Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold962
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1469792
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.31
Warning! 91164 characters in sequence are not A, C, G, or T
File 5 of 4
Found at i:1162631 original size:4 final size:4
Alignment explanation
Indices: 1162622--1162679 Score: 62
Period size: 4 Copynumber: 14.5 Consensus size: 4
1162612 AATTTTTGTT
* * * * * *
1162622 ACGG ACGG ACAG ACAG ACGG ACAG ACAG ACAG ACGG ACGG ACGG ACAG
1 ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG
1162670 ACGG ACGG AC
1 ACGG ACGG AC
1162680 AGACAGACAC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.36, C:0.26, G:0.38, T:0.00
Consensus pattern (4 bp):
ACGG
Found at i:1162642 original size:12 final size:12
Alignment explanation
Indices: 1162625--1162687 Score: 90
Period size: 12 Copynumber: 5.2 Consensus size: 12
1162615 TTTTGTTACG
1162625 GACGGACAGACA
1 GACGGACAGACA
1162637 GACGGACAGACA
1 GACGGACAGACA
* * *
1162649 GACAGACGGACG
1 GACGGACAGACA
*
1162661 GACGGACAGACG
1 GACGGACAGACA
1162673 GACGGACAGACA
1 GACGGACAGACA
1162685 GAC
1 GAC
1162688 ACACAAGGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 45 1.00
ACGTcount: A:0.38, C:0.25, G:0.37, T:0.00
Consensus pattern (12 bp):
GACGGACAGACA
Found at i:1162643 original size:16 final size:16
Alignment explanation
Indices: 1162622--1162687 Score: 114
Period size: 16 Copynumber: 4.1 Consensus size: 16
1162612 AATTTTTGTT
1162622 ACGGACGGACAGACAG
1 ACGGACGGACAGACAG
*
1162638 ACGGACAGACAGACAG
1 ACGGACGGACAGACAG
*
1162654 ACGGACGGACGGACAG
1 ACGGACGGACAGACAG
1162670 ACGGACGGACAGACAG
1 ACGGACGGACAGACAG
1162686 AC
1 AC
1162688 ACACAAGGGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.38, C:0.26, G:0.36, T:0.00
Consensus pattern (16 bp):
ACGGACGGACAGACAG
Found at i:1162684 original size:4 final size:4
Alignment explanation
Indices: 1162629--1162688 Score: 66
Period size: 4 Copynumber: 15.0 Consensus size: 4
1162619 GTTACGGACG
* * * * * *
1162629 GACA GACA GACG GACA GACA GACA GACG GACG GACG GACA GACG GACG
1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA
1162677 GACA GACA GACA
1 GACA GACA GACA
1162689 CACAAGGGTA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.40, C:0.25, G:0.35, T:0.00
Consensus pattern (4 bp):
GACA
Found at i:1164386 original size:2 final size:2
Alignment explanation
Indices: 1164381--1164455 Score: 143
Period size: 2 Copynumber: 38.0 Consensus size: 2
1164371 TCAAAAAATA
1164381 TC TC TC 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 TC TC TC
1164423 TC T- 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
1164456 CACACATTGA
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 71 0.99
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1165322 original size:23 final size:22
Alignment explanation
Indices: 1165303--1165345 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1165293 TACTATAGGT
1165303 ATAAAAAAAATATTTTTATATAG
1 ATAAAAAAAA-ATTTTTATATAG
*
1165326 ATATAAAAAAATTTTTATAT
1 ATAAAAAAAAATTTTTATAT
1165346 GAATCATCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
ATAAAAAAAAATTTTTATATAG
Found at i:1172868 original size:38 final size:38
Alignment explanation
Indices: 1172825--1173417 Score: 942
Period size: 38 Copynumber: 15.4 Consensus size: 38
1172815 TAATGGCCAC
1172825 TTTACCTGCACTATGACTATGGGAGTTTTATTTGATAT
1 TTTACCTGCACTATGACTATGGGAGTTTTATTTGATAT
1172863 TTTACCTGCACTATGACTATGGGAGTTTTATTTGATAT
1 TTTACCTGCACTATGACTATGGGAGTTTTATTTGATAT
1172901 TTTACCTGCACTATGACTATGGGAGTTTTATTTGATAT
1 TTTACCTGCACTATGACTATGGGAGTTTTATTTGATAT
* *
1172939 TTTACCTGCACTATGACTATGGGAGTTTTGTTTAATAT
1 TTTACCTGCACTATGACTATGGGAGTTTTATTTGATAT
1172977 TTTACCTGCACTATGACTATGGGAGTTTTATTTGATAT
1 TTTACCTGCACTATGACTATGGGAGTTTTATTTGATAT
* *
1173015 TTTACCTGCACTATGACTATGGGAGTTTTGTTTAATAT
1 TTTACCTGCACTATGACTATGGGAGTTTTATTTGATAT
1173053 TTTACCTGCACTATGACTATGGGAGTTTTATTTGATAT
1 TTTACCTGCACTATGACTATGGGAGTTTTATTTGATAT
* *
1173091 TTTACCTGCACTATGACTATGGGAGTTTTGTTTAATAT
1 TTTACCTGCACTATGACTATGGGAGTTTTATTTGATAT
1173129 TTTACCTGCACTATGACTATGGGAGTTTTATTTGATAT
1 TTTACCTGCACTATGACTATGGGAGTTTTATTTGATAT
1173167 TTTACCTGCACTATGACTATGGGAGTTTTATTTGATAT
1 TTTACCTGCACTATGACTATGGGAGTTTTATTTGATAT
1173205 TTTA-CTGCACTATGACTATCATAATGGGAGTTTTATTTGATAT
1 TTTACCTGCACTATG---A-C-T-ATGGGAGTTTTATTTGATAT
* * *
1173248 TTTA-CTGAACTAGGACTATGTGAGTTTTATTTGATAT
1 TTTACCTGCACTATGACTATGGGAGTTTTATTTGATAT
1173285 TTTACCTGCACTATGACTATGGGAGTTTTATTTGATAT
1 TTTACCTGCACTATGACTATGGGAGTTTTATTTGATAT
1173323 TTTA-CTGCACTATGACTATCATAATGGGAGTTTTATTTGATAT
1 TTTACCTGCACTATG---A-C-T-ATGGGAGTTTTATTTGATAT
* * *
1173366 TTTA-CTGAACTAGGACTATGTGAGTTTTATTTGATAT
1 TTTACCTGCACTATGACTATGGGAGTTTTATTTGATAT
1173403 TTTACCTGCACTATG
1 TTTACCTGCACTATG
1173418 GTTGTTATTA
Statistics
Matches: 518, Mismatches: 23, Indels: 28
0.91 0.04 0.05
Matches are distributed among these distances:
37 66 0.13
38 378 0.73
39 2 0.00
40 4 0.01
41 2 0.00
42 2 0.00
43 64 0.12
ACGTcount: A:0.25, C:0.13, G:0.18, T:0.45
Consensus pattern (38 bp):
TTTACCTGCACTATGACTATGGGAGTTTTATTTGATAT
Found at i:1181976 original size:163 final size:164
Alignment explanation
Indices: 1181785--1182136 Score: 537
Period size: 165 Copynumber: 2.1 Consensus size: 164
1181775 TTGCATTATA
* * *
1181785 GTTCTTAAGAAGAAGATTTTAAAACATTTTCCTAT-ATAAT-TATGTTAAAATCTAAACCCCTCC
1 GTTCTTGAGAAGAAGATTTTTAAACATTTTCCTATCAT-ATCTATGTTAAAATCTAAACCCCGCC
* * * *
1181848 TGGGGCCCCACTTTTTGTTCGGGGGTCACGATTTTTACAATTTAGAATTTTCACTATATATACAA
65 TGGGGCCCCACTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACAA
*
1181913 GCTTTTGTGTAAATATTGGCATTTCTGGTGCAGTG
130 GCTTTTGTGTAAAAATTGGCATTTCTGGTGCAGTG
* * * * * *
1181948 GTTCTTGAGAAGAAGATTTTTTAACATTTTCCTATGCATTTCTATGTTTAACTTTGAACCCCGCC
1 GTTCTTGAGAAGAAGATTTTTAAACATTTTCCTAT-CATATCTATGTTAAAATCTAAACCCCGCC
*
1182013 TGGGGCCCCAGTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACAA
65 TGGGGCCCCACTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACAA
1182078 GCTTTTGTGTAAAAATTGGCATTTCTGGTGCAGTG
130 GCTTTTGTGTAAAAATTGGCATTTCTGGTGCAGTG
1182113 GTTCTTGAGAAGAAGATTTTTAAA
1 GTTCTTGAGAAGAAGATTTTTAAA
1182137 GACATGCACC
Statistics
Matches: 170, Mismatches: 16, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
163 32 0.19
164 1 0.01
165 137 0.81
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.38
Consensus pattern (164 bp):
GTTCTTGAGAAGAAGATTTTTAAACATTTTCCTATCATATCTATGTTAAAATCTAAACCCCGCCT
GGGGCCCCACTTTTGGTCCGAGGGTCACGATTTTTACAATTTAGAATCTTCACTATATATACAAG
CTTTTGTGTAAAAATTGGCATTTCTGGTGCAGTG
Found at i:1182320 original size:12 final size:12
Alignment explanation
Indices: 1182303--1182340 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1182293 TGAAAAGTTT
1182303 ACAGACAGACGG
1 ACAGACAGACGG
1182315 ACAGACAGACGG
1 ACAGACAGACGG
*
1182327 ACGGAC-GACGG
1 ACAGACAGACGG
1182338 ACA
1 ACA
1182341 AGGGGTGATC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 7 0.29
12 17 0.71
ACGTcount: A:0.39, C:0.26, G:0.34, T:0.00
Consensus pattern (12 bp):
ACAGACAGACGG
Found at i:1188269 original size:2 final size:2
Alignment explanation
Indices: 1188262--1188296 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1188252 ATCTATTTTA
1188262 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1188297 CTAGCATACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1195656 original size:3 final size:3
Alignment explanation
Indices: 1195648--1195706 Score: 91
Period size: 3 Copynumber: 19.3 Consensus size: 3
1195638 GTAATTATCG
* *
1195648 TCA TCA TCA TCA TCA TCA TCAA TCA TCT TCA TCA CCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TC-A TCA TCA TCA TCA TCA TCA TCA TCA
1195694 TCA TCA TCA TCA T
1 TCA TCA TCA TCA T
1195707 TTATTCCTTC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
3 48 0.94
4 3 0.06
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:1196584 original size:16 final size:16
Alignment explanation
Indices: 1196563--1196612 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1196553 TAACAAATTT
1196563 ACTCTTGATTTCTCGA
1 ACTCTTGATTTCTCGA
* *
1196579 ACTCTTGATCTCTCAAA
1 ACTCTTGATTTCTC-GA
* *
1196596 ACCCTTGATTCCTCGA
1 ACTCTTGATTTCTCGA
1196612 A
1 A
1196613 GTCAAACTGC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
16 15 0.56
17 12 0.44
ACGTcount: A:0.24, C:0.30, G:0.10, T:0.36
Consensus pattern (16 bp):
ACTCTTGATTTCTCGA
Found at i:1197342 original size:16 final size:16
Alignment explanation
Indices: 1197321--1197356 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1197311 CGGAAAATTC
1197321 CGAACTCTTGAAAACT
1 CGAACTCTTGAAAACT
*
1197337 CGAACTCTTGAAACCT
1 CGAACTCTTGAAAACT
1197353 CGAA
1 CGAA
1197357 GTTTTTCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.28, G:0.14, T:0.22
Consensus pattern (16 bp):
CGAACTCTTGAAAACT
Found at i:1199602 original size:2 final size:2
Alignment explanation
Indices: 1199597--1199639 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1199587 TGATTTGATT
1199597 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1199639 G
1 G
1199640 GGGGGGGGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1204316 original size:171 final size:170
Alignment explanation
Indices: 1203978--1204514 Score: 678
Period size: 171 Copynumber: 3.2 Consensus size: 170
1203968 AAAGAATCAT
* * *
1203978 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTTAAGATTTACTCTATATATTCATATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGGAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* * * * * *
1204043 TT-AACATCCCCCCAATGTGGCCCCACCCTACCCCCCGGGATCACGATTTTCACAACTTTGAATC
66 TTCCACAACCCCCCATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAACTTTGAATC
1204107 TACACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTC
131 TACACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTC
* *
1204147 TTGGCTGATTAGTTTATGAGGAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGGAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* ** * *
1204212 TTCCCCCCCCCCCCCCATTGT-GCCCCAGCCTACCACCAGGGGTCATGATTTTCACAACTTTGAA
66 TT--CCACAACCCCCCATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAACTTTGAA
*
1204276 TCTACACTACCTGAGGATACCTCCACACAAGTTTCAGCTTTC
129 TCTACACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTC
* * *
1204318 CTGGCTGATTAATTCCTG-GGAAGAAGATTTTTAAAGATTTACTCTATATATTTCTATGTAAAA-
1 CTGGCTGATTAGTTTCTGAGG-AGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAAC
* * ** * *
1204381 ---CCTCGACTTCCCATTGTGGTCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAAT
65 TTTCCACAACCCCCCATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAACTTTGAAT
* ** *
1204443 CTACATTACCTGAAAATGCTTCCACACAAGTTTCAGCTTTC
130 CTACACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTC
* *
1204484 CTGGCT--TTATGGTTCTTGAGAAGAAGATTTT
1 CTGGCTGATTA-GTTTC-TGAGGAGAAGATTTT
1204515 GAAAATTCTC
Statistics
Matches: 321, Mismatches: 39, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
164 3 0.01
165 14 0.04
166 94 0.29
167 1 0.00
169 62 0.19
170 2 0.01
171 134 0.42
172 11 0.03
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (170 bp):
CTGGCTGATTAGTTTCTGAGGAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
TTCCACAACCCCCCATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAACTTTGAATC
TACACTACCTGAGGATACTTCCACACAAGTTTCAGCTTTC
Found at i:1244003 original size:2 final size:2
Alignment explanation
Indices: 1243998--1244026 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1243988 TTATTAAAAA
1243998 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1244027 AAATCAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1246032 original size:165 final size:164
Alignment explanation
Indices: 1245759--1246089 Score: 644
Period size: 165 Copynumber: 2.0 Consensus size: 164
1245749 TCGTTCACGT
1245759 TAATATTCTGTTCTAAAAACAAGGATTCCATCATATCACATTTGACCTCGAAGCCGTATTTTTTG
1 TAATATTCTGTTCTAAAAACAAGGATTCCATCATATCACATTTGACCTCGAAGCCGTATTTTTTG
1245824 AGCTTGTTACACATGGTTAGCACCTCCTTGATATGATATTTAGAATCATCAGCTAGTGAGACAAA
66 AGCTTGTTACACATGGTTAGCACCTCCTTGATATGATATTTAGAATCATCAGCTAGTGAGACAAA
1245889 CACCGTCCTGGGTCCTGTAAAGAAAAATACACAG
131 CACCGTCCTGGGTCCTGTAAAGAAAAATACACAG
*
1245923 TNAATATTCTGTTCTAAAAACAAGGATTCCATCATATCACATTTGCCCTCGAAGCCGTATTTTTT
1 T-AATATTCTGTTCTAAAAACAAGGATTCCATCATATCACATTTGACCTCGAAGCCGTATTTTTT
1245988 GAGCTTGTTACACATGGTTAGCACCTCCTTGATATGATATTTAGAATCATCAGCTAGTGAGACAA
65 GAGCTTGTTACACATGGTTAGCACCTCCTTGATATGATATTTAGAATCATCAGCTAGTGAGACAA
1246053 ACACCGTCCTGGGTCCTGTAAAGAAAAATACACAG
130 ACACCGTCCTGGGTCCTGTAAAGAAAAATACACAG
1246088 TA
1 TA
1246090 GCTTAATTAT
Statistics
Matches: 165, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
164 2 0.01
165 163 0.99
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (164 bp):
TAATATTCTGTTCTAAAAACAAGGATTCCATCATATCACATTTGACCTCGAAGCCGTATTTTTTG
AGCTTGTTACACATGGTTAGCACCTCCTTGATATGATATTTAGAATCATCAGCTAGTGAGACAAA
CACCGTCCTGGGTCCTGTAAAGAAAAATACACAG
Found at i:1246124 original size:2 final size:2
Alignment explanation
Indices: 1246117--1246191 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
1246107 AAGACACAAT
1246117 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1246159 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1246192 NNNNNNNNNN
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1246885 original size:2 final size:2
Alignment explanation
Indices: 1246880--1246908 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1246870 TTATTAAAAA
1246880 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1246909 AAATCAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1248371 original size:198 final size:197
Alignment explanation
Indices: 1248033--1248428 Score: 783
Period size: 198 Copynumber: 2.0 Consensus size: 197
1248023 ACAACACCCA
1248033 TTTATCCTATAGATTATTTATTGTGAATAACATACTCATAACATATGTACATAAGAATTATAAAC
1 TTTATCCTATAGATTATTTATTGTGAATAACATACTCATAACATATGTACATAAGAATTATAAAC
1248098 CGATAACAAATATCTTATTCATCTTGCAACAATAATGGAAAGTGCCTGCAAAATATATAGTATAT
66 CGATAACAAATATCTTATTCATCTTGCAACAATAATGGAAAGTGCCTGCAAAATATATAGTATAT
1248163 AATACATTTATAACTGTATCTTTATCTAGCGAGTTTATATATCTGGTAACATATTGGGTATATGT
131 AATACATTTATAACTGTATCTTTATCTAGCGAGTTTATATATCTGGTAACATATTGGGTATATGT
1248228 TT
196 TT
1248230 NTTTATCCTATAGATTATTTATTGTGAATAACATACTCATAACATATGTACATAAGAATTATAAA
1 -TTTATCCTATAGATTATTTATTGTGAATAACATACTCATAACATATGTACATAAGAATTATAAA
1248295 CCGATAACAAATATCTTATTCATCTTGCAACAATAATGGAAAGTGCCTGCAAAATATATAGTATA
65 CCGATAACAAATATCTTATTCATCTTGCAACAATAATGGAAAGTGCCTGCAAAATATATAGTATA
1248360 TAATACATTTATAACTGTATCTTTATCTAGCGAGTTTATATATCTGGTAACATATTGGGTATATG
130 TAATACATTTATAACTGTATCTTTATCTAGCGAGTTTATATATCTGGTAACATATTGGGTATATG
1248425 TTT
195 TTT
1248428 T
1 T
1248429 AACAATCTGT
Statistics
Matches: 198, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
197 1 0.01
198 197 0.99
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (197 bp):
TTTATCCTATAGATTATTTATTGTGAATAACATACTCATAACATATGTACATAAGAATTATAAAC
CGATAACAAATATCTTATTCATCTTGCAACAATAATGGAAAGTGCCTGCAAAATATATAGTATAT
AATACATTTATAACTGTATCTTTATCTAGCGAGTTTATATATCTGGTAACATATTGGGTATATGT
TT
Found at i:1249030 original size:2 final size:2
Alignment explanation
Indices: 1249023--1249098 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
1249013 ATCGTACATA
1249023 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1249065 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1249099 GTTTATAGTT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1254215 original size:27 final size:27
Alignment explanation
Indices: 1254179--1254253 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
1254169 TATGTCTTTG
*
1254179 AAAGACCATGAATATCTTAATTGTTGA
1 AAAGTCCATGAATATCTTAATTGTTGA
* *
1254206 ACATTCCATGAATATC-TATATTGTTGA
1 AAAGTCCATGAATATCTTA-ATTGTTGA
1254233 AAAGTCCATGAATAT-TTAATT
1 AAAGTCCATGAATATCTTAATT
1254254 TGTTTGACTC
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
26 5 0.12
27 36 0.88
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (27 bp):
AAAGTCCATGAATATCTTAATTGTTGA
Found at i:1254550 original size:16 final size:17
Alignment explanation
Indices: 1254529--1254561 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1254519 CACACGTTGA
1254529 ACAAGTGTAC-TAAAGT
1 ACAAGTGTACTTAAAGT
1254545 ACAAGTGTACTTAAAGT
1 ACAAGTGTACTTAAAGT
1254562 GTACTCAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.27
Consensus pattern (17 bp):
ACAAGTGTACTTAAAGT
Found at i:1262614 original size:16 final size:17
Alignment explanation
Indices: 1262593--1262627 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1262583 CAAACTCCAA
1262593 TTTTTT-CAATTTGATT
1 TTTTTTCCAATTTGATT
*
1262609 TTTTTTCCAGTTTGATT
1 TTTTTTCCAATTTGATT
1262626 TT
1 TT
1262628 AATTTTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.14, C:0.09, G:0.09, T:0.69
Consensus pattern (17 bp):
TTTTTTCCAATTTGATT
Found at i:1262919 original size:17 final size:16
Alignment explanation
Indices: 1262897--1262933 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
1262887 TTTGGTCAGT
1262897 TTTACACATAGAACTTA
1 TTTACACA-AGAACTTA
1262914 TTT--ACAAGAACTTA
1 TTTACACAAGAACTTA
1262928 TTTACA
1 TTTACA
1262934 GAATTAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 5
0.78 0.00 0.22
Matches are distributed among these distances:
14 11 0.61
15 3 0.17
16 1 0.06
17 3 0.17
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (16 bp):
TTTACACAAGAACTTA
Found at i:1262925 original size:14 final size:14
Alignment explanation
Indices: 1262906--1262933 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1262896 TTTTACACAT
1262906 AGAACTTATTTACA
1 AGAACTTATTTACA
1262920 AGAACTTATTTACA
1 AGAACTTATTTACA
1262934 GAATTAATTC
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:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
AGAACTTATTTACA
Found at i:1270494 original size:182 final size:182
Alignment explanation
Indices: 1270187--1270623 Score: 856
Period size: 182 Copynumber: 2.4 Consensus size: 182
1270177 CTCGGTAAAT
*
1270187 AGGCGCAAGGCGCCTAAACTAGGACTTGTGACAATTAGGTGACCCCGGATTCCTGAGGGTGGGGG
1 AGGCGCAGGGCGCCTAAACTAGGACTTGTGACAATTAGGTGACCCCGGATTCCTGAGGGTGGGGG
1270252 TCCTGCCCGGGGGTGACCGGTCTCAGAACCTTCAATAATTATGCCGTTCTTGGCCCCACGGCGCC
66 TCCTGCCCGGGGGTGACCGGTCTCAGAACCTTCAATAATTATGCCGTTCTTGGCCCCACGGCGCC
*
1270317 CTGAATAATTGTTATAATAACTATATTATCATATTATATAGGGACATAAACA
131 CTGAATAATCGTTATAATAACTATATTATCATATTATATAGGGACATAAACA
1270369 AGGCGCAGGGCGCCTAAACTAGGACTTGTGACAATTAGGTGACCCCGGATTCCTGAGGGTGGGGG
1 AGGCGCAGGGCGCCTAAACTAGGACTTGTGACAATTAGGTGACCCCGGATTCCTGAGGGTGGGGG
1270434 TCCTGCCCGGGGGTGACCGGTCTCAGAACCTTCAATAATTATGCCGTTCTTGGCCCCACGGCGCC
66 TCCTGCCCGGGGGTGACCGGTCTCAGAACCTTCAATAATTATGCCGTTCTTGGCCCCACGGCGCC
1270499 CTGAATAATCGTTATAATAACTATATTATCATATTATATAGGGACATAAACA
131 CTGAATAATCGTTATAATAACTATATTATCATATTATATAGGGACATAAACA
1270551 AGGCGCAGGGCGCCTAAACTAGGACTTGTGACAATTAGGTGACCCCGGATTCCTGAGGGTGGGGG
1 AGGCGCAGGGCGCCTAAACTAGGACTTGTGACAATTAGGTGACCCCGGATTCCTGAGGGTGGGGG
1270616 TCCTGCCC
66 TCCTGCCC
1270624 NNNNNNNNNN
Statistics
Matches: 253, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
182 253 1.00
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (182 bp):
AGGCGCAGGGCGCCTAAACTAGGACTTGTGACAATTAGGTGACCCCGGATTCCTGAGGGTGGGGG
TCCTGCCCGGGGGTGACCGGTCTCAGAACCTTCAATAATTATGCCGTTCTTGGCCCCACGGCGCC
CTGAATAATCGTTATAATAACTATATTATCATATTATATAGGGACATAAACA
Found at i:1271533 original size:182 final size:182
Alignment explanation
Indices: 1271226--1271625 Score: 791
Period size: 182 Copynumber: 2.2 Consensus size: 182
1271216 NNNNNNNNNN
1271226 AATTGTCACAAGTCCTAGTTTAGGCGCCCTGCGCCTTGTTTATGTCCCTATATAATATGATAATA
1 AATTGTCACAAGTCCTAGTTTAGGCGCCCTGCGCCTTGTTTATGTCCCTATATAATATGATAATA
1271291 TAGTTATTATAACAATTATTCAGGGCGCCGTGGGGCCAAGAACGGCATAATTATTGAAGGTTCTG
66 TAGTTATTATAACAATTATTCAGGGCGCCGTGGGGCCAAGAACGGCATAATTATTGAAGGTTCTG
1271356 AGACCGGTCACCCCCGGGCAGGACCCCCACCCTCAGGAATCCGGGGTCACCT
131 AGACCGGTCACCCCCGGGCAGGACCCCCACCCTCAGGAATCCGGGGTCACCT
1271408 AATTGTCACAAGTCCTAGTTTAGGCGCCCTGCGCCTTGTTTATGTCCCTATATAATATGATAATA
1 AATTGTCACAAGTCCTAGTTTAGGCGCCCTGCGCCTTGTTTATGTCCCTATATAATATGATAATA
1271473 TAGTTATTATAACAATTATTCAGGGCGCCGTGGGGCCAAGAACGGCATAATTATTGAAGGTTCTG
66 TAGTTATTATAACAATTATTCAGGGCGCCGTGGGGCCAAGAACGGCATAATTATTGAAGGTTCTG
1271538 AGACCGGTCACCCCCGGGCAGGACCCCCACCCTCAGGAATCCGGGGTCACCT
131 AGACCGGTCACCCCCGGGCAGGACCCCCACCCTCAGGAATCCGGGGTCACCT
*
1271590 AATTGTCACAAGTCCTAGTTTAGGCGCCTTGCGCCT
1 AATTGTCACAAGTCCTAGTTTAGGCGCCCTGCGCCT
1271626 ATTTACCGAG
Statistics
Matches: 217, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
182 217 1.00
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (182 bp):
AATTGTCACAAGTCCTAGTTTAGGCGCCCTGCGCCTTGTTTATGTCCCTATATAATATGATAATA
TAGTTATTATAACAATTATTCAGGGCGCCGTGGGGCCAAGAACGGCATAATTATTGAAGGTTCTG
AGACCGGTCACCCCCGGGCAGGACCCCCACCCTCAGGAATCCGGGGTCACCT
Found at i:1271834 original size:2 final size:2
Alignment explanation
Indices: 1271827--1271897 Score: 124
Period size: 2 Copynumber: 35.5 Consensus size: 2
1271817 GAAATTCAAC
* *
1271827 GA GA GA GA GA GA GA GA GA GA GA CA GA GA GA CA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1271869 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1271898 GGAGGATATT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.03, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1273628 original size:172 final size:167
Alignment explanation
Indices: 1273296--1273876 Score: 686
Period size: 168 Copynumber: 3.4 Consensus size: 167
1273286 CTCCCCATGT
* * * *
1273296 CCTGAACCCCTGACCCAGGGGCCATGAATTTCATAATTTTGGTAGAGGAG--TAAGTGGACATCA
1 CCTGAACCCCTGACACAGGGGTCATGAATTTCACAATTTTGGTAGAGG-GCTTCA-TGGACATCA
* * ** ** * * * * * * * * *
1273359 TAACCATGTATTCAGTTTTTTGCCCACATGTTTGGGATTAAAAAAGAAGATTTTTTAAGATTTAT
64 TAACCATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATGTTCTAAGATTTAA
* *
1273424 TACATTTTTACCATATGGT-CATATTAGCCCAACCCTAGAG
129 TACATTTTTACTATAT--TCCATATTGGCCCAACCCTAGAG
* * *
1273464 CCTGAACCCCTGACACAGGGGTAATTAATTTCACAATTTTGGTAGATGGGCTTCATAGACATCAT
1 CCTGAACCCCTGACACAGGGGTCATGAATTTCACAATTTTGGTAGA-GGGCTTCATGGACATCAT
* * *
1273529 AATCATGCATTTATTTTTTAACAAATATATCTGGGATCAGTAGAGAAGAAGATGTTCTAAGATTT
65 AACCATGCATTTAGTTTTTAACAAATATATATGGG---AGTAGAGAAGAAGATGTTCTAAGATTT
*
1273594 AATACATTTTTTCTATATATCCATATTGGCCCAACCCTAGAG
127 AATACATTTTTACTATAT-TCCATATTGGCCCAACCCTAGAG
* * *
1273636 CCTAAACCCCTGAAAGAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACAT-ACT
1 CCTGAACCCCTGACACAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCA-T
*
1273700 AACCATGCATTTAGTTTTTAACAAATGTATATGGGAGTAGAGAAGAAGATGTTCTAAGATTTAAT
65 AACCATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATGTTCTAAGATTTAAT
1273765 ACATTTTTACTATATTGCCATATTGGTCCC-ACCCTAGAG
130 ACATTTTTACTATATT-CCATATTGG-CCCAACCCTAGAG
* * * * *
1273804 GCAGAACCACTGACCCAGGGGCCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATA
1 CCTGAACCCCTGACACAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATA
1273869 ACCATGCA
66 ACCATGCA
1273877 ACCATTTTAT
Statistics
Matches: 355, Mismatches: 47, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
167 1 0.00
168 167 0.47
169 39 0.11
170 3 0.01
171 47 0.13
172 98 0.28
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (167 bp):
CCTGAACCCCTGACACAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCTTCATGGACATCATA
ACCATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATGTTCTAAGATTTAATA
CATTTTTACTATATTCCATATTGGCCCAACCCTAGAG
Found at i:1274200 original size:2 final size:2
Alignment explanation
Indices: 1274193--1274227 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1274183 CACTTTAAAA
*
1274193 TC TC TC TC TC TC TC TC TC TC TC CC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1274228 TAGCGTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:1286503 original size:1 final size:1
Alignment explanation
Indices: 1286497--1286522 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1286487 NNNAAACATT
1286497 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
1286523 TTTATTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1286684 original size:2 final size:2
Alignment explanation
Indices: 1286677--1286709 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
1286667 AATGTTTCTT
1286677 TA TA TA TA TA TA TA TA TNA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
1286710 AAATTCTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1286700 original size:15 final size:14
Alignment explanation
Indices: 1286677--1286709 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
1286667 AATGTTTCTT
1286677 TATATATATATATA
1 TATATATATATATA
1286691 TATNATATATATATA
1 TAT-ATATATATATA
1286706 TATA
1 TATA
1286710 AAATTCTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TATATATATATATA
Found at i:1289773 original size:12 final size:12
Alignment explanation
Indices: 1289756--1289787 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1289746 GATAACATTA
1289756 ATTTACATCGAT
1 ATTTACATCGAT
1289768 ATTTACATCGAT
1 ATTTACATCGAT
*
1289780 AATTACAT
1 ATTTACAT
1289788 TATAACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.41
Consensus pattern (12 bp):
ATTTACATCGAT
Found at i:1305098 original size:21 final size:21
Alignment explanation
Indices: 1305074--1305121 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1305064 ATGGTTTAAC
*
1305074 TTGTTTGTCTTGTTTT-TTGTT
1 TTGTTTGGCTT-TTTTGTTGTT
*
1305095 TTGTTTGGGTTTTTTGTTGTT
1 TTGTTTGGCTTTTTTGTTGTT
1305116 TTGTTT
1 TTGTTT
1305122 ATTATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.00, C:0.02, G:0.23, T:0.75
Consensus pattern (21 bp):
TTGTTTGGCTTTTTTGTTGTT
Found at i:1340558 original size:22 final size:22
Alignment explanation
Indices: 1340533--1340575 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1340523 CAAATTTGTC
1340533 TATTGTTCGATCAATATAATTA
1 TATTGTTCGATCAATATAATTA
*
1340555 TATTTTTCGATCAATATAATT
1 TATTGTTCGATCAATATAATT
1340576 CTGTGAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (22 bp):
TATTGTTCGATCAATATAATTA
Found at i:1352598 original size:12 final size:12
Alignment explanation
Indices: 1352581--1352635 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
1352571 ATCTTCAGTT
*
1352581 GTCATCATCGTC
1 GTCATCATCATC
1352593 GTCATCATCATC
1 GTCATCATCATC
* * *
1352605 ATCATCGTCGTC
1 GTCATCATCATC
1352617 GTCATCATCATC
1 GTCATCATCATC
1352629 GTCATCA
1 GTCATCA
1352636 ACGAATAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.22, C:0.33, G:0.13, T:0.33
Consensus pattern (12 bp):
GTCATCATCATC
Found at i:1352600 original size:3 final size:3
Alignment explanation
Indices: 1352582--1352635 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
1352572 TCTTCAGTTG
* * * * * *
1352582 TCA TCA TCG TCG TCA TCA TCA TCA TCA TCG TCG TCG TCA TCA TCA TCG
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1352630 TCA TCA
1 TCA TCA
1352636 ACGAATAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.22, C:0.33, G:0.11, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:1352605 original size:18 final size:18
Alignment explanation
Indices: 1352582--1352635 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
1352572 TCTTCAGTTG
*
1352582 TCATCATCGTCGTCATCA
1 TCATCATCATCGTCATCA
* *
1352600 TCATCATCATCGTCGTCG
1 TCATCATCATCGTCATCA
1352618 TCATCATCATCGTCATCA
1 TCATCATCATCGTCATCA
1352636 ACGAATAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.22, C:0.33, G:0.11, T:0.33
Consensus pattern (18 bp):
TCATCATCATCGTCATCA
Found at i:1352608 original size:21 final size:21
Alignment explanation
Indices: 1352582--1352628 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1352572 TCTTCAGTTG
1352582 TCATCATCGTCGTCATCATCA
1 TCATCATCGTCGTCATCATCA
*
1352603 TCATCATCGTCGTCGTCATCA
1 TCATCATCGTCGTCATCATCA
1352624 TCATC
1 TCATC
1352629 GTCATCAACG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.34, G:0.11, T:0.34
Consensus pattern (21 bp):
TCATCATCGTCGTCATCATCA
Found at i:1361229 original size:15 final size:15
Alignment explanation
Indices: 1361209--1361240 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1361199 ACTATATCTG
1361209 CGAATTCGTTATAAC
1 CGAATTCGTTATAAC
1361224 CGAATTCGTTATAAC
1 CGAATTCGTTATAAC
1361239 CG
1 CG
1361241 TAAAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (15 bp):
CGAATTCGTTATAAC
Found at i:1371561 original size:21 final size:21
Alignment explanation
Indices: 1371535--1371675 Score: 129
Period size: 21 Copynumber: 6.7 Consensus size: 21
1371525 TACAAGATAA
1371535 ACGATAGGATAGGATTCACGC
1 ACGATAGGATAGGATTCACGC
* *
1371556 ACGATAGGATAGCATTAACGC
1 ACGATAGGATAGGATTCACGC
* * * *
1371577 ACGATAGAACAGTATACACGC
1 ACGATAGGATAGGATTCACGC
* *
1371598 ACGAAAGGATAGGATTAACGC
1 ACGATAGGATAGGATTCACGC
* * * *
1371619 ACGATAGAACAGTATACACGC
1 ACGATAGGATAGGATTCACGC
* * **
1371640 ACGATATGATAGGATTGATAC
1 ACGATAGGATAGGATTCACGC
*
1371661 ACGATAGGAAAGGAT
1 ACGATAGGATAGGAT
1371676 AAACGATGTT
Statistics
Matches: 91, Mismatches: 29, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 91 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (21 bp):
ACGATAGGATAGGATTCACGC
Found at i:1371667 original size:42 final size:42
Alignment explanation
Indices: 1371551--1371655 Score: 183
Period size: 42 Copynumber: 2.5 Consensus size: 42
1371541 GGATAGGATT
*
1371551 CACGCACGATAGGATAGCATTAACGCACGATAGAACAGTATA
1 CACGCACGATAGGATAGGATTAACGCACGATAGAACAGTATA
*
1371593 CACGCACGAAAGGATAGGATTAACGCACGATAGAACAGTATA
1 CACGCACGATAGGATAGGATTAACGCACGATAGAACAGTATA
*
1371635 CACGCACGATATGATAGGATT
1 CACGCACGATAGGATAGGATT
1371656 GATACACGAT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (42 bp):
CACGCACGATAGGATAGGATTAACGCACGATAGAACAGTATA
Found at i:1372700 original size:21 final size:21
Alignment explanation
Indices: 1372666--1372799 Score: 110
Period size: 21 Copynumber: 6.4 Consensus size: 21
1372656 CGATAAACCT
*
1372666 GATAGGATTCACGCACGATAG
1 GATAGGATTAACGCACGATAG
*
1372687 GATAGCATTAACGCACGATAG
1 GATAGGATTAACGCACGATAG
* * * *
1372708 AACAGTA-TACACGCACGAAAG
1 GATAGGATTA-ACGCACGATAG
1372729 GATAGGATTAACGCACGATAG
1 GATAGGATTAACGCACGATAG
* * * *
1372750 AACAGTA-TACACGCACGATAC
1 GATAGGATTA-ACGCACGATAG
* ** *
1372771 GATAGGATTGATACACGATAC
1 GATAGGATTAACGCACGATAG
1372792 GATAGGAT
1 GATAGGAT
1372800 AGGATTGTAA
Statistics
Matches: 89, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
20 4 0.04
21 82 0.92
22 3 0.03
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.18
Consensus pattern (21 bp):
GATAGGATTAACGCACGATAG
Found at i:1372790 original size:42 final size:42
Alignment explanation
Indices: 1372675--1372779 Score: 183
Period size: 42 Copynumber: 2.5 Consensus size: 42
1372665 TGATAGGATT
*
1372675 CACGCACGATAGGATAGCATTAACGCACGATAGAACAGTATA
1 CACGCACGATAGGATAGGATTAACGCACGATAGAACAGTATA
*
1372717 CACGCACGAAAGGATAGGATTAACGCACGATAGAACAGTATA
1 CACGCACGATAGGATAGGATTAACGCACGATAGAACAGTATA
*
1372759 CACGCACGATACGATAGGATT
1 CACGCACGATAGGATAGGATT
1372780 GATACACGAT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.16
Consensus pattern (42 bp):
CACGCACGATAGGATAGGATTAACGCACGATAGAACAGTATA
Found at i:1387586 original size:19 final size:19
Alignment explanation
Indices: 1387549--1387588 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1387539 GAATACACTT
*
1387549 TTTTATGTATTTTTATGTA
1 TTTTATGTATTTCTATGTA
* *
1387568 TTTTGTGTATTTCTGTGTA
1 TTTTATGTATTTCTATGTA
1387587 TT
1 TT
1387589 GCAATAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.15, C:0.03, G:0.15, T:0.68
Consensus pattern (19 bp):
TTTTATGTATTTCTATGTA
Found at i:1394492 original size:2 final size:2
Alignment explanation
Indices: 1394485--1394511 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1394475 AGAATAATTT
1394485 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1394512 TGTTTCAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1394828 original size:2 final size:2
Alignment explanation
Indices: 1394821--1394874 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1394811 TGCAATTCTC
1394821 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1394863 AG AG AG AG AG AG
1 AG AG AG AG AG AG
1394875 GGGGGGATGG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1395241 original size:16 final size:16
Alignment explanation
Indices: 1395220--1395254 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1395210 CTAAATGGAT
*
1395220 CATGTGAAAATAGTTC
1 CATGTGAAAATAATTC
1395236 CATGTGAAAATAATTC
1 CATGTGAAAATAATTC
1395252 CAT
1 CAT
1395255 ATGAGAAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (16 bp):
CATGTGAAAATAATTC
Found at i:1398485 original size:23 final size:23
Alignment explanation
Indices: 1398455--1398503 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
1398445 TAATGCATTA
*
1398455 CTTTAAGGTACACTATTCACTAC
1 CTTTAAGGTACACTATCCACTAC
1398478 CTTTAAGGTACACTATCCACTAC
1 CTTTAAGGTACACTATCCACTAC
1398501 CTT
1 CTT
1398504 GAGGTATGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.35
Consensus pattern (23 bp):
CTTTAAGGTACACTATCCACTAC
Found at i:1404802 original size:2 final size:2
Alignment explanation
Indices: 1404791--1404826 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1404781 GCAAGTTTTT
*
1404791 TC TC TT 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
1404827 CAACAATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:1408779 original size:2 final size:2
Alignment explanation
Indices: 1408772--1408838 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
1408762 AATATTACAA
*
1408772 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1408814 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1408839 ATCCACTTAC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1420500 original size:10 final size:10
Alignment explanation
Indices: 1420485--1420509 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1420475 ACTCAATCTG
1420485 AAATATCTAA
1 AAATATCTAA
1420495 AAATATCTAA
1 AAATATCTAA
1420505 AAATA
1 AAATA
1420510 CAAAACATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (10 bp):
AAATATCTAA
Found at i:1447245 original size:16 final size:15
Alignment explanation
Indices: 1447220--1447250 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1447210 TAACACTTTG
1447220 TTCCTATACTGTAAA
1 TTCCTATACTGTAAA
1447235 TTCCTTATACTGTAAA
1 TTCC-TATACTGTAAA
1447251 CGTACTACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.42
Consensus pattern (15 bp):
TTCCTATACTGTAAA
Found at i:1450961 original size:49 final size:49
Alignment explanation
Indices: 1450885--1451232 Score: 479
Period size: 49 Copynumber: 7.0 Consensus size: 49
1450875 TACATGTATT
* *
1450885 TTACCTGTATGTTGACTTCGATTTGAGAGTGAGGACTTGTGAGGAGAAA
1 TTACCTGTATGTTGACCTGGATTTGAGAGTGAGGACTTGTGAGGAGAAA
* * *
1450934 TAAACTGTATGTTGACCTGGATTTGAGAGTGAGGAC-T-TGAGGGGAAA
1 TTACCTGTATGTTGACCTGGATTTGAGAGTGAGGACTTGTGAGGAGAAA
* * *
1450981 TTACCAGTATGTTGACCTGGATTTGAGAGTGAGGACTTGTCATGAGAAA
1 TTACCTGTATGTTGACCTGGATTTGAGAGTGAGGACTTGTGAGGAGAAA
*
1451030 TTACCTGTATGTTGACCTGGGTTGACCTGGATTTGAGAGTGAGGACTTGTGATGAGAAA
1 TTACC----TG-T-A--T--GTTGACCTGGATTTGAGAGTGAGGACTTGTGAGGAGAAA
1451089 TTACC--TATGTTGACCTGGATTTGAGAGTGAGGACTTGTGAGGAGAAA
1 TTACCTGTATGTTGACCTGGATTTGAGAGTGAGGACTTGTGAGGAGAAA
* *
1451136 TTACCTATATGTTGACCTGGATTTGAGAGTGAGGACATGTGAGGAGAAA
1 TTACCTGTATGTTGACCTGGATTTGAGAGTGAGGACTTGTGAGGAGAAA
1451185 TTACCTGTATGTTGACCTGGATTTGAGAGTGAGGACTTGTGAGGAGAA
1 TTACCTGTATGTTGACCTGGATTTGAGAGTGAGGACTTGTGAGGAGAA
1451233 TCCTGCAGAT
Statistics
Matches: 268, Mismatches: 17, Indels: 28
0.86 0.05 0.09
Matches are distributed among these distances:
47 85 0.32
48 2 0.01
49 132 0.49
51 1 0.00
52 1 0.00
53 1 0.00
54 1 0.00
55 1 0.00
57 1 0.00
59 43 0.16
ACGTcount: A:0.27, C:0.11, G:0.32, T:0.30
Consensus pattern (49 bp):
TTACCTGTATGTTGACCTGGATTTGAGAGTGAGGACTTGTGAGGAGAAA
Found at i:1451049 original size:96 final size:98
Alignment explanation
Indices: 1450885--1451232 Score: 479
Period size: 96 Copynumber: 3.5 Consensus size: 98
1450875 TACATGTATT
* * * *
1450885 TTACCTGTATGTTGACTTCGATTTGAGAGTGAGGACTTGTGAGGAGAAATAAACTGTATGTTGAC
1 TTACCTGTATGTTGACCTGGATTTGAGAGTGAGGACTTGTGAGGAGAAATTACCTGTATGTTGAC
*
1450950 CTGGATTTGAGAGTGAGGAC-T-TGAGGGGAAA
66 CTGGATTTGAGAGTGAGGACATGTGAGGAGAAA
* * *
1450981 TTACCAGTATGTTGACCTGGATTTGAGAGTGAGGACTTGTCATGAGAAATTACCTGTATGTTGAC
1 TTACCTGTATGTTGACCTGGATTTGAGAGTGAGGACTTGTGAGGAGAAATTACC----TG-T-A-
* *
1451046 CTGGGTTGACCTGGATTTGAGAGTGAGGACTTGTGATGAGAAA
59 -T--GTTGACCTGGATTTGAGAGTGAGGACATGTGAGGAGAAA
*
1451089 TTACC--TATGTTGACCTGGATTTGAGAGTGAGGACTTGTGAGGAGAAATTACCTATATGTTGAC
1 TTACCTGTATGTTGACCTGGATTTGAGAGTGAGGACTTGTGAGGAGAAATTACCTGTATGTTGAC
1451152 CTGGATTTGAGAGTGAGGACATGTGAGGAGAAA
66 CTGGATTTGAGAGTGAGGACATGTGAGGAGAAA
1451185 TTACCTGTATGTTGACCTGGATTTGAGAGTGAGGACTTGTGAGGAGAA
1 TTACCTGTATGTTGACCTGGATTTGAGAGTGAGGACTTGTGAGGAGAA
1451233 TCCTGCAGAT
Statistics
Matches: 224, Mismatches: 14, Indels: 26
0.85 0.05 0.10
Matches are distributed among these distances:
96 89 0.40
98 42 0.19
100 3 0.01
101 2 0.01
102 2 0.01
104 1 0.00
106 71 0.32
107 1 0.00
108 13 0.06
ACGTcount: A:0.27, C:0.11, G:0.32, T:0.30
Consensus pattern (98 bp):
TTACCTGTATGTTGACCTGGATTTGAGAGTGAGGACTTGTGAGGAGAAATTACCTGTATGTTGAC
CTGGATTTGAGAGTGAGGACATGTGAGGAGAAA
Found at i:1451183 original size:155 final size:155
Alignment explanation
Indices: 1450904--1451204 Score: 491
Period size: 155 Copynumber: 1.9 Consensus size: 155
1450894 TGTTGACTTC
*
1450904 GATTTGAGAGTGAGGACTTGTGAGGAGAAATAAACTGTATGTTGACCTGGATTTGAGAGTGAGGA
1 GATTTGAGAGTGAGGACTTGTGAGGAGAAATAAACTCTATGTTGACCTGGATTTGAGAGTGAGGA
* * *
1450969 CTTGAGGGGAAATTACCAGTATGTTGACCTGGATTTGAGAGTGAGGACTTGTCATGAGAAATTAC
66 CTTGAGGAGAAATTACCAGTATGTTGACCTGGATTTGAGAGTGAGGACATGTCAGGAGAAATTAC
1451034 CTGTATGTTGACCTGGGTTGACCTG
131 CTGTATGTTGACCTGGGTTGACCTG
* *
1451059 GATTTGAGAGTGAGGACTTGTGATGAGAAAT-TAC-CTATGTTGACCTGGATTTGAGAGTGAGGA
1 GATTTGAGAGTGAGGACTTGTGAGGAGAAATAAACTCTATGTTGACCTGGATTTGAGAGTGAGGA
*
1451122 CTTGTGAGGAGAAATTACCTA-TATGTTGACCTGGATTTGAGAGTGAGGACATGTGAGGAGAAAT
66 C-T-TGAGGAGAAATTACC-AGTATGTTGACCTGGATTTGAGAGTGAGGACATGTCAGGAGAAAT
1451186 TACCTGTATGTTGACCTGG
128 TACCTGTATGTTGACCTGG
1451205 ATTTGAGAGT
Statistics
Matches: 136, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
153 29 0.21
154 3 0.02
155 103 0.76
156 1 0.01
ACGTcount: A:0.28, C:0.11, G:0.32, T:0.30
Consensus pattern (155 bp):
GATTTGAGAGTGAGGACTTGTGAGGAGAAATAAACTCTATGTTGACCTGGATTTGAGAGTGAGGA
CTTGAGGAGAAATTACCAGTATGTTGACCTGGATTTGAGAGTGAGGACATGTCAGGAGAAATTAC
CTGTATGTTGACCTGGGTTGACCTG
Found at i:1451557 original size:2 final size:2
Alignment explanation
Indices: 1451552--1451582 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1451542 GGGTTCCCCC
1451552 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1451583 CAAAATGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1452811 original size:2 final size:2
Alignment explanation
Indices: 1452804--1452841 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1452794 ATTTTGTATT
*
1452804 TC TC TC TC TC TC TC TC TT 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 TC
1452842 AAAAATTCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:1452897 original size:2 final size:2
Alignment explanation
Indices: 1452890--1452924 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1452880 TAAAACAAAA
1452890 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1452925 TCAACCACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1454695 original size:88 final size:89
Alignment explanation
Indices: 1454546--1454711 Score: 271
Period size: 88 Copynumber: 1.9 Consensus size: 89
1454536 TTGTATGTGA
* * *
1454546 ATATCTTTGTTGTGCAAAGATGTTTAATAATGACATGTGTGCATAGGAATATACCATTTAC-ATA
1 ATATCTTTGCTGTGCAAAGATGTTTAATAATGAAATGTGTGCAAAGGAATATACCATTTACAATA
1454610 ACTATATATTGATGCTGAACTTGG
66 ACTATATATTGATGCTGAACTTGG
*
1454634 ATATCTTTGCTGTGCAAAGATGTTTAATAATGAAATGTGTGCAAAGGAATATGCCATTTACATAT
1 ATATCTTTGCTGTGCAAAGATGTTTAATAATGAAATGTGTGCAAAGGAATATACCATTTACA-AT
*
1454699 AACTATATGTTGA
65 AACTATATATTGA
1454712 CACTGAGCTT
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
88 57 0.80
90 14 0.20
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (89 bp):
ATATCTTTGCTGTGCAAAGATGTTTAATAATGAAATGTGTGCAAAGGAATATACCATTTACAATA
ACTATATATTGATGCTGAACTTGG
Found at i:1458991 original size:2 final size:2
Alignment explanation
Indices: 1458984--1459032 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1458974 ATCAAACCTC
1458984 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1459026 CT CT CT C
1 CT CT CT C
1459033 ATGGGTATGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1464231 original size:172 final size:168
Alignment explanation
Indices: 1463831--1464455 Score: 853
Period size: 168 Copynumber: 3.7 Consensus size: 168
1463821 CCAAATTTCA
* ** * *
1463831 AAAATCGTCTTCTCTACTCCCACACATGTGAGG-AAAAAACTGGTTGCATAGTTATGATGTCCAT
1 AAAATCTTCTTCTCTACTCCCACACATGTG-GGCAAAAAACTGAATACATGGTTATGATGTCCAT
** * *
1463895 GTTGCCCTCTACCAAAATTGTGAAATTCATGGCCCCTGGATCAGGGGTTCAGGCTCTAGGGTGGG
65 GAAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGTGGG
*
1463960 GCCAATATGGCCATATAGTAAAAATGTGTTAAATCTTAG
130 GCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAG
*
1463999 AAAATCTTCTTCTCTACTCCCACACATGTGGGCAAAAAACTGAATACATGATTATGATGTCCATG
1 AAAATCTTCTTCTCTACTCCCACACATGTGGGCAAAAAACTGAATACATGGTTATGATGTCCATG
* * * * * * *
1464064 AAGCCCTCTATCAAAATTGTAAAATTTATGACCCTTGTGTTAGGGGTTCAGGTTCTAGGGTGGGG
66 AAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGTGGGG
*
1464129 CCAAT-TGGCCATATAGTAAAAATGTATTAAATCTTTAAAA
131 CCAATATGGCCATATAGTAAAAATGTATTAAATC-TT--AG
1464169 AATCAATCTTCTTCTCTACTCCCACACATGTGGGCAAAAAACTGAATACATGGTTATGATGTCCA
1 AA--AATCTTCTTCTCTACTCCCACACATGTGGGCAAAAAACTGAATACATGGTTATGATGTCCA
* * * * *
1464234 -CAAACTCCTCTACCAAAATTGTGAGATTCGTGACCCCTGGGTCATGGGTTCAGGCTCTAGGGTG
64 TGAAGC-CCTCTACCAAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGTG
1464298 GGGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAG
128 GGGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAG
* * *
1464339 AAAATCTTCTTCTCTACTCCCACACATGTGGGCAAAAAATTTAATACATGGTTATGATCTCCTAT
1 AAAATCTTCTTCTCTACTCCCACACATGTGGGCAAAAAACTGAATACATGGTTATGATGTCC-AT
* * * * * *
1464404 -AACCCCTCTGCCTAAATTTTGAAATTCATGGCCCCTGGGTTAGGGGTTCAGG
65 GAAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGG
1464456 ACATTGGGGG
Statistics
Matches: 402, Mismatches: 45, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
167 29 0.07
168 214 0.53
169 4 0.01
170 6 0.01
171 3 0.01
172 118 0.29
173 28 0.07
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Consensus pattern (168 bp):
AAAATCTTCTTCTCTACTCCCACACATGTGGGCAAAAAACTGAATACATGGTTATGATGTCCATG
AAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGTGGGG
CCAATATGGCCATATAGTAAAAATGTATTAAATCTTAG
Done.