Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2097
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: 58251
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Found at i:6592 original size:42 final size:42
Alignment explanation
Indices: 6533--6668 Score: 165
Period size: 45 Copynumber: 3.2 Consensus size: 42
6523 TTCGAGCATA
6533 AGTGTGCGGGC-ATAAGTG-TCACGGATTGTGAGATTGGCACT
1 AGTGTGCGGGCAATAAGTGTTCACGG-TTGTGAGATTGGCACT
*
6574 AGTGTGCTGGCAATAAGTGTTCTCACGTGTTGTGAGATTGGC-CT
1 AGTGTGCGGGCAATAAGTG-T-TCACG-GTTGTGAGATTGGCACT
*
6618 AAGTGTGCGGGCAATAAG-GTTC-CGGTTGTGAGATTGCCAACT
1 -AGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTGGC-ACT
6660 AGTGTGCGG
1 AGTGTGCGG
6669 CTTGAAATGC
Statistics
Matches: 84, Mismatches: 3, Indels: 16
0.82 0.03 0.16
Matches are distributed among these distances:
40 13 0.15
41 21 0.25
42 11 0.13
43 1 0.01
44 3 0.04
45 34 0.40
46 1 0.01
ACGTcount: A:0.21, C:0.15, G:0.35, T:0.29
Consensus pattern (42 bp):
AGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTGGCACT
Found at i:10873 original size:47 final size:47
Alignment explanation
Indices: 10710--11245 Score: 880
Period size: 47 Copynumber: 11.3 Consensus size: 47
10700 GATTCGAATG
*
10710 ATATATATGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
10757 ATAT-TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--T
10805 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
*
10852 ATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--T
10901 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--T
10950 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
10997 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
11044 ATATATAGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 ATATAT-GTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
11092 ATATATGTGATAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
11138 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAATA-TGT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA-AGTGT
* * * * * * * *
11185 ATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGC
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
*
11232 ATAAATGTGATAAG
1 ATATATGTGATAAG
11246 TCCCGAAGGG
Statistics
Matches: 466, Mismatches: 14, Indels: 18
0.94 0.03 0.04
Matches are distributed among these distances:
46 87 0.19
47 190 0.41
48 53 0.11
49 136 0.29
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
Found at i:10905 original size:96 final size:94
Alignment explanation
Indices: 10710--11245 Score: 880
Period size: 96 Copynumber: 5.6 Consensus size: 94
10700 GATTCGAATG
*
10710 ATATATATGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT-TGTGATAAGGCCT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
10774 AATGGCCGATGTGATGAATGTGAAAGTGTAT
66 AATGGCCGATGTGATGAATGTGAAAGTG--T
*
10805 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
10870 AATGGCCGATGTGATGAATGTGAAAGTGTAT
66 AATGGCCGATGTGATGAATGTGAAAGTG--T
10901 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGC
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGC
10966 CTAATGGCCGATGTGATGAATGTGAAAGTGT
64 CTAATGGCCGATGTGATGAATGTGAAAGTGT
10997 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATAGTGATAAGGCC
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT-GTGATAAGGCC
11062 TAATGGCCGATGTGATGAATGTGAAAGTGT
65 TAATGGCCGATGTGATGAATGTGAAAGTGT
11092 ATATATGTGATAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
11156 AATGGCCGATGTGATGAATGTGAATA-TGT
66 AATGGCCGATGTGATGAATGTGAA-AGTGT
* * * * * * * * *
11185 ATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGATAAG
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
11246 TCCCGAAGGG
Statistics
Matches: 424, Mismatches: 11, Indels: 13
0.95 0.02 0.03
Matches are distributed among these distances:
93 56 0.13
94 73 0.17
95 112 0.26
96 137 0.32
98 46 0.11
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.29
Consensus pattern (94 bp):
ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCT
AATGGCCGATGTGATGAATGTGAAAGTGT
Found at i:12671 original size:43 final size:43
Alignment explanation
Indices: 12623--12721 Score: 198
Period size: 43 Copynumber: 2.3 Consensus size: 43
12613 TTGGTTTTCA
12623 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
12666 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
12709 GCACTAAGTGTGC
1 GCACTAAGTGTGC
12722 TAAAACTAAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.23, C:0.15, G:0.34, T:0.27
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:12732 original size:43 final size:43
Alignment explanation
Indices: 12623--12734 Score: 163
Period size: 43 Copynumber: 2.6 Consensus size: 43
12613 TTGGTTTTCA
**
12623 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGAAAATAAGTGTTCACGGTTGTGAGATTG
**
12666 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGAAAATAAGTGTTCACGGTTGTGAGATTG
*
12709 GCACTAAGTGTGC-TAAAACTAAGTGT
1 GCACTAAGTGTGCGGAAAA-TAAGTGT
12735 GCGAGTTTAA
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
42 2 0.03
43 63 0.97
ACGTcount: A:0.26, C:0.14, G:0.32, T:0.28
Consensus pattern (43 bp):
GCACTAAGTGTGCGGAAAATAAGTGTTCACGGTTGTGAGATTG
Found at i:13260 original size:36 final size:37
Alignment explanation
Indices: 13205--13280 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 37
13195 CCGAGCTCTA
* *
13205 AAGACCCGATGACTACGTGTGG-GATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
13241 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
13278 AAG
1 AAG
13281 GCTTCGTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
36 20 0.56
37 16 0.44
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:14999 original size:31 final size:31
Alignment explanation
Indices: 14956--15039 Score: 152
Period size: 31 Copynumber: 2.7 Consensus size: 31
14946 TTAGTCTTGA
14956 CATAT-ACTGGGCCGAAGCCTTTCCATAAAT
1 CATATCACTGGGCCGAAGCCTTTCCATAAAT
*
14986 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTCCATAAAT
15017 CATATCACTGGGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
15040 ACTGTAAAAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 5 0.10
31 47 0.90
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTCCATAAAT
Found at i:15315 original size:26 final size:26
Alignment explanation
Indices: 15249--15515 Score: 317
Period size: 26 Copynumber: 10.3 Consensus size: 26
15239 CTGGAGGCCT
*
15249 AGCCTCTTTT-AAT-AACTGGGGCAAA
1 AGCC-CTTTTCAATAAACTGGGGCATA
** *
15274 AGCCC-TTTCGGTAAACTGGGGCGTA
1 AGCCCTTTTCAATAAACTGGGGCATA
**
15299 AGCCCTTTTCAATAAACTAAGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
**
15325 AGCCCTTTTCGGTAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
15351 AG-CCTTTTCCAATAAACTGGGGCATA
1 AGCCCTTTT-CAATAAACTGGGGCATA
* *** *
15377 ATCCCTTTTTTGTAAACTGAGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
** *
15403 AAACCTTTCCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
15429 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
* * *
15455 AACTCTTTTCAATAAACTAGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
15481 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
15507 AGCCCTTTT
1 AGCCCTTTT
15516 GCACTTCCTC
Statistics
Matches: 201, Mismatches: 36, Indels: 9
0.82 0.15 0.04
Matches are distributed among these distances:
23 3 0.01
24 2 0.01
25 25 0.12
26 165 0.82
27 6 0.03
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.28
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:16698 original size:54 final size:53
Alignment explanation
Indices: 16534--16717 Score: 228
Period size: 54 Copynumber: 3.4 Consensus size: 53
16524 TGTAAATCCA
* * *
16534 GGGTATTTTGGTAATTTTACAAA-TTGAGGGTATTTCGGTAATTTCACAAACTAG
1 GGGTATTTCGGTAATTTTACAAACTAG-GGGTATTTTGGTAATTT-ACAAACTAG
*
16588 TGGTATTTCGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTCGGTAATTTTACAAACTAGGGGTATTTTGGTAA-TTTACAAACTAG
* **
16642 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTCTATCCTAC-AG
1 GGGTATTTCGGTAATTTTACAAACTAGGGGTATTTTGGTAATT-TA-CAAACTAG
* *
16696 GGGTATTTCAGTAATTTCACAA
1 GGGTATTTCGGTAATTTTACAA
16718 TCGAAGGTAA
Statistics
Matches: 115, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
53 2 0.02
54 105 0.91
55 8 0.07
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (53 bp):
GGGTATTTCGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTACAAACTAG
Found at i:16703 original size:27 final size:27
Alignment explanation
Indices: 16424--16684 Score: 249
Period size: 27 Copynumber: 9.6 Consensus size: 27
16414 CATCCTACAA
* * * * *
16424 GGGTGTTTTGGTAAATCTACAAACCAA
1 GGGTATTTTGGTAATTTTACAAACTAG
* ** *
16451 GGGTATTTTAGTAATTTTGTAAACTAA
1 GGGTATTTTGGTAATTTTACAAACTAG
* * * * *
16478 TGGTATTTCT-ATAATTTTTAGAAAGTCAA
1 GGGTATTT-TGGTAA-TTTTACAAACT-AG
* ** *
16507 GGGTATTTTTGTAATTTTGTAAATCCA-
1 GGGTATTTTGGTAATTTTACAAA-CTAG
*
16534 GGGTATTTTGGTAATTTTACAAA-TTG
1 GGGTATTTTGGTAATTTTACAAACTAG
* *
16560 AGGGTATTTCGGTAATTTCACAAACTAG
1 -GGGTATTTTGGTAATTTTACAAACTAG
* *
16588 TGGTATTTCGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
16615 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
16642 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACTAG
16669 GGGTATTTTGGTAATT
1 GGGTATTTTGGTAATT
16685 CTATCCTACA
Statistics
Matches: 196, Mismatches: 30, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
27 164 0.84
28 20 0.10
29 12 0.06
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACTAG
Found at i:16754 original size:27 final size:27
Alignment explanation
Indices: 16716--16901 Score: 158
Period size: 27 Copynumber: 6.9 Consensus size: 27
16706 GTAATTTCAC
*
16716 AATCGAAGGTAAAACGGTAATTTTGTA
1 AATCAAAGGTAAAACGGTAATTTTGTA
*
16743 AA-CTAAAGGTAAAATGGTAATTTTGTA
1 AATC-AAAGGTAAAACGGTAATTTTGTA
* * * *
16770 AATCGAGGGTAAAACGGTAATTCTATA
1 AATCAAAGGTAAAACGGTAATTTTGTA
* * * * *
16797 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCAAAGGTAAAACGGTAATTTTGTA
* * * *
16824 AATCAAGGGTAAAACGATAATTCTATA
1 AATCAAAGGTAAAACGGTAATTTTGTA
* * * *
16851 AATCGAGGGTAAAATGGTAATTCTGTA
1 AATCAAAGGTAAAACGGTAATTTTGTA
* * *
16878 AATCGAGGGTAAAATGGTAATTTT
1 AATCAAAGGTAAAACGGTAATTTT
16902 ACAAATTGAG
Statistics
Matches: 141, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 1 0.01
27 139 0.99
28 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (27 bp):
AATCAAAGGTAAAACGGTAATTTTGTA
Found at i:16784 original size:54 final size:54
Alignment explanation
Indices: 16716--16913 Score: 263
Period size: 54 Copynumber: 3.7 Consensus size: 54
16706 GTAATTTCAC
* * * * * *
16716 AATCGAAGGTAAAACGGTAATTTTGTAAA-CTAAAGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTATAAATC-GAGGGTAAAATGGTAATTCTGTA
*
16770 AATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTGTA
* *
16824 AATCAAGGGTAAAACGATAATTCTATAAATCGAGGGTAAAATGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTGTA
* * * *
16878 AATCGAGGGTAAAATGGTAATTTTACAAATTGAGGG
1 AATCGAGGGTAAAACGGTAATTCTATAAATCGAGGG
16914 CTTTTCAGTA
Statistics
Matches: 127, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
54 126 0.99
55 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.29
Consensus pattern (54 bp):
AATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTGTA
Found at i:16835 original size:81 final size:81
Alignment explanation
Indices: 16716--16899 Score: 253
Period size: 81 Copynumber: 2.3 Consensus size: 81
16706 GTAATTTCAC
* * * * * * * *
16716 AATCGAAGGTAAAACGGTAATTTTGTAAACTAAAGGTAAAATGGTAATTTTGTAAATCGAGGGTA
1 AATCGAGGGTAAAATGGTAATTCTATAAACTAAAGGTAAAACGATAATTCTATAAATCGAGGGTA
16781 AAACGGTAATTCTATA
66 AAACGGTAATTCTATA
*
16797 AATCGAGGGTAAAATGGTAATTCTATAAA-TCAAGGGTAAAACGATAATTCTATAAATCGAGGGT
1 AATCGAGGGTAAAATGGTAATTCTATAAACT-AAAGGTAAAACGATAATTCTATAAATCGAGGGT
* *
16861 AAAATGGTAATTCTGTA
65 AAAACGGTAATTCTATA
16878 AATCGAGGGTAAAATGGTAATT
1 AATCGAGGGTAAAATGGTAATT
16900 TTACAAATTG
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
80 1 0.01
81 90 0.99
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.29
Consensus pattern (81 bp):
AATCGAGGGTAAAATGGTAATTCTATAAACTAAAGGTAAAACGATAATTCTATAAATCGAGGGTA
AAACGGTAATTCTATA
Found at i:16907 original size:27 final size:27
Alignment explanation
Indices: 16750--16913 Score: 238
Period size: 27 Copynumber: 6.1 Consensus size: 27
16740 GTAAACTAAA
* *
16750 GGTAAAATGGTAATTTTGTAAATCGAG
1 GGTAAAATGGTAATTCTATAAATCGAG
*
16777 GGTAAAACGGTAATTCTATAAATCGAG
1 GGTAAAATGGTAATTCTATAAATCGAG
*
16804 GGTAAAATGGTAATTCTATAAATCAAG
1 GGTAAAATGGTAATTCTATAAATCGAG
* *
16831 GGTAAAACGATAATTCTATAAATCGAG
1 GGTAAAATGGTAATTCTATAAATCGAG
*
16858 GGTAAAATGGTAATTCTGTAAATCGAG
1 GGTAAAATGGTAATTCTATAAATCGAG
* * *
16885 GGTAAAATGGTAATTTTACAAATTGAG
1 GGTAAAATGGTAATTCTATAAATCGAG
16912 GG
1 GG
16914 CTTTTCAGTA
Statistics
Matches: 122, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 122 1.00
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.29
Consensus pattern (27 bp):
GGTAAAATGGTAATTCTATAAATCGAG
Found at i:24371 original size:12 final size:12
Alignment explanation
Indices: 24346--24384 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
24336 TCAGAGAGTT
* *
24346 ACACGGGGTAGG
1 ACACGGGCTGGG
24358 ACACGGGCTGGG
1 ACACGGGCTGGG
*
24370 ACACAGGCTGGG
1 ACACGGGCTGGG
24382 ACA
1 ACA
24385 TAGCCATGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.26, C:0.23, G:0.44, T:0.08
Consensus pattern (12 bp):
ACACGGGCTGGG
Found at i:32727 original size:38 final size:38
Alignment explanation
Indices: 32676--32752 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
32666 TCTAATAGCT
32676 ATGGAACATTAAAGTGGAGGTCCTTATGTGGTAATTAG
1 ATGGAACATTAAAGTGGAGGTCCTTATGTGGTAATTAG
32714 ATGGAACATTAAAGTGGAGGTCCTTATGTGGTAATTAG
1 ATGGAACATTAAAGTGGAGGTCCTTATGTGGTAATTAG
32752 A
1 A
32753 CCATTTGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.32, C:0.08, G:0.29, T:0.31
Consensus pattern (38 bp):
ATGGAACATTAAAGTGGAGGTCCTTATGTGGTAATTAG
Found at i:36009 original size:44 final size:43
Alignment explanation
Indices: 35945--36115 Score: 174
Period size: 43 Copynumber: 4.0 Consensus size: 43
35935 ATAGGACTCT
* *
35945 GATATGTGATTT-CATGTAAGACCATGTCTGGGACGTTGGCATC
1 GATAT-TGATTTACGTGTAAGACCATATCTGGGACGTTGGCATC
* * *
35988 GAT-TTGAGGTTTACGTGTAAGACCATGTCTAGGACATTGGCATC
1 GATATTGA--TTTACGTGTAAGACCATATCTGGGACGTTGGCATC
*
36032 -ATATATGATTT-CGTGTAAGACCTTATCTGGGACAG-TGGCATC
1 GATAT-TGATTTACGTGTAAGACCATATCTGGGAC-GTTGGCATC
* *
36074 GATAGTTGA-TTACATGTAAGACCACATCTGGGACGTTGGCAT
1 GATA-TTGATTTACGTGTAAGACCATATCTGGGACGTTGGCAT
36116 TGTATGAGCT
Statistics
Matches: 108, Mismatches: 10, Indels: 20
0.78 0.07 0.14
Matches are distributed among these distances:
41 3 0.03
42 30 0.28
43 42 0.39
44 30 0.28
45 3 0.03
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (43 bp):
GATATTGATTTACGTGTAAGACCATATCTGGGACGTTGGCATC
Found at i:39585 original size:125 final size:125
Alignment explanation
Indices: 39363--39615 Score: 470
Period size: 125 Copynumber: 2.0 Consensus size: 125
39353 ATACTGCTAA
* *
39363 ACCTAGTCAAAATAAAAGTGTATAGTTAGGATATGTTTACTTATGAATTAGCTATTTAGGTTTGG
1 ACCTAGTCAAAATAAAAGTGTATAGTTAGGATATCTTTACTTATGAATTAGCTATTTAGGTTCGG
39428 TCATGAATCTCAATGAATGAATAAAATTTTTAAAAGTCACATTGAAGTTATTTTCCATTG
66 TCATGAATCTCAATGAATGAATAAAATTTTTAAAAGTCACATTGAAGTTATTTTCCATTG
*
39488 ACCTAGTCCAAATAAAAGTGTATAGTTAGGATATCTTTACTTATGAATTAGCTATTTAGGTTCGG
1 ACCTAGTCAAAATAAAAGTGTATAGTTAGGATATCTTTACTTATGAATTAGCTATTTAGGTTCGG
*
39553 TCATGAATCTCAATGAATGAATAAAATTTTTAAAAGTCACATTGAAGTTATTTTCTATTG
66 TCATGAATCTCAATGAATGAATAAAATTTTTAAAAGTCACATTGAAGTTATTTTCCATTG
39613 ACC
1 ACC
39616 GAATGTTGGC
Statistics
Matches: 124, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
125 124 1.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (125 bp):
ACCTAGTCAAAATAAAAGTGTATAGTTAGGATATCTTTACTTATGAATTAGCTATTTAGGTTCGG
TCATGAATCTCAATGAATGAATAAAATTTTTAAAAGTCACATTGAAGTTATTTTCCATTG
Found at i:41401 original size:47 final size:47
Alignment explanation
Indices: 41282--41454 Score: 186
Period size: 44 Copynumber: 3.8 Consensus size: 47
41272 ACTAGGATGT
*
41282 TGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA
1 TGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCAA
* *
41330 T-G--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATGTAA
1 TGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAA
41372 CTAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-ATGGATGCGAA
1 -T-GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGC-AA
* *
41422 ---C-GCCGAGCTCGTTGAGTTGAGTCCGAGTTCACT
1 TGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT
41455 TATGGGCGGG
Statistics
Matches: 109, Mismatches: 7, Indels: 22
0.79 0.05 0.16
Matches are distributed among these distances:
42 6 0.06
43 1 0.01
44 32 0.29
45 31 0.28
47 31 0.28
48 2 0.02
49 4 0.04
50 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28
Consensus pattern (47 bp):
TGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAA
Found at i:44384 original size:15 final size:15
Alignment explanation
Indices: 44364--44427 Score: 89
Period size: 15 Copynumber: 4.4 Consensus size: 15
44354 GTATCTTGGG
44364 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
44379 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
44394 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
44409 TTTCTTTATTC-GG-
1 TTTCTTTATTCTGGA
44422 TTTCTT
1 TTTCTT
44428 GTTATCTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
13 6 0.13
14 4 0.09
15 33 0.73
16 2 0.04
ACGTcount: A:0.11, C:0.16, G:0.12, T:0.61
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:46834 original size:45 final size:45
Alignment explanation
Indices: 46785--46957 Score: 199
Period size: 45 Copynumber: 3.8 Consensus size: 45
46775 ATGTTTGGCA
*
46785 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACG
* * * * *
46830 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGA--GATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGC-A-ACG
*
46875 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AACG
* * *
46921 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
46958 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
43 1 0.01
44 6 0.06
45 58 0.55
46 39 0.37
47 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACG
Found at i:50458 original size:68 final size:67
Alignment explanation
Indices: 50386--50535 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
50376 CATCATGTGT
* * * *
50386 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
50448 ATGTAG
62 ATGTAG
** * *
50454 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
50519 AG
66 AG
50521 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
50536 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:50491 original size:64 final size:64
Alignment explanation
Indices: 50410--50593 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
50400 AGACATTATG
* *
50410 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
50474 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
50539 AA
63 AA
* * * *
50541 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
50594 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:56109 original size:39 final size:39
Alignment explanation
Indices: 56065--56139 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
56055 TGAGATGTTG
* *
56065 CATTCTTGAGTTCTAAAGTACGTGGGAATGATACTTTTT
1 CATTCTTGAGTTCTAAAGTACATGGGAACGATACTTTTT
56104 CATTCTTGAGTTCTAAAGTACATGGGAACGATACTT
1 CATTCTTGAGTTCTAAAGTACATGGGAACGATACTT
56140 ACCTCTGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (39 bp):
CATTCTTGAGTTCTAAAGTACATGGGAACGATACTTTTT
Done.