Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold191
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: 842153
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 45129 characters in sequence are not A, C, G, or T
File 3 of 6
Found at i:298130 original size:80 final size:78
Alignment explanation
Indices: 297994--298236 Score: 294
Period size: 80 Copynumber: 3.1 Consensus size: 78
297984 AAGAGATGCA
* * *
297994 AAATTTGGTGTTTTAAAAGTAAAAATAGAGTTAGAGTATCC-CTTCGGTGATGGTGGGGTTGGAG
1 AAATTCGGTGTTTTAGAAGTAAAAATAG-GTT-GAGTATCCTC-TCGGAGATGGTGGGGTTGGAG
298058 TATCCCCAAATATGAG
63 TATCCCCAAATATGAG
** * *
298074 AAATTCGGTGTTTTAGAAGTAAAAATGAGGTTGGAGTATCCTCTCAAAGATAGTGGGGTTAGAGT
1 AAATTCGGTGTTTTAGAAGTAAAAAT-AGGTT-GAGTATCCTCTCGGAGATGGTGGGGTTGGAGT
298139 ATCCCCAAATATGAG
64 ATCCCCAAATATGAG
** * *
298154 AAATTCAATGTTTTAGAAGTAAAAACAAGGTTGAGTAT-CTCCTCGGAGATGGTAGGGTTGGAGT
1 AAATTCGGTGTTTTAGAAGTAAAAA-TAGGTTGAGTATCCT-CTCGGAGATGGTGGGGTTGGAGT
*
298218 ATCCCCAAAGATGA-
64 ATCCCCAAATATGAG
298232 AAATT
1 AAATT
298237 TTGGCATTTT
Statistics
Matches: 142, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
78 7 0.05
79 37 0.26
80 95 0.67
81 3 0.02
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (78 bp):
AAATTCGGTGTTTTAGAAGTAAAAATAGGTTGAGTATCCTCTCGGAGATGGTGGGGTTGGAGTAT
CCCCAAATATGAG
Found at i:303025 original size:33 final size:33
Alignment explanation
Indices: 302988--303054 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
302978 AGTAGCTTAA
302988 ATTGTATCGAGACAAAAAAATATGTATCGATAC
1 ATTGTATCGAGACAAAAAAATATGTATCGATAC
* * ***
303021 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGAGACAAAAAAATATGTATCGATAC
303054 A
1 A
303055 AATCATTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.31
Consensus pattern (33 bp):
ATTGTATCGAGACAAAAAAATATGTATCGATAC
Found at i:303028 original size:13 final size:13
Alignment explanation
Indices: 303010--303034 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
303000 CAAAAAAATA
303010 TGTATCGATACAT
1 TGTATCGATACAT
303023 TGTATCGATACA
1 TGTATCGATACA
303035 ACACTTTATG
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:304049 original size:32 final size:32
Alignment explanation
Indices: 304008--304081 Score: 139
Period size: 32 Copynumber: 2.3 Consensus size: 32
303998 TTTAATAGTG
304008 TATCGATACATCTGGGCAAATTTGCCTGCATC
1 TATCGATACATCTGGGCAAATTTGCCTGCATC
*
304040 TATCGATACATCTGGGCAAATTTGCCTGCATG
1 TATCGATACATCTGGGCAAATTTGCCTGCATC
304072 TATCGATACA
1 TATCGATACA
304082 AAGATCAGTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (32 bp):
TATCGATACATCTGGGCAAATTTGCCTGCATC
Found at i:304179 original size:33 final size:33
Alignment explanation
Indices: 304142--304208 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
304132 AGTAGCTTAA
304142 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
304175 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
304208 A
1 A
304209 AATCATTGAA
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:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:304182 original size:13 final size:13
Alignment explanation
Indices: 304164--304188 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
304154 CAAAAAAATA
304164 TGTATCGATACAT
1 TGTATCGATACAT
304177 TGTATCGATACA
1 TGTATCGATACA
304189 ACACTTTATG
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:305332 original size:21 final size:22
Alignment explanation
Indices: 305303--305361 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
305293 GGGTCAAAAC
*
305303 CTAGAATGTATC-ATTACATT-A
1 CTAGTATGTATCGA-TACATTCA
305324 CTAGTATGTATCGATACATTCA
1 CTAGTATGTATCGATACATTCA
*
305346 CT--TATGTATCGGTACA
1 CTAGTATGTATCGATACA
305362 ATTTTTTCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 13 0.38
21 17 0.50
22 4 0.12
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (22 bp):
CTAGTATGTATCGATACATTCA
Found at i:308649 original size:79 final size:78
Alignment explanation
Indices: 308487--308705 Score: 298
Period size: 79 Copynumber: 2.8 Consensus size: 78
308477 CAGGGCTAGA
*
308487 AGTATCCCCGATTATGGAAAATCGGTGTTTTAGAAATAAAAATCGGGGTTGGAGTATCCCCTCAG
1 AGTATCCCCGATTAT-GAAAATCGATGTTTTAGAAAT-AAAATCGGGGTTGGAGTATCCCCTCAG
308552 AAATAATAGGGTTGG
64 AAATAATAGGGTTGG
* * * *
308567 AGTATCCCCGATTATAGAAAATCGCTGTTTT-GAAAATAAAATTGGGATTGGAGTATCCCCGTGA
1 AGTATCCCCGATTAT-GAAAATCGATGTTTTAG-AAATAAAATCGGGGTTGGAGTATCCCC-TCA
308631 -AAATAATAGGGTTGG
63 GAAATAATAGGGTTGG
* * *
308646 AGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAGTCGGGGTTGGAGTATCCCC
1 AGTATCCCCGATTATGA-AAATCGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCC
308706 AATTGTGAAA
Statistics
Matches: 124, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
78 2 0.02
79 86 0.69
80 36 0.29
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.28
Consensus pattern (78 bp):
AGTATCCCCGATTATGAAAATCGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCAGAA
ATAATAGGGTTGG
Found at i:308704 original size:51 final size:50
Alignment explanation
Indices: 308639--308807 Score: 221
Period size: 51 Copynumber: 3.3 Consensus size: 50
308629 GAAAATAATA
* * *
308639 GGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAAGTCG
1 GGGTTGGAGTATCCCCGATTATGA-AAATCGATGTTTTAGAAATAAAATCG
* * *
308690 GGGTTGGAGTATCCCCAATTGTGAAAATCTGATGTTTTGGAAATAAAATCG
1 GGGTTGGAGTATCCCCGATTATGAAAATC-GATGTTTTAGAAATAAAATCG
* * * *
308741 GAGTTGGAGTATCCCCGATTATGAAAATTTGATGTTTTAAAAATAAAACCG
1 GGGTTGGAGTATCCCCGATTATGAAAA-TCGATGTTTTAGAAATAAAATCG
308792 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
308808 TTGGAAATAA
Statistics
Matches: 102, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
50 5 0.05
51 96 0.94
52 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (50 bp):
GGGTTGGAGTATCCCCGATTATGAAAATCGATGTTTTAGAAATAAAATCG
Found at i:308864 original size:79 final size:77
Alignment explanation
Indices: 308747--308989 Score: 242
Period size: 79 Copynumber: 3.1 Consensus size: 77
308737 ATCGGAGTTG
* *
308747 GAGTATCCCCGATTATGAAAATTTGATGTTTTAAAAATAAAACCGGGGTTGGAGTATCCCCTTGG
1 GAGTATCCCCGA-TATGAAAA-TCGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTTGG
308812 AAATAACGGGGTTA
64 AAATAACGGGGTTA
* * *
308826 GAGTATCCCCGATAGTGGAAAATCGATGTTTTGGAAAT-AAACCGGGATTGGAGTAT--CCTCGC
1 GAGTATCCCCGATA-T-GAAAATCGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTTG-
* *
308888 GAAATAATGGGGTTG
63 GAAATAACGGGGTTA
* * * ** * * *
308903 GAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGTCGAGGTTGGAGTAT-TCCTTCA
1 GAGTATCCCCGA-TATGA-AAATCGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTT-G
*
308967 GAAATAACGGGGTTG
63 GAAATAACGGGGTTA
308982 GAGTATCC
1 GAGTATCC
308990 TCAATGAAAT
Statistics
Matches: 138, Mismatches: 18, Indels: 16
0.80 0.10 0.09
Matches are distributed among these distances:
76 6 0.04
77 42 0.30
78 34 0.25
79 51 0.37
80 5 0.04
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (77 bp):
GAGTATCCCCGATATGAAAATCGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTTGGAA
ATAACGGGGTTA
Found at i:309016 original size:28 final size:27
Alignment explanation
Indices: 308949--309017 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 27
308939 ATAAAGTCGA
308949 GGTTGGAGTATTCCTTCAGAAATAACGG
1 GGTTGGAGTA-TCCTTCAGAAATAACGG
308977 GGTTGGAGTATCC-TCAATGAAATAACGG
1 GGTTGGAGTATCCTTC-A-GAAATAACGG
309005 GGTTGGAGTATCC
1 GGTTGGAGTATCC
309018 CCGATTGTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
26 2 0.05
27 4 0.10
28 33 0.85
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (27 bp):
GGTTGGAGTATCCTTCAGAAATAACGG
Found at i:309098 original size:50 final size:51
Alignment explanation
Indices: 309006--309120 Score: 135
Period size: 50 Copynumber: 2.3 Consensus size: 51
308996 AAATAACGGG
* * * **
309006 GTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTGGGAAATAAAATC-GGA
1 GTTGGAGTATCCCCAATTATGAAAAATTGAGGTTTGAAAAAT-AAATCTGGA
* * *
309057 GTTGG-GTATCCCCAATTATGGAAAATTGAGGTTTTAAAAATAAATCTGGG
1 GTTGGAGTATCCCCAATTATGAAAAATTGAGGTTTGAAAAATAAATCTGGA
309107 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
309121 TTGGAAATAA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
49 5 0.09
50 36 0.67
51 13 0.24
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCAATTATGAAAAATTGAGGTTTGAAAAATAAATCTGGA
Found at i:309199 original size:51 final size:51
Alignment explanation
Indices: 309134--309250 Score: 146
Period size: 51 Copynumber: 2.3 Consensus size: 51
309124 GAAATAACGA
* *
309134 GGTTAGAGTATCCCCGATGGTGGAAAA-TCAATGTTTTGGAAATAAAACCGG
1 GGTTAGAGTATCCCCGATGAT-GAAAATTCAATGTTTTAGAAATAAAACCGG
* * *** *
309185 GGTTGGAGTATCCCCGATTATGAAAATTTGGTGTTTTAGAAATAAAACTGG
1 GGTTAGAGTATCCCCGATGATGAAAATTCAATGTTTTAGAAATAAAACCGG
309236 GGTTAGAGTATCCCC
1 GGTTAGAGTATCCCC
309251 TTGGAAATAA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
50 5 0.09
51 51 0.91
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTAGAGTATCCCCGATGATGAAAATTCAATGTTTTAGAAATAAAACCGG
Found at i:309250 original size:130 final size:130
Alignment explanation
Indices: 308995--309329 Score: 469
Period size: 130 Copynumber: 2.6 Consensus size: 130
308985 TATCCTCAAT
* * * *
308995 GAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTGGGAAATAAAATCGGAGTT
1 GAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAATGTTTTGGAAATAAAACCGGGGTT
* *
309060 GG-GTATCCCCAATTATGGAAAATTGAGGTTTTAAAAATAAATCTGGGGTTGGAGTATCCCCTTG
66 GGAGTATCCCCAATTATGGAAAATTGAGGTTTTAAAAATAAAACTGGGGTTAGAGTATCCCCTTG
* * * * *
309124 GAAATAACGAGGTTAGAGTATCCCCGATGGTGGAAAATCAATGTTTTGGAAATAAAACCGGGGTT
1 GAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAATGTTTTGGAAATAAAACCGGGGTT
* *
309189 GGAGTATCCCCGATTAT-GAAAATTTG-GTGTTTTAGAAATAAAACTGGGGTTAGAGTATCCCCT
66 GGAGTATCCCCAATTATGGAAAA-TTGAG-GTTTTAAAAATAAAACTGGGGTTAGAGTATCCCCT
309252 TG
129 TG
* * * *
309254 GAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGAAAATAAAACCGAGGTT
1 GAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAATGTTTTGGAAATAAAACCGGGGTT
*
309319 TGAGTATCCCC
66 GGAGTATCCCC
309330 TCGGAAATAA
Statistics
Matches: 180, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
129 64 0.36
130 116 0.64
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.29
Consensus pattern (130 bp):
GAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAATGTTTTGGAAATAAAACCGGGGTT
GGAGTATCCCCAATTATGGAAAATTGAGGTTTTAAAAATAAAACTGGGGTTAGAGTATCCCCTTG
Found at i:309265 original size:79 final size:78
Alignment explanation
Indices: 309182--309389 Score: 290
Period size: 79 Copynumber: 2.6 Consensus size: 78
309172 GAAATAAAAC
* * * *
309182 CGGGGTTGGAGTATCCCCGATTATGAAAATTTGGTGTTTTAGAAATAAAACTGGGGTTAGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTT-GAAATAAAACCGAGGTTAGAGTAT
*
309247 CCCCTTGGAAATAA
65 CCCCTCGGAAATAA
*
309261 CGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGAAAATAAAACCGAGGTTTGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTG-AAATAAAACCGAGGTTAGAGTAT
309326 CCCCTCGGAAATAA
65 CCCCTCGGAAATAA
** * * *
309340 TAGGGTTAGAGTATCCCCGATTGTAAAAAATTAGTGTTTTGGAAATAAAA
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTT-GAAATAAAA
309390 ATATGAATGA
Statistics
Matches: 116, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
78 1 0.01
79 114 0.98
80 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGAAATAAAACCGAGGTTAGAGTATC
CCCTCGGAAATAA
Found at i:311825 original size:20 final size:20
Alignment explanation
Indices: 311800--311876 Score: 127
Period size: 20 Copynumber: 3.9 Consensus size: 20
311790 ATGTACCAAT
311800 ACAATGTATCGATACAATGA
1 ACAATGTATCGATACAATGA
311820 ACAATGTATCGATACAATGA
1 ACAATGTATCGATACAATGA
* *
311840 ATAATGTATCGATACAGTGA
1 ACAATGTATCGATACAATGA
*
311860 ACAATGTATCAATACAA
1 ACAATGTATCGATACAA
311877 ATTGTGAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.26
Consensus pattern (20 bp):
ACAATGTATCGATACAATGA
Found at i:312619 original size:42 final size:43
Alignment explanation
Indices: 312544--312715 Score: 145
Period size: 42 Copynumber: 4.0 Consensus size: 43
312534 AGTGAAAAAT
* * *
312544 AGTACGTCCTGCTTTTTGAGGACAAAGGGAAAAAGGAAAACGAA
1 AGTACATCCTGCTCTTTGAGGACAAAGAGAAAAAGGAAAA-GAA
* * *
312588 A-TGCATCCTGCTCTTTGAGGATAAA-AGAAAAAGGAAAATAA
1 AGTACATCCTGCTCTTTGAGGACAAAGAGAAAAAGGAAAAGAA
* * * *
312629 AGTACATCCTACTCTTTGAGAACTAGAAGGGAAAAGAAGGAAATG-A
1 AGTACATCCTGCTCTTTGAGGAC-A-AAGAG-AAA-AAGGAAAAGAA
* * *
312675 AGTGCATCATGCTTTTTGAGGACAAAG-GAAAAAAGGAAAAG
1 AGTACATCCTGCTCTTTGAGGACAAAGAG-AAAAAGGAAAAG
312716 GTGTACTGCT
Statistics
Matches: 103, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
41 3 0.03
42 37 0.36
43 26 0.25
44 6 0.06
45 2 0.02
46 22 0.21
47 7 0.07
ACGTcount: A:0.44, C:0.12, G:0.24, T:0.20
Consensus pattern (43 bp):
AGTACATCCTGCTCTTTGAGGACAAAGAGAAAAAGGAAAAGAA
Found at i:312747 original size:37 final size:37
Alignment explanation
Indices: 312692--312763 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
312682 CATGCTTTTT
*
312692 GAGGACAAAGGAAAAAAGGAAAAGGTGTACTGCTCAA
1 GAGGACAAAGGAAAAAAGGAAAAGGCGTACTGCTCAA
* * *
312729 GAGGGCAAAGGAGAAAAGGAAAAGGCGTCCTGCTC
1 GAGGACAAAGGAAAAAAGGAAAAGGCGTACTGCTC
312764 TTTGAGGACT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.43, C:0.14, G:0.33, T:0.10
Consensus pattern (37 bp):
GAGGACAAAGGAAAAAAGGAAAAGGCGTACTGCTCAA
Found at i:312817 original size:61 final size:61
Alignment explanation
Indices: 312742--313291 Score: 663
Period size: 61 Copynumber: 9.1 Consensus size: 61
312732 GGCAAAGGAG
*
312742 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTATGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
* * *
312803 AAAAGGAGAAGGCGTCCTGCTCTTTGAGGACTG-AAGGTGCCACCAGCTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
* *
312863 AAAAGGAAAAGGCGTCCTACTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
* ** * * *
312924 ------AAAAGGCATTATGCTCTTTGAAGACTGGGAAA-TGCCACCAACATGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT
* * * * *
312979 AAAAGGAAAAGGCATCCTGCTCTTCGAGGACT-AGAAGGTGCCAACGACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGA-AAAGTGCCACCAACTTGTGTGGGCTTT
*
313040 AAAAGGAAAAAGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT
* *
313102 AAAAGGAAAAGGCGTCTTGCTCTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGA-AAAGTGCCACCAACTTGTGTGGGCTTT
* ** * * **
313163 AAAAGGAAAAGGTGTCCTATTTTTTGAGGACT-AGAAGGTGCCACCAACTTGTGTGAACTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGA-AAAGTGCCACCAACTTGTGTGGGCTTT
* * * * * *
313224 AAAAGGAAAAGGTGTCCAGCTCTTTGAGGACTAAAAAAATGTCACCAACTTGTGTAGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTGTGGGCTTT
*
313286 GAAAGG
1 AAAAGG
313292 CATCCTGCTC
Statistics
Matches: 424, Mismatches: 50, Indels: 29
0.84 0.10 0.06
Matches are distributed among these distances:
55 43 0.10
56 5 0.01
60 58 0.14
61 236 0.56
62 80 0.19
63 2 0.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.25
Consensus pattern (61 bp):
AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:313113 original size:123 final size:122
Alignment explanation
Indices: 312742--313312 Score: 695
Period size: 123 Copynumber: 4.8 Consensus size: 122
312732 GGCAAAGGAG
*
312742 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTATGGGCTTTAAA
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAG-AAAGTGCCACCAACTTGTGTGGGCTTTAAA
* * *
312806 AGGAGAAGGCGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAGCTTGTGTGGGCTTT
65 AGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTT
* *
312863 AAAAGGAAAAGGCGTCCTACTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT----
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
* ** * * *
312924 --AAAAGGCATTATGCTCTTTGAAGACTGGGAAA-TGCCACCAACATGTGTGGGCTTT
66 GGAAAAGGCGTCCTGCTCTTTGAGGACT-AGAAAGTGCCACCAACTTGTGTGGGCTTT
* * * * *
312979 AAAAGGAAAAGGCATCCTGCTCTTCGAGGACTAGAAGGTGCCAACGACTTGTGTGGGCTTTAAAA
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
*
313044 GGAAAAAGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT
66 GGAAAAGGCGTCCTGCTCTTTGAGGACTAG-AAAGTGCCACCAACTTGTGTGGGCTTT
* *
313102 AAAAGGAAAAGGCGTCTTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
* ** * * **
313167 GGAAAAGGTGTCCTATTTTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGAACTTT
66 GGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTT
* * * * * *
313224 AAAAGGAAAAGGTGTCCAGCTCTTTGAGGACTAAAAAAATGTCACCAACTTGTGTAGGCTTT---
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT-AGAAAGTGCCACCAACTTGTGTGGGCTTTAAA
*
313286 --G-AAAGGCATCCTGCTCTTTGAGGACTA
65 AGGAAAAGGCGTCCTGCTCTTTGAGGACTA
313313 AAGGGTGAAA
Statistics
Matches: 388, Mismatches: 50, Indels: 28
0.83 0.11 0.06
Matches are distributed among these distances:
115 21 0.05
116 75 0.19
117 24 0.06
118 1 0.00
121 58 0.15
122 78 0.20
123 131 0.34
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26
Consensus pattern (122 bp):
AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
GGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:313194 original size:184 final size:182
Alignment explanation
Indices: 312742--313291 Score: 713
Period size: 184 Copynumber: 3.0 Consensus size: 182
312732 GGCAAAGGAG
* *
312742 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTGAAAAGTGCCACCAACTTGTATGGGCTTTAAAA
1 AAAAGGAAAAGGCGTCTTGCTCTTTGAGGACTG--AAGTGCCACCAACTTGTGTGGGCTTTAAAA
* * *
312807 GGAGAAGGCGTCCTGCTCTTTGAGGACT-GAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGAA
64 GGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAGGTGCCAACAACTTGTGTGGGCTTTAAAAGGAA
* *
312871 AAGGCGTCCTACTCTTTGAGGACT-GGAAAGTGCCACCAACTTGTGTGGGCTTT
129 AAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT
* * * *
312924 ------AAAAGGCAT-TATGCTCTTTGAAGACTGGGAAATGCCACCAACATGTGTGGGCTTTAAA
1 AAAAGGAAAAGGCGTCT-TGCTCTTTGAGGACT--GAAGTGCCACCAACTTGTGTGGGCTTTAAA
* * *
312982 AGGAAAAGGCATCCTGCTCTTCGAGGACTAGAAGGTGCCAACGACTTGTGTGGGCTTTAAAAGGA
63 AGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAGGTGCCAACAACTTGTGTGGGCTTTAAAAGGA
*
313047 AAAAGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT
128 AAAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT
313102 AAAAGGAAAAGGCGTCTTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
1 AAAAGGAAAAGGCGTCTTGCTCTTTGAGGACT-GAA-GTGCCACCAACTTGTGTGGGCTTTAAAA
* ** * * **
313167 GGAAAAGGTGTCCTATTTTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGAACTTTAAAAGGAA
64 GGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAGGTGCCAACAACTTGTGTGGGCTTTAAAAGGAA
* * * * * *
313232 AAGGTGTCCAGCTCTTTGAGGACTAAAAAAATGTCACCAACTTGTGTAGGCTTT
129 AAGGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT
*
313286 GAAAGG
1 AAAAGG
313292 CATCCTGCTC
Statistics
Matches: 317, Mismatches: 38, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
176 74 0.23
177 55 0.17
178 29 0.09
183 3 0.01
184 155 0.49
185 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.25
Consensus pattern (182 bp):
AAAAGGAAAAGGCGTCTTGCTCTTTGAGGACTGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG
AAAAGGCGTCCTGCTCTTTGAGGACTAGAAGGTGCCAACAACTTGTGTGGGCTTTAAAAGGAAAA
GGCGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:315956 original size:21 final size:21
Alignment explanation
Indices: 315932--315978 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
315922 TTTGATGATG
315932 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
315952 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
315973 ATTTTG
1 ATTTTG
315979 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:316117 original size:13 final size:13
Alignment explanation
Indices: 316099--316124 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
316089 ATAATCACCC
316099 TGTATCGATACAA
1 TGTATCGATACAA
316112 TGTATCGATACAA
1 TGTATCGATACAA
316125 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:318232 original size:15 final size:15
Alignment explanation
Indices: 318196--318233 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
318186 TTCATCAATT
* *
318196 TCATTTGGAGCTTCT
1 TCATTTTGAGCTTCC
318211 TCATTTTGAGCTTCC
1 TCATTTTGAGCTTCC
318226 TCATTTTG
1 TCATTTTG
318234 GACATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.16, T:0.50
Consensus pattern (15 bp):
TCATTTTGAGCTTCC
Found at i:320066 original size:21 final size:21
Alignment explanation
Indices: 320037--320081 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
320027 AAGTTTTCAT
*
320037 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
320057 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
320079 TTT
1 TTT
320082 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:322315 original size:13 final size:13
Alignment explanation
Indices: 322297--322322 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
322287 CAATTTTTTG
322297 TGTATCGATACAT
1 TGTATCGATACAT
322310 TGTATCGATACAT
1 TGTATCGATACAT
322323 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:323202 original size:18 final size:16
Alignment explanation
Indices: 323181--323222 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
323171 CTTTTCTCTC
323181 TTTTTTTCTTTTTTTGTG
1 TTTTTTT-TTTTTTT-TG
*
323199 TTTTTTGTTTTTTTTG
1 TTTTTTTTTTTTTTTG
323215 TTTTTTTT
1 TTTTTTTT
323223 AAAAAAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 9 0.41
17 7 0.32
18 6 0.27
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (16 bp):
TTTTTTTTTTTTTTTG
Found at i:333541 original size:16 final size:16
Alignment explanation
Indices: 333512--333546 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
333502 TAGTGATTGT
333512 ACAAAAAATAAAACAA
1 ACAAAAAATAAAACAA
333528 ACAAATAAAT-AAACAA
1 ACAAA-AAATAAAACAA
333544 ACA
1 ACA
333547 CCTCAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.77, C:0.14, G:0.00, T:0.09
Consensus pattern (16 bp):
ACAAAAAATAAAACAA
Found at i:337578 original size:52 final size:52
Alignment explanation
Indices: 337429--337557 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
337419 CGAAATACGA
* *
337429 AAATTTACCTACATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
* * *
337481 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATGGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
337533 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
337558 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
Found at i:337623 original size:19 final size:18
Alignment explanation
Indices: 337599--337663 Score: 68
Period size: 19 Copynumber: 3.8 Consensus size: 18
337589 TAGCTTACAT
337599 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAA-TTA
337618 TGTATCGATAC---A-T-
1 TGTATCGATACAAAATTA
*
337631 TGTATCGATACAACAGTTA
1 TGTATCGATACAA-AATTA
337650 TGTATCGATACAAA
1 TGTATCGATACAAA
337664 TCGTTGAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 1 0.03
18 2 0.05
19 24 0.62
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.32
Consensus pattern (18 bp):
TGTATCGATACAAAATTA
Found at i:337635 original size:32 final size:32
Alignment explanation
Indices: 337594--337661 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
337584 GGCAGTAGCT
337594 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAAAACTTATGTATCGA
* *
337626 TACATTGTATCGATACAACAGTTATGTATCGA
1 TACATTGTATCGATACAAAACTTATGTATCGA
337658 TACA
1 TACA
337662 AATCGTTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (32 bp):
TACATTGTATCGATACAAAACTTATGTATCGA
Found at i:337636 original size:13 final size:13
Alignment explanation
Indices: 337618--337642 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
337608 ACAAAACTTA
337618 TGTATCGATACAT
1 TGTATCGATACAT
337631 TGTATCGATACA
1 TGTATCGATACA
337643 ACAGTTATGT
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:338362 original size:55 final size:55
Alignment explanation
Indices: 338301--338719 Score: 252
Period size: 52 Copynumber: 7.6 Consensus size: 55
338291 GAACCAATAC
* * *
338301 GCTGATTCACGGCCAATGATATTGGGTTTAAAGATGAGAAAAAGGATGTCAATGT
1 GCTGATTCAAGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAATGT
* * * * * * * *
338356 GCTGATTCACGGTCAGCGACATTAGACTTGAAGATGAG-AAAA--ATGCCAATGT
1 GCTGATTCAAGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAATGT
* * * * *
338408 GCTGATTCAAGGCCAACAACATTGGGTTTTAAAGATGATG---AAGG-TGCCAATAT
1 GCTGATTCAAGGCCAACGATATTGGG-CTTAAAGATGA-GAAAAAGGATGTCAATGT
* * * *
338461 GCTAATTCAAGGCCAGCAATATTGGACTTAAAGATGATGGTGAGAAAAGTGATAAAGATGCCAAT
1 GCTGATTCAAGGCCAACGATATTGGGCTTAAAGATGA----GA-AAAAG-GAT---G-T--CAAT
*
338526 AT
54 GT
* * *
338528 GTTGATTCACGGCCAATGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAATGT
1 GCTGATTCAAGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAATGT
* * * ** * *
338583 GCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG-G-AAAAGG-TGCCAATAT
1 GCTGATTCAAGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAATGT
* * * * * *
338635 GCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTG-G-AAAAGG-TGCCAATAT
1 GCTGATTCAAGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAATGT
* * * *
338687 GTTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GCTGATTCAAGGCCAACGATATTGGGCTTAAAG
338720 GTGCCAATGT
Statistics
Matches: 299, Mismatches: 46, Indels: 41
0.77 0.12 0.11
Matches are distributed among these distances:
52 129 0.43
53 45 0.15
54 6 0.02
55 65 0.22
57 1 0.00
58 1 0.00
59 3 0.01
60 1 0.00
61 4 0.01
62 5 0.02
63 2 0.01
64 1 0.00
67 36 0.12
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (55 bp):
GCTGATTCAAGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAATGT
Found at i:338430 original size:52 final size:52
Alignment explanation
Indices: 338328--339270 Score: 389
Period size: 49 Copynumber: 19.1 Consensus size: 52
338318 GATATTGGGT
* * * * *
338328 TTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCACGGTCAGCGACATTAGAC
1 TTAAAGATGAG-AAAA--ATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* * **
338383 TTGAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAACAACATTGGGTT
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATT-GGAC
** * * *
338436 TTAAAGATGATG-AAGGTGCCAATATGCTAATTCAAGGCCAGCAATATTGGAC
1 TTAAAGATGA-GAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* * * *** *
338488 TTAAAGATGATGGTGAGAAAAGTGATAAAGATGCCAATATGTTGATTCACGGCCAATGATATTGG
1 TT-AA-A-GA---T--G---A--GA-AAA-ATGCCAATGTGCTGATTCAAGGCCAGCAACATTGG
*
338553 GC
51 AC
* * *
338555 TTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAAC
1 TTAAAGATGAG-AAAA--ATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* * * *
338610 TTAAAGATG-GAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAGAAAA-ATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* * * * * *
338662 TTAAAGGTG-GAAAAGGTGCCAATATGTTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAGAAAA-ATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* *
338714 TT-AA-A-G-G-----TGCCAATGTGCTGATTCAAGGCCAGCTACATCGGAC
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
** * * *
338757 TTAAAGA--A-AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
*
338806 TT-AA-A-G-G-----TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
** * * * *
338849 TTAAAGAT---AAAGGTGCCAATATGTTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* * *
338898 TT---GA--AG----GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
** * * * *
338941 TTAAAGA--AG-AAGGTGCCAATATGCTGATTCAAGGCTAGCTATATTGGAC
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* * *
338990 TT-AA-A-G-G-----TGTCAATGTGCTGATTCAAGGCCAGCTACGTTGGAC
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
** * * *
339033 TTAAAGAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* * *
339082 TT-AA-A-G-G-----TGCCAATGTGTTGATTCAAGGCCAGCTACGTTGGAC
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
** * * *
339125 TTAAAGAT--G-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* * *
339174 TT-AA-A-G-G-----TGCCAATGTGCTGATTCAAGGCCAACTACGTTGGAC
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
** * * * *
339217 TTAAAGAT--G-AAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
339266 TTAAA
1 TTAAA
339271 AAGGGTTGCC
Statistics
Matches: 727, Mismatches: 90, Indels: 148
0.75 0.09 0.15
Matches are distributed among these distances:
43 207 0.28
44 10 0.01
45 7 0.01
46 6 0.01
47 6 0.01
48 8 0.01
49 211 0.29
51 2 0.00
52 117 0.16
53 46 0.06
54 11 0.02
55 50 0.07
56 1 0.00
58 1 0.00
59 1 0.00
60 1 0.00
61 1 0.00
63 1 0.00
64 4 0.01
65 1 0.00
66 4 0.01
67 31 0.04
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (52 bp):
TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
Found at i:338469 original size:53 final size:52
Alignment explanation
Indices: 338399--338499 Score: 139
Period size: 53 Copynumber: 1.9 Consensus size: 52
338389 ATGAGAAAAA
* * **
338399 TGCCAATGTGCTGATTCAAGGCCAACAACATTGGGTTTTAAAGATGATGAAGG
1 TGCCAATATGCTAATTCAAGGCCAACAACATT-GGACTTAAAGATGATGAAGG
* *
338452 TGCCAATATGCTAATTCAAGGCCAGCAATATTGGACTTAAAGATGATG
1 TGCCAATATGCTAATTCAAGGCCAACAACATTGGACTTAAAGATGATG
338500 GTGAGAAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
52 14 0.33
53 28 0.67
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.27
Consensus pattern (52 bp):
TGCCAATATGCTAATTCAAGGCCAACAACATTGGACTTAAAGATGATGAAGG
Found at i:338560 original size:67 final size:68
Alignment explanation
Indices: 338438--338564 Score: 166
Period size: 67 Copynumber: 1.9 Consensus size: 68
338428 ATTGGGTTTT
* * *
338438 AAAGATGATGAAGGTGCCAATATGCTAATTCAAGGCCAGCAATATTGGACTTAAAGATGATGGTG
1 AAAGATGATAAAGATGCCAATATGCTAATTCAAGGCCAACAATATTGGACTTAAAGATGATGGTG
338503 AGA
66 AGA
* * * ** *
338506 AAAG-TGATAAAGATGCCAATATGTTGATTCACGGCCAATGATATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTAATTCAAGGCCAACAATATTGGACTTAAAGATGA
338565 GAAAAAGGAT
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
67 46 0.92
68 4 0.08
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTAATTCAAGGCCAACAATATTGGACTTAAAGATGATGGTG
AGA
Found at i:338640 original size:227 final size:227
Alignment explanation
Indices: 338258--338719 Score: 630
Period size: 227 Copynumber: 2.0 Consensus size: 227
338248 GCCACACTAA
* *
338258 ACTTAAAGATGATGAGGATAAGGAGTGATAAAAGAACCAATACGCTGATTCACGGCCAATGATAT
1 ACTTAAAGATGATGAGGAGAAGAAGTGATAAAAGAACCAATACGCTGATTCACGGCCAATGATAT
* * * *
338323 TGGGTTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCACGGTCAGCGACATTAGACTTGAA
66 TGGGCTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAA
* ** *
338388 GATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAACAACATTGGGTTTTAAAGAT-GATGAAGG
131 GATGAGAAAAATGCCAATATGCTGATTCAAGGCCAACAACATT-GGACTTAAAGATGGA-AAAGG
338452 TGCCAATATGCTAATTCAAGGCCAGCAATATTGG
194 TGCCAATATGCTAATTCAAGGCCAGCAATATTGG
* * *
338486 ACTTAAAGATGATG-GTGAGAA-AAGTGAT-AAAGATGCCAATATGTTGATTCACGGCCAATGAT
1 ACTTAAAGATGATGAG-GAGAAGAAGTGATAAAAGA-ACCAATACGCTGATTCACGGCCAATGAT
*
338548 ATTGGGCTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATT-GAACTT
64 ATTGGGCTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCGACATTAG-ACTT
* * * * *
338612 AAAGATG-GAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGAAAA
128 AAAGATGAGAAAA-ATGCCAATATGCTGATTCAAGGCCAACAACATTGGACTTAAAGATGGAAAA
* * *
338676 GGTGCCAATATGTTGATTCAAGGCCAGCTATATTGG
192 GGTGCCAATATGCTAATTCAAGGCCAGCAATATTGG
338712 ACTTAAAG
1 ACTTAAAG
338720 GTGCCAATGT
Statistics
Matches: 207, Mismatches: 22, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
226 63 0.30
227 126 0.61
228 18 0.09
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (227 bp):
ACTTAAAGATGATGAGGAGAAGAAGTGATAAAAGAACCAATACGCTGATTCACGGCCAATGATAT
TGGGCTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAA
GATGAGAAAAATGCCAATATGCTGATTCAAGGCCAACAACATTGGACTTAAAGATGGAAAAGGTG
CCAATATGCTAATTCAAGGCCAGCAATATTGG
Found at i:338806 original size:92 final size:92
Alignment explanation
Indices: 338621--339270 Score: 1068
Period size: 92 Copynumber: 7.0 Consensus size: 92
338611 TAAAGATGGA
* * *
338621 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGAAAAGGTGCCAATA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAATA
*
338686 TGTTGATTCAAGGCCAGCTATATTGGACTT
63 TGCTGATTCAAGGCCAGCTATATTGGACTT
* *
338716 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATCGGACTTAAAGAAAAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
338781 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
*
338808 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
*
338873 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* *
338900 GAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGGTGCCAATATG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGCCAATATG
*
338964 CTGATTCAAGGCTAGCTATATTGGACTT
65 CTGATTCAAGGCCAGCTATATTGGACTT
* *
338992 AAAGGTGTCAATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAAGATAAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
339057 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* * *
339084 AAAGGTGCCAATGTGTTGATTCAAGGCCAGCTACGTTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
339149 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* * *
339176 AAAGGTGCCAATGTGCTGATTCAAGGCCAACTACGTTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
* *
339241 TAATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
339268 AAA
1 AAA
339271 AAGGGTTGCC
Statistics
Matches: 526, Mismatches: 27, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
91 1 0.00
92 480 0.91
93 1 0.00
95 44 0.08
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTT
Found at i:339316 original size:33 final size:32
Alignment explanation
Indices: 339271--339438 Score: 219
Period size: 32 Copynumber: 5.1 Consensus size: 32
339261 TGGACTTAAA
*
339271 AAGGGTTGCCACCGACTTATGTGGGCTTTAGAG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTT-GAG
* * *
339304 AATGGTTGCCACCAACTTGTGTGGGCTTTAAG
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAG
* * *
339336 AAGAAGGTTGCCACCGACTTATATGGGCTTTGAA
1 AAG--GGTTGCCACCGACTTGTGTGGGCTTTGAG
* *
339370 AAGGGTTGCCATCGACTTGTGTGGGCTTTGAA
1 AAGGGTTGCCACCGACTTGTGTGGGCTTTGAG
339402 AAGGGTTGCCACCGACTTGTGTGGGCTTTTGAG
1 AAGGGTTGCCACCGACTTGTGTGGGC-TTTGAG
339435 AAGG
1 AAGG
339439 AGAAAGATGC
Statistics
Matches: 117, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
32 55 0.47
33 35 0.30
34 27 0.23
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (32 bp):
AAGGGTTGCCACCGACTTGTGTGGGCTTTGAG
Found at i:339593 original size:32 final size:32
Alignment explanation
Indices: 339472--339756 Score: 258
Period size: 32 Copynumber: 9.1 Consensus size: 32
339462 ACTTAAAAGG
* * * *
339472 GAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAA
1 GAAAAGGA-TGCCACTGAGTCGTGGACTTTGAA
* * **
339505 -AAGAAGG-TGCCACGGAGTTGTGGACTTAAAA
1 GAA-AAGGATGCCACTGAGTCGTGGACTTTGAA
*
339536 GGAACAAGG-TGCCAC-GAAGTTGTGGACTTTGAA
1 -GAA-AAGGATGCCACTG-AGTCGTGGACTTTGAA
339569 GAAAAGGATGCCACTGAGTCGTGGACTTTGAA
1 GAAAAGGATGCCACTGAGTCGTGGACTTTGAA
*
339601 GAAAAGGATGCCACTAAGTCGTGGACTTTG-A
1 GAAAAGGATGCCACTGAGTCGTGGACTTTGAA
* * *
339632 GACAAA--ACGCCACTAAGTCATGGACTTTGAA
1 GA-AAAGGATGCCACTGAGTCGTGGACTTTGAA
*
339663 GAAAAGGATGCCACTGAGTTGTGGACTTTG-A
1 GAAAAGGATGCCACTGAGTCGTGGACTTTGAA
339694 GATAAA--ATGCCACTGAGTCGT-GAGCTTTG-A
1 GA-AAAGGATGCCACTGAGTCGTGGA-CTTTGAA
339724 GACAAA--ATGCCACTGAGTCGTGGACTTT-AA
1 GA-AAAGGATGCCACTGAGTCGTGGACTTTGAA
339754 GAA
1 GAA
339757 GGTATTTGAA
Statistics
Matches: 220, Mismatches: 18, Indels: 32
0.81 0.07 0.12
Matches are distributed among these distances:
29 3 0.01
30 71 0.32
31 35 0.16
32 81 0.37
33 30 0.14
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (32 bp):
GAAAAGGATGCCACTGAGTCGTGGACTTTGAA
Found at i:339662 original size:62 final size:61
Alignment explanation
Indices: 339512--339756 Score: 257
Period size: 62 Copynumber: 4.0 Consensus size: 61
339502 GAAAAGAAGG
* * ** * *
339512 TGCCACGGAGTTGTGGACTTAAAAGGAACAAGG-TGCCACGAAGTTGTGGACTTTGAAGAAAAGG
1 TGCCACTGAGTCGTGGACTTTGAA-GAA-AAGGATGCCACTAAGTCGTGGACTTTG-AGAAAA--
339576 A
61 A
339577 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTAAGTCGTGGACTTTGAGACAAAA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTAAGTCGTGGACTTTGAGA-AAAA
* * * * *
339639 CGCCACTAAGTCATGGACTTTGAAGAAAAGGATGCCACTGAGTTGTGGACTTTGAGATAAAA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTAAGTCGTGGACTTTGAGA-AAAA
* *
339701 TGCCACTGAGTCGT-GAGCTTTG-AGACAAA--ATGCCACTGAGTCGTGGACTTTAAGAA
1 TGCCACTGAGTCGTGGA-CTTTGAAGA-AAAGGATGCCACTAAGTCGTGGACTTTGAGAA
339757 GGTATTTGAA
Statistics
Matches: 159, Mismatches: 17, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
59 1 0.01
60 24 0.15
61 5 0.03
62 76 0.48
63 7 0.04
64 26 0.16
65 20 0.13
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (61 bp):
TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTAAGTCGTGGACTTTGAGAAAAA
Found at i:342952 original size:52 final size:52
Alignment explanation
Indices: 342867--342995 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
342857 CGAAATACGA
*
342867 AAATTTGCCTGCATGTATCGATAAATTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
* *
342919 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
342971 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
342996 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
Found at i:343006 original size:52 final size:52
Alignment explanation
Indices: 342867--343015 Score: 205
Period size: 52 Copynumber: 2.9 Consensus size: 52
342857 CGAAATACGA
*
342867 AAATTTGCCTGCATGTATCGAT--AAATTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACAAATATC--AGTGTATCGATACATCTAGGC
** *
342919 AAATTTGCCTGCATGTATCGATACATTTTAT-AGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-AATATCAGTGTATCGATACATCTAGGC
*
342971 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACAAATATCAGTGTATCGATACA
343016 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
51 2 0.02
52 81 0.94
54 1 0.01
55 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACAAATATCAGTGTATCGATACATCTAGGC
Found at i:343022 original size:13 final size:13
Alignment explanation
Indices: 343004--343028 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
342994 CAAAGATCAG
343004 TGTATCGATACAA
1 TGTATCGATACAA
343017 TGTATCGATACA
1 TGTATCGATACA
343029 TTTGAGTAAT
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:343805 original size:54 final size:52
Alignment explanation
Indices: 343742--343875 Score: 142
Period size: 54 Copynumber: 2.5 Consensus size: 52
343732 GAACCAATAC
* *
343742 GCTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAAAGGATGTCAATGT
1 GCTGATTCACGGCCAACGACATTGGGTTTAAAGATGAGAAAA--ATGCCAATGT
*** * * ** *
343796 GCTGATTCACGATTAGCGACATTAGACTTGAAGATGAGAAAAATGCCAATGT
1 GCTGATTCACGGCCAACGACATTGGGTTTAAAGATGAGAAAAATGCCAATGT
* *
343848 GCTGATTCAAGGCCAACAACATTGGGTT
1 GCTGATTCACGGCCAACGACATTGGGTT
343876 GGAGTGTCCC
Statistics
Matches: 61, Mismatches: 19, Indels: 2
0.74 0.23 0.02
Matches are distributed among these distances:
52 28 0.46
54 33 0.54
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (52 bp):
GCTGATTCACGGCCAACGACATTGGGTTTAAAGATGAGAAAAATGCCAATGT
Found at i:346026 original size:13 final size:13
Alignment explanation
Indices: 346008--346032 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
345998 CAAAGATTAG
346008 TGTATCGATACAA
1 TGTATCGATACAA
346021 TGTATCGATACA
1 TGTATCGATACA
346033 TTTGAGTAAT
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:346099 original size:19 final size:18
Alignment explanation
Indices: 346075--346170 Score: 68
Period size: 19 Copynumber: 5.7 Consensus size: 18
346065 TAGCTTACAT
346075 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
346094 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
346107 TGTATCGATATAACACTTA
1 TGTATCGATACAA-ACTTA
*
346126 TGTATCTATAC--A--T-
1 TGTATCGATACAAACTTA
346139 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
346159 TGTATCGATACA
1 TGTATCGATACA
346171 GATCTTTGAA
Statistics
Matches: 60, Mismatches: 4, Indels: 25
0.67 0.04 0.28
Matches are distributed among these distances:
13 20 0.33
14 2 0.03
16 4 0.07
18 1 0.02
19 21 0.35
20 12 0.20
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.36
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:346111 original size:32 final size:32
Alignment explanation
Indices: 346070--346170 Score: 166
Period size: 32 Copynumber: 3.1 Consensus size: 32
346060 GGCAGTAGCT
*
346070 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
* *
346102 TACATTGTATCGATATAACACTTATGTATCTA
1 TACATTGTATCGATACAACACTTATGTATCGA
346134 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
346167 TACA
1 TACA
346171 GATCTTTGAA
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 49 0.78
33 14 0.22
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.37
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:346112 original size:13 final size:13
Alignment explanation
Indices: 346094--346150 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
346084 ACAAAACTTA
346094 TGTATCGATACAT
1 TGTATCGATACAT
346107 TGTATCGATATAACACTT
1 TGTATCG--AT-ACA--T
*
346125 ATGTATCTATACAT
1 -TGTATCGATACAT
346139 TGTATCGATACA
1 TGTATCGATACA
346151 ACACTTTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 18 0.50
14 1 0.03
15 2 0.06
16 6 0.17
17 2 0.06
18 1 0.03
19 6 0.17
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:347884 original size:79 final size:76
Alignment explanation
Indices: 347726--348027 Score: 270
Period size: 79 Copynumber: 3.8 Consensus size: 76
347716 ACAACAAGGC
* * *
347726 TGGAGTATCCTTGATTATGGAAAATCTG-TGTTCTAGAAATAAAAATCGGGGTTGGAGTATCCCC
1 TGGAGTATCCCTGATTAT-GAAAATC-GATGTTTTAGAAAT-AAAATCGGGATTGGAGTATCCCC
* *
347790 AAGGAAATAACGGGT
63 GA-GAAATAAGGGGT
* *
347805 TAGAGTATCCCTGATTATAGAAAATCGATGTTTT-GAAAATAAAATCGGGATTAGAGTATCCCCG
1 TGGAGTATCCCTGATTAT-GAAAATCGATGTTTTAG-AAATAAAATCGGGATTGGAGTATCCCCG
*
347869 TGAAAATAATGGGGT
64 AG-AAATAA-GGGGT
* * * * * *
347884 TGGAGTATCCCTAATTGTGAGAAATCAATATTTTAGAAATAAAGTCGGGGTTGGAGTATCCCCGA
1 TGGAGTATCCCTGATTATGA-AAATCGATGTTTTAGAAATAAAATCGGGATTGGAGTATCCCCGA
* *
347949 CGAAATAACGAGAT
65 -GAAATAA-GGGGT
* * * *
347963 TGGAGTAT-CCTCGATTGTGAAAAATTGATGTTTTGGAAATAAAATC-AGAGTTGGAGTATCCCC
1 TGGAGTATCCCT-GATTATG-AAAATCGATGTTTTAGAAATAAAATCGGGA-TTGGAGTATCCCC
348026 GA
63 GA
348028 TTGTGAAAAA
Statistics
Matches: 184, Mismatches: 29, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
77 1 0.01
78 35 0.19
79 145 0.79
80 3 0.02
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (76 bp):
TGGAGTATCCCTGATTATGAAAATCGATGTTTTAGAAATAAAATCGGGATTGGAGTATCCCCGAG
AAATAAGGGGT
Found at i:348148 original size:208 final size:209
Alignment explanation
Indices: 347807--348233 Score: 463
Period size: 208 Copynumber: 2.0 Consensus size: 209
347797 TAACGGGTTA
* * *
347807 GAGTATCCCTGATTATAGAAAATCGATGTTTTGAAAATAAAATCGGGATTAGAGTATCCCCGTGA
1 GAGTATCCCCGATTATAGAAAATCGATGTTTTGAAAATAAAACCGGGATTAGAGTATCCCCGTAA
** * * * ** * *
347872 AAATAATGGGGTTGGAGTATCCCTAATTGTGAGAAATCAATATTTTAGAAATAAAGTCGGGGTTG
66 AAATAACAGGGTTAGAGTATCCCCAATGGTGAGAAATCAATATTTTAGAAATAAAACCAGGATTG
* ** * *
347937 GAGTATCCCCGACG-AAATAACGAGATTGGAGTATCCTCGATTGTGAA-AAATTGATGTTTTGGA
131 GAGTATCCCCG-CGAAAATAACGAGATTGGAGTATCCCCGATTGT-AAGAAATCAATATTTTAGA
348000 AATAAAATCAGAGTTG
194 AATAAAATCAGAGTTG
* *
348016 GAGTATCCCCGATTGT-GAAAAATTGATGTTTT-AGAAATAAAACCGGG-TTAGAGTATCCCC-T
1 GAGTATCCCCGATTATAG-AAAATCGATGTTTTGA-AAATAAAACCGGGATTAGAGTATCCCCGT
* * * *
348077 CAAAAATTACAGGGTTAGAGTATCCCCAATGGTG-GAAAATCGATGTTTTGGAAATAAAACCAGG
64 -AAAAATAACAGGGTTAGAGTATCCCCAATGGTGAG-AAATCAATATTTTAGAAATAAAACCAGG
* ** ** *
348141 ATTGGAGTATTCTTGCGAAAATAATTAGGTTGGAGTATCCCCGATTGTAAGAAATCAATATTTTA
127 ATTGGAGTATCCCCGCGAAAATAACGAGATTGGAGTATCCCCGATTGTAAGAAATCAATATTTTA
* * *
348206 GAAATAAAGTCGGGGTTG
192 GAAATAAAATCAGAGTTG
348224 GAGTATCCCC
1 GAGTATCCCC
348234 TTAGAAATAA
Statistics
Matches: 180, Mismatches: 32, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
207 6 0.03
208 135 0.75
209 39 0.22
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (209 bp):
GAGTATCCCCGATTATAGAAAATCGATGTTTTGAAAATAAAACCGGGATTAGAGTATCCCCGTAA
AAATAACAGGGTTAGAGTATCCCCAATGGTGAGAAATCAATATTTTAGAAATAAAACCAGGATTG
GAGTATCCCCGCGAAAATAACGAGATTGGAGTATCCCCGATTGTAAGAAATCAATATTTTAGAAA
TAAAATCAGAGTTG
Found at i:348181 original size:79 final size:78
Alignment explanation
Indices: 348012--348261 Score: 209
Period size: 79 Copynumber: 3.2 Consensus size: 78
348002 TAAAATCAGA
* * * *
348012 GTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAACCGGGTTAGAGTATCCCCT
1 GTTGGAGTATCCCCAATGGTGAAAAATCGATGTTTTAGAAATAAAACCGGATTAGAGTATCCCCT
*
348077 CAAAAATTACAGG
66 CAAAAATAACAGG
* * * * * *
348090 GTTAGAGTATCCCCAATGGTGGAAAATCGATGTTTTGGAAATAAAACCAGGATTGGAGTAT-TCT
1 GTTGGAGTATCCCCAATGGTGAAAAATCGATGTTTTAGAAATAAAACC-GGATTAGAGTATCCCC
* *
348154 TGCGAAAATAATTA-G
65 T-CAAAAATAA-CAGG
* * * * * * * *
348169 GTTGGAGTATCCCCGATTGT-AAGAAATCAATATTTTAGAAATAAAGTCGGGGTTGGAGTATCCC
1 GTTGGAGTATCCCCAATGGTGAA-AAATCGATGTTTTAGAAATAAA-ACCGGATTAGAGTATCCC
* *
348233 CTTAGAAATAACAGG
64 CTCAAAAATAACAGG
* *
348248 GATGGCGTATCCCC
1 GTTGGAGTATCCCC
348262 GATGAAATAA
Statistics
Matches: 134, Mismatches: 31, Indels: 13
0.75 0.17 0.07
Matches are distributed among these distances:
78 46 0.34
79 84 0.63
80 4 0.03
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.28
Consensus pattern (78 bp):
GTTGGAGTATCCCCAATGGTGAAAAATCGATGTTTTAGAAATAAAACCGGATTAGAGTATCCCCT
CAAAAATAACAGG
Found at i:348268 original size:28 final size:28
Alignment explanation
Indices: 348222--348292 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
348212 AAGTCGGGGT
*
348222 TGGAGTATCCCC-TTAGAAATAACAGGGA
1 TGGAGTATCCCCGAT-GAAATAACAGGGA
* * *
348250 TGGCGTATCCCCGATGAAATAACGGGGT
1 TGGAGTATCCCCGATGAAATAACAGGGA
*
348278 TGGAGTATCCTCGAT
1 TGGAGTATCCCCGAT
348293 TGTGAAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
28 35 0.97
29 1 0.03
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (28 bp):
TGGAGTATCCCCGATGAAATAACAGGGA
Found at i:348342 original size:51 final size:50
Alignment explanation
Indices: 348274--348389 Score: 171
Period size: 51 Copynumber: 2.3 Consensus size: 50
348264 TGAAATAACG
* *
348274 GGGTTGGAGTATCCTCGATTGTGAAAAATTGATGTTTTGGAAATAAAA-T
1 GGGTTGGAGTATCCTCGATGGTGAAAAATTGATGTTTTAGAAATAAAACT
*
348323 CGGAGTTGGAGTATCCTCGATGGTGGAAAATTGATGTTTTAGAAATAAAACT
1 -GG-GTTGGAGTATCCTCGATGGTGAAAAATTGATGTTTTAGAAATAAAACT
348375 GGGTTTGGAGTATCC
1 GGG-TTGGAGTATCC
348390 CTTTGTAAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
50 3 0.05
51 56 0.93
52 1 0.02
ACGTcount: A:0.30, C:0.09, G:0.28, T:0.33
Consensus pattern (50 bp):
GGGTTGGAGTATCCTCGATGGTGAAAAATTGATGTTTTAGAAATAAAACT
Found at i:348438 original size:130 final size:129
Alignment explanation
Indices: 348266--348519 Score: 384
Period size: 130 Copynumber: 2.0 Consensus size: 129
348256 ATCCCCGATG
* * * * *
348266 AAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGATGTTTTGGAAATAAAATCGGAGTTG
1 AAATAACGGGGTTAGAGTATCCCCGATGGTGAAAAATCGATGTTTTGGAAATAAAACCGGAGTTG
* *
348331 GAGTATCCTCGATGGTGGAAAATTGATGTTTTAGAAATAAAA-CTGGGTTTGGAGTATCCCTTTG
66 GAGTATCC-CGATGATGGAAAATTGATGTTTTAGAAATAAAACCAGGG-TTGGAGTATCCCTTTG
348395 T
129 T
* *
348396 AAATAACGGGGTTAGAGTATCCCCGATGGTGGAAAATCGATGTTTTGGAAATAAAACCGGGGTTG
1 AAATAACGGGGTTAGAGTATCCCCGATGGTGAAAAATCGATGTTTTGGAAATAAAACCGGAGTTG
* *
348461 GAGTATCCCGATTATGGAAAATTGGTGTTTTAGAAATAAAACCAGGGTTGGAGTATCCC
66 GAGTATCCCGATGATGGAAAATTGATGTTTTAGAAATAAAACCAGGGTTGGAGTATCCC
348520 CGATTATGAA
Statistics
Matches: 112, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
129 42 0.38
130 70 0.62
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.30
Consensus pattern (129 bp):
AAATAACGGGGTTAGAGTATCCCCGATGGTGAAAAATCGATGTTTTGGAAATAAAACCGGAGTTG
GAGTATCCCGATGATGGAAAATTGATGTTTTAGAAATAAAACCAGGGTTGGAGTATCCCTTTGT
Found at i:348490 original size:50 final size:51
Alignment explanation
Indices: 348402--348571 Score: 234
Period size: 51 Copynumber: 3.4 Consensus size: 51
348392 TTGTAAATAA
** * *
348402 CGGGGTTAGAGTATCCCCGATGGTGGAAAATCGATGTTTTGGAAATAAAAC
1 CGGGGTTAGAGTATCCCCGATTATGGAAAATTGGTGTTTTGGAAATAAAAC
* *
348453 CGGGGTTGGAGTAT-CCCGATTATGGAAAATTGGTGTTTTAGAAATAAAAC
1 CGGGGTTAGAGTATCCCCGATTATGGAAAATTGGTGTTTTGGAAATAAAAC
* * * * *
348503 CAGGGTTGGAGTATCCCCGATTATGAAAAATTCGTGTTTTGAAAATAAAAC
1 CGGGGTTAGAGTATCCCCGATTATGGAAAATTGGTGTTTTGGAAATAAAAC
348554 CGGGGTTAGAGTATCCCC
1 CGGGGTTAGAGTATCCCC
348572 TCGAAAATAA
Statistics
Matches: 105, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
50 44 0.42
51 61 0.58
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (51 bp):
CGGGGTTAGAGTATCCCCGATTATGGAAAATTGGTGTTTTGGAAATAAAAC
Found at i:348516 original size:180 final size:181
Alignment explanation
Indices: 348272--348631 Score: 449
Period size: 180 Copynumber: 2.0 Consensus size: 181
348262 GATGAAATAA
* * *
348272 CGGGGTTGGAGTATCCTCGATTGTGAAAAATTGATGTTTTGGAAATAAAATCGGAGTTGGAGTAT
1 CGGGGTTGGAGTATCCTCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGAGTTGGAGTAT
* * * * * * * * *
348337 CCTCGATGGTGGAAAATT-GATGTTTT-AGAAATAAAACTGGGTTTGGAGTATCCCTTTGTAAAT
66 CCCCGATGATGAAAAATTCG-TGTTTTGA-AAATAAAACCGGGGTTAGAGTATCCCCTCGAAAAT
* ** *
348400 AACGGGGTTAGAGTATCCCCGATGGTGGAAAATCGATGTTTTGGAAATAAAAC
129 AACAGGGTTAGAGTATCCCCGATGGTAAAAAATCGATGTTTTGAAAATAAAAC
* *
348453 CGGGGTTGGAGTATCC-CGATTATGGAAAATTGGTGTTTTAGAAATAAAACCAGG-GTTGGAGTA
1 CGGGGTTGGAGTATCCTCGATTATGAAAAATTGATGTTTTAGAAATAAAACC-GGAGTTGGAGTA
*
348516 TCCCCGATTATGAAAAATTCGTGTTTTGAAAATAAAACCGGGGTTAGAGTATCCCCTCGAAAATA
65 TCCCCGATGATGAAAAATTCGTGTTTTGAAAATAAAACCGGGGTTAGAGTATCCCCTCGAAAATA
* * * * *
348581 ATAGGGTTAGAGTATCTCCGATTGTAAAAAATTGGTGTTTTGAAAATAAAA
130 ACAGGGTTAGAGTATCCCCGATGGTAAAAAATCGATGTTTTGAAAATAAAA
348632 ACATGAATGA
Statistics
Matches: 152, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
180 132 0.87
181 20 0.13
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (181 bp):
CGGGGTTGGAGTATCCTCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGAGTTGGAGTAT
CCCCGATGATGAAAAATTCGTGTTTTGAAAATAAAACCGGGGTTAGAGTATCCCCTCGAAAATAA
CAGGGTTAGAGTATCCCCGATGGTAAAAAATCGATGTTTTGAAAATAAAAC
Found at i:350737 original size:13 final size:13
Alignment explanation
Indices: 350719--350748 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
350709 GTAAACCCTG
*
350719 AATGTATCGATAC
1 AATGTATCAATAC
350732 AATGTATCAATAC
1 AATGTATCAATAC
350745 AATG
1 AATG
350749 AGCAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (13 bp):
AATGTATCAATAC
Found at i:352260 original size:20 final size:20
Alignment explanation
Indices: 352235--352289 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
352225 TTTTACCCAG
* *
352235 ATGTATCAATACATTTGTCA
1 ATGTATCGATACATTTATCA
* * *
352255 ATGTATCGATATATGTATGA
1 ATGTATCGATACATTTATCA
352275 ATGTATCGATACATT
1 ATGTATCGATACATT
352290 CTATTTTTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTATCA
Found at i:352334 original size:20 final size:20
Alignment explanation
Indices: 352306--352453 Score: 107
Period size: 20 Copynumber: 6.8 Consensus size: 20
352296 TTTTACCCAG
352306 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
352326 ATTTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
352346 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
352366 ATGTATCGATACATTCTTTCTTTTTACCCA
1 ATGTATCGATACA-------TTTTT---CA
* *
352396 GATGTATCGACATATTTTTCA
1 -ATGTATCGATACATTTTTCA
* * *
352417 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
352437 ATGTATCGATACATTTT
1 ATGTATCGATACATTTT
352454 GTCTTTTTTC
Statistics
Matches: 98, Mismatches: 19, Indels: 22
0.71 0.14 0.16
Matches are distributed among these distances:
20 74 0.76
21 2 0.02
24 5 0.05
27 4 0.04
30 2 0.02
31 11 0.11
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:352342 original size:71 final size:71
Alignment explanation
Indices: 352224--352362 Score: 242
Period size: 71 Copynumber: 2.0 Consensus size: 71
352214 AAAAGTCACA
*
352224 TTTTTACCCAGATGTATCAATACATTTGTCAATGTATCGATATATGTATGAATGTATCGATACAT
1 TTTTTACCCAGATGTATCAATACATTTGTCAATGTATCGATACATGTATGAATGTATCGATACAT
352289 TCTATT
66 TCTATT
* * *
352295 TTTTTACCCAGATGTATCGATACATTTTTCAATTTATCGATACATGTATGAATGTATCGATACAT
1 TTTTTACCCAGATGTATCAATACATTTGTCAATGTATCGATACATGTATGAATGTATCGATACAT
352360 TCT
66 TCT
352363 TCAATGTATC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 64 1.00
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (71 bp):
TTTTTACCCAGATGTATCAATACATTTGTCAATGTATCGATACATGTATGAATGTATCGATACAT
TCTATT
Found at i:352398 original size:91 final size:91
Alignment explanation
Indices: 352274--352451 Score: 313
Period size: 91 Copynumber: 2.0 Consensus size: 91
352264 TATATGTATG
* *
352274 AATGTATCGATACATTCTATTTTTTTACCCAGATGTATCGATACATTTTTCAATTTATCGATACA
1 AATGTATCGATACATTCTATTTTTTTACCCAGATGTATCGACACATTTTTCAATGTATCGATACA
352339 TGTATGAATGTATCGATACATTCTTC
66 TGTATGAATGTATCGATACATTCTTC
*
352365 AATGTATCGATACATTCT-TTCTTTTTACCCAGATGTATCGACATATTTTTCAATGTATCGATAC
1 AATGTATCGATACATTCTATT-TTTTTACCCAGATGTATCGACACATTTTTCAATGTATCGATAC
352429 ATGTATGAATGTATCGATACATT
65 ATGTATGAATGTATCGATACATT
352452 TTGTCTTTTT
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
90 2 0.02
91 81 0.98
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (91 bp):
AATGTATCGATACATTCTATTTTTTTACCCAGATGTATCGACACATTTTTCAATGTATCGATACA
TGTATGAATGTATCGATACATTCTTC
Found at i:352404 original size:71 final size:70
Alignment explanation
Indices: 352329--352501 Score: 206
Period size: 71 Copynumber: 2.4 Consensus size: 70
352319 TTTTTCAATT
* *
352329 TATCGATACATGTATGAATGTATCGATACAT-TCTTCAATGTATCGATACATTCTT-TCTTTTTA
1 TATCGATACAT-TATAAATGTATCGATACATGT-ATCAATGTATCGATACATT-TTGTCTTTTTA
352392 CCCAGATG
63 CCCAGATG
* * * * * *
352400 TATCGACATATTTTTCAATGTATCGATACATGTATGAATGTATCGATACATTTTGTCTTTTTTCC
1 TATCGATACA-TTATAAATGTATCGATACATGTATCAATGTATCGATACATTTTGTCTTTTTACC
352465 CAGATG
65 CAGATG
*
352471 TATCGATACATTGAAAAATGTATCGATACAT
1 TATCGATACATT-ATAAATGTATCGATACAT
352502 CTAGTTAAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
70 4 0.05
71 80 0.93
72 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.40
Consensus pattern (70 bp):
TATCGATACATTATAAATGTATCGATACATGTATCAATGTATCGATACATTTTGTCTTTTTACCC
AGATG
Found at i:361181 original size:28 final size:27
Alignment explanation
Indices: 360975--361820 Score: 950
Period size: 27 Copynumber: 30.9 Consensus size: 27
360965 TGGTATTCCT
360975 TTTTAAGTCCACAACTCCGTGGCTA-CC
1 TTTTAAGTCCACAACTCCGTGGC-ACCC
361002 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
361029 TTTTAAG-CCTACAACTCCGTGGCAACC
1 TTTTAAGTCC-ACAACTCCGTGGCACCC
* * * *
361056 TTTTACGCCCATAACTCCGTGGCAACC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* * *
361083 TTTTAAGTCCATAACTCCATGGCAACC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
361110 TTTTAAGTCCACAACTCCGTGGCAACC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* *
361137 TTGTAAGTCTACAACTCCGTGGCAGCCC
1 TTTTAAGTCCACAACTCCGTGGCA-CCC
*
361165 TTTTTAAGT-CATAACTCCGTGGCACCC
1 -TTTTAAGTCCACAACTCCGTGGCACCC
* * *
361192 TTTTAAGCCCACAACTCCATGGTAGCCC
1 TTTTAAGTCCACAACTCCGTGGCA-CCC
*
361220 TTTTTAAGTCCACAACTCTGTGGCACCC
1 -TTTTAAGTCCACAACTCCGTGGCACCC
* *
361248 TTTTAAG-CCTACAACTCTGT-GCAACC
1 TTTTAAGTCC-ACAACTCCGTGGCACCC
* *
361274 ATTTAAGTCCACAACTCCGTGGCAACC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* *
361301 TTTTAAGCCCACAACTCCGTGGCAACC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* * *
361328 -TTTAAGTCCACAACTCTGTGGTAACC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
361354 TTTTAAAGTCCAAAACTCCGTGGCAGCCC
1 TTTT-AAGTCCACAACTCCGTGGCA-CCC
*
361383 TTTTTAAGTCCACAACTCCGTGGCACCT
1 -TTTTAAGTCCACAACTCCGTGGCACCC
* ** *
361411 TTTTAAGCCCACAACTCTATGGCAACC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* *
361438 TTTTAAGTCCACAACTCCATGGCAACC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* *
361465 TTTTAAGTCCACAACTCTGTGGCAACC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
361492 TTTTAAAGAT-CACAACTCCATGGCACCC
1 TTTT-AAG-TCCACAACTCCGTGGCACCC
361520 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
361547 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
*
361575 TTTTAAAGTCCACAACTTCGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
* * * *
361603 TTTTAAAGTCCACAACTTCATGGTATCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
361631 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
* *
361659 TTTTAAGTCCACAACTCCATAGCAACCC
1 TTTTAAGTCCACAACTCCGTGGC-ACCC
*
361687 TTTTTAAGTCCACAACTCTGTGGCACCC
1 -TTTTAAGTCCACAACTCCGTGGCACCC
* * * *
361715 TTTTAAGTCCACAAGTCAGTGGCATCA
1 TTTTAAGTCCACAACTCCGTGGCACCC
* * * * * * *
361742 TTTCAAAGCCCATAAGTCAGTGGCATCA
1 TTT-TAAGTCCACAACTCCGTGGCACCC
361770 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* * *
361797 TTTAAAGTCCACAAGTCAGTGGCA
1 TTTTAAGTCCACAACTCCGTGGCA
361821 TCATTTCAAA
Statistics
Matches: 718, Mismatches: 79, Indels: 44
0.85 0.09 0.05
Matches are distributed among these distances:
26 56 0.08
27 390 0.54
28 199 0.28
29 69 0.10
30 4 0.01
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.27
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCGTGGCACCC
Found at i:361837 original size:28 final size:28
Alignment explanation
Indices: 361528--362292 Score: 618
Period size: 28 Copynumber: 27.2 Consensus size: 28
361518 CCTTTTAAGT
* * * * *
361528 CCACAACTCCGTGGCACCCTTTTAAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * * *
361556 CCACAACTCCGTGGCACCCTTTTAAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * *
361584 CCACAACTTC-GTGGCACCCTTTTAAAGT
1 CCACAA-GTCAGTGGCATCCTTTCAAAGC
* * * *
361612 CCACAACTTCA-TGGTATCCTTTTAAAGT
1 CCACAA-GTCAGTGGCATCCTTTCAAAGC
* * * * *
361640 CCACAACTCCGTGGCACCCTTT-TAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * ** *
361667 CCACAACTCCA-TAGCAACCCTTTTTAAGT
1 CCACAAGT-CAGTGGC-ATCCTTTCAAAGC
* * * * *
361696 CCACAACTCTGTGGCACCCTTT-TAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
*
361723 CCACAAGTCAGTGGCATCATTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * *
361751 CCATAAGTCAGTGGCATCATTT-TAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * *
361778 CCACAACTCCGTGGCACCCTTT-AAAGT
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
*
361805 CCACAAGTCAGTGGCATCATTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
361833 CCACAAGTCAATGGCATCATTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
*
361861 CTACAAGTCAGTGGCATCCTTTTCAAAGC
1 CCACAAGTCAGTGGCATCC-TTTCAAAGC
* * * * *
361890 CCACAAATTAATGGCACCCTTTCAAAAC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
361918 CCACAAGTCAGTGGCATCTTTTCCAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * * * *
361946 CAATAAGTCAATGGCATCTTTTCCAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
361974 CCACAAGTCAGTGACA-CCTTTTTCATAGC
1 CCACAAGTCAGTGGCATCC--TTTCAAAGC
* *
362003 CCATGAA-TCAGTGGCA-CCTTTTCATAGC
1 CCA-CAAGTCAGTGGCATCC-TTTCAAAGC
362031 CCACAAGTCAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
362059 CCACAAGTCAGTGGCAT-CTCTTCAAAGC
1 CCACAAGTCAGTGGCATCCT-TTCAAAGC
* *
362087 TCACAAGTTAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
*
362115 CCACAAGTCAGTGGCATCCTTTCAAATC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
362143 CCACAAGTCAATGGCATCCTTTCAAAAC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * *
362171 CCACAAGTCAATAGCAACCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
362199 CAACACAAATCAGTGGCATCTTTTCCAAAGC
1 C--CACAAGTCAGTGGCATCCTTT-CAAAGC
* *
362230 CCACAAGTCAGTAGCATTCTTCTCAAAGCC
1 CCACAAGTCAGTGGCATCCTT-TCAAAG-C
*
362260 CACACAAATCAGTGGCATCC-TTCAAAGC
1 C-CACAAGTCAGTGGCATCCTTTCAAAGC
362288 CCACA
1 CCACA
362293 TAAATTAGTG
Statistics
Matches: 629, Mismatches: 85, Indels: 47
0.83 0.11 0.06
Matches are distributed among these distances:
27 91 0.14
28 402 0.64
29 92 0.15
30 22 0.03
31 22 0.03
ACGTcount: A:0.30, C:0.31, G:0.14, T:0.25
Consensus pattern (28 bp):
CCACAAGTCAGTGGCATCCTTTCAAAGC
Found at i:361958 original size:113 final size:113
Alignment explanation
Indices: 361528--362292 Score: 669
Period size: 113 Copynumber: 6.8 Consensus size: 113
361518 CCTTTTAAGT
* * * * * * * * *
361528 CCACAACTCCGTGGCACCCTTTT-AAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACT
1 CCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAATCAGTGGCACCCTTTCAAAGCCCACAA-G
* * * * * * * *
361592 TC-GTGGCACCCTTTTAAAGTCCACAACTTC-ATGGTATCCTTTTAAAGT
65 TCAGTGGCATCCTTTCAAAGCCCACAA-GTCAATGGCATCATTTCAAAGC
* * * * * * ** *
361640 CCACAACTCCGTGGCACCCTTTT--AAGTCCACAACTCCA-TAGCAACCCTTTTTAAGTCCACAA
1 CCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAAT-CAGTGGC-ACCCTTTCAAAGCCCACAA
* * * * * *
361702 CTCTGTGGCACCCTTT-TAAGTCCACAAGTCAGTGGCATCATTTCAAAGC
64 GTCAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCATCATTTCAAAGC
* * * * * *
361751 CCATAAGTCAGTGGCATCATTTT--AAGTCCACAACTCCGTGGCACCCTTT-AAAGTCCACAAGT
1 CCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAATCAGTGGCACCCTTTCAAAGCCCACAAGT
*
361813 CAGTGGCATCATTTCAAAGCCCACAAGTCAATGGCATCATTTCAAAGC
66 CAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCATCATTTCAAAGC
* * * *
361861 CTACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAATTAATGGCACCCTTTCAAAACCCACAAGT
1 CCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAATCAGTGGCACCCTTTCAAAGCCCACAAGT
* * * * * *
361926 CAGTGGCATCTTTTCCAAGCCAATAAGTCAATGGCATCTTTTCCAAGC
66 CAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCATCATTTCAAAGC
* * ** * *
361974 CCACAAGTCAGTGACA-CCTTTTTCATAGCCCATGAATCAGTGGCACCTTTTCATAGCCCACAAG
1 CCACAAGTCAGTGGCATCC-TTTTCAAAGCCCACAAATCAGTGGCACCCTTTCAAAGCCCACAAG
*
362038 TCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATC-TCTTCAAAGC
65 TCAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCATCAT-TTCAAAGC
* * * * *
362087 TCACAAGTTAGTGGCATCC-TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAATCCCACAAGT
1 CCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAATCAGTGGCACCCTTTCAAAGCCCACAAGT
* * * * *
362151 CAATGGCATCCTTTCAAAACCCACAAGTCAATAGCAACCTTTCAAAGC
66 CAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCATCATTTCAAAGC
* * * **
362199 CAACACAAATCAGTGGCAT-CTTTTCCAAAGCCCACAAGTCAGTAGCATTCTTCTCAAAGCCCAC
1 C--CACAAGTCAGTGGCATCCTTTT-CAAAGCCCACAAATCAGTGGCACCCTT-TCAAAG-CC-C
*
362263 ACAAATCAGTGGCATCC-TTCAAAGCCCACA
60 ACAAGTCAGTGGCATCCTTTCAAAGCCCACA
362293 TAAATTAGTG
Statistics
Matches: 550, Mismatches: 83, Indels: 35
0.82 0.12 0.05
Matches are distributed among these distances:
109 22 0.04
110 60 0.11
111 73 0.13
112 156 0.28
113 160 0.29
114 19 0.03
115 25 0.05
116 5 0.01
117 14 0.03
118 16 0.03
ACGTcount: A:0.30, C:0.31, G:0.14, T:0.25
Consensus pattern (113 bp):
CCACAAGTCAGTGGCATCCTTTTCAAAGCCCACAAATCAGTGGCACCCTTTCAAAGCCCACAAGT
CAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCATCATTTCAAAGC
Found at i:363183 original size:20 final size:20
Alignment explanation
Indices: 363158--363374 Score: 78
Period size: 20 Copynumber: 9.8 Consensus size: 20
363148 TTTTTACCCA
*
363158 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTATC
* * *
363178 AATGTATCAATACATGTATG
1 AATGTATCGATACATTTATC
363198 AATGTATCGATACATTCTATCTTTTTACCC
1 AATGTATCGATACATT-TA------T---C
* *
363228 AGATGTATTGATACATTTTTC
1 A-ATGTATCGATACATTTATC
* * *
363249 AATGTATTGATACATGTATG
1 AATGTATCGATACATTTATC
363269 AATGTATCGATACATTCTATCTTTTTACCC
1 AATGTATCGATACATT-TA------T---C
* **
363299 AAATGTATCGATACATTGAAG
1 -AATGTATCGATACATTTATC
* *
363320 AATGTACCGATACATTCAT-
1 AATGTATCGATACATTTATC
*
363339 AATGTATCGATTCATTCT-TC
1 AATGTATCGATACATT-TATC
363359 AATGTATCGATACATT
1 AATGTATCGATACATT
363375 CTTTCTTTTT
Statistics
Matches: 148, Mismatches: 25, Indels: 48
0.67 0.11 0.22
Matches are distributed among these distances:
19 15 0.10
20 91 0.61
21 6 0.04
24 1 0.01
27 2 0.01
30 3 0.02
31 30 0.20
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTTATC
Found at i:363324 original size:71 final size:71
Alignment explanation
Indices: 363148--363356 Score: 305
Period size: 71 Copynumber: 3.0 Consensus size: 71
363138 AAAAGTCACA
*
363148 TTTTTACCCAAATGTATCGATACATTTTTCAATGTATCAATACATGTATGAATGTATCGATACAT
1 TTTTTACCCAAATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
363213 TCTATC
66 TCTATC
* * *
363219 TTTTTACCCAGATGTATTGATACATTTTTCAATGTATTGATACATGTATGAATGTATCGATACAT
1 TTTTTACCCAAATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
363284 TCTATC
66 TCTATC
**** * *
363290 TTTTTACCCAAATGTATCGATACATTGAAGAATGTACCGATACAT-TCAT-AATGTATCGATTCA
1 TTTTTACCCAAATGTATCGATACATTTTTCAATGTATCGATACATGT-ATGAATGTATCGATACA
363353 TTCT
65 TTCT
363357 TCAATGTATC
Statistics
Matches: 124, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
70 18 0.15
71 106 0.85
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (71 bp):
TTTTTACCCAAATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
TCTATC
Found at i:363377 original size:20 final size:19
Alignment explanation
Indices: 363300--363375 Score: 89
Period size: 20 Copynumber: 3.9 Consensus size: 19
363290 TTTTTACCCA
* *
363300 AATGTATCGATACATTGAAG
1 AATGTATCGATACATT-CAT
*
363320 AATGTACCGATACATTCAT
1 AATGTATCGATACATTCAT
* *
363339 AATGTATCGATTCATTCTT
1 AATGTATCGATACATTCAT
363358 CAATGTATCGATACATTC
1 -AATGTATCGATACATTC
363376 TTTCTTTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 17 0.35
20 31 0.65
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (19 bp):
AATGTATCGATACATTCAT
Found at i:368892 original size:21 final size:21
Alignment explanation
Indices: 368859--368903 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
368849 TTGCAAGATG
*
368859 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
368881 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
368901 AAA
1 AAA
368904 ATGAAAGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:370721 original size:15 final size:15
Alignment explanation
Indices: 370701--370730 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
370691 AAAAATGTCT
*
370701 AAAATGAGGAAGCTC
1 AAAATGAAGAAGCTC
370716 AAAATGAAGAAGCTC
1 AAAATGAAGAAGCTC
370731 CAAACGAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.23, T:0.13
Consensus pattern (15 bp):
AAAATGAAGAAGCTC
Found at i:372827 original size:13 final size:13
Alignment explanation
Indices: 372809--372834 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
372799 ACATTTTTCC
372809 TTGTATCGATACA
1 TTGTATCGATACA
372822 TTGTATCGATACA
1 TTGTATCGATACA
372835 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:372998 original size:20 final size:20
Alignment explanation
Indices: 372955--373000 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
372945 AAATCTTTTG
372955 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
372976 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
372996 CAAAA
1 CAAAA
373001 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:375412 original size:20 final size:20
Alignment explanation
Indices: 375367--375418 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
375357 GTAGCCAAAC
* **
375367 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACAAAAAA
375387 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
375406 TTGTATCGATACA
1 TTGTATCGATACA
375419 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:379497 original size:54 final size:55
Alignment explanation
Indices: 379399--379539 Score: 126
Period size: 54 Copynumber: 2.5 Consensus size: 55
379389 ATATCAGTTG
* * * * * * * *
379399 GCACATGAATCAAAACCCACATTAGCTAGCATC-CAAGTCTAAGCCCATACTGGCTA
1 GCACAT-AATCGAAGCCCACATTAACTGGCA-CACGAGTCGAAGCCCACACTAGCTA
* * *
379455 GCACCT-AT-GTAAGCCCACATTAACTGGCACACGAGTCGAAGCCCACATTAGTTA
1 GCACATAATCG-AAGCCCACATTAACTGGCACACGAGTCGAAGCCCACACTAGCTA
379509 GCACATGAATCGAAGCCCACATTAACTGGCA
1 GCACAT-AATCGAAGCCCACATTAACTGGCA
379540 TTTAAGTCTA
Statistics
Matches: 68, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
53 1 0.01
54 40 0.59
56 26 0.38
57 1 0.01
ACGTcount: A:0.34, C:0.30, G:0.17, T:0.19
Consensus pattern (55 bp):
GCACATAATCGAAGCCCACATTAACTGGCACACGAGTCGAAGCCCACACTAGCTA
Found at i:379498 original size:28 final size:28
Alignment explanation
Indices: 379465--379539 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 28
379455 GCACCTATGT
*
379465 AAGCCCACATTAACTGGCACACGAGTCG
1 AAGCCCACATTAACTGGCACACGAATCG
** * *
379493 AAGCCCACATTAGTTAGCACATGAATCG
1 AAGCCCACATTAACTGGCACACGAATCG
379521 AAGCCCACATTAACTGGCA
1 AAGCCCACATTAACTGGCA
379540 TTTAAGTCTA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.17
Consensus pattern (28 bp):
AAGCCCACATTAACTGGCACACGAATCG
Found at i:379620 original size:28 final size:28
Alignment explanation
Indices: 379465--379706 Score: 104
Period size: 28 Copynumber: 8.7 Consensus size: 28
379455 GCACCTATGT
** *
379465 AAGCCCACATTAACTGGCACACGAGTCG
1 AAGCCCACATTAGTTGGCACACAAGTCG
* *
379493 AAGCCCACATTAGTTAGCACATGAA-TCG
1 AAGCCCACATTAGTTGGCACA-CAAGTCG
** *** *
379521 AAGCCCACATTAACTGGCATTTAAGTCT
1 AAGCCCACATTAGTTGGCACACAAGTCG
* * *
379549 AAACCCACACTAGCTGGCAC-CTAAGT--
1 AAGCCCACATTAGTTGGCACAC-AAGTCG
* * *
379575 ATGCCCTA-ACTAGCTGGCACACAAGTCG
1 AAGCCC-ACATTAGTTGGCACACAAGTCG
** **
379603 AAGCCCACATTAGTTGGCATTTGC-A-TTA
1 AAGCCCACATTAGTTGGCA--CACAAGTCG
* **
379631 AAACCCACATTAGTTGGCACATGAGTCG
1 AAGCCCACATTAGTTGGCACACAAGTCG
* * * * *
379659 AAGCCCATACTAGTTGGTAC-CTTAGTCC
1 AAGCCCACATTAGTTGGCACAC-AAGTCG
*
379687 AAGCCCACACTAGTTGGCAC
1 AAGCCCACATTAGTTGGCAC
379707 TTTAGTCCAA
Statistics
Matches: 160, Mismatches: 41, Indels: 26
0.70 0.18 0.11
Matches are distributed among these distances:
26 20 0.12
27 6 0.04
28 131 0.82
29 2 0.01
30 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.22
Consensus pattern (28 bp):
AAGCCCACATTAGTTGGCACACAAGTCG
Found at i:379671 original size:110 final size:110
Alignment explanation
Indices: 379394--379698 Score: 299
Period size: 110 Copynumber: 2.8 Consensus size: 110
379384 AACCCATATC
* * * * * *
379394 AGTTGGCACATGAATCAAAACCCACATTAGCTAGCATC-CAAGTCTAAGCCCATACTGGCTAGCA
1 AGTTAGCACATGAATCAAAACCCACATTAACTGGCA-CATAAGTCTAAGCCCATACTAGCTGGCA
* * *
379458 CCTATGTAAGCCCACATTAACTGGCACACGAGTCGAAGCCCACATT
65 CCTAAGTAAGCCCACACTAACTGGCACACAAGTCGAAGCCCACATT
* * ** * *
379504 AGTTAGCACATGAATCGAAGCCCACATTAACTGGCATTTAAGTCTAAACCCACACTAGCTGGCAC
1 AGTTAGCACATGAATCAAAACCCACATTAACTGGCACATAAGTCTAAGCCCATACTAGCTGGCAC
* *
379569 CTAAGTATGCCCTA-ACTAGCTGGCACACAAGTCGAAGCCCACATT
66 CTAAGTAAGCCC-ACACTAACTGGCACACAAGTCGAAGCCCACATT
* ** * * ** * * * *
379614 AGTTGGCATTTGCATTAAAACCCACATTAGTTGGCACATGAGTCGAAGCCCATACTAGTTGGTAC
1 AGTTAGCACATGAATCAAAACCCACATTAACTGGCACATAAGTCTAAGCCCATACTAGCTGGCAC
*
379679 CTTAGTCCAAGCCCACACTA
66 CTAAGT--AAGCCCACACTA
379699 GTTGGCACTT
Statistics
Matches: 155, Mismatches: 35, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
110 144 0.93
111 2 0.01
112 9 0.06
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.22
Consensus pattern (110 bp):
AGTTAGCACATGAATCAAAACCCACATTAACTGGCACATAAGTCTAAGCCCATACTAGCTGGCAC
CTAAGTAAGCCCACACTAACTGGCACACAAGTCGAAGCCCACATT
Found at i:379711 original size:28 final size:28
Alignment explanation
Indices: 379634--379727 Score: 107
Period size: 28 Copynumber: 3.4 Consensus size: 28
379624 TGCATTAAAA
* * *
379634 CCCACATTAGTTGGCACATGAGTCGAAG
1 CCCACACTAGTTGGCACATTAGTCCAAG
* * *
379662 CCCATACTAGTTGGTACCTTAGTCCAAG
1 CCCACACTAGTTGGCACATTAGTCCAAG
*
379690 CCCACACTAGTTGGCACTTTAGTCCAAG
1 CCCACACTAGTTGGCACATTAGTCCAAG
**
379718 TTCACACTAG
1 CCCACACTAG
379728 CTAGCACCTA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 55 1.00
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.26
Consensus pattern (28 bp):
CCCACACTAGTTGGCACATTAGTCCAAG
Found at i:379734 original size:28 final size:28
Alignment explanation
Indices: 379680--379734 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
379670 AGTTGGTACC
* *
379680 TTAGTCCAAGCCCACACTAGTTGGCACT
1 TTAGTCCAAGCCCACACTAGCTAGCACT
**
379708 TTAGTCCAAGTTCACACTAGCTAGCAC
1 TTAGTCCAAGCCCACACTAGCTAGCAC
379735 CTAAGTTAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.25
Consensus pattern (28 bp):
TTAGTCCAAGCCCACACTAGCTAGCACT
Found at i:379748 original size:56 final size:56
Alignment explanation
Indices: 379687--379811 Score: 146
Period size: 56 Copynumber: 2.2 Consensus size: 56
379677 ACCTTAGTCC
* * * *
379687 AAGCCCACACTAGTTGGCACTTTA-GTCCAAGT-TCACACTAGCTAGCACCTAAGTTA
1 AAGCCCACACTAGTTGACAC-TTAGGTCAAAGTCT-ACACTAGCTAGAAACTAAGTTA
* * *
379743 GAGCCCACATTAGTTGACACTTAGGTCAAAGTCTACATTAGCTAGAAACTAAGTTA
1 AAGCCCACACTAGTTGACACTTAGGTCAAAGTCTACACTAGCTAGAAACTAAGTTA
*
379799 AAACCCACACTAG
1 AAGCCCACACTAG
379812 CTAACACCTC
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
55 3 0.05
56 53 0.93
57 1 0.02
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (56 bp):
AAGCCCACACTAGTTGACACTTAGGTCAAAGTCTACACTAGCTAGAAACTAAGTTA
Found at i:380727 original size:11 final size:11
Alignment explanation
Indices: 380711--380759 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
380701 ACTTTGAACT
*
380711 AGAAAAGAGAG
1 AGAAAAGAGAA
*
380722 AGAAAAGAAAA
1 AGAAAAGAGAA
*
380733 AGAAAAAAGAA
1 AGAAAAGAGAA
*
380744 AGAAAAAAAGAA
1 AG-AAAAGAGAA
380756 AGAA
1 AGAA
380760 CAAAAAAGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
11 22 0.67
12 11 0.33
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AGAAAAGAGAA
Found at i:380737 original size:22 final size:23
Alignment explanation
Indices: 380731--380800 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 23
380721 GAGAAAAGAA
380731 AAAGAAAAAAGAAAGAAAAAAAG
1 AAAGAAAAAAGAAAGAAAAAAAG
*
380754 AAAGAACAAAA-AAGAGGGAAACAAA-
1 AAAGAA-AAAAGAA-A--GAAAAAAAG
*
380779 AAAGAAAGAAGAAA-AAAAAAAG
1 AAAGAAAAAAGAAAGAAAAAAAG
380801 GTGGCATGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 13
0.70 0.06 0.24
Matches are distributed among these distances:
21 6 0.16
23 8 0.21
24 9 0.24
25 8 0.21
26 7 0.18
ACGTcount: A:0.79, C:0.03, G:0.19, T:0.00
Consensus pattern (23 bp):
AAAGAAAAAAGAAAGAAAAAAAG
Found at i:383373 original size:78 final size:77
Alignment explanation
Indices: 383242--383395 Score: 204
Period size: 78 Copynumber: 2.0 Consensus size: 77
383232 GACCACTTCA
* * * *
383242 CGGTGGTCATCAAAAGGTTAGCAGATAAGTGAGTTGTCTGATGACCTTCCCTAATCAATACAAGA
1 CGGTGGTCATCAAAAGATTAGCAGATAAGTGAATTATCTGATAACCTTCCCTAATCAATACAAGA
383307 AAATTTCTTTCG
66 AAATTTCTTTCG
* * *
383319 CGGTGG-CTATCAAAAGATTAGTCA-AGTAAGTGAATTATCTGATAACCTTTCCTAATTAATATA
1 CGGTGGTC-ATCAAAAGATTAG-CAGA-TAAGTGAATTATCTGATAACCTTCCCTAATCAATACA
383382 AGAAAATTTCTTTC
63 AGAAAATTTCTTTC
383396 TCAACCTATC
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
76 1 0.01
77 19 0.28
78 47 0.70
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (77 bp):
CGGTGGTCATCAAAAGATTAGCAGATAAGTGAATTATCTGATAACCTTCCCTAATCAATACAAGA
AAATTTCTTTCG
Found at i:386122 original size:7 final size:7
Alignment explanation
Indices: 386110--386146 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
386100 AAATTAATAA
386110 AAAATTT
1 AAAATTT
386117 AAAATTT
1 AAAATTT
386124 AAAAATTT
1 -AAAATTT
386132 AAAATTT
1 AAAATTT
*
386139 AAATTTT
1 AAAATTT
386146 A
1 A
386147 TTAAATATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
7 21 0.75
8 7 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AAAATTT
Found at i:386124 original size:25 final size:26
Alignment explanation
Indices: 386076--386127 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
386066 CTTAAAAATT
***
386076 ATTAATTAAAAAATTTATTTTTTAAA
1 ATTAATTAAAAAATTTAAAATTTAAA
386102 ATTAA-TAAAAAATTTAAAATTTAAA
1 ATTAATTAAAAAATTTAAAATTTAAA
386127 A
1 A
386128 ATTTAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
ATTAATTAAAAAATTTAAAATTTAAA
Found at i:386128 original size:26 final size:26
Alignment explanation
Indices: 386076--386130 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
386066 CTTAAAAATT
** *
386076 ATTAATTAAAAAATTTATTTTTTAAA
1 ATTAATTAAAAAATTTAAATTTAAAA
386102 ATTAA-TAAAAAATTTAAAATTTAAAA
1 ATTAATTAAAAAATTT-AAATTTAAAA
386128 ATT
1 ATT
386131 TAAAATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATTAATTAAAAAATTTAAATTTAAAA
Found at i:386129 original size:15 final size:15
Alignment explanation
Indices: 386109--386141 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
386099 AAAATTAATA
386109 AAAAATTTAAAATTT
1 AAAAATTTAAAATTT
386124 AAAAATTTAAAATTT
1 AAAAATTTAAAATTT
386139 AAA
1 AAA
386142 TTTTATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAAATTTAAAATTT
Found at i:391928 original size:21 final size:21
Alignment explanation
Indices: 391895--391944 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
391885 TTGCAAGTTG
*
391895 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
391917 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
391938 AAATAAA
1 AAATAAA
391945 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:393762 original size:15 final size:15
Alignment explanation
Indices: 393742--393772 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
393732 TAAAAATATC
*
393742 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
393757 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
393772 C
1 C
393773 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:395874 original size:13 final size:13
Alignment explanation
Indices: 395856--395893 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
395846 CATTTTTCTT
395856 TGTATCGATACAA
1 TGTATCGATACAA
*
395869 TGTATCGATACAC
1 TGTATCGATACAA
395882 TGTATCGATACA
1 TGTATCGATACA
395894 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:396048 original size:20 final size:20
Alignment explanation
Indices: 396005--396050 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
395995 AAATCTTTTG
396005 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
396026 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
396046 CAAAA
1 CAAAA
396051 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:398444 original size:19 final size:19
Alignment explanation
Indices: 398420--398484 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 19
398410 TAGCCAAACT
398420 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
398439 TGTATCGAT--AC---A-A
1 TGTATCGATACACAAAATA
398452 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC--AAAATA
398473 TGTATCGATACA
1 TGTATCGATACA
398485 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 9 0.24
20 1 0.03
21 13 0.34
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:398456 original size:13 final size:13
Alignment explanation
Indices: 398438--398463 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
398428 TACACAAAAT
398438 ATGTATCGATACA
1 ATGTATCGATACA
398451 ATGTATCGATACA
1 ATGTATCGATACA
398464 CAAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:398461 original size:32 final size:33
Alignment explanation
Indices: 398420--398484 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
398410 TAGCCAAACT
398420 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
398452 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATACAC-AAAAATATGTATCGATACA
398485 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.42
34 18 0.58
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:401948 original size:18 final size:18
Alignment explanation
Indices: 401922--401956 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
401912 GCTCATCTGG
* *
401922 TTTTTTTTTTAATTATTA
1 TTTTATTTTTAAATATTA
401940 TTTTATTTTTAAATATT
1 TTTTATTTTTAAATATT
401957 TAATTTTGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTATTTTTAAATATTA
Found at i:402637 original size:14 final size:13
Alignment explanation
Indices: 402614--402655 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
402604 AATCGATTAA
402614 TTTTAATTTAATT
1 TTTTAATTTAATT
402627 TTTTAAATTTAATT
1 TTTT-AATTTAATT
**
402641 TACTAATTTAATT
1 TTTTAATTTAATT
402654 TT
1 TT
402656 ATGAATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTAATTTAATT
Found at i:402662 original size:14 final size:13
Alignment explanation
Indices: 402617--402663 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
402607 CGATTAATTT
*
402617 TAATTTAATTTTT
1 TAATTTAATTTTA
402630 TAAATTTAA-TTTA
1 T-AATTTAATTTTA
402643 CTAATTTAATTTTA
1 -TAATTTAATTTTA
402657 TGAATTT
1 T-AATTT
402664 TAAGATAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 12 0.41
14 17 0.59
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (13 bp):
TAATTTAATTTTA
Found at i:403108 original size:5 final size:5
Alignment explanation
Indices: 403093--403156 Score: 55
Period size: 5 Copynumber: 13.2 Consensus size: 5
403083 AATTATTTTC
* *
403093 TAATA -AATA TAATA TAATA T-ATT TAAATA TAAT- TATTA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA T-AATA TAATA TAATA TAATA TAATA
*
403141 T-ATA TTATA TTAATA T
1 TAATA TAATA -TAATA T
403157 TTAATAATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
4 14 0.29
5 27 0.56
6 7 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (5 bp):
TAATA
Found at i:403154 original size:29 final size:28
Alignment explanation
Indices: 403100--403162 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 28
403090 TTCTAATAAA
403100 TATAATATAATATATTTAAATATAATTAT
1 TATAATATAATATATTTAAATATAA-TAT
*
403129 TATAATATAATATATATTATAT-TAATAT
1 TATAATATAATATAT-TTAAATATAATAT
403157 T-TAATA
1 TATAATA
403163 ATTTATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 5 0.16
28 4 0.12
29 18 0.56
30 5 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
TATAATATAATATATTTAAATATAATAT
Found at i:404226 original size:18 final size:18
Alignment explanation
Indices: 404203--404242 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
404193 TGAAAATAAT
*
404203 TTGATGAGTACATGAAAA
1 TTGATGAGCACATGAAAA
404221 TTGATGAGCACATGAAAA
1 TTGATGAGCACATGAAAA
404239 TTGA
1 TTGA
404243 ATATCGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.42, C:0.07, G:0.23, T:0.28
Consensus pattern (18 bp):
TTGATGAGCACATGAAAA
Found at i:404525 original size:22 final size:22
Alignment explanation
Indices: 404483--404525 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
404473 ATTAAAAATA
* *
404483 TAATTAAAATAATTAATTCAAT
1 TAATTAAAATAATAAAATCAAT
*
404505 TAATTAAATTAATAAAATCAA
1 TAATTAAAATAATAAAATCAA
404526 AAATAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (22 bp):
TAATTAAAATAATAAAATCAAT
Found at i:404746 original size:11 final size:11
Alignment explanation
Indices: 404716--404791 Score: 55
Period size: 11 Copynumber: 6.7 Consensus size: 11
404706 GATGTAATTT
*
404716 TAAATATGATA
1 TAAATATTATA
404727 TAATTATATTATA
1 TAA--ATATTATA
404740 TAAATA-TATAA
1 TAAATATTAT-A
* *
404751 TAAAAATAATA
1 TAAATATTATA
* *
404762 AAAATATAATA
1 TAAATATTATA
*
404773 TAAAAATTATA
1 TAAATATTATA
*
404784 TAATTATT
1 TAAATATT
404792 TAAATATGTT
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
10 3 0.06
11 36 0.71
12 2 0.04
13 10 0.20
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (11 bp):
TAAATATTATA
Found at i:404768 original size:20 final size:21
Alignment explanation
Indices: 404739--404777 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
404729 ATTATATTAT
*
404739 ATAAATATATAATA-AAAATA
1 ATAAAAATATAATATAAAATA
404759 ATAAAAATATAATATAAAA
1 ATAAAAATATAATATAAAA
404778 ATTATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
ATAAAAATATAATATAAAATA
Found at i:404805 original size:27 final size:28
Alignment explanation
Indices: 404763--404864 Score: 93
Period size: 27 Copynumber: 3.5 Consensus size: 28
404753 AAAATAATAA
404763 AAATATAATATAAAAATTATATAATTATTT
1 AAATAT-ATAT-AAAATTATATAATTATTT
* *
404793 AAATATGT-TAAAATTA-ATAATATATTA
1 AAATATATATAAAATTATATAAT-TATTT
* *
404820 AAATTTATATAAAAATATATAA-TATTTT
1 AAATATATATAAAATTATATAATTA-TTT
404848 AAATATAATTATAAAAT
1 AAATAT-A-TATAAAAT
404865 AAAAAAATAA
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
26 5 0.09
27 19 0.33
28 15 0.26
29 6 0.10
30 13 0.22
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (28 bp):
AAATATATATAAAATTATATAATTATTT
Found at i:404865 original size:29 final size:29
Alignment explanation
Indices: 404763--404863 Score: 86
Period size: 30 Copynumber: 3.5 Consensus size: 29
404753 AAAATAATAA
*
404763 AAATATAATATAAAAATTATATAAT-TATTT
1 AAATATATTATAAAAA-TATATAATAT-TTT
* * *
404793 AAATAT-GT-TAAAATTA-ATAATATATT
1 AAATATATTATAAAAATATATAATATTTT
*
404819 AAA-ATTTATATAAAAATATATAATATTTT
1 AAATATAT-TATAAAAATATATAATATTTT
404848 AAATATAATTATAAAA
1 AAATAT-ATTATAAAA
404864 TAAAAAAATA
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
25 2 0.04
26 10 0.18
27 4 0.07
28 12 0.21
29 13 0.23
30 15 0.26
31 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (29 bp):
AAATATATTATAAAAATATATAATATTTT
Found at i:405531 original size:13 final size:14
Alignment explanation
Indices: 405508--405539 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
405498 TAATATTTTA
405508 ATAAA-TTAATAAT
1 ATAAATTTAATAAT
405521 A-AAATTTAATAAT
1 ATAAATTTAATAAT
405534 ATAAAT
1 ATAAAT
405540 ACATTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 10 0.59
14 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAAATTTAATAAT
Found at i:405548 original size:22 final size:21
Alignment explanation
Indices: 405481--405548 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 21
405471 ACATAATTTT
*
405481 TTAATTTAAT-ATATAATTAA
1 TTAATTTAATAATATAAATAA
* *
405501 -TATTTTAATAA-ATTAATAA
1 TTAATTTAATAATATAAATAA
*
405520 TAAAATTTAATAATATAAATACA
1 T-TAATTTAATAATATAAATA-A
405543 TTAATT
1 TTAATT
405549 ATGTATAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
19 14 0.39
20 1 0.03
21 9 0.25
22 10 0.28
23 2 0.06
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (21 bp):
TTAATTTAATAATATAAATAA
Found at i:406197 original size:18 final size:17
Alignment explanation
Indices: 406176--406218 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
406166 TATAAATAAA
* *
406176 ATATAAAATATAATAATT
1 ATATAAAAAAT-ATAACT
406194 ATATTAAAAAATATAACT
1 ATA-TAAAAAATATAACT
406212 ATATAAA
1 ATATAAA
406219 GATTTAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 4 0.18
18 11 0.50
19 7 0.32
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
ATATAAAAAATATAACT
Found at i:406395 original size:21 final size:23
Alignment explanation
Indices: 406359--406406 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
406349 ACTTTGTATT
406359 TTATTAATATTTTAATAA-ATTAA
1 TTATTAATATTTTAATAATA-TAA
406382 TTATTAA-A-TTTAATAATATAA
1 TTATTAATATTTTAATAATATAA
406403 TTAT
1 TTAT
406407 ATTCATTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 15 0.62
22 2 0.08
23 7 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTATTAATATTTTAATAATATAA
Found at i:406596 original size:25 final size:22
Alignment explanation
Indices: 406529--406598 Score: 68
Period size: 25 Copynumber: 3.0 Consensus size: 22
406519 TTAAATATTT
*
406529 TAATTTATTTAAATTCAAAAATTA
1 TAATTTAATTAAATT-AAAAA-TA
* *
406553 TAATTTAAATAAATAAAAAATA
1 TAATTTAATTAAATTAAAAATA
406575 TAATATAATAATTAAATTAAAAAT
1 TAAT-T--TAATTAAATTAAAAAT
406599 TACAATTATA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
22 6 0.16
23 6 0.16
24 12 0.32
25 14 0.37
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (22 bp):
TAATTTAATTAAATTAAAAATA
Found at i:406605 original size:18 final size:19
Alignment explanation
Indices: 406584--406619 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
406574 ATAATATAAT
406584 AATTAAATTAAAA-ATTAC
1 AATTAAATTAAAATATTAC
*
406602 AATTATATTAAAATATTA
1 AATTAAATTAAAATATTA
406620 TAAAAATCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTAAATTAAAATATTAC
Found at i:407052 original size:19 final size:21
Alignment explanation
Indices: 407028--407082 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 21
407018 TAAATATCTT
407028 TAATTTTATTTT-ATTTT-TG
1 TAATTTTATTTTAATTTTATG
*
407047 TAATTTGATTTTAAATTTTATG
1 TAATTTTATTTT-AATTTTATG
407069 TAA-TTT-TTTTAATT
1 TAATTTTATTTTAATT
407083 AAATTAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 15 0.48
20 4 0.13
21 7 0.23
22 5 0.16
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.67
Consensus pattern (21 bp):
TAATTTTATTTTAATTTTATG
Found at i:407299 original size:11 final size:11
Alignment explanation
Indices: 407274--407308 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
407264 TCATCAAAAA
*
407274 ATATATATATAT
1 ATATA-ATATGT
407286 ATATAATATGT
1 ATATAATATGT
407297 ATATAATATGT
1 ATATAATATGT
407308 A
1 A
407309 CTGCTTTAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 17 0.77
12 5 0.23
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (11 bp):
ATATAATATGT
Found at i:408046 original size:18 final size:17
Alignment explanation
Indices: 408019--408054 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
408009 TATATATTTT
408019 TTAAAATTTTTGATATA
1 TTAAAATTTTTGATATA
408036 TTAATAATTTTTGATATA
1 TTAA-AATTTTTGATATA
408054 T
1 T
408055 AAATTTTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
TTAAAATTTTTGATATA
Found at i:410069 original size:3 final size:3
Alignment explanation
Indices: 410055--410092 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
410045 TAATTAGATT
*
410055 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
410093 TTGTTTTCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:411821 original size:19 final size:18
Alignment explanation
Indices: 411778--411824 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
411768 TAATTTGTAT
* *
411778 ATTATAATTATATTTAAA
1 ATTATATTTATAATTAAA
411796 A-TATATTTATAAATTAAA
1 ATTATATTTAT-AATTAAA
411814 ATTATATTTAT
1 ATTATATTTAT
411825 TATTTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.32
18 8 0.32
19 9 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTATATTTATAATTAAA
Found at i:411836 original size:16 final size:18
Alignment explanation
Indices: 411815--411857 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
411805 TAAATTAAAA
*
411815 TTATATTTATT-A-TTTT
1 TTATATTAATTAATTTTT
411831 TTATATTAATTAATTTTT
1 TTATATTAATTAATTTTT
411849 TTATATTAA
1 TTATATTAA
411858 GTATTTGGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 10 0.42
17 1 0.04
18 13 0.54
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATATTAATTAATTTTT
Found at i:411850 original size:18 final size:16
Alignment explanation
Indices: 411815--411863 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 16
411805 TAAATTAAAA
*
411815 TTATATTTATTATTTT
1 TTATATTAATTATTTT
411831 TTATATTAATTAATTTTT
1 TTATATTAATT-A-TTTT
*
411849 TTATATTAAGTATTT
1 TTATATTAATTATTT
411864 GGAGAAAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 13 0.45
17 2 0.07
18 14 0.48
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
TTATATTAATTATTTT
Found at i:412479 original size:13 final size:13
Alignment explanation
Indices: 412453--412491 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
412443 AGATCTCCAA
*
412453 AAAAAAAAAAAAT
1 AAAAAAACAAAAT
* *
412466 AAATAAATAAAAT
1 AAAAAAACAAAAT
412479 AAAAAAACAAAAT
1 AAAAAAACAAAAT
412492 TTTAAACTCT
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:0.85, C:0.03, G:0.00, T:0.13
Consensus pattern (13 bp):
AAAAAAACAAAAT
Done.