Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007418.1 Hibiscus syriacus cultivar Beakdansim tig00020063_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: 1198774
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 6
Found at i:912313 original size:96 final size:96
Alignment explanation
Indices: 912114--912313 Score: 208
Period size: 96 Copynumber: 2.1 Consensus size: 96
912104 ATCACTGATT
* * * * *
912114 TACTGGTTTATAAACTATTGTTACTTGAAATATGTTCTCTGGTTACGAATTTTCACTGTAAAGTA
1 TACTGGTTTATAAACTATTGTTACCTGAAATATGTTATCTGGTTACCAATTTTCACTGGAAAATA
* * *
912179 TGATCTTTTCTGATTTATAGATCATGGAACC
66 TGATCTTTCCTGATATATAGATCATGAAACC
* * * * * **
912210 TATTGGTTTATGAACTA-TGATTACCTGAAATGTGTTATTTGGTTTCCTGTTTTCACTGGAAAAT
1 TACTGGTTTATAAACTATTG-TTACCTGAAATATGTTATCTGGTTACCAATTTTCACTGGAAAAT
*
912274 ATGAT-TGTTCCTGATATAT-GTATCATGAAATC
65 ATGATCT-TTCCTGATATATAG-ATCATGAAACC
912306 TACTGGTT
1 TACTGGTT
912314 AATACTTGAA
Statistics
Matches: 84, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
95 4 0.05
96 80 0.95
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.43
Consensus pattern (96 bp):
TACTGGTTTATAAACTATTGTTACCTGAAATATGTTATCTGGTTACCAATTTTCACTGGAAAATA
TGATCTTTCCTGATATATAGATCATGAAACC
Found at i:915673 original size:17 final size:16
Alignment explanation
Indices: 915644--915676 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
915634 TGAAAACAAA
915644 CAAATAAAATAATAAC
1 CAAATAAAATAATAAC
915660 CAAATAATAATAATAAC
1 CAAATAA-AATAATAAC
915677 ATTAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (16 bp):
CAAATAAAATAATAAC
Found at i:917462 original size:524 final size:524
Alignment explanation
Indices: 916373--918461 Score: 4050
Period size: 524 Copynumber: 4.0 Consensus size: 524
916363 GGGCGGGTGG
*
916373 GGCAGTCATTCTCCTGAAATTTTCAATGTCTCCAATATTTTAGATTTTTTATGTATATCTTTAAA
1 GGCAGTCGTTCTCCTGAAATTTTCAATGTCTCCAATATTTTAGATTTTTTATGTATATCTTTAAA
916438 TTGATAATTTTTTTGTACTCCTTAAATTTTATAAATTCACTCTCTTAGCATAAAATTCTACGTTC
66 TTGATAATTTTTTTGTACTCCTTAAATTTTATAAATTCACTCTCTTAGCATAAAATTCTACGTTC
*
916503 GTCGCTGAGTCAATAGCATAAGATGTTAGAATTAGAGAATAAGTAGATATTGTAAATAAATGACC
131 GTCACTGAGTCAATAGCATAAGATGTTAGAATTAGAGAATAAGTAGATATTGTAAATAAATGACC
916568 CTATCAAATTTTAATGAAACTTTATGTCTTTTGATATGGTTAAATTTCGATCAATCCATGAATCA
196 CTATCAAATTTTAATGAAACTTTATGTCTTTTGATATGGTTAAATTTCGATCAATCCATGAATCA
*
916633 TGTGTATACATATTTATGATTGTATTTTACATATGAGTAAACATTTAACAC--T--G---T-ATT
261 TGTGTATACATATTTATGATTGTATTTTAAATATGAGTAAACATTTAACACTGTAGGACATGATT
916690 AAAATGAAAATGGTAATCTAAGGACATGATTAATATATTTTACAATTTAGGGTTCAGTTTAAAAC
326 AAAATGAAAATGGTAATCTAAGGACATGATTAATATATTTTACAATTTAGGGTTCAGTTTAAAAC
916755 TAAAATATAATTTTTAGGTGTTTGATATAATTAGCACTTAATAGTTGGGTTTAAATATTGTTATA
391 TAAAATATAATTTTTAGGTGTTTGATATAATTAGCACTTAATAGTTGGGTTTAAATATTGTTATA
*
916820 CATGTCATAATATAATTTATTATTCATTTTTTAACACAATCCTTAATTTGCTTTTATTAATTCAA
456 CATGTCATAATATAATTTATTATTCATTTTTTAACACAATCCTTAATTTGCTTTTATTGATTCAA
916885 TTAT
521 TTAT
* *
916889 GGCAGTCGTTCTCCTAAAATTTTCAATGTCTCCAATATTTTAGATTTTTTATGTATATATTTAAA
1 GGCAGTCGTTCTCCTGAAATTTTCAATGTCTCCAATATTTTAGATTTTTTATGTATATCTTTAAA
*
916954 TTGATAATTTTTTTGTACTCCTTAAATTTTATAAATTCACTCTCTTAGCATAAAATTCTACATTC
66 TTGATAATTTTTTTGTACTCCTTAAATTTTATAAATTCACTCTCTTAGCATAAAATTCTACGTTC
917019 GTCACTGAGTCAATAGCATAAGATGTTAGAATTAGAGAATAAGTAGATATTGTAAATAAATGACC
131 GTCACTGAGTCAATAGCATAAGATGTTAGAATTAGAGAATAAGTAGATATTGTAAATAAATGACC
917084 CTATCAAATTTTAATGAAACTTTATGTCTTTTGATATGGTTAAATTTCGATCAATCCATGAATCA
196 CTATCAAATTTTAATGAAACTTTATGTCTTTTGATATGGTTAAATTTCGATCAATCCATGAATCA
917149 TGTGTATACATATTTATGATTGTATTTTAAATATGAGTAAACATTTAACACTGTAGGACATGATT
261 TGTGTATACATATTTATGATTGTATTTTAAATATGAGTAAACATTTAACACTGTAGGACATGATT
917214 AAAATGAAAATGGTAATCTAAGGACATGATTAATATATTTTACAATTTAGGGTTCAGTTTAAAAC
326 AAAATGAAAATGGTAATCTAAGGACATGATTAATATATTTTACAATTTAGGGTTCAGTTTAAAAC
917279 TAAAATATAATTTTTAGGTGTTTGATATAATTAGCACTTAATAGTTGGGTTTAAATATTGTTATA
391 TAAAATATAATTTTTAGGTGTTTGATATAATTAGCACTTAATAGTTGGGTTTAAATATTGTTATA
917344 CATGTCATAATATAATTTATTATTCATTTTTTAACACAATCCTTAATTTGCTTTTATTGATTCAA
456 CATGTCATAATATAATTTATTATTCATTTTTTAACACAATCCTTAATTTGCTTTTATTGATTCAA
917409 TTAT
521 TTAT
917413 GGCAGTCGTTCTCCTGAAATTTTCAATGTCTCCAATATTTTAGATTTTTTATGTATATCTTTAAA
1 GGCAGTCGTTCTCCTGAAATTTTCAATGTCTCCAATATTTTAGATTTTTTATGTATATCTTTAAA
917478 TTGATAATTTTTTTGTACTCCTTAAATTTTATAAATTCACTCTCTTAGCATAAAATTCTACGTTC
66 TTGATAATTTTTTTGTACTCCTTAAATTTTATAAATTCACTCTCTTAGCATAAAATTCTACGTTC
*
917543 GTCACTGAGTCAATAGCATAAGATGTTAGAATTAGAGAATAAGTAGATATTGTAAATAAATAACC
131 GTCACTGAGTCAATAGCATAAGATGTTAGAATTAGAGAATAAGTAGATATTGTAAATAAATGACC
917608 CTATCAAATTTTAATGAAACTTTATGTCTTTTGATATGGTTAAATTTCGATCAATCCATGAATCA
196 CTATCAAATTTTAATGAAACTTTATGTCTTTTGATATGGTTAAATTTCGATCAATCCATGAATCA
917673 TGTGTATACATATTTATGATTGTATTTTAAATATGAGTAAACATTTAACACTGTAGGACATGATT
261 TGTGTATACATATTTATGATTGTATTTTAAATATGAGTAAACATTTAACACTGTAGGACATGATT
917738 AAAATGAAAATGGTAATCTAAGGACATGATTAATATATTTTACAATTTAGGGTTCAGTTTAAAAC
326 AAAATGAAAATGGTAATCTAAGGACATGATTAATATATTTTACAATTTAGGGTTCAGTTTAAAAC
917803 TAAAATATAATTTTTAGGTGTTTGATATAATTAGCACTTAATAGTTGGGTTTAAATATTGTTATA
391 TAAAATATAATTTTTAGGTGTTTGATATAATTAGCACTTAATAGTTGGGTTTAAATATTGTTATA
917868 CATGTCATAATATAATTTATTATTCATTTTTTAACACAATCCTTAATTTGCTTTTATTGATTCAA
456 CATGTCATAATATAATTTATTATTCATTTTTTAACACAATCCTTAATTTGCTTTTATTGATTCAA
917933 TTAT
521 TTAT
917937 GGCAGTCGTTCTCCTGAAATTTTCAATGTCTCCAATATTTTAGATTTTTTATGTATATCTTTAAA
1 GGCAGTCGTTCTCCTGAAATTTTCAATGTCTCCAATATTTTAGATTTTTTATGTATATCTTTAAA
918002 TTGATAATTTTTTTGTACTCCTTAAATTTTATAAATTCACTCTCTTAGCATAAAATTCTACGTTC
66 TTGATAATTTTTTTGTACTCCTTAAATTTTATAAATTCACTCTCTTAGCATAAAATTCTACGTTC
918067 GTCACTGAGTCAATAGCATAAGATGTTAGAATTAGAGAATAAGTAGATATTGTAAATAAATGACC
131 GTCACTGAGTCAATAGCATAAGATGTTAGAATTAGAGAATAAGTAGATATTGTAAATAAATGACC
918132 CTATCAAATTTTAATGAAACTTTATGTCTTTTGATATGGTTAAATTTCGATCAATCCATGAATCA
196 CTATCAAATTTTAATGAAACTTTATGTCTTTTGATATGGTTAAATTTCGATCAATCCATGAATCA
918197 TGTGTATACATATTTATGATTGTATTTTAAATATGAGTAAACATTTAACACTGTAGGACATGATT
261 TGTGTATACATATTTATGATTGTATTTTAAATATGAGTAAACATTTAACACTGTAGGACATGATT
918262 AAAATGAAAATGGTAATCTAAGGACATGATTAATATATTTTACAATTTAGGGTTCAGTTTAAAAC
326 AAAATGAAAATGGTAATCTAAGGACATGATTAATATATTTTACAATTTAGGGTTCAGTTTAAAAC
918327 TAAAATATAATTTTTAGGTGTTTGATATAATTAGCACTTAATAGTTGGGTTTAAATATTGTTATA
391 TAAAATATAATTTTTAGGTGTTTGATATAATTAGCACTTAATAGTTGGGTTTAAATATTGTTATA
918392 CATGTCATAATATAATTTATTATTCATTTTTTAACACAATCCTTAATTTGCTTTTATTGATTCAA
456 CATGTCATAATATAATTTATTATTCATTTTTTAACACAATCCTTAATTTGCTTTTATTGATTCAA
918457 TTAT
521 TTAT
918461 G
1 G
918462 AGACCTATTT
Statistics
Matches: 1553, Mismatches: 12, Indels: 8
0.99 0.01 0.01
Matches are distributed among these distances:
516 305 0.20
518 1 0.00
520 1 0.00
523 1 0.00
524 1245 0.80
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (524 bp):
GGCAGTCGTTCTCCTGAAATTTTCAATGTCTCCAATATTTTAGATTTTTTATGTATATCTTTAAA
TTGATAATTTTTTTGTACTCCTTAAATTTTATAAATTCACTCTCTTAGCATAAAATTCTACGTTC
GTCACTGAGTCAATAGCATAAGATGTTAGAATTAGAGAATAAGTAGATATTGTAAATAAATGACC
CTATCAAATTTTAATGAAACTTTATGTCTTTTGATATGGTTAAATTTCGATCAATCCATGAATCA
TGTGTATACATATTTATGATTGTATTTTAAATATGAGTAAACATTTAACACTGTAGGACATGATT
AAAATGAAAATGGTAATCTAAGGACATGATTAATATATTTTACAATTTAGGGTTCAGTTTAAAAC
TAAAATATAATTTTTAGGTGTTTGATATAATTAGCACTTAATAGTTGGGTTTAAATATTGTTATA
CATGTCATAATATAATTTATTATTCATTTTTTAACACAATCCTTAATTTGCTTTTATTGATTCAA
TTAT
Found at i:934976 original size:38 final size:41
Alignment explanation
Indices: 934934--935034 Score: 154
Period size: 38 Copynumber: 2.5 Consensus size: 41
934924 ATTTCCAGAT
934934 AGAGTTCATAATGAGAAGAACTCGTCATCT-A-AA-GAAGA
1 AGAGTTCATAATGAGAAGAACTCGTCATCTAAGAAGGAAGA
*
934972 AGAGTTCATAATGAGAAGAATTCGTCATCTGAAGAAGGAAGA
1 AGAGTTCATAATGAGAAGAACTCGTCATCT-AAGAAGGAAGA
935014 AGAAGTTCATAATGAGAAGAA
1 AG-AGTTCATAATGAGAAGAA
935035 TTTGTTCAAC
Statistics
Matches: 57, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
38 29 0.51
40 1 0.02
41 2 0.04
42 7 0.12
43 18 0.32
ACGTcount: A:0.46, C:0.10, G:0.24, T:0.21
Consensus pattern (41 bp):
AGAGTTCATAATGAGAAGAACTCGTCATCTAAGAAGGAAGA
Found at i:935129 original size:116 final size:116
Alignment explanation
Indices: 934973--935350 Score: 590
Period size: 113 Copynumber: 3.3 Consensus size: 116
934963 TAAAGAAGAA
934973 GAGTTCATAATGAGAAGAATTCGTCATCTGAAGAAG-GAAGAAGAAGTTCATAATGAGAAGAATT
1 GAGTTCATAATGAGAAGAA-TCGTCATCTGAAGAAGTGAAGAAGAAGTTCATAATGAGAAGAATT
935037 TGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGTTC
65 TGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGTTC
935089 GAGTTCATAATGAGAAGAA-C-TCATCTGAAGAAGT-AAGAAGAAGTTCATAATGAGAAGAATTT
1 GAGTTCATAATGAGAAGAATCGTCATCTGAAGAAGTGAAGAAGAAGTTCATAATGAGAAGAATTT
*
935151 GTTCAACCTTTTACTCAAATCCATCACTTGATGGATCAACTTTTCCAGTTC
66 GTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGTTC
*
935202 GAGTTCATAATGAGAAGAA-C-TCATCTGAAGAA-TGAAGAAGAAGTTCATAATAAGAAGAATTT
1 GAGTTCATAATGAGAAGAATCGTCATCTGAAGAAGTGAAGAAGAAGTTCATAATGAGAAGAATTT
* * * * * * * * *
935264 GTTCAACCTTTTGTTTAAATTCATCAATTGATGGATTAACATTGCCAGGTA
66 GTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGTTC
935315 GAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
1 GAGTTCATAATGAGAAGAA-TCGTCATCTGAAGAAG
935351 AATTTGTTCA
Statistics
Matches: 244, Mismatches: 12, Indels: 11
0.91 0.04 0.04
Matches are distributed among these distances:
112 1 0.00
113 210 0.86
114 1 0.00
115 1 0.00
116 31 0.13
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (116 bp):
GAGTTCATAATGAGAAGAATCGTCATCTGAAGAAGTGAAGAAGAAGTTCATAATGAGAAGAATTT
GTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGTTC
Found at i:935376 original size:205 final size:205
Alignment explanation
Indices: 935141--935650 Score: 914
Period size: 205 Copynumber: 2.5 Consensus size: 205
935131 GTTCATAATG
935141 AGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGT
1 AGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGT
935206 TCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAAC
66 TCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAAC
935271 CTTTTGTTTAAATTCATCAATTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACT
131 CTTTTGTTTAAATTCATCAATTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACT
935336 CGTCATCTGA
196 CGTCATCTGA
935346 AGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGT
1 AGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGT
*
935411 TCATAATGAGAATAACTCATCTGAAGAATGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAAC
66 TCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAAC
935476 CTTTTGTTTAAATTCATCAATTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACT
131 CTTTTGTTTAAATTCATCAATTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACT
935541 CGTCATCTGA
196 CGTCATCTGA
* * * * * ****
935551 AGAAGAATTTGTTCAACCTTTTGCCCAAATCCATCACTTGATGGATTAGCTTTTCTAGAGAAAGT
1 AGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGT
*
935616 TCATAATGAGAAGAACTCATTTGAAGAA-GAAGAAG
66 TCATAATGAGAAGAACTCATCTGAAGAATGAAGAAG
935651 TTCACAATGA
Statistics
Matches: 293, Mismatches: 12, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
204 7 0.02
205 286 0.98
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.31
Consensus pattern (205 bp):
AGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGT
TCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAAC
CTTTTGTTTAAATTCATCAATTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACT
CGTCATCTGA
Found at i:935411 original size:92 final size:92
Alignment explanation
Indices: 935253--935633 Score: 260
Period size: 92 Copynumber: 3.9 Consensus size: 92
935243 AGTTCATAAT
** * * *
935253 AAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCAATTGATGGATTAACATTGCCAGGTAGAG
1 AAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCAATTGATGGATCAACATTGCCAGGTAGAG
935318 TTCATAATGAGAAGAACTCGTCATCTG
66 TTCATAATGAGAAGAACTCGTCATCTG
* * * * *
935345 AAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAG
1 AAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCAATTGATGGATCAACATTGCCAGGTAGAG
* * **
935410 TTCATAATGAGAATAACTCATCTGAAGAATG
66 TTCATAATGAGAAGAACTCGTC---A-TCTG
* ** *** ** * *
935441 AAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCAATTGATGGATT
1 AAGAAGAA-TT--T-GT-TCAACCTTTTACTCAA------------ATCCATCAATTGATGGATC
935506 AACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTG
49 AACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTG
* * * * * * * * *
935550 AAGAAGAATTTGTTCAACCTTTTGCCCAAATCCATCACTTGATGGATTAGCTTTTCTAGAG-AAA
1 AAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCAATTGATGGATCAACATTGCCAG-GTAGA
935614 GTTCATAATGAGAAGAACTC
65 GTTCATAATGAGAAGAACTC
935634 ATTTGAAGAA
Statistics
Matches: 219, Mismatches: 48, Indels: 44
0.70 0.15 0.14
Matches are distributed among these distances:
92 121 0.55
93 1 0.00
95 1 0.00
96 10 0.05
97 2 0.01
99 1 0.00
100 1 0.00
101 9 0.04
104 9 0.04
105 1 0.00
106 1 0.00
108 2 0.01
109 10 0.05
110 1 0.00
113 49 0.22
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (92 bp):
AAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCAATTGATGGATCAACATTGCCAGGTAGAG
TTCATAATGAGAAGAACTCGTCATCTG
Found at i:935909 original size:3 final size:3
Alignment explanation
Indices: 935903--935994 Score: 143
Period size: 3 Copynumber: 30.7 Consensus size: 3
935893 TTTTTACTCA
*
935903 TAT TAT TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
935951 TAT TAT TAT TA- TAT ATAT TAT TA- TAT ATAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT -TAT TAT TAT TAT TAT TA
935995 AAAAAAATTT
Statistics
Matches: 83, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
2 4 0.05
3 73 0.88
4 6 0.07
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:936408 original size:14 final size:15
Alignment explanation
Indices: 936381--936413 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
936371 AGAGAGAGAC
*
936381 AGAAACAGAGAACAA
1 AGAAACAGAAAACAA
936396 AGAAACA-AAAACAA
1 AGAAACAGAAAACAA
936410 AGAA
1 AGAA
936414 TAAATAACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.73, C:0.12, G:0.15, T:0.00
Consensus pattern (15 bp):
AGAAACAGAAAACAA
Found at i:937385 original size:15 final size:15
Alignment explanation
Indices: 937365--937411 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
937355 ATATAATAAA
937365 TAATAATTTATTTTT
1 TAATAATTTATTTTT
*
937380 TAATAAATTA--TTT
1 TAATAATTTATTTTT
937393 TAAT-ATTTATTTTT
1 TAATAATTTATTTTT
*
937407 CAATA
1 TAATA
937412 TCGAAGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
12 4 0.15
13 7 0.27
14 6 0.23
15 9 0.35
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TAATAATTTATTTTT
Found at i:941821 original size:26 final size:27
Alignment explanation
Indices: 941736--941821 Score: 102
Period size: 27 Copynumber: 3.2 Consensus size: 27
941726 ATGAAAGGAT
941736 TGAAATACCCATGAACTCAAAAATGAC
1 TGAAATACCCATGAACTCAAAAATGAC
* *
941763 TGAAATACCCTTAAACTCAAAAATGAC
1 TGAAATACCCATGAACTCAAAAATGAC
** * **
941790 CAAAATACCC-TGAGCTCTGAAATGAC
1 TGAAATACCCATGAACTCAAAAATGAC
941816 TGAAAT
1 TGAAAT
941822 GCTCTTGGGC
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
26 16 0.33
27 33 0.67
ACGTcount: A:0.45, C:0.22, G:0.12, T:0.21
Consensus pattern (27 bp):
TGAAATACCCATGAACTCAAAAATGAC
Found at i:943813 original size:44 final size:43
Alignment explanation
Indices: 943627--943960 Score: 443
Period size: 44 Copynumber: 7.7 Consensus size: 43
943617 GCAAAAATGA
* * * * *
943627 TAAGGTCTTATCCTTGCACATAGCAAAAGAGCCTGGGGAAACTG
1 TAAGG-CTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTG
*
943671 TAAGGCTTATCCTTGCACACAACAAAGGAACCTGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTG
943714 TAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTG
1 TAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTG
* * *
943757 TAAGGCTTACCCTTGCATACAACAAAGGGACATGGGAGAAACTG
1 TAAGGCTTACCCTTGCACACAACAAAGGAACCTGGG-GAAACTG
* *
943801 TAAGGCTTACCCTTGCACATAACAAAAGGAACCTGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAAC-AAAGGAACCTGGGGAAACTG
* *
943845 TAAGGCTTACCCTTGCACACAACAAAAGGAACCCGGGGGAACTG
1 TAAGGCTTACCCTTGCACACAAC-AAAGGAACCTGGGGAAACTG
* * ** *
943889 TAAGGCTTACCCTTGAACACAGCAAAGGGGCCTGGGGGACACTG
1 TAAGGCTTACCCTTGCACACAACAAAGGAACCT-GGGGAAACTG
* *
943933 TAAGGCTTACCTTTGCACACAGCAAAGG
1 TAAGGCTTACCCTTGCACACAACAAAGG
943961 GACTTGCTGT
Statistics
Matches: 263, Mismatches: 24, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
43 116 0.44
44 136 0.52
45 11 0.04
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.18
Consensus pattern (43 bp):
TAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGGAAACTG
Found at i:946880 original size:15 final size:14
Alignment explanation
Indices: 946856--946896 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
946846 CGAGTGACGT
*
946856 TTATTATATATCTTA
1 TTATT-TATATATTA
946871 TTATATTATATATTA
1 TTAT-TTATATATTA
946886 TTATTTATATA
1 TTATTTATATA
946897 GCCCGAATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 7 0.29
15 16 0.67
16 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (14 bp):
TTATTTATATATTA
Found at i:948770 original size:24 final size:24
Alignment explanation
Indices: 948753--948840 Score: 133
Period size: 24 Copynumber: 3.7 Consensus size: 24
948743 ATCATAACAT
948753 AATCCAGGTCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATCAGATCAA
*
948777 AATCCAGGTCAAGTATTCA-ATCAG
1 AATCCAGGTCAAGTA-TCAGATCAA
*
948801 AATCCAGGTCAAGTATCCGATCAA
1 AATCCAGGTCAAGTATCAGATCAA
*
948825 AATCCAGGTCAGGTAT
1 AATCCAGGTCAAGTAT
948841 TATAATAGAA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
23 2 0.03
24 53 0.91
25 3 0.05
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.23
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCAGATCAA
Found at i:948788 original size:12 final size:13
Alignment explanation
Indices: 948753--948835 Score: 61
Period size: 12 Copynumber: 6.8 Consensus size: 13
948743 ATCATAACAT
948753 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
948766 TAT-CAGATCAA-
1 AATCCAGGTCAAG
948777 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* * *
948790 TATTCA-ATC-AG
1 AATCCAGGTCAAG
948801 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
948814 TATCC-GATCAA-
1 AATCCAGGTCAAG
948825 AATCCAGGTCA
1 AATCCAGGTCA
948836 GGTATTATAA
Statistics
Matches: 51, Mismatches: 14, Indels: 11
0.67 0.18 0.14
Matches are distributed among these distances:
11 12 0.24
12 27 0.53
13 12 0.24
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.22
Consensus pattern (13 bp):
AATCCAGGTCAAG
Found at i:950003 original size:18 final size:18
Alignment explanation
Indices: 949982--950016 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
949972 TTCCATCCGG
*
949982 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
950000 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
950017 GTGATTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:951306 original size:18 final size:18
Alignment explanation
Indices: 951283--951333 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
951273 ACAGTCAATG
951283 GGTCAACGGGTCGGGCCA
1 GGTCAACGGGTCGGGCCA
* * *
951301 GGTCAATC-AGTCGGGTCG
1 GGTCAA-CGGGTCGGGCCA
*
951319 GGTAAACGGGTCGGG
1 GGTCAACGGGTCGGG
951334 TCGGGTTGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 1 0.04
18 24 0.92
19 1 0.04
ACGTcount: A:0.18, C:0.22, G:0.45, T:0.16
Consensus pattern (18 bp):
GGTCAACGGGTCGGGCCA
Found at i:953442 original size:24 final size:24
Alignment explanation
Indices: 953415--953519 Score: 81
Period size: 24 Copynumber: 4.5 Consensus size: 24
953405 TATATCAAAA
*
953415 ATCATAACATAATCCATGTCAAGT
1 ATCATAACATAATCCAGGTCAAGT
* * *
953439 ATCAGATCAAAATCCAGGTCAAGT
1 ATCATAACATAATCCAGGTCAAGT
*
953463 AT--TCA-ATAATCCAGGTCAAGT
1 ATCATAACATAATCCAGGTCAAGT
** * * *
953484 ATCCGATCAAAATCCAGGTCAGGT
1 ATCATAACATAATCCAGGTCAAGT
* *
953508 ATTATAATATAA
1 ATCATAACATAA
953520 ATCAAATCGG
Statistics
Matches: 59, Mismatches: 19, Indels: 6
0.70 0.23 0.07
Matches are distributed among these distances:
21 17 0.29
24 42 0.71
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (24 bp):
ATCATAACATAATCCAGGTCAAGT
Found at i:953474 original size:45 final size:45
Alignment explanation
Indices: 953423--953510 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
953413 AAATCATAAC
*
953423 ATAATCCATGTCAAGTATCAGATCAAAATCCAGGTCAAGTATTCA
1 ATAATCCAGGTCAAGTATCAGATCAAAATCCAGGTCAAGTATTCA
* *
953468 ATAATCCAGGTCAAGTATCCGATCAAAATCCAGGTCAGGTATT
1 ATAATCCAGGTCAAGTATCAGATCAAAATCCAGGTCAAGTATT
953511 ATAATATAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (45 bp):
ATAATCCAGGTCAAGTATCAGATCAAAATCCAGGTCAAGTATTCA
Found at i:953475 original size:21 final size:20
Alignment explanation
Indices: 953445--953510 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 20
953435 AAGTATCAGA
953445 TCAAAATCCAGGTCAAGTAT
1 TCAAAATCCAGGTCAAGTAT
953465 TCAATAATCCAGGTCAAGTAT
1 TCAA-AATCCAGGTCAAGTAT
*
953486 CCGATCAAAATCCAGGTCAGGTAT
1 ----TCAAAATCCAGGTCAAGTAT
953510 T
1 T
953511 ATAATATAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
20 5 0.12
21 16 0.40
24 15 0.38
25 4 0.10
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (20 bp):
TCAAAATCCAGGTCAAGTAT
Found at i:954671 original size:18 final size:18
Alignment explanation
Indices: 954650--954707 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
954640 TTCCATCCGG
* *
954650 TCTTATTATTTAATTCAA
1 TCTTATCATTTACTTCAA
* *
954668 TCTTATCATTTGCTTTAA
1 TCTTATCATTTACTTCAA
*
954686 TCTTATCATTTACTTCAG
1 TCTTATCATTTACTTCAA
954704 TCTT
1 TCTT
954708 TTCGAACAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.24, C:0.17, G:0.03, T:0.55
Consensus pattern (18 bp):
TCTTATCATTTACTTCAA
Found at i:963311 original size:23 final size:22
Alignment explanation
Indices: 963291--963339 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
963281 TACATTTTGT
*
963291 AAAGATGATAGATTCTATTTTC
1 AAAGATGATAAATTCTATTTTC
* *
963313 AAATATGATAAATTCTCTTTTC
1 AAAGATGATAAATTCTATTTTC
963335 AAAGA
1 AAAGA
963340 CCAAAACTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (22 bp):
AAAGATGATAAATTCTATTTTC
Found at i:964062 original size:125 final size:125
Alignment explanation
Indices: 963840--964479 Score: 867
Period size: 125 Copynumber: 5.1 Consensus size: 125
963830 ATCTGAACTC
* * *
963840 CACGGAAGAGTAGTGGAACGGATTTTTCAGTAAAGTATAAAATCTTCACAGAAGAATAGTGAAGT
1 CACGGAAGAGTAGTGGAATGGATTTTTCAGCAAAGTATGAAATCTTCACAGAAGAATAGTGAAGT
* * * *
963905 AATCTGATGGTGAGTCTGATCTTCACGGAAGAGTAGTTAAATTAGATTCTCATCCATTTT
66 AATCCGATGGTGAGTCTGATCTTCACGGAAGAGTAGTGAAATTAGATTCTCATTCGTTTT
* * * *
963965 CACGGAAGAGTAGTGGAATGGATTTTTCAACAAAGTATTAAATCTTCATAGAAGAGTAGTGAAGT
1 CACGGAAGAGTAGTGGAATGGATTTTTCAGCAAAGTATGAAATCTTCACAGAAGAATAGTGAAGT
* *
964030 AATCCGATGGTGAGTCTGATCTTCACAGAAGAGTAGTGAAATTAGATTCTCATTTGTTTT
66 AATCCGATGGTGAGTCTGATCTTCACGGAAGAGTAGTGAAATTAGATTCTCATTCGTTTT
* * ** * *
964090 CACGGAAGAGTAGTGAAACT-GATTTTTCAGCAAAGTATGGAATCTTCATGGAAAAATAGTGAAA
1 CACGGAAGAGTAGTGGAA-TGGATTTTTCAGCAAAGTATGAAATCTTCACAGAAGAATAGTGAAG
* * *
964154 TAATCTGATCGTGAGTCTGATCTTCACGGAAGAGCAGTGAAATTAGATTCTCATTCGTTTT
65 TAATCCGATGGTGAGTCTGATCTTCACGGAAGAGTAGTGAAATTAGATTCTCATTCGTTTT
* *
964215 CATC-GAAGAGTAGTGGAATGAATTTTTCAGCAAAGTATGAAATCTTCACGGAAGAATAGTGAAG
1 CA-CGGAAGAGTAGTGGAATGGATTTTTCAGCAAAGTATGAAATCTTCACAGAAGAATAGTGAAG
* * *
964279 TAATCCAATGGTGAGTCTGATCTTCACGGAAGAGTAGTGAAACTAGATTCTCATACGTTTT
65 TAATCCGATGGTGAGTCTGATCTTCACGGAAGAGTAGTGAAATTAGATTCTCATTCGTTTT
** *** * *
964340 CACATAAGAGTAGTGGAACAAATATTTTTAGCAAAATATGAAATCTTCA-AGGAA-AATAGTGAA
1 CACGGAAGAGTAGTGGAATGGAT-TTTTCAGCAAAGTATGAAATCTTCACA-GAAGAATAGTGAA
* *
964403 GTAATTCGATGGTGAGTCTGATCTTCAAGGAAGAGTAGTGAAATTAGATTCTCATTCGTTTT
64 GTAATCCGATGGTGAGTCTGATCTTCACGGAAGAGTAGTGAAATTAGATTCTCATTCGTTTT
*
964465 TACGGAA-AGGTAGTG
1 CACGGAAGA-GTAGTG
964480 AAATTAGATT
Statistics
Matches: 457, Mismatches: 51, Indels: 14
0.88 0.10 0.03
Matches are distributed among these distances:
124 3 0.01
125 426 0.93
126 28 0.06
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (125 bp):
CACGGAAGAGTAGTGGAATGGATTTTTCAGCAAAGTATGAAATCTTCACAGAAGAATAGTGAAGT
AATCCGATGGTGAGTCTGATCTTCACGGAAGAGTAGTGAAATTAGATTCTCATTCGTTTT
Found at i:965982 original size:23 final size:22
Alignment explanation
Indices: 965934--965982 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
965924 CGAAATCAGG
* *
965934 TTTTGCATTTTTTTTAATTTGG
1 TTTTGCATTTTTTATAATTTGA
* *
965956 TTTTCGCATTTTTTATATTTTTA
1 TTTT-GCATTTTTTATAATTTGA
965979 TTTT
1 TTTT
965983 AGTCCTTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.71
Consensus pattern (22 bp):
TTTTGCATTTTTTATAATTTGA
Found at i:970770 original size:22 final size:24
Alignment explanation
Indices: 970744--970804 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 24
970734 ATACCCTCCT
970744 GGGGGTATCGGTACCTAC-TCAAA
1 GGGGGTATCGGTACCTACTTCAAA
* *
970767 GGGGGGATCGGTACC-CCTTC-AA
1 GGGGGTATCGGTACCTACTTCAAA
*
970789 GGGGGTATCGATACCT
1 GGGGGTATCGGTACCT
970805 CCTGCACCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 16 0.50
23 16 0.50
ACGTcount: A:0.21, C:0.23, G:0.34, T:0.21
Consensus pattern (24 bp):
GGGGGTATCGGTACCTACTTCAAA
Found at i:977615 original size:22 final size:23
Alignment explanation
Indices: 977581--977624 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
977571 GTACAACCAC
*
977581 TGTTTACGAGTACTGTTCATCAT
1 TGTTCACGAGTACTGTTCATCAT
977604 TGTTCACG-GTACTGTTCATCA
1 TGTTCACGAGTACTGTTCATCA
977625 CTATTCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.41
Consensus pattern (23 bp):
TGTTCACGAGTACTGTTCATCAT
Found at i:977631 original size:22 final size:22
Alignment explanation
Indices: 977590--977631 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
977580 CTGTTTACGA
* *
977590 GTACTGTTCATCATTGTTCACG
1 GTACTGTTCATCACTATTCACG
977612 GTACTGTTCATCACTATTCA
1 GTACTGTTCATCACTATTCA
977632 TAAAAAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.40
Consensus pattern (22 bp):
GTACTGTTCATCACTATTCACG
Found at i:980453 original size:42 final size:41
Alignment explanation
Indices: 980352--980556 Score: 268
Period size: 42 Copynumber: 4.8 Consensus size: 41
980342 CTATACACCA
* * *
980352 GTAAGGCTTAACCTGTGCACAAAG-AAAAGGAGCCTAGGAAAACT
1 GTAAGGCTT-ACCT-TGCACACAGCAAAGGGA-CCT-GGGAAACT
* *
980396 GTAAGGTTTATCCTTGCACACAACAAAGGGACCTGGGAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
*
980438 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
980480 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAACT
*
980522 GTAAGGCTTACCTTCTCACACAGCAAAGGGACCTG
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTG
980557 ATAATACTTC
Statistics
Matches: 147, Mismatches: 11, Indels: 8
0.89 0.07 0.05
Matches are distributed among these distances:
41 4 0.03
42 115 0.78
43 11 0.07
44 17 0.12
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (41 bp):
GTAAGGCTTACCTTGCACACAGCAAAGGGACCTGGGAAACT
Found at i:981529 original size:29 final size:28
Alignment explanation
Indices: 981497--981659 Score: 238
Period size: 29 Copynumber: 5.7 Consensus size: 28
981487 TTTTTTAAAA
* * *
981497 TAATTACCAAAATAGAACCTTTTTCGAAT
1 TAATTCCCAAAATAGCACCATTTT-GAAT
981526 TAATTCCCAAAATAGCACCCATTTTGAAT
1 TAATTCCCAAAATAGCA-CCATTTTGAAT
981555 TAATTCCCAAAATAGCACCATTTTGAAT
1 TAATTCCCAAAATAGCACCATTTTGAAT
981583 TAATTCCCAAAATAGCACCCATTTCT-AAT
1 TAATTCCCAAAATAGCA-CCATTT-TGAAT
*
981612 TAATTCCCAAAATAGCACCCATTTGGAAT
1 TAATTCCCAAAATAGCA-CCATTTTGAAT
981641 TAATTCCCAAAATAGCACC
1 TAATTCCCAAAATAGCACC
981660 TGGTCAACGG
Statistics
Matches: 126, Mismatches: 4, Indels: 9
0.91 0.03 0.06
Matches are distributed among these distances:
28 30 0.24
29 89 0.71
30 7 0.06
ACGTcount: A:0.39, C:0.24, G:0.07, T:0.30
Consensus pattern (28 bp):
TAATTCCCAAAATAGCACCATTTTGAAT
Found at i:981623 original size:86 final size:86
Alignment explanation
Indices: 981497--981659 Score: 272
Period size: 86 Copynumber: 1.9 Consensus size: 86
981487 TTTTTTAAAA
** *
981497 TAATTACCAAAATAGAACCTTTTTCGAATTAATTCCCAAAATAGCACCCATTTTGAATTAATTCC
1 TAATTACCAAAATAGAACCCATTTCGAATTAATTCCCAAAATAGCACCCATTTGGAATTAATTCC
981562 CAAAATAGCACCATTTTGAAT
66 CAAAATAGCACCATTTTGAAT
* * *
981583 TAATTCCCAAAATAGCACCCATTTCTAATTAATTCCCAAAATAGCACCCATTTGGAATTAATTCC
1 TAATTACCAAAATAGAACCCATTTCGAATTAATTCCCAAAATAGCACCCATTTGGAATTAATTCC
981648 CAAAATAGCACC
66 CAAAATAGCACC
981660 TGGTCAACGG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
86 71 1.00
ACGTcount: A:0.39, C:0.24, G:0.07, T:0.30
Consensus pattern (86 bp):
TAATTACCAAAATAGAACCCATTTCGAATTAATTCCCAAAATAGCACCCATTTGGAATTAATTCC
CAAAATAGCACCATTTTGAAT
Found at i:987893 original size:42 final size:41
Alignment explanation
Indices: 987792--987996 Score: 268
Period size: 42 Copynumber: 4.8 Consensus size: 41
987782 CTATACACCA
* *
987792 GTAAGGCTTAACCTGTGCACAAAGCAAA-GGAGCCTAGGAAAACT
1 GTAAGGCTT-ACCT-TGCACACAGCAAAGGGA-CCT-GGGAAACT
*
987836 GTAAGGCTTATCCTTGCACACAGTAAAGGGACCTGGGAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
* *
987878 GTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
*
987920 GTAAGGCTTACCTTCGCACATAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAACT
*
987962 GTAAGGCTTACCTTCGCACACAACAAAGGGACCTG
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTG
987997 ATAATACTTC
Statistics
Matches: 146, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
41 4 0.03
42 112 0.77
43 15 0.10
44 15 0.10
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (41 bp):
GTAAGGCTTACCTTGCACACAGCAAAGGGACCTGGGAAACT
Found at i:988973 original size:29 final size:29
Alignment explanation
Indices: 988940--989106 Score: 142
Period size: 29 Copynumber: 5.8 Consensus size: 29
988930 AATAGCACCC
* * *
988940 TTTTTTAAAATAATTACCAAAATAACACA
1 TTTTTTGAATTAATTCCCAAAATAACACA
*
988969 TTTTTTGAATTAATTCCCAAAATAGCACCA
1 TTTTTTGAATTAATTCCCAAAATAACA-CA
*
988999 --TTTTGAATTAATTCCCAAAATAACACC
1 TTTTTTGAATTAATTCCCAAAATAACACA
** * *
989026 CATTTCGAATTAATTCCCAAAATAGCAC-
1 TTTTTTGAATTAATTCCCAAAATAACACA
** * * * *
989054 CCTTTTGAATTAATTCCAAAAACAGCACC
1 TTTTTTGAATTAATTCCCAAAATAACACA
** *
989083 CATTTCGAATTAATTCCCAAAATA
1 TTTTTTGAATTAATTCCCAAAATA
989107 GCACCCGGTC
Statistics
Matches: 118, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
27 1 0.01
28 48 0.41
29 67 0.57
30 2 0.02
ACGTcount: A:0.41, C:0.22, G:0.05, T:0.32
Consensus pattern (29 bp):
TTTTTTGAATTAATTCCCAAAATAACACA
Found at i:988974 original size:30 final size:30
Alignment explanation
Indices: 988929--989030 Score: 93
Period size: 29 Copynumber: 3.5 Consensus size: 30
988919 CATTTTACAG
* *
988929 AAATAGCACCCTTTTTTAAAATAATTACCA
1 AAATAACACCATTTTTTAAAATAATTACCA
* * *
988959 AAATAACA-CATTTTTTGAATTAATTCCCA
1 AAATAACACCATTTTTTAAAATAATTACCA
* * * *
988988 AAATAGCACCA--TTTTGAATTAATTCCCA
1 AAATAACACCATTTTTTAAAATAATTACCA
989016 AAATAACACCCATTT
1 AAATAACA-CCATTT
989031 CGAATTAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
28 24 0.39
29 27 0.44
30 9 0.15
31 1 0.02
ACGTcount: A:0.42, C:0.21, G:0.04, T:0.33
Consensus pattern (30 bp):
AAATAACACCATTTTTTAAAATAATTACCA
Found at i:989019 original size:57 final size:57
Alignment explanation
Indices: 988950--989111 Score: 243
Period size: 57 Copynumber: 2.8 Consensus size: 57
988940 TTTTTTAAAA
* *** *
988950 TAATTACCAAAATAACACATTTTTTGAATTAATTCCCAAAATAGCACCATTTTGAAT
1 TAATTCCCAAAATAACACCCATTTCGAATTAATTCCCAAAATAGCACCATTTTGAAT
*
989007 TAATTCCCAAAATAACACCCATTTCGAATTAATTCCCAAAATAGCACCCTTTTGAAT
1 TAATTCCCAAAATAACACCCATTTCGAATTAATTCCCAAAATAGCACCATTTTGAAT
* * *
989064 TAATTCCAAAAACAGCACCCATTTCGAATTAATTCCCAAAATAGCACC
1 TAATTCCCAAAATAACACCCATTTCGAATTAATTCCCAAAATAGCACC
989112 CGGTCAACGG
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 96 1.00
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.30
Consensus pattern (57 bp):
TAATTCCCAAAATAACACCCATTTCGAATTAATTCCCAAAATAGCACCATTTTGAAT
Found at i:989109 original size:29 final size:29
Alignment explanation
Indices: 988975--989112 Score: 217
Period size: 29 Copynumber: 4.8 Consensus size: 29
988965 CACATTTTTT
*
988975 GAATTAATTCCCAAAATAGCA-CCATTTT
1 GAATTAATTCCCAAAATAGCACCCATTTC
*
989003 GAATTAATTCCCAAAATAACACCCATTTC
1 GAATTAATTCCCAAAATAGCACCCATTTC
*
989032 GAATTAATTCCCAAAATAGCACCC-TTTT
1 GAATTAATTCCCAAAATAGCACCCATTTC
* *
989060 GAATTAATTCCAAAAACAGCACCCATTTC
1 GAATTAATTCCCAAAATAGCACCCATTTC
989089 GAATTAATTCCCAAAATAGCACCC
1 GAATTAATTCCCAAAATAGCACCC
989113 GGTCAACGGT
Statistics
Matches: 99, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
28 45 0.45
29 54 0.55
ACGTcount: A:0.40, C:0.26, G:0.07, T:0.28
Consensus pattern (29 bp):
GAATTAATTCCCAAAATAGCACCCATTTC
Found at i:989137 original size:12 final size:13
Alignment explanation
Indices: 989120--989148 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
989110 CCCGGTCAAC
989120 GGTCAAC-GGTCG
1 GGTCAACAGGTCG
989132 GGTCAACAGGTCG
1 GGTCAACAGGTCG
989145 GGTC
1 GGTC
989149 GGGTCAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (13 bp):
GGTCAACAGGTCG
Found at i:990014 original size:17 final size:16
Alignment explanation
Indices: 989982--990075 Score: 75
Period size: 16 Copynumber: 5.9 Consensus size: 16
989972 AAAAAGAAGG
*
989982 AAGAAAA-AGAAAAAA
1 AAGAAAACAAAAAAAA
*
989997 AACAAAACAAACAAAAA
1 AAGAAAACAAA-AAAAA
* *
990014 AAGAAAAGAAAAGAAA
1 AAGAAAACAAAAAAAA
* *
990030 AAGAAAACGAAGAAAA
1 AAGAAAACAAAAAAAA
* * *
990046 AA-AATAGAAAAAGAA
1 AAGAAAACAAAAAAAA
*
990061 AAGAAAAGAAAAAAA
1 AAGAAAACAAAAAAA
990076 TGAGAGACAA
Statistics
Matches: 60, Mismatches: 16, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
15 16 0.27
16 30 0.50
17 14 0.23
ACGTcount: A:0.82, C:0.04, G:0.13, T:0.01
Consensus pattern (16 bp):
AAGAAAACAAAAAAAA
Found at i:990020 original size:5 final size:5
Alignment explanation
Indices: 990012--990072 Score: 63
Period size: 5 Copynumber: 11.8 Consensus size: 5
990002 AACAAACAAA
*
990012 AAAAG AAAAG AAAAG AAAAAG AAAACG AAGAA- AAAA- AATAG AAAAAG
1 AAAAG AAAAG AAAAG -AAAAG AAAA-G AA-AAG AAAAG AAAAG -AAAAG
990059 AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAA
990073 AAATGAGAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
4 5 0.10
5 30 0.61
6 12 0.24
7 2 0.04
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:990026 original size:36 final size:38
Alignment explanation
Indices: 989959--990075 Score: 121
Period size: 40 Copynumber: 2.9 Consensus size: 38
989949 AATAATATAA
*
989959 GAAAACAAACAGGAAAAAGAAGGAAGAAAAAGAAAAAAAAC
1 GAAAACAAACAGAAAAAAGAA--AAG-AAAAGAAAAAAAAC
990000 -AAAACAAACA-AAAAAAGAAAAGAAAAGAAAAAGAAAAC
1 GAAAACAAACAGAAAAAAGAAAAGAAAAG-AAAA-AAAAC
* * *
990038 GAAGAAAAAAAATAGAAAAAGAAAAGAAAAGAAAAAAA
1 GAA-AACAAACAGA-AAAAAGAAAAGAAAAGAAAAAAA
990076 TGAGAGACAA
Statistics
Matches: 67, Mismatches: 3, Indels: 13
0.81 0.04 0.16
Matches are distributed among these distances:
36 5 0.07
37 7 0.10
38 5 0.07
39 10 0.15
40 19 0.28
41 5 0.07
42 16 0.24
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.01
Consensus pattern (38 bp):
GAAAACAAACAGAAAAAAGAAAAGAAAAGAAAAAAAAC
Found at i:990093 original size:42 final size:42
Alignment explanation
Indices: 989973--990073 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
989963 ACAAACAGGA
** * * *
989973 AAAAGAAGGAAGAAAAAGAAAAAAAACAAAACAAACAAAAAAAG
1 AAAAGAA--AAGAAAAAGAAAACGAACAAAAAAAATAGAAAAAG
*
990017 AAAAGAAAAGAAAAAGAAAACGAAGAAAAAAAATAGAAAAAG
1 AAAAGAAAAGAAAAAGAAAACGAACAAAAAAAATAGAAAAAG
990059 AAAAGAAAAGAAAAA
1 AAAAGAAAAGAAAAA
990074 AATGAGAGAC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
42 44 0.86
44 7 0.14
ACGTcount: A:0.80, C:0.04, G:0.15, T:0.01
Consensus pattern (42 bp):
AAAAGAAAAGAAAAAGAAAACGAACAAAAAAAATAGAAAAAG
Found at i:994070 original size:47 final size:45
Alignment explanation
Indices: 993976--994101 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
993966 GTAACCATGC
* *
993976 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATTGGAA
1 AAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATATTGGAA
* *
994020 AAATAAGCTTATGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTATGAGCTTATGGAA--TAAATGGTAAGTATATTGGAA
** *
994067 AAATAAGCTTACAAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTATGAGCTTATGGAATAAATGGTAAG
994102 AGATTTTATA
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 23 0.32
45 11 0.15
46 1 0.01
47 37 0.51
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATATTGGAA
Found at i:995249 original size:2 final size:2
Alignment explanation
Indices: 995242--995283 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
995232 AACGAACATA
995242 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
995284 TAACACATGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:999335 original size:31 final size:31
Alignment explanation
Indices: 999269--999339 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
999259 TCGAGTGACC
* * * **
999269 AATTTATTATAAATTGATAATGTTAACGATT
1 AATTTATTATAAATCGATAACGTTAACAAAG
*
999300 AATTTATTATAAATCGATAACGTTAATAAAG
1 AATTTATTATAAATCGATAACGTTAACAAAG
999331 AATTTATTA
1 AATTTATTA
999340 CTCTTTAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.42
Consensus pattern (31 bp):
AATTTATTATAAATCGATAACGTTAACAAAG
Found at i:1000112 original size:118 final size:119
Alignment explanation
Indices: 999904--1000134 Score: 374
Period size: 118 Copynumber: 1.9 Consensus size: 119
999894 AAAAAATATG
*
999904 ATAACATAACCGGTTAATTACTAGAAACATTATCAAACATAATAACATATTAGGTAGCGCTTATA
1 ATAACATAACCGGTTAACTACTAGAAACATTATCAAACATAATAACATATTAGGTAGCGCTTATA
***
999969 TAACATAATAGGTATTGCCTTTTTAAAGCTGATAGGGC-TTTGGAAATCTGACA
66 TAACATAATAGGTAACACCTTTTTAAAGCTGATAGGGCTTTTGGAAATCTGACA
* * *
1000022 ATAACATAACCGGTTAACTATTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTATA
1 ATAACATAACCGGTTAACTACTAGAAACATTATCAAACATAATAACATATTAGGTAGCGCTTATA
* *
1000087 TAACGTAATAGGTAACACCTTTTTAAAGCTGATGGGGCTTTTGGAAAT
66 TAACATAATAGGTAACACCTTTTTAAAGCTGATAGGGCTTTTGGAAAT
1000135 TCGACGATAA
Statistics
Matches: 103, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
118 94 0.91
119 9 0.09
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.31
Consensus pattern (119 bp):
ATAACATAACCGGTTAACTACTAGAAACATTATCAAACATAATAACATATTAGGTAGCGCTTATA
TAACATAATAGGTAACACCTTTTTAAAGCTGATAGGGCTTTTGGAAATCTGACA
Found at i:1000515 original size:2 final size:2
Alignment explanation
Indices: 1000508--1000546 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1000498 TTATGGAGTG
1000508 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1000547 TCTATGATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1002969 original size:31 final size:31
Alignment explanation
Indices: 1002922--1002993 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
1002912 AGTGGAGACG
*
1002922 AAATTG-AAATTGAAATTCAAACTCAAATTA
1 AAATTGAAAATTCAAATTCAAACTCAAATTA
* * *
1002952 AACTTTAAAATTCAAATTCAAACTCGAATTA
1 AAATTGAAAATTCAAATTCAAACTCAAATTA
1002983 AAATTGAAAAT
1 AAATTGAAAAT
1002994 GAAAATGAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
30 4 0.11
31 31 0.89
ACGTcount: A:0.53, C:0.11, G:0.06, T:0.31
Consensus pattern (31 bp):
AAATTGAAAATTCAAATTCAAACTCAAATTA
Found at i:1006854 original size:194 final size:193
Alignment explanation
Indices: 1006523--1006907 Score: 531
Period size: 194 Copynumber: 2.0 Consensus size: 193
1006513 TTTTCTTTTA
* *
1006523 AAAGTATCGATAATATGATACATATACTTATTAAAGTATTGATACCTTCAACATATCTGATAACG
1 AAAGTATCGATAATATGATACATATACTTATAAAAGTATTGATACCTTCAACATATCCGATAACG
** * *
1006588 CTTTACCGGTTTTGTCATAATGAAATCGATTTTGTCATATTTTAACTTGTTATATTGTCATGTAT
66 CTTTACCAATTTTGTCATAATAAAATCGATTTTGTCATATTTTAACTGGTTATATTGTCATGTAT
* * * *
1006653 CGATACATGTTTCTAAAGTATTGATACTTTATAGGAGCCATTATTGCAATTCTTTTAAATTCTT
131 AGATACATGTGTATAAAGTATTGATACTTTATAGGAGCCATTATTGCAAGT-TTTTAAATTCTT
* * *
1006717 AAAGTATCGATAATATGATACATATACTTATAAAAGTATTGATACCTTCAACATATCCGGTAGCT
1 AAAGTATCGATAATATGATACATATACTTATAAAAGTATTGATACCTTCAACATATCCGATAACG
* * * * *
1006782 CTTTATCAATTTTGTCATATTAAAA-CTGGTTTTGTCGTATTTTTA-TCGGTTATATTGTCATGT
66 CTTTACCAATTTTGTCATAATAAAATC-GATTTTGTCATATTTTAACT-GGTTATATTGTCATGT
* * * *
1006845 ATAGATACATGTGTATAAAGTATTGATAGTTTATATGTGCTATTATTGCAAGTTTTTAAATTC
129 ATAGATACATGTGTATAAAGTATTGATACTTTATAGGAGCCATTATTGCAAGTTTTTAAATTC
1006908 AGAAAATATC
Statistics
Matches: 167, Mismatches: 22, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
193 12 0.07
194 155 0.93
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (193 bp):
AAAGTATCGATAATATGATACATATACTTATAAAAGTATTGATACCTTCAACATATCCGATAACG
CTTTACCAATTTTGTCATAATAAAATCGATTTTGTCATATTTTAACTGGTTATATTGTCATGTAT
AGATACATGTGTATAAAGTATTGATACTTTATAGGAGCCATTATTGCAAGTTTTTAAATTCTT
Found at i:1008371 original size:15 final size:16
Alignment explanation
Indices: 1008348--1008381 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1008338 GTTTATTTGA
1008348 TTTTAAGTATTTA-AT
1 TTTTAAGTATTTATAT
*
1008363 TTTTTAGTATTTATAT
1 TTTTAAGTATTTATAT
1008379 TTT
1 TTT
1008382 AGTCACATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (16 bp):
TTTTAAGTATTTATAT
Found at i:1008383 original size:14 final size:15
Alignment explanation
Indices: 1008347--1008384 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1008337 TGTTTATTTG
1008347 ATTTTAAGTATTTAAT
1 ATTTT-AGTATTTAAT
*
1008363 TTTTTAGTATTT-AT
1 ATTTTAGTATTTAAT
1008377 ATTTTAGT
1 ATTTTAGT
1008385 CACATTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 9 0.45
15 7 0.35
16 4 0.20
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (15 bp):
ATTTTAGTATTTAAT
Found at i:1009180 original size:30 final size:30
Alignment explanation
Indices: 1009115--1009180 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
1009105 ATATTTTTAC
* * *
1009115 TATTCTAGTCTTTTAAATTTCTGTTTGTGT
1 TATTTTAGCCTTTTAAATTTCTATTTGTGT
* *
1009145 CATTTTAGCCTTTTAATTTTCTAATTT-TGT
1 TATTTTAGCCTTTTAAATTTCT-ATTTGTGT
1009175 TATTTT
1 TATTTT
1009181 GATTCCTAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
30 26 0.90
31 3 0.10
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (30 bp):
TATTTTAGCCTTTTAAATTTCTATTTGTGT
Found at i:1011849 original size:14 final size:13
Alignment explanation
Indices: 1011833--1011875 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
1011823 GGATCAACAT
1011833 TTTTGCATTTGCA
1 TTTTGCATTTGCA
1011846 TTTT-CATCTTTGCA
1 TTTTGCA--TTTGCA
*
1011860 TTTTGCATTTTCA
1 TTTTGCATTTGCA
1011873 TTT
1 TTT
1011876 CATTTTTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 2 0.08
13 12 0.46
14 10 0.38
15 2 0.08
ACGTcount: A:0.14, C:0.16, G:0.09, T:0.60
Consensus pattern (13 bp):
TTTTGCATTTGCA
Found at i:1011866 original size:21 final size:20
Alignment explanation
Indices: 1011834--1011873 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
1011824 GATCAACATT
1011834 TTTGCATTTGCATTTTCATC
1 TTTGCATTTGCATTTTCATC
1011854 TTTGCATTTTGCATTTTCAT
1 TTTGCA-TTTGCATTTTCAT
1011874 TTCATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.57
Consensus pattern (20 bp):
TTTGCATTTGCATTTTCATC
Found at i:1012864 original size:2 final size:2
Alignment explanation
Indices: 1012844--1012935 Score: 157
Period size: 2 Copynumber: 46.0 Consensus size: 2
1012834 TCATTTATCC
* * *
1012844 AT AT AT GT AT GT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1012886 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1012928 AT AT AT AT
1 AT AT AT AT
1012936 CCCTTGTTGT
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1013154 original size:9 final size:9
Alignment explanation
Indices: 1013119--1013159 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
1013109 CAAAAAGAGG
1013119 AAATAAA-A
1 AAATAAATA
*
1013127 AAATAAAAA
1 AAATAAATA
*
1013136 AAATATATA
1 AAATAAATA
1013145 AAATAAAT-
1 AAATAAATA
1013153 AAATAAA
1 AAATAAA
1013160 GATAAAGGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 14 0.48
9 15 0.52
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATAAATA
Found at i:1014231 original size:32 final size:32
Alignment explanation
Indices: 1014190--1014292 Score: 136
Period size: 32 Copynumber: 3.2 Consensus size: 32
1014180 GAAACAATAG
1014190 AGGGCATCTTTGAAGATTCAACATCAAATGTT
1 AGGGCATCTTTGAAGATTCAACATCAAATGTT
1014222 AGGGCATCTTTGGAA-ATTCAACATCAAATGTT
1 AGGGCATCTTT-GAAGATTCAACATCAAATGTT
* * * * *
1014254 GGGGCATCTTTGGAGATTCAATATCGAATATT
1 AGGGCATCTTTGAAGATTCAACATCAAATGTT
*
1014286 GGGGCAT
1 AGGGCAT
1014293 TCAATATCCT
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
31 2 0.03
32 59 0.92
33 3 0.05
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (32 bp):
AGGGCATCTTTGAAGATTCAACATCAAATGTT
Found at i:1014438 original size:34 final size:34
Alignment explanation
Indices: 1014400--1014590 Score: 256
Period size: 34 Copynumber: 5.6 Consensus size: 34
1014390 AAAAAAAAAA
*
1014400 TTGTCTCACTTGAGATAATTTCTCAAAACAAATT
1 TTGTCTCACTTGAGACAATTTCTCAAAACAAATT
1014434 TTGTCTCACTTGAGACAATTTCTCAAAACAAATT
1 TTGTCTCACTTGAGACAATTTCTCAAAACAAATT
* * *** * *
1014468 TTCTATTGTTTGAGACAATTTGTCAAAATAAATT
1 TTGTCTCACTTGAGACAATTTCTCAAAACAAATT
* *
1014502 CTGTCTCACTTGAGACAATTTCTCAAAATAAATT
1 TTGTCTCACTTGAGACAATTTCTCAAAACAAATT
* *
1014536 TCGTCTCGCTTGAGACAATTTCTCAAAACAAATT
1 TTGTCTCACTTGAGACAATTTCTCAAAACAAATT
* *
1014570 TTGTCTCGCTTGAGAAAATTT
1 TTGTCTCACTTGAGACAATTT
1014591 TTCTCTGAGA
Statistics
Matches: 136, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 136 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.38
Consensus pattern (34 bp):
TTGTCTCACTTGAGACAATTTCTCAAAACAAATT
Found at i:1014583 original size:102 final size:102
Alignment explanation
Indices: 1014401--1014590 Score: 299
Period size: 102 Copynumber: 1.9 Consensus size: 102
1014391 AAAAAAAAAT
* *
1014401 TGTCTCACTTGAGATAATTTCTCAAAACAAATTTTGTCTCACTTGAGACAATTTCTCAAAACAAA
1 TGTCTCACTTGAGACAATTTCTCAAAACAAATTTCGTCTCACTTGAGACAATTTCTCAAAACAAA
* * *
1014466 TTTTCTATTGTTTGAGACAATTTGTCAAAATAAATTC
66 TTTTCTATCGCTTGAGAAAATTTGTCAAAATAAATTC
* *
1014503 TGTCTCACTTGAGACAATTTCTCAAAATAAATTTCGTCTCGCTTGAGACAATTTCTCAAAACAAA
1 TGTCTCACTTGAGACAATTTCTCAAAACAAATTTCGTCTCACTTGAGACAATTTCTCAAAACAAA
* *
1014568 TTTTGTCTCGCTTGAGAAAATTT
66 TTTTCTATCGCTTGAGAAAATTT
1014591 TTCTCTGAGA
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
102 79 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (102 bp):
TGTCTCACTTGAGACAATTTCTCAAAACAAATTTCGTCTCACTTGAGACAATTTCTCAAAACAAA
TTTTCTATCGCTTGAGAAAATTTGTCAAAATAAATTC
Found at i:1014882 original size:76 final size:76
Alignment explanation
Indices: 1014756--1015058 Score: 301
Period size: 76 Copynumber: 3.9 Consensus size: 76
1014746 GTTTCATTTG
* * ** * * * *
1014756 AAACAA-AGTTGTCTCACTTGAGATTG-TTTTACTTGAAAGAAGTCATTTCATTTGACTCAAGAT
1 AAACAAGATTTGTCTCGCTTGAGACAGTTTTTACTCGAAACAAGACATTTCATTTCACTCAAGAT
*
1014819 TGTTTTTCTCA
66 TGTTTTTCTTA
* * * *
1014830 AAACAAGATTTGTCTCGCTTGAGACAGGTTTTATTCAAAACAAGACATTTCATTTCATTTCACTA
1 AAACAAGATTTGTCTCGCTTGAGACAGTTTTTACTCGAAACAAGACATTTCATTTCA-CTCA--A
* *
1014895 CATGTTCTTTTTCTTA
63 GA--TTGTTTTTCTTA
* * * * *
1014911 AAACAA-CTTTCATCTCGCTTGAGACATTTTTTACTCGAAATAAGA-AGATTCATTTCACTCAAG
1 AAACAAGATTT-GTCTCGCTTGAGACAGTTTTTACTCGAAACAAGACA-TTTCATTTCACTCAAG
1014974 ATTGTTTTTCTTA
64 ATTGTTTTTCTTA
* *
1014987 AAACAAGATTTGTCTCGCTTGAGAC-GATTTTTACTCGAAAGAAGGCATTTCATTTCACTCAAGA
1 AAACAAGATTTGTCTCGCTTGAGACAG-TTTTTACTCGAAACAAGACATTTCATTTCACTCAAGA
1015051 TTGTTTTT
65 TTGTTTTT
1015059 AAAGAATATT
Statistics
Matches: 186, Mismatches: 31, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
74 6 0.03
75 16 0.09
76 93 0.50
77 7 0.04
78 2 0.01
79 2 0.01
80 7 0.04
81 53 0.28
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (76 bp):
AAACAAGATTTGTCTCGCTTGAGACAGTTTTTACTCGAAACAAGACATTTCATTTCACTCAAGAT
TGTTTTTCTTA
Found at i:1014906 original size:81 final size:81
Alignment explanation
Indices: 1014798--1015043 Score: 283
Period size: 81 Copynumber: 3.1 Consensus size: 81
1014788 TTGAAAGAAG
* * *
1014798 TCATTTCATTTGACTCAAGATTGTTTTTCTCAAAACAAGATTTGTCTCGCTTGAGACAGGTTTTA
1 TCATTTCATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGTTTTTA
* *
1014863 TTCAAAACAAGACATT
66 CTCGAAACAAGACATT
* * * * *
1014879 TCATTTCATTTCACTACATG-TTCTTTTTCTTAAAACAA-CTTTCATCTCGCTTGAGACATTTTT
1 TCATTTCATTTCACT-CAAGATTGTTTTTCTTAAAACAAGATTT-GTCTCGCTTGAGACAGTTTT
*
1014942 TACTCGAAATAAGA-A--
64 TACTCGAAACAAGACATT
*
1014957 -GA-TTCATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGAC-GATTTTT
1 TCATTTCATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAG-TTTTT
* *
1015019 ACTCGAAAGAAGGCATT
65 ACTCGAAACAAGACATT
1015036 TCATTTCA
1 TCATTTCA
1015044 CTCAAGATTG
Statistics
Matches: 135, Mismatches: 20, Indels: 20
0.77 0.11 0.11
Matches are distributed among these distances:
75 3 0.02
76 57 0.42
77 5 0.04
80 5 0.04
81 62 0.46
82 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (81 bp):
TCATTTCATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAGTTTTTA
CTCGAAACAAGACATT
Found at i:1015157 original size:40 final size:36
Alignment explanation
Indices: 1015066--1015427 Score: 413
Period size: 36 Copynumber: 9.9 Consensus size: 36
1015056 TTTAAAGAAT
* * * * *
1015066 ATTTTATCTCGCTTGATATAGTTTCCCTCGAAGCAGAA
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAA--ACAA
* * *
1015104 GATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAAAAA
1 -ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAAC---AA
* *
1015144 GATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAA
1 -ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAA
1015181 A-TTTAGTCTCCCTTGAGACAGTTTCCCTTGAAACAA
1 ATTTTA-TCTCCCTTGAGACAGTTTCCCTTGAAACAA
* *
1015217 ATTTTGTCTCCCTTGAGACGGTTTCCCTTGAAACAA
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAA
*
1015253 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAA
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAA
* ** *
1015289 ATTTTTTCTCGTTTGAGACGGTTTCCCTTGAAACAA
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAA
* *
1015325 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAA
* * *
1015361 ATTTTGTCTCCTTTGAGACGGTTTCCCTTGAAACAA
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAA
* *
1015397 ATTTTGTCTCCTTTGAGAC-GATTTCCCTTGA
1 ATTTTATCTCCCTTGAGACAG-TTTCCCTTGA
1015428 GACAGTCTCC
Statistics
Matches: 297, Mismatches: 20, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
35 5 0.02
36 219 0.74
37 6 0.02
39 31 0.10
40 36 0.12
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (36 bp):
ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAA
Found at i:1015192 original size:21 final size:21
Alignment explanation
Indices: 1015163--1015232 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
1015153 TCGCTTGAGA
*
1015163 TAGTTTCCCTTGAAACAAATT
1 TAGTCTCCCTTGAAACAAATT
*
1015184 TAGTCTCCCTTGAGAC-----
1 TAGTCTCCCTTGAAACAAATT
*
1015200 -AGTTTCCCTTGAAACAAATT
1 TAGTCTCCCTTGAAACAAATT
*
1015220 TTGTCTCCCTTGA
1 TAGTCTCCCTTGA
1015233 GACGGTTTCC
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
15 13 0.35
21 24 0.65
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (21 bp):
TAGTCTCCCTTGAAACAAATT
Found at i:1015204 original size:36 final size:36
Alignment explanation
Indices: 1015105--1015427 Score: 441
Period size: 36 Copynumber: 8.9 Consensus size: 36
1015095 GAAGCAGAAG
* * * *
1015105 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAAAAA
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC---AA
* * *
1015144 GATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAA
1 -ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAA
*
1015181 ATTTAGTCTCCCTTGAGACAGTTTCCCTTGAAACAA
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAA
*
1015217 ATTTTGTCTCCCTTGAGACGGTTTCCCTTGAAACAA
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAA
1015253 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAA
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAA
* ** *
1015289 ATTTTTTCTCGTTTGAGACGGTTTCCCTTGAAACAA
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAA
*
1015325 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAA
* *
1015361 ATTTTGTCTCCTTTGAGACGGTTTCCCTTGAAACAA
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAA
*
1015397 ATTTTGTCTCCTTTGAGAC-GATTTCCCTTGA
1 ATTTTGTCTCCCTTGAGACAG-TTTCCCTTGA
1015428 GACAGTCTCC
Statistics
Matches: 262, Mismatches: 20, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
35 1 0.00
36 226 0.86
37 2 0.01
40 33 0.13
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (36 bp):
ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAA
Found at i:1015338 original size:21 final size:21
Alignment explanation
Indices: 1015312--1015376 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
1015302 TGAGACGGTT
1015312 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
* *
1015333 TCCCTTGAGAC--A-GTT-TC
1 TCCCTTGAAACAAATTTTGTC
1015350 T--CTTGAAACAAATTTTGTC
1 TCCCTTGAAACAAATTTTGTC
*
1015369 TCCTTTGA
1 TCCCTTGA
1015377 GACGGTTTCC
Statistics
Matches: 33, Mismatches: 5, Indels: 12
0.66 0.10 0.24
Matches are distributed among these distances:
15 7 0.21
17 4 0.12
18 4 0.12
19 4 0.12
21 14 0.42
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (21 bp):
TCCCTTGAAACAAATTTTGTC
Found at i:1015412 original size:21 final size:20
Alignment explanation
Indices: 1015314--1015409 Score: 59
Period size: 21 Copynumber: 5.2 Consensus size: 20
1015304 AGACGGTTTC
1015314 CCTTGAAACAAATTTTGTCT
1 CCTTGAAACAAATTTTGTCT
* *
1015334 CCCTTGAGAC--A-GTT-TCT
1 -CCTTGAAACAAATTTTGTCT
1015351 -CTTGAAACAAATTTTGTCT
1 CCTTGAAACAAATTTTGTCT
* **
1015370 CCTTTGAGAC---GGTT-TC-
1 CC-TTGAAACAAATTTTGTCT
1015386 CCTTGAAACAAATTTTGTCT
1 CCTTGAAACAAATTTTGTCT
1015406 CCTT
1 CCTT
1015410 TGAGACGATT
Statistics
Matches: 54, Mismatches: 10, Indels: 23
0.62 0.11 0.26
Matches are distributed among these distances:
15 13 0.24
16 2 0.04
17 6 0.11
18 8 0.15
19 6 0.11
20 5 0.09
21 14 0.26
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.40
Consensus pattern (20 bp):
CCTTGAAACAAATTTTGTCT
Found at i:1015429 original size:15 final size:15
Alignment explanation
Indices: 1015402--1015476 Score: 73
Period size: 15 Copynumber: 5.0 Consensus size: 15
1015392 AACAAATTTT
*
1015402 GTCTCCTTTGAGAC-
1 GTCTCCCTTGAGACA
*
1015416 GATTTCCCTTGAGACA
1 G-TCTCCCTTGAGACA
1015432 GTCTCCCTTGAGACAA
1 GTCTCCCTTGAGAC-A
* * *
1015448 AT-TCACTTGAAACA
1 GTCTCCCTTGAGACA
1015462 GTCTCCCTTGAGACA
1 GTCTCCCTTGAGACA
1015477 AATTCACTTG
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
14 3 0.06
15 42 0.88
16 3 0.06
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.29
Consensus pattern (15 bp):
GTCTCCCTTGAGACA
Found at i:1015443 original size:30 final size:30
Alignment explanation
Indices: 1015402--1015492 Score: 137
Period size: 30 Copynumber: 3.0 Consensus size: 30
1015392 AACAAATTTT
* * * * *
1015402 GTCTCCTTTGAGACGATTTCCCTTGAGACA
1 GTCTCCCTTGAGACAAATTCACTTGAAACA
1015432 GTCTCCCTTGAGACAAATTCACTTGAAACA
1 GTCTCCCTTGAGACAAATTCACTTGAAACA
1015462 GTCTCCCTTGAGACAAATTCACTTGAAACA
1 GTCTCCCTTGAGACAAATTCACTTGAAACA
1015492 G
1 G
1015493 AAGATTTTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (30 bp):
GTCTCCCTTGAGACAAATTCACTTGAAACA
Found at i:1015486 original size:15 final size:15
Alignment explanation
Indices: 1015438--1015487 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1015428 GACAGTCTCC
1015438 CTTGAGACAAATTCA
1 CTTGAGACAAATTCA
* * *
1015453 CTTGAAAC-AGTCTCC
1 CTTGAGACAAAT-TCA
1015468 CTTGAGACAAATTCA
1 CTTGAGACAAATTCA
1015483 CTTGA
1 CTTGA
1015488 AACAGAAGAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 2 0.07
15 23 0.85
16 2 0.07
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (15 bp):
CTTGAGACAAATTCA
Found at i:1015625 original size:43 final size:43
Alignment explanation
Indices: 1015563--1015793 Score: 236
Period size: 43 Copynumber: 5.4 Consensus size: 43
1015553 TGATTTTCAG
* *
1015563 GGGTTTCTTGAAGAAAAGCTTGAGAGACCATCGTGATATGTAA
1 GGGTTTCTTGATGACAAGCTTGAGAGACCATCGTGATATGTAA
* * *
1015606 GGGTTTATTGAGGACAAGCTTGA-AGGACCATCGTGATATGTAG
1 GGGTTTCTTGATGACAAGCTTGAGA-GACCATCGTGATATGTAA
*
1015649 GGGTTCCTTGATGACAAGCTTGA-AGGACCATCGTGATATGT-A
1 GGGTTTCTTGATGACAAGCTTGAGA-GACCATCGTGATATGTAA
* * * * *
1015691 GGGGTTCTTTGATGATAAGTTTGAGAAACCATCGTGATATAT-A
1 GGGTTTC-TTGATGACAAGCTTGAGAGACCATCGTGATATGTAA
* * * * * *
1015734 GGGTTTCTTGATGTCAAGTTTTAGGGACCATCGTGATATGCAG
1 GGGTTTCTTGATGACAAGCTTGAGAGACCATCGTGATATGTAA
* *
1015777 GGGTTCCTTGGTGACAA
1 GGGTTTCTTGATGACAA
1015794 TTAAGAAACT
Statistics
Matches: 158, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
42 33 0.21
43 124 0.78
44 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (43 bp):
GGGTTTCTTGATGACAAGCTTGAGAGACCATCGTGATATGTAA
Found at i:1015722 original size:86 final size:87
Alignment explanation
Indices: 1015561--1015782 Score: 265
Period size: 86 Copynumber: 2.6 Consensus size: 87
1015551 CCTGATTTTC
* * *
1015561 AGGGGTTTCTTGAAGAAAAGCTTG-AGAGACCATCGTGATATGTAAGGGTT-TATTGAGGACAAG
1 AGGGGTTTCTTGATGACAAGCTTGAAG-GACCATCGTGATATGTAGGGGTTCTATTGAGGACAAG
* *
1015624 CTTGAAGGACCATCGTGATATGT
65 CTTGAAGAACCATCGTGATATAT
* * * *
1015647 AGGGGTTCCTTGATGACAAGCTTGAAGGACCATCGTGATATGTAGGGGTTCT-TTGATGATAAGT
1 AGGGGTTTCTTGATGACAAGCTTGAAGGACCATCGTGATATGTAGGGGTTCTATTGAGGACAAGC
1015711 TTG-AGAAACCATCGTGATATAT
66 TTGAAG-AACCATCGTGATATAT
* * * * *
1015733 A-GGGTTTCTTGATGTCAAGTTTTAGGGACCATCGTGATATGCAGGGGTTC
1 AGGGGTTTCTTGATGACAAGCTTGAAGGACCATCGTGATATGTAGGGGTTC
1015783 CTTGGTGACA
Statistics
Matches: 118, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
85 45 0.38
86 70 0.59
87 3 0.03
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.31
Consensus pattern (87 bp):
AGGGGTTTCTTGATGACAAGCTTGAAGGACCATCGTGATATGTAGGGGTTCTATTGAGGACAAGC
TTGAAGAACCATCGTGATATAT
Found at i:1016198 original size:9 final size:9
Alignment explanation
Indices: 1016183--1016228 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
1016173 AGGCTTAAAA
1016183 AATATTATT
1 AATATTATT
*
1016192 TATATTATT
1 AATATTATT
1016201 AATATTATT
1 AATATTATT
*
1016210 ATTA-TATT
1 AATATTATT
1016218 --TATTATT
1 AATATTATT
1016225 AATA
1 AATA
1016229 AAATTATTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
6 2 0.06
7 4 0.13
8 4 0.13
9 21 0.68
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
AATATTATT
Found at i:1016209 original size:12 final size:13
Alignment explanation
Indices: 1016194--1016228 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
1016184 ATATTATTTA
1016194 TATTATTAATA-T
1 TATTATTAATATT
1016206 TATTATT-ATATT
1 TATTATTAATATT
1016218 TATTATTAATA
1 TATTATTAATA
1016229 AAATTATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.14
12 15 0.71
13 3 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTATTAATATT
Found at i:1016221 original size:24 final size:24
Alignment explanation
Indices: 1016177--1016237 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
1016167 TTGATCAGGC
1016177 TTAA-AAAA-TATTATTTATATTA
1 TTAATAAAATTATTATTTATATTA
**
1016199 TTAATATTATTATTATATT-TATTA
1 TTAATAAAATTATTAT-TTATATTA
1016223 TTAATAAAATTATTA
1 TTAATAAAATTATTA
1016238 CATGTGCTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 4 0.12
23 2 0.06
24 24 0.75
25 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTAATAAAATTATTATTTATATTA
Found at i:1024032 original size:19 final size:19
Alignment explanation
Indices: 1024008--1024045 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1023998 ACCATGCCAC
*
1024008 ACTAAGGACATCTTCTTCA
1 ACTAAGGACATCTTATTCA
1024027 ACTAAGGACATCTTATTCA
1 ACTAAGGACATCTTATTCA
1024046 GATGTGAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (19 bp):
ACTAAGGACATCTTATTCA
Found at i:1030038 original size:3 final size:3
Alignment explanation
Indices: 1030032--1030082 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
1030022 ATACTTTACC
1030032 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1030080 ATT
1 ATT
1030083 GTATACAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1030907 original size:22 final size:21
Alignment explanation
Indices: 1030881--1030938 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
1030871 AAGTCTGCCC
1030881 ATATTATTTTATTTTTAATATA
1 ATATTATTTTATTTTTAATA-A
*
1030903 ATATTTTTTTA-TTTTAATAA
1 ATATTATTTTATTTTTAATAA
*
1030923 A-AGTATTTTAATTTTT
1 ATATTATTTT-ATTTTT
1030939 TATACGTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 6 0.19
20 3 0.10
21 12 0.39
22 10 0.32
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
ATATTATTTTATTTTTAATAA
Found at i:1030917 original size:21 final size:22
Alignment explanation
Indices: 1030881--1030931 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
1030871 AAGTCTGCCC
* *
1030881 ATATTATTTTATTTTTAATATA
1 ATATTTTTTTATTTTTAATAAA
1030903 ATATTTTTTTA-TTTTAATAAA
1 ATATTTTTTTATTTTTAATAAA
1030924 AGTATTTT
1 A-TATTTT
1030932 AATTTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
ATATTTTTTTATTTTTAATAAA
Found at i:1030939 original size:22 final size:20
Alignment explanation
Indices: 1030885--1030940 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 20
1030875 CTGCCCATAT
*
1030885 TATTTTA-TTTTTAATATAA
1 TATTTTATTTTTTAATAAAA
*
1030904 TATTTTTTTATTTTAATAAAA
1 TATTTTATT-TTTTAATAAAA
1030925 GTATTTTAATTTTTTA
1 -TATTTT-ATTTTTTA
1030941 TACGTTACCA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 6 0.20
20 1 0.03
21 10 0.33
22 11 0.37
23 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TATTTTATTTTTTAATAAAA
Found at i:1032034 original size:2 final size:2
Alignment explanation
Indices: 1032029--1032062 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1032019 TAGAAAAGTA
1032029 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1032063 GTAAATATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1032244 original size:31 final size:31
Alignment explanation
Indices: 1032216--1032276 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
1032206 TGGAGTGATC
*
1032216 AGTTTATTACAAATTAATAACT-TTAGTGACT
1 AGTTTATTACAAATCAATAA-TGTTAGTGACT
* *
1032247 ATTTTATTACAAGTCAATAATGTTAGTGAC
1 AGTTTATTACAAATCAATAATGTTAGTGAC
1032277 CAATTTGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (31 bp):
AGTTTATTACAAATCAATAATGTTAGTGACT
Found at i:1038043 original size:2 final size:2
Alignment explanation
Indices: 1038036--1038063 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1038026 TTATTTTTCA
1038036 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
1038064 TTCAATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1043027 original size:272 final size:272
Alignment explanation
Indices: 1042606--1043109 Score: 742
Period size: 272 Copynumber: 1.9 Consensus size: 272
1042596 CGAATTACCT
* * *
1042606 TGAATCGAGCAATAGGTCGAACAAGTTATTTTCATTATGAACTTATTCTCCCTCTGTCAGATGAG
1 TGAATCGAGCAATAGGTCGAACAAGTTATTCTCATAATGAACTTATTATCCCTCTGTCAGATGAG
* ** * *
1042671 TTGTTCTCATTATGAAGTCTCCAATGGAATTATCAATCCCTCAAGCGAGGCGTTGCTGATTTAAA
66 TTATTCTCATTACAAACTCTCCAATGGAATTATCAATCCCTCAAGCGAGGCGTTGCTGATTCAAA
* * *
1042736 GTGTTGTGAATCGAGCAATAGGTCGAATAAGTTCTTCTCATTATGAATTTATTCTCTCTCTGTCG
131 GTGTTGTGAATCGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCTGTCG
* * *
1042801 TATGAGTTCTTCTCATTATGAACTTTTC-ATTGGAAATGTCAGACCCTCAAGCAAGGTGTTGCTG
196 GATGAGTTCTTCTCATTAAGAAC-TCTCAATTGGAAATGTCAGACCCTCAAGCAAGGTGTTGCTG
1042865 ATTTAAAGTGTTG
260 ATTTAAAGTGTTG
* * * * *
1042878 TGAATCTAGCAATAGGTCGAACAAGTTCTTCTCATAATGAATTTTTTATCCCTTTGTCAGATGAG
1 TGAATCGAGCAATAGGTCGAACAAGTTATTCTCATAATGAACTTATTATCCCTCTGTCAGATGAG
* * *
1042943 TTATTCTCATTACAAACTCTCTAGTGGAAATT-TCAATCCCTCAAGCGAGGCGTTGCTGATTCGA
66 TTATTCTCATTACAAACTCTCCAATGG-AATTATCAATCCCTCAAGCGAGGCGTTGCTGATTCAA
* * *
1043007 AGTGTTGTGAATCTAGCAATAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTC
130 AGTGTTGTGAATCGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCTGTC
*
1043072 GGATGAGTTCTTCTTATTAAGAACTCTCAATTGGAAAT
195 GGATGAGTTCTTCTCATTAAGAACTCTCAATTGGAAAT
1043110 ATTGATCGGT
Statistics
Matches: 204, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
271 3 0.01
272 197 0.97
273 4 0.02
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (272 bp):
TGAATCGAGCAATAGGTCGAACAAGTTATTCTCATAATGAACTTATTATCCCTCTGTCAGATGAG
TTATTCTCATTACAAACTCTCCAATGGAATTATCAATCCCTCAAGCGAGGCGTTGCTGATTCAAA
GTGTTGTGAATCGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCTGTCG
GATGAGTTCTTCTCATTAAGAACTCTCAATTGGAAATGTCAGACCCTCAAGCAAGGTGTTGCTGA
TTTAAAGTGTTG
Found at i:1043108 original size:136 final size:136
Alignment explanation
Indices: 1042570--1043109 Score: 662
Period size: 136 Copynumber: 4.0 Consensus size: 136
1042560 GGAAATGATG
* * ** *
1042570 ATCCCTCAAGCGAGGCGTTGCTGATTCGAATTACCT-TGAATCGAGCAATAGGTCGAACAAGTTA
1 ATCCCTCAAGCGAGGCGTTGCTGATTCAAAGT-GTTGTGAATCGAGCAATAGGTCGAACAAGTTC
* * * *
1042634 TTTTCATTATGAACTTATTCTCCCTCTGTCAGATGAGTTGTTCTCATTATGAAGTCTCCAA-TGG
65 TTCTCATTATGAACTTATTCTCCCTCTGTCAGATGAGTTCTTCTCATTAAGAACTCT-CAATTGG
1042698 -AATTATCA
129 AAATT-TCA
* *
1042706 ATCCCTCAAGCGAGGCGTTGCTGATTTAAAGTGTTGTGAATCGAGCAATAGGTCGAATAAGTTCT
1 ATCCCTCAAGCGAGGCGTTGCTGATTCAAAGTGTTGTGAATCGAGCAATAGGTCGAACAAGTTCT
* * * *
1042771 TCTCATTATGAATTTATTCTCTCTCTGTC-GTATGAGTTCTTCTCATTATGAACTTTTC-ATTGG
66 TCTCATTATGAACTTATTCTCCCTCTGTCAG-ATGAGTTCTTCTCATTAAGAAC-TCTCAATTGG
*
1042834 AAATGTCA
129 AAATTTCA
* * * *
1042842 GA-CCCTCAAGCAAGGTGTTGCTGATTTAAAGTGTTGTGAATCTAGCAATAGGTCGAACAAGTTC
1 -ATCCCTCAAGCGAGGCGTTGCTGATTCAAAGTGTTGTGAATCGAGCAATAGGTCGAACAAGTTC
* * * * * * * *
1042906 TTCTCATAATGAATTTTTTATCCCTTTGTCAGATGAGTTATTCTCATTACA-AACTCTCTAGTGG
65 TTCTCATTATGAACTTATTCTCCCTCTGTCAGATGAGTTCTTCTCATTA-AGAACTCTCAATTGG
1042970 AAATTTCA
129 AAATTTCA
* * *
1042978 ATCCCTCAAGCGAGGCGTTGCTGATTCGAAGTGTTGTGAATCTAGCAATAGGTTGAACAAGTTCT
1 ATCCCTCAAGCGAGGCGTTGCTGATTCAAAGTGTTGTGAATCGAGCAATAGGTCGAACAAGTTCT
* * *
1043043 TCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTTATTAAGAACTCTCAATTGGAA
66 TCTCATTATGAACTTATTCTCCCTCTGTCAGATGAGTTCTTCTCATTAAGAACTCTCAATTGGAA
1043108 AT
131 AT
1043110 ATTGATCGGT
Statistics
Matches: 350, Mismatches: 43, Indels: 22
0.84 0.10 0.05
Matches are distributed among these distances:
135 8 0.02
136 335 0.96
137 7 0.02
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (136 bp):
ATCCCTCAAGCGAGGCGTTGCTGATTCAAAGTGTTGTGAATCGAGCAATAGGTCGAACAAGTTCT
TCTCATTATGAACTTATTCTCCCTCTGTCAGATGAGTTCTTCTCATTAAGAACTCTCAATTGGAA
ATTTCA
Found at i:1044047 original size:6 final size:6
Alignment explanation
Indices: 1044036--1044105 Score: 50
Period size: 6 Copynumber: 10.7 Consensus size: 6
1044026 GAACCTCTCA
* * *
1044036 TTTTCT TTTTCTT TTTTCC TTTTCC TTTTCATT TTTTCCC TTTTCAT TTTTCT
1 TTTTCT TTTTC-T TTTTCT TTTTCT TTTTC--T TTTT-CT TTTTC-T TTTTCT
*
1044089 TTTTGT CTTTTCT TTTT
1 TTTTCT -TTTTCT TTTT
1044106 TAGGCATAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
6 27 0.52
7 20 0.38
8 4 0.08
9 1 0.02
ACGTcount: A:0.03, C:0.20, G:0.01, T:0.76
Consensus pattern (6 bp):
TTTTCT
Found at i:1044070 original size:20 final size:20
Alignment explanation
Indices: 1044036--1044092 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
1044026 GAACCTCTCA
*
1044036 TTTTCTTTTTCTTTTTT-CC
1 TTTTCATTTTCTTTTTTCCC
*
1044055 TTTTCCTTTTCATTTTTTCCC
1 TTTTCATTTTC-TTTTTTCCC
1044076 TTTTCATTTTTCTTTTT
1 TTTTCA-TTTTCTTTTT
1044093 GTCTTTTCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.30
20 6 0.18
21 12 0.36
22 5 0.15
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTCATTTTCTTTTTTCCC
Found at i:1044079 original size:15 final size:14
Alignment explanation
Indices: 1044055--1044086 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
1044045 TCTTTTTTCC
1044055 TTTTCCTTTTCATT
1 TTTTCCTTTTCATT
1044069 TTTTCCCTTTTCATT
1 TTTT-CCTTTTCATT
1044084 TTT
1 TTT
1044087 CTTTTTGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTCCTTTTCATT
Found at i:1044106 original size:20 final size:19
Alignment explanation
Indices: 1044036--1044105 Score: 88
Period size: 19 Copynumber: 3.5 Consensus size: 19
1044026 GAACCTCTCA
1044036 TTTTCTTTTTCTTTTTTCC
1 TTTTCTTTTTCTTTTTTCC
*
1044055 TTTTCCTTTTCATTTTTTCCC
1 TTTTCTTTTTC-TTTTTT-CC
1044076 TTTTCATTTTTCTTTTTGT-C
1 TTTTC-TTTTTCTTTTT-TCC
1044096 TTTTCTTTTT
1 TTTTCTTTTT
1044106 TAGGCATAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
19 15 0.33
20 12 0.27
21 12 0.27
22 6 0.13
ACGTcount: A:0.03, C:0.20, G:0.01, T:0.76
Consensus pattern (19 bp):
TTTTCTTTTTCTTTTTTCC
Found at i:1051653 original size:21 final size:21
Alignment explanation
Indices: 1051608--1051654 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1051598 ATCATTAGAA
* *
1051608 AAAAATCCAAGAATAATTCAT
1 AAAAATCAAAGAATAATTCAC
1051629 AAAAATCAAAGAATAATT-AGC
1 AAAAATCAAAGAATAATTCA-C
1051650 AAAAA
1 AAAAA
1051655 CAATTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.64, C:0.11, G:0.06, T:0.19
Consensus pattern (21 bp):
AAAAATCAAAGAATAATTCAC
Found at i:1053499 original size:15 final size:14
Alignment explanation
Indices: 1053474--1053503 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1053464 CAAAAAAAAC
1053474 ATAAAATAAATACA
1 ATAAAATAAATACA
1053488 ATAAACATAAATACA
1 ATAAA-ATAAATACA
1053503 A
1 A
1053504 GGACCTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.20
Consensus pattern (14 bp):
ATAAAATAAATACA
Found at i:1056996 original size:20 final size:19
Alignment explanation
Indices: 1056948--1056997 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1056938 TGCCCATATC
*
1056948 ATTTTATTTTTAATATAAT
1 ATTTTAATTTTAATATAAT
*
1056967 ATTTTTATTTTAATA-AGAGT
1 ATTTTAATTTTAATATA-A-T
1056987 ATTTTAATTTT
1 ATTTTAATTTT
1056998 GTTATACATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 1 0.04
19 14 0.54
20 11 0.42
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (19 bp):
ATTTTAATTTTAATATAAT
Found at i:1057516 original size:2 final size:2
Alignment explanation
Indices: 1057509--1057560 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1057499 GAAAAACTGA
1057509 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1057551 AT AT AT AT AT
1 AT AT AT AT AT
1057561 GAATAGGTTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1060531 original size:3 final size:3
Alignment explanation
Indices: 1060525--1060562 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
1060515 ATAATAAAGG
* *
1060525 AAT AAT AAT AAT AAT AAT ATT AAT AAT ATT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1060563 GCCTAACAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:1065359 original size:12 final size:12
Alignment explanation
Indices: 1065344--1065408 Score: 51
Period size: 12 Copynumber: 5.4 Consensus size: 12
1065334 TCGACTTGAA
1065344 TTCTGTTCTGAT
1 TTCTGTTCTGAT
* *
1065356 TTCTGATATGGA-
1 TTCTGTTCT-GAT
*
1065368 TTATGTTCTGAT
1 TTCTGTTCTGAT
* * *
1065380 ATCTGATCTGAA
1 TTCTGTTCTGAT
*
1065392 TTCTGTTTTGAT
1 TTCTGTTCTGAT
1065404 TTCTG
1 TTCTG
1065409 ATATCTCCAT
Statistics
Matches: 38, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
11 2 0.05
12 34 0.89
13 2 0.05
ACGTcount: A:0.17, C:0.12, G:0.18, T:0.52
Consensus pattern (12 bp):
TTCTGTTCTGAT
Found at i:1065374 original size:24 final size:24
Alignment explanation
Indices: 1065340--1065412 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
1065330 ATAATCGACT
*
1065340 TGAATTCTGTTCTGATTTCTGATA
1 TGAATTATGTTCTGATTTCTGATA
* * *
1065364 TGGATTATGTTCTGATATCTGATC
1 TGAATTATGTTCTGATTTCTGATA
* *
1065388 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTATGTTCTGATTTCTGATA
1065412 T
1 T
1065413 CTCCATTTAC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.51
Consensus pattern (24 bp):
TGAATTATGTTCTGATTTCTGATA
Found at i:1071505 original size:28 final size:27
Alignment explanation
Indices: 1071446--1071502 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
1071436 GAAAGGATTT
*
1071446 AAATACCTTGGATATGTGAATTGACCA
1 AAATACCTTGGATATGTGAAATGACCA
1071473 AAATACCATTGGA-ATG-GAAATGAACCA
1 AAATACC-TTGGATATGTGAAATG-ACCA
1071500 AAA
1 AAA
1071503 ATATCACCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 5 0.19
27 17 0.63
28 5 0.19
ACGTcount: A:0.46, C:0.14, G:0.18, T:0.23
Consensus pattern (27 bp):
AAATACCTTGGATATGTGAAATGACCA
Found at i:1072582 original size:24 final size:24
Alignment explanation
Indices: 1072555--1072616 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
1072545 TTCAATTTGA
* * *
1072555 ATTCTGTTGTGATACCTGACCTAG
1 ATTCTATTATGATACATGACCTAG
1072579 ATTCTATTATGATACATGACCTAG
1 ATTCTATTATGATACATGACCTAG
* *
1072603 ATTATATTCTGATA
1 ATTCTATTATGATA
1072617 TCTGAAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (24 bp):
ATTCTATTATGATACATGACCTAG
Found at i:1074801 original size:22 final size:22
Alignment explanation
Indices: 1074775--1074827 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
1074765 CCGTTAACTG
1074775 CGTTGACCG-TCATTAACCGGAC
1 CGTTGACCGAT-ATTAACCGGAC
* *
1074797 CGTTGACCGATGTTGACCGGAC
1 CGTTGACCGATATTAACCGGAC
1074819 CGTTGACCG
1 CGTTGACCG
1074828 CCTTTGACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.19, C:0.30, G:0.28, T:0.23
Consensus pattern (22 bp):
CGTTGACCGATATTAACCGGAC
Found at i:1074834 original size:22 final size:21
Alignment explanation
Indices: 1074775--1074836 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 21
1074765 CCGTTAACTG
* *
1074775 CGTTGACCGTCATTAACCGGAC
1 CGTTGACCG-CTTTGACCGGAC
*
1074797 CGTTGACCGATGTTGACCGGAC
1 CGTTGACCGCT-TTGACCGGAC
1074819 CGTTGACCGCCTTTGACC
1 CGTTGACCG-CTTTGACC
1074837 AGCCATTGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
22 33 0.97
23 1 0.03
ACGTcount: A:0.18, C:0.32, G:0.26, T:0.24
Consensus pattern (21 bp):
CGTTGACCGCTTTGACCGGAC
Found at i:1074856 original size:11 final size:11
Alignment explanation
Indices: 1074794--1074856 Score: 60
Period size: 11 Copynumber: 5.8 Consensus size: 11
1074784 TCATTAACCG
1074794 GACCGTTGACC
1 GACCGTTGACC
*
1074805 GA-TGTTGACC
1 GACCGTTGACC
1074815 GGACCGTTGACC
1 -GACCGTTGACC
*
1074827 G-CCTTTGACC
1 GACCGTTGACC
*
1074837 -AGCCATTGACC
1 GA-CCGTTGACC
1074848 GACCGTTGA
1 GACCGTTGA
1074857 TTTGTTTTGG
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
10 15 0.36
11 19 0.45
12 8 0.19
ACGTcount: A:0.19, C:0.32, G:0.27, T:0.22
Consensus pattern (11 bp):
GACCGTTGACC
Found at i:1076780 original size:24 final size:24
Alignment explanation
Indices: 1076759--1076841 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 24
1076749 ATTTCTGATT
1076759 TGAATTTTGTTATGATACCTGACC
1 TGAATTTTGTTATGATACCTGACC
* **
1076783 TGGATTTTGTTATGATAAATGACC
1 TGAATTTTGTTATGATACCTGACC
* **
1076807 T-AGATTCTGTTATGATAAATGACC
1 TGA-ATTTTGTTATGATACCTGACC
* *
1076831 TGGATTCTGTT
1 TGAATTTTGTT
1076842 CTAATATCTA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (24 bp):
TGAATTTTGTTATGATACCTGACC
Found at i:1087212 original size:22 final size:22
Alignment explanation
Indices: 1087184--1087227 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1087174 CAATTCTAAC
1087184 GGGAGAATTGAAACAGACCCTT
1 GGGAGAATTGAAACAGACCCTT
1087206 GGGAGAATTGAAACAGACCCTT
1 GGGAGAATTGAAACAGACCCTT
1087228 AATATTTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.18
Consensus pattern (22 bp):
GGGAGAATTGAAACAGACCCTT
Found at i:1091676 original size:14 final size:14
Alignment explanation
Indices: 1091631--1091684 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
1091621 GTGAAATTAA
1091631 ACGGGTTAACTCAG
1 ACGGGTTAACTCAG
* * * * *
1091645 ATGAGTTGAGTCAT
1 ACGGGTTAACTCAG
*
1091659 ACGGGTTGACTCAG
1 ACGGGTTAACTCAG
1091673 ACGGGTTAACTC
1 ACGGGTTAACTC
1091685 GAATCGATTT
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (14 bp):
ACGGGTTAACTCAG
Found at i:1091712 original size:14 final size:15
Alignment explanation
Indices: 1091681--1091713 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1091671 AGACGGGTTA
*
1091681 ACTCGAATCGATTTG
1 ACTCGAATCGAGTTG
1091696 ACTCGAAT-GAGTTG
1 ACTCGAATCGAGTTG
1091710 ACTC
1 ACTC
1091714 AGAGACTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (15 bp):
ACTCGAATCGAGTTG
Found at i:1092393 original size:103 final size:103
Alignment explanation
Indices: 1092214--1092419 Score: 412
Period size: 103 Copynumber: 2.0 Consensus size: 103
1092204 AAACAACAAA
1092214 CAGTGGTCAAACGGTGGTGGAATCGGGTGACAAAAAGGGTTAGCCGGGGAATTTTTTTGGAAATG
1 CAGTGGTCAAACGGTGGTGGAATCGGGTGACAAAAAGGGTTAGCCGGGGAATTTTTTTGGAAATG
1092279 GGTATTTGGCAGCTGTGCTTGAATCTAATCGTGAGGGG
66 GGTATTTGGCAGCTGTGCTTGAATCTAATCGTGAGGGG
1092317 CAGTGGTCAAACGGTGGTGGAATCGGGTGACAAAAAGGGTTAGCCGGGGAATTTTTTTGGAAATG
1 CAGTGGTCAAACGGTGGTGGAATCGGGTGACAAAAAGGGTTAGCCGGGGAATTTTTTTGGAAATG
1092382 GGTATTTGGCAGCTGTGCTTGAATCTAATCGTGAGGGG
66 GGTATTTGGCAGCTGTGCTTGAATCTAATCGTGAGGGG
1092420 GCAGAATTTA
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.24, C:0.12, G:0.37, T:0.27
Consensus pattern (103 bp):
CAGTGGTCAAACGGTGGTGGAATCGGGTGACAAAAAGGGTTAGCCGGGGAATTTTTTTGGAAATG
GGTATTTGGCAGCTGTGCTTGAATCTAATCGTGAGGGG
Found at i:1094335 original size:31 final size:31
Alignment explanation
Indices: 1094300--1094373 Score: 139
Period size: 31 Copynumber: 2.4 Consensus size: 31
1094290 TTAGGCTCAT
*
1094300 AAGGAATTACCATTCGGTGCTGAACCTATAA
1 AAGGAATTACCATTCGATGCTGAACCTATAA
1094331 AAGGAATTACCATTCGATGCTGAACCTATAA
1 AAGGAATTACCATTCGATGCTGAACCTATAA
1094362 AAGGAATTACCA
1 AAGGAATTACCA
1094374 ACATCGATTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (31 bp):
AAGGAATTACCATTCGATGCTGAACCTATAA
Found at i:1094386 original size:31 final size:30
Alignment explanation
Indices: 1094300--1094388 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 30
1094290 TTAGGCTCAT
* *
1094300 AAGGAATTACCATTCGGTGCTGAACCTATAA
1 AAGGAATTACCAATCGAT-CTGAACCTATAA
*
1094331 AAGGAATTACCATTCGATGCTGAACCTATAA
1 AAGGAATTACCAATCGAT-CTGAACCTATAA
1094362 AAGGAATTACCAACATCGAT-TGAACCT
1 AAGGAATTACC-A-ATCGATCTGAACCT
1094389 GTTAGAGATA
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
31 48 0.89
32 1 0.02
33 5 0.09
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (30 bp):
AAGGAATTACCAATCGATCTGAACCTATAA
Found at i:1097872 original size:208 final size:206
Alignment explanation
Indices: 1097498--1097918 Score: 720
Period size: 208 Copynumber: 2.0 Consensus size: 206
1097488 TATCCCATCT
*
1097498 ATTTCTTATATGTAATGGAATATTCTCCCCTTAAATTGCTTGAAAATATTAAAATCGAATAAGAA
1 ATTTATTATATGTAATGGAATATTCTCCCCTTAAATTGCTTGAAAATATTAAAATCGAATAAGAA
*
1097563 ATCAATATCGTAATTTTACATGAAATTATCTGAAAACATAAATTGTCATTACCTAAATTTAAGTA
66 ATCAATATCGTAATTTTACATGAAATTATATGAAAACATAAATTGTCATTACCTAAATTTAAGTA
*
1097628 AAACAGAATAAAATTAAAATAAAATAACATAAAAATAGAATACAAATATTACTATCATTTAATAA
131 AAACAAAATAAAATTAAAATAAAATAACATAAAAATA-AATA-AAATATTACTATCATTTAATAA
1097693 ATAAAAATGTTCA
194 ATAAAAATGTTCA
* * * *
1097706 CTTTATTATATGTAATGGATTATTCTCCGCTTGAATTGCTTGAAAATATTAAAATCGAATAAGAA
1 ATTTATTATATGTAATGGAATATTCTCCCCTTAAATTGCTTGAAAATATTAAAATCGAATAAGAA
1097771 ATCAATATCGTAATTTTACATGAAATTATATGAAAACATAAATTGTCATTACCTAAATTTAAGTA
66 ATCAATATCGTAATTTTACATGAAATTATATGAAAACATAAATTGTCATTACCTAAATTTAAGTA
*
1097836 AAACAAAAT-AAA-TAAAATAAAATAACATAAAAAAATAATTAAAATATTACTATCATTTAATAA
131 AAACAAAATAAAATTAAAATAAAATAACAT--AAAAATAAATAAAATATTACTATCATTTAATAA
1097899 ATAAAAATGTTCA
194 ATAAAAATGTTCA
1097912 ATTTATT
1 ATTTATT
1097919 TCAAATTCAC
Statistics
Matches: 202, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
206 57 0.28
207 6 0.03
208 139 0.69
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (206 bp):
ATTTATTATATGTAATGGAATATTCTCCCCTTAAATTGCTTGAAAATATTAAAATCGAATAAGAA
ATCAATATCGTAATTTTACATGAAATTATATGAAAACATAAATTGTCATTACCTAAATTTAAGTA
AAACAAAATAAAATTAAAATAAAATAACATAAAAATAAATAAAATATTACTATCATTTAATAAAT
AAAAATGTTCA
Found at i:1099380 original size:17 final size:18
Alignment explanation
Indices: 1099355--1099389 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1099345 TTGAGTTTTA
*
1099355 GACTGATTT-GGTTGATT
1 GACTAATTTGGGTTGATT
1099372 GACTAATTTGGGTTGATT
1 GACTAATTTGGGTTGATT
1099390 TTCCTACTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.20, C:0.06, G:0.29, T:0.46
Consensus pattern (18 bp):
GACTAATTTGGGTTGATT
Found at i:1099751 original size:6 final size:6
Alignment explanation
Indices: 1099742--1099885 Score: 74
Period size: 7 Copynumber: 22.3 Consensus size: 6
1099732 TAGTATTTTA
* * * * * *
1099742 AATATT AATAAT AATAAT AAGCACT ACTAAC AATTAAT AACAAT AAATAAT
1 AATAAT AATAAT AATAAT AA-TAAT AATAAT AA-TAAT AATAAT -AATAAT
* * * * *
1099793 AATAAT AATAAAT ATTGAT AAAAATT AATAAA AATTAAT AATTATT AATAA-
1 AATAAT AAT-AAT AATAAT AATAA-T AATAAT AA-TAAT AA-TAAT AATAAT
*
1099844 CATCAAT AATAAAT AATAAAT AATAAT AATAACT AATAAT AA
1 AAT-AAT AAT-AAT AAT-AAT AATAAT AATAA-T AATAAT AA
1099886 CCAATAAGAA
Statistics
Matches: 105, Mismatches: 24, Indels: 18
0.71 0.16 0.12
Matches are distributed among these distances:
5 2 0.02
6 48 0.46
7 55 0.52
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (6 bp):
AATAAT
Found at i:1099755 original size:3 final size:3
Alignment explanation
Indices: 1099742--1099885 Score: 74
Period size: 3 Copynumber: 44.7 Consensus size: 3
1099732 TAGTATTTTA
* * * * * *
1099742 AAT ATT AAT AAT AAT AAT AAGC ACT ACT AAC AATT AAT AAC AAT AAAT
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AA-T AAT AAT AAT -AAT
* * * * *
1099790 AAT AAT AAT AAT AAAT ATT GAT AAA AATT AAT AAA AATT AAT AATT ATT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AA-T AAT AAT AA-T AAT AA-T AAT
*
1099839 AAT AA- CAT CAAT AAT AAAT AAT AAAT AAT AAT AAT AACT AAT AAT AA
1 AAT AAT AAT -AAT AAT -AAT AAT -AAT AAT AAT AAT AA-T AAT AAT AA
1099886 CCAATAAGAA
Statistics
Matches: 107, Mismatches: 22, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
2 1 0.01
3 80 0.75
4 26 0.24
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1099797 original size:16 final size:16
Alignment explanation
Indices: 1099776--1099885 Score: 87
Period size: 16 Copynumber: 6.6 Consensus size: 16
1099766 TACTAACAAT
*
1099776 TAATAACAATAAATAA
1 TAATAATAATAAATAA
*
1099792 TAATAATAATAAATAT
1 TAATAATAATAAATAA
* * *
1099808 TGATAAAAATTAATAA
1 TAATAATAATAAATAA
* * *
1099824 AAATTAATAATTATTAA
1 TAA-TAATAATAAATAA
1099841 TAACATCAATAATAAATAA
1 T-A-AT-AATAATAAATAA
1099860 TAAATAATAAT-AATAA
1 T-AATAATAATAAATAA
1099876 CTAATAATAA
1 -TAATAATAA
1099886 CCAATAAGAA
Statistics
Matches: 76, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
16 40 0.53
17 18 0.24
18 4 0.05
19 14 0.18
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.32
Consensus pattern (16 bp):
TAATAATAATAAATAA
Found at i:1099806 original size:26 final size:26
Alignment explanation
Indices: 1099776--1099882 Score: 69
Period size: 29 Copynumber: 3.8 Consensus size: 26
1099766 TACTAACAAT
*
1099776 TAATAACAATAAATAATAAT-AATAA
1 TAATAATAATAAATAATAATAAATAA
1099801 TAAATATTGATAA-AAATTAATAA-AAATTAA
1 T-AATA---ATAATAAA-TAATAATAAA-TAA
*
1099831 TAATTATTAATAACATCAATAATAAATAA
1 TAA-TAATAATAA-AT-AATAATAAATAA
1099860 TAAATAATAAT-AATAACTAATAA
1 T-AATAATAATAAATAA-TAATAA
1099883 TAACCAATAA
Statistics
Matches: 65, Mismatches: 3, Indels: 26
0.69 0.03 0.28
Matches are distributed among these distances:
25 1 0.02
26 6 0.09
27 11 0.17
28 7 0.11
29 29 0.45
30 11 0.17
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.32
Consensus pattern (26 bp):
TAATAATAATAAATAATAATAAATAA
Found at i:1099819 original size:42 final size:40
Alignment explanation
Indices: 1099741--1099885 Score: 109
Period size: 42 Copynumber: 3.5 Consensus size: 40
1099731 TTAGTATTTT
* ** * *
1099741 AAATATTAATAATAATAATAAGCACTACTAACAATTAATAA
1 AAATAATAATAATAATAATAAATAATA-TAAAAATTAATAA
* *
1099782 CAATAAATAATAATAATAATAAATATTGATAAAAATTAATAA
1 AAAT-AATAATAATAATAATAAATAAT-ATAAAAATTAATAA
* *
1099824 AAAT--TAATAATTATTAATAACATCAATA-ATAAA-TAATAA
1 AAATAATAATAA-TAATAATAA-AT-AATATAAAAATTAATAA
1099863 ATAATAATAATAACTAATAATAA
1 A-AATAATAATAA-TAATAATAA
1099886 CCAATAAGAA
Statistics
Matches: 84, Mismatches: 12, Indels: 15
0.76 0.11 0.14
Matches are distributed among these distances:
39 13 0.15
40 15 0.18
41 6 0.07
42 49 0.58
43 1 0.01
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (40 bp):
AAATAATAATAATAATAATAAATAATATAAAAATTAATAA
Found at i:1099823 original size:36 final size:38
Alignment explanation
Indices: 1099783--1099882 Score: 100
Period size: 39 Copynumber: 2.6 Consensus size: 38
1099773 AATTAATAAC
* **
1099783 AATAAATAATAATAATAAT-A-AATATTGATAA-AAATT
1 AATAAATAATAATAATAATAATAACATCAATAATAAA-T
*
1099819 AATAAA-AATTAATAATTATTAATAACATCAATAATAAAT
1 AATAAATAA-TAATAA-TAATAATAACATCAATAATAAAT
1099858 AATAAATAATAATAATAACTAATAA
1 AATAAATAATAATAATAA-TAATAA
1099883 TAACCAATAA
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
35 2 0.04
36 12 0.23
37 3 0.06
38 3 0.06
39 27 0.52
40 5 0.10
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (38 bp):
AATAAATAATAATAATAATAATAACATCAATAATAAAT
Found at i:1099861 original size:10 final size:10
Alignment explanation
Indices: 1099787--1099885 Score: 80
Period size: 10 Copynumber: 9.8 Consensus size: 10
1099777 AATAACAATA
1099787 AATAAT-AAT
1 AATAATAAAT
1099796 AATAATAAAT
1 AATAATAAAT
* *
1099806 ATTGATAAA-
1 AATAATAAAT
1099815 AATTAATAAA-
1 AA-TAATAAAT
*
1099825 AATTAATAATT
1 AA-TAATAAAT
*
1099836 ATTAATAACAT
1 AATAATAA-AT
1099847 CAATAATAAAT
1 -AATAATAAAT
1099858 AATAA-ATAAT
1 AATAATA-AAT
*
1099868 AATAATAACT
1 AATAATAAAT
1099878 AATAATAA
1 AATAATAA
1099886 CCAATAAGAA
Statistics
Matches: 74, Mismatches: 9, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
9 8 0.11
10 54 0.73
11 5 0.07
12 7 0.09
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (10 bp):
AATAATAAAT
Found at i:1099886 original size:10 final size:9
Alignment explanation
Indices: 1099742--1099885 Score: 74
Period size: 10 Copynumber: 14.9 Consensus size: 9
1099732 TAGTATTTTA
*
1099742 AATATTAAT
1 AATAATAAT
1099751 AATAATAAT
1 AATAATAAT
* * *
1099760 AAGCACTACT
1 AA-TAATAAT
*
1099770 AACAATTAAT
1 AATAA-TAAT
*
1099780 AACAATAAAT
1 AATAAT-AAT
1099790 AATAATAAT
1 AATAATAAT
*
1099799 AATAAATATT
1 AAT-AATAAT
* *
1099809 GATAAAAATT
1 AATAATAA-T
*
1099819 AATAAAAATT
1 AATAATAA-T
*
1099829 AATAATTATT
1 AATAA-TAAT
*
1099839 AATAA-CAT
1 AATAATAAT
1099847 CAATAATAAAT
1 -AATAAT-AAT
1099858 AATAAATAAT
1 AAT-AATAAT
1099868 AATAATAACT
1 AATAATAA-T
1099878 AATAATAA
1 AATAATAA
1099886 CCAATAAGAA
Statistics
Matches: 107, Mismatches: 17, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
8 1 0.01
9 32 0.30
10 68 0.64
11 6 0.06
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (9 bp):
AATAATAAT
Found at i:1103117 original size:4 final size:4
Alignment explanation
Indices: 1103108--1103144 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
1103098 ATTGGAATAA
*
1103108 AAAT AAAT AAA- CAA- AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1103145 AATTGAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 4 0.13
4 26 0.87
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:1103147 original size:14 final size:14
Alignment explanation
Indices: 1103103--1103144 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
1103093 ATCTGATTGG
1103103 AATAAAAATAAATA
1 AATAAAAATAAATA
*
1103117 AACAAAAATAAATA
1 AATAAAAATAAATA
1103131 AAT--AAATAAATA
1 AATAAAAATAAATA
1103143 AA
1 AA
1103145 AATTGAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 11 0.42
14 15 0.58
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (14 bp):
AATAAAAATAAATA
Found at i:1103160 original size:22 final size:21
Alignment explanation
Indices: 1103106--1103157 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
1103096 TGATTGGAAT
1103106 AAAAATAAATAAACAAAAATA
1 AAAAATAAATAAACAAAAATA
* *
1103127 AATAAATAAATAAATAAAAATT
1 AA-AAATAAATAAACAAAAATA
*
1103149 GAAAATAAA
1 AAAAATAAA
1103158 ATACTAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (21 bp):
AAAAATAAATAAACAAAAATA
Found at i:1103212 original size:17 final size:17
Alignment explanation
Indices: 1103190--1103250 Score: 74
Period size: 17 Copynumber: 3.7 Consensus size: 17
1103180 CTTTCGAAAA
*
1103190 ATATGTTTTAAAAAACT
1 ATATGTTTTCAAAAACT
1103207 ATATGTTCTTCAAAAAC-
1 ATATGTT-TTCAAAAACT
*
1103224 -CAT-TTTTCAAAAACT
1 ATATGTTTTCAAAAACT
1103239 ATATGTTTTCAA
1 ATATGTTTTCAA
1103251 GTATAATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 9 0.24
15 2 0.05
16 4 0.11
17 14 0.38
18 8 0.22
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.41
Consensus pattern (17 bp):
ATATGTTTTCAAAAACT
Found at i:1103304 original size:37 final size:36
Alignment explanation
Indices: 1103263--1103495 Score: 164
Period size: 37 Copynumber: 6.5 Consensus size: 36
1103253 ATAATTTAAA
*
1103263 AAAAACTTTATATTATATG-TTTCAAAAATACGTTTCC
1 AAAAAC-TTATATTATATGTTTTCAAAAATA-GTTTTC
1103300 AAAAAC-TATATTAAATATTGTTTTCAAAAATA--TTT-
1 AAAAACTTATATT--ATA-TGTTTTCAAAAATAGTTTTC
* * *
1103335 AAAAATTATATATTATA-CTTTTCAAAAATGTGTTTTC
1 AAAAACT-TATATTATATGTTTTCAAAAAT-AGTTTTC
* * *
1103372 -GAAACTATATATTATAAGTTTTCAAAAATGTGTTTTC
1 AAAAACT-TATATTATATGTTTTCAAAAAT-AGTTTTC
* * ** *
1103409 -AAAAC-CATATTATATGTTTTCCAAAACCGATTTTT
1 AAAAACTTATATTATATGTTTTCAAAAATAG-TTTTC
*
1103444 AAAAACTATATATTATCTGTTTTCAAAAATA-TTTTC
1 AAAAACT-TATATTATATGTTTTCAAAAATAGTTTTC
*
1103480 AAAAAC-TATACTATAT
1 AAAAACTTATATTATAT
1103496 TATTATATAT
Statistics
Matches: 159, Mismatches: 22, Indels: 33
0.74 0.10 0.15
Matches are distributed among these distances:
33 11 0.07
34 9 0.06
35 36 0.23
36 34 0.21
37 38 0.24
38 20 0.13
39 11 0.07
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (36 bp):
AAAAACTTATATTATATGTTTTCAAAAATAGTTTTC
Done.