Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold390
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: 51630
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2150 original size:2 final size:2
Alignment explanation
Indices: 2143--2175 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2133 AGGTGGGTGG
*
2143 GT GT GT GT GT GT GT GT GT GT GG GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
2176 GGTCATAGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.55, T:0.45
Consensus pattern (2 bp):
GT
Found at i:2176 original size:12 final size:12
Alignment explanation
Indices: 2139--2178 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
2129 GTGAAGGTGG
2139 GTGGGTGTGTGT
1 GTGGGTGTGTGT
2151 GT--GTGTGTGT
1 GTGGGTGTGTGT
2161 GTGGGTGTGTGT
1 GTGGGTGTGTGT
2173 GTGGGT
1 GTGGGT
2179 CATAGCATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.38
12 16 0.62
ACGTcount: A:0.00, C:0.00, G:0.57, T:0.42
Consensus pattern (12 bp):
GTGGGTGTGTGT
Found at i:6943 original size:21 final size:20
Alignment explanation
Indices: 6910--6954 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
6900 GCTTTAACAG
6910 AACTACTAATGTGGCAAGTT
1 AACTACTAATGTGGCAAGTT
* *
6930 AACTAGCTGATGTGGCCAGTT
1 AACTA-CTAATGTGGCAAGTT
6951 AACT
1 AACT
6955 TGCCACGTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (20 bp):
AACTACTAATGTGGCAAGTT
Found at i:8939 original size:21 final size:20
Alignment explanation
Indices: 8913--8957 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
8903 CTACGTGGCA
8913 AGTTAACTGGCCACATCAGC
1 AGTTAACTGGCCACATCAGC
**
8933 TAGTTAACTTTCCACATCAGC
1 -AGTTAACTGGCCACATCAGC
8954 AGTT
1 AGTT
8958 TTGTTAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (20 bp):
AGTTAACTGGCCACATCAGC
Found at i:9053 original size:30 final size:31
Alignment explanation
Indices: 8986--9054 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
8976 AAACTGTTAA
* * *
8986 TTAGTGACTGTTTTGTCACTTTTTTATAACG
1 TTAGTGACAGTTTTGTCACTTTTTCATAAAG
*
9017 TTAGTGACAGTTTTGTTA-TTTTTCA-AAAG
1 TTAGTGACAGTTTTGTCACTTTTTCATAAAG
9046 TTGAGTGAC
1 TT-AGTGAC
9055 TGAAATGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 5 0.15
30 12 0.36
31 16 0.48
ACGTcount: A:0.23, C:0.10, G:0.19, T:0.48
Consensus pattern (31 bp):
TTAGTGACAGTTTTGTCACTTTTTCATAAAG
Found at i:16801 original size:19 final size:17
Alignment explanation
Indices: 16769--16811 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
16759 TTACTTGTGC
*
16769 ATTTATGTTTTGAACTTG
1 ATTTATGTTATGAA-TTG
16787 ATTTGATGTTATGAATTG
1 ATTT-ATGTTATGAATTG
*
16805 AATTATG
1 ATTTATG
16812 ATAATACCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 3 0.14
18 10 0.45
19 9 0.41
ACGTcount: A:0.28, C:0.02, G:0.19, T:0.51
Consensus pattern (17 bp):
ATTTATGTTATGAATTG
Found at i:20432 original size:77 final size:77
Alignment explanation
Indices: 20305--20755 Score: 443
Period size: 77 Copynumber: 5.8 Consensus size: 77
20295 TAAAATTCTA
* * * * * * *
20305 AAACAAAATTAAGATCAATTCTGTTAAAC-ATCAGGATTAAAACCCGAAACA-AATTTATTTAAT
1 AAACAAAATCAAAATAAAATCTGTTAAACGAT-GGGAATAAATCCCGAAACAGAA-TTATTTAAT
*
20368 TAAATCTTATTTGG
64 TAAATCTTGTTTGG
* *
20382 AAACAAAATCAAAATAAAATCTGTTAAACGAAGGGAATAAATCCCGAAACAGAATTATTTAACTA
1 AAACAAAATCAAAATAAAATCTGTTAAACGATGGGAATAAATCCCGAAACAGAATTATTTAATTA
20447 AATCTTGTTTGG
66 AATCTTGTTTGG
* * * * * *
20459 AAACAAAATCAAAATAAAATATGTTAAACGGTGGGAATAAATCACAAAACAAAATTATTTGATTA
1 AAACAAAATCAAAATAAAATCTGTTAAACGATGGGAATAAATCCCGAAACAGAATTATTTAATTA
*
20524 AATATTGTTTGG
66 AATCTTGTTTGG
* * *
20536 AAACAAAATCAAAATAAAATCTGTTAAAC-AGCGGGAATAAATCCCTAAACAAAATTATTTAATT
1 AAACAAAATCAAAATAAAATCTGTTAAACGA-TGGGAATAAATCCCGAAACAGAATTATTTAATT
20600 AAATCTTCGTTTGG
65 AAATCTT-GTTTGG
* * * * * *
20614 AAATAAAATC-----AAAATCTATTAAATG-GGGAGAATAAATCCCGAAATAGAATTATTCAATT
1 AAACAAAATCAAAATAAAATCTGTTAAACGATGG-GAATAAATCCCGAAACAGAATTATTTAATT
* * *
20673 AATTCTTGCTTGA
65 AAATCTTGTTTGG
* * * *
20686 AAACAAAATCAAAATGGAATACAATCTGTTAAACGGTGAGAATAAACCCCGAAACAGATTTTATT
1 AAACAAAATCAAAAT---A-A-AATCTGTTAAACGATGGGAATAAATCCCGAAACAGA-ATTATT
20751 TAATT
60 TAATT
20756 TTAATTTTTA
Statistics
Matches: 310, Mismatches: 46, Indels: 30
0.80 0.12 0.08
Matches are distributed among these distances:
72 15 0.05
73 44 0.14
77 193 0.62
78 18 0.06
80 1 0.00
81 1 0.00
82 28 0.09
83 10 0.03
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (77 bp):
AAACAAAATCAAAATAAAATCTGTTAAACGATGGGAATAAATCCCGAAACAGAATTATTTAATTA
AATCTTGTTTGG
Found at i:33474 original size:31 final size:31
Alignment explanation
Indices: 33295--33473 Score: 227
Period size: 31 Copynumber: 5.8 Consensus size: 31
33285 ACAAATGACA
*
33295 AGTG-AAAGTGGTAGTTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
**
33325 AGTGAAAAGTGGTAGCTTTTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
*
33356 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
* * *
33387 AGTGAAAAATGGTAGC-TCCGACAACCTGATC
1 AGTGAAAAGTGGTAGCTTCAG-CTACCTGATC
* * *
33418 AGTGAAAAATGGTAGCTCCAGCTACATGATC
1 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
* *
33449 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCAGCTAC
33474 AAGTGACAAG
Statistics
Matches: 131, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
30 7 0.05
31 122 0.93
32 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
Found at i:33577 original size:47 final size:46
Alignment explanation
Indices: 33491--33613 Score: 138
Period size: 47 Copynumber: 2.7 Consensus size: 46
33481 AAGTGATTTC
* * * *
33491 CGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTA
1 CGTATAAGACCATGTCTGGGATATGGCATCAGTGAGATATATGATA
* * *
33537 CTGTATAAGACCATGTCTGGGATATGGCATCATTGAGATATGTGATT
1 C-GTATAAGACCATGTCTGGGATATGGCATCAGTGAGATATATGATA
* * * *
33584 CGTGTAAGACCATGACTGGGCTATGACATC
1 CGTATAAGACCATGTCTGGGATATGGCATC
33614 GATAAATGAA
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
46 26 0.40
47 39 0.60
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (46 bp):
CGTATAAGACCATGTCTGGGATATGGCATCAGTGAGATATATGATA
Found at i:35170 original size:18 final size:18
Alignment explanation
Indices: 35147--35182 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
35137 AGTTAAAAAA
*
35147 TATTTTATTAATTATTTT
1 TATTTTATTAATGATTTT
35165 TATTTTATTAATGATTTT
1 TATTTTATTAATGATTTT
35183 ATTAATGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TATTTTATTAATGATTTT
Found at i:38235 original size:16 final size:15
Alignment explanation
Indices: 38209--38243 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
38199 TGATGTGAAT
38209 AATATAAAATATTAA
1 AATATAAAATATTAA
*
38224 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
38240 AATA
1 AATA
38244 ATAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:38431 original size:20 final size:21
Alignment explanation
Indices: 38389--38431 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
38379 CCTTTTTTAG
* *
38389 AATAATAATTAAATATACGAA
1 AATAATAATTAAATACACAAA
*
38410 AATAAT-ATTATATACACAAA
1 AATAATAATTAAATACACAAA
38430 AA
1 AA
38432 GGTATATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (21 bp):
AATAATAATTAAATACACAAA
Found at i:39123 original size:13 final size:13
Alignment explanation
Indices: 39077--39127 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
39067 GAAAATGTAA
39077 TTTTTT-TTATAT
1 TTTTTTATTATAT
*
39089 TTGTTTTGTATATAT
1 TT-TTTTAT-TATAT
*
39104 ATTTTTATTATAT
1 TTTTTTATTATAT
39117 TTTTTTATTAT
1 TTTTTTATTAT
39128 GATGTATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 2 0.06
13 19 0.58
14 6 0.18
15 6 0.18
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.75
Consensus pattern (13 bp):
TTTTTTATTATAT
Found at i:39199 original size:18 final size:18
Alignment explanation
Indices: 39164--39217 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
39154 CGAAAAAACG
39164 AAAAA-AATAAA-AA-AT
1 AAAAATAATAAAGAAGAT
*
39179 AAAAATAA-AAATAAGAGT
1 AAAAATAATAAAGAAGA-T
39197 -AAAATAATAAAGAAGAT
1 AAAAATAATAAAGAAGAT
39214 AAAA
1 AAAA
39218 TCACCTTTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
15 8 0.25
16 4 0.12
17 9 0.28
18 11 0.34
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (18 bp):
AAAAATAATAAAGAAGAT
Found at i:39202 original size:17 final size:17
Alignment explanation
Indices: 39180--39218 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
39170 ATAAAAAATA
*
39180 AAAATAA-AAATAAGAGT
1 AAAATAATAAAGAAGA-T
39197 AAAATAATAAAGAAGAT
1 AAAATAATAAAGAAGAT
39214 AAAAT
1 AAAAT
39219 CACCTTTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (17 bp):
AAAATAATAAAGAAGAT
Found at i:39471 original size:27 final size:27
Alignment explanation
Indices: 39431--39488 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 27
39421 GGTTTCTTGG
39431 TTTTTTTTAGGGGGGGTTAGGTTTTTCC
1 TTTTTTTTA-GGGGGGTTAGGTTTTTCC
* *
39459 TTTTTTTT-TGGGGGTTAGGTTTTTTC
1 TTTTTTTTAGGGGGGTTAGGTTTTTCC
39485 TTTT
1 TTTT
39489 GGGGGACTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 20 0.71
28 8 0.29
ACGTcount: A:0.05, C:0.05, G:0.28, T:0.62
Consensus pattern (27 bp):
TTTTTTTTAGGGGGGTTAGGTTTTTCC
Found at i:40389 original size:92 final size:87
Alignment explanation
Indices: 40163--40415 Score: 238
Period size: 87 Copynumber: 2.8 Consensus size: 87
40153 ACTAGACATT
* * * * *
40163 AAAAACATAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAG
1 AAAAACAT-AATTGAAAATACCTCGGCATGTG-GCCGAGGCTCAACTCACCTCTCGCAATATGAG
***
40228 TTGATTTTTAAAACAAAATTTGTA
64 TTGATTTTTAAAACAAAATTAAAA
** * * ** * * *
40252 AAGCAGATTA-TGAAAATACCTCGATATGTGACCCGAAGCTCAACTCACCTCTCGTAATATGAGT
1 AAAAACATAATTGAAAATACCTCGGCATGTG-GCCGAGGCTCAACTCACCTCTCGCAATATGAGT
*
40316 TGATTTTTGCAAAGCATAAATTAAAA
65 TGATTTTT--AAAACA-AAATTAAAA
* *
40342 AAAAACATCAATTGAAAATACCTCGGCGTGTGGCCTGAGGCTCAACTCACCACTCGCAATATGAG
1 AAAAACAT-AATTGAAAATACCTCGGCATGTGGCC-GAGGCTCAACTCACCTCTCGCAATATGAG
*
40407 CTGATTTTT
64 TTGATTTTT
40416 TTTAAACACA
Statistics
Matches: 128, Mismatches: 30, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
87 52 0.41
88 1 0.01
89 10 0.08
90 11 0.09
91 3 0.02
92 51 0.40
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (87 bp):
AAAAACATAATTGAAAATACCTCGGCATGTGGCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTTTAAAACAAAATTAAAA
Found at i:40560 original size:76 final size:74
Alignment explanation
Indices: 40437--40578 Score: 221
Period size: 76 Copynumber: 1.9 Consensus size: 74
40427 AAATTGAAGA
*
40437 ACAGAAATGGAAAACACCTCAGCGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTT
1 ACAGAAATGGAAAACACCTCAGCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTT
40502 TTTTGAAAG
66 TTTTGAAAG
* * * *
40511 ACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
1 ACAGAAATGGAAAACACCTC-A-GCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATT
40576 TTT
64 TTT
40579 GAAACTTAAC
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
74 18 0.30
75 1 0.02
76 42 0.69
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Consensus pattern (74 bp):
ACAGAAATGGAAAACACCTCAGCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTT
TTTTGAAAG
Found at i:40648 original size:87 final size:81
Alignment explanation
Indices: 40606--40914 Score: 242
Period size: 92 Copynumber: 3.8 Consensus size: 81
40596 GCAGATTTTG
40606 AAAATACCTC-GATATGTGA-CTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA
1 AAAATACCTCAG-TATGTGATCTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA
40669 AAATATAAATTGAAAAA
65 AAATATAAATTGAAAAA
* *
40686 AAAATACCTCAGTGTGTGATCTGAA-GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGA
1 AAAATACCTCAGTATGTGATCTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGA
* * *
40750 AAGACAGAAATTG-----
64 AAAATATAAATTGAAAAA
* *** * * *
40763 AAAATAGCTCAGCGCGTGAGC-CAAGGCTCAACTCACCTCTCGTAATATGAGTCGATTTTTTTTG
1 AAAATACCTCAGTATGTGATCTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTG
** *
40827 AAAGGTAGAAATTGAAAAATGGAAA
63 AAAAATATAAATTG---AA---AAA
* ** *
40852 TTGAAAATACCTCGGCGTGTGATCT-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 ---AAAATACCTCAGTATGTGATCTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
40915 TTGAAAGACA
Statistics
Matches: 187, Mismatches: 21, Indels: 33
0.78 0.09 0.14
Matches are distributed among these distances:
76 2 0.01
77 45 0.24
78 20 0.11
80 46 0.25
81 5 0.03
82 17 0.09
89 5 0.03
92 47 0.25
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (81 bp):
AAAATACCTCAGTATGTGATCTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
AATATAAATTGAAAAA
Found at i:40812 original size:77 final size:78
Alignment explanation
Indices: 40621--40844 Score: 260
Period size: 77 Copynumber: 2.9 Consensus size: 78
40611 ACCTCGATAT
* *
40621 GTGA-CTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAATATAAATTGAA
1 GTGAGCTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGATAGAAATTG--
* *
40683 AAAAAAATACCTCAGTGT
64 ---AAAATACCTCAGCGC
* * *
40701 GTGATCTGAA-GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAA
1 GTGAGCTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGATAGAAATTGAA
*
40765 AATAGCTCAGCGC
66 AATACCTCAGCGC
* * *
40778 GTGAGC-CAAGGCTCAACTCACCTCTCGTAATATGAGTCGATTTTTTTTGAAAGGTAGAAATTGA
1 GTGAGCTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAAGATAGAAATTGA
40842 AAA
65 AAA
40845 ATGGAAATTG
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
76 2 0.02
77 45 0.36
78 24 0.19
80 34 0.27
81 4 0.03
82 17 0.13
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (78 bp):
GTGAGCTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGATAGAAATTGAA
AATACCTCAGCGC
Found at i:40886 original size:169 final size:169
Alignment explanation
Indices: 40686--41162 Score: 719
Period size: 169 Copynumber: 2.8 Consensus size: 169
40676 AATTGAAAAA
* * *
40686 AAAATACCTCAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
1 AAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
*
40751 AGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGTAATATGAGTC
66 AGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTC
* *
40816 GATTTTTTTTGAAAGGTAGAAATTGAAAAATGGAAATTG
131 GATTTTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTG
40855 AAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
1 AAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
* *
40920 AGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTTAACTCACCCCTCGCAATATGAGTC
66 AGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTC
40985 GATTTTTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTG
131 GA-TTTTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTG
* * * *
41025 AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCGCTCGCAATACGAGTTGATTTTTTTTTT
1 AAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTT
* * * * *
41090 GACA-ACAGAAATTGAAATTACCTCA--GCGT-ATCCTGAGGCTCAACTCACCTCTCGCAATATG
63 GAAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATG
*
41151 AGTTGATTTTTT
127 AGTCGATTTTTT
41163 AAAATACCTC
Statistics
Matches: 283, Mismatches: 20, Indels: 10
0.90 0.06 0.03
Matches are distributed among these distances:
169 135 0.48
170 119 0.42
172 19 0.07
173 10 0.04
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (169 bp):
AAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAA
AGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTC
GATTTTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTG
Found at i:40891 original size:249 final size:239
Alignment explanation
Indices: 40470--41014 Score: 614
Period size: 249 Copynumber: 2.2 Consensus size: 239
40460 GTCTTGAGGT
*
40470 TCAACTCACCTCTCGCAATATGAGCTGATTTTTTTTGAAAGACAGAAATTGAAAATACCTCAACG
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAGACAGAAATTGAAAATACCTCAACG
* ** * * * *
40535 TGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACTTAACTTGAAAAGCAG
66 TGGCTCAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTGAAACTGAAATTGAAAAACAG
** *
40600 ATTTTGAAAATACCTCGATATGTGACTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTT
131 AAATTGAAAATACCTCGACATGTGACTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
* * * * * *
40664 TTGAAAAATATAAATTGAAAAAAAAATACCTCAGTGTGTGATCTGAA-GC
196 TTGAAAAACAGAAATTG-----AAAATACCTCAGCGCGTGAGC-CAAGGC
* *
40713 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAAGACAGAAATTGAAAATAGCTCAGCG
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAGACAGAAATTGAAAATACCTCA--A
* *
40777 CGTGAGC-CAAGGCTCAACTCACCTCTCGTAATATGAGTCGATTTTTTTTGAAAGGTAGAAATTG
64 CGTG-GCTCAAGGCTCAACTCACCTCTCGCAATATGAGTCGA---TTTTTGAAA-CT-GAAATTG
** * * *
40841 AAAAATGGAAATTGAAAATACCTCGGCGTGTGA-TCTGAGGCTCAACTCACCTCTCGCAATATGA
123 AAAAACAGAAATTGAAAATACCTCGACATGTGACTC-AAGGCTCAACTCACCTCTCGCAATATGA
* *
40905 GTTGATTTTTTTGAAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGC
187 GTTGA-TTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGCCAAGGC
* * * *
40959 TTAACTCACCCCTCGCAATATGAGTCGATTTTTTTTTGAAAGGCAGAAATTGAAAA
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTTGAAAGACAGAAATTGAAAA
41015 ACGGAAATTG
Statistics
Matches: 256, Mismatches: 32, Indels: 23
0.82 0.10 0.07
Matches are distributed among these distances:
242 32 0.12
243 27 0.11
244 34 0.13
245 3 0.01
246 44 0.17
247 9 0.04
248 28 0.11
249 62 0.24
251 17 0.07
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (239 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAGACAGAAATTGAAAATACCTCAACG
TGGCTCAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTTTTGAAACTGAAATTGAAAAACAG
AAATTGAAAATACCTCGACATGTGACTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
TTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGCCAAGGC
Found at i:40903 original size:92 final size:91
Alignment explanation
Indices: 40756--40935 Score: 261
Period size: 92 Copynumber: 2.0 Consensus size: 91
40746 TTGAAAGACA
* *
40756 GAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGTAATATGAGTCGATTT
1 GAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTCGA-TT
**
40821 TTTTTGAAAGGTAGAAATTGAAAAATG
65 TTTTTGAAAGACAGAAATTGAAAAATG
* * * ** *
40848 GAAATTGAAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 GAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTT
40913 TTTTGAAAGACAGAAATTGAAAA
66 TTTTGAAAGACAGAAATTGAAAA
40936 TAGCTCAGCG
Statistics
Matches: 78, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
91 24 0.31
92 54 0.69
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (91 bp):
GAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTCGATTT
TTTTGAAAGACAGAAATTGAAAAATG
Found at i:40965 original size:77 final size:78
Alignment explanation
Indices: 40848--41014 Score: 228
Period size: 77 Copynumber: 2.1 Consensus size: 78
40838 TTGAAAAATG
* * * ** * *
40848 GAAATTGAAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TT
1 GAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCCCTCGCAATATGAGTCGATTT
40912 TTTTTGAAAGACA
66 TTTTTGAAAGACA
* *
40925 GAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTTAACTCACCCCTCGCAATATGAGTCGATTT
1 GAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCCCTCGCAATATGAGTCGA-TT
*
40990 TTTTTTGAAAGGCA
65 TTTTTTGAAAGACA
41004 GAAATTGAAAA
1 GAAATTGAAAA
41015 ACGGAAATTG
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
77 53 0.68
79 25 0.32
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (78 bp):
GAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCCCTCGCAATATGAGTCGATTT
TTTTTGAAAGACA
Found at i:41082 original size:93 final size:93
Alignment explanation
Indices: 40915--41106 Score: 237
Period size: 93 Copynumber: 2.1 Consensus size: 93
40905 GTTGATTTTT
* * * *
40915 TTGAAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTTAACTCACCCCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCCCTCGCAATAC
40980 GAGTCGA-TTTTTTTTTGA-AAGGCAGAAA
66 GAGTCGATTTTTTTTTTGACAA--CAGAAA
* * * * * *
41008 TTGAAAAACGGAAATTGAAAATACCTCGGCGTGTGA-CCTGAGGCTCAACTCGCCGCTCGCAATA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGCC-AAGGCTCAACTCACCCCTCGCAATA
*
41072 CGAGTTGATTTTTTTTTTGACAACAGAAA
65 CGAGTCGATTTTTTTTTTGACAACAGAAA
41101 TTGAAA
1 TTGAAA
41107 TTACCTCAGC
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
92 2 0.02
93 70 0.82
94 11 0.13
95 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (93 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCCCTCGCAATAC
GAGTCGATTTTTTTTTTGACAACAGAAA
Found at i:41147 original size:77 final size:78
Alignment explanation
Indices: 41018--41162 Score: 220
Period size: 77 Copynumber: 1.9 Consensus size: 78
41008 TTGAAAAACG
* * *
41018 GAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCGCTCGCAATACGAGTTGATTT
1 GAAATTGAAAATACCTCAGCGTAT-ACCTGAGGCTCAACTCACCGCTCGCAATACGAGTTGATTT
41083 TTTTTTTGACAACA
65 TTTTTTTGACAACA
* * *
41097 GAAATTGAAATTACCTCAGCGTAT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 GAAATTGAAAATACCTCAGCGTATACCTGAGGCTCAACTCACCGCTCGCAATACGAGTTGATTTT
41161 TT
66 TT
41163 AAAATACCTC
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
77 39 0.65
79 21 0.35
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (78 bp):
GAAATTGAAAATACCTCAGCGTATACCTGAGGCTCAACTCACCGCTCGCAATACGAGTTGATTTT
TTTTTTGACAACA
Found at i:51102 original size:44 final size:44
Alignment explanation
Indices: 51023--51185 Score: 149
Period size: 44 Copynumber: 3.8 Consensus size: 44
51013 TATCATTATT
* * *
51023 TTTAGACGGCGTTTGTG-AGAAAAGTGCCGCTAAAGGTTATGATC
1 TTTAG-CGGCGTTTGTGAAAAAAAGCGCCGCTAAAGGTTATGGTC
*
51067 TTTAGCGGCGTTTGTGAAAAAAAGCCGCCGC-AAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGAAAAAAAG-CGCCGCTAAAGGTTATGGTC
* ** *
51111 TTTTAGCAGCGTTTGCT-TTAAAAAGCGCCGCTACA-G-TATGGTC
1 -TTTAGCGGCGTTTG-TGAAAAAAAGCGCCGCTAAAGGTTATGGTC
* * *
51154 TTTAGCGGCGTTTTTTAAAAAAA-CGCCCCTAA
1 TTTAGCGGCGTTTGTGAAAAAAAGCGCCGCTAA
51186 TTTTTGCAGC
Statistics
Matches: 98, Mismatches: 15, Indels: 15
0.77 0.12 0.12
Matches are distributed among these distances:
41 8 0.08
42 17 0.17
43 17 0.17
44 29 0.30
45 26 0.27
46 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (44 bp):
TTTAGCGGCGTTTGTGAAAAAAAGCGCCGCTAAAGGTTATGGTC
Done.