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: 45801
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:2022 original size:28 final size:28
Alignment explanation
Indices: 1953--2278 Score: 368
Period size: 28 Copynumber: 11.4 Consensus size: 28
1943 CACCTTTTCC
* * *
1953 AAAGCCCACAAGTCCGTGGCATCCTTTCC
1 AAAGCCCACAAGTCAGTGGCAACC-TTCA
1982 AAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* *
2010 AAAGCCCACAAGTCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAACC--TTCA
*
2040 AAAGCCCACAAGTCAGTGGCAACCTTCC
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* *
2068 AAAGCCCACAAGTCCA-TGGCATCCTTTCC
1 AAAGCCCACAAGT-CAGTGGCAACC-TTCA
2097 AAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* * *
2125 AAAGCCCACAAGCCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAACC--TTCA
*
2155 AAAGCCCTCAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* * * *
2183 AAAGCCCACAAGTTAGTGGTATCTTTTCA
1 AAAGCCCACAAGTCAGTGGCAAC-CTTCA
*
2212 AAAGCCCACAAGTCAGTGTCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* **
2240 AAAGCACACAAGTTGGT-GCAACCCTATCA
1 AAAGCCCACAAGTCAGTGGCAA-CCT-TCA
2269 AAAGCCCACA
1 AAAGCCCACA
2279 TAAGTTGGTG
Statistics
Matches: 256, Mismatches: 31, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
27 3 0.01
28 120 0.47
29 83 0.32
30 50 0.20
ACGTcount: A:0.32, C:0.33, G:0.17, T:0.18
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCAACCTTCA
Found at i:2123 original size:57 final size:58
Alignment explanation
Indices: 1953--2252 Score: 457
Period size: 57 Copynumber: 5.2 Consensus size: 58
1943 CACCTTTTCC
1953 AAAGCCCACAAGTCC-GTGGCATCCTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCCAGTGGCATCCTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
* *
2010 AAAGCCCACAAGT-CAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCC
1 AAAGCCCACAAGTCCAGTGGCATCC-TTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
2068 AAAGCCCACAAGTCCA-TGGCATCCTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCCAGTGGCATCCTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
* *
2125 AAAGCCCACAAG-CCAGTGGCACCCTTTTCCAAAGCCCTCAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCCAGTGGCATCC-TTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
* * * * *
2183 AAAGCCCACAAGT-TAGTGGTATCTTTTCAAAAGCCCACAAGTCAGTGTCAACCTTCA
1 AAAGCCCACAAGTCCAGTGGCATCCTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
*
2240 AAAGCACACAAGT
1 AAAGCCCACAAGT
2253 TGGTGCAACC
Statistics
Matches: 223, Mismatches: 14, Indels: 12
0.90 0.06 0.05
Matches are distributed among these distances:
56 4 0.02
57 114 0.51
58 103 0.46
59 2 0.01
ACGTcount: A:0.32, C:0.33, G:0.17, T:0.18
Consensus pattern (58 bp):
AAAGCCCACAAGTCCAGTGGCATCCTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCA
Found at i:2151 original size:115 final size:115
Alignment explanation
Indices: 1949--2251 Score: 500
Period size: 115 Copynumber: 2.6 Consensus size: 115
1939 TCCTCACCTT
*
1949 TTCCAAAGCCCACAAGTCCGTGGCATCCTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAG
1 TTCCAAAGCCCACAAGTCCATGGCATCCTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAG
*
2014 CCCACAAGTCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCAACC
66 CCCACAAGCCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCAACC
2064 TTCCAAAGCCCACAAGTCCATGGCATCCTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAG
1 TTCCAAAGCCCACAAGTCCATGGCATCCTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAG
*
2129 CCCACAAGCCAGTGGCACCCTTTTCCAAAGCCCTCAAGTCAGTGGCAACC
66 CCCACAAGCCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCAACC
* * * * * *
2179 TTCAAAAGCCCACAAGT-TAGTGGTATCTTTTCAAAAGCCCACAAGTCAGTGTCAACCTTCAAAA
1 TTCCAAAGCCCACAAGTCCA-TGGCATCCTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAA
*
2243 GCACACAAG
65 GCCCACAAG
2252 TTGGTGCAAC
Statistics
Matches: 177, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
114 1 0.01
115 176 0.99
ACGTcount: A:0.31, C:0.34, G:0.17, T:0.18
Consensus pattern (115 bp):
TTCCAAAGCCCACAAGTCCATGGCATCCTTTCCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAG
CCCACAAGCCAGTGGCACCCTTTTCCAAAGCCCACAAGTCAGTGGCAACC
Found at i:2357 original size:49 final size:49
Alignment explanation
Indices: 2298--2756 Score: 552
Period size: 49 Copynumber: 9.6 Consensus size: 49
2288 GGCATCTTTT
*
2298 TTTAAGTCCAATATCGCTGGCCTTGAATCAGTATATTGGCACTGTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTGTCATC
* * *
2347 TTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCA----C--C
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTGTCATC
2390 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTGTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTGTCATC
* * *
2439 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCT-TCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTGTCATC
** * * *
2488 TTTAAGTCCGGTATCGTTGGCTTTGAATCAGCATATTGGCACCGTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTGTCATC
* * *
2537 TTAAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA----C--C
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTGTCATC
*
2580 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTGTCATC
* * * *
2629 TTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCT-TCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTGTCATC
** * *
2678 TTTAAGTCCGGTATCGCTGGCTTTGAATCAGCATATTGGCACCGTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTGTCATC
* *
2727 TTTAAGAT-CAATGTCGCTGGCCATGAATCA
1 TTTAAG-TCCAATATCGCTGGCCTTGAATCA
2757 AAACATTGTC
Statistics
Matches: 347, Mismatches: 46, Indels: 34
0.81 0.11 0.08
Matches are distributed among these distances:
43 78 0.22
45 2 0.01
47 2 0.01
48 2 0.01
49 259 0.75
50 4 0.01
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (49 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTGTCATC
Found at i:2487 original size:141 final size:141
Alignment explanation
Indices: 2298--2756 Score: 545
Period size: 141 Copynumber: 3.2 Consensus size: 141
2288 GGCATCTTTT
* *
2298 TTTAAGTCCAATATCGCTGGCCTTGAATCAGTATATTGGCACTGTCATCTTTAAGTCCAATGTCG
1 TTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACT-TCATCTTTAAGTCCAATGTCG
* *
2363 CTAGCCTTGAATCAGCACATTGGCA-C-CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATAT
65 TTGGCCTTGAATCAGCACATTGGCATCTCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATAT
2426 TGGCACTGTCATC
130 TGGCAC-GTCATC
* * ** *
2439 TTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCGGTATCG
1 TTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTTCATCTTTAAGTCCAATGTCG
* * * *
2504 TTGGCTTTGAATCAGCATATTGGCACCGTCATCTTAAAGTCCAATGTCGCTGGCCTTGAATCAGC
65 TTGGCCTTGAATCAGCACATTGGCA---TC-TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGC
*
2569 ACATTGGCA---C--C
126 ATATTGGCACGTCATC
* * *
2580 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCATCTTTAAGACCAATGTCG
1 TTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTTCATCTTTAAGTCCAATGTCG
** *
2645 TTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCGGTATCGCTGGCTTTGAATCAGC
65 TTGGCCTTGAATCAGCACATTGGCA---TC-TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGC
2710 ATATTGGCACCGTCATC
126 ATATTGGCA-CGTCATC
* * *
2727 TTTAAGATCAATGTCGCTGGCCATGAATCA
1 TTTAAGACCAATATCGCTGGCCTTGAATCA
2757 AAACATTGTC
Statistics
Matches: 268, Mismatches: 37, Indels: 20
0.82 0.11 0.06
Matches are distributed among these distances:
141 197 0.74
142 2 0.01
143 1 0.00
145 2 0.01
147 66 0.25
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (141 bp):
TTTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTCATCTTTAAGTCCAATGTCGT
TGGCCTTGAATCAGCACATTGGCATCTCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT
GGCACGTCATC
Found at i:2621 original size:190 final size:190
Alignment explanation
Indices: 2298--2756 Score: 803
Period size: 190 Copynumber: 2.4 Consensus size: 190
2288 GGCATCTTTT
** * * *
2298 TTTAAGTCCAATATCGCTGGCCTTGAATCAGTATATTGGCACTGTCATCTTTAAGTCCAATGTCG
1 TTTAAGTCCGGTATCGCTGGCTTTGAATCAGCATATTGGCACCGTCATCTTTAAGTCCAATGTCG
*
2363 CTAGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
66 CTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
*
2428 GCACTGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
131 GCACCGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
* *
2488 TTTAAGTCCGGTATCGTTGGCTTTGAATCAGCATATTGGCACCGTCATCTTAAAGTCCAATGTCG
1 TTTAAGTCCGGTATCGCTGGCTTTGAATCAGCATATTGGCACCGTCATCTTTAAGTCCAATGTCG
2553 CTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
66 CTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
*
2618 GCACCGTCATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCATC
131 GCACCGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
2678 TTTAAGTCCGGTATCGCTGGCTTTGAATCAGCATATTGGCACCGTCATCTTTAAGAT-CAATGTC
1 TTTAAGTCCGGTATCGCTGGCTTTGAATCAGCATATTGGCACCGTCATCTTTAAG-TCCAATGTC
*
2742 GCTGGCCATGAATCA
65 GCTGGCCTTGAATCA
2757 AAACATTGTC
Statistics
Matches: 255, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
190 254 1.00
191 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (190 bp):
TTTAAGTCCGGTATCGCTGGCTTTGAATCAGCATATTGGCACCGTCATCTTTAAGTCCAATGTCG
CTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
GCACCGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
Found at i:3516 original size:13 final size:13
Alignment explanation
Indices: 3498--3522 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3488 CATAAAGTGT
3498 TGTATCGATACAA
1 TGTATCGATACAA
3511 TGTATCGATACA
1 TGTATCGATACA
3523 TATTTTTTTG
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:3520 original size:33 final size:33
Alignment explanation
Indices: 3478--3544 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3468 TTCAACGATT
3478 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
3511 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
3544 T
1 T
3545 TTAAGCTTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:3648 original size:52 final size:50
Alignment explanation
Indices: 3585--3730 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 50
3575 CATTACTCAA
*
3585 ATGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAG
1 ATGTATCGATACACT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAG
* *
3637 ATGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAG
1 ATGTATCGATACACTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAG
*
3689 ATGTATCGATACACTATTAAATGTATCGATACATGCAAGCAA
1 ATGTATCGATACACTATT--ATGTATCGATACATGCAGGCAA
3731 CTTTTCATAT
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
51 2 0.02
52 82 0.98
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.29
Consensus pattern (50 bp):
ATGTATCGATACACTATTATGTATCGATACATGCAGGCAAATTTGCCCAG
Found at i:6866 original size:52 final size:52
Alignment explanation
Indices: 6803--6926 Score: 212
Period size: 52 Copynumber: 2.4 Consensus size: 52
6793 CGTTACGACA
* *
6803 ATACATGCAGGCAAACTTTCCCAGATGTATCGATACACTATGAAATGTATCG
1 ATACATGCAGGCAAATTTTCCCAGATGTATCAATACACTATGAAATGTATCG
* *
6855 ATACATACAGGCAAATTTTCCCAGATGTATCAATACATTATGAAATGTATCG
1 ATACATGCAGGCAAATTTTCCCAGATGTATCAATACACTATGAAATGTATCG
6907 ATACATGCAGGCAAATTTTC
1 ATACATGCAGGCAAATTTTC
6927 ATATTTCGGG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.29
Consensus pattern (52 bp):
ATACATGCAGGCAAATTTTCCCAGATGTATCAATACACTATGAAATGTATCG
Found at i:12161 original size:13 final size:13
Alignment explanation
Indices: 12143--12181 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
12133 TCATTACTTA
*
12143 TATTTCGGGGCAT
1 TATTTCGGGGCAC
*
12156 TATTTCGAGGCAC
1 TATTTCGGGGCAC
*
12169 TATTTCAGGGCAC
1 TATTTCGGGGCAC
12182 AATGACAAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.33
Consensus pattern (13 bp):
TATTTCGGGGCAC
Found at i:12802 original size:16 final size:15
Alignment explanation
Indices: 12772--12819 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
12762 ATAAGGGAAT
12772 AAAAGAAAAGAAAAA
1 AAAAGAAAAGAAAAA
12787 AAAAGAAAAAGGAAAAA
1 AAAAG-AAAA-GAAAAA
* *
12804 AACATGAAATGAAAAA
1 AA-AAGAAAAGAAAAA
12820 GATGAGGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 5 0.18
16 10 0.36
17 11 0.39
18 2 0.07
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.04
Consensus pattern (15 bp):
AAAAGAAAAGAAAAA
Found at i:21829 original size:157 final size:157
Alignment explanation
Indices: 21365--22028 Score: 751
Period size: 157 Copynumber: 4.3 Consensus size: 157
21355 TAGGGTCCAC
** *
21365 TAGGGTTACCGAGATACTTTCATGTTTAAGGTATACCCT-TAGGGGTATTTTTGTAATTTTTTAA
1 TAGGGTTACCGAGATACTTTCATGTCGAAGGTATACCCTATAGGGGCATTTTTGTAATTTTTTAA
* * *
21429 AACCTAGTCCTAGGTTGTCACCGGGTCAGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTAA
66 AACCTAGTCCTAGGTTGTCACCGGGTCTGCTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCA
*
21494 TCCCATCTCTAATCTTTTTAAGTCTTT
131 TCCCATCTCTAATCTTTTTAAGTCCTT
* *
21521 TAGGGTTACCGAGATACTTTCATGTCGAAGGTATA-CCTATAGAGGGCATTTTCGTAA--TTTCA
1 TAGGGTTACCGAGATACTTTCATGTCGAAGGTATACCCTATAG-GGGCATTTTTGTAATTTTTTA
* * * * ** *
21583 AAACCTAGTCTTAGGTTGTCACCCGGTCCGTTTTTATGTTGAAGGTAGGTATTTAGGATAGGTTC
65 AAACCTAGTCCTAGGTTGTCACCGGGTCTGCTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTC
*
21648 ATCCCATCTTTAATCTTTTTAAGTCCTT
130 ATCCCATCTCTAATCTTTTTAAGTCCTT
* *
21676 TAGGGTTACC-AGGATACGTTT-ATGTCAAAGATATA-CCTATAGGGGCATTTTTGTAATTTTTT
1 TAGGGTTACCGA-GATAC-TTTCATGTCGAAGGTATACCCTATAGGGGCATTTTTGTAATTTTTT
* ** * * * * *
21738 -AGAGTTAAATCCTAGGTTTTTCACTGGGTCTGCTTTTATGCTGAAGGTGGGTATTTAGGATAGT
64 AAAACCT-AGTCCTAGG-TTGTCACCGGGTCTGCTTTTATGCCGAAGGTGGGTATTTAGGATAGG
* *
21802 TTCATCCCCTCTCTAATCTTTTCAAGTCCTT
127 TTCATCCCATCTCTAATCTTTTTAAGTCCTT
* ** * * * *
21833 TAAGGTTACTAAGATACTTTTATGTCGAAGGTATATCC-ATAGGGGTATTTTTGAAATTTTTTAA
1 TAGGGTTACCGAGATACTTTCATGTCGAAGGTATACCCTATAGGGGCATTTTTGTAATTTTTTAA
* * *
21897 AACCTAGTCTTAGGTTGTCACCGGGT-TCGCTTTTATGCCAAAGGTGAGTATTTAGGATAGGTTC
66 AACCTAGTCCTAGGTTGTCACCGGGTCT-GCTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTC
* * *
21961 ATCCCATTTGTAATCCTTTTTAACTCCTT
130 ATCCCATCTCTAAT-CTTTTTAAGTCCTT
* * *
21990 TAGGGGTATCGAG-TA-TTTC-TGCGTCGAAGGTATCCCCTA
1 TAGGGTTACCGAGATACTTTCAT--GTCGAAGGTATACCCTA
22029 AAGGTATTTT
Statistics
Matches: 425, Mismatches: 66, Indels: 33
0.81 0.13 0.06
Matches are distributed among these distances:
154 15 0.04
155 130 0.31
156 120 0.28
157 154 0.36
158 6 0.01
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.39
Consensus pattern (157 bp):
TAGGGTTACCGAGATACTTTCATGTCGAAGGTATACCCTATAGGGGCATTTTTGTAATTTTTTAA
AACCTAGTCCTAGGTTGTCACCGGGTCTGCTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCA
TCCCATCTCTAATCTTTTTAAGTCCTT
Found at i:22048 original size:312 final size:310
Alignment explanation
Indices: 21436--21997 Score: 772
Period size: 312 Copynumber: 1.8 Consensus size: 310
21426 TAAAACCTAG
21436 TCCTAGGTTGTCACCGGGTCAGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTAATCCCATC
1 TCCTAGGTTGTCACCGGGTCAGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTAATCCCATC
* * * *
21501 TCTAATCTTTTTAAGTCTTTTAGGGTTACCGAGATACTTTCATGTCGAAGGTATACCTATAGAGG
66 TCTAATCTTTTCAAGTCCTTTAAGGTTACCAAGATACTTTCATGTCGAAGGTATACCTATAGAGG
* * ***
21566 GCATTTTCGTAATTTCAAAACCTAGTCTTAGGTTGTCACCCGGTCCGTTTTTATGTTGAAGGTAG
131 GCATTTTCGAAATTTCAAAACCTAGTCTTAGGTTGTCACCCGGTCCGCTTTTATGCCAAAGGTAG
* *
21631 GTATTTAGGATAGGTTCATCCCATCTTTAATCTTTTTAAGTCCTTTAGGGTTACCAGGATACGTT
196 GTATTTAGGATAGGTTCATCCCATCTTTAATCTTTTTAACTCCTTTAGGGGTACCAGGATAC-TT
* *
21696 TATGTCAAAGATATACCTATAGGGGCATTTTTGTAATTTTTTAGAGTTAAA
260 TATGTCAAAGATATACCTATAGAGGCATTTTCGTAATTTTTTAGAGTTAAA
* * * * * * * *
21747 TCCTAGGTTTTTCACTGGGTCTGCTTTTATGCTGAAGGTGGGTATTTAGGATAGTTTCATCCCCT
1 TCCTAGG-TTGTCACCGGGTCAGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTAATCCCAT
* *
21812 CTCTAATCTTTTCAAGTCCTTTAAGGTTACTAAGATACTTTTATGTCGAAGGTATATCC-ATAG-
65 CTCTAATCTTTTCAAGTCCTTTAAGGTTACCAAGATACTTTCATGTCGAAGGTATA-CCTATAGA
* * * * *
21875 GGGTATTTTTGAAATTTTTTAAAACCTAGTCTTAGGTTGTCACCGGGTTCGCTTTTATGCCAAAG
129 GGGCATTTTCGAAA--TTTCAAAACCTAGTCTTAGGTTGTCACCCGGTCCGCTTTTATGCCAAAG
21940 GT-GAGTATTTAGGATAGGTTCATCCCAT-TTGTAATCCTTTTTAACTCCTTTAGGGGTA
192 GTAG-GTATTTAGGATAGGTTCATCCCATCTT-TAAT-CTTTTTAACTCCTTTAGGGGTA
21998 TCGAGTATTT
Statistics
Matches: 218, Mismatches: 26, Indels: 11
0.85 0.10 0.04
Matches are distributed among these distances:
311 18 0.08
312 106 0.49
313 74 0.34
314 20 0.09
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (310 bp):
TCCTAGGTTGTCACCGGGTCAGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTAATCCCATC
TCTAATCTTTTCAAGTCCTTTAAGGTTACCAAGATACTTTCATGTCGAAGGTATACCTATAGAGG
GCATTTTCGAAATTTCAAAACCTAGTCTTAGGTTGTCACCCGGTCCGCTTTTATGCCAAAGGTAG
GTATTTAGGATAGGTTCATCCCATCTTTAATCTTTTTAACTCCTTTAGGGGTACCAGGATACTTT
ATGTCAAAGATATACCTATAGAGGCATTTTCGTAATTTTTTAGAGTTAAA
Found at i:24197 original size:13 final size:13
Alignment explanation
Indices: 24179--24203 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24169 ATTATGCCTA
24179 AAAAAACAAAAAC
1 AAAAAACAAAAAC
24192 AAAAAACAAAAA
1 AAAAAACAAAAA
24204 AATCGAATGA
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:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAAAC
Found at i:25767 original size:44 final size:44
Alignment explanation
Indices: 25591--26130 Score: 247
Period size: 44 Copynumber: 12.3 Consensus size: 44
25581 CTAACATATC
* * **
25591 GTTACCACCCTGGTCAGATTGTTTTCATTCTGA-TTGACATATG
1 GTTACCACCCTGGTCAAATTTTTTTCATTCTGATTTGATGTATG
** * *
25634 GTTACCACCCTGGTCAAATTTTCCTCCTTCTTG-TTTGATGCATG
1 GTTACCACCCTGGTCAAATTTTTTTCATTC-TGATTTGATGTATG
* * * * * **
25678 GCTACCACCTTGGTCAAATTTTTTTTATT-TCAGTCTGACATATG
1 GTTACCACCCTGGTCAAATTTTTTTCATTCTGA-TTTGATGTATG
* * * *
25722 GTTATCACCCTAGTCAGATTTTTTTCATTCTGATTTGATGCATG
1 GTTACCACCCTGGTCAAATTTTTTTCATTCTGATTTGATGTATG
* * *** * *
25766 GTTAGCACCCTGGTC-AATCTGCCTCCTTCTTG-TTTGACGTATG
1 GTTACCACCCTGGTCAAATTTTTTTCATTC-TGATTTGATGTATG
* * * * *
25809 TTTACCACCCTAGTTAAACTCTTTTT-ATT-TTAGTTTGATGTATG
1 GTTACCACCCTGGTCAAA-TTTTTTTCATTCTGA-TTTGATGTATG
* * * * * *
25853 GTTACCACCTTGGTTATATTCTTTTCATTCTGATTTAATGCATG
1 GTTACCACCCTGGTCAAATTTTTTTCATTCTGATTTGATGTATG
* * * ***** *
25897 GTTATCACCTTAGTCAAATCAGCCTCCTTCCTG-TTTGATGTATG
1 GTTACCACCCTGGTCAAATTTTTTTCATT-CTGATTTGATGTATG
* * * * * *
25941 GTTACCACCTTGGTTAGATTCTTTTCATTCTGATTTAATGCATG
1 GTTACCACCCTGGTCAAATTTTTTTCATTCTGATTTGATGTATG
* * * ***** * *
25985 GTTATCACCTTAGTCAAATCAGCCTCCTTCCTG-TTTAATGTATG
1 GTTACCACCCTGGTCAAATTTTTTTCATT-CTGATTTGATGTATG
* * * * * **
26029 GTTACCACCTTGGTCAAACTCTTTTCAGGTCAG-TTTGACATATG
1 GTTACCACCCTGGTCAAATTTTTTTCA-TTCTGATTTGATGTATG
* * ** * *
26073 GATACCACCCTGGTCAGATTCCTTTCATTCCTG-CTTGACGTATG
1 GTTACCACCCTGGTCAAATTTTTTTCATT-CTGATTTGATGTATG
26117 GTTACCACCCTGGT
1 GTTACCACCCTGGT
26131 TAAGCTCTTT
Statistics
Matches: 362, Mismatches: 118, Indels: 33
0.71 0.23 0.06
Matches are distributed among these distances:
42 2 0.01
43 62 0.17
44 283 0.78
45 15 0.04
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (44 bp):
GTTACCACCCTGGTCAAATTTTTTTCATTCTGATTTGATGTATG
Found at i:25795 original size:131 final size:132
Alignment explanation
Indices: 25573--25954 Score: 435
Period size: 131 Copynumber: 2.9 Consensus size: 132
25563 AATTCTTCTC
* * * * ***
25573 ATTTCGGTCTAACATATCGTTACCACCCTGGTCAGATTGTTTTCATTCTGA-TTGACATATGGTT
1 ATTTCAGTCTGACATATGGTTACCACCCTGGTCAGATTCTTTTCATTCTGATTTGATGCATGGTT
* * * * * *
25637 ACCACCCTGGTCAAATTTTCCTCCTTCTTGTTTGATGCATGGCTACCACCTTGGTCAAATTTTTT
66 ACCACCCTGGTCAAATCTGCCTCCTTCTTGTTTGATGTATGGTTACCACCTTGGTCAAACTCTTT
25702 TT
131 TT
* * *
25704 ATTTCAGTCTGACATATGGTTATCACCCTAGTCAGATTTTTTTCATTCTGATTTGATGCATGGTT
1 ATTTCAGTCTGACATATGGTTACCACCCTGGTCAGATTCTTTTCATTCTGATTTGATGCATGGTT
* * * * * *
25769 AGCACCCTGGTC-AATCTGCCTCCTTCTTGTTTGACGTATGTTTACCACCCTAGTTAAACTCTTT
66 ACCACCCTGGTCAAATCTGCCTCCTTCTTGTTTGATGTATGGTTACCACCTTGGTCAAACTCTTT
25833 TT
131 TT
* * ** * * * *
25835 ATTTTAGTTTGATGTATGGTTACCACCTTGGTTATATTCTTTTCATTCTGATTTAATGCATGGTT
1 ATTTCAGTCTGACATATGGTTACCACCCTGGTCAGATTCTTTTCATTCTGATTTGATGCATGGTT
* * * * *
25900 ATCACCTTAGTCAAATCAGCCTCCTTCCTGTTTGATGTATGGTTACCACCTTGGT
66 ACCACCCTGGTCAAATCTGCCTCCTTCTTGTTTGATGTATGGTTACCACCTTGGT
25955 TAGATTCTTT
Statistics
Matches: 208, Mismatches: 41, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
131 151 0.73
132 57 0.27
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (132 bp):
ATTTCAGTCTGACATATGGTTACCACCCTGGTCAGATTCTTTTCATTCTGATTTGATGCATGGTT
ACCACCCTGGTCAAATCTGCCTCCTTCTTGTTTGATGTATGGTTACCACCTTGGTCAAACTCTTT
TT
Found at i:25986 original size:132 final size:131
Alignment explanation
Indices: 25743--25995 Score: 328
Period size: 132 Copynumber: 1.9 Consensus size: 131
25733 AGTCAGATTT
* * * *
25743 TTTTCATTCTGATTTGATGCATGGTTAGCACCCTGGTCAATCTGCCTCCTTCTTGTTTGACGTAT
1 TTTTCATTCTGATTTAATGCATGGTTAGCACCCTAGTCAATCAGCCTCCTTCCTGTTTGACGTAT
* * * * *
25808 GTTTACCACCCTAGTTAAACTCTTTTTATTTTAGTTTGATGTATGGTTACCACCTTGGTTATATT
66 GGTTACCACCCTAGTTAAACTCTTTTCATTTGAGTTTAATGCATGGTTACCACCTTGGTTATATT
25873 C
131 C
* * *
25874 TTTTCATTCTGATTTAATGCATGGTTATCACCTTAGTCAAATCAGCCTCCTTCCTGTTTGATGTA
1 TTTTCATTCTGATTTAATGCATGGTTAGCACCCTAGTC-AATCAGCCTCCTTCCTGTTTGACGTA
* * * * *
25939 TGGTTACCACCTTGGTTAGATTCTTTTCATTCTGA-TTTAATGCATGGTTATCACCTT
65 TGGTTACCACCCTAGTTAAACTCTTTTCATT-TGAGTTTAATGCATGGTTACCACCTT
25996 AGTCAAATCA
Statistics
Matches: 103, Mismatches: 17, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
131 34 0.33
132 67 0.65
133 2 0.02
ACGTcount: A:0.19, C:0.21, G:0.15, T:0.45
Consensus pattern (131 bp):
TTTTCATTCTGATTTAATGCATGGTTAGCACCCTAGTCAATCAGCCTCCTTCCTGTTTGACGTAT
GGTTACCACCCTAGTTAAACTCTTTTCATTTGAGTTTAATGCATGGTTACCACCTTGGTTATATT
C
Found at i:25990 original size:88 final size:88
Alignment explanation
Indices: 25841--26042 Score: 386
Period size: 88 Copynumber: 2.3 Consensus size: 88
25831 TTTTATTTTA
*
25841 GTTTGATGTATGGTTACCACCTTGGTTATATTCTTTTCATTCTGATTTAATGCATGGTTATCACC
1 GTTTGATGTATGGTTACCACCTTGGTTAGATTCTTTTCATTCTGATTTAATGCATGGTTATCACC
25906 TTAGTCAAATCAGCCTCCTTCCT
66 TTAGTCAAATCAGCCTCCTTCCT
25929 GTTTGATGTATGGTTACCACCTTGGTTAGATTCTTTTCATTCTGATTTAATGCATGGTTATCACC
1 GTTTGATGTATGGTTACCACCTTGGTTAGATTCTTTTCATTCTGATTTAATGCATGGTTATCACC
25994 TTAGTCAAATCAGCCTCCTTCCT
66 TTAGTCAAATCAGCCTCCTTCCT
*
26017 GTTTAATGTATGGTTACCACCTTGGT
1 GTTTGATGTATGGTTACCACCTTGGT
26043 CAAACTCTTT
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 112 1.00
ACGTcount: A:0.20, C:0.21, G:0.16, T:0.43
Consensus pattern (88 bp):
GTTTGATGTATGGTTACCACCTTGGTTAGATTCTTTTCATTCTGATTTAATGCATGGTTATCACC
TTAGTCAAATCAGCCTCCTTCCT
Found at i:26143 original size:44 final size:44
Alignment explanation
Indices: 26024--26174 Score: 135
Period size: 44 Copynumber: 3.4 Consensus size: 44
26014 CCTGTTTAAT
* * * *
26024 GTATGGTTACCACCTTGGTCAAACTCTTTTCAGGT-CAGTTTGAC
1 GTATGGTTACCACCCTGGTTAAGCTCTTTTCA-TTCCAGTTTGAC
* * * * * * *
26068 ATATGGATACCACCCTGG-TCAGATTCCTTTCATTCCTGCTTGAC
1 GTATGGTTACCACCCTGGTTAAG-CTCTTTTCATTCCAGTTTGAC
*
26112 GTATGGTTACCACCCTGGTTAAGCTCTTTTCATTCCCGTTTGAC
1 GTATGGTTACCACCCTGGTTAAGCTCTTTTCATTCCAGTTTGAC
* * *
26156 GTGTGATTACCACTCTGGT
1 GTATGGTTACCACCCTGGT
26175 CAAACGTTTC
Statistics
Matches: 83, Mismatches: 21, Indels: 6
0.75 0.19 0.05
Matches are distributed among these distances:
43 2 0.02
44 78 0.94
45 3 0.04
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (44 bp):
GTATGGTTACCACCCTGGTTAAGCTCTTTTCATTCCAGTTTGAC
Found at i:27969 original size:156 final size:151
Alignment explanation
Indices: 27720--28023 Score: 385
Period size: 156 Copynumber: 2.0 Consensus size: 151
27710 CTGTAAGATC
** *
27720 ATTTTCAAAATATGAAGTTTTTTACTCTGTAAATTTTCGGTAGGATTTTTCTAAGTTTATAATTT
1 ATTTTCAAAATATGAAGTTTTTTACTCCATAAATTTTCAGTAGGATTTTTCTAAGTTTATAATTT
* * * *
27785 TCAAAATTCTTTAAATATTATTGTTTAATTCATATTAAATTAG-TTTTGAAAATTTCAACTTATT
66 TAAAAATTCTTCAAATATTATTGTTTAATTCACATTAAATCAGTTTTTGAAAA-TTCAACTTATT
27849 TTATAAGTTTTAGAATTTTTCCT
130 TTATAAGTTTT-GAATTTTTCCT
* * *
27872 ATTTTCAAAATATGGAATTTTTTTACTCCATAAATTTCTCTAGTAGTATTTTTCTTAGTTTATAA
1 ATTTTCAAAATAT-GAAGTTTTTTACTCCATAAATTT-TC-AGTAGGATTTTTCTAAGTTTATAA
* * * * *
27937 TTTTTAAAAATTCTTCGAATATTGTTGTTTAATTCACATTGAATCAGTTTTTTTAAAATTCAATT
63 -TTTTAAAAATTCTTCAAATATTATTGTTTAATTCACATTAAATCAG-TTTTTGAAAATTCAACT
* *
28002 TATTTTGTGAGTTTTGAATTTT
126 TATTTTATAAGTTTTGAATTTT
28024 ATATAACCAT
Statistics
Matches: 129, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
152 13 0.10
153 20 0.16
154 2 0.02
155 21 0.16
156 46 0.36
157 19 0.15
158 8 0.06
ACGTcount: A:0.31, C:0.08, G:0.09, T:0.52
Consensus pattern (151 bp):
ATTTTCAAAATATGAAGTTTTTTACTCCATAAATTTTCAGTAGGATTTTTCTAAGTTTATAATTT
TAAAAATTCTTCAAATATTATTGTTTAATTCACATTAAATCAGTTTTTGAAAATTCAACTTATTT
TATAAGTTTTGAATTTTTCCT
Found at i:29379 original size:23 final size:25
Alignment explanation
Indices: 29336--29393 Score: 93
Period size: 23 Copynumber: 2.4 Consensus size: 25
29326 TTGTTGTTTT
29336 TTTTATGTATGTACATTTTCATATGA
1 TTTTATG-ATGTACATTTTCATATGA
29362 TTTTATGATG-A-ATTTTCATATGA
1 TTTTATGATGTACATTTTCATATGA
29385 TTTTATGAT
1 TTTTATGAT
29394 ATTTTAACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 3 0.09
26 7 0.22
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.55
Consensus pattern (25 bp):
TTTTATGATGTACATTTTCATATGA
Found at i:29384 original size:12 final size:11
Alignment explanation
Indices: 29350--29388 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
29340 ATGTATGTAC
29350 ATTTTCATATG
1 ATTTTCATATG
29361 ATTTT-ATGATG
1 ATTTTCAT-ATG
29372 AATTTTCATATG
1 -ATTTTCATATG
29384 ATTTT
1 ATTTT
29389 ATGATATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 2 0.08
11 13 0.52
12 8 0.32
13 2 0.08
ACGTcount: A:0.28, C:0.05, G:0.10, T:0.56
Consensus pattern (11 bp):
ATTTTCATATG
Found at i:29399 original size:10 final size:11
Alignment explanation
Indices: 29358--29399 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
29348 ACATTTTCAT
29358 ATGATTTTATG
1 ATGATTTTATG
29369 ATGAATTTTCAT-
1 ATG-ATTTT-ATG
29381 ATGATTTTATG
1 ATGATTTTATG
29392 AT-ATTTTA
1 ATGATTTTA
29400 ACATGTAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 8 0.29
11 10 0.36
12 8 0.29
13 2 0.07
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (11 bp):
ATGATTTTATG
Found at i:29901 original size:166 final size:165
Alignment explanation
Indices: 29414--29932 Score: 636
Period size: 165 Copynumber: 3.1 Consensus size: 165
29404 GTAAGGACTA
* * * *
29414 AAATGAAAATTTTTAAAAGTTTAGGGATTAAATAGCAAATTTTAGTTTTTAAAGGTATAATCATC
1 AAATGAAAA-TTTCAAAAGTTTAGAGATTAAATAGCAAATTTTAGTTTTTAAAGATAAAATCATC
* *
29479 ATTTTAGTCATTTTTAAAGATTTGTATTATTCCTATGGCCTT-CTTAGA-GCTATAAAAATTTTC
65 ATTTTAGTCATTTTTAAAGATTTCTATTATTCCTATGGCCTTCCATAGAGGC-ATAAAAATTTTC
* * *
29542 AAAACTTTTCGTATCCTCTTGGTTTTTCATGAGGTAAG
129 AAGACTTTT-GTATCCTCTCGGTTTTTCATTAGGTAAG
* *
29580 AAAT-AAATTTTTCAAAAGTTTA-AGGATTAAATAGCAAATTTTAGTTTTTAAAGCTAAAA-CAT
1 AAATGAAA-ATTTCAAAAGTTTAGA-GATTAAATAGCAAATTTTAGTTTTTAAAGATAAAATCAT
* * *
29642 TATTTTAGTCATTTTTAAAGATTTCTATTATTCCTATGGCCTTCCATAGGGGCATAAAAACTTTC
64 CATTTTAGTCATTTTTAAAGATTTCTATTATTCCTATGGCCTTCCATAGAGGCATAAAAATTTTC
** * * *
29707 AAGACTTATCATATCCTTTCGGTTTTTCATTAGATACG
129 AAGACTT-TTGTATCCTCTCGGTTTTTCATTAGGTAAG
* * * *
29745 AAATGAAAATTTGAAAAGTTTAGAGATTAAATAGCAAATTTTAGTTTTTAGAGAAAAAATAATCA
1 AAATGAAAATTTCAAAAGTTTAGAGATTAAATAGCAAATTTTAGTTTTTAAAGATAAAATCATCA
* * * * *
29810 TTTTAGTCATTTTTAGAGATTTCTATTATTTCTATGGCCTTCCGTAGAGGCATAGATATTTTCAA
66 TTTTAGTCATTTTTAAAGATTTCTATTATTCCTATGGCCTTCCATAGAGGCATAAAAATTTTCAA
** *
29875 GACCTTTTGTATCCTCTCAATTTTTCATTGGGTATA-
131 GA-CTTTTGTATCCTCTCGGTTTTTCATTAGGTA-AG
*
29911 AAATGAAATTTTCAAAAGTTTA
1 AAATGAAAATTTCAAAAGTTTA
29933 AGGGCTTAAT
Statistics
Matches: 301, Mismatches: 42, Indels: 20
0.83 0.12 0.06
Matches are distributed among these distances:
164 44 0.15
165 139 0.46
166 115 0.38
167 3 0.01
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.41
Consensus pattern (165 bp):
AAATGAAAATTTCAAAAGTTTAGAGATTAAATAGCAAATTTTAGTTTTTAAAGATAAAATCATCA
TTTTAGTCATTTTTAAAGATTTCTATTATTCCTATGGCCTTCCATAGAGGCATAAAAATTTTCAA
GACTTTTGTATCCTCTCGGTTTTTCATTAGGTAAG
Found at i:30520 original size:156 final size:154
Alignment explanation
Indices: 30265--30649 Score: 375
Period size: 155 Copynumber: 2.5 Consensus size: 154
30255 TTGTCATTGG
* * ** *
30265 GATGCTTTTATGCCAAAGGTGTGCATTTGGGATAAGTTTATCCCATTTATGATCATTTTCAAGTC
1 GATGCTTTTATGCCAAAGGTGTGCATTTAGGATAAATTTATATCATTTATGATCATTTTTAAGTC
** * * * * * * * *
30330 TGTTGGGGTTACTAGGATACTTTTATGTTGAAGGTATACT-TTAGGGAAATTTTTATAATTTT-T
66 T-TTAAGGTTACTAGGATACTCTCAAGCTAAAGGTATA-TACTAAGG-AATTTTCATAATTTTCT
*
30393 CTA-AAGCCGAGTCTTAGGTTATCACCAA
128 -TATAA-CCAAGTCTTAGGTTATCACCAA
* * * *
30421 GATGCTTTTATGCTAAAAGTGTGCATTTAGGATAATTTTATTTCATTTATGATCATTTTTAAGTC
1 GATGCTTTTATGCCAAAGGTGTGCATTTAGGATAAATTTATATCATTTATGATCATTTTTAAGT-
* *
30486 CTTTAAGGTTACT-GAGATACTCTCAAGCTAAAGGTATATACTAAGGCATTTTCGTAATTTTCTT
65 CTTTAAGGTTACTAG-GATACTCTCAAGCTAAAGGTATATACTAAGGAATTTTCATAATTTTCTT
* * ***
30550 ATAACTAAGTCTTAGGTTGTCACTGG
129 ATAACCAAGTCTTAGGTTATCACCAA
* * *
30576 GATGCTTTTATGCCCAAGGTGTGCATTTAGGATAAATTCATCAT-ATTTACGATCATTTTTAAGT
1 GATGCTTTTATGCCAAAGGTGTGCATTTAGGATAAATTTAT-ATCATTTATGATCATTTTTAAG-
*
30640 TTTTTAAGGT
64 TCTTTAAGGT
30650 GTAAACACCT
Statistics
Matches: 189, Mismatches: 33, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
155 94 0.50
156 93 0.49
157 2 0.01
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (154 bp):
GATGCTTTTATGCCAAAGGTGTGCATTTAGGATAAATTTATATCATTTATGATCATTTTTAAGTC
TTTAAGGTTACTAGGATACTCTCAAGCTAAAGGTATATACTAAGGAATTTTCATAATTTTCTTAT
AACCAAGTCTTAGGTTATCACCAA
Found at i:30610 original size:155 final size:155
Alignment explanation
Indices: 30246--30649 Score: 397
Period size: 156 Copynumber: 2.6 Consensus size: 155
30236 TCTAAAATTT
* * * * **
30246 AGTCCTAGGTTGTCATTGGGATGCTTTTATGCCAAAGGTGTGCATTTGGGATAAGTTTATCCCAT
1 AGTCTTAGGTTGTCACTGGGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAAATTTATATCAT
* ** * * * * * * *
30311 TTATGATCATTTTCAAGTCTGTTGGGGTTACTAGGATACTTTTATGTTGAAGGTATACTTTAGGG
66 TTATGATCATTTTTAAGTCT-TTAAGGTTACTAGGATACTCTCAAGCTAAAGGTATACTCTAAGG
* *
30376 AAATTTTTATAATTTTTCTAAAGCCG
130 AAATTTTCATAATTTTTCTAAAGCCA
* *** * * * *
30402 AGTCTTAGGTTATCACCAAGATGCTTTTATGCTAAAAGTGTGCATTTAGGATAATTTTATTTCAT
1 AGTCTTAGGTTGTCACTGGGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAAATTTATATCAT
30467 TTATGATCATTTTTAAGTCCTTTAAGGTTACT-GAGATACTCTCAAGCTAAAGGTATA-TACTAA
66 TTATGATCATTTTTAAGT-CTTTAAGGTTACTAG-GATACTCTCAAGCTAAAGGTATACT-CTAA
* * *
30530 GG-CATTTTCGTAA-TTTTCTTATAA-CTA
128 GGAAATTTTCATAATTTTTC-TA-AAGCCA
* *
30557 AGTCTTAGGTTGTCACTGGGATGCTTTTATGCCCAAGGTGTGCATTTAGGATAAATTCATCAT-A
1 AGTCTTAGGTTGTCACTGGGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAAATTTAT-ATCA
* *
30621 TTTACGATCATTTTTAAGTTTTTTAAGGT
65 TTTATGATCATTTTTAAG-TCTTTAAGGT
30650 GTAAACACCT
Statistics
Matches: 202, Mismatches: 39, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
154 5 0.02
155 90 0.45
156 105 0.52
157 2 0.01
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (155 bp):
AGTCTTAGGTTGTCACTGGGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAAATTTATATCAT
TTATGATCATTTTTAAGTCTTTAAGGTTACTAGGATACTCTCAAGCTAAAGGTATACTCTAAGGA
AATTTTCATAATTTTTCTAAAGCCA
Found at i:30977 original size:20 final size:21
Alignment explanation
Indices: 30935--30979 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
30925 TTCTACAATT
30935 TGTATCGATACAATAAGATAA
1 TGTATCGATACAATAAGATAA
*
30956 TGTATGGATAC-ATAAG-TGAA
1 TGTATCGATACAATAAGAT-AA
30976 TGTA
1 TGTA
30980 GCAATACATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 11 0.50
21 10 0.45
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (21 bp):
TGTATCGATACAATAAGATAA
Found at i:31103 original size:52 final size:52
Alignment explanation
Indices: 31061--31162 Score: 159
Period size: 52 Copynumber: 2.0 Consensus size: 52
31051 TCGATATATT
* *
31061 TTTCATTATATCGATACATTCTGGGTTTTCAACTCAAATGTATCAATACAAG
1 TTTCATTATATCGATACATTCTGAGTTTTCAACCCAAATGTATCAATACAAG
* **
31113 TTTCATTCTATCGATACATTCTGAGTTTTTGACCCAAATGTATCAATACA
1 TTTCATTATATCGATACATTCTGAGTTTTCAACCCAAATGTATCAATACA
31163 TTCTTCAATG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (52 bp):
TTTCATTATATCGATACATTCTGAGTTTTCAACCCAAATGTATCAATACAAG
Found at i:37125 original size:81 final size:81
Alignment explanation
Indices: 37008--37158 Score: 266
Period size: 81 Copynumber: 1.9 Consensus size: 81
36998 TTTTTAAAAC
* * *
37008 AATATATGGAACTATAATTAAATATTTATTTAAACCAAATTAATCAAAACTTATTTAACACATAA
1 AATATAGGGAACCATAATTAAATATTTATTAAAACCAAATTAATCAAAACTTATTTAACACATAA
37073 ATAATCTCTTTTTTTT
66 ATAATCTCTTTTTTTT
37089 AATATAGGGAACCATAATTAAATATTTATTAAAACCAAATTAATCAAAACTTATTTAACACATAA
1 AATATAGGGAACCATAATTAAATATTTATTAAAACCAAATTAATCAAAACTTATTTAACACATAA
*
37154 TTAAT
66 ATAAT
37159 TTTAGGCCTG
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 66 1.00
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (81 bp):
AATATAGGGAACCATAATTAAATATTTATTAAAACCAAATTAATCAAAACTTATTTAACACATAA
ATAATCTCTTTTTTTT
Found at i:38978 original size:146 final size:146
Alignment explanation
Indices: 38708--38990 Score: 399
Period size: 146 Copynumber: 1.9 Consensus size: 146
38698 TGAAAGGCCA
* * *
38708 TAAGAATAATAGAAATCTTTAAAAGTGGCTAAAATGATGATTTTACCTCTAAAAACTAAAATTTG
1 TAAGAATAAAAGAAATCTTTAAAAGTGACTAAAATGATGATTTTACCACTAAAAACTAAAATTTG
*
38773 CTATTTAATCCCTAAAATTTTAAAAATCTCATTTCGTACCTGACGAAAAACAAAGAGGATGCAAA
66 CTATTTAATCCCTAAAATTTTAAAAATCTCATTTCGTACCTGACGAAAAACAAAGAGGATACAAA
38838 AAGTTTTGTAAATTTC
131 AAGTTTTGTAAATTTC
*
38854 TAAGAATAAAAGAAATATTTTAAAA-TGACTAAAATGATGATTTTACCACTAAAAACTAAAATTT
1 TAAGAATAAAAGAAAT-CTTTAAAAGTGACTAAAATGATGATTTTACCACTAAAAACTAAAATTT
* ** * * * * * * *
38918 TCTATTTAATCTTTAAAGTTTTAAAATTTTCATTTCGTACCTGATGGAAAACCGAA-AGGATACG
65 GCTATTTAATCCCTAAAATTTTAAAAATCTCATTTCGTACCTGA-CGAAAAACAAAGAGGATACA
38982 AAAAGTTTT
129 AAAAGTTTT
38991 AAAAATTGCT
Statistics
Matches: 120, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
146 105 0.88
147 15 0.12
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (146 bp):
TAAGAATAAAAGAAATCTTTAAAAGTGACTAAAATGATGATTTTACCACTAAAAACTAAAATTTG
CTATTTAATCCCTAAAATTTTAAAAATCTCATTTCGTACCTGACGAAAAACAAAGAGGATACAAA
AAGTTTTGTAAATTTC
Found at i:42701 original size:167 final size:162
Alignment explanation
Indices: 42474--42951 Score: 460
Period size: 164 Copynumber: 2.9 Consensus size: 162
42464 TTAAATTTCG
* * * *
42474 GAGTTTTCTTCTTCATAAATTTTTT-GGAAGGATTTTCATGGGTTTAAAATTTTCAAAATTCATT
1 GAGTTTTCTTCTCCAT-AATTTTTTCGGAGGGATTTTC-TAGGTTTAAAATTTTTAAAATTCATT
* * *
42538 AAATATTATTATTTAATTCACATTAAATCATTTTTCAAAAACTCCTTAATTTTCATGAGTTTTTG
64 AAATATTATTATTTAATTCAAATTAAATCATTTTTAAAAAACTCCTTCATTTTCATGAGTTTTTG
*
42603 AATTTTTTCCTTAAAATTTCTCGGTTTTCTAAATATA
129 AATTTTTT-CTTAAAATTT-TCGGTTTTCGAAATA-A
42640 GAGTTTTCTTCTCCATAATTTATTTCGGAGGGATTTTTCTAGGTTTAAAATTTTTAAAATTCATT
1 GAGTTTTCTTCTCCATAATTT-TTTCGGAGGGA-TTTTCTAGGTTTAAAATTTTTAAAATTCATT
* * * * * *
42705 AAATTTTATGATTTAACTCAAATTAAATCAATTTTAAAAAACTCCTTCATTTTCCTAAG--TTTG
64 AAATATTATTATTTAATTCAAATTAAATCATTTTTAAAAAACTCCTTCATTTTCATGAGTTTTTG
* *** *
42768 AATTTTTTTCTTGAAATTTTTTTTTTTCGAAATAC
129 AA-TTTTTTCTTAAAATTTTCGGTTTTCGAAATAA
* * ** * ** * ** *
42803 GAAATTTTCTAATTTGTA-AATGTTTTCCAAGGGACTTTTCTTGGTTTTTAATTTTTAAAATTTA
1 G-AGTTTTCT--TCTCCATAATTTTTTCGGAGGGA-TTTTCTAGGTTTAAAATTTTTAAAATTCA
* * * * * ** *
42867 TCAAATATTATTATTTAATTCATATTTAATCATTTTTGAAAAATTAATTCATCTTCATGAGTTAT
62 TTAAATATTATTATTTAATTCAAATTAAATCATTTTTAAAAAACTCCTTCATTTTCATGAGTT-T
42932 TTGAATTTTTTCTTGAAAAT
126 TTGAATTTTTTCTT-AAAAT
42952 CCATTTTTTC
Statistics
Matches: 255, Mismatches: 46, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
163 1 0.00
164 99 0.39
165 24 0.09
166 36 0.14
167 90 0.35
168 5 0.02
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.50
Consensus pattern (162 bp):
GAGTTTTCTTCTCCATAATTTTTTCGGAGGGATTTTCTAGGTTTAAAATTTTTAAAATTCATTAA
ATATTATTATTTAATTCAAATTAAATCATTTTTAAAAAACTCCTTCATTTTCATGAGTTTTTGAA
TTTTTTCTTAAAATTTTCGGTTTTCGAAATAA
Found at i:42977 original size:19 final size:18
Alignment explanation
Indices: 42935--42979 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
42925 GAGTTATTTG
**
42935 AATTTTTTCTTGAAAATC
1 AATTTTTTCTAAAAAATC
*
42953 CATTTTTTCTAAAAAATC
1 AATTTTTTCTAAAAAATC
42971 AAGTTTTTT
1 AA-TTTTTT
42980 ATTCCACAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.51
Consensus pattern (18 bp):
AATTTTTTCTAAAAAATC
Done.