Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1846
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: 186639
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:178014 original size:32 final size:32
Alignment explanation
Indices: 177909--178034 Score: 125
Period size: 32 Copynumber: 4.0 Consensus size: 32
177899 TTCAAATACC
* * * *
177909 TTCTTAAAGTCCATGACTTAGTGGCAAT-C-TC
1 TTCTCAAAGTCCACGACTCAGTGGC-ATCCTTT
*
177940 TTCTCAAAGCCCACGACTCAGTGGCAT--TTT
1 TTCTCAAAGTCCACGACTCAGTGGCATCCTTT
*
177970 GTCTCAAAGTCCACGACTCAGTGGCATCCTTT
1 TTCTCAAAGTCCACGACTCAGTGGCATCCTTT
* * * *
178002 TTTTCAAAGTCCACAACTCTGTGGCACCCTTT
1 TTCTCAAAGTCCACGACTCAGTGGCATCCTTT
178034 T
1 T
178035 AAGTCCACAA
Statistics
Matches: 80, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
30 28 0.35
31 21 0.26
32 31 0.39
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.33
Consensus pattern (32 bp):
TTCTCAAAGTCCACGACTCAGTGGCATCCTTT
Found at i:178042 original size:27 final size:27
Alignment explanation
Indices: 178008--178209 Score: 172
Period size: 27 Copynumber: 7.0 Consensus size: 27
177998 CTTTTTTTCA
*
178008 AAGTCCACAACTCTGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
178035 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
178062 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAGTCCACAACTCCGTGGCA--C-----CCTTTT
*
178096 AAGTCCACAACTCTGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* * *
178123 AAGCCCACAACTCCATGGCACTCTTTTTCCTTCT
1 AAGTCCACAACTCCGTGGCA--C-----CCTTTT
*
178157 AAGTCCACAACT-CGTGGCTCCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* * *
178183 AAGCCCATAACTCCGTGGCACTCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
178210 TCCTTCTAAG
Statistics
Matches: 142, Mismatches: 18, Indels: 30
0.75 0.09 0.16
Matches are distributed among these distances:
26 15 0.11
27 79 0.56
29 2 0.01
31 1 0.01
32 1 0.01
33 5 0.04
34 39 0.27
ACGTcount: A:0.21, C:0.36, G:0.13, T:0.30
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCACCCTTTT
Found at i:178114 original size:34 final size:34
Alignment explanation
Indices: 178056--178242 Score: 181
Period size: 34 Copynumber: 6.0 Consensus size: 34
178046 TCCGTGGCAC
*
178056 CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTT
1 CCTTCTAAGCCCACAACTCCGTGGCACTCTTTTT
* *
178090 CCTTCTAAGTCCACAACTCTGTGGCA--C-----
1 CCTTCTAAGCCCACAACTCCGTGGCACTCTTTTT
* *
178117 CCTTTTAAGCCCACAACTCCATGGCACTCTTTTT
1 CCTTCTAAGCCCACAACTCCGTGGCACTCTTTTT
*
178151 CCTTCTAAGTCCACAACT-CGTGG--CTC-----
1 CCTTCTAAGCCCACAACTCCGTGGCACTCTTTTT
* *
178177 CCTTTTAAGCCCATAACTCCGTGGCACTCTTTTT
1 CCTTCTAAGCCCACAACTCCGTGGCACTCTTTTT
*
178211 CCTTCTAAGTCCACAACTCCGTGGCAC-CTTTT
1 CCTTCTAAGCCCACAACTCCGTGGCACTCTTTT
178243 CTTTTCAAAG
Statistics
Matches: 122, Mismatches: 16, Indels: 31
0.72 0.09 0.18
Matches are distributed among these distances:
26 15 0.12
27 27 0.22
29 4 0.03
31 3 0.02
32 1 0.01
33 9 0.07
34 63 0.52
ACGTcount: A:0.19, C:0.36, G:0.12, T:0.33
Consensus pattern (34 bp):
CCTTCTAAGCCCACAACTCCGTGGCACTCTTTTT
Found at i:178180 original size:26 final size:27
Alignment explanation
Indices: 178151--178201 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
178141 CACTCTTTTT
*
178151 CCTTCTAAGTCCACAACT-CGTGGCTC
1 CCTTCTAAGCCCACAACTCCGTGGCTC
* *
178177 CCTTTTAAGCCCATAACTCCGTGGC
1 CCTTCTAAGCCCACAACTCCGTGGC
178202 ACTCTTTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.20, C:0.37, G:0.16, T:0.27
Consensus pattern (27 bp):
CCTTCTAAGCCCACAACTCCGTGGCTC
Found at i:178203 original size:60 final size:61
Alignment explanation
Indices: 178029--178242 Score: 369
Period size: 61 Copynumber: 3.5 Consensus size: 61
178019 TCTGTGGCAC
*
178029 CCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTT
1 CCTTCTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTT
* *
178090 CCTTCTAAGTCCACAACTCTGTGGCACCCTTTTAAGCCCACAACTCCATGGCACTCTTTTT
1 CCTTCTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTT
* *
178151 CCTTCTAAGTCCACAACT-CGTGGCTCCCTTTTAAGCCCATAACTCCGTGGCACTCTTTTT
1 CCTTCTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTT
178211 CCTTCTAAGTCCACAACTCCGTGGCA-CCTTTT
1 CCTTCTAAGTCCACAACTCCGTGGCACCCTTTT
178243 CTTTTCAAAG
Statistics
Matches: 144, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
60 62 0.43
61 82 0.57
ACGTcount: A:0.20, C:0.36, G:0.13, T:0.32
Consensus pattern (61 bp):
CCTTCTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTT
Found at i:178286 original size:33 final size:32
Alignment explanation
Indices: 178244--178375 Score: 201
Period size: 33 Copynumber: 4.1 Consensus size: 32
178234 GCACCTTTTC
* *
178244 TTTTCAAAGCCCACACAAGTAGGTGGTAACCT
1 TTTTCAAAGCCCACACAAGTCGGTGGCAACCT
*
178276 TTTTCTAAAGCCCACACAAGTCGGTGGCAACCC
1 TTTTC-AAAGCCCACACAAGTCGGTGGCAACCT
178309 TTTTCAAAGCCCACACAAGTCGGTGGCAACCT
1 TTTTCAAAGCCCACACAAGTCGGTGGCAACCT
* *
178341 TTTTCTAAAGCCCACACAAGTTGGTGGTAACCT
1 TTTTC-AAAGCCCACACAAGTCGGTGGCAACCT
178374 TT
1 TT
178376 CTAAGCCCAA
Statistics
Matches: 92, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
32 36 0.39
33 56 0.61
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (32 bp):
TTTTCAAAGCCCACACAAGTCGGTGGCAACCT
Found at i:178312 original size:65 final size:64
Alignment explanation
Indices: 178243--178384 Score: 223
Period size: 65 Copynumber: 2.2 Consensus size: 64
178233 GGCACCTTTT
*
178243 CTTTTCAAAGCCCACACAAGTAGGTGGTAACCTTTTTCTAAAGCCCACACAAGTCGGTGGCAACC
1 CTTTTCAAAGCCCACACAAGTAGGTGGCAACCTTTTTCTAAAGCCCACACAAGTCGGTGGCAA-C
* * *
178308 CTTTTCAAAGCCCACACAAGTCGGTGGCAACCTTTTTCTAAAGCCCACACAAGTTGGTGGTAAC
1 CTTTTCAAAGCCCACACAAGTAGGTGGCAACCTTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
*
178372 C-TTTCTAAGCCCA
1 CTTTTCAAAGCCCA
178385 ATATCATTGG
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
63 11 0.15
64 2 0.03
65 59 0.82
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.25
Consensus pattern (64 bp):
CTTTTCAAAGCCCACACAAGTAGGTGGCAACCTTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
Found at i:178486 original size:43 final size:43
Alignment explanation
Indices: 178421--179569 Score: 939
Period size: 43 Copynumber: 25.0 Consensus size: 43
178411 TGGCACCATT
* *
178421 ATCTTTAAGTCCAACGTAGCTGGCCTTGAATCAGCACATTGGC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
178464 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
* * * *
178507 ACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG---C
* * * *
178553 TTTATCTTTTAGACCAATGTCGCTGGCCTTGAATCAGCACATTAGA
1 ---ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
* * * * *
178599 ACCTTCAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG---C
* *
178645 TTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAACACATTGGC
1 ---ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
* *
178691 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCTGCACATTGGA
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
* * * * *
178734 ACCTTTAAGTCCAATATAGATGGCCTTGAATCAGCATATTGGCACC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG---C
* *
178780 TTTATCTTTAAGACCAATGTAGCTGGCCTTGAATCAGCACATTGGC
1 ---ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
*
178826 ATCTTTAAGTCCAATGTCGCTCGCCTTGAATCAGCACATTGGC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
* * * * * *
178869 ACCTTTAAGTCCAATATAGATGGCCTTGATTCAGCATATTGGCACC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG---C
* * *
178915 TTTATCTTTAAGACCAACGTCGCTGGCCTTGAATCAGCGCATTGGC
1 ---ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
* ** * *
178961 ACCTTTAAGTCCAATACCGCTAGCCTTGAATCAGCATATTGGCACC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG---C
* * *
179007 TTTATCTTTAAGACCAATGTCACTGGCCTTGAATCGGCACATTGGC
1 ---ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
* * * *
179053 ACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG------C
*
179102 ATCTTTAAGTCCAATGTGGCTGGCCTTGAATCAGCACATTGGC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
* * * *
179145 ACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG------C
*
179194 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
* * * *
179237 ACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG------C
* *
179286 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACCTTGGC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
* ** * * * *
179329 ACCTCCAAGTCCAATATCGCTAGCCTTGAATCAACATATTGGCACCCTC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG------C
* * *
179378 ATCTTTTAAGCCCAATGTCGCTGGCCTTAAATCAGCACATTGAC
1 ATC-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
* * * *
179422 ACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATAATGGCACCTTTGTC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGC---A---CA---TTGGC
* *
179474 ATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTGCCTTTGTC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACA-T--TG-----G-C
* *
179526 ATTTTTAAGTCCAATGTCGCTGGCCTTTAATCAGCACATTGGC
1 ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
179569 A
1 A
179570 CCTTCATCTT
Statistics
Matches: 895, Mismatches: 139, Indels: 144
0.76 0.12 0.12
Matches are distributed among these distances:
43 475 0.53
44 6 0.01
46 11 0.01
49 300 0.34
50 30 0.03
51 1 0.00
52 72 0.08
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31
Consensus pattern (43 bp):
ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC
Found at i:178560 original size:92 final size:92
Alignment explanation
Indices: 178423--179515 Score: 1439
Period size: 92 Copynumber: 12.0 Consensus size: 92
178413 GCACCATTAT
** *
178423 CTTTAAGTCCAACGTAGCTGGCCTTGAATCAGCACATTGG---C---ATCTTTAAGTCCAATGTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
178482 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* *
178509 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTTAGACCAATGTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
* *
178574 GCTGGCCTTGAATCAGCACATTAGAAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * * *
178601 CTTCAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
* *
178666 GCTGGCCTTGAATCAACACATTGGCAT
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * * * * * *
178693 CTTTAAGTCCAATGTCGCTGGCCTTGAATCTGCACATTGG-A-----ACCTTTAAGTCCAATATA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
* *
178752 GATGGCCTTGAATCAGCATATTGGCACC
66 GCTGGCCTTGAATCAGCACATTGGCA-C
* * *
178780 TTTATCTTTAAGACCAATGTAGCTGGCCTTGAATCAGCACATTGG---C---ATCTTTAAGTCCA
1 -----CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCA
*
178839 ATGTCGCTCGCCTTGAATCAGCACATTGGCAC
61 ATGTCGCTGGCCTTGAATCAGCACATTGGCAC
* * * *
178871 CTTTAAGTCCAATATAGATGGCCTTGATTCAGCATATTGGCACCTTTATCTTTAAGACCAACGTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
*
178936 GCTGGCCTTGAATCAGCGCATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
** * *
178963 CTTTAAGTCCAATACCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
* *
179028 ACTGGCCTTGAATCGGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* *
179055 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
179120 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* *
179147 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
179212 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* *
179239 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
*
179304 GCTGGCCTTGAATCAGCACCTTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
** * * * * * *
179331 CTCCAAGTCCAATATCGCTAGCCTTGAATCAACATATTGGCACCCTCATCTTTTAAGCCCAATGT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATC-TTTAAGTCCAATGT
* *
179396 CGCTGGCCTTAAATCAGCACATTGACAC
65 CGCTGGCCTTGAATCAGCACATTGGCAC
* * *
179424 CTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATAATGGCACCTTTGTCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TT-T-ATCTTTAAGTCCAAT
* *
179489 ATCGCTGGCCTTGAATCAGCATATTGG
63 GTCGCTGGCCTTGAATCAGCACATTGG
179516 TGCCTTTGTC
Statistics
Matches: 897, Mismatches: 87, Indels: 37
0.88 0.09 0.04
Matches are distributed among these distances:
86 111 0.12
89 2 0.00
91 2 0.00
92 667 0.74
93 77 0.09
94 1 0.00
95 34 0.04
96 3 0.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (92 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
GCTGGCCTTGAATCAGCACATTGGCAC
Found at i:178625 original size:135 final size:137
Alignment explanation
Indices: 178392--179573 Score: 1166
Period size: 135 Copynumber: 8.6 Consensus size: 137
178382 CCAATATCAT
* * *
178392 TGGCCTTGAATCAGCATATTGGCACCATTATCTTTAAGTCCAACGTAGCTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCA
* * *
178457 CATTGGCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C-CTTTAAGTCCA
66 CATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCTTTAAGTCCA
178520 ATATAGC
131 ATATAGC
* *
178527 TGGCCTTGAATCAGCATATTGGCACCTTTATCTTTTAGACCAATGTCGCTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCA
* * * * * *
178592 CATTAGAACCTTCAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAG
66 CATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC----TCTTTAAG
*
178657 TCCAATGTAGC
127 TCCAATATAGC
* * *
178668 TGGCCTTGAATCAACACATTGG---C---ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCTGCA
1 TGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCA
* * *
178727 CATTGGAACCTTTAAGTCCAATATAGATGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAG
66 CATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC----TCTTTAAG
* *
178792 ACCAATGTAGC
127 TCCAATATAGC
* *
178803 TGGCCTTGAATCAGCACATTGG---C---ATCTTTAAGTCCAATGTCGCTCGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCA
* * *
178862 CATTGGCACCTTTAAGTCCAATATAGATGGCCTTGATTCAGCATATTGGCACCTTTATCTTTAAG
66 CATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC----TCTTTAAG
* ** *
178927 ACCAACGTCGC
127 TCCAATATAGC
** ** *
178938 TGGCCTTGAATCAGCGCATTGGCA-C-----CTTTAAGTCCAATACCGCTAGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCA
* * * *
178997 TATTGGCACCTTTATCTTTAAGACCAATGTCA-CTGGCCTTGAATCGGCACATTGGCA-C-CTTT
66 CATTGGCA-C-----CTTTAAGTCCAATAT-AGCTGGCCTTGAATCAGCACATTGGCACCTCTTT
179059 AAGTCCAATATAGC
124 AAGTCCAATATAGC
* *
179073 TGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTGGCTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCA
*
179138 CATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAG
66 CATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-C--C-TCTTTAAG
*
179203 TCCAATGTAGC
127 TCCAATATAGC
* * *
179214 TGGCCTTGAATCAGCACATTGGCA-C-----CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCA
* * * *
179273 TATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACCTTGGCACCTC--CA
66 CATTGGCA----C--CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCTTTA
*
179336 AGTCCAATATCGC
125 AGTCCAATATAGC
* * * * * *
179349 TAGCCTTGAATCAACATATTGGCACCCTCATCTTTTAAGCCCAATGTCGCTGGCCTTAAATCAGC
1 TGGCCTTGAATCAGCATATTGGCACCTTTATC-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGC
* * * * *
179414 ACATTGACACCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATAATGGCACCTTTGTCATCTT
65 ACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-C-----C-TCTT
*
179479 TAAGTCCAATATCGC
123 TAAGTCCAATATAGC
** * *
179494 TGGCCTTGAATCAGCATATTGGTGCCTTTGTCATTTTTAAGTCCAATGTCGCTGGCCTTTAATCA
1 TGGCCTTGAATCAGCATATTGGCACC-TT-T-ATCTTTAAGTCCAATGTCGCTGGCCTTGAATCA
179559 GCACATTGGCACCTT
63 GCACATTGGCACCTT
179574 CATCTTTAAC
Statistics
Matches: 900, Mismatches: 94, Indels: 94
0.83 0.09 0.09
Matches are distributed among these distances:
134 1 0.00
135 538 0.60
136 40 0.04
137 4 0.00
138 3 0.00
139 2 0.00
140 4 0.00
141 188 0.21
142 37 0.04
143 2 0.00
145 36 0.04
146 1 0.00
147 42 0.05
148 2 0.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31
Consensus pattern (137 bp):
TGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCA
CATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCTTTAAGTCCA
ATATAGC
Found at i:179502 original size:52 final size:52
Alignment explanation
Indices: 179424--179778 Score: 240
Period size: 52 Copynumber: 6.8 Consensus size: 52
179414 ACATTGACAC
* *
179424 CTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATAATGGCACCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCAT
**
179476 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTGCCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCAT
* * * * * * *
179528 TTTTAAGTCCAATGTCGCTGGCCTTTAATCAGCACATTGGCACCTTCATCTTTAA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT--T-GTCAT
* * * ** *
179583 CATTCCTAAGCCCGATGTCGCTGGCCTTGCCTCAGCACATTGGCA--TTT-T--T
1 C-TT--TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCAT
* ** * * * * *
179633 CTTCAAGTTTAAATGTCGTTGGCCATGAATCAGCACATTGTCA--TTTGTTGCAT
1 CTTTAAG-TCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTG-T-CAT
* * * * *
179686 CTTCAAGTCCAATATTGCTGGCCTTGAATCAGCATATTAGCA-TTTTCTTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-GTCAT
** * * *
179738 CTTTAAAACCCAATATCGTTGGCCGTGAATCAACATATTGG
1 CTTT-AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
179779 TCCTTTTATC
Statistics
Matches: 240, Mismatches: 48, Indels: 29
0.76 0.15 0.09
Matches are distributed among these distances:
47 3 0.01
48 29 0.12
49 2 0.01
50 2 0.01
52 121 0.50
53 41 0.17
54 2 0.01
55 2 0.01
56 4 0.02
58 34 0.14
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (52 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCAT
Found at i:180464 original size:13 final size:13
Alignment explanation
Indices: 180446--180470 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
180436 CATAAAGTGT
180446 TGTATCGATACAA
1 TGTATCGATACAA
180459 TGTATCGATACA
1 TGTATCGATACA
180471 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:180486 original size:32 final size:33
Alignment explanation
Indices: 180428--180494 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 33
180418 CAACGATTTA
180428 TATCGATACATAAAGTGTTGTATCGATACAATG
1 TATCGATACATAAAGTGTTGTATCGATACAATG
* *
180461 TATCGATACAT-AAGTTTTGTATCGATGCAATG
1 TATCGATACATAAAGTGTTGTATCGATACAATG
180493 TA
1 TA
180495 AGCTACTGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 21 0.66
33 11 0.34
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (33 bp):
TATCGATACATAAAGTGTTGTATCGATACAATG
Found at i:180661 original size:52 final size:52
Alignment explanation
Indices: 180564--180691 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
180554 CACGGATCTT
*
180564 TGTATCGATACATGCAGGC-AATCTGCCCAGATGCAGCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGCAGCGATACACTATGAAA
* * *
180615 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGCAGCGATACACTATGAAA
180667 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
180692 TCATATTTCG
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
51 18 0.25
52 53 0.75
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGCAGCGATACACTATGAAA
Found at i:183759 original size:13 final size:13
Alignment explanation
Indices: 183741--183765 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
183731 ACGACATTCA
183741 TGTATCGATACAT
1 TGTATCGATACAT
183754 TGTATCGATACA
1 TGTATCGATACA
183766 ATGTGCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:183854 original size:13 final size:13
Alignment explanation
Indices: 183836--183860 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
183826 CAATGATCAT
183836 GTATCGATACAAG
1 GTATCGATACAAG
183849 GTATCGATACAA
1 GTATCGATACAA
183861 AGCATAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (13 bp):
GTATCGATACAAG
Found at i:183878 original size:33 final size:32
Alignment explanation
Indices: 183817--183879 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
183807 CCAGTTTCAT
* *
183817 GTATCGATACAATGATCATGTATCGATACAAG
1 GTATCGATACAAAGATAATGTATCGATACAAG
*
183849 GTATCGATACAAAGCATAATGTATTGATACA
1 GTATCGATACAAAG-ATAATGTATCGATACA
183880 TCTAGATGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (32 bp):
GTATCGATACAAAGATAATGTATCGATACAAG
Found at i:184988 original size:147 final size:148
Alignment explanation
Indices: 184717--185201 Score: 412
Period size: 147 Copynumber: 3.3 Consensus size: 148
184707 TCAGATATCA
* * * * *
184717 CTAAGACCTACCATCGACGTAGAAGTGCCCGAAGATCCT-AGTGGACTTAAAAAGACAAAAACAA
1 CTAAGGCCTACCATCGACTTAGAAGTGCCTGATGATCCTAAG-GGACTT-GAAAGACAAAAACAA
* * * *
184781 ACCTACTCCTAATTCTTACCTTCGACATAGAAGCAGACCTAGTAATTTTATAGAACTAGGTTTTG
64 ACCTACCCCTAATTCTTACCTTCGACATAGAAACAGACCTAGTAATTTCATAGAACTAGGTTTCG
* * *
184846 GGAGAAATGCTAAAAGGTCC
129 GGAAAAAGGCTAAAAGATCC
* * * * *
184866 CTAAGGCCTACCATCGACTTAGAAGTGCTTGGTGATCCTAAGGGACTTGAAAGA-TAAAATAAGC
1 CTAAGGCCTACCATCGACTTAGAAGTGCCTGATGATCCTAAGGGACTTGAAAGACAAAAACAAAC
* ***
184930 CTACCCCTAATT-TATACTTTCGACATAGAAAC-GAACCTAGTAATTTCATAGGGTTAGGTTTCG
66 CTACCCCTAATTCT-TACCTTCGACATAGAAACAG-ACCTAGTAATTTCATAGAACTAGGTTTCG
*
184993 GGAAAAAGGCTAAAATATCC
129 GGAAAAAGGCTAAAAGATCC
** * * **
185013 CTAAGGTTTACCATCGACTTAGAAGTGCCTGATGATCTTAAGGGACTTGAAAAAGCAAAAATGAA
1 CTAAGGCCTACCATCGACTTAGAAGTGCCTGATGATCCTAAGGGACTTGAAAGA-CAAAAACAAA
** ** * * * * * *
185078 CCTATTCCTAATT-TATACCTTC-AGTGTAGAAACAGATCC-GGTAGTTTTATAGGATTAGCTTT
65 CCTACCCCTAATTCT-TACCTTCGA-CATAGAAACAGA-CCTAGTAATTTCATAGAACTAGGTTT
** *
185140 TAGG-AAAAGTGCTAAAATAT-C
127 CGGGAAAAAG-GCTAAAAGATCC
* * * * *
185161 CTAAGGCTTGCCATCGACTTAGGAGTACCCGATGATCCTAA
1 CTAAGGCCTACCATCGACTTAGAAGTGCCTGATGATCCTAA
185202 AAAACTTGAA
Statistics
Matches: 278, Mismatches: 49, Indels: 19
0.80 0.14 0.05
Matches are distributed among these distances:
146 2 0.01
147 122 0.44
148 47 0.17
149 102 0.37
150 5 0.02
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (148 bp):
CTAAGGCCTACCATCGACTTAGAAGTGCCTGATGATCCTAAGGGACTTGAAAGACAAAAACAAAC
CTACCCCTAATTCTTACCTTCGACATAGAAACAGACCTAGTAATTTCATAGAACTAGGTTTCGGG
AAAAAGGCTAAAAGATCC
Done.