Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 325 of 325
Found at i:98487139 original size:10 final size:10
Alignment explanation
Indices: 98487085--98487150 Score: 62
Period size: 10 Copynumber: 6.2 Consensus size: 10
98487075 CTTTAGTTTA
98487085 AATATATATAT
1 AATATA-ATAT
98487096 AA-ATATATAT
1 AATATA-ATAT
98487106 ATATATAAATAT
1 A-ATAT-AATAT
*
98487118 AATATAACAT
1 AATATAATAT
98487128 AATATAATAT
1 AATATAATAT
*
98487138 AATTATAACAT
1 AA-TATAATAT
98487149 AA
1 AA
98487151 AATATCTTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
10 24 0.50
11 16 0.33
12 7 0.15
13 1 0.02
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (10 bp):
AATATAATAT
Found at i:98495187 original size:24 final size:24
Alignment explanation
Indices: 98495152--98495208 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
98495142 ATTTTATGGT
*
98495152 ATTTTATACGAGACCATTCTAATA
1 ATTTTATTCGAGACCATTCTAATA
*
98495176 ATTTTATTCGAGACTATTCTAATA
1 ATTTTATTCGAGACCATTCTAATA
98495200 ATTTTATTC
1 ATTTTATTC
98495209 ATAAATATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.46
Consensus pattern (24 bp):
ATTTTATTCGAGACCATTCTAATA
Found at i:98512452 original size:26 final size:26
Alignment explanation
Indices: 98512423--98512475 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
98512413 TCAAACATGC
98512423 ATTTAAGTCAATTTAAC-CCTAGGGGT
1 ATTTAAGT-AATTTAACTCCTAGGGGT
** *
98512449 ATTTCGGTAATTTATCTCCTAGGGGT
1 ATTTAAGTAATTTAACTCCTAGGGGT
98512475 A
1 A
98512476 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (26 bp):
ATTTAAGTAATTTAACTCCTAGGGGT
Found at i:98513992 original size:26 final size:26
Alignment explanation
Indices: 98513956--98514065 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
98513946 CATGAAATTC
98513956 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
98513982 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
98514008 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
98514034 TTATCATTG-AACATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
98514060 TTATCA
1 TTATCA
98514066 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
26 79 0.98
27 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:98515929 original size:50 final size:51
Alignment explanation
Indices: 98515852--98515980 Score: 181
Period size: 50 Copynumber: 2.5 Consensus size: 51
98515842 GACCATGGCA
98515852 ACAAGTGATAAGTGATAGCTTCGGCTACACTAATCTGATCAAAGA-AAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTAATCTGATCAAAGACAAA-TG
* *
98515903 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTAATCTGATCAAAGACAAATG
* * * *
98515953 ACAAATGAAAAGTGGTAGCTTCAGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
98515981 CTGATCAGTG
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
50 44 0.63
51 26 0.37
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTAATCTGATCAAAGACAAATG
Found at i:98515996 original size:31 final size:31
Alignment explanation
Indices: 98515958--98516135 Score: 268
Period size: 31 Copynumber: 5.7 Consensus size: 31
98515948 AAATGACAAA
*
98515958 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
*
98515989 TGAAAAGTGGTAGCTTCTGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
*
98516020 TGAAAAGTGGTAG-TTCCGCCTACCTGATCAG
1 TGAAAAGTGGTAGCTT-CGGCTACCTGATCAG
*
98516051 TGAAAAGTGGTAGCTCCGGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
* * *
98516082 TGAAAAATGGTAGCTCCGGTTACCTGATCAG
1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
*
98516113 TGAATAGTGGTAGCTTCGGCTAC
1 TGAAAAGTGGTAGCTTCGGCTAC
98516136 AAGTGACAAG
Statistics
Matches: 134, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
30 2 0.01
31 131 0.98
32 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (31 bp):
TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
Found at i:98516278 original size:46 final size:47
Alignment explanation
Indices: 98516159--98516282 Score: 171
Period size: 47 Copynumber: 2.7 Consensus size: 47
98516149 CAAGTGATTT
* *
98516159 CTGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTA
1 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGCTA
*
98516206 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATGTG--A
1 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGCTA
* * *
98516251 CTCGTGTAAGACCATAGCTGGGTTATGGCATC
1 CT-GTATAAGACCATATCTGGGATATGGCATC
98516283 GATATATGAA
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
45 3 0.04
46 26 0.37
47 41 0.59
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (47 bp):
CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGCTA
Found at i:98516320 original size:42 final size:42
Alignment explanation
Indices: 98516254--98516350 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
98516244 TATGTGACTC
* * *
98516254 GTGTAAGACCATAGCTGGGTTATGGCATCGA-TATATGAATAT
1 GTGTAAGACCATAGCCGGGCTATGGCATC-ATTATATGAAGAT
*
98516296 GTGTAAGACCATAGCCGGGCTATGGCATCATTATGTGAAGAT
1 GTGTAAGACCATAGCCGGGCTATGGCATCATTATATGAAGAT
98516338 GTGTAAGACCATA
1 GTGTAAGACCATA
98516351 ATTGAACTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 1 0.02
42 49 0.98
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (42 bp):
GTGTAAGACCATAGCCGGGCTATGGCATCATTATATGAAGAT
Found at i:98516361 original size:42 final size:42
Alignment explanation
Indices: 98516274--98516368 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 42
98516264 ATAGCTGGGT
* * **
98516274 TATGGCATCGATATATGAATATGTGTAAGACCATAGCCGGGC
1 TATGGCATCGATATATGAAGATGTGTAAGACCATAACCGAAC
* **
98516316 TATGGCATC-ATTATGTGAAGATGTGTAAGACCATAATTGAAC
1 TATGGCATCGA-TATATGAAGATGTGTAAGACCATAACCGAAC
98516358 TATGGCATCGA
1 TATGGCATCGA
98516369 GAAAACGAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 1 0.02
42 42 0.95
43 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (42 bp):
TATGGCATCGATATATGAAGATGTGTAAGACCATAACCGAAC
Found at i:98521382 original size:21 final size:21
Alignment explanation
Indices: 98521345--98521427 Score: 71
Period size: 21 Copynumber: 4.0 Consensus size: 21
98521335 TGATCAGAAT
98521345 ACGACACAT-AAGTGCCTGAA
1 ACGACACATAAAGTGCCTGAA
* * **
98521365 ACGACACATGAGGTGCCTGCT
1 ACGACACATAAAGTGCCTGAA
* * *
98521386 GCGACACACAAGGTG-CTGAAA
1 ACGACACATAAAGTGCCTG-AA
98521407 TACGACACATAAAGTGCCTGA
1 -ACGACACATAAAGTGCCTGA
98521428 TCAGTAAAGC
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
20 12 0.25
21 20 0.42
22 13 0.27
23 3 0.06
ACGTcount: A:0.35, C:0.25, G:0.24, T:0.16
Consensus pattern (21 bp):
ACGACACATAAAGTGCCTGAA
Found at i:98521405 original size:41 final size:43
Alignment explanation
Indices: 98521346--98521426 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
98521336 GATCAGAATA
* * *
98521346 CGACACATAAGTGCCTG-AA-ACGACACATGAGGTGCCTGCTG
1 CGACACACAAGTGCCTGAAATACGACACATAAAGTGCCTGCTG
98521387 CGACACACAAGGTG-CTGAAATACGACACATAAAGTGCCTG
1 CGACACACAA-GTGCCTGAAATACGACACATAAAGTGCCTG
98521427 ATCAGTAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 12 0.35
42 5 0.15
43 17 0.50
ACGTcount: A:0.33, C:0.26, G:0.25, T:0.16
Consensus pattern (43 bp):
CGACACACAAGTGCCTGAAATACGACACATAAAGTGCCTGCTG
Found at i:98521687 original size:23 final size:23
Alignment explanation
Indices: 98521618--98521715 Score: 79
Period size: 28 Copynumber: 3.8 Consensus size: 23
98521608 AAATGTCCAA
*
98521618 CCAAAACACACCAGGATAATCCT
1 CCAAAACACACCAGAATAATCCT
98521641 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAG----A-ATAATCCT
*
98521669 CCCAAACACACCAGAATAATATAATCCAT
1 CCAAAACACACCAG----A-ATAATCC-T
98521698 CCAAAACACACCAGAATA
1 CCAAAACACACCAGAATA
98521716 GTACAAAGTG
Statistics
Matches: 64, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
23 14 0.22
24 3 0.05
25 1 0.02
28 32 0.50
29 14 0.22
ACGTcount: A:0.47, C:0.33, G:0.05, T:0.15
Consensus pattern (23 bp):
CCAAAACACACCAGAATAATCCT
Found at i:98521714 original size:29 final size:28
Alignment explanation
Indices: 98521633--98521715 Score: 130
Period size: 28 Copynumber: 2.9 Consensus size: 28
98521623 ACACACCAGG
* *
98521633 ATAATCCTCCAAAACACACCAGTATCAT
1 ATAATCCTCCAAAACACACCAGAATAAT
*
98521661 ATAATCCTCCCAAACACACCAGAATAAT
1 ATAATCCTCCAAAACACACCAGAATAAT
98521689 ATAATCCATCCAAAACACACCAGAATA
1 ATAATCC-TCCAAAACACACCAGAATA
98521716 GTACAAAGTG
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 32 0.64
29 18 0.36
ACGTcount: A:0.47, C:0.31, G:0.04, T:0.18
Consensus pattern (28 bp):
ATAATCCTCCAAAACACACCAGAATAAT
Found at i:98526984 original size:30 final size:31
Alignment explanation
Indices: 98526950--98527285 Score: 226
Period size: 30 Copynumber: 11.3 Consensus size: 31
98526940 TGACCAAGGG
98526950 AAAGGGATAGCTTCAG-CTATCAAATTATGA
1 AAAGGGATAGCTTCAGACTATCAAATTATGA
*
98526980 AAAGGGATAGCTTC-GACTGTCAAATTATGA
1 AAAGGGATAGCTTCAGACTATCAAATTATGA
* ** *
98527010 AAAGGGATAACTTC-GGTTGTCAAATTATGA
1 AAAGGGATAGCTTCAGACTATCAAATTATGA
* *
98527040 AAAGAGATAGCTTC-GACTATGAAATTAT-A
1 AAAGGGATAGCTTCAGACTATCAAATTATGA
* * *
98527069 CAAAGGGAT-G-GTGACGACCATCAACA--ATGA
1 -AAAGGGATAGCTTCA-GACTATCAA-ATTATGA
* * *
98527099 AAAGGGAT-G-GTAATGACCATCGAAA-TATGA
1 AAAGGGATAGCTTCA-GACTATC-AAATTATGA
* ** *
98527129 AAAGAGATAG-TTTTGGCTATCAAATTATGA
1 AAAGGGATAGCTTCAGACTATCAAATTATGA
*
98527159 AAAGGGATAGCTTC-GGCTATCAAATTATGA
1 AAAGGGATAGCTTCAGACTATCAAATTATGA
* * * *
98527189 AAAGGGAT-G-GTAACGACCATC-AACTATGA
1 AAAGGGATAGCTTCA-GACTATCAAATTATGA
* * *
98527218 AAAGGGATAG--TGACGACCATCAAAATATGA
1 AAAGGGATAGCTTCA-GACTATCAAATTATGA
*
98527248 AAAGGGATAGCTTC-GACTATCGAATTATGA
1 AAAGGGATAGCTTCAGACTATCAAATTATGA
*
98527278 GAAGGGAT
1 AAAGGGAT
98527286 GGTGACAACA
Statistics
Matches: 252, Mismatches: 37, Indels: 34
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.01
29 54 0.21
30 190 0.75
31 5 0.02
32 1 0.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGGATAGCTTCAGACTATCAAATTATGA
Found at i:98527135 original size:89 final size:88
Alignment explanation
Indices: 98526950--98527288 Score: 276
Period size: 89 Copynumber: 3.8 Consensus size: 88
98526940 TGACCAAGGG
* * **
98526950 AAAGGGATAGCTTC-AGCTATCAAATTATGAAAAGGGATAGCTTCGACTGTCAAATTATGAAAAG
1 AAAGAGATAGCTTCGA-CTATCAAATTATGAAAAGGGATAGCTACGACCATCAAA-TATGAAAAG
** * ****
98527014 GGATAACT-TCGGTTGTCAAATTATGA
64 GGAT-GGTAACGACCATCAAA-TATGA
* *
98527040 AAAGAGATAGCTTCGACTATGAAATTAT-ACAAAGGGAT-GGTGACGACCATCAACA-ATGAAAA
1 AAAGAGATAGCTTCGACTATCAAATTATGA-AAAGGGATAGCT-ACGACCATCAA-ATATGAAAA
*
98527102 GGGATGGTAATGACCATCGAAATATGA
63 GGGATGGTAACGACCATC-AAATATGA
* * * * * *
98527129 AAAGAGATAGTTTTGGCTATCAAATTATGAAAAGGGATAGCTTCGGCTATCAAATTATGAAAAGG
1 AAAGAGATAGCTTCGACTATCAAATTATGAAAAGGGATAGCTACGACCATCAAA-TATGAAAAGG
*
98527194 GATGGTAACGACCATCAACTATGA
65 GATGGTAACGACCATCAAATATGA
* * * * * * * *
98527218 AAAGGGATAG-TGACGACCATCAAAATATGAAAAGGGATAGCTTCGACTATCGAATTATGAGAAG
1 AAAGAGATAGCT-TCGACTATCAAATTATGAAAAGGGATAGCTACGACCATC-AAATATGAAAAG
98527282 GGATGGT
64 GGATGGT
98527289 GACAACAATT
Statistics
Matches: 204, Mismatches: 33, Indels: 25
0.78 0.13 0.10
Matches are distributed among these distances:
88 3 0.01
89 127 0.62
90 72 0.35
91 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (88 bp):
AAAGAGATAGCTTCGACTATCAAATTATGAAAAGGGATAGCTACGACCATCAAATATGAAAAGGG
ATGGTAACGACCATCAAATATGA
Found at i:98527283 original size:119 final size:118
Alignment explanation
Indices: 98526975--98527285 Score: 390
Period size: 119 Copynumber: 2.6 Consensus size: 118
98526965 GCTATCAAAT
* ** * * * *
98526975 TATGAAAAGGGATAGCTTCGACTGTCAAATTATGAAAAGGGATAACTTCGGTTGTCAAATTATGA
1 TATGAAAAGGGATAG-TACGACCATCAAAATATGAAAAGGGATAGCTTCGGCTATCAAATTATGA
* * *
98527040 AAAGAGATAGCTTCGACTATGAAATTATACAAAGGGATGGTGACGACCATCAAC
65 AAAGGGATAGCTTCGACTATCAAATTATACAAAGGGATGGTAACGACCATCAAC
* * * * * * *
98527094 AATGAAAAGGGATGGTAATGACCATCGAAATATGAAAAGAGATAGTTTTGGCTATCAAATTATGA
1 TATGAAAAGGGATAGT-ACGACCATCAAAATATGAAAAGGGATAGCTTCGGCTATCAAATTATGA
*
98527159 AAAGGGATAGCTTCGGCTATCAAATTATGA-AAAGGGATGGTAACGACCATCAAC
65 AAAGGGATAGCTTCGACTATCAAATTAT-ACAAAGGGATGGTAACGACCATCAAC
* *
98527213 TATGAAAAGGGATAGTGACGACCATCAAAATATGAAAAGGGATAGCTTCGACTATCGAATTATGA
1 TATGAAAAGGGATAGT-ACGACCATCAAAATATGAAAAGGGATAGCTTCGGCTATCAAATTATGA
*
98527278 GAAGGGAT
65 AAAGGGAT
98527286 GGTGACAACA
Statistics
Matches: 161, Mismatches: 29, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
118 1 0.01
119 159 0.99
120 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (118 bp):
TATGAAAAGGGATAGTACGACCATCAAAATATGAAAAGGGATAGCTTCGGCTATCAAATTATGAA
AAGGGATAGCTTCGACTATCAAATTATACAAAGGGATGGTAACGACCATCAAC
Found at i:98530590 original size:20 final size:20
Alignment explanation
Indices: 98530547--98530590 Score: 58
Period size: 18 Copynumber: 2.3 Consensus size: 20
98530537 AATTATTTGC
98530547 TCACTAAAAAATTAAATTGA
1 TCACTAAAAAATTAAATTGA
98530567 --ACTAGAAAAA-TAAATTGA
1 TCACTA-AAAAATTAAATTGA
98530585 TCACTA
1 TCACTA
98530591 CTTGGACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
18 12 0.57
19 5 0.24
20 4 0.19
ACGTcount: A:0.55, C:0.11, G:0.07, T:0.27
Consensus pattern (20 bp):
TCACTAAAAAATTAAATTGA
Found at i:98542305 original size:40 final size:40
Alignment explanation
Indices: 98542268--98542453 Score: 243
Period size: 40 Copynumber: 4.7 Consensus size: 40
98542258 GCTACTCGTT
*** *
98542268 CAAATGCCTTCGGAAAATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATT-TAGTAACTCGCA
98542308 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCA
98542348 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCA
* * * *
98542388 CGAATGCCTTCGGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAAC-TCGCA
*
98542429 CAAA-GCCTTCGGGA-CTTAGCCCGGA
1 CAAATGCCTTC-GGATCTTAGTCCGGA
98542454 CATCATTCGA
Statistics
Matches: 133, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
40 121 0.91
41 12 0.09
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGATCTTAGTCCGGATTTAGTAACTCGCA
Found at i:98545171 original size:21 final size:21
Alignment explanation
Indices: 98545147--98545187 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
98545137 TCCACCGGGC
*
98545147 ATGTGATCTAACAACATGGCA
1 ATGTGACCTAACAACATGGCA
* *
98545168 ATGTGACCTAGCGACATGGC
1 ATGTGACCTAACAACATGGC
98545188 CGAGTGAGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (21 bp):
ATGTGACCTAACAACATGGCA
Found at i:98546276 original size:2 final size:2
Alignment explanation
Indices: 98546269--98546300 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
98546259 CACCAAGCAC
98546269 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
98546301 TGCACCTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:98547143 original size:39 final size:39
Alignment explanation
Indices: 98547089--98547163 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
98547079 CGAAATCTAG
98547089 CTGAAGCACATAAGTGCTAAACGGAAACCCGGAGGCTAA
1 CTGAAGCACATAAGTGCTAAACGGAAACCCGGAGGCTAA
*
98547128 CTGAAGCACATAAGTGCTAAACGGAAGCCCGGAGGC
1 CTGAAGCACATAAGTGCTAAACGGAAACCCGGAGGC
98547164 ACATAAGTGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.36, C:0.24, G:0.28, T:0.12
Consensus pattern (39 bp):
CTGAAGCACATAAGTGCTAAACGGAAACCCGGAGGCTAA
Found at i:98547175 original size:29 final size:29
Alignment explanation
Indices: 98547133--98547192 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
98547123 GCTAACTGAA
*
98547133 GCACATAAGTGCTAAACGGAAGCCCGGAG
1 GCACATAAGTGCTAAACGGAAGCCAGGAG
98547162 GCACATAAGTGCTAAACGGAAGCCAGGAG
1 GCACATAAGTGCTAAACGGAAGCCAGGAG
98547191 GC
1 GC
98547193 TAACTAAAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.35, C:0.23, G:0.32, T:0.10
Consensus pattern (29 bp):
GCACATAAGTGCTAAACGGAAGCCAGGAG
Found at i:98549433 original size:27 final size:27
Alignment explanation
Indices: 98549403--98549457 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
98549393 TACAATTAAG
98549403 TAAACAAATAACTAATTTTATACGATT
1 TAAACAAATAACTAATTTTATACGATT
98549430 TAAACAAATAACTAATTTTATACGATT
1 TAAACAAATAACTAATTTTATACGATT
98549457 T
1 T
98549458 CCTGTCAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (27 bp):
TAAACAAATAACTAATTTTATACGATT
Found at i:98562822 original size:14 final size:15
Alignment explanation
Indices: 98562803--98562834 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
98562793 ATTCTTGTGA
98562803 AAAATAAAT-AAAAT
1 AAAATAAATAAAAAT
98562817 AAAATAAATAAAAAT
1 AAAATAAATAAAAAT
98562832 AAA
1 AAA
98562835 GAACACATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
AAAATAAATAAAAAT
Found at i:98569314 original size:50 final size:50
Alignment explanation
Indices: 98569239--98569337 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 50
98569229 TAATGATTAA
98569239 AGGTGTTCACTGTCCTAGGTGTGGCTTAGATTTAAATTGTACTAATTGTG
1 AGGTGTTCACTGTCCTAGGTGTGGCTTAGATTTAAATTGTACTAATTGTG
* *
98569289 AGGTGTTCACTGTCCTATGTGTGGCTTAGATTTAAATTGTGCTAATTGT
1 AGGTGTTCACTGTCCTAGGTGTGGCTTAGATTTAAATTGTACTAATTGT
98569338 ATTTATTTGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.21, C:0.12, G:0.25, T:0.41
Consensus pattern (50 bp):
AGGTGTTCACTGTCCTAGGTGTGGCTTAGATTTAAATTGTACTAATTGTG
Found at i:98577133 original size:21 final size:20
Alignment explanation
Indices: 98577095--98577134 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
98577085 ACTAAAAAAT
*
98577095 AACAAATTTAATTAAAATAA
1 AACAAATATAATTAAAATAA
*
98577115 AACAAATAATAATTTAAATA
1 AACAAAT-ATAATTAAAATA
98577135 CTAAAAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (20 bp):
AACAAATATAATTAAAATAA
Found at i:98578665 original size:15 final size:15
Alignment explanation
Indices: 98578645--98578674 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
98578635 ATAATTCTAA
*
98578645 TAATTATCTTAATAT
1 TAATTATCCTAATAT
98578660 TAATTATCCTAATAT
1 TAATTATCCTAATAT
98578675 AAATAAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:98579277 original size:3 final size:3
Alignment explanation
Indices: 98579269--98579346 Score: 54
Period size: 3 Copynumber: 27.0 Consensus size: 3
98579259 CCTGGGCAGT
* * * * *
98579269 AGA AGA AG- AGG AGA AAA AGA AGA ATA AG- AGA AGA ATA AGA AGA ATA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * * *
98579315 AGA AAA AGA AGA TG- AGG AGA AGA AGA ATA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
98579347 GAAAATGGAA
Statistics
Matches: 56, Mismatches: 16, Indels: 6
0.72 0.21 0.08
Matches are distributed among these distances:
2 5 0.09
3 51 0.91
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.06
Consensus pattern (3 bp):
AGA
Found at i:98579297 original size:20 final size:20
Alignment explanation
Indices: 98579269--98579317 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
98579259 CCTGGGCAGT
* *
98579269 AGAAGAAGAGGAGAAAAAGA
1 AGAATAAGAGAAGAAAAAGA
*
98579289 AGAATAAGAGAAGAATAAGA
1 AGAATAAGAGAAGAAAAAGA
98579309 AGAATAAGA
1 AGAATAAGA
98579318 AAAAGAAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.29, T:0.06
Consensus pattern (20 bp):
AGAATAAGAGAAGAAAAAGA
Found at i:98579317 original size:29 final size:29
Alignment explanation
Indices: 98579269--98579351 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
98579259 CCTGGGCAGT
* * *
98579269 AGAAGAAGAGGAGAAAAAGAAGAATAAGA-G
1 AGAAGAAGA--AGAATAAGAAAAAGAAGATG
*
98579299 AAGAATAAGAAGAATAAGAAAAAGAAGATG
1 -AGAAGAAGAAGAATAAGAAAAAGAAGATG
*
98579329 AGGAGAAGAAGAATAAGAGAAAA
1 AGAAGAAGAAGAATAAGA-AAAA
98579352 TGGAAGGAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 31 0.70
30 5 0.11
31 8 0.18
ACGTcount: A:0.65, C:0.00, G:0.29, T:0.06
Consensus pattern (29 bp):
AGAAGAAGAAGAATAAGAAAAAGAAGATG
Found at i:98580509 original size:21 final size:21
Alignment explanation
Indices: 98580485--98580525 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
98580475 CAACATGGCA
98580485 AGTTAACTGGCCACATCAGCT
1 AGTTAACTGGCCACATCAGCT
*
98580506 AGTTAACTTGCCACATCAGC
1 AGTTAACTGGCCACATCAGC
98580526 ACTCCCGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (21 bp):
AGTTAACTGGCCACATCAGCT
Found at i:98580950 original size:19 final size:19
Alignment explanation
Indices: 98580915--98580952 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
98580905 AATCCAAATT
*
98580915 GAAACCTCAAACCAAAACC
1 GAAACCTCAAACAAAAACC
*
98580934 GAAACCTCAAATAAAAACC
1 GAAACCTCAAACAAAAACC
98580953 CAAATTGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.55, C:0.32, G:0.05, T:0.08
Consensus pattern (19 bp):
GAAACCTCAAACAAAAACC
Found at i:98584400 original size:22 final size:22
Alignment explanation
Indices: 98584372--98584416 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
98584362 AACTTGTTCT
*
98584372 AAAGATGAAAACCACAATACCC
1 AAAGATGAAAACCAAAATACCC
98584394 AAAGATGAAAACCAAAATACCC
1 AAAGATGAAAACCAAAATACCC
98584416 A
1 A
98584417 CAGAAATAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.58, C:0.24, G:0.09, T:0.09
Consensus pattern (22 bp):
AAAGATGAAAACCAAAATACCC
Found at i:98589174 original size:3 final size:3
Alignment explanation
Indices: 98589166--98589194 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
98589156 ACGACGCAAA
98589166 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
98589195 GATGTTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Done.