Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 160 of 322
Found at i:52621314 original size:20 final size:20
Alignment explanation
Indices: 52621289--52621331 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
52621279 CTCAGTATTC
52621289 TTATCCTGAATTTTAGGATT
1 TTATCCTGAATTTTAGGATT
*
52621309 TTATCCTGAATTTTAGTATT
1 TTATCCTGAATTTTAGGATT
52621329 TTA
1 TTA
52621332 ATTTGGATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.09, G:0.12, T:0.53
Consensus pattern (20 bp):
TTATCCTGAATTTTAGGATT
Found at i:52622770 original size:70 final size:70
Alignment explanation
Indices: 52622657--52622797 Score: 273
Period size: 70 Copynumber: 2.0 Consensus size: 70
52622647 GCCTATCCAC
52622657 ATACAAAAATCAAAGAATAAAACAAAATATTAACCCAATTACATGAGACACGCTCCATACCCATG
1 ATACAAAAATCAAAGAATAAAACAAAATATTAACCCAATTACATGAGACACGCTCCATACCCATG
52622722 GCCCA
66 GCCCA
*
52622727 ATACAAAAATCAAAGAATAAAACAAAATATTAACCCAATTACATTAGACACGCTCCATACCCATG
1 ATACAAAAATCAAAGAATAAAACAAAATATTAACCCAATTACATGAGACACGCTCCATACCCATG
52622792 GCCCA
66 GCCCA
52622797 A
1 A
52622798 AATCTAAGTT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.49, C:0.26, G:0.08, T:0.18
Consensus pattern (70 bp):
ATACAAAAATCAAAGAATAAAACAAAATATTAACCCAATTACATGAGACACGCTCCATACCCATG
GCCCA
Found at i:52623327 original size:16 final size:16
Alignment explanation
Indices: 52623306--52623362 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
52623296 TTTGGTTCGC
*
52623306 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
52623322 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
52623338 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
52623354 TGTAATGGA
1 TGTAATGGA
52623363 AAAGCTGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:52635148 original size:265 final size:265
Alignment explanation
Indices: 52634675--52635180 Score: 940
Period size: 265 Copynumber: 1.9 Consensus size: 265
52634665 CATTCAATTC
*
52634675 TGTCCAACATACCGGTGATCGACACCTTCGACCATATAATGCTTCATACGGAGCCATTTGAATAC
1 TGTCCAACATACCGGTGATCGACACCTTCAACCATATAATGCTTCATACGGAGCCATTTGAATAC
*
52634740 TAGATTGGAAACTATTGTTATAGACAAATTCAGCTAATGGCAAATAACGTTCCCAACCTGATTCA
66 TAGATTGGAAACTATTGTTATAGACAAATTCAGCTAATGACAAATAACGTTCCCAACCTGATTCA
52634805 AAATCAATGATACAAGCCCGAAGCATATCTTCTAATATCTGTATTACCCGTTCGGACTGTCCATC
131 AAATCAATGATACAAGCCCGAAGCATATCTTCTAATATCTGTATTACCCGTTCGGACTGTCCATC
* *
52634870 TGTTTGCGGATGAAAAGCCGTACTAAAGTTAAGTCGAGTACCCAATCTGGACCAATCATTTTTCT
196 TGTTTACGGATGAAAAGACGTACTAAAGTTAAGTCGAGTACCCAATCTGGACCAATCATTTTTCT
52634935 TTCAT
261 TTCAT
* *
52634940 TGTCCAACGTACCGGTGATTGACACCTTCAACCATATAATGCTTCATACGGAGCCATTTGAATAC
1 TGTCCAACATACCGGTGATCGACACCTTCAACCATATAATGCTTCATACGGAGCCATTTGAATAC
*
52635005 TAGATTGGAAACTATTGTTATAGATAAATTCAGCTAATGACAAATAACGTTCCCAACCTGATTCA
66 TAGATTGGAAACTATTGTTATAGACAAATTCAGCTAATGACAAATAACGTTCCCAACCTGATTCA
52635070 AAATCAATGATACAAGCCCGAAGCATATCTTCTAATATCTGTATTACCCGTTCGGACTGTCCATC
131 AAATCAATGATACAAGCCCGAAGCATATCTTCTAATATCTGTATTACCCGTTCGGACTGTCCATC
*
52635135 TGTTTACGGATGAAAAGACGTACTAACGTTAAGTCGAGTACCCAAT
196 TGTTTACGGATGAAAAGACGTACTAAAGTTAAGTCGAGTACCCAAT
52635181 GATTCATGTA
Statistics
Matches: 233, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
265 233 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (265 bp):
TGTCCAACATACCGGTGATCGACACCTTCAACCATATAATGCTTCATACGGAGCCATTTGAATAC
TAGATTGGAAACTATTGTTATAGACAAATTCAGCTAATGACAAATAACGTTCCCAACCTGATTCA
AAATCAATGATACAAGCCCGAAGCATATCTTCTAATATCTGTATTACCCGTTCGGACTGTCCATC
TGTTTACGGATGAAAAGACGTACTAAAGTTAAGTCGAGTACCCAATCTGGACCAATCATTTTTCT
TTCAT
Found at i:52642407 original size:23 final size:22
Alignment explanation
Indices: 52642355--52642429 Score: 91
Period size: 21 Copynumber: 3.5 Consensus size: 22
52642345 CCTGATCAGT
** *
52642355 ATACGACACATAAAGTGCCT-A
1 ATACGACACACGAGGTGCCTGA
*
52642376 AAACGACACACGAGGTGCCTG-
1 ATACGACACACGAGGTGCCTGA
52642397 ATACGACACACGAGGTGCCTGA
1 ATACGACACACGAGGTGCCTGA
52642419 TATACGACACA
1 -ATACGACACA
52642430 TAAAGTGCCT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 36 0.78
23 10 0.22
ACGTcount: A:0.37, C:0.27, G:0.21, T:0.15
Consensus pattern (22 bp):
ATACGACACACGAGGTGCCTGA
Found at i:52642437 original size:23 final size:23
Alignment explanation
Indices: 52642354--52642442 Score: 87
Period size: 21 Copynumber: 4.0 Consensus size: 23
52642344 ACCTGATCAG
*
52642354 TATACGACACATAAAGTGCCT-A
1 TATACGACACACAAAGTGCCTGA
* * *
52642376 -AAACGACACACGAGGTGCCTG-
1 TATACGACACACAAAGTGCCTGA
* *
52642397 -ATACGACACACGAGGTGCCTGA
1 TATACGACACACAAAGTGCCTGA
*
52642419 TATACGACACATAAAGTGCCTGA
1 TATACGACACACAAAGTGCCTGA
52642442 T
1 T
52642443 CAGTAAAGCC
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
21 36 0.64
23 20 0.36
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.18
Consensus pattern (23 bp):
TATACGACACACAAAGTGCCTGA
Found at i:52649273 original size:177 final size:177
Alignment explanation
Indices: 52648977--52649493 Score: 797
Period size: 177 Copynumber: 2.9 Consensus size: 177
52648967 GCGACATCGG
*
52648977 TGAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCAAAAATGGTAAGTCTTATC
1 TGAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCAAAAATGGCAAGTCTTATC
* *
52649042 TTCATGTATCAGCTATGGAGCAGATTTTAGCCACCAAGCCTTATCTCTCTGAAGTTGCAAAGAGC
66 TCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAAGCCTTATCTCTCTGAAGTTGCAAAGAGC
*
52649107 AGGTTGAAGATACAAGTCTTATCTTCCTAAAGTTACAGGAAGCAGAC
131 AGGTTGAAGATACAAGTCTTATCTTCCTGAAGTTACAGGAAGCAGAC
* * *
52649154 TGAAAATTACAGATCTTATCTCCATGTATCGGATATGGAGCAGATCAGAAATGGCGAGTCTTATC
1 TGAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCAAAAATGGCAAGTCTTATC
*
52649219 TCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAAGCCTTATCTCTCTGAAGTTGCAGAGAGC
66 TCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAAGCCTTATCTCTCTGAAGTTGCAAAGAGC
* *
52649284 AGGTTGAAGATACAAGTCTTATCTTCCTGAAGTTGCAGGAAGTAGAC
131 AGGTTGAAGATACAAGTCTTATCTTCCTGAAGTTACAGGAAGCAGAC
* * *
52649331 TGAAAATTACAGATCTTATCTCTATGTATCGGCT-TGGAGCAGATAAAAAATGGCTAGTCTTATC
1 TGAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCAAAAATGGCAAGTCTTATC
* * * * **
52649395 TCCATGTATCGGCTATGGAGTAGATTTTAGCCA-CAGGCCCTGTCTCTCTGAAGTTGCAGCGGAG
66 TCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAAGCCTTATCTCTCTGAAGTTGCA-AAGAG
* **
52649459 CAAGTTGAAG-TCACAAACCTTATCTTCCTGAAGTT
130 CAGGTTGAAGAT-ACAAGTCTTATCTTCCTGAAGTT
52649494 GCTATAGGAC
Statistics
Matches: 314, Mismatches: 24, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
175 23 0.07
176 92 0.29
177 199 0.63
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (177 bp):
TGAAAATTACAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCAAAAATGGCAAGTCTTATC
TCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAAGCCTTATCTCTCTGAAGTTGCAAAGAGC
AGGTTGAAGATACAAGTCTTATCTTCCTGAAGTTACAGGAAGCAGAC
Found at i:52655355 original size:15 final size:15
Alignment explanation
Indices: 52655313--52655355 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
52655303 CCCGGCCCGT
52655313 AAAATAAATAAATACAA
1 AAAAT-AATAAA-ACAA
*
52655330 AAAA-AACAAAACAA
1 AAAATAATAAAACAA
52655344 AAAATAATAAAA
1 AAAATAATAAAA
52655356 GTCCTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 8 0.35
15 11 0.48
17 4 0.17
ACGTcount: A:0.81, C:0.07, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAATAATAAAACAA
Found at i:52656641 original size:12 final size:12
Alignment explanation
Indices: 52656624--52656798 Score: 99
Period size: 12 Copynumber: 15.1 Consensus size: 12
52656614 GAATGTAAAA
52656624 ATTATTATATAT
1 ATTATTATATAT
52656636 ATTATT-T-T-T
1 ATTATTATATAT
*
52656645 ATTTTTATAT-T
1 ATTATTATATAT
52656656 A-T-TTAT-TAT
1 ATTATTATATAT
52656665 ATTATT-TATAT
1 ATTATTATATAT
*
52656676 TTTATTATATAT
1 ATTATTATATAT
* *
52656688 TTTGATTTATACAT
1 ATT-A-TTATATAT
*
52656702 TTTATTATATAT
1 ATTATTATATAT
52656714 CATTTTATTATATAT
1 -A--TTATTATATAT
52656729 ATTATTCAT-TAT
1 ATTATT-ATATAT
*
52656741 ATT-TTTTATAT
1 ATTATTATATAT
*
52656752 -TTTTTAT-TAT
1 ATTATTATATAT
52656762 A-TATTATATA-
1 ATTATTATATAT
*
52656772 ATTATTTATTATTT
1 ATTA-TTA-TATAT
*
52656786 ATTATTATGTAT
1 ATTATTATATAT
52656798 A
1 A
52656799 ATTTTAAAAA
Statistics
Matches: 131, Mismatches: 11, Indels: 42
0.71 0.06 0.23
Matches are distributed among these distances:
8 1 0.01
9 12 0.09
10 17 0.13
11 26 0.20
12 39 0.30
13 10 0.08
14 15 0.11
15 11 0.08
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.65
Consensus pattern (12 bp):
ATTATTATATAT
Found at i:52656653 original size:21 final size:21
Alignment explanation
Indices: 52656626--52656790 Score: 93
Period size: 22 Copynumber: 8.0 Consensus size: 21
52656616 ATGTAAAAAT
*
52656626 TATTATATATATTA-TT-TT-
1 TATTATTTATATTATTTATTA
52656644 TATT-TTTATATTATTTATTA
1 TATTATTTATATTATTTATTA
*
52656664 TATTATTTATATTTTATTATATA
1 TATTATTTATATTAT-TTAT-TA
* *
52656687 TTTTGATTTATA-CATTTTATTA
1 TATT-ATTTATATTA-TTTATTA
52656709 TATATCATTT-TATTA--TA-TA
1 TAT-T-ATTTATATTATTTATTA
* *
52656728 TATTATTCAT-TATATTTTTTA
1 TATTATTTATAT-TATTTATTA
*
52656749 TATT-TTT-TATTATATATTA
1 TATTATTTATATTATTTATTA
* *
52656768 TATAATTATTTATTATTTATTA
1 TATTATT-TATATTATTTATTA
52656790 T
1 T
52656791 TATGTATAAT
Statistics
Matches: 113, Mismatches: 15, Indels: 34
0.70 0.09 0.21
Matches are distributed among these distances:
17 12 0.11
18 10 0.09
19 18 0.16
20 12 0.11
21 16 0.14
22 22 0.19
23 15 0.13
24 8 0.07
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (21 bp):
TATTATTTATATTATTTATTA
Found at i:52656662 original size:7 final size:7
Alignment explanation
Indices: 52656625--52656791 Score: 74
Period size: 7 Copynumber: 22.1 Consensus size: 7
52656615 AATGTAAAAA
52656625 TTATTAT
1 TTATTAT
52656632 ATATATTAT
1 -T-TATTAT
52656641 TT-TTAT
1 TTATTAT
52656647 TT-TTAT
1 TTATTAT
52656653 ATTATTTAT
1 -TTA-TTAT
52656662 TATATTAT
1 T-TATTAT
52656670 TTA-TATT
1 TTATTA-T
52656677 TTATTAT
1 TTATTAT
*
52656684 ATATTTTGAT
1 -T-TATT-AT
*
52656694 TTATACATT
1 TTAT-TA-T
52656703 TTATTAT
1 TTATTAT
* *
52656710 ATATCATT
1 TTATTA-T
52656718 TTATTAT
1 TTATTAT
52656725 ATATATTAT
1 -T-TATTAT
*
52656734 TCATTAT
1 TTATTAT
52656741 ATT-TT-T
1 -TTATTAT
*
52656747 TATATTTT
1 T-TATTAT
52656755 TTATTAT
1 TTATTAT
*
52656762 ATATTAT
1 TTATTAT
*
52656769 ATAATTAT
1 -TTATTAT
52656777 TTATTAT
1 TTATTAT
52656784 TTATTAT
1 TTATTAT
52656791 T
1 T
52656792 ATGTATAATT
Statistics
Matches: 124, Mismatches: 15, Indels: 41
0.69 0.08 0.23
Matches are distributed among these distances:
5 1 0.01
6 14 0.11
7 50 0.40
8 30 0.24
9 27 0.22
10 2 0.02
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.66
Consensus pattern (7 bp):
TTATTAT
Found at i:52656708 original size:52 final size:52
Alignment explanation
Indices: 52656624--52656784 Score: 170
Period size: 52 Copynumber: 3.1 Consensus size: 52
52656614 GAATGTAAAA
* * *
52656624 ATTATTATATATATTATTTTTATTTTTATATTATTTATTATATTATT-TATAT
1 ATTATTATATATTTTATTTATATTTTT-TATTATATATTATATTATTATATAT
* ** * *
52656676 TTTATTATATATTTTGATTTATACATTTTATTATATATCATTTTATTATATAT
1 ATTATTATATATTTT-ATTTATATTTTTTATTATATATTATATTATTATATAT
*
52656729 ATTATTCAT-TATATTT-TTTATATTTTTTATTATATATTATATAATTAT-T-T
1 ATTATT-ATATAT-TTTATTTATATTTTTTATTATATATTATATTATTATATAT
52656779 ATTATT
1 ATTATT
52656785 TATTATTATG
Statistics
Matches: 91, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
50 7 0.08
51 1 0.01
52 56 0.62
53 22 0.24
54 5 0.05
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (52 bp):
ATTATTATATATTTTATTTATATTTTTTATTATATATTATATTATTATATAT
Found at i:52656790 original size:57 final size:65
Alignment explanation
Indices: 52656652--52656804 Score: 153
Period size: 67 Copynumber: 2.4 Consensus size: 65
52656642 TTTATTTTTA
* *
52656652 TATTATTTATTATATTATTTATATTTTATTATATATTTTGATTTATACATTTTATTATATATCAT
1 TATTATTTATTAT-TCATTTATATTTTATTATATATTTTGATTTATA-ATATTATTATATATCAT
52656717 TT
64 TT
* *
52656719 TATTATATATATTATTCA-TTATATTTT-TTATAT-TTTTTA-TTAT-ATATTA-TATA-ATTA-
1 TATTAT-T-TATTATTCATTTATATTTTATTATATATTTTGATTTATAATATTATTATATATCAT
52656776 TT
64 TT
*
52656778 TATTATTTATTATT-ATGTATAATTTTA
1 TATTATTTATTATTCATTTAT-ATTTTA
52656805 AAAATTTATA
Statistics
Matches: 76, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
56 1 0.01
57 10 0.13
58 6 0.08
59 8 0.11
60 3 0.04
61 4 0.05
62 5 0.07
64 4 0.05
65 5 0.07
66 6 0.08
67 15 0.20
68 3 0.04
69 6 0.08
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (65 bp):
TATTATTTATTATTCATTTATATTTTATTATATATTTTGATTTATAATATTATTATATATCATTT
Found at i:52656804 original size:25 final size:25
Alignment explanation
Indices: 52656625--52656804 Score: 79
Period size: 29 Copynumber: 6.8 Consensus size: 25
52656615 AATGTAAAAA
*
52656625 TTATTA-TATATATTATTTTTATT-T
1 TTATTATTATATA-TAATTTTATTAT
*
52656649 TTA-TATTAT-T-T-ATTATATTAT
1 TTATTATTATATATAATTTTATTAT
*
52656670 TTA-TATTTTATTATATATTTTGATTTAT
1 TTATTATTATA-TATA-ATTTT-A-TTAT
*
52656698 ACATT-TTATTATATATCATTTTATTAT
1 ---TTATTATTATATATAATTTTATTAT
** *
52656725 ATATATTATTCATTATATTTTTTATATTTT
1 -T-TATTATT-A-TATATAATTT-TATTAT
52656755 TTATTATATATTATATAATTATTTATTAT
1 TTATTAT-TA-TATATAA-T-TTTATTAT
*
52656784 TTATTATTATGTATAATTTTA
1 TTATTATTATATATAATTTTA
52656805 AAAATTTATA
Statistics
Matches: 122, Mismatches: 13, Indels: 41
0.69 0.07 0.23
Matches are distributed among these distances:
20 6 0.05
21 10 0.08
23 4 0.03
24 7 0.06
25 6 0.05
26 6 0.05
27 16 0.13
28 21 0.17
29 28 0.23
30 10 0.08
31 8 0.07
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (25 bp):
TTATTATTATATATAATTTTATTAT
Found at i:52657181 original size:18 final size:18
Alignment explanation
Indices: 52657158--52657192 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52657148 ATCTCATAAA
*
52657158 TTATTTGTTATTTTTATG
1 TTATTTATTATTTTTATG
*
52657176 TTATTTATTGTTTTTAT
1 TTATTTATTATTTTTAT
52657193 ATATTCGCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (18 bp):
TTATTTATTATTTTTATG
Found at i:52664178 original size:30 final size:30
Alignment explanation
Indices: 52664144--52664203 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
52664134 ACTTAATACG
52664144 AACTTTGGCAAAATTAC-CATTTTGCCCCTA
1 AACTTTGGCAAAATTACAC-TTTTGCCCCTA
* *
52664174 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
52664204 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.28, C:0.27, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:52671378 original size:45 final size:45
Alignment explanation
Indices: 52671326--52671636 Score: 312
Period size: 45 Copynumber: 6.9 Consensus size: 45
52671316 TTAGACGGGG
52671326 AGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGA
1 AGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGA
* * * * * * *
52671371 AGTAGATCGAAGAT-GACAGATTTGGCGTCTC-TGT-ATTAGA-CGGG
1 AGCAGATCGAAGATAG-CAGATCTGACAT-TCGTGTGTTTACATC-GA
* * * *
52671415 AGGAGATCGAAGATAGTAGATCTGGCATTCATGTGTTTACATCGA
1 AGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGA
*
52671460 AGCAGGTCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGA
1 AGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGA
* * * * * *
52671505 AGCAGATCGAAGAT-GACAGATTTGACGTCCCTGT-ATTAGA-CGA
1 AGCAGATCGAAGATAG-CAGATCTGACATTCGTGTGTTTACATCGA
* ** *
52671548 GGAGCAGATCAAAGATAGTGGTTCTGACATTCGTGTGTTTACATCGA
1 --AGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGA
*
52671595 AGCAGGTCGAAGATAGCAGATCTGACATTCGTGTGTTTACAT
1 AGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACAT
52671637 GTAATGACCC
Statistics
Matches: 212, Mismatches: 41, Indels: 26
0.76 0.15 0.09
Matches are distributed among these distances:
43 6 0.03
44 36 0.17
45 159 0.75
46 8 0.04
47 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (45 bp):
AGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGA
Found at i:52671456 original size:89 final size:90
Alignment explanation
Indices: 52671282--52671473 Score: 305
Period size: 89 Copynumber: 2.1 Consensus size: 90
52671272 AGGGGGCAAT
*
52671282 GTAGATCAAAGATGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGAT
1 GTAGATCGAAGATGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGAT
*
52671347 CTGACATTCGTGTGTTTACATCGAA
66 CTGACATTCATGTGTTTACATCGAA
* * *
52671372 GTAGATCGAAGATGACAGATTTGGCGTCTCTGTATTAGAC-GGGAGGAGATCGAAGATAGTAGAT
1 GTAGATCGAAGATGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGAT
*
52671436 CTGGCATTCATGTGTTTACATCGAA
66 CTGACATTCATGTGTTTACATCGAA
* *
52671461 GCAGGTCGAAGAT
1 GTAGATCGAAGAT
52671474 AGCAGATCTG
Statistics
Matches: 94, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
89 56 0.60
90 38 0.40
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.27
Consensus pattern (90 bp):
GTAGATCGAAGATGACAGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGAT
CTGACATTCATGTGTTTACATCGAA
Found at i:52671524 original size:134 final size:135
Alignment explanation
Indices: 52671326--52671636 Score: 525
Period size: 134 Copynumber: 2.3 Consensus size: 135
52671316 TTAGACGGGG
* *
52671326 AGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGTAGATCGAAGATGACAGA
1 AGCAGGTCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACAGA
* * * * *
52671391 TTTGGCGTCTCTGTATTAGACG-GGAGGAGATCGAAGATAGTAGATCTGGCATTCATGTGTTTAC
66 TTTGACGTCCCTGTATTAGACGAGGAGCAGATCAAAGATAGTAGATCTGACATTCATGTGTTTAC
52671455 ATCGA
131 ATCGA
52671460 AGCAGGTCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACAGA
1 AGCAGGTCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACAGA
* * *
52671525 TTTGACGTCCCTGTATTAGACGAGGAGCAGATCAAAGATAGTGGTTCTGACATTCGTGTGTTTAC
66 TTTGACGTCCCTGTATTAGACGAGGAGCAGATCAAAGATAGTAGATCTGACATTCATGTGTTTAC
52671590 ATCGA
131 ATCGA
52671595 AGCAGGTCGAAGATAGCAGATCTGACATTCGTGTGTTTACAT
1 AGCAGGTCGAAGATAGCAGATCTGACATTCGTGTGTTTACAT
52671637 GTAATGACCC
Statistics
Matches: 166, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
134 83 0.50
135 83 0.50
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (135 bp):
AGCAGGTCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACAGA
TTTGACGTCCCTGTATTAGACGAGGAGCAGATCAAAGATAGTAGATCTGACATTCATGTGTTTAC
ATCGA
Found at i:52671950 original size:8 final size:8
Alignment explanation
Indices: 52671937--52671965 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
52671927 TTATGTTTAG
52671937 TATATTAT
1 TATATTAT
52671945 TATATTAT
1 TATATTAT
52671953 TATATTAT
1 TATATTAT
52671961 TATAT
1 TATAT
52671966 AATAAAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:52675990 original size:45 final size:45
Alignment explanation
Indices: 52675941--52676338 Score: 327
Period size: 45 Copynumber: 8.9 Consensus size: 45
52675931 GACGGGGAGG
52675941 AGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGC
1 AGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGC
* * * ** * *
52675986 AGATC-AACGAT-GACCGATTTG--GTGTC-TCCGTATTAGA-CGGGGAGC
1 AGATCGAA-GATAG-CAGATCTGACAT-TCGTGTGT-TTACATC--GAAGC
*
52676031 AGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGT
1 AGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGC
* * * * * * *
52676076 AGATCGAAGAT-GACAGATTTGGCGTCTC-TGT-ATTAGA-CGGGAGG
1 AGATCGAAGATAG-CAGATCTGACAT-TCGTGTGTTTACATC-GAAGC
* * *
52676120 AGATCGAAGATAGTAGATCTGGCATTCATGTGTTTACATCGAAGC
1 AGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGC
*
52676165 AGGTCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGC
1 AGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGC
* * * * * *
52676210 AGATCGAAGAT-GACAGATTTGACGTCCCTGT-ATTAGA-CGAGGAGC
1 AGATCGAAGATAG-CAGATCTGACATTCGTGTGTTTACATCGA--AGC
* ** *
52676255 AGATCAAAGATAGTGGTTCTGACATTCGTGTGTTTACATCGAAGC
1 AGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGC
*
52676300 AGGTCGAAGATAGCAGATCTGACATTCGTGTGTTTACAT
1 AGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACAT
52676339 GTAATGACCC
Statistics
Matches: 273, Mismatches: 55, Indels: 50
0.72 0.15 0.13
Matches are distributed among these distances:
43 11 0.04
44 45 0.16
45 192 0.70
46 17 0.06
47 8 0.03
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (45 bp):
AGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGC
Found at i:52676049 original size:90 final size:89
Alignment explanation
Indices: 52675896--52676175 Score: 427
Period size: 90 Copynumber: 3.1 Consensus size: 89
52675886 GGGGCAATGT
*
52675896 AGATCAAAGATGACAGATTTGGCATCTCTGTATTAGACGGGGAGGAGATCGAAGATAGCAGATCT
1 AGATC-AAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGGAGATCGAAGATAGCAGATCT
52675961 GACATTCGTGTGTTTACATCGAAGC
65 GACATTCGTGTGTTTACATCGAAGC
* * * *
52675986 AGATCAACGATGACCGATTTGGTGTCTCCGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCT
1 AGATCAA-GATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGGAGATCGAAGATAGCAGATCT
*
52676051 GACATTCGTGTGTTTACATCGAAGT
65 GACATTCGTGTGTTTACATCGAAGC
*
52676076 AGATCGAAGATGACAGATTTGGCGTCTCTGTATTAGAC-GGGAGGAGATCGAAGATAGTAGATCT
1 AGATC-AAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGGAGATCGAAGATAGCAGATCT
* *
52676140 GGCATTCATGTGTTTACATCGAAGC
65 GACATTCGTGTGTTTACATCGAAGC
*
52676165 AGGTCGAAGAT
1 AGATC-AAGAT
52676176 AGCAGATCTG
Statistics
Matches: 173, Mismatches: 15, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
89 58 0.34
90 113 0.65
91 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.26
Consensus pattern (89 bp):
AGATCAAGATGACAGATTTGGCGTCTCTGTATTAGACGGGGAGGAGATCGAAGATAGCAGATCTG
ACATTCGTGTGTTTACATCGAAGC
Found at i:52676197 original size:134 final size:135
Alignment explanation
Indices: 52676028--52676338 Score: 525
Period size: 134 Copynumber: 2.3 Consensus size: 135
52676018 TTAGACGGGG
* *
52676028 AGCAGATCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGTAGATCGAAGATGACAGA
1 AGCAGGTCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACAGA
* * * * *
52676093 TTTGGCGTCTCTGTATTAGACG-GGAGGAGATCGAAGATAGTAGATCTGGCATTCATGTGTTTAC
66 TTTGACGTCCCTGTATTAGACGAGGAGCAGATCAAAGATAGTAGATCTGACATTCATGTGTTTAC
52676157 ATCGA
131 ATCGA
52676162 AGCAGGTCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACAGA
1 AGCAGGTCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACAGA
* * *
52676227 TTTGACGTCCCTGTATTAGACGAGGAGCAGATCAAAGATAGTGGTTCTGACATTCGTGTGTTTAC
66 TTTGACGTCCCTGTATTAGACGAGGAGCAGATCAAAGATAGTAGATCTGACATTCATGTGTTTAC
52676292 ATCGA
131 ATCGA
52676297 AGCAGGTCGAAGATAGCAGATCTGACATTCGTGTGTTTACAT
1 AGCAGGTCGAAGATAGCAGATCTGACATTCGTGTGTTTACAT
52676339 GTAATGACCC
Statistics
Matches: 166, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
134 83 0.50
135 83 0.50
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (135 bp):
AGCAGGTCGAAGATAGCAGATCTGACATTCGTGTGTTTACATCGAAGCAGATCGAAGATGACAGA
TTTGACGTCCCTGTATTAGACGAGGAGCAGATCAAAGATAGTAGATCTGACATTCATGTGTTTAC
ATCGA
Found at i:52676652 original size:8 final size:8
Alignment explanation
Indices: 52676639--52676667 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
52676629 TTATGTTTAG
52676639 TATATTAT
1 TATATTAT
52676647 TATATTAT
1 TATATTAT
52676655 TATATTAT
1 TATATTAT
52676663 TATAT
1 TATAT
52676668 AATAAAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:52678028 original size:14 final size:15
Alignment explanation
Indices: 52678000--52678028 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52677990 TTGATTGAAA
52678000 TGATTGAATTTATAT
1 TGATTGAATTTATAT
52678015 TGATTGAA-TTATAT
1 TGATTGAATTTATAT
52678029 AATATATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (15 bp):
TGATTGAATTTATAT
Found at i:52678439 original size:23 final size:23
Alignment explanation
Indices: 52678413--52678473 Score: 94
Period size: 21 Copynumber: 2.8 Consensus size: 23
52678403 AGGCACTTTA
52678413 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
52678436 TGTGTCGTA--TCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
52678457 TGTGTCGT-TTT-AGGCAC
1 TGTGTCGTATTTCAGGCAC
52678474 TTTATGTGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
21 26 0.72
22 1 0.03
23 9 0.25
ACGTcount: A:0.13, C:0.25, G:0.28, T:0.34
Consensus pattern (23 bp):
TGTGTCGTATTTCAGGCACCTCG
Found at i:52678481 original size:21 final size:21
Alignment explanation
Indices: 52678403--52678483 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
52678393 TTTATCGACC
* *
52678403 AGGCACTTTATGTGTCGTATTT
1 AGGCACCTCATGTGTCGT-TTT
* * *
52678425 CAGGCACCTCGTGTGTCGTATC
1 -AGGCACCTCATGTGTCGTTTT
*
52678447 AGGCACCTCGTGTGTCGTTTT
1 AGGCACCTCATGTGTCGTTTT
* *
52678468 AGGCACTTTATGTGTC
1 AGGCACCTCATGTGTC
52678484 ATATACTGAT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
21 32 0.67
22 1 0.02
23 15 0.31
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (21 bp):
AGGCACCTCATGTGTCGTTTT
Found at i:52679688 original size:45 final size:45
Alignment explanation
Indices: 52679639--52679784 Score: 118
Period size: 45 Copynumber: 3.2 Consensus size: 45
52679629 TTAGACGGGG
52679639 AGCAGATCAAAGATAGCAGATCTGACATTCGTGTGTTTACATCGA
1 AGCAGATCAAAGATAGCAGATCTGACATTCGTGTGTTTACATCGA
* * * * * * * * *
52679684 AGCAGATCGAAGAT-GACAGATTTGGCGTCTC-TATATTAGACA-AGG
1 AGCAGATCAAAGATAG-CAGATCTGACAT-TCGTGTGTT-TACATCGA
* * * * *
52679729 AGTAGATCAAAAATAGCAGATCTGATATTTGTGTGTTTACATCAA
1 AGCAGATCAAAGATAGCAGATCTGACATTCGTGTGTTTACATCGA
52679774 AGCAGATCAAA
1 AGCAGATCAAA
52679785 AATGACAGAT
Statistics
Matches: 71, Mismatches: 24, Indels: 12
0.66 0.22 0.11
Matches are distributed among these distances:
44 5 0.07
45 60 0.85
46 6 0.08
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (45 bp):
AGCAGATCAAAGATAGCAGATCTGACATTCGTGTGTTTACATCGA
Found at i:52679738 original size:90 final size:89
Alignment explanation
Indices: 52679585--52679832 Score: 352
Period size: 90 Copynumber: 2.8 Consensus size: 89
52679575 AGACGTTACA
* *
52679585 TTACATCGAAGCAGATCGAAGATGACAGATTTGGCATCCCTATATTAGACGGGGAGCAGATCAAA
1 TTACATCGAAGCAGATCGAAGATGACAGATTTGGCGT-CCTATATTAGACGGGGAGTAGATCAAA
52679650 GATAGCAGATCTGACATTCGTGTGT
65 GATAGCAGATCTGACATTCGTGTGT
**
52679675 TTACATCGAAGCAGATCGAAGATGACAGATTTGGCGTCTCTATATTAGACAAGGAGTAGATCAAA
1 TTACATCGAAGCAGATCGAAGATGACAGATTTGGCGTC-CTATATTAGACGGGGAGTAGATCAAA
* * *
52679740 AATAGCAGATCTGATATTTGTGTGT
65 GATAGCAGATCTGACATTCGTGTGT
* * * * * *
52679765 TTACATCAAAGCAGATCAAAAATGACAGATTTGACGTCCTTGTATTAGGCGGGGAGTAGATCAAA
1 TTACATCGAAGCAGATCGAAGATGACAGATTTGGCGTCC-TATATTAGACGGGGAGTAGATCAAA
52679830 GAT
65 GAT
52679833 TTCAGCATGG
Statistics
Matches: 140, Mismatches: 16, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
89 2 0.01
90 138 0.99
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.26
Consensus pattern (89 bp):
TTACATCGAAGCAGATCGAAGATGACAGATTTGGCGTCCTATATTAGACGGGGAGTAGATCAAAG
ATAGCAGATCTGACATTCGTGTGT
Found at i:52681314 original size:16 final size:17
Alignment explanation
Indices: 52681295--52681332 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
52681285 TTTTTAAATT
*
52681295 TTTTATAAT-TTATTTA
1 TTTTATAATATTATATA
52681311 TTTTA-AATATTATATA
1 TTTTATAATATTATATA
52681327 TTTTAT
1 TTTTAT
52681333 TTATTTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTATAATATTATATA
Found at i:52681318 original size:25 final size:25
Alignment explanation
Indices: 52681286--52681339 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
52681276 TTTTAATCCT
* *
52681286 TTTTAAATTTTTTATAATTTATTTA
1 TTTTAAATATTATATAATTTATTTA
*
52681311 TTTTAAATATTATATATTTTATTTA
1 TTTTAAATATTATATAATTTATTTA
52681336 TTTT
1 TTTT
52681340 TACTATAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTAAATATTATATAATTTATTTA
Found at i:52681429 original size:17 final size:17
Alignment explanation
Indices: 52681373--52681518 Score: 56
Period size: 17 Copynumber: 8.4 Consensus size: 17
52681363 GTAAAAATTA
52681373 TTATATATATTATTTTTAT
1 TTAT-TATA-TATTTTTAT
*
52681392 TT-TTATATTTTTTATATT
1 TTATTATATATTTT-TA-T
*
52681410 TTATTATATATTTTGAT
1 TTATTATATATTTTTAT
*
52681427 TTA-TACAT-TTTATTAT
1 TTATTATATATTT-TTAT
* * * *
52681443 ATATCATTTTATTATATAT
1 TTATTA-TATATT-TTTAT
52681462 ATTATTCAT-TATATTTT-T
1 -TTATT-ATATAT-TTTTAT
*
52681480 TTATTATATA-TTATA-
1 TTATTATATATTTTTAT
*
52681495 TAATTATATATTATTTA-
1 TTATTATATATT-TTTAT
52681512 TTATTAT
1 TTATTAT
52681519 GTATAATTTT
Statistics
Matches: 95, Mismatches: 17, Indels: 32
0.66 0.12 0.22
Matches are distributed among these distances:
15 15 0.16
16 17 0.18
17 27 0.28
18 7 0.07
19 22 0.23
20 6 0.06
21 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (17 bp):
TTATTATATATTTTTAT
Found at i:52681442 original size:29 final size:27
Alignment explanation
Indices: 52681370--52681515 Score: 102
Period size: 29 Copynumber: 5.3 Consensus size: 27
52681360 AATGTAAAAA
* *
52681370 TTATTATATATATTATT-TT-TATTTT
1 TTATTATATATTTTATTATTATATATT
* * *
52681395 TATATTTTTTATATT-TTATTATATATT
1 T-TATTATATATTTTATTATTATATATT
*
52681422 TTGATTTATACATTTTATTA-TATATCATT
1 TT-A-TTATATATTTTATTATTATAT-ATT
* *
52681451 TTATTATATATATTATTCATTATATTTTT
1 TTATTATATATTTTATT-ATTATA-TATT
* *
52681480 TTATTATATATTATATAATTATATATTAT
1 TTATTATATATTTTATTATTATATA-T-T
52681509 TTATTAT
1 TTATTAT
52681516 TATGTATAAT
Statistics
Matches: 95, Mismatches: 14, Indels: 20
0.74 0.11 0.16
Matches are distributed among these distances:
25 3 0.03
26 14 0.15
27 20 0.21
28 21 0.22
29 36 0.38
30 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (27 bp):
TTATTATATATTTTATTATTATATATT
Found at i:52681491 original size:7 final size:7
Alignment explanation
Indices: 52681376--52681515 Score: 72
Period size: 7 Copynumber: 21.4 Consensus size: 7
52681366 AAAATTATTA
52681376 TATATAT
1 TATATAT
*
52681383 TAT-TTT
1 TATATAT
*
52681389 TAT-TTT
1 TATATAT
*
52681395 TATATTT
1 TATATAT
*
52681402 TTTATAT
1 TATATAT
52681409 T-T-TAT
1 TATATAT
52681414 TATATAT
1 TATATAT
*
52681421 TTTGAT-T
1 TAT-ATAT
*
52681428 TATACAT
1 TATATAT
52681435 T-T-TAT
1 TATATAT
52681440 TATATAT
1 TATATAT
*
52681447 CAT-T-T
1 TATATAT
52681452 TAT-TA-
1 TATATAT
52681457 TATATAT
1 TATATAT
52681464 TAT-TCAT
1 TATAT-AT
52681471 TATAT-T
1 TATATAT
* *
52681477 TTTTTAT
1 TATATAT
52681484 TATATAT
1 TATATAT
52681491 TATATAAT
1 TATAT-AT
52681499 TATATAT
1 TATATAT
*
52681506 TATTTAT
1 TATATAT
52681513 TAT
1 TAT
52681516 TATGTATAAT
Statistics
Matches: 105, Mismatches: 14, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
5 14 0.13
6 24 0.23
7 57 0.54
8 10 0.10
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (7 bp):
TATATAT
Found at i:52681501 original size:44 final size:45
Alignment explanation
Indices: 52681434--52681518 Score: 120
Period size: 44 Copynumber: 1.9 Consensus size: 45
52681424 GATTTATACA
* *
52681434 TTTTATTATATATCATTTTATTATATA-TA-TTATTCATTATATTT
1 TTTTATTATATATCATATAATTATATATTATTTATT-ATTATATTT
*
52681478 TTTTATTATATATTATATAATTATATATTATTTATTATTAT
1 TTTTATTATATATCATATAATTATATATTATTTATTATTAT
52681519 GTATAATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
44 24 0.67
45 7 0.19
46 5 0.14
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (45 bp):
TTTTATTATATATCATATAATTATATATTATTTATTATTATATTT
Found at i:52681919 original size:18 final size:18
Alignment explanation
Indices: 52681896--52681930 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52681886 ATCTCATAAA
*
52681896 TTATTTGTTATTTTTATG
1 TTATTTATTATTTTTATG
*
52681914 TTATTTATTGTTTTTAT
1 TTATTTATTATTTTTAT
52681931 ATATTCGCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (18 bp):
TTATTTATTATTTTTATG
Found at i:52682869 original size:28 final size:27
Alignment explanation
Indices: 52682825--52682895 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 27
52682815 GTAATTTGAA
* **
52682825 AATCAATTGCACCCTTAGTTGAAAAAT
1 AATCAATTGCACCCTTAATAAAAAAAT
*
52682852 GAATCAATTAG-ACTCTTAATAAAAAAAT
1 -AATCAATT-GCACCCTTAATAAAAAAAT
*
52682880 AATCAATTGAACCCTT
1 AATCAATTGCACCCTT
52682896 CGAATTGTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
26 1 0.03
27 13 0.36
28 21 0.58
29 1 0.03
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.30
Consensus pattern (27 bp):
AATCAATTGCACCCTTAATAAAAAAAT
Found at i:52701977 original size:13 final size:13
Alignment explanation
Indices: 52701940--52701990 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
52701930 TTTGGTAATA
52701940 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
* *
52701953 CTGTAGAAAAGTG
1 CTTTTGAAAAGTG
* *
52701966 TTTTTGAGAAGTG
1 CTTTTGAAAAGTG
52701979 CTTTTGAAAAGT
1 CTTTTGAAAAGT
52701991 TTAGTTTAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.37
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:52701977 original size:26 final size:26
Alignment explanation
Indices: 52701941--52701990 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
52701931 TTGGTAATAC
52701941 TTTTGAAAAGTGCTGTAGAAAAGTGT
1 TTTTGAAAAGTGCTGTAGAAAAGTGT
* * *
52701967 TTTTGAGAAGTGCTTTTGAAAAGT
1 TTTTGAAAAGTGCTGTAGAAAAGT
52701991 TTAGTTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (26 bp):
TTTTGAAAAGTGCTGTAGAAAAGTGT
Found at i:52711822 original size:16 final size:17
Alignment explanation
Indices: 52711798--52711831 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
52711788 TTTCATTTTT
52711798 TAATATATATT-TTAAA
1 TAATATATATTATTAAA
*
52711814 TAATTTATATTATTAAA
1 TAATATATATTATTAAA
52711831 T
1 T
52711832 TACATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATATATATTATTAAA
Found at i:52722042 original size:18 final size:18
Alignment explanation
Indices: 52722019--52722060 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
52722009 AGATAGGGAA
52722019 AGAAAA-AAAAATTAAAAG
1 AGAAAACAAAAATT-AAAG
52722037 AGAAAACAAAAATTAAAG
1 AGAAAACAAAAATTAAAG
52722055 AGAAAA
1 AGAAAA
52722061 TATGGTGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.76, C:0.02, G:0.12, T:0.10
Consensus pattern (18 bp):
AGAAAACAAAAATTAAAG
Found at i:52727511 original size:105 final size:105
Alignment explanation
Indices: 52727276--52727589 Score: 317
Period size: 105 Copynumber: 3.0 Consensus size: 105
52727266 TGTGATATTG
* * * * * * * * *
52727276 TCACATATAATATATTGATCGATGCACATTGTAAGGAGGGGATGATTTATAAAGCTGTAGATATC
1 TCACGTATAATATACTGATTGATGCATATTGTAAAGAGGGAATGGTTTCTAAAGCTATAGATATC
* * * * * *
52727341 GTTGATACAATGGGGAAGCAAGGCATTGAACCTAATATTG
66 GTTGACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTA
* * * * *
52727381 TCACGTATAATATATTTATTGATGCATATTGCAAAGAGGGAATGGTTTCTAAAGCTATAGAAACC
1 TCACGTATAATATACTGATTGATGCATATTGTAAAGAGGGAATGGTTTCTAAAGCTATAGATATC
* *
52727446 ATTGACACAATGAGAAAGCAAGGTATTGAGCCTAATGTTA
66 GTTGACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTA
* * * * * *
52727486 TCACGTATAATATACTGGTTTATGCATATTTTAACA-AGGCAATGGTTACTGAAGCTGA-AGATA
1 TCACGTATAATATACTGATTGATGCATATTGTAA-AGAGGGAATGGTTTCTAAAGCT-ATAGATA
* * *
52727549 TTGTTGACACAATGATAAAGCAAGGCATTGAGCCTGATGTT
64 TCGTTGACACAATGAGAAAGCAAGGCATTGAGCCTAATGTT
52727590 GTTACCTATA
Statistics
Matches: 171, Mismatches: 36, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
105 169 0.99
106 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (105 bp):
TCACGTATAATATACTGATTGATGCATATTGTAAAGAGGGAATGGTTTCTAAAGCTATAGATATC
GTTGACACAATGAGAAAGCAAGGCATTGAGCCTAATGTTA
Found at i:52729934 original size:21 final size:19
Alignment explanation
Indices: 52729910--52729981 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 19
52729900 TCTAATTACT
52729910 AATATTTAATTATTATATTTA
1 AATATTTAATTA-TAT-TTTA
*
52729931 AATATTTAAATATATTTTA
1 AATATTTAATTATATTTTA
* *
52729950 TATATTCTAATTAAATTTAATA
1 AATATT-TAATTATATTT--TA
*
52729972 AATAATTAAT
1 AATATTTAAT
52729982 ATTAATTACT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 9 0.21
20 12 0.29
21 15 0.36
22 6 0.14
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (19 bp):
AATATTTAATTATATTTTA
Found at i:52730223 original size:13 final size:13
Alignment explanation
Indices: 52730202--52730233 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
52730192 AAATTTTTCT
52730202 AAAGCACTTCTCA
1 AAAGCACTTCTCA
*
52730215 AAAGTACTTCTCA
1 AAAGCACTTCTCA
52730228 AAAGCA
1 AAAGCA
52730234 TTTTTCCACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.44, C:0.25, G:0.09, T:0.22
Consensus pattern (13 bp):
AAAGCACTTCTCA
Found at i:52748325 original size:3 final size:3
Alignment explanation
Indices: 52748317--52748361 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
52748307 AAGAATTGCT
52748317 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
52748362 AAGAATTAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:52755890 original size:107 final size:107
Alignment explanation
Indices: 52755694--52755892 Score: 233
Period size: 107 Copynumber: 1.9 Consensus size: 107
52755684 AGGCAATCCA
* * * * *
52755694 GCCTTGACCTAAGATAAACCCTGAACTACTTCGCTATGCAGATCGTTATGTTGTTAAAGAAACCA
1 GCCTTGACCTAACATAAACCCGGAACTACTTCGCTATGCAGATCATTAAGTTGCTAAAGAAACCA
* **
52755759 TGAAACTAGAATCAGATGTTCTCATCTATCCGAAGCAGGTTT
66 GGAAACTAGAATCAGATGACCTCATCTATCCGAAGCAGGTTT
* * * *
52755801 GCCTTGACCGT-ACATAAACCCGGGAA-TACTTTGCTATGCTGATCATTAAGTTGCTAGATAAAC
1 GCCTTGACC-TAACATAAACCC-GGAACTACTTCGCTATGCAGATCATTAAGTTGCTAAAGAAAC
*
52755864 CAGGTAACTAGAATC-GAATGACCTCATCT
64 CAGGAAACTAGAATCAG-ATGACCTCATCT
52755893 GGCTAACCAG
Statistics
Matches: 76, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
106 1 0.01
107 71 0.93
108 4 0.05
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (107 bp):
GCCTTGACCTAACATAAACCCGGAACTACTTCGCTATGCAGATCATTAAGTTGCTAAAGAAACCA
GGAAACTAGAATCAGATGACCTCATCTATCCGAAGCAGGTTT
Found at i:52759909 original size:21 final size:19
Alignment explanation
Indices: 52759883--52759921 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
52759873 GGTTTATTTT
52759883 ATTATATTTACTATTAATATA
1 ATTATATTTA-T-TTAATATA
52759904 ATTATATTTATTTAATAT
1 ATTATATTTATTTAATAT
52759922 TAATAGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 1 0.06
21 10 0.56
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTATATTTATTTAATATA
Found at i:52762636 original size:23 final size:23
Alignment explanation
Indices: 52762587--52762636 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
52762577 ATTCGTATGG
* *
52762587 TATTAATTTTTTACAAATATTTA
1 TATTAATTTTATACAAATAGTTA
*
52762610 TATTAATTTTCATACCAATAGTT-
1 TATTAATTTT-ATACAAATAGTTA
52762633 TATT
1 TATT
52762637 GTATATTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.54
Consensus pattern (23 bp):
TATTAATTTTATACAAATAGTTA
Found at i:52766611 original size:21 final size:21
Alignment explanation
Indices: 52766587--52766628 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
52766577 CTCCACGACC
*
52766587 GCCTCCTCTACCACCACCTCT
1 GCCTCCTCCACCACCACCTCT
*
52766608 GCCTCCTCCACGACCACCTCT
1 GCCTCCTCCACCACCACCTCT
52766629 TCCACCACCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.57, G:0.07, T:0.21
Consensus pattern (21 bp):
GCCTCCTCCACCACCACCTCT
Found at i:52768496 original size:28 final size:28
Alignment explanation
Indices: 52768465--52768520 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
52768455 TTTTATATTA
* * * *
52768465 TATAATTTAATTTTAATTTATTTTAAAT
1 TATAATTAAAATTAAATTAATTTTAAAT
52768493 TATAATTAAAATTAAATTAATTTTAAAT
1 TATAATTAAAATTAAATTAATTTTAAAT
52768521 AGAAAATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TATAATTAAAATTAAATTAATTTTAAAT
Found at i:52776061 original size:23 final size:23
Alignment explanation
Indices: 52776002--52776061 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 23
52775992 ATGTATAGAC
52776002 TAAAT-AA-AATAA-TAAAATAA
1 TAAATAAATAATAATTAAAATAA
* * *
52776022 T-AATAAATATTTTATTAAAATAT
1 TAAATAAATA-ATAATTAAAATAA
52776045 TAAATAAATAATAATTA
1 TAAATAAATAATAATTA
52776062 TCTAATTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
19 3 0.10
20 3 0.10
21 1 0.03
22 2 0.07
23 13 0.43
24 8 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
TAAATAAATAATAATTAAAATAA
Found at i:52776070 original size:31 final size:31
Alignment explanation
Indices: 52776001--52776071 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
52775991 CATGTATAGA
*
52776001 CTAAATAAAATAATAAAATAATAATAAATAT
1 CTAATTAAAATAATAAAATAATAATAAATAT
* * * *
52776032 TTTATTAAAAT-ATTAAATAAATAATAATTAT
1 CTAATTAAAATAATAAAAT-AATAATAAATAT
52776063 CTAATTAAA
1 CTAATTAAA
52776072 TAACTATAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
30 6 0.19
31 26 0.81
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (31 bp):
CTAATTAAAATAATAAAATAATAATAAATAT
Found at i:52784972 original size:4 final size:4
Alignment explanation
Indices: 52784963--52785006 Score: 88
Period size: 4 Copynumber: 11.0 Consensus size: 4
52784953 CAAAGTCAAA
52784963 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
52785007 CAATGGGGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:52788272 original size:124 final size:125
Alignment explanation
Indices: 52788087--52788333 Score: 381
Period size: 124 Copynumber: 2.0 Consensus size: 125
52788077 GTAGAATGTA
* * * *
52788087 TATTAATTATGTCATTTTAAGTTTTAGTTTAATGTATTGTAATAATGAGAATAACATAAGTTCAA
1 TATTAATTATGTCATTTTAAGTTTTAGTTTAATCTATTGTAATAATAAGAAGAACAAAAGTTCAA
* *
52788152 GTGTGCTTAATCATGCATTTTTCTTTGATTTAAGAGTTTGAGAGAATTATAAGTAAAATG
66 GCGTGCTTAATCATGCATTTTTCTTCGATTTAAGAGTTTGAGAGAATTATAAGTAAAATG
*
52788212 TATTAATTATGTCA-TTTGAGTTTTAGTTTAATCTATTGTAATAATCAAG-AGAACAAAAGTTCA
1 TATTAATTATGTCATTTTAAGTTTTAGTTTAATCTATTGTAATAAT-AAGAAGAACAAAAGTTCA
* * *
52788275 AGCGTGCTTAATCATGTATTTTTCTTCGATTTAAGAGTTTGAGAGGATTTTAAGTAAAA
65 AGCGTGCTTAATCATGCATTTTTCTTCGATTTAAGAGTTTGAGAGAATTATAAGTAAAA
52788334 ATAGACATTC
Statistics
Matches: 111, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
124 95 0.86
125 16 0.14
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (125 bp):
TATTAATTATGTCATTTTAAGTTTTAGTTTAATCTATTGTAATAATAAGAAGAACAAAAGTTCAA
GCGTGCTTAATCATGCATTTTTCTTCGATTTAAGAGTTTGAGAGAATTATAAGTAAAATG
Found at i:52791481 original size:23 final size:24
Alignment explanation
Indices: 52791455--52791501 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
52791445 AAATATCTAA
52791455 TATGATGTATA-AAAAATTAAAAT
1 TATGATGTATATAAAAATTAAAAT
* * *
52791478 TATGGTTTATATAAAATTTAAAAT
1 TATGATGTATATAAAAATTAAAAT
52791502 GGAAACGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (24 bp):
TATGATGTATATAAAAATTAAAAT
Found at i:52797571 original size:18 final size:20
Alignment explanation
Indices: 52797536--52797578 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
52797526 AAAAGTTATT
* *
52797536 ATTTTTTTTAAATTATAA-A
1 ATTTTTATTAAATAATAACA
52797555 ATTTTTATTAAA-AATAACA
1 ATTTTTATTAAATAATAACA
52797574 ATTTT
1 ATTTT
52797579 GTTATTAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTTTATTAAATAATAACA
Found at i:52798766 original size:11 final size:11
Alignment explanation
Indices: 52798752--52798777 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
52798742 TGAAATTTTC
52798752 TCAAAATTCTA
1 TCAAAATTCTA
52798763 TCAAAATTCTA
1 TCAAAATTCTA
52798774 TCAA
1 TCAA
52798778 TTTATTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (11 bp):
TCAAAATTCTA
Found at i:52799031 original size:48 final size:48
Alignment explanation
Indices: 52798913--52799047 Score: 150
Period size: 48 Copynumber: 2.8 Consensus size: 48
52798903 AGTGATAATT
* * *
52798913 TTAAATTTTCAATACTA-TTCGATATTTTCTTAATTTATGCAAATTTAA
1 TTAAATTTGCAATACTACTT-GATATTTTTTTCATTTATGCAAATTTAA
* *
52798961 TTAAATTTGCAATACTATTTGATATTTTTTTCATTTATGC-AGTTATAA
1 TTAAATTTGCAATACTACTTGATATTTTTTTCATTTATGCAAATT-TAA
* * *
52799009 TTAAAATTT-CAATATTGCTTGATTTTTTTTTCATTTATG
1 TT-AAATTTGCAATACTACTTGATATTTTTTTCATTTATG
52799048 ATGTTTGCAT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
47 3 0.04
48 65 0.86
49 8 0.11
ACGTcount: A:0.31, C:0.09, G:0.07, T:0.53
Consensus pattern (48 bp):
TTAAATTTGCAATACTACTTGATATTTTTTTCATTTATGCAAATTTAA
Found at i:52800668 original size:18 final size:18
Alignment explanation
Indices: 52800645--52800687 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
52800635 CGCGAGGTGC
*
52800645 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
*
52800663 GTATCCTAACCTTTATAT
1 GTATCCTAACCCTTATAT
*
52800681 GTTTCCT
1 GTATCCT
52800688 TTTTCTAGTC
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:0.21, C:0.26, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:52803673 original size:75 final size:75
Alignment explanation
Indices: 52803594--52803773 Score: 270
Period size: 75 Copynumber: 2.4 Consensus size: 75
52803584 GGTACATATC
* *
52803594 CCATCCACTAACGGAGTGTCGTGCAGGGGTTGGGTATTCCATACTCCTACTAAACACGGGCACTT
1 CCATCCACTAACGGAGTGTCGTGCAGGGGTTGGGTATTCCATAATCCTACTAAACACGGGAACTT
52803659 CCGTGTTTTG
66 CCGTGTTTTG
* * * * *
52803669 CCATCCACTGACGGAGTGTCATGTAGGGGTTGGGTATTCCATAATGCTACTAAACATGGGAACTT
1 CCATCCACTAACGGAGTGTCGTGCAGGGGTTGGGTATTCCATAATCCTACTAAACACGGGAACTT
**
52803734 TGGTGTTTTG
66 CCGTGTTTTG
*
52803744 CCATCCACTAACGGAGTGTCGGGCAGGGGT
1 CCATCCACTAACGGAGTGTCGTGCAGGGGT
52803774 CGTGTACTCC
Statistics
Matches: 92, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 92 1.00
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (75 bp):
CCATCCACTAACGGAGTGTCGTGCAGGGGTTGGGTATTCCATAATCCTACTAAACACGGGAACTT
CCGTGTTTTG
Found at i:52804473 original size:126 final size:126
Alignment explanation
Indices: 52804236--52804614 Score: 548
Period size: 126 Copynumber: 3.0 Consensus size: 126
52804226 GCTCATTTGT
52804236 AGGCTCATTTTTCTGCGAACTACTGTAGCAAAAGAGCGTCCACGT-GAGAGCTTTTTTCAGAACT
1 AGGCTCATTTTTCTGCGAACTACTGTAGCAAAAGAGCGTCCACGTGGA-AGCTTTTTTCAGAAC-
* *
52804300 TTTTGCTGACAGTGCATCTTGCTTGAAGCATTTTCGATACTATTTGTTCAGAAACGTCTACTC
64 TTTTGCTGACAGTGCATCTTGCTTGAAGCGTTTTCGACACTATTTGTTCAGAAACGTCTACTC
* * *
52804363 AGGCTCATTTTCCTGCAAATTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTTTTTTCAGAACTT
1 AGGCTCATTTTTCTGCGAACTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTTTTTTCAGAACTT
* * *
52804428 TTGTTGACAGTGCATCCTACTTGAAGCGTTTTCGACACTATTTGTTCAGAAACGTCTACTC
66 TTGCTGACAGTGCATCTTGCTTGAAGCGTTTTCGACACTATTTGTTCAGAAACGTCTACTC
** * * * * *
52804489 AGATTTATTTTTCTACGAACTACTGTAGCAAAAGAGTGTCCACGTGGGAG-TTTTTTCCAGAAAT
1 AGGCTCATTTTTCTGCGAACTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTTTTTT-CAGAACT
* * *
52804553 TTT-CTGACACTGCATCTTGCTTGAAGTGTTTTCGACACTATTTGTTCAGAAATGTCTACTC
65 TTTGCTGACAGTGCATCTTGCTTGAAGCGTTTTCGACACTATTTGTTCAGAAACGTCTACTC
52804614 A
1 A
52804615 AAATTATTCT
Statistics
Matches: 226, Mismatches: 24, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
125 59 0.26
126 108 0.48
127 57 0.25
128 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (126 bp):
AGGCTCATTTTTCTGCGAACTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTTTTTTCAGAACTT
TTGCTGACAGTGCATCTTGCTTGAAGCGTTTTCGACACTATTTGTTCAGAAACGTCTACTC
Found at i:52804749 original size:59 final size:59
Alignment explanation
Indices: 52804686--52804817 Score: 135
Period size: 59 Copynumber: 2.2 Consensus size: 59
52804676 GTTTTTTTTT
52804686 CTAATACCCTAAACACAAATTTA-T-TTAAAAATACTAA-ACCCTAATTTAATCAATTAACC
1 CTAATACCCTAAACACAAATTTAGTATTAAAAAT--TAATA-CCTAATTTAATCAATTAACC
* ** * * ** *
52804745 CTAATATCCTAAATTCTAATTTAGTATTTAAAATTAATATTTAATTTAATGAATTAACC
1 CTAATACCCTAAACACAAATTTAGTATTAAAAATTAATACCTAATTTAATCAATTAACC
*
52804804 CTAAAACCCTAAAC
1 CTAATACCCTAAAC
52804818 TTTAATTCAA
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
59 50 0.85
60 2 0.03
61 7 0.12
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (59 bp):
CTAATACCCTAAACACAAATTTAGTATTAAAAATTAATACCTAATTTAATCAATTAACC
Found at i:52805177 original size:19 final size:19
Alignment explanation
Indices: 52805155--52805207 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
52805145 ACGATTATGT
52805155 ATCAATTAACCCTAATTTA
1 ATCAATTAACCCTAATTTA
52805174 ATCAATTAACCCTAATTTA
1 ATCAATTAACCCTAATTTA
52805193 ATCAATTAACCCTAA
1 ATCAATTAACCCTAA
52805208 ACCCTTAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.34
Consensus pattern (19 bp):
ATCAATTAACCCTAATTTA
Found at i:52805318 original size:24 final size:26
Alignment explanation
Indices: 52805285--52805347 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 26
52805275 ATTTTTTTAT
*
52805285 AAACCCTAAAAACCT-TTAAACCTT-A
1 AAACCATAAAAACCTCTT-AACCTTAA
*
52805310 AAA-CATAAAAA-ATCTTAACCTTAA
1 AAACCATAAAAACCTCTTAACCTTAA
52805334 AAACCATAAAAACC
1 AAACCATAAAAACC
52805348 CTAACGTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
23 7 0.23
24 13 0.42
25 11 0.35
ACGTcount: A:0.56, C:0.24, G:0.00, T:0.21
Consensus pattern (26 bp):
AAACCATAAAAACCTCTTAACCTTAA
Found at i:52805320 original size:25 final size:25
Alignment explanation
Indices: 52805292--52805345 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
52805282 TATAAACCCT
52805292 AAAAACCTTTAAACCTT-AAAA-CATA
1 AAAAACC-TT-AACCTTAAAAACCATA
*
52805317 AAAAATCTTAACCTTAAAAACCATA
1 AAAAACCTTAACCTTAAAAACCATA
52805342 AAAA
1 AAAA
52805346 CCCTAACGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 6 0.23
24 6 0.23
25 14 0.54
ACGTcount: A:0.59, C:0.19, G:0.00, T:0.22
Consensus pattern (25 bp):
AAAAACCTTAACCTTAAAAACCATA
Found at i:52805352 original size:24 final size:24
Alignment explanation
Indices: 52805285--52805360 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
52805275 ATTTTTTTAT
*
52805285 AAACCCTAAAAACCTTTAAACCTT-A
1 AAACCATAAAAACC-TT-AACCTTAA
*
52805310 AAA-CATAAAAAATCTTAACCTTAA
1 AAACCAT-AAAAACCTTAACCTTAA
* *
52805334 AAACCATAAAAACCCTAA-CGTAA
1 AAACCATAAAAACCTTAACCTTAA
52805357 AAAC
1 AAAC
52805361 GGGCAAAATG
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
23 14 0.33
24 17 0.40
25 12 0.28
ACGTcount: A:0.55, C:0.24, G:0.01, T:0.20
Consensus pattern (24 bp):
AAACCATAAAAACCTTAACCTTAA
Found at i:52807768 original size:3 final size:3
Alignment explanation
Indices: 52807760--52807784 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
52807750 ATCACCACTT
52807760 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
52807785 CCTCCTCCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:52811740 original size:3 final size:3
Alignment explanation
Indices: 52811695--52811726 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
52811685 TATTTTATTT
52811695 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
52811727 TTCTTTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:52812147 original size:23 final size:23
Alignment explanation
Indices: 52812103--52812149 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
52812093 TTATAATCTC
*
52812103 AAAAGTTAAATTTCATTATTTTT
1 AAAAGTTAAATTTAATTATTTTT
*
52812126 AAAAGATTAAA-TTAATTTTTTTT
1 AAAAG-TTAAATTTAATTATTTTT
52812149 A
1 A
52812150 TTTTTAAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (23 bp):
AAAAGTTAAATTTAATTATTTTT
Found at i:52812587 original size:90 final size:88
Alignment explanation
Indices: 52812478--52812709 Score: 383
Period size: 79 Copynumber: 2.7 Consensus size: 88
52812468 TTGTGTCTCC
52812478 ATTGTTTTGTTTTATTTTATTTTTTTTGAAAATATGAAGCATTTATATATTTTCTAAATTTAAAA
1 ATTGTTTTGTTTTATTTTATTTTTTTTGAAAATATGAAGCATTTATATATTTTCTAAATTT--AA
52812543 TAAATTTAAGATTTTCTCATCAATT
64 TAAATTTAAGATTTTCTCATCAATT
52812568 ATTGTTTTGTTTTATTTTATTTTTTTTGAAAATATGAAGCATTTATATATTTTC---------TA
1 ATTGTTTTGTTTTATTTTATTTTTTTTGAAAATATGAAGCATTTATATATTTTCTAAATTTAATA
52812624 AATTTAAGATTTTCTCATCAATT
66 AATTTAAGATTTTCTCATCAATT
52812647 ATTGTTTTGTTTTATTTTATTTTTTTTGAAAATATGAAGCATTTATATATTTTCTAAATTTAA
1 ATTGTTTTGTTTTATTTTATTTTTTTTGAAAATATGAAGCATTTATATATTTTCTAAATTTAA
52812710 GATTTTCTCA
Statistics
Matches: 133, Mismatches: 0, Indels: 20
0.87 0.00 0.13
Matches are distributed among these distances:
79 79 0.59
90 54 0.41
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.56
Consensus pattern (88 bp):
ATTGTTTTGTTTTATTTTATTTTTTTTGAAAATATGAAGCATTTATATATTTTCTAAATTTAATA
AATTTAAGATTTTCTCATCAATT
Found at i:52812637 original size:79 final size:79
Alignment explanation
Indices: 52812543--52812728 Score: 372
Period size: 79 Copynumber: 2.4 Consensus size: 79
52812533 AAATTTAAAA
52812543 TAAATTTAAGATTTTCTCATCAATTATTGTTTTGTTTTATTTTATTTTTTTTGAAAATATGAAGC
1 TAAATTTAAGATTTTCTCATCAATTATTGTTTTGTTTTATTTTATTTTTTTTGAAAATATGAAGC
52812608 ATTTATATATTTTC
66 ATTTATATATTTTC
52812622 TAAATTTAAGATTTTCTCATCAATTATTGTTTTGTTTTATTTTATTTTTTTTGAAAATATGAAGC
1 TAAATTTAAGATTTTCTCATCAATTATTGTTTTGTTTTATTTTATTTTTTTTGAAAATATGAAGC
52812687 ATTTATATATTTTC
66 ATTTATATATTTTC
52812701 TAAATTTAAGATTTTCTCATCAATTATT
1 TAAATTTAAGATTTTCTCATCAATTATT
52812729 TTAAATTTAA
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 107 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (79 bp):
TAAATTTAAGATTTTCTCATCAATTATTGTTTTGTTTTATTTTATTTTTTTTGAAAATATGAAGC
ATTTATATATTTTC
Found at i:52813419 original size:26 final size:27
Alignment explanation
Indices: 52813380--52813437 Score: 100
Period size: 26 Copynumber: 2.2 Consensus size: 27
52813370 TATCAATATC
52813380 AGGGGCAAAACTAGGAAAAAAAATTT-
1 AGGGGCAAAACTAGGAAAAAAAATTTA
*
52813406 AGGGGCAAAGCTAGGAAAAAAAATTTA
1 AGGGGCAAAACTAGGAAAAAAAATTTA
52813433 AGGGG
1 AGGGG
52813438 AGTCGAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 25 0.83
27 5 0.17
ACGTcount: A:0.50, C:0.07, G:0.29, T:0.14
Consensus pattern (27 bp):
AGGGGCAAAACTAGGAAAAAAAATTTA
Found at i:52828798 original size:33 final size:33
Alignment explanation
Indices: 52828761--52828884 Score: 230
Period size: 33 Copynumber: 3.8 Consensus size: 33
52828751 CTCTGTTTCA
52828761 GGTTGCTGGACAGGAGCTGGAATGTGAGTGTTT
1 GGTTGCTGGACAGGAGCTGGAATGTGAGTGTTT
*
52828794 GGTTGCTGGACGGGAGCTGGAATGTGAGTGTTT
1 GGTTGCTGGACAGGAGCTGGAATGTGAGTGTTT
52828827 GGTTGCTGGACAGGAGCTGGAATGTGAGTGTTT
1 GGTTGCTGGACAGGAGCTGGAATGTGAGTGTTT
*
52828860 GGTTGCTGGACAGTAGCTGGAATGT
1 GGTTGCTGGACAGGAGCTGGAATGT
52828885 CAAGAAGAAA
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.18, C:0.10, G:0.43, T:0.30
Consensus pattern (33 bp):
GGTTGCTGGACAGGAGCTGGAATGTGAGTGTTT
Found at i:52828946 original size:60 final size:60
Alignment explanation
Indices: 52828853--52828970 Score: 227
Period size: 60 Copynumber: 2.0 Consensus size: 60
52828843 CTGGAATGTG
*
52828853 AGTGTTTGGTTGCTGGACAGTAGCTGGAATGTCAAGAAGAAAGAATTCTCTGTCCTTACA
1 AGTGTTTGGTTGCTAGACAGTAGCTGGAATGTCAAGAAGAAAGAATTCTCTGTCCTTACA
52828913 AGTGTTTGGTTGCTAGACAGTAGCTGGAATGTCAAGAAGAAAGAATTCTCTGTCCTTA
1 AGTGTTTGGTTGCTAGACAGTAGCTGGAATGTCAAGAAGAAAGAATTCTCTGTCCTTA
52828971 TCTTCTGTGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (60 bp):
AGTGTTTGGTTGCTAGACAGTAGCTGGAATGTCAAGAAGAAAGAATTCTCTGTCCTTACA
Found at i:52833861 original size:41 final size:41
Alignment explanation
Indices: 52833804--52833886 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
52833794 TGTTAACAGT
52833804 AGCAGCATATCCCAATCTAAATCCCATTACCAAAACTCGAA
1 AGCAGCATATCCCAATCTAAATCCCATTACCAAAACTCGAA
52833845 AGCAGCATATCCCAATCTAAATCCCATTACCAAAACTCGAA
1 AGCAGCATATCCCAATCTAAATCCCATTACCAAAACTCGAA
52833886 A
1 A
52833887 CCCCTAATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.42, C:0.31, G:0.07, T:0.19
Consensus pattern (41 bp):
AGCAGCATATCCCAATCTAAATCCCATTACCAAAACTCGAA
Found at i:52837844 original size:17 final size:19
Alignment explanation
Indices: 52837822--52837857 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
52837812 AGACTTAAAA
52837822 AGAAGTCTA-AA-AGGAGT
1 AGAAGTCTACAAGAGGAGT
52837839 AGAAGTCTACAAGAGGAGT
1 AGAAGTCTACAAGAGGAGT
52837858 GGGACTGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 2 0.12
19 6 0.35
ACGTcount: A:0.44, C:0.08, G:0.31, T:0.17
Consensus pattern (19 bp):
AGAAGTCTACAAGAGGAGT
Found at i:52839594 original size:10 final size:11
Alignment explanation
Indices: 52839567--52839592 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
52839557 AAAAAATATT
52839567 AAAAATTAGAA
1 AAAAATTAGAA
52839578 AAAAATTAGAA
1 AAAAATTAGAA
52839589 AAAA
1 AAAA
52839593 TTGTAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (11 bp):
AAAAATTAGAA
Found at i:52839700 original size:21 final size:21
Alignment explanation
Indices: 52839672--52839731 Score: 56
Period size: 19 Copynumber: 3.0 Consensus size: 21
52839662 TTTTATAAAG
52839672 TCGT-AAGAAAATTATAAAAAA
1 TCGTAAAGAAAA-TATAAAAAA
*
52839693 T-GTAAAG-AAATAT-AAAAT
1 TCGTAAAGAAAATATAAAAAA
*
52839711 TCGTAAAAAAAACTATAAAAA
1 TCGTAAAGAAAA-TATAAAAA
52839732 TTATCGTACC
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 5 0.16
19 8 0.25
20 8 0.25
21 7 0.22
22 4 0.12
ACGTcount: A:0.63, C:0.05, G:0.08, T:0.23
Consensus pattern (21 bp):
TCGTAAAGAAAATATAAAAAA
Found at i:52840975 original size:32 final size:33
Alignment explanation
Indices: 52840917--52840982 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
52840907 AAAATTTGCA
*
52840917 ACATAAGCCCCTCTACTTTTTTTATATAAATTT
1 ACATAAACCCCTCTACTTTTTTTATATAAATTT
52840950 ACATAAACCCCTCTAC-TTTTTTATATAAATTT
1 ACATAAACCCCTCTACTTTTTTTATATAAATTT
52840982 A
1 A
52840983 AGTGGTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.33, C:0.21, G:0.02, T:0.44
Consensus pattern (33 bp):
ACATAAACCCCTCTACTTTTTTTATATAAATTT
Found at i:52841315 original size:12 final size:12
Alignment explanation
Indices: 52841298--52841322 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52841288 TCTAACATTT
52841298 ACACTCGAATTC
1 ACACTCGAATTC
52841310 ACACTCGAATTC
1 ACACTCGAATTC
52841322 A
1 A
52841323 AGTAACATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.32, G:0.08, T:0.24
Consensus pattern (12 bp):
ACACTCGAATTC
Found at i:52842346 original size:24 final size:24
Alignment explanation
Indices: 52842319--52842367 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
52842309 AAATGTTCGT
* *
52842319 GGATTGATCAATCCTAGAATGAAG
1 GGATTGAGCAATCCTAGAACGAAG
52842343 GGATTGAGCAATCCTAGAACGAAG
1 GGATTGAGCAATCCTAGAACGAAG
52842367 G
1 G
52842368 AAGGAAGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.14, G:0.29, T:0.20
Consensus pattern (24 bp):
GGATTGAGCAATCCTAGAACGAAG
Found at i:52845125 original size:84 final size:86
Alignment explanation
Indices: 52844996--52845168 Score: 251
Period size: 84 Copynumber: 2.0 Consensus size: 86
52844986 CCAACTGATT
* * *
52844996 AGGGGTCACTCTATTAGATAATCCAGAGGAAATAACACCAGAATCAGCTCTTGGACCTGATAATG
1 AGGGGTCACTCTATTA-ATAATCCAGAAGAAATAACACCAGAATCACCACTTGGACCTGATAATG
*
52845061 AAGGTAACACTTCTGCAGTTCC
65 AAGGCAACACTTCTGCAGTTCC
* * **
52845083 AGGGGTCACTCTA-T-ATAATCCTGAAGAACTAACAGTAGAATCACCACTTGGACCTGATAATGA
1 AGGGGTCACTCTATTAATAATCCAGAAGAAATAACACCAGAATCACCACTTGGACCTGATAATGA
52845146 AGGCAACACTTCTGCAGTTCC
66 AGGCAACACTTCTGCAGTTCC
52845167 AG
1 AG
52845169 TACTTGACCC
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
84 64 0.82
86 1 0.01
87 13 0.17
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (86 bp):
AGGGGTCACTCTATTAATAATCCAGAAGAAATAACACCAGAATCACCACTTGGACCTGATAATGA
AGGCAACACTTCTGCAGTTCC
Found at i:52853192 original size:31 final size:31
Alignment explanation
Indices: 52853156--52853214 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
52853146 AAATGGTCAT
* *
52853156 TAAACTATTTGAAAGTTTTTATTTAAATCAC
1 TAAACTATTCGAAAGTTTTCATTTAAATCAC
*
52853187 TAAACTATTCGGAAGTTTTCATTTAAAT
1 TAAACTATTCGAAAGTTTTCATTTAAAT
52853215 TATAAGTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.44
Consensus pattern (31 bp):
TAAACTATTCGAAAGTTTTCATTTAAATCAC
Found at i:52857870 original size:18 final size:16
Alignment explanation
Indices: 52857828--52857870 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 16
52857818 ATTAAATAAA
52857828 TATATTTTTTAATTTT
1 TATATTTTTTAATTTT
52857844 TATACTTTTTTGAATGTTT
1 TATA-TTTTTT-AAT-TTT
52857863 TATATTTT
1 TATATTTT
52857871 AAAAAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.17
17 6 0.25
18 7 0.29
19 7 0.29
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (16 bp):
TATATTTTTTAATTTT
Found at i:52860025 original size:21 final size:22
Alignment explanation
Indices: 52859999--52860045 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
52859989 CTCTGCTCAA
*
52859999 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
52860020 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
52860042 ACTC
1 ACTC
52860046 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:52871389 original size:63 final size:63
Alignment explanation
Indices: 52871311--52871436 Score: 234
Period size: 63 Copynumber: 2.0 Consensus size: 63
52871301 GCAAAGTCAA
52871311 TAATTAGATATTTAATTCAAATCAAAATCTCACTTTAAAAGTGAATCCAGTTATACTTGAAGT
1 TAATTAGATATTTAATTCAAATCAAAATCTCACTTTAAAAGTGAATCCAGTTATACTTGAAGT
* *
52871374 TAATTAGATATTTAATTCAAATCAAAATCTCACTTTAAAAGTGGATTCAGTTATACTTGAAGT
1 TAATTAGATATTTAATTCAAATCAAAATCTCACTTTAAAAGTGAATCCAGTTATACTTGAAGT
52871437 GAACTTCAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.37
Consensus pattern (63 bp):
TAATTAGATATTTAATTCAAATCAAAATCTCACTTTAAAAGTGAATCCAGTTATACTTGAAGT
Found at i:52873447 original size:51 final size:51
Alignment explanation
Indices: 52873371--52873472 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
52873361 TATTCAACAC
*
52873371 TAGTTCGAGTCTGGATAATGATTCAAGATAGAGGAAGAAACCTGCAAAGGG
1 TAGTTCGAGTCTGGATAATGATTCAAGATAGAAGAAGAAACCTGCAAAGGG
52873422 TAGTTCGAGTCTGGATAATGATTCAAGATAGAAGAAGAAACCTGCAAAGGG
1 TAGTTCGAGTCTGGATAATGATTCAAGATAGAAGAAGAAACCTGCAAAGGG
52873473 GAACTACTTC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.22
Consensus pattern (51 bp):
TAGTTCGAGTCTGGATAATGATTCAAGATAGAAGAAGAAACCTGCAAAGGG
Found at i:52875710 original size:150 final size:149
Alignment explanation
Indices: 52875303--52876115 Score: 527
Period size: 150 Copynumber: 5.3 Consensus size: 149
52875293 TACTAATGGA
* * * * * * *
52875303 AATGGAAAAGCAGG-TCTACCAACAAATCTTAGGCATGATGCTAACAGATTCATTTTGAAAATGC
1 AATGGAAAAGCAGGCACAACAAAGAAATCTCAAGCATGATGCTAACAGATTCACTTT-AAAA---
* * * **
52875367 CCTGTTATGTTATATGCTAT-TGGGTTCATATGGCTACTTTTAAGTTCAATGTTTCATCGCTTCT
62 --TGTT-TGTTATATGCTATAT-GGTTCATATGGCTGCTTTCAAGTTCAACGTTTCATTACTTCT
* * ** *
52875431 ATTTCAGTTATACAATGTTTGACGACT
123 ATTTCAGTTCTACAATGCTCAATGACT
* * * * * * ** * *
52875458 AATGAAAACAGAAAGACAAGCACTACCAAA-TAATCTTAGGCATGATGCTAATGGACTCACTCTG
1 AATG----GA-AAAG-CAGGCAC-AACAAAGAAATCTCAAGCATGATGCTAACAGATTCACT-TT
* * *
52875522 AAAATGTTATGTTATATGCTATTTGGTTCATATGGCTGCCTTCTGAGTTCAACGTTTCATTACTT
58 AAAATGTT-TGTTATATGCTATATGGTTCATATGGCTGCTTTC-AAGTTCAACGTTTCATTACTT
* *
52875587 CTGTTTCAGTTCTAGAATG-TCAATGACT
121 CTATTTCAGTTCTACAATGCTCAATGACT
52875615 AATGGAAAAGCAGGC-CAAACAAAGAAATCTCAAGCATGATGCTAACAGATTCACTTTAAAATGT
1 AATGGAAAAGCAGGCAC-AACAAAGAAATCTCAAGCATGATGCTAACAGATTCACTTTAAAATGT
* * * * *
52875679 ATTGTTATATGCTATACGGTTCATGTAGCTGCTTTCAAGTTC-ACTCTTTCATTTCTTCTATTTC
65 -TTGTTATATGCTATATGGTTCATATGGCTGCTTTCAAGTTCAAC-GTTTCATTACTTCTATTTC
*
52875743 AGTTCTACAATGCTCAATGGCT
128 AGTTCTACAATGCTCAATGACT
* * * * * *
52875765 AATGGAAAGGCAGGCACTACCAATAAATCTCAGGCTTGATGCTAACAGATTCACTTTGAAAATGT
1 AATGGAAAAGCAGGCACAACAAAGAAATCTCAAGCATGATGCTAACAGATTCACTTT-AAAATGT
* * * *
52875830 CTTGTTATAATGCTA-ATGGCTTCATATGGATGCTTTCAAGTTCAATGCTTCATTGCTTCTATTT
65 -TTGTTAT-ATGCTATATGG-TTCATATGGCTGCTTTCAAGTTCAACGTTTCATTACTTCTATTT
* * *
52875894 CAGCTCTACAATGTTCGATGACT
127 CAGTTCTACAATGCTCAATGACT
* * * * * * * *
52875917 AATGGAAACCAAAAAGGCAGGCACTACAAA-ATAATCTTAGGCACGATGTTAA-GGATTTAATCT
1 AATGG------AAAA-GCAGGCACAACAAAGA-AATCTCAAGCATGATGCTAACAGATTCACT-T
* * * * * * * *
52875980 GAACATG-TCGTTTATAAGCTA-ATTGGTTCACATGGCTGGTTTCAAGTTCAATGTTTCTTTACT
57 TAAAATGTTTG-TTATATGCTATA-TGGTTCATATGGCTGCTTTCAAGTTCAACGTTTCATTACT
* * *
52876043 TCTATTCCAGCTCTACAATGTTCAATGACT
120 TCTATTTCAGTTCTACAATGCTCAATGACT
* * * *
52876073 AATGGAAAGGCAGACA-ATACCAAGAAAGCT-AAGGCATGATGCT
1 AATGGAAAAGCAGGCACA-ACAAAGAAATCTCAA-GCATGATGCT
52876116 CAAGCGAAAA
Statistics
Matches: 529, Mismatches: 95, Indels: 74
0.76 0.14 0.11
Matches are distributed among these distances:
148 3 0.01
149 54 0.10
150 104 0.20
151 48 0.09
152 69 0.13
153 2 0.00
155 4 0.01
156 72 0.14
157 51 0.10
158 49 0.09
159 31 0.06
160 4 0.01
161 3 0.01
162 31 0.06
163 4 0.01
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Consensus pattern (149 bp):
AATGGAAAAGCAGGCACAACAAAGAAATCTCAAGCATGATGCTAACAGATTCACTTTAAAATGTT
TGTTATATGCTATATGGTTCATATGGCTGCTTTCAAGTTCAACGTTTCATTACTTCTATTTCAGT
TCTACAATGCTCAATGACT
Found at i:52884149 original size:18 final size:18
Alignment explanation
Indices: 52884126--52884162 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
52884116 TTTGTTTTTC
52884126 TAATTTAAATCTTAGGAT
1 TAATTTAAATCTTAGGAT
*
52884144 TAATTTAGATCTTAGGAT
1 TAATTTAAATCTTAGGAT
52884162 T
1 T
52884163 TAAATAGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.46
Consensus pattern (18 bp):
TAATTTAAATCTTAGGAT
Found at i:52889118 original size:27 final size:28
Alignment explanation
Indices: 52889088--52889140 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
52889078 TATTTTTTGA
* * *
52889088 AATTATG-AAAATATTTTTAAAAATTGT
1 AATTATGTAAAAAAATTATAAAAATTGT
52889115 AATTATGTAAAAAAATTATAAAAATT
1 AATTATGTAAAAAAATTATAAAAATT
52889141 TTATAACAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.40
Consensus pattern (28 bp):
AATTATGTAAAAAAATTATAAAAATTGT
Found at i:52894739 original size:22 final size:23
Alignment explanation
Indices: 52894714--52894758 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
52894704 TCATATGGTT
*
52894714 GAATATATATTT-AGTTTTTTTA
1 GAATATATATTTGAGTTATTTTA
*
52894736 GAATTTATATTTGAGTTATTTTA
1 GAATATATATTTGAGTTATTTTA
52894759 AGATAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (23 bp):
GAATATATATTTGAGTTATTTTA
Found at i:52899124 original size:14 final size:15
Alignment explanation
Indices: 52899096--52899132 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
52899086 AGATATTATT
52899096 TTATGTTA-T-TTTA
1 TTATGTTATTATTTA
52899109 TTAT-TTATTATTTA
1 TTATGTTATTATTTA
52899123 TTATGTTATT
1 TTATGTTATT
52899133 TTATTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 3 0.14
13 5 0.24
14 8 0.38
15 5 0.24
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.70
Consensus pattern (15 bp):
TTATGTTATTATTTA
Found at i:52899990 original size:22 final size:23
Alignment explanation
Indices: 52899965--52900010 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
52899955 CAACCAAATC
52899965 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
52899987 AATTCATTCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
52900010 A
1 A
52900011 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:52900016 original size:23 final size:23
Alignment explanation
Indices: 52899972--52900016 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
52899962 ATCAATTCAA
*
52899972 CATATTTTCAAGATAAATTCATT
1 CATATTTTCAAGATAAAGTCATT
*
52899995 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
52900017 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATT
Found at i:52905816 original size:21 final size:21
Alignment explanation
Indices: 52905790--52905830 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
52905780 AGCTTAAATG
52905790 ATGGTTGAATAAGTA-GAATTC
1 ATGGTTGAA-AAGTATGAATTC
52905811 ATGGTTGAAAAGTATGAATT
1 ATGGTTGAAAAGTATGAATT
52905831 GAAATTGCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.34
Consensus pattern (21 bp):
ATGGTTGAAAAGTATGAATTC
Found at i:52907176 original size:39 final size:39
Alignment explanation
Indices: 52907122--52907198 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
52907112 TGGTATTTGA
* * *
52907122 AATATATCCGGACATGAGGTCTGTAGGCTATATGCTGGG
1 AATATATCCGGACATGAAGTCCGCAGGCTATATGCTGGG
*
52907161 AATATATCCGGACATGAAGTCCGCAGGCTATGTGCTGG
1 AATATATCCGGACATGAAGTCCGCAGGCTATATGCTGG
52907199 AATGGTACCC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (39 bp):
AATATATCCGGACATGAAGTCCGCAGGCTATATGCTGGG
Found at i:52909715 original size:19 final size:20
Alignment explanation
Indices: 52909678--52909715 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
52909668 ATAAGGTGGT
52909678 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
52909698 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
52909716 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:52910387 original size:18 final size:18
Alignment explanation
Indices: 52910364--52910646 Score: 124
Period size: 18 Copynumber: 15.3 Consensus size: 18
52910354 GAATAATTAT
52910364 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAGTCAG
* * *
52910382 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAGTCAG
* * **
52910400 TTATTCAATAATAACCAG
1 TTATTCAGTAACAGTCAG
* *
52910418 TTATTCAATATCGATCAATTGATCGG
1 TTATTCAGTA---A-C-A--G-TCAG
* *
52910444 TTATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
*
52910462 TTATTCAGTAA-AATCAG
1 TTATTCAGTAACAGTCAG
* * *
52910479 ATATTCAGTAACTATTAAG
1 TTATTCAGTAAC-AGTCAG
* * *
52910498 GTATTTAGTAGCAGTCA-
1 TTATTCAGTAACAGTCAG
* * *
52910515 TTCATTTAGTGACAATCAG
1 TT-ATTCAGTAACAGTCAG
* *
52910534 TTATTCAGTAA-TGATCAA
1 TTATTCAGTAACAG-TCAG
* *
52910552 TTATTCAGTAATATTCAG
1 TTATTCAGTAACAGTCAG
*
52910570 TTATTCAGTAATAGTCTA-
1 TTATTCAGTAACAGTC-AG
* * *
52910588 ATATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* * *
52910606 TTATCCGGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* *
52910624 TTATTCAGTAATAATCAG
1 TTATTCAGTAACAGTCAG
52910642 TTATT
1 TTATT
52910647 TTATACCTTT
Statistics
Matches: 199, Mismatches: 50, Indels: 32
0.71 0.18 0.11
Matches are distributed among these distances:
17 16 0.08
18 151 0.76
19 17 0.09
21 2 0.01
22 1 0.01
23 2 0.01
26 10 0.05
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAG
Found at i:52910406 original size:36 final size:36
Alignment explanation
Indices: 52910364--52910646 Score: 151
Period size: 36 Copynumber: 7.6 Consensus size: 36
52910354 GAATAATTAT
* *
52910364 TTATTCAGTAACAGTCAGTTATTCGGTAACAATCAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
* * * * * *
52910400 TTATTCAATAATAACCAGTTATTCAATATCGATCAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
* *
52910436 TTGATCGGTTATCCAGTAACAGTCAATTATTCAGTAA-AATCAGA
1 TT-A-----T-T-CAGTAACAATCAGTTATTCAGTAACAATCA-A
* * * * * *
52910480 -TATTCAGTAACTATTAAGGTATTTAGTAGCAGTC-A
1 TTATTCAGTAAC-AATCAGTTATTCAGTAACAATCAA
* * **
52910515 TTCATTTAGTGACAATCAGTTATTCAGTAATGATCAA
1 TT-ATTCAGTAACAATCAGTTATTCAGTAACAATCAA
* * * *
52910552 TTATTCAGTAATATTCAGTTATTCAGTAATAGTCTAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATC-AA
* * * * * *
52910589 -TATCCAGTAACAGTCAATTATCCGGTAACAGTCAA
1 TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
*
52910624 TTATTCAGTAATAATCAGTTATT
1 TTATTCAGTAACAATCAGTTATT
52910647 TTATACCTTT
Statistics
Matches: 180, Mismatches: 51, Indels: 32
0.68 0.19 0.12
Matches are distributed among these distances:
35 10 0.06
36 126 0.70
37 18 0.10
42 2 0.01
43 6 0.03
44 18 0.10
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (36 bp):
TTATTCAGTAACAATCAGTTATTCAGTAACAATCAA
Found at i:52910865 original size:45 final size:45
Alignment explanation
Indices: 52910810--52911002 Score: 280
Period size: 45 Copynumber: 4.3 Consensus size: 45
52910800 ACAAATCCGG
* *
52910810 AACAGTAACAGTAACAGTATTC-ATCACACAAAGTGCTGAATCGGT
1 AACAGTAACAGTAACAATATTCGA-CACACAAAGTGCCGAATCGGT
* * *
52910855 AACGGTAACAGTAACAATATTCAACACACAAAGTGTCGAATCGGT
1 AACAGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCGGT
* *
52910900 AACGGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCGAT
1 AACAGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCGGT
* *
52910945 AACAGTAGCAGTAACAATATTCGACACACAAAGTGCCGAATTGGT
1 AACAGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCGGT
*
52910990 AACAGTAGCAGTA
1 AACAGTAACAGTA
52911003 GCGGTAACAG
Statistics
Matches: 136, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
45 135 0.99
46 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (45 bp):
AACAGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCGGT
Found at i:52911422 original size:5 final size:5
Alignment explanation
Indices: 52911411--52911457 Score: 67
Period size: 5 Copynumber: 9.2 Consensus size: 5
52911401 AATTAATCAT
* *
52911411 AATTC CATTC CATTC AATTC AATTC AATTC AATTC AATTC AAATTC A
1 AATTC AATTC AATTC AATTC AATTC AATTC AATTC AATTC -AATTC A
52911458 CTTATCCACT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
5 34 0.87
6 5 0.13
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (5 bp):
AATTC
Found at i:52918504 original size:13 final size:13
Alignment explanation
Indices: 52918486--52918536 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
52918476 ATAGGAGATT
52918486 TTATTTTATTTTA
1 TTATTTTATTTTA
52918499 TTA-TTTA-TTT-
1 TTATTTTATTTTA
52918509 TTATTTTTATTTTA
1 TTA-TTTTATTTTA
*
52918523 TTAATTTATCTTTA
1 TTATTTTAT-TTTA
52918537 GCATATTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
10 3 0.09
11 3 0.09
12 8 0.25
13 11 0.34
14 7 0.22
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:52918513 original size:6 final size:6
Alignment explanation
Indices: 52918484--52918521 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
52918474 AAATAGGAGA
52918484 TTTTA- TTTTA- TTTTAT TATTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT T-TTTAT TTTTAT TTTTAT TTT
52918522 ATTAATTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 10 0.32
6 15 0.48
7 6 0.19
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:52918521 original size:24 final size:24
Alignment explanation
Indices: 52918484--52918536 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
52918474 AAATAGGAGA
52918484 TTTTATTTTATTTTATT-ATTTAT
1 TTTTATTTTATTTTATTAATTTAT
52918507 TTTTATTTTTATTTTATTAATTTAT
1 TTTTA-TTTTATTTTATTAATTTAT
*
52918532 CTTTA
1 TTTTA
52918537 GCATATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 5 0.19
24 12 0.44
25 10 0.37
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTATTTTATTTTATTAATTTAT
Found at i:52920865 original size:43 final size:44
Alignment explanation
Indices: 52920761--52920911 Score: 154
Period size: 44 Copynumber: 3.5 Consensus size: 44
52920751 TAAAAAAAAA
*
52920761 TTAGATCTT-AGGACTT-AAATAGGTTAAAGTTTTATTTTTCTCAT
1 TTAGATCTTAAGGA-TTCAAATAGGTTAAA-TTTTATTTTTCTAAT
* * *
52920805 TTATAT-TTTAGGATTCAAATAGGTTAAATTTTACTTTTCTAAT
1 TTAGATCTTAAGGATTCAAATAGGTTAAATTTTATTTTTCTAAT
*
52920848 TTAGATCTTAAGG-TTCAAATAGGGTAGAAATTTGT-TTTTTCTAAT
1 TTAGATCTTAAGGATTCAAATA-GGT-TAAATTT-TATTTTTCTAAT
*
52920893 TTAAATCTT-AGGATT-AAAT
1 TTAGATCTTAAGGATTCAAAT
52920912 TTTATTTTTT
Statistics
Matches: 92, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
43 30 0.33
44 36 0.39
45 25 0.27
46 1 0.01
ACGTcount: A:0.32, C:0.07, G:0.13, T:0.47
Consensus pattern (44 bp):
TTAGATCTTAAGGATTCAAATAGGTTAAATTTTATTTTTCTAAT
Found at i:52926669 original size:16 final size:16
Alignment explanation
Indices: 52926650--52926697 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
52926640 TTTACATGAT
52926650 TATAATTTTAAAAAAA
1 TATAATTTTAAAAAAA
* *
52926666 TATAATTTCAAATAAA
1 TATAATTTTAAAAAAA
52926682 TGATGAATTTTCAAAA
1 T-AT-AATTTT-AAAA
52926698 TAATTTAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 15 0.60
17 2 0.08
18 5 0.20
19 3 0.12
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (16 bp):
TATAATTTTAAAAAAA
Found at i:52929720 original size:18 final size:18
Alignment explanation
Indices: 52929697--52929731 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52929687 ATTTATACTT
52929697 ATAATTTATTATAATTTA
1 ATAATTTATTATAATTTA
* *
52929715 ATAATTTTTTATGATTT
1 ATAATTTATTATAATTT
52929732 TTTTATATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
ATAATTTATTATAATTTA
Found at i:52932459 original size:18 final size:18
Alignment explanation
Indices: 52932412--52932460 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
52932402 TCAATGCAGT
52932412 GATTCTCTAAATTTGATTG
1 GATTCTC-AAATTTGATTG
*
52932431 GATTTTC-AATTTGAATTG
1 GATTCTCAAATTTG-ATTG
52932449 G-TTCTCAAATTT
1 GATTCTCAAATTT
52932461 ACATGTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 10 0.38
18 10 0.38
19 6 0.23
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (18 bp):
GATTCTCAAATTTGATTG
Found at i:52935683 original size:27 final size:25
Alignment explanation
Indices: 52935629--52935683 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
52935619 CAGATGGCCC
* **
52935629 AAAGTAAAAAAATCTAAATATTTTT
1 AAAGTAAAAAAATCTAAATAATCCT
52935654 AAAGTAAAAAAATCTAGATATAATCCT
1 AAAGTAAAAAAATCTA-A-ATAATCCT
52935681 AAA
1 AAA
52935684 AAAAGGCACC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 16 0.64
26 1 0.04
27 8 0.32
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.29
Consensus pattern (25 bp):
AAAGTAAAAAAATCTAAATAATCCT
Found at i:52939325 original size:15 final size:15
Alignment explanation
Indices: 52939305--52939333 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52939295 TCTCTATCAT
52939305 TATTGTATTTCTATG
1 TATTGTATTTCTATG
52939320 TATTGTATTTCTAT
1 TATTGTATTTCTAT
52939334 ATCATTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.10, T:0.62
Consensus pattern (15 bp):
TATTGTATTTCTATG
Found at i:52942479 original size:19 final size:19
Alignment explanation
Indices: 52942442--52942485 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
52942432 TGAAACTAGT
*
52942442 ATCAATATTCTCAATAATA
1 ATCAATATTCTCAAGAATA
52942461 ATCAATATT-TCCAAGAATA
1 ATCAATATTCT-CAAGAATA
52942480 AGTCAA
1 A-TCAA
52942486 AAGGAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 17 0.77
20 4 0.18
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.32
Consensus pattern (19 bp):
ATCAATATTCTCAAGAATA
Found at i:52956363 original size:19 final size:19
Alignment explanation
Indices: 52956326--52956369 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
52956316 TGAAACTAGT
*
52956326 ATCAATATTCTCAATAATA
1 ATCAATATTCTCAAGAATA
52956345 ATCAATATT-TCCAAGAATA
1 ATCAATATTCT-CAAGAATA
52956364 AGTCAA
1 A-TCAA
52956370 AAGGAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 17 0.77
20 4 0.18
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.32
Consensus pattern (19 bp):
ATCAATATTCTCAAGAATA
Found at i:52961326 original size:32 final size:33
Alignment explanation
Indices: 52961283--52961344 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
52961273 CAAAACAAAT
*
52961283 TTATTTGTAAAAATTATAATAATAAATTTAAAA
1 TTATTTGTAAAAATAATAATAATAAATTTAAAA
**
52961316 TTATTT-TAAAAATAATAATTTTAAATTTA
1 TTATTTGTAAAAATAATAATAATAAATTTA
52961345 CGAGTTGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 20 0.77
33 6 0.23
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (33 bp):
TTATTTGTAAAAATAATAATAATAAATTTAAAA
Found at i:52965325 original size:12 final size:12
Alignment explanation
Indices: 52965308--52965332 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52965298 CTTGAAATGC
52965308 CTTCTCTTCACT
1 CTTCTCTTCACT
52965320 CTTCTCTTCACT
1 CTTCTCTTCACT
52965332 C
1 C
52965333 CTTTCTGCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.44, G:0.00, T:0.48
Consensus pattern (12 bp):
CTTCTCTTCACT
Found at i:52967495 original size:21 final size:21
Alignment explanation
Indices: 52967446--52967501 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
52967436 TAAGAAAACA
52967446 AAATATAAA-AAT-TTACCAT
1 AAATATAAATAATATTACCAT
* *
52967465 AAA-AGGAAATAATATTATCAT
1 AAATA-TAAATAATATTACCAT
*
52967486 AAATATAAATATTATT
1 AAATATAAATAATATT
52967502 TATCTTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
18 1 0.03
19 6 0.21
20 3 0.10
21 18 0.62
22 1 0.03
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.34
Consensus pattern (21 bp):
AAATATAAATAATATTACCAT
Found at i:52970997 original size:7 final size:7
Alignment explanation
Indices: 52970985--52971010 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
52970975 TTGTTATTTA
52970985 TTTTATT
1 TTTTATT
52970992 TTTTATT
1 TTTTATT
52970999 TTTTATT
1 TTTTATT
52971006 TTTTA
1 TTTTA
52971011 ATATATGGTG
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTATT
Found at i:52972846 original size:15 final size:15
Alignment explanation
Indices: 52972826--52972854 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52972816 TACTCGGTAT
52972826 AAAGATAACATATCC
1 AAAGATAACATATCC
52972841 AAAGATAACATATC
1 AAAGATAACATATC
52972855 TGTGTCGATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.21
Consensus pattern (15 bp):
AAAGATAACATATCC
Found at i:52975501 original size:12 final size:12
Alignment explanation
Indices: 52975484--52975512 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
52975474 CCATATAATC
52975484 TCTCTTTTACTG
1 TCTCTTTTACTG
52975496 TCTCTTTTACTG
1 TCTCTTTTACTG
52975508 TCTCT
1 TCTCT
52975513 ATATACTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.28, G:0.07, T:0.59
Consensus pattern (12 bp):
TCTCTTTTACTG
Found at i:52976916 original size:26 final size:26
Alignment explanation
Indices: 52976865--52976918 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
52976855 CTTCGTATTA
52976865 TATAGATATATAATATCCATATCTCT
1 TATAGATATATAATATCCATATCTCT
52976891 TATAGATATATAATATCCATATCTCT
1 TATAGATATATAATATCCATATCTCT
52976917 TA
1 TA
52976919 CATGTGTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.15, G:0.04, T:0.43
Consensus pattern (26 bp):
TATAGATATATAATATCCATATCTCT
Found at i:52993680 original size:19 final size:18
Alignment explanation
Indices: 52993633--52993680 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
52993623 TTCAAATATC
52993633 AATATTTTAATAATAAAAT
1 AATA-TTTAATAATAAAAT
* *
52993652 ATTATATTAATATTAAGAAT
1 AATAT-TTAATAATAA-AAT
52993672 AATATTTAA
1 AATATTTAA
52993681 ATTTTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 1 0.04
19 16 0.67
20 7 0.29
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
AATATTTAATAATAAAAT
Done.