Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 35 of 362
Found at i:10261853 original size:25 final size:25
Alignment explanation
Indices: 10261821--10261869 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
10261811 ATATATCTTA
**
10261821 ACTATATTATGTATGTATTTTTAAC
1 ACTATATTATGTACATATTTTTAAC
10261846 ACTATATTATGTACATATTTTTAA
1 ACTATATTATGTACATATTTTTAA
10261870 TATTATCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (25 bp):
ACTATATTATGTACATATTTTTAAC
Found at i:10262052 original size:24 final size:22
Alignment explanation
Indices: 10262016--10262073 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 22
10262006 CAATATTAAT
10262016 TATTATTATTATTCTAATATTTTGA
1 TATT-TTA-TATTCTAATATTTT-A
*
10262041 TATTTTGATATTTTAATATTTTA
1 TATTTT-ATATTCTAATATTTTA
10262064 TATTTTATAT
1 TATTTTATAT
10262074 ATTTTATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 4 0.13
23 7 0.23
24 15 0.48
25 5 0.16
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (22 bp):
TATTTTATATTCTAATATTTTA
Found at i:10262068 original size:7 final size:8
Alignment explanation
Indices: 10262032--10262073 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
10262022 TATTATTCTA
10262032 ATATTTTG
1 ATATTTTG
10262040 ATATTTTG
1 ATATTTTG
*
10262048 ATATTTTA
1 ATATTTTG
10262056 ATATTTT-
1 ATATTTTG
10262063 ATATTTT-
1 ATATTTTG
10262070 ATAT
1 ATAT
10262074 ATTTTATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
7 11 0.33
8 22 0.67
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (8 bp):
ATATTTTG
Found at i:10262084 original size:24 final size:25
Alignment explanation
Indices: 10262032--10262084 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
10262022 TATTATTCTA
*
10262032 ATATTTTGATATTTTGATATTTTA-
1 ATATTTTAATATTTTGATATTTTAT
*
10262056 ATATTTT-ATATTTTATATATTTTAT
1 ATATTTTAATATTTT-GATATTTTAT
10262081 -TATT
1 ATATT
10262085 CACATCATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (25 bp):
ATATTTTAATATTTTGATATTTTAT
Found at i:10263984 original size:17 final size:18
Alignment explanation
Indices: 10263964--10263999 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
10263954 AAAATCATTA
10263964 ATTA-AATTCTTGAAAAT
1 ATTATAATTCTTGAAAAT
*
10263981 ATTATAATTTTTGAAAAT
1 ATTATAATTCTTGAAAAT
10263999 A
1 A
10264000 AAAATTTCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (18 bp):
ATTATAATTCTTGAAAAT
Found at i:10266216 original size:79 final size:82
Alignment explanation
Indices: 10266078--10266234 Score: 198
Period size: 79 Copynumber: 1.9 Consensus size: 82
10266068 TTATACAAAA
* *
10266078 ATTTCTAAAACTTTACCAATATTTCTAAGGCTCTACCAAAGGTTTCCTTAGTGTCCCAAATCCAA
1 ATTTCTAAAACTTTACCAATATTTCTAAGGCTCTACCAAA-GTTTCCTTAATGTCCCAAACCCAA
10266143 -CTAACTCAACATTTTGCC
65 TC-AACTCAACATTTTGCC
* * * *
10266161 ATTTC-AAAA-TTTACCAATATTTTTAAGAG-TTTATCAAA-TTTCCTTAATGTGCCAAACCCAA
1 ATTTCTAAAACTTTACCAATATTTCTAAG-GCTCTACCAAAGTTTCCTTAATGTCCCAAACCCAA
10266222 TCAACTCAACATT
65 TCAACTCAACATT
10266235 ATGACATACA
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
79 31 0.47
80 1 0.02
81 24 0.36
82 5 0.08
83 5 0.08
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.35
Consensus pattern (82 bp):
ATTTCTAAAACTTTACCAATATTTCTAAGGCTCTACCAAAGTTTCCTTAATGTCCCAAACCCAAT
CAACTCAACATTTTGCC
Found at i:10266249 original size:79 final size:81
Alignment explanation
Indices: 10266084--10266251 Score: 184
Period size: 79 Copynumber: 2.1 Consensus size: 81
10266074 AAAAATTTCT
* * *
10266084 AAAACTTTACCAATATTTCTAAGGCTCTACCAAAGGTTTCCTTAGTGTCCCAAATCCAACTAACT
1 AAAAATTTACCAATATTTCTAAGGCTCTACCAAA-GTTTCCTTAATGTCCCAAACCCAACTAACT
* * *
10266149 CAACATTTTGCCATTTC
65 CAACATTATGACATTAC
* * * *
10266166 -AAAATTTACCAATATTTTTAAGAG-TTTATCAAA-TTTCCTTAATGTGCCAAACCCAA-TCAAC
1 AAAAATTTACCAATATTTCTAAG-GCTCTACCAAAGTTTCCTTAATGTCCCAAACCCAACT-AAC
10266227 TCAACATTATGACA-TAC
64 TCAACATTATGACATTAC
10266244 AAAAATTT
1 AAAAATTT
10266252 CTAAGGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
78 3 0.04
79 42 0.58
81 27 0.37
82 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.33
Consensus pattern (81 bp):
AAAAATTTACCAATATTTCTAAGGCTCTACCAAAGTTTCCTTAATGTCCCAAACCCAACTAACTC
AACATTATGACATTAC
Found at i:10266270 original size:20 final size:20
Alignment explanation
Indices: 10266245--10266381 Score: 93
Period size: 20 Copynumber: 6.8 Consensus size: 20
10266235 ATGACATACA
10266245 AAAATTTCTAAGGATTTATC
1 AAAATTTCTAAGGATTTATC
* *
10266265 AAAATTTTTAAAGATTTA-C
1 AAAATTTCTAAGGATTTATC
* *
10266284 AAAAATATT-TGAGGATTTCTC
1 -AAAAT-TTCTAAGGATTTATC
*
10266305 AAAATTTCT-ATG-TTTATACC
1 AAAATTTCTAAGGATTTAT--C
* *
10266325 AAAATATCTAAGGATTTACC
1 AAAATTTCTAAGGATTTATC
* * * * *
10266345 ATAATTTGTAAAGATTCACC
1 AAAATTTCTAAGGATTTATC
*
10266365 AAAATTTATAAGGATTT
1 AAAATTTCTAAGGATTT
10266382 TGCCAAAACT
Statistics
Matches: 90, Mismatches: 19, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
18 4 0.04
19 5 0.06
20 72 0.80
21 5 0.06
22 4 0.04
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (20 bp):
AAAATTTCTAAGGATTTATC
Found at i:10266285 original size:40 final size:40
Alignment explanation
Indices: 10266241--10266381 Score: 133
Period size: 40 Copynumber: 3.5 Consensus size: 40
10266231 CATTATGACA
*
10266241 TACAAAAATTTCTAAGGATTTATCAAAATTTTTAAAGATT
1 TACAAAAATTTCTAAGGATTTATCAAAATTTCTAAAGATT
* * * *
10266281 TACAAAAATATT-TGAGGATTTCTCAAAATTTCT-ATGTTT
1 TACAAAAAT-TTCTAAGGATTTATCAAAATTTCTAAAGATT
* * * * *
10266320 ATACCAAAATATCTAAGGATTTACCATAATTTGTAAAGATT
1 -TACAAAAATTTCTAAGGATTTATCAAAATTTCTAAAGATT
* * *
10266361 CACCAAAATTTATAAGGATTT
1 TACAAAAATTTCTAAGGATTT
10266382 TGCCAAAACT
Statistics
Matches: 80, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
39 5 0.06
40 69 0.86
41 6 0.08
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (40 bp):
TACAAAAATTTCTAAGGATTTATCAAAATTTCTAAAGATT
Found at i:10266438 original size:33 final size:33
Alignment explanation
Indices: 10266396--10266458 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
10266386 AAAACTTATT
10266396 AGGTTATACTAAAATAACTAAAGATTTACTATA
1 AGGTTATACTAAAATAACTAAAGATTTACTATA
* *
10266429 AGGTTATACTAAAATATCTAAGGATTTACT
1 AGGTTATACTAAAATAACTAAAGATTTACT
10266459 TGAATCTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (33 bp):
AGGTTATACTAAAATAACTAAAGATTTACTATA
Found at i:10266498 original size:20 final size:20
Alignment explanation
Indices: 10266439--10266507 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
10266429 AGGTTATACT
* *
10266439 AAAATATCTAAGGATTTACT
1 AAAATTTCTAAGGATTTACC
** *
10266459 TGAATCTT-TAAGGATATACC
1 AAAAT-TTCTAAGGATTTACC
10266479 AAAATTTCTAAGGATTTACC
1 AAAATTTCTAAGGATTTACC
10266499 -AAATTTCTA
1 AAAATTTCTA
10266508 GAGTATACTA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
19 11 0.28
20 27 0.69
21 1 0.03
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (20 bp):
AAAATTTCTAAGGATTTACC
Found at i:10266616 original size:20 final size:19
Alignment explanation
Indices: 10266583--10266660 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 19
10266573 ACTAATCTTG
* *
10266583 TTAAGGTTTAACCAAAATT
1 TTAAGATTTTACCAAAATT
10266602 TGTAAGATTTTACCAAAAATT
1 T-TAAGATTTTACC-AAAATT
10266623 TTAAAGA-TTTACCAAAATT
1 TT-AAGATTTTACCAAAATT
* *
10266642 TATAAGGTTATACCAAAAT
1 T-TAAGATTTTACCAAAAT
10266661 ATCTAAGAGT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
19 11 0.22
20 28 0.56
21 11 0.22
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.36
Consensus pattern (19 bp):
TTAAGATTTTACCAAAATT
Found at i:10266698 original size:20 final size:21
Alignment explanation
Indices: 10266673--10266725 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
10266663 CTAAGAGTAT
10266673 CAAAATTTCTAAA-GCCTTAC
1 CAAAATTTCTAAAGGCCTTAC
* ** *
10266693 CAAAATCTC-AAAGGGTTTGC
1 CAAAATTTCTAAAGGCCTTAC
10266713 CAAAATTTCTAAA
1 CAAAATTTCTAAA
10266726 AATTTCCTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 3 0.12
20 20 0.77
21 3 0.12
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (21 bp):
CAAAATTTCTAAAGGCCTTAC
Found at i:10266890 original size:20 final size:20
Alignment explanation
Indices: 10266867--10266994 Score: 95
Period size: 20 Copynumber: 6.5 Consensus size: 20
10266857 CAAAAAAGTT
*
10266867 TAAGGATCTACCAAAATTTC
1 TAAGGATTTACCAAAATTTC
* *
10266887 TAAGG-TGTTA-C-TAATATC
1 TAAGGAT-TTACCAAAATTTC
*
10266905 TAAGGATTTACAAAAATTTC
1 TAAGGATTTACCAAAATTTC
* *
10266925 TAA-GATTATAACAAAATATC
1 TAAGGATT-TACCAAAATTTC
* * *
10266945 TAAGTATTTATCAATATTTC
1 TAAGGATTTACCAAAATTTC
* *
10266965 GAAGGCA-TTACAAAAATTTC
1 TAAGG-ATTTACCAAAATTTC
10266985 TAAGGATTTA
1 TAAGGATTTA
10266995 ACAGTATTTC
Statistics
Matches: 81, Mismatches: 19, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
18 13 0.16
19 8 0.10
20 56 0.69
21 4 0.05
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (20 bp):
TAAGGATTTACCAAAATTTC
Found at i:10266964 original size:40 final size:39
Alignment explanation
Indices: 10266899--10267007 Score: 105
Period size: 40 Copynumber: 2.7 Consensus size: 39
10266889 AGGTGTTACT
*
10266899 AATATCTAAGGATTTACAAAAATTTCTAA-G-ATTATAACAA
1 AATATCTAAGGATTTAC-AATATTTCTAAGGCATTA-AA-AA
* * *
10266939 AATATCTAAGTATTTATCAATATTTCGAAGGCATTACAAA
1 AATATCTAAGGATTTA-CAATATTTCTAAGGCATTAAAAA
* *
10266979 AATTTCTAAGGATTTAACAGTATTTCTAA
1 AATATCTAAGGATTT-ACAATATTTCTAA
10267008 AAATTTACCG
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
40 49 0.86
41 4 0.07
42 4 0.07
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (39 bp):
AATATCTAAGGATTTACAATATTTCTAAGGCATTAAAAA
Found at i:10267196 original size:20 final size:20
Alignment explanation
Indices: 10267164--10267267 Score: 97
Period size: 20 Copynumber: 5.2 Consensus size: 20
10267154 ACAAAAATGC
*
10267164 CCTTAGAATTTTTGGTAAAT
1 CCTTAGAAATTTTGGTAAAT
* * * *
10267184 CCCTAGATATTTTGATTCAA-
1 CCTTAGAAATTTTG-GTAAAT
10267204 CCTTAGAAATTTTTTGG-AAAT
1 CCTTAGAAA--TTTTGGTAAAT
* *
10267225 CCTTATAAATTTTGGTAAAA
1 CCTTAGAAATTTTGGTAAAT
10267245 CCTTAGAAATTTTGGTAAA-
1 CCTTAGAAATTTTGGTAAAT
10267264 CCTT
1 CCTT
10267268 TACAAAATAT
Statistics
Matches: 67, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
19 10 0.15
20 41 0.61
21 11 0.16
22 5 0.07
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
CCTTAGAAATTTTGGTAAAT
Found at i:10267225 original size:41 final size:42
Alignment explanation
Indices: 10267164--10267257 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 42
10267154 ACAAAAATGC
* **
10267164 CCTTAG-AA-TTTTTGGTAAATCCCTAGATATTTTGATTCAA
1 CCTTAGAAATTTTTTGGTAAATCCCTAGAAATTTTGATAAAA
* * *
10267204 CCTTAGAAATTTTTTGG-AAATCCTTATAAATTTTGGTAAAA
1 CCTTAGAAATTTTTTGGTAAATCCCTAGAAATTTTGATAAAA
10267245 CCTTAGAAATTTT
1 CCTTAGAAATTTT
10267258 GGTAAACCTT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 6 0.13
41 33 0.72
42 7 0.15
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.43
Consensus pattern (42 bp):
CCTTAGAAATTTTTTGGTAAATCCCTAGAAATTTTGATAAAA
Found at i:10268932 original size:12 final size:12
Alignment explanation
Indices: 10268910--10268943 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
10268900 AGGGCGAGAA
10268910 AAAAGGAGGTGGT
1 AAAA-GAGGTGGT
10268923 AAAAGAGGTGGT
1 AAAAGAGGTGGT
*
10268935 AAGAGAGGT
1 AAAAGAGGT
10268944 ACACATTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.44, T:0.15
Consensus pattern (12 bp):
AAAAGAGGTGGT
Found at i:10270432 original size:93 final size:93
Alignment explanation
Indices: 10270319--10270491 Score: 301
Period size: 93 Copynumber: 1.9 Consensus size: 93
10270309 CGCCCATAAG
* * *
10270319 CGAACTCGGACTCTACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
10270384 ACGAGCTCGGATGCCTAGTTACATCTCT
66 ACGAGCTCGGATGCCTAGTTACATCTCT
*
10270412 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
10270477 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
10270492 CAAATATCCT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.31, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCT
Found at i:10270487 original size:46 final size:46
Alignment explanation
Indices: 10270312--10270487 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
10270302 TGTAACCCGC
* * * *
10270312 CCATAAGCGAACTCGGACTCTACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
10270358 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
10270404 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
10270451 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
10270488 TGCCCAAATA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 68 0.62
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:10270506 original size:46 final size:44
Alignment explanation
Indices: 10270363--10270506 Score: 116
Period size: 46 Copynumber: 3.1 Consensus size: 44
10270353 CGCATCCATA
* *
10270363 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA---A-ATC-CT
* * *
10270412 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC--ATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCAAATCC-T
10270455 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC-AA-ATCCT
10270502 AGTGA
1 AGTGA
10270507 CATGTCACTT
Statistics
Matches: 77, Mismatches: 8, Indels: 23
0.71 0.07 0.21
Matches are distributed among these distances:
42 1 0.01
43 4 0.05
44 4 0.05
46 33 0.43
47 28 0.36
48 4 0.05
49 3 0.04
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATCCT
Found at i:10274723 original size:42 final size:42
Alignment explanation
Indices: 10274664--10274745 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
10274654 AGGCAAGAGT
10274664 TAGCTTGGGCGATATTGAAACTTAGAGAAAAGTCCTTGCTGC
1 TAGCTTGGGCGATATTGAAACTTAGAGAAAAGTCCTTGCTGC
10274706 TAGCTTGGGCGATATTGAAACTTAGAGAAAAGTCCTTGCT
1 TAGCTTGGGCGATATTGAAACTTAGAGAAAAGTCCTTGCT
10274746 ACTTGTTATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (42 bp):
TAGCTTGGGCGATATTGAAACTTAGAGAAAAGTCCTTGCTGC
Found at i:10275236 original size:3 final size:3
Alignment explanation
Indices: 10275228--10275277 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
10275218 TACCAACCTG
10275228 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
10275276 AA
1 AA
10275278 AACCCATACC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:10276332 original size:2 final size:2
Alignment explanation
Indices: 10276325--10276353 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
10276315 GAAGAAAATA
10276325 AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
10276354 GGGGGGGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10278952 original size:11 final size:10
Alignment explanation
Indices: 10278873--10278948 Score: 50
Period size: 11 Copynumber: 7.3 Consensus size: 10
10278863 ATACCAACAT
*
10278873 AATTGTTAAA
1 AATTATTAAA
10278883 TAATTATTAAA
1 -AATTATTAAA
10278894 AATTA-TAAA
1 AATTATTAAA
*
10278903 AGTATT-GTAGAA
1 A--ATTATTA-AA
*
10278915 AATTATTTGAA
1 AATTA-TTAAA
10278926 AATTA-TAAA
1 AATTATTAAA
10278935 AATATATTAAA
1 AAT-TATTAAA
10278946 AAT
1 AAT
10278949 ATATAGCTAT
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
9 11 0.21
10 10 0.19
11 28 0.53
12 4 0.08
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (10 bp):
AATTATTAAA
Found at i:10279611 original size:22 final size:24
Alignment explanation
Indices: 10279559--10279612 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
10279549 TTTTTTATGA
*
10279559 TTAAATTATTGTTATTAAATATGTT
1 TTAAATTATTGTTATT-AATATCTT
*
10279584 TGAAATTATTG-TATT-ATATCTT
1 TTAAATTATTGTTATTAATATCTT
10279606 TTAAATT
1 TTAAATT
10279613 GAATTTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 12 0.46
24 4 0.15
25 10 0.38
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (24 bp):
TTAAATTATTGTTATTAATATCTT
Found at i:10284369 original size:48 final size:48
Alignment explanation
Indices: 10284313--10284579 Score: 227
Period size: 48 Copynumber: 5.6 Consensus size: 48
10284303 TGTGTGCTAA
* * *
10284313 TGTAAGACCATGTCTAGAACATGGCATTGGCCACATTATGAGAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCCAG
* *** * *
10284361 TGTAAGACCATGTTTGGGACATGGCATCGGCGTTGA-TATGTGTA-CTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGC-CACATTATGAG-AGCCAG
* * * *
10284409 TGTAAGACTATGTCTGGGATATAGCATCGGCCACATTATGAGAGTCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCCAG
*** * * *
10284457 TGTAAGACCATGTCTGGGACATGGCATCGG-CGTTTATATGTGTGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCACAT-TATGAGAGCCAG
* * * * ** * *
10284505 TGTAAGACCATGTCCGGGATATGACATCGG-TATTGTTATGAGAGCTAC
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCA-CATTATGAGAGCCAG
10284553 TGTAAGACCATGTCTGGGACATGGCAT
1 TGTAAGACCATGTCTGGGACATGGCAT
10284580 TGGCAACTTA
Statistics
Matches: 172, Mismatches: 41, Indels: 12
0.76 0.18 0.05
Matches are distributed among these distances:
47 4 0.02
48 164 0.95
49 4 0.02
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (48 bp):
TGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCCAG
Found at i:10284460 original size:96 final size:94
Alignment explanation
Indices: 10284296--10284579 Score: 372
Period size: 96 Copynumber: 3.0 Consensus size: 94
10284286 ATGGCATTTG
* * * * *
10284296 GTTGATATGTGTGCTAATGTAAGACCATGTCTAGAACATGGCATTGGCCACATTATGAGAGCCAG
1 GTTGATATGTGTGCTAGTGTAAGACCATGTCTGGGATAT-GCATCGGCCACATTATGAGAG-CAG
*
10284361 TGTAAGACCATGTTTGGGACATGGCATCGGC
64 TGTAAGACCATGTCTGGGACATGGCATCGGC
* *
10284392 GTTGATATGTGTACTAGTGTAAGACTATGTCTGGGATATAGCATCGGCCACATTATGAGAGTCAG
1 GTTGATATGTGTGCTAGTGTAAGACCATGTCTGGGATAT-GCATCGGCCACATTATGAGAG-CAG
10284457 TGTAAGACCATGTCTGGGACATGGCATCGGC
64 TGTAAGACCATGTCTGGGACATGGCATCGGC
* * * **
10284488 GTTTATATGTGTGCTAGTGTAAGACCATGTCCGGGATATGACATCGG-TATTGTTATGAGAGCTA
1 GTTGATATGTGTGCTAGTGTAAGACCATGTCTGGGATATG-CATCGGCCA-CATTATGAGAGC-A
*
10284552 CTGTAAGACCATGTCTGGGACATGGCAT
63 GTGTAAGACCATGTCTGGGACATGGCAT
10284580 TGGCAACTTA
Statistics
Matches: 167, Mismatches: 18, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
95 3 0.02
96 164 0.98
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (94 bp):
GTTGATATGTGTGCTAGTGTAAGACCATGTCTGGGATATGCATCGGCCACATTATGAGAGCAGTG
TAAGACCATGTCTGGGACATGGCATCGGC
Found at i:10291482 original size:48 final size:48
Alignment explanation
Indices: 10291407--10291627 Score: 227
Period size: 48 Copynumber: 4.6 Consensus size: 48
10291397 TGATATGTGT
* * * *
10291407 GCTAGTGTAAGATCATGTCTGGGACATGGCATCAGCCACATTATGAGA
1 GCTAGTGTAAGACCATGTCTAGGACATGGCATCAGCTATATTATGAGA
* * * *
10291455 GCTCGTGTAAAACCATGTCTAGGACATGGCATCAGCGT-TGA-TATGTGT
1 GCTAGTGTAAGACCATGTCTAGGACATGGCATCAGC-TAT-ATTATGAGA
* * *
10291503 GCTAGTGTAAGATCATGTCTGGGACATGGCATCGGCTATATTAT-AGGA
1 GCTAGTGTAAGACCATGTCTAGGACATGGCATCAGCTATATTATGA-GA
* * *
10291551 G-TCAGTGTAAGTCCATGTCTAGGACATGGCATC-GGTATTGTTATGAGA
1 GCT-AGTGTAAGACCATGTCTAGGACATGGCATCAGCTA-TATTATGAGA
*
10291599 GCTAGTGTAAGACCATGTCTAAGACATGG
1 GCTAGTGTAAGACCATGTCTAGGACATGG
10291628 TATCTGCCTT
Statistics
Matches: 142, Mismatches: 22, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
47 6 0.04
48 133 0.94
49 3 0.02
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (48 bp):
GCTAGTGTAAGACCATGTCTAGGACATGGCATCAGCTATATTATGAGA
Found at i:10291559 original size:96 final size:96
Alignment explanation
Indices: 10291395--10291627 Score: 308
Period size: 96 Copynumber: 2.4 Consensus size: 96
10291385 ATGACATTTG
10291395 GTTGATATGTGTGCTAGTGTAAGATCATGTCTGGGACATGGCATCAGCCACATTATGAGAGCTCG
1 GTTGATATGTGTGCTAGTGTAAGATCATGTCTGGGACATGGCATCAGCCACATTATGAGAGCTCG
10291460 TGTAAAACCATGTCTAGGACATGGCATCAGC
66 TGTAAAACCATGTCTAGGACATGGCATCAGC
* * *
10291491 GTTGATATGTGTGCTAGTGTAAGATCATGTCTGGGACATGGCATCGGCTATATTAT-AGGAG-TC
1 GTTGATATGTGTGCTAGTGTAAGATCATGTCTGGGACATGGCATCAGCCACATTATGA-GAGCTC
** * *
10291554 AGTGTAAGTCCATGTCTAGGACATGGCATCGGT
65 -GTGTAAAACCATGTCTAGGACATGGCATCAGC
* * * * * **
10291587 ATTGTTATGAGAGCTAGTGTAAGACCATGTCTAAGACATGG
1 GTTGATATGTGTGCTAGTGTAAGATCATGTCTGGGACATGG
10291628 TATCTGCCTT
Statistics
Matches: 121, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
95 3 0.02
96 118 0.98
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (96 bp):
GTTGATATGTGTGCTAGTGTAAGATCATGTCTGGGACATGGCATCAGCCACATTATGAGAGCTCG
TGTAAAACCATGTCTAGGACATGGCATCAGC
Found at i:10296605 original size:26 final size:26
Alignment explanation
Indices: 10296576--10296632 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
10296566 CATTACTTTT
*
10296576 GAAAAGT-ATTTTTAAAAAGTACTGTG
1 GAAAAGTGATTTTGAAAAA-TACTGTG
* *
10296602 GAAAAGTGATTTTGAGAAATACTTTG
1 GAAAAGTGATTTTGAAAAATACTGTG
10296628 GAAAA
1 GAAAA
10296633 ATTTAAGTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.44, C:0.04, G:0.21, T:0.32
Consensus pattern (26 bp):
GAAAAGTGATTTTGAAAAATACTGTG
Found at i:10297818 original size:21 final size:22
Alignment explanation
Indices: 10297794--10297834 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
10297784 AAACAATATA
10297794 ATTTTG-CTTTTTAA-TTTAATG
1 ATTTTGAC-TTTTAACTTTAATG
10297815 ATTTTGACTTTTAACTTTAA
1 ATTTTGACTTTTAACTTTAA
10297835 AAAAAGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.59
Consensus pattern (22 bp):
ATTTTGACTTTTAACTTTAATG
Found at i:10298155 original size:32 final size:34
Alignment explanation
Indices: 10298119--10298184 Score: 91
Period size: 35 Copynumber: 2.0 Consensus size: 34
10298109 CAATATAGAA
* *
10298119 TTTTAGACTTTT-AAT-ATTGTTTTAAAAATCAT
1 TTTTAGAATTTTAAATAATAGTTTTAAAAATCAT
10298151 TTTTAGAATTTTAAATAGATAGTTTTAAAAATCA
1 TTTTAGAATTTTAAATA-ATAGTTTTAAAAATCA
10298185 AAAGCTCGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 11 0.38
33 3 0.10
35 15 0.52
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (34 bp):
TTTTAGAATTTTAAATAATAGTTTTAAAAATCAT
Found at i:10298604 original size:14 final size:14
Alignment explanation
Indices: 10298585--10298623 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
10298575 TGATTGGCAG
10298585 TAAAATGTTTTCTA
1 TAAAATGTTTTCTA
* *
10298599 TAAAATGATTTCTG
1 TAAAATGTTTTCTA
*
10298613 GAAAATGTTTT
1 TAAAATGTTTT
10298624 ACTTTTCTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (14 bp):
TAAAATGTTTTCTA
Found at i:10298632 original size:20 final size:20
Alignment explanation
Indices: 10298607--10298646 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
10298597 TATAAAATGA
*
10298607 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
10298627 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
10298647 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:10298637 original size:34 final size:35
Alignment explanation
Indices: 10298592--10298658 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
10298582 CAGTAAAATG
*
10298592 TTTTCTATAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCTATAAAATGATTTACTGGAAAATATTTTAC
*
10298626 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCTATAAAATGATTTACTGGAAAATATTTT
10298659 CTAGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48
Consensus pattern (35 bp):
TTTTCTATAAAATGATTTACTGGAAAATATTTTAC
Found at i:10298723 original size:32 final size:32
Alignment explanation
Indices: 10298639--10298724 Score: 86
Period size: 33 Copynumber: 2.6 Consensus size: 32
10298629 TCTGTAAAAT
* **
10298639 GATTTACTGGAAAATATTTTCTAGTGTTTGATT
1 GATTT-CTTGAAAATATTTTCTAGTGTTTGACA
*
10298672 GA-ATCTGTGTAAAATATTTTCT-GCTGTTTGACA
1 GATTTCT-TG-AAAATATTTTCTAG-TGTTTGACA
10298705 GATTTCTTGAAAATATTTTC
1 GATTTCTTGAAAATATTTTC
10298725 CGGAAAAGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
31 2 0.05
32 14 0.32
33 25 0.57
34 3 0.07
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.47
Consensus pattern (32 bp):
GATTTCTTGAAAATATTTTCTAGTGTTTGACA
Found at i:10298764 original size:18 final size:18
Alignment explanation
Indices: 10298738--10298787 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
10298728 AAAAGTTGTT
*
10298738 TTTACATATATTAATAAA
1 TTTATATATATTAATAAA
10298756 TTTATATATATTAATAAA
1 TTTATATATATTAATAAA
* *
10298774 TTTTTATATTTTAA
1 TTTATATATATTAA
10298788 ATTATTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTATATATATTAATAAA
Found at i:10301719 original size:14 final size:14
Alignment explanation
Indices: 10301700--10301730 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
10301690 GGTAGACCGA
10301700 AGGTGGACCGGTGG
1 AGGTGGACCGGTGG
*
10301714 AGGTGGATCGGTGG
1 AGGTGGACCGGTGG
10301728 AGG
1 AGG
10301731 ACGGAGGTAG
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:0.16, C:0.10, G:0.58, T:0.16
Consensus pattern (14 bp):
AGGTGGACCGGTGG
Found at i:10309741 original size:30 final size:29
Alignment explanation
Indices: 10309707--10309793 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 29
10309697 AATTTTAATA
10309707 TTTAATTTGGTATTTAAGTTTTTTTTATG
1 TTTAATTTGGTATTTAAGTTTTTTTTATG
* * **
10309736 TTTTAATTTGGTATTTGAGTTTGACTTCAATG
1 -TTTAATTTGGTATTTAAGTTT--TTTTTATG
* *
10309768 TTTAATTTGATAATTAAGTTTTTTTT
1 TTTAATTTGGTATTTAAGTTTTTTTT
10309794 GTCCTATACA
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
29 2 0.04
30 20 0.44
31 18 0.40
32 5 0.11
ACGTcount: A:0.23, C:0.02, G:0.14, T:0.61
Consensus pattern (29 bp):
TTTAATTTGGTATTTAAGTTTTTTTTATG
Found at i:10310144 original size:21 final size:20
Alignment explanation
Indices: 10310114--10310153 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
10310104 GAATGATGAG
*
10310114 TAAGAACTCTTATAAAATAAA
1 TAAGAACTCTT-CAAAATAAA
*
10310135 TAAGATCTCTTCAAAATAA
1 TAAGAACTCTTCAAAATAA
10310154 TAAAAAAAAA
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:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (20 bp):
TAAGAACTCTTCAAAATAAA
Found at i:10321407 original size:35 final size:34
Alignment explanation
Indices: 10321333--10321496 Score: 134
Period size: 35 Copynumber: 4.8 Consensus size: 34
10321323 CAATCAACCA
* * * * *
10321333 AAACACACCAGATGCTCACAAGAGCCAATCCATCG
1 AAACACA-CAAATGCTTATAAGAGCTAATCCCTCG
*
10321368 --ACACACAAATGCTTATAAGAGTTAATCCCTCTG
1 AAACACACAAATGCTTATAAGAGCTAATCCCTC-G
* *
10321401 AAACACACTAATGCTTGTAAGAGCTAATCCCTACG
1 AAACACACAAATGCTTATAAGAGCTAATCCCT-CG
* * * *
10321436 AAACACACCAATGCTCATAAGAGCTAGTCCCTCCA
1 AAACACACAAATGCTTATAAGAGCTAATCCCT-CG
* * * *
10321471 AAATACACCAATACTCATAAGAGCTA
1 AAACACACAAATGCTTATAAGAGCTA
10321497 GTCCAACCGA
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
32 20 0.19
33 6 0.06
35 81 0.75
36 1 0.01
ACGTcount: A:0.40, C:0.29, G:0.12, T:0.20
Consensus pattern (34 bp):
AAACACACAAATGCTTATAAGAGCTAATCCCTCG
Found at i:10321492 original size:70 final size:67
Alignment explanation
Indices: 10321330--10321501 Score: 173
Period size: 70 Copynumber: 2.5 Consensus size: 67
10321320 CGACAATCAA
* * * *
10321330 CCAAAACACACCAGATGCTCACAAGAGCCAATCCATCGACACACAAATGCTTATAAGAGTTAATC
1 CCAAAACACACCA-ATGCTCATAAGAGCTAATCCATCGACACACAAATGCTCATAAGAGCTAATC
10321395 CCT
65 CCT
** * ** * * *
10321398 CTGAAACACACTAATGCTTGTAAGAGCTAATCCCTACGAAACACACCAATGCTCATAAGAGCTAG
1 CCAAAACACACCAATGCTCATAAGAGCTAATCCAT-CG--ACACACAAATGCTCATAAGAGCTAA
10321463 TCCCT
63 TCCCT
* * *
10321468 CCAAAATACACCAATACTCATAAGAGCTAGTCCA
1 CCAAAACACACCAATGCTCATAAGAGCTAATCCA
10321502 ACCGAATCAT
Statistics
Matches: 80, Mismatches: 21, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
67 17 0.21
68 12 0.15
70 51 0.64
ACGTcount: A:0.39, C:0.30, G:0.12, T:0.19
Consensus pattern (67 bp):
CCAAAACACACCAATGCTCATAAGAGCTAATCCATCGACACACAAATGCTCATAAGAGCTAATCC
CT
Found at i:10324640 original size:26 final size:26
Alignment explanation
Indices: 10324611--10324662 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
10324601 ACTTTCATAT
10324611 TCCCCCATAAATCATCAAAGAACAAA
1 TCCCCCATAAATCATCAAAGAACAAA
10324637 TCCCCCATAAATCATCAAAGAACAAA
1 TCCCCCATAAATCATCAAAGAACAAA
10324663 CATGTCACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.31, G:0.04, T:0.15
Consensus pattern (26 bp):
TCCCCCATAAATCATCAAAGAACAAA
Found at i:10329569 original size:46 final size:46
Alignment explanation
Indices: 10329458--10329612 Score: 193
Period size: 46 Copynumber: 3.3 Consensus size: 46
10329448 TTATCTTTGA
* * * * * **
10329458 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTGTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATGT
10329505 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
* * * **
10329551 CACGCTGCCATGGTATCTTTCAACCATGGTCTTATTTATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
10329597 CATGTTGCCATGGTAT
1 CATGTTGCCATGGTAT
10329613 AGAAACTAGA
Statistics
Matches: 94, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
46 61 0.65
47 33 0.35
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.42
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
Found at i:10337859 original size:6 final size:6
Alignment explanation
Indices: 10337850--10337888 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
10337840 ATGTTGGAGT
10337850 AGGTGA AGGTGA AGGTGA AGGTGA AGGTGA AGGTGA AGG
1 AGGTGA AGGTGA AGGTGA AGGTGA AGGTGA AGGTGA AGG
10337889 CGTGATTCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.51, T:0.15
Consensus pattern (6 bp):
AGGTGA
Found at i:10351013 original size:21 final size:21
Alignment explanation
Indices: 10350984--10351023 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
10350974 ATAAGAAATT
*
10350984 TTTTTTGTTAGTATTATGTAG
1 TTTTGTGTTAGTATTATGTAG
* *
10351005 TTTTGTGTTATTTTTATGT
1 TTTTGTGTTAGTATTATGT
10351024 TTTGTTTAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.17, T:0.68
Consensus pattern (21 bp):
TTTTGTGTTAGTATTATGTAG
Found at i:10351143 original size:27 final size:27
Alignment explanation
Indices: 10351108--10351160 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
10351098 GAAATTTTTT
*
10351108 AATATATTTGATATTGTTAGAAATGGC
1 AATAAATTTGATATTGTTAGAAATGGC
10351135 AATAAATTTGATATTGTTAGAAATGG
1 AATAAATTTGATATTGTTAGAAATGG
10351161 ACTATTATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.40
Consensus pattern (27 bp):
AATAAATTTGATATTGTTAGAAATGGC
Found at i:10357926 original size:23 final size:21
Alignment explanation
Indices: 10357889--10357932 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 21
10357879 TTTACCTACA
10357889 TAAAAAATAAAAAAATAGCAT
1 TAAAAAATAAAAAAATAGCAT
10357910 TAAAATAATTAAAAAAATAGCAT
1 TAAAA-AA-TAAAAAAATAGCAT
10357933 GCCAAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.24
22 2 0.10
23 14 0.67
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (21 bp):
TAAAAAATAAAAAAATAGCAT
Found at i:10357939 original size:24 final size:23
Alignment explanation
Indices: 10357896--10357941 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
10357886 ACATAAAAAA
*
10357896 TAAAAAAATAGCATTAAAATAAT
1 TAAAAAAATAGCATCAAAATAAT
*
10357919 TAAAAAAATAGCATGCCAAATAA
1 TAAAAAAATAGCAT-CAAAATAA
10357942 ATTTCATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.63, C:0.09, G:0.07, T:0.22
Consensus pattern (23 bp):
TAAAAAAATAGCATCAAAATAAT
Found at i:10360436 original size:42 final size:42
Alignment explanation
Indices: 10360389--10360480 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
10360379 ACTGCCTGAG
* *
10360389 ACACGACCGTGTGTATTAGCTCAATGTGTTACATGGTCTAGC
1 ACACGACCGTGTGTATTAGCTCAATATGTTACACGGTCTAGC
* *
10360431 ACACGACGGTGTGTATTAGCTCAATATGTTACACGGTCTAGT
1 ACACGACCGTGTGTATTAGCTCAATATGTTACACGGTCTAGC
10360473 ACACGACC
1 ACACGACC
10360481 ATGTATCACT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (42 bp):
ACACGACCGTGTGTATTAGCTCAATATGTTACACGGTCTAGC
Found at i:10385452 original size:75 final size:75
Alignment explanation
Indices: 10385324--10385471 Score: 208
Period size: 75 Copynumber: 2.0 Consensus size: 75
10385314 GGAAAACCAA
* * * *
10385324 GATTATTCCCTTATTAATAGAGAAGGCAAAAGGAAAGCTAGAAAAATGAATTATATTCTTTCTAA
1 GATTATTCCCTTATTAATAGAGAAAGCAAAAGGAAAGCTAAAAAAACGAATTATATTCTTTCCAA
*
10385389 ATGAATATAG
66 AAGAATATAG
* * *
10385399 GATTATTCCCTTATTAATAGAGAAAGCAAATGGAAAGTTACAAAAAACG-ATTATATTTTTTCCA
1 GATTATTCCCTTATTAATAGAGAAAGCAAAAGGAAAGCTA-AAAAAACGAATTATATTCTTTCCA
10385463 AAAGAATAT
65 AAAGAATAT
10385472 TAATTTCCAT
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
75 58 0.91
76 6 0.09
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (75 bp):
GATTATTCCCTTATTAATAGAGAAAGCAAAAGGAAAGCTAAAAAAACGAATTATATTCTTTCCAA
AAGAATATAG
Found at i:10386044 original size:140 final size:138
Alignment explanation
Indices: 10385448--10386144 Score: 1083
Period size: 138 Copynumber: 5.0 Consensus size: 138
10385438 ACAAAAAACG
* * **
10385448 ATTATATTTTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCAAAATTAATTAAT
1 ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACTGAAATTAATTAAT
* *
10385513 ATAA-TTTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAACCAAATTC
66 ATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTC
*
10385577 ATATTTTA
131 ATATATTA
** * * * * *
10385585 ATTATATTCTTTTGAAAAGAATATTGATTTCCATATCTTTTATATTTTGACGGAAGTTAATTAAT
1 ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACTGAAATTAATTAAT
* *
10385650 ATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATGAGTCAAATTC
66 ATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTC
10385715 ATATATTA
131 ATATATTA
* *
10385723 ATTATACTCTTTCCAAAAGAATATTGATTTTCATGTCTTTTATATTTTGACTGAAATTAATTAAT
1 ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACTGAAATTAATTAAT
* * *
10385788 ATAACTTTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGACTCAAAATT
66 ATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATC-AAATT
10385853 CATATATTA
130 CATATATTA
* *
10385862 ATTATATTCTTTCCAAAAGAATATTAATTTTCAAGTCTTTTATAGTTTGACTGAAATTAATTAAT
1 ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACTGAAATTAATTAAT
*
10385927 ATAACTGTTTATATTAATAAATTCGGTAAAATATTTATACAATTAATATTTTGTATGAATCAAAC
66 ATAACTGTTTATATTAATAAATTCGGTAAAATA--TATACAATTAATATTTTGTATGAATCAAAT
10385992 TCATATATTA
129 TCATATATTA
*
10386002 ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTAT-TTTCTGACTAAAATTAATTAA
1 ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTT-TGACTGAAATTAATTAA
* *
10386066 TATAACTGTTTATATTAATAAATTCGGTAAATTTTTTATACAATTAATATTTTGTATGAATCAAA
65 TATAACTGTTTATATTAATAAATTCGGTAAA--ATATATACAATTAATATTTTGTATGAATCAAA
10386131 TTCATATATTA
128 TTCATATATTA
10386142 ATT
1 ATT
10386145 TTATCTATAT
Statistics
Matches: 515, Mismatches: 38, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
137 61 0.12
138 176 0.34
139 108 0.21
140 144 0.28
141 25 0.05
142 1 0.00
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (138 bp):
ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACTGAAATTAATTAAT
ATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTC
ATATATTA
Found at i:10386080 original size:279 final size:276
Alignment explanation
Indices: 10385448--10386144 Score: 1096
Period size: 279 Copynumber: 2.5 Consensus size: 276
10385438 ACAAAAAACG
* * *
10385448 ATTATATTTTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCAAAATTAATTAAT
1 ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACTAAAATTAATTAAT
10385513 ATAA-TTTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAAC-CAAATT
66 ATAACTTTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATG-ACTCAAATT
* ** * * *
10385576 CATATTTTAATTATATTCTTTTGAAAAGAATATTGATTTCCATATCTTTTATATTTTGACGGAAG
130 CATATATTAATTATATTCTTTCCAAAAGAATATTAATTTCCATATCTTTTATAGTTTGACGGAAA
10385641 TTAATTAATATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATGA
195 TTAATTAATATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATGA
* *
10385706 GTCAAATTCATATATTA
260 ATCAAACTCATATATTA
* * *
10385723 ATTATACTCTTTCCAAAAGAATATTGATTTTCATGTCTTTTATATTTTGACTGAAATTAATTAAT
1 ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACTAAAATTAATTAAT
*
10385788 ATAACTTTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGACTCAAAATT
66 ATAACTTTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGACTC-AAATT
* *
10385853 CATATATTAATTATATTCTTTCCAAAAGAATATTAATTTTCA-AGTCTTTTATAGTTTGACTGAA
130 CATATATTAATTATATTCTTTCCAAAAGAATATTAATTTCCATA-TCTTTTATAGTTTGACGGAA
*
10385917 ATTAATTAATATAACTGTTTATATTAATAAATTCGGTAAAATATTTATACAATTAATATTTTGTA
194 ATTAATTAATATAACTGTTTATATTAATAAATTCGGTAAAATA--TATACAATTAATATTTTATA
10385982 TGAATCAAACTCATATATTA
257 TGAATCAAACTCATATATTA
10386002 ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTAT-TTTCTGACTAAAATTAATTAA
1 ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTT-TGACTAAAATTAATTAA
* * * *
10386066 TATAACTGTTTATATTAATAAATTCGGTAAATTTTTTATACAATTAATATTTTGTATGAATCAAA
65 TATAACTTTTTATATTAATAAATTCGGTAAA--ATATATACAATTAATATTTTGTATGACTCAAA
10386131 TTCATATATTAATT
128 TTCATATATTAATT
10386145 TTATCTATAT
Statistics
Matches: 387, Mismatches: 26, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
275 65 0.17
276 51 0.13
277 102 0.26
278 3 0.01
279 123 0.32
280 17 0.04
281 26 0.07
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (276 bp):
ATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACTAAAATTAATTAAT
ATAACTTTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGACTCAAATTC
ATATATTAATTATATTCTTTCCAAAAGAATATTAATTTCCATATCTTTTATAGTTTGACGGAAAT
TAATTAATATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTATATGAA
TCAAACTCATATATTA
Found at i:10390317 original size:12 final size:12
Alignment explanation
Indices: 10390300--10390329 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
10390290 CGTATACTGT
*
10390300 CACACGGGTGAC
1 CACACGGGCGAC
10390312 CACACGGGCGAC
1 CACACGGGCGAC
10390324 CACACG
1 CACACG
10390330 CCTGTGTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.40, G:0.30, T:0.03
Consensus pattern (12 bp):
CACACGGGCGAC
Found at i:10393326 original size:23 final size:22
Alignment explanation
Indices: 10393284--10393337 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
10393274 TGTTAAAGTT
*
10393284 AAAAA-TTTAAATTTGCTAAATA
1 AAAAATTTTAAATTAGCTAAA-A
10393306 AAAAATTTTAAAGTTAG-TAAAA
1 AAAAATTTTAAA-TTAGCTAAAA
*
10393328 AATAATTTTA
1 AAAAATTTTA
10393338 TCTATTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 15 0.54
23 10 0.36
24 3 0.11
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (22 bp):
AAAAATTTTAAATTAGCTAAAA
Found at i:10397848 original size:25 final size:25
Alignment explanation
Indices: 10397791--10397848 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
10397781 AACTCATATG
* * **
10397791 AGCCATATAACGAGAAGCTTATCCA
1 AGCCATATAACAAGAAGCTCATAAA
* *
10397816 GGCTATATAACAAGAAGCTCATAAA
1 AGCCATATAACAAGAAGCTCATAAA
10397841 AGCCATAT
1 AGCCATAT
10397849 TTGTGAAGCT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.21
Consensus pattern (25 bp):
AGCCATATAACAAGAAGCTCATAAA
Found at i:10397948 original size:23 final size:23
Alignment explanation
Indices: 10397921--10397966 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
10397911 GATAACCATG
* *
10397921 TATCGGGAAG-TTCAAGCGAGCCA
1 TATCGAGAAGCTTC-AGAGAGCCA
10397944 TATCGAGAAGCTTCAGAGAGCCA
1 TATCGAGAAGCTTCAGAGAGCCA
10397967 CTAACAGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.33, C:0.22, G:0.28, T:0.17
Consensus pattern (23 bp):
TATCGAGAAGCTTCAGAGAGCCA
Found at i:10398112 original size:24 final size:26
Alignment explanation
Indices: 10398085--10398137 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
10398075 CGATCTAGAT
*
10398085 GCTCCG-AAGAGCAAT-TAACGGGAA
1 GCTCCGCAAGAACAATATAACGGGAA
*
10398109 GCT-CGCAAGAACCATATAACGGGAA
1 GCTCCGCAAGAACAATATAACGGGAA
10398134 GCTC
1 GCTC
10398138 AAGAGGGCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
23 2 0.08
24 10 0.42
25 12 0.50
ACGTcount: A:0.36, C:0.25, G:0.26, T:0.13
Consensus pattern (26 bp):
GCTCCGCAAGAACAATATAACGGGAA
Found at i:10409216 original size:45 final size:45
Alignment explanation
Indices: 10409163--10409251 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
10409153 TTGATGCTTT
*
10409163 GTAAGTTCGTATAACGGGAAATTACCTTACCATTTATTTACATTA
1 GTAAGTTCGTATAACGGGAAATTAACTTACCATTTATTTACATTA
10409208 GTAAGTTCGTATAACGGGAAATTAACTTACCATTTATTTACATT
1 GTAAGTTCGTATAACGGGAAATTAACTTACCATTTATTTACATT
10409252 TAAAATAAGC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (45 bp):
GTAAGTTCGTATAACGGGAAATTAACTTACCATTTATTTACATTA
Found at i:10409731 original size:23 final size:25
Alignment explanation
Indices: 10409715--10409794 Score: 90
Period size: 26 Copynumber: 3.2 Consensus size: 25
10409705 GAGCCATATC
*
10409715 AGGAAGCTC-CAGAGAGCCATTAAT
1 AGGAAGCTCACAAAGAGCCATTAAT
**
10409739 AGGAAGCTCACAAAGAGCTTTTAATT
1 AGGAAGCTCACAAAGAGCCATTAA-T
* *
10409765 GGGAAGCTCACGAAGAGCCATATAAT
1 AGGAAGCTCACAAAGAGCCAT-TAAT
10409791 AGGA
1 AGGA
10409795 CACTCATAAG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
24 9 0.20
25 11 0.24
26 22 0.49
27 3 0.07
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (25 bp):
AGGAAGCTCACAAAGAGCCATTAAT
Found at i:10414819 original size:2 final size:2
Alignment explanation
Indices: 10414812--10414839 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10414802 TATAAAATTC
10414812 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
10414840 TAGATCATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10415088 original size:16 final size:15
Alignment explanation
Indices: 10415046--10415093 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
10415036 ACTCTATCCA
*
10415046 AATCTAAGAAAATTT
1 AATCTAAAAAAATTT
* *
10415061 AACCTTAAAAAATTT
1 AATCTAAAAAAATTT
*
10415076 GAATCTAAAAAAACTT
1 -AATCTAAAAAAATTT
10415092 AA
1 AA
10415094 ACCCAAAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.56, C:0.10, G:0.04, T:0.29
Consensus pattern (15 bp):
AATCTAAAAAAATTT
Found at i:10425391 original size:37 final size:36
Alignment explanation
Indices: 10425311--10425398 Score: 85
Period size: 37 Copynumber: 2.4 Consensus size: 36
10425301 CATCTAAAAT
* *
10425311 AAATAATATACAAAGAAATATAAATACTTTAGTATAA
1 AAAT-ATATACAAAAAAATATAAATACTTTAATATAA
10425348 ATAATATATACAAAAAAATATATAATA-TTTGAAT-TAA
1 A-AATATATACAAAAAAATATA-AATACTTT-AATATAA
10425385 CAAATAT-T-CAAAAA
1 -AAATATATACAAAAA
10425399 GGAAATTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
35 6 0.13
36 1 0.02
37 28 0.62
38 10 0.22
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (36 bp):
AAATATATACAAAAAAATATAAATACTTTAATATAA
Found at i:10427151 original size:177 final size:177
Alignment explanation
Indices: 10426865--10427460 Score: 844
Period size: 177 Copynumber: 3.4 Consensus size: 177
10426855 CACTGCAACG
* * * *
10426865 TTAGGGAGATAAG-GCTGCAATTTTTAGTCTACTTCCTTGCTACCTTAGGAAGATAATG-CTTGT
1 TTAGGGAGATAAGATCTACAATTTTCAGTCTACTTCCTTGCTACCTCAGGAAGATAA-GACTTGT
* * * * *
10426928 AACTTCAACCTGCTCTCTTGCTACCTCGGAGAGATATGGTTGGTGGCTGAAATCTACTCCATTGC
65 ATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTACTCCATTGC
10426993 CGATACATGGAGATAAGATTCGCCATCTTTGATCTTCTCCACTACTGC
130 CGATACATGGAGATAAGATTCGCCATCTTTGATCTTCTCCACTACTGC
* *
10427041 TTAGGGAGATAAGATCTATAATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTGTA
1 TTAGGGAGATAAGATCTACAATTTTCAGTCTACTTCCTTGCTACCTCAGGAAGATAAGACTTGTA
* * *
10427106 TCTTCAACCTGCTCTTTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTACTCTATTGCT
66 TCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTACTCCATTGCC
* *
10427171 GATACATGGAGATAAGA-TCTGCCGTCTTCGAT-TTGCTCCACTACTGC
131 GATACATGGAGATAAGATTC-GCCATCTTTGATCTT-CTCCACTACTGC
* **
10427218 TTAGGGAGATAAGATCTACAATTTTCAGTCTGCTTCCTTGCTACCTCAAAAAGATAAGACTTGTA
1 TTAGGGAGATAAGATCTACAATTTTCAGTCTACTTCCTTGCTACCTCAGGAAGATAAGACTTGTA
* * *
10427283 TCTTCAACCTACTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAACCTGCTCCATTGCC
66 TCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTACTCCATTGCC
* * *
10427348 GATACATGGAGATAAGATTCACCAT-TTTCGATCTACTCCACTACTAC
131 GATACATGGAGATAAGATTCGCCATCTTT-GATCTTCTCCACTACTGC
* * * *
10427395 TTAGGGAGATAACATCTATAATTTTCAGTCTACTTCAC-TGCAACCTCAGGGAGATAAGACTTGT
1 TTAGGGAGATAAGATCTACAATTTTCAGTCTACTTC-CTTGCTACCTCAGGAAGATAAGACTTGT
10427459 AT
65 AT
10427461 ATTGAGCCTG
Statistics
Matches: 375, Mismatches: 37, Indels: 15
0.88 0.09 0.04
Matches are distributed among these distances:
176 20 0.05
177 351 0.94
178 4 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.32
Consensus pattern (177 bp):
TTAGGGAGATAAGATCTACAATTTTCAGTCTACTTCCTTGCTACCTCAGGAAGATAAGACTTGTA
TCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTACTCCATTGCC
GATACATGGAGATAAGATTCGCCATCTTTGATCTTCTCCACTACTGC
Found at i:10427538 original size:354 final size:353
Alignment explanation
Indices: 10426865--10427546 Score: 888
Period size: 354 Copynumber: 1.9 Consensus size: 353
10426855 CACTGCAACG
* * * **
10426865 TTAGGGAGATAAGGCTGCAATTTTTAGTCTACTTCCTTGCTACCTTAGGAAGATAATGCTTGTAA
1 TTAGGGAGATAAGGCTACAATTTTCAGTCTACTTCCTTGCTACCTCAAAAAGATAATGCTTGTAA
* * * * * *
10426930 CTTCAACCTGCTCTCTTGCTACCTCGGAGAGATATGGTTGGTGGCTGAAATCTACTCCATTGCCG
66 CTTCAACCTACTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAACCTACTCCATTGCCG
* * * *
10426995 ATACATGGAGATAAGATTCGCCATCTTTGATCTTCTCCACTACTGCTTAGGGAGATAAGATCTAT
131 ATACATGGAGATAAGATTCACCATCTTTGATCTACTCCACTACTACTTAGGGAGATAACATCTAT
* * * ***
10427060 AATTTTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTGTATCTTCAACCTGCTCTTTTG
196 AATTTTCAGTCTACTTCCTTGCAACCTCAGGAAGATAAGACTTGTATATTCAACCTGCTCCACTG
* * ** * * * *
10427125 CTACCTCAGAGAGATAAGGCTGGTGGCTAAAATCTACTCTATTGCTGATACATGGAGATAAGATC
261 CAACCTCAGAGAGATAAGGCTGCTCACTAAAACCTACTCTACTGCTAATACAGGGAGATAAGATC
10427190 TGCCGTCTTCGATTTGCTCCACTACTGC
326 TGCCGTCTTCGATTTGCTCCACTACTGC
* *
10427218 TTAGGGAGATAAGATCTACAATTTTCAGTCTGCTTCCTTGCTACCTCAAAAAGATAA-GACTTGT
1 TTAGGGAGATAAG-GCTACAATTTTCAGTCTACTTCCTTGCTACCTCAAAAAGATAATG-CTTGT
* *
10427282 ATCTTCAACCTACTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAACCTGCTCCATTGC
64 AACTTCAACCTACTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAACCTACTCCATTGC
10427347 CGATACATGGAGATAAGATTCACCAT-TTTCGATCTACTCCACTACTACTTAGGGAGATAACATC
129 CGATACATGGAGATAAGATTCACCATCTTT-GATCTACTCCACTACTACTTAGGGAGATAACATC
* * *
10427411 TATAATTTTCAGTCTACTTCAC-TGCAACCTCAGGGAGATAAGACTTGTATATTGAGCCTGCTCC
193 TATAATTTTCAGTCTACTTC-CTTGCAACCTCAGGAAGATAAGACTTGTATATTCAACCTGCTCC
* * ** * *
10427475 ACTGCAACTTCA-AGGAGATAAGGCTTCTCACTTCAACCTGCTCTACTGC-AACTTCAGGGAGAT
257 ACTGCAACCTCAGA-GAGATAAGGCTGCTCACTAAAACCTACTCTACTGCTAA-TACAGGGAGAT
*
10427538 AAGGTCTGC
320 AAGATCTGC
10427547 TATGATCTGC
Statistics
Matches: 280, Mismatches: 43, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
353 19 0.07
354 260 0.93
355 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (353 bp):
TTAGGGAGATAAGGCTACAATTTTCAGTCTACTTCCTTGCTACCTCAAAAAGATAATGCTTGTAA
CTTCAACCTACTCTCTTGCTACCTCAGAGAGATAAGGCTGGTGGCTAAAACCTACTCCATTGCCG
ATACATGGAGATAAGATTCACCATCTTTGATCTACTCCACTACTACTTAGGGAGATAACATCTAT
AATTTTCAGTCTACTTCCTTGCAACCTCAGGAAGATAAGACTTGTATATTCAACCTGCTCCACTG
CAACCTCAGAGAGATAAGGCTGCTCACTAAAACCTACTCTACTGCTAATACAGGGAGATAAGATC
TGCCGTCTTCGATTTGCTCCACTACTGC
Found at i:10427541 original size:44 final size:42
Alignment explanation
Indices: 10427431--10427581 Score: 144
Period size: 44 Copynumber: 3.5 Consensus size: 42
10427421 AGTCTACTTC
* * * * * *
10427431 ACTGCAACCTCAGGGAGATAAGACTTGTATATTGAGCCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGGCTTCTA-CTT-AACCTGCTCT
*
10427475 ACTGCAACTTCAAGGAGATAAGGCTTCTCACTTCAACCTGCTCT
1 ACTGCAACTTCAGGGAGATAAGGCTTCT-ACTT-AACCTGCTCT
* * *
10427519 ACTGCAACTTCAGGGAGATAAGG--TCTGCTATGATCTGCTCT
1 ACTGCAACTTCAGGGAGATAAGGCTTCTACT-TAACCTGCTCT
*
10427560 ACTGCAACTTCAGAGAGATAAG
1 ACTGCAACTTCAGGGAGATAAG
10427582 ATCTGTTTAT
Statistics
Matches: 92, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
41 31 0.34
42 4 0.04
44 56 0.61
45 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (42 bp):
ACTGCAACTTCAGGGAGATAAGGCTTCTACTTAACCTGCTCT
Found at i:10427569 original size:41 final size:44
Alignment explanation
Indices: 10427467--10427586 Score: 140
Period size: 41 Copynumber: 2.8 Consensus size: 44
10427457 GTATATTGAG
* * *
10427467 CCTGCTCCACTGCAACTTCAAGGAGATAAGG-CTTCTCACTTCAA
1 CCTGCTCTACTGCAACTTCAGGGAGATAAGGTCTGCTCAC-TCAA
*
10427511 CCTGCTCTACTGCAACTTCAGGGAGATAAGGTCTGCT-A-T-GA
1 CCTGCTCTACTGCAACTTCAGGGAGATAAGGTCTGCTCACTCAA
* * *
10427552 TCTGCTCTACTGCAACTTCAGAGAGATAAGATCTG
1 CCTGCTCTACTGCAACTTCAGGGAGATAAGGTCTG
10427587 TTTATTTATA
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
41 33 0.49
42 1 0.01
44 30 0.44
45 4 0.06
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (44 bp):
CCTGCTCTACTGCAACTTCAGGGAGATAAGGTCTGCTCACTCAA
Found at i:10427918 original size:64 final size:64
Alignment explanation
Indices: 10427817--10427942 Score: 207
Period size: 64 Copynumber: 2.0 Consensus size: 64
10427807 ATGTATCTAT
*
10427817 GCTTATGCCAAATAATTAGGATGATATGATCAAAATGAATCAAATGCTCCTAACTAGGTGTGAC
1 GCTTATGCCAAATAATTAGGATGATATGATCAAAATGAATCAAATGCTCCTAACTAGATGTGAC
* * * *
10427881 GCTTATGTCAAATAATTAGGATGTTATGATCGAAATGAATCAAATGCTCTTAACTAGATGTG
1 GCTTATGCCAAATAATTAGGATGATATGATCAAAATGAATCAAATGCTCCTAACTAGATGTG
10427943 TTATGAATGA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (64 bp):
GCTTATGCCAAATAATTAGGATGATATGATCAAAATGAATCAAATGCTCCTAACTAGATGTGAC
Found at i:10440370 original size:15 final size:15
Alignment explanation
Indices: 10440350--10440380 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
10440340 TTGCTTGTGC
10440350 ATGAAAAAATAAAAA
1 ATGAAAAAATAAAAA
10440365 ATGAAAAAATAAAAA
1 ATGAAAAAATAAAAA
10440380 A
1 A
10440381 AATGTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.13
Consensus pattern (15 bp):
ATGAAAAAATAAAAA
Found at i:10444665 original size:35 final size:38
Alignment explanation
Indices: 10444577--10444665 Score: 103
Period size: 38 Copynumber: 2.4 Consensus size: 38
10444567 AAAAGAAAGT
* * *
10444577 TAAAGTAAATAATATACAAAGCAATATATAGATCCATC
1 TAAAATAAATAATATACAAAGCAATATATAAATACATC
*
10444615 TAAAATAAATAATATACAAAG-AA-ATATAAATAC-TT
1 TAAAATAAATAATATACAAAGCAATATATAAATACATC
**
10444650 TAGTATAAATAATATA
1 TAAAATAAATAATATA
10444666 TACAAAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
35 15 0.33
36 8 0.18
37 2 0.04
38 20 0.44
ACGTcount: A:0.57, C:0.08, G:0.06, T:0.29
Consensus pattern (38 bp):
TAAAATAAATAATATACAAAGCAATATATAAATACATC
Found at i:10446273 original size:20 final size:22
Alignment explanation
Indices: 10446248--10446287 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
10446238 TGAAACGTTG
10446248 TAGCAT-A-TAAATTGTATATA
1 TAGCATGAGTAAATTGTATATA
*
10446268 TAGCATGAGTAAATTTTATA
1 TAGCATGAGTAAATTGTATA
10446288 AACTAACCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 1 0.06
22 10 0.59
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.40
Consensus pattern (22 bp):
TAGCATGAGTAAATTGTATATA
Found at i:10450488 original size:27 final size:30
Alignment explanation
Indices: 10450458--10450521 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
10450448 TGTTAACATG
* *
10450458 TGATGGACG-TTT-TTTT-TTGGATCATTT
1 TGATGGACGATTTATTTTGTTGAATCATTC
10450485 TGATGGACGATTTAATTTTGTTGAATCATTC
1 TGATGGACGATTT-ATTTTGTTGAATCATTC
10450516 TGATGG
1 TGATGG
10450522 TAATATTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 9 0.29
28 3 0.10
30 4 0.13
31 15 0.48
ACGTcount: A:0.20, C:0.08, G:0.23, T:0.48
Consensus pattern (30 bp):
TGATGGACGATTTATTTTGTTGAATCATTC
Found at i:10457103 original size:35 final size:35
Alignment explanation
Indices: 10457063--10457143 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 35
10457053 TACCTTTTGA
* *
10457063 AGTGTCACCCCCAAGGACCTCTATAGCGTTTACAT
1 AGTGTCACCCCCAAGGACCTCTATACCGTTTACAC
* * ** * *
10457098 AGTGTCGCCTCGTAGGACTTGTATACCGTTTACAC
1 AGTGTCACCCCCAAGGACCTCTATACCGTTTACAC
10457133 AGTGTCACCCC
1 AGTGTCACCCC
10457144 ATAGGTCTAT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (35 bp):
AGTGTCACCCCCAAGGACCTCTATACCGTTTACAC
Found at i:10464271 original size:31 final size:32
Alignment explanation
Indices: 10464235--10464296 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
10464225 TATTTTTGAG
**
10464235 TTAAATTTGGCCTTCAACCTTTT-AAAAAGAT
1 TTAAATTTAACCTTCAACCTTTTGAAAAAGAT
*
10464266 TTAAATTTAACCTTCAATCTTTTGAAAAAGA
1 TTAAATTTAACCTTCAACCTTTTGAAAAAGA
10464297 GTTGAAATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.39
Consensus pattern (32 bp):
TTAAATTTAACCTTCAACCTTTTGAAAAAGAT
Found at i:10468375 original size:26 final size:26
Alignment explanation
Indices: 10468346--10468428 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
10468336 TTGAGAGCAA
10468346 AGGGCTCAAGTAAACTAGTTGAAATT
1 AGGGCTCAAGTAAACTAGTTGAAATT
** * * * *
10468372 AGGGGACAA-AAATACAAATTTGAACA-A
1 AGGGCTCAAGTAA-AC-TAGTTGAA-ATT
*
10468399 AGGGCTCGAGTAAACTAGTTGAAATT
1 AGGGCTCAAGTAAACTAGTTGAAATT
10468425 AGGG
1 AGGG
10468429 GACAAAAATA
Statistics
Matches: 39, Mismatches: 13, Indels: 10
0.63 0.21 0.16
Matches are distributed among these distances:
25 3 0.08
26 19 0.49
27 14 0.36
28 3 0.08
ACGTcount: A:0.42, C:0.11, G:0.25, T:0.22
Consensus pattern (26 bp):
AGGGCTCAAGTAAACTAGTTGAAATT
Found at i:10474052 original size:2 final size:2
Alignment explanation
Indices: 10474045--10474072 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10474035 TTTATTAGAG
10474045 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
10474073 ATAAAGCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:10475473 original size:6 final size:6
Alignment explanation
Indices: 10475462--10475487 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
10475452 AATTAATGTT
10475462 TTTATA TTTATA TTTATA TTTATA TT
1 TTTATA TTTATA TTTATA TTTATA TT
10475488 CCTTTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTATA
Found at i:10478632 original size:19 final size:21
Alignment explanation
Indices: 10478601--10478653 Score: 76
Period size: 19 Copynumber: 2.7 Consensus size: 21
10478591 ACAATTATCA
10478601 AAATATTAT-AAAAAAT-TAG
1 AAATATTATAAAAAAATCTAG
*
10478620 AAAT-TTATAAAAAAATCTAT
1 AAATATTATAAAAAAATCTAG
10478640 AAATATTATAAAAA
1 AAATATTATAAAAA
10478654 CAAAAAATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 4 0.13
19 11 0.37
20 6 0.20
21 9 0.30
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (21 bp):
AAATATTATAAAAAAATCTAG
Found at i:10478664 original size:26 final size:26
Alignment explanation
Indices: 10478629--10478703 Score: 125
Period size: 26 Copynumber: 2.9 Consensus size: 26
10478619 GAAATTTATA
10478629 AAAAAATCTATAAATATTATAAAAAC
1 AAAAAATCTATAAATATTATAAAAAC
10478655 AAAAAATCTATAAATATTATAAAAAC
1 AAAAAATCTATAAATATTATAAAAAC
* *
10478681 AAAAAATATATAAA-AATATAAAA
1 AAAAAATCTATAAATATTATAAAA
10478704 TTTATAAAAC
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
25 8 0.17
26 39 0.83
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.25
Consensus pattern (26 bp):
AAAAAATCTATAAATATTATAAAAAC
Found at i:10478694 original size:17 final size:17
Alignment explanation
Indices: 10478666--10478712 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
10478656 AAAAATCTAT
10478666 AAATATTATAAAAACAAA
1 AAATA-TATAAAAACAAA
* *
10478684 AAATATATAAAAATATA
1 AAATATATAAAAACAAA
*
10478701 AAATTTATAAAA
1 AAATATATAAAA
10478713 CAATTATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 21 0.81
18 5 0.19
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATATATAAAAACAAA
Found at i:10478695 original size:9 final size:9
Alignment explanation
Indices: 10478631--10478737 Score: 62
Period size: 9 Copynumber: 11.9 Consensus size: 9
10478621 AATTTATAAA
*
10478631 AAAATCTAT
1 AAAATATAT
10478640 -AAATATTAT
1 AAAATA-TAT
* *
10478649 AAAA-ACAA
1 AAAATATAT
*
10478657 AAAATCTAT
1 AAAATATAT
10478666 -AAATATTAT
1 AAAATA-TAT
* *
10478675 AAAA-ACAA
1 AAAATATAT
10478683 AAAATATAT
1 AAAATATAT
10478692 AAAA-ATAT
1 AAAATATAT
*
10478700 AAAATTTAT
1 AAAATATAT
*
10478709 AAAACAATTAT
1 AAAA-TA-TAT
10478720 AAAAATATAT
1 -AAAATATAT
10478730 AAAATATA
1 AAAATATA
10478738 GAGAAATTAA
Statistics
Matches: 73, Mismatches: 15, Indels: 20
0.68 0.14 0.19
Matches are distributed among these distances:
8 26 0.36
9 30 0.41
10 9 0.12
11 4 0.05
12 4 0.05
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (9 bp):
AAAATATAT
Found at i:10478697 original size:10 final size:10
Alignment explanation
Indices: 10478600--10478849 Score: 61
Period size: 9 Copynumber: 25.4 Consensus size: 10
10478590 AACAATTATC
10478600 AAAATATTATA
1 AAAATA-TATA
10478611 AAAA-AT-TA
1 AAAATATATA
* *
10478619 GAAATTTATA
1 AAAATATATA
* *
10478629 AAAAAATCTA
1 AAAATATATA
*
10478639 TAAATAT-TA
1 AAAATATATA
*
10478648 TAAAA-ACA-A
1 -AAAATATATA
*
10478657 AAAATCTATA
1 AAAATATATA
*
10478667 AATAT-TAT-
1 AAAATATATA
*
10478675 AAAA-ACA-A
1 AAAATATATA
10478683 AAAATATATA
1 AAAATATATA
10478693 AAAATATA-A
1 AAAATATATA
**
10478702 AATTTATA-A
1 AAAATATATA
10478711 AACAAT-TATA
1 AA-AATATATA
10478721 AAAATATATA
1 AAAATATATA
* *
10478731 AAATATAGAGA
1 AAA-ATATATA
*
10478742 AATTAATTTTAATA
1 AA--AA-TAT-ATA
10478756 AAAA-ATATGA
1 AAAATATAT-A
10478766 AAGAATA-ATGA
1 AA-AATATAT-A
10478777 AAAATATTATA
1 AAAATA-TATA
*
10478788 AAAAT-TTTA
1 AAAATATATA
10478797 AAAAT-TATA
1 AAAATATATA
*
10478806 GAGAAAT-TATT
1 -A-AAATATATA
* *
10478817 AAAATGGTAAA
1 AAAAT-ATATA
*
10478828 AAAAT-TAAA
1 AAAATATATA
10478837 AAAATAT-TA
1 AAAATATATA
10478846 AAAA
1 AAAA
10478850 CATGTATTTT
Statistics
Matches: 179, Mismatches: 32, Indels: 58
0.67 0.12 0.22
Matches are distributed among these distances:
8 17 0.09
9 58 0.32
10 53 0.30
11 39 0.22
12 6 0.03
13 2 0.01
14 4 0.02
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (10 bp):
AAAATATATA
Found at i:10478737 original size:28 final size:27
Alignment explanation
Indices: 10478611--10478737 Score: 109
Period size: 26 Copynumber: 4.6 Consensus size: 27
10478601 AAATATTATA
* *
10478611 AAAAATTAGAAATTTATAAAAAAATCTAT
1 AAAAATTATAAA-ATAT-AAAAAATCTAT
* *
10478640 AAATATTATAAAA-ACAAAAAATCTAT
1 AAAAATTATAAAATATAAAAAATCTAT
* * *
10478666 AAATATTATAAAA-ACAAAAAATATAT
1 AAAAATTATAAAATATAAAAAATCTAT
10478692 AAAAA-TATAAAATTTATAAAACAAT-TAT
1 AAAAATTATAAAA--TATAAAA-AATCTAT
10478720 AAAAATATATAAAATATA
1 AAAAAT-TATAAAATATA
10478738 GAGAAATTAA
Statistics
Matches: 85, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
25 7 0.08
26 40 0.47
27 1 0.01
28 17 0.20
29 13 0.15
30 7 0.08
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.29
Consensus pattern (27 bp):
AAAAATTATAAAATATAAAAAATCTAT
Found at i:10478812 original size:20 final size:20
Alignment explanation
Indices: 10478777--10478849 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 20
10478767 AGAATAATGA
10478777 AAAATATTATAAAAATT-TT
1 AAAATATTATAAAAATTATT
10478796 AAAA-ATTATAGAGAAATTATT
1 AAAATATTATA-A-AAATTATT
** * **
10478817 AAAATGGTAAAAAAATTAAA
1 AAAATATTATAAAAATTATT
10478837 AAAATATTA-AAAA
1 AAAATATTATAAAA
10478850 CATGTATTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
18 6 0.14
19 9 0.21
20 18 0.42
21 7 0.16
22 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.30
Consensus pattern (20 bp):
AAAATATTATAAAAATTATT
Found at i:10486759 original size:24 final size:24
Alignment explanation
Indices: 10486732--10486779 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
10486722 TAAGGGAAAA
*
10486732 TAAAAA-TAATTAGTAGATTATTAT
1 TAAAAAGTAATTA-TAAATTATTAT
*
10486756 TAAAAAGTTATTATAAATTATTAT
1 TAAAAAGTAATTATAAATTATTAT
10486780 AAATTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (24 bp):
TAAAAAGTAATTATAAATTATTAT
Found at i:10486778 original size:10 final size:10
Alignment explanation
Indices: 10486751--10486785 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
10486741 TTAGTAGATT
*
10486751 ATTATTAAAA
1 ATTATTATAA
10486761 AGTTATTATAA
1 A-TTATTATAA
10486772 ATTATTATAA
1 ATTATTATAA
10486782 ATTA
1 ATTA
10486786 AAAAAATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (10 bp):
ATTATTATAA
Found at i:10493807 original size:33 final size:33
Alignment explanation
Indices: 10493770--10493843 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
10493760 CTCTGTTTAG
*
10493770 TGTGTTGGTTAGATTAGCTCTTATGAACATTAA
1 TGTGTTGGTTAGATTAACTCTTATGAACATTAA
* * **
10493803 TGTGTTGGTTGGATTAACTCTTATGAGCATTGG
1 TGTGTTGGTTAGATTAACTCTTATGAACATTAA
10493836 TGTGTTGG
1 TGTGTTGG
10493844 AGGGATTGGC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.20, C:0.08, G:0.28, T:0.43
Consensus pattern (33 bp):
TGTGTTGGTTAGATTAACTCTTATGAACATTAA
Found at i:10496840 original size:11 final size:11
Alignment explanation
Indices: 10496824--10496851 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
10496814 TTTTGCACAC
10496824 ATTCACTACAT
1 ATTCACTACAT
10496835 ATTCACTACAT
1 ATTCACTACAT
10496846 ATTCAC
1 ATTCAC
10496852 ATTATAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.29, G:0.00, T:0.36
Consensus pattern (11 bp):
ATTCACTACAT
Found at i:10498346 original size:32 final size:35
Alignment explanation
Indices: 10498310--10498398 Score: 107
Period size: 32 Copynumber: 2.7 Consensus size: 35
10498300 ATTATTTGAA
10498310 AATTTTATATAAATATTATAATTATAA-C-TT-AT
1 AATTTTATATAAATATTATAATTATAATCATTAAT
* *
10498342 AATTTAATAT-AATATTAAAACTTATAATCATTAAT
1 AATTTTATATAAATATTATAA-TTATAATCATTAAT
*
10498377 AA-TTTATATAAATATTTTAATT
1 AATTTTATATAAATATTATAATT
10498399 TATGTTTAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
31 9 0.19
32 15 0.32
33 1 0.02
34 10 0.21
35 12 0.26
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (35 bp):
AATTTTATATAAATATTATAATTATAATCATTAAT
Found at i:10498363 original size:25 final size:26
Alignment explanation
Indices: 10498321--10498369 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
10498311 ATTTTATATA
* *
10498321 AATATTATAATTATAACTTATAATTT
1 AATATAATAATTAAAACTTATAATTT
10498347 AATATAAT-ATTAAAACTTATAAT
1 AATATAATAATTAAAACTTATAAT
10498370 CATTAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (26 bp):
AATATAATAATTAAAACTTATAATTT
Found at i:10498549 original size:12 final size:12
Alignment explanation
Indices: 10498532--10498569 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
10498522 ATTCTTACAC
10498532 AAAAAAATGTAA
1 AAAAAAATGTAA
10498544 AAAAAAA-GTTAA
1 AAAAAAATG-TAA
10498556 AAAAACAATGTAA
1 AAAAA-AATGTAA
10498569 A
1 A
10498570 TATATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 1 0.04
12 15 0.65
13 6 0.26
14 1 0.04
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAAAAATGTAA
Found at i:10500125 original size:21 final size:22
Alignment explanation
Indices: 10500101--10500153 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
10500091 TACCACTGTT
10500101 TCTAATCTCACT-GCTACAATA
1 TCTAATCTCACTCGCTACAATA
*
10500122 TCTAATCTCA-TCGCTACAGTA
1 TCTAATCTCACTCGCTACAATA
*
10500143 ACTAATCTCAC
1 TCTAATCTCAC
10500154 CGCCGCTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.32, C:0.30, G:0.06, T:0.32
Consensus pattern (22 bp):
TCTAATCTCACTCGCTACAATA
Found at i:10513638 original size:40 final size:41
Alignment explanation
Indices: 10513552--10513648 Score: 110
Period size: 40 Copynumber: 2.4 Consensus size: 41
10513542 CTACAATGTT
*
10513552 TGGCACTTAGTGTGCG-TTTGAAAATAGCTTTGGCTATAAA
1 TGGCACTTAGTGTGCGAATTGAAAATAGCTTTGGCTATAAA
* * **
10513592 TAGCACTTAGTGTGCGAATTG-AAATAG-TTTCGGCTTTATG
1 TGGCACTTAGTGTGCGAATTGAAAATAGCTTT-GGCTATAAA
*
10513632 TGGCACTAAGTGTGCGA
1 TGGCACTTAGTGTGCGA
10513649 TACCGAGATA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
39 3 0.06
40 42 0.88
41 3 0.06
ACGTcount: A:0.26, C:0.13, G:0.27, T:0.34
Consensus pattern (41 bp):
TGGCACTTAGTGTGCGAATTGAAAATAGCTTTGGCTATAAA
Found at i:10515065 original size:21 final size:21
Alignment explanation
Indices: 10515039--10515093 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
10515029 GACCTAGGGG
10515039 ACACGCCCGTGTGCCCTTCTT
1 ACACGCCCGTGTGCCCTTCTT
* *
10515060 ACACGCCCATGTACCCTTCTT
1 ACACGCCCGTGTGCCCTTCTT
*
10515081 ACACGTCCGTGTG
1 ACACGCCCGTGTG
10515094 GGAACACCGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.15, C:0.40, G:0.18, T:0.27
Consensus pattern (21 bp):
ACACGCCCGTGTGCCCTTCTT
Found at i:10516257 original size:13 final size:12
Alignment explanation
Indices: 10516231--10516265 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
10516221 CTCCGTATTG
*
10516231 GTAACAGTATCA
1 GTAACAGTAACA
10516243 GTAACGAGTAACA
1 GTAAC-AGTAACA
10516256 GTAACAGTAA
1 GTAACAGTAA
10516266 TGGTACACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.20
Consensus pattern (12 bp):
GTAACAGTAACA
Found at i:10516258 original size:6 final size:6
Alignment explanation
Indices: 10516231--10516265 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
10516221 CTCCGTATTG
*
10516231 GTAACA GTATCA GTAACGA GTAACA GTAACA GTAA
1 GTAACA GTAACA GTAAC-A GTAACA GTAACA GTAA
10516266 TGGTACACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.20
Consensus pattern (6 bp):
GTAACA
Found at i:10516368 original size:57 final size:59
Alignment explanation
Indices: 10516241--10516369 Score: 156
Period size: 57 Copynumber: 2.2 Consensus size: 59
10516231 GTAACAGTAT
*
10516241 CAGTAACGAGTAACAGTAACAGTAATGGTACACAAAGTACCTCATCGGAACAAATCTGAAA
1 CAGTAAC-AGTAACAGTAACAGTAATGGTA-ACAAAGTACCTCATCGAAACAAATCTGAAA
* * * *
10516302 CAGTAACAGTAACAGTAACAGTTA-GGT-ACAGAGTACCTCTTCGAAACGAATCCTG-AA
1 CAGTAACAGTAACAGTAACAGTAATGGTAACAAAGTACCTCATCGAAACAAAT-CTGAAA
*
10516359 CAGTCACAGTA
1 CAGTAACAGTA
10516370 GTTGACACAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
57 32 0.52
58 3 0.05
59 3 0.05
60 16 0.26
61 7 0.11
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (59 bp):
CAGTAACAGTAACAGTAACAGTAATGGTAACAAAGTACCTCATCGAAACAAATCTGAAA
Found at i:10516678 original size:3 final size:3
Alignment explanation
Indices: 10516670--10516696 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
10516660 ATTCAATACC
10516670 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
10516697 CTTACCATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:10517331 original size:9 final size:9
Alignment explanation
Indices: 10517317--10517347 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
10517307 TTTCTCTTTT
10517317 TTTTATTTC
1 TTTTATTTC
10517326 TTTTATTTC
1 TTTTATTTC
*
10517335 ATTTATTTC
1 TTTTATTTC
10517344 TTTT
1 TTTT
10517348 TTTTAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTATTTC
Found at i:10517768 original size:25 final size:25
Alignment explanation
Indices: 10517712--10517761 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
10517702 TTATCCTTAA
*
10517712 TTTAAGTTAATTCACTTCATTAAAC
1 TTTAAATTAATTCACTTCATTAAAC
*
10517737 TTTAAATTAA-TCAC-TCATTTAAC
1 TTTAAATTAATTCACTTCATTAAAC
10517760 TT
1 TT
10517762 CGTAAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 10 0.43
24 4 0.17
25 9 0.39
ACGTcount: A:0.36, C:0.16, G:0.02, T:0.46
Consensus pattern (25 bp):
TTTAAATTAATTCACTTCATTAAAC
Found at i:10526279 original size:12 final size:12
Alignment explanation
Indices: 10526262--10526286 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10526252 TTCATATCTT
10526262 ATTCAATCTCTA
1 ATTCAATCTCTA
10526274 ATTCAATCTCTA
1 ATTCAATCTCTA
10526286 A
1 A
10526287 AATTTTTGGT
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:0.24, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTCAATCTCTA
Found at i:10526407 original size:40 final size:40
Alignment explanation
Indices: 10526352--10526431 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
10526342 TGCAATATGA
*
10526352 TGATAACTATCATAAGTTCATTTCAACTAATCATGAACTT
1 TGATAACTATCATAAGTTCATTTCAACTAATAATGAACTT
*
10526392 TGATAATTATCATAAGTTCATTTCAACTAATAATGAACTT
1 TGATAACTATCATAAGTTCATTTCAACTAATAATGAACTT
10526432 ACCATTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (40 bp):
TGATAACTATCATAAGTTCATTTCAACTAATAATGAACTT
Found at i:10527012 original size:43 final size:43
Alignment explanation
Indices: 10526951--10527036 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
10526941 ATCACATGTA
* *
10526951 TCGCATCCATTATGAACTCAGACCAT-TCAACGAGCTCGGATGC
1 TCGCATCCATAATGAACTCAGACC-TCTCAACGAGCTCAGATGC
* *
10526994 TCGCATCCATAATGAACTCGGACCTCTCAACTAGCTCAGATGC
1 TCGCATCCATAATGAACTCAGACCTCTCAACGAGCTCAGATGC
10527037 CACATATATC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 1 0.03
43 37 0.97
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.23
Consensus pattern (43 bp):
TCGCATCCATAATGAACTCAGACCTCTCAACGAGCTCAGATGC
Found at i:10555222 original size:203 final size:203
Alignment explanation
Indices: 10554883--10555285 Score: 601
Period size: 203 Copynumber: 2.0 Consensus size: 203
10554873 ATCATCCCCC
* * *
10554883 CTCACTCTCATCGGCCAGATATCCCCACGGGGCATCTCGAGCATGCTAAATATGAGAATGATCAA
1 CTCACTCTCATCGGCCAAATATCCCCACAGGGCATATCGAGCATGCTAAATATGAGAATGATCAA
* * * *
10554948 GAAACGATATGGCACATACCCTTCTCAATACCGCCGAGTCTAGTCGACTGAGGAGAAGGACCCAA
66 GAAACGATATGGCACATACCCTTCTCAATACCACCGAGTCCAGTCCACCGAGGAGAAGGACCCAA
10555013 AGGACATTACTGATGATGTCTCC-ACACGTCATGAGGACCCACCGTCTCAGCCACCACCCATCCA
131 AGGACATTACTGATGATGTC-CCTACACGTCATGAGGACCCACCGTCTCAGCCACCACCCATCCA
10555077 TCATCCTTT
195 TCATCCTTT
* *
10555086 CTCACTCTCATCGGCCAAATGTCCCCACAGGGCATATCGAGCATGCTAAATATGAGGATGATCAA
1 CTCACTCTCATCGGCCAAATATCCCCACAGGGCATATCGAGCATGCTAAATATGAGAATGATCAA
* * * * ** * * *
10555151 GAAACGATGTGGCACCTACCCTTCTCAGTACTACCTCGTCCAGTCCACCGAGGAGGAGGACTCAG
66 GAAACGATATGGCACATACCCTTCTCAATACCACCGAGTCCAGTCCACCGAGGAGAAGGACCCAA
* * *
10555216 AGGACATTATTGATGATGTCCCTCCACGTCATGAGGACCCACCGTCTCAGCCACCACCTATCCAT
131 AGGACATTACTGATGATGTCCCTACACGTCATGAGGACCCACCGTCTCAGCCACCACCCATCCAT
10555281 CATCC
196 CATCC
10555286 AGTTCATGCG
Statistics
Matches: 178, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
202 2 0.01
203 176 0.99
ACGTcount: A:0.28, C:0.32, G:0.20, T:0.21
Consensus pattern (203 bp):
CTCACTCTCATCGGCCAAATATCCCCACAGGGCATATCGAGCATGCTAAATATGAGAATGATCAA
GAAACGATATGGCACATACCCTTCTCAATACCACCGAGTCCAGTCCACCGAGGAGAAGGACCCAA
AGGACATTACTGATGATGTCCCTACACGTCATGAGGACCCACCGTCTCAGCCACCACCCATCCAT
CATCCTTT
Found at i:10563185 original size:13 final size:13
Alignment explanation
Indices: 10563167--10563197 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
10563157 AATGAGGGCA
*
10563167 CACGGGTGTGCCC
1 CACGGGTATGCCC
10563180 CACGGGTATGCCC
1 CACGGGTATGCCC
10563193 CACGG
1 CACGG
10563198 CCGTGAGCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.39, G:0.35, T:0.13
Consensus pattern (13 bp):
CACGGGTATGCCC
Found at i:10566540 original size:20 final size:20
Alignment explanation
Indices: 10566499--10566541 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
10566489 CTAGTGCTGT
* *
10566499 ATAGAGGCACCGAAATGTAA
1 ATAGAGACACCGAAATGCAA
10566519 ATAGAGACACC-AAAGTGCAA
1 ATAGAGACACCGAAA-TGCAA
10566539 ATA
1 ATA
10566542 AAGAGCACAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.49, C:0.16, G:0.21, T:0.14
Consensus pattern (20 bp):
ATAGAGACACCGAAATGCAA
Found at i:10569048 original size:23 final size:22
Alignment explanation
Indices: 10569021--10569068 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
10569011 GGATTTGCAC
*
10569021 TAATAATTTC-TAACTTGATAGAT
1 TAATAATTGCTTAACTT-ATA-AT
10569044 TAATAATTGCTTAACTTATAAT
1 TAATAATTGCTTAACTTATAAT
10569066 TAA
1 TAA
10569069 CTTGATAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 5 0.22
23 12 0.52
24 6 0.26
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (22 bp):
TAATAATTGCTTAACTTATAAT
Found at i:10569296 original size:17 final size:17
Alignment explanation
Indices: 10569274--10569308 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
10569264 TTCTTATATG
10569274 AATTCAAGTACTAGCTT
1 AATTCAAGTACTAGCTT
*
10569291 AATTCATGTACTAGCTT
1 AATTCAAGTACTAGCTT
10569308 A
1 A
10569309 TTGAAGATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.37
Consensus pattern (17 bp):
AATTCAAGTACTAGCTT
Found at i:10571977 original size:18 final size:17
Alignment explanation
Indices: 10571954--10572006 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
10571944 GTACAATTCA
10571954 AATAATTTATTTTAATTT
1 AATAATTTA-TTTAATTT
* *
10571972 AATAATATATTTCATTT
1 AATAATTTATTTAATTT
* *
10571989 AATTATTTTACTTAATTT
1 AA-TAATTTATTTAATTT
10572007 TTTATTTCTA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
17 9 0.32
18 19 0.68
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (17 bp):
AATAATTTATTTAATTT
Found at i:10581372 original size:20 final size:21
Alignment explanation
Indices: 10581341--10581395 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 21
10581331 ATAAAATCAA
*
10581341 TAAAATTT-ATAAAAAATA-T
1 TAAATTTTAATAAAAAATATT
*
10581360 TAATTTTTAAT-AAAAATATT
1 TAAATTTTAATAAAAAATATT
*
10581380 TAAATTTTATTAAAAA
1 TAAATTTTAATAAAAA
10581396 TTAGAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 13 0.45
20 12 0.41
21 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAATTTTAATAAAAAATATT
Found at i:10581396 original size:20 final size:19
Alignment explanation
Indices: 10581341--10581396 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 19
10581331 ATAAAATCAA
* *
10581341 TAAAATTTATAAAAAATAT
1 TAAATTTTATTAAAAATAT
* *
10581360 TAATTTTTAATAAAAATATT
1 TAAATTTTATTAAAAATA-T
10581380 TAAATTTTATTAAAAAT
1 TAAATTTTATTAAAAAT
10581397 TAGAAAAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAATTTTATTAAAAATAT
Found at i:10581422 original size:29 final size:29
Alignment explanation
Indices: 10581390--10581462 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 29
10581380 TAAATTTTAT
10581390 TAAAAATTAGAAAAAAATTATAAAAATAG
1 TAAAAATTAGAAAAAAATTATAAAAATAG
* * ** * *
10581419 TAAAAATTTGTAAAATTTTATAAATATCG
1 TAAAAATTAGAAAAAAATTATAAAAATAG
*
10581448 TAAAAAATTATAAAA
1 T-AAAAATTAGAAAA
10581463 TGCATAAAAA
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
29 24 0.71
30 10 0.29
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (29 bp):
TAAAAATTAGAAAAAAATTATAAAAATAG
Found at i:10581463 original size:29 final size:29
Alignment explanation
Indices: 10581407--10581463 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
10581397 TAGAAAAAAA
* *
10581407 TTATAAAAATAGTAAAAATTTGTAAAATT
1 TTATAAAAATAGTAAAAAATTATAAAATT
* *
10581436 TTATAAATATCGTAAAAAATTATAAAAT
1 TTATAAAAATAGTAAAAAATTATAAAAT
10581464 GCATAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (29 bp):
TTATAAAAATAGTAAAAAATTATAAAATT
Found at i:10585729 original size:7 final size:7
Alignment explanation
Indices: 10585719--10585752 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
10585709 TTGTGTTTGT
10585719 GGTTTAG
1 GGTTTAG
10585726 GGTTTAG
1 GGTTTAG
*
10585733 GGTTTAT
1 GGTTTAG
*
10585740 GTTTTAG
1 GGTTTAG
10585747 GGTTTA
1 GGTTTA
10585753 AGGTCTCAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (7 bp):
GGTTTAG
Found at i:10585729 original size:21 final size:21
Alignment explanation
Indices: 10585713--10585752 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
10585703 TAGGTTTTGT
10585713 GTTTGTGGTTTAGGGTTTAGG
1 GTTTGTGGTTTAGGGTTTAGG
* *
10585734 GTTTATGTTTTAGGGTTTA
1 GTTTGTGGTTTAGGGTTTA
10585753 AGGTCTCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.35, T:0.53
Consensus pattern (21 bp):
GTTTGTGGTTTAGGGTTTAGG
Found at i:10585766 original size:21 final size:20
Alignment explanation
Indices: 10585720--10585778 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
10585710 TGTGTTTGTG
* * *
10585720 GTTTAGGGTTTAGGGTTTAT
1 GTTTAGGGTTTAAGGTTCAA
10585740 GTTTTAGGGTTTAAGGTCTCAA
1 G-TTTAGGGTTTAAGGT-TCAA
*
10585762 GTTTAGGGTTTCAGGTT
1 GTTTAGGGTTTAAGGTT
10585779 TAGAGTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 2 0.06
21 28 0.85
22 3 0.09
ACGTcount: A:0.17, C:0.05, G:0.32, T:0.46
Consensus pattern (20 bp):
GTTTAGGGTTTAAGGTTCAA
Found at i:10585781 original size:14 final size:15
Alignment explanation
Indices: 10585719--10585781 Score: 53
Period size: 14 Copynumber: 4.5 Consensus size: 15
10585709 TTGTGTTTGT
10585719 GGTTTAGGGTTT-AG
1 GGTTTAGGGTTTCAG
* *
10585733 GGTTTA-TGTTTTAG
1 GGTTTAGGGTTTCAG
* *
10585747 GGTTTAAGGTCTCA-
1 GGTTTAGGGTTTCAG
*
10585761 AGTTTAGGGTTTCA-
1 GGTTTAGGGTTTCAG
10585775 GGTTTAG
1 GGTTTAG
10585782 AGTATAATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
13 4 0.10
14 31 0.79
15 4 0.10
ACGTcount: A:0.17, C:0.05, G:0.33, T:0.44
Consensus pattern (15 bp):
GGTTTAGGGTTTCAG
Found at i:10588247 original size:39 final size:39
Alignment explanation
Indices: 10588204--10588281 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
10588194 AGGTAGAGAA
*
10588204 CTTAAATTTGTTATTTTGCATGATTATTTGAGATCTGCT
1 CTTAAATTTGTTATTCTGCATGATTATTTGAGATCTGCT
*
10588243 CTTAAATTTGTTATTCTGCATGATTATTTGAGATTTGCT
1 CTTAAATTTGTTATTCTGCATGATTATTTGAGATCTGCT
10588282 TCTGTCAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.51
Consensus pattern (39 bp):
CTTAAATTTGTTATTCTGCATGATTATTTGAGATCTGCT
Found at i:10588271 original size:20 final size:20
Alignment explanation
Indices: 10588209--10588272 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
10588199 GAGAACTTAA
*
10588209 ATTTGTTATTTTGCATGATT
1 ATTTGTTATTCTGCATGATT
** *
10588229 ATTTGAGA-TCTGC-T-CTT
1 ATTTGTTATTCTGCATGATT
10588246 AAATTTGTTATTCTGCATGATT
1 --ATTTGTTATTCTGCATGATT
10588268 ATTTG
1 ATTTG
10588273 AGATTTGCTT
Statistics
Matches: 32, Mismatches: 7, Indels: 10
0.65 0.14 0.20
Matches are distributed among these distances:
17 2 0.06
18 1 0.03
19 10 0.31
20 16 0.50
21 1 0.03
22 2 0.06
ACGTcount: A:0.22, C:0.09, G:0.16, T:0.53
Consensus pattern (20 bp):
ATTTGTTATTCTGCATGATT
Done.