Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 18 of 444
Found at i:5135174 original size:91 final size:91
Alignment explanation
Indices: 5135006--5135212 Score: 281
Period size: 91 Copynumber: 2.3 Consensus size: 91
5134996 TACGCTGAGG
* * *
5135006 TGTTTTTCAATTTTTGTGTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
1 TGTTTTTCAATTTCTGTGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGC
* * * * *
5135071 TCATATTCTGAGGTGTTTTCCATTTC
66 TCACAGTCTGAGGTATTTTCAAATTC
* * *
5135097 TGTTCTTCAATTTCTGTGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGGGCCTTGGC
1 TGTTTTTCAATTTCTGTGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGC
5135162 TCACACGT-TGAGGTATTTTCAAATTC
66 TCACA-GTCTGAGGTATTTTCAAATTC
* *
5135188 TGTTTTTCAAATTCTGTTTTTCAAA
1 TGTTTTTCAATTTCTGTGTTTCAAA
5135213 TTCTGTTTTT
Statistics
Matches: 101, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
91 100 0.99
92 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (91 bp):
TGTTTTTCAATTTCTGTGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGC
TCACAGTCTGAGGTATTTTCAAATTC
Found at i:5135225 original size:15 final size:14
Alignment explanation
Indices: 5135177--5135222 Score: 92
Period size: 14 Copynumber: 3.3 Consensus size: 14
5135167 CGTTGAGGTA
5135177 TTTTCAAATTCTGT
1 TTTTCAAATTCTGT
5135191 TTTTCAAATTCTGT
1 TTTTCAAATTCTGT
5135205 TTTTCAAATTCTGT
1 TTTTCAAATTCTGT
5135219 TTTT
1 TTTT
5135223 TCAGAAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.20, C:0.13, G:0.07, T:0.61
Consensus pattern (14 bp):
TTTTCAAATTCTGT
Found at i:5135315 original size:76 final size:77
Alignment explanation
Indices: 5135205--5135424 Score: 257
Period size: 76 Copynumber: 2.8 Consensus size: 77
5135195 CAAATTCTGT
* * *
5135205 TTTTCAAATTCTGTTTTTTCAGAAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG-
1 TTTTCAATTTCTGTTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGC
5135269 ACATGCTGAGGTA
65 ACATGCTGAGGTA
* *
5135282 GTTTT-AATTTCTG-TTCTTCAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGC
1 -TTTTCAATTTCTGTTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG-
*
5135345 TCACGTGCTGAGGTA
64 -CACATGCTGAGGTA
* * *
5135360 TTTTCAATTTCTGTTTTTTTAATTTTTCAAATATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TTTTCAATTTCTGTTTTTTCAA-----AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
5135425 TTAATTTTCG
Statistics
Matches: 121, Mismatches: 11, Indels: 14
0.83 0.08 0.10
Matches are distributed among these distances:
75 2 0.02
76 43 0.36
77 11 0.09
78 24 0.20
79 6 0.05
84 35 0.29
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (77 bp):
TTTTCAATTTCTGTTTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGCA
CATGCTGAGGTA
Found at i:5135509 original size:13 final size:13
Alignment explanation
Indices: 5135491--5135515 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5135481 TGAGTTGAGC
5135491 CTTTTAATTTCTG
1 CTTTTAATTTCTG
5135504 CTTTTAATTTCT
1 CTTTTAATTTCT
5135516 ATGTTTCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.04, T:0.64
Consensus pattern (13 bp):
CTTTTAATTTCTG
Found at i:5135523 original size:68 final size:68
Alignment explanation
Indices: 5135383--5135559 Score: 218
Period size: 68 Copynumber: 2.6 Consensus size: 68
5135373 TTTTTTTAAT
*
5135383 TTTTCAAATATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TTTAATTTTCGTTTTTCAAAATC
1 TTTTCAAATATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTTCGCTTTTCAAAATC
5135447 TAC
66 TAC
* * **
5135450 TTTTCAAATTATTAACTCATGTTGCGAGAGGTGAGTTGAGCCTTTTAA-TTTCTGCTTTT-AATT
1 TTTTCAAA-TATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTTC-GCTTTTCAAAA
5135513 TCTA-
64 TCTAC
* * **
5135517 TGTTTCAAAAATCAACCCATATTGCGAGAAATGAGTTGAGCCT
1 T-TTTCAAATATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
5135560 CAGTTCACCT
Statistics
Matches: 95, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
67 37 0.39
68 48 0.51
69 10 0.11
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (68 bp):
TTTTCAAATATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTTCGCTTTTCAAAATC
TAC
Found at i:5136086 original size:25 final size:25
Alignment explanation
Indices: 5136052--5136099 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
5136042 AAAAGTCTTT
5136052 ACTCTATTCTCGTTACACGACAACA
1 ACTCTATTCTCGTTACACGACAACA
*
5136077 ACTCTGTTCTCGTTACACGACAA
1 ACTCTATTCTCGTTACACGACAA
5136100 TAAGTAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.31, G:0.10, T:0.29
Consensus pattern (25 bp):
ACTCTATTCTCGTTACACGACAACA
Found at i:5136518 original size:14 final size:14
Alignment explanation
Indices: 5136496--5136656 Score: 144
Period size: 14 Copynumber: 10.7 Consensus size: 14
5136486 AAAAGGGGGA
5136496 AGCAAAAAAATTTTCC
1 AGCAAAAAAA--TTCC
5136512 AGCAAAAAAATTCCAGC
1 AGCAAAAAAATT-C--C
*
5136529 AGCAAAAAAATTTTTTC
1 AGCAAAAAAA---TTCC
5136546 AGCAAAAAAATTCCAGC
1 AGCAAAAAAATT-C--C
5136563 AGCAAAAAAATTCC
1 AGCAAAAAAATTCC
*
5136577 AGCAAAAAAAATCC
1 AGCAAAAAAATTCC
*
5136591 AGC-AAAAAATTCT
1 AGCAAAAAAATTCC
* *
5136604 AGCCAAAAAATTTC
1 AGCAAAAAAATTCC
5136618 AGCAAAGAAAATTCC
1 AGCAAA-AAAATTCC
*
5136633 AGCAAAAAATTTCC
1 AGCAAAAAAATTCC
*
5136647 AGTAAAAAAA
1 AGCAAAAAAA
5136657 ACCAAAAAAG
Statistics
Matches: 122, Mismatches: 12, Indels: 24
0.77 0.08 0.15
Matches are distributed among these distances:
13 11 0.09
14 49 0.40
15 14 0.11
16 11 0.09
17 35 0.29
20 2 0.02
ACGTcount: A:0.55, C:0.19, G:0.09, T:0.18
Consensus pattern (14 bp):
AGCAAAAAAATTCC
Found at i:5136549 original size:34 final size:33
Alignment explanation
Indices: 5136496--5136594 Score: 157
Period size: 34 Copynumber: 3.0 Consensus size: 33
5136486 AAAAGGGGGA
5136496 AGCAAAAAAATTTTCCAGCAAAAAAATTCCAGC
1 AGCAAAAAAATTTTCCAGCAAAAAAATTCCAGC
*
5136529 AGCAAAAAAATTTTTTCAGCAAAAAAATTCCAGC
1 AGCAAAAAAA-TTTTCCAGCAAAAAAATTCCAGC
*
5136563 AGCAAAAAAA--TTCCAGCAAAAAAAATCCAGC
1 AGCAAAAAAATTTTCCAGCAAAAAAATTCCAGC
5136594 A
1 A
5136595 AAAAATTCTA
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
31 20 0.32
33 10 0.16
34 32 0.52
ACGTcount: A:0.54, C:0.20, G:0.09, T:0.17
Consensus pattern (33 bp):
AGCAAAAAAATTTTCCAGCAAAAAAATTCCAGC
Found at i:5137149 original size:31 final size:34
Alignment explanation
Indices: 5137081--5137153 Score: 85
Period size: 36 Copynumber: 2.1 Consensus size: 34
5137071 GGGTGATATG
* *
5137081 TTAAGTTAGTGGGTTGGGTTGGTTGTGTTGGGTTTA
1 TTAAGTTAGTGAGTTGGGTTGGTTGTGTT--GATTA
*
5137117 TTAAGTTAGTGAGTTGGGTTGGTT-TGTATTATTA
1 TTAAGTTAGTGAGTTGGGTTGGTTGTGT-TGATTA
5137151 TTA
1 TTA
5137154 TTATTTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 6 0.18
35 3 0.09
36 24 0.73
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.49
Consensus pattern (34 bp):
TTAAGTTAGTGAGTTGGGTTGGTTGTGTTGATTA
Found at i:5137822 original size:16 final size:17
Alignment explanation
Indices: 5137779--5137823 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
5137769 AAAATTCAGG
5137779 TTTCAAAAATTTTCGTGA
1 TTTC-AAAATTTTCGTGA
5137797 TTTCAAAATTTTCGTG-
1 TTTCAAAATTTTCGTGA
*
5137813 TTTTAAAATTT
1 TTTCAAAATTT
5137824 CTCATTTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 10 0.38
17 12 0.46
18 4 0.15
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (17 bp):
TTTCAAAATTTTCGTGA
Found at i:5139485 original size:19 final size:19
Alignment explanation
Indices: 5139461--5139498 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5139451 GAAATGAATA
5139461 ATTTCAAGCAAATAGGTTG
1 ATTTCAAGCAAATAGGTTG
5139480 ATTTCAAGCAAATAGGTTG
1 ATTTCAAGCAAATAGGTTG
5139499 GCAATCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (19 bp):
ATTTCAAGCAAATAGGTTG
Found at i:5139886 original size:26 final size:26
Alignment explanation
Indices: 5139849--5139932 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
5139839 TGATACAAAT
* *
5139849 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5139875 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5139901 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5139927 TGATAA
1 TGATAA
5139933 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:5140560 original size:23 final size:23
Alignment explanation
Indices: 5140526--5140569 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
5140516 GAAAATCACC
*
5140526 ATAAATTGTGTAATTAAAGCTGA
1 ATAAATTATGTAATTAAAGCTGA
5140549 ATAAATTATGTAATTAAAGCT
1 ATAAATTATGTAATTAAAGCT
5140570 TATTGAGTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (23 bp):
ATAAATTATGTAATTAAAGCTGA
Found at i:5141404 original size:28 final size:26
Alignment explanation
Indices: 5141373--5141443 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 26
5141363 AGCAGTTAAC
*
5141373 TTACTATAATACCCCTATGTATGGAAAA
1 TTACTATAATACCCCTA-G-ATGCAAAA
* * *
5141401 TTACTGTTATACCCCTAGGTGCAAAA
1 TTACTATAATACCCCTAGATGCAAAA
*
5141427 TTACCA-AATACCCCTAG
1 TTACTATAATACCCCTAG
5141444 GGTTAAATTG
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
25 10 0.28
26 10 0.28
27 1 0.03
28 15 0.42
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (26 bp):
TTACTATAATACCCCTAGATGCAAAA
Found at i:5142514 original size:2 final size:2
Alignment explanation
Indices: 5142507--5142540 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5142497 GTAGCTAAAT
5142507 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5142541 CACATAAACA
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):
TA
Found at i:5143143 original size:2 final size:2
Alignment explanation
Indices: 5143136--5143169 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5143126 TTAAATTATG
*
5143136 TA TA TA TA TA GA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5143170 AAATAAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5143200 original size:19 final size:20
Alignment explanation
Indices: 5143167--5143206 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
5143157 ATATATATAT
5143167 ATAAAATAAAGAAAAT-AAA
1 ATAAAATAAAGAAAATGAAA
5143186 ATAAAATAACA-AAAATGAAA
1 ATAAAATAA-AGAAAATGAAA
5143206 A
1 A
5143207 ATGAAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (20 bp):
ATAAAATAAAGAAAATGAAA
Found at i:5143486 original size:9 final size:9
Alignment explanation
Indices: 5143456--5143497 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
5143446 AGAGGTTAGG
*
5143456 TTTTTTTTC
1 TTTTTTTTA
*
5143465 TTTTTCTTCA
1 TTTTT-TTTA
5143475 TTTTTTTTA
1 TTTTTTTTA
5143484 -TTTTTTTA
1 TTTTTTTTA
5143492 TTTTTT
1 TTTTTT
5143498 ATTTTGGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
8 8 0.29
9 13 0.46
10 7 0.25
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:5145148 original size:54 final size:54
Alignment explanation
Indices: 5145085--5145197 Score: 226
Period size: 54 Copynumber: 2.1 Consensus size: 54
5145075 TTTTCTATTG
5145085 AAGCTAAAGCTGTGTTAGAAATATTGAAATTAGAGTGGAACAAAGATTTTAGAC
1 AAGCTAAAGCTGTGTTAGAAATATTGAAATTAGAGTGGAACAAAGATTTTAGAC
5145139 AAGCTAAAGCTGTGTTAGAAATATTGAAATTAGAGTGGAACAAAGATTTTAGAC
1 AAGCTAAAGCTGTGTTAGAAATATTGAAATTAGAGTGGAACAAAGATTTTAGAC
5145193 AAGCT
1 AAGCT
5145198 GAATTGGAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.27
Consensus pattern (54 bp):
AAGCTAAAGCTGTGTTAGAAATATTGAAATTAGAGTGGAACAAAGATTTTAGAC
Found at i:5145570 original size:31 final size:32
Alignment explanation
Indices: 5145514--5145577 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
5145504 TTCGTGTATC
*
5145514 AAAAATATATATATATTAATGAAATAAAATATT
1 AAAAATATATATATATGAATGAAATAAAA-ATT
*
5145547 AAAAATATATAT-TA-GAATTAAATAAAAATT
1 AAAAATATATATATATGAATGAAATAAAAATT
5145577 A
1 A
5145578 TTTTGAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 4 0.14
31 11 0.38
32 2 0.07
33 12 0.41
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (32 bp):
AAAAATATATATATATGAATGAAATAAAAATT
Found at i:5146092 original size:29 final size:29
Alignment explanation
Indices: 5146050--5146105 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
5146040 ATGCACCCTC
5146050 TAGTATATTCTTACAATCTTTTTCATTTT
1 TAGTATATTCTTACAATCTTTTTCATTTT
5146079 TAGTATATTCTTACAATCTTTTTCATT
1 TAGTATATTCTTACAATCTTTTTCATT
5146106 AAAGTGGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.25, C:0.14, G:0.04, T:0.57
Consensus pattern (29 bp):
TAGTATATTCTTACAATCTTTTTCATTTT
Found at i:5149610 original size:18 final size:16
Alignment explanation
Indices: 5149564--5149602 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
5149554 AGGAAAACAA
5149564 AGTA-ATAAAAAATGG
1 AGTATATAAAAAATGG
5149579 AGTATATAAAAAATGG
1 AGTATATAAAAAATGG
5149595 AGTATATA
1 AGTATATA
5149603 TACAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.56, C:0.00, G:0.18, T:0.26
Consensus pattern (16 bp):
AGTATATAAAAAATGG
Found at i:5151221 original size:12 final size:12
Alignment explanation
Indices: 5151187--5151243 Score: 60
Period size: 12 Copynumber: 4.8 Consensus size: 12
5151177 GATTGACAAA
5151187 TAATAATAATAG
1 TAATAATAATAG
***
5151199 TAATTGCAATAG
1 TAATAATAATAG
*
5151211 TAATAGTAATAG
1 TAATAATAATAG
* *
5151223 AAATAATAATAA
1 TAATAATAATAG
5151235 TAATAATAA
1 TAATAATAA
5151244 AAGTCCAAAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.32
Consensus pattern (12 bp):
TAATAATAATAG
Found at i:5151227 original size:18 final size:18
Alignment explanation
Indices: 5151188--5151239 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
5151178 ATTGACAAAT
* *
5151188 AATAATAATAGTAATTGC
1 AATAATAATAGTAATAGA
*
5151206 AATAGTAATAGTAATAGA
1 AATAATAATAGTAATAGA
*
5151224 AATAATAATAATAATA
1 AATAATAATAGTAATA
5151240 ATAAAAGTCC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.58, C:0.02, G:0.10, T:0.31
Consensus pattern (18 bp):
AATAATAATAGTAATAGA
Found at i:5154908 original size:3 final size:3
Alignment explanation
Indices: 5154902--5155004 Score: 57
Period size: 3 Copynumber: 34.0 Consensus size: 3
5154892 ATGAAAACAG
* * * * * * * *
5154902 TAA TAA TAA TAA TAC TAA TAG TAG CAA TAG TAA TAG TAA TAG TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
5154950 GTAA TAA TAA TAA TAA TGAA -AA TAA AAA TAG TAA T-A TAA TGA TAT
1 -TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5154995 TAA TATA TAA
1 TAA TA-A TAA
5155005 ATATAAATAG
Statistics
Matches: 73, Mismatches: 22, Indels: 10
0.70 0.21 0.10
Matches are distributed among these distances:
2 4 0.05
3 62 0.85
4 7 0.10
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:5154980 original size:49 final size:49
Alignment explanation
Indices: 5154886--5154989 Score: 122
Period size: 49 Copynumber: 2.1 Consensus size: 49
5154876 AAAAACGACA
* * * **
5154886 ATAATAATGAAAACAGTAATAATAATAATACTAATAGTAGCAATAGTAAT
1 ATAATAGT-AAAACAGTAATAATAATAATAATAATAATAAAAATAGTAAT
5154936 AGTAATAGTAAAA-AGTAATAATAATAATAATGAA-AATAAAAATAGTAAT
1 A-TAATAGTAAAACAGTAATAATAATAATAAT-AATAATAAAAATAGTAAT
5154985 ATAAT
1 ATAAT
5154990 GATATTAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
48 4 0.09
49 30 0.64
50 7 0.15
51 6 0.13
ACGTcount: A:0.60, C:0.03, G:0.10, T:0.28
Consensus pattern (49 bp):
ATAATAGTAAAACAGTAATAATAATAATAATAATAATAAAAATAGTAAT
Found at i:5155131 original size:3 final size:3
Alignment explanation
Indices: 5155123--5155178 Score: 51
Period size: 3 Copynumber: 19.0 Consensus size: 3
5155113 AGGTGAGAAT
* * * * *
5155123 ATA ATA ATA GTA ATA AT- ACA ATA GTA ATA ATA ATA ATA ACA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
5155170 GTA ATA ATA
1 ATA ATA ATA
5155179 GTATGTTAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
2 1 0.02
3 40 0.98
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:5162285 original size:216 final size:213
Alignment explanation
Indices: 5162063--5162474 Score: 693
Period size: 216 Copynumber: 1.9 Consensus size: 213
5162053 TGAGGCGGGT
5162063 TGGGTCGGGTCGGACCAAGGGCAAAACAACGTCATTTTG-GCATTTGAGGCCAGTCCCAAAATGA
1 TGGGTCGGGTCGGACCAAGGGCAAAACAACGTCATTTTGAG-ATTTGAGGCCAGTCCCAAAATGA
* * *
5162127 CGTCTTTTTGGGGCCTATATAAGTCAATTTTTTTGGAAAAAAAATCATTTCATCCTTTGTTTTTT
65 CATCGTTTTGGGGCCTATATAAGTCAA-TTTTTTGG-AAAAAAATCATTTCATCCTTTATTTTTT
5162192 T-TAAAAAAAAAAAACTCAAAAGCTCTCTCTTCTCTCTCAAATATCTCTCCCCTCAGGCCAAGCT
128 TCT--AAAAAAAAAACTCAAAAGCTCTCTCTTCTCTCTCAAATATCTCTCCCCTCAGGCCAAGCT
5162256 CCGGCTTCACCGGCGTCTTGAGG
191 CCGGCTTCACCGGCGTCTTGAGG
** *
5162279 TGGGTCGGGTCGGACCAAGGGCAAAATTACGTCGTTTTGAGATTTGAGGCCAGTCCCAAAATGAC
1 TGGGTCGGGTCGGACCAAGGGCAAAACAACGTCATTTTGAGATTTGAGGCCAGTCCCAAAATGAC
5162344 ATCGTTTTGGGGCCTATATAAGTCAATTTTTTGGAAAAAAATCATTTCATCCTTTATTTTTTTCT
66 ATCGTTTTGGGGCCTATATAAGTCAATTTTTTGGAAAAAAATCATTTCATCCTTTATTTTTTTCT
* *
5162409 AAAAAAAAACCTCAAAAGCTCTCTCTTCTCTCTCAAATATCTCTCCCCTCAGGCTAAGCTCCGGC
131 AAAAAAAAAACTCAAAAGCTCTCTCTTCTCTCTCAAATATCTCTCCCCTCAGGCCAAGCTCCGGC
5162474 T
196 T
5162475 CCGTCCACTG
Statistics
Matches: 186, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
213 64 0.34
214 28 0.15
215 9 0.05
216 84 0.45
217 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.31
Consensus pattern (213 bp):
TGGGTCGGGTCGGACCAAGGGCAAAACAACGTCATTTTGAGATTTGAGGCCAGTCCCAAAATGAC
ATCGTTTTGGGGCCTATATAAGTCAATTTTTTGGAAAAAAATCATTTCATCCTTTATTTTTTTCT
AAAAAAAAAACTCAAAAGCTCTCTCTTCTCTCTCAAATATCTCTCCCCTCAGGCCAAGCTCCGGC
TTCACCGGCGTCTTGAGG
Found at i:5162531 original size:7 final size:8
Alignment explanation
Indices: 5162514--5162543 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
5162504 AAGGTGCCCC
5162514 TTTTTATT
1 TTTTTATT
5162522 TTTTTATT
1 TTTTTATT
5162530 TTTTTGATT
1 TTTTT-ATT
5162539 TTTTT
1 TTTTT
5162544 TATATACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.10, C:0.00, G:0.03, T:0.87
Consensus pattern (8 bp):
TTTTTATT
Found at i:5162532 original size:9 final size:9
Alignment explanation
Indices: 5162514--5162546 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
5162504 AAGGTGCCCC
5162514 TTTTTA-TT
1 TTTTTATTT
5162522 TTTTTATTT
1 TTTTTATTT
*
5162531 TTTTGATTT
1 TTTTTATTT
5162540 TTTTTAT
1 TTTTTAT
5162547 ATACATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 6 0.27
9 16 0.73
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.85
Consensus pattern (9 bp):
TTTTTATTT
Found at i:5168273 original size:3 final size:3
Alignment explanation
Indices: 5168258--5168297 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
5168248 TCCATGTTTT
* *
5168258 TTA TTA TTC TTA TTA TTA TTA TTA TTA TTA CTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
5168298 GTATACGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:5168362 original size:26 final size:27
Alignment explanation
Indices: 5168329--5168388 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
5168319 GTGAATGTTG
*
5168329 TATA-TATT-TATGTATAATATTATTTT
1 TATATTATTGTAT-TATAATATTATTAT
*
5168355 TA-ATTATTGTATTTTAATATTATTAT
1 TATATTATTGTATTATAATATTATTAT
5168381 TATATTAT
1 TATATTAT
5168389 ATATACTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 1 0.03
26 20 0.69
27 8 0.28
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (27 bp):
TATATTATTGTATTATAATATTATTAT
Found at i:5168398 original size:29 final size:26
Alignment explanation
Indices: 5168343--5168398 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 26
5168333 TATTTATGTA
* *
5168343 TAATATTATTTTTAATTATTGTATTT
1 TAATATTATTATTAATTATTATATTT
5168369 TAATATTATTATTATATTATATATACTTT
1 TAATATTATTATTA-ATTAT-TATA-TTT
5168398 T
1 T
5168399 TCGTATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 13 0.52
27 5 0.20
28 3 0.12
29 4 0.16
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (26 bp):
TAATATTATTATTAATTATTATATTT
Found at i:5181236 original size:71 final size:71
Alignment explanation
Indices: 5181115--5181248 Score: 207
Period size: 71 Copynumber: 1.9 Consensus size: 71
5181105 GTTTTCCAAG
* *
5181115 AAAATCAGCTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
5181180 GTTTCA
66 GTTTCA
* * *
5181186 AAAATCAACTCATATTGCGAGA-AGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAGA-TGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
5181249 CTGCTTTTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
70 1 0.02
71 56 0.98
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.30
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
GTTTCA
Found at i:5181288 original size:160 final size:157
Alignment explanation
Indices: 5181024--5181399 Score: 671
Period size: 160 Copynumber: 2.4 Consensus size: 157
5181014 TTGTTTTTTC
5181024 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
*
5181089 CTGCTTTTTAGTTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGATGAGTTGAGCCTCAA
66 CTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGATGAGTTGAGCCTCAA
5181154 GACACGTTGAGGTAATTTCAATTTATGTTT
131 G--ACGTTGAGGTAATTTCAATTTATG-TT
5181184 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
*
5181249 CTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
66 CTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGATGAGTTGAGCCTCAA
*
5181314 GACGTTGAGGTAATTTTAATTTATGTT
131 GACGTTGAGGTAATTTCAATTTATGTT
* * *
5181341 CCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTT
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTT
5181400 TAGTTTATGT
Statistics
Matches: 210, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
157 58 0.28
158 23 0.11
160 129 0.61
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (157 bp):
CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
CTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGATGAGTTGAGCCTCAA
GACGTTGAGGTAATTTCAATTTATGTT
Found at i:5181692 original size:56 final size:56
Alignment explanation
Indices: 5181550--5181706 Score: 246
Period size: 58 Copynumber: 2.8 Consensus size: 56
5181540 TTAATTCCTG
5181550 TTTTTT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTCAATTTATAT
1 TTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTCAATTTATAT
* *
5181605 TTTTTTCAAATAAATCAACCCATATTGCGAGAGGTGAGTTGAGCCTTTCAACTTT-TGT
1 TTTTTTC-AA-AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTCAA-TTTATAT
*
5181663 TTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
1 TTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
5181707 CAAGGCACGC
Statistics
Matches: 94, Mismatches: 4, Indels: 7
0.90 0.04 0.07
Matches are distributed among these distances:
55 6 0.06
56 33 0.35
57 4 0.04
58 48 0.51
59 3 0.03
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (56 bp):
TTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTCAATTTATAT
Found at i:5181861 original size:73 final size:72
Alignment explanation
Indices: 5181760--5181962 Score: 257
Period size: 73 Copynumber: 2.8 Consensus size: 72
5181750 GTTTTCCAAG
* *
5181760 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCTGAGGTATTTTTAATT-
1 AAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGT--CACGCTGAGGTA-TTTTAATTC
5181824 T-ATGTTTCA
63 TGATGTTTCA
* ** **
5181833 AAATTTGACTCATATTGTGAGAGGTGAGTCAAGCCTCAGGTCACGCTGAGGTATTTTAATTCCTG
1 AAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTAATT-CTG
*
5181898 TTGTTTCA
65 ATGTTTCA
* * *
5181906 AAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGGCATGCTGAGGTATTTT
1 AAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTT
5181963 CAGTTTCTAC
Statistics
Matches: 111, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
70 8 0.07
71 12 0.11
72 1 0.01
73 90 0.81
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (72 bp):
AAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTAATTCTGA
TGTTTCA
Found at i:5182228 original size:138 final size:138
Alignment explanation
Indices: 5181896--5182296 Score: 650
Period size: 138 Copynumber: 2.9 Consensus size: 138
5181886 TTTTAATTCC
5181896 TGTTGTTTC-AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGGCATGCTGAGGTAT
1 TGTT-TTTCAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGGCATGCTGAGGTAT
5181960 TTTCAGTTTCTACTTTCCAATTCCTGTTTTTT--AAAAATCAACTCATATTGCGAGAGGTGAGTT
65 TTTCAGTTTCTACTTTCCAATTCCTGTTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTT
5182023 GTACCTTTT
130 GTACCTTTT
5182032 TGTTTTTCAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGGCATGCTGAGGTATT
1 TGTTTTTCAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGGCATGCTGAGGTATT
5182097 TTCAGTTTCTACTTTCCAATTCCTGTTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
66 TTCAGTTTCTACTTTCCAATTCCTGTTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
5182162 TACCTTTT
131 TACCTTTT
* * *
5182170 TGTTTTTCAAAAAATCAACCCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTACT
1 TGTTTTTCAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGGCATGCTGAGGTA-T
* * * ** * * *
5182235 TTCCA-TTTCTGCTTTTCAATTCCTACTGTTCAAAAAAATCAGCTCATATTGCGAGA-GTGAGT
65 TTTCAGTTTCTACTTTCCAATTCCTGTTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGT
5182297 CAAGCTTTAG
Statistics
Matches: 250, Mismatches: 11, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
135 4 0.02
136 91 0.36
137 6 0.02
138 144 0.58
139 5 0.02
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (138 bp):
TGTTTTTCAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGGCATGCTGAGGTATT
TTCAGTTTCTACTTTCCAATTCCTGTTTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
TACCTTTT
Found at i:5183905 original size:3 final size:3
Alignment explanation
Indices: 5183890--5183929 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
5183880 TCCATGTTTT
* *
5183890 TTA TTA TTC TTA TTA TTA TTA TTA TTA TTA CTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
5183930 GTATACGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:5183994 original size:26 final size:27
Alignment explanation
Indices: 5183961--5184020 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
5183951 GTGAATGTTG
*
5183961 TATA-TATT-TATGTATAATATTATTTT
1 TATATTATTGTAT-TATAATATTATTAT
*
5183987 TA-ATTATTGTATTTTAATATTATTAT
1 TATATTATTGTATTATAATATTATTAT
5184013 TATATTAT
1 TATATTAT
5184021 ATATACTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 1 0.03
26 20 0.69
27 8 0.28
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (27 bp):
TATATTATTGTATTATAATATTATTAT
Found at i:5184030 original size:29 final size:26
Alignment explanation
Indices: 5183975--5184030 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 26
5183965 TATTTATGTA
* *
5183975 TAATATTATTTTTAATTATTGTATTT
1 TAATATTATTATTAATTATTATATTT
5184001 TAATATTATTATTATATTATATATACTTT
1 TAATATTATTATTA-ATTAT-TATA-TTT
5184030 T
1 T
5184031 TCGTATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 13 0.52
27 5 0.20
28 3 0.12
29 4 0.16
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (26 bp):
TAATATTATTATTAATTATTATATTT
Found at i:5184156 original size:23 final size:24
Alignment explanation
Indices: 5184112--5184157 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
5184102 TATACACATT
*
5184112 TCATATAGTATTATCTTTTTACTA
1 TCATATAGTATTATCTTCTTACTA
5184136 TCATAT-GTATTAT-TATCTTACT
1 TCATATAGTATTATCT-TCTTACT
5184158 TATTTTCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 13 0.65
24 6 0.30
ACGTcount: A:0.28, C:0.13, G:0.04, T:0.54
Consensus pattern (24 bp):
TCATATAGTATTATCTTCTTACTA
Found at i:5184171 original size:21 final size:21
Alignment explanation
Indices: 5184143--5184195 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 21
5184133 CTATCATATG
5184143 TATTATTATCTTACTTATTTTCAC
1 TATTATTA--TTA-TTATTTTCAC
5184167 TATTATTATTATTATTTTCA-
1 TATTATTATTATTATTTTCAC
5184187 TCATTATTA
1 T-ATTATTA
5184196 CACGTATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 1 0.04
21 16 0.57
22 3 0.11
24 8 0.29
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTATTATTATTATTTTCAC
Found at i:5192252 original size:24 final size:24
Alignment explanation
Indices: 5192223--5192302 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 24
5192213 AAATTTTAAG
* *
5192223 ATAAAAATTTAAAATAAGTAATAT
1 ATAAAAATTTAAAATAAATAACAT
* *
5192247 ATAAAAAGTTCAAAACAAATAACA-
1 ATAAAAA-TTTAAAATAAATAACAT
* *
5192271 ATAAAAGAATTTAAAATCATTAACAT
1 AT-AAA-AATTTAAAATAAATAACAT
5192297 ATAAAA
1 ATAAAA
5192303 GATATATATA
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
24 10 0.23
25 30 0.68
26 4 0.09
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (24 bp):
ATAAAAATTTAAAATAAATAACAT
Found at i:5192618 original size:3 final size:3
Alignment explanation
Indices: 5192612--5192636 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5192602 AAAAAAAAAA
5192612 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
5192637 TGCGTAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5192695 original size:2 final size:2
Alignment explanation
Indices: 5192690--5192716 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5192680 TGTGTGTGTG
5192690 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 T
5192717 GTAAGGATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5195574 original size:15 final size:15
Alignment explanation
Indices: 5195554--5195584 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5195544 ATATGGTTGA
*
5195554 TGATTCAATTCCATT
1 TGATTCAATTCAATT
5195569 TGATTCAATTCAATT
1 TGATTCAATTCAATT
5195584 T
1 T
5195585 TATATTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.48
Consensus pattern (15 bp):
TGATTCAATTCAATT
Found at i:5198743 original size:25 final size:25
Alignment explanation
Indices: 5198708--5198758 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
5198698 TCAGTATTGC
* *
5198708 TCTGCTATATTCTATTTTGTTCTAT
1 TCTGCTATATTCAATTCTGTTCTAT
* *
5198733 TCTGCTTTATTGAATTCTGTTCTAT
1 TCTGCTATATTCAATTCTGTTCTAT
5198758 T
1 T
5198759 TGAAATTCGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.16, C:0.16, G:0.10, T:0.59
Consensus pattern (25 bp):
TCTGCTATATTCAATTCTGTTCTAT
Found at i:5202002 original size:13 final size:13
Alignment explanation
Indices: 5201984--5202010 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5201974 CGTGATTTTG
5201984 ATGTACATATTTA
1 ATGTACATATTTA
5201997 ATGTACATATTTA
1 ATGTACATATTTA
5202010 A
1 A
5202011 GATTATTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (13 bp):
ATGTACATATTTA
Found at i:5207314 original size:21 final size:21
Alignment explanation
Indices: 5207288--5207328 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5207278 ATCTGCTCAA
* *
5207288 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
5207309 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
5207329 TCGCTTGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:5210966 original size:39 final size:39
Alignment explanation
Indices: 5210935--5211095 Score: 234
Period size: 39 Copynumber: 4.1 Consensus size: 39
5210925 AGGGCTCGAG
* *
5210935 CCGGAGTT-GGTAAACCTATTTCCCGTTCCAGGGCTTGGA
1 CCGGA-TTCGGTAAACTTATTTCCCGTTCCAGGGCTTGGT
* * * *
5210974 CTGGAGTCGGTAAACTTATTTCCTGTCCCAGGGCTTGGT
1 CCGGATTCGGTAAACTTATTTCCCGTTCCAGGGCTTGGT
*
5211013 CTGGATTCGGTAAACTTATTTCCCGTTCCAGGGCTTGGT
1 CCGGATTCGGTAAACTTATTTCCCGTTCCAGGGCTTGGT
*
5211052 CCGGATTCAGTAAACTTATTTCCCGTTCCAGGGCTTGGT
1 CCGGATTCGGTAAACTTATTTCCCGTTCCAGGGCTTGGT
5211091 CCGGA
1 CCGGA
5211096 GTCCTTGATG
Statistics
Matches: 110, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
38 1 0.01
39 109 0.99
ACGTcount: A:0.17, C:0.25, G:0.27, T:0.32
Consensus pattern (39 bp):
CCGGATTCGGTAAACTTATTTCCCGTTCCAGGGCTTGGT
Found at i:5223343 original size:22 final size:22
Alignment explanation
Indices: 5223315--5223360 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
5223305 ATCAGAGGGT
5223315 TGACAAGTATCCTATA-AAAGTA
1 TGACAAGTATCCTATAGAAA-TA
5223337 TGACAAGTATCCTATAGAAATA
1 TGACAAGTATCCTATAGAAATA
5223359 TG
1 TG
5223361 GTAAATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.28
Consensus pattern (22 bp):
TGACAAGTATCCTATAGAAATA
Found at i:5223389 original size:45 final size:45
Alignment explanation
Indices: 5223337--5223427 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
5223327 TATAAAAGTA
5223337 TGACAAGTATCCTATAGAAATATGGTAAATTATTAAAAATACATT
1 TGACAAGTATCCTATAGAAATATGGTAAATTATTAAAAATACATT
5223382 TGACAAGTATCCTATAGAAATATGGTAAATTATTAAAAATACATT
1 TGACAAGTATCCTATAGAAATATGGTAAATTATTAAAAATACATT
5223427 T
1 T
5223428 AAAAAAAAGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (45 bp):
TGACAAGTATCCTATAGAAATATGGTAAATTATTAAAAATACATT
Found at i:5224714 original size:22 final size:22
Alignment explanation
Indices: 5224697--5224753 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
5224687 ACAATATTTA
5224697 AATATTAATAATAAAATAATAAC
1 AATA-TAATAATAAAATAATAAC
* *
5224720 AATATAATAATAAAACAATGAC
1 AATATAATAATAAAATAATAAC
* *
5224742 AAAACAATAATA
1 AATATAATAATA
5224754 TTTTCTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.25
Consensus pattern (22 bp):
AATATAATAATAAAATAATAAC
Found at i:5224718 original size:11 final size:11
Alignment explanation
Indices: 5224702--5224753 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
5224692 ATTTAAATAT
5224702 TAATAATAAAA
1 TAATAATAAAA
* *
5224713 TAATAACAATA
1 TAATAATAAAA
5224724 TAATAATAAAA
1 TAATAATAAAA
* * *
5224735 CAATGACAAAA
1 TAATAATAAAA
*
5224746 CAATAATA
1 TAATAATA
5224754 TTTTCTTTTT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.67, C:0.08, G:0.02, T:0.23
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:5231799 original size:2 final size:2
Alignment explanation
Indices: 5231792--5231822 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5231782 TTATTAGTAT
5231792 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 T
5231823 TAACTGTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5234851 original size:17 final size:17
Alignment explanation
Indices: 5234829--5234889 Score: 54
Period size: 16 Copynumber: 3.6 Consensus size: 17
5234819 ATTTTAATTA
5234829 ATATTTATCATTTATAT
1 ATATTTATCATTTATAT
*
5234846 ATATTTACTGCAGTTATAT
1 ATATTTA-T-CATTTATAT
* *
5234865 AT-TTTTTCTTTTAT-T
1 ATATTTATCATTTATAT
*
5234880 AAATTTATCA
1 ATATTTATCA
5234890 ATATTTACAA
Statistics
Matches: 34, Mismatches: 7, Indels: 7
0.71 0.15 0.15
Matches are distributed among these distances:
15 2 0.06
16 10 0.29
17 8 0.24
18 4 0.12
19 10 0.29
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.57
Consensus pattern (17 bp):
ATATTTATCATTTATAT
Found at i:5238477 original size:15 final size:16
Alignment explanation
Indices: 5238431--5238481 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 16
5238421 AAAATATTTG
*
5238431 AAATATTTTAATAT-A
1 AAATAATTTAATATAA
*
5238446 ATATAATTTAATATAA
1 AAATAATTTAATATAA
*
5238462 AAATAATTTTAT-TAA
1 AAATAATTTAATATAA
5238477 AAATA
1 AAATA
5238482 TTATTAAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 20 0.65
16 11 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATAATTTAATATAA
Found at i:5238562 original size:7 final size:7
Alignment explanation
Indices: 5238550--5238576 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5238540 ATATGATTAA
5238550 ATTATTT
1 ATTATTT
5238557 ATTATTT
1 ATTATTT
5238564 ATTATTT
1 ATTATTT
5238571 ATTATT
1 ATTATT
5238577 AAATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
ATTATTT
Found at i:5238762 original size:16 final size:16
Alignment explanation
Indices: 5238724--5238762 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
5238714 TGAATTACTA
* *
5238724 ATTACAACTCTATTTT
1 ATTACAGCTCTATTCT
5238740 ATTACAGCTCTATTCT
1 ATTACAGCTCTATTCT
5238756 ATTACAG
1 ATTACAG
5238763 TTAATCAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.44
Consensus pattern (16 bp):
ATTACAGCTCTATTCT
Found at i:5250318 original size:11 final size:11
Alignment explanation
Indices: 5250302--5250337 Score: 54
Period size: 11 Copynumber: 3.1 Consensus size: 11
5250292 TCAGTTCAGT
5250302 ACAAAAAAAAA
1 ACAAAAAAAAA
5250313 ACAAAAAAAAA
1 ACAAAAAAAAA
5250324 AGCAAAAACAAAA
1 A-CAAAAA-AAAA
5250337 A
1 A
5250338 ATTGAAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 12 0.52
12 6 0.26
13 5 0.22
ACGTcount: A:0.86, C:0.11, G:0.03, T:0.00
Consensus pattern (11 bp):
ACAAAAAAAAA
Found at i:5250321 original size:12 final size:12
Alignment explanation
Indices: 5250304--5250338 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
5250294 AGTTCAGTAC
5250304 AAAAAAAAAACA
1 AAAAAAAAAACA
*
5250316 AAAAAAAAAGCA
1 AAAAAAAAAACA
5250328 AAAACAAAAAA
1 AAAA-AAAAAA
5250339 TTGAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.89, C:0.09, G:0.03, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAACA
Found at i:5255165 original size:29 final size:29
Alignment explanation
Indices: 5255129--5255209 Score: 126
Period size: 29 Copynumber: 2.8 Consensus size: 29
5255119 ATTTTGAAAT
*
5255129 AATAGAATTAAATTAATTCTTATAAATAA
1 AATAGAATTAAATTAATGCTTATAAATAA
*
5255158 AATAGAATTAAATTAATGCTTATAAATGA
1 AATAGAATTAAATTAATGCTTATAAATAA
* *
5255187 AATGGAATTAAATTAATGATTAT
1 AATAGAATTAAATTAATGCTTAT
5255210 GCATTACTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.37
Consensus pattern (29 bp):
AATAGAATTAAATTAATGCTTATAAATAA
Found at i:5258139 original size:2 final size:2
Alignment explanation
Indices: 5258132--5258166 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5258122 CACATTTATT
5258132 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 T
5258167 TTAAGTGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5258847 original size:41 final size:40
Alignment explanation
Indices: 5258770--5258856 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 40
5258760 TCAAATACAT
5258770 TTAAAACAAATATTAAAATAAGAAACAAATAAAAAATGATA
1 TTAAAACAAATATTAAAATAAGAAACAAATAAAAAAT-ATA
* * * * **
5258811 TTAAAACAATTCTTAAAATAATACACAAATTGAAAATATA
1 TTAAAACAAATATTAAAATAAGAAACAAATAAAAAATATA
*
5258851 ATAAAA
1 TTAAAA
5258857 AGTGATTATA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 8 0.21
41 31 0.79
ACGTcount: A:0.64, C:0.07, G:0.03, T:0.25
Consensus pattern (40 bp):
TTAAAACAAATATTAAAATAAGAAACAAATAAAAAATATA
Found at i:5258907 original size:28 final size:27
Alignment explanation
Indices: 5258843--5258907 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
5258833 ACACAAATTG
* * *
5258843 AAAATATAATAAAAAGTGATTATATTA
1 AAAATAAAATAAAAAGTAAGTATATTA
* *
5258870 AAATTGAAAATAAAATGTAAGTATGATTA
1 AAAAT-AAAATAAAAAGTAAGTAT-ATTA
5258899 AAAATAAAA
1 AAAATAAAA
5258908 ATATATATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
27 4 0.13
28 18 0.60
29 8 0.27
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (27 bp):
AAAATAAAATAAAAAGTAAGTATATTA
Found at i:5259262 original size:36 final size:37
Alignment explanation
Indices: 5259189--5259263 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 37
5259179 ATTTTCCTAT
* *
5259189 TTCTTGAATAGGGGGTAAAATACAATCCAATTTCTTA
1 TTCTTGAATAGGGGGTAAAATACAATCAAATTCCTTA
**
5259226 TTCTTGAATA-GGGGTAAAATGTAATCAAATTCCTTA
1 TTCTTGAATAGGGGGTAAAATACAATCAAATTCCTTA
5259262 TT
1 TT
5259264 TAAATACCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
36 24 0.71
37 10 0.29
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (37 bp):
TTCTTGAATAGGGGGTAAAATACAATCAAATTCCTTA
Found at i:5262044 original size:2 final size:2
Alignment explanation
Indices: 5262037--5262088 Score: 70
Period size: 2 Copynumber: 25.5 Consensus size: 2
5262027 TTGAAAACTC
*
5262037 AT AT AT AT AGT CAT -T AT CT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5262080 AT AT AT AT A
1 AT AT AT AT A
5262089 ATTCGAGGCC
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
1 1 0.02
2 41 0.91
3 2 0.04
4 1 0.02
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5262613 original size:2 final size:2
Alignment explanation
Indices: 5262608--5262646 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5262598 TGTAAGAAGC
5262608 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
5262647 TCAATTCAAC
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:5270476 original size:15 final size:15
Alignment explanation
Indices: 5270429--5270478 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
5270419 GAGATTTATT
*
5270429 TTAATTA-TAGTTAA
1 TTAATTATTAATTAA
*
5270443 TTAATT-TAAATTTAA
1 TTAATTATTAA-TTAA
*
5270458 TTAATTATTAATTAT
1 TTAATTATTAATTAA
5270473 TTAATT
1 TTAATT
5270479 CAATGCTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
14 7 0.24
15 19 0.66
16 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
TTAATTATTAATTAA
Found at i:5278313 original size:3 final size:3
Alignment explanation
Indices: 5278305--5278340 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
5278295 CTACTTTAAT
5278305 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5278341 CTTCTAATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5278576 original size:23 final size:23
Alignment explanation
Indices: 5278534--5278578 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5278524 AATACTACGC
***
5278534 TATATATATTTTTTTGTATTATG
1 TATATATATTTTTAAATATTATG
5278557 TATATATATTTTTAAATATTAT
1 TATATATATTTTTAAATATTAT
5278579 ATATTGAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (23 bp):
TATATATATTTTTAAATATTATG
Found at i:5281722 original size:26 final size:26
Alignment explanation
Indices: 5281686--5281792 Score: 196
Period size: 26 Copynumber: 4.1 Consensus size: 26
5281676 AAAATTCCAG
5281686 TCATGGAACATTTACCTAACCCATTA
1 TCATGGAACATTTACCTAACCCATTA
5281712 TCATGGAACATTTACCTAACCCATTA
1 TCATGGAACATTTACCTAACCCATTA
*
5281738 TCATGAAACATTTACCTAACCCATTA
1 TCATGGAACATTTACCTAACCCATTA
*
5281764 TCATGGAACATTTACCTAACCTATTA
1 TCATGGAACATTTACCTAACCCATTA
5281790 TCA
1 TCA
5281793 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.36, C:0.26, G:0.07, T:0.32
Consensus pattern (26 bp):
TCATGGAACATTTACCTAACCCATTA
Found at i:5293417 original size:43 final size:43
Alignment explanation
Indices: 5293361--5293442 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
5293351 ATTATGCTTG
*
5293361 AAAAAGGAAATCAAGATGAAAACTCGAAAACGGCATCTTAAAA
1 AAAAAGGAAATCAAGATGAAAACCCGAAAACGGCATCTTAAAA
** * * *
5293404 AAAAAGGTGATCAAGGTGAAAACCCGAAAAGGGCGTCTT
1 AAAAAGGAAATCAAGATGAAAACCCGAAAACGGCATCTT
5293443 GATTAAACAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.49, C:0.15, G:0.22, T:0.15
Consensus pattern (43 bp):
AAAAAGGAAATCAAGATGAAAACCCGAAAACGGCATCTTAAAA
Found at i:5294486 original size:89 final size:90
Alignment explanation
Indices: 5294260--5294505 Score: 379
Period size: 89 Copynumber: 2.7 Consensus size: 90
5294250 TCTGTTTTTC
* *
5294260 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
* *
5294325 TGTTTTCTTCAATTTATGTTTGTCAA
66 TGCTTTC-TCAATTTATGTCTGTCAA
* * *
5294351 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCGATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
*
5294416 TGCTTTC-CAATTTTTGCTCT-TCAA
66 TGCTTTCTCAATTTATG-TCTGTCAA
*
5294440 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
5294505 T
66 T
5294506 ATTTGTCAAA
Statistics
Matches: 142, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
89 74 0.52
90 2 0.01
91 66 0.46
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (90 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
TGCTTTCTCAATTTATGTCTGTCAA
Found at i:5294574 original size:75 final size:73
Alignment explanation
Indices: 5294440--5294589 Score: 192
Period size: 73 Copynumber: 2.0 Consensus size: 73
5294430 TGCTCTTCAA
* * * *
5294440 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATCGCGAGAGGTGAGTTGAACCTCAGCACACGCTGAGGTAATTTCAATTTC
5294505 TATTTGTC
66 TATTTGTC
* * **
5294513 AAAAATCAACTCATATCGCGAGAGGTGAGTTGAACCTCGACTCACATGCTGAGGTCTTTTCAATT
1 AAAAATCAACTCATATCGCGAGAGGTGAGTTGAACCTC-A-GCACACGCTGAGGTAATTTCAATT
* *
5294578 TCTGTTTTTC
64 TCTATTTGTC
5294588 AA
1 AA
5294590 TTTCTGTTTG
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
73 35 0.54
74 1 0.02
75 29 0.45
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (73 bp):
AAAAATCAACTCATATCGCGAGAGGTGAGTTGAACCTCAGCACACGCTGAGGTAATTTCAATTTC
TATTTGTC
Found at i:5294588 original size:14 final size:14
Alignment explanation
Indices: 5294569--5294603 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
5294559 TGCTGAGGTC
5294569 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
5294583 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
*
5294597 TTGTCAA
1 TTTTCAA
5294604 AATCAACTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.17, C:0.14, G:0.09, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:5294704 original size:75 final size:72
Alignment explanation
Indices: 5294584--5294729 Score: 247
Period size: 75 Copynumber: 2.0 Consensus size: 72
5294574 AATTTCTGTT
*
5294584 TTTCAATTTCTGTTTGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
1 TTTCAATTTATGTTTGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
5294649 GAGGTAA
66 GAGGTAA
*
5294656 TTTCAATTTATGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCAC
1 TTTCAATTTATGTTTGTC---AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
5294721 GCTGAGGTA
63 GCTGAGGTA
5294730 TTTTTGATTT
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
72 17 0.25
75 52 0.75
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (72 bp):
TTTCAATTTATGTTTGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
GAGGTAA
Found at i:5294890 original size:75 final size:73
Alignment explanation
Indices: 5294765--5294914 Score: 210
Period size: 73 Copynumber: 2.0 Consensus size: 73
5294755 TGCTCTTCAA
* * *
5294765 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGGACATGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTCAGCACATGCTGAGGTAATTTCAATTTC
5294830 TGTTTGTC
66 TGTTTGTC
* **
5294838 AAAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTCGACTCACATGCTGAGGTCTTTTCAATT
1 AAAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTC-A-GCACATGCTGAGGTAATTTCAATT
* *
5294903 TTTGTTTTTC
64 TCTGTTTGTC
5294913 AA
1 AA
5294915 TTTCTGTTCG
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
73 36 0.54
74 1 0.01
75 30 0.45
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.33
Consensus pattern (73 bp):
AAAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTCAGCACATGCTGAGGTAATTTCAATTTC
TGTTTGTC
Found at i:5294922 original size:325 final size:325
Alignment explanation
Indices: 5294332--5294995 Score: 1204
Period size: 325 Copynumber: 2.0 Consensus size: 325
5294322 TTTTGTTTTC
5294332 TTCAATTTATGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACG
1 TTCAATTTATGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACG
* *
5294397 CTGAGGTATTTTCGATTTCTGCTTTCCAATTTTTGCTCTTCAAAAAAATCAACTCATATTGTGAG
66 CTGAGGTATTTTCGATTTCTGCTTTCCAATTTCTGCTCTTCAAAAAAATCAACTCATATTGCGAG
5294462 AGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTATTTGTCAAAAATCAACTCAT
131 AGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTATTTGTCAAAAATCAACTCAT
5294527 ATCGCGAGAGGTGAGTTGAACCTCGACTCACATGCTGAGGTCTTTTCAATTTCTGTTTTTCAATT
196 ATCGCGAGAGGTGAGTTGAACCTCGACTCACATGCTGAGGTCTTTTCAATTTCTGTTTTTCAATT
* *
5294592 TCTGTTTGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGACACGCTGAGGTAA
261 TCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGAGG-CACGCTGAGGTAA
5294656 T
325 T
5294657 TTCAATTTATGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACG
1 TTCAATTTATGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACG
*
5294722 CTGAGGTATTTTTGATTTCTGCTTTCCAATTTCTGCTCTTCAAAAAAATCAACTCATATTGCGAG
66 CTGAGGTATTTTCGATTTCTGCTTTCCAATTTCTGCTCTTCAAAAAAATCAACTCATATTGCGAG
* * *
5294787 AGGTGAGTTGAGCTTCAGGACATGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATCAACTCAT
131 AGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTATTTGTCAAAAATCAACTCAT
* *
5294852 ATCGCGAGAGGTGAGTTGAGCCTCGACTCACATGCTGAGGTCTTTTCAATTTTTGTTTTTCAATT
196 ATCGCGAGAGGTGAGTTGAACCTCGACTCACATGCTGAGGTCTTTTCAATTTCTGTTTTTCAATT
*
5294917 TCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGAGGCACGCTGAGGTATT
261 TCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGAGGCACGCTGAGGTAAT
*
5294982 TTCAATTAATGTTT
1 TTCAATTTATGTTT
5294996 TTTCAATTTA
Statistics
Matches: 326, Mismatches: 12, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
325 323 0.99
326 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (325 bp):
TTCAATTTATGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACG
CTGAGGTATTTTCGATTTCTGCTTTCCAATTTCTGCTCTTCAAAAAAATCAACTCATATTGCGAG
AGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTATTTGTCAAAAATCAACTCAT
ATCGCGAGAGGTGAGTTGAACCTCGACTCACATGCTGAGGTCTTTTCAATTTCTGTTTTTCAATT
TCTGTTCGTCAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGAGGCACGCTGAGGTAAT
Found at i:5295114 original size:176 final size:176
Alignment explanation
Indices: 5294820--5295138 Score: 435
Period size: 176 Copynumber: 1.8 Consensus size: 176
5294810 GCTGAGGTAA
* *
5294820 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTCGACTCACAT
1 TTTCAATTTATGTTTGTCAAAAATCAACTCATATCACGAGAGGTGAGTTGAGCCTCGACTCACAT
* ** * * ** * * *
5294885 GCTGAGGTCTTTTCAATTTTTGTTTTTCAATTTCTGTTCGTCAAAATCAACTCATATTGCGAGAG
66 GCTGAGGTATTTTCAAAATCTATTTGGCAAATTCTATTCGTCAAAATCAACTCATATTGCGAGAA
5294950 GTGAGTTAAGCCTCGAGGCACGCTGAGGTATTTTCAATTAATGTTT
131 GTGAGTTAAGCCTCGAGGCACGCTGAGGTATTTTCAATTAATGTTT
* * **
5294996 TTTCAATTTATGCTTT-TCAAGAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACA
1 TTTCAATTTATG-TTTGTCAAAAATCAACTCATATCACGAGAGGTGAGTTGAGCCTCGACTCACA
* *
5295060 TGCTGAGGTATTTTCAAAATCTATTTGGCAAATTCTATT-TTCAAAAATCAACTCATATTGTGAG
65 TGCTGAGGTATTTTCAAAATCTATTTGGCAAATTCTATTCGTC-AAAATCAACTCATATTGCGAG
*
5295124 AAGTGAGTTGAGCCT
129 AAGTGAGTTAAGCCT
5295139 TTGCTCACGT
Statistics
Matches: 122, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
175 2 0.02
176 117 0.96
177 3 0.02
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.36
Consensus pattern (176 bp):
TTTCAATTTATGTTTGTCAAAAATCAACTCATATCACGAGAGGTGAGTTGAGCCTCGACTCACAT
GCTGAGGTATTTTCAAAATCTATTTGGCAAATTCTATTCGTCAAAATCAACTCATATTGCGAGAA
GTGAGTTAAGCCTCGAGGCACGCTGAGGTATTTTCAATTAATGTTT
Found at i:5295152 original size:88 final size:87
Alignment explanation
Indices: 5294820--5295213 Score: 384
Period size: 88 Copynumber: 4.5 Consensus size: 87
5294810 GCTGAGGTAA
*
5294820 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATCGCGAGAGGTGAGTTGAGCCTCGACTCACAT
1 TTTCAATTTCTGTTT-TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGACTCACAT
* ** *
5294885 GCTGAGGTCTTTTCAATTTTTGTT
65 GCTGAGGTATTTTCAAAATCT-TT
* * **
5294909 TTTCAATTTCTGTTCGTC-AAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGAGGCAC--
1 TTTCAATTTCTGTT-TTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGACTCACAT
*
5294971 GCTGAGGTATTTTCAATTAATGTTT
65 GCTGAGGTATTTTCAA--AATCTTT
* * * **
5294996 TTTCAATTTATGCTTTTCAAGAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACAT
1 TTTCAATTTCTG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGACTCACAT
5295061 GCTGAGGTATTTTCAAAATCTATT
65 GCTGAGGTATTTTCAAAATCT-TT
** * * * * * *
5295085 TGGCAAATTCTATTTTCAAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTTTG-CTCACGT
1 TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TCGACTCACAT
* **
5295149 GCTGAGCTATTTTTCAATTTCTATT
65 GCTGAGGTA-TTTTCAAAATCT-TT
* * * *
5295174 TTT-AATGTCTAGTTTTTAAAAGTCAATTCATATTGCGAGA
1 TTTCAATTTCT-GTTTTCAAAAATCAACTCATATTGCGAGA
5295214 AATGAGTAGA
Statistics
Matches: 253, Mismatches: 41, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
86 15 0.06
87 15 0.06
88 142 0.56
89 65 0.26
90 16 0.06
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.38
Consensus pattern (87 bp):
TTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGACTCACATG
CTGAGGTATTTTCAAAATCTTT
Found at i:5296933 original size:3 final size:3
Alignment explanation
Indices: 5296925--5296985 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
5296915 CTCTACTTTA
5296925 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
5296973 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
5296986 CTTCTAATGT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5297224 original size:23 final size:23
Alignment explanation
Indices: 5297182--5297226 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5297172 AATACTACGC
***
5297182 TATATATATTTTTTTGTATTATG
1 TATATATATTTTTAAATATTATG
5297205 TATATATATTTTTAAATATTAT
1 TATATATATTTTTAAATATTAT
5297227 ATATTGAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (23 bp):
TATATATATTTTTAAATATTATG
Found at i:5297479 original size:24 final size:26
Alignment explanation
Indices: 5297434--5297481 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
5297424 TTAATACATG
5297434 TTTTATATATGTATATATTATGTATA
1 TTTTATATATGTATATATTATGTATA
5297460 TTTTA-ATAT-TATAT-TATATGTA
1 TTTTATATATGTATATAT-TATGTA
5297482 CGTATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 1 0.05
24 11 0.52
25 4 0.19
26 5 0.24
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (26 bp):
TTTTATATATGTATATATTATGTATA
Found at i:5298989 original size:26 final size:26
Alignment explanation
Indices: 5298953--5299114 Score: 247
Period size: 26 Copynumber: 6.2 Consensus size: 26
5298943 TGATACAAAT
*
5298953 TGATAATAGGTTAGGTAAATATTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
5298979 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
5299005 TGATAATGGGTTAGGTAAATGCTT-CA
1 TGATAATAGGTTAGGTAAATG-TTCCA
5299031 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
5299057 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
5299083 TGATAAT-GAGTTAGGTAAATGTTTCA
1 TGATAATAG-GTTAGGTAAATGTTCCA
5299109 TGATAA
1 TGATAA
5299115 GAATTTCATG
Statistics
Matches: 128, Mismatches: 5, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
25 3 0.02
26 123 0.96
27 2 0.02
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:5299085 original size:78 final size:78
Alignment explanation
Indices: 5298953--5299114 Score: 279
Period size: 78 Copynumber: 2.1 Consensus size: 78
5298943 TGATACAAAT
*
5298953 TGATAATAGGTTAGGTAAATATTCCATGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTA
1 TGATAATAGGTTAGGTAAATATTCCATGATAATAGGTTAGGTAAATGTTCCATGATAATGAGTTA
5299018 GGTAAATGCTTCA
66 GGTAAATGCTTCA
* * *
5299031 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCATGATAATGAGTTA
1 TGATAATAGGTTAGGTAAATATTCCATGATAATAGGTTAGGTAAATGTTCCATGATAATGAGTTA
*
5299096 GGTAAATGTTTCA
66 GGTAAATGCTTCA
5299109 TGATAA
1 TGATAA
5299115 GAATTTCATG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.36
Consensus pattern (78 bp):
TGATAATAGGTTAGGTAAATATTCCATGATAATAGGTTAGGTAAATGTTCCATGATAATGAGTTA
GGTAAATGCTTCA
Found at i:5303083 original size:13 final size:13
Alignment explanation
Indices: 5303065--5303089 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5303055 TGTCTCGCAG
5303065 TGATTCCAGGCCA
1 TGATTCCAGGCCA
5303078 TGATTCCAGGCC
1 TGATTCCAGGCC
5303090 TCGAATCTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.32, G:0.24, T:0.24
Consensus pattern (13 bp):
TGATTCCAGGCCA
Found at i:5306085 original size:26 final size:26
Alignment explanation
Indices: 5306055--5306138 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
5306045 TGATACAAAT
* *
5306055 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5306081 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5306107 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5306133 TGATAA
1 TGATAA
5306139 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:5313090 original size:26 final size:26
Alignment explanation
Indices: 5313061--5313144 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
5313051 TGATACAAAT
* *
5313061 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5313087 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5313113 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5313139 TGATAA
1 TGATAA
5313145 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:5320162 original size:7 final size:7
Alignment explanation
Indices: 5320147--5320338 Score: 51
Period size: 7 Copynumber: 27.1 Consensus size: 7
5320137 TGAATTTTAA
*
5320147 AATAGAT
1 AATATAT
5320154 AATATAT
1 AATATAT
5320161 AATAGTAT
1 AATA-TAT
* *
5320169 ATAAAAAT
1 A-ATATAT
* *
5320177 AATAAAA
1 AATATAT
*
5320184 AATGAAAT
1 AAT-ATAT
*
5320192 AATTTAT
1 AATATAT
5320199 AATATAT
1 AATATAT
5320206 AATATA-
1 AATATAT
* *
5320212 AAAATGT
1 AATATAT
* *
5320219 AAGTTTTT
1 AA-TATAT
5320227 AA-A-AT
1 AATATAT
*
5320232 AATGTAT
1 AATATAT
5320239 AATATA-
1 AATATAT
*
5320245 AATAAAT
1 AATATAT
5320252 AAATATAT
1 -AATATAT
5320260 AAGATATAT
1 -A-ATATAT
5320269 AAGT-TA-
1 AA-TATAT
*
5320275 AA-GTAT
1 AATATAT
5320281 AATATAT
1 AATATAT
5320288 AATA-AT
1 AATATAT
* *
5320294 AATTTAC
1 AATATAT
*
5320301 AA-ATTTT
1 AATA-TAT
*
5320308 GAAAATAT
1 -AATATAT
5320316 AATAATAT
1 AAT-ATAT
*
5320324 AATAAAT
1 AATATAT
5320331 AATATAT
1 AATATAT
5320338 A
1 A
5320339 TAATAAATTA
Statistics
Matches: 136, Mismatches: 30, Indels: 38
0.67 0.15 0.19
Matches are distributed among these distances:
5 5 0.04
6 18 0.13
7 66 0.49
8 38 0.28
9 9 0.07
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.36
Consensus pattern (7 bp):
AATATAT
Found at i:5320261 original size:28 final size:29
Alignment explanation
Indices: 5320230--5320290 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 29
5320220 AGTTTTTAAA
5320230 ATAATGTATAATATAA-ATAAA-TA-AATAT
1 ATAATG-AT-ATATAAGATAAAGTATAATAT
*
5320258 ATAA-GATATATAAGTTAAAGTATAATAT
1 ATAATGATATATAAGATAAAGTATAATAT
5320286 ATAAT
1 ATAAT
5320291 AATAATTTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
25 6 0.21
26 6 0.21
27 3 0.11
28 13 0.46
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (29 bp):
ATAATGATATATAAGATAAAGTATAATAT
Found at i:5320295 original size:42 final size:41
Alignment explanation
Indices: 5320196--5320295 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 41
5320186 TGAAATAATT
* * * *
5320196 TATAATATATAAT-ATAAAAATGTAAGTTTTTAAAATAATG
1 TATAATATATAATAATAAAAATATAAGTATATAAAATAAAG
* **
5320236 TATAATATA-AATAAATAAATATATAAGATATATAAGTTAAAG
1 TATAATATATAAT-AATAAAAATATAAG-TATATAAAATAAAG
5320278 TATAATATATAATAATAA
1 TATAATATATAATAATAA
5320296 TTTACAAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
39 3 0.06
40 9 0.18
41 11 0.22
42 23 0.47
43 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (41 bp):
TATAATATATAATAATAAAAATATAAGTATATAAAATAAAG
Found at i:5320341 original size:16 final size:15
Alignment explanation
Indices: 5320314--5320346 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
5320304 TTTTGAAAAT
5320314 ATAATAATATAATAA
1 ATAATAATATAATAA
5320329 ATAATATATATAATAA
1 ATAATA-ATATAATAA
5320345 AT
1 AT
5320347 TAAAAATAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATAATAATATAATAA
Found at i:5320343 original size:12 final size:12
Alignment explanation
Indices: 5320312--5320344 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5320302 AATTTTGAAA
5320312 ATATAATAATAT
1 ATATAATAATAT
5320324 A-ATAAATAATAT
1 ATAT-AATAATAT
5320336 ATATAATAA
1 ATATAATAA
5320345 ATTAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.11
12 15 0.79
13 2 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
ATATAATAATAT
Found at i:5320354 original size:20 final size:19
Alignment explanation
Indices: 5320309--5320354 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
5320299 ACAAATTTTG
5320309 AAAATATAATAATATAATA
1 AAAATATAATAATATAATA
5320328 AATAATATATATAATA-AATTA
1 AA-AATATA-ATAATATAA-TA
5320349 AAAATA
1 AAAATA
5320355 AGTTTAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 2 0.08
20 12 0.50
21 10 0.42
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATATAATAATATAATA
Found at i:5321623 original size:30 final size:29
Alignment explanation
Indices: 5321589--5321645 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
5321579 TTGGGTAGGG
5321589 TGTAACAGGTCTG-GGCTATTTTGGGTTTGC
1 TGTAACAGGTCTGAGG-TA-TTTGGGTTTGC
*
5321619 TGTAACGGGTCTGAGGTATTTGGGTTT
1 TGTAACAGGTCTGAGGTATTTGGGTTT
5321646 TGTGTTTGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 9 0.36
30 14 0.56
31 2 0.08
ACGTcount: A:0.14, C:0.11, G:0.35, T:0.40
Consensus pattern (29 bp):
TGTAACAGGTCTGAGGTATTTGGGTTTGC
Found at i:5322309 original size:205 final size:204
Alignment explanation
Indices: 5321946--5322467 Score: 780
Period size: 205 Copynumber: 2.5 Consensus size: 204
5321936 GATTTGTTCT
* * * * * *
5321946 CCAAATCATCTTAGATTTGCTTTAGCGTAAGCACGCGAAAACCAAATCAGCTATGTCTTCGATTC
1 CCAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAACCAAATCAGTTATGTCTTCGATTT
* * * **
5322011 GTTCCTTGTAAGCACAAGGATACCAAGCCATCTTGGATCTTGCTTCAGTGAAATCATCTGAAGTA
66 GCTCCTTGTAAGCACAAGGATGCTAAATCATCTTGGATC-TGCTTCAGTGAAATCATCTGAAGTA
* * *
5322076 AGATCTGCTATATTTCTACCCTCCGTTGAAGTGGAGATGCCAGACTTCGATTTGCTCTCTGCCAA
130 AGATCTGCTATATATCTACCCTCCGTTGAAGTGGAGATGCCAGACTTCAATTTGCTCTCTGACAA
5322141 TACAGAGATG
195 TACAGAGATG
*
5322151 CCAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAACCAAATCAGTTATGTTTTCGATTT
1 CCAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAACCAAATCAGTTATGTCTTCGATTT
*
5322216 GCTCGTTGTAAGCACAAGGATGCTAAATCATCTTGGATCTGCTTCAGTGTAAA-CATCTGAAGGT
66 GCTCCTTGTAAGCACAAGGATGCTAAATCATCTTGGATCTGCTTCAGTG-AAATCATCTGAA-GT
* * *
5322280 GAGATCTGCTATGTATCTGCTCC-CCGTTGAAGTGGAGATGCCAGACTTCAATTTGCTCTCTGAC
129 AAGATCTGCTATATATCTAC-CCTCCGTTGAAGTGGAGATGCCAGACTTCAATTTGCTCTCTGAC
5322344 AATACAGAGATG
193 AATACAGAGATG
*
5322356 CCAAATCATCTTAGATTTGCTTCATCGTAAACACGT-AAAAGCCAAATCAGTTATGTCTTCAATT
1 CCAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAA-CCAAATCAGTTATGTCTTCGATT
* *
5322420 TGCTCCTTGTAAGTACAAGGATGCTAAATCATCTTAGATCTGCTTCAG
65 TGCTCCTTGTAAGCACAAGGATGCTAAATCATCTTGGATCTGCTTCAG
5322468 CCAGATCTGC
Statistics
Matches: 289, Mismatches: 24, Indels: 8
0.90 0.07 0.02
Matches are distributed among these distances:
204 22 0.08
205 265 0.92
206 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (204 bp):
CCAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAACCAAATCAGTTATGTCTTCGATTT
GCTCCTTGTAAGCACAAGGATGCTAAATCATCTTGGATCTGCTTCAGTGAAATCATCTGAAGTAA
GATCTGCTATATATCTACCCTCCGTTGAAGTGGAGATGCCAGACTTCAATTTGCTCTCTGACAAT
ACAGAGATG
Found at i:5328776 original size:499 final size:499
Alignment explanation
Indices: 5327838--5328837 Score: 1730
Period size: 499 Copynumber: 2.0 Consensus size: 499
5327828 GGATGTCGAT
5327838 TCGTCCCATCACTTTCCTTTCAATTCCATCAAAGGCTCTTACCACATTATGACATGTTTTCATAT
1 TCGTCCCATCACTTTCCTTTCAATTCCATCAAAGGCTCTTACCACATTATGACATGTTTTCATAT
* *
5327903 GCGAACTGTCAATGGGTAATCTGTTCAAGGTGGATAATGGCAGGACATTCAAAGTAGACCCATTA
66 GCGAACTATCAATGGGTAATCTGTTCAAGGTGGATAATGGCAGGACATTCAAAGCAGACCCATTA
* * *
5327968 TCAACGAGTGTACTTGGTAGCATGTATCCTTTGCATCGAGTAGTGATGTGCAAGGCTTTGGTTGA
131 TCAACGAGTGCACTTGGCAGCATGTATCCTTTGCACCGAGTAGTGATGTGCAAGGCTTTGGTTGA
*
5328033 CCCTATACCCCCAGGTGGAATTTCATCATCATTAAAATAGATGAAATTGTTAGCACTGATGTTAT
196 CCCTATACCCCCAGGTGGAATTTCATCATCATTAAAATAGATGAAATTGTCAGCACTGATGTTAT
** *
5328098 TTACCAATTGATCCAATTTGTTAACGGATATGTCGTGGGTGATATATGTTTCGTTAAGCACCTGC
261 TTACCAACCGATCCAATTTGTTAACGGATATGTCGTGGGTGACATATGTTTCGTTAAGCACCTGC
** *
5328163 AATAATGTATCTCGATGCACCTCAGAACTCAGAAGCAAGGCTAATACTGATATACGCGCTGGCTG
326 AATAATACATCCCGATGCACCTCAGAACTCAGAAGCAAGGCTAATACTGATATACGCGCTGGCTG
* * *
5328228 CTTACGTAACTGCTCGACCACACTATACTCGCTATGCTTAAGGAACTTTAAGAACTCTTTAGCCT
391 CTTACGCAACTGCTCGACCACACTATACTCACTATGCTTAAGGAACTTTAAGAACTCCTTAGCCT
* *
5328293 CCTCCTTATTTACTGGCTCATTGATGGGTATTTCAGTCTCTTTC
456 CCTCCTCATTTACTGGCTCATTGATGGGTATTTCAATCTCTTTC
* *
5328337 TCGTCCCATCACTTTCTTTTCAGTTCCATCAAAGGCTCTTACCACATTATGACATGTTTTCATAT
1 TCGTCCCATCACTTTCCTTTCAATTCCATCAAAGGCTCTTACCACATTATGACATGTTTTCATAT
* *
5328402 GCGAACTATCAATGGGTAATCTGTTCAAGGTGGATAATGGCAGGGCGTTCAAAGCAGACCCATTA
66 GCGAACTATCAATGGGTAATCTGTTCAAGGTGGATAATGGCAGGACATTCAAAGCAGACCCATTA
*
5328467 TCAACGAGTGCACTTGGCAGCATTTATCCTTTGCACCGAGTAGTGATGTGCAAGGCTTTGGTTGA
131 TCAACGAGTGCACTTGGCAGCATGTATCCTTTGCACCGAGTAGTGATGTGCAAGGCTTTGGTTGA
* *
5328532 CCCTATACCCCCAGGTGGAATTTCATCATCATTGAAATAGATGAAATTGTCAGCATTGATGTTAT
196 CCCTATACCCCCAGGTGGAATTTCATCATCATTAAAATAGATGAAATTGTCAGCACTGATGTTAT
* * *
5328597 TTACCAACCGGTCCAATTTGTTAATGGATATGTCGTGGGTGACATATGTTTCGTTAAGCACCTTC
261 TTACCAACCGATCCAATTTGTTAACGGATATGTCGTGGGTGACATATGTTTCGTTAAGCACCTGC
* *
5328662 AATGATACATCCCGATGCACCTCAGAACTCAGAAGCAGGGCTAATACTGATATACGCGCTGGCTG
326 AATAATACATCCCGATGCACCTCAGAACTCAGAAGCAAGGCTAATACTGATATACGCGCTGGCTG
5328727 CTTACGCAACTGCTCGACCACACTATACTCACTATGCTTAAGGAACTTTAAGAACTCCTTAGCCT
391 CTTACGCAACTGCTCGACCACACTATACTCACTATGCTTAAGGAACTTTAAGAACTCCTTAGCCT
*
5328792 CCTTCTCATTTACTGGCTCATTGATGGGTATTTCAATCTCTTTC
456 CCTCCTCATTTACTGGCTCATTGATGGGTATTTCAATCTCTTTC
5328836 TC
1 TC
5328838 TTTTCAACAT
Statistics
Matches: 471, Mismatches: 30, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
499 471 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (499 bp):
TCGTCCCATCACTTTCCTTTCAATTCCATCAAAGGCTCTTACCACATTATGACATGTTTTCATAT
GCGAACTATCAATGGGTAATCTGTTCAAGGTGGATAATGGCAGGACATTCAAAGCAGACCCATTA
TCAACGAGTGCACTTGGCAGCATGTATCCTTTGCACCGAGTAGTGATGTGCAAGGCTTTGGTTGA
CCCTATACCCCCAGGTGGAATTTCATCATCATTAAAATAGATGAAATTGTCAGCACTGATGTTAT
TTACCAACCGATCCAATTTGTTAACGGATATGTCGTGGGTGACATATGTTTCGTTAAGCACCTGC
AATAATACATCCCGATGCACCTCAGAACTCAGAAGCAAGGCTAATACTGATATACGCGCTGGCTG
CTTACGCAACTGCTCGACCACACTATACTCACTATGCTTAAGGAACTTTAAGAACTCCTTAGCCT
CCTCCTCATTTACTGGCTCATTGATGGGTATTTCAATCTCTTTC
Found at i:5334972 original size:7 final size:7
Alignment explanation
Indices: 5334957--5335100 Score: 52
Period size: 7 Copynumber: 20.6 Consensus size: 7
5334947 TGAATTTTAA
*
5334957 AATAGAT
1 AATATAT
5334964 AATATAT
1 AATATAT
5334971 AATAGTAT
1 AATA-TAT
* *
5334979 ATAAAAAT
1 A-ATATAT
*
5334987 AATA-AA
1 AATATAT
*
5334993 AATGAAAT
1 AAT-ATAT
*
5335001 AATTTAT
1 AATATAT
5335008 AATATAT
1 AATATAT
5335015 AATATA-
1 AATATAT
* *
5335021 AAAATGT
1 AATATAT
* *
5335028 AAGTTTTT
1 AA-TATAT
5335036 AA-A-AT
1 AATATAT
*
5335041 AATGTAT
1 AATATAT
5335048 AATATA-
1 AATATAT
*
5335054 AATAAAT
1 AATATAT
5335061 AAATATAT
1 -AATATAT
5335069 AAGATATAT
1 -A-ATATAT
5335078 AAGT-TA-
1 AA-TATAT
5335084 AA-ATAT
1 AATATAT
5335090 AATATAT
1 AATATAT
5335097 AATA
1 AATA
5335101 ATTTGCAAAT
Statistics
Matches: 102, Mismatches: 20, Indels: 30
0.67 0.13 0.20
Matches are distributed among these distances:
5 5 0.05
6 17 0.17
7 47 0.46
8 25 0.25
9 8 0.08
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (7 bp):
AATATAT
Found at i:5335069 original size:21 final size:21
Alignment explanation
Indices: 5335037--5335101 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
5335027 TAAGTTTTTA
*
5335037 AAAT-AATGTATAATATAAAT
1 AAATAAATATATAATATAAAT
* *
5335057 AAATAAATATATAAGATATAT
1 AAATAAATATATAATATAAAT
*
5335078 AAGTTAAA-ATATAATATATAAT
1 AA-ATAAATATATAATATA-AAT
5335100 AA
1 AA
5335102 TTTGCAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 4 0.11
21 24 0.67
22 8 0.22
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.34
Consensus pattern (21 bp):
AAATAAATATATAATATAAAT
Found at i:5335070 original size:28 final size:29
Alignment explanation
Indices: 5335039--5335099 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 29
5335029 AGTTTTTAAA
5335039 ATAATGTATAATATAA-AT-AAATA-AATAT
1 ATAATG-AT-ATATAAGATAAAATATAATAT
*
5335067 ATAA-GATATATAAGTTAAAATATAATAT
1 ATAATGATATATAAGATAAAATATAATAT
5335095 ATAAT
1 ATAAT
5335100 AATTTGCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
25 6 0.21
26 3 0.11
27 6 0.21
28 13 0.46
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (29 bp):
ATAATGATATATAAGATAAAATATAATAT
Found at i:5336454 original size:30 final size:30
Alignment explanation
Indices: 5336395--5336451 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
5336385 TTGGGTAGGG
5336395 TGTAACAGGTCTGGGCTATTTTGGGTTTGT
1 TGTAACAGGTCTGGGCTATTTTGGGTTTGT
*
5336425 TGTAACGGGTCTGAGG-TA-TTTGGGTTT
1 TGTAACAGGTCTG-GGCTATTTTGGGTTT
5336452 TGTGTTTGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 9 0.36
30 14 0.56
31 2 0.08
ACGTcount: A:0.14, C:0.09, G:0.35, T:0.42
Consensus pattern (30 bp):
TGTAACAGGTCTGGGCTATTTTGGGTTTGT
Found at i:5339503 original size:26 final size:26
Alignment explanation
Indices: 5339467--5339550 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
5339457 CATGAAATTC
5339467 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5339493 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
5339519 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
5339545 TTATCA
1 TTATCA
5339551 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:5344368 original size:29 final size:30
Alignment explanation
Indices: 5344311--5344368 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
5344301 TGATAATTTT
*
5344311 ATTTTTTATTAATTAATTATTGTTCTATTC
1 ATTTTTTATTAATTAATTATTGTTATATTC
*
5344341 ATTTTTTATT-A-TAATTTATTTTTATATT
1 ATTTTTTATTAATTAA-TTATTGTTATATT
5344369 TAGACTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 12 0.48
30 10 0.40
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (30 bp):
ATTTTTTATTAATTAATTATTGTTATATTC
Found at i:5345330 original size:3 final size:3
Alignment explanation
Indices: 5345322--5345382 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
5345312 CAGGATAAAG
5345322 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5345370 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
5345383 AATCCAAAGT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5345864 original size:3 final size:3
Alignment explanation
Indices: 5345856--5345998 Score: 55
Period size: 3 Copynumber: 47.0 Consensus size: 3
5345846 ATTAACAATG
* * * *
5345856 ATA ATA ATA ATA GTA ATA ATA TTA A-A ATA A-A AAA AGA ATA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
5345901 AT- ATA ATA AAA ATA ATA A-A GTA ATTA AAA ATA ATA CTA TATA TATA
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA -ATA -ATA
* * * * *
5345947 CAT- GTA CATA GGTA ATA AAA ATA TATA CTA CTA TATA ATA ATA ATA
1 -ATA ATA -ATA -ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA
5345993 ATA ATA
1 ATA ATA
5345999 TTAAAATACG
Statistics
Matches: 105, Mismatches: 24, Indels: 22
0.70 0.16 0.15
Matches are distributed among these distances:
2 10 0.10
3 75 0.71
4 20 0.19
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:5345917 original size:9 final size:9
Alignment explanation
Indices: 5345856--5345935 Score: 56
Period size: 10 Copynumber: 8.7 Consensus size: 9
5345846 ATTAACAATG
*
5345856 ATAATAATA
1 ATAATAAAA
* *
5345865 ATAGTAATA
1 ATAATAAAA
*
5345874 AT-ATTAAA
1 ATAATAAAA
*
5345882 ATAAAAAAAGA
1 AT-AATAAA-A
5345893 ATAATAAAA
1 ATAATAAAA
5345902 TATAATAAAA
1 -ATAATAAAA
5345912 ATAAT-AAA
1 ATAATAAAA
*
5345920 GTAATTAAAA
1 ATAA-TAAAA
5345930 ATAATA
1 ATAATA
5345936 CTATATATAT
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
8 11 0.20
9 19 0.34
10 23 0.41
11 3 0.05
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.28
Consensus pattern (9 bp):
ATAATAAAA
Found at i:5345930 original size:18 final size:19
Alignment explanation
Indices: 5345873--5345935 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
5345863 TAATAGTAAT
* *
5345873 AATATTAAAATA-AAAAAA
1 AATAATAAAATATAATAAA
5345891 GAATAATAAAATATAATAAA
1 -AATAATAAAATATAATAAA
* *
5345911 AATAATAAAGTA-ATTAAA
1 AATAATAAAATATAATAAA
5345929 AATAATA
1 AATAATA
5345936 CTATATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
18 12 0.31
19 22 0.56
20 5 0.13
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.25
Consensus pattern (19 bp):
AATAATAAAATATAATAAA
Found at i:5346118 original size:3 final size:3
Alignment explanation
Indices: 5346110--5346139 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
5346100 ACGCTATTGT
*
5346110 ATA ATA ATA TTA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5346140 GCAAAATACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:5346400 original size:123 final size:118
Alignment explanation
Indices: 5346160--5346499 Score: 415
Period size: 123 Copynumber: 2.8 Consensus size: 118
5346150 AAAAACACGC
* *
5346160 ATAATAAAAATATTAAAATAAAATAATAAAAAAG--CTA-TA-A-AAATAGATATACATATACGC
1 ATAAT-AAAATATTAAAATAAAATAATAAAAAAGCACTACTATATATATATATATACATATACG-
* *
5346220 ACATAAAAAATATATACTAATATATATATAATAATATTGCAATGCAAAAAAGCAAAT
64 -TATAAAAAA-ATATACTAATATATATATAATAATATTGCAATGAAAAAAAGCAAAT
* *
5346277 ATAATAAAATATTAAAATAAAGTAATAAAAAAGAGCACTACTATATATATATATATGCATATACG
1 ATAATAAAATATTAAAATAAAATAAT-AAAAA-AGCACTACTATATATATATATATACATATACG
*
5346342 TATGAAAAAAATATACTAATATATATATAATAATATTGCGATGAAAAAAAAAGCAAAT
64 TAT-AAAAAAATATACTAATATATATATAATAATATTGCAATG--AAAAAAAGCAAAT
* *
5346400 ATAATAAAATATTAAAATAAAATAATGAAAAA-CACTACTATATATATATACATATACATGTACG
1 ATAATAAAATATTAAAATAAAATAATAAAAAAGCACTACTATATATATAT--ATATACATATACG
*
5346464 TATATAACAAATATGCACTAATATATA-ATAATAATA
64 TATA-AAAAAATAT--ACTAATATATATATAATAATA
5346500 ATAACGATAC
Statistics
Matches: 196, Mismatches: 12, Indels: 24
0.84 0.05 0.10
Matches are distributed among these distances:
116 20 0.10
117 10 0.05
118 2 0.01
120 20 0.10
121 38 0.19
122 33 0.17
123 62 0.32
124 11 0.06
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.29
Consensus pattern (118 bp):
ATAATAAAATATTAAAATAAAATAATAAAAAAGCACTACTATATATATATATATACATATACGTA
TAAAAAAATATACTAATATATATATAATAATATTGCAATGAAAAAAAGCAAAT
Found at i:5347531 original size:23 final size:23
Alignment explanation
Indices: 5347505--5347549 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
5347495 ATGTGTTGGG
5347505 TTTTGAGATTTAATGTAAATGGA
1 TTTTGAGATTTAATGTAAATGGA
5347528 TTTTGAGATTTAATGTAAATGG
1 TTTTGAGATTTAATGTAAATGG
5347550 GCTAAAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (23 bp):
TTTTGAGATTTAATGTAAATGGA
Found at i:5351187 original size:63 final size:64
Alignment explanation
Indices: 5351043--5351189 Score: 233
Period size: 64 Copynumber: 2.3 Consensus size: 64
5351033 TACAACTATG
* * * *
5351043 ATTCTCAATTTTCCAAATTGTGGGCCCAGCTAATTTGATTTTTGCTCTAGTTGTGATTAATTTC
1 ATTCTCAATTTTCCAAAATATGGGCCCAACTAATTAGATTTTTGCTCTAGTTGTGATTAATTTC
*
5351107 ATTCTCAATTTTCCAAAATATGGGCCCAACTAATTAGATTTTTGC-CTAGTTGTGGTTAATTTC
1 ATTCTCAATTTTCCAAAATATGGGCCCAACTAATTAGATTTTTGCTCTAGTTGTGATTAATTTC
*
5351170 ATTTTCAATTTTCCAAAATA
1 ATTCTCAATTTTCCAAAATA
5351190 AGATTGATTG
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
63 36 0.47
64 41 0.53
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.44
Consensus pattern (64 bp):
ATTCTCAATTTTCCAAAATATGGGCCCAACTAATTAGATTTTTGCTCTAGTTGTGATTAATTTC
Found at i:5358064 original size:14 final size:14
Alignment explanation
Indices: 5358041--5358071 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5358031 GGATTAAATC
*
5358041 TAATATAAATTAAA
1 TAATAGAAATTAAA
5358055 TAATAGAAATTAAA
1 TAATAGAAATTAAA
5358069 TAA
1 TAA
5358072 AAACAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (14 bp):
TAATAGAAATTAAA
Found at i:5358114 original size:21 final size:20
Alignment explanation
Indices: 5358056--5358119 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
5358046 TAAATTAAAT
5358056 AATAGAAATTAAATAAAAACAA
1 AATA-AAATTAAAT-AAAACAA
** *
5358078 AATAAAAACAAGTAAAACAA
1 AATAAAATTAAATAAAACAA
* *
5358098 AATTAAATTTAAATAAAGCAA
1 AA-TAAAATTAAATAAAACAA
5358119 A
1 A
5358120 TATGATTCTC
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
20 9 0.27
21 20 0.61
22 4 0.12
ACGTcount: A:0.70, C:0.06, G:0.05, T:0.19
Consensus pattern (20 bp):
AATAAAATTAAATAAAACAA
Found at i:5359039 original size:29 final size:27
Alignment explanation
Indices: 5358998--5359055 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 27
5358988 GTAATTAGGG
* * *
5358998 CTAAATTGCAAAAATAATAAATTGAAGGA
1 CTAAAATGC-AAAATAAAAAAGTG-AGGA
*
5359027 CTAAAATGTAAAATAAAAAAGTGAGGA
1 CTAAAATGCAAAATAAAAAAGTGAGGA
5359054 CT
1 CT
5359056 TGTTTGGGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 6 0.24
28 12 0.48
29 7 0.28
ACGTcount: A:0.55, C:0.07, G:0.16, T:0.22
Consensus pattern (27 bp):
CTAAAATGCAAAATAAAAAAGTGAGGA
Found at i:5359237 original size:15 final size:15
Alignment explanation
Indices: 5359196--5359238 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
5359186 TATGTTGTTG
*
5359196 GATTAAATTGAATGA
1 GATTAATTTGAATGA
* *
5359211 AATTGTATTTGAATGA
1 GATT-AATTTGAATGA
5359227 GATTAATTTGAA
1 GATTAATTTGAA
5359239 AATTGTATAG
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.40
Consensus pattern (15 bp):
GATTAATTTGAATGA
Found at i:5360259 original size:131 final size:131
Alignment explanation
Indices: 5360090--5360468 Score: 544
Period size: 131 Copynumber: 2.9 Consensus size: 131
5360080 GATATGAATG
* * *
5360090 AAATTTTGAAGGGATACTT-GATTATTTTGAGCAAACGCGAAATTGCAACCCAACACGTTAGGTC
1 AAATTTCGAAGCGATA-TTCGATTATTTTGAGCAAACGCGAAATTGCAACCCAACACGTTAGGGC
* * * ** *
5360154 ACGATTCTGCGAATTGCTAATTATCAAACCTCGTCTTCATTTTGAAGAATTTTAGAAGACGTGAG
65 ACGATTCCGCGAATCGCCAAACATCAAACCTCGTCTTCATTTTAAAGAATTTTAGAAGACGTGAG
5360219 TA
130 TA
5360221 AAATTTCGAAGCGATATTCGATTATTTTGAGCAAACGCGAAATTGCAACCCAACACGTTAGGGCA
1 AAATTTCGAAGCGATATTCGATTATTTTGAGCAAACGCGAAATTGCAACCCAACACGTTAGGGCA
* * *
5360286 CGATTCCGTGAATCGCCAAACATCGAATCTCGTCTTCATTTTAAAGAATTTTAGAAGACGTGAGT
66 CGATTCCGCGAATCGCCAAACATCAAACCTCGTCTTCATTTTAAAGAATTTTAGAAGACGTGAGT
*
5360351 G
131 A
* * * *
5360352 AAATTTCGAAGCGATATTCGATTATTTTGAGCAAACACAAAATTGCAACCCAACATGTTGGGGCA
1 AAATTTCGAAGCGATATTCGATTATTTTGAGCAAACGCGAAATTGCAACCCAACACGTTAGGGCA
* * * * *
5360417 CGCTTCCGCGAATCGCCAAACATCGAATCTCGTTTTCGTTTTAAAGAATTTT
66 CGATTCCGCGAATCGCCAAACATCAAACCTCGTCTTCATTTTAAAGAATTTT
5360469 TGAATAAATG
Statistics
Matches: 226, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
130 2 0.01
131 224 0.99
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (131 bp):
AAATTTCGAAGCGATATTCGATTATTTTGAGCAAACGCGAAATTGCAACCCAACACGTTAGGGCA
CGATTCCGCGAATCGCCAAACATCAAACCTCGTCTTCATTTTAAAGAATTTTAGAAGACGTGAGT
A
Found at i:5363143 original size:44 final size:44
Alignment explanation
Indices: 5363075--5363817 Score: 876
Period size: 44 Copynumber: 16.9 Consensus size: 44
5363065 TGTTATTTTT
* * * * *
5363075 GATCTTCTCTCTGCTAATATAGAGATGTCAAATCTG-TCATCTTC
1 GATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCT-ATCTTC
* * * *
5363119 GATCTGCTCTCTGTCGACACAGAGATGCCAAATCTGCTATCTTC
1 GATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTC
* * ** * ** * *
5363163 GATCTGCGCTCTGATAACACAGAGGCGCCAAATCTGCCATCTTT
1 GATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTC
* *
5363207 GATCTACTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTT
1 GATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTC
* * *
5363251 GATCTGTTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTT
1 GATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTC
*
5363295 GATCTGCTCTCCGCCAATACAGAGATGGCAAATCTGCTATCTTC
1 GATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTC
* *
5363339 GATCTGCTCTCCGCCAATACAGAGATGGCAAATCTGCTATCTTT
1 GATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTC
* * *
5363383 GATCTGCTCTCCGCCAATATAGAGACGCCAAATCTGCTATCTTT
1 GATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTC
* * *
5363427 GATCTGCTCTCCGCCAATACAGAGACGCCAAATTTGCTATTTTC
1 GATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTC
* * *
5363471 GATCTGCTTTCCGCCAATACAGAGACGCCAAATCTGCTACCTTC
1 GATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTC
* * * ** * *
5363515 GATCTGCCCTCTGACAATACAGAGACACTAAATCTGTTATCTTC
1 GATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTC
* * ** * * * *
5363559 GATCTGCCCTCTGATAGTACAGAGACGCCAAATCTACTATCTTT
1 GATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTC
5363603 GATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTC
1 GATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTC
* *
5363647 GATCTGCTCTCCGCCAATATAGAGATGCCAAATCTGCTATCTTT
1 GATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTC
* * * *
5363691 GATCTACTCTCCACCAATACAGAAACGCCAAATCTGCTATCTTC
1 GATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTC
* * *
5363735 GATCTGCTCCCCACCAATACAGAGACGCCAAATCTGCTATCTTC
1 GATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTC
* **** * *
5363779 GATCTGCCCTCTAATAATACAAAGACGCCAAATCTGCTA
1 GATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTA
5363818 GATTCGCCAA
Statistics
Matches: 615, Mismatches: 83, Indels: 2
0.88 0.12 0.00
Matches are distributed among these distances:
44 614 1.00
45 1 0.00
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (44 bp):
GATCTGCTCTCCGCCAATACAGAGATGCCAAATCTGCTATCTTC
Found at i:5370416 original size:12 final size:12
Alignment explanation
Indices: 5370399--5370423 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5370389 GTGAATGACA
5370399 AAAGCCGACTCC
1 AAAGCCGACTCC
5370411 AAAGCCGACTCC
1 AAAGCCGACTCC
5370423 A
1 A
5370424 CCACTTGCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.40, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAGCCGACTCC
Done.