Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold481
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1334154
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 122349 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:5768 original size:25 final size:25
Alignment explanation
Indices: 5732--5980 Score: 198
Period size: 25 Copynumber: 9.8 Consensus size: 25
5722 CATTAATTGA
*
5732 TGTATATCCTCTCCTTTGAATTAAT
1 TGTAGATCCTCTCCTTTGAATTAAT
* *
5757 TATAGATCCTCTCCCTTT-AATGAAT
1 TGTAGATCCTCT-CCTTTGAATTAAT
** *
5782 TGTAGATCCTCTTTTTTGAATAAAT
1 TGTAGATCCTCTCCTTTGAATTAAT
*
5807 TGTAGATCCTCTCCCTTGAATACCGGTAATT
1 TGTAGATCCTCTCCTTTGAAT-----TAA-T
* * *
5838 TGTAGATCCTCCCCCTTGAATAAAT
1 TGTAGATCCTCTCCTTTGAATTAAT
* * *
5863 TGTAAATCCTTTTCTTTGAACTT-AT
1 TGTAGATCCTCTCCTTTGAA-TTAAT
* * * *
5888 TGTAGATCGTCTCATTTAAATTTAT
1 TGTAGATCCTCTCCTTTGAATTAAT
* *
5913 TGAAGATCCTCTCCTTTGAATTTAT
1 TGTAGATCCTCTCCTTTGAATTAAT
* * * *
5938 TCTAGATCCTCACCTTTTAACT-AT
1 TGTAGATCCTCTCCTTTGAATTAAT
5962 TGTAGATCCTCTCCTTTGA
1 TGTAGATCCTCTCCTTTGA
5981 GGAAGTGATG
Statistics
Matches: 177, Mismatches: 37, Indels: 21
0.75 0.16 0.09
Matches are distributed among these distances:
24 23 0.13
25 123 0.69
26 8 0.05
30 2 0.01
31 21 0.12
ACGTcount: A:0.25, C:0.21, G:0.11, T:0.43
Consensus pattern (25 bp):
TGTAGATCCTCTCCTTTGAATTAAT
Found at i:30360 original size:224 final size:223
Alignment explanation
Indices: 29970--30416 Score: 885
Period size: 224 Copynumber: 2.0 Consensus size: 223
29960 GGAACAGCCG
29970 CATTGATCTCTTAAAAATAAAGATTCGAGGCAATACACATTGTTTTGACTGGAACTAACACGTGA
1 CATTGATCTCTTAAAAATAAAGATTCGAGGCAATACACATTGTTTTGACTGGAACTAACACGTGA
30035 AATTGACATGGTTTGAAAACTTTTTACGGTTTGAAGTTGTACTTCCATGATCAGTGCGAGACAAA
66 AATTGACATGGTTTGAAAACTTTTTACGGTTTGAAGTTGTACTTCCATGATCAGTGCGAGACAAA
30100 TAGGTATTTCTGATCTGATAATTTACTGATGACGTTCGTGGTATATTGGAGAATAATGTCCGCGG
131 TAGGTATTTCTGATCTGATAATTTACTGATGACGTTCGTGGTATATTGGAGAATAATGTCCGCGG
30165 CATCTCTTTGATCTCGGCAATAACTGTA
196 CATCTCTTTGATCTCGGCAATAACTGTA
30193 NCATTGATCTCTTAAAAATAAAGATTCGAGGCAATACACATTGTTTTGACTGGAACTAACACGTG
1 -CATTGATCTCTTAAAAATAAAGATTCGAGGCAATACACATTGTTTTGACTGGAACTAACACGTG
30258 AAATTGACATGGTTTGAAAACTTTTTACGGTTTGAAGTTGTACTTCCATGATCAGTGCGAGACAA
65 AAATTGACATGGTTTGAAAACTTTTTACGGTTTGAAGTTGTACTTCCATGATCAGTGCGAGACAA
30323 ATAGGTATTTCTGATCTGATAATTTACTGATGACGTTCGTGGTATATTGGAGAATAATGTCCGCG
130 ATAGGTATTTCTGATCTGATAATTTACTGATGACGTTCGTGGTATATTGGAGAATAATGTCCGCG
30388 GCATCTCTTTGATCTCGGCAATAACTGTA
195 GCATCTCTTTGATCTCGGCAATAACTGTA
30417 GTAGAATTCT
Statistics
Matches: 223, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
224 223 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.34
Consensus pattern (223 bp):
CATTGATCTCTTAAAAATAAAGATTCGAGGCAATACACATTGTTTTGACTGGAACTAACACGTGA
AATTGACATGGTTTGAAAACTTTTTACGGTTTGAAGTTGTACTTCCATGATCAGTGCGAGACAAA
TAGGTATTTCTGATCTGATAATTTACTGATGACGTTCGTGGTATATTGGAGAATAATGTCCGCGG
CATCTCTTTGATCTCGGCAATAACTGTA
Found at i:31647 original size:14 final size:14
Alignment explanation
Indices: 31628--31656 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
31618 CCACGAGTTG
31628 TATTCCATACACCC
1 TATTCCATACACCC
31642 TATTCCATACACCC
1 TATTCCATACACCC
31656 T
1 T
31657 GAGGCGGCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.41, G:0.00, T:0.31
Consensus pattern (14 bp):
TATTCCATACACCC
Found at i:31969 original size:20 final size:20
Alignment explanation
Indices: 31904--32000 Score: 97
Period size: 20 Copynumber: 4.7 Consensus size: 20
31894 AGGTATTTTC
31904 TGATATCAAAAAATAAATAT-T
1 TGATATCAAAAAAT-AAT-TCT
* * *
31925 TGATATCAATAATTCGAATTAT
1 TGATATCAAAAAAT--AATTCT
*
31947 TGATATCAGAAAATAATTCT
1 TGATATCAAAAAATAATTCT
*
31967 TGATATAAAAAAATAATTCT
1 TGATATCAAAAAATAATTCT
*
31987 TGATTTCAAAAAAT
1 TGATATCAAAAAAT
32001 CTATTTTGTG
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
20 35 0.56
21 13 0.21
22 15 0.24
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.36
Consensus pattern (20 bp):
TGATATCAAAAAATAATTCT
Found at i:32070 original size:22 final size:21
Alignment explanation
Indices: 32048--32172 Score: 67
Period size: 21 Copynumber: 5.7 Consensus size: 21
32038 ATTCGAATTC
32048 TTGATATCAAAAAATGATTTT
1 TTGATATCAAAAAATGATTTT
* *
32069 CT--TATCACAAAATTGATTTT
1 TTGATATCA-AAAAATGATTTT
*
32089 TTGATAGCAAGAATTAAAGTTGATTTT
1 TTGATATC-A-AA--AAA--TGATTTT
** * *
32116 TT-ATAGAAAAAAATCGAATTC
1 TTGATATCAAAAAAT-GATTTT
* *
32137 TTGATATCAGAAAATAATTTT
1 TTGATATCAAAAAATGATTTT
*
32158 TTGATATTAAAAAAT
1 TTGATATCAAAAAAT
32173 CAATTGTATT
Statistics
Matches: 77, Mismatches: 17, Indels: 20
0.68 0.15 0.18
Matches are distributed among these distances:
19 5 0.06
20 13 0.17
21 23 0.30
22 15 0.19
23 3 0.04
24 2 0.03
25 3 0.04
26 4 0.05
27 9 0.12
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.40
Consensus pattern (21 bp):
TTGATATCAAAAAATGATTTT
Found at i:33583 original size:23 final size:22
Alignment explanation
Indices: 33536--33585 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
33526 TTCAATATCT
* * *
33536 GATAT-CAAAAAATCATTTTCG
1 GATATCCAAAAAATCAATCTCA
33557 GATATCCAAAAAATCGAATCTCA
1 GATATCCAAAAAATC-AATCTCA
33580 GATATC
1 GATATC
33586 ATAAAATGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 5 0.21
22 9 0.38
23 10 0.42
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (22 bp):
GATATCCAAAAAATCAATCTCA
Found at i:33623 original size:22 final size:22
Alignment explanation
Indices: 33482--33630 Score: 101
Period size: 22 Copynumber: 6.7 Consensus size: 22
33472 TTTATTTGAA
* *
33482 TTTCTGATATCAGAAAATGCAAT
1 TTTCTGATATCAAAAAAT-CGAT
* *
33505 TCT-TGATATCAAAAAATCAGTT
1 TTTCTGATATCAAAAAATC-GAT
33527 TCAATATCTGATATCAAAAAATC-AT
1 T---T-TCTGATATCAAAAAATCGAT
* *
33552 TTTCGGATATCCAAAAAATCGAA
1 TTTCTGATAT-CAAAAAATCGAT
* * *
33575 TCTCAGATATCATAAAAT-GAT
1 TTTCTGATATCAAAAAATCGAT
*
33596 TTT-TGATATCACAAAATCGAT
1 TTTCTGATATCAAAAAATCGAT
*
33617 TTTTTGATAT-AAAA
1 TTTCTGATATCAAAA
33631 GAAATGGATC
Statistics
Matches: 100, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
20 12 0.12
21 21 0.21
22 38 0.38
23 11 0.11
25 2 0.02
26 1 0.01
27 15 0.15
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.35
Consensus pattern (22 bp):
TTTCTGATATCAAAAAATCGAT
Found at i:33753 original size:22 final size:22
Alignment explanation
Indices: 33727--33777 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
33717 TATCAGAAAA
*
33727 TGATATCAGTAATTCGAATTCT
1 TGATATCAGGAATTCGAATTCT
33749 TGATATCAGGAATTCGAATTCT
1 TGATATCAGGAATTCGAATTCT
*
33771 TGTTATC
1 TGATATC
33778 TAAAAATCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (22 bp):
TGATATCAGGAATTCGAATTCT
Found at i:65087 original size:2 final size:2
Alignment explanation
Indices: 65080--65140 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
65070 TATAGTGAAA
65080 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
65122 CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT C
65141 ACACACATGG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:70801 original size:466 final size:465
Alignment explanation
Indices: 69930--70860 Score: 1853
Period size: 466 Copynumber: 2.0 Consensus size: 465
69920 TGTTTATAAC
69930 CTTCGAGATATCCGAGACATTTACGGTAAAATACATGTACTTAAAATTAAGTGGTTGGTACTTAC
1 CTTCGAGATATCCGAGACATTTACGGTAAAATACATGTACTTAAAATTAAGTGGTTGGTACTTAC
69995 AAATCACTTTGATATATCCATTGTATTCGAGATATCAGTGTTTCAGATATCAAAGTTCAACTGTA
66 AAATCACTTTGATATATCCATTGTATTCGAGATATCAGTGTTTCAGATATCAAAGTTCAACTGTA
70060 GTTTTTAGAATTGTTTGAATGTAAGAAATTTGAAAAAAACTAAACTTCGGAACTTTATTTATTTT
131 GTTTTTAGAATTGTTTGAATGTAAGAAATTTGAAAAAAACTAAACTTCGGAACTTTATTTATTTT
70125 AATAGAATTTATGAACTACAGGAGAGATTACGAGCCAATGAACTGAGACAACAGCTGATCGACCA
196 AATAGAATTTATGAACTACAGGAGAGATTACGAGCCAATGAACTGAGACAACAGCTGATCGACCA
70190 ACAACTCAAGAACCTGGATGATGGGGCTGTCCATTCCTAGCTGTTAGCAGTGTAGTATAGCATCA
261 ACAACTCAAGAACCTGGATGATGGGGCTGTCCATTCCTAGCTGTTAGCAGTGTAGTATAGCATCA
70255 AGTTTACCAAAGACTTCATCATAACAAGACAGACTAATGCTTTGACCCAGCCCTCTGCCTGGGCA
326 AGTTTACCAAAGACTTCATCATAACAAGACAGACTAATGCTTTGACCCAGCCCTCTGCCTGGGCA
70320 TTAAATTATTCTCTGAACAATCATTAACAACAAAGATTGGTATCCCTATTAAATAAATGAGATTT
391 TTAAATTATTCTCTGAACAATCATTAACAACAAAGATTGGTATCCCTATTAAATAAATGAGATTT
70385 TTATACTTTT
456 TTATACTTTT
70395 NCTTCGAGATATCCGAGACATTTACGGTAAAATACATGTACTTAAAATTAAGTGGTTGGTACTTA
1 -CTTCGAGATATCCGAGACATTTACGGTAAAATACATGTACTTAAAATTAAGTGGTTGGTACTTA
70460 CAAATCACTTTGATATATCCATTGTATTCGAGATATCAGTGTTTCAGATATCAAAGTTCAACTGT
65 CAAATCACTTTGATATATCCATTGTATTCGAGATATCAGTGTTTCAGATATCAAAGTTCAACTGT
70525 AGTTTTTAGAATTGTTTGAATGTAAGAAATTTGAAAAAAACTAAACTTCGGAACTTTATTTATTT
130 AGTTTTTAGAATTGTTTGAATGTAAGAAATTTGAAAAAAACTAAACTTCGGAACTTTATTTATTT
70590 TAATAGAATTTATGAACTACAGGAGAGATTACGAGCCAATGAACTGAGACAACAGCTGATCGACC
195 TAATAGAATTTATGAACTACAGGAGAGATTACGAGCCAATGAACTGAGACAACAGCTGATCGACC
70655 AACAACTCAAGAACCTGGATGATGGGGCTGTCCATTCCTAGCTGTTAGCAGTGTAGTATAGCATC
260 AACAACTCAAGAACCTGGATGATGGGGCTGTCCATTCCTAGCTGTTAGCAGTGTAGTATAGCATC
70720 AAGTTTACCAAAGACTTCATCATAACAAGACAGACTAATGCTTTGACCCAGCCCTCTGCCTGGGC
325 AAGTTTACCAAAGACTTCATCATAACAAGACAGACTAATGCTTTGACCCAGCCCTCTGCCTGGGC
70785 ATTAAATTATTCTCTGAACAATCATTAACAACAAAGATTGGTATCCCTATTAAATAAATGAGATT
390 ATTAAATTATTCTCTGAACAATCATTAACAACAAAGATTGGTATCCCTATTAAATAAATGAGATT
70850 TTTATACTTTT
455 TTTATACTTTT
70861 ATGTCAGTGC
Statistics
Matches: 465, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
466 465 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (465 bp):
CTTCGAGATATCCGAGACATTTACGGTAAAATACATGTACTTAAAATTAAGTGGTTGGTACTTAC
AAATCACTTTGATATATCCATTGTATTCGAGATATCAGTGTTTCAGATATCAAAGTTCAACTGTA
GTTTTTAGAATTGTTTGAATGTAAGAAATTTGAAAAAAACTAAACTTCGGAACTTTATTTATTTT
AATAGAATTTATGAACTACAGGAGAGATTACGAGCCAATGAACTGAGACAACAGCTGATCGACCA
ACAACTCAAGAACCTGGATGATGGGGCTGTCCATTCCTAGCTGTTAGCAGTGTAGTATAGCATCA
AGTTTACCAAAGACTTCATCATAACAAGACAGACTAATGCTTTGACCCAGCCCTCTGCCTGGGCA
TTAAATTATTCTCTGAACAATCATTAACAACAAAGATTGGTATCCCTATTAAATAAATGAGATTT
TTATACTTTT
Found at i:75940 original size:26 final size:21
Alignment explanation
Indices: 75879--75977 Score: 182
Period size: 21 Copynumber: 4.8 Consensus size: 21
75869 ATTCAAATAT
*
75879 TTGTACCTATCTTCAAAT-AA
1 TTGTACCTATCTTCAATTCAA
75899 TTGTACCTATCTTCAATTCAA
1 TTGTACCTATCTTCAATTCAA
75920 TTGTACCTATCTTCAATTCAA
1 TTGTACCTATCTTCAATTCAA
75941 TTGTACCTATCTTCAATTCAA
1 TTGTACCTATCTTCAATTCAA
75962 TTGTACCTATCTTCAA
1 TTGTACCTATCTTCAA
75978 ATTGAATTAG
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
20 17 0.22
21 60 0.78
ACGTcount: A:0.29, C:0.23, G:0.05, T:0.42
Consensus pattern (21 bp):
TTGTACCTATCTTCAATTCAA
Found at i:76015 original size:43 final size:42
Alignment explanation
Indices: 75954--76048 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 42
75944 TACCTATCTT
*
75954 CAATTCAATTGTACCTATCTTCAAATTGAATTAG-AGATAGGTA
1 CAATTCAATTATACCTATCTT-AAATT-AATTAGAAGATAGGTA
* * *
75997 CAATTCAATTATACCTATCTTTAATTCATTTGAAGATAGGTA
1 CAATTCAATTATACCTATCTTAAATTAATTAGAAGATAGGTA
*
76039 CAATTGAATT
1 CAATTCAATT
76049 GAAGATAGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
41 4 0.09
42 22 0.48
43 20 0.43
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.38
Consensus pattern (42 bp):
CAATTCAATTATACCTATCTTAAATTAATTAGAAGATAGGTA
Found at i:76015 original size:64 final size:63
Alignment explanation
Indices: 75882--76024 Score: 173
Period size: 64 Copynumber: 2.3 Consensus size: 63
75872 CAAATATTTG
* * * * *
75882 TACCTATCTTCAAAT-AATTGTACCTATCTTCAATTCAATTGTACCTATCTTCAATTCAATTG
1 TACCTATCTTCAATTCAATTGTACCTATCTTCAATTCAATTGTACATAGCTACAATTCAATTA
* * *
75944 TACCTATCTTCAATTCAATTGTACCTATCTTCAAATTGAATTAG-AGATAGGTACAATTCAATTA
1 TACCTATCTTCAATTCAATTGTACCTATCTTC-AATTCAATT-GTACATAGCTACAATTCAATTA
*
76008 TACCTATCTTTAATTCA
1 TACCTATCTTCAATTCA
76025 TTTGAAGATA
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
62 14 0.20
63 16 0.23
64 38 0.55
65 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (63 bp):
TACCTATCTTCAATTCAATTGTACCTATCTTCAATTCAATTGTACATAGCTACAATTCAATTA
Found at i:76043 original size:21 final size:21
Alignment explanation
Indices: 76019--76119 Score: 103
Period size: 21 Copynumber: 4.6 Consensus size: 21
76009 ACCTATCTTT
*
76019 AATTCATTTGAAGATAGGTAC
1 AATTCAATTGAAGATAGGTAC
*
76040 AATTGAATTGAAGATAGGTAC
1 AATTCAATTGAAGATAGGTAC
*
76061 AAATGCAATGAATTGAAGATAGGTAC
1 -AAT----TCAATTGAAGATAGGTAC
* *
76087 AATTGAATTAAAGATAGGTAC
1 AATTCAATTGAAGATAGGTAC
*
76108 AATTGAATTGAA
1 AATTCAATTGAA
76120 CCTATCTTCA
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
21 47 0.66
22 3 0.04
25 3 0.04
26 18 0.25
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.29
Consensus pattern (21 bp):
AATTCAATTGAAGATAGGTAC
Found at i:77614 original size:21 final size:21
Alignment explanation
Indices: 77582--77650 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
77572 TAGATATGTC
*
77582 TGAATTGAACCTATCTTCAAA
1 TGAATTGTACCTATCTTCAAA
* *
77603 TCAATTGTACCTATCTTTAAA
1 TGAATTGTACCTATCTTCAAA
*
77624 TGAATTTTACCTATCTTCAAA
1 TGAATTGTACCTATCTTCAAA
77645 TGAATT
1 TGAATT
77651 AGAGATAGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (21 bp):
TGAATTGTACCTATCTTCAAA
Found at i:77681 original size:63 final size:63
Alignment explanation
Indices: 77603--77741 Score: 190
Period size: 63 Copynumber: 2.2 Consensus size: 63
77593 TATCTTCAAA
* **
77603 TCAATTGTACCTATCTTTAAATGAATTTTACCTATCTTCAAATGAATT-AGAGATAGGTATAAT
1 TCAATTGTACCTATCTTTAAATCAATTGAACCTATCTTCAAATGAATTGA-AGATAGGTATAAT
* * * *
77666 TCAATTGAACCTATCTTTAATTCAATTGAACCTATCTTTAATTGAATTGAAGATAGGTATAAT
1 TCAATTGTACCTATCTTTAAATCAATTGAACCTATCTTCAAATGAATTGAAGATAGGTATAAT
*
77729 TCATTTGTACCTA
1 TCAATTGTACCTA
77742 GGTATAATTC
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
63 65 0.98
64 1 0.02
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (63 bp):
TCAATTGTACCTATCTTTAAATCAATTGAACCTATCTTCAAATGAATTGAAGATAGGTATAAT
Found at i:77686 original size:21 final size:21
Alignment explanation
Indices: 77662--77848 Score: 153
Period size: 21 Copynumber: 9.0 Consensus size: 21
77652 GAGATAGGTA
*
77662 TAATTCAATTGAACCTATCTT
1 TAATTCAATTGTACCTATCTT
*
77683 TAATTCAATTGAACCTATCTT
1 TAATTCAATTGTACCTATCTT
* * ** ** *
77704 TAATTGAATTGAAGATAGGTA
1 TAATTCAATTGTACCTATCTT
* ** *
77725 TAATTCATTTGTACCTAGGTA
1 TAATTCAATTGTACCTATCTT
* ** *
77746 TAATTCATTTGTACCTAGGTA
1 TAATTCAATTGTACCTATCTT
* **
77767 TAATT-ATTTACACCTATCTT
1 TAATTCAATTGTACCTATCTT
*
77787 CAATTCAATTGTACCTATCTT
1 TAATTCAATTGTACCTATCTT
* *
77808 CAAAT-AATTGTACCTATCTT
1 TAATTCAATTGTACCTATCTT
77828 TAATTCAATTGTACCTATCTT
1 TAATTCAATTGTACCTATCTT
77849 CAAATGATTT
Statistics
Matches: 141, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
20 32 0.23
21 109 0.77
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.43
Consensus pattern (21 bp):
TAATTCAATTGTACCTATCTT
Found at i:77708 original size:42 final size:42
Alignment explanation
Indices: 77584--77853 Score: 167
Period size: 42 Copynumber: 6.5 Consensus size: 42
77574 GATATGTCTG
* * * *
77584 AATTGAACCTATCTTCAAATCAATTGTACCTATCTTTAAATG
1 AATTGTACCTATCTTCAAATCAATTGAACCTATCTTTAATTC
* * ** *
77626 AATTTTACCTATCTTCAAATGAATTAGAGA--TAGGTATAATTC
1 AATTGTACCTATCTTCAAATCAATT-GA-ACCTATCTTTAATTC
* * * *
77668 AATTGAACCTATCTTTAATTCAATTGAACCTATCTTTAATTG
1 AATTGTACCTATCTTCAAATCAATTGAACCTATCTTTAATTC
* ** ** * * * ** *
77710 AATTGAAGATAGGTAT-AATTCATTTGTACCTAGGTATAATTC
1 AATTGTACCTATCT-TCAAATCAATTGAACCTATCTTTAATTC
* ** * * *
77752 ATTTGTACCTA-GGT-ATAAT-TATTTACACCTATCTTCAATTC
1 AATTGTACCTATCTTCA-AATCAATTGA-ACCTATCTTTAATTC
*
77793 AATTGTACCTATCTTCAAAT-AATTGTACCTATCTTTAATTC
1 AATTGTACCTATCTTCAAATCAATTGAACCTATCTTTAATTC
77834 AATTGTACCTATCTTCAAAT
1 AATTGTACCTATCTTCAAAT
77854 GATTTGAAGA
Statistics
Matches: 170, Mismatches: 49, Indels: 19
0.71 0.21 0.08
Matches are distributed among these distances:
40 5 0.03
41 60 0.35
42 101 0.59
43 3 0.02
44 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (42 bp):
AATTGTACCTATCTTCAAATCAATTGAACCTATCTTTAATTC
Found at i:77750 original size:63 final size:63
Alignment explanation
Indices: 77632--77762 Score: 165
Period size: 63 Copynumber: 2.1 Consensus size: 63
77622 AATGAATTTT
* *
77632 ACCTATCTTCAAATGAATTAGAGATAGGTATAATTCAATTGAACCTATCTTTAATTCAATTGA
1 ACCTATCTTCAAATGAATTAGAGATAGGTATAATTCAATTGAACCTAGCTATAATTCAATTGA
* * * * * * *
77695 ACCTATCTTTAATTGAATT-GAAGATAGGTATAATTCATTTGTACCTAGGTATAATTCATTTGT
1 ACCTATCTTCAAATGAATTAG-AGATAGGTATAATTCAATTGAACCTAGCTATAATTCAATTGA
77758 ACCTA
1 ACCTA
77763 GGTATAATTA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
62 1 0.02
63 57 0.98
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (63 bp):
ACCTATCTTCAAATGAATTAGAGATAGGTATAATTCAATTGAACCTAGCTATAATTCAATTGA
Found at i:77917 original size:20 final size:20
Alignment explanation
Indices: 77849--77921 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
77839 TACCTATCTT
77849 CAAATGATTTGAAGATAGGTA
1 CAAAT-ATTTGAAGATAGGTA
* *
77870 CAATTAATTGAAGATAGGTA
1 CAAATATTTGAAGATAGGTA
*
77890 CAATTATTTGAAGATAGGTA
1 CAAATATTTGAAGATAGGTA
77910 CAAATATTTGAA
1 CAAATATTTGAA
77922 TATATGTTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
20 44 0.92
21 4 0.08
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32
Consensus pattern (20 bp):
CAAATATTTGAAGATAGGTA
Found at i:78957 original size:15 final size:15
Alignment explanation
Indices: 78934--78963 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
78924 CCCGCCTTCT
78934 TTTCCTTCCAGTTTC
1 TTTCCTTCCAGTTTC
*
78949 TTTCTTTCCAGTTTC
1 TTTCCTTCCAGTTTC
78964 CTCATGGTAT
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:0.07, C:0.30, G:0.07, T:0.57
Consensus pattern (15 bp):
TTTCCTTCCAGTTTC
Found at i:94750 original size:15 final size:15
Alignment explanation
Indices: 94730--94759 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
94720 TGAACGTTTT
94730 TAGTCTCGTTCAACC
1 TAGTCTCGTTCAACC
94745 TAGTCTCGTTCAACC
1 TAGTCTCGTTCAACC
94760 AGACGCTCGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.33
Consensus pattern (15 bp):
TAGTCTCGTTCAACC
Found at i:95296 original size:2 final size:2
Alignment explanation
Indices: 95289--95319 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
95279 ACTGAAAATA
95289 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
95320 GTTGTATGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:96208 original size:8 final size:8
Alignment explanation
Indices: 96197--96274 Score: 93
Period size: 8 Copynumber: 9.8 Consensus size: 8
96187 AGTGTGACGG
*
96197 ACGGACGC
1 ACGGACAC
96205 ACGGACAC
1 ACGGACAC
96213 ACGGACAC
1 ACGGACAC
*
96221 ACGGACCC
1 ACGGACAC
96229 ACGGACAC
1 ACGGACAC
* *
96237 ACAGACCC
1 ACGGACAC
*
96245 ATGGACAC
1 ACGGACAC
*
96253 ACGGACCC
1 ACGGACAC
*
96261 ATGGACAC
1 ACGGACAC
96269 ACGGAC
1 ACGGAC
96275 GGACGCCCGG
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 57 1.00
ACGTcount: A:0.33, C:0.38, G:0.26, T:0.03
Consensus pattern (8 bp):
ACGGACAC
Found at i:96218 original size:16 final size:16
Alignment explanation
Indices: 96197--96274 Score: 111
Period size: 16 Copynumber: 4.9 Consensus size: 16
96187 AGTGTGACGG
* *
96197 ACGGACGCACGGACAC
1 ACGGACACACGGACCC
96213 ACGGACACACGGACCC
1 ACGGACACACGGACCC
*
96229 ACGGACACACAGACCC
1 ACGGACACACGGACCC
*
96245 ATGGACACACGGACCC
1 ACGGACACACGGACCC
*
96261 ATGGACACACGGAC
1 ACGGACACACGGAC
96275 GGACGCCCGG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 57 1.00
ACGTcount: A:0.33, C:0.38, G:0.26, T:0.03
Consensus pattern (16 bp):
ACGGACACACGGACCC
Found at i:100458 original size:46 final size:46
Alignment explanation
Indices: 100385--100475 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 46
100375 CACAAACACA
100385 AGCAGTCAGTAAAGAAAAAGATACATCAAAGTACTGAGAGTACTCT
1 AGCAGTCAGTAAAGAAAAAGATACATCAAAGTACTGAGAGTACTCT
* * * *
100431 AGCAGTCGGTAAAGAAGAAGGTGCATCAAAGTACTGAGAGTACTC
1 AGCAGTCAGTAAAGAAAAAGATACATCAAAGTACTGAGAGTACTC
100476 GACCGGGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.42, C:0.15, G:0.24, T:0.19
Consensus pattern (46 bp):
AGCAGTCAGTAAAGAAAAAGATACATCAAAGTACTGAGAGTACTCT
Found at i:100764 original size:12 final size:11
Alignment explanation
Indices: 100743--100779 Score: 56
Period size: 12 Copynumber: 3.2 Consensus size: 11
100733 ATCTGAAGCT
100743 TATAATAATAA
1 TATAATAATAA
100754 TATATATAATAA
1 TATA-ATAATAA
100766 TATAATAATTAA
1 TATAATAA-TAA
100778 TA
1 TA
100780 ATAGCAGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TATAATAATAA
Found at i:100778 original size:15 final size:17
Alignment explanation
Indices: 100744--100782 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
100734 TCTGAAGCTT
100744 ATAATAATAATATATATA
1 ATAAT-ATAATATATATA
100762 ATAATATAATA-AT-TA
1 ATAATATAATATATATA
100777 ATAATA
1 ATAATA
100783 GCAGCAAGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 2 0.10
17 6 0.29
18 5 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAATATAATATATATA
Found at i:111801 original size:12 final size:11
Alignment explanation
Indices: 111771--111803 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
111761 CATATTATGT
111771 AAAAAAAAA-A
1 AAAAAAAAAGA
*
111781 AAAAAAAAGGA
1 AAAAAAAAAGA
111792 AAAAAAAAAGA
1 AAAAAAAAAGA
111803 A
1 A
111804 CACGTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 8 0.40
11 12 0.60
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:115932 original size:21 final size:21
Alignment explanation
Indices: 115908--115994 Score: 104
Period size: 21 Copynumber: 4.2 Consensus size: 21
115898 TGTTTCTACC
*
115908 AAATATGTCGACATGTAAGAT
1 AAATATGTCGACATGCAAGAT
*
115929 AAATATGTTGACATGCAAGAT
1 AAATATGTCGACATGCAAGAT
* * *
115950 AATTATGTCAACATGCAACAT
1 AAATATGTCGACATGCAAGAT
* *
115971 AATTATGTTGACATGCAAGA-
1 AAATATGTCGACATGCAAGAT
115991 AAAT
1 AAAT
115995 TGCAATCAGA
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
20 3 0.05
21 53 0.95
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (21 bp):
AAATATGTCGACATGCAAGAT
Found at i:115978 original size:42 final size:42
Alignment explanation
Indices: 115911--115995 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
115901 TTCTACCAAA
* * * *
115911 TATGTCGACATGTAAGATAAATATGTTGACATGCAAGATAAT
1 TATGTCAACATGCAACATAAATATGTTGACATGCAAGAAAAT
*
115953 TATGTCAACATGCAACATAATTATGTTGACATGCAAGAAAAT
1 TATGTCAACATGCAACATAAATATGTTGACATGCAAGAAAAT
115995 T
1 T
115996 GCAATCAGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (42 bp):
TATGTCAACATGCAACATAAATATGTTGACATGCAAGAAAAT
Found at i:116107 original size:21 final size:21
Alignment explanation
Indices: 116081--116291 Score: 145
Period size: 21 Copynumber: 10.0 Consensus size: 21
116071 GCTACTTTTT
116081 TTTATGTCGACATGCAACTTA
1 TTTATGTCGACATGCAACTTA
** **
116102 TTTATGTTAACATGCAAGATA
1 TTTATGTCGACATGCAACTTA
** *
116123 AATATG-CTGATATGCAACTTA
1 TTTATGTC-GACATGCAACTTA
*
116144 TTTATGTCAACATGCAACTTA
1 TTTATGTCGACATGCAACTTA
*
116165 TTTATTTCGACATGCAACTTA
1 TTTATGTCGACATGCAACTTA
* *
116186 TTTATGTCAACATGGAACTTA
1 TTTATGTCGACATGCAACTTA
** * * **
116207 CGTATGTTGACATGCGAGATA
1 TTTATGTCGACATGCAACTTA
** *
116228 AATATGTTGACATGCAACTTA
1 TTTATGTCGACATGCAACTTA
* ** * **
116249 GTTATGTTTACATGCGAGATA
1 TTTATGTCGACATGCAACTTA
** *
116270 AATATGTTGACATGCAACTTA
1 TTTATGTCGACATGCAACTTA
116291 T
1 T
116292 AAGTTGTATG
Statistics
Matches: 142, Mismatches: 46, Indels: 4
0.74 0.24 0.02
Matches are distributed among these distances:
21 141 0.99
22 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (21 bp):
TTTATGTCGACATGCAACTTA
Found at i:116219 original size:42 final size:42
Alignment explanation
Indices: 116083--116221 Score: 163
Period size: 42 Copynumber: 3.3 Consensus size: 42
116073 TACTTTTTTT
* * **
116083 TATGTCGACATGCAACTTATTTATGTTAACATGCAAGATAAA
1 TATGTTGACATGCAACTTATTTATGTCAACATGCAACTTAAA
* * **
116125 TATGCTGATATGCAACTTATTTATGTCAACATGCAACTTATT
1 TATGTTGACATGCAACTTATTTATGTCAACATGCAACTTAAA
* **
116167 TAT-TTCGACATGCAACTTATTTATGTCAACATGGAACTTACG
1 TATGTT-GACATGCAACTTATTTATGTCAACATGCAACTTAAA
116209 TATGTTGACATGC
1 TATGTTGACATGC
116222 GAGATAAATA
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
41 1 0.01
42 79 0.96
43 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (42 bp):
TATGTTGACATGCAACTTATTTATGTCAACATGCAACTTAAA
Found at i:116378 original size:63 final size:63
Alignment explanation
Indices: 116299--116460 Score: 209
Period size: 63 Copynumber: 2.6 Consensus size: 63
116289 TATAAGTTGT
* * *** *
116299 ATGTCAACATAACTAAGTTGCATGTCGACATTAATATGTTGCATGTCAACATATTTATCTTGC
1 ATGTTAACATAACTAAGTTGCATGTCGACATTAATAAGTTGCATGTCAACATAAAGAACTTGC
* *
116362 ATGTTAACATAACTAAGTTGCATGTCGACA-TAATTAAGTTGCATGTCGACATAAAGAAGTTGC
1 ATGTTAACATAACTAAGTTGCATGTCGACATTAA-TAAGTTGCATGTCAACATAAAGAACTTGC
* * *
116425 ATGTTAACATAAATAAGTTGCATGTTGACATCAATA
1 ATGTTAACATAACTAAGTTGCATGTCGACATTAATA
116461 GGTAGCGTAT
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
62 3 0.03
63 81 0.94
64 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (63 bp):
ATGTTAACATAACTAAGTTGCATGTCGACATTAATAAGTTGCATGTCAACATAAAGAACTTGC
Found at i:116455 original size:21 final size:21
Alignment explanation
Indices: 116290--116449 Score: 176
Period size: 21 Copynumber: 7.6 Consensus size: 21
116280 CATGCAACTT
*
116290 ATAAGTTGTATGTCAACATAA
1 ATAAGTTGCATGTCAACATAA
* * *
116311 CTAAGTTGCATGTCGACATTA
1 ATAAGTTGCATGTCAACATAA
* *
116332 ATATGTTGCATGTCAACATAT
1 ATAAGTTGCATGTCAACATAA
* ** *
116353 TTATCTTGCATGTTAACATAA
1 ATAAGTTGCATGTCAACATAA
* *
116374 CTAAGTTGCATGTCGACATAA
1 ATAAGTTGCATGTCAACATAA
* *
116395 TTAAGTTGCATGTCGACATAA
1 ATAAGTTGCATGTCAACATAA
* *
116416 AGAAGTTGCATGTTAACATAA
1 ATAAGTTGCATGTCAACATAA
116437 ATAAGTTGCATGT
1 ATAAGTTGCATGT
116450 TGACATCAAT
Statistics
Matches: 115, Mismatches: 24, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 115 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (21 bp):
ATAAGTTGCATGTCAACATAA
Found at i:116590 original size:21 final size:21
Alignment explanation
Indices: 116566--116619 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
116556 GTTATGTTGT
*
116566 ATGTTGACATAACTATCTTGC
1 ATGTCGACATAACTATCTTGC
* ***
116587 ATGTCAACATCTTTATCTTGC
1 ATGTCGACATAACTATCTTGC
116608 ATGTCGACATAA
1 ATGTCGACATAA
116620 TTAATAGAAA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (21 bp):
ATGTCGACATAACTATCTTGC
Found at i:116617 original size:42 final size:42
Alignment explanation
Indices: 116539--116619 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
116529 ATTGCTGTTT
* * *
116539 TCTTGCATGTAAACATAGTTATGTTGTATGTTGACATAACTA
1 TCTTGCATGTAAACATAGTTATCTTGCATGTCGACATAACTA
* **
116581 TCTTGCATGTCAACATCTTTATCTTGCATGTCGACATAA
1 TCTTGCATGTAAACATAGTTATCTTGCATGTCGACATAA
116620 TTAATAGAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (42 bp):
TCTTGCATGTAAACATAGTTATCTTGCATGTCGACATAACTA
Found at i:120693 original size:203 final size:203
Alignment explanation
Indices: 120320--120725 Score: 787
Period size: 203 Copynumber: 2.0 Consensus size: 203
120310 AGAATTTTTT
120320 AAATAACAACAAACTCTCAATCTCCTATTTTATTTGAACAAACTTGAATTCTCTTTAAACAATAC
1 AAATAACAACAAACTCTCAATCTCCTATTTTATTTGAACAAACTTGAATTCTCTTTAAACAATAC
120385 TGCTTTGTGCCAAGTTTGGTTGAAATTGGCACAGTGGTTTTTAAGAAACAAAAAGAAAATGTAAA
66 TGCTTTGTGCCAAGTTTGGTTGAAATTGGCACAGTGGTTTTTAAGAAACAAAAAGAAAATGTAAA
120450 TGTTTACGATGACAACATCAACGACAGACAACGGCAAATTTTGATTAGAAAGCTTACTTAAGCCT
131 TGTTTACGATGACAACATCAACGACAGACAACGGCAAATTTTGATTAGAAAGCTTACTTAAGCCT
120515 TCGGCTCA
196 TCGGCTCA
120523 NAAATAACAACAAACTCTCAATCTCCTATTTTATTTGAACAAACTTGAATTCTCTTTAAACAATA
1 -AAATAACAACAAACTCTCAATCTCCTATTTTATTTGAACAAACTTGAATTCTCTTTAAACAATA
120588 CTGCTTTGTGCCAAGTTTGG-TGAAATTGGCACAGTGGTTTTTAAGAAACAAAAAGAAAATGTAA
65 CTGCTTTGTGCCAAGTTTGGTTGAAATTGGCACAGTGGTTTTTAAGAAACAAAAAGAAAATGTAA
*
120652 ATGTTTACGATGACAACATCAACGACAGACAGCGGCAAATTTTGATTAGAAAGCTTACTTAAGCC
130 ATGTTTACGATGACAACATCAACGACAGACAACGGCAAATTTTGATTAGAAAGCTTACTTAAGCC
120717 TTCGGCTCA
195 TTCGGCTCA
120726 GGTGAGCTAT
Statistics
Matches: 201, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
203 117 0.58
204 84 0.42
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (203 bp):
AAATAACAACAAACTCTCAATCTCCTATTTTATTTGAACAAACTTGAATTCTCTTTAAACAATAC
TGCTTTGTGCCAAGTTTGGTTGAAATTGGCACAGTGGTTTTTAAGAAACAAAAAGAAAATGTAAA
TGTTTACGATGACAACATCAACGACAGACAACGGCAAATTTTGATTAGAAAGCTTACTTAAGCCT
TCGGCTCA
Found at i:124171 original size:2 final size:2
Alignment explanation
Indices: 124164--124203 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
124154 ATACTTTAGT
124164 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
124204 GCTTTTTCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:125721 original size:44 final size:44
Alignment explanation
Indices: 125671--125761 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
125661 GTATGTTACA
125671 TTAAAAGTTTAGACTTTATCAAGTTAAACTTATCTATAACAGTC
1 TTAAAAGTTTAGACTTTATCAAGTTAAACTTATCTATAACAGTC
125715 TTAAAAGTTTAGACTTTATCAAGTTAAACTTATCTATAACAGTC
1 TTAAAAGTTTAGACTTTATCAAGTTAAACTTATCTATAACAGTC
125759 TTA
1 TTA
125762 CTGTAATAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (44 bp):
TTAAAAGTTTAGACTTTATCAAGTTAAACTTATCTATAACAGTC
Found at i:126793 original size:21 final size:21
Alignment explanation
Indices: 126767--126907 Score: 138
Period size: 21 Copynumber: 6.7 Consensus size: 21
126757 TACAAGATAA
126767 ACGATAGGATAGGATTCACGC
1 ACGATAGGATAGGATTCACGC
*
126788 ACGATAGGATAGGATTAACGC
1 ACGATAGGATAGGATTCACGC
* * * *
126809 ACGATAGAACAGTATACACGC
1 ACGATAGGATAGGATTCACGC
* *
126830 ACGAAAGGATAGGATTAACGC
1 ACGATAGGATAGGATTCACGC
* * * *
126851 ACGATAGAACAGTATACACGC
1 ACGATAGGATAGGATTCACGC
* * **
126872 ACGATATGATAGGATTGATAC
1 ACGATAGGATAGGATTCACGC
*
126893 ACGATAGGAAAGGAT
1 ACGATAGGATAGGAT
126908 AAACGATGTT
Statistics
Matches: 92, Mismatches: 28, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 92 1.00
ACGTcount: A:0.40, C:0.16, G:0.26, T:0.18
Consensus pattern (21 bp):
ACGATAGGATAGGATTCACGC
Found at i:126899 original size:42 final size:42
Alignment explanation
Indices: 126783--126887 Score: 192
Period size: 42 Copynumber: 2.5 Consensus size: 42
126773 GGATAGGATT
126783 CACGCACGATAGGATAGGATTAACGCACGATAGAACAGTATA
1 CACGCACGATAGGATAGGATTAACGCACGATAGAACAGTATA
*
126825 CACGCACGAAAGGATAGGATTAACGCACGATAGAACAGTATA
1 CACGCACGATAGGATAGGATTAACGCACGATAGAACAGTATA
*
126867 CACGCACGATATGATAGGATT
1 CACGCACGATAGGATAGGATT
126888 GATACACGAT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (42 bp):
CACGCACGATAGGATAGGATTAACGCACGATAGAACAGTATA
Found at i:159828 original size:24 final size:24
Alignment explanation
Indices: 159796--159841 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
159786 CAACGAAGTT
159796 GAAGTTTATATTAATCAATCATAA
1 GAAGTTTATATTAATCAATCATAA
159820 GAAGTTTATATTAATCAATCAT
1 GAAGTTTATATTAATCAATCAT
159842 TAGAGACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (24 bp):
GAAGTTTATATTAATCAATCATAA
Found at i:165647 original size:7 final size:7
Alignment explanation
Indices: 165637--165710 Score: 76
Period size: 7 Copynumber: 10.0 Consensus size: 7
165627 TGTGTTTTGC
165637 TTTTATTT
1 TTTTA-TT
*
165645 TTTTAAT
1 TTTTATT
165652 TTTTATTT
1 TTTTA-TT
165660 TTTTATT
1 TTTTATT
165667 TATTTATTT
1 T-TTTA-TT
165676 TTTTATT
1 TTTTATT
*
165683 TTTTTTT
1 TTTTATT
165690 TTTTATT
1 TTTTATT
*
165697 TATTATT
1 TTTTATT
*
165704 TATTATT
1 TTTTATT
165711 ATTATCATAA
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
7 36 0.62
8 19 0.33
9 3 0.05
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTATT
Found at i:165648 original size:8 final size:8
Alignment explanation
Indices: 165637--165697 Score: 83
Period size: 8 Copynumber: 8.0 Consensus size: 8
165627 TGTGTTTTGC
165637 TTTTATTT
1 TTTTATTT
*
165645 TTTTA-AT
1 TTTTATTT
165652 TTTTATTT
1 TTTTATTT
165660 TTTTATTT
1 TTTTATTT
*
165668 ATTTATTT
1 TTTTATTT
165676 TTTTA-TT
1 TTTTATTT
165683 TTTT-TTT
1 TTTTATTT
165690 TTTTATTT
1 TTTTATTT
165698 ATTATTTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
7 18 0.39
8 28 0.61
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTATTT
Found at i:165661 original size:38 final size:38
Alignment explanation
Indices: 165634--165707 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 38
165624 TTTTGTGTTT
165634 TGCTTTTATTTTTTTAATTTTTATTTTTTTATTTATTTA
1 TGCTTTTATTTTTTT-ATTTTTATTTTTTTATTTATTTA
** * *
165673 TTTTTTTATTTTTTTTTTTTTA-TTTATTATTTATT
1 TGCTTTTATTTTTTTATTTTTATTTTTTTATTTATT
165708 ATTATTATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 12 0.39
38 6 0.19
39 13 0.42
ACGTcount: A:0.16, C:0.01, G:0.01, T:0.81
Consensus pattern (38 bp):
TGCTTTTATTTTTTTATTTTTATTTTTTTATTTATTTA
Found at i:165677 original size:30 final size:30
Alignment explanation
Indices: 165638--165704 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
165628 GTGTTTTGCT
165638 TTTATTTTTTTAATTTTTATTTTTTTATTTA
1 TTTA-TTTTTTAATTTTTATTTTTTTATTTA
* *
165669 TTTATTTTTTTATTTTTTTTTTTTTATTTA
1 TTTATTTTTTAATTTTTATTTTTTTATTTA
165699 -TTATTT
1 TTTATTT
165705 ATTATTATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 6 0.18
30 24 0.71
31 4 0.12
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (30 bp):
TTTATTTTTTAATTTTTATTTTTTTATTTA
Found at i:165694 original size:26 final size:28
Alignment explanation
Indices: 165657--165710 Score: 85
Period size: 26 Copynumber: 2.0 Consensus size: 28
165647 TTAATTTTTA
165657 TTTTTTTATTTATTTATT-TTT-TTATT
1 TTTTTTTATTTATTTATTATTTATTATT
*
165683 TTTTTTTTTTTATTTATTATTTATTATT
1 TTTTTTTATTTATTTATTATTTATTATT
165711 ATTATCATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 17 0.68
27 3 0.12
28 5 0.20
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (28 bp):
TTTTTTTATTTATTTATTATTTATTATT
Found at i:165698 original size:4 final size:4
Alignment explanation
Indices: 165638--165707 Score: 67
Period size: 4 Copynumber: 18.5 Consensus size: 4
165628 GTGTTTTGCT
* * * *
165638 TTTA TTTT TTTA ATT- TTTA TTTT TTTA TTTA TTTA TTTT TTTA TTT-
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
*
165684 TTT- TTTT TTTA TTTA -TTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
165708 ATTATTATCA
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
3 11 0.20
4 43 0.80
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (4 bp):
TTTA
Found at i:166457 original size:16 final size:17
Alignment explanation
Indices: 166436--166473 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
166426 CCCCCATCCC
166436 TAAAAAAAAAAT-AAAA
1 TAAAAAAAAAATAAAAA
*
166452 T-AAAAAAAAGTAAAAA
1 TAAAAAAAAAATAAAAA
166468 TAAAAA
1 TAAAAA
166474 GAGGAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 9 0.47
16 6 0.32
17 4 0.21
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (17 bp):
TAAAAAAAAAATAAAAA
Found at i:166458 original size:15 final size:16
Alignment explanation
Indices: 166438--166473 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
166428 CCCATCCCTA
166438 AAAAAAAAAT-AAAAT
1 AAAAAAAAATAAAAAT
*
166453 AAAAAAAAGTAAAAAT
1 AAAAAAAAATAAAAAT
166469 AAAAA
1 AAAAA
166474 GAGGAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (16 bp):
AAAAAAAAATAAAAAT
Found at i:170059 original size:4 final size:4
Alignment explanation
Indices: 170052--170112 Score: 77
Period size: 4 Copynumber: 15.2 Consensus size: 4
170042 TTTTGTCTGT
* * * *
170052 CGTC CGTC TGTC CGTC CGTC TGTC CGTC CGTC TGTC CGTC CGTC TGTC
1 CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC CGTC
*
170100 CGTC CGTC TGTC C
1 CGTC CGTC CGTC C
170113 TAAACTTTTC
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.00, C:0.43, G:0.25, T:0.33
Consensus pattern (4 bp):
CGTC
Found at i:170069 original size:12 final size:12
Alignment explanation
Indices: 170046--170112 Score: 127
Period size: 12 Copynumber: 5.7 Consensus size: 12
170036 ATCACATTTT
170046 GTCTGT-CGTCC
1 GTCTGTCCGTCC
170057 GTCTGTCCGTCC
1 GTCTGTCCGTCC
170069 GTCTGTCCGTCC
1 GTCTGTCCGTCC
170081 GTCTGTCCGTCC
1 GTCTGTCCGTCC
170093 GTCTGTCCGTCC
1 GTCTGTCCGTCC
170105 GTCTGTCC
1 GTCTGTCC
170113 TAAACTTTTC
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
11 6 0.11
12 49 0.89
ACGTcount: A:0.00, C:0.40, G:0.25, T:0.34
Consensus pattern (12 bp):
GTCTGTCCGTCC
Found at i:170658 original size:166 final size:167
Alignment explanation
Indices: 170275--170985 Score: 1087
Period size: 166 Copynumber: 4.2 Consensus size: 167
170265 AAATTTCGAG
* * * *
170275 AAATTTTTAAAAATCTTCTTCTCA-AGAACCAGA-AAGCCAGGAAAGCTGAATCTTGTGTGGAAG
1 AAATCTTTAAAAATCTTCTTCTCAGA-AACTA-ATCAGCCAGGAAAGCTGAAACTTGTGTGGAAG
* *
170338 CATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCAC
64 CATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGAGGCCAC
170403 AATGGGGGGGTCG-AAGTTTTACATAGGAATATATAGAGT
129 AATGGGGGGGT-GTAAGTTTTACATAGGAATATATAGAGT
*
170442 AAATCTTTAAAAATCTTCTTCTCAGAAACTAAACAGCCAGGAAAGCTGAAACTTGTGTGGAAGCA
1 AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCA
*
170507 TCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACAA
66 TCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGAGGCCACAA
170572 T-GGGGGGTCG-AAGTTTTACATAGGAATATATAGAGT
131 TGGGGGGGT-GTAAGTTTTACATAGGAATATATAGAGT
170608 AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCA
1 AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCA
* * * *
170673 TCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTAAGGCCACAT
66 TCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGAGGCCACAA
*
170738 TGGGGGGGGGGGTGTTAAAATTTTACATAGGAATATATAGAGT
131 T----GGGGGGGTG-T-AAGTTTTACATAGGAATATATAGAGT
*
170781 AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTG-GGAAGTA
1 AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCA
*
170845 TCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGGTGAGGCCACAG
66 TCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGAGGCCACA-
**
170910 GGGGGGGGGGTGTTAAAGTTTTACATAGGAATA-A-AGAGT
130 -ATGGGGGGGTG-T-AAGTTTTACATAGGAATATATAGAGT
170949 AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGC
1 AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGC
170986 AAGATGATTC
Statistics
Matches: 514, Mismatches: 18, Indels: 23
0.93 0.03 0.04
Matches are distributed among these distances:
166 161 0.31
167 122 0.24
168 43 0.08
169 1 0.00
170 30 0.06
171 7 0.01
172 68 0.13
173 82 0.16
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.26
Consensus pattern (167 bp):
AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCA
TCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTGAGGCCACAA
TGGGGGGGTGTAAGTTTTACATAGGAATATATAGAGT
Found at i:170736 original size:333 final size:332
Alignment explanation
Indices: 170275--170985 Score: 1083
Period size: 333 Copynumber: 2.1 Consensus size: 332
170265 AAATTTCGAG
* * * *
170275 AAATTTTTAAAAATCTTCTTCTCA-AGAACCAGA-AAGCCAGGAAAGCTGAATCTTGTGTGGAAG
1 AAATCTTTAAAAATCTTCTTCTCAGA-AACTA-ATCAGCCAGGAAAGCTGAAACTTGTGTGGAAG
* **
170338 CATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAATTCATGACCCCCGGGGGTAGGGTGGGGCCAC
64 CATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTAAGGCCAC
*
170403 AAT-GGGGGGGTCG-AAGTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCA
129 AATGGGGGGGGT-GTAAATTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCA
170466 GAAACTAAACAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAG
193 GAAACTAAACAGCCAGGAAAGCTGAAACTTGTG-GGAAGCATCCTCAGGTAGTGTAGATTCAAAG
* *
170531 TTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCACA-ATGGGGGGTCG-AAGTTTTACATA
257 TTGTGAAAATCATGACCCCCGGGGGTAGGGTGAGGCCACAGAGGGGGGGT-GTAAGTTTTACATA
170594 GGAATATATAGAGT
321 GGAATA-A-AGAGT
170608 AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCA
1 AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCA
* * *
170673 TCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGATCCCTGGGGGTAGGGTAAGGCCACAT
66 TCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTAAGGCCACAA
170738 TGGGGGGGGGGGTGTTAAAATTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCT
131 T---GGGGGGGGTG-T-AAATTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCT
* *
170803 CAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGGGAAGTATCCTCAGGTAGTGTAGATTCAAA
191 CAGAAACTAAACAGCCAGGAAAGCTGAAACTTGTGGGAAGCATCCTCAGGTAGTGTAGATTCAAA
* *
170868 GTTGTGAAAATCATGACCCCTGGGGGTAGGGTGAGGCCACAGGGGGGGGGGGTGTTAAAGTTTTA
256 GTTGTGAAAATCATGACCCCCGGGGGTAGGGTGAGGCCACA--GAGGGGGGGTG-T-AAGTTTTA
170933 CATAGGAATAAAGAGT
317 CATAGGAATAAAGAGT
170949 AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGC
1 AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGC
170986 AAGATGATTC
Statistics
Matches: 346, Mismatches: 17, Indels: 22
0.90 0.04 0.06
Matches are distributed among these distances:
332 1 0.00
333 117 0.34
334 1 0.00
336 1 0.00
337 8 0.02
338 68 0.20
339 81 0.23
340 1 0.00
341 49 0.14
342 1 0.00
343 18 0.05
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.26
Consensus pattern (332 bp):
AAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCA
TCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCGGGGGTAGGGTAAGGCCACAA
TGGGGGGGGTGTAAATTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAA
ACTAAACAGCCAGGAAAGCTGAAACTTGTGGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGT
GAAAATCATGACCCCCGGGGGTAGGGTGAGGCCACAGAGGGGGGGTGTAAGTTTTACATAGGAAT
AAAGAGT
Found at i:172759 original size:24 final size:24
Alignment explanation
Indices: 172732--172780 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
172722 AAACAGTCCC
172732 ATCTAGTTCGAGATGAAAACTTTG
1 ATCTAGTTCGAGATGAAAACTTTG
*
172756 ATCTAGTTCGAGATGAGAACTTTG
1 ATCTAGTTCGAGATGAAAACTTTG
172780 A
1 A
172781 CTGTATATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (24 bp):
ATCTAGTTCGAGATGAAAACTTTG
Found at i:176894 original size:2 final size:2
Alignment explanation
Indices: 176887--176949 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
176877 GAAATAAATT
176887 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
176929 GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA G
176950 GGNNNNNNNN
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:177023 original size:2 final size:2
Alignment explanation
Indices: 177016--177056 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
177006 TAAAAGTGAT
*
177016 AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
177057 TTTTGTGAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:184109 original size:23 final size:23
Alignment explanation
Indices: 184079--184126 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
184069 TAACTGCAAA
*
184079 GGCTATTGTG-AATCTAATTTACG
1 GGCTATTGTGAAAT-TAATGTACG
184102 GGCTATTGTGAAATTAATGTACG
1 GGCTATTGTGAAATTAATGTACG
184125 GG
1 GG
184127 GCTTACATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.27, C:0.10, G:0.27, T:0.35
Consensus pattern (23 bp):
GGCTATTGTGAAATTAATGTACG
Found at i:189150 original size:166 final size:167
Alignment explanation
Indices: 188776--190101 Score: 943
Period size: 167 Copynumber: 7.9 Consensus size: 167
188766 CTTACATGAG
* * * * *
188776 GATGCTTCCACATAAGTTTCAGCTTTCATGGCTACGTAGTTT-T-AG-AG-ATATTATAATAAAG
1 GATGCTTCCACATAAGTTTCAGCTTTCCTGGCTACTTATTTTCTGAGAAGAAGATT-T-TTAAAG
* * * * * * *
188837 ATTTTCTCTATATAATTCTATGT-AAAAATTCGA--CCCCCATTGTGACCTCA-CCCTACCCCAG
64 ATTTACTCTATATATTTCTATGTCAAAAATTCAACCCCCCCATTGTGGCCCCATCCATACCCCCG
*
188898 -GGGTCATGATTTTCACAGCTTTGAATCTACAGC-AGCTGA
129 AGGGTCATGATTTTCACAACTTT-AATCTACA-CTAGCTGA
* * * ** *
188937 GGATGCTTTCACATAAGTTTCAGCCTTCCTGCCTACTTAGATTCTGAGAAAAAGATTTTTAAAGA
1 -GATGCTTCCACATAAGTTTCAGCTTTCCTGGCTACTTATTTTCTGAGAAGAAGATTTTTAAAGA
* *
189002 TTTACTCTATATATTTCTATGTCAAAAA-TCAACCCCTCCTTTGTGGCCCCATCCAT-CCCCCGA
65 TTTACTCTATATATTTCTATGTCAAAAATTCAACCCCCCCATTGTGGCCCCATCCATACCCCCGA
* * * *
189065 GGATTATGA-TTTCACAACTTTAAATTTACATTAGCTGA
130 GGGTCATGATTTTCACAACTTT-AATCTACACTAGCTGA
* *
189103 GCATGCTTCCACTTAAGTTTCAGCTTTCCTGGTTACTTATTTTCTGAGAAGAAGATTTTTAAAGA
1 G-ATGCTTCCACATAAGTTTCAGCTTTCCTGGCTACTTATTTTCTGAGAAGAAGATTTTTAAAGA
* * * *
189168 TTTACTACATATATATTTATATTTTCCTATATAAAACGTTGACACGCCCCCCCCCAATTGTGACC
65 TTTACT-C-TATATATTTCTA-TGT-C---A-AAAA--TT--CA---ACCCCCCC-ATTGTGGCC
* * * * * *
189233 CTATCCA-GCCTCC-AGGGGTCCTGATTTTTACAACTTTGATTCTACA-T---T-A
114 CCATCCATACCCCCGA-GGGTCATGATTTTCACAACTTT-AATCTACACTAGCTGA
* * *
189282 -ATTCTTCCACATAAGTTTCAGCTTTTCTTGGCTGA-TAAATTTT-TGAGAAGAAG-TTTCTTAA
1 GATGCTTCCACATAAGTTTCAGC-TTTCCTGGCT-ACT-TATTTTCTGAGAAGAAGATTT-TTAA
* ** * *
189343 AGATTTACTCTATATATTCCTAT-TCAAAAATTCGGCCCCCCCATTGTGGACCCA-CCCTACCCC
62 AGATTTACTCTATATATTTCTATGTCAAAAATTCAACCCCCCCATTGTGGCCCCATCCATACCCC
* * * *
189406 CGGGGGTCACGATTTTTACATCTTTAAATCTACACTAGCTGA
127 CGAGGGTCATGATTTTCACAACTTT-AATCTACACTAGCTGA
* *
189448 GGATGCTTCCACATAAGTTTCAGCTTTCCTGGCCGA-TTAGTTTT-GGAGAAGAAGATTTTTAAA
1 -GATGCTTCCACATAAGTTTCAGCTTTCCTGG-CTACTTA-TTTTCTGAGAAGAAGATTTTTAAA
* * ** * * *
189511 GATTTACTCTATATATTCCTATGT--AAAATTCGA-TTCCCCAATGTGGCCCTA-CCCTACCCCC
63 GATTTACTCTATATATTTCTATGTCAAAAATTCAACCCCCCCATTGTGGCCCCATCCATACCCCC
*
189572 G-GGGTCATGATTTTCACATCTTTAATTCTACACTAGCTGAA
128 GAGGGTCATGATTTTCACAACTTTAA-TCTACACTAGCTG-A
* * * * * * *
189613 GATAC-T-CACATAAGTTTCACCTTTCCTGCCTACTTAGTTTATGTGAAAAAGATTTTTAAAGAT
1 GATGCTTCCACATAAGTTTCAGCTTTCCTGGCTACTTATTTTCTGAGAAGAAGATTTTTAAAGAT
* * *
189676 TTACTCTTTATATTTCTATGT-AAAAATTCGACCCCCTCC-TTGTAGCCCCATCC-TACCCCCGA
66 TTACTCTATATATTTCTATGTCAAAAATTCAACCCCC-CCATTGTGGCCCCATCCATACCCCCGA
*
189738 GGGTCATGATTTTCACAACTTTGAATCTACACTAGCTAA
130 GGGTCATGATTTTCACAACTTT-AATCTACACTAGCTGA
*
189777 GAATGCTTCCACATAAGTTTCAGCTTTCCTGGCTACTTATTTTCT--G-AGAAGATTTTTAAACA
1 G-ATGCTTCCACATAAGTTTCAGCTTTCCTGGCTACTTATTTTCTGAGAAGAAGATTTTTAAAGA
* * * *
189839 TTTTCTATATACACATGTATATATATTCCTATGT-AAAAATTCGA-CCGCGCATTGTGGCCCCA-
65 -----T-T-T--AC-TCTATATAT-TT-CTATGTCAAAAATTCAACCCCCCCATTGTGGCCCCAT
* ** *
189901 CCTTACTCCTTG-GGGTTATGATTTTCACAACTTTGAATCTACACTAGCTGA
118 CCATAC-CCCCGAGGGTCATGATTTTCACAACTTT-AATCTACACTAGCTGA
* * * *
189952 GGATGCTTCGACATATAAGTTTCAGCATTT-CTGGCTACTTAGTTTATGAGAAGAAGATTTTAAA
1 -GATGCTTC--CACATAAGTTTCAGC-TTTCCTGGCTACTTATTTTCTGAGAAGAAGATTTTTAA
** * * ** ** * * *
190016 AGATTTACAATATATATTCCTATGT--AAAATTCGA-TTCCTTAATGTGGCCCTA-CCCTACCCC
62 AGATTTACTCTATATATTTCTATGTCAAAAATTCAACCCCCCCATTGTGGCCCCATCCATACCCC
*
190077 CGAGGGTCATGATTTTAACAACTTT
127 CGAGGGTCATGATTTTCACAACTTT
190102 GATTCTACTC
Statistics
Matches: 946, Mismatches: 134, Indels: 163
0.76 0.11 0.13
Matches are distributed among these distances:
160 2 0.00
161 44 0.05
162 106 0.11
163 13 0.01
164 102 0.11
165 76 0.08
166 123 0.13
167 139 0.15
168 43 0.05
169 8 0.01
170 10 0.01
171 3 0.00
173 5 0.01
174 16 0.02
175 64 0.07
176 30 0.03
177 54 0.06
178 35 0.04
179 10 0.01
180 15 0.02
182 7 0.01
183 24 0.03
184 17 0.02
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (167 bp):
GATGCTTCCACATAAGTTTCAGCTTTCCTGGCTACTTATTTTCTGAGAAGAAGATTTTTAAAGAT
TTACTCTATATATTTCTATGTCAAAAATTCAACCCCCCCATTGTGGCCCCATCCATACCCCCGAG
GGTCATGATTTTCACAACTTTAATCTACACTAGCTGA
Found at i:189788 original size:329 final size:330
Alignment explanation
Indices: 188772--190101 Score: 1144
Period size: 329 Copynumber: 4.0 Consensus size: 330
188762 AGTCCTTACA
* * * * * *
188772 TGAGGATGCTTCCACATAAGTTTCAGCTTTCATGGCTACGTAGTTTT-AGAG-ATATTATAATAA
1 TGAGAATGCTTCCACATAAGTTTCAGCTTTCCTGGCGACTTA-TTTTGAGAGAAGATT-T-TTAA
* * *
188835 AGATTTTCTCTATATAATT-CTATGTAAAAATTCGACCCCCATTGT-GACCTCACCCTACCCCAG
63 AGATTTACTCTATAT-ATTCCTATGTAAAAATTCGACCCCCAATGTGGCCCT-ACCCTACCCCAG
* *
188898 GGGTCATGATTTTCACAGCTTTGAATCTACAGC-AGCTGAGGATGCTTTCACATAAGTTTCAGCC
126 GGGTCATGATTTTCACAACTTTGAATCTACA-CTAGCTGAAGATGC-TTCACATAAGTTTCAGCC
* * *
188962 -TTCCTGCCTACTTAGATTCTGAGAAAAAGATTTTTAAAGATTTACTCTATATATTTCTATGTCA
189 TTTCCTGCCTACTTAGTTTATGAGAAAAAGATTTTTAAAGATTTACTCTATATATTCCTATGTCA
* * * * *
189026 AAAA-TC-AACCCCTCCTTTGTGGCCCCATCC-ATCCCCCGAGGATTATGA-TTTCACAACTTTA
254 AAAATTCGACCCCCTCCATTGTGGCCCCACCCTA-CCCCCGAGGGTCATGATTTTCACAACTTTA
* *
189087 AATTTACATTAGC
318 AATCTACACTAGC
* * **
189100 TGAGCATGCTTCCACTTAAGTTTCAGCTTTCCTGGTTACTTATTTTCTGAGAAGAAGATTTTTAA
1 TGAGAATGCTTCCACATAAGTTTCAGCTTTCCTGGCGACTTA-TTT-TGAG-AGAAGATTTTTAA
* * *
189165 AGATTTACTACATATATATTTATATTTTCCTATATAAAACGTTGACACGCCCCCCCCCAATTGTG
63 AGATTTACT-C-----TA--TATA--TTCCTATGTAAAA-ATT----CG---ACCCCCAA-TGTG
* * * * * *
189230 ACCCTATCC-AGCCTCCAGGGGTCCTGATTTTTACAACTTTGATTCTACA-T---T--A-ATTCT
109 GCCCTACCCTA-CC-CCAGGGGTCATGATTTTCACAACTTTGAATCTACACTAGCTGAAGATGCT
* * * * * * *
189287 TCCACATAAGTTTCAGCTTTTCTTGGCTGA-TAAATTTTTGAGAAGAAG-TTTCTTAAAGATTTA
172 T-CACATAAGTTTCAGCCTTTCCTGCCT-ACTTAGTTTATGAGAAAAAGATTT-TTAAAGATTTA
* * *
189350 CTCTATATATTCCTAT-TCAAAAATTCGGCCCCC-CCATTGTGGACCCACCCTACCCCCGGGGGT
234 CTCTATATATTCCTATGTCAAAAATTCGACCCCCTCCATTGTGGCCCCACCCTACCCCCGAGGGT
* * *
189413 CACGATTTTTACATCTTTAAATCTACACTAGC
299 CATGATTTTCACAACTTTAAATCTACACTAGC
*
189445 TGAGGATGCTTCCACATAAGTTTCAGCTTTCCTGGCCGA-TTAGTTTTGGAGAAGAAGATTTTTA
1 TGAGAATGCTTCCACATAAGTTTCAGCTTTCCTGG-CGACTTA-TTTT-GAG-AGAAGATTTTTA
* *
189509 AAGATTTACTCTATATATTCCTATGT-AAAATTCGATTCCCCAATGTGGCCCTACCCTACCCCCG
62 AAGATTTACTCTATATATTCCTATGTAAAAATTCGA-CCCCCAATGTGGCCCTACCCTACCCCAG
* *
189573 GGGTCATGATTTTCACATCTTT-AATTCTACACTAGCTGAAGATAC-TCACATAAGTTTCA-CCT
126 GGGTCATGATTTTCACAACTTTGAA-TCTACACTAGCTGAAGATGCTTCACATAAGTTTCAGCCT
* * *
189635 TTCCTGCCTACTTAGTTTATGTGAAAAAGATTTTTAAAGATTTACTCTTTATATTTCTATGT-AA
190 TTCCTGCCTACTTAGTTTATGAGAAAAAGATTTTTAAAGATTTACTCTATATATTCCTATGTCAA
* * *
189699 AAATTCGACCCCCTCC-TTGTAGCCCCATCCTACCCCCGAGGGTCATGATTTTCACAACTTTGAA
255 AAATTCGACCCCCTCCATTGTGGCCCCACCCTACCCCCGAGGGTCATGATTTTCACAACTTTAAA
189763 TCTACACTAGC
320 TCTACACTAGC
* * ** *
189774 TAAGAATGCTTCCACATAAGTTTCAGCTTTCCTGGCTACTTATTTTCTGAGAAGATTTTTAAACA
1 TGAGAATGCTTCCACATAAGTTTCAGCTTTCCTGGCGACTTATTTTGAGAGAAGATTTTTAAAGA
* * * * *
189839 TTTTCTATATACACATGTATATATATTCCTATGTAAAAATTCGACCGCGCATTGTGGCCCCACCT
66 -----T-T-T--AC---TCTATATATTCCTATGTAAAAATTCGACC-CCCAATGTGGCCCTACCC
** * *
189904 TACTCCTTGGGGTTATGATTTTCACAACTTTGAATCTACACTAGCTGAGGATGCTTCGACATATA
118 TAC-CCCAGGGGTCATGATTTTCACAACTTTGAATCTACACTAGCTGAAGATGCTTC-AC--ATA
* * * * **
189969 AGTTTCAGCATTT-CTGGCTACTTAGTTTATGAGAAGAAGATTTTAAAAGATTTACAATATATAT
179 AGTTTCAGCCTTTCCTGCCTACTTAGTTTATGAGAAAAAGATTTTTAAAGATTTACTCTATATAT
** * * * *
190033 TCCTATGT--AAAATTCGA-TTCCT-TAATGTGGCCCTACCCTACCCCCGAGGGTCATGATTTTA
244 TCCTATGTCAAAAATTCGACCCCCTCCATTGTGGCCCCACCCTACCCCCGAGGGTCATGATTTTC
190094 ACAACTTT
309 ACAACTTT
190102 GATTCTACTC
Statistics
Matches: 812, Mismatches: 115, Indels: 136
0.76 0.11 0.13
Matches are distributed among these distances:
324 1 0.00
325 28 0.03
326 29 0.04
327 8 0.01
328 47 0.06
329 152 0.19
330 32 0.04
331 7 0.01
332 8 0.01
333 3 0.00
334 3 0.00
335 10 0.01
336 2 0.00
337 5 0.01
338 20 0.02
339 30 0.04
340 50 0.06
341 6 0.01
342 47 0.06
343 37 0.05
344 137 0.17
345 99 0.12
346 2 0.00
348 7 0.01
349 8 0.01
350 34 0.04
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (330 bp):
TGAGAATGCTTCCACATAAGTTTCAGCTTTCCTGGCGACTTATTTTGAGAGAAGATTTTTAAAGA
TTTACTCTATATATTCCTATGTAAAAATTCGACCCCCAATGTGGCCCTACCCTACCCCAGGGGTC
ATGATTTTCACAACTTTGAATCTACACTAGCTGAAGATGCTTCACATAAGTTTCAGCCTTTCCTG
CCTACTTAGTTTATGAGAAAAAGATTTTTAAAGATTTACTCTATATATTCCTATGTCAAAAATTC
GACCCCCTCCATTGTGGCCCCACCCTACCCCCGAGGGTCATGATTTTCACAACTTTAAATCTACA
CTAGC
Found at i:194965 original size:14 final size:14
Alignment explanation
Indices: 194946--194990 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
194936 CCATATTTAA
194946 TTTTACTCTTACTT
1 TTTTACTCTTACTT
*
194960 TTTTA--CTTA--A
1 TTTTACTCTTACTT
194970 TTTTACTCTTACTT
1 TTTTACTCTTACTT
194984 TTTTACT
1 TTTTACT
194991 TTCGCGTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
10 5 0.20
12 8 0.32
14 12 0.48
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTACTCTTACTT
Found at i:194974 original size:24 final size:24
Alignment explanation
Indices: 194942--194991 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
194932 AGTACCATAT
194942 TTAATTTTACTCTTACTTTTTTAC
1 TTAATTTTACTCTTACTTTTTTAC
194966 TTAATTTTACTCTTACTTTTTTAC
1 TTAATTTTACTCTTACTTTTTTAC
194990 TT
1 TT
194992 TCGCGTCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (24 bp):
TTAATTTTACTCTTACTTTTTTAC
Found at i:196136 original size:146 final size:146
Alignment explanation
Indices: 195978--196316 Score: 484
Period size: 146 Copynumber: 2.3 Consensus size: 146
195968 GACCCTTGGT
* * * * **
195978 TCAAGGTCATGACACACCCTAAGGTTATAAGCAATATTTATGTGAATTAAGAACTT-CAATATTT
1 TCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGGAAGAACTTCCAATATTT
* * * * *
196042 GTCCG-TAAAAAAGATATGGACTGGACACCAATTTTGCACTTTTTTCTGCCAGTGACCTTGACCC
66 CT-CGTTAAAAAAGATATGAACCGGACACAAATTTTGCA-TTTTATCTGCCAGTGACCTTGACCC
* *
196106 TGTCCGAATGACCTTGAG
129 TGCCCAAATGACCTTGAG
*
196124 TCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGGAAGAACTTCCAATGTTT
1 TCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGGAAGAACTTCCAATATTT
*
196189 CTCGTTAAGAAAGATATGAACCGGACACAAATTTTGCATTTTATCTGCCAGTGACCTTGACCCTG
66 CTCGTTAAAAAAGATATGAACCGGACACAAATTTTGCATTTTATCTGCCAGTGACCTTGACCCTG
*
196254 CCCAAATGACCTTGGG
131 CCCAAATGACCTTGAG
**
196270 TCAAGACCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAG
1 TCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAG
196317 TAAAAATTCT
Statistics
Matches: 173, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
146 136 0.79
147 37 0.21
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (146 bp):
TCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGGAAGAACTTCCAATATTT
CTCGTTAAAAAAGATATGAACCGGACACAAATTTTGCATTTTATCTGCCAGTGACCTTGACCCTG
CCCAAATGACCTTGAG
Found at i:197844 original size:16 final size:16
Alignment explanation
Indices: 197820--197855 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
197810 ATCTGAAGTG
197820 GGACAGACAGACAGAC
1 GGACAGACAGACAGAC
*
197836 GGACGGACAGACAGAC
1 GGACAGACAGACAGAC
197852 GGAC
1 GGAC
197856 TGACGGACGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.25, G:0.36, T:0.00
Consensus pattern (16 bp):
GGACAGACAGACAGAC
Found at i:197846 original size:12 final size:12
Alignment explanation
Indices: 197829--197864 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
197819 GGGACAGACA
197829 GACAGACGGACG
1 GACAGACGGACG
*
197841 GACAGACAGACG
1 GACAGACGGACG
*
197853 GACTGACGGACG
1 GACAGACGGACG
197865 CAGAGGAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.25, G:0.39, T:0.03
Consensus pattern (12 bp):
GACAGACGGACG
Found at i:197862 original size:8 final size:8
Alignment explanation
Indices: 197820--197863 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
197810 ATCTGAAGTG
197820 GGACAGAC
1 GGACAGAC
*
197828 AGACAGAC
1 GGACAGAC
*
197836 GGACGGAC
1 GGACAGAC
*
197844 AGACAGAC
1 GGACAGAC
*
197852 GGACTGAC
1 GGACAGAC
197860 GGAC
1 GGAC
197864 GCAGAGGAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.36, C:0.25, G:0.36, T:0.02
Consensus pattern (8 bp):
GGACAGAC
Found at i:200998 original size:166 final size:158
Alignment explanation
Indices: 200655--201003 Score: 389
Period size: 166 Copynumber: 2.2 Consensus size: 158
200645 GATCCCTATA
* *
200655 ATGATCCCTCGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAACAGTA
1 ATGACCCCTCGGTCAGGGGTTCAGGCTCCAGGGTGGGGCCAATATGGCCAAATAGTAAAACAGTA
* ** * * *
200720 TTTAATCTACTTCTCTACTCCCACTTATGTGAGCTAAAACCTGAATACATGGTTATGATGTCCAT
66 TTTAATCTACTTCTCTACACCCACACATGTGAGCTAAAAACTGAATACATGGTTATGATATCCAC
* *
200785 GAGGGCCTCTACTAAAATTGTGAAATTC
131 AAGCGCCTCTACTAAAATTGTGAAATTC
* * *
200813 ATGATCCCTCGGTCAGGGGTTCAGGCTCCAGGGTGGGGCTAATATGGCCATATAGTAAAA-ATGT
1 ATGACCCCTCGGTCAGGGGTTCAGGCTCCAGGGTGGGGCCAATATGGCCAAATAGTAAAACA-GT
* *
200877 TTTTAAATCTTAAAAAAATCTTCTCTACACCCACACATGTGGGC-AAAAACTGAATACATGGTTA
65 ATTT-AATC-T------A-CTTCTCTACACCCACACATGTGAGCTAAAAACTGAATACATGGTTA
* * * *
200941 TGATATCTACAATCTCCTTTACCT-AAATTGTGAAATTC
121 TGATATCCACAAGCGCCTCTA-CTAAAATTGTGAAATTC
* *
200979 ATGGCCCCTGGGTCAGGGGTTCAGG
1 ATGACCCCTCGGTCAGGGGTTCAGG
201004 ACATGGGGGG
Statistics
Matches: 160, Mismatches: 20, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
157 1 0.01
158 62 0.39
159 4 0.03
160 1 0.01
166 69 0.43
167 23 0.14
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (158 bp):
ATGACCCCTCGGTCAGGGGTTCAGGCTCCAGGGTGGGGCCAATATGGCCAAATAGTAAAACAGTA
TTTAATCTACTTCTCTACACCCACACATGTGAGCTAAAAACTGAATACATGGTTATGATATCCAC
AAGCGCCTCTACTAAAATTGTGAAATTC
Found at i:201849 original size:166 final size:158
Alignment explanation
Indices: 201506--201854 Score: 389
Period size: 166 Copynumber: 2.2 Consensus size: 158
201496 GATCCCTATA
* *
201506 ATGATCCCTCGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCAAATAGTAAAACAGTA
1 ATGACCCCTCGGTCAGGGGTTCAGGCTCCAGGGTGGGGCCAATATGGCCAAATAGTAAAACAGTA
* ** * * *
201571 TTTAATCTACTTCTCTACTCCCACTTATGTGAGCTAAAACCTGAATACATGGTTATGATGTCCAT
66 TTTAATCTACTTCTCTACACCCACACATGTGAGCTAAAAACTGAATACATGGTTATGATATCCAC
* *
201636 GAGGGCCTCTACTAAAATTGTGAAATTC
131 AAGCGCCTCTACTAAAATTGTGAAATTC
* * *
201664 ATGATCCCTCGGTCAGGGGTTCAGGCTCCAGGGTGGGGCTAATATGGCCATATAGTAAAA-ATGT
1 ATGACCCCTCGGTCAGGGGTTCAGGCTCCAGGGTGGGGCCAATATGGCCAAATAGTAAAACA-GT
* *
201728 TTTTAAATCTTAAAAAAATCTTCTCTACACCCACACATGTGGGC-AAAAACTGAATACATGGTTA
65 ATTT-AATC-T------A-CTTCTCTACACCCACACATGTGAGCTAAAAACTGAATACATGGTTA
* * * *
201792 TGATATCTACAATCTCCTTTACCT-AAATTGTGAAATTC
121 TGATATCCACAAGCGCCTCTA-CTAAAATTGTGAAATTC
* *
201830 ATGGCCCCTGGGTCAGGGGTTCAGG
1 ATGACCCCTCGGTCAGGGGTTCAGG
201855 ACATGGGGGG
Statistics
Matches: 160, Mismatches: 20, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
157 1 0.01
158 62 0.39
159 4 0.03
160 1 0.01
166 69 0.43
167 23 0.14
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (158 bp):
ATGACCCCTCGGTCAGGGGTTCAGGCTCCAGGGTGGGGCCAATATGGCCAAATAGTAAAACAGTA
TTTAATCTACTTCTCTACACCCACACATGTGAGCTAAAAACTGAATACATGGTTATGATATCCAC
AAGCGCCTCTACTAAAATTGTGAAATTC
Found at i:213865 original size:13 final size:13
Alignment explanation
Indices: 213839--213874 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
213829 AAAACATTTT
*
213839 TAAAGAGTTAAAG
1 TAAAGGGTTAAAG
*
213852 TAAAGGGTTTAAG
1 TAAAGGGTTAAAG
213865 TAAAGGGTTA
1 TAAAGGGTTA
213875 TATAAGCCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (13 bp):
TAAAGGGTTAAAG
Found at i:216371 original size:4 final size:4
Alignment explanation
Indices: 216364--216390 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
216354 GCTGCTGTCT
216364 GTCG GTCG GTCG GTCG GTCG GTCG GTC
1 GTCG GTCG GTCG GTCG GTCG GTCG GTC
216391 CACCAACAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.26, G:0.48, T:0.26
Consensus pattern (4 bp):
GTCG
Found at i:216557 original size:95 final size:95
Alignment explanation
Indices: 216394--216583 Score: 362
Period size: 95 Copynumber: 2.0 Consensus size: 95
216384 GTCGGTCCAC
*
216394 CAACAGTTTCCGTTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGCT
1 CAACAGTTTCCGTTCATTTTCTTCGCAGAGGATAAACATATTGAAATGAAATTTGGTATACAGCT
216459 TTATCATGATAATATCGAGGTCAAGTTCGA
66 TTATCATGATAATATCGAGGTCAAGTTCGA
216489 CAACAGTTTCCGTTCATTTTCTTCGCAGAGGATAAACATATTGAAATGAAATTTGGTATACAGCT
1 CAACAGTTTCCGTTCATTTTCTTCGCAGAGGATAAACATATTGAAATGAAATTTGGTATACAGCT
*
216554 TTATCATGATAATATCTAGGTCAAGTTCGA
66 TTATCATGATAATATCGAGGTCAAGTTCGA
216584 TATTGGGTAC
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 93 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (95 bp):
CAACAGTTTCCGTTCATTTTCTTCGCAGAGGATAAACATATTGAAATGAAATTTGGTATACAGCT
TTATCATGATAATATCGAGGTCAAGTTCGA
Found at i:220003 original size:160 final size:160
Alignment explanation
Indices: 219714--220003 Score: 373
Period size: 160 Copynumber: 1.8 Consensus size: 160
219704 ACAGGAGAAA
* * * * * * *
219714 GGGTAATCCTCAAGAGATAAATGTCGCTGGTATACATGGTTGGTCACAGATAGCTTCTCTCCTCT
1 GGGTAATCCTCAAGAGATAAATGTCGCTGATACACATGGTTCGTAACAGATAACGTCTCCCCTCT
* * * * * *
219779 GTACCCACAGGGCTTACAGGACCACACTCTACCACGTTTCCCAGCGGAGGCATCCATTATGACCA
66 GTACCCACAGGGCTTACAGGACCAAACACGACCACGTTTCCCAGCCGAGACATCCATAATGACCA
219844 AGGATATAGAGATCTCTACCACAGGAAACC
131 AGGATATAGAGATCTCTACCACAGGAAACC
* * * *
219874 GGGTAGTCCTCAAGAGATAAGTGTCGCTGATACACGTGGTTCGTAACAGCTAACGTCTCCCCTCT
1 GGGTAATCCTCAAGAGATAAATGTCGCTGATACACATGGTTCGTAACAGATAACGTCTCCCCTCT
* * * * * *
219939 GTACCCGCAGGGCTTGCATGACCAAACACGACCACGTTTCCCATCCGAGACGTCCGTAATGACCA
66 GTACCCACAGGGCTTACAGGACCAAACACGACCACGTTTCCCAGCCGAGACATCCATAATGACCA
220004 TAGACAGCAA
Statistics
Matches: 107, Mismatches: 23, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
160 107 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (160 bp):
GGGTAATCCTCAAGAGATAAATGTCGCTGATACACATGGTTCGTAACAGATAACGTCTCCCCTCT
GTACCCACAGGGCTTACAGGACCAAACACGACCACGTTTCCCAGCCGAGACATCCATAATGACCA
AGGATATAGAGATCTCTACCACAGGAAACC
Found at i:221207 original size:152 final size:152
Alignment explanation
Indices: 221041--221619 Score: 461
Period size: 161 Copynumber: 3.6 Consensus size: 152
221031 TCAAATTTTC
*
221041 TAAAATCTTCTTCTCTACTTCCACACATATGAGGAAAAAACTGAATGCATGGTTATGATGTCCAT
1 TAAAATCTTCTTCTCTACTTCCACACATATGAGGAAAAAACTAAATGCATGGTTATGATGTCCAT
* *
221106 GAAGCCCTCTACCAAAATTGTGAAATTCATGGCCTCT-GGTAGAGGCTCTA-GGTGGGGCCAATA
66 GAAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTAGGTAGAGGCTCTAGGGTGGGGCCAATA
221169 TGGCCATATAGTAAAAATATCT
131 TGGCCATATAGTAAAAATATCT
* * *** ** ** * * *
221191 TGGAAAATCTTTTTCTCTACTCCCATTTATATTTGTTAAAAACTAAATGCATGATTATAATATCC
1 T--AAAATCTTCTTCTCTACTTCCACACATATGAGGAAAAAACTAAATGCATGGTTATGATGTCC
* * * * *
221256 ATGAGGCCCTCTATCAAAATTGTTAAATTCATTACCCCTGGGTTAGGGGTTCAGGCTCTAGGGTG
64 ATGAAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTAGG-TA---G---AGGCTCTAGGGTG
* * *
221321 TGGCCAATATGGCCATATAGTAAAAATGTAT
122 GGGCCAATATGGCCATATAGTAAAAATATCT
* * * * *
221352 TAAAATCTTCTTCTCTACTACC-C-TATATAATGGTAAAAACTAAATGCATGATGATGATGATGT
1 TAAAATCTTCTTCTCTACTTCCACACATATGA-GGAAAAAACTAAATGCATG--G-TTATGATGT
* * * *
221415 CCATGAGGCCCTCTACTAAAATTGTGAAATTCATGACCCCTAGTTTAGGGGTTCGGGTTCTAGGG
62 CCATGAAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTAG-GTAGAGG--C----TCTAGGG
221480 TGGGGCCAATATGGCCATATAGTAAAAATGTATTAAATCTT
120 TGGGGCCAATATGGCCATATAGT-AAAA---A-T--ATC-T
* * * *
221521 TAAAAACATCTTCTTCTCTGCTTCCACACATATTG-GCAAAAAACTGAATACATGGTTATGATGT
1 T--AAA-ATCTTCTTCTCTACTTCCACACATA-TGAGGAAAAAACTAAATGCATGGTTATGATGT
* *
221585 CCACT-AA-CTCATCTACCTAAATTGTGAAATTCATG
62 CCA-TGAAGC-CCTCTACCAAAATTGTGAAATTCATG
221620 GCCTCATGGG
Statistics
Matches: 336, Mismatches: 55, Indels: 56
0.75 0.12 0.13
Matches are distributed among these distances:
150 1 0.00
152 82 0.24
153 2 0.01
154 2 0.01
155 2 0.01
157 7 0.02
158 19 0.06
159 19 0.06
160 8 0.02
161 108 0.32
162 4 0.01
165 1 0.00
166 1 0.00
168 1 0.00
169 3 0.01
170 35 0.10
171 5 0.01
172 16 0.05
173 16 0.05
174 3 0.01
175 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (152 bp):
TAAAATCTTCTTCTCTACTTCCACACATATGAGGAAAAAACTAAATGCATGGTTATGATGTCCAT
GAAGCCCTCTACCAAAATTGTGAAATTCATGACCCCTAGGTAGAGGCTCTAGGGTGGGGCCAATA
TGGCCATATAGTAAAAATATCT
Found at i:221420 original size:161 final size:157
Alignment explanation
Indices: 221041--221520 Score: 554
Period size: 161 Copynumber: 3.1 Consensus size: 157
221031 TCAAATTTTC
* * * * *
221041 TAAAATCTTCTTCTCTACTTCCACACATATGA-GGAAAAAACTGAATGCATGGT-TATGATGTCC
1 TAAAATCTTCTTCTCTAC-TCC-CATATATAATGGTAAAAACTAAATGCATGATGTATGATGTCC
* * *
221104 ATGAAGCCCTCTACCAAAATTGTGAAATTCATGGCCTCTGG-TA---G---AGGCTCTA-GGTGG
64 ATGAGGCCCTCTA-CAAAATTGTGAAATTCATGACCCCTGGTTAGGGGTTCAGGCTCTAGGGTGG
* *
221161 GGCCAATATGGCCATATAGTAAAAATATCT
128 GGCCAATATGGCCATATAGTAAAAATGTAT
* * * * * *
221191 TGGAAAATCTTTTTCTCTACTCCCATTTATATTTGTTAAAAACTAAATGCATGAT-TATAATATC
1 T--AAAATCTTCTTCTCTACTCCCATATATA-ATGGTAAAAACTAAATGCATGATGTATGATGTC
* *
221255 CATGAGGCCCTCTATCAAAATTGTTAAATTCATTACCCCTGGGTTAGGGGTTCAGGCTCTAGGGT
63 CATGAGGCCCTCTA-CAAAATTGTGAAATTCATGACCCCT-GGTTAGGGGTTCAGGCTCTAGGGT
*
221320 GTGGCCAATATGGCCATATAGTAAAAATGTAT
126 GGGGCCAATATGGCCATATAGTAAAAATGTAT
221352 TAAAATCTTCTTCTCTACTACCC-TATATAATGGTAAAAACTAAATGCATGATGATGATGATGTC
1 TAAAATCTTCTTCTCTACT-CCCATATATAATGGTAAAAACTAAATGCATGATG-T-ATGATGTC
* * *
221416 CATGAGGCCCTCTACTAAAATTGTGAAATTCATGACCCCTAGTTTAGGGGTTCGGGTTCTAGGGT
63 CATGAGGCCCTCTAC-AAAATTGTGAAATTCATGACCCCT-GGTTAGGGGTTCAGGCTCTAGGGT
221481 GGGGCCAATATGGCCATATAGTAAAAATGTAT
126 GGGGCCAATATGGCCATATAGTAAAAATGTAT
221513 T-AAATCTT
1 TAAAATCTT
221521 TAAAAACATC
Statistics
Matches: 279, Mismatches: 33, Indels: 26
0.83 0.10 0.08
Matches are distributed among these distances:
150 6 0.02
151 3 0.01
152 74 0.27
153 2 0.01
154 2 0.01
157 1 0.00
158 21 0.08
159 22 0.08
160 20 0.07
161 128 0.46
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (157 bp):
TAAAATCTTCTTCTCTACTCCCATATATAATGGTAAAAACTAAATGCATGATGTATGATGTCCAT
GAGGCCCTCTACAAAATTGTGAAATTCATGACCCCTGGTTAGGGGTTCAGGCTCTAGGGTGGGGC
CAATATGGCCATATAGTAAAAATGTAT
Found at i:224415 original size:25 final size:26
Alignment explanation
Indices: 224364--224416 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
224354 TATATTCCAT
* *
224364 TTATAAACTGGGCGTGTTTTATTCCC
1 TTATAAACTGGGCCTGATTTATTCCC
224390 TTATAAACTGGGCCT-ATTTATTCCC
1 TTATAAACTGGGCCTGATTTATTCCC
224415 TT
1 TT
224417 GTAGGGTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.43
Consensus pattern (26 bp):
TTATAAACTGGGCCTGATTTATTCCC
Found at i:230624 original size:20 final size:20
Alignment explanation
Indices: 230595--230632 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
230585 TCAATAGAAT
* *
230595 AAACATTTCATTATTTTACG
1 AAACAATTCATCATTTTACG
230615 AAACAATTCATCATTTTA
1 AAACAATTCATCATTTTA
230633 TAATACTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.16, G:0.03, T:0.42
Consensus pattern (20 bp):
AAACAATTCATCATTTTACG
Found at i:234653 original size:2 final size:2
Alignment explanation
Indices: 234648--234683 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
234638 TTTTTTTTAT
234648 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
234684 AACGAATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:238458 original size:15 final size:15
Alignment explanation
Indices: 238420--238458 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
238410 CGATGATGGT
** *
238420 AGGGAGACCGCTGGG
1 AGGGAGACTACTGGA
238435 AGGGAGACTACTGGA
1 AGGGAGACTACTGGA
238450 AGGGAGACT
1 AGGGAGACT
238459 GCCGGGGACG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.28, C:0.15, G:0.46, T:0.10
Consensus pattern (15 bp):
AGGGAGACTACTGGA
Found at i:249958 original size:27 final size:27
Alignment explanation
Indices: 249926--250190 Score: 354
Period size: 27 Copynumber: 9.9 Consensus size: 27
249916 AATCGTTCTA
* *
249926 GTTACAGTACATACAGGTAACTTAACT
1 GTTACAGTACATACAGGTAACTTTATT
* *
249953 GTTACAGTACATACAGGTAACTTAACT
1 GTTACAGTACATACAGGTAACTTTATT
* *
249980 GTTACAGTTCATACAGGTAACTTTGTT
1 GTTACAGTACATACAGGTAACTTTATT
*
250007 GTTACAGTACATACAGGTAACTTTGTT
1 GTTACAGTACATACAGGTAACTTTATT
*
250034 GTTACAGTACATACAGGTAACTTTGTT
1 GTTACAGTACATACAGGTAACTTTATT
* *
250061 GTTACAGTACATACAGGTAACTTAACT
1 GTTACAGTACATACAGGTAACTTTATT
* * *
250088 GTTACAGTTCATAAAGGTAACTTTTTT
1 GTTACAGTACATACAGGTAACTTTATT
*
250115 GTTACAGTACATACAGGTAACTTTGTT
1 GTTACAGTACATACAGGTAACTTTATT
* *
250142 GTTACAGTACATACACGT--CGTTACTT
1 GTTACAGTACATACAGGTAACTTTA-TT
*
250168 GTTACAGTACATACAAGTAACTT
1 GTTACAGTACATACAGGTAACTT
250191 ACACATTATA
Statistics
Matches: 214, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
25 3 0.01
26 19 0.09
27 190 0.89
28 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (27 bp):
GTTACAGTACATACAGGTAACTTTATT
Found at i:269293 original size:1 final size:1
Alignment explanation
Indices: 269287--269313 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
269277 CTTTTCTGAT
269287 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGG
269314 TTGTTGGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:271719 original size:22 final size:22
Alignment explanation
Indices: 271692--271810 Score: 193
Period size: 22 Copynumber: 5.4 Consensus size: 22
271682 TTTACAAAGG
*
271692 AAAGATTTACAGAACAAGGAAC
1 AAAGATTTACAGAATAAGGAAC
*
271714 AAAGATTTACAGAACAAGGAAC
1 AAAGATTTACAGAATAAGGAAC
271736 AAAGATTTACAGAATAAGGAAC
1 AAAGATTTACAGAATAAGGAAC
*
271758 ACAGATTTACAGAATAAGGAAC
1 AAAGATTTACAGAATAAGGAAC
*
271780 ACAGATTTACAGAATAAGGAAC
1 AAAGATTTACAGAATAAGGAAC
*
271802 ACAGATTTA
1 AAAGATTTA
271811 AAAAGAATTA
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 95 1.00
ACGTcount: A:0.52, C:0.13, G:0.18, T:0.18
Consensus pattern (22 bp):
AAAGATTTACAGAATAAGGAAC
Found at i:275670 original size:37 final size:37
Alignment explanation
Indices: 275625--275697 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
275615 ACGCCTCGAG
275625 GTGTTTTTCCGAGCCTGCCGGAAAGGCCCGAGAAGTC
1 GTGTTTTTCCGAGCCTGCCGGAAAGGCCCGAGAAGTC
275662 GTGTTTTTCCGAGCCTGCCGGAAAGGCCCGAGAAGT
1 GTGTTTTTCCGAGCCTGCCGGAAAGGCCCGAGAAGT
275698 TGGGATTGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.19, C:0.26, G:0.33, T:0.22
Consensus pattern (37 bp):
GTGTTTTTCCGAGCCTGCCGGAAAGGCCCGAGAAGTC
Found at i:277457 original size:20 final size:21
Alignment explanation
Indices: 277413--277457 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
277403 TGAAACTCAC
* *
277413 TTTCATTTAATTAAATTGTAG
1 TTTCATTGAATGAAATTGTAG
277434 -TTCATTGAATGAAATTG-AG
1 TTTCATTGAATGAAATTGTAG
277453 TTTCA
1 TTTCA
277458 CATGTTTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (21 bp):
TTTCATTGAATGAAATTGTAG
Found at i:277846 original size:3 final size:3
Alignment explanation
Indices: 277838--277902 Score: 76
Period size: 3 Copynumber: 21.7 Consensus size: 3
277828 AATATCGCTA
** * *
277838 TCG TCG TCG TCG TCG TTA TCA TCA TCG TCG TCG TCG TCG TCG TCG TCG
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG
* *
277886 TCG TCA TCA TCG TCG TC
1 TCG TCG TCG TCG TCG TC
277903 ATCATCATCA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.08, C:0.32, G:0.25, T:0.35
Consensus pattern (3 bp):
TCG
Found at i:277867 original size:15 final size:15
Alignment explanation
Indices: 277856--277911 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
277846 GTCGTCGTTA
*
277856 TCATCATCGTCGTCG
1 TCATCATCATCGTCG
* * *
277871 TCGTCGTCGTCGTCG
1 TCATCATCATCGTCG
*
277886 TCGTCATCATCGTCG
1 TCATCATCATCGTCG
277901 TCATCATCATC
1 TCATCATCATC
277912 ATTCTCTCTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.12, C:0.34, G:0.20, T:0.34
Consensus pattern (15 bp):
TCATCATCATCGTCG
Found at i:279934 original size:6 final size:6
Alignment explanation
Indices: 279924--279963 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
279914 AAAAAAACCC
279924 CAAAAA -AAAAA CAAAAA CAAAAA CAAAAA C-AAAA CAAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA
279964 AAACCCCTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 10 0.31
6 22 0.69
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:279939 original size:23 final size:23
Alignment explanation
Indices: 279894--279970 Score: 79
Period size: 23 Copynumber: 3.4 Consensus size: 23
279884 CAAATGAAAC
*
279894 AAAAACCCCAAACAGC-AAA-AAA
1 AAAAACCCCAAA-AACAAAACAAA
*
279916 AAAAACCCCAAAAAAAAAACAAA
1 AAAAACCCCAAAAACAAAACAAA
**
279939 AACAAA-AACAAAAACAAAACAAA
1 AA-AAACCCCAAAAACAAAACAAA
279962 AAAAACCCC
1 AAAAACCCC
279971 TCTCCTTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.02
22 18 0.41
23 22 0.50
24 3 0.07
ACGTcount: A:0.74, C:0.25, G:0.01, T:0.00
Consensus pattern (23 bp):
AAAAACCCCAAAAACAAAACAAA
Found at i:279940 original size:12 final size:12
Alignment explanation
Indices: 279909--279966 Score: 64
Period size: 12 Copynumber: 4.8 Consensus size: 12
279899 CCCCAAACAG
279909 CAAAAAAAAAAA
1 CAAAAAAAAAAA
*
279921 CCCCAAAAAAAAAA
1 --CAAAAAAAAAAA
*
279935 CAAAAACAAAAA
1 CAAAAAAAAAAA
*
279947 C-AAAAACAAAA
1 CAAAAAAAAAAA
279958 CAAAAAAAA
1 CAAAAAAAA
279967 CCCCTCTCCT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
11 9 0.24
12 17 0.46
14 11 0.30
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:289013 original size:1 final size:1
Alignment explanation
Indices: 289007--289031 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
288997 TTTTCTATAA
289007 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
289032 ACCGGGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:289862 original size:2 final size:2
Alignment explanation
Indices: 289855--289896 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
289845 TATACCTTTC
289855 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
289897 NNNNNNNNNN
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:292231 original size:29 final size:29
Alignment explanation
Indices: 292189--292669 Score: 660
Period size: 29 Copynumber: 16.6 Consensus size: 29
292179 NNNNNNNNNN
292189 TCGTTTGGCATACTCTTCAAATATGCTGG
1 TCGTTTGGCATACTCTTCAAATATGCTGG
* * *
292218 TCGTTTGGCATACTCTTTAAATATACTGA
1 TCGTTTGGCATACTCTTCAAATATGCTGG
292247 TCGTTTGGCATACTCTTCAAATATGCTGG
1 TCGTTTGGCATACTCTTCAAATATGCTGG
* *
292276 TCGTTTGGCATACTCTTGAAATATGCTGC
1 TCGTTTGGCATACTCTTCAAATATGCTGG
*
292305 TCGTTTGGCATACTCTTAAAATATGCTGG
1 TCGTTTGGCATACTCTTCAAATATGCTGG
* *
292334 TCGTTTGGCATACTCTTCAAATTTGCTGT
1 TCGTTTGGCATACTCTTCAAATATGCTGG
* * *
292363 TTGTTTGGCATACTCTTCAAATATGATGA
1 TCGTTTGGCATACTCTTCAAATATGCTGG
* * *
292392 TCGTTTGGCATACTCTTCAAAAATGTTGA
1 TCGTTTGGCATACTCTTCAAATATGCTGG
* * *
292421 TGGTTTGGCATACTCTTTAAATTTGCTGG
1 TCGTTTGGCATACTCTTCAAATATGCTGG
292450 TCGTTTGGCATACTCTTCAAATATGCTGG
1 TCGTTTGGCATACTCTTCAAATATGCTGG
*
292479 TCGTTTGGCATACTCTTCAAATATGCTGA
1 TCGTTTGGCATACTCTTCAAATATGCTGG
* * * * * *
292508 TCG-TTGGACATGCTGTGCAAAAATGTTGA
1 TCGTTTGG-CATACTCTTCAAATATGCTGG
* * *
292537 TGGTTTGGCATACTCTTTAAATTTGCTGG
1 TCGTTTGGCATACTCTTCAAATATGCTGG
*
292566 TCGTTTGGCATACTCTTCAGAA-ATGCTGC
1 TCGTTTGGCATACTCTTCA-AATATGCTGG
292595 TCGTTTGGCATACTCTTCAAATATGCTGG
1 TCGTTTGGCATACTCTTCAAATATGCTGG
*
292624 TCGTTTGGCATACTTTTCAAATATGCTGG
1 TCGTTTGGCATACTCTTCAAATATGCTGG
*
292653 TCGTTTGTCATACTCTT
1 TCGTTTGGCATACTCTT
292670 AAGACATGTT
Statistics
Matches: 396, Mismatches: 52, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
28 6 0.02
29 384 0.97
30 6 0.02
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.40
Consensus pattern (29 bp):
TCGTTTGGCATACTCTTCAAATATGCTGG
Found at i:292838 original size:29 final size:29
Alignment explanation
Indices: 292684--292838 Score: 121
Period size: 29 Copynumber: 5.1 Consensus size: 29
292674 CATGTTGTTT
* *
292684 AAATATGCTGATCGTTGAGCATGCTGTTC
1 AAATATGCTGATCGTTGGGCATGCTCTTC
* * *
292713 AGATATGCTGATCGTTTGACATGCTCTTC
1 AAATATGCTGATCGTTGGGCATGCTCTTC
* * * *
292742 GAATACTAGTATGCTGCTCTTTTGGCATACTCTTC
1 --A-A--A-TATGCTGATCGTTGGGCATGCTCTTC
* * * * *
292777 AGATATGCTGATTGTTGTGCATACTGTTC
1 AAATATGCTGATCGTTGGGCATGCTCTTC
*
292806 AAATATGCTGATCGTTGGGCATGCTCTTT
1 AAATATGCTGATCGTTGGGCATGCTCTTC
292835 AAAT
1 AAAT
292839 TATAATAATC
Statistics
Matches: 97, Mismatches: 23, Indels: 12
0.73 0.17 0.09
Matches are distributed among these distances:
29 71 0.73
30 1 0.01
31 1 0.01
33 1 0.01
34 1 0.01
35 22 0.23
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (29 bp):
AAATATGCTGATCGTTGGGCATGCTCTTC
Found at i:292858 original size:93 final size:93
Alignment explanation
Indices: 292208--292838 Score: 252
Period size: 87 Copynumber: 7.0 Consensus size: 93
292198 ATACTCTTCA
* * * * * *
292208 AATATGCTGGTCGTTTGGCATACTCTTTAAATATACTGATCGTTTG-GCATACTCTTCAAATATG
1 AATATGCTGCTCTTTTGGCATACTCTTCAGATATGCTGATCG-TTGAGCATACTGTTCAAATATG
* * *
292272 CTGGTCGTTTGG-CATACTCTT----GA--
65 CTGATCG-TTGGACATGCTCTTCAAATACT
* * * * * *
292295 AATATGCTGCTCGTTTGGCATACTCTTAAAATATGCTGGTCGTTTG-GCATACTCTTCAAATTTG
1 AATATGCTGCTCTTTTGGCATACTCTTCAGATATGCTGATCG-TTGAGCATACTGTTCAAATATG
* * *
292359 CTGTTTGTTTGG-CATACTCTTCAAATA-T
65 CTGATCG-TTGGACATGCTCTTCAAATACT
* * * * * * * *
292387 GATGAT-C-G----TTTGGCATACTCTTCAAAAATGTTGATGGTTTG-GCATACTCTTTAAATTT
1 AAT-ATGCTGCTCTTTTGGCATACTCTTCAGATATGCTGATCG-TTGAGCATACTGTTCAAATAT
* *
292445 GCTGGTCGTTTGG-CATACTCTTC----A--
64 GCTGATCG-TTGGACATGCTCTTCAAATACT
* * * * * *
292469 AATATGCTGGTCGTTTGGCATACTCTTCAAATATGCTGATCGTTG-GACATGCTGTGCAAAAATG
1 AATATGCTGCTCTTTTGGCATACTCTTCAGATATGCTGATCGTTGAG-CATACTGTTCAAATATG
* * *
292533 TTGATGGTTTGG-CATACTCTT----TA--
65 CTGATCG-TTGGACATGCTCTTCAAATACT
* * * * * *
292556 AATTTGCTGGTCGTTTGGCATACTCTTCAGAAATGCTGCTCGTTTG-GCATACTCTTCAAATATG
1 AATATGCTGCTCTTTTGGCATACTCTTCAGATATGCTGATCG-TTGAGCATACTGTTCAAATATG
* * *
292620 CTGGTCGTTTGG-CATACTTTTCAAATATGCTGGT
65 CTGATCG-TTGGACATGCTCTTCAAATA--C---T
** * * ** * ** * * * * *
292654 CGTTTGTCATACTCTTAAGACATGTTGTTTAAATATGCTGATCGTTGAGCATGCTGTTCAGATAT
1 AATATG-C-TGCTCTTTTGGCATACTCTTCAGATATGCTGATCGTTGAGCATACTGTTCAAATAT
* *
292719 GCTGATCGTTTGACATGCTCTTCGAATACT
64 GCTGATCGTTGGACATGCTCTTCAAATACT
* * *
292749 AGTATGCTGCTCTTTTGGCATACTCTTCAGATATGCTGATTGTTGTGCATACTGTTCAAATATGC
1 AATATGCTGCTCTTTTGGCATACTCTTCAGATATGCTGATCGTTGAGCATACTGTTCAAATATGC
* *
292814 TGATCGTTGGGCATGCTCTTTAAAT
66 TGATCGTTGGACATGCTCTTCAAAT
292839 TATAATAATC
Statistics
Matches: 430, Mismatches: 84, Indels: 54
0.76 0.15 0.10
Matches are distributed among these distances:
81 2 0.00
82 3 0.01
83 2 0.00
86 4 0.01
87 267 0.62
88 4 0.01
91 4 0.01
92 3 0.01
93 68 0.16
94 1 0.00
95 5 0.01
98 5 0.01
99 7 0.02
100 55 0.13
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (93 bp):
AATATGCTGCTCTTTTGGCATACTCTTCAGATATGCTGATCGTTGAGCATACTGTTCAAATATGC
TGATCGTTGGACATGCTCTTCAAATACT
Found at i:299216 original size:15 final size:16
Alignment explanation
Indices: 299190--299219 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
299180 AAATTATCTG
299190 CTTTTCTTTTCTTTCC
1 CTTTTCTTTTCTTTCC
299206 CTTTT-TTTTCTTTC
1 CTTTTCTTTTCTTTC
299220 TGATTGTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (16 bp):
CTTTTCTTTTCTTTCC
Found at i:305426 original size:2 final size:2
Alignment explanation
Indices: 305413--305482 Score: 122
Period size: 2 Copynumber: 35.0 Consensus size: 2
305403 GCATATGATT
* *
305413 TC TC TC TA TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
305455 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
305483 ATATGAAAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.01, C:0.47, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:305930 original size:12 final size:12
Alignment explanation
Indices: 305910--305940 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
305900 TCTATCAATA
305910 TATCCATCCTTC
1 TATCCATCCTTC
*
305922 TATCTATCCTTC
1 TATCCATCCTTC
305934 TATCCAT
1 TATCCAT
305941 TTACTCTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.19, C:0.35, G:0.00, T:0.45
Consensus pattern (12 bp):
TATCCATCCTTC
Found at i:305951 original size:2 final size:2
Alignment explanation
Indices: 305944--305980 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
305934 TATCCATTTA
305944 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
305981 CCCACACACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:312920 original size:1 final size:1
Alignment explanation
Indices: 312916--312947 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
312906 GTTTTTTGTA
312916 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
312948 GCAATTTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:312921 original size:9 final size:9
Alignment explanation
Indices: 312902--312948 Score: 53
Period size: 8 Copynumber: 5.2 Consensus size: 9
312892 TAAGTAATGC
312902 TGTTGTTTTT
1 TGTT-TTTTT
312912 TGTATTTTTT
1 TGT-TTTTTT
312922 T-TTTTTTT
1 TGTTTTTTT
312930 T-TTTTTTT
1 TGTTTTTTT
*
312938 TTTTTTTTT
1 TGTTTTTTT
312947 TG
1 TG
312949 CAATTTGTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
8 15 0.44
9 9 0.26
10 9 0.26
11 1 0.03
ACGTcount: A:0.02, C:0.00, G:0.09, T:0.89
Consensus pattern (9 bp):
TGTTTTTTT
Found at i:313276 original size:2 final size:2
Alignment explanation
Indices: 313271--313346 Score: 136
Period size: 2 Copynumber: 38.5 Consensus size: 2
313261 TATGTGTGTT
313271 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
313313 AG AG AG AG AG AG AG AG AG AG AA AG A- AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
313347 TTCGGCATAT
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
1 1 0.01
2 70 0.99
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:317137 original size:18 final size:18
Alignment explanation
Indices: 317114--317155 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
317104 CCAACTGATG
*
317114 TATTATTACTATCACTAT
1 TATTATTAATATCACTAT
*
317132 TATTATTAATATTACTAT
1 TATTATTAATATCACTAT
317150 TATTAT
1 TATTAT
317156 CATTATTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTATTAATATCACTAT
Found at i:317138 original size:6 final size:6
Alignment explanation
Indices: 317114--317173 Score: 57
Period size: 6 Copynumber: 10.0 Consensus size: 6
317104 CCAACTGATG
* * * * * *
317114 TATTAT TACTAT CACTAT TATTAT TAATAT TACTAT TATTAT CATTAT
1 TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT
*
317162 TATCAT TATTAT
1 TATTAT TATTAT
317174 AATCATTTGA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (6 bp):
TATTAT
Found at i:320905 original size:18 final size:17
Alignment explanation
Indices: 320893--320927 Score: 61
Period size: 17 Copynumber: 2.0 Consensus size: 17
320883 TAAAATGAAT
320893 ACAATGAAAAAAAAAATA
1 ACAA-GAAAAAAAAAATA
320911 ACAAGAAAAAAAAAATA
1 ACAAGAAAAAAAAAATA
320928 TCCACCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.80, C:0.06, G:0.06, T:0.09
Consensus pattern (17 bp):
ACAAGAAAAAAAAAATA
Found at i:324250 original size:23 final size:23
Alignment explanation
Indices: 324220--324263 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
324210 CCTCTACTTT
*
324220 TGTAAGAAAATCTAATTGAATTC
1 TGTAAGAAAATATAATTGAATTC
324243 TGTAAGAAAATATAATTGAAT
1 TGTAAGAAAATATAATTGAAT
324264 AAAGAACAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.34
Consensus pattern (23 bp):
TGTAAGAAAATATAATTGAATTC
Found at i:324800 original size:132 final size:132
Alignment explanation
Indices: 324563--324958 Score: 792
Period size: 132 Copynumber: 3.0 Consensus size: 132
324553 TTCTCATAGA
324563 AATTCACACTTCGTCTCATTGTAAAAAAATTATAAAAATAAGTGATACAGTATGATAGTATGTGT
1 AATTCACACTTCGTCTCATTGTAAAAAAATTATAAAAATAAGTGATACAGTATGATAGTATGTGT
324628 CCTCCCCCCTGCCCCGGACAAGGGGCTAGGGGGAGGACACATTCATAACCCAACAACTTGCATTA
66 CCTCCCCCCTGCCCCGGACAAGGGGCTAGGGGGAGGACACATTCATAACCCAACAACTTGCATTA
324693 GG
131 GG
324695 AATTCACACTTCGTCTCATTGTAAAAAAATTATAAAAATAAGTGATACAGTATGATAGTATGTGT
1 AATTCACACTTCGTCTCATTGTAAAAAAATTATAAAAATAAGTGATACAGTATGATAGTATGTGT
324760 CCTCCCCCCTGCCCCGGACAAGGGGCTAGGGGGAGGACACATTCATAACCCAACAACTTGCATTA
66 CCTCCCCCCTGCCCCGGACAAGGGGCTAGGGGGAGGACACATTCATAACCCAACAACTTGCATTA
324825 GG
131 GG
324827 AATTCACACTTCGTCTCATTGTAAAAAAATTATAAAAATAAGTGATACAGTATGATAGTATGTGT
1 AATTCACACTTCGTCTCATTGTAAAAAAATTATAAAAATAAGTGATACAGTATGATAGTATGTGT
324892 CCTCCCCCCTGCCCCGGACAAGGGGCTAGGGGGAGGACACATTCATAACCCAACAACTTGCATTA
66 CCTCCCCCCTGCCCCGGACAAGGGGCTAGGGGGAGGACACATTCATAACCCAACAACTTGCATTA
324957 GG
131 GG
324959 CACCAAGAAT
Statistics
Matches: 264, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
132 264 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (132 bp):
AATTCACACTTCGTCTCATTGTAAAAAAATTATAAAAATAAGTGATACAGTATGATAGTATGTGT
CCTCCCCCCTGCCCCGGACAAGGGGCTAGGGGGAGGACACATTCATAACCCAACAACTTGCATTA
GG
Found at i:327483 original size:3 final size:3
Alignment explanation
Indices: 327470--327518 Score: 53
Period size: 3 Copynumber: 15.3 Consensus size: 3
327460 ATGACAGGAT
* *
327470 TGA TAA TGA TGA TGA TACA TGTA TTGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA T-GA TG-A -TGA TGA TGA TGA TGA TGA TGA TGA
327518 T
1 T
327519 TATAATGATT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 33 0.85
4 4 0.10
5 2 0.05
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.37
Consensus pattern (3 bp):
TGA
Found at i:327485 original size:12 final size:12
Alignment explanation
Indices: 327470--327527 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
327460 ATGACAGGAT
327470 TGATAATGATGA
1 TGATAATGATGA
327482 TGATACATG-T-A
1 TGATA-ATGATGA
*
327493 TTGATGATGATGA
1 -TGATAATGATGA
*
327506 TGATGATGATGA
1 TGATAATGATGA
*
327518 TTATAATGAT
1 TGATAATGAT
327528 TGTTTGGCGA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
11 4 0.10
12 31 0.79
13 4 0.10
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (12 bp):
TGATAATGATGA
Found at i:327485 original size:24 final size:25
Alignment explanation
Indices: 327458--327527 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
327448 TACTTCTTTC
327458 TGATGACA-GGATTGATAATGATGA
1 TGATGACATGGATTGATAATGATGA
* *
327482 TGAT-ACATGTATTGATGATGATGA
1 TGATGACATGGATTGATAATGATGA
*
327506 TGATGATGAT-GATT-ATAATGAT
1 TGATGA-CATGGATTGATAATGAT
327528 TGTTTGGCGA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
23 3 0.08
24 29 0.76
25 4 0.11
26 2 0.05
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.36
Consensus pattern (25 bp):
TGATGACATGGATTGATAATGATGA
Found at i:327786 original size:26 final size:26
Alignment explanation
Indices: 327751--327835 Score: 116
Period size: 26 Copynumber: 3.3 Consensus size: 26
327741 ATAAGTTATA
327751 ATAGTTTGATAGCTTGGTGGTTTGGT
1 ATAGTTTGATAGCTTGGTGGTTTGGT
* *
327777 ATAGTTTGATGGCTTGGTGGTTTGAT
1 ATAGTTTGATAGCTTGGTGGTTTGGT
* * * *
327803 ACAGTTTGATACCTAGGAGGTTTGGT
1 ATAGTTTGATAGCTTGGTGGTTTGGT
327829 ATAGTTT
1 ATAGTTT
327836 AATGGTTTAG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.19, C:0.06, G:0.32, T:0.44
Consensus pattern (26 bp):
ATAGTTTGATAGCTTGGTGGTTTGGT
Found at i:327850 original size:26 final size:26
Alignment explanation
Indices: 327751--327850 Score: 94
Period size: 26 Copynumber: 3.8 Consensus size: 26
327741 ATAAGTTATA
* *
327751 ATAGTTTGATAGCTTGGTGGTTTGGT
1 ATAGTTTGATGGCTTAGTGGTTTGGT
* *
327777 ATAGTTTGATGGCTTGGTGGTTTGAT
1 ATAGTTTGATGGCTTAGTGGTTTGGT
* * * *
327803 ACAGTTTGAT-ACCTAGGAGGTTTGGT
1 ATAGTTTGATGGCTTA-GTGGTTTGGT
* *
327829 ATAGTTTAATGGTTTAGTGGTT
1 ATAGTTTGATGGCTTAGTGGTT
327851 ATAGTTTGGT
Statistics
Matches: 58, Mismatches: 14, Indels: 4
0.76 0.18 0.05
Matches are distributed among these distances:
25 2 0.03
26 54 0.93
27 2 0.03
ACGTcount: A:0.19, C:0.05, G:0.32, T:0.44
Consensus pattern (26 bp):
ATAGTTTGATGGCTTAGTGGTTTGGT
Found at i:328027 original size:26 final size:26
Alignment explanation
Indices: 327998--328196 Score: 90
Period size: 26 Copynumber: 7.4 Consensus size: 26
327988 TTTGTTGTGG
327998 TTTGGTAGCTTTGGCTAGTTATACCA
1 TTTGGTAGCTTTGGCTAGTTATACCA
* * **
328024 TTTGATAGCTTGGGGGTCT-GTTAT--GG
1 TTTGGTAGCTT--TGG-CTAGTTATACCA
328050 TTTGGTAGCTTTTCGGCTAGTTATACCA
1 TTTGGTAGC-TTT-GGCTAGTTATACCA
* * * **
328078 TTTGGTAGCTTGGGGGTTTGTTAT--GG
1 TTTGGTAGCTT--TGGCTAGTTATACCA
*
328104 TTTGGTAGCTTTTGGGCTAGTTACACCA
1 TTTGGTAGC-TTT-GGCTAGTTATACCA
* * **
328132 TTTGATAGCTTGGGGGTCT-GTTATGGC-
1 TTTGGTAGCTT--TGG-CTAGTTATACCA
328159 -TTGGTAGCTTTTTGGCTAGTTATACCA
1 TTTGGTAGC--TTTGGCTAGTTATACCA
328186 TTTGGTAGCTT
1 TTTGGTAGCTT
328197 GGGGTTTGTT
Statistics
Matches: 123, Mismatches: 28, Indels: 44
0.63 0.14 0.23
Matches are distributed among these distances:
25 4 0.03
26 58 0.47
27 8 0.07
28 49 0.40
29 4 0.03
ACGTcount: A:0.15, C:0.13, G:0.30, T:0.43
Consensus pattern (26 bp):
TTTGGTAGCTTTGGCTAGTTATACCA
Found at i:328087 original size:54 final size:53
Alignment explanation
Indices: 327979--328264 Score: 369
Period size: 54 Copynumber: 5.2 Consensus size: 53
327969 TCTATTTGTG
* *
327979 GCTTGGTGGTTTGTTGTGGTTTGGTAGC-TTTGGCTAGTTATACCATTTGATA
1 GCTTGGGGGTTTGTTATGGTTTGGTAGCTTTTGGCTAGTTATACCATTTGATA
* *
328031 GCTTGGGGGTCTGTTATGGTTTGGTAGCTTTTCGGCTAGTTATACCATTTGGTA
1 GCTTGGGGGTTTGTTATGGTTTGGTAGCTTTT-GGCTAGTTATACCATTTGATA
*
328085 GCTTGGGGGTTTGTTATGGTTTGGTAGCTTTTGGGCTAGTTACACCATTTGATA
1 GCTTGGGGGTTTGTTATGGTTTGGTAGCTTTT-GGCTAGTTATACCATTTGATA
* * *
328139 GCTTGGGGGTCTGTTATGGCTTGGTAGCTTTTTGGCTAGTTATACCATTTGGTA
1 GCTTGGGGGTTTGTTATGGTTTGGTAGC-TTTTGGCTAGTTATACCATTTGATA
* *
328193 GCTT-GGGGTTTGTTATGGTTTCAAATTGGTAGATTTTTGGCTAGTTACACCATTTGATA
1 GCTTGGGGGTTTGTTATGG--T----TTGGTAG-CTTTTGGCTAGTTATACCATTTGATA
*
328252 GCTTGGTGGTTTG
1 GCTTGGGGGTTTG
328265 GATTGTGGTT
Statistics
Matches: 205, Mismatches: 18, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
52 25 0.12
53 16 0.08
54 119 0.58
55 4 0.02
59 34 0.17
60 7 0.03
ACGTcount: A:0.14, C:0.11, G:0.31, T:0.44
Consensus pattern (53 bp):
GCTTGGGGGTTTGTTATGGTTTGGTAGCTTTTGGCTAGTTATACCATTTGATA
Found at i:328147 original size:108 final size:107
Alignment explanation
Indices: 327979--328257 Score: 418
Period size: 108 Copynumber: 2.6 Consensus size: 107
327969 TCTATTTGTG
* * *
327979 GCTTGGTGGTTTGTTGTGGTTTGGTAGC-TTTGGCTAGTTATACCATTTGATAGCTTGGGGGTCT
1 GCTTGGGGGTTTGTTATGGTTTGGTAGCTTTTGGCTAGTTACACCATTTGATAGCTTGGGGGTCT
*
328043 GTTATGGTTTGGTAGCTTTTCGGCTAGTTATACCATTTGGTA
66 GTTATGGCTTGGTAGCTTTTCGGCTAGTTATACCATTTGGTA
328085 GCTTGGGGGTTTGTTATGGTTTGGTAGCTTTTGGGCTAGTTACACCATTTGATAGCTTGGGGGTC
1 GCTTGGGGGTTTGTTATGGTTTGGTAGCTTTT-GGCTAGTTACACCATTTGATAGCTTGGGGGTC
*
328150 TGTTATGGCTTGGTAGCTTTTTGGCTAGTTATACCATTTGGTA
65 TGTTATGGCTTGGTAGCTTTTCGGCTAGTTATACCATTTGGTA
*
328193 GCTT-GGGGTTTGTTATGGTTTCAAATTGGTAGATTTTTGGCTAGTTACACCATTTGATAGCTTG
1 GCTTGGGGGTTTGTTATGG--T----TTGGTAG-CTTTTGGCTAGTTACACCATTTGATAGCTTG
328257 G
59 G
328258 TGGTTTGGAT
Statistics
Matches: 158, Mismatches: 6, Indels: 11
0.90 0.03 0.06
Matches are distributed among these distances:
106 26 0.16
107 17 0.11
108 76 0.48
109 1 0.01
113 34 0.22
114 4 0.03
ACGTcount: A:0.15, C:0.11, G:0.30, T:0.43
Consensus pattern (107 bp):
GCTTGGGGGTTTGTTATGGTTTGGTAGCTTTTGGCTAGTTACACCATTTGATAGCTTGGGGGTCT
GTTATGGCTTGGTAGCTTTTCGGCTAGTTATACCATTTGGTA
Found at i:334451 original size:2 final size:2
Alignment explanation
Indices: 334446--334529 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
334436 CAACAATTCA
334446 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
334488 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
334530 AACAGGTTAT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:335012 original size:12 final size:12
Alignment explanation
Indices: 334977--335017 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
334967 ATGTGCAACA
334977 CCATTTGCTGTT
1 CCATTTGCTGTT
**
334989 CCATTAACTGTT
1 CCATTTGCTGTT
*
335001 CCATTTGTTGTT
1 CCATTTGCTGTT
335013 CCATT
1 CCATT
335018 ACTTTTTACT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.15, C:0.24, G:0.12, T:0.49
Consensus pattern (12 bp):
CCATTTGCTGTT
Found at i:336249 original size:2 final size:2
Alignment explanation
Indices: 336242--336296 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
336232 AAAGAATGTA
336242 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
336284 CT CT CT CT CT CT C
1 CT CT CT CT CT CT C
336297 AACAATGCAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:344195 original size:2 final size:2
Alignment explanation
Indices: 344188--344238 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
344178 AGTTGCATTG
344188 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
344230 CT CT CT CT C
1 CT CT CT CT C
344239 CCCCCCACGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:355336 original size:25 final size:21
Alignment explanation
Indices: 355308--355362 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 21
355298 CCCCAACCAT
355308 CCATAAAGTGCATACCCTAACACTC
1 CCATAAAGTGC---CCCT-ACACTC
* *
355333 CCATAACGTGCCCCTACTCTC
1 CCATAAAGTGCCCCTACACTC
355354 CCATAAAGT
1 CCATAAAGT
355363 ACTGTTACTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 13 0.48
22 4 0.15
25 10 0.37
ACGTcount: A:0.31, C:0.38, G:0.09, T:0.22
Consensus pattern (21 bp):
CCATAAAGTGCCCCTACACTC
Found at i:355631 original size:21 final size:21
Alignment explanation
Indices: 355578--355834 Score: 90
Period size: 21 Copynumber: 11.7 Consensus size: 21
355568 TGTACCCTCT
355578 CTCCCATAGAGTA-CACTTACC
1 CTCCCATAGAGTATC-CTTACC
**
355599 CTCAAATAGAGTATCCTTACC
1 CTCCCATAGAGTATCCTTACC
* **
355620 CTCCCATGGAGTA-CCCCAGCC
1 CTCCCATAGAGTATCCTTA-CC
* * * *
355641 TTCCCATAGAGTAAAAACCCTAATC
1 CTCCCATAGAGT----ATCCTTACC
* *
355666 CTCCCATTGAGTATCCTTACT
1 CTCCCATAGAGTATCCTTACC
* **
355687 CTCCCATGGAGTA-CCCCAGCC
1 CTCCCATAGAGTATCCTTA-CC
* * *
355708 TTCCCATAGAGTAAATACCCTAATC
1 CTCCCATAGAGT--AT--CCTTACC
*
355733 CTCCCATAGAGTATCCTTACT
1 CTCCCATAGAGTATCCTTACC
* **
355754 CTCCCATGGAGTA-CCCCAGCC
1 CTCCCATAGAGTATCCTTA-CC
* * *
355775 TTCCCATAGAGTAGATACCCTAATC
1 CTCCCATAGAGT--AT--CCTTACC
* * * *
355800 CTCCCATAGGGTACCCTAACT
1 CTCCCATAGAGTATCCTTACC
355821 CTCCCATAGAGTAT
1 CTCCCATAGAGTAT
355835 TCTCACTCTC
Statistics
Matches: 170, Mismatches: 47, Indels: 38
0.67 0.18 0.15
Matches are distributed among these distances:
20 9 0.05
21 111 0.65
22 1 0.01
23 5 0.03
25 35 0.21
26 9 0.05
ACGTcount: A:0.27, C:0.35, G:0.12, T:0.25
Consensus pattern (21 bp):
CTCCCATAGAGTATCCTTACC
Done.