Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 8 of 163
Found at i:2541332 original size:205 final size:204
Alignment explanation
Indices: 2540907--2541620 Score: 914
Period size: 205 Copynumber: 3.5 Consensus size: 204
2540897 AAAATCAATT
* * * ** * *
2540907 CAAATTAATCAGAAAAGAAACACCAATAAAAATCGAACTAAAAAGAGAGAGGAAATGTTGATGAA
1 CAAATTAATCAGCAAAGAAACACCAATACAAATCAAACTAAAAA-A-ACCGGAAATATCGATGAA
* * * **
2540972 CTTCGAAACCAAT-ACGAGGTCTAGAAGGAGAAAATGGCTCAAAACCAATTCAAACTAATCAGCA
64 CTTCGAAACGAATAACGAGGTCTAGAAGGAGAAAATAGCTAAAAATGAATTCAAACTAATCAGCA
**
2541036 AAGAAAAACTATTATAAATCAAATTAACAAAAAGGAATGGAAATATAAATGAATAGCGAGATCTA
129 AAGAAAAACTATTATAAATCAAATT-TTAAAAA--AA-GGAAATATAAATGAATAGCGAGATCTA
*
2541101 GAAGGAGAAATTGAA
190 GAACGAGAAATTGAA
* * * *
2541116 CAAAATAATCAGCAAAGAAACACTAATTCAAATCAAAGTAAAAAAACCGGAAATATCGATGAACT
1 CAAATTAATCAGCAAAGAAACACCAATACAAATCAAACTAAAAAAACCGGAAATATCGATGAACT
* * * *
2541181 TTGAAATGAATAACGAGGTCTAGAAGGAGAAAATAAGCTAAAAATGAATTCACACTAATCGGCAA
66 TCGAAACGAATAACGAGGTCTAGAAGGAGAAAAT-AGCTAAAAATGAATTCAAACTAATCAGCAA
*
2541246 AGAAAAACAATTATAAATCAAATTTTAAAAAAAGGAAATATAAATGAATAGCGAGATCTAGAACG
130 AGAAAAACTATTATAAATCAAATTTTAAAAAAAGGAAATATAAATGAATAGCGAGATCTAGAACG
2541311 AGAAATTGAA
195 AGAAATTGAA
* *
2541321 CAAAGTAATCAGCAAAGAAACACCAATACAAATCAAACTAAAAAAACCGGAAATATAGATGAACT
1 CAAATTAATCAGCAAAGAAACACCAATACAAATCAAACTAAAAAAACCGGAAATATCGATGAACT
* * * *
2541386 TCGAAATGAATAACGAGGTCTGGAAGGAGAAAGTGAGCTAAAAATGAATTCAAACTAATCAGTAA
66 TCGAAACGAATAACGAGGTCTAGAAGGAGAAAAT-AGCTAAAAATGAATTCAAACTAATCAGCAA
* * ** * * *
2541451 AGAAATACTATTAT-AATTATTTTTTTAAAAAAGGAAATATAAACGAAGAGCGAGATCTAGAACG
130 AGAAAAACTATTATAAATCAAATTTTAAAAAAAGGAAATATAAATGAATAGCGAGATCTAGAACG
2541515 A-AAGATTGAA
195 AGAA-ATTGAA
* * * *
2541525 CAAATTAATCAGCAAAGAAGCACTAACACAAATCAAACTAAAAAAACCAGAAATATCGAT-AACT
1 CAAATTAATCAGCAAAGAAACACCAATACAAATCAAACTAAAAAAACCGGAAATATCGATGAACT
* * * *
2541589 TTGAAACGAACAGCGAGATCTAGAAGGAGAAA
66 TCGAAACGAATAACGAGGTCTAGAAGGAGAAA
2541621 TGGAACTAAC
Statistics
Matches: 446, Mismatches: 56, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
203 32 0.07
204 105 0.24
205 171 0.38
206 2 0.00
207 24 0.05
208 28 0.06
209 84 0.19
ACGTcount: A:0.53, C:0.13, G:0.16, T:0.19
Consensus pattern (204 bp):
CAAATTAATCAGCAAAGAAACACCAATACAAATCAAACTAAAAAAACCGGAAATATCGATGAACT
TCGAAACGAATAACGAGGTCTAGAAGGAGAAAATAGCTAAAAATGAATTCAAACTAATCAGCAAA
GAAAAACTATTATAAATCAAATTTTAAAAAAAGGAAATATAAATGAATAGCGAGATCTAGAACGA
GAAATTGAA
Found at i:2544088 original size:10 final size:10
Alignment explanation
Indices: 2544065--2544095 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
2544055 CCAACATGTA
2544065 ATTTATTATAT
1 ATTTATT-TAT
2544076 ATTTATTTAT
1 ATTTATTTAT
2544086 ATTTATTTAT
1 ATTTATTTAT
2544096 TTATAAAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.65
11 7 0.35
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
ATTTATTTAT
Found at i:2544094 original size:14 final size:14
Alignment explanation
Indices: 2544065--2544100 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
2544055 CCAACATGTA
2544065 ATTTATTATATATTT
1 ATTTA-TATATATTT
*
2544080 ATTTATATTTATTT
1 ATTTATATATATTT
2544094 ATTTATA
1 ATTTATA
2544101 AAAGGATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTTATATATATTT
Found at i:2547147 original size:20 final size:18
Alignment explanation
Indices: 2547102--2547154 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 18
2547092 ACTATTATTT
*
2547102 AATTCAAATTTAAATAAA
1 AATTCGAATTTAAATAAA
*
2547120 ATACTCGAATTTAACATAAA
1 A-ATTCGAATTTAA-ATAAA
*
2547140 CAATTCGAGTTTAAA
1 -AATTCGAATTTAAA
2547155 ATAACTATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 1 0.04
19 11 0.39
20 15 0.54
21 1 0.04
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.32
Consensus pattern (18 bp):
AATTCGAATTTAAATAAA
Found at i:2552563 original size:53 final size:53
Alignment explanation
Indices: 2552483--2552641 Score: 318
Period size: 53 Copynumber: 3.0 Consensus size: 53
2552473 TTGAGAAAGG
2552483 TTCTAAAACTCACCATAAAGTTTACTATTCATCAGCCAATAACCTCTTAATTT
1 TTCTAAAACTCACCATAAAGTTTACTATTCATCAGCCAATAACCTCTTAATTT
2552536 TTCTAAAACTCACCATAAAGTTTACTATTCATCAGCCAATAACCTCTTAATTT
1 TTCTAAAACTCACCATAAAGTTTACTATTCATCAGCCAATAACCTCTTAATTT
2552589 TTCTAAAACTCACCATAAAGTTTACTATTCATCAGCCAATAACCTCTTAATTT
1 TTCTAAAACTCACCATAAAGTTTACTATTCATCAGCCAATAACCTCTTAATTT
2552642 AATAGTAAGA
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 106 1.00
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.36
Consensus pattern (53 bp):
TTCTAAAACTCACCATAAAGTTTACTATTCATCAGCCAATAACCTCTTAATTT
Found at i:2553552 original size:147 final size:145
Alignment explanation
Indices: 2553298--2553561 Score: 350
Period size: 147 Copynumber: 1.8 Consensus size: 145
2553288 CGCAATATCC
* * * * * * *
2553298 TACACATGACCACATGATGTTACACCTTGATACCAATTAGATCAATGAAATAGTGGCCAACATTG
1 TACACATGACCACACGATGTCACACCTTAATACCAATTAGATCAATAAAACAATGGCCAACATTA
* * *
2553363 TGGCTTCCTATGTACGACGTCGTGACATCACACCTTGATCACCAATAAATCAATGACATAATAAC
66 CGACTTCCTATGTAC-ACATCGTGACATCACACCTTGATCACCAATAAATCAATGACATAATAAC
2553428 TAAGGTCGCAATGTTG
130 TAAGGTCGCAATGTTG
** * *
2553444 TACACATGACGTCACGATGTCATACCTTAATGACCTATTAGATCAATAAAACAATGGCCAACATT
1 TACACATGACCACACGATGTCACACCTTAAT-ACCAATTAGATCAATAAAACAATGGCCAACATT
*
2553509 ACGACTTCCTGCATGTA-ACATCGTGACATCACACCTTGGTCACCAATAAATCA
65 ACGACTTCCT--ATGTACACATCGTGACATCACACCTTGATCACCAATAAATCA
2553562 GTGGGACAAT
Statistics
Matches: 100, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
146 25 0.25
147 70 0.70
149 5 0.05
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (145 bp):
TACACATGACCACACGATGTCACACCTTAATACCAATTAGATCAATAAAACAATGGCCAACATTA
CGACTTCCTATGTACACATCGTGACATCACACCTTGATCACCAATAAATCAATGACATAATAACT
AAGGTCGCAATGTTG
Found at i:2553584 original size:147 final size:147
Alignment explanation
Indices: 2553298--2553607 Score: 331
Period size: 147 Copynumber: 2.1 Consensus size: 147
2553288 CGCAATATCC
** * * * * * * *
2553298 TACACATGACCACATGATGTTACACCTTGATACCAATTAGATCAATGAAATAGTGGCCAACATTG
1 TACACATGACGTCACGATGTCACACCTTAATACCAATTAGATCAATAAAACAATGGCCAACATTA
* * * *
2553363 TGGCTTCCTATGTACGACGTCGTGACATCACACCTTGATCACCAATAAATCAATGACATAATAAC
66 CGACTTCCTATGTAC-ACATCGTGACATCACACCTTGATCACCAATAAATCAATGACACAATAAC
* ** *
2553428 TAAGGTCGCAAT-GT-TG
130 GAACATCGCAATGGTATA
* *
2553444 TACACATGACGTCACGATGTCATACCTTAATGACCTATTAGATCAATAAAACAATGGCCAACATT
1 TACACATGACGTCACGATGTCACACCTTAAT-ACCAATTAGATCAATAAAACAATGGCCAACATT
* * **
2553509 ACGACTTCCTGCATGTA-ACATCGTGACATCACACCTTGGTCACCAATAAATCAGTGGGACAATA
65 ACGACTTCCT--ATGTACACATCGTGACATCACACCTTGATCACCAATAAATCAATGACACAATA
2553573 GA-GAACATCGCAATGGTATA
128 -ACGAACATCGCAATGGTATA
*
2553593 TACACATAACGTCAC
1 TACACATGACGTCAC
2553608 AACGCTACAT
Statistics
Matches: 134, Mismatches: 24, Indels: 9
0.80 0.14 0.05
Matches are distributed among these distances:
146 25 0.19
147 86 0.64
148 3 0.02
149 20 0.15
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (147 bp):
TACACATGACGTCACGATGTCACACCTTAATACCAATTAGATCAATAAAACAATGGCCAACATTA
CGACTTCCTATGTACACATCGTGACATCACACCTTGATCACCAATAAATCAATGACACAATAACG
AACATCGCAATGGTATA
Found at i:2555622 original size:38 final size:40
Alignment explanation
Indices: 2555542--2555630 Score: 128
Period size: 38 Copynumber: 2.2 Consensus size: 40
2555532 TAAAAAGTAT
* *
2555542 TTATATTAAAAAACACTACCATAAATATAATAAATGTTTTA
1 TTATATT-AAAAACACTACAATAAATATAATAAATATTTTA
2555583 TTATATTAAAAACAC-A-AATAAATATAATAAATATTTTA
1 TTATATTAAAAACACTACAATAAATATAATAAATATTTTA
*
2555621 TTTTATTAAA
1 TTATATTAAA
2555631 TATAATTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
38 29 0.64
39 1 0.02
40 8 0.18
41 7 0.16
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.39
Consensus pattern (40 bp):
TTATATTAAAAACACTACAATAAATATAATAAATATTTTA
Found at i:2556963 original size:77 final size:78
Alignment explanation
Indices: 2556835--2556989 Score: 303
Period size: 77 Copynumber: 2.0 Consensus size: 78
2556825 TCAATTAAAG
2556835 TTCTTAAATATTTTTATATTTTATATAAAGTTTTTAAAATATGTTTGAAGGAATAAATTGGTAAA
1 TTCTTAAATATTTTTATATTTTATATAAAGTTTTTAAAATATGTTTGAAGGAATAAATTGGTAAA
2556900 AGTTGTCAAGTTC
66 AGTTGTCAAGTTC
2556913 TTCTTAAATA-TTTTATATTTTATATAAAGTTTTTAAAATATGTTTGAAGGAATAAATTGGTAAA
1 TTCTTAAATATTTTTATATTTTATATAAAGTTTTTAAAATATGTTTGAAGGAATAAATTGGTAAA
2556977 AGTTGTCAAGTTC
66 AGTTGTCAAGTTC
2556990 AAAAATTAAT
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 67 0.87
78 10 0.13
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (78 bp):
TTCTTAAATATTTTTATATTTTATATAAAGTTTTTAAAATATGTTTGAAGGAATAAATTGGTAAA
AGTTGTCAAGTTC
Found at i:2561569 original size:138 final size:139
Alignment explanation
Indices: 2561311--2561586 Score: 536
Period size: 138 Copynumber: 2.0 Consensus size: 139
2561301 TAGCCCCACT
2561311 ATCATATTATTGGCTTTCCCTTGTTTGAATTACCATCTGAATCCGACTTTGATATGATGTTGTCT
1 ATCATATTATTGGCTTTCCCTTGTTTGAATTACCATCTGAATCCGACTTTGATATGATGTTGTCT
2561376 AATTAATTCTTGGTAAGAATCTATTAAATGCATGACAAAATGGTAGTCTCTAAGATTATAATATT
66 AATTAATTCTTGGTAAGAATCTATTAAATGCATGACAAAATGGTAGTCTCTAAGATTATAATATT
2561441 TTCATATAA
131 TTCATATAA
2561450 ATCATATTA-TGGCTTTCCCTTGTTTGAATTACCATCTGAATCCGACTTTGATATGATGTTGTCT
1 ATCATATTATTGGCTTTCCCTTGTTTGAATTACCATCTGAATCCGACTTTGATATGATGTTGTCT
*
2561514 AATTAATTCTTGGTAAGAATCTATTAAATTCATGACAAAATGGTAGTCTCTAAGATTATAATATT
66 AATTAATTCTTGGTAAGAATCTATTAAATGCATGACAAAATGGTAGTCTCTAAGATTATAATATT
2561579 TTCATATA
131 TTCATATA
2561587 TATATANNNN
Statistics
Matches: 136, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
138 127 0.93
139 9 0.07
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (139 bp):
ATCATATTATTGGCTTTCCCTTGTTTGAATTACCATCTGAATCCGACTTTGATATGATGTTGTCT
AATTAATTCTTGGTAAGAATCTATTAAATGCATGACAAAATGGTAGTCTCTAAGATTATAATATT
TTCATATAA
Found at i:2563756 original size:183 final size:183
Alignment explanation
Indices: 2563448--2563816 Score: 738
Period size: 183 Copynumber: 2.0 Consensus size: 183
2563438 NNNNNACGAG
2563448 AGGCTGCTATGAGCTCCATACTTTCAGCAATTCATTTAAAATATTGGCCCAAAGGTTGATGAATT
1 AGGCTGCTATGAGCTCCATACTTTCAGCAATTCATTTAAAATATTGGCCCAAAGGTTGATGAATT
2563513 TGCATTTAAGGTCAGGCATGGAAGTTTGATGACTTATTTTAATGGTCAAAAGTACAACTCATGGT
66 TGCATTTAAGGTCAGGCATGGAAGTTTGATGACTTATTTTAATGGTCAAAAGTACAACTCATGGT
2563578 GTTTCTTGTGATATTTTCTCTTATATATTACCTCCATTTTTTTATTGTATTTT
131 GTTTCTTGTGATATTTTCTCTTATATATTACCTCCATTTTTTTATTGTATTTT
2563631 AGGCTGCTATGAGCTCCATACTTTCAGCAATTCATTTAAAATATTGGCCCAAAGGTTGATGAATT
1 AGGCTGCTATGAGCTCCATACTTTCAGCAATTCATTTAAAATATTGGCCCAAAGGTTGATGAATT
2563696 TGCATTTAAGGTCAGGCATGGAAGTTTGATGACTTATTTTAATGGTCAAAAGTACAACTCATGGT
66 TGCATTTAAGGTCAGGCATGGAAGTTTGATGACTTATTTTAATGGTCAAAAGTACAACTCATGGT
2563761 GTTTCTTGTGATATTTTCTCTTATATATTACCTCCATTTTTTTATTGTATTTT
131 GTTTCTTGTGATATTTTCTCTTATATATTACCTCCATTTTTTTATTGTATTTT
2563814 AGG
1 AGG
2563817 GATGAATTTA
Statistics
Matches: 186, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
183 186 1.00
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (183 bp):
AGGCTGCTATGAGCTCCATACTTTCAGCAATTCATTTAAAATATTGGCCCAAAGGTTGATGAATT
TGCATTTAAGGTCAGGCATGGAAGTTTGATGACTTATTTTAATGGTCAAAAGTACAACTCATGGT
GTTTCTTGTGATATTTTCTCTTATATATTACCTCCATTTTTTTATTGTATTTT
Found at i:2572265 original size:23 final size:24
Alignment explanation
Indices: 2572222--2572267 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
2572212 TTTATCCCTT
*
2572222 AAAAAAAAAGGAACGTTAAAAGAGA
1 AAAAAAAAAGGAAAG-TAAAAGAGA
2572247 AAAAAAAAAGGAAAG-AAAAGA
1 AAAAAAAAAGGAAAGTAAAAGA
2572268 AATTGAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
25 14 0.70
ACGTcount: A:0.74, C:0.02, G:0.20, T:0.04
Consensus pattern (24 bp):
AAAAAAAAAGGAAAGTAAAAGAGA
Found at i:2573397 original size:6 final size:6
Alignment explanation
Indices: 2573386--2573414 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2573376 TAAAATGTGA
2573386 TGGTTG TGGTTG TGGTTG TGGTTG TGGTT
1 TGGTTG TGGTTG TGGTTG TGGTTG TGGTT
2573415 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (6 bp):
TGGTTG
Found at i:2574580 original size:52 final size:51
Alignment explanation
Indices: 2574523--2574629 Score: 162
Period size: 52 Copynumber: 2.1 Consensus size: 51
2574513 TGTGGCATGT
* *
2574523 AAATGGACCCCTGCAATAACCCTTTTTCAGCA-AAATAAAGAAATCCCGACCA
1 AAATGGACCCCTGAAAGAACCCTTTTTCA--ATAAATAAAGAAATCCCGACCA
*
2574575 AAATGGACCCCTGAAAGAACCCTTTTTCAATAAATAAAGAATTCCCGACCA
1 AAATGGACCCCTGAAAGAACCCTTTTTCAATAAATAAAGAAATCCCGACCA
2574626 AAAT
1 AAAT
2574630 TCACAAGAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
50 1 0.02
51 23 0.45
52 27 0.53
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (51 bp):
AAATGGACCCCTGAAAGAACCCTTTTTCAATAAATAAAGAAATCCCGACCA
Found at i:2582831 original size:257 final size:257
Alignment explanation
Indices: 2582374--2582858 Score: 792
Period size: 257 Copynumber: 1.9 Consensus size: 257
2582364 CAATATTCCA
* *
2582374 TATAGAATTCAAGATCATTACAATTACTATGATTCTATCGTTAACCAGACCGATTAAAAATCACT
1 TATAGAATTCAAGATCATTACAACTACTATGATTCTATCATTAACCAGACCGATTAAAAATCACT
* *
2582439 TAAATTAAGAACAAAAAAAATGGAATTCAAGCAAGCAAACGATTCGGTGCATGCTTTTTAAACAA
66 TAAACTAAGAACAAAAAAAA-GGAATTCAAGCAAGCAAACGATTCGGCGCATGCTTTTTAAACAA
* * *
2582504 ACAATTCAAGTAATATTTAAACATGATAATCATGCAAGTAATTATGGTACCTAAACAGAGATCGA
130 AAAATTAAAGTAATATTTAAACATGATAATCATGCAAGTAATTAGGGTACCTAAACAGAGATCGA
*
2582569 GAAGAAGATCTGGCATCGTCTCGCAGTTTTTCCCTAGGTTTTTATTTCGACGACACCGATCCT
195 GAAGAAGATCCGGCATCGTCTCGCAGTTTTTCCCTAGGTTTTTATTTCGACGACACCGATCCT
* * *
2582632 TATAGAATTCAAGATCATTTCAACTATTATGATTCTATCATTAACCAGACCGATTCAAAATCACT
1 TATAGAATTCAAGATCATTACAACTACTATGATTCTATCATTAACCAGACCGATTAAAAATCACT
*** *
2582697 TAAACTAAGGGGGAAAATAAA-GAATTCAAGCAAGCAAACGATTCGGCGCATGCTTTTTAAACAA
66 TAAACTAA-GAACAAAAAAAAGGAATTCAAGCAAGCAAACGATTCGGCGCATGCTTTTTAAACAA
* *
2582761 AAAATTAAAGTAATATTTAAACATGATAATTATGCAAGTAATTAGGGTACCTAAACAGAGGTCGA
130 AAAATTAAAGTAATATTTAAACATGATAATCATGCAAGTAATTAGGGTACCTAAACAGAGATCGA
2582826 GAAGAAGATCCGGCATCGTCTCGCAGTTTTTCC
195 GAAGAAGATCCGGCATCGTCTCGCAGTTTTTCC
2582859 TTCGACGCCA
Statistics
Matches: 209, Mismatches: 17, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
257 134 0.64
258 67 0.32
259 8 0.04
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.28
Consensus pattern (257 bp):
TATAGAATTCAAGATCATTACAACTACTATGATTCTATCATTAACCAGACCGATTAAAAATCACT
TAAACTAAGAACAAAAAAAAGGAATTCAAGCAAGCAAACGATTCGGCGCATGCTTTTTAAACAAA
AAATTAAAGTAATATTTAAACATGATAATCATGCAAGTAATTAGGGTACCTAAACAGAGATCGAG
AAGAAGATCCGGCATCGTCTCGCAGTTTTTCCCTAGGTTTTTATTTCGACGACACCGATCCT
Found at i:2592011 original size:43 final size:41
Alignment explanation
Indices: 2591950--2592037 Score: 149
Period size: 43 Copynumber: 2.1 Consensus size: 41
2591940 ATTGACCATA
*
2591950 AAATAAATATGAATGATACTTTGATTATACAAAAAAAAAATCG
1 AAATAAATATGAATGATACTTTGATCATAC--AAAAAAAATCG
2591993 AAATAAATATGAATGATACTTTGATCATACAAAAAAAATCG
1 AAATAAATATGAATGATACTTTGATCATACAAAAAAAATCG
2592034 AAAT
1 AAAT
2592038 TGTAAAACTA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
41 15 0.34
43 29 0.66
ACGTcount: A:0.56, C:0.08, G:0.09, T:0.27
Consensus pattern (41 bp):
AAATAAATATGAATGATACTTTGATCATACAAAAAAAATCG
Found at i:2592849 original size:33 final size:33
Alignment explanation
Indices: 2592811--2592880 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
2592801 CCCGGAAAGC
* *
2592811 ATGGGGATGTTAAAGGATTTA-AAGTGCATGGAA
1 ATGGGGATCTTAAAGGATTTAGAA-TCCATGGAA
*
2592844 ATGGGGATCTTAGAGGATTTAGAATCCATGGAA
1 ATGGGGATCTTAAAGGATTTAGAATCCATGGAA
2592877 ATGG
1 ATGG
2592881 AAACATTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 31 0.94
34 2 0.06
ACGTcount: A:0.34, C:0.06, G:0.33, T:0.27
Consensus pattern (33 bp):
ATGGGGATCTTAAAGGATTTAGAATCCATGGAA
Found at i:2599768 original size:18 final size:17
Alignment explanation
Indices: 2599740--2599774 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2599730 ATTTTTAAGA
*
2599740 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
2599757 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
2599775 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:2600024 original size:45 final size:44
Alignment explanation
Indices: 2599934--2600029 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 44
2599924 TTACACCTCT
*
2599934 ATTACACTCAACCAAACACAGGATTACTATTACGCCTCTATTCC
1 ATTACACTCAACCAAACACAGGATTACTATTACGCCTCTACTCC
* *** *
2599978 ATTACATTCAACCAAACAGTTGATTTGCTATTACGCCTCTACTCC
1 ATTACACTCAACCAAACACAGGA-TTACTATTACGCCTCTACTCC
2600023 ATTACAC
1 ATTACAC
2600030 CTCTAATCCA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.43
45 25 0.57
ACGTcount: A:0.32, C:0.30, G:0.07, T:0.30
Consensus pattern (44 bp):
ATTACACTCAACCAAACACAGGATTACTATTACGCCTCTACTCC
Found at i:2600032 original size:16 final size:16
Alignment explanation
Indices: 2600013--2600060 Score: 78
Period size: 16 Copynumber: 3.0 Consensus size: 16
2600003 TGCTATTACG
* *
2600013 CCTCTACTCCATTACA
1 CCTCTAATCCAATACA
2600029 CCTCTAATCCAATACA
1 CCTCTAATCCAATACA
2600045 CCTCTAATCCAATACA
1 CCTCTAATCCAATACA
2600061 GCGAACCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.33, C:0.40, G:0.00, T:0.27
Consensus pattern (16 bp):
CCTCTAATCCAATACA
Found at i:2601198 original size:101 final size:101
Alignment explanation
Indices: 2601023--2601262 Score: 363
Period size: 101 Copynumber: 2.4 Consensus size: 101
2601013 TGAATTGACG
* * *
2601023 GATAAGACCATAACTGGGTTATGGCACTATGAACGTGAGACCATGGTTGGACCATGGCAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTAGACCATGACAGTGTTT
* * *
2601088 ATATGTAAGATCATAGCTGGGTTATGACATTCTGAT
66 ATATGTAAGACCATAGCTGGGCTATGACATTCTAAT
* *
2601124 GATAAGACTATAACTGGGTTATGGCACTATGAACGTAAGGCCATGGTTAGACCATGACAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTAGACCATGACAGTGTTT
*
2601189 ATATGTAAGACCATAGCTGGGCTATGGCATTCTAAT
66 ATATGTAAGACCATAGCTGGGCTATGACATTCTAAT
* * * *
2601225 GATAATACCATAAATGGGTTATGGCACTACGAATGTAA
1 GATAAGACCATAACTGGGTTATGGCACTATGAACGTAA
2601263 AGGATGAATT
Statistics
Matches: 125, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
101 125 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (101 bp):
GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTAGACCATGACAGTGTTT
ATATGTAAGACCATAGCTGGGCTATGACATTCTAAT
Found at i:2601287 original size:24 final size:24
Alignment explanation
Indices: 2601260--2601307 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2601250 ACTACGAATG
2601260 TAAAGGATGAATTGACGGAAAATT
1 TAAAGGATGAATTGACGGAAAATT
*
2601284 TAAAGGATGAATTGACGGCAAATT
1 TAAAGGATGAATTGACGGAAAATT
2601308 ACCCAAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.06, G:0.25, T:0.25
Consensus pattern (24 bp):
TAAAGGATGAATTGACGGAAAATT
Found at i:2601752 original size:26 final size:26
Alignment explanation
Indices: 2601716--2601766 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
2601706 CATGAAAGAG
2601716 TGGTAAGATTGAAGTTATGCAATTTA
1 TGGTAAGATTGAAGTTATGCAATTTA
2601742 TGGTAAGATTGAAGTTATGCAATTT
1 TGGTAAGATTGAAGTTATGCAATTT
2601767 CTTATGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.24, T:0.39
Consensus pattern (26 bp):
TGGTAAGATTGAAGTTATGCAATTTA
Found at i:2605346 original size:17 final size:17
Alignment explanation
Indices: 2605326--2605360 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2605316 ACTTTGAGAC
* *
2605326 TTAAGTTATTTTGGGTT
1 TTAAATTATTTAGGGTT
2605343 TTAAATTATTTAGGGTT
1 TTAAATTATTTAGGGTT
2605360 T
1 T
2605361 GAATTGTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (17 bp):
TTAAATTATTTAGGGTT
Found at i:2605399 original size:15 final size:15
Alignment explanation
Indices: 2605364--2605401 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2605354 AGGGTTTGAA
2605364 TTGTTTCAGGTTAGG
1 TTGTTTCAGGTTAGG
*
2605379 TAGTTT-AGGTTAGGG
1 TTGTTTCAGGTTA-GG
2605394 TTGTTTCA
1 TTGTTTCA
2605402 TTTTCAGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 6 0.32
15 12 0.63
16 1 0.05
ACGTcount: A:0.16, C:0.05, G:0.32, T:0.47
Consensus pattern (15 bp):
TTGTTTCAGGTTAGG
Found at i:2610912 original size:39 final size:39
Alignment explanation
Indices: 2610858--2610937 Score: 126
Period size: 39 Copynumber: 2.1 Consensus size: 39
2610848 AAAAGCTATC
2610858 TGAAGGTGGTGATGATT-TTTGCTTAGGAGGAGGAGGTGA
1 TGAAGGTGGTGATGATTGTTT-CTTAGGAGGAGGAGGTGA
* *
2610897 TGAAGGTGGTGATGATTGTTTCTTAGGAGGTGGCGGTGA
1 TGAAGGTGGTGATGATTGTTTCTTAGGAGGAGGAGGTGA
2610936 TG
1 TG
2610938 GTGACGGTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 35 0.92
40 3 0.08
ACGTcount: A:0.20, C:0.04, G:0.44, T:0.33
Consensus pattern (39 bp):
TGAAGGTGGTGATGATTGTTTCTTAGGAGGAGGAGGTGA
Found at i:2610947 original size:39 final size:39
Alignment explanation
Indices: 2610865--2610947 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
2610855 ATCTGAAGGT
**
2610865 GGTGATGATTTTTGCTTAGGAGGAGGAGGTGATGAAGGT
1 GGTGATGATTTTTGCTTAGGAGGAGGAGGTGATGAAGAC
* * **
2610904 GGTGATGATTGTTT-CTTAGGAGGTGGCGGTGATGGTGAC
1 GGTGATGATT-TTTGCTTAGGAGGAGGAGGTGATGAAGAC
2610943 GGTGA
1 GGTGA
2610948 AAGAGGTGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
39 34 0.92
40 3 0.08
ACGTcount: A:0.19, C:0.05, G:0.45, T:0.31
Consensus pattern (39 bp):
GGTGATGATTTTTGCTTAGGAGGAGGAGGTGATGAAGAC
Found at i:2611010 original size:3 final size:3
Alignment explanation
Indices: 2611004--2611034 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2610994 GATTGTTCCT
*
2611004 GAG GAG GAG GAG GAG AAG GAG GAG GAG GAG G
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG G
2611035 TGAAGGTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:2611064 original size:18 final size:18
Alignment explanation
Indices: 2611041--2611086 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
2611031 GAGGTGAAGG
2611041 TGGTGGTGATGATGATGA
1 TGGTGGTGATGATGATGA
* *
2611059 TGGTGGTGGTGATGGTGA
1 TGGTGGTGATGATGATGA
* *
2611077 AGGAGGTGAT
1 TGGTGGTGAT
2611087 TGCTTATTAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.20, C:0.00, G:0.50, T:0.30
Consensus pattern (18 bp):
TGGTGGTGATGATGATGA
Found at i:2611084 original size:21 final size:20
Alignment explanation
Indices: 2611038--2611084 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
2611028 GAGGAGGTGA
*
2611038 AGGTGGTGGTGATGATGATG
1 AGGTGGTGGTGATGATGAGG
*
2611058 ATGGTGGTGGTGATGGTGAAGG
1 A-GGTGGTGGTGATGATG-AGG
2611080 AGGTG
1 AGGTG
2611085 ATTGCTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 19 0.83
22 3 0.13
ACGTcount: A:0.19, C:0.00, G:0.53, T:0.28
Consensus pattern (20 bp):
AGGTGGTGGTGATGATGAGG
Found at i:2623732 original size:193 final size:193
Alignment explanation
Indices: 2623403--2623791 Score: 751
Period size: 193 Copynumber: 2.0 Consensus size: 193
2623393 ATATATTAAG
*
2623403 TAAATTTTTAATGACAAGCATCGACAGCATGGTCCCAACGTGTCTTGTCTCCTTAAATTTCACAA
1 TAAATTTTTAATGACAAGCATCGACAGCATGGTCCCAACCTGTCTTGTCTCCTTAAATTTCACAA
2623468 TCGCAATTATTATATATATGGGTTAATGTAGTTTTTAGTCTTTCAATTTAGTAATTGGGTTTATT
66 TCGCAATTATTATATATATGGGTTAATGTAGTTTTTAGTCTTTCAATTTAGTAATTGGGTTTATT
2623533 TTGGTGTTTATATATATTTTGAGGATAAATTCCATTAAACAATAAATAAATAAAATAATGAAA
131 TTGGTGTTTATATATATTTTGAGGATAAATTCCATTAAACAATAAATAAATAAAATAATGAAA
*
2623596 TAAATTTTTAATGACAAGCATCGACAGCATTGTCCCAACCTGTCTTGTCTCCTTAAATTTCACAA
1 TAAATTTTTAATGACAAGCATCGACAGCATGGTCCCAACCTGTCTTGTCTCCTTAAATTTCACAA
2623661 TCGCAATTATTATATATATGGGTTAATGTAGTTTTTAGTCTTTCAATTTAGTAATTGGGTTTATT
66 TCGCAATTATTATATATATGGGTTAATGTAGTTTTTAGTCTTTCAATTTAGTAATTGGGTTTATT
*
2623726 TTGGTGTTTATATATATTTTGAGGATAAATTCGATTAAACAATAAATAAATAAAATAATGAAA
131 TTGGTGTTTATATATATTTTGAGGATAAATTCCATTAAACAATAAATAAATAAAATAATGAAA
2623789 TAA
1 TAA
2623792 TAGGAAAGAT
Statistics
Matches: 193, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
193 193 1.00
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (193 bp):
TAAATTTTTAATGACAAGCATCGACAGCATGGTCCCAACCTGTCTTGTCTCCTTAAATTTCACAA
TCGCAATTATTATATATATGGGTTAATGTAGTTTTTAGTCTTTCAATTTAGTAATTGGGTTTATT
TTGGTGTTTATATATATTTTGAGGATAAATTCCATTAAACAATAAATAAATAAAATAATGAAA
Found at i:2647137 original size:26 final size:26
Alignment explanation
Indices: 2647108--2647161 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
2647098 ATAACACATG
*
2647108 TTTTGAATT-TTTGAAAATATTTATAT
1 TTTTAAATTGTTT-AAAATATTTATAT
* *
2647134 TTTTAAATTGTTTAAAATTTTTTTAT
1 TTTTAAATTGTTTAAAATATTTATAT
2647160 TT
1 TT
2647162 AAAGTGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (26 bp):
TTTTAAATTGTTTAAAATATTTATAT
Found at i:2647164 original size:15 final size:16
Alignment explanation
Indices: 2647144--2647177 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2647134 TTTTAAATTG
2647144 TTTAAAAT-TTTTTTA
1 TTTAAAATGTTTTTTA
*
2647159 TTTAAAGTGTTTTTTA
1 TTTAAAATGTTTTTTA
2647175 TTT
1 TTT
2647178 TGCATACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (16 bp):
TTTAAAATGTTTTTTA
Found at i:2650727 original size:4 final size:4
Alignment explanation
Indices: 2650718--2650765 Score: 96
Period size: 4 Copynumber: 12.0 Consensus size: 4
2650708 TGTACTAATC
2650718 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
2650766 GCCTTTTTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:2655985 original size:18 final size:17
Alignment explanation
Indices: 2655958--2655991 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
2655948 GGCCCGACCC
2655958 ATATTAATATATATTTA
1 ATATTAATATATATTTA
2655975 ATATATAATATATATTT
1 ATAT-TAATATATATTT
2655992 GATTAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTAATATATATTTA
Found at i:2656011 original size:26 final size:27
Alignment explanation
Indices: 2655977--2656040 Score: 94
Period size: 26 Copynumber: 2.4 Consensus size: 27
2655967 TATATTTAAT
*
2655977 ATATAATATATATTTGATTAAAAATAA
1 ATATAATATATATTTGATCAAAAATAA
2656004 ATAT-ATATATATTTGATCAAAAATAA
1 ATATAATATATATTTGATCAAAAATAA
* *
2656030 AAAAAATATAT
1 ATATAATATAT
2656041 TTAATATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 23 0.70
27 10 0.30
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (27 bp):
ATATAATATATATTTGATCAAAAATAA
Found at i:2663826 original size:13 final size:13
Alignment explanation
Indices: 2663808--2663839 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
2663798 TAAGTTCATA
2663808 AATATTATTATTT
1 AATATTATTATTT
2663821 AATATTATTATTT
1 AATATTATTATTT
2663834 AATATT
1 AATATT
2663840 TATGAGTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
AATATTATTATTT
Found at i:2667715 original size:46 final size:46
Alignment explanation
Indices: 2667641--2667773 Score: 176
Period size: 46 Copynumber: 2.9 Consensus size: 46
2667631 CATGGCAAAG
** *
2667641 TGTGAAACGTAGGTATGAAAATTCAGTAAAGAAAACCATACCGAGT
1 TGTGAAACGTAGGTATGGTATTTCAGTAAAGAAAACCATACCGAGT
* * * *
2667687 TGTGGAACGTAGGTATGGTATTTTAGTAACGAAAACCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTTCAGTAAAGAAAACCATACCGAGT
* * *
2667733 TGTGAAAAGTATGTATGGTATTTCAGTGAAGAAAACCATAC
1 TGTGAAACGTAGGTATGGTATTTCAGTAAAGAAAACCATAC
2667774 TAAGTTATAA
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 74 1.00
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.27
Consensus pattern (46 bp):
TGTGAAACGTAGGTATGGTATTTCAGTAAAGAAAACCATACCGAGT
Found at i:2669930 original size:11 final size:13
Alignment explanation
Indices: 2669914--2669946 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
2669904 ATTTCACGGA
2669914 AAAATTTCG-T-G
1 AAAATTTCGTTCG
2669925 AAAATTTCGTTCG
1 AAAATTTCGTTCG
2669938 AAAATTTCG
1 AAAATTTCG
2669947 ACATTTGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 1 0.05
13 10 0.50
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (13 bp):
AAAATTTCGTTCG
Found at i:2680525 original size:31 final size:32
Alignment explanation
Indices: 2680464--2680548 Score: 124
Period size: 31 Copynumber: 2.8 Consensus size: 32
2680454 TATTTGTTTA
*
2680464 TTTAGTTATTGTA--TTTT-AATTTGATCAAT
1 TTTAGTTTTTGTATTTTTTGAATTTGATCAAT
2680493 TTTAGTTTTTGTATTTTTTGAATTT-ATCAAT
1 TTTAGTTTTTGTATTTTTTGAATTTGATCAAT
*
2680524 TTTAGTTTTTGTATTTTTCGAATTT
1 TTTAGTTTTTGTATTTTTTGAATTT
2680549 TAAAATTTCA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
29 12 0.24
31 34 0.67
32 5 0.10
ACGTcount: A:0.22, C:0.04, G:0.11, T:0.64
Consensus pattern (32 bp):
TTTAGTTTTTGTATTTTTTGAATTTGATCAAT
Found at i:2680532 original size:23 final size:23
Alignment explanation
Indices: 2680507--2680550 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
2680497 GTTTTTGTAT
2680507 TTTTTGAATTTATC-AATTTTAG
1 TTTTTGAATTTATCGAATTTTAG
* *
2680529 TTTTTGTATTTTTCGAATTTTA
1 TTTTTGAATTTATCGAATTTTA
2680551 AAATTTCAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.23, C:0.05, G:0.09, T:0.64
Consensus pattern (23 bp):
TTTTTGAATTTATCGAATTTTAG
Found at i:2680556 original size:31 final size:31
Alignment explanation
Indices: 2680464--2680563 Score: 109
Period size: 31 Copynumber: 3.3 Consensus size: 31
2680454 TATTTGTTTA
* *
2680464 TTTAGTTATTGTA-TTTT--AATTTGATCAAT
1 TTTAGTTTTTGTATTTTTCGAATTT-ATAAAT
* *
2680493 TTTAGTTTTTGTATTTTTTGAATTTATCAAT
1 TTTAGTTTTTGTATTTTTCGAATTTATAAAT
2680524 TTTAGTTTTTGTATTTTTCGAATTT-TAAAAT
1 TTTAGTTTTTGTATTTTTCGAATTTAT-AAAT
*
2680555 TTCAGTTTT
1 TTTAGTTTT
2680564 GATGCAAATG
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
29 12 0.19
30 5 0.08
31 41 0.65
32 5 0.08
ACGTcount: A:0.24, C:0.04, G:0.10, T:0.62
Consensus pattern (31 bp):
TTTAGTTTTTGTATTTTTCGAATTTATAAAT
Found at i:2682304 original size:31 final size:31
Alignment explanation
Indices: 2682269--2682328 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2682259 TTTTTAGTTA
* * * *
2682269 AATTTGACCCTTAACCTTTTAGAAAGAGTCT
1 AATTTGACCATCAACCTTTCAAAAAGAGTCT
2682300 AATTTGACCATCAACCTTTCAAAAAGAGT
1 AATTTGACCATCAACCTTTCAAAAAGAGT
2682329 AGACTTGCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (31 bp):
AATTTGACCATCAACCTTTCAAAAAGAGTCT
Found at i:2684145 original size:3 final size:3
Alignment explanation
Indices: 2684137--2684167 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2684127 TTAAAACTCT
2684137 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2684168 AGTTTCAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2688584 original size:75 final size:76
Alignment explanation
Indices: 2688479--2688637 Score: 302
Period size: 75 Copynumber: 2.1 Consensus size: 76
2688469 TTTTAAAAGA
*
2688479 TTATTATTTGATGTCAAATATTTTATATCACCAAATCAATTCTCCATGATAATATTTTACCCTTA
1 TTATTTTTTGATGTCAAATATTTTATATCACCAAATCAATTCTCCATGATAATATTTTACCCTTA
2688544 ATTA-TTTATT
66 ATTATTTTATT
2688554 TTATTTTTTGATGTCAAATATTTTATATCACCAAATCAATTCTCCATGATAATATTTTACCCTTA
1 TTATTTTTTGATGTCAAATATTTTATATCACCAAATCAATTCTCCATGATAATATTTTACCCTTA
2688619 ATTATTTTATT
66 ATTATTTTATT
2688630 TTATTTTT
1 TTATTTTT
2688638 ATTTTTTTCA
Statistics
Matches: 82, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
75 68 0.83
76 14 0.17
ACGTcount: A:0.31, C:0.14, G:0.04, T:0.51
Consensus pattern (76 bp):
TTATTTTTTGATGTCAAATATTTTATATCACCAAATCAATTCTCCATGATAATATTTTACCCTTA
ATTATTTTATT
Found at i:2700190 original size:208 final size:208
Alignment explanation
Indices: 2699832--2700238 Score: 814
Period size: 208 Copynumber: 2.0 Consensus size: 208
2699822 CGTACAGCTG
2699832 GGTAACGTTCATATAACGGCTAATAAATTAGGCCGACAAAAGAAAATAAATTGAAATTGTGTGAA
1 GGTAACGTTCATATAACGGCTAATAAATTAGGCCGACAAAAGAAAATAAATTGAAATTGTGTGAA
2699897 ACGTTCACTTAACGTTTATATATAATTTGGTTATCTACCAGCTGCCACATCATCACTTCAATTAT
66 ACGTTCACTTAACGTTTATATATAATTTGGTTATCTACCAGCTGCCACATCATCACTTCAATTAT
2699962 TCCATTTAAATTTTTAAAAATAATATTCCTTCAATTTAAAAAATTTTAATTATACTAAATATTTT
131 TCCATTTAAATTTTTAAAAATAATATTCCTTCAATTTAAAAAATTTTAATTATACTAAATATTTT
2700027 TCAAATACTATTT
196 TCAAATACTATTT
2700040 GGTAACGTTCATATAACGGCTAATAAATTAGGCCGACAAAAGAAAATAAATTGAAATTGTGTGAA
1 GGTAACGTTCATATAACGGCTAATAAATTAGGCCGACAAAAGAAAATAAATTGAAATTGTGTGAA
2700105 ACGTTCACTTAACGTTTATATATAATTTGGTTATCTACCAGCTGCCACATCATCACTTCAATTAT
66 ACGTTCACTTAACGTTTATATATAATTTGGTTATCTACCAGCTGCCACATCATCACTTCAATTAT
2700170 TCCATTTAAATTTTTAAAAATAATATTCCTTCAATTTAAAAAATTTTAATTATACTAAATATTTT
131 TCCATTTAAATTTTTAAAAATAATATTCCTTCAATTTAAAAAATTTTAATTATACTAAATATTTT
2700235 TCAA
196 TCAA
2700239 TTAAAATACT
Statistics
Matches: 199, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
208 199 1.00
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.37
Consensus pattern (208 bp):
GGTAACGTTCATATAACGGCTAATAAATTAGGCCGACAAAAGAAAATAAATTGAAATTGTGTGAA
ACGTTCACTTAACGTTTATATATAATTTGGTTATCTACCAGCTGCCACATCATCACTTCAATTAT
TCCATTTAAATTTTTAAAAATAATATTCCTTCAATTTAAAAAATTTTAATTATACTAAATATTTT
TCAAATACTATTT
Found at i:2701302 original size:21 final size:21
Alignment explanation
Indices: 2701278--2701328 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
2701268 ACATAACTAA
*
2701278 TTAGTCTCGAGACAATTGCTC
1 TTAGTCTCGAGACAAGTGCTC
* *
2701299 TTAGGTCTCGGGACAAGTGGTC
1 TTA-GTCTCGAGACAAGTGCTC
*
2701321 TTTGTCTC
1 TTAGTCTC
2701329 AAGATAGAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (21 bp):
TTAGTCTCGAGACAAGTGCTC
Found at i:2703230 original size:43 final size:43
Alignment explanation
Indices: 2703134--2703230 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 43
2703124 ATATTAGACA
**
2703134 TCATGTAAGACCATGTTTGGGACATTGGCATCGATATGTGATT
1 TCATGTAAGACCATGGCTGGGACATTGGCATCGATATGTGATT
* *
2703177 TCGTGCAAGACCATGGCTGGG-CTATTGGCATCGATATGTGATT
1 TCATGTAAGACCATGGCTGGGAC-ATTGGCATCGATATGTGATT
2703220 AT-ATGTAAGAC
1 -TCATGTAAGAC
2703231 TATATCTAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
42 1 0.02
43 44 0.96
44 1 0.02
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (43 bp):
TCATGTAAGACCATGGCTGGGACATTGGCATCGATATGTGATT
Found at i:2705384 original size:57 final size:58
Alignment explanation
Indices: 2705229--2705387 Score: 133
Period size: 57 Copynumber: 2.7 Consensus size: 58
2705219 TTAGCTCTCT
* * * *
2705229 AATATTTATACATTCTATCAATTT-GATCCTAAATATAAAAACATCAACAGATTTAACCCTC
1 AATATTTATAAAATCTATCAATTTAG-TCCTAAATCT-AAAA-A-CAACAAATTTAACCCTC
* * * * * * ** * *
2705290 AATGTTTACAAAATTTGTCATTTTAATTATAATTCTAAAAA-AACAAATTTGACCCTC
1 AATATTTATAAAATCTATCAATTTAGTCCTAAATCTAAAAACAACAAATTTAACCCTC
*
2705347 AATATTTATAAAATCTATCAATTTAGTCCTAACTCTAAAAA
1 AATATTTATAAAATCTATCAATTTAGTCCTAAATCTAAAAA
2705388 TTTAAATATA
Statistics
Matches: 74, Mismatches: 23, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
57 46 0.62
59 1 0.01
60 4 0.05
61 23 0.31
ACGTcount: A:0.43, C:0.16, G:0.04, T:0.36
Consensus pattern (58 bp):
AATATTTATAAAATCTATCAATTTAGTCCTAAATCTAAAAACAACAAATTTAACCCTC
Found at i:2706338 original size:5 final size:5
Alignment explanation
Indices: 2706328--2706354 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2706318 TTCTCTTACC
2706328 AAATA AAATA AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AA
2706355 NNNNNNNNNN
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:2714454 original size:29 final size:29
Alignment explanation
Indices: 2714412--2714471 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
2714402 CCTCGATACA
2714412 TAACTAATTAGTCTCGAGACAATTGCTCC
1 TAACTAATTAGTCTCGAGACAATTGCTCC
2714441 TAACTAATTAGTCTCGAGACAATTGCTCC
1 TAACTAATTAGTCTCGAGACAATTGCTCC
2714470 TA
1 TA
2714472 GGTTTCGGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (29 bp):
TAACTAATTAGTCTCGAGACAATTGCTCC
Found at i:2717061 original size:5 final size:5
Alignment explanation
Indices: 2717051--2717079 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
2717041 TTCTCTTACC
2717051 AAATA AAATA AAATA AAATA AAATA AAAT
1 AAATA AAATA AAATA AAATA AAATA AAAT
2717080 CCCCTTACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:2717642 original size:12 final size:12
Alignment explanation
Indices: 2717625--2717649 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2717615 TGAACGAATA
2717625 TTTTATTTTATT
1 TTTTATTTTATT
2717637 TTTTATTTTATT
1 TTTTATTTTATT
2717649 T
1 T
2717650 GTAAGAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:2718500 original size:22 final size:22
Alignment explanation
Indices: 2718459--2718500 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2718449 TAACTAATTA
*
2718459 GTCTCGAGACAATTGCTCTTAG
1 GTCTCGAGACAAGTGCTCTTAG
* *
2718481 GTCTCGGGACAAGTGGTCTT
1 GTCTCGAGACAAGTGCTCTT
2718501 TGTCTCAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.31
Consensus pattern (22 bp):
GTCTCGAGACAAGTGCTCTTAG
Found at i:2732014 original size:7 final size:7
Alignment explanation
Indices: 2731985--2732013 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2731975 TGAACGAATA
2731985 TTATATT
1 TTATATT
2731992 TTATATT
1 TTATATT
2731999 TTATATT
1 TTATATT
2732006 TTAT-TT
1 TTATATT
2732012 TT
1 TT
2732014 TGAAAGAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTATATT
Found at i:2734892 original size:145 final size:145
Alignment explanation
Indices: 2734619--2734902 Score: 370
Period size: 145 Copynumber: 2.0 Consensus size: 145
2734609 GACTGCCATC
* * * * *
2734619 TAGGGTTGTTGTTAGGAAGGTAACGGAGATGAATGACAAAGTGATTACTTCGTAACAAAACGATA
1 TAGGATTGTCGTTAGGAAGGTAACGGAGATGAACGACAAAGTGACTACTTCATAACAAAACGATA
** * * *
2734684 ATACAAGTGACTAAAACATAACATTTCAAATAGAAGTGACTAAAATGTATTATAAGACAAACAAA
66 ATACAAAAGACTAAAACATAACATTTCAAATAGAAATGACTAAAATATAATATAAGACAAACAAA
2734749 AGTGACTATCCCACA
131 AGTGACTATCCCACA
* * * * * *
2734764 TAGGATTGTCGTTAGGGAGGTAATGGAGCTGAACGGCAGAGTGACTACTTCATAACAAAATGATA
1 TAGGATTGTCGTTAGGAAGGTAACGGAGATGAACGACAAAGTGACTACTTCATAACAAAACGATA
** * * * *
2734829 ATGTAAAAGACTAAAACGTAACATTTCAAATATAAATGACTAAAATATAATCTAATACAAACAAA
66 ATACAAAAGACTAAAACATAACATTTCAAATAGAAATGACTAAAATATAATATAAGACAAACAAA
2734894 AGTGACTAT
131 AGTGACTAT
2734903 TTTTACAGTT
Statistics
Matches: 117, Mismatches: 22, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
145 117 1.00
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.25
Consensus pattern (145 bp):
TAGGATTGTCGTTAGGAAGGTAACGGAGATGAACGACAAAGTGACTACTTCATAACAAAACGATA
ATACAAAAGACTAAAACATAACATTTCAAATAGAAATGACTAAAATATAATATAAGACAAACAAA
AGTGACTATCCCACA
Found at i:2737196 original size:19 final size:19
Alignment explanation
Indices: 2737172--2737208 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2737162 CATCTTATTA
*
2737172 TATAATATTTGCATATAAC
1 TATAATATTTACATATAAC
2737191 TATAATATTTACATATAA
1 TATAATATTTACATATAA
2737209 ATTATCAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (19 bp):
TATAATATTTACATATAAC
Found at i:2740017 original size:41 final size:42
Alignment explanation
Indices: 2739954--2740071 Score: 123
Period size: 41 Copynumber: 2.8 Consensus size: 42
2739944 TTTCGGACGA
* * * *
2739954 ATTAGTGGCGTTTTTAGTAAAGCGCCGCTAATGCTCTG-GTT
1 ATTAGCGGCGCTTTTAATAAAGCGCCGCTAATGCTCAGTGTT
* * * *
2739995 ATTAGCTGTGTTTTTTAA-AAAGCGCCGCTAATGGTCAGTGTT
1 ATTAGCGGCG-CTTTTAATAAAGCGCCGCTAATGCTCAGTGTT
* *
2740037 TTTAGCGGCGCTTTTAATATAGCGCCGCTAATGCT
1 ATTAGCGGCGCTTTTAATAAAGCGCCGCTAATGCT
2740072 AAGACTTTTA
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
41 31 0.50
42 31 0.50
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (42 bp):
ATTAGCGGCGCTTTTAATAAAGCGCCGCTAATGCTCAGTGTT
Found at i:2744981 original size:12 final size:12
Alignment explanation
Indices: 2744964--2744988 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2744954 TGAACGAATA
2744964 TTTTATTTTATT
1 TTTTATTTTATT
2744976 TTTTATTTTATT
1 TTTTATTTTATT
2744988 T
1 T
2744989 GTAAGAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:2746747 original size:15 final size:16
Alignment explanation
Indices: 2746716--2746748 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2746706 AATTTCTAAT
*
2746716 ATTTTTATAAATTTTA
1 ATTTTTATAAATATTA
2746732 ATTTTTAT-AATATTA
1 ATTTTTATAAATATTA
2746747 AT
1 AT
2746749 GATTTTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTTATAAATATTA
Found at i:2746755 original size:18 final size:16
Alignment explanation
Indices: 2746712--2746758 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
2746702 AATTAATTTC
2746712 TAATATTTTTATAAAT
1 TAATATTTTTATAAAT
*
2746728 T-TTAATTTTTATAATAT
1 TAAT-ATTTTTATAA-AT
2746745 TAATGATTTTTATA
1 TAAT-ATTTTTATA
2746759 CTTTTTTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 1 0.04
16 11 0.44
17 3 0.12
18 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TAATATTTTTATAAAT
Found at i:2749481 original size:21 final size:22
Alignment explanation
Indices: 2749443--2749537 Score: 70
Period size: 24 Copynumber: 4.2 Consensus size: 22
2749433 TCCCATCATA
*
2749443 TTTTTTTGGTACTATCTCAT-ATT
1 TTTTTTTCGTA-T-TCTCATAATT
2749466 TTTTTTTCGTATTCTCTTATAATT
1 TTTTTTTCGTATTCTC--ATAATT
* * *
2749490 TTTTTTTTGTATT-TCTTCA-T
1 TTTTTTTCGTATTCTCATAATT
*
2749510 TTTTTTTAGTATTGCCTCATAATT
1 TTTTTTTCGTATT--CTCATAATT
2749534 TTTT
1 TTTT
2749538 GTATTGTCTC
Statistics
Matches: 58, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
20 13 0.22
21 6 0.10
22 1 0.02
23 18 0.31
24 20 0.34
ACGTcount: A:0.16, C:0.12, G:0.06, T:0.66
Consensus pattern (22 bp):
TTTTTTTCGTATTCTCATAATT
Found at i:2749491 original size:23 final size:23
Alignment explanation
Indices: 2749465--2749537 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 23
2749455 TATCTCATAT
*
2749465 TTTTTTTTCGTATTCTCTTATAA
1 TTTTTTTTAGTATTCTCTTATAA
* *
2749488 TTTTTTTTTTGTATT-TC-T-TCA
1 -TTTTTTTTAGTATTCTCTTATAA
*
2749509 TTTTTTTTAGTATTGC-CTCATAA
1 TTTTTTTTAGTATT-CTCTTATAA
2749532 TTTTTT
1 TTTTTT
2749538 GTATTGTCTC
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
20 13 0.32
21 3 0.08
22 1 0.03
23 10 0.25
24 13 0.32
ACGTcount: A:0.15, C:0.11, G:0.05, T:0.68
Consensus pattern (23 bp):
TTTTTTTTAGTATTCTCTTATAA
Found at i:2749514 original size:20 final size:20
Alignment explanation
Indices: 2749489--2749554 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
2749479 CTCTTATAAT
* *
2749489 TTTTTTTTTGTATTTCTTCA
1 TTTTTTTTTGTATTGCCTCA
*
2749509 TTTTTTTTAGTATTGCCTCA
1 TTTTTTTTTGTATTGCCTCA
** *
2749529 TAATTTTTTGTATTGTCTCA
1 TTTTTTTTTGTATTGCCTCA
2749549 TATTTT
1 T-TTTT
2749555 AAGGTACTTT
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
20 34 0.94
21 2 0.06
ACGTcount: A:0.15, C:0.11, G:0.08, T:0.67
Consensus pattern (20 bp):
TTTTTTTTTGTATTGCCTCA
Found at i:2749580 original size:20 final size:20
Alignment explanation
Indices: 2749512--2749584 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
2749502 TTCTTCATTT
* *
2749512 TTTTTAGTATTGCCTCATAA
1 TTTTTGGTATTGTCTCATAA
*
2749532 TTTTTTGTATTGTCTCAT-A
1 TTTTTGGTATTGTCTCATAA
*
2749551 TTTTAAGGTACTT-TCTCATAA
1 TTTT-TGGTA-TTGTCTCATAA
2749572 TTTTTGGTATTGT
1 TTTTTGGTATTGT
2749585 TTCAAAAAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
19 7 0.16
20 30 0.68
21 7 0.16
ACGTcount: A:0.21, C:0.11, G:0.12, T:0.56
Consensus pattern (20 bp):
TTTTTGGTATTGTCTCATAA
Found at i:2753850 original size:27 final size:26
Alignment explanation
Indices: 2753816--2753866 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
2753806 ACATAAAAAT
* *
2753816 TGTCAAATTGTACTTGTTTTTTTAGC
1 TGTCAAATTCTAATTGTTTTTTTAGC
*
2753842 TGTCGAAATTCTAATTTTTTTTTTA
1 TGTC-AAATTCTAATTGTTTTTTTA
2753867 AAAATTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 4 0.19
27 17 0.81
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.57
Consensus pattern (26 bp):
TGTCAAATTCTAATTGTTTTTTTAGC
Found at i:2754716 original size:6 final size:6
Alignment explanation
Indices: 2754705--2754734 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2754695 CCATAGCTAA
*
2754705 TTCAAC TTCAAC TTCAAT TTCAAC TTCAAC
1 TTCAAC TTCAAC TTCAAC TTCAAC TTCAAC
2754735 ACCAACACCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (6 bp):
TTCAAC
Found at i:2764043 original size:4 final size:4
Alignment explanation
Indices: 2764034--2764059 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2764024 TAATTAACAG
2764034 TGTA TGTA TGTA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TG
2764060 ATTCCATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:2791591 original size:44 final size:44
Alignment explanation
Indices: 2791541--2791648 Score: 146
Period size: 44 Copynumber: 2.5 Consensus size: 44
2791531 CTTGTCGAAT
* * *
2791541 TGCAAGCCGAAGTGGCGGACAGTCTAAATGCTAACCTGAA-TGGG
1 TGCAAGCCGAAATGGCAGACAGTCTAAATGC-AACCTCAAGTGGG
* *
2791585 TGCAAGCCGAAATGGCAGACGGTCTAAATGCAAGCTCAAGTGGG
1 TGCAAGCCGAAATGGCAGACAGTCTAAATGCAACCTCAAGTGGG
*
2791629 TGCAAGCCAAAATGGCAGAC
1 TGCAAGCCGAAATGGCAGAC
2791649 TAAAGGCAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 6 0.11
44 51 0.89
ACGTcount: A:0.32, C:0.21, G:0.31, T:0.16
Consensus pattern (44 bp):
TGCAAGCCGAAATGGCAGACAGTCTAAATGCAACCTCAAGTGGG
Found at i:2792528 original size:21 final size:21
Alignment explanation
Indices: 2792504--2792556 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2792494 CATTGTTTCT
* *
2792504 AATCTCACTGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
* *
2792525 AATCTCACCGTTACAGTAACT
1 AATCTCACCGCTACAGTAACC
2792546 AATCTCACCGC
1 AATCTCACCGC
2792557 CACCGCTGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.34, G:0.09, T:0.26
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:2794571 original size:21 final size:21
Alignment explanation
Indices: 2794547--2794599 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2794537 CATTGTTTCT
* *
2794547 AATCTCACTGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
* *
2794568 AATCTCACCGTTACAGTAACT
1 AATCTCACCGCTACAGTAACC
2794589 AATCTCACCGC
1 AATCTCACCGC
2794600 CACCGCTGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.34, G:0.09, T:0.26
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:2804881 original size:24 final size:24
Alignment explanation
Indices: 2804849--2804896 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2804839 TGAAGAAGAT
2804849 GGACCCCAAGTGGTGGTTGGAGGC
1 GGACCCCAAGTGGTGGTTGGAGGC
2804873 GGACCCCAAGTGGTGGTTGGAGGC
1 GGACCCCAAGTGGTGGTTGGAGGC
2804897 TAGCATCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.21, G:0.46, T:0.17
Consensus pattern (24 bp):
GGACCCCAAGTGGTGGTTGGAGGC
Found at i:2805770 original size:29 final size:29
Alignment explanation
Indices: 2805735--2805790 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
2805725 TAACTATTTG
*
2805735 AACTAATTAATTACATTATAAAAATATTA
1 AACTAATTAATAACATTATAAAAATATTA
2805764 AACTAATTAATAACATTATAAAAATAT
1 AACTAATTAATAACATTATAAAAATAT
2805791 AAAGATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (29 bp):
AACTAATTAATAACATTATAAAAATATTA
Found at i:2816901 original size:12 final size:12
Alignment explanation
Indices: 2816884--2816910 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2816874 ATTAATCTCA
2816884 TTGAATATATCT
1 TTGAATATATCT
2816896 TTGAATATATCT
1 TTGAATATATCT
2816908 TTG
1 TTG
2816911 CATTGATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.52
Consensus pattern (12 bp):
TTGAATATATCT
Found at i:2820976 original size:16 final size:16
Alignment explanation
Indices: 2820957--2820995 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2820947 GCTGAGTTCT
* *
2820957 TTTCTTTTGTTTTTTC
1 TTTCTTTCGTTTTTGC
*
2820973 TTTCATTCGTTTTTGC
1 TTTCTTTCGTTTTTGC
2820989 TTTCTTT
1 TTTCTTT
2820996 GCTACTGCCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.03, C:0.15, G:0.08, T:0.74
Consensus pattern (16 bp):
TTTCTTTCGTTTTTGC
Found at i:2832006 original size:34 final size:36
Alignment explanation
Indices: 2831968--2832047 Score: 96
Period size: 34 Copynumber: 2.3 Consensus size: 36
2831958 ATGTGAAAGT
*
2831968 ATAATATATT-ATATTTAAATTTAA-ATTTTTAA-AA
1 ATAATATATTCATATATAAATTTAATA-TTTTAAGAA
*
2832002 ATAATAT-TTCATATATAAATTTTATATTTTAAGAA
1 ATAATATATTCATATATAAATTTAATATTTTAAGAA
2832037 ATAATAATATT
1 ATAAT-ATATT
2832048 TAAAAAAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
33 2 0.05
34 25 0.64
35 8 0.21
36 2 0.05
37 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (36 bp):
ATAATATATTCATATATAAATTTAATATTTTAAGAA
Found at i:2832304 original size:29 final size:29
Alignment explanation
Indices: 2832245--2832303 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
2832235 TATGATTTAA
* *
2832245 TGTGTAATTGTATACATGAATTTTTATTT
1 TGTGTAATTGTATACATGAAATTTGATTT
*
2832274 TGTGTAATTTTATACATGAAAATTTGATTT
1 TGTGTAATTGTATACATG-AAATTTGATTT
2832304 GATCCAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.53
Consensus pattern (29 bp):
TGTGTAATTGTATACATGAAATTTGATTT
Found at i:2837444 original size:16 final size:19
Alignment explanation
Indices: 2837404--2837441 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2837394 GGAAAATGTT
*
2837404 TTTAGGATATATATATAAA
1 TTTAGGATATATATAGAAA
2837423 TTTAGGA-ATATA-AGAAA
1 TTTAGGATATATATAGAAA
2837440 TT
1 TT
2837442 AGGTATTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 5 0.28
19 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.39
Consensus pattern (19 bp):
TTTAGGATATATATAGAAA
Found at i:2848656 original size:17 final size:16
Alignment explanation
Indices: 2848636--2848669 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2848626 TTTTACTCAC
2848636 AATTTAAATTATTTTTT
1 AATTTAAATT-TTTTTT
*
2848653 AATTTTAATTTTTTTT
1 AATTTAAATTTTTTTT
2848669 A
1 A
2848670 TATATTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
AATTTAAATTTTTTTT
Found at i:2855045 original size:16 final size:16
Alignment explanation
Indices: 2855026--2855061 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
2855016 TATATATATA
*
2855026 TTATTTTATTTTATTT
1 TTATCTTATTTTATTT
2855042 TTATCTTATTTTATTT
1 TTATCTTATTTTATTT
2855058 TTAT
1 TTAT
2855062 AATTCACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (16 bp):
TTATCTTATTTTATTT
Found at i:2856610 original size:46 final size:45
Alignment explanation
Indices: 2856504--2856716 Score: 221
Period size: 46 Copynumber: 4.8 Consensus size: 45
2856494 CATATGACCT
*
2856504 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
2856547 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
2856593 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
* * * *
2856630 CTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAG-CTAAGCTACCA
2856676 CTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGC
1 CTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGC
2856717 NNNNNNNNNN
Statistics
Matches: 141, Mismatches: 11, Indels: 28
0.78 0.06 0.16
Matches are distributed among these distances:
37 29 0.21
39 1 0.01
40 3 0.02
42 1 0.01
43 11 0.08
44 6 0.04
45 21 0.15
46 44 0.31
48 1 0.01
51 1 0.01
52 23 0.16
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:2856631 original size:37 final size:37
Alignment explanation
Indices: 2856590--2856665 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
2856580 GCTGAAGCTA
*
2856590 CCACTTATCACTTTATCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTATCACTTGATCAGATAAGTATAG
* *
2856627 CCACTTATCACTTTGTCTCTTGATCAGATAAGTATAG
1 CCACTTATCACTTTATCACTTGATCAGATAAGTATAG
2856664 CC
1 CC
2856666 GAAGCTATCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.36
Consensus pattern (37 bp):
CCACTTATCACTTTATCACTTGATCAGATAAGTATAG
Found at i:2856649 original size:83 final size:85
Alignment explanation
Indices: 2856544--2856716 Score: 251
Period size: 83 Copynumber: 2.0 Consensus size: 85
2856534 AGCTAGGCTA
* *
2856544 CCACTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTT-A-TC
1 CCACTTATCACTTTGCCACTTGATCAGATAAGTATAGCCGAAGCTACCACTTATCACTTTCATTC
2856607 ACTTGATCAGATAAGTGTAG
66 ACTTGATCAGATAAGTGTAG
* * *
2856627 CCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACT
1 CCACTTATCACTTTGCCACTTGATCAGATAAGTATAGCCGAAGCTACCACTTATCACTTT-CA--
2856692 TGTCACTTGATCAGATAAGTGTAG
63 T-TCACTTGATCAGATAAGTGTAG
2856716 C
1 C
2856717 NNNNNNNNNN
Statistics
Matches: 79, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
83 55 0.70
85 1 0.01
89 23 0.29
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.34
Consensus pattern (85 bp):
CCACTTATCACTTTGCCACTTGATCAGATAAGTATAGCCGAAGCTACCACTTATCACTTTCATTC
ACTTGATCAGATAAGTGTAG
Found at i:2864470 original size:54 final size:54
Alignment explanation
Indices: 2864383--2864495 Score: 217
Period size: 54 Copynumber: 2.1 Consensus size: 54
2864373 GGAGCCTCAG
2864383 TTCTCAAGGTTTTTGCCTTAAGCTTCTTTGATAGTGCTTCTAACTGATCTAAAT
1 TTCTCAAGGTTTTTGCCTTAAGCTTCTTTGATAGTGCTTCTAACTGATCTAAAT
*
2864437 TTCTTAAGGTTTTTGCCTTAAGCTTCTTTGATAGTGCTTCTAACTGATCTAAAT
1 TTCTCAAGGTTTTTGCCTTAAGCTTCTTTGATAGTGCTTCTAACTGATCTAAAT
2864491 TTCTC
1 TTCTC
2864496 TGAATAAAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.21, C:0.19, G:0.14, T:0.46
Consensus pattern (54 bp):
TTCTCAAGGTTTTTGCCTTAAGCTTCTTTGATAGTGCTTCTAACTGATCTAAAT
Found at i:2865591 original size:375 final size:375
Alignment explanation
Indices: 2864901--2865694 Score: 1563
Period size: 375 Copynumber: 2.1 Consensus size: 375
2864891 CCTTTGTTCG
*
2864901 TATTTTTTTC-CAAGATTTTATTACTTTTAAAAAATATACTATTTTCTAATTTATTATTTTACAT
1 TATTTTTTTCTCGA-ATTTTATTACTTTTAAAAAATATACTATTTTCTAATTTATTATTTTACAT
2864965 TATTTTAGTACATTATGCTTGAAATGTATTCATTTAGTGTGTTTTTTATTGAAAGTAATAAAATC
65 TATTTTAGTACATTATGCTTGAAATGTATTCATTTAGTGTGTTTTTTATTGAAAGTAATAAAATC
2865030 CAGAAAAAAAATATGAACAAAGGGCCGAAATAAGAGTTTTTTTAAAATTTATTTAAAAAACACAC
130 CAGAAAAAAAATATGAACAAAGGGCCGAAATAAGAGTTTTTTTAAAATTTATTTAAAAAACACAC
2865095 TAAACGAATACATTTCAAACATAATGAACTAAAATAATGTAAAATAATATATTTAAAAAATAGTA
195 TAAACGAATACATTTCAAACATAATGAACTAAAATAATGTAAAATAATATATTTAAAAAATAGTA
2865160 TTTTTTTAAAGTAATAAAATCCGAAAAAAAATACAAACAAAGGGCTGAAAGGTAATATTTTAGTA
260 TTTTTTTAAAGTAATAAAATCCGAAAAAAAATACAAACAAAGGGCTGAAAGGTAATATTTTAGTA
2865225 AAAAAATTACGAAAAAAAAAAATATATATTTTTAAAGTAATAAAATATTCT
325 AAAAAATTACGAAAAAAAAAAATATATATTTTTAAAGTAATAAAATATTCT
2865276 TATTTTTTTCTCGAATTTTATTACTTTTAAAAAATATACTATTTTCTAATTTATTATTTTACATT
1 TATTTTTTTCTCGAATTTTATTACTTTTAAAAAATATACTATTTTCTAATTTATTATTTTACATT
2865341 ATTTTAGTACATTATGCTTGAAATGTATTCATTTAGTGTGTTTTTTATTGAAAGTAATAAAATCC
66 ATTTTAGTACATTATGCTTGAAATGTATTCATTTAGTGTGTTTTTTATTGAAAGTAATAAAATCC
2865406 AGAAAAAAAATATGAACAAAGGGCCGAAATAAGAGTTTTTTTAAAATTTATTTAAAAAACACACT
131 AGAAAAAAAATATGAACAAAGGGCCGAAATAAGAGTTTTTTTAAAATTTATTTAAAAAACACACT
2865471 AAACGAATACATTTCAAACATAATGAACTAAAATAATGTAAAATAATATATTTAAAAAATAGTAT
196 AAACGAATACATTTCAAACATAATGAACTAAAATAATGTAAAATAATATATTTAAAAAATAGTAT
2865536 TTTTTTAAAGTAATAAAATCCGAAAAAAAATACAAACAAAGGGCTGAAAGGTAATATTTTAGTAA
261 TTTTTTAAAGTAATAAAATCCGAAAAAAAATACAAACAAAGGGCTGAAAGGTAATATTTTAGTAA
2865601 AAAAATTACGAAAAAAAAAAATATATATTTTTAAAGTAATAAAATATTCT
326 AAAAATTACGAAAAAAAAAAATATATATTTTTAAAGTAATAAAATATTCT
2865651 TATTTTTTTCTCGAATTTTATTACTTTTAAAAAATATACTATTT
1 TATTTTTTTCTCGAATTTTATTACTTTTAAAAAATATACTATTT
2865695 CACCAAAAAG
Statistics
Matches: 417, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
375 415 1.00
376 2 0.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (375 bp):
TATTTTTTTCTCGAATTTTATTACTTTTAAAAAATATACTATTTTCTAATTTATTATTTTACATT
ATTTTAGTACATTATGCTTGAAATGTATTCATTTAGTGTGTTTTTTATTGAAAGTAATAAAATCC
AGAAAAAAAATATGAACAAAGGGCCGAAATAAGAGTTTTTTTAAAATTTATTTAAAAAACACACT
AAACGAATACATTTCAAACATAATGAACTAAAATAATGTAAAATAATATATTTAAAAAATAGTAT
TTTTTTAAAGTAATAAAATCCGAAAAAAAATACAAACAAAGGGCTGAAAGGTAATATTTTAGTAA
AAAAATTACGAAAAAAAAAAATATATATTTTTAAAGTAATAAAATATTCT
Found at i:2866130 original size:146 final size:141
Alignment explanation
Indices: 2865952--2866441 Score: 603
Period size: 146 Copynumber: 3.4 Consensus size: 141
2865942 TCTAAATTAA
**
2865952 AAAAAATAGTATATTTTTTAAAAGTAATAAAATACAGGGAAAAAATACGAACATAGGACCGAAAT
1 AAAAAATAGTATATTTTTTAAAAGTAATAAAAT-C-GAAAAAAAATACGAACATAGG-CCGAAAT
* *
2866017 AAGAATTTTTTTTTAAATTTATTTAAAAAACATACTAAATTAATACATTTCTAATATAATATACT
63 AAG-A-TTTTTTTTAAATTTATTTAAAAAACACACTAAATTAATACATTTCAAATATAATATACT
2866082 AAAATAATGTAAAATT
126 AAAATAATGTAAAATT
*
2866098 AAAAAATAGTATATTTTTTAAAAGTAATAAAATTCGAAAAAAAAATACGAACATAGGGCCAAAAT
1 AAAAAATAGTATATTTTTTAAAAGTAATAAAA-TCG-AAAAAAAATACGAACATA-GGCCGAAAT
* * *
2866163 AAGATTTTTTTT-AATTTATTT-AAAAACACACCAAATTAATTCATTTCAAATATAGTATACTAA
63 AAGATTTTTTTTAAATTTATTTAAAAAACACACTAAATTAATACATTTCAAATATAATATACTAA
2866226 AATAATGTAAAA-T
128 AATAATGTAAAATT
* * *
2866239 -AAAAA-AGTATATTTTTTAAAAGTAATAAAATCCGAAAAAATAATAAGAACAAATGGCTGAAAT
1 AAAAAATAGTATATTTTTTAAAAGTAATAAAAT-CGAAAAAA-AATACGAACATA-GGCCGAAAT
* * * * *
2866302 AAGGTTTTTTTAAAATTTATTTAAAAAACACACTAAATCAAAACATTTCAAATATAATGTACTAA
63 AAGATTTTTTTTAAATTTATTTAAAAAACACACTAAATTAATACATTTCAAATATAATATACTAA
2866367 AATAATGTAAAATTTAAAAATT
128 AATAATG-------T-AAAATT
*
2866389 AAAAAATAGTACATTTTTTAAAAGTAATAAAATTCGAAAAAAAAATACGAACA
1 AAAAAATAGTATATTTTTTAAAAGTAATAAAA-TCG-AAAAAAAATACGAACA
2866442 AAGGGGAGTG
Statistics
Matches: 301, Mismatches: 23, Indels: 34
0.84 0.06 0.09
Matches are distributed among these distances:
138 7 0.02
139 54 0.18
140 14 0.05
141 44 0.15
142 49 0.16
143 9 0.03
144 8 0.03
145 2 0.01
146 58 0.19
147 3 0.01
148 1 0.00
149 4 0.01
150 1 0.00
151 5 0.02
152 35 0.12
153 7 0.02
ACGTcount: A:0.53, C:0.08, G:0.07, T:0.32
Consensus pattern (141 bp):
AAAAAATAGTATATTTTTTAAAAGTAATAAAATCGAAAAAAAATACGAACATAGGCCGAAATAAG
ATTTTTTTTAAATTTATTTAAAAAACACACTAAATTAATACATTTCAAATATAATATACTAAAAT
AATGTAAAATT
Found at i:2866234 original size:142 final size:143
Alignment explanation
Indices: 2865952--2866446 Score: 631
Period size: 139 Copynumber: 3.4 Consensus size: 143
2865942 TCTAAATTAA
* ** * *
2865952 AAAAAATAGTATATTTTTTAAAAGTAATAAAATAC-AGGGAAAAAATACGAACATAGGACCGAAA
1 AAAAAATAGTATATTTTTTAAAAGTAATAAAATTCGA-AAAAAAAATACGAACAAAGGGCCGAAA
* *
2866016 TAAGAATTTTTTTTTAAATTTATTTAAAAAACATACTAAATTAATACATTTCTAATATAATATAC
65 TAAG-A-TTTTTTTT-AATTTATTTAAAAAACACACTAAATTAATACATTTCAAATATAATATAC
2866081 TAAAATAATGTAAAATT
127 TAAAATAATGTAAAATT
* *
2866098 AAAAAATAGTATATTTTTTAAAAGTAATAAAATTCGAAAAAAAAATACGAACATAGGGCCAAAAT
1 AAAAAATAGTATATTTTTTAAAAGTAATAAAATTCGAAAAAAAAATACGAACAAAGGGCCGAAAT
* * *
2866163 AAGATTTTTTTTAATTTATTT-AAAAACACACCAAATTAATTCATTTCAAATATAGTATACTAAA
66 AAGATTTTTTTTAATTTATTTAAAAAACACACTAAATTAATACATTTCAAATATAATATACTAAA
2866227 ATAATGTAAAA-T
131 ATAATGTAAAATT
* * * * *
2866239 -AAAAA-AGTATATTTTTTAAAAGTAATAAAATCCGAAAAAATAATAAGAACAAATGGCTGAAAT
1 AAAAAATAGTATATTTTTTAAAAGTAATAAAATTCGAAAAAAAAATACGAACAAAGGGCCGAAAT
* * * * *
2866302 AAGGTTTTTTTAAAATTTATTTAAAAAACACACTAAATCAAAACATTTCAAATATAATGTACTAA
66 AAGATTTTTTT-TAATTTATTTAAAAAACACACTAAATTAATACATTTCAAATATAATATACTAA
2866367 AATAATGTAAAATTTAAAAATT
130 AATAATG-------T-AAAATT
*
2866389 AAAAAATAGTACATTTTTTAAAAGTAATAAAATTCGAAAAAAAAATACGAACAAAGGG
1 AAAAAATAGTATATTTTTTAAAAGTAATAAAATTCGAAAAAAAAATACGAACAAAGGG
2866447 GAGTGCCGCC
Statistics
Matches: 305, Mismatches: 30, Indels: 22
0.85 0.08 0.06
Matches are distributed among these distances:
139 61 0.20
140 14 0.05
141 44 0.14
142 49 0.16
143 9 0.03
144 8 0.03
145 1 0.00
146 61 0.20
147 1 0.00
148 1 0.00
149 4 0.01
150 1 0.00
151 5 0.02
152 46 0.15
ACGTcount: A:0.53, C:0.07, G:0.08, T:0.31
Consensus pattern (143 bp):
AAAAAATAGTATATTTTTTAAAAGTAATAAAATTCGAAAAAAAAATACGAACAAAGGGCCGAAAT
AAGATTTTTTTTAATTTATTTAAAAAACACACTAAATTAATACATTTCAAATATAATATACTAAA
ATAATGTAAAATT
Found at i:2867718 original size:2 final size:2
Alignment explanation
Indices: 2867711--2867739 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2867701 AATTGATATT
2867711 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2867740 TAACGGGACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2868647 original size:19 final size:16
Alignment explanation
Indices: 2868609--2868643 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
2868599 ATATGTATTT
2868609 AATATATATTTGATTA
1 AATATATATTTGATTA
2868625 AATAGTATATTTGATTA
1 AATA-TATATTTGATTA
2868642 AA
1 AA
2868644 AATAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (16 bp):
AATATATATTTGATTA
Found at i:2868903 original size:13 final size:12
Alignment explanation
Indices: 2868881--2868910 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
2868871 ATGTTAAGTT
2868881 ATTTGTGTGAAA
1 ATTTGTGTGAAA
2868893 ATTTCGTGTGAAA
1 ATTT-GTGTGAAA
2868906 ATTTG
1 ATTTG
2868911 ATCGTTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.30, C:0.03, G:0.23, T:0.43
Consensus pattern (12 bp):
ATTTGTGTGAAA
Found at i:2870870 original size:102 final size:102
Alignment explanation
Indices: 2870717--2871425 Score: 1321
Period size: 102 Copynumber: 7.0 Consensus size: 102
2870707 CCAGTGATCC
* * * * * *
2870717 GGGG-ATCAACACTTAGCAACCCCTTTCAAATTCAAAGATATGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAACAACCCCCTTCACATTTAAA-ATACGGTGGAATCAGCACTTAGCAACC
* *
2870781 ACCAATGATTCGGAGAATCAGCACTTAGCAACCTCTTG
65 ACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTG
2870819 GGGGAATCAGCACTTAACAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAACAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
*
2870884 CCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTG
66 CCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTG
2870921 GGGGAATCAGCACTTAACAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAACAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
2870986 CCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTG
66 CCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTG
2871023 GGGGAATCAGCACTTAACAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAACAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
2871088 CCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTG
66 CCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTG
2871125 GGGGAATCAGCACTTAACAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAACAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
2871190 CCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTG
66 CCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTG
2871227 GGGGAATCAGCACTTAACAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAACAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
2871292 CCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTG
66 CCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTG
2871329 GGGGAATCAGCACTTAACAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAACAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
2871394 CCAATGATTCGGGGAATCAGCACTTAGCAACC
66 CCAATGATTCGGGGAATCAGCACTTAGCAACC
2871426 NNNNNNNNNN
Statistics
Matches: 596, Mismatches: 10, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
102 569 0.95
103 27 0.05
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.21
Consensus pattern (102 bp):
GGGGAATCAGCACTTAACAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
CCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTG
Found at i:2873876 original size:17 final size:17
Alignment explanation
Indices: 2873835--2873868 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2873825 GTAAATCACT
2873835 CATCTCGATTCGAGAAG
1 CATCTCGATTCGAGAAG
2873852 CATCTCGATTCGAGAAG
1 CATCTCGATTCGAGAAG
2873869 GGTCTCGAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (17 bp):
CATCTCGATTCGAGAAG
Found at i:2874188 original size:16 final size:16
Alignment explanation
Indices: 2874167--2874222 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
2874157 CATTTGATTC
*
2874167 ACTGTAATTGAATAGA
1 ACTGTAATGGAATAGA
2874183 ACTGTAATGGAATAGA
1 ACTGTAATGGAATAGA
**
2874199 GTTGTAATGGAATA-A
1 ACTGTAATGGAATAGA
2874214 AGCTGTAAT
1 A-CTGTAAT
2874223 TAATAATTCC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
15 1 0.03
16 33 0.97
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.30
Consensus pattern (16 bp):
ACTGTAATGGAATAGA
Found at i:2875281 original size:38 final size:38
Alignment explanation
Indices: 2875239--2875316 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
2875229 TTGATACCCT
2875239 TTTACATGTTAATAACACAAAATACCATCATCTTTCAA
1 TTTACATGTTAATAACACAAAATACCATCATCTTTCAA
2875277 TTTACATGTTAATAACACAAAATACCATCATCTTTCAA
1 TTTACATGTTAATAACACAAAATACCATCATCTTTCAA
2875315 TT
1 TT
2875317 GTTAAAATGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.41, C:0.21, G:0.03, T:0.36
Consensus pattern (38 bp):
TTTACATGTTAATAACACAAAATACCATCATCTTTCAA
Found at i:2878637 original size:24 final size:25
Alignment explanation
Indices: 2878581--2878637 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
2878571 CTGCTTAGAT
2878581 CAAAGATAAAGAAACCAAAATTAAAG
1 CAAAGA-AAAGAAACCAAAATTAAAG
* *
2878607 CATAGAAAATAAA-CAAAATTCAAA-
1 CAAAGAAAAGAAACCAAAATT-AAAG
2878631 CAAAGAA
1 CAAAGAA
2878638 GAAAAAGAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 13 0.48
25 9 0.33
26 5 0.19
ACGTcount: A:0.67, C:0.12, G:0.09, T:0.12
Consensus pattern (25 bp):
CAAAGAAAAGAAACCAAAATTAAAG
Found at i:2880802 original size:21 final size:20
Alignment explanation
Indices: 2880765--2880803 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2880755 ATATATAAAA
*
2880765 ATTTTTAAAATATTTTTTTT
1 ATTTTTAAAATAATTTTTTT
2880785 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAAT-AATTTTT
2880804 GGTGTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTTTTAAAATAATTTTTTT
Found at i:2882025 original size:17 final size:16
Alignment explanation
Indices: 2881999--2882033 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
2881989 GTATATATTT
2881999 AATATATATTTGATTA
1 AATATATATTTGATTA
2882015 AATAGTATATTTGATTA
1 AATA-TATATTTGATTA
2882032 AA
1 AA
2882034 AAAATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (16 bp):
AATATATATTTGATTA
Found at i:2882957 original size:18 final size:17
Alignment explanation
Indices: 2882910--2882961 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 17
2882900 CTTTATATGA
2882910 CTAAAAACTATGAATTTTT
1 CTAAAAA-TA-GAATTTTT
2882929 CTCAGAAAATAGAATTTATT
1 CT-A-AAAATAGAATTT-TT
2882949 CTAAAAATA-AATT
1 CTAAAAATAGAATT
2882962 ATCACTACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 4 0.13
18 6 0.20
19 9 0.30
20 7 0.23
21 4 0.13
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.37
Consensus pattern (17 bp):
CTAAAAATAGAATTTTT
Found at i:2884224 original size:309 final size:302
Alignment explanation
Indices: 2883672--2884281 Score: 1139
Period size: 309 Copynumber: 2.0 Consensus size: 302
2883662 AATTAATTAG
*
2883672 TTAATTTGAATATATTTGATTAATAGCATTATTATTTGGTTTTAAATTAGAAAACAATAAAATGC
1 TTAATTTGAATATATTTGATTAATAGCATTATTATTTGATTTTAAATTAGAAAACAATAAAATGC
2883737 TAAAATAATTTTCAAAAATAAAATTATAAATTTGAAACATTAATTTTAAAAATTAATAGTTAATG
66 TAAAATAATTTTCAAAAATAAAATTATAAATTTGAAACATTAATTTTAAAAATTAATAGTTAATG
2883802 CGATAATTTTAATACATTAAAATAATAATTAATTTTTATTTATGGTTGGTGTGCATGTGCAAATT
131 CGATAATTTTAATACATTAAAATAATAATTAATTTTTATTTATGGTTGGTGTGCATGTGCAAATT
2883867 AAATCAAACTCTAATCTTAATTCTCAAAATATATTTTTTTTATATTTTAATGAGATATTTACATA
196 AAATCAAACTCTAATCTTAATTCTCAAAATATATTTTTTTTATATTTTAATGAGATATTTACATA
2883932 TATTTTTAAGATAGTTGTTTTTATATTTATTCAAACTCATAC
261 TATTTTTAAGATAGTTGTTTTTATATTTATTCAAACTCATAC
*
2883974 TTAATTTTAATATATTTGATTAATAGCATTATTATTTGATTTTAAATTAGAAAACAATAAAATGT
1 TTAATTTGAATATATTTGATTAATAGCATTATTATTTGATTTTAAATTAGAAAAC-----AA--T
2884039 AAAATGCTAAAATAATTTTCAAAAATAAAATTATAAATTTGAAACATTAATTTTAAAAATTAATA
59 AAAATGCTAAAATAATTTTCAAAAATAAAATTATAAATTTGAAACATTAATTTTAAAAATTAATA
2884104 GTTAATGCGATAATTTTAATACATTAAAATAATAATTAATTTTTATTTATGGTTGGTGTGCATGT
124 GTTAATGCGATAATTTTAATACATTAAAATAATAATTAATTTTTATTTATGGTTGGTGTGCATGT
2884169 GCAAATTAAATCAAACTCTAATCTTAATTCTCAAAATATATTTTTTTTATATTTTAATGAGATAT
189 GCAAATTAAATCAAACTCTAATCTTAATTCTCAAAATATATTTTTTTTATATTTTAATGAGATAT
2884234 TTACATATATTTTTAAGATAGTTGTTTTTATATTTATTCAAACTCATA
254 TTACATATATTTTTAAGATAGTTGTTTTTATATTTATTCAAACTCATA
2884282 ATAAGTGTTT
Statistics
Matches: 299, Mismatches: 2, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
302 53 0.18
307 2 0.01
309 244 0.82
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.44
Consensus pattern (302 bp):
TTAATTTGAATATATTTGATTAATAGCATTATTATTTGATTTTAAATTAGAAAACAATAAAATGC
TAAAATAATTTTCAAAAATAAAATTATAAATTTGAAACATTAATTTTAAAAATTAATAGTTAATG
CGATAATTTTAATACATTAAAATAATAATTAATTTTTATTTATGGTTGGTGTGCATGTGCAAATT
AAATCAAACTCTAATCTTAATTCTCAAAATATATTTTTTTTATATTTTAATGAGATATTTACATA
TATTTTTAAGATAGTTGTTTTTATATTTATTCAAACTCATAC
Found at i:2886307 original size:32 final size:32
Alignment explanation
Indices: 2886263--2886326 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
2886253 TTTGGTTCGC
*
2886263 TATAATGGAATAGAGCTGTAATGGAATAGAGG
1 TATAATGAAATAGAGCTGTAATGGAATAGAGG
2886295 TATAATGAAATAGAGCTGTAATGGAATAGAGG
1 TATAATGAAATAGAGCTGTAATGGAATAGAGG
2886327 CGTAATAGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.42, C:0.03, G:0.30, T:0.25
Consensus pattern (32 bp):
TATAATGAAATAGAGCTGTAATGGAATAGAGG
Found at i:2886332 original size:16 final size:16
Alignment explanation
Indices: 2886265--2886325 Score: 95
Period size: 16 Copynumber: 3.8 Consensus size: 16
2886255 TGGTTCGCTA
2886265 TAATGGAATAGAGCTG
1 TAATGGAATAGAGCTG
* *
2886281 TAATGGAATAGAGGTA
1 TAATGGAATAGAGCTG
*
2886297 TAATGAAATAGAGCTG
1 TAATGGAATAGAGCTG
2886313 TAATGGAATAGAG
1 TAATGGAATAGAG
2886326 GCGTAATAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.43, C:0.03, G:0.30, T:0.25
Consensus pattern (16 bp):
TAATGGAATAGAGCTG
Found at i:2886377 original size:45 final size:44
Alignment explanation
Indices: 2886314--2886406 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
2886304 ATAGAGCTGT
*
2886314 AATGGAATAGAGGCGTAATAGTAATTCAAT-TGTTTGGTTGAATGA
1 AATGGAATAGAGACGTAATAGT-ATTC-ATGTGTTTGGTTGAATGA
* *
2886359 AATGGAATAGA-ACTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGAC-GTAATAGTATTCATGTGTTTGGTTGAATGA
2886403 AATG
1 AATG
2886407 ATGCTATAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
43 1 0.02
44 23 0.53
45 19 0.44
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGACGTAATAGTATTCATGTGTTTGGTTGAATGA
Found at i:2893275 original size:18 final size:18
Alignment explanation
Indices: 2893252--2893291 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
2893242 TACCAATATG
*
2893252 TTATTTGAGTTATTCGAA
1 TTATTTGAGTTATTCAAA
2893270 TTATTTGAGTTATTCAAA
1 TTATTTGAGTTATTCAAA
2893288 TTAT
1 TTAT
2893292 AAAATTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.53
Consensus pattern (18 bp):
TTATTTGAGTTATTCAAA
Found at i:2895987 original size:14 final size:14
Alignment explanation
Indices: 2895968--2895994 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2895958 TTTGTTAAGA
2895968 CTGTTAAAATTATC
1 CTGTTAAAATTATC
2895982 CTGTTAAAATTAT
1 CTGTTAAAATTAT
2895995 TGACGTGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.44
Consensus pattern (14 bp):
CTGTTAAAATTATC
Found at i:2899017 original size:41 final size:41
Alignment explanation
Indices: 2898970--2899050 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
2898960 TTTTACAAAG
*
2898970 AAAAAATATTTGTTTTTGATAGAACTAGTCCCCACTTACCT
1 AAAAAATATTTGTGTTTGATAGAACTAGTCCCCACTTACCT
2899011 AAAAAATATTTGTGTTTGATAGAACTAGTCCCCACTTACC
1 AAAAAATATTTGTGTTTGATAGAACTAGTCCCCACTTACC
2899051 CTTTCTCGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.35
Consensus pattern (41 bp):
AAAAAATATTTGTGTTTGATAGAACTAGTCCCCACTTACCT
Found at i:2902701 original size:126 final size:126
Alignment explanation
Indices: 2902476--2902869 Score: 510
Period size: 126 Copynumber: 3.1 Consensus size: 126
2902466 GGCCAAACAA
* *
2902476 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAG-TTTTTTTCATTAATTTTGCTGATAGTGCAT
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTT-AGTAATTTTGCTGACAGTGCAT
* * *
2902540 CCTGCTTGAAGCGTTTTTAACACCACTTGTTCAGAACCGTCTTCTTAAAATTATTTTTTTAG
65 CCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTTAAAATTATTTTTTTAG
* * * * * *
2902602 GAACTATTGTAGAAAAAGAGTGCCCACGTGGGAGCTTTTTTTAGTATTTTTGTTGACAGTGCATT
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATC
* * *
2902667 CTGCTTAAAGCATTTTTGACACTATTTGTTCAGAACTGTCTTCTTAAAATTATTTTTTTAG
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTTAAAATTATTTTTTTAG
* * *
2902728 AAACTACTGTAGAAAAAGAGCATCCACGTGGGAGC-TTTTTGAGTAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATC
* * * *
2902792 CTGCTTGAAGTGTTTTTGACA-TTTTCTTTTCAGAACCGTCTT-TTCAAAATTAATTTTTCT-G
66 CTGCTTGAAGCGTTTTTGACACTATT-TGTTCAGAACCGTCTTCTT-AAAATT-ATTTTTTTAG
* *
2902853 AAAATACTGTAGAAAAA
1 GAACTACTGTAGAAAAA
2902870 AATATTATTG
Statistics
Matches: 233, Mismatches: 31, Indels: 9
0.85 0.11 0.03
Matches are distributed among these distances:
124 5 0.02
125 80 0.34
126 141 0.61
127 7 0.03
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATC
CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAACCGTCTTCTTAAAATTATTTTTTTAG
Found at i:2902965 original size:34 final size:34
Alignment explanation
Indices: 2902927--2903033 Score: 115
Period size: 34 Copynumber: 3.1 Consensus size: 34
2902917 AATTATTTAA
*
2902927 AAAAAAACTAAACCCTAATTTAAATAATTTTTTT
1 AAAAAAACTAAACCCTAATTTAATTAATTTTTTT
* * *
2902961 AAAAAACTCTAAACCCTAATTTAATTTATTTATTT
1 AAAAAA-ACTAAACCCTAATTTAATTAATTTTTTT
*** * * *
2902996 AAAACCCCTAAAACTTAATTTAATTATTTTTTTT
1 AAAAAAACTAAACCCTAATTTAATTAATTTTTTT
2903030 AAAA
1 AAAA
2903034 CTTTAAACCC
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
34 32 0.53
35 28 0.47
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (34 bp):
AAAAAAACTAAACCCTAATTTAATTAATTTTTTT
Found at i:2902973 original size:35 final size:34
Alignment explanation
Indices: 2902934--2903050 Score: 128
Period size: 33 Copynumber: 3.4 Consensus size: 34
2902924 TAAAAAAAAA
*
2902934 CTAAACCCTAATTTAAATAATTTTTTTAAAAAACT
1 CTAAACCCTAATTTAAATTATTTTTTT-AAAAACT
* * * *
2902969 CTAAACCCTAATTTAATTTATTTATTTAAAACCC
1 CTAAACCCTAATTTAAATTATTTTTTTAAAAACT
* * *
2903003 CTAAAACTTAATTT-AATTATTTTTTTTAAAACT
1 CTAAACCCTAATTTAAATTATTTTTTTAAAAACT
* *
2903036 TTAAACCCTGATTTA
1 CTAAACCCTAATTTA
2903051 TTTTTTAAAA
Statistics
Matches: 65, Mismatches: 16, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
33 24 0.37
34 17 0.26
35 24 0.37
ACGTcount: A:0.40, C:0.15, G:0.01, T:0.44
Consensus pattern (34 bp):
CTAAACCCTAATTTAAATTATTTTTTTAAAAACT
Found at i:2903116 original size:28 final size:28
Alignment explanation
Indices: 2903072--2903143 Score: 112
Period size: 27 Copynumber: 2.6 Consensus size: 28
2903062 TCTTAAACCT
2903072 AAAACCCTAAACC-TAAATTATTTTAAC
1 AAAACCCTAAACCTTAAATTATTTTAAC
* *
2903099 ACAACCATAAACCTTAAATTATTTTAAC
1 AAAACCCTAAACCTTAAATTATTTTAAC
2903127 AAAACCCT-AACCTTAAA
1 AAAACCCTAAACCTTAAA
2903144 CCCTAAACCC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 20 0.50
28 20 0.50
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.28
Consensus pattern (28 bp):
AAAACCCTAAACCTTAAATTATTTTAAC
Found at i:2904114 original size:24 final size:23
Alignment explanation
Indices: 2904078--2904125 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
2904068 GAGGAGGAGA
2904078 AAGAAGAAAAAAAAGAGAGAAAAG
1 AAGAAGAAAAAAAAG-GAGAAAAG
* *
2904102 AAGAAGAAGAAAATGGAGAAAAG
1 AAGAAGAAAAAAAAGGAGAAAAG
2904125 A
1 A
2904126 GAGGGAGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (23 bp):
AAGAAGAAAAAAAAGGAGAAAAG
Found at i:2904121 original size:15 final size:14
Alignment explanation
Indices: 2904078--2904114 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2904068 GAGGAGGAGA
2904078 AAGAAGAAAA-AA-
1 AAGAAGAAAAGAAG
2904090 AAGAGAGAAAAGAAG
1 AAGA-AGAAAAGAAG
2904105 AAGAAGAAAA
1 AAGAAGAAAA
2904115 TGGAGAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 8 0.36
15 4 0.18
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
AAGAAGAAAAGAAG
Found at i:2905943 original size:16 final size:16
Alignment explanation
Indices: 2905922--2905952 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2905912 TTCACTATTA
*
2905922 TGTCTTTTGTATTTTC
1 TGTCTTTTATATTTTC
2905938 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
2905953 ACATGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:2913600 original size:43 final size:39
Alignment explanation
Indices: 2913539--2913713 Score: 140
Period size: 33 Copynumber: 4.6 Consensus size: 39
2913529 AGTGATTCGG
* *
2913539 GGAATCAGCATTTAGCAACCCCTTTCACATTCAAGGATATGGT
1 GGAATCAGCACTTAGCAACCCC-TTCA-ATT-AA-GATACGGT
* *
2913582 GGAATCAGCACTTAGCAACCAC--CAAAT-AG-T-CGG-
1 GGAATCAGCACTTAGCAACCCCTTCAATTAAGATACGGT
*
2913615 GGAATCAGCACTTAGCAACCCCATTCAAATTTAAAATACGGT
1 GGAATCAGCACTTAGCAACCCC-TTC-AA-TTAAGATACGGT
* *
2913657 GGAATCAGCACTTAGCAACCAC--CAA-TGAG-T-CGG-
1 GGAATCAGCACTTAGCAACCCCTTCAATTAAGATACGGT
2913690 GGAATCAGCACTTAGCAACCCCTT
1 GGAATCAGCACTTAGCAACCCCTT
2913714 TGGGGGAATC
Statistics
Matches: 110, Mismatches: 11, Indels: 30
0.73 0.07 0.20
Matches are distributed among these distances:
33 42 0.38
34 5 0.05
35 2 0.02
36 4 0.04
37 3 0.03
38 3 0.03
39 4 0.04
40 3 0.03
41 3 0.03
42 21 0.19
43 20 0.18
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (39 bp):
GGAATCAGCACTTAGCAACCCCTTCAATTAAGATACGGT
Found at i:2913624 original size:33 final size:33
Alignment explanation
Indices: 2913582--2913737 Score: 135
Period size: 33 Copynumber: 4.6 Consensus size: 33
2913572 AGGATATGGT
2913582 GGAATCAGCACTTAGCAACCACCAA-ATAGTCGG
1 GGAATCAGCACTTAGCAACCACCAATA-AGTCGG
* *
2913615 GGAATCAGCACTTAGCAACCCCATTCAAATTTAAAATACGG
1 GGAATCAGCACTTAGCAA--CCA--CCAA--T-AAGT-CGG
*
2913656 TGGAATCAGCACTTAGCAACCACCAATGAGTCGG
1 -GGAATCAGCACTTAGCAACCACCAATAAGTCGG
* *
2913690 GGAATCAGCACTTAGCAACC-CC--T--TTGGG
1 GGAATCAGCACTTAGCAACCACCAATAAGTCGG
2913718 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
2913738 CCCTTTGTAT
Statistics
Matches: 106, Mismatches: 7, Indels: 25
0.77 0.05 0.18
Matches are distributed among these distances:
28 23 0.22
30 1 0.01
32 2 0.02
33 38 0.36
34 3 0.03
35 5 0.05
36 1 0.01
37 3 0.03
38 3 0.03
40 5 0.05
41 4 0.04
42 18 0.17
ACGTcount: A:0.34, C:0.27, G:0.21, T:0.19
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATAAGTCGG
Found at i:2913679 original size:75 final size:76
Alignment explanation
Indices: 2913502--2913711 Score: 307
Period size: 76 Copynumber: 2.8 Consensus size: 76
2913492 TAACCGTTAT
* * * * * * *
2913502 CGGTGGATTCAGCACTTAGCAACCACTAGTGATTCGGGGAATCAGCATTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCATTCAA
*
2913567 ATTCAAGGATA
66 ATTCAAGAATA
*
2913578 TGGTGGAATCAGCACTTAGCAACCACCAAAT-AGTCGGGGAATCAGCACTTAGCAACCCCATTCA
1 CGGTGGAATCAGCACTTAGCAACCACC-AATGAGTCGGGGAATCAGCACTTAGCAACCCCATTCA
*
2913642 AATTTAA-AATA
65 AATTCAAGAATA
2913653 CGGTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCC
2913712 TTTGGGGGAA
Statistics
Matches: 121, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
74 3 0.02
75 57 0.47
76 59 0.49
77 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (76 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCATTCAA
ATTCAAGAATA
Found at i:2913719 original size:28 final size:29
Alignment explanation
Indices: 2913688--2913744 Score: 107
Period size: 28 Copynumber: 2.0 Consensus size: 29
2913678 CCAATGAGTC
2913688 GGGGAATCAGCACTTAGCAA-CCCCTTTG
1 GGGGAATCAGCACTTAGCAACCCCCTTTG
2913716 GGGGAATCAGCACTTAGCAACCCCCTTTG
1 GGGGAATCAGCACTTAGCAACCCCCTTTG
2913745 TATTCAATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 20 0.71
29 8 0.29
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.21
Consensus pattern (29 bp):
GGGGAATCAGCACTTAGCAACCCCCTTTG
Found at i:2915623 original size:9 final size:9
Alignment explanation
Indices: 2915594--2915630 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
2915584 TGAGTTTTCG
2915594 AATTCGAAT
1 AATTCGAAT
*
2915603 AACTCGAAT
1 AATTCGAAT
2915612 AATTCGAAT
1 AATTCGAAT
*
2915621 AATTTGAAT
1 AATTCGAAT
2915630 A
1 A
2915631 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:2916418 original size:5 final size:5
Alignment explanation
Indices: 2916408--2916433 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2916398 CTCAAAAATT
2916408 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
2916434 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:2927345 original size:2 final size:2
Alignment explanation
Indices: 2927338--2927375 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2927328 ATATTCATTC
* *
2927338 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2927376 TTTCCTCCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2929656 original size:27 final size:27
Alignment explanation
Indices: 2929617--2929678 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
2929607 CTTTATATAT
*
2929617 TTTTTAGAATTTTTTTAAA-AATATAAA
1 TTTTT-GAATTTTTATAAATAATATAAA
* *
2929644 TTTTTGAATTTTTATAAATATTTTAAA
1 TTTTTGAATTTTTATAAATAATATAAA
2929671 TTTTTGAA
1 TTTTTGAA
2929679 AATTATTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 12 0.39
27 19 0.61
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (27 bp):
TTTTTGAATTTTTATAAATAATATAAA
Done.