Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 138 of 328
Found at i:40166997 original size:20 final size:20
Alignment explanation
Indices: 40166972--40167019 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
40166962 ATTCCGACTG
40166972 TGTGTCGATGAGACACTATA
1 TGTGTCGATGAGACACTATA
*
40166992 TGTGTCAATGAGACACTATA
1 TGTGTCGATGAGACACTATA
40167012 TGTGTCGA
1 TGTGTCGA
40167020 CTACTGTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (20 bp):
TGTGTCGATGAGACACTATA
Found at i:40195364 original size:32 final size:32
Alignment explanation
Indices: 40195327--40195390 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
40195317 TGAGTTTATT
40195327 TAGTAAATATAGTATAAAGACATCATAATGTG
1 TAGTAAATATAGTATAAAGACATCATAATGTG
*
40195359 TAGTAAATATAGTATAGAGACATCATAATGTG
1 TAGTAAATATAGTATAAAGACATCATAATGTG
40195391 GAAAAGGCGA
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:0.45, C:0.06, G:0.17, T:0.31
Consensus pattern (32 bp):
TAGTAAATATAGTATAAAGACATCATAATGTG
Found at i:40199565 original size:27 final size:27
Alignment explanation
Indices: 40199535--40199596 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
40199525 AAAGAATTCT
* * **
40199535 TTTGTGGCGCAATATGAAAGGAATGCA
1 TTTGTGGCGCAATATAAAAGAAAAACA
*
40199562 TTTGTGGTGCAATATAAAAGAAAAACA
1 TTTGTGGCGCAATATAAAAGAAAAACA
40199589 TTTGTGGC
1 TTTGTGGC
40199597 AAATAATGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.29
Consensus pattern (27 bp):
TTTGTGGCGCAATATAAAAGAAAAACA
Found at i:40200888 original size:3 final size:3
Alignment explanation
Indices: 40200863--40200968 Score: 126
Period size: 3 Copynumber: 35.0 Consensus size: 3
40200853 GGTACAACTT
40200863 ATA ATA A-A ATA CATAA ATGA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA -AT-A AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
40200910 ATA ATA ATA ATA ATA GTA GTA GTA GTA ATA ATA ATA ATA ATA ATA TTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
40200958 A-A ATA ATA ATA
1 ATA ATA ATA ATA
40200969 TTATTATTAT
Statistics
Matches: 94, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
2 4 0.04
3 82 0.87
4 7 0.07
5 1 0.01
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:40200983 original size:23 final size:23
Alignment explanation
Indices: 40200888--40201002 Score: 81
Period size: 24 Copynumber: 4.7 Consensus size: 23
40200878 AATGAATAAT
40200888 AATAATAATAATAATAATAAT-AA
1 AATAATAATAATAATAAT-ATCAA
* * *
40200911 TAATAATAATAATAGTAGTAGT-AGT
1 -AATAATAATAATAATAATA-TCA-A
*
40200936 AATAATAATAATAATAATATTAA
1 AATAATAATAATAATAATATCAA
* * *
40200959 AATAATAATATTATTATTATCAA
1 AATAATAATAATAATAATATCAA
40200982 AATTAATTAATCTAATAATAA
1 AA-TAA-TAA--TAATAATAA
40201003 AATGGCCAAA
Statistics
Matches: 71, Mismatches: 13, Indels: 11
0.75 0.14 0.12
Matches are distributed among these distances:
23 23 0.32
24 39 0.55
25 3 0.04
27 6 0.08
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (23 bp):
AATAATAATAATAATAATATCAA
Found at i:40203644 original size:20 final size:20
Alignment explanation
Indices: 40203615--40203652 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
40203605 ATAATATATG
*
40203615 ATAATTTATAATATATATCT
1 ATAATCTATAATATATATCT
40203635 ATAATCTATAATATATAT
1 ATAATCTATAATATATAT
40203653 AAAAGCACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAATCTATAATATATATCT
Found at i:40204950 original size:21 final size:19
Alignment explanation
Indices: 40204896--40204950 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
40204886 TTTAAATTAC
*
40204896 AATTTTATAAATAATAATC
1 AATTTTATAAATAATAATA
* **
40204915 AACTTTATATTTAATATATGA
1 AATTTTATAAATAATA-AT-A
40204936 AATTTTATAAATAAT
1 AATTTTATAAATAAT
40204951 GCATTTATAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 13 0.48
20 2 0.07
21 12 0.44
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (19 bp):
AATTTTATAAATAATAATA
Found at i:40207143 original size:51 final size:51
Alignment explanation
Indices: 40207058--40207175 Score: 157
Period size: 51 Copynumber: 2.3 Consensus size: 51
40207048 TTATGATCAG
*
40207058 TGACAAGTGATAAGTGGTAGCCTCAGCTATACTTATCTGATCAGTGACAAA
1 TGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGACAAA
* * * * *
40207109 TGACAAGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATTAGTGACAAG
1 TGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGACAAA
*
40207160 TGATC-AGTGACAAGTG
1 TGA-CAAGTGATAAGTG
40207176 ACAAGTGATA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 58 0.98
52 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (51 bp):
TGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGACAAA
Found at i:40207168 original size:14 final size:14
Alignment explanation
Indices: 40207146--40207198 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
40207136 TGCACTTATC
*
40207146 TGATTAGTGACAAG
1 TGATCAGTGACAAG
40207160 TGATCAGTGACAAG
1 TGATCAGTGACAAG
*
40207174 TGA-CAAGTGATAAATG
1 TGATC-AGTGA-CAA-G
40207190 TGATCAGTG
1 TGATCAGTG
40207199 TAAGACCGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 1 0.03
14 21 0.64
15 2 0.06
16 8 0.24
17 1 0.03
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.26
Consensus pattern (14 bp):
TGATCAGTGACAAG
Found at i:40207175 original size:7 final size:7
Alignment explanation
Indices: 40207151--40207183 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
40207141 TTATCTGATT
40207151 AGTGACA
1 AGTGACA
40207158 AGTGATC-
1 AGTGA-CA
40207165 AGTGACA
1 AGTGACA
40207172 AGTGACA
1 AGTGACA
40207179 AGTGA
1 AGTGA
40207184 TAAATGTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 1 0.04
7 22 0.92
8 1 0.04
ACGTcount: A:0.39, C:0.12, G:0.30, T:0.18
Consensus pattern (7 bp):
AGTGACA
Found at i:40208635 original size:23 final size:23
Alignment explanation
Indices: 40208604--40208648 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
40208594 ATAATAGTAT
40208604 TAAAATAAA-GTTTTAATTGATGG
1 TAAAATAAATGTTTT-ATTGATGG
*
40208627 TAAATTAAATGTTTTATTGATG
1 TAAAATAAATGTTTTATTGATG
40208649 CAATCGACGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (23 bp):
TAAAATAAATGTTTTATTGATGG
Found at i:40210908 original size:28 final size:28
Alignment explanation
Indices: 40210868--40210925 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
40210858 CTATGACAAG
40210868 TTAGAAACTTTTCTGCATTTAGATTAAT
1 TTAGAAACTTTTCTGCATTTAGATTAAT
40210896 TTAGAAACTTTTCTGCATTTAGATTAAT
1 TTAGAAACTTTTCTGCATTTAGATTAAT
40210924 TT
1 TT
40210926 TCGTTTCTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (28 bp):
TTAGAAACTTTTCTGCATTTAGATTAAT
Found at i:40220238 original size:2 final size:2
Alignment explanation
Indices: 40220231--40220260 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
40220221 TAAGCCTTAC
*
40220231 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40220261 ACTAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:40224049 original size:44 final size:44
Alignment explanation
Indices: 40224001--40224088 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
40223991 AGTCAAATAT
* * *
40224001 TATTAAAAAAACCTACATTAATTAGAGTTTAAGTGGGAAACTAA
1 TATTAAAAAAACCTACACTAATTAAAGTTTAAGTGAGAAACTAA
* *
40224045 TATTAAAATAAGCTACACTAATTAAAGTTTAAGTGAGAAACTAA
1 TATTAAAAAAACCTACACTAATTAAAGTTTAAGTGAGAAACTAA
40224089 AATCAGAGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (44 bp):
TATTAAAAAAACCTACACTAATTAAAGTTTAAGTGAGAAACTAA
Found at i:40224610 original size:30 final size:31
Alignment explanation
Indices: 40224567--40224626 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
40224557 TACAAAATGA
*
40224567 TCATTAAATTATTTTG-AATTTTTTATTTAAG
1 TCATTAAATTA-TTTGAAAATTTTTATTTAAG
*
40224598 TCATTGAA-TATTTGAAAATTTTTATTTAA
1 TCATTAAATTATTTGAAAATTTTTATTTAA
40224627 ATAATTGAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 4 0.15
30 15 0.58
31 7 0.27
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (31 bp):
TCATTAAATTATTTGAAAATTTTTATTTAAG
Found at i:40225225 original size:19 final size:18
Alignment explanation
Indices: 40225201--40225288 Score: 65
Period size: 19 Copynumber: 4.7 Consensus size: 18
40225191 ATTTTTATTT
40225201 ATTAAATAAAATTTAAATA
1 ATTAAATAAAA-TTAAATA
*
40225220 ATTAAATTAAATTAAATA
1 ATTAAATAAAATTAAATA
* *
40225238 ATATATCAATTACA-TAAGATA
1 AT-TA--AATAAAATTAA-ATA
*
40225259 ATTTAAGTAAAATT-AA-A
1 A-TTAAATAAAATTAAATA
40225276 ATTAAATAAAATT
1 ATTAAATAAAATT
40225289 TTAAATTATT
Statistics
Matches: 57, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
16 11 0.19
17 2 0.04
18 10 0.18
19 17 0.30
20 4 0.07
21 12 0.21
22 1 0.02
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (18 bp):
ATTAAATAAAATTAAATA
Found at i:40225296 original size:17 final size:16
Alignment explanation
Indices: 40225201--40225288 Score: 53
Period size: 16 Copynumber: 5.8 Consensus size: 16
40225191 ATTTTTATTT
*
40225201 ATTAAATAAAATTTAA
1 ATTAAATAAAATTAAA
*
40225217 A-T-AATTAAATT-AA
1 ATTAAATAAAATTAAA
* *
40225230 ATTAAATAATA-TATCA
1 ATTAAATAAAATTA-AA
* *
40225246 ATTACATAAGA-T-AA
1 ATTAAATAAAATTAAA
* *
40225260 TTTAAGTAAAATTAAA
1 ATTAAATAAAATTAAA
40225276 ATTAAATAAAATT
1 ATTAAATAAAATT
40225289 TTAAATTATT
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
13 3 0.06
14 18 0.34
15 7 0.13
16 25 0.47
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (16 bp):
ATTAAATAAAATTAAA
Found at i:40227444 original size:22 final size:23
Alignment explanation
Indices: 40227400--40227445 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
40227390 AGTTTAAAAA
* **
40227400 TTAATTTTTAAAATATTTTATAT
1 TTAATTTTCAAAATATTAAATAT
40227423 TTAATTTTCAAAATA-TAAATAT
1 TTAATTTTCAAAATATTAAATAT
40227445 T
1 T
40227446 ATTTTTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TTAATTTTCAAAATATTAAATAT
Found at i:40228275 original size:22 final size:23
Alignment explanation
Indices: 40228245--40228292 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
40228235 TTGTGAAATG
40228245 TTATAAAATAAAAATAA-TATTT
1 TTATAAAATAAAAATAAGTATTT
*
40228267 TTATTAAATAAAAATAAGGTATTT
1 TTATAAAATAAAAATAA-GTATTT
40228291 TT
1 TT
40228293 CTGCATCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 16 0.70
24 7 0.30
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
TTATAAAATAAAAATAAGTATTT
Found at i:40229668 original size:21 final size:20
Alignment explanation
Indices: 40229630--40229669 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
40229620 TCAAGCTAAC
* *
40229630 AAGGGCACACGTCTGTGTGG
1 AAGGGCACACGCCCGTGTGG
40229650 AAGGGCAACACGCCCGTGTG
1 AAGGGC-ACACGCCCGTGTG
40229670 TCTTCTTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.23, C:0.25, G:0.38, T:0.15
Consensus pattern (20 bp):
AAGGGCACACGCCCGTGTGG
Found at i:40231002 original size:96 final size:95
Alignment explanation
Indices: 40230837--40231161 Score: 346
Period size: 96 Copynumber: 3.4 Consensus size: 95
40230827 AAGGGTGAAT
* * * *
40230837 TGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTCGAGGCCGATGCCATGTCCT
1 TGCCGATGCCAT-TTCCAGACATGGTCTTACACTGGCTCTCATGTCGTGGCCGATGCCATGTCCC
*
40230902 AGACATGGTCTTACACTAGCTCTCATCTCAA
65 AGACATGGTCTTACACTAGCTCTCATATCAA
* * * *
40230933 TGCCGGTGCCATTTCCTAGACATGGTTTTACACTGGCTCTCGTGTTGTGGCCGATGCCATGTCCC
1 TGCCGATGCCATTTCC-AGACATGGTCTTACACTGGCTCTCATGTCGTGGCCGATGCCATGTCCC
* * *
40230998 AGACATGGTCTTACACTAGCACACATATGAA
65 AGACATGGTCTTACACTAGCTCTCATATCAA
* * * *** * * * *
40231029 TGCCGATGCCATGTCCCAGACATGGTCTTACATTAGCTCTCACAACATCGCTGATGCCATGTTCC
1 TGCCGATGCCAT-TTCCAGACATGGTCTTACACTGGCTCTCATGTCGTGGCCGATGCCATGTCCC
* * *
40231094 AAACATGGTCTTACACTGGCTCTCATATC-G
65 AGACATGGTCTTACACTAGCTCTCATATCAA
* * *
40231124 TGGCCAACGCCATGTCCCAGACATGGTCTTACACTGGC
1 T-GCCGATGCCAT-TTCCAGACATGGTCTTACACTGGC
40231162 ATACATATCA
Statistics
Matches: 190, Mismatches: 36, Indels: 6
0.82 0.16 0.03
Matches are distributed among these distances:
95 5 0.03
96 182 0.96
97 3 0.02
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (95 bp):
TGCCGATGCCATTTCCAGACATGGTCTTACACTGGCTCTCATGTCGTGGCCGATGCCATGTCCCA
GACATGGTCTTACACTAGCTCTCATATCAA
Found at i:40231100 original size:144 final size:144
Alignment explanation
Indices: 40230838--40231170 Score: 431
Period size: 144 Copynumber: 2.3 Consensus size: 144
40230828 AGGGTGAATT
* * * * *
40230838 GCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTCGAGGCCGATGCCATGTCCTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCGAGGCCGATGCCATGTCCCA
* * * *
40230903 GACATGGTCTTACACTAGCTCTCATCTCAATGCCGGTGCCATTTCCTAGACATGGTTTTACACTG
66 GACATGGTCTTACACTAGCTCTCATCACAATGCCGATGCCATTTCCTAAACATGGTCTTACACTG
* * *
40230968 GCTCTCGTGTTGTG
131 GCTCTCATATCGTG
* *
40230982 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATAT-GAATGCCGATGCCATGTCCC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCG-AGGCCGATGCCATGTCCC
* *
40231046 AGACATGGTCTTACATTAGCTCTCA-CA-ACATCGCTGATGCCATGTTCC-AAACATGGTCTTAC
65 AGACATGGTCTTACACTAGCTCTCATCACA-AT-GCCGATGCCAT-TTCCTAAACATGGTCTTAC
40231108 ACTGGCTCTCATATCGTG
127 ACTGGCTCTCATATCGTG
* * *
40231126 GCCAACGCCATGTCCCAGACATGGTCTTACACTGGCATACATATC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATC
40231171 ACCCAAATGT
Statistics
Matches: 164, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
142 1 0.01
143 4 0.02
144 155 0.95
145 4 0.02
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (144 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCGAGGCCGATGCCATGTCCCA
GACATGGTCTTACACTAGCTCTCATCACAATGCCGATGCCATTTCCTAAACATGGTCTTACACTG
GCTCTCATATCGTG
Found at i:40231169 original size:48 final size:48
Alignment explanation
Indices: 40230838--40231170 Score: 314
Period size: 48 Copynumber: 6.9 Consensus size: 48
40230828 AGGGTGAATT
* * * *
40230838 GCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCGTG
* * * * *
40230886 GCCGATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCATCTCAAT-
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATC-GTG
* * * * * * * *
40230934 GCCGGTGCCATTTCCTAGACATGGTTTTACACTGGCTCTCGTGTTGTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCGTG
* *
40230982 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATAT-GAAT-
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCG--TG
* * * * * * *
40231030 GCCGATGCCATGTCCCAGACATGGTCTTACATTAGCTCTCACAACATC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCGTG
* * * *
40231078 GCTGATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATATCGTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCGTG
* *
40231126 GCCAACGCCATGTCCCAGACATGGTCTTACACTGGCAT-ACATATC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGC-TCACATATC
40231171 ACCCAAATGT
Statistics
Matches: 232, Mismatches: 46, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
47 3 0.01
48 227 0.98
49 2 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATATCGTG
Found at i:40241669 original size:7 final size:7
Alignment explanation
Indices: 40241657--40241818 Score: 189
Period size: 7 Copynumber: 22.3 Consensus size: 7
40241647 TAAAGCTTCC
40241657 ACCCTAA
1 ACCCTAA
40241664 ACCCTAA
1 ACCCTAA
40241671 ACCCTAA
1 ACCCTAA
40241678 ACCCTAA
1 ACCCTAA
*
40241685 ACCCAAAA
1 ACCC-TAA
*
40241693 ACCTTAAA
1 ACCCT-AA
40241701 ACCCTAA
1 ACCCTAA
40241708 ACCCTAA
1 ACCCTAA
40241715 ACCCTAA
1 ACCCTAA
**
40241722 ACTATAA
1 ACCCTAA
40241729 ACCCTAA
1 ACCCTAA
40241736 ACCCTAA
1 ACCCTAA
40241743 ACCCTAA
1 ACCCTAA
*
40241750 ACCATAA
1 ACCCTAA
*
40241757 ACCATAAA
1 ACCCT-AA
40241765 ACCCTAAA
1 ACCCT-AA
*
40241773 ACCATAA
1 ACCCTAA
40241780 ACCCTAAA
1 ACCCT-AA
*
40241788 ACACTAAA
1 ACCCT-AA
*
40241796 ACCATAA
1 ACCCTAA
40241803 ACCCTAA
1 ACCCTAA
40241810 ACCCTAA
1 ACCCTAA
40241817 AC
1 AC
40241819 TTACTACTAT
Statistics
Matches: 135, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
7 99 0.73
8 36 0.27
ACGTcount: A:0.49, C:0.36, G:0.00, T:0.14
Consensus pattern (7 bp):
ACCCTAA
Found at i:40241712 original size:37 final size:35
Alignment explanation
Indices: 40241657--40241818 Score: 207
Period size: 37 Copynumber: 4.5 Consensus size: 35
40241647 TAAAGCTTCC
40241657 ACCCTAAACCCTAAACCCTAAACCCTAAACCCAAAA
1 ACCCTAAACCCTAAACCCTAAACCCTAAA-CCAAAA
* * *
40241693 ACCTTAAAACCCTAAACCCTAAACCCTAAACTATAA
1 ACCCT-AAACCCTAAACCCTAAACCCTAAACCAAAA
*
40241729 ACCCTAAACCCTAAACCCTAAACCATAAACCATAAA
1 ACCCTAAACCCTAAACCCTAAACCCTAAACCA-AAA
* * *
40241765 ACCCTAAAACCATAAACCCTAAAACACTAAAACCATAA
1 ACCCT-AAACCCTAAACCCT-AAACCCT-AAACCAAAA
40241803 ACCCTAAACCCTAAAC
1 ACCCTAAACCCTAAAC
40241819 TTACTACTAT
Statistics
Matches: 109, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
35 25 0.23
36 19 0.17
37 47 0.43
38 12 0.11
39 6 0.06
ACGTcount: A:0.49, C:0.36, G:0.00, T:0.14
Consensus pattern (35 bp):
ACCCTAAACCCTAAACCCTAAACCCTAAACCAAAA
Found at i:40243837 original size:137 final size:137
Alignment explanation
Indices: 40243599--40243874 Score: 516
Period size: 137 Copynumber: 2.0 Consensus size: 137
40243589 AACCCATTCA
* *
40243599 GGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGAGCTTTAGCCCCTTATT
1 GGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACCGAGCCTTAGCCCCTTATT
40243664 CAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGC
66 CAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGC
40243729 CCATTTG
131 CCATTTG
*
40243736 GGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACCGGGCCTTAGCCCCTTATT
1 GGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACCGAGCCTTAGCCCCTTATT
*
40243801 CAGATAACAGTATGGCCCATAGGCCCATTTTAAAATACATGCAACATCAGTAAACATATGCAAGC
66 CAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGC
40243866 CCATTTG
131 CCATTTG
40243873 GG
1 GG
40243875 AGACTACTCA
Statistics
Matches: 135, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 135 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (137 bp):
GGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACCGAGCCTTAGCCCCTTATT
CAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAACATATGCAAGC
CCATTTG
Found at i:40245697 original size:26 final size:25
Alignment explanation
Indices: 40245661--40245744 Score: 132
Period size: 26 Copynumber: 3.2 Consensus size: 25
40245651 CATGAAATTC
40245661 TTATCATGAAACATTTACCTAACTCA
1 TTATCATGAAACATTTACCTAAC-CA
40245687 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAA-CCA
*
40245713 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACC-A
40245739 TTATCA
1 TTATCA
40245745 ATTTGTATCA
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
25 2 0.04
26 52 0.95
27 1 0.02
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (25 bp):
TTATCATGAAACATTTACCTAACCA
Found at i:40247207 original size:43 final size:43
Alignment explanation
Indices: 40247141--40247311 Score: 186
Period size: 43 Copynumber: 4.0 Consensus size: 43
40247131 AGCTCGTACA
* * *
40247141 ATGCCAATGTCCTAGACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATATCG
* * *
40247184 ATGCCACTGTCCCAGACAG-GGTCTTACACGAAATTAAATA-AG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACACGAAATCAAATATCG
* *
40247226 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAA-ATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACG-AAATC-AAATATCG
** * *
40247270 ATGCCAACATCCCAGACGTGGTCTTACATGAAATCACATATC
1 ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATATC
40247312 AGAAATCCTA
Statistics
Matches: 105, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
42 29 0.28
43 46 0.44
44 30 0.29
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATATCG
Found at i:40247293 original size:86 final size:85
Alignment explanation
Indices: 40247141--40247303 Score: 215
Period size: 86 Copynumber: 1.9 Consensus size: 85
40247131 AGCTCGTACA
* * * *
40247141 ATGCCAATGTCCTAGACGTGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGACAGGGT
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCAAATATCGATGCCACTATCCCAGACAGGGT
40247206 CTTACACGAAATTAAATAAG
66 CTTACACGAAATTAAATAAG
*
40247226 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAA-ATCGATGCCAAC-ATCCCAGAC-G
1 ATGCCAATGTCCCAGACATGGTCTTACACGT-AATC-AAATATCGATGCC-ACTATCCCAGACAG
*
40247288 TGGTCTTACATGAAAT
63 -GGTCTTACACGAAAT
40247304 CACATATCAG
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
85 29 0.43
86 35 0.51
87 4 0.06
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (85 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAATCAAATATCGATGCCACTATCCCAGACAGGGT
CTTACACGAAATTAAATAAG
Found at i:40253752 original size:23 final size:22
Alignment explanation
Indices: 40253710--40253752 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
40253700 ATAATCCATA
**
40253710 CCAAATCATACCAATTCATAAG
1 CCAAATCATACCAAAACATAAG
40253732 CCAAAGTCATACCAAAACATA
1 CCAAA-TCATACCAAAACATA
40253753 TGTTTCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.49, C:0.28, G:0.05, T:0.19
Consensus pattern (22 bp):
CCAAATCATACCAAAACATAAG
Found at i:40255428 original size:43 final size:43
Alignment explanation
Indices: 40255351--40255520 Score: 186
Period size: 43 Copynumber: 4.0 Consensus size: 43
40255341 TCGTACAATA
* * *
40255351 CCAAAGTCCCAGAC-GTGGTCTTACATGTAATCAAATATCGATG
1 CCAATGTCCCAGACAG-GGTCTTACACGAAATCAAATATCGATG
* **
40255394 CCACTGTCATAGACAGGGTCTTACACGAAATCAAATA-CGATG
1 CCAATGTCCCAGACAGGGTCTTACACGAAATCAAATATCGATG
* *
40255436 TCAATGTCCCAGACATGGTCTTACACGTAAATCTAAA-ATCGATG
1 CCAATGTCCCAGACAGGGTCTTACACG-AAATC-AAATATCGATG
* *
40255480 CCAATGTCCCAGAC-GTGGTCTTACATGAAATCACATATCGA
1 CCAATGTCCCAGACAG-GGTCTTACACGAAATCAAATATCGA
40255521 AAATCCTATG
Statistics
Matches: 106, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
42 29 0.27
43 45 0.42
44 32 0.30
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.25
Consensus pattern (43 bp):
CCAATGTCCCAGACAGGGTCTTACACGAAATCAAATATCGATG
Found at i:40255504 original size:86 final size:85
Alignment explanation
Indices: 40255356--40255512 Score: 219
Period size: 86 Copynumber: 1.8 Consensus size: 85
40255346 CAATACCAAA
* * * *
40255356 GTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCCACTGTCATAGACAGGGTCTTACACG
1 GTCCCAGACATGGTCTTACACGTAATCAAATATCGATGCCAATGTCACAGACAGGGTCTTACACG
40255421 AAATCAAATACGATGTCAAT
66 AAATCAAATACGATGTCAAT
*
40255441 GTCCCAGACATGGTCTTACACGTAAATCTAAA-ATCGATGCCAATGTCCCAGAC-GTGGTCTTAC
1 GTCCCAGACATGGTCTTACACGT-AATC-AAATATCGATGCCAATGTCACAGACAG-GGTCTTAC
*
40255504 ATGAAATCA
63 ACGAAATCA
40255513 CATATCGAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
85 22 0.35
86 38 0.60
87 3 0.05
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (85 bp):
GTCCCAGACATGGTCTTACACGTAATCAAATATCGATGCCAATGTCACAGACAGGGTCTTACACG
AAATCAAATACGATGTCAAT
Found at i:40255888 original size:34 final size:34
Alignment explanation
Indices: 40255850--40255920 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
40255840 AAATCCATAA
40255850 ACACATATTTAGGGCATTTTACAAATTAGCTCAC
1 ACACATATTTAGGGCATTTTACAAATTAGCTCAC
40255884 ACACATATTTAGGGCATTTTACAAATTAGCTCAC
1 ACACATATTTAGGGCATTTTACAAATTAGCTCAC
40255918 ACA
1 ACA
40255921 TTTTCTCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.31
Consensus pattern (34 bp):
ACACATATTTAGGGCATTTTACAAATTAGCTCAC
Found at i:40257921 original size:18 final size:18
Alignment explanation
Indices: 40257900--40257936 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
40257890 AGATGCAATT
40257900 TGAATTATAGATACAAAA
1 TGAATTATAGATACAAAA
*
40257918 TGAATTTTAGATACAAAA
1 TGAATTATAGATACAAAA
40257936 T
1 T
40257937 CAGATGCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.32
Consensus pattern (18 bp):
TGAATTATAGATACAAAA
Found at i:40265304 original size:17 final size:18
Alignment explanation
Indices: 40265274--40265307 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
40265264 ATGTGGTTTG
40265274 CCCGTGTGGGCCCACACA
1 CCCGTGTGGGCCCACACA
40265292 CCCGTGT-GGCCCACAC
1 CCCGTGTGGGCCCACAC
40265308 GGCCTGCCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.15, C:0.47, G:0.26, T:0.12
Consensus pattern (18 bp):
CCCGTGTGGGCCCACACA
Found at i:40268265 original size:21 final size:21
Alignment explanation
Indices: 40268229--40268268 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
40268219 CACTAGACAC
40268229 AGGGGAACACGCCCGTGTGGG
1 AGGGGAACACGCCCGTGTGGG
40268250 AGGGGCAACACG-CCGTGTG
1 AGGGG-AACACGCCCGTGTG
40268269 ACCAATTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.20, C:0.25, G:0.45, T:0.10
Consensus pattern (21 bp):
AGGGGAACACGCCCGTGTGGG
Found at i:40269498 original size:46 final size:44
Alignment explanation
Indices: 40269410--40269524 Score: 160
Period size: 46 Copynumber: 2.5 Consensus size: 44
40269400 ATACCGATAC
*
40269410 CATGTCCCAGACATGGTCTTACACTGACACATCTTGTAGCCGATG
1 CATGTCCCAGACAT-GTCTTACACTGACACATCTTGAAGCCGATG
* *
40269455 CATGTCCCAGACATGTTTTACACTGGCTTACATCTT-AAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTGAC--ACATCTTGAA-GCCGATG
40269501 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
40269525 AGCACACAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
44 11 0.17
45 15 0.24
46 37 0.59
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (44 bp):
CATGTCCCAGACATGTCTTACACTGACACATCTTGAAGCCGATG
Found at i:40272762 original size:40 final size:40
Alignment explanation
Indices: 40272707--40272930 Score: 270
Period size: 40 Copynumber: 5.5 Consensus size: 40
40272697 TATTCGGATG
*
40272707 ATATCCGGGCTAAGTCACGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
40272747 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * *
40272790 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* ** * * *
40272830 ATATCTGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
40272870 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
40272910 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
40272931 ATACTTGGGT
Statistics
Matches: 158, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 13 0.08
40 108 0.68
41 1 0.01
43 36 0.23
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:40272850 original size:83 final size:79
Alignment explanation
Indices: 40272711--40272930 Score: 264
Period size: 83 Copynumber: 2.7 Consensus size: 79
40272701 CGGATGATAT
* * **
40272711 CCGGGCTAAGTCACGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATAT-CGGGCTAAGTCCCGAAGGCATTCA
*
40272776 TGCGAGTAGCTG-CTATAC
65 TGC---TAG-TGACCATAC
*
40272794 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCTGGGCTAAGTCCCGAAGGCATTCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATC-GGGCTAAGTCCCGAAGGCATTCA
*
40272859 TGCTAGTGACCATAT
65 TGCTAGTGACCATAC
* * * *
40272874 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCCGGCTAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCGGGCTAAGTCCCGAAG
40272931 ATACTTGGGT
Statistics
Matches: 123, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
79 16 0.13
80 43 0.35
81 2 0.02
82 1 0.01
83 61 0.50
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCGGGCTAAGTCCCGAAGGCATTCAT
GCTAGTGACCATAC
Found at i:40280884 original size:40 final size:40
Alignment explanation
Indices: 40280822--40281044 Score: 252
Period size: 40 Copynumber: 5.5 Consensus size: 40
40280812 TATTCGGATG
*
40280822 ATATTCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
40280862 ATATCCAGGCTAAGTCCCGAAGGCATTTGTACGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * *
40280905 ATA-CCTGGGCTAAGTTCCGAAGGCATTTGTGCTAGTGACT
1 ATATCC-GGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
** * * *
40280945 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
40280985 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
40281025 ATATCC-GGCTAAATCCCGAA
1 ATATCCGGGCTAAGTCCCGAA
40281045 TATACTTGGG
Statistics
Matches: 155, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
39 12 0.08
40 106 0.68
41 3 0.02
42 2 0.01
43 32 0.21
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:40295860 original size:22 final size:22
Alignment explanation
Indices: 40295815--40295871 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
40295805 TATGGAGTCA
* * *
40295815 ACACACCCATATG-AAATAGGC
1 ACACACCCGTGTGAAAAGAGGC
40295836 ACACACCCGTGTGAAAAGAGGC
1 ACACACCCGTGTGAAAAGAGGC
**
40295858 ACATGCCCGTGTGA
1 ACACACCCGTGTGA
40295872 CTATGACACA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 11 0.37
22 19 0.63
ACGTcount: A:0.35, C:0.28, G:0.23, T:0.14
Consensus pattern (22 bp):
ACACACCCGTGTGAAAAGAGGC
Found at i:40296205 original size:12 final size:12
Alignment explanation
Indices: 40296188--40296214 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40296178 GTCAGAATCA
40296188 GCTCCAAAATAG
1 GCTCCAAAATAG
40296200 GCTCCAAAATAG
1 GCTCCAAAATAG
40296212 GCT
1 GCT
40296215 GCATAATGTG
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:0.37, C:0.26, G:0.19, T:0.19
Consensus pattern (12 bp):
GCTCCAAAATAG
Found at i:40300475 original size:15 final size:17
Alignment explanation
Indices: 40300442--40300475 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
40300432 ATTAAGGTAG
40300442 TATTATTGTTTTTTATA
1 TATTATTGTTTTTTATA
40300459 TATTATTGTTTTTTATA
1 TATTATTGTTTTTTATA
40300476 AAATTTTTAA
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:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TATTATTGTTTTTTATA
Found at i:40301666 original size:21 final size:21
Alignment explanation
Indices: 40301640--40301713 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
40301630 TAACTCATGA
40301640 GTTTCAGTTTAACCCTTTTGG
1 GTTTCAGTTTAACCCTTTTGG
* * *
40301661 GTTTCAGTTTAGCTCTTTTGA
1 GTTTCAGTTTAACCCTTTTGG
* * * * *
40301682 GCTTCAGATTAATCCTTATAG
1 GTTTCAGTTTAACCCTTTTGG
*
40301703 GTTTCCGTTTA
1 GTTTCAGTTTA
40301714 GCTCCTACGA
Statistics
Matches: 39, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (21 bp):
GTTTCAGTTTAACCCTTTTGG
Found at i:40301706 original size:42 final size:42
Alignment explanation
Indices: 40301637--40301757 Score: 109
Period size: 42 Copynumber: 2.9 Consensus size: 42
40301627 AGTTAACTCA
* * * *
40301637 TGAGTTTCAGTTTAACCCTTTTGGGTTTCAGTTTAGCTCTTT
1 TGAGCTTCAGATTAACCCTTATAGGTTTCAGTTTAGCTCTTT
* * * *
40301679 TGAGCTTCAGATTAATCCTTATAGGTTTCCGTTTAGCTCCTA
1 TGAGCTTCAGATTAACCCTTATAGGTTTCAGTTTAGCTCTTT
* * * * *
40301721 CGAGCTTCCA-TTTAACCCTTACAAGTTTCCGTTTAGC
1 TGAGCTT-CAGATTAACCCTTATAGGTTTCAGTTTAGC
40301758 ACTTATGTGC
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 63 0.97
43 2 0.03
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (42 bp):
TGAGCTTCAGATTAACCCTTATAGGTTTCAGTTTAGCTCTTT
Found at i:40301729 original size:21 final size:21
Alignment explanation
Indices: 40301705--40301762 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
40301695 CCTTATAGGT
*
40301705 TTCCGTTTAGCTCC-TACGAGC
1 TTCCGTTTAGC-CCTTACAAGC
* * *
40301726 TTCCATTTAACCCTTACAAGT
1 TTCCGTTTAGCCCTTACAAGC
*
40301747 TTCCGTTTAGCACTTA
1 TTCCGTTTAGCCCTTA
40301763 TGTGCAGCCT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.21, C:0.29, G:0.12, T:0.38
Consensus pattern (21 bp):
TTCCGTTTAGCCCTTACAAGC
Found at i:40304241 original size:177 final size:177
Alignment explanation
Indices: 40303945--40304300 Score: 676
Period size: 177 Copynumber: 2.0 Consensus size: 177
40303935 TCTAACCGCC
*
40303945 AAACCTGACATTTGACGAAAACCATGTCAGCAACACTGAGTTCAATTCAAAAATTAGAATTTTGA
1 AAACCTGACATTTGAAGAAAACCATGTCAGCAACACTGAGTTCAATTCAAAAATTAGAATTTTGA
40304010 ATACTTGGTAAAATAATACTAGGCCATAACCAATTCATATCAAAAGGATCTACCCTTAGAACCTG
66 ATACTTGGTAAAATAATACTAGGCCATAACCAATTCATATCAAAAGGATCTACCCTTAGAACCTG
*
40304075 CATCGTTGTGTTAGATGTTAGATAGGATATATTATAAGTCAAATATT
131 CATCGTTGTGTTAGATGTAAGATAGGATATATTATAAGTCAAATATT
*
40304122 AAACCTGGCATTTGAAGAAAACCATGTCAGCAACACTGAGTTCAATTCAAAAATTAGAATTTTGA
1 AAACCTGACATTTGAAGAAAACCATGTCAGCAACACTGAGTTCAATTCAAAAATTAGAATTTTGA
40304187 ATACTTGGTAAAATAATACTAGGCCATAACCAATTCATATCAAAAGGATCTACCCTTAGAACCTG
66 ATACTTGGTAAAATAATACTAGGCCATAACCAATTCATATCAAAAGGATCTACCCTTAGAACCTG
*
40304252 CATCGTTGTGTTAGATGTAAGATAGTATATATTATAAGTCAAATATT
131 CATCGTTGTGTTAGATGTAAGATAGGATATATTATAAGTCAAATATT
40304299 AA
1 AA
40304301 GATTTGTTTT
Statistics
Matches: 175, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
177 175 1.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.30
Consensus pattern (177 bp):
AAACCTGACATTTGAAGAAAACCATGTCAGCAACACTGAGTTCAATTCAAAAATTAGAATTTTGA
ATACTTGGTAAAATAATACTAGGCCATAACCAATTCATATCAAAAGGATCTACCCTTAGAACCTG
CATCGTTGTGTTAGATGTAAGATAGGATATATTATAAGTCAAATATT
Found at i:40306872 original size:96 final size:95
Alignment explanation
Indices: 40306708--40306943 Score: 280
Period size: 96 Copynumber: 2.5 Consensus size: 95
40306698 GGTGAATTGC
* * * * * *
40306708 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTCGAGGCCGAAGCCATGTCCCAGA
1 CGATGCCATGTTCC-AACATGGTCTTACACTAGCACACATATCAAGACCGAAGCCATGTACCAGA
* *
40306773 CATGGTCTTACACTGGCTCTCA-TA-ATGTGGT
65 CATGGTCTTACACTGGATCTCATTACAT-T-AT
* * * *
40306804 CGATGCCATG-TCCTAGACATGGTCTTACACTAGCGCACATATCAATATCGATGCCATGTACCAG
1 CGATGCCATGTTCC-A-ACATGGTCTTACACTAGCACACATATCAAGACCGAAGCCATGTACCAG
40306868 ACATGGTCTTACACTGGATCTCATTACATTAT
64 ACATGGTCTTACACTGGATCTCATTACATTAT
*
40306900 CGATGCCATGTTCCCAACATGGTCTTACACTAGCACACGTATCA
1 CGATGCCATGTT-CCAACATGGTCTTACACTAGCACACATATCA
40306944 CCCAAATGTC
Statistics
Matches: 121, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
95 4 0.03
96 108 0.89
97 5 0.04
98 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (95 bp):
CGATGCCATGTTCCAACATGGTCTTACACTAGCACACATATCAAGACCGAAGCCATGTACCAGAC
ATGGTCTTACACTGGATCTCATTACATTAT
Found at i:40306901 original size:48 final size:47
Alignment explanation
Indices: 40306708--40306930 Score: 218
Period size: 48 Copynumber: 4.7 Consensus size: 47
40306698 GGTGAATTGC
* * * ***
40306708 CGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTCGA-GGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACAT-AC-ATTAT
* * *
40306756 CGAAGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-ATGTGGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATACAT-T-AT
* * * *
40306804 CGATGCCATGTCCTAGACATGGTCTTACACTAGCGCACATATCAATAT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATA-CATTAT
* * *
40306852 CGATGCCATGTACCAGACATGGTCTTACACTGGATCTCATTACATTAT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACA-TACATTAT
40306900 CGATGCCATGTTCCCA-ACATGGTCTTACACT
1 CGATGCCATG-TCCCAGACATGGTCTTACACT
40306931 AGCACACGTA
Statistics
Matches: 146, Mismatches: 22, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
45 1 0.01
48 137 0.94
49 7 0.05
50 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATACATTAT
Found at i:40307333 original size:25 final size:25
Alignment explanation
Indices: 40307305--40307361 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
40307295 ACAAAAATTA
40307305 CGATTTTACCACTAGGCTCGTAAAT
1 CGATTTTACCACTAGGCTCGTAAAT
* *
40307330 CGATTTTACCCCTAGGCTTGTAAAT
1 CGATTTTACCACTAGGCTCGTAAAT
40307355 CGATTTT
1 CGATTTT
40307362 TATTGAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.37
Consensus pattern (25 bp):
CGATTTTACCACTAGGCTCGTAAAT
Found at i:40311164 original size:37 final size:37
Alignment explanation
Indices: 40311118--40311190 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
40311108 GAGGTTTTGG
40311118 GTTTGAATCTTTTCCTTGAGTTTTTGTTATTTTTTTT
1 GTTTGAATCTTTTCCTTGAGTTTTTGTTATTTTTTTT
40311155 GTTTGAATCTTTTCCTTGAGTTTTTGTTATTTTTTT
1 GTTTGAATCTTTTCCTTGAGTTTTTGTTATTTTTTT
40311191 GGTAATCTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.11, C:0.08, G:0.14, T:0.67
Consensus pattern (37 bp):
GTTTGAATCTTTTCCTTGAGTTTTTGTTATTTTTTTT
Found at i:40313141 original size:40 final size:40
Alignment explanation
Indices: 40313095--40313281 Score: 211
Period size: 39 Copynumber: 4.7 Consensus size: 40
40313085 ACTACTTGCT
*
40313095 CAAATGCCTTCGGGACTT-GACCCGGTTATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAG-CCCGGTTATAGTAACTCGCA
*
40313135 CAAATGCCTTCGGGACTTAGCCCGGTT-CAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* ** *
40313174 CCAATGCCTTCGGGACTTAGCCCGGAAATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *** * *
40313214 CAATTGCCTTCGGG-TTTAGCCC-AAAATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
40313253 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
40313282 CATCCGAATT
Statistics
Matches: 123, Mismatches: 19, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
38 3 0.02
39 63 0.51
40 55 0.45
41 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:40313209 original size:79 final size:78
Alignment explanation
Indices: 40313095--40313277 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 78
40313085 ACTACTTGCT
** *
40313095 CAAATGCCTTCGGGACTT-GACCCGGTTATAGTAACTCACACAAATGCCTTCGGGACTTAGCCC-
1 CAAATGCCTTCGGGACTTAG-CCCGGAAATAATAACTCACACAAATGCCTTCGGG-CTTAGCCCA
** *
40313158 GGTTCAGTAACTCGCA
64 AATT-AGTAACTAGCA
* * * *
40313174 CCAATGCCTTCGGGACTTAGCCCGGAAATAATAACTCGCACAATTGCCTTCGGGTTTAGCCCAAA
1 CAAATGCCTTCGGGACTTAGCCCGGAAATAATAACTCACACAAATGCCTTCGGGCTTAGCCC-AA
*
40313239 ATTAGTCACTAGCA
65 ATTAGTAACTAGCA
40313253 CAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
40313278 TTATCATCCG
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
78 7 0.08
79 79 0.89
80 3 0.03
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.23
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAGCCCGGAAATAATAACTCACACAAATGCCTTCGGGCTTAGCCCAAA
TTAGTAACTAGCA
Found at i:40314733 original size:93 final size:93
Alignment explanation
Indices: 40314604--40314775 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
40314594 CGCCCATAAG
* * * *
40314604 CGAACTCGGGCTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
40314669 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
40314697 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
40314762 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
40314776 TCAACCATCC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:40314772 original size:46 final size:46
Alignment explanation
Indices: 40314597--40314772 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
40314587 TGTAACCCGC
* * * * *
40314597 CCATAAGCGAACTCGGGCTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
40314643 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
40314693 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
40314736 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
40314773 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 61 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:40314791 original size:46 final size:44
Alignment explanation
Indices: 40314648--40314791 Score: 141
Period size: 46 Copynumber: 3.1 Consensus size: 44
40314638 CGCATCCATA
40314648 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT
* * * *
40314695 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCT
40314741 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CT
40314787 AGTGA
1 AGTGA
40314792 CATGTCACTT
Statistics
Matches: 80, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
44 9 0.11
45 1 0.01
46 33 0.41
47 31 0.39
48 1 0.01
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCT
Found at i:40322675 original size:39 final size:40
Alignment explanation
Indices: 40322593--40322697 Score: 153
Period size: 39 Copynumber: 2.6 Consensus size: 40
40322583 ACTTGCTCAT
*
40322593 ATGCCTTCGGGACTT-GACCCGGTTATAGTAACTTGCACAA
1 ATGCCTTCGGGACTTAG-CCCGGTTATAGTAACTCGCACAA
*
40322633 ATGCCTTCGGGACTTAGCCCGGTTCA-A-TAACTCGCACCA
1 ATGCCTTCGGGACTTAGCCCGGTT-ATAGTAACTCGCACAA
40322672 ATGCCTTCGGGACTTAGCCCGGTTAT
1 ATGCCTTCGGGACTTAGCCCGGTTAT
40322698 CATCCGAATA
Statistics
Matches: 60, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
38 1 0.02
39 34 0.57
40 23 0.38
41 2 0.03
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.27
Consensus pattern (40 bp):
ATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAA
Found at i:40325219 original size:43 final size:43
Alignment explanation
Indices: 40325164--40325379 Score: 265
Period size: 43 Copynumber: 5.0 Consensus size: 43
40325154 ATATTGTGCA
* * *
40325164 ATGCCAAC-GTCCCAGATATGGTTTTACACGTAATCACATATTG
1 ATGCC-ACTGTCCCAGACATGGTCTTACACGTAATCACATATCG
* * *
40325207 ATGCCACTGTCCCAGATAGGGTCTTACACGTAATCACATATTG
1 ATGCCACTGTCCCAGACATGGTCTTACACGTAATCACATATCG
* *
40325250 ATGCCAAC-ATCCCAGACGTGGTCTTACACGTAATCACATATCG
1 ATGCC-ACTGTCCCAGACATGGTCTTACACGTAATCACATATCG
* * * *
40325293 ATGCCATTTTCCCAGACGTGGTCTTACACATAATCACATATCG
1 ATGCCACTGTCCCAGACATGGTCTTACACGTAATCACATATCG
* * *
40325336 ATGCCATTGTCCCGGACAGGGTCTTACACGTAATCACATATCG
1 ATGCCACTGTCCCAGACATGGTCTTACACGTAATCACATATCG
40325379 A
1 A
40325380 AAATCCTATG
Statistics
Matches: 155, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
42 3 0.02
43 150 0.97
44 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACATGGTCTTACACGTAATCACATATCG
Found at i:40327027 original size:33 final size:34
Alignment explanation
Indices: 40326950--40327030 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
40326940 TCTTATATAT
*
40326950 TATGACATTTTGATATGATATATGTTTCTAAAAA
1 TATGACATTCTGATATGATATATGTTTCTAAAAA
* * * **
40326984 TATGATATTCTGATCTGGTATATGTTT-TGGAAA
1 TATGACATTCTGATATGATATATGTTTCTAAAAA
40327017 TATGACATTCTGAT
1 TATGACATTCTGAT
40327031 TTGACATTCG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 17 0.43
34 23 0.57
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.44
Consensus pattern (34 bp):
TATGACATTCTGATATGATATATGTTTCTAAAAA
Found at i:40341155 original size:12 final size:11
Alignment explanation
Indices: 40341136--40341168 Score: 57
Period size: 12 Copynumber: 2.9 Consensus size: 11
40341126 CAACAAAATG
40341136 CATTTTTTTTT
1 CATTTTTTTTT
40341147 CACTTTTTTTTT
1 CA-TTTTTTTTT
40341159 CATTTTTTTT
1 CATTTTTTTT
40341169 GAGAACAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (11 bp):
CATTTTTTTTT
Found at i:40342190 original size:3 final size:3
Alignment explanation
Indices: 40342182--40342236 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
40342172 AAGGAAGATA
40342182 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40342230 AAT AAT A
1 AAT AAT A
40342237 GACTCAATGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:40342314 original size:14 final size:13
Alignment explanation
Indices: 40342296--40342370 Score: 60
Period size: 15 Copynumber: 5.1 Consensus size: 13
40342286 AACAAATACA
*
40342296 AAAAAATAGAAAT
1 AAAAAATAAAAAT
40342309 AGAAAAATAAAAAT
1 A-AAAAATAAAAAT
40342323 AAAAATAATAAAACATAT
1 -AAAA-AAT-AAA-A-AT
40342341 AAAAAATTAAAATAT
1 AAAAAA-TAAAA-AT
40342356 AAAAAATTAAAAAT
1 AAAAAA-TAAAAAT
40342370 A
1 A
40342371 TAAGTATAAG
Statistics
Matches: 54, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
13 1 0.02
14 17 0.31
15 20 0.37
16 8 0.15
17 6 0.11
18 2 0.04
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:40342327 original size:7 final size:7
Alignment explanation
Indices: 40342296--40342370 Score: 55
Period size: 8 Copynumber: 10.1 Consensus size: 7
40342286 AACAAATACA
40342296 AAAAAAT
1 AAAAAAT
*
40342303 -AGAAAT
1 AAAAAAT
40342309 AGAAAAAT
1 A-AAAAAT
40342317 -AAAAAT
1 AAAAAAT
40342323 AAAAATAAT
1 -AAAA-AAT
40342332 AAAACATAT
1 AAAA-A-AT
40342341 AAAAAATT
1 AAAAAA-T
*
40342349 AAAATAT
1 AAAAAAT
40342356 AAAAAAT
1 AAAAAAT
*
40342363 TAAAAAT
1 AAAAAAT
40342370 A
1 A
40342371 TAAGTATAAG
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
6 11 0.20
7 14 0.26
8 20 0.37
9 9 0.17
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (7 bp):
AAAAAAT
Found at i:40342332 original size:15 final size:14
Alignment explanation
Indices: 40342295--40342370 Score: 80
Period size: 14 Copynumber: 5.1 Consensus size: 14
40342285 AAACAAATAC
*
40342295 AAAAAAATAGAAAT
1 AAAAAAATAAAAAT
*
40342309 AGAAAAATAAAAAT
1 AAAAAAATAAAAAT
40342323 AAAAATAATAAAACAT
1 AAAAA-AATAAAA-AT
40342339 ATAAAAAATTAAAATAT
1 A-AAAAAA-TAAAA-AT
*
40342356 AAAAAATTAAAAAT
1 AAAAAAATAAAAAT
40342370 A
1 A
40342371 TAAGTATAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
14 19 0.36
15 12 0.23
16 10 0.19
17 12 0.23
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (14 bp):
AAAAAAATAAAAAT
Found at i:40342353 original size:31 final size:31
Alignment explanation
Indices: 40342289--40342373 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 31
40342279 ATAGTAAAAC
* * * *
40342289 AAATACAAAAAAATAGAAATA-GAAAAATAA
1 AAATATAAAAAATTAAAAATATAAAAAATAA
*
40342319 AAATA-AAAATAA-TAAAACATATAAAAAATTA
1 AAATATAAAA-AATTAAAA-ATATAAAAAATAA
40342350 AAATATAAAAAATTAAAAATATAA
1 AAATATAAAAAATTAAAAATATAA
40342374 GTATAAGAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
29 8 0.17
30 10 0.21
31 20 0.43
32 9 0.19
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.20
Consensus pattern (31 bp):
AAATATAAAAAATTAAAAATATAAAAAATAA
Found at i:40342368 original size:16 final size:15
Alignment explanation
Indices: 40342296--40342373 Score: 88
Period size: 16 Copynumber: 5.1 Consensus size: 15
40342286 AACAAATACA
*
40342296 AAAAAATAGAAATA-
1 AAAAAATAAAAATAT
*
40342310 GAAAAATAAAAATA-
1 AAAAAATAAAAATAT
40342324 AAAATAATAAAACATAT
1 AAAA-AATAAAA-ATAT
*
40342341 AAAAAATTAAAATAT
1 AAAAAATAAAAATAT
40342356 AAAAAATTAAAAATAT
1 AAAAAA-TAAAAATAT
40342372 AA
1 AA
40342374 GTATAAGAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
14 15 0.27
15 17 0.31
16 19 0.35
17 4 0.07
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.21
Consensus pattern (15 bp):
AAAAAATAAAAATAT
Found at i:40342424 original size:15 final size:15
Alignment explanation
Indices: 40342396--40342436 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
40342386 TTAATTAATT
* *
40342396 AATTAGTAAAATAAA
1 AATTAATAATATAAA
40342411 AATTAATAATATAAA
1 AATTAATAATATAAA
40342426 AATTAATAATA
1 AATTAATAATA
40342437 AATAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (15 bp):
AATTAATAATATAAA
Found at i:40345710 original size:39 final size:39
Alignment explanation
Indices: 40345655--40345743 Score: 164
Period size: 39 Copynumber: 2.3 Consensus size: 39
40345645 TACCAGAAGC
40345655 AAATAAAA-G-AAAAGTTAGTAAATTAAAGTAAAAACAA
1 AAATAAAATGCAAAAGTTAGTAAATTAAAGTAAAAACAA
40345692 AAATAAAATGCAAAAGTTAGTAAATTAAAGTAAAAACAA
1 AAATAAAATGCAAAAGTTAGTAAATTAAAGTAAAAACAA
40345731 AAATAAAATGCAA
1 AAATAAAATGCAA
40345744 TAAAAATAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
37 8 0.16
38 1 0.02
39 41 0.82
ACGTcount: A:0.66, C:0.04, G:0.10, T:0.19
Consensus pattern (39 bp):
AAATAAAATGCAAAAGTTAGTAAATTAAAGTAAAAACAA
Found at i:40355899 original size:82 final size:84
Alignment explanation
Indices: 40355762--40355981 Score: 295
Period size: 84 Copynumber: 2.6 Consensus size: 84
40355752 TATTCGGGCT
* * * * *
40355762 TTATTGCCTAGCAAGCTTTGTGCCGCTGTATTAAATCAGGCTTATTTCCTAGCAGGC-TT-TGTG
1 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTATATCAGGCTTATTGCCTAGCAGGCTTTATATG
*
40355825 CCGGTGTATTAAATCAGGC
66 CCGGTGTATTAAATCAGAC
*
40355844 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTATATCAGGCTTATTGCCTAGCAGGCTTTATATT
1 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTATATCAGGCTTATTGCCTAGCAGGCTTTATATG
* *
40355909 TCGGTGTATTATATCAGAC
66 CCGGTGTATTAAATCAGAC
* *
40355928 TTATTGCCTAGCAGGCTCTGTGTCGGTGTATTATA-CTAGGCTT-TATGCCTAGCA
1 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTATATC-AGGCTTAT-TGCCTAGCA
40355982 AATTTTATGT
Statistics
Matches: 123, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
82 53 0.43
83 4 0.03
84 66 0.54
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (84 bp):
TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTATATCAGGCTTATTGCCTAGCAGGCTTTATATG
CCGGTGTATTAAATCAGAC
Found at i:40355931 original size:43 final size:41
Alignment explanation
Indices: 40355762--40355981 Score: 282
Period size: 41 Copynumber: 5.3 Consensus size: 41
40355752 TATTCGGGCT
* *
40355762 TTATTGCCTAGCAAGCTTTGTGCCGCTGTATTAAATCAGGC
1 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTAAATCAGGC
*
40355803 TTATTTCCTAGCAGGCTTTGTGCCGGTGTATTAAATCAGGC
1 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTAAATCAGGC
*
40355844 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTATATCAGGC
1 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTAAATCAGGC
* ** * *
40355885 TTATTGCCTAGCAGGCTTTATATTTCGGTGTATTATATCAGAC
1 TTATTGCCTAGCAGGC-TT-TGTGCCGGTGTATTAAATCAGGC
* * *
40355928 TTATTGCCTAGCAGGCTCTGTGTCGGTGTATTATA-CTAGGC
1 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTAAATC-AGGC
40355969 TT-TATGCCTAGCA
1 TTAT-TGCCTAGCA
40355982 AATTTTATGT
Statistics
Matches: 162, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
40 2 0.01
41 122 0.75
42 3 0.02
43 35 0.22
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (41 bp):
TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTAAATCAGGC
Found at i:40361205 original size:28 final size:28
Alignment explanation
Indices: 40361142--40361242 Score: 114
Period size: 28 Copynumber: 3.6 Consensus size: 28
40361132 AATCACAAAT
* *
40361142 TAGCACTAAGTGTGCGGGTTCAAATTATA
1 TAGCACTAAGTGTGCGAGTT-AGATTATA
* * *
40361171 CAGCACTAAGTGTGCAAGTTTGATTATA
1 TAGCACTAAGTGTGCGAGTTAGATTATA
* *
40361199 TAGCACTAAGTGTGCGAGTTCGACTAT-
1 TAGCACTAAGTGTGCGAGTTAGATTATA
40361226 TAAGCACTAAGTGTGCG
1 T-AGCACTAAGTGTGCG
40361243 GGCTTATTGC
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
27 1 0.02
28 44 0.71
29 17 0.27
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (28 bp):
TAGCACTAAGTGTGCGAGTTAGATTATA
Found at i:40371798 original size:21 final size:21
Alignment explanation
Indices: 40371772--40371814 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
40371762 CTGACCATAT
40371772 GGGCGTGTCCCCAGAGCACAC
1 GGGCGTGTCCCCAGAGCACAC
* *
40371793 GGGCGTGTGCCCAGATCACAC
1 GGGCGTGTCCCCAGAGCACAC
40371814 G
1 G
40371815 ATCGTGTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.35, G:0.35, T:0.12
Consensus pattern (21 bp):
GGGCGTGTCCCCAGAGCACAC
Found at i:40371820 original size:21 final size:21
Alignment explanation
Indices: 40371774--40371822 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
40371764 GACCATATGG
* *
40371774 GCGTGTCCCCAGAGCACACGG
1 GCGTGTGCCCAGAGCACACGA
*
40371795 GCGTGTGCCCAGATCACACGA
1 GCGTGTGCCCAGAGCACACGA
*
40371816 TCGTGTG
1 GCGTGTG
40371823 AGCCCTGCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.33, G:0.33, T:0.16
Consensus pattern (21 bp):
GCGTGTGCCCAGAGCACACGA
Found at i:40373321 original size:14 final size:14
Alignment explanation
Indices: 40373302--40373331 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40373292 TTAAACCTAG
40373302 ACCAATCCAAATCA
1 ACCAATCCAAATCA
*
40373316 ACCAATCCAATTCA
1 ACCAATCCAAATCA
40373330 AC
1 AC
40373332 ATATTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACCAATCCAAATCA
Found at i:40373870 original size:41 final size:41
Alignment explanation
Indices: 40373787--40374005 Score: 305
Period size: 41 Copynumber: 5.4 Consensus size: 41
40373777 TGTTTTACCA
* * * *
40373787 AAAACACCGCTAAAAA-CAGTGCAATAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGT
* *
40373827 AAAACGCCACTAAAAACCAGAGCATTAGCAGCGCTTTCGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGT
40373868 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGT
* **
40373909 AAAACGCCGCTAAAAACCAGAGCAATAGCGATGCTTTCGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGT
* * * **
40373950 AAAACGCCGCTAAAAACCAGAACATTAACGGTGCTTTCAAT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGT
40373991 AAAACGCCGCTAAAA
1 AAAACGCCGCTAAAA
40374006 GTTATATAAC
Statistics
Matches: 161, Mismatches: 17, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
40 14 0.09
41 147 0.91
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.17
Consensus pattern (41 bp):
AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGT
Found at i:40374088 original size:17 final size:17
Alignment explanation
Indices: 40374066--40374101 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40374056 CCTAAAACAC
* *
40374066 AAAAACTCTAAACCCTA
1 AAAAACCCTAAACACTA
40374083 AAAAACCCTAAACACTA
1 AAAAACCCTAAACACTA
40374100 AA
1 AA
40374102 CTATAACCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.58, C:0.28, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAAACCCTAAACACTA
Found at i:40374904 original size:8 final size:8
Alignment explanation
Indices: 40374886--40374981 Score: 139
Period size: 8 Copynumber: 12.4 Consensus size: 8
40374876 AAATCAAAAT
40374886 AAAAATT-
1 AAAAATTA
40374893 AAAAATT-
1 AAAAATTA
40374900 AAAAATT-
1 AAAAATTA
40374907 AAAAATT-
1 AAAAATTA
40374914 -AAAATTA
1 AAAAATTA
40374921 AAAAATTA
1 AAAAATTA
40374929 AAAAATTA
1 AAAAATTA
40374937 AAAAATTAA
1 AAAAATT-A
40374946 AAAAATTAA
1 AAAAATT-A
40374955 AAAAATTA
1 AAAAATTA
40374963 AAAAATTA
1 AAAAATTA
40374971 AAAAATTA
1 AAAAATTA
40374979 AAA
1 AAA
40374982 TTAATATTTT
Statistics
Matches: 86, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
6 6 0.07
7 21 0.24
8 42 0.49
9 17 0.20
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
AAAAATTA
Found at i:40374904 original size:14 final size:15
Alignment explanation
Indices: 40374881--40374985 Score: 130
Period size: 14 Copynumber: 7.0 Consensus size: 15
40374871 ACATTAAATC
40374881 AAAA-TAAAAATT-A
1 AAAATTAAAAATTAA
40374894 AAAATTAAAAATT-A
1 AAAATTAAAAATTAA
40374908 AAAATT-AAAATTAA
1 AAAATTAAAAATTAA
40374922 AAAATTAAAAAATTAA
1 AAAATT-AAAAATTAA
40374938 AAAATTAAAAAAATTAAA
1 AAAATT--AAAAATT-AA
40374956 AAAATTAAAAAATTAA
1 AAAATT-AAAAATTAA
40374972 AAAATT-AAAATTAA
1 AAAATTAAAAATTAA
40374986 TATTTTAGTC
Statistics
Matches: 86, Mismatches: 0, Indels: 11
0.89 0.00 0.11
Matches are distributed among these distances:
13 10 0.12
14 30 0.35
16 22 0.26
17 16 0.19
18 8 0.09
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATTAAAAATTAA
Found at i:40374963 original size:34 final size:33
Alignment explanation
Indices: 40374886--40374981 Score: 141
Period size: 34 Copynumber: 3.1 Consensus size: 33
40374876 AAATCAAAAT
40374886 AAAAATT-AAAAATT-AAAAATT-AAAAATT--
1 AAAAATTAAAAAATTAAAAAATTAAAAAATTAA
40374914 -AAAATTAAAAAATTAAAAAATTAAAAAATTAA
1 AAAAATTAAAAAATTAAAAAATTAAAAAATTAA
40374946 AAAAATTAAAAAAATTAAAAAATTAAAAAATTAA
1 AAAAATT-AAAAAATTAAAAAATTAAAAAATTAA
40374980 AA
1 AA
40374982 TTAATATTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
27 6 0.10
28 7 0.11
29 7 0.11
30 7 0.11
33 6 0.10
34 28 0.46
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (33 bp):
AAAAATTAAAAAATTAAAAAATTAAAAAATTAA
Found at i:40374965 original size:6 final size:6
Alignment explanation
Indices: 40374876--40374923 Score: 51
Period size: 7 Copynumber: 7.5 Consensus size: 6
40374866 ATTACACATT
* *
40374876 AAATCA AAATAA AAATTAA AAATTAA AAATTAA AAATTA AAATTA AAA
1 AAATTA AAATTA AAATT-A AAATT-A AAATT-A AAATTA AAATTA AAA
40374924 AATTAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
6 19 0.49
7 20 0.51
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (6 bp):
AAATTA
Found at i:40375091 original size:20 final size:20
Alignment explanation
Indices: 40375068--40375155 Score: 78
Period size: 20 Copynumber: 4.6 Consensus size: 20
40375058 ATTTGAAAGA
40375068 AAAAATAAAAAATATATGTT
1 AAAAATAAAAAATATATGTT
40375088 AAAAATGAAAAAA-A-A---T
1 AAAAAT-AAAAAATATATGTT
* * * * **
40375104 AAAATTAAACAATAAAAGAA
1 AAAAATAAAAAATATATGTT
40375124 AAAAATAAAAAATATATGTT
1 AAAAATAAAAAATATATGTT
40375144 AAAAATAAAAAA
1 AAAAATAAAAAA
40375156 AATAAAATTA
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
15 5 0.09
16 7 0.13
17 1 0.02
19 1 0.02
20 33 0.62
21 6 0.11
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.20
Consensus pattern (20 bp):
AAAAATAAAAAATATATGTT
Found at i:40375122 original size:55 final size:55
Alignment explanation
Indices: 40375063--40375172 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
40375053 AAAAAATTTG
40375063 AAAG-AAAAAATAAAAAATATATGTTAAAAATGAAAAAAAATAAAATTAAACAATA
1 AAAGAAAAAAATAAAAAATATATGTTAAAAAT-AAAAAAAATAAAATTAAACAATA
40375118 AAAGAAAAAAATAAAAAATATATGTTAAAAATAAAAAAAATAAAATTAAACAATA
1 AAAGAAAAAAATAAAAAATATATGTTAAAAATAAAAAAAATAAAATTAAACAATA
40375173 GTGGCGTTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
55 27 0.50
56 27 0.50
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.20
Consensus pattern (55 bp):
AAAGAAAAAAATAAAAAATATATGTTAAAAATAAAAAAAATAAAATTAAACAATA
Found at i:40378992 original size:19 final size:19
Alignment explanation
Indices: 40378970--40379010 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
40378960 TTTATTGATA
40378970 TTTTTA-TATTTAATCTAG
1 TTTTTATTATTTAATCTAG
* *
40378988 TTTTTATTATTTATTTTAG
1 TTTTTATTATTTAATCTAG
40379007 TTTT
1 TTTT
40379011 GATTCTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTATTATTTAATCTAG
Found at i:40399820 original size:17 final size:17
Alignment explanation
Indices: 40399798--40399836 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
40399788 AACCAGAACT
*
40399798 ACACCAGAATAAGCTCA
1 ACACCAGAACAAGCTCA
40399815 ACACCAGAACAAGCTCA
1 ACACCAGAACAAGCTCA
40399832 ACACC
1 ACACC
40399837 TTCCCACATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.46, C:0.36, G:0.10, T:0.08
Consensus pattern (17 bp):
ACACCAGAACAAGCTCA
Found at i:40406740 original size:17 final size:18
Alignment explanation
Indices: 40406718--40406751 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
40406708 AAATACTAAC
40406718 AATTAAAT-AAATTGAAA
1 AATTAAATAAAATTGAAA
40406735 AATTAAATAAAATTGAA
1 AATTAAATAAAATTGAA
40406752 TTTTGGGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
AATTAAATAAAATTGAAA
Found at i:40407575 original size:30 final size:31
Alignment explanation
Indices: 40407517--40407576 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
40407507 TGCTTTTGAA
* *
40407517 AATATTTACAAAAAAGAGATATCTAATTTTT
1 AATATTTACAAAAAAGAGATACCAAATTTTT
40407548 AATATTTAC-AAAAAGAGCA-ACCAAATTTT
1 AATATTTACAAAAAAGAG-ATACCAAATTTT
40407577 GAAAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (31 bp):
AATATTTACAAAAAAGAGATACCAAATTTTT
Found at i:40409521 original size:27 final size:27
Alignment explanation
Indices: 40409490--40409649 Score: 182
Period size: 27 Copynumber: 5.9 Consensus size: 27
40409480 CTGCCAGAAT
* *
40409490 AGATA-ATGTGACAGAGTCACCAGATAC
1 AGATATATGTGGCAGAGCCACCAGAT-C
* * *
40409517 AGATA-ATCATGGCA-AGGCCACTAGAAC
1 AGATATAT-GTGGCAGA-GCCACCAGATC
*
40409544 AGATATCTGTGGCAGAGCCACCAGATC
1 AGATATATGTGGCAGAGCCACCAGATC
*
40409571 AGATATTTGTGGCAGAGCCACCAGATC
1 AGATATATGTGGCAGAGCCACCAGATC
*
40409598 AGATATTTGTGGCAGAGCCACCAGATC
1 AGATATATGTGGCAGAGCCACCAGATC
* *
40409625 AGATATTTGTGGCATAGCCACCAGA
1 AGATATATGTGGCAGAGCCACCAGA
40409650 ACGCTTCCTC
Statistics
Matches: 118, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
27 105 0.89
28 13 0.11
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (27 bp):
AGATATATGTGGCAGAGCCACCAGATC
Found at i:40409601 original size:81 final size:82
Alignment explanation
Indices: 40409496--40409649 Score: 204
Period size: 81 Copynumber: 1.9 Consensus size: 82
40409486 GAATAGATAA
* *
40409496 TGTGACAGAGTCACCAGATACAGATAATCATGGCA-AGGCCACTAGAACAGATATCTGTGGCAGA
1 TGTGACAGAGCCACCAGATACAGATAATCATGGCAGA-GCCACCAGAACAGATATCTGTGGCAGA
40409560 GCCACCAGATCAGATATT
65 GCCACCAGATCAGATATT
* * ** * * *
40409578 TGTGGCAGAGCCACCAGAT-CAGATATTTGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAG
1 TGTGACAGAGCCACCAGATACAGATAATCATGGCAGAGCCACCAGAACAGATATCTGTGGCAGAG
40409642 CCACCAGA
66 CCACCAGA
40409650 ACGCTTCCTC
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
81 44 0.71
82 18 0.29
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (82 bp):
TGTGACAGAGCCACCAGATACAGATAATCATGGCAGAGCCACCAGAACAGATATCTGTGGCAGAG
CCACCAGATCAGATATT
Found at i:40411304 original size:26 final size:26
Alignment explanation
Indices: 40411268--40411403 Score: 218
Period size: 26 Copynumber: 5.2 Consensus size: 26
40411258 CATGATATTC
40411268 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
40411294 TTATCATGAAATATTTACCTAACCCG
1 TTATCATGAAACATTTACCTAACCCA
* *
40411320 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
40411346 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
40411372 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
40411398 TTATCA
1 TTATCA
40411404 ATTTGTATCA
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 100 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:40415231 original size:19 final size:21
Alignment explanation
Indices: 40415207--40415245 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40415197 TGCTATTTAG
40415207 AGTTTC-CA-AAGAAAAATCC
1 AGTTTCACAGAAGAAAAATCC
*
40415226 AGTTTCACAGCAGAAAAATC
1 AGTTTCACAGAAGAAAAATC
40415246 AGTGTCCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.46, C:0.21, G:0.13, T:0.21
Consensus pattern (21 bp):
AGTTTCACAGAAGAAAAATCC
Found at i:40415255 original size:21 final size:21
Alignment explanation
Indices: 40415216--40415255 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
40415206 GAGTTTCCAA
*
40415216 AGAAAAATCCAGTTTCACAGC
1 AGAAAAATCCAGTTCCACAGC
40415237 AGAAAAAT-CAGTGTCCACA
1 AGAAAAATCCAGT-TCCACA
40415256 ACCATAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.45, C:0.23, G:0.15, T:0.17
Consensus pattern (21 bp):
AGAAAAATCCAGTTCCACAGC
Found at i:40416825 original size:31 final size:31
Alignment explanation
Indices: 40416784--40416847 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
40416774 CCTTTTCATA
*
40416784 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
40416815 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
40416846 TT
1 TT
40416848 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:40417086 original size:23 final size:24
Alignment explanation
Indices: 40417055--40417205 Score: 227
Period size: 23 Copynumber: 6.4 Consensus size: 24
40417045 CTGGAGGCCT
40417055 AGCCTCTTTTAATAACTGGGGCA-A
1 AGCC-CTTTTAATAACTGGGGCATA
40417079 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
**
40417103 AGCCC-TTTAATAACTGGGGTGTA
1 AGCCCTTTTAATAACTGGGGCATA
*
40417126 AGCCCTTTTGATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
40417150 AGCCCTTTTGATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
40417174 AGCCC-TTTAATAACTGGGGCCTA
1 AGCCCTTTTAATAACTGGGGCATA
40417197 AGCCCTTTT
1 AGCCCTTTT
40417206 TCACTTCCTC
Statistics
Matches: 117, Mismatches: 7, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
23 60 0.51
24 57 0.49
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.30
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:40417205 original size:47 final size:48
Alignment explanation
Indices: 40417055--40417205 Score: 227
Period size: 47 Copynumber: 3.2 Consensus size: 48
40417045 CTGGAGGCCT
40417055 AGCCTCTTTTAATAACTGGGGCA-AAGCCCTTTTAATAACTGGGGCATA
1 AGCC-CTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATA
** *
40417103 AGCCC-TTTAATAACTGGGGTGTAAGCCCTTTTGATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATA
* *
40417150 AGCCCTTTTGATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCCTA
1 AGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATA
40417197 AGCCCTTTT
1 AGCCCTTTT
40417206 TCACTTCCTC
Statistics
Matches: 93, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
46 14 0.15
47 55 0.59
48 24 0.26
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.30
Consensus pattern (48 bp):
AGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATA
Found at i:40417277 original size:9 final size:9
Alignment explanation
Indices: 40417263--40417288 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
40417253 ACATCATGTG
40417263 CATATCATA
1 CATATCATA
40417272 CATATCATA
1 CATATCATA
40417281 CATATCAT
1 CATATCAT
40417289 GTGCAGATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:40417298 original size:20 final size:20
Alignment explanation
Indices: 40417275--40417330 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
40417265 TATCATACAT
40417275 ATCATACATATCATGTGCAG
1 ATCATACATATCATGTGCAG
* ***
40417295 ATCATACATTTCATGTGTTT
1 ATCATACATATCATGTGCAG
*
40417315 ATCATACATACCATGT
1 ATCATACATATCATGT
40417331 TTATCAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (20 bp):
ATCATACATATCATGTGCAG
Found at i:40417347 original size:17 final size:18
Alignment explanation
Indices: 40417310--40417347 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
40417300 ACATTTCATG
*
40417310 TGTTTATCATACATACCA
1 TGTTTATCATAAATACCA
*
40417328 TGTTTATCA-AAATCCCA
1 TGTTTATCATAAATACCA
40417345 TGT
1 TGT
40417348 ATTAAAATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (18 bp):
TGTTTATCATAAATACCA
Found at i:40417399 original size:25 final size:25
Alignment explanation
Indices: 40417367--40417414 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
40417357 ATACATAAAC
* * *
40417367 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
40417392 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
40417415 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:40421071 original size:16 final size:17
Alignment explanation
Indices: 40421052--40421083 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
40421042 GAAAGTGACA
40421052 AAATTAAA-AGATAATT
1 AAATTAAATAGATAATT
40421068 AAATTAAATAGATAAT
1 AAATTAAATAGATAAT
40421084 ATCATCTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (17 bp):
AAATTAAATAGATAATT
Found at i:40423367 original size:42 final size:42
Alignment explanation
Indices: 40423320--40423413 Score: 179
Period size: 42 Copynumber: 2.2 Consensus size: 42
40423310 AGAGACACAG
40423320 GCGTGTGTCTCAGCTGTGTGTACTACACAGCCCAGAACACGA
1 GCGTGTGTCTCAGCTGTGTGTACTACACAGCCCAGAACACGA
*
40423362 GCGTGTGTCTCAGCTGTGTGTACTACACAGCCCAGAACACGG
1 GCGTGTGTCTCAGCTGTGTGTACTACACAGCCCAGAACACGA
40423404 GCGTGTGTCT
1 GCGTGTGTCT
40423414 TGGCCATATG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.20, C:0.28, G:0.29, T:0.23
Consensus pattern (42 bp):
GCGTGTGTCTCAGCTGTGTGTACTACACAGCCCAGAACACGA
Found at i:40425464 original size:27 final size:29
Alignment explanation
Indices: 40425434--40425518 Score: 75
Period size: 30 Copynumber: 3.0 Consensus size: 29
40425424 ATACAAGAGC
*
40425434 ATATA-GTGAATC-CGCACACTTAGTGCT
1 ATATATGTGAAGCTCGCACACTTAGTGCT
* **
40425461 ATATATTTTCAGCTCGCACACTTAGTGCT
1 ATATATGTGAAGCTCGCACACTTAGTGCT
* * * *
40425490 ATATAATTTTAAACCCGCACACTTAGTGC
1 ATAT-ATGTGAAGCTCGCACACTTAGTGC
40425519 CAATCTTGTC
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
27 5 0.10
28 3 0.06
29 19 0.40
30 21 0.44
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (29 bp):
ATATATGTGAAGCTCGCACACTTAGTGCT
Found at i:40425478 original size:29 final size:30
Alignment explanation
Indices: 40425445--40425518 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
40425435 TATAGTGAAT
* *
40425445 CCGCACACTTAGTGCTATAT-ATTTTCAGC
1 CCGCACACTTAGTGCTATATAATTTTAAAC
*
40425474 TCGCACACTTAGTGCTATATAATTTTAAAC
1 CCGCACACTTAGTGCTATATAATTTTAAAC
40425504 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
40425519 CAATCTTGTC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 19 0.47
30 21 0.52
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (30 bp):
CCGCACACTTAGTGCTATATAATTTTAAAC
Found at i:40427980 original size:40 final size:40
Alignment explanation
Indices: 40427918--40428173 Score: 260
Period size: 40 Copynumber: 6.4 Consensus size: 40
40427908 AAACCAAGTA
* * *
40427918 CCTTCGGGATTTA-ACCGGATA-TAGCTAATCACTCAAATG
1 CCTTCGGGACTTAGCCCGGATATTAG-TAATCACACAAATG
* * *
40427957 CCTTCGGGACTTAGCCCGGATA-TAGTAGTTCGCACAAACG
1 CCTTCGGGACTTAGCCCGGATATTAGTA-ATCACACAAATG
*
40427997 CCTTCGGGACTTAGCCCGGAT-TTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATTAGTAA-TCACACAAATG
*
40428037 CCTTCGGGACTTAGCCCGGA-ATTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATTAGTAA-TCACACAAATG
* * *
40428077 CCTTCGGGACTTAGCTC-GAAATTAGTCA-CTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATTAGTAATC-A-CACAAATG
* *
40428117 CCTTCGGGACTTAGCCCAGA-ATTAGTCA-CTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATTAGTAATC-A-CACAAATG
40428157 CCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
40428174 CGTTATCATC
Statistics
Matches: 196, Mismatches: 12, Indels: 17
0.87 0.05 0.08
Matches are distributed among these distances:
38 1 0.01
39 16 0.08
40 177 0.90
41 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATTAGTAATCACACAAATG
Found at i:40428050 original size:80 final size:79
Alignment explanation
Indices: 40427951--40428173 Score: 322
Period size: 80 Copynumber: 2.8 Consensus size: 79
40427941 GCTAATCACT
* *
40427951 CAAATGCCTTCGGGACTTAGCCCGG-ATATAGTAGTTCGCACAAACGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA-CTCGCACAAATGCCTTCGGGACTTAGCCCG
* * *
40428015 GATTTAGTAACTCGCA
64 AAATTAGTAACTAGCA
*
40428031 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGGACTTAGCTCGA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGA
*
40428096 AATTAGTCACTAGCA
65 AATTAGTAACTAGCA
* *
40428111 CAAATGCCTTCGGGACTTAGCCCAGAATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCC
40428174 CGTTATCATC
Statistics
Matches: 130, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
80 127 0.98
81 3 0.02
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGAA
ATTAGTAACTAGCA
Found at i:40428152 original size:120 final size:120
Alignment explanation
Indices: 40427951--40428173 Score: 333
Period size: 120 Copynumber: 1.9 Consensus size: 120
40427941 GCTAATCACT
* * * *
40427951 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAGTTCGCACAAACGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGAATATAGTAGCTAGCACAAACGCCTTCGGGACTTAGCCCAG
* *
40428016 ATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
66 AATTAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* *
40428071 CAAATGCCTTCGGGACTTAGCTCGAA-ATTAGTCA-CTAGCACAAATGCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCCGAATA-TAGT-AGCTAGCACAAACGCCTTCGGGACTTAGCCC
*
40428134 AGAATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCC
64 AGAATTAGTAACTAGCACAAATGCCTTCGGGACTTAGCCC
40428174 CGTTATCATC
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
119 1 0.01
120 90 0.98
121 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (120 bp):
CAAATGCCTTCGGGACTTAGCCCGAATATAGTAGCTAGCACAAACGCCTTCGGGACTTAGCCCAG
AATTAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:40436006 original size:40 final size:40
Alignment explanation
Indices: 40435944--40436196 Score: 347
Period size: 39 Copynumber: 6.4 Consensus size: 40
40435934 AAACCAAGTA
* * *
40435944 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
**
40435983 CCTTCGGGACTTAGCCCGGATATAGTAGTTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
40436023 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
40436063 CCTTCGGGACTTAGCCCGAAT-TAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
40436102 CCTTCGGGACTTAGCCCGAAT-TAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
40436141 CCTTCGGGACTTAG-CCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
40436180 CCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
40436197 CGTTATCATC
Statistics
Matches: 198, Mismatches: 11, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
38 4 0.02
39 114 0.58
40 80 0.40
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:40448018 original size:20 final size:20
Alignment explanation
Indices: 40447993--40448043 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
40447983 TGTCAAAATA
40447993 ACACGGGCGTGTGCCTGTAT
1 ACACGGGCGTGTGCCTGTAT
40448013 ACACGGGCGTGTGCCTGTAT
1 ACACGGGCGTGTGCCTGTAT
*
40448033 ACACAGGCGTG
1 ACACGGGCGTG
40448044 GGAGAAACGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.18, C:0.25, G:0.35, T:0.22
Consensus pattern (20 bp):
ACACGGGCGTGTGCCTGTAT
Found at i:40454428 original size:55 final size:54
Alignment explanation
Indices: 40454341--40454595 Score: 244
Period size: 55 Copynumber: 4.8 Consensus size: 54
40454331 ATTAGGGTTT
* *
40454341 AAGGATACCGTGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAA-GTTTCTAAGGC
* * * * *
40454396 AAGGAAATCATGTAAGACCATGTCAAGACATGGC-ATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTT--TCTAAGGC
* * *
40454451 AAAGG-TCCCATGTAAGACCATGCCAAGGCAT--CACATTGGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCA-ATTGGTAAGTTTC-TAAGGC
* *
40454504 AAGGCTACCATGTAAGACCATGTCAAGACATGGCAA-TGGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGGC
* * *
40454553 AAGGATACCACGTAAGACCATGACAAGTCATGGCAA-TGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAG
40454596 GTACCCGTGT
Statistics
Matches: 167, Mismatches: 23, Indels: 26
0.77 0.11 0.12
Matches are distributed among these distances:
49 39 0.23
52 7 0.04
53 39 0.23
54 12 0.07
55 66 0.40
56 4 0.02
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGTTTCTAAGGC
Found at i:40454547 original size:108 final size:109
Alignment explanation
Indices: 40454351--40454548 Score: 294
Period size: 108 Copynumber: 1.8 Consensus size: 109
40454341 AAGGATACCG
*
40454351 TGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGACCA
1 TGTAAGACCATGCCAAGGCAT-GCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGACCA
*
40454416 TGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTCCCA
65 TGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCCCA
* **
40454461 TGTAAGACCATGCCAAGGCAT-CACATTGGTGA-G-TTCATAAGGCAAGGCTACCATGTAAGACC
1 TGTAAGACCATGCCAAGGCATGCA-ATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAGACC
*
40454523 ATGTCAAGACATGGCAATGGTAAGTT
64 ATGTCAAGACATGGCAATGATAAGTT
40454549 TCAAAAGGAT
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
107 3 0.04
108 49 0.61
109 7 0.09
110 21 0.26
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (109 bp):
TGTAAGACCATGCCAAGGCATGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGACCAT
GTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCCCA
Found at i:40454808 original size:16 final size:16
Alignment explanation
Indices: 40454787--40454817 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40454777 ATAAATTTGA
40454787 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
40454803 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
40454818 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:40473019 original size:55 final size:55
Alignment explanation
Indices: 40472932--40473180 Score: 234
Period size: 55 Copynumber: 4.7 Consensus size: 55
40472922 ATTAGGGTTT
* * *
40472932 AAGGATACCGTGTAAGACCATGCCAAGGCATGGCAATTGGTTAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTTAAGTTTCTAAGGC
* * * * *
40472987 AAGGAAATCATGTAAGACCATGTCAAGACATGGC-ATT-GATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTTAAGTT--TCTAAGGC
* * *
40473042 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGC-ATTGG-TGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTTAAGTTTC-TAAGGC
* * *
40473095 AAGGCTACCATGTAAGACCATGTCAAGACATGG-AAATGG-TAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTTAAGTTTCTAAGGC
* *
40473144 AAGGATACCATGTAAGACCATGACAAGTCATGGCAAT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAAT
40473181 GGTAAGGTAC
Statistics
Matches: 161, Mismatches: 24, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
49 30 0.19
50 2 0.01
52 7 0.04
53 44 0.27
54 7 0.04
55 66 0.41
56 5 0.03
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (55 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTTAAGTTTCTAAGGC
Found at i:40473138 original size:108 final size:110
Alignment explanation
Indices: 40472942--40473139 Score: 303
Period size: 108 Copynumber: 1.8 Consensus size: 110
40472932 AAGGATACCG
* *
40472942 TGTAAGACCATGCCAAGGCATGGCAATTGGTTAGGTTTCTAAGGCAAGGAAATCATGTAAGACCA
1 TGTAAGACCATGCCAAGGCATGGCAATTGGTGAGGTTTCTAAGGCAAGGAAACCATGTAAGACCA
* *
40473007 TGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTCCCA
66 TGTCAAGACATGGAAATGATAAGTTACTATAAGGCAAAGGTCCCA
**
40473052 TGTAAGACCATGCCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGCTACCATGTAAGACC
1 TGTAAGACCATGCCAAGGCATGGCAATTGGTGAGGTTTC-TAAGGCAAGGAAACCATGTAAGACC
*
40473114 ATGTCAAGACATGGAAATGGTAAGTT
65 ATGTCAAGACATGGAAATGATAAGTT
40473140 TCAAAAGGAT
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
107 3 0.04
108 46 0.57
109 7 0.09
110 24 0.30
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (110 bp):
TGTAAGACCATGCCAAGGCATGGCAATTGGTGAGGTTTCTAAGGCAAGGAAACCATGTAAGACCA
TGTCAAGACATGGAAATGATAAGTTACTATAAGGCAAAGGTCCCA
Found at i:40473399 original size:16 final size:16
Alignment explanation
Indices: 40473378--40473408 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40473368 ATAAATTTGA
40473378 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
40473394 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
40473409 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:40477451 original size:17 final size:17
Alignment explanation
Indices: 40477429--40477465 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
40477419 TGCACAGGTC
*
40477429 ACCCGAGACGACTGTGG
1 ACCCGAGACGACTATGG
40477446 ACCCGAGACGACTATGG
1 ACCCGAGACGACTATGG
40477463 ACC
1 ACC
40477466 TACTGTTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.27, C:0.32, G:0.30, T:0.11
Consensus pattern (17 bp):
ACCCGAGACGACTATGG
Found at i:40478108 original size:20 final size:20
Alignment explanation
Indices: 40478080--40478119 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40478070 GAGGTGGCCA
*
40478080 CACATCTGCATGGACTTTCT
1 CACAACTGCATGGACTTTCT
*
40478100 CACAACTGCGTGGACTTTCT
1 CACAACTGCATGGACTTTCT
40478120 TATTACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.30, G:0.17, T:0.33
Consensus pattern (20 bp):
CACAACTGCATGGACTTTCT
Found at i:40479072 original size:25 final size:25
Alignment explanation
Indices: 40478994--40479076 Score: 103
Period size: 25 Copynumber: 3.3 Consensus size: 25
40478984 GCTATAATCG
* *
40478994 GTAAGCTCATACGAGCTGAGTAACA
1 GTAAGCTCATACGAGCTGAATAATA
**
40479019 GTAAGCTCATACGAATTGAATAATA
1 GTAAGCTCATACGAGCTGAATAATA
* * *
40479044 GTAAGCTCATACGAGCTAAATATTG
1 GTAAGCTCATACGAGCTGAATAATA
40479069 GTAAGCTC
1 GTAAGCTC
40479077 TCTCGAGATG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.25
Consensus pattern (25 bp):
GTAAGCTCATACGAGCTGAATAATA
Found at i:40480616 original size:29 final size:28
Alignment explanation
Indices: 40480582--40480684 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
40480572 TACTCAATCA
*
40480582 CGCACACTTAGTGCCATATGATTCAAGCC
1 CGCACACTTAGTGCCATAT-ATTCAAGCT
* * *
40480611 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATATA-TTCAAGCT
* *
40480640 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCATATATT-CAAGCT
*
40480669 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
40480685 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTCAAGCT
Found at i:40485185 original size:45 final size:45
Alignment explanation
Indices: 40485083--40485489 Score: 552
Period size: 45 Copynumber: 9.1 Consensus size: 45
40485073 TTTTCTCAAA
* * * *
40485083 TCACCTGCATT-TCGCCTGCTAGGCTCGAA-GCCCG-ATATCATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
* * ** *
40485125 TCACCTGCATTATAGCCTGTTAGGCTCGAAA-GCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTC-AAAGGCCCGAATAACATT
* * * *
40485170 TCACCGGCATTATAGCCTACTAGGCTCAAAGGCCTGAATAATATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
* * *
40485215 TCACCGGCATTATAACCTGCTAGGCTCAAAGGCCCGAATAATATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
*
40485260 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCAGAATAACATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
40485305 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
* * *
40485350 TCATCAGCATTATAGCCTGCTAAGCTCAAAGGCCCGAATAACATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
* *
40485395 TCACCGGCATTATAGCCTGCTAGGCTCAAAAGCCCAAATAACATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
* * *
40485440 TCACCGACATTATAGGCTGCTAGGCTTAAAGGCCCGAATAACATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
40485485 TCACC
1 TCACC
40485490 AGTTCTTTCC
Statistics
Matches: 329, Mismatches: 32, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
42 11 0.03
43 13 0.04
44 10 0.03
45 295 0.90
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.24
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
Found at i:40495528 original size:79 final size:79
Alignment explanation
Indices: 40495408--40495625 Score: 345
Period size: 79 Copynumber: 2.8 Consensus size: 79
40495398 TATTCGAATG
40495408 ATATCCGGGCTAAGT-CCGAAGGCA-TTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTG-CTATATCCGGGCTAAGTCCCGAAGGCA
*
40495471 TTTGTGCTATTGACT
65 TTTGTGCTAGTGACT
*
40495486 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGCTATATCCGGGCTAAGTCCCGAAGGCTT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGCTATATCCGGGCTAAGTCCCGAAGGCAT
40495551 TTGTGCTAGTGACT
66 TTGTGCTAGTGACT
* * *
40495565 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT-C-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGCTATATCCGGGCTAAGTCCCGAAGG
40495626 TACTTGGGTT
Statistics
Matches: 132, Mismatches: 5, Indels: 6
0.92 0.03 0.04
Matches are distributed among these distances:
78 30 0.23
79 83 0.63
80 19 0.14
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (79 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGCTATATCCGGGCTAAGTCCCGAAGGCAT
TTGTGCTAGTGACT
Found at i:40495538 original size:39 final size:40
Alignment explanation
Indices: 40495408--40495625 Score: 340
Period size: 40 Copynumber: 5.6 Consensus size: 40
40495398 TATTCGAATG
40495408 ATATCCGGGCTAAGT-CCGAAGGCA-TTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
40495446 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
40495486 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
40495525 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
40495565 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
40495605 ATAT-C-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
40495626 TACTTGGGTT
Statistics
Matches: 168, Mismatches: 8, Indels: 8
0.91 0.04 0.04
Matches are distributed among these distances:
38 29 0.17
39 48 0.29
40 89 0.53
41 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Done.