Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 134 of 187
Found at i:39860128 original size:120 final size:120
Alignment explanation
Indices: 39859912--39860174 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
39859902 TTGAATGCTG
* *
39859912 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
39859976 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
39860032 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
39860095 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
39860151 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
39860175 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:39860194 original size:79 final size:80
Alignment explanation
Indices: 39859913--39860209 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
39859903 TGAATGCTGT
* ** * * * **
39859913 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
39859976 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
39859993 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
39860057 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
39860073 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
39860137 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
39860152 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
39860210 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:39864109 original size:49 final size:49
Alignment explanation
Indices: 39864049--39864166 Score: 186
Period size: 48 Copynumber: 2.4 Consensus size: 49
39864039 TTGATTTTTA
* * *
39864049 AAAACTCTTTTAGATAATAATTTAAATTCTATTTAATTATCT-TTTATTT
1 AAAACTCTTTTAAATAATAATTTAAATTCCATTTAATTAT-TATTTATCT
39864098 AAAACTCTTTTAAATAATAA-TTAAATTCCATTTAATTATTATTTATCT
1 AAAACTCTTTTAAATAATAATTTAAATTCCATTTAATTATTATTTATCT
39864146 AAAACTCTTTTAAATAATAAT
1 AAAACTCTTTTAAATAATAAT
39864167 ATAATTATTA
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
47 1 0.02
48 44 0.69
49 19 0.30
ACGTcount: A:0.42, C:0.09, G:0.01, T:0.48
Consensus pattern (49 bp):
AAAACTCTTTTAAATAATAATTTAAATTCCATTTAATTATTATTTATCT
Found at i:39864173 original size:38 final size:38
Alignment explanation
Indices: 39864130--39864204 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
39864120 AAATTCCATT
*
39864130 TAATTATTATTTATCTAAAACTCTTTTAAATAATAATA
1 TAATTATTATTTATCTAAAAATCTTTTAAATAATAATA
39864168 TAATTATTATTTATCTAAAAATCTTTTAAATAATAAT
1 TAATTATTATTTATCTAAAAATCTTTTAAATAATAAT
39864205 TCTATTTCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (38 bp):
TAATTATTATTTATCTAAAAATCTTTTAAATAATAATA
Found at i:39864358 original size:94 final size:88
Alignment explanation
Indices: 39864168--39864334 Score: 217
Period size: 94 Copynumber: 1.8 Consensus size: 88
39864158 AATAATAATA
* *
39864168 TAATTATTATTTATCTAAAAATCTTTTAAATAATAATTCTATTTCCTTATCTGATAAGGAATATA
1 TAATTATTATTTAGCTAAAAATCTTTTAAATAATAATTCTATTTCCTTATCTAATAAGGAATATA
* * *
39864233 GCAAATTCTTTTGATTTTGAATTT
66 GCAAATCCTTTTGATCTCG-ATTT
*
39864257 TAATTATTATTTAGCTAAAACTCTTTATAATAATAATTAAATTCTATTTCCTTATCTAATAAGGA
1 TAATTATTATTTAGCTAAAAATCTTT-T-A-AATAA-T-AATTCTATTTCCTTATCTAATAAGGA
*
39864322 ATATATCAAATCC
61 ATATAGCAAATCC
39864335 CCTTTTATCT
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
89 24 0.35
90 1 0.01
91 1 0.01
92 5 0.07
93 1 0.01
94 36 0.53
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (88 bp):
TAATTATTATTTAGCTAAAAATCTTTTAAATAATAATTCTATTTCCTTATCTAATAAGGAATATA
GCAAATCCTTTTGATCTCGATTT
Found at i:39866373 original size:15 final size:16
Alignment explanation
Indices: 39866353--39866382 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39866343 TGATGCATTG
39866353 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
39866368 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
39866383 AGTATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:39867034 original size:30 final size:30
Alignment explanation
Indices: 39866998--39867063 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
39866988 ACGGCCTAAG
*
39866998 ACACGGACGTGTGTCTTAGCCGTGTGTGAC
1 ACACGGACGTGTGTCTCAGCCGTGTGTGAC
*
39867028 ACACGGACGTGTGTCTCAGCTGTGTGTGAC
1 ACACGGACGTGTGTCTCAGCCGTGTGTGAC
39867058 ACACGG
1 ACACGG
39867064 CAATGTGACA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.18, C:0.24, G:0.33, T:0.24
Consensus pattern (30 bp):
ACACGGACGTGTGTCTCAGCCGTGTGTGAC
Found at i:39887554 original size:13 final size:14
Alignment explanation
Indices: 39887536--39887565 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
39887526 ACAATGTTAT
39887536 ATTTTAAA-ATTTC
1 ATTTTAAATATTTC
39887549 ATTTTAAATATTTC
1 ATTTTAAATATTTC
39887563 ATT
1 ATT
39887566 AATCAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTTAAATATTTC
Found at i:39897215 original size:232 final size:232
Alignment explanation
Indices: 39896809--39897274 Score: 932
Period size: 232 Copynumber: 2.0 Consensus size: 232
39896799 GTGGCACACA
39896809 ACTAGATAGAGTTGACAAGAGTGTTGTTGCTGAAACAGCGAATTCAAAATTTGATCAAAGCAAAC
1 ACTAGATAGAGTTGACAAGAGTGTTGTTGCTGAAACAGCGAATTCAAAATTTGATCAAAGCAAAC
39896874 TCTTGAAAAAAACAAGAAAAGCACCATAAATGAGAAAACTTGACCAAGCGATGCTAAAGCAAACT
66 TCTTGAAAAAAACAAGAAAAGCACCATAAATGAGAAAACTTGACCAAGCGATGCTAAAGCAAACT
39896939 CAGATAGTATTGTTGAACACAAAGCTCAGGCAAAACAATCACTGCAACCTAAAGTTCGCCCAACC
131 CAGATAGTATTGTTGAACACAAAGCTCAGGCAAAACAATCACTGCAACCTAAAGTTCGCCCAACC
39897004 CCACCATTTCCCCAATGATTTCAAAATCACAGACAAG
196 CCACCATTTCCCCAATGATTTCAAAATCACAGACAAG
39897041 ACTAGATAGAGTTGACAAGAGTGTTGTTGCTGAAACAGCGAATTCAAAATTTGATCAAAGCAAAC
1 ACTAGATAGAGTTGACAAGAGTGTTGTTGCTGAAACAGCGAATTCAAAATTTGATCAAAGCAAAC
39897106 TCTTGAAAAAAACAAGAAAAGCACCATAAATGAGAAAACTTGACCAAGCGATGCTAAAGCAAACT
66 TCTTGAAAAAAACAAGAAAAGCACCATAAATGAGAAAACTTGACCAAGCGATGCTAAAGCAAACT
39897171 CAGATAGTATTGTTGAACACAAAGCTCAGGCAAAACAATCACTGCAACCTAAAGTTCGCCCAACC
131 CAGATAGTATTGTTGAACACAAAGCTCAGGCAAAACAATCACTGCAACCTAAAGTTCGCCCAACC
39897236 CCACCATTTCCCCAATGATTTCAAAATCACAGACAAG
196 CCACCATTTCCCCAATGATTTCAAAATCACAGACAAG
39897273 AC
1 AC
39897275 CAACAATTCA
Statistics
Matches: 234, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
232 234 1.00
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (232 bp):
ACTAGATAGAGTTGACAAGAGTGTTGTTGCTGAAACAGCGAATTCAAAATTTGATCAAAGCAAAC
TCTTGAAAAAAACAAGAAAAGCACCATAAATGAGAAAACTTGACCAAGCGATGCTAAAGCAAACT
CAGATAGTATTGTTGAACACAAAGCTCAGGCAAAACAATCACTGCAACCTAAAGTTCGCCCAACC
CCACCATTTCCCCAATGATTTCAAAATCACAGACAAG
Found at i:39911892 original size:72 final size:73
Alignment explanation
Indices: 39911809--39911956 Score: 192
Period size: 72 Copynumber: 2.0 Consensus size: 73
39911799 TTTAATGCTA
* * *
39911809 TCCCAAGTCCCATGCACACACTAAATTCGGCTG-GTTGGGAAAATACAACAG-CAACTTTCGCTT
1 TCCCAAGTCCCATGCACACAATAAATTCGGCAGCGTTGGAAAAATACAACAGCCAACTTT-GCTT
39911872 TAAATGCCG
65 TAAATGCCG
* * * * * *
39911881 TCCCAAGTCCCATGCACTCAATAAATTCGGCAGCTTTGGAAAAATGCAGCAGCCACCTTTTCTTT
1 TCCCAAGTCCCATGCACACAATAAATTCGGCAGCGTTGGAAAAATACAACAGCCAACTTTGCTTT
39911946 AAATGCCG
66 AAATGCCG
39911954 TCC
1 TCC
39911957 ATGTACCTGC
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
72 30 0.46
73 29 0.45
74 6 0.09
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (73 bp):
TCCCAAGTCCCATGCACACAATAAATTCGGCAGCGTTGGAAAAATACAACAGCCAACTTTGCTTT
AAATGCCG
Found at i:39912164 original size:16 final size:16
Alignment explanation
Indices: 39912143--39912174 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
39912133 CATTCTGCAT
39912143 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
39912159 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
39912175 AAACACATTA
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:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:39913977 original size:20 final size:20
Alignment explanation
Indices: 39913954--39914000 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
39913944 GGGTTAAGAT
*
39913954 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
39913974 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
39913994 TGAGCTG
1 TGAGCTG
39914001 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:39915726 original size:48 final size:48
Alignment explanation
Indices: 39915671--39915776 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
39915661 TTGTCTTTTC
*
39915671 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
39915719 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
39915767 TTTCTTTTTC
1 TTTCTTTTTC
39915777 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:39925804 original size:40 final size:40
Alignment explanation
Indices: 39925751--39925939 Score: 193
Period size: 40 Copynumber: 4.8 Consensus size: 40
39925741 GAGTTACTAG
* * * * *
39925751 AGTATAAATAGGGGCACGAAAGTGCATTTAGGGGTAACAA
1 AGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTAACAA
* * * *
39925791 AGTACAAACAGGGGCACGTATGTGCATTCAAGGGT-ACTGA
1 AGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTAAC-AA
* * * * *
39925831 AGTACAAACAAGGGCATGTAAGTGCAATCAGAGGTACCGA
1 AGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTAACAA
* *
39925871 AGTACAAATAGGGGCACGTAAGTGCAATCAGGGGTACCAA
1 AGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTAACAA
* *
39925911 AGTACATACA-AGGCACGTAAGTGCAATCA
1 AGTACAAACAGGGGCACGTAAGTGCAATCA
39925940 TCAATAATTA
Statistics
Matches: 125, Mismatches: 22, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
39 20 0.16
40 104 0.83
41 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.28, T:0.17
Consensus pattern (40 bp):
AGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTAACAA
Found at i:39925896 original size:80 final size:79
Alignment explanation
Indices: 39925763--39925939 Score: 219
Period size: 80 Copynumber: 2.2 Consensus size: 79
39925753 TATAAATAGG
* * * * * * * *
39925763 GGCACGAAAGTGCATTTAGGGGTAACAAAGTACAAACAGGGGCACGTATGTGCATTCAAGGGTAC
1 GGCACGTAAGTGCAATCAGAGGTACCGAAGTACAAACAGGGGCACGTAAGTGCAATCAAGGGTAC
**
39925828 TGAAGTACAAACAA
66 CAAAGTACAAACAA
* * *
39925842 GGGCATGTAAGTGCAATCAGAGGTACCGAAGTACAAATAGGGGCACGTAAGTGCAATCAGGGGTA
1 -GGCACGTAAGTGCAATCAGAGGTACCGAAGTACAAACAGGGGCACGTAAGTGCAATCAAGGGTA
*
39925907 CCAAAGTACATACAA
65 CCAAAGTACAAACAA
39925922 GGCACGTAAGTGCAATCA
1 GGCACGTAAGTGCAATCA
39925940 TCAATAATTA
Statistics
Matches: 82, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
79 17 0.21
80 65 0.79
ACGTcount: A:0.37, C:0.18, G:0.28, T:0.17
Consensus pattern (79 bp):
GGCACGTAAGTGCAATCAGAGGTACCGAAGTACAAACAGGGGCACGTAAGTGCAATCAAGGGTAC
CAAAGTACAAACAA
Found at i:39925903 original size:20 final size:20
Alignment explanation
Indices: 39925799--39925939 Score: 67
Period size: 20 Copynumber: 7.1 Consensus size: 20
39925789 AAAGTACAAA
* *
39925799 CAGGGGCACGTATGTGCATT
1 CAGGGGCACGTAAGTGCAAT
* * * *
39925819 CAAGGGTAC-TGAAGTACAAA
1 CAGGGGCACGT-AAGTGCAAT
* *
39925839 CAAGGGCATGTAAGTGCAAT
1 CAGGGGCACGTAAGTGCAAT
* * *
39925859 CAGAGGTACCG-AAGTACAAAT
1 CAGGGGCA-CGTAAGTGC-AAT
39925880 -AGGGGCACGTAAGTGCAAT
1 CAGGGGCACGTAAGTGCAAT
* ** *
39925899 CAGGGGTACCAAAGTAC-AT
1 CAGGGGCACGTAAGTGCAAT
*
39925918 ACA-AGGCACGTAAGTGCAAT
1 -CAGGGGCACGTAAGTGCAAT
39925938 CA
1 CA
39925940 TCAATAATTA
Statistics
Matches: 86, Mismatches: 27, Indels: 17
0.66 0.21 0.13
Matches are distributed among these distances:
19 19 0.22
20 62 0.72
21 5 0.06
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.17
Consensus pattern (20 bp):
CAGGGGCACGTAAGTGCAAT
Found at i:39937628 original size:381 final size:381
Alignment explanation
Indices: 39937023--39937783 Score: 1513
Period size: 381 Copynumber: 2.0 Consensus size: 381
39937013 TTTGTTATAT
39937023 GTTTTAGGAAAATGTTAATATATTATTATTTAATTTATTATTCATTAATACACATTTTTGACGAT
1 GTTTTAGGAAAATGTTAATATATTATTATTTAATTTATTATTCATTAATACACATTTTTGACGAT
39937088 TTGATATAATTTATATGTATATTTTGTTTTATCTTTGTTTAAAAATTTATCTTTTTAATATATTA
66 TTGATATAATTTATATGTATATTTTGTTTTATCTTTGTTTAAAAATTTATCTTTTTAATATATTA
*
39937153 TATATCAAATATTTACATAATAATATTTTTTACATATAACACAATTCTTTATACACAGGTGAATT
131 TATATAAAATATTTACATAATAATATTTTTTACATATAACACAATTCTTTATACACAGGTGAATT
39937218 ATTAATTATTTTAAAAATGTGTTAACGTTATGATATTGGATATTATTAAGATTATGGATTTCAAG
196 ATTAATTATTTTAAAAATGTGTTAACGTTATGATATTGGATATTATTAAGATTATGGATTTCAAG
39937283 AGTTTTTAATATGTTTATGTATGTATTTTAAATCGATTTTACTTATATGTAATTCATTAAAAAAA
261 AGTTTTTAATATGTTTATGTATGTATTTTAAATCGATTTTACTTATATGTAATTCATTAAAAAAA
39937348 CTTATTTATGTATGAAATTTTATATATATATGTATGGTATATTTATATGATTATGC
326 CTTATTTATGTATGAAATTTTATATATATATGTATGGTATATTTATATGATTATGC
39937404 GTTTTAGGAAAATGTTAATATATTATTATTTAATTTATTATTCATTAATACACATTTTTGACGAT
1 GTTTTAGGAAAATGTTAATATATTATTATTTAATTTATTATTCATTAATACACATTTTTGACGAT
39937469 TTGATATAATTTATATGTATATTTTGTTTTATCTTTGTTTAAAAATTTATCTTTTTAATATATTA
66 TTGATATAATTTATATGTATATTTTGTTTTATCTTTGTTTAAAAATTTATCTTTTTAATATATTA
39937534 TATATAAAATATTTACATAATAATATTTTTTACATATAACACAATTCTTTATACACAGGTGAATT
131 TATATAAAATATTTACATAATAATATTTTTTACATATAACACAATTCTTTATACACAGGTGAATT
39937599 ATTAATTATTTTAAAAATGTGTTAACGTTATGATATTGGATATTATTAAGATTATGGATTTCAAG
196 ATTAATTATTTTAAAAATGTGTTAACGTTATGATATTGGATATTATTAAGATTATGGATTTCAAG
39937664 AGTTTTTAATATGTTTATGTATGTATTTTAAATCGATTTTACTTATATGTAATTCATTAAAAAAA
261 AGTTTTTAATATGTTTATGTATGTATTTTAAATCGATTTTACTTATATGTAATTCATTAAAAAAA
39937729 CTTATTTATGTATGAAATTTTATATATATATGTATGGTATATTTATATGATTATG
326 CTTATTTATGTATGAAATTTTATATATATATGTATGGTATATTTATATGATTATG
39937784 TTGTATACTA
Statistics
Matches: 379, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
381 379 1.00
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.49
Consensus pattern (381 bp):
GTTTTAGGAAAATGTTAATATATTATTATTTAATTTATTATTCATTAATACACATTTTTGACGAT
TTGATATAATTTATATGTATATTTTGTTTTATCTTTGTTTAAAAATTTATCTTTTTAATATATTA
TATATAAAATATTTACATAATAATATTTTTTACATATAACACAATTCTTTATACACAGGTGAATT
ATTAATTATTTTAAAAATGTGTTAACGTTATGATATTGGATATTATTAAGATTATGGATTTCAAG
AGTTTTTAATATGTTTATGTATGTATTTTAAATCGATTTTACTTATATGTAATTCATTAAAAAAA
CTTATTTATGTATGAAATTTTATATATATATGTATGGTATATTTATATGATTATGC
Found at i:39937783 original size:23 final size:21
Alignment explanation
Indices: 39937734--39937784 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
39937724 AAAAACTTAT
39937734 TTATGTATGAAATTTTATATA
1 TTATGTATGAAATTTTATATA
**
39937755 TATATGTATGGTATATTTATATGA
1 T-TATGTATGAAAT-TTTATAT-A
39937779 TTATGT
1 TTATGT
39937785 TGTATACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 1 0.04
22 10 0.40
23 12 0.48
24 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (21 bp):
TTATGTATGAAATTTTATATA
Found at i:39939828 original size:39 final size:40
Alignment explanation
Indices: 39939733--39939994 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
39939723 TTGAATGATG
*
39939733 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
39939771 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
39939812 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
39939851 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
39939890 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
39939929 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
39939968 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
39939995 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:39955402 original size:14 final size:14
Alignment explanation
Indices: 39955378--39955420 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
39955368 AAGACAATGA
39955378 ATTGCAAAAAAAAAT
1 ATTG-AAAAAAAAAT
*
39955393 ATTGAAAAAAATAT
1 ATTGAAAAAAAAAT
39955407 ATTGAAAAAGAAAA
1 ATTGAAAAA-AAAA
39955421 AAGAGATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 18 0.72
15 7 0.28
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.21
Consensus pattern (14 bp):
ATTGAAAAAAAAAT
Found at i:39955442 original size:13 final size:13
Alignment explanation
Indices: 39955426--39955461 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
39955416 GAAAAAAGAG
39955426 ATGAAAAATGAAA
1 ATGAAAAATGAAA
39955439 ATGAAAAATGAAA
1 ATGAAAAATGAAA
39955452 A-GTAAAAATG
1 ATG-AAAAATG
39955462 GAGAGGCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 1 0.05
13 21 0.95
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (13 bp):
ATGAAAAATGAAA
Found at i:39956908 original size:50 final size:50
Alignment explanation
Indices: 39956753--39956911 Score: 178
Period size: 50 Copynumber: 3.2 Consensus size: 50
39956743 ACAGTGGAAC
39956753 AGATTAAAACCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAACCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * * * ** ** *
39956803 ACACTAAAGCCACAACGCG-GAATCTTACTTTCCC-AGGTGGTGCAGTGGAAC
1 AGATTAAAACCACATCG-GTGAATCTTGCTTCCCCGACAT--TGCAGTTAAAA
39956854 AGATTAAAACCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAACCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
39956904 AGATTAAA
1 AGATTAAA
39956912 GCTACAACAG
Statistics
Matches: 82, Mismatches: 22, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
49 2 0.02
50 43 0.52
51 35 0.43
52 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (50 bp):
AGATTAAAACCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
Found at i:39956919 original size:101 final size:101
Alignment explanation
Indices: 39956744--39957057 Score: 447
Period size: 101 Copynumber: 3.1 Consensus size: 101
39956734 TCTGAGATTA
*
39956744 CAGTGGAACAGATTAAAACCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAACACTA
1 CAGTGGAACAGATTAAAACCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGACTA
39956809 AAGCCACAACGCGGAATCTTACTTTCCCAGGTGGTG
66 AAGCCACAACGCGGAATCTTACTTTCCCAGGTGGTG
*
39956845 CAGTGGAACAGATTAAAACCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTA
1 CAGTGGAACAGATTAAAACCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGACTA
* * * *
39956910 AAGCTACAACAGC-G-A-CTTAC-TTCTCAAGCGGTG
66 AAGCCACAAC-GCGGAATCTTACTTTCCCAGGTGGTG
* ** * * * * * *
39956943 CAGTGGAATAGATTAACGCCATAGCGGCGAACCTTGTTTCCCCAACATTGCAGTTAAAAAGACTA
1 CAGTGGAACAGATTAAAACCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGACTA
*
39957008 AAGCCACAACGGGGAATCTTACTTTCCCAGGTGGTG
66 AAGCCACAACGCGGAATCTTACTTTCCCAGGTGGTG
39957044 CAGTGGAACAGATT
1 CAGTGGAACAGATT
39957058 GAAGCTACAA
Statistics
Matches: 186, Mismatches: 22, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
97 1 0.01
98 75 0.40
99 6 0.03
100 6 0.03
101 96 0.52
102 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (101 bp):
CAGTGGAACAGATTAAAACCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGACTA
AAGCCACAACGCGGAATCTTACTTTCCCAGGTGGTG
Found at i:39957086 original size:199 final size:199
Alignment explanation
Indices: 39956744--39957109 Score: 516
Period size: 199 Copynumber: 1.8 Consensus size: 199
39956734 TCTGAGATTA
* * * *
39956744 CAGTGGAACAGATTAAAACCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAACACTA
1 CAGTGGAACAGATTAAAACCACAGCGGCGAACCTTGCTTCCCCAACATTGCAGTTAAAAACACTA
* * **
39956809 AAGCCACAACGCGGAATCTTACTTTCCCAGGTGGTGCAGTGGAACAGATTAAAACCACATCGGTG
66 AAGCCACAACGCGGAATCTTACTTTCCCAGGTGGTGCAGTGGAACAGATTAAAACCACAACAGCA
** **
39956874 AATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGACTTACTTCTCAAGC
131 AATCTCACTTCCCCGACATCACAGTTAAAAAGATTAAAGCTACAACAGCGACTTACTTCTCAAGC
39956939 GGTG
196 GGTG
* ** * * *
39956943 CAGTGGAATAGATTAACGCCATAGCGGCGAACCTTGTTTCCCCAACATTGCAGTTAAAAAGACTA
1 CAGTGGAACAGATTAAAACCACAGCGGCGAACCTTGCTTCCCCAACATTGCAGTTAAAAACACTA
* * * *
39957008 AAGCCACAACGGGGAATCTTACTTTCCCAGGTGGTGCAGTGGAACAGATTGAAGCTACAACAGCA
66 AAGCCACAACGCGGAATCTTACTTTCCCAGGTGGTGCAGTGGAACAGATTAAAACCACAACAGCA
**
39957073 AATCTCACTTCCCCGACATCACAGTTAAGCAGATTAA
131 AATCTCACTTCCCCGACATCACAGTTAAAAAGATTAA
39957110 GGTTACGAGT
Statistics
Matches: 143, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
199 143 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (199 bp):
CAGTGGAACAGATTAAAACCACAGCGGCGAACCTTGCTTCCCCAACATTGCAGTTAAAAACACTA
AAGCCACAACGCGGAATCTTACTTTCCCAGGTGGTGCAGTGGAACAGATTAAAACCACAACAGCA
AATCTCACTTCCCCGACATCACAGTTAAAAAGATTAAAGCTACAACAGCGACTTACTTCTCAAGC
GGTG
Found at i:39957099 original size:101 final size:100
Alignment explanation
Indices: 39956744--39957100 Score: 405
Period size: 101 Copynumber: 3.6 Consensus size: 100
39956734 TCTGAGATTA
* * * *
39956744 CAGTGGAACAGATTAAAACCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAACACTA
1 CAGTGGAACAGATT-AAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGACTA
*
39956809 AAGCCACAACGCGGAATCTTACTTTCCCAGGTGGTG
65 AAGCCACAACGGGGAATCTTACTTTCCCAGGTGGTG
* * * *
39956845 CAGTGGAACAGATTAAAACCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTA
1 CAGTGGAACAGATT-AAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGACTA
* * * * * *
39956910 AAGCTACAACAGCG-A-CTTAC-TTCTCAAGCGGTG
65 AAGCCACAACGGGGAATCTTACTTTCCCAGGTGGTG
* * * * * *
39956943 CAGTGGAATAGATTAACGCCATAGCGGCGAACCTTGTTTCCCCAACATTGCAGTTAAAAAGACTA
1 CAGTGGAACAGATTAA-GCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGACTA
39957008 AAGCCACAACGGGGAATCTTACTTTCCCAGGTGGTG
65 AAGCCACAACGGGGAATCTTACTTTCCCAGGTGGTG
* * * ** **
39957044 CAGTGGAACAGATTGAAGCTACAACAGCAAATCTCACTTCCCCGACATCACAGTTAA
1 CAGTGGAACAGATT-AAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAA
39957101 GCAGATTAAG
Statistics
Matches: 214, Mismatches: 37, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
97 2 0.01
98 74 0.35
99 6 0.03
100 6 0.03
101 124 0.58
102 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (100 bp):
CAGTGGAACAGATTAAGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGACTAA
AGCCACAACGGGGAATCTTACTTTCCCAGGTGGTG
Found at i:39961791 original size:50 final size:50
Alignment explanation
Indices: 39961722--39961855 Score: 223
Period size: 50 Copynumber: 2.7 Consensus size: 50
39961712 GTAAGTCTGG
*
39961722 TGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGT
1 TGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATAGTGT
*
39961772 TGGCACCAAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATAGTGT
1 TGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATAGTGT
* **
39961822 TGGCACCGAGATGAGAGTTCCCCCGTAAGACCAT
1 TGGCACCGAGATGAGAGGTCCCATGTAAGACCAT
39961856 ATTAGATTAT
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 78 1.00
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21
Consensus pattern (50 bp):
TGGCACCGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATAGTGT
Found at i:39974309 original size:50 final size:50
Alignment explanation
Indices: 39974206--39974398 Score: 172
Period size: 50 Copynumber: 3.7 Consensus size: 50
39974196 GGGAATGAGA
* **
39974206 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGAGATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGC---A---CCGAGATGAGAGG
*
39974262 TCCCACGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * * **
39974312 TCCC-CTATAAGACCATGTCTGAGACATAGCATGGGCACCGATATGAGAAC
1 TCCCAC-GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * ** *
39974362 TGCCATGTAAGACCATACCTGGGATATGGCATTGGCA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
39974399 GTACAGGAAA
Statistics
Matches: 114, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
49 1 0.01
50 78 0.68
53 1 0.01
56 34 0.30
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:39978736 original size:21 final size:21
Alignment explanation
Indices: 39978710--39978752 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
39978700 TCATGCATAT
39978710 ATCGGTTAAGCAATTTACCTA
1 ATCGGTTAAGCAATTTACCTA
39978731 ATCGGTTAAGCAATTTACCTA
1 ATCGGTTAAGCAATTTACCTA
39978752 A
1 A
39978753 ATCTAACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (21 bp):
ATCGGTTAAGCAATTTACCTA
Found at i:39980566 original size:21 final size:22
Alignment explanation
Indices: 39980541--39980591 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
39980531 AAAATATATT
39980541 AAATCAATTTTTAAA-AATTTG
1 AAATCAATTTTTAAATAATTTG
* * *
39980562 AAATC-TTTTTTAAATCATTTT
1 AAATCAATTTTTAAATAATTTG
39980583 AAATCAATT
1 AAATCAATT
39980592 CACGAGTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 8 0.33
21 14 0.58
22 2 0.08
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (22 bp):
AAATCAATTTTTAAATAATTTG
Found at i:39984691 original size:4 final size:4
Alignment explanation
Indices: 39984684--39984708 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
39984674 AAAAAAAAAA
39984684 GAGG GAGG GAGG GAGG GAGG GAGG G
1 GAGG GAGG GAGG GAGG GAGG GAGG G
39984709 GTCGGGGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.76, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:39986822 original size:18 final size:17
Alignment explanation
Indices: 39986793--39986835 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
39986783 TCTCTCAATT
39986793 CTTTCT-AATCTCCTAA
1 CTTTCTCAATCTCCTAA
*
39986809 CTTTCTCAACTCTCTTAA
1 CTTTCTCAA-TCTCCTAA
*
39986827 ATTTCTCAA
1 CTTTCTCAA
39986836 GTTCTTGTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 6 0.26
17 2 0.09
18 15 0.65
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.44
Consensus pattern (17 bp):
CTTTCTCAATCTCCTAA
Found at i:39991358 original size:11 final size:11
Alignment explanation
Indices: 39991342--39991380 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
39991332 TGTCCTTAAG
39991342 AAAACTAAATA
1 AAAACTAAATA
39991353 AAAACTAAA-A
1 AAAACTAAATA
39991363 ATAAACTAAACTA
1 A-AAACTAAA-TA
39991376 AAAAC
1 AAAAC
39991381 AGAAAATAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.08
11 17 0.68
12 4 0.16
13 2 0.08
ACGTcount: A:0.72, C:0.13, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAACTAAATA
Found at i:39991386 original size:23 final size:22
Alignment explanation
Indices: 39991343--39991389 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
39991333 GTCCTTAAGA
39991343 AAACTAAATAAAAACTAAAAAT
1 AAACTAAATAAAAACTAAAAAT
39991365 AAACTAAACTAAAAAC-AGAAAAT
1 AAACTAAA-TAAAAACTA-AAAAT
39991388 AA
1 AA
39991390 CATGCAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.72, C:0.11, G:0.02, T:0.15
Consensus pattern (22 bp):
AAACTAAATAAAAACTAAAAAT
Found at i:39993004 original size:20 final size:21
Alignment explanation
Indices: 39992965--39993004 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
39992955 TACATCAATT
*
39992965 AGTTCATGCATTCTTTCCATA
1 AGTTCATGCATTCATTCCATA
*
39992986 AGTTCATGC-TTGATTCCAT
1 AGTTCATGCATTCATTCCAT
39993005 TTGAATACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (21 bp):
AGTTCATGCATTCATTCCATA
Found at i:39997529 original size:39 final size:40
Alignment explanation
Indices: 39997484--39997668 Score: 178
Period size: 40 Copynumber: 4.7 Consensus size: 40
39997474 GCTCCTCGTT
* * *
39997484 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
39997524 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
39997563 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * * * * *
39997603 CAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CATAACCCGGATTTAGTAAC-TCGCA
* *
39997644 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACATAACCCGGA
39997669 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 37 0.30
40 74 0.61
41 11 0.09
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:39997584 original size:40 final size:39
Alignment explanation
Indices: 39997451--39997668 Score: 165
Period size: 40 Copynumber: 5.5 Consensus size: 39
39997441 AAATCACGTA
* * **
39997451 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCA-AATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCG--CACAATG
* * * * *
39997490 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
* *
39997529 CCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * *
39997569 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * * * *
39997609 CCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCACAAAG
1 CCTTCGGGA-CTTAACCCGGATTTA-GCAAC-TCGCACAATG
*
39997649 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
39997669 CAGCATTCAA
Statistics
Matches: 143, Mismatches: 29, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
38 2 0.01
39 48 0.34
40 85 0.59
41 8 0.06
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
Found at i:40003524 original size:27 final size:27
Alignment explanation
Indices: 40003485--40003653 Score: 196
Period size: 27 Copynumber: 6.2 Consensus size: 27
40003475 NNNNNNNNNC
* * *
40003485 AGTGCTATATAATCAACTCGCACACTT
1 AGTGCTACATAGTCAAATCGCACACTT
* *
40003512 AGTGCTACGTAATCAAATCGCACACTT
1 AGTGCTACATAGTCAAATCGCACACTT
40003539 AGTGCTACATAGTCAAACTCGCACACTT
1 AGTGCTACATAGTCAAA-TCGCACACTT
** * *
40003567 AGTGCCGCATGGTCAATTCGCACACTT
1 AGTGCTACATAGTCAAATCGCACACTT
* **
40003594 AGTGC-ATCATATTCATTTCGCACACTT
1 AGTGCTA-CATAGTCAAATCGCACACTT
*
40003621 AGTGCAACATAGTCAAATCGCACACTT
1 AGTGCTACATAGTCAAATCGCACACTT
40003648 AGTGCT
1 AGTGCT
40003654 GTACAATTTA
Statistics
Matches: 122, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 98 0.80
28 24 0.20
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (27 bp):
AGTGCTACATAGTCAAATCGCACACTT
Found at i:40003622 original size:82 final size:81
Alignment explanation
Indices: 40003497--40003652 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40003487 TGCTATATAA
* *
40003497 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40003562 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40003579 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40003643 CACTTAGTGC
65 CACTTAGTGC
40003653 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40008603 original size:504 final size:503
Alignment explanation
Indices: 40007624--40008606 Score: 1815
Period size: 502 Copynumber: 2.0 Consensus size: 503
40007614 TCACCTTTGT
*
40007624 AATTTTTTTCACTCATCCCTCCATCAATCCTAGCATCTAAAACCCACCAAGTACCAAATCACCTA
1 AATTTTTTTCACTCATCCCTCCATCAATCCTAGCATCCAAAACCCACCAAGTACCAAATCACCTA
40007689 GTGCCGAACTCTCTAGCCCGCAACACCGCCCAGCTTCGCACGTCACCTTTACGCCTAGCAACAGC
66 GTGCCGAACTCTCTAGCCCGCAACACCGCCCAGCTTCGCACGTCACCTTTACGCCTAGCAACAGC
*
40007754 CCCATTTGGCCAGCAGCCCAAGCACGCACCAGTAGCTTACGCCGCTACTGCCGCTCCCATCAGAC
131 CCCATTTGGCCAGCAGCCCAAGCACGCACCAGTAGCTTACACCGCTACTGCCGCTCCCATCAGAC
*
40007819 CTACACTCACGCACCCGCTCATGTGCACCAATGCACCAGCCCTACCATTCGCCCGACAATGCCAC
196 CTACACTCACGCACCCGCTCATGTGCACCAACGCACCAGCCCTACCATTCGCCCGACAATGCCAC
*
40007884 CTGCTGTTCACACATCTGCTCACATCGCCTTGCTACTCGGACCAACACCCTTTCCTATCGTACCA
261 CTGCTGTTCACACATCTGCTCACATCGCCTTGCTACTCGGACCAACACCCTTTCCTATCGCACCA
*
40007949 TACCATCAAGAAACCCTACAACCATCCCTAAACCAAACCCTTTTGCTTTATATTTATTTTCTTTG
326 CACCATCAAGAAACCCTACAACCATCCCTAAACCAAACCCTTTTGCTTTATATTTATTTTCTTTG
40008014 AGTTCTTACCAAAGTGAGATACGAAAGCGTTTTCAAGAATCAACAGACGCACCTAGAAAAAGGCT
391 AGTTCTTACCAAAGTGAGATACGAAAGCGTTTTCAAGAATCAACAGACGCACCTAGAAAAAGGCT
40008079 TTACGCTGAAAGAAAACAACTATAAAGAAAACAACGAAAGTCTGATGC
456 TTACGCTGAAAGAAAACAACTATAAAGAAAACAACGAAAGTCTGATGC
40008127 AATTTTTTTCACTCATCCCTCCATCAATCCTAGCATCCAAAACCCACCAAGTACCAAATCACCTA
1 AATTTTTTTCACTCATCCCTCCATCAATCCTAGCATCCAAAACCCACCAAGTACCAAATCACCTA
*
40008192 GTGCCGAACTCTCTAG-CCGCAACACCGCCCAGCTTCGCACGTCACCTTTACGCCTAGCAATAGC
66 GTGCCGAACTCTCTAGCCCGCAACACCGCCCAGCTTCGCACGTCACCTTTACGCCTAGCAACAGC
* * *
40008256 CCCATTTGGCTAGCAGCCCAAGCACGCACCAGTAGCTTACACTGCTACTGCCGCTCGCATCAGAC
131 CCCATTTGGCCAGCAGCCCAAGCACGCACCAGTAGCTTACACCGCTACTGCCGCTCCCATCAGAC
* * * *
40008321 CTACTCTCACGCACCCGCTCATGTGCACCAACGCACCAGCCCTACTATTCGCTCGACAGTGCCAC
196 CTACACTCACGCACCCGCTCATGTGCACCAACGCACCAGCCCTACCATTCGCCCGACAATGCCAC
40008386 CTGCTGTTCACACATCTGCTCACATCGCGCCTTGCTACTCGGACCAACACCCTTTCCTATCGCAC
261 CTGCTGTTCACACATCTGCTCACAT--CGCCTTGCTACTCGGACCAACACCCTTTCCTATCGCAC
40008451 CACACCATCAAGAAACCCTACAACCATCCCTAAACCAAACCCTTTTGCTTTATATTTATTTTCTT
324 CACACCATCAAGAAACCCTACAACCATCCCTAAACCAAACCCTTTTGCTTTATATTTATTTTCTT
*
40008516 TGAGTTCTTACCAAAGTGAGATACGAAAGCGTTTTCAAGAATCAACAGATGCACCTAGAAAAAGG
389 TGAGTTCTTACCAAAGTGAGATACGAAAGCGTTTTCAAGAATCAACAGACGCACCTAGAAAAAGG
40008581 CTTTACGCTGAAAGAAAACAACTATA
454 CTTTACGCTGAAAGAAAACAACTATA
40008607 TTGATTTCAT
Statistics
Matches: 464, Mismatches: 14, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
502 193 0.42
503 80 0.17
504 191 0.41
ACGTcount: A:0.29, C:0.35, G:0.14, T:0.23
Consensus pattern (503 bp):
AATTTTTTTCACTCATCCCTCCATCAATCCTAGCATCCAAAACCCACCAAGTACCAAATCACCTA
GTGCCGAACTCTCTAGCCCGCAACACCGCCCAGCTTCGCACGTCACCTTTACGCCTAGCAACAGC
CCCATTTGGCCAGCAGCCCAAGCACGCACCAGTAGCTTACACCGCTACTGCCGCTCCCATCAGAC
CTACACTCACGCACCCGCTCATGTGCACCAACGCACCAGCCCTACCATTCGCCCGACAATGCCAC
CTGCTGTTCACACATCTGCTCACATCGCCTTGCTACTCGGACCAACACCCTTTCCTATCGCACCA
CACCATCAAGAAACCCTACAACCATCCCTAAACCAAACCCTTTTGCTTTATATTTATTTTCTTTG
AGTTCTTACCAAAGTGAGATACGAAAGCGTTTTCAAGAATCAACAGACGCACCTAGAAAAAGGCT
TTACGCTGAAAGAAAACAACTATAAAGAAAACAACGAAAGTCTGATGC
Found at i:40010591 original size:12 final size:12
Alignment explanation
Indices: 40010576--40010616 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
40010566 ATGCTCGTGA
40010576 AAAAAAGAAAAG
1 AAAAAAGAAAAG
40010588 AAAAAAGAAAAG
1 AAAAAAGAAAAG
*
40010600 AAAAGA-AAAAG
1 AAAAAAGAAAAG
40010611 AAAAAA
1 AAAAAA
40010617 TGAAGAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:40010600 original size:17 final size:16
Alignment explanation
Indices: 40010578--40010614 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 16
40010568 GCTCGTGAAA
40010578 AAAAGAAAAGAAAAAAG
1 AAAAGAAAAG-AAAAAG
40010595 AAAAGAAAAGAAAAAG
1 AAAAGAAAAGAAAAAG
40010611 AAAA
1 AAAA
40010615 AATGAAGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAGAAAAAG
Found at i:40010606 original size:22 final size:25
Alignment explanation
Indices: 40010578--40010625 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
40010568 GCTCGTGAAA
40010578 AAAAG-AAAAGAAAAAA-GAA-AAG
1 AAAAGAAAAAGAAAAAATGAAGAAG
40010600 AAAAGAAAAAGAAAAAATGAAGAAG
1 AAAAGAAAAAGAAAAAATGAAGAAG
40010625 A
1 A
40010626 GAACAACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.22
23 11 0.48
24 3 0.13
25 4 0.17
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (25 bp):
AAAAGAAAAAGAAAAAATGAAGAAG
Found at i:40010615 original size:17 final size:16
Alignment explanation
Indices: 40010575--40010615 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 16
40010565 AATGCTCGTG
40010575 AAAAAAAGAAAAGAAA
1 AAAAAAAGAAAAGAAA
40010591 AAAGAAAAGAAAAGAAA
1 AAA-AAAAGAAAAGAAA
40010608 AAGAAAAA
1 AA-AAAAA
40010616 ATGAAGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.13
17 19 0.83
18 1 0.04
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAAGAAA
Found at i:40012178 original size:20 final size:18
Alignment explanation
Indices: 40012147--40012183 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
40012137 TGTAATGCTG
40012147 ATATGCTTAATTTAATTA
1 ATATGCTTAATTTAATTA
40012165 ATATGGCTTAAATTTAATT
1 ATAT-GCTT-AATTTAATT
40012184 TCTGTTAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (18 bp):
ATATGCTTAATTTAATTA
Found at i:40019391 original size:51 final size:49
Alignment explanation
Indices: 40019329--40019566 Score: 260
Period size: 51 Copynumber: 4.7 Consensus size: 49
40019319 ATACTCGGTT
* * *
40019329 CACATAGTAGCCTGCACATAGTACTACACATGTGAGCGTTTTCATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-C-CTATCATCCGATA
* * * *
40019380 CACGTAGTAGCCTGCACATAGTACTACACACGTGATCCAAGCTATCCGCTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCTATC-ATCCGATA
* * * *
40019431 CGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCTATCA-TCCGATA
* * * * *
40019481 CACGTAGTAGACTACACATAGTACTATACACGTGACCATTTTCATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACC--TATCATCCGATA
*
40019532 CACATAGTAGCCTACACATAGTACTACACACGTGA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA
40019567 TCTAGCAACT
Statistics
Matches: 156, Mismatches: 27, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
49 1 0.01
50 41 0.26
51 110 0.71
52 4 0.03
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.24
Consensus pattern (49 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCTATCATCCGATA
Found at i:40019513 original size:101 final size:102
Alignment explanation
Indices: 40019329--40019561 Score: 310
Period size: 101 Copynumber: 2.3 Consensus size: 102
40019319 ATACTCGGTT
* * * * *
40019329 CACATAGTAGCCTGCACATAGTACTACACATGTGAGCGTTTTCATCCGATACACGTAGTAGCCTG
1 CACATAGTAGCCTGCACATAGTACTACACATGCGAGCGCTATCATCCGATACACGTAGTAGACTA
*
40019394 CACATAGTACTACACACGTGATCCAAGCT-ATCCGCTA
66 CACATAGTACTACACACGTGA-CCAAGCTCATCCGATA
* *
40019431 CGCATAGTAGCCTGCACATAGTACTACACATGCGA-C-CTATCATTCCGGTACACGTAGTAGACT
1 CACATAGTAGCCTGCACATAGTACTACACATGCGAGCGCTATCA-TCCGATACACGTAGTAGACT
* ***
40019494 ACACATAGTACTATACACGTGACCATTTTCATCCGATA
65 ACACATAGTACTACACACGTGACCAAGCTCATCCGATA
*
40019532 CACATAGTAGCCTACACATAGTACTACACA
1 CACATAGTAGCCTGCACATAGTACTACACA
40019562 CGTGATCTAG
Statistics
Matches: 115, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
100 8 0.07
101 74 0.64
102 33 0.29
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.24
Consensus pattern (102 bp):
CACATAGTAGCCTGCACATAGTACTACACATGCGAGCGCTATCATCCGATACACGTAGTAGACTA
CACATAGTACTACACACGTGACCAAGCTCATCCGATA
Found at i:40025207 original size:23 final size:23
Alignment explanation
Indices: 40025177--40025220 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
40025167 GTTACTGAGT
40025177 ATGACGTTATGCATACATGTAAA
1 ATGACGTTATGCATACATGTAAA
40025200 ATGACGTTATGCATACATGTA
1 ATGACGTTATGCATACATGTA
40025221 TGATTTATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (23 bp):
ATGACGTTATGCATACATGTAAA
Found at i:40025277 original size:26 final size:25
Alignment explanation
Indices: 40025237--40025292 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
40025227 ATGACACGAC
* *
40025237 ATACTGTATTGGCAGCTTTGCTGCG
1 ATACTGTACTGGCAGCTTTACTGCG
40025262 ATACTGATACTGGCAGCTTTACTGCG
1 ATACTG-TACTGGCAGCTTTACTGCG
*
40025288 TTACT
1 ATACT
40025293 ATTACGAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (25 bp):
ATACTGTACTGGCAGCTTTACTGCG
Found at i:40025464 original size:28 final size:26
Alignment explanation
Indices: 40025424--40025483 Score: 93
Period size: 28 Copynumber: 2.2 Consensus size: 26
40025414 ACTGTACTGA
40025424 TACTGTAATGGGCTAAGGCCCACATTG
1 TACTGTAATGGGCTAAGG-CCACATTG
*
40025451 TTACTGTATTGGGCTAAGGCCACATTG
1 -TACTGTAATGGGCTAAGGCCACATTG
40025478 TACTGT
1 TACTGT
40025484 GACTAAATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 6 0.19
27 8 0.26
28 17 0.55
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (26 bp):
TACTGTAATGGGCTAAGGCCACATTG
Found at i:40032445 original size:13 final size:12
Alignment explanation
Indices: 40032408--40032460 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 12
40032398 CTAATCTTTG
*
40032408 ATTTATTTTTCT
1 ATTTATTTTTTT
40032420 ATTTTATTTATTTT
1 A-TTTATTT-TTTT
40032434 ATTTATTTATTTT
1 ATTTATTT-TTTT
* *
40032447 AATTAATTTTTT
1 ATTTATTTTTTT
40032459 AT
1 AT
40032461 CTGACTTGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
12 6 0.17
13 25 0.71
14 4 0.11
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (12 bp):
ATTTATTTTTTT
Found at i:40032872 original size:14 final size:14
Alignment explanation
Indices: 40032833--40032873 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
40032823 AATTCATGAG
40032833 TATCTCTTTCCTTTA
1 TATCTCTTT-CTTTA
*
40032848 T-TCT-ATTCTTTA
1 TATCTCTTTCTTTA
40032860 TATCTCTTTCTTTA
1 TATCTCTTTCTTTA
40032874 ACATTGTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
12 6 0.27
13 5 0.23
14 10 0.45
15 1 0.05
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (14 bp):
TATCTCTTTCTTTA
Found at i:40037593 original size:24 final size:24
Alignment explanation
Indices: 40037566--40037658 Score: 132
Period size: 24 Copynumber: 3.9 Consensus size: 24
40037556 ACACACCACG
*
40037566 TTGTGGCCAAGCCACTCCATAGCA
1 TTGTGGCCAAGCCACTCAATAGCA
* *
40037590 TTGTGGCCAAGCAACTCAATAGCG
1 TTGTGGCCAAGCCACTCAATAGCA
* * *
40037614 TTTTGGTCAAGCCACTCAATAACA
1 TTGTGGCCAAGCCACTCAATAGCA
40037638 TTGTGGCCAAGCCACTCAATA
1 TTGTGGCCAAGCCACTCAATA
40037659 TTGCAGATAA
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (24 bp):
TTGTGGCCAAGCCACTCAATAGCA
Found at i:40045781 original size:50 final size:50
Alignment explanation
Indices: 40045706--40045895 Score: 164
Period size: 50 Copynumber: 3.7 Consensus size: 50
40045696 TTTCTTGTAC
* * * * **
40045706 TGCCAATGTCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATATCGG
* * * ** * *
40045756 TGCCCATGTCTTGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATATCGG
* * *
40045806 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCAT-A--TC---GG
* *
40045862 TGCCAATGCCATCTCCCAGACATGGTCTTACATG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATG
40045896 GGATCTCTTT
Statistics
Matches: 114, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
50 78 0.68
53 2 0.02
56 34 0.30
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATATCGG
Found at i:40050075 original size:50 final size:50
Alignment explanation
Indices: 40049962--40050154 Score: 224
Period size: 50 Copynumber: 3.8 Consensus size: 50
40049952 GATAATAACA
* * * * ** *
40049962 TGCCAAAGCCATGTCCCAGGCATGGTATTAAATGGGATGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * * ** * *
40050013 TGCCCATGCCATGCCCCAAACATGGTCTTACGGGGGACCTTTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
40050063 TGCCAACGCCATGTCCCAGACATGGTATTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
40050113 TGCCAACGCCATGTCCCAGACATGATCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
40050155 TTACCCAAAT
Statistics
Matches: 117, Mismatches: 25, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
50 89 0.76
51 28 0.24
ACGTcount: A:0.22, C:0.30, G:0.23, T:0.25
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:40050150 original size:100 final size:101
Alignment explanation
Indices: 40049962--40050152 Score: 258
Period size: 100 Copynumber: 1.9 Consensus size: 101
40049952 GATAATAACA
* ** * *
40049962 TGCCAAAGCCATGTCCCAGGCATGGTATTAAATGGGATGTTCTCATATCGGTGCCCATGCCATGC
1 TGCCAAAGCCATGTCCCAGACATGGTATTAAATGGGATCCTCTCATATCGGTGCCAACGCCATGC
* *
40050027 CCCAAACATGGTCTTACGGGGGACCTTTCATCTTGG
66 CCCAAACATGATCTTACAGGGGACCTTTCATCTTGG
* * * *
40050063 TGCCAACGCCATGTCCCAGACATGGTATTACATGGGA-CCTCTCATCTCGGTGCCAACGCCATGT
1 TGCCAAAGCCATGTCCCAGACATGGTATTAAATGGGATCCTCTCATATCGGTGCCAACGCCATGC
* *
40050127 CCCAGACATGATCTTACATGGGACCT
66 CCCAAACATGATCTTACAGGGGACCT
40050153 CTTTACCCAA
Statistics
Matches: 77, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
100 43 0.56
101 34 0.44
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (101 bp):
TGCCAAAGCCATGTCCCAGACATGGTATTAAATGGGATCCTCTCATATCGGTGCCAACGCCATGC
CCCAAACATGATCTTACAGGGGACCTTTCATCTTGG
Found at i:40053981 original size:50 final size:50
Alignment explanation
Indices: 40053919--40054049 Score: 138
Period size: 50 Copynumber: 2.6 Consensus size: 50
40053909 CAATGTCATA
* ** * * * *
40053919 TCCCAGATATGGTCTTACATGGGAGTTCTCAGATCGGTGCTC-ATGTCTTG
1 TCCCAGACATGGTCTTACATGGGACCTCTCAGATCGGTAC-CAACGCCATG
* ** **
40053969 TCCCAGACATGGTCATACGGGGGACCTCTCATCTCGGTACCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCAGATCGGTACCAACGCCATG
40054019 TCCCAGACATGGTCTTACATGGGACCTCTCA
1 TCCCAGACATGGTCTTACATGGGACCTCTCA
40054050 TAACCTCAAT
Statistics
Matches: 65, Mismatches: 15, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
49 1 0.02
50 64 0.98
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACATGGGACCTCTCAGATCGGTACCAACGCCATG
Found at i:40067166 original size:25 final size:25
Alignment explanation
Indices: 40067138--40067190 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
40067128 TAACCACAAT
40067138 TATTACAAGCCACTATTCAAAAAAC
1 TATTACAAGCCACTATTCAAAAAAC
40067163 TATTACAAGCCACTATTCAAAAAAC
1 TATTACAAGCCACTATTCAAAAAAC
40067188 TAT
1 TAT
40067191 GGTCTATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.47, C:0.23, G:0.04, T:0.26
Consensus pattern (25 bp):
TATTACAAGCCACTATTCAAAAAAC
Found at i:40067179 original size:13 final size:13
Alignment explanation
Indices: 40067138--40067179 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
40067128 TAACCACAAT
40067138 TATTACAAGCCAC
1 TATTACAAGCCAC
***
40067151 TATT-CAAAAAAC
1 TATTACAAGCCAC
40067163 TATTACAAGCCAC
1 TATTACAAGCCAC
40067176 TATT
1 TATT
40067180 CAAAAAACTA
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.43, C:0.24, G:0.05, T:0.29
Consensus pattern (13 bp):
TATTACAAGCCAC
Found at i:40069070 original size:186 final size:183
Alignment explanation
Indices: 40068722--40069080 Score: 454
Period size: 186 Copynumber: 1.9 Consensus size: 183
40068712 GGGTTTAGGT
* * * * * *
40068722 TGTAACAACCTATTTTCAGTGAAATCGAAACAGTGGTTTTGGGACCACAAATCTGACGTGAAAAT
1 TGTAACAACCCATTTTCAGTGAAATCAAAACAGTGGTTTTGAGACCACAAATCTAAAGTAAAAAT
** * *
40068787 ATTTTATTTATTATTTTAATGTCTACCACATGCTAGTACTGCCCTATAAAAATTTCATTAAAAAA
66 ATTTTATTTATTATTTTAATGTCTACCACATGCTAGTAAAGCCATAGAAAAATTTCATTAAAAAA
40068852 TTTTATCATTTGCATGCTTAATTAAGTAAAAAGGACTAAATCGTAAAAGGTGA
131 TTTTATCATTTGCATGCTTAATTAAGTAAAAAGGACTAAATCGTAAAAGGTGA
* ** *
40068905 TGTAACATCCCATTTTTGGTGAAATCAAAATAGTGGTTTTGAGACCACAAATAC-AAAGTAAAAA
1 TGTAACAACCCATTTTCAGTGAAATCAAAACAGTGGTTTTGAGACCACAAAT-CTAAAGTAAAAA
* * * * *
40068969 TATTTATTTTATTATTATTTTAATGTTTA-CAGCATGTTAGTAAAGTCATAGAAAAATTTCGTTA
65 TA-TT-TTAT-TTATTATTTTAATGTCTACCA-CATGCTAGTAAAGCCATAGAAAAATTTCATTA
* *
40069033 AGAAATTTTATCATTTGCATGCTTAATT-CGATAAAAAGGACTAAATCG
126 AAAAATTTTATCATTTGCATGCTTAATTAAG-TAAAAAGGACTAAATCG
40069081 CTTAAAATGT
Statistics
Matches: 149, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
183 54 0.36
184 3 0.02
185 6 0.04
186 86 0.58
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.36
Consensus pattern (183 bp):
TGTAACAACCCATTTTCAGTGAAATCAAAACAGTGGTTTTGAGACCACAAATCTAAAGTAAAAAT
ATTTTATTTATTATTTTAATGTCTACCACATGCTAGTAAAGCCATAGAAAAATTTCATTAAAAAA
TTTTATCATTTGCATGCTTAATTAAGTAAAAAGGACTAAATCGTAAAAGGTGA
Found at i:40089861 original size:26 final size:26
Alignment explanation
Indices: 40089805--40089861 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
40089795 CTTTTATGAT
*
40089805 TTTTTTATAAATTTTTTTAATTTTAA
1 TTTTTTATAAATTTTTTTAATTATAA
40089831 TTTTTTATAAATTTTTATTAAATTAT-A
1 TTTTTTATAAATTTTT-TT-AATTATAA
40089858 TTTT
1 TTTT
40089862 GATATAACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 16 0.57
27 7 0.25
28 5 0.18
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTTTTATAAATTTTTTTAATTATAA
Found at i:40094509 original size:113 final size:111
Alignment explanation
Indices: 40094286--40094510 Score: 344
Period size: 113 Copynumber: 2.0 Consensus size: 111
40094276 ATACAGTGTT
* * *
40094286 TTGTGATAGTCAATGTTATTTTCCTTACGAATGATCAAATGTTTCACTAGAGAACAAATCACATC
1 TTGTGATAGTCAATGTCATCTTCCTTACAAATGATCAAATGTTTCACTAGAGAACAAATCACATC
* *
40094351 GATGTTCAATGTCATTTTATACGTGATATTATTGCTCATGTTGATG
66 GATGTTCAATGTCATTTTATACATGATATTATTGCTCATGGTGATG
40094397 TTGTGATAGTCAGAGTGTCATCTTCCTTACAAATGATCAAATGTTTCA-TGAGAGAACAAATCAC
1 TTGTGATAGTCA-A-TGTCATCTTCCTTACAAATGATCAAATGTTTCACT-AGAGAACAAATCAC
** *
40094461 ATCGATGTTCGGTGTCATTTTATGCATGATATTATTGCTCATGGTGATG
63 ATCGATGTTCAATGTCATTTTATACATGATATTATTGCTCATGGTGATG
40094510 T
1 T
40094511 GAGCAAAGTT
Statistics
Matches: 103, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
111 12 0.12
112 2 0.02
113 89 0.86
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (111 bp):
TTGTGATAGTCAATGTCATCTTCCTTACAAATGATCAAATGTTTCACTAGAGAACAAATCACATC
GATGTTCAATGTCATTTTATACATGATATTATTGCTCATGGTGATG
Found at i:40104343 original size:25 final size:25
Alignment explanation
Indices: 40104290--40104376 Score: 99
Period size: 25 Copynumber: 3.5 Consensus size: 25
40104280 TACCAGTTTT
* *
40104290 AGCTCTTATGAGCTTACCGATACTT-
1 AGCTCGTATGAGCTTACCGTTA-TTC
40104315 AGCTCGTATGAGCTTACCGTTATTC
1 AGCTCGTATGAGCTTACCGTTATTC
* *
40104340 AGCTCAG-AGGAGCTTACCGTTA-AC
1 AGCTC-GTATGAGCTTACCGTTATTC
40104364 AGCTCGTATGAGC
1 AGCTCGTATGAGC
40104377 ATACATGTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
23 1 0.02
24 13 0.24
25 39 0.72
26 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (25 bp):
AGCTCGTATGAGCTTACCGTTATTC
Found at i:40125421 original size:26 final size:24
Alignment explanation
Indices: 40125392--40125442 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
40125382 AGTTGTAGAG
40125392 AGAAAATTCTCTAAAGAGATTATTTT
1 AGAAAATT-TCTAAAGAGATT-TTTT
* *
40125418 AGAAAATTTCTAGAGATATTTTTT
1 AGAAAATTTCTAAAGAGATTTTTT
40125442 A
1 A
40125443 TTTTTACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 5 0.22
25 10 0.43
26 8 0.35
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (24 bp):
AGAAAATTTCTAAAGAGATTTTTT
Found at i:40134909 original size:21 final size:21
Alignment explanation
Indices: 40134883--40134925 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
40134873 CTAATGAAAT
40134883 CCATTTTC-TTCAGTTTTCTCA
1 CCATTTTCATT-AGTTTTCTCA
40134904 CCATTTTCATTAGTTTTCTCA
1 CCATTTTCATTAGTTTTCTCA
40134925 C
1 C
40134926 TAAACAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.16, C:0.28, G:0.05, T:0.51
Consensus pattern (21 bp):
CCATTTTCATTAGTTTTCTCA
Found at i:40137303 original size:68 final size:68
Alignment explanation
Indices: 40137224--40137358 Score: 200
Period size: 68 Copynumber: 2.0 Consensus size: 68
40137214 TTATTTATTG
* *
40137224 CCATATCCGAGCTATGGTCTTACACCTTATAAC-CCTATGTTTAGTGTCCTGGCAAACTCTATTG
1 CCATAGCCGAGCTATGGTCTTACACCTTATAACACC-ATGTTTAATGTCCTGGCAAACTCTATTG
40137288 GTTC
65 GTTC
* * * *
40137292 CCATAGCCGAGCTATGGTCTTACACCTTGTAACACCATGTTTAATGTCTTGGTAGACTCTATTGG
1 CCATAGCCGAGCTATGGTCTTACACCTTATAACACCATGTTTAATGTCCTGGCAAACTCTATTGG
40137357 TT
66 TT
40137359 GTGTAACATC
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
68 58 0.97
69 2 0.03
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (68 bp):
CCATAGCCGAGCTATGGTCTTACACCTTATAACACCATGTTTAATGTCCTGGCAAACTCTATTGG
TTC
Found at i:40138201 original size:29 final size:29
Alignment explanation
Indices: 40138164--40138222 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
40138154 TCCGAGCTTT
*
40138164 GGGGAAAAAGTGTAATTATGTAAAAGTTA
1 GGGGAAAAAGTGTAATTATATAAAAGTTA
* * *
40138193 GGGGCAAAATTGTAATTTTATAAAAGTTA
1 GGGGAAAAAGTGTAATTATATAAAAGTTA
40138222 G
1 G
40138223 AGTTGAGGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.42, C:0.02, G:0.25, T:0.31
Consensus pattern (29 bp):
GGGGAAAAAGTGTAATTATATAAAAGTTA
Found at i:40138707 original size:50 final size:50
Alignment explanation
Indices: 40138612--40138751 Score: 147
Period size: 50 Copynumber: 2.8 Consensus size: 50
40138602 CATTGAGATT
* * ** *
40138612 ATGAGAGGTCCTATGTAAGACCATGTCTGGGACATGGTGTTGGCAC-TGAG
1 ATGAGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATGGGCACAT-AG
** *
40138662 ATGAGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACATAT
1 ATGAGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATGGGCACATAG
** * * *
40138712 ATGAGAACTCCCATGTAAGACCATATTTTGGATATGGCAT
1 ATGAGAGGTCCCATGTAAGACCATGTTTGGGACATGGCAT
40138752 TTTTAGTACA
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
50 73 0.99
51 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.26
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATGGGCACATAG
Found at i:40147054 original size:47 final size:47
Alignment explanation
Indices: 40147000--40147092 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 47
40146990 ACCTAAGTGC
40147000 GAGACAAGAGGGAATAGAGAGATTCAATCAAGTTGTCTAGGAATAGA
1 GAGACAAGAGGGAATAGAGAGATTCAATCAAGTTGTCTAGGAATAGA
*
40147047 GAGACAAGAGGGAATAGAGAGATTCAGTCAAGTTGTCTAGGAATAG
1 GAGACAAGAGGGAATAGAGAGATTCAATCAAGTTGTCTAGGAATAG
40147093 TATTCTCCAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.41, C:0.09, G:0.31, T:0.19
Consensus pattern (47 bp):
GAGACAAGAGGGAATAGAGAGATTCAATCAAGTTGTCTAGGAATAGA
Found at i:40165816 original size:31 final size:31
Alignment explanation
Indices: 40165749--40165821 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
40165739 GCTCTTCCGG
40165749 TTTTTTCATTTTTCTAAATTTCATCCTATAC-
1 TTTTTT-ATTTTTCTAAATTTCATCCTATACA
* * *
40165780 CTTTTTATTTATTTTAAATTTCATCCATTTA-A
1 TTTTTTATTT-TTCTAAATTTCATCC-TATACA
40165812 TTTTTTATTT
1 TTTTTTATTT
40165822 CCTTAAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 4 0.11
31 19 0.54
32 12 0.34
ACGTcount: A:0.23, C:0.14, G:0.00, T:0.63
Consensus pattern (31 bp):
TTTTTTATTTTTCTAAATTTCATCCTATACA
Found at i:40169539 original size:17 final size:16
Alignment explanation
Indices: 40169517--40169550 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40169507 GGGGATGGCG
40169517 TTTGTTTGATGTTTATT
1 TTTGTTTG-TGTTTATT
*
40169534 TTTGTTTGTTTTTATT
1 TTTGTTTGTGTTTATT
40169550 T
1 T
40169551 CATAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.09, C:0.00, G:0.15, T:0.76
Consensus pattern (16 bp):
TTTGTTTGTGTTTATT
Found at i:40178590 original size:39 final size:40
Alignment explanation
Indices: 40178495--40178756 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
40178485 TTGAATGATG
*
40178495 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
40178533 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
40178574 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
40178613 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
40178652 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
40178691 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
40178730 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
40178757 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:40191089 original size:5 final size:5
Alignment explanation
Indices: 40191067--40191147 Score: 56
Period size: 5 Copynumber: 15.6 Consensus size: 5
40191057 TTTTATTGAA
* * ** *
40191067 TTTAT CTTTAT CTTTAT TTTAT TTTAT TTTAGT TTTTT TTTGT TCAAG
1 TTTAT -TTTAT -TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTTAT
* *
40191115 CTTGT TTTAT TTT-T ATTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT -TTTAT TTTAT TTTAT TTT
40191148 TGCAGAATAA
Statistics
Matches: 59, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
4 1 0.02
5 42 0.71
6 16 0.27
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:40209768 original size:75 final size:75
Alignment explanation
Indices: 40209672--40209845 Score: 258
Period size: 75 Copynumber: 2.3 Consensus size: 75
40209662 TATATATTGA
* *
40209672 GCATTAGCGGCGCTTTTTGAAAAACACCGCAAAAAAATTAAGAACAACGCCGTCGTTTTATGTTG
1 GCATTAGCGGCGCTTTTTGAAAAACACCGCAAAAAAATTAAGAACAACGCCGCCGTTTTATGTTA
40209737 AGCTTTAGTG
66 AGCTTTAGTG
* * * * * * *
40209747 GTATTAGAGGCACTTTTTGAAAAACGCGGCAAAAAAATTCAGCACAACGCCGCCGTTTTATGTTA
1 GCATTAGCGGCGCTTTTTGAAAAACACCGCAAAAAAATTAAGAACAACGCCGCCGTTTTATGTTA
40209812 AGCTTTAGTG
66 AGCTTTAGTG
*
40209822 GCATTAGCGGTGCTTTTTGAAAAA
1 GCATTAGCGGCGCTTTTTGAAAAA
40209846 TGTCGCTATA
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 86 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.29
Consensus pattern (75 bp):
GCATTAGCGGCGCTTTTTGAAAAACACCGCAAAAAAATTAAGAACAACGCCGCCGTTTTATGTTA
AGCTTTAGTG
Found at i:40210265 original size:7 final size:7
Alignment explanation
Indices: 40210255--40210438 Score: 79
Period size: 7 Copynumber: 25.9 Consensus size: 7
40210245 TATTATTATA
40210255 GTTTAGG
1 GTTTAGG
*
40210262 GTTTATG
1 GTTTAGG
40210269 GTTTAGG
1 GTTTAGG
* *
40210276 GTATAAG
1 GTTTAGG
40210283 GTTTAGG
1 GTTTAGG
*
40210290 GTTTAAG
1 GTTTAGG
*
40210297 GTTTAAG
1 GTTTAGG
*
40210304 GTTTAAGA
1 GTTT-AGG
40210312 GTTACTA--
1 GTT--TAGG
* *
40210319 TTTTAAG
1 GTTTAGG
*
40210326 GTTTATG
1 GTTTAGG
*
40210333 GATTATGG
1 GTTTA-GG
40210341 GTTTAGG
1 GTTTAGG
* *
40210348 GATTATG
1 GTTTAGG
**
40210355 GTTTATA
1 GTTTAGG
*
40210362 GTTTATG
1 GTTTAGG
40210369 GTTTAAGG
1 GTTT-AGG
*
40210377 G-TTGGG
1 GTTTAGG
**
40210383 GTTTAAA
1 GTTTAGG
40210390 GTTTAGG
1 GTTTAGG
* *
40210397 GGTTAGAA
1 GTTTAG-G
*
40210405 GTTAAGG
1 GTTTAGG
40210412 G-TTAGG
1 GTTTAGG
*
40210418 GGTTAGGG
1 GTTTA-GG
40210426 GTTTAGG
1 GTTTAGG
40210433 GTTTAG
1 GTTTAG
40210439 ATTAATTAAT
Statistics
Matches: 132, Mismatches: 34, Indels: 22
0.70 0.18 0.12
Matches are distributed among these distances:
5 2 0.02
6 8 0.06
7 98 0.74
8 22 0.17
9 1 0.01
10 1 0.01
ACGTcount: A:0.23, C:0.01, G:0.35, T:0.42
Consensus pattern (7 bp):
GTTTAGG
Found at i:40222891 original size:40 final size:40
Alignment explanation
Indices: 40222847--40223108 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
40222837 GCTCCTCGTT
* *
40222847 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
40222887 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
40222927 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
40222966 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
40223005 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
40223044 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
40223085 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40223109 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:40246139 original size:18 final size:17
Alignment explanation
Indices: 40246111--40246145 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40246101 ATTATTAAGA
*
40246111 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
40246128 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
40246146 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:40246283 original size:18 final size:17
Alignment explanation
Indices: 40246255--40246289 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40246245 ATTATTAAGA
*
40246255 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
40246272 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
40246290 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:40246500 original size:44 final size:45
Alignment explanation
Indices: 40246451--40246545 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
40246441 TTACACCTCT
* *
40246451 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
40246495 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
40246540 ATTACA
1 ATTACA
40246546 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:40246573 original size:16 final size:16
Alignment explanation
Indices: 40246526--40246575 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
40246516 GATTTGCTAT
* *
40246526 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
40246542 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
40246558 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
40246574 TA
1 TA
40246576 TAGCGAACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.34, C:0.36, G:0.00, T:0.30
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:40248719 original size:13 final size:13
Alignment explanation
Indices: 40248701--40248730 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
40248691 TATTCGATAG
40248701 TACAAACTGTAAT
1 TACAAACTGTAAT
*
40248714 TACAAATTGTAAT
1 TACAAACTGTAAT
40248727 TACA
1 TACA
40248731 CAGTTATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (13 bp):
TACAAACTGTAAT
Found at i:40249762 original size:20 final size:20
Alignment explanation
Indices: 40249739--40249777 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
40249729 ATGTAAATTA
40249739 ATTTTATAATATACTTTTTT
1 ATTTTATAATATACTTTTTT
40249759 ATTTTATAATATACTTTTT
1 ATTTTATAATATACTTTTT
40249778 GACCACGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTTTATAATATACTTTTTT
Found at i:40254599 original size:19 final size:19
Alignment explanation
Indices: 40254554--40254600 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
40254544 ACTCTCAATC
40254554 TCTTTTTGCTCTTTTTCAT
1 TCTTTTTGCTCTTTTTCAT
* *
40254573 TCTCTTTTTCT-TTTTTGATT
1 TCT-TTTTGCTCTTTTTCA-T
40254593 TCTTTTTG
1 TCTTTTTG
40254601 TGTCTTGCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.04, C:0.17, G:0.06, T:0.72
Consensus pattern (19 bp):
TCTTTTTGCTCTTTTTCAT
Found at i:40278085 original size:61 final size:61
Alignment explanation
Indices: 40277990--40278106 Score: 198
Period size: 61 Copynumber: 1.9 Consensus size: 61
40277980 AATTAATCAC
* * *
40277990 ATTAATATTATATTAATAAAATATTATCTAGATAAATATTAAATTAAATTTAATATCTCAT
1 ATTAATATTACATTAATAAAATACTATCTAGATAAATACTAAATTAAATTTAATATCTCAT
*
40278051 ATTAATATTACATTAATAAAATACTATCTAGATAAATACTAAATTTAATTTAATAT
1 ATTAATATTACATTAATAAAATACTATCTAGATAAATACTAAATTAAATTTAATAT
40278107 TAAATTCATT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.43
Consensus pattern (61 bp):
ATTAATATTACATTAATAAAATACTATCTAGATAAATACTAAATTAAATTTAATATCTCAT
Found at i:40279427 original size:71 final size:71
Alignment explanation
Indices: 40279334--40279476 Score: 189
Period size: 71 Copynumber: 2.0 Consensus size: 71
40279324 TCTATCGACG
* * * * *
40279334 CCTTGAGGACTTCTACTGAAACAAGTCAAGTTAGCAGCCAAAGTTCAACATCTCCTACACTTCTA
1 CCTTAAGGACTTCTACTAAAACAAGTCAAGTCAGCAGCAAAAGTTCAACATCCCCTACACTTCTA
40279399 CCGATA
66 CCGATA
* * *
40279405 CCTTAAGGACTTCTAAC-AAAACAATTCAAGTCAGTAGCAAAAGTTCAGCATCCCCTACACTTCT
1 CCTTAAGGACTTCT-ACTAAAACAAGTCAAGTCAGCAGCAAAAGTTCAACATCCCCTACACTTCT
*
40279469 ACTGATA
65 ACCGATA
40279476 C
1 C
40279477 TCTGATGGGT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
71 60 0.97
72 2 0.03
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (71 bp):
CCTTAAGGACTTCTACTAAAACAAGTCAAGTCAGCAGCAAAAGTTCAACATCCCCTACACTTCTA
CCGATA
Found at i:40303473 original size:71 final size:71
Alignment explanation
Indices: 40303352--40303484 Score: 185
Period size: 71 Copynumber: 1.9 Consensus size: 71
40303342 GCTTAGGACT
* * * * * * *
40303352 TCTATCGATACCTTAAGGACTTCGACCGAAACAAGTCTAGTTAGTAGCCAAATTTTAGCATCTCC
1 TCTACCGATACCTTAAGGACTTCGACCAAAACAAGTCAAGTCAATAGCCAAAGTTCAGCATCTCC
40303417 TACACC
66 TACACC
* *
40303423 TCTACCGATACCTTAAGGACTTCTACCAAAACAATTCAAGTCAATAGCCAAAGTTCAGCATC
1 TCTACCGATACCTTAAGGACTTCGACCAAAACAAGTCAAGTCAATAGCCAAAGTTCAGCATC
40303485 CCCTGTATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
71 53 1.00
ACGTcount: A:0.34, C:0.27, G:0.13, T:0.26
Consensus pattern (71 bp):
TCTACCGATACCTTAAGGACTTCGACCAAAACAAGTCAAGTCAATAGCCAAAGTTCAGCATCTCC
TACACC
Found at i:40314796 original size:63 final size:63
Alignment explanation
Indices: 40314720--40314845 Score: 225
Period size: 63 Copynumber: 2.0 Consensus size: 63
40314710 TTTTTAAGAC
*
40314720 ATAAAGTGGGTCATGCATGATTAAATTAAATAATAAAATATAAAATTATATTTAATAATTTAT
1 ATAAAGTCGGTCATGCATGATTAAATTAAATAATAAAATATAAAATTATATTTAATAATTTAT
* *
40314783 ATAAAGTCGGTCATGCCTGATTAAATTGAATAATAAAATATAAAATTATATTTAATAATTTAT
1 ATAAAGTCGGTCATGCATGATTAAATTAAATAATAAAATATAAAATTATATTTAATAATTTAT
40314846 TTTAAAATAT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.38
Consensus pattern (63 bp):
ATAAAGTCGGTCATGCATGATTAAATTAAATAATAAAATATAAAATTATATTTAATAATTTAT
Found at i:40316641 original size:36 final size:36
Alignment explanation
Indices: 40316601--40316669 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
40316591 GACATCATAG
* *
40316601 ATGCAGGGCACG-CTAACGTTGTTAAGAATGATACTT
1 ATGCAGGGCA-GACTAACGTTATTAAAAATGATACTT
40316637 ATGCAGGGCAGACTAACGTTATTAAAAATGATA
1 ATGCAGGGCAGACTAACGTTATTAAAAATGATA
40316670 TTTTACAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 1 0.03
36 29 0.97
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.26
Consensus pattern (36 bp):
ATGCAGGGCAGACTAACGTTATTAAAAATGATACTT
Found at i:40317646 original size:28 final size:28
Alignment explanation
Indices: 40317603--40317657 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
40317593 GAGTAAGGAT
40317603 TAAGGAAATCACTGAATCAACATAATCA
1 TAAGGAAATCACTGAATCAACATAATCA
* *
40317631 TAAGGAAATCATTGAATCTACATAATC
1 TAAGGAAATCACTGAATCAACATAATC
40317658 CTGGACTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.25
Consensus pattern (28 bp):
TAAGGAAATCACTGAATCAACATAATCA
Found at i:40321193 original size:18 final size:19
Alignment explanation
Indices: 40321170--40321211 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
40321160 TGTTTTAAAG
40321170 TTTATAG-T-TTAATTTTAT
1 TTTATAGTTATTAATTTT-T
40321188 TTTATAGTTATTAATTTTT
1 TTTATAGTTATTAATTTTT
40321207 TTTAT
1 TTTAT
40321212 CTTTTAAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.32
19 7 0.32
20 8 0.36
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTATAGTTATTAATTTTT
Found at i:40330086 original size:269 final size:269
Alignment explanation
Indices: 40329607--40330145 Score: 1078
Period size: 269 Copynumber: 2.0 Consensus size: 269
40329597 ATGTCCTAGA
40329607 TGGAGAGATTTTATACAAAAGAGGGAAGGATCAAGTACTATTGAGATGCGTGGATAGGGTGGAAG
1 TGGAGAGATTTTATACAAAAGAGGGAAGGATCAAGTACTATTGAGATGCGTGGATAGGGTGGAAG
40329672 CCAAGAAAATCCTAGAAGAAGTTCACGAAGGCATTTGTGGAACGCATGCCAATGGATTTACAATG
66 CCAAGAAAATCCTAGAAGAAGTTCACGAAGGCATTTGTGGAACGCATGCCAATGGATTTACAATG
40329737 GCTAGACAGATCATGAGATTCGGCTATTACTGGTCCACCATGGAAGGAGATTGCATCAATTATGC
131 GCTAGACAGATCATGAGATTCGGCTATTACTGGTCCACCATGGAAGGAGATTGCATCAATTATGC
40329802 CAAGAAGTGCCATAAATGCCAAATCTATGCAGACAAAATACACGCGCCTCCGTCACCTCTTCACA
196 CAAGAAGTGCCATAAATGCCAAATCTATGCAGACAAAATACACGCGCCTCCGTCACCTCTTCACA
40329867 TTATGACTT
261 TTATGACTT
40329876 TGGAGAGATTTTATACAAAAGAGGGAAGGATCAAGTACTATTGAGATGCGTGGATAGGGTGGAAG
1 TGGAGAGATTTTATACAAAAGAGGGAAGGATCAAGTACTATTGAGATGCGTGGATAGGGTGGAAG
40329941 CCAAGAAAATCCTAGAAGAAGTTCACGAAGGCATTTGTGGAACGCATGCCAATGGATTTACAATG
66 CCAAGAAAATCCTAGAAGAAGTTCACGAAGGCATTTGTGGAACGCATGCCAATGGATTTACAATG
40330006 GCTAGACAGATCATGAGATTCGGCTATTACTGGTCCACCATGGAAGGAGATTGCATCAATTATGC
131 GCTAGACAGATCATGAGATTCGGCTATTACTGGTCCACCATGGAAGGAGATTGCATCAATTATGC
40330071 CAAGAAGTGCCATAAATGCCAAATCTATGCAGACAAAATACACGCGCCTCCGTCACCTCTTCACA
196 CAAGAAGTGCCATAAATGCCAAATCTATGCAGACAAAATACACGCGCCTCCGTCACCTCTTCACA
40330136 TTATGACTT
261 TTATGACTT
40330145 T
1 T
40330146 TCCATGGCCT
Statistics
Matches: 270, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
269 270 1.00
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.24
Consensus pattern (269 bp):
TGGAGAGATTTTATACAAAAGAGGGAAGGATCAAGTACTATTGAGATGCGTGGATAGGGTGGAAG
CCAAGAAAATCCTAGAAGAAGTTCACGAAGGCATTTGTGGAACGCATGCCAATGGATTTACAATG
GCTAGACAGATCATGAGATTCGGCTATTACTGGTCCACCATGGAAGGAGATTGCATCAATTATGC
CAAGAAGTGCCATAAATGCCAAATCTATGCAGACAAAATACACGCGCCTCCGTCACCTCTTCACA
TTATGACTT
Found at i:40332929 original size:44 final size:44
Alignment explanation
Indices: 40332380--40332916 Score: 788
Period size: 44 Copynumber: 12.2 Consensus size: 44
40332370 CACAAAGCCA
*
40332380 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGCCC
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
*
40332424 TATCTCCCTGACCAGCAGTGGAATAGGCTGAAGATTGTAAGTCC
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
* * * * *
40332468 TAGCTCCCTGAACAGCAGTGGAATAGGTCGAAGATGGTAAGCCC
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
40332512 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
* * *
40332556 TATCTCCCTGACCAGCAGTGGAATAGGTCGAAGATGGTAAGCCC
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
* *
40332600 TATCTCCCTGAACAGCAGTGGAATAGGTCGAAGATTGTAAGTCC
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
* * * * * * * *
40332644 TAGCTCCCTGAACAACAGTAGAATAGGTCGAAGATGGTAGGCCC
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
* * * *
40332688 TATCTCCCTGACCAGCAGTAGAATAAGTTGAAAATCGTAAGTCC
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
*
40332732 TATCTCCCTGACCAGAAGTGGAATAGGTTGAAGATTGTAAGTCC
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
40332776 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
* *
40332820 TATCTCTCGGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
* *
40332864 TATCTCCCTGACCAACAGTGGAATAGGTTGAAAATTGT-AGATCC
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAG-TCC
*
40332908 TGTCTCCCT
1 TATCTCCCT
40332917 AAGCAGTAGT
Statistics
Matches: 445, Mismatches: 47, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
43 2 0.00
44 443 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.25
Consensus pattern (44 bp):
TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGTAAGTCC
Found at i:40337513 original size:48 final size:48
Alignment explanation
Indices: 40337461--40337552 Score: 114
Period size: 47 Copynumber: 1.9 Consensus size: 48
40337451 CACGATTTTC
*
40337461 ATTATGTGGCAGTATACCTACAATTTTGGTGGC-TTGTCCACAATATTG
1 ATTAT-TGGCAGTATACCTACAATTTTGGTGACATTGTCCACAATATTG
* * * * *
40337509 ATTATTGGTAGTTTATCTACGATTTTGGTGACATTGTTCACAAT
1 ATTATTGGCAGTATACCTACAATTTTGGTGACATTGTCCACAAT
40337553 TTGGTGTGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
47 22 0.59
48 15 0.41
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (48 bp):
ATTATTGGCAGTATACCTACAATTTTGGTGACATTGTCCACAATATTG
Found at i:40341446 original size:19 final size:19
Alignment explanation
Indices: 40341419--40341462 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
40341409 TTTATGTTTT
40341419 ATTTA-TTTATTTACTTA-A
1 ATTTATTTTATTT-CTTATA
*
40341437 ATTTATTTTATTTTTTATA
1 ATTTATTTTATTTCTTATA
40341456 ATTTATT
1 ATTTATT
40341463 AATGCGGAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTATTTTATTTCTTATA
Found at i:40349894 original size:20 final size:20
Alignment explanation
Indices: 40349869--40349910 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
40349859 CTTATAAACC
40349869 GAATCAAACCATATCTTTCT
1 GAATCAAACCATATCTTTCT
40349889 GAATCAAACCATATCTTTCT
1 GAATCAAACCATATCTTTCT
40349909 GA
1 GA
40349911 GACCTCTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.33
Consensus pattern (20 bp):
GAATCAAACCATATCTTTCT
Found at i:40350929 original size:21 final size:21
Alignment explanation
Indices: 40350900--40350939 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40350890 GGGTCTACTC
*
40350900 GCCCATGTGAAGGCCACACAT
1 GCCCATGTGAAAGCCACACAT
*
40350921 GCCCCTGTGAAAGCCACAC
1 GCCCATGTGAAAGCCACAC
40350940 GCGCTTGTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.38, G:0.23, T:0.12
Consensus pattern (21 bp):
GCCCATGTGAAAGCCACACAT
Found at i:40353259 original size:21 final size:20
Alignment explanation
Indices: 40353235--40353274 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40353225 ATCTTATAAT
40353235 ATTTGGAAAAATATAATTTTA
1 ATTT-GAAAAATATAATTTTA
* *
40353256 ATTTGATAAATATTATTTT
1 ATTTGAAAAATATAATTTT
40353275 TTTAAACTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (20 bp):
ATTTGAAAAATATAATTTTA
Found at i:40354030 original size:15 final size:15
Alignment explanation
Indices: 40354006--40354036 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40353996 TCTTTCTCTC
40354006 TTTTCGTTTCTTTTT
1 TTTTCGTTTCTTTTT
*
40354021 TTTTCTTTTCTTTTT
1 TTTTCGTTTCTTTTT
40354036 T
1 T
40354037 ATATTATTAA
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:0.00, C:0.13, G:0.03, T:0.84
Consensus pattern (15 bp):
TTTTCGTTTCTTTTT
Found at i:40354663 original size:3 final size:3
Alignment explanation
Indices: 40354657--40354690 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
40354647 AGTTTAATAA
* *
40354657 TAT TAT TAT TAC TAT TAT TAT TAT TAG TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
40354691 TTTTATCAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:40354793 original size:21 final size:24
Alignment explanation
Indices: 40354739--40354793 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 24
40354729 TTATTATGTA
40354739 GTATTATTTTAAGTTTTCCATATAT
1 GTATTATTTTAAG-TTTCCATATAT
40354764 -TATTA-TTTAA-TTT-CATA-AT
1 GTATTATTTTAAGTTTCCATATAT
40354783 GTATTATTTTA
1 GTATTATTTTA
40354794 TATATATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 2 0.07
20 9 0.32
21 7 0.25
23 5 0.18
24 5 0.18
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.58
Consensus pattern (24 bp):
GTATTATTTTAAGTTTCCATATAT
Found at i:40359592 original size:14 final size:14
Alignment explanation
Indices: 40359573--40359606 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
40359563 CAAAATGAAA
*
40359573 GTGGAAGATCTTAT
1 GTGGAAGACCTTAT
40359587 GTGGAAGACCTTAT
1 GTGGAAGACCTTAT
*
40359601 CTGGAA
1 GTGGAA
40359607 TAACATTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (14 bp):
GTGGAAGACCTTAT
Found at i:40359703 original size:15 final size:15
Alignment explanation
Indices: 40359673--40359725 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
40359663 GATTCAATCA
40359673 AAAAAAAAAGAAGAAC
1 AAAAAAAAA-AAGAAC
* *
40359689 AGAACAAAAAAGAAC
1 AAAAAAAAAAAGAAC
40359704 AAAAAACAAAAAGAAAC
1 AAAAAA-AAAAAG-AAC
40359721 AAAAA
1 AAAAA
40359726 CCTCTACTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
15 10 0.32
16 13 0.42
17 8 0.26
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAGAAC
Found at i:40359711 original size:17 final size:17
Alignment explanation
Indices: 40359672--40359725 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
40359662 AGATTCAATC
*
40359672 AAAA-AAAAAAGAAGAA
1 AAAACAAAAAAGAACAA
*
40359688 CAGAACAAAAAAGAACAA
1 -AAAACAAAAAAGAACAA
40359706 AAAAC-AAAAAGAAACAA
1 AAAACAAAAAAG-AACAA
40359723 AAA
1 AAA
40359726 CCTCTACTGG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 6 0.19
17 15 0.47
18 11 0.34
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAACAAAAAAGAACAA
Found at i:40361697 original size:88 final size:88
Alignment explanation
Indices: 40361502--40361705 Score: 259
Period size: 88 Copynumber: 2.3 Consensus size: 88
40361492 CATAAATCTC
* * * * * *
40361502 ATCTCCCTGAGCAACAGTGAAGTAGGTTAAAAATAGCAGATCTTTTCTTCATGTATTGGTAGCGA
1 ATCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAATAGCAGATCTTGTCTTCATGTATCGGCAACGA
*
40361567 AATAGATTGAAGACACCAGCCTT
66 AATAGATCGAAGACACCAGCCTT
* * *
40361590 ATCTCCCTGAGTAGCAGTGGAGTAGGTTAAAAATAGCAGATCTTGTCTTCCTGTATCGGCAATGA
1 ATCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAATAGCAGATCTTGTCTTCATGTATCGGCAACGA
*
40361655 AGTAGATCGAAGAC-CTCAGCCTT
66 AATAGATCGAAGACAC-CAGCCTT
* *
40361678 ATCTCCCTG-GACAGTAGTGGAATAGGTT
1 ATCTCCCTGAG-CAGCAGTGGAGTAGGTT
40361706 GATGATTGTA
Statistics
Matches: 100, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
87 2 0.02
88 98 0.98
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (88 bp):
ATCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAATAGCAGATCTTGTCTTCATGTATCGGCAACGA
AATAGATCGAAGACACCAGCCTT
Found at i:40361870 original size:44 final size:44
Alignment explanation
Indices: 40361804--40362122 Score: 254
Period size: 44 Copynumber: 7.2 Consensus size: 44
40361794 TTAAGCTGCC
* * *
40361804 AGTCCTACCTCCCTGGATAGCAGTGGAATAGGTTGAAGATTGTA
1 AGTCCTATCTCCCTAGACAGCAGTGGAATAGGTTGAAGATTGTA
*
40361848 AGTCCTATCTCCCTAGACAGCAGTGGAATAGGTTGAAGGTTGTA
1 AGTCCTATCTCCCTAGACAGCAGTGGAATAGGTTGAAGATTGTA
* *
40361892 AGTCCTATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATTGT-
1 AGTCCTATCTCCCTAGACAGCAGTGGAATAGGTTGAAGATTGTA
* * * ** * ** *
40361935 AGATCCTGTCTCCCTA-AGCAGTAATGGAGCAGATCAAAGATGGTGA
1 AG-TCCTATCTCCCTAGA-CAGCAGTGGAATAGGTTGAAGATTGT-A
* * * ** * * * * *****
40361981 A-TCTTATCTTCATAGGGTAGTAG-GGAAGCAGATTTAAG-CCACC
1 AGTCCTATCTCCCTA-GACAGCAGTGGAA-TAGGTTGAAGATTGTA
40362024 AGTCCTATCTCCCT-GAACAGCAGTGGAATAGGTTGAAGATTGTA
1 AGTCCTATCTCCCTAG-ACAGCAGTGGAATAGGTTGAAGATTGTA
*
40362068 AGTCCTATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTA
1 AGTCCTATCTCCCTAGACAGCAGTGGAATAGGTTGAAGATTGTA
* *
40362112 CGTCCTGTCTC
1 AGTCCTATCTC
40362123 TTTAAGCAGT
Statistics
Matches: 216, Mismatches: 47, Indels: 24
0.75 0.16 0.08
Matches are distributed among these distances:
42 1 0.00
43 15 0.07
44 186 0.86
45 13 0.06
46 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (44 bp):
AGTCCTATCTCCCTAGACAGCAGTGGAATAGGTTGAAGATTGTA
Found at i:40361917 original size:88 final size:88
Alignment explanation
Indices: 40361804--40362122 Score: 281
Period size: 88 Copynumber: 3.6 Consensus size: 88
40361794 TTAAGCTGCC
* *
40361804 AGTCCTACCTCCCTGGATAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTAGACAGC
1 AGTCCTATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTAGACAGC
*
40361869 AGTGGAATAGGTTGAAGGTTGTA
66 AGTGGAATAGGTTGAAGATTGTA
* *
40361892 AGTCCTATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATTGT-AGATCCTGTCTCCCTA-AGCA
1 AGTCCTATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTAAG-TCCTATCTCCCTAGA-CA
* * ** * ** *
40361955 GTAATGGAGCAGATCAAAGATGGTGA
64 GCAGTGGAATAGGTTGAAGATTGT-A
* * * ** * * * * *****
40361981 A-TCTTATCTTCATAGGGTAGTAG-GGAAGCAGATTTAAG-CCACCAGTCCTATCTCCCT-GAAC
1 AGTCCTATCTCCCT-GGACAGCAGTGGAA-TAGGTTGAAGATTGTAAGTCCTATCTCCCTAG-AC
40362042 AGCAGTGGAATAGGTTGAAGATTGTA
63 AGCAGTGGAATAGGTTGAAGATTGTA
* *
40362068 AGTCCTATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTACGTCCTGTCTC
1 AGTCCTATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTC
40362123 TTTAAGCAGT
Statistics
Matches: 170, Mismatches: 50, Indels: 22
0.70 0.21 0.09
Matches are distributed among these distances:
87 18 0.11
88 133 0.78
89 19 0.11
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (88 bp):
AGTCCTATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTAGACAGC
AGTGGAATAGGTTGAAGATTGTA
Found at i:40361974 original size:220 final size:220
Alignment explanation
Indices: 40361677--40362122 Score: 712
Period size: 220 Copynumber: 2.0 Consensus size: 220
40361667 ACCTCAGCCT
* * *
40361677 TATCTCCCTGGACAGTAGTGGAATAGGTTGATGATTGTAGATCATGTCTGCCTAAACAATAGTGG
1 TATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATTGTAGATCATGTCTCCCTAAACAATAATGG
* **
40361742 AACAGATCAAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCTGCCAGT
66 AACAGATCAAAGACGGTGAATCTTATCTTCACAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGT
* *
40361807 CCTACCTCCCTGGATAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTAGACAGCAGT
131 CCTACCTCCCTGAACAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTAGACAGCAGT
*
40361872 GGAATAGGTTGAAGGTTGTAAGTCC
196 GGAATAGGTTGAAGATTGTAAGTCC
* * *
40361897 TATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAATGG
1 TATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATTGTAGATCATGTCTCCCTAAACAATAATGG
* * * *
40361962 AGCAGATCAAAGATGGTGAATCTTATCTTCATAGGGTAGTAGGGAAGCAGATTTAAGCCACCAGT
66 AACAGATCAAAGACGGTGAATCTTATCTTCACAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGT
* *
40362027 CCTATCTCCCTGAACAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGACAGCAGT
131 CCTACCTCCCTGAACAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTAGACAGCAGT
*
40362092 GGAATAGGTTGAAGATTGTACGTCC
196 GGAATAGGTTGAAGATTGTAAGTCC
*
40362117 TGTCTC
1 TATCTC
40362123 TTTAAGCAGT
Statistics
Matches: 206, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
220 206 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (220 bp):
TATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATTGTAGATCATGTCTCCCTAAACAATAATGG
AACAGATCAAAGACGGTGAATCTTATCTTCACAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGT
CCTACCTCCCTGAACAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTAGACAGCAGT
GGAATAGGTTGAAGATTGTAAGTCC
Found at i:40362033 original size:176 final size:177
Alignment explanation
Indices: 40361848--40362215 Score: 589
Period size: 176 Copynumber: 2.1 Consensus size: 177
40361838 GAAGATTGTA
*
40361848 AGTCCTATCTCCCTAG-ACAGCAGTGGAATAGGTTGAAGGTTGTAAGTCCTATCTCCCTGGACAG
1 AGTCCTATCTCCCTAGAACAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGACAG
* * *
40361912 TAGTGGAATAGGTTGAAGATTGTA-GATCCTGTCTCCCTAAGCAGTAATGGAGCAGATCAAAGAT
66 CAGTGGAATAGGTTGAAGATTGTACG-TCCTGTCTCCCTAAGCAGTAATGAAGCAGATCAAAGAC
* * *
40361976 GGTGAATCTTATCTTCATAGGGTAGTAGGGAAGCAGATTTAAGCCACC
130 GGTGAATCTTATCTACACAAGGTAGTAGGGAAGCAGATTTAAGCCACC
40362024 AGTCCTATCTCCCT-GAACAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGACAG
1 AGTCCTATCTCCCTAGAACAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGACAG
** *
40362088 CAGTGGAATAGGTTGAAGATTGTACGTCCTGTCTCTTTAAGCAGTAGTGAAGCAGATCAAAGACG
66 CAGTGGAATAGGTTGAAGATTGTACGTCCTGTCTCCCTAAGCAGTAATGAAGCAGATCAAAGACG
* *
40362153 GTGAATCTTATCTACCCAAGGTAGTAGGGAAGCAGATTTAAGCCGCC
131 GTGAATCTTATCTACACAAGGTAGTAGGGAAGCAGATTTAAGCCACC
*
40362200 AGCCCTATCTCCCTAG
1 AGTCCTATCTCCCTAG
40362216 TTGCAGTGGA
Statistics
Matches: 176, Mismatches: 13, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
175 1 0.01
176 173 0.98
177 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (177 bp):
AGTCCTATCTCCCTAGAACAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGACAG
CAGTGGAATAGGTTGAAGATTGTACGTCCTGTCTCCCTAAGCAGTAATGAAGCAGATCAAAGACG
GTGAATCTTATCTACACAAGGTAGTAGGGAAGCAGATTTAAGCCACC
Found at i:40363160 original size:18 final size:19
Alignment explanation
Indices: 40363139--40363177 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
40363129 TCTTTTTTAG
40363139 TTCTTTCTCTCTTTTC-GT
1 TTCTTTCTCTCTTTTCTGT
* *
40363157 TTCTTTTTTTCTTTTCTGT
1 TTCTTTCTCTCTTTTCTGT
40363176 TT
1 TT
40363178 TTATATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.00, C:0.21, G:0.05, T:0.74
Consensus pattern (19 bp):
TTCTTTCTCTCTTTTCTGT
Found at i:40370697 original size:20 final size:20
Alignment explanation
Indices: 40370672--40370716 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
40370662 TAAATACACA
40370672 TAATTAAAATT-AGACACAAT
1 TAATT-AAATTAAGACACAAT
*
40370692 TAATTAAGTTAAGACACAAT
1 TAATTAAATTAAGACACAAT
40370712 TAATT
1 TAATT
40370717 CGGTTGGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (20 bp):
TAATTAAATTAAGACACAAT
Found at i:40372890 original size:14 final size:16
Alignment explanation
Indices: 40372871--40372905 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
40372861 TTCTTTTTCA
40372871 ATTTTC-TTTTCT-TC
1 ATTTTCTTTTTCTCTC
40372885 ATTTTCTTTTTCTCTC
1 ATTTTCTTTTTCTCTC
40372901 ATTTT
1 ATTTT
40372906 TTCGATTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 6 0.32
16 7 0.37
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTTCTTTTTCTCTC
Found at i:40372895 original size:15 final size:15
Alignment explanation
Indices: 40372854--40372905 Score: 56
Period size: 13 Copynumber: 3.6 Consensus size: 15
40372844 TTTTTCTGAA
*
40372854 TCTCAATTTCTTTT-
1 TCTCATTTTCTTTTC
*
40372868 TC-AATTTTCTTTTC
1 TCTCATTTTCTTTTC
40372882 T-TCATTTTCTTTTTC
1 TCTCATTTTC-TTTTC
40372897 TCTCATTTT
1 TCTCATTTT
40372906 TTCGATTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 9 0.29
14 9 0.29
15 6 0.19
16 7 0.23
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.67
Consensus pattern (15 bp):
TCTCATTTTCTTTTC
Found at i:40372924 original size:18 final size:17
Alignment explanation
Indices: 40372903--40372958 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 17
40372893 TTTCTCTCAT
40372903 TTTTTCGATTTCTTTTTC
1 TTTTTC-ATTTCTTTTTC
*
40372921 TTTTGCAATTTCTTTTTC
1 TTTTTC-ATTTCTTTTTC
40372939 TTTTTCACTTTCTTTTTC
1 TTTTTCA-TTTCTTTTTC
40372957 TT
1 TT
40372959 CTTTTTCATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
17 1 0.03
18 33 0.97
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.71
Consensus pattern (17 bp):
TTTTTCATTTCTTTTTC
Found at i:40372970 original size:6 final size:6
Alignment explanation
Indices: 40372860--40372958 Score: 56
Period size: 6 Copynumber: 16.0 Consensus size: 6
40372850 TGAATCTCAA
* * ** **
40372860 TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTCT CAT-TT TTTCGA
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCT-T TTTCTT TTTCTT
* ** **
40372911 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCAC TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
40372959 CTTTTTCATT
Statistics
Matches: 66, Mismatches: 23, Indels: 8
0.68 0.24 0.08
Matches are distributed among these distances:
5 2 0.03
6 50 0.76
7 11 0.17
8 3 0.05
ACGTcount: A:0.08, C:0.19, G:0.02, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:40373863 original size:18 final size:18
Alignment explanation
Indices: 40373823--40373866 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
40373813 ACTTCTTCTT
*
40373823 TTTTTTATACTTCGAAATT
1 TTTTTT-TACTTCGAAATC
* *
40373842 TTTTTTTACTTCGTACTC
1 TTTTTTTACTTCGAAATC
40373860 TTTTTTT
1 TTTTTTT
40373867 TTGTAATTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.16, C:0.14, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTTTTTACTTCGAAATC
Found at i:40373863 original size:20 final size:18
Alignment explanation
Indices: 40373819--40373868 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
40373809 TTTCACTTCT
40373819 TCTTTTTTTTATACTTCGA
1 TCTTTTTTTT-TACTTCGA
**
40373838 AATTTTTTTTTACTTCGTA
1 TCTTTTTTTTTACTTCG-A
40373857 CTCTTTTTTTTT
1 -TCTTTTTTTTT
40373869 GTAATTTCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 7 0.28
19 9 0.36
20 9 0.36
ACGTcount: A:0.14, C:0.14, G:0.04, T:0.68
Consensus pattern (18 bp):
TCTTTTTTTTTACTTCGA
Found at i:40374243 original size:70 final size:69
Alignment explanation
Indices: 40374154--40374291 Score: 231
Period size: 70 Copynumber: 2.0 Consensus size: 69
40374144 TTACAAAGTG
* *
40374154 AATTTTGAAATGATAGAAGGTTTAGAAAGATGTAGGTTCGATTTAATAAATGAATCAAAGGATAT
1 AATTTTGAAATGATAGAAGGTTTAGAAAGATGTAGGTTC-ATTTAATAAAGGAATCAAAGGATAG
40374219 TTAAT
65 TTAAT
* *
40374224 AATTTTGTAATGTTAGAAGGTTTAGAAAGATGTAGGTTCATTTAATAAAGGAATCAAAGGATAGT
1 AATTTTGAAATGATAGAAGGTTTAGAAAGATGTAGGTTCATTTAATAAAGGAATCAAAGGATAGT
40374289 TAA
66 TAA
40374292 CTTGGGATAA
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
69 27 0.42
70 37 0.58
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34
Consensus pattern (69 bp):
AATTTTGAAATGATAGAAGGTTTAGAAAGATGTAGGTTCATTTAATAAAGGAATCAAAGGATAGT
TAAT
Found at i:40375174 original size:20 final size:20
Alignment explanation
Indices: 40375149--40375193 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
40375139 TAAATACACA
40375149 TAATTAAAATT-AGACACAAT
1 TAATT-AAATTAAGACACAAT
* *
40375169 TAATTAAGTTAAGATACAAT
1 TAATTAAATTAAGACACAAT
40375189 TAATT
1 TAATT
40375194 TGATTGGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.36
Consensus pattern (20 bp):
TAATTAAATTAAGACACAAT
Found at i:40377572 original size:15 final size:15
Alignment explanation
Indices: 40377554--40377583 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40377544 AGTTTCATTA
40377554 TCTACAGTTTCACAG
1 TCTACAGTTTCACAG
*
40377569 TCTATAGTTTCACAG
1 TCTACAGTTTCACAG
40377584 CCTGTAGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (15 bp):
TCTACAGTTTCACAG
Found at i:40377591 original size:15 final size:15
Alignment explanation
Indices: 40377559--40377595 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
40377549 CATTATCTAC
*
40377559 AGTTTCACAGTCTAT
1 AGTTTCACAGCCTAT
*
40377574 AGTTTCACAGCCTGT
1 AGTTTCACAGCCTAT
40377589 AGTTTCA
1 AGTTTCA
40377596 ATATATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (15 bp):
AGTTTCACAGCCTAT
Found at i:40382442 original size:30 final size:30
Alignment explanation
Indices: 40382407--40382467 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
40382397 ATTATATAAG
40382407 TAAGATGATTTTATATGTGTATGAAATTGA
1 TAAGATGATTTTATATGTGTATGAAATTGA
*
40382437 TAAGATGATTTTATATGTGTATGAGATTGA
1 TAAGATGATTTTATATGTGTATGAAATTGA
40382467 T
1 T
40382468 TAAACTTGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.44
Consensus pattern (30 bp):
TAAGATGATTTTATATGTGTATGAAATTGA
Done.