Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold516
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: 103685
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.30
Warning! 11080 characters in sequence are not A, C, G, or T
Found at i:17828 original size:47 final size:47
Alignment explanation
Indices: 17771--17901 Score: 174
Period size: 48 Copynumber: 2.8 Consensus size: 47
17761 TCAATCGATA
** *
17771 AGTACCTATACCATGGCCTATAGCCAAATCAAGGTAACTTATC-CTAG
1 AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCT-G
* * *
17818 AGTACTTATACCATGGCCCCGTAGACAAATCAAGGTAACTCCTCTCTG
1 AGTACCTATACCATGG-CCCGTAGCCAAATCAAGGTAACTCATCTCTG
*
17866 AATACCTATACCATGGCCCGTAGCCAAATCAAGGTA
1 AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTA
17902 TTATTCACAC
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
47 34 0.47
48 37 0.51
49 2 0.03
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (47 bp):
AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCTG
Found at i:19764 original size:15 final size:15
Alignment explanation
Indices: 19741--19778 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
19731 ATTTGCCAGT
*
19741 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTAG
19755 AAAATGA-TTTCTAG
1 AAAATGATTTTCTAG
19769 AAAATGATTT
1 AAAATGATTT
19779 ACTTTTCTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 18 0.86
15 3 0.14
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.39
Consensus pattern (15 bp):
AAAATGATTTTCTAG
Found at i:19791 original size:20 final size:19
Alignment explanation
Indices: 19762--19807 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
19752 TGGAAAATGA
19762 TTTCTAGAAAATGATTTACT
1 TTTCTAG-AAATGATTTACT
* *
19782 TTTCTGGAAATGATTTGCT
1 TTTCTAGAAATGATTTACT
19801 TTTCTAG
1 TTTCTAG
19808 TGTTTGGATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.48
Consensus pattern (19 bp):
TTTCTAGAAATGATTTACT
Found at i:20506 original size:13 final size:13
Alignment explanation
Indices: 20490--20514 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20480 GAGAAGTCAT
20490 AGCTAGAAGACTG
1 AGCTAGAAGACTG
20503 AGCTAGAAGACT
1 AGCTAGAAGACT
20515 AGACCCTTTC
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:0.28, T:0.16
Consensus pattern (13 bp):
AGCTAGAAGACTG
Found at i:24055 original size:32 final size:32
Alignment explanation
Indices: 24014--24074 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
24004 TTTTTGAAAG
* * *
24014 TTTTAATTAAACTCTCCTTTTTTTAAAAAAAA
1 TTTTAATTAAACTCACATATTTTTAAAAAAAA
* *
24046 TTTTCATTAATCTCACATATTTTTAAAAA
1 TTTTAATTAAACTCACATATTTTTAAAAA
24075 TTGTAATCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (32 bp):
TTTTAATTAAACTCACATATTTTTAAAAAAAA
Found at i:37406 original size:59 final size:59
Alignment explanation
Indices: 37334--37452 Score: 202
Period size: 59 Copynumber: 2.0 Consensus size: 59
37324 AAGCCTTGAG
* ** *
37334 AGAATTCTATTGAATCCTTTGTCGTTGCAAGTTAGGCTGACTTAGGGGTTTTTGGGGCA
1 AGAATTCTATTGAATCCTTTATCGTTGCAAGTTAGGCTGACTTAGGCATGTTTGGGGCA
37393 AGAATTCTATTGAATCCTTTATCGTTGCAAGTTAGGCTGACTTAGGCATGTTTGGGGCA
1 AGAATTCTATTGAATCCTTTATCGTTGCAAGTTAGGCTGACTTAGGCATGTTTGGGGCA
37452 A
1 A
37453 AGAAACTGCC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (59 bp):
AGAATTCTATTGAATCCTTTATCGTTGCAAGTTAGGCTGACTTAGGCATGTTTGGGGCA
Found at i:42524 original size:59 final size:55
Alignment explanation
Indices: 42452--42565 Score: 174
Period size: 59 Copynumber: 2.0 Consensus size: 55
42442 AAGACTTGAG
* *
42452 GGAATTCTATTGAATCCTTTGTCGTTGCAAGTTAGACTGACTTAGGCGTTTTTGGGGCA
1 GGAATTCTATTGAATCCTTTATCGTTGCAAGTTAG---G-CTTAGGCATTTTTGGGGCA
42511 GGAATTCTATTGAATCCTTTATCGTTGCAAGTTAGGCTTAGGCATTTTTGGGGCA
1 GGAATTCTATTGAATCCTTTATCGTTGCAAGTTAGGCTTAGGCATTTTTGGGGCA
42566 AAGAAACTGC
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
55 18 0.34
56 1 0.02
59 34 0.64
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (55 bp):
GGAATTCTATTGAATCCTTTATCGTTGCAAGTTAGGCTTAGGCATTTTTGGGGCA
Found at i:43826 original size:47 final size:47
Alignment explanation
Indices: 43728--43852 Score: 126
Period size: 47 Copynumber: 2.7 Consensus size: 47
43718 CGATAAGTAC
* * * * *
43728 CTATACCATGGCCCATAGCCAAATCAAGGTAACTTATCCCGGAGTAC
1 CTATACCATGGCCCGTAGACAAATCAAGGTAACTCATCCCGGAATAA
** * * * *
43775 CTATATTAT-GCCTTGTAGACAAATCAAGGTAACTCCTCTCTGAATAA
1 CTATACCATGGCC-CGTAGACAAATCAAGGTAACTCATCCCGGAATAA
*
43822 CTATACCATGGCCCGTAGCCAAATCAAGGTA
1 CTATACCATGGCCCGTAGACAAATCAAGGTA
43853 TTATTCGCAC
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
46 3 0.05
47 55 0.90
48 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (47 bp):
CTATACCATGGCCCGTAGACAAATCAAGGTAACTCATCCCGGAATAA
Found at i:50844 original size:13 final size:13
Alignment explanation
Indices: 50822--50859 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
50812 CTTCTTATTC
*
50822 TTCTTCTTTTCTCT
1 TTCTTTTTTTCT-T
50836 TT-TTTTTTTCTT
1 TTCTTTTTTTCTT
50848 TTCTTTTTTTCT
1 TTCTTTTTTTCT
50860 GCTGCCCTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 3 0.14
13 17 0.77
14 2 0.09
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTCTTTTTTTCTT
Found at i:50855 original size:11 final size:11
Alignment explanation
Indices: 50813--50855 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
50803 TGTCCATTTC
*
50813 TTCTTATTCTT
1 TTCTTTTTCTT
50824 CTTCTTTTCTCTT
1 -TTCTTTT-TCTT
*
50837 TTTTTTTTCTT
1 TTCTTTTTCTT
50848 TTCTTTTT
1 TTCTTTTT
50856 TTCTGCTGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 11 0.41
12 12 0.44
13 4 0.15
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:50856 original size:12 final size:12
Alignment explanation
Indices: 50809--50856 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 12
50799 GGTATGTCCA
50809 TTTCTTCTTATTCT
1 TTTCTT-TT-TTCT
*
50823 TCTTCTTTTCTCT
1 T-TTCTTTTTTCT
50836 TTT-TTTTTTCT
1 TTTCTTTTTTCT
50847 TTTCTTTTTT
1 TTTCTTTTTT
50857 TCTGCTGCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
11 10 0.33
12 8 0.27
13 4 0.13
14 3 0.10
15 5 0.17
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTCTTTTTTCT
Found at i:52959 original size:6 final size:6
Alignment explanation
Indices: 52950--53034 Score: 62
Period size: 6 Copynumber: 14.2 Consensus size: 6
52940 TGAAAATTTT
* * ** * * *
52950 AGATAC AGATGC AGTTAC AGATGT AAATAC ATATAC ATATAC AGATAC
1 AGATAC AGATAC AGATAC AGATAC AGATAC AGATAC AGATAC AGATAC
* * * * *
52998 AGATAC AGGTGC AAATAC AGATGC AAATAC AGATAC A
1 AGATAC AGATAC AGATAC AGATAC AGATAC AGATAC A
53035 AATATAGACA
Statistics
Matches: 58, Mismatches: 21, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.47, C:0.15, G:0.16, T:0.21
Consensus pattern (6 bp):
AGATAC
Found at i:52980 original size:12 final size:12
Alignment explanation
Indices: 52952--53038 Score: 84
Period size: 12 Copynumber: 7.2 Consensus size: 12
52942 AAAATTTTAG
*
52952 ATACAGATGCAG
1 ATACAGATGCAA
* *
52964 TTACAGATGTAA
1 ATACAGATGCAA
* * *
52976 ATACATATACAT
1 ATACAGATGCAA
* *
52988 ATACAGATACAG
1 ATACAGATGCAA
*
53000 ATACAGGTGCAA
1 ATACAGATGCAA
53012 ATACAGATGCAA
1 ATACAGATGCAA
*
53024 ATACAGATACAA
1 ATACAGATGCAA
53036 ATA
1 ATA
53039 TAGACACAAA
Statistics
Matches: 60, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 60 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (12 bp):
ATACAGATGCAA
Found at i:53005 original size:36 final size:36
Alignment explanation
Indices: 52952--53034 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 36
52942 AAAATTTTAG
* * * * *
52952 ATACAGATGCAGTTACAGATGTAAATACATATACAT
1 ATACAGATACAGATACAGATGCAAATACAGATACAA
* *
52988 ATACAGATACAGATACAGGTGCAAATACAGATGCAA
1 ATACAGATACAGATACAGATGCAAATACAGATACAA
53024 ATACAGATACA
1 ATACAGATACA
53035 AATATAGACA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.22
Consensus pattern (36 bp):
ATACAGATACAGATACAGATGCAAATACAGATACAA
Found at i:53048 original size:24 final size:24
Alignment explanation
Indices: 52965--53049 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
52955 CAGATGCAGT
** * *
52965 TACAGATGTAAATACATATACATA
1 TACAGATACAAATACAGATACAAA
* * *
52989 TACAGATACAGATACAGGTGCAAA
1 TACAGATACAAATACAGATACAAA
*
53013 TACAGATGCAAATACAGATACAAA
1 TACAGATACAAATACAGATACAAA
* *
53037 TATAGACACAAAT
1 TACAGATACAAAT
53050 GTAAATACAT
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.51, C:0.15, G:0.13, T:0.21
Consensus pattern (24 bp):
TACAGATACAAATACAGATACAAA
Found at i:62216 original size:41 final size:41
Alignment explanation
Indices: 62171--62374 Score: 302
Period size: 41 Copynumber: 5.0 Consensus size: 41
62161 CATTTCGGAC
* *
62171 TATAAGTCTAACAGGCTAAGTGCCGGTGATCTGAACCAGGT
1 TATAAGCCTAACAGGCTAAGTGCCGGTGATCTGAATCAGGT
* * *
62212 TATAAGCCTAGA-AGGCTAAGTGCCGATTATCTGAATCAGGC
1 TATAAGCCTA-ACAGGCTAAGTGCCGGTGATCTGAATCAGGT
* * *
62253 TATAAGCCTAGCAAGCTAAGTGCCGGTGAACTGAATCAGGT
1 TATAAGCCTAACAGGCTAAGTGCCGGTGATCTGAATCAGGT
*
62294 TATAAGCCTAACAGGCTAAGTGCCGGTGATCTGAACCAGGT
1 TATAAGCCTAACAGGCTAAGTGCCGGTGATCTGAATCAGGT
*
62335 TATAAGCCTAACAGGCTAAGTGCCAGTGATCTGAATCAGG
1 TATAAGCCTAACAGGCTAAGTGCCGGTGATCTGAATCAGG
62375 CTAAATGCCA
Statistics
Matches: 144, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
41 143 0.99
42 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (41 bp):
TATAAGCCTAACAGGCTAAGTGCCGGTGATCTGAATCAGGT
Found at i:62374 original size:25 final size:25
Alignment explanation
Indices: 62346--62399 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
62336 ATAAGCCTAA
*
62346 CAGGCTAAGTGCCAGTGATCTGAAT
1 CAGGCTAAATGCCAGTGATCTGAAT
62371 CAGGCTAAATGCCAGTGATCTGAAT
1 CAGGCTAAATGCCAGTGATCTGAAT
62396 CAGG
1 CAGG
62400 TTATAAGCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (25 bp):
CAGGCTAAATGCCAGTGATCTGAAT
Found at i:62416 original size:66 final size:66
Alignment explanation
Indices: 62305--62442 Score: 222
Period size: 66 Copynumber: 2.1 Consensus size: 66
62295 ATAAGCCTAA
* *
62305 CAGGCTAAGTGCCGGTGATCTGAACCAGGTTATAAGCCTAACAGGCTAAGTGCCAGTGATCTGAA
1 CAGGCTAAATGCCAGTGATCTGAACCAGGTTATAAGCCTAACAGGCTAAGTGCCAGTGATCTGAA
62370 T
66 T
* ** *
62371 CAGGCTAAATGCCAGTGATCTGAATCAGGTTATAAGCCTGGCAGGCTAAGTGCCGGTGATCTGAA
1 CAGGCTAAATGCCAGTGATCTGAACCAGGTTATAAGCCTAACAGGCTAAGTGCCAGTGATCTGAA
62436 T
66 T
62437 CAGGCT
1 CAGGCT
62443 TTAAGCCTAA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (66 bp):
CAGGCTAAATGCCAGTGATCTGAACCAGGTTATAAGCCTAACAGGCTAAGTGCCAGTGATCTGAA
T
Found at i:62430 original size:41 final size:41
Alignment explanation
Indices: 62371--62468 Score: 144
Period size: 41 Copynumber: 2.4 Consensus size: 41
62361 TGATCTGAAT
* * **
62371 CAGGCTAAATGCCAGTGATCTGAATCAGG-TTATAAGCCTGG
1 CAGGCTAAGTGCCGGTGATCTGAATCAGGCTT-TAAGCCTAA
62412 CAGGCTAAGTGCCGGTGATCTGAATCAGGCTTTAAGCCTAA
1 CAGGCTAAGTGCCGGTGATCTGAATCAGGCTTTAAGCCTAA
62453 CAGGCTAAGTGCCGGT
1 CAGGCTAAGTGCCGGT
62469 AAATCTGTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
41 50 0.96
42 2 0.04
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (41 bp):
CAGGCTAAGTGCCGGTGATCTGAATCAGGCTTTAAGCCTAA
Found at i:62453 original size:107 final size:107
Alignment explanation
Indices: 62267--62465 Score: 328
Period size: 107 Copynumber: 1.9 Consensus size: 107
62257 AGCCTAGCAA
* *
62267 GCTAAGTGCCGGTGAACTGAATCAGGTTATAAGCCTAACAGGCTAAGTGCCGGTGATCTGAACCA
1 GCTAAATGCCAGTGAACTGAATCAGGTTATAAGCCTAACAGGCTAAGTGCCGGTGATCTGAACCA
62332 GGTTATAAGCCTAACAGGCTAAGTGCCAGTGATCTGAATCAG
66 GGTTATAAGCCTAACAGGCTAAGTGCCAGTGATCTGAATCAG
* ** *
62374 GCTAAATGCCAGTGATCTGAATCAGGTTATAAGCCTGGCAGGCTAAGTGCCGGTGATCTGAATCA
1 GCTAAATGCCAGTGAACTGAATCAGGTTATAAGCCTAACAGGCTAAGTGCCGGTGATCTGAACCA
62439 GGCTT-TAAGCCTAACAGGCTAAGTGCC
66 GG-TTATAAGCCTAACAGGCTAAGTGCC
62466 GGTAAATCTG
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
107 83 0.98
108 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (107 bp):
GCTAAATGCCAGTGAACTGAATCAGGTTATAAGCCTAACAGGCTAAGTGCCGGTGATCTGAACCA
GGTTATAAGCCTAACAGGCTAAGTGCCAGTGATCTGAATCAG
Found at i:62744 original size:36 final size:37
Alignment explanation
Indices: 62693--62770 Score: 95
Period size: 36 Copynumber: 2.1 Consensus size: 37
62683 TTACAAGTAT
*
62693 ATATGTGCATTTGGCACATGTAATTG-ATAAGTATAA
1 ATATATGCATTTGGCACATGTAATTGAATAAGTATAA
* * * * *
62729 ATATATGCTTTTGGCATATGTATTTGAATAATTATAG
1 ATATATGCATTTGGCACATGTAATTGAATAAGTATAA
62766 ATATA
1 ATATA
62771 AATGTATTCG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
36 22 0.63
37 13 0.37
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.41
Consensus pattern (37 bp):
ATATATGCATTTGGCACATGTAATTGAATAAGTATAA
Found at i:70625 original size:19 final size:19
Alignment explanation
Indices: 70593--70631 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
70583 AAAAATTAAA
*
70593 TTAAAAATTATTATAAGAAT
1 TTAAAAAATATTATAA-AAT
70613 TTAAAAAAT-TTATAAAAT
1 TTAAAAAATATTATAAAAT
70631 T
1 T
70632 GAAATTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 6 0.33
20 8 0.44
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
TTAAAAAATATTATAAAAT
Found at i:80889 original size:51 final size:51
Alignment explanation
Indices: 80777--80893 Score: 173
Period size: 51 Copynumber: 2.3 Consensus size: 51
80767 ACTTTTGATC
*
80777 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGGGACA
* * *
80828 AGCGGCAAGTGATAAGT-GATAGCTTTAGCTACACTTATCTGATCAGGGACA
1 AGTGACAAGTGATAAGTAG-TAGCTTCAGCTACACTTATCTGATCAGGGACA
*
80879 AGTGAAAAGTGATAA
1 AGTGACAAGTGATAA
80894 ATACGATCCG
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 1 0.02
51 57 0.98
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGGGACA
Found at i:82675 original size:19 final size:19
Alignment explanation
Indices: 82639--82732 Score: 101
Period size: 18 Copynumber: 5.1 Consensus size: 19
82629 AAACACGAGA
**
82639 TTTTGAAACACAATAATAAT
1 TTTTGAAA-ACACGAATAAT
82659 TTTTGAAAACACGAAT-AT
1 TTTTGAAAACACGAATAAT
82677 TTTTG-AAACACGAA-AAT
1 TTTTGAAAACACGAATAAT
82694 ATTTTGAAAACACGGAAT--T
1 -TTTTGAAAACAC-GAATAAT
82713 TTTTGAAAACACGAA-AAT
1 TTTTGAAAACACGAATAAT
82731 TT
1 TT
82733 GTCAAACACG
Statistics
Matches: 65, Mismatches: 2, Indels: 16
0.78 0.02 0.19
Matches are distributed among these distances:
17 14 0.22
18 27 0.42
19 13 0.20
20 11 0.17
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (19 bp):
TTTTGAAAACACGAATAAT
Found at i:82685 original size:17 final size:18
Alignment explanation
Indices: 82656--82732 Score: 111
Period size: 18 Copynumber: 4.3 Consensus size: 18
82646 ACACAATAAT
82656 AATTTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
*
82674 TATTTTTG-AAACACGAA
1 AATTTTTGAAAACACGAA
*
82691 AATATTTTGAAAACACGGA
1 AAT-TTTTGAAAACACGAA
*
82710 ATTTTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
82728 AATTT
1 AATTT
82733 GTCAAACACG
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
17 11 0.22
18 30 0.59
19 10 0.20
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.32
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:82698 original size:37 final size:38
Alignment explanation
Indices: 82623--82730 Score: 131
Period size: 36 Copynumber: 2.9 Consensus size: 38
82613 CTTTTTTTTG
*
82623 TTTTT-AAAACACG-AGA-TTTTGAAACAC-AATAATAA
1 TTTTTGAAAACACGAATATTTTTGAAACACGAA-AATAA
82658 TTTTTGAAAACACGAATATTTTTGAAACACGAAAAT-A
1 TTTTTGAAAACACGAATATTTTTGAAACACGAAAATAA
82695 -TTTTGAAAACACGGAAT-TTTTTGAAAACACGAAAAT
1 TTTTTGAAAACAC-GAATATTTTTG-AAACACGAAAAT
82731 TTGTCAAACA
Statistics
Matches: 66, Mismatches: 1, Indels: 10
0.86 0.01 0.13
Matches are distributed among these distances:
35 5 0.08
36 26 0.39
37 19 0.29
38 14 0.21
39 2 0.03
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.31
Consensus pattern (38 bp):
TTTTTGAAAACACGAATATTTTTGAAACACGAAAATAA
Found at i:82740 original size:54 final size:54
Alignment explanation
Indices: 82658--82761 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 54
82648 ACAATAATAA
* * *
82658 TTTTTGAAAACACGAATATTTTTGAAACACGAAAATATTTTGAAAACACGGAAT
1 TTTTTGAAAACACGAAAATTTGTCAAACACGAAAATATTTTGAAAACACGGAAT
** * *
82712 TTTTTGAAAACACGAAAATTTGTCAAACACGGGAGTTTTTTGAAAACACG
1 TTTTTGAAAACACGAAAATTTGTCAAACACGAAAATATTTTGAAAACACG
82762 ATAACATCAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.31
Consensus pattern (54 bp):
TTTTTGAAAACACGAAAATTTGTCAAACACGAAAATATTTTGAAAACACGGAAT
Found at i:82751 original size:36 final size:37
Alignment explanation
Indices: 82662--82762 Score: 129
Period size: 36 Copynumber: 2.8 Consensus size: 37
82652 TAATAATTTT
*
82662 TGAAAACAC-GAATATTTTTG-AAACACGAAAATATTT
1 TGAAAACACGGAAT-TTTTTGAAAACACGAAAATATTG
82698 TGAAAACACGGAATTTTTTGAAAACACGAAAAT-TTG
1 TGAAAACACGGAATTTTTTGAAAACACGAAAATATTG
* *
82734 T-CAAACACGGGAGTTTTTTGAAAACACGA
1 TGAAAACAC-GGAATTTTTTGAAAACACGA
82763 TAACATCAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
35 6 0.10
36 37 0.63
37 16 0.27
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.28
Consensus pattern (37 bp):
TGAAAACACGGAATTTTTTGAAAACACGAAAATATTG
Found at i:82823 original size:17 final size:17
Alignment explanation
Indices: 82795--82852 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
82785 GAGAAAATTT
82795 TTTTTTGAAAACACGAAC
1 TTTTTT-AAAACACGAAC
*
82813 TTTTTTCAAACACTGGAA-
1 TTTTTTAAAACAC--GAAC
*
82831 -TTTTGAAAACACGAAC
1 TTTTTTAAAACACGAAC
82847 TTTTTT
1 TTTTTT
82853 TTTAATTCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
15 3 0.09
17 20 0.62
18 6 0.19
19 3 0.09
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (17 bp):
TTTTTTAAAACACGAAC
Found at i:82942 original size:28 final size:28
Alignment explanation
Indices: 82911--82964 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
82901 AACAGGAATA
* * *
82911 TATTTTTTTGAAACACGGGAAATTTTAT
1 TATTATTTTCAAACACGAGAAATTTTAT
82939 TATTATTTTCAAACACGAGAAATTTT
1 TATTATTTTCAAACACGAGAAATTTT
82965 GAAGACACGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.44
Consensus pattern (28 bp):
TATTATTTTCAAACACGAGAAATTTTAT
Found at i:82974 original size:18 final size:17
Alignment explanation
Indices: 82944--83084 Score: 99
Period size: 17 Copynumber: 7.8 Consensus size: 17
82934 TTTATTATTA
* *
82944 TTTTCAAACACGAGAAA
1 TTTTGAAACACGAGAAT
82961 TTTTGAAGACACGA-AGAT
1 TTTTGAA-ACACGAGA-AT
*
82979 TTTTGAAACATGAGAAT
1 TTTTGAAACACGAGAAT
82996 TTTTGAAAACACGA-AATTTT
1 TTTTG-AAACACGAGAA---T
*
83016 TTTTAAAACACG-GAAGT
1 TTTTGAAACACGAGAA-T
*
83033 TTTTGAAACACAAGAAATTTT
1 TTTTGAAACACGAG-AA---T
*
83054 TTTTGAAAACACGAAAAT
1 TTTTG-AAACACGAGAAT
83072 TTTTGAAACACGA
1 TTTTGAAACACGA
83085 TTTTTTTTAA
Statistics
Matches: 100, Mismatches: 11, Indels: 26
0.73 0.08 0.19
Matches are distributed among these distances:
17 40 0.40
18 29 0.29
19 11 0.11
20 5 0.05
21 8 0.08
22 7 0.07
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (17 bp):
TTTTGAAACACGAGAAT
Found at i:82988 original size:35 final size:34
Alignment explanation
Indices: 82944--83016 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 34
82934 TTTATTATTA
*
82944 TTTTCAAACACGAGAAATTTTGAAGACACGAAGAT
1 TTTTCAAACACGAGAAATTTTGAAAACACGAA-AT
* * *
82979 TTTTGAAACATGAGAATTTTTGAAAACACGAAAT
1 TTTTCAAACACGAGAAATTTTGAAAACACGAAAT
83013 TTTT
1 TTTT
83017 TTTAAAACAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
34 6 0.18
35 28 0.82
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (34 bp):
TTTTCAAACACGAGAAATTTTGAAAACACGAAAT
Found at i:83035 original size:20 final size:19
Alignment explanation
Indices: 82995--83084 Score: 96
Period size: 19 Copynumber: 4.8 Consensus size: 19
82985 AACATGAGAA
82995 TTTTTGAAAACACGAAATT
1 TTTTTGAAAACACGAAATT
* * *
83014 TTTTTTAAAACACGGAA-G
1 TTTTTGAAAACACGAAATT
*
83032 TTTTTGAAACACAAGAAATTT
1 TTTTTGAAA-ACACGAAA-TT
*
83053 TTTTTGAAAACACGAAA-A
1 TTTTTGAAAACACGAAATT
83071 TTTTTG-AAACACGA
1 TTTTTGAAAACACGA
83085 TTTTTTTTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
17 8 0.14
18 14 0.24
19 21 0.36
20 7 0.12
21 9 0.15
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (19 bp):
TTTTTGAAAACACGAAATT
Found at i:83066 original size:39 final size:38
Alignment explanation
Indices: 82978--83082 Score: 135
Period size: 37 Copynumber: 2.8 Consensus size: 38
82968 GACACGAAGA
* *
82978 TTTTTG-AAACATGAGAATTTTTGAAA-ACACGAAATTT
1 TTTTTGAAAACACG-GAATTTTTGAAACACAAGAAATTT
83015 TTTTT-AAAACACGGAAGTTTTTGAAACACAAGAAATTT
1 TTTTTGAAAACACGGAA-TTTTTGAAACACAAGAAATTT
*
83053 TTTTTGAAAACACGAAAATTTTTGAAACAC
1 TTTTTGAAAACACG-GAATTTTTGAAACAC
83083 GATTTTTTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
36 3 0.05
37 20 0.33
38 15 0.25
39 20 0.33
40 2 0.03
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (38 bp):
TTTTTGAAAACACGGAATTTTTGAAACACAAGAAATTT
Found at i:83438 original size:22 final size:21
Alignment explanation
Indices: 83390--83444 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
83380 TGAAATTATT
*
83390 TAAATTTAAAATTAAATTAAA
1 TAAATTTAAAATTAAAATAAA
83411 TTAAATTTAAAATATAAAATACAA
1 -TAAATTTAAAAT-TAAAATA-AA
*
83435 -AAATATAAAA
1 TAAATTTAAAA
83445 ATGCATAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 21 0.72
23 6 0.21
24 2 0.07
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAATTTAAAATTAAAATAAA
Found at i:83709 original size:7 final size:7
Alignment explanation
Indices: 83697--83788 Score: 73
Period size: 7 Copynumber: 13.0 Consensus size: 7
83687 AATTTTTTTA
83697 TTTCTTT
1 TTTCTTT
83704 TTTCTTT
1 TTTCTTT
83711 TTTCTTT
1 TTTCTTT
*
83718 CTT-TTT
1 TTTCTTT
* *
83724 CTTCTTC
1 TTTCTTT
*
83731 CTTCTTT
1 TTTCTTT
83738 CTTTCTCTT
1 -TTTCT-TT
83747 TTTCTTT
1 TTTCTTT
*
83754 TTT-TTC
1 TTTCTTT
83760 TTTCTTCT
1 TTTCTT-T
83768 TTT-TCTT
1 TTTCT-TT
*
83775 CTTCTTT
1 TTTCTTT
83782 TTTCTTT
1 TTTCTTT
83789 CTTCCCCGTT
Statistics
Matches: 70, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
6 11 0.16
7 43 0.61
8 14 0.20
9 2 0.03
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTCTTT
Found at i:83724 original size:6 final size:6
Alignment explanation
Indices: 83697--83788 Score: 75
Period size: 6 Copynumber: 15.2 Consensus size: 6
83687 AATTTTTTTA
* * *
83697 TTTCTTT TTTCTT TTT-TC TTTCTT TTTCTT CTTCCTT CTTTCTT TCTCTT
1 TTTC-TT TTTCTT TTTCTT TTTCTT TTTCTT -TTTCTT -TTTCTT TTTCTT
*
83747 TTTC-- TTT-TT TTTCTT TCTTCTT TTTCTT CTTCTTT TTTCTT T
1 TTTCTT TTTCTT TTTCTT T-TTCTT TTTCTT TTTC-TT TTTCTT T
83789 CTTCCCCGTT
Statistics
Matches: 70, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
4 3 0.04
5 7 0.10
6 34 0.49
7 26 0.37
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTCTT
Found at i:83765 original size:45 final size:42
Alignment explanation
Indices: 83699--83786 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 42
83689 TTTTTTTATT
83699 TCTTTTTTCTTTTTTCTTTCTT-TTTCTTCTTCCTTCTTTCTTTC
1 TCTTTTTTCTTTTTTCTTTCTTCTTT-TTCTT-CTTCTTT-TTTC
*
83743 TCTTTTTCTTTTTTTTCTTTCTTCTTTTTCTTCTTCTTTTTTC
1 TCTTTTT-TCTTTTTTCTTTCTTCTTTTTCTTCTTCTTTTTTC
83786 T
1 T
83787 TTCTTCCCCG
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
43 5 0.12
44 14 0.34
45 19 0.46
46 3 0.07
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (42 bp):
TCTTTTTTCTTTTTTCTTTCTTCTTTTTCTTCTTCTTTTTTC
Found at i:83940 original size:17 final size:16
Alignment explanation
Indices: 83875--83941 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 16
83865 CGCTCCTCCC
* *
83875 TTTTCTTTCTCTTCTTT
1 TTTTTTTTCT-TTCTTG
*
83892 TCTTTTTTTCTTCCTTG
1 T-TTTTTTTCTTTCTTG
83909 TTTTTTCTTGC-TTCTTG
1 TTTTTT-TT-CTTTCTTG
83926 TTGTTTTTTCTTTCTT
1 TT-TTTTTTCTTTCTT
83942 TCTTTTTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
16 6 0.15
17 22 0.54
18 13 0.32
ACGTcount: A:0.00, C:0.19, G:0.06, T:0.75
Consensus pattern (16 bp):
TTTTTTTTCTTTCTTG
Found at i:83944 original size:21 final size:22
Alignment explanation
Indices: 83889--83945 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 22
83879 CTTTCTCTTC
*
83889 TTTTCTTTTTTTCTTCCTTGTT
1 TTTTCTTTCTTTCTTCCTTGTT
* *
83911 TTTTCTTGC-TTCTT-GTTGTT
1 TTTTCTTTCTTTCTTCCTTGTT
83931 TTTTCTTTCTTTCTT
1 TTTTCTTTCTTTCTT
83946 TTTTATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 13 0.43
21 10 0.33
22 7 0.23
ACGTcount: A:0.00, C:0.18, G:0.07, T:0.75
Consensus pattern (22 bp):
TTTTCTTTCTTTCTTCCTTGTT
Found at i:84376 original size:30 final size:30
Alignment explanation
Indices: 84335--84423 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
84325 GAAATTTTAA
* ** *
84335 TTTAGAAAAGTTTAGGGGTTGAACTGTAAT
1 TTTAGAAAAGTTTAGGGGTTAAAAGGCAAT
*
84365 TTTA-AGAAAGTTTGGGGGTTAAAAGGCAAT
1 TTTAGA-AAAGTTTAGGGGTTAAAAGGCAAT
* *
84395 TTTAGAAAAGTTTAGGGGTCAAAATGCAA
1 TTTAGAAAAGTTTAGGGGTTAAAAGGCAA
84424 AAAAAATAAG
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 1 0.02
30 47 0.96
31 1 0.02
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.31
Consensus pattern (30 bp):
TTTAGAAAAGTTTAGGGGTTAAAAGGCAAT
Found at i:87073 original size:26 final size:23
Alignment explanation
Indices: 87027--87081 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
87017 ACTTCATCTC
87027 TTTAT-ATATTTATTTTATAATTG
1 TTTATAATATTTATTTTATAA-TG
*
87050 TTTATAATATTTATATTATGTAATG
1 TTTATAATATTTAT-TT-TATAATG
87075 -TTATAAT
1 TTTATAAT
87082 TGTGATATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 5 0.18
24 15 0.54
25 4 0.14
26 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (23 bp):
TTTATAATATTTATTTTATAATG
Found at i:87525 original size:29 final size:30
Alignment explanation
Indices: 87481--87586 Score: 139
Period size: 29 Copynumber: 3.7 Consensus size: 30
87471 AGAAATTTGT
* *
87481 ATTTTGACCCCT-AACTTT-TTTAAATTTC
1 ATTTTGACCCCTAAACTTTCTTAAAATTAC
87509 ATTTTGACCCCTAAACTTTCTTAAAATTAC
1 ATTTTGACCCCTAAACTTTCTTAAAATTAC
* *
87539 ATTTT-AACCCTTAACTTTCTTAAAATTAC
1 ATTTTGACCCCTAAACTTTCTTAAAATTAC
*
87568 ATTTTGACCCC-AAATTTTC
1 ATTTTGACCCCTAAACTTTC
87587 CAAAATTTAC
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
28 12 0.18
29 39 0.57
30 17 0.25
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.44
Consensus pattern (30 bp):
ATTTTGACCCCTAAACTTTCTTAAAATTAC
Found at i:87597 original size:58 final size:58
Alignment explanation
Indices: 87481--87607 Score: 150
Period size: 58 Copynumber: 2.2 Consensus size: 58
87471 AGAAATTTGT
* * * *
87481 ATTTTGACCCCTAACTTTTTTAAATTTCATTTTGACCCCTAAACTTTCTTAAAATTAC
1 ATTTTAACCCCTAACTTTTTAAAATTACATTTTGACCCCTAAACTTTCTCAAAATTAC
* *
87539 ATTTTAACCCTTAACTTTCTTAAAATTACATTTTGACCCC-AAATTTTC-CAAAATTTAC
1 ATTTTAACCCCTAACTTT-TTAAAATTACATTTTGACCCCTAAACTTTCTCAAAA-TTAC
* *
87597 ACTTTATCCCC
1 ATTTTAACCCC
87608 AAAGGTTTTG
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
57 4 0.07
58 35 0.60
59 19 0.33
ACGTcount: A:0.31, C:0.24, G:0.02, T:0.43
Consensus pattern (58 bp):
ATTTTAACCCCTAACTTTTTAAAATTACATTTTGACCCCTAAACTTTCTCAAAATTAC
Found at i:87941 original size:9 final size:9
Alignment explanation
Indices: 87919--88013 Score: 64
Period size: 9 Copynumber: 10.6 Consensus size: 9
87909 TTTTGGTTAA
87919 AAATTAACC
1 AAATTAACC
* *
87928 GAATTAGCC
1 AAATTAACC
87937 AAATTAACC
1 AAATTAACC
* *
87946 GAATTACCC
1 AAATTAACC
* *
87955 GACTTAACC
1 AAATTAACC
* *
87964 GAATTACCC
1 AAATTAACC
* *
87973 GAATTACCC
1 AAATTAACC
*
87982 GAATTAACC
1 AAATTAACC
*
87991 GAATTAACC
1 AAATTAACC
*
88000 GAATTAACC
1 AAATTAACC
*
88009 TAATT
1 AAATT
88014 GAATCAAACA
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 74 1.00
ACGTcount: A:0.41, C:0.25, G:0.09, T:0.24
Consensus pattern (9 bp):
AAATTAACC
Found at i:87942 original size:18 final size:18
Alignment explanation
Indices: 87920--88005 Score: 127
Period size: 18 Copynumber: 4.8 Consensus size: 18
87910 TTTGGTTAAA
* *
87920 AATTAACCGAATTAGCCA
1 AATTAACCGAATTACCCG
87938 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
*
87956 ACTTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
* *
87974 AATTACCCGAATTAACCG
1 AATTAACCGAATTACCCG
87992 AATTAACCGAATTA
1 AATTAACCGAATTA
88006 ACCTAATTGA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.41, C:0.26, G:0.10, T:0.23
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:87956 original size:27 final size:27
Alignment explanation
Indices: 87920--88005 Score: 127
Period size: 27 Copynumber: 3.2 Consensus size: 27
87910 TTTGGTTAAA
* * *
87920 AATTAACCGAATTAGCCAAATTAACCG
1 AATTACCCGAATTAACCGAATTAACCG
* *
87947 AATTACCCGACTTAACCGAATTACCCG
1 AATTACCCGAATTAACCGAATTAACCG
87974 AATTACCCGAATTAACCGAATTAACCG
1 AATTACCCGAATTAACCGAATTAACCG
88001 AATTA
1 AATTA
88006 ACCTAATTGA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.41, C:0.26, G:0.10, T:0.23
Consensus pattern (27 bp):
AATTACCCGAATTAACCGAATTAACCG
Found at i:88137 original size:13 final size:13
Alignment explanation
Indices: 88119--88143 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88109 ATTGGGTTGG
88119 GTTGGGTAATTGA
1 GTTGGGTAATTGA
88132 GTTGGGTAATTG
1 GTTGGGTAATTG
88144 GGTTAGATTG
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:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (13 bp):
GTTGGGTAATTGA
Found at i:88530 original size:19 final size:20
Alignment explanation
Indices: 88489--88531 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
88479 ATAGCAACCA
* *
88489 AAAAATAAATAAATAGAAGC
1 AAAAATAAATAAAAAAAAGC
*
88509 AAAAA-AAATAAAAAAAATC
1 AAAAATAAATAAAAAAAAGC
88528 AAAA
1 AAAA
88532 CAGCAGCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.12
Consensus pattern (20 bp):
AAAAATAAATAAAAAAAAGC
Found at i:88803 original size:22 final size:22
Alignment explanation
Indices: 88778--88859 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 22
88768 AGGTCGAAGG
*
88778 GAAAGAAG-AAGAAGAGAAGAAA
1 GAAAGAAGAAAAAAGA-AAGAAA
88800 GAAAGAAGAAAAAAGAAAGAAA
1 GAAAGAAGAAAAAAGAAAGAAA
* **
88822 AAAAGAAAGAAAAGGGAAAG-AA
1 GAAAG-AAGAAAAAAGAAAGAAA
*
88844 -AAAGAA-AAAATAGAAA
1 GAAAGAAGAAAAAAGAAA
88860 AGGCGGTTGA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
19 8 0.15
20 2 0.04
21 4 0.08
22 20 0.38
23 18 0.35
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.01
Consensus pattern (22 bp):
GAAAGAAGAAAAAAGAAAGAAA
Found at i:88828 original size:30 final size:29
Alignment explanation
Indices: 88794--88859 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
88784 AGAAGAAGAG
88794 AAGAAAG-AAAGAAGAAAAAAGAAAGAAAAA
1 AAGAAAGAAAAG-AGAAAAAA-AAAGAAAAA
* *
88824 AAGAAAGAAAAGGGAAAGAAAAAGAAAAA
1 AAGAAAGAAAAGAGAAAAAAAAAGAAAAA
88853 ATAGAAA
1 A-AGAAA
88860 AGGCGGTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 10 0.31
30 18 0.56
31 4 0.12
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (29 bp):
AAGAAAGAAAAGAGAAAAAAAAAGAAAAA
Found at i:88831 original size:23 final size:23
Alignment explanation
Indices: 88778--88846 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 23
88768 AGGTCGAAGG
*
88778 GAAAGAAGAAGAAGAGAAGAAAGAAA
1 GAAAGAA-AA-AAGA-AAGAAAAAAA
88804 G-AAGAAAAAAGAAAGAAAAAAA
1 GAAAGAAAAAAGAAAGAAAAAAA
**
88826 GAAAGAAAAGGGAAAGAAAAA
1 GAAAGAAAAAAGAAAGAAAAA
88847 GAAAAAATAG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
22 10 0.26
23 21 0.54
24 2 0.05
25 5 0.13
26 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (23 bp):
GAAAGAAAAAAGAAAGAAAAAAA
Found at i:88841 original size:27 final size:26
Alignment explanation
Indices: 88811--88862 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
88801 AAAGAAGAAA
88811 AAAGAAAGAA-AAAAAGAAAGAAAAGGG
1 AAAGAAA-AAGAAAAA-AAAGAAAAGGG
*
88838 AAAGAAAAAGAAAAAATAGAAAAGG
1 AAAGAAAAAGAAAAAAAAGAAAAGG
88863 CGGTTGACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (26 bp):
AAAGAAAAAGAAAAAAAAGAAAAGGG
Found at i:88844 original size:4 final size:4
Alignment explanation
Indices: 88778--88833 Score: 59
Period size: 4 Copynumber: 15.0 Consensus size: 4
88768 AGGTCGAAGG
88778 GAAA G-AA G-AA G-AA GAGAA GAAA GAAA G-AA GAAA -AAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
*
88822 AAAA GAAA GAAA
1 GAAA GAAA GAAA
88834 AGGGAAAGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
3 15 0.33
4 27 0.59
5 4 0.09
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:88846 original size:12 final size:12
Alignment explanation
Indices: 88783--88848 Score: 61
Period size: 11 Copynumber: 5.8 Consensus size: 12
88773 GAAGGGAAAG
*
88783 AAGAAGAAGAG-
1 AAGAAAAAGAGA
88794 AAGAAAGAA-AG-
1 AAGAAA-AAGAGA
88805 AAGAAAAA-AGA
1 AAGAAAAAGAGA
*
88816 AAGAAAAAAAGA
1 AAGAAAAAGAGA
*
88828 AAG-AAAAGGGA
1 AAGAAAAAGAGA
88839 AAGAAAAAGA
1 AAGAAAAAGA
88849 AAAAATAGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
10 4 0.09
11 30 0.64
12 13 0.28
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AAGAAAAAGAGA
Found at i:88851 original size:26 final size:27
Alignment explanation
Indices: 88811--88862 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
88801 AAAGAAGAAA
88811 AAAGAAAGAAAAAAAGAA-AGAAAAGGG
1 AAAGAAAGAAAAAAA-AATAGAAAAGGG
*
88838 AAAGAAA-AAGAAAAAATAGAAAAGG
1 AAAGAAAGAAAAAAAAATAGAAAAGG
88863 CGGTTGACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 2 0.09
26 14 0.61
27 7 0.30
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (27 bp):
AAAGAAAGAAAAAAAAATAGAAAAGGG
Found at i:89105 original size:17 final size:17
Alignment explanation
Indices: 89083--89130 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
89073 AGGCCCGGTT
89083 GCAGCAGCCCAGCACCA
1 GCAGCAGCCCAGCACCA
* *
89100 GCAGCAGCCCTGCAGCA
1 GCAGCAGCCCAGCACCA
*
89117 GCGAGCAGGCCAGC
1 GC-AGCAGCCCAGC
89131 CCACGAAAGC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.25, C:0.42, G:0.31, T:0.02
Consensus pattern (17 bp):
GCAGCAGCCCAGCACCA
Found at i:89396 original size:16 final size:15
Alignment explanation
Indices: 89375--89408 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
89365 GTATTTATAT
89375 TTTTAATTTAATTCAA
1 TTTTAATTTAATT-AA
89391 TTTTAATTTAATTAA
1 TTTTAATTTAATTAA
89406 TTT
1 TTT
89409 CAATAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTAATTTAATTAA
Found at i:89709 original size:17 final size:17
Alignment explanation
Indices: 89686--89870 Score: 144
Period size: 17 Copynumber: 10.6 Consensus size: 17
89676 AAAAAAAGGA
89686 TCGTGTTTCAAAAATTT
1 TCGTGTTTCAAAAATTT
* *
89703 TCATGTTTTCAAAAATTC
1 TCGTG-TTTCAAAAATTT
89721 TCGTGTTTCAAAAAAATTT
1 TCGTGTTTC--AAAAATTT
89740 CTCGTGTTTC--AAATTT
1 -TCGTGTTTCAAAAATTT
* *
89756 TCATGTTTTCAAAAAATTC
1 TCGTG-TTTC-AAAAATTT
*
89775 TCGTGTTTCACAAA-TT
1 TCGTGTTTCAAAAATTT
* *
89791 TCTGTATTTTAAAAAATTT
1 TC-GT-GTTTCAAAAATTT
89810 TCGTGTTTCAAAAATTT
1 TCGTGTTTCAAAAATTT
* * *
89827 TTGTGCTTC-AAAATTC
1 TCGTGTTTCAAAAATTT
* **
89843 TCGTGTTTTAAAAAAAT
1 TCGTGTTTCAAAAATTT
*
89860 TCATGTTTCAA
1 TCGTGTTTCAA
89871 TCAGATCACG
Statistics
Matches: 131, Mismatches: 25, Indels: 24
0.73 0.14 0.13
Matches are distributed among these distances:
15 4 0.03
16 25 0.19
17 45 0.34
18 28 0.21
19 20 0.15
20 9 0.07
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (17 bp):
TCGTGTTTCAAAAATTT
Found at i:89725 original size:35 final size:34
Alignment explanation
Indices: 89686--89870 Score: 137
Period size: 35 Copynumber: 5.3 Consensus size: 34
89676 AAAAAAAGGA
*
89686 TCGTGTTTCAAAAATTTTCATGTTTTCAAAAATT
1 TCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATT
*
89720 CTCGTGTTTCAAAAAAATTTCTCGTG-TTTC-AAATTT
1 -TCGTGTTTC--AAAAATTT-TCGTGTTTTCAAAAATT
* * *
89756 TCATGTTTTCAAAAAATTCTCGTG-TTTCACAAATT
1 TCGTG-TTTC-AAAAATTTTCGTGTTTTCAAAAATT
* *
89791 TCTGTATTTTAAAAAATTTTCGTG-TTTCAAAAATTT
1 TC-GT-GTTTCAAAAATTTTCGTGTTTTCAAAAA-TT
* * * * *
89827 TTGTGCTTC-AAAATTCTCGTGTTTTAAAAAAAT
1 TCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATT
*
89860 TCATGTTTCAA
1 TCGTGTTTCAA
89871 TCAGATCACG
Statistics
Matches: 119, Mismatches: 21, Indels: 21
0.74 0.13 0.13
Matches are distributed among these distances:
33 18 0.15
34 20 0.17
35 49 0.41
36 16 0.13
37 12 0.10
38 4 0.03
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (34 bp):
TCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATT
Found at i:89776 original size:34 final size:34
Alignment explanation
Indices: 89691--89855 Score: 140
Period size: 35 Copynumber: 4.8 Consensus size: 34
89681 AAGGATCGTG
* * * *
89691 TTTC-AAAAATTTTCATGTTTTCAAAAATTCTCGTG
1 TTTCAAAAAATTCTCGTG-TTTCAAAATTTCT-GTA
*
89726 TTTCAAAAAAATTTCTCGTGTTTCAAATTTTCATGT-
1 TTTC-AAAAAA-TTCTCGTGTTTCAAAATTTC-TGTA
89762 TTTCAAAAAATTCTCGTGTTTCACAAATTTCTGTA
1 TTTCAAAAAATTCTCGTGTTTCA-AAATTTCTGTA
* * * *
89797 TTTTAAAAAATTTTCGTGTTTCAAAAATTTTTGTG
1 TTTCAAAAAATTCTCGTGTTTC-AAAATTTCTGTA
* *
89832 CTTC--AAAATTCTCGTGTTTTAAAA
1 TTTCAAAAAATTCTCGTGTTTCAAAA
89856 AAATTCATGT
Statistics
Matches: 110, Mismatches: 13, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
32 4 0.04
33 14 0.13
34 16 0.15
35 47 0.43
36 5 0.05
37 17 0.15
38 7 0.06
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.46
Consensus pattern (34 bp):
TTTCAAAAAATTCTCGTGTTTCAAAATTTCTGTA
Found at i:90448 original size:6 final size:6
Alignment explanation
Indices: 90437--90462 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
90427 GTTAGTCTAA
90437 AAATTT AAATTT AAATTT AAATTT AA
1 AAATTT AAATTT AAATTT AAATTT AA
90463 TAAATTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
AAATTT
Found at i:91617 original size:105 final size:105
Alignment explanation
Indices: 91433--91661 Score: 316
Period size: 105 Copynumber: 2.2 Consensus size: 105
91423 TCACTTGATA
* * * * *
91433 TTGTCATGTATAATACATTGGTTGATGCTCTTTGCAAGGAAGGAACGATTTCTAAAGCTGTAGAG
1 TTGTCACGTATAATACATTGGTTGATGCGCATTGCAAGGAAGGAACGATCTCTAAAGCAGTAGAG
91498 ATCGTTGACACAATGAGAAAGCAAGGCATTGAGCCTAATG
66 ATCGTTGACACAATGAGAAAGCAAGGCATTGAGCCTAATG
* * * * *
91538 TTGTCACGTACAATACATTGGTTGATGCGCATTGCAAGGAAGGTATGGTCTCTGAAGCAG-AGGA
1 TTGTCACGTATAATACATTGGTTGATGCGCATTGCAAGGAAGGAACGATCTCTAAAGCAGTA-GA
* * * *
91602 TATTGTTGACGCAATGATAAAGCAAGGCATTGAGCCTAATG
65 GATCGTTGACACAATGAGAAAGCAAGGCATTGAGCCTAATG
91643 TTGTCACGTATAATACATT
1 TTGTCACGTATAATACATT
91662 AGTTAATGGC
Statistics
Matches: 108, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
104 1 0.01
105 107 0.99
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (105 bp):
TTGTCACGTATAATACATTGGTTGATGCGCATTGCAAGGAAGGAACGATCTCTAAAGCAGTAGAG
ATCGTTGACACAATGAGAAAGCAAGGCATTGAGCCTAATG
Found at i:96324 original size:16 final size:15
Alignment explanation
Indices: 96288--96326 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
96278 TTACCCTAAA
96288 AATTAATTAAAAAAT
1 AATTAATTAAAAAAT
*
96303 ATATTATTTAAAAAATT
1 A-ATTAATTAAAAAA-T
96320 AATTAAT
1 AATTAAT
96327 AATTAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 1 0.05
16 17 0.85
17 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTAATTAAAAAAT
Found at i:97066 original size:16 final size:17
Alignment explanation
Indices: 97035--97068 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
97025 TAAATTTGAT
*
97035 TGAAAATATACCAAAAA
1 TGAAAACATACCAAAAA
97052 TGAAAACAT-CCAAAAA
1 TGAAAACATACCAAAAA
97068 T
1 T
97069 TCAAGATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.62, C:0.15, G:0.06, T:0.18
Consensus pattern (17 bp):
TGAAAACATACCAAAAA
Found at i:97457 original size:22 final size:23
Alignment explanation
Indices: 97424--97471 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
97414 TAGTTTACCC
* *
97424 TTTGAAATAAAA-ACATATTATT
1 TTTGAAATAAAATAAATAGTATT
97446 TTTGTAAA-AAAATAAATAGTATT
1 TTTG-AAATAAAATAAATAGTATT
97469 TTT
1 TTT
97472 TAAGTAAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (23 bp):
TTTGAAATAAAATAAATAGTATT
Found at i:99810 original size:21 final size:23
Alignment explanation
Indices: 99766--99812 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 23
99756 AAATTGTTAG
99766 TAAATATTATTATATTTATTAAT
1 TAAATATTATTATATTTATTAAT
99789 TAAAT-TTATT-TAATTT-TTAAT
1 TAAATATTATTAT-ATTTATTAAT
99810 TAA
1 TAA
99813 TTTTCAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 9 0.39
22 9 0.39
23 5 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TAAATATTATTATATTTATTAAT
Done.