Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 128 of 190
Found at i:38106381 original size:2 final size:2
Alignment explanation
Indices: 38106374--38106401 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38106364 TAAAACCCAT
38106374 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38106402 AACAAAGTTT
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):
TA
Found at i:38109638 original size:2 final size:2
Alignment explanation
Indices: 38109631--38109673 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
38109621 ATGTTTATTT
* *
38109631 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA -A AA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38109671 TA T
1 TA T
38109674 TTTAAATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:38109674 original size:18 final size:18
Alignment explanation
Indices: 38109644--38109679 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
38109634 ATATATATAT
*
38109644 ATATATATATATTATAAA
1 ATATAAATATATTATAAA
*
38109662 ATATAAATATATTTTAAA
1 ATATAAATATATTATAAA
38109680 TAATTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATAAATATATTATAAA
Found at i:38116109 original size:20 final size:20
Alignment explanation
Indices: 38116076--38116116 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
38116066 TAGACATTTG
** *
38116076 TTTTATTACCATTTTATATA
1 TTTTATTAAAATTTTAAATA
38116096 TTTTATTAAAATTTTAAATA
1 TTTTATTAAAATTTTAAATA
38116116 T
1 T
38116117 AAAAAGCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTATTAAAATTTTAAATA
Found at i:38116243 original size:20 final size:21
Alignment explanation
Indices: 38116218--38116259 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
38116208 ATTCATCTCA
38116218 TATTTTAATTG-ATTT-ATTAT
1 TATTTT-ATTGAATTTCATTAT
38116238 TATTTTATTGAATTTCATTAT
1 TATTTTATTGAATTTCATTAT
38116259 T
1 T
38116260 CAAGTTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 10 0.50
21 6 0.30
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (21 bp):
TATTTTATTGAATTTCATTAT
Found at i:38117319 original size:43 final size:42
Alignment explanation
Indices: 38117272--38117518 Score: 262
Period size: 43 Copynumber: 5.8 Consensus size: 42
38117262 GTGGAGAAAT
*
38117272 GCTGCTATAGAACATGACCTTTAGCGGCGCTTATCCCAGAAAC
1 GCTGCTATAGAACATGACCTTTAGCGGCGCTT-TCCCACAAAC
* * *
38117315 GCTGCTATAGATCATGACATTTAGCGGCACTTTTCCCACAAAC
1 GCTGCTATAGAACATGACCTTTAGCGGCGC-TTTCCCACAAAC
* *
38117358 -CTTGCTATAGAACATGACCTTTAGCGGCGCCTTCCCCACAATC
1 GC-TGCTATAGAACATGACCTTTAGCGGCG-CTTTCCCACAAAC
* * * *
38117401 GCTGCTATAGAATATAACCTTTTGCGGCACTTTCCCACAAAC
1 GCTGCTATAGAACATGACCTTTAGCGGCGCTTTCCCACAAAC
* * * * *
38117443 GCCGCTATAGAGCATGACCTTTAGTGACGCTTTCCCTACAAAT
1 GCTGCTATAGAACATGACCTTTAGCGGCGCTTTCCC-ACAAAC
* * * * *
38117486 GCCGCTAAAGAATATGACTTTTAGTGGCGCTTT
1 GCTGCTATAGAACATGACCTTTAGCGGCGCTTT
38117519 TTACCATAAA
Statistics
Matches: 170, Mismatches: 29, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
42 40 0.24
43 126 0.74
44 4 0.02
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (42 bp):
GCTGCTATAGAACATGACCTTTAGCGGCGCTTTCCCACAAAC
Found at i:38117478 original size:85 final size:86
Alignment explanation
Indices: 38117275--38117551 Score: 278
Period size: 86 Copynumber: 3.2 Consensus size: 86
38117265 GAGAAATGCT
* * *
38117275 GCTATAGAACATGACCTTTAGCGGCGCTTAT-CCCAGAAACGCTGCTATAG-ATCATGACATTTA
1 GCTATAGAACATGACCTTTAGCGGCGCTT-TCCCCACAATCGCTGCTATAGAAT-ATAACATTTA
*
38117338 GCGGCACTTTTCCCACAAACCTT
64 GCGGCACTTTTCCCACAAACCTC
* * *
38117361 GCTATAGAACATGACCTTTAGCGGCGCCTTCCCCACAATCGCTGCTATAGAATATAACCTTTTGC
1 GCTATAGAACATGACCTTTAGCGGCGCTTTCCCCACAATCGCTGCTATAGAATATAACATTTAGC
38117426 GGCAC-TTTCCCACAAACGC-C
66 GGCACTTTTCCCACAAAC-CTC
* * * * * * * *
38117446 GCTATAGAGCATGACCTTTAGTGACGCTTTCCCTACAAAT-GCCGCTAAAGAATATGACTTTTAG
1 GCTATAGAACATGACCTTTAGCGGCGCTTTCCCCAC-AATCGCTGCTATAGAATATAACATTTAG
* * * * *
38117510 TGGCGCTTTTTACCATAAAAC-C
65 CGGCAC-TTTTCCCACAAACCTC
*
38117532 GCTAAAGAACATGACCTTTA
1 GCTATAGAACATGACCTTTA
38117552 ATGGTGCTTT
Statistics
Matches: 161, Mismatches: 24, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
85 67 0.42
86 83 0.52
87 11 0.07
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (86 bp):
GCTATAGAACATGACCTTTAGCGGCGCTTTCCCCACAATCGCTGCTATAGAATATAACATTTAGC
GGCACTTTTCCCACAAACCTC
Found at i:38117850 original size:16 final size:16
Alignment explanation
Indices: 38117825--38117860 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
38117815 AATGAAATAA
*
38117825 CAAAATTTATTATATT
1 CAAAAGTTATTATATT
38117841 CAAAAGTTATTATATT
1 CAAAAGTTATTATATT
38117857 -AAAA
1 CAAAA
38117861 TATTCTTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (16 bp):
CAAAAGTTATTATATT
Found at i:38122487 original size:9 final size:9
Alignment explanation
Indices: 38122473--38122542 Score: 74
Period size: 9 Copynumber: 8.0 Consensus size: 9
38122463 TAAGTATAAT
38122473 TAAGTTATG
1 TAAGTTATG
38122482 TAAGTTATG
1 TAAGTTATG
* * *
38122491 ATATGATATA
1 -TAAGTTATG
*
38122501 T-ATTTATG
1 TAAGTTATG
38122509 T-A-TTATG
1 TAAGTTATG
38122516 TAAGTTATG
1 TAAGTTATG
38122525 TAAGTTATG
1 TAAGTTATG
38122534 TAAGTTATG
1 TAAGTTATG
38122543 ATCCAAAGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
7 6 0.12
8 6 0.12
9 33 0.65
10 6 0.12
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (9 bp):
TAAGTTATG
Found at i:38122542 original size:34 final size:34
Alignment explanation
Indices: 38122477--38122542 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
38122467 TATAATTAAG
* *
38122477 TTATGTAAGTTATGATATGATATATATTTATGTA
1 TTATGTAAGTTATGATAAGATATATAGTTATGTA
* *
38122511 TTATGTAAGTTATG-TAAGTTATGTAAGTTATG
1 TTATGTAAGTTATGATAAGATATAT-AGTTATG
38122543 ATCCAAAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 7 0.26
34 20 0.74
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (34 bp):
TTATGTAAGTTATGATAAGATATATAGTTATGTA
Found at i:38122613 original size:13 final size:13
Alignment explanation
Indices: 38122595--38122620 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38122585 TGATTATCAT
38122595 CTTTAAATTTTAA
1 CTTTAAATTTTAA
38122608 CTTTAAATTTTAA
1 CTTTAAATTTTAA
38122621 TAATTATATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
CTTTAAATTTTAA
Found at i:38124883 original size:15 final size:15
Alignment explanation
Indices: 38124863--38124894 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
38124853 TGGCAGATAA
38124863 CAGAAAACTGGATGG
1 CAGAAAACTGGATGG
*
38124878 CAGAAAATTGGATGG
1 CAGAAAACTGGATGG
38124893 CA
1 CA
38124895 AATCTAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.12, G:0.31, T:0.16
Consensus pattern (15 bp):
CAGAAAACTGGATGG
Found at i:38126170 original size:20 final size:20
Alignment explanation
Indices: 38126147--38126185 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38126137 TTTATGTAAT
38126147 ATTTAAAATAATTATATAAA
1 ATTTAAAATAATTATATAAA
* **
38126167 ATTTGAAATTTTTATATAA
1 ATTTAAAATAATTATATAA
38126186 TTTTTTATGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
ATTTAAAATAATTATATAAA
Found at i:38126791 original size:41 final size:41
Alignment explanation
Indices: 38126734--38126826 Score: 107
Period size: 41 Copynumber: 2.3 Consensus size: 41
38126724 CGACGTTTAA
* * *
38126734 AAACGTCGCTAATGCTTGA-CTTTTTGTGGCATTTTTCTCAT
1 AAACGCCGCTAATGCTTGATC-GTTTGCGGCATTTTTCTCAT
* *
38126775 AAACGCCGCTATTGCTTGATCGTTTGCGGCGTTTTTCTCAT
1 AAACGCCGCTAATGCTTGATCGTTTGCGGCATTTTTCTCAT
* *
38126816 AAGCCCCGCTA
1 AAACGCCGCTA
38126827 CTGTTTTACC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 43 0.98
42 1 0.02
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (41 bp):
AAACGCCGCTAATGCTTGATCGTTTGCGGCATTTTTCTCAT
Found at i:38128414 original size:24 final size:24
Alignment explanation
Indices: 38128395--38128444 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
38128385 AGATTTAGTA
*
38128395 TTTATGAGTATAATATATTTAACT
1 TTTATGAGCATAATATATTTAACT
* *
38128419 TTTATTAGCATAATATATTTGACT
1 TTTATGAGCATAATATATTTAACT
38128443 TT
1 TT
38128445 GATTAGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.06, G:0.08, T:0.52
Consensus pattern (24 bp):
TTTATGAGCATAATATATTTAACT
Found at i:38128449 original size:24 final size:24
Alignment explanation
Indices: 38128404--38128450 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
38128394 ATTTATGAGT
*
38128404 ATAATATATTTAACTTTTATTAGC
1 ATAATATATTTAACTTTGATTAGC
*
38128428 ATAATATATTTGACTTTGATTAG
1 ATAATATATTTAACTTTGATTAG
38128451 AATTAGGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (24 bp):
ATAATATATTTAACTTTGATTAGC
Found at i:38129776 original size:28 final size:28
Alignment explanation
Indices: 38129744--38129799 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
38129734 TGTTTGACGG
*
38129744 AGTTGTCAGAACACTTAGTGATGTGCGA
1 AGTTGTCAGAACACTTAGTGACGTGCGA
38129772 AGTTGTCAGAACACTTAGTGACGTGCGA
1 AGTTGTCAGAACACTTAGTGACGTGCGA
38129800 CATGTTCCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.27
Consensus pattern (28 bp):
AGTTGTCAGAACACTTAGTGACGTGCGA
Found at i:38137314 original size:126 final size:125
Alignment explanation
Indices: 38137089--38137358 Score: 470
Period size: 126 Copynumber: 2.2 Consensus size: 125
38137079 GATAAAATCA
* * *
38137089 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAATCGCGCCCACGTGGACGCGCTTTTGCTATAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCACGCCCACGTGGACGCGCTTTTGCTACAGT
38137154 AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAAAAACGCTTC
66 AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTAT-AAAAAACGCTTC
38137215 AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCACGCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCACGCCCACGTGGACGCGCTTTTGCTACAGT
* *
38137280 AGGT-CTTACAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
66 AGGTCCTGA-AAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAAAACGCTTC
38137340 AAGCAGGATGCTTTATCAG
1 AAGCAGGATGCTTTATCAG
38137359 GATGCTTCAA
Statistics
Matches: 138, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
125 34 0.25
126 104 0.75
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (125 bp):
AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCACGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGAAAATAGTATAAAAAACGCTTC
Found at i:38137361 original size:13 final size:13
Alignment explanation
Indices: 38137341--38137381 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
38137331 AAACGCTTCA
38137341 AGCAGGATGCTTT
1 AGCAGGATGCTTT
* *
38137354 ATCAGGATGCTTCA
1 AGCAGGATGCTT-T
38137368 AGCAGGATGCTTT
1 AGCAGGATGCTTT
38137381 A
1 A
38137382 AGTTAAGGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (13 bp):
AGCAGGATGCTTT
Found at i:38137375 original size:14 final size:14
Alignment explanation
Indices: 38137335--38137379 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
38137325 TATAAAAAAC
38137335 GCTTCAAGCAGGAT
1 GCTTCAAGCAGGAT
* *
38137349 GCTT-TATCAGGAT
1 GCTTCAAGCAGGAT
38137362 GCTTCAAGCAGGAT
1 GCTTCAAGCAGGAT
38137376 GCTT
1 GCTT
38137380 TAAGTTAAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (14 bp):
GCTTCAAGCAGGAT
Found at i:38137404 original size:21 final size:21
Alignment explanation
Indices: 38137378--38137419 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
38137368 AGCAGGATGC
38137378 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
38137399 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
38137420 AGGGTTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.43
Consensus pattern (21 bp):
TTTAAGTTAAGGGTTAGGGTT
Found at i:38137457 original size:12 final size:12
Alignment explanation
Indices: 38137442--38137484 Score: 59
Period size: 12 Copynumber: 3.3 Consensus size: 12
38137432 AGGGTTTGTC
38137442 AATTAAATTATA
1 AATTAAATTATA
38137454 AATTAAATTATA
1 AATTAAATTATA
38137466 AATTATAAATTTATA
1 AA-T-TAAA-TTATA
38137481 AATT
1 AATT
38137485 TTTAATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 14 0.50
13 2 0.07
14 5 0.18
15 7 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AATTAAATTATA
Found at i:38137485 original size:8 final size:7
Alignment explanation
Indices: 38137445--38137484 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
38137435 GTTTGTCAAT
38137445 TAAATTA
1 TAAATTA
38137452 TAAA-T-
1 TAAATTA
38137457 TAAATTA
1 TAAATTA
38137464 TAAATTA
1 TAAATTA
38137471 TAAATTTA
1 TAAA-TTA
38137479 TAAATT
1 TAAATT
38137485 TTTAATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 4 0.13
6 2 0.07
7 17 0.57
8 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TAAATTA
Found at i:38137703 original size:21 final size:22
Alignment explanation
Indices: 38137679--38137737 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
38137669 GTCCGGCTTT
* *
38137679 CGGCAGGGG-TTGTGGTTGCTC
1 CGGCAGGGGATTCTGGTTCCTC
38137700 CGGC-GGGGATTCTGGTTCCTC
1 CGGCAGGGGATTCTGGTTCCTC
* *
38137721 CGGTAGGGCA-TCTGGTT
1 CGGCAGGGGATTCTGGTT
38137738 GTCGGTGTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 4 0.12
21 24 0.75
22 4 0.12
ACGTcount: A:0.07, C:0.22, G:0.42, T:0.29
Consensus pattern (22 bp):
CGGCAGGGGATTCTGGTTCCTC
Found at i:38138004 original size:18 final size:18
Alignment explanation
Indices: 38137978--38138020 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
38137968 AACTCGAAAA
* * *
38137978 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
38137996 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
38138014 AGGATAC
1 AGGATAC
38138021 GCACCTGGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:38138676 original size:7 final size:7
Alignment explanation
Indices: 38138666--38138691 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
38138656 TTATATACAT
38138666 AATACTA
1 AATACTA
38138673 AATACTA
1 AATACTA
38138680 AATACTA
1 AATACTA
38138687 AATAC
1 AATAC
38138692 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:38139914 original size:22 final size:22
Alignment explanation
Indices: 38139889--38139961 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
38139879 ATATGGATTG
*
38139889 GAGAGAAATTTG-GAAGGAAATT
1 GAGAGAAATTTGAG-AGCAAATT
38139911 GAGAGCAAA-TTGAGAGCAAATT
1 GAGAG-AAATTTGAGAGCAAATT
**
38139933 GAGAGGAAA-TTGAGAAAATAATT
1 GAGA-GAAATTTGAGAGCA-AATT
38139956 GAGAGA
1 GAGAGA
38139962 GGATTAGTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
22 31 0.70
23 13 0.30
ACGTcount: A:0.48, C:0.03, G:0.30, T:0.19
Consensus pattern (22 bp):
GAGAGAAATTTGAGAGCAAATT
Found at i:38139922 original size:11 final size:11
Alignment explanation
Indices: 38139906--38139947 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
38139896 ATTTGGAAGG
38139906 AAATTGAGAGC
1 AAATTGAGAGC
38139917 AAATTGAGAGC
1 AAATTGAGAGC
*
38139928 AAATTGAGAGG
1 AAATTGAGAGC
38139939 AAATTGAGA
1 AAATTGAGA
38139948 AAATAATTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.48, C:0.05, G:0.29, T:0.19
Consensus pattern (11 bp):
AAATTGAGAGC
Found at i:38140875 original size:30 final size:29
Alignment explanation
Indices: 38140811--38140878 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
38140801 TTTGAAATTT
* *
38140811 GAAATTTAATTTTTATATTTTTATTTTCA
1 GAAATTTAATTTTTATATTTTTAATGTCA
38140840 GAAATTTAATTTCTT-TAATTTTTAAATGTCA
1 GAAATTTAATTT-TTAT-ATTTTT-AATGTCA
38140871 -AAATTTAA
1 GAAATTTAA
38140879 ATTTAACTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 13 0.38
30 16 0.47
31 5 0.15
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (29 bp):
GAAATTTAATTTTTATATTTTTAATGTCA
Found at i:38141523 original size:14 final size:14
Alignment explanation
Indices: 38141482--38141531 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
38141472 TACTGTTTTT
*
38141482 TACTATTTTCTTGT
1 TACTATTTTCTTGC
* *
38141496 TACTTTTTTTTTGC
1 TACTATTTTCTTGC
*
38141510 TACTATTTTGTTGC
1 TACTATTTTCTTGC
*
38141524 TATTATTT
1 TACTATTT
38141532 GGATATTGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.14, C:0.12, G:0.08, T:0.66
Consensus pattern (14 bp):
TACTATTTTCTTGC
Found at i:38145260 original size:17 final size:17
Alignment explanation
Indices: 38145240--38145298 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
38145230 TTAATAGATA
38145240 ATTGAAGTGAATATGAT
1 ATTGAAGTGAATATGAT
*
38145257 ATTG-AGTTGATTAATAGAT
1 ATTGAAG-TGAAT-AT-GAT
*
38145276 AATTGAAGTGAATGTGAT
1 -ATTGAAGTGAATATGAT
38145294 ATTGA
1 ATTGA
38145299 GATTATGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
16 2 0.06
17 13 0.38
18 5 0.15
19 4 0.12
20 8 0.24
21 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (17 bp):
ATTGAAGTGAATATGAT
Found at i:38145268 original size:37 final size:37
Alignment explanation
Indices: 38145227--38145299 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
38145217 AATTAATGAA
38145227 TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
1 TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
*
38145264 TGATTAATAGATAATTGAAGTGAATGTGATATTGAG
1 TGATTAATAGATAATTGAAGTGAATATGATATTGAG
38145300 ATTATGAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.37
Consensus pattern (37 bp):
TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
Found at i:38145280 original size:20 final size:19
Alignment explanation
Indices: 38145227--38145286 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
38145217 AATTAATGAA
38145227 TGATTAATAGATAATTGAAG
1 TGATTAATAGATAATTG-AG
*
38145247 TGAAT-AT-GAT-ATTGAG
1 TGATTAATAGATAATTGAG
38145263 TTGATTAATAGATAATTGAAG
1 -TGATTAATAGATAATTG-AG
38145284 TGA
1 TGA
38145287 ATGTGATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
16 2 0.06
17 8 0.24
18 5 0.15
19 5 0.15
20 11 0.33
21 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TGATTAATAGATAATTGAG
Found at i:38145438 original size:40 final size:39
Alignment explanation
Indices: 38145384--38145507 Score: 121
Period size: 40 Copynumber: 3.2 Consensus size: 39
38145374 AATCATTGTT
*
38145384 GGTTCATCCAACTAGAGCTGGGCTCACTATTTTTATCATC
1 GGTTTATCCAACTAGAGCTGGGCTCACTATTTTTATC-TC
* * * * * *
38145424 GGTTTATCCGACTAGCGCTGGGCGCA--AATATT-GCT-
1 GGTTTATCCAACTAGAGCTGGGCTCACTATTTTTATCTC
* *
38145459 AGTTTATCCAACTAGAGCTGGGCTCACTATTTATATCGTC
1 GGTTTATCCAACTAGAGCTGGGCTCACTATTTTTATC-TC
38145499 GGTTTATCC
1 GGTTTATCC
38145508 GACAAGTACT
Statistics
Matches: 63, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
35 22 0.35
36 1 0.02
37 4 0.06
38 5 0.08
39 1 0.02
40 30 0.48
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (39 bp):
GGTTTATCCAACTAGAGCTGGGCTCACTATTTTTATCTC
Found at i:38145470 original size:75 final size:75
Alignment explanation
Indices: 38145341--38145599 Score: 351
Period size: 75 Copynumber: 3.5 Consensus size: 75
38145331 TGAGTAATTG
* * *
38145341 ATATTGTCGGTTCATCCGACTAGCGCTGGGCGC-AATCATTGTTGGTTCATCCAACTAGAGCTGG
1 ATATCGTCGGTTTATCCGACTAGCGCTGGGCGCAAAT-ATTGTTGGTTTATCCAACTAGAGCTGG
38145405 GCTCACTATTT
65 GCTCACTATTT
* * * *
38145416 TTATCATCGGTTTATCCGACTAGCGCTGGGCGCAAATATTGCTAGTTTATCCAACTAGAGCTGGG
1 ATATCGTCGGTTTATCCGACTAGCGCTGGGCGCAAATATTGTTGGTTTATCCAACTAGAGCTGGG
38145481 CTCACTATTT
66 CTCACTATTT
* ** * * *
38145491 ATATCGTCGGTTTATCCGACAAGTACTGGGTGCAAATATCGTTGGTTTATCCAACCAGAGCTGGG
1 ATATCGTCGGTTTATCCGACTAGCGCTGGGCGCAAATATTGTTGGTTTATCCAACTAGAGCTGGG
*
38145556 CTCACTAATT
66 CTCACTATTT
* *
38145566 AT-TCGTCGGTATATCCGACTAGCGCTAGGCGCAA
1 ATATCGTCGGTTTATCCGACTAGCGCTGGGCGCAA
38145600 CTTCCGTCAG
Statistics
Matches: 159, Mismatches: 24, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
74 26 0.16
75 130 0.82
76 3 0.02
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (75 bp):
ATATCGTCGGTTTATCCGACTAGCGCTGGGCGCAAATATTGTTGGTTTATCCAACTAGAGCTGGG
CTCACTATTT
Found at i:38145555 original size:35 final size:35
Alignment explanation
Indices: 38145424--38145555 Score: 97
Period size: 35 Copynumber: 3.6 Consensus size: 35
38145414 TTTTATCATC
* * * * *
38145424 GGTTTATCCGACTAGCGCTGGGCGCAAATATTGCT
1 GGTTTATCCAACTAGAGCTGGGTGCAAATATCGTT
* *
38145459 AGTTTATCCAACTAGAGCTGGGCT-CACTATTTATATCGTC
1 GGTTTATCCAACTAGAGCTGGG-TGCA--A---ATATCGTT
* *
38145499 GGTTTATCCGACAAGTA-CTGGGTGCAAATATCGTT
1 GGTTTATCCAACTAG-AGCTGGGTGCAAATATCGTT
*
38145534 GGTTTATCCAACCAGAGCTGGG
1 GGTTTATCCAACTAGAGCTGGG
38145556 CTCACTAATT
Statistics
Matches: 75, Mismatches: 13, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
34 1 0.01
35 46 0.61
37 1 0.01
38 1 0.01
39 1 0.01
40 24 0.32
41 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (35 bp):
GGTTTATCCAACTAGAGCTGGGTGCAAATATCGTT
Found at i:38147376 original size:2 final size:2
Alignment explanation
Indices: 38147369--38147402 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
38147359 TATTATATTC
38147369 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38147403 TGCATTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38149871 original size:19 final size:19
Alignment explanation
Indices: 38149847--38149884 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
38149837 TTACTTATGA
*
38149847 ATTGGTTGTTAATACTTTG
1 ATTGGTTGGTAATACTTTG
*
38149866 ATTGGTTGGTAATATTTTG
1 ATTGGTTGGTAATACTTTG
38149885 TAACCCTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.03, G:0.24, T:0.53
Consensus pattern (19 bp):
ATTGGTTGGTAATACTTTG
Found at i:38154113 original size:16 final size:16
Alignment explanation
Indices: 38154092--38154143 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
38154082 TTTGGTTCGC
38154092 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
38154108 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
38154124 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
38154140 TGTA
1 TGTA
38154144 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:38154229 original size:39 final size:43
Alignment explanation
Indices: 38154124--38154233 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
38154114 GGATTAGAGG
38154124 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
38154169 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
38154209 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
38154234 TAATGGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:38154406 original size:14 final size:15
Alignment explanation
Indices: 38154367--38154408 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
38154357 TTTTAACATA
*
38154367 ATTATTATTAAATAT
1 ATTATAATTAAATAT
38154382 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
38154396 A-TATAATTTAATA
1 ATTATAATTAAATA
38154409 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:38154718 original size:24 final size:27
Alignment explanation
Indices: 38154667--38154719 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
38154657 TATATGTAAT
*
38154667 ATTATTAAAATAATATTTTTTATTTTA
1 ATTATTAAAATAATATTTTTTATATTA
*
38154694 ATTATTTAAA-AATA-TTTTTA-ATTA
1 ATTATTAAAATAATATTTTTTATATTA
38154718 AT
1 AT
38154720 GCGGTGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.21
25 6 0.25
26 4 0.17
27 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
ATTATTAAAATAATATTTTTTATATTA
Found at i:38158533 original size:28 final size:28
Alignment explanation
Indices: 38158471--38158541 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
38158461 AAAAACTCCC
**
38158471 TATAT-AATATTTTAATATTATTTTTAT
1 TATATAAATATTAAAATATTATTTTTAT
*
38158498 TATTTAAATA-TAAAATATTTATTTTTA-
1 TATATAAATATTAAAATA-TTATTTTTAT
38158525 TATCATAAATATTAAAA
1 TAT-ATAAATATTAAAA
38158542 ATAACAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
27 12 0.33
28 19 0.53
29 5 0.14
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (28 bp):
TATATAAATATTAAAATATTATTTTTAT
Found at i:38158534 original size:21 final size:22
Alignment explanation
Indices: 38158493--38158537 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
38158483 TAATATTATT
38158493 TTTATTATTTAAATATAAAATA
1 TTTATTATTTAAATATAAAATA
*
38158515 TTTATT-TTTATATCAT-AAATA
1 TTTATTATTTAAAT-ATAAAATA
38158536 TT
1 TT
38158538 AAAAATAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTATTATTTAAATATAAAATA
Found at i:38162178 original size:14 final size:14
Alignment explanation
Indices: 38162159--38162188 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
38162149 ATTATTTGTT
38162159 TTATTTATTTTTAA
1 TTATTTATTTTTAA
*
38162173 TTATTTGTTTTTAA
1 TTATTTATTTTTAA
38162187 TT
1 TT
38162189 TTAAATCCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (14 bp):
TTATTTATTTTTAA
Found at i:38164626 original size:17 final size:18
Alignment explanation
Indices: 38164600--38164637 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
38164590 TTTTTTATAA
38164600 TTATTAAGGA-TTTTAAG
1 TTATTAAGGAGTTTTAAG
* *
38164617 TTATTTAGGAGTTTTATG
1 TTATTAAGGAGTTTTAAG
38164635 TTA
1 TTA
38164638 GCAAGAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (18 bp):
TTATTAAGGAGTTTTAAG
Found at i:38165067 original size:17 final size:18
Alignment explanation
Indices: 38165047--38165083 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
38165037 ATTATTCTAA
*
38165047 TATTTTATTTA-TTATTT
1 TATTTTAGTTATTTATTT
38165064 TATTTTAGTTATTTATTT
1 TATTTTAGTTATTTATTT
38165082 TA
1 TA
38165084 ATTGTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (18 bp):
TATTTTAGTTATTTATTT
Found at i:38165070 original size:13 final size:13
Alignment explanation
Indices: 38165047--38165095 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
38165037 ATTATTCTAA
38165047 TATTTTA-TTTAT
1 TATTTTATTTTAT
38165059 TATTTTATTTTAGT
1 TATTTTATTTTA-T
38165073 TA-TTTATTTTAAT
1 TATTTTATTTT-AT
*
38165086 TGTTTTATTT
1 TATTTTATTT
38165096 GACTTGGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 7 0.22
13 14 0.44
14 11 0.34
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.73
Consensus pattern (13 bp):
TATTTTATTTTAT
Found at i:38170231 original size:47 final size:46
Alignment explanation
Indices: 38170180--38170268 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
38170170 TTCTGGAAGT
*
38170180 TTGGCTACAATTATAGTGGCCCGACCACACATATCTGTTCTAGCAAC
1 TTGGCTACAA-TATAGTGGCCCGACCACACATATCTGATCTAGCAAC
* * ** *
38170227 TTGGCTGCAATATGGTGGCTTGACCACATATATCTGATCTAG
1 TTGGCTACAATATAGTGGCCCGACCACACATATCTGATCTAG
38170269 TAGTTTAACT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
46 27 0.75
47 9 0.25
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (46 bp):
TTGGCTACAATATAGTGGCCCGACCACACATATCTGATCTAGCAAC
Found at i:38171851 original size:11 final size:11
Alignment explanation
Indices: 38171835--38171859 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
38171825 TAGTAACTTT
38171835 ATTTAAACATA
1 ATTTAAACATA
38171846 ATTTAAACATA
1 ATTTAAACATA
38171857 ATT
1 ATT
38171860 AATTATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTTAAACATA
Found at i:38186354 original size:25 final size:25
Alignment explanation
Indices: 38186326--38186375 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
38186316 TTAAACCAAG
*
38186326 TAAAATGAAACTACGAAAGGGCACA
1 TAAAATGAAACTACGAAAGAGCACA
38186351 TAAAATGAAACTACGAAAGAGCACA
1 TAAAATGAAACTACGAAAGAGCACA
38186376 AGTTACCACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.54, C:0.16, G:0.18, T:0.12
Consensus pattern (25 bp):
TAAAATGAAACTACGAAAGAGCACA
Found at i:38193642 original size:30 final size:32
Alignment explanation
Indices: 38193606--38193667 Score: 101
Period size: 30 Copynumber: 2.0 Consensus size: 32
38193596 ATAAATTATA
*
38193606 AAAAATATTAATTAA-ATTAAAAAA-TGAAAT
1 AAAAATATTAAATAATATTAAAAAAGTGAAAT
38193636 AAAAATATTAAATAATATTAAAAAAGTGAAAT
1 AAAAATATTAAATAATATTAAAAAAGTGAAAT
38193668 TAACCTTTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 14 0.48
31 9 0.31
32 6 0.21
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (32 bp):
AAAAATATTAAATAATATTAAAAAAGTGAAAT
Found at i:38195334 original size:13 final size:13
Alignment explanation
Indices: 38195314--38195349 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
38195304 TTTATTAAAA
38195314 CAACGAGTTTGGT
1 CAACGAGTTTGGT
*
38195327 CCACGAGTTTGGT
1 CAACGAGTTTGGT
38195340 CAACGA-TTTG
1 CAACGAGTTTG
38195350 ATTAGCACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (13 bp):
CAACGAGTTTGGT
Found at i:38196579 original size:22 final size:22
Alignment explanation
Indices: 38196525--38196572 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
38196515 ATAAAAGGGC
38196525 AAATAA-AACTAATAATGATAAT
1 AAATAATAA-TAATAATGATAAT
*
38196547 AATTAATAATAATAATGATAAT
1 AAATAATAATAATAATGATAAT
38196569 AAAT
1 AAAT
38196573 GCTAATACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (22 bp):
AAATAATAATAATAATGATAAT
Found at i:38199507 original size:22 final size:22
Alignment explanation
Indices: 38199482--38199724 Score: 299
Period size: 22 Copynumber: 11.0 Consensus size: 22
38199472 CCAACATTCA
* * *
38199482 GACAACATTTAATTAACATTTG
1 GACAGCATTTAATCAACAATTG
38199504 GACAGCATTTAATCAACAATTG
1 GACAGCATTTAATCAACAATTG
* *
38199526 GACAACATTAAATCAAC-ATGTG
1 GACAGCATTTAATCAACAAT-TG
* *
38199548 GACAACATTTAATTAACAATTG
1 GACAGCATTTAATCAACAATTG
* * * *
38199570 GACAACATTCAATCAATATTTG
1 GACAGCATTTAATCAACAATTG
38199592 GACAGCATTTAATCAACAATTG
1 GACAGCATTTAATCAACAATTG
** *
38199614 GACAGCATAAAATCAACATTTG
1 GACAGCATTTAATCAACAATTG
38199636 GACAGCATTTAATCAACAATTG
1 GACAGCATTTAATCAACAATTG
* * *
38199658 GACAGCATTCAATCAATATTTG
1 GACAGCATTTAATCAACAATTG
*
38199680 GACAACATTTAATCAACAATTG
1 GACAGCATTTAATCAACAATTG
*
38199702 GATAGCATTTAATCAACAATTG
1 GACAGCATTTAATCAACAATTG
38199724 G
1 G
38199725 CACTACACCA
Statistics
Matches: 189, Mismatches: 30, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
21 2 0.01
22 185 0.98
23 2 0.01
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (22 bp):
GACAGCATTTAATCAACAATTG
Found at i:38199530 original size:44 final size:44
Alignment explanation
Indices: 38199482--38199724 Score: 333
Period size: 44 Copynumber: 5.5 Consensus size: 44
38199472 CCAACATTCA
* *
38199482 GACAACATTTAATTAACATTTGGACAGCATTTAATCAACAATTG
1 GACAACATTAAATCAACATTTGGACAGCATTTAATCAACAATTG
* * *
38199526 GACAACATTAAATCAACATGTGGACAACATTTAATTAACAATTG
1 GACAACATTAAATCAACATTTGGACAGCATTTAATCAACAATTG
* *
38199570 GACAACATTCAATCAATATTTGGACAGCATTTAATCAACAATTG
1 GACAACATTAAATCAACATTTGGACAGCATTTAATCAACAATTG
* *
38199614 GACAGCATAAAATCAACATTTGGACAGCATTTAATCAACAATTG
1 GACAACATTAAATCAACATTTGGACAGCATTTAATCAACAATTG
* * * *
38199658 GACAGCATTCAATCAATATTTGGACAACATTTAATCAACAATTG
1 GACAACATTAAATCAACATTTGGACAGCATTTAATCAACAATTG
* * * *
38199702 GATAGCATTTAATCAACAATTGG
1 GACAACATTAAATCAACATTTGG
38199725 CACTACACCA
Statistics
Matches: 177, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 177 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (44 bp):
GACAACATTAAATCAACATTTGGACAGCATTTAATCAACAATTG
Found at i:38199591 original size:88 final size:88
Alignment explanation
Indices: 38199482--38199719 Score: 368
Period size: 88 Copynumber: 2.7 Consensus size: 88
38199472 CCAACATTCA
* * * *
38199482 GACAACATTTAATTAACATTTGGACAGCATTTAATCAACAATTGGACAACATTAAATCAACATGT
1 GACAACATTCAATCAATATTTGGACAGCATTTAATCAACAATTGGACAGCATTAAATCAACATGT
*
38199547 GGACAACATTTAATTAACAATTG
66 GGACAACATTTAATCAACAATTG
* *
38199570 GACAACATTCAATCAATATTTGGACAGCATTTAATCAACAATTGGACAGCATAAAATCAACATTT
1 GACAACATTCAATCAATATTTGGACAGCATTTAATCAACAATTGGACAGCATTAAATCAACATGT
*
38199635 GGACAGCATTTAATCAACAATTG
66 GGACAACATTTAATCAACAATTG
* * * *
38199658 GACAGCATTCAATCAATATTTGGACAACATTTAATCAACAATTGGATAGCATTTAATCAACA
1 GACAACATTCAATCAATATTTGGACAGCATTTAATCAACAATTGGACAGCATTAAATCAACA
38199720 ATTGGCACTA
Statistics
Matches: 137, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 137 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (88 bp):
GACAACATTCAATCAATATTTGGACAGCATTTAATCAACAATTGGACAGCATTAAATCAACATGT
GGACAACATTTAATCAACAATTG
Found at i:38199961 original size:43 final size:43
Alignment explanation
Indices: 38199860--38200084 Score: 242
Period size: 43 Copynumber: 5.3 Consensus size: 43
38199850 TTATTTTTAT
* * * * *** *
38199860 AAACGCTGCTAAAGGTCATGTTCTTTAGCGGTGC-TATGAAAA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAC
38199902 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAC
* * *
38199945 AAACGTCGCTAAAGATCATGTTCCTTAGCGACGCTTTTTCCAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAC
* *
38199988 AAACGCCGCTAAAGATAATGTTCTTTAGCGGCG-TTTCTTCCGC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTT-TTCCAC
* * *
38200031 AAACGCCACTAAATG-TCATGTTCTTTTAGCGGAG-TTTTTACAC
1 AAACGCCGCTAAA-GATCATGTTC-TTTAGCGGCGCTTTTTCCAC
*
38200074 AAATGCCGCTA
1 AAACGCCGCTA
38200085 TTTCTTTGGT
Statistics
Matches: 156, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
42 34 0.22
43 109 0.70
44 13 0.08
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAC
Found at i:38200543 original size:21 final size:21
Alignment explanation
Indices: 38200519--38200569 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
38200509 TTCTTTTGAA
* *
38200519 CCTCTGCTTCTCTCGTTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
*
38200540 CCTCTGCTTCCCTCGCTGCCG
1 CCTCTGCTTCCCTCGCTGCAG
38200561 CCTCTGCTT
1 CCTCTGCTT
38200570 TAAGTTGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.02, C:0.45, G:0.18, T:0.35
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Found at i:38200560 original size:87 final size:87
Alignment explanation
Indices: 38200434--38200609 Score: 280
Period size: 87 Copynumber: 2.0 Consensus size: 87
38200424 TCTGCTCTGT
** *
38200434 TCTGCTTCCCTCGCTGCAGTGTCTGCTTCTCTCGATGCCGCATCTGCTTTAAGTTGTAGCTGGAG
1 TCTGCTTCCCTCGCTGCAGCCTCTGCTTCCCTCGATGCCGCATCTGCTTTAAGTTGTAGCTGGAG
*
38200499 TTCTTCATATTTCTTTTGAACC
66 TTCTTCATATTTCCTTTGAACC
* * * *
38200521 TCTGCTTCTCTCGTTGCAGCCTCTGCTTCCCTCGCTGCCGCCTCTGCTTTAAGTTGTAGCTGGAG
1 TCTGCTTCCCTCGCTGCAGCCTCTGCTTCCCTCGATGCCGCATCTGCTTTAAGTTGTAGCTGGAG
38200586 TTCTTCATATTTCCTTTGAACC
66 TTCTTCATATTTCCTTTGAACC
38200608 TC
1 TC
38200610 AACTGTGGTC
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.11, C:0.30, G:0.19, T:0.40
Consensus pattern (87 bp):
TCTGCTTCCCTCGCTGCAGCCTCTGCTTCCCTCGATGCCGCATCTGCTTTAAGTTGTAGCTGGAG
TTCTTCATATTTCCTTTGAACC
Found at i:38206132 original size:9 final size:9
Alignment explanation
Indices: 38206118--38206709 Score: 295
Period size: 9 Copynumber: 69.6 Consensus size: 9
38206108 CATCATATAT
38206118 TTATGTAAG
1 TTATGTAAG
38206127 TTATGT-A-
1 TTATGTAAG
* *
38206134 TTAAGTAAA
1 TTATGTAAG
38206143 TTATGTAAG
1 TTATGTAAG
38206152 TTATGT-A-
1 TTATGTAAG
* *
38206159 TTAAGTAAA
1 TTATGTAAG
38206168 TTATGTAAG
1 TTATGTAAG
38206177 TTATGT-A-
1 TTATGTAAG
38206184 TTATGTAAG
1 TTATGTAAG
38206193 TTATGTAAG
1 TTATGTAAG
38206202 TTATGT-A-
1 TTATGTAAG
* *
38206209 TTAAGTAAA
1 TTATGTAAG
38206218 TTATGTAAG
1 TTATGTAAG
38206227 TTATGT-A-
1 TTATGTAAG
38206234 TTATGTAAG
1 TTATGTAAG
38206243 TTATGTAAG
1 TTATGTAAG
*
38206252 TTGTGT-A-
1 TTATGTAAG
* *
38206259 TTATGAAAC
1 TTATGTAAG
38206268 TTATGTAAG
1 TTATGTAAG
*
38206277 TTATGT--C
1 TTATGTAAG
*
38206284 TTATGTAGG
1 TTATGTAAG
38206293 TTATGTAAG
1 TTATGTAAG
38206302 TTATGT-A-
1 TTATGTAAG
38206309 TTATGTAAG
1 TTATGTAAG
38206318 TTATGT-A-
1 TTATGTAAG
*
38206325 TTAAT-TAAA
1 TT-ATGTAAG
38206334 TTATGTAAG
1 TTATGTAAG
*
38206343 -T-TGT--C
1 TTATGTAAG
*
38206348 TTATATAAG
1 TTATGTAAG
38206357 TTATGTAAG
1 TTATGTAAG
38206366 TTATGTAAG
1 TTATGTAAG
*
38206375 TTGTGT-A-
1 TTATGTAAG
38206382 TTATGTAAG
1 TTATGTAAG
38206391 TTATGT-A-
1 TTATGTAAG
* *
38206398 TTAAGTAGG
1 TTATGTAAG
38206407 TTATGTAAG
1 TTATGTAAG
38206416 TTATGT-A-
1 TTATGTAAG
38206423 TTATGTAAG
1 TTATGTAAG
38206432 TTATGTAAG
1 TTATGTAAG
* **
38206441 TTTTTGT-TT
1 -TTATGTAAG
*
38206450 TTGTGT-A-
1 TTATGTAAG
*
38206457 TTATGTAAC
1 TTATGTAAG
* *
38206466 TTATTTAAT
1 TTATGTAAG
*
38206475 TTATGTAGG
1 TTATGTAAG
*
38206484 TCATGTATTA-
1 TTATGTA--AG
38206494 TTATGTAAG
1 TTATGTAAG
*
38206503 TTAT-TATG
1 TTATGTAAG
*
38206511 -TA-GGATA-
1 TTATGTA-AG
38206518 TTATGTAAG
1 TTATGTAAG
38206527 TTATGTAAG
1 TTATGTAAG
* ***
38206536 TTTTTTGTTTT
1 --TTATGTAAG
*
38206547 TTGTGT-A-
1 TTATGTAAG
*
38206554 TTATGTAAC
1 TTATGTAAG
* *
38206563 TTATTTAAT
1 TTATGTAAG
*
38206572 TTATGTAGG
1 TTATGTAAG
* *
38206581 GTA-GGATA-
1 TTATGTA-AG
38206589 TTATGTAAG
1 TTATGTAAG
38206598 TTATGTAAG
1 TTATGTAAG
* **
38206607 TTTTTGT-TT
1 -TTATGTAAG
* *
38206616 TTTTGTGTA-
1 TTATGT-AAG
*
38206625 TTATGTAAC
1 TTATGTAAG
* *
38206634 TTATTTAAT
1 TTATGTAAG
* *
38206643 TTATATAGG
1 TTATGTAAG
38206652 TTATGTATTA-
1 TTATGTA--AG
38206662 TTATGTAAG
1 TTATGTAAG
38206671 TTATG-AA-
1 TTATGTAAG
38206678 TTATGTAAG
1 TTATGTAAG
*
38206687 TTATGTAAA
1 TTATGTAAG
*
38206696 TTACGTAAG
1 TTATGTAAG
38206705 TTATG
1 TTATG
38206710 AAATTTGAAC
Statistics
Matches: 446, Mismatches: 80, Indels: 114
0.70 0.12 0.18
Matches are distributed among these distances:
6 1 0.00
7 85 0.19
8 57 0.13
9 275 0.62
10 23 0.05
11 5 0.01
ACGTcount: A:0.31, C:0.01, G:0.18, T:0.49
Consensus pattern (9 bp):
TTATGTAAG
Found at i:38206146 original size:16 final size:17
Alignment explanation
Indices: 38206143--38206438 Score: 177
Period size: 16 Copynumber: 17.9 Consensus size: 17
38206133 ATTAAGTAAA
*
38206143 TTATGTAAGTTATGTA-
1 TTATGTAAATTATGTAG
*
38206159 TTAAGTAAATTATGTAAG
1 TTATGTAAATTATGT-AG
38206177 TTATGT--ATTATGTAAG
1 TTATGTAAATTATGT-AG
*
38206193 TTATGTAAGTTATGTA-
1 TTATGTAAATTATGTAG
*
38206209 TTAAGTAAATTATGTAAG
1 TTATGTAAATTATGT-AG
38206227 TTATGT--ATTATGTAAG
1 TTATGTAAATTATGT-AG
* *
38206243 TTATGTAAGTTGTGTA-
1 TTATGTAAATTATGTAG
38206259 TTATG-AAACTTATGTAAG
1 TTATGTAAA-TTATGT-AG
*
38206277 TTATGT--CTTATGTAGG
1 TTATGTAAATTATGTA-G
*
38206293 TTATGTAAGTTATGTA-
1 TTATGTAAATTATGTAG
*
38206309 TTATGTAAGTTATGTA-
1 TTATGTAAATTATGTAG
38206325 TTAAT-TAAATTATGTAAG
1 TT-ATGTAAATTATGT-AG
* *
38206343 -T-TGT--CTTATATAAG
1 TTATGTAAATTATGT-AG
*
38206357 TTATGTAAGTTATGTAAG
1 TTATGTAAATTATGT-AG
*
38206375 TTGTGT--ATTATGTAAG
1 TTATGTAAATTATGT-AG
*
38206391 TTATGT--ATTAAGTAGG
1 TTATGTAAATTATGTA-G
*
38206407 TTATGTAAGTTATGTA-
1 TTATGTAAATTATGTAG
*
38206423 TTATGTAAGTTATGTA
1 TTATGTAAATTATGTA
38206439 AGTTTTTGTT
Statistics
Matches: 230, Mismatches: 24, Indels: 52
0.75 0.08 0.17
Matches are distributed among these distances:
14 8 0.03
15 6 0.03
16 155 0.67
17 9 0.04
18 52 0.23
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (17 bp):
TTATGTAAATTATGTAG
Found at i:38206391 original size:25 final size:25
Alignment explanation
Indices: 38206118--38206533 Score: 360
Period size: 25 Copynumber: 16.6 Consensus size: 25
38206108 CATCATATAT
* *
38206118 TTATGTAAGTTATGTATTAAGTAAA
1 TTATGTAAGTTATGTATTATGTAAG
* *
38206143 TTATGTAAGTTATGTATTAAGTAAA
1 TTATGTAAGTTATGTATTATGTAAG
38206168 TTATGTAAGTTATGTATTATGTAAG
1 TTATGTAAGTTATGTATTATGTAAG
* *
38206193 TTATGTAAGTTATGTATTAAGTAAA
1 TTATGTAAGTTATGTATTATGTAAG
38206218 TTATGTAAGTTATGTATTATGTAAG
1 TTATGTAAGTTATGTATTATGTAAG
* * *
38206243 TTATGTAAGTTGTGTATTATGAAAC
1 TTATGTAAGTTATGTATTATGTAAG
* *
38206268 TTATGTAAGTTATGTCTTATGTAGG
1 TTATGTAAGTTATGTATTATGTAAG
38206293 TTATGTAAGTTATGTATTATGTAAG
1 TTATGTAAGTTATGTATTATGTAAG
38206318 TTATGT-A-TTAAT-TAAATTATGTAAG
1 TTATGTAAGTT-ATGT--ATTATGTAAG
* *
38206343 -T-TGT--CTTATATAAGTTATGTAAG
1 TTATGTAAGTTATGT-A-TTATGTAAG
*
38206366 TTATGTAAGTTGTGTATTATGTAAG
1 TTATGTAAGTTATGTATTATGTAAG
*
38206391 TTATGT-A-TTAAGTAGGTTATGTAAG
1 TTATGTAAGTTATGTA--TTATGTAAG
38206416 TTATGT-A-TTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGT-A-TTATGTAAG
* ** * *
38206441 TTTTTGT-TTTTGTGTATTATGTAAC
1 -TTATGTAAGTTATGTATTATGTAAG
* * *
38206466 TTATTTAATTTATGTAGGTCATGTATTA-
1 TTATGTAAGTTATGTA--TTATGTA--AG
*
38206494 TTATGTAAGTTAT-TATGTA-GGATA-
1 TTATGTAAGTTATGTAT-TATGTA-AG
38206518 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
38206534 AGTTTTTTGT
Statistics
Matches: 334, Mismatches: 35, Indels: 44
0.81 0.08 0.11
Matches are distributed among these distances:
22 4 0.01
23 23 0.07
24 25 0.07
25 244 0.73
26 9 0.03
27 17 0.05
28 11 0.03
29 1 0.00
ACGTcount: A:0.32, C:0.01, G:0.19, T:0.48
Consensus pattern (25 bp):
TTATGTAAGTTATGTATTATGTAAG
Found at i:38206508 original size:12 final size:12
Alignment explanation
Indices: 38206491--38206530 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
38206481 AGGTCATGTA
38206491 TTATTATGTAAG
1 TTATTATGTAAG
*
38206503 TTATTATGTAGG
1 TTATTATGTAAG
*
38206515 ATATTATGTAAG
1 TTATTATGTAAG
38206527 TTAT
1 TTAT
38206531 GTAAGTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (12 bp):
TTATTATGTAAG
Found at i:38206530 original size:95 final size:95
Alignment explanation
Indices: 38206421--38206601 Score: 305
Period size: 97 Copynumber: 1.9 Consensus size: 95
38206411 GTAAGTTATG
38206421 TATTATGTAAGTTATGTAAG-TTTTTG-TTTTTGTGTATTATGTAACTTATTTAATTTATGTA-G
1 TATTATGTAAGTTATGTAAGTTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGG
*
38206483 GTCATGTATTATTATGTAAGTTATTATGTAGGA
66 GT-A-GGA-TATTATGTAAGTTATTATGTAGGA
38206516 TATTATGTAAGTTATGTAAGTTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGG
1 TATTATGTAAGTTATGTAAGTTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGG
38206581 GTAGGATATTATGTAAGTTAT
66 GTAGGATATTATGTAAGTTAT
38206602 GTAAGTTTTT
Statistics
Matches: 82, Mismatches: 1, Indels: 6
0.92 0.01 0.07
Matches are distributed among these distances:
95 35 0.43
96 8 0.10
97 36 0.44
98 3 0.04
ACGTcount: A:0.27, C:0.02, G:0.18, T:0.53
Consensus pattern (95 bp):
TATTATGTAAGTTATGTAAGTTTTTTGTTTTTTGTGTATTATGTAACTTATTTAATTTATGTAGG
GTAGGATATTATGTAAGTTATTATGTAGGA
Found at i:38206593 original size:71 final size:71
Alignment explanation
Indices: 38206510--38206675 Score: 271
Period size: 71 Copynumber: 2.3 Consensus size: 71
38206500 AAGTTATTAT
38206510 GTAGGATATTATGTAAGTTATGTAAGTTTTT-TGTTTTTTGTGTATTATGTAACTTATTTAATTT
1 GTAGGATATTATGTAAGTTATGTAAGTTTTTGT-TTTTTTGTGTATTATGTAACTTATTTAATTT
*
38206574 ATGTAGG
65 ATATAGG
38206581 GTAGGATATTATGTAAGTTATGTAAGTTTTTGTTTTTTTGTGTATTATGTAACTTATTTAATTTA
1 GTAGGATATTATGTAAGTTATGTAAGTTTTTGTTTTTTTGTGTATTATGTAACTTATTTAATTTA
38206646 TATAGG
66 TATAGG
* *
38206652 TTATGTATTATTATGTAAGTTATG
1 GTA-GGA-TATTATGTAAGTTATG
38206676 AATTATGTAA
Statistics
Matches: 89, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
71 70 0.79
72 3 0.03
73 16 0.18
ACGTcount: A:0.27, C:0.01, G:0.19, T:0.54
Consensus pattern (71 bp):
GTAGGATATTATGTAAGTTATGTAAGTTTTTGTTTTTTTGTGTATTATGTAACTTATTTAATTTA
TATAGG
Found at i:38206680 original size:16 final size:16
Alignment explanation
Indices: 38206661--38206711 Score: 75
Period size: 16 Copynumber: 3.1 Consensus size: 16
38206651 GTTATGTATT
38206661 ATTATGTAAGTTATGA
1 ATTATGTAAGTTATGA
38206677 ATTATGTAAGTTATGTAA
1 ATTATGTAAGTTATG--A
*
38206695 ATTACGTAAGTTATGA
1 ATTATGTAAGTTATGA
38206711 A
1 A
38206712 ATTTGAACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 17 0.53
18 15 0.47
ACGTcount: A:0.39, C:0.02, G:0.18, T:0.41
Consensus pattern (16 bp):
ATTATGTAAGTTATGA
Found at i:38210504 original size:114 final size:114
Alignment explanation
Indices: 38210253--38210742 Score: 642
Period size: 114 Copynumber: 4.3 Consensus size: 114
38210243 AGACAAATAA
* * * * * ** *
38210253 TTTTTTTGCAGCGCTTTCCCACAAACGCCGCTAAATCCCAGAGCATTAGCGGCG-TTGTATTAAA
1 TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTT-CCTCAAA
* * * * * * * *
38210317 AATGCCACTAAAGCCCCCGAAAGGTCAGAAAATGGCATCGTTGGGCTTATG
65 AACGCCGCTAAA-TCCCCGAATGCTCAGAAAACGGCGTCGTTGGGCTTAGG
* * * * *
38210368 TTTTTTTGCGGTGCTTTATCAAAAACGTCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAA
1 TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTCAAAA
38210433 ACGCCGCTAAATCCCCGAATGCTCAGAAAACGGCGTCGTTGGGCTTAGG
66 ACGCCGCTAAATCCCCGAATGCTCAGAAAACGGCGTCGTTGGGCTTAGG
* *
38210482 TTTTTTTGTGGCGCTTTCTCAAAAACGCCGCTAAAACCCTGAGCATTAGCGGCGCTTCCTCAAAA
1 TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTCAAAA
* **
38210547 ATGCCGCTAAATCCCCGAATGCTCAGAAAATAGCGTCGTTGGGCTTAGG
66 ACGCCGCTAAATCCCCGAATGCTCAGAAAACGGCGTCGTTGGGCTTAGG
* * *
38210596 TTTTTTTACGGCACTTTCTCAAAAACACCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTCAAAA
1 TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTCAAAA
* *
38210661 ACGGCGCTAAATCCCCGAATGCTCAAAAAACGGCGTCGTTGGGCTTAGG
66 ACGCCGCTAAATCCCCGAATGCTCAGAAAACGGCGTCGTTGGGCTTAGG
* * *
38210710 -TTTTTTGAGGCGCTTTCTGAAAAACGCTGCTAA
1 TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAA
38210743 TACTTATTTT
Statistics
Matches: 331, Mismatches: 43, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
113 27 0.08
114 240 0.73
115 62 0.19
116 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (114 bp):
TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTCAAAA
ACGCCGCTAAATCCCCGAATGCTCAGAAAACGGCGTCGTTGGGCTTAGG
Found at i:38210873 original size:22 final size:23
Alignment explanation
Indices: 38210845--38210910 Score: 91
Period size: 22 Copynumber: 3.0 Consensus size: 23
38210835 GTGTAGTGTG
38210845 GACAACATTTAATCAACAATTT-
1 GACAACATTTAATCAACAATTTA
* *
38210867 GACAACATTCAATCAA-TATTTA
1 GACAACATTTAATCAACAATTTA
*
38210889 GACAGCATTTAATCAACAATTT
1 GACAACATTTAATCAACAATTT
38210911 TTTACTTCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 4 0.11
22 29 0.78
23 4 0.11
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (23 bp):
GACAACATTTAATCAACAATTTA
Found at i:38211767 original size:43 final size:42
Alignment explanation
Indices: 38211731--38211859 Score: 111
Period size: 42 Copynumber: 3.0 Consensus size: 42
38211721 TCTTTCATGT
*
38211731 AATCAAACAACGATGCCACTGTCCCAGATAGAGTCTTACACGA
1 AATCAAA-AACGATGCCAATGTCCCAGATAGAGTCTTACACGA
* * *
38211774 AATCATATACGATGCCAATGTCCCAGACATG-GTCTTACACGTA
1 AATCAAAAACGATGCCAATGTCCCAGATA-GAGTCTTACACG-A
* * * *
38211817 AATCTCAAATCGA-GCCCAACT-TCCCAGACATAGTCTTACACGA
1 AATC-AAAAACGATG-CCAA-TGTCCCAGATAGAGTCTTACACGA
38211860 TGTCACATTT
Statistics
Matches: 71, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
42 29 0.41
43 14 0.20
44 27 0.38
45 1 0.01
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.22
Consensus pattern (42 bp):
AATCAAAAACGATGCCAATGTCCCAGATAGAGTCTTACACGA
Found at i:38211799 original size:42 final size:43
Alignment explanation
Indices: 38211700--38211858 Score: 132
Period size: 43 Copynumber: 3.7 Consensus size: 43
38211690 AGCTTGTACA
* * * * * *
38211700 ATGCCAACGTCCCAGACGTGGTCTTTCATGT-AATCAAACAACG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCATA-TACG
* *
38211743 ATGCCACTGTCCCAGATA-GAGTCTTACACG-AAATCATATACG
1 ATGCCAATGTCCCAGACATG-GTCTTACACGTAAATCATATACG
*
38211785 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATC-TCAAATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCAT-ATA-CG
*
38211829 A-GCCCAACT-TCCCAGACATAGTCTTACACG
1 ATG-CCAA-TGTCCCAGACATGGTCTTACACG
38211859 ATGTCACATT
Statistics
Matches: 96, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
42 31 0.32
43 37 0.39
44 27 0.28
45 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.23
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCATATACG
Found at i:38213498 original size:16 final size:16
Alignment explanation
Indices: 38213477--38213542 Score: 52
Period size: 16 Copynumber: 4.3 Consensus size: 16
38213467 CCTCTCCTTG
*
38213477 TATTTATTTTATTTAT
1 TATTTATTTTACTTAT
38213493 TATTTA-TTTAGCTTA-
1 TATTTATTTTA-CTTAT
* *
38213508 T-TTAATTTTATTTGAT
1 TATTTATTTTACTT-AT
38213524 T-TTTATTTTACTT-T
1 TATTTATTTTACTTAT
38213538 TATTT
1 TATTT
38213543 TAGTTCTAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
14 7 0.17
15 13 0.32
16 20 0.50
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (16 bp):
TATTTATTTTACTTAT
Found at i:38213500 original size:11 final size:10
Alignment explanation
Indices: 38213477--38213542 Score: 55
Period size: 11 Copynumber: 6.5 Consensus size: 10
38213467 CCTCTCCTTG
38213477 TATTTA-TTT
1 TATTTATTTT
38213486 TATTTATTATT
1 TATTTATT-TT
**
38213497 TATTTA-GCT
1 TATTTATTTT
*
38213506 TATTTAATTT
1 TATTTATTTT
38213516 TATTTGATTTT
1 TATTT-ATTTT
*
38213527 TATTTTACTTT
1 TA-TTTATTTT
38213538 TATTT
1 TATTT
38213543 TAGTTCTAGA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
9 13 0.28
10 10 0.22
11 20 0.43
12 3 0.07
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (10 bp):
TATTTATTTT
Found at i:38213735 original size:24 final size:23
Alignment explanation
Indices: 38213705--38213751 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
38213695 ATTCGTAGGT
* *
38213705 TCTATTTTTATTATCTTTTCATCA
1 TCTATTTTCATCATC-TTTCATCA
38213729 TCTATTTTCATCATCTTTCATCA
1 TCTATTTTCATCATCTTTCATCA
38213752 AAAAACATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.57
Consensus pattern (23 bp):
TCTATTTTCATCATCTTTCATCA
Found at i:38213738 original size:13 final size:13
Alignment explanation
Indices: 38213720--38213744 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38213710 TTTTATTATC
38213720 TTTTCATCATCTA
1 TTTTCATCATCTA
38213733 TTTTCATCATCT
1 TTTTCATCATCT
38213745 TTCATCAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTCATCATCTA
Found at i:38214612 original size:25 final size:24
Alignment explanation
Indices: 38214584--38214694 Score: 87
Period size: 25 Copynumber: 4.5 Consensus size: 24
38214574 ACAGCTCTCT
*
38214584 TGAGCTTCCCGATACTTGGCTCTTA
1 TGAGCTTCCCGATA-TTGGCTCATA
* * *
38214609 TGAGTTTCTCGATATTTGGCTCACA
1 TGAGCTTCCCGATA-TTGGCTCATA
* ** *
38214634 AGAGCTTCCCGATATACAGCTCGTA
1 TGAGCTTCCCGATAT-TGGCTCATA
* *
38214659 TGAGCTTCCCGTTATATGGCTCAGA
1 TGAGCTTCCCGATAT-TGGCTCATA
*
38214684 AGAGCTTCCCG
1 TGAGCTTCCCG
38214695 TTTACATGCT
Statistics
Matches: 66, Mismatches: 19, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
24 1 0.02
25 65 0.98
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.32
Consensus pattern (24 bp):
TGAGCTTCCCGATATTGGCTCATA
Found at i:38214661 original size:50 final size:50
Alignment explanation
Indices: 38214585--38214694 Score: 132
Period size: 50 Copynumber: 2.2 Consensus size: 50
38214575 CAGCTCTCTT
** * * * *
38214585 GAGCTTCCCGATACTTGGCTCTTATGAGTTTCTCGATATTTGGCTCACAA
1 GAGCTTCCCGATACTCAGCTCGTATGAGCTTCCCGATATATGGCTCACAA
* *
38214635 GAGCTTCCCGATA-TACAGCTCGTATGAGCTTCCCGTTATATGGCTCAGAA
1 GAGCTTCCCGATACT-CAGCTCGTATGAGCTTCCCGATATATGGCTCACAA
38214685 GAGCTTCCCG
1 GAGCTTCCCG
38214695 TTTACATGCT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
49 1 0.02
50 50 0.98
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (50 bp):
GAGCTTCCCGATACTCAGCTCGTATGAGCTTCCCGATATATGGCTCACAA
Found at i:38215450 original size:28 final size:28
Alignment explanation
Indices: 38215411--38215524 Score: 142
Period size: 28 Copynumber: 4.1 Consensus size: 28
38215401 CTATACAGTA
*
38215411 ACAGT-ACAGTGTGGGCCTTAGCCTAGA-
1 ACAGTAACAGTGTGGGCCTTAGCCCA-AT
*
38215438 ACAGTAACAGTGTGGGCTTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* *
38215466 ATAGTAATAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* * *
38215494 ATAGTAACAGTTTAGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
38215522 ACA
1 ACA
38215525 ATAATAGTAC
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
27 6 0.08
28 70 0.92
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (28 bp):
ACAGTAACAGTGTGGGCCTTAGCCCAAT
Found at i:38215810 original size:2 final size:2
Alignment explanation
Indices: 38215803--38215840 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
38215793 AGTAACAGTC
38215803 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
38215841 ATGAATCAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:38215911 original size:27 final size:26
Alignment explanation
Indices: 38215873--38216096 Score: 197
Period size: 27 Copynumber: 8.3 Consensus size: 26
38215863 AAGGCTATAA
38215873 CAGTCATTTTACCCTAT-GAGGGTATTT
1 CAGTCATTTTACCCT-TCG-GGGTATTT
*
38215900 CAGTCATTTTACCCTTTCGCGGTATTT
1 CAGTCATTTTACCC-TTCGGGGTATTT
*
38215927 CGGTCATTTTACCCTTCGGAGGTATTT
1 CAGTCATTTTACCCTTCGG-GGTATTT
*
38215954 C-GATCATTTTACCC-TCATGGGTATTT
1 CAG-TCATTTTACCCTTC-GGGGTATTT
* *
38215980 CGGTCATTTTACCCTCCGGGGGTATTT
1 CAGTCATTTTACCCTTC-GGGGTATTT
*
38216007 C-GATCATTTTACCCTTCGAGGGTGTTT
1 CAG-TCATTTTACCCTTCG-GGGTATTT
*
38216034 -AGATTATTTTACCCTTCGAGGGTATTT
1 CAG-TCATTTTACCCTTCG-GGGTATTT
** *
38216061 TGGTCATTTTACCCTTCAAGGGTATTT
1 CAGTCATTTTACCCTTC-GGGGTATTT
* *
38216088 TAGTTATTT
1 CAGTCATTT
38216097 GCCCATGAAT
Statistics
Matches: 169, Mismatches: 16, Indels: 24
0.81 0.08 0.11
Matches are distributed among these distances:
26 28 0.17
27 138 0.82
28 3 0.02
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (26 bp):
CAGTCATTTTACCCTTCGGGGTATTT
Found at i:38216068 original size:107 final size:108
Alignment explanation
Indices: 38215875--38216087 Score: 272
Period size: 107 Copynumber: 2.0 Consensus size: 108
38215865 GGCTATAACA
* * *
38215875 GTCATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTTTCGCGGTATTTCGGTCATTTTACC
1 GTCATTTTACCCTACGAGGGTATTTCAGTCATTTTACCCTTTCGCGGTATTTAGATCATTTTACC
*
38215940 CTTCGGAGGTATTTCGATCATTTTACCC-TCATGGGTATTTCG
66 CTTCGGAGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCG
* * * * *
38215982 GTCATTTTACCCTCCGGGGGTATTTC-GATCATTTTACCC-TTCGAGGGTGTTTAGATTATTTTA
1 GTCATTTTACCCTACGAGGGTATTTCAG-TCATTTTACCCTTTCG-CGGTATTTAGATCATTTTA
* *
38216045 CCCTTC-GAGGGTATTTTGGTCATTTTACCCTTCAAGGGTATTT
64 CCCTTCGGA-GGTATTTCGATCATTTTACCCTTCAAGGGTATTT
38216088 TAGTTATTTG
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
106 7 0.08
107 73 0.80
108 11 0.12
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.42
Consensus pattern (108 bp):
GTCATTTTACCCTACGAGGGTATTTCAGTCATTTTACCCTTTCGCGGTATTTAGATCATTTTACC
CTTCGGAGGTATTTCGATCATTTTACCCTTCAAGGGTATTTCG
Found at i:38216077 original size:54 final size:54
Alignment explanation
Indices: 38215875--38216087 Score: 240
Period size: 54 Copynumber: 4.0 Consensus size: 54
38215865 GGCTATAACA
* *
38215875 GTCATTTTACCCTAT-GAGGGTATTTC-AGTCATTTTACCCTTTCG-CGGTATTTCG
1 GTCATTTTACCCT-TCGAGGGTATTTCGA-TCATTTTACCC-TTCGAGGGTATTTAG
*
38215929 GTCATTTTACCCTTCG-GAGGTATTTCGATCATTTTACCC-TC-ATGGGTATTTCG
1 GTCATTTTACCCTTCGAG-GGTATTTCGATCATTTTACCCTTCGA-GGGTATTTAG
* * *
38215982 GTCATTTTACCCTCCGGGGGTATTTCGATCATTTTACCCTTCGAGGGTGTTTAG
1 GTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTAG
* * * * *
38216036 ATTATTTTACCCTTCGAGGGTATTTTGGTCATTTTACCCTTCAAGGGTATTT
1 GTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCGAGGGTATTT
38216088 TAGTTATTTG
Statistics
Matches: 139, Mismatches: 12, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
52 2 0.01
53 47 0.34
54 88 0.63
55 2 0.01
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.42
Consensus pattern (54 bp):
GTCATTTTACCCTTCGAGGGTATTTCGATCATTTTACCCTTCGAGGGTATTTAG
Found at i:38222039 original size:21 final size:21
Alignment explanation
Indices: 38222013--38222052 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
38222003 AGATCATTAA
38222013 TTTTATCTATTTT-ATTTTTAG
1 TTTTAT-TATTTTCATTTTTAG
*
38222034 TTTTATTTTTTTCATTTTT
1 TTTTATTATTTTCATTTTT
38222053 TTTGTTTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.78
Consensus pattern (21 bp):
TTTTATTATTTTCATTTTTAG
Found at i:38227141 original size:63 final size:63
Alignment explanation
Indices: 38227042--38227172 Score: 244
Period size: 63 Copynumber: 2.1 Consensus size: 63
38227032 AGGAGCTAGC
*
38227042 TTACTGATATCATTAAGAATAAGAGAGGCCTAATTCTAACCAATAAACACACACAAGCGGGTT
1 TTACTGATATCATTAAGAATAAGAGAGGCCTAATTCTAACAAATAAACACACACAAGCGGGTT
*
38227105 TTACTGATATCATTAAGAATGAGAGAGGCCTAATTCTAACAAATAAACACACACAAGCGGGTT
1 TTACTGATATCATTAAGAATAAGAGAGGCCTAATTCTAACAAATAAACACACACAAGCGGGTT
38227168 TTACT
1 TTACT
38227173 TAGATGAGAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.25
Consensus pattern (63 bp):
TTACTGATATCATTAAGAATAAGAGAGGCCTAATTCTAACAAATAAACACACACAAGCGGGTT
Found at i:38237878 original size:21 final size:22
Alignment explanation
Indices: 38237839--38237879 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
38237829 TCAAAAAAAA
*
38237839 TAATACAAATGGATGAATTTTT
1 TAATACAAATGGATCAATTTTT
*
38237861 TAATAGAAA-GGATCAATTT
1 TAATACAAATGGATCAATTT
38237880 ACTATTTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.37
Consensus pattern (22 bp):
TAATACAAATGGATCAATTTTT
Found at i:38240995 original size:20 final size:20
Alignment explanation
Indices: 38240970--38241007 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38240960 GCAGTGGAAA
38240970 TTTATTTTCTTA-GAATAAAT
1 TTTATTTT-TTAGGAATAAAT
38240990 TTTATTTTTTAGGAATAA
1 TTTATTTTTTAGGAATAA
38241008 TAATTTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (20 bp):
TTTATTTTTTAGGAATAAAT
Found at i:38244951 original size:29 final size:27
Alignment explanation
Indices: 38244919--38244996 Score: 95
Period size: 26 Copynumber: 2.9 Consensus size: 27
38244909 AGTGCATTAA
*
38244919 CAGAACAGAGGTGCACCGAAGTGCAATGC
1 CAGAACAGAGG-ACACCGAAGTGCAAT-C
* *
38244948 CAGAACGGAGGACACCGTAGTGCAATC
1 CAGAACAGAGGACACCGAAGTGCAATC
*
38244975 C-GAATAGAGGACACCGAAGTGC
1 CAGAACAGAGGACACCGAAGTGC
38244997 TAATAGAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
26 18 0.42
27 2 0.05
28 13 0.30
29 10 0.23
ACGTcount: A:0.35, C:0.24, G:0.31, T:0.10
Consensus pattern (27 bp):
CAGAACAGAGGACACCGAAGTGCAATC
Found at i:38244995 original size:26 final size:26
Alignment explanation
Indices: 38244932--38245010 Score: 88
Period size: 26 Copynumber: 3.0 Consensus size: 26
38244922 AACAGAGGTG
**
38244932 CACCGAAGTGCAATGCCAGAACGGAGGA
1 CACCGAAGTGCAAT-CC-GAATAGAGGA
*
38244960 CACCGTAGTGCAATCCGAATAGAGGA
1 CACCGAAGTGCAATCCGAATAGAGGA
*
38244986 CACCGAAGTGCTAAT-AGAATAGAGG
1 CACCGAAGTGC-AATCCGAATAGAGG
38245011 GCGCACTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
26 27 0.60
27 5 0.11
28 13 0.29
ACGTcount: A:0.37, C:0.22, G:0.29, T:0.13
Consensus pattern (26 bp):
CACCGAAGTGCAATCCGAATAGAGGA
Found at i:38248099 original size:6 final size:6
Alignment explanation
Indices: 38248090--38248114 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
38248080 TTATATTTGT
38248090 TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA T
38248115 ATTTTATTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:38259781 original size:203 final size:200
Alignment explanation
Indices: 38259432--38259834 Score: 754
Period size: 203 Copynumber: 2.0 Consensus size: 200
38259422 AATGCGTACT
38259432 ACAGGGCGTTTTTACTGATGTGGCAGTGAAAAGGCGCCCTGTAGGACGCGTTTTCCTTTCTCTAT
1 ACAGGGCGTTTTTACTGATGTGGCAGTGAAAAGGCGCCCTGTAGGACGCGTTTTCCTTTCTCTAT
*
38259497 AAAAAACAACGTAGATTAGTAAATTTTTAGAAAATCAGCATAGTTTATCAAAAAAAAAAGAAATT
66 AAAAAACAACATAGATTAGTAAATTTTTAGAAAATCAGCATAGTTTATCAAAAAAAAAAGAAATT
38259562 TCAACATATTTAGATAAATCCGCCGCCATATTCGCTTATTATTATTATTATTATTATTTGGCATA
131 TCAACATATTTAGATAAATCCGCCGCCATATTCGC---TTATTATTATTATTATTATTTGGCATA
38259627 ACCACTTA
193 ACCACTTA
38259635 ACAGGGCGTTTTTACTGATGTGGCAGTGAAAAGGCGCCCTGTAGGACGCGTTTTCCTTTCTCTAT
1 ACAGGGCGTTTTTACTGATGTGGCAGTGAAAAGGCGCCCTGTAGGACGCGTTTTCCTTTCTCTAT
38259700 AAAAAAACAACATAGATTAGTAAATTTTTAGAAAATCAGCATAGTTTATC-AAAAAAAAAGAAAT
66 -AAAAAACAACATAGATTAGTAAATTTTTAGAAAATCAGCATAGTTTATCAAAAAAAAAAGAAAT
38259764 TTCAACATATTTAGATAAATCCGCCGCCATATTCGCTTATTATTATTATTATTATTTGGCATAAC
130 TTCAACATATTTAGATAAATCCGCCGCCATATTCGCTTATTATTATTATTATTATTTGGCATAAC
38259829 CACTTA
195 CACTTA
38259835 TTTGGCCCTC
Statistics
Matches: 198, Mismatches: 1, Indels: 5
0.97 0.00 0.02
Matches are distributed among these distances:
200 35 0.18
203 115 0.58
204 48 0.24
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (200 bp):
ACAGGGCGTTTTTACTGATGTGGCAGTGAAAAGGCGCCCTGTAGGACGCGTTTTCCTTTCTCTAT
AAAAAACAACATAGATTAGTAAATTTTTAGAAAATCAGCATAGTTTATCAAAAAAAAAAGAAATT
TCAACATATTTAGATAAATCCGCCGCCATATTCGCTTATTATTATTATTATTATTTGGCATAACC
ACTTA
Found at i:38265498 original size:21 final size:21
Alignment explanation
Indices: 38265472--38265512 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
38265462 CCACCGCCAG
38265472 CCTTTTTCTGCTCCCCTCCAC
1 CCTTTTTCTGCTCCCCTCCAC
38265493 CCTTTTTCTGCTCCCCTCCA
1 CCTTTTTCTGCTCCCCTCCA
38265513 GCCATATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.05, C:0.51, G:0.05, T:0.39
Consensus pattern (21 bp):
CCTTTTTCTGCTCCCCTCCAC
Found at i:38272846 original size:38 final size:40
Alignment explanation
Indices: 38272793--38272867 Score: 109
Period size: 38 Copynumber: 1.9 Consensus size: 40
38272783 ACACAAAAAA
* *
38272793 TATTTTAAAAATAAAAA-ATAA-AAAATATATTTTTAAAG
1 TATTTTAAAAATAAAAATAAAATAAAATATATATTTAAAG
*
38272831 TATTTTAAAATTAAAAATAAAATAAAATATATATTTA
1 TATTTTAAAAATAAAAATAAAATAAAATATATATTTA
38272868 TTATATTCGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 16 0.50
39 3 0.09
40 13 0.41
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (40 bp):
TATTTTAAAAATAAAAATAAAATAAAATATATATTTAAAG
Found at i:38273372 original size:21 final size:21
Alignment explanation
Indices: 38273348--38273387 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
38273338 TTACAATTTT
*
38273348 TAAAGTTAAAAGTTAAAACCA
1 TAAAGTTAAAAGATAAAACCA
38273369 TAAAGTTAAAAGATAAAAC
1 TAAAGTTAAAAGATAAAAC
38273388 TACGTCACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.07, G:0.10, T:0.23
Consensus pattern (21 bp):
TAAAGTTAAAAGATAAAACCA
Found at i:38281992 original size:27 final size:28
Alignment explanation
Indices: 38281962--38282014 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
38281952 CCATTTGCTA
* *
38281962 TTATATTTAAATTTTTAAAT-ATTTAAT
1 TTATAATTAAATTTATAAATAATTTAAT
*
38281989 TTATAATTGAATTTATAAATAATTTA
1 TTATAATTAAATTTATAAATAATTTA
38282015 TTAATTATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
TTATAATTAAATTTATAAATAATTTAAT
Found at i:38282126 original size:33 final size:33
Alignment explanation
Indices: 38282089--38282208 Score: 107
Period size: 33 Copynumber: 3.4 Consensus size: 33
38282079 TTAATTTATT
38282089 TTTTAATTTTCAATATCATGTATAAAATGAACA
1 TTTTAATTTTCAATATCATGTATAAAATGAACA
* * * *
38282122 TTTTAATTTCTCAAGA-CAAATATTTAATTTTCATTAGAACA
1 TTTTAATTT-TCAATATC--ATGTATAA-----AAT-GAACA
38282163 TTTTAATTTTCAATATCATGTATAAAATGAACA
1 TTTTAATTTTCAATATCATGTATAAAATGAACA
*
38282196 TTTTAATATTCAA
1 TTTTAATTTTCAA
38282209 AAACATTTCT
Statistics
Matches: 68, Mismatches: 9, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
33 27 0.40
34 7 0.10
35 6 0.09
39 6 0.09
40 7 0.10
41 15 0.22
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (33 bp):
TTTTAATTTTCAATATCATGTATAAAATGAACA
Found at i:38282169 original size:20 final size:18
Alignment explanation
Indices: 38282117--38282175 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 18
38282107 TGTATAAAAT
38282117 GAACATTTTAATTTCTCAA
1 GAACATTTTAATTT-TCAA
*
38282136 GACAAATATTTAATTTTCATTA
1 GA-ACAT-TTTAATTTTCA--A
38282158 GAACATTTTAATTTTCAA
1 GAACATTTTAATTTTCAA
38282176 TATCATGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
18 1 0.03
19 2 0.06
20 17 0.50
21 11 0.32
22 3 0.09
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (18 bp):
GAACATTTTAATTTTCAA
Found at i:38282802 original size:16 final size:16
Alignment explanation
Indices: 38282781--38282818 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
38282771 TTTGGTTCGC
38282781 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
38282797 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
38282813 CGTAAT
1 TGTAAT
38282819 AGTAATTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.03, G:0.34, T:0.26
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:38285270 original size:105 final size:108
Alignment explanation
Indices: 38285008--38285311 Score: 321
Period size: 108 Copynumber: 2.9 Consensus size: 108
38284998 TAAATAAGGT
* * * *
38285008 AATATTTTGTGTTTAGAAAATCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTCTCGTTCG
1 AATATTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTTTG
* *
38285073 ACCCAAATAGCCAAATACCCTTTTTAAACTTTCAAAATAAGAC
66 ACCCAAATAGCCAAATACCCTTTTGAAACTTTCAAAACAAGAC
* * * * *
38285116 CATATTTCGCATTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTACTCGTTTG
1 AATATTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTTTG
* * * * * * *
38285181 -GCCAAATAGTCGAATA-TCTTTTCGAAA-TTTTAAAACGAGGC
66 ACCCAAATAGCCAAATACCCTTTT-GAAACTTTCAAAACAAGAC
* * * *
38285222 AATGTTTTGCGTTTAGAAATTTGAG-GAACGTGCCCTAAGGTGCTGGGTTTCGATTTCTCGTTT-
1 AATATTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTTTG
** * * *
38285285 AATCAAATTGCCAAATATCCTCTTGAA
66 ACCCAAATAGCCAAATACCCTTTTGAA
38285312 TTTTAATCTA
Statistics
Matches: 159, Mismatches: 34, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
105 49 0.31
106 38 0.24
107 16 0.10
108 56 0.35
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (108 bp):
AATATTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTCGTTTG
ACCCAAATAGCCAAATACCCTTTTGAAACTTTCAAAACAAGAC
Found at i:38289335 original size:48 final size:48
Alignment explanation
Indices: 38289281--38289377 Score: 131
Period size: 48 Copynumber: 2.0 Consensus size: 48
38289271 ATCCGATTCG
* *
38289281 AAAAAAAGGAAAAGAAAAAGAGAAAAAAATCAAAATCAAAATCAAAAT
1 AAAAAAAGAAAAAGAAAAAGAGAAAAAAATCAAAATCAAAATAAAAAT
* * ** *
38289329 AAAAAAATAAAAAGAAAAATAGAAATCAATCAAAGTCAAAATAAAAAT
1 AAAAAAAGAAAAAGAAAAAGAGAAAAAAATCAAAATCAAAATAAAAAT
38289377 A
1 A
38289378 TGAAAAGCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.74, C:0.06, G:0.08, T:0.11
Consensus pattern (48 bp):
AAAAAAAGAAAAAGAAAAAGAGAAAAAAATCAAAATCAAAATAAAAAT
Found at i:38292463 original size:17 final size:17
Alignment explanation
Indices: 38292441--38292474 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
38292431 AACGATAGAG
38292441 ATAAAAAATCTTAACTC
1 ATAAAAAATCTTAACTC
*
38292458 ATAAAAAATCTTGACTC
1 ATAAAAAATCTTAACTC
38292475 CAAGTTTATT
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:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (17 bp):
ATAAAAAATCTTAACTC
Found at i:38295256 original size:27 final size:27
Alignment explanation
Indices: 38295226--38295286 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
38295216 TATCTCGGTT
38295226 GACTATCCCATATTTAA-TGTCTCGTCA
1 GACTATCCCATATTTAACTGTCT-GTCA
* * * *
38295253 GACTATCTCGTGTTTAACTTTCTGTCA
1 GACTATCCCATATTTAACTGTCTGTCA
38295280 GACTATC
1 GACTATC
38295287 TATGATACCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39
Consensus pattern (27 bp):
GACTATCCCATATTTAACTGTCTGTCA
Found at i:38298347 original size:20 final size:20
Alignment explanation
Indices: 38298322--38298361 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
38298312 AATATTTTCC
*
38298322 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
38298342 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
38298362 TCATTTTACG
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:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:38298367 original size:34 final size:35
Alignment explanation
Indices: 38298310--38298376 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
38298300 CAAACACTAG
*
38298310 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
38298345 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
38298377 TATTTTACTG
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:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:38299609 original size:29 final size:29
Alignment explanation
Indices: 38299559--38299614 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
38299549 ATAAGAACTT
*
38299559 GATCAATTTAGTCCATGCACTATTAAATG
1 GATCAAATTAGTCCATGCACTATTAAATG
** *
38299588 GATCAAATTAGTCTTTGTACTATTAAA
1 GATCAAATTAGTCCATGCACTATTAAA
38299615 AAGAATTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (29 bp):
GATCAAATTAGTCCATGCACTATTAAATG
Found at i:38317608 original size:13 final size:13
Alignment explanation
Indices: 38317590--38317620 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
38317580 GTCATGTGTC
*
38317590 ACACACGGCTGAA
1 ACACACGCCTGAA
38317603 ACACACGCCTGAA
1 ACACACGCCTGAA
38317616 ACACA
1 ACACA
38317621 TGCCCGTGTC
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:0.42, C:0.35, G:0.16, T:0.06
Consensus pattern (13 bp):
ACACACGCCTGAA
Found at i:38318822 original size:51 final size:50
Alignment explanation
Indices: 38318719--38318841 Score: 124
Period size: 51 Copynumber: 2.4 Consensus size: 50
38318709 TATAAAACTT
* * * *
38318719 ATATATATATATATATATAAAATACATAATGCATTTATGAAAACAAGGAAA
1 ATATAAATATATA-ATATAAAATACATAATGCATTTATCAAAAAAAAGAAA
* * *
38318770 ATATAAATATATACATATAAAATATATTCATGCATTTA-CAAAAAAAATAAA
1 ATATAAATATATA-ATATAAAATACA-TAATGCATTTATCAAAAAAAAGAAA
*
38318821 ATATATAA-GTATAATATAAAA
1 ATATA-AATATATAATATAAAA
38318842 CGTGGAAAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
50 8 0.13
51 41 0.67
52 12 0.20
ACGTcount: A:0.58, C:0.06, G:0.05, T:0.32
Consensus pattern (50 bp):
ATATAAATATATAATATAAAATACATAATGCATTTATCAAAAAAAAGAAA
Found at i:38319119 original size:3 final size:3
Alignment explanation
Indices: 38319106--38319148 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
38319096 ATATGTAGGT
* *
38319106 ATA AAA ATA ATA ATA TATA AT- ATA ATA ATA ATA ATA AAA ATA A
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA A
38319149 CAAAATTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:38319148 original size:18 final size:18
Alignment explanation
Indices: 38319106--38319162 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
38319096 ATATGTAGGT
38319106 ATAAAAATAATAAT-AT-
1 ATAAAAATAATAATAATA
*
38319122 AT-AATATAATAATAATA
1 ATAAAAATAATAATAATA
*
38319139 ATAAAAATAACAA-AATTA
1 ATAAAAATAATAATAA-TA
38319157 ATAAAA
1 ATAAAA
38319163 TAGACTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 10 0.29
16 4 0.12
17 4 0.12
18 16 0.47
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (18 bp):
ATAAAAATAATAATAATA
Found at i:38319405 original size:19 final size:21
Alignment explanation
Indices: 38319367--38319405 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
38319357 CCTTTTTTAA
*
38319367 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
38319388 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
38319406 AAGAAAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:38319632 original size:21 final size:21
Alignment explanation
Indices: 38319606--38319662 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
38319596 AATCATATCT
38319606 TCTAAGATTGTATATATCATA
1 TCTAAGATTGTATATATCATA
* *
38319627 TCTAAGATTGCACATATCATA
1 TCTAAGATTGTATATATCATA
38319648 TCTAAGATTGTATAT
1 TCTAAGATTGTATAT
38319663 CCTCGAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (21 bp):
TCTAAGATTGTATATATCATA
Found at i:38320049 original size:44 final size:44
Alignment explanation
Indices: 38319973--38320305 Score: 201
Period size: 44 Copynumber: 7.7 Consensus size: 44
38319963 CTCTAATCCA
* * * * *
38319973 CTCCACTACAACTT-AGGGAGACAGGATTTGTTTATTTAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTACTTAGTCTG
38320016 C-CTCACTGCAACTTCA-GGAGGATAAGACTTGTTTACTTAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGACTTGTTTACTTAGTCTG
* **
38320060 CTCCACTGCAACTTCAGGGAGATAAGACTAG---AC-GCGATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTACTTAG-TCTG
* * ** * *
38320101 CT-CTCTGCAACTTCAGAGAGATAAGATCCAAGGTT--TT-GATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGA--CTTGTTTACTTAG-TCTG
* * *** *
38320144 CTCCACTGCAACTTCAGGGAGATAGGA-TTATCGGCTCTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTACT-TAGTCTG
* ** *
38320188 CTCCACTGCAACTTCAGGGAGATAAGATTTG-CCATCTTCAGTCTA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTA-CTT-AGTCTG
* * *
38320233 C-CTCACTGCAACTTCA-GGAGGATAAGACTTGCTTGCTGAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGACTTGTTTACTTAGTCTG
* *
38320277 CTCCACTACAACTTCAGGGAGAAAAGACT
1 CTCCACTGCAACTTCAGGGAGATAAGACT
38320306 AGATGCGATC
Statistics
Matches: 227, Mismatches: 38, Indels: 49
0.72 0.12 0.16
Matches are distributed among these distances:
40 23 0.10
41 8 0.04
42 4 0.02
43 22 0.10
44 128 0.56
45 42 0.19
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.27
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGTTTACTTAGTCTG
Found at i:38320393 original size:217 final size:217
Alignment explanation
Indices: 38319963--38320444 Score: 754
Period size: 217 Copynumber: 2.2 Consensus size: 217
38319953 AAATCCATCA
** * * * ** *
38319963 CTCTAATCCACTCCACTACAACTT-AGGGAGACAGGATTTGTTTAT-TT-AGTCTGCCTCACTGC
1 CTCTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-CCATCTTCAGTCTACCTCACTGC
* * * *
38320025 AACTTCAGGAGGATAAGACTTGTTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
65 AACTTCAGGAGGATAAGACTTGCTTACTGAGTCTGCTCCACTACAACTTCAGGGAGAAAAGACTA
*
38320090 GACGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTGATCCGCTCCACTGCAA
130 GACGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTCCACTGCAA
**
38320155 CTTCAGGGAGATAGGATTATCGG
195 CTTCAACGAGATAGGATTATCGG
38320178 CTCTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTACCTCACTGCA
1 CTCTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTACCTCACTGCA
*
38320243 ACTTCAGGAGGATAAGACTTGCTTGCTGAGTCTGCTCCACTACAACTTCAGGGAGAAAAGACTAG
66 ACTTCAGGAGGATAAGACTTGCTTACTGAGTCTGCTCCACTACAACTTCAGGGAGAAAAGACTAG
* *
38320308 ATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTCCACTGTAAC
131 ACGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTCCACTGCAAC
*
38320373 TTCAACGAGATAGTATTATCGG
196 TTCAACGAGATAGGATTATCGG
*
38320395 CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCA
1 CTCTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCA
38320445 ACCTACTCCG
Statistics
Matches: 244, Mismatches: 20, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
215 23 0.09
216 16 0.07
217 205 0.84
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (217 bp):
CTCTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTACCTCACTGCA
ACTTCAGGAGGATAAGACTTGCTTACTGAGTCTGCTCCACTACAACTTCAGGGAGAAAAGACTAG
ACGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTCCACTGCAAC
TTCAACGAGATAGGATTATCGG
Found at i:38320427 original size:44 final size:42
Alignment explanation
Indices: 38320056--38320433 Score: 184
Period size: 44 Copynumber: 8.8 Consensus size: 42
38320046 GTTTACTTAG
* * ***
38320056 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTA-GAC-GCGA
1 TCTGCTCCACTGCAACTTCAGGGAGAT-AGATTATGGCTTTAA
* * * * * *
38320097 TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTGA
1 TCTGCTCCACTGCAACTTCAGGGAGAT-AGAT-TATGGCTTTAA
* *
38320140 TCCGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTCTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATA-GATTAT-GGCTTTAA
* *
38320184 TCTGCTCCACTGCAACTTCAGGGAGATAAGATT-TGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGAT-AGATTATGGC-T-TT-AA
* * *
38320229 TCTAC-CTCACTGCAACTTCA-GGAGGATAAGACT-T-GCTTGCTGAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GAT-AGATTATGGCTT--T-AA
* * * * ***
38320273 TCTGCTCCACTACAACTTCAGGGAGAAAAGACTA--GATGCGA
1 TCTGCTCCACTGCAACTTCAGGGAG-ATAGATTATGGCTTTAA
* * * * *
38320314 TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGAT-AGAT-TATGGCTTTAA
* * **
38320357 TCCGCTCCACTGTAACTTCAACGAGATAGTATTATCGGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAG-ATTAT-GGCTTTAA
38320401 TCTGCTCCACTGCAACTTCAGGGAGATAAGATT
1 TCTGCTCCACTGCAACTTCAGGGAGAT-AGATT
38320434 TGCCATCTTC
Statistics
Matches: 257, Mismatches: 54, Indels: 49
0.71 0.15 0.14
Matches are distributed among these distances:
39 1 0.00
40 40 0.16
41 14 0.05
42 4 0.02
43 23 0.09
44 140 0.54
45 35 0.14
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.27
Consensus pattern (42 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAGATTATGGCTTTAA
Found at i:38320674 original size:127 final size:129
Alignment explanation
Indices: 38320400--38320741 Score: 517
Period size: 127 Copynumber: 2.6 Consensus size: 129
38320390 ATCGGCTTTA
* ** * * * *
38320400 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAACCTACTCCGCTGCTGCTCA
1 ATCTGCTCCACTACTGCTT-AGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCA
* *
38320465 GGGAGATAAGGCTTGGTGGCTTAAATTTACTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCT
65 GGGAGACAAGGCTTGGTGGCTTAAATCTACTTCCCACTA---TGGAAAGATAAGATTTGCCGTCT
*
38320530 TTG
127 TCG
38320533 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGC-GCTGCTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAG
* *
38320597 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCTCACTA-GGAAAGATAAGATTTGCCGTCTTCG
66 GGAGACAAGGCTTGGTGGCTTAAATCTACTTCCCACTATGGAAAGATAAGATTTGCCGTCTTCG
*
38320660 ATCTGCTCTACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAG
38320725 GGAGACAAGGCTTGGTG
66 GGAGACAAGGCTTGGTG
38320742 TTTCACCGGT
Statistics
Matches: 195, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
127 78 0.40
128 26 0.13
131 43 0.22
132 32 0.16
133 16 0.08
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (129 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAG
GGAGACAAGGCTTGGTGGCTTAAATCTACTTCCCACTATGGAAAGATAAGATTTGCCGTCTTCG
Found at i:38321994 original size:22 final size:23
Alignment explanation
Indices: 38321968--38322020 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
38321958 CTCCTTTTGC
38321968 TTTTCTTTTCCTT-TTTCT-TTCT
1 TTTTCTTTTCCTTCTTTCTCTT-T
*
38321990 TTTTCTTTTCTTTCTTTCTCTTT
1 TTTTCTTTTCCTTCTTTCTCTTT
38322013 TTTT-TTTT
1 TTTTCTTTT
38322021 GAAAAATTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 16 0.57
23 10 0.36
24 2 0.07
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTTCTTTTCCTTCTTTCTCTTT
Found at i:38322000 original size:15 final size:15
Alignment explanation
Indices: 38321969--38322013 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
38321959 TCCTTTTGCT
*
38321969 TTTCTTTTCCTTTTTC
1 TTTCTTTTTC-TTTTC
38321985 TTTCTTTTTCTTTTC
1 TTTCTTTTTCTTTTC
*
38322000 TTTCTTTCTCTTTT
1 TTTCTTTTTCTTTT
38322014 TTTTTTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 18 0.67
16 9 0.33
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTCTTTTTCTTTTC
Found at i:38322005 original size:19 final size:19
Alignment explanation
Indices: 38321981--38322017 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
38321971 TCTTTTCCTT
38321981 TTTCTTTCT-TTTTCTTTTC
1 TTTCTTTCTCTTTT-TTTTC
38322000 TTTCTTTCTCTTTTTTTT
1 TTTCTTTCTCTTTTTTTT
38322018 TTTGAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTCTTTCTCTTTTTTTTC
Found at i:38329184 original size:19 final size:21
Alignment explanation
Indices: 38329146--38329184 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
38329136 CCTTTTTTAA
*
38329146 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
38329167 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
38329185 GAAAACAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:38329409 original size:21 final size:21
Alignment explanation
Indices: 38329376--38329455 Score: 105
Period size: 21 Copynumber: 4.0 Consensus size: 21
38329366 ATTACAAAAT
38329376 CATATC-T-TCTAAGATTGTA
1 CATATCATATCTAAGATTGTA
* *
38329395 TATATCATATCTAAGATTGCA
1 CATATCATATCTAAGATTGTA
*
38329416 CATATCATATTTAAGATTG--
1 CATATCATATCTAAGATTGTA
38329435 CATATCATATCTAAGATTGTA
1 CATATCATATCTAAGATTGTA
38329456 TATCCTCGAA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
19 23 0.44
20 1 0.02
21 28 0.54
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (21 bp):
CATATCATATCTAAGATTGTA
Found at i:38329440 original size:19 final size:19
Alignment explanation
Indices: 38329396--38329459 Score: 92
Period size: 19 Copynumber: 3.3 Consensus size: 19
38329386 AAGATTGTAT
38329396 ATATCATATCTAAGATTGCAC
1 ATATCATATCTAAGATTG--C
*
38329417 ATATCATATTTAAGATTGC
1 ATATCATATCTAAGATTGC
*
38329436 ATATCATATCTAAGATTGT
1 ATATCATATCTAAGATTGC
38329455 ATATC
1 ATATC
38329460 CTCGAAAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 23 0.57
21 17 0.43
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (19 bp):
ATATCATATCTAAGATTGC
Done.