Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008252.1 Hibiscus syriacus cultivar Beakdansim tig00110904_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2928487
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 13
Found at i:913752 original size:356 final size:353
Alignment explanation
Indices: 913246--913917 Score: 1068
Period size: 356 Copynumber: 1.9 Consensus size: 353
913236 GTAAATTAAC
*
913246 AGTGTCGATACTTTAATATAAGTATCGACACTTTTGGAAATAAAAAGAGAAGAAGTTATAGCGCC
1 AGTGTCGATACTTAAATATAAGTATCGACACTTTTGGAAATAAAAAGAGAAGAAGTTATAGCGCC
*
913311 TAAAAAGTGTCAATACTTTAAAAAAATGTATCGATCCATAACAATATTACAGGTAAAAATATGAC
66 TAAAAAGTGTCAATACTTTAAAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAC
* * *
913376 AAAATCGATCTCAAAATGACAAAACCGGTAAAATGCTACCAGATATATTGCAAGTGTCGATAATT
131 AAAACCGATCTCAAAATGACAAAACCGGTAAAAGGCTACCAGATATATTGAAAGTGTCGATAATT
*
913441 TAATATAAGTATCGATACTTTCTGAATTTAAAAGAGAAG-A-TATAGCGCCTAAAAAGTGTCGAC
196 TAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTATAGCGCCTAAAAAGTGTCGAC
* * *
913504 ACTTTATGAAAA-T-T-GATCTATAACAATATAACAGCTAAAAATATGATAAAACCGTTCTCAAA
261 ACTTTATGAAAAGTATCGATCGATAACAATATAACAACTAAAAATATGAGAAAACCGTTCTCAAA
913566 ATGACAAAACAGGTAAATAACTACCAGA
326 ATGACAAAACAGGTAAATAACTACCAGA
*
913594 AGTGTCGATACTTAAATATAAGTATCGACACTTTTTGAATTTAAATAAAAGAAAAGAGAAGAAGT
1 AGTGTCGATACTTAAATATAAGTATCGACAC-TTTTG----GAAAT---A-AAAAGAGAAGAAGT
* *
913659 TATAGCGCCTATAAAGTGTCGATAC-TTAAAAAAATGTATCGATCCATAACAATATAACAGGTAA
57 TATAGCGCCTAAAAAGTGTCAATACTTTAAAAAAATGTATCGATCCATAACAATATAACAGGTAA
* * *
913723 AAATATGACAAAACCGGTCTCAAAATGACAAAACCGGTAAAAGGCTACCGGATATGTTGAAAGTG
122 AAATATGACAAAACCGATCTCAAAATGACAAAACCGGTAAAAGGCTACCAGATATATTGAAAGTG
913788 TCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAA
187 TCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAG-TATAGCGCCTAAA
913853 AAGTGTCGACACTTTATGAAAATGTATCGATCGATAACAATATAACAACTAAAAATATGAGAAAA
251 AAGTGTCGACACTTTATGAAAA-GTATCGATCGATAACAATATAACAACTAAAAATATGAGAAAA
913918 TATGTCAACA
Statistics
Matches: 293, Mismatches: 15, Indels: 17
0.90 0.05 0.05
Matches are distributed among these distances:
348 30 0.10
349 5 0.02
353 4 0.01
356 145 0.49
357 38 0.13
359 35 0.12
361 1 0.00
362 1 0.00
363 34 0.12
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (353 bp):
AGTGTCGATACTTAAATATAAGTATCGACACTTTTGGAAATAAAAAGAGAAGAAGTTATAGCGCC
TAAAAAGTGTCAATACTTTAAAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAC
AAAACCGATCTCAAAATGACAAAACCGGTAAAAGGCTACCAGATATATTGAAAGTGTCGATAATT
TAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTATAGCGCCTAAAAAGTGTCGAC
ACTTTATGAAAAGTATCGATCGATAACAATATAACAACTAAAAATATGAGAAAACCGTTCTCAAA
ATGACAAAACAGGTAAATAACTACCAGA
Found at i:914330 original size:23 final size:23
Alignment explanation
Indices: 914301--914348 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
914291 AAATAGGTCA
* *
914301 ATATAAGCGCTACCTATTATATT
1 ATATAAGCGCTACCAAATATATT
914324 ATATAAGCGCTACCAAATATATT
1 ATATAAGCGCTACCAAATATATT
914347 AT
1 AT
914349 TGTACTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (23 bp):
ATATAAGCGCTACCAAATATATT
Found at i:914447 original size:87 final size:87
Alignment explanation
Indices: 914301--914461 Score: 241
Period size: 87 Copynumber: 1.9 Consensus size: 87
914291 AAATAGGTCA
* *
914301 ATATAAGCGCTACCTATTATATTATATAAGCGCTACCAAATATATTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAACGCTACCAAATATATTATTGTACTTGATAATATTT
*
914366 CCGGTTAAATACTTATTTTATT
66 CCAGTTAAATACTTATTTTATT
* * * * *
914388 ATATAAGCGCTACCTATTACATTATATAAACGTTAGCTAATATGTTATTGTGCTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAACGCTACCAAATATATTATTGTACTTGATAATATTT
*
914453 TCAGTTAAA
66 CCAGTTAAA
914462 CGATATAACA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 65 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAACGCTACCAAATATATTATTGTACTTGATAATATTT
CCAGTTAAATACTTATTTTATT
Found at i:915136 original size:14 final size:16
Alignment explanation
Indices: 915117--915148 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
915107 TCATAATTTT
915117 AATTTAAT-T-TAATA
1 AATTTAATCTCTAATA
915131 AATTTAATCTCTAATA
1 AATTTAATCTCTAATA
915147 AA
1 AA
915149 ATTATTGCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 1 0.06
16 7 0.44
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTTAATCTCTAATA
Found at i:920286 original size:14 final size:15
Alignment explanation
Indices: 920267--920317 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 15
920257 ATACCTATAT
920267 ATTCT-ATCAATTTA
1 ATTCTAATCAATTTA
920281 ATTCTAATCTTAATTTA
1 ATTCTAATC--AATTTA
920298 ATT-TAAT-ATATTTA
1 ATTCTAATCA-ATTTA
920312 ATTCTA
1 ATTCTA
920318 CACAACATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
13 1 0.03
14 13 0.41
15 5 0.16
16 4 0.12
17 9 0.28
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTCTAATCAATTTA
Found at i:920297 original size:17 final size:16
Alignment explanation
Indices: 920275--920317 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
920265 ATATTCTATC
*
920275 AATTTAATTCTAATCTT
1 AATTTAATTCTAAT-AT
920292 AATTTAATT-TAATAT
1 AATTTAATTCTAATAT
920307 -ATTTAATTCTA
1 AATTTAATTCTA
920318 CACAACATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 8 0.33
15 3 0.12
16 4 0.17
17 9 0.38
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTTAATTCTAATAT
Found at i:920899 original size:2 final size:2
Alignment explanation
Indices: 920892--920923 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
920882 ATTTTTATTA
920892 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
920924 TCAAAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:920976 original size:2 final size:2
Alignment explanation
Indices: 920969--921000 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
920959 TTTAACAATA
920969 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
921001 CATTAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:921895 original size:21 final size:21
Alignment explanation
Indices: 921871--921910 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
921861 CAAACTTCTC
*
921871 TTAACTAACTAATAACAACCT
1 TTAACCAACTAATAACAACCT
*
921892 TTAACCAACTCATAACAAC
1 TTAACCAACTAATAACAAC
921911 TTAGTTGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (21 bp):
TTAACCAACTAATAACAACCT
Found at i:928478 original size:22 final size:21
Alignment explanation
Indices: 928422--928468 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
928412 CATTAAGAAC
928422 ATTCAATAATTCATATTTTTA
1 ATTCAATAATTCATATTTTTA
928443 ATTCAATAATTCATATTTTTA
1 ATTCAATAATTCATATTTTTA
928464 ATTCA
1 ATTCA
928469 GTGAGTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTCAATAATTCATATTTTTA
Found at i:930423 original size:3 final size:3
Alignment explanation
Indices: 930417--930470 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
930407 AAACAACAAC
930417 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
930465 AAT AAT
1 AAT AAT
930471 CCACTTTCTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:932905 original size:19 final size:19
Alignment explanation
Indices: 932881--932931 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
932871 GAAAAACATA
932881 AAAAAATAAAATATTTTTT
1 AAAAAATAAAATATTTTTT
932900 AAAAAATAAAATATTTTTT
1 AAAAAATAAAATATTTTTT
*
932919 AAATAATAAAATA
1 AAAAAATAAAATA
932932 ATGGATGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAAATAAAATATTTTTT
Found at i:934012 original size:24 final size:24
Alignment explanation
Indices: 933985--934040 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 24
933975 GGTCCAGTTA
933985 AAGGTGGGGCAA-TTGATGGTGATG
1 AAGGTGGGG-AAGTTGATGGTGATG
934009 AAGGTGGGGAAGTTGATGGTGATG
1 AAGGTGGGGAAGTTGATGGTGATG
*
934033 AAGATGGG
1 AAGGTGGG
934041 CCAGTTAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 2 0.07
24 28 0.93
ACGTcount: A:0.27, C:0.02, G:0.48, T:0.23
Consensus pattern (24 bp):
AAGGTGGGGAAGTTGATGGTGATG
Found at i:934046 original size:24 final size:24
Alignment explanation
Indices: 933991--934046 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
933981 GTTAAAGGTG
*
933991 GGGCAA-TTGATGGTGATGAAGGT
1 GGGCAAGTTGATGGTGATGAAGAT
*
934014 GGGGAAGTTGATGGTGATGAAGAT
1 GGGCAAGTTGATGGTGATGAAGAT
*
934038 GGGCCAGTT
1 GGGCAAGTT
934047 AAAGGTGGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.25, C:0.05, G:0.45, T:0.25
Consensus pattern (24 bp):
GGGCAAGTTGATGGTGATGAAGAT
Found at i:934053 original size:24 final size:24
Alignment explanation
Indices: 934002--934053 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
933992 GGCAATTGAT
* * * *
934002 GGTGATGAAGGTGGGGAAGTTGAT
1 GGTGATGAAGATGGGCAAGTTAAA
*
934026 GGTGATGAAGATGGGCCAGTTAAA
1 GGTGATGAAGATGGGCAAGTTAAA
934050 GGTG
1 GGTG
934054 GGTCGATGAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.04, G:0.46, T:0.23
Consensus pattern (24 bp):
GGTGATGAAGATGGGCAAGTTAAA
Found at i:935690 original size:21 final size:21
Alignment explanation
Indices: 935664--935703 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
935654 AAAAATGTGT
935664 ATCGATGCACTGCTACAGTGC
1 ATCGATGCACTGCTACAGTGC
*
935685 ATCGATGCACTGTTACAGT
1 ATCGATGCACTGCTACAGT
935704 AACTTCCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (21 bp):
ATCGATGCACTGCTACAGTGC
Found at i:936225 original size:46 final size:45
Alignment explanation
Indices: 936107--936259 Score: 261
Period size: 45 Copynumber: 3.4 Consensus size: 45
936097 TTCAAAATAT
* *
936107 TTACCATTTATCCCATAAGCTCGTAAACTTATTTTACTAACATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACTAACATAC
*
936152 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACTAATATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACTAACATAC
*
936197 TTACCATTTTATTCCATAAGCTTGTAAGCTTATTTTACTAACATAC
1 TTACCA-TTTATTCCATAAGCTCGTAAGCTTATTTTACTAACATAC
936243 TTACCATTTATTCCATA
1 TTACCATTTATTCCATA
936260 TAAGCTTATT
Statistics
Matches: 102, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
45 59 0.58
46 43 0.42
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.42
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACTAACATAC
Found at i:940330 original size:21 final size:21
Alignment explanation
Indices: 940306--940381 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
940296 CTGTAATAGC
* *
940306 TTCATCTCAGCCTGCAGCAGT
1 TTCATCTCAGCCTGCAACAAT
* * * *
940327 TTCATCTTAGTCTACAACAAC
1 TTCATCTCAGCCTGCAACAAT
* *
940348 TTCATCTCAGCCAGTAACAAT
1 TTCATCTCAGCCTGCAACAAT
940369 TTCATCTCAGCCT
1 TTCATCTCAGCCT
940382 CTAAGAAGGA
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.26, C:0.32, G:0.11, T:0.32
Consensus pattern (21 bp):
TTCATCTCAGCCTGCAACAAT
Found at i:940474 original size:57 final size:58
Alignment explanation
Indices: 940348--940474 Score: 150
Period size: 57 Copynumber: 2.2 Consensus size: 58
940338 CTACAACAAC
* * * * *
940348 TTCATCTCAGCCAGTAACAATTTCATCTCAGCCTCTAAGAAGGATGCACCCTCCATCT
1 TTCATCTCAGCCTGCAACAATTTCATCTCAACCTCAAAGAAGGATGCAACCTCCATCT
* * * *
940406 TT-ATATCAGCCTGCAACAATTTCATCTCAACTTGAAAGAAGGATGCAACCTTCAT-T
1 TTCATCTCAGCCTGCAACAATTTCATCTCAACCTCAAAGAAGGATGCAACCTCCATCT
*
940462 TTCATCTTAGCCT
1 TTCATCTCAGCCT
940475 CCACCAGGCT
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
56 3 0.05
57 52 0.91
58 2 0.04
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (58 bp):
TTCATCTCAGCCTGCAACAATTTCATCTCAACCTCAAAGAAGGATGCAACCTCCATCT
Found at i:940570 original size:49 final size:49
Alignment explanation
Indices: 940498--940645 Score: 278
Period size: 49 Copynumber: 3.0 Consensus size: 49
940488 CACCTTTAAC
940498 ATTTTCTCAAACTCCACCAACTTCCAAGAAATCACATGGAGGAAGCACA
1 ATTTTCTCAAACTCCACCAACTTCCAAGAAATCACATGGAGGAAGCACA
940547 ATTTTCTCAAACTCCACCAACTTCCAAGAAATCACATGGAGGAAGCACA
1 ATTTTCTCAAACTCCACCAACTTCCAAGAAATCACATGGAGGAAGCACA
* *
940596 ATTTTCTCAAACTCCACCAACTTCTAAGAAATCAAATGGAGGAAGCACA
1 ATTTTCTCAAACTCCACCAACTTCCAAGAAATCACATGGAGGAAGCACA
940645 A
1 A
940646 GACCCAAATT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 97 1.00
ACGTcount: A:0.40, C:0.27, G:0.12, T:0.21
Consensus pattern (49 bp):
ATTTTCTCAAACTCCACCAACTTCCAAGAAATCACATGGAGGAAGCACA
Found at i:945040 original size:17 final size:16
Alignment explanation
Indices: 944994--945042 Score: 71
Period size: 16 Copynumber: 3.0 Consensus size: 16
944984 CGGATATCCG
*
944994 ATCCGAAATTTAGGAT
1 ATCCGAAATTTCGGAT
945010 ATCCGAAATTTCGGAT
1 ATCCGAAATTTCGGAT
*
945026 ATCCGAATTTTTCGGAT
1 ATCCGAA-ATTTCGGAT
945043 CAGATACGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 22 0.73
17 8 0.27
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (16 bp):
ATCCGAAATTTCGGAT
Found at i:945097 original size:16 final size:17
Alignment explanation
Indices: 945066--945099 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
945056 TTACTTTAAG
945066 TATCCGAAATTTTCGGA
1 TATCCGAAATTTTCGGA
945083 TATCCGAAA-TTTCGGA
1 TATCCGAAATTTTCGGA
945099 T
1 T
945100 CGGATAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (17 bp):
TATCCGAAATTTTCGGA
Found at i:948200 original size:24 final size:24
Alignment explanation
Indices: 948142--948200 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
948132 GTTCAATTTA
*
948142 AATCGGTT-GAATCGTTACTAGTG
1 AATCGGTTAGAATCGCTACTAGTG
* * *
948165 AACCGATCAGAATCGCTACTAGTG
1 AATCGGTTAGAATCGCTACTAGTG
948189 AATCGGTTAGAA
1 AATCGGTTAGAA
948201 CCGTTGAATC
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (24 bp):
AATCGGTTAGAATCGCTACTAGTG
Found at i:948220 original size:17 final size:18
Alignment explanation
Indices: 948187--948220 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
948177 TCGCTACTAG
948187 TGAATCGGTTAGAACCGT
1 TGAATCGGTTAGAACCGT
*
948205 TGAATC-GTTCGAACCG
1 TGAATCGGTTAGAACCG
948221 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (18 bp):
TGAATCGGTTAGAACCGT
Found at i:950053 original size:22 final size:22
Alignment explanation
Indices: 950007--950052 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
949997 GCATGATAAA
* *
950007 TTTAGTCAATAAATTAGAATAT
1 TTTAGTCAAAAAAATAGAATAT
950029 TTTAGTCAAAAAAATAGAA-AT
1 TTTAGTCAAAAAAATAGAATAT
950050 TTT
1 TTT
950053 TTTAGCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (22 bp):
TTTAGTCAAAAAAATAGAATAT
Found at i:950054 original size:23 final size:23
Alignment explanation
Indices: 950007--950063 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
949997 GCATGATAAA
* *
950007 TTTAGTCAATAAATTAGAA-TAT
1 TTTAGTCAAAAAAATAGAATTAT
*
950029 TTTAGTCAAAAAAATAGAAATTTT
1 TTTAGTCAAAAAAATAG-AATTAT
950053 TTTAG-CAAAAA
1 TTTAGTCAAAAA
950064 TGTTTTTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 15 0.50
23 8 0.27
24 7 0.23
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (23 bp):
TTTAGTCAAAAAAATAGAATTAT
Found at i:950638 original size:21 final size:21
Alignment explanation
Indices: 950614--950655 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
950604 TTCCCAAGAA
* *
950614 GAGATTATCTGAGTGCTCCTT
1 GAGATGATCTCAGTGCTCCTT
*
950635 GAGATGCTCTCAGTGCTCCTT
1 GAGATGATCTCAGTGCTCCTT
950656 ACTTCACGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.36
Consensus pattern (21 bp):
GAGATGATCTCAGTGCTCCTT
Found at i:951521 original size:172 final size:175
Alignment explanation
Indices: 951235--951581 Score: 673
Period size: 172 Copynumber: 2.0 Consensus size: 175
951225 CTTTGAACCT
951235 ACTTGTGAAAACACTCACACGCTAAGTCTTTGACTTAGTGAGGCATAAATGAGCATAATAAAACA
1 ACTTGTGAAAACACTCACACGCTAAGTCTTTGACTTAGTGAGGCATAAATGAGCATAATAAAACA
951300 TTAAAAACACTTTCTTAAACATTTCAGAGAAAACATTGAATACGGAAAACAAGATACATTTCATA
66 TTAAAAACACTTTCTTAAACATTTCAGAGAAAACATTGAATACGGAAAACAAGATACATTTCATA
951365 TAAAT-ACA-ATATTGTTATGCACTTTTCAATCC-TATCAAATAG
131 TAAATAACATATATTGTTATGCACTTTTCAATCCATATCAAATAG
951407 ACTTGTGAAAACACTCACACGCTAAGTCTTTGACTTAGTGAGGCATAAATGAGCATAATAAAACA
1 ACTTGTGAAAACACTCACACGCTAAGTCTTTGACTTAGTGAGGCATAAATGAGCATAATAAAACA
951472 TTAAAAACACTTTCTTAAACATTTCAGAGAAAACATTGAATACGGAAAACAAGATACATTTCATA
66 TTAAAAACACTTTCTTAAACATTTCAGAGAAAACATTGAATACGGAAAACAAGATACATTTCATA
951537 TAAATAACATATATTGTTATGCACTTTTCAATCCATATCAAATAG
131 TAAATAACATATATTGTTATGCACTTTTCAATCCATATCAAATAG
951582 TTTAATTAGC
Statistics
Matches: 172, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
172 135 0.78
173 3 0.02
174 24 0.14
175 10 0.06
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.29
Consensus pattern (175 bp):
ACTTGTGAAAACACTCACACGCTAAGTCTTTGACTTAGTGAGGCATAAATGAGCATAATAAAACA
TTAAAAACACTTTCTTAAACATTTCAGAGAAAACATTGAATACGGAAAACAAGATACATTTCATA
TAAATAACATATATTGTTATGCACTTTTCAATCCATATCAAATAG
Found at i:957650 original size:13 final size:13
Alignment explanation
Indices: 957632--957658 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
957622 AAGGTAATTT
957632 GTTACAAATCCAA
1 GTTACAAATCCAA
957645 GTTACAAATCCAA
1 GTTACAAATCCAA
957658 G
1 G
957659 CAGTTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.22
Consensus pattern (13 bp):
GTTACAAATCCAA
Found at i:963882 original size:47 final size:48
Alignment explanation
Indices: 963778--964002 Score: 256
Period size: 48 Copynumber: 4.7 Consensus size: 48
963768 CAGGAGTAGC
* * * * *
963778 ACCTTTCTGCCAAAATGCACTGTTATGCATTTGAGTTTCATTTGTGGC
1 ACCTTTCTGCCAAAATGCACCGTTATGCATTTAATTTTCATTAGTGGA
*
963826 ACCTTTCTGCTAAAATGCACCGTTATGCATTT-ATTTTCATTAGTGGA
1 ACCTTTCTGCCAAAATGCACCGTTATGCATTTAATTTTCATTAGTGGA
* *
963873 ACCTTTCTGCCAAAATGCACCGTTATGCATTTATTTTTCATTAGTAGA
1 ACCTTTCTGCCAAAATGCACCGTTATGCATTTAATTTTCATTAGTGGA
* * * * * *
963921 TCATTTCTACCAATAATGCACTGTTACGCATTTAATTTTCATTAAT-GA
1 ACCTTTCTGCCAA-AATGCACCGTTATGCATTTAATTTTCATTAGTGGA
* * *
963969 CATCTTTCTGCCAATAATGCATCGTTATACATTT
1 -ACCTTTCTGCCAA-AATGCACCGTTATGCATTT
964003 TCATTTATGG
Statistics
Matches: 151, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
47 43 0.28
48 55 0.36
49 53 0.35
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.40
Consensus pattern (48 bp):
ACCTTTCTGCCAAAATGCACCGTTATGCATTTAATTTTCATTAGTGGA
Found at i:964019 original size:44 final size:44
Alignment explanation
Indices: 963955--964058 Score: 136
Period size: 44 Copynumber: 2.4 Consensus size: 44
963945 TACGCATTTA
* * * *
963955 ATTTTCATTAATGACATCTTTCTGCCAATAATGCATCGTTATAC
1 ATTTTCATTTATGGCATCTTTCTGCCAATAATGCACCATTATAC
* * *
963999 ATTTTCATTTATGGCTTCTTTTTGCCAATAATGCACCATTATGC
1 ATTTTCATTTATGGCATCTTTCTGCCAATAATGCACCATTATAC
*
964043 AATTTCATTTATGGCA
1 ATTTTCATTTATGGCA
964059 CATTTCTCTC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.27, C:0.19, G:0.11, T:0.43
Consensus pattern (44 bp):
ATTTTCATTTATGGCATCTTTCTGCCAATAATGCACCATTATAC
Found at i:969362 original size:49 final size:48
Alignment explanation
Indices: 969137--969450 Score: 419
Period size: 47 Copynumber: 6.6 Consensus size: 48
969127 AGAATGACAT
* * * *
969137 CTTTCTACCAAAATGCACCGTTATGCATTTAAGTTTCATTTGTGGAAC
1 CTTTCTGCCAAAATGCACCGTTATGCATTTAATTTTCATTAGTGGCAC
* *
969185 CTTTTTGCCAAAATGCACCGTTATGCATTTAATTTTCATTAGTGCCAC
1 CTTTCTGCCAAAATGCACCGTTATGCATTTAATTTTCATTAGTGGCAC
*
969233 C-TTCTGCCAAAATGCACCGTTATGCATTTAATTTTCATTAGTGGCAT
1 CTTTCTGCCAAAATGCACCGTTATGCATTTAATTTTCATTAGTGGCAC
*
969280 C-TTCTGCCAAAATGCACCGTTATGCATTTAATTTTCATTAGTGGCAT
1 CTTTCTGCCAAAATGCACCGTTATGCATTTAATTTTCATTAGTGGCAC
* *
969327 CTTTCTGCCAATAATGCACCATTATGCGTTTAATTTTCATTAGTGGCAC
1 CTTTCTGCCAA-AATGCACCGTTATGCATTTAATTTTCATTAGTGGCAC
* *
969376 CTTTCTGCCAATAATTCATCGTTATGC-----ATTTTCATTTA-TGGCAC
1 CTTTCTGCCAA-AATGCACCGTTATGCATTTAATTTTCA-TTAGTGGCAC
*
969420 CTTTTTGCCAATAATGCACCGTTATGCATTT
1 CTTTCTGCCAA-AATGCACCGTTATGCATTT
969451 TCATTTTTGG
Statistics
Matches: 241, Mismatches: 18, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
44 37 0.15
45 3 0.01
47 91 0.38
48 52 0.22
49 58 0.24
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (48 bp):
CTTTCTGCCAAAATGCACCGTTATGCATTTAATTTTCATTAGTGGCAC
Found at i:969422 original size:44 final size:44
Alignment explanation
Indices: 969137--969502 Score: 241
Period size: 47 Copynumber: 7.9 Consensus size: 44
969127 AGAATGACAT
* * *
969137 CTTTCTACCAA-AATGCACCGTTATGCATTTAAGTTTCATTTGTGGAAC
1 CTTTCTGCCAATAATGCACCGTTATGCA--T---TTTCATTTATGGCAC
* *
969185 CTTTTTGCCAA-AATGCACCGTTATGCATTTAATTTTCA-TTAGTGCCAC
1 CTTTCTGCCAATAATGCACCGTTATGC-----ATTTTCATTTA-TGGCAC
*
969233 C-TTCTGCCAA-AATGCACCGTTATGCATTTAATTTTCA-TTAGTGGCAT
1 CTTTCTGCCAATAATGCACCGTTATGC-----ATTTTCATTTA-TGGCAC
*
969280 C-TTCTGCCAA-AATGCACCGTTATGCATTTAATTTTCA-TTAGTGGCAT
1 CTTTCTGCCAATAATGCACCGTTATGC-----ATTTTCATTTA-TGGCAC
*
969327 CTTTCTGCCAATAATGCACCATTATGCGTTTAATTTTCA-TTAGTGGCAC
1 CTTTCTGCCAATAATGCACCGTTATGC-----ATTTTCATTTA-TGGCAC
* *
969376 CTTTCTGCCAATAATTCATCGTTATGCATTTTCATTTATGGCAC
1 CTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCAC
* * *
969420 CTTTTTGCCAATAATGCACCGTTATGCATTTTCATTTTTGGAAC
1 CTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCAC
* * *
969464 CATTATG-CAATTAATGCACCGTTATGTATTTTCATTTAT
1 CTTTCTGCCAA-TAATGCACCGTTATGCATTTTCATTTAT
969503 TCATTCATTT
Statistics
Matches: 285, Mismatches: 23, Indels: 24
0.86 0.07 0.07
Matches are distributed among these distances:
43 3 0.01
44 83 0.29
45 3 0.01
47 93 0.33
48 43 0.15
49 58 0.20
51 1 0.00
53 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (44 bp):
CTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTATGGCAC
Found at i:969436 original size:142 final size:138
Alignment explanation
Indices: 969139--969450 Score: 403
Period size: 142 Copynumber: 2.2 Consensus size: 138
969129 AATGACATCT
* * *
969139 TTCTACCAAAATGCACCGTTATGCATTTAAGTTTCATTTGTGGAACCTTTTTGCCAAAATGCACC
1 TTCTGCCAAAATGCACCGTTATGCATTTAAGTTTCATTAGTGGAACCTTTCTGCCAAAATGCACC
*
969204 GTTATGCATTTAATTTTCATTAGTGCCACCTTCTGCCAAAATGCACCGTTATGCATTTAATTTTC
66 ATTATGCATTTAATTTTCATTAGTGCCACCTTCTGCCAAAATGCACCGTTATGC---T-ATTTTC
*
969269 ATTAGTGGCATC
127 ATTAGTGGCACC
* * *
969281 TTCTGCCAAAATGCACCGTTATGCATTTAATTTTCATTAGTGGCATCTTTCTGCCAATAATGCAC
1 TTCTGCCAAAATGCACCGTTATGCATTTAAGTTTCATTAGTGGAACCTTTCTGCCAA-AATGCAC
* * * *
969346 CATTATGCGTTTAATTTTCATTAGTGGCACCTTTCTGCCAATAATTCATCGTTATGC-ATTTTCA
65 CATTATGCATTTAATTTTCATTAGTGCCACC-TTCTGCCAA-AATGCACCGTTATGCTATTTTCA
969410 TTTA-TGGCACC
128 -TTAGTGGCACC
*
969421 TTTTTGCCAATAATGCACCGTTATGCATTT
1 -TTCTGCCAA-AATGCACCGTTATGCATTT
969451 TCATTTTTGG
Statistics
Matches: 151, Mismatches: 13, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
140 13 0.09
141 11 0.07
142 70 0.46
143 35 0.23
144 9 0.06
145 13 0.09
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (138 bp):
TTCTGCCAAAATGCACCGTTATGCATTTAAGTTTCATTAGTGGAACCTTTCTGCCAAAATGCACC
ATTATGCATTTAATTTTCATTAGTGCCACCTTCTGCCAAAATGCACCGTTATGCTATTTTCATTA
GTGGCACC
Found at i:981400 original size:45 final size:46
Alignment explanation
Indices: 981351--981441 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
981341 GAACATCGAA
* * *
981351 TGCATTTTATGCATCGATGCAC-ATACCATGTATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
*
981396 TGCATTTGATGCATCGATGCACAAGATCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
981442 CCTTTTTCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 21 0.51
46 20 0.49
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
Found at i:993926 original size:17 final size:18
Alignment explanation
Indices: 993879--993918 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
993869 GATTTTGGTA
*
993879 AAAAGATATTAAAATAAT
1 AAAAGAGATTAAAATAAT
*
993897 AAAAGAGAATAAAA-AAT
1 AAAAGAGATTAAAATAAT
993914 AAAAG
1 AAAAG
993919 CAATTAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.17
Consensus pattern (18 bp):
AAAAGAGATTAAAATAAT
Found at i:999503 original size:18 final size:18
Alignment explanation
Indices: 999468--999510 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
999458 AAAGTTATTA
*
999468 AAAT-AATAAAAACGATT
1 AAATAAATAAAAACAATT
*
999485 AAATAAATAAAAGCAATT
1 AAATAAATAAAAACAATT
999503 AAAGTAAA
1 AAA-TAAA
999511 AATAAGAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.18
18 14 0.64
19 4 0.18
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAATAAAAACAATT
Found at i:1002581 original size:17 final size:17
Alignment explanation
Indices: 1002530--1002582 Score: 52
Period size: 20 Copynumber: 2.9 Consensus size: 17
1002520 GTTTGCATAA
1002530 CATTCATTGCATTTAAT
1 CATTCATTGCATTTAAT
* * *
1002547 AAGTGTGATGTTCATTTAAT
1 CA-T-TCAT-TGCATTTAAT
1002567 CATTCATTGCATTTAA
1 CATTCATTGCATTTAA
1002583 ATCAAACTAG
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
17 9 0.33
18 4 0.15
19 4 0.15
20 10 0.37
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.45
Consensus pattern (17 bp):
CATTCATTGCATTTAAT
Found at i:1002648 original size:17 final size:17
Alignment explanation
Indices: 1002626--1002678 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
1002616 TGAATAATGT
1002626 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
1002643 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
*
1002660 TAGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
1002677 TA
1 TA
1002679 CTCTTAATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:1011585 original size:40 final size:37
Alignment explanation
Indices: 1011501--1011594 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 37
1011491 AATGTTGATT
* * *
1011501 TTTTCTTAACATTTTCGGTTGAATCGAAGATGTTATA
1 TTTTCATAACATTTTCGGTTGAAACGAAGATGTTAAA
1011538 TTCTTCATAACATTTTCGGTTAGCAAACG-AGAATGTTACAA
1 TT-TTCATAACATTTTCGGTT-G-AAACGAAG-ATGTTA-AA
1011579 TTTTCATAACATTTTC
1 TTTTCATAACATTTTC
1011595 TGCAATAGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
37 2 0.04
38 17 0.35
39 3 0.06
40 24 0.49
41 3 0.06
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (37 bp):
TTTTCATAACATTTTCGGTTGAAACGAAGATGTTAAA
Found at i:1014811 original size:21 final size:21
Alignment explanation
Indices: 1014773--1014827 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
1014763 TATTTTTGCC
* * *
1014773 TCAATATATATATTAATTTTAT
1 TCAATA-AAATATGAATTTAAT
1014795 TCAATAAAATATGAATTTAAT
1 TCAATAAAATATGAATTTAAT
* *
1014816 TGAAGAAAATAT
1 TCAATAAAATAT
1014828 ACATGGGTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (21 bp):
TCAATAAAATATGAATTTAAT
Found at i:1019513 original size:3 final size:3
Alignment explanation
Indices: 1019500--1019555 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
1019490 ATAAATAAGC
1019500 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1019546 ATA ATA ATA A
1 ATA ATA ATA A
1019556 CAATTAGATA
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.08
3 47 0.92
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1019534 original size:29 final size:29
Alignment explanation
Indices: 1019474--1019555 Score: 114
Period size: 29 Copynumber: 2.9 Consensus size: 29
1019464 CAAAAATTTT
* * *
1019474 TAATATATTAATAACAAT-A-AATAAGCA
1 TAATATAATAATAATAATAATAATAAGAA
*
1019501 TAATATAATAATAATAATAATAATAATAA
1 TAATATAATAATAATAATAATAATAAGAA
1019530 TAATATAATAATAATAATAATAATAA
1 TAATATAATAATAATAATAATAATAA
1019556 CAATTAGATA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 16 0.33
28 1 0.02
29 32 0.65
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.33
Consensus pattern (29 bp):
TAATATAATAATAATAATAATAATAAGAA
Found at i:1019795 original size:43 final size:44
Alignment explanation
Indices: 1019725--1020085 Score: 207
Period size: 43 Copynumber: 8.4 Consensus size: 44
1019715 GGACGCCACT
* * * * * *
1019725 GCTCATACGTGATGAAGAGTTCGGGTCGTCTAAGGG-TGACATG
1 GCTCCTACGTGATGAGGAGATCTGGTCATCTAAGGGATGACACG
* * * * *
1019768 GTTCCTACGTGATGAGGAAATCTGG---TC-GAGGGTTGACACT
1 GCTCCTACGTGATGAGGAGATCTGGTCATCTAAGGGATGACACG
* * * * *
1019808 GCTCATACGTGATGAAGAGTTCTTGGCCATCTTAAGGTGATAACACG
1 GCTCCTACGTGATGAGGAGATC-TGGTCATC-TAAGG-GATGACACG
* * * * *
1019855 GTTCCTACGTGATGAGGACG-GCTGGTTATCT-ACGGTTGACACG
1 GCTCCTACGTGATGAGGA-GATCTGGTCATCTAAGGGATGACACG
* *
1019898 GCTCCTACGTGATGAGGAGATCTGG---TCT-GGGGAATGACATG
1 GCTCCTACGTGATGAGGAGATCTGGTCATCTAAGGG-ATGACACG
* * * * *
1019939 GCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACG
1 GCTCCTACGTGATGAGGAGATCTGGTCATCT-AAGG-GATGACACG
* * * * *
1019985 GTTCCTACGTGATGAGGACG-GCTGGTTATCT-ATGGTTGACACG
1 GCTCCTACGTGATGAGGA-GATCTGGTCATCTAAGGGATGACACG
*
1020028 GCTCCTACGTGATGAGGAGATCTGG---TCT-GGGGATGACACG
1 GCTCCTACGTGATGAGGAGATCTGGTCATCTAAGGGATGACACG
* *
1020068 GTTCCTACATGATGAGGA
1 GCTCCTACGTGATGAGGA
1020086 CGGCTGGCCA
Statistics
Matches: 244, Mismatches: 55, Indels: 41
0.72 0.16 0.12
Matches are distributed among these distances:
39 4 0.02
40 57 0.23
41 31 0.13
42 2 0.01
43 75 0.31
44 9 0.04
45 1 0.00
46 40 0.16
47 24 0.10
48 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (44 bp):
GCTCCTACGTGATGAGGAGATCTGGTCATCTAAGGGATGACACG
Found at i:1019965 original size:130 final size:130
Alignment explanation
Indices: 1019761--1020066 Score: 510
Period size: 130 Copynumber: 2.4 Consensus size: 130
1019751 CGTCTAAGGG
* * * *
1019761 TGACATGGTTCCTACGTGATGAGGAAATCTGGTC-GAGGGTTGACACTGCTCATACGTGATGAAG
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTG-GGGATGACACTGCTCATACGTGATGAAG
*
1019825 AGTTCTTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTACGG
65 AGTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTACGG
1019890 T
130 T
1019891 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGAATGACA-TGGCTCATACGTGATGAA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGG-ATGACACT-GCTCATACGTGATGAA
*
1019955 GAGTTC-TGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATG
64 GAGTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTACG
1020019 GT
129 GT
1020021 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACAC
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACAC
1020067 GGTTCCTACA
Statistics
Matches: 166, Mismatches: 6, Indels: 8
0.92 0.03 0.04
Matches are distributed among these distances:
129 6 0.04
130 132 0.80
131 28 0.17
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.26
Consensus pattern (130 bp):
TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACTGCTCATACGTGATGAAGA
GTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTACGGT
Found at i:1020151 original size:28 final size:28
Alignment explanation
Indices: 1020131--1020192 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
1020121 AAACCAAATT
1020131 AAAGATTTGTTTCAAAAGAAACAAACCC
1 AAAGATTTGTTTCAAAAGAAACAAACCC
* *
1020159 AAAGATTTGTTTCAAGAA-AAATAAACTC
1 AAAGATTTGTTTCAA-AAGAAACAAACCC
1020187 AAAGAT
1 AAAGAT
1020193 GATATTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 29 0.94
29 2 0.06
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAAACCC
Found at i:1020819 original size:67 final size:65
Alignment explanation
Indices: 1020586--1021097 Score: 424
Period size: 67 Copynumber: 7.9 Consensus size: 65
1020576 GTATCTTAGT
* * * *
1020586 GAGACAAAATTTTGTTTCCAAAGAAACAGACTC--AGA-TTTTTCTTCAAAAGAAACTGTTTTAA
1 GAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTTTTTCAAAAGAAATTATTTAAA
* * ** * * * * * *
1020648 GTGATAAAACCTTGTTTCCAGAGAAACAAACTCAAAGATGATCTTGTTTT-AAGAGAAAATGTTT
1 GAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGAT--T-TTTTTTTCAAAAGAAATTATTT
*
1020712 CAA
63 AAA
* * *
1020715 GAGACAAAA-TTCGTTT-GAAGGGAAAC-GACTCAAAGATTTTTTTTTCAAAAGAAATTATCTTA
1 GAGACAAAATTTTGTTTCCAA-AGAAACAGACTCAAAGATTTTTTTTTCAAAAGAAATTAT-TTA
1020777 AGA
64 A-A
* *
1020780 GAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCCTAA
1 GAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTTTTTCAAAAGAAATTAT-TTAA
1020845 GA
65 -A
* * * * * *
1020847 GAAACAACATTTTGTTTCCAAAGAAACAGACTC--AGA-TTTTTCTTCAAAAGAAACTGTTTTAA
1 GAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTTTTTCAAAAGAAATTATTTAAA
* * ** * * * * * *
1020909 GTGATAAAACCTTGTTTCCAGAGAAACAAACTCAAAGATGATCTTGTTTT-AAGAGAAAATGTTT
1 GAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGAT--T-TTTTTTTCAAAAGAAATTATTT
*
1020973 CAA
63 AAA
* * *
1020976 GAGACAAAA-TTCGTTT-GAAGGGAAAC-GACTCAAAGA-TTTTTTTTCAAAAGAAATTATCTTA
1 GAGACAAAATTTTGTTTCCAA-AGAAACAGACTCAAAGATTTTTTTTTCAAAAGAAATTAT-TTA
1021037 AGA
64 A-A
*
1021040 GAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATT
1 GAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTTTTTCAAAAGAAATT
1021098 CTCAAAGATT
Statistics
Matches: 356, Mismatches: 67, Indels: 49
0.75 0.14 0.10
Matches are distributed among these distances:
61 6 0.02
62 69 0.19
63 15 0.04
64 36 0.10
65 45 0.13
66 43 0.12
67 132 0.37
68 10 0.03
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (65 bp):
GAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTTTTTCAAAAGAAATTATTTAAA
Found at i:1021102 original size:28 final size:29
Alignment explanation
Indices: 1021044--1021131 Score: 101
Period size: 28 Copynumber: 3.1 Consensus size: 29
1021034 TTAAGAGAGA
* * * *
1021044 CAAA-ATTTTGTTTCCAAAGAAACAGACT
1 CAAAGATTTTTTTTCAAAAGAAACTGTCT
1021072 CAAAGATTTTTGTTTCAAAAGAAA-T-TCT
1 CAAAGATTTTT-TTTCAAAAGAAACTGTCT
*
1021100 CAAAGATTTTTTTTCAAGAGAAACTGTCT
1 CAAAGATTTTTTTTCAAAAGAAACTGTCT
1021129 CAA
1 CAA
1021132 GAGAAACAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
27 11 0.22
28 18 0.35
29 11 0.22
30 11 0.22
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (29 bp):
CAAAGATTTTTTTTCAAAAGAAACTGTCT
Found at i:1021121 original size:27 final size:30
Alignment explanation
Indices: 1021049--1021131 Score: 109
Period size: 30 Copynumber: 2.9 Consensus size: 30
1021039 AGAGACAAAA
* * *
1021049 TTTTGTTTCCAAAGAAACAGACTCAAAGAT
1 TTTTGTTTCAAAAGAAACTGTCTCAAAGAT
1021079 TTTTGTTTCAAAAGAAA-T-TCTCAAAGAT
1 TTTTGTTTCAAAAGAAACTGTCTCAAAGAT
*
1021107 TTTT-TTTCAAGAGAAACTGTCTCAA
1 TTTTGTTTCAAAAGAAACTGTCTCAA
1021132 GAGAAACAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 11 0.23
28 14 0.30
29 6 0.13
30 16 0.34
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.36
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACTGTCTCAAAGAT
Found at i:1022050 original size:4 final size:4
Alignment explanation
Indices: 1022035--1022081 Score: 80
Period size: 4 Copynumber: 12.2 Consensus size: 4
1022025 ATGTATCATA
1022035 TATG TATG --TG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1022081 T
1 T
1022082 GTATACTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
4 39 0.95
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:1023946 original size:26 final size:24
Alignment explanation
Indices: 1023916--1023986 Score: 78
Period size: 20 Copynumber: 3.0 Consensus size: 24
1023906 TAAGGTGGAA
1023916 AGAATATTTCAAGGTCTCAAAGAG
1 AGAATATTTCAAGGTCTCAAAGAG
* *
1023940 AGGGAATGTTTCAAGG--TCGAA-A-
1 A--GAATATTTCAAGGTCTCAAAGAG
1023962 AGAATATTTCAAGGTCTCAAAGAG
1 AGAATATTTCAAGGTCTCAAAGAG
1023986 A
1 A
1023987 TAGAATGTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
20 12 0.32
22 5 0.14
23 2 0.05
24 6 0.16
26 12 0.32
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (24 bp):
AGAATATTTCAAGGTCTCAAAGAG
Found at i:1023991 original size:26 final size:26
Alignment explanation
Indices: 1023913--1023992 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 26
1023903 TTTTAAGGTG
1023913 GAAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
** *
1023939 GAGGGAATGTTTCAAGG--TC---GA
1 GAAAGAATATTTCAAGGTCTCAAAGA
1023960 -AAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
*
1023985 GATAGAAT
1 GAAAGAAT
1023993 GTCAAAAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
20 13 0.32
21 2 0.05
22 2 0.05
24 2 0.05
25 2 0.05
26 20 0.49
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.24
Consensus pattern (26 bp):
GAAAGAATATTTCAAGGTCTCAAAGA
Found at i:1023993 original size:46 final size:45
Alignment explanation
Indices: 1023901--1023994 Score: 143
Period size: 46 Copynumber: 2.1 Consensus size: 45
1023891 ATAAATACAG
* * *
1023901 TGTTTTAAGGTGGAAAGAATATTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
*
1023946 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
1023992 TGT
1 TGT
1023995 CAAAAATTGG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 10 0.23
46 34 0.77
ACGTcount: A:0.38, C:0.09, G:0.26, T:0.28
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
Found at i:1029504 original size:3 final size:3
Alignment explanation
Indices: 1029491--1029562 Score: 137
Period size: 3 Copynumber: 24.3 Consensus size: 3
1029481 ATAAATAAGC
1029491 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1029538 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1029563 CAATTAGATA
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 66 0.97
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1033625 original size:24 final size:24
Alignment explanation
Indices: 1033598--1033659 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
1033588 TAGTCACCAC
1033598 TGCCACGTAAAATTTGCACCGAAG
1 TGCCACGTAAAATTTGCACCGAAG
* * *
1033622 TGCCACGTAGAATATGCACTGAAG
1 TGCCACGTAAAATTTGCACCGAAG
*
1033646 TGCCACATAAAATT
1 TGCCACGTAAAATT
1033660 CTCCCGAAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (24 bp):
TGCCACGTAAAATTTGCACCGAAG
Found at i:1033826 original size:15 final size:15
Alignment explanation
Indices: 1033805--1033881 Score: 84
Period size: 15 Copynumber: 5.2 Consensus size: 15
1033795 GAGTATTGTT
1033805 TATTCACATAGAACA
1 TATTCACATAGAACA
* * *
1033820 CATTCACTTAGCACA
1 TATTCACATAGAACA
1033835 TATTCACATAG-ACA
1 TATTCACATAGAACA
* *
1033849 TTTTCACATATAACA
1 TATTCACATAGAACA
* *
1033864 TATTCACCTATAACA
1 TATTCACATAGAACA
1033879 TAT
1 TAT
1033882 ACTTATAGTA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
14 12 0.23
15 40 0.77
ACGTcount: A:0.40, C:0.23, G:0.04, T:0.32
Consensus pattern (15 bp):
TATTCACATAGAACA
Found at i:1033864 original size:29 final size:30
Alignment explanation
Indices: 1033805--1033870 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
1033795 GAGTATTGTT
* *
1033805 TATTCACATAGAACACATTCACTTAGCACA
1 TATTCACATAGAACACATTCACATAGAACA
** *
1033835 TATTCACATAG-ACATTTTCACATATAACA
1 TATTCACATAGAACACATTCACATAGAACA
1033864 TATTCAC
1 TATTCAC
1033871 CTATAACATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.39, C:0.24, G:0.05, T:0.32
Consensus pattern (30 bp):
TATTCACATAGAACACATTCACATAGAACA
Found at i:1034526 original size:20 final size:20
Alignment explanation
Indices: 1034501--1034550 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
1034491 CCTTATTTTG
1034501 GTATCGATAC-CTCCACATCA
1 GTATCGATACACTCCA-ATCA
* *
1034521 GTATCGACACTACTTCAATCA
1 GTATCGATAC-ACTCCAATCA
1034542 GTATCGATA
1 GTATCGATA
1034551 TTGTTCATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 9 0.36
21 12 0.48
22 4 0.16
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (20 bp):
GTATCGATACACTCCAATCA
Found at i:1038341 original size:18 final size:19
Alignment explanation
Indices: 1038320--1038355 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1038310 TATCTAAATC
1038320 AAAT-CAAATATCATTGGA
1 AAATACAAATATCATTGGA
*
1038338 AAATACAATTATCATTGG
1 AAATACAAATATCATTGG
1038356 CTTTCATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (19 bp):
AAATACAAATATCATTGGA
Found at i:1039275 original size:9 final size:9
Alignment explanation
Indices: 1039261--1039287 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1039251 GTCCTGCCCT
1039261 TGCTTACTC
1 TGCTTACTC
1039270 TGCTTACTC
1 TGCTTACTC
1039279 TGCTTACTC
1 TGCTTACTC
1039288 CTCTGAACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.33, G:0.11, T:0.44
Consensus pattern (9 bp):
TGCTTACTC
Found at i:1039633 original size:24 final size:24
Alignment explanation
Indices: 1039606--1039668 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
1039596 CAGTCACCAC
*
1039606 TGCCACATAGAATTTGGACCGAAA
1 TGCCACATAGAATTTGCACCGAAA
** * *
1039630 TGCCATGTAGAATATGCACCGAAG
1 TGCCACATAGAATTTGCACCGAAA
1039654 TGCCACATAG-ATTTG
1 TGCCACATAGAATTTG
1039669 TCCCGAAGGA
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
23 4 0.13
24 27 0.87
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (24 bp):
TGCCACATAGAATTTGCACCGAAA
Found at i:1039687 original size:23 final size:23
Alignment explanation
Indices: 1039661--1039735 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
1039651 AAGTGCCACA
*
1039661 TAGATTTGTCCCGAAGGACCGCG
1 TAGAATTGTCCCGAAGGACCGCG
** *
1039684 TAGAACTTGTCTTGAAGGACCACG
1 TAGAA-TTGTCCCGAAGGACCGCG
* *
1039708 TAGAATTGTCCCGAATGACCGTG
1 TAGAATTGTCCCGAAGGACCGCG
1039731 TAGAA
1 TAGAA
1039736 CCCTCAACTC
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
23 22 0.52
24 20 0.48
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (23 bp):
TAGAATTGTCCCGAAGGACCGCG
Found at i:1039700 original size:24 final size:24
Alignment explanation
Indices: 1039666--1039736 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
1039656 CCACATAGAT
1039666 TTGTCCCGAAGGACCGCGTAGAAC
1 TTGTCCCGAAGGACCGCGTAGAAC
** *
1039690 TTGTCTTGAAGGACCACGTAGAA-
1 TTGTCCCGAAGGACCGCGTAGAAC
* *
1039713 TTGTCCCGAATGACCGTGTAGAAC
1 TTGTCCCGAAGGACCGCGTAGAAC
1039737 CCTCAACTCT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
23 18 0.47
24 20 0.53
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.23
Consensus pattern (24 bp):
TTGTCCCGAAGGACCGCGTAGAAC
Found at i:1039907 original size:15 final size:15
Alignment explanation
Indices: 1039837--1039913 Score: 57
Period size: 15 Copynumber: 5.2 Consensus size: 15
1039827 GATTATTGTT
*
1039837 TATTCACATAGAACA
1 TATTCACATATAACA
* * **
1039852 CATTCACTTAGCACA
1 TATTCACATATAACA
* *
1039867 AATTCACATA-AATA
1 TATTCACATATAACA
*
1039881 TTTTCACATATAACA
1 TATTCACATATAACA
* *
1039896 TATTCACCTATACCA
1 TATTCACATATAACA
1039911 TAT
1 TAT
1039914 ACTCATAGTA
Statistics
Matches: 48, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
14 10 0.21
15 38 0.79
ACGTcount: A:0.42, C:0.23, G:0.03, T:0.32
Consensus pattern (15 bp):
TATTCACATATAACA
Found at i:1040583 original size:21 final size:20
Alignment explanation
Indices: 1040554--1040594 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1040544 ATACCTCCAC
1040554 ATCAATATTGACACTACTTCA
1 ATCAATATTGACACTA-TTCA
* *
1040575 ATCAGTATTGATACTATTCA
1 ATCAATATTGACACTATTCA
1040595 TCTGATTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.37
Consensus pattern (20 bp):
ATCAATATTGACACTATTCA
Found at i:1045728 original size:20 final size:18
Alignment explanation
Indices: 1045705--1045744 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
1045695 TGCGTTATAA
1045705 ATATTATAATAAATATAATT
1 ATATTATAAT-AAT-TAATT
*
1045725 ATATTATTATAATTAATT
1 ATATTATAATAATTAATT
1045743 AT
1 AT
1045745 TACAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 3 0.16
20 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATTATAATAATTAATT
Found at i:1045745 original size:13 final size:14
Alignment explanation
Indices: 1045718--1045751 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1045708 TTATAATAAA
1045718 TATAATTATATTAT
1 TATAATTATATTAT
1045732 TATAATTA-ATTAT
1 TATAATTATATTAT
*
1045745 TACAATT
1 TATAATT
1045752 TTACAGGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
TATAATTATATTAT
Found at i:1046753 original size:18 final size:18
Alignment explanation
Indices: 1046730--1046764 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1046720 TAGAGAGATG
*
1046730 TGAGAGTTTCTCTCTCTT
1 TGAGAGCTTCTCTCTCTT
1046748 TGAGAGCTTCTCTCTCT
1 TGAGAGCTTCTCTCTCT
1046765 AAAGAGAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (18 bp):
TGAGAGCTTCTCTCTCTT
Found at i:1057884 original size:13 final size:13
Alignment explanation
Indices: 1057866--1057897 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1057856 TATGTGAGTT
1057866 CACTGAGGTTGTG
1 CACTGAGGTTGTG
1057879 CACTGAGGTTGTG
1 CACTGAGGTTGTG
1057892 CACTGA
1 CACTGA
1057898 TGCTATCACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (13 bp):
CACTGAGGTTGTG
Found at i:1057969 original size:18 final size:18
Alignment explanation
Indices: 1057946--1057998 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
1057936 ACTGTATATT
* *
1057946 TGTCCCGAATGACCATTA
1 TGTCCCGAAGGACCACTA
1057964 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1057982 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1057999 CCTTAAGAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.26, C:0.32, G:0.21, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1063281 original size:18 final size:18
Alignment explanation
Indices: 1063258--1063346 Score: 178
Period size: 18 Copynumber: 4.9 Consensus size: 18
1063248 ACTGTATATT
1063258 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1063276 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1063294 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1063312 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1063330 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1063347 CCTTAAGAGC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 71 1.00
ACGTcount: A:0.27, C:0.34, G:0.22, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1065761 original size:14 final size:14
Alignment explanation
Indices: 1065744--1065772 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1065734 GGTAGTACAC
1065744 AAGTTACCAATAAA
1 AAGTTACCAATAAA
1065758 AAGTTACCAATAAA
1 AAGTTACCAATAAA
1065772 A
1 A
1065773 TCAGTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.14, G:0.07, T:0.21
Consensus pattern (14 bp):
AAGTTACCAATAAA
Found at i:1067602 original size:3 final size:3
Alignment explanation
Indices: 1067594--1067628 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
1067584 TCTTAACATT
* *
1067594 GAA GAA GAA GAA GAA TAA GAA GAA TAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1067629 GAATCCTTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.06
Consensus pattern (3 bp):
GAA
Found at i:1069979 original size:20 final size:18
Alignment explanation
Indices: 1069956--1069995 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
1069946 TACGTTATAA
1069956 ATATTATAATAAATATAATT
1 ATATTATAAT-AAT-TAATT
*
1069976 ATATTATTATAATTAATT
1 ATATTATAATAATTAATT
1069994 AT
1 AT
1069996 TTCAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 3 0.16
20 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATTATAATAATTAATT
Found at i:1071476 original size:24 final size:20
Alignment explanation
Indices: 1071420--1071473 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
1071410 TAATCATTAA
1071420 TAATTAGTATATTATGTGAT
1 TAATTAGTATATTATGTGAT
1071440 TAATTAGTATATTATGTGAT
1 TAATTAGTATATTATGTGAT
1071460 TAATTAGTAT-TTAT
1 TAATTAGTATATTAT
1071474 ATTTTAAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 4 0.12
20 30 0.88
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (20 bp):
TAATTAGTATATTATGTGAT
Found at i:1073748 original size:23 final size:21
Alignment explanation
Indices: 1073697--1073736 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1073687 GGTCACTGAT
1073697 ATAATTTACCTTTTATTTTAA
1 ATAATTTACCTTTTATTTTAA
*
1073718 ATAATTTACCTTTAATTTT
1 ATAATTTACCTTTTATTTT
1073737 TTAACTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (21 bp):
ATAATTTACCTTTTATTTTAA
Found at i:1074085 original size:15 final size:15
Alignment explanation
Indices: 1074067--1074101 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1074057 GGCACATCAA
1074067 TTTTAATTTATATTT
1 TTTTAATTTATATTT
* *
1074082 TTTTCATTTTTATTT
1 TTTTAATTTATATTT
1074097 TTTTA
1 TTTTA
1074102 CGAAATCAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTAATTTATATTT
Found at i:1076841 original size:25 final size:25
Alignment explanation
Indices: 1076781--1076843 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
1076771 GTGTACATTC
*
1076781 TATGTGGCACTTTCGAGTGTAACTA
1 TATGTGGCACTTTCGAGTGCAACTA
* * * *
1076806 TAAGCGACACTTTCGAGTGCAATTA
1 TATGTGGCACTTTCGAGTGCAACTA
1076831 TATGTGGCACTTT
1 TATGTGGCACTTT
1076844 ATGTGTAATT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.35
Consensus pattern (25 bp):
TATGTGGCACTTTCGAGTGCAACTA
Found at i:1079432 original size:20 final size:20
Alignment explanation
Indices: 1079403--1079452 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1079393 GATTTAAGTG
* *
1079403 GTATCGATACCAAGAGGGGA
1 GTATCAATACCAAGAGGAGA
* *
1079423 GTATCAATACCATGAGGATA
1 GTATCAATACCAAGAGGAGA
1079443 GTATCAATAC
1 GTATCAATAC
1079453 TGTCGACAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (20 bp):
GTATCAATACCAAGAGGAGA
Found at i:1080895 original size:25 final size:26
Alignment explanation
Indices: 1080867--1080921 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
1080857 TATGTGATTA
1080867 TAATAT-AATATTATAATATTA-CTAG
1 TAATATCAATATTA-AATATTATCTAG
* *
1080892 TAATATCTATATTAAATATTATTTAG
1 TAATATCAATATTAAATATTATCTAG
1080918 TAAT
1 TAAT
1080922 TATTTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (26 bp):
TAATATCAATATTAAATATTATCTAG
Found at i:1080905 original size:26 final size:27
Alignment explanation
Indices: 1080874--1080933 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
1080864 TTATAATATA
1080874 ATATTATAATATTA-CTAGTAA-TATCT
1 ATATTA-AATATTATCTAGTAATTATCT
* *
1080900 ATATTAAATATTATTTAGTAATTATTT
1 ATATTAAATATTATCTAGTAATTATCT
1080927 ATATTAA
1 ATATTAA
1080934 GTTATTAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 7 0.23
26 12 0.40
27 11 0.37
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (27 bp):
ATATTAAATATTATCTAGTAATTATCT
Found at i:1085565 original size:45 final size:45
Alignment explanation
Indices: 1085478--1085598 Score: 208
Period size: 45 Copynumber: 2.7 Consensus size: 45
1085468 ATAACATTTC
*
1085478 TTACCAGTATA-TTAACCATTTATTCCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTT-ACCATTTATT-CCATAAGCTCGTAAGCTTATT
1085524 TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
1085569 TTACCAATATACTTACCATTTATTCCATAA
1 TTACCAATATACTTACCATTTATTCCATAA
1085599 TCTTATAAAC
Statistics
Matches: 73, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
45 51 0.70
46 20 0.27
47 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (45 bp):
TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
Found at i:1085781 original size:59 final size:59
Alignment explanation
Indices: 1085681--1085808 Score: 175
Period size: 59 Copynumber: 2.2 Consensus size: 59
1085671 GTAGTGCTAA
* * * **
1085681 CCCGAGTATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAGT
1 CCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAGT
* ** *
1085740 CCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTATT
1 CCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAGT
1085799 CCCGAATATG
1 CCCGAATATG
1085809 CTGCATGTTG
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (59 bp):
CCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAGT
Found at i:1086721 original size:29 final size:30
Alignment explanation
Indices: 1086656--1086721 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
1086646 ACAACCCAGT
* * *
1086656 AATTTTTCCAAAATTGCCAAATTGATCCCC
1 AATTTTTCAAAAATTGACAAAATGATCCCC
* * *
1086686 CACTTTTCAAAAATT-ACAAAATGGTCCCC
1 AATTTTTCAAAAATTGACAAAATGATCCCC
1086715 AATTTTT
1 AATTTTT
1086722 TCTAAGGCTT
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35
Consensus pattern (30 bp):
AATTTTTCAAAAATTGACAAAATGATCCCC
Found at i:1090559 original size:20 final size:20
Alignment explanation
Indices: 1090534--1090579 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1090524 CTATTTCCAC
1090534 TCATTTGTAAAGCCTTCGGG
1 TCATTTGTAAAGCCTTCGGG
*
1090554 TCATTTGTAAAGCCTTTGGG
1 TCATTTGTAAAGCCTTCGGG
1090574 TCATTT
1 TCATTT
1090580 ATCAGTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (20 bp):
TCATTTGTAAAGCCTTCGGG
Found at i:1091457 original size:15 final size:15
Alignment explanation
Indices: 1091437--1091469 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1091427 GTGACATTTT
1091437 ATATTATATATTATA
1 ATATTATATATTATA
1091452 ATATTATATATTATA
1 ATATTATATATTATA
1091467 ATA
1 ATA
1091470 ACATATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATTATATATTATA
Found at i:1091475 original size:15 final size:15
Alignment explanation
Indices: 1091442--1091481 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1091432 ATTTTATATT
**
1091442 ATATATTATAATATT
1 ATATATTATAATAAC
1091457 ATATATTATAATAAC
1 ATATATTATAATAAC
1091472 ATATTATTAT
1 ATA-TATTAT
1091482 TATTTATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATATTATAATAAC
Found at i:1092393 original size:27 final size:28
Alignment explanation
Indices: 1092316--1092400 Score: 76
Period size: 27 Copynumber: 3.2 Consensus size: 28
1092306 TCTCCATACG
1092316 TAAATTTATTGCAAAGACATTAA-TTAA
1 TAAATTTATTGCAAAGACATTAATTTAA
* *
1092343 TAAATTTAAATT-TAAAGAGC---AATTTTA
1 TAAATTT--ATTGCAAAGA-CATTAATTTAA
1092370 T-AATTTATTGCAAAGACATTAA-TTAA
1 TAAATTTATTGCAAAGACATTAATTTAA
1092396 TAAAT
1 TAAAT
1092401 ACCGGTACCA
Statistics
Matches: 45, Mismatches: 4, Indels: 18
0.67 0.06 0.27
Matches are distributed among these distances:
24 4 0.09
25 5 0.11
26 11 0.24
27 16 0.36
28 5 0.11
29 4 0.09
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.39
Consensus pattern (28 bp):
TAAATTTATTGCAAAGACATTAATTTAA
Found at i:1092398 original size:26 final size:26
Alignment explanation
Indices: 1092318--1092398 Score: 80
Period size: 26 Copynumber: 3.1 Consensus size: 26
1092308 TCCATACGTA
1092318 AATTTATTGCAAAGACATTAATTAAT
1 AATTTATTGCAAAGACATTAATTAAT
*
1092344 AAATTTAAATT-TAAAGAGCAATT--TT-AT
1 -AATTT--ATTGCAAAGA-C-ATTAATTAAT
1092371 AATTTATTGCAAAGACATTAATTAAT
1 AATTTATTGCAAAGACATTAATTAAT
1092397 AA
1 AA
1092399 ATACCGGTAC
Statistics
Matches: 44, Mismatches: 2, Indels: 17
0.70 0.03 0.27
Matches are distributed among these distances:
23 3 0.07
24 4 0.09
25 7 0.16
26 9 0.20
27 7 0.16
28 7 0.16
29 4 0.09
30 3 0.07
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.38
Consensus pattern (26 bp):
AATTTATTGCAAAGACATTAATTAAT
Found at i:1093285 original size:56 final size:56
Alignment explanation
Indices: 1093123--1093285 Score: 149
Period size: 56 Copynumber: 2.9 Consensus size: 56
1093113 TGATTATCAA
* * **
1093123 ATGGCACTAAGCGTGCAAAAACTTAAGAAATTCATACTAAGTG-TT-TGAA-TTTCAGT
1 ATGGGACTAAGTGTGCAAAAAC-TAAGAAATTCATA--ATTTGCTTATGAATTTTCAGT
* * * *
1093179 ATGGGCACTATGTATGC-AAAACTAAGATATTCATAATTT-CTTTATAAATTTTC-GT
1 ATGGG-ACTAAGTGTGCAAAAACTAAGAAATTCATAATTTGC-TTATGAATTTTCAGT
*
1093234 ATGGGACTAAGTGTGCAAAAAGGTAAGAAATTCATAATTTGCTTATGAATTT
1 ATGGGACTAAGTGTGCAAAAA-CTAAGAAATTCATAATTTGCTTATGAATTT
1093286 CTGTATAAGA
Statistics
Matches: 86, Mismatches: 13, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
53 2 0.02
54 11 0.13
55 26 0.30
56 38 0.44
57 9 0.10
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (56 bp):
ATGGGACTAAGTGTGCAAAAACTAAGAAATTCATAATTTGCTTATGAATTTTCAGT
Found at i:1093766 original size:67 final size:67
Alignment explanation
Indices: 1093497--1093748 Score: 409
Period size: 67 Copynumber: 3.8 Consensus size: 67
1093487 AAAGATTATA
*
1093497 AGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAGGTGCCTT
1 AGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
1093562 TG
66 TG
* *
1093564 AGGCCTAACTGTGCATTGACAGAAAGGTATCAATTGTGCCAGTTAGATGAAAGGCTAAGTGCCTT
1 AGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
1093629 TG
66 TG
*
1093631 AGGCCTAACTGTGCATTGACAGAAAGGTGGT-AATTGTGCCAGTTAGAT-AATAGGCTAAGTGCC
1 AGGCCTAACTGTGCATTGACAGAAAGGT-GTCAATTATGCCAGTTAGATGAA-AGGCTAAGTGCC
1093694 TTTG
64 TTTG
* * *
1093698 AGGCCTAATTGTGCATTGACAGAAAGATGTCAATTATGCTAGTTAGATGAA
1 AGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1093749 TGGTTAAATA
Statistics
Matches: 173, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
66 4 0.02
67 166 0.96
68 3 0.02
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (67 bp):
AGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
TG
Found at i:1093832 original size:80 final size:80
Alignment explanation
Indices: 1093699--1093860 Score: 245
Period size: 80 Copynumber: 2.0 Consensus size: 80
1093689 GTGCCTTTGA
* * * * *
1093699 GGCCTAATTGTGCATTGACAGAAAGATGTCAATTATGCTAGTTAGATGAATGGTTAAATACCGTT
1 GGCCTAACTGTGCATTGACAAAAAGATGACAATTATGCCAGTTAGATGAATGGTTAAACACCGTT
1093764 GAGTAAAAGATAAAT
66 GAGTAAAAGATAAAT
1093779 GGCCTAACTGTGCATTGACAAAAA-AGTGACAATTATGCCAGTTAGATGAATGGTTAAACACCGT
1 GGCCTAACTGTGCATTGACAAAAAGA-TGACAATTATGCCAGTTAGATGAATGGTTAAACACCGT
**
1093843 TTTGTAAAAGATAAAT
65 TGAGTAAAAGATAAAT
1093859 GG
1 GG
1093861 AAAAAAGTTG
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
79 1 0.01
80 73 0.99
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (80 bp):
GGCCTAACTGTGCATTGACAAAAAGATGACAATTATGCCAGTTAGATGAATGGTTAAACACCGTT
GAGTAAAAGATAAAT
Found at i:1095931 original size:27 final size:28
Alignment explanation
Indices: 1095900--1095952 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
1095890 TAGCATATTA
*
1095900 AAAAAAAT-AAAGCTTGAAAA-TAAAAG
1 AAAAAAATGAAAACTTGAAAAGTAAAAG
1095926 AAAAAAATGAAAACTTGAAAAGTAAAA
1 AAAAAAATGAAAACTTGAAAAGTAAAA
1095953 AGAGAAAGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 8 0.33
27 11 0.46
28 5 0.21
ACGTcount: A:0.70, C:0.04, G:0.11, T:0.15
Consensus pattern (28 bp):
AAAAAAATGAAAACTTGAAAAGTAAAAG
Found at i:1100016 original size:6 final size:6
Alignment explanation
Indices: 1100001--1100034 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1099991 GCTTAATCAA
*
1100001 AAAAAT AAAAAC AAAAAC AAAAAC -AAAAC AAAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAA
1100035 ATGTAACGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.85, C:0.12, G:0.00, T:0.03
Consensus pattern (6 bp):
AAAAAC
Found at i:1107863 original size:7 final size:7
Alignment explanation
Indices: 1107851--1107880 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1107841 ACTCTAGTTC
1107851 CTTTGTT
1 CTTTGTT
1107858 CTTTGTT
1 CTTTGTT
1107865 CTTTGTT
1 CTTTGTT
*
1107872 CTTTATT
1 CTTTGTT
1107879 CT
1 CT
1107881 CTTGGTGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.03, C:0.17, G:0.10, T:0.70
Consensus pattern (7 bp):
CTTTGTT
Found at i:1108704 original size:13 final size:13
Alignment explanation
Indices: 1108688--1108726 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1108678 CTATTTAATG
*
1108688 ATTAAATTTATTT
1 ATTATATTTATTT
*
1108701 ATTATATTAATTT
1 ATTATATTTATTT
*
1108714 AATATATTTATTT
1 ATTATATTTATTT
1108727 TCTACCAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTATATTTATTT
Found at i:1110019 original size:2 final size:2
Alignment explanation
Indices: 1110012--1110046 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1110002 AAAAACATGA
1110012 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1110047 CTAGCCATTC
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:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1113241 original size:25 final size:25
Alignment explanation
Indices: 1113207--1113256 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1113197 GAATTGCTTG
1113207 AAGAAACTAACATTTTATATATAAT
1 AAGAAACTAACATTTTATATATAAT
1113232 AAGAAACTAACATTTTATATATAAT
1 AAGAAACTAACATTTTATATATAAT
1113257 TGCAGTCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.36
Consensus pattern (25 bp):
AAGAAACTAACATTTTATATATAAT
Found at i:1114514 original size:17 final size:17
Alignment explanation
Indices: 1114492--1114530 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1114482 ATGAAGACAA
* *
1114492 TTTAATTAATGTACTAG
1 TTTAATGAATGAACTAG
*
1114509 TTTAATGAATGAACTAT
1 TTTAATGAATGAACTAG
1114526 TTTAA
1 TTTAA
1114531 CTAGTAAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.46
Consensus pattern (17 bp):
TTTAATGAATGAACTAG
Found at i:1117888 original size:24 final size:25
Alignment explanation
Indices: 1117829--1117888 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
1117819 TTAGTTACTA
*
1117829 ACTTTTATTTTCTTTCATTTTAGTC
1 ACTTTTATTTTATTTCATTTTAGTC
*
1117854 ATTTTTATTTTATTTCGA-TTTAG-C
1 ACTTTTATTTTATTTC-ATTTTAGTC
*
1117878 CCTTTTATTTT
1 ACTTTTATTTT
1117889 GTTTTGTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 10 0.33
25 19 0.63
26 1 0.03
ACGTcount: A:0.17, C:0.13, G:0.05, T:0.65
Consensus pattern (25 bp):
ACTTTTATTTTATTTCATTTTAGTC
Found at i:1117995 original size:17 final size:18
Alignment explanation
Indices: 1117973--1118025 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
1117963 TAGGTCCTCA
1117973 TATTTTATTTTTATTTT-
1 TATTTTATTTTTATTTTG
1117990 TATTTTATGTTTT-TTATTG
1 TATTTTAT-TTTTATT-TTG
*
1118009 TTTTTTATTTTTTATTT
1 TATTTTA-TTTTTATTT
1118026 GTTGTTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
17 10 0.33
18 6 0.20
19 11 0.37
20 3 0.10
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.81
Consensus pattern (18 bp):
TATTTTATTTTTATTTTG
Found at i:1118042 original size:22 final size:22
Alignment explanation
Indices: 1118006--1118051 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1117996 ATGTTTTTTA
*
1118006 TTGTTTTTTATTTTTTATT-TG
1 TTGTTTTTTAATTTTTATTATG
1118027 TTGTTTTTATAATTTTTATTATG
1 TTGTTTTT-TAATTTTTATTATG
1118050 TT
1 TT
1118052 TATTAATTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.36
22 10 0.45
23 4 0.18
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (22 bp):
TTGTTTTTTAATTTTTATTATG
Found at i:1118043 original size:30 final size:30
Alignment explanation
Indices: 1117980--1118043 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
1117970 TCATATTTTA
**
1117980 TTTTTATTTTTATTTTATGTTTTTTATTGT
1 TTTTTATTTTTATTTTATGTTTTTTATAAT
1118010 TTTTTATTTTTTATTTGT-TG-TTTTTATAAT
1 TTTTTA-TTTTTATTT-TATGTTTTTTATAAT
1118040 TTTT
1 TTTT
1118044 ATTATGTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 18 0.60
31 11 0.37
32 1 0.03
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.80
Consensus pattern (30 bp):
TTTTTATTTTTATTTTATGTTTTTTATAAT
Found at i:1125097 original size:31 final size:31
Alignment explanation
Indices: 1125038--1125097 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
1125028 ATATAGATCA
1125038 TTTCCATATAATTTGCATGTCACATATATCT
1 TTTCCATATAATTTGCATGTCACATATATCT
*
1125069 TTTCTCATAT-ATTT-CATGTACCCATATAT
1 TTTC-CATATAATTTGCATGT-CACATATAT
1125098 ATATTATATG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 5 0.19
31 16 0.62
32 5 0.19
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.47
Consensus pattern (31 bp):
TTTCCATATAATTTGCATGTCACATATATCT
Found at i:1127408 original size:17 final size:17
Alignment explanation
Indices: 1127384--1127427 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1127374 TAAATAAGAC
* *
1127384 AATTTAATTAATGTACT
1 AATTTAATTAACGAACT
* *
1127401 AGTTTAATGAACGAACT
1 AATTTAATTAACGAACT
1127418 AATTTAATTA
1 AATTTAATTA
1127428 GAGAACTAGC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (17 bp):
AATTTAATTAACGAACT
Found at i:1130138 original size:15 final size:16
Alignment explanation
Indices: 1130109--1130142 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1130099 GAATTAGATA
1130109 TTTAGATTTTGGGGAT
1 TTTAGATTTTGGGGAT
1130125 TTTAGATTTT-GGGAT
1 TTTAGATTTTGGGGAT
1130140 TTT
1 TTT
1130143 GGGTGACAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.18, C:0.00, G:0.26, T:0.56
Consensus pattern (16 bp):
TTTAGATTTTGGGGAT
Found at i:1130190 original size:14 final size:14
Alignment explanation
Indices: 1130171--1130197 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1130161 CGATTGATTA
1130171 ATGGGTGGGTGACG
1 ATGGGTGGGTGACG
1130185 ATGGGTGGGTGAC
1 ATGGGTGGGTGAC
1130198 CGTTCGGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.07, G:0.56, T:0.22
Consensus pattern (14 bp):
ATGGGTGGGTGACG
Found at i:1134351 original size:20 final size:22
Alignment explanation
Indices: 1134303--1134351 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
1134293 GAAATATTTT
*
1134303 ATATATTTGTACCATTCTTTCA
1 ATATATATGTACCATTCTTTCA
1134325 ATATATATGTA-CATT-TTT-A
1 ATATATATGTACCATTCTTTCA
1134344 AGTATATA
1 A-TATATA
1134352 CTAAAACATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 2 0.08
20 9 0.36
21 4 0.16
22 10 0.40
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.49
Consensus pattern (22 bp):
ATATATATGTACCATTCTTTCA
Found at i:1134533 original size:23 final size:23
Alignment explanation
Indices: 1134498--1134545 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1134488 TTAGTTTATT
**
1134498 TTTATCTTTTAAAATATTATAAA
1 TTTATCTCATAAAATATTATAAA
*
1134521 TTTATCTCATAAAATATTTTAAA
1 TTTATCTCATAAAATATTATAAA
1134544 TT
1 TT
1134546 CGTCAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTATCTCATAAAATATTATAAA
Found at i:1134958 original size:20 final size:21
Alignment explanation
Indices: 1134928--1134966 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1134918 ATTACATATA
*
1134928 CAAATATGACAAAATCGGTCC
1 CAAATATGACAAAACCGGTCC
1134949 CAAA-ATGACAAAACCGGT
1 CAAATATGACAAAACCGGT
1134967 AAAACGCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.46, C:0.23, G:0.15, T:0.15
Consensus pattern (21 bp):
CAAATATGACAAAACCGGTCC
Found at i:1135333 original size:164 final size:168
Alignment explanation
Indices: 1135058--1135739 Score: 647
Period size: 164 Copynumber: 3.9 Consensus size: 168
1135048 TAGCGCCTAT
* ** * *
1135058 AAAGTGTCGATACTTTAAAAAAATATATCGATCCATAATAATATAATAGGTAAAAATATGATAAA
1 AAAGTGTCGACACTTTATGAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
* * * *
1135123 ACAGGTCTCAAAATTGACCAAACCAGTAAAACGATACCGAATATGTTGAAAGTGTCGATACTTTA
66 ACAGGTCTCAAAAATGACAAAACCAGTAAAACGATACCGGATATGTTGAAAGTGTCGATAATTTA
1135188 ATATAAGTATCGACACTTTCT--AAAA-TTA-AACTAA
131 ATATAAGTATCGACACTTTCTAAAAAAGTTATAACTAA
* * *
1135222 AAAGTGTCGACACTTTATGAAAATGTATCGATCCATAAGAATATACCAGGTAAAAATATGATAAA
1 AAAGTGTCGACACTTTATGAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
* * * *
1135287 ACAGGTCTCAAAAATGACAAAACCGGAAAAAAGATACCGGATATGTTAAAAGTGTCGATAATTTA
66 ACAGGTCTCAAAAATGACAAAACCAGTAAAACGATACCGGATATGTTGAAAGTGTCGATAATTTA
* *
1135352 ATATAAGTATCGGCACTTTCTGAATTTAAAAGAGAAGTTATAGCGCCTAA
131 ATATAAGTATCGACACTTTC------T-AAA-A-AAGTTATA---ACTAA
* **
1135402 AAAGTGTCGACACTTTATGAAAATATATCGATCTATAACAATATAACATCTAAAAATATGATAAA
1 AAAGTGTCGACACTTTATGAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
* * * * * * *
1135467 ACCGGCCTCAACAATGAAAAAACCGGTAAAACGATATCAGATATGTTGAAAGTGTCAATACTTTA
66 ACAGGTCTCAAAAATGACAAAACCAGTAAAACGATACCGGATATGTTGAAAGTG----T-C----
* * * *
1135532 ATATAACTTTAATATAACTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAACGCCTAT
122 -GATAA-TTTAATATAAGTATCGACAC--TT----TCTAAAA------AAGTTATAA---CTAA
* *
1135596 AAAGTGTCGATACTTTA--AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
1 AAAGTGTCGACACTTTATGAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGAT-AA
* *
1135659 AACAGGTCTCAAAATTGACAAAACCAGTAAAACGCTACCGGATATGTTGAAAGTGTCGATAATTT
65 AACAGGTCTCAAAAATGACAAAACCAGTAAAACGATACCGGATATGTTGAAAGTGTCGATAATTT
1135724 AATATAAGTATCGACA
130 AATATAAGTATCGACA
1135740 TTTTATGAAT
Statistics
Matches: 422, Mismatches: 54, Indels: 66
0.78 0.10 0.12
Matches are distributed among these distances:
164 134 0.32
170 1 0.00
173 1 0.00
174 1 0.00
175 2 0.00
176 3 0.01
177 1 0.00
180 108 0.26
182 18 0.04
183 4 0.01
184 1 0.00
185 1 0.00
188 1 0.00
189 2 0.00
190 7 0.02
191 19 0.05
192 39 0.09
193 50 0.12
194 28 0.07
197 1 0.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (168 bp):
AAAGTGTCGACACTTTATGAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
ACAGGTCTCAAAAATGACAAAACCAGTAAAACGATACCGGATATGTTGAAAGTGTCGATAATTTA
ATATAAGTATCGACACTTTCTAAAAAAGTTATAACTAA
Found at i:1135521 original size:180 final size:181
Alignment explanation
Indices: 1135218--1135909 Score: 860
Period size: 180 Copynumber: 3.8 Consensus size: 181
1135208 TAAAATTAAA
* *
1135218 CTAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAAGAATATACCAGGTAAAAATATGA
1 CTAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGA
* * * *
1135283 TAAAACAGGTCTCAAAAATGACAAAACCGGAAAAAAGATACCGGATATGTTAAAAGTGTCGATAA
66 TAAAACAGGTCTC-AAAATGAAAAAACCGGTAAAACGATACCGGATATGTTGAAAGTGTCGATAA
*
1135348 TTTAATATAAGTATCGGCACTTTCTGAATTT-AAA-AG-AGAAGTTATAGCGC
130 TTTAATATAAGTATCGACACTTT-TGAATTTAAAAGAGAAGAAGTTATAGCGC
* * **
1135398 CTAAAAAGTGTCGACACTTTATGAAAATATATCGATCTATAACAATATAACATCTAAAAATATGA
1 CTAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGA
* * * *
1135463 TAAAACCGGCCTCAACAATGAAAAAACCGGTAAAACGATATCAGATATGTTGAAAGTGTCAATAC
66 TAAAACAGGTCTCAA-AATGAAAAAACCGGTAAAACGATACCGGATATGTTGAAAGTG----T-C
* * *
1135528 TTTAATATAACTTTAATATAACTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAACGC
125 -----GATAA-TTTAATATAAGTATCGACACTTTT-GAATTTAAAAGAGAAGAAGTTATAGCGC
* *
1135592 CTATAAAGTGTCGATACTTTA--AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGA
1 CTAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGA
* * *
1135655 TAAAAACAGGTCTCAAAATTGACAAAACCAGTAAAACGCTACCGGATATGTTGAAAGTGTCGATA
66 T-AAAACAGGTCTCAAAA-TGAAAAAACCGGTAAAACGATACCGGATATGTTGAAAGTGTCGATA
*
1135720 ATTTAATATAAGTATCGACATTTTATGAATTTAAAAGAGAAGAAGTTATAGCGC
129 ATTTAATATAAGTATCGACACTTT-TGAATTTAAAAGAGAAGAAGTTATAGCGC
* * *
1135774 CTATAAAA-TGTCGATACTTT-TAAAAAATGTATCGATCCATAACAATATAATAGGTAAAAATAT
1 CTA-AAAAGTGTCGACACTTTAT-GAAAATGTATCGATCCATAACAATATAACAGGTAAAAATAT
* * *
1135837 GATAAAACCGGTCTCAAAATGAAAAAACCGGT-AAAGGATTATCGGATATGTTGAAAGTGTCGAT
64 GATAAAACAGGTCTCAAAATGAAAAAACCGGTAAAACGA-TACCGGATATGTTGAAAGTGTCGAT
*
1135901 ACTTTAATA
128 AATTTAATA
1135910 AGTACACGTA
Statistics
Matches: 444, Mismatches: 44, Indels: 46
0.83 0.08 0.09
Matches are distributed among these distances:
179 2 0.00
180 106 0.24
181 4 0.01
182 106 0.24
183 23 0.05
184 43 0.10
185 1 0.00
188 1 0.00
189 1 0.00
190 5 0.01
191 27 0.06
192 44 0.10
193 49 0.11
194 32 0.07
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.27
Consensus pattern (181 bp):
CTAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGA
TAAAACAGGTCTCAAAATGAAAAAACCGGTAAAACGATACCGGATATGTTGAAAGTGTCGATAAT
TTAATATAAGTATCGACACTTTTGAATTTAAAAGAGAAGAAGTTATAGCGC
Found at i:1135542 original size:11 final size:11
Alignment explanation
Indices: 1135526--1135550 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1135516 AAGTGTCAAT
1135526 ACTTTAATATA
1 ACTTTAATATA
1135537 ACTTTAATATA
1 ACTTTAATATA
1135548 ACT
1 ACT
1135551 ATCGACACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (11 bp):
ACTTTAATATA
Found at i:1135762 original size:182 final size:180
Alignment explanation
Indices: 1135222--1135909 Score: 846
Period size: 182 Copynumber: 3.7 Consensus size: 180
1135212 ATTAAACTAA
* *
1135222 AAAGTGTCGACACTTTATGAAAATGTATCGATCCATAAGAATATACCAGGTAAAAATATGATAAA
1 AAAGTGTCGACACTTTA-GAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
* * * *
1135287 ACAGGTCTCAAAAATGACAAAACCGGAAAAAAGATACCGGATATGTTAAAAGTGTCGATAATTTA
65 ACAGGTCTC-AAAATGAAAAAACCGGTAAAACGATACCGGATATGTTGAAAGTGTCGATAATTTA
* * *
1135352 ATATAAGTATCGGCACTTTCTGAATTT-AAA-AG-AGAAGTTATAGCGCCTAA
129 ATATAAGTATCGACA-TTTTTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAT
* * **
1135402 AAAGTGTCGACACTTTATGAAAATATATCGATCTATAACAATATAACATCTAAAAATATGATAAA
1 AAAGTGTCGACACTTTA-GAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
* * * *
1135467 ACCGGCCTCAACAATGAAAAAACCGGTAAAACGATATCAGATATGTTGAAAGTGTCAATACTTTA
65 ACAGGTCTCAA-AATGAAAAAACCGGTAAAACGATACCGGATATGTTGAAAGTG----T-C----
* * * *
1135532 ATATAACTTTAATATAACTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAACGCCTAT
120 -GATAA-TTTAATATAAGTATCGACA-TTTTTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAT
*
1135596 AAAGTGTCGATACTTTA-AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAA
1 AAAGTGTCGACACTTTAGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAT-AAA
* * *
1135660 ACAGGTCTCAAAATTGACAAAACCAGTAAAACGCTACCGGATATGTTGAAAGTGTCGATAATTTA
65 ACAGGTCTCAAAA-TGAAAAAACCGGTAAAACGATACCGGATATGTTGAAAGTGTCGATAATTTA
1135725 ATATAAGTATCGACATTTTATGAATTTAAAAGAGAAGAAGTTATAGCGCCTAT
129 ATATAAGTATCGACATTTT-TGAATTTAAAAGAGAAGAAGTTATAGCGCCTAT
* * * *
1135778 AAAATGTCGATACTTTTAAAAAATGTATCGATCCATAACAATATAATAGGTAAAAATATGATAAA
1 AAAGTGTCGACAC-TTTAGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
* * * *
1135843 ACCGGTCTCAAAATGAAAAAACCGGT-AAAGGATTATCGGATATGTTGAAAGTGTCGATACTTTA
65 ACAGGTCTCAAAATGAAAAAACCGGTAAAACGA-TACCGGATATGTTGAAAGTGTCGATAATTTA
1135907 ATA
129 ATA
1135910 AGTACACGTA
Statistics
Matches: 441, Mismatches: 46, Indels: 40
0.84 0.09 0.08
Matches are distributed among these distances:
179 2 0.00
180 102 0.23
181 8 0.02
182 104 0.24
183 23 0.05
184 43 0.10
185 1 0.00
188 1 0.00
189 1 0.00
190 4 0.01
191 27 0.06
192 44 0.10
193 49 0.11
194 32 0.07
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.27
Consensus pattern (180 bp):
AAAGTGTCGACACTTTAGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAA
CAGGTCTCAAAATGAAAAAACCGGTAAAACGATACCGGATATGTTGAAAGTGTCGATAATTTAAT
ATAAGTATCGACATTTTTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAT
Found at i:1136320 original size:16 final size:16
Alignment explanation
Indices: 1136299--1136333 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1136289 ATTTAATATT
1136299 TATAGGTAAAAAATGA
1 TATAGGTAAAAAATGA
*
1136315 TATAGGTAGAAAATGA
1 TATAGGTAAAAAATGA
1136331 TAT
1 TAT
1136334 TTTAGGTTGT
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:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (16 bp):
TATAGGTAAAAAATGA
Found at i:1137653 original size:22 final size:22
Alignment explanation
Indices: 1137602--1137657 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
1137592 AATGTTTTTG
*
1137602 TTTTTTTATATAAAATGATAGTA
1 TTTTATTATATAAAATGATAG-A
*
1137625 TAGTTATTATATAAAATGATA-A
1 T-TTTATTATATAAAATGATAGA
1137647 CTTTTATTATA
1 -TTTTATTATA
1137658 AATACAGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 9 0.32
23 2 0.07
24 17 0.61
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (22 bp):
TTTTATTATATAAAATGATAGA
Found at i:1137907 original size:9 final size:9
Alignment explanation
Indices: 1137895--1137946 Score: 59
Period size: 9 Copynumber: 5.8 Consensus size: 9
1137885 TCAAGGAGTT
1137895 AGAGGAGGC
1 AGAGGAGGC
*
1137904 AGAGGAAGC
1 AGAGGAGGC
*
1137913 AGAGGAGGA
1 AGAGGAGGC
*
1137922 AGAGGAAGC
1 AGAGGAGGC
*
1137931 AAAGGAGGC
1 AGAGGAGGC
*
1137940 AGTGGAG
1 AGAGGAG
1137947 AAGGAAGAAG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.40, C:0.08, G:0.50, T:0.02
Consensus pattern (9 bp):
AGAGGAGGC
Found at i:1137916 original size:18 final size:18
Alignment explanation
Indices: 1137895--1137941 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
1137885 TCAAGGAGTT
1137895 AGAGGAGGCAGAGGAAGC
1 AGAGGAGGCAGAGGAAGC
*
1137913 AGAGGAGGAAGAGGAAGC
1 AGAGGAGGCAGAGGAAGC
*
1137931 AAAGGAGGCAG
1 AGAGGAGGCAG
1137942 TGGAGAAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.43, C:0.09, G:0.49, T:0.00
Consensus pattern (18 bp):
AGAGGAGGCAGAGGAAGC
Found at i:1137926 original size:27 final size:27
Alignment explanation
Indices: 1137895--1137946 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1137885 TCAAGGAGTT
* *
1137895 AGAGGAGGCAGAGGAAGCAGAGGAGGA
1 AGAGGAAGCAAAGGAAGCAGAGGAGGA
* *
1137922 AGAGGAAGCAAAGGAGGCAGTGGAG
1 AGAGGAAGCAAAGGAAGCAGAGGAG
1137947 AAGGAAGAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.40, C:0.08, G:0.50, T:0.02
Consensus pattern (27 bp):
AGAGGAAGCAAAGGAAGCAGAGGAGGA
Found at i:1138376 original size:18 final size:18
Alignment explanation
Indices: 1138353--1138391 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1138343 GAAAAAATTT
* *
1138353 GAAGAAGAGAAGATGGAG
1 GAAGAAGAAAAGATAGAG
1138371 GAAGAAGAAAAGATAGAG
1 GAAGAAGAAAAGATAGAG
1138389 GAA
1 GAA
1138392 ATGAGGAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.38, T:0.05
Consensus pattern (18 bp):
GAAGAAGAAAAGATAGAG
Done.