Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_264
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: 110808
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:114 original size:43 final size:43
Alignment explanation
Indices: 33--118 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
23 AAACAGTATA
* **
33 ATGCCAATGTCCCAGACGTGGTCTTACATGTAGTCACATATCG
1 ATGCCAATATCCCAGACGTGGTCTTACATGTAAACACATATCG
*
76 ATGCCACTATCCCAGACAG-GGTCTTAC-TCGTAAACACATATCG
1 ATGCCAATATCCCAGAC-GTGGTCTTACAT-GTAAACACATATCG
119 GAATCACATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
42 1 0.03
43 35 0.95
44 1 0.03
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (43 bp):
ATGCCAATATCCCAGACGTGGTCTTACATGTAAACACATATCG
Found at i:3033 original size:27 final size:27
Alignment explanation
Indices: 2959--3056 Score: 126
Period size: 27 Copynumber: 3.7 Consensus size: 27
2949 AGCTGAACCT
* *
2959 TTATGAGACAAAATGACTATTTTGCCC
1 TTATGTGATAAAATGACTATTTTGCCC
*
2986 TTATGTGGT-AAATGACTATTTTGCCC
1 TTATGTGATAAAATGACTATTTTGCCC
* *
3012 TCATGTGATAAAATGACGATTTTGCCC
1 TTATGTGATAAAATGACTATTTTGCCC
* *
3039 TTATGAGATAAACTGACT
1 TTATGTGATAAAATGACT
3057 GAAATACCCC
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
26 24 0.40
27 36 0.60
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (27 bp):
TTATGTGATAAAATGACTATTTTGCCC
Found at i:3077 original size:27 final size:27
Alignment explanation
Indices: 3047--3166 Score: 134
Period size: 27 Copynumber: 4.4 Consensus size: 27
3037 CCTTATGAGA
*
3047 TAAACTGACTGAAATACCCCTATAAGG
1 TAAAATGACTGAAATACCCCTATAAGG
* * * *
3074 TAAAATGACTGTAATACCCTTGTAGGG
1 TAAAATGACTGAAATACCCCTATAAGG
* * * *
3101 TGAAATGACTGTAATACCCCTGTAGGG
1 TAAAATGACTGAAATACCCCTATAAGG
*
3128 TAAAATGACT-ATAATACCCTTATAAGG
1 TAAAATGACTGA-AATACCCCTATAAGG
3155 TAAAATGACTGA
1 TAAAATGACTGA
3167 TTTGCCCTAT
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
27 78 0.99
28 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (27 bp):
TAAAATGACTGAAATACCCCTATAAGG
Found at i:3094 original size:54 final size:52
Alignment explanation
Indices: 3036--3166 Score: 154
Period size: 54 Copynumber: 2.4 Consensus size: 52
3026 GACGATTTTG
* *
3036 CCCTTATGAGATAAACTGACTGAAATACCCCTATAAGGTAAAATGACTGTAATA
1 CCCTTAT-AGGTAAA-TGACTGAAATACCCCTATAAGGTAAAATGACTATAATA
* * * *
3090 CCCTTGTAGGGTGAAATGACTGTAATACCCCTGTAGGGTAAAATGACTATAATA
1 CCCTTATA-GGT-AAATGACTGAAATACCCCTATAAGGTAAAATGACTATAATA
3144 CCCTTATAAGGTAAAATGACTGA
1 CCCTTAT-AGGT-AAATGACTGA
3167 TTTGCCCTAT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
53 1 0.02
54 60 0.92
55 4 0.06
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (52 bp):
CCCTTATAGGTAAATGACTGAAATACCCCTATAAGGTAAAATGACTATAATA
Found at i:24533 original size:30 final size:30
Alignment explanation
Indices: 24499--24556 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
24489 CCTTAACTCT
*
24499 AACTTTTGTAAAATTACAATTTTGCCCCTA
1 AACTTTTGCAAAATTACAATTTTGCCCCTA
* *
24529 AACTTTTGCATAATTACACTTTTGCCCC
1 AACTTTTGCAAAATTACAATTTTGCCCC
24557 AAAGCTCGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (30 bp):
AACTTTTGCAAAATTACAATTTTGCCCCTA
Found at i:33937 original size:28 final size:28
Alignment explanation
Indices: 33885--33996 Score: 163
Period size: 28 Copynumber: 4.0 Consensus size: 28
33875 GCACACCCAA
33885 TGCTATATAATC-AACTCGCACACTTAG
1 TGCTATATAATCAAACTCGCACACTTAG
33912 TGCTATATAATCAAACTCGCACACTTAG
1 TGCTATATAATCAAACTCGCACACTTAG
*
33940 TGCTACATAATCAAACTCGCACACTTAG
1 TGCTATATAATCAAACTCGCACACTTAG
* * * *
33968 TGCTGTACAATTTAAACCCGCACACTTAG
1 TGCTATATAA-TCAAACTCGCACACTTAG
33997 CGCCAATCTC
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 12 0.16
28 49 0.64
29 16 0.21
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.28
Consensus pattern (28 bp):
TGCTATATAATCAAACTCGCACACTTAG
Found at i:43660 original size:40 final size:45
Alignment explanation
Indices: 43611--43693 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 45
43601 CAAAATTTTG
*
43611 TTTTAAAAATTTAAAC-TT-TTC-TT-AAAAAACA-TATTTTTAT
1 TTTTAAAAATCTAAACTTTCTTCTTTAAAAAAACACTATTTTTAT
*
43651 TTTTCAAAATCTAAACTTTCTTCTTTAAAAAAACACTATTTTT
1 TTTTAAAAATCTAAACTTTCTTCTTTAAAAAAACACTATTTTT
43694 TCTTAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
40 14 0.39
41 2 0.06
42 3 0.08
43 2 0.06
44 8 0.22
45 7 0.19
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (45 bp):
TTTTAAAAATCTAAACTTTCTTCTTTAAAAAAACACTATTTTTAT
Found at i:43726 original size:138 final size:139
Alignment explanation
Indices: 43492--43767 Score: 364
Period size: 137 Copynumber: 2.0 Consensus size: 139
43482 AAATGATTTA
* *
43492 AAAAAACAGATTTTTATTTTTCAAAATCCGAACTTTCTCCCTTTTTTTAAAAAAAAAATTATTTT
1 AAAAAACAGATTTTTATTTTTCAAAATCCAAACTTTCT-CCTTTCTTTAAAAAAAAAATTATTTT
** * * *
43557 CTTAAAAATTAAAGCTTTTATTTTAAAATAGTTGAAAAAAAAATCAAAATTTTGTTTTAAAAATT
65 CTTAAAAATTAAAAATTTTACTTTAAAATAGTTG-AAAAAAAATCAAAACTTTGTTTAAAAAATT
43622 TAAACTTTTCTT
129 TAAA-TTTTCTT
* * *
43634 AAAAAACATATTTTTATTTTTCAAAATCTAAAC-TT-T-C-TTCTTTAAAAAAACACTATT-TTT
1 AAAAAACAGATTTTTATTTTTCAAAATCCAAACTTTCTCCTTTCTTTAAAAAAA-A-AATTATTT
* *
43694 TCTTAAAAATTAAAAATTTTACTTTGAAATAGTTGAAAAAAACTCAAAACTTTGTTTAAAAAATT
64 TCTTAAAAATTAAAAATTTTACTTTAAAATAGTTGAAAAAAAATCAAAACTTTGTTTAAAAAATT
43759 TAAATTTTC
129 TAAATTTTC
43768 CTTTCAAATA
Statistics
Matches: 120, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
136 5 0.04
137 43 0.36
138 36 0.30
139 3 0.03
140 1 0.01
141 2 0.02
142 30 0.25
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (139 bp):
AAAAAACAGATTTTTATTTTTCAAAATCCAAACTTTCTCCTTTCTTTAAAAAAAAAATTATTTTC
TTAAAAATTAAAAATTTTACTTTAAAATAGTTGAAAAAAAATCAAAACTTTGTTTAAAAAATTTA
AATTTTCTT
Found at i:44193 original size:3 final size:3
Alignment explanation
Indices: 44185--44247 Score: 54
Period size: 3 Copynumber: 20.7 Consensus size: 3
44175 GTAAAAAATG
* * * * *
44185 ATA ATA ATA ATA ATA ATA TTTA CTA ATA ATA ATA GTA ATA GTA ATG
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
44231 CTG ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
44248 TTGGGCCTTT
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
3 46 0.96
4 2 0.04
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:44603 original size:34 final size:34
Alignment explanation
Indices: 44558--44639 Score: 121
Period size: 34 Copynumber: 2.4 Consensus size: 34
44548 ATAAGTGATT
44558 CATTATGAAATGGTTGATCTTGTAAATTG-TATTG
1 CATTATGAAATGGTTGATCTTGTAAA-TGATATTG
*
44592 CATTATTAAATGGTTGATCTTGTAAATGATATTG
1 CATTATGAAATGGTTGATCTTGTAAATGATATTG
* *
44626 CACTATGAATTGGT
1 CATTATGAAATGGT
44640 AAGATACACA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 2 0.05
34 41 0.95
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (34 bp):
CATTATGAAATGGTTGATCTTGTAAATGATATTG
Found at i:44619 original size:16 final size:16
Alignment explanation
Indices: 44565--44619 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
44555 ATTCATTATG
44565 AAATGGTTGATCTTGT
1 AAATGGTTGATCTTGT
*
44581 AAATTGTATTGCAT-TAT-T
1 AAA-TG-GTTG-ATCT-TGT
44599 AAATGGTTGATCTTGT
1 AAATGGTTGATCTTGT
44615 AAATG
1 AAATG
44620 ATATTGCACT
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
15 3 0.10
16 13 0.42
17 4 0.13
18 8 0.26
19 3 0.10
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (16 bp):
AAATGGTTGATCTTGT
Found at i:46010 original size:21 final size:21
Alignment explanation
Indices: 45982--46024 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
45972 TTACATGGCC
45982 TGTTCACAAGGCCGTGT-CCT
1 TGTTCACAAGGCCGTGTGCCT
* *
46002 TGTTACACACGGGCGTGTGCCT
1 TGTT-CACAAGGCCGTGTGCCT
46024 T
1 T
46025 AGCCACACGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.14, C:0.28, G:0.28, T:0.30
Consensus pattern (21 bp):
TGTTCACAAGGCCGTGTGCCT
Found at i:47833 original size:41 final size:41
Alignment explanation
Indices: 47706--47891 Score: 252
Period size: 41 Copynumber: 4.6 Consensus size: 41
47696 CTTGCACAAG
* * * * * * *
47706 GCCTTCGGGTCTTAACCCGAATATGGTCAC-TAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
*
47746 GCCTTCGGGACTTAGCCCGGATATAGTCGC-TAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
* *
47786 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGCTTAGCACAAAA
47827 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
47868 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
47892 CATTCGAGTA
Statistics
Matches: 132, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
39 3 0.02
40 58 0.44
41 68 0.52
42 3 0.02
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (41 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAA
Found at i:47834 original size:81 final size:82
Alignment explanation
Indices: 47736--47889 Score: 249
Period size: 81 Copynumber: 1.9 Consensus size: 82
47726 ATATGGTCAC
* * *
47736 TAGCATAAATGCCTTCGGGACTTAGCCCGGATATAGTCGC-TAGCACAAATGCCTTC-GGATCTT
1 TAGCACAAAAGCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAAGCCTTCGGGA-CTT
*
47799 AGTCCGGATGTAGTCGCT
65 AGCCCGGATGTAGTCGCT
47817 TAGCACAAAAGCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAAGCCTTCGGGACTTA
1 TAGCACAAAAGCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAAGCCTTCGGGACTTA
47882 GCCCGGAT
66 GCCCGGAT
47890 ATCATTCGAG
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
81 38 0.57
82 26 0.39
83 3 0.04
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.24
Consensus pattern (82 bp):
TAGCACAAAAGCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAAGCCTTCGGGACTTA
GCCCGGATGTAGTCGCT
Found at i:54606 original size:43 final size:42
Alignment explanation
Indices: 54559--54726 Score: 228
Period size: 42 Copynumber: 4.0 Consensus size: 42
54549 CATAGTATCG
* * *
54559 TATCGATGCCAGTAGCCCAGCTATGGTCTTACATGTAATCTCA
1 TATCGATGCCA-TAGCCCAGATATGGTCTTACACGAAATCTCA
* * *
54602 TATCGATGCCAATAGCCTAGCTATGATCTTACACGAAATCTCA
1 TATCGATGCC-ATAGCCCAGATATGGTCTTACACGAAATCTCA
** *
54645 TATCGATGCCATATACCAAATATGGTCTTACACGAAATCTCA
1 TATCGATGCCATAGCCCAGATATGGTCTTACACGAAATCTCA
*
54687 TATCGATGCCATATCCCAGATATGGTCTTACACGAAATCT
1 TATCGATGCCATAGCCCAGATATGGTCTTACACGAAATCT
54727 TAGTAACCCT
Statistics
Matches: 112, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
42 64 0.57
43 47 0.42
44 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (42 bp):
TATCGATGCCATAGCCCAGATATGGTCTTACACGAAATCTCA
Found at i:59536 original size:36 final size:36
Alignment explanation
Indices: 59464--59533 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
59454 ATGATTAAAC
* *
59464 AATTCAATAATATATATAGTAAAAAATGTAAAAATT
1 AATTCAATAATATAAATAGTAAAAAATATAAAAATT
*
59500 AATTTAATAATATAAATAGTATATAAAA-ATAAAA
1 AATTCAATAATATAAATAGTA-A-AAAATATAAAA
59534 TTATTACTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 19 0.66
37 6 0.21
38 4 0.14
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (36 bp):
AATTCAATAATATAAATAGTAAAAAATATAAAAATT
Found at i:61675 original size:42 final size:43
Alignment explanation
Indices: 61575--61690 Score: 146
Period size: 43 Copynumber: 2.7 Consensus size: 43
61565 AGCTCGTACA
* *
61575 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCAAATATCG
1 ATGCCAACGTCCCAGACAG-GGTCTTACACGAAATCAAATATCG
* ** *
61618 ATGTCATTGTCCCAGACAGGGTCATACACGAAATCAAATA-CG
1 ATGCCAACGTCCCAGACAGGGTCTTACACGAAATCAAATATCG
*
61660 ATGCCAACGTCCCAGACATGGTCTTACACGA
1 ATGCCAACGTCCCAGACAGGGTCTTACACGA
61691 TAACACATGC
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
42 28 0.46
43 32 0.52
44 1 0.02
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACAGGGTCTTACACGAAATCAAATATCG
Found at i:69255 original size:43 final size:43
Alignment explanation
Indices: 69191--69331 Score: 121
Period size: 44 Copynumber: 3.3 Consensus size: 43
69181 GCACGTACAT
* * *
69191 CGTGGTCTTACATGT-CATCAAATATCGATTCC-ACTATCCCAAA
1 CGTGGTCTTACACGTAAATCAAATAT-GATGCCAAC-ATCCCAAA
* *
69234 CAG-GGTCTTACACG-AAATCAAATATGATGCCAACGTCCCAGA
1 C-GTGGTCTTACACGTAAATCAAATATGATGCCAACATCCCAAA
* * * *
69276 CGTGGTCTTACACGTAAATCATAAGT-CGACGCCAACGTTCCAAA
1 CGTGGTCTTACACGTAAATCA-AA-TATGATGCCAACATCCCAAA
69320 CGTGGTCTTACA
1 CGTGGTCTTACA
69332 TGATAACACA
Statistics
Matches: 82, Mismatches: 9, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
41 1 0.01
42 23 0.28
43 28 0.34
44 29 0.35
45 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (43 bp):
CGTGGTCTTACACGTAAATCAAATATGATGCCAACATCCCAAA
Found at i:69286 original size:42 final size:44
Alignment explanation
Indices: 69227--69331 Score: 128
Period size: 44 Copynumber: 2.4 Consensus size: 44
69217 GATTCCACTA
* *
69227 TCCCAAACAG-GGTCTTACACG-AAATCA-AA-TATGATGCCAACG
1 TCCCAAAC-GTGGTCTTACACGTAAATCATAAGT-CGACGCCAACG
*
69269 TCCCAGACGTGGTCTTACACGTAAATCATAAGTCGACGCCAACG
1 TCCCAAACGTGGTCTTACACGTAAATCATAAGTCGACGCCAACG
*
69313 TTCCAAACGTGGTCTTACA
1 TCCCAAACGTGGTCTTACA
69332 TGATAACACA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
41 1 0.02
42 18 0.33
43 6 0.11
44 28 0.52
45 1 0.02
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (44 bp):
TCCCAAACGTGGTCTTACACGTAAATCATAAGTCGACGCCAACG
Found at i:75586 original size:7 final size:7
Alignment explanation
Indices: 75574--75599 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
75564 GTTGAATGTA
75574 GGCTTTG
1 GGCTTTG
75581 GGCTTTG
1 GGCTTTG
75588 GGCTTTG
1 GGCTTTG
75595 GGCTT
1 GGCTT
75600 GTGGAGTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.15, G:0.42, T:0.42
Consensus pattern (7 bp):
GGCTTTG
Found at i:76450 original size:34 final size:34
Alignment explanation
Indices: 76406--76475 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
76396 ATTATGCAAT
76406 TGTTACTGTAATGGGCTAAGGCCCACACTGATAC
1 TGTTACTGTAATGGGCTAAGGCCCACACTGATAC
*
76440 TGTTATTGTAATGGGCTAAGGCCCACACTGATAC
1 TGTTACTGTAATGGGCTAAGGCCCACACTGATAC
76474 TG
1 TG
76476 GACTTTACTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (34 bp):
TGTTACTGTAATGGGCTAAGGCCCACACTGATAC
Found at i:85657 original size:29 final size:28
Alignment explanation
Indices: 85621--85698 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
85611 TCATGAGATT
85621 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
85651 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
85678 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
85699 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:85916 original size:174 final size:174
Alignment explanation
Indices: 85651--86012 Score: 697
Period size: 174 Copynumber: 2.1 Consensus size: 174
85641 AAATTGTACA
85651 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
85716 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTACCGAGTCGA
*
85781 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TCTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
*
85825 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
*
85890 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTATCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTACCGAGTCGA
85955 TCTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TCTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
85999 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
86013 CGGTTGATTA
Statistics
Matches: 184, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 184 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTACCGAGTCGA
TCTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:86096 original size:145 final size:145
Alignment explanation
Indices: 85850--86123 Score: 494
Period size: 145 Copynumber: 1.9 Consensus size: 145
85840 GTTTAAAGTA
*
85850 CATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATGTGTGCGAACCCAATATATATTTTCT
1 CATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATGTGTGCGAACCCAATATATATTTTCT
* * *
85915 ATAAATTATTTACATTAAGGGTGCGACCTTATCGAGTCGATCTTGGACAGCGGAAAAGGTAAGTG
66 ATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAATCTTGGACAGCGGAAAAGGTAAGTG
85980 TGCGAACTTGAAATG
131 TGCGAACTTGAAATG
85995 CATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATGTGTGCGAACCCAATATATATTTTCT
1 CATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATGTGTGCGAACCCAATATATATTTTCT
* *
86060 ATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAATTTTGGACAGCGGAAAAGGTAAGT
66 ATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAATCTTGGACAGCGGAAAAGGTAAGT
86124 ACCTTGAGTT
Statistics
Matches: 123, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
145 123 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (145 bp):
CATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATGTGTGCGAACCCAATATATATTTTCT
ATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAATCTTGGACAGCGGAAAAGGTAAGTG
TGCGAACTTGAAATG
Found at i:88622 original size:40 final size:39
Alignment explanation
Indices: 88578--88801 Score: 217
Period size: 40 Copynumber: 5.6 Consensus size: 39
88568 GCTCCTCGTT
*
88578 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGTTATAGTAATTCGCA
* *
88618 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGG-TTATAGTAATTCGCA
*
88658 CAAATGCCTTCGGGACTTAGCCCGG-AATTAGT-ATCTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGTTA-TAGTAAT-TCGCA
*
88698 CAAATGCCTTCGGATCTTAGTCCGGATT-TAGT-ATCTCGCA
1 CAAATGCCTTCGGA-CTTAGCCCGG-TTATAGTAAT-TCGCA
* * * * *
88738 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGA-CTTAGCCCGGTTATAGT-AATTCGCA
88779 CAAA-GCCTTCGGACTTAGCCCGG
1 CAAATGCCTTCGGACTTAGCCCGG
88802 ACATCATTCA
Statistics
Matches: 161, Mismatches: 13, Indels: 21
0.83 0.07 0.11
Matches are distributed among these distances:
39 14 0.09
40 136 0.84
41 10 0.06
42 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGACTTAGCCCGGTTATAGTAATTCGCA
Found at i:88679 original size:80 final size:78
Alignment explanation
Indices: 88578--88802 Score: 276
Period size: 80 Copynumber: 2.8 Consensus size: 78
88568 GCTCCTCGTT
* *
88578 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTC-GGACTTAGCCCGG
88643 ATTTAGTAACTCGCA
64 ATTTAGTAACTCGCA
* *
88658 CAAATGCCTTCGGGACTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGA-CTTAGCCCG
*
88722 GATTTAGTATCTCGCA
63 GATTTAGTAACTCGCA
* * * *
88738 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGACTTAGCCCG
88801 GA
63 GA
88803 CATCATTCAA
Statistics
Matches: 127, Mismatches: 11, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
79 19 0.15
80 98 0.77
81 9 0.07
82 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGACTTAGCCCGGAT
TTAGTAACTCGCA
Found at i:88787 original size:120 final size:119
Alignment explanation
Indices: 88578--88802 Score: 289
Period size: 120 Copynumber: 1.9 Consensus size: 119
88568 GCTCCTCGTT
88578 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
88643 ATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
66 ATATAGTAACTAGCACAAATGCCTTC-GGACTTAGCCCGGAATTAGTATCTCGCA
* * **
88698 CAAATGCCTTC-GGATCTTAGTCCGGATT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CAAATGCCTTCGGGA-CATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAAC
* *
88759 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGACTTAGCCCGGA
62 CCGGATATAGTAAC-TAGCACAAATGCCTTCGGACTTAGCCCGGA
88803 CATCATTCAA
Statistics
Matches: 92, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
119 22 0.24
120 60 0.65
121 10 0.11
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (119 bp):
CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTAGCACAAATGCCTTCGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:96683 original size:119 final size:120
Alignment explanation
Indices: 96477--96699 Score: 274
Period size: 119 Copynumber: 1.9 Consensus size: 120
96467 TCCTCGTTCA
* *
96477 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAACCCGGAT
* * * *
96542 TTAGTAACTCGCACGAATGCCTTTGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * **
96597 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCACACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCACACAAATGCCTTCGGGA-CTTAACCCGG
* * *
96659 ATATGGTCACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAAC-TAGCACGAAAGCCTTCGGGACTTAACCCGGA
96700 CATCATTCAA
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
118 4 0.05
119 66 0.76
120 17 0.20
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCACACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:96699 original size:40 final size:40
Alignment explanation
Indices: 96475--96699 Score: 260
Period size: 40 Copynumber: 5.7 Consensus size: 40
96465 GCTCCTCGTT
* *
96475 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
96515 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * * *
96555 CGAATGCCTTTGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
96595 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
96634 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
96675 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
96700 CATCATTCAA
Statistics
Matches: 159, Mismatches: 20, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
38 2 0.01
39 30 0.19
40 116 0.73
41 11 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:99639 original size:49 final size:49
Alignment explanation
Indices: 99582--99810 Score: 282
Period size: 49 Copynumber: 4.7 Consensus size: 49
99572 CTTATACGCA
*
99582 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
* * ** * *
99631 TAGTAGCCTGCACTTTGTACTACACACATGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCCGGTACACG
* * * * *
99681 TAGTAGCCTGCACTTAATACTACACACGTGATCGAAGTAT-CGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAATTATCCGGTACACG
* * * *
99730 TAGTAGCC-GCATTTAGTACTACACATGCGACCAATTATCCGGTACATG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
99778 TAGTAGCCTGCACTTAGTACTACACACGTGACC
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC
99811 TCACAATAGA
Statistics
Matches: 147, Mismatches: 29, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
47 6 0.04
48 32 0.22
49 64 0.44
50 44 0.30
51 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
Done.