Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008650.1 Hibiscus syriacus cultivar Beakdansim tig00111640_pilon, 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: 1713193
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:345328 original size:30 final size:30
Alignment explanation
Indices: 345294--345469 Score: 248
Period size: 30 Copynumber: 5.9 Consensus size: 30
345284 CCGAAGAAGG
345294 TACTTCTTGATGGGGCACTTCATGACAACC
1 TACTTCTTGATGGGGCACTTCATGACAACC
*
345324 TACTTCCTGATGGGGCACTTCATGACAACC
1 TACTTCTTGATGGGGCACTTCATGACAACC
*
345354 TACTTCCTGATGGGGCACTTCATGACAACC
1 TACTTCTTGATGGGGCACTTCATGACAACC
** *
345384 TACAACTTGATGGGGCACTTCATGACAAGC
1 TACTTCTTGATGGGGCACTTCATGACAACC
* *
345414 -ATCTTCTTGATGGGGCATTTCATGACAAGC
1 TA-CTTCTTGATGGGGCACTTCATGACAACC
*
345444 -ATCTTCTTGATGGGGCATTTCATGAC
1 TA-CTTCTTGATGGGGCACTTCATGAC
345470 GAGCATCTTC
Statistics
Matches: 137, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
29 1 0.01
30 136 0.99
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.30
Consensus pattern (30 bp):
TACTTCTTGATGGGGCACTTCATGACAACC
Found at i:352712 original size:30 final size:30
Alignment explanation
Indices: 352650--352712 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
352640 TGTTTTTCTG
* **
352650 ATATGTGTTCATATCAGTTTATAATTTCTT
1 ATATGTGTTCATATCAGTTTACAATTAATT
352680 ATATGTGTTCATATCAGTTT-CAATTGAATT
1 ATATGTGTTCATATCAGTTTACAATT-AATT
352710 ATA
1 ATA
352713 AGTTGCAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.30, C:0.10, G:0.11, T:0.49
Consensus pattern (30 bp):
ATATGTGTTCATATCAGTTTACAATTAATT
Found at i:362490 original size:37 final size:37
Alignment explanation
Indices: 362440--362510 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
362430 ATTTAGATTT
*
362440 AATCGATTTTATTTTTAGAGTATTTATCAATAGAATA
1 AATCGATTTTATTTTTAAAGTATTTATCAATAGAATA
*
362477 AATCGGTTTTATTTTTAAAGTATTTATCAATAGA
1 AATCGATTTTATTTTTAAAGTATTTATCAATAGA
362511 TTAAGAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (37 bp):
AATCGATTTTATTTTTAAAGTATTTATCAATAGAATA
Found at i:363502 original size:31 final size:31
Alignment explanation
Indices: 363400--363502 Score: 116
Period size: 31 Copynumber: 3.2 Consensus size: 31
363390 CCTCATTTCC
* * *
363400 AAGTGACCAAAACTTAATAAAACAATAACAT
1 AAGTGACAAAAACTTAATAAAACGATAACGT
* *
363431 AAGTGAAAAAAACCTAATGATAAAACGATAACGT
1 AAGTGACAAAAA-CT--TAATAAAACGATAACGT
* *
363465 AAGTGACTAAAACTTAATAAAACGATAATGT
1 AAGTGACAAAAACTTAATAAAACGATAACGT
363496 AAGTGAC
1 AAGTGAC
363503 CAAATATATA
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
31 32 0.53
32 2 0.03
33 2 0.03
34 24 0.40
ACGTcount: A:0.54, C:0.13, G:0.13, T:0.20
Consensus pattern (31 bp):
AAGTGACAAAAACTTAATAAAACGATAACGT
Found at i:364711 original size:25 final size:25
Alignment explanation
Indices: 364627--364711 Score: 66
Period size: 25 Copynumber: 3.4 Consensus size: 25
364617 TTTTATATAC
* *
364627 ATATAATATAATTGTAATAATATTATG
1 ATATTATAT-ATTATAATAATA-TATG
* * * *
364654 TTTTTA-ATATTATATTAATATATA
1 ATATTATATATTATAATAATATATG
*
364678 ATCA-GATATATTATAATAATATATG
1 AT-ATTATATATTATAATAATATATG
364703 ATATTATAT
1 ATATTATAT
364712 TTTTAAATAA
Statistics
Matches: 43, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
24 6 0.14
25 32 0.74
26 2 0.05
27 3 0.07
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (25 bp):
ATATTATATATTATAATAATATATG
Found at i:364810 original size:6 final size:6
Alignment explanation
Indices: 364799--364848 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
364789 TCTTTTAAAA
*
364799 AATATT AATATT AAT-TA AATATTT AATATT AATA-T AATAATTT AATATT
1 AATATT AATATT AATATT AATA-TT AATATT AATATT AAT-A-TT AATATT
364848 A
1 A
364849 TGTTAATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
5 8 0.22
6 19 0.51
7 6 0.16
8 4 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATATT
Found at i:364826 original size:18 final size:17
Alignment explanation
Indices: 364793--364848 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 17
364783 CCCGTTTCTT
*
364793 TTAAAAAATA-TTAATA
1 TTAATAAATATTTAATA
364809 TTAATTAAATATTTAATA
1 TTAA-TAAATATTTAATA
364827 TTAATATAATAATTTAATA
1 TTAATA-AAT-ATTTAATA
364846 TTA
1 TTA
364849 TGTTAATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
16 4 0.11
17 7 0.20
18 13 0.37
19 11 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAATAAATATTTAATA
Found at i:364846 original size:26 final size:24
Alignment explanation
Indices: 364799--364847 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
364789 TCTTTTAAAA
364799 AATATTAATATTAATTAAATATTT
1 AATATTAATATTAATTAAATATTT
*
364823 AATATTAATATAATAATTTAATATT
1 AATATTAATAT--TAATTAAATATT
364848 ATGTTAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.50
26 11 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AATATTAATATTAATTAAATATTT
Found at i:364857 original size:19 final size:19
Alignment explanation
Indices: 364803--364848 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
364793 TTAAAAAATA
364803 TTAATATTAAT-TAA-ATAT
1 TTAATATTAATATAATA-AT
364821 TTAATATTAATATAATAAT
1 TTAATATTAATATAATAAT
364840 TTAATATTA
1 TTAATATTA
364849 TGTTAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 11 0.42
19 14 0.54
20 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAATATTAATATAATAAT
Found at i:366503 original size:2 final size:2
Alignment explanation
Indices: 366496--366535 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
366486 TAATTTTAAA
366496 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
366536 GAAATAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:367445 original size:27 final size:27
Alignment explanation
Indices: 367415--367470 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
367405 GGTCGAGTTT
*
367415 GGGTCAGGTGAAAGG-TGTATATTTTTC
1 GGGTCAGGTG-AAGGATGTATAATTTTC
* *
367442 GGGTCGGGTGGAGGATGTATAATTTTC
1 GGGTCAGGTGAAGGATGTATAATTTTC
367469 GG
1 GG
367471 TTAGATCGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 3 0.12
27 22 0.88
ACGTcount: A:0.20, C:0.07, G:0.39, T:0.34
Consensus pattern (27 bp):
GGGTCAGGTGAAGGATGTATAATTTTC
Found at i:374237 original size:10 final size:10
Alignment explanation
Indices: 374222--374247 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
374212 AGGCAGTAAG
374222 AGCCAAAAGA
1 AGCCAAAAGA
374232 AGCCAAAAGA
1 AGCCAAAAGA
374242 AGCCAA
1 AGCCAA
374248 GTTGCTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.58, C:0.23, G:0.19, T:0.00
Consensus pattern (10 bp):
AGCCAAAAGA
Found at i:380557 original size:32 final size:32
Alignment explanation
Indices: 380487--380649 Score: 103
Period size: 34 Copynumber: 4.6 Consensus size: 32
380477 AGGCCCAATC
380487 ATTATATAGTTTTCAAAATGATTTTTAAAAAT
1 ATTATATAGTTTTCAAAATGATTTTTAAAAAT
*
380519 ATTATATAAGTTTTCCAAAATGTTTTTTAAACTATAT
1 ATTATAT-AGTTTT-CAAAATGATTTTTAAA--A-AT
* * *
380556 ATTATATAAATTTTCCAAAAAATGTTTTTTTTAAAACT
1 ATTATAT-AGTTTT-C--AAAATG--ATTTTTAAAAAT
* **
380594 ATACATTATA-TTTTCAAAATGATTTCAAAACTATAT
1 AT-TA-TATAGTTTTCAAAATGATTTTTAAA--A-AT
*
380630 ATTATATAATTTTCAAAATG
1 ATTATATAGTTTTCAAAATG
380650 CTTTAAAACT
Statistics
Matches: 107, Mismatches: 9, Indels: 27
0.75 0.06 0.19
Matches are distributed among these distances:
32 7 0.07
33 12 0.11
34 19 0.18
35 19 0.18
36 4 0.04
37 18 0.17
38 7 0.07
39 9 0.08
40 3 0.03
41 9 0.08
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.46
Consensus pattern (32 bp):
ATTATATAGTTTTCAAAATGATTTTTAAAAAT
Found at i:380642 original size:35 final size:35
Alignment explanation
Indices: 380487--380756 Score: 184
Period size: 37 Copynumber: 7.5 Consensus size: 35
380477 AGGCCCAATC
*
380487 ATTATATAGTTTTCAAAATGATTTTT-AAA--A-AT
1 ATTATATAATTTTCAAAATG-TTTTTAAAACTATAT
*
380519 ATTATATAAGTTTTCCAAAATGTTTTTTAAACTATAT
1 ATTATATAA-TTTT-CAAAATGTTTTTAAAACTATAT
*
380556 ATTATATAAATTTTCCAAAAAATGTTTTTTTTAAAACTATAC
1 ATTATAT-AATTTT-C--AAAATG---TTTTTAAAACTATAT
* *
380598 A-T-TAT-ATTTTCAAAATGATTTCAAAACTATAT
1 ATTATATAATTTTCAAAATGTTTTTAAAACTATAT
*
380630 ATTATATAATTTTCAAAATG-CTTTAAAACTTATAT
1 ATTATATAATTTTCAAAATGTTTTTAAAAC-TATAT
* * *
380665 ATTGTATATAAGCTTTCAAAAACGTTTTAAAAACTATAT
1 A-T-TATATAA-TTTTC-AAAATGTTTTTAAAACTATAT
* * **
380704 AATAAAT-ATTTTCGGAAACCGTTTTTGAAAACTATAT
1 ATTATATAATTTTC--AAAATGTTTTT-AAAACTATAT
380741 ATTATAT--TTTTCAAAA
1 ATTATATAATTTTCAAAA
380757 ACATTTTCAA
Statistics
Matches: 194, Mismatches: 21, Indels: 44
0.75 0.08 0.17
Matches are distributed among these distances:
32 21 0.11
33 10 0.05
34 23 0.12
35 28 0.14
36 17 0.09
37 42 0.22
38 11 0.06
39 17 0.09
40 10 0.05
41 1 0.01
42 14 0.07
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (35 bp):
ATTATATAATTTTCAAAATGTTTTTAAAACTATAT
Found at i:380703 original size:39 final size:34
Alignment explanation
Indices: 380585--380704 Score: 102
Period size: 35 Copynumber: 3.4 Consensus size: 34
380575 AAATGTTTTT
* * *
380585 TTTAAAACTATACATTATAT---TTTCAAAATGA
1 TTTAAAACTATATATTATATAACTTTCAAAACGC
* *
380616 TTTCAAAACTATATATTATATAATTTTCAAAATGC
1 TTT-AAAACTATATATTATATAACTTTCAAAACGC
*
380651 TTTAAAACTTATATATTGTATATAAGCTTTCAAAAACGT
1 TTTAAAAC-TATATA-T-TATATAA-CTTTC-AAAACGC
380690 TTTAAAAACTATATA
1 TTT-AAAACTATATA
380705 ATAAATATTT
Statistics
Matches: 74, Mismatches: 5, Indels: 12
0.81 0.05 0.13
Matches are distributed among these distances:
31 3 0.04
32 16 0.22
34 5 0.07
35 19 0.26
36 1 0.01
37 7 0.09
38 4 0.05
39 14 0.19
40 5 0.07
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (34 bp):
TTTAAAACTATATATTATATAACTTTCAAAACGC
Found at i:380813 original size:10 final size:9
Alignment explanation
Indices: 380771--380813 Score: 58
Period size: 8 Copynumber: 5.2 Consensus size: 9
380761 TTTCAAAAAT
380771 TATACTATA
1 TATACTATA
380780 T-TACTATA
1 TATACTATA
380788 TATA-TATA
1 TATACTATA
380796 TATA-TATA
1 TATACTATA
380804 TATACT-TA
1 TATACTATA
380812 TA
1 TA
380814 ATAAAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 28 0.88
9 4 0.12
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (9 bp):
TATACTATA
Found at i:381377 original size:120 final size:120
Alignment explanation
Indices: 381164--381403 Score: 480
Period size: 120 Copynumber: 2.0 Consensus size: 120
381154 GATTCCACCA
381164 TGTAGTTGACAGGCCTTTGAGCTGAATGAAATCGAACTCGAAAGGTCTTCGTTGATAGATAACTT
1 TGTAGTTGACAGGCCTTTGAGCTGAATGAAATCGAACTCGAAAGGTCTTCGTTGATAGATAACTT
381229 TTGTCACTTAGGCACGGTTAACTTGGGTCTTCTTCTCGACTTGAAAACCTCTATT
66 TTGTCACTTAGGCACGGTTAACTTGGGTCTTCTTCTCGACTTGAAAACCTCTATT
381284 TGTAGTTGACAGGCCTTTGAGCTGAATGAAATCGAACTCGAAAGGTCTTCGTTGATAGATAACTT
1 TGTAGTTGACAGGCCTTTGAGCTGAATGAAATCGAACTCGAAAGGTCTTCGTTGATAGATAACTT
381349 TTGTCACTTAGGCACGGTTAACTTGGGTCTTCTTCTCGACTTGAAAACCTCTATT
66 TTGTCACTTAGGCACGGTTAACTTGGGTCTTCTTCTCGACTTGAAAACCTCTATT
381404 GCAGCCGGAC
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 120 1.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (120 bp):
TGTAGTTGACAGGCCTTTGAGCTGAATGAAATCGAACTCGAAAGGTCTTCGTTGATAGATAACTT
TTGTCACTTAGGCACGGTTAACTTGGGTCTTCTTCTCGACTTGAAAACCTCTATT
Found at i:381676 original size:84 final size:83
Alignment explanation
Indices: 381560--382334 Score: 705
Period size: 84 Copynumber: 9.4 Consensus size: 83
381550 TTGGCAGTAG
* * *
381560 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
*
381625 GTCTTTTGGTCACAGATAA
66 GTC-TTTGGTGACAGATAA
* * * * * * * * * **
381644 CCCTTTTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
1 CCCTTCTAGACTTAAGTTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAA
*
381709 GGTCTTTGGT---AGATAG
65 GGTCTTTGGTGACAGATAA
* * * * *
381725 CCCTTCTCGACTTAAGCTATGTTGCAAATGATATGCCTTAGAGCTAAGCGTAGTCGAACTCGAAG
1 CCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
*
381790 GTCTTTGGTTGGCAGATAA
66 GTCTTTGG-TGACAGATAA
* * * * * * * **
381809 CCCTTCTTGACTTAAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGCAATCGAACTCGGG
1 CCCTTCTAGACTTAAGTTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAA
*
381874 GGTCTTT-G-G-CAGATAG
65 GGTCTTTGGTGACAGATAA
* * * * *
381890 CCATTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAA
1 CCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCC-TTGGAGCTGAGCGTAGTCGAACTCGAA
* * *
381954 GGTCTTTTGTTGGCAGACAA
65 GGTC-TTTGGTGACAGATAA
* *
381974 CCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAG
1 CCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
** *
382039 GTCTTTGGTGAC-TTTAT
66 GTCTTTGGTGACAGATAA
* * * * * * * * * *
382056 CCCTTATAGCCTTGAGTTATGTTGTAAAATGATATGCCCTCGAATCTGAGTGTAATCGAACTC-A
1 CCCTTCTAGACTTAAGTTATGCTG-CAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGA
* * *
382120 GGGGTCTTT-G-G-CATATAG
64 -AGGTCTTTGGTGACAGATAA
* ** *
382138 CCCTTCTCGACTTAAACTATGCTGCAAATGATATGTCTTGGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
382203 GTCTTTGGTTGGA-AGATAA
66 GTCTTTGG-T-GACAGATAA
* * * * * * *
382222 CCCTTCTCGACTTAAGTTATGCTGCAAATGATATTCCCTTGAAGTTGAGTGCAATCGAACTCGAA
1 CCCTTCTAGACTTAAGTTATGCTGCAAATGATA-TGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
382287 GGTCTTT-GTGACAGATAA
65 GGTCTTTGGTGACAGATAA
* *
382305 CCCTTCTAGCCTTGAGTTATGCTGCAAATG
1 CCCTTCTAGACTTAAGTTATGCTGCAAATG
382335 CTATCTTTTA
Statistics
Matches: 553, Mismatches: 114, Indels: 49
0.77 0.16 0.07
Matches are distributed among these distances:
80 80 0.14
81 86 0.16
82 44 0.08
83 56 0.10
84 202 0.37
85 85 0.15
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (83 bp):
CCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
GTCTTTGGTGACAGATAA
Found at i:381736 original size:165 final size:163
Alignment explanation
Indices: 381531--382334 Score: 796
Period size: 165 Copynumber: 4.9 Consensus size: 163
381521 AAGTTGAATA
* * *
381531 TAATCGAACTCGGTGGTCTTTGGCAG-TAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGGAGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATG
* * * *
381595 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTTTAGCCTTGAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGACTTAAG
* * *
381660 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
130 TTATGCTGCAAATGATATG-CCTCGAAGCTGAGCG
* *
381695 TAATCGAACTCGGGGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATGATATG
1 TAATCGAACTCGGAGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATG
* * * *
381760 CCTTAGAGCTAAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTTGACTTAAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGACTTAAG
* *
381825 TTATGCTGTAAATGATATGCCCTCGAAGCTGAGTG
130 TTATGCTGCAAATGATATG-CCTCGAAGCTGAGCG
* * * * *
381860 CAATCGAACTCGGGGGTCTTTGGCAGATAGCCATTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGGAGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATG
* * * *
381925 CCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAA
66 CC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGACTTAA
* * *
381989 GTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCG
129 GTTATGCTGCAAATGATATGCCTCGAAGCTGAGCG
* ** * * * * * * * *
382024 TAGTCGAACTCAAAGGTCTTTGGT-GACTTTATCCCTTATAGCCTTGAGTTATGTTGTAAAATGA
1 TAATCGAACTCGGAGGTCTTTGGTAGA---TAGCCCTTCTCGACTTAAGCTATGCTG-CAAATGA
* * * * * * * * *
382088 TATGCCCTCGAATCTGAGTGTAATCGAACTC-AGGGGTCTTT-G-G-CATATAGCCCTTCTCGAC
62 TATG-CCTTGGAGCTGAGCGTAGTCGAACTCGA-AGGTCTTTGGTGACAGATAACCCTTCTAGAC
** * * *
382149 TTAAACTATGCTGCAAATGATATGTCTTGGAGCTGAGCG
125 TTAAGTTATGCTGCAAATGATATGCCTCGAAGCTGAGCG
* * * *
382188 TAGTCGAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
1 TAATCGAACTCGGAGGTCTTTGG-T---AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
* * * * * * *
382253 TATTCCCTTGAAGTTGAGTGCAATCGAACTCGAAGGTCTTT-GTGACAGATAACCCTTCTAGCCT
62 TA-TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACT
*
382317 TGAGTTATGCTGCAAATG
126 TAAGTTATGCTGCAAATG
382335 CTATCTTTTA
Statistics
Matches: 540, Mismatches: 80, Indels: 37
0.82 0.12 0.06
Matches are distributed among these distances:
163 2 0.00
164 130 0.24
165 290 0.54
166 49 0.09
167 44 0.08
168 23 0.04
169 2 0.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (163 bp):
TAATCGAACTCGGAGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATG
CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTAAGT
TATGCTGCAAATGATATGCCTCGAAGCTGAGCG
Found at i:382151 original size:248 final size:248
Alignment explanation
Indices: 381725--382334 Score: 848
Period size: 248 Copynumber: 2.5 Consensus size: 248
381715 TGGTAGATAG
* * * *
381725 CCCTTCTCGACTTAAGCTATGTTGCAAATGATATGCCTTAGAGCTAAGCGTAGTCGAACTCGAAG
1 CCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* * * *
381790 GTCTTTGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGTAAATGATATGCCCTCGAAGCT
66 GTCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCT
* *
381855 GAGTGCAATCGAACTCGGGGGTCTTTGGCAGATAGCCATTCTCGACTTAAGCTATGCTGCAAATG
130 GAGTGCAATCGAACTCAGGGGTCTTTGGCAGATAGCCATTCTCGACTTAAACTATGCTGCAAATG
* * *
381920 ATGTGCCGTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAA
195 ATATGCC-TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGAAGACAA
* * *
381974 CCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAG
1 CCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
** * * * *
382039 GTCTTTGGTGAC-TTTATCCCTTATAGCCTTGAGTTATGTTGTAAAATGATATGCCCTCGAATCT
66 GTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGT-AAATGATATGCCCTCGAAGCT
* * *
382103 GAGTGTAATCGAACTCAGGGGTCTTTGGCATATAGCCCTTCTCGACTTAAACTATGCTGCAAATG
130 GAGTGCAATCGAACTCAGGGGTCTTTGGCAGATAGCCATTCTCGACTTAAACTATGCTGCAAATG
* * *
382168 ATATGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGATAA
195 ATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGAAGACAA
* * * * * *
382222 CCCTTCTCGACTTAAGTTATGCTGCAAATGATATTCCCTTGAAGTTGAGTGCAATCGAACTCGAA
1 CCCTTCTCGACTTAAGTTATGCTGCAAATGATA-TGCCTTGGAGCTGAGCGTAGTCGAACTCGAA
*
382287 GGTCTTT-GTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
65 GGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATG
382335 CTATCTTTTA
Statistics
Matches: 314, Mismatches: 43, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
247 24 0.08
248 169 0.54
249 121 0.39
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (248 bp):
CCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
GTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTG
AGTGCAATCGAACTCAGGGGTCTTTGGCAGATAGCCATTCTCGACTTAAACTATGCTGCAAATGA
TATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGAAGACAA
Found at i:382222 original size:413 final size:416
Alignment explanation
Indices: 381560--382334 Score: 1198
Period size: 413 Copynumber: 1.9 Consensus size: 416
381550 TTGGCAGTAG
* * *
381560 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTAGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAG
* *
381625 GTCTTTTGGTCACAGATAACCCTTTTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCT
66 GTCTTTTGGTCACAGATAACCCTTATAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCT
* * * *
381690 GAGTGTAATCGAACTCGGGGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATG
131 GAGTGTAATCGAACTCAGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAACTATGCTGCAAATG
* *
381755 ATATGCCTTAGAGCTAAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTTGAC
196 ATATGCCTTAGAGCTAAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGAC
* **
381820 TTAAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGCAATCGAACTCGGGGGTCTTTG-G-
261 TTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGCAATCGAACTCGAAGGTCTTTGTGA
* *
381883 CAGATAGCCATTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
326 CAGATAACCATTCTAGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
381948 CTCAAAGGTCTTTTGTTGGCAGACAA
391 CTCAAAGGTCTTTTGTTGGCAGACAA
* *
381974 CCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAG
1 CCCTTCTAGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAG
* ** * * *
382039 GTC-TTTGGTGAC-TTTATCCCTTATAGCCTTGAGTTATGTTGTAAAATGATATGCCCTCGAATC
66 GTCTTTTGGTCACAGATAACCCTTATAGCCTTGAGTTATGCTGT-AAATGATATGCCCTCGAAGC
*
382102 TGAGTGTAATCGAACTCAGGGGTCTTTGGCATATAGCCCTTCTCGACTTAAACTATGCTGCAAAT
130 TGAGTGTAATCGAACTCAGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAACTATGCTGCAAAT
* * *
382167 GATATGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGA
195 GATATGCCTTAGAGCTAAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGA
* * *
382232 CTTAAGTTATGCTGCAAATGATATTCCCTTGAAGTTGAGTGCAATCGAACTCGAAGGTCTTTGTG
260 CTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGCAATCGAACTCGAAGGTCTTTGTG
* * * *
382297 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATG
325 ACAGATAACCATTCTAGACTTAAGCTATGCTGCAAATG
382335 CTATCTTTTA
Statistics
Matches: 323, Mismatches: 35, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
412 25 0.08
413 203 0.63
414 64 0.20
415 31 0.10
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (416 bp):
CCCTTCTAGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAG
GTCTTTTGGTCACAGATAACCCTTATAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCT
GAGTGTAATCGAACTCAGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAACTATGCTGCAAATG
ATATGCCTTAGAGCTAAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGAC
TTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGCAATCGAACTCGAAGGTCTTTGTGA
CAGATAACCATTCTAGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
CTCAAAGGTCTTTTGTTGGCAGACAA
Found at i:395050 original size:21 final size:20
Alignment explanation
Indices: 395023--395102 Score: 115
Period size: 21 Copynumber: 3.9 Consensus size: 20
395013 TTTGCCTCCG
395023 GTTGTCCCTAAACTCCCCCC
1 GTTGTCCCTAAACTCCCCCC
* *
395043 GCTTGTCCCTGAACTCCCTCCG
1 G-TTGTCCCTAAACTCCC-CCC
395065 GTTGTCCCTAAACTCCCCCC
1 GTTGTCCCTAAACTCCCCCC
395085 AGTTGTCCCTAAACTCCC
1 -GTTGTCCCTAAACTCCC
395103 TCCGGTTACA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
20 3 0.06
21 47 0.89
22 3 0.06
ACGTcount: A:0.15, C:0.46, G:0.12, T:0.26
Consensus pattern (20 bp):
GTTGTCCCTAAACTCCCCCC
Found at i:395076 original size:42 final size:42
Alignment explanation
Indices: 395017--395109 Score: 161
Period size: 42 Copynumber: 2.2 Consensus size: 42
395007 AATCAATTTG
*
395017 CCTCCGGTTGTCCCTAAACTCCCCCC-GCTTGTCCCTGAACTC
1 CCTCCGGTTGTCCCTAAACTCCCCCCAG-TTGTCCCTAAACTC
395059 CCTCCGGTTGTCCCTAAACTCCCCCCAGTTGTCCCTAAACTC
1 CCTCCGGTTGTCCCTAAACTCCCCCCAGTTGTCCCTAAACTC
395101 CCTCCGGTT
1 CCTCCGGTT
395110 ACAGTTCCCC
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
42 48 0.98
43 1 0.02
ACGTcount: A:0.13, C:0.46, G:0.14, T:0.27
Consensus pattern (42 bp):
CCTCCGGTTGTCCCTAAACTCCCCCCAGTTGTCCCTAAACTC
Found at i:395131 original size:15 final size:15
Alignment explanation
Indices: 395099--395138 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
395089 GTCCCTAAAC
*
395099 TCCCTCCGGTTACAGT
1 TCCC-CCGGTAACAGT
*
395115 TCCCCCGGTAACGGT
1 TCCCCCGGTAACAGT
395130 TCCCCCGGT
1 TCCCCCGGT
395139 TATCACAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.10, C:0.42, G:0.23, T:0.25
Consensus pattern (15 bp):
TCCCCCGGTAACAGT
Found at i:408223 original size:19 final size:19
Alignment explanation
Indices: 408188--408236 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
408178 TGTCTAATTT
* *
408188 TAAAATATTTCTTTTTTCTC
1 TAAAATATAT-TTTTTTATC
408208 ATAAAATATATTTTTTTATC
1 -TAAAATATATTTTTTTATC
408228 TAAAATATA
1 TAAAATATA
408237 AAACTTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 9 0.35
20 8 0.31
21 9 0.35
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (19 bp):
TAAAATATATTTTTTTATC
Found at i:411958 original size:12 final size:10
Alignment explanation
Indices: 411934--411964 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
411924 ACCCACAATC
411934 CTCTCTCCTT
1 CTCTCTCCTT
411944 CTCTCTCCTT
1 CTCTCTCCTT
411954 CTCTCTCCTT
1 CTCTCTCCTT
411964 C
1 C
411965 AACTCAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (10 bp):
CTCTCTCCTT
Found at i:416560 original size:2 final size:2
Alignment explanation
Indices: 416553--416590 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
416543 GCATCTCTTA
416553 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
416591 TATTAAGCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:435213 original size:31 final size:31
Alignment explanation
Indices: 435155--435287 Score: 149
Period size: 31 Copynumber: 4.3 Consensus size: 31
435145 AGTTTTAAAA
* * *
435155 GTAACAAATTGATCACTAATGTTATCGATTT
1 GTAACAAAATAATTACTAATGTTATCGATTT
* * *
435186 GTAATAAAATAATTATTAATGTAATCGATTT
1 GTAACAAAATAATTACTAATGTTATCGATTT
* **
435217 GTAACAAAATGATTACTAACATTATCGATTT
1 GTAACAAAATAATTACTAATGTTATCGATTT
* * * *
435248 GTAACAAAATGATCACTAACGTTGTCGATTT
1 GTAACAAAATAATTACTAATGTTATCGATTT
435279 GTAACAAAA
1 GTAACAAAA
435288 AAATACTCTA
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 87 1.00
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.35
Consensus pattern (31 bp):
GTAACAAAATAATTACTAATGTTATCGATTT
Found at i:435223 original size:62 final size:62
Alignment explanation
Indices: 435155--435287 Score: 167
Period size: 62 Copynumber: 2.1 Consensus size: 62
435145 AGTTTTAAAA
* ** * * * *
435155 GTAACAAATTGATCACTAATGTTATCGATTTGTAATAAAATAATTATTAATGTAATCGATTT
1 GTAACAAAATGATCACTAACATTATCGATTTGTAACAAAATAATCACTAACGTAATCGATTT
* * **
435217 GTAACAAAATGATTACTAACATTATCGATTTGTAACAAAATGATCACTAACGTTGTCGATTT
1 GTAACAAAATGATCACTAACATTATCGATTTGTAACAAAATAATCACTAACGTAATCGATTT
435279 GTAACAAAA
1 GTAACAAAA
435288 AAATACTCTA
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.35
Consensus pattern (62 bp):
GTAACAAAATGATCACTAACATTATCGATTTGTAACAAAATAATCACTAACGTAATCGATTT
Found at i:435252 original size:16 final size:16
Alignment explanation
Indices: 435208--435257 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
435198 TTATTAATGT
435208 AATCGATTTGTAACAA
1 AATCGATTTGTAACAA
** *
435224 AAT-GATTACTAACAT
1 AATCGATTTGTAACAA
*
435239 TATCGATTTGTAACAA
1 AATCGATTTGTAACAA
435255 AAT
1 AAT
435258 GATCACTAAC
Statistics
Matches: 25, Mismatches: 8, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (16 bp):
AATCGATTTGTAACAA
Found at i:438585 original size:23 final size:24
Alignment explanation
Indices: 438550--438595 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
438540 CAATTTGATG
* * *
438550 ATTACATTTATTTTATTTTAATTA
1 ATTACATTAATTTAAATTTAATTA
438574 ATTA-ATTAATTTAAATTTAATT
1 ATTACATTAATTTAAATTTAATT
438596 TATGTGTCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTACATTAATTTAAATTTAATTA
Found at i:438877 original size:18 final size:18
Alignment explanation
Indices: 438851--438889 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
438841 GATAAAATTA
438851 AAATTAAAAATATA-TTT
1 AAATTAAAAATATATTTT
438868 AAATTAAAAATATATTTT
1 AAATTAAAAATATATTTT
438886 AAAT
1 AAAT
438890 ATACTTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATTAAAAATATATTTT
Found at i:447666 original size:26 final size:26
Alignment explanation
Indices: 447629--447682 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
447619 CTCACTCATT
447629 CTACCTACTGAACTACGAAAGCACGC
1 CTACCTACTGAACTACGAAAGCACGC
* *
447655 CTACCTATTGAACTACGAAAGCATGC
1 CTACCTACTGAACTACGAAAGCACGC
447681 CT
1 CT
447683 TTCTCGACGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.31, G:0.15, T:0.20
Consensus pattern (26 bp):
CTACCTACTGAACTACGAAAGCACGC
Found at i:447999 original size:14 final size:14
Alignment explanation
Indices: 447980--448006 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
447970 TTAAGTAATT
447980 TTCTTTCTCTTCCC
1 TTCTTTCTCTTCCC
447994 TTCTTTCTCTTCC
1 TTCTTTCTCTTCC
448007 TCGTTAGTCT
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:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (14 bp):
TTCTTTCTCTTCCC
Found at i:457098 original size:21 final size:21
Alignment explanation
Indices: 457069--457110 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
457059 AGAATTATTA
*
457069 TAATATTTTAAAATTAATAAT
1 TAATATTTTAAAATAAATAAT
* *
457090 TAATTTTTTATAATAAATAAT
1 TAATATTTTAAAATAAATAAT
457111 ATTAATTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATATTTTAAAATAAATAAT
Found at i:457128 original size:22 final size:24
Alignment explanation
Indices: 457083--457131 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
457073 ATTTTAAAAT
*
457083 TAATAATTAATTTTTTATAATAAA
1 TAATAATTAATTTATTATAATAAA
*
457107 TAAT-ATTAA-TTATTATACTAAA
1 TAATAATTAATTTATTATAATAAA
457129 TAA
1 TAA
457132 ATATCATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 14 0.61
23 5 0.22
24 4 0.17
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
TAATAATTAATTTATTATAATAAA
Found at i:457167 original size:25 final size:24
Alignment explanation
Indices: 457125--457175 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
457115 ATTATTATAC
* * *
457125 TAAATAAATATCATAAAATAATTTT
1 TAAATAAAAATCA-AAAAAAATATT
*
457150 TAAATAAAAATTAAAAAAAATATT
1 TAAATAAAAATCAAAAAAAATATT
457174 TA
1 TA
457176 GGTGTACATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
TAAATAAAAATCAAAAAAAATATT
Found at i:457499 original size:20 final size:20
Alignment explanation
Indices: 457474--457513 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
457464 TAATCTGAGT
457474 CTCTTTCGTTTCCTATGGGC
1 CTCTTTCGTTTCCTATGGGC
457494 CTCTTTCGTTTCCTATGGGC
1 CTCTTTCGTTTCCTATGGGC
457514 GGAAACTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.05, C:0.30, G:0.20, T:0.45
Consensus pattern (20 bp):
CTCTTTCGTTTCCTATGGGC
Found at i:459032 original size:20 final size:20
Alignment explanation
Indices: 459007--459044 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
458997 ATAACTGCAA
459007 ACAAAAAA-AATATAATTAGT
1 ACAAAAAATAAT-TAATTAGT
459027 ACAAAAAATAATTAATTA
1 ACAAAAAATAATTAATTA
459045 ATAAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (20 bp):
ACAAAAAATAATTAATTAGT
Found at i:459065 original size:17 final size:17
Alignment explanation
Indices: 459043--459106 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 17
459033 AATAATTAAT
459043 TAATAAATTTATATAAA
1 TAATAAATTTATATAAA
459060 TAAT-AA-TTATATAAA
1 TAATAAATTTATATAAA
* *
459075 T-ATTATTTTA-ATAAA
1 TAATAAATTTATATAAA
459090 -AATTAATATTTATATAA
1 TAA-TAA-ATTTATATAA
459107 TTATATTACT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
14 2 0.05
15 17 0.45
16 7 0.18
17 8 0.21
18 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATAAATTTATATAAA
Found at i:459069 original size:15 final size:15
Alignment explanation
Indices: 459014--459076 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
459004 CAAACAAAAA
*
459014 AAAT-ATAATTAGTAC
1 AAATAATAATTA-TAT
*
459029 AAAAAATAATTA-AT
1 AAATAATAATTATAT
* *
459043 TAATAA-ATTTATAT
1 AAATAATAATTATAT
459057 AAATAATAATTATAT
1 AAATAATAATTATAT
459072 AAATA
1 AAATA
459077 TTATTTTAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 4 0.11
14 12 0.32
15 15 0.39
16 7 0.18
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (15 bp):
AAATAATAATTATAT
Found at i:459108 original size:15 final size:15
Alignment explanation
Indices: 459039--459113 Score: 53
Period size: 15 Copynumber: 4.7 Consensus size: 15
459029 AAAAAATAAT
459039 TAATTAATAAATTTATA
1 TAATTAAT--ATTTATA
* *
459056 TAAATAATAATTATA
1 TAATTAATATTTATA
* *
459071 TAAATATTATTTTAATAA
1 TAATTAATA-TTT-AT-A
*
459089 AAATTAATATTTATA
1 TAATTAATATTTATA
459104 TAATT-ATATT
1 TAATTAATATT
459114 ACTATAAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
14 5 0.11
15 19 0.40
16 4 0.09
17 12 0.26
18 7 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATTAATATTTATA
Found at i:460539 original size:21 final size:19
Alignment explanation
Indices: 460501--460541 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
460491 GGTAATGTAA
460501 TTATTTTAATATATTATTT
1 TTATTTTAATATATTATTT
460520 TTATTTTATATATGATTATTT
1 TTATTTTA-ATAT-ATTATTT
460541 T
1 T
460542 AAAAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.40
20 4 0.20
21 8 0.40
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
TTATTTTAATATATTATTT
Found at i:461661 original size:34 final size:34
Alignment explanation
Indices: 461587--461662 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 34
461577 TTATAACTGT
*
461587 AAAAAATAATAAAAAGTTAATATAATACAATTTA
1 AAAAAATAATAAAAAGTTAATATAATACAATATA
* * * * *
461621 ACAAAATAATAAATTA-TTAATTTATTATAATATA
1 AAAAAATAATAAA-AAGTTAATATAATACAATATA
461655 AAAAAATA
1 AAAAAATA
461663 TTTTACATTC
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
34 33 0.97
35 1 0.03
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (34 bp):
AAAAAATAATAAAAAGTTAATATAATACAATATA
Found at i:461720 original size:27 final size:27
Alignment explanation
Indices: 461690--461741 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
461680 AATCTGGTCG
* *
461690 AGTTTGAGCTTTAAGAGTATTTGAGCT
1 AGTTTGAACTTTAAGAGGATTTGAGCT
*
461717 AGTTTGAACTTTGAGAGGATTTGAG
1 AGTTTGAACTTTAAGAGGATTTGAG
461742 AATTTGGTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.27, C:0.06, G:0.29, T:0.38
Consensus pattern (27 bp):
AGTTTGAACTTTAAGAGGATTTGAGCT
Found at i:468652 original size:16 final size:17
Alignment explanation
Indices: 468631--468663 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
468621 ACATTTTGTT
468631 AAATTAA-TTTTATTAA
1 AAATTAATTTTTATTAA
468647 AAATTAATTTTTATTAA
1 AAATTAATTTTTATTAA
468664 CATTAAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AAATTAATTTTTATTAA
Found at i:476032 original size:185 final size:183
Alignment explanation
Indices: 475715--476102 Score: 643
Period size: 185 Copynumber: 2.1 Consensus size: 183
475705 ATTAAATTTT
* *
475715 AAATTTTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
* *
475780 TTTAAGATCTAATAACTTTTAAACCTAAATAAATATTAATTAATTAAAAAAATTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACATAAATAAATATTAATTAATTAAAAAAATTATATAAAATTT
*
475845 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAAC--TTTTTTTAATTAAA
475900 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
* * * *
475965 TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAATTTATCTGAAATTT
66 TTTAAGATCCAATAACTTTTAAACATAAATAAATATTAATTAATTAAAAAAATTATATAAAATTT
476030 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTAATTAAA
* * *
476083 AAACATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
476103 AATTAGAAAA
Statistics
Matches: 191, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
182 8 0.04
183 23 0.12
185 160 0.84
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (183 bp):
AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACATAAATAAATATTAATTAATTAAAAAAATTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTAATTAAA
Found at i:476241 original size:15 final size:14
Alignment explanation
Indices: 476216--476254 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
476206 AAGAAAAACA
476216 AAGTTTGATTAATT
1 AAGTTTGATTAATT
*
476230 CAGTTATGATTAATT
1 AAGTT-TGATTAATT
*
476245 AAGTTCGATT
1 AAGTTTGATT
476255 CGATTTTAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.46
Consensus pattern (14 bp):
AAGTTTGATTAATT
Found at i:478562 original size:2 final size:2
Alignment explanation
Indices: 478555--478602 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
478545 TGGGCTTTTA
478555 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
478597 AT AT AT
1 AT AT AT
478603 TTTCTGTAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:484883 original size:2 final size:2
Alignment explanation
Indices: 484876--484901 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
484866 TATGTATGTG
484876 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
484902 AATGCAGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:490818 original size:21 final size:21
Alignment explanation
Indices: 490789--490840 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
490779 GAGTGATGAT
490789 GACGATGAGAAAGACGACGAC
1 GACGATGAGAAAGACGACGAC
* * *
490810 GAGGATGAGGACGACGACGAC
1 GACGATGAGAAAGACGACGAC
490831 GACGATGAGA
1 GACGATGAGA
490841 GTGAAGAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.17, G:0.38, T:0.06
Consensus pattern (21 bp):
GACGATGAGAAAGACGACGAC
Found at i:490959 original size:26 final size:26
Alignment explanation
Indices: 490923--490975 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
490913 CAAGGAGACA
*
490923 TCGATAGATCTAATAAAATTGTAATC
1 TCGATAAATCTAATAAAATTGTAATC
490949 TCGATAAATCTAATAAAATTGTAATC
1 TCGATAAATCTAATAAAATTGTAATC
490975 T
1 T
490976 TTTCATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.36
Consensus pattern (26 bp):
TCGATAAATCTAATAAAATTGTAATC
Found at i:492872 original size:39 final size:39
Alignment explanation
Indices: 492794--492872 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 39
492784 ACTATTTAAG
* * *
492794 GCTCAATCCCACATAGTATTGGGAACAAGTGTTGATAAT
1 GCTCAATCCCACATAGTATTGGAAACAACTATTGATAAT
*
492833 GCTCAAATCCCACATAGTATTGGAAAC-ACTATTGGTAAT
1 GCTC-AATCCCACATAGTATTGGAAACAACTATTGATAAT
492872 G
1 G
492873 GTATTTAAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 14 0.40
40 21 0.60
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (39 bp):
GCTCAATCCCACATAGTATTGGAAACAACTATTGATAAT
Found at i:493047 original size:13 final size:13
Alignment explanation
Indices: 493029--493067 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
493019 TTTTTAACTA
493029 TCACAACGAATTT
1 TCACAACGAATTT
493042 TCACAACGAATTT
1 TCACAACGAATTT
*
493055 TCGCAACGAATTT
1 TCACAACGAATTT
493068 AGAAAATCGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (13 bp):
TCACAACGAATTT
Found at i:493101 original size:22 final size:22
Alignment explanation
Indices: 493076--493125 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
493066 TTAGAAAATC
493076 GCAACGACAACTGTAGACTATA
1 GCAACGACAACTGTAGACTATA
* *
493098 GCAACAACAACTGTAGACTATC
1 GCAACGACAACTGTAGACTATA
493120 GCAACG
1 GCAACG
493126 CGATTTTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.26, G:0.18, T:0.16
Consensus pattern (22 bp):
GCAACGACAACTGTAGACTATA
Found at i:497784 original size:44 final size:40
Alignment explanation
Indices: 497731--497816 Score: 100
Period size: 40 Copynumber: 2.0 Consensus size: 40
497721 TTTTCATTAT
* *
497731 TATTATATTTTATTCCTTTATTCATATACATATATATATATGTA
1 TATTATATTTTA-T--TTTATT-ATACACATATATATATACGTA
* *
497775 TATTTTATTTTATTTTATTATACATATATATATATACGTA
1 TATTATATTTTATTTTATTATACACATATATATATACGTA
497815 TA
1 TA
497817 ATCATCGTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
40 20 0.53
41 6 0.16
43 1 0.03
44 11 0.29
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (40 bp):
TATTATATTTTATTTTATTATACACATATATATATACGTA
Found at i:497828 original size:40 final size:39
Alignment explanation
Indices: 497755--497836 Score: 96
Period size: 38 Copynumber: 2.1 Consensus size: 39
497745 CCTTTATTCA
* * *
497755 TATACATATATATATATGTATATTTTATTTTA-TTTTAT
1 TATACATATATATATATGTATATATCATGTTATTTTTAT
497793 TATACATATATATATATACGTATA-ATCATCGTTATTTTTAT
1 TATACATATATATATAT--GTATATATCAT-GTTATTTTTAT
497834 TAT
1 TAT
497837 TTTAAGTATC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
38 17 0.46
39 3 0.08
40 8 0.22
41 9 0.24
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (39 bp):
TATACATATATATATATGTATATATCATGTTATTTTTAT
Found at i:498094 original size:17 final size:17
Alignment explanation
Indices: 498060--498105 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
498050 TATTTGATCA
498060 TAGTTATTTATTTATTT
1 TAGTTATTTATTTATTT
*
498077 TAGTT-TTTTTTTAGTTT
1 TAGTTATTTATTTA-TTT
*
498094 TATTTATTTATT
1 TAGTTATTTATT
498106 AATATTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 7 0.29
17 12 0.50
18 5 0.21
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.74
Consensus pattern (17 bp):
TAGTTATTTATTTATTT
Found at i:502282 original size:21 final size:21
Alignment explanation
Indices: 502236--502292 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
502226 AATTTGATGA
*
502236 AGAAGATAAAGCTAAAAAGAT
1 AGAAGATAAAGATAAAAAGAT
* *
502257 GGAAGA-AAAGATAAAAATATT
1 AGAAGATAAAGATAAAAAGA-T
*
502278 AGAAGATCAA-ATAAA
1 AGAAGATAAAGATAAA
502293 GATGGTCCAG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 11 0.38
21 16 0.55
22 2 0.07
ACGTcount: A:0.63, C:0.04, G:0.18, T:0.16
Consensus pattern (21 bp):
AGAAGATAAAGATAAAAAGAT
Found at i:508894 original size:1 final size:1
Alignment explanation
Indices: 508857--508882 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
508847 TCTTAAGTTG
508857 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
508883 GAGAGAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:510195 original size:105 final size:105
Alignment explanation
Indices: 509690--510467 Score: 1466
Period size: 105 Copynumber: 7.4 Consensus size: 105
509680 AGGTTTTACC
509690 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
509755 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
509796 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
509861 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
509902 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
509967 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
510007 CAGAGCCAATTTCAAACTTCACAACGAAGGATATTGGACTCCGGACAACGTAAGTTCAACTTCAC
1 CAGAGCCAATTTC-AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
510072 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
65 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
510113 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
510178 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
510218 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
510283 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
510323 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
510388 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
510428 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
510468 GAAAACAACA
Statistics
Matches: 664, Mismatches: 7, Indels: 3
0.99 0.01 0.00
Matches are distributed among these distances:
105 364 0.55
106 300 0.45
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:511887 original size:41 final size:41
Alignment explanation
Indices: 511841--511925 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
511831 ATATTTTCAT
511841 TATTAT-TATATTTTATTCCTT-TATTCA-TATACATATATATA
1 TATTATGTATATTTTATT--TTAT-TTCATTATACATATATATA
*
511882 TATTATGTATATTTTATTTTATTTTATTATACATATATATA
1 TATTATGTATATTTTATTTTATTTCATTATACATATATATA
511923 TAT
1 TAT
511926 ACGTATAATC
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
40 5 0.12
41 24 0.60
42 11 0.28
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (41 bp):
TATTATGTATATTTTATTTTATTTCATTATACATATATATA
Found at i:511948 original size:41 final size:41
Alignment explanation
Indices: 511868--511952 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 41
511858 CCTTTATTCA
* * * *
511868 TATACATATATATATATTATGTATATTTTATTTTATTTTAT
1 TATACATATATATATATTACGTATATATCATGTTATTTTAT
511909 TATACATATATATATA-TACGTATA-ATCATCGTTATTTTTAT
1 TATACATATATATATATTACGTATATATCAT-GTTA-TTTTAT
511950 TAT
1 TAT
511953 TTTAAGTATC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
39 3 0.08
40 10 0.26
41 25 0.66
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (41 bp):
TATACATATATATATATTACGTATATATCATGTTATTTTAT
Found at i:512210 original size:17 final size:17
Alignment explanation
Indices: 512176--512221 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
512166 TATTTGATCA
512176 TAGTTATTTATTTATTT
1 TAGTTATTTATTTATTT
*
512193 TAGTT-TTTTTTTAGTTT
1 TAGTTATTTATTTA-TTT
*
512210 TATTTATTTATT
1 TAGTTATTTATT
512222 AATATTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 7 0.29
17 12 0.50
18 5 0.21
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.74
Consensus pattern (17 bp):
TAGTTATTTATTTATTT
Found at i:512359 original size:12 final size:12
Alignment explanation
Indices: 512344--512377 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
512334 TAATATTTTA
512344 TATATTTATATG
1 TATATTTATATG
*
512356 TATATATATATG
1 TATATTTATATG
512368 TATACTTTAT
1 TATA-TTTAT
512378 GTAATTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (12 bp):
TATATTTATATG
Found at i:513296 original size:23 final size:24
Alignment explanation
Indices: 513265--513311 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
513255 TATTATGATA
*
513265 AAAAATTCTGTTTAA-AATATATT
1 AAAAATTCTGCTTAACAATATATT
* *
513288 AAAATTTCTGCTTAACATTATATT
1 AAAAATTCTGCTTAACAATATATT
513312 TAGAATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.45
Consensus pattern (24 bp):
AAAAATTCTGCTTAACAATATATT
Found at i:513309 original size:24 final size:23
Alignment explanation
Indices: 513256--513311 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
513246 AATAATTATT
* *
513256 ATTATGATAAAAAATTCTGTTTAA
1 ATTAT-ATTAAAAATTCTGCTTAA
* *
513280 AATATATTAAAATTTCTGCTTAA
1 ATTATATTAAAAATTCTGCTTAA
513303 CATTATATT
1 -ATTATATT
513312 TAGAATAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (23 bp):
ATTATATTAAAAATTCTGCTTAA
Found at i:514879 original size:18 final size:17
Alignment explanation
Indices: 514851--514884 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
514841 GAAAGCGCTT
514851 AGAGAGAAGGAAGAAGC
1 AGAGAGAAGGAAGAAGC
*
514868 AGAGAGGAAGGATGAAG
1 AGAGA-GAAGGAAGAAG
514885 AGGTTGATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.03, G:0.44, T:0.03
Consensus pattern (17 bp):
AGAGAGAAGGAAGAAGC
Found at i:521977 original size:117 final size:117
Alignment explanation
Indices: 521767--522000 Score: 450
Period size: 117 Copynumber: 2.0 Consensus size: 117
521757 AGCCAACATA
*
521767 TAAATGGGTTCATCAATTAAAAAATATGAAAAAGAATTCAAATTCAGTTTCTATAGTAATTCTAA
1 TAAATGGGTTCATCAATTAAAAAATACGAAAAAGAATTCAAATTCAGTTTCTATAGTAATTCTAA
*
521832 AAAGAATAACACTAGTTATATAGTATTGCTAAAAGTGAATAAAGGCAATATT
66 AAAGAATAACACTAGTTATATAGCATTGCTAAAAGTGAATAAAGGCAATATT
521884 TAAATGGGTTCATCAATTAAAAAATACGAAAAAGAATTCAAATTCAGTTTCTATAGTAATTCTAA
1 TAAATGGGTTCATCAATTAAAAAATACGAAAAAGAATTCAAATTCAGTTTCTATAGTAATTCTAA
521949 AAAGAATAACACTAGTTATATAGCATTGCTAAAAGTGAATAAAGGCAATATT
66 AAAGAATAACACTAGTTATATAGCATTGCTAAAAGTGAATAAAGGCAATATT
522001 GAATGAGAAG
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
117 115 1.00
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (117 bp):
TAAATGGGTTCATCAATTAAAAAATACGAAAAAGAATTCAAATTCAGTTTCTATAGTAATTCTAA
AAAGAATAACACTAGTTATATAGCATTGCTAAAAGTGAATAAAGGCAATATT
Found at i:533514 original size:27 final size:27
Alignment explanation
Indices: 533484--533538 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
533474 CTGTATGTAG
* *
533484 GAAGATTCGTTCTGGTATTACGTAATT
1 GAAGATTCGTACTGATATTACGTAATT
*
533511 GAAGATTCGTACTGATATTACTTAATT
1 GAAGATTCGTACTGATATTACGTAATT
533538 G
1 G
533539 TTCAGTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (27 bp):
GAAGATTCGTACTGATATTACGTAATT
Found at i:534448 original size:37 final size:36
Alignment explanation
Indices: 534372--534448 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
534362 TTTTTATATT
*
534372 TTTAATTTTGTAAAAAAATTTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAA-TTATATAAATATTATCAA
* *
534409 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
534446 TTT
1 TTT
534449 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 13 0.37
37 18 0.51
38 4 0.11
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:545920 original size:2 final size:2
Alignment explanation
Indices: 545913--545944 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
545903 AAGTTTTTAT
545913 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
545945 ATAAAAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:546195 original size:31 final size:31
Alignment explanation
Indices: 546160--546220 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
546150 ATATTTTATC
* *
546160 ACTTTTGTTTTTATTTAATTAAGATTTGATT
1 ACTTTCGTTTTTATTTAATTAAGATGTGATT
*
546191 ACTTTCGTTTTTGTTTAATTAAGATGTGAT
1 ACTTTCGTTTTTATTTAATTAAGATGTGAT
546221 CACTAAGGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.25, C:0.05, G:0.13, T:0.57
Consensus pattern (31 bp):
ACTTTCGTTTTTATTTAATTAAGATGTGATT
Found at i:547413 original size:19 final size:18
Alignment explanation
Indices: 547384--547429 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
547374 TAATTTGTAT
*
547384 ATAATATAATTATTAAGATA
1 ATAA-ATAATT-TTAAAATA
547404 ATAAATAATTTTAAAATA
1 ATAAATAATTTTAAAATA
547422 ATTAAATA
1 A-TAAATA
547430 CACCTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 8 0.33
19 12 0.50
20 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
ATAAATAATTTTAAAATA
Found at i:548071 original size:15 final size:15
Alignment explanation
Indices: 548051--548095 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
548041 TAATAAGGTT
*
548051 ATTTATTTTAAAATA
1 ATTTATTATAAAATA
548066 ATTTATTATAAAATA
1 ATTTATTATAAAATA
548081 ATTTATTATAAAATA
1 ATTTATTATAAAATA
548096 TGGATTGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTTATTATAAAATA
Found at i:548136 original size:33 final size:36
Alignment explanation
Indices: 548066--548150 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 36
548056 TTTTAAAATA
*
548066 ATTTATTATAAAATAATTTATTATAAAATATGGATTG
1 ATTTATTTTAAAATAATTTATTAT-AAATATGGATTG
*
548103 ATTTATTTTAAAATAATTTA-T-T-AGTATGGATTG
1 ATTTATTTTAAAATAATTTATTATAAATATGGATTG
548136 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
548151 TGGATTGATT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
33 25 0.54
35 1 0.02
36 1 0.02
37 19 0.41
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.49
Consensus pattern (36 bp):
ATTTATTTTAAAATAATTTATTATAAATATGGATTG
Found at i:548141 original size:18 final size:18
Alignment explanation
Indices: 548118--548165 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
548108 TTTTAAAATA
*
548118 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
548136 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
548158 ATTTATTA
1 ATTTATTA
548166 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:548159 original size:55 final size:52
Alignment explanation
Indices: 548051--548164 Score: 165
Period size: 55 Copynumber: 2.1 Consensus size: 52
548041 TAATAAGGTT
548051 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTATAAAATATGGATTG
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTATAAAATATGGATTG
* * * *
548103 ATTTATTTTAAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATAATTTATTA-TA--AAATAATTTATTATAAAATATGGATTG
548158 ATTTATT
1 ATTTATT
548165 ATTGTAGTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
52 23 0.42
53 2 0.04
55 30 0.55
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (52 bp):
ATTTATTTTAAAATAATTTATTATAAAATAATTTATTATAAAATATGGATTG
Found at i:548216 original size:32 final size:32
Alignment explanation
Indices: 548174--549313 Score: 825
Period size: 32 Copynumber: 38.7 Consensus size: 32
548164 TATTGTAGTT
*
548174 GTATGAATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
548206 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
548229 -TATGGATTGATTTATTTTAAATAATTTATCA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
548260 GTATGTATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
548283 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
548314 GTATGAATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
548337 -TATGGATTGATTTATTTCAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* **
548368 GTATGAATTGATTTATTTTAAA-ATATGGATT-
1 GTATGGATTGATTTATTTTAAATA-ATTTATTA
** * *
548399 G-ATTTATT-ATTGTAGTTGTATGAATTGATTTATTTTAAA
1 GTATGGATTGATT-TA-TT-T-T-AAATAATTTA--TT--A
*
548438 ATATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
548461 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
548492 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
**
548524 GTATTAATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
548556 GTATGAATTGATTTATTTTAAA-AATTTTATTA
1 GTATGGATTGATTTATTTTAAATAA-TTTATTA
* **
548588 GTATGAATTGATTTATTTTAAA-ATATGGATT-
1 GTATGGATTGATTTATTTTAAATA-ATTTATTA
** * * *
548619 G-ATTTATT-ATTGTAGTTGTATCGATTGATTTATT-
1 GTATGGATTGATT-TA-TT-T-T-AAATAATTTATTA
* * * * * *
548653 -T-T-AAATAATTTATTAGTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATT--T-T-AAATAATTTA--TT--A
*
548690 ATATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
548722 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
548754 GTATGAATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
548777 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
548808 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
548831 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
548862 GTATGTATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
548885 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
548916 GTATAGATTGATTTATTTTAAATAATTTATCA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
548948 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
548980 GTATAGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
549012 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
549035 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
549066 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
549089 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
549120 GTATAGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
549152 GTATGGATTGATTTATTTT--A-AA---A-TA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
549177 -TA--GATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
549206 GTATGAATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
549229 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
549260 GTATAGATTGATTTATTTTAAATAATTTATCA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
549292 GTATGAATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
549314 ATATGGATTT
Statistics
Matches: 905, Mismatches: 60, Indels: 286
0.72 0.05 0.23
Matches are distributed among these distances:
22 149 0.16
23 39 0.04
24 3 0.00
25 13 0.01
26 31 0.03
28 28 0.03
29 21 0.02
30 17 0.02
31 48 0.05
32 499 0.55
33 7 0.01
34 15 0.02
36 10 0.01
37 2 0.00
38 3 0.00
39 1 0.00
40 16 0.02
41 3 0.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:548232 original size:22 final size:22
Alignment explanation
Indices: 548207--548249 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
548197 AATTTATTAG
548207 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
548229 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
548250 TAATTTATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:548249 original size:54 final size:54
Alignment explanation
Indices: 548175--549425 Score: 1047
Period size: 54 Copynumber: 22.6 Consensus size: 54
548165 ATTGTAGTTG
*
548175 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* *
548229 TATGGATTGATTTATTTTAAATAATTTATCAGTATGTATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
548283 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* *
548337 TATGGATTGATTTATTTCAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* *
548391 TATGGATTGATTTA--TT--AT--TGTAGTT-GTATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAA
** ** * ** * * *
548439 TATGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAA
**
548493 TATGGATTGATTTATTTTAAATAATTTATTAGTATTAATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA
*
548549 TTTATTAGTATGAATTGATTTATTTTAAA-AATTTTATTAGTATGAATTGATTTATTTTAAAA
1 --TA-T-G---G-ATTGATTTATTTTAAATAA-TTTATTAGTATGGATTGATTTATTTTAAAA
* * * * * * *
548611 TATGGATTGATTTATTATT--GTAGTTGTA-TCG-ATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATT-TTAAATAATT-TATTAGTATGGATTGA-TTT--AT--TTTA-AAA
** ** * ** * * *
548669 TATGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAA
*
548723 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
548777 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
548831 TATGGATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
548885 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATCA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-TTT---TAA---A--A
*
548948 GTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTT-AAA
1 -TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
** ** * ** * * *
549002 TAATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTTT-AAA
1 T-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
** ** * ** * * *
549056 TAATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTTTAAATAA
1 T-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA
549113 TTTATTAGTATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 --TA-T-G----GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* *
549175 TATAGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
549229 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA
** ** *
549285 TTTATCAGTATGAATTGATTTATTTTAAA-ATATGGATT--TATTTATT-ATTGTAGTTGT---A
1 --TAT--G---G-ATTGATTTATTTTAAATA-ATTTATTAGTATGGATTGATT-TA-TTTTAAAA
*
549343 TA--AATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
549395 TATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
549426 TTGTAGTTGT
Statistics
Matches: 1013, Mismatches: 95, Indels: 178
0.79 0.07 0.14
Matches are distributed among these distances:
48 61 0.06
49 6 0.01
50 12 0.01
51 3 0.00
52 14 0.01
53 20 0.02
54 599 0.59
55 41 0.04
56 19 0.02
57 8 0.01
58 36 0.04
59 12 0.01
60 7 0.01
61 4 0.00
62 15 0.01
63 26 0.03
64 130 0.13
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:548277 original size:22 final size:22
Alignment explanation
Indices: 548261--548303 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
548251 AATTTATCAG
*
548261 TATGTATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
548283 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
548304 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:548324 original size:86 final size:85
Alignment explanation
Indices: 548229--549425 Score: 761
Period size: 86 Copynumber: 14.0 Consensus size: 85
548219 TATTTTAAAA
*
548229 TATGGATTGATTTATTTTAAATAATTTATCAGTATGTATTGATTTATTTTAAAATATGGATTGAT
1 TATGAATTGATTTATTTTAAATAATTTAT-AGTATGTATTGATTTATTTTAAAATATGGATTGAT
548294 TTATTTTAAATAATTTATTAG
65 TTATTTTAAATAATTTATTAG
** * * * ** * * * *
548315 TATGAATTGATTTATTTTAAA-ATATGGATTG-ATTTATTTCAAATAATTTATTAGTATGAATTG
1 TATGAATTGATTTATTTTAAATA-ATTTATAGTATGTA-TTGATTTATTTTA-AAATATGGATTG
* *
548378 ATTTATTTTAAAATATGGATTGATTTAT
63 ATTTATTTT-AAATA---ATTTA-TTAG
* * * * ** * * * *
548406 TATTGTAGTTG-TATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
1 TA-TG-AATTGAT-TTATTTTAAATAATTTATAGTATGTATTGATTTATTTTAAAATATGGATTG
548470 ATTTATTTTAAATAATTTATTAG
63 ATTTATTTTAAATAATTTATTAG
*
548493 TATGGATTGATTTATTTTAAATAATTTATTAGTAT-TAATTGATTTATTTTAAATAATTTATTAG
1 TATGAATTGATTTATTTTAAATAATTTA-TAGTATGT-ATTGATTTATTTT-AA-AA--TA-T-G
548557 TATGAATTGATTTATTTTAAA-AATTTTATTAG
58 ---G-ATTGATTTATTTTAAATAA-TTTATTAG
* * * *** *
548589 TATGAATTGATTTATTTT-AA-AA--TAT-GGAT-TGATTTA-TTATTGTAGTTGTATCGATTGA
1 TATGAATTGATTTATTTTAAATAATTTATAGTATGT-ATTGATTTATTTTA-AAATATGGATTGA
548647 TTTATTTTAAATAATTTATTAG
64 TTTATTTTAAATAATTTATTAG
* ** * * * ** * * *
548669 TATGGATTGATTTATTTTAAA-ATATGGATTG-ATTTATTTTAAATAATTTATTAGTATGGATTG
1 TATGAATTGATTTATTTTAAATA-ATTTATAGTATGTA-TTGATTTATTTTA-AAATATGGATTG
548732 ATTTATTTTAAATAATTTATTAG
63 ATTTATTTTAAATAATTTATTAG
** * * * ** * * *
548755 TATGAATTGATTTATTTTAAA-ATATGGATTG-ATTTATTTTAAATAATTTATTAGTATGGATTG
1 TATGAATTGATTTATTTTAAATA-ATTTATAGTATGTA-TTGATTTATTTTA-AAATATGGATTG
548818 ATTTATTTT-AA-AA--TA-T-G
63 ATTTATTTTAAATAATTTATTAG
548835 ---G-ATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATGGATTGAT
1 TATGAATTGATTTATTTTAAATAATTTA-TAGTATGTATTGATTTATTTTAAAATATGGATTGAT
548896 TTATTTTAAATAATTTATTAG
65 TTATTTTAAATAATTTATTAG
*
548917 TAT-AGATTGATTTATTTTAAATAATTTATCAGTATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGA-ATTGATTTATTTTAAATAATTTAT-AGTATGTATTGATTTATTTT-AA-AA--TA-T-G
548981 TATAGATTGATTTATTTTAAATAATTTATTAG
58 ----GATTGATTTATTTTAAATAATTTATTAG
* ** * * * ** * * *
549013 TATGGATTGATTTATTTTAAA-ATATGGATTG-ATTTATTTTAAATAATTTATTAGTATGGATTG
1 TATGAATTGATTTATTTTAAATA-ATTTATAGTATGTA-TTGATTTATTTTA-AAATATGGATTG
549076 ATTTATTTT-AA-AA--TA-T-G
63 ATTTATTTTAAATAATTTATTAG
**
549093 ---G-ATTGATTTATTTTAAATAATTTATTAGTATAG-ATTGATTTATTTT-AAATAATTTATTA
1 TATGAATTGATTTATTTTAAATAATTTA-TAGTAT-GTATTGATTTATTTTAAAAT-ATGGATT-
** * ** * * *
549152 GTATGGA-TTGATTTATTTTA-AAA
62 G-ATTTATTTTAAATAATTTATTAG
*
549175 TAT-AGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGA
1 TATGA-ATTGATTTATTTTAAATAATTTA-TAGTATGTATTGATTTATTTTAAAATATGGATTGA
549239 TTTATTTTAAATAATTTATTAG
64 TTTATTTTAAATAATTTATTAG
* *
549261 TAT-AGATTGATTTATTTTAAATAATTTATCAGTATGAATTGATTTATTTTAAAATATGGATTTA
1 TATGA-ATTGATTTATTTTAAATAATTTAT-AGTATGTATTGATTTATTTTAAAATATGGATTGA
*
549325 TTTA--TT--AT--TGTAGTT-G
64 TTTATTTTAAATAATTTA-TTAG
* *
549341 TATAAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGAATTGATTTATTTTAAATAATTTA-TAGTATGTATTGATTTATTTTAAAATATGGATTGAT
549406 TTATTTTAAATAATTTATTA
65 TTATTTTAAATAATTTATTA
549426 TTGTAGTTGT
Statistics
Matches: 889, Mismatches: 124, Indels: 196
0.74 0.10 0.16
Matches are distributed among these distances:
75 2 0.00
76 62 0.07
77 30 0.03
78 12 0.01
79 1 0.00
80 111 0.12
81 15 0.02
82 10 0.01
84 20 0.02
85 51 0.06
86 346 0.39
87 18 0.02
88 9 0.01
89 6 0.01
90 17 0.02
91 14 0.02
92 27 0.03
93 20 0.02
94 11 0.01
95 15 0.02
96 92 0.10
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (85 bp):
TATGAATTGATTTATTTTAAATAATTTATAGTATGTATTGATTTATTTTAAAATATGGATTGATT
TATTTTAAATAATTTATTAG
Found at i:548329 original size:18 final size:18
Alignment explanation
Indices: 548306--548384 Score: 51
Period size: 22 Copynumber: 4.4 Consensus size: 18
548296 ATTTTAAATA
548306 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
* *
548324 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AGTATGAATTG
*
548346 ATTTATT--TCA--AA-TA
1 ATTTATTAGT-ATGAATTG
548360 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
548378 ATTTATT
1 ATTTATT
548385 TTAAAATATG
Statistics
Matches: 46, Mismatches: 5, Indels: 20
0.65 0.07 0.28
Matches are distributed among these distances:
14 8 0.17
15 2 0.04
16 2 0.04
17 3 0.07
18 13 0.28
20 4 0.09
22 14 0.30
ACGTcount: A:0.35, C:0.01, G:0.11, T:0.52
Consensus pattern (18 bp):
ATTTATTAGTATGAATTG
Found at i:548394 original size:22 final size:22
Alignment explanation
Indices: 548369--548481 Score: 145
Period size: 22 Copynumber: 5.0 Consensus size: 22
548359 AATTTATTAG
*
548369 TATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
***
548391 TATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTA-T-TT-TA-AAA
*
548417 TATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
548439 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
548461 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
548482 TAATTTATTA
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
22 55 0.71
23 3 0.04
24 4 0.05
25 3 0.04
26 13 0.17
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:548489 original size:14 final size:14
Alignment explanation
Indices: 548470--548554 Score: 53
Period size: 14 Copynumber: 5.5 Consensus size: 14
548460 ATATGGATTG
548470 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* * *
548484 ATTTATTAGTATGGATTG
1 ATTTATT--T-T-AAATA
548502 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
548516 ATTTATTAGTATTAATTG
1 ATTTA-T--T-TTAAATA
548534 ATTTATTTTAAATA
1 ATTTATTTTAAATA
548548 ATTTATT
1 ATTTATT
548555 AGTATGAATT
Statistics
Matches: 53, Mismatches: 10, Indels: 16
0.67 0.13 0.20
Matches are distributed among these distances:
14 26 0.49
15 3 0.06
16 2 0.04
17 3 0.06
18 19 0.36
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.56
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:548537 original size:18 final size:18
Alignment explanation
Indices: 548516--548572 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
548506 ATTTTAAATA
548516 ATTTATTAGTATTAATTG
1 ATTTATTAGTATTAATTG
* *
548534 ATTTA-T--T-TTAAATA
1 ATTTATTAGTATTAATTG
*
548548 ATTTATTAGTATGAATTG
1 ATTTATTAGTATTAATTG
548566 ATTTATT
1 ATTTATT
548573 TTAAAAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 10 0.33
15 2 0.07
17 2 0.07
18 16 0.53
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (18 bp):
ATTTATTAGTATTAATTG
Found at i:548571 original size:140 final size:140
Alignment explanation
Indices: 548416--549393 Score: 811
Period size: 140 Copynumber: 6.9 Consensus size: 140
548406 TATTGTAGTT
548416 GTATGAATTGATTTATTTTAAAA-TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTA
1 GTAT-AATTGATTTATTTTAAAATTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTA
**
548480 AATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATTAATTGATTTATTTTAA
65 AATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAA
548545 ATAATTTATTA
130 ATAATTTATTA
548556 GTATGAATTGATTTATTTTAAAAATTTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGA
1 GTAT-AATTGATTTATTTT-AAAA--TTA-T-G---G-ATTGATTTATTTTAAAATATGGATTGA
* *
548621 TTTA--TT--AT--TGTAGTT-GTATCGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
56 TTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
**
548679 TTTATTTTAAA-ATATGGATT-
120 TTTATTTTAAATA-ATTTATTA
* * * ** * ** * * * *
548699 GATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAATA---ATTTA-TTAGTATG
1 G-TATAATTGATTTATTTTAAAATTATGGATTGATTTATTTTAAAATATGGATTGATTTA-TTTT
* * *
548759 AATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAT
64 AAATAATTTA--TT--AGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAT
**
548824 TTTAAA-ATATGGATT-
125 TTTAAATA-ATTTATTA
* * * ** * ** * *
548839 GATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATGGATTGATTTATTTTA
1 G-TATAATTGATTTATTTTAAAATTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTA
* *
548904 AATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATCAGTATGGATTGATTTATTTTAA
65 AATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAA
548969 ATAATTTATTA
130 ATAATTTATTA
548980 GTATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
1 GTATA-ATTGATTTATTTT--A-AA---A-T--TATGGATTGATTTATTTTAAAATATGGATTGA
549045 TTTATTTTAAATAATTTATTAGTATGGATTGATTTA-TTT---TAA---A--A-TATGGATTGAT
56 TTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
549100 TTATTTTAAATAATTTATTA
121 TTATTTTAAATAATTTATTA
*
549120 GTATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGA
1 GTATA-ATTGATTTATTTT--A-AA---A-T--TATGGATTGATTTATTTTAAAATATGGATTGA
*
549185 TTTATTTTAAATAATTTATTAGTATGAATTGATTTA-TTT---TAA---A--A-TATGGATTGAT
56 TTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
549240 TTATTTTAAATAATTTATTA
121 TTATTTTAAATAATTTATTA
*
549260 GTATAGATTGATTTATTTTAAATAATTTATCAGTATGAATTGATTTATTTTAAAATATGGATTTA
1 GTATA-ATTGATTTATTTT-AA-AA-TTAT--G---G-ATTGATTTATTTTAAAATATGGATTGA
* **
549325 TTTA--TT--AT--TGTAGTT-GTATAAATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
56 TTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
549383 TTTATTTTAAA
120 TTTATTTTAAA
549394 ATATGGATTG
Statistics
Matches: 729, Mismatches: 50, Indels: 114
0.82 0.06 0.13
Matches are distributed among these distances:
129 3 0.00
130 4 0.01
132 1 0.00
133 5 0.01
134 34 0.05
135 6 0.01
136 9 0.01
137 2 0.00
138 7 0.01
139 5 0.01
140 400 0.55
141 21 0.03
142 4 0.01
143 14 0.02
144 98 0.13
145 6 0.01
146 6 0.01
147 1 0.00
148 2 0.00
149 4 0.01
150 97 0.13
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (140 bp):
GTATAATTGATTTATTTTAAAATTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
ATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
TAATTTATTA
Found at i:548694 original size:22 final size:22
Alignment explanation
Indices: 548669--548711 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
548659 AATTTATTAG
548669 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
548691 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
548712 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:548780 original size:22 final size:22
Alignment explanation
Indices: 548755--548797 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
548745 AATTTATTAG
548755 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
548777 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
548798 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:548834 original size:22 final size:22
Alignment explanation
Indices: 548809--548851 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
548799 AATTTATTAG
548809 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
548831 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
548852 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:548879 original size:22 final size:22
Alignment explanation
Indices: 548863--548905 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
548853 AATTTATTAG
*
548863 TATGTATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
548885 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
548906 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:549038 original size:22 final size:22
Alignment explanation
Indices: 549013--549055 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
549003 AATTTATTAG
549013 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
549035 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
549056 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:549092 original size:22 final size:22
Alignment explanation
Indices: 549067--549109 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
549057 AATTTATTAG
549067 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
549089 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
549110 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:549117 original size:14 final size:14
Alignment explanation
Indices: 549098--549150 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
549088 ATATGGATTG
549098 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
549112 ATTTATTAGTATAGATTG
1 ATTTATT--T-TA-AATA
549130 ATTTATTTTAAATA
1 ATTTATTTTAAATA
549144 ATTTATT
1 ATTTATT
549151 AGTATGGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 16 0.52
15 2 0.06
16 2 0.06
17 2 0.06
18 9 0.29
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:549232 original size:22 final size:22
Alignment explanation
Indices: 549207--549249 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
549197 AATTTATTAG
549207 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
549229 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
549250 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:549257 original size:14 final size:14
Alignment explanation
Indices: 549238--549289 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
549228 ATATGGATTG
549238 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
549252 ATTTATTAGTATAGATTG
1 ATTTATT--T-TA-AATA
549270 ATTTATTTTAAATA
1 ATTTATTTTAAATA
549284 ATTTAT
1 ATTTAT
549290 CAGTATGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
14 15 0.50
15 2 0.07
16 2 0.07
17 2 0.07
18 9 0.30
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:549398 original size:22 final size:22
Alignment explanation
Indices: 549373--549415 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
549363 AATTTATTAG
549373 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
549395 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
549416 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:549475 original size:31 final size:31
Alignment explanation
Indices: 549440--549498 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
549430 AGTTGTATGT
* *
549440 ATTATTTAAATTTTAATATTGT-AAAACTAAA
1 ATTATTTAAATCTCAATATT-TCAAAACTAAA
549471 ATTATTTAAATCTCAATATTTCAAAACT
1 ATTATTTAAATCTCAATATTTCAAAACT
549499 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (31 bp):
ATTATTTAAATCTCAATATTTCAAAACTAAA
Found at i:552857 original size:21 final size:21
Alignment explanation
Indices: 552831--552870 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
552821 GTAAAGCGCC
552831 AATAATAACATTTTCGATAGA
1 AATAATAACATTTTCGATAGA
*
552852 AATAATAATATTTTCGATA
1 AATAATAACATTTTCGATA
552871 ATTCTTTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.38
Consensus pattern (21 bp):
AATAATAACATTTTCGATAGA
Found at i:553066 original size:42 final size:42
Alignment explanation
Indices: 553020--553104 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
553010 CGTCTGAATA
553020 AACTTTTGTAAATATAAAACATCGTTGATTGTGTATGTAGCT
1 AACTTTTGTAAATATAAAACATCGTTGATTGTGTATGTAGCT
553062 AACTTTTGTAAATATAAAACATCGTTGATTGTGTATGTAGCT
1 AACTTTTGTAAATATAAAACATCGTTGATTGTGTATGTAGCT
553104 A
1 A
553105 TTTTTATTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.40
Consensus pattern (42 bp):
AACTTTTGTAAATATAAAACATCGTTGATTGTGTATGTAGCT
Found at i:561895 original size:60 final size:60
Alignment explanation
Indices: 561766--561904 Score: 172
Period size: 60 Copynumber: 2.3 Consensus size: 60
561756 TAATGAATAT
* * * *
561766 TCGGGTGATCATTTTGTAAATTTTAATAGTCGAGGGACTCAACAAAGTAATATTATATGA
1 TCGGGGGACCATTTTGTAAATTTTAATAGTCGAGGGACTCAACAAAGTAATATCATATAA
** * * *
561826 TCGAAGGACCATTTTGTAACA-TTTAATAGTCGAGGGACTTAATAAAGTAATATCCTATAA
1 TCGGGGGACCATTTTGTAA-ATTTTAATAGTCGAGGGACTCAACAAAGTAATATCATATAA
561886 TCGGGGGACCATTTGTGTA
1 TCGGGGGACCATTT-TGTA
561905 CTTTATCCTA
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
60 61 0.92
61 5 0.08
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (60 bp):
TCGGGGGACCATTTTGTAAATTTTAATAGTCGAGGGACTCAACAAAGTAATATCATATAA
Found at i:562496 original size:21 final size:23
Alignment explanation
Indices: 562452--562510 Score: 77
Period size: 21 Copynumber: 2.6 Consensus size: 23
562442 AACGTATTAT
*
562452 TATAAATTATTTATAAATTTAAA
1 TATAAATTATTTATAAATTAAAA
562475 TATAAATTATTTA-AAA-TAAAA
1 TATAAATTATTTATAAATTAAAA
*
562496 TATTAATTATATTAT
1 TATAAATTAT-TTAT
562511 TTTATAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 13 0.41
22 6 0.19
23 13 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TATAAATTATTTATAAATTAAAA
Found at i:562788 original size:12 final size:12
Alignment explanation
Indices: 562737--562788 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
562727 TACTCATACT
562737 ATATATATAATA
1 ATATATATAATA
562749 ATA-ATAATAATA
1 ATATAT-ATAATA
*
562761 ATAAATAT-AT-
1 ATATATATAATA
*
562771 ATATATATACTA
1 ATATATATAATA
562783 ATATAT
1 ATATAT
562789 GTAGAAGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
10 7 0.21
11 5 0.15
12 20 0.59
13 2 0.06
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATATATAATA
Found at i:567885 original size:24 final size:24
Alignment explanation
Indices: 567858--567905 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
567848 TCAATTCATG
567858 TAAATT-TTTAATTAATAATTTTGT
1 TAAATTATTTAATTAAT-ATTTTGT
*
567882 TAAATTATTTAGTTAATATTTTGT
1 TAAATTATTTAATTAATATTTTGT
567906 GATTTTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (24 bp):
TAAATTATTTAATTAATATTTTGT
Found at i:568121 original size:20 final size:20
Alignment explanation
Indices: 568096--568149 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
568086 TAATTTATTT
*
568096 TTTAAATAATGTTTAATATA
1 TTTAAATAATATTTAATATA
*
568116 TTTAAATAATATTTTATATA
1 TTTAAATAATATTTAATATA
*
568136 TTTATATTAATATT
1 TTTA-AATAATATT
568150 ATGTTTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 22 0.73
21 8 0.27
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTAAATAATATTTAATATA
Found at i:568146 original size:21 final size:21
Alignment explanation
Indices: 568063--568149 Score: 64
Period size: 20 Copynumber: 4.5 Consensus size: 21
568053 TGTGTAAATT
568063 TATTAAATATTTT-TAT-TTTA
1 TATT-AATATTTTATATATTTA
*
568083 TATT-A-A-TTTAT-TTTTTA
1 TATTAATATTTTATATATTTA
* * *
568100 -AATAATGTTTAATATATTTA
1 TATTAATATTTTATATATTTA
*
568120 -AATAATATTTTATATATTTA
1 TATTAATATTTTATATATTTA
568140 TATTAATATT
1 TATTAATATT
568150 ATGTTTTTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
16 6 0.11
17 7 0.13
18 1 0.02
19 4 0.08
20 27 0.51
21 8 0.15
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (21 bp):
TATTAATATTTTATATATTTA
Found at i:572345 original size:16 final size:15
Alignment explanation
Indices: 572315--572348 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
572305 TCAGTTAATC
572315 ATATGAAATTATTAA
1 ATATGAAATTATTAA
*
572330 ATATTAAATATATTAA
1 ATATGAAAT-TATTAA
572346 ATA
1 ATA
572349 CATATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
ATATGAAATTATTAA
Found at i:574506 original size:21 final size:21
Alignment explanation
Indices: 574476--574521 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
574466 ATATATTATT
* *
574476 TTTTTTAAATTTAGAATAATA
1 TTTTTAAAATTTAAAATAATA
574497 TTTTTAAAATTTAAAATAATA
1 TTTTTAAAATTTAAAATAATA
574518 TTTT
1 TTTT
574522 CATCAACCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTTTAAAATTTAAAATAATA
Found at i:574926 original size:20 final size:20
Alignment explanation
Indices: 574901--574938 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
574891 ACATTTTTAC
574901 ATTTTTTAATAAAATTTATA
1 ATTTTTTAATAAAATTTATA
*
574921 ATTTTTTTATAAAATTTA
1 ATTTTTTAATAAAATTTA
574939 AAAGATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTTTTAATAAAATTTATA
Found at i:578368 original size:20 final size:21
Alignment explanation
Indices: 578343--578381 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
578333 TATTTTTTTA
*
578343 TTTTTTAATA-ATAAAAATAT
1 TTTTTTAAAAGATAAAAATAT
578363 TTTTTTAAAAGATAAAAAT
1 TTTTTTAAAAGATAAAAAT
578382 TTAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (21 bp):
TTTTTTAAAAGATAAAAATAT
Found at i:583178 original size:103 final size:103
Alignment explanation
Indices: 582982--583180 Score: 283
Period size: 103 Copynumber: 1.9 Consensus size: 103
582972 TCCAGATGCA
* * *
582982 AGAAACCAACCACATTCACAAAAGTTCCCTATCTTCCTCGAACTCTAATTAAACGGGATTAGAAA
1 AGAAACCAACCACATTCACAAAAGTTCCCTATCTTCCTCAAACTCGAATTAAAAGGGATTAGAAA
* *
583047 CCACAATTCATATATAAGTGATACTTAAAAAAGAGATT
66 CCAAAATTCATATATAAGTGACACTTAAAAAAGAGATT
* * *
583085 AGAAACTAACCACATTCACAAAAGTTCCCTGTCTTCTTCAAACTCGAATTAAAAGGGATTAGAAA
1 AGAAACCAACCACATTCACAAAAGTTCCCTATCTTCCTCAAACTCGAATTAAAAGGGATTAGAAA
** *
583150 CCAAAATTTC-TATATCGGTGACATTTAAAAA
66 CCAAAA-TTCATATATAAGTGACACTTAAAAA
583181 GGGTTTAATT
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
103 81 0.96
104 3 0.04
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (103 bp):
AGAAACCAACCACATTCACAAAAGTTCCCTATCTTCCTCAAACTCGAATTAAAAGGGATTAGAAA
CCAAAATTCATATATAAGTGACACTTAAAAAAGAGATT
Found at i:586646 original size:25 final size:26
Alignment explanation
Indices: 586618--586684 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
586608 ATTGGCATTA
*
586618 ATTTATGTTTTTAAA-AAAAATAAAT
1 ATTTATATTTTTAAACAAAAATAAAT
* *
586643 ATTTATATATTTAAATCAAAAATATAT
1 ATTTATATTTTTAAA-CAAAAATAAAT
*
586670 ATTTATCTTTATTAA
1 ATTTATATTT-TTAA
586685 CTTATTACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 13 0.38
27 17 0.50
28 4 0.12
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (26 bp):
ATTTATATTTTTAAACAAAAATAAAT
Found at i:587841 original size:31 final size:32
Alignment explanation
Indices: 587794--587853 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
587784 ATTTAATATT
*
587794 TTTTTAATTTAGATATT-AATTGA-ATAATTA
1 TTTTTAATTTAAATATTAAATTGAGATAATTA
587824 TTTTTAAGTTTAAATATTAAATTGAGATAA
1 TTTTTAA-TTTAAATATTAAATTGAGATAA
587854 AAATTTTGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 7 0.27
31 9 0.35
32 6 0.23
33 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (32 bp):
TTTTTAATTTAAATATTAAATTGAGATAATTA
Found at i:594085 original size:261 final size:261
Alignment explanation
Indices: 593621--594146 Score: 1025
Period size: 261 Copynumber: 2.0 Consensus size: 261
593611 CAACAATGCC
593621 ATCCATAAATTAAATGAAGCAACAAGGTGCAAATCCCAGTACACATCTCTGGTCAAATGATGAGA
1 ATCCATAAATTAAATGAAGCAACAAGGTGCAAATCCCAGTACACATCTCTGGTCAAATGATGAGA
593686 TCTTGGAAGATAGCCAAGCCTCTCATGAAATAATCTTAGCAACAAAAGAATGCTCTAATGTTCCC
66 TCTTGGAAGATAGCCAAGCCTCTCATGAAATAATCTTAGCAACAAAAGAATGCTCTAATGTTCCC
*
593751 ATAACACCCTCGAATCAATGCTTTGTTACAACAATAATAATAACCCCACTCGGGCTACTCCCATT
131 ATAACACCCTCGAATCAATGCCTTGTTACAACAATAATAATAACCCCACTCGGGCTACTCCCATT
593816 AAATAACTCGGAAACTAGATAACTAAATGCAAACATGTCCTGCACCCAACGCTGAAACTATCACT
196 AAATAACTCGGAAACTAGATAACTAAATGCAAACATGTCCTGCACCCAACGCTGAAACTATCACT
593881 T
261 T
593882 ATCCATAAATTAAATGAAGCAACAAGGTGCAAATCCCAGTACACATCTCTGGTCAAATGATGAGA
1 ATCCATAAATTAAATGAAGCAACAAGGTGCAAATCCCAGTACACATCTCTGGTCAAATGATGAGA
* *
593947 TCTTGGAAGATAGCCAAGCCTCTCATGAAATTATCTTGGCAACAAAAGAATGCTCTAATGTTCCC
66 TCTTGGAAGATAGCCAAGCCTCTCATGAAATAATCTTAGCAACAAAAGAATGCTCTAATGTTCCC
594012 ATAACACCCTCGAATCAATGCCTTGTTACAACAATAATAATAACCCCACTCGGGCTACTCCCATT
131 ATAACACCCTCGAATCAATGCCTTGTTACAACAATAATAATAACCCCACTCGGGCTACTCCCATT
594077 AAATAACTCGGAAACTAGATAACTAAATGCAAACATGTCCTGCACCCAACGCTGAAACTATCACT
196 AAATAACTCGGAAACTAGATAACTAAATGCAAACATGTCCTGCACCCAACGCTGAAACTATCACT
594142 T
261 T
594143 ATCC
1 ATCC
594147 TGTGTTATGC
Statistics
Matches: 262, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
261 262 1.00
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.24
Consensus pattern (261 bp):
ATCCATAAATTAAATGAAGCAACAAGGTGCAAATCCCAGTACACATCTCTGGTCAAATGATGAGA
TCTTGGAAGATAGCCAAGCCTCTCATGAAATAATCTTAGCAACAAAAGAATGCTCTAATGTTCCC
ATAACACCCTCGAATCAATGCCTTGTTACAACAATAATAATAACCCCACTCGGGCTACTCCCATT
AAATAACTCGGAAACTAGATAACTAAATGCAAACATGTCCTGCACCCAACGCTGAAACTATCACT
T
Found at i:604705 original size:19 final size:19
Alignment explanation
Indices: 604683--604736 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 19
604673 CAATAAATAT
604683 TTACAATCACAATCGTAAA
1 TTACAATCACAATCGTAAA
*
604702 TTACAAT-A-AA--G--AT
1 TTACAATCACAATCGTAAA
604715 TTACAATCACAATCGTAAA
1 TTACAATCACAATCGTAAA
604734 TTA
1 TTA
604737 AGCACATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
13 8 0.30
14 1 0.04
15 3 0.11
17 3 0.11
18 1 0.04
19 11 0.41
ACGTcount: A:0.48, C:0.17, G:0.06, T:0.30
Consensus pattern (19 bp):
TTACAATCACAATCGTAAA
Found at i:604708 original size:32 final size:32
Alignment explanation
Indices: 604667--604736 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
604657 GAAAAATCTC
*
604667 AAATTACAATAAATATTTACAATCACAATCGT
1 AAATTACAATAAAGATTTACAATCACAATCGT
604699 AAATTACAATAAAGATTTACAATCACAATCGT
1 AAATTACAATAAAGATTTACAATCACAATCGT
604731 AAATTA
1 AAATTA
604737 AGCACATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.30
Consensus pattern (32 bp):
AAATTACAATAAAGATTTACAATCACAATCGT
Found at i:611968 original size:30 final size:31
Alignment explanation
Indices: 611925--611982 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
611915 AATTTTAAAT
611925 TCCTTTTGAATTTTCTGT-TTTTTTATCAAA
1 TCCTTTTGAATTTTCTGTATTTTTTATCAAA
* *
611955 TCCTTTT-ATATTTTTTTTATTTTTTATC
1 TCCTTTTGA-ATTTTCTGTATTTTTTATC
611983 TTAACAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 1 0.04
30 14 0.58
31 9 0.38
ACGTcount: A:0.17, C:0.12, G:0.03, T:0.67
Consensus pattern (31 bp):
TCCTTTTGAATTTTCTGTATTTTTTATCAAA
Found at i:613013 original size:12 final size:13
Alignment explanation
Indices: 612983--613017 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
612973 TGTTGGGTTT
*
612983 TTTTTTGTTTGAAG
1 TTTTTT-TTTAAAG
612997 TTTTTTTTTAAAG
1 TTTTTTTTTAAAG
613010 TTTTTTTT
1 TTTTTTTT
613018 CTTGAAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.74
Consensus pattern (13 bp):
TTTTTTTTTAAAG
Found at i:613472 original size:28 final size:29
Alignment explanation
Indices: 613414--613472 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
613404 AAACAGAACA
613414 AAAACAAGAGGGAGGGCAGGAAGAAGATG
1 AAAACAAGAGGGAGGGCAGGAAGAAGATG
* *
613443 AAAACGAGAGGGAGGG-GGGAAGAAGATG
1 AAAACAAGAGGGAGGGCAGGAAGAAGATG
613471 AA
1 AA
613473 CATGTGCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 13 0.46
29 15 0.54
ACGTcount: A:0.47, C:0.05, G:0.44, T:0.03
Consensus pattern (29 bp):
AAAACAAGAGGGAGGGCAGGAAGAAGATG
Done.