Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008177.1 Hibiscus syriacus cultivar Beakdansim tig00110773_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: 1003138
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:4196 original size:372 final size:369
Alignment explanation
Indices: 3510--4244 Score: 1313
Period size: 372 Copynumber: 2.0 Consensus size: 369
3500 TGTAACCAAC
3510 TTCAAAAACCTCACAATAAGTTATTAACCACACGTGAGAAACCAGCAAACAGCTCGTTCAACAAC
1 TTCAAAAACCTCACAATAAGTTATTAACCACACGTGAGAAACCAGCAAACAGCTCGTTCAACAAC
3575 AAAGCAGACCCAGGTCATCCAAGACCATACTCCAACATTCCCCCTACTGGAAAACCTTTTTACTA
66 AAAGCAGACCCAGGTCATCCAAGACCATACTCCAACATTCCCCCTACTGGAAAACCTTTTTACTA
3640 ACAAGTCACACTCCAACATTCCCCCTACTAACACACCTCTTTAAAAGAGACATTCACTCTACACT
131 ACAAGTCACACTCCAACATTCCCCCTACTAACACACCTCTTTAAAAGAGACATTCACTCTACACT
3705 CCTCATCACTTGACTCAAAGAATTAACTTGAACTTGAGAACAAGCAACAGTTGCCTATGTTTAAG
196 CCTCATCACTTGACTCAAAGAATTAACTTGAACTTGAGAACAAGCAACAGTTGCCTATGTTTAAG
3770 AAACATAGAGCAAACAATGATTTAGTTAATATATCAACAACCTGCTCAAAGGCAGGAACCT-CTG
261 AAACATAGAGCAAACAATGATTTAGTTAATATATCAACAACCTGCTCAAAGGCAGGAACCTCCTG
3834 AACTGAAAGCTTGCCAGCAACAACCAT-T-CCTAACAAGCAGCA
326 AACTGAAAGCTTGCCAGCAACAACCATCTCCCTAACAAGCAGCA
3876 TTCAAAAACCTCACAATAAAGTTATTAACCACACGTGAGAAACCAGCAAAGCAGCTCGTTCAACA
1 TTCAAAAACCTCACAAT-AAGTTATTAACCACACGTGAGAAACCAGCAAA-CAGCTCGTTCAACA
*
3941 ACAAAGCAGCATGACCCATGTCATCCAAGACCATACTCCAACA-TCCCCCTACTGG-AAACCTTT
64 AC-AA--AGCA-GACCCAGGTCATCCAAGACCATACTCCAACATTCCCCCTACTGGAAAACCTTT
4004 TTACTAACAAGTCACACTCCAACATTCCCCCTACTAACACACCTCTTTAAAAGAGACATTCACTC
125 TTACTAACAAGTCACACTCCAACATTCCCCCTACTAACACACCTCTTTAAAAGAGACATTCACTC
*
4069 TACACTCCTCATCACTTGACTCCAAAGAATTAACTTGAACTTGAGAAACAAGCAACCGTTGCCTA
190 TACACTCCTCATCACTTGACT-CAAAGAATTAACTTGAACTTGAG-AACAAGCAACAGTTGCCTA
4134 TGTTTAAGAAACATAGGAG-AAGACAATGATTTAG-TAATATATCAACAACCTGCTCAAAGGCAG
253 TGTTTAAGAAACATA-GAGCAA-ACAATGATTTAGTTAATATATCAACAACCTGCTCAAAGGCAG
4197 GAACCTCCTGAACTGAAAGCTTGCCAGCAACAACCATCTCCCTAACAA
316 GAACCTCCTGAACTGAAAGCTTGCCAGCAACAACCATCTCCCTAACAA
4245 AGAACAAATC
Statistics
Matches: 354, Mismatches: 2, Indels: 17
0.95 0.01 0.05
Matches are distributed among these distances:
366 17 0.05
367 32 0.09
368 16 0.05
369 2 0.01
370 94 0.27
371 39 0.11
372 100 0.28
373 45 0.13
374 1 0.00
375 8 0.02
ACGTcount: A:0.38, C:0.29, G:0.12, T:0.21
Consensus pattern (369 bp):
TTCAAAAACCTCACAATAAGTTATTAACCACACGTGAGAAACCAGCAAACAGCTCGTTCAACAAC
AAAGCAGACCCAGGTCATCCAAGACCATACTCCAACATTCCCCCTACTGGAAAACCTTTTTACTA
ACAAGTCACACTCCAACATTCCCCCTACTAACACACCTCTTTAAAAGAGACATTCACTCTACACT
CCTCATCACTTGACTCAAAGAATTAACTTGAACTTGAGAACAAGCAACAGTTGCCTATGTTTAAG
AAACATAGAGCAAACAATGATTTAGTTAATATATCAACAACCTGCTCAAAGGCAGGAACCTCCTG
AACTGAAAGCTTGCCAGCAACAACCATCTCCCTAACAAGCAGCA
Found at i:11479 original size:20 final size:20
Alignment explanation
Indices: 11432--11489 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
11422 AAATAACTAA
11432 CAAATTCGCAACACGAACTC
1 CAAATTCGCAACACGAACTC
* * ***
11452 TAATTTCGCAACACGGTTTC
1 CAAATTCGCAACACGAACTC
* *
11472 CAAATTCGTAACTCGAAC
1 CAAATTCGCAACACGAAC
11490 ATAAATATTT
Statistics
Matches: 26, Mismatches: 12, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.24
Consensus pattern (20 bp):
CAAATTCGCAACACGAACTC
Found at i:11672 original size:20 final size:22
Alignment explanation
Indices: 11647--11690 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
11637 CAAATTCGCC
11647 AATTTGA-AAA-TTGAGTTGCA
1 AATTTGACAAATTTGAGTTGCA
*
11667 AATTTGACAAATTTGTGTTGCA
1 AATTTGACAAATTTGAGTTGCA
11689 AA
1 AA
11691 ATGTAAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
21 3 0.14
22 11 0.52
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (22 bp):
AATTTGACAAATTTGAGTTGCA
Found at i:13376 original size:24 final size:24
Alignment explanation
Indices: 13366--13483 Score: 141
Period size: 24 Copynumber: 4.9 Consensus size: 24
13356 CATAATTCAC
* *
13366 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAAAATCCAA
*
13390 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAAAATCCAA
*
13414 GTCAAGTATCAGATCAGAATCCATA
1 GTCAAGTATCAGATCAAAATCCA-A
* *
13439 -TC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAAAATCCAA
13462 GTCAAGTATCAGATCAGAAATC
1 GTCAAGTATCAGATCA-AAATC
13484 AAATCGAAAA
Statistics
Matches: 84, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
23 2 0.02
24 75 0.89
25 7 0.08
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAAAATCCAA
Found at i:13435 original size:48 final size:48
Alignment explanation
Indices: 13366--13480 Score: 169
Period size: 48 Copynumber: 2.4 Consensus size: 48
13356 CATAATTCAC
* * *
13366 GTCAAGTATCATATCAAAATCCAGGTCA-AGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAGATCAGA-TATCAGATCAGAATCCAA
* *
13414 GTCAAGTATCAGATCAGAATCCATATCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGATCAGATATCAGATCAGAATCCAA
13462 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
13481 ATCAAATCGA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
48 60 0.98
49 1 0.02
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGATCAGATATCAGATCAGAATCCAA
Found at i:13497 original size:48 final size:48
Alignment explanation
Indices: 13342--13497 Score: 147
Period size: 48 Copynumber: 3.2 Consensus size: 48
13332 AAACGGATAT
* * * * * * * *
13342 ATCAAAAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAG
1 ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
* * *
13390 GTCA-AGTATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAT
1 ATCAGA-AATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
* *
13438 ATCAGATATCAGATCAGAATCCATGTCAAGTATCAGATCAGAAAT-CAA
1 ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAG-AATCCAA
13486 ATC-GAAAATCAG
1 ATCAG-AAATCAG
13498 GTAAAATATT
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
47 2 0.02
48 85 0.93
49 4 0.04
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAA
Found at i:16001 original size:13 final size:13
Alignment explanation
Indices: 15983--16027 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
15973 CAACGGTTAA
15983 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
15996 CGGGTCAATGGGT
1 CGGGTCAACGGGT
*
16009 CGGGTCAACAGGT
1 CGGGTCAACGGGT
16022 CGGGTC
1 CGGGTC
16028 GGGTAAACGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.16, C:0.22, G:0.44, T:0.18
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:16014 original size:18 final size:18
Alignment explanation
Indices: 16005--16051 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
15995 TCGGGTCAAT
16005 GGGTCGGGTCAACAGGTC
1 GGGTCGGGTCAACAGGTC
* *
16023 GGGTCGGGTAAACGGGTC
1 GGGTCGGGTCAACAGGTC
16041 GGGTCGGGTCA
1 GGGTCGGGTCA
16052 TGACCGGTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.15, C:0.19, G:0.49, T:0.17
Consensus pattern (18 bp):
GGGTCGGGTCAACAGGTC
Found at i:16038 original size:13 final size:13
Alignment explanation
Indices: 15983--16044 Score: 52
Period size: 13 Copynumber: 4.4 Consensus size: 13
15973 CAACGGTTAA
*
15983 CGGGTCAACGGGT
1 CGGGTAAACGGGT
* *
15996 CGGGTCAATGGGT
1 CGGGTAAACGGGT
16009 CGGGTCAACAGGTCGGGT
1 CGGGT-AA-A---CGGGT
16027 CGGGTAAACGGGT
1 CGGGTAAACGGGT
16040 CGGGT
1 CGGGT
16045 CGGGTCATGA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
13 27 0.66
14 1 0.02
15 1 0.02
16 1 0.02
17 2 0.05
18 9 0.22
ACGTcount: A:0.16, C:0.19, G:0.47, T:0.18
Consensus pattern (13 bp):
CGGGTAAACGGGT
Found at i:17209 original size:35 final size:35
Alignment explanation
Indices: 17161--17227 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
17151 CTTTTTGTAC
*
17161 AAGTAAGGTCCTGAGCACACAGCCGAGGAACCGGT
1 AAGTAAGGCCCTGAGCACACAGCCGAGGAACCGGT
17196 AAGTAAGGCCCTGAGCACACAGCCGAGGAACC
1 AAGTAAGGCCCTGAGCACACAGCCGAGGAACC
17228 TCCAGGTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.33, C:0.28, G:0.30, T:0.09
Consensus pattern (35 bp):
AAGTAAGGCCCTGAGCACACAGCCGAGGAACCGGT
Found at i:17326 original size:24 final size:24
Alignment explanation
Indices: 17316--17406 Score: 139
Period size: 24 Copynumber: 3.8 Consensus size: 24
17306 CATAATTCAC
*
17316 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
17340 GTAAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
*
17364 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
17388 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
17407 ATCAAATCGA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
23 2 0.03
24 56 0.93
25 2 0.03
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:25905 original size:33 final size:33
Alignment explanation
Indices: 25868--25946 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
25858 AGTTGGCAAG
25868 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
25901 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
*
25934 TTGGGAATTTCAT
1 TTGGAAATTTCAT
25947 ATTTGGTGGC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.41
Consensus pattern (33 bp):
TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
Found at i:25955 original size:30 final size:32
Alignment explanation
Indices: 25868--25962 Score: 122
Period size: 33 Copynumber: 3.0 Consensus size: 32
25858 AGTTGGCAAG
*
25868 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCAT-GTTGGTGGCCAACTTA
*
25901 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCAT-GTTGGTGGCCAACTTA
* *
25934 TTGGGAATTTCAT-AT-TTGGTGGCTAACTT
1 TTGGAAATTTCATCATGTTGGTGGCCAACTT
25963 GTACACATCG
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
30 13 0.22
32 1 0.02
33 45 0.76
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (32 bp):
TTGGAAATTTCATCATGTTGGTGGCCAACTTA
Found at i:43464 original size:18 final size:18
Alignment explanation
Indices: 43430--43489 Score: 61
Period size: 19 Copynumber: 3.4 Consensus size: 18
43420 TCTCCATCAC
*
43430 AAAAAAAAA-TGTT-GAA
1 AAAAAAAAACAGTTCGAA
* *
43446 AAAAAATAGCAGTTCGAAA
1 AAAAAAAAACAGTTCG-AA
*
43465 AAAAAAAAACTGTTCGAA
1 AAAAAAAAACAGTTCGAA
43483 AAAAAAA
1 AAAAAAA
43490 GACATGAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
16 7 0.20
17 3 0.09
18 10 0.29
19 15 0.43
ACGTcount: A:0.67, C:0.07, G:0.12, T:0.15
Consensus pattern (18 bp):
AAAAAAAAACAGTTCGAA
Found at i:43468 original size:19 final size:19
Alignment explanation
Indices: 43444--43489 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
43434 AAAAATGTTG
* *
43444 AAAAAAAATAGCAGTTCGA
1 AAAAAAAAAAACAGTTCGA
*
43463 AAAAAAAAAAACTGTTCGA
1 AAAAAAAAAAACAGTTCGA
43482 AAAAAAAA
1 AAAAAAAA
43490 GACATGAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.67, C:0.09, G:0.11, T:0.13
Consensus pattern (19 bp):
AAAAAAAAAAACAGTTCGA
Found at i:50316 original size:32 final size:32
Alignment explanation
Indices: 50247--50313 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
50237 AGTTGGCAAG
50247 TTTG-AAATTTCATCTTGGTTGGTGGCCAACT
1 TTTGAAAATTTCATCTTGGTTGGTGGCCAACT
50278 TATTGAAAATTTCATCTTGGTTGGTGGCCAAACT
1 T-TTGAAAATTTCATCTTGGTTGGTGGCC-AACT
50312 TT
1 TT
50314 GAATATGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 1 0.03
32 3 0.09
33 24 0.73
34 5 0.15
ACGTcount: A:0.22, C:0.15, G:0.21, T:0.42
Consensus pattern (32 bp):
TTTGAAAATTTCATCTTGGTTGGTGGCCAACT
Found at i:53108 original size:18 final size:17
Alignment explanation
Indices: 53087--53124 Score: 53
Period size: 15 Copynumber: 2.3 Consensus size: 17
53077 TATGTCCCAT
53087 AGGACCACTACGTCCCGA
1 AGGA-CACTACGTCCCGA
53105 AGG--ACTACGTCCCGA
1 AGGACACTACGTCCCGA
53120 AGGAC
1 AGGAC
53125 TACAATACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 5
0.78 0.00 0.22
Matches are distributed among these distances:
15 15 0.83
18 3 0.17
ACGTcount: A:0.29, C:0.34, G:0.26, T:0.11
Consensus pattern (17 bp):
AGGACACTACGTCCCGA
Found at i:53113 original size:15 final size:15
Alignment explanation
Indices: 53093--53127 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
53083 CCATAGGACC
53093 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
53108 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
53123 ACTAC
1 ACTAC
53128 AATACCCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.34, G:0.23, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:53797 original size:20 final size:20
Alignment explanation
Indices: 53769--53809 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
53759 ATTTTTCCTT
*
53769 TAGGTGGAATCGATACCCCC
1 TAGGGGGAATCGATACCCCC
53789 TAGGGGGAATCGATACCCCC
1 TAGGGGGAATCGATACCCCC
53809 T
1 T
53810 GGACATACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.20
Consensus pattern (20 bp):
TAGGGGGAATCGATACCCCC
Found at i:60012 original size:15 final size:15
Alignment explanation
Indices: 59989--60022 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
59979 CCGTAGGACC
* *
59989 ACTAGGTCCCGAAGT
1 ACTAAGTCCCGAAGG
60004 ACTAAGTCCCGAAGG
1 ACTAAGTCCCGAAGG
60019 ACTA
1 ACTA
60023 CAATACCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (15 bp):
ACTAAGTCCCGAAGG
Found at i:96317 original size:2 final size:2
Alignment explanation
Indices: 96310--96337 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
96300 CAATAAATAA
96310 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
96338 CCCTTGTTGT
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:96639 original size:33 final size:32
Alignment explanation
Indices: 96597--96730 Score: 131
Period size: 33 Copynumber: 4.2 Consensus size: 32
96587 AATATATAGC
96597 AAAAAAAAGAGAAAGAAAAAGGAAAAGAAAAAG
1 AAAAAAAA-AGAAAGAAAAAGGAAAAGAAAAAG
*
96630 -AAAAAAAAGAAAGAGAAAGAGAAAGAGAAAAAG
1 AAAAAAAAAGAAAGAAAAAG-GAAA-AGAAAAAG
96663 -AAAAAAAAG-AAG-AAAA--AAAA-AAAAAG
1 AAAAAAAAAGAAAGAAAAAGGAAAAGAAAAAG
* *
96689 AGAAAAAAAAGAAA-AATAAGGGAAAGAACGAAAG
1 A-AAAAAAAAGAAAGAAAAAGGAAAAGAA--AAAG
96723 AAAAAAAA
1 AAAAAAAA
96731 TTGATCAAAT
Statistics
Matches: 86, Mismatches: 4, Indels: 22
0.77 0.04 0.20
Matches are distributed among these distances:
26 6 0.07
27 1 0.01
28 12 0.14
29 5 0.06
31 17 0.20
32 16 0.19
33 24 0.28
34 5 0.06
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.01
Consensus pattern (32 bp):
AAAAAAAAAGAAAGAAAAAGGAAAAGAAAAAG
Found at i:96704 original size:6 final size:6
Alignment explanation
Indices: 96600--96695 Score: 90
Period size: 6 Copynumber: 15.8 Consensus size: 6
96590 ATATAGCAAA
* * *
96600 AAAAAG AGAAAG AAAAAG GAAAAG AAAAAG AAAAAA AAGAAAG AGAAAGAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AA-AAAG A-AAA-AG
* *
96651 AAAGAG AAAAAG AAAAA- AAAGAAG AAAAA- AAAAA- AAAGAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAA
96696 AAAGAAAAAT
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
5 12 0.16
6 47 0.64
7 11 0.15
8 4 0.05
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:103048 original size:23 final size:23
Alignment explanation
Indices: 102991--103042 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
102981 TTGCATGCTA
*
102991 GGTATCGATACCATCCTTGAATG
1 GGTACCGATACCATCCTTGAATG
103014 GGTACCGATACCATCCTTGAATG
1 GGTACCGATACCATCCTTGAATG
103037 GGTACC
1 GGTACC
103043 ACTACCCCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (23 bp):
GGTACCGATACCATCCTTGAATG
Found at i:103555 original size:14 final size:13
Alignment explanation
Indices: 103520--103544 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
103510 CTATATATTG
103520 ATTTTCAAACATT
1 ATTTTCAAACATT
103533 ATTTTCAAACAT
1 ATTTTCAAACAT
103545 AGTTTTTCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTTTCAAACATT
Found at i:106134 original size:6 final size:7
Alignment explanation
Indices: 106112--106141 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
106102 GTCAAAGGAA
106112 GTCAACG
1 GTCAACG
106119 GTCAACG
1 GTCAACG
106126 GTC-ACG
1 GTCAACG
106132 GTCAACG
1 GTCAACG
106139 GTC
1 GTC
106142 GGGTCTGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:106134 original size:13 final size:13
Alignment explanation
Indices: 106116--106141 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
106106 AAGGAAGTCA
106116 ACGGTCAACGGTC
1 ACGGTCAACGGTC
106129 ACGGTCAACGGTC
1 ACGGTCAACGGTC
106142 GGGTCTGGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:106182 original size:9 final size:9
Alignment explanation
Indices: 106170--106251 Score: 65
Period size: 10 Copynumber: 8.4 Consensus size: 9
106160 CAGGTCAGAA
106170 CGGTCAAAC
1 CGGTCAAAC
*
106179 CGGTTCATAC
1 CGG-TCAAAC
106189 CGGTCAAAC
1 CGGTCAAAC
*
106198 CGGTTCGAAC
1 CGG-TCAAAC
106208 CGGTCGAAAC
1 CGGTC-AAAC
*
106218 CGATCAGAAC
1 CGGTCA-AAC
* *
106228 CGATTGAAAAC
1 CG-GT-CAAAC
106239 CGGTCAAAC
1 CGGTCAAAC
106248 CGGT
1 CGGT
106252 TTCCAGCCCT
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
9 22 0.38
10 29 0.50
11 6 0.10
12 1 0.02
ACGTcount: A:0.30, C:0.29, G:0.24, T:0.16
Consensus pattern (9 bp):
CGGTCAAAC
Found at i:106194 original size:19 final size:19
Alignment explanation
Indices: 106170--106219 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
106160 CAGGTCAGAA
106170 CGGTCAAACCGGTTC-ATAC
1 CGGTCAAACCGGTTCGA-AC
106189 CGGTCAAACCGGTTCGAAC
1 CGGTCAAACCGGTTCGAAC
106208 CGGTCGAAACCG
1 CGGTC-AAACCG
106220 ATCAGAACCG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 22 0.76
20 7 0.24
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.16
Consensus pattern (19 bp):
CGGTCAAACCGGTTCGAAC
Found at i:109241 original size:28 final size:28
Alignment explanation
Indices: 109201--109277 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
109191 GAAGCCAACT
*
109201 TGAAACACATTACCTCCCTAAATTAACC
1 TGAAACACATTACCTCCCCAAATTAACC
** *
109229 TGAAACATGTTACTTCCCCAAATTAACC
1 TGAAACACATTACCTCCCCAAATTAACC
* *
109257 TGAAACGCATTACCTTCCCAA
1 TGAAACACATTACCTCCCCAA
109278 GTCAGCCTAA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.36, C:0.31, G:0.06, T:0.26
Consensus pattern (28 bp):
TGAAACACATTACCTCCCCAAATTAACC
Found at i:110989 original size:110 final size:108
Alignment explanation
Indices: 110568--111732 Score: 752
Period size: 104 Copynumber: 10.7 Consensus size: 108
110558 TTTTTTTAGG
*
110568 AACTAAGTCTGATTTTCAGAGGTTTCTTGACATGGTATTTTTTAAAATGAG-TTTCAAAGAAACT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGAC---G-A-TTTTT-AAATGAGCTTTCAAAGAAACT
* * *
110632 AAGTCTAATTTTCAGAGGTTTCTTGACATGGTATTTTTAAAATGAGTTTTCAAAGA
60 AAGTCTGATTTTTAGAAGTTTCTTG--AT--TA-TTTT-AAATGAGTTTT-AAAGA
* * * * *
110688 AACTAAGTCTTATTTTCAAAAGTTTCTTG-C-TTATTTTAAATGAGTTTTCAAAGAAACTAAGTT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGAT-TTTTAAATGAGCTTTCAAAGAAACTAAGTC
* * * *
110751 TGATTTTCAGAGGTTT-TTGACATGAAATTTTTCAAAATGAGTTTCAAAGA
65 TGATTTTTAGAAGTTTCTTG--AT--TA-TTTT--AAATGAGTTTTAAAGA
* * * * *
110801 AACAAATTCTGATTTTCATAAGTTTCTTGATGA-TTTTAAATGAGTTTTCAAAGAAACTAAGTCT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGCTTTCAAAGAAACTAAGTCT
* *
110865 GATTTTTAGGAGTTTGTTGATTATTTCTAAATGAGATTTTAAAGA
66 GATTTTTAGAAGTTTCTTGATTATTT-TAAATGAG-TTTTAAAGA
* * *
110910 AACTAAGTATGATTTTCAGAAGTTTTTTGACAATTTTTAAATGAGCTTTCAAAGAAACTAAGTCT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGCTTTCAAAGAAACTAAGTCT
** *
110975 GATTTTTAGAAGTTTCTTGACGATTTTCAAGTGAGTTTTTAAAGA
66 GATTTTTAGAAGTTTCTTGATTATTTT-AAATGAG-TTTTAAAGA
* * * ** *
111020 AATTAAGTCTGATTTTCAAAAGTTTCTTAATTATTTTTAAATGAGCTTTCAAAGAAACTAAGTTT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGCTTTCAAAGAAACTAAGTCT
* **
111085 GATTTTTAGATGTTTCTTGACGATTTTCAAATGAGTTTTAAAGA
66 GATTTTTAGAAGTTTCTTGATTATTTT-AAATGAGTTTTAAAGA
* * * * * * *
111129 AACTAAGCCTGGTCTTCAGAAGTTTCTTGATGA-TTTTAAATGAACTTTCAAAGAAATTAAGCCT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGCTTTCAAAGAAACTAAGTCT
* * ** * * * *
111193 AATTTGTAGGGGTTTCTTAATGT-TTTCAAATGAATTTCAAAGA
66 GATTTTTAGAAGTTTCTTGAT-TATTTTAAATGAGTTTTAAAGA
* * *
111236 AACTAAGTCAT-ATTTTCATAAGTTTCTTGACGATTTTCAAATGAGCTTTTAAAGAAACTAAGTC
1 AACTAAGTC-TGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGCTTTCAAAGAAACTAAGTC
* * *
111300 CGA-TTTTCGTAAGTTTCTTGATTA-TTTAAATGAGCTTTCAAAGA
65 TGATTTTTAG-AAGTTTCTTGATTATTTTAAATGAG-TTTTAAAGA
* ** * * *
111344 AATTAAGTCTGATTTTCAGTGGTTTCTT-A--ATTTTTCCATATGA--ATT-AAAAAAACTAAGT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTT--AAATGAGCTTTCAAAGAAACTAAGT
* ** * * *
111403 CTAATTTTTAGGGGTTTCTTGATGT-TTTCAAATGAATTTGAAAGA
64 CTGATTTTTAGAAGTTTCTTGAT-TATTTTAAATGAGTTTTAAAGA
* * * ** * * * *
111448 AGA-TAAGCCTAATTTTTAGGGGTTTCTTGA-TATTTTCAAATGA--ATT-AAAAAAAGCTAAG-
1 A-ACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGCTTTCAAAGAAA-CTAAGT
* * * * * *
111507 CATAATTTTAAG-GGTTTCTTGATGT-TTTCAAATGAATTTGAAAGA
64 C-TGATTTTTAGAAGTTTCTTGAT-TATTTTAAATGAGTTTTAAAGA
* * * * ** * * * * * * *
111552 AGCTAAGCCTAATTTTTAGGGGTTTCTTAATG-TTTTCAAATGA-ATTTGAAAGAAGCTAAGCCT
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGCTTTCAAAGAAACTAAGTCT
** * * * * *
111615 -A-TTTTAGGGGTTTCTTGACGT-TTTCAAATGAATTTGAAAAA
66 GATTTTTAGAAGTTTCTTGA-TTATTTTAAATGAGTTTTAAAGA
** * * * *
111656 AACTAAGTCTGATTTTCAGGGGTTTCTTGATGATAATTTTCAATGAGTTTTAAAAGAAAGCTAAG
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGACGAT--TTTTAAATGAGCTTTCAAAGAAA-CTAAG
* *
111721 CCTAATTTTTAG
63 TCTGATTTTTAG
111733 GGGTTCCTTG
Statistics
Matches: 877, Mismatches: 127, Indels: 91
0.80 0.12 0.08
Matches are distributed among these distances:
103 5 0.01
104 199 0.23
105 46 0.05
106 11 0.01
107 68 0.08
108 128 0.15
109 81 0.09
110 160 0.18
111 6 0.01
112 2 0.00
113 94 0.11
114 50 0.06
119 1 0.00
120 26 0.03
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.41
Consensus pattern (108 bp):
AACTAAGTCTGATTTTCAGAAGTTTCTTGACGATTTTTAAATGAGCTTTCAAAGAAACTAAGTCT
GATTTTTAGAAGTTTCTTGATTATTTTAAATGAGTTTTAAAGA
Found at i:111261 original size:53 final size:53
Alignment explanation
Indices: 110607--111687 Score: 762
Period size: 55 Copynumber: 20.0 Consensus size: 53
110597 ACATGGTATT
* * * *
110607 TTTTAAAATGAGTTTCAAAGAAACTAAGTCTAATTTTCAGAGGTTTCTTGACATGG
1 TTTTCAAATGAATTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTG--AT-G
* * * * *
110663 TATTTTTAAAATGAGTTTTCAAAGAAACTAAGTCTTATTTTCAAAAGTTTCTTGCT-
1 ---TTTTCAAATGA-ATTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATG
* * * *
110719 TATTTTAAATGAGTTTTCAAAGAAACTAAGTTTGATTTTCAGAGGTTT-TTGACATG
1 T-TTTCAAATGA-ATTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTG--ATG
* * * *
110775 AAATTTTTCAAAATGAGTTTCAAAGAAACAAATTCTGATTTTCATAAGTTTCTTGATG
1 ----TTTTC-AAATGAATTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATG
* * * *
110833 ATTTT-AAATGAGTTTTCAAAGAAACTAAGTCTGATTTTTAGGAGTTTGTTGAT-
1 -TTTTCAAATGA-ATTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATG
* * * **
110886 TATTTCTAAATGAGATTTTAAAGAAACTAAGTATGATTTTCAGAAGTTTTTTGACAA
1 T-TTTC-AAATGA-ATTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGA-TG
* * * *
110943 TTTTTAAATGAGCTTTCAAAGAAACTAAGTCTGATTTTTAGAAGTTTCTTGACG
1 TTTTCAAATGA-ATTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATG
* * * * * * *
110997 ATTTTCAAGTGAGTTTTTAAAGAAATTAAGTCTGATTTTCAAAAGTTTCTTAATTA
1 -TTTTCAAATGA-ATTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGA-TG
* * * * * *
111053 TTTTTAAATGAGCTTTCAAAGAAACTAAGTTTGATTTTTAGATGTTTCTTGACG
1 TTTTCAAATGA-ATTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATG
* * * * *
111107 ATTTTCAAATGAGTTTTAAAGAAACTAAGCCTGGTCTTCAGAAGTTTCTTGATG
1 -TTTTCAAATGAATTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATG
* * * ** *
111161 ATTTT-AAATGAACTTTCAAAGAAATTAAGCCTAATTTGT-AGGGGTTTCTTAATG
1 -TTTTCAAATGAA-TTTCAAAGAAACTAAGTCTGATTT-TCAGAAGTTTCTTGATG
* *
111215 TTTTCAAATGAATTTCAAAGAAACTAAGTCAT-ATTTTCATAAGTTTCTTGACG
1 TTTTCAAATGAATTTCAAAGAAACTAAGTC-TGATTTTCAGAAGTTTCTTGATG
* * *
111268 ATTTTCAAATGAGCTTTTAAAGAAACTAAGTCCGATTTTC-GTAAGTTTCTTGAT-
1 -TTTTCAAATGA-ATTTCAAAGAAACTAAGTCTGATTTTCAG-AAGTTTCTTGATG
* * ** *
111322 TATTT-AAATGAGCTTTCAAAGAAATTAAGTCTGATTTTCAGTGGTTTCTTAAT-
1 T-TTTCAAATGA-ATTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATG
* * * * **
111375 TTTTCCATATGAA-TT-AAAAAAACTAAGTCTAATTTTTAGGGGTTTCTTGATG
1 TTTT-CAAATGAATTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATG
* * * * ** *
111427 TTTTCAAATGAATTTGAAAGAAGA-TAAGCCTAATTTTTAGGGGTTTCTTGATA
1 TTTTCAAATGAATTTCAAAGAA-ACTAAGTCTGATTTTCAGAAGTTTCTTGATG
* * * *
111480 TTTTCAAATGAA-TT-AAAAAAAGCTAAG-CATAATTTTAAG-GGTTTCTTGATG
1 TTTTCAAATGAATTTCAAAGAAA-CTAAGTC-TGATTTTCAGAAGTTTCTTGATG
* * * * * ** *
111531 TTTTCAAATGAATTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTAATG
1 TTTTCAAATGAATTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATG
* * * ** *
111584 TTTTCAAATGAATTTGAAAGAAGCTAAGCCT-ATTTT-AGGGGTTTCTTGACG
1 TTTTCAAATGAATTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATG
* * **
111635 TTTTCAAATGAATTTGAAAAAAACTAAGTCTGATTTTCAGGGGTTTCTTGATG
1 TTTTCAAATGAATTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATG
111688 ATAATTTTCA
Statistics
Matches: 851, Mismatches: 125, Indels: 98
0.79 0.12 0.09
Matches are distributed among these distances:
50 1 0.00
51 107 0.13
52 54 0.06
53 201 0.24
54 173 0.20
55 219 0.26
56 3 0.00
57 1 0.00
58 4 0.00
59 43 0.05
60 45 0.05
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.41
Consensus pattern (53 bp):
TTTTCAAATGAATTTCAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATG
Found at i:111419 original size:51 final size:53
Alignment explanation
Indices: 111108--111737 Score: 448
Period size: 53 Copynumber: 11.8 Consensus size: 53
111098 TTCTTGACGA
* * * ** * * ** *
111108 TTTTCAAATGAGTTTTAAAGAAACTAAGCCTGGTCTTCAGAAGTTTCTTGATG
1 TTTTCAAATGAATTTGAAAAAAACTAAGCCTAATTTTTAGGGGTTTCTTAATG
* * * *
111161 ATTTT-AAATGAACTTTCAAAGAAATTAAGCCTAATTTGTAGGGGTTTCTTAATG
1 -TTTTCAAATGAA-TTTGAAAAAAACTAAGCCTAATTTTTAGGGGTTTCTTAATG
* * * * *** * *
111215 TTTTCAAATGAATTTCAAAGAAACTAAGTC-ATATTTTCATAAGTTTCTTGACG
1 TTTTCAAATGAATTTGAAAAAAACTAAGCCTA-ATTTTTAGGGGTTTCTTAATG
* * * * * *
111268 ATTTTCAAATGAGCTTTTAAAGAAACTAAGTCC-GATTTTCGTA--AGTTTCTTGAT-
1 -TTTTCAAATGA-ATTTGAAAAAAACTAAG-CCTAATTTT--TAGGGGTTTCTTAATG
* * * * * * * *
111322 TATTT-AAATGAGCTTTCAAAGAAATTAAGTCTGATTTTCAGTGGTTTCTTAAT-
1 T-TTTCAAATGA-ATTTGAAAAAAACTAAGCCTAATTTTTAGGGGTTTCTTAATG
* * *
111375 TTTTCCATATGAA-TT-AAAAAAACTAAGTCTAATTTTTAGGGGTTTCTTGATG
1 TTTT-CAAATGAATTTGAAAAAAACTAAGCCTAATTTTTAGGGGTTTCTTAATG
* * *
111427 TTTTCAAATGAATTTGAAAGAAGA-TAAGCCTAATTTTTAGGGGTTTCTTGATA
1 TTTTCAAATGAATTTGAAA-AAAACTAAGCCTAATTTTTAGGGGTTTCTTAATG
* * *
111480 TTTTCAAATGAA-TT-AAAAAAAGCTAAGCATAA-TTTTAAGGGTTTCTTGATG
1 TTTTCAAATGAATTTGAAAAAAA-CTAAGCCTAATTTTTAGGGGTTTCTTAATG
* *
111531 TTTTCAAATGAATTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTAATG
1 TTTTCAAATGAATTTGAAAAAAACTAAGCCTAATTTTTAGGGGTTTCTTAATG
* * * *
111584 TTTTCAAATGAATTTGAAAGAAGCTAAGCCT-A-TTTTAGGGGTTTCTTGACG
1 TTTTCAAATGAATTTGAAAAAAACTAAGCCTAATTTTTAGGGGTTTCTTAATG
* * * *
111635 TTTTCAAATGAATTTGAAAAAAACTAAGTCTGATTTTCAGGGGTTTCTTGATGATAA
1 TTTTCAAATGAATTTGAAAAAAACTAAGCCTAATTTTTAGGGGTTTCTT-A--AT-G
* *
111692 TTTTC-AATGAGTTTTAAAAGAAAGCTAAGCCTAATTTTTAGGGGTT
1 TTTTCAAATGAATTTGAAAA-AAA-CTAAGCCTAATTTTTAGGGGTT
111738 CCTTGACAAT
Statistics
Matches: 478, Mismatches: 67, Indels: 58
0.79 0.11 0.10
Matches are distributed among these distances:
50 3 0.01
51 115 0.24
52 36 0.08
53 188 0.39
54 64 0.13
55 30 0.06
56 14 0.03
57 9 0.02
58 19 0.04
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (53 bp):
TTTTCAAATGAATTTGAAAAAAACTAAGCCTAATTTTTAGGGGTTTCTTAATG
Found at i:112559 original size:73 final size:73
Alignment explanation
Indices: 112168--112549 Score: 525
Period size: 73 Copynumber: 5.2 Consensus size: 73
112158 GATCAACATA
* *
112168 TCGCTTGAGACAGTTTCACTCGAAACAAAATTTTATCTCACTTAAGATTGTTTTTCTTAAAACAA
1 TCGCTTGAGACAGTTTCACTCGAAACAAAATTTTATCTCACTTGAGATCGTTTTTCTTAAAACAA
*
112233 ACTTCATC
66 ACTTCGTC
* * * *
112241 TCTCTAGAGACAGTTTCACTTGAAACAAAATTTTATCTCACTTGAGATCGTTTTTCTAAAAACAA
1 TCGCTTGAGACAGTTTCACTCGAAACAAAATTTTATCTCACTTGAGATCGTTTTTCTTAAAACAA
112306 ACTTCGTC
66 ACTTCGTC
* * * *
112314 TTGCTAGAGACAGTTTCATTCGAAACAAAATTTTATCTCACTTGAGATCGTTTTCCTTAAAACAA
1 TCGCTTGAGACAGTTTCACTCGAAACAAAATTTTATCTCACTTGAGATCGTTTTTCTTAAAACAA
112379 ACTTCGTC
66 ACTTCGTC
*
112387 TCGCTTGAGACAGTTTTCACTCAAAACAAAATTTTATCTCACTTGAGATCG-TTTTCTTAAAACA
1 TCGCTTGAGACAG-TTTCACTCGAAACAAAATTTTATCTCACTTGAGATCGTTTTTCTTAAAACA
112451 AACTTCGTC
65 AACTTCGTC
* * * * * * * *
112460 TTGCTTGAGAAATTTTTACTCGAAATAATAAATTTATCTCACTCGAGATTGTTTTTCTTAAAACA
1 TCGCTTGAGACAGTTTCACTCGAAACAA-AATTTTATCTCACTTGAGATCGTTTTTCTTAAAACA
*
112525 AACTT-ATC
65 AACTTCGTC
* *
112533 TCGTTTGAGAAAGTTTC
1 TCGCTTGAGACAGTTTC
112550 CCTTGAAATA
Statistics
Matches: 274, Mismatches: 32, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
72 12 0.04
73 209 0.76
74 53 0.19
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.37
Consensus pattern (73 bp):
TCGCTTGAGACAGTTTCACTCGAAACAAAATTTTATCTCACTTGAGATCGTTTTTCTTAAAACAA
ACTTCGTC
Found at i:112680 original size:35 final size:36
Alignment explanation
Indices: 112634--112702 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
112624 TCAAACTTCG
* *
112634 TCTCACTTGAGACA-TTTCTC-TCGAAACAAATTTTA
1 TCTCACCTGAGACAGTTTATCTTC-AAACAAATTTTA
*
112669 TCTCACCTGAGATAGTTTATCTTCAAACAAATTT
1 TCTCACCTGAGACAGTTTATCTTCAAACAAATTT
112703 CTTTTGGTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 12 0.41
36 15 0.52
37 2 0.07
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.38
Consensus pattern (36 bp):
TCTCACCTGAGACAGTTTATCTTCAAACAAATTTTA
Found at i:113317 original size:25 final size:22
Alignment explanation
Indices: 113265--113316 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
113255 GGTTCATAAT
113265 GAGAAGAACTCATCTGATGAGG
1 GAGAAGAACTCATCTGATGAGG
113287 GAGAAGAACTCATCTGATGAGG
1 GAGAAGAACTCATCTGATGAGG
113309 GAGAAGAA
1 GAGAAGAA
113317 GTTCATAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.12, G:0.33, T:0.15
Consensus pattern (22 bp):
GAGAAGAACTCATCTGATGAGG
Found at i:113326 original size:168 final size:160
Alignment explanation
Indices: 113118--113437 Score: 471
Period size: 159 Copynumber: 1.9 Consensus size: 160
113108 AGTTCATAAT
*
113118 GAGAAGAACTCATCCGAAAGAGTGAGAAGAAGATCATAATGAGAAGAACTTGTTCAACTTTCAAC
1 GAGAAGAACTCATCCGAAAGAGGGAGAAGAAGATCATAATGAGAAGAACTTG------TTT-AAC
* * *
113183 TTTAGCTTGATTTATCGCATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACATTTCC
59 CTTAGCTTGATTCAT--CACATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACATTTCC
*
113248 AATGGAGGGTTCATAATGAGAAGAACTCATCTGATGAGG
122 AATGGAGAGTTCATAATGAGAAGAACTCATCTGATGAGG
* * *
113287 GAGAAGAACTCATCTG-ATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTAGCT
1 GAGAAGAACTCATCCGAAAGAGGGAGAAGAAGATCATAATGAGAAGAACTTGTTTAACCTTAGCT
*
113351 TGATTCATCACATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACATTTCCAGTGGAGAG
66 TGATTCATCACATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACATTTCCAATGGAGAG
113416 TTCATAATGAGAAGAACTCATC
131 TTCATAATGAGAAGAACTCATC
113438 CAACAGAGGG
Statistics
Matches: 142, Mismatches: 9, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
159 76 0.54
161 16 0.11
162 3 0.02
168 32 0.23
169 15 0.11
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (160 bp):
GAGAAGAACTCATCCGAAAGAGGGAGAAGAAGATCATAATGAGAAGAACTTGTTTAACCTTAGCT
TGATTCATCACATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACATTTCCAATGGAGAG
TTCATAATGAGAAGAACTCATCTGATGAGG
Found at i:113654 original size:139 final size:139
Alignment explanation
Indices: 113287--113900 Score: 856
Period size: 139 Copynumber: 4.4 Consensus size: 139
113277 TCTGATGAGG
* * * *
113287 GAGAAGAACTCATCTGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTAGCTT
1 GAGAAGAACTCATCTGATGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTAACTC
* * *
113352 GATTCAT--CACATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACATTTCCAGTGGAGA
66 GATTCATCGCATATGGAGTTGAATCAGCAACACATCACTCGAGGGATCAACATTTCCAGTAGAGA
113415 GTTCATAAT
131 GTTCATAAT
** * *
113424 GAGAAGAACTCATCCAACAGAGGGAGAAAAAGTTCATAATGAGAATAACTTGTTCAACCTTAACT
1 GAGAAGAACTCATCTGA-TGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTAACT
* * ** * * * *
113489 CGATTCATCGCATATGGATTTTAATCAATAACACATCACTTGAGGGATCAACATTTCTAATGGAG
65 CGATTCATCGCATATGGAGTTGAATCAGCAACACATCACTCGAGGGATCAACATTTCCAGTAGAG
113554 AGTTCATAAT
130 AGTTCATAAT
* * * *
113564 GAGAAGAACTAATATAATGAGGGAGAAAAAGTTCATAATGAAAAGAACTTGTTCAACCTTAACTC
1 GAGAAGAACTCATCTGATGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTAACTC
* * * *
113629 GATTCATCGCATGTGGAGTTGAATCAGCAATACCTCACTTGAGGGATCAACATTTCCAGTAGAGA
66 GATTCATCGCATATGGAGTTGAATCAGCAACACATCACTCGAGGGATCAACATTTCCAGTAGAGA
113694 GTTCATAAT
131 GTTCATAAT
* * * * * * *
113703 GAAAAGAACTCATCCGATGAGGGGGGAAAAGTTCAAAATGAGAAGAACTTGTTCAACATTAGCTC
1 GAGAAGAACTCATCTGATGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTAACTC
*
113768 GATTCATTGCATATGGAGTTGAATCAGCAACACATCACTCGAGGGATCAACATTTCCAGTAGAGA
66 GATTCATCGCATATGGAGTTGAATCAGCAACACATCACTCGAGGGATCAACATTTCCAGTAGAGA
113833 GTTCATAAT
131 GTTCATAAT
* *
113842 GAGAATAACTCATCTGATGAGGGA-AAAGAAGTTCATAATGAGAATAACTTGTTCAACCT
1 GAGAAGAACTCATCTGATGAGGGAGAAA-AAGTTCATAATGAGAAGAACTTGTTCAACCT
113901 CAGCAGTTTC
Statistics
Matches: 416, Mismatches: 57, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
137 15 0.04
138 51 0.12
139 280 0.67
140 70 0.17
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.26
Consensus pattern (139 bp):
GAGAAGAACTCATCTGATGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTAACTC
GATTCATCGCATATGGAGTTGAATCAGCAACACATCACTCGAGGGATCAACATTTCCAGTAGAGA
GTTCATAAT
Found at i:119042 original size:11 final size:12
Alignment explanation
Indices: 119015--119045 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
119005 AAATAGAAAT
119015 AAAAAATACAAG
1 AAAAAATACAAG
119027 AAAAAATACAAG
1 AAAAAATACAAG
119039 AAAAAAT
1 AAAAAAT
119046 TCTAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.10
Consensus pattern (12 bp):
AAAAAATACAAG
Found at i:121551 original size:22 final size:22
Alignment explanation
Indices: 121523--121568 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
121513 GTGAATCCTC
*
121523 ATATTACATTTGTTTATAAAAA
1 ATATTACATTTGTTGATAAAAA
121545 ATATTACATTTGTTGATAAAAA
1 ATATTACATTTGTTGATAAAAA
121567 AT
1 AT
121569 TGTGGTTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (22 bp):
ATATTACATTTGTTGATAAAAA
Found at i:123582 original size:36 final size:36
Alignment explanation
Indices: 123535--123650 Score: 205
Period size: 36 Copynumber: 3.2 Consensus size: 36
123525 GCTTTACCAG
123535 TGTGAACAGCAGCATGCAATTTAAACATTCTTGCAT
1 TGTGAACAGCAGCATGCAATTTAAACATTCTTGCAT
123571 TGTGAACAGCAGCATGCAATTTAAACATTCTTGCAT
1 TGTGAACAGCAGCATGCAATTTAAACATTCTTGCAT
* *
123607 TGTGAACAGCAGCATGCATTTTAAACATTCTTCCAT
1 TGTGAACAGCAGCATGCAATTTAAACATTCTTGCAT
*
123643 GGTGAACA
1 TGTGAACA
123651 AGAGGATATT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 77 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (36 bp):
TGTGAACAGCAGCATGCAATTTAAACATTCTTGCAT
Found at i:123626 original size:19 final size:19
Alignment explanation
Indices: 123566--123626 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
123556 TAAACATTCT
123566 TGCATTGTGAACAGCAGCA
1 TGCATTGTGAACAGCAGCA
* *
123585 TGCAATT-T-AA-A-CATTCT
1 TGC-ATTGTGAACAGCA-GCA
123602 TGCATTGTGAACAGCAGCA
1 TGCATTGTGAACAGCAGCA
123621 TGCATT
1 TGCATT
123627 TTAAACATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
16 5 0.16
17 6 0.19
18 4 0.12
19 12 0.38
20 5 0.16
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (19 bp):
TGCATTGTGAACAGCAGCA
Found at i:123633 original size:19 final size:19
Alignment explanation
Indices: 123539--123633 Score: 54
Period size: 19 Copynumber: 5.2 Consensus size: 19
123529 TACCAGTGTG
*
123539 AACAGCAGCATGCAATTTA
1 AACAGCAGCATGCATTTTA
** * * *
123558 AACA--TTCTTGCATTGTG
1 AACAGCAGCATGCATTTTA
*
123575 AACAGCAGCATGCAATTTA
1 AACAGCAGCATGCATTTTA
** * * *
123594 AACA--TTCTTGCATTGTG
1 AACAGCAGCATGCATTTTA
123611 AACAGCAGCATGCATTTTA
1 AACAGCAGCATGCATTTTA
123630 AACA
1 AACA
123634 TTCTTCCATG
Statistics
Matches: 49, Mismatches: 23, Indels: 8
0.61 0.29 0.10
Matches are distributed among these distances:
17 22 0.45
19 27 0.55
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (19 bp):
AACAGCAGCATGCATTTTA
Found at i:130736 original size:104 final size:103
Alignment explanation
Indices: 130576--130872 Score: 364
Period size: 104 Copynumber: 2.9 Consensus size: 103
130566 TTCTTCAAAA
* * * * * *
130576 AAAAAAAATTTCGTCTCGCTTGAGACCTTTTCCCTTGGATATACAAATTTCGAATTTGTTCACAT
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTCAAATTTGTTCACAT
* * *
130641 TAAGCAAAGTTAATATCACTTGAGATTGTTGTTTCTTTT
66 TAAACAAA-TTAATATCACTTGAGATTGTTGTTTATTTC
* *
130680 AAAACAAACTTCGTCTCGCTTGAGATATTTTTCCTTTGAGATACAAATTTCAAATTTGCTTCACA
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTCAAATTTG-TTCACA
* *
130745 TGAAACAAATTAATCTCACTTGAGATTGTTGTTTATTTC
65 TTAAACAAATTAATATCACTTGAGATTGTTGTTTATTTC
* * * * * *
130784 GAAACAAATTTCGTTTCGCTTGAGACATTTTTTCTCTGGGATACAAATTT-AAATTTGTTGTAC-
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTCAAATTTGTT-CACA
130847 TTGAAACAAAATTAATATCACTTGAG
65 TT-AAAC-AAATTAATATCACTTGAG
130873 TTTTCAAAAT
Statistics
Matches: 166, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
102 3 0.02
103 13 0.08
104 137 0.83
105 13 0.08
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (103 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTCAAATTTGTTCACAT
TAAACAAATTAATATCACTTGAGATTGTTGTTTATTTC
Found at i:131049 original size:27 final size:27
Alignment explanation
Indices: 131014--131089 Score: 66
Period size: 27 Copynumber: 2.7 Consensus size: 27
131004 ACAGTTTCTC
131014 TTGAGATAAATCTTTGAGTCTGTTCCTA
1 TTGA-ATAAATCTTTGAGTCTGTTCCTA
* *
131042 TTGAATAAAAATC-TTGAGT-TGTTTCTT
1 TTGAAT--AAATCTTTGAGTCTGTTCCTA
* *
131069 TTGAAACAAATATTTGAGTCT
1 TTG-AATAAATCTTTGAGTCT
131090 ATTTCTGTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
26 4 0.10
27 17 0.44
28 13 0.33
29 5 0.13
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (27 bp):
TTGAATAAATCTTTGAGTCTGTTCCTA
Found at i:131195 original size:62 final size:63
Alignment explanation
Indices: 131076--131226 Score: 225
Period size: 62 Copynumber: 2.4 Consensus size: 63
131066 CTTTTGAAAC
* * *
131076 AAATATTTGAGTCTATTTCTGTTAAAACAAAGTTTTGTCTCTCTGGAGACAATTTCGTAAAAA
1 AAATCTTTGAGTCTATTTCTTTTGAAACAAAGTTTTGTCTCTCTGGAGACAATTTCGTAAAAA
* * *
131139 AAATCTTTGAGTCTATTTATTTTGAAACAAAG-TTTGTCTCTCTTGAGACAATTTCGTGAAAA
1 AAATCTTTGAGTCTATTTCTTTTGAAACAAAGTTTTGTCTCTCTGGAGACAATTTCGTAAAAA
*
131201 AAATCTTTGAGT-TGTTTCTTTTGAAA
1 AAATCTTTGAGTCTATTTCTTTTGAAA
131227 AAAATCTTTG
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
61 12 0.15
62 40 0.50
63 28 0.35
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (63 bp):
AAATCTTTGAGTCTATTTCTTTTGAAACAAAGTTTTGTCTCTCTGGAGACAATTTCGTAAAAA
Found at i:131223 original size:152 final size:154
Alignment explanation
Indices: 131043--131390 Score: 391
Period size: 152 Copynumber: 2.2 Consensus size: 154
131033 CTGTTCCTAT
*
131043 TGAATAAAAATC-TTGAGTTGTTTCTTTTGAAACAAATATTTGAGTCTATTT-CTGTTAAAACAA
1 TGAA-AAAAATCTTTGAGTTGTTTCTTTTGAAACAAATATTTGAGTCTATTTCCT-TGAAAACAA
* * **
131106 AGTTTTGTCTCTC-TGGAGACAATTTC-GTAAAAAAAATCTTTGAGTCTATTTATTTTGAAACAA
64 AATTTTGTCTCTCTTGG-GACAATTTCTGTAAAAAAAATCTTTGAGTATATTTATTTAAAAACAA
* *
131169 AGTTTGTCTCTCTTGAGACAATTTC-G
128 AGTTTGCCTCTCTTGAGACAATTTCAA
* * * *
131195 TGAAAAAAATCTTTGAGTTGTTTCTTTTGAAAAAAATCTTTGAGTCTGTTTCCTTGGAAACAAAA
1 TGAAAAAAATCTTTGAGTTGTTTCTTTTGAAACAAATATTTGAGTCTATTTCCTTGAAAACAAAA
* * ** * *
131260 TTTTGTCTCTCTTGGGACAATTTCTTTTGAAAATCATCTTTGAGTATATTTCTTTAAAAACAAAT
66 TTTTGTCTCTCTTGGGACAATTTC-TGTAAAAAAAATCTTTGAGTATATTTATTTAAAAACAAAG
* *
131325 TTTGCCTCTCTTGAGATAGTTTCTAA
130 TTTGCCTCTCTTGAGACAATTTC-AA
* * *
131351 TGAAAAAATAACCTTTGGGATTGTTTCCTTTGAAACAAAT
1 TG-AAAAA-AATCTTTGAG-TTGTTTCTTTTGAAACAAAT
131391 TTCGTCTCAC
Statistics
Matches: 163, Mismatches: 23, Indels: 13
0.82 0.12 0.07
Matches are distributed among these distances:
151 7 0.04
152 68 0.42
153 5 0.03
154 50 0.31
156 2 0.01
157 5 0.03
158 8 0.05
159 18 0.11
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (154 bp):
TGAAAAAAATCTTTGAGTTGTTTCTTTTGAAACAAATATTTGAGTCTATTTCCTTGAAAACAAAA
TTTTGTCTCTCTTGGGACAATTTCTGTAAAAAAAATCTTTGAGTATATTTATTTAAAAACAAAGT
TTGCCTCTCTTGAGACAATTTCAA
Found at i:131232 original size:27 final size:28
Alignment explanation
Indices: 131195--131264 Score: 99
Period size: 27 Copynumber: 2.5 Consensus size: 28
131185 GACAATTTCG
*
131195 TGAAAAAAATCTTTGAGT-TGTTTCTTT
1 TGAAAAAAATCTTTGAGTCTGTTTCCTT
131222 TGAAAAAAATCTTTGAGTCTGTTTCCTT
1 TGAAAAAAATCTTTGAGTCTGTTTCCTT
*
131250 GGAAACAAAAT-TTTG
1 TGAAA-AAAATCTTTG
131265 TCTCTCTTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
27 18 0.46
28 16 0.41
29 5 0.13
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (28 bp):
TGAAAAAAATCTTTGAGTCTGTTTCCTT
Found at i:131319 original size:89 final size:87
Alignment explanation
Indices: 131136--131319 Score: 217
Period size: 90 Copynumber: 2.1 Consensus size: 87
131126 AATTTCGTAA
* *
131136 AAAAAATCTTTGAGTCTATTTATTTTGAAACAAAGTTTGTCTCTCTTGAGACAATTTCGTGAAAA
1 AAAAAATCTTTGAGTCTATTTACTTGGAAACAAAGTTTGTCTCTCTTGAGACAATTTCGTGAAAA
*
131201 AAATCTTTGAGTTGTTTCTTTT
66 AAATCTTTGAGTTATTTCTTTT
* * * * *
131223 GAAAAAAATCTTTGAGTCTGTTTCCTTGGAAACAAAATTTTGTCTCTCTTGGGACAATTTCTTTT
1 --AAAAAATCTTTGAGTCTATTTACTTGGAAAC-AAAGTTTGTCTCTCTTGAGACAATTTC--GT
**
131288 GAAAATCATCTTTGAGTATATTTC-TTT
61 GAAAAAAATCTTTGAGT-TATTTCTTTT
131315 AAAAA
1 AAAAA
131320 CAAATTTTGC
Statistics
Matches: 81, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
89 27 0.33
90 30 0.37
92 19 0.23
93 5 0.06
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (87 bp):
AAAAAATCTTTGAGTCTATTTACTTGGAAACAAAGTTTGTCTCTCTTGAGACAATTTCGTGAAAA
AAATCTTTGAGTTATTTCTTTT
Found at i:131319 original size:90 final size:88
Alignment explanation
Indices: 131135--131328 Score: 228
Period size: 89 Copynumber: 2.1 Consensus size: 88
131125 CAATTTCGTA
* *
131135 AAAAAAATCTTTGAGTCTATTTATTTTGAAACAAAGTTTGTCTCTCTTGAGACAATTTCGTGAAA
1 AAAAAAATCTTTGAGTCTATTTACTTGGAAACAAAGTTTGTCTCTCTTGAGACAATTTCGTGAAA
*
131200 AAAATCTTTGAGTTGTTTCTTTT
66 AAAATCTTTGAGTTATTTCTTTT
* * * * *
131223 GAAAAAAATCTTTGAGTCTGTTTCCTTGGAAACAAAATTTTGTCTCTCTTGGGACAATTTCTTTT
1 -AAAAAAATCTTTGAGTCTATTTACTTGGAAAC-AAAGTTTGTCTCTCTTGAGACAATTTC--GT
** *
131288 GAAAATCATCTTTGAGTATATTTCTTTA
62 GAAAAAAATCTTTGAGT-TATTTCTTTT
131316 AAAACAAAT-TTTG
1 AAAA-AAATCTTTG
131329 CCTCTCTTGA
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
89 28 0.31
90 25 0.28
92 24 0.27
93 12 0.13
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.42
Consensus pattern (88 bp):
AAAAAAATCTTTGAGTCTATTTACTTGGAAACAAAGTTTGTCTCTCTTGAGACAATTTCGTGAAA
AAAATCTTTGAGTTATTTCTTTT
Found at i:131321 original size:65 final size:64
Alignment explanation
Indices: 131215--131337 Score: 165
Period size: 65 Copynumber: 1.9 Consensus size: 64
131205 CTTTGAGTTG
* * ** *
131215 TTTCTTTTGAAAAAAATCTTTGAGTCTGTTTCCTTGGAAACAAAATTTTGTCTCTCTTGGGACAA
1 TTTCTTTTGAAAAAAATCTTTGAGTATATTTCCTTAAAAAC-AAATTTTGCCTCTCTTGGGACAA
** *
131280 TTTCTTTTGAAAATCATCTTTGAGTATATTTCTTTAAAAACAAATTTTGCCTCTCTTG
1 TTTCTTTTGAAAAAAATCTTTGAGTATATTTCCTTAAAAACAAATTTTGCCTCTCTTG
131338 AGATAGTTTC
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
64 16 0.32
65 34 0.68
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (64 bp):
TTTCTTTTGAAAAAAATCTTTGAGTATATTTCCTTAAAAACAAATTTTGCCTCTCTTGGGACAA
Found at i:132148 original size:28 final size:28
Alignment explanation
Indices: 132084--132178 Score: 113
Period size: 28 Copynumber: 3.3 Consensus size: 28
132074 GAGACAGTTG
132084 CTTTTGAAACACATTATCTTTGAG-CTGTTT
1 CTTTTGAAACA-A--ATCTTTGAGTCTGTTT
132114 -TTCTTGAAACAAATCTTTGAGTCTGTTT
1 CTT-TTGAAACAAATCTTTGAGTCTGTTT
* *
132142 CTTTTGAAACAAATCTTTGAATCGGTTT
1 CTTTTGAAACAAATCTTTGAGTCTGTTT
*
132170 CTCTTGAAA
1 CTTTTGAAA
132179 TCATAACTCC
Statistics
Matches: 59, Mismatches: 3, Indels: 8
0.84 0.04 0.11
Matches are distributed among these distances:
27 9 0.15
28 37 0.63
29 5 0.08
30 8 0.14
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (28 bp):
CTTTTGAAACAAATCTTTGAGTCTGTTT
Found at i:132438 original size:86 final size:84
Alignment explanation
Indices: 132285--132530 Score: 386
Period size: 86 Copynumber: 2.9 Consensus size: 84
132275 TAACCAGTCG
*
132285 TCCTCATCAAGTAGGAACCGAGTTATCACCCTTAGATGGCCAAAAACTCTTCATCACGTATGAGC
1 TCCTCATCACGTAGGAACCGAG---TCACCCTTAGATGGCCAAAAACTCTTCATCACGTATGAGC
132350 AGTGTCATCCCCTGACCAGATT
63 AGTGTCATCCCCTGACCAGATT
132372 TCCTCATCACGTAGGAACCGAGTCACCCTTAGATGGCCAAAAAAACTCTTCATCACGTATGAGCA
1 TCCTCATCACGTAGGAACCGAGTCACCCTTAGATGGCC--AAAAACTCTTCATCACGTATGAGCA
132437 GTGTCATCCCCTGACCAGATT
64 GTGTCATCCCCTGACCAGATT
* * * *
132458 TCCTCATCACGTAGGAACCGAGTCACCCTTAGACGACC-AGAACTCTTCATCACGTATGAGTAGT
1 TCCTCATCACGTAGGAACCGAGTCACCCTTAGATGGCCAAAAACTCTTCATCACGTATGAGCAGT
*
132522 GTCGTCCCC
66 GTCATCCCC
132531 ACCAACACAC
Statistics
Matches: 151, Mismatches: 6, Indels: 8
0.92 0.04 0.05
Matches are distributed among these distances:
83 32 0.21
84 16 0.11
86 82 0.54
87 21 0.14
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (84 bp):
TCCTCATCACGTAGGAACCGAGTCACCCTTAGATGGCCAAAAACTCTTCATCACGTATGAGCAGT
GTCATCCCCTGACCAGATT
Found at i:132508 original size:43 final size:42
Alignment explanation
Indices: 132288--132513 Score: 113
Period size: 40 Copynumber: 5.2 Consensus size: 42
132278 CCAGTCGTCC
* * *
132288 TCATCAAGTAGGAACCGAGTTATCACCCTTAGATGGCCAAAAACTCT
1 TCATCACGTAGGAACCGAG---TCACCCTTAGA-GACC-AGAACTCT
* * * * * ** *
132335 TCATCACGTATGAGCAGTGTCATCCCCT---GACCAGATTTCC
1 TCATCACGTAGGAACCGAGTCA-CCCTTAGAGACCAGAACTCT
* *
132375 TCATCACGTAGGAACCGAGTCACCCTTAGATGGCCAAAAAAACTCT
1 TCATCACGTAGGAACCGAGTCACCCTTAGA-GACC---AGAACTCT
* * * * * ** *
132421 TCATCACGTATGAGCAGTGTCATCCCCT---GACCAGATTTCC
1 TCATCACGTAGGAACCGAGTCA-CCCTTAGAGACCAGAACTCT
132461 TCATCACGTAGGAACCGAGTCACCCTTAGACGACCAGAACTCT
1 TCATCACGTAGGAACCGAGTCACCCTTAGA-GACCAGAACTCT
132504 TCATCACGTA
1 TCATCACGTA
132514 TGAGTAGTGT
Statistics
Matches: 127, Mismatches: 39, Indels: 30
0.65 0.20 0.15
Matches are distributed among these distances:
39 8 0.06
40 44 0.35
41 3 0.02
43 25 0.20
44 3 0.02
45 4 0.03
46 22 0.17
47 18 0.14
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.23
Consensus pattern (42 bp):
TCATCACGTAGGAACCGAGTCACCCTTAGAGACCAGAACTCT
Found at i:132720 original size:14 final size:14
Alignment explanation
Indices: 132685--132738 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
132675 TTAAAATTAT
132685 TATTATTA-ATTGT-
1 TATTATTATATT-TA
*
132698 TATTTTTATATTTA
1 TATTATTATATTTA
132712 TATTATTAT-TTTA
1 TATTATTATATTTA
*
132725 TTAATATTATATTT
1 -TATTATTATATTT
132739 TTACATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 12 0.35
14 19 0.56
15 3 0.09
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TATTATTATATTTA
Found at i:132726 original size:17 final size:17
Alignment explanation
Indices: 132680--132739 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
132670 TTTTTTTAAA
*
132680 ATTATTATTATTAATTGTT
1 ATTATT-TTATTAA-TATT
*
132699 ATT-TTTATATTTATATT
1 ATTATTT-TATTAATATT
132716 ATTATTTTATTAATATT
1 ATTATTTTATTAATATT
132733 A-TATTTT
1 ATTATTTT
132740 TACATATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
16 6 0.17
17 17 0.47
18 10 0.28
19 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
ATTATTTTATTAATATT
Found at i:132740 original size:17 final size:16
Alignment explanation
Indices: 132670--132741 Score: 58
Period size: 17 Copynumber: 4.4 Consensus size: 16
132660 TGTCCGGGTC
*
132670 TTTTT-TTAAAATTA-
1 TTTTTATTAATATTAT
* *
132684 TTATTATTAATTGTTAT
1 TTTTTATTAA-TATTAT
*
132701 TTTTATATTTATATTAT
1 TTTT-TATTAATATTAT
132718 TATTTTATTAATATTAT
1 T-TTTTATTAATATTAT
132735 ATTTTTA
1 -TTTTTA
132742 CATATTTTGG
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
14 4 0.09
15 4 0.09
16 3 0.07
17 25 0.56
18 9 0.20
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (16 bp):
TTTTTATTAATATTAT
Found at i:134161 original size:27 final size:27
Alignment explanation
Indices: 134131--134187 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
134121 TTTGGTTTAA
* * *
134131 TTTCTATTTAGCCCTTTAAGTTTCTGT
1 TTTCCATTTAGCCCTCTAACTTTCTGT
*
134158 TTTCCATTTAGTCCTCTAACTTTCTGT
1 TTTCCATTTAGCCCTCTAACTTTCTGT
134185 TTT
1 TTT
134188 AGCTTTTTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.14, C:0.21, G:0.09, T:0.56
Consensus pattern (27 bp):
TTTCCATTTAGCCCTCTAACTTTCTGT
Found at i:135629 original size:36 final size:36
Alignment explanation
Indices: 135579--135694 Score: 196
Period size: 36 Copynumber: 3.2 Consensus size: 36
135569 GCTTTACCAG
*
135579 TGTGAACAGAAGCATGCAATTTAAACATTCTTGCAT
1 TGTGAACAGCAGCATGCAATTTAAACATTCTTGCAT
135615 TGTGAACAGCAGCATGCAATTTAAACATTCTTGCAT
1 TGTGAACAGCAGCATGCAATTTAAACATTCTTGCAT
* *
135651 TGTGAACAGCAGCATGCACTTTAAACATTCTTCCAT
1 TGTGAACAGCAGCATGCAATTTAAACATTCTTGCAT
*
135687 GGTGAACA
1 TGTGAACA
135695 AGAGGATATT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 76 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (36 bp):
TGTGAACAGCAGCATGCAATTTAAACATTCTTGCAT
Found at i:150034 original size:32 final size:32
Alignment explanation
Indices: 149983--150049 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
149973 TCCCATGATT
*
149983 TACCCAAGGAAGTGCCTTGGGGCCTAAGAGCC
1 TACCCAAGAAAGTGCCTTGGGGCCTAAGAGCC
** **
150015 TACCCAAGAAAGTTTCTTGGGGCCTCGGAGCC
1 TACCCAAGAAAGTGCCTTGGGGCCTAAGAGCC
150047 TAC
1 TAC
150050 TCAAACATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.24, C:0.28, G:0.28, T:0.19
Consensus pattern (32 bp):
TACCCAAGAAAGTGCCTTGGGGCCTAAGAGCC
Found at i:156892 original size:12 final size:12
Alignment explanation
Indices: 156875--156901 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
156865 TTTACCATTT
156875 TTTCATTTTATC
1 TTTCATTTTATC
156887 TTTCATTTTATC
1 TTTCATTTTATC
156899 TTT
1 TTT
156902 TTTAGAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTCATTTTATC
Found at i:160685 original size:2 final size:2
Alignment explanation
Indices: 160678--160777 Score: 92
Period size: 2 Copynumber: 49.0 Consensus size: 2
160668 AGACAGACAT
* * *
160678 AC AC AC AC AC AC AC AC GC TC AC AC AC AC AC AC GC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * ** *
160720 AC GC TC AC AC AC AC AC GC GC AC AC AC AC AC GT AC AC AC CC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
160762 AC GAGC AC AC AC AC AC
1 AC -A-C AC AC AC AC AC
160778 GCACGTACGT
Statistics
Matches: 80, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
2 77 0.96
3 2 0.03
4 1 0.01
ACGTcount: A:0.40, C:0.49, G:0.08, T:0.03
Consensus pattern (2 bp):
AC
Found at i:160702 original size:14 final size:14
Alignment explanation
Indices: 160683--160779 Score: 131
Period size: 14 Copynumber: 6.9 Consensus size: 14
160673 GACATACACA
*
160683 CACACACACACGCT
1 CACACACACACGCG
*
160697 CACACACACACACG
1 CACACACACACGCG
*
160711 CACACACACACGCT
1 CACACACACACGCG
160725 CACACACACACGCG
1 CACACACACACGCG
**
160739 CACACACACACGTA
1 CACACACACACGCG
* *
160753 CACACCCACACGAG
1 CACACACACACGCG
160767 CACACACACACGC
1 CACACACACACGC
160780 ACGTACGTAC
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 71 1.00
ACGTcount: A:0.38, C:0.49, G:0.09, T:0.03
Consensus pattern (14 bp):
CACACACACACGCG
Found at i:160718 original size:28 final size:28
Alignment explanation
Indices: 160678--160779 Score: 145
Period size: 28 Copynumber: 3.6 Consensus size: 28
160668 AGACAGACAT
*
160678 ACACACACACACACACGCTCACACACAC
1 ACACGCACACACACACGCTCACACACAC
160706 ACACGCACACACACACGCTCACACACAC
1 ACACGCACACACACACGCTCACACACAC
* *
160734 ACGCGCACACACACACG-T-ACACACCC
1 ACACGCACACACACACGCTCACACACAC
160760 ACACGAGCACACACACACGC
1 ACAC--GCACACACACACGC
160780 ACGTACGTAC
Statistics
Matches: 67, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
26 10 0.15
27 1 0.01
28 56 0.84
ACGTcount: A:0.39, C:0.49, G:0.09, T:0.03
Consensus pattern (28 bp):
ACACGCACACACACACGCTCACACACAC
Found at i:162632 original size:138 final size:138
Alignment explanation
Indices: 162462--162716 Score: 406
Period size: 138 Copynumber: 1.8 Consensus size: 138
162452 TGTGTATGAT
162462 AGTTATCGATCGATTTTGATTAATGCATAACGGTGCATTTTCGTATTAATACTATGTGTACTTTT
1 AGTTATCGATCGATTTTGATTAATGCATAACGGTGCATTTTCGTATTAATACTATGTGTACTTTT
*
162527 GGCACTA-GATGTGCAAT-CATGGAATTCATAATGAGTTTATGAATTACCATTTCGATATACAAT
66 GGCACTATGA-CTGC-ATCCATGGAATTCATAATGAGTTTATGAATTACCATTTCGATATACAAT
162590 TATGTATAAA
129 TATGTATAAA
* * *
162600 AGTTATTGATCGATTTTGTTTAATGCATAACGGTGCATTTTCGTATTAGTACTATGTGTACTTTT
1 AGTTATCGATCGATTTTGATTAATGCATAACGGTGCATTTTCGTATTAATACTATGTGTACTTTT
* * * *
162665 GGTACTATGACTGCATCCATGGAATTCATAATGTGTTTGTGAATTTCCATTT
66 GGCACTATGACTGCATCCATGGAATTCATAATGAGTTTATGAATTACCATTT
162717 TGGCACTTCG
Statistics
Matches: 107, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
137 2 0.02
138 103 0.96
139 2 0.02
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.42
Consensus pattern (138 bp):
AGTTATCGATCGATTTTGATTAATGCATAACGGTGCATTTTCGTATTAATACTATGTGTACTTTT
GGCACTATGACTGCATCCATGGAATTCATAATGAGTTTATGAATTACCATTTCGATATACAATTA
TGTATAAA
Found at i:165020 original size:28 final size:28
Alignment explanation
Indices: 164986--165052 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 28
164976 CAAATATCAA
* *
164986 CAATAAATAAATGTCAGTGGTTAATAT-G
1 CAATAAATAAAAGTCAGTAGTTAAT-TCG
*
165014 CAATAAAATAAAAGTTAGTAGTTAATTCG
1 CAAT-AAATAAAAGTCAGTAGTTAATTCG
*
165043 AAATAAATAA
1 CAATAAATAA
165053 CATAGCAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 11 0.33
29 22 0.67
ACGTcount: A:0.51, C:0.06, G:0.13, T:0.30
Consensus pattern (28 bp):
CAATAAATAAAAGTCAGTAGTTAATTCG
Found at i:170352 original size:2 final size:2
Alignment explanation
Indices: 170345--170392 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
170335 AATCTTCTAG
170345 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
170387 AT AT AT
1 AT AT AT
170393 TTGTAACATC
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:173995 original size:11 final size:11
Alignment explanation
Indices: 173979--174028 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
173969 ATAATAGAAA
173979 TATTTTTATTT
1 TATTTTTATTT
*
173990 TATTTTTTATTC
1 TA-TTTTTATTT
*
174002 TATTTTTATGT
1 TATTTTTATTT
*
174013 TA-TTTTACTT
1 TATTTTTATTT
174023 TATTTT
1 TATTTT
174029 ACCTTATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
10 8 0.25
11 14 0.44
12 10 0.31
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:173998 original size:12 final size:12
Alignment explanation
Indices: 173981--174018 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
173971 AATAGAAATA
173981 TTTTTATTTTAT
1 TTTTTATTTTAT
*
173993 TTTTTATTCTA-
1 TTTTTATTTTAT
*
174004 TTTTTATGTTAT
1 TTTTTATTTTAT
174016 TTT
1 TTT
174019 ACTTTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.79
Consensus pattern (12 bp):
TTTTTATTTTAT
Found at i:174549 original size:10 final size:10
Alignment explanation
Indices: 174534--174564 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
174524 CAATGGCAAC
174534 TAATTCAAAA
1 TAATTCAAAA
*
174544 TAATTCAAAC
1 TAATTCAAAA
174554 TAATTCAAAA
1 TAATTCAAAA
174564 T
1 T
174565 CCCAATTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (10 bp):
TAATTCAAAA
Found at i:180867 original size:3 final size:3
Alignment explanation
Indices: 180859--180920 Score: 79
Period size: 3 Copynumber: 19.7 Consensus size: 3
180849 CCAAAAATAA
* *
180859 ATT ATT ATT CTT AATT ATT ATT ATT ATT ATT ATT AATT ATT ATT AGTA
1 ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT A-TT
180907 ATT ATT ATT ATT AT
1 ATT ATT ATT ATT AT
180921 AAAATAAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
3 45 0.87
4 7 0.13
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:180874 original size:13 final size:13
Alignment explanation
Indices: 180859--180919 Score: 81
Period size: 13 Copynumber: 4.8 Consensus size: 13
180849 CCAAAAATAA
*
180859 ATTATTATT-CTT
1 ATTATTATTAATT
180871 AATTATTATT-ATT
1 -ATTATTATTAATT
180884 ATTATTATTAATT
1 ATTATTATTAATT
*
180897 ATTATTAGTAATT
1 ATTATTATTAATT
180910 ATTATTATTA
1 ATTATTATTA
180920 TAAAATAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
12 9 0.20
13 35 0.80
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (13 bp):
ATTATTATTAATT
Found at i:180880 original size:16 final size:16
Alignment explanation
Indices: 180859--180919 Score: 79
Period size: 16 Copynumber: 3.8 Consensus size: 16
180849 CCAAAAATAA
*
180859 ATTATTATTCTTAATT
1 ATTATTATTATTAATT
180875 ATTATTATTATT-ATT
1 ATTATTATTATTAATT
* *
180890 ATTAATTATTATTAGTA
1 ATT-ATTATTATTAATT
180907 ATTATTATTATTA
1 ATTATTATTATTA
180920 TAAAATAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
15 6 0.15
16 30 0.75
17 4 0.10
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (16 bp):
ATTATTATTATTAATT
Found at i:182860 original size:5 final size:5
Alignment explanation
Indices: 182850--182914 Score: 69
Period size: 5 Copynumber: 13.0 Consensus size: 5
182840 ATAGAAATAT
* *
182850 TTTTA TTTTA TTTTA TTTTA -TTTA TTCTA TTTTTA TGTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA
** *
182900 CCTTA TTTTA ATTTA
1 TTTTA TTTTA TTTTA
182915 AGTATTGACA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
4 4 0.08
5 41 0.84
6 4 0.08
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.72
Consensus pattern (5 bp):
TTTTA
Found at i:183426 original size:10 final size:10
Alignment explanation
Indices: 183411--183440 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
183401 TGCCGGCTCC
183411 AATTCAAAAT
1 AATTCAAAAT
*
183421 AATTCAAACT
1 AATTCAAAAT
183431 AATTCAAAAT
1 AATTCAAAAT
183441 CTCAATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (10 bp):
AATTCAAAAT
Found at i:194973 original size:3 final size:3
Alignment explanation
Indices: 194965--195010 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
194955 AAATAAATTG
194965 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
195011 AAATAAAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:198641 original size:15 final size:15
Alignment explanation
Indices: 198617--198646 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
198607 TTTTAAAATA
*
198617 AAAACTTATTTTTTT
1 AAAACCTATTTTTTT
198632 AAAACCTATTTTTTT
1 AAAACCTATTTTTTT
198647 TTTAAATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (15 bp):
AAAACCTATTTTTTT
Found at i:199606 original size:5 final size:5
Alignment explanation
Indices: 199596--199621 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
199586 TTAATTAGGA
199596 TTAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT T
199622 ACTTTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTAAT
Found at i:206802 original size:82 final size:82
Alignment explanation
Indices: 206697--206974 Score: 249
Period size: 82 Copynumber: 3.4 Consensus size: 82
206687 TAAAATGGTA
* * *
206697 ACTTTAGCGGCGCTTGTT-TACAAATGCCGTAATAGTGTTCACTTATAGTGGCGTTTTTTCGACA
1 ACTTTAGCGGCG-TTTTTATACAAACGCCGTAATAGTGTTCAC-TATAGTGGCGTTTTTTCAACA
206761 AACACCGCAATAGAGTAGT
64 AACACCGCAATAGAGTAGT
* ** * * * * * *
206780 A-TTTAGCGGTGTTTTTATACAAACGCCACAATAGGGTTAACCTATAGTGGCATTTGTGCAATAA
1 ACTTTAGCGGCGTTTTTATACAAACGCCGTAATAGTGTTCA-CTATAGTGGCGTTTTTTCAACAA
* *
206844 ACGCCGCAATAGATTAGT
65 ACACCGCAATAGAGTAGT
* *
206862 ACTTTAGCGGCGTTTTTATACAAACACCGTAATA-TGGTTCAACTATAGTGGCGTTTTTT-AATA
1 ACTTTAGCGGCGTTTTTATACAAACGCCGTAATAGT-GTTC-ACTATAGTGGCGTTTTTTCAACA
** * * * *
206925 AATGCTGCAACATATTAGT
64 AACACCGCAATAGAGTAGT
**
206944 ACTTTAGCGATGTTTTTGTATACAAACGCCG
1 ACTTTAGCGGCG-TTTT-TATACAAACGCCG
206975 CGATAACTCG
Statistics
Matches: 158, Mismatches: 30, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
81 4 0.03
82 90 0.57
83 51 0.32
84 13 0.08
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (82 bp):
ACTTTAGCGGCGTTTTTATACAAACGCCGTAATAGTGTTCACTATAGTGGCGTTTTTTCAACAAA
CACCGCAATAGAGTAGT
Found at i:213106 original size:65 final size:64
Alignment explanation
Indices: 212994--213142 Score: 212
Period size: 65 Copynumber: 2.3 Consensus size: 64
212984 GGGGGTGTTA
* *
212994 CATAAAATGCATTCGATGTTTTAAAATAGCCTGAGTGCATCAATGCAT-GTCTTGTGCATCGATG
1 CATAAAATGCATTCGATGTTTTAAAATAACCTGAGTGCATCAATGCATGGT-ATGTGCATCGATG
* *
213058 CATCAAATGCATTCGATGTTTTCATAAA-AACCTGAGTGCATCGATGCATGGTATGTGCATCGAT
1 CATAAAATGCATTCGATGTTTT-A-AAATAACCTGAGTGCATCAATGCATGGTATGTGCATCGAT
213122 G
64 G
*
213123 CATAAAATGCATTAGATGTT
1 CATAAAATGCATTCGATGTT
213143 CAATATATTC
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
64 21 0.28
65 50 0.66
66 5 0.07
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (64 bp):
CATAAAATGCATTCGATGTTTTAAAATAACCTGAGTGCATCAATGCATGGTATGTGCATCGATG
Found at i:213181 original size:65 final size:63
Alignment explanation
Indices: 212994--213184 Score: 183
Period size: 65 Copynumber: 3.0 Consensus size: 63
212984 GGGGGTGTTA
* * * *
212994 CATAAAATGCATTCGATGTTT--TAAAATAGCCTGAGTGCATCAATGCATGTCTTGTGCATCGAT
1 CATAAAATGCATTAGATGTTTCATAAAA-A-CATGAGTGCATCGATGCATG-GTTGTGCATCGAT
213057 G
63 G
* * *
213058 CATCAAATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCGATGCATGGTATGTGCATCGATG
1 CATAAAATGCATTAGATG-TTTCATAAAAACATGAGTGCATCGATGCATGGT-TGTGCATCGATG
* **
213123 CATAAAATGCATTAGATG-TTCAATATATTCAATG-GTGCATCGATGCATGGATTGGTGCATCG
1 CATAAAATGCATTAGATGTTTC-ATAAAAAC-ATGAGTGCATCGATGCATGG-TT-GTGCATCG
213185 GTACACTCTT
Statistics
Matches: 110, Mismatches: 9, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
63 3 0.03
64 40 0.36
65 61 0.55
66 1 0.01
67 5 0.05
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (63 bp):
CATAAAATGCATTAGATGTTTCATAAAAACATGAGTGCATCGATGCATGGTTGTGCATCGATG
Found at i:215920 original size:23 final size:23
Alignment explanation
Indices: 215890--215971 Score: 73
Period size: 23 Copynumber: 3.6 Consensus size: 23
215880 GCATGGCAGT
215890 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* *
215913 GTGCATCGGTGCATC-TTC-ATGA
1 GTGCATCGATGCA-CATTCAAGGA
* *
215935 -TGTATTGATGCACATTCAAAGG-
1 GTGCATCGATGCACATTC-AAGGA
215957 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
215972 TATTTGGTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 11
0.70 0.12 0.17
Matches are distributed among these distances:
20 1 0.02
21 12 0.27
22 3 0.07
23 17 0.38
24 12 0.27
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:222029 original size:45 final size:44
Alignment explanation
Indices: 221934--222038 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 44
221924 GTGCACTAAG
* *
221934 GGTGCATCGATGCATAAAATGCATTCGATGTTTTAAAATAGCCT
1 GGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCAT
** *
221978 GAGTGCATCGATGCATAAAATGCATTCGATG-TTCAATTTATTCAAT
1 G-GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATA-GC-AT
222024 GGTGCATCGATGCAT
1 GGTGCATCGATGCAT
222039 GGATTGGTGC
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
44 7 0.13
45 44 0.83
46 2 0.04
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.32
Consensus pattern (44 bp):
GGTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCAT
Found at i:223925 original size:35 final size:35
Alignment explanation
Indices: 223879--223949 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
223869 ATACTGCTTA
223879 ATATATATACACCAAAACTTAGTATATCACAAAAG
1 ATATATATACACCAAAACTTAGTATATCACAAAAG
*
223914 ATATATATACACCAAAACTTAGTGTATCACAAAAG
1 ATATATATACACCAAAACTTAGTATATCACAAAAG
223949 A
1 A
223950 CTCCCAAAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.51, C:0.17, G:0.07, T:0.25
Consensus pattern (35 bp):
ATATATATACACCAAAACTTAGTATATCACAAAAG
Found at i:223929 original size:18 final size:18
Alignment explanation
Indices: 223879--223931 Score: 65
Period size: 17 Copynumber: 3.0 Consensus size: 18
223869 ATACTGCTTA
223879 ATATATATACACCAAAAC
1 ATATATATACACCAAAAC
* *
223897 TTAGTATAT-CA-CAAAAG
1 ATA-TATATACACCAAAAC
223914 ATATATATACACCAAAAC
1 ATATATATACACCAAAAC
223932 TTAGTGTATC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
16 5 0.18
17 9 0.32
18 9 0.32
19 5 0.18
ACGTcount: A:0.53, C:0.19, G:0.04, T:0.25
Consensus pattern (18 bp):
ATATATATACACCAAAAC
Found at i:224637 original size:41 final size:43
Alignment explanation
Indices: 224592--224678 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 43
224582 GAGAAAGAAG
* *
224592 ATAGTTCAATTACTAAATT-T-ATATATCCAAATAATTAAATA
1 ATAGTTCAATTACTAAATTATAATATACCCAAACAATTAAATA
* *
224633 ATAGTTCAATTGCTAAATTAGTAATTTACCCAAACAATTAAATA
1 ATAGTTCAATTACTAAATTA-TAATATACCCAAACAATTAAATA
224677 AT
1 AT
224679 CTTAAGTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
41 18 0.46
43 1 0.03
44 20 0.51
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (43 bp):
ATAGTTCAATTACTAAATTATAATATACCCAAACAATTAAATA
Found at i:232373 original size:18 final size:17
Alignment explanation
Indices: 232346--232382 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
232336 TATTTTTTTT
232346 ATTTATTAAAAATAATA
1 ATTTATTAAAAATAATA
232363 ATTTGATTAAAAATAATA
1 ATTT-ATTAAAAATAATA
232381 AT
1 AT
232383 ATATAATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
ATTTATTAAAAATAATA
Found at i:232539 original size:15 final size:15
Alignment explanation
Indices: 232519--232547 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
232509 AATCGATCTG
232519 ATCAAATCAAATTAA
1 ATCAAATCAAATTAA
232534 ATCAAATCAAATTA
1 ATCAAATCAAATTA
232548 TTTTTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.28
Consensus pattern (15 bp):
ATCAAATCAAATTAA
Found at i:235606 original size:14 final size:14
Alignment explanation
Indices: 235589--235616 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
235579 ATCATAACAA
235589 AATTATATAACTAT
1 AATTATATAACTAT
235603 AATTATATAACTAT
1 AATTATATAACTAT
235617 TCTTTCATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:238776 original size:51 final size:51
Alignment explanation
Indices: 238715--238814 Score: 182
Period size: 51 Copynumber: 2.0 Consensus size: 51
238705 TTGGTCATCT
*
238715 ATCATTGAAAAGTTAATGATGATGTTGATGCGATAATTTTTAAAATTATCC
1 ATCATCGAAAAGTTAATGATGATGTTGATGCGATAATTTTTAAAATTATCC
*
238766 ATCATCGAAAAGTTAATGATGATGTTGATGTGATAATTTTTAAAATTAT
1 ATCATCGAAAAGTTAATGATGATGTTGATGCGATAATTTTTAAAATTAT
238815 TTATAATTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.40
Consensus pattern (51 bp):
ATCATCGAAAAGTTAATGATGATGTTGATGCGATAATTTTTAAAATTATCC
Found at i:239555 original size:31 final size:31
Alignment explanation
Indices: 239520--239582 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
239510 GATAAGAATG
239520 TTTACAGAGTTCTACAAGTAAATTACTAAAT
1 TTTACAGAGTTCTACAAGTAAATTACTAAAT
239551 TTTACAGAGTTCTACAAGTAAATTACTAAAT
1 TTTACAGAGTTCTACAAGTAAATTACTAAAT
239582 T
1 T
239583 ATTTGTGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.37
Consensus pattern (31 bp):
TTTACAGAGTTCTACAAGTAAATTACTAAAT
Found at i:241380 original size:37 final size:39
Alignment explanation
Indices: 241329--241404 Score: 104
Period size: 37 Copynumber: 2.0 Consensus size: 39
241319 TTACTTTTTG
*
241329 AAATTTAGTTTTTATATTAATTAT-AATT-TGTATATTAT
1 AAATTTAGATTTTATATTAATT-TCAATTCTGTATATTAT
*
241367 AAATTT-GATTTTATATTAATTTCAATTCTTTATATTAT
1 AAATTTAGATTTTATATTAATTTCAATTCTGTATATTAT
241405 TTATAATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 1 0.03
37 18 0.53
38 15 0.44
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.58
Consensus pattern (39 bp):
AAATTTAGATTTTATATTAATTTCAATTCTGTATATTAT
Found at i:241398 original size:19 final size:20
Alignment explanation
Indices: 241376--241421 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
241366 TAAATTTGAT
241376 TTTATATTAATTT-CAATTC
1 TTTATATTAATTTACAATTC
*
241395 TTTATATT-ATTTATAATTC
1 TTTATATTAATTTACAATTC
241414 -TTATATTA
1 TTTATATTA
241422 TAAATTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTATATTAATTTACAATTC
Found at i:241422 original size:18 final size:18
Alignment explanation
Indices: 241376--241422 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
241366 TAAATTTGAT
241376 TTTATATTAATTTCAATTC
1 TTTATATT-ATTTCAATTC
*
241395 TTTATATTATTTATAATTC
1 TTTATATTATTT-CAATTC
241414 -TTATATTAT
1 TTTATATTAT
241423 AAATTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 13 0.50
19 13 0.50
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTATATTATTTCAATTC
Found at i:241435 original size:13 final size:14
Alignment explanation
Indices: 241401--241437 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
241391 ATTCTTTATA
241401 TTATTTAT-AATTC
1 TTATTTATAAATTC
241414 TTATATTATAAATT-
1 TTAT-TTATAAATTC
241428 TTATTTATAA
1 TTATTTATAA
241438 TCACTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 8 0.36
15 4 0.18
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTTATAAATTC
Found at i:241914 original size:20 final size:20
Alignment explanation
Indices: 241889--241926 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
241879 ATTGAGAAGG
241889 GATGCACCGATGCACTCATT
1 GATGCACCGATGCACTCATT
*
241909 GATGCATCGATGCACTCA
1 GATGCACCGATGCACTCA
241927 CCATATCGAA
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:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (20 bp):
GATGCACCGATGCACTCATT
Found at i:247799 original size:45 final size:44
Alignment explanation
Indices: 247735--247833 Score: 112
Period size: 45 Copynumber: 2.2 Consensus size: 44
247725 TTTGTGCATA
* *
247735 ATGCATCGATACACTATGAA-AGTGCATCGATGCATCCCTTTGAAT
1 ATGCATCGATACACTATGAAGA-TGCACCGATGCAACCC-TTGAAT
* *
247780 ATGCATCGATACA-TCATGAAGATTCACCGATGCAAGCCTTGAAT
1 ATGCATCGATACACT-ATGAAGATGCACCGATGCAACCCTTGAAT
*
247824 GTGCATCGAT
1 ATGCATCGAT
247834 GCACAAGGTC
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
44 16 0.34
45 30 0.64
46 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.27
Consensus pattern (44 bp):
ATGCATCGATACACTATGAAGATGCACCGATGCAACCCTTGAAT
Found at i:251690 original size:15 final size:15
Alignment explanation
Indices: 251670--251703 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
251660 ACATTATTGC
251670 ATCAATTCAGCAAGA
1 ATCAATTCAGCAAGA
*
251685 ATCAATTCAGCAAGC
1 ATCAATTCAGCAAGA
251700 ATCA
1 ATCA
251704 TGCATTAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.24, G:0.12, T:0.21
Consensus pattern (15 bp):
ATCAATTCAGCAAGA
Found at i:253800 original size:19 final size:19
Alignment explanation
Indices: 253776--253825 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
253766 AAATAACCAA
253776 CGAATTCGCAACTCAGTTT
1 CGAATTCGCAACTCAGTTT
253795 CGAATTCGCAACTCAGTTT
1 CGAATTCGCAACTCAGTTT
253814 CGAATTCGCAAC
1 CGAATTCGCAAC
253826 ACGAACTCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (19 bp):
CGAATTCGCAACTCAGTTT
Found at i:253893 original size:21 final size:21
Alignment explanation
Indices: 253868--253909 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
253858 TTTGCAACTG
253868 AAATTTGGAATTCGTAACACA
1 AAATTTGGAATTCGTAACACA
253889 AAATTTGGAATTCGTAACACA
1 AAATTTGGAATTCGTAACACA
253910 GAAGTCGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (21 bp):
AAATTTGGAATTCGTAACACA
Found at i:253965 original size:42 final size:40
Alignment explanation
Indices: 253919--254008 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
253909 AGAAGTCGAA
*
253919 TTCGCAACTCGAATTTGACAATTTCGCAACACAAATTTCTTT
1 TTCGCAACTCGAATTTGA-AA-TTCGCAACACAAATTTCCTT
* * * * *
253961 TTCGCAACTTGATTTTTAAATTCGCAACACGAGTTTCCTT
1 TTCGCAACTCGAATTTGAAATTCGCAACACAAATTTCCTT
254001 TTCGCAAC
1 TTCGCAAC
254009 AAGATTTTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 25 0.60
41 2 0.05
42 15 0.36
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (40 bp):
TTCGCAACTCGAATTTGAAATTCGCAACACAAATTTCCTT
Found at i:254003 original size:40 final size:40
Alignment explanation
Indices: 253941--254049 Score: 112
Period size: 40 Copynumber: 2.7 Consensus size: 40
253931 ATTTGACAAT
* * * **
253941 TTCGCAACACAAATTTCTTTTTCGCAACTTGATTTT-TAAA
1 TTCGCAACACGAGTTTCATTTTCGCAACAAGATTTTCT-AA
*
253981 TTCGCAACACGAGTTTCCTTTTCGCAACAAGATTTTCTAA
1 TTCGCAACACGAGTTTCATTTTCGCAACAAGATTTTCTAA
* * * *
254021 TTTGTAACGCGAGTTTCAATTTCGCAACA
1 TTCGCAACACGAGTTTCATTTTCGCAACA
254050 GTAATTTCTT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 57 0.98
41 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (40 bp):
TTCGCAACACGAGTTTCATTTTCGCAACAAGATTTTCTAA
Found at i:254102 original size:60 final size:60
Alignment explanation
Indices: 253974--254110 Score: 143
Period size: 60 Copynumber: 2.3 Consensus size: 60
253964 GCAACTTGAT
* * * * *
253974 TTTTAAATTCGCAACACGAGTTTCCTTTTCGCAACAAGATTTTCTAATTTGTAACGCGAG
1 TTTTAATTTCGCAACACGAATTTCCTTTTCGCAACAAGATTTTCTAATTCGCAACGCGAA
* * ** *
254034 TTTCAATTTCGCAACA-GTAATTTCTTTTTCGCAACTCGATTTT-TGAATTCGCAATGCGAA
1 TTTTAATTTCGCAACACG-AATTTCCTTTTCGCAACAAGATTTTCT-AATTCGCAACGCGAA
*
254094 TTTTAATTTTGCAACAC
1 TTTTAATTTCGCAACAC
254111 ATCTTTTAAT
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
59 2 0.03
60 60 0.97
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (60 bp):
TTTTAATTTCGCAACACGAATTTCCTTTTCGCAACAAGATTTTCTAATTCGCAACGCGAA
Found at i:254117 original size:20 final size:20
Alignment explanation
Indices: 254094--254131 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
254084 GCAATGCGAA
*
254094 TTTTAATTTTGCAACACATC
1 TTTTAATTTCGCAACACATC
254114 TTTTAATTTCGCAACACA
1 TTTTAATTTCGCAACACA
254132 AATATTTTAG
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:0.32, C:0.21, G:0.05, T:0.42
Consensus pattern (20 bp):
TTTTAATTTCGCAACACATC
Found at i:254285 original size:14 final size:15
Alignment explanation
Indices: 254266--254303 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
254256 TCCCTATCTC
254266 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
254280 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
254296 TAATTTTT
1 TAATTTTT
254304 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:254918 original size:12 final size:12
Alignment explanation
Indices: 254897--254930 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
254887 ACCACATTTC
*
254897 CAATACCAAACA
1 CAATATCAAACA
254909 CAATATCAAACA
1 CAATATCAAACA
*
254921 CAATCTCAAA
1 CAATATCAAA
254931 ATCCACAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:255107 original size:24 final size:24
Alignment explanation
Indices: 255060--255109 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
255050 TCAAAATTTA
* *
255060 ATCTTGGTCAATACCCGGACTTTG
1 ATCTTGGTAAATACCCAGACTTTG
* *
255084 ATCTTGGTAAATACTCAGATTTTG
1 ATCTTGGTAAATACCCAGACTTTG
255108 AT
1 AT
255110 GATGTTTCAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (24 bp):
ATCTTGGTAAATACCCAGACTTTG
Found at i:258026 original size:27 final size:27
Alignment explanation
Indices: 257992--258047 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
257982 GCCTAATGAA
** *
257992 AATTCGCAACTGGAAAATTGAATTCGC
1 AATTCGCAACACGAAAATCGAATTCGC
258019 AATTCGCAACACGAAAATCGAATTCGC
1 AATTCGCAACACGAAAATCGAATTCGC
258046 AA
1 AA
258048 CTTGAAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.21
Consensus pattern (27 bp):
AATTCGCAACACGAAAATCGAATTCGC
Found at i:258069 original size:20 final size:20
Alignment explanation
Indices: 258019--258070 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
258009 TTGAATTCGC
*
258019 AATTCGCAACACGAAAATCG
1 AATTCGCAACTCGAAAATCG
*
258039 AATTCGCAACTTGAAAAT-G
1 AATTCGCAACTCGAAAATCG
258058 AAATTCGCAACTC
1 -AATTCGCAACTC
258071 AATTTCGAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.21
Consensus pattern (20 bp):
AATTCGCAACTCGAAAATCG
Found at i:258098 original size:20 final size:21
Alignment explanation
Indices: 258073--258152 Score: 85
Period size: 20 Copynumber: 4.0 Consensus size: 21
258063 CGCAACTCAA
*
258073 TTTCGAGTTGTGAATTTC-AT
1 TTTCGAGTTGCGAATTTCGAT
*
258093 TTTCGATTTGCGAA-TTCGAT
1 TTTCGAGTTGCGAATTTCGAT
* *
258113 TTTCGAGTTGCGAATTT-TAA
1 TTTCGAGTTGCGAATTTCGAT
* *
258133 TATCGAGTTGCGATTTTCGA
1 TTTCGAGTTGCGAATTTCGA
258153 GTTGCGAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
19 3 0.06
20 43 0.88
21 3 0.06
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.45
Consensus pattern (21 bp):
TTTCGAGTTGCGAATTTCGAT
Found at i:258147 original size:34 final size:34
Alignment explanation
Indices: 258109--258213 Score: 192
Period size: 34 Copynumber: 3.1 Consensus size: 34
258099 TTTGCGAATT
258109 CGATTTTCGAGTTGCGAATTTTAATATCGAGTTG
1 CGATTTTCGAGTTGCGAATTTTAATATCGAGTTG
258143 CGATTTTCGAGTTGCGAATTTTAATATCGAGTTG
1 CGATTTTCGAGTTGCGAATTTTAATATCGAGTTG
* *
258177 CGATTTTCGTGTTGTGAATTTTAATATCGAGTTG
1 CGATTTTCGAGTTGCGAATTTTAATATCGAGTTG
258211 CGA
1 CGA
258214 ATTTGATTTT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 69 1.00
ACGTcount: A:0.23, C:0.11, G:0.24, T:0.42
Consensus pattern (34 bp):
CGATTTTCGAGTTGCGAATTTTAATATCGAGTTG
Found at i:258174 original size:20 final size:20
Alignment explanation
Indices: 258115--258217 Score: 104
Period size: 20 Copynumber: 5.8 Consensus size: 20
258105 AATTCGATTT
258115 TCGAGTTGCGAATTTTAATA
1 TCGAGTTGCGAATTTTAATA
258135 TCGAGTTGCG-A--TT--T-
1 TCGAGTTGCGAATTTTAATA
258149 TCGAGTTGCGAATTTTAATA
1 TCGAGTTGCGAATTTTAATA
258169 TCGAGTTGCG-A--TT--T-
1 TCGAGTTGCGAATTTTAATA
* *
258183 TCGTGTTGTGAATTTTAATA
1 TCGAGTTGCGAATTTTAATA
258203 TCGAGTTGCGAATTT
1 TCGAGTTGCGAATTT
258218 GATTTTCTTA
Statistics
Matches: 67, Mismatches: 4, Indels: 24
0.71 0.04 0.25
Matches are distributed among these distances:
14 18 0.27
15 4 0.06
17 8 0.12
19 4 0.06
20 33 0.49
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (20 bp):
TCGAGTTGCGAATTTTAATA
Found at i:258477 original size:24 final size:24
Alignment explanation
Indices: 258445--258530 Score: 163
Period size: 24 Copynumber: 3.6 Consensus size: 24
258435 CCTTGAATAC
258445 ATATTCAACTAGTTTAGATGATGG
1 ATATTCAACTAGTTTAGATGATGG
*
258469 ATATTCAACAAGTTTAGATGATGG
1 ATATTCAACTAGTTTAGATGATGG
258493 ATATTCAACTAGTTTAGATGATGG
1 ATATTCAACTAGTTTAGATGATGG
258517 ATATTCAACTAGTT
1 ATATTCAACTAGTT
258531 GAAAAATCAG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (24 bp):
ATATTCAACTAGTTTAGATGATGG
Found at i:260537 original size:21 final size:21
Alignment explanation
Indices: 260492--260621 Score: 120
Period size: 21 Copynumber: 6.2 Consensus size: 21
260482 GTATGGAATG
* *
260492 TGGATCATGAACGATGCGG-GG
1 TGGATCCTGAACGATG-GGAGA
*
260513 TGGATCCTAAACGATGGGAGA
1 TGGATCCTGAACGATGGGAGA
**
260534 TGGATCCTGAATAATGGGAGA
1 TGGATCCTGAACGATGGGAGA
260555 TGGATCCTGAACGATGGGAG-
1 TGGATCCTGAACGATGGGAGA
* * * * *
260575 GGGCCTCTTGAACGATGAGAGG
1 TGG-ATCCTGAACGATGGGAGA
* *
260597 TGAATCCTGAACAATGGGAGA
1 TGGATCCTGAACGATGGGAGA
260618 TGGA
1 TGGA
260622 CCTTGAATAA
Statistics
Matches: 86, Mismatches: 20, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
20 4 0.05
21 81 0.94
22 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.37, T:0.20
Consensus pattern (21 bp):
TGGATCCTGAACGATGGGAGA
Found at i:260628 original size:21 final size:21
Alignment explanation
Indices: 260513--260643 Score: 104
Period size: 21 Copynumber: 6.2 Consensus size: 21
260503 CGATGCGGGG
* *
260513 TGGATCCTAAACGATGGGAGA
1 TGGATCCTGAACAATGGGAGA
*
260534 TGGATCCTGAATAATGGGAGA
1 TGGATCCTGAACAATGGGAGA
*
260555 TGGATCCTGAACGATGGGAG-
1 TGGATCCTGAACAATGGGAGA
* * * * * *
260575 GGGCCTCTTGAACGATGAGAGG
1 TGG-ATCCTGAACAATGGGAGA
*
260597 TGAATCCTGAACAATGGGAGA
1 TGGATCCTGAACAATGGGAGA
* * *
260618 TGGA-CCTTGAATAATGGTAGG
1 TGGATCC-TGAACAATGGGAGA
260639 TGGAT
1 TGGAT
260644 AAGGCTTCTT
Statistics
Matches: 86, Mismatches: 20, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
20 4 0.05
21 81 0.94
22 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.35, T:0.22
Consensus pattern (21 bp):
TGGATCCTGAACAATGGGAGA
Found at i:260640 original size:42 final size:41
Alignment explanation
Indices: 260511--260643 Score: 135
Period size: 42 Copynumber: 3.2 Consensus size: 41
260501 AACGATGCGG
*
260511 GGTGGATCCTAAACGATGGGAGATGGATCC-TGAATAATGGGA
1 GGTGGATCCTGAACGATGGGAGATGGA-CCTTGAATAAT-GGA
* * * **
260553 GATGGATCCTGAACGATGGGAG-GGGCCTCTTGAACGATGAGA
1 GGTGGATCCTGAACGATGGGAGATGGAC-CTTGAATAATG-GA
* *
260595 GGTGAATCCTGAACAATGGGAGATGGACCTTGAATAATGGTA
1 GGTGGATCCTGAACGATGGGAGATGGACCTTGAATAATGG-A
260637 GGTGGAT
1 GGTGGAT
260644 AAGGCTTCTT
Statistics
Matches: 72, Mismatches: 14, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
40 1 0.01
41 5 0.07
42 63 0.88
43 3 0.04
ACGTcount: A:0.29, C:0.13, G:0.36, T:0.22
Consensus pattern (41 bp):
GGTGGATCCTGAACGATGGGAGATGGACCTTGAATAATGGA
Found at i:261013 original size:63 final size:63
Alignment explanation
Indices: 260939--261079 Score: 192
Period size: 63 Copynumber: 2.2 Consensus size: 63
260929 TCTCATGTAG
* * * * *
260939 AGCACCTACCTCATCACGTAAAGAACCATTGTCATCACGTAAAGTAGCTACCTCACCACATAA
1 AGCACCTACCTCATCACATAAAGAACCATTATCATCACGTAAAGCACCGACCTCACCACATAA
* * * *
261002 AGCACCTACCTCATCATATAAAGCACCATTATCATCACGTAAAGCACCGACCTCATCACGTAA
1 AGCACCTACCTCATCACATAAAGAACCATTATCATCACGTAAAGCACCGACCTCACCACATAA
*
261065 AGCACCTAACTCATC
1 AGCACCTACCTCATC
261080 CCGTGGAGGT
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.36, C:0.33, G:0.10, T:0.21
Consensus pattern (63 bp):
AGCACCTACCTCATCACATAAAGAACCATTATCATCACGTAAAGCACCGACCTCACCACATAA
Found at i:261078 original size:21 final size:21
Alignment explanation
Indices: 260939--261079 Score: 135
Period size: 21 Copynumber: 6.7 Consensus size: 21
260929 TCTCATGTAG
260939 AGCACCTACCTCATCACGTAA
1 AGCACCTACCTCATCACGTAA
* **
260960 AGAACC-ATTGTCATCACGTAA
1 AGCACCTA-CCTCATCACGTAA
* * * *
260981 AGTAGCTACCTCACCACATAA
1 AGCACCTACCTCATCACGTAA
**
261002 AGCACCTACCTCATCATATAA
1 AGCACCTACCTCATCACGTAA
261023 AGCACCATTA--TCATCACGTAA
1 AGCACC--TACCTCATCACGTAA
*
261044 AGCACCGACCTCATCACGTAA
1 AGCACCTACCTCATCACGTAA
*
261065 AGCACCTAACTCATC
1 AGCACCTACCTCATC
261080 CCGTGGAGGT
Statistics
Matches: 96, Mismatches: 18, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 91 0.95
22 1 0.01
23 2 0.02
ACGTcount: A:0.36, C:0.33, G:0.10, T:0.21
Consensus pattern (21 bp):
AGCACCTACCTCATCACGTAA
Found at i:261226 original size:42 final size:42
Alignment explanation
Indices: 261179--261303 Score: 162
Period size: 42 Copynumber: 3.0 Consensus size: 42
261169 GTGATGGAAT
* * * *
261179 AGGTGATGGATCTTGGTGTCGAGGTGTAGAATC-AGCTTGATA
1 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCGA-CTCGATA
*
261221 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCGACTCGATG
1 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCGACTCGATA
* **
261263 AGGTGATAGATCTCCATGTCGAAGTGGAGAATCGACTCGAT
1 AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCGACTCGAT
261304 GAAAAAGTGG
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 73 0.99
43 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.34, T:0.26
Consensus pattern (42 bp):
AGGTGATGGATCTCGGTGTCGAAGTGGAGAATCGACTCGATA
Found at i:261567 original size:12 final size:12
Alignment explanation
Indices: 261552--261582 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
261542 ATTATTTAAA
*
261552 CGGGTATCGGGT
1 CGGGTATCGGGC
261564 CGGGTATCGGGC
1 CGGGTATCGGGC
261576 CGGGTAT
1 CGGGTAT
261583 ATATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.19, G:0.48, T:0.23
Consensus pattern (12 bp):
CGGGTATCGGGC
Done.