Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003278.1 Hibiscus syriacus cultivar Beakdansim tig00006893_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: 90429
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:10310 original size:25 final size:26
Alignment explanation
Indices: 10273--10328 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 26
10263 TATCTCAATG
* *
10273 TATAAATACTTAAATTCATAATATTC
1 TATATATACTTAAATTCAAAATATTC
* * *
10299 TATATATA-TTAACTTGAAAATATTT
1 TATATATACTTAAATTCAAAATATTC
10324 TATAT
1 TATAT
10329 TAACTTATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (26 bp):
TATATATACTTAAATTCAAAATATTC
Found at i:11695 original size:89 final size:88
Alignment explanation
Indices: 11585--11754 Score: 261
Period size: 89 Copynumber: 1.9 Consensus size: 88
11575 ACAGAAACCA
* *
11585 GTTACACCATCCGACCCTCCAAACCGGTTAGAATCCGAACCGGTTTTTTTAAAATCCGA-TTTTT
1 GTTACACCATCCGACCATCCAAACCGGTTAGAATCCGAA-CGGATTTTTTAAAAT-CGAGTTTTT
*
11649 TGGCTAGGTGAAAAAACCAGATCGG
64 TGGCTAGATGAAAAAACCAGATCGG
* *
11674 GTTACACCATCCGACCATCCAAACCGGTTAGAATCCGAACTGATTTTTTAAAATCTAGTTTTTTG
1 GTTACACCATCCGACCATCCAAACCGGTTAGAATCCGAACGGATTTTTTAAAATCGAGTTTTTTG
*
11739 GTTAGATGAAAAAACC
66 GCTAGATGAAAAAACC
11755 GTATCGATTT
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
87 2 0.03
88 34 0.46
89 38 0.51
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (88 bp):
GTTACACCATCCGACCATCCAAACCGGTTAGAATCCGAACGGATTTTTTAAAATCGAGTTTTTTG
GCTAGATGAAAAAACCAGATCGG
Found at i:13310 original size:17 final size:17
Alignment explanation
Indices: 13276--13310 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
13266 ACAAATACTG
* *
13276 AAAACAAATAGATCATA
1 AAAACAAATAAATAATA
13293 AAAACAAATAAATAATA
1 AAAACAAATAAATAATA
13310 A
1 A
13311 TAAAACCCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.09, G:0.03, T:0.17
Consensus pattern (17 bp):
AAAACAAATAAATAATA
Found at i:14488 original size:19 final size:18
Alignment explanation
Indices: 14464--14503 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
14454 GCTGCTGGAA
14464 ACCGGTTTAACCGGTTCTG
1 ACCGGTTTAACCGGTT-TG
*
14483 ACCGGTTTGACCGGTTTG
1 ACCGGTTTAACCGGTTTG
14501 ACC
1 ACC
14504 CGACCGACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.15, C:0.28, G:0.28, T:0.30
Consensus pattern (18 bp):
ACCGGTTTAACCGGTTTG
Found at i:14500 original size:9 final size:9
Alignment explanation
Indices: 14464--14503 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
14454 GCTGCTGGAA
*
14464 ACCGGTTTA
1 ACCGGTTTG
14473 ACCGGTTCTG
1 ACCGGTT-TG
14483 ACCGGTTTG
1 ACCGGTTTG
14492 ACCGGTTTG
1 ACCGGTTTG
14501 ACC
1 ACC
14504 CGACCGACCC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.15, C:0.28, G:0.28, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:14532 original size:22 final size:22
Alignment explanation
Indices: 14507--14575 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
14497 TTTGACCCGA
*
14507 CCGACCCAACCCGACCGTTGAG
1 CCGACCCAACCCGACCGTTGAC
* *
14529 CCGAGCCGACCCGACCGTTGAC
1 CCGACCCAACCCGACCGTTGAC
* *
14551 CCGACCCGACCGTTGACCGTTGAC
1 CCGACCCAACC--CGACCGTTGAC
14575 C
1 C
14576 GTTGACTTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 29 0.73
24 11 0.28
ACGTcount: A:0.19, C:0.45, G:0.25, T:0.12
Consensus pattern (22 bp):
CCGACCCAACCCGACCGTTGAC
Found at i:14554 original size:17 final size:17
Alignment explanation
Indices: 14534--14568 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
14524 TTGAGCCGAG
14534 CCGACCCGACCGTTGAC
1 CCGACCCGACCGTTGAC
14551 CCGACCCGACCGTTGAC
1 CCGACCCGACCGTTGAC
14568 C
1 C
14569 GTTGACCGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.49, G:0.23, T:0.11
Consensus pattern (17 bp):
CCGACCCGACCGTTGAC
Found at i:21791 original size:20 final size:19
Alignment explanation
Indices: 21739--21795 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
21729 GGCTGCTGGA
* *
21739 AACCGGTTTAACCAGTTTTC
1 AACCGGTTTGACC-GGTTTC
21759 AACCGGTTCTGACCGGTTTC
1 AACCGGTT-TGACCGGTTTC
21779 GAACCGGTTTGACCGGT
1 -AACCGGTTTGACCGGT
21796 CTGACCCGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 21 0.64
21 12 0.36
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.30
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTTC
Found at i:21818 original size:17 final size:17
Alignment explanation
Indices: 21796--21835 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
21786 TTTGACCGGT
21796 CTGACCCGACCCGACCG
1 CTGACCCGACCCGACCG
21813 CTGACCCGACCCGACCG
1 CTGACCCGACCCGACCG
*
21830 TTGACC
1 CTGACC
21836 GTTGACCGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.17, C:0.50, G:0.23, T:0.10
Consensus pattern (17 bp):
CTGACCCGACCCGACCG
Found at i:25300 original size:44 final size:44
Alignment explanation
Indices: 25199--25297 Score: 132
Period size: 44 Copynumber: 2.3 Consensus size: 44
25189 TCAGGCCAGG
25199 TATATA-TATTTTAAATTAAATATATAAATATTATATATATATA
1 TATATATTATTTTAAATTAAATATATAAATATTATATATATATA
* * * *
25242 TATATGTTAATTTAAATTAAATTTATTAATATTATATATATA-A
1 TATATATTATTTTAAATTAAATATATAAATATTATATATATATA
25285 TA-ATAATTATTTT
1 TATAT-ATTATTTT
25298 TAATATTTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
42 2 0.04
43 14 0.29
44 32 0.67
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (44 bp):
TATATATTATTTTAAATTAAATATATAAATATTATATATATATA
Found at i:25406 original size:30 final size:30
Alignment explanation
Indices: 25372--25446 Score: 123
Period size: 30 Copynumber: 2.5 Consensus size: 30
25362 CATCCCCATT
25372 CCCGTCCCCGTTTAACATAAACAATTTTTC
1 CCCGTCCCCGTTTAACATAAACAATTTTTC
* * *
25402 CCCGTCCCCGTTTAGCTTAAACGATTTTTC
1 CCCGTCCCCGTTTAACATAAACAATTTTTC
25432 CCCGTCCCCGTTTAA
1 CCCGTCCCCGTTTAA
25447 TTCAGTTTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.20, C:0.36, G:0.11, T:0.33
Consensus pattern (30 bp):
CCCGTCCCCGTTTAACATAAACAATTTTTC
Found at i:25731 original size:30 final size:30
Alignment explanation
Indices: 25690--25751 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
25680 ATATATGGTA
25690 ACTTTCATTTTATTTAATTAAGAGATGATC
1 ACTTTCATTTTATTTAATTAAGAGATGATC
* * *
25720 ACTTTCGTTTTATTTAATTAAGATATGGTC
1 ACTTTCATTTTATTTAATTAAGAGATGATC
25750 AC
1 AC
25752 CATGGGTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (30 bp):
ACTTTCATTTTATTTAATTAAGAGATGATC
Found at i:25999 original size:30 final size:30
Alignment explanation
Indices: 25927--26046 Score: 93
Period size: 30 Copynumber: 4.0 Consensus size: 30
25917 AAATTTTCAA
* * *
25927 AAATATATTTTATTTTTATTTTAAAATTTCAT
1 AAATATATTATATTTTTATCTT--AATTTAAT
*
25959 -AGTATA-TATATTTTTATCTTAATTTAAT
1 AAATATATTATATTTTTATCTTAATTTAAT
* * *
25987 AAATATATTATATTATTA-CTTTAAATTATT
1 AAATATATTATATTTTTATC-TTAATTTAAT
* * *
26017 AAATATATTTTATTCTTATATTAACTTTAA
1 AAATATATTATATTTTTATCTTAA-TTTAA
26047 AATATTTTAA
Statistics
Matches: 70, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
28 7 0.10
29 6 0.09
30 49 0.70
31 8 0.11
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (30 bp):
AAATATATTATATTTTTATCTTAATTTAAT
Found at i:26083 original size:20 final size:19
Alignment explanation
Indices: 26048--26092 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
26038 TAACTTTAAA
*
26048 ATATTTTAATATTAAATAT
1 ATATTTAAATATTAAATAT
26067 ATATTTAAATCATTAAATAT
1 ATATTTAAAT-ATTAAATAT
26087 AT-TTTA
1 ATATTTA
26093 TTCAATTAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATTTAAATATTAAATAT
Found at i:26086 original size:18 final size:17
Alignment explanation
Indices: 26043--26090 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
26033 TATATTAACT
*
26043 TTAAA-ATATTTTAATA
1 TTAAATATATTTAAATA
26059 TTAAATATATATTTAAATCA
1 TT-AA-ATATATTTAAAT-A
26079 TTAAATATATTT
1 TTAAATATATTT
26091 TATTCAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 2 0.07
17 2 0.07
18 9 0.33
19 11 0.41
20 3 0.11
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
TTAAATATATTTAAATA
Found at i:29375 original size:20 final size:19
Alignment explanation
Indices: 29315--29376 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
29305 AAATTTATAA
*
29315 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
29334 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
29352 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
29372 ATTTT
1 ATTTT
29377 GATTTAAGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:31581 original size:21 final size:21
Alignment explanation
Indices: 31538--31584 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
31528 ACATGTTTTA
* * * *
31538 TTTAGAGTTAAAATTTGATAT
1 TTTAAAGTTAAAATCTAAAAT
31559 TTTAAAGTTAAAATCTAAAAT
1 TTTAAAGTTAAAATCTAAAAT
31580 TTTAA
1 TTTAA
31585 GATTTAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.45
Consensus pattern (21 bp):
TTTAAAGTTAAAATCTAAAAT
Found at i:33638 original size:56 final size:56
Alignment explanation
Indices: 33574--33752 Score: 182
Period size: 56 Copynumber: 3.2 Consensus size: 56
33564 GTTCTGAATT
* * * *
33574 GAATATATCTATTAGTTGTTGTCATTAATAGGCATAAAAGCAGAGGTGTCAAAATC
1 GAATATATCTATTAGTTGTTGTCATTAATAAGCATAAAAACAAAGGTCTCAAAATC
* * * * *
33630 GAATATATCTATCAGTGGTTGTCATTAATAAGTATAAAAATAAAGGTCTCGAAATC
1 GAATATATCTATTAGTTGTTGTCATTAATAAGCATAAAAACAAAGGTCTCAAAATC
* * * * * * *
33686 GAGTATATATATTAATTGTTGAT-ATTAAGAATCATAAAAA-TAAGGACCTCAAAATC
1 GAATATATCTATTAGTTGTTG-TCATTAATAAGCATAAAAACAAAGG-TCTCAAAATC
33742 GAATATATCTA
1 GAATATATCTA
33753 AAAAATAAAG
Statistics
Matches: 99, Mismatches: 22, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
55 4 0.04
56 94 0.95
57 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (56 bp):
GAATATATCTATTAGTTGTTGTCATTAATAAGCATAAAAACAAAGGTCTCAAAATC
Found at i:34359 original size:20 final size:21
Alignment explanation
Indices: 34336--34379 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
34326 TATATAATTA
34336 TTTAAGATTTT-CTTT-AATAT
1 TTTAA-ATTTTCCTTTAAATAT
*
34356 TTTAACTTTTCCTTTAAATAT
1 TTTAAATTTTCCTTTAAATAT
34377 TTT
1 TTT
34380 TTAATTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 9 0.43
21 8 0.38
ACGTcount: A:0.27, C:0.09, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTAAATTTTCCTTTAAATAT
Found at i:41482 original size:31 final size:31
Alignment explanation
Indices: 41447--41557 Score: 109
Period size: 31 Copynumber: 3.5 Consensus size: 31
41437 ATTCATATAT
*
41447 TCGGGTCGGGTCGGGTGAAACTTTATTTTGG
1 TCGGGTCGGATCGGGTGAAACTTTATTTTGG
* * * **
41478 TCGGGTCGGATCGGGT--TATTTTAAGTGTGATAT
1 TCGGGTCGGATCGGGTGAAACTTT-A-T-T-TTGG
*
41511 TCGGGTCGGGTCGGGTGAAACTTTATTTTGG
1 TCGGGTCGGATCGGGTGAAACTTTATTTTGG
41542 TCGGGTCGGATCGGGT
1 TCGGGTCGGATCGGGT
41558 TTTTTTAAGT
Statistics
Matches: 61, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
29 4 0.07
30 1 0.02
31 32 0.52
32 2 0.03
33 17 0.28
34 1 0.02
35 4 0.07
ACGTcount: A:0.14, C:0.13, G:0.39, T:0.35
Consensus pattern (31 bp):
TCGGGTCGGATCGGGTGAAACTTTATTTTGG
Found at i:41511 original size:64 final size:64
Alignment explanation
Indices: 41443--41585 Score: 277
Period size: 64 Copynumber: 2.2 Consensus size: 64
41433 TCTAATTCAT
41443 ATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGATCGGGTTATTTTAAGTGTG
1 ATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGATCGGGTTATTTTAAGTGTG
*
41507 ATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGATCGGGTTTTTTTAAGTGTG
1 ATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGATCGGGTTATTTTAAGTGTG
41571 ATATTCGGGTCGGGT
1 ATATTCGGGTCGGGT
41586 TTAGGTTTAG
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 78 1.00
ACGTcount: A:0.15, C:0.11, G:0.36, T:0.38
Consensus pattern (64 bp):
ATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGATCGGGTTATTTTAAGTGTG
Found at i:41517 original size:33 final size:33
Alignment explanation
Indices: 41478--41583 Score: 103
Period size: 33 Copynumber: 3.3 Consensus size: 33
41468 TTTATTTTGG
41478 TCGGGTCGGATCGGGTTATTTTAAGTGTGATAT
1 TCGGGTCGGATCGGGTTATTTTAAGTGTGATAT
* * * * **
41511 TCGGGTCGGGTCGGGTGAAACTTT-A-T-T-TTGG
1 TCGGGTCGGATCGGGT--TATTTTAAGTGTGATAT
*
41542 TCGGGTCGGATCGGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGATCGGGTTATTTTAAGTGTGATAT
41575 TCGGGTCGG
1 TCGGGTCGG
41584 GTTTAGGTTT
Statistics
Matches: 54, Mismatches: 13, Indels: 12
0.68 0.16 0.15
Matches are distributed among these distances:
29 3 0.06
30 1 0.02
31 17 0.31
32 2 0.04
33 26 0.48
34 1 0.02
35 4 0.07
ACGTcount: A:0.14, C:0.11, G:0.37, T:0.38
Consensus pattern (33 bp):
TCGGGTCGGATCGGGTTATTTTAAGTGTGATAT
Found at i:41842 original size:38 final size:37
Alignment explanation
Indices: 41759--41844 Score: 111
Period size: 38 Copynumber: 2.3 Consensus size: 37
41749 TTTATTTTGT
*
41759 TCGGGTCGGGTCGGGTTTTTTAAGTGTTATATTCGGA
1 TCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGA
* * *
41796 TTGAGTCGGGTCGGATTTTTTTAAGTGTGATATTCAGG-
1 TCGGGTCGGGTCGG-GTTTTTTAAGTGTGATATTC-GGA
41834 TCGGGTCGGGT
1 TCGGGTCGGGT
41845 TCGAGTTTAG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
37 12 0.29
38 27 0.66
39 2 0.05
ACGTcount: A:0.14, C:0.10, G:0.36, T:0.40
Consensus pattern (37 bp):
TCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGA
Found at i:42012 original size:254 final size:248
Alignment explanation
Indices: 41546--42138 Score: 848
Period size: 259 Copynumber: 2.4 Consensus size: 248
41536 TTTTGGTCGG
* * *
41546 GTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGT---TTAGGTTTAGAGTGAAAAAAAC
1 GTCGGGTC-GGTTTTTTTAAGTGTGATATTC-GGTCGGGTCGGTTCGGTTTAGGGTGAAAAAAAC
* *
41608 CGGACCGACCCGAAAATATATATAATTCAGGTCGGGTCAGATTAAGTCACTGTTTTTATTAAATA
64 CGGACCGACCCAAAAATATATATAATTTAGGTCGGGTCAGATTAAGTCACTGTTTTTATTAAATA
*
41673 AAAATAATTTTTTATTATTTCGGGTCAGGTCGAGTTGGATTTCTAATTCATATATTCGGGTCGGG
129 AAAATAATTTTTTATTATTTCGGGTCA-G-CGAGTCGGATTTCTAATTCATATATTCGGGTCGGG
*
41738 TCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTTATATTCGGATTGA
192 TCGGATGAAACTTTATTTTG-T----TCGGGTCGGGTTTTTTAAGTGTGATATTCGGATTGA
41800 GTCGGGTCGGATTTTTTTAAGTGTGATATTCAGGTCGGGTCGGGTTCGAGTTTAGGGTGAAAAAA
1 GTCGGGTCGG-TTTTTTTAAGTGTGATATTC-GGTCGGGTC-GGTTCG-GTTTAGGGTGAAAAAA
* *
41865 ACCGGACCGACCCAAAAATATATATAATTTGGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAA
62 ACCGGACCGACCCAAAAATATATATAATTTAGGTCGGGTCAGATTAAGTCACTGTTTTTATTAAA
*
41930 TAAAAATATTTTTTTATTATTTCGGGTC-G-G-GTCGGATTTCTAATTCATATATTCGGGTCGGG
127 TAAAAATAATTTTTTATTATTTCGGGTCAGCGAGTCGGATTTCTAATTCATATATTCGGGTCGGG
*
41992 TCGGATGAAACTTTATTTTGTTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTTGA
192 TCGGATGAAACTTTATTTTGTTCGGGTCGGGTTTTTTAAGTGTGATATTCGGATTGA
42049 GTC-GGTCAGGTTTTTTTAAGTGTGATA-T---TCGGGTCAGGTTCGGGTTTAGGGTGAAAAAAA
1 GTCGGGTC-GGTTTTTTTAAGTGTGATATTCGGTCGGGTC-GGTTC-GGTTTAGGGTGAAAAAAA
*
42109 CCGGACCGACCCGAAAAAAATATATAATTT
63 CCGGACCGACCC-AAAAATATATATAATTT
42139 TACCTTATAT
Statistics
Matches: 316, Mismatches: 14, Indels: 28
0.88 0.04 0.08
Matches are distributed among these distances:
243 41 0.13
244 17 0.05
247 1 0.00
248 21 0.07
249 39 0.12
253 3 0.01
254 86 0.27
255 1 0.00
257 1 0.00
258 3 0.01
259 103 0.33
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.37
Consensus pattern (248 bp):
GTCGGGTCGGTTTTTTTAAGTGTGATATTCGGTCGGGTCGGTTCGGTTTAGGGTGAAAAAAACCG
GACCGACCCAAAAATATATATAATTTAGGTCGGGTCAGATTAAGTCACTGTTTTTATTAAATAAA
AATAATTTTTTATTATTTCGGGTCAGCGAGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGG
ATGAAACTTTATTTTGTTCGGGTCGGGTTTTTTAAGTGTGATATTCGGATTGA
Found at i:43494 original size:18 final size:19
Alignment explanation
Indices: 43459--43495 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
43449 CACGGAATGT
43459 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
43479 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
43496 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:47056 original size:30 final size:29
Alignment explanation
Indices: 47006--47135 Score: 176
Period size: 30 Copynumber: 4.4 Consensus size: 29
46996 AGTTAGTTAG
47006 AAAA-ATATTTTTAAAAGTTAAGATAAAAAT
1 AAAATATATTTTT--AAGTTAAGATAAAAAT
47036 AAAATATATTATTTAAGTTAAGAT-AAAAT
1 AAAATATATT-TTTAAGTTAAGATAAAAAT
*
47065 AAAATATA-TTTTAAGTTAAAATAAAAAT
1 AAAATATATTTTTAAGTTAAGATAAAAAT
* *
47093 AATATATATTTCTAAGTTAAAGATAAAAAT
1 AAAATATATTTTTAAGTT-AAGATAAAAAT
47123 AAAATATATTTTT
1 AAAATATATTTTT
47136 GAAAAATTAA
Statistics
Matches: 89, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
27 12 0.13
28 13 0.15
29 21 0.24
30 35 0.39
31 5 0.06
32 3 0.03
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (29 bp):
AAAATATATTTTTAAGTTAAGATAAAAAT
Found at i:47081 original size:57 final size:59
Alignment explanation
Indices: 47007--47134 Score: 183
Period size: 57 Copynumber: 2.2 Consensus size: 59
46997 GTTAGTTAGA
* *
47007 AAAATAT-TTTTAAAAGTTAAGATAAAAATAAAATATATTATTTAAGTT-AAGAT-AAAAT
1 AAAATATATTTT-AAAGTTAAAATAAAAATAAAATATATT-TCTAAGTTAAAGATAAAAAT
*
47065 AAAATATATTTT-AAGTTAAAATAAAAATAATATATATTTCTAAGTTAAAGATAAAAAT
1 AAAATATATTTTAAAGTTAAAATAAAAATAAAATATATTTCTAAGTTAAAGATAAAAAT
47123 AAAATATATTTT
1 AAAATATATTTT
47135 TGAAAAATTA
Statistics
Matches: 64, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
56 7 0.11
57 29 0.45
58 24 0.38
59 4 0.06
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (59 bp):
AAAATATATTTTAAAGTTAAAATAAAAATAAAATATATTTCTAAGTTAAAGATAAAAAT
Found at i:47165 original size:18 final size:18
Alignment explanation
Indices: 47139--47186 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
47129 TATTTTTGAA
47139 AAATTAATATATGAATTT
1 AAATTAATATATGAATTT
* *
47157 AATTTAATATTTGAATTT
1 AAATTAATATATGAATTT
*
47175 AAATTAAGATAT
1 AAATTAATATAT
47187 ATATTAAGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (18 bp):
AAATTAATATATGAATTT
Found at i:58266 original size:20 final size:19
Alignment explanation
Indices: 58235--58280 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 19
58225 TAATCTCAAA
58235 ATTTTATTTATTTTTTATAAT
1 ATTTTATTTA-TTTTTA-AAT
58256 ATTTT-TTTATTTTTAAAT
1 ATTTTATTTATTTTTAAAT
58274 ATTTTAT
1 ATTTTAT
58281 ATGGCGTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.33
19 7 0.29
20 4 0.17
21 5 0.21
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
ATTTTATTTATTTTTAAAT
Found at i:59714 original size:15 final size:14
Alignment explanation
Indices: 59674--59705 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
59664 AAATAATAAC
59674 CTACATGGAACCCA
1 CTACATGGAACCCA
59688 CTACATGGAACCCA
1 CTACATGGAACCCA
59702 CTAC
1 CTAC
59706 GTTGGAACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.38, G:0.12, T:0.16
Consensus pattern (14 bp):
CTACATGGAACCCA
Found at i:62881 original size:9 final size:9
Alignment explanation
Indices: 62867--62891 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
62857 ATTTCCCATT
62867 TTATATCTA
1 TTATATCTA
62876 TTATATCTA
1 TTATATCTA
62885 TTATATC
1 TTATATC
62892 AAACTCTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (9 bp):
TTATATCTA
Found at i:70864 original size:12 final size:12
Alignment explanation
Indices: 70847--70882 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
70837 AATTAGCCGA
70847 GGCCAAGTGATG
1 GGCCAAGTGATG
70859 GGCCAAGTGATG
1 GGCCAAGTGATG
70871 GGCCAAGTGATG
1 GGCCAAGTGATG
70883 AATAATGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.25, C:0.17, G:0.42, T:0.17
Consensus pattern (12 bp):
GGCCAAGTGATG
Found at i:74116 original size:15 final size:15
Alignment explanation
Indices: 74072--74123 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
74062 TTAATGTCAT
74072 ATTAAAATAAAAATA
1 ATTAAAATAAAAATA
* *
74087 A--AATAATTCAGAATA
1 ATTAA-AA-TAAAAATA
74102 ATTAAAATAAAAATA
1 ATTAAAATAAAAATA
74117 ATTAAAA
1 ATTAAAA
74124 ATTCATTGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
13 2 0.07
14 2 0.07
15 21 0.72
16 2 0.07
17 2 0.07
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (15 bp):
ATTAAAATAAAAATA
Found at i:76723 original size:2 final size:2
Alignment explanation
Indices: 76716--76760 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
76706 CTAAATTTAC
76716 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
76758 AT A
1 AT A
76761 ATTAAAATTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:77002 original size:21 final size:21
Alignment explanation
Indices: 76976--77040 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
76966 GTTTCCAGAT
*
76976 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
76997 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
77018 TCGCAATGCGAACTGCGA-TA
1 TCGCAATGCGAACTTCGACTA
77038 TCG
1 TCG
77041 ACTATCGCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 5 0.12
21 35 0.88
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:77054 original size:20 final size:20
Alignment explanation
Indices: 77031--77162 Score: 87
Period size: 20 Copynumber: 6.5 Consensus size: 20
77021 CAATGCGAAC
77031 TGCGATATCGACTATCGCAA
1 TGCGATATCGACTATCGCAA
*
77051 TGCGA-AT-GTA-AATCGCAA
1 TGCGATATCG-ACTATCGCAA
*
77069 TGCGATAGTCGACTATCGCAT
1 TGCGATA-TCGACTATCGCAA
* * * *
77090 TGCGATTTAC-ATTTTCGCAT
1 TGCGATAT-CGACTATCGCAA
*
77110 TGCGATAGTCGACTATTGCAA
1 TGCGATA-TCGACTATCGCAA
*
77131 TGCGAATAT-GTA-AATCGCAA
1 TGCG-ATATCG-ACTATCGCAA
77151 TGCGATAGTCGA
1 TGCGATA-TCGA
77163 AGTTCGCATT
Statistics
Matches: 87, Mismatches: 13, Indels: 24
0.70 0.10 0.19
Matches are distributed among these distances:
18 13 0.15
19 7 0.08
20 36 0.41
21 28 0.32
22 3 0.03
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.29
Consensus pattern (20 bp):
TGCGATATCGACTATCGCAA
Found at i:77120 original size:41 final size:39
Alignment explanation
Indices: 77031--77162 Score: 160
Period size: 41 Copynumber: 3.3 Consensus size: 39
77021 CAATGCGAAC
*
77031 TGCGATA-TCGACTATCGCAATGCGAATGTAAATCGCAA
1 TGCGATAGTCGACTATCGCAATGCGAATTTAAATCGCAA
* * *
77069 TGCGATAGTCGACTATCGCATTGCG-ATTTACATTTTCGCAT
1 TGCGATAGTCGACTATCGCAATGCGAATTTA-A--ATCGCAA
*
77110 TGCGATAGTCGACTATTGCAATGCGAATATGTAAATCGCAA
1 TGCGATAGTCGACTATCGCAATGCGAAT-T-TAAATCGCAA
77151 TGCGATAGTCGA
1 TGCGATAGTCGA
77163 AGTTCGCATT
Statistics
Matches: 79, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
38 11 0.14
39 17 0.22
41 45 0.57
42 2 0.03
43 2 0.03
44 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.29
Consensus pattern (39 bp):
TGCGATAGTCGACTATCGCAATGCGAATTTAAATCGCAA
Found at i:77156 original size:82 final size:79
Alignment explanation
Indices: 77031--77197 Score: 255
Period size: 82 Copynumber: 2.1 Consensus size: 79
77021 CAATGCGAAC
77031 TGCGATATCGACTATCGCAATGCGAATGTAAATCGCAATGCGATAGTCG-ACTATCGCATTGCGA
1 TGCGATATCGACTATCGCAATGCGAATGTAAATCGCAATGCGATAGTCGAACT-TCGCATTGCGA
* *
77095 TTTACATTTTCGCAT
65 TTTACATATTCACAT
* *
77110 TGCGATAGTCGACTATTGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCATTGC
1 TGCGATA-TCGACTATCGCAATGCG-A-ATGTAAATCGCAATGCGATAGTCGAACTTCGCATTGC
77175 GATTTACATATTCACAT
63 GATTTACATATTCACAT
77192 TGCGAT
1 TGCGAT
77198 TTATTCCAAA
Statistics
Matches: 80, Mismatches: 4, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
79 7 0.09
80 16 0.20
81 1 0.01
82 54 0.68
83 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31
Consensus pattern (79 bp):
TGCGATATCGACTATCGCAATGCGAATGTAAATCGCAATGCGATAGTCGAACTTCGCATTGCGAT
TTACATATTCACAT
Found at i:77196 original size:41 final size:40
Alignment explanation
Indices: 77063--77197 Score: 125
Period size: 41 Copynumber: 3.3 Consensus size: 40
77053 CGAATGTAAA
* * *
77063 TCGCAATGCGATAGTCGACTATCGCATTGCGATTTACATTT
1 TCGCATTGCGATAGTCGAAT-TCGCATTGCGATTTACATAT
*
77104 TCGCATTGCGATAGTCGACTATT-GCAATGCGAATATGTA-A-A-
1 TCGCATTGCGATAGTCGA--ATTCGCATTGCG-AT-T-TACATAT
*
77145 TCGCAATGCGATAGTCGAAGTTCGCATTGCGATTTACATAT
1 TCGCATTGCGATAGTCGAA-TTCGCATTGCGATTTACATAT
*
77186 TCACATTGCGAT
1 TCGCATTGCGAT
77198 TTATTCCAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
38 2 0.03
39 3 0.04
40 5 0.07
41 58 0.76
42 3 0.04
43 3 0.04
44 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (40 bp):
TCGCATTGCGATAGTCGAATTCGCATTGCGATTTACATAT
Found at i:77867 original size:6 final size:6
Alignment explanation
Indices: 77845--77882 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
77835 GCCCGTCTCG
*
77845 GGTCG- GGTCGT GATCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
77883 AATACGTGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.03, C:0.16, G:0.50, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:78033 original size:13 final size:13
Alignment explanation
Indices: 78015--78096 Score: 62
Period size: 13 Copynumber: 6.2 Consensus size: 13
78005 AATGCGAACT
78015 TGGACTATCGCAA
1 TGGACTATCGCAA
78028 TGGACTATCGCAA
1 TGGACTATCGCAA
* *
78041 TGCGAATAT-GTAAA
1 TG-GACTATCG-CAA
* *
78055 TCG-CAAT-GCGAA
1 TGGACTATCGC-AA
78067 CTTGGACTATCGCAA
1 --TGGACTATCGCAA
78082 TGGACTATCGCAA
1 TGGACTATCGCAA
78095 TG
1 TG
78097 CGAATATGTA
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
12 5 0.09
13 32 0.59
14 10 0.19
15 5 0.09
16 2 0.04
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (13 bp):
TGGACTATCGCAA
Found at i:78059 original size:20 final size:20
Alignment explanation
Indices: 78034--78120 Score: 73
Period size: 20 Copynumber: 4.7 Consensus size: 20
78024 GCAATGGACT
78034 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
78054 ATCGCAATGCGAACT-TGGACT
1 ATCGCAATGCGAA-TATGTA-A
*
78075 ATCGCAATG-G---A-CT--
1 ATCGCAATGCGAATATGTAA
78088 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
78108 ATCGCAATGCGAA
1 ATCGCAATGCGAA
78121 CTTGGACTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 20
0.68 0.06 0.26
Matches are distributed among these distances:
13 9 0.17
14 1 0.02
17 1 0.02
18 1 0.02
20 30 0.58
21 10 0.19
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:78062 original size:54 final size:54
Alignment explanation
Indices: 77997--78137 Score: 282
Period size: 54 Copynumber: 2.6 Consensus size: 54
77987 GAATTTGGAA
77997 TAAATCGCAATGCGAACTTGGACTATCGCAATGGACTATCGCAATGCGAATATG
1 TAAATCGCAATGCGAACTTGGACTATCGCAATGGACTATCGCAATGCGAATATG
78051 TAAATCGCAATGCGAACTTGGACTATCGCAATGGACTATCGCAATGCGAATATG
1 TAAATCGCAATGCGAACTTGGACTATCGCAATGGACTATCGCAATGCGAATATG
78105 TAAATCGCAATGCGAACTTGGACTATCGCAATG
1 TAAATCGCAATGCGAACTTGGACTATCGCAATG
78138 CGAACTTCGA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 87 1.00
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (54 bp):
TAAATCGCAATGCGAACTTGGACTATCGCAATGGACTATCGCAATGCGAATATG
Found at i:78134 original size:21 final size:21
Alignment explanation
Indices: 78082--78161 Score: 101
Period size: 21 Copynumber: 3.9 Consensus size: 21
78072 ACTATCGCAA
78082 TGGACTATCGCAATGCGAA-T
1 TGGACTATCGCAATGCGAACT
* *
78102 ATGTA-AATCGCAATGCGAACT
1 -TGGACTATCGCAATGCGAACT
78123 TGGACTATCGCAATGCGAACT
1 TGGACTATCGCAATGCGAACT
* *
78144 TCGACTATCGCATTGCGA
1 TGGACTATCGCAATGCGA
78162 TTTACATATT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
20 16 0.31
21 35 0.69
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (21 bp):
TGGACTATCGCAATGCGAACT
Found at i:78216 original size:21 final size:21
Alignment explanation
Indices: 78170--78278 Score: 134
Period size: 21 Copynumber: 5.2 Consensus size: 21
78160 GATTTACATA
* * *
78170 TTCGCATTGTGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
78190 TATCGCATTGCGATAGTCCAAG
1 T-TCGCATTGCGATAGTCCAAG
78212 TTCGCATTGCGATAGTTCGCAAG
1 TTCGCATTGCGATAG-TC-CAAG
78235 TTCGCA-TGCGATAGT-CAAG
1 TTCGCATTGCGATAGTCCAAG
*
78254 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
78275 TTCG
1 TTCG
78279 TTGCGAATCT
Statistics
Matches: 79, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
19 10 0.13
20 10 0.13
21 36 0.46
22 13 0.16
23 10 0.13
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:78254 original size:42 final size:42
Alignment explanation
Indices: 78170--78278 Score: 152
Period size: 42 Copynumber: 2.6 Consensus size: 42
78160 GATTTACATA
* *
78170 TTCGCATTGTGATAGTCG-ACTATCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCGAAGT-TCGCATTGCGATAGTCCAAG
78212 TTCGCATTGCGATAGTTCGCAAGTTCGCA-TGCGATAGT-CAAG
1 TTCGCATTGCGATAG-TCG-AAGTTCGCATTGCGATAGTCCAAG
78254 TTCGCATTGCGATAGTCGAAGTTCG
1 TTCGCATTGCGATAGTCGAAGTTCG
78279 TTGCGAATCT
Statistics
Matches: 62, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
40 7 0.11
41 3 0.05
42 33 0.53
43 12 0.19
44 5 0.08
45 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (42 bp):
TTCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAG
Found at i:78827 original size:98 final size:98
Alignment explanation
Indices: 78717--78951 Score: 294
Period size: 88 Copynumber: 2.5 Consensus size: 98
78707 GGTCACATCA
78717 ATTTGAAGATTAATTTA-TTTAATTTATTAAAATTAGGACTAAATTAAAATAAAATAAATATAAT
1 ATTTGAAGATTAATTTATTTTAATTTATTAAAATTA-GACTAAATTAAAATAAAATAAATATAAT
*
78781 CATCAAATTGAATGGTGACACATGGCACCATTCC
65 CATCAAATTGAATGGTGACACATGACACCATTCC
*
78815 ATTTGAAGATTAATTTATTTTAATTTA-TAAAA-T----T--A--AAAATAAAATAAATGTAATC
1 ATTTGAAGATTAATTTATTTTAATTTATTAAAATTAGACTAAATTAAAATAAAATAAATATAATC
* **
78870 ATCAAATTGAATGGTGATATTTGACACCATTCC
66 ATCAAATTGAATGGTGACACATGACACCATTCC
** *
78903 ATTTGAAGATTAATTTTATTTTAACGTATTAAAATTATGACAAAATTAA
1 ATTTGAAGATTAA-TTTATTTTAATTTATTAAAATTA-GACTAAATTAA
78952 TAGAATATAT
Statistics
Matches: 116, Mismatches: 8, Indels: 24
0.78 0.05 0.16
Matches are distributed among these distances:
88 61 0.53
89 12 0.10
90 6 0.05
91 1 0.01
92 1 0.01
97 1 0.01
98 23 0.20
99 9 0.08
100 2 0.02
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (98 bp):
ATTTGAAGATTAATTTATTTTAATTTATTAAAATTAGACTAAATTAAAATAAAATAAATATAATC
ATCAAATTGAATGGTGACACATGACACCATTCC
Found at i:84619 original size:21 final size:22
Alignment explanation
Indices: 84590--84645 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
84580 TTGTCCAGGT
*
84590 TTTTTTTATTTAACT-TTATTG
1 TTTTATTATTTAACTATTATTG
* *
84611 TTTTATTATTATTACTATTATTT
1 TTTTATTATT-TAACTATTATTG
84634 TTATTATTATTT
1 TT-TTATTATTT
84646 TAATACAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 9 0.31
22 4 0.14
23 8 0.28
24 8 0.28
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTATTATTTAACTATTATTG
Found at i:84645 original size:12 final size:12
Alignment explanation
Indices: 84613--84646 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
84603 CTTTATTGTT
*
84613 TTATTATTATTA
1 TTATTATTTTTA
*
84625 CTATTATTTTTA
1 TTATTATTTTTA
84637 TTATTATTTT
1 TTATTATTTT
84647 AATACAAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (12 bp):
TTATTATTTTTA
Found at i:85381 original size:32 final size:34
Alignment explanation
Indices: 85345--85451 Score: 98
Period size: 33 Copynumber: 3.2 Consensus size: 34
85335 TGGTAAAAAT
* *
85345 TTATTTTTATGTTAGTAT-TTT-T-TAAATAGTTA
1 TTATTTTTATATTAATATATTTATGTAAATA-TTA
85377 TTATTTTTTATATTAATATATTTATGTAAATATTA
1 TTA-TTTTTATATTAATATATTTATGTAAATATTA
* * *
85412 TT-TTTTTAT-TAAATAATATTTATATAATTATTA
1 TTATTTTTATATTAAT-ATATTTATGTAAATATTA
85445 TTTATTT
1 -TTATTT
85452 AGAATTATTA
Statistics
Matches: 63, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
32 7 0.11
33 36 0.57
34 5 0.08
35 9 0.14
36 6 0.10
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.63
Consensus pattern (34 bp):
TTATTTTTATATTAATATATTTATGTAAATATTA
Found at i:85417 original size:33 final size:33
Alignment explanation
Indices: 85375--85452 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
85365 TTTAAATAGT
*
85375 TATTATTTTTTATATT-AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAATAATATTTATATAAA
*
85407 TATTATTTTTTTATTAAATAATATTTATATAAT
1 TATTATTTTTTTATTAAATAATATTTATATAAA
*
85440 TATTATTTATTTA
1 TATTATTTTTTTA
85453 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
31 4 0.10
32 14 0.34
33 23 0.56
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (33 bp):
TATTATTTTTTTATTAAATAATATTTATATAAA
Found at i:85426 original size:18 final size:19
Alignment explanation
Indices: 85397--85432 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
85387 TATTAATATA
*
85397 TTTATGTAAATATTATTTT
1 TTTATGTAAATAATATTTT
85416 TTTAT-TAAATAATATTT
1 TTTATGTAAATAATATTT
85433 ATATAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTATGTAAATAATATTTT
Found at i:85613 original size:17 final size:17
Alignment explanation
Indices: 85591--85644 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
85581 AATGTTAATA
85591 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
85608 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
85625 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
85642 TTT
1 TTT
85645 TATAATGTAT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:87176 original size:21 final size:21
Alignment explanation
Indices: 87146--87193 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
87136 GCAGGGGTAC
* *
87146 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
87167 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
87188 ATGCCA
1 ATGCCA
87194 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:87208 original size:21 final size:21
Alignment explanation
Indices: 87184--87269 Score: 68
Period size: 21 Copynumber: 4.1 Consensus size: 21
87174 GCCCACCAGT
*
87184 TTATATGCC-ATCTCCGCAGGG
1 TTATATGCCGAGC-CCGCAGGG
*
87205 TTATATTCCGAGCCCGCAGGG
1 TTATATGCCGAGCCCGCAGGG
* * *
87226 TTACATTCCTAGCCCGCCA-GG
1 TTATATGCCGAGCCCG-CAGGG
* * *
87247 TTACATTCCTAGCCCGCAGGG
1 TTATATGCCGAGCCCGCAGGG
87268 TT
1 TT
87270 TTATACCATA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
20 2 0.03
21 52 0.90
22 4 0.07
ACGTcount: A:0.19, C:0.31, G:0.23, T:0.27
Consensus pattern (21 bp):
TTATATGCCGAGCCCGCAGGG
Found at i:87830 original size:30 final size:30
Alignment explanation
Indices: 87784--87873 Score: 99
Period size: 34 Copynumber: 2.9 Consensus size: 30
87774 AAATGTTTTT
*
87784 AAAATACAAATTATATTCAAATTTAAAATA
1 AAAATAAAAATTATATTCAAATTTAAAATA
* *
87814 AAAATAAAAATAATATTATTCGAAATTTAAATTT
1 AAAATAAAAAT--TA-TATTC-AAATTTAAAATA
* *
87848 AAAATATAAATTATATTCGAATTTAA
1 AAAATAAAAATTATATTCAAATTTAA
87874 CATTAAATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
30 17 0.33
31 5 0.10
32 4 0.08
33 5 0.10
34 20 0.39
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (30 bp):
AAAATAAAAATTATATTCAAATTTAAAATA
Found at i:87880 original size:30 final size:29
Alignment explanation
Indices: 87782--87880 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 29
87772 ATAAATGTTT
* *
87782 TTAAAATACAAATTATATTCAAATTTAAAA
1 TTAAAATAAAAATTATATTCGAATTT-AAA
*
87812 TAAAAATAAAAATAATATTATTCGAAATTTAAA
1 TTAAAATAAAAAT--TA-TATTCG-AATTTAAA
*
87845 TTTAAAATATAAATTATATTCGAATTTAACA
1 -TTAAAATAAAAATTATATTCGAATTTAA-A
87876 TTAAA
1 TTAAA
87881 TTTCAACTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
30 23 0.40
31 7 0.12
32 4 0.07
33 8 0.14
34 16 0.28
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAAAATAAAAATTATATTCGAATTTAAA
Found at i:88011 original size:14 final size:14
Alignment explanation
Indices: 87992--88018 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
87982 ATCATTAACA
87992 TATATATTAAAATG
1 TATATATTAAAATG
88006 TATATATTAAAAT
1 TATATATTAAAAT
88019 CAACTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (14 bp):
TATATATTAAAATG
Done.