Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold501
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: 1397941
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 110142 characters in sequence are not A, C, G, or T
File 5 of 5
Found at i:1021410 original size:2 final size:2
Alignment explanation
Indices: 1021403--1021451 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1021393 AGATAGATAG
1021403 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1021445 GT GT GT G
1 GT GT GT G
1021452 CAAAAAGAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:1023437 original size:3 final size:3
Alignment explanation
Indices: 1023425--1023467 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
1023415 TAATTATAAA
* *
1023425 ATC ATT ATC ATC ATC ATC ATC ATA ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1023468 GTCCTCTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.37, C:0.28, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:1023556 original size:15 final size:16
Alignment explanation
Indices: 1023523--1023565 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
1023513 CTGATTACAT
1023523 TTGTCCGTTGTCTGTCG
1 TTGT-CGTTGTCTGTCG
1023540 TTGTCGTTGTC-GTCG
1 TTGTCGTTGTCTGTCG
*
1023555 TTGTCGATGTC
1 TTGTCGTTGTC
1023566 AACTTTTCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.56
16 7 0.28
17 4 0.16
ACGTcount: A:0.02, C:0.21, G:0.30, T:0.47
Consensus pattern (16 bp):
TTGTCGTTGTCTGTCG
Found at i:1024018 original size:166 final size:163
Alignment explanation
Indices: 1023734--1024344 Score: 711
Period size: 166 Copynumber: 3.7 Consensus size: 163
1023724 GGTATTTTTC
* * * * *** **
1023734 AAAAATCTTCTTCTCAAAAACTATTCGGCCTGAAAAGCTAAAACTTGTGTGGCGGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGACCAGAAAAGCT-CAACTTAAATGGTAGCATCCTCAGG
* * *
1023799 TAGTGGAGATTCAAGTCTGTTCAAATCATGGTCCCCGGGGGTAGGGAGGGGCCACAAGAAGGGGA
65 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAAG--GGGGA
1023864 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
128 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* *
1023900 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAATTTAAAATGGTAGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGACCAGAAAAGCTCAACTT-AAATGGTAGCATCCTCAGG
*
1023965 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTACGGTGGGGCCACAATTGGGGGA
65 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAA--GGGGGA
*
1024030 TCAAGTTTTACAAAGGAATATATAGAGAAAATCTTT
128 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
* * **** * **
1024066 AAAAATCTTCTTCTCAAAAACTATTTGACCA-AGAAAGCTCAAATTGGCGGGTAATCATCCTGTG
1 AAAAATCTTCTTCTCAAAAACTATTAGACCAGA-AAAGCTCAACTTAAATGGT-AGCATCCTCAG
* * * ** * *
1024130 ATAATGTCGATTCAAGTTTGTTCAAATCATGGTCCATGGGGGTAGGGCGGGGCCACAATGGTGGA
64 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAA-GGGGGA
* *
1024195 T-ACA-TTTT---T----ATATAGAGAGAAAATCTTC
128 TCA-AGTTTTACATAGGAATATATAGAGAAAATCTTT
* *
1024223 AAAAATCTTCTTCTCAAAAAATATTAGACCAGAAAAGCTCAACTTAAATTGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGACCAGAAAAGCTCAACTTAAA-TGGTAGCATCCTCAGG
* *
1024288 TAGTTTAGATTCAAGTTTGTTCAAATCATTGTCCCCGGGGGTAGGGTGGGGCCACAA
65 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAA
1024345 TGGGTGATAA
Statistics
Matches: 383, Mismatches: 54, Indels: 25
0.83 0.12 0.05
Matches are distributed among these distances:
157 115 0.30
158 3 0.01
164 5 0.01
165 16 0.04
166 243 0.63
168 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (163 bp):
AAAAATCTTCTTCTCAAAAACTATTAGACCAGAAAAGCTCAACTTAAATGGTAGCATCCTCAGGT
AGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAAGGGGGATCA
AGTTTTACATAGGAATATATAGAGAAAATCTTT
Found at i:1024452 original size:127 final size:128
Alignment explanation
Indices: 1024226--1024480 Score: 386
Period size: 127 Copynumber: 2.0 Consensus size: 128
1024216 AATCTTCAAA
* * * *
1024226 AATCTTCTTCTCAAAAAATATTAGACCAGAAAAGCTCAACTTAAATTGGAAGCATCCTCAGGTAG
1 AATCTTCTTCTCAAAAAATATAAGACCAGAAAAGCTCAAATTAAAGTGGAAGCATCCTCAGATAG
* *
1024291 TTTAGATTCAAGTTTGTTCAAATCATTGTCCCCGGGGGTAGGGTGGGGCCACAA-TGGGTGAT
66 TGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGTGAT
* ** * * **
1024353 AATCTTCTTCTCAAAAACTATAAGGTCAGGAATGCTCAAATTTGAGTGGAAGCATCCTCAGATAG
1 AATCTTCTTCTCAAAAAATATAAGACCAGAAAAGCTCAAATTAAAGTGGAAGCATCCTCAGATAG
1024418 TGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGTGAT
66 TGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGTGAT
1024481 CAAGTTTTAC
Statistics
Matches: 114, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
127 106 0.93
128 8 0.07
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (128 bp):
AATCTTCTTCTCAAAAAATATAAGACCAGAAAAGCTCAAATTAAAGTGGAAGCATCCTCAGATAG
TGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGTGAT
Found at i:1024626 original size:293 final size:284
Alignment explanation
Indices: 1024069--1024646 Score: 680
Period size: 293 Copynumber: 2.0 Consensus size: 284
1024059 AATCTTTAAA
** * * **
1024069 AATCTTCTTCTCAAAAACTATTTGACCAAGAAAGCTCAAATTGGCGGGTAATCATCCTGTGATAA
1 AATCTTCTTCTCAAAAACTATAAGACCAAGAAAGCTCAAATTGGAGGGTAAGCATCCTCAGATAA
* *
1024134 TGTCGATTCAAGTTTGTTCAAATCATGGTCCATGGGGGTAGGGCGGGGCCACAATGGTGGATACA
66 TGTAGATTCAAGTTTGTTCAAATCATGGTCCACGGGGGTAGGGCGGGGCCACAATGGTGGATACA
*
1024199 TTTTTATATAGAGAGAAAATCTTCAAAAATCTTCTTCTCAAAAAATATTAGACCAGAAAAGCTCA
131 TTTTTATATAGAGAGAAAATCTTCAAAAATCTTCTTCTCAAAAAATATTACACCAGAAAAGCTCA
* ** * * * * * * *
1024264 ACTTAAATTGGAAGCATCCTCAGGTAGTTTAGATTCAAGTTTGTTCAAATCATTGTCCCCGGGGG
196 AATTAAACGGGAACCATCCTCAGATAATGTAGATTCAAGTTCGTTCAAATCATGGTCCCCGGCGG
*
1024329 TAGGGTGGGGCCACAATGGGTGAT
261 TAGGGTGGGGCCACAATGGGGGAT
** * * *
1024353 AATCTTCTTCTCAAAAACTATAAGGTCAGGAATGCTCAAATTTGAGTGG-AAGCATCCTCAGATA
1 AATCTTCTTCTCAAAAACTATAAGACCAAGAAAGCTCAAATTGGAG-GGTAAGCATCCTCAGATA
* * *
1024417 GTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGG-GTGAT
65 ATGTAGATTCAAGTTTGTTCAAATCATGGTCCACGGGGGTAGGGCGGGGCCACAA-TGGTG-GAT
* * * *
1024481 -CAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTTCAC
128 AC-A-TTTT---T----ATATAGAGAGAAAATCTTCAAAAATCTTCTTCTCAAAAAATATTACAC
**
1024545 CA-AGAAAGCTCAAATT-GGCGGGTAACCATCCTCAGATAATGTAGATTCAAGTTCGTTCAAATC
184 CAGA-AAAGCTCAAATTAAACGGG-AACCATCCTCAGATAATGTAGATTCAAGTTCGTTCAAATC
*
1024608 ATGGTCCCTGGCGGTAGGGTGGGGCCACAATGGGGGAT
247 ATGGTCCCCGGCGGTAGGGTGGGGCCACAATGGGGGAT
1024646 A
1 A
1024647 CATTTTTATA
Statistics
Matches: 245, Mismatches: 35, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
284 102 0.42
285 9 0.04
286 4 0.02
289 1 0.00
292 3 0.01
293 126 0.51
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.28
Consensus pattern (284 bp):
AATCTTCTTCTCAAAAACTATAAGACCAAGAAAGCTCAAATTGGAGGGTAAGCATCCTCAGATAA
TGTAGATTCAAGTTTGTTCAAATCATGGTCCACGGGGGTAGGGCGGGGCCACAATGGTGGATACA
TTTTTATATAGAGAGAAAATCTTCAAAAATCTTCTTCTCAAAAAATATTACACCAGAAAAGCTCA
AATTAAACGGGAACCATCCTCAGATAATGTAGATTCAAGTTCGTTCAAATCATGGTCCCCGGCGG
TAGGGTGGGGCCACAATGGGGGAT
Found at i:1024627 original size:166 final size:162
Alignment explanation
Indices: 1024389--1024870 Score: 488
Period size: 157 Copynumber: 3.0 Consensus size: 162
1024379 CAGGAATGCT
* * * * *
1024389 CAAATTTGAGTGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGG
1 CAAATCTGAGGGGAACCATCCTCAGATAGTGTAGATTCAAGTTCGTTCAAATCATGGT-CCCGGC
* *
1024454 GGTAGGGTGGGGCCACAATTGGGTGATCAAGTTTTACATAGGAATATATAGAGAAAATCTTTAAA
65 GGTAGGGTGGGGCCACAA-TGGGGGAT-AA-TTTTACATAGGAATATATAGAGAAAATCTTAAAA
*
1024519 AATCTTCTTCTCAAAAACTATTTCACCAAGAAAGCT
127 AATCTTCTTCTCAAAAACTATTTCACCAAGAAAGCC
*
1024555 CAAAT-TG-GCGGGTAACCATCCTCAGATAATGTAGATTCAAGTTCGTTCAAATCATGGTCCCTG
1 CAAATCTGAG-GGG-AACCATCCTCAGATAGTGTAGATTCAAGTTCGTTCAAATCATGGTCCC-G
*
1024618 GCGGTAGGGTGGGGCCACAATGGGGGATACATTTT---T----ATACATAGAGAAAATCTCTAAA
63 GCGGTAGGGTGGGGCCACAATGGGGGATA-ATTTTACATAGGAATATATAGAGAAAATCT-TAAA
*
1024676 AAATCTTCTTCTC-AAAACTA-TTCAGCCAGGAAAGCC
126 AAATCTTCTTCTCAAAAACTATTTCA-CCAAGAAAGCC
* * * * * * * * * * * *
1024712 CAAATCTGAGTGGAAGCAT-TTCTAAATCGTATAGATTCAAGTTGGTTAAAATAATAGT-CCAGT
1 CAAATCTGAGGGGAACCATCCTC-AGATAGTGTAGATTCAAGTTCGTTCAAATCATGGTCCCGGC
* * * * *
1024775 GGTATGGTGAGGCCACAGTGGGGGATGAATTTTTACATAGGAATATATACAGAAAATCTTCAAAA
65 GGTAGGGTGGGGCCACAATGGGGGAT-AA-TTTTACATAGGAATATATAGAGAAAATCTTAAAAA
*
1024840 ATCTTCTTCTCAAAAACTATTTGACC-AGAAA
128 ATCTTCTTCTCAAAAACTATTTCACCAAGAAA
1024871 AGCTATAACT
Statistics
Matches: 265, Mismatches: 31, Indels: 44
0.78 0.09 0.13
Matches are distributed among these distances:
155 25 0.09
156 13 0.05
157 69 0.26
158 20 0.08
159 2 0.01
161 1 0.00
162 20 0.08
163 24 0.09
164 9 0.03
165 15 0.06
166 67 0.25
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (162 bp):
CAAATCTGAGGGGAACCATCCTCAGATAGTGTAGATTCAAGTTCGTTCAAATCATGGTCCCGGCG
GTAGGGTGGGGCCACAATGGGGGATAATTTTACATAGGAATATATAGAGAAAATCTTAAAAAATC
TTCTTCTCAAAAACTATTTCACCAAGAAAGCC
Found at i:1024748 original size:157 final size:160
Alignment explanation
Indices: 1024353--1024860 Score: 466
Period size: 166 Copynumber: 3.1 Consensus size: 160
1024343 AATGGGTGAT
* * *
1024353 AATCTTCTTCTCAAAAACTA-TAAGGTCAGGAATGCTCAAATTTGAGTGGAAGCATCCTCAGATA
1 AATCTTCTTCTCAAAAACTATTCA-GCCAGGAAAGCTCAAA-TTGAGTGGAAGCATCCTCAGATA
* * *
1024417 GTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGTGATC
64 GTGTAGATTCAAGTTCGTTCAAATCATGGTCCCCGGCGGTAGGGTGGGGCCACAATTGGGGGATC
* *
1024482 AAGTTTTACATAGGAATATATAGAGAAAATCTTTAAA
129 AAGTTTT--AT---AATACATAGAGAAAATCTTAAAA
* * *
1024519 AATCTTCTTCTCAAAAACTATTTCA-CCAAGAAAGCTCAAATTG-GCGGGTAACCATCCTCAGAT
1 AATCTTCTTCTCAAAAACTA-TTCAGCCAGGAAAGCTCAAATTGAG-TGG-AAGCATCCTCAGAT
* *
1024582 AATGTAGATTCAAGTTCGTTCAAATCATGGTCCCTGGCGGTAGGGTGGGGCCACAA-TGGGGGAT
63 AGTGTAGATTCAAGTTCGTTCAAATCATGGTCCCCGGCGGTAGGGTGGGGCCACAATTGGGGGAT
1024646 -ACA-TTTT-T-ATACATAGAGAAAATCTCTAAAA
128 CA-AGTTTTATAATACATAGAGAAAATCT-TAAAA
* * * *
1024677 AATCTTCTTCTC-AAAACTATTCAGCCAGGAAAGCCCAAATCTGAGTGGAAGCAT-TTCTAAATC
1 AATCTTCTTCTCAAAAACTATTCAGCCAGGAAAGCTCAAAT-TGAGTGGAAGCATCCTC-AGATA
* * * * * * * * * * *
1024740 GTATAGATTCAAGTTGGTTAAAATAATAGT--CCAGTGGTATGGTGAGGCCAC-AGTGGGGGATG
64 GTGTAGATTCAAGTTCGTTCAAATCATGGTCCCCGGCGGTAGGGTGGGGCCACAATTGGGGGATC
* * * *
1024802 AATTTTTACATAGGAATATATACAGAAAATCTTCAAA
129 AAGTTTT--AT---AATACATAGAGAAAATCTTAAAA
1024839 AATCTTCTTCTCAAAAACTATT
1 AATCTTCTTCTCAAAAACTATT
1024861 TGACCAGAAA
Statistics
Matches: 287, Mismatches: 34, Indels: 45
0.78 0.09 0.12
Matches are distributed among these distances:
154 1 0.00
155 25 0.09
156 11 0.04
157 69 0.24
158 20 0.07
159 2 0.01
161 1 0.00
162 16 0.06
163 24 0.08
164 6 0.02
165 13 0.05
166 97 0.34
168 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (160 bp):
AATCTTCTTCTCAAAAACTATTCAGCCAGGAAAGCTCAAATTGAGTGGAAGCATCCTCAGATAGT
GTAGATTCAAGTTCGTTCAAATCATGGTCCCCGGCGGTAGGGTGGGGCCACAATTGGGGGATCAA
GTTTTATAATACATAGAGAAAATCTTAAAA
Found at i:1024749 original size:450 final size:450
Alignment explanation
Indices: 1023903--1024763 Score: 1309
Period size: 450 Copynumber: 1.9 Consensus size: 450
1023893 AATCTTTAAA
* * *
1023903 AATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAATTTAAAATGGTAGCATCCTCAGGTAG
1 AATCTTCTTCTCAAAAACTATAAGGCCAGAAAAGCTCAATTTAAAATGGAAGCATCCTCAGATAG
1023968 TGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTACGGTGGGGCCACAATTGGGGGATCA
66 TGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTACGGTGGGGCCACAATTGGGGGATCA
*
1024033 AGTTTTACAAAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTTGACCAA
131 AGTTTTACAAAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTTCACCAA
* ** * *
1024098 GAAAGCTCAAATTGGCGGGTAATCATCCTGTGATAATGTCGATTCAAGTTTGTTCAAATCATGGT
196 GAAAGCTCAAATTGGCGGGTAACCATCCTCAGATAATGTAGATTCAAGTTCGTTCAAATCATGGT
* * * *
1024163 CCATGGGGGTAGGGCGGGGCCACAATGGTGGATACATTTTTATATAGAGAGAAAATCTTCAAAAA
261 CCATGGCGGTAGGGCGGGGCCACAATGGGGGATACATTTTTATACAGAGAGAAAATCTTAAAAAA
* * * ** *
1024228 TCTTCTTCTCAAAAAATATTAGACCAGAAAAGCTCAACTTAAATTGGAAGCATCCTCAGGTAGTT
326 TCTTCTTCTCAAAAAATATTAGACCAGAAAAGCCCAAATTAAAGTGGAAGCATCCTCAAATAGTA
* *
1024293 TAGATTCAAGTTTGTTCAAATCATTGTCCCCGGGGGTAGGGTGGGGCCACAATGGGTGAT
391 TAGATTCAAGTTGGTTAAAATCATTGTCCCCGGGGGTAGGGTGGGGCCACAATGGGTGAT
* * * * *
1024353 AATCTTCTTCTCAAAAACTATAAGGTCAGGAATGCTCAAATTT-GAGTGGAAGCATCCTCAGATA
1 AATCTTCTTCTCAAAAACTATAAGGCCAGAAAAGCTC-AATTTAAAATGGAAGCATCCTCAGATA
* *
1024417 GTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGGTGATC
65 GTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTACGGTGGGGCCACAATTGGGGGATC
*
1024482 AAGTTTTACATAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTTCACCA
130 AAGTTTTACAAAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTTCACCA
1024547 AGAAAGCTCAAATTGGCGGGTAACCATCCTCAGATAATGTAGATTCAAGTTCGTTCAAATCATGG
195 AGAAAGCTCAAATTGGCGGGTAACCATCCTCAGATAATGTAGATTCAAGTTCGTTCAAATCATGG
* * *
1024612 TCCCTGGCGGTAGGGTGGGGCCACAATGGGGGATACATTTTTATACATAGAGAAAATCTCTAAAA
260 TCCATGGCGGTAGGGCGGGGCCACAATGGGGGATACATTTTTATACAGAGAGAAAATCT-TAAAA
* * * *
1024677 AATCTTCTTCTC-AAAACTATTCAG-CCAGGAAAGCCCAAATCT-GAGTGGAAGCAT-TTCTAAA
324 AATCTTCTTCTCAAAAAATATT-AGACCAGAAAAGCCCAAAT-TAAAGTGGAAGCATCCTC-AAA
*
1024738 TCGTATAGATTCAAGTTGGTTAAAAT
386 TAGTATAGATTCAAGTTGGTTAAAAT
1024764 AATAGTCCAG
Statistics
Matches: 369, Mismatches: 37, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
449 2 0.01
450 343 0.93
451 24 0.07
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (450 bp):
AATCTTCTTCTCAAAAACTATAAGGCCAGAAAAGCTCAATTTAAAATGGAAGCATCCTCAGATAG
TGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTACGGTGGGGCCACAATTGGGGGATCA
AGTTTTACAAAGGAATATATAGAGAAAATCTTTAAAAATCTTCTTCTCAAAAACTATTTCACCAA
GAAAGCTCAAATTGGCGGGTAACCATCCTCAGATAATGTAGATTCAAGTTCGTTCAAATCATGGT
CCATGGCGGTAGGGCGGGGCCACAATGGGGGATACATTTTTATACAGAGAGAAAATCTTAAAAAA
TCTTCTTCTCAAAAAATATTAGACCAGAAAAGCCCAAATTAAAGTGGAAGCATCCTCAAATAGTA
TAGATTCAAGTTGGTTAAAATCATTGTCCCCGGGGGTAGGGTGGGGCCACAATGGGTGAT
Found at i:1027972 original size:14 final size:14
Alignment explanation
Indices: 1027955--1027985 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1027945 TATGCAAAGG
*
1027955 TCAATAGGTCAATA
1 TCAAAAGGTCAATA
1027969 TCAAAAGGTCAATA
1 TCAAAAGGTCAATA
1027983 TCA
1 TCA
1027986 TAAAATATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (14 bp):
TCAAAAGGTCAATA
Found at i:1028184 original size:14 final size:14
Alignment explanation
Indices: 1028167--1028197 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1028157 TATGCAAAGG
*
1028167 TCAATAGGTCAATA
1 TCAAAAGGTCAATA
1028181 TCAAAAGGTCAATA
1 TCAAAAGGTCAATA
1028195 TCA
1 TCA
1028198 TAAAATATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (14 bp):
TCAAAAGGTCAATA
Found at i:1028252 original size:212 final size:211
Alignment explanation
Indices: 1027883--1028302 Score: 831
Period size: 212 Copynumber: 2.0 Consensus size: 211
1027873 GTCAGTAAAG
1027883 CCGGACGCATTAATATAAACAAGATCACCGATGTTTTCATGTCTGTGAAAACTTTCCATAAATAT
1 CCGGACGCATTAATATAAACAAGATCACCGATGTTTTCATGTCTGTGAAAACTTTCCATAAATAT
1027948 GCAAAGGTCAATAGGTCAATATCAAAAGGTCAATATCATAAAATATAGGTTTTTGACCCAGGTAT
66 GCAAAGGTCAATAGGTCAATATCAAAAGGTCAATATCATAAAATATAGGTTTTTGACCCAGGTAT
1028013 TTGAAAGTGAAAAAACACTTCAATAGCACTACAATCGAAGTGTAAAAGTTACCAGAATTTGTGCC
131 TTGAAAGTGAAAAAACACTTCAATAGCACTACAATCGAAGTGTAAAAGTTACCAGAATTTGTGCC
1028078 CCCCCCCTCCTCCCCC
196 CCCCCCCTCCTCCCCC
1028094 CCNGGACGCATTAATATAAACAAGATCACCGATGTTTTCATGTCTGTGAAAACTTTCCATAAATA
1 CC-GGACGCATTAATATAAACAAGATCACCGATGTTTTCATGTCTGTGAAAACTTTCCATAAATA
1028159 TGCAAAGGTCAATAGGTCAATATCAAAAGGTCAATATCATAAAATATAGGTTTTTGACCCAGGTA
65 TGCAAAGGTCAATAGGTCAATATCAAAAGGTCAATATCATAAAATATAGGTTTTTGACCCAGGTA
1028224 TTTGAAAGTGAAAAAACACTTCAATAGCACTACAATCGAAGTGTAAAAGTTACCAGAATTTGTGC
130 TTTGAAAGTGAAAAAACACTTCAATAGCACTACAATCGAAGTGTAAAAGTTACCAGAATTTGTGC
1028289 CCCCCCCCTCCTCC
195 CCCCCCCCTCCTCC
1028303 NNNNNNNNNN
Statistics
Matches: 208, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
211 2 0.01
212 206 0.99
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (211 bp):
CCGGACGCATTAATATAAACAAGATCACCGATGTTTTCATGTCTGTGAAAACTTTCCATAAATAT
GCAAAGGTCAATAGGTCAATATCAAAAGGTCAATATCATAAAATATAGGTTTTTGACCCAGGTAT
TTGAAAGTGAAAAAACACTTCAATAGCACTACAATCGAAGTGTAAAAGTTACCAGAATTTGTGCC
CCCCCCCTCCTCCCCC
Found at i:1030688 original size:9 final size:9
Alignment explanation
Indices: 1030676--1030708 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
1030666 TCCTCCGGCA
1030676 CCACCTAGT
1 CCACCTAGT
1030685 CCACCTAGT
1 CCACCTAGT
1030694 CCACCTAGT
1 CCACCTAGT
1030703 CCACCT
1 CCACCT
1030709 CCTACCAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.21, C:0.48, G:0.09, T:0.21
Consensus pattern (9 bp):
CCACCTAGT
Found at i:1030736 original size:33 final size:33
Alignment explanation
Indices: 1030694--1030762 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
1030684 TCCACCTAGT
*
1030694 CCACCTAGTCCACCTCCTACCAATCCTCCGGCA
1 CCACCTAGTCCACCTCCTACCAATCCTCCGCCA
* *
1030727 CCACCTAGTCCACCTCCTATCGATCCTCCGCCA
1 CCACCTAGTCCACCTCCTACCAATCCTCCGCCA
1030760 CCA
1 CCA
1030763 GCACCTAGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.20, C:0.52, G:0.09, T:0.19
Consensus pattern (33 bp):
CCACCTAGTCCACCTCCTACCAATCCTCCGCCA
Found at i:1030984 original size:24 final size:24
Alignment explanation
Indices: 1030940--1030989 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 24
1030930 CTGAAGCATG
1030940 AAAATTAAATAAATATTTTTTTTAA
1 AAAATTAAAT-AATATTTTTTTTAA
1030965 NAAAATTAAAT-ATATTTTTTTTAA
1 -AAAATTAAATAATATTTTTTTTAA
1030989 A
1 A
1030990 TCAAAATTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 1 0.04
24 13 0.54
26 10 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATTAAATAATATTTTTTTTAA
Found at i:1030995 original size:26 final size:25
Alignment explanation
Indices: 1030940--1030997 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 25
1030930 CTGAAGCATG
*
1030940 AAAATTAAATAAATATTTTTTTTAAN
1 AAAATTAAAT-AATATTTTTTTTAAC
1030966 AAAATTAAAT-ATATTTTTTTTAAATC
1 AAAATTAAATAATATTTTTTTT-AA-C
1030992 AAAATT
1 AAAATT
1030998 CGTAACAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 11 0.38
25 2 0.07
26 16 0.55
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
AAAATTAAATAATATTTTTTTTAAC
Found at i:1031775 original size:29 final size:29
Alignment explanation
Indices: 1031738--1031793 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1031728 TTAATAACTC
* *
1031738 CATTTTGAAGAAGCAAGGGAAGATAACAA
1 CATTATGAAGAAGCAAGGGAAAATAACAA
*
1031767 CATTATGAAGGAGCAAGGGAAAATAAC
1 CATTATGAAGAAGCAAGGGAAAATAAC
1031794 TCATTTAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.48, C:0.11, G:0.25, T:0.16
Consensus pattern (29 bp):
CATTATGAAGAAGCAAGGGAAAATAACAA
Found at i:1036859 original size:2 final size:2
Alignment explanation
Indices: 1036852--1036907 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1036842 TGTTTTTAAC
1036852 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
1036894 CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT
1036908 GCTTTCCATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1042838 original size:114 final size:114
Alignment explanation
Indices: 1042638--1042976 Score: 678
Period size: 114 Copynumber: 3.0 Consensus size: 114
1042628 ATTATTTGAA
1042638 ATTTTGCAGAGTGTTAATTCAGACTCGAAAGAATAATCAAATCATATCTGCTATCTGATTTAATA
1 ATTTTGCAGAGTGTTAATTCAGACTCGAAAGAATAATCAAATCATATCTGCTATCTGATTTAATA
1042703 TTCATCATTTCAAGTAAACATATTTTGCAAAATGAAATGTTTATATTTC
66 TTCATCATTTCAAGTAAACATATTTTGCAAAATGAAATGTTTATATTTC
1042752 ATTTTGCAGAGTGTTAATTCAGACTCGAAAGAATAATCAAATCATATCTGCTATCTGATTTAATA
1 ATTTTGCAGAGTGTTAATTCAGACTCGAAAGAATAATCAAATCATATCTGCTATCTGATTTAATA
1042817 TTCATCATTTCAAGTAAACATATTTTGCAAAATGAAATGTTTATATTTC
66 TTCATCATTTCAAGTAAACATATTTTGCAAAATGAAATGTTTATATTTC
1042866 ATTTTGCAGAGTGTTAATTCAGACTCGAAAGAATAATCAAATCATATCTGCTATCTGATTTAATA
1 ATTTTGCAGAGTGTTAATTCAGACTCGAAAGAATAATCAAATCATATCTGCTATCTGATTTAATA
1042931 TTCATCATTTCAAGTAAACATATTTTGCAAAATGAAATGTTTATAT
66 TTCATCATTTCAAGTAAACATATTTTGCAAAATGAAATGTTTATAT
1042977 GTTTATGTTT
Statistics
Matches: 225, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 225 1.00
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (114 bp):
ATTTTGCAGAGTGTTAATTCAGACTCGAAAGAATAATCAAATCATATCTGCTATCTGATTTAATA
TTCATCATTTCAAGTAAACATATTTTGCAAAATGAAATGTTTATATTTC
Found at i:1047367 original size:6 final size:6
Alignment explanation
Indices: 1047356--1047382 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1047346 TTAAAAAGTT
1047356 AATGAC AATGAC AATGAC AATGAC AAT
1 AATGAC AATGAC AATGAC AATGAC AAT
1047383 TTCTTTATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.19
Consensus pattern (6 bp):
AATGAC
Found at i:1064705 original size:20 final size:20
Alignment explanation
Indices: 1064681--1065092 Score: 401
Period size: 20 Copynumber: 18.8 Consensus size: 20
1064671 TCGCTGTGAG
*
1064681 GATCTCCTCACAGCGACATG
1 GATCTCCTCACAGCGACATA
1064701 GATCTCCTCACAGCGACATA
1 GATCTCCTCACAGCGACATA
*
1064721 AATCTCCTCACAGCGACATA
1 GATCTCCTCACAGCGACATA
*
1064741 GATCCCCTCACGGCGACAGCGACATA
1 GAT---CTC-C-TC-ACAGCGACATA
1064767 GATCTCCTCACAGCGACAGCAACATA
1 GATCTCCTCACA--G-C-G--ACATA
1064793 GATCTCCTCACAGCGACAGCAACATA
1 GATCTCCTCACA--G-C-G--ACATA
*
1064819 GATCTCCTCACAGCGACATT
1 GATCTCCTCACAGCGACATA
1064839 GATCTCCTCACAGCGACATA
1 GATCTCCTCACAGCGACATA
1064859 GATCTCCTCACAGCGACAGCGACATA
1 GATCTCCT-----C-ACAGCGACATA
*
1064885 GATTTCCTCACAGCGACATA
1 GATCTCCTCACAGCGACATA
1064905 GATCTCCTCACAGCGACAGCGACATA
1 GATCTCCT-----C-ACAGCGACATA
1064931 GATCTCCTCACAGCGACATA
1 GATCTCCTCACAGCGACATA
1064951 GATCTCCTCACAGCGACATA
1 GATCTCCTCACAGCGACATA
*
1064971 AATCTCCTCACAGCGACATA
1 GATCTCCTCACAGCGACATA
*
1064991 GATCTACTCACAGCGACATA
1 GATCTCCTCACAGCGACATA
* *
1065011 AATCTCCTCATAGCGACATA
1 GATCTCCTCACAGCGACATA
*
1065031 GTTCTCCTCACAGCGACAGCGACATA
1 GATCTCCT-----C-ACAGCGACATA
*
1065057 GATCTCCTCACAGAGACATA
1 GATCTCCTCACAGCGACATA
1065077 GATCTCCTCACAGCGA
1 GATCTCCTCACAGCGA
1065093 AATATCAAAT
Statistics
Matches: 341, Mismatches: 21, Indels: 60
0.81 0.05 0.14
Matches are distributed among these distances:
20 208 0.61
21 4 0.01
22 3 0.01
23 8 0.02
24 3 0.01
25 4 0.01
26 111 0.33
ACGTcount: A:0.31, C:0.34, G:0.16, T:0.19
Consensus pattern (20 bp):
GATCTCCTCACAGCGACATA
Found at i:1064766 original size:26 final size:26
Alignment explanation
Indices: 1064730--1064948 Score: 258
Period size: 26 Copynumber: 9.1 Consensus size: 26
1064720 AAATCTCCTC
* *
1064730 ACAGCGACATAGATCCCCTCACGGCG
1 ACAGCGACATAGATCTCCTCACAGCG
1064756 ACAGCGACATAGATCTCCTCACAGCG
1 ACAGCGACATAGATCTCCTCACAGCG
*
1064782 ACAGCAACATAGATCTCCTCACAGCG
1 ACAGCGACATAGATCTCCTCACAGCG
*
1064808 ACAGCAACATAGATCTCCT-----C-
1 ACAGCGACATAGATCTCCTCACAGCG
*
1064828 ACAGCGACATTGATCTCCTCAC----
1 ACAGCGACATAGATCTCCTCACAGCG
1064850 --AGCGACATAGATCTCCTCACAGCG
1 ACAGCGACATAGATCTCCTCACAGCG
*
1064874 ACAGCGACATAGAT-T--TC-C-TC-
1 ACAGCGACATAGATCTCCTCACAGCG
1064894 ACAGCGACATAGATCTCCTCACAGCG
1 ACAGCGACATAGATCTCCTCACAGCG
1064920 ACAGCGACATAGATCTCCTCACAGCG
1 ACAGCGACATAGATCTCCTCACAGCG
1064946 ACA
1 ACA
1064949 TAGATCTCCT
Statistics
Matches: 170, Mismatches: 8, Indels: 30
0.82 0.04 0.14
Matches are distributed among these distances:
20 50 0.29
21 3 0.02
22 1 0.01
23 4 0.02
24 1 0.01
25 2 0.01
26 109 0.64
ACGTcount: A:0.31, C:0.35, G:0.17, T:0.17
Consensus pattern (26 bp):
ACAGCGACATAGATCTCCTCACAGCG
Found at i:1065050 original size:66 final size:66
Alignment explanation
Indices: 1064681--1065092 Score: 429
Period size: 66 Copynumber: 6.2 Consensus size: 66
1064671 TCGCTGTGAG
* *
1064681 GATCTCCTCACAGCGACATGGATCTCCT-----C-ACAGCGACATAAATCTCCTCACAGCGACAT
1 GATCTCCTCACAGCGACATAGATCTCCTCACAGCGACAGCGACATAGATCTCCTCACAGCGACAT
1064740 A
66 A
* *
1064741 GATCCCCTCACGGCGACAGCGACATAGATCTCCTCACAGCGACAGCAACATAGATCTCCTCACAG
1 GAT---CTC-C-TC-ACAGCGACATAGATCTCCTCACAGCGACAGCGACATAGATCTCCTCACA-
1064806 CGACAGCAACATA
59 -G-C-G--ACATA
* ** ** * **
1064819 GATCTCCTCACAGCGACATTGATCTCCTCACAGCGACATAGATC-T-CCTCACAGCGACAGCGAC
1 GATCTCCTCACAGCGACATAGATCTCCTCACAGCGACAGCGA-CATAGATCTCCTC-ACAGCGAC
1064882 ATA
64 ATA
*
1064885 GATTTCCTCACAGCGACATAGATCTCCTCACAGCGACAGCGACATAGATCTCCTCACAGCGACAT
1 GATCTCCTCACAGCGACATAGATCTCCTCACAGCGACAGCGACATAGATCTCCTCACAGCGACAT
1064950 A
66 A
* *
1064951 GATCTCCTCACAGCGACATAAATCTCCT-----C-ACAGCGACATAGATCTACTCACAGCGACAT
1 GATCTCCTCACAGCGACATAGATCTCCTCACAGCGACAGCGACATAGATCTCCTCACAGCGACAT
1065010 A
66 A
* * * *
1065011 AATCTCCTCATAGCGACATAGTTCTCCTCACAGCGACAGCGACATAGATCTCCTCACAGAGACAT
1 GATCTCCTCACAGCGACATAGATCTCCTCACAGCGACAGCGACATAGATCTCCTCACAGCGACAT
1065076 A
66 A
1065077 GATCTCCTCACAGCGA
1 GATCTCCTCACAGCGA
1065093 AATATCAAAT
Statistics
Matches: 290, Mismatches: 34, Indels: 50
0.78 0.09 0.13
Matches are distributed among these distances:
60 57 0.20
61 1 0.00
63 3 0.01
64 1 0.00
65 3 0.01
66 142 0.49
67 4 0.01
68 1 0.00
69 1 0.00
70 1 0.00
71 5 0.02
72 54 0.19
73 2 0.01
74 2 0.01
75 4 0.01
76 1 0.00
78 8 0.03
ACGTcount: A:0.31, C:0.34, G:0.16, T:0.19
Consensus pattern (66 bp):
GATCTCCTCACAGCGACATAGATCTCCTCACAGCGACAGCGACATAGATCTCCTCACAGCGACAT
A
Found at i:1065075 original size:46 final size:46
Alignment explanation
Indices: 1064690--1065092 Score: 425
Period size: 46 Copynumber: 9.0 Consensus size: 46
1064680 GGATCTCCTC
* *
1064690 ACAGCGACATGGATCTCCTCACAGCGACATAAATCTCCTCACAGCG
1 ACAGCGACATAGATCTCCTCACAGCGACATAGATCTCCTCACAGCG
* * *** *
1064736 ACA--TAGAT-CCCCTCACGGCGACAGCGACATAGATCTCCTCACAGCG
1 ACAGCGACATAGATCTC-C-TC-ACAGCGACATAGATCTCCTCACAGCG
*
1064782 ACAGCAACATAGATCTCCTCACAGCGACAGCAACATAGATCTCCT-----C-
1 ACAGCGACATAGATCTCCTCACA--G-C-G--ACATAGATCTCCTCACAGCG
*
1064828 ACAGCGACATTGATCTCCTCACAGCGACATAGATCTCCTCACAGCG
1 ACAGCGACATAGATCTCCTCACAGCGACATAGATCTCCTCACAGCG
*
1064874 ACAGCGACATAGATTTCCTCACAGCGACATAGATCTCCTCACAGCG
1 ACAGCGACATAGATCTCCTCACAGCGACATAGATCTCCTCACAGCG
1064920 ACAGCGACATAGATCTCCTCACAGCGACATAGATCTCCT-----C-
1 ACAGCGACATAGATCTCCTCACAGCGACATAGATCTCCTCACAGCG
* *
1064960 ACAGCGACATAAATCTCCTCACAGCGACATAGA--T-CT-AC-TC-
1 ACAGCGACATAGATCTCCTCACAGCGACATAGATCTCCTCACAGCG
* * *
1065000 ACAGCGACATAAATCTCCTCATAGCGACATAGTTCTCCTCACAGCG
1 ACAGCGACATAGATCTCCTCACAGCGACATAGATCTCCTCACAGCG
*
1065046 ACAGCGACATAGATCTCCTCACAGAGACATAGATCTCCTCACAGCG
1 ACAGCGACATAGATCTCCTCACAGCGACATAGATCTCCTCACAGCG
1065092 A
1 A
1065093 AATATCAAAT
Statistics
Matches: 304, Mismatches: 26, Indels: 54
0.79 0.07 0.14
Matches are distributed among these distances:
37 2 0.01
38 1 0.00
40 77 0.25
41 1 0.00
42 2 0.01
43 6 0.02
44 7 0.02
45 3 0.01
46 180 0.59
47 2 0.01
48 5 0.02
49 4 0.01
50 1 0.00
52 13 0.04
ACGTcount: A:0.31, C:0.34, G:0.16, T:0.19
Consensus pattern (46 bp):
ACAGCGACATAGATCTCCTCACAGCGACATAGATCTCCTCACAGCG
Found at i:1067422 original size:18 final size:17
Alignment explanation
Indices: 1067383--1067419 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
1067373 CAATTTTTTT
1067383 TTATTTATTTATTTTAA
1 TTATTTATTTATTTTAA
1067400 TTATTTCATTTATTATTAA
1 TTATTT-ATTTATT-TTAA
1067419 T
1 T
1067420 ATTCAGGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 7 0.39
19 5 0.28
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATTTATTTATTTTAA
Found at i:1080474 original size:23 final size:23
Alignment explanation
Indices: 1080448--1080501 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
1080438 GTTTTGGTCA
1080448 ATTTATTTGAAATATCCAAAATG
1 ATTTATTTGAAATATCCAAAATG
1080471 ATTTATTTGAAATATCCAAAATG
1 ATTTATTTGAAATATCCAAAATG
*
1080494 ATATATTT
1 ATTTATTT
1080502 ACCATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (23 bp):
ATTTATTTGAAATATCCAAAATG
Found at i:1081967 original size:16 final size:16
Alignment explanation
Indices: 1081942--1081972 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1081932 GAATTTCTTA
*
1081942 TACGGTTATAACGAAT
1 TACGGATATAACGAAT
1081958 TACGGATATAACGAA
1 TACGGATATAACGAA
1081973 GTAATTTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (16 bp):
TACGGATATAACGAAT
Found at i:1087000 original size:39 final size:39
Alignment explanation
Indices: 1086946--1087047 Score: 159
Period size: 39 Copynumber: 2.6 Consensus size: 39
1086936 GATTCTTCTT
*
1086946 TAACGTCTTCCTTCTTTTCTGCTTTAGAAGATCCATCTC
1 TAACGTCTTCCTTCTTTTCTGCTTTAGAAGATCCATCTA
* *
1086985 TAACGTCTTCCTTCTTTTCTGCTTTAGCATATCCATCTA
1 TAACGTCTTCCTTCTTTTCTGCTTTAGAAGATCCATCTA
* *
1087024 TAATGTCTTCTTTCTTTTCTGCTT
1 TAACGTCTTCCTTCTTTTCTGCTT
1087048 GCACGGGTGT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.16, C:0.26, G:0.09, T:0.49
Consensus pattern (39 bp):
TAACGTCTTCCTTCTTTTCTGCTTTAGAAGATCCATCTA
Found at i:1089508 original size:28 final size:28
Alignment explanation
Indices: 1089466--1089519 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
1089456 AATATTCTTA
* *
1089466 TTTAATCATATCCAGAATTTGTAGTTCG
1 TTTAATCATACCCAGAATTTGAAGTTCG
1089494 TTTAATCATACCCAGAATTTGAAGTT
1 TTTAATCATACCCAGAATTTGAAGTT
1089520 TTGCTGTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (28 bp):
TTTAATCATACCCAGAATTTGAAGTTCG
Found at i:1095171 original size:22 final size:25
Alignment explanation
Indices: 1095127--1095171 Score: 69
Period size: 22 Copynumber: 1.9 Consensus size: 25
1095117 CTAAGTCCTT
1095127 GTATATATAATTTTAGTAAATTATA
1 GTATATATAATTTTAGTAAATTATA
1095152 GTATA-ATAA-TTTA-TAAATTA
1 GTATATATAATTTTAGTAAATTA
1095172 AACAACAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.35
23 4 0.20
24 4 0.20
25 5 0.25
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (25 bp):
GTATATATAATTTTAGTAAATTATA
Found at i:1097218 original size:2 final size:2
Alignment explanation
Indices: 1097211--1097278 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
1097201 TATGGAGGGG
1097211 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
1097253 GA GA GA GA GA G- GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1097279 GAGCGCGAGA
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1117699 original size:42 final size:43
Alignment explanation
Indices: 1117640--1117837 Score: 256
Period size: 42 Copynumber: 4.7 Consensus size: 43
1117630 CAAATTAATA
* * *
1117640 GTACAGTGCCGTACAGTGGGGTACAGTGCTGGTCAGT-GCCCG
1 GTACAGTGGCGTACAGTGGGGTACAGTGCTGGTCAGTAGCACT
*
1117682 GTACAGTGGCGTACAGTGGGGTACAGTGCTGGTCAGT-GCCCT
1 GTACAGTGGCGTACAGTGGGGTACAGTGCTGGTCAGTAGCACT
*** *
1117724 GTACAGTGGCGTACAGTGGGGTACAGTGGAAGTCAGTAGGACT
1 GTACAGTGGCGTACAGTGGGGTACAGTGCTGGTCAGTAGCACT
* * * *
1117767 GTACAGTGGTGTACAGTGGGATACAGTGCTGTTCAGTAGCAAT
1 GTACAGTGGCGTACAGTGGGGTACAGTGCTGGTCAGTAGCACT
* *
1117810 GTACAGTGGGGTACAGTGGGATACAGTG
1 GTACAGTGGCGTACAGTGGGGTACAGTG
1117838 GAAGTCAGTG
Statistics
Matches: 139, Mismatches: 16, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
42 74 0.53
43 65 0.47
ACGTcount: A:0.22, C:0.17, G:0.38, T:0.23
Consensus pattern (43 bp):
GTACAGTGGCGTACAGTGGGGTACAGTGCTGGTCAGTAGCACT
Found at i:1117709 original size:32 final size:31
Alignment explanation
Indices: 1117640--1117752 Score: 108
Period size: 32 Copynumber: 3.6 Consensus size: 31
1117630 CAAATTAATA
* *
1117640 GTACAGTGCC-GTACAGTGGGGTACAGTGCTG
1 GTACAGTGCCGGTACAGTGGCGTACAGTG-GG
1117671 GT-CAGTGCCCGGTACAGTGGCGTACAGTGGG
1 GTACAGTG-CCGGTACAGTGGCGTACAGTGGG
* * *
1117702 GTACAGTGCTGGT-CAGTGCCCTGTACAGTGGC
1 GTACAGTGCCGGTACAGTG-GC-GTACAGTGGG
*
1117734 GTACAGTG-GGGTACAGTGG
1 GTACAGTGCCGGTACAGTGG
1117753 AAGTCAGTAG
Statistics
Matches: 69, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
30 10 0.14
31 15 0.22
32 44 0.64
ACGTcount: A:0.18, C:0.20, G:0.40, T:0.22
Consensus pattern (31 bp):
GTACAGTGCCGGTACAGTGGCGTACAGTGGG
Found at i:1117752 original size:10 final size:10
Alignment explanation
Indices: 1117640--1117838 Score: 89
Period size: 10 Copynumber: 18.9 Consensus size: 10
1117630 CAAATTAATA
**
1117640 GTACAGTGCC
1 GTACAGTGGG
1117650 GTACAGTGGG
1 GTACAGTGGG
*
1117660 GTACAGTGCTG
1 GTACAGTG-GG
*
1117671 GT-CAGTGCCCG
1 GTACAGTG--GG
*
1117682 GTACAGTGGC
1 GTACAGTGGG
1117692 GTACAGTGGG
1 GTACAGTGGG
*
1117702 GTACAGTGCTG
1 GTACAGTG-GG
**
1117713 GT-CAGTGCCCT
1 GTACAGTG--GG
*
1117724 GTACAGTGGC
1 GTACAGTGGG
1117734 GTACAGTGGG
1 GTACAGTGGG
*
1117744 GTACAGTGGAA
1 GTACAGTGG-G
*
1117755 GT-CAGTAGGACT
1 GTACAGT-GG--G
*
1117767 GTACAGTGGT
1 GTACAGTGGG
1117777 GTACAGTGGG
1 GTACAGTGGG
* **
1117787 ATACAGTGCT
1 GTACAGTGGG
* **
1117797 GTTCAGTAGCAAT
1 GTACAGT-G--GG
1117810 GTACAGTGGG
1 GTACAGTGGG
1117820 GTACAGTGGG
1 GTACAGTGGG
*
1117830 ATACAGTGG
1 GTACAGTGG
1117839 AAGTCAGTGA
Statistics
Matches: 149, Mismatches: 27, Indels: 26
0.74 0.13 0.13
Matches are distributed among these distances:
10 105 0.70
11 18 0.12
12 15 0.10
13 11 0.07
ACGTcount: A:0.22, C:0.17, G:0.38, T:0.23
Consensus pattern (10 bp):
GTACAGTGGG
Found at i:1120660 original size:13 final size:13
Alignment explanation
Indices: 1120644--1120670 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1120634 TTTCAATATT
1120644 TTTGAAATGTCAA
1 TTTGAAATGTCAA
1120657 TTTGAAATGTCAA
1 TTTGAAATGTCAA
1120670 T
1 T
1120671 ATTCATTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (13 bp):
TTTGAAATGTCAA
Found at i:1123839 original size:4 final size:4
Alignment explanation
Indices: 1123830--1124009 Score: 297
Period size: 4 Copynumber: 45.0 Consensus size: 4
1123820 GTGCCGCCCC
* * * * *
1123830 CTCT CTCT CTGT CTCT CTCT CTGT CTGT CTGT CTCT CTCT CTCT ATCT
1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
*
1123878 CTCT CTCT CTCT CTCT CTCT CTAT CTCT CTCT CTCT CTCT CTCT CTCT
1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
1123926 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
*
1123974 CTCT ATCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
1124010 AACAACTTTA
Statistics
Matches: 166, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 166 1.00
ACGTcount: A:0.02, C:0.46, G:0.02, T:0.50
Consensus pattern (4 bp):
CTCT
Found at i:1130197 original size:16 final size:16
Alignment explanation
Indices: 1130178--1130209 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1130168 GTCAAATGCT
1130178 TTTGAGGTATCGTAGA
1 TTTGAGGTATCGTAGA
*
1130194 TTTGAGGTATTGTAGA
1 TTTGAGGTATCGTAGA
1130210 ATACAAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.03, G:0.31, T:0.41
Consensus pattern (16 bp):
TTTGAGGTATCGTAGA
Found at i:1135023 original size:36 final size:35
Alignment explanation
Indices: 1134983--1135054 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 35
1134973 CATTAACATG
*
1134983 ACAATGAAATTACCCTGCATGGTTTACAGTAACAAA
1 ACAATAAAATTACCCTGCATGGTTTACAGTAA-AAA
1135019 ACAATAAAATTACCCTGCATGGTTTACAGTAAAAA
1 ACAATAAAATTACCCTGCATGGTTTACAGTAAAAA
1135054 A
1 A
1135055 GCCAATGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 4 0.11
36 31 0.89
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.25
Consensus pattern (35 bp):
ACAATAAAATTACCCTGCATGGTTTACAGTAAAAA
Found at i:1137789 original size:9 final size:9
Alignment explanation
Indices: 1137767--1137822 Score: 76
Period size: 9 Copynumber: 6.1 Consensus size: 9
1137757 ACAATTTGTC
1137767 CGTTGTCTGT
1 CGTTGTC-GT
1137777 CGTTGTCGT
1 CGTTGTCGT
*
1137786 CGTTGTCGG
1 CGTTGTCGT
1137795 CGTTGTCGT
1 CGTTGTCGT
*
1137804 CGTTGTCGG
1 CGTTGTCGT
*
1137813 AGTTGTCGT
1 CGTTGTCGT
1137822 C
1 C
1137823 ATCGGCGTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
9 33 0.82
10 7 0.17
ACGTcount: A:0.02, C:0.21, G:0.36, T:0.41
Consensus pattern (9 bp):
CGTTGTCGT
Found at i:1137800 original size:18 final size:18
Alignment explanation
Indices: 1137767--1137822 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
1137757 ACAATTTGTC
*
1137767 CGTTGTCTGTCGTTGTCGT
1 CGTTGTC-GGCGTTGTCGT
1137786 CGTTGTCGGCGTTGTCGT
1 CGTTGTCGGCGTTGTCGT
*
1137804 CGTTGTCGGAGTTGTCGT
1 CGTTGTCGGCGTTGTCGT
1137822 C
1 C
1137823 ATCGGCGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
18 28 0.80
19 7 0.20
ACGTcount: A:0.02, C:0.21, G:0.36, T:0.41
Consensus pattern (18 bp):
CGTTGTCGGCGTTGTCGT
Found at i:1140864 original size:2 final size:2
Alignment explanation
Indices: 1140859--1140891 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1140849 TTGTGATATA
1140859 TC 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 TC T
1140892 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1140956 original size:14 final size:14
Alignment explanation
Indices: 1140937--1140963 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1140927 GAATAATAAA
1140937 AAGTGTTTTAAAAT
1 AAGTGTTTTAAAAT
1140951 AAGTGTTTTAAAA
1 AAGTGTTTTAAAA
1140964 GTTTTTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (14 bp):
AAGTGTTTTAAAAT
Found at i:1146039 original size:36 final size:36
Alignment explanation
Indices: 1145992--1146066 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
1145982 AATAAAACAT
*
1145992 TAACAAGACAATGAAATTACCCTGCATGGTTTACAG
1 TAACAAGACAATGAAATTACCCCGCATGGTTTACAG
1146028 TAACAAGACAATGAAATTACCCCGCATGGTTTACAG
1 TAACAAGACAATGAAATTACCCCGCATGGTTTACAG
1146064 TAA
1 TAA
1146067 AAAAGCCAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (36 bp):
TAACAAGACAATGAAATTACCCCGCATGGTTTACAG
Found at i:1151253 original size:13 final size:13
Alignment explanation
Indices: 1151235--1151260 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1151225 GAAAATGTAA
1151235 CATTGTTTCAACG
1 CATTGTTTCAACG
1151248 CATTGTTTCAACG
1 CATTGTTTCAACG
1151261 TTAGACTGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (13 bp):
CATTGTTTCAACG
Found at i:1152037 original size:21 final size:21
Alignment explanation
Indices: 1151994--1152040 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1151984 AAAACCTCAT
*
1151994 CGTTGAATAACGTTGATTCAA
1 CGTTGAATAACGTTGATTAAA
*
1152015 CGTTGAATAATTGTTGA-TAAA
1 CGTTGAATAA-CGTTGATTAAA
1152036 CGTTG
1 CGTTG
1152041 CAACTTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (21 bp):
CGTTGAATAACGTTGATTAAA
Found at i:1166282 original size:166 final size:166
Alignment explanation
Indices: 1165682--1166803 Score: 1456
Period size: 166 Copynumber: 6.8 Consensus size: 166
1165672 GTGAATATGC
* ** * * * * * * *
1165682 AAAATAAGCAAAGTCAACATGTAACAGAAAGCTGGCATCCGATTGGTACAGAAATATATCCCACA
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* * * * *
1165747 ATATGGCATCCCTAAACAAATAGTGTGTTACAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
66 ATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
*
1165812 AATCTTTGAGGAAAATTTGTTTGAAAATTTTGGCT-
131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA
*
1165847 AAAATAAACAAAGTAC-TCATTTAACAGGAAGTCGACGTCCGATTGGTAC-AAAATATATCCCAC
1 AAAATAAACAAAGT-CGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCAC
* * * * * *
1165910 GATATGGCACGCCTTAACAAACACTGTGTGAAAATTTCAAGCATCTGCGATAAATTGCTGCTGAG
65 GATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
*
1165975 AAATCTTTGACGAAAATTTGTTTGTAAATTTTGGCT-
130 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA
* * * *
1166011 AAAATAAACAAAG--GTCCTTTTCACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCAA
1 AAAATAAACAAAGTCGT-CATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCAC
* * * * * *
1166074 GAAATGGCATGCCAAAACAAATAGTATGTTAAAATTTCAAGCATCTGCGATAAATGGTTGCTGAG
65 GATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
* *
1166139 AAATCTTTGACGGAAATTAGTTTGAAAATTTTGGCTA
130 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA
* *
1166176 AAAATAAACAAAGTAC-TCATTCAACAGGAAGTTGACGTCCGATTGGTACAAAAATACATCCCAC
1 AAAATAAACAAAGT-CGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCAC
* ** *
1166240 GATATAGCATGCCTTTACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAG
65 GATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
* * * *
1166305 -AATTTTTGACAAAAATTAGTTTGAAAATTTTTGCTA
130 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA
* * *
1166341 AAAATAAACAAAGTCGTCATTTAACAGGAAGATGACGTCTGATTGGTACAAAAATATATCACACG
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* * * * * *
1166406 ATTTTGCATGTCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCAATAAACAGTTGCTTAGA
66 ATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
* *
1166471 ATTCTTTGACAAAAATTTGTTTGAAAATTGTT-GCTA
131 AATCTTTGACGAAAATTTGTTTGAAAATT-TTGGCTA
* * * **
1166507 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTAACGTCTGATTGTTACAAAAATATATCAAACG
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* *
1166572 ATATAGCATGCCTAAACAAATATTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
66 ATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
* *
1166637 TATCTTTGACGAAAATTTGTTTGAAAATGTTGG-TGAA
131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCT--A
* * **
1166674 AAAATAAGCAAAGTCATCATTTAACAGGAAGTTGACGTCCGATTATTACAAAAATATATCCCACG
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* *
1166739 ATATGGCATGCCCT-AACAAACACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTACTGAG
66 ATATGGCATG-CCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
1166803 A
130 A
1166804 TAAATGCGAC
Statistics
Matches: 843, Mismatches: 99, Indels: 28
0.87 0.10 0.03
Matches are distributed among these distances:
162 1 0.00
163 28 0.03
164 218 0.26
165 202 0.24
166 272 0.32
167 119 0.14
168 3 0.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.29
Consensus pattern (166 bp):
AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
ATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTA
Found at i:1166495 original size:331 final size:331
Alignment explanation
Indices: 1165682--1166803 Score: 1479
Period size: 331 Copynumber: 3.4 Consensus size: 331
1165672 GTGAATATGC
* ** * * * * * * *
1165682 AAAATAAGCAAAGTCAACATGTAACAGAAAGCTGGCATCCGATTGGTACAGAAATATATCCCACA
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* * * * *
1165747 ATATGGCATCCCTAAACAAATAGTGTGTTACAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
66 ATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
*
1165812 AATCTTTGAGGAAAATTTGTTTGAAAATTTTGGCT-AAAATAAACAAAGTACTCATTTAACAGGA
131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTAAAAATAAACAAAGTACTCATTTAACAGGA
* * * * *
1165876 AGTCGACGTCCGATTGGTAC-AAAATATATCCCACGATATGGCACGCCTTAACAAACACTGTGTG
196 AGTTGACGTCCGATTGGTACAAAAATATATCCCACGATATAGCATGCCTTAACAAATACTGTGTA
* * *
1165940 AAAATTTCAAGCATCTGCGATAAATTGCTGCTGAGAAATCTTTGACGAAAATTTGTTTGTAAATT
261 AAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG-AATCTTTGACGAAAATTTGTTTGAAAATT
*
1166005 TTGGCT-
325 TTTGCTA
* * * *
1166011 AAAATAAACAAAG--GTCCTTTTCACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCAA
1 AAAATAAACAAAGTCGT-CATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCAC
* * * * * *
1166074 GAAATGGCATGCCAAAACAAATAGTATGTTAAAATTTCAAGCATCTGCGATAAATGGTTGCTGAG
65 GATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
* * *
1166139 AAATCTTTGACGGAAATTAGTTTGAAAATTTTGGCTAAAAATAAACAAAGTACTCATTCAACAGG
130 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTAAAAATAAACAAAGTACTCATTTAACAGG
* *
1166204 AAGTTGACGTCCGATTGGTACAAAAATACATCCCACGATATAGCATGCCTTTACAAATACTGTGT
195 AAGTTGACGTCCGATTGGTACAAAAATATATCCCACGATATAGCATGCCTTAACAAATACTGTGT
* * * *
1166269 AAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAGAATTTTTGACAAAAATTAGTTTGAAAATT
260 AAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAATCTTTGACGAAAATTTGTTTGAAAATT
1166334 TTTGCTA
325 TTTGCTA
* * *
1166341 AAAATAAACAAAGTCGTCATTTAACAGGAAGATGACGTCTGATTGGTACAAAAATATATCACACG
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* * * * * *
1166406 ATTTTGCATGTCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCAATAAACAGTTGCTTAGA
66 ATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
* *
1166471 ATTCTTTGACAAAAATTTGTTTGAAAATTGTT-GCTAAAAATAAACAAAGT-CGTCATTTAACAG
131 AATCTTTGACGAAAATTTGTTTGAAAATT-TTGGCTAAAAATAAACAAAGTAC-TCATTTAACAG
* * * ** * *
1166534 GAAGTTAACGTCTGATTGTTACAAAAATATATCAAACGATATAGCATGCCTAAACAAATATTGTG
194 GAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGATATAGCATGCCTTAACAAATACTGTG
1166599 TAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGATATCTTTGACGAAAATTTGTTTGAAAA
259 TAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA-ATCTTTGACGAAAATTTGTTTGAAAA
* *
1166664 TGTTGGTG-AA
323 T-TT-TTGCTA
* * **
1166674 AAAATAAGCAAAGTCATCATTTAACAGGAAGTTGACGTCCGATTATTACAAAAATATATCCCACG
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* *
1166739 ATATGGCATGCCCT-AACAAACACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTACTGAG
66 ATATGGCATG-CCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
1166803 A
130 A
1166804 TAAATGCGAC
Statistics
Matches: 687, Mismatches: 94, Indels: 20
0.86 0.12 0.02
Matches are distributed among these distances:
328 127 0.18
329 89 0.13
330 84 0.12
331 240 0.35
332 28 0.04
333 115 0.17
334 4 0.01
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.29
Consensus pattern (331 bp):
AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
ATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
AATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTAAAAATAAACAAAGTACTCATTTAACAGGA
AGTTGACGTCCGATTGGTACAAAAATATATCCCACGATATAGCATGCCTTAACAAATACTGTGTA
AAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAATCTTTGACGAAAATTTGTTTGAAAATTT
TTGCTA
Found at i:1168035 original size:20 final size:20
Alignment explanation
Indices: 1168010--1168050 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1168000 ATTAACGTAT
1168010 ACAGACTCATTCCCTGCAAA
1 ACAGACTCATTCCCTGCAAA
* *
1168030 ACAGACTGATTCCCTGTAAA
1 ACAGACTCATTCCCTGCAAA
1168050 A
1 A
1168051 AGGTGCGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.29, G:0.12, T:0.22
Consensus pattern (20 bp):
ACAGACTCATTCCCTGCAAA
Found at i:1172801 original size:2 final size:2
Alignment explanation
Indices: 1172796--1172838 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1172786 ATATATATAT
1172796 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
1172838 A
1 A
1172839 ATTTTATAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1175338 original size:146 final size:146
Alignment explanation
Indices: 1174967--1175678 Score: 940
Period size: 152 Copynumber: 4.9 Consensus size: 146
1174957 ATTTTCGAAA
* * * **
1174967 CAATGACCTTGAACTTCCTC-AATTGACCTTGGGTCAAGGTCATGACACACCCTTCCGTCATAAG
1 CAATGACCTTGACCTTGCACGAA-TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAG
* * *
1175031 CAATATTTGTGTGAAGTAAGAACATT-CAATGCTTCTCCATAAGGAAGATATGGACCGGACACGA
65 CAATCTTTGTGTGAAGTAAGAAC-TTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGA
1175095 ATTTTGCATTTTTT-T--
129 ATTTTGCATTTTTTCTGC
** * * *
1175110 C--TGACAGTGACCTTGCACGAATGACCTTGAGTGAAAGTCATGACACACCCTTAGGTCATAAGC
1 CAATGACCTTGACCTTGCACGAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGC
* *
1175173 AATCTTTGTGTGAAGTAAGAACTTCCAATATTTCTCCCTAAGAAAGATATGGACCGGACACGAAT
66 AATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAAT
1175238 TTTGCATTTTTTCTGC
131 TTTGCATTTTTTCTGC
* * * * *
1175254 CAATGACCTTGACCTTGTACAAATGATCTTGGGTCAAGGTCATTACACATCCTTAGGTCATAAGC
1 CAATGACCTTGACCTTGCACGAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGC
* * *
1175319 AATCTTTGTGTGAACTAAGAACTTCCAATGTCAATGTTTCTCTATAAGAAAGATATGGACCGGAG
66 AATCTTTGTGTGAAGTAAGAACTT-C-----CAATGTTTCTCCATAAGAAAGATATGGACCGGAC
1175384 ACGAATTTTGCATTTTTTCTGC
125 ACGAATTTTGCATTTTTTCTGC
* * * *
1175406 CAGTGACCTTGACCTTGC-CTGAATGAACTTAGGTCATA-GTCATGACACACCCTTAGGTCATAG
1 CAATGACCTTGACCTTGCAC-GAATGACCTTGGGTCA-AGGTCATGACACACCCTTAGGTCATAA
* * *
1175469 GCAATCTTTGTGTGAAGTAAGACCCTCCAATGTTTCTCCATAAGAAAAATATGGACCGGACACGA
64 GCAATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGA
*
1175534 ATTTTG-AATTTTTCTGC
129 ATTTTGCATTTTTTCTGC
* * * *
1175551 CAGTGACCTTGACCTTGCCCGAATGACCTTGGGTCAAGGTCTTGACACACCTTTAGGTCATAAGC
1 CAATGACCTTGACCTTGCACGAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGC
*
1175616 AATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACGGGACACGA
66 AATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGA
1175679 TTTCACAGAC
Statistics
Matches: 498, Mismatches: 54, Indels: 32
0.85 0.09 0.05
Matches are distributed among these distances:
140 2 0.00
141 118 0.24
142 3 0.01
143 1 0.00
144 2 0.00
145 125 0.25
146 117 0.23
147 1 0.00
151 2 0.00
152 126 0.25
153 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (146 bp):
CAATGACCTTGACCTTGCACGAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGC
AATCTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAAT
TTTGCATTTTTTCTGC
Found at i:1175507 original size:298 final size:290
Alignment explanation
Indices: 1174967--1175678 Score: 923
Period size: 298 Copynumber: 2.5 Consensus size: 290
1174957 ATTTTCGAAA
* * * * **
1174967 CAATGACCTTGAACTTCCTCAATTGACCTTGGGTCAAGGTCATGACACACCCTTCCGTCATAAGC
1 CAATGACCTTGACCTT-GTCAAATGACCTTGGGTCAAGGTCATTACACA-CCTTAGGTCATAAGC
* *
1175032 AATATTTGTGTGAAGTAAGAA----C-AT-TCAATGCTTCTCCATAAGGAAGATATGGACCGGAC
64 AATCTTTGTGTGAAGTAAGAACTTCCAATGTCAATGCTTCTCCATAAGAAAGATATGGACCGGAC
* *
1175091 ACGAATTTTGCATTTTTTTCTGACAGTGACCTTGCACGAATGACCTTGAGTGAAAGTCATGACAC
129 ACGAATTTTGCATTTTTTTCTGACAGTGACCTTGCACGAATGAACTTGAGTCAAAGTCATGACAC
* * *
1175156 ACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCCAATATTTCTCCCTAAGAAAGAT
194 ACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACCTCCAATATTTCTCCATAAGAAAAAT
*
1175221 ATGGACCGGACACGAATTTTGCATTTTTTCTGC
259 ATGGACCGGACACGAATTTTG-AATTTTTCTGC
*
1175254 CAATGACCTTGACCTTGTACAAATGATCTTGGGTCAAGGTCATTACACATCCTTAGGTCATAAGC
1 CAATGACCTTGACCTTGT-CAAATGACCTTGGGTCAAGGTCATTACACA-CCTTAGGTCATAAGC
* * * *
1175319 AATCTTTGTGTGAACTAAGAACTTCCAATGTCAATGTTTCTCTATAAGAAAGATATGGACCGGAG
64 AATCTTTGTGTGAAGTAAGAACTTCCAATGTCAATGCTTCTCCATAAGAAAGATATGGACCGGAC
* * *
1175384 ACGAATTTTGCA-TTTTTTCTGCCAGTGACCTTGACCTTGCCTGAATGAACTT-AGGTCATAGTC
129 ACGAATTTTGCATTTTTTTCTGACAGTGACCTTG--C---AC-GAATGAACTTGA-GTCAAAGTC
* * *
1175447 ATGACACACCCTTAGGTCATAGGCAATCTTTGTGTGAAGTAAGACCCTCCAATGTTTCTCCATAA
187 ATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACCTCCAATATTTCTCCATAA
1175512 GAAAAATATGGACCGGACACGAATTTTGAATTTTTCTGC
252 GAAAAATATGGACCGGACACGAATTTTGAATTTTTCTGC
* * *
1175551 CAGTGACCTTGACCTTGCCCGAATGACCTTGGGTCAAGGTC-TTGACACACCTTTAGGTCATAAG
1 CAATGACCTTGACCTTG-TCAAATGACCTTGGGTCAAGGTCATT-ACACACC-TTAGGTCATAAG
*
1175615 CAATCTTTGTGTGAAGTAAGAACTTCCAATG----T--TTCTCCATAAGAAAGATATGGACGGGA
63 CAATCTTTGTGTGAAGTAAGAACTTCCAATGTCAATGCTTCTCCATAAGAAAGATATGGACCGGA
1175674 CACGA
128 CACGA
1175679 TTTCACAGAC
Statistics
Matches: 374, Mismatches: 34, Indels: 30
0.85 0.08 0.07
Matches are distributed among these distances:
286 1 0.00
287 74 0.20
291 30 0.08
292 22 0.06
293 44 0.12
294 1 0.00
296 4 0.01
297 95 0.25
298 103 0.28
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (290 bp):
CAATGACCTTGACCTTGTCAAATGACCTTGGGTCAAGGTCATTACACACCTTAGGTCATAAGCAA
TCTTTGTGTGAAGTAAGAACTTCCAATGTCAATGCTTCTCCATAAGAAAGATATGGACCGGACAC
GAATTTTGCATTTTTTTCTGACAGTGACCTTGCACGAATGAACTTGAGTCAAAGTCATGACACAC
CCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACCTCCAATATTTCTCCATAAGAAAAATAT
GGACCGGACACGAATTTTGAATTTTTCTGC
Found at i:1175600 original size:145 final size:146
Alignment explanation
Indices: 1174990--1175678 Score: 908
Period size: 145 Copynumber: 4.7 Consensus size: 146
1174980 CTTCCTCAAT
** * *
1174990 TGACCTTGGGTCAAGGTCATGACACACCCTTCCGTCATAAGCAATATTTGTGTGAAGTAAGAACA
1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACC
* * * *
1175055 TTCAATGCTTCTCCATAAGGAAGATATGGACCGGACACGAATTTTGC-ATTTTT-T-TC--TGAC
66 TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCAATTTTTCTGCCAGTGAC
**
1175115 AGTGACCTTGCACGAA
131 CTTGACCTTGCACGAA
* * * *
1175131 TGACCTTGAGTGAAAGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT
1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACC
* * * *
1175196 TCCAATATTTCTCCCTAAGAAAGATATGGACCGGACACGAATTTTGCATTTTTTCTGCCAATGAC
66 TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCAATTTTTCTGCCAGTGAC
* *
1175261 CTTGACCTTGTACAAA
131 CTTGACCTTGCACGAA
* * * *
1175277 TGATCTTGGGTCAAGGTCATTACACATCCTTAGGTCATAAGCAATCTTTGTGTGAACTAAGAACT
1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAA--
* * * *
1175342 TCCAATGTCAATGTTTCTCTATAAGAAAGATATGGACCGGAGACGAATTTTGCATTTTTTCTGCC
64 -CC--T-CCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCAATTTTTCTGCC
1175407 AGTGACCTTGACCTTGC-CTGAA
125 AGTGACCTTGACCTTGCAC-GAA
* * * *
1175429 TGAACTTAGGTCATA-GTCATGACACACCCTTAGGTCATAGGCAATCTTTGTGTGAAGTAAGACC
1 TGACCTTGGGTCA-AGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAAC
*
1175493 CTCCAATGTTTCTCCATAAGAAAAATATGGACCGGACACGAATTTTG-AATTTTTCTGCCAGTGA
65 CTCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCAATTTTTCTGCCAGTGA
*
1175557 CCTTGACCTTGCCCGAA
130 CCTTGACCTTGCACGAA
* * *
1175574 TGACCTTGGGTCAAGGTCTTGACACACCTTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACT
1 TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACC
*
1175639 TCCAATGTTTCTCCATAAGAAAGATATGGACGGGACACGA
66 TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGA
1175679 TTTCACAGAC
Statistics
Matches: 478, Mismatches: 55, Indels: 26
0.86 0.10 0.05
Matches are distributed among these distances:
141 100 0.21
142 5 0.01
143 1 0.00
144 2 0.00
145 125 0.26
146 114 0.24
147 1 0.00
149 3 0.01
151 2 0.00
152 124 0.26
153 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (146 bp):
TGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACC
TCCAATGTTTCTCCATAAGAAAGATATGGACCGGACACGAATTTTGCAATTTTTCTGCCAGTGAC
CTTGACCTTGCACGAA
Found at i:1184418 original size:26 final size:26
Alignment explanation
Indices: 1184389--1184462 Score: 103
Period size: 26 Copynumber: 2.8 Consensus size: 26
1184379 ATAAAACTAA
* * *
1184389 ACAGATACGACTTACGTCAGACTTAT
1 ACAGATACGACTTACCTCAGACGTAC
* *
1184415 ACAGATACAATTTACCTCAGACGTAC
1 ACAGATACGACTTACCTCAGACGTAC
1184441 ACAGATACGACTTACCTCAGAC
1 ACAGATACGACTTACCTCAGAC
1184463 CTATCGGAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (26 bp):
ACAGATACGACTTACCTCAGACGTAC
Found at i:1185638 original size:10 final size:10
Alignment explanation
Indices: 1185620--1185653 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1185610 GGCTTCATGA
*
1185620 TATGGTATGG
1 TATGGTATGC
*
1185630 TATGCTATGC
1 TATGGTATGC
1185640 TATGGTATGC
1 TATGGTATGC
1185650 TATG
1 TATG
1185654 AGATTTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.09, G:0.29, T:0.41
Consensus pattern (10 bp):
TATGGTATGC
Found at i:1185643 original size:15 final size:15
Alignment explanation
Indices: 1185620--1185653 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1185610 GGCTTCATGA
*
1185620 TATGGTATGGTATGC
1 TATGCTATGGTATGC
1185635 TATGCTATGGTATGC
1 TATGCTATGGTATGC
1185650 TATG
1 TATG
1185654 AGATTTGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.09, G:0.29, T:0.41
Consensus pattern (15 bp):
TATGCTATGGTATGC
Found at i:1185885 original size:21 final size:20
Alignment explanation
Indices: 1185847--1185934 Score: 122
Period size: 21 Copynumber: 4.2 Consensus size: 20
1185837 GAATGCGATT
**
1185847 CTATGAGATTGTATGCTATG
1 CTATGAGATTCAATGCTATG
*
1185867 GTATGAGATTCCAATGCTATG
1 CTATGAGATT-CAATGCTATG
1185888 CTATGAGAGTTCAATGCTATG
1 CTATGAGA-TTCAATGCTATG
1185909 CTATGAGATTTCAATGCTATG
1 CTATGAGA-TTCAATGCTATG
1185930 CTATG
1 CTATG
1185935 CTATCGTGTA
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
20 9 0.15
21 50 0.82
22 2 0.03
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (20 bp):
CTATGAGATTCAATGCTATG
Found at i:1192824 original size:200 final size:200
Alignment explanation
Indices: 1192481--1192872 Score: 775
Period size: 200 Copynumber: 2.0 Consensus size: 200
1192471 GATACGTAAC
1192481 ATGTCCATTATTTTTATCTTACAACACATTTATACTTTTGTCAATATCTTTTTTCGACGAAAAAT
1 ATGTCCATTATTTTTATCTTACAACACATTTATACTTTTGTCAATATCTTTTTTCGACGAAAAAT
1192546 GCTAAAAAGCTGTGATTCACATTGTTATCATCTACTGATGAAAAATGTCGACATTATTTTGAACT
66 GCTAAAAAGCTGTGATTCACATTGTTATCATCTACTGATGAAAAATGTCGACATTATTTTGAACT
1192611 TGTAACTCAATAATAATACCGTGTGTTTGCGACAATTAATGAGTCGCAGAAAATAAATCAGCTTT
131 TGTAACTCAATAATAATACCGTGTGTTTGCGACAATTAATGAGTCGCAGAAAATAAATCAGCTTT
1192676 TTTTT
196 TTTTT
*
1192681 ATGTCCATTATTTTTATCTTACAACACATTTATACTTTTGTCAATATCTTTTTTCGACGATAAAT
1 ATGTCCATTATTTTTATCTTACAACACATTTATACTTTTGTCAATATCTTTTTTCGACGAAAAAT
1192746 GCTAAAAAGCTGTGATTCACATTGTTATCATCTACTGATGAAAAATGTCGACATTATTTTGAACT
66 GCTAAAAAGCTGTGATTCACATTGTTATCATCTACTGATGAAAAATGTCGACATTATTTTGAACT
1192811 TGTAACTCAATAATAATACCGTGTGTTTGCGACAATTAATGAGTCGCAGAAAATAAATCAGC
131 TGTAACTCAATAATAATACCGTGTGTTTGCGACAATTAATGAGTCGCAGAAAATAAATCAGC
1192873 NTTTGAAGAT
Statistics
Matches: 191, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
200 191 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (200 bp):
ATGTCCATTATTTTTATCTTACAACACATTTATACTTTTGTCAATATCTTTTTTCGACGAAAAAT
GCTAAAAAGCTGTGATTCACATTGTTATCATCTACTGATGAAAAATGTCGACATTATTTTGAACT
TGTAACTCAATAATAATACCGTGTGTTTGCGACAATTAATGAGTCGCAGAAAATAAATCAGCTTT
TTTTT
Found at i:1192982 original size:10 final size:11
Alignment explanation
Indices: 1192966--1193090 Score: 136
Period size: 10 Copynumber: 11.9 Consensus size: 11
1192956 TGCGTCTTTT
1192966 TACCCCAATGA
1 TACCCCAATGA
1192977 -ACCCCAATGA
1 TACCCCAATGA
1192987 -ACCCCAATGA
1 TACCCCAATGA
1192997 TACCCCAATGA
1 TACCCCAATGA
1193008 -ACCCCAATGA
1 TACCCCAATGA
*
1193018 TATCCCAATGA
1 TACCCCAATGA
*
1193029 TA-CCTAATGA
1 TACCCCAATGA
* *
1193039 TACCCCTATTA
1 TACCCCAATGA
*
1193050 TA-CCAAATGA
1 TACCCCAATGA
*
1193060 TATCCCAATGA
1 TACCCCAATGA
*
1193071 -ACCCTAATGA
1 TACCCCAATGA
*
1193081 TACCCTAATG
1 TACCCCAATG
1193091 GACTTTGAAA
Statistics
Matches: 98, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
10 54 0.55
11 44 0.45
ACGTcount: A:0.38, C:0.32, G:0.09, T:0.22
Consensus pattern (11 bp):
TACCCCAATGA
Found at i:1193003 original size:21 final size:21
Alignment explanation
Indices: 1192967--1193090 Score: 137
Period size: 21 Copynumber: 6.0 Consensus size: 21
1192957 GCGTCTTTTT
1192967 ACCCCAATGA-ACCCCAATGA
1 ACCCCAATGATACCCCAATGA
1192987 ACCCCAATGATACCCCAATGA
1 ACCCCAATGATACCCCAATGA
*
1193008 ACCCCAATGATATCCCAATGA
1 ACCCCAATGATACCCCAATGA
* * *
1193029 TA-CCTAATGATACCCCTATTA
1 -ACCCCAATGATACCCCAATGA
* *
1193050 TA-CCAAATGATATCCCAATGA
1 -ACCCCAATGATACCCCAATGA
* *
1193071 ACCCTAATGATACCCTAATG
1 ACCCCAATGATACCCCAATG
1193091 GACTTTGAAA
Statistics
Matches: 89, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.12
21 77 0.87
22 1 0.01
ACGTcount: A:0.38, C:0.32, G:0.09, T:0.21
Consensus pattern (21 bp):
ACCCCAATGATACCCCAATGA
Found at i:1193038 original size:42 final size:43
Alignment explanation
Indices: 1192966--1193090 Score: 159
Period size: 42 Copynumber: 3.0 Consensus size: 43
1192956 TGCGTCTTTT
* *
1192966 TACCCCAATGA-ACCCCAATGAACCCCAATGATACCCCAATGA
1 TACCCCAATGATATCCCAATGAACCCTAATGATACCCCAATGA
* *
1193008 -ACCCCAATGATATCCCAATGATA-CCTAATGATACCCCTATTA
1 TACCCCAATGATATCCCAATGA-ACCCTAATGATACCCCAATGA
* *
1193050 TA-CCAAATGATATCCCAATGAACCCTAATGATACCCTAATG
1 TACCCCAATGATATCCCAATGAACCCTAATGATACCCCAATG
1193091 GACTTTGAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
41 11 0.15
42 58 0.82
43 2 0.03
ACGTcount: A:0.38, C:0.32, G:0.09, T:0.22
Consensus pattern (43 bp):
TACCCCAATGATATCCCAATGAACCCTAATGATACCCCAATGA
Found at i:1194871 original size:2 final size:2
Alignment explanation
Indices: 1194866--1194944 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
1194856 AATAGGATGG
*
1194866 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GG
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1194908 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1194945 TTAACATTGT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1195231 original size:2 final size:2
Alignment explanation
Indices: 1195224--1195265 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1195214 AGTTTAACAG
1195224 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
1195266 CAGATATCCC
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):
GA
Found at i:1198019 original size:11 final size:11
Alignment explanation
Indices: 1198003--1198087 Score: 131
Period size: 11 Copynumber: 8.0 Consensus size: 11
1197993 TATTTAAAGT
*
1198003 TCATTGGAGTA
1 TCATTGGGGTA
1198014 TCATTGGGGT-
1 TCATTGGGGTA
1198024 TCATTGGGGTA
1 TCATTGGGGTA
1198035 TCATTGGGGTA
1 TCATTGGGGTA
1198046 TCATTGGGGT-
1 TCATTGGGGTA
1198056 TCATTGGGGTA
1 TCATTGGGGTA
*
1198067 TCATTGAGGT-
1 TCATTGGGGTA
1198077 TCATTGGGGTA
1 TCATTGGGGTA
1198088 AAAAGACGCA
Statistics
Matches: 68, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
10 29 0.43
11 39 0.57
ACGTcount: A:0.18, C:0.09, G:0.35, T:0.38
Consensus pattern (11 bp):
TCATTGGGGTA
Found at i:1198027 original size:21 final size:21
Alignment explanation
Indices: 1198003--1198087 Score: 111
Period size: 21 Copynumber: 4.0 Consensus size: 21
1197993 TATTTAAAGT
1198003 TCATTGGAGTATCATTGGGGT-
1 TCATTGGAGT-TCATTGGGGTA
*
1198024 TCATTGGGGTATCATTGGGGTA
1 TCATTGGAGT-TCATTGGGGTA
*
1198046 TCATTGGGGTTCATTGGGGTA
1 TCATTGGAGTTCATTGGGGTA
1198067 TCATT-GAGGTTCATTGGGGTA
1 TCATTGGA-GTTCATTGGGGTA
1198088 AAAAGACGCA
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
20 1 0.02
21 49 0.82
22 10 0.17
ACGTcount: A:0.18, C:0.09, G:0.35, T:0.38
Consensus pattern (21 bp):
TCATTGGAGTTCATTGGGGTA
Found at i:1198047 original size:32 final size:32
Alignment explanation
Indices: 1198003--1198086 Score: 143
Period size: 32 Copynumber: 2.7 Consensus size: 32
1197993 TATTTAAAGT
*
1198003 TCATTGGAGTATCATTGGGGTTCATTGGGGTA
1 TCATTGGGGTATCATTGGGGTTCATTGGGGTA
1198035 TCATTGGGGTATCATTGGGGTTCATTGGGGTA
1 TCATTGGGGTATCATTGGGGTTCATTGGGGTA
*
1198067 TCATTGAGGT-TCATTGGGGT
1 TCATTGGGGTATCATTGGGGT
1198087 AAAAAGACGC
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
31 10 0.20
32 40 0.80
ACGTcount: A:0.17, C:0.10, G:0.36, T:0.38
Consensus pattern (32 bp):
TCATTGGGGTATCATTGGGGTTCATTGGGGTA
Found at i:1209770 original size:32 final size:33
Alignment explanation
Indices: 1209722--1209798 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 33
1209712 ATTGACCCGG
1209722 GTTGAAAATTGACCC-GGGGGTCATTTTTCAAC
1 GTTGAAAATTGACCCGGGGGGTCATTTTTCAAC
1209754 GTT-AAATATTGACCCGGGGGGTCATTTTTCAAC
1 GTTGAAA-ATTGACCCGGGGGGTCATTTTTCAAC
1209787 GTTGAAAATTGA
1 GTTGAAAATTGA
1209799 GACCAAAATC
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
31 3 0.07
32 11 0.26
33 25 0.60
34 3 0.07
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (33 bp):
GTTGAAAATTGACCCGGGGGGTCATTTTTCAAC
Found at i:1224895 original size:11 final size:11
Alignment explanation
Indices: 1224876--1224919 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
1224866 CAAAAATGTG
*
1224876 TTGCTGCAATA
1 TTGCCGCAATA
1224887 TTGCCGCAATA
1 TTGCCGCAATA
* *
1224898 TTGCCGCATTG
1 TTGCCGCAATA
*
1224909 TTGCAGCAATA
1 TTGCCGCAATA
1224920 ATTTTACTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (11 bp):
TTGCCGCAATA
Found at i:1226743 original size:20 final size:19
Alignment explanation
Indices: 1226718--1226777 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 19
1226708 ATTATAATAT
1226718 TGTATCATATAATATGATA
1 TGTATCATATAATATGATA
* *
1226737 GTGTATCATAAAATATAAATA
1 -TGTATCATATAATAT-GATA
* *
1226758 TGAATCATATGATATGATA
1 TGTATCATATAATATGATA
1226777 T
1 T
1226778 CATAGTTTGC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 4 0.12
20 26 0.79
21 3 0.09
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (19 bp):
TGTATCATATAATATGATA
Found at i:1242447 original size:22 final size:22
Alignment explanation
Indices: 1242422--1242473 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1242412 TATCGCTTCT
1242422 TCGCCTTTGCAA-CTTCGCACTC
1 TCGCCTTTG-AATCTTCGCACTC
* *
1242444 TCGCCTTTGAATCTTTGCACTT
1 TCGCCTTTGAATCTTCGCACTC
1242466 TCGCCTTT
1 TCGCCTTT
1242474 TTAACTCACC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 2 0.07
22 25 0.93
ACGTcount: A:0.12, C:0.35, G:0.13, T:0.40
Consensus pattern (22 bp):
TCGCCTTTGAATCTTCGCACTC
Found at i:1243701 original size:10 final size:10
Alignment explanation
Indices: 1243676--1243720 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
1243666 TTATGTATCA
*
1243676 AATATGATAC
1 AATATCATAC
*
1243686 AGTATCATAC
1 AATATCATAC
1243696 AATATCATAC
1 AATATCATAC
* *
1243706 TATATTATAC
1 AATATCATAC
1243716 AATAT
1 AATAT
1243721 AATATTATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (10 bp):
AATATCATAC
Found at i:1243705 original size:20 final size:20
Alignment explanation
Indices: 1243688--1243730 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1243678 TATGATACAG
1243688 TATCATACAATATCATACTA
1 TATCATACAATATCATACTA
* * *
1243708 TATTATACAATATAATATTA
1 TATCATACAATATCATACTA
1243728 TAT
1 TAT
1243731 GTGCCAATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.42
Consensus pattern (20 bp):
TATCATACAATATCATACTA
Found at i:1246531 original size:181 final size:181
Alignment explanation
Indices: 1246230--1247183 Score: 1453
Period size: 181 Copynumber: 5.3 Consensus size: 181
1246220 ACAGATCGCC
* * * * * *
1246230 CTGCGCCCAAACTAGGACTTGTCCTCACTAGGTGATCCCGGATTCCTCGGGGGACGGGTGTACCC
1 CTGCGCCCAAACTAGGACTTGTGCTCATTAGGTGAGCCCGGATTCCTTGGGGGAGGGGTGTTCCC
* *
1246295 TCGAAGATTCCGGACCCAAACCAGGCACTAGTGACACCGATTCCTGGCGCCAGTGCGCTGAGTTG
66 TCGAGGATTCCGGACCCAAATCAGGCACTAGTGACACCGATTCCTGGCGCCAGTGCGCTGAGTTG
** * *
1246360 ACCTTAAGTGAACAAATTATTTCTGTTATGTAGGGATCTAAACTGGGTGCC
131 ACCTTAAGTGAACAAATTATTTCTGTTATGTAGGGATCTAAACAAGGCGCT
* *
1246411 CTGCGCACAAACTAGGACTTGTGCTCATTAAGTGAGCCCGGATTCCTTGGGGGAGGGGTGTTCCC
1 CTGCGCCCAAACTAGGACTTGTGCTCATTAGGTGAGCCCGGATTCCTTGGGGGAGGGGTGTTCCC
* * *
1246476 TCGAGGATTCCGGACCCAAACCAGGCACTAGTGACACCGTTTCTTGGCGCCAGTGCGCTGAGTTG
66 TCGAGGATTCCGGACCCAAATCAGGCACTAGTGACACCGATTCCTGGCGCCAGTGCGCTGAGTTG
* *
1246541 ACCTAAAGTGAACAAATTATTTCTGTTATGTAGGGATTTAAACAAGGCGCT
131 ACCTTAAGTGAACAAATTATTTCTGTTATGTAGGGATCTAAACAAGGCGCT
* * * * * * *
1246592 CTGTGCCAAAACTAGGACTTGTGCTCATTAGGTGATCCCGGATTCCTTGGGGGAGAGGTTTTACT
1 CTGCGCCCAAACTAGGACTTGTGCTCATTAGGTGAGCCCGGATTCCTTGGGGGAGGGGTGTTCCC
*** *
1246657 TCGAGGATTCCGGTGTCAAATCAGGCACTAGTGACACCGATTACTGGCGCCAGTGCGCTGAGTTG
66 TCGAGGATTCCGGACCCAAATCAGGCACTAGTGACACCGATTCCTGGCGCCAGTGCGCTGAGTTG
*
1246722 ACCTTAAGTGAACAAATTATTCCTGTTATGTAGGGATCTAAACAAGGCGCT
131 ACCTTAAGTGAACAAATTATTTCTGTTATGTAGGGATCTAAACAAGGCGCT
* * * *
1246773 CTGCGCCCAAACTAGGAATTGTGCTCATTAGGTGAGCCCGGATTCCTTGGGGGAGAGGTGTTACT
1 CTGCGCCCAAACTAGGACTTGTGCTCATTAGGTGAGCCCGGATTCCTTGGGGGAGGGGTGTTCCC
***
1246838 TCGAGGATTCCGGTGTCAAATCAGGCACTAGTGACA-CGAATTCCTGGCGCCAGTGCGCTGAGTT
66 TCGAGGATTCCGGACCCAAATCAGGCACTAGTGACACCG-ATTCCTGGCGCCAGTGCGCTGAGTT
* *
1246902 GACCTTAAGTGAACAAATAATTCCTGTTATGTAGGGATCTAAACAAGGCGCT
130 GACCTTAAGTGAACAAATTATTTCTGTTATGTAGGGATCTAAACAAGGCGCT
* * * * *
1246954 CTGCGCCCAAACTGGGAATTGTGCTCATTAGGTGAGCCCGGATTCCTTGGGGAAAGGTTGTTCCC
1 CTGCGCCCAAACTAGGACTTGTGCTCATTAGGTGAGCCCGGATTCCTTGGGGGAGGGGTGTTCCC
*
1247019 TCGAGGATTCCGGACCCAAATCAGGCAATAGTGACACCGATTCCTGGCGCCAGTGCGCTGAGTTG
66 TCGAGGATTCCGGACCCAAATCAGGCACTAGTGACACCGATTCCTGGCGCCAGTGCGCTGAGTTG
1247084 ACCTTAAGTGAACAAATT-TTTCCTGTTATGTAGGGATCTAAACAAGGCGCT
131 ACCTTAAGTGAACAAATTATTT-CTGTTATGTAGGGATCTAAACAAGGCGCT
*
1247135 CTGCGCCCAAACTAGGACTTGTGCTCATTAGGTGAGCCAGGATTCCTTG
1 CTGCGCCCAAACTAGGACTTGTGCTCATTAGGTGAGCCCGGATTCCTTG
1247184 ATCACTAGTG
Statistics
Matches: 711, Mismatches: 59, Indels: 6
0.92 0.08 0.01
Matches are distributed among these distances:
180 4 0.01
181 705 0.99
182 2 0.00
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (181 bp):
CTGCGCCCAAACTAGGACTTGTGCTCATTAGGTGAGCCCGGATTCCTTGGGGGAGGGGTGTTCCC
TCGAGGATTCCGGACCCAAATCAGGCACTAGTGACACCGATTCCTGGCGCCAGTGCGCTGAGTTG
ACCTTAAGTGAACAAATTATTTCTGTTATGTAGGGATCTAAACAAGGCGCT
Found at i:1247904 original size:31 final size:31
Alignment explanation
Indices: 1247851--1247941 Score: 112
Period size: 31 Copynumber: 2.9 Consensus size: 31
1247841 TCAGGCAAAA
*
1247851 GGGTCATTTTTC-GACGTTGAATAATGACCGG
1 GGGTCATTTTTCTG-CGTAGAATAATGACCGG
*
1247882 GGGTAATTTTTCTGCGTAGAATAATGACCGG
1 GGGTCATTTTTCTGCGTAGAATAATGACCGG
* * * *
1247913 GGGTCATTATTCTACGTCGAAAAATGACC
1 GGGTCATTTTTCTGCGTAGAATAATGACC
1247942 CCAGTCATTA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
31 51 0.98
32 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.31
Consensus pattern (31 bp):
GGGTCATTTTTCTGCGTAGAATAATGACCGG
Found at i:1251335 original size:15 final size:15
Alignment explanation
Indices: 1251315--1251345 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1251305 GATTTGAGAT
1251315 AAAAAAAAAAAAGAA
1 AAAAAAAAAAAAGAA
*
1251330 AAAAAAAGAAAAGAA
1 AAAAAAAAAAAAGAA
1251345 A
1 A
1251346 TTATGCTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAGAA
Found at i:1252943 original size:13 final size:13
Alignment explanation
Indices: 1252927--1252952 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1252917 TCCCTCATTC
1252927 TCTCTCTCTCTCT
1 TCTCTCTCTCTCT
1252940 TCTCTCTCTCTCT
1 TCTCTCTCTCTCT
1252953 NCATTTCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (13 bp):
TCTCTCTCTCTCT
Found at i:1252944 original size:15 final size:15
Alignment explanation
Indices: 1252924--1252952 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1252914 TTCTCCCTCA
1252924 TTCTCTCTCTCTCTC
1 TTCTCTCTCTCTCTC
1252939 TTCTCTCTCTCTCT
1 TTCTCTCTCTCTCT
1252953 NCATTTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (15 bp):
TTCTCTCTCTCTCTC
Found at i:1253648 original size:4 final size:4
Alignment explanation
Indices: 1253647--1253698 Score: 68
Period size: 4 Copynumber: 13.0 Consensus size: 4
1253637 GGGACAGACA
* * * *
1253647 GACG GACG GACG GACA GACG GACG GACG GACA GACA GACG GACT GACG
1 GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG GACG
1253695 GACG
1 GACG
1253699 CAGTGGAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.31, C:0.25, G:0.42, T:0.02
Consensus pattern (4 bp):
GACG
Found at i:1253662 original size:16 final size:16
Alignment explanation
Indices: 1253638--1253689 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
1253628 AACTGAAGTG
*
1253638 GGACAGACAGACGGAC
1 GGACGGACAGACGGAC
1253654 GGACGGACAGACGGAC
1 GGACGGACAGACGGAC
*
1253670 GGACGGACAGACAGAC
1 GGACGGACAGACGGAC
1253686 GGAC
1 GGAC
1253690 TGACGGACGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.25, G:0.40, T:0.00
Consensus pattern (16 bp):
GGACGGACAGACGGAC
Found at i:1255414 original size:16 final size:16
Alignment explanation
Indices: 1255393--1255424 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1255383 AACTGTAGTG
1255393 GGACAGACAGACGGAC
1 GGACAGACAGACGGAC
1255409 GGACAGACAGACGGAC
1 GGACAGACAGACGGAC
1255425 TGATGGACGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.38, T:0.00
Consensus pattern (16 bp):
GGACAGACAGACGGAC
Found at i:1256801 original size:17 final size:17
Alignment explanation
Indices: 1256781--1256813 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1256771 AACTCTCAGA
1256781 TTAGCCGATAACTGGTC
1 TTAGCCGATAACTGGTC
1256798 TTAGCCGATAACTGGT
1 TTAGCCGATAACTGGT
1256814 ACAGTACCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (17 bp):
TTAGCCGATAACTGGTC
Found at i:1260459 original size:189 final size:189
Alignment explanation
Indices: 1260137--1260515 Score: 742
Period size: 189 Copynumber: 2.0 Consensus size: 189
1260127 GGGAGGCTTC
1260137 GCCCCCTGAACCCCCCGGCCCCCAGACCCCCTGCCGCAATAAATTTGCCTCACTAGAATATTATC
1 GCCCCCTGAACCCCCCGGCCCCCAGACCCCCTGCCGCAATAAATTTGCCTCACTAGAATATTATC
1260202 TCAAGCTACGCCCCTGCATCTGTGTATAACCCGTCCCGATTTAACTTCGGCTTGAGCATGAATCG
66 TCAAGCTACGCCCCTGCATCTGTGTATAACCCGTCCCGATTTAACTTCGGCTTGAGCATGAATCG
1260267 AAGATTGGTAGTATTCAGGTCAAAGATTGTCAAAATAAAATTCACAATTCTTCAAAATT
131 AAGATTGGTAGTATTCAGGTCAAAGATTGTCAAAATAAAATTCACAATTCTTCAAAATT
1260326 GNCCCCCTGAACCCCCCGGCCCCCAGA-CCCCTGCCGCAATAAATTTGCCTCACTAGAATATTAT
1 G-CCCCCTGAACCCCCCGGCCCCCAGACCCCCTGCCGCAATAAATTTGCCTCACTAGAATATTAT
1260390 CTCAAGCTACGCCCCTGCATCTGTGTATAACCCGTCCCGATTTAACTTCGGCTTGAGCATGAATC
65 CTCAAGCTACGCCCCTGCATCTGTGTATAACCCGTCCCGATTTAACTTCGGCTTGAGCATGAATC
1260455 GAAGATTGGTAGTATTCAGGTCAAAGATTGTCAAAATAAAATTCACAATTCTTCAAAATT
130 GAAGATTGGTAGTATTCAGGTCAAAGATTGTCAAAATAAAATTCACAATTCTTCAAAATT
1260515 G
1 G
1260516 GCACATTGCA
Statistics
Matches: 189, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
189 164 0.87
190 25 0.13
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.26
Consensus pattern (189 bp):
GCCCCCTGAACCCCCCGGCCCCCAGACCCCCTGCCGCAATAAATTTGCCTCACTAGAATATTATC
TCAAGCTACGCCCCTGCATCTGTGTATAACCCGTCCCGATTTAACTTCGGCTTGAGCATGAATCG
AAGATTGGTAGTATTCAGGTCAAAGATTGTCAAAATAAAATTCACAATTCTTCAAAATT
Found at i:1268606 original size:18 final size:18
Alignment explanation
Indices: 1268583--1268620 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1268573 AAATATTACT
1268583 GCTCCTCCGACACAAGCG
1 GCTCCTCCGACACAAGCG
*
1268601 GCTCCTCCGACACCAGCG
1 GCTCCTCCGACACAAGCG
1268619 GC
1 GC
1268621 NNNNNNNNNN
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.47, G:0.24, T:0.11
Consensus pattern (18 bp):
GCTCCTCCGACACAAGCG
Found at i:1269354 original size:2 final size:2
Alignment explanation
Indices: 1269347--1269371 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1269337 NNNNNNNNNN
1269347 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1269372 AAGCACTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1270041 original size:146 final size:145
Alignment explanation
Indices: 1269599--1270402 Score: 1128
Period size: 146 Copynumber: 5.5 Consensus size: 145
1269589 AAAAACTGTT
* * * *
1269599 GGTCATAAGCAATATTTGTGTGAAGTAAGAACATTCAATGCTTCTCCATAAGAAAGATAAT-AAC
1 GGTCATAAGCAATCTTTGTATGAAGTAAGAAC-TTCAATGTTTCTCCATAAGAAAGAT-ATGGAC
1269663 CGGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAG
64 CGGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAG
*
1269728 GTCATGACACACCCTTT
129 GTCATGACACACCCTTA
* * * * * *
1269745 GGTCCTAAGCAATATTTGTGTGAAGTTAGAACATTCAATGCTTCTTCATAAGAAAGATAAT-GAC
1 GGTCATAAGCAATCTTTGTATGAAGTAAGAAC-TTCAATGTTTCTCCATAAGAAAGAT-ATGGAC
* * * * ** *
1269809 CGGACACGAATTTTGCATTATTTTTTTCCCAACGACCTTGACCTTGCCCAAATGACCTTGGATCA
64 CGGACACAAATTTTGCA--CTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCA
*
1269874 AGGTCATGACACACCCATA
127 AGGTCATGACACACCCTTA
* * * *
1269893 GGTCATTAGCAATCTTTGTATGAATTAAGAATTTCAAATGTTTCTCCATAAGAAAGATATGGGCC
1 GGTCATAAGCAATCTTTGTATGAAGTAAGAACTTC-AATGTTTCTCCATAAGAAAGATATGGACC
*
1269958 GGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCTAATGACCTTGGGTCAAGG
65 GGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG
1270023 TCATGACACACCCTTA
130 TCATGACACACCCTTA
* *
1270039 GGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCAAATGTTTCTCCATTAGAAAGATATGGACC
1 GGTCATAAGCAATCTTTGTATGAAGTAAGAACTTC-AATGTTTCTCCATAAGAAAGATATGGACC
* * * * *
1270104 GGACACGAATTTTTGTA-TGTTTTCTGCCAGTGACCATGAACTTGCCCGAATGACCTTGGGTCAA
65 GGACAC-AAATTTTGCACT-TTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAA
1270168 GGTCATGACACACCCTTA
128 GGTCATGACACACCCTTA
1270186 GGTCATAAGCAATCTTTGTATGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
1 GGTCATAAGCAATCTTTGTATGAAGTAAGAACTT-CAATGTTTCTCCATAAGAAAGATATGGACC
* * * * * *
1270251 GGACACTAATATCGTATTTTTTCTGCCAGTGACCTTGACCTTGCCCGAATGACCTTGGGTCAAGG
65 GGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG
*
1270316 TCATGACACACCCTAA
130 TCATGACACACCCTTA
*
1270332 GGTCATAAGCGATCTTTGTATGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
1 GGTCATAAGCAATCTTTGTATGAAGTAAGAACTT-CAATGTTTCTCCATAAGAAAGATATGGACC
1270397 GGACAC
65 GGACAC
1270403 GATTGCACAG
Statistics
Matches: 597, Mismatches: 53, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
146 335 0.56
147 141 0.24
148 121 0.20
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (145 bp):
GGTCATAAGCAATCTTTGTATGAAGTAAGAACTTCAATGTTTCTCCATAAGAAAGATATGGACCG
GACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGT
CATGACACACCCTTA
Found at i:1270304 original size:293 final size:291
Alignment explanation
Indices: 1269599--1270404 Score: 1179
Period size: 293 Copynumber: 2.7 Consensus size: 291
1269589 AAAAACTGTT
* * * *
1269599 GGTCATAAGCAATATTTGTGTGAAGTAAGAACATT-CAATGCTTCTCCATAAGAAAGATAAT-AA
1 GGTCATAAGCAATCTTTGTATGAAGTAAGAAC-TTCCAATGTTTCTCCATAAGAAAGAT-ATGGA
1269662 CCGGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAA
64 CCGGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAA
* * * * * *
1269727 GGTCATGACACACCCTTTGGTCCTAAGCAATATTTGTGTGAAGTTAGAACATTCAATGCTTCTTC
129 GGTCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAAC-TTCAATGTTTCTCC
* * *
1269792 ATAAGAAAGATAAT-GACCGGACACGAATTTTGCATTATTTTTTTCCCAACGACCTTGACCTTGC
193 ATAAGAAAGAT-ATGGACCGGACACGAATTTTG-A-TATTTTTCTCCCAACGACCATGAACTTGC
1269856 CCAAATGACCTTGGATCAAGGTCATGACACACCCATA
255 CCAAATGACCTTGGATCAAGGTCATGACACACCCATA
* * * * *
1269893 GGTCATTAGCAATCTTTGTATGAATTAAGAATTTCAAATGTTTCTCCATAAGAAAGATATGGGCC
1 GGTCATAAGCAATCTTTGTATGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
*
1269958 GGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCTAATGACCTTGGGTCAAGG
66 GGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG
1270023 TCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCAAATGTTTCTCCAT
131 TCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTC-AATGTTTCTCCAT
* * ** *
1270088 TAGAAAGATATGGACCGGACACGAATTTTTG-TATGTTTTCTGCCAGTGACCATGAACTTGCCCG
195 AAGAAAGATATGGACCGGACACGAA-TTTTGATAT-TTTTCTCCCAACGACCATGAACTTGCCCA
* *
1270152 AATGACCTTGGGTCAAGGTCATGACACACCCTTA
258 AATGACCTTGGATCAAGGTCATGACACACCCATA
1270186 GGTCATAAGCAATCTTTGTATGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
1 GGTCATAAGCAATCTTTGTATGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
* * * * * *
1270251 GGACACTAATATCGTATTTTTTCTGCCAGTGACCTTGACCTTGCCCGAATGACCTTGGGTCAAGG
66 GGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG
* * *
1270316 TCATGACACACCCTAAGGTCATAAGCGATCTTTGTATGAAGTAAGAACTTCCAATGTTTCTCCAT
131 TCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACTT-CAATGTTTCTCCAT
1270381 AAGAAAGATATGGACCGGACACGA
195 AAGAAAGATATGGACCGGACACGA
1270405 TTGCACAGAC
Statistics
Matches: 464, Mismatches: 41, Indels: 15
0.89 0.08 0.03
Matches are distributed among these distances:
292 3 0.01
293 265 0.57
294 191 0.41
295 5 0.01
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (291 bp):
GGTCATAAGCAATCTTTGTATGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAGATATGGACC
GGACACAAATTTTGCACTTTTTCTGCCAGTGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGG
TCATGACACACCCTTAGGTCATAAGCAATCTTTGTGTGAAGTAAGAACTTCAATGTTTCTCCATA
AGAAAGATATGGACCGGACACGAATTTTGATATTTTTCTCCCAACGACCATGAACTTGCCCAAAT
GACCTTGGATCAAGGTCATGACACACCCATA
Found at i:1270429 original size:12 final size:12
Alignment explanation
Indices: 1270412--1270463 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
1270402 CGATTGCACA
*
1270412 GACAGACGGACG
1 GACAGACAGACG
*
1270424 GACAGACGGACG
1 GACAGACAGACG
*
1270436 GACAAACAGACG
1 GACAGACAGACG
*
1270448 GACGGACAGACG
1 GACAGACAGACG
1270460 GACA
1 GACA
1270464 AGGTGATTCC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.38, C:0.25, G:0.37, T:0.00
Consensus pattern (12 bp):
GACAGACAGACG
Found at i:1270430 original size:16 final size:16
Alignment explanation
Indices: 1270409--1270458 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
1270399 ACACGATTGC
* *
1270409 ACAGACAGACGGACGG
1 ACAGACGGACGGACAG
*
1270425 ACAGACGGACGGACAA
1 ACAGACGGACGGACAG
1270441 ACAGACGGACGGACAG
1 ACAGACGGACGGACAG
1270457 AC
1 AC
1270459 GGACAAGGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.40, C:0.26, G:0.34, T:0.00
Consensus pattern (16 bp):
ACAGACGGACGGACAG
Found at i:1270660 original size:18 final size:18
Alignment explanation
Indices: 1270639--1270678 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1270629 ACCACTAAAC
*
1270639 TAAAAACTAAATAATATA
1 TAAAAACTAAAAAATATA
*
1270657 TAAAAACTAAAAAATGTA
1 TAAAAACTAAAAAATATA
1270675 TAAA
1 TAAA
1270679 CACCGGATCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.25
Consensus pattern (18 bp):
TAAAAACTAAAAAATATA
Found at i:1274932 original size:26 final size:21
Alignment explanation
Indices: 1274851--1274970 Score: 206
Period size: 21 Copynumber: 5.8 Consensus size: 21
1274841 ATTCAAATAT
*
1274851 TTGTACCTATCTTCAAAT-AA
1 TTGTACCTATCTTCAATTCAA
*
1274871 TTGTACCTATCTTCAATTCAG
1 TTGTACCTATCTTCAATTCAA
*
1274892 TTGTACTTATCTTCAATTCAA
1 TTGTACCTATCTTCAATTCAA
1274913 TTGTACCTATCTTCAATTCAA
1 TTGTACCTATCTTCAATTCAA
1274934 TTGTACCTATCTTCAATTCAA
1 TTGTACCTATCTTCAATTCAA
1274955 TTGTACCTATCTTCAA
1 TTGTACCTATCTTCAA
1274971 ATTGAATTAG
Statistics
Matches: 94, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
20 17 0.18
21 77 0.82
ACGTcount: A:0.28, C:0.23, G:0.06, T:0.43
Consensus pattern (21 bp):
TTGTACCTATCTTCAATTCAA
Found at i:1275310 original size:17 final size:17
Alignment explanation
Indices: 1275280--1275313 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1275270 TATATAAGTG
*
1275280 ACCCTAACTACGTCACT
1 ACCCTAACGACGTCACT
*
1275297 ACCCTAACGCCGTCACT
1 ACCCTAACGACGTCACT
1275314 TTTGGGGTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.44, G:0.09, T:0.21
Consensus pattern (17 bp):
ACCCTAACGACGTCACT
Found at i:1275380 original size:2 final size:2
Alignment explanation
Indices: 1275375--1275415 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1275365 ACACACACAG
* *
1275375 AT AT AT AG AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1275416 ATTTTGAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1275628 original size:21 final size:21
Alignment explanation
Indices: 1275596--1275664 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
1275586 TAGATATGTC
* *
1275596 TGAATTGAACCTGTCTTCAAA
1 TGAATTGTACCTATCTTCAAA
* * *
1275617 TCAATTGTACCTATTTTTAAA
1 TGAATTGTACCTATCTTCAAA
* *
1275638 TGAATTTTTCCTATCTTCAAA
1 TGAATTGTACCTATCTTCAAA
1275659 TGAATT
1 TGAATT
1275665 AGAGATAGGT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (21 bp):
TGAATTGTACCTATCTTCAAA
Found at i:1275693 original size:42 final size:42
Alignment explanation
Indices: 1275647--1275734 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
1275637 ATGAATTTTT
1275647 CCTATCTTCAAATGAATT-AGAGATAGGTATAATTCAATTGAA
1 CCTATCTTCAAATGAATTGA-AGATAGGTATAATTCAATTGAA
* * * *
1275689 CCTATCTTTAATTGAATTGAAGATAGGTATAATTCATTTGTA
1 CCTATCTTCAAATGAATTGAAGATAGGTATAATTCAATTGAA
1275731 CCTA
1 CCTA
1275735 GGTATAATTC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 40 0.98
43 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (42 bp):
CCTATCTTCAAATGAATTGAAGATAGGTATAATTCAATTGAA
Found at i:1275721 original size:21 final size:21
Alignment explanation
Indices: 1275669--1275764 Score: 84
Period size: 21 Copynumber: 4.6 Consensus size: 21
1275659 TGAATTAGAG
1275669 ATAGGTATAATTCAATTGAAC
1 ATAGGTATAATTCAATTGAAC
* ** * * *
1275690 CTATCTTTAATTGAATTGAAG
1 ATAGGTATAATTCAATTGAAC
* *
1275711 ATAGGTATAATTCATTTGTAC
1 ATAGGTATAATTCAATTGAAC
* * *
1275732 CTAGGTATAATTCATTTGTAC
1 ATAGGTATAATTCAATTGAAC
*
1275753 CTAGGTATAATT
1 ATAGGTATAATT
1275765 ATTTAGAGAT
Statistics
Matches: 60, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (21 bp):
ATAGGTATAATTCAATTGAAC
Found at i:1275789 original size:20 final size:21
Alignment explanation
Indices: 1275711--1275788 Score: 99
Period size: 21 Copynumber: 3.8 Consensus size: 21
1275701 TGAATTGAAG
1275711 ATAGGTATAATTCATTTGTAC
1 ATAGGTATAATTCATTTGTAC
*
1275732 CTAGGTATAATTCATTTGTAC
1 ATAGGTATAATTCATTTGTAC
* *
1275753 CTAGGTATAATT-ATTTAG-AG
1 ATAGGTATAATTCATTT-GTAC
1275773 ATAGGTATAATT-ATTT
1 ATAGGTATAATTCATTT
1275789 ACACCTATCT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
20 20 0.38
21 33 0.62
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (21 bp):
ATAGGTATAATTCATTTGTAC
Found at i:1275815 original size:21 final size:21
Alignment explanation
Indices: 1275791--1275864 Score: 105
Period size: 21 Copynumber: 3.6 Consensus size: 21
1275781 AATTATTTAC
1275791 ACCTATCTTCAATTCAATTGT
1 ACCTATCTTCAATTCAATTGT
*
1275812 ACCTATCTTCAAAT-AATTGT
1 ACCTATCTTCAATTCAATTGT
* *
1275832 ACCTATCTTTAATGCAATTGT
1 ACCTATCTTCAATTCAATTGT
*
1275853 AGCTATCTTCAA
1 ACCTATCTTCAA
1275865 ATGATTTGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 17 0.37
21 29 0.63
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.41
Consensus pattern (21 bp):
ACCTATCTTCAATTCAATTGT
Found at i:1275930 original size:20 final size:20
Alignment explanation
Indices: 1275862--1275934 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1275852 TAGCTATCTT
1275862 CAAATGATTTGAAGATAGGTA
1 CAAAT-ATTTGAAGATAGGTA
* * *
1275883 CAATTAATTGAAGATGGGTA
1 CAAATATTTGAAGATAGGTA
*
1275903 CAATTATTTGAAGATAGGTA
1 CAAATATTTGAAGATAGGTA
1275923 CAAATATTTGAA
1 CAAATATTTGAA
1275935 TATATGTTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
20 42 0.91
21 4 0.09
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (20 bp):
CAAATATTTGAAGATAGGTA
Found at i:1276211 original size:4 final size:4
Alignment explanation
Indices: 1276202--1276231 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1276192 AATATTGAAA
1276202 TATT TATT TATT TATT T-TT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TAT
1276232 CTAAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TATT
Found at i:1276222 original size:11 final size:12
Alignment explanation
Indices: 1276202--1276231 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
1276192 AATATTGAAA
1276202 TATTTATTTATT
1 TATTTATTTATT
1276214 TATTT-TTTATT
1 TATTTATTTATT
1276225 TATTTAT
1 TATTTAT
1276232 CTAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TATTTATTTATT
Found at i:1280651 original size:91 final size:90
Alignment explanation
Indices: 1280494--1280662 Score: 268
Period size: 91 Copynumber: 1.9 Consensus size: 90
1280484 TTCATGGCCA
* **
1280494 CTGGGTCAGAGGTTCAGGCTCTCAGGTGGGGTTAATATGGCATTATAGTAAAACTGTATTAAATC
1 CTGGGTCAGAGGTTCAGGCTCTAAGGTGGGGCCAATATGGCATTATAGTAAAACTGTATTAAATC
1280559 TTAGAAAGTCTTCTATTTCCTTAAAT
66 TTAGAAAGT-TTCTATTTCCTTAAAT
* *
1280585 CTGGGTCAGAGGTTCAGGGTCTAAGG-GTGGGCCAATATGGCATTATAGTAAAACTGTATTATAT
1 CTGGGTCAGAGGTTCAGGCTCTAAGGTG-GGGCCAATATGGCATTATAGTAAAACTGTATTAAAT
1280649 CTTAGAAAGTTTCT
65 CTTAGAAAGTTTCT
1280663 CTATTCCCAT
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
90 5 0.07
91 67 0.93
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (90 bp):
CTGGGTCAGAGGTTCAGGCTCTAAGGTGGGGCCAATATGGCATTATAGTAAAACTGTATTAAATC
TTAGAAAGTTTCTATTTCCTTAAAT
Found at i:1281173 original size:24 final size:21
Alignment explanation
Indices: 1281126--1281168 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1281116 CTTAAGTATG
*
1281126 TAATGTTGAAGTATCATAATA
1 TAATATTGAAGTATCATAATA
*
1281147 TAATATTGAAGTATCATCATA
1 TAATATTGAAGTATCATAATA
1281168 T
1 T
1281169 TATAACGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.40
Consensus pattern (21 bp):
TAATATTGAAGTATCATAATA
Found at i:1291420 original size:4 final size:4
Alignment explanation
Indices: 1291411--1291477 Score: 73
Period size: 4 Copynumber: 16.8 Consensus size: 4
1291401 AAATGGAGTG
* * * *
1291411 CACA CACA CACA TACA TACA CACA CACA TACA CACA CACA CATA CACA
1 CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA CACA
*
1291459 CACA TACGA -ACA CACA CAC
1 CACA CAC-A CACA CACA CAC
1291478 GCACGGTAGA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
3 1 0.02
4 52 0.96
5 1 0.02
ACGTcount: A:0.49, C:0.42, G:0.01, T:0.07
Consensus pattern (4 bp):
CACA
Found at i:1291472 original size:10 final size:10
Alignment explanation
Indices: 1291414--1291465 Score: 68
Period size: 10 Copynumber: 5.2 Consensus size: 10
1291404 TGGAGTGCAC
1291414 ACACACACAT
1 ACACACACAT
* *
1291424 ACATACACAC
1 ACACACACAT
* *
1291434 ACACATACAC
1 ACACACACAT
1291444 ACACACACAT
1 ACACACACAT
1291454 ACACACACAT
1 ACACACACAT
1291464 AC
1 AC
1291466 GAACACACAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 36 1.00
ACGTcount: A:0.50, C:0.40, G:0.00, T:0.10
Consensus pattern (10 bp):
ACACACACAT
Found at i:1291473 original size:16 final size:14
Alignment explanation
Indices: 1291411--1291477 Score: 91
Period size: 14 Copynumber: 4.6 Consensus size: 14
1291401 AAATGGAGTG
1291411 CACACACACACATA
1 CACACACACACATA
1291425 CATACACACACACATA
1 C--ACACACACACATA
1291441 CACACACACACATA
1 CACACACACACATA
*
1291455 CACACACATACGA-A
1 CACACACACAC-ATA
1291469 CACACACAC
1 CACACACAC
1291478 GCACGGTAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
14 33 0.69
15 1 0.02
16 14 0.29
ACGTcount: A:0.49, C:0.42, G:0.01, T:0.07
Consensus pattern (14 bp):
CACACACACACATA
Found at i:1298273 original size:162 final size:161
Alignment explanation
Indices: 1298043--1298335 Score: 464
Period size: 162 Copynumber: 1.8 Consensus size: 161
1298033 CTAACAAAGT
* * *
1298043 GGTCATGAATTTCACAATTTTAGTAGAGGACTTCATGGACATTATAATCAGGTATTTAGTTTTTA
1 GGTCATGAATTTCACAATTTTAGTAGAGGACCTCATGGACATCATAATCAGGCATTTAGTTTTTA
1298108 ACAAATATATATTTAGGAGTAGAGAAGAAGATTTTCT-AAGATTTAATACATTCTTT-CTATATG
66 ACAAATATATA--TAGGAGTAGAGAAGAAGATTTTCTAAAGATTTAATAC-TTCTTTACTATATG
1298171 GCCACATTGGCCCCACCCTAGAGCCTGACCCAGG
128 GCCACATTGGCCCCACCCTAGAGCCTGACCCAGG
* * *
1298205 GGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGGACATCATAATCATGCATTTAGTTTTTA
1 GGTCATGAATTTCACAATTTTAGTAGAGGACCTCATGGACATCATAATCAGGCATTTAGTTTTTA
* * *
1298270 ACAAATATATATGGGAGTAGAGAAGAAGATTTTTTAAAGATTTAATACTTTTTTACTATATGGCC
66 ACAAATATATATAGGAGTAGAGAAGAAGATTTTCTAAAGATTTAATACTTCTTTACTATATGGCC
1298335 A
131 A
1298336 TACTCTAGCG
Statistics
Matches: 120, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
160 27 0.22
161 23 0.19
162 70 0.58
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (161 bp):
GGTCATGAATTTCACAATTTTAGTAGAGGACCTCATGGACATCATAATCAGGCATTTAGTTTTTA
ACAAATATATATAGGAGTAGAGAAGAAGATTTTCTAAAGATTTAATACTTCTTTACTATATGGCC
ACATTGGCCCCACCCTAGAGCCTGACCCAGG
Found at i:1298686 original size:25 final size:25
Alignment explanation
Indices: 1298658--1298706 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
1298648 AATTTTGGAG
1298658 TTTTGGAGGATAACAGTTGAAATTT
1 TTTTGGAGGATAACAGTTGAAATTT
1298683 TTTTGGAGGATAACAGTTGAAATT
1 TTTTGGAGGATAACAGTTGAAATT
1298707 GACACCCCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.24, T:0.39
Consensus pattern (25 bp):
TTTTGGAGGATAACAGTTGAAATTT
Found at i:1314754 original size:1 final size:1
Alignment explanation
Indices: 1314748--1314772 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1314738 GTACATGTTA
1314748 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
1314773 ATTCCACCAA
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:1316031 original size:167 final size:166
Alignment explanation
Indices: 1315601--1316221 Score: 730
Period size: 168 Copynumber: 3.7 Consensus size: 166
1315591 CCAAATTTTC
* * * * *
1315601 AAAAATCTTCTTCTCTAATCCCACGCATGTGAGG-AAAAAAC-CAGTTGCATGGTTATGATGTCC
1 AAAAATCTTCTTCTCTACTCCCACACATGTG-GGCAAAAAACTGA-ATACATGGTTATGATGTCC
* * * * * *
1315664 ATAAAGCCCTCTACCAAAATTGTGAAATTTATGGCCCCAGGGTCAGGGGTTCTGGCTCTAGGGTG
64 ATGAAG-CCTCTACCTAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGTG
*
1315729 GGGCCAATATGGCCATATAGTAAAAATGTATTAAATCTT
128 GGGCCAATATGGCCATATAGTAAAAATGTTTTAAATCTT
* * * * * **** * * *
1315768 AGAAAATCTTCTTCTTTACTACCATATATATTTTTAAAAAACTAAATGCATGATTATGATGTCCA
1 A-AAAATCTTCTTCTCTACTCCCACACATGTGGGCAAAAAACTGAATACATGGTTATGATGTCCA
* *
1315833 TGAAGCCTTCTACCTAAATTATGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGTCG
65 TGAAGCC-TCTACCTAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGTGG
* * * *
1315898 GGCCAATGTGGCCATAAAGTAAAACTGTTTTAGATCTT
129 GGCCAATATGGCCATATAGTAAAAATGTTTTAAATCTT
1315936 AAAAATCTTCTTCTCTACTCCCACACATGTGGGCAAAAAACTGAATACATGGTTATGATGTCCAT
1 AAAAATCTTCTTCTCTACTCCCACACATGTGGGCAAAAAACTGAATACATGGTTATGATGTCCAT
* ** * *
1316001 GAGAGCCTCTA-CTAAAACTGTGAAATTCATGACCCCTTTGTTAGGTGTTCAGGCTCTAGGGTGG
66 GA-AGCCTCTACCT-AAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGTGG
*
1316065 GGCCAATATGGCCATATAGTAAAAGTGTTTTAAATCTT
129 GGCCAATATGGCCATATAGTAAAAATGTTTTAAATCTT
*
1316103 AAAAAATCTTCTTCTCTACTCCCACACATGTGGGCAAAAAACTGAATACATGGTTCA-GATATCC
1 -AAAAATCTTCTTCTCTACTCCCACACATGTGGGCAAAAAACTGAATACATGGTT-ATGATGTCC
* * * * *
1316167 A-GAATCTCCTTTACCTAAATTGTGGAATTCATGACACCTTGGTCAGGGGTTCAGG
64 ATGAA--GCCTCTACCTAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGG
1316222 ACATGAAAGG
Statistics
Matches: 385, Mismatches: 58, Indels: 21
0.83 0.12 0.05
Matches are distributed among these distances:
166 3 0.01
167 140 0.36
168 238 0.62
169 4 0.01
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (166 bp):
AAAAATCTTCTTCTCTACTCCCACACATGTGGGCAAAAAACTGAATACATGGTTATGATGTCCAT
GAAGCCTCTACCTAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGTGGGG
CCAATATGGCCATATAGTAAAAATGTTTTAAATCTT
Found at i:1316213 original size:335 final size:335
Alignment explanation
Indices: 1315601--1316221 Score: 813
Period size: 335 Copynumber: 1.9 Consensus size: 335
1315591 CCAAATTTTC
* * *
1315601 AAAAATCTTCTTCTCTAATCCCACGCATGTGAGGAAAAAACCAGTTGCATGGTTATGATGTCCAT
1 AAAAATCTTCTTCTCTAATCCCACACATGTGAGGAAAAAACCAGATACATGGTTATGATGTCCAT
* * * *
1315666 AAAGCCCTCTACCAAAATTGTGAAATTTATGGCCCCAGGGTCAGGGGTTCTGGCTCTAGGGTGGG
66 AAAGCCCTCTACCAAAACTGTGAAATTCATGACCCCAGGGTCAGGGGTTCAGGCTCTAGGGTGGG
* * * *
1315731 GCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAGAAAATCTTCTTCTTTACTACCATATA
131 GCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAAAAAATCTTCTTCTCTACTACCACACA
**** * *
1315796 TATTTTTAAAAAACTAAATGCATGATTATGATGTCCATGAAGCCTTCTACCTAAATTATGAAATT
196 TATGGGCAAAAAACTAAATACATGATTATGATATCCATGAAGCCTTCTACCTAAATTATGAAATT
*
1315861 CATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGTCGGGCCAATGTGGCCATAAAGTAAAACTGT
261 CATGACACCTGGGTCAGGGGTTCAGGCTCTAGGGTCGGGCCAATGTGGCCATAAAGTAAAACTGT
1315926 TTTAGATCTT
326 TTTAGATCTT
* *
1315936 AAAAATCTTCTTCTCTACTCCCACACATGTG-GGCAAAAAA-CTGAATACATGGTTATGATGTCC
1 AAAAATCTTCTTCTCTAATCCCACACATGTGAGG-AAAAAACCAG-ATACATGGTTATGATGTCC
* * *** * *
1315999 ATGAGAG-CCTCTACTAAAACTGTGAAATTCATGACCCCTTTGTTAGGTGTTCAGGCTCTAGGGT
64 AT-AAAGCCCTCTACCAAAACTGTGAAATTCATGACCCCAGGGTCAGGGGTTCAGGCTCTAGGGT
* * *
1316063 GGGGCCAATATGGCCATATAGTAAAAGTGTTTTAAATCTTAAAAAATCTTCTTCTCTACTCCCAC
128 GGGGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAAAAAATCTTCTTCTCTACTACCAC
* * * * *
1316128 ACATGTGGGCAAAAAACTGAATACATGGTTCA-GATATCCA-GAATCTCCTT-TACCTAAATTGT
193 ACATATGGGCAAAAAACTAAATACATGATT-ATGATATCCATGAA--GCCTTCTACCTAAATTAT
* *
1316190 GGAATTCATGACACCTTGGTCAGGGGTTCAGG
255 GAAATTCATGACACCTGGGTCAGGGGTTCAGG
1316222 ACATGAAAGG
Statistics
Matches: 243, Mismatches: 37, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
334 7 0.03
335 228 0.94
336 8 0.03
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (335 bp):
AAAAATCTTCTTCTCTAATCCCACACATGTGAGGAAAAAACCAGATACATGGTTATGATGTCCAT
AAAGCCCTCTACCAAAACTGTGAAATTCATGACCCCAGGGTCAGGGGTTCAGGCTCTAGGGTGGG
GCCAATATGGCCATATAGTAAAAATGTATTAAATCTTAAAAAATCTTCTTCTCTACTACCACACA
TATGGGCAAAAAACTAAATACATGATTATGATATCCATGAAGCCTTCTACCTAAATTATGAAATT
CATGACACCTGGGTCAGGGGTTCAGGCTCTAGGGTCGGGCCAATGTGGCCATAAAGTAAAACTGT
TTTAGATCTT
Found at i:1318513 original size:134 final size:135
Alignment explanation
Indices: 1318230--1318497 Score: 312
Period size: 135 Copynumber: 2.0 Consensus size: 135
1318220 CCCTTTAATT
* * * * * * *
1318230 AAGGATCAAGCATATATATGGTTAAGGGGTGGGGATCTCAACCGTTTTCGAGATATTCGTGCATT
1 AAGGAACAAGAATATATATGGTTAAGGGGCGGGGATCCCAACCGTTTTCGAGATATTAGTGAACT
* * *
1318295 TCCTGTTCGAGGGGGGTCACGACCACCCACGGGGCCCATGATATACATACTGTTTGATGCCCCTT
66 TCCTGTTCGAGGGGGGTCACGACCACCCACAGGGCCCATGACATACATACTATTTGATGCCCCTT
1318360 GACAC
131 GACAC
*
1318365 AAGGAACAAGAATATATATGGTTTAA-GGGCGGGGATCCCAACTGTTTT-GAAGATATTAAG-GA
1 AAGGAACAAGAATATATATGG-TTAAGGGGCGGGGATCCCAACCGTTTTCG-AGATATT-AGTGA
* * * * * *
1318427 ACTTGCTGTTTGA-GGGGGTCAGGACCATCCACAGGGCCCATGACCTACATAAC-ATTTGATGCT
63 ACTTCCTGTTCGAGGGGGGTCACGACCACCCACAGGGCCCATGACATACAT-ACTATTTGATGCC
1318490 CCTTGACA
127 CCTTGACA
1318498 TCAGAACCAT
Statistics
Matches: 112, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
134 49 0.44
135 58 0.52
136 5 0.04
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (135 bp):
AAGGAACAAGAATATATATGGTTAAGGGGCGGGGATCCCAACCGTTTTCGAGATATTAGTGAACT
TCCTGTTCGAGGGGGGTCACGACCACCCACAGGGCCCATGACATACATACTATTTGATGCCCCTT
GACAC
Found at i:1321717 original size:21 final size:21
Alignment explanation
Indices: 1321693--1321734 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1321683 CTTTTTTTTA
1321693 AATCAATTTTCATATAATTAG
1 AATCAATTTTCATATAATTAG
1321714 AATCAATTTTCATATAATTAG
1 AATCAATTTTCATATAATTAG
1321735 CAATAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.43
Consensus pattern (21 bp):
AATCAATTTTCATATAATTAG
Found at i:1326303 original size:2 final size:2
Alignment explanation
Indices: 1326296--1326320 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1326286 TCCTGTCATT
1326296 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
1326321 GAGCAAGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1327393 original size:2 final size:2
Alignment explanation
Indices: 1327386--1327421 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1327376 AAAAATAAAC
1327386 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
1327422 CAGGGATGGG
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1327541 original size:11 final size:11
Alignment explanation
Indices: 1327525--1327562 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
1327515 ATATTGTGTA
1327525 TTTTCAATTAC
1 TTTTCAATTAC
1327536 TTTTCAATTAC
1 TTTTCAATTAC
* *
1327547 ATCTCAATTAC
1 TTTTCAATTAC
1327558 TTTTC
1 TTTTC
1327563 TCCAAGTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (11 bp):
TTTTCAATTAC
Found at i:1328174 original size:32 final size:33
Alignment explanation
Indices: 1328119--1328180 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 33
1328109 AAATAAAACT
1328119 AAAGTAATTGAAATGTAATTAATTACATTTATC
1 AAAGTAATTGAAATGTAATTAATTACATTTATC
*
1328152 AAAGTAATTGAGA-GTAATTAATTACATTT
1 AAAGTAATTGAAATGTAATTAATTACATTT
1328181 TAAAAAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (33 bp):
AAAGTAATTGAAATGTAATTAATTACATTTATC
Found at i:1328285 original size:2 final size:2
Alignment explanation
Indices: 1328278--1328304 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1328268 CCCCAACTCT
1328278 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1328305 TGAGTGTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1348794 original size:165 final size:165
Alignment explanation
Indices: 1348509--1349089 Score: 796
Period size: 165 Copynumber: 3.5 Consensus size: 165
1348499 CATATGAGCG
* * * * * *
1348509 ACTATTTATTGCAGATGCTTGAAATTTTTACACAGTATATGTATAGGCATGCTATATCGTGGGAT
1 ACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGT-TTGGCATGCCATATCGTGGGAT
* * *
1348574 GTATTTTTGTACCAATCGGACGTCAACTTCCTGTT-TATGAGTACTTTGTTTTTTTTTAGCAAAA
65 ATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGAGTACTTTGTTTTTTTTTAGCCAAA
*
1348638 ATTTTAAAACAAATTTCCGTCAAAGATTTCTCAGCA
130 ATTTTCAAACAAATTTCCGTCAAAGATTTCTCAGCA
* * * * *
1348674 ACTATTAATTGCAGGTGCTTGAAATTTTAACACACTATTTGTTCTGGCATGCCATGTTGTGGGAT
1 ACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTT-TGGCATGCCATATCGTGGGAT
* * *
1348739 ATATTTTTGTATCAATCGGGCGTCAACTTCCTGTTAAAT-AATGACTTTGTTTTTTTTTAGCCAA
65 ATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGAGT-ACTTTGTTTTTTTTTAGCCAA
*
1348803 AATTTTCAAACAAATTTTCGTCAAAGATTTCTCAG-A
129 AATTTTCAAACAAATTTCCGTCAAAGATTTCTCAGCA
* *
1348839 AGCTATTTATCGCAGATGCTTGAAATATTT-ACACAGTGTTTGTTCTGGCATGCCATATCGTGGG
1 A-CTATTTATCGCAGATGCTTGAAAT-TTTAACACACTATTTGTT-TGGCATGCCATATCGTGGG
* *
1348903 ATATATTTTTGAACCAATCGGACGTCAACTTCCTGTTAAATGAGTACTTTG-TTTATTTTAGCCA
63 ATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGAGTACTTTGTTTTTTTTTAGCCA
1348967 AAATTTTCAAACAAAATTTCC-TCAAAGATTTCTCAGCA
128 AAATTTTCAAAC-AAATTTCCGTCAAAGATTTCTCAGCA
* * * *
1349005 CCTTTTTATCGCAGATGCTTGACATTTTAACACACTATTTGTTTAGGCATGCCATATTGTGGGAT
1 ACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTT-GGCATGCCATATCGTGGGAT
*
1349070 ATATTTCTGTACCAATCGGA
65 ATATTTTTGTACCAATCGGA
1349090 TGCCAGCTCT
Statistics
Matches: 368, Mismatches: 38, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
164 5 0.01
165 200 0.54
166 158 0.43
167 5 0.01
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (165 bp):
ACTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTGGCATGCCATATCGTGGGATA
TATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGAGTACTTTGTTTTTTTTTAGCCAAAA
TTTTCAAACAAATTTCCGTCAAAGATTTCTCAGCA
Found at i:1349118 original size:331 final size:331
Alignment explanation
Indices: 1348510--1349108 Score: 893
Period size: 331 Copynumber: 1.8 Consensus size: 331
1348500 ATATGAGCGA
* * * *
1348510 CTATTTATTGCAGATGCTTGAAATTTTTACACAGTATATGTATAGGCATGCTATATCGTGGGATG
1 CTATTTATCGCAGATGCTTGAAATATTTACACAGTATATGTATAGGCATGCCATATCGTGGGATA
* * *
1348575 TATTTTTGTACCAATCGGACGTCAACTTCCTGTTTATGAGTACTTTGTTTTTTTTTAGCAAAAAT
66 TATTTTTGAACCAATCGGACGTCAACTTCCTGTTAATGAGTACTTTGTTTTATTTTAGCAAAAAT
* *
1348640 TTTAAAACAAATTTCCGTCAAAGATTTCTCAGCAACTATTAATTGCAGGTGCTTGAAATTTTAAC
131 TTTAAAACAAATTTCCGTCAAAGATTTCTCAGCAACTATTAATCGCAGATGCTTGAAATTTTAAC
* * * * *
1348705 ACACTATTTGTTCTGGCATGCCATGTTGTGGGATATATTTTTGTATCAATCGGGCGTCAACTTCC
196 ACACTATTTGTTCTGGCATGCCATATTGTGGGATATATTTCTGTACCAATCGGACGCCAACTTCC
1348770 TGTTAAATAATGACTTTGTTTTTTTTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCT
261 TGTTAAATAATGACTTTGTTTTTTTTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCT
1348835 CAGAAG
326 CAGAAG
* * *
1348841 CTATTTATCGCAGATGCTTGAAATATTTACACAGTGTTTGT-TCTGGCATGCCATATCGTGGGAT
1 CTATTTATCGCAGATGCTTGAAATATTTACACAGTATATGTAT-AGGCATGCCATATCGTGGGAT
*
1348905 ATATTTTTGAACCAATCGGACGTCAACTTCCTGTTAAATGAGTACTTTG-TTTATTTTAGCCAAA
65 ATATTTTTGAACCAATCGGACGTCAACTTCCTGTT-AATGAGTACTTTGTTTTATTTTAGCAAAA
* * * * *
1348969 ATTTTCAAACAAAATTTCC-TCAAAGATTTCTCAGCACCTTTTTATCGCAGATGCTTGACATTTT
129 ATTTTAAAAC-AAATTTCCGTCAAAGATTTCTCAGCAACTATTAATCGCAGATGCTTGAAATTTT
* *
1349033 AACACACTATTTGTT-TAGGCATGCCATATTGTGGGATATATTTCTGTACCAATCGGATGCCAGC
193 AACACACTATTTGTTCT-GGCATGCCATATTGTGGGATATATTTCTGTACCAATCGGACGCCAAC
1349097 -TCTCTGTTAAAT
257 TTC-CTGTTAAAT
1349109 GTCGACTTTG
Statistics
Matches: 238, Mismatches: 25, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
330 4 0.02
331 214 0.90
332 20 0.08
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (331 bp):
CTATTTATCGCAGATGCTTGAAATATTTACACAGTATATGTATAGGCATGCCATATCGTGGGATA
TATTTTTGAACCAATCGGACGTCAACTTCCTGTTAATGAGTACTTTGTTTTATTTTAGCAAAAAT
TTTAAAACAAATTTCCGTCAAAGATTTCTCAGCAACTATTAATCGCAGATGCTTGAAATTTTAAC
ACACTATTTGTTCTGGCATGCCATATTGTGGGATATATTTCTGTACCAATCGGACGCCAACTTCC
TGTTAAATAATGACTTTGTTTTTTTTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATTTCT
CAGAAG
Found at i:1349693 original size:2 final size:2
Alignment explanation
Indices: 1349686--1349742 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
1349676 ACTCCATTAA
1349686 CT CT CT CT CT CT CT CT C- 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
1349727 CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT
1349743 AATTAAGCCA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1350008 original size:20 final size:20
Alignment explanation
Indices: 1349962--1350010 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
1349952 TTTAAAAAAG
* * *
1349962 CCCTGAGCAAACCCCGAGTGG
1 CCCTGAG-AAAACCCAAGTGA
*
1349983 CGCTGAGAAAACCCAAGTGA
1 CCCTGAGAAAACCCAAGTGA
1350003 CCCTGAGA
1 CCCTGAGA
1350011 TTTGCACTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.10
Consensus pattern (20 bp):
CCCTGAGAAAACCCAAGTGA
Done.