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 30 of 325
Found at i:6981746 original size:6 final size:6
Alignment explanation
Indices: 6981731--6981789 Score: 86
Period size: 6 Copynumber: 10.2 Consensus size: 6
6981721 AGTCCATTTA
*
6981731 TTTA-T TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATC
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
6981778 TTT-CT TTTATT T
1 TTTATT TTTATT T
6981790 ATTTCTAAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
5 7 0.15
6 41 0.85
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTATT
Found at i:6987704 original size:2 final size:2
Alignment explanation
Indices: 6987692--6987730 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
6987682 ACATAAGAAG
6987692 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6987731 CTCTGCTTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6991839 original size:33 final size:33
Alignment explanation
Indices: 6991787--6991855 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
6991777 GAAAGACCTT
* * *
6991787 TTGGTAAAACGATTGAACTTCGACGAGCCTAAG
1 TTGGGAAAACAATTCAACTTCGACGAGCCTAAG
*
6991820 TTGGGAAAACAATTCAACTTCGACGAGTCTAAG
1 TTGGGAAAACAATTCAACTTCGACGAGCCTAAG
6991853 TTG
1 TTG
6991856 AGGGACTATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.26
Consensus pattern (33 bp):
TTGGGAAAACAATTCAACTTCGACGAGCCTAAG
Found at i:6993401 original size:5 final size:6
Alignment explanation
Indices: 6993384--6993411 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
6993374 CTACTTTAGC
6993384 TATTTT TATTTT TATTTT TATTTT TATT
1 TATTTT TATTTT TATTTT TATTTT TATT
6993412 GCAATTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TATTTT
Found at i:6998723 original size:6 final size:6
Alignment explanation
Indices: 6998708--6998778 Score: 101
Period size: 6 Copynumber: 12.2 Consensus size: 6
6998698 AGTCCATTTA
*
6998708 TTTA-T TTTATT TTTATT TTTATT TTTACT TTTATT TTTATT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
* *
6998755 TTTATT TTTATA TTT-CT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT T
6998779 ATTTCCGAAG
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
5 7 0.12
6 51 0.88
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTATT
Found at i:6999753 original size:9 final size:10
Alignment explanation
Indices: 6999726--6999756 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
6999716 TAGTCCCTGA
6999726 ATTATTTTTT
1 ATTATTTTTT
6999736 ATTATTTTTT
1 ATTATTTTTT
*
6999746 CTTATTTTTT
1 ATTATTTTTT
6999756 A
1 A
6999757 AAAAAAAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (10 bp):
ATTATTTTTT
Found at i:7016923 original size:30 final size:30
Alignment explanation
Indices: 7016889--7016951 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
7016879 ATTTATTTTA
7016889 TTGTTAATTTTCTTATTATTTTA-AAGGCAT
1 TTGTTAATTTTCTTATTATTTTAGAA-GCAT
*
7016919 TTGTTAATTTTTTTATTATTTTAGAAGCAT
1 TTGTTAATTTTCTTATTATTTTAGAAGCAT
7016949 TTG
1 TTG
7016952 CTTGTTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.94
31 2 0.06
ACGTcount: A:0.25, C:0.05, G:0.11, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTCTTATTATTTTAGAAGCAT
Found at i:7019136 original size:3 final size:3
Alignment explanation
Indices: 7019128--7019167 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
7019118 AGTAAAACTT
7019128 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
7019168 AAGAAGAAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:7020313 original size:2 final size:2
Alignment explanation
Indices: 7020306--7020342 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
7020296 TCACTTCCCT
7020306 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7020343 GCACACACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7022188 original size:67 final size:66
Alignment explanation
Indices: 7022081--7022219 Score: 260
Period size: 67 Copynumber: 2.1 Consensus size: 66
7022071 CAAGGAATAA
7022081 AAGTATTTATTAATTATAAAAAAATAAAAGGAAAAACTAACTTAACGAGTAAGTAGTTACTTGGG
1 AAGTATTTATTAATTATAAAAAAATAAAAGGAAAAACTAACTTAACGAGTAAGTAGTTACTTGGG
7022146 T
66 T
7022147 AAGTATTTATTAATTATAAAAAAAATAAAAGGAAAAACTAACTTAACGAGTAAGTAGTTACTTGG
1 AAGTATTTATTAATTAT-AAAAAAATAAAAGGAAAAACTAACTTAACGAGTAAGTAGTTACTTGG
7022212 GT
65 GT
7022214 ACAGTA
1 A-AGTA
7022220 ATGACTGAAA
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
66 17 0.24
67 50 0.70
68 4 0.06
ACGTcount: A:0.49, C:0.06, G:0.15, T:0.29
Consensus pattern (66 bp):
AAGTATTTATTAATTATAAAAAAATAAAAGGAAAAACTAACTTAACGAGTAAGTAGTTACTTGGG
T
Found at i:7024399 original size:14 final size:14
Alignment explanation
Indices: 7024380--7024407 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
7024370 CAATGTCAAT
7024380 GAAAAATAAATAAG
1 GAAAAATAAATAAG
7024394 GAAAAATAAATAAG
1 GAAAAATAAATAAG
7024408 ATGAGGGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
GAAAAATAAATAAG
Found at i:7025440 original size:18 final size:19
Alignment explanation
Indices: 7025398--7025441 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
7025388 GAAATCCTAT
*
7025398 ATAAATATTTTATTATAAT
1 ATAAATATTTTATTATAAC
*
7025417 AGAAATATTTTA-TATAAC
1 ATAAATATTTTATTATAAC
7025435 ATAAATA
1 ATAAATA
7025442 AAATTCTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
ATAAATATTTTATTATAAC
Found at i:7028740 original size:26 final size:26
Alignment explanation
Indices: 7028702--7028811 Score: 132
Period size: 26 Copynumber: 4.2 Consensus size: 26
7028692 TGATACAAAT
7028702 TGATAA-AAGGTTAGGTAAATATTCCA
1 TGATAATAA-GTTAGGTAAATATTCCA
7028728 TGATAATAAGTTAGGTAAATATTCCA
1 TGATAATAAGTTAGGTAAATATTCCA
** * *
7028754 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAAGTTAGGTAAATATTCCA
** * *
7028780 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAAGTTAGGTAAATATTCCA
7028806 TGATAA
1 TGATAA
7028812 GAATTTCATG
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
26 77 0.97
27 2 0.03
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.35
Consensus pattern (26 bp):
TGATAATAAGTTAGGTAAATATTCCA
Found at i:7028759 original size:52 final size:52
Alignment explanation
Indices: 7028702--7028811 Score: 148
Period size: 52 Copynumber: 2.1 Consensus size: 52
7028692 TGATACAAAT
7028702 TGATAAAAGGTTAGGTAAATATTCCATGATAATAAGTTAGGTAAATATTCCA
1 TGATAAAAGGTTAGGTAAATATTCCATGATAATAAGTTAGGTAAATATTCCA
** * * ** * *
7028754 TGATAATGGGTTAGGTAAATGTTTCATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAAAAGGTTAGGTAAATATTCCATGATAATAAGTTAGGTAAATATTCCA
7028806 TGATAA
1 TGATAA
7028812 GAATTTCATG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.35
Consensus pattern (52 bp):
TGATAAAAGGTTAGGTAAATATTCCATGATAATAAGTTAGGTAAATATTCCA
Found at i:7040428 original size:20 final size:20
Alignment explanation
Indices: 7040391--7040430 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
7040381 AGCCGAGTCA
* *
7040391 TGATAACATGGTAGATTGAT
1 TGATAACATGGCACATTGAT
*
7040411 TGATAATATGGCACATTGAT
1 TGATAACATGGCACATTGAT
7040431 CAAGTTAATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (20 bp):
TGATAACATGGCACATTGAT
Found at i:7041036 original size:27 final size:28
Alignment explanation
Indices: 7040997--7041049 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
7040987 ATGTTTTGCA
* * *
7040997 ATTTTTGCGATTTTTTTAAATTTTTTTT
1 ATTTTTACGATTTTTATAAATCTTTTTT
7041025 ATTTTTAC-ATTTTTATAAATCTTTT
1 ATTTTTACGATTTTTATAAATCTTTT
7041050 GATGAATTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.23, C:0.06, G:0.04, T:0.68
Consensus pattern (28 bp):
ATTTTTACGATTTTTATAAATCTTTTTT
Found at i:7041206 original size:42 final size:42
Alignment explanation
Indices: 7041158--7041257 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 42
7041148 TTTTTCAATA
*
7041158 TTTTAAATTGTTTTTATA-TATTTTTATTAGATTTT-AA-AATTT
1 TTTTAAATT-TTTTTATACTAGTTTTA-TA-ATTTTGAATAATTT
7041200 TTTTAAATATTTTTT-TACTAGTTTTATAATTTTGAATAATTT
1 TTTTAAAT-TTTTTTATACTAGTTTTATAATTTTGAATAATTT
* *
7041242 TTTCAAGTTTTTTTAT
1 TTTTAAATTTTTTTAT
7041258 TTTTAATTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
40 5 0.10
41 12 0.24
42 32 0.64
43 1 0.02
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (42 bp):
TTTTAAATTTTTTTATACTAGTTTTATAATTTTGAATAATTT
Found at i:7041214 original size:32 final size:32
Alignment explanation
Indices: 7041157--7041232 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
7041147 ATTTTTCAAT
* *
7041157 ATTTT-AAATTGTTTTTATATA-TTTTTATTAG
1 ATTTTAAAATT-TTTTTAAATATTTTTTACTAG
7041188 ATTTTAAAATTTTTTTAAATATTTTTTTACTAG
1 ATTTTAAAATTTTTTTAAATA-TTTTTTACTAG
*
7041221 -TTTTATAATTTT
1 ATTTTAAAATTTT
7041233 GAATAATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
31 14 0.36
32 16 0.41
33 9 0.23
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.64
Consensus pattern (32 bp):
ATTTTAAAATTTTTTTAAATATTTTTTACTAG
Found at i:7041834 original size:12 final size:10
Alignment explanation
Indices: 7041809--7041843 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
7041799 TACAATTTCC
7041809 ATTTTTTATA
1 ATTTTTTATA
7041819 ATTTTTTATA
1 ATTTTTTATA
* *
7041829 ATATTTTACA
1 ATTTTTTATA
7041839 ATTTT
1 ATTTT
7041844 AATATTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:7041842 original size:8 final size:8
Alignment explanation
Indices: 7041831--7041887 Score: 53
Period size: 8 Copynumber: 7.1 Consensus size: 8
7041821 TTTTTATAAT
*
7041831 ATTTTACA
1 ATTTTAAA
*
7041839 ATTTTAAT
1 ATTTTAAA
*
7041847 ATTTTATA
1 ATTTTAAA
*
7041855 TTTTTAAA
1 ATTTTAAA
7041863 ATTTTTAAA
1 A-TTTTAAA
*
7041872 ATTTTATA
1 ATTTTAAA
7041880 A-TTTAAA
1 ATTTTAAA
7041887 A
1 A
7041888 AACTATGTGT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
7 6 0.15
8 25 0.64
9 8 0.21
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (8 bp):
ATTTTAAA
Found at i:7041848 original size:16 final size:16
Alignment explanation
Indices: 7041827--7041887 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
7041817 TAATTTTTTA
*
7041827 TAATATTTTACAATTT
1 TAATATTTTAAAATTT
* *
7041843 TAATATTTTATATTTT
1 TAATATTTTAAAATTT
*
7041859 TAAAATTTTTAAAATTT
1 TAATA-TTTTAAAATTT
*
7041876 T-ATAATTTAAAA
1 TAATATTTTAAAA
7041888 AACTATGTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
15 7 0.19
16 20 0.54
17 10 0.27
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
TAATATTTTAAAATTT
Found at i:7041875 original size:25 final size:24
Alignment explanation
Indices: 7041822--7041888 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 24
7041812 TTTTATAATT
* *
7041822 TTTTATAATATTTTACAATTTTAATA
1 TTTTAT-AT-TTTTAAAATTTTAAAA
7041848 TTTTATATTTTTAAAATTTTTAAAA
1 TTTTATATTTTTAAAA-TTTTAAAA
* *
7041873 TTTTATAATTTAAAAA
1 TTTTATATTTTTAAAA
7041889 ACTATGTGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 7 0.19
25 23 0.64
26 6 0.17
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTATATTTTTAAAATTTTAAAA
Found at i:7043216 original size:2 final size:2
Alignment explanation
Indices: 7043209--7043243 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
7043199 ATATGTGCAA
* *
7043209 AT AT AT AT AT AT AT AT AT AT AT AC AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7043244 AAATATACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:7043263 original size:19 final size:19
Alignment explanation
Indices: 7043207--7043259 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 19
7043197 TGATATGTGC
*
7043207 AAATATATATATATATAT-
1 AAATATACATATATATATA
* *
7043225 ATATATACATATGTATATA
1 AAATATACATATATATATA
7043244 AAATATACATA-ATATA
1 AAATATACATATATATA
7043260 ATAATAGTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
18 19 0.66
19 10 0.34
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (19 bp):
AAATATACATATATATATA
Found at i:7043344 original size:2 final size:2
Alignment explanation
Indices: 7043331--7043474 Score: 81
Period size: 2 Copynumber: 75.0 Consensus size: 2
7043321 GGAATTTAAA
* *
7043331 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
7043372 AGT AT TT A- AG A- AT AT AT AC AT A- AG AA AT AT AT A- ACT A- AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
** * * *
7043411 GGC AT AT AT AC AT A- AT AT AT AT AT A- AT AC AC AT A- AT AT AT
1 -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
7043451 AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
7043475 TAAAATGATA
Statistics
Matches: 110, Mismatches: 20, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
1 9 0.08
2 98 0.89
3 3 0.03
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.40
Consensus pattern (2 bp):
AT
Found at i:7044327 original size:14 final size:15
Alignment explanation
Indices: 7044292--7044327 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
7044282 TCTATTGTTT
7044292 TTTTTTTGCTGGAAA
1 TTTTTTTGCTGGAAA
7044307 TTTTTTT-CTGGAAA
1 TTTTTTTGCTGGAAA
7044321 TTTTTTT
1 TTTTTTT
7044328 TTGGTGCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.17, C:0.06, G:0.14, T:0.64
Consensus pattern (15 bp):
TTTTTTTGCTGGAAA
Found at i:7044328 original size:15 final size:16
Alignment explanation
Indices: 7044291--7044328 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
7044281 TTCTATTGTT
7044291 TTTTTTTTGCTGGAAA
1 TTTTTTTTGCTGGAAA
7044307 -TTTTTTT-CTGGAAA
1 TTTTTTTTGCTGGAAA
7044321 TTTTTTTT
1 TTTTTTTT
7044329 TGGTGCTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.16, C:0.05, G:0.13, T:0.66
Consensus pattern (16 bp):
TTTTTTTTGCTGGAAA
Found at i:7044336 original size:34 final size:31
Alignment explanation
Indices: 7044289--7044362 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 31
7044279 CGTTCTATTG
*
7044289 TTTTTTTTT-TGCTGGAAATTTTTTTCTGGAAA
1 TTTTTTTTTGTGCTGG-AATTTTTTGCT-GAAA
**
7044321 TTTTTTTTTGGTGCTGGAATTTTTTGCTGATT
1 TTTTTTTTT-GTGCTGGAATTTTTTGCTGAAA
7044353 TTTTTTTTTG
1 TTTTTTTTTG
7044363 CTTCCCCTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
31 1 0.03
32 20 0.54
33 10 0.27
34 6 0.16
ACGTcount: A:0.12, C:0.05, G:0.18, T:0.65
Consensus pattern (31 bp):
TTTTTTTTTGTGCTGGAATTTTTTGCTGAAA
Found at i:7044806 original size:35 final size:35
Alignment explanation
Indices: 7044766--7044871 Score: 194
Period size: 35 Copynumber: 3.0 Consensus size: 35
7044756 GGGGTGTGTG
*
7044766 ATGGTGCTGGCGGCAGACAGCATGGGAGAGTGGGA
1 ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
*
7044801 GTGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1 ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
7044836 ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1 ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
7044871 A
1 A
7044872 GAGGCAAGTG
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.23, C:0.12, G:0.49, T:0.16
Consensus pattern (35 bp):
ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
Found at i:7045656 original size:48 final size:50
Alignment explanation
Indices: 7045580--7045726 Score: 183
Period size: 54 Copynumber: 2.9 Consensus size: 50
7045570 ATATGACCTA
**
7045580 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAAAACAA-AA-
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAATAAC
* *
7045628 AGG-TACAACTCACCTCTCGCAATATGAGTTGCTTTTTGAAAGACAGAAATTAAC
1 AGGCT-CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA-A-A-CAA-TAAC
*
7045682 AGGCTCAACTCACCTCTCGCAATGTGAGTTGATTTTTGAAAAACA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
7045727 GGAATTGGAA
Statistics
Matches: 84, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
47 1 0.01
48 36 0.43
49 1 0.01
50 1 0.01
51 3 0.04
52 1 0.01
53 3 0.04
54 37 0.44
55 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (50 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAATAAC
Found at i:7045751 original size:24 final size:24
Alignment explanation
Indices: 7045719--7045768 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
7045709 GTTGATTTTT
7045719 GAAAAACAGGAATTGGAAAGTAGA
1 GAAAAACAGGAATTGGAAAGTAGA
7045743 GAAAAACAGGAATTGGAAAGTAGA
1 GAAAAACAGGAATTGGAAAGTAGA
7045767 GA
1 GA
7045769 CTGAAAATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.54, C:0.04, G:0.30, T:0.12
Consensus pattern (24 bp):
GAAAAACAGGAATTGGAAAGTAGA
Found at i:7046019 original size:70 final size:70
Alignment explanation
Indices: 7045906--7046178 Score: 510
Period size: 70 Copynumber: 3.9 Consensus size: 70
7045896 CATAAATTGA
*
7045906 AAATTGAAATTACCTCAACGTGTTTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGA
1 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGA
7045971 AACAT
66 AACAT
*
7045976 AAATTGAAATTACCTCAACGTGTCTTGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTGA
1 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGA
7046041 AACAT
66 AACAT
*
7046046 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCCATATGAGTTGATTTTGA
1 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGA
7046111 AACAT
66 AACAT
*
7046116 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATGTGAGTTGATTTT
1 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
7046179 CTGTCACTTG
Statistics
Matches: 197, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 197 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (70 bp):
AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGA
AACAT
Found at i:7046135 original size:140 final size:143
Alignment explanation
Indices: 7045807--7046178 Score: 633
Period size: 140 Copynumber: 2.6 Consensus size: 143
7045797 TCAACTCACC
7045807 TATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTC
1 TATGAGTTGA-TTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTC
* *
7045872 TCGCCATATGAGTTGATTTTGAAACATAAATTGAAAATTGAAATTACCTCAACGTGTTTTGAGGC
65 TCGCAATATGAGTTGATTTTGAAAC---AATT-AAAATTGAAATTACCTCAACGTGTCTTGAGGC
7045937 TCAACTCACCTCTCGCAA
126 TCAACTCACCTCTCGCAA
*
7045955 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTTAACTCACCTCT
1 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
7046020 CGCAATATGAGTTGATTTTGAAAC-A-T-AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAAC
66 CGCAATATGAGTTGATTTTGAAACAATTAAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAAC
*
7046082 TCACCTCTCGCCA
131 TCACCTCTCGCAA
7046095 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
1 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
*
7046160 CGCAATGTGAGTTGATTTT
66 CGCAATATGAGTTGATTTT
7046179 CTGTCACTTG
Statistics
Matches: 218, Mismatches: 6, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
140 129 0.59
142 1 0.00
143 1 0.00
147 77 0.35
148 10 0.05
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (143 bp):
TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
CGCAATATGAGTTGATTTTGAAACAATTAAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAAC
TCACCTCTCGCAA
Found at i:7056625 original size:2 final size:2
Alignment explanation
Indices: 7056618--7056654 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
7056608 ATGTGCAAAA
* *
7056618 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7056655 AAATATACAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:7056846 original size:22 final size:21
Alignment explanation
Indices: 7056814--7056863 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 21
7056804 AACTAATGGC
*
7056814 ATATATACATAATATATATAT
1 ATATACACATAATATATATAT
7056835 ATAATACACATAATATATATAT
1 AT-ATACACATAATATATATAT
7056857 ATATACA
1 ATATACA
7056864 TATTAGAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATACACATAATATATATAT
Found at i:7057400 original size:11 final size:12
Alignment explanation
Indices: 7057384--7057420 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
7057374 AGAAAAAAAA
7057384 GGAAGAGAG-AG
1 GGAAGAGAGAAG
7057395 GGAAGAGAGAAG
1 GGAAGAGAGAAG
7057407 GG-AGAGAGAAG
1 GGAAGAGAGAAG
7057418 GGA
1 GGA
7057421 GGGGAAGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 20 0.83
12 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (12 bp):
GGAAGAGAGAAG
Found at i:7057421 original size:11 final size:11
Alignment explanation
Indices: 7057382--7057430 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
7057372 AAAGAAAAAA
*
7057382 AAGGAAGAGAG
1 AAGGGAGAGAG
7057393 -AGGGAAGAGAG
1 AAGGG-AGAGAG
7057404 AAGGGAGAGAG
1 AAGGGAGAGAG
*
7057415 AAGGGAG-GGG
1 AAGGGAGAGAG
7057425 AAGGGA
1 AAGGGA
7057431 AATCCGGTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 11 0.32
11 19 0.56
12 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (11 bp):
AAGGGAGAGAG
Found at i:7058209 original size:35 final size:35
Alignment explanation
Indices: 7058170--7058238 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
7058160 GGGTGTGTGA
7058170 TGGTGCTGGCGGCAGACAGCATGGGAGAGTGGGAG
1 TGGTGCTGGCGGCAGACAGCATGGGAGAGTGGGAG
*
7058205 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1 TGGTGCTGGCGGCAGACAGCATGGGAGAGTGGGA
7058239 AGAGGCAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.20, C:0.13, G:0.51, T:0.16
Consensus pattern (35 bp):
TGGTGCTGGCGGCAGACAGCATGGGAGAGTGGGAG
Found at i:7068735 original size:12 final size:12
Alignment explanation
Indices: 7068714--7068743 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
7068704 CTTTTAAAAG
*
7068714 AATGGCGATATA
1 AATGGTGATATA
7068726 AATGGTGATATA
1 AATGGTGATATA
7068738 AATGGT
1 AATGGT
7068744 TAGCAATACA
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:0.40, C:0.03, G:0.27, T:0.30
Consensus pattern (12 bp):
AATGGTGATATA
Found at i:7069862 original size:136 final size:137
Alignment explanation
Indices: 7069609--7069894 Score: 538
Period size: 136 Copynumber: 2.1 Consensus size: 137
7069599 TATTGGGCCT
**
7069609 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
7069674 AGCCCCTTATTCAGATAACAGCATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGCATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
7069739 CATATGC
131 CATATGC
7069746 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACT-GGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
7069810 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGCATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
7069875 CATATGC
131 CATATGC
7069882 AAGCCCATTTGGG
1 AAGCCCATTTGGG
7069895 GAGACTACTC
Statistics
Matches: 146, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
136 90 0.62
137 56 0.38
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGCATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
CATATGC
Found at i:7070171 original size:26 final size:26
Alignment explanation
Indices: 7070142--7070195 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
7070132 TCAAACATGC
7070142 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGT-AATTTAACACCTAGGGGT
* **
7070168 ATTTTGGTAATTTTGCACCTAGGGGT
1 ATTTAGGTAATTTAACACCTAGGGGT
7070194 AT
1 AT
7070196 AACAGTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (26 bp):
ATTTAGGTAATTTAACACCTAGGGGT
Found at i:7070203 original size:26 final size:27
Alignment explanation
Indices: 7070174--7070234 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 27
7070164 GGGTATTTTG
* *
7070174 GTAATTTTGC-ACCTAGGGGTATAACA
1 GTAATTTTCCAACATAGGGGTATAACA
* *
7070200 GTAATTTTCCATACATAGGGGTATTATA
1 GTAATTTTCCA-ACATAGGGGTATAACA
7070228 GTAATTT
1 GTAATTT
7070235 AGCTGCTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 9 0.31
28 20 0.69
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (27 bp):
GTAATTTTCCAACATAGGGGTATAACA
Found at i:7071721 original size:26 final size:26
Alignment explanation
Indices: 7071683--7071766 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
7071673 CATGATATTC
* *
7071683 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
7071709 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
7071735 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
7071761 TTATCA
1 TTATCA
7071767 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.35
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCTA
Found at i:7073009 original size:3 final size:3
Alignment explanation
Indices: 7073001--7073031 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
7072991 GTTTATGTGT
7073001 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
7073032 CCCTACATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:7075395 original size:31 final size:28
Alignment explanation
Indices: 7075345--7075401 Score: 87
Period size: 31 Copynumber: 1.9 Consensus size: 28
7075335 CGGATGGGGA
7075345 AGTTTTTTTATTTATTTAATATTAATTT
1 AGTTTTTTTATTTATTTAATATTAATTT
7075373 AGTTATTTTTATTTAATATTAATATTAAT
1 AGTT-TTTTTATTT-AT-TTAATATTAAT
7075402 ATAAAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 4 0.15
29 9 0.35
30 2 0.08
31 11 0.42
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (28 bp):
AGTTTTTTTATTTATTTAATATTAATTT
Found at i:7078063 original size:19 final size:18
Alignment explanation
Indices: 7078036--7078071 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7078026 CCCCTTTTTT
*
7078036 TTTTGTTTTATTATTAATA
1 TTTTATTTTATT-TTAATA
7078055 TTTTATTTTATTTTAAT
1 TTTTATTTTATTTTAAT
7078072 TGTATTGTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTATTTTATTTTAATA
Found at i:7079000 original size:18 final size:18
Alignment explanation
Indices: 7078977--7079014 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
7078967 CTTCTTTGGT
7078977 GCTTCTCTTCTTTAAGTA
1 GCTTCTCTTCTTTAAGTA
*
7078995 GCTTCTCTTTTTTAAGTA
1 GCTTCTCTTCTTTAAGTA
7079013 GC
1 GC
7079015 ATCATTCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.21, G:0.13, T:0.50
Consensus pattern (18 bp):
GCTTCTCTTCTTTAAGTA
Found at i:7079220 original size:44 final size:44
Alignment explanation
Indices: 7079058--7079285 Score: 181
Period size: 44 Copynumber: 5.0 Consensus size: 44
7079048 GGAATTAGTA
* *** * * *
7079058 CTTCAATCTACTCCACTGTTGCTTCAAGGAGATTAGACTCGCAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCAT
* * * * *
7079102 CTACAATTTGCTCCACTGCAACTTCAGGGGGATAAGATTTGTAACTCGTAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA----T---TCGCAT
* **
7079153 CTTTAATCTATTCCACTGCAACTTCAGGG-GAATAAGATTCGCAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAG-ATAAGATTCGCAT
* * *
7079197 CTTCAATCTGCTCCACTGCAACTTGAGGGAGATAAGATTTG-AGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCA-T
*
7079241 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTCTGCAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTC-GCAT
7079286 GGTAAATTTA
Statistics
Matches: 143, Mismatches: 29, Indels: 23
0.73 0.15 0.12
Matches are distributed among these distances:
43 1 0.01
44 103 0.72
45 2 0.01
46 1 0.01
47 1 0.01
50 1 0.01
51 34 0.24
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCAT
Found at i:7086077 original size:40 final size:40
Alignment explanation
Indices: 7086018--7086124 Score: 124
Period size: 40 Copynumber: 2.7 Consensus size: 40
7086008 CAATTGAATG
* * * *
7086018 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGAAACT
* * * **
7086058 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGAAACT
*
7086098 ACATCCGGGCTAAGACCCGAAGGCATT
1 ATATCCGGGCTAAGACCCGAAGGCATT
7086125 CGTGCAAGTC
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGAAACT
Found at i:7086182 original size:39 final size:39
Alignment explanation
Indices: 7086056--7086184 Score: 154
Period size: 40 Copynumber: 3.3 Consensus size: 39
7086046 ATGCTGGAAA
* *
7086056 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGA
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-AGTGG
* * *
7086096 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGC-AGTGG
*
7086136 TTCTATCCGGGCTAAGACCCG-AGGCATTCGTGCACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCA-GTGG
7086175 TTATATCCGG
1 TTATATCCGG
7086185 TTGTATTCCG
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
38 1 0.01
39 27 0.36
40 48 0.63
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (39 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCAGTGG
Found at i:7092825 original size:20 final size:20
Alignment explanation
Indices: 7092796--7092833 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
7092786 TGAGAGAAAC
*
7092796 AAAAACAAAGAAAGAAAAAA
1 AAAAAAAAAGAAAGAAAAAA
*
7092816 AAAAAAAAAGGAAGAAAA
1 AAAAAAAAAGAAAGAAAA
7092834 GTGTTCATCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.84, C:0.03, G:0.13, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGAAAGAAAAAA
Found at i:7094121 original size:40 final size:40
Alignment explanation
Indices: 7094062--7094168 Score: 124
Period size: 40 Copynumber: 2.7 Consensus size: 40
7094052 CAATTGAATG
* * * *
7094062 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGAAACT
* * * **
7094102 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGAAACT
*
7094142 ACATCCGGGCTAAGACCCGAAGGCATT
1 ATATCCGGGCTAAGACCCGAAGGCATT
7094169 CGTGCAAGTC
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGAAACT
Found at i:7094188 original size:40 final size:39
Alignment explanation
Indices: 7094103--7094229 Score: 141
Period size: 40 Copynumber: 3.2 Consensus size: 39
7094093 CTGGAAATTA
* * *
7094103 TATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTG-AC
1 TATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTGTTC
7094141 TACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCGTTC
1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGT-GTTC
* * *
7094183 TATCCGGGCTAAGACCCGAGGGCATTCGTGCACGTGGTTA
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGT-GTTC
7094223 TATCCGG
1 TATCCGG
7094230 TTGTATTCCG
Statistics
Matches: 77, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
38 1 0.01
39 3 0.04
40 70 0.91
41 1 0.01
42 2 0.03
ACGTcount: A:0.23, C:0.25, G:0.29, T:0.23
Consensus pattern (39 bp):
TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTGTTC
Found at i:7102505 original size:18 final size:18
Alignment explanation
Indices: 7102478--7102519 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
7102468 CGTACATGAG
* *
7102478 AGAAACAAAAACAAAGAA
1 AGAAAAAAAAAAAAAGAA
*
7102496 AGAAAAAAAAAAAAAGGA
1 AGAAAAAAAAAAAAAGAA
7102514 AGAAAA
1 AGAAAA
7102520 GTGTTCATCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (18 bp):
AGAAAAAAAAAAAAAGAA
Found at i:7103808 original size:40 final size:40
Alignment explanation
Indices: 7103749--7103855 Score: 124
Period size: 40 Copynumber: 2.7 Consensus size: 40
7103739 CAATTGAATG
* * * *
7103749 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGAAACT
* * * **
7103789 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGAAACT
*
7103829 ACATCCGGGCTAAGACCCGAAGGCATT
1 ATATCCGGGCTAAGACCCGAAGGCATT
7103856 CGTGCAAGTC
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGAAACT
Found at i:7103913 original size:39 final size:40
Alignment explanation
Indices: 7103787--7103915 Score: 156
Period size: 40 Copynumber: 3.2 Consensus size: 40
7103777 ATGCTGGAAA
* *
7103787 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGC-TAGTGA
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAT-GTGG
* * * *
7103827 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGG
*
7103867 TTCTATCCGGGCTAAGACCCG-AGGCATTCGTGCATGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGG
7103906 TTATATCCGG
1 TTATATCCGG
7103916 TTGTATTCCG
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
39 28 0.37
40 47 0.63
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGG
Found at i:7110488 original size:17 final size:17
Alignment explanation
Indices: 7110456--7110496 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
7110446 CGTACATGAG
*
7110456 AGAAACAAAAACAAAGAA
1 AGAAA-AAAAAAAAAGAA
*
7110474 AGAAAAAAAAAAAAGGA
1 AGAAAAAAAAAAAAGAA
7110491 AGAAAA
1 AGAAAA
7110497 GTGTTCATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (17 bp):
AGAAAAAAAAAAAAGAA
Found at i:7111784 original size:40 final size:40
Alignment explanation
Indices: 7111725--7111831 Score: 124
Period size: 40 Copynumber: 2.7 Consensus size: 40
7111715 CAATTGAATG
* * * *
7111725 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGAAACT
* * * **
7111765 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGAAACT
*
7111805 ACATCCGGGCTAAGACCCGAAGGCATT
1 ATATCCGGGCTAAGACCCGAAGGCATT
7111832 CGTGCAAGTC
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGAAACT
Found at i:7111889 original size:39 final size:40
Alignment explanation
Indices: 7111763--7111891 Score: 156
Period size: 40 Copynumber: 3.2 Consensus size: 40
7111753 ATGCTGGAAA
* *
7111763 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGC-TAGTGA
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAT-GTGG
* * * *
7111803 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGG
*
7111843 TTCTATCCGGGCTAAGACCCG-AGGCATTCGTGCATGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGG
7111882 TTATATCCGG
1 TTATATCCGG
7111892 TTGTATTCCG
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
39 28 0.37
40 47 0.63
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGG
Found at i:7119942 original size:22 final size:22
Alignment explanation
Indices: 7119917--7119958 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
7119907 AATGTTTAAT
7119917 AATAACATAA-AATAGATGATAA
1 AATAACATAATAATA-ATGATAA
*
7119939 AATATCATAATAATAATGAT
1 AATAACATAATAATAATGAT
7119959 GTAATTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.29
Consensus pattern (22 bp):
AATAACATAATAATAATGATAA
Found at i:7120118 original size:16 final size:16
Alignment explanation
Indices: 7120099--7120131 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
7120089 ACAAGTGCAC
7120099 AAAATAA-AATCAAATA
1 AAAATAACAAT-AAATA
7120115 AAAATAACAATAAATA
1 AAAATAACAATAAATA
7120131 A
1 A
7120132 CAAGTGTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAATAACAATAAATA
Found at i:7120202 original size:16 final size:16
Alignment explanation
Indices: 7120173--7120218 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
7120163 TTTAATTTTT
*
7120173 AAGTG-TAAAAAAATG
1 AAGTGATAAATAAATG
7120188 AAGTGATAAATAAATG
1 AAGTGATAAATAAATG
*
7120204 AA-TGAATGAATAAAT
1 AAGTG-ATAAATAAAT
7120219 AAATAGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 7 0.26
16 20 0.74
ACGTcount: A:0.59, C:0.00, G:0.17, T:0.24
Consensus pattern (16 bp):
AAGTGATAAATAAATG
Found at i:7120207 original size:20 final size:20
Alignment explanation
Indices: 7120184--7120222 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
7120174 AGTGTAAAAA
7120184 AATGAAGTG-ATAAATAAATG
1 AATGAA-TGAATAAATAAATG
7120204 AATGAATGAATAAATAAAT
1 AATGAATGAATAAATAAAT
7120223 AGTTTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (20 bp):
AATGAATGAATAAATAAATG
Found at i:7122105 original size:44 final size:44
Alignment explanation
Indices: 7122049--7122209 Score: 142
Period size: 44 Copynumber: 3.7 Consensus size: 44
7122039 TTTAATCTTT
*
7122049 TCCACTGCAACTTCAGGGAAATAAAATTCGCATCTTCAATCTGC
1 TCCACTGCAACTTCAGGGAAATAAAATTCGCAGCTTCAATCTGC
* * * * * **
7122093 TCCACCGCAACTTTAGGGAGATAAGATTTGTGGCTTCAATCTGC
1 TCCACTGCAACTTCAGGGAAATAAAATTCGCAGCTTCAATCTGC
* ** * * * ** *
7122137 TCCACTGCAACTTGATAGAGATAAGATTTGTGGCTTCAATCTAC
1 TCCACTGCAACTTCAGGGAAATAAAATTCGCAGCTTCAATCTGC
* * *
7122181 TCCACTGTAACTTCAGGGAGATAAGATTC
1 TCCACTGCAACTTCAGGGAAATAAAATTC
7122210 AGCATGGTAG
Statistics
Matches: 99, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 99 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGGAAATAAAATTCGCAGCTTCAATCTGC
Found at i:7122367 original size:228 final size:227
Alignment explanation
Indices: 7122022--7122436 Score: 584
Period size: 228 Copynumber: 1.8 Consensus size: 227
7122012 AGGGTGATAA
7122022 GATTTGTAACTCGTAGCTTTAATCTTTTCCACTGCAACTTCAGGGAAATAAAATTCGCATCTTCA
1 GATTTGTAACTCGTAGCTTTAATCTTTTCCACTGCAACTTCAGGGAAATAAAATTCGCATCTTCA
** * *
7122087 ATCTGCTCCACCGCAACTTTAGGGAGATAAGATTTGTGGCTTCAATCTGCTCCACTGCAACTTGA
66 ATCTGCTCCACCGCAACTTTAGGGAGATAAGATTTGTAACTTCAACCTGCTCCACTGCAACTTCA
* *
7122152 TAGAGATAAGATTTGTGGCTTCAATCTACTCCACTGTAACTTCAGGGAGATAAGATTCAGCATGG
131 GAGAGATAAGATTTGT-GCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTCAGCATGG
7122217 TAGATTTAATCCGCCCTACTACAAGAGGTATAG
195 TAGATTTAATCCGCCCTACTACAAGAGGTATAG
* * * * *
7122250 GATTTGTGACTTGTAGCTTTAAT-TTGTTTCACTGCAAC-TCTAGGGAAATGAGATTCGCTATCT
1 GATTTGTAACTCGTAGCTTTAATCTT-TTCCACTGCAACTTC-AGGGAAATAAAATTCGC-ATCT
* * * *
7122313 TCAATCTGCTCCACTGCAACTTTAGGGAGATGAGATTT-TAACTTCAACCTGCTCCATTGTAACT
63 TCAATCTGCTCCACCGCAACTTTAGGGAGATAAGATTTGTAACTTCAACCTGCTCCACTGCAACT
* * * * * *
7122377 TCAGGGAGATAAGGTTTGTGCTTTAATTTGCTCCACTGCAACTTTAGGGAGATAAGATTC
128 TCAGAGAGATAAGATTTGTGCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTC
7122437 GCCACGATGA
Statistics
Matches: 163, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
227 40 0.25
228 83 0.51
229 40 0.25
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (227 bp):
GATTTGTAACTCGTAGCTTTAATCTTTTCCACTGCAACTTCAGGGAAATAAAATTCGCATCTTCA
ATCTGCTCCACCGCAACTTTAGGGAGATAAGATTTGTAACTTCAACCTGCTCCACTGCAACTTCA
GAGAGATAAGATTTGTGCTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTCAGCATGGT
AGATTTAATCCGCCCTACTACAAGAGGTATAG
Found at i:7122377 original size:43 final size:43
Alignment explanation
Indices: 7122279--7122435 Score: 163
Period size: 43 Copynumber: 3.6 Consensus size: 43
7122269 TAATTTGTTT
* * * *
7122279 CACTGCAACTCTAGGGAAATGAGATTCGCTATCTTCAATCTGCTC
1 CACTGCAACTTTAGGGAGATAAGATTTG-TA-CTTCAATCTGCTC
* *
7122324 CACTGCAACTTTAGGGAGATGAGATTT-TAACTTCAACCTGCTC
1 CACTGCAACTTTAGGGAGATAAGATTTGT-ACTTCAATCTGCTC
* * * * * * *
7122367 CATTGTAACTTCAGGGAGATAAGGTTTGTGCTTTAATTTGCTC
1 CACTGCAACTTTAGGGAGATAAGATTTGTACTTCAATCTGCTC
7122410 CACTGCAACTTTAGGGAGATAAGATT
1 CACTGCAACTTTAGGGAGATAAGATT
7122436 CGCCACGATG
Statistics
Matches: 93, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
43 67 0.72
44 2 0.02
45 24 0.26
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (43 bp):
CACTGCAACTTTAGGGAGATAAGATTTGTACTTCAATCTGCTC
Found at i:7125392 original size:11 final size:11
Alignment explanation
Indices: 7125378--7125417 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
7125368 TGTTTTCCCT
*
7125378 CTATTTTGCTA
1 CTATTTTACTA
7125389 CTATTTTACTA
1 CTATTTTACTA
* *
7125400 TTATGTTACTA
1 CTATTTTACTA
7125411 CTATTTT
1 CTATTTT
7125418 GTTGTTGTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.23, C:0.15, G:0.05, T:0.57
Consensus pattern (11 bp):
CTATTTTACTA
Found at i:7126269 original size:22 final size:22
Alignment explanation
Indices: 7126241--7126306 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
7126231 CTAGGAGATG
**
7126241 AAACTCAAGTTTTTCCTTGTAA
1 AAACTCAAGTTTCCCCTTGTAA
7126263 AAACTCAAGTTTCCCCTTGTAA
1 AAACTCAAGTTTCCCCTTGTAA
7126285 AAACTCAAGTTTCCCCCTTGTA
1 AAACTCAAGTTT-CCCCTTGTA
7126307 TTAAAAAGCT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 32 0.78
23 9 0.22
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (22 bp):
AAACTCAAGTTTCCCCTTGTAA
Found at i:7126377 original size:21 final size:21
Alignment explanation
Indices: 7126336--7126375 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
7126326 TCTAAACAAG
7126336 ATAAAACTCAAGTTATTCCCT
1 ATAAAACTCAAGTTATTCCCT
*
7126357 ATAAAACTTAAGTT-TTCCC
1 ATAAAACTCAAGTTATTCCC
7126376 CTCCTACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.35
Consensus pattern (21 bp):
ATAAAACTCAAGTTATTCCCT
Found at i:7126423 original size:16 final size:17
Alignment explanation
Indices: 7126402--7126439 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
7126392 AAATTAATTC
7126402 TAAAAAAA-TAAAAATA
1 TAAAAAAATTAAAAATA
7126418 TAAAAAAATTAAAAATA
1 TAAAAAAATTAAAAATA
7126435 TAAAA
1 TAAAA
7126440 TGGTTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
TAAAAAAATTAAAAATA
Found at i:7126467 original size:95 final size:94
Alignment explanation
Indices: 7126368--7126550 Score: 235
Period size: 95 Copynumber: 1.9 Consensus size: 94
7126358 TAAAACTTAA
*
7126368 GTTTTCCCCTCCTACT-AAAAATTAAAATTAATTCTAAAAA-AATAAAAATATAAAAAAATTAAA
1 GTTTTCCCCTCCTACTAAAAAATTAAAATAAATTCTAAAAAGAA-AAAAATA-AAAAAAATTAAA
*
7126431 AATATAAAATGGTTTTTCTATGTAAACCCCAT
64 AAGATAAAATGGTTTTTCT-TGTAAACCCCAT
* * ** * * **
7126463 GTTTTTCTCTTTTAGTAAAAAATTAAAATAAATTCTAAAAAGGAAAAAATAAATGAAATTAAAAA
1 GTTTTCCCCTCCTACTAAAAAATTAAAATAAATTCTAAAAAGAAAAAAATAAAAAAAATTAAAAA
7126528 GATAAAATGGTTTTTCTTGTAAA
66 GATAAAATGGTTTTTCTTGTAAA
7126551 AACAAGTAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
94 6 0.08
95 39 0.51
96 30 0.39
97 1 0.01
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.34
Consensus pattern (94 bp):
GTTTTCCCCTCCTACTAAAAAATTAAAATAAATTCTAAAAAGAAAAAAATAAAAAAAATTAAAAA
GATAAAATGGTTTTTCTTGTAAACCCCAT
Found at i:7127515 original size:43 final size:43
Alignment explanation
Indices: 7127468--7127583 Score: 130
Period size: 43 Copynumber: 2.7 Consensus size: 43
7127458 ATTTATGTGG
*
7127468 AAAAACGCCGCTATAGAACATGACCTTTAGTAG-TG-TTTCTCAC
1 AAAAATGCCGCTATAGAACATGACCTTTAGTAGATGCTTTC-C-C
* * *
7127511 AAAAATACCGCTGTAGAACATGACCTTTAG-CGATGCTTTCCC
1 AAAAATGCCGCTATAGAACATGACCTTTAGTAGATGCTTTCCC
* * *
7127553 ACAAATGCCACTATAGAACATGACATTTAGT
1 AAAAATGCCGCTATAGAACATGACCTTTAGT
7127584 GGCACTTTTC
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
42 27 0.44
43 30 0.49
44 4 0.07
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (43 bp):
AAAAATGCCGCTATAGAACATGACCTTTAGTAGATGCTTTCCC
Found at i:7133245 original size:78 final size:78
Alignment explanation
Indices: 7133116--7133272 Score: 271
Period size: 78 Copynumber: 2.0 Consensus size: 78
7133106 ATAACAATAT
* *
7133116 AAGCAGAATATCAGAAGAGAGGGAGAGAAGCAAAATTGCCCTGAATATTTGGATGAGATCCTTGG
1 AAGCAGAATATCAGAAGAGAGGAAGAGAAGCAAAACTGCCCTGAATATTTGGATGAGATCCTTGG
7133181 AGTAGCGAGAGCA
66 AGTAGCGAGAGCA
7133194 AAGCAGAATATCAGAAGAGAGGAAGAGAAG-AGAAACTGCCCTGAATATTTGGATGAGATCCTTG
1 AAGCAGAATATCAGAAGAGAGGAAGAGAAGCA-AAACTGCCCTGAATATTTGGATGAGATCCTTG
*
7133258 GAGTAGCTAGAGCA
65 GAGTAGCGAGAGCA
7133272 A
1 A
7133273 GAATTGTAGA
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
77 1 0.01
78 74 0.99
ACGTcount: A:0.39, C:0.13, G:0.30, T:0.18
Consensus pattern (78 bp):
AAGCAGAATATCAGAAGAGAGGAAGAGAAGCAAAACTGCCCTGAATATTTGGATGAGATCCTTGG
AGTAGCGAGAGCA
Found at i:7133455 original size:6 final size:6
Alignment explanation
Indices: 7133441--7133472 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
7133431 AATAAAATTT
7133441 AAATAAA AAATAA AAATAA AAATAA AAATAA A
1 AAAT-AA AAATAA AAATAA AAATAA AAATAA A
7133473 GTAATAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.84
7 4 0.16
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:7135125 original size:9 final size:9
Alignment explanation
Indices: 7135111--7135158 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 9
7135101 AACAAATAAT
7135111 AAATAAAGA
1 AAATAAAGA
7135120 AAATAAA-A
1 AAATAAAGA
7135128 ACTAATCAAAG-
1 A--AAT-AAAGA
7135139 AAATAAAGA
1 AAATAAAGA
7135148 AAATAAAGA
1 AAATAAAGA
7135157 AA
1 AA
7135159 TGAATAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
8 6 0.18
9 21 0.62
10 3 0.09
11 4 0.12
ACGTcount: A:0.75, C:0.04, G:0.08, T:0.12
Consensus pattern (9 bp):
AAATAAAGA
Found at i:7135174 original size:32 final size:30
Alignment explanation
Indices: 7135105--7135177 Score: 89
Period size: 28 Copynumber: 2.5 Consensus size: 30
7135095 AAAGAGAACA
*
7135105 AATAAT-AAATAAAGAAAATAAAAACTAAT
1 AATAATGAAATAAAGAAAATAAAAAATAAT
*
7135134 CA-AA-GAAATAAAGAAAATAAAGAAATGAAT
1 AATAATGAAATAAAGAAAATAAA-AAAT-AAT
7135164 AATAATGAAATAAA
1 AATAATGAAATAAA
7135178 ATAAAAGAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
28 18 0.50
29 4 0.11
30 4 0.11
31 2 0.06
32 8 0.22
ACGTcount: A:0.71, C:0.03, G:0.08, T:0.18
Consensus pattern (30 bp):
AATAATGAAATAAAGAAAATAAAAAATAAT
Found at i:7139978 original size:53 final size:53
Alignment explanation
Indices: 7139917--7140020 Score: 156
Period size: 53 Copynumber: 2.0 Consensus size: 53
7139907 GACGGAAAAT
*
7139917 ATGTGATAATGTAATTCCGTATAAGACCATAGT-TAGGCTATGGCATCGGTACA
1 ATGTGATAATGTAATTCCGTATAAGACCAT-GTCTAGGATATGGCATCGGTACA
* * *
7139970 ATGTGATAATGTGATTTCGTATAAGACCATGTCTAGGATATGGCTTCGGTA
1 ATGTGATAATGTAATTCCGTATAAGACCATGTCTAGGATATGGCATCGGTA
7140021 TGATATGTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 2 0.04
53 44 0.96
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (53 bp):
ATGTGATAATGTAATTCCGTATAAGACCATGTCTAGGATATGGCATCGGTACA
Found at i:7140604 original size:17 final size:21
Alignment explanation
Indices: 7140562--7140604 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
7140552 GATTGGAAAA
7140562 TGAAATATACTTGTTTTGGCT
1 TGAAATATACTTGTTTTGGCT
7140583 TGAAATA-A-TTG-TTTGG-T
1 TGAAATATACTTGTTTTGGCT
7140600 TGAAA
1 TGAAA
7140605 ATTTTTAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.27
18 5 0.23
19 3 0.14
20 1 0.05
21 7 0.32
ACGTcount: A:0.30, C:0.05, G:0.21, T:0.44
Consensus pattern (21 bp):
TGAAATATACTTGTTTTGGCT
Found at i:7140606 original size:18 final size:20
Alignment explanation
Indices: 7140562--7140606 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
7140552 GATTGGAAAA
*
7140562 TGAAATATACTTGTTTTGGCT
1 TGAAA-ATAATTGTTTTGGCT
7140583 TG-AAATAATTG-TTTGG-T
1 TGAAAATAATTGTTTTGGCT
7140600 TGAAAAT
1 TGAAAAT
7140607 TTTTAGGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 3 0.14
18 9 0.41
19 6 0.27
20 2 0.09
21 2 0.09
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.44
Consensus pattern (20 bp):
TGAAAATAATTGTTTTGGCT
Found at i:7140863 original size:20 final size:20
Alignment explanation
Indices: 7140838--7140890 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
7140828 ACGGCTGCAG
* *
7140838 CACACGGGCATGTTCCAGGA
1 CACACGGGCATGTCCCAAGA
* *
7140858 CACACGGGCGTGTCCCAAGC
1 CACACGGGCATGTCCCAAGA
*
7140878 CACACAGGCATGT
1 CACACGGGCATGT
7140891 GCCCCTATCT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.34, G:0.28, T:0.13
Consensus pattern (20 bp):
CACACGGGCATGTCCCAAGA
Found at i:7144871 original size:7 final size:7
Alignment explanation
Indices: 7144849--7144881 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
7144839 ATAAATAAAT
7144849 TATATTA
1 TATATTA
7144856 TATTATTA
1 TA-TATTA
7144864 TATATTA
1 TATATTA
7144871 TATATTA
1 TATATTA
7144878 TATA
1 TATA
7144882 AATTGAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TATATTA
Found at i:7145914 original size:13 final size:13
Alignment explanation
Indices: 7145892--7145924 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
7145882 AAGGGTTTGT
7145892 TTAT-TAAACTAA
1 TTATCTAAACTAA
7145904 TTATCTAAACTAA
1 TTATCTAAACTAA
*
7145917 TTAACTAA
1 TTATCTAA
7145925 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:7148194 original size:30 final size:31
Alignment explanation
Indices: 7148160--7148220 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
7148150 ATATGTGAAC
7148160 ATATG-TTCATGTTTAAAACAACTAAGTGAT
1 ATATGTTTCATGTTTAAAACAACTAAGTGAT
*
7148190 ATATGTTTCATGTTTAAAACAATTAAGTGAT
1 ATATGTTTCATGTTTAAAACAACTAAGTGAT
7148221 GTGTTTTGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (31 bp):
ATATGTTTCATGTTTAAAACAACTAAGTGAT
Found at i:7151348 original size:17 final size:17
Alignment explanation
Indices: 7151322--7151355 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
7151312 TCCATTTGGC
*
7151322 TCTTCCTCAAGTACACT
1 TCTTCATCAAGTACACT
7151339 TCTTCATCAAGTACACT
1 TCTTCATCAAGTACACT
7151356 GGATTAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.32, G:0.06, T:0.35
Consensus pattern (17 bp):
TCTTCATCAAGTACACT
Found at i:7151888 original size:36 final size:37
Alignment explanation
Indices: 7151848--7151934 Score: 101
Period size: 36 Copynumber: 2.4 Consensus size: 37
7151838 TCCAAAGTTT
* * *
7151848 TATGTAAGTTATGATATG-ATAT-ATAT-ATTTATGTAT
1 TATGTAAGTTATGATAAGTA-ATGATATGATATATAT-T
7151884 TATGTAAGTTATG-TAAGTAATGATATGATATATATT
1 TATGTAAGTTATGATAAGTAATGATATGATATATATT
7151920 TATGTAAGTTATGAT
1 TATGTAAGTTATGAT
7151935 CCAAAGTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
35 5 0.11
36 32 0.73
37 7 0.16
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (37 bp):
TATGTAAGTTATGATAAGTAATGATATGATATATATT
Found at i:7152002 original size:13 final size:13
Alignment explanation
Indices: 7151984--7152010 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
7151974 TGATTATCAT
7151984 CTTTAAATTTTAA
1 CTTTAAATTTTAA
7151997 CTTTAAATTTTAA
1 CTTTAAATTTTAA
7152010 C
1 C
7152011 CCTTTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (13 bp):
CTTTAAATTTTAA
Found at i:7155185 original size:11 final size:11
Alignment explanation
Indices: 7155165--7155194 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
7155155 TTGTGTGTTC
7155165 TTTA-TTTTAT
1 TTTATTTTTAT
7155175 TTTATTTTTAT
1 TTTATTTTTAT
7155186 TTTATTTTT
1 TTTATTTTT
7155195 TTCACAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.21
11 15 0.79
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:7159614 original size:13 final size:14
Alignment explanation
Indices: 7159596--7159624 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
7159586 TTGTGTGTTC
7159596 TTTATTTTA-TTTT
1 TTTATTTTACTTTT
7159609 TTTATTTTACTTTT
1 TTTATTTTACTTTT
7159623 TT
1 TT
7159625 CACAGACAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTATTTTACTTTT
Found at i:7166408 original size:41 final size:41
Alignment explanation
Indices: 7166349--7166481 Score: 216
Period size: 41 Copynumber: 3.3 Consensus size: 41
7166339 TTACCAAAAA
7166349 CGCCGCT-AAAAACAGAGCAATAGCGGCTTTTTTGGCAAAG
1 CGCCGCTAAAAAACAGAGCAATAGCGGCTTTTTTGGCAAAG
*
7166389 CGCCGCTAAAAAACAGAGCAATAGCGGCGTTTTTGGCAAAG
1 CGCCGCTAAAAAACAGAGCAATAGCGGCTTTTTTGGCAAAG
* *
7166430 CGGCGCTAAAAAACATAGCAATAGCGGCATTTTTT-GCAAAG
1 CGCCGCTAAAAAACAGAGCAATAGCGGC-TTTTTTGGCAAAG
7166471 CGCCGCTAAAA
1 CGCCGCTAAAA
7166482 GTCATATAAC
Statistics
Matches: 86, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
40 7 0.08
41 74 0.86
42 5 0.06
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.19
Consensus pattern (41 bp):
CGCCGCTAAAAAACAGAGCAATAGCGGCTTTTTTGGCAAAG
Found at i:7167247 original size:19 final size:20
Alignment explanation
Indices: 7167211--7167255 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
7167201 TATTAGATTT
7167211 TAAAAAAATTGATAAATAAA
1 TAAAAAAATTGATAAATAAA
*
7167231 TAAAAACATTGAT-AATAAA
1 TAAAAAAATTGATAAATAAA
7167250 TAAAAA
1 TAAAAA
7167256 TGAAATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (20 bp):
TAAAAAAATTGATAAATAAA
Found at i:7168148 original size:7 final size:7
Alignment explanation
Indices: 7168135--7168213 Score: 95
Period size: 8 Copynumber: 10.6 Consensus size: 7
7168125 AATCTTCAAA
7168135 AAAAATT
1 AAAAATT
*
7168142 GAAAATT
1 AAAAATT
7168149 AAAAATT
1 AAAAATT
7168156 AAAAATT
1 AAAAATT
*
7168163 AAAAAATAA
1 -AAAAAT-T
7168172 AAAAATT
1 AAAAATT
7168179 AAAAATT
1 AAAAATT
7168186 AAAAACTT
1 AAAAA-TT
7168194 AAAAACTT
1 AAAAA-TT
7168202 AAAAACTT
1 AAAAA-TT
7168210 AAAA
1 AAAA
7168214 TTTTAATATT
Statistics
Matches: 65, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
7 31 0.48
8 34 0.52
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.24
Consensus pattern (7 bp):
AAAAATT
Found at i:7168159 original size:23 final size:23
Alignment explanation
Indices: 7168143--7168213 Score: 83
Period size: 23 Copynumber: 3.0 Consensus size: 23
7168133 AAAAAAATTG
7168143 AAAATTAAAAATTAAAAATT-AA
1 AAAATTAAAAATTAAAAATTAAA
*
7168165 AAAATAAAAAAATTAAAAATT-AA
1 AAAAT-TAAAAATTAAAAATTAAA
*
7168188 AAACTTAAAAACTTAAAAACTTAAA
1 AAAATTAAAAA-TTAAAAA-TTAAA
7168213 A
1 A
7168214 TTTTAATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
22 10 0.24
23 27 0.64
24 2 0.05
25 3 0.07
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (23 bp):
AAAATTAAAAATTAAAAATTAAA
Found at i:7168219 original size:16 final size:15
Alignment explanation
Indices: 7168135--7168213 Score: 99
Period size: 15 Copynumber: 5.3 Consensus size: 15
7168125 AATCTTCAAA
*
7168135 AAAAATTGAAAA-TT
1 AAAAATTAAAAACTT
7168149 AAAAATTAAAAA-TT
1 AAAAATTAAAAACTT
* *
7168163 AAAAAATAAAAAAATT
1 -AAAAATTAAAAACTT
7168179 AAAAATTAAAAACTT
1 AAAAATTAAAAACTT
7168194 AAAAACTTAAAAACTT
1 AAAAA-TTAAAAACTT
7168210 AAAA
1 AAAA
7168214 TTTTAATATT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
14 13 0.22
15 29 0.50
16 16 0.28
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.24
Consensus pattern (15 bp):
AAAAATTAAAAACTT
Found at i:7168421 original size:41 final size:41
Alignment explanation
Indices: 7168369--7168478 Score: 141
Period size: 41 Copynumber: 2.7 Consensus size: 41
7168359 AAAAATAAAT
* * *
7168369 TTGAGCAATAGTGGCGTTTTTACTGAAAACGCCACAAAAAG
1 TTGAGCTATAGTGGCGTTTTTACTAAAAACGCCACAAAAAA
* **
7168410 TTGAGCTATAGTGGTGTTTTTGGTAAAAACGCCACAAAAAA
1 TTGAGCTATAGTGGCGTTTTTACTAAAAACGCCACAAAAAA
* *
7168451 TTGAGATACAGTGGCGTTTTT-CTAAAAA
1 TTGAGCTATAGTGGCGTTTTTACTAAAAA
7168479 TGCAGCAAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
40 6 0.10
41 53 0.90
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (41 bp):
TTGAGCTATAGTGGCGTTTTTACTAAAAACGCCACAAAAAA
Found at i:7174679 original size:19 final size:21
Alignment explanation
Indices: 7174651--7174698 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
7174641 TTATTATTTA
7174651 TTTTAGTTTTGATTATAA-AT
1 TTTTAGTTTTGATTATAATAT
* *
7174671 TTTTA-TTTTTATTTTAATAT
1 TTTTAGTTTTGATTATAATAT
7174691 TTTTAGTT
1 TTTTAGTT
7174699 AAAATTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.42
20 12 0.50
21 2 0.08
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (21 bp):
TTTTAGTTTTGATTATAATAT
Found at i:7174680 original size:20 final size:20
Alignment explanation
Indices: 7174639--7174698 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
7174629 TTAATCTAAT
*
7174639 TTTTATTAT-TTA-TTTTAG
1 TTTTATTATAATATTTTTAG
*
7174657 TTTTGATTATAA-ATTTTTAT
1 TTTT-ATTATAATATTTTTAG
*
7174677 TTTTATTTTAATATTTTTAG
1 TTTTATTATAATATTTTTAG
7174697 TT
1 TT
7174699 AAAATTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 4 0.12
19 12 0.35
20 18 0.53
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (20 bp):
TTTTATTATAATATTTTTAG
Found at i:7175387 original size:30 final size:30
Alignment explanation
Indices: 7175329--7175387 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
7175319 CACACGGGCA
* *
7175329 AAAGACACGGCCATGTGTCTCAGCCGTGTG
1 AAAGACACGGCCATGTGACACAGCCGTGTG
*
7175359 AAAGACACGGCCATAG-GACACAGGCGTGT
1 AAAGACACGGCCAT-GTGACACAGCCGTGT
7175388 ACCTTGACCG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.29, C:0.25, G:0.31, T:0.15
Consensus pattern (30 bp):
AAAGACACGGCCATGTGACACAGCCGTGTG
Found at i:7175930 original size:21 final size:21
Alignment explanation
Indices: 7175892--7175932 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
7175882 GTGTCTAATG
*
7175892 CTGATGGAATGGGGCGTGTGA
1 CTGATGGAATAGGGCGTGTGA
* *
7175913 CTGATGGGATAGGTCGTGTG
1 CTGATGGAATAGGGCGTGTG
7175933 CCTAATGCTT
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:0.17, C:0.10, G:0.46, T:0.27
Consensus pattern (21 bp):
CTGATGGAATAGGGCGTGTGA
Found at i:7176051 original size:24 final size:23
Alignment explanation
Indices: 7175997--7176066 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 23
7175987 TATAGCAGAC
7175997 CACAATTTGGGTGTGATTTTGGG
1 CACAATTTGGGTGTGATTTTGGG
* *
7176020 -ACTGATTTGGGTCGTGGTTTTGGG
1 CAC-AATTTGGGT-GTGATTTTGGG
* *
7176044 CACAATTTTGGGCGCGATTTTGG
1 CACAA-TTTGGGTGTGATTTTGG
7176067 ACGTGAAATG
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
22 2 0.05
23 8 0.22
24 19 0.51
25 8 0.22
ACGTcount: A:0.14, C:0.11, G:0.36, T:0.39
Consensus pattern (23 bp):
CACAATTTGGGTGTGATTTTGGG
Found at i:7178518 original size:103 final size:103
Alignment explanation
Indices: 7178339--7178540 Score: 395
Period size: 103 Copynumber: 2.0 Consensus size: 103
7178329 TAGGTACCTG
7178339 GGTGTGACTTTAACGAAACATTTAACCCAGTGATCAAACCTGCTACTATCTGAACCATCTTATCT
1 GGTGTGACTTTAACGAAACATTTAACCCAGTGATCAAACCTGCTACTATCTGAACCATCTTATCT
7178404 ATTGCTGTATCCAATGGTTGGCAATTGCGTCAAGCTGA
66 ATTGCTGTATCCAATGGTTGGCAATTGCGTCAAGCTGA
7178442 GGTGTGACTTTAACGAAACATTTAACCCAGTGATCAAACCTGCTACTATCTGAACCATCTTATCT
1 GGTGTGACTTTAACGAAACATTTAACCCAGTGATCAAACCTGCTACTATCTGAACCATCTTATCT
*
7178507 ATTGTTGTATCCAATGGTTGGCAATTGCGTCAAG
66 ATTGCTGTATCCAATGGTTGGCAATTGCGTCAAG
7178541 TCAATGTAAA
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 98 1.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (103 bp):
GGTGTGACTTTAACGAAACATTTAACCCAGTGATCAAACCTGCTACTATCTGAACCATCTTATCT
ATTGCTGTATCCAATGGTTGGCAATTGCGTCAAGCTGA
Found at i:7182271 original size:26 final size:25
Alignment explanation
Indices: 7182242--7182290 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
7182232 AAATTATTAG
*
7182242 TATTT-ATTATATTATTTTTTAAAATA
1 TATTTAATTA-ATT-TTTTTAAAAATA
7182268 TATTTAATTAATTTTTTTAAAAA
1 TATTTAATTAATTTTTTTAAAAA
7182291 AAAAATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 9 0.43
26 8 0.38
27 4 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TATTTAATTAATTTTTTTAAAAATA
Found at i:7189216 original size:30 final size:30
Alignment explanation
Indices: 7189180--7189249 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
7189170 ATCTCGAGAT
* * *
7189180 AGGATGTTTGAAAACTATCTTGGGATTTCC
1 AGGATGTCTGAAAACTATCTTGAGATTCCC
* *
7189210 AGGATGTCTGATAATTATCTTGAGATTCCC
1 AGGATGTCTGAAAACTATCTTGAGATTCCC
7189240 A-GAT-TCTGAA
1 AGGATGTCTGAA
7189250 TTTTTAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 5 0.15
29 3 0.09
30 26 0.76
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (30 bp):
AGGATGTCTGAAAACTATCTTGAGATTCCC
Found at i:7200471 original size:10 final size:10
Alignment explanation
Indices: 7200458--7200482 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
7200448 AAAATCTTTA
7200458 AAAATTTTGT
1 AAAATTTTGT
7200468 AAAATTTTGT
1 AAAATTTTGT
7200478 AAAAT
1 AAAAT
7200483 ACTTAGGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (10 bp):
AAAATTTTGT
Found at i:7209469 original size:29 final size:29
Alignment explanation
Indices: 7209427--7209485 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
7209417 AGTTAGCCCC
7209427 GCAGTCGAATGCTCCTATTTCTCGAGGTA
1 GCAGTCGAATGCTCCTATTTCTCGAGGTA
7209456 GCAGTCGAATGCTCCTATTTCTCGAGGTA
1 GCAGTCGAATGCTCCTATTTCTCGAGGTA
7209485 G
1 G
7209486 ACCCTCGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (29 bp):
GCAGTCGAATGCTCCTATTTCTCGAGGTA
Found at i:7224728 original size:29 final size:30
Alignment explanation
Indices: 7224696--7224781 Score: 79
Period size: 31 Copynumber: 2.9 Consensus size: 30
7224686 ATTCAATTTA
7224696 CAATTTGATACAT-AAACTTTAATTTGGTG
1 CAATTTGATACATGAAACTTTAATTTGGTG
* * * *
7224725 CAATTAT-ACACATGAAATTTTTATTGTGGTT
1 CAATT-TGATACATGAAACTTTAATT-TGGTG
*
7224756 CAA-ATGTATACATGAAACTTTAATTT
1 CAATTTG-ATACATGAAACTTTAATTT
7224782 TAATTCAATC
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
29 11 0.25
30 11 0.25
31 22 0.50
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (30 bp):
CAATTTGATACATGAAACTTTAATTTGGTG
Found at i:7226946 original size:18 final size:18
Alignment explanation
Indices: 7226923--7226962 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
7226913 GCTTATTTAT
7226923 AAAATTAAACCATAGTAG
1 AAAATTAAACCATAGTAG
* *
7226941 AAAATTAAACCTTTGTAG
1 AAAATTAAACCATAGTAG
7226959 AAAA
1 AAAA
7226963 GTTTCAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.25
Consensus pattern (18 bp):
AAAATTAAACCATAGTAG
Found at i:7233545 original size:22 final size:21
Alignment explanation
Indices: 7233514--7233560 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
7233504 TGAATCGAGT
*
7233514 TTTATAATTTTTAATATTTTTA
1 TTTATAATTTTTAATA-ATTTA
*
7233536 TTTATTATTTTTAATAATTTA
1 TTTATAATTTTTAATAATTTA
7233557 TTTA
1 TTTA
7233561 ATTGAAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTATAATTTTTAATAATTTA
Found at i:7235049 original size:12 final size:12
Alignment explanation
Indices: 7235032--7235065 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
7235022 GCCACACAGG
7235032 CGTGTGGTAGCC
1 CGTGTGGTAGCC
* *
7235044 CGTGTGGGAGGC
1 CGTGTGGTAGCC
7235056 CGTGTGGTAG
1 CGTGTGGTAG
7235066 TACACAGCCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.09, C:0.18, G:0.50, T:0.24
Consensus pattern (12 bp):
CGTGTGGTAGCC
Found at i:7243426 original size:30 final size:30
Alignment explanation
Indices: 7243390--7243449 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
7243380 TTCTCGAGCC
7243390 TAGGGGCAAAA-GTGTAATTATGCAAAAGTT
1 TAGGGGCAAAATG-GTAATTATGCAAAAGTT
*
7243420 TAGGGGCAAAATGGTAATTTTGCAAAAGTT
1 TAGGGGCAAAATGGTAATTATGCAAAAGTT
7243450 CGTATTAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAATGGTAATTATGCAAAAGTT
Found at i:7244177 original size:49 final size:50
Alignment explanation
Indices: 7244097--7244343 Score: 300
Period size: 49 Copynumber: 5.0 Consensus size: 50
7244087 AGCTATTGTG
*
7244097 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * *
7244147 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAACTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * * * * **
7244197 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAAATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* *
7244247 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * * *
7244297 -GGTCGCATATGTAGTACTAAGTGCAAGCTACTATGCGTACCAGATAA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA
7244344 CTTCAGCTAC
Statistics
Matches: 166, Mismatches: 29, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
49 82 0.49
50 47 0.28
51 37 0.22
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:7250028 original size:16 final size:16
Alignment explanation
Indices: 7249999--7250044 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
7249989 ATTATTTATT
* *
7249999 AAATTATTTAAATTAA
1 AAATTTTTTCAATTAA
7250015 AAATTTTTTCAATTAA
1 AAATTTTTTCAATTAA
*
7250031 ATAATTTTCTCAAT
1 A-AATTTTTTCAAT
7250045 CCAACTCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 15 0.58
17 11 0.42
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATTTTTTCAATTAA
Found at i:7250038 original size:17 final size:16
Alignment explanation
Indices: 7250009--7250044 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
7249999 AAATTATTTA
*
7250009 AATTAAAAATTTTTTC
1 AATTAAAAATTTTCTC
7250025 AATTAAATAATTTTCTC
1 AATTAAA-AATTTTCTC
7250042 AAT
1 AAT
7250045 CCAACTCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTAAAAATTTTCTC
Found at i:7259171 original size:31 final size:32
Alignment explanation
Indices: 7259130--7259192 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
7259120 TTATTTATAA
*
7259130 AAGATATTTAT-TAATTAAATAT-TTATATTAT
1 AAGATATTTATGTAA-TAAATATATTAAATTAT
*
7259161 AAGATTTTTATGTAATAAATATATTAAATTAT
1 AAGATATTTATGTAATAAATATATTAAATTAT
7259193 GACAAGTGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (32 bp):
AAGATATTTATGTAATAAATATATTAAATTAT
Found at i:7259474 original size:28 final size:28
Alignment explanation
Indices: 7259443--7259505 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
7259433 TCCCATATTA
7259443 ATGGGGTATAGGAAAAGTCTCATAACTT
1 ATGGGGTATAGGAAAAGTCTCATAACTT
* * *
7259471 ATGGGGTATAGGAAGAGTTTTATAACTT
1 ATGGGGTATAGGAAAAGTCTCATAACTT
7259499 ATGGGGT
1 ATGGGGT
7259506 TGATAATGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.06, G:0.30, T:0.32
Consensus pattern (28 bp):
ATGGGGTATAGGAAAAGTCTCATAACTT
Found at i:7266480 original size:16 final size:16
Alignment explanation
Indices: 7266459--7266492 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
7266449 ATATATAGTT
7266459 AATTAATT-AAAATATG
1 AATTAATTGAAAAT-TG
7266475 AATTAATTGAAAATTG
1 AATTAATTGAAAATTG
7266491 AA
1 AA
7266493 AAGTGAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (16 bp):
AATTAATTGAAAATTG
Found at i:7266628 original size:6 final size:6
Alignment explanation
Indices: 7266608--7266641 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
7266598 ATGTGTCGAA
*
7266608 TACTGT TACTGGT TACTGT TACCGT TACTGT TAC
1 TACTGT TACT-GT TACTGT TACTGT TACTGT TAC
7266642 CGATTTAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.44
Consensus pattern (6 bp):
TACTGT
Found at i:7266748 original size:6 final size:6
Alignment explanation
Indices: 7266737--7266761 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
7266727 ACAGTATTGC
7266737 TACTGT TACTGT TACTGT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT T
7266762 TCGGCTTCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TACTGT
Found at i:7266924 original size:18 final size:18
Alignment explanation
Indices: 7266881--7267068 Score: 143
Period size: 18 Copynumber: 10.4 Consensus size: 18
7266871 CTGATTATTT
*
7266881 CTGAATAAATGACTGTTA
1 CTGAATAATTGACTGTTA
7266899 GC-GAATAATTGACTGTTA
1 -CTGAATAATTGACTGTTA
* * *
7266917 CTGGATAATAGACTGCTA
1 CTGAATAATTGACTGTTA
* *
7266935 CTGAATAATTGAATATTA
1 CTGAATAATTGACTGTTA
* *
7266953 CTGAATAAATGA-TCATTA
1 CTGAATAATTGACT-GTTA
* * * *
7266971 CTAAATAACTGATTGTCA
1 CTGAATAATTGACTGTTA
7266989 CTGAATGAA-TGACTGTTA
1 CTGAAT-AATTGACTGTTA
* * *
7267007 CTAAATAACTTAATTGTTA
1 CTGAATAA-TTGACTGTTA
*
7267026 CTGAAT-ATCTGA-TTTTA
1 CTGAATAAT-TGACTGTTA
7267043 CTGAATAATTGACTGTTA
1 CTGAATAATTGACTGTTA
*
7267061 CTGGATAA
1 CTGAATAA
7267069 CCGATCAATT
Statistics
Matches: 135, Mismatches: 25, Indels: 19
0.75 0.14 0.11
Matches are distributed among these distances:
17 18 0.13
18 101 0.75
19 16 0.12
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (18 bp):
CTGAATAATTGACTGTTA
Found at i:7267128 original size:18 final size:18
Alignment explanation
Indices: 7267107--7267147 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
7267097 AGTTATTATT
* *
7267107 GAATAATTGATTGTTACC
1 GAATAACTGACTGTTACC
*
7267125 GAATAACTGACTGTTACT
1 GAATAACTGACTGTTACC
7267143 GAATA
1 GAATA
7267148 GATAATTGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (18 bp):
GAATAACTGACTGTTACC
Found at i:7267146 original size:36 final size:36
Alignment explanation
Indices: 7266866--7267163 Score: 151
Period size: 36 Copynumber: 8.1 Consensus size: 36
7266856 AAATGTATAA
* * * *
7266866 AATAACTGATTATTTCTGAATAAATGACTGTTAGC-G
1 AATAACTGATTGTTACTGAATAATTGATTGTTA-CTG
* * * * * *
7266902 AATAATTGACTGTTACTGGATAATAGACTGCTACTG
1 AATAACTGATTGTTACTGAATAATTGATTGTTACTG
* * * * ** *
7266938 AATAATTGAATATTACTGAATAAATGATCATTACTA
1 AATAACTGATTGTTACTGAATAATTGATTGTTACTG
* * *
7266974 AATAACTGATTGTCACTGAATGAA-TGACTGTTACTA
1 AATAACTGATTGTTACTGAAT-AATTGATTGTTACTG
*
7267010 AATAACTTAATTGTTACTGAAT-ATCTGATT-TTACTG
1 AATAAC-TGATTGTTACTGAATAAT-TGATTGTTACTG
* * * *
7267046 AATAATTGACTGTTACTGGATAACCGATCAATTGATCGATACTG
1 AATAACTGATTGTTACT-G---A---AT-AATTGATTGTTACTG
* * *
7267090 AATAACT-AGTTATTATTGAATAATTGATTGTTACCG
1 AATAACTGA-TTGTTACTGAATAATTGATTGTTACTG
* *
7267126 AATAACTGACTGTTACTGAATAGA-TAATTGTT-CTG
1 AATAACTGATTGTTACTGAATA-ATTGATTGTTACTG
7267161 AAT
1 AAT
7267164 GTTAATGAAC
Statistics
Matches: 198, Mismatches: 46, Indels: 37
0.70 0.16 0.13
Matches are distributed among these distances:
35 16 0.08
36 131 0.66
37 23 0.12
39 1 0.01
40 1 0.01
42 2 0.01
43 6 0.03
44 18 0.09
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (36 bp):
AATAACTGATTGTTACTGAATAATTGATTGTTACTG
Done.