Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold156
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1175753
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.30
Warning! 90626 characters in sequence are not A, C, G, or T
File 4 of 3
Found at i:889509 original size:13 final size:13
Alignment explanation
Indices: 889493--889517 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
889483 AAGTTAGAAT
889493 AATTAATTTTCAA
1 AATTAATTTTCAA
889506 AATTAATTTTCA
1 AATTAATTTTCA
889518 GATATTCAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
AATTAATTTTCAA
Found at i:896026 original size:2 final size:2
Alignment explanation
Indices: 896019--896063 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
896009 TTGACAGAAT
* *
896019 AG AG AG AG GG AG TG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
896061 AG A
1 AG A
896064 CTTTCACCGG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.51, T:0.02
Consensus pattern (2 bp):
AG
Found at i:896530 original size:200 final size:200
Alignment explanation
Indices: 896187--896587 Score: 802
Period size: 200 Copynumber: 2.0 Consensus size: 200
896177 CTANGGGGGG
896187 CGTAGCCACTGCCACTGCTTCTAAAGCATGCCTTATTTCTTTTTGTAAAAATATGTTTATGATCT
1 CGTAGCCACTGCCACTGCTTCTAAAGCATGCCTTATTTCTTTTTGTAAAAATATGTTTATGATCT
896252 GTAAAACAATGAAATACAACAAACTATTCAACATTGTTGTTTTTGCATTTATTTCATTGTAATAG
66 GTAAAACAATGAAATACAACAAACTATTCAACATTGTTGTTTTTGCATTTATTTCATTGTAATAG
896317 CCCGAAACCGCAATTTCCAGGCAATTTCGATACCTAAACACCAACTAATTTTCATTCAAGTTTTA
131 CCCGAAACCGCAATTTCCAGGCAATTTCGATACCTAAACACCAACTAATTTTCATTCAAGTTTTA
896382 CCCCC
196 CCCCC
896387 CGTAGCCACTGCCACTGCTTCTAAAGCATGCCTTATTTCTTTTTGTAAAAATATGTTTATGATCT
1 CGTAGCCACTGCCACTGCTTCTAAAGCATGCCTTATTTCTTTTTGTAAAAATATGTTTATGATCT
896452 GTAAAACAATGAAATACAACAAACTATTCAACATTGTTGTTTTTGCATTTATTTCATTGTAATAG
66 GTAAAACAATGAAATACAACAAACTATTCAACATTGTTGTTTTTGCATTTATTTCATTGTAATAG
896517 CCCGAAACCGCAATTTCCAGGCAATTTCGATACCTAAACACCAACTAATTTTCATTCAAGTTTTA
131 CCCGAAACCGCAATTTCCAGGCAATTTCGATACCTAAACACCAACTAATTTTCATTCAAGTTTTA
896582 CCCCC
196 CCCCC
896587 C
1 C
896588 CCCCCCAAAA
Statistics
Matches: 201, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 201 1.00
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (200 bp):
CGTAGCCACTGCCACTGCTTCTAAAGCATGCCTTATTTCTTTTTGTAAAAATATGTTTATGATCT
GTAAAACAATGAAATACAACAAACTATTCAACATTGTTGTTTTTGCATTTATTTCATTGTAATAG
CCCGAAACCGCAATTTCCAGGCAATTTCGATACCTAAACACCAACTAATTTTCATTCAAGTTTTA
CCCCC
Found at i:909181 original size:15 final size:15
Alignment explanation
Indices: 909161--909195 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
909151 AGTAAAAGGG
*
909161 GCGAAACCACTCGGC
1 GCGAAACCACTCAGC
*
909176 GCGAAACCTCTCAGC
1 GCGAAACCACTCAGC
909191 GCGAA
1 GCGAA
909196 CAAGTGATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.37, G:0.26, T:0.09
Consensus pattern (15 bp):
GCGAAACCACTCAGC
Found at i:913125 original size:19 final size:19
Alignment explanation
Indices: 913097--913136 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
913087 TACATTAGTT
*
913097 AATTCTATTTT-CAAATTCA
1 AATTCAATTTTGCAAA-TCA
913116 AATTCAATTTTGCAAATCA
1 AATTCAATTTTGCAAATCA
913135 AA
1 AA
913137 AGCCTAGCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (19 bp):
AATTCAATTTTGCAAATCA
Found at i:915743 original size:83 final size:83
Alignment explanation
Indices: 915604--915792 Score: 333
Period size: 83 Copynumber: 2.3 Consensus size: 83
915594 ATTAACTGGC
* * * *
915604 AAGATTGGAAATATACAGCTTACTAACACAGAATATACAAGATCTATTCAACAGGTGTGTCGTGT
1 AAGATTGGAAATATACAGCTAACTAACACAGAATATACAAAATATACTCAACAGGTGTGTCGTGT
915669 GCCCATGTGCGCGGGGGG
66 GCCCATGTGCGCGGGGGG
*
915687 AAGATTGGAAATATACAGCTAACTAACACATAATATACAAAATATACTCAACAGGTGTGTCGTGT
1 AAGATTGGAAATATACAGCTAACTAACACAGAATATACAAAATATACTCAACAGGTGTGTCGTGT
915752 GCCCATGTGCGCGGGGGG
66 GCCCATGTGCGCGGGGGG
915770 AAGATTGGAAATATACAGCTAAC
1 AAGATTGGAAATATACAGCTAAC
915793 ACAAATATTT
Statistics
Matches: 101, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 101 1.00
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.23
Consensus pattern (83 bp):
AAGATTGGAAATATACAGCTAACTAACACAGAATATACAAAATATACTCAACAGGTGTGTCGTGT
GCCCATGTGCGCGGGGGG
Found at i:915981 original size:16 final size:16
Alignment explanation
Indices: 915960--916019 Score: 93
Period size: 16 Copynumber: 3.8 Consensus size: 16
915950 GACCCGTCTT
*
915960 GGCCGAGGAGTCCTGG
1 GGCCGAGGTGTCCTGG
915976 GGCCGAGGTGTCCTGG
1 GGCCGAGGTGTCCTGG
* *
915992 GGCCGAGGTGTCGTTG
1 GGCCGAGGTGTCCTGG
916008 GGCCGAGGTGTC
1 GGCCGAGGTGTC
916020 TGACATTCTC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.08, C:0.23, G:0.50, T:0.18
Consensus pattern (16 bp):
GGCCGAGGTGTCCTGG
Found at i:917239 original size:15 final size:15
Alignment explanation
Indices: 917219--917251 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
917209 TGGTTACTTG
917219 TTGTGAAATGTAATA
1 TTGTGAAATGTAATA
917234 TTGTGAAATGTAATA
1 TTGTGAAATGTAATA
917249 TTG
1 TTG
917252 CTTGCACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (15 bp):
TTGTGAAATGTAATA
Found at i:919932 original size:2 final size:2
Alignment explanation
Indices: 919925--919966 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
919915 TCTTATGAAT
919925 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
919967 ATGAGAATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:920529 original size:21 final size:22
Alignment explanation
Indices: 920488--920529 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
920478 TCCAGATGGC
*
920488 CGAGCTTGTCCTCTTGTTGAAG
1 CGAGCTTGTCCTCTTGATGAAG
*
920510 CGAGCTT-TCTTCTTGATGAA
1 CGAGCTTGTCCTCTTGATGAA
920530 TAATTCATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (22 bp):
CGAGCTTGTCCTCTTGATGAAG
Found at i:920963 original size:2 final size:2
Alignment explanation
Indices: 920956--921003 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
920946 TCCTCAAAAT
920956 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
920998 AG AG AG
1 AG AG AG
921004 CTGCATATGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:923282 original size:18 final size:18
Alignment explanation
Indices: 923261--923297 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
923251 CAGCCATTCG
923261 CTCCTCAAACTTCCTCCT
1 CTCCTCAAACTTCCTCCT
**
923279 CTCCTCAGCCTTCCTCCT
1 CTCCTCAAACTTCCTCCT
923297 C
1 C
923298 AACCTCTCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.54, G:0.03, T:0.32
Consensus pattern (18 bp):
CTCCTCAAACTTCCTCCT
Found at i:925089 original size:172 final size:172
Alignment explanation
Indices: 924803--925255 Score: 843
Period size: 172 Copynumber: 2.6 Consensus size: 172
924793 GTATCGAGTC
*
924803 TATCGACCAAGGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
1 TATCGACCAAAGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
924868 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
66 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
924933 GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG
131 GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG
924975 TATCGACCAAAGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
1 TATCGACCAAAGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
* *
925040 TAATGAAAATCCGGCAAAGTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
66 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
*
925105 GAGTCATTATTGTGGTCAAAGTCCCATAACTCCTACAAAAAG
131 GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG
* * *
925147 TATCGACCAATGCTGATTTTCGAACTTGACCAAGATAATAGTGGTATAAACATTTGGTATAAATT
1 TATCGACCAAAGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
925212 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAA
66 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAA
925256 AAAAGCGTGA
Statistics
Matches: 272, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
172 272 1.00
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (172 bp):
TATCGACCAAAGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG
Found at i:925516 original size:27 final size:27
Alignment explanation
Indices: 925486--925724 Score: 203
Period size: 27 Copynumber: 8.9 Consensus size: 27
925476 ATTATAGCTG
925486 CCTCATACCTGAGCCTCTGTTTCACCA
1 CCTCATACCTGAGCCTCTGTTTCACCA
* * *
925513 CCTCATACCAGA-CTCTATATTTCACCA
1 CCTCATACCTGAGC-CTCTGTTTCACCA
*
925540 CCT-AGTACTTGAGCCTCTGTTTCACCA
1 CCTCA-TACCTGAGCCTCTGTTTCACCA
* * * * * *
925567 CCTCATACCAGAACCCCTATTCCTCCA
1 CCTCATACCTGAGCCTCTGTTTCACCA
* ** *
925594 CCTCATACCTGAGCTTCAATTTCAACA
1 CCTCATACCTGAGCCTCTGTTTCACCA
* * *
925621 ACTCAAACCTGAGCCTCTGATTCACCA
1 CCTCATACCTGAGCCTCTGTTTCACCA
* * * * * * *
925648 CCTCATTCCAGAACCCCTATTCCTCCA
1 CCTCATACCTGAGCCTCTGTTTCACCA
* **
925675 CCTCATAACTGAGCCTCTGTTTCACTG
1 CCTCATACCTGAGCCTCTGTTTCACCA
925702 CCTCATACCTGAGCCTCTGTTTC
1 CCTCATACCTGAGCCTCTGTTTC
925725 TCCTGCTCCT
Statistics
Matches: 158, Mismatches: 50, Indels: 8
0.73 0.23 0.04
Matches are distributed among these distances:
26 2 0.01
27 154 0.97
28 2 0.01
ACGTcount: A:0.23, C:0.39, G:0.09, T:0.29
Consensus pattern (27 bp):
CCTCATACCTGAGCCTCTGTTTCACCA
Found at i:925616 original size:81 final size:80
Alignment explanation
Indices: 925510--925724 Score: 263
Period size: 81 Copynumber: 2.6 Consensus size: 80
925500 CTCTGTTTCA
* *
925510 CCACCTCATACCAGA-CTCTATATTTCACCACCT-AGTACTTGAGCCTCTGTTTCACCACCTCAT
1 CCACCTCATACCTGAGCTC-A-ATTTCACCACCTCA-TACCTGAGCCTCTGTTTCACCACCTCAT
925573 ACCAGAACCCCTATTCCT
63 ACCAGAACCCCTATTCCT
* * * * *
925591 CCACCTCATACCTGAGCTTCAATTTCAACAACTCAAACCTGAGCCTCTGATTCACCACCTCATTC
1 CCACCTCATACCTGAGC-TCAATTTCACCACCTCATACCTGAGCCTCTGTTTCACCACCTCATAC
925656 CAGAACCCCTATTCCT
65 CAGAACCCCTATTCCT
* ** **
925672 CCACCTCATAACTGAGCCTCTGTTTCACTGCCTCATACCTGAGCCTCTGTTTC
1 CCACCTCATACCTGAG-CTCAATTTCACCACCTCATACCTGAGCCTCTGTTTC
925725 TCCTGCTCCT
Statistics
Matches: 114, Mismatches: 16, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
81 108 0.95
82 4 0.04
83 2 0.02
ACGTcount: A:0.24, C:0.39, G:0.09, T:0.28
Consensus pattern (80 bp):
CCACCTCATACCTGAGCTCAATTTCACCACCTCATACCTGAGCCTCTGTTTCACCACCTCATACC
AGAACCCCTATTCCT
Found at i:928407 original size:62 final size:62
Alignment explanation
Indices: 928229--928430 Score: 316
Period size: 62 Copynumber: 3.3 Consensus size: 62
928219 CTTTGCCTTC
*
928229 CTCTAAGGTTGTGTCATTAGACTGTGCTATTCTCTAAGGTTGTGTCATTAGACTGTGCTATT
1 CTCTAAGGTTGTGTCATTAGACTGTGCTATTCTCTAAGGTTGTGTCATTAGACTTTGCTATT
*
928291 CTCTAAGGTTGTGTCATTAGACTGTGCTATTCTCTAAGGTTGTATCATTAGACTTTGCTATT
1 CTCTAAGGTTGTGTCATTAGACTGTGCTATTCTCTAAGGTTGTGTCATTAGACTTTGCTATT
* * * * *
928353 CTCTGAGGTTGTGTCATTAGACTGTGCTACTCTCTGAGGTTGTGTCATTAGACTTCGCCTA-C
1 CTCTAAGGTTGTGTCATTAGACTGTGCTATTCTCTAAGGTTGTGTCATTAGACTTTG-CTATT
*
928415 CTCTGAGGTTGTGTCA
1 CTCTAAGGTTGTGTCA
928431 CTTTCTCTCT
Statistics
Matches: 131, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
62 128 0.98
63 3 0.02
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (62 bp):
CTCTAAGGTTGTGTCATTAGACTGTGCTATTCTCTAAGGTTGTGTCATTAGACTTTGCTATT
Found at i:928424 original size:93 final size:93
Alignment explanation
Indices: 928222--928426 Score: 306
Period size: 93 Copynumber: 2.2 Consensus size: 93
928212 TATTTAGCTT
* *
928222 TGCCTTCCTCTAAGGTTGTGTCATTAGACTGTGCTATTCTCTAAGGTTGTGTCATTAGACTGTGC
1 TGCCTACCTCTAAGGTTGTATCATTAGACTGTGCTATTCTCTAAGGTTGTGTCATTAGACTGTGC
*
928287 TATTCTCTAAGGTTGTGTCATTAGACTG
66 TACTCTCTAAGGTTGTGTCATTAGACTG
* * *
928315 TG-CTATTCTCTAAGGTTGTATCATTAGACTTTGCTATTCTCTGAGGTTGTGTCATTAGACTGTG
1 TGCCTA-CCTCTAAGGTTGTATCATTAGACTGTGCTATTCTCTAAGGTTGTGTCATTAGACTGTG
*
928379 CTACTCTCTGAGGTTGTGTCATTAGACT-
65 CTACTCTCTAAGGTTGTGTCATTAGACTG
*
928407 TCGCCTACCTCTGAGGTTGT
1 T-GCCTACCTCTAAGGTTGT
928427 GTCACTTTCT
Statistics
Matches: 100, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
92 3 0.03
93 94 0.94
94 3 0.03
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.41
Consensus pattern (93 bp):
TGCCTACCTCTAAGGTTGTATCATTAGACTGTGCTATTCTCTAAGGTTGTGTCATTAGACTGTGC
TACTCTCTAAGGTTGTGTCATTAGACTG
Found at i:928430 original size:31 final size:31
Alignment explanation
Indices: 928229--928406 Score: 311
Period size: 31 Copynumber: 5.7 Consensus size: 31
928219 CTTTGCCTTC
928229 CTCTAAGGTTGTGTCATTAGACTGTGCTATT
1 CTCTAAGGTTGTGTCATTAGACTGTGCTATT
928260 CTCTAAGGTTGTGTCATTAGACTGTGCTATT
1 CTCTAAGGTTGTGTCATTAGACTGTGCTATT
928291 CTCTAAGGTTGTGTCATTAGACTGTGCTATT
1 CTCTAAGGTTGTGTCATTAGACTGTGCTATT
* *
928322 CTCTAAGGTTGTATCATTAGACTTTGCTATT
1 CTCTAAGGTTGTGTCATTAGACTGTGCTATT
* *
928353 CTCTGAGGTTGTGTCATTAGACTGTGCTACT
1 CTCTAAGGTTGTGTCATTAGACTGTGCTATT
*
928384 CTCTGAGGTTGTGTCATTAGACT
1 CTCTAAGGTTGTGTCATTAGACT
928407 TCGCCTACCT
Statistics
Matches: 141, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 141 1.00
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.42
Consensus pattern (31 bp):
CTCTAAGGTTGTGTCATTAGACTGTGCTATT
Found at i:930839 original size:15 final size:15
Alignment explanation
Indices: 930819--930849 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
930809 ATCAGTATAA
930819 GCAGTGAACTGCATG
1 GCAGTGAACTGCATG
930834 GCAGTGAACTGCATG
1 GCAGTGAACTGCATG
930849 G
1 G
930850 GTTGAAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.35, T:0.19
Consensus pattern (15 bp):
GCAGTGAACTGCATG
Found at i:937713 original size:2 final size:2
Alignment explanation
Indices: 937706--937741 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
937696 ATGCAAACAA
* *
937706 CT CT CT CT CT CT CC CT CT CT CT CT CT CC CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
937742 GTAGATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (2 bp):
CT
Found at i:937725 original size:14 final size:14
Alignment explanation
Indices: 937706--937741 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
937696 ATGCAAACAA
937706 CTCTCTCTCTCTCC
1 CTCTCTCTCTCTCC
937720 CTCTCTCTCTCTCC
1 CTCTCTCTCTCTCC
937734 CTCTCTCT
1 CTCTCTCT
937742 GTAGATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (14 bp):
CTCTCTCTCTCTCC
Found at i:941659 original size:2 final size:2
Alignment explanation
Indices: 941652--941686 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
941642 AATTATAAGT
941652 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
941687 TTTTCTCAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:943718 original size:59 final size:56
Alignment explanation
Indices: 943537--943742 Score: 216
Period size: 56 Copynumber: 3.6 Consensus size: 56
943527 GTTTAACATG
* * * *
943537 TCCAGATGAATACCAAATTTTGTCTTATTTATTCGGTAGGTTACATTTATACAGAT
1 TCCAGATAAATACCGAATTTTGTCTTATTGATTCAGTAGGTTACATTTATACAGAT
* ** * * * *
943593 TCCAAATGGATGCTGAATTTTGTCTTATTGAATT-AGGAGGTTATATTTATACAGAT
1 TCCAGATAAATACCGAATTTTGTCTTATTG-ATTCAGTAGGTTACATTTATACAGAT
* * *
943649 TCCAGATAAATACTGAATTTTGTCTTAATGATTCAGTAGCTTACATTTAGTATACAGAT
1 TCCAGATAAATACCGAATTTTGTCTTATTGATTCAGTAGGTTACA-TT--TATACAGAT
* *
943708 TCCAGATAAATACCGAATTTCGTTTTTATTGATTC
1 TCCAGATAAATACCGAATTTTG-TCTTATTGATTC
943743 TGAATCAGTA
Statistics
Matches: 123, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
55 3 0.02
56 76 0.62
57 5 0.04
59 29 0.24
60 10 0.08
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (56 bp):
TCCAGATAAATACCGAATTTTGTCTTATTGATTCAGTAGGTTACATTTATACAGAT
Found at i:949656 original size:2 final size:2
Alignment explanation
Indices: 949649--949690 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
949639 GTAGTTCATA
* *
949649 TC TC TC TC TC TC TC TC TT TC TC TT TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
949691 AGTATTGTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:957531 original size:20 final size:19
Alignment explanation
Indices: 957402--957544 Score: 83
Period size: 20 Copynumber: 7.3 Consensus size: 19
957392 GTGCAGGGTA
*
957402 GGTTGATCTGACCTCTCTGA
1 GGTTG-TCTGACCTCTCTGT
* * *
957422 GGTTGTTTTAACCTCTTTGT
1 GGTTG-TCTGACCTCTCTGT
*
957442 GGTCTGTCTGACCTTTCTGT
1 GGT-TGTCTGACCTCTCTGT
*
957462 GGTTGATTTGA-C-CTCTGT
1 GGTTG-TCTGACCTCTCTGT
* *
957480 GGTTAGCCTGACCTCTCTCT
1 GGTT-GTCTGACCTCTCTGT
** * *
957500 AACTGGTTTGACCTCTCTGT
1 -GGTTGTCTGACCTCTCTGT
* *
957520 GGTCTGTCTGACTTCTTTGT
1 GGT-TGTCTGACCTCTCTGT
957540 GGTTG
1 GGTTG
957545 ATATGACATC
Statistics
Matches: 90, Mismatches: 26, Indels: 15
0.69 0.20 0.11
Matches are distributed among these distances:
18 12 0.13
19 8 0.09
20 67 0.74
21 3 0.03
ACGTcount: A:0.10, C:0.22, G:0.24, T:0.43
Consensus pattern (19 bp):
GGTTGTCTGACCTCTCTGT
Found at i:962679 original size:18 final size:17
Alignment explanation
Indices: 962652--962686 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
962642 TAAAACTTTA
962652 ACATTATACATATACAT
1 ACATTATACATATACAT
962669 ACATATATACATATACAT
1 ACAT-TATACATATACAT
962687 TTAAGAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (17 bp):
ACATTATACATATACAT
Found at i:979934 original size:2 final size:2
Alignment explanation
Indices: 979879--979926 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
979869 NNNNNNNNNG
* *
979879 GA GA GA AA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
979921 GA GA GA
1 GA GA GA
979927 TGGAGAGATG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
GA
Found at i:984018 original size:2 final size:2
Alignment explanation
Indices: 984011--984038 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
984001 NNNNNNNNNN
984011 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
984039 GGGTTCACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:996021 original size:15 final size:15
Alignment explanation
Indices: 996003--996037 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
995993 CGTATCATAC
996003 GATATTGGATAATAT
1 GATATTGGATAATAT
* *
996018 GATATTGGTTTATAT
1 GATATTGGATAATAT
996033 GATAT
1 GATAT
996038 ATAGAGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (15 bp):
GATATTGGATAATAT
Found at i:1000562 original size:10 final size:10
Alignment explanation
Indices: 1000547--1000573 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1000537 TTAGTTAGAC
1000547 TTCTTTACGT
1 TTCTTTACGT
1000557 TTCTTTACGT
1 TTCTTTACGT
1000567 TTCTTTA
1 TTCTTTA
1000574 GTATTCCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.07, T:0.63
Consensus pattern (10 bp):
TTCTTTACGT
Found at i:1009207 original size:9 final size:9
Alignment explanation
Indices: 1009193--1009227 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1009183 GTCTGCCGTT
1009193 GTCGTTGTC
1 GTCGTTGTC
1009202 GTCGTTGTC
1 GTCGTTGTC
* *
1009211 GTCGTCGGC
1 GTCGTTGTC
1009220 GTCGTTGT
1 GTCGTTGT
1009228 TGTAATCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.37, T:0.40
Consensus pattern (9 bp):
GTCGTTGTC
Found at i:1015152 original size:437 final size:436
Alignment explanation
Indices: 1014335--1015320 Score: 1421
Period size: 437 Copynumber: 2.3 Consensus size: 436
1014325 TGTTTACAAT
*
1014335 ACCTTTCATTTGATATCAAGAAAAAGGGACTGGCCCCTTAAATTAGGGGACCAAAGGGCTCTAAA
1 ACCTTTCATTTGATATCAAGAAAAAGGGGCTGGCCCCTTAAATTAGGGGACCAAAGGGCTCTAAA
* *
1014400 GTGTTTAATCTGTAGCCCTTTACTGAGAGATATTTTGTGAAATGTTATAGAAGCAAATATGTTTA
66 GAGTTTAATCTGTAGCCCTTTACTGAGAGATATTTTGTGAAATGTTATAGAAGCAAATATCTTTA
** * *
1014465 TCCTACAGTTATATATTTAAGCAATGTAACGATTTTTTCATGTGTTACGTAATTAAGGGTTTTTA
131 TCCTACAGTTATATATCCAAGCAATGTAACGATTTTATCATATGTTACGTAATTAAGGGTTTTTA
*
1014530 GGGGCCGAAAATTCAAAATTTCGATCACCCATATCTCAGAAAGGAAAAATATTTTTAAATGCAAA
196 GGGGCCGAAAATCCAAAATTTCGATCACCCATATCTCAGAAAGGAAAAATATTTTTAAATGCAAA
*
1014595 ACCGAAGAAAAGTTGTTCAAAATGATGATCTTAACAATATGCAACCTTCAAAATTTCGTTAAACA
261 ACCGAAGAAAAGTTGTTCAAAAAGATGATCTTAACAATATGCAACCTTCAAAATTTCGTTAAACA
* *
1014660 GCCACTATAAGGAAATAAGGGATCGGCCCCTAAAACATTCTTTCTCATATATCTCCAAATCGGTA
326 GCCACTATAAGGAAATAAGGGATCGGCCCCTAAAACATCCTTTCTCATATATCTCCAAAACGGTA
* * *
1014725 ACGAATTTGTAAACACTTGTT-GAACAAAATTTGTTTAGAATTAAATG
391 ACGAATTTCTAAACACTTGTTCG--CAAAATGTGTTCAGAATTAAATG
* * *
1014772 ACTTTTCATTTGATATCAAGAGAAAGGGGCTGGCCCCTCAAATTAGGGGACCAAAGGGCTCTAAA
1 ACCTTTCATTTGATATCAAGAAAAAGGGGCTGGCCCCTTAAATTAGGGGACCAAAGGGCTCTAAA
* * *
1014837 GAGTTTAATCTGTAGCCCTTTACTGAGAGATATTTTATGAAATGTTATAGTAGCAAATGTCTTTA
66 GAGTTTAATCTGTAGCCCTTTACTGAGAGATATTTTGTGAAATGTTATAGAAGCAAATATCTTTA
* * * * * *
1014902 TCTTGCAGTTATGTATCCAAGCAATTTAATGATTTTATCATATGTTATGTAA-TAAGGGGTTTTT
131 TCCTACAGTTATATATCCAAGCAATGTAACGATTTTATCATATGTTACGTAATTAA-GGGTTTTT
*
1014966 AGGGGCC-AAAAGTCCAAAATTTTGATCACCCATATCTCAGAAAGGAAAAATATTTTTAAATGCA
195 AGGGGCCGAAAA-TCCAAAATTTCGATCACCCATATCTCAGAAAGGAAAAATATTTTTAAATGCA
* * *
1015030 GTAGA-C-AAGAAAAGTTGTTCAAAAAGATGTTCTTAACAATATGTAACCTTCAAAATTTCGTTA
259 --AAACCGAAGAAAAGTTGTTCAAAAAGATGATCTTAACAATATGCAACCTTCAAAATTTCGTTA
* * * * *
1015093 AACAGCCCCTTTAAGGAGATATGGGATCGGCCCCTAAAACCTCCTTTCTCATATATCTCCAAAAC
322 AACAGCCACTATAAGGAAATAAGGGATCGGCCCCTAAAACATCCTTTCTCATATATCTCCAAAAC
* * * *
1015158 GGTAACGAATTTCTGAACATTTGTTCGCGAAATGTGTTCAGAATTAATTG
387 GGTAACGAATTTCTAAACACTTGTTCGCAAAATGTGTTCAGAATTAAATG
* * *
1015208 TCCTTTCATTTAATATCAAGAAAAAGGGGCTGGCCCCTTAAATTAGGGGATCAAAGGGCTCTAAA
1 ACCTTTCATTTGATATCAAGAAAAAGGGGCTGGCCCCTTAAATTAGGGGACCAAAGGGCTCTAAA
* ** *
1015273 -ATCGTTT-ATCTATAGCCCTTT-CATGAGAGCCATTTTGTGAAAGGTTAT
66 GA--GTTTAATCTGTAGCCCTTTAC-TGAGAGATATTTTGTGAAATGTTAT
1015321 TAAAGCTAGA
Statistics
Matches: 491, Mismatches: 50, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
435 2 0.00
436 119 0.24
437 366 0.75
438 2 0.00
439 2 0.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (436 bp):
ACCTTTCATTTGATATCAAGAAAAAGGGGCTGGCCCCTTAAATTAGGGGACCAAAGGGCTCTAAA
GAGTTTAATCTGTAGCCCTTTACTGAGAGATATTTTGTGAAATGTTATAGAAGCAAATATCTTTA
TCCTACAGTTATATATCCAAGCAATGTAACGATTTTATCATATGTTACGTAATTAAGGGTTTTTA
GGGGCCGAAAATCCAAAATTTCGATCACCCATATCTCAGAAAGGAAAAATATTTTTAAATGCAAA
ACCGAAGAAAAGTTGTTCAAAAAGATGATCTTAACAATATGCAACCTTCAAAATTTCGTTAAACA
GCCACTATAAGGAAATAAGGGATCGGCCCCTAAAACATCCTTTCTCATATATCTCCAAAACGGTA
ACGAATTTCTAAACACTTGTTCGCAAAATGTGTTCAGAATTAAATG
Found at i:1015800 original size:2 final size:2
Alignment explanation
Indices: 1015793--1015856 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
1015783 AAACATATGT
1015793 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1015835 GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA
1015857 AAGCGATTGG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1020772 original size:138 final size:134
Alignment explanation
Indices: 1020383--1020790 Score: 482
Period size: 132 Copynumber: 3.0 Consensus size: 134
1020373 CTGACCCCCC
** *
1020383 CCCCCCTAAACAGGAAGTGCCCAAATATTTTGAAAACGGTTGAGATCCATACCCCTAAACTATAT
1 CCCCCCTAAACAGGAAGTGCCCAAATATTTTGAAAACGGTTGAGATCCACCCCCCTAAACCATAT
* * ** * *
1020448 ATATTCTTAATCCTTGTGTTAAGGGGCATCAATTGGTATGCAGGTCAAGGGCCCCAGGGGTAGTC
66 ATATTCATAATCCTTGTGTTAAGGGGCATCAAATGGTATTTAGGTCATGGGCCCCGGGGGTAGTC
1020513 CTGA
131 CTGA
* * * * *
1020517 CCCTCC-AAACAGGAAGTGCCTAAATATTCTGAAAACGGTTGAGAT-CTCCACCCTAAACCATAT
1 CCCCCCTAAACAGGAAGTGCCCAAATATTTTGAAAACGGTTGAGATCCACCCCCCTAAACCATAT
** * **
1020580 ATATT-ATTGTTCTTTGTGTTAAGGGGCATCAAATGGTATGTT-GGTCATATGCCCCGGGGGTAG
66 ATATTCA-TAATCCTTGTGTTAAGGGGCATCAAATGGTAT-TTAGGTCATGGGCCCCGGGGGTAG
**
1020643 TTATGA
129 TCCTGA
* *
1020649 CCCCCCTTAAACAGGAAGTGCCCAAATATTTTGAAAATGGTTGAGATCCCCCCCCCCCCTAAACC
1 CCCCCC-TAAACAGGAAGTGCCCAAATATTTTGAAAACGGTTGAGAT---CCACCCCCCTAAACC
* * * **
1020714 ATATATATTCATAATCCTAGTATTAAGAGGCATCAAATGGTATTTAGGTTGTGGGCCCCGGGGGT
62 ATATATATTCATAATCCTTGTGTTAAGGGGCATCAAATGGTATTTAGGTCATGGGCCCCGGGGGT
1020779 AGTCCTGA
127 AGTCCTGA
1020787 CCCC
1 CCCC
1020791 TGTTGAACAG
Statistics
Matches: 225, Mismatches: 39, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
132 72 0.32
133 37 0.16
134 41 0.18
137 2 0.01
138 72 0.32
139 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (134 bp):
CCCCCCTAAACAGGAAGTGCCCAAATATTTTGAAAACGGTTGAGATCCACCCCCCTAAACCATAT
ATATTCATAATCCTTGTGTTAAGGGGCATCAAATGGTATTTAGGTCATGGGCCCCGGGGGTAGTC
CTGA
Found at i:1020800 original size:138 final size:134
Alignment explanation
Indices: 1020389--1020800 Score: 454
Period size: 138 Copynumber: 3.1 Consensus size: 134
1020379 CCCCCCCCCC
** *
1020389 TAAACAGGAAGTGCCCAAATATTTTGAAAACGGTTGAGATCCATACCCCTAAACTATATATATTC
1 TAAACAGGAAGTGCCCAAATATTTTGAAAACGGTTGAGATCCACCCCCCTAAACCATATATATTC
* * ** * *
1020454 TTAATCCTTGTGTTAAGGGGCATCAATTGGTATGCAGGTCAAGGGCCCCAGGGGTAGTCCTGA-C
66 ATAATCCTTGTGTTAAGGGGCATCAAATGGTATTTAGGTCATGGGCCCCGGGGGTAGTCCTGACC
*
1020518 CCTC
131 CCTT
* * * * *
1020522 CAAACAGGAAGTGCCTAAATATTCTGAAAACGGTTGAGAT-CTCCACCCTAAACCATATATATT-
1 TAAACAGGAAGTGCCCAAATATTTTGAAAACGGTTGAGATCCACCCCCCTAAACCATATATATTC
** * ** **
1020585 ATTGTTCTTTGTGTTAAGGGGCATCAAATGGTATGTT-GGTCATATGCCCCGGGGGTAGTTATGA
66 A-TAATCCTTGTGTTAAGGGGCATCAAATGGTAT-TTAGGTCATGGGCCCCGGGGGTAGTCCTGA
*
1020649 CCCCCCT
129 -CCCCTT
* *
1020656 TAAACAGGAAGTGCCCAAATATTTTGAAAATGGTTGAGATCCCCCCCCCCCCTAAACCATATATA
1 TAAACAGGAAGTGCCCAAATATTTTGAAAACGGTTGAGAT---CCACCCCCCTAAACCATATATA
* * * **
1020721 TTCATAATCCTAGTATTAAGAGGCATCAAATGGTATTTAGGTTGTGGGCCCCGGGGGTAGTCCTG
63 TTCATAATCCTTGTGTTAAGGGGCATCAAATGGTATTTAGGTCATGGGCCCCGGGGGTAGTCCTG
1020786 ACCCCTGT
128 ACCCCT-T
*
1020794 TGAACAG
1 TAAACAG
1020801 ACAATTTCCA
Statistics
Matches: 225, Mismatches: 43, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
132 67 0.30
133 37 0.16
134 39 0.17
137 6 0.03
138 75 0.33
139 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Consensus pattern (134 bp):
TAAACAGGAAGTGCCCAAATATTTTGAAAACGGTTGAGATCCACCCCCCTAAACCATATATATTC
ATAATCCTTGTGTTAAGGGGCATCAAATGGTATTTAGGTCATGGGCCCCGGGGGTAGTCCTGACC
CCTT
Found at i:1029566 original size:13 final size:13
Alignment explanation
Indices: 1029548--1029576 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1029538 AAAAAGCTTT
1029548 TAAATAAATAATG
1 TAAATAAATAATG
1029561 TAAATAAATAATG
1 TAAATAAATAATG
1029574 TAA
1 TAA
1029577 CATTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (13 bp):
TAAATAAATAATG
Found at i:1030211 original size:25 final size:26
Alignment explanation
Indices: 1030164--1030212 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1030154 TCTTCACAAC
1030164 AGGCTACACGTAAATTGTAAAAATTT
1 AGGCTACACGTAAATTGTAAAAATTT
* *
1030190 AGGCTACATGTACA-TGTAAAAAT
1 AGGCTACACGTAAATTGTAAAAAT
1030213 CAACAGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (26 bp):
AGGCTACACGTAAATTGTAAAAATTT
Found at i:1032215 original size:17 final size:18
Alignment explanation
Indices: 1032193--1032233 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1032183 CATATGTATA
*
1032193 TATATGCATTA-ATACAT
1 TATATGCAGTATATACAT
1032210 TATATGC-GTATATACAT
1 TATATGCAGTATATACAT
1032227 TA-ATGCA
1 TATATGCA
1032234 AAGCAGGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (18 bp):
TATATGCAGTATATACAT
Found at i:1033016 original size:18 final size:18
Alignment explanation
Indices: 1032968--1033016 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
1032958 TTTTCTTTTT
*
1032968 TATTGTTGAAAATAAAGA
1 TATTTTTGAAAATAAAGA
1032986 T-TTTCTT-AAAATAAAGA
1 TATTT-TTGAAAATAAAGA
1033003 TATTTTTGAAAATA
1 TATTTTTGAAAATA
1033017 TGTTCCCCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (18 bp):
TATTTTTGAAAATAAAGA
Found at i:1033641 original size:19 final size:19
Alignment explanation
Indices: 1033617--1033667 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
1033607 CGCTTTAAAT
1033617 TTATATCCCATTTGGGCTA
1 TTATATCCCATTTGGGCTA
**
1033636 TTATATCCCCA--ACGGCTA
1 TTATAT-CCCATTTGGGCTA
1033654 TTATATCCCATTTG
1 TTATATCCCATTTG
1033668 AGAGATTGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
17 4 0.16
18 11 0.44
19 6 0.24
20 4 0.16
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (19 bp):
TTATATCCCATTTGGGCTA
Found at i:1039524 original size:33 final size:33
Alignment explanation
Indices: 1039485--1039547 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
1039475 AATATTTGCC
*
1039485 TGCCACCGTATATTTTGAGATTTTTCTGAGCCA
1 TGCCACCGTATATTTCGAGATTTTTCTGAGCCA
1039518 TGCCACCGTATATTTCGAGATTTTTCTGAG
1 TGCCACCGTATATTTCGAGATTTTTCTGAG
1039548 ATGGCTCAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (33 bp):
TGCCACCGTATATTTCGAGATTTTTCTGAGCCA
Found at i:1039607 original size:2 final size:2
Alignment explanation
Indices: 1039600--1039666 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
1039590 GTTTCTCTGC
1039600 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1039642 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1039667 TTTGTACCCT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1042566 original size:2 final size:2
Alignment explanation
Indices: 1042559--1042600 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1042549 TTTCTTCTAT
1042559 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1042601 CCTACCAACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1043332 original size:39 final size:39
Alignment explanation
Indices: 1043249--1043332 Score: 116
Period size: 39 Copynumber: 2.2 Consensus size: 39
1043239 GTCATGAACC
*
1043249 TTGTAACATTTATACAGGACTTGTAGAAGTAAACAAACA
1 TTGTAACATTTATACAGGACTTGCAGAAGTAAACAAACA
* * *
1043288 ATGTAACATTTATAGAGGACTTGCAGAATTAAACATAA-A
1 TTGTAACATTTATACAGGACTTGCAGAAGTAAACA-AACA
1043327 TTGTAA
1 TTGTAA
1043333 GTTTTTATCA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 37 0.95
40 2 0.05
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (39 bp):
TTGTAACATTTATACAGGACTTGCAGAAGTAAACAAACA
Found at i:1045315 original size:11 final size:11
Alignment explanation
Indices: 1045308--1045338 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1045298 TTTAGAGTGG
1045308 ACCCAGAGTAA
1 ACCCAGAGTAA
*
1045319 ACCCAAAGTAA
1 ACCCAGAGTAA
1045330 ACCCAGAGT
1 ACCCAGAGT
1045339 GGACACAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.45, C:0.29, G:0.16, T:0.10
Consensus pattern (11 bp):
ACCCAGAGTAA
Found at i:1050775 original size:21 final size:20
Alignment explanation
Indices: 1050741--1051003 Score: 148
Period size: 22 Copynumber: 12.2 Consensus size: 20
1050731 AATTATTTTT
*
1050741 ATCTCGTAATTACGAGAAAA
1 ATCTCGTTATTACGAGAAAA
* *
1050761 AGTCACGTTATTACGAGATAATT
1 A-TCTCGTTATTACGAGA-AA-A
1050784 ATCTCGTTATTACGAGAAAAA
1 ATCTCGTTATTACGAG-AAAA
* **
1050805 ATCTCGTTATCACGAGTTAATT
1 ATCTCGTTATTACGAG--AAAA
*
1050827 ATCTCGTTATTACGAGTTAAAT
1 ATCTCGTTATTACGAG--AAAA
*
1050849 ATCTCGTAATTACGAGAAAA
1 ATCTCGTTATTACGAGAAAA
* * ** **
1050869 TATCTCGTAATAACGACTTTATT
1 -ATCTCGTTATTACGA--GAAAA
**
1050892 ATCTCGTTATTACGAGTTAATT
1 ATCTCGTTATTACGAG--AAAA
* *
1050914 ATCTCGTTATTACGAGTTAAG
1 ATCTCGTTATTACGAG-AAAA
* *
1050935 ATCTCGTAATTACGAGTAAATT
1 ATCTCGTTATTACGAG-AAA-A
* **
1050957 ATCTCGTTATTATGAGTTAATT
1 ATCTCGTTATTACGAG--AAAA
1050979 ATCTCGTTATTACGAGAAAA
1 ATCTCGTTATTACGAGAAAA
1050999 GATCT
1 -ATCT
1051004 TTTTTAAAAT
Statistics
Matches: 196, Mismatches: 34, Indels: 25
0.77 0.13 0.10
Matches are distributed among these distances:
20 6 0.03
21 67 0.34
22 117 0.60
23 6 0.03
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (20 bp):
ATCTCGTTATTACGAGAAAA
Found at i:1050794 original size:22 final size:22
Alignment explanation
Indices: 1050766--1050994 Score: 284
Period size: 22 Copynumber: 10.5 Consensus size: 22
1050756 GAAAAAGTCA
*
1050766 CGTTATTACGAGATAATTATCT
1 CGTTATTACGAGTTAATTATCT
* **
1050788 CGTTATTACGAG-AAAAAATCT
1 CGTTATTACGAGTTAATTATCT
*
1050809 CGTTATCACGAGTTAATTATCT
1 CGTTATTACGAGTTAATTATCT
*
1050831 CGTTATTACGAGTTAAATATCT
1 CGTTATTACGAGTTAATTATCT
* * *
1050853 CGTAATTACGAG-AAAATATCT
1 CGTTATTACGAGTTAATTATCT
* * * *
1050874 CGTAATAACGACTTTATTATCT
1 CGTTATTACGAGTTAATTATCT
1050896 CGTTATTACGAGTTAATTATCT
1 CGTTATTACGAGTTAATTATCT
*
1050918 CGTTATTACGAGTTAA-GATCT
1 CGTTATTACGAGTTAATTATCT
* *
1050939 CGTAATTACGAGTAAATTATCT
1 CGTTATTACGAGTTAATTATCT
*
1050961 CGTTATTATGAGTTAATTATCT
1 CGTTATTACGAGTTAATTATCT
1050983 CGTTATTACGAG
1 CGTTATTACGAG
1050995 AAAAGATCTT
Statistics
Matches: 176, Mismatches: 28, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
21 53 0.30
22 123 0.70
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (22 bp):
CGTTATTACGAGTTAATTATCT
Found at i:1050800 original size:43 final size:42
Alignment explanation
Indices: 1050739--1050995 Score: 230
Period size: 43 Copynumber: 5.9 Consensus size: 42
1050729 AAAATTATTT
* *
1050739 TTATCTCGTAATTACGAGAAAAAGTCACGTTATTACGAGATAA
1 TTATCTCGTTATTACGAGAAAAA-TCTCGTTATTACGAGATAA
* *
1050782 TTATCTCGTTATTACGAGAAAAAATCTCGTTATCACGAGTTAA
1 TTATCTCGTTATTACGAG-AAAAATCTCGTTATTACGAGATAA
* *
1050825 TTATCTCGTTATTACGAGTTAAATATCTCGTAATTACGAGA-AA
1 TTATCTCGTTATTACGAG--AAAAATCTCGTTATTACGAGATAA
* * * ** ** *
1050868 ATATCTCGTAATAACGACTTTATTATCTCGTTATTACGAGTTAA
1 TTATCTCGTTATTACGA--GAAAAATCTCGTTATTACGAGATAA
* * *
1050912 TTATCTCGTTATTACGAGTTAAGATCTCGTAATTACGAG-TAAA
1 TTATCTCGTTATTACGAG-AAAAATCTCGTTATTACGAGAT-AA
* **
1050955 TTATCTCGTTATTATGAGTTAATTATCTCGTTATTACGAGA
1 TTATCTCGTTATTACGAG--AAAAATCTCGTTATTACGAGA
1050996 AAAGATCTTT
Statistics
Matches: 176, Mismatches: 29, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
42 1 0.01
43 120 0.68
44 55 0.31
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (42 bp):
TTATCTCGTTATTACGAGAAAAATCTCGTTATTACGAGATAA
Found at i:1050842 original size:65 final size:65
Alignment explanation
Indices: 1050766--1051003 Score: 350
Period size: 65 Copynumber: 3.7 Consensus size: 65
1050756 GAAAAAGTCA
* * * *
1050766 CGTTATTACGAGATAATTATCTCGTTATTACGAGAAAAAATCTCGTTATCACGAGTTAATTATCT
1 CGTTATTACGAGTTAATTATCTCGTTATTACGAGAAAAGATCTCGTAATAACGAGTTAATTATCT
* * * * *
1050831 CGTTATTACGAGTTAAATATCTCGTAATTACGAGAAAATATCTCGTAATAACGACTTTATTATCT
1 CGTTATTACGAGTTAATTATCTCGTTATTACGAGAAAAGATCTCGTAATAACGAGTTAATTATCT
** * *
1050896 CGTTATTACGAGTTAATTATCTCGTTATTACGAGTTAAGATCTCGTAATTACGAGTAAATTATCT
1 CGTTATTACGAGTTAATTATCTCGTTATTACGAGAAAAGATCTCGTAATAACGAGTTAATTATCT
*
1050961 CGTTATTATGAGTTAATTATCTCGTTATTACGAGAAAAGATCT
1 CGTTATTACGAGTTAATTATCTCGTTATTACGAGAAAAGATCT
1051004 TTTTTAAAAT
Statistics
Matches: 153, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 153 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (65 bp):
CGTTATTACGAGTTAATTATCTCGTTATTACGAGAAAAGATCTCGTAATAACGAGTTAATTATCT
Found at i:1050908 original size:87 final size:87
Alignment explanation
Indices: 1050805--1050994 Score: 292
Period size: 87 Copynumber: 2.2 Consensus size: 87
1050795 ACGAGAAAAA
* *
1050805 ATCTCGTTATCACGAGTTAATTATCTCGTTATTACGAGTTAAATATCTCGTAATTACGAG-AAAA
1 ATCTCGTTATTACGAGTTAATTATCTCGTTATTACGAGTT-AAGATCTCGTAATTACGAGTAAAA
*
1050869 TATCTCGTAATAACGACTTTATT
65 TATCTCGTAATAACGACTTAATT
*
1050892 ATCTCGTTATTACGAGTTAATTATCTCGTTATTACGAGTTAAGATCTCGTAATTACGAGTAAATT
1 ATCTCGTTATTACGAGTTAATTATCTCGTTATTACGAGTTAAGATCTCGTAATTACGAGTAAAAT
* * * *
1050957 ATCTCGTTATTATGAGTTAATT
66 ATCTCGTAATAACGACTTAATT
1050979 ATCTCGTTATTACGAG
1 ATCTCGTTATTACGAG
1050995 AAAAGATCTT
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
86 18 0.19
87 76 0.81
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (87 bp):
ATCTCGTTATTACGAGTTAATTATCTCGTTATTACGAGTTAAGATCTCGTAATTACGAGTAAAAT
ATCTCGTAATAACGACTTAATT
Found at i:1051658 original size:22 final size:22
Alignment explanation
Indices: 1051633--1051710 Score: 59
Period size: 22 Copynumber: 3.5 Consensus size: 22
1051623 TAAATCTTTT
1051633 CTCGTAATAACGAGATAATTAA
1 CTCGTAATAACGAGATAATTAA
* * * **
1051655 CTCGTTATTACGAGAT-CTTTT
1 CTCGTAATAACGAGATAATTAA
*
1051676 CTCGTATTAATAACAAGATAATTAA
1 CTCG---TAATAACGAGATAATTAA
*
1051701 CTCTTAATAA
1 CTCGTAATAA
1051711 TTAGATCTTT
Statistics
Matches: 40, Mismatches: 12, Indels: 8
0.67 0.20 0.13
Matches are distributed among these distances:
21 6 0.15
22 20 0.50
24 9 0.22
25 5 0.12
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (22 bp):
CTCGTAATAACGAGATAATTAA
Found at i:1051696 original size:46 final size:46
Alignment explanation
Indices: 1051626--1051731 Score: 130
Period size: 46 Copynumber: 2.3 Consensus size: 46
1051616 TTTTATATAA
* *
1051626 ATCTTTTCTCG---TAATAACGAGATAATTAACTCGTT-ATTACGAG
1 ATCTTTTCTCGTATTAATAACAAGATAATTAACTC-TTAATAACGAG
**
1051669 ATCTTTTCTCGTATTAATAACAAGATAATTAACTCTTAATAATTAG
1 ATCTTTTCTCGTATTAATAACAAGATAATTAACTCTTAATAACGAG
1051715 ATCTTTTCTCGTTATTA
1 ATCTTTTCTCG-TATTA
1051732 CGAGATCTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
43 11 0.20
45 2 0.04
46 36 0.67
47 5 0.09
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.42
Consensus pattern (46 bp):
ATCTTTTCTCGTATTAATAACAAGATAATTAACTCTTAATAACGAG
Found at i:1051737 original size:21 final size:21
Alignment explanation
Indices: 1051713--1051758 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1051703 CTTAATAATT
* *
1051713 AGATCTTTTCTCGTTATTACG
1 AGATCTTTTCTCGTAATTACA
1051734 AGATCTTTTCTCGTAATTACA
1 AGATCTTTTCTCGTAATTACA
1051755 AGAT
1 AGAT
1051759 AAAAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.43
Consensus pattern (21 bp):
AGATCTTTTCTCGTAATTACA
Found at i:1056107 original size:163 final size:165
Alignment explanation
Indices: 1055778--1056177 Score: 470
Period size: 163 Copynumber: 2.4 Consensus size: 165
1055768 GGTGTGTGTC
* * * *
1055778 TTTAAAAATATTCTTCTCAATAACCACAGCACCAGAAATGCCAATATTTAAACAAAAGCTTGATT
1 TTTAAGAATA-TCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTAAACAAAAGCTTGTTT
* * * * * *
1055843 ATACATTGAAGATTCTAAACTGTAAAAATTGTGATCCTCGGTCCAAAACTGGGGCCCCAGGCGGG
65 ATATAGTGAAGATTCTAAACTGTAAAAATCGAGACCCTCGGACCAAAACTGGGGCCCCAGGCGGG
* * *
1055908 GTTCAAAGTTTAACATAGAAATACGTAGCTAAAATG
130 GCTCAAAGTTTAACATAGAAATACATAGATAAAATG
** * *
1055944 TTTAA-AA-ATCTTCTCAAGAACCACTGCACCAGTGATGCCAAAATTTAAACAAAAGCTTGTTTT
1 TTTAAGAATATCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTAAACAAAAGCTTGTTTA
* * *
1056007 TATAGTGAAGATTCTAAATTGTAAAAATCGAGACCCTCGGACCAAAACTGTGGCCCTAGGCGGGG
66 TATAGTGAAGATTCTAAACTGTAAAAATCGAGACCCTCGGACCAAAACTGGGGCCCCAGGCGGGG
* * **
1056072 CTCAAATTTTAATATAGAGTTACATA-ATAAAAATG
131 CTCAAAGTTTAACATAGAAATACATAGAT-AAAATG
* * *
1056107 TTTAAGAATTTTCTTCTTCATAG--CCATTGCACCAGAAATGCCAATATTTACAC-AAAGCTTGT
1 TTTAAGAA-TATCTTC-TCA-AGAACCACTGCACCAGAAATGCCAATATTTAAACAAAAGCTTGT
1056169 TTATATAGT
63 TTATATAGT
1056178 AAAAAAAAAA
Statistics
Matches: 198, Mismatches: 30, Indels: 13
0.82 0.12 0.05
Matches are distributed among these distances:
162 1 0.01
163 135 0.68
164 3 0.02
165 19 0.10
166 35 0.18
167 3 0.02
168 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.29
Consensus pattern (165 bp):
TTTAAGAATATCTTCTCAAGAACCACTGCACCAGAAATGCCAATATTTAAACAAAAGCTTGTTTA
TATAGTGAAGATTCTAAACTGTAAAAATCGAGACCCTCGGACCAAAACTGGGGCCCCAGGCGGGG
CTCAAAGTTTAACATAGAAATACATAGATAAAATG
Found at i:1056497 original size:13 final size:13
Alignment explanation
Indices: 1056479--1056503 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1056469 GAACTCTGGG
1056479 AATCAGTTCTCAA
1 AATCAGTTCTCAA
1056492 AATCAGTTCTCA
1 AATCAGTTCTCA
1056504 CAATACGTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (13 bp):
AATCAGTTCTCAA
Found at i:1062196 original size:12 final size:12
Alignment explanation
Indices: 1062181--1062294 Score: 71
Period size: 12 Copynumber: 9.6 Consensus size: 12
1062171 AATCCCCCCC
*
1062181 AAAAAACCAACA
1 AAAAAACAAACA
1062193 AAAAAACAAACA
1 AAAAAACAAACA
*
1062205 AACAAACAAACA
1 AAAAAACAAACA
*
1062217 AACCGAAAACAAATA
1 AA---AAAACAAACA
*
1062232 TTTAAAAA-AAAC-
1 --AAAAAACAAACA
*
1062244 AAGAAA-AAAC-
1 AAAAAACAAACA
1062254 AAAAAACAAA-A
1 AAAAAACAAACA
1062265 AAAACAAC-AACA
1 AAAA-AACAAACA
*
1062277 AAAAAACAGA-A
1 AAAAAACAAACA
1062288 AAAAAAC
1 AAAAAAC
1062295 CCCAAATCGG
Statistics
Matches: 82, Mismatches: 10, Indels: 21
0.73 0.09 0.19
Matches are distributed among these distances:
10 13 0.16
11 20 0.24
12 33 0.40
13 3 0.04
14 4 0.05
15 8 0.10
17 1 0.01
ACGTcount: A:0.77, C:0.17, G:0.03, T:0.04
Consensus pattern (12 bp):
AAAAAACAAACA
Found at i:1062200 original size:8 final size:8
Alignment explanation
Indices: 1062189--1062291 Score: 59
Period size: 8 Copynumber: 12.2 Consensus size: 8
1062179 CCAAAAAACC
1062189 AACAAAAA
1 AACAAAAA
*
1062197 AACAAACA
1 AACAAAAA
*
1062205 AACAAACA
1 AACAAAAA
1062213 AACAAACCGAA
1 AACAAA---AA
*
1062224 AACAAATATT
1 AACAAA-A-A
*
1062234 TA-AAAAA
1 AACAAAAA
1062241 AACAAGAAA
1 AACAA-AAA
1062250 AA-ACAAAA
1 AACA-AAAA
1062258 AACAAAAA
1 AACAAAAA
* *
1062266 AA-ACAAC
1 AACAAAAA
1062273 AACAAAAA
1 AACAAAAA
1062281 AACAGAAAA
1 AACA-AAAA
1062290 AA
1 AA
1062292 AACCCCAAAT
Statistics
Matches: 74, Mismatches: 11, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
7 6 0.08
8 43 0.58
9 17 0.23
10 1 0.01
11 7 0.09
ACGTcount: A:0.78, C:0.16, G:0.03, T:0.04
Consensus pattern (8 bp):
AACAAAAA
Found at i:1062205 original size:4 final size:4
Alignment explanation
Indices: 1062180--1062219 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
1062170 AAATCCCCCC
* *
1062180 CAAA -AAA CCAA CAAA AAAA CAAA CAAA CAAA CAAA CAAA C
1 CAAA CAAA CAAA CAAA CAAA CAAA CAAA CAAA CAAA CAAA C
1062220 CGAAAACAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.75, C:0.25, G:0.00, T:0.00
Consensus pattern (4 bp):
CAAA
Found at i:1062257 original size:15 final size:14
Alignment explanation
Indices: 1062235--1062282 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 14
1062225 ACAAATATTT
*
1062235 AAAAAAAACAAGA-
1 AAAAAAAACAAAAC
*
1062248 AAAAACAA-AAAAC
1 AAAAAAAACAAAAC
1062261 AAAAAAAACAACAAC
1 AAAAAAAACAA-AAC
1062276 AAAAAAA
1 AAAAAAA
1062283 CAGAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 3 0.10
13 14 0.48
14 2 0.07
15 10 0.34
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.00
Consensus pattern (14 bp):
AAAAAAAACAAAAC
Found at i:1062257 original size:17 final size:16
Alignment explanation
Indices: 1062237--1062282 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
1062227 AAATATTTAA
1062237 AAAAAACAAGAAAAAAC
1 AAAAAACAA-AAAAAAC
1062254 AAAAAACAAAAAAAAC
1 AAAAAACAAAAAAAAC
*
1062270 -AACAACAAAAAAA
1 AAAAAACAAAAAAA
1062283 CAGAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 12 0.43
16 7 0.25
17 9 0.32
ACGTcount: A:0.85, C:0.13, G:0.02, T:0.00
Consensus pattern (16 bp):
AAAAAACAAAAAAAAC
Found at i:1062264 original size:26 final size:25
Alignment explanation
Indices: 1062235--1062294 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 25
1062225 ACAAATATTT
*
1062235 AAAAAAAACAAGAAAAAACAAAAAAC
1 AAAAAAAACAACAAAAAA-AAAAAAC
* * *
1062261 AAAAAAAACAACAACAAAAAAACAG
1 AAAAAAAACAACAAAAAAAAAAAAC
1062286 AAAAAAAAC
1 AAAAAAAAC
1062295 CCCAAATCGG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 14 0.47
26 16 0.53
ACGTcount: A:0.83, C:0.13, G:0.03, T:0.00
Consensus pattern (25 bp):
AAAAAAAACAACAAAAAAAAAAAAC
Found at i:1067526 original size:2 final size:2
Alignment explanation
Indices: 1067519--1067577 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1067509 ACATACAAAT
1067519 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1067561 AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG A
1067578 TGTGGGTTTG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1073299 original size:2 final size:2
Alignment explanation
Indices: 1073292--1073333 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1073282 AAGGTTTTAC
* *
1073292 TA TA TA TA TA AA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1073334 AAGAACAACC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1080566 original size:4 final size:4
Alignment explanation
Indices: 1080557--1080634 Score: 59
Period size: 4 Copynumber: 17.8 Consensus size: 4
1080547 TCGTATCATA
* *
1080557 AAAC AAAC AAAC AAAC AAAC ATATAC ACA- AAAC AAAAC AAAAC AAGC
1 AAAC AAAC AAAC AAAC AAAC A-A-AC AAAC AAAC -AAAC -AAAC AAAC
1080604 AAAC GAAAC GAAAC AAAAC AAAAC AAAC AAA
1 AAAC -AAAC -AAAC -AAAC -AAAC AAAC AAA
1080635 AACAACCCCT
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
3 2 0.03
4 31 0.48
5 28 0.44
6 3 0.05
ACGTcount: A:0.72, C:0.22, G:0.04, T:0.03
Consensus pattern (4 bp):
AAAC
Found at i:1080593 original size:5 final size:5
Alignment explanation
Indices: 1080583--1080635 Score: 58
Period size: 5 Copynumber: 11.2 Consensus size: 5
1080573 AAACATATAC
* * *
1080583 ACAAA ACAAA ACAAA AC-AA GC-AA ACGAA ACGAA ACAAA ACAAA AC-AA
1 ACAAA ACAAA ACAAA ACAAA ACAAA ACAAA ACAAA ACAAA ACAAA ACAAA
1080630 ACAAA A
1 ACAAA A
1080636 ACAACCCCTG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
4 10 0.23
5 33 0.77
ACGTcount: A:0.74, C:0.21, G:0.06, T:0.00
Consensus pattern (5 bp):
ACAAA
Found at i:1080598 original size:10 final size:9
Alignment explanation
Indices: 1080556--1080635 Score: 65
Period size: 10 Copynumber: 8.4 Consensus size: 9
1080546 GTCGTATCAT
1080556 AAAACAAAC
1 AAAACAAAC
1080565 -AAACAAAC
1 AAAACAAAC
*
1080573 AAACATATACAC
1 AAA-ACA-A-AC
1080585 AAAACAAAAC
1 AAAAC-AAAC
*
1080595 AAAACAAGC
1 AAAACAAAC
1080604 -AAACGAAAC
1 AAAAC-AAAC
*
1080613 GAAACAAAAC
1 AAAAC-AAAC
1080623 AAAACAAAC
1 AAAACAAAC
1080632 AAAA
1 AAAA
1080636 ACAACCCCTG
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
8 12 0.21
9 16 0.28
10 21 0.36
11 3 0.05
12 6 0.10
ACGTcount: A:0.72, C:0.21, G:0.04, T:0.03
Consensus pattern (9 bp):
AAAACAAAC
Found at i:1080620 original size:14 final size:13
Alignment explanation
Indices: 1080557--1080634 Score: 68
Period size: 13 Copynumber: 5.5 Consensus size: 13
1080547 TCGTATCATA
1080557 AAACAAAC-AAAC
1 AAACAAACAAAAC
1080569 AAACAAACATATACAC
1 AAACAAACA-A-A-AC
1080585 AAAACAAAACAAAAC
1 -AAAC-AAACAAAAC
* *
1080600 AAGCAAACGAAAC
1 AAACAAACAAAAC
1080613 GAAACAAAACAAAAC
1 -AAAC-AAACAAAAC
1080628 AAACAAA
1 AAACAAA
1080635 AACAACCCCT
Statistics
Matches: 54, Mismatches: 4, Indels: 15
0.74 0.05 0.21
Matches are distributed among these distances:
12 8 0.15
13 11 0.20
14 11 0.20
15 11 0.20
16 3 0.06
17 5 0.09
18 5 0.09
ACGTcount: A:0.72, C:0.22, G:0.04, T:0.03
Consensus pattern (13 bp):
AAACAAACAAAAC
Found at i:1080675 original size:1 final size:1
Alignment explanation
Indices: 1080669--1080694 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1080659 AAACCCCTAA
1080669 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
1080695 GAAAATACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1091708 original size:12 final size:12
Alignment explanation
Indices: 1091691--1091734 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
1091681 TAAATTATTG
1091691 ATATTATTTTTT
1 ATATTATTTTTT
* *
1091703 ATATTACTTTAT
1 ATATTATTTTTT
1091715 ATATTATTTATTT
1 ATATTATTT-TTT
1091728 A-ATTATT
1 ATATTATT
1091735 AAATACTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 24 0.89
13 3 0.11
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (12 bp):
ATATTATTTTTT
Found at i:1098607 original size:37 final size:37
Alignment explanation
Indices: 1098560--1098642 Score: 148
Period size: 37 Copynumber: 2.2 Consensus size: 37
1098550 AAAAAGATAC
* *
1098560 CAATCTTCTGTACCCTTGTTAACATCAACACTGTCAT
1 CAATGTTCTGTACCCTTGTTAACATCAACACCGTCAT
1098597 CAATGTTCTGTACCCTTGTTAACATCAACACCGTCAT
1 CAATGTTCTGTACCCTTGTTAACATCAACACCGTCAT
1098634 CAATGTTCT
1 CAATGTTCT
1098643 AAGAAGACCT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.35
Consensus pattern (37 bp):
CAATGTTCTGTACCCTTGTTAACATCAACACCGTCAT
Found at i:1112157 original size:2 final size:2
Alignment explanation
Indices: 1112150--1112193 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1112140 TTTGTTTCAT
1112150 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1112192 TC
1 TC
1112194 CTGACAATAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1114640 original size:15 final size:14
Alignment explanation
Indices: 1114617--1114656 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 14
1114607 GTTATTTGAT
1114617 ACAAAAAAAAGCAAAA
1 ACAAAAAAAA--AAAA
1114633 ACAAAAAACAAAAAA
1 ACAAAAAA-AAAAAA
1114648 ACAAAAAAA
1 ACAAAAAAA
1114657 CATAGTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 1 0.04
15 12 0.52
16 8 0.35
17 2 0.09
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (14 bp):
ACAAAAAAAAAAAA
Found at i:1114647 original size:9 final size:8
Alignment explanation
Indices: 1114629--1114658 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1114619 AAAAAAAAGC
1114629 AAAAAC-A
1 AAAAACAA
1114636 AAAAACAA
1 AAAAACAA
1114644 AAAAACAA
1 AAAAACAA
1114652 AAAAACA
1 AAAAACA
1114659 TAGTATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAACAA
Found at i:1115202 original size:11 final size:11
Alignment explanation
Indices: 1115186--1115210 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1115176 CTTTCAAATT
1115186 ACATTAAGGCA
1 ACATTAAGGCA
1115197 ACATTAAGGCA
1 ACATTAAGGCA
1115208 ACA
1 ACA
1115211 ACATAATCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.20, G:0.16, T:0.16
Consensus pattern (11 bp):
ACATTAAGGCA
Found at i:1115624 original size:5 final size:5
Alignment explanation
Indices: 1115614--1115661 Score: 68
Period size: 5 Copynumber: 10.4 Consensus size: 5
1115604 ATGTCTTCAG
1115614 TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT T-TTT T-TTT T-TTT T-TTT
1 TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT TGTTT
1115660 TG
1 TG
1115662 GGGGGGGGGG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 16 0.38
5 26 0.62
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (5 bp):
TGTTT
Found at i:1116004 original size:2 final size:2
Alignment explanation
Indices: 1115997--1116037 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1115987 ACTCCATGTA
1115997 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1116038 GTAGGTAAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1116651 original size:2 final size:2
Alignment explanation
Indices: 1116644--1116706 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
1116634 TTGTACATAT
*
1116644 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GT GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1116686 GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA G
1116707 NNNNNNNNNN
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.48, C:0.00, G:0.51, T:0.02
Consensus pattern (2 bp):
GA
Found at i:1130204 original size:57 final size:56
Alignment explanation
Indices: 1130116--1130232 Score: 216
Period size: 57 Copynumber: 2.1 Consensus size: 56
1130106 TGCTCTAGTT
1130116 ATTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTCTTTTTC
1 ATTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTT-TTTTTC
*
1130173 ATTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTTTTTTT
1 ATTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTTTTTTC
1130229 ATTA
1 ATTA
1130233 TTATTATTCT
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 9 0.15
57 50 0.85
ACGTcount: A:0.17, C:0.19, G:0.15, T:0.49
Consensus pattern (56 bp):
ATTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTATTGTTTTTTTTC
Found at i:1130903 original size:31 final size:30
Alignment explanation
Indices: 1130844--1130908 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
1130834 TCGGAAATGT
* *
1130844 TTTTGTTAAGTCGTACTTAAAATCATTCGTA
1 TTTTGTTAAGTCGTACTCAAAATAATTCG-A
*
1130875 TTTTGTTAAGTCGTAC-CAGGAATAATTCGA
1 TTTTGTTAAGTCGTACTCA-AAATAATTCGA
1130905 TTTT
1 TTTT
1130909 TTCATCTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 6 0.20
31 24 0.80
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (30 bp):
TTTTGTTAAGTCGTACTCAAAATAATTCGA
Found at i:1131681 original size:31 final size:32
Alignment explanation
Indices: 1131611--1131689 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
1131601 TCGGATTTTT
* * *
1131611 TTTTGTTAAGTTGTTCTTAAAATCAAGAAGGT
1 TTTTGTTAAGTCGTACTTAAAATCAAGAAGGA
***
1131643 TTTTGTTAAGTCGTACTTAAAATC-ATTCGGA
1 TTTTGTTAAGTCGTACTTAAAATCAAGAAGGA
1131674 TTTTGTTAAGTCGTAC
1 TTTTGTTAAGTCGTAC
1131690 CAGGAATAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
31 19 0.46
32 22 0.54
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.44
Consensus pattern (32 bp):
TTTTGTTAAGTCGTACTTAAAATCAAGAAGGA
Found at i:1131702 original size:31 final size:30
Alignment explanation
Indices: 1131643--1131707 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
1131633 TCAAGAAGGT
* *
1131643 TTTTGTTAAGTCGTACTTAAAATCATTCGGA
1 TTTTGTTAAGTCGTACTCAAAATAATTC-GA
*
1131674 TTTTGTTAAGTCGTAC-CAGGAATAATTCGA
1 TTTTGTTAAGTCGTACTCA-AAATAATTCGA
1131704 TTTT
1 TTTT
1131708 TTCATCTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 7 0.23
31 23 0.77
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (30 bp):
TTTTGTTAAGTCGTACTCAAAATAATTCGA
Found at i:1132484 original size:31 final size:32
Alignment explanation
Indices: 1132414--1132492 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
1132404 TTCGGATTTT
* * *
1132414 TTTTGTTAAGTTGTTCTTAAAATCAAGAAGGT
1 TTTTGTTAAGTCGTACTTAAAATCAAGAAGGA
***
1132446 TTTTGTTAAGTCGTACTTAAAATC-ATTCGGA
1 TTTTGTTAAGTCGTACTTAAAATCAAGAAGGA
1132477 TTTTGTTAAGTCGTAC
1 TTTTGTTAAGTCGTAC
1132493 CAGGAATTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
31 19 0.46
32 22 0.54
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.44
Consensus pattern (32 bp):
TTTTGTTAAGTCGTACTTAAAATCAAGAAGGA
Found at i:1132505 original size:31 final size:30
Alignment explanation
Indices: 1132446--1132510 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
1132436 TCAAGAAGGT
*
1132446 TTTTGTTAAGTCGTACTTAAAATCATTCGGA
1 TTTTGTTAAGTCGTACTCAAAATCATTC-GA
* *
1132477 TTTTGTTAAGTCGTAC-CAGGAATTATTCGA
1 TTTTGTTAAGTCGTACTCA-AAATCATTCGA
1132507 TTTT
1 TTTT
1132511 TTCATCTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 7 0.23
31 23 0.77
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (30 bp):
TTTTGTTAAGTCGTACTCAAAATCATTCGA
Found at i:1135152 original size:340 final size:333
Alignment explanation
Indices: 1134419--1135159 Score: 843
Period size: 340 Copynumber: 2.2 Consensus size: 333
1134409 GGCTCATGCC
* * * * *
1134419 TTTCACAACTTTGAATCTACACTACCTCAGGATGCTTCCACTCAAGTTACAGCTTTCCTGGCTTA
1 TTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAACTTTCAGCTTTCCTGGCTAA
* * * *
1134484 TTAGTTTCTGAGTAGAAGGTTTTTAAAGATTTACTCTATATATTCCTATATTAAACTTTGACCCC
66 TTAGTTTCTGAGTAGAAGATCTATAAAGATTTACTCTATATATTCCTACATTAAACTTTGACCCC
** * *
1134549 CCTCCCCCATTGTGGCCCCACTCAACCTCTGGGGGTCATGATTTTCACAACTTTAAATTTACACT
131 CCT-CCCCATTGTGGCCCCACTCAACCTCCAGGGGTCATGATTTTCACAACTTTAAATTAACACC
* **
1134614 ATCTGAGGCTGCTCCCACACAAATTTCAGCTTTCCTGACTGAAAAGCTCCGAGAAGATTTTTAAA
195 ACCTGAGAATGCTCCCACACAAATTTCAGCTTTCCTGACTGAAAAGCTCCGAGAAGATTTTTAAA
* * *
1134679 GATTTACTCTATATATACCTTAGTAAAACTTCAAACCCCCATTGTTGCCCCATCCTACCCCCGGG
260 GATTTACTCTATATATACCTTAGTAAAACGTCAAACCCCCATTGTGGCCCCATCCTACCCCCGAG
1134744 GGTCAATAT
325 GGTCAATAT
* * * * *
1134753 TTTCACAGCATTGAATTTACACTACCTGAGGATGCTTGCGCAC-ACGTTTCAGCTTTCCTGGCTA
1 TTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAC-TTTCAGCTTTCCTGGCTA
* * * *
1134817 ATTAGTTTTTGAG-AGGAAGAATAACTATAAATATATATATTAACTATATATTCCTACGTTAAAC
65 ATTAGTTTCTGAGTA-GAAG-AT--CTATAAAGAT-T-TACT--CTATATATTCCTACATTAAAC
* * *
1134881 TTTGA-CCCCCT-TCCATTGTGGCCCCAC-CTTACCTCCAGGGGTCATGATTTTCACAACTTTGA
122 TTTGACCCCCCTCCCCATTGTGGCCCCACTC-AACCTCCAGGGGTCATGATTTTCACAACTTTAA
* * * ** * *
1134943 ATTAACACCACCTGAGAAT-TTTCCACACAAATTTCAGCTTTCCTGGCTGATGAGTTCATGAGAA
186 ATTAACACCACCTGAGAATGCTCCCACACAAATTTCAGCTTTCCTGACTGAAAAGCTC-CGAGAA
* * * * *
1135007 GAATGTTTTTTAAGATTTACTCTATATATTCCTTTGTAAAA-GTCGATCCCCCATTGTGGCCCCA
250 G-A--TTTTTAAAGATTTACTCTATATATACCTTAGTAAAACGTCAAACCCCCATTGTGGCCCCA
*
1135071 -CTCTACCCCTGAGGGTC-ATGAT
312 TC-CTACCCCCGAGGGTCAAT-AT
* *
1135093 TTTCACAACTTTAAATCTACACTACCTGAGGATGCTTCCACACAACTTTCAGGTTTCCTGGCCTA
1 TTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAACTTTCAGCTTTCCTGG-CTA
1135158 AT
65 AT
1135160 GGTTCTTGAG
Statistics
Matches: 338, Mismatches: 51, Indels: 29
0.81 0.12 0.07
Matches are distributed among these distances:
333 2 0.01
334 68 0.20
335 1 0.00
337 40 0.12
338 65 0.19
339 7 0.02
340 91 0.27
341 64 0.19
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (333 bp):
TTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAACTTTCAGCTTTCCTGGCTAA
TTAGTTTCTGAGTAGAAGATCTATAAAGATTTACTCTATATATTCCTACATTAAACTTTGACCCC
CCTCCCCATTGTGGCCCCACTCAACCTCCAGGGGTCATGATTTTCACAACTTTAAATTAACACCA
CCTGAGAATGCTCCCACACAAATTTCAGCTTTCCTGACTGAAAAGCTCCGAGAAGATTTTTAAAG
ATTTACTCTATATATACCTTAGTAAAACGTCAAACCCCCATTGTGGCCCCATCCTACCCCCGAGG
GTCAATAT
Found at i:1138494 original size:163 final size:168
Alignment explanation
Indices: 1138075--1138495 Score: 430
Period size: 170 Copynumber: 2.5 Consensus size: 168
1138065 TTTACATTGC
* *
1138075 AGTATATAGAGTTAATCTTTAAAAATCTTCTTCTCAAAATCCATTTGGTCAGAAAAGCTGAAACT
1 AGTATATAGAGTTAATC-TTAAAAATCTTCTTCTCAAAAACCATTTGGCCAGAAAAGCTGAAACT
* * * ** * * *
1138140 CGTGTGGAAGCATCCTCAGATAGTGTAGATTCAAGTTTGTCAAATCATATTACCTGGGTTAAGGT
65 TGTGTGGAAGCATCCTCAGGTAGCGTAGATAAAAGTATGTCAAATCATAGTACCTGGGGTAAGGT
**
1138205 GGGGCCACAATGGAAGGGGGCGTTAAGATTTTAACATGGG
130 GGGGCCACAA-GGAAGGGGGCGTTAAGATTTTAACAAAGG
* *
1138245 AGTGTATAGAGTTAATCTATAGAAATCTTCTTCTCAAAAACCATTTGGCCAGAAAAGCCT-AAAC
1 AGTATATAGAGTTAATCT-TAAAAATCTTCTTCTCAAAAACCATTTGGCCAGAAAAG-CTGAAAC
* * * * *
1138309 GTGTGTTGAAGCA-CATTCAGGTAGCGTAGATAAAAGTATGTCCAATTCATGGT-CCTTGAGGGT
64 TTGTGTGGAAGCATC-CTCAGGTAGCGTAGATAAAAGTATGT-CAAATCATAGTACC-TG-GGGT
** * *
1138372 AAGGTGGGGCCAC-A-G-TTGGGGTG-TAA-ATTTT-TCAAAGG
125 AAGGTGGGGCCACAAGGAAGGGGGCGTTAAGATTTTAACAAAGG
*** * * *
1138410 AGTATATAGAGTTAATCTTAAAAAAAAT-TTCTCCAAAGCCATTTGGCCAAAAAAGCTGAAACTT
1 AGTATATAGAGTTAATCTTAAAAATCTTCTTCTCAAAAACCATTTGGCCAGAAAAGCTGAAACTT
*
1138474 GTATGGAAGCATCCTCAGGTAG
66 GTGTGGAAGCATCCTCAGGTAG
1138496 TGTAATTTCA
Statistics
Matches: 208, Mismatches: 35, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
162 2 0.01
163 46 0.22
164 7 0.03
165 21 0.10
166 5 0.02
167 3 0.01
168 5 0.02
169 3 0.01
170 87 0.42
171 13 0.06
172 16 0.08
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (168 bp):
AGTATATAGAGTTAATCTTAAAAATCTTCTTCTCAAAAACCATTTGGCCAGAAAAGCTGAAACTT
GTGTGGAAGCATCCTCAGGTAGCGTAGATAAAAGTATGTCAAATCATAGTACCTGGGGTAAGGTG
GGGCCACAAGGAAGGGGGCGTTAAGATTTTAACAAAGG
Found at i:1139329 original size:18 final size:17
Alignment explanation
Indices: 1139288--1139330 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
1139278 ACTATACTGT
*
1139288 GACAAAAAGAAATCAAT
1 GACAAAAAGAAATCAAG
* *
1139305 GATAAAAAGAATATCCAG
1 GACAAAAAGAA-ATCAAG
1139323 GACAAAAA
1 GACAAAAA
1139331 TTGATTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.63, C:0.12, G:0.14, T:0.12
Consensus pattern (17 bp):
GACAAAAAGAAATCAAG
Found at i:1150799 original size:171 final size:167
Alignment explanation
Indices: 1150403--1150850 Score: 577
Period size: 171 Copynumber: 2.7 Consensus size: 167
1150393 CACCCTATTC
* * *
1150403 CCGGGGGTCATTATTTTCACAACTTTGAATCTACTCTACCTGATGATGCTTCAACACAAGTTTA-
1 CCGGGGGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCAACACAAGTTTAC
* * *
1150467 AGCTTTCCTGGCTGATTAGTTTCTAAGAAGAATATTTTTAAAGATTTACTCTATATATTCCTTTG
66 AGCTTTCCTGGCTGATTAGTTTTTAAGAAGAAGATTTTTAAAGATTTACTATATATATTCCTTTG
1150532 TTAAACCTTGACCCTCAATTGTGGCCCAATCCTACCA
131 TTAAACCTTGACCCTCAATTGTGGCCCAATCCTACCA
* * *
1150569 CCGGGGGTCATGATTTTCACAACTTTGAATCTACAATACATGAGAATGCTTCAACACAAGTTTCA
1 CCGGGGGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCAACACAAGTTT-A
1150634 GCAGCTTTCCTGGCTGATTAGTTTTTAAGAAGAAGATTTTTAAAGATTTACTATATATATATTCC
65 -CAGCTTTCCTGGCTGATTAGTTTTTAAGAAGAAGATTTTTAAAGATTTAC--TATATATATTCC
* * *
1150699 TTTGTTTAACTTTGACACC-C-ATTGTGGCCC-GTCCATGACC-
127 TTTGTTAAACCTTGAC-CCTCAATTGTGGCCCAATCC-T-ACCA
* * * *
1150739 CCTGGGGATCATGATTTTCACAACTTTAAATCTACGCTACCTGAGGATGCTTCTACACAAGTTT-
1 CC-GGGGGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCAACACAAGTTTA
* * * * *
1150803 CAGCTTTCCTGGCTTAATGGTTCTTGAGAAGAAGATTTTTGAAA-ATTT
65 CAGCTTTCCTGGCTGATTAGTTTTTAAGAAGAAGATTTTT-AAAGATTT
1150851 CTCAAATTTT
Statistics
Matches: 248, Mismatches: 24, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
166 57 0.23
167 1 0.00
168 39 0.16
169 53 0.21
170 13 0.05
171 83 0.33
172 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (167 bp):
CCGGGGGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCAACACAAGTTTAC
AGCTTTCCTGGCTGATTAGTTTTTAAGAAGAAGATTTTTAAAGATTTACTATATATATTCCTTTG
TTAAACCTTGACCCTCAATTGTGGCCCAATCCTACCA
Found at i:1156928 original size:16 final size:15
Alignment explanation
Indices: 1156901--1156931 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
1156891 CGGAAAACCT
1156901 TAAAAATAAATAAAA
1 TAAAAATAAATAAAA
1156916 TAAAAATAGAATAAAA
1 TAAAAATA-AATAAAA
1156932 ATAGAACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (15 bp):
TAAAAATAAATAAAA
Found at i:1156942 original size:12 final size:11
Alignment explanation
Indices: 1156908--1156942 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1156898 CCTTAAAAAT
*
1156908 AAATAAAATAA
1 AAATAGAATAA
1156919 AAATAGAATAA
1 AAATAGAATAA
1156930 AAATAGAACTAA
1 AAATAGAA-TAA
1156942 A
1 A
1156943 TTCAACTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 18 0.82
12 4 0.18
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.17
Consensus pattern (11 bp):
AAATAGAATAA
Found at i:1161936 original size:17 final size:17
Alignment explanation
Indices: 1161911--1162003 Score: 100
Period size: 17 Copynumber: 5.4 Consensus size: 17
1161901 CCCCCCCCCC
1161911 AAAAA-AAAAAAACAAA
1 AAAAACAAAAAAACAAA
1161927 AAAAACAAAAAAACAAA
1 AAAAACAAAAAAACAAA
1161944 AAACAA-AAAACAAACAAA
1 AAA-AACAAAA-AAACAAA
* *
1161962 AACAAATAAAAAAAACCAA
1 AA-AAA-CAAAAAAACAAA
* *
1161981 ACAAACAAAAAAACCAA
1 AAAAACAAAAAAACAAA
1161998 AAAAAC
1 AAAAAC
1162004 GAAACACTTA
Statistics
Matches: 67, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
16 5 0.07
17 34 0.51
18 16 0.24
19 8 0.12
20 4 0.06
ACGTcount: A:0.84, C:0.15, G:0.00, T:0.01
Consensus pattern (17 bp):
AAAAACAAAAAAACAAA
Found at i:1161944 original size:24 final size:24
Alignment explanation
Indices: 1161911--1162003 Score: 95
Period size: 24 Copynumber: 4.0 Consensus size: 24
1161901 CCCCCCCCCC
1161911 AAAAAA-AAAAAACAAAAAAAACA
1 AAAAAACAAAAAACAAAAAAAACA
1161934 AAAAAACAAAAAACAAAAAACAA-A
1 AAAAAACAAAAAACAAAAAA-AACA
* * *
1161958 CAAAAAC-AAATA-AAAAAAACCA
1 AAAAAACAAAAAACAAAAAAAACA
* *
1161980 AACAAACAAAAAAACCAAAAAAAC
1 AAAAAAC-AAAAAACAAAAAAAAC
1162004 GAAACACTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
21 1 0.02
22 12 0.21
23 10 0.18
24 24 0.43
25 9 0.16
ACGTcount: A:0.84, C:0.15, G:0.00, T:0.01
Consensus pattern (24 bp):
AAAAAACAAAAAACAAAAAAAACA
Found at i:1161993 original size:1 final size:1
Alignment explanation
Indices: 1161911--1161976 Score: 60
Period size: 1 Copynumber: 66.0 Consensus size: 1
1161901 CCCCCCCCCC
* * * * * * * *
1161911 AAAAAAAAAAAACAAAAAAAACAAAAAAACAAAAAACAAAAAACAAACAAAAACAAATAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1161976 A
1 A
1161977 CCAAACAAAC
Statistics
Matches: 49, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.88, C:0.11, G:0.00, T:0.02
Consensus pattern (1 bp):
A
Found at i:1162003 original size:9 final size:9
Alignment explanation
Indices: 1161915--1162003 Score: 67
Period size: 9 Copynumber: 9.9 Consensus size: 9
1161905 CCCCCCAAAA
*
1161915 AAAAAAAAC
1 AAAAAAACC
*
1161924 AAAAAAAAC
1 AAAAAAACC
1161933 AAAAAAA-C
1 AAAAAAACC
*
1161941 -AAAAAACAA
1 AAAAAAAC-C
*
1161950 AAAACAAACA
1 AAAA-AAACC
**
1161960 AAAACAAATA
1 AAAA-AAACC
1161970 AAAAAAACC
1 AAAAAAACC
*
1161979 AAACAAA-C
1 AAAAAAACC
1161987 AAAAAAACC
1 AAAAAAACC
1161996 AAAAAAAC
1 AAAAAAAC
1162004 GAAACACTTA
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
7 6 0.09
8 8 0.12
9 34 0.49
10 17 0.25
11 4 0.06
ACGTcount: A:0.83, C:0.16, G:0.00, T:0.01
Consensus pattern (9 bp):
AAAAAAACC
Done.