Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015091.1 Kokia drynarioides strain JFW-HI SEQ_130135, whole genome shotgun sequence
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: 803680
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 595 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:322044 original size:20 final size:20
Alignment explanation
Indices: 322019--322056 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
322009 AATGGCAAAA
322019 CAGTCACTT-AACTTTCAATT
1 CAGTCA-TTCAACTTTCAATT
322039 CAGTCATTCAACTTTCAA
1 CAGTCATTCAACTTTCAA
322057 AAAATAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (20 bp):
CAGTCATTCAACTTTCAATT
Found at i:322997 original size:29 final size:29
Alignment explanation
Indices: 322942--322998 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
322932 GTATAAACAA
* **
322942 ATTGGGTCATTTACGCAAAAAGTAAAAAT
1 ATTGGGTCATTTACGAAAAAACAAAAAAT
**
322971 ATTGGGTCATTTATTAAAAAACAAAAAA
1 ATTGGGTCATTTACGAAAAAACAAAAAA
322999 GGAAAGATGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (29 bp):
ATTGGGTCATTTACGAAAAAACAAAAAAT
Found at i:323932 original size:18 final size:19
Alignment explanation
Indices: 323909--323947 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
323899 TTATTTAATA
*
323909 ATAATTTTAA-AAACAATT
1 ATAATTTTAATAAAAAATT
323927 ATAATTTTAATAAAAAATT
1 ATAATTTTAATAAAAAATT
323946 AT
1 AT
323948 TAGATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
ATAATTTTAATAAAAAATT
Found at i:345760 original size:29 final size:29
Alignment explanation
Indices: 345727--345784 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
345717 TAGTGGAGAA
*
345727 TAAAATGTTACAGTTTAGTCATTTATGTT
1 TAAAATGTTACAGTTTAGTCACTTATGTT
* *
345756 TAAAATGTTATATTTTAGTCACTTATGTT
1 TAAAATGTTACAGTTTAGTCACTTATGTT
345785 AGCATTTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (29 bp):
TAAAATGTTACAGTTTAGTCACTTATGTT
Found at i:347277 original size:17 final size:19
Alignment explanation
Indices: 347246--347283 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
347236 ATCAATTAAA
*
347246 ATAATAAAAATATAAATTT
1 ATAATAAAAATATAAAGTT
347265 ATAA-AAAAA-ATAAAGTT
1 ATAATAAAAATATAAAGTT
347282 AT
1 AT
347284 CAATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 5 0.28
19 4 0.22
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
ATAATAAAAATATAAAGTT
Found at i:348672 original size:14 final size:14
Alignment explanation
Indices: 348649--348679 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
348639 TTCAAGTGAT
*
348649 AAAAGGAAAAGAAA
1 AAAAGAAAAAGAAA
348663 AAAAGAAAAAGAAA
1 AAAAGAAAAAGAAA
348677 AAA
1 AAA
348680 CAGACAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAGAAA
Found at i:356749 original size:15 final size:16
Alignment explanation
Indices: 356729--356758 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
356719 AAAATAATCA
356729 CCTCTTA-TTTTCTTT
1 CCTCTTACTTTTCTTT
356744 CCTCTTACTTTTCTT
1 CCTCTTACTTTTCTT
356759 CTCTACCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.07, C:0.30, G:0.00, T:0.63
Consensus pattern (16 bp):
CCTCTTACTTTTCTTT
Found at i:361137 original size:18 final size:18
Alignment explanation
Indices: 361114--361162 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
361104 TAACAATTTT
361114 TTTAATTTTTAGTTATAA
1 TTTAATTTTTAGTTATAA
* *
361132 TTTAATATTTAAGTTTTAA
1 TTTAAT-TTTTAGTTATAA
361151 TTAATAATTTTT
1 TT--TAATTTTT
361163 TTGGTTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 6 0.24
19 12 0.48
20 3 0.12
21 4 0.16
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (18 bp):
TTTAATTTTTAGTTATAA
Found at i:362730 original size:43 final size:43
Alignment explanation
Indices: 362669--362751 Score: 166
Period size: 43 Copynumber: 1.9 Consensus size: 43
362659 TTATGCTTCC
362669 TTAGCCTCGTATGACAAGATGAAGTATCTTGTGGCTGGATCTT
1 TTAGCCTCGTATGACAAGATGAAGTATCTTGTGGCTGGATCTT
362712 TTAGCCTCGTATGACAAGATGAAGTATCTTGTGGCTGGAT
1 TTAGCCTCGTATGACAAGATGAAGTATCTTGTGGCTGGAT
362752 TTGACTCTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.34
Consensus pattern (43 bp):
TTAGCCTCGTATGACAAGATGAAGTATCTTGTGGCTGGATCTT
Found at i:366418 original size:24 final size:24
Alignment explanation
Indices: 366390--366452 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
366380 AGAAATAATC
366390 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAGTTAAACTCTGTTTAATTG
* * *
366414 TTTCAATTAAACTTTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTAATTG
* *
366438 TTTAAGTCAAACTCT
1 TTTCAGTTAAACTCT
366453 TATTAATCTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTAATTG
Found at i:367803 original size:33 final size:33
Alignment explanation
Indices: 367761--367826 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
367751 AATAAAATAA
367761 TTTATGGTAACTCATTGTTAAAATTATTATTAT
1 TTTATGGTAACTCATTGTTAAAATTATTATTAT
367794 TTTATGGTAACTCATTGTTAAAATTATTATTAT
1 TTTATGGTAACTCATTGTTAAAATTATTATTAT
367827 AAAATATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (33 bp):
TTTATGGTAACTCATTGTTAAAATTATTATTAT
Found at i:370960 original size:16 final size:18
Alignment explanation
Indices: 370939--370971 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
370929 GGCACTTTTT
370939 AAATTTA-ATA-AAAAAG
1 AAATTTAGATAGAAAAAG
370955 AAATTTAGATAGAAAAA
1 AAATTTAGATAGAAAAA
370972 AGGGATACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (18 bp):
AAATTTAGATAGAAAAAG
Found at i:371414 original size:40 final size:40
Alignment explanation
Indices: 371362--371444 Score: 121
Period size: 40 Copynumber: 2.1 Consensus size: 40
371352 AAATACACTT
* *
371362 AAAAATATTAAAACAAATATTGAAACAACAAACAAATTAA
1 AAAAATATTAAAACAAATAGTAAAACAACAAACAAATTAA
* * *
371402 AAAAATATTAAAACAATTCGTAAAACAACAAACAAATTGA
1 AAAAATATTAAAACAAATAGTAAAACAACAAACAAATTAA
371442 AAA
1 AAA
371445 TACAATAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.66, C:0.11, G:0.04, T:0.19
Consensus pattern (40 bp):
AAAAATATTAAAACAAATAGTAAAACAACAAACAAATTAA
Found at i:371707 original size:45 final size:45
Alignment explanation
Indices: 371657--371756 Score: 107
Period size: 45 Copynumber: 2.2 Consensus size: 45
371647 CTAAAATAGA
*
371657 ACCAAAAACA-CTACCAAA-ATGCACCAAAAACAGAACCAAAACTGC
1 ACCAAAAACAGC-ACCAAATA-GCACCAAAAACAGAACCAAAACTAC
* * * *
371702 ACCAAAAA-AGCATCAAATCAGCACCAAAAACAGTACTAAATCTAC
1 ACCAAAAACAGCACCAAAT-AGCACCAAAAACAGAACCAAAACTAC
371747 ACCAAAAACA
1 ACCAAAAACA
371757 ACCTGCAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
44 6 0.13
45 38 0.83
46 2 0.04
ACGTcount: A:0.56, C:0.29, G:0.06, T:0.09
Consensus pattern (45 bp):
ACCAAAAACAGCACCAAATAGCACCAAAAACAGAACCAAAACTAC
Found at i:371718 original size:22 final size:23
Alignment explanation
Indices: 371657--371756 Score: 96
Period size: 22 Copynumber: 4.4 Consensus size: 23
371647 CTAAAATAGA
**
371657 ACCAAAAACACTACCAAAA-TGC
1 ACCAAAAACAGAACCAAAACTGC
371679 ACCAAAAACAGAACCAAAACTGC
1 ACCAAAAACAGAACCAAAACTGC
* * * *
371702 ACCAAAAA-AGCATCAAATCAGC
1 ACCAAAAACAGAACCAAAACTGC
* * * *
371724 ACCAAAAACAGTACTAAATCTAC
1 ACCAAAAACAGAACCAAAACTGC
371747 ACCAAAAACA
1 ACCAAAAACA
371757 ACCTGCAAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
22 35 0.54
23 30 0.46
ACGTcount: A:0.56, C:0.29, G:0.06, T:0.09
Consensus pattern (23 bp):
ACCAAAAACAGAACCAAAACTGC
Found at i:371742 original size:23 final size:23
Alignment explanation
Indices: 371638--371756 Score: 79
Period size: 22 Copynumber: 5.3 Consensus size: 23
371628 CACAGCACTG
* *
371638 AAAATAGTACTAAAAT-AGAACCA
1 AAAACAGTACT-AAATCAGCACCA
* *
371661 AAAACACTACCAAA--ATGCACCA
1 AAAACAGTACTAAATCA-GCACCA
* * * *
371683 AAAACAGAACCAAAACTGCACCA
1 AAAACAGTACTAAATCAGCACCA
*
371706 AAAA-AGCA-TCAAATCAGCACCA
1 AAAACAGTACT-AAATCAGCACCA
371728 AAAACAGTACTAAATCTA-CACCA
1 AAAACAGTACTAAATC-AGCACCA
371751 AAAACA
1 AAAACA
371757 ACCTGCAAAA
Statistics
Matches: 77, Mismatches: 12, Indels: 14
0.75 0.12 0.14
Matches are distributed among these distances:
21 1 0.01
22 37 0.48
23 37 0.48
24 2 0.03
ACGTcount: A:0.57, C:0.25, G:0.07, T:0.11
Consensus pattern (23 bp):
AAAACAGTACTAAATCAGCACCA
Found at i:372788 original size:18 final size:18
Alignment explanation
Indices: 372767--372802 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
372757 AATAATTTTT
*
372767 AAAATTCAAATATTTATA
1 AAAATTCAAAAATTTATA
*
372785 AAAATTTAAAAATTTATA
1 AAAATTCAAAAATTTATA
372803 TTTAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAATTCAAAAATTTATA
Found at i:393997 original size:3 final size:3
Alignment explanation
Indices: 393991--394022 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
393981 TTTTTTTTGT
393991 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
394023 TGAGTATGTT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:398344 original size:16 final size:17
Alignment explanation
Indices: 398311--398349 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
398301 ATTATATTTT
*
398311 AAAAAATTATTTAAAAA
1 AAAAAACTATTTAAAAA
398328 AAAAAACTA-TTACAAAA
1 AAAAAACTATTTA-AAAA
398345 AAAAA
1 AAAAA
398350 GGGCGTCCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAAACTATTTAAAAA
Found at i:406035 original size:10 final size:11
Alignment explanation
Indices: 406008--406034 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
405998 ATCATATGTC
406008 ATTTTTAAAAT
1 ATTTTTAAAAT
406019 ATTTTTAAAAT
1 ATTTTTAAAAT
406030 ATTTT
1 ATTTT
406035 ACTAGACCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTTTTAAAAT
Found at i:407573 original size:30 final size:30
Alignment explanation
Indices: 407548--407925 Score: 159
Period size: 30 Copynumber: 12.7 Consensus size: 30
407538 TCGAGGATAT
* *
407548 AATGTGAATTTTTGGAAGGTTCGAGGTCAA
1 AATGTGAATTTTTGGAAAGTTCGAGGTAAA
*
407578 AATG-GAA-TTTTGGAAAGTTTGAGGGTAAA
1 AATGTGAATTTTTGGAAAGTTCGA-GGTAAA
* *
407607 AATAT-AATTTTTGGAAAGTTCGTGGTCAAAA
1 AATGTGAATTTTTGGAAAGTTCGAGGT--AAA
* *
407638 AATG-GAA-TTTTGGAAAGTTCAAGGGAAAA
1 AATGTGAATTTTTGGAAAGTTCGA-GGTAAA
* *
407667 AATAT-AATTTTTGGAAAGTT-TAGGGTCAAA
1 AATGTGAATTTTTGGAAAGTTCGA-GGT-AAA
* * *
407697 AAT-AGAA--TTTGGAAAGTTTAGGGGTAAA
1 AATGTGAATTTTTGGAAAG-TTCGAGGTAAA
* *** * *
407725 AATAT-AATTTTCAAAAAGATTGGGGGTCAAA
1 AATGTGAATTTTTGGAAAG-TTCGAGGT-AAA
** * * *
407756 AAAATAGAA-TTTGGGAAAGTTTGGGGGTAAA
1 AATGT-GAATTTTTGGAAAG-TTCGAGGTAAA
* * *
407787 ATTAT-AATTTTTGGAAAGTT-TAGGGTTAAAA
1 AATGTGAATTTTTGGAAAGTTCGA-GG-T-AAA
*
407818 AATG-GAA-TTTTGGAAAGTTTGAGGGTAAA
1 AATGTGAATTTTTGGAAAGTTCGA-GGTAAA
* * *
407847 AATGT-AATTTTTGGATAGTTTG-GTGTTAA
1 AATGTGAATTTTTGGAAAGTTCGAG-GTAAA
*
407876 AATG-GAA-TTTTGGAAAGTTTGAGGGTAAA
1 AATGTGAATTTTTGGAAAGTTCGA-GGTAAA
* *
407905 AATAT-AATTTTTGGATAGTTC
1 AATGTGAATTTTTGGAAAGTTC
407926 AAGGACCTTC
Statistics
Matches: 273, Mismatches: 42, Indels: 66
0.72 0.11 0.17
Matches are distributed among these distances:
28 44 0.16
29 67 0.25
30 111 0.41
31 34 0.12
32 15 0.05
33 2 0.01
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.34
Consensus pattern (30 bp):
AATGTGAATTTTTGGAAAGTTCGAGGTAAA
Found at i:407585 original size:29 final size:29
Alignment explanation
Indices: 407486--407925 Score: 123
Period size: 30 Copynumber: 14.8 Consensus size: 29
407476 GCTTCGGGAA
* * *
407486 CAAAATGGTAATTTTCGGAAGGTTCGGGGTT
1 CAAAATGG-AATTTTTGGAAAGTTCGAGG-T
* ** * *
407517 AAAAATAAAATTTTTAGATA-TTCGAGGAT
1 CAAAATGGAATTTTTGGAAAGTTCGAGG-T
* *
407546 -ATAATGTGAATTTTTGGAAGGTTCGAGGT
1 CAAAATG-GAATTTTTGGAAAGTTCGAGGT
*
407575 CAAAATGGAA-TTTTGGAAAGTTTGAGGGT
1 CAAAATGGAATTTTTGGAAAGTTCGA-GGT
* ** *
407604 AAAAATATAATTTTTGGAAAGTTCGTGGT
1 CAAAATGGAATTTTTGGAAAGTTCGAGGT
* *
407633 CAAAAAATGGAA-TTTTGGAAAGTTCAAGGGA
1 C--AAAATGGAATTTTTGGAAAGTTCGA-GGT
* ** *
407664 AAAAATATAATTTTTGGAAAGTT-TAGGGT
1 CAAAATGGAATTTTTGGAAAGTTCGA-GGT
* * *
407693 CAAAAATAGAA--TTTGGAAAGTTTAGGGGT
1 C-AAAATGGAATTTTTGGAAAG-TTCGAGGT
* ** *** * *
407722 AAAAATATAATTTTCAAAAAGATTGGGGGT
1 CAAAATGGAATTTTTGGAAAG-TTCGAGGT
* * * *
407752 CAAAAAAATAGAA-TTTGGGAAAGTTTGGGGGT
1 C---AAAATGGAATTTTTGGAAAG-TTCGAGGT
** *
407784 -AAAATTATAATTTTTGGAAAGTT-TAGGGTT
1 CAAAA-TGGAATTTTTGGAAAGTTCGA-GG-T
* *
407814 AAAAAATGGAA-TTTTGGAAAGTTTGAGGGT
1 -CAAAATGGAATTTTTGGAAAGTTCGA-GGT
* * * *
407844 AAAAATGTAATTTTTGGATAGTTTG-GTGT
1 CAAAATGGAATTTTTGGAAAGTTCGAG-GT
* *
407873 TAAAATGGAA-TTTTGGAAAGTTTGAGGGT
1 CAAAATGGAATTTTTGGAAAGTTCGA-GGT
* ** *
407902 AAAAATATAATTTTTGGATAGTTC
1 CAAAATGGAATTTTTGGAAAGTTC
407926 AAGGACCTTC
Statistics
Matches: 312, Mismatches: 68, Indels: 59
0.71 0.15 0.13
Matches are distributed among these distances:
28 52 0.17
29 85 0.27
30 127 0.41
31 21 0.07
32 19 0.06
33 8 0.03
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (29 bp):
CAAAATGGAATTTTTGGAAAGTTCGAGGT
Found at i:407668 original size:60 final size:59
Alignment explanation
Indices: 407554--407925 Score: 425
Period size: 58 Copynumber: 6.3 Consensus size: 59
407544 ATATAATGTG
*
407554 AATTTTTGGAAGGTTCGAGGTC--AAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATAT
1 AATTTTTGGAAAGTTCG-GGTCAAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATAT
** *
407612 AATTTTTGGAAAGTTCGTGGTCAAAAAATGGAATTTTGGAAAGTTCAAGGGAAAAAATAT
1 AATTTTTGGAAAGTTCG-GGTCAAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATAT
* *
407672 AATTTTTGGAAAGTTTAGGGTC-AAAAATAGAA-TTTGGAAAGTTT-AGGGGTAAAAATAT
1 AATTTTTGGAAAG-TTCGGGTCAAAAAATGGAATTTTGGAAAGTTTGA-GGGTAAAAATAT
*** * * * * *
407730 AATTTTCAAAAAGATTGGGGGTCAAAAAAATAGAATTTGGGAAAGTTTGGGGGTAAAATTAT
1 AATTTTTGGAAAG-TT-CGGGTC-AAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATAT
* * *
407792 AATTTTTGGAAAGTTTAGGGTTAAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATGT
1 AATTTTTGGAAAG-TTCGGGTCAAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATAT
* * *
407852 AATTTTTGGATAGTTTGGTGT--TAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATAT
1 AATTTTTGGAAAGTTCGG-GTCAAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATAT
*
407910 AATTTTTGGATAGTTC
1 AATTTTTGGAAAGTTC
407926 AAGGACCTTC
Statistics
Matches: 271, Mismatches: 33, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
57 1 0.00
58 104 0.38
59 18 0.07
60 97 0.36
61 17 0.06
62 34 0.13
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.34
Consensus pattern (59 bp):
AATTTTTGGAAAGTTCGGGTCAAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATAT
Found at i:407795 original size:180 final size:180
Alignment explanation
Indices: 407576--407915 Score: 499
Period size: 180 Copynumber: 1.9 Consensus size: 180
407566 GTTCGAGGTC
* * *
407576 AAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATATAATTTTTGGAAAG-TTCGTGGTCAAAAAA
1 AAAATAGAATTTGGGAAAGTTTGAGGGTAAAAATATAATTTTTGGAAAGTTTAG-GGTCAAAAAA
407640 TGGAATTTTGGAAAGTTCAAGGGAAAAAATATAATTTTTGGAAAGTTTAGG-GTCAAAAATAGAA
65 TGGAATTTTGGAAAGTTCAAGGGAAAAAATATAATTTTTGGAAAGTTT-GGTGT-AAAAATAGAA
407704 -TTTGGAAAGTTT-AGGGGTAAAAATATAATTTTCAAAAAGATTGGGGGTCAAA
128 TTTTGGAAAGTTTGA-GGGTAAAAATATAATTTTCAAAAAGATTGGGGGTCAAA
* * *
407756 AAAATAGAATTTGGGAAAGTTTGGGGGTAAAATTATAATTTTTGGAAAGTTTAGGGTTAAAAAAT
1 AAAATAGAATTTGGGAAAGTTTGAGGGTAAAAATATAATTTTTGGAAAGTTTAGGGTCAAAAAAT
** * * * * *
407821 GGAATTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTTGGATAGTTTGGTGTTAAAATGGAATTT
66 GGAATTTTGGAAAGTTCAAGGGAAAAAATATAATTTTTGGAAAGTTTGGTGTAAAAATAGAATTT
407886 TGGAAAGTTTGAGGGTAAAAATATAATTTT
131 TGGAAAGTTTGAGGGTAAAAATATAATTTT
407916 TGGATAGTTC
Statistics
Matches: 143, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
179 10 0.07
180 129 0.90
181 4 0.03
ACGTcount: A:0.40, C:0.02, G:0.25, T:0.34
Consensus pattern (180 bp):
AAAATAGAATTTGGGAAAGTTTGAGGGTAAAAATATAATTTTTGGAAAGTTTAGGGTCAAAAAAT
GGAATTTTGGAAAGTTCAAGGGAAAAAATATAATTTTTGGAAAGTTTGGTGTAAAAATAGAATTT
TGGAAAGTTTGAGGGTAAAAATATAATTTTCAAAAAGATTGGGGGTCAAA
Found at i:407940 original size:58 final size:56
Alignment explanation
Indices: 407578--407924 Score: 205
Period size: 60 Copynumber: 5.9 Consensus size: 56
407568 TCGAGGTCAA
* * ***
407578 AATGGAATTTTGGAAAGTTTGAGGGTAAAAATATAATTTTTGGAAAGTTCGTGGTCAAAA
1 AATGGAATTTTGGAAAGTTTGAGGGTAAAAATATAATTTTTGGATAGTT--AGG-C-CTT
** * * ***
407638 AATGGAATTTTGGAAAGTTCAAGGGAAAAAATATAATTTTTGGAAAGTTTAGGGTCAAA
1 AATGGAATTTTGGAAAGTTTGAGGGTAAAAATATAATTTTTGGATAG-TTA-GG-CCTT
* *** * * ***
407697 AATAGAA-TTTGGAAAGTTT-AGGGGTAAAAATATAATTTTCAAAAAGATTGGGGGTCAAAAA
1 AATGGAATTTTGGAAAGTTTGA-GGGTAAAAATATAATTTTTGGATAG-TT--AGG-C--CTT
* * * * * *
407758 AATAGAATTTGGGAAAGTTTGGGGGTAAAATTATAATTTTTGGAAAGTTTAGG-GTT
1 AATGGAATTTTGGAAAGTTTGAGGGTAAAAATATAATTTTTGGATAG-TTAGGCCTT
* * **
407814 AAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTTGGATAGTTTGGTGTT
1 ----AATGGAATTTTGGAAAGTTTGAGGGTAAAAATATAATTTTTGGATAGTTAGGCCTT
407874 AAAATGGAATTTTGGAAAGTTTGAGGGTAAAAATATAATTTTTGGATAGTT
1 --AATGGAATTTTGGAAAGTTTGAGGGTAAAAATATAATTTTTGGATAGTT
407925 CAAGGACCTT
Statistics
Matches: 242, Mismatches: 31, Indels: 30
0.80 0.10 0.10
Matches are distributed among these distances:
57 1 0.00
58 84 0.35
59 17 0.07
60 94 0.39
61 12 0.05
62 34 0.14
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.34
Consensus pattern (56 bp):
AATGGAATTTTGGAAAGTTTGAGGGTAAAAATATAATTTTTGGATAGTTAGGCCTT
Found at i:410090 original size:11 final size:11
Alignment explanation
Indices: 410061--410145 Score: 54
Period size: 11 Copynumber: 8.0 Consensus size: 11
410051 TTTGGACATT
410061 ATAAATTTAAA
1 ATAAATTTAAA
*
410072 CTTAAATTTAAA
1 -ATAAATTTAAA
410084 ATAAATTT-AA
1 ATAAATTTAAA
*
410094 AT---TCT-AA
1 ATAAATTTAAA
*
410101 ATAGATTTAAA
1 ATAAATTTAAA
* * *
410112 CTTAATATAAA
1 ATAAATTTAAA
*
410123 CTTAAATTTAAA
1 -ATAAATTTAAA
410135 ATAAATTTAAA
1 ATAAATTTAAA
410146 TCCTGTTAGG
Statistics
Matches: 56, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
7 6 0.11
10 6 0.11
11 26 0.46
12 18 0.32
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (11 bp):
ATAAATTTAAA
Found at i:410093 original size:17 final size:17
Alignment explanation
Indices: 410068--410146 Score: 97
Period size: 17 Copynumber: 4.6 Consensus size: 17
410058 ATTATAAATT
*
410068 TAAACTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
410085 TAAATTTAAATTCT-AAA
1 TAAATTTAAATT-TAAAA
* * *
410102 TAGATTTAAACTTAATA
1 TAAATTTAAATTTAAAA
*
410119 TAAACTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
410136 TAAATTTAAAT
1 TAAATTTAAAT
410147 CCTGTTAGGC
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
16 1 0.02
17 49 0.96
18 1 0.02
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:410101 original size:7 final size:6
Alignment explanation
Indices: 410062--410146 Score: 63
Period size: 6 Copynumber: 14.8 Consensus size: 6
410052 TTGGACATTA
* * *
410062 TAAATT TAAACT TAAATT TAAA-A TAAATT TAAATT CTAAA-- TAGATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT -TAAATT TAAATT
* * * *
410108 TAAACT T-AATA TAAACT TAAATT TAAA-A TAAATT TAAAT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAAT
410147 CCTGTTAGGC
Statistics
Matches: 59, Mismatches: 14, Indels: 12
0.69 0.16 0.14
Matches are distributed among these distances:
4 3 0.05
5 11 0.19
6 41 0.69
7 4 0.07
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (6 bp):
TAAATT
Found at i:410795 original size:209 final size:209
Alignment explanation
Indices: 410496--410971 Score: 677
Period size: 209 Copynumber: 2.3 Consensus size: 209
410486 TTTGATCCAT
* * * * * * * *
410496 TTCTCTTTGTCTCATCAAGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAAGAAGGTAACC
1 TTCTCTATATCTCATCAGGAAGACGGATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACC
* * * * *
410561 GCTTTATTGCTTCAACTTACTTCTCAGTATCTCATCAGGAAGCTGGTGTTCGAAGATTT-GCTCA
66 ACTTTATTGCTTCAACCTACTTCTCAATATCTCATCAGGAAGCTGGGGTTCGAAG-TTTCACTCA
*
410625 C-TCTGAGCCTGGCTTCATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATC
130 CAT-TGAGCATGGCTTCATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATC
* *
410689 ACTTGTTTCAATTCGC
194 ACTTGTTACAATCCGC
* ** *
410705 TTTTCTATATCTCATCAGGAAGACAAATTTGGTCCACTTCTCAGTATCTCATCCGGAAGCTAACC
1 TTCTCTATATCTCATCAGGAAGACGGATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACC
* * * *
410770 ATTTTTTTGCTTCGACCTGCTTCTCAATATCTCATCAGGAAGCTGGGGTTCGAAGTTTCACTCAC
66 ACTTTATTGCTTCAACCTACTTCTCAATATCTCATCAGGAAGCTGGGGTTCGAAGTTTCACTCAC
* *
410835 ATTGAGCATTGCTTCATTTATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCAC
131 ATTGAGCATGGCTTCATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCAC
410900 TTGTTACAATCCGC
196 TTGTTACAATCCGC
*
410914 TTCTCTGTATCTCATCAGGAAGACGGATTTGGTCCACTTCTCAGTATCTCATCAGGAA
1 TTCTCTATATCTCATCAGGAAGACGGATTTGGTCCACTTCTCAGTATCTCATCAGGAA
410972 AATGACCAAC
Statistics
Matches: 234, Mismatches: 31, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
208 3 0.01
209 230 0.98
210 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (209 bp):
TTCTCTATATCTCATCAGGAAGACGGATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACC
ACTTTATTGCTTCAACCTACTTCTCAATATCTCATCAGGAAGCTGGGGTTCGAAGTTTCACTCAC
ATTGAGCATGGCTTCATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCAC
TTGTTACAATCCGC
Found at i:411467 original size:5 final size:5
Alignment explanation
Indices: 411459--411484 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
411449 GAGATAGAAT
411459 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
411485 ATATTTGTTC
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:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:412227 original size:58 final size:58
Alignment explanation
Indices: 412035--412212 Score: 311
Period size: 58 Copynumber: 3.1 Consensus size: 58
412025 AAAAGCAGTT
* ** *
412035 GTTTATGAGTGTTATTTAGGAATAAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGTTTTTTAATAATGAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
412093 GTTTATGAGTGTTTTTTAATAATGAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGTTTTTTAATAATGAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
*
412151 GTTTATGAGTGTTTTTTAATAATGAAATTATATTTGAGTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGTTTTTTAATAATGAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
412209 GTTT
1 GTTT
412213 GTTGATGGGT
Statistics
Matches: 115, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 115 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.49
Consensus pattern (58 bp):
GTTTATGAGTGTTTTTTAATAATGAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
Found at i:412442 original size:9 final size:9
Alignment explanation
Indices: 412428--412453 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
412418 TCGATTCGTT
412428 TAACTCGAA
1 TAACTCGAA
412437 TAACTCGAA
1 TAACTCGAA
412446 TAACTCGA
1 TAACTCGA
412454 TTCGAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (9 bp):
TAACTCGAA
Found at i:413616 original size:24 final size:24
Alignment explanation
Indices: 413585--413633 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
413575 GCTCCATTCA
413585 TTTTTTGGCGATAGGGAGATGAGT
1 TTTTTTGGCGATAGGGAGATGAGT
413609 TTTTTTGGCGATAGGGAGATGAGT
1 TTTTTTGGCGATAGGGAGATGAGT
413633 T
1 T
413634 GTGATGCTTG
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:0.04, G:0.37, T:0.39
Consensus pattern (24 bp):
TTTTTTGGCGATAGGGAGATGAGT
Found at i:424133 original size:29 final size:30
Alignment explanation
Indices: 424046--424133 Score: 85
Period size: 29 Copynumber: 3.0 Consensus size: 30
424036 AATTTTTGGA
*
424046 AGGTTAAAAATGGAAATTTTAGATATT-AG
1 AGGTTAAAAATGGAATTTTTAGATATTCAG
* * *
424075 AGGAT-AGAATGGTAATTTTTGGA-AGGTTCAG
1 AGGTTAAAAATGG-AATTTTTAGATA--TTCAG
424106 -GGTTAAAAATGGAATTTTTAGATATTCA
1 AGGTTAAAAATGGAATTTTTAGATATTCA
424134 CACTGAATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
28 7 0.15
29 16 0.35
30 14 0.30
31 9 0.20
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (30 bp):
AGGTTAAAAATGGAATTTTTAGATATTCAG
Found at i:429436 original size:49 final size:49
Alignment explanation
Indices: 429374--430145 Score: 379
Period size: 49 Copynumber: 15.8 Consensus size: 49
429364 AAGGATATGG
* *
429374 AGGGAAA-AGTTTAAGTCGCAACGGTGAA-CATTGTACCTCAGAAGCATGA
1 AGGGAAAGA-TTTAAGTCGCAACGGCGAATCATTGTACCAC-GAAGCATGA
* * * *
429423 GGGGAAAGATTTAAGCCGCAACGGCGAATC-TAGTACCACGAAGATATAGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAATCATTGTACCACGAAG-CAT-GA
* * * * *
429473 A-GGAAAGGTTTAAGTCGCAACGG-AAAACCTTGTACCTCAGAAGCATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAATCATTGTACCAC-GAAGCATGA
* * * ** *
429521 AGGGAAAGATTTAAGTCGTAATGGTGAATC-TAATACCACGAAGATATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAATCATTGTACCACGAAG-CATGA
* * * * *
429570 AGGGAAAGATTTAAGTCGCAATGGCGAATCCA--ATACCACGAGGATATGG
1 AGGGAAAGATTTAAGTCGCAACGGCGAAT-CATTGTACCACGAAG-CATGA
* * * * * * * * *
429619 AGGGAAAGGTTTAAATCGCAACGAC-AAACCTTGTACCTCAAAAGTATAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAATCATTGTACCAC-GAAGCATGA
* * * * *
429668 AGGGAAATATTTAAGCCGTAACGGCGAATCCA--GTACCACGAGGATATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAAT-CATTGTACCACGAAG-CATGA
* * ** * *
429717 AGGGAAAGTTTTAAGTCGTAACGATGAA-CCTTGTACCTCAGAAGCATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAATCATTGTACCAC-GAAGCATGA
* *
429766 AGGGAAAGATTTAAGTCGCAACGGCGAATCCA--GTACCACG-AGGATATA
1 AGGGAAAGATTTAAGTCGCAACGGCGAAT-CATTGTACCACGAAGCAT-GA
* * * * *
429814 GAGGGAAAGGTTTAAGTCGCAACGG-TAAACTTTGTACCTCAGAAGCATGA
1 -AGGGAAAGATTTAAGTCGCAACGGCGAATCATTGTACCAC-GAAGCATGA
* * * ** * ***
429864 AGGGAAAGATTTAA-ACTACAACGACGAATC-TAATACCTCAGAAATTTGA
1 AGGGAAAGATTTAAGTC-GCAACGGCGAATCATTGTACCAC-GAAGCATGA
* * * **
429913 AGGGAAAGATTTAAGTCACAACAGCGAATC-TAGTACCACGAAAATATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAATCATTGTACCACG-AAGCATGA
* * * * * *
429962 AAGGAAAGATTTAAGCCGCAACGACGAATC-TAGTACCACGAAGATATGG
1 AGGGAAAGATTTAAGTCGCAACGGCGAATCATTGTACCACGAAG-CATGA
* * * * * * *
430011 AGTGAAAGGTTTAAGTCGTAACGACGAA-CCTTGTACCTCAGAAACATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAATCATTGTACCAC-GAAGCATGA
* * * * * *
430060 AGGGAAAAATTTAAGCCGTAACAGCAAATCCA--ATACCACGAAG-ATTTGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAAT-CATTGTACCACGAAGCA--TGA
* * * *
430109 AGGGAAAGGTTTAAGTTGCAACGACGAA-CCTTGTACC
1 AGGGAAAGATTTAAGTCGCAACGGCGAATCATTGTACC
430146 TAAAAAACAT
Statistics
Matches: 552, Mismatches: 130, Indels: 82
0.72 0.17 0.11
Matches are distributed among these distances:
47 9 0.02
48 30 0.05
49 478 0.87
50 28 0.05
51 7 0.01
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (49 bp):
AGGGAAAGATTTAAGTCGCAACGGCGAATCATTGTACCACGAAGCATGA
Found at i:429623 original size:98 final size:98
Alignment explanation
Indices: 429419--430146 Score: 619
Period size: 98 Copynumber: 7.4 Consensus size: 98
429409 CCTCAGAAGC
* * * * * * *
429419 ATGAGGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATAGAA-GGAAAGGTT
1 ATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCGAAGATAT-GAAGGGAAAGATT
* * * * * * *
429483 TAAGTCGCAACGG-AAAACCTTGTACCTC-AGAAGC
65 TAAGCCGCAACGGCGAATCC-AGTACCACGAGGA-T
* * * * * ** *
429517 ATGAAGGGAAAGATTTAAGTCGTAATGGTGAATCTAATACCACGAAGATATGAAGGGAAAGATTT
1 ATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCGAAGATATGAAGGGAAAGATTT
* * *
429582 AAGTCGCAATGGCGAATCCAATACCACGAGGAT
66 AAGCCGCAACGGCGAATCCAGTACCACGAGGAT
* * * * * * *
429615 ATGGAGGGAAAGGTTTAAATCGCAACGACAAACCTTGTACCTC-AAAAGTATAAAGGGAAATATT
1 ATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCGAAGA-TATGAAGGGAAAGATT
*
429679 TAAGCCGTAACGGCGAATCCAGTACCACGAGGAT
65 TAAGCCGCAACGGCGAATCCAGTACCACGAGGAT
* * ** *
429713 ATGAAGGGAAAGTTTTAAGTCGTAACGATGAACCTTGTACCTCAGAAG-CATGAAGGGAAAGATT
1 ATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTC-GAAGATATGAAGGGAAAGATT
*
429777 TAAGTCGCAACGGCGAATCCAGTACCACGAGGAT
65 TAAGCCGCAACGGCGAATCCAGTACCACGAGGAT
** * *
429811 AT-AGAGGGAAAGGTTTAAGTCGCAACGGTAAACTTTGTACCTCAGAAG-CATGAAGGGAAAGAT
1 ATGA-AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTC-GAAGATATGAAGGGAAAGAT
* ** * * * * *
429874 TTAAACTACAACGACGAATCTAATACCTC-AGAAAT
64 TTAAGCCGCAACGGCGAATCCAGTACCACGAG-GAT
* * * * * * * * *
429909 TTGAAGGGAAAGATTTAAGTCACAACAGCGAATCTAGTACCACGAAAATATGAAAGGAAAGATTT
1 ATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCGAAGATATGAAGGGAAAGATTT
* * *
429974 AAGCCGCAACGACGAATCTAGTACCACGAAGAT
66 AAGCCGCAACGGCGAATCCAGTACCACGAGGAT
* * * * * *
430007 ATGGAGTGAAAGGTTTAAGTCGTAACGACGAACCTTGTACCTCAGAA-ACATGAAGGGAAAAATT
1 ATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTC-GAAGATATGAAGGGAAAGATT
* * * * *
430071 TAAGCCGTAACAGCAAATCCAATACCACGAAGAT
65 TAAGCCGCAACGGCGAATCCAGTACCACGAGGAT
* * *
430105 TTGAAGGGAAAGGTTTAAGTTGCAACGACGAACCTTGTACCT
1 ATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCT
430147 AAAAAACATA
Statistics
Matches: 513, Mismatches: 105, Indels: 24
0.80 0.16 0.04
Matches are distributed among these distances:
97 12 0.02
98 487 0.95
99 12 0.02
100 2 0.00
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (98 bp):
ATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCGAAGATATGAAGGGAAAGATTT
AAGCCGCAACGGCGAATCCAGTACCACGAGGAT
Found at i:429736 original size:196 final size:196
Alignment explanation
Indices: 429517--430124 Score: 736
Period size: 196 Copynumber: 3.1 Consensus size: 196
429507 CCTCAGAAGC
* *
429517 ATGAAGGGAAAGATTTAAGTCGTAATGGTGAATCTAATACCACGAAGATATGAAGGGAAAGATTT
1 ATGAAGGGAAAGATTTAAGTCGTAACGGTGAATCTAGTACCACGAAGATATGAAGGGAAAGATTT
* * *
429582 AAGTCGCAATGGCGAATCCAATACCACGAGGATATGGAGGGAAAGGTTTAAATCGCAACGACAAA
66 AAGTCGCAACGGCGAATCCAGTACCACGAGGATATGGAGGGAAAGGTTTAAGTCGCAACGACAAA
* * * *
429647 CCTTGTACCTCAAAAGTATAAAGGGAAATATTTAAGCCGTAACGGCGAATCCAGTACCACGAGGA
131 CCTTGTACCTCAAAAGCATGAAGGGAAAAATTTAAGCCGTAACGGCGAATCCAATACCACGAGGA
429712 T
196 T
* * * * * *
429713 ATGAAGGGAAAGTTTTAAGTCGTAACGATGAACCTTGTACCTCAGAAG-CATGAAGGGAAAGATT
1 ATGAAGGGAAAGATTTAAGTCGTAACGGTGAATCTAGTACCAC-GAAGATATGAAGGGAAAGATT
* **
429777 TAAGTCGCAACGGCGAATCCAGTACCACGAGGATATAGAGGGAAAGGTTTAAGTCGCAACGGTAA
65 TAAGTCGCAACGGCGAATCCAGTACCACGAGGATATGGAGGGAAAGGTTTAAGTCGCAACGACAA
* * * * *** * * *
429842 ACTTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAACTACAACGACGAATCTAATACCTC-AGA
130 ACCTTGTACCTCAAAAGCATGAAGGGAAAAATTTAAGCCGTAACGGCGAATCCAATACCACGAG-
*
429906 AAT
194 GAT
* ** * * * *
429909 TTGAAGGGAAAGATTTAAGTCACAACAGCGAATCTAGTACCACGAAAATATGAAAGGAAAGATTT
1 ATGAAGGGAAAGATTTAAGTCGTAACGGTGAATCTAGTACCACGAAGATATGAAGGGAAAGATTT
* * * * * * *
429974 AAGCCGCAACGACGAATCTAGTACCACGAAGATATGGAGTGAAAGGTTTAAGTCGTAACGACGAA
66 AAGTCGCAACGGCGAATCCAGTACCACGAGGATATGGAGGGAAAGGTTTAAGTCGCAACGACAAA
* * *
430039 CCTTGTACCTCAGAAA-CATGAAGGGAAAAATTTAAGCCGTAACAGCAAATCCAATACCACGAAG
131 CCTTGTACCTCA-AAAGCATGAAGGGAAAAATTTAAGCCGTAACGGCGAATCCAATACCACGAGG
430103 AT
195 AT
* *
430105 TTGAAGGGAAAGGTTTAAGT
1 ATGAAGGGAAAGATTTAAGT
430125 TGCAACGACG
Statistics
Matches: 341, Mismatches: 66, Indels: 10
0.82 0.16 0.02
Matches are distributed among these distances:
195 5 0.01
196 329 0.96
197 7 0.02
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (196 bp):
ATGAAGGGAAAGATTTAAGTCGTAACGGTGAATCTAGTACCACGAAGATATGAAGGGAAAGATTT
AAGTCGCAACGGCGAATCCAGTACCACGAGGATATGGAGGGAAAGGTTTAAGTCGCAACGACAAA
CCTTGTACCTCAAAAGCATGAAGGGAAAAATTTAAGCCGTAACGGCGAATCCAATACCACGAGGA
T
Found at i:429770 original size:147 final size:147
Alignment explanation
Indices: 429419--430074 Score: 503
Period size: 147 Copynumber: 4.5 Consensus size: 147
429409 CCTCAGAAGC
* * * * * * * * *
429419 ATGAGGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCAC-GAAGATATAGAA-GGAAAGGT
1 ATGAAGGGAAAGATTTAAGTCGTAACGACGAACCTAATACCTCAGAA-ACAT-GAAGGGAAAGAT
* * * * * * * * *
429482 TTAAGTCGCAACGGA-AAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGTCGTAATGGT
64 TTAAGTCGCAAC-GACAAACCTAGTACCACAAAAGTATAAAGGGAAAGATTTAAGCCGCAACGGC
*
429546 GAATCTAATACCACGAAGAT
128 GAATCTAGTACCACGAAGAT
* * * * * * * *
429566 ATGAAGGGAAAGATTTAAGTCGCAATGGCGAATCC-AATACCAC-GAGGATATGGAGGGAAAGGT
1 ATGAAGGGAAAGATTTAAGTCGTAACGACGAA-CCTAATACCTCAGA-AACATGAAGGGAAAGAT
* * * * *
429629 TTAAATCGCAACGACAAACCTTGTACCTCAAAAGTATAAAGGGAAATATTTAAGCCGTAACGGCG
64 TTAAGTCGCAACGACAAACCTAGTACCACAAAAGTATAAAGGGAAAGATTTAAGCCGCAACGGCG
* *
429694 AATCCAGTACCACGAGGAT
129 AATCTAGTACCACGAAGAT
* * ** *
429713 ATGAAGGGAAAGTTTTAAGTCGTAACGATGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTT
1 ATGAAGGGAAAGATTTAAGTCGTAACGACGAACCTAATACCTCAGAAACATGAAGGGAAAGATTT
* * * * * * * *
429778 AAGTCGCAACGGCGAATCC-AGTACCAC-GAGGATATAGAGGGAAAGGTTTAAGTCGCAACGG-T
66 AAGTCGCAACGAC-AAACCTAGTACCACAAAAG-TATAAAGGGAAAGATTTAAGCCGCAACGGCG
* * * *
429840 AAACTTTGTACCTCAGAAG-C
129 AATC-TAGTACCAC-GAAGAT
* * **
429860 ATGAAGGGAAAGATTTAA-AC-TACAACGACGAATCTAATACCTCAGAAATTTGAAGGGAAAGAT
1 ATGAAGGGAAAGATTTAAGTCGT--AACGACGAACCTAATACCTCAGAAACATGAAGGGAAAGAT
* * *
429923 TTAAGTCACAAC-AGCGAATCTAGTACCACGAAAA-TATGAAA-GGAAAGATTTAAGCCGCAACG
64 TTAAGTCGCAACGA-CAAACCTAGTACCAC-AAAAGTAT-AAAGGGAAAGATTTAAGCCGCAACG
*
429985 ACGAATCTAGTACCACGAAGAT
126 GCGAATCTAGTACCACGAAGAT
* * * ** *
430007 ATGGAGTGAAAGGTTTAAGTCGTAACGACGAACCTTGTACCTCAGAAACATGAAGGGAAAAATTT
1 ATGAAGGGAAAGATTTAAGTCGTAACGACGAACCTAATACCTCAGAAACATGAAGGGAAAGATTT
430072 AAG
66 AAG
430075 CCGTAACAGC
Statistics
Matches: 403, Mismatches: 85, Indels: 42
0.76 0.16 0.08
Matches are distributed among these distances:
145 1 0.00
146 18 0.04
147 366 0.91
148 16 0.04
149 2 0.00
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.20
Consensus pattern (147 bp):
ATGAAGGGAAAGATTTAAGTCGTAACGACGAACCTAATACCTCAGAAACATGAAGGGAAAGATTT
AAGTCGCAACGACAAACCTAGTACCACAAAAGTATAAAGGGAAAGATTTAAGCCGCAACGGCGAA
TCTAGTACCACGAAGAT
Found at i:430083 original size:147 final size:147
Alignment explanation
Indices: 429517--430145 Score: 524
Period size: 147 Copynumber: 4.3 Consensus size: 147
429507 CCTCAGAAGC
* * * ** *
429517 ATGAAGGGAAAGATTTAAGTCGTAATGGTGAATCTAATACCACGAAGATATGAAGGGAAAGATTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAGATATGAAGGGAAAGATTT
* * * ** * * * * * *
429582 AAGTCGCAATGGCGAATCC-AATACCAC-GAGGATATGGAGGGAAAGGTTTAAATCGCAAC-GAC
66 AAGTCGTAACGACGAA-CCTTGTACCTCAGA-AACATGAAGGGAAAGATTTAAGTCGCAACAG-C
* * * *
429644 -AAACCTTGTACCTC-AAAAGT
128 GAATCC-AGTACCACGAAGA-T
* * * * * * *
429664 ATAAAGGGAAATATTTAAGCCGTAACGGCGAATCCAGTACCACGAGGATATGAAGGGAAAGTTTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAGATATGAAGGGAAAGATTT
* * *
429729 AAGTCGTAACGATGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGTCGCAACGGCGAA
66 AAGTCGTAACGACGAACCTTGTACCTCAGAAACATGAAGGGAAAGATTTAAGTCGCAACAGCGAA
*
429794 TCCAGTACCACGAGGAT
131 TCCAGTACCACGAAGAT
* * * * * *
429811 AT-AGAGGGAAAGGTTTAAGTCGCAACG--GTAAACTTTGTACCTCAGAAG-CATGAAGGGAAAG
1 ATGA-AGGGAAAGATTTAAGCCGCAACGACG-AATC-TAGTACCAC-GAAGATATGAAGGGAAAG
* * ** ** *
429872 ATTTAA-AC-TACAACGACGAATCTAATACCTCAGAAATTTGAAGGGAAAGATTTAAGTCACAAC
62 ATTTAAGTCGT--AACGACGAACCTTGTACCTCAGAAACATGAAGGGAAAGATTTAAGTCGCAAC
* *
429935 AGCGAATCTAGTACCACGAAAAT
125 AGCGAATCCAGTACCACGAAGAT
* * * *
429958 ATGAAAGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAGATATGGAGTGAAAGGTTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAGATATGAAGGGAAAGATTT
* * * *
430023 AAGTCGTAACGACGAACCTTGTACCTCAGAAACATGAAGGGAAAAATTTAAGCCGTAACAGCAAA
66 AAGTCGTAACGACGAACCTTGTACCTCAGAAACATGAAGGGAAAGATTTAAGTCGCAACAGCGAA
*
430088 TCCAATACCACGAAGAT
131 TCCAGTACCACGAAGAT
* * ** * *
430105 TTGAAGGGAAAGGTTTAAGTTGCAACGACGAACCTTGTACC
1 ATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACC
430146 TAAAAAACAT
Statistics
Matches: 383, Mismatches: 82, Indels: 34
0.77 0.16 0.07
Matches are distributed among these distances:
145 2 0.01
146 11 0.03
147 351 0.92
148 17 0.04
149 2 0.01
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (147 bp):
ATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAGATATGAAGGGAAAGATTT
AAGTCGTAACGACGAACCTTGTACCTCAGAAACATGAAGGGAAAGATTTAAGTCGCAACAGCGAA
TCCAGTACCACGAAGAT
Found at i:430154 original size:98 final size:98
Alignment explanation
Indices: 429566--430163 Score: 635
Period size: 98 Copynumber: 6.1 Consensus size: 98
429556 CCACGAAGAT
* * * *
429566 ATGAAGGGAAAGATTTAAGTCGCAATGGCGAATCCAATACCACGAGGATATGGAGGGAAAGGTTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGATATGAAGGGAAAGGTTT
* * **
429631 AAATCGCAACGACAAACCTTGTACCTCAAAAGT
66 AAGTCGCAACGACGAACCTTGTACCTCAAAAAC
* * * * * *
429664 ATAAAGGGAAATATTTAAGCCGTAACGGCGAATCCAGTACCACGAGGATATGAAGGGAAAGTTTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGATATGAAGGGAAAGGTTT
* * * *
429729 AAGTCGTAACGATGAACCTTGTACCTCAGAAGC
66 AAGTCGCAACGACGAACCTTGTACCTCAAAAAC
* * *
429762 ATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCCAGTACCACGAGGATAT-AGAGGGAAAGGTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGATATGA-AGGGAAAGGTT
*** * * *
429826 TAAGTCGCAACGGTAAACTTTGTACCTCAGAAGC
65 TAAGTCGCAACGACGAACCTTGTACCTCAAAAAC
* ** * * * * *
429860 ATGAAGGGAAAGATTTAAACTACAACGACGAATCTAATACCTCAGAA-ATTTGAAGGGAAAGATT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCAC-GAAGATATGAAGGGAAAGGTT
* * * * * *
429924 TAAGTCACAAC-AGCGAATCTAGTACCACGAAAAT
65 TAAGTCGCAACGA-CGAACCTTGTACCTCAAAAAC
* * * * * *
429958 ATGAAAGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAGATATGGAGTGAAAGGTTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGATATGAAGGGAAAGGTTT
* *
430023 AAGTCGTAACGACGAACCTTGTACCTCAGAAAC
66 AAGTCGCAACGACGAACCTTGTACCTCAAAAAC
* * * * *
430056 ATGAAGGGAAAAATTTAAGCCGTAACAGCAAATCCAATACCACGAAGATTTGAAGGGAAAGGTTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGATATGAAGGGAAAGGTTT
* *
430121 AAGTTGCAACGACGAACCTTGTACCTAAAAAAC
66 AAGTCGCAACGACGAACCTTGTACCTCAAAAAC
*
430154 ATAAAGGGAA
1 ATGAAGGGAA
430164 GGTTGAGGCC
Statistics
Matches: 414, Mismatches: 80, Indels: 12
0.82 0.16 0.02
Matches are distributed among these distances:
97 4 0.01
98 406 0.98
99 4 0.01
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (98 bp):
ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGATATGAAGGGAAAGGTTT
AAGTCGCAACGACGAACCTTGTACCTCAAAAAC
Found at i:430536 original size:42 final size:42
Alignment explanation
Indices: 430471--430614 Score: 173
Period size: 42 Copynumber: 3.4 Consensus size: 42
430461 GTTACGTTAC
* * *
430471 CATCCAATCTTTTACCCCAATCATGAGGTATATTGAAAACAT
1 CATCCAATCTCTTACCCCGATCATGAGGTAGATTGAAAACAT
* * * * *
430513 CATCCAATCTCTTACCTCGATCATAAGGCAGATTGCAACCAT
1 CATCCAATCTCTTACCCCGATCATGAGGTAGATTGAAAACAT
* *
430555 CATTCAATCTCTTACCCCGATCATG-GGATAGATTGAAAACCT
1 CATCCAATCTCTTACCCCGATCATGAGG-TAGATTGAAAACAT
*
430597 CATCCAATCTTTTACCCC
1 CATCCAATCTCTTACCCC
430615 TAAGTTAAGC
Statistics
Matches: 84, Mismatches: 17, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
41 2 0.02
42 82 0.98
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.29
Consensus pattern (42 bp):
CATCCAATCTCTTACCCCGATCATGAGGTAGATTGAAAACAT
Found at i:434976 original size:61 final size:61
Alignment explanation
Indices: 434874--435000 Score: 150
Period size: 61 Copynumber: 2.1 Consensus size: 61
434864 CTAATGTCAT
* *
434874 GACATCCGACCTTCAATGTCGAAACATTAGAATCAATAGAGTAATTTG-TCTCTGGTGTCGC
1 GACATCCAACCTTCAATGTCGAAACATTAGAATCAATAGAGTAATTTGTTCTC-GATGTCGC
* ** * * *
434935 GACATCCAACCTTCAGTGTCGCGACATTGGAGTC-ATAAGAGTAATTTGTTCTCGATGTCTC
1 GACATCCAACCTTCAATGTCGAAACATTAGAATCAAT-AGAGTAATTTGTTCTCGATGTCGC
434996 GACAT
1 GACAT
435001 TAGGAGATCA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
60 2 0.04
61 50 0.89
62 4 0.07
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (61 bp):
GACATCCAACCTTCAATGTCGAAACATTAGAATCAATAGAGTAATTTGTTCTCGATGTCGC
Found at i:437327 original size:19 final size:18
Alignment explanation
Indices: 437283--437345 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
437273 AACAAATAAT
*
437283 TTAAAAATTATAAAAATA
1 TTAAAAATTAAAAAAATA
*
437301 TTCCAAAATTAAAAAAATA
1 TT-AAAAATTAAAAAAATA
*
437320 TATAAAAAGTTAATAAAA-A
1 T-TAAAAA-TTAAAAAAATA
437339 TTAAAAA
1 TTAAAAA
437346 AAAGCATGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
18 8 0.21
19 21 0.55
20 9 0.24
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.29
Consensus pattern (18 bp):
TTAAAAATTAAAAAAATA
Found at i:437337 original size:10 final size:9
Alignment explanation
Indices: 437305--437347 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
437295 AAAATATTCC
437305 AAAATTAAA
1 AAAATTAAA
437314 AAAATATATAA
1 AAAAT-TA-AA
*
437325 AAAGTTAATA
1 AAAATTAA-A
437335 AAAATTAAA
1 AAAATTAAA
437344 AAAA
1 AAAA
437348 AGCATGAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
9 11 0.38
10 12 0.41
11 6 0.21
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (9 bp):
AAAATTAAA
Found at i:437945 original size:2 final size:2
Alignment explanation
Indices: 437938--437967 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
437928 TAATTTCTTA
437938 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
437968 ATACGCTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:441375 original size:2 final size:2
Alignment explanation
Indices: 441368--441398 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
441358 CAAAAATGCT
441368 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
441399 TTGTCGATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:441783 original size:41 final size:41
Alignment explanation
Indices: 441676--441783 Score: 135
Period size: 41 Copynumber: 2.6 Consensus size: 41
441666 AGAGTTTAAT
*
441676 ATTTAAGGTTTAGGATTTAATGTTTATAATTCAAGTTTGGG
1 ATTTAAGGTTTAGGATTTAGTGTTTATAATTCAAGTTTGGG
* * * * *
441717 GTTTAAGATCTAGGGTTTAGTGTTTATAATTTAAGTTTGGG
1 ATTTAAGGTTTAGGATTTAGTGTTTATAATTCAAGTTTGGG
* * *
441758 ATTTAAGGTTTAAGATTCAGGGTTTA
1 ATTTAAGGTTTAGGATTTAGTGTTTA
441784 GGGTTCAGAA
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.28, C:0.03, G:0.24, T:0.45
Consensus pattern (41 bp):
ATTTAAGGTTTAGGATTTAGTGTTTATAATTCAAGTTTGGG
Found at i:442889 original size:21 final size:20
Alignment explanation
Indices: 442858--442912 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 20
442848 TTCATCAACA
442858 ATTTTATAATTATTATTTTTAT
1 ATTTTATAATTA--ATTTTTAT
442880 ATTTT-TAATTAATTTTTA-
1 ATTTTATAATTAATTTTTAT
*
442898 ATTGTATAA-TAATTT
1 ATTTTATAATTAATTT
442913 ATAACTTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 10 0.32
19 10 0.32
21 6 0.19
22 5 0.16
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
ATTTTATAATTAATTTTTAT
Found at i:445176 original size:3 final size:3
Alignment explanation
Indices: 445168--445192 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
445158 TTCAAGCTAT
445168 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
445193 CGTTATGCAG
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:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:464089 original size:21 final size:21
Alignment explanation
Indices: 464063--464106 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
464053 CTTCAAAAGT
464063 ATGCTTTCCTACAACACAATC
1 ATGCTTTCCTACAACACAATC
464084 ATGCTTTCCTACAACACAATC
1 ATGCTTTCCTACAACACAATC
464105 AT
1 AT
464107 AGTGATGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
ATGCTTTCCTACAACACAATC
Found at i:469693 original size:24 final size:23
Alignment explanation
Indices: 469634--469698 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 23
469624 ACGCAAGTTC
* *
469634 AAGA-CATTTATGCTCATCAGCT
1 AAGATCATTTACGCTCACCAGCT
*
469656 AAGAT-ACTTACGCTCACCAGCT
1 AAGATCATTTACGCTCACCAGCT
* *
469678 AATATGCATTTACGCTAACCA
1 AAGAT-CATTTACGCTCACCA
469699 ACTATTCAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 22 0.65
24 12 0.35
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.28
Consensus pattern (23 bp):
AAGATCATTTACGCTCACCAGCT
Found at i:470501 original size:16 final size:16
Alignment explanation
Indices: 470477--470508 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
470467 TCCTTACAAA
*
470477 TTTATTTCTTTAACAT
1 TTTAGTTCTTTAACAT
470493 TTTAGTTCTTTAACAT
1 TTTAGTTCTTTAACAT
470509 AAAAATTACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.12, G:0.03, T:0.59
Consensus pattern (16 bp):
TTTAGTTCTTTAACAT
Found at i:480486 original size:57 final size:57
Alignment explanation
Indices: 480423--480543 Score: 206
Period size: 57 Copynumber: 2.1 Consensus size: 57
480413 CTTATCGTAG
* *
480423 CATGTTTTATGTAATTTATTACAGTGATTGAATTTAGAGAATATTTTATTTATTTAT
1 CATGTTTTATGTAATTTATTACAGTGATTGAATTTAGAAAATATTTTATTTACTTAT
*
480480 CATGTTTTATGTAATTTATTATAGTGATTGAATTTAGAAAATATTTTATTTACTTAT
1 CATGTTTTATGTAATTTATTACAGTGATTGAATTTAGAAAATATTTTATTTACTTAT
*
480537 CGTGTTT
1 CATGTTT
480544 GCGTTTAATT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.53
Consensus pattern (57 bp):
CATGTTTTATGTAATTTATTACAGTGATTGAATTTAGAAAATATTTTATTTACTTAT
Found at i:481533 original size:6 final size:6
Alignment explanation
Indices: 481524--481584 Score: 56
Period size: 6 Copynumber: 10.0 Consensus size: 6
481514 TATACATATA
*
481524 TATTTT TA-TTT TATTTT TATCTTT TGTTATT TA-TTT TATTTT TATTGTT
1 TATTTT TATTTT TATTTT TAT-TTT TATT-TT TATTTT TATTTT TATT-TT
481573 ATATTTT T-TTTT
1 -TATTTT TATTTT
481585 CGAAACTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
5 13 0.28
6 18 0.38
7 12 0.26
8 4 0.09
ACGTcount: A:0.16, C:0.02, G:0.03, T:0.79
Consensus pattern (6 bp):
TATTTT
Found at i:483029 original size:38 final size:41
Alignment explanation
Indices: 482960--483039 Score: 101
Period size: 43 Copynumber: 2.0 Consensus size: 41
482950 TAAAATAAGC
* * *
482960 AAATGAAAGTTTGAATTGAAAAATAACAAAATGTAGTAAAAAT
1 AAATGAAAGTTTGAAAT-AAAAATAA-AAATTGTAGCAAAAAT
483003 AAATGAAAGTTTGAAAT-AAAAT-AAAATTGTAGCAAAA
1 AAATGAAAGTTTGAAATAAAAATAAAAATTGTAGCAAAA
483040 TTGTAAAACA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
39 12 0.35
40 1 0.03
41 5 0.15
43 16 0.47
ACGTcount: A:0.59, C:0.03, G:0.14, T:0.25
Consensus pattern (41 bp):
AAATGAAAGTTTGAAATAAAAATAAAAATTGTAGCAAAAAT
Found at i:483380 original size:29 final size:28
Alignment explanation
Indices: 483347--483468 Score: 79
Period size: 29 Copynumber: 4.2 Consensus size: 28
483337 AAAGGAAAAA
483347 TAGGGTCAAAATGAAATTTTGGAAAGTT
1 TAGGGTCAAAATGAAATTTTGGAAAGTT
* **
483375 TGAGGGAT-AAATTTG-AATTTTTTAAGAGTT
1 T-AGGG-TCAAA-ATGAAATTTTGGAA-AGTT
* * *
483405 TAGGGGTCAAAAAGTAAATTTTGAAAACTT
1 TA-GGGTCAAAATG-AAATTTTGGAAAGTT
* *
483435 CGAGGGTCAAAAT-ATATTTTTGGAAAGTT
1 -TAGGGTCAAAATGA-AATTTTGGAAAGTT
483464 TAGGG
1 TAGGG
483469 ACTTTTTGGG
Statistics
Matches: 70, Mismatches: 14, Indels: 20
0.67 0.13 0.19
Matches are distributed among these distances:
28 6 0.09
29 29 0.41
30 26 0.37
31 9 0.13
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (28 bp):
TAGGGTCAAAATGAAATTTTGGAAAGTT
Found at i:484285 original size:4 final size:4
Alignment explanation
Indices: 484270--484316 Score: 58
Period size: 4 Copynumber: 11.8 Consensus size: 4
484260 ATATGAATTT
* * * *
484270 TATA TCTA TATA TATA TATA TATA TGTA TGTA TATA TGTA TATA TAT
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TAT
484317 TAAAAACAGG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.51
Consensus pattern (4 bp):
TATA
Found at i:485791 original size:2 final size:2
Alignment explanation
Indices: 485784--485816 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
485774 TCCGCTATTA
485784 AG AG AG AG AG 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
485817 AAACTACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:488985 original size:15 final size:15
Alignment explanation
Indices: 488965--489017 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
488955 ATACTACAAA
488965 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
488980 ATATTTATAATTGTAATT
1 ATATTTATTA-T-TAA-T
*
488998 AATATTTATTATTAAA
1 -ATATTTATTATTAAT
489014 ATAT
1 ATAT
489018 CAATATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 13 0.42
16 1 0.03
17 6 0.19
18 2 0.06
19 9 0.29
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:489070 original size:16 final size:15
Alignment explanation
Indices: 489051--489090 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
489041 TTGTGAAGAA
489051 TATTATTTAAAAATAT
1 TATTATTTAAAAAT-T
489067 TATT-TTT-AAAATT
1 TATTATTTAAAAATT
489080 TATTA-TTAAAA
1 TATTATTTAAAA
489091 TAAAATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 7 0.32
14 8 0.36
15 3 0.14
16 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTATTTAAAAATT
Found at i:489082 original size:13 final size:14
Alignment explanation
Indices: 489049--489092 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 14
489039 ATTTGTGAAG
*
489049 AATATTATT-TAAA
1 AATATTATTATTAA
*
489062 AATATTATTTTTAA
1 AATATTATTATTAA
489076 AAT-TTATTATTAA
1 AATATTATTATTAA
489089 AATA
1 AATA
489093 AAATTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 21 0.78
14 6 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATATTATTATTAA
Found at i:489165 original size:53 final size:53
Alignment explanation
Indices: 489092--489208 Score: 182
Period size: 53 Copynumber: 2.2 Consensus size: 53
489082 TTATTAAAAT
*
489092 AAAATTAAAAT-ATAAAATATAAATAATTAAATACGCATGTTTAATAGTATTG
1 AAAATTATAATAATAAAATATAAATAATTAAATACGCATGTTTAATAGTATTG
* * *
489144 AAAATTATAATAATTAAATATAAATAATTAAATATGTATGTTTAATAGTATTG
1 AAAATTATAATAATAAAATATAAATAATTAAATACGCATGTTTAATAGTATTG
*
489197 AAAAATATAATA
1 AAAATTATAATA
489209 TTTTATATTA
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
52 10 0.17
53 49 0.83
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.37
Consensus pattern (53 bp):
AAAATTATAATAATAAAATATAAATAATTAAATACGCATGTTTAATAGTATTG
Found at i:489169 original size:14 final size:14
Alignment explanation
Indices: 489152--489178 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
489142 TGAAAATTAT
489152 AATAATTAAATATA
1 AATAATTAAATATA
489166 AATAATTAAATAT
1 AATAATTAAATAT
489179 GTATGTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AATAATTAAATATA
Found at i:491382 original size:3 final size:3
Alignment explanation
Indices: 491374--491412 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
491364 AATATATCTA
491374 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
491413 TTGGGAGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:493415 original size:18 final size:18
Alignment explanation
Indices: 493392--493435 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
493382 TTTTTAGCTA
493392 ATAATTATAAATTAAAT-T
1 ATAATTAT-AATTAAATGT
**
493410 ATAATTATTTTTAAATGT
1 ATAATTATAATTAAATGT
493428 ATAATTAT
1 ATAATTAT
493436 CACAACTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
ATAATTATAATTAAATGT
Found at i:494669 original size:67 final size:67
Alignment explanation
Indices: 494596--494727 Score: 178
Period size: 67 Copynumber: 2.0 Consensus size: 67
494586 TTTGTGATCA
* *
494596 TGTGTGAGTGTCCCTAACTTTGTAACCAAAAACTAAAATTC-CTATTGAAAAC-CTAACTTTGTA
1 TGTGTGAGTGTACCTAACTTTGTAACCAAAAACTAAAATTCTC-ATTAAAAACTC-AACTTTGTA
494659 ATTG
64 ATTG
*** *
494663 TGTGTGAGTGTACCTAACTTTGTAATTGAATACTAAAATTCTCATTAAAAACTCAACTTTGTAAT
1 TGTGTGAGTGTACCTAACTTTGTAACCAAAAACTAAAATTCTCATTAAAAACTCAACTTTGTAAT
494728 AAAATGCTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
67 55 0.96
68 2 0.04
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (67 bp):
TGTGTGAGTGTACCTAACTTTGTAACCAAAAACTAAAATTCTCATTAAAAACTCAACTTTGTAAT
TG
Found at i:494797 original size:82 final size:82
Alignment explanation
Indices: 494651--494878 Score: 287
Period size: 82 Copynumber: 2.8 Consensus size: 82
494641 TGAAAACCTA
* * *
494651 ACTTTGTAATTGTGTGTGAGTGTACCTAACTTTGTAATTGAATACTAAAATT-CTCATTAAAAAC
1 ACTTTGTAATTGTGTGTGAGTGTACCCAACTTTGTAATCGAATACTAAAATTCCT-ATTGAAAAC
*
494715 TCAACTTTGTAATAAAAT
65 TCAACTTTGTAACAAAAT
* * * * * *
494733 GCTTTGTAATTGTGTGTGAGTGTGCCCAACTTTGTAATCAAAAATTAAAATTCCTATTGGAAACT
1 ACTTTGTAATTGTGTGTGAGTGTACCCAACTTTGTAATCGAATACTAAAATTCCTATTGAAAACT
* *
494798 TAACTTTGTAACAAAGT
66 CAACTTTGTAACAAAAT
* * * * *
494815 ACTTTGTAAATGTGTGTGGGTGTACCCAATTTTCTAACCGAATACTAAAATTCCTATTGAAAAC
1 ACTTTGTAATTGTGTGTGAGTGTACCCAACTTTGTAATCGAATACTAAAATTCCTATTGAAAAC
494879 CTAATTTTAT
Statistics
Matches: 122, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
82 120 0.98
83 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (82 bp):
ACTTTGTAATTGTGTGTGAGTGTACCCAACTTTGTAATCGAATACTAAAATTCCTATTGAAAACT
CAACTTTGTAACAAAAT
Found at i:495132 original size:58 final size:58
Alignment explanation
Indices: 495012--495134 Score: 149
Period size: 58 Copynumber: 2.1 Consensus size: 58
495002 AAAAGAGTTG
* * * * * *
495012 TTATATAAATAGATATGTTGGTATATATTATAGATTTTGGTATCAGTATAAAATATTT
1 TTATATAAATAGACATGTTGGTATACATTATAAATTTTGATATCAGTATAAAATAATA
* **
495070 TTATATAAATAGACATGTTGTTATACATTATAAATTTTGATATTTGTTATAAAA-AATA
1 TTATATAAATAGACATGTTGGTATACATTATAAATTTTGATATCAG-TATAAAATAATA
495128 TTATATA
1 TTATATA
495135 TTATATAAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 48 0.87
59 7 0.13
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (58 bp):
TTATATAAATAGACATGTTGGTATACATTATAAATTTTGATATCAGTATAAAATAATA
Found at i:495495 original size:39 final size:39
Alignment explanation
Indices: 495452--495526 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
495442 GGGTTTTCAT
**
495452 TTTTCAATAAAAATTTTAATATTTGGTTACAAAGTTAAG
1 TTTTCAATAAAAATTTTAATATTTAATTACAAAGTTAAG
* * *
495491 TTTTCAGTAGAAATTTTAGTATTTAATTACAAAGTT
1 TTTTCAATAAAAATTTTAATATTTAATTACAAAGTT
495527 GGGTACATGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (39 bp):
TTTTCAATAAAAATTTTAATATTTAATTACAAAGTTAAG
Found at i:495565 original size:36 final size:36
Alignment explanation
Indices: 495516--495587 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
495506 TTAGTATTTA
*
495516 ATTACAAAGTTGGGTACATGCACATAAACGAATATT
1 ATTACAAAATTGGGTACATGCACATAAACGAATATT
495552 ATTACAAAATTGGGTACATGCACATAAACGAATATT
1 ATTACAAAATTGGGTACATGCACATAAACGAATATT
495588 CGATTATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (36 bp):
ATTACAAAATTGGGTACATGCACATAAACGAATATT
Found at i:496579 original size:16 final size:16
Alignment explanation
Indices: 496542--496572 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
496532 ATTTCATCTT
*
496542 TATTTATTTTTATGTC
1 TATTTATATTTATGTC
496558 TATTTATATTTATGT
1 TATTTATATTTATGT
496573 TTTTTTACAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.68
Consensus pattern (16 bp):
TATTTATATTTATGTC
Found at i:497126 original size:27 final size:27
Alignment explanation
Indices: 497092--497167 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
497082 CTGAGGATAC
*
497092 TACTCCTATTGTCCCTCCACTTAAGGA
1 TACTCCTATTGTCCCTCCACCTAAGGA
* * * * *
497119 TCCTCCTACTGTTCCTCTACCTGAGGA
1 TACTCCTATTGTCCCTCCACCTAAGGA
497146 TACTCCTACTTCTGTCCCTCCA
1 TACTCCTA--T-TGTCCCTCCA
497168 ATCTTTTCCC
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
27 28 0.78
30 8 0.22
ACGTcount: A:0.17, C:0.38, G:0.11, T:0.34
Consensus pattern (27 bp):
TACTCCTATTGTCCCTCCACCTAAGGA
Found at i:499599 original size:27 final size:26
Alignment explanation
Indices: 499548--499603 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
499538 CTAAGGATAC
* *
499548 TACTCCTATTGTCCTTCCACCTGAGGA
1 TACTCCTACTGTCCCTCCACCTGA-GA
* *
499575 TACTCCTACTGTCCCTCTACTTGAGA
1 TACTCCTACTGTCCCTCCACCTGAGA
499601 TAC
1 TAC
499604 ATTTACTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.20, C:0.34, G:0.12, T:0.34
Consensus pattern (26 bp):
TACTCCTACTGTCCCTCCACCTGAGA
Found at i:504870 original size:21 final size:21
Alignment explanation
Indices: 504846--504887 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
504836 ATTATAGAAG
504846 CAAGCTAAATTGGAAAAGGTC
1 CAAGCTAAATTGGAAAAGGTC
* *
504867 CAAGTTGAATTGGAAAAGGTC
1 CAAGCTAAATTGGAAAAGGTC
504888 TTCAAAGAAG
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:0.40, C:0.12, G:0.26, T:0.21
Consensus pattern (21 bp):
CAAGCTAAATTGGAAAAGGTC
Found at i:509837 original size:24 final size:24
Alignment explanation
Indices: 509771--509828 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
509761 TAAACTCTAC
509771 CTGGGCTCGTAAGAGCTAACCATT
1 CTGGGCTCGTAAGAGCTAACCATT
509795 CTGGGCTCGTAAGAGCTAACCATT
1 CTGGGCTCGTAAGAGCTAACCATT
*
509819 TTGGGCTCGT
1 CTGGGCTCGT
509829 GTGCACTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.28
Consensus pattern (24 bp):
CTGGGCTCGTAAGAGCTAACCATT
Found at i:511970 original size:15 final size:16
Alignment explanation
Indices: 511933--511967 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
511923 TAAAAAAACA
*
511933 AAAATAAATAGACATG
1 AAAATAAATAAACATG
*
511949 AAAATAAATAAAGATG
1 AAAATAAATAAACATG
511965 AAA
1 AAA
511968 TAAGAATAAA
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:0.69, C:0.03, G:0.11, T:0.17
Consensus pattern (16 bp):
AAAATAAATAAACATG
Found at i:514781 original size:25 final size:26
Alignment explanation
Indices: 514731--514800 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 26
514721 CCAAAAAGTC
514731 TATTTA-AATTT-ATATTAAAATTATA
1 TATTTATAATTTAATATTAAAA-TATA
*
514756 TATTTATAATTTAATTTTAAAA-ATA
1 TATTTATAATTTAATATTAAAATATA
* *
514781 TTTTTATATTTTAA-ATTAAA
1 TATTTATAATTTAATATTAAA
514801 TTATGATTGG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
24 5 0.13
25 21 0.54
26 5 0.13
27 8 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TATTTATAATTTAATATTAAAATATA
Found at i:519637 original size:22 final size:21
Alignment explanation
Indices: 519589--519650 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
519579 TAAAAAATTT
*
519589 ATAAAATTATTAAATATTAAA
1 ATAAAATAATTAAATATTAAA
*
519610 ATAAAATAATATAAATATTTTAA
1 ATAAAATAAT-TAAATA-TTAAA
*
519633 A-AAAAT-ATTAAAAATTAA
1 ATAAAATAATTAAATATTAA
519651 TATTGACATG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 3 0.09
20 5 0.14
21 11 0.31
22 11 0.31
23 5 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAAAATAATTAAATATTAAA
Found at i:519985 original size:21 final size:21
Alignment explanation
Indices: 519960--520010 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
519950 TATGTTTTGA
*
519960 TAATTTAAAAAAAATATTTAT-
1 TAATTTAAAAAAAA-ATTGATC
**
519981 TAA-TTAAATGAAAATTGATC
1 TAATTTAAAAAAAAATTGATC
520001 TAATTTAAAA
1 TAATTTAAAA
520011 TATAGTCTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
19 5 0.21
20 11 0.46
21 8 0.33
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (21 bp):
TAATTTAAAAAAAAATTGATC
Found at i:521419 original size:26 final size:26
Alignment explanation
Indices: 521383--521433 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
521373 ATTTTTTAAA
*
521383 AAATATAAAATCT-TTAAATATTTTTT
1 AAATATAAAAT-TATTAAATAATTTTT
521409 AAATATAAAATTATTAAATAATTTT
1 AAATATAAAATTATTAAATAATTTT
521434 AATTTTCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
AAATATAAAATTATTAAATAATTTTT
Found at i:522329 original size:31 final size:28
Alignment explanation
Indices: 522287--522381 Score: 109
Period size: 29 Copynumber: 3.2 Consensus size: 28
522277 ATTGGAAATT
*
522287 AAAATTATTTAATAATTTTATTATTTCAAA
1 AAAATAATTTAATAATTTTA-TATTT-AAA
*
522317 AAAATAATTTTAATAATTTTATATTTTAA
1 AAAATAA-TTTAATAATTTTATATTTAAA
* * *
522346 AAAATAAATTAAAAAGTTTTATATTTTAA
1 AAAATAATTTAATAA-TTTTATATTTAAA
522375 AAAATAA
1 AAAATAA
522382 AATTTAAATT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
28 6 0.10
29 29 0.49
30 11 0.19
31 13 0.22
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (28 bp):
AAAATAATTTAATAATTTTATATTTAAA
Found at i:525299 original size:26 final size:25
Alignment explanation
Indices: 525269--525326 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 25
525259 TAGAATGATT
525269 ATATAAAA-ATTTCAATAAATAAAAAA
1 ATATAAAATATTT-AAT-AATAAAAAA
*
525295 ATATAAAATTATTTAATAATAAAATA
1 ATATAAAA-TATTTAATAATAAAAAA
525321 ATATAA
1 ATATAA
525327 TATAAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 22 0.76
27 3 0.10
28 4 0.14
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (25 bp):
ATATAAAATATTTAATAATAAAAAA
Found at i:525318 original size:16 final size:15
Alignment explanation
Indices: 525294--525341 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
525284 TAAATAAAAA
525294 AATATAAAATTATTT
1 AATATAAAATTATTT
* *
525309 AATAATAAAATAATAT
1 AAT-ATAAAATTATTT
525325 AATATAAATATT-TTT
1 AATATAAA-ATTATTT
525340 AA
1 AA
525342 AAAAATTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATAAAATTATTT
Found at i:529017 original size:17 final size:18
Alignment explanation
Indices: 528985--529018 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
528975 TTATAAAAAT
528985 AATTCAAAATATTTATAA
1 AATTCAAAATATTTATAA
*
529003 AATTCCAAA-ATTTATA
1 AATTCAAAATATTTATA
529019 TTTTTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTCAAAATATTTATAA
Found at i:530863 original size:59 final size:56
Alignment explanation
Indices: 530788--530964 Score: 178
Period size: 59 Copynumber: 3.0 Consensus size: 56
530778 AAAAAAATTG
* *
530788 GGTGTTGGCCATGCAATGGCCGACACTCCTTTTCTGTTAGATAAAAAATTAAATTTTTT
1 GGTGTTGGCCATGCAATGGCCGACACACCTTTT-TG--AGAAAAAAAATTAAATTTTTT
* * *
530847 GGTGTTGGCCATGCAATGACAGACACACTCTTTTTGAGAAAAAAAAATTACA-TTTTT
1 GGTGTTGGCCATGCAATGGCCGACACAC-CTTTTTGAG-AAAAAAAATTAAATTTTTT
* *
530904 GAGTGTTTGCCATTGC-ATGGCCGACACCCCTTTTTTGAGAAAAAAAAAATTAAAATTTTTT
1 G-GTGTTGGCCA-TGCAATGGCCGACACACC-TTTTTGAG--AAAAAAAATT-AAATTTTTT
530965 TATCCGAGAA
Statistics
Matches: 100, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
57 9 0.09
58 38 0.38
59 41 0.41
60 7 0.07
61 5 0.05
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (56 bp):
GGTGTTGGCCATGCAATGGCCGACACACCTTTTTGAGAAAAAAAATTAAATTTTTT
Found at i:531047 original size:64 final size:62
Alignment explanation
Indices: 530944--531153 Score: 278
Period size: 62 Copynumber: 3.4 Consensus size: 62
530934 TTTTTTGAGA
* * * *
530944 AAAAAAAAATTAAAATTTTTTTATCCGAGAAAAGAGGGTGTCGACCATTGCATGGCAAACAC
1 AAAAAAAATTTAAAATTTTTTTATCCGAGAACAGGGGGTGTCGACCATTGCATGGCTAACAC
*
531006 AAAAAAAATTTAAAATTTTTTTTTATCCGAGAACAGGGGGTGTCGGCCATTGCATGGCTAACAC
1 AAAAAAAATTTAAAA--TTTTTTTATCCGAGAACAGGGGGTGTCGACCATTGCATGGCTAACAC
* * * *
531070 CAAAAAAATTTGAAAA-TTTTTTATCCGAGAACATGGGGTGTCGTCCATTGCATGTCTAACAC
1 AAAAAAAATTT-AAAATTTTTTTATCCGAGAACAGGGGGTGTCGACCATTGCATGGCTAACAC
* * *
531132 CAAAAAAATTTGAATTTTTTTT
1 AAAAAAAATTTAAAATTTTTTT
531154 TCTCAAAAAG
Statistics
Matches: 133, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
61 2 0.02
62 74 0.56
64 53 0.40
65 4 0.03
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (62 bp):
AAAAAAAATTTAAAATTTTTTTATCCGAGAACAGGGGGTGTCGACCATTGCATGGCTAACAC
Found at i:531096 original size:126 final size:124
Alignment explanation
Indices: 530945--531200 Score: 315
Period size: 126 Copynumber: 2.0 Consensus size: 124
530935 TTTTTGAGAA
530945 AAAAAAAATTAAAATTTTTTTATCCGAGAA-AAGAGGGTGTCGACCATTGCATGGCAAACACAAA
1 AAAAAAAATTAAAATTTTTTTATCCGAGAACAAG-GGGTGTCGACCATTGCATGGCAAACACAAA
* *
531009 AAAAATTTAAAATTTTTTTTTATCCGAGAACA-GGG-GGTGTCGGCCATTGC-ATGGCTAACACC
65 AAAAATTT-AAATTTTTTTTTAT-C-A-AAAAGGGGAGGTGTCGGCCA-TGCAATGGCCAACACC
* * * * * *
531071 AAAAAAATTTGAAAA-TTTTTTATCCGAGAACATGGGGTGTCGTCCATTGCATGTCTAACACCAA
1 AAAAAAAATT-AAAATTTTTTTATCCGAGAACAAGGGGTGTCGACCATTGCATGGCAAACACAAA
* * *
531135 AAAAATTTGAATTTTTTTTTCTCAAAAAGGGGAGGTGTCGGCTATGCAATGGCCAACACC
65 AAAAATTTAAATTTTTTTTTATCAAAAAGGGGAGGTGTCGGCCATGCAATGGCCAACACC
531195 AAAAAA
1 AAAAAA
531201 TGCAATTTTT
Statistics
Matches: 114, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
122 3 0.03
123 7 0.06
124 28 0.25
125 12 0.11
126 58 0.51
127 6 0.05
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (124 bp):
AAAAAAAATTAAAATTTTTTTATCCGAGAACAAGGGGTGTCGACCATTGCATGGCAAACACAAAA
AAAATTTAAATTTTTTTTTATCAAAAAGGGGAGGTGTCGGCCATGCAATGGCCAACACC
Found at i:531172 original size:62 final size:60
Alignment explanation
Indices: 530946--531281 Score: 254
Period size: 62 Copynumber: 5.5 Consensus size: 60
530936 TTTTGAGAAA
** * * * * *
530946 AAAAAAATTAAAATTTTTTTATC-CGAGAAAAGAGGGTGTCGACCATTGCATGGCAAACACA
1 AAAAAAATTTGAATTTTTTTTTCTC-A-AAAAGGGGGTGTCGGCCATTGCATGGCCAACACC
* * * *
531007 AAAAAAATTTAAAATTTTTTTTTATCCGAGAACAGGGGGTGTCGGCCATTGCATGGCTAACACC
1 AAAAAAATTT-GAATTTTTTTTTCT-C-A-AAAAGGGGGTGTCGGCCATTGCATGGCCAACACC
* * * * * * *
531071 AAAAAAATTTGAAAATTTTTTATC-CGAGAACATGGGGTGTCGTCCATTGCATGTCTAACACC
1 AAAAAAATTTG-AATTTTTTTTTCTC-A-AAAAGGGGGTGTCGGCCATTGCATGGCCAACACC
*
531133 AAAAAAATTTGAATTTTTTTTTCTCAAAAAGGGGAGGTGTCGGCTA-TGCAATGGCCAACACC
1 AAAAAAATTTGAATTTTTTTTTCTCAAAAA-GGG-GGTGTCGGCCATTGC-ATGGCCAACACC
* *** * * **
531195 -AAAAAA--TGCAA-TTTTTTTTCTGAAAAAGGGGGTGTCAATCATTGCACGACCAACATT
1 AAAAAAATTTG-AATTTTTTTTTCTCAAAAAGGGGGTGTCGGCCATTGCATGGCCAACACC
*
531252 AAAAAATTTTGAATTTTTTTTTCTCAAAAA
1 AAAAAAATTTGAATTTTTTTTTCTCAAAAA
531282 AAATGCAATT
Statistics
Matches: 227, Mismatches: 34, Indels: 29
0.78 0.12 0.10
Matches are distributed among these distances:
57 15 0.07
58 11 0.05
59 19 0.08
60 22 0.10
61 31 0.14
62 77 0.34
64 52 0.23
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (60 bp):
AAAAAAATTTGAATTTTTTTTTCTCAAAAAGGGGGTGTCGGCCATTGCATGGCCAACACC
Found at i:531285 original size:84 final size:83
Alignment explanation
Indices: 531195--531365 Score: 263
Period size: 84 Copynumber: 2.0 Consensus size: 83
531185 GGCCAACACC
* * * *
531195 AAAAAATGCAATTTTTTTTCTGAAAAAGGGGGTGTCAATCATTGCACGA-CCAACATTAAAAAAT
1 AAAAAATGCAATTTTTTTTCTGAAAAAGAGGATGTCAACCATTGCA-GAGCCAACATAAAAAAAT
531259 TTTGAATTTTTTTTTCTCAA
65 TTTGAA-TTTTTTTTCTCAA
* *
531279 AAAAAATGCAATTTTTTTTCTGAAAAAGAGGATGTCGACCATTGCATAGCCAACATAAAAAAATT
1 AAAAAATGCAATTTTTTTTCTGAAAAAGAGGATGTCAACCATTGCAGAGCCAACATAAAAAAATT
531344 TTGAATTTTTTTTCTCAA
66 TTGAATTTTTTTTCTCAA
531362 AAAA
1 AAAA
531366 GGGGTGTCAA
Statistics
Matches: 80, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
83 18 0.22
84 62 0.77
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (83 bp):
AAAAAATGCAATTTTTTTTCTGAAAAAGAGGATGTCAACCATTGCAGAGCCAACATAAAAAAATT
TTGAATTTTTTTTCTCAA
Found at i:531339 original size:58 final size:55
Alignment explanation
Indices: 531277--531451 Score: 181
Period size: 58 Copynumber: 3.0 Consensus size: 55
531267 TTTTTTTCTC
531277 AAAAAAAATGCAATTTTTTTTCTGAAAAAGAGGATGTCGACCATTGCATAGCCAACAT
1 AAAAAAAATG-AATTTTTTTTCTGAAAAAGAGG-TGTCGACCATTGCAT-GCCAACAT
* * * *
531335 AAAAAAATTTTGAATTTTTTTTCTCAAAAAAGGGGTGTCAACCATTGCATGGCCAACAT
1 AAAAAAA--ATGAATTTTTTTTCT-GAAAAAGAGGTGTCGACCATTGCAT-GCCAACAT
* * *
531394 -AAAAAAATTAATTTTTTATCTGAGAAAAAAGAGGTGTTGACCATTGCATGACCAACAT
1 AAAAAAAATGAATTTTTTTTCT--G-AAAAAGAGGTGTCGACCATTGCATG-CCAACAT
531452 CCAAAATTAT
Statistics
Matches: 98, Mismatches: 13, Indels: 12
0.80 0.11 0.10
Matches are distributed among these distances:
56 12 0.12
57 1 0.01
58 41 0.42
59 34 0.35
60 10 0.10
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (55 bp):
AAAAAAAATGAATTTTTTTTCTGAAAAAGAGGTGTCGACCATTGCATGCCAACAT
Found at i:531379 original size:59 final size:59
Alignment explanation
Indices: 531288--531451 Score: 178
Period size: 59 Copynumber: 2.8 Consensus size: 59
531278 AAAAAAATGC
* *
531288 AATTTTTTTTCTGAAAAAGAGGATGTCGACCATTGCATAGCCAACATAAAAAAATTTTG
1 AATTTTTTTTCTAAAAAAGAGGATGTCAACCATTGCATAGCCAACATAAAAAAATTTTG
* *
531347 AATTTTTTTTCTCAAAAAAG-GGGTGTCAACCATTGCATGGCCAACATAAAAAAA--TT-
1 AATTTTTTTTCT-AAAAAAGAGGATGTCAACCATTGCATAGCCAACATAAAAAAATTTTG
* **
531403 AATTTTTTATCTGAGAAAAAAGAGG-TGTTGACCATTGCAT-GACCAACAT
1 AATTTTTTTTCT---AAAAAAGAGGATGTCAACCATTGCATAG-CCAACAT
531452 CCAAAATTAT
Statistics
Matches: 92, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
56 11 0.12
57 3 0.03
58 27 0.29
59 45 0.49
60 6 0.07
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (59 bp):
AATTTTTTTTCTAAAAAAGAGGATGTCAACCATTGCATAGCCAACATAAAAAAATTTTG
Found at i:533553 original size:27 final size:26
Alignment explanation
Indices: 533513--533586 Score: 94
Period size: 27 Copynumber: 2.8 Consensus size: 26
533503 CATTTTATAT
533513 TTTTTTTCTAATTTTTAATAAAATTTA
1 TTTTTTTCT-ATTTTTAATAAAATTTA
* *
533540 TTTTATTTCTATTTGTATTAAAATTTA
1 TTTT-TTTCTATTTTTAATAAAATTTA
* *
533567 TTTTTTTATATTTTTTATAA
1 TTTTTTTCTATTTTTAATAA
533587 TTTTTACTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
26 12 0.30
27 23 0.57
28 5 0.12
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (26 bp):
TTTTTTTCTATTTTTAATAAAATTTA
Found at i:536387 original size:220 final size:220
Alignment explanation
Indices: 535999--536439 Score: 733
Period size: 220 Copynumber: 2.0 Consensus size: 220
535989 TTCAACTCAT
535999 ATTTTAAATAGGTCTAATTTTTTTTGTCCAAACTTATTTTTCGAGCTTAATATTTTTATCCAAAC
1 ATTTTAAATAGGTCTAATTTTTTTTGTCCAAACTTATTTTTCGAGCTTAATATTTTTATCCAAAC
*
536064 TCTTCTACATTTAGGATGGACCTTCAAACCTAGACAAATAACGCAACCCATAAACAAATTTAGGT
66 TCTTCTAAATTTAGGATGGACCTTCAAACCTAGACAAATAACGCAACCCATAAACAAATTTAGGT
536129 TTAAGATGTTGGCAAATGTTTTCAAAATGTAGCAATGTAATAATAAAAATAACAATAAGATTTAA
131 TTAAGATGTTGGCAAATGTTTTCAAAATGTAGCAATGTAATAATAAAAATAACAATAAGATTTAA
536194 TTACTCTTTGAATGTTTGAAATCTA
196 TTACTCTTTGAATGTTTGAAATCTA
* * * *
536219 ATTTTTAATAGGTTTAATTTTTTTTGTCCAAACTTATTTTTCGAGTTTAATATTTTTA-CTCAGA
1 ATTTTAAATAGGTCTAATTTTTTTTGTCCAAACTTATTTTTCGAGCTTAATATTTTTATC-CAAA
* * * * *
536283 C-CTTCCTAAATTTCGGATGGACCTTCAAACCTGGACAAGTAGCGCAACCTATAAACAAATTTAG
65 CTCTT-CTAAATTTAGGATGGACCTTCAAACCTAGACAAATAACGCAACCCATAAACAAATTTAG
*
536347 GTTTAAGATGTTGGCAAATGTTTTCAAAATGTAGCAATGTAATAATAAAAATAACAATATGATTT
129 GTTTAAGATGTTGGCAAATGTTTTCAAAATGTAGCAATGTAATAATAAAAATAACAATAAGATTT
* *
536412 AATTATTCTTTGTATGTTTGAAATCTA
194 AATTACTCTTTGAATGTTTGAAATCTA
536439 A
1 A
536440 CTCCATATAC
Statistics
Matches: 206, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
219 4 0.02
220 202 0.98
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (220 bp):
ATTTTAAATAGGTCTAATTTTTTTTGTCCAAACTTATTTTTCGAGCTTAATATTTTTATCCAAAC
TCTTCTAAATTTAGGATGGACCTTCAAACCTAGACAAATAACGCAACCCATAAACAAATTTAGGT
TTAAGATGTTGGCAAATGTTTTCAAAATGTAGCAATGTAATAATAAAAATAACAATAAGATTTAA
TTACTCTTTGAATGTTTGAAATCTA
Found at i:545052 original size:22 final size:22
Alignment explanation
Indices: 545027--545083 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
545017 AAGTTGTTGT
* * *
545027 TTTTGTTATTATTTTGGTGTTA
1 TTTTATTATTATTTTGATATTA
*
545049 TTTTATTATTATATTGATATTA
1 TTTTATTATTATTTTGATATTA
*
545071 TTTTATTGTTATT
1 TTTTATTATTATT
545084 GTTTTGATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.21, C:0.00, G:0.11, T:0.68
Consensus pattern (22 bp):
TTTTATTATTATTTTGATATTA
Found at i:545088 original size:14 final size:14
Alignment explanation
Indices: 545046--545088 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
545036 TATTTTGGTG
545046 TTATT-TTATTATT
1 TTATTGTTATTATT
* *
545059 ATATTGATATTATT
1 TTATTGTTATTATT
*
545073 TTATTGTTATTGTT
1 TTATTGTTATTATT
545087 TT
1 TT
545089 GATATTATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (14 bp):
TTATTGTTATTATT
Found at i:545466 original size:31 final size:32
Alignment explanation
Indices: 545424--545501 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 32
545414 CACCCTTAAG
* *
545424 GTCACTAAACTATGAGTCATTTTCTTT-T-TTA
1 GTCACTCAACTATGA-ACATTTTCTTTATATTA
* *
545455 GTCACTCAACTATGAACTTTTTTTTTATATTA
1 GTCACTCAACTATGAACATTTTCTTTATATTA
*
545487 GTCACCCAACTATGA
1 GTCACTCAACTATGA
545502 TTTTTTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
30 8 0.20
31 15 0.38
32 17 0.43
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (32 bp):
GTCACTCAACTATGAACATTTTCTTTATATTA
Found at i:545510 original size:31 final size:32
Alignment explanation
Indices: 545452--545528 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 32
545442 ATTTTCTTTT
* *
545452 TTAGTCACTCAACTATGAACTTTTTTTTTATA
1 TTAGTCACCCAACTATGAACTTTTTTTTTAAA
*
545484 TTAGTCACCCAACTATG-ATTTTTTTTTTAAA
1 TTAGTCACCCAACTATGAACTTTTTTTTTAAA
545515 TT-GATCA-CCAACTA
1 TTAG-TCACCCAACTA
545529 AACGAGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
30 8 0.20
31 17 0.41
32 16 0.39
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (32 bp):
TTAGTCACCCAACTATGAACTTTTTTTTTAAA
Found at i:547393 original size:23 final size:24
Alignment explanation
Indices: 547358--547407 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
547348 TTTTACAGAA
* *
547358 AAAACTTAGTAAA-TGAGCTTAATT
1 AAAACTTAATAAACGGA-CTTAATT
547382 AAAA-TTAATAAACGGACTTAATT
1 AAAACTTAATAAACGGACTTAATT
547405 AAA
1 AAA
547408 TTCTGAGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (24 bp):
AAAACTTAATAAACGGACTTAATT
Found at i:558421 original size:12 final size:11
Alignment explanation
Indices: 558400--558431 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
558390 AATTTTGTTT
558400 TTATTTTATTA
1 TTATTTTATTA
558411 TTATATTTATTA
1 TTAT-TTTATTA
558423 TTATTTTAT
1 TTATTTTAT
558432 AAATAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:558451 original size:16 final size:16
Alignment explanation
Indices: 558430--558478 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
558420 TTATTATTTT
558430 ATAAATAAATAAACAA
1 ATAAATAAATAAACAA
558446 ATAAATAAATAATA-AA
1 ATAAATAAATAA-ACAA
*
558462 ATTAAA-AAATATACAA
1 A-TAAATAAATAAACAA
558478 A
1 A
558479 CCCAATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 1 0.03
16 23 0.79
17 5 0.17
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (16 bp):
ATAAATAAATAAACAA
Found at i:559351 original size:30 final size:30
Alignment explanation
Indices: 559317--559502 Score: 137
Period size: 30 Copynumber: 6.3 Consensus size: 30
559307 AAAATTATGT
*
559317 TTTGACCTCTAAATTTTTCAAAAATTCAAA
1 TTTGACCTCTAAATTTTCCAAAAATTCAAA
* * *
559347 TTTGA-CTCCAAATTTTCAAAAAATTCGAA
1 TTTGACCTCTAAATTTTCCAAAAATTCAAA
* * **
559376 TTTAACCCCTAAAATTTTCCAAAAATTTGAA
1 TTTGACCTCT-AAATTTTCCAAAAATTCAAA
* *
559407 TTT-A-GTCCTAAA-TTTCCAAAAATTCCAA
1 TTTGACCT-CTAAATTTTCCAAAAATTCAAA
* * * * ***
559435 TTTAACCCCAAAATTTTCCAAAACTTTTGA
1 TTTGACCTCTAAATTTTCCAAAAATTCAAA
* ** *
559465 TTTGACCCCTAAAGCTTCCAAAAATTCAAG
1 TTTGACCTCTAAATTTTCCAAAAATTCAAA
559495 TTTGACCT
1 TTTGACCT
559503 GGTTTTATTT
Statistics
Matches: 120, Mismatches: 30, Indels: 12
0.74 0.19 0.07
Matches are distributed among these distances:
28 17 0.14
29 32 0.27
30 50 0.42
31 21 0.17
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.35
Consensus pattern (30 bp):
TTTGACCTCTAAATTTTCCAAAAATTCAAA
Found at i:559360 original size:29 final size:28
Alignment explanation
Indices: 559331--559457 Score: 112
Period size: 29 Copynumber: 4.4 Consensus size: 28
559321 ACCTCTAAAT
* *
559331 TTTTCAAAAATTCAAATTTGACTCCAAA
1 TTTTCAAAAATTCGAATTTAACTCCAAA
*
559359 TTTTCAAAAAATTCGAATTTAACCCCTAAAA
1 TTTTC-AAAAATTCGAATTTAACTCC--AAA
* *
559390 TTTTCCAAAAATTTGAATTT-AGTCCTAAA
1 TTTT-CAAAAATTCGAATTTAACTCC-AAA
* * *
559419 TTTCCAAAAATTCCAATTTAACCCCAAAA
1 TTTTCAAAAATTCGAATTTAACTCC-AAA
*
559448 TTTTCCAAAA
1 TTTTCAAAAA
559458 CTTTTGATTT
Statistics
Matches: 79, Mismatches: 15, Indels: 9
0.77 0.15 0.09
Matches are distributed among these distances:
28 18 0.23
29 37 0.47
30 3 0.04
31 20 0.25
32 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.03, T:0.35
Consensus pattern (28 bp):
TTTTCAAAAATTCGAATTTAACTCCAAA
Found at i:559464 original size:59 final size:60
Alignment explanation
Indices: 559327--559491 Score: 176
Period size: 59 Copynumber: 2.8 Consensus size: 60
559317 TTTGACCTCT
* ** * * * *
559327 AAATTTTTCAAAAATTCAAATTTGACTCC-AAATTTTCAAAAAATTCGAATTTAACCCCTA
1 AAATTTTCCAAAAATT-TGATTTGACCCCTAAAGTTTCCAAAAATTCCAATTTAACCCCTA
**
559387 AAATTTTCCAAAAATTTGAATTT-AGTCCTAAA-TTTCCAAAAATTCCAATTTAACCCC-A
1 AAATTTTCCAAAAATTTG-ATTTGACCCCTAAAGTTTCCAAAAATTCCAATTTAACCCCTA
* *
559445 AAATTTTCCAAAACTTTTGATTTGACCCCTAAAGCTTCCAAAAATTC
1 AAATTTTCCAAAA-ATTTGATTTGACCCCTAAAGTTTCCAAAAATTC
559492 AAGTTTGACC
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
58 18 0.20
59 38 0.42
60 34 0.38
ACGTcount: A:0.41, C:0.21, G:0.04, T:0.35
Consensus pattern (60 bp):
AAATTTTCCAAAAATTTGATTTGACCCCTAAAGTTTCCAAAAATTCCAATTTAACCCCTA
Found at i:559549 original size:26 final size:27
Alignment explanation
Indices: 559520--559578 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
559510 TTTTTATTTA
* *
559520 TTTATTTTATCTTATATGTATATTAT-
1 TTTATTGTATCTTATATATATATTATC
* * *
559546 TTTATTGTATGTTATGTATATATTGTC
1 TTTATTGTATCTTATATATATATTATC
559573 TTTATT
1 TTTATT
559579 ATGTGTACTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 21 0.78
27 6 0.22
ACGTcount: A:0.24, C:0.03, G:0.08, T:0.64
Consensus pattern (27 bp):
TTTATTGTATCTTATATATATATTATC
Found at i:560860 original size:21 final size:21
Alignment explanation
Indices: 560836--560881 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
560826 ATAAAATATT
*
560836 ATAAATTTTATAATGATTTGC
1 ATAAATTCTATAATGATTTGC
* * *
560857 ATAAATTCTGTAATGTTTTGT
1 ATAAATTCTATAATGATTTGC
560878 ATAA
1 ATAA
560882 TTAGTGTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (21 bp):
ATAAATTCTATAATGATTTGC
Found at i:565507 original size:13 final size:14
Alignment explanation
Indices: 565489--565517 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
565479 AGGCTCATCT
565489 ATTTTT-TAAAAAA
1 ATTTTTGTAAAAAA
565502 ATTTTTGTAAAAAA
1 ATTTTTGTAAAAAA
565516 AT
1 AT
565518 ATTTATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (14 bp):
ATTTTTGTAAAAAA
Found at i:567025 original size:65 final size:65
Alignment explanation
Indices: 566946--567077 Score: 228
Period size: 65 Copynumber: 2.0 Consensus size: 65
566936 CTTTCTACAT
* * * *
566946 TGACAATAATACACATGTTAATTTAGTTAAGATTTAATCGATTTATTGATAATATTATTTAAGAA
1 TGACAATAATACACATGTCAATTTAATTAAGACTCAATCGATTTATTGATAATATTATTTAAGAA
567011 TGACAATAATACACATGTCAATTTAATTAAGACTCAATCGATTTATTGATAATATTATTTAAGAA
1 TGACAATAATACACATGTCAATTTAATTAAGACTCAATCGATTTATTGATAATATTATTTAAGAA
567076 TG
1 TG
567078 TAGAGTTTGA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (65 bp):
TGACAATAATACACATGTCAATTTAATTAAGACTCAATCGATTTATTGATAATATTATTTAAGAA
Found at i:567074 original size:32 final size:31
Alignment explanation
Indices: 566964--567076 Score: 77
Period size: 32 Copynumber: 3.5 Consensus size: 31
566954 ATACACATGT
* * *
566964 TAATTTAGTTAAGATTTAATCGATTTATTGA
1 TAATTTATTTAAGAATCAATCGATTTATTGA
* ** *
566995 TAATATTATTTAAGAATGACAAT-AATACACATG-
1 TAAT-TTATTTAAGAAT--CAATCGATTTA-TTGA
* *
567028 TCAATTTAATTAAGACTCAATCGATTTATTGA
1 T-AATTTATTTAAGAATCAATCGATTTATTGA
567060 TAATATTATTTAAGAAT
1 TAAT-TTATTTAAGAAT
567077 GTAGAGTTTG
Statistics
Matches: 59, Mismatches: 15, Indels: 15
0.66 0.17 0.17
Matches are distributed among these distances:
31 13 0.22
32 24 0.41
33 14 0.24
34 8 0.14
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
TAATTTATTTAAGAATCAATCGATTTATTGA
Found at i:585892 original size:23 final size:23
Alignment explanation
Indices: 585771--585892 Score: 138
Period size: 23 Copynumber: 5.2 Consensus size: 23
585761 AGCGCACTCA
*
585771 CTGTTTAGCAC-GTCTTGTGCTCT
1 CTGTTTAGCACTGT-GTGTGCTCT
585794 CTGTTATTAGCACTGTGTGTGCTCT
1 CTG-T-TTAGCACTGTGTGTGCTCT
* *
585819 CTGATTAGCACTTTGTGTGCTCT
1 CTGTTTAGCACTGTGTGTGCTCT
* * * *
585842 CTGATTAGTACTTTGTGTACTCT
1 CTGTTTAGCACTGTGTGTGCTCT
*
585865 CTGTTTAGTACTGTGTGTGCTCT
1 CTGTTTAGCACTGTGTGTGCTCT
585888 CTGTT
1 CTGTT
585893 GCCCAGCACT
Statistics
Matches: 88, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
23 67 0.76
24 1 0.01
25 18 0.20
26 2 0.02
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.46
Consensus pattern (23 bp):
CTGTTTAGCACTGTGTGTGCTCT
Found at i:585933 original size:69 final size:69
Alignment explanation
Indices: 585790--585939 Score: 191
Period size: 69 Copynumber: 2.1 Consensus size: 69
585780 ACGTCTTGTG
*
585790 CTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTT
1 CTCTCTG-T-TTAGCACTGTGTGTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGTACTT
585855 TGTGTA
64 TGTGTA
*
585861 CTCTCTGTTTAGTACTGTGTGTGCTCTCTG-TTGCCCAGCAC-TTATGTGCTCTCTG-TTAGTAC
1 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGATT----AGCACTTTATGTGCTCTCTGATTAGTAC
585923 TTTG-GTA
62 TTTGTGTA
*
585930 CTCTTTGTTT
1 CTCTCTGTTT
585940 GTTTCGTATA
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
68 2 0.03
69 33 0.46
70 12 0.17
71 20 0.28
72 5 0.07
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (69 bp):
CTCTCTGTTTAGCACTGTGTGTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGTACTTTG
TGTA
Found at i:586804 original size:15 final size:15
Alignment explanation
Indices: 586763--586826 Score: 76
Period size: 15 Copynumber: 4.2 Consensus size: 15
586753 ACCATTTGAT
* *
586763 TAAAATTAAGAAT-T
1 TAAAATTAAAAATAA
586777 TAAAATTTAAAAAGTAA
1 TAAAA-TTAAAAA-TAA
586794 TAAAATTAAAAATAA
1 TAAAATTAAAAATAA
*
586809 TCAAATTAAAAATAA
1 TAAAATTAAAAATAA
586824 TAA
1 TAA
586827 TTTACATATA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
14 5 0.12
15 25 0.58
16 8 0.19
17 5 0.12
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.30
Consensus pattern (15 bp):
TAAAATTAAAAATAA
Found at i:586910 original size:12 final size:12
Alignment explanation
Indices: 586893--586926 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
586883 TCATATACAA
*
586893 ATATTATTATGT
1 ATATTATTATGC
586905 ATATTATTATGC
1 ATATTATTATGC
*
586917 ATATTGTTAT
1 ATATTATTAT
586927 AACTTATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (12 bp):
ATATTATTATGC
Found at i:595112 original size:38 final size:38
Alignment explanation
Indices: 595025--595725 Score: 598
Period size: 38 Copynumber: 18.4 Consensus size: 38
595015 ATTAGGAACT
* * * * * *
595025 AAGCTCGATAAACACCAGCACATAGTCTGTTTGGCATGA
1 AAGCCCGATAAACACCGGCACATAGCCTGCTAGGCA-CA
* * *
595064 AA-CCAGATAAACACCGGCACATAGCTTGTTAGGCACA
1 AAGCCCGATAAACACCGGCACATAGCCTGCTAGGCACA
* * *
595101 AAGCCCAATAAAACACTGGCACATAGCCTACTAGGCACA
1 AAGCCCGAT-AAACACCGGCACATAGCCTGCTAGGCACA
* ** * * * * *
595140 AAGCCCGATAAATATTGACATAAAGCTTGCTAGGCACT
1 AAGCCCGATAAACACCGGCACATAGCCTGCTAGGCACA
* * *
595178 AACCCCGATAAACACCAGCACATAGCCTGCTAGGCATA
1 AAGCCCGATAAACACCGGCACATAGCCTGCTAGGCACA
* * * * * **
595216 AAGCCCAATAAACATCAGCAAAAAGCCTGCTAGGCATT
1 AAGCCCGATAAACACCGGCACATAGCCTGCTAGGCACA
** *
595254 AAGCCCGATAAACACTTGCACATAGCCTGCTAAGCACA
1 AAGCCCGATAAACACCGGCACATAGCCTGCTAGGCACA
* * * * * * * *
595292 AAGCCCAATAAATATCGACACAAAGCCTACTAAGCACT
1 AAGCCCGATAAACACCGGCACATAGCCTGCTAGGCACA
* * * *
595330 AAGCCCGATAAATACCGGTACATAACCTGTTAGGCACA
1 AAGCCCGATAAACACCGGCACATAGCCTGCTAGGCACA
* * * * * * * *
595368 AAGCTCGATATATATCGGCATAAAGCTTGCTAGGCACT
1 AAGCCCGATAAACACCGGCACATAGCCTGCTAGGCACA
* *
595406 AAGCCCAATAAACACCGGCACATAGCCTGTTAGGCACA
1 AAGCCCGATAAACACCGGCACATAGCCTGCTAGGCACA
* * *
595444 AAGCCCGATAAACACCAGCACAAAGCTTGCTAGGCA-A
1 AAGCCCGATAAACACCGGCACATAGCCTGCTAGGCACA
*
595481 TAAGCCCGATAAACACCGGCACATAGCCTGCTAGGTACA
1 -AAGCCCGATAAACACCGGCACATAGCCTGCTAGGCACA
* * * *
595520 AAGCCTGATAAACACCGGCATAAAGCCTGCTAGGCACT
1 AAGCCCGATAAACACCGGCACATAGCCTGCTAGGCACA
* * *
595558 AAGCCCGATAAATACAGGCACATAGCTTGCTAGGCACA
1 AAGCCCGATAAACACCGGCACATAGCCTGCTAGGCACA
* * * * * **
595596 AAGCCCGATAAACACTGGAAAAAAGCCTACTAGGCATT
1 AAGCCCGATAAACACCGGCACATAGCCTGCTAGGCACA
** *
595634 AAGCCCGATAAACACAAGCACATAG-TTGCTAGGCACA
1 AAGCCCGATAAACACCGGCACATAGCCTGCTAGGCACA
* * * * * **
595671 AAGCTCGATAAATACCAGCACAAAACCTGCTAGGCATT
1 AAGCCCGATAAACACCGGCACATAGCCTGCTAGGCACA
*
595709 GAGCCCGATAAACACCG
1 AAGCCCGATAAACACCG
595726 ACATAATCAC
Statistics
Matches: 519, Mismatches: 138, Indels: 11
0.78 0.21 0.02
Matches are distributed among these distances:
37 32 0.06
38 451 0.87
39 36 0.07
ACGTcount: A:0.38, C:0.28, G:0.18, T:0.16
Consensus pattern (38 bp):
AAGCCCGATAAACACCGGCACATAGCCTGCTAGGCACA
Found at i:595213 original size:76 final size:76
Alignment explanation
Indices: 594992--595725 Score: 690
Period size: 76 Copynumber: 9.7 Consensus size: 76
594982 GCATTAACCT
* * * ** * * * * * *
594992 CGATAACCATCGACACAAACCCTATTAGGAACTAAGCTCGATAAACACCAGCACATAGTCTGTTT
1 CGATAAACATCGACATAAAGCCTGCTAGGCACTAAGCCCGATAAACACCGGCACATAGCCTGCTA
*
595057 GGCATGAAA-CC
66 GGCA-CAAAGCC
* * * * * * * * * * *
595068 AGATAAACACCGGCACATAGCTTGTTAGGCACAAAGCCCAATAAAACACTGGCACATAGCCTACT
1 CGATAAACATCGACATAAAGCCTGCTAGGCACTAAGCCCGAT-AAACACCGGCACATAGCCTGCT
595133 AGGCACAAAGCC
65 AGGCACAAAGCC
* * * * *
595145 CGATAAATATTGACATAAAGCTTGCTAGGCACTAACCCCGATAAACACCAGCACATAGCCTGCTA
1 CGATAAACATCGACATAAAGCCTGCTAGGCACTAAGCCCGATAAACACCGGCACATAGCCTGCTA
*
595210 GGCATAAAGCC
66 GGCACAAAGCC
* * * **
595221 CAATAAACATC-AGCAAAAAGCCTGCTAGGCATTAAGCCCGATAAACACTTGCACATAGCCTGCT
1 CGATAAACATCGA-CATAAAGCCTGCTAGGCACTAAGCCCGATAAACACCGGCACATAGCCTGCT
*
595285 AAGCACAAAGCC
65 AGGCACAAAGCC
* * * * * * * * *
595297 CAATAAATATCGACACAAAGCCTACTAAGCACTAAGCCCGATAAATACCGGTACATAACCTGTTA
1 CGATAAACATCGACATAAAGCCTGCTAGGCACTAAGCCCGATAAACACCGGCACATAGCCTGCTA
*
595362 GGCACAAAGCT
66 GGCACAAAGCC
* * * * * *
595373 CGATATATATCGGCATAAAGCTTGCTAGGCACTAAGCCCAATAAACACCGGCACATAGCCTGTTA
1 CGATAAACATCGACATAAAGCCTGCTAGGCACTAAGCCCGATAAACACCGGCACATAGCCTGCTA
595438 GGCACAAAGCC
66 GGCACAAAGCC
* * * *
595449 CGATAAACA-CCAGCACAAAGCTTGCTAGGCAATAAGCCCGATAAACACCGGCACATAGCCTGCT
1 CGATAAACATCGA-CATAAAGCCTGCTAGGCACTAAGCCCGATAAACACCGGCACATAGCCTGCT
*
595513 AGGTACAAAGCC
65 AGGCACAAAGCC
* * * * * *
595525 TGATAAACACCGGCATAAAGCCTGCTAGGCACTAAGCCCGATAAATACAGGCACATAGCTTGCTA
1 CGATAAACATCGACATAAAGCCTGCTAGGCACTAAGCCCGATAAACACCGGCACATAGCCTGCTA
595590 GGCACAAAGCC
66 GGCACAAAGCC
* * * * ** *
595601 CGATAAACACTGGA-AAAAAGCCTACTAGGCATTAAGCCCGATAAACACAAGCACATAG-TTGCT
1 CGATAAACA-TCGACATAAAGCCTGCTAGGCACTAAGCCCGATAAACACCGGCACATAGCCTGCT
*
595664 AGGCACAAAGCT
65 AGGCACAAAGCC
* * * *
595676 CGATAAATACCAGCACA-AAA-CCTGCTAGGCATTGAGCCCGATAAACACCG
1 CGATAAACATC-G-ACATAAAGCCTGCTAGGCACTAAGCCCGATAAACACCG
595726 ACATAATCAC
Statistics
Matches: 542, Mismatches: 106, Indels: 21
0.81 0.16 0.03
Matches are distributed among these distances:
75 53 0.10
76 431 0.80
77 58 0.11
ACGTcount: A:0.38, C:0.28, G:0.18, T:0.16
Consensus pattern (76 bp):
CGATAAACATCGACATAAAGCCTGCTAGGCACTAAGCCCGATAAACACCGGCACATAGCCTGCTA
GGCACAAAGCC
Found at i:595337 original size:152 final size:152
Alignment explanation
Indices: 594992--595723 Score: 772
Period size: 152 Copynumber: 4.8 Consensus size: 152
594982 GCATTAACCT
* * * * * * * *
594992 CGATAACCATCGACACAAACCCTATTAGGAACTAAGCTCGATAAACACCAGCACATAGTCTGTTT
1 CGATAAACATCGACACAAAGCCTACTAGGCACTAAGCCCGATAAACACCAGCACATAGCCTGCTA
* * * * * * * *
595057 GGCATGAAA-CCAGATAAACACCGGCACATAGCTTGTTAGGCACAAAGCCCAATAAAACACTGGC
66 GGCA-CAAAGCCCGATAAACACCGGCAAAAAGCCTGCTAGGCACTAAGCCCGAT-AAACACTGGC
*
595121 ACATAGCCTACTAGGCACAAAGCC
129 ACATAGCCTGCTAGGCACAAAGCC
* * * * * *
595145 CGATAAATATTGACATAAAGCTTGCTAGGCACTAACCCCGATAAACACCAGCACATAGCCTGCTA
1 CGATAAACATCGACACAAAGCCTACTAGGCACTAAGCCCGATAAACACCAGCACATAGCCTGCTA
* * * * * *
595210 GGCATAAAGCCCAATAAACATCAGCAAAAAGCCTGCTAGGCATTAAGCCCGATAAACACTTGCAC
66 GGCACAAAGCCCGATAAACACCGGCAAAAAGCCTGCTAGGCACTAAGCCCGATAAACACTGGCAC
*
595275 ATAGCCTGCTAAGCACAAAGCC
131 ATAGCCTGCTAGGCACAAAGCC
* * * * * * * *
595297 CAATAAATATCGACACAAAGCCTACTAAGCACTAAGCCCGATAAATACCGGTACATAACCTGTTA
1 CGATAAACATCGACACAAAGCCTACTAGGCACTAAGCCCGATAAACACCAGCACATAGCCTGCTA
* * * * * * * *
595362 GGCACAAAGCTCGATATATATCGGCATAAAGCTTGCTAGGCACTAAGCCCAATAAACACCGGCAC
66 GGCACAAAGCCCGATAAACACCGGCAAAAAGCCTGCTAGGCACTAAGCCCGATAAACACTGGCAC
*
595427 ATAGCCTGTTAGGCACAAAGCC
131 ATAGCCTGCTAGGCACAAAGCC
* * * * *
595449 CGATAAACA-CCAGCACAAAGCTTGCTAGGCAATAAGCCCGATAAACACCGGCACATAGCCTGCT
1 CGATAAACATCGA-CACAAAGCCTACTAGGCACTAAGCCCGATAAACACCAGCACATAGCCTGCT
* * * * *
595513 AGGTACAAAGCCTGATAAACACCGGCATAAAGCCTGCTAGGCACTAAGCCCGATAAATACAGGCA
65 AGGCACAAAGCCCGATAAACACCGGCAAAAAGCCTGCTAGGCACTAAGCCCGATAAACACTGGCA
*
595578 CATAGCTTGCTAGGCACAAAGCC
130 CATAGCCTGCTAGGCACAAAGCC
* * * * *
595601 CGATAAACACTGGA-AAAAAGCCTACTAGGCATTAAGCCCGATAAACACAAGCACATAG-TTGCT
1 CGATAAACA-TCGACACAAAGCCTACTAGGCACTAAGCCCGATAAACACCAGCACATAGCCTGCT
* * * * *
595664 AGGCACAAAGCTCGATAAATACCAGCACAAAA-CCTGCTAGGCATTGAGCCCGATAAACAC
65 AGGCACAAAGCCCGATAAACACCGGCA-AAAAGCCTGCTAGGCACTAAGCCCGATAAACAC
595724 CGACATAATC
Statistics
Matches: 478, Mismatches: 96, Indels: 12
0.82 0.16 0.02
Matches are distributed among these distances:
151 53 0.11
152 336 0.70
153 88 0.18
154 1 0.00
ACGTcount: A:0.38, C:0.28, G:0.18, T:0.17
Consensus pattern (152 bp):
CGATAAACATCGACACAAAGCCTACTAGGCACTAAGCCCGATAAACACCAGCACATAGCCTGCTA
GGCACAAAGCCCGATAAACACCGGCAAAAAGCCTGCTAGGCACTAAGCCCGATAAACACTGGCAC
ATAGCCTGCTAGGCACAAAGCC
Found at i:611269 original size:22 final size:23
Alignment explanation
Indices: 611237--611279 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
611227 TTTACATAAA
611237 CGCCGCAAAAGGT-AGAGCAAAG
1 CGCCGCAAAAGGTCAGAGCAAAG
*
611259 CGCCGCTAAAGGTCAGAGCAA
1 CGCCGCAAAAGGTCAGAGCAA
611280 TAACGGCGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.37, C:0.26, G:0.30, T:0.07
Consensus pattern (23 bp):
CGCCGCAAAAGGTCAGAGCAAAG
Found at i:611312 original size:41 final size:41
Alignment explanation
Indices: 611255--611697 Score: 530
Period size: 41 Copynumber: 10.8 Consensus size: 41
611245 AAGGTAGAGC
* *
611255 AAAGCGCCGCTAAAGGTCAGAGCAATAACGGCGCTTATGGA
1 AAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGG
611296 AAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGG
1 AAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGG
* ** * **
611337 CAAGCATCGCTAAAGGTCAGAGCAATAGCGACGCTTATGTT
1 AAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGG
** * *
611378 AAAGCGTGGCTAAAGGTCAGAGCAATAGTGGCGCTTGTGGG
1 AAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGG
* *
611419 AAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGTTTATGGT
1 AAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGG
* * *
611460 CAAGCACCGCTAAAGGTCATAGCAATAGCGGCGCTTATGGG
1 AAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGG
* * * *
611501 AAAGCACCGCTAAAGGTCATATCAATAGCAGCGCTTATGGG
1 AAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGG
* *
611542 CAAGCGCCGCTAAAGGTCAGAGCAATAGCGGTGCTTATGGG
1 AAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGG
* * * ** *
611583 AAAGTGCCGCTAAAGGTCAGAGCATTAGCGACATTTATGGT
1 AAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGG
* * *
611624 AAAGCGCCGTTAAAGGTTAGAG-AATTAGCGGCGTTTACT-GG
1 AAAGCGCCGCTAAAGGTCAGAGCAA-TAGCGGCGCTTA-TGGG
* * * *
611665 AAAACGTCGCTAAAGGTCAGAGCATTAGTGGCG
1 AAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCG
611698 TTTTCCCATA
Statistics
Matches: 342, Mismatches: 57, Indels: 6
0.84 0.14 0.01
Matches are distributed among these distances:
40 1 0.00
41 339 0.99
42 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.19
Consensus pattern (41 bp):
AAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGG
Found at i:616903 original size:13 final size:14
Alignment explanation
Indices: 616887--616915 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
616877 TTTTAAATAT
616887 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
616900 TTATAATGGTTTAA
1 TTATAATGGTTTAA
616914 TT
1 TT
616916 CATCGTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:617819 original size:43 final size:43
Alignment explanation
Indices: 617701--618141 Score: 427
Period size: 43 Copynumber: 10.3 Consensus size: 43
617691 ATCTGTTAAT
* * *
617701 TTTAGCGGCGTCTGT--GGAAAGAACGCCGCTAAAGAACACTATT-
1 TTTAGCGGCGTTTGTGAGGAAAG--CGCCGCTAAAGACCA-TGTTC
* * * *
617744 TATAGC-GCGTTTGTG-GAGTAAGTGCCGTTAAAGA-CAGTGTTC
1 TTTAGCGGCGTTTGTGAG-GAAAGCGCCGCTAAAGACCA-TGTTC
* * * *
617786 TTTAGCGGCATTTGTGAGAAAAGCGCTGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGAGGAAAGCGCCGCTAAAGACCATGTTC
* * *
617829 TTTAGTGGCGTTTGTGGGGGAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGAGGAAAGCGCCGCTAAAGACCATGTTC
*
617872 TTTAGCGGCGTTTGTGAGGGAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGAGGAAAGCGCCGCTAAAGACCATGTTC
* * * *
617915 TTTAACAGCTTTTGTTGA-GAAAGCGCCTCTAAAGACCATGTTC
1 TTTAGCGGCGTTTG-TGAGGAAAGCGCCGCTAAAGACCATGTTC
* *
617958 TTTAACGGCGTTTGTG-GGAAAGCGCTGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGAGGAAAGCGCCGCTAAAGACCATGTTC
* * * *
618000 TTTAGCGGCATTTGTGGGGGAAGCACCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGAGGAAAGCGCCGCTAAAGACCATGTTC
*
618043 TATAGCGGCGTTTGTG-GGTAAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGAGG-AAAGCGCCGCTAAAGACCATGTTC
* * * * * *
618086 TTTAACGACATTTGTTGA-AAAAGTGTCGCTAAAGACCATGTT-
1 TTTAGCGGCGTTTG-TGAGGAAAGCGCCGCTAAAGACCATGTTC
*
618128 TTATAGCGGGGTTT
1 TT-TAGCGGCGTTT
618142 TTTCTTATAA
Statistics
Matches: 333, Mismatches: 52, Indels: 26
0.81 0.13 0.06
Matches are distributed among these distances:
41 5 0.02
42 65 0.20
43 251 0.75
44 12 0.04
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGAGGAAAGCGCCGCTAAAGACCATGTTC
Found at i:617986 original size:171 final size:172
Alignment explanation
Indices: 617767--618127 Score: 532
Period size: 171 Copynumber: 2.1 Consensus size: 172
617757 TGGAGTAAGT
* * *
617767 GCCGTTAAAGA-CAGTGTTCTTTAGCGGCATTTGTGAGAAAAGCGCTGCTAAAGATCATGTTCTT
1 GCCGCTAAAGACCA-TGTTCTTTAACGGCATTTGTGAGAAAAGCGCTGCTAAAGACCATGTTCTT
* * * * *
617831 TAGTGGCGTTTGTGGGGGAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGAGG-GAAG
65 TAGCGGCATTTGTGGGGGAAGCACCGCTAAAGACCATGTTCTATAGCGGCGTTTGTG-GGTAAAG
* *
617895 CGCCGCTAAAGACCATGTTCTTTAAC-AGCTTTTGTTGAGAAAGC
129 CGCCGCTAAAGACCATGTTCTTTAACGA-CATTTGTTGAAAAAGC
* * *
617939 GCCTCTAAAGACCATGTTCTTTAACGGCGTTTGTG-GGAAAGCGCTGCTAAAGACCATGTTCTTT
1 GCCGCTAAAGACCATGTTCTTTAACGGCATTTGTGAGAAAAGCGCTGCTAAAGACCATGTTCTTT
618003 AGCGGCATTTGTGGGGGAAGCACCGCTAAAGACCATGTTCTATAGCGGCGTTTGTGGGTAAAGCG
66 AGCGGCATTTGTGGGGGAAGCACCGCTAAAGACCATGTTCTATAGCGGCGTTTGTGGGTAAAGCG
*
618068 CCGCTAAAGACCATGTTCTTTAACGACATTTGTTGAAAAAGT
131 CCGCTAAAGACCATGTTCTTTAACGACATTTGTTGAAAAAGC
*
618110 GTCGCTAAAGACCATGTT
1 GCCGCTAAAGACCATGTT
618128 TTATAGCGGG
Statistics
Matches: 170, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
170 2 0.01
171 137 0.81
172 29 0.17
173 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (172 bp):
GCCGCTAAAGACCATGTTCTTTAACGGCATTTGTGAGAAAAGCGCTGCTAAAGACCATGTTCTTT
AGCGGCATTTGTGGGGGAAGCACCGCTAAAGACCATGTTCTATAGCGGCGTTTGTGGGTAAAGCG
CCGCTAAAGACCATGTTCTTTAACGACATTTGTTGAAAAAGC
Done.