Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007768.1 Hibiscus syriacus cultivar Beakdansim tig00110044_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: 2539099
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 11
Found at i:441430 original size:20 final size:20
Alignment explanation
Indices: 441405--441444 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
441395 AATCCAACAT
441405 TTCATTCAAGGACAAAGCAC
1 TTCATTCAAGGACAAAGCAC
441425 TTCATTCAAGGACAAAGCAC
1 TTCATTCAAGGACAAAGCAC
441445 ATACGAGTTC
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:0.40, C:0.25, G:0.15, T:0.20
Consensus pattern (20 bp):
TTCATTCAAGGACAAAGCAC
Found at i:443560 original size:30 final size:30
Alignment explanation
Indices: 443524--443606 Score: 112
Period size: 30 Copynumber: 2.7 Consensus size: 30
443514 ATATCAGATT
443524 GATTGATTTCGGGTCAGATCAAATCAAAGC
1 GATTGATTTCGGGTCAGATCAAATCAAAGC
* * *
443554 GATTGATTTCGGGTCAGATTAAATCAGATC
1 GATTGATTTCGGGTCAGATCAAATCAAAGC
* *
443584 GATTGATTTTCGAGTCAGGTCAA
1 GATTGA-TTTCGGGTCAGATCAA
443607 TATCCAATCG
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 33 0.72
31 13 0.28
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (30 bp):
GATTGATTTCGGGTCAGATCAAATCAAAGC
Found at i:443625 original size:28 final size:28
Alignment explanation
Indices: 443588--443647 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
443578 CAGATCGATT
443588 GATTTTCGAGTCAGGTCAATATCCAATC
1 GATTTTCGAGTCAGGTCAATATCCAATC
443616 GATTTTCGAGTCAGGTCAATATCCAATC
1 GATTTTCGAGTCAGGTCAATATCCAATC
443644 GATT
1 GATT
443648 ATTTTCGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (28 bp):
GATTTTCGAGTCAGGTCAATATCCAATC
Found at i:443664 original size:31 final size:31
Alignment explanation
Indices: 443601--443690 Score: 80
Period size: 31 Copynumber: 3.0 Consensus size: 31
443591 TTTCGAGTCA
**
443601 GGTCAATATCCAATCG---ATTTTCGAG-TCA
1 GGTCAATATCCAATCGATTATTTTCG-GTTTG
443629 GGTCAATATCCAATCGATTATTTTCGGTTTG
1 GGTCAATATCCAATCGATTATTTTCGGTTTG
* ** * *
443660 GGTCACTATCTGATCAATTATTTTCGATTTG
1 GGTCAATATCCAATCGATTATTTTCGGTTTG
443691 AGTTAACTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
28 16 0.31
30 1 0.02
31 34 0.67
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (31 bp):
GGTCAATATCCAATCGATTATTTTCGGTTTG
Found at i:444497 original size:59 final size:60
Alignment explanation
Indices: 444356--444499 Score: 157
Period size: 60 Copynumber: 2.4 Consensus size: 60
444346 TCATATGTCT
** * * **
444356 TAAACTATGACCCTCATT-TCAAATTAGTCCTTAAACTTTTAAATATTTCAATTTCATCTT
1 TAAACTATGAATCTCATTCT-AAATTAATCCTTAAACTTTTAAACATTTCAATTTCATCCC
* * ** *
444416 TGAATTATGCCTCTCATTCTAAATTAATCCTTAAACTTTTTAACATTT-AATTTCATCCC
1 TAAACTATGAATCTCATTCTAAATTAATCCTTAAACTTTTAAACATTTCAATTTCATCCC
*
444475 TAAACTATGAATGTCATTCTAAATT
1 TAAACTATGAATCTCATTCTAAATT
444500 GGTTCATACA
Statistics
Matches: 69, Mismatches: 14, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
59 29 0.42
60 39 0.57
61 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.43
Consensus pattern (60 bp):
TAAACTATGAATCTCATTCTAAATTAATCCTTAAACTTTTAAACATTTCAATTTCATCCC
Found at i:448772 original size:2 final size:2
Alignment explanation
Indices: 448726--448753 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
448716 AACAGTGAGG
448726 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
448754 TGATTTTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:450237 original size:19 final size:19
Alignment explanation
Indices: 450215--450297 Score: 60
Period size: 19 Copynumber: 4.2 Consensus size: 19
450205 TCGTTGCGAT
*
450215 TTTGGACTATCGTAACGAA
1 TTTGGACTATCGCAACGAA
*
450234 TTTGGAATAAATCGCAACGCGAA
1 TTTGGACT--ATCGCAA--CGAA
* *
450257 CTTCGACTATCGCAAC-AA
1 TTTGGACTATCGCAACGAA
* *
450275 TCTTGGACTATTGTAACGAA
1 T-TTGGACTATCGCAACGAA
450295 TTT
1 TTT
450298 ATAATAAATC
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
18 2 0.04
19 22 0.45
20 3 0.06
21 13 0.27
23 9 0.18
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (19 bp):
TTTGGACTATCGCAACGAA
Found at i:450311 original size:61 final size:61
Alignment explanation
Indices: 450216--450342 Score: 193
Period size: 61 Copynumber: 2.1 Consensus size: 61
450206 CGTTGCGATT
* *
450216 TTGGACTATCGTAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAAC-AATC
1 TTGGACTATCGTAACGAATTTAGAATAAATCGCAACGCGAACTTAGACTATCGCAACGAA-C
* * *
450277 TTGGACTATTGTAACGAATTTATAATAAATCGCAACGCGAACTTAGAGTATCGCAACGAAC
1 TTGGACTATCGTAACGAATTTAGAATAAATCGCAACGCGAACTTAGACTATCGCAACGAAC
450338 TTGGA
1 TTGGA
450343 ATAAATCGCA
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (61 bp):
TTGGACTATCGTAACGAATTTAGAATAAATCGCAACGCGAACTTAGACTATCGCAACGAAC
Found at i:450352 original size:21 final size:19
Alignment explanation
Indices: 450216--450345 Score: 55
Period size: 19 Copynumber: 6.4 Consensus size: 19
450206 CGTTGCGATT
* * *
450216 TTGGACTATCGTAACGAAT
1 TTGGAATATCGCAACGAAC
450235 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
* *
450258 TTCGACTATCGCAAC-AATC
1 TTGGAATATCGCAACGAA-C
* * * *
450277 TTGGACTATTGTAACGAAT
1 TTGGAATATCGCAACGAAC
**
450296 TTATAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
* *
450319 TTAGAGTATCGCAACGAAC
1 TTGGAATATCGCAACGAAC
450338 TTGGAATA
1 TTGGAATA
450346 AATCGCAGCG
Statistics
Matches: 82, Mismatches: 19, Indels: 20
0.68 0.16 0.17
Matches are distributed among these distances:
18 2 0.02
19 35 0.43
20 2 0.02
21 25 0.30
23 18 0.22
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (19 bp):
TTGGAATATCGCAACGAAC
Found at i:450361 original size:23 final size:22
Alignment explanation
Indices: 450300--450365 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
450290 ACGAATTTAT
*
450300 AATAAATCGCAACGCGAACTTAG
1 AATAAATCGC-ACGCGAACTTGG
* *
450323 AGT--ATCGCA-ACGAACTTGG
1 AATAAATCGCACGCGAACTTGG
450342 AATAAATCGCAGCGCGAACTTGG
1 AATAAATCGCA-CGCGAACTTGG
450365 A
1 A
450366 CTATCACAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
19 10 0.29
20 1 0.03
21 11 0.32
23 12 0.35
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (22 bp):
AATAAATCGCACGCGAACTTGG
Found at i:451096 original size:16 final size:15
Alignment explanation
Indices: 451066--451105 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
451056 GTTTATTTCA
*
451066 GAATGATTAAGTGTT
1 GAATGATTAAATGTT
451081 GAATGATTTAAATGTT
1 GAATGA-TTAAATGTT
*
451097 GAATAATTA
1 GAATGATTA
451106 GAGATGGCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (15 bp):
GAATGATTAAATGTT
Found at i:454632 original size:22 final size:23
Alignment explanation
Indices: 454602--454647 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
454592 AAAATATATC
454602 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
454625 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
454647 T
1 T
454648 CAATGTTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:454827 original size:12 final size:12
Alignment explanation
Indices: 454810--454841 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
454800 CAATCCAGGC
454810 GACATACGGGGT
1 GACATACGGGGT
454822 GACATACGGGGT
1 GACATACGGGGT
454834 GACATACG
1 GACATACG
454842 AGCCATACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.28, C:0.19, G:0.38, T:0.16
Consensus pattern (12 bp):
GACATACGGGGT
Found at i:454876 original size:35 final size:35
Alignment explanation
Indices: 454836--455058 Score: 304
Period size: 35 Copynumber: 6.0 Consensus size: 35
454826 TACGGGGTGA
454836 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
1 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
454871 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
1 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
**
454906 CATACGAGCCATACGAGCCAATGGTTCT-CCGGTG
1 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
454940 ACATACGGGGTGACATACGAGCCATACGAGCCAATGGTTCTCCCCATG
1 -CATAC-----G-------AGCCATACGAGCCAATGGTTCTCCCCATG
454988 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
1 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
455023 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
1 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
455058 C
1 C
455059 GAGGTTGCCA
Statistics
Matches: 170, Mismatches: 4, Indels: 28
0.84 0.02 0.14
Matches are distributed among these distances:
34 4 0.02
35 133 0.78
40 1 0.01
42 1 0.01
47 27 0.16
48 4 0.02
ACGTcount: A:0.26, C:0.33, G:0.22, T:0.20
Consensus pattern (35 bp):
CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
Found at i:455025 original size:117 final size:117
Alignment explanation
Indices: 454819--455052 Score: 468
Period size: 117 Copynumber: 2.0 Consensus size: 117
454809 CGACATACGG
454819 GGTGACATACGGGGTGACATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATA
1 GGTGACATACGGGGTGACATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATA
454884 CGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCC
66 CGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCC
454936 GGTGACATACGGGGTGACATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATA
1 GGTGACATACGGGGTGACATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATA
455001 CGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCC
66 CGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCC
455053 CCATGCGAGG
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 117 1.00
ACGTcount: A:0.26, C:0.31, G:0.24, T:0.20
Consensus pattern (117 bp):
GGTGACATACGGGGTGACATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATA
CGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCC
Found at i:455027 original size:82 final size:82
Alignment explanation
Indices: 454871--455028 Score: 282
Period size: 82 Copynumber: 1.9 Consensus size: 82
454861 TCTCCCCATG
454871 CATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCC
1 CATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCC
**
454936 GGTGACATACGGGGTGA
66 CATGACATACGGGGTGA
454953 CATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCC
1 CATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCT-C
455018 CCATG-CATACG
65 CCATGACATACG
455029 AGCCATACGA
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
82 69 0.95
83 4 0.05
ACGTcount: A:0.26, C:0.32, G:0.23, T:0.20
Consensus pattern (82 bp):
CATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCC
CATGACATACGGGGTGA
Found at i:455143 original size:29 final size:29
Alignment explanation
Indices: 455093--455172 Score: 126
Period size: 29 Copynumber: 2.8 Consensus size: 29
455083 AGGAATAGAG
* *
455093 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
455122 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
455151 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
455173 CCATTCCCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 46 0.96
30 2 0.04
ACGTcount: A:0.15, C:0.31, G:0.33, T:0.21
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:455388 original size:25 final size:25
Alignment explanation
Indices: 455359--455410 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
455349 TGTACAATTA
455359 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTGAGGCAGCCGG
455384 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTGAGGCAGCCGG
455409 TT
1 TT
455411 ATAAAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.35, T:0.27
Consensus pattern (25 bp):
TTGGTGAAATAATTGAGGCAGCCGG
Found at i:455451 original size:23 final size:23
Alignment explanation
Indices: 455423--455468 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
455413 AAAAGAAAGA
455423 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
455446 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
455469 CCGAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.39, T:0.09
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:455483 original size:25 final size:23
Alignment explanation
Indices: 455423--455483 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
455413 AAAAGAAAGA
**
455423 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
455446 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
455469 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
455484 AGGGAGAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 23 0.70
25 10 0.30
ACGTcount: A:0.51, C:0.07, G:0.36, T:0.07
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:455497 original size:21 final size:21
Alignment explanation
Indices: 455473--455525 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
455463 TTGCAGCCGA
455473 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
455494 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
*
455515 GAAAGTAAGAA
1 GAAAGAAAGAA
455526 GAAGAAAGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (21 bp):
GAAAGAAAGAAAGGGAGAAAG
Found at i:455519 original size:17 final size:16
Alignment explanation
Indices: 455471--455502 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
455461 GATTGCAGCC
455471 GAGAAAGAAAGAAAGG
1 GAGAAAGAAAGAAAGG
455487 GAGAAAGGAAAGAAAG
1 GAGAAA-GAAAGAAAG
455503 AAAGGGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
GAGAAAGAAAGAAAGG
Found at i:455731 original size:41 final size:41
Alignment explanation
Indices: 455685--455794 Score: 118
Period size: 44 Copynumber: 2.6 Consensus size: 41
455675 GTATACATAA
455685 ATTAAAAATTATTTAATTAGTATATG-TTTG-ATAGTTA-TAT
1 ATTAAAAATTATTTAATTAGT-T-TGTTTTGTATAGTTAGTAT
* *
455725 AGTTAAAAAATAATTAATTAGTTTGTTTTGTTAATAGTTAGTTAT
1 A-TTAAAAATTATTTAATTAGTTTGTTTTG-T-ATAGTTAG-TAT
*
455770 ATAAAAAATTATTTAATTAGTTTGT
1 ATTAAAAATTATTTAATTAGTTTGT
455795 GTTAGTTAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
39 2 0.03
40 6 0.10
41 18 0.31
43 7 0.12
44 21 0.36
45 4 0.07
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (41 bp):
ATTAAAAATTATTTAATTAGTTTGTTTTGTATAGTTAGTAT
Found at i:455791 original size:44 final size:46
Alignment explanation
Indices: 455728--455818 Score: 134
Period size: 44 Copynumber: 2.0 Consensus size: 46
455718 GTTATATAGT
*
455728 TAAAAAATAATTAATTAGTTTGT-TTTGTT-AATAGTT-AGTTATA
1 TAAAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATA
*
455771 TAAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATA
1 TAAAAAA-TAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATA
455818 T
1 T
455819 TTGTTTGTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 7 0.17
44 15 0.36
45 5 0.12
46 7 0.17
47 8 0.19
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (46 bp):
TAAAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATA
Found at i:456013 original size:16 final size:16
Alignment explanation
Indices: 455981--456027 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
455971 TTTAAAAAGT
*
455981 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
455997 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
456013 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
456028 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:456022 original size:15 final size:14
Alignment explanation
Indices: 456002--456032 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
455992 GTTTATTAGT
456002 TTATTATATTATAAG
1 TTATTATATTA-AAG
456017 TTATTATATTAAAG
1 TTATTATATTAAAG
456031 TT
1 TT
456033 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:458205 original size:17 final size:17
Alignment explanation
Indices: 458183--458215 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
458173 CAATGATTTT
*
458183 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
458200 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
458216 AATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:458232 original size:24 final size:22
Alignment explanation
Indices: 458200--458268 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
458190 AAATCATTAC
458200 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
* *
458222 TAGTAAATCAACTATTTTAAATCA-T
1 TAGT--ATCAAATA-ATTAAAT-ATT
458247 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
458269 AACAATAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
21 1 0.03
22 11 0.29
23 7 0.18
24 7 0.18
25 11 0.29
26 1 0.03
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (22 bp):
TAGTATCAAATAATTAAATATT
Found at i:460441 original size:26 final size:24
Alignment explanation
Indices: 460383--460441 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
460373 CTAATAAACC
*
460383 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
460407 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
460435 TAATAAT
1 TAATAAT
460442 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:461232 original size:41 final size:45
Alignment explanation
Indices: 461187--461295 Score: 127
Period size: 47 Copynumber: 2.4 Consensus size: 45
461177 GTTTAAAGAC
* *
461187 ACTAACAAATTAATTAATATTTTT-TAT-AT-TTA-ATAACTTAA
1 ACTAACAAACTAATTAATATTTTTATATAATAATATATAACTTAA
*
461228 ACTAAGAAACTAATTAACTAATTTTTATATAATAATATATAACTTAA
1 ACTAACAAACTAATTAA-T-ATTTTTATATAATAATATATAACTTAA
*
461275 ACTAATAAACTAATATAATAT
1 ACTAACAAACTAAT-TAATAT
461296 AACTTAAACT
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
41 15 0.26
42 1 0.02
43 6 0.11
44 3 0.05
45 2 0.04
46 4 0.07
47 23 0.40
48 3 0.05
ACGTcount: A:0.50, C:0.08, G:0.01, T:0.40
Consensus pattern (45 bp):
ACTAACAAACTAATTAATATTTTTATATAATAATATATAACTTAA
Found at i:461324 original size:28 final size:28
Alignment explanation
Indices: 461257--461324 Score: 102
Period size: 28 Copynumber: 2.4 Consensus size: 28
461247 AATTTTTATA
*
461257 TAATAATATATAACTTAAACTAATAAAC
1 TAATAATATATAACTTAAACTAACAAAC
461285 TAAT-ATAATATAACTTAAACTAACAAAC
1 TAATAAT-ATATAACTTAAACTAACAAAC
*
461313 TAATAATTTATA
1 TAATAATATATA
461325 CTAACAAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 32 0.89
29 2 0.06
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATAATATATAACTTAAACTAACAAAC
Found at i:461327 original size:21 final size:21
Alignment explanation
Indices: 461294--461342 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
461284 CTAATATAAT
461294 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
461315 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
461336 ATTAACT
1 A-TAACT
461343 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:461829 original size:46 final size:45
Alignment explanation
Indices: 461770--461863 Score: 179
Period size: 46 Copynumber: 2.1 Consensus size: 45
461760 CATGGCCATG
461770 CACAGTTCCCACGTCCAATGCACCATCCCCTCCCCCCATGCATTCC
1 CACAGTTCCCACGTCCAATGCACCATCCCCT-CCCCCATGCATTCC
461816 CACAGTTCCCACGTCCAATGCACCATCCCCTCCCCCATGCATTCC
1 CACAGTTCCCACGTCCAATGCACCATCCCCTCCCCCATGCATTCC
461861 CAC
1 CAC
461864 GTCCCATGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 17 0.35
46 31 0.65
ACGTcount: A:0.20, C:0.52, G:0.09, T:0.19
Consensus pattern (45 bp):
CACAGTTCCCACGTCCAATGCACCATCCCCTCCCCCATGCATTCC
Found at i:461952 original size:29 final size:29
Alignment explanation
Indices: 461910--461999 Score: 171
Period size: 29 Copynumber: 3.1 Consensus size: 29
461900 AAAATACACA
*
461910 AAGGTTGCCCGGATGCCATGGCGACCTCC
1 AAGGTCGCCCGGATGCCATGGCGACCTCC
461939 AAGGTCGCCCGGATGCCATGGCGACCTCC
1 AAGGTCGCCCGGATGCCATGGCGACCTCC
461968 AAGGTCGCCCGGATGCCATGGCGACCTCC
1 AAGGTCGCCCGGATGCCATGGCGACCTCC
461997 AAG
1 AAG
462000 ACCACTGTAG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.19, C:0.36, G:0.31, T:0.14
Consensus pattern (29 bp):
AAGGTCGCCCGGATGCCATGGCGACCTCC
Found at i:462444 original size:28 final size:28
Alignment explanation
Indices: 462377--462430 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
462367 ATCATGTTTG
* *
462377 TATATGCATCAGTCATTCTATGTTCTAC
1 TATATGTATCGGTCATTCTATGTTCTAC
462405 TATATGTATCGGTCATTCTATGTTCT
1 TATATGTATCGGTCATTCTATGTTCT
462431 CGTACTTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.46
Consensus pattern (28 bp):
TATATGTATCGGTCATTCTATGTTCTAC
Found at i:464091 original size:21 final size:20
Alignment explanation
Indices: 464005--464162 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
463995 AAATGACCAA
**
464005 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
464024 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
464044 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
464064 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
464085 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
464106 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
464126 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
464147 AAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
464163 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 42 0.40
21 46 0.44
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:464155 original size:20 final size:20
Alignment explanation
Indices: 464130--464181 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
464120 GATTTTCAAG
* *
464130 AATCGCAACGCGAATATAAA
1 AATCGCAACGCGAACACAAA
*
464150 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACAAA
464170 AATCGCAACGCG
1 AATCGCAACGCG
464182 TATCCGTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.27, G:0.17, T:0.12
Consensus pattern (20 bp):
AATCGCAACGCGAACACAAA
Found at i:464191 original size:20 final size:20
Alignment explanation
Indices: 464149--464358 Score: 210
Period size: 20 Copynumber: 10.5 Consensus size: 20
464139 GCGAATATAA
* *
464149 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
464169 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
464189 AAACCGCAACGTGTATCTGT
1 AAATCGCAACGCGTATCCGT
*
464209 AAATAGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
464229 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
464249 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
464269 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * * *
464289 AAATCGTAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
464309 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
464329 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
464349 AAATCACAAC
1 AAATCGCAAC
464359 ACTGAAATTT
Statistics
Matches: 158, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
19 1 0.01
20 155 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:465090 original size:24 final size:24
Alignment explanation
Indices: 465051--465097 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
465041 AAATTTGGTC
465051 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
465075 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
465098 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:467631 original size:33 final size:33
Alignment explanation
Indices: 467580--467830 Score: 186
Period size: 33 Copynumber: 7.2 Consensus size: 33
467570 CGGAAATTAC
* *
467580 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
*
467613 AATCCCAACAAGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGC-GAAATGAA
* * *
467647 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AA-GAAAATCGCAATGCGA-AAT-GAA
* *
467686 AATGCGGAA-ATGAAAATCGCAATGCGAAATGAA
1 AAT-CGCAACAAGAAAATCGCAATGCGAAATGAA
* *
467719 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
* * *
467752 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AA-GAAAATCGCAATGCGA-AAT-GAA
* *
467791 AATGCGGAA-ATGAAAATCGCAATGCGAAATGAA
1 AAT-CGCAACAAGAAAATCGCAATGCGAAATGAA
467824 AATCGCA
1 AATCGCA
467831 TTGCGATTCT
Statistics
Matches: 171, Mismatches: 27, Indels: 41
0.72 0.11 0.17
Matches are distributed among these distances:
32 9 0.05
33 63 0.37
34 43 0.25
35 3 0.02
36 1 0.01
37 1 0.01
38 17 0.10
39 24 0.14
40 10 0.06
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
AATCGCAACAAGAAAATCGCAATGCGAAATGAA
Found at i:467657 original size:53 final size:53
Alignment explanation
Indices: 467594--467830 Score: 440
Period size: 53 Copynumber: 4.5 Consensus size: 53
467584 GCAACGAGAG
* * *
467594 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
467647 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
467700 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
467752 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
467805 AATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
467831 TTGCGATTCT
Statistics
Matches: 180, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
52 52 0.29
53 128 0.71
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:467663 original size:19 final size:19
Alignment explanation
Indices: 467594--467836 Score: 274
Period size: 19 Copynumber: 13.7 Consensus size: 19
467584 GCAACGAGAG
467594 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
467613 AATCCCAA--C--AA-GAA
1 AATCGCAATGCGAAATGAA
467627 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
467647 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
467666 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
467680 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
467700 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
467719 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
467733 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
467752 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
467771 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
467785 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
467805 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
467824 AATCGCATTGCGA
1 AATCGCAATGCGA
467837 TTCTCTCGTT
Statistics
Matches: 192, Mismatches: 9, Indels: 46
0.78 0.04 0.19
Matches are distributed among these distances:
14 40 0.21
15 5 0.03
16 5 0.03
17 9 0.05
18 1 0.01
19 92 0.48
20 40 0.21
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:467737 original size:86 final size:84
Alignment explanation
Indices: 467580--467759 Score: 242
Period size: 86 Copynumber: 2.1 Consensus size: 84
467570 CGGAAATTAC
467580 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATG
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAA-GCGG-AATG
467645 AAAATCGCAATGCGAAATGAA
64 AAAATCGCAATGCGAAATGAA
*
467666 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-C-G
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C--AA-GAAAATCGCAAGCGG
*
467729 -A-GAGAATCGCAATGCGAAATGAA
60 AATGAAAATCGCAATGCGAAATGAA
467752 AATCGCAA
1 AATCGCAA
467760 TGCGAAATGA
Statistics
Matches: 86, Mismatches: 2, Indels: 12
0.86 0.02 0.12
Matches are distributed among these distances:
86 54 0.63
87 16 0.19
89 2 0.02
90 1 0.01
91 2 0.02
92 11 0.13
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (84 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAAGCGGAATGAA
AATCGCAATGCGAAATGAA
Found at i:467780 original size:105 final size:106
Alignment explanation
Indices: 467594--467830 Score: 440
Period size: 105 Copynumber: 2.2 Consensus size: 106
467584 GCAACGAGAG
*
467594 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
467659 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
66 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
* *
467700 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
467764 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
66 AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
467805 AATCGCAATGCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
467831 TTGCGATTCT
Statistics
Matches: 128, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
105 87 0.68
106 41 0.32
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (106 bp):
AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:467870 original size:53 final size:52
Alignment explanation
Indices: 467807--467922 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
467797 GAAATGAAAA
*
467807 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
467859 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
467912 TCGCATTGCGA
1 TCGCATTGCGA
467923 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:467885 original size:19 final size:19
Alignment explanation
Indices: 467845--467932 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
467835 GATTCTCTCG
467845 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
467865 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
467884 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
467898 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
467917 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
467933 AACATAATGC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.11
17 7 0.11
19 26 0.43
20 15 0.25
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:468042 original size:14 final size:14
Alignment explanation
Indices: 468023--468059 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
468013 CATCAATTAC
468023 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
468037 ACAAATCATCTTTT
1 ACAAATCAACTTTT
468051 ACAAATCAA
1 ACAAATCAA
468060 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:470025 original size:19 final size:19
Alignment explanation
Indices: 469985--470122 Score: 133
Period size: 19 Copynumber: 7.5 Consensus size: 19
469975 GTTTACTTTT
* *
469985 GCAACACGAAACTTAAAATC
1 GCAACGCGAAA-TCAAAATC
* *
470005 GCAACGCGAAATGAGAATC
1 GCAACGCGAAATCAAAATC
* *
470024 GCAACGAGAAACCAAAATC
1 GCAACGCGAAATCAAAATC
*
470043 GCAACGCGAAACCAAAATC
1 GCAACGCGAAATCAAAATC
*
470062 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATCAAAATC
*
470081 GCAA--CG--A-CAGAATC
1 GCAACGCGAAATCAAAATC
*
470095 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATCAAAATC
*
470114 GCAATGCGA
1 GCAACGCGA
470123 TTTTGGTTTC
Statistics
Matches: 98, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
14 9 0.09
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 73 0.74
20 10 0.10
ACGTcount: A:0.46, C:0.25, G:0.20, T:0.09
Consensus pattern (19 bp):
GCAACGCGAAATCAAAATC
Found at i:470151 original size:19 final size:19
Alignment explanation
Indices: 470118--470162 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
470108 AAAATCGCAA
**
470118 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
470137 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
470156 TGCGATT
1 TGCGATT
470163 CTCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.47
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:470451 original size:93 final size:93
Alignment explanation
Indices: 470292--470793 Score: 986
Period size: 93 Copynumber: 5.4 Consensus size: 93
470282 TCAGGGTATT
470292 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
470357 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
470385 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
470450 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
470478 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
470543 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
470571 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACGAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
470636 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
470664 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
470729 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
470757 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
470794 AAGCAATCTA
Statistics
Matches: 406, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 406 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:472491 original size:20 final size:20
Alignment explanation
Indices: 472460--472556 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
472450 TTTTGGTTGA
472460 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
472480 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
472500 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
472519 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
472534 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
472554 AAT
1 AAT
472557 CGCAACACGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:472512 original size:21 final size:21
Alignment explanation
Indices: 472458--472522 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
472448 TCTTTTGGTT
472458 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
472479 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
472499 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
472520 GAA
1 GAA
472523 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:472526 original size:14 final size:14
Alignment explanation
Indices: 472507--472562 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
472497 GAGAAATGAA
472507 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
472521 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
472540 AATCGCAACGAGAG
1 AATCGCAACGAGAG
472554 AATCGCAAC
1 AATCGCAAC
472563 ACGAAATGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:472539 original size:33 final size:33
Alignment explanation
Indices: 472458--472580 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
472448 TCTTTTGGTT
*
472458 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
472499 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
472532 GAAATGAAAATCGCAACGAGAGAATCGCAACAC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
472565 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
472581 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
33 49 0.61
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.28
ACGTcount: A:0.47, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:472616 original size:14 final size:14
Alignment explanation
Indices: 472597--472653 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
472587 TTTGGTTTCG
472597 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
472611 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
472630 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
472644 CGTTGCGATT
1 CGTTGCGATT
472654 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:472629 original size:33 final size:33
Alignment explanation
Indices: 472581--472660 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
472571 AAAATCGCAA
**
472581 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
472614 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
472647 TGCGATTTTCATTT
1 TGCGATTTTCATTT
472661 TTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:472666 original size:21 final size:21
Alignment explanation
Indices: 472641--472714 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
472631 GTTGCGATTC
472641 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
472662 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
472683 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
472704 TCTCGTTGCGA
1 TCTCGTTGCGA
472715 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:472836 original size:33 final size:33
Alignment explanation
Indices: 472794--472864 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
472784 AATACTAACT
472794 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
472827 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
472860 TGAAA
1 TGAAA
472865 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:473269 original size:20 final size:20
Alignment explanation
Indices: 473244--473395 Score: 205
Period size: 20 Copynumber: 7.6 Consensus size: 20
473234 CTTTAAAAAT
473244 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
473264 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
473284 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
473304 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
473324 CACGTTACGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
473344 CGCGTTGCGATTTATGTATT
1 CGCGTTGCGATTTACGGATA
* ** *
473364 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
473384 CGCGTTGCGATT
1 CGCGTTGCGATT
473396 CTGGAAAATC
Statistics
Matches: 118, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 118 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:473739 original size:21 final size:21
Alignment explanation
Indices: 473715--473759 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
473705 TAAGTTTTAA
*
473715 AAAATTAAAAATTTAGATACT
1 AAAACTAAAAATTTAGATACT
* * *
473736 AAAACTGATAATTTAGGTACT
1 AAAACTAAAAATTTAGATACT
473757 AAA
1 AAA
473760 TGTATAGTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.31
Consensus pattern (21 bp):
AAAACTAAAAATTTAGATACT
Found at i:490820 original size:4 final size:4
Alignment explanation
Indices: 490811--490845 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
490801 GTGATACATG
490811 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
490846 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:490861 original size:2 final size:2
Alignment explanation
Indices: 490856--490883 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
490846 TATATATATA
490856 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
490884 ATATTGTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:492614 original size:18 final size:20
Alignment explanation
Indices: 492577--492616 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
492567 CGAATTTATA
492577 AAATTTTAAGATGACGAAAAT
1 AAATTTTAAGAT-ACGAAAAT
492598 AAATTTTAA-AT-CGAAAAT
1 AAATTTTAAGATACGAAAAT
492616 A
1 A
492617 TAAAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
20 2 0.11
21 9 0.47
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.30
Consensus pattern (20 bp):
AAATTTTAAGATACGAAAAT
Found at i:493584 original size:24 final size:25
Alignment explanation
Indices: 493552--493598 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
493542 CTATTCTTTC
493552 ACTTCAATCAAGC-TCGAATTTTAG
1 ACTTCAATCAAGCTTCGAATTTTAG
* *
493576 ACTTCAATCGAGCTTCTAATTTT
1 ACTTCAATCAAGCTTCGAATTTT
493599 TTTTTGAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (25 bp):
ACTTCAATCAAGCTTCGAATTTTAG
Found at i:521344 original size:81 final size:81
Alignment explanation
Indices: 521209--521368 Score: 302
Period size: 81 Copynumber: 2.0 Consensus size: 81
521199 ACATTTGACC
*
521209 TGTGTGCCTGTTTTCGGATTTAGAAATTCCTATTTTCTTTTAGTTAATTTGTGGTTGCTGTCGAG
1 TGTGTGCCTGTTTTCGGATTTAGAAATCCCTATTTTCTTTTAGTTAATTTGTGGTTGCTGTCGAG
521274 AGAATATAATCGTGCT
66 AGAATATAATCGTGCT
*
521290 TGTGTGCCTGTTTTTGGATTTAGAAATCCCTATTTTCTTTTAGTTAATTTGTGGTTGCTGTCGAG
1 TGTGTGCCTGTTTTCGGATTTAGAAATCCCTATTTTCTTTTAGTTAATTTGTGGTTGCTGTCGAG
521355 AGAATATAATCGTG
66 AGAATATAATCGTG
521369 TTCTCTTAAC
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.20, C:0.12, G:0.23, T:0.46
Consensus pattern (81 bp):
TGTGTGCCTGTTTTCGGATTTAGAAATCCCTATTTTCTTTTAGTTAATTTGTGGTTGCTGTCGAG
AGAATATAATCGTGCT
Found at i:527832 original size:20 final size:19
Alignment explanation
Indices: 527796--527838 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
527786 GACGATTTTA
527796 TTTATTTACAGATTTAAATG
1 TTTATTTACAGATTT-AATG
*
527816 TTTATTTAGA-ATATTAATG
1 TTTATTTACAGAT-TTAATG
527835 TTTA
1 TTTA
527839 ATATTAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTATTTACAGATTTAATG
Found at i:532747 original size:21 final size:21
Alignment explanation
Indices: 532681--532749 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
532671 ACCTATGGTT
*
532681 CATTTCAGAAGTTCAAGTTAG
1 CATTTCAGAAGTTCAAGTTAA
*
532702 CATTT-AAACAG--C-AGTTCATA
1 CATTTCAGA-AGTTCAAGTT-A-A
*
532722 GATTTCAGAAGTTCAAGTTAA
1 CATTTCAGAAGTTCAAGTTAA
532743 CATTTCA
1 CATTTCA
532750 TAATAAATGA
Statistics
Matches: 36, Mismatches: 5, Indels: 14
0.65 0.09 0.25
Matches are distributed among these distances:
18 4 0.11
19 2 0.06
20 8 0.22
21 16 0.44
22 2 0.06
23 4 0.11
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (21 bp):
CATTTCAGAAGTTCAAGTTAA
Found at i:539660 original size:15 final size:15
Alignment explanation
Indices: 539640--539687 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
539630 TTTTTTATTA
539640 TAAATTTTATAAATT
1 TAAATTTTATAAATT
***
539655 TAAA-TTTATCTTTT
1 TAAATTTTATAAATT
539669 TAAAATTTTATAAATT
1 T-AAATTTTATAAATT
539685 TAA
1 TAA
539688 GTTGTCTCTT
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
14 8 0.32
15 9 0.36
16 8 0.32
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
TAAATTTTATAAATT
Found at i:540498 original size:38 final size:42
Alignment explanation
Indices: 540456--540541 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 42
540446 AACAAAATGC
* *
540456 TAATAAATAA-AAAAATGAAA-AAA-ATAT-ATAAATAATAA
1 TAATAAATAATAAAAATGAAAGAAAGAAATAATAAAAAATAA
*
540494 TAAT-AATAATAATAATGAAAGAAAGAAATAATAAAAAATAA
1 TAATAAATAATAAAAATGAAAGAAAGAAATAATAAAAAATAA
540535 TAATAAA
1 TAATAAA
540542 AGGTTAAGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
37 5 0.12
38 13 0.32
39 3 0.08
40 3 0.08
41 14 0.35
42 2 0.05
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (42 bp):
TAATAAATAATAAAAATGAAAGAAAGAAATAATAAAAAATAA
Found at i:541856 original size:6 final size:6
Alignment explanation
Indices: 541847--541894 Score: 62
Period size: 6 Copynumber: 7.8 Consensus size: 6
541837 CTGAAAAAGA
*
541847 AAAAAT AAAAAAT AAAAAT AAATAA- ATAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT -AAAAAT AAAAAT AAA-AAT AAAAAT AAAAAT AAAAAT AAAAA
541895 GGAACATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
5 2 0.05
6 27 0.73
7 8 0.22
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:541863 original size:14 final size:14
Alignment explanation
Indices: 541840--541894 Score: 58
Period size: 16 Copynumber: 3.8 Consensus size: 14
541830 TTTGGTCCTG
*
541840 AAAAAGAAAAAATA
1 AAAAATAAAAAATA
541854 AAAAAT-AAAAATA
1 AAAAATAAAAAATA
*
541867 AATAAATAAATAAAAA
1 AA-AAATAAA-AAATA
541883 TAAAAATAAAAA
1 -AAAAATAAAAA
541895 GGAACATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
13 9 0.26
14 9 0.26
15 4 0.11
16 11 0.31
17 2 0.06
ACGTcount: A:0.84, C:0.00, G:0.02, T:0.15
Consensus pattern (14 bp):
AAAAATAAAAAATA
Found at i:541998 original size:37 final size:38
Alignment explanation
Indices: 541907--541998 Score: 95
Period size: 37 Copynumber: 2.5 Consensus size: 38
541897 AACATTTTAA
*
541907 AAAATAATATATTATATATATGTTTTAAAATGTATTTTT
1 AAAATAATATATTATATATATGTTTGAAAA-GTATTTTT
*
541946 AAAATCATATA--ATATATAT-TTTCGAATAA-TA-TTTT
1 AAAATAATATATTATATATATGTTT-GAA-AAGTATTTTT
*
541981 AAAATTATATATTATATA
1 AAAATAATATATTATATA
541999 CATACTTTCT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
35 14 0.30
36 5 0.11
37 15 0.33
38 2 0.04
39 10 0.22
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (38 bp):
AAAATAATATATTATATATATGTTTGAAAAGTATTTTT
Found at i:542242 original size:42 final size:41
Alignment explanation
Indices: 542150--542243 Score: 109
Period size: 42 Copynumber: 2.3 Consensus size: 41
542140 ACTCTATATA
* *
542150 TATTTCCAAAATGTTTTTAAAAAAAATATATAATATATATG
1 TATTTCCAAAATGTTTTTAAAAAAAATATATAATATACATC
* * *
542191 T-TTTCCAAAATGCTTTTTTTAAAAAACTATATATTATACATC
1 TATTTCCAAAATG--TTTTTAAAAAAAATATATAATATACATC
*
542233 TATTTCAAAAA
1 TATTTCCAAAA
542244 CCATTAGCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
40 11 0.25
41 1 0.02
42 24 0.55
43 8 0.18
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.43
Consensus pattern (41 bp):
TATTTCCAAAATGTTTTTAAAAAAAATATATAATATACATC
Found at i:544612 original size:12 final size:13
Alignment explanation
Indices: 544588--544616 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
544578 GTCGTCAATC
544588 AACATTGAATGAT
1 AACATTGAATGAT
544601 AACATT-AATGAT
1 AACATTGAATGAT
544613 AACA
1 AACA
544617 CAATTAGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (13 bp):
AACATTGAATGAT
Found at i:550408 original size:2 final size:2
Alignment explanation
Indices: 550401--550434 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
550391 CAAAACATCA
550401 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
550435 GTATCCTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:551649 original size:23 final size:23
Alignment explanation
Indices: 551623--551671 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
551613 GACCTTTAAT
* * *
551623 AATAAAAAATATTATTTTTATTA
1 AATAAAAAATAATAATTTAATTA
551646 AAT-AAAAATAATAATTTAATTA
1 AATAAAAAATAATAATTTAATTA
551668 AATA
1 AATA
551672 TATATTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AATAAAAAATAATAATTTAATTA
Found at i:551683 original size:19 final size:17
Alignment explanation
Indices: 551625--551696 Score: 54
Period size: 18 Copynumber: 3.9 Consensus size: 17
551615 CCTTTAATAA
*
551625 TAAAAAATATTATTTTTAT
1 TAAAAAATATTA-TTAT-T
* * *
551644 TAAATAAAAATAATAATT
1 TAAA-AAATATTATTATT
*
551662 TAATTAAATATATATTATT
1 TAA-AAAATAT-TATTATT
551681 TAAAAAATATTATTAT
1 TAAAAAATATTATTAT
551697 AATTATTATT
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
17 6 0.15
18 15 0.37
19 14 0.34
20 6 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAAAAATATTATTATT
Found at i:552135 original size:24 final size:23
Alignment explanation
Indices: 552084--552138 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
552074 ATGTAAATTT
552084 TAATTTT-AATTAGAATATAATA
1 TAATTTTAAATTAGAATATAATA
* *
552106 TTATTTTAAATATATAATA-AATAA
1 TAATTTTAAAT-TAGAATATAAT-A
552130 TAATTTTAA
1 TAATTTTAA
552139 CATTTAAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 6 0.22
23 6 0.22
24 15 0.56
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TAATTTTAAATTAGAATATAATA
Found at i:552341 original size:16 final size:16
Alignment explanation
Indices: 552320--552352 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
552310 TAATAAATAA
552320 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
552336 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
552352 A
1 A
552353 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:552439 original size:16 final size:16
Alignment explanation
Indices: 552418--552488 Score: 115
Period size: 16 Copynumber: 4.4 Consensus size: 16
552408 CATTTAATAA
*
552418 ATAAACGAACATGAAC
1 ATAAACGAACACGAAC
552434 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
*
552450 ATAAACGAACATGAAC
1 ATAAACGAACACGAAC
*
552466 ATAAATGAACACGAAC
1 ATAAACGAACACGAAC
552482 ATAAACG
1 ATAAACG
552489 TTGGAGACCC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.56, C:0.20, G:0.13, T:0.11
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:552454 original size:32 final size:32
Alignment explanation
Indices: 552418--552488 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
552408 CATTTAATAA
552418 ATAAACGAACATGAACATAAACGAACACGAAC
1 ATAAACGAACATGAACATAAACGAACACGAAC
*
552450 ATAAACGAACATGAACATAAATGAACACGAAC
1 ATAAACGAACATGAACATAAACGAACACGAAC
552482 ATAAACG
1 ATAAACG
552489 TTGGAGACCC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.56, C:0.20, G:0.13, T:0.11
Consensus pattern (32 bp):
ATAAACGAACATGAACATAAACGAACACGAAC
Found at i:553252 original size:14 final size:14
Alignment explanation
Indices: 553235--553265 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
553225 AATGAACATA
*
553235 AACGAACATAATCG
1 AACGAACATAAACG
553249 AACGAACATAAACG
1 AACGAACATAAACG
553263 AAC
1 AAC
553266 ATAACCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.23, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:553255 original size:24 final size:24
Alignment explanation
Indices: 553215--553289 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
553205 GATTGTGTTA
*
553215 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAAAGAACATAAACG
*
553239 AACATAATCGAACGAACATAAACG
1 AACATAATCGAAAGAACATAAACG
* * *
553263 AACATAACCAAAAGAACATAACCG
1 AACATAATCGAAAGAACATAAACG
553287 AAC
1 AAC
553290 GTTCACGAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
23 3 0.07
24 42 0.93
ACGTcount: A:0.57, C:0.20, G:0.11, T:0.12
Consensus pattern (24 bp):
AACATAATCGAAAGAACATAAACG
Found at i:553994 original size:16 final size:14
Alignment explanation
Indices: 553951--553999 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 14
553941 GAGTTGAGAC
*
553951 TAAATAATTTA-TG
1 TAAATAATTTATTT
553964 T-AA-AATTTATTT
1 TAAATAATTTATTT
553976 TAAATAATTTATGTAT
1 TAAATAATTTAT-T-T
553992 TAAATAAT
1 TAAATAAT
554000 AATATTTCAG
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
11 6 0.20
12 4 0.13
13 3 0.10
14 7 0.23
15 1 0.03
16 9 0.30
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (14 bp):
TAAATAATTTATTT
Found at i:556141 original size:17 final size:17
Alignment explanation
Indices: 556119--556155 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
556109 ATAACTCAAA
*
556119 ATATGCATAAATACTGC
1 ATATGCATAAATAATGC
556136 ATATGCATAAATAATGC
1 ATATGCATAAATAATGC
556153 ATA
1 ATA
556156 AAATCAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (17 bp):
ATATGCATAAATAATGC
Found at i:556714 original size:3 final size:3
Alignment explanation
Indices: 556706--556760 Score: 76
Period size: 3 Copynumber: 18.0 Consensus size: 3
556696 TCTAATTTTA
*
556706 ATT ATT ATT ATT ATT GTT ATT ATT ATT ATGT -TT ATT AATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT -ATT ATT ATT
556752 ATT ATT ATT
1 ATT ATT ATT
556761 TTTTGCAGGC
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 1 0.02
3 42 0.89
4 4 0.09
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:564870 original size:36 final size:35
Alignment explanation
Indices: 564782--564880 Score: 128
Period size: 36 Copynumber: 2.8 Consensus size: 35
564772 AGTTTCCTTC
*
564782 GAAAACAAATTTTGTCTCGCTTGAGAC-AGTTCTT
1 GAAAACAAATTTTGTCTCGCTTGAGACAAGTTATT
* * *
564816 GAAAAACAAATTTTGTCTCACTTAAGACAATTTATCT
1 G-AAAACAAATTTTGTCTCGCTTGAGACAAGTTAT-T
*
564853 GAAAACAAATTTCGTCTCGCTTGAGACA
1 GAAAACAAATTTTGTCTCGCTTGAGACA
564881 TTTTTCCTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
34 1 0.02
35 24 0.44
36 28 0.51
37 2 0.04
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.32
Consensus pattern (35 bp):
GAAAACAAATTTTGTCTCGCTTGAGACAAGTTATT
Found at i:564965 original size:104 final size:105
Alignment explanation
Indices: 564854--565138 Score: 443
Period size: 105 Copynumber: 2.7 Consensus size: 105
564844 AATTTATCTG
564854 AAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGCTTCACT
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGCTTCACT
*
564919 TGAAACAAAATTAATCTCACTTGAGATTGTTGTTT-TTTT
66 TGAAACAAAATTAATCTCACTTGAGATTGTTGTTTATTTC
* *
564958 AAAACAAATTTCGTCTCGCTTGGGACATTTTTTTCCTTTGA-AAACAAATTTTGAATTTGCTTCA
1 AAAACAAATTTCGTCTCGCTTGAGACA--TTTTTCCTTTGAGATACAAATTTTGAATTTGCTTCA
565022 CTTGAAACAAAATTAATCTCACTTGAGATTGTTGTTTATTTC
64 CTTGAAACAAAATTAATCTCACTTGAGATTGTTGTTTATTTC
* * * * *
565064 AAAACAAATTTCGTCTCGCTTGAGACATTTTTTCTATGAGATACAAA-TTTAAATTTG-TTGTAT
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGCTT-CAC
565127 TTGAAACAAAAT
65 TTGAAACAAAAT
565139 AAACACCTTT
Statistics
Matches: 166, Mismatches: 10, Indels: 10
0.89 0.05 0.05
Matches are distributed among these distances:
103 2 0.01
104 58 0.35
105 65 0.39
106 41 0.25
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (105 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGCTTCACT
TGAAACAAAATTAATCTCACTTGAGATTGTTGTTTATTTC
Found at i:565852 original size:36 final size:35
Alignment explanation
Indices: 565791--565887 Score: 99
Period size: 35 Copynumber: 2.7 Consensus size: 35
565781 TTTGGAAAAA
* * ** *
565791 ATCTTTGAGTTTGTTT-CTTTGGAAACAAAAGTTACC
1 ATCTTTGAGTATGTTTCCCTT-GAAAC-AAAGCAAAC
565827 ATCTTTGAGTATGTTTCCCTTGAAACAAAGCAAAC
1 ATCTTTGAGTATGTTTCCCTTGAAACAAAGCAAAC
*
565862 ATCTTTGAG-ATCGTTTCTCTTGAAAC
1 ATCTTTGAGTAT-GTTTCCCTTGAAAC
565888 GAATTTTGTC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
34 2 0.04
35 28 0.53
36 20 0.38
37 3 0.06
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (35 bp):
ATCTTTGAGTATGTTTCCCTTGAAACAAAGCAAAC
Found at i:566082 original size:28 final size:28
Alignment explanation
Indices: 566051--566132 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
566041 GAAACACATC
*
566051 ATCTTTGAGTTTGTTTTTCTTGAAACGA
1 ATCTTTGAGTTTGTTTTTCTTGAAACAA
*
566079 ATCTTTGGGTTTGTTTCTT-TTGAAACAA
1 ATCTTTGAGTTTGTTT-TTCTTGAAACAA
* *
566107 ATCTTT-AATTTGGTTTCTCTTGAAAC
1 ATCTTTGAGTTT-GTTTTTCTTGAAAC
566133 CATAACTCCT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
27 4 0.09
28 40 0.87
29 2 0.04
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (28 bp):
ATCTTTGAGTTTGTTTTTCTTGAAACAA
Found at i:566349 original size:40 final size:40
Alignment explanation
Indices: 566294--566488 Score: 124
Period size: 40 Copynumber: 4.5 Consensus size: 40
566284 CCAGAACTCT
*
566294 TCATCACGTATGAGCCGTGTCATCCCCCGACCAAATCTCC
1 TCATCACGTAGGAGCCGTGTCATCCCCCGACCAAATCTCC
* * *
566334 TCATCACGTAGGAGCCGTTTCA-CCCCTAGATAACC-AACCGTCC
1 TCATCACGTAGGAGCCGTGTCATCCCC-CG---ACCAAATC-TCC
* * * *
566377 TCATCACGTAGGAACCGTGTTATCACCTTCCTAAAGATGGCCAAAACTCT
1 TCATCACGTAGGAGCCGTGTCATC-CC--CC----GA---CCAAATCTCC
** *
566427 TCATCACGTATAAGCCGTGTCATCCACCGACCAAATCTCC
1 TCATCACGTAGGAGCCGTGTCATCCCCCGACCAAATCTCC
* *
566467 TCATCACGTAGGAACCGGGTCA
1 TCATCACGTAGGAGCCGTGTCA
566489 CCCTTAGACG
Statistics
Matches: 117, Mismatches: 21, Indels: 34
0.68 0.12 0.20
Matches are distributed among these distances:
39 4 0.03
40 47 0.40
42 3 0.03
43 27 0.23
44 1 0.01
45 2 0.02
47 4 0.03
49 1 0.01
50 25 0.21
51 3 0.03
ACGTcount: A:0.27, C:0.34, G:0.16, T:0.23
Consensus pattern (40 bp):
TCATCACGTAGGAGCCGTGTCATCCCCCGACCAAATCTCC
Found at i:566377 original size:133 final size:133
Alignment explanation
Indices: 566139--566488 Score: 531
Period size: 133 Copynumber: 2.6 Consensus size: 133
566129 AAACCATAAC
* * * * ** * *
566139 TCCTAAAGATGGCCAG-CCGTCCTCATCATGTAGGAATCGTGTCATCCCCAGACCAGATCTCCTC
1 TCCTAAAGATGGCCAGAAC-TCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAAATCTCCTC
*
566203 ATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATC
65 ATCACGTAGGAGCCGTGTCAACCATAGATAACCAACCGTCCTCATCACGTAGGAACCGTGTTATC
566268 ACCT
130 ACCT
566272 TCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAAATCTCCTCA
1 TCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAAATCTCCTCA
* * *
566337 TCACGTAGGAGCCGTTTCACCCCTAGATAACCAACCGTCCTCATCACGTAGGAACCGTGTTATCA
66 TCACGTAGGAGCCGTGTCAACCATAGATAACCAACCGTCCTCATCACGTAGGAACCGTGTTATCA
566402 CCT
131 CCT
* * *
566405 TCCTAAAGATGGCCAAAACTCTTCATCACGTATAAGCCGTGTCATCCACCGACCAAATCTCCTCA
1 TCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAAATCTCCTCA
* *
566470 TCACGTAGGAACCGGGTCA
66 TCACGTAGGAGCCGTGTCA
566489 CCCTTAGACG
Statistics
Matches: 198, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
133 197 0.99
134 1 0.01
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.23
Consensus pattern (133 bp):
TCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAAATCTCCTCA
TCACGTAGGAGCCGTGTCAACCATAGATAACCAACCGTCCTCATCACGTAGGAACCGTGTTATCA
CCT
Found at i:566383 original size:43 final size:42
Alignment explanation
Indices: 566197--566396 Score: 147
Period size: 43 Copynumber: 4.6 Consensus size: 42
566187 CAGACCAGAT
* * *
566197 CTCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGC
1 CTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAAC
* ** *
566239 CGTCCTCATCACGTAGGAACCGTGTTATCACCTTCCTAAAGATGGCCAGAA
1 C-TCCTCATCACGTAGGAGCCGTG---TCACC--CCT--AGATAACCA-AC
* * * *
566290 CTCTTCATCACGTATGAGCCGTGTCATCCCC-CG---ACCAAAT
1 CTCCTCATCACGTAGGAGCCGTGTCA-CCCCTAGATAACC-AAC
*
566330 CTCCTCATCACGTAGGAGCCGTTTCACCCCTAGATAACCAAC
1 CTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAAC
*
566372 CGTCCTCATCACGTAGGAACCGTGT
1 C-TCCTCATCACGTAGGAGCCGTGT
566397 TATCACCTTC
Statistics
Matches: 122, Mismatches: 20, Indels: 31
0.71 0.12 0.18
Matches are distributed among these distances:
39 4 0.03
40 27 0.22
41 1 0.01
42 4 0.03
43 46 0.38
46 6 0.05
47 3 0.02
48 4 0.03
50 26 0.21
51 1 0.01
ACGTcount: A:0.26, C:0.34, G:0.18, T:0.23
Consensus pattern (42 bp):
CTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAAC
Found at i:566704 original size:3 final size:3
Alignment explanation
Indices: 566696--566750 Score: 76
Period size: 3 Copynumber: 18.0 Consensus size: 3
566686 TCTAATTTTA
*
566696 ATT ATT ATT ATT ATT GTT ATT ATT ATT ATGT -TT ATT AATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT -ATT ATT ATT
566742 ATT ATT ATT
1 ATT ATT ATT
566751 TTTTGCAGGC
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 1 0.02
3 42 0.89
4 4 0.09
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:568770 original size:15 final size:15
Alignment explanation
Indices: 568747--568785 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
568737 GACCACGACC
* *
568747 ACGACACGACCCGAG
1 ACGAGACGACACGAG
*
568762 ACGAGACGAGACGAG
1 ACGAGACGACACGAG
568777 ACGAGACGA
1 ACGAGACGA
568786 GACGGACGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.28, G:0.33, T:0.00
Consensus pattern (15 bp):
ACGAGACGACACGAG
Found at i:568786 original size:5 final size:5
Alignment explanation
Indices: 568758--568793 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
568748 CGACACGACC
568758 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG-GA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
568794 GCGGCGGCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.36, C:0.22, G:0.42, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:569274 original size:5 final size:5
Alignment explanation
Indices: 569261--569292 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
569251 CCGCCGTCGC
*
569261 CGTCC CGTCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
569293 GGTCGTGGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.44, G:0.22, T:0.34
Consensus pattern (5 bp):
CGTCT
Found at i:569890 original size:17 final size:17
Alignment explanation
Indices: 569868--569903 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
569858 ATTTTCTGGG
569868 AATAAAGCATCATCAGA
1 AATAAAGCATCATCAGA
569885 AATAAAGCATCATCAGA
1 AATAAAGCATCATCAGA
569902 AA
1 AA
569904 GTTGGATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.17, G:0.11, T:0.17
Consensus pattern (17 bp):
AATAAAGCATCATCAGA
Found at i:584979 original size:23 final size:23
Alignment explanation
Indices: 584960--585013 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
584950 AAATGCACGT
584960 AAGTGCCACGTAGAATTGCACCG
1 AAGTGCCACGTAGAATTGCACCG
*
584983 AAGTGCCGCGTAGAATTGCACCG
1 AAGTGCCACGTAGAATTGCACCG
585006 AAGTGCCA
1 AAGTGCCA
585014 TATAAAATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.30, C:0.26, G:0.28, T:0.17
Consensus pattern (23 bp):
AAGTGCCACGTAGAATTGCACCG
Found at i:586607 original size:24 final size:24
Alignment explanation
Indices: 586551--586632 Score: 118
Period size: 24 Copynumber: 3.6 Consensus size: 24
586541 TCCCCTTGAA
*
586551 GTGCATCGATGCAT-TC-T-ACA-
1 GTGCATCGATGCATCCCTTAACAT
*
586571 GTGTATCGATGCATCCCTTAACAT
1 GTGCATCGATGCATCCCTTAACAT
586595 GTGCATCGATGCATCCCTTAACAT
1 GTGCATCGATGCATCCCTTAACAT
586619 GTGCATCGATGCAT
1 GTGCATCGATGCAT
586633 GCACTCCTTA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
20 13 0.24
21 1 0.02
22 1 0.02
23 3 0.05
24 37 0.67
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTAACAT
Found at i:599832 original size:10 final size:10
Alignment explanation
Indices: 599819--599863 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
599809 TATTTATCTA
599819 ATTTTAATAT
1 ATTTTAATAT
* *
599829 ATTTTTATCT
1 ATTTTAATAT
599839 ATTTT-ATA-
1 ATTTTAATAT
599847 A-TTTAATAT
1 ATTTTAATAT
599856 ATTTTAAT
1 ATTTTAAT
599864 TAAAAAACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
7 3 0.10
8 4 0.14
9 3 0.10
10 19 0.66
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTTTAATAT
Found at i:609529 original size:18 final size:20
Alignment explanation
Indices: 609491--609534 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
609481 AATATTATTT
609491 ATAATATATTTATATTATAA
1 ATAATATATTTATATTATAA
*
609511 ATAATAT-TTTA-ATTTTAA
1 ATAATATATTTATATTATAA
*
609529 AAAATA
1 ATAATA
609535 AATTATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 11 0.50
19 4 0.18
20 7 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATAATATATTTATATTATAA
Found at i:636273 original size:8 final size:8
Alignment explanation
Indices: 636260--636315 Score: 63
Period size: 7 Copynumber: 7.9 Consensus size: 8
636250 AAAATGAGTG
636260 AAAATGAA
1 AAAATGAA
636268 AAAATG-A
1 AAAATGAA
636275 AAAAT-AA
1 AAAATGAA
636282 AAAAT-AA
1 AAAATGAA
636289 AAAATG--
1 AAAATGAA
636295 --AATGAA
1 AAAATGAA
636301 AAAATGAA
1 AAAATGAA
636309 AAAATGA
1 AAAATGA
636316 GGGTTCAAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
4 4 0.10
7 19 0.45
8 19 0.45
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (8 bp):
AAAATGAA
Found at i:636304 original size:21 final size:22
Alignment explanation
Indices: 636260--636315 Score: 75
Period size: 20 Copynumber: 2.7 Consensus size: 22
636250 AAAATGAGTG
636260 AAAATGAAAAAATGAAAAATAA
1 AAAATGAAAAAATGAAAAATAA
636282 AAAAT-AAAAAATG---AATGAA
1 AAAATGAAAAAATGAAAAAT-AA
636301 AAAATGAAAAAATGA
1 AAAATGAAAAAATGA
636316 GGGTTCAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
18 3 0.10
19 7 0.23
20 8 0.26
21 8 0.26
22 5 0.16
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (22 bp):
AAAATGAAAAAATGAAAAATAA
Found at i:637398 original size:55 final size:55
Alignment explanation
Indices: 637314--637849 Score: 753
Period size: 55 Copynumber: 9.7 Consensus size: 55
637304 CCAACGATAA
* * *
637314 TTGAAGATTGATCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCGATTG
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
*
637369 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
* *
637424 TTGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
637479 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
637534 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAAATAGGGAGCAGACACGATTG
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAG-AAATAGGGAGCAGACACGATTG
637590 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACG-TTCG
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATT-G
* * *
637645 TTGAAGATTGTTCGAGTCTCATTCTCTCTGAAGAAAATAGGGAGCAGGCACGATTA
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAG-AAATAGGGAGCAGACACGATTG
* * *
637701 TTG-AGAATTGTTCGAGTCTCATACTCTCTGAAAAAAATAGGGAGCAGACATGATTA
1 TTGAAG-ATTGTTCGAGTCTCATACTCTCTG-AAGAAATAGGGAGCAGACACGATTG
* * * ** *
637757 TCG-AGAATCGTTTGAGTCTTGTACTCTCTGGAA-AAATGGGGAGCAGACACGATTG
1 TTGAAG-ATTGTTCGAGTCTCATACTCTCT-GAAGAAATAGGGAGCAGACACGATTG
** * * *
637812 ACGAAGATT-TTCGAGT-T-TTACTCCCTGAAGCAATAGGG
1 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGG
637850 GATAAAACCA
Statistics
Matches: 445, Mismatches: 27, Indels: 21
0.90 0.05 0.04
Matches are distributed among these distances:
51 3 0.01
52 13 0.03
53 1 0.00
54 8 0.02
55 269 0.60
56 146 0.33
57 5 0.01
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (55 bp):
TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
Found at i:637636 original size:111 final size:111
Alignment explanation
Indices: 637314--637849 Score: 766
Period size: 111 Copynumber: 4.9 Consensus size: 111
637304 CCAACGATAA
* *
637314 TTGAAGATTGATCGAGTCTTATACTCTCTGAAG-AAATAGGGAGCAGACGCGATTGTTGAAGATT
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAAATAGGGAGCAGACACGATTGTTGAAGATT
*
637378 GTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
66 GTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
*
637424 TTGAAAATTGTTCGAGTCTTATACTCTCTGAAG-AAATAGGGAGCAGACACGATTGTTGAAGATT
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAAATAGGGAGCAGACACGATTGTTGAAGATT
637488 GTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
66 GTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
*
637534 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAAATAGGGAGCAGACACGATTGTTGAAGATT
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAAATAGGGAGCAGACACGATTGTTGAAGATT
637599 GTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACG-TTCG
66 GTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATT-G
* * * *
637645 TTGAAGATTGTTCGAGTCTCATTCTCTCTGAAGAAAATAGGGAGCAGGCACGATTATTG-AGAAT
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAAATAGGGAGCAGACACGATTGTTGAAG-AT
* * *
637709 TGTTCGAGTCTCATACTCTCTGAAAAAAATAGGGAGCAGACATGATTA
65 TGTTCGAGTCTCATACTCTCTG-AAGAAATAGGGAGCAGACACGATTG
* * * * * * **
637757 TCG-AGAATCGTTTGAGTCTTGTACTCTCTGGA-AAAATGGGGAGCAGACACGATTGACGAAGAT
1 TTGAAG-ATTGTTCGAGTCTTATACTCTCTGAAGAAAATAGGGAGCAGACACGATTGTTGAAGAT
* * *
637820 T-TTCGAGT-T-TTACTCCCTGAAGCAATAGGG
65 TGTTCGAGTCTCATACTCTCTGAAGAAATAGGG
637850 GATAAAACCA
Statistics
Matches: 391, Mismatches: 28, Indels: 17
0.90 0.06 0.04
Matches are distributed among these distances:
107 9 0.02
108 8 0.02
109 1 0.00
110 148 0.38
111 180 0.46
112 43 0.11
113 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (111 bp):
TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAAATAGGGAGCAGACACGATTGTTGAAGATT
GTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
Found at i:638591 original size:16 final size:16
Alignment explanation
Indices: 638572--638607 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
638562 AGCAGAACGA
638572 GAGGCACGGAGAAATC
1 GAGGCACGGAGAAATC
638588 GAGGCACGGAGAAATC
1 GAGGCACGGAGAAATC
638604 GAGG
1 GAGG
638608 ATAGAAAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.36, C:0.17, G:0.42, T:0.06
Consensus pattern (16 bp):
GAGGCACGGAGAAATC
Found at i:643117 original size:21 final size:21
Alignment explanation
Indices: 643078--643117 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
643068 CTAGTTCATG
* **
643078 ATGCTGATGTGGCGGTCCACA
1 ATGCTGACGTGGCAATCCACA
643099 ATGCTGACGTGGCAATCCA
1 ATGCTGACGTGGCAATCCA
643118 TTTGTTATGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.25, G:0.30, T:0.23
Consensus pattern (21 bp):
ATGCTGACGTGGCAATCCACA
Found at i:646890 original size:17 final size:17
Alignment explanation
Indices: 646868--646906 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
646858 TCAATTTATC
646868 ATTTTCGCTCCTATCGT
1 ATTTTCGCTCCTATCGT
646885 ATTTTCGCTCCTATCGT
1 ATTTTCGCTCCTATCGT
646902 ATTTT
1 ATTTT
646907 TGCATCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.13, C:0.26, G:0.10, T:0.51
Consensus pattern (17 bp):
ATTTTCGCTCCTATCGT
Found at i:648674 original size:31 final size:32
Alignment explanation
Indices: 648633--648693 Score: 90
Period size: 31 Copynumber: 1.9 Consensus size: 32
648623 GGGGGTAAAT
648633 TATGTATTTAGTA-TCTAAACTATTAATTTTGG
1 TATGTATTTAGTACT-TAAACTATTAATTTTGG
*
648665 TATGT-TTTAGTACTTAAACTTTTAATTTT
1 TATGTATTTAGTACTTAAACTATTAATTTT
648694 TTTAAATACA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 21 0.78
32 6 0.22
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.54
Consensus pattern (32 bp):
TATGTATTTAGTACTTAAACTATTAATTTTGG
Found at i:656794 original size:6 final size:6
Alignment explanation
Indices: 656783--656819 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
656773 ATCAACGGTG
*
656783 ATGGCA ATGGCA ATGGCA ATGGCA GTGGCA ATGGCA A
1 ATGGCA ATGGCA ATGGCA ATGGCA ATGGCA ATGGCA A
656820 ACCAAAGGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.32, C:0.16, G:0.35, T:0.16
Consensus pattern (6 bp):
ATGGCA
Found at i:663513 original size:9 final size:9
Alignment explanation
Indices: 663501--663550 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
663491 GAAGGAGAAT
663501 GAGGAAGAG
1 GAGGAAGAG
*
663510 GAGGAGGAG
1 GAGGAAGAG
*
663519 GAGGAGGAG
1 GAGGAAGAG
663528 GAGG-AGAAG
1 GAGGAAG-AG
663537 GA-GAAGGAG
1 GAGGAA-GAG
663546 GAGGA
1 GAGGA
663551 GGAGAAGGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
8 2 0.06
9 30 0.86
10 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (9 bp):
GAGGAAGAG
Found at i:663571 original size:3 final size:3
Alignment explanation
Indices: 663553--664698 Score: 988
Period size: 3 Copynumber: 383.3 Consensus size: 3
663543 GAGGAGGAGG
* * * * * *
663553 AGA AGG AGA AGG AGA AGA AGA AGT AGA TGG AGA AGG AGA ATG- AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA
* * * * *
663598 AGG AGA TGG AGA AGGA A-A AGG AGA AGA AGA ATG- AGA AGG AGA AGA
1 AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA
* *
663643 AGA ATG- AGA AGG AGA AGA AGA ATG- AGA AGA AGA AGG AGA AGA AGA
1 AGA A-GA AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA
* * * * * * *
663688 AGG AGA TGG AGA AGG AGA A-A GAGA AGG AGA AGG AGA AGGA A-A AGG
1 AGA AGA AGA AGA AGA AGA AGA -AGA AGA AGA AGA AGA A-GA AGA AGA
* *
663733 AGA AGG AGA AGG AGA AGA AGGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA
*
663779 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGG AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * *
663827 AGA AGA AGG AGA AGA AGA AGA AGA ATG- AGA AGA AGG AGA AGA AGG
1 AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA
* * * *
663872 AGA AGAA AGA A-A GAGA ATA AGG AGA AGA AGG AGA AGA AGG AGA AGA
1 AGA AG-A AGA AGA -AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* *
663918 AGGA AGA AGG AGA AGA ATG- AGA AGA ATG- AGA AGA ATG- AGA AGA AGG
1 A-GA AGA AGA AGA AGA A-GA AGA AGA A-GA AGA AGA A-GA AGA AGA AGA
* * *
663964 AGA AGA A-A GAGA AGA AGG AGA AGA AGG AGA AGA AGGA AGA AGG AGA
1 AGA AGA AGA -AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA AGA AGA
* * * *
664010 AGA TGA AGA AG- AGA ATG- AGA AG- AGA AGG AGA AGG AGA AGG AGA
1 AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* *
664053 AGG AGA AG- AGA ATG- AGA AGA AGG AGA AGA ATG- AGA AGGA AGA AGA
1 AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA A-GA AGA A-GA AGA AGA
*
664098 AGA AGA AGGA AGA GGA AGA AGA AGA AGA AGA AGA AGA AGA AGGA AGGA
1 AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA A-GA
* * * * * *
664146 AGA AGA AGA AGA AGA AGA AGGA AGA AGG AGG AGG AG- AGG AGG AGG
1 AGA AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA
* * * * * * * * * *
664191 AGG AGA GGA GGG AGG AGG AGG AGG AGG AGA GGA AGAA AGAA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AG-A AGA AGA
* * * * *
664238 GGA AGA AAA AGA AGA AGA TGA AGA GGA AGA GAGA AG- AGA AGA GGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA -AGA AGA AGA AGA AGA
* * * * * *
664283 AGA TGA AGA GGA AGA TGA AG- AGA AGA TGA AGA AGA AGA TGA AGA GGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * *
664330 AGA GGA AGA GGA AGA AGA AGA GGA AGA AGA AG- AGA AG- AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
664376 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
664424 AGA AG- AGA AGA AG- AGA AG- AGA GGA AGAA AGA AG- AGA AG- AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA
* * *
664465 AGA TGA AG- AGA GGA AGA AGGA AG- AGA AGA GGA AG- AGA AGA GAGA
1 AGA AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA -AGA
664509 AG- AGAA AGA AGA A-A AG- AGA AGA AG- AGA AGA AGA AGAA AGA AG-
1 AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA
664551 AGA AGA AGA AG- AGA AGA AGGA AGA AGA AG- AGA AGA AGA A-A GAGA
1 AGA AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA AGA -AGA
664595 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-A AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
664642 AGA ATGGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA A--GA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
664689 AGA AGA AGA A
1 AGA AGA AGA A
664699 TGGATTTGCA
Statistics
Matches: 939, Mismatches: 128, Indels: 152
0.77 0.11 0.12
Matches are distributed among these distances:
2 67 0.07
3 793 0.84
4 76 0.08
5 3 0.00
ACGTcount: A:0.58, C:0.00, G:0.40, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:668678 original size:23 final size:23
Alignment explanation
Indices: 668641--668697 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
668631 AGAAATCAAG
668641 AATTTAT-TATG-TAAT-GATCA
1 AATTTATATATGTTAATAGATCA
* *
668661 ATTTTATTATATGTTAATAGATGA
1 AATTTA-TATATGTTAATAGATCA
668685 AATTTATATATGT
1 AATTTATATATGT
668698 GATATATCAC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 5 0.17
21 1 0.03
22 4 0.13
23 11 0.37
24 9 0.30
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.49
Consensus pattern (23 bp):
AATTTATATATGTTAATAGATCA
Found at i:669054 original size:17 final size:18
Alignment explanation
Indices: 669029--669063 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
669019 GTGATCCGTT
669029 GTGTGTTCTTC-TTCTTG
1 GTGTGTTCTTCATTCTTG
*
669046 GTGTTTTCTTCATTCTTG
1 GTGTGTTCTTCATTCTTG
669064 CAGTTCAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.03, C:0.17, G:0.20, T:0.60
Consensus pattern (18 bp):
GTGTGTTCTTCATTCTTG
Found at i:675159 original size:21 final size:21
Alignment explanation
Indices: 675133--675185 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
675123 TTATGTTAAT
* *
675133 GTGGTAGTTCACAGTGCTGAC
1 GTGGTAGTCCACAGTACTGAC
*
675154 GTGGTAGTCCACGGTACTGAC
1 GTGGTAGTCCACAGTACTGAC
*
675175 GTGGCAGTCCA
1 GTGGTAGTCCA
675186 TCTATTATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.19, C:0.23, G:0.34, T:0.25
Consensus pattern (21 bp):
GTGGTAGTCCACAGTACTGAC
Found at i:676892 original size:13 final size:13
Alignment explanation
Indices: 676874--676900 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
676864 TATATAATAC
676874 AAGAATTATTATA
1 AAGAATTATTATA
676887 AAGAATTATTATA
1 AAGAATTATTATA
676900 A
1 A
676901 TCTCTGGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (13 bp):
AAGAATTATTATA
Found at i:676916 original size:2 final size:2
Alignment explanation
Indices: 676909--676933 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
676899 AATCTCTGGT
676909 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
676934 TAATTTCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:677240 original size:117 final size:117
Alignment explanation
Indices: 677023--677253 Score: 329
Period size: 117 Copynumber: 2.0 Consensus size: 117
677013 TATTGTCTAA
* * * *
677023 GGATGTTAAACGGTTATAATTTCGTCGATTTCGTACAGTATCCGCTCCAATTGGGGTGGGATGAG
1 GGATGTCAAACGGGTATAATTTCGTCGATTCCGCACAGTATCCGCTCCAATTGGGGTGGGATGAG
*
677088 TATAATTTTAGTAGATAGTGAACATGTGTGAATTTAGAAAGTGATACCCTAG
66 TATAATTTTAGTAGATAGTGAACATATGTGAATTTAGAAAGTGATACCCTAG
* * * *
677140 GGATGTCAAACGGGTATAATTTTGTGGATTCCGCACAGTATCCGCTCCAATTGGGGTGGGGTGGG
1 GGATGTCAAACGGGTATAATTTCGTCGATTCCGCACAGTATCCGCTCCAATTGGGGTGGGATGAG
* * **
677205 TATAATTTTAGTGGGTAGTGGGCATATGT-AGATTTAGAAAGTGATACCC
66 TATAATTTTAGTAGATAGTGAACATATGTGA-ATTTAGAAAGTGATACCC
677254 ATCGCGAATA
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
116 1 0.01
117 99 0.99
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (117 bp):
GGATGTCAAACGGGTATAATTTCGTCGATTCCGCACAGTATCCGCTCCAATTGGGGTGGGATGAG
TATAATTTTAGTAGATAGTGAACATATGTGAATTTAGAAAGTGATACCCTAG
Found at i:677909 original size:197 final size:197
Alignment explanation
Indices: 677562--677957 Score: 713
Period size: 197 Copynumber: 2.0 Consensus size: 197
677552 TTTATGTTTG
677562 TTGCTTATGCATAACTTAAGGTTGTTGTCAGGCGAGTCTAGCCGGATACGTCTCCAATTAAATAG
1 TTGCTTATGCATAACTTAAGGTTGTTGTCAGGCGAGTCTAGCCGGATACGTCTCCAATTAAATAG
677627 TAGGTGTGAGGATGAATTTAAAAATGTGACTACGTGGGTGGATGTAGATTTGAAAAAATTTACCC
66 TAGGTGTGAGGATGAATTTAAAAATGTGACTACGTGGGTGGATGTAGATTTGAAAAAATTTACCC
* * * *
677692 TTCATAAGTGGTGGGCGGATAGTGGATTTAAAAATATTAAATAGATATGAAAATAGAAGAGAGGG
131 TTCATAAATAGTGAGCGGATAGTGAATTTAAAAATATTAAATAGATATGAAAATAGAAGAGAGGG
677757 TA
196 TA
* *
677759 TTGCTTATGCATAACTTAAGGTTGTTGTCAGGCGAGTCTAGCCGGATACGTCTCCAGTTAGATAG
1 TTGCTTATGCATAACTTAAGGTTGTTGTCAGGCGAGTCTAGCCGGATACGTCTCCAATTAAATAG
*
677824 TAGGTGTGAGGATGAATTTAAAAATGT-ACCTACGTGGGTGGATGTGGATTTGAAAAAATTTACC
66 TAGGTGTGAGGATGAATTTAAAAATGTGA-CTACGTGGGTGGATGTAGATTTGAAAAAATTTACC
677888 CTTCATAAATAGTGAGCGGATAGTGAATTTAAAAATATTAAATAGATATGAAAATAGAAGAGAGG
130 CTTCATAAATAGTGAGCGGATAGTGAATTTAAAAATATTAAATAGATATGAAAATAGAAGAGAGG
677953 GTA
195 GTA
677956 TT
1 TT
677958 TGCACCTTAC
Statistics
Matches: 191, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
196 1 0.01
197 190 0.99
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.30
Consensus pattern (197 bp):
TTGCTTATGCATAACTTAAGGTTGTTGTCAGGCGAGTCTAGCCGGATACGTCTCCAATTAAATAG
TAGGTGTGAGGATGAATTTAAAAATGTGACTACGTGGGTGGATGTAGATTTGAAAAAATTTACCC
TTCATAAATAGTGAGCGGATAGTGAATTTAAAAATATTAAATAGATATGAAAATAGAAGAGAGGG
TA
Done.