Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 74 of 199
Found at i:20977653 original size:3 final size:3
Alignment explanation
Indices: 20977645--20977680 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
20977635 AATATTATGG
20977645 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20977681 AACGCAAGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:20977970 original size:11 final size:11
Alignment explanation
Indices: 20977954--20977997 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
20977944 AGATTAATTT
20977954 GAATTTTTTTA
1 GAATTTTTTTA
*
20977965 GAATTTTTATA
1 GAATTTTTTTA
20977976 -AGATTTTTTTA
1 GA-ATTTTTTTA
*
20977987 AAATTTTTTTA
1 GAATTTTTTTA
20977998 TAAAATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 1 0.03
11 27 0.93
12 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (11 bp):
GAATTTTTTTA
Found at i:20977986 original size:13 final size:12
Alignment explanation
Indices: 20977968--20978006 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
20977958 TTTTTTAGAA
20977968 TTTTTATAAGATT
1 TTTTTATAA-ATT
20977981 TTTTTA-AAATT
1 TTTTTATAAATT
20977992 TTTTTATAAAATT
1 TTTTTAT-AAATT
20978005 TT
1 TT
20978007 AATAATTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.38
12 2 0.08
13 13 0.54
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (12 bp):
TTTTTATAAATT
Found at i:20978006 original size:11 final size:11
Alignment explanation
Indices: 20977955--20978011 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
20977945 GATTAATTTG
* *
20977955 AATTTTTTTAG
1 AATTTTTATAA
20977966 AATTTTTATAA
1 AATTTTTATAA
* *
20977977 GATTTTTTTAA
1 AATTTTTATAA
20977988 AATTTTTTTATAA
1 AA--TTTTTATAA
*
20978001 AATTTTAATAA
1 AATTTTTATAA
20978012 TTACTAATAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
11 27 0.73
13 10 0.27
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (11 bp):
AATTTTTATAA
Found at i:20982478 original size:41 final size:41
Alignment explanation
Indices: 20982432--20982515 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
20982422 ATAATTGTTG
20982432 ATTGCCGTCTTGATGATTTAATGTCATTAAATAAGTTATTA
1 ATTGCCGTCTTGATGATTTAATGTCATTAAATAAGTTATTA
*
20982473 ATTGCCTTCTTGATGATTTAATGTCATTAAATAAGTTATTA
1 ATTGCCGTCTTGATGATTTAATGTCATTAAATAAGTTATTA
20982514 AT
1 AT
20982516 GCTTCAAGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (41 bp):
ATTGCCGTCTTGATGATTTAATGTCATTAAATAAGTTATTA
Found at i:20997441 original size:27 final size:27
Alignment explanation
Indices: 20997379--20997597 Score: 222
Period size: 27 Copynumber: 8.1 Consensus size: 27
20997369 GCTGATTGCC
* * **
20997379 AGGCTGGTGTTCAAATTGCTGCTGACT
1 AGGCCGGTGTTCGAATTGCTGCTGGGT
*** *
20997406 AGATTGGTGTTCAAATTGCTGCTGGGT
1 AGGCCGGTGTTCGAATTGCTGCTGGGT
* *
20997433 AGGCCGGTGATCGAATTGCTGCTGGTT
1 AGGCCGGTGTTCGAATTGCTGCTGGGT
* * * *
20997460 AGGCCGGTGCTCGAATGGCTGTTGGTT
1 AGGCCGGTGTTCGAATTGCTGCTGGGT
* * * *
20997487 AGGCCGGTGTTCGAATGGTTGTTGGTT
1 AGGCCGGTGTTCGAATTGCTGCTGGGT
* * *
20997514 AGGCCGGTGATCAAATTGCTGTTGGGT
1 AGGCCGGTGTTCGAATTGCTGCTGGGT
* *
20997541 AGGCCGGTGTTCGAATGGCTGTTGGGT
1 AGGCCGGTGTTCGAATTGCTGCTGGGT
*
20997568 AGGCCGGTGATCGAATTGCTGCTGGGT
1 AGGCCGGTGTTCGAATTGCTGCTGGGT
20997595 AGG
1 AGG
20997598 GCAATAGTCG
Statistics
Matches: 166, Mismatches: 26, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 166 1.00
ACGTcount: A:0.15, C:0.16, G:0.38, T:0.31
Consensus pattern (27 bp):
AGGCCGGTGTTCGAATTGCTGCTGGGT
Found at i:20997496 original size:81 final size:81
Alignment explanation
Indices: 20997411--20997597 Score: 275
Period size: 81 Copynumber: 2.3 Consensus size: 81
20997401 TGACTAGATT
* * *
20997411 GGTGTTCAAATTGCTGCTGGGTAGGCCGGTGATCGAATTGCTGCTGGTTAGGCCGGTGCTCGAAT
1 GGTGTTCGAATTGCTGCTGGGTAGGCCGGTGATCAAATTGCTGCTGGGTAGGCCGGTGCTCGAAT
*
20997476 GGCTGTTGGTTAGGCC
66 GGCTGTTGGGTAGGCC
* * * * * *
20997492 GGTGTTCGAATGGTTGTTGGTTAGGCCGGTGATCAAATTGCTGTTGGGTAGGCCGGTGTTCGAAT
1 GGTGTTCGAATTGCTGCTGGGTAGGCCGGTGATCAAATTGCTGCTGGGTAGGCCGGTGCTCGAAT
20997557 GGCTGTTGGGTAGGCC
66 GGCTGTTGGGTAGGCC
*
20997573 GGTGATCGAATTGCTGCTGGGTAGG
1 GGTGTTCGAATTGCTGCTGGGTAGG
20997598 GCAATAGTCG
Statistics
Matches: 91, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 91 1.00
ACGTcount: A:0.14, C:0.16, G:0.40, T:0.30
Consensus pattern (81 bp):
GGTGTTCGAATTGCTGCTGGGTAGGCCGGTGATCAAATTGCTGCTGGGTAGGCCGGTGCTCGAAT
GGCTGTTGGGTAGGCC
Found at i:20997610 original size:54 final size:54
Alignment explanation
Indices: 20997419--20997597 Score: 259
Period size: 54 Copynumber: 3.3 Consensus size: 54
20997409 TTGGTGTTCA
* * * *
20997419 AATTGCTGCTGGGTAGGCCGGTGATCGAATTGCTGCTGGTTAGGCCGGTGCTCG
1 AATTGCTGCTGGGTAGGCCGGTGTTCGAATGGCTGTTGGTTAGGCCGGTGATCG
* * * * *
20997473 AATGGCTGTTGGTTAGGCCGGTGTTCGAATGGTTGTTGGTTAGGCCGGTGATCA
1 AATTGCTGCTGGGTAGGCCGGTGTTCGAATGGCTGTTGGTTAGGCCGGTGATCG
* *
20997527 AATTGCTGTTGGGTAGGCCGGTGTTCGAATGGCTGTTGGGTAGGCCGGTGATCG
1 AATTGCTGCTGGGTAGGCCGGTGTTCGAATGGCTGTTGGTTAGGCCGGTGATCG
20997581 AATTGCTGCTGGGTAGG
1 AATTGCTGCTGGGTAGG
20997598 GCAATAGTCG
Statistics
Matches: 110, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 110 1.00
ACGTcount: A:0.14, C:0.16, G:0.40, T:0.30
Consensus pattern (54 bp):
AATTGCTGCTGGGTAGGCCGGTGTTCGAATGGCTGTTGGTTAGGCCGGTGATCG
Found at i:21002268 original size:33 final size:32
Alignment explanation
Indices: 21002152--21002274 Score: 131
Period size: 33 Copynumber: 3.8 Consensus size: 32
21002142 GCAGTAGTCA
* * * *
21002152 CACCCTCCCCATCAGCTTTTACCTTTTCAACAT
1 CACCCTCCCTAGCAGCTTCTACC-CTTCAACAT
* *
21002185 CACCCTCCCTAACAACTTCTATCCCTTCAACAT
1 CACCCTCCCTAGCAGCTTCTA-CCCTTCAACAT
*
21002218 CACCCT-CTTCAGCAGCTTCTACACCTTCAACAT
1 CACCCTCCCT-AGCAGCTTCTAC-CCTTCAACAT
*
21002251 CACCCTCCCTAGTAGCTTCTACCC
1 CACCCTCCCTAGCAGCTTCTACCC
21002275 CCTCCCTAGT
Statistics
Matches: 76, Mismatches: 10, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
32 5 0.07
33 67 0.88
34 4 0.05
ACGTcount: A:0.23, C:0.45, G:0.04, T:0.28
Consensus pattern (32 bp):
CACCCTCCCTAGCAGCTTCTACCCTTCAACAT
Found at i:21002277 original size:21 final size:21
Alignment explanation
Indices: 21002253--21002295 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
21002243 TTCAACATCA
*
21002253 CCCTCCCTAGTAGCTTCTACC
1 CCCTCCCTAGTAACTTCTACC
*
21002274 CCCTCCCTAGTAACTTTTACC
1 CCCTCCCTAGTAACTTCTACC
21002295 C
1 C
21002296 ATTCAACAAC
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:0.16, C:0.47, G:0.07, T:0.30
Consensus pattern (21 bp):
CCCTCCCTAGTAACTTCTACC
Found at i:21002302 original size:54 final size:54
Alignment explanation
Indices: 21002234--21002361 Score: 152
Period size: 54 Copynumber: 2.4 Consensus size: 54
21002224 CTTCAGCAGC
* *
21002234 TTCTACACC-TTCAACATCACCCTCCCTAGTAGCTTCTACCCCCTCCCTAGTAACT
1 TTCTAC-CCATTCAACATCACCCTCCCTAGCAGCTTCTACCCCCTCCCCA-TAACT
* * * * * *
21002289 TT-TACCCATTCAACAACACCCTCCTTAGCAGTTTGTACCCCCTCCCCATCAGT
1 TTCTACCCATTCAACATCACCCTCCCTAGCAGCTTCTACCCCCTCCCCATAACT
21002342 TTCTACCCATTCAACATCAC
1 TTCTACCCATTCAACATCAC
21002362 ACTCTCCATC
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
53 7 0.11
54 53 0.85
55 2 0.03
ACGTcount: A:0.23, C:0.42, G:0.05, T:0.29
Consensus pattern (54 bp):
TTCTACCCATTCAACATCACCCTCCCTAGCAGCTTCTACCCCCTCCCCATAACT
Found at i:21008990 original size:134 final size:134
Alignment explanation
Indices: 21008745--21009441 Score: 731
Period size: 134 Copynumber: 5.2 Consensus size: 134
21008735 TAAGTAAAAG
* * * * * *
21008745 GTCGTGATCGTAAATCAGCGAACTGATTAAGTGGAGTCGCGATTGTAAATCAACGAACTGTTTAA
1 GTCGTGATCGTAAATCAGCGAACTGTTTAAGTGGAGTCGCGATCGTAAATCGATGAACTCTTTAT
* * * * * * *
21008810 AAAGTGGTCATGATCGTAAATCGATGAATTGAAGATGTGATCGTAAATTAGCGAGCTTTAAAAAT
66 GAAGTGTTCATGATCGTAAATCAATGAACTGAAGATGTAATCGTAAATCAACGAGCTTTAAAAAT
*
21008875 GATA
131 GACA
* * * *
21008879 GTCGTGATCATAAATCAGCGAACTGTTTAAGTGAAGTCGCGACCGTAAATCGATGAACTCTTTTT
1 GTCGTGATCGTAAATCAGCGAACTGTTTAAGTGGAGTCGCGATCGTAAATCGATGAACTCTTTAT
* * * *
21008944 GAAGTGTTTATGATCGTAAATCAATAAACTGAAGCTGTAATTGTAAATCAACGAGCTTTAAAAAT
66 GAAGTGTTCATGATCGTAAATCAATGAACTGAAGATGTAATCGTAAATCAACGAGCTTTAAAAAT
*
21009009 GATA
131 GACA
* * * * *
21009013 GTCGTGATCGTAAATCAGCTAACTGTTTAAGTGGAGTTGCAATCGTAAATCGATGAACTGTTTAA
1 GTCGTGATCGTAAATCAGCGAACTGTTTAAGTGGAGTCGCGATCGTAAATCGATGAACTCTTTAT
* * * * * *
21009078 GAAGTGATCATGATCGTAAGTCGATGAACTGAAGCTATGATCGTAAATCAACGAGCTTTAAAAAT
66 GAAGTGTTCATGATCGTAAATCAATGAACTGAAGATGTAATCGTAAATCAACGAGCTTTAAAAAT
21009143 GACA
131 GACA
* ** * * * * *
21009147 GTTGTGATTATAAATCAGTGAA-TCGTTTAAGTGGAGTAGCAATCGTAAATTG-TCAAACTCTTT
1 GTCGTGATCGTAAATCAGCGAACT-GTTTAAGTGGAGTCGCGATCGTAAATCGAT-GAACTCTTT
* * * *
21009210 ATAAAGTGTTCATGATCGTAAATCAATGAACT-AAAATCGTAATAGTAAATCATCGAGCTTTAAA
64 ATGAAGTGTTCATGATCGTAAATCAATGAACTGAAGAT-GTAATCGTAAATCAACGAGCTTTAAA
21009274 AATGACA
128 AATGACA
* * * * *
21009281 GTCATGATCGTAAATCAGCGAATTGTTTTAGTGGAGT-GTTGATCGTAAATCGACGAACTCTTTA
1 GTCGTGATCGTAAATCAGCGAACTGTTTAAGTGGAGTCG-CGATCGTAAATCGATGAACTCTTTA
* * * * * * * * *
21009345 TGAAGTGTTTACGATTGTAAATTAACGAACTTAA-ATCGTGATTGTAAATCAACAAGCTTTAAAA
65 TGAAGTGTTCATGATCGTAAATCAATGAACTGAAGAT-GTAATCGTAAATCAACGAGCTTTAAAA
21009409 ATGACA
129 ATGACA
* * *
21009415 ATCAG-GATTGTAAATCAACGAACTGTT
1 GTC-GTGATCGTAAATCAGCGAACTGTT
21009442 AGAAAATCGA
Statistics
Matches: 470, Mismatches: 85, Indels: 16
0.82 0.15 0.03
Matches are distributed among these distances:
133 6 0.01
134 461 0.98
135 3 0.01
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.30
Consensus pattern (134 bp):
GTCGTGATCGTAAATCAGCGAACTGTTTAAGTGGAGTCGCGATCGTAAATCGATGAACTCTTTAT
GAAGTGTTCATGATCGTAAATCAATGAACTGAAGATGTAATCGTAAATCAACGAGCTTTAAAAAT
GACA
Found at i:21009469 original size:39 final size:39
Alignment explanation
Indices: 21009424--21009499 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
21009414 AATCAGGATT
* *
21009424 GTAAATCAACGAACTGTTAGAAAATCGAATGTCGTGATC
1 GTAAATCAACGAACTGTAAGAAAATCGAAGGTCGTGATC
** * *
21009463 GTAAATCAGTGGACTGTAAGAAAGTCGAAGGTCGTGA
1 GTAAATCAACGAACTGTAAGAAAATCGAAGGTCGTGA
21009500 CTGTATTTTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (39 bp):
GTAAATCAACGAACTGTAAGAAAATCGAAGGTCGTGATC
Found at i:21031740 original size:23 final size:23
Alignment explanation
Indices: 21031670--21031755 Score: 110
Period size: 21 Copynumber: 4.0 Consensus size: 23
21031660 CCTGATCAAT
21031670 ATACGACACAT-AAGTGCCTGA-
1 ATACGACACATAAAGTGCCTGAG
** *
21031691 A-ACGACACACGAGGTGCCT--G
1 ATACGACACATAAAGTGCCTGAG
21031711 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCTGAG
21031734 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
21031756 TCGGCAAAGC
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
20 9 0.16
21 23 0.42
23 23 0.42
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.16
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAG
Found at i:21031752 original size:44 final size:41
Alignment explanation
Indices: 21031670--21031756 Score: 120
Period size: 44 Copynumber: 2.0 Consensus size: 41
21031660 CCTGATCAAT
* *
21031670 ATACGACACATAAGTGCCTGAAACGACACACGAGGTGCCTG
1 ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
*
21031711 ATACGACACATAAAGTGCCTGAGATACGACACATAAAGTGCCTG
1 ATACGACACAT-AAGTGCCTGA-A-ACGACACACAAAGTGCCTG
21031755 AT
1 AT
21031757 CGGCAAAGCT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
41 11 0.28
42 10 0.25
43 1 0.03
44 18 0.45
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (41 bp):
ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
Found at i:21032131 original size:16 final size:17
Alignment explanation
Indices: 21032110--21032141 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
21032100 TAATAATAGT
21032110 ACTTACCTTA-TATTTC
1 ACTTACCTTATTATTTC
21032126 ACTTACCTTATTATTT
1 ACTTACCTTATTATTT
21032142 GCTTGTCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (17 bp):
ACTTACCTTATTATTTC
Found at i:21035819 original size:16 final size:17
Alignment explanation
Indices: 21035791--21035826 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
21035781 TTAGAATTGG
*
21035791 ATTGAGAAAATTATTTA
1 ATTGAGAAAATTAATTA
21035808 ATTGAG-AAATTAATTA
1 ATTGAGAAAATTAATTA
21035824 ATT
1 ATT
21035827 TAAATTAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (17 bp):
ATTGAGAAAATTAATTA
Found at i:21042923 original size:24 final size:24
Alignment explanation
Indices: 21042891--21042939 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
21042881 CAAGTAGGAG
* *
21042891 TTGTGTTACTCTTTGTAGGGAGCA
1 TTGTCTTACTCTTTGTAGAGAGCA
*
21042915 TTGTCTTACTGTTTGTAGAGAGCA
1 TTGTCTTACTCTTTGTAGAGAGCA
21042939 T
1 T
21042940 CAAAAATCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.18, C:0.12, G:0.27, T:0.43
Consensus pattern (24 bp):
TTGTCTTACTCTTTGTAGAGAGCA
Found at i:21047392 original size:22 final size:24
Alignment explanation
Indices: 21047366--21047409 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
21047356 GAAAAATATT
21047366 AAATAT-ATA-TTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
21047388 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
21047410 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:21047541 original size:59 final size:59
Alignment explanation
Indices: 21047475--21047644 Score: 322
Period size: 59 Copynumber: 2.9 Consensus size: 59
21047465 TCAAGTTTGT
*
21047475 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
21047534 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
*
21047593 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATT
21047645 AATAATTTGA
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 109 1.00
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (59 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
Found at i:21047676 original size:16 final size:16
Alignment explanation
Indices: 21047655--21047696 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
21047645 AATAATTTGA
*
21047655 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
21047671 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
21047687 TAGTTTTAAT
1 TAATTTTAAT
21047697 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:21047680 original size:22 final size:23
Alignment explanation
Indices: 21047670--21047725 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
21047660 TTACTAACAA
* * *
21047670 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
21047692 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
21047715 TTAATTTTAAT
1 TTAATTTTAAT
21047726 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:21047987 original size:28 final size:27
Alignment explanation
Indices: 21047956--21048025 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
21047946 AAATAAAAAA
*
21047956 TTACCAAAATGT-TATAACTTTTTTTTAT
1 TTACCAAAATATATATAA--TTTTTTTAT
*
21047984 TTACCAAAAAATATATAATTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTAT
21048011 TTACCAAAATATATA
1 TTACCAAAATATATA
21048026 AAAAATAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 23 0.61
28 10 0.26
29 5 0.13
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.47
Consensus pattern (27 bp):
TTACCAAAATATATATAATTTTTTTAT
Found at i:21048166 original size:4 final size:4
Alignment explanation
Indices: 21048157--21048287 Score: 94
Period size: 4 Copynumber: 32.0 Consensus size: 4
21048147 GAAGAAGAGG
* *
21048157 GAAA GAAA GAAA GAAA GAAA GGAGAG GAAA GAAA G-AA -AAA GAAG GAAA
1 GAAA GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA
* *
21048205 GAAAA GGAAA G-GA GAAGA GAAA AAAA GAAA GAAA G-AA -AAA GAAAA
1 G-AAA -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA G-AAA
*
21048250 GGAAA GGAGAA GAAA -AAA GAAA GAAA GAAG GAAA GAAA
1 -GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
21048288 AGGAAAGGAG
Statistics
Matches: 103, Mismatches: 10, Indels: 28
0.73 0.07 0.20
Matches are distributed among these distances:
3 13 0.13
4 60 0.58
5 25 0.24
6 5 0.05
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:21048186 original size:18 final size:18
Alignment explanation
Indices: 21048165--21048298 Score: 85
Period size: 18 Copynumber: 6.9 Consensus size: 18
21048155 GGGAAAGAAA
21048165 GAAAGAAAGAAAGGAGAG
1 GAAAGAAAGAAAGGAGAG
*
21048183 GAAAGAAAGAAA-AAGAAG
1 GAAAGAAAGAAAGGAG-AG
21048201 GAAAGAAAAGGAAAGGAGAAG
1 GAAAG-AAA-GAAAGGAG-AG
* *
21048222 AGAAAAAAAGAAA-GAAAG
1 -GAAAGAAAGAAAGGAGAG
* *
21048240 AAAAAGAAAAGGAAAGGAGAA
1 -GAAAG-AAA-GAAAGGAGAG
*
21048261 GAAA-AAAGAAAGAAAGAAG
1 GAAAGAAAGAAAG-GAG-AG
21048280 GAAAGAAAAGGAAAGGAGA
1 GAAAG-AAA-GAAAGGAGA
21048299 AGAGAAGAGA
Statistics
Matches: 91, Mismatches: 12, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
17 7 0.08
18 30 0.33
19 13 0.14
20 16 0.18
21 16 0.18
22 9 0.10
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (18 bp):
GAAAGAAAGAAAGGAGAG
Found at i:21048232 original size:40 final size:39
Alignment explanation
Indices: 21048158--21048353 Score: 196
Period size: 40 Copynumber: 5.1 Consensus size: 39
21048148 AAGAAGAGGG
*
21048158 AAAGAAAGAAAG-AAA-GAAAGGAG-AG-GAAAGAAAGAA
1 AAAG-AAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAA
21048194 AAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAAA
1 AAAGAA-GAAAGAAAAGGAAAGGAGAAGAGAAAAAAAG-AA
*
21048235 GAAAGAA-AAAGAAAAGGAAAGGAGAAGA-AAAAAGAA-AG
1 -AAAGAAGAAAGAAAAGGAAAGGAGAAGAGAAAAA-AAGAA
*
21048273 AAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAGAGAAAAAAA
1 AAAGAA-GAAAGAAAAGGAAAGGAGAAGAGAA-A-AAAAGAA
* * *
21048315 AAAGAAG-AAGAAGAGGGAAGGA-AGGA-AAAAAAAGAA
1 AAAGAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAA
21048351 AAA
1 AAA
21048354 AAAAGAATTT
Statistics
Matches: 139, Mismatches: 7, Indels: 28
0.80 0.04 0.16
Matches are distributed among these distances:
35 2 0.01
36 18 0.13
37 10 0.07
38 11 0.08
39 31 0.22
40 46 0.33
41 6 0.04
42 15 0.11
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (39 bp):
AAAGAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAGAA
Found at i:21048296 original size:79 final size:79
Alignment explanation
Indices: 21048157--21048353 Score: 250
Period size: 79 Copynumber: 2.5 Consensus size: 79
21048147 GAAGAAGAGG
*
21048157 GAAAGAAAG--AAAG-AAA-GAAAGGAGAGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGA
1 GAAAGAAAGAAAAAGAAAAGGAAAGGAGAAGAAA-AAAGAAAAAGAAGGAAAGAAAAGGAAAGGA
21048218 GAAGAGAA-A-AAAA
65 GAAGAGAAGAGAAAA
21048231 GAAAGAAAGAAAAAGAAAAGGAAAGGAGAAGAAAAAAGAAAGAAAGAAGGAAAGAAAAGGAAAGG
1 GAAAGAAAGAAAAAGAAAAGGAAAGGAGAAGAAAAAAG-AA-AAAGAAGGAAAGAAAAGGAAAGG
21048296 AGAAGAGAAGAGAAAA
64 AGAAGAGAAGAGAAAA
* * *
21048312 -AAA-AAAGAAGAAGAAGAGGGAAGGAAGGAA-AAAAAAGAAAAA
1 GAAAGAAAGAAAAAGAAAAGGAAAGG-A-GAAGAAAAAAGAAAAA
21048354 AAAAGAATTT
Statistics
Matches: 109, Mismatches: 4, Indels: 16
0.84 0.03 0.12
Matches are distributed among these distances:
74 9 0.08
76 4 0.04
77 7 0.06
78 18 0.17
79 52 0.48
80 12 0.11
81 7 0.06
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (79 bp):
GAAAGAAAGAAAAAGAAAAGGAAAGGAGAAGAAAAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAG
AAGAGAAGAGAAAA
Found at i:21053764 original size:18 final size:18
Alignment explanation
Indices: 21053741--21053785 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
21053731 ATCCCAATGA
21053741 TCGCCACCACATTCTTCT
1 TCGCCACCACATTCTTCT
* *
21053759 TCGCCAGCACCTTCTTCT
1 TCGCCACCACATTCTTCT
*
21053777 TCACCACCA
1 TCGCCACCA
21053786 ACCATGTCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.18, C:0.47, G:0.07, T:0.29
Consensus pattern (18 bp):
TCGCCACCACATTCTTCT
Found at i:21054643 original size:3 final size:3
Alignment explanation
Indices: 21054635--21054669 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
21054625 TCTTAATACT
21054635 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
21054670 TAATAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:21054944 original size:27 final size:27
Alignment explanation
Indices: 21054914--21054998 Score: 161
Period size: 27 Copynumber: 3.1 Consensus size: 27
21054904 CCAATCAGTA
21054914 TGGCACCATTGGTGCCGCCAATGGCAT
1 TGGCACCATTGGTGCCGCCAATGGCAT
21054941 TGGCACCATTGGTGCCGCCAATGGCAT
1 TGGCACCATTGGTGCCGCCAATGGCAT
*
21054968 TGGCACCATTGGTGCCGCCAATGCCAT
1 TGGCACCATTGGTGCCGCCAATGGCAT
21054995 TGGC
1 TGGC
21054999 GTGACCAAGG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.18, C:0.31, G:0.29, T:0.22
Consensus pattern (27 bp):
TGGCACCATTGGTGCCGCCAATGGCAT
Found at i:21055117 original size:27 final size:27
Alignment explanation
Indices: 21055061--21055129 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
21055051 TTTGTTTTTG
*
21055061 ATATATTTTGGTAAATAAAAAAATTAT
1 ATATATTTTGGTAAATAAAAAAAGTAT
*
21055088 ATATTTTTTGGTAAATAAAAAAAAGT-T
1 ATATATTTTGGTAAAT-AAAAAAAGTAT
*
21055115 ATAACATTTTGGTAA
1 AT-ATATTTTGGTAA
21055130 TTTTTTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 18 0.50
28 18 0.50
ACGTcount: A:0.48, C:0.01, G:0.10, T:0.41
Consensus pattern (27 bp):
ATATATTTTGGTAAATAAAAAAAGTAT
Found at i:21055124 original size:28 final size:27
Alignment explanation
Indices: 21055065--21055129 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 27
21055055 TTTTTGATAT
*
21055065 ATTTTGGTAAATAAAAAAATTATATAT
1 ATTTTGGTAAATAAAAAAATTATATAC
*
21055092 TTTTTGGTAAATAAAAAAAAGTTATA-AC
1 ATTTTGGTAAAT-AAAAAAA-TTATATAC
21055120 ATTTTGGTAA
1 ATTTTGGTAA
21055130 TTTTTTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 11 0.33
28 17 0.52
29 5 0.15
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.40
Consensus pattern (27 bp):
ATTTTGGTAAATAAAAAAATTATATAC
Found at i:21056588 original size:25 final size:23
Alignment explanation
Indices: 21056505--21056584 Score: 151
Period size: 23 Copynumber: 3.5 Consensus size: 23
21056495 ATATATATAA
21056505 AAAATATATATTTGATTAAAAAT
1 AAAATATATATTTGATTAAAAAT
21056528 AAAATATATATTTGATTAAAAAT
1 AAAATATATATTTGATTAAAAAT
21056551 AAAATATATATTTGATTAAAAAT
1 AAAATATATATTTGATTAAAAAT
*
21056574 AAAAAATATAT
1 AAAATATATAT
21056585 ATTTAATATA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (23 bp):
AAAATATATATTTGATTAAAAAT
Found at i:21059365 original size:18 final size:20
Alignment explanation
Indices: 21059341--21059383 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
21059331 TTTATTTGTT
*
21059341 TTATTATAATAATATAATATA
1 TTATTAT-ATAATAAAATATA
21059362 TTATTATATAATAAAATATA
1 TTATTATATAATAAAATATA
21059382 TT
1 TT
21059384 TACTCAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTATATAATAAAATATA
Found at i:21060470 original size:6 final size:6
Alignment explanation
Indices: 21060421--21060451 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
21060411 ACTATTAAAT
21060421 TAAAAA TAAAAA TAAAAA TAAAAA TAGAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TA-AAAA
21060452 GATCAAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
TAAAAA
Found at i:21065673 original size:27 final size:26
Alignment explanation
Indices: 21065642--21065837 Score: 230
Period size: 27 Copynumber: 7.3 Consensus size: 26
21065632 TATAACAGTT
*
21065642 ATTTTATCCTATGGGGATATTTCGGTC
1 ATTTTACCCTATGGGG-TATTTCGGTC
* * *
21065669 ATTTTACCCTATCAGGGCATTTTGGTC
1 ATTTTACCCTAT-GGGGTATTTCGGTC
*
21065696 ATTTTACCCTATGGGGGTATTTCAGTC
1 ATTTTACCCTAT-GGGGTATTTCGGTC
*
21065723 ATTTTACCCTATGGAGGTATTTCGATC
1 ATTTTACCCTATGG-GGTATTTCGGTC
* *
21065750 ATTTTACCCTATGAGGGTGTTTTGGTC
1 ATTTTACCCTATG-GGGTATTTCGGTC
* * *
21065777 ATTTTACCCTATGGGATATTTTGGTT
1 ATTTTACCCTATGGGGTATTTCGGTC
*
21065803 ATTTTACCCTATAGGGGTATTTCGGTT
1 ATTTTACCCTAT-GGGGTATTTCGGTC
21065830 ATTTTACC
1 ATTTTACC
21065838 TTAATTTAGG
Statistics
Matches: 146, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
26 24 0.16
27 118 0.81
28 4 0.03
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.44
Consensus pattern (26 bp):
ATTTTACCCTATGGGGTATTTCGGTC
Found at i:21065752 original size:81 final size:79
Alignment explanation
Indices: 21065624--21065837 Score: 277
Period size: 81 Copynumber: 2.7 Consensus size: 79
21065614 CATTTCATCT
** *
21065624 CCTA-GGGGTATAACAGTTATTTTATCCTATGGGGATATTTCGGTCATTTTACCCTATCAGGGCA
1 CCTATGGGGTATTTCAGTTATTTTACCCTATGGGG-TATTTCGGTCATTTTACCCTATCAGGGCA
21065688 TTTTGGTCATTTTAC
65 TTTTGGTCATTTTAC
* * * *
21065703 CCTATGGGGGTATTTCAGTCATTTTACCCTATGGAGGTATTTCGATCATTTTACCCTATGAGGGT
1 CCTAT-GGGGTATTTCAGTTATTTTACCCTATGG-GGTATTTCGGTCATTTTACCCTATCAGGGC
*
21065768 GTTTTGGTCATTTTAC
64 ATTTTGGTCATTTTAC
* ** *
21065784 CCTATGGGATATTTTGGTTATTTTACCCTATAGGGGTATTTCGGTTATTTTACC
1 CCTATGGGGTATTTCAGTTATTTTACCCTAT-GGGGTATTTCGGTCATTTTACC
21065838 TTAATTTAGG
Statistics
Matches: 117, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
79 4 0.03
80 40 0.34
81 71 0.61
82 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.43
Consensus pattern (79 bp):
CCTATGGGGTATTTCAGTTATTTTACCCTATGGGGTATTTCGGTCATTTTACCCTATCAGGGCAT
TTTGGTCATTTTAC
Found at i:21072086 original size:37 final size:37
Alignment explanation
Indices: 21072036--21072251 Score: 115
Period size: 37 Copynumber: 5.8 Consensus size: 37
21072026 TTCAAAGTAA
21072036 TAAATTGACACCCAGTGTCTCATCGACTAAATCGAAG
1 TAAATTGACACCCAGTGTCTCATCGACTAAATCGAAG
* * *
21072073 TAAATTGGCACCCAGTGCCTCATTGA--AACA-C-ACCAG
1 TAAATTGACACCCAGTGTCTCATCGACTAA-ATCGA--AG
* * * * *
21072109 T---TTGGCATCCAGTG-CGTCATCGAATAATTCAAAG
1 TAAATTGACACCCAGTGTC-TCATCGACTAAATCGAAG
* * *
21072143 TAATAAATTGACACCCAGTGTCTCATTGGCTAAACCGAAG
1 ---TAAATTGACACCCAGTGTCTCATCGACTAAATCGAAG
* * * * * *
21072183 TAAATTGGCACCTAGTGTCTTATTGAATTAATCCGAAG
1 TAAATTGACACCCAGTGTCTCATCGACTAAAT-CGAAG
*
21072221 TAACAAATTGACACCCAGTGTCTCACCGACT
1 T---AAATTGACACCCAGTGTCTCATCGACT
21072252 CGAAGTCGAA
Statistics
Matches: 133, Mismatches: 27, Indels: 34
0.69 0.14 0.18
Matches are distributed among these distances:
32 1 0.01
33 18 0.14
34 3 0.02
35 6 0.05
36 5 0.04
37 49 0.37
38 6 0.05
40 23 0.17
41 22 0.17
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (37 bp):
TAAATTGACACCCAGTGTCTCATCGACTAAATCGAAG
Found at i:21072182 original size:110 final size:110
Alignment explanation
Indices: 21071988--21072209 Score: 374
Period size: 110 Copynumber: 2.0 Consensus size: 110
21071978 GATCCAACCA
21071988 AAACACACCAGTTTGGCACCTAGTGCGTCATCGAATAATTCAAAGTAATAAATTGACACCCAGTG
1 AAACACACCAGTTTGGCACCTAGTGCGTCATCGAATAATTCAAAGTAATAAATTGACACCCAGTG
*
21072053 TCTCATCGACTAAATCGAAGTAAATTGGCACCCAGTGCCTCATTG
66 TCTCATCGACTAAACCGAAGTAAATTGGCACCCAGTGCCTCATTG
21072098 AAACACACCAGTTTGGCATCC-AGTGCGTCATCGAATAATTCAAAGTAATAAATTGACACCCAGT
1 AAACACACCAGTTTGGCA-CCTAGTGCGTCATCGAATAATTCAAAGTAATAAATTGACACCCAGT
* * * * *
21072162 GTCTCATTGGCTAAACCGAAGTAAATTGGCACCTAGTGTCTTATTG
65 GTCTCATCGACTAAACCGAAGTAAATTGGCACCCAGTGCCTCATTG
21072208 AA
1 AA
21072210 TTAATCCGAA
Statistics
Matches: 105, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
110 103 0.98
111 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.26
Consensus pattern (110 bp):
AAACACACCAGTTTGGCACCTAGTGCGTCATCGAATAATTCAAAGTAATAAATTGACACCCAGTG
TCTCATCGACTAAACCGAAGTAAATTGGCACCCAGTGCCTCATTG
Found at i:21072241 original size:41 final size:39
Alignment explanation
Indices: 21072140--21072245 Score: 117
Period size: 37 Copynumber: 2.7 Consensus size: 39
21072130 GAATAATTCA
*
21072140 AAGTAATAAATTGACACCCAGTGTCTCATTGGCTAAACCG
1 AAGTAA-AAATTGACACCCAGTGTCTCATTGACTAAACCG
* * * * *
21072180 AAGT--AAATTGGCACCTAGTGTCTTATTGAATTAATCCG
1 AAGTAAAAATTGACACCCAGTGTCTCATTG-ACTAAACCG
21072218 AAGTAACAAATTGACACCCAGTGTCTCA
1 AAGTAA-AAATTGACACCCAGTGTCTCA
21072246 CCGACTCGAA
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
37 21 0.40
38 10 0.19
40 4 0.08
41 18 0.34
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (39 bp):
AAGTAAAAATTGACACCCAGTGTCTCATTGACTAAACCG
Found at i:21073171 original size:19 final size:16
Alignment explanation
Indices: 21073122--21073192 Score: 53
Period size: 16 Copynumber: 4.4 Consensus size: 16
21073112 TAATTTTTCC
21073122 TTCTTTCTTT-TC--T
1 TTCTTTCTTTCTCTAT
*
21073135 TTCTTT-TTCTCCCTAT
1 TTCTTTCTT-TCTCTAT
21073151 TTCGTTTGGCTTTCTCTAT
1 TTC-TTT--CTTTCTCTAT
21073170 TTCTTTCTTTCTCT-T
1 TTCTTTCTTTCTCTAT
21073185 TCTCTTTC
1 T-TCTTTC
21073193 CTTTTTCTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 15
0.73 0.03 0.23
Matches are distributed among these distances:
12 2 0.04
13 7 0.15
14 1 0.02
15 2 0.04
16 18 0.38
17 3 0.06
18 3 0.06
19 9 0.19
20 2 0.04
ACGTcount: A:0.03, C:0.27, G:0.04, T:0.66
Consensus pattern (16 bp):
TTCTTTCTTTCTCTAT
Found at i:21073201 original size:17 final size:16
Alignment explanation
Indices: 21073160--21073202 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
21073150 TTTCGTTTGG
21073160 CTTTCTCTATT-TCTTT
1 CTTTCTCT-TTCTCTTT
21073176 CTTTCTCTTTCTCTTT
1 CTTTCTCTTTCTCTTT
*
21073192 CCTTTTTCTTT
1 -CTTTCTCTTT
21073203 TTAGTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 2 0.08
16 13 0.54
17 9 0.38
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (16 bp):
CTTTCTCTTTCTCTTT
Found at i:21082161 original size:15 final size:15
Alignment explanation
Indices: 21082141--21082175 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
21082131 AGCAGAAAGA
21082141 TTCCTCATGAAGTAT
1 TTCCTCATGAAGTAT
21082156 TTCCTCATGAAGTAT
1 TTCCTCATGAAGTAT
21082171 TTCCT
1 TTCCT
21082176 GCCTAGCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (15 bp):
TTCCTCATGAAGTAT
Found at i:21091110 original size:18 final size:18
Alignment explanation
Indices: 21091087--21091132 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
21091077 GGCAACCCAC
21091087 ATTTATTTTCATTTA-GTA
1 ATTTATTTT-ATTTATGTA
*
21091105 ATTTATTTTATTTATTTA
1 ATTTATTTTATTTATGTA
21091123 ATTTAATTTT
1 ATTT-ATTTT
21091133 GAATTCTAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 5 0.20
18 15 0.60
19 5 0.20
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
ATTTATTTTATTTATGTA
Found at i:21091479 original size:20 final size:22
Alignment explanation
Indices: 21091433--21091479 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
21091423 AAATGACCAA
*
21091433 GAAAGAAAAAGAAGGAAAAAAG
1 GAAAGAAAAAGAAAGAAAAAAG
21091455 G--AGAAAAA-AAAG-AAAAAG
1 GAAAGAAAAAGAAAGAAAAAAG
21091473 GAAAGAA
1 GAAAGAA
21091480 TGGCTTGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
18 7 0.32
19 3 0.14
20 11 0.50
22 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (22 bp):
GAAAGAAAAAGAAAGAAAAAAG
Found at i:21096658 original size:16 final size:16
Alignment explanation
Indices: 21096633--21096676 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
21096623 CCGATATAAT
* * *
21096633 AAATTATTTATTTTTA
1 AAATTTTTTAATTTAA
21096649 AAATTTTTTAATTTAA
1 AAATTTTTTAATTTAA
21096665 AAATATTTTTAA
1 AAAT-TTTTTAA
21096677 AATACTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AAATTTTTTAATTTAA
Found at i:21096680 original size:11 final size:11
Alignment explanation
Indices: 21096664--21096726 Score: 73
Period size: 11 Copynumber: 6.0 Consensus size: 11
21096654 TTTTAATTTA
21096664 AAAATATTTTT
1 AAAATATTTTT
21096675 AAAATACTTTTT
1 AAAATA-TTTTT
21096687 ---A-A-TTTT
1 AAAATATTTTT
21096693 AAAATATTTTT
1 AAAATATTTTT
21096704 AAAATATTTTT
1 AAAATATTTTT
21096715 AAAATACTTTTT
1 AAAATA-TTTTT
21096727 TTAAAAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
6 4 0.09
8 1 0.02
9 2 0.04
10 1 0.02
11 27 0.60
12 10 0.22
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:21096704 original size:17 final size:18
Alignment explanation
Indices: 21096671--21096705 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
21096661 TTAAAAATAT
21096671 TTTTAAAATACTTTTTAA
1 TTTTAAAATACTTTTTAA
21096689 TTTTAAAATA-TTTTTAA
1 TTTTAAAATACTTTTTAA
21096706 AATATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTAAAATACTTTTTAA
Found at i:21096710 original size:40 final size:41
Alignment explanation
Indices: 21096656--21096774 Score: 145
Period size: 40 Copynumber: 2.9 Consensus size: 41
21096646 TTAAAATTTT
*
21096656 TTAATTTAAAAATATTTTTAAAATACTTTTTAATTTTAAAA
1 TTAATTTTAAAATATTTTTAAAATACTTTTTAATTTTAAAA
* **
21096697 -TATTTTTAAAATATTTTTAAAATACTTTTT--TTAAAAAAAA
1 TTAATTTTAAAATATTTTTAAAATACTTTTTAATT--TTAAAA
*
21096737 TTAATTTTAAAATATTTTAAAAATACTTTTTAAATTTT
1 TTAATTTTAAAATATTTTTAAAATACTTTTT-AATTTT
21096775 TTTTAATTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
38 2 0.03
40 32 0.50
41 28 0.44
44 2 0.03
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (41 bp):
TTAATTTTAAAATATTTTTAAAATACTTTTTAATTTTAAAA
Found at i:21096784 original size:40 final size:39
Alignment explanation
Indices: 21096643--21096770 Score: 139
Period size: 41 Copynumber: 3.2 Consensus size: 39
21096633 AAATTATTTA
** *
21096643 TTTTTAAAATTTTTTAATTTAAAAATATTTTTAAAATAC
1 TTTTTAAAATTAATTAATTTTAAAATATTTTTAAAATAC
** * *
21096682 TTTTTAATTTTAAAATATTTTTAAAATATTTTTAAAATAC
1 TTTTTAAAATT-AATTAATTTTAAAATATTTTTAAAATAC
** *
21096722 TTTTTTTAAAAAAAATTAATTTTAAAATATTTTAAAAATAC
1 --TTTTTAAAATTAATTAATTTTAAAATATTTTTAAAATAC
21096763 TTTTTAAA
1 TTTTTAAA
21096771 TTTTTTTTAA
Statistics
Matches: 72, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
39 17 0.24
40 23 0.32
41 25 0.35
42 7 0.10
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (39 bp):
TTTTTAAAATTAATTAATTTTAAAATATTTTTAAAATAC
Found at i:21097117 original size:19 final size:18
Alignment explanation
Indices: 21097088--21097137 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
21097078 TTAATTCAAC
21097088 TTTTGGAATTTTTATAAATA
1 TTTT-GAATTTTTA-AAATA
*
21097108 TTTTGAA-TTTTAAAATT
1 TTTTGAATTTTTAAAATA
21097125 TATTTGAATTTTT
1 T-TTTGAATTTTT
21097138 TGTTGAGAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 5 0.19
18 11 0.41
19 7 0.26
20 4 0.15
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (18 bp):
TTTTGAATTTTTAAAATA
Found at i:21097603 original size:30 final size:30
Alignment explanation
Indices: 21097567--21097626 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
21097557 CCTAAGATCA
21097567 GTATCGGATGTAAAAGCTAATTAAGGCATT
1 GTATCGGATGTAAAAGCTAATTAAGGCATT
21097597 GTATCGGATGTAAAAGCTAATTAAGGCATT
1 GTATCGGATGTAAAAGCTAATTAAGGCATT
21097627 AACAGCCTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (30 bp):
GTATCGGATGTAAAAGCTAATTAAGGCATT
Found at i:21098802 original size:19 final size:20
Alignment explanation
Indices: 21098757--21098839 Score: 89
Period size: 20 Copynumber: 4.1 Consensus size: 20
21098747 ATTTTAAATT
*
21098757 TTTTTAAAATATAAATTTTGAAA
1 TTTTTAAAA-AT-TATTTTG-AA
*
21098780 TTTTTATAAA-TATTTTGAA
1 TTTTTAAAAATTATTTTGAA
21098799 -TTTTAAAAATTATTTTGAA
1 TTTTTAAAAATTATTTTGAA
* *
21098818 TTTTTGAAAATTATTTTAAA
1 TTTTTAAAAATTATTTTGAA
21098838 TT
1 TT
21098840 ATTTTTGTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
18 8 0.15
19 11 0.21
20 25 0.47
22 1 0.02
23 8 0.15
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
TTTTTAAAAATTATTTTGAA
Found at i:21098838 original size:10 final size:10
Alignment explanation
Indices: 21098747--21098844 Score: 51
Period size: 10 Copynumber: 9.5 Consensus size: 10
21098737 ATCTCAGAAA
21098747 ATTTTAAATT
1 ATTTTAAATT
*
21098757 TTTTTAAAATAT
1 ATTTT-AAAT-T
21098769 AAATTTTGAAATT
1 --ATTTT-AAATT
21098782 -TTTATAAA-T
1 ATTT-TAAATT
*
21098791 ATTTTGAATT
1 ATTTTAAATT
**
21098801 -TTAAAAATT
1 ATTTTAAATT
*
21098810 ATTTTGAATT
1 ATTTTAAATT
*
21098820 -TTTGAAAATT
1 ATTT-TAAATT
21098830 ATTTTAAATT
1 ATTTTAAATT
21098840 ATTTT
1 ATTTT
21098845 TGTAATTTTT
Statistics
Matches: 65, Mismatches: 13, Indels: 20
0.66 0.13 0.20
Matches are distributed among these distances:
9 13 0.20
10 34 0.52
11 8 0.12
12 1 0.02
13 1 0.02
14 8 0.12
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (10 bp):
ATTTTAAATT
Found at i:21102153 original size:27 final size:27
Alignment explanation
Indices: 21102099--21102214 Score: 126
Period size: 27 Copynumber: 4.3 Consensus size: 27
21102089 AATAACGATC
* * *
21102099 ATTTTACCCTTC-GGGGTATTTCGATA
1 ATTTTACCCATCAAGGGTATTTCGGTA
* ** *
21102125 ATTTTACTCATTTAGAGTATTTCGGTA
1 ATTTTACCCATCAAGGGTATTTCGGTA
* *
21102152 ATTTTTCCCATCAAGGGTATTTCAGTA
1 ATTTTACCCATCAAGGGTATTTCGGTA
* *
21102179 ATTTTACCCATCGAGGGTATTTCGGTC
1 ATTTTACCCATCAAGGGTATTTCGGTA
21102206 ATTTTACCC
1 ATTTTACCC
21102215 TAAAGGGGTC
Statistics
Matches: 73, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
26 9 0.12
27 64 0.88
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.42
Consensus pattern (27 bp):
ATTTTACCCATCAAGGGTATTTCGGTA
Found at i:21102223 original size:27 final size:27
Alignment explanation
Indices: 21102141--21102223 Score: 80
Period size: 27 Copynumber: 3.1 Consensus size: 27
21102131 CTCATTTAGA
* *
21102141 GTATTTCGGTAATTTTTCCCATCAA-GG
1 GTATTTCGGTAATTTTACCC-TAAAGGG
* **
21102168 GTATTTCAGTAATTTTACCC-ATCGAGG
1 GTATTTCGGTAATTTTACCCTAAAG-GG
*
21102195 GTATTTCGGTCATTTTACCCTAAAGGG
1 GTATTTCGGTAATTTTACCCTAAAGGG
21102222 GT
1 GT
21102224 CTCGGTGTAA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
27 42 0.95
28 2 0.05
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (27 bp):
GTATTTCGGTAATTTTACCCTAAAGGG
Found at i:21106989 original size:10 final size:11
Alignment explanation
Indices: 21106963--21106987 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21106953 ACACCTAATT
21106963 AAAATTAAAAA
1 AAAATTAAAAA
21106974 AAAATTAAAAA
1 AAAATTAAAAA
21106985 AAA
1 AAA
21106988 TTGAACCAGA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAATTAAAAA
Found at i:21107066 original size:2 final size:2
Alignment explanation
Indices: 21107059--21107090 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
21107049 ATCGAAAGAA
21107059 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
21107091 TAGACAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21107310 original size:14 final size:14
Alignment explanation
Indices: 21107257--21107310 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
21107247 TGTTTAGGGT
21107257 TTTTGAGTTTGGGGA
1 TTTTGA-TTTGGGGA
* * *
21107272 TTTAGGATTTTGGGT
1 TTT-TGATTTGGGGA
21107287 TTTTGAATTTGGGGA
1 TTTTG-ATTTGGGGA
21107302 TTTTGATTT
1 TTTTGATTT
21107311 AAGGTTGTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
14 5 0.16
15 24 0.77
16 2 0.06
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (14 bp):
TTTTGATTTGGGGA
Found at i:21107310 original size:29 final size:30
Alignment explanation
Indices: 21107270--21107333 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
21107260 TGAGTTTGGG
*
21107270 GATTTAGGATTTTGGGTTTTTGAATTTGGG
1 GATTTAGGATTTAGGGTTTTTGAATTTGGG
* * * *
21107300 GATTT-TGATTTAAGGTTGTCGAATTTGGG
1 GATTTAGGATTTAGGGTTTTTGAATTTGGG
21107329 GATTT
1 GATTT
21107334 GGGCTAGGGG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.19, C:0.02, G:0.31, T:0.48
Consensus pattern (30 bp):
GATTTAGGATTTAGGGTTTTTGAATTTGGG
Found at i:21107411 original size:30 final size:29
Alignment explanation
Indices: 21107363--21107419 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
21107353 TGGGGATTTG
* ** *
21107363 TTTAGGGTTTTTTGATTTTAGGGATTTTCA
1 TTTAAGGTTTTTAAATTTT-GGAATTTTCA
21107393 TTTAAGGTTTTTAAATTTTGGAATTTT
1 TTTAAGGTTTTTAAATTTTGGAATTTT
21107420 TGTTTATTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 7 0.30
30 16 0.70
ACGTcount: A:0.21, C:0.02, G:0.19, T:0.58
Consensus pattern (29 bp):
TTTAAGGTTTTTAAATTTTGGAATTTTCA
Found at i:21115423 original size:5 final size:5
Alignment explanation
Indices: 21115415--21115442 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
21115405 TAACTTTTCT
21115415 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
21115443 ATCAAATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:21116244 original size:160 final size:161
Alignment explanation
Indices: 21115968--21116286 Score: 419
Period size: 160 Copynumber: 2.0 Consensus size: 161
21115958 GGTGAGGGTC
* * *
21115968 ACAATAGAAGATCATGCATTCAACCTAACACAACTGGATCACAAATATATCATTAACACTTTTTC
1 ACAACAGAAGATCATGCAATCAACCTAACACAACTGGATCACAAATATATCATAAACACTTTTTC
* * * * *
21116033 ACTATCAAGTTCTTAAATATTTAAGTCTAATTTGGGGTTTTACAATTTTTTT-TCTCAGTCTGGT
66 ACTATCAAGTTCTAAAATATTTAAATCTAATTTAGGGTTTGACAATTTTTTTGTCTCAGTCTAGT
21116097 ACGAGTACAAGAACTAAAAGCCAAAAAAAGA
131 ACGAGTACAAGAACTAAAAGCCAAAAAAAGA
* **
21116128 ACAACAGAAGATCATGCAATCAACCTACCACAACTGGATCACAGGTATAT-AGTAAACACTTTTT
1 ACAACAGAAGATCATGCAATCAACCTAACACAACTGGATCACAAATATATCA-TAAACACTTTTT
* * ***
21116192 TACTGTCAAGTT-TCAAAATATTTAAATCTAATTTAGGGTTGTGATTTTTTTTTTGTCTCAGTCT
65 CACTATCAAGTTCT-AAAATATTTAAATCTAATTTAGGGTT-TGACAATTTTTTTGTCTCAGTCT
* * *
21116256 AGTATGAGTGCAAGAACTAGAAGCCAAAAAA
128 AGTACGAGTACAAGAACTAAAAGCCAAAAAA
21116287 GGATGGTATA
Statistics
Matches: 136, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
159 2 0.01
160 89 0.65
161 9 0.07
162 36 0.26
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (161 bp):
ACAACAGAAGATCATGCAATCAACCTAACACAACTGGATCACAAATATATCATAAACACTTTTTC
ACTATCAAGTTCTAAAATATTTAAATCTAATTTAGGGTTTGACAATTTTTTTGTCTCAGTCTAGT
ACGAGTACAAGAACTAAAAGCCAAAAAAAGA
Found at i:21118378 original size:17 final size:17
Alignment explanation
Indices: 21118339--21118380 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
21118329 TAAAAGCAAA
*
21118339 TTTTATTAAATTGTTTT
1 TTTTATAAAATTGTTTT
*
21118356 TGTTATAAAATT-TTTGT
1 TTTTATAAAATTGTTT-T
21118373 TTTTATAA
1 TTTTATAA
21118381 TTTCAACATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (17 bp):
TTTTATAAAATTGTTTT
Found at i:21123598 original size:41 final size:42
Alignment explanation
Indices: 21123522--21123617 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
21123512 ATACACCGGT
* * *
21123522 TTAAGCCTGCTAGACTTATAGTCCGAATTTATTTCACCGGCA
1 TTAAGCCTGCTAGACGTAAAGTCCGAATTGATTTCACCGGCA
* * *
21123564 TTAAGCCTGCTAGACGTAAAGTCTGAA-TGGTTTCACTGGCA
1 TTAAGCCTGCTAGACGTAAAGTCCGAATTGATTTCACCGGCA
**
21123605 ACAAGCCTGCTAG
1 TTAAGCCTGCTAG
21123618 GTACTGAGCC
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
41 22 0.48
42 24 0.52
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (42 bp):
TTAAGCCTGCTAGACGTAAAGTCCGAATTGATTTCACCGGCA
Found at i:21128290 original size:24 final size:24
Alignment explanation
Indices: 21128263--21128314 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
21128253 TTAGTAAGTC
*
21128263 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
21128287 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
21128311 AAAT
1 AAAT
21128315 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:21130465 original size:18 final size:18
Alignment explanation
Indices: 21130442--21130477 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
21130432 ACAATGGTCT
21130442 AGCAATTTTGATTTGACC
1 AGCAATTTTGATTTGACC
21130460 AGCAATTTTGATTTGACC
1 AGCAATTTTGATTTGACC
21130478 CTATATATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (18 bp):
AGCAATTTTGATTTGACC
Found at i:21134739 original size:30 final size:30
Alignment explanation
Indices: 21134705--21134773 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
21134695 AGTTTCATTT
** *
21134705 CAGTCACTCAAC-TTTCGAAAAGTTACAAAA
1 CAGTCACT-AACGTTTAAAAAAGTGACAAAA
21134735 CAGTCACTAACGTTTTAAAAAAGTGACAAAA
1 CAGTCACTAACG-TTTAAAAAAGTGACAAAA
*
21134766 TAGTCACT
1 CAGTCACT
21134774 GATTAACAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 3 0.09
30 8 0.24
31 22 0.67
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (30 bp):
CAGTCACTAACGTTTAAAAAAGTGACAAAA
Found at i:21134833 original size:21 final size:20
Alignment explanation
Indices: 21134805--21134846 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
21134795 TGTTAACGGG
21134805 ACCACTGACATGGCAAGTTA
1 ACCACTGACATGGCAAGTTA
**
21134825 ACCAGCTGATGTGGCAAGTTA
1 ACCA-CTGACATGGCAAGTTA
21134846 A
1 A
21134847 TTTGCCACGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (20 bp):
ACCACTGACATGGCAAGTTA
Found at i:21135329 original size:12 final size:12
Alignment explanation
Indices: 21135312--21135376 Score: 64
Period size: 12 Copynumber: 5.6 Consensus size: 12
21135302 ATTTAGAGTT
21135312 ATTTTGATTTCG
1 ATTTTGATTTCG
21135324 ATTTTGA-TTCTG
1 ATTTTGATTTC-G
21135336 A-TTT-ATTTCG
1 ATTTTGATTTCG
** *
21135346 ATTTCAATTTAG
1 ATTTTGATTTCG
*
21135358 ATTTTGATTTCA
1 ATTTTGATTTCG
21135370 ATTTTGA
1 ATTTTGA
21135377 AACACTCACT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
10 3 0.07
11 11 0.26
12 29 0.67
ACGTcount: A:0.23, C:0.08, G:0.12, T:0.57
Consensus pattern (12 bp):
ATTTTGATTTCG
Found at i:21135350 original size:28 final size:28
Alignment explanation
Indices: 21135310--21135367 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
21135300 TTATTTAGAG
* * *
21135310 TTATTTTGATTTCGATTTTGATTCTGAT
1 TTATTTCGATTTCAATTTAGATTCTGAT
*
21135338 TTATTTCGATTTCAATTTAGATTTTGAT
1 TTATTTCGATTTCAATTTAGATTCTGAT
21135366 TT
1 TT
21135368 CAATTTTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.21, C:0.07, G:0.12, T:0.60
Consensus pattern (28 bp):
TTATTTCGATTTCAATTTAGATTCTGAT
Found at i:21135414 original size:12 final size:12
Alignment explanation
Indices: 21135393--21135427 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
21135383 CACTGGTTCT
*
21135393 GATTTTGATTTC
1 GATTTAGATTTC
*
21135405 GATTTCGATTTC
1 GATTTAGATTTC
21135417 GATTTAGATTT
1 GATTTAGATTT
21135428 TGGTTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.20, C:0.09, G:0.17, T:0.54
Consensus pattern (12 bp):
GATTTAGATTTC
Found at i:21135420 original size:18 final size:18
Alignment explanation
Indices: 21135393--21135427 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21135383 CACTGGTTCT
* *
21135393 GATTTTGATTTCGATTTC
1 GATTTCGATTTAGATTTC
21135411 GATTTCGATTTAGATTT
1 GATTTCGATTTAGATTT
21135428 TGGTTTTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.09, G:0.17, T:0.54
Consensus pattern (18 bp):
GATTTCGATTTAGATTTC
Found at i:21135691 original size:20 final size:22
Alignment explanation
Indices: 21135651--21135691 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
21135641 TTACCTTCTA
21135651 TATTGTACTAGTTATTATCTGT
1 TATTGTACTAGTTATTATCTGT
*
21135673 TATTGT-CTA-TTATTGTCTG
1 TATTGTACTAGTTATTATCTG
21135692 CCATGTGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 3 0.17
22 6 0.33
ACGTcount: A:0.20, C:0.10, G:0.15, T:0.56
Consensus pattern (22 bp):
TATTGTACTAGTTATTATCTGT
Found at i:21137662 original size:28 final size:28
Alignment explanation
Indices: 21137625--21137679 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
21137615 AAGTGTTTTT
*
21137625 TAATATGCATGCAGTGAGTATTTTTTAA
1 TAATATGCATGCAGTGACTATTTTTTAA
* *
21137653 TAATATGCATGTAGTGACTTTTTTTTA
1 TAATATGCATGCAGTGACTATTTTTTA
21137680 GGTGTGTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.29, C:0.07, G:0.16, T:0.47
Consensus pattern (28 bp):
TAATATGCATGCAGTGACTATTTTTTAA
Found at i:21138383 original size:21 final size:21
Alignment explanation
Indices: 21138357--21138408 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
21138347 CAAGTGGTTG
* *
21138357 CCCCAACTCAGCAA-CAGGCTA
1 CCCCAACTCAGCAAGAAAG-TA
*
21138378 CCCCAAATCAGCAAGAAAGTA
1 CCCCAACTCAGCAAGAAAGTA
21138399 CCCCAACTCA
1 CCCCAACTCA
21138409 ACAGGCTGCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.38, C:0.40, G:0.12, T:0.10
Consensus pattern (21 bp):
CCCCAACTCAGCAAGAAAGTA
Found at i:21138897 original size:22 final size:23
Alignment explanation
Indices: 21138846--21138890 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
21138836 CTTCTCTTCT
*
21138846 AACATATGAGAATTGAAAAAATA
1 AACATGTGAGAATTGAAAAAATA
*
21138869 AACATGTGAGAATT-AAGAAATA
1 AACATGTGAGAATTGAAAAAATA
21138891 CAAATGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.58, C:0.04, G:0.16, T:0.22
Consensus pattern (23 bp):
AACATGTGAGAATTGAAAAAATA
Found at i:21140050 original size:346 final size:347
Alignment explanation
Indices: 21139392--21140087 Score: 1340
Period size: 346 Copynumber: 2.0 Consensus size: 347
21139382 GCCAAATTTC
21139392 TTACACCCAAAAAACCTCCTACCTGGGTTGTCATTGGACCAAGACGTGTTTAATTTGGCTAGGTT
1 TTACACCCAAAAAACCTCCTACCTGGGTTGTCATTGGACCAAGACGTGTTTAATTTGGCTAGGTT
21139457 TCCAAAATAGCACACCGAAATCACTTCAGGCATCTCCATTTACAAATATTTAATATTTTTATTTA
66 TCCAAAATAGCACACCGAAATCACTTCAGGCATCTCCATTTACAAATATTTAATATTTTTATTTA
21139522 CCTTGAATAAATTAAGATTGATCGTATTTATGATCTTGAATTTCATGAATATTGATTATAAATAT
131 CCTTGAATAAATTAAGATTGATCGTATTTATGATCTTGAATTTCATGAATATTGATTATAAATAT
21139587 TTAATATTTTTATTTACAAATTGTTGTTGTTAGTGTGAATTTTGTGTTTGTGTTAATCGTGCATT
196 TTAATATTTTTATTTACAAATTGTTGTTGTTAGTGTGAATTTTGTGTTTGTGTTAATCGTGCATT
21139652 TGACATATTACATTGATCTTGAAACACCAAAATATGTGGTTTTTACTTTTGCAAAAAACTAATAA
261 TGACATATTACATTGATCTTGAAACACCAAAATATGTGGTTTTTACTTTTGCAAAAAACTAATAA
21139717 TCTTTTAATACAATGTCTAGAA
326 TCTTTTAATACAATGTCTAGAA
* *
21139739 TTACACCCAAAAAACCTCCTA-CTTGGTTGTCATTGGACCAAGACGTGTTTAATTTGGCTGGGTT
1 TTACACCCAAAAAACCTCCTACCTGGGTTGTCATTGGACCAAGACGTGTTTAATTTGGCTAGGTT
*
21139803 TCCACAATAGCACACCGAAATCACTTCAGGCATCTCCATTTACAAATATTTAATATTTTTATTTA
66 TCCAAAATAGCACACCGAAATCACTTCAGGCATCTCCATTTACAAATATTTAATATTTTTATTTA
21139868 CCTTGAATAAATTAAGATTGATCGTATTTATGATCTTGAATTTCATGAATATTGATTATAAATAT
131 CCTTGAATAAATTAAGATTGATCGTATTTATGATCTTGAATTTCATGAATATTGATTATAAATAT
21139933 TTAATATTTTTATTTACAAATTGTTGTTGTTAGTGTGAATTTTGTGTTTGTGTTAATCGTGCATT
196 TTAATATTTTTATTTACAAATTGTTGTTGTTAGTGTGAATTTTGTGTTTGTGTTAATCGTGCATT
*
21139998 TGACATATTACATTGATCTTGCAACACCAAAATATGTGGTTTTTACTTTTGCAAAAAACTAATAA
261 TGACATATTACATTGATCTTGAAACACCAAAATATGTGGTTTTTACTTTTGCAAAAAACTAATAA
*
21140063 TCTTTTAATACAATGTCTAGGA
326 TCTTTTAATACAATGTCTAGAA
21140085 TTA
1 TTA
21140088 TCTGTAATCC
Statistics
Matches: 344, Mismatches: 5, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
346 323 0.94
347 21 0.06
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.40
Consensus pattern (347 bp):
TTACACCCAAAAAACCTCCTACCTGGGTTGTCATTGGACCAAGACGTGTTTAATTTGGCTAGGTT
TCCAAAATAGCACACCGAAATCACTTCAGGCATCTCCATTTACAAATATTTAATATTTTTATTTA
CCTTGAATAAATTAAGATTGATCGTATTTATGATCTTGAATTTCATGAATATTGATTATAAATAT
TTAATATTTTTATTTACAAATTGTTGTTGTTAGTGTGAATTTTGTGTTTGTGTTAATCGTGCATT
TGACATATTACATTGATCTTGAAACACCAAAATATGTGGTTTTTACTTTTGCAAAAAACTAATAA
TCTTTTAATACAATGTCTAGAA
Found at i:21140307 original size:29 final size:30
Alignment explanation
Indices: 21140265--21140322 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
21140255 AATGAAAATT
21140265 TAAATACTTCAATTT-TAGTATAGAAATTGA
1 TAAATACTTCAATTTATAGTATA-AAATTGA
* *
21140295 TAAATA-TTGAATTTATATTATAAAATTG
1 TAAATACTTCAATTTATAGTATAAAATTG
21140323 TTTAGTATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (30 bp):
TAAATACTTCAATTTATAGTATAAAATTGA
Found at i:21152811 original size:18 final size:17
Alignment explanation
Indices: 21152788--21152822 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
21152778 TACTGCTTTC
*
21152788 TTGTTGTTTTTTATTGTT
1 TTGTTGATTTTT-TTGTT
21152806 TTGTTGATTTTTTTGTT
1 TTGTTGATTTTTTTGTT
21152823 GTTTTTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.06, C:0.00, G:0.17, T:0.77
Consensus pattern (17 bp):
TTGTTGATTTTTTTGTT
Found at i:21156840 original size:42 final size:42
Alignment explanation
Indices: 21156781--21156867 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
21156771 ATTAAATTTG
21156781 AATAGTAAAATGAGCTTTTTAAGTTGAATGGGATGACTAGAA
1 AATAGTAAAATGAGCTTTTTAAGTTGAATGGGATGACTAGAA
21156823 AATAGTAAAATGAGCTTTTTAAGTTGAATGGGATGACTAGAA
1 AATAGTAAAATGAGCTTTTTAAGTTGAATGGGATGACTAGAA
21156865 AAT
1 AAT
21156868 GAACTCAGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (42 bp):
AATAGTAAAATGAGCTTTTTAAGTTGAATGGGATGACTAGAA
Found at i:21160076 original size:19 final size:20
Alignment explanation
Indices: 21160034--21160076 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
21160024 TCATGCTTTC
*
21160034 TATTCACATTTTCATATTCA
1 TATTCACATTTTCATAATCA
21160054 -ATTCACATTTTCA-AATCA
1 TATTCACATTTTCATAATCA
21160072 TATTC
1 TATTC
21160077 CACAATCACG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTCACATTTTCATAATCA
Found at i:21160311 original size:23 final size:23
Alignment explanation
Indices: 21160267--21160319 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
21160257 GTGTCTGAAA
* *
21160267 CGACACACGAGGTGCCTTAAATAT
1 CGACACACAAGGTGCCTGAAAT-T
*
21160291 -GACACACAAGGTGTCTGAAATT
1 CGACACACAAGGTGCCTGAAATT
21160313 CGACACA
1 CGACACA
21160320 TAAACTGCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.19
Consensus pattern (23 bp):
CGACACACAAGGTGCCTGAAATT
Found at i:21160361 original size:23 final size:23
Alignment explanation
Indices: 21160333--21160409 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
21160323 ACTGCCTGAT
*
21160333 TAAAGTGCATAAAATACAACACA
1 TAAAGTGCATGAAATACAACACA
* * *
21160356 TAAAGTGCCTGATATCCAACACA
1 TAAAGTGCATGAAATACAACACA
* * *
21160379 TAAAGTGCTTGAAATACGACAGA
1 TAAAGTGCATGAAATACAACACA
21160402 TAAAGTGC
1 TAAAGTGC
21160410 CTGAGCGGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.21
Consensus pattern (23 bp):
TAAAGTGCATGAAATACAACACA
Found at i:21164153 original size:21 final size:21
Alignment explanation
Indices: 21164127--21164168 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
21164117 ATTTTTCCAA
* *
21164127 AGATGTGTATTGGATTGAATT
1 AGATGTGAATTGGATTAAATT
*
21164148 AGATGTGAATTGTATTAAATT
1 AGATGTGAATTGGATTAAATT
21164169 GAGCTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (21 bp):
AGATGTGAATTGGATTAAATT
Found at i:21164535 original size:25 final size:26
Alignment explanation
Indices: 21164507--21164592 Score: 97
Period size: 25 Copynumber: 3.4 Consensus size: 26
21164497 CTTATGAGCA
*
21164507 TCCCAATAATTGGCTCTCACGAG-TT
1 TCCCATTAATTGGCTCTCACGAGCTT
* *
21164532 TCCCGTTATTTGGCTCTCACGAGCTT
1 TCCCATTAATTGGCTCTCACGAGCTT
**
21164558 T-CCATTAATTGGCTCTCATAAGC-T
1 TCCCATTAATTGGCTCTCACGAGCTT
21164582 TCCCAATTAAT
1 TCCC-ATTAAT
21164593 GACTCTCCGG
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
24 2 0.04
25 40 0.78
26 9 0.18
ACGTcount: A:0.22, C:0.28, G:0.14, T:0.36
Consensus pattern (26 bp):
TCCCATTAATTGGCTCTCACGAGCTT
Found at i:21164654 original size:24 final size:24
Alignment explanation
Indices: 21164603--21164655 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
21164593 GACTCTCCGG
*
21164603 AGCTTCTCGATATTGGCTCGCATG
1 AGCTTCTCGATATTGGCTCGCATA
* *
21164627 AGCTTCTCGA-ATTTGGCTCTCTTA
1 AGCTTCTCGATA-TTGGCTCGCATA
21164651 AGCTT
1 AGCTT
21164656 TCTGTTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.38
Consensus pattern (24 bp):
AGCTTCTCGATATTGGCTCGCATA
Found at i:21164719 original size:25 final size:24
Alignment explanation
Indices: 21164691--21164772 Score: 74
Period size: 25 Copynumber: 3.3 Consensus size: 24
21164681 CCGATAATTG
21164691 GCTCGCAAGAGCTTCCCATTACAT
1 GCTCGCAAGAGCTTCCCATTACAT
** * * *
21164715 CGCTCATATGAGCTTCCCGTTATAT
1 -GCTCGCAAGAGCTTCCCATTACAT
* *
21164740 GGTTCGAAAGAGCTTCCCGATTACAT
1 -GCTCGCAAGAGCTTCCC-ATTACAT
21164766 GCTCGCA
1 GCTCGCA
21164773 TGGGCATACC
Statistics
Matches: 42, Mismatches: 14, Indels: 2
0.72 0.24 0.03
Matches are distributed among these distances:
25 37 0.88
26 5 0.12
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (24 bp):
GCTCGCAAGAGCTTCCCATTACAT
Found at i:21164751 original size:50 final size:50
Alignment explanation
Indices: 21164671--21164769 Score: 130
Period size: 50 Copynumber: 2.0 Consensus size: 50
21164661 TTATAACTCG
* *
21164671 TATGAGCTTTCCGATAATTGGCTCGCAAGAGCTTCCC-ATTACATCGCTCA
1 TATGAGCTTCCCGATAATTGGCTCGAAAGAGCTTCCCGATTACAT-GCTCA
* *
21164721 TATGAGCTTCCCG-TTATATGGTTCGAAAGAGCTTCCCGATTACATGCTC
1 TATGAGCTTCCCGATAAT-TGGCTCGAAAGAGCTTCCCGATTACATGCTC
21164770 GCATGGGCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
49 3 0.07
50 33 0.77
51 7 0.16
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.31
Consensus pattern (50 bp):
TATGAGCTTCCCGATAATTGGCTCGAAAGAGCTTCCCGATTACATGCTCA
Found at i:21168394 original size:5 final size:5
Alignment explanation
Indices: 21168384--21168416 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
21168374 TTTTTATGTT
*
21168384 TATAA TATAA TATAA TATAA TGTAA TATAA TAT
1 TATAA TATAA TATAA TATAA TATAA TATAA TAT
21168417 TTTATTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:21172142 original size:5 final size:5
Alignment explanation
Indices: 21172127--21172170 Score: 56
Period size: 5 Copynumber: 8.8 Consensus size: 5
21172117 AGCTATTAGG
21172127 TTTTGC TTTTC TTTTC TTTT- TTTTC TTTTC -TTTC TTTCTC TTTT
1 TTTT-C TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTT-TC TTTT
21172171 TTTACTTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
4 8 0.23
5 18 0.51
6 9 0.26
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:21172152 original size:14 final size:15
Alignment explanation
Indices: 21172133--21172170 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
21172123 TAGGTTTTGC
21172133 TTTTCTTTTCTTT-T
1 TTTTCTTTTCTTTCT
21172147 TTTTCTTTTCTTTCT
1 TTTTCTTTTCTTTCT
*
21172162 TTCTCTTTT
1 TTTTCTTTT
21172171 TTTACTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCTTTTCTTTCT
Found at i:21174108 original size:17 final size:17
Alignment explanation
Indices: 21174086--21174120 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
21174076 CTCATTTTCT
21174086 GTTGCTTAGTCTAGTGA
1 GTTGCTTAGTCTAGTGA
21174103 GTTGCTTAGTCTAGTGA
1 GTTGCTTAGTCTAGTGA
21174120 G
1 G
21174121 GTTAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.11, G:0.31, T:0.40
Consensus pattern (17 bp):
GTTGCTTAGTCTAGTGA
Found at i:21174439 original size:23 final size:23
Alignment explanation
Indices: 21174413--21174458 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
21174403 ATGAGAATTT
**
21174413 TTAAAATTTTTAAATCAAAATAA
1 TTAAAATTTAAAAATCAAAATAA
*
21174436 TTAAAATTTAAAAATTAAAATAA
1 TTAAAATTTAAAAATCAAAATAA
21174459 ATAATCTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
TTAAAATTTAAAAATCAAAATAA
Found at i:21177460 original size:44 final size:45
Alignment explanation
Indices: 21177405--21177695 Score: 164
Period size: 44 Copynumber: 6.6 Consensus size: 45
21177395 TCATTCTAAC
* * * *
21177405 CCACTGTAACTTTAGAGGTAGA-GGATTTGTCA-CTTTAATCTATT
1 CCACTGCAACTTTAGAGGAAGATAGATTTGT-AGCTTTAATCTACT
* *
21177449 CCACTGCAAC-TT-CAGGAAGATTAGATTTGTAGCTTTAATCTGCT
1 CCACTGCAACTTTAGAGGAAGA-TAGATTTGTAGCTTTAATCTACT
* * * * *
21177493 CCACTGCAACTTTAG-GG-AGATGAGACTCGAATCTTCAATCTACT
1 CCACTGCAACTTTAGAGGAAGAT-AGATTTGTAGCTTTAATCTACT
* * * *
21177537 CCACTGCAACTTCA-A-GAAGATGAGAATTGTAACTTTAATCTGCT
1 CCACTGCAACTTTAGAGGAAGAT-AGATTTGTAGCTTTAATCTACT
* * * * * *
21177581 CCACTACAAC-TT-CAGGAAGATAAGACTTGTAACTTCT-ATTTGCT
1 CCACTGCAACTTTAGAGGAAGAT-AGATTTGTAGCTT-TAATCTACT
* * *
21177625 CCACTGCAACTTCT---GGAAGATAAGACTCGTAGCTTTAATCTGCT
1 CCACTGCAACTT-TAGAGGAAGAT-AGATTTGTAGCTTTAATCTACT
*
21177669 CCATTGCAACTTTAG-GG-AGATAAGATT
1 CCACTGCAACTTTAGAGGAAGAT-AGATT
21177696 CGCTATCTTC
Statistics
Matches: 200, Mismatches: 31, Indels: 32
0.76 0.12 0.12
Matches are distributed among these distances:
42 6 0.03
43 9 0.05
44 176 0.88
45 8 0.04
46 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (45 bp):
CCACTGCAACTTTAGAGGAAGATAGATTTGTAGCTTTAATCTACT
Found at i:21177556 original size:88 final size:89
Alignment explanation
Indices: 21177441--21177738 Score: 339
Period size: 88 Copynumber: 3.4 Consensus size: 89
21177431 TTGTCACTTT
* * *
21177441 AATCTATTCCACTGCAACTTCAGGAAGATTAGATTTGTAGCTTTAATCTGCTCCACTGCAACTTT
1 AATCTACTCCACTGCAACTTCAGGAAGATAAGAATTGTAGCTTTAATCTGCTCCACTGCAACTTT
*
21177506 AGGGAGATGAGACTCG-AATCTTC
66 AGGGAGATAAGACTCGCAATCTTC
* * * * *
21177529 AATCTACTCCACTGCAACTTCAAGAAGATGAGAATTGTAACTTTAATCTGCTCCACTACAACTTC
1 AATCTACTCCACTGCAACTTCAGGAAGATAAGAATTGTAGCTTTAATCTGCTCCACTGCAACTTT
* * *
21177594 AGGAAGATAAGACTTGTAA-CTTC
66 AGGGAGATAAGACTCGCAATCTTC
* * * * * * *
21177617 TATTTGCTCCACTGCAACTTCTGGAAGATAAGACTCGTAGCTTTAATCTGCTCCATTGCAACTTT
1 AATCTACTCCACTGCAACTTCAGGAAGATAAGAATTGTAGCTTTAATCTGCTCCACTGCAACTTT
* *
21177682 AGGGAGATAAGATTCGCTATCTTC
66 AGGGAGATAAGACTCGCAATCTTC
* * * * * *
21177706 AATTTGCTCTACTACAAATTCAGGGAGATAAGA
1 AATCTACTCCACTGCAACTTCAGGAAGATAAGA
21177739 TTTGCCACGA
Statistics
Matches: 175, Mismatches: 33, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
88 142 0.81
89 33 0.19
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (89 bp):
AATCTACTCCACTGCAACTTCAGGAAGATAAGAATTGTAGCTTTAATCTGCTCCACTGCAACTTT
AGGGAGATAAGACTCGCAATCTTC
Found at i:21177630 original size:132 final size:131
Alignment explanation
Indices: 21177431--21177738 Score: 332
Period size: 132 Copynumber: 2.3 Consensus size: 131
21177421 GGTAGAGGAT
* ** * * * *
21177431 TTGTCACTTTAATCTATTCCACTGCAACTTCAGGAAGATTAGATTTGTAGCTTTAATCTGCTCCA
1 TTGTAACTTTAATCTGCTCCACTACAACTTCAGGAAGATAAGACTTGTAACTTTAATCTGCTCCA
* * * *
21177496 CTGCAACTT-TAGGGAGATGAGACTCGAATCTTCAATCTACTCCACTGCAACTTCAAGAAGATGA
66 CTGCAACTTCT-GGAAGATAAGACTCGAAGCTTCAATCTACTCCACTGCAACTTCAAGAAGATAA
21177560 GAA
130 G-A
*
21177563 TTGTAACTTTAATCTGCTCCACTACAACTTCAGGAAGATAAGACTTGTAACTTCT-ATTTGCTCC
1 TTGTAACTTTAATCTGCTCCACTACAACTTCAGGAAGATAAGACTTGTAACTT-TAATCTGCTCC
* * * * * * *
21177627 ACTGCAACTTCTGGAAGATAAGACTCGTAGCTTTAATCTGCTCCATTGCAACTTTAGGGAGATAA
65 ACTGCAACTTCTGGAAGATAAGACTCGAAGCTTCAATCTACTCCACTGCAACTTCAAGAAGATAA
21177692 GA
130 GA
* * * * * *
21177694 TTCGCTATCTTCAATTTGCTCTACTACAAATTCAGGGAGATAAGA
1 TT-G-TAACTTTAATCTGCTCCACTACAACTTCAGGAAGATAAGA
21177739 TTTGCCACGA
Statistics
Matches: 147, Mismatches: 25, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
131 3 0.02
132 108 0.73
133 36 0.24
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (131 bp):
TTGTAACTTTAATCTGCTCCACTACAACTTCAGGAAGATAAGACTTGTAACTTTAATCTGCTCCA
CTGCAACTTCTGGAAGATAAGACTCGAAGCTTCAATCTACTCCACTGCAACTTCAAGAAGATAAG
A
Found at i:21177731 original size:45 final size:44
Alignment explanation
Indices: 21177448--21177740 Score: 232
Period size: 44 Copynumber: 6.6 Consensus size: 44
21177438 TTTAATCTAT
* * * * * *
21177448 TCCACTGCAACTTCAGGAAGATTAGATTTGTAGCTTTAATCTGC
1 TCCACTACAACTTCAGGAAGATAAGATTCGTAACTTCAATTTGC
* * * * * * *
21177492 TCCACTGCAACTTTAGGGAGATGAGACTCG-AATCTTCAATCTAC
1 TCCACTACAACTTCAGGAAGATAAGATTCGTAA-CTTCAATTTGC
* * * * *
21177536 TCCACTGCAACTTCAAGAAGATGAGAATT-GTAACTTTAATCTGC
1 TCCACTACAACTTCAGGAAGATAAG-ATTCGTAACTTCAATTTGC
*
21177580 TCCACTACAACTTCAGGAAGATAAGACTT-GTAACTTCTATTTGC
1 TCCACTACAACTTCAGGAAGATAAGA-TTCGTAACTTCAATTTGC
* * * * * *
21177624 TCCACTGCAACTTCTGGAAGATAAGACTCGTAGCTTTAATCTGC
1 TCCACTACAACTTCAGGAAGATAAGATTCGTAACTTCAATTTGC
* * * * *
21177668 TCCATTGCAACTTTAGGGAGATAAGATTCGCTATCTTCAATTTGC
1 TCCACTACAACTTCAGGAAGATAAGATTCG-TAACTTCAATTTGC
* * *
21177713 TCTACTACAAATTCAGGGAGATAAGATT
1 TCCACTACAACTTCAGGAAGATAAGATT
21177741 TGCCACGATG
Statistics
Matches: 203, Mismatches: 40, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
43 3 0.01
44 162 0.80
45 38 0.19
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (44 bp):
TCCACTACAACTTCAGGAAGATAAGATTCGTAACTTCAATTTGC
Found at i:21185805 original size:19 final size:21
Alignment explanation
Indices: 21185783--21185829 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
21185773 TTGTGAAACT
*
21185783 TAATGCAT-ATG-ATGAAATA
1 TAATGCATGATGAATGAAAAA
21185802 TAATGC-TGATGAATGAAAAA
1 TAATGCATGATGAATGAAAAA
21185822 TGAATGCA
1 T-AATGCA
21185830 AAGAAAGGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 1 0.04
19 9 0.39
20 8 0.35
21 5 0.22
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (21 bp):
TAATGCATGATGAATGAAAAA
Found at i:21191226 original size:669 final size:668
Alignment explanation
Indices: 21189950--21191269 Score: 2505
Period size: 669 Copynumber: 2.0 Consensus size: 668
21189940 CATTTCTGCT
21189950 TATTTATGGCATGTATAGACTGACTTTCACACATATTTTATTTGTCCGAGAACCGACTAAACCGT
1 TATTTATGGCATGTATAGACTGACTTTCACACATATTTTATTTGTCCGAGAACCGACTAAACCGT
*
21190015 AGCTCTGATACCACTAAAATGTAACACCCCTTACCCGTATTCCTTAACAGAACAGAGTATGAGGT
66 AACTCTGATACCACTAAAATGTAACACCCCTTACCCGTATTCCTTAACAGAACAGAGTATGAGGT
21190080 ATTACTATTTTTTTTAAATTTCGACAGCATTTCTGCTTATTTTTACGTACAACCCCCTGCAAGTT
131 ATTACTATTTTTTTTAAATTTCGACAGCATTTCTGCTTATTTTTACGTACAACCCCCTGCAAGTT
21190145 TTCAATCACACTTTCAAACAATTCCAATAATCCAACCAAAAACAGTTGTATGATCATACTCAATT
196 TTCAATCACACTTTCAAACAATTCCAATAATCCAACCAAAAACAGTTGTATGATCATACTCAATT
*
21190210 TGTCTAATAATAAACATCAACATTTTAAACCGAAACATACTATATATTTGTTTACGCCATAATAC
261 TGTCTAATAATAAACATCAAAATTTTAAACCGAAACATACTATATATTTGTTTACGCCATAATAC
21190275 ATAAAGTCGTCTATACATGCCATGTTTCCAAAATATGAGTTGCAAAATACCCAAGCGTTGATGAT
326 ATAAAGTCGTCTATACATGCCATGTTTCCAAAATATGAGTTGCAAAATACCCAAGCGTTGATGAT
21190340 AGTGTAGATGATTATCTCACTCCGCCCAAGTTCCGAGTTGATTGATGTCACTCGGTGCAAAATAT
391 AGTGTAGATGATTATCTCACTCCGCCCAAGTTCCGAGTTGATTGATGTCACTCGGTGCAAAATAT
21190405 CGTAACTTTTCAATTTACTCCACTACTTTCTCTTTTCCCCGTTTGAGGTATTCTTCTCGTCTTTC
456 CGTAACTTTTCAATTTACTCCACTACTTTCTCTTTTCCCCGTTTGAGGTATTCTTCTCGTCTTTC
* *
21190470 TTGTTTATGGAGCTTGGAAGCTTGAAAACCCTAACTATGGCTTCCCCCTTGCTGATTTCGTTCAC
521 TTGATTATAGAGCTTGGAAGCTTGAAAACCCTAACTATGGCTTCCCCCTTGCTGATTTCGTTCAC
* *
21190535 CATGAAGAAGATGAGCATATTTTTCCATCTTTTTCCTACTTAATTCTATTTAATTACCAAATGAC
586 CATAAAGAAGATGAGCATATTTTTCCATCTTTTTCCCACTTAATTCTATTTAATTACCAAATGAC
21190600 TTTCACACTATCACAATA
651 TTTCACACTATCACAATA
*
21190618 TATTTATGGCATGTATAGACTGACTTTCACACATATTTTATTTGTCCGAGAACCGACTCAACCGT
1 TATTTATGGCATGTATAGACTGACTTTCACACATATTTTATTTGTCCGAGAACCGACTAAACCGT
21190683 AACTCTGATACCACTAAAATGTAACACCCCTTACCCGTATTCCTTAACAGAACAGAGTATGAGGT
66 AACTCTGATACCACTAAAATGTAACACCCCTTACCCGTATTCCTTAACAGAACAGAGTATGAGGT
21190748 ATTACTATTTTTTTTTAAATTTCGACAGCATTTCTGCTTATTTTTACGTACAACCCCCTGCAAGT
131 ATTACTA-TTTTTTTTAAATTTCGACAGCATTTCTGCTTATTTTTACGTACAACCCCCTGCAAGT
21190813 TTTCAATCACACTTTCAAACAATTCCAATAATCCAACCAAAAACAGTTGTATGATCATACTCAAT
195 TTTCAATCACACTTTCAAACAATTCCAATAATCCAACCAAAAACAGTTGTATGATCATACTCAAT
*
21190878 TTGTCTAATAATAAACATCAAAATTTTAAACCGAAACATACTATATATTTGTTTATGCCATAATA
260 TTGTCTAATAATAAACATCAAAATTTTAAACCGAAACATACTATATATTTGTTTACGCCATAATA
21190943 CATAAAGTCGTCTATACATGCCATGTTTCCAAAATATGAGTTGCAAAATACCCAAGCGTTGATGA
325 CATAAAGTCGTCTATACATGCCATGTTTCCAAAATATGAGTTGCAAAATACCCAAGCGTTGATGA
* *
21191008 TAGTGTAGATGATTATCTGACTCCGCCCAAGTTTCGAGTTGATTGATGTCACTCGGTGCAAAATA
390 TAGTGTAGATGATTATCTCACTCCGCCCAAGTTCCGAGTTGATTGATGTCACTCGGTGCAAAATA
* *
21191073 TCGTAATTTTTCAATTTACTCCACTACTTTCTCTTTTCCCTGTTTGAGGTATTCTTCTCGTCTTT
455 TCGTAACTTTTCAATTTACTCCACTACTTTCTCTTTTCCCCGTTTGAGGTATTCTTCTCGTCTTT
*
21191138 CTTGATTATAGAGCTTGGAAGCTTGAAAACCCTAACTATGGTTTCCCCCTTGCTGATTTCGTTCA
520 CTTGATTATAGAGCTTGGAAGCTTGAAAACCCTAACTATGGCTTCCCCCTTGCTGATTTCGTTCA
*
21191203 CCATAAAGAAGATGAGCATATTTTTCCATCTTTTTCCCATTTAATTCTATTTAATTACCAAATGA
585 CCATAAAGAAGATGAGCATATTTTTCCATCTTTTTCCCACTTAATTCTATTTAATTACCAAATGA
21191268 CT
650 CT
21191270 AAAATGCCCT
Statistics
Matches: 637, Mismatches: 14, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
668 135 0.21
669 502 0.79
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.35
Consensus pattern (668 bp):
TATTTATGGCATGTATAGACTGACTTTCACACATATTTTATTTGTCCGAGAACCGACTAAACCGT
AACTCTGATACCACTAAAATGTAACACCCCTTACCCGTATTCCTTAACAGAACAGAGTATGAGGT
ATTACTATTTTTTTTAAATTTCGACAGCATTTCTGCTTATTTTTACGTACAACCCCCTGCAAGTT
TTCAATCACACTTTCAAACAATTCCAATAATCCAACCAAAAACAGTTGTATGATCATACTCAATT
TGTCTAATAATAAACATCAAAATTTTAAACCGAAACATACTATATATTTGTTTACGCCATAATAC
ATAAAGTCGTCTATACATGCCATGTTTCCAAAATATGAGTTGCAAAATACCCAAGCGTTGATGAT
AGTGTAGATGATTATCTCACTCCGCCCAAGTTCCGAGTTGATTGATGTCACTCGGTGCAAAATAT
CGTAACTTTTCAATTTACTCCACTACTTTCTCTTTTCCCCGTTTGAGGTATTCTTCTCGTCTTTC
TTGATTATAGAGCTTGGAAGCTTGAAAACCCTAACTATGGCTTCCCCCTTGCTGATTTCGTTCAC
CATAAAGAAGATGAGCATATTTTTCCATCTTTTTCCCACTTAATTCTATTTAATTACCAAATGAC
TTTCACACTATCACAATA
Found at i:21198163 original size:21 final size:21
Alignment explanation
Indices: 21198117--21198164 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
21198107 TGTTATGGAC
*
21198117 TTTTGATTTTTGGTTTTATTT
1 TTTTTATTTTTGGTTTTATTT
* *
21198138 ATTTTATTTTTGGTTTGTTTTT
1 TTTTTATTTTTGGTTT-TATTT
21198160 TTTTT
1 TTTTT
21198165 CGGGCCCAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.08, C:0.00, G:0.12, T:0.79
Consensus pattern (21 bp):
TTTTTATTTTTGGTTTTATTT
Found at i:21198393 original size:6 final size:6
Alignment explanation
Indices: 21198384--21198426 Score: 50
Period size: 6 Copynumber: 6.7 Consensus size: 6
21198374 AAAAAATTTG
*
21198384 AATTCC AATTCC TTAAATTCC AATCCC AATTCC AATTCC AATT
1 AATTCC AATTCC ---AATTCC AATTCC AATTCC AATTCC AATT
21198427 TTTATTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 26 0.81
9 6 0.19
ACGTcount: A:0.35, C:0.30, G:0.00, T:0.35
Consensus pattern (6 bp):
AATTCC
Found at i:21204421 original size:21 final size:22
Alignment explanation
Indices: 21204397--21204448 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
21204387 CTCGTATATA
* *
21204397 GGTCAAAATGGGTT-AAATACT
1 GGTCAAAATGGATTAAAATACG
*
21204418 GGTCAAAATGGATTAAAATAGG
1 GGTCAAAATGGATTAAAATACG
21204440 GGTCAAAAT
1 GGTCAAAAT
21204449 ATGAAAATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.42, C:0.08, G:0.25, T:0.25
Consensus pattern (22 bp):
GGTCAAAATGGATTAAAATACG
Found at i:21204821 original size:65 final size:65
Alignment explanation
Indices: 21204743--21204868 Score: 166
Period size: 65 Copynumber: 1.9 Consensus size: 65
21204733 AGAAAATGAA
* * *
21204743 GAAGGTGAAAAAGAAAAGAAAA-AGTTAGCAGAAAAGATAAAAGAGAAAGAAA-GTAGAAGGAGA
1 GAAGGTAAAAAAGAAAA-AAAACAATTAACAGAAAAGATAAAAGAGAAAGAAATG-AGAAGGAGA
21204806 AG
64 AG
* * *
21204808 GAAGGTAAAAAAGAAAAAAAACAATTAATAGAGAAGGTAAAAGAGAAAGAAATGAGAAGGA
1 GAAGGTAAAAAAGAAAAAAAACAATTAACAGAAAAGATAAAAGAGAAAGAAATGAGAAGGA
21204869 AAAAAAGAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
64 4 0.08
65 48 0.91
66 1 0.02
ACGTcount: A:0.63, C:0.02, G:0.27, T:0.09
Consensus pattern (65 bp):
GAAGGTAAAAAAGAAAAAAAACAATTAACAGAAAAGATAAAAGAGAAAGAAATGAGAAGGAGAAG
Found at i:21205938 original size:44 final size:44
Alignment explanation
Indices: 21205867--21205978 Score: 170
Period size: 44 Copynumber: 2.5 Consensus size: 44
21205857 ATACATGCAA
* *
21205867 AAATTAGATGCATTGGAAGAAATTTGGAACAAACTTCGTAATTT
1 AAATTAGATGCATTGGAACAAACTTGGAACAAACTTCGTAATTT
* * * *
21205911 AAATGAGATGCATTGCACCAAACTTGGAACAAACTTTGTAATTT
1 AAATTAGATGCATTGGAACAAACTTGGAACAAACTTCGTAATTT
21205955 AAATTAGATGCATTGGAACAAACT
1 AAATTAGATGCATTGGAACAAACT
21205979 CTGTAAAATA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 59 1.00
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (44 bp):
AAATTAGATGCATTGGAACAAACTTGGAACAAACTTCGTAATTT
Found at i:21218700 original size:3 final size:3
Alignment explanation
Indices: 21218692--21218761 Score: 72
Period size: 3 Copynumber: 24.0 Consensus size: 3
21218682 TATATATAGG
* ** *
21218692 AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AA- AAG GCT AAT AAT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
21218738 AAT AAT AAT GAT AAT AAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
21218762 GGGGCTATTA
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
2 4 0.07
3 50 0.93
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:21223587 original size:18 final size:18
Alignment explanation
Indices: 21223564--21223608 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
21223554 GTTTTGAAAA
**
21223564 TGGTCAAAATTATGTTTC
1 TGGTCAAAATTATAATTC
21223582 TGGTCAAAATTATAATTC
1 TGGTCAAAATTATAATTC
*
21223600 TAGTCAAAA
1 TGGTCAAAA
21223609 GTGGCTTGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (18 bp):
TGGTCAAAATTATAATTC
Found at i:21223857 original size:21 final size:20
Alignment explanation
Indices: 21223831--21223878 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
21223821 ATGATGGGAT
21223831 TGGTGGTACTGTTGGGCCGAA
1 TGGTGGTA-TGTTGGGCCGAA
21223852 TGGTGG--TGTTGGGCCGAA
1 TGGTGGTATGTTGGGCCGAA
21223870 -GGATGGTAT
1 TGG-TGGTAT
21223879 TGGGCCTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
17 2 0.08
18 15 0.62
20 1 0.04
21 6 0.25
ACGTcount: A:0.15, C:0.10, G:0.46, T:0.29
Consensus pattern (20 bp):
TGGTGGTATGTTGGGCCGAA
Found at i:21223876 original size:18 final size:18
Alignment explanation
Indices: 21223840--21223884 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
21223830 TTGGTGGTAC
21223840 TGTTGGGCCGAATGGTGG
1 TGTTGGGCCGAATGGTGG
21223858 TGTTGGGCCGAA-GGATGG
1 TGTTGGGCCGAATGG-TGG
*
21223876 TATTGGGCC
1 TGTTGGGCC
21223885 TAATATTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 2 0.08
18 23 0.92
ACGTcount: A:0.13, C:0.13, G:0.47, T:0.27
Consensus pattern (18 bp):
TGTTGGGCCGAATGGTGG
Found at i:21229706 original size:17 final size:16
Alignment explanation
Indices: 21229665--21229706 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
21229655 AATTCAATTT
*
21229665 TAATATAAATATTCAA
1 TAATATAAAAATTCAA
21229681 T-ATACTAAACAATTCAA
1 TAATA-TAAA-AATTCAA
21229698 TAATATAAA
1 TAATATAAA
21229707 TAATATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 3 0.14
16 5 0.23
17 11 0.50
18 3 0.14
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (16 bp):
TAATATAAAAATTCAA
Found at i:21230171 original size:9 final size:9
Alignment explanation
Indices: 21230157--21230193 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
21230147 TATAGTTTGA
21230157 TATTCGAAT
1 TATTCGAAT
21230166 TATTCGAAT
1 TATTCGAAT
*
21230175 TATTCGAGT
1 TATTCGAAT
*
21230184 TATTTGAAT
1 TATTCGAAT
21230193 T
1 T
21230194 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:21231924 original size:104 final size:104
Alignment explanation
Indices: 21231744--21231942 Score: 326
Period size: 104 Copynumber: 1.9 Consensus size: 104
21231734 TTGCTTTCAT
* * * * * * *
21231744 TTTATCTTTTGATTCATTTTGAGCACGATAAAGTGGATGTTATCATAAATTTATATGGTTTCTAA
1 TTTATCTTTTGACTCATTTTAAGCACAATAAAGTGGATGTTATCATAAATTCATATAGCTTATAA
*
21231809 TCTAGCATTCATCAATATACAATGTCTTCTCTTAAAGAA
66 TCTAGCATTCATCAATATACAAGGTCTTCTCTTAAAGAA
21231848 TTTATCTTTTGACTCATTTTAAGCACAATAAAGTGGATGTTATCATAAATTCATATAGCTTATAA
1 TTTATCTTTTGACTCATTTTAAGCACAATAAAGTGGATGTTATCATAAATTCATATAGCTTATAA
21231913 TCTAGCATTCATCAATATACAAGGTCTTCT
66 TCTAGCATTCATCAATATACAAGGTCTTCT
21231943 TCCAAAAAAT
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
104 87 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.41
Consensus pattern (104 bp):
TTTATCTTTTGACTCATTTTAAGCACAATAAAGTGGATGTTATCATAAATTCATATAGCTTATAA
TCTAGCATTCATCAATATACAAGGTCTTCTCTTAAAGAA
Found at i:21240109 original size:2 final size:2
Alignment explanation
Indices: 21240104--21240140 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
21240094 TCAACAGGTT
21240104 TC 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 TC T
21240141 TTTTTCCCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:21244457 original size:31 final size:29
Alignment explanation
Indices: 21244376--21244457 Score: 76
Period size: 31 Copynumber: 2.7 Consensus size: 29
21244366 ATAACTATTG
*
21244376 CATAAAAATATTTTAT-ATTCATAATTAA
1 CATAAAAATATATTATAATTCATAATTAA
* * *
21244404 CAATTTTAAAATTTATTTTAATTCATTAATTTAA
1 C-A--TAAAAATATATTATAATTCA-TAA-TTAA
21244438 CATAAAAATATATTATAATT
1 CATAAAAATATATTATAATT
21244458 ACTTTTCTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
28 1 0.02
29 1 0.02
31 25 0.61
32 5 0.12
33 4 0.10
34 5 0.12
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (29 bp):
CATAAAAATATATTATAATTCATAATTAA
Found at i:21245550 original size:14 final size:14
Alignment explanation
Indices: 21245531--21245569 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
21245521 CTAAAAAAAT
21245531 AAATCATTTTTCAA
1 AAATCATTTTTCAA
21245545 AAATCATTTTTCAA
1 AAATCATTTTTCAA
21245559 AAATCATTTTT
1 AAATCATTTTT
21245570 AGTAAACCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (14 bp):
AAATCATTTTTCAA
Found at i:21245904 original size:22 final size:23
Alignment explanation
Indices: 21245842--21245906 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 23
21245832 ATTTAAATTA
* *
21245842 TAAAATTATTTGATATAT-TATT
1 TAAAATTATTTGATAAATATAAT
* *
21245864 TAAAATTAATT-ACAGAATATAAT
1 TAAAATTATTTGATA-AATATAAT
21245887 T-AAATTATTTGATAAATATA
1 TAAAATTATTTGATAAATATA
21245907 GATTTTAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 2 0.06
22 26 0.76
23 6 0.18
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.45
Consensus pattern (23 bp):
TAAAATTATTTGATAAATATAAT
Found at i:21247436 original size:36 final size:36
Alignment explanation
Indices: 21247396--21247467 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
21247386 ACATAATTGT
21247396 TAACAAATCATCAAAGTGGTGTTCATTGATAATGGG
1 TAACAAATCATCAAAGTGGTGTTCATTGATAATGGG
21247432 TAACAAATCATCAAAGTGGTGTTCATTGATAATGGG
1 TAACAAATCATCAAAGTGGTGTTCATTGATAATGGG
21247468 ATGCTCATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (36 bp):
TAACAAATCATCAAAGTGGTGTTCATTGATAATGGG
Found at i:21253154 original size:32 final size:33
Alignment explanation
Indices: 21253113--21253178 Score: 125
Period size: 32 Copynumber: 2.0 Consensus size: 33
21253103 TGTAAATCAA
21253113 TACAATCTCATGCTGAAATAGAAAGTTTT-TTT
1 TACAATCTCATGCTGAAATAGAAAGTTTTATTT
21253145 TACAATCTCATGCTGAAATAGAAAGTTTTATTT
1 TACAATCTCATGCTGAAATAGAAAGTTTTATTT
21253178 T
1 T
21253179 CTCATAAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 29 0.88
33 4 0.12
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (33 bp):
TACAATCTCATGCTGAAATAGAAAGTTTTATTT
Found at i:21255757 original size:26 final size:25
Alignment explanation
Indices: 21255711--21255761 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
21255701 ACAAACAAAT
* *
21255711 AATCAACCTAGTTATTATAATATAAG
1 AATCAACATAGTTAATATAAT-TAAG
21255737 AATCAACATCAGTTAAT-TAATTAAG
1 AATCAACAT-AGTTAATATAATTAAG
21255762 CCTAGTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 4 0.18
26 12 0.55
27 6 0.27
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (25 bp):
AATCAACATAGTTAATATAATTAAG
Found at i:21258810 original size:18 final size:18
Alignment explanation
Indices: 21258787--21258830 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
21258777 TTAGTCTACA
21258787 AGCTCGTCTCACTCGAAG
1 AGCTCGTCTCACTCGAAG
21258805 AGCTCGTCTCACTCGAAG
1 AGCTCGTCTCACTCGAAG
*
21258823 ACCTCGTC
1 AGCTCGTC
21258831 AGTCGTGACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.20, C:0.36, G:0.20, T:0.23
Consensus pattern (18 bp):
AGCTCGTCTCACTCGAAG
Done.