Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 133 of 198
Found at i:42413436 original size:20 final size:20
Alignment explanation
Indices: 42413411--42413451 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
42413401 AGAGATGAAG
42413411 AAAGGATGAGGGGAAATCGA
1 AAAGGATGAGGGGAAATCGA
42413431 AAAGGATGAGGGGAAATCGA
1 AAAGGATGAGGGGAAATCGA
42413451 A
1 A
42413452 GAAAGACAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.05, G:0.39, T:0.10
Consensus pattern (20 bp):
AAAGGATGAGGGGAAATCGA
Found at i:42418227 original size:31 final size:31
Alignment explanation
Indices: 42418186--42418255 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
42418176 ACTTAACAGA
* ** *
42418186 TTAATAACTTAAATAAAAATTTTCAAATAAT
1 TTAATGACTTAAATAAAAACATCCAAATAAT
* *
42418217 TTAGTGACTTAAATGAAAACATCCAAATAAT
1 TTAATGACTTAAATAAAAACATCCAAATAAT
42418248 TTAATGAC
1 TTAATGAC
42418256 CGTTTGTAAC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.34
Consensus pattern (31 bp):
TTAATGACTTAAATAAAAACATCCAAATAAT
Found at i:42422344 original size:42 final size:41
Alignment explanation
Indices: 42422287--42422475 Score: 299
Period size: 42 Copynumber: 4.5 Consensus size: 41
42422277 GTTTACAAAC
42422287 AAAAACGCCGCTAAAGACTATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAC-ATGTTCTTTAGCGGCGCTTAGAA
42422329 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAG-ACATGTTCTTTAGCGGCGCTTAGAA
*
42422371 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAG-ACATGTTCTTTAGCGGCGCTTAGAA
* *
42422413 AAAAA-GCCTCTAAAGACCATGTTCTTTAGCGGTGCTTAGAA
1 AAAAACGCCGCTAAAGA-CATGTTCTTTAGCGGCGCTTAGAA
42422454 AAAAACGCCGCTAAAGAACATG
1 AAAAACGCCGCTAAAG-ACATG
42422476 AAAAATAGTA
Statistics
Matches: 139, Mismatches: 4, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
40 1 0.01
41 37 0.27
42 98 0.71
43 3 0.02
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGACATGTTCTTTAGCGGCGCTTAGAA
Found at i:42422441 original size:83 final size:84
Alignment explanation
Indices: 42422287--42422475 Score: 319
Period size: 83 Copynumber: 2.3 Consensus size: 84
42422277 GTTTACAAAC
42422287 AAAAACGCCGCTAAAG-ACTATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATG
1 AAAAACGCCGCTAAAGAAC-ATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATG
42422351 TTCTTTAGCGGCGCTTAGAA
65 TTCTTTAGCGGCGCTTAGAA
* * *
42422371 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAAA-GCCTCTAAAGACCATGT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGT
*
42422435 TCTTTAGCGGTGCTTAGAA
66 TCTTTAGCGGCGCTTAGAA
42422454 AAAAACGCCGCTAAAGAACATG
1 AAAAACGCCGCTAAAGAACATG
42422476 AAAAATAGTA
Statistics
Matches: 99, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
83 54 0.55
84 43 0.43
85 2 0.02
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (84 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGT
TCTTTAGCGGCGCTTAGAA
Found at i:42422871 original size:21 final size:21
Alignment explanation
Indices: 42422845--42422891 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
42422835 TGGCCTACTA
* * *
42422845 TGCTTCTCTCGTTGCAGCTTC
1 TGCTTCCCTCGCTGCAGCCTC
*
42422866 TGCTTCCCTCGCTGCCGCCTC
1 TGCTTCCCTCGCTGCAGCCTC
42422887 TGCTT
1 TGCTT
42422892 TAAGTTGTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.02, C:0.40, G:0.19, T:0.38
Consensus pattern (21 bp):
TGCTTCCCTCGCTGCAGCCTC
Found at i:42426396 original size:9 final size:9
Alignment explanation
Indices: 42426384--42426614 Score: 162
Period size: 9 Copynumber: 26.4 Consensus size: 9
42426374 ATTAAGTCAA
42426384 TTATGTAAG
1 TTATGTAAG
*
42426393 TTATGTACG
1 TTATGTAAG
42426402 TGTA--TAAG
1 T-TATGTAAG
42426410 TTATGTAAG
1 TTATGTAAG
42426419 TTATGT-A-
1 TTATGTAAG
*
42426426 TTAAGTAAG
1 TTATGTAAG
* *
42426435 CTATTTAAG
1 TTATGTAAG
*
42426444 TTGTGT-A-
1 TTATGTAAG
42426451 TTATGTAAG
1 TTATGTAAG
42426460 TTATGTAAG
1 TTATGTAAG
**
42426469 TTATCAAAG
1 TTATGTAAG
* *
42426478 TAATGTATG
1 TTATGTAAG
42426487 TTATGTAAG
1 TTATGTAAG
42426496 -T-TGTAAG
1 TTATGTAAG
*
42426503 TTAT-TATG
1 TTATGTAAG
*
42426511 TATTATGTAGG
1 --TTATGTAAG
42426522 TTATGTAAG
1 TTATGTAAG
42426531 TTATGTAAG
1 TTATGTAAG
*
42426540 TTTTGT-A-
1 TTATGTAAG
*
42426547 TTATTTAAG
1 TTATGTAAG
*
42426556 TTGTGTAAG
1 TTATGTAAG
*
42426565 TTATGTATG
1 TTATGTAAG
*
42426574 CTATGTAAG
1 TTATGTAAG
* *
42426583 TAATGTGTA-
1 TTATGT-AAG
42426592 TTATGTAAG
1 TTATGTAAG
*
42426601 TTTATATAAG
1 -TTATGTAAG
42426611 TTAT
1 TTAT
42426615 TATGTAACTA
Statistics
Matches: 169, Mismatches: 36, Indels: 34
0.71 0.15 0.14
Matches are distributed among these distances:
7 22 0.13
8 16 0.09
9 113 0.67
10 15 0.09
11 3 0.02
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:42426450 original size:25 final size:25
Alignment explanation
Indices: 42426368--42426472 Score: 117
Period size: 25 Copynumber: 4.2 Consensus size: 25
42426358 TGATATATAT
42426368 TTATGTATTAAGTCAA-TTATGTAAG
1 TTATGTATTAAGT-AAGTTATGTAAG
42426393 TTATGTACGTGT-A-TAAGTTATGTAAG
1 TTATGTA--T-TAAGTAAGTTATGTAAG
* *
42426419 TTATGTATTAAGTAAGCTATTTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
* *
42426444 TTGTGTATTATGTAAGTTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
42426469 TTAT
1 TTAT
42426473 CAAAGTAATG
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
23 1 0.01
24 2 0.03
25 44 0.66
26 17 0.25
27 2 0.03
28 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.46
Consensus pattern (25 bp):
TTATGTATTAAGTAAGTTATGTAAG
Found at i:42426468 original size:34 final size:33
Alignment explanation
Indices: 42426383--42426565 Score: 123
Period size: 34 Copynumber: 5.6 Consensus size: 33
42426373 TATTAAGTCA
* * *
42426383 ATTATGTAAGTTATGTACGTGTATAAGTTATGT
1 ATTATGTAAGTTATGTAAGTATTTAAGTTATGT
* *
42426416 AAGTTATGT-A-TTAAGTAAGCTATTTAAGTTGTGT
1 -A-TTATGTAAGTTATGTAAG-TATTTAAGTTATGT
** *
42426450 ATTATGTAAGTTATGTAAGTTATCAAAGTAATGT
1 ATTATGTAAGTTATGTAAG-TATTTAAGTTATGT
42426484 ATGTTATGTAAG-T-TGTAAG---TT-A-TTATGT
1 A--TTATGTAAGTTATGTAAGTATTTAAGTTATGT
* * *
42426512 ATTATGTAGGTTATGTAAGTTATGTAAGTTTTGT
1 ATTATGTAAGTTATGTAAG-TATTTAAGTTATGT
* *
42426546 ATTATTTAAGTTGTGTAAGT
1 ATTATGTAAGTTATGTAAGT
42426566 TATGTATGCT
Statistics
Matches: 115, Mismatches: 20, Indels: 29
0.70 0.12 0.18
Matches are distributed among these distances:
26 8 0.07
27 1 0.01
28 12 0.10
29 1 0.01
32 7 0.06
33 11 0.10
34 59 0.51
35 7 0.06
36 9 0.08
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (33 bp):
ATTATGTAAGTTATGTAAGTATTTAAGTTATGT
Found at i:42426547 original size:62 final size:63
Alignment explanation
Indices: 42426447--42426573 Score: 161
Period size: 62 Copynumber: 2.0 Consensus size: 63
42426437 ATTTAAGTTG
42426447 TGTATTATGTAAGTTATGTAAGTTATCAAAGTAATGTATGTTATGTAAG-T-TGTAAGTTAT-TA
1 TGTATTATGTAAGTTATGTAAGTTATCAAAGTAATGTA--TTATGTAAGTTGTGTAAGTTATGTA
* ** ** *
42426509 TGTATTATGTAGGTTATGTAAGTTATGTAAGTTTTGTATTATTTAAGTTGTGTAAGTTATGTA
1 TGTATTATGTAAGTTATGTAAGTTATCAAAGTAATGTATTATGTAAGTTGTGTAAGTTATGTA
42426572 TG
1 TG
42426574 CTATGTAAGT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
60 8 0.14
61 1 0.02
62 43 0.77
63 4 0.07
ACGTcount: A:0.30, C:0.01, G:0.21, T:0.48
Consensus pattern (63 bp):
TGTATTATGTAAGTTATGTAAGTTATCAAAGTAATGTATTATGTAAGTTGTGTAAGTTATGTA
Found at i:42426550 original size:25 final size:25
Alignment explanation
Indices: 42426506--42426707 Score: 74
Period size: 25 Copynumber: 7.7 Consensus size: 25
42426496 TTGTAAGTTA
*
42426506 TTATGTATTATGTAGGTTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
* *
42426531 TTATGTAAGTTTTGT-A-TTATTTAAG
1 TTATGT-A-TTATGTAAGTTATGTAAG
* * *
42426556 TTGTGTAAGTTATGTATGCTATGTAAG
1 TTATGT-A-TTATGTAAGTTATGTAAG
* *
42426583 TAATGTGTATTATGTAAGTTTATATAAG
1 T--TATGTATTATGTAAG-TTATGTAAG
** *
42426611 TTAT-TATGTAACTAA-TGTAT-TATG
1 TTATGTAT-TATGTAAGT-TATGTAAG
* * * * *
42426635 TAAGTTTATT-TGAGAATTTTATATAAG
1 TTA-TGTATTATG-TAA-GTTATGTAAG
*
42426662 TCATGTATTATGTAAGTTAACATGTAAG
1 TTATGTATTATGTAAGTT---ATGTAAG
42426690 TTATGTATTATGTAAGTT
1 TTATGTATTATGTAAGTT
42426708 TAATAAGTGT
Statistics
Matches: 132, Mismatches: 26, Indels: 35
0.68 0.13 0.18
Matches are distributed among these distances:
24 6 0.05
25 39 0.30
26 21 0.16
27 29 0.22
28 32 0.24
29 5 0.04
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.48
Consensus pattern (25 bp):
TTATGTATTATGTAAGTTATGTAAG
Found at i:42426582 original size:43 final size:44
Alignment explanation
Indices: 42426460--42426602 Score: 114
Period size: 44 Copynumber: 3.2 Consensus size: 44
42426450 ATTATGTAAG
* ** * * *
42426460 TTATGTAAGTTATCAAAGTAATGTATGTTATGTAAGT-TGTAAGTTA
1 TTATGTAAGTTGTGTAAGTTATGTAAGCTATGTAAGTATGT--G-TA
* * * *
42426506 TTATGT-A-TTATGTAGGTTATGTAAGTTATGTAAGT-TTTGTA
1 TTATGTAAGTTGTGTAAGTTATGTAAGCTATGTAAGTATGTGTA
* *
42426547 TTATTTAAGTTGTGTAAGTTATGTATGCTATGTAAGTAATGTGTA
1 TTATGTAAGTTGTGTAAGTTATGTAAGCTATGTAAGT-ATGTGTA
42426592 TTATGTAAGTT
1 TTATGTAAGTT
42426603 TATATAAGTT
Statistics
Matches: 80, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
41 7 0.09
42 2 0.03
43 24 0.30
44 25 0.31
45 16 0.20
46 6 0.08
ACGTcount: A:0.30, C:0.01, G:0.21, T:0.48
Consensus pattern (44 bp):
TTATGTAAGTTGTGTAAGTTATGTAAGCTATGTAAGTATGTGTA
Found at i:42426638 original size:38 final size:39
Alignment explanation
Indices: 42426588--42426679 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 39
42426578 GTAAGTAATG
* *
42426588 TGTATTATGTAAGTTTATAT-A-AGTTATTATGTAACTAA
1 TGTATTATGTAAGTTTATATGAGAATT-TTATATAACTAA
* * *
42426626 TGTATTATGTAAGTTTATTTGAGAATTTTATATAAGTCA
1 TGTATTATGTAAGTTTATATGAGAATTTTATATAACTAA
42426665 TGTATTATGTAAGTT
1 TGTATTATGTAAGTT
42426680 AACATGTAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
38 19 0.40
39 25 0.53
40 3 0.06
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (39 bp):
TGTATTATGTAAGTTTATATGAGAATTTTATATAACTAA
Found at i:42427692 original size:67 final size:67
Alignment explanation
Indices: 42427584--42427722 Score: 269
Period size: 67 Copynumber: 2.1 Consensus size: 67
42427574 NNTTTTGAGA
*
42427584 ATTCATTATATAATGAATTTATTAAACATTCAATCAATTAACTAACCAAAATTGATAATTCATTG
1 ATTCATTATATAATGAATTTATTAAACATTCAATCAATTAACTAACCAAAATTGAAAATTCATTG
42427649 AC
66 AC
42427651 ATTCATTATATAATGAATTTATTAAACATTCAATCAATTAACTAACCAAAATTGAAAATTCATTG
1 ATTCATTATATAATGAATTTATTAAACATTCAATCAATTAACTAACCAAAATTGAAAATTCATTG
42427716 AC
66 AC
42427718 ATTCA
1 ATTCA
42427723 ATCAATTAAT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 71 1.00
ACGTcount: A:0.45, C:0.14, G:0.04, T:0.37
Consensus pattern (67 bp):
ATTCATTATATAATGAATTTATTAAACATTCAATCAATTAACTAACCAAAATTGAAAATTCATTG
AC
Found at i:42427803 original size:16 final size:16
Alignment explanation
Indices: 42427782--42427817 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
42427772 ATTAATTGAA
42427782 ATAAAATTGAAAATCG
1 ATAAAATTGAAAATCG
*
42427798 ATAAAATTGTAAATCG
1 ATAAAATTGAAAATCG
42427814 ATAA
1 ATAA
42427818 TTATAAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.11, T:0.28
Consensus pattern (16 bp):
ATAAAATTGAAAATCG
Found at i:42427873 original size:10 final size:10
Alignment explanation
Indices: 42427858--42427896 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
42427848 TTCGAATAAT
42427858 TATAAAATTA
1 TATAAAATTA
42427868 TATAAAATTA
1 TATAAAATTA
*
42427878 TTTAAAATTA
1 TATAAAATTA
*
42427888 TTTAAAATT
1 TATAAAATT
42427897 TACCCATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
TATAAAATTA
Found at i:42430144 original size:21 final size:21
Alignment explanation
Indices: 42430079--42430130 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
42430069 TATAATTTGT
* * **
42430079 AAACCTTAAACCTCAAAAACC
1 AAACCCTAAACCCCAAACCCC
42430100 AAACCCTAAACCCCAAACCCC
1 AAACCCTAAACCCCAAACCCC
42430121 AAACCCTAAA
1 AAACCCTAAA
42430131 TGCTAAACTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.50, C:0.40, G:0.00, T:0.10
Consensus pattern (21 bp):
AAACCCTAAACCCCAAACCCC
Found at i:42430159 original size:29 final size:28
Alignment explanation
Indices: 42430105--42430159 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
42430095 AAACCAAACC
* *
42430105 CTAAACCCCAAACCCCAAACCCTAAATG
1 CTAAACCCAAAACCCCAAACACTAAATG
*
42430133 CTAAACTCCAAAACCCCAAACAGTAAA
1 CTAAAC-CCAAAACCCCAAACACTAAA
42430160 AGTCAAAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.47, C:0.38, G:0.04, T:0.11
Consensus pattern (28 bp):
CTAAACCCAAAACCCCAAACACTAAATG
Found at i:42431445 original size:114 final size:112
Alignment explanation
Indices: 42431254--42431515 Score: 269
Period size: 113 Copynumber: 2.3 Consensus size: 112
42431244 ATTCCGGTAT
* * *
42431254 ACATCAAGAACTAAACACTGTGTTTTGGTTAAGATACTTTGCGGCGCGTTCCACAAACACCGCTA
1 ACATCAAG-ACCAAACACTGCGTTTTGGTTAAGATACTTTGAGGCGCGTTCCACAAACACCGCTA
* * *
42431319 ATGATATACTTTAGC-GGCGTTTTTCATCAAGCGCCACTAATTCTAATAC
65 ATAATATACTTTA-CTGGCG-TTTTCATCAAACGCCACTAATTATAATAC
* * * ***
42431368 ACCTCAAGACCAAACTCTGCGTTTTGGTTAAGATATTTTGAGGCGC-TTACCACCAAACGTTGCT
1 ACATCAAGACCAAACACTGCGTTTTGGTTAAGATACTTTGAGGCGCGTT-CCA-CAAACACCGCT
* * * * *
42431432 -ATAACTATCCTTTACTGGCGTTTTCCTTAAACGCCACTAATTATATTAT
64 AATAA-TATACTTTACTGGCGTTTTCATCAAACGCCACTAATTATAATAC
* *
42431481 ACATCAGGACCAACACACTGCGTTTTGATTAAGAT
1 ACATCAAGACCAA-ACACTGCGTTTTGGTTAAGAT
42431516 GTCTTGCAGC
Statistics
Matches: 122, Mismatches: 21, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
112 2 0.02
113 74 0.61
114 46 0.38
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (112 bp):
ACATCAAGACCAAACACTGCGTTTTGGTTAAGATACTTTGAGGCGCGTTCCACAAACACCGCTAA
TAATATACTTTACTGGCGTTTTCATCAAACGCCACTAATTATAATAC
Found at i:42431663 original size:114 final size:114
Alignment explanation
Indices: 42431194--42431737 Score: 386
Period size: 114 Copynumber: 4.8 Consensus size: 114
42431184 GTTTCGGTAA
* * ** **
42431194 AAGCGCCGCTAATACTATGC-TTCAGCGGCGTTTTC-CCATGTGCGCCACTAATTCCGGTATACA
1 AAGCGCCGCTAATACTATACATT-AGCGGCGTTTTCTTCATAAGCGCCACTAATT-CAATATACA
* *
42431257 TCAAGAACTAAACACTGTGTTTTGGTTAAGATAC-TTTGCGGCGCGTT-CCAC-
64 TCAAG-ACCAAACACTGCGTTTTGGTTAAGAT-CTTTTGCGGCGC-TTACCACT
* * * *
42431308 AAACACCGCTAATGA-TATACTTTAGCGGCG-TTT-TTCATCAAGCGCCACTAATTCTAATACAC
1 AAGCGCCGCTAAT-ACTATACATTAGCGGCGTTTTCTTCAT-AAGCGCCACTAATTC-AATATAC
* * * * *
42431370 CTCAAGACCAAACTCTGCGTTTTGGTTAAGATATTTTGAGGCGCTTACCACC
63 ATCAAGACCAAACACTGCGTTTTGGTTAAGATCTTTTGCGGCGCTTACCACT
* ** * *
42431422 AAACGTTGCT-ATAACTATCCTTTA-CTGGCGTTTTCCTT-A-AA-CGCCACTAATT-ATATTAT
1 AAGCGCCGCTAAT-ACTATACATTAGC-GGCGTTTT-CTTCATAAGCGCCACTAATTCA-A-TAT
* * * * * * * *
42431481 ACATCAGGACCAACACACTGCGTTTTGATTAAGATGTCTTGCAGCGTTTAACGCT
61 ACATCAAGACCAA-ACACTGCGTTTTGGTTAAGATCTTTTGCGGCGCTTACCACT
** * * *
42431536 CGGTGCCGCTAATACTATACATTAGCGGCATTTTCTTTATAAGCGCCACTAATTGCAATATACAT
1 AAGCGCCGCTAATACTATACATTAGCGGCGTTTTCTTCATAAGCGCCACTAATT-CAATATACAT
* ** * *
42431601 CAAGACTAAACTTTGCGTTTTGGTTAACATCTTTTGCGGCGCTT-CCTCT
65 CAAGACCAAACACTGCGTTTTGGTTAAGATCTTTTGCGGCGCTTACCACT
* * * *
42431650 AAGCGCCGCTAATACTATACATTA-CTAGCG-TTTGTTCGTAAGCGCCACTAATGCCAA-ATACA
1 AAGCGCCGCTAATACTATACATTAGC-GGCGTTTTCTTCATAAGCGCCACTAAT-TCAATATACA
* *
42431712 TCAAGACCAGAACACTACGTGTTGGT
64 TCAAGACCA-AACACTGCGTTTTGGT
42431738 CTTGAGATTT
Statistics
Matches: 336, Mismatches: 68, Indels: 53
0.74 0.15 0.12
Matches are distributed among these distances:
111 1 0.00
112 16 0.05
113 109 0.32
114 142 0.42
115 38 0.11
116 26 0.08
117 3 0.01
118 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (114 bp):
AAGCGCCGCTAATACTATACATTAGCGGCGTTTTCTTCATAAGCGCCACTAATTCAATATACATC
AAGACCAAACACTGCGTTTTGGTTAAGATCTTTTGCGGCGCTTACCACT
Found at i:42435212 original size:23 final size:23
Alignment explanation
Indices: 42435185--42435234 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
42435175 TGATTTTTAA
**
42435185 ATTTTAAATTATTTAGGGATAAT
1 ATTTTAAATTATTTAGCAATAAT
*
42435208 ATTTTGAATTATTTAGCAATAAT
1 ATTTTAAATTATTTAGCAATAAT
42435231 ATTT
1 ATTT
42435235 AGGGAAAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (23 bp):
ATTTTAAATTATTTAGCAATAAT
Found at i:42436157 original size:22 final size:21
Alignment explanation
Indices: 42436088--42436164 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 21
42436078 TTATTTTTCC
42436088 ATTTATTTTATTTTATTAAATTT
1 ATTTATTTTATTTT-TT-AATTT
** * *
42436111 ATTT-TTGCATTTTTGAACATT
1 ATTTATTTTATTTTTTAA-TTT
42436132 -TTTATTTTATTTTTTATATTT
1 ATTTATTTTATTTTTTA-ATTT
42436153 ATTTATTTTATT
1 ATTTATTTTATT
42436165 ATCTTAATCA
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
20 5 0.12
21 14 0.33
22 19 0.45
23 4 0.10
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (21 bp):
ATTTATTTTATTTTTTAATTT
Found at i:42441602 original size:26 final size:27
Alignment explanation
Indices: 42441573--42441627 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
42441563 ATAGAAAACA
42441573 AAATAATATACACAATAATA-ATATAT
1 AAATAATATACACAATAATATATATAT
* * *
42441599 AAATAATATATATAATAATATATGTAT
1 AAATAATATACACAATAATATATATAT
42441626 AA
1 AA
42441628 GTTGAAGCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (27 bp):
AAATAATATACACAATAATATATATAT
Found at i:42441605 original size:11 final size:12
Alignment explanation
Indices: 42441587--42441621 Score: 63
Period size: 11 Copynumber: 3.0 Consensus size: 12
42441577 AATATACACA
42441587 ATAATAATATAT
1 ATAATAATATAT
42441599 A-AATAATATAT
1 ATAATAATATAT
42441610 ATAATAATATAT
1 ATAATAATATAT
42441622 GTATAAGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATAATATAT
Found at i:42441618 original size:15 final size:14
Alignment explanation
Indices: 42441574--42441618 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 14
42441564 TAGAAAACAA
*
42441574 AATAATATACACAAT
1 AATAATATATA-AAT
42441589 AATAATATATAAAT
1 AATAATATATAAAT
42441603 AAT-ATATAT-AAT
1 AATAATATATAAAT
42441615 AATA
1 AATA
42441619 TATGTATAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 6 0.21
13 6 0.21
14 6 0.21
15 10 0.36
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAATATATAAAT
Found at i:42441667 original size:16 final size:16
Alignment explanation
Indices: 42441648--42441685 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
42441638 GTAAAAATAA
42441648 AATAAAGTACTA-AAAT
1 AATAAAGTA-TATAAAT
*
42441664 AATAAAGTATATATAT
1 AATAAAGTATATAAAT
42441680 AATAAA
1 AATAAA
42441686 AAATAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 2 0.10
16 18 0.90
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (16 bp):
AATAAAGTATATAAAT
Found at i:42443801 original size:100 final size:100
Alignment explanation
Indices: 42443502--42444097 Score: 657
Period size: 100 Copynumber: 6.0 Consensus size: 100
42443492 GATCTGCTCC
* * * * * * *
42443502 ACTGCAATG-CTAGGGAAGTAAGATTCATTGTTGTTGCTTTAATCTATTCCACTGTAACACTC-G
1 ACTGCAATGTCGA-GGAAGTAAGATTCGTCGTTGTAGCTTTAATCTGTTCCACTGCACCAC-CAG
* * * * *
42443565 AGAAGTAAGATTCGTTGTTGTAGCTTTAATCCATTTC
64 GGAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTA
* * * * * * * * *
42443602 ACTGCAATGCCGGGGAAGTAAGATTTGTTGTTGTAGCTTT-ATCTGTTTCGCCGCAACGCC-GAG
1 ACTGCAATGTCGAGGAAGTAAGATTCGTCGTTGTAGCTTTAATCTGTTCCACTGCACCACCAG-G
* * * *
42443665 GAAGTAAGATTTGCTATTGTAGCTTCAATTTGTTTA
65 GAAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTA
* * *
42443701 ACTGCAATGTTGAGGAAGTAAGATTCATCGTTGTAGCTTTAATCTGTTCCACTGCACCACTAGGG
1 ACTGCAATGTCGAGGAAGTAAGATTCGTCGTTGTAGCTTTAATCTGTTCCACTGCACCACCAGGG
* * *
42443766 AAATAAGATTCGCTGTTGTAGCTGT-AATTTGTTTA
66 AAGTAAGATTCGCTGTTGTAGCT-TCAATCTATTTA
* * * * * * **
42443801 ACTGTAACGTCGGGGAAGTAAGATTCGCCGTCGTAGCTTTAATCTGTTCCACTGAACTGCCAGGG
1 ACTGCAATGTCGAGGAAGTAAGATTCGTCGTTGTAGCTTTAATCTGTTCCACTGCACCACCAGGG
*
42443866 AAGTAAGATTTGCTGTTGTAGCTTCAATCTATTTA
66 AAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTA
* * * *
42443901 ACTGTAATGTCGAGGAAGTAAGATTCGTTGTTGTAGCTTTAATCTATTCCACTGCAACACCAGGG
1 ACTGCAATGTCGAGGAAGTAAGATTCGTCGTTGTAGCTTTAATCTGTTCCACTGCACCACCAGGG
42443966 AAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTA
66 AAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTA
* *
42444001 ACTGCAATGTCGGGGAAGTAAGATTCG-CTGTCGTAGCTTTAATCTGTTCCACTGCACCACCAGG
1 ACTGCAATGTCGAGGAAGTAAGATTCGTC-GTTGTAGCTTTAATCTGTTCCACTGCACCACCAGG
* *
42444065 GAAATAAGATTCGCTG-TGATAACTTCAATCTAT
65 GAAGTAAGATTCGCTGTTG-TAGCTTCAATCTAT
42444098 CCCACTACAA
Statistics
Matches: 419, Mismatches: 69, Indels: 16
0.83 0.14 0.03
Matches are distributed among these distances:
98 2 0.00
99 78 0.19
100 336 0.80
101 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (100 bp):
ACTGCAATGTCGAGGAAGTAAGATTCGTCGTTGTAGCTTTAATCTGTTCCACTGCACCACCAGGG
AAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTA
Found at i:42443936 original size:200 final size:198
Alignment explanation
Indices: 42443502--42444097 Score: 759
Period size: 200 Copynumber: 3.0 Consensus size: 198
42443492 GATCTGCTCC
* * * * *
42443502 ACTGCAATG-CTAGGGAAGTAAGATTCATTGTTGTTGCTTTAATCTATTCCACTGTAACACTCGA
1 ACTGCAATGTCGA-GGAAGTAAGATTCATTGTTGTAGCTTTAATCTATTCCACTGCAACACTAGG
* * * * * *
42443566 GAAGTAAGATTCGTTGTTGTAGCTTTAATCCATTTCACTGCAATGCCGGGGAAGTAAGATTTGTT
65 GAAGTAAGATTCGCTGTTGTAGC-TTAATCTATTTAACTGCAATGTCGGGGAAGTAAGATTCGCT
* * * * *
42443631 GTTGTAGCTTT-ATCTGTTTCGCCGCAACGCC-GAGGAAGTAAGATTTGCTATTGTAGCTTCAAT
129 GTCGTAGCTTTAATCTGTTCCACTG-AACGCCAG-GGAAGTAAGATTTGCTGTTGTAGCTTCAAT
* *
42443694 TTGTTTA
192 CTATTTA
* * * *
42443701 ACTGCAATGTTGAGGAAGTAAGATTCATCGTTGTAGCTTTAATCTGTTCCACTGCACCACTAGGG
1 ACTGCAATGTCGAGGAAGTAAGATTCATTGTTGTAGCTTTAATCTATTCCACTGCAACACTAGGG
* * * * * *
42443766 AAATAAGATTCGCTGTTGTAGCTGTAATTTGTTTAACTGTAACGTCGGGGAAGTAAGATTCGCCG
66 AAGTAAGATTCGCTGTTGTAGCT-TAATCTATTTAACTGCAATGTCGGGGAAGTAAGATTCGCTG
42443831 TCGTAGCTTTAATCTGTTCCACTGAACTGCCAGGGAAGTAAGATTTGCTGTTGTAGCTTCAATCT
130 TCGTAGCTTTAATCTGTTCCACTGAAC-GCCAGGGAAGTAAGATTTGCTGTTGTAGCTTCAATCT
42443896 ATTTA
194 ATTTA
* * *
42443901 ACTGTAATGTCGAGGAAGTAAGATTCGTTGTTGTAGCTTTAATCTATTCCACTGCAACACCAGGG
1 ACTGCAATGTCGAGGAAGTAAGATTCATTGTTGTAGCTTTAATCTATTCCACTGCAACACTAGGG
42443966 AAGTAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGTAAGATTCGCTG
66 AAGTAAGATTCGCTGTTGTAGCTT-AATCTATTTAACTGCAATGTCGGGGAAGTAAGATTCGCTG
* * * * *
42444031 TCGTAGCTTTAATCTGTTCCACTGCACCACCAGGGAAATAAGATTCGCTG-TGATAACTTCAATC
130 TCGTAGCTTTAATCTGTTCCACTG-AACGCCAGGGAAGTAAGATTTGCTGTTG-TAGCTTCAATC
42444095 TAT
193 TAT
42444098 CCCACTACAA
Statistics
Matches: 343, Mismatches: 46, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
198 1 0.00
199 120 0.35
200 219 0.64
201 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (198 bp):
ACTGCAATGTCGAGGAAGTAAGATTCATTGTTGTAGCTTTAATCTATTCCACTGCAACACTAGGG
AAGTAAGATTCGCTGTTGTAGCTTAATCTATTTAACTGCAATGTCGGGGAAGTAAGATTCGCTGT
CGTAGCTTTAATCTGTTCCACTGAACGCCAGGGAAGTAAGATTTGCTGTTGTAGCTTCAATCTAT
TTA
Found at i:42444095 original size:50 final size:50
Alignment explanation
Indices: 42443487--42444095 Score: 444
Period size: 50 Copynumber: 12.2 Consensus size: 50
42443477 AAGGCTGGTG
* * * * ** *
42443487 GCTTCGATCTGCTCCACTGCAATGCTAGGGAAGTAAGATTCATTGTTGTT
1 GCTTCAATCTGTTCCACTGCAACGCCAGGGAAGTAAGATTCGCTGTTGTA
* * * * * *
42443537 GCTTTAATCTATTCCACTGTAACACTC-GAGAAGTAAGATTCGTTGTTGTA
1 GCTTCAATCTGTTCCACTGCAACGC-CAGGGAAGTAAGATTCGCTGTTGTA
* ** * * * * *
42443587 GCTTTAATCCATTTCACTGCAATGCCGGGGAAGTAAGATTTGTTGTTGTA
1 GCTTCAATCTGTTCCACTGCAACGCCAGGGAAGTAAGATTCGCTGTTGTA
* * * * * *
42443637 GCTT-TATCTGTTTCGCCGCAACGCC-GAGGAAGTAAGATTTGCTATTGTA
1 GCTTCAATCTGTTCCACTGCAACGCCAG-GGAAGTAAGATTCGCTGTTGTA
* ** * ** *
42443686 GCTTCAATTTGTTTAACTGCAATG-TTGAGGAAGTAAGATTC-ATCGTTGTA
1 GCTTCAATCTGTTCCACTGCAACGCCAG-GGAAGTAAGATTCGCT-GTTGTA
* * * * *
42443736 GCTTTAATCTGTTCCACTGCACCACTAGGGAAATAAGATTCGCTGTTGTA
1 GCTTCAATCTGTTCCACTGCAACGCCAGGGAAGTAAGATTCGCTGTTGTA
* ** * * * * *
42443786 GCTGT-AATTTGTTTAACTGTAACGTCGGGGAAGTAAGATTCGCCGTCGTA
1 GCT-TCAATCTGTTCCACTGCAACGCCAGGGAAGTAAGATTCGCTGTTGTA
* *
42443836 GCTTTAATCTGTTCCACTG-AACTGCCAGGGAAGTAAGATTTGCTGTTGTA
1 GCTTCAATCTGTTCCACTGCAAC-GCCAGGGAAGTAAGATTCGCTGTTGTA
* ** * * * *
42443886 GCTTCAATCTATTTAACTGTAATGTC-GAGGAAGTAAGATTCGTTGTTGTA
1 GCTTCAATCTGTTCCACTGCAACGCCAG-GGAAGTAAGATTCGCTGTTGTA
* * *
42443936 GCTTTAATCTATTCCACTGCAACACCAGGGAAGTAAGATTCGCTGTTGTA
1 GCTTCAATCTGTTCCACTGCAACGCCAGGGAAGTAAGATTCGCTGTTGTA
* ** * * * *
42443986 GCTTCAATCTATTTAACTGCAATGTCGGGGAAGTAAGATTCGCTGTCGTA
1 GCTTCAATCTGTTCCACTGCAACGCCAGGGAAGTAAGATTCGCTGTTGTA
* * * *
42444036 GCTTTAATCTGTTCCACTGCACCACCAGGGAAATAAGATTCGCTG-TGATA
1 GCTTCAATCTGTTCCACTGCAACGCCAGGGAAGTAAGATTCGCTGTTG-TA
*
42444086 ACTTCAATCT
1 GCTTCAATCT
42444096 ATCCCACTAC
Statistics
Matches: 441, Mismatches: 103, Indels: 30
0.77 0.18 0.05
Matches are distributed among these distances:
48 1 0.00
49 47 0.11
50 386 0.88
51 7 0.02
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (50 bp):
GCTTCAATCTGTTCCACTGCAACGCCAGGGAAGTAAGATTCGCTGTTGTA
Found at i:42447985 original size:34 final size:34
Alignment explanation
Indices: 42447942--42448011 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
42447932 GGTGGGTACC
*
42447942 AAAGAATATACAAATAATATATGAATTTATGAAT
1 AAAGAATATACAAAGAATATATGAATTTATGAAT
42447976 AAAGAATATACAAAGAATATATGAATTTATGAAT
1 AAAGAATATACAAAGAATATATGAATTTATGAAT
42448010 AA
1 AA
42448012 CTATTTGTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.30
Consensus pattern (34 bp):
AAAGAATATACAAAGAATATATGAATTTATGAAT
Found at i:42450050 original size:19 final size:19
Alignment explanation
Indices: 42450008--42450054 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
42449998 TTGTGGACTT
*
42450008 TAATGCAAATGATGTAATG
1 TAATGCAAATGATGAAATG
*
42450027 TAATGCAAATGCGTGAAATG
1 TAATGCAAATG-ATGAAATG
42450047 -AATGCAAA
1 TAATGCAAA
42450055 AAGGGGTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.26
Consensus pattern (19 bp):
TAATGCAAATGATGAAATG
Found at i:42450541 original size:16 final size:16
Alignment explanation
Indices: 42450516--42450550 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
42450506 TTCTATGATG
*
42450516 AAATGCCATGCAGTCA
1 AAATGCCATGCAGCCA
*
42450532 AAATGTCATGCAGCCA
1 AAATGCCATGCAGCCA
42450548 AAA
1 AAA
42450551 CAAAACACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (16 bp):
AAATGCCATGCAGCCA
Found at i:42452309 original size:11 final size:12
Alignment explanation
Indices: 42452291--42452325 Score: 63
Period size: 11 Copynumber: 3.0 Consensus size: 12
42452281 AATATACACA
42452291 ATAATAATATAT
1 ATAATAATATAT
42452303 A-AATAATATAT
1 ATAATAATATAT
42452314 ATAATAATATAT
1 ATAATAATATAT
42452326 GTAAAAGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATAATATAT
Found at i:42452319 original size:26 final size:25
Alignment explanation
Indices: 42452277--42452330 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
42452267 ACAGAAAACA
42452277 AAATAATATACACAATAATAATATAT
1 AAATAATATACACAATAAT-ATATAT
* * *
42452303 AAATAATATATATAATAATATATGT
1 AAATAATATACACAATAATATATAT
42452328 AAA
1 AAA
42452331 AGTTGAAGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (25 bp):
AAATAATATACACAATAATATATAT
Found at i:42452322 original size:15 final size:14
Alignment explanation
Indices: 42452278--42452322 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 14
42452268 CAGAAAACAA
*
42452278 AATAATATACACAAT
1 AATAATATATA-AAT
42452293 AATAATATATAAAT
1 AATAATATATAAAT
42452307 AAT-ATATAT-AAT
1 AATAATATATAAAT
42452319 AATA
1 AATA
42452323 TATGTAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 6 0.21
13 6 0.21
14 6 0.21
15 10 0.36
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAATATATAAAT
Found at i:42452371 original size:16 final size:16
Alignment explanation
Indices: 42452352--42452389 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
42452342 GTAAAAATAA
42452352 AATAAAGTACTA-AAAT
1 AATAAAGTA-TATAAAT
*
42452368 AATAAAGTATATATAT
1 AATAAAGTATATAAAT
42452384 AATAAA
1 AATAAA
42452390 AAATAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 2 0.10
16 18 0.90
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (16 bp):
AATAAAGTATATAAAT
Found at i:42452605 original size:25 final size:26
Alignment explanation
Indices: 42452577--42452634 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
42452567 AAATGAAATG
42452577 ATAATATATGGAA-AACTTAAAATAA
1 ATAATATATGGAACAACTTAAAATAA
* * *
42452602 ATAAT-TATTGAACAATTTAAAATGA
1 ATAATATATGGAACAACTTAAAATAA
42452627 ATAATATA
1 ATAATATA
42452635 AAGTTCAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 6 0.21
25 20 0.71
26 2 0.07
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (26 bp):
ATAATATATGGAACAACTTAAAATAA
Found at i:42457240 original size:23 final size:24
Alignment explanation
Indices: 42457214--42457263 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
42457204 TGATTTTTAA
*
42457214 ATTTTAA-ATTATTTAGTGATAAT
1 ATTTTAAGATTATTTAGTAATAAT
42457237 A-TTTAAGATTATTTAGTAATAAT
1 ATTTTAAGATTATTTAGTAATAAT
42457260 ATTT
1 ATTT
42457264 CGGGAAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 5 0.21
23 17 0.71
24 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTTAAGATTATTTAGTAATAAT
Found at i:42458066 original size:19 final size:17
Alignment explanation
Indices: 42458028--42458069 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
42458018 GCTTATAAAG
*
42458028 TATTTTATTTTTTCATT
1 TATTTTATTTTTTAATT
42458045 TATTTTATTTTCTTAAATT
1 TATTTTATTTT-TT-AATT
42458064 TATTTT
1 TATTTT
42458070 TGCATTTTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.50
18 2 0.09
19 9 0.41
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (17 bp):
TATTTTATTTTTTAATT
Found at i:42460545 original size:31 final size:32
Alignment explanation
Indices: 42460486--42460550 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
42460476 GGCAAATTAC
42460486 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
42460518 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
42460549 AA
1 AA
42460551 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:42483083 original size:16 final size:16
Alignment explanation
Indices: 42483048--42483081 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
42483038 CAATGGTAAC
42483048 TTTTCTTTCTTCTTCT
1 TTTTCTTTCTTCTTCT
42483064 TTTTCTTT-TTCTT-T
1 TTTTCTTTCTTCTTCT
42483078 TTTT
1 TTTT
42483082 TTATTTCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 5 0.28
16 8 0.44
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTCTTTCTTCTTCT
Found at i:42498906 original size:2 final size:2
Alignment explanation
Indices: 42498894--42498935 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
42498884 CGTGAGAAAG
42498894 AT AT A- AT 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 AT AT AT AT
42498935 A
1 A
42498936 AATGCTAGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42505403 original size:40 final size:39
Alignment explanation
Indices: 42505333--42505419 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 39
42505323 NTTTTTAATT
*
42505333 TAAATTTTT-TAATACTTTTTTAAATTTTTAATTTTAAA
1 TAAATTTTTAAAATACTTTTTTAAATTTTTAATTTTAAA
* *
42505371 -ATATTTTTAAAATACTTTTTTTAATTTGTTTAATTTTAAA
1 TAAATTTTTAAAATAC-TTTTTTAAATT-TTTAATTTTAAA
42505411 TAAATTTTT
1 TAAATTTTT
42505420 TGGGTATTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
37 7 0.17
38 5 0.12
39 10 0.24
40 12 0.29
41 7 0.17
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (39 bp):
TAAATTTTTAAAATACTTTTTTAAATTTTTAATTTTAAA
Found at i:42512722 original size:21 final size:21
Alignment explanation
Indices: 42512696--42512740 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
42512686 TTTAAGGGTA
* *
42512696 TGTCGTGACACCCTCAGTCTG
1 TGTCGTGAAACCCTCAATCTG
42512717 TGTCGTGAAACCCTCAATCTG
1 TGTCGTGAAACCCTCAATCTG
42512738 TGT
1 TGT
42512741 TGCAACATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.29, G:0.22, T:0.31
Consensus pattern (21 bp):
TGTCGTGAAACCCTCAATCTG
Found at i:42518718 original size:22 final size:24
Alignment explanation
Indices: 42518680--42518723 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
42518670 CTGGCCCGAT
*
42518680 TTTTAATAAATACAAAA-AAAATA
1 TTTTAATAAATAAAAAATAAAATA
42518703 TTTTAA-AAATAAAAAATAAAA
1 TTTTAATAAATAAAAAATAAAA
42518724 AAATATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (24 bp):
TTTTAATAAATAAAAAATAAAATA
Found at i:42519931 original size:3 final size:3
Alignment explanation
Indices: 42519914--42519985 Score: 62
Period size: 3 Copynumber: 25.3 Consensus size: 3
42519904 GGTTTTCTTT
* * * *
42519914 TTA TT- TTA ATA TTA TTA TT- GTA TTA TT- GTA TTA TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
42519959 TTA TAA TTA TTA TTT TTA TT- TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
42519986 AACCATGTAT
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
2 6 0.11
3 47 0.89
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:42521709 original size:3 final size:3
Alignment explanation
Indices: 42521701--42521764 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
42521691 GATATCGACG
42521701 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42521749 ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
42521765 ATAAATAAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:42521769 original size:4 final size:4
Alignment explanation
Indices: 42521760--42521790 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
42521750 TAATAATAAT
42521760 AATA AATA AATA AATA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AATA AAT
42521791 TGATTAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:42523573 original size:44 final size:45
Alignment explanation
Indices: 42523525--42523709 Score: 114
Period size: 44 Copynumber: 4.2 Consensus size: 45
42523515 ACTACTGCTT
42523525 AGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGCCAAC-C
1 AGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGCCAACAC
* * * * *
42523569 AGGGAAAT-AGAAT-TACT-AGCTTCAATGTACTCCACTG-TAACCAC
1 AGGGAGATAAG-ATCTA-TAATCTTCAATCTATTCCACTGCCAA-CAC
* * * *** * * * ** **
42523613 AGAGAGGTAAAATCTGCCATCTTCGATCTGTTCCACT-ACTGCTT
1 AGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGCCAACAC
* *
42523657 AGGGAGATAAGATCTGTAATCTTCAATCTATTCCAATGCCAAC-C
1 AGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGCCAACAC
42523701 AGGGAGATA
1 AGGGAGATA
42523710 GAATTACCAA
Statistics
Matches: 99, Mismatches: 33, Indels: 18
0.66 0.22 0.12
Matches are distributed among these distances:
42 2 0.02
43 22 0.22
44 57 0.58
45 18 0.18
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (45 bp):
AGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGCCAACAC
Found at i:42523595 original size:132 final size:132
Alignment explanation
Indices: 42523305--42524160 Score: 1267
Period size: 132 Copynumber: 6.5 Consensus size: 132
42523295 ACTGCAATTT
* * *
42523305 CAGGGAGATATG-ATTAGT-GCTTTCAATATACTCCACTGTAACCTCAGGGAGGTAAAATCCGCC
1 CAGGGAGATA-GAATTACTAGC-TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCC
* * * *
42523368 ATCTCCGATCTGCTCCACTACCGCTTAGGGAG-TAAGATCTGTAATCTTCAATCTATTTCACTGT
64 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGC
***
42523432 TGCC
129 CAAC
* * *
42523436 CAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCTCAAGGAGGTAAAATCTGTCAT
1 CAGGGAGATAGAATTACTAGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCAT
* ** *
42523501 CTTCGTTCTGCTTTACTACTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGCCA
66 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCCA
42523566 AC
131 AC
* * *
42523568 CAGGGAAATAGAATTACTAGCTTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCTGCCAT
1 CAGGGAGATAGAATTACTAGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCAT
* *
42523633 CTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCAATGCCA
66 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCCA
42523698 AC
131 AC
* * * *
42523700 CAGGGAGATAGAATTACCAACTTCAATGTACTCCACTGTAACCTCAGGGAGGTAGAATCCGCCAT
1 CAGGGAGATAGAATTACTAGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCAT
* *
42523765 CTTCGATCTGCTCCACTACTGGTTAGGGAGATAAGATCTGCAATCTTCAATCTATTCCACTGCTG
66 CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGC--
42523830 C-A-
129 CAAC
* * *
42523832 CAGGGA-AGTAGAATTACTGGTTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCA
1 CAGGGAGA-TAGAATTACTAGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCA
*
42523896 TCTTCGATCTGCTGCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCC
65 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCC
*
42523961 AAT
130 AAC
*
42523964 CAGGGAGATAGAATTACTAGCTTCAATGTACTCCACTGTAACCAT-AGAGAGGTAAAATCTGCCA
1 CAGGGAGATAGAATTACTAGCTTCAATGTACTCCACTGTAACC-TCAGGGAGGTAAAATCTGCCA
*
42524028 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAATCTATTCCACTGCC
65 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCC
42524093 AAC
130 AAC
* * *
42524096 CAGGGACATAGAATTACCAGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCAT
1 CAGGGAGATAGAATTACTAGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCAT
42524161 TAACCTGCTC
Statistics
Matches: 656, Mismatches: 58, Indels: 21
0.89 0.08 0.03
Matches are distributed among these distances:
130 2 0.00
131 82 0.12
132 568 0.87
133 3 0.00
134 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (132 bp):
CAGGGAGATAGAATTACTAGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCAT
CTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCCA
AC
Found at i:42523824 original size:44 final size:44
Alignment explanation
Indices: 42523624--42524089 Score: 169
Period size: 44 Copynumber: 10.6 Consensus size: 44
42523614 GAGAGGTAAA
* * ** *
42523624 ATCTGCCATCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAG
1 ATCTGCAATCTTCAATCTACTCCACTACTGCTCAGGGAGATAAG
* * * * **
42523668 ATCTGTAATCTTCAATCTATTCCAATGCCAAC-CAGGGAGAT-AG
1 ATCTGCAATCTTCAATCTACTCCACT-ACTGCTCAGGGAGATAAG
* * *
42523711 AAT-TACCAA-CTTCAATGTACTCCACTGTAAC--CTCAGGGAGGT-AG
1 -ATCT-GCAATCTTCAATCTACTCCAC--T-ACTGCTCAGGGAGATAAG
* * * * * *
42523755 AATCCGCCATCTTCGATCTGCTCCACTACTGGTTAGGGAGATAAG
1 -ATCTGCAATCTTCAATCTACTCCACTACTGCTCAGGGAGATAAG
* * *
42523800 ATCTGCAATCTTCAATCTATTCCACTGCTGCACAGGGA-AGT-AG
1 ATCTGCAATCTTCAATCTACTCCACTACTGCTCAGGGAGA-TAAG
* * * *
42523843 AATTACTG--GT-TTCAATGTACTCCACTGTAAC--CTCAGGGAGGTAAA
1 -A-T-CTGCAATCTTCAATCTACTCCAC--T-ACTGCTCAGGGAGATAAG
* * * * * *
42523888 ATCCGCCATCTTCGATCTGCTGCACTACTGCTTAGGGAGATAAG
1 ATCTGCAATCTTCAATCTACTCCACTACTGCTCAGGGAGATAAG
* * * ***
42523932 ATCTGTAATCTTCAATCTATTCCACTGCCAATCAGGGAGAT-AG
1 ATCTGCAATCTTCAATCTACTCCACTACTGCTCAGGGAGATAAG
* * * * * * *
42523975 AAT-TACTAGCTTCAATGTACTCCACTGTAAC--CAT-AGAGAGGTAAA
1 -ATCTGCAATCTTCAATCTACTCCAC--T-ACTGC-TCAGGGAGATAAG
* * * *
42524020 ATCTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAG
1 ATCTGCAATCTTCAATCTACTCCACTACTGCTCAGGGAGATAAG
*
42524064 ATCTGCAATCTTCAATCTATTCCACT
1 ATCTGCAATCTTCAATCTACTCCACT
42524090 GCCAACCAGG
Statistics
Matches: 300, Mismatches: 87, Indels: 70
0.66 0.19 0.15
Matches are distributed among these distances:
42 8 0.03
43 56 0.19
44 179 0.60
45 52 0.17
46 5 0.02
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (44 bp):
ATCTGCAATCTTCAATCTACTCCACTACTGCTCAGGGAGATAAG
Found at i:42523996 original size:396 final size:395
Alignment explanation
Indices: 42523326--42524160 Score: 1402
Period size: 396 Copynumber: 2.1 Consensus size: 395
42523316 GATTAGTGCT
*
42523326 TTCAATATACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTCCGATCTGCTCCACTACCG
1 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTCCGATCTGCTCCACTACCG
* * * *
42523391 CTTAGGGAGTAAGATCTGTAATCTTCAATCTATTTCACTGTTGCCCAGGGAGATAGAATTACTGG
66 CTTAGGGAGTAAGATCTGCAATCTTCAATCTATTCCACTGCTGCACAGGGAGATAGAATTACTGG
* * * **
42523456 CTTCAATGTACTCCACTGTAACCTCAAGGAGGTAAAATCTGTCATCTTCGTTCTGCTTTACTACT
131 CTTCAATGTACTCCACTGTAACCTCAAGGAGGTAAAATCCGCCATCTTCGATCTGCTGCACTACT
42523521 GCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGCCAACCAGGGAAATAGAATTACT
196 GCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGCCAACCAGGGAAATAGAATTACT
*
42523586 AGCTTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCTGCCATCTTCGATCTGTTCCACTA
261 AGCTTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTA
* *
42523651 CTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCAATGCCAACCAGGGAGATAGAATTA
326 CTGCTTAGGGAGATAAGATCTGCAATCTTCAATCTATTCCAATGCCAACCAGGGACATAGAATTA
42523716 CCAAC
391 CCAAC
* * *
42523721 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAGAATCCGCCATCTTCGATCTGCTCCACTACTG
1 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTCCGATCTGCTCCACTACCG
*
42523786 GTTAGGGAGATAAGATCTGCAATCTTCAATCTATTCCACTGCTGCACAGGGA-AGTAGAATTACT
66 CTTAGGGAG-TAAGATCTGCAATCTTCAATCTATTCCACTGCTGCACAGGGAGA-TAGAATTACT
* *
42523850 GGTTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTGCACTA
129 GGCTTCAATGTACTCCACTGTAACCTCAAGGAGGTAAAATCCGCCATCTTCGATCTGCTGCACTA
* * *
42523915 CTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCCAATCAGGGAGATAGAATTA
194 CTGCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGCCAACCAGGGAAATAGAATTA
*
42523980 CTAGCTTCAATGTACTCCACTGTAACCATAGAGAGGTAAAATCTGCCATCTTCGATCTGCTCCAC
259 CTAGCTTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCTGCCATCTTCGATCTGCTCCAC
*
42524045 TACTGCTTAGGGAGATAAGATCTGCAATCTTCAATCTATTCCACTGCCAACCAGGGACATAGAAT
324 TACTGCTTAGGGAGATAAGATCTGCAATCTTCAATCTATTCCAATGCCAACCAGGGACATAGAAT
*
42524110 TACCAGC
389 TACCAAC
* *
42524117 TTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCAT
1 TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCAT
42524161 TAACCTGCTC
Statistics
Matches: 410, Mismatches: 28, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
395 70 0.17
396 340 0.83
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (395 bp):
TTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTCCGATCTGCTCCACTACCG
CTTAGGGAGTAAGATCTGCAATCTTCAATCTATTCCACTGCTGCACAGGGAGATAGAATTACTGG
CTTCAATGTACTCCACTGTAACCTCAAGGAGGTAAAATCCGCCATCTTCGATCTGCTGCACTACT
GCTTAGGGAGATAAGATCTATAATCTTCAATCTATTCCACTGCCAACCAGGGAAATAGAATTACT
AGCTTCAATGTACTCCACTGTAACCACAGAGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTA
CTGCTTAGGGAGATAAGATCTGCAATCTTCAATCTATTCCAATGCCAACCAGGGACATAGAATTA
CCAAC
Found at i:42524334 original size:87 final size:88
Alignment explanation
Indices: 42524160--42524335 Score: 230
Period size: 87 Copynumber: 2.0 Consensus size: 88
42524150 AAATCTGCCA
* * *
42524160 TTAACCTGCTCCACTGCAACCGAGGGAGGCAAGGTTAGTATCTTCAATCTGCTTCGCTGTCAATG
1 TTAACCTGCTCCACTGCAACCGAGGGAGACAAGGTTAGTATCTTCAATCTGCTTCACTGTCAATA
* *
42524225 TAGGAAGGTAAGATCTACTATCT
66 CAGGAAGGCAAGATCTACTATCT
* * * *
42524248 TTAACCTGCTCCATTGCAACCGAGGGAGACAAGGCTTTGT-T-TTCGATCTGCTTCACTGTCTAT
1 TTAACCTGCTCCACTGCAACCGAGGGAGACAAGG-TTAGTATCTTCAATCTGCTTCACTGTCAAT
* *
42524311 ACAGGAAGGCAAGATTTGCTATCT
65 ACAGGAAGGCAAGATCTACTATCT
42524335 T
1 T
42524336 CACTGATCTG
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
87 39 0.51
88 33 0.43
89 4 0.05
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (88 bp):
TTAACCTGCTCCACTGCAACCGAGGGAGACAAGGTTAGTATCTTCAATCTGCTTCACTGTCAATA
CAGGAAGGCAAGATCTACTATCT
Found at i:42525582 original size:7 final size:7
Alignment explanation
Indices: 42525563--42525616 Score: 69
Period size: 7 Copynumber: 7.9 Consensus size: 7
42525553 TTAGCCTCTC
42525563 CATTTTT
1 CATTTTT
42525570 -ACTTTTT
1 CA-TTTTT
42525577 CATTTTT
1 CATTTTT
42525584 CA-TTTT
1 CATTTTT
42525590 CATTTTT
1 CATTTTT
42525597 CA-TTTT
1 CATTTTT
42525603 CATTTTTT
1 CA-TTTTT
42525611 CATTTT
1 CATTTT
42525617 CCATATTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
6 13 0.31
7 22 0.52
8 7 0.17
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (7 bp):
CATTTTT
Found at i:42525582 original size:13 final size:13
Alignment explanation
Indices: 42525563--42525617 Score: 83
Period size: 13 Copynumber: 4.1 Consensus size: 13
42525553 TTAGCCTCTC
*
42525563 CATTTTTACTTTTT
1 CATTTTT-CATTTT
42525577 CATTTTTCATTTT
1 CATTTTTCATTTT
42525590 CATTTTTCATTTT
1 CATTTTTCATTTT
42525603 CATTTTTTCATTTT
1 CA-TTTTTCATTTT
42525617 C
1 C
42525618 CATATTTTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
13 20 0.51
14 19 0.49
ACGTcount: A:0.15, C:0.16, G:0.00, T:0.69
Consensus pattern (13 bp):
CATTTTTCATTTT
Found at i:42525610 original size:14 final size:14
Alignment explanation
Indices: 42525563--42525627 Score: 80
Period size: 13 Copynumber: 4.6 Consensus size: 14
42525553 TTAGCCTCTC
* *
42525563 CATTTTTACTTTTT
1 CATTTTTTCATTTT
42525577 CA-TTTTTCATTTT
1 CATTTTTTCATTTT
42525590 CA-TTTTTCATTTT
1 CATTTTTTCATTTT
42525603 CATTTTTTCATTTT
1 CATTTTTTCATTTT
42525617 CCATATTTTTC
1 -CAT-TTTTTC
42525628 TGACTCAAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
13 24 0.52
14 13 0.28
15 3 0.07
16 6 0.13
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (14 bp):
CATTTTTTCATTTT
Found at i:42525617 original size:6 final size:6
Alignment explanation
Indices: 42525573--42525608 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
42525563 CATTTTTACT
42525573 TTTTCA TTTTTCA TTTTCA TTTTTCA TTTTCA TTTT
1 TTTTCA -TTTTCA TTTTCA -TTTTCA TTTTCA TTTT
42525609 TTCATTTTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 16 0.57
7 12 0.43
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (6 bp):
TTTTCA
Found at i:42527086 original size:41 final size:43
Alignment explanation
Indices: 42527033--42527125 Score: 163
Period size: 41 Copynumber: 2.2 Consensus size: 43
42527023 GTGATTCGCA
42527033 TTTTTTTTGGTGCTCTTTCTCTTCTCTGTTTCTTTTC-TTTT-
1 TTTTTTTTGGTGCTCTTTCTCTTCTCTGTTTCTTTTCATTTTC
42527074 TTTTTTTTGGTGCTCTTTCTCTTCTCTGTTTCTTTTCATTTTC
1 TTTTTTTTGGTGCTCTTTCTCTTCTCTGTTTCTTTTCATTTTC
42527117 TATTTTTTT
1 T-TTTTTTT
42527126 ATATGTGCGA
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
41 37 0.76
42 4 0.08
43 1 0.02
44 7 0.14
ACGTcount: A:0.02, C:0.18, G:0.09, T:0.71
Consensus pattern (43 bp):
TTTTTTTTGGTGCTCTTTCTCTTCTCTGTTTCTTTTCATTTTC
Found at i:42540544 original size:44 final size:44
Alignment explanation
Indices: 42540363--42540547 Score: 124
Period size: 44 Copynumber: 4.2 Consensus size: 44
42540353 AAGATAACAG
* * ** *
42540363 ATCTTATCTCCCTAAGCAGTAGTAGAGCAGATAGAAGATGGCGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGCAA
* * * * *
42540407 ATCTTACCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAGCCACCAA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGACAGCAA
** * * ** * * * *
42540451 GCCTTGTCTCCCTTAGCAGCGGCGGAGCAGGTTGAAGATAGCAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGCAA
* *
42540495 GTCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGCAA
42540539 ATCTTATCT
1 ATCTTATCT
42540548 TCTCCAGGAG
Statistics
Matches: 99, Mismatches: 36, Indels: 12
0.67 0.24 0.08
Matches are distributed among these distances:
42 4 0.04
43 5 0.05
44 83 0.84
45 6 0.06
46 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACAGCAA
Found at i:42542163 original size:3 final size:3
Alignment explanation
Indices: 42542155--42542200 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
42542145 GATATCGACG
42542155 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
42542201 ATTGATTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:42543595 original size:17 final size:17
Alignment explanation
Indices: 42543575--42543619 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
42543565 ATAATTTACT
42543575 TATATAT-CATACTTTTA
1 TATATATACATA-TTTTA
*
42543592 TATATATACATATTTTG
1 TATATATACATATTTTA
42543609 TA-A-ATACATAT
1 TATATATACATAT
42543620 ACACGTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 8 0.31
16 1 0.04
17 13 0.50
18 4 0.15
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (17 bp):
TATATATACATATTTTA
Found at i:42552623 original size:12 final size:12
Alignment explanation
Indices: 42552608--42552633 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42552598 AAAAAACTTT
42552608 AAAATATTATAA
1 AAAATATTATAA
42552620 AAAATATTATAA
1 AAAATATTATAA
42552632 AA
1 AA
42552634 GTATTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATATTATAA
Found at i:42555351 original size:18 final size:18
Alignment explanation
Indices: 42555328--42555363 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
42555318 TCAAAATAGG
42555328 CTCTCCTTAACATTAGAA
1 CTCTCCTTAACATTAGAA
42555346 CTCTCCTTAACATTAGAA
1 CTCTCCTTAACATTAGAA
42555364 GAGCTTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.33
Consensus pattern (18 bp):
CTCTCCTTAACATTAGAA
Found at i:42558827 original size:16 final size:16
Alignment explanation
Indices: 42558788--42558828 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
42558778 TAGGCCCATC
42558788 ATCCCATGATCTCATG
1 ATCCCATGATCTCATG
** *
42558804 ATTTCATGATCTTATG
1 ATCCCATGATCTCATG
42558820 ATCCCATGA
1 ATCCCATGA
42558829 ATTTTTCCTC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (16 bp):
ATCCCATGATCTCATG
Found at i:42566618 original size:43 final size:43
Alignment explanation
Indices: 42566557--42566646 Score: 180
Period size: 43 Copynumber: 2.1 Consensus size: 43
42566547 TGGTTTGATT
42566557 TTGTAAATACCTTATATTTTCTTACTATACAACCTTGGGAAAC
1 TTGTAAATACCTTATATTTTCTTACTATACAACCTTGGGAAAC
42566600 TTGTAAATACCTTATATTTTCTTACTATACAACCTTGGGAAAC
1 TTGTAAATACCTTATATTTTCTTACTATACAACCTTGGGAAAC
42566643 TTGT
1 TTGT
42566647 TACTTTCGTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (43 bp):
TTGTAAATACCTTATATTTTCTTACTATACAACCTTGGGAAAC
Found at i:42570051 original size:50 final size:50
Alignment explanation
Indices: 42569934--42570180 Score: 282
Period size: 50 Copynumber: 4.8 Consensus size: 50
42569924 GATAATAACA
* ** * *
42569934 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * **
42569983 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * *
42570033 TGCCCATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
42570083 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC--GG
*
42570138 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
42570181 TTACCCAAAT
Statistics
Matches: 168, Mismatches: 22, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
48 1 0.01
49 39 0.23
50 83 0.49
53 2 0.01
55 2 0.01
56 41 0.24
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:42586700 original size:24 final size:25
Alignment explanation
Indices: 42586673--42586728 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
42586663 AAACTTAATT
* *
42586673 CTAATCAAA-GCTAAATTTATTATG
1 CTAATCAAATGCTAAATATATTATA
42586697 CTAAT-AAATGCTAAATATATTATA
1 CTAATCAAATGCTAAATATATTATA
*
42586721 CTCATCAA
1 CTAATCAA
42586729 TACAAAATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 3 0.11
24 22 0.81
25 2 0.07
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (25 bp):
CTAATCAAATGCTAAATATATTATA
Found at i:42594689 original size:45 final size:44
Alignment explanation
Indices: 42594577--42595375 Score: 271
Period size: 44 Copynumber: 18.3 Consensus size: 44
42594567 TCGCAGTAGG
* * **
42594577 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGA-CTG-AGTAAGCA-GG
1 TCTTATCTCCCTCAGGTTGCAGTGGAGCAGATC-GAAG-ACG-ATAA
* * * *
42594621 TCTTATCCCCCTGAGGTTGCAGTGGGGCAGATCGAAGATGATAAA
1 TCTTATCTCCCTCAGGTTGCAGTGGAGCAGATCGAAGACGAT-AA
* * *
42594666 TCTTCTCTCCCTCAGGTTGCAGTGGAGTAGATTGAAGACGATAA
1 TCTTATCTCCCTCAGGTTGCAGTGGAGCAGATCGAAGACGATAA
* * * * **
42594710 TCTTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTA--ATAGA
1 TCTTATCTCCCTCAGGTTGCAGTGGAGCAGATCGAAG-ACGATA-A
* * * * ** * **
42594754 TCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCAG-C-A-GG
1 TCTTATCTCCCTCAGGTTGCAGTGGAGCAGATCGAAGACGATAA
* * **
42594795 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGA-CTG-AGTAAGCA-GG
1 TCTTATCTCCCTCAGGTTGCAGTGGAGCAGATC-GAAG-ACG-ATAA
* * * * * * * *
42594839 TCTTATCCCCCTGAGGTTTCATTGGGGCATATCAAAGATGATAAA
1 TCTTATCTCCCTCAGGTTGCAGTGGAGCAGATCGAAGACGAT-AA
* *
42594884 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGACGATAA
1 TCTTATCTCCCTCAGGTTGCAGTGGAGCAGATCGAAGACGATAA
* * * * ** **
42594928 TCCTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAGTA--ATAGA
1 TCTTATCTCCCTCAGGTTGCAGTGGAGCAGATCGAAG-ACGATA-A
* * * * ** * **
42594972 TCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCAG-C-A-GG
1 TCTTATCTCCCTCAGGTTGCAGTGGAGCAGATCGAAGACGATAA
* * * **
42595013 TCTTATCTCCCTAAGGTTACAGTGGAGCAGA-CTG-AGTAAGCA-GG
1 TCTTATCTCCCTCAGGTTGCAGTGGAGCAGATC-GAAG-ACG-ATAA
* * * *
42595057 TCTTATC-CCATTGAGGTTTCAGTAGG-GCAGATCGAAGATGATAAA
1 TCTTATCTCC-CTCAGGTTGCAGT-GGAGCAGATCGAAGACGAT-AA
*
42595102 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGATCGAAGACGATAA
1 TCTTATCTCCCTCAGGTTGCAGTGGAGCAGATCGAAGACGATAA
* * * * **
42595146 TCCTATCTCCCTGAAGTTGTAGTGGAGC-GAATTAAAGTA--ATAGA
1 TCTTATCTCCCTCAGGTTGCAGTGGAGCAG-ATCGAAG-ACGATA-A
* * * * * ** *
42595190 TCTTATCTCTCTGAAGTTACAGTAGAGTGGATC-ACAG-CAGGT--
1 TCTTATCTCCCTCAGGTTGCAGTGGAGCAGATCGA-AGAC-GATAA
* * **
42595232 T-TTATCTCCCTGAGGTTGCAGTGGAGCAGA-CTG-AGTAAGCA-GG
1 TCTTATCTCCCTCAGGTTGCAGTGGAGCAGATC-GAAG-ACG-ATAA
* * * *
42595275 TCTTA-CCCTCCTAAGGTTGCAGTGGGGCAGATCGAAGATGATAAA
1 TCTTATCTC-CCTCAGGTTGCAGTGGAGCAGATCGAAGACGAT-AA
* *
42595320 TCTTATCTCCCTGAGGTTGCAGTAGAGCAGAAT-GAAGACGATAA
1 TCTTATCTCCCTCAGGTTGCAGTGGAGCAG-ATCGAAGACGATAA
*
42595364 TCCTATCTCCCT
1 TCTTATCTCCCT
42595376 GAATTTGTAG
Statistics
Matches: 584, Mismatches: 116, Indels: 110
0.72 0.14 0.14
Matches are distributed among these distances:
40 9 0.02
41 76 0.13
42 1 0.00
43 22 0.04
44 318 0.54
45 152 0.26
46 6 0.01
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (44 bp):
TCTTATCTCCCTCAGGTTGCAGTGGAGCAGATCGAAGACGATAA
Found at i:42594823 original size:218 final size:218
Alignment explanation
Indices: 42594445--42595578 Score: 1866
Period size: 218 Copynumber: 5.2 Consensus size: 218
42594435 ATCGAAATCA
*
42594445 AAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATCGAAGACGATAATCCTATCTCCCTGAAGTT
1 AAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGACGATAATCCTATCTCCCTGAAGTT
* * * *
42594510 GTAGTGGAGTGGATTAAAGTAACAGATCTTATATCTCTGAAGTTGCAATAGAGTGGATCGCAGTA
66 GTAGTGGAGTGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCAGCA
42594575 GGTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTGAGGTTG
131 GGTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTGAGGTTG
42594640 CAGTGGGGCAGATCGAAGATGAT
196 CAGTGGGGCAGATCGAAGATGAT
* * * *
42594663 AAATCTTCTCTCCCTCAGGTTGCAGTGGAGTAGATTGAAGACGATAATCTTATCTCCCTGAAGTT
1 AAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGACGATAATCCTATCTCCCTGAAGTT
*
42594728 GTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCAGCA
66 GTAGTGGAGTGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCAGCA
*
42594793 GGTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTGAGGTTT
131 GGTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTGAGGTTG
* * *
42594858 CATTGGGGCATATCAAAGATGAT
196 CAGTGGGGCAGATCGAAGATGAT
42594881 AAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGACGATAATCCTATCTCCCTGAAGTT
1 AAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGACGATAATCCTATCTCCCTGAAGTT
42594946 GTAGTGGAGTGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCAGCA
66 GTAGTGGAGTGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCAGCA
* * ** *
42595011 GGTCTTATCTCCCTAAGGTTACAGTGGAGCAGACTGAGTAAGCAGGTCTTATCCCATTGAGGTTT
131 GGTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTGAGGTTG
*
42595076 CAGTAGGGCAGATCGAAGATGAT
196 CAGTGGGGCAGATCGAAGATGAT
*
42595099 AAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATCGAAGACGATAATCCTATCTCCCTGAAGTT
1 AAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGACGATAATCCTATCTCCCTGAAGTT
* * * *
42595164 GTAGTGGAGCGAATTAAAGTAATAGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCACAGCA
66 GTAGTGGAGTGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCAGCA
* *
42595229 GGTTTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGTAAGCAGGTCTTA-CCCTCCTAAGGTT
131 GGTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGTAAGCAGGTCTTATCCC-CCTGAGGTT
42595293 GCAGTGGGGCAGATCGAAGATGAT
195 GCAGTGGGGCAGATCGAAGATGAT
* * *
42595317 AAATCTTATCTCCCTGAGGTTGCAGTAGAGCAGAATGAAGACGATAATCCTATCTCCCTGAATTT
1 AAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGACGATAATCCTATCTCCCTGAAGTT
* * * *
42595382 GTAGTAGAGTAGATTAAAGTAATAGATCTTATCTCTTTGAAGTTACAGTAGAGTGGATCGCAGCA
66 GTAGTGGAGTGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCAGCA
* * *
42595447 GGTCTTATCTCCCTGAGGTTGCAGGGGAGCAGACTGAGTAAGCAAGTCTTATCCCCTTGAGGTTG
131 GGTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTGAGGTTG
*
42595512 CAGTGGGGCAAATCGAAGATGAT
196 CAGTGGGGCAGATCGAAGATGAT
*
42595535 -AA----ATCTCCCTGAGGTTGCAGTGAAGCAGATTGAAGACGATAATC
1 AAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGACGATAATC
42595579 TTATAGAGTG
Statistics
Matches: 855, Mismatches: 59, Indels: 9
0.93 0.06 0.01
Matches are distributed among these distances:
213 39 0.05
217 5 0.01
218 808 0.95
219 3 0.00
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.28
Consensus pattern (218 bp):
AAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGACGATAATCCTATCTCCCTGAAGTT
GTAGTGGAGTGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCAGCA
GGTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGTAAGCAGGTCTTATCCCCCTGAGGTTG
CAGTGGGGCAGATCGAAGATGAT
Found at i:42595740 original size:44 final size:44
Alignment explanation
Indices: 42595601--42595799 Score: 131
Period size: 44 Copynumber: 4.5 Consensus size: 44
42595591 TCGCATCAGT
* **
42595601 TCTTATCTCCCTGAGGTTGCAGTGGAACAGACTGAGGAAG-CA-GG
1 TCTTATCTCCCTGAGGTTGCAGTGGAACAGACT-A-GAAGTGATAA
* * *** *
42595645 TCTTATCCCCCTGAGATTGCAG-GGGGGAGA-TCGAAGATGATAAA
1 TCTTATCTCCCTGAGGTTGCAGTGGAACAGACTAGAAG-TGAT-AA
*
42595689 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGA-TAGAAGTCGATAA
1 TCTTATCTCCCTGAGGTTGCAGTGGAACAGACTAGAAGT-GATAA
* * * * * * *
42595733 TCCTATCTTCTTGAAGTTGTAGTGGAACAGATTA-AAGTAATAGA
1 TCTTATCTCCCTGAGGTTGCAGTGGAACAGACTAGAAGTGATA-A
* *
42595777 TCTTATCTCTCTGAAGTTGCAGT
1 TCTTATCTCCCTGAGGTTGCAGT
42595800 AGAGTGGATC
Statistics
Matches: 121, Mismatches: 26, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
40 4 0.03
42 2 0.02
43 8 0.07
44 91 0.75
45 16 0.13
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.29
Consensus pattern (44 bp):
TCTTATCTCCCTGAGGTTGCAGTGGAACAGACTAGAAGTGATAA
Found at i:42620329 original size:37 final size:37
Alignment explanation
Indices: 42620288--42620358 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
42620278 CCATCCCTAT
42620288 ACACCATATAGGGTATTAAATACACATCCAACCCTGC
1 ACACCATATAGGGTATTAAATACACATCCAACCCTGC
* *
42620325 ACACCATATAGGGTATTAAATACCCATCTAACCC
1 ACACCATATAGGGTATTAAATACACATCCAACCC
42620359 CACACACCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.30, G:0.10, T:0.23
Consensus pattern (37 bp):
ACACCATATAGGGTATTAAATACACATCCAACCCTGC
Found at i:42620365 original size:37 final size:37
Alignment explanation
Indices: 42620288--42620366 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
42620278 CCATCCCTAT
**
42620288 ACACCATATAGGGTATTAAATACACATCCAACCCTGC
1 ACACCATATAGGGTATTAAATACACATCCAACCCCAC
* *
42620325 ACACCATATAGGGTATTAAATACCCATCTAACCCCAC
1 ACACCATATAGGGTATTAAATACACATCCAACCCCAC
42620362 ACACC
1 ACACC
42620367 TCTTAGTGTC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.38, C:0.33, G:0.09, T:0.20
Consensus pattern (37 bp):
ACACCATATAGGGTATTAAATACACATCCAACCCCAC
Found at i:42620655 original size:21 final size:21
Alignment explanation
Indices: 42620612--42620655 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
42620602 CGAATAGCAA
**
42620612 ATCATACATAACATATTTTAG
1 ATCATACATAACATATTACAG
*
42620633 ATCATACATAACGTATTACAG
1 ATCATACATAACATATTACAG
42620654 AT
1 AT
42620656 TATGCTTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (21 bp):
ATCATACATAACATATTACAG
Found at i:42627493 original size:92 final size:93
Alignment explanation
Indices: 42627370--42627541 Score: 233
Period size: 92 Copynumber: 1.9 Consensus size: 93
42627360 CATTTTTTTT
* * * **
42627370 ATTTTCCAAAGCATTGAACCTTAAATCGGTATCGATACCA-G-ACAGGGTATTGATAAATTTTG-
1 ATTTTCCAAAACATTGAAACTCAAATCGGTATCGATACCAGGTA-AGGGTATCAATAAATTTTGC
*
42627432 AAAGGTATCGATACTTTTTATTTTTGTTCA
65 AAA-GTATCAATACTTTTTATTTTTGTTCA
* *
42627462 ATTTTCCAAAACATTGAAACTCAAATTGGTATCGATACCAGGTAAGGGTATCAATAATTTTTGCA
1 ATTTTCCAAAACATTGAAACTCAAATCGGTATCGATACCAGGTAAGGGTATCAATAAATTTTGCA
42627527 AAGTATCAATACTTT
66 AAGTATCAATACTTT
42627542 GTTAAGGGTA
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
92 36 0.52
93 29 0.42
94 4 0.06
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (93 bp):
ATTTTCCAAAACATTGAAACTCAAATCGGTATCGATACCAGGTAAGGGTATCAATAAATTTTGCA
AAGTATCAATACTTTTTATTTTTGTTCA
Found at i:42630830 original size:29 final size:29
Alignment explanation
Indices: 42630763--42630824 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
42630753 CAAGTAATCT
*
42630763 CACAAACGATAGGTTGCGATTTGCTAACA
1 CACAAATGATAGGTTGCGATTTGCTAACA
*
42630792 CACAAATGATAGGTTGCGATTTGCTAACT
1 CACAAATGATAGGTTGCGATTTGCTAACA
42630821 CACA
1 CACA
42630825 TGTGATTATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (29 bp):
CACAAATGATAGGTTGCGATTTGCTAACA
Found at i:42632240 original size:13 final size:13
Alignment explanation
Indices: 42632218--42632251 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
42632208 TCTAAAATAG
42632218 TAAC-AAATTTAA
1 TAACAAAATTTAA
42632230 TAACAAAATTTAA
1 TAACAAAATTTAA
*
42632243 TAATAAAAT
1 TAACAAAAT
42632252 AATAGTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (13 bp):
TAACAAAATTTAA
Found at i:42632974 original size:5 final size:5
Alignment explanation
Indices: 42632930--42632955 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
42632920 CTTGTTTTAA
42632930 TTATT TTATT TTATT TTATT TTATT T
1 TTATT TTATT TTATT TTATT TTATT T
42632956 AAAATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:42632986 original size:5 final size:5
Alignment explanation
Indices: 42632978--42633005 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
42632968 ATTTTATCCT
42632978 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
42633006 TGCCAAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:42640184 original size:34 final size:35
Alignment explanation
Indices: 42640101--42640174 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 35
42640091 CTAGTCTGAT
* *
42640101 ATGACATTCTGATATGATATATGTGCTTCTGAAAAC
1 ATGACATTCTGATCTGATATATGT-CTTATGAAAAC
*
42640137 ATGACATTCTGATCTGATATATGT-TTATGAAAAT
1 ATGACATTCTGATCTGATATATGTCTTATGAAAAC
42640171 ATGA
1 ATGA
42640175 TACTTTGATC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
34 12 0.34
36 23 0.66
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (35 bp):
ATGACATTCTGATCTGATATATGTCTTATGAAAAC
Found at i:42644603 original size:23 final size:21
Alignment explanation
Indices: 42644576--42644630 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
42644566 CTAATTATTA
42644576 TTTTAGTTAGTATGATTGTTAGT
1 TTTTAGTTA-TATGATTGTTA-T
* *
42644599 TTTTACATTATATTATTGTTAT
1 TTTTA-GTTATATGATTGTTAT
*
42644621 TGTTAGTTAT
1 TTTTAGTTAT
42644631 TATTTTTAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 4 0.15
22 5 0.19
23 15 0.56
24 3 0.11
ACGTcount: A:0.24, C:0.02, G:0.15, T:0.60
Consensus pattern (21 bp):
TTTTAGTTATATGATTGTTAT
Found at i:42644695 original size:82 final size:82
Alignment explanation
Indices: 42644487--42644724 Score: 261
Period size: 82 Copynumber: 2.9 Consensus size: 82
42644477 GTTTAGTTAT
* * * * *
42644487 TAATAATTATTGTTACTTAGTATTATTGTTAGTAAAAAACTA-A-TATTATTATTGTTAGTTCTT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGTATAAAACTATATTATTGTTATTGTTAGTTATT
*
42644550 AGGATTAGTAAAAACCC
66 ATGATTAGTAAAAACCC
* * * * *
42644567 TAATTATTATT-TTAGTTAGTATGATTGTTAGTTTTTACATTATATTATTGTTATTGTTAGTTAT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAG-TATAAAACTATATTATTGTTATTGTTAGTTAT
**
42644631 TATTTTTAGT-AAAACCC
65 TATGATTAGTAAAAACCC
* *
42644648 TAATTATTCTTGTTAGTTAGTATTATT-TTGAGTATAAAACTATTATTATTGCTATTGTGTTAGT
1 TAATTATTATTGTTAGTTAGTATTATTGTT-AGTATAAAACTA-TATTATTGTTA-T-TGTTAGT
42644712 TATTATGATTAGT
62 TATTATGATTAGT
42644725 GGTTAAACGT
Statistics
Matches: 128, Mismatches: 22, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
79 18 0.14
80 15 0.12
81 26 0.20
82 50 0.39
83 1 0.01
84 18 0.14
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (82 bp):
TAATTATTATTGTTAGTTAGTATTATTGTTAGTATAAAACTATATTATTGTTATTGTTAGTTATT
ATGATTAGTAAAAACCC
Found at i:42648154 original size:18 final size:18
Alignment explanation
Indices: 42648131--42648170 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
42648121 GAATATGACT
42648131 GCTCGGGATCTGGCTCGG
1 GCTCGGGATCTGGCTCGG
* *
42648149 GCTCGGGCTTTGGCTCGG
1 GCTCGGGATCTGGCTCGG
42648167 GCTC
1 GCTC
42648171 TGGTTTGGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.03, C:0.30, G:0.42, T:0.25
Consensus pattern (18 bp):
GCTCGGGATCTGGCTCGG
Found at i:42650338 original size:4 final size:4
Alignment explanation
Indices: 42650329--42650390 Score: 52
Period size: 4 Copynumber: 13.5 Consensus size: 4
42650319 CTCTTTTCTT
42650329 TTTC TTTC TTCTCC TTTC TATTTC TTTC TTTC TTCTCC TTTCC TTTTC TTTC
1 TTTC TTTC TT-T-C TTTC --TTTC TTTC TTTC TT-T-C TTT-C -TTTC TTTC
42650381 TTTC TTTC TT
1 TTTC TTTC TT
42650391 CTCCTTTCCA
Statistics
Matches: 51, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
4 31 0.61
5 7 0.14
6 13 0.25
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:42650339 original size:20 final size:20
Alignment explanation
Indices: 42650314--42650387 Score: 78
Period size: 20 Copynumber: 3.5 Consensus size: 20
42650304 TTCCCTCTTC
42650314 TTCTTCTCTTTTCTTTTTCT
1 TTCTTCTCTTTTCTTTTTCT
*
42650334 TTCTTCTCCTTTCTATTTCTTTCT
1 TTCTTCT-CTTT-T-CTT-TTTCT
* *
42650358 TTCTTCTCCTTTCCTTTTCT
1 TTCTTCTCTTTTCTTTTTCT
42650378 TTCTT-TCTTT
1 TTCTTCTCTTT
42650388 CTTCTCCTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
19 4 0.09
20 17 0.38
21 5 0.11
22 2 0.04
23 5 0.11
24 12 0.27
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.70
Consensus pattern (20 bp):
TTCTTCTCTTTTCTTTTTCT
Found at i:42650361 original size:24 final size:24
Alignment explanation
Indices: 42650329--42650386 Score: 100
Period size: 24 Copynumber: 2.4 Consensus size: 24
42650319 CTCTTTTCTT
42650329 TTTCTTTCTTCTCCTTT-CTATTTC
1 TTTCTTTCTTCTCCTTTCCT-TTTC
42650353 TTTCTTTCTTCTCCTTTCCTTTTC
1 TTTCTTTCTTCTCCTTTCCTTTTC
42650377 TTTCTTTCTT
1 TTTCTTTCTT
42650387 TCTTCTCCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 31 0.94
25 2 0.06
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTCTTTCTTCTCCTTTCCTTTTC
Found at i:42650380 original size:28 final size:28
Alignment explanation
Indices: 42650321--42650399 Score: 107
Period size: 28 Copynumber: 3.0 Consensus size: 28
42650311 TTCTTCTTCT
42650321 CTTTTC-TT-TTTCTTTCTTCTCCTTT-
1 CTTTTCTTTCTTTCTTTCTTCTCCTTTC
*
42650346 C---TATTTCTTTCTTTCTTCTCCTTTC
1 CTTTTCTTTCTTTCTTTCTTCTCCTTTC
42650371 CTTTTCTTTCTTTCTTTCTTCTCCTTTC
1 CTTTTCTTTCTTTCTTTCTTCTCCTTTC
42650399 C
1 C
42650400 ATCTCCTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
22 1 0.02
23 2 0.04
24 17 0.37
25 2 0.04
28 24 0.52
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (28 bp):
CTTTTCTTTCTTTCTTTCTTCTCCTTTC
Found at i:42650512 original size:27 final size:26
Alignment explanation
Indices: 42650454--42650512 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
42650444 ATAAGGGGAG
* * * *
42650454 TGGTGCCGCCTGTGGCAGTGGCATCA
1 TGGTGCCGCCTCTGCCACTGGCACCA
42650480 TCGGTGCCGCCTCTGCCACTGGCACCA
1 T-GGTGCCGCCTCTGCCACTGGCACCA
42650507 CTGGTG
1 -TGGTG
42650513 TCACCTGTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 1 0.04
27 25 0.93
28 1 0.04
ACGTcount: A:0.10, C:0.34, G:0.34, T:0.22
Consensus pattern (26 bp):
TGGTGCCGCCTCTGCCACTGGCACCA
Found at i:42650898 original size:9 final size:10
Alignment explanation
Indices: 42650866--42650900 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
42650856 TTATTAAATT
*
42650866 ATTTTTTATA
1 ATTTTTAATA
42650876 ATTTTTAATA
1 ATTTTTAATA
42650886 ATTTTTAAT-
1 ATTTTTAATA
42650895 ATTTTT
1 ATTTTT
42650901 TTACATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 6 0.25
10 18 0.75
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:42650901 original size:10 final size:10
Alignment explanation
Indices: 42650865--42650915 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
42650855 TTTATTAAAT
42650865 TATTTTTT-A
1 TATTTTTTAA
*
42650874 TAATTTTTAA
1 TATTTTTTAA
*
42650884 TAATTTTTAA
1 TATTTTTTAA
42650894 TATTTTTTTACA
1 TA-TTTTTTA-A
42650906 TATTTATTTA
1 TATTT-TTTA
42650916 TTTATTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
9 7 0.19
10 13 0.36
11 9 0.25
12 7 0.19
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (10 bp):
TATTTTTTAA
Found at i:42652642 original size:20 final size:19
Alignment explanation
Indices: 42652617--42652664 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
42652607 TTAATTAAAA
*
42652617 TTAATTAATAATGTTTTATC
1 TTAATTAATAATATTTTA-C
**
42652637 TTAATTAATCTTATTTTAC
1 TTAATTAATAATATTTTAC
42652656 TTAATTAAT
1 TTAATTAAT
42652665 CAACATGATC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.56
Consensus pattern (19 bp):
TTAATTAATAATATTTTAC
Found at i:42655980 original size:10 final size:10
Alignment explanation
Indices: 42655947--42655981 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
42655937 AATTTAATTC
42655947 TTTTCTTTTA
1 TTTTCTTTTA
*
42655957 TGTTCTTTTAA
1 TTTTCTTTT-A
42655968 TTTTCTTTTA
1 TTTTCTTTTA
42655978 TTTT
1 TTTT
42655982 TCATTCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.11, C:0.09, G:0.03, T:0.77
Consensus pattern (10 bp):
TTTTCTTTTA
Found at i:42658765 original size:31 final size:29
Alignment explanation
Indices: 42658701--42658769 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
42658691 ACGATAACGT
** *
42658701 AAGTGACTAAAATGTAACATTTTAAACAT
1 AAGTGACTAAAATGTAACATGGTAAACAA
*
42658730 AAGTGACTAAAATGTAACCTGAGGTAAACAA
1 AAGTGACTAAAATGTAACAT--GGTAAACAA
42658761 AAGTGACTA
1 AAGTGACTA
42658770 TTTTAATAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.56
31 15 0.44
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.25
Consensus pattern (29 bp):
AAGTGACTAAAATGTAACATGGTAAACAA
Found at i:42663537 original size:14 final size:14
Alignment explanation
Indices: 42663518--42663546 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
42663508 AAAGAATTGG
42663518 AGCTAAAAGGATGC
1 AGCTAAAAGGATGC
42663532 AGCTAAAAGGATGC
1 AGCTAAAAGGATGC
42663546 A
1 A
42663547 TACATCCTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.28, T:0.14
Consensus pattern (14 bp):
AGCTAAAAGGATGC
Found at i:42664002 original size:2 final size:2
Alignment explanation
Indices: 42663995--42664027 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
42663985 TTATATTAAA
*
42663995 AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
42664028 AAGTACTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:42666858 original size:20 final size:20
Alignment explanation
Indices: 42666826--42666868 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
42666816 GGGGAAGTGG
*
42666826 GAGGAAGTAAAAA-TTTTGA
1 GAGGAAGTAAAAAGGTTTGA
*
42666845 GAGGAAAGTGAAAAGGTTTGA
1 GAGG-AAGTAAAAAGGTTTGA
42666866 GAG
1 GAG
42666869 TTTGGGGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 8 0.40
21 8 0.40
ACGTcount: A:0.44, C:0.00, G:0.35, T:0.21
Consensus pattern (20 bp):
GAGGAAGTAAAAAGGTTTGA
Found at i:42679610 original size:34 final size:34
Alignment explanation
Indices: 42679568--42679641 Score: 141
Period size: 34 Copynumber: 2.2 Consensus size: 34
42679558 TAATCTATGA
42679568 AACT-TAATGTTTTTTAAAAAATAATAACATAAT
1 AACTCTAATGTTTTTTAAAAAATAATAACATAAT
42679601 AACTCTAATGTTTTTTAAAAAATAATAACATAAT
1 AACTCTAATGTTTTTTAAAAAATAATAACATAAT
42679635 AACTCTA
1 AACTCTA
42679642 GGGTTTTTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 4 0.10
34 36 0.90
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (34 bp):
AACTCTAATGTTTTTTAAAAAATAATAACATAAT
Found at i:42687498 original size:17 final size:17
Alignment explanation
Indices: 42687466--42687510 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
42687456 TTAATTAATT
* *
42687466 TTTTAAAATTTTAAAAA
1 TTTTAAAAATTCAAAAA
42687483 TTTTAAAAATTCAAAAA
1 TTTTAAAAATTCAAAAA
* *
42687500 ATATAAAAATT
1 TTTTAAAAATT
42687511 ATTTTTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
TTTTAAAAATTCAAAAA
Found at i:42687581 original size:34 final size:34
Alignment explanation
Indices: 42687516--42687581 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
42687506 AAATTATTTT
42687516 TAAAAATTAAAAATCATTAGAATTATTAAAATGTA
1 TAAAAATTAAAAA-CATTAGAATTATTAAAATGTA
*
42687551 TAAAAATATAAAAA-ATTA-ATATTTTTAAAAT
1 TAAAAAT-TAAAAACATTAGA-ATTATTAAAAT
42687582 TAATTAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
33 1 0.04
34 14 0.50
35 7 0.25
36 6 0.21
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (34 bp):
TAAAAATTAAAAACATTAGAATTATTAAAATGTA
Found at i:42695127 original size:3 final size:3
Alignment explanation
Indices: 42695119--42695164 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
42695109 TGGGCTAAGG
42695119 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
42695165 GGTGAGTTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:42695927 original size:17 final size:17
Alignment explanation
Indices: 42695900--42695932 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
42695890 TGTATTTTTA
42695900 TGAATTGTG-AATAAAG
1 TGAATTGTGAAATAAAG
42695916 TGAATATGTGAAATAAA
1 TGAAT-TGTGAAATAAA
42695933 AATGTAGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 4 0.27
18 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.30
Consensus pattern (17 bp):
TGAATTGTGAAATAAAG
Found at i:42696782 original size:22 final size:24
Alignment explanation
Indices: 42696742--42696785 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
42696732 TGATAAAATA
42696742 TTTTGATATAACAAATTAAAGTGT
1 TTTTGATATAACAAATTAAAGTGT
*
42696766 TTTTGA-AT-ACAAGTTAAAGT
1 TTTTGATATAACAAATTAAAGT
42696786 TTAACAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 2 0.11
24 6 0.32
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAGTGT
Found at i:42698307 original size:2 final size:2
Alignment explanation
Indices: 42698300--42698331 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
42698290 AAACTAAATA
42698300 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
42698332 TTAAATGTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42702009 original size:9 final size:9
Alignment explanation
Indices: 42701990--42702027 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
42701980 CGAGTGAACA
42701990 AAAACTTGAG
1 AAAA-TTGAG
42702000 AAAATTGAG
1 AAAATTGAG
42702009 AAAATTGAG
1 AAAATTGAG
*
42702018 AGAATTGAG
1 AAAATTGAG
42702027 A
1 A
42702028 GAGTTAGGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
9 23 0.85
10 4 0.15
ACGTcount: A:0.53, C:0.03, G:0.24, T:0.21
Consensus pattern (9 bp):
AAAATTGAG
Found at i:42702028 original size:9 final size:9
Alignment explanation
Indices: 42701995--42702056 Score: 56
Period size: 9 Copynumber: 6.9 Consensus size: 9
42701985 GAACAAAAAC
*
42701995 TTGAGAAAA
1 TTGAGAGAA
*
42702004 TTGAGAAAA
1 TTGAGAGAA
42702013 TTGAGAGAA
1 TTGAGAGAA
*
42702022 TTGAGAGAG
1 TTGAGAGAA
42702031 TT-AG-GAGA
1 TTGAGAGA-A
*
42702039 TTAGAAAGAA
1 TT-GAGAGAA
42702049 TTGAGAGA
1 TTGAGAGA
42702057 CTATGATGTG
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
7 2 0.05
8 4 0.09
9 32 0.73
10 4 0.09
11 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.23
Consensus pattern (9 bp):
TTGAGAGAA
Found at i:42702306 original size:5 final size:5
Alignment explanation
Indices: 42702296--42702321 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
42702286 ATAAATATGA
42702296 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
42702322 TTTTTTTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:42704425 original size:24 final size:24
Alignment explanation
Indices: 42704398--42704446 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
42704388 CTCAATTATA
42704398 CCGTGCTTGCATTAATCTTAAGTT
1 CCGTGCTTGCATTAATCTTAAGTT
42704422 CCGTGCTTGCATTAATCTTAAGTT
1 CCGTGCTTGCATTAATCTTAAGTT
42704446 C
1 C
42704447 ATAATCAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.41
Consensus pattern (24 bp):
CCGTGCTTGCATTAATCTTAAGTT
Found at i:42706366 original size:7 final size:7
Alignment explanation
Indices: 42706356--42706395 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
42706346 TTAGTTTTTG
42706356 GATTTCA
1 GATTTCA
42706363 GATTTCA
1 GATTTCA
42706370 GATTTCA
1 GATTTCA
42706377 GATTTCA
1 GATTTCA
* *
42706384 TATTTTA
1 GATTTCA
42706391 GATTT
1 GATTT
42706396 TGAATTATGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (7 bp):
GATTTCA
Found at i:42706396 original size:7 final size:7
Alignment explanation
Indices: 42706323--42706396 Score: 58
Period size: 7 Copynumber: 10.6 Consensus size: 7
42706313 CTCTTTCGAG
*
42706323 TTTTAAA
1 TTTTAGA
*
42706330 TTTTAGG
1 TTTTAGA
*
42706337 TTTTAGT
1 TTTTAGA
*
42706344 TTTTAGT
1 TTTTAGA
*
42706351 TTTTGGA
1 TTTTAGA
*
42706358 TTTCAGA
1 TTTTAGA
*
42706365 TTTCAGA
1 TTTTAGA
*
42706372 TTTCAGA
1 TTTTAGA
* *
42706379 TTTCATA
1 TTTTAGA
42706386 TTTTAGA
1 TTTTAGA
42706393 TTTT
1 TTTT
42706397 GAATTATGGT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 57 1.00
ACGTcount: A:0.23, C:0.05, G:0.14, T:0.58
Consensus pattern (7 bp):
TTTTAGA
Found at i:42706428 original size:22 final size:22
Alignment explanation
Indices: 42706400--42706446 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
42706390 AGATTTTGAA
42706400 TTATGGTTTTGATTTTCGAATT
1 TTATGGTTTTGATTTTCGAATT
42706422 TTATGGTTTTGATTTTCGAATT
1 TTATGGTTTTGATTTTCGAATT
42706444 TTA
1 TTA
42706447 AGTTTTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.19, C:0.04, G:0.17, T:0.60
Consensus pattern (22 bp):
TTATGGTTTTGATTTTCGAATT
Found at i:42707775 original size:19 final size:18
Alignment explanation
Indices: 42707739--42707778 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
42707729 CTCAAATGCC
*
42707739 ATACAAATATATTATAAT
1 ATACAAATATAGTATAAT
42707757 ATACAAATAATAGTATAAT
1 ATACAAAT-ATAGTATAAT
42707776 ATA
1 ATA
42707779 ATATAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (18 bp):
ATACAAATATAGTATAAT
Found at i:42709191 original size:37 final size:37
Alignment explanation
Indices: 42709123--42709204 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 37
42709113 GAAAATTTTG
*
42709123 TGAGTGAACAAAAGCAATGTGAAGGTTAAAAGCATAA
1 TGAGTGAACAAAAGCAATGTGAAGGTCAAAAGCATAA
* **
42709160 TGAGTGAATAAAAGC-AT-TGAATGTGTCAAAAGCATTG
1 TGAGTGAACAAAAGCAATGTGAA-G-GTCAAAAGCATAA
42709197 TGAGTGAA
1 TGAGTGAA
42709205 AAGAGTGATA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 4 0.10
36 3 0.08
37 32 0.82
ACGTcount: A:0.44, C:0.07, G:0.26, T:0.23
Consensus pattern (37 bp):
TGAGTGAACAAAAGCAATGTGAAGGTCAAAAGCATAA
Found at i:42719244 original size:19 final size:17
Alignment explanation
Indices: 42719207--42719241 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
42719197 ATCGTTGCTC
42719207 ATCTGATTGGGAAAAAA
1 ATCTGATTGGGAAAAAA
42719224 ATCTGATTGGGAAAAAA
1 ATCTGATTGGGAAAAAA
42719241 A
1 A
42719242 AATATGCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.06, G:0.23, T:0.23
Consensus pattern (17 bp):
ATCTGATTGGGAAAAAA
Found at i:42719260 original size:8 final size:8
Alignment explanation
Indices: 42719244--42719275 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
42719234 GAAAAAAAAA
42719244 TATGCATG
1 TATGCATG
*
42719252 TATGTATG
1 TATGCATG
42719260 TATGCATG
1 TATGCATG
42719268 TATGCATG
1 TATGCATG
42719276 CATATATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (8 bp):
TATGCATG
Found at i:42719276 original size:12 final size:12
Alignment explanation
Indices: 42719244--42719278 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
42719234 GAAAAAAAAA
*
42719244 TATGCATGTATG
1 TATGCATGCATG
*
42719256 TATGTATGCATG
1 TATGCATGCATG
42719268 TATGCATGCAT
1 TATGCATGCAT
42719279 ATATTAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (12 bp):
TATGCATGCATG
Found at i:42720551 original size:7 final size:7
Alignment explanation
Indices: 42720539--42720568 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
42720529 TTAACAGTTA
42720539 TAAAATT
1 TAAAATT
42720546 TAAAATT
1 TAAAATT
42720553 TAAAATT
1 TAAAATT
42720560 TAAAATT
1 TAAAATT
42720567 TA
1 TA
42720569 CAACTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TAAAATT
Found at i:42723282 original size:20 final size:20
Alignment explanation
Indices: 42723257--42723298 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
42723247 TTGAGAACTA
*
42723257 AATCTAGTTCAGTTAGAATG
1 AATCTAGTTCAGTCAGAATG
42723277 AATCTAGTTCAGTCAGAATG
1 AATCTAGTTCAGTCAGAATG
42723297 AA
1 AA
42723299 CCAGCTGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (20 bp):
AATCTAGTTCAGTCAGAATG
Found at i:42739814 original size:16 final size:16
Alignment explanation
Indices: 42739793--42739838 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
42739783 CTAAAAATGA
42739793 AAAGAAAACGAAAAG-G
1 AAAGAAAA-GAAAAGAG
42739809 AAAGAAAA-AGAAAGAG
1 AAAGAAAAGA-AAAGAG
42739825 AAAGAGAAAGAAAA
1 AAAGA-AAAGAAAA
42739839 CCTAACCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.04
15 4 0.15
16 14 0.54
17 6 0.23
18 1 0.04
ACGTcount: A:0.74, C:0.02, G:0.24, T:0.00
Consensus pattern (16 bp):
AAAGAAAAGAAAAGAG
Found at i:42746544 original size:17 final size:18
Alignment explanation
Indices: 42746511--42746544 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
42746501 ATGATGTCTC
*
42746511 AAACTATTTTTATGCTTG
1 AAACTATTTTGATGCTTG
42746529 AAACTA-TTTGATGCTT
1 AAACTATTTTGATGCTT
42746545 ACTATTCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (18 bp):
AAACTATTTTGATGCTTG
Found at i:42749168 original size:41 final size:41
Alignment explanation
Indices: 42749111--42749194 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
42749101 TTGAACAAGA
* * *
42749111 AAACCTAAAGAGACAGTTGATTATGATTACTGAAGCAAGCT
1 AAACCCAAAAAGACAGTTGATTATGATTACCGAAGCAAGCT
*
42749152 AAACCCAAAAAGACAGTTGGTTATGATTACCGAAGCAAGCT
1 AAACCCAAAAAGACAGTTGATTATGATTACCGAAGCAAGCT
42749193 AA
1 AA
42749195 TCACCCATAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (41 bp):
AAACCCAAAAAGACAGTTGATTATGATTACCGAAGCAAGCT
Found at i:42750361 original size:18 final size:18
Alignment explanation
Indices: 42750334--42750371 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
42750324 TAGGAAAATT
*
42750334 TAGGAAGTGCTGAAGACC
1 TAGGAAGTGCCGAAGACC
*
42750352 TAGGATGTGCCGAAGACC
1 TAGGAAGTGCCGAAGACC
42750370 TA
1 TA
42750372 ATTCAGGCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.32, T:0.18
Consensus pattern (18 bp):
TAGGAAGTGCCGAAGACC
Found at i:42752330 original size:25 final size:25
Alignment explanation
Indices: 42752299--42752346 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
42752289 TGTCTCATAC
*
42752299 GGCCGAGTCATACGCCCGTGTCTCT
1 GGCCGAGTCACACGCCCGTGTCTCT
42752324 GGCCGAGTCACACGCCCGTGTCT
1 GGCCGAGTCACACGCCCGTGTCT
42752347 TTGACCGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.12, C:0.38, G:0.29, T:0.21
Consensus pattern (25 bp):
GGCCGAGTCACACGCCCGTGTCTCT
Done.