Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2462
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: 42367
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:2725 original size:17 final size:17
Alignment explanation
Indices: 2703--2737 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2693 TGACCTTGAA
2703 TCATCAGGGGACAATTC
1 TCATCAGGGGACAATTC
2720 TCATCAGGGGACAATTC
1 TCATCAGGGGACAATTC
2737 T
1 T
2738 TGCAACCTTA
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:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (17 bp):
TCATCAGGGGACAATTC
Found at i:5734 original size:72 final size:67
Alignment explanation
Indices: 5587--5734 Score: 197
Period size: 72 Copynumber: 2.1 Consensus size: 67
5577 CGGGGATCAT
* * *
5587 CACTTAGCAACCTCGGGGGAATCAGCACATAGCAACCCTTTTCATTTCAAATATACAATGGATAT
1 CACTTAGCAACCTCGGAGGAATCAGCACATAGCAACCCTTTACATTTCAAAGATACAATGGATAT
5652 CG
66 CG
***
5654 CACTTAGCAACCCCTCGGAGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 CACTTAGCAA--CCTCGGAGGAATCAGCACATAGCAA--CCCTTT-ACATTTCAAAGATACAATG
5719 GATATCG
61 GATATCG
5726 CACTTAGCA
1 CACTTAGCA
5735 CCACCAATGA
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
67 10 0.14
69 24 0.34
71 6 0.09
72 30 0.43
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.24
Consensus pattern (67 bp):
CACTTAGCAACCTCGGAGGAATCAGCACATAGCAACCCTTTACATTTCAAAGATACAATGGATAT
CG
Found at i:5775 original size:25 final size:25
Alignment explanation
Indices: 5747--5795 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
5737 ACCAATGAAC
*
5747 CGGGGAATCAGCACTTAGCAACCCT
1 CGGGGAATCAGCACATAGCAACCCT
5772 CGGGGAATCAGCACATAGCAACCC
1 CGGGGAATCAGCACATAGCAACCC
5796 CTTTCACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.33, G:0.24, T:0.12
Consensus pattern (25 bp):
CGGGGAATCAGCACATAGCAACCCT
Found at i:5835 original size:101 final size:103
Alignment explanation
Indices: 5653--5872 Score: 347
Period size: 101 Copynumber: 2.1 Consensus size: 103
5643 AATGGATATC
5653 GCACTTAGCAACCCCTCGGAGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAA-CCCTCGGAGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
5718 GGATATCGCACTTAGCACCACCAATGAACCGGGGAATCA
65 GGATATCGCACATAGCACCACCAATAAACCGGGGAATCA
5757 GCACTTAGCAACCCTCGG-GGAATCAGCACATAGCAA-CCCCTTTCACATTTCAAAGATATGGTG
1 GCACTTAGCAACCCTCGGAGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
* *
5820 GATCA-CGCACATAGCACCACCCATAAATCGGGGAATCA
66 GAT-ATCGCACATAGCACCACCAATAAACCGGGGAATCA
**
5858 GCACACAGCAACCCT
1 GCACTTAGCAACCCT
5873 TTTATATACA
Statistics
Matches: 109, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
101 72 0.66
102 19 0.17
103 7 0.06
104 11 0.10
ACGTcount: A:0.32, C:0.31, G:0.19, T:0.18
Consensus pattern (103 bp):
GCACTTAGCAACCCTCGGAGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
GATATCGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:12685 original size:17 final size:18
Alignment explanation
Indices: 12663--12698 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
12653 ATACTCTGGT
*
12663 TTTTATTGTTTTAA-TGC
1 TTTTATTATTTTAACTGC
12680 TTTTATTATTTTAACTGC
1 TTTTATTATTTTAACTGC
12698 T
1 T
12699 ATGATTGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.19, C:0.08, G:0.08, T:0.64
Consensus pattern (18 bp):
TTTTATTATTTTAACTGC
Found at i:16075 original size:6 final size:6
Alignment explanation
Indices: 16064--16138 Score: 64
Period size: 6 Copynumber: 12.7 Consensus size: 6
16054 AATATATAAA
* * * *
16064 AAATTG AAATTG AAAGTTG -TATTG -AATTG AAATTC AATTTG AAATTC
1 AAATTG AAATTG AAA-TTG AAATTG AAATTG AAATTG AAATTG AAATTG
* * *
16111 AAATTG GAATTA AAAATG AAATTG AAAT
1 AAATTG AAATTG AAATTG AAATTG AAAT
16139 GAATTTATAT
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
5 7 0.13
6 43 0.81
7 3 0.06
ACGTcount: A:0.48, C:0.03, G:0.15, T:0.35
Consensus pattern (6 bp):
AAATTG
Found at i:16430 original size:17 final size:17
Alignment explanation
Indices: 16410--16450 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
16400 TGAAATTTGT
*
16410 ATTGAAATGAAATTCAA
1 ATTGAAAAGAAATTCAA
*
16427 ATTGAAAAGAAATTGAA
1 ATTGAAAAGAAATTCAA
16444 A-TGAAAA
1 ATTGAAAA
16451 CATATTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.59, C:0.02, G:0.15, T:0.24
Consensus pattern (17 bp):
ATTGAAAAGAAATTCAA
Found at i:16783 original size:25 final size:24
Alignment explanation
Indices: 16732--16798 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 24
16722 AGAAAAATTG
16732 AAATGAAATTCAAAT-AACATTAGAA
1 AAATGAAATTCAAATGAA-ATT-GAA
*
16757 AAATGAAATTCAAATGAAATTTAA
1 AAATGAAATTCAAATGAAATTGAA
*
16781 AAAT-AAATTGAAATGAAA
1 AAATGAAATTCAAATGAAA
16799 AAACATTGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
23 13 0.33
24 6 0.15
25 18 0.46
26 2 0.05
ACGTcount: A:0.61, C:0.04, G:0.09, T:0.25
Consensus pattern (24 bp):
AAATGAAATTCAAATGAAATTGAA
Found at i:16883 original size:132 final size:131
Alignment explanation
Indices: 16727--16987 Score: 355
Period size: 131 Copynumber: 2.0 Consensus size: 131
16717 AAAAAAGAAA
* * * *
16727 AATTGAAATGAAATTCAAATAACATTAG-AAAAATGAAATTCAAATGAAATTTAAAAATAAATTG
1 AATTGAAATGAAATTCAAAAAACATGAGAAAAAATAAAATTCAAATGAAATTT---AAGAAATTG
* *
16791 AAATGAAAAAACA-TTGACATGAGAAAAAAAATTTTAATTAAAAAAGAAAAAAAATGAAATGAAA
63 AAATGAAAAAAAATTTGACATGACAAAAAAAATTTTAATTAAAAAAGAAAAAAAATGAAATGAAA
16855 TTAG
128 TTAG
*
16859 AATTGAAATGAAATTCAAAAAACATGAGAAAAAATAAAATTCAAATGAACTTTAAGAAATTGAAA
1 AATTGAAATGAAATTCAAAAAACATGAGAAAAAATAAAATTCAAATGAAATTTAAGAAATTGAAA
** * * * * *
16924 TGAAAAAAAATTTGACATGACAAATGAAGTTTTAATTACAAAGGAAAAAAAGTTAAATGAAATT
66 TGAAAAAAAATTTGACATGACAAAAAAAATTTTAATTAAAAAAGAAAAAAAATGAAATGAAATT
16988 CAAATAACAT
Statistics
Matches: 113, Mismatches: 14, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
130 20 0.18
131 45 0.40
132 26 0.23
133 22 0.19
ACGTcount: A:0.59, C:0.05, G:0.11, T:0.25
Consensus pattern (131 bp):
AATTGAAATGAAATTCAAAAAACATGAGAAAAAATAAAATTCAAATGAAATTTAAGAAATTGAAA
TGAAAAAAAATTTGACATGACAAAAAAAATTTTAATTAAAAAAGAAAAAAAATGAAATGAAATTA
G
Found at i:16982 original size:114 final size:112
Alignment explanation
Indices: 16862--17208 Score: 348
Period size: 114 Copynumber: 3.2 Consensus size: 112
16852 AAATTAGAAT
16862 TGAAATGAAATTCAAAAAACATGAGAAAAAATAAAATTCAAATGAACTTTAAG-A-A-ATTGAAA
1 TGAAATGAAATTCAAAAAACATGAGAAAAAATAAAATTCAAATGAACTTTAAGAAGAGATTGAAA
*
16924 TGAAAAAAAATTTGACATGACAAATGAAGTTTTAATTACAAAGGAAAAAAAG
66 TGAAAAAAAAATTGACATGACAAATGAAGTTTTAATT---AA--AAAAAAAG
* * * ** *
16976 TTAAATGAAATTCAAATAACATGAGAAAACATGGAATTCAAATGAATTTTAAGAAGAGATTGAAA
1 TGAAATGAAATTCAAAAAACATGAGAAAAAATAAAATTCAAATGAACTTTAAGAAGAGATTGAAA
*
17041 TGAAAAAAAAATTGACATGACAAATGAGGTTTTAATTAAAAAAAAAG
66 TGAAAAAAAAATTGACATGACAAATGAAGTTTTAATTAAAAAAAAAG
* * * * * *
17088 TGAAATGAAATTC----AA-AT-TG---AAATAAAATTCAAATG-AC-ATGAGAAAAAAATGAAA
1 TGAAATGAAATTCAAAAAACATGAGAAAAAATAAAATTCAAATGAACTTTAAGAAGAGATTGAAA
* *
17142 TTGAAATTAAAAAAGTTAGACATGAGAAATAAAGTTTTAATT-AAAAAAAAG
66 -TGAAA--AAAAAA-TT-GACATGACAAATGAAGTTTTAATTAAAAAAAAAG
17193 TGAAATGAAATT-AAAA
1 TGAAATGAAATTCAAAA
17209 TTCAAATGAC
Statistics
Matches: 199, Mismatches: 22, Indels: 30
0.79 0.09 0.12
Matches are distributed among these distances:
101 12 0.06
102 6 0.03
103 13 0.07
104 6 0.03
105 23 0.12
106 22 0.11
107 2 0.01
108 2 0.01
112 20 0.10
114 49 0.25
115 1 0.01
116 1 0.01
117 42 0.21
ACGTcount: A:0.57, C:0.05, G:0.14, T:0.24
Consensus pattern (112 bp):
TGAAATGAAATTCAAAAAACATGAGAAAAAATAAAATTCAAATGAACTTTAAGAAGAGATTGAAA
TGAAAAAAAAATTGACATGACAAATGAAGTTTTAATTAAAAAAAAAG
Found at i:17110 original size:17 final size:17
Alignment explanation
Indices: 17088--17121 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17078 AAAAAAAAAG
*
17088 TGAAATGAAATTCAAAT
1 TGAAATAAAATTCAAAT
17105 TGAAATAAAATTCAAAT
1 TGAAATAAAATTCAAAT
17122 GACATGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.29
Consensus pattern (17 bp):
TGAAATAAAATTCAAAT
Found at i:17208 original size:17 final size:16
Alignment explanation
Indices: 17188--17258 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 16
17178 TTAATTAAAA
17188 AAAAGTGAAATGAAATT
1 AAAA-TGAAATGAAATT
* *
17205 AAAATTCAAATGACATT
1 AAAA-TGAAATGAAATT
*
17222 AGAAA-AAAATGAAATT
1 A-AAATGAAATGAAATT
* *
17238 CAAATGAAATTGAAATG
1 AAAATGAAA-TGAAATT
17255 AAAA
1 AAAA
17259 AAAATAAAGG
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
15 3 0.07
16 12 0.29
17 24 0.57
18 3 0.07
ACGTcount: A:0.61, C:0.04, G:0.13, T:0.23
Consensus pattern (16 bp):
AAAATGAAATGAAATT
Found at i:17243 original size:105 final size:105
Alignment explanation
Indices: 17034--17261 Score: 264
Period size: 105 Copynumber: 2.2 Consensus size: 105
17024 TTAAGAAGAG
* *
17034 ATTGAAATGAAAAAAAAATTGACATGACAAATGAGGTTTTAATTAAAAAAAAAGTGAAATGAAAT
1 ATTGAAATG--AAAAAAATTGACATGACAAATAAAGTTTTAATTAAAAAAAAAGTGAAATGAAAT
* * ** *
17099 TCAAATTGAAATAAAATTCAAATGACATGAGAAAAAAATGAA
64 TAAAATTCAAATAAAATTCAAAAAAAATGAGAAAAAAATGAA
* * *
17141 ATTGAAATTAAAAAAGTTAGACATGAGAAATAAAGTTTTAATT-AAAAAAAAGTGAAATGAAATT
1 ATTGAAATGAAAAAAATT-GACATGACAAATAAAGTTTTAATTAAAAAAAAAGTGAAATGAAATT
* * **
17205 AAAATTCAAATGACATT-AGAAAAAAATGA-AATTCAAATGAA
65 AAAATTCAAATAAAATTCA-AAAAAAATGAGAA-AAAAATGAA
17246 ATTGAAATGAAAAAAA
1 ATTGAAATGAAAAAAA
17262 ATAAAGGTTG
Statistics
Matches: 102, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
104 3 0.03
105 70 0.69
106 21 0.21
107 8 0.08
ACGTcount: A:0.59, C:0.04, G:0.13, T:0.24
Consensus pattern (105 bp):
ATTGAAATGAAAAAAATTGACATGACAAATAAAGTTTTAATTAAAAAAAAAGTGAAATGAAATTA
AAATTCAAATAAAATTCAAAAAAAATGAGAAAAAAATGAA
Found at i:17244 original size:11 final size:11
Alignment explanation
Indices: 17228--17257 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
17218 CATTAGAAAA
17228 AAATGAAATTC
1 AAATGAAATTC
*
17239 AAATGAAATTG
1 AAATGAAATTC
17250 AAATGAAA
1 AAATGAAA
17258 AAAAATAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.60, C:0.03, G:0.13, T:0.23
Consensus pattern (11 bp):
AAATGAAATTC
Found at i:17248 original size:38 final size:38
Alignment explanation
Indices: 17181--17255 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 38
17171 TAAAGTTTTA
*
17181 ATTAAAAAAAAGTGAAATGAAATTAAAATTCAAATGAC
1 ATTAAAAAAAAGTGAAATCAAATTAAAATTCAAATGAC
* *
17219 ATTAGAAAAAAA-TGAAATTCAAA-TGAAATTGAAATGA
1 ATTA-AAAAAAAGTGAAA-TCAAATTAAAATTCAAATGA
17256 AAAAAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 21 0.66
39 11 0.34
ACGTcount: A:0.60, C:0.04, G:0.12, T:0.24
Consensus pattern (38 bp):
ATTAAAAAAAAGTGAAATCAAATTAAAATTCAAATGAC
Found at i:17263 original size:27 final size:27
Alignment explanation
Indices: 17193--17263 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
17183 TAAAAAAAAG
* *
17193 TGAAATGAAATTAAAATTCAAATGACAT
1 TGAAATGAAA-AAAAATTCAAATGAAAT
*
17221 TAGAAA--AAAATGAAATTCAAATGAAAT
1 T-GAAATGAAAA-AAAATTCAAATGAAAT
17248 TGAAATGAAAAAAAAT
1 TGAAATGAAAAAAAAT
17264 AAAGGTTGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
26 4 0.11
27 22 0.63
28 5 0.14
29 4 0.11
ACGTcount: A:0.61, C:0.04, G:0.11, T:0.24
Consensus pattern (27 bp):
TGAAATGAAAAAAAATTCAAATGAAAT
Found at i:17577 original size:20 final size:20
Alignment explanation
Indices: 17552--17591 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17542 ACCTAATCAC
*
17552 CACCGCCATTAACTATCGTT
1 CACCGCCATTAACCATCGTT
*
17572 CACCGCCATTCACCATCGTT
1 CACCGCCATTAACCATCGTT
17592 TACTATCGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.40, G:0.10, T:0.28
Consensus pattern (20 bp):
CACCGCCATTAACCATCGTT
Found at i:20032 original size:83 final size:83
Alignment explanation
Indices: 19817--20053 Score: 253
Period size: 89 Copynumber: 2.8 Consensus size: 83
19807 AATAAAACAA
* * *
19817 ATATATAATTC-AAAAAAATAATAATAC-GCACCAAATTAAATTTACAGATACAAGAAAATACAA
1 ATATATAATTCGAACAACA-AATAATACAG-ACTAAATTAAATTTACAGATACAAGAAAATACAA
* * *
19880 ATATTCTAGAATATTAATAC
64 ACATTCTAAAAAATTAATAC
* *
19900 ATGAAAATATAAAATTTGAACAACAAATAATACAGACTAAATTAAATTTATAGATACAAGAAAAT
1 AT----ATAT--AATTCGAACAACAAATAATACAGACTAAATTAAATTTACAGATACAAGAAAAT
* *
19965 TCAAACATTTTAAAAAATTAATAC
60 ACAAACATTCTAAAAAATTAATAC
** * *
19989 ATATATAATTCGAACAACAAATAATACAGACTAAATTTTATTTACAGACACAAAAATAATACAAA
1 ATATATAATTCGAACAACAAATAATACAGACTAAATTAAATTTACAGATACAAGAA-AATACAAA
20054 AATCTTGAAT
Statistics
Matches: 128, Mismatches: 17, Indels: 17
0.79 0.10 0.10
Matches are distributed among these distances:
83 46 0.36
84 7 0.05
85 4 0.03
87 4 0.03
89 61 0.48
90 6 0.05
ACGTcount: A:0.56, C:0.11, G:0.05, T:0.27
Consensus pattern (83 bp):
ATATATAATTCGAACAACAAATAATACAGACTAAATTAAATTTACAGATACAAGAAAATACAAAC
ATTCTAAAAAATTAATAC
Found at i:22040 original size:5 final size:5
Alignment explanation
Indices: 22030--22091 Score: 124
Period size: 5 Copynumber: 12.4 Consensus size: 5
22020 TTATGTTTTA
22030 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
22080 ATTAT ATTAT AT
1 ATTAT ATTAT AT
22092 AAACTAAAGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 57 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:22924 original size:15 final size:15
Alignment explanation
Indices: 22876--22925 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
22866 TTTATCAAAT
22876 TTATATTGATTGAAA
1 TTATATTGATTGAAA
* *
22891 TCATTTTGATT-AAA
1 TTATATTGATTGAAA
22905 TTTATATTGATTGAAA
1 -TTATATTGATTGAAA
22921 TTATA
1 TTATA
22926 ATATATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 3 0.10
15 23 0.79
16 3 0.10
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (15 bp):
TTATATTGATTGAAA
Found at i:24265 original size:24 final size:22
Alignment explanation
Indices: 24222--24265 Score: 52
Period size: 24 Copynumber: 1.9 Consensus size: 22
24212 ATAAATATTG
* *
24222 AAAATTGAATTAAGGGCTGAAT
1 AAAATTGAATTAAAGCCTGAAT
24244 AAAATATGAGATTAAAGCCTGA
1 AAAAT-TGA-ATTAAAGCCTGA
24266 TGAGTCTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 3 0.17
24 10 0.56
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.25
Consensus pattern (22 bp):
AAAATTGAATTAAAGCCTGAAT
Found at i:25214 original size:67 final size:66
Alignment explanation
Indices: 25093--25313 Score: 295
Period size: 68 Copynumber: 3.3 Consensus size: 66
25083 AAAGAAATAC
* * * * *
25093 TCATTGCATACCTATTAAAAAATAGTC--AACATGTATATTAAAAAACAGTTATACACACTAACA
1 TCATTGCATGCATATTAAAAAATAGTCAAAATATGTATATTAAAAAACAGTCATACACACCAACA
25156 A
66 A
* *
25157 TAACTGCATGCATATTAAAAAATAGTCAATAATATGTATATTAAAAAACAGTCATACACACCAAC
1 TCATTGCATGCATATTAAAAAATAGTCAA-AATATGTATATTAAAAAACAGTCATACACACCAAC
25222 AA
65 AA
* * *
25224 TCATTGCATGCATATTAAAAAAATAGTTAACATCATGTATATTAAAAAACCA-TCATAGACACCA
1 TCATTGCATGCATATT-AAAAAATAGTCAAAAT-ATGTATATTAAAAAA-CAGTCATACACACCA
25288 ACAA
63 ACAA
25292 TCATTGCATGCATATTAAAAAA
1 TCATTGCATGCATATTAAAAAA
25314 CACTTATTAA
Statistics
Matches: 139, Mismatches: 12, Indels: 9
0.87 0.08 0.06
Matches are distributed among these distances:
64 23 0.17
67 56 0.40
68 58 0.42
69 2 0.01
ACGTcount: A:0.49, C:0.17, G:0.07, T:0.27
Consensus pattern (66 bp):
TCATTGCATGCATATTAAAAAATAGTCAAAATATGTATATTAAAAAACAGTCATACACACCAACA
A
Found at i:27003 original size:15 final size:15
Alignment explanation
Indices: 26982--27029 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
26972 AACTCTTATC
26982 CTATTAGACACATCA
1 CTATTAGACACATCA
* **
26997 CTTTTAGATGCATCA
1 CTATTAGACACATCA
**
27012 CTACCAGACACATCA
1 CTATTAGACACATCA
27027 CTA
1 CTA
27030 CTTGACATTC
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.35, C:0.29, G:0.08, T:0.27
Consensus pattern (15 bp):
CTATTAGACACATCA
Found at i:27522 original size:6 final size:6
Alignment explanation
Indices: 27504--27702 Score: 68
Period size: 6 Copynumber: 33.7 Consensus size: 6
27494 TATTAATAAC
* ** **
27504 AAAT-A AAACCA AAATCA AAAT-A ACCT-A A-ATCA AAATTG AAATCA
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
* ** * * * * * *
27548 AAATCG AAATTG AAATCG AAATCG AAATCC AAATCG AAATCG AAATCG
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
* * * * * * *
27596 AAATAAA AAATCA GAATCG AAATAAA AAAT-G AAATCA AAATCG AAATTA
1 AAAT-CA AAATCA AAATCA AAAT-CA AAATCA AAATCA AAATCA AAATCA
** ** * * * *
27645 AAATCA AAATTG AAAT-A GAAATTG AAATCA AAATCG AAATTA GAATCG
1 AAATCA AAATCA AAATCA -AAATCA AAATCA AAATCA AAATCA AAATCA
27693 AAATCA AAAT
1 AAATCA AAAT
27703 TGAGATCGAA
Statistics
Matches: 144, Mismatches: 42, Indels: 15
0.72 0.21 0.07
Matches are distributed among these distances:
4 1 0.01
5 14 0.10
6 121 0.84
7 8 0.06
ACGTcount: A:0.59, C:0.12, G:0.09, T:0.20
Consensus pattern (6 bp):
AAATCA
Found at i:27533 original size:15 final size:15
Alignment explanation
Indices: 27510--27539 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
27500 TAACAAATAA
27510 AACCAAAATCAAAAT
1 AACCAAAATCAAAAT
*
27525 AACCTAAATCAAAAT
1 AACCAAAATCAAAAT
27540 TGAAATCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.20, G:0.00, T:0.17
Consensus pattern (15 bp):
AACCAAAATCAAAAT
Found at i:27547 original size:12 final size:12
Alignment explanation
Indices: 27530--27724 Score: 122
Period size: 12 Copynumber: 16.8 Consensus size: 12
27520 AAAATAACCT
*
27530 AAATCAAAATTG
1 AAATCAAAATCG
27542 AAATCAAAATCG
1 AAATCAAAATCG
**
27554 AAATTGAAATCG
1 AAATCAAAATCG
* *
27566 AAATCGAAATCC
1 AAATCAAAATCG
*
27578 AAATCGAAATCG
1 AAATCAAAATCG
* **
27590 AAATCGAAATAAA
1 AAATCAAAAT-CG
*
27603 AAATCAGAATCG
1 AAATCAAAATCG
*
27615 AAATAAAAAAT-G
1 AAAT-CAAAATCG
27627 AAATCAAAATCG
1 AAATCAAAATCG
*
27639 AAAT-----T-A
1 AAATCAAAATCG
*
27645 AAATCAAAATTG
1 AAATCAAAATCG
*
27657 AAAT-AGAAATTG
1 AAATCA-AAATCG
27669 AAATCAAAATCG
1 AAATCAAAATCG
* *
27681 AAATTAGAATCG
1 AAATCAAAATCG
*
27693 AAATCAAAATTG
1 AAATCAAAATCG
* *
27705 AGATCGAAAT--
1 AAATCAAAATCG
27715 AAATCAAAAT
1 AAATCAAAAT
27725 AAATAGAAAT
Statistics
Matches: 145, Mismatches: 27, Indels: 24
0.74 0.14 0.12
Matches are distributed among these distances:
6 4 0.03
7 1 0.01
10 8 0.06
11 7 0.05
12 112 0.77
13 13 0.09
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.21
Consensus pattern (12 bp):
AAATCAAAATCG
Found at i:27557 original size:18 final size:18
Alignment explanation
Indices: 27530--27724 Score: 129
Period size: 18 Copynumber: 11.2 Consensus size: 18
27520 AAAATAACCT
* *
27530 AAATCAAAATTGAAATCA
1 AAATCGAAATCGAAATCA
* *
27548 AAATCGAAATTGAAATCG
1 AAATCGAAATCGAAATCA
* *
27566 AAATCGAAATCCAAATCG
1 AAATCGAAATCGAAATCA
*
27584 AAATCGAAATCGAAATAAA
1 AAATCGAAATCGAAAT-CA
27603 AAATC-AGAATCGAAAT--
1 AAATCGA-AATCGAAATCA
27619 AAA---AAAT-GAAATCA
1 AAATCGAAATCGAAATCA
**
27633 AAATCGAAATTAAAATCA
1 AAATCGAAATCGAAATCA
* * **
27651 AAATTGAAATAGAAATTG
1 AAATCGAAATCGAAATCA
* *
27669 AAATCAAAATCGAAATTA
1 AAATCGAAATCGAAATCA
* * **
27687 GAATCGAAATCAAAATTG
1 AAATCGAAATCGAAATCA
*
27705 AGATCGAAAT--AAATCA
1 AAATCGAAATCGAAATCA
27721 AAAT
1 AAAT
27725 AAATAGAAAT
Statistics
Matches: 143, Mismatches: 26, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
12 5 0.03
13 3 0.02
14 4 0.03
16 10 0.07
17 4 0.03
18 103 0.72
19 14 0.10
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.21
Consensus pattern (18 bp):
AAATCGAAATCGAAATCA
Found at i:28329 original size:22 final size:22
Alignment explanation
Indices: 28299--28341 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
28289 AGCACACGGT
* *
28299 AAATTGGTTTCAAATCAAAATA
1 AAATCGGTTGCAAATCAAAATA
28321 AAATCGGTTGCAAATCAAAAT
1 AAATCGGTTGCAAATCAAAAT
28342 CAACCTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.28
Consensus pattern (22 bp):
AAATCGGTTGCAAATCAAAATA
Found at i:29700 original size:20 final size:19
Alignment explanation
Indices: 29668--29705 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
29658 TCTTTTGGTA
29668 CTATTATTATTAATCTATTG
1 CTATTATTATTAA-CTATTG
29688 CTATT-TTATTTAACTATT
1 CTATTATTA-TTAACTATT
29706 TTAGGTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.58
Consensus pattern (19 bp):
CTATTATTATTAACTATTG
Found at i:42021 original size:43 final size:43
Alignment explanation
Indices: 41818--42154 Score: 168
Period size: 43 Copynumber: 7.7 Consensus size: 43
41808 AATCATCAGC
*
41818 CTTATCTTCACTGAGCAGGAGTGAAGCAGGCTATAA-ACCAGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTA-AATACCAGAT
* * * * ***
41861 CTTATCTTCA-TGAGCAGGAGTGAAGCAGATCGAATTTTGATGAAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAG-GCTAAATACCA-G-AT
* * * ** * * *
41906 CTTATCTCCAC-GTA-CCGGCGATGGAGCAGATTCCAATCATCAG-C
1 CTTATCTTCACTG-AGCAGGAG-TGGAGCAGGCT-AAAT-ACCAGAT
*
41950 CTTATCTTCACTGAGTAGGAGTGGAGCAGGCTAAATACCAGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATACCAGAT
* * * * * ***
41993 CTTATCTTCACTGAGCAGAAGTGAAGCAGATCGAATTTTGATGAAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAG-GCTAAATACCA-G-AT
* * * ** * *
42039 CTTATCTCCAC-GTA-CCGGCGATGGAGCAGATTCCAATCACCAG-C
1 CTTATCTTCACTG-AGCAGGAG-TGGAGCAGGCT-AAAT-ACCAGAT
* *
42083 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTATATACTAGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATACCAGAT
*
42126 CTTATCTTCACTGAGCAGGAGTGAAGCAG
1 CTTATCTTCACTGAGCAGGAGTGGAGCAG
42155 ATCAAATTTG
Statistics
Matches: 212, Mismatches: 60, Indels: 44
0.67 0.19 0.14
Matches are distributed among these distances:
42 27 0.13
43 72 0.34
44 46 0.22
45 30 0.14
46 34 0.16
47 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (43 bp):
CTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATACCAGAT
Found at i:42096 original size:133 final size:133
Alignment explanation
Indices: 41675--42163 Score: 813
Period size: 133 Copynumber: 3.7 Consensus size: 133
41665 GATTACAGAT
* *
41675 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGG-TAAATATAACAGATCTTATCTTCGC
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCT-AA-ATACCAGATCTTATCTTCAC
* *
41739 TGAGCAGGAGTGGAGCAGATCAAATTTTGGTGAATCTTATCTCCACGTACCGGCGATGGAGCAGA
64 TGAGCAGGAGTGAAGCAGATCAAATTTTGATGAATCTTATCTCCACGTACCGGCGATGGAGCAGA
41804 TTCCA
129 TTCCA
41809 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTATAA-ACCAGATCTTATCTTCA-T
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTA-AATACCAGATCTTATCTTCACT
*
41872 GAGCAGGAGTGAAGCAGATCGAATTTTGATGAATCTTATCTCCACGTACCGGCGATGGAGCAGAT
65 GAGCAGGAGTGAAGCAGATCAAATTTTGATGAATCTTATCTCCACGTACCGGCGATGGAGCAGAT
41937 TCCA
130 TCCA
* *
41941 ATCATCAGCCTTATCTTCACTGAGTAGGAGTGGAGCAGGCTAAATACCAGATCTTATCTTCACTG
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTAAATACCAGATCTTATCTTCACTG
* *
42006 AGCAGAAGTGAAGCAGATCGAATTTTGATGAATCTTATCTCCACGTACCGGCGATGGAGCAGATT
66 AGCAGGAGTGAAGCAGATCAAATTTTGATGAATCTTATCTCCACGTACCGGCGATGGAGCAGATT
42071 CCA
131 CCA
* * * *
42074 ATCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTATATACTAGATCTTATCTTCACTG
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTAAATACCAGATCTTATCTTCACTG
42139 AGCAGGAGTGAAGCAGATCAAATTT
66 AGCAGGAGTGAAGCAGATCAAATTT
42164 GGCGAGTCTT
Statistics
Matches: 337, Mismatches: 14, Indels: 9
0.94 0.04 0.03
Matches are distributed among these distances:
131 2 0.01
132 124 0.37
133 168 0.50
134 41 0.12
135 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (133 bp):
ATCATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTAAATACCAGATCTTATCTTCACTG
AGCAGGAGTGAAGCAGATCAAATTTTGATGAATCTTATCTCCACGTACCGGCGATGGAGCAGATT
CCA
Found at i:42176 original size:265 final size:266
Alignment explanation
Indices: 41675--42178 Score: 825
Period size: 265 Copynumber: 1.9 Consensus size: 266
41665 GATTACAGAT
*
41675 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGTAAATATAACAGATCTTATCTTCGCT
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGTAAATATAACAGATCTTATCTTCACT
* * *
41740 GAGCAGGAGTGGAGCAGATCAAATTTTGGTGAATCTTATCTCCACGTACCGGCGATGGAGCAGAT
66 GAGCAGAAGTGAAGCAGATCAAATTTTGATGAATCTTATCTCCACGTACCGGCGATGGAGCAGAT
*
41805 TCCAATCATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTATAAACCAGATCTTATCTTC
131 TCCAATCACCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTATAAACCAGATCTTATCTTC
* *
41870 ATGAGCAGGAGTGAAGCAGATCGAATTTTGATGAATCTTATCTCCACGTACCGGCGATGGAGCAG
196 ATGAGCAGGAGTGAAGCAGATCGAAATTTGACGAATCTTATCTCCACGTACCGGCGATGGAGCAG
41935 ATTCCA
261 ATTCCA
* * *
41941 ATCATCAGCCTTATCTTCACTGAGTAGGAGTGGAGCAGGCT-AA-ATACCAGATCTTATCTTCAC
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGG-TAAATATAACAGATCTTATCTTCAC
*
42004 TGAGCAGAAGTGAAGCAGATCGAATTTTGATGAATCTTATCTCCACGTACCGGCGATGGAGCAGA
65 TGAGCAGAAGTGAAGCAGATCAAATTTTGATGAATCTTATCTCCACGTACCGGCGATGGAGCAGA
* * *
42069 TTCCAATCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTATATACTAGATCTTATCTT
130 TTCCAATCACCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTATAAACCAGATCTTATCTT
* *
42134 CACTGAGCAGGAGTGAAGCAGATC-AAATTTGGCGAGTCTTATCTC
195 CA-TGAGCAGGAGTGAAGCAGATCGAAATTTGACGAATCTTATCTC
42179 TATATATCGC
Statistics
Matches: 220, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
265 159 0.72
266 60 0.27
267 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (266 bp):
ATCATCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGTAAATATAACAGATCTTATCTTCACT
GAGCAGAAGTGAAGCAGATCAAATTTTGATGAATCTTATCTCCACGTACCGGCGATGGAGCAGAT
TCCAATCACCAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTATAAACCAGATCTTATCTTC
ATGAGCAGGAGTGAAGCAGATCGAAATTTGACGAATCTTATCTCCACGTACCGGCGATGGAGCAG
ATTCCA
Done.