCACCATACTATTACAAGTCCCCA
1 CCACCATACTATTACAAGTCCCCA
1315799 CCACCA
1 CCACCA
1315805 CCAGTCCACT
Statistics
Matches: 56, Mismatches: 18, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
23 5 0.09
24 44 0.79
25 6 0.11
26 1 0.02
ACGTcount: A:0.29, C:0.48, G:0.03, T:0.20
Consensus pattern (24 bp):
CCACCATACTATTACAAGTCCCCA
Found at i:1315779 original size:48 final size:48
Alignment explanation
Indices: 1315727--1316125 Score: 336
Period size: 48 Copynumber: 8.3 Consensus size: 48
1315717 CAAGTCCCCA
* * * *
1315727 CCACCATACTACTACAAGTCTCCACCACCACC-TTCTCCCTCACCACCT
1 CCACCATACTACTACAAATCCCCACCACCACCAGTC-CACTCACCACCT
* * * *
1315775 CCACCATACTATTACAAGTCCCCACCACCACCAGTCCACTCTCCACCC
1 CCACCATACTACTACAAATCCCCACCACCACCAGTCCACTCACCACCT
*
1315823 CCACCATACTACTACAAATCCCCACCACCACCAGTCCACTCTCCACCT
1 CCACCATACTACTACAAATCCCCACCACCACCAGTCCACTCACCACCT
1315871 CCACCATACTACTACAAATCCCCACCACCACCA-TCTC-CTTCACCACCT
1 CCACCATACTACTACAAATCCCCACCACCACCAGTC-CAC-TCACCACCT
* * ** *
1315919 CTACCATACTACTACAAATCACCC-CCACCTCCAGTGAAAGCTCCAGCACCT
1 CCACCATACTACTACAAATC-CCCACCACCACCAGT-CCA-CT-CACCACCT
* * * * * *
1315970 --ACC-TACCACTACAACTCCCCTCCTCCACCA-T-CACCATCTCCTCCT
1 CCACCATACTACTACAAATCCCCACCACCACCAGTCCA-C-TCACCACCT
* * ** * *
1316015 CCCCCATACTACTACAAATCTCCC-CCCCCACCAGTCCACTTTCCCCCA
1 CCACCATACTACTACAAATC-CCCACCACCACCAGTCCACTCACCACCT
* * *
1316063 CCACCATACTACTACAAATCTCCACCTCCTCCA-TCTC-CGTCACCACCT
1 CCACCATACTACTACAAATCCCCACCACCACCAGTC-CAC-TCACCACCT
*
1316111 CCTCCATACTACTAC
1 CCACCATACTACTAC
1316126 CACTCACCTC
Statistics
Matches: 291, Mismatches: 40, Indels: 40
0.78 0.11 0.11
Matches are distributed among these distances:
45 7 0.02
46 1 0.00
47 14 0.05
48 244 0.84
49 14 0.05
50 3 0.01
51 8 0.03
ACGTcount: A:0.27, C:0.51, G:0.03, T:0.20
Consensus pattern (48 bp):
CCACCATACTACTACAAATCCCCACCACCACCAGTCCACTCACCACCT
Found at i:1315820 original size:21 final size:21
Alignment explanation
Indices: 1315796--1315876 Score: 65
Period size: 21 Copynumber: 3.6 Consensus size: 21
1315786 TTACAAGTCC
1315796 CCACCACCACCAGTCCACTCT
1 CCACCACCACCAGTCCACTCT
* *
1315817 CCACCCCCACCA-TACTACTACAAATCC
1 CCACCACCACCAGT-C--C-AC---TCT
1315844 CCACCACCACCAGTCCACTCT
1 CCACCACCACCAGTCCACTCT
*
1315865 CCACCTCCACCA
1 CCACCACCACCA
1315877 TACTACTACA
Statistics
Matches: 47, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
20 1 0.02
21 25 0.53
23 1 0.02
24 4 0.09
25 1 0.02
27 14 0.30
28 1 0.02
ACGTcount: A:0.27, C:0.57, G:0.02, T:0.14
Consensus pattern (21 bp):
CCACCACCACCAGTCCACTCT
Found at i:1315840 original size:165 final size:165
Alignment explanation
Indices: 1315559--1315900 Score: 469
Period size: 165 Copynumber: 2.1 Consensus size: 165
1315549 TCATTCCCCA
1315559 CCACCACCATACTACTACAAGTCTCCACCACCACCTTCTCCCTCACCACCTCCACCATACTATTA
1 CCACCACCATACTACTACAAGTCTCCACCACCACCTTCTCCCTCACCACCTCCACCATACTATTA
* * * * *
1315624 CAAGTCCCCACCACCACCAAAACACGTAGAGGAGCCCCCATACATCTACAAATCTCCTCCACCAC
66 CAAGTCCCCACCACCACCAAAACACCTACA-GACCCCCCATACATCTACAAATCCCCACCACCAC
* *
1315689 CA-TCGC-CATCT-CCTCCACCATACTATTACAAGTCC
130 CAGTC-CAC-TCTCCCTCCACCATACTACTACAAATCC
1315724 CCACCACCATACTACTACAAGTCTCCACCACCACCTTCTCCCTCACCACCTCCACCATACTATTA
1 CCACCACCATACTACTACAAGTCTCCACCACCACCTTCTCCCTCACCACCTCCACCATACTATTA
*** * *
1315789 CAAGTCCCCACCACCACCAGTCCACTCTCCA-CCCCCACCATAC-TACTACAAATCCCCACCACC
66 CAAGTCCCCACCACCACCAAAACAC-CTACAGACCCC-CCATACAT-CTACAAATCCCCACCACC
1315852 ACCAGTCCACTCTCCACCTCCACCATACTACTACAAATCC
128 ACCAGTCCACTCT-C-CCTCCACCATACTACTACAAATCC
1315892 CCACCACCA
1 CCACCACCA
1315901 CCATCTCCTT
Statistics
Matches: 157, Mismatches: 12, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
164 4 0.03
165 117 0.75
166 5 0.03
168 31 0.20
ACGTcount: A:0.29, C:0.49, G:0.04, T:0.18
Consensus pattern (165 bp):
CCACCACCATACTACTACAAGTCTCCACCACCACCTTCTCCCTCACCACCTCCACCATACTATTA
CAAGTCCCCACCACCACCAAAACACCTACAGACCCCCCATACATCTACAAATCCCCACCACCACC
AGTCCACTCTCCCTCCACCATACTACTACAAATCC
Found at i:1315884 original size:144 final size:144
Alignment explanation
Indices: 1315727--1316082 Score: 389
Period size: 144 Copynumber: 2.5 Consensus size: 144
1315717 CAAGTCCCCA
* * *
1315727 CCACCATACTACTACAAGTCTCCACCACCACCTTCTCCCTCACCACCTCCACCATACTATTACAA
1 CCACCATACTACTACAAATCTCCACCACCACCATCTCCCTCACCACCTCCACCATACTACTACAA
* * ** * *
1315792 GTC-CCCACCACCACCAGTCCACTCTCCA-CCCCCACCATACTACTACAAATCCCCACCACCACC
66 ATCACCC-CCACCACCAGTCAAAGCTCCAGCACCCACC-TACCACTACAAATCCCCACCACCACC
1315855 AGT--CCACTCTCCACCT
129 A-TCACCA-TCTCCACCT
* * *
1315871 CCACCATACTACTACAAATCCCCACCACCACCATCTCCTTCACCACCTCTACCATACTACTACAA
1 CCACCATACTACTACAAATCTCCACCACCACCATCTCCCTCACCACCTCCACCATACTACTACAA
* * * * * *
1315936 ATCACCCCCACCTCCAGTGAAAGCTCCAGCACCTACCTACCACTACAACTCCCCTCCTCCACCAT
66 ATCACCCCCACCACCAGTCAAAGCTCCAGCACCCACCTACCACTACAAATCCCCACCACCACCAT
*
1316001 CACCATCTCCTCCT
131 CACCATCTCCACCT
* * * * ** * *
1316015 CCCCCATACTACTACAAATCTCCCCCCCCACCAGTC-CACTTTCCCCCACCACCATACTACTACA
1 CCACCATACTACTACAAATCTCCACCACCACCA-TCTCCCTCACCACCTCCACCATACTACTACA
1316079 AATC
65 AATC
1316083 TCCACCTCCT
Statistics
Matches: 177, Mismatches: 30, Indels: 10
0.82 0.14 0.05
Matches are distributed among these distances:
143 1 0.01
144 162 0.92
145 14 0.08
ACGTcount: A:0.28, C:0.51, G:0.03, T:0.19
Consensus pattern (144 bp):
CCACCATACTACTACAAATCTCCACCACCACCATCTCCCTCACCACCTCCACCATACTACTACAA
ATCACCCCCACCACCAGTCAAAGCTCCAGCACCCACCTACCACTACAAATCCCCACCACCACCAT
CACCATCTCCACCT
Found at i:1315940 original size:27 final size:27
Alignment explanation
Indices: 1315817--1315941 Score: 78
Period size: 27 Copynumber: 5.1 Consensus size: 27
1315807 AGTCCACTCT
* *
1315817 CCACCCCCACCATACTACTACAAATCC
1 CCACCTCCACCATACTACTACAAATCA
* *
1315844 CCACCACCACCAGT-C--C-AC---TCT
1 CCACCTCCACCA-TACTACTACAAATCA
*
1315865 CCACCTCCACCATACTACTACAAATCC
1 CCACCTCCACCATACTACTACAAATCA
* *
1315892 CCACCACCACCAT-CT-C--C--TTCA
1 CCACCTCCACCATACTACTACAAATCA
*
1315913 CCACCTCTACCATACTACTACAAATCA
1 CCACCTCCACCATACTACTACAAATCA
1315940 CC
1 CC
1315942 CCCACCTCCA
Statistics
Matches: 74, Mismatches: 10, Indels: 28
0.66 0.09 0.25
Matches are distributed among these distances:
20 1 0.01
21 27 0.36
22 2 0.03
23 3 0.04
24 4 0.05
25 3 0.04
26 2 0.03
27 31 0.42
28 1 0.01
ACGTcount: A:0.30, C:0.51, G:0.01, T:0.18
Consensus pattern (27 bp):
CCACCTCCACCATACTACTACAAATCA
Found at i:1322823 original size:15 final size:15
Alignment explanation
Indices: 1322799--1322828 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1322789 TAAAATTTTG
1322799 GGGTCATTTCAAGTT
1 GGGTCATTTCAAGTT
*
1322814 GGGTCGTTTCAAGTT
1 GGGTCATTTCAAGTT
1322829 TCGATTCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.13, G:0.30, T:0.40
Consensus pattern (15 bp):
GGGTCATTTCAAGTT
Found at i:1327838 original size:22 final size:22
Alignment explanation
Indices: 1327798--1327842 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1327788 ACATAAGAAG
*
1327798 TGGTGATAAAAGTTGAATTAAA
1 TGGTGATAAAAATTGAATTAAA
1327820 TGGTAGATAAAAATT-AATTAAA
1 TGGT-GATAAAAATTGAATTAAA
1327842 T
1 T
1327843 CATTAATAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (22 bp):
TGGTGATAAAAATTGAATTAAA
Found at i:1341110 original size:9 final size:9
Alignment explanation
Indices: 1341098--1341217 Score: 50
Period size: 9 Copynumber: 13.0 Consensus size: 9
1341088 ACAATAATTT
1341098 TTATAAAAA
1 TTATAAAAA
*
1341107 TTAT-TAAA
1 TTATAAAAA
*
1341115 TTTTAATAAA
1 TTATAA-AAA
*
1341125 -AATAAAAA
1 TTATAAAAA
*
1341133 -TATAAAAT
1 TTATAAAAA
1341141 TTATTAAAAA
1 TTA-TAAAAA
* *
1341151 TTACAAATATTT
1 TTATAAA-A--A
1341163 TTATAAAAA
1 TTATAAAAA
*
1341172 TCATAAAAA
1 TTATAAAAA
*
1341181 -AATAAAATA
1 TTATAAAA-A
* *
1341190 TTGTAAAATT
1 TTATAAAA-A
1341200 TTATAAAAA
1 TTATAAAAA
*
1341209 TCATAAAAA
1 TTATAAAAA
1341218 AAATCAACGA
Statistics
Matches: 82, Mismatches: 20, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
8 21 0.26
9 29 0.35
10 25 0.30
11 1 0.01
12 6 0.07
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.36
Consensus pattern (9 bp):
TTATAAAAA
Found at i:1341143 original size:24 final size:24
Alignment explanation
Indices: 1341100--1341160 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 24
1341090 AATAATTTTT
*
1341100 ATAAAAATTATTAAATTTTAATAAAA
1 ATAAAAA-TA-TAAAATTTAATAAAA
*
1341126 ATAAAAATATAAAATTTATTAAAA
1 ATAAAAATATAAAATTTAATAAAA
*
1341150 ATTACAAATAT
1 A-TAAAAATAT
1341161 TTTTATAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.45
25 10 0.32
26 7 0.23
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
ATAAAAATATAAAATTTAATAAAA
Found at i:1341447 original size:19 final size:19
Alignment explanation
Indices: 1341425--1341468 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
1341415 TTCTTACGAC
1341425 TTTATAAAATTTTA-TGATT
1 TTTATAAAATTTTACT-ATT
1341444 TTTATAAAATTTTACTATT
1 TTTATAAAATTTTACTATT
1341463 TTTATA
1 TTTATA
1341469 TTTTTTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTATAAAATTTTACTATT
Found at i:1341475 original size:19 final size:21
Alignment explanation
Indices: 1341453--1341493 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1341443 TTTTATAAAA
1341453 TTTTACT-ATTTTT-ATATTT
1 TTTTACTAATTTTTAATATTT
*
1341472 TTTTCCTAATTTTTAATATTT
1 TTTTACTAATTTTTAATATTT
1341493 T
1 T
1341494 AATTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 6 0.32
21 7 0.37
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTACTAATTTTTAATATTT
Found at i:1341475 original size:29 final size:27
Alignment explanation
Indices: 1341442--1341522 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 27
1341432 AATTTTATGA
*
1341442 TTTTTATAAAATTTTACTATTTTTATATT
1 TTTTTATAAAATTTTAATA-TTTTA-ATT
* *
1341471 TTTTTCCT-AATTTTTAATATTTTAATT
1 TTTTT-ATAAAATTTTAATATTTTAATT
1341498 TTTTTATTAAAATTTAATAATATTT
1 TTTTTA-TAAAATTT--TAATATTT
1341523 ATAGCTTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
27 9 0.21
28 10 0.24
29 14 0.33
30 9 0.21
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTTTATAAAATTTTAATATTTTAATT
Found at i:1341513 original size:27 final size:28
Alignment explanation
Indices: 1341442--1341525 Score: 73
Period size: 27 Copynumber: 2.9 Consensus size: 28
1341432 AATTTTATGA
*
1341442 TTTTTATAAAATTTTACTATTTTTATATT
1 TTTTTATAAAA-TTTAATATTTTTATATT
* **
1341471 TTTTTCCTAATTTTTAATA-TTTTA-ATT
1 TTTTT-ATAAAATTTAATATTTTTATATT
*
1341498 TTTTTATTAAAATTTAATAATATTTATA
1 TTTTTA-TAAAATTTAAT-ATTTTTATA
1341526 GCTTTTATTG
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
27 17 0.40
28 6 0.14
29 15 0.36
30 4 0.10
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (28 bp):
TTTTTATAAAATTTAATATTTTTATATT
Found at i:1341556 original size:13 final size:13
Alignment explanation
Indices: 1341540--1341570 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1341530 TTATTGATTC
1341540 TTTTTTTTTATAA
1 TTTTTTTTTATAA
*
1341553 TTTTTTTTTCTAA
1 TTTTTTTTTATAA
1341566 TTTTT
1 TTTTT
1341571 AATAAAAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTTTTATAA
Found at i:1346493 original size:22 final size:21
Alignment explanation
Indices: 1346458--1346498 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1346448 AAAGGTATAA
**
1346458 AGAGGTTTTTTTAATAATTTTG
1 AGAGGTTTAATTAA-AATTTTG
1346480 AGAGGTTTAATTAAAATTT
1 AGAGGTTTAATTAAAATTT
1346499 CTAAAAGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (21 bp):
AGAGGTTTAATTAAAATTTTG
Found at i:1350464 original size:3 final size:3
Alignment explanation
Indices: 1350458--1350482 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1350448 TGTATTTCAA
1350458 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1350483 GTACATTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1350557 original size:14 final size:14
Alignment explanation
Indices: 1350540--1350590 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
1350530 TTTTTATTAC
1350540 TTTATTTTAATATT
1 TTTATTTTAATATT
*
1350554 TTTATTATAATAGCTT
1 TTTATTTTAATA--TT
1350570 TTGTATTTTAATATT
1 TT-TATTTTAATATT
*
1350585 ATTATT
1 TTTATT
1350591 ATTATCATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 15 0.48
15 3 0.10
16 4 0.13
17 9 0.29
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (14 bp):
TTTATTTTAATATT
Found at i:1350800 original size:22 final size:23
Alignment explanation
Indices: 1350772--1350826 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
1350762 AATTTTTTTA
1350772 ATATATATTATATGAATA-ATTT
1 ATATATATTATATGAATATATTT
* *
1350794 ATATATAATATTATGTATATATTT
1 ATATATATTA-TATGAATATATTT
1350818 -TA-ATATTAT
1 ATATATATTAT
1350827 CAGTTATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 1 0.04
22 14 0.50
23 9 0.32
24 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
ATATATATTATATGAATATATTT
Found at i:1357132 original size:22 final size:21
Alignment explanation
Indices: 1357097--1357137 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1357087 AAAGGTATAA
**
1357097 AGAGGTTTTTTTAATAATTTTG
1 AGAGGTTTAATTAA-AATTTTG
1357119 AGAGGTTTAATTAAAATTT
1 AGAGGTTTAATTAAAATTT
1357138 CTAAAAGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (21 bp):
AGAGGTTTAATTAAAATTTTG
Found at i:1361107 original size:3 final size:3
Alignment explanation
Indices: 1361101--1361128 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1361091 TGTATTTCAA
1361101 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1361129 GTACATTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1361203 original size:14 final size:14
Alignment explanation
Indices: 1361186--1361236 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
1361176 TTTTTATTAC
1361186 TTTATTTTAATATT
1 TTTATTTTAATATT
*
1361200 TTTATTATAATAGCTT
1 TTTATTTTAATA--TT
1361216 TTGTATTTTAATATT
1 TT-TATTTTAATATT
*
1361231 ATTATT
1 TTTATT
1361237 ATTATCATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 15 0.48
15 3 0.10
16 4 0.13
17 9 0.29
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (14 bp):
TTTATTTTAATATT
Found at i:1361446 original size:22 final size:23
Alignment explanation
Indices: 1361418--1361472 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
1361408 AATTTTTTTA
1361418 ATATATATTATATGAATA-ATTT
1 ATATATATTATATGAATATATTT
* *
1361440 ATATATAATATTATGTATATATTT
1 ATATATATTA-TATGAATATATTT
1361464 -TA-ATATTAT
1 ATATATATTAT
1361473 CAGTTATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 1 0.04
22 14 0.50
23 9 0.32
24 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
ATATATATTATATGAATATATTT
Found at i:1366104 original size:6 final size:6
Alignment explanation
Indices: 1366095--1366120 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1366085 TTGAGGAAGT
1366095 GGCAGA GGCAGA GGCAGA GGCAGA GG
1 GGCAGA GGCAGA GGCAGA GGCAGA GG
1366121 GTGGGTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.15, G:0.54, T:0.00
Consensus pattern (6 bp):
GGCAGA
Found at i:1367349 original size:22 final size:21
Alignment explanation
Indices: 1367324--1367364 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1367314 ATTTTTTATA
*
1367324 TAATAAAATATATCAAAAACAC
1 TAATAAAATA-ATAAAAAACAC
*
1367346 TAATAATATAATAAAAAAC
1 TAATAAAATAATAAAAAAC
1367365 CCCTTAACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (21 bp):
TAATAAAATAATAAAAAACAC
Found at i:1377915 original size:27 final size:27
Alignment explanation
Indices: 1377877--1377932 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1377867 CACCATCTTC
1377877 CATTATTTATTTATTTTTATAATAACA
1 CATTATTTATTTATTTTTATAATAACA
1377904 CATTATTTATTTATTTTTATAATAACA
1 CATTATTTATTTATTTTTATAATAACA
1377931 CA
1 CA
1377933 CTAGCTGACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.54
Consensus pattern (27 bp):
CATTATTTATTTATTTTTATAATAACA
Found at i:1378139 original size:16 final size:16
Alignment explanation
Indices: 1378118--1378149 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1378108 AATAACAACG
1378118 CTTTGATTTCATAAAA
1 CTTTGATTTCATAAAA
1378134 CTTTGATTTCATAAAA
1 CTTTGATTTCATAAAA
1378150 AAAAGGTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (16 bp):
CTTTGATTTCATAAAA
Found at i:1378920 original size:13 final size:13
Alignment explanation
Indices: 1378904--1378928 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1378894 CTGAATTTTT
1378904 TTTTCAATTTAAG
1 TTTTCAATTTAAG
1378917 TTTTCAATTTAA
1 TTTTCAATTTAA
1378929 ATTTAGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (13 bp):
TTTTCAATTTAAG
Found at i:1378933 original size:19 final size:17
Alignment explanation
Indices: 1378909--1378963 Score: 56
Period size: 19 Copynumber: 3.0 Consensus size: 17
1378899 TTTTTTTTTC
1378909 AATTTAAGTTTTCAATTT
1 AATTT-AGTTTTCAATTT
*
1378927 AAATTTAGTTGTTTAATTT
1 -AATTTAGTT-TTCAATTT
*
1378946 AATTTCAGTTTTCTATTT
1 AATTT-AGTTTTCAATTT
1378964 CATAAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.58
Consensus pattern (17 bp):
AATTTAGTTTTCAATTT
Found at i:1379607 original size:16 final size:17
Alignment explanation
Indices: 1379588--1379619 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1379578 AAGTTATATA
1379588 TATTT-GAAAATTTTAT
1 TATTTAGAAAATTTTAT
1379604 TATTTAGAAAATTTTA
1 TATTTAGAAAATTTTA
1379620 ATTTTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
TATTTAGAAAATTTTAT
Found at i:1384498 original size:21 final size:21
Alignment explanation
Indices: 1384472--1384512 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1384462 AGACGAGCAA
* *
1384472 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1384493 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1384513 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:1395362 original size:27 final size:27
Alignment explanation
Indices: 1395324--1395379 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
1395314 CACTCTCTAA
1395324 CATCTTCAAGTTCTTCATCACCATTTT
1 CATCTTCAAGTTCTTCATCACCATTTT
*
1395351 CATCTTCAAGTTCTTCATGACCATTTT
1 CATCTTCAAGTTCTTCATCACCATTTT
1395378 CA
1 CA
1395380 GTGGAAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.23, C:0.29, G:0.05, T:0.43
Consensus pattern (27 bp):
CATCTTCAAGTTCTTCATCACCATTTT
Found at i:1397790 original size:36 final size:36
Alignment explanation
Indices: 1397715--1397798 Score: 91
Period size: 36 Copynumber: 2.3 Consensus size: 36
1397705 AGTATGCATT
** * *
1397715 TCTTACATTGCATATTACCAATGAATGTGTTGCATC
1 TCTTACATTTTATATTACCAATGAATGTGTTGAACC
*
1397751 TCTTACATTTTATATTACCAATGGATG-GCTTGAACC
1 TCTTACATTTTATATTACCAATGAATGTG-TTGAACC
1397787 TCTT-CTATTTTA
1 TCTTAC-ATTTTA
1397799 CATTTTCAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
35 2 0.05
36 39 0.95
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.43
Consensus pattern (36 bp):
TCTTACATTTTATATTACCAATGAATGTGTTGAACC
Found at i:1408793 original size:18 final size:18
Alignment explanation
Indices: 1408753--1408838 Score: 106
Period size: 18 Copynumber: 4.9 Consensus size: 18
1408743 GACCGTTTAC
1408753 GTACTATTCA--TATAC-
1 GTACTATTCACGTATACG
* *
1408768 GCACTATTTACGTATACG
1 GTACTATTCACGTATACG
*
1408786 GTACTATTCACATATACG
1 GTACTATTCACGTATACG
*
1408804 GCACTATTCACGTATACG
1 GTACTATTCACGTATACG
*
1408822 GTACTGTTCACGTATAC
1 GTACTATTCACGTATAC
1408839 AGTAGTTGGG
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
15 8 0.14
17 5 0.08
18 46 0.78
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (18 bp):
GTACTATTCACGTATACG
Found at i:1408817 original size:36 final size:35
Alignment explanation
Indices: 1408753--1408838 Score: 122
Period size: 36 Copynumber: 2.5 Consensus size: 35
1408743 GACCGTTTAC
*
1408753 GTACTATT--CATATACGCACTATTTACGTATACG
1 GTACTATTCACATATACGCACTATTCACGTATACG
1408786 GTACTATTCACATATACGGCACTATTCACGTATACG
1 GTACTATTCACATATAC-GCACTATTCACGTATACG
* *
1408822 GTACTGTTCACGTATAC
1 GTACTATTCACATATAC
1408839 AGTAGTTGGG
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
33 8 0.17
35 7 0.15
36 32 0.68
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (35 bp):
GTACTATTCACATATACGCACTATTCACGTATACG
Found at i:1424495 original size:14 final size:14
Alignment explanation
Indices: 1424476--1424517 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1424466 AAAAATATAA
1424476 TAATAATATAATAG
1 TAATAATATAATAG
* *
1424490 TAATAATACAATGG
1 TAATAATATAATAG
1424504 TAATAATACTAATA
1 TAATAATA-TAATA
1424518 AAAGTTAGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 20 0.87
15 3 0.13
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (14 bp):
TAATAATATAATAG
Found at i:1424962 original size:19 final size:20
Alignment explanation
Indices: 1424871--1424964 Score: 61
Period size: 20 Copynumber: 4.7 Consensus size: 20
1424861 TAGTAACGAT
1424871 AATAATAATATATAAAA-ATAG
1 AATAATAATA-ATAAAATA-AG
***
1424892 AA-AATAATAATATGGTAA-
1 AATAATAATAATAAAATAAG
* *
1424910 AATATTAAT-ATATTAATAAG
1 AATAATAATAATA-AAATAAG
*
1424930 AATAATAGTAATAAAATAAG
1 AATAATAATAATAAAATAAG
1424950 ATTATAATAATAATA
1 A--ATAATAATAATA
1424965 TTAACAAGAA
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
18 5 0.09
19 13 0.23
20 22 0.39
21 5 0.09
22 11 0.20
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (20 bp):
AATAATAATAATAAAATAAG
Found at i:1448499 original size:10 final size:10
Alignment explanation
Indices: 1448484--1448509 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1448474 TGTAGTGTAA
1448484 ATATTATGAT
1 ATATTATGAT
1448494 ATATTATGAT
1 ATATTATGAT
1448504 ATATTA
1 ATATTA
1448510 ATTCAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (10 bp):
ATATTATGAT
Found at i:1451131 original size:46 final size:46
Alignment explanation
Indices: 1451061--1451426 Score: 475
Period size: 46 Copynumber: 8.0 Consensus size: 46
1451051 GCTCTCTGAA
* *
1451061 ATGAAATGCGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
1451107 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
1451153 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
1451199 ATGAAAAGAATAAGACCATGGTTGAAATATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** ** * *
1451245 GGGAAATGAAAAAGACCATGGTTGAAAGATACCATGGCAGCGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
1451291 ATGGAACGAATAAGACCATGGTTGAAAGATACCATGGCAACTTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
1451337 ATGGAAAGGA-TAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 AT-GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
1451383 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATG
1451427 TCAAAGATAA
Statistics
Matches: 285, Mismatches: 32, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
44 1 0.00
45 5 0.02
46 274 0.96
47 5 0.02
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:1452499 original size:129 final size:128
Alignment explanation
Indices: 1452349--1452628 Score: 326
Period size: 129 Copynumber: 2.2 Consensus size: 128
1452339 GTTTATTTAA
* * ** * * *** * *
1452349 AAAACGCCGCTAAAGACCATGATTTTTAGCGACGCTTTTTTTACAAACGCCGCTAAATACCATAA
1 AAAACGCCGCTAAAAATCATGACCTTTAACGACACTTTTCCCACAAACGCCACTAAAAACCATAA
* * *
1452414 CCTTTAGCGGCGCTTTTCCAAAAAACGCCGCTAAAGATCATGACTTTTAACGGCACTTTTCCC
66 CCTTTAGCGGCACTTTTCCAAAAAACGCCACTAAAGAACATGACTTTTAACGGCACTTTTCCC
* *
1452477 GAAAACGCCGCTAAAAATCATGACCTTTAACGATACTTTTCCCACAAACGCCACTAAAAATCATA
1 -AAAACGCCGCTAAAAATCATGACCTTTAACGACACTTTTCCCACAAACGCCACTAAAAACCATA
* * * ** *
1452542 ACCTTTAGCGGCACTTTTCCCACAAACGCCACTAAAGAACATGACTTTTAGCGGCGTTTTTCTC
65 ACCTTTAGCGGCACTTTTCCAAAAAACGCCACTAAAGAACATGACTTTTAACGGCACTTTTCCC
* *
1452606 ACAAACACCACTAAAAATCATGA
1 A-AAACGCCGCTAAAAATCATGA
1452629 ACTTCAAAAA
Statistics
Matches: 126, Mismatches: 24, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
128 1 0.01
129 125 0.99
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (128 bp):
AAAACGCCGCTAAAAATCATGACCTTTAACGACACTTTTCCCACAAACGCCACTAAAAACCATAA
CCTTTAGCGGCACTTTTCCAAAAAACGCCACTAAAGAACATGACTTTTAACGGCACTTTTCCC
Found at i:1452503 original size:86 final size:85
Alignment explanation
Indices: 1452347--1452603 Score: 264
Period size: 86 Copynumber: 3.0 Consensus size: 85
1452337 GCGTTTATTT
* * * * *** *
1452347 AAAAAACGCCGCTAAAGACCATGATTTTTAGCGACGCTTTTTTTACAAACGCCGCTAAATACCAT
1 AAAAAACGCCGCTAAAGATCATGACTTTTAGCGGCACTTTTCCCACAAACGCCGCTAAA-AACAT
*
1452412 AACCTTTAGCGGCGCTTTTCC
65 GACCTTTAGCGGCGCTTTTCC
*
1452433 AAAAAACGCCGCTAAAGATCATGACTTTTAACGGCACTTTTCCCGA-AAACGCCGCTAAAAATCA
1 AAAAAACGCCGCTAAAGATCATGACTTTTAGCGGCACTTTTCCC-ACAAACGCCGCTAAAAA-CA
* ***
1452497 TGACCTTTAACGATACTTTTCC
64 TGACCTTTAGCGGCGCTTTTCC
* * * * * * *
1452519 CACAAACGCCACTAAAAATCATAACCTTTAGCGGCACTTTTCCCACAAACGCCACTAAAGAACAT
1 AAAAAACGCCGCTAAAGATCATGACTTTTAGCGGCACTTTTCCCACAAACGCCGCTAAA-AACAT
* *
1452584 GACTTTTAGCGGCGTTTTTC
65 GACCTTTAGCGGCGCTTTTC
1452604 TCACAAACAC
Statistics
Matches: 139, Mismatches: 28, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
85 2 0.01
86 134 0.96
87 3 0.02
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.26
Consensus pattern (85 bp):
AAAAAACGCCGCTAAAGATCATGACTTTTAGCGGCACTTTTCCCACAAACGCCGCTAAAAACATG
ACCTTTAGCGGCGCTTTTCC
Found at i:1452609 original size:43 final size:42
Alignment explanation
Indices: 1452350--1452628 Score: 227
Period size: 43 Copynumber: 6.5 Consensus size: 42
1452340 TTTATTTAAA
* ** * * ***
1452350 AAACGCCGCTAAAGACCATGATTTTTAGCGACGCTTTTTTTAC
1 AAACGCCGCTAAA-AACATGACCTTTAGCGGCACTTTTCCCAC
* * * * *
1452393 AAACGCCGCTAAATACCATAACCTTTAGCGGCGCTTTTCCAAA
1 AAACGCCGCTAAA-AACATGACCTTTAGCGGCACTTTTCCCAC
* * *
1452436 AAACGCCGCTAAAGATCATGACTTTTAACGGCACTTTTCCCGA-
1 AAACGCCGCTAAA-AACATGACCTTTAGCGGCACTTTTCCC-AC
* **
1452479 AAACGCCGCTAAAAATCATGACCTTTAACGATACTTTTCCCAC
1 AAACGCCGCTAAAAA-CATGACCTTTAGCGGCACTTTTCCCAC
* *
1452522 AAACGCCACTAAAAATCATAACCTTTAGCGGCACTTTTCCCAC
1 AAACGCCGCTAAAAA-CATGACCTTTAGCGGCACTTTTCCCAC
* * ** *
1452565 AAACGCCACTAAAGAACATGACTTTTAGCGGCGTTTTTCTCAC
1 AAACGCCGCTAAA-AACATGACCTTTAGCGGCACTTTTCCCAC
* *
1452608 AAACACCACTAAAAATCATGA
1 AAACGCCGCTAAAAA-CATGA
1452629 ACTTCAAAAA
Statistics
Matches: 200, Mismatches: 31, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
42 4 0.02
43 193 0.96
44 3 0.01
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (42 bp):
AAACGCCGCTAAAAACATGACCTTTAGCGGCACTTTTCCCAC
Found at i:1454402 original size:21 final size:22
Alignment explanation
Indices: 1454370--1454422 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
1454360 CAACTTTCAG
1454370 ACACCATAAA-TTGCAGCATTTA
1 ACACC-TAAATTTGCAGCATTTA
*
1454392 ACACCTAAATTTTCAGCATTTA
1 ACACCTAAATTTGCAGCATTTA
*
1454414 ACACATAAA
1 ACACCTAAA
1454423 ATGGTTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 4 0.14
22 24 0.86
ACGTcount: A:0.43, C:0.23, G:0.06, T:0.28
Consensus pattern (22 bp):
ACACCTAAATTTGCAGCATTTA
Found at i:1456606 original size:6 final size:6
Alignment explanation
Indices: 1456595--1456625 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1456585 TTTCAAAACT
*
1456595 AAAGGG AAAGGG AAAGGG AAAGGG GAAGGG A
1 AAAGGG AAAGGG AAAGGG AAAGGG AAAGGG A
1456626 TCGTATGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (6 bp):
AAAGGG
Found at i:1456854 original size:7 final size:6
Alignment explanation
Indices: 1456821--1456854 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
1456811 TATTTTATAC
1456821 ATTTTT ATTTTT ATATTTT ATTTTT ATTTATT AT
1 ATTTTT ATTTTT AT-TTTT ATTTTT ATTT-TT AT
1456855 CAATGTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 16 0.62
7 10 0.38
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (6 bp):
ATTTTT
Found at i:1456854 original size:13 final size:12
Alignment explanation
Indices: 1456821--1456854 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
1456811 TATTTTATAC
1456821 ATTTTTATTTTT
1 ATTTTTATTTTT
1456833 ATATTTTATTTTT
1 AT-TTTTATTTTT
1456846 ATTTATTAT
1 ATTT-TTAT
1456855 CAATGTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
ATTTTTATTTTT
Found at i:1456864 original size:20 final size:20
Alignment explanation
Indices: 1456841--1456889 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1456831 TTATATTTTA
1456841 TTTTTATTTA-TTATCAATG
1 TTTTTATTTATTTATCAATG
1456860 TTTTTATTTATTTATCAATG
1 TTTTTATTTATTTATCAATG
*
1456880 TTTTTTTTTA
1 TTTTTATTTA
1456890 AATCTAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.69
Consensus pattern (20 bp):
TTTTTATTTATTTATCAATG
Found at i:1456889 original size:16 final size:19
Alignment explanation
Indices: 1456842--1456883 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
1456832 TATATTTTAT
1456842 TTTTATTTA-TTATCAATG
1 TTTTATTTATTTATCAATG
1456860 TTTTTATTTATTTATCAATG
1 -TTTTATTTATTTATCAATG
1456880 TTTT
1 TTTT
1456884 TTTTTAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTATTTATTTATCAATG
Found at i:1457339 original size:14 final size:15
Alignment explanation
Indices: 1457299--1457344 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1457289 CATGGCCATT
1457299 AAACCTTAAATCATA
1 AAACCTTAAATCATA
*
1457314 AAACCCTAAATCAT-
1 AAACCTTAAATCATA
* *
1457328 AGACCTTAAATCTTA
1 AAACCTTAAATCATA
1457343 AA
1 AA
1457345 TATTAAACCC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.50, C:0.22, G:0.02, T:0.26
Consensus pattern (15 bp):
AAACCTTAAATCATA
Found at i:1457532 original size:17 final size:18
Alignment explanation
Indices: 1457497--1457531 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1457487 AAGGTTATAG
1457497 ATTAGTGTTTAGGGTTTT
1 ATTAGTGTTTAGGGTTTT
1457515 ATTAG-GTTTAAGGGTTT
1 ATTAGTGTTT-AGGGTTT
1457532 AAGAGTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (18 bp):
ATTAGTGTTTAGGGTTTT
Found at i:1459403 original size:16 final size:16
Alignment explanation
Indices: 1459356--1459407 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
1459346 AGGGGTTATA
1459356 GTTTAGT-TTTTAGGGG
1 GTTTAGTGTTTTA-GGG
*
1459372 GTTTTTA-TGATTTAGGG
1 G--TTTAGTGTTTTAGGG
1459389 GTTTAGTGTTTTAGGG
1 GTTTAGTGTTTTAGGG
1459405 GTT
1 GTT
1459408 ATAGATTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
15 4 0.13
16 13 0.43
17 5 0.17
18 8 0.27
ACGTcount: A:0.13, C:0.00, G:0.35, T:0.52
Consensus pattern (16 bp):
GTTTAGTGTTTTAGGG
Found at i:1459527 original size:41 final size:41
Alignment explanation
Indices: 1459462--1459641 Score: 288
Period size: 41 Copynumber: 4.4 Consensus size: 41
1459452 ATTATATGAC
* *
1459462 TTTTAGCGGCTTTTTTACCAAAAGCGCCGTTAATGCTCTGGT
1 TTTTAGCGGC-GTTTTACCAAAAGCGCCGCTAATGCTCTGGT
*
1459504 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
*
1459545 TTTTAGCGGCGCTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* *
1459586 TTTTAACGGCGTTTCACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
*
1459627 TTTTAGCGGTGTTTT
1 TTTTAGCGGCGTTTT
1459642 TTGATAAAAC
Statistics
Matches: 127, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
41 117 0.92
42 10 0.08
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.34
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
Found at i:1459841 original size:12 final size:12
Alignment explanation
Indices: 1459824--1459853 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1459814 ACAAAATCCG
1459824 AATTTAATTTCC
1 AATTTAATTTCC
*
1459836 AATTTAATTTCT
1 AATTTAATTTCC
1459848 AATTTA
1 AATTTA
1459854 TTTAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (12 bp):
AATTTAATTTCC
Found at i:1466260 original size:13 final size:13
Alignment explanation
Indices: 1466242--1466266 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1466232 TGAAGTGTTA
1466242 AAGATCAAGCTGG
1 AAGATCAAGCTGG
1466255 AAGATCAAGCTG
1 AAGATCAAGCTG
1466267 TTGGAATATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.28, T:0.16
Consensus pattern (13 bp):
AAGATCAAGCTGG
Found at i:1471452 original size:16 final size:13
Alignment explanation
Indices: 1471419--1471446 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1471409 GGATGAAGTG
1471419 TGGAAGATCAAGC
1 TGGAAGATCAAGC
1471432 TGGAAGATCAAGC
1 TGGAAGATCAAGC
1471445 TG
1 TG
1471447 CTGGAATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.14, G:0.32, T:0.18
Consensus pattern (13 bp):
TGGAAGATCAAGC
Done.