Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 134 of 295
Found at i:41001143 original size:14 final size:17
Alignment explanation
Indices: 41001111--41001148 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
41001101 GATTATAAAG
41001111 TATATTATTAAATTAAT
1 TATATTATTAAATTAAT
41001128 TATATTA-TAAA-T-AT
1 TATATTATTAAATTAAT
41001142 TATATTA
1 TATATTA
41001149 AGAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 1 0.05
16 4 0.19
17 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTATTAAATTAAT
Found at i:41004261 original size:12 final size:12
Alignment explanation
Indices: 41004246--41004272 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
41004236 TAAAAATATT
41004246 AATAAAAAATAG
1 AATAAAAAATAG
41004258 AATAAAAAATAG
1 AATAAAAAATAG
41004270 AAT
1 AAT
41004273 TTGAATAGAA
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:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (12 bp):
AATAAAAAATAG
Found at i:41004618 original size:29 final size:27
Alignment explanation
Indices: 41004569--41004627 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
41004559 TTTCCACCAT
* *
41004569 TTTTTAAAAAATTGACCTATTTCCTTAA
1 TTTTTAAAAAAATGACCTA-TTCCATAA
* *
41004597 TTTTTAAAAAAATGGCTTTATTCCATAA
1 TTTTTAAAAAAATGAC-CTATTCCATAA
41004625 TTT
1 TTT
41004628 ATCCCATGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 24 0.92
29 2 0.08
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.47
Consensus pattern (27 bp):
TTTTTAAAAAAATGACCTATTCCATAA
Found at i:41023759 original size:18 final size:18
Alignment explanation
Indices: 41023723--41023759 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
41023713 TTGGTTTTCG
* *
41023723 AATTCGAATAACTCTAAT
1 AATTCGAATAAATCAAAT
41023741 AATTCGAATAAATCAAAT
1 AATTCGAATAAATCAAAT
41023759 A
1 A
41023760 CCAAATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (18 bp):
AATTCGAATAAATCAAAT
Found at i:41023878 original size:31 final size:31
Alignment explanation
Indices: 41023812--41023878 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
41023802 CTCTTTACTT
****
41023812 CCCCCAAAACTTTTACTCCCTCCCACTTTTT
1 CCCCCAAAACTTTTACTCCCTCCCACTCCCA
41023843 CCCCCAAAACTTTTACTCCCCTCCCA-TCCCA
1 CCCCCAAAACTTTTACT-CCCTCCCACTCCCA
41023874 CCCCC
1 CCCCC
41023879 TTCTACCCCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 23 0.74
32 8 0.26
ACGTcount: A:0.19, C:0.54, G:0.00, T:0.27
Consensus pattern (31 bp):
CCCCCAAAACTTTTACTCCCTCCCACTCCCA
Found at i:41027079 original size:50 final size:50
Alignment explanation
Indices: 41027014--41027351 Score: 258
Period size: 50 Copynumber: 6.7 Consensus size: 50
41027004 ACCGAAGCTC
* *
41027014 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
* * * * ** * *
41027064 TCTGGTACACGTAGTAGCCTACA-TTAGTACTACGCACGTGATTTAACCA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
* * * * * ** *
41027113 TTTGATACACGTAGTAGCCTACACTTAGTACTACACACGTGATCGAAGTTAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGA-CCTA-TCAA
* * * * * * *
41027165 -CGGGTACGCATAGTAGTCTGCACTTAGTACTACACACATG-G-CTTAACCA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACT--ACACATGCGACCTATCAA
* **
41027214 TCTGATACACGTAGTAGCCTGCACTTAGTACTACACACATGATCGAAGT-T-AA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACT--ACACATG--CGACCTATCAA
* ** *
41027266 T-GGGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
*
41027315 TCTAGTACACGTAGTAGCCTGCACTTAGTACTACACA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACA
41027352 CGTGACTCAC
Statistics
Matches: 222, Mismatches: 53, Indels: 26
0.74 0.18 0.09
Matches are distributed among these distances:
47 4 0.02
48 1 0.00
49 51 0.23
50 104 0.47
51 50 0.23
52 4 0.02
53 7 0.03
54 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (50 bp):
TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
Found at i:41027196 original size:51 final size:51
Alignment explanation
Indices: 41027124--41027301 Score: 207
Period size: 51 Copynumber: 3.5 Consensus size: 51
41027114 TTGATACACG
* *
41027124 TAGTAGCCTACACTTAGTACTACACACGTGATCGAAGTTAACGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACATGATCGAAGTTAACGGGTACGCA
* * * ** * * * * *
41027175 TAGTAGTCTGCACTTAGTACTACACACATG-GCTTAA-CCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACATGATC-GAAGTTAACGGGTACGCA
* *
41027225 TAGTAGCCTGCACTTAGTACTACACACATGATCGAAGTTAATGGGTATGCA
1 TAGTAGCCTGCACTTAGTACTACACACATGATCGAAGTTAACGGGTACGCA
41027276 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
41027302 TGCGACCTAT
Statistics
Matches: 100, Mismatches: 24, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
50 39 0.39
51 61 0.61
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (51 bp):
TAGTAGCCTGCACTTAGTACTACACACATGATCGAAGTTAACGGGTACGCA
Found at i:41027222 original size:101 final size:101
Alignment explanation
Indices: 41027025--41027356 Score: 388
Period size: 101 Copynumber: 3.3 Consensus size: 101
41027015 CTGGTACGCA
* * ** * * * * *
41027025 TAGTAGCCTGCACTTAGTACTACACATGCGA-CCTA-TCAATCTGGTACACGTAGTAGCCTACA-
1 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTAA-CGGGTACGCATAGTAGCCTGCAC
* * ** *
41027087 TTAGTACTACGCACGTGATTTAACCATTTGATACACG
65 TTAGTACTACACACATGGCTTAACCATCTGATACACG
* *
41027124 TAGTAGCCTACACTTAGTACTACACACGTGATCGAAGTTAACGGGTACGCATAGTAGTCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTAACGGGTACGCATAGTAGCCTGCACT
41027189 TAGTACTACACACATGGCTTAACCATCTGATACACG
66 TAGTACTACACACATGGCTTAACCATCTGATACACG
* * *
41027225 TAGTAGCCTGCACTTAGTACTACACACATGATCGAAGTTAATGGGTATGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTAACGGGTACGCATAGTAGCCTGCACT
* * *
41027290 TAGTACT--ACACATGCGACCTATCAATCT-AGTACACG
66 TAGTACTACACACATG-G-CTTAACCATCTGA-TACACG
41027326 TAGTAGCCTGCACTTAGTACTACACACGTGA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA
41027357 CTCACAATGG
Statistics
Matches: 202, Mismatches: 25, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
99 35 0.17
100 21 0.10
101 146 0.72
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (101 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTAACGGGTACGCATAGTAGCCTGCACT
TAGTACTACACACATGGCTTAACCATCTGATACACG
Found at i:41029928 original size:42 final size:42
Alignment explanation
Indices: 41029881--41029966 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
41029871 ATACTCAATA
41029881 TATACCCATCAATCAGTCAGTTCACACAATTAGGGTCCTAAG
1 TATACCCATCAATCAGTCAGTTCACACAATTAGGGTCCTAAG
41029923 TATACCCATCAATCAGTCAGTTCACACAATTAGGGTCCTAAG
1 TATACCCATCAATCAGTCAGTTCACACAATTAGGGTCCTAAG
41029965 TA
1 TA
41029967 ATGCTTACTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.27
Consensus pattern (42 bp):
TATACCCATCAATCAGTCAGTTCACACAATTAGGGTCCTAAG
Found at i:41042558 original size:27 final size:27
Alignment explanation
Indices: 41042528--41042705 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
41042518 ATATCGAGTC
* * * *
41042528 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
41042555 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41042582 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
* ** * *
41042610 CGCGCACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
41042637 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
41042664 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41042691 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41042706 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 107 0.82
28 23 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:41042645 original size:82 final size:81
Alignment explanation
Indices: 41042549--41042704 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41042539 TGCTATATAA
*
41042549 TCAACTCGCACACTTAGTGC-TACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGC
1 TCAACTCGCACACTTAGTGCAT-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGC
*
41042613 GCACTTAGTGCCGCATGG
64 ACACTTAGTGCCGCATGG
* * **
41042631 TCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCAC
1 TCAACTCGCACACTTAGTGCATCATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
41042696 ACTTAGTGC
66 ACTTAGTGC
41042705 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 14 0.21
82 52 0.78
83 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCATCATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:41050471 original size:27 final size:27
Alignment explanation
Indices: 41050441--41050618 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
41050431 ATATCGAGTC
* * * *
41050441 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
41050468 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41050495 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
* ** * *
41050523 CGCGCACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
41050550 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
41050577 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41050604 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41050619 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 107 0.82
28 23 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:41050558 original size:82 final size:81
Alignment explanation
Indices: 41050462--41050617 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41050452 TGCTATATAA
*
41050462 TCAACTCGCACACTTAGTGC-TACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGC
1 TCAACTCGCACACTTAGTGCAT-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGC
*
41050526 GCACTTAGTGCCGCATGG
64 ACACTTAGTGCCGCATGG
* * **
41050544 TCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCAC
1 TCAACTCGCACACTTAGTGCATCATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
41050609 ACTTAGTGC
66 ACTTAGTGC
41050618 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 14 0.21
82 52 0.78
83 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCATCATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:41054932 original size:38 final size:38
Alignment explanation
Indices: 41054841--41054993 Score: 198
Period size: 38 Copynumber: 4.0 Consensus size: 38
41054831 GAATCCAGTC
* * *
41054841 ACCAGCACAAAGCCTGCGGGACTTTAAGCTCGGATATAAT
1 ACCAGCACGAAGCCTGCGGGA-TTTAA-CCCGGATATATT
* *
41054881 ACTAGCACTAAGCCTGCGGGATTTAACCCGGATATATT
1 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATT
* *
41054919 ACCAGTACGAAGCCTGTGGGATTTAACCCGGATATATT
1 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATT
* * *
41054957 ACCAGCACGGAGCCTACGGGACTTAACCCGGATATAT
1 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATAT
41054994 ATCGAGTGCT
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
38 76 0.76
39 5 0.05
40 19 0.19
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (38 bp):
ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATT
Found at i:41064321 original size:93 final size:93
Alignment explanation
Indices: 41064167--41064345 Score: 247
Period size: 93 Copynumber: 1.9 Consensus size: 93
41064157 CTTACATACG
* **
41064167 TCAAGGCCGATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCACTTATCTGTGTTGATGCCAT
1 TCAAGGCCGATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCAC-TATCTGGGCCGATGCCAT
41064232 GTCCTAAACAGGTCTTACACTAACAAACC
65 GTCCTAAACAGGTCTTACACTAACAAACC
*
41064261 TCAA-GCCGATGCCATGTCCTAGACAGGTCTTACACTAGCT-TGCA-TATCTTGAGGCCGATGCC
1 TCAAGGCCGATGCCATGTCCCAGACAGGTCTTACACTAGCTCT-CACTATC-TG-GGCCGATGCC
* *
41064323 ATGTCCTAGACAGGTTTTACACT
63 ATGTCCTAAACAGGTCTTACACT
41064346 GGCTCTCACT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
91 4 0.05
92 3 0.04
93 65 0.86
94 4 0.05
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.27
Consensus pattern (93 bp):
TCAAGGCCGATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCACTATCTGGGCCGATGCCATG
TCCTAAACAGGTCTTACACTAACAAACC
Found at i:41064395 original size:49 final size:48
Alignment explanation
Indices: 41064172--41064394 Score: 215
Period size: 49 Copynumber: 4.7 Consensus size: 48
41064162 ATACGTCAAG
*
41064172 GCCGATGCCATGTCCCAGACAGGTCTTACACTAGCTCTCACTTATCTGT
1 GCCGATGCCATGTCCTAGACAGGTCTTACACTAGCTCTCAC-TATCTGT
** * * ** * **
41064221 GTTGATGCCATGTCCTAAACAGGTCTTACACTA--ACAAAC-CTC-AA
1 GCCGATGCCATGTCCTAGACAGGTCTTACACTAGCTCTCACTATCTGT
*
41064265 GCCGATGCCATGTCCTAGACAGGTCTTACACTAGCT-TGCA-TATCTTGAG
1 GCCGATGCCATGTCCTAGACAGGTCTTACACTAGCTCT-CACTATC-TG-T
* *
41064314 GCCGATGCCATGTCCTAGACAGGTTTTACACTGGCTCTCACTTATCTGT
1 GCCGATGCCATGTCCTAGACAGGTCTTACACTAGCTCTCAC-TATCTGT
* * *
41064363 GTCGATGTCATGTCCTAGACAGGTTTTACACT
1 GCCGATGCCATGTCCTAGACAGGTCTTACACT
41064395 GACACACACA
Statistics
Matches: 140, Mismatches: 24, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
44 30 0.21
45 2 0.01
46 3 0.02
47 3 0.02
49 95 0.68
50 3 0.02
51 4 0.03
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (48 bp):
GCCGATGCCATGTCCTAGACAGGTCTTACACTAGCTCTCACTATCTGT
Found at i:41069903 original size:3 final size:3
Alignment explanation
Indices: 41069895--41069920 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
41069885 ATCTGAGAAC
41069895 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
41069921 ATTTTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:41071183 original size:54 final size:54
Alignment explanation
Indices: 41071093--41071200 Score: 162
Period size: 54 Copynumber: 2.0 Consensus size: 54
41071083 AAAAAGGAAA
* * * * *
41071093 AGGAAGGAATGGATGCACGCTAGTCAAACTTTGAAGAAACACCAGATTTGTCTT
1 AGGAAGGAACGGAAGCACGCTAGTCAAACTTCGAAGAAACACCAAATTTATCTT
*
41071147 AGGAAGGAACGGAAGCACGCTAGTCAGACTTCGAAGAAACACCAAATTTATCTT
1 AGGAAGGAACGGAAGCACGCTAGTCAAACTTCGAAGAAACACCAAATTTATCTT
41071201 CTAACTCTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (54 bp):
AGGAAGGAACGGAAGCACGCTAGTCAAACTTCGAAGAAACACCAAATTTATCTT
Found at i:41085727 original size:40 final size:40
Alignment explanation
Indices: 41085622--41085838 Score: 298
Period size: 40 Copynumber: 5.5 Consensus size: 40
41085612 CGGATGATAA
* *
41085622 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
41085662 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
41085701 CCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
41085741 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
41085781 CCGAGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
41085821 CC-GGCTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
41085839 TACTTGGTTT
Statistics
Matches: 162, Mismatches: 12, Indels: 7
0.90 0.07 0.04
Matches are distributed among these distances:
39 50 0.31
40 112 0.69
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:41093308 original size:12 final size:12
Alignment explanation
Indices: 41093291--41093319 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
41093281 TTATAATTTA
41093291 TTCTTAACAACT
1 TTCTTAACAACT
41093303 TTCTTAACAACT
1 TTCTTAACAACT
41093315 TTCTT
1 TTCTT
41093320 CATCTTCTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (12 bp):
TTCTTAACAACT
Found at i:41095590 original size:40 final size:39
Alignment explanation
Indices: 41095492--41095714 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
41095482 TCCTCGTTCA
* * ** * *
41095492 AATGCCTTCGGGACATAGCCCGGATTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAACAATTCGCAC
*
41095531 AATGCCTTCGGGACATAACCCGGATTTAACAATTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAACAATTCGCAC
*
41095570 GAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAACAATTCGCAC
**
41095610 GAATGCCTTCGGGACTTAACCCGGATTT-AGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAACAAT-TCGCAC
* * * * * *
41095650 AAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAATTCGCAC
* *
41095691 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
41095715 CAGCATTCAA
Statistics
Matches: 156, Mismatches: 22, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
39 39 0.25
40 108 0.69
41 8 0.05
42 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAATTCGCAC
Found at i:41095648 original size:80 final size:79
Alignment explanation
Indices: 41095490--41095714 Score: 240
Period size: 80 Copynumber: 2.8 Consensus size: 79
41095480 GCTCCTCGTT
* * ** * *
41095490 CAAATGCCTTCGGGACATAGCCCGGATTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAATGCCTTCGGGACTTAACCCGGA
41095555 TTTAACAATTCGCA
66 TTTAACAATTCGCA
*
41095569 CGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCAC-AATGCCTTCGGGACTTAACCCGG
**
41095634 ATTT-AGTATCTCGCA
65 ATTTAACAAT-TCGCA
* * * * * * *
41095649 CAAAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCACAAAGCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACAATGCCTTCGGGACTTAACCC
41095712 GGA
63 GGA
41095715 CAGCATTCAA
Statistics
Matches: 124, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
79 41 0.33
80 77 0.62
81 6 0.05
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAATGCCTTCGGGACTTAACCCGGA
TTTAACAATTCGCA
Found at i:41095714 original size:120 final size:119
Alignment explanation
Indices: 41095492--41095714 Score: 288
Period size: 120 Copynumber: 1.9 Consensus size: 119
41095482 TCCTCGTTCA
* * *
41095492 AATGCCTTCGGGACATAGCCCGGATTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATA
* *
41095557 TAACAATTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
66 TAACAATTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
41095611 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAATCCGGA
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGA-CATAACCCGGA
* * *
41095675 TATATTCACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGGA
64 TATA-ACAATTAGCACGAAAGCCTTCGGGACTTAACCCGGA
41095715 CAGCATTCAA
Statistics
Matches: 88, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
119 38 0.43
120 42 0.48
121 8 0.09
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (119 bp):
AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATA
TAACAATTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:41099661 original size:21 final size:20
Alignment explanation
Indices: 41099637--41099675 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
41099627 GAGTATTTTG
41099637 ATGTTTAATGATAGATTATGA
1 ATGTTTAATGATAG-TTATGA
*
41099658 ATGTTTGATGATAGTTAT
1 ATGTTTAATGATAGTTAT
41099676 ATTAGGTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (20 bp):
ATGTTTAATGATAGTTATGA
Found at i:41100316 original size:48 final size:48
Alignment explanation
Indices: 41100239--41100465 Score: 312
Period size: 48 Copynumber: 4.7 Consensus size: 48
41100229 TTAGGGGATA
* *
41100239 CATTGTTTTGGCTTCGGGCCATGATATTGGCACTTCGAGTGCAAGCTT
1 CATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGAGTGCGAGCTT
* * * *
41100287 CATTCATTTGGATTTGGGCCATGATATTGGCACTTCAAGTGCGAGCTT
1 CATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGAGTGCGAGCTT
* * *
41100335 CATTAATTTGGCTTTGGGCCATGATATTGGCACTTCGGGTGCGAGCTT
1 CATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGAGTGCGAGCTT
* * * *
41100383 AATTGATTTGGCTTCAGGCCATGATATTAGCACTTCGAGTGCGAGATAT
1 CATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGAGTGCGAGCT-T
*
41100432 -ATTGAATTGGCTTCGGGCCATGATATTGGCACTT
1 CATTGATTTGGCTTCGGGCCATGATATTGGCACTT
41100466 AGTGTGTGGG
Statistics
Matches: 158, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
48 157 0.99
49 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (48 bp):
CATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGAGTGCGAGCTT
Found at i:41109351 original size:42 final size:41
Alignment explanation
Indices: 41109304--41109456 Score: 139
Period size: 42 Copynumber: 3.6 Consensus size: 41
41109294 TGTGATTTTT
* *
41109304 TGTAAGACCATATCTTGGATATGGCATCGATATGTGATTTCA
1 TGTAAGACCATAT-TTGGATATGGCATCGATATATGATTCCA
* * * ** *
41109346 TGTAAGACCATGTTTGGGACATGGCATCGATATAAGACACCG
1 TGTAAGACCATATTT-GGATATGGCATCGATATATGATTCCA
* *
41109388 TGTAAGA-CATAGTTGGGCTATTGGCATCGATATATGA-TCCTA
1 TGTAAGACCATA-TTTGGATA-TGGCATCGATATATGATTCC-A
*
41109430 TGTAAGACCATATATCGGATATGGCAT
1 TGTAAGACCATAT-TTGGATATGGCAT
41109457 TGGCATCTTA
Statistics
Matches: 88, Mismatches: 17, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
41 10 0.11
42 69 0.78
43 9 0.10
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.31
Consensus pattern (41 bp):
TGTAAGACCATATTTGGATATGGCATCGATATATGATTCCA
Found at i:41117253 original size:43 final size:43
Alignment explanation
Indices: 41117117--41117288 Score: 192
Period size: 43 Copynumber: 4.0 Consensus size: 43
41117107 ACATAGGATC
* *
41117117 CGATATGTGCTTTCGTGTAAGACCACGTCT-GAGACGTTGGCAT
1 CGATATTTGATTTCGTGTAAGACCACGTCTAG-GACGTTGGCAT
* *
41117160 CGACT-TATGATTTACGTGTAAGACCACGTCTAGAACGTTGGCAT
1 CGA-TATTTGATTT-CGTGTAAGACCACGTCTAGGACGTTGGCAT
*
41117204 CG-TATTTGATTTCGTGTAAGACC-CTGTCTGGGACAG-TGGCAT
1 CGATATTTGATTTCGTGTAAGACCAC-GTCTAGGAC-GTTGGCAT
* * *
41117246 CGATATTTGATTACATGTAAGACCACGTCTAGGACATTGGCAT
1 CGATATTTGATTTCGTGTAAGACCACGTCTAGGACGTTGGCAT
41117289 TGTATGAGCT
Statistics
Matches: 110, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
41 1 0.01
42 27 0.25
43 50 0.45
44 31 0.28
45 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (43 bp):
CGATATTTGATTTCGTGTAAGACCACGTCTAGGACGTTGGCAT
Found at i:41117303 original size:86 final size:86
Alignment explanation
Indices: 41117127--41117296 Score: 213
Period size: 85 Copynumber: 2.0 Consensus size: 86
41117117 CGATATGTGC
*
41117127 TTTCGTGTAAGACCACGTCTGAGACGTTGGCATCGACTTATGATTTACGTGTAAGACCACGTCTA
1 TTTCGTGTAAGACCACGTCTGAGACGTTGGCATCGACTTATGATTTACATGTAAGACCACGTCTA
* **
41117192 GAACGTTGGCATCGTATTTGA
66 GAACATTGGCATCGTATGAGA
* *
41117213 TTTCGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGA-TATTTGA-TTACATGTAAGACCACGT
1 TTTCGTGTAAGACCAC-GTCTGAGAC-GTTGGCATCGACT-TATGATTTACATGTAAGACCACGT
* *
41117274 CTAGGACATTGGCATTGTATGAG
63 CTAGAACATTGGCATCGTATGAG
41117297 CTTTTCGAGC
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
85 37 0.51
86 35 0.48
87 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (86 bp):
TTTCGTGTAAGACCACGTCTGAGACGTTGGCATCGACTTATGATTTACATGTAAGACCACGTCTA
GAACATTGGCATCGTATGAGA
Found at i:41120830 original size:24 final size:24
Alignment explanation
Indices: 41120798--41120868 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
41120788 CTGTCAGGAG
41120798 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
41120822 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
**
41120846 AGGATTTAGGAGAAGATAAGGGA
1 AGGATTTAGGAGTTGATAAGGGA
41120869 GGAAATCTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.37, C:0.00, G:0.38, T:0.25
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:41120880 original size:48 final size:48
Alignment explanation
Indices: 41120798--41120891 Score: 111
Period size: 48 Copynumber: 1.9 Consensus size: 48
41120788 CTGTCAGGAG
** * *
41120798 AGGATTTAGGAGTTGATAAGGGATAGGATTTAGGAGTTGAT-AAGGGAT
1 AGGATTTAGGAGAAGATAAGGGA-AGGATCTAGGAGCTGATCAAGGGAT
41120846 AGGATTTAGGAGAAGATAAGGG-AGGAAATCTAGGAGCTGATCAAGG
1 AGGATTTAGGAGAAGATAAGGGAAGG--ATCTAGGAGCTGATCAAGG
41120892 AACAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
46 3 0.08
48 32 0.82
49 4 0.10
ACGTcount: A:0.36, C:0.03, G:0.37, T:0.23
Consensus pattern (48 bp):
AGGATTTAGGAGAAGATAAGGGAAGGATCTAGGAGCTGATCAAGGGAT
Found at i:41122324 original size:27 final size:26
Alignment explanation
Indices: 41122284--41122368 Score: 116
Period size: 27 Copynumber: 3.2 Consensus size: 26
41122274 AGGAAACGTC
* *
41122284 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
41122311 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
*
41122338 CTGGTGGTTCTGCCACGATTATCTGTT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
41122365 CTGG
1 CTGG
41122369 CAGCCATGCT
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
26 2 0.04
27 49 0.92
28 2 0.04
ACGTcount: A:0.15, C:0.24, G:0.25, T:0.36
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:41123433 original size:28 final size:29
Alignment explanation
Indices: 41123360--41123447 Score: 94
Period size: 28 Copynumber: 3.1 Consensus size: 29
41123350 AGCATGGCTG
* * * *
41123360 CCAGATACAGA-AA-ATGTGACAGAGTCA
1 CCAGATACAGATAATTTGTGGCATAGCCA
*
41123387 CCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAATTTGTGGCA-TAGCCA
41123416 CCAGA-ACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAATTTGTGGCATAGCCA
41123444 CCAG
1 CCAG
41123448 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
27 12 0.24
28 25 0.49
29 14 0.27
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (29 bp):
CCAGATACAGATAATTTGTGGCATAGCCA
Found at i:41123600 original size:28 final size:28
Alignment explanation
Indices: 41123553--41123617 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
41123543 AAATTAACCC
* *
41123553 TAGGGGTACAAAGGTCATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
*
41123581 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
41123609 TAGGGGTAT
1 TAGGGGTAT
41123618 TCTAGTACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.31, C:0.09, G:0.28, T:0.32
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCATACA
Found at i:41123880 original size:8 final size:8
Alignment explanation
Indices: 41123864--41123895 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
41123854 CCCAAAATAC
41123864 CGGCTTTT
1 CGGCTTTT
*
41123872 CGGCATTT
1 CGGCTTTT
41123880 CGGCTTTT
1 CGGCTTTT
41123888 CGGCTTTT
1 CGGCTTTT
41123896 GCCGATCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.03, C:0.25, G:0.25, T:0.47
Consensus pattern (8 bp):
CGGCTTTT
Found at i:41132683 original size:28 final size:28
Alignment explanation
Indices: 41132641--41132705 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
41132631 ATGTACTAGA
* *
41132641 ATACCCCTATTTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
41132669 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
41132697 ATACCCCTA
1 ATACCCCTA
41132706 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:41132870 original size:27 final size:27
Alignment explanation
Indices: 41132822--41132901 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 27
41132812 CTAGTGGCTA
*
41132822 TGCCACAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAA-TATCTGTTCTGGTGGCAC
*
41132850 TGCCACATATATCTGTTCTGGTGGCAC
1 TGCCACAAATATCTGTTCTGGTGGCAC
41132877 TGCCACAAAATATCTGTATCTGGTG
1 TGCCAC-AAATATCTGT-TCTGGTG
41132902 ACTCTGTCAC
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
27 23 0.49
28 17 0.36
29 7 0.15
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (27 bp):
TGCCACAAATATCTGTTCTGGTGGCAC
Found at i:41132920 original size:55 final size:56
Alignment explanation
Indices: 41132822--41132926 Score: 142
Period size: 55 Copynumber: 1.9 Consensus size: 56
41132812 CTAGTGGCTA
* *
41132822 TGCCACAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-TCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTATCTGGTGGCAC
* * *
41132877 TGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTATCTGG
1 TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTATCTGG
41132927 CAGCCATGCT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
55 22 0.51
56 21 0.49
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (56 bp):
TGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTATCTGGTGGCAC
Found at i:41138853 original size:3 final size:3
Alignment explanation
Indices: 41138845--41138916 Score: 94
Period size: 3 Copynumber: 24.0 Consensus size: 3
41138835 ATTTTCGGCA
*
41138845 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AGAG AAG AAG -GG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A-AG AAG AAG AAG AAG
*
41138890 AAG -AG AAG AAG AAG AAAG AAA AAG AAG
1 AAG AAG AAG AAG AAG -AAG AAG AAG AAG
41138917 GAGAGGAGGA
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
2 3 0.05
3 52 0.85
4 6 0.10
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:41139002 original size:14 final size:14
Alignment explanation
Indices: 41138953--41139015 Score: 58
Period size: 14 Copynumber: 4.4 Consensus size: 14
41138943 TGAGAGAAGA
41138953 AAAAAGAA--AAAG
1 AAAAAGAAGGAAAG
41138965 AAAAAGAGAAGGAGAAG
1 -AAAA-AGAAGGA-AAG
* * *
41138982 AAGAAGAGGGAAGG
1 AAAAAGAAGGAAAG
41138996 AAAAAGAAGGAAAG
1 AAAAAGAAGGAAAG
41139010 AAAAAG
1 AAAAAG
41139016 GTAATTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
13 4 0.10
14 23 0.57
15 6 0.15
16 4 0.10
17 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (14 bp):
AAAAAGAAGGAAAG
Found at i:41139002 original size:17 final size:17
Alignment explanation
Indices: 41138958--41139015 Score: 50
Period size: 19 Copynumber: 3.4 Consensus size: 17
41138948 GAAGAAAAAA
*
41138958 GAAAAAGAAAAAGAGAAG
1 GAAAAAG-AAGAGAGAAG
*
41138976 GAGAAGAAGAAGAGGGAAG
1 GA-AA-AAGAAGAGAGAAG
41138995 GAAAAAGAAG-GA-AA-
1 GAAAAAGAAGAGAGAAG
41139009 GAAAAAG
1 GAAAAAG
41139016 GTAATTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 7 0.20
15 2 0.06
16 1 0.03
17 6 0.17
18 4 0.11
19 12 0.34
20 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (17 bp):
GAAAAAGAAGAGAGAAG
Found at i:41139632 original size:132 final size:133
Alignment explanation
Indices: 41139481--41139720 Score: 295
Period size: 132 Copynumber: 1.8 Consensus size: 133
41139471 ATGAAATATG
* ** * * *
41139481 AAAATAGTATAATTAAAAAAAATCCGAAAATAAAAAAATACGAACAATGTGCCAAAGTCA-GGTT
1 AAAATAATATAATT-AAAAAAATAAGAAAAGAAAAAAATACGAACAAAGTGCCAAAATCAGGGTT
**
41139545 ACTTATTAAATTAATATAAAAAA-ACTTAAATAATACATTTGAAAGATTTTATGCTACAATAAAA
65 ACTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAAGATTTTATGCTACAATAAAA
41139609 TACC
130 TACC
* * * * * * * * *
41139613 AAAATAATATATTTTAAAAAATAATATACGAAAAAAATATGAATAAAGTGCTAAAATTAGGGTTA
1 AAAATAATATAATTAAAAAAATAAGAAAAGAAAAAAATACGAACAAAGTGCCAAAATCAGGGTTA
*
41139678 TTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAA
66 CTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAA
41139721 GCATTATGTA
Statistics
Matches: 88, Mismatches: 18, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
131 32 0.36
132 36 0.41
133 20 0.23
ACGTcount: A:0.55, C:0.07, G:0.08, T:0.29
Consensus pattern (133 bp):
AAAATAATATAATTAAAAAAATAAGAAAAGAAAAAAATACGAACAAAGTGCCAAAATCAGGGTTA
CTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAAGATTTTATGCTACAATAAAAT
ACC
Found at i:41139763 original size:146 final size:146
Alignment explanation
Indices: 41139602--41140512 Score: 968
Period size: 146 Copynumber: 6.1 Consensus size: 146
41139592 TTTATGCTAC
* *
41139602 AATAAAATACCAAAATAATATATTTTAAAAAATAATATACGAAAAAAATATGAATAAAGTGCT-A
1 AATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCTCA
* *
41139666 AAATTAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAGCATTATGTA
66 AAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGTA
41139731 CTAAAATAATATAAAGA
131 CTAAAATAATATAAA-A
*
41139748 AATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAATAAAAAAATTACGAAGAAAG
1 AATAAAATACGAAAATAATATATTTTAAAAAATAATATACG-----AAAAAAA-TACGAATAAAG
* * * ** *
41139813 T-ATCAAAATCAGGGTTATTTAGTATAAAACCCTTAATATAAAGAAACAGATAATTAATACATTT
60 TGCTCAAAATCAGGGTTATTTA-T-TAAAA----AAATATAAA-AAATACTTAAATAATACATTT
*** * * *
41139877 G-ATTTTTTTTTGCTAAAATAATATAAAA
118 GAAACATTATGTACTAAAATAATATAAAA
* *
41139905 AATAAAATAAGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATATGAATAAAGTGCT-A
1 AATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCTCA
* * *
41139969 AAATCAGGGATATTTATTGAAAAAATATAAAAAAATACTGAAATAATACATTTGAAACATTATGT
66 AAATCAGGGTTATTTATTAAAAAAATAT-AAAAAATACTTAAATAATACATTTGAAACATTATGT
*
41140034 ACTAAAATAATATGAAGA
130 ACTAAAATAATAT-AAAA
* *
41140052 AATAAAATACGAAAATAATATATTTTAAAAAATAAGATAC-AAAAAAATACGAAAAAAGTG-TCA
1 AATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCTCA
** * *
41140115 AAATCAGGGTTATTTATTAAATTAGTATAAAAAAACACTTACATAATATACCTAATACATTTGAA
66 AAATCAGGGTTATTTATTAAA--AAAATATAAAAA-A--TAC-T--TA-A-ATAATACATTTGAA
* * *
41140180 ACATTTTTTGCTAAAATAATATAAAA
121 ACATTATGTACTAAAATAATATAAAA
* *
41140206 AATAAAATAGGAAAATAATATATTTTAAAAAATAATATACG-AAAAAATATGAATAAAGTGCT-A
1 AATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCTCA
** * * *
41140269 AAATCAGGGTTATTTATT-AAAAAATATTTAAAACACTTAAATAATATATTTAAAACATTATGTA
66 AAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGTA
* *
41140333 CTAAAATAAGGGTTTTAAA
131 CTAAAATAA---TATAAAA
* * *
41140352 ATTAAATAATACGAAAGTAATATA-TTTAAAAAA-AAGATACGAAAAAAATACGAA-AAAGTG-T
1 AAT-AA-AATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
* ** * *
41140413 CAAAATCAGTGTTATTTATTAAATTAATATAAAAAAATACTTACATAATACATTTAAAACATT-T
64 CAAAATCAGGGTTATTTATTAAAAAAATAT-AAAAAATACTTAAATAATACATTTGAAACATTAT
* *
41140477 TTTCTAAAATAATATAAAA
128 GTACTAAAATAATATAAAA
*
41140496 AATAATATACGAAAATA
1 AATAAAATACGAAAATA
41140513 TTTTACTTAT
Statistics
Matches: 637, Mismatches: 88, Indels: 84
0.79 0.11 0.10
Matches are distributed among these distances:
142 10 0.02
143 29 0.05
144 8 0.01
145 26 0.04
146 136 0.21
147 87 0.14
148 49 0.08
149 4 0.01
150 5 0.01
151 42 0.07
152 34 0.05
153 4 0.01
154 83 0.13
155 33 0.05
157 41 0.06
158 28 0.04
159 18 0.03
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.30
Consensus pattern (146 bp):
AATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCTCA
AAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGTA
CTAAAATAATATAAAA
Found at i:41139908 original size:12 final size:13
Alignment explanation
Indices: 41139891--41139926 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
41139881 TTTTTTTGCT
41139891 AAAATAATATAA-
1 AAAATAATATAAG
*
41139903 AAAATAAAATAAG
1 AAAATAATATAAG
41139916 AAAATAATATA
1 AAAATAATATA
41139927 TTTTAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (13 bp):
AAAATAATATAAG
Found at i:41140308 original size:20 final size:22
Alignment explanation
Indices: 41140285--41140325 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
41140275 GGGTTATTTA
41140285 TTAAA-AA-ATATTTAAAACAC
1 TTAAATAATATATTTAAAACAC
41140305 TTAAATAATATATTTAAAACA
1 TTAAATAATATATTTAAAACA
41140326 TTATGTACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 2 0.11
22 12 0.63
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (22 bp):
TTAAATAATATATTTAAAACAC
Found at i:41140446 original size:300 final size:295
Alignment explanation
Indices: 41139602--41140512 Score: 1215
Period size: 300 Copynumber: 3.1 Consensus size: 295
41139592 TTTATGCTAC
*
41139602 AATAAAATACCAAAATAATATATTTTAAAAAATAATATACGAAAAAAATATGAATAAAGTGCTAA
1 AATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATATGAATAAAGTGCTAA
* *
41139667 AATTAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAGCATTATGTAC
66 AATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGTAC
*
41139732 TAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAATAAA
131 TAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACG-----AAA
* *
41139797 AAAATTACGAAGAAAGTATCAAAATCAGGGTTATTTAGTATAAAACCCTTAATATAAAGAAAC-A
191 AAAA-TACGAA-AAAGTGTCAAAATCAGGGTTATTTA-T-T-AAA---TTAATATAAAAAAACTA
* ***
41139861 GATA-AT--TAATACATTTG-ATTTTTTTTTGCTAAAATAATATAAAA
248 CATATATACTAATACATTTGAAACATTTTTTGCTAAAATAATATAAAA
*
41139905 AATAAAATAAGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATATGAATAAAGTGCTAA
1 AATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATATGAATAAAGTGCTAA
* * *
41139970 AATCAGGGATATTTATTGAAAAAATATAAAAAAATACTGAAATAATACATTTGAAACATTATGTA
66 AATCAGGGTTATTTATTAAAAAAATAT-AAAAAATACTTAAATAATACATTTGAAACATTATGTA
*
41140035 CTAAAATAATATGAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATAC-AAAAAAA
130 CTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAAAA
*
41140099 TACGAAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAGTATAAAAAAACACTTACATAATAT
195 TACG-AAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATAT-AAAAAA-AC-TACAT-ATAT
41140164 ACCTAATACATTTGAAACATTTTTTGCTAAAATAATATAAAA
255 A-CTAATACATTTGAAACATTTTTTGCTAAAATAATATAAAA
*
41140206 AATAAAATAGGAAAATAATATATTTTAAAAAATAATATACG-AAAAAATATGAATAAAGTGCTAA
1 AATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATATGAATAAAGTGCTAA
** * * *
41140270 AATCAGGGTTATTTATT-AAAAAATATTTAAAACACTTAAATAATATATTTAAAACATTATGTAC
66 AATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGTAC
* * * *
41140334 TAAAATAAGGGTTTTAA-AATTAAATAATACGAAAGTAATATA-TTTAAAAAA-AAGATACGAAA
131 TAAAATAA---TATAAAGAAAT-AA-AATACGAAAATAATATATTTTAAAAAATAAGATACGAAA
* *
41140396 AAAATACGAAAAAGTGTCAAAATCAGTGTTATTTATTAAATTAATATAAAAAAA-TAC-T-TACA
191 AAAATACGAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAACTACATATATA
*
41140458 -TAATACATTTAAAACATTTTTT-CTAAAATAATATAAAA
256 CTAATACATTTGAAACATTTTTTGCTAAAATAATATAAAA
*
41140496 AATAATATACGAAAATA
1 AATAAAATACGAAAATA
41140513 TTTTACTTAT
Statistics
Matches: 556, Mismatches: 34, Indels: 49
0.87 0.05 0.08
Matches are distributed among these distances:
290 31 0.06
291 27 0.05
292 5 0.01
293 5 0.01
294 3 0.01
295 5 0.01
296 5 0.01
297 30 0.05
298 50 0.09
299 15 0.03
300 97 0.17
301 90 0.16
302 16 0.03
303 87 0.16
304 90 0.16
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.30
Consensus pattern (295 bp):
AATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATATGAATAAAGTGCTAA
AATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGTAC
TAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAAAAT
ACGAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAACTACATATATACTAAT
ACATTTGAAACATTTTTTGCTAAAATAATATAAAA
Found at i:41140535 original size:300 final size:289
Alignment explanation
Indices: 41139454--41140512 Score: 1172
Period size: 300 Copynumber: 3.6 Consensus size: 289
41139444 AGTTTTTTGT
* * * * ** ** * **
41139454 TAAAATAATATAAAAAAATGAAATATGAAAATAGTATAATTAAAAAAAATCCGAAAATAAAAAAA
1 TAAAATAATATAAAGAAATAAAATACGAAAATAATAT-ATTTTAAAAAATAAGATACGAAAAAAA
* * * * *
41139519 TACGAACAATGTGCCAAAGTCA-GGTTACTTATTAAATTAATAT-AAAAAA-ACTTAAATAATAC
65 TACGAA-AAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAATACTTACATAATAC
* * * **
41139581 ATTTGAAAGATTTTATGCT---A-CA-AT--AAAAT---A-CCAAAATAATATATTTTAAAAAAT
129 ATTT-AAACATTTTTTGCTAAAATAATATAAAAAATAAAATAGAAAATAATATATTTTAAAAAAT
*
41139635 AATATACGAAAAAAATATGAATAAAGTGCTAAAATTAGGGTTATTTATTAAAAAAATATAAAAAA
193 AATATACGAAAAAAATATGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATAAAAAA
*
41139700 TACTTAAATAATACATTTGAAGCATTATGTAC
258 TACTTAAATAATACATTTGAAACATTATGTAC
*
41139732 TAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAATAAA
1 TAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACG-----AAA
* * * *
41139797 AAAATTACGAAGAAAGTATCAAAATCAGGGTTATTTAGTATAAAACCCTTAATATAAAGAAACAG
61 AAAA-TACGAA-AAAGTGTCAAAATCAGGGTTATTTA-T-T-AAA---TTAATATAAAAAAATAC
* * ***
41139862 ATA-ATTAATACATTTGATTTTTTTTTGCTAAAATAATATAAAAAATAAAATAAGAAAATAATAT
118 TTACA-TAATACATTTAAACATTTTTTGCTAAAATAATATAAAAAATAAAAT-AGAAAATAATAT
* *
41139926 ATTTTAAAAAATAATATACGAAAAAAATATGAATAAAGTGCTAAAATCAGGGATATTTATTGAAA
181 ATTTTAAAAAATAATATACGAAAAAAATATGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAA
*
41139991 AAATATAAAAAAATACTGAAATAATACATTTGAAACATTATGTAC
246 AAATAT-AAAAAATACTTAAATAATACATTTGAAACATTATGTAC
*
41140036 TAAAATAATATGAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATAC-AAAAAAAT
1 TAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAAAAT
*
41140100 ACGAAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAGTATAAAAAAACACTTACATAATATA
66 ACG-AAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATAT-AAAAAA-A--TAC----T-TA
*
41140165 CCTAATACATTTGAAACATTTTTTGCTAAAATAATATAAAAAATAAAATAGGAAAATAATATATT
121 CATAATACATTT-AAACATTTTTTGCTAAAATAATATAAAAAATAAAATA-GAAAATAATATATT
41140230 TTAAAAAATAATATACG-AAAAAATATGAATAAAGTGCTAAAATCAGGGTTATTTATT-AAAAAA
184 TTAAAAAATAATATACGAAAAAAATATGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAA
** * * *
41140293 TATTTAAAACACTTAAATAATATATTTAAAACATTATGTAC
249 TATAAAAAATACTTAAATAATACATTTGAAACATTATGTAC
* * * *
41140334 TAAAATAAGGGTTTTAA-AATTAAATAATACGAAAGTAATATA-TTTAAAAAA-AAGATACGAAA
1 TAAAATAA---TATAAAGAAAT-AA-AATACGAAAATAATATATTTTAAAAAATAAGATACGAAA
*
41140396 AAAATACGAAAAAGTGTCAAAATCAGTGTTATTTATTAAATTAATATAAAAAAATACTTACATAA
61 AAAATACGAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAATACTTACATAA
*
41140461 TACATTTAAAACATTTTTT-CTAAAATAATATAAAAAATAATATACGAAAATA
126 TACATTT-AAACATTTTTTGCTAAAATAATATAAAAAATAAAATA-GAAAATA
41140513 TTTTACTTAT
Statistics
Matches: 669, Mismatches: 64, Indels: 84
0.82 0.08 0.10
Matches are distributed among these distances:
277 12 0.02
278 33 0.05
282 7 0.01
283 17 0.03
284 8 0.01
285 1 0.00
286 1 0.00
287 3 0.00
290 38 0.06
291 45 0.07
292 19 0.03
293 1 0.00
294 4 0.01
295 3 0.00
296 6 0.01
297 28 0.04
298 55 0.08
299 15 0.02
300 99 0.15
301 90 0.13
302 16 0.02
303 78 0.12
304 90 0.13
ACGTcount: A:0.56, C:0.07, G:0.08, T:0.30
Consensus pattern (289 bp):
TAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACGAAAAAAAT
ACGAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAATACTTACATAATACAT
TTAAACATTTTTTGCTAAAATAATATAAAAAATAAAATAGAAAATAATATATTTTAAAAAATAAT
ATACGAAAAAAATATGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATAAAAAATAC
TTAAATAATACATTTGAAACATTATGTAC
Found at i:41142475 original size:72 final size:72
Alignment explanation
Indices: 41142382--41142522 Score: 219
Period size: 72 Copynumber: 2.0 Consensus size: 72
41142372 AGTCCGAGCG
* *
41142382 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGTAATGACTATTTCCCGG
1 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTCCCGG
41142447 GCTCGTC
66 GCTCGTC
* * * * *
41142454 ATCGCATTCACTTTCGGCTGATACTTCTTATCATCCGGATTTTGCGGGCAATGACAATTTCTCGG
1 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTCCCGG
41142519 GCTC
66 GCTC
41142523 ATCGGGGGGC
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.34
Consensus pattern (72 bp):
ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACAATTTCCCGG
GCTCGTC
Found at i:41145489 original size:25 final size:25
Alignment explanation
Indices: 41145461--41145539 Score: 65
Period size: 25 Copynumber: 3.3 Consensus size: 25
41145451 GTAATGACCG
41145461 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* *** ****
41145486 ATGTGAT-AAGGCCTAA-TG-GCCG
1 ATGTGATGAATGTGAAAGTGTATAT
41145508 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
41145533 ATGTGAT
1 ATGTGAT
41145540 AAGGCCTAAT
Statistics
Matches: 35, Mismatches: 16, Indels: 6
0.61 0.28 0.11
Matches are distributed among these distances:
22 7 0.20
23 7 0.20
24 7 0.20
25 14 0.40
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:41145511 original size:47 final size:47
Alignment explanation
Indices: 41145452--41145636 Score: 289
Period size: 47 Copynumber: 3.9 Consensus size: 47
41145442 TAGTATGGCG
*
41145452 TAATGACCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
41145499 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
* *
41145546 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
* * * * * *
41145593 GAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
41145637 TCCCGAAGGG
Statistics
Matches: 127, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 127 1.00
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
Found at i:41145811 original size:37 final size:37
Alignment explanation
Indices: 41145755--41145833 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
41145745 CCGAGCTCTA
* * *
41145755 AAGACCCGATGACTACGTGTGGGGATTTTGCCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGCCCGGGT
* *
41145792 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGCCCGGGT
41145829 AAGAC
1 AAGAC
41145834 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGCCCGGGT
Found at i:41150330 original size:15 final size:16
Alignment explanation
Indices: 41150311--41150369 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 16
41150301 TACCTTCTTT
41150311 TTTTCTTCTCCTTCT-
1 TTTTCTTCTCCTTCTA
*
41150326 TTTTCTTCCTTCTCTTCTC
1 TTTTCTT-C-TC-CTTCTA
* *
41150345 CTTTCTT-TCCTTTTA
1 TTTTCTTCTCCTTCTA
41150360 TTTTCTTCTC
1 TTTTCTTCTC
41150370 ATTGTTGCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
15 17 0.49
16 5 0.14
17 2 0.06
18 5 0.14
19 6 0.17
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTCTTCTCCTTCTA
Found at i:41150508 original size:27 final size:27
Alignment explanation
Indices: 41150451--41150548 Score: 160
Period size: 27 Copynumber: 3.6 Consensus size: 27
41150441 GACCCACACA
* **
41150451 ACTGGTGCCGTCTCTGTTTAGAGACAAC
1 ACTGGTGCCGCCTCTG-CCAGAGACAAC
41150479 ACTGGTGCCGCCTCTGCCAGAGACAAC
1 ACTGGTGCCGCCTCTGCCAGAGACAAC
41150506 ACTGGTGCCGCCTCTGCCAGAGACAAC
1 ACTGGTGCCGCCTCTGCCAGAGACAAC
41150533 ACTGGTGCCGCCTCTG
1 ACTGGTGCCGCCTCTG
41150549 GCACCCACAT
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
27 52 0.78
28 15 0.22
ACGTcount: A:0.19, C:0.34, G:0.27, T:0.20
Consensus pattern (27 bp):
ACTGGTGCCGCCTCTGCCAGAGACAAC
Found at i:41156117 original size:20 final size:19
Alignment explanation
Indices: 41156088--41156131 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
41156078 TCGTAAACGC
*
41156088 ATTTTTTATTTTTATTTTA
1 ATTTTTTATTTTAATTTTA
41156107 ATTTTTATATTTTAATTTTA
1 ATTTTT-TATTTTAATTTTA
41156127 ATTTT
1 ATTTT
41156132 GAGACATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (19 bp):
ATTTTTTATTTTAATTTTA
Found at i:41156119 original size:14 final size:13
Alignment explanation
Indices: 41156096--41156125 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
41156086 GCATTTTTTA
41156096 TTTTTATTTTAAT
1 TTTTTATTTTAAT
41156109 TTTTATATTTTAAT
1 TTTT-TATTTTAAT
41156123 TTT
1 TTT
41156126 AATTTTGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTATTTTAAT
Found at i:41156353 original size:21 final size:20
Alignment explanation
Indices: 41156329--41156388 Score: 59
Period size: 23 Copynumber: 2.8 Consensus size: 20
41156319 AATAAAATCA
41156329 TAAAAATAAAATGTATATTTT
1 TAAAAATAAAAT-TATATTTT
*
41156350 TAAAAAAATTAAAAATCAT-TTTT
1 T--AAAAA-T-AAAATTATATTTT
41156373 TAAAAATAAAATTATA
1 TAAAAATAAAATTATA
41156389 ATTTATAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
19 7 0.22
20 1 0.03
21 6 0.19
23 10 0.31
24 3 0.09
25 5 0.16
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
TAAAAATAAAATTATATTTT
Found at i:41156392 original size:22 final size:22
Alignment explanation
Indices: 41156328--41156397 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 22
41156318 AAATAAAATC
41156328 ATAAAAATAAAATGTATATTTTT
1 ATAAAAATAAAAT-TATATTTTT
*
41156351 AAAAAAATTAAAA--ATCATTTTT
1 ATAAAAA-TAAAATTAT-ATTTTT
*
41156373 -TAAAAATAAAATTATA-ATTT
1 ATAAAAATAAAATTATATTTTT
41156393 ATAAA
1 ATAAA
41156398 TTATGAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
20 8 0.21
21 12 0.31
22 8 0.21
23 6 0.15
24 5 0.13
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (22 bp):
ATAAAAATAAAATTATATTTTT
Found at i:41163626 original size:27 final size:27
Alignment explanation
Indices: 41163573--41163626 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
41163563 ATGACATCAA
* *
41163573 AGATAGTCTGACGGGACGTTAAGCACG
1 AGATAGTCTGACGAGACGTTAAACACG
41163600 AGATAGTCTGACGAGAC-TCTAAACACG
1 AGATAGTCTGACGAGACGT-TAAACACG
41163627 TAAATTCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.19
Consensus pattern (27 bp):
AGATAGTCTGACGAGACGTTAAACACG
Found at i:41164967 original size:19 final size:18
Alignment explanation
Indices: 41164945--41164990 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
41164935 AATAATAACG
*
41164945 ATAATATTAAAAATAAGTA
1 ATAATAATAAAAAT-AGTA
*
41164964 ATAATAATGAAAATAGTA
1 ATAATAATAAAAATAGTA
*
41164982 AGAATAATA
1 ATAATAATA
41164991 TGGTATTAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (18 bp):
ATAATAATAAAAATAGTA
Found at i:41164978 original size:28 final size:28
Alignment explanation
Indices: 41164935--41164988 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
41164925 CATATATGTA
* *
41164935 AATAATAACGATAATATTAAAAATAAGT
1 AATAATAACGAAAATAGTAAAAATAAGT
* *
41164963 AATAATAATGAAAATAGTAAGAATAA
1 AATAATAACGAAAATAGTAAAAATAA
41164989 TATGGTATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.26
Consensus pattern (28 bp):
AATAATAACGAAAATAGTAAAAATAAGT
Found at i:41164987 original size:18 final size:19
Alignment explanation
Indices: 41164954--41164989 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
41164944 GATAATATTA
*
41164954 AAAATAAGTAATAATAATG
1 AAAATAAGTAAGAATAATG
41164973 AAAAT-AGTAAGAATAAT
1 AAAATAAGTAAGAATAAT
41164990 ATGGTATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (19 bp):
AAAATAAGTAAGAATAATG
Found at i:41167688 original size:90 final size:89
Alignment explanation
Indices: 41167535--41167826 Score: 364
Period size: 90 Copynumber: 3.3 Consensus size: 89
41167525 TCACTTCATT
* * ** *
41167535 TCTCGCAATATGAATTGACTCTTT-AAAAATAGACGTT--AAAACAGAAATTAAAAATAGCTCAG
1 TCTCGCAATATGAGTTGA-TTTTTGAAAAATAGAAATTGAAAAACAGAAATTAAAAATACCTCAG
*
41167597 CACGTGAGCCAAGGCTCAACTCACC
65 CACGTGAGCCGAGGCTCAACTCACC
* *
41167622 TCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAAACAGAAATTTAAAATACCTCAG
1 TCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTG-AAAAACAGAAATTAAAAATACCTCAG
*
41167687 CATGTGAGCCGAGGCTCAACTCACC
65 CACGTGAGCCGAGGCTCAACTCACC
* * *
41167712 TCTCGCAATATGAGTTGATTTTTTGAAAAGTAGAAATTGAAAAACAGAAATTGAAAATTCCTCAG
1 TCTCGCAATATGAGTTGA-TTTTTGAAAAATAGAAATTGAAAAACAGAAATTAAAAATACCTCAG
* *
41167777 --CGTG-CCCTGAGGCTCAACTCACT
65 CACGTGAGCC-GAGGCTCAACTCACC
*
41167800 TATCGCAATATGAGTTGA-TTTTGAAAA
1 TCTCGCAATATGAGTTGATTTTTGAAAA
41167827 CAGAAATAAA
Statistics
Matches: 182, Mismatches: 17, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
86 13 0.07
87 29 0.16
88 34 0.19
90 88 0.48
91 18 0.10
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.27
Consensus pattern (89 bp):
TCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAAAAACAGAAATTAAAAATACCTCAGC
ACGTGAGCCGAGGCTCAACTCACC
Found at i:41181830 original size:49 final size:49
Alignment explanation
Indices: 41181743--41181864 Score: 201
Period size: 49 Copynumber: 2.5 Consensus size: 49
41181733 AATAACACGC
*
41181743 CAAATAAATTTCAT-AAAAATAAATCTAATCAACCTAAAACACACATAA
1 CAAATAAATTTCATAAAAAATAAATCTAATAAACCTAAAACACACATAA
*
41181791 CAAATAAATTTCATAAAAAATAAATCTAATAAACTTAAAACACACATAA
1 CAAATAAATTTCATAAAAAATAAATCTAATAAACCTAAAACACACATAA
*
41181840 CAAATAAATTACATAAAAAAATAAA
1 CAAATAAATTTCAT-AAAAAATAAA
41181865 ACATTCTTTG
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
48 14 0.20
49 45 0.65
50 10 0.14
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (49 bp):
CAAATAAATTTCATAAAAAATAAATCTAATAAACCTAAAACACACATAA
Found at i:41182253 original size:50 final size:51
Alignment explanation
Indices: 41182162--41182259 Score: 146
Period size: 51 Copynumber: 1.9 Consensus size: 51
41182152 TATTTATTTA
* *
41182162 TTTTTCCTTCTTTTTCCCATTCCCATTCCCTCTCTCTATTCTCCTTCTCAT
1 TTTTTCCTTCTTTTTCCCATTCCCATTCCCGCCCTCTATTCTCCTTCTCAT
*
41182213 TTTTTCTTTCTTTTTCCC-TTCCC-TTCCCGCCCTCTCATTCTCCTTCT
1 TTTTTCCTTCTTTTTCCCATTCCCATTCCCGCCCTCT-ATTCTCCTTCT
41182260 TCTCCTTCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
49 10 0.23
50 16 0.37
51 17 0.40
ACGTcount: A:0.05, C:0.41, G:0.01, T:0.53
Consensus pattern (51 bp):
TTTTTCCTTCTTTTTCCCATTCCCATTCCCGCCCTCTATTCTCCTTCTCAT
Found at i:41182262 original size:9 final size:9
Alignment explanation
Indices: 41182250--41182274 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
41182240 CGCCCTCTCA
41182250 TTCTCCTTC
1 TTCTCCTTC
41182259 TTCTCCTTC
1 TTCTCCTTC
41182268 TTCTCCT
1 TTCTCCT
41182275 AAAAATAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (9 bp):
TTCTCCTTC
Found at i:41184712 original size:16 final size:16
Alignment explanation
Indices: 41184691--41184722 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41184681 GTCTTAATTC
41184691 TTAAAAAAATTTAAAA
1 TTAAAAAAATTTAAAA
*
41184707 TTAAAAATATTTAAAA
1 TTAAAAAAATTTAAAA
41184723 GTTCATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TTAAAAAAATTTAAAA
Found at i:41184827 original size:20 final size:20
Alignment explanation
Indices: 41184804--41184842 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
41184794 TTATTTAAAT
41184804 AATAATTTTATAAATAAAAA
1 AATAATTTTATAAATAAAAA
*
41184824 AATATTTTTATAAATAAAA
1 AATAATTTTATAAATAAAA
41184843 TAATTTAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATTTTATAAATAAAAA
Found at i:41185462 original size:19 final size:20
Alignment explanation
Indices: 41185422--41185470 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
41185412 ATAATTTTGC
41185422 ATGTATTTTT-TTAAATATT
1 ATGTATTTTTATTAAATATT
41185441 ATGTATTTTTATTGAAA-A-T
1 ATGTATTTTTATT-AAATATT
*
41185460 ATGAATTTTTA
1 ATGTATTTTTA
41185471 ATTTTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 21 0.78
20 3 0.11
21 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (20 bp):
ATGTATTTTTATTAAATATT
Found at i:41186278 original size:11 final size:11
Alignment explanation
Indices: 41186249--41186285 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
41186239 TTAATATTTT
*
41186249 ATTATAAAATA
1 ATTATTAAATA
41186260 A-T-TTAAATA
1 ATTATTAAATA
41186269 ATTATTAAATA
1 ATTATTAAATA
41186280 ATTATT
1 ATTATT
41186286 TTCTCCAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 7 0.30
10 2 0.09
11 14 0.61
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATTATTAAATA
Found at i:41186467 original size:10 final size:10
Alignment explanation
Indices: 41186448--41186484 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
41186438 AGAAATTATA
41186448 AAATTA-TTT
1 AAATTATTTT
41186457 AAATTATTTT
1 AAATTATTTT
41186467 AAATATATTTT
1 AAAT-TATTTT
41186478 AAATTAT
1 AAATTAT
41186485 ATTATTGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 6 0.23
10 10 0.38
11 10 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
AAATTATTTT
Found at i:41186487 original size:12 final size:11
Alignment explanation
Indices: 41186454--41186487 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
41186444 TATAAAATTA
41186454 TTTAAAT-TAT
1 TTTAAATATAT
41186464 TTTAAATATAT
1 TTTAAATATAT
41186475 TTTAAATTATAT
1 TTTAAA-TATAT
41186487 T
1 T
41186488 ATTGTGATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 7 0.32
11 9 0.41
12 6 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTAAATATAT
Found at i:41186694 original size:25 final size:25
Alignment explanation
Indices: 41186666--41186716 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
41186656 AAAATATTAA
*
41186666 AGTAAATCTTTTAAAATAATTAGAT
1 AGTAAATCTTTTAAAAGAATTAGAT
41186691 AGTAAATCTTTTAAAAGAATTAGAT
1 AGTAAATCTTTTAAAAGAATTAGAT
41186716 A
1 A
41186717 AAGATTCCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (25 bp):
AGTAAATCTTTTAAAAGAATTAGAT
Found at i:41188804 original size:20 final size:20
Alignment explanation
Indices: 41188775--41188873 Score: 99
Period size: 20 Copynumber: 4.8 Consensus size: 20
41188765 CGTGGAATAG
* *
41188775 GCACACGCCCATGTGAGGAA
1 GCACAAGCCCGTGTGAGGAA
*
41188795 GCACAAGCCCGTGTAAGGAA
1 GCACAAGCCCGTGTGAGGAA
*
41188815 GCACAAGCCCGTGTGAAAGGAG
1 GCACAAGCCCGTGTG--AGGAA
* * *
41188837 GCACATGGCCGTGTGAGGAT
1 GCACAAGCCCGTGTGAGGAA
*
41188857 GACACACGCCCGTGTGA
1 G-CACAAGCCCGTGTGA
41188874 CCGAGTGACA
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
20 36 0.55
21 13 0.20
22 17 0.26
ACGTcount: A:0.28, C:0.26, G:0.33, T:0.12
Consensus pattern (20 bp):
GCACAAGCCCGTGTGAGGAA
Found at i:41195750 original size:40 final size:40
Alignment explanation
Indices: 41195695--41195884 Score: 296
Period size: 40 Copynumber: 4.8 Consensus size: 40
41195685 CGGATGATAA
41195695 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
* *
41195735 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
41195775 CC-GGCTAAG-CCCGAAGGCATTTGTGCGAGTTACCAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
* *
41195813 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCA-AAT
* *
41195853 CCGGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
41195885 AGTTATATCC
Statistics
Matches: 138, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
38 29 0.21
39 14 0.10
40 93 0.67
41 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.23
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
Found at i:41195835 original size:78 final size:80
Alignment explanation
Indices: 41195691--41195884 Score: 322
Period size: 78 Copynumber: 2.5 Consensus size: 80
41195681 TATTCGGATG
41195691 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAATCCGGGCTAAGTCCCGAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAATCCGGGCTAAGTCCCGAAGGCA
*
41195756 TTTGTGCGAGTTACT
66 TTGGTGCGAGTTACT
*
41195771 A-ATTCC-GGCTAAG-CCCGAAGGCATTTGTGCGAGTTACCAAATCCGGGCTAAGTCCCGAAGGC
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAATCCGGGCTAAGTCCCGAAGGC
41195833 ATTGGTGCGAGTTACT
65 ATTGGTGCGAGTTACT
* *
41195849 ATAACCGGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
41195885 AGTTATATCC
Statistics
Matches: 105, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
78 67 0.64
79 15 0.14
80 23 0.22
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (80 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAATCCGGGCTAAGTCCCGAAGGCA
TTGGTGCGAGTTACT
Found at i:41197545 original size:19 final size:20
Alignment explanation
Indices: 41197501--41197548 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
41197491 ACAAATTATT
*
41197501 TATAAATTTTAATTTAAATA
1 TATAAATTATAATTTAAATA
*
41197521 TATAAATTATATTTTAAATA
1 TATAAATTATAATTTAAATA
41197541 T-TAAATTA
1 TATAAATTA
41197549 CATTACAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TATAAATTATAATTTAAATA
Found at i:41197646 original size:17 final size:18
Alignment explanation
Indices: 41197621--41197658 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
41197611 AAGAAATAAA
*
41197621 ATAATTATA-CATTTAAT
1 ATAAATATAGCATTTAAT
41197638 ATAAATATATGCATTTAAT
1 ATAAATATA-GCATTTAAT
41197657 AT
1 AT
41197659 TTATAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
19 10 0.56
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (18 bp):
ATAAATATAGCATTTAAT
Found at i:41200778 original size:24 final size:25
Alignment explanation
Indices: 41200751--41200811 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
41200741 TTTAGTTATA
*
41200751 AATATTTATTATTATTT-TGATAAT
1 AATATTTATTATAATTTGTGATAAT
*
41200775 AATATATTAATATAATTTGTGATAAT
1 AATAT-TTATTATAATTTGTGATAAT
*
41200801 AAAATTATATT
1 AATATT-TATT
41200812 TTTAATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 5 0.17
25 11 0.37
26 14 0.47
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (25 bp):
AATATTTATTATAATTTGTGATAAT
Found at i:41200810 original size:23 final size:25
Alignment explanation
Indices: 41200751--41200802 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
41200741 TTTAGTTATA
* *
41200751 AATAT-TTATTATTATTTTGATAAT
1 AATATATTAATATAATTTTGATAAT
41200775 AATATATTAATATAATTTGTGATAAT
1 AATATATTAATATAATTT-TGATAAT
41200801 AA
1 AA
41200803 AATTATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.21
25 10 0.42
26 9 0.38
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (25 bp):
AATATATTAATATAATTTTGATAAT
Found at i:41200827 original size:21 final size:22
Alignment explanation
Indices: 41200774--41200827 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 22
41200764 ATTTTGATAA
41200774 TAATATAT-TAA-TATAATTTG
1 TAATATATATAATTATAATTTG
* * *
41200794 TGATA-ATAAAATTAT-ATTTT
1 TAATATATATAATTATAATTTG
41200814 TAATATATATAATT
1 TAATATATATAATT
41200828 TATGTAACTT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
19 2 0.08
20 14 0.54
21 10 0.38
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (22 bp):
TAATATATATAATTATAATTTG
Found at i:41205314 original size:25 final size:27
Alignment explanation
Indices: 41205277--41205329 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
41205267 TCAAACATGC
41205277 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
41205303 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
41205329 A
1 A
41205330 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:41216888 original size:28 final size:28
Alignment explanation
Indices: 41216825--41216947 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
41216815 ATATTAAGTC
*
41216825 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
41216852 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
41216880 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
41216908 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
41216937 CGCACACTTAG
1 CGCACACTTAG
41216948 CGCCAATCTC
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.25
28 49 0.56
29 16 0.18
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:41225092 original size:28 final size:27
Alignment explanation
Indices: 41225029--41225126 Score: 151
Period size: 28 Copynumber: 3.6 Consensus size: 27
41225019 ATATTAAGTC
*
41225029 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
41225056 CGCACACTTAGTGCTATATAATCGAACT
1 CGCACACTTAGTGCTATATAATC-AACT
* *
41225084 CCCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
41225112 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41225127 GTACAATTTA
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
27 22 0.34
28 43 0.66
ACGTcount: A:0.32, C:0.30, G:0.12, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:41240431 original size:24 final size:22
Alignment explanation
Indices: 41240377--41240433 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
41240367 TTATCTCGAA
41240377 AGAGCTTACTGTTCAGCTCAAT
1 AGAGCTTACTGTTCAGCTCAAT
* *
41240399 AGAGTTTACTGTTTTTAGCTCAA-
1 AGAGCTTACTG--TTCAGCTCAAT
41240422 AGGAGCTTACTG
1 A-GAGCTTACTG
41240434 ACCATGACTC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 10 0.34
23 1 0.03
24 18 0.62
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (22 bp):
AGAGCTTACTGTTCAGCTCAAT
Found at i:41246349 original size:47 final size:47
Alignment explanation
Indices: 41246297--41246642 Score: 491
Period size: 47 Copynumber: 7.3 Consensus size: 47
41246287 TGCACAAGTA
* * *
41246297 TATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGAA-AGTA
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG
41246344 TATATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
1 TATATAT--GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
* *
41246393 TGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
* *
41246440 TGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
* **
41246487 TGTACGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
* *
41246534 CATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG
* *
41246581 TATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGGAA-GTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGT-GAACATG
*
41246628 TATAAATGTGATAAG
1 TATATATGTGATAAG
41246643 TCCCGAAGGG
Statistics
Matches: 278, Mismatches: 16, Indels: 10
0.91 0.05 0.03
Matches are distributed among these distances:
46 1 0.00
47 233 0.84
48 3 0.01
49 40 0.14
50 1 0.00
ACGTcount: A:0.32, C:0.10, G:0.31, T:0.27
Consensus pattern (47 bp):
TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATG
Found at i:41246520 original size:22 final size:22
Alignment explanation
Indices: 41246493--41246614 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
41246483 CATGTGTACG
41246493 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
41246515 TGTGATGAATG-TGAACAT-GCATATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
*
41246540 TGAGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * ***
41246562 TGTGATGAATG-TGAAAGTGTATATA
1 TGTGAT-AAGGCCG-AA-TGGCCA-A
41246587 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
41246609 TGTGAT
1 TGTGAT
41246615 GGATGTGGAA
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 21 0.30
23 17 0.24
24 17 0.24
25 15 0.21
ACGTcount: A:0.34, C:0.11, G:0.30, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:41250718 original size:79 final size:81
Alignment explanation
Indices: 41250582--41250766 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
41250572 TTGAATGATG
*
41250582 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
41250646 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
41250661 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
41250723 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
41250741 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
41250767 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:41250780 original size:40 final size:40
Alignment explanation
Indices: 41250583--41250766 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
41250573 TGAATGATGT
* * * *
41250583 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
41250623 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
41250663 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
41250701 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
41250742 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
41250767 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:41250788 original size:79 final size:79
Alignment explanation
Indices: 41250635--41250799 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
41250625 GGACTAAGAT
* **
41250635 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
41250700 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
41250714 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
41250777 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
41250793 CCGAAGG
1 CCGAAGG
41250800 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:41255574 original size:17 final size:17
Alignment explanation
Indices: 41255552--41255586 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
41255542 AAACAATCAC
41255552 CCTTCAAG-CTCGTAATT
1 CCTTCAAGCCT-GTAATT
41255569 CCTTCAAGCCTGTAATT
1 CCTTCAAGCCTGTAATT
41255586 C
1 C
41255587 GAATAACACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.23, C:0.31, G:0.11, T:0.34
Consensus pattern (17 bp):
CCTTCAAGCCTGTAATT
Found at i:41261705 original size:68 final size:67
Alignment explanation
Indices: 41261598--41261759 Score: 211
Period size: 68 Copynumber: 2.4 Consensus size: 67
41261588 CTCATCATGT
* *
41261598 CTCATGTTTAATGTCTTGGCAGACTCTACTGGTCTCCATAG-TCGAGTTATGGTCTTACACCTGT
1 CTCATGTTTAATGTCTTGGCGGACT-TACTGGTCTCCATAGCT-GAGCTATGGTCTTACACCTGT
41261662 AATC
64 AATC
* * *
41261666 CTCATGTCTAATGTCCTGGCGGACTTAATTGGT-TGCCATAGCTGAGCTATGGTCTTACACCTGT
1 CTCATGTTTAATGTCTTGGCGGACTT-ACTGGTCT-CCATAGCTGAGCTATGGTCTTACACCTGT
41261730 AATC
64 AATC
* *
41261734 CCCATGTTTAATGTCTTGGCGAACTT
1 CTCATGTTTAATGTCTTGGCGGACTT
41261760 TCACGTGTTT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
67 2 0.02
68 79 0.96
69 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (67 bp):
CTCATGTTTAATGTCTTGGCGGACTTACTGGTCTCCATAGCTGAGCTATGGTCTTACACCTGTAA
TC
Found at i:41264911 original size:40 final size:40
Alignment explanation
Indices: 41264679--41264904 Score: 289
Period size: 40 Copynumber: 5.7 Consensus size: 40
41264669 TTGAATGATG
* * * *
41264679 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAGGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGA-GTTACTAAA
* *
41264719 TCCGGACTAAGAT-CCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
41264759 TCCAGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
41264799 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
41264839 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
41264880 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
41264905 AACGAGTAGC
Statistics
Matches: 169, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
39 1 0.01
40 158 0.93
41 10 0.06
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:41264911 original size:120 final size:120
Alignment explanation
Indices: 41264679--41264937 Score: 287
Period size: 120 Copynumber: 2.2 Consensus size: 120
41264669 TTGAATGATG
* * *
41264679 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAGGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
**
41264744 GTACGAGTTACTAAATCCAGACTAAGATCCGAAGGCATTTGTGCGAGTTA-CTAAA
66 GTACGAGTTACTAAATCCAGACTAAGATCCGAAGGCATTTGAACGAG-TAGCTAAA
* * **
41264799 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-GTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCGAGGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * *
41264862 TTGTGCGAGTTACTATAA-CCGGGCTATG-TCCCGAAGGCATTTGAACGAGTAGCTATA
64 TTGTACGAGTTACTA-AATCCAGACTAAGAT-CCGAAGGCATTTGAACGAGTAGCTAAA
* *
41264919 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
41264938 TATGTGATTT
Statistics
Matches: 118, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
119 18 0.15
120 90 0.76
121 10 0.08
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (120 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTACGAGTTACTAAATCCAGACTAAGATCCGAAGGCATTTGAACGAGTAGCTAAA
Found at i:41272809 original size:79 final size:81
Alignment explanation
Indices: 41272673--41272857 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
41272663 TTGAATGATG
*
41272673 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
41272737 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
41272752 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
41272814 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
41272832 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
41272858 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:41272871 original size:40 final size:40
Alignment explanation
Indices: 41272674--41272857 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
41272664 TGAATGATGT
* * * *
41272674 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
41272714 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
41272754 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
41272792 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
41272833 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
41272858 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:41272879 original size:79 final size:79
Alignment explanation
Indices: 41272726--41272880 Score: 208
Period size: 79 Copynumber: 2.0 Consensus size: 79
41272716 GGACTAAGAT
* **
41272726 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
41272791 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* *
41272805 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
*
41272868 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
41272881 ATTCCAAAGG
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
78 2 0.03
79 40 0.60
80 25 0.37
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:41284229 original size:43 final size:43
Alignment explanation
Indices: 41284181--41284265 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
41284171 ATCGACATCG
* *
41284181 TATTTGATTTCGTGTAAAACC-CTGTCTGGGATAG-TGGCATTGA
1 TATTTGATTACATGTAAAACCAC-GTCTGGGAT-GTTGGCATTGA
*
41284224 TATTTGATTACATGTAAGACCACGTCTGGGATGTTGGCATTG
1 TATTTGATTACATGTAAAACCACGTCTGGGATGTTGGCATTG
41284266 TACAAGCTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 1 0.03
43 35 0.95
44 1 0.03
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (43 bp):
TATTTGATTACATGTAAAACCACGTCTGGGATGTTGGCATTGA
Found at i:41300929 original size:29 final size:29
Alignment explanation
Indices: 41300895--41300968 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
41300885 TAATCAGCCA
* *
41300895 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACC
*
41300924 CGCACACTTAGTGCCATGCATTTCAAGCC
1 CGCACACTTAGTGCCATGCATTTCAAACC
41300953 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
41300969 ATCTCACAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 3 0.07
29 38 0.93
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACC
Found at i:41312668 original size:29 final size:29
Alignment explanation
Indices: 41312634--41312705 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
41312624 TAATCAGCCA
* *
41312634 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACC
*
41312663 CGCACACTTAGTGCCATGCATTTCAAGCC
1 CGCACACTTAGTGCCATGCATTTCAAACC
41312692 CGCACACTTAGTGC
1 CGCACACTTAGTGC
41312706 AAATCTCACA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
28 3 0.08
29 36 0.92
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACC
Found at i:41319698 original size:49 final size:48
Alignment explanation
Indices: 41319590--41319764 Score: 191
Period size: 49 Copynumber: 3.7 Consensus size: 48
41319580 AGACGTAAGC
* * *
41319590 CAGTGTAAGA-CATATCTGGGACAT-GCATCGG-CT-GCAATATG-T-G
1 CAGTATAAGACCATGTCTGGGACATGGCATCGGCCTCG-AAGATGATAG
* *
41319633 TCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGAAGATGATAG
1 -CAGTATAAGACCATGTCTGGGACATGGCATCGGCCTCGAAGATGATAG
* **
41319682 CTAGTATAAGACCATGTCTGGGACATGGGATTAGCCTCGAAGATGATAG
1 C-AGTATAAGACCATGTCTGGGACATGGCATCGGCCTCGAAGATGATAG
* *
41319731 CAGTGTAAGACCATGTCTGAGACATGGCATCGGC
1 CAGTATAAGACCATGTCTGGGACATGGCATCGGC
41319765 ACCTTACCCA
Statistics
Matches: 112, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
44 10 0.09
45 13 0.12
46 7 0.06
47 7 0.06
48 31 0.28
49 44 0.39
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (48 bp):
CAGTATAAGACCATGTCTGGGACATGGCATCGGCCTCGAAGATGATAG
Found at i:41326348 original size:46 final size:48
Alignment explanation
Indices: 41326206--41326568 Score: 348
Period size: 49 Copynumber: 7.6 Consensus size: 48
41326196 TGTGAGCTAA
* * * *
41326206 TGTAAGA-CATGTCTGGGACAT-GCATCAGCCACAATATGAGAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGAGAGCCAG
* * * * * *
41326252 TGTAAGACCATGTCTGGGACGTGGCATCGGCATCAAGAGGAGTGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGAGAGCCAG
*
41326300 TGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGACGTA-AGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATG-AGAGCCAG
* * *** * *
41326346 TGTAAGA-CATGTCCGGGACAT-GCATCAGTAGCGAGAT--GTGTCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGAGAGCCAG
* * * * ** *
41326390 TGTAAGACCATGTCTGGGATATGGGATCGGCATGGTTATGTAAGAGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATG--AGAGCCAG
* *
41326440 TGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAAGATGATAGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCTCG-AGATGAGAGCCAG
* *
41326489 TGTAAGACCATGTCCGGGACATGGCATCGGCCTCGAAGATGATAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCTCG-AGATGAGAGCCAG
*
41326538 TATAAGACCATGTCTGGGACATGGCATCGGC
1 TGTAAGACCATGTCTGGGACATGGCATCGGC
41326569 ACCTTACCCA
Statistics
Matches: 261, Mismatches: 45, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
44 11 0.04
45 12 0.05
46 65 0.25
47 27 0.10
48 25 0.10
49 83 0.32
50 35 0.13
51 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (48 bp):
TGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGAGAGCCAG
Found at i:41333457 original size:49 final size:49
Alignment explanation
Indices: 41333345--41333462 Score: 164
Period size: 49 Copynumber: 2.4 Consensus size: 49
41333335 TAGTGTAAAG
* * * *
41333345 CCATGTCCGAGACATAGCATTGGCCTCAAAGATGATAGCCAGTGTAAGA
1 CCATGTCCGAGACATGGCATCGGCCTCAAAGATGATAGCCAATATAAGA
* *
41333394 CCATGTCCGAGACATGGCATCGGCCTCGAATATGATAGCCAATATAAGA
1 CCATGTCCGAGACATGGCATCGGCCTCAAAGATGATAGCCAATATAAGA
* *
41333443 CCATGTCTGGGACATGGCAT
1 CCATGTCCGAGACATGGCAT
41333463 GTTTGAGTCT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 61 1.00
ACGTcount: A:0.31, C:0.24, G:0.25, T:0.21
Consensus pattern (49 bp):
CCATGTCCGAGACATGGCATCGGCCTCAAAGATGATAGCCAATATAAGA
Found at i:41335848 original size:55 final size:54
Alignment explanation
Indices: 41335770--41335881 Score: 179
Period size: 55 Copynumber: 2.1 Consensus size: 54
41335760 TCGAGAAAGA
* *
41335770 AAAATTTTAGAGTACAAGGCCGGGTAGTATGGCTACAAAAGGGAGACATTCGAG
1 AAAATTTTAAAGTACAAGGCCGGGTAGTACGGCTACAAAAGGGAGACATTCGAG
* *
41335824 AAAATTTTCAAAGTACAAGGCCGGGTAGTACGGTTACAAAAGGGAGACCTTCGAG
1 AAAATTTT-AAAGTACAAGGCCGGGTAGTACGGCTACAAAAGGGAGACATTCGAG
41335879 AAA
1 AAA
41335882 TGGCAGTAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
54 8 0.15
55 45 0.85
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.20
Consensus pattern (54 bp):
AAAATTTTAAAGTACAAGGCCGGGTAGTACGGCTACAAAAGGGAGACATTCGAG
Found at i:41346616 original size:79 final size:81
Alignment explanation
Indices: 41346480--41346662 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
41346470 TTGAATGATG
* *
41346480 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
41346544 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
41346559 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
41346621 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
41346639 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
41346663 TGAACGAGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.65
80 30 0.34
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:41346678 original size:40 final size:40
Alignment explanation
Indices: 41346481--41346664 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
41346471 TGAATGATGT
* * * *
41346481 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
41346521 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
41346561 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
41346599 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
41346640 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
41346665 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 34 0.27
40 80 0.65
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:41346686 original size:79 final size:79
Alignment explanation
Indices: 41346533--41346697 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
41346523 GGACTAAGAT
* **
41346533 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
41346598 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
41346612 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
41346675 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
41346691 CCGAAGG
1 CCGAAGG
41346698 TATGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.65
80 24 0.32
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:41350042 original size:28 final size:25
Alignment explanation
Indices: 41349982--41350080 Score: 94
Period size: 25 Copynumber: 3.9 Consensus size: 25
41349972 CATCTCTTAT
* * *
41349982 GAGCTTACCGATACTCAGCTC-GTAT
1 GAGCTTACCGTTATTCAGCTCAG-AG
41350007 GAGCTTACCGTTATTCAGCTCGAAGAAG
1 GAGCTTACCGTTATTCAGCTC--AG-AG
* *
41350035 GAGCTTACCATTATTCAGCTCAGAT
1 GAGCTTACCGTTATTCAGCTCAGAG
*
41350060 GAGCTTACCGTT-TACAGCTCA
1 GAGCTTACCGTTATTCAGCTCA
41350081 TATGAGCATA
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
24 8 0.13
25 31 0.49
26 2 0.03
28 22 0.35
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28
Consensus pattern (25 bp):
GAGCTTACCGTTATTCAGCTCAGAG
Found at i:41353240 original size:16 final size:17
Alignment explanation
Indices: 41353219--41353251 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
41353209 TTACTTTAGC
41353219 CATTTT-ATTTTTATTG
1 CATTTTAATTTTTATTG
41353235 CATTTTAAATTTTTATT
1 CATTTT-AATTTTTATT
41353252 TTCTTTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.67
Consensus pattern (17 bp):
CATTTTAATTTTTATTG
Found at i:41359338 original size:27 final size:27
Alignment explanation
Indices: 41359308--41359485 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
41359298 ATATTGAGTC
* * * *
41359308 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
41359335 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41359362 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
41359390 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
41359417 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
41359444 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41359471 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41359486 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:41359447 original size:82 final size:81
Alignment explanation
Indices: 41359329--41359484 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41359319 TGCTATATAA
* *
41359329 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
41359394 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
41359411 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
41359475 CACTTAGTGC
65 CACTTAGTGC
41359485 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:41367425 original size:27 final size:27
Alignment explanation
Indices: 41367395--41367572 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
41367385 ATATTGAGTC
* * * *
41367395 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
41367422 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41367449 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
41367477 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
41367504 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
41367531 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41367558 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41367573 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:41367534 original size:82 final size:81
Alignment explanation
Indices: 41367416--41367571 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41367406 TGCTATATAA
* *
41367416 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
41367481 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
41367498 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
41367562 CACTTAGTGC
65 CACTTAGTGC
41367572 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:41369778 original size:25 final size:24
Alignment explanation
Indices: 41369743--41369790 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
41369733 CACTTTTGTC
41369743 TTTATTTATCTTC-TTTAACTACTT
1 TTTATTTATCTTCATTTAA-TACTT
41369767 TTTATTTTATCTTCATTTAATACT
1 TTTA-TTTATCTTCATTTAATACT
41369791 GTGTCATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.18
25 13 0.59
26 5 0.23
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTATTTATCTTCATTTAATACTT
Found at i:41369799 original size:26 final size:25
Alignment explanation
Indices: 41369747--41369800 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
41369737 TTTGTCTTTA
* *
41369747 TTTATCTTCTTTAACTACTTTTTAT
1 TTTATCTTCTTTAACTACTTGTCAT
41369772 TTTATCTTCATTTAA-TACTGTGTCAT
1 TTTATCTTC-TTTAACTACT-TGTCAT
41369798 TTT
1 TTT
41369801 TAGGTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.20, C:0.15, G:0.04, T:0.61
Consensus pattern (25 bp):
TTTATCTTCTTTAACTACTTGTCAT
Found at i:41403985 original size:44 final size:44
Alignment explanation
Indices: 41403937--41404211 Score: 191
Period size: 44 Copynumber: 6.2 Consensus size: 44
41403927 AGCCACCGAC
* * * *
41403937 CTTATCTCTCTGAAGTAGAAAGGGAGCAGGCTAAAGATTGTAGT
1 CTTATCTCTCTGAGGTAGCAAGGGAGCAGACTGAAGATTGTAGT
*
41403981 CTTATCT-TCTTGAGGTAGCAAGGGAGCAGAATGAAGATTGTAGAT
1 CTTATCTCTC-TGAGGTAGCAAGGGAGCAGACTGAAGATTGTAG-T
* * ** * * ** * *
41404026 CTTGTCTCCCTGAAATAG-TAGTGGAGCAGA-TCAAAGACCGCAAAT
1 CTTATCTCTCTGAGGTAGCAAG-GGAGCAGACT-GAAGATTG-TAGT
* * ** **** *
41404071 CTTATCT-TCCCGAGGTAGCAAGGGAGCAGATTTTAGCCACTAGC
1 CTTATCTCT-CTGAGGTAGCAAGGGAGCAGACTGAAGATTGTAGT
* *
41404115 CTTATCTCTCTGAGGTAGCAAGGGAGCAGGCTGAATATTGTAGT
1 CTTATCTCTCTGAGGTAGCAAGGGAGCAGACTGAAGATTGTAGT
* *
41404159 CTTATCT-TCCTGAGGTAGTAAAGGAGCAGACTGAAGATTGTAGAT
1 CTTATCTCT-CTGAGGTAGCAAGGGAGCAGACTGAAGATTGTAG-T
41404204 CTTATCTC
1 CTTATCTC
41404212 CCTAAGCAGT
Statistics
Matches: 174, Mismatches: 44, Indels: 24
0.72 0.18 0.10
Matches are distributed among these distances:
43 3 0.02
44 107 0.61
45 59 0.34
46 5 0.03
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (44 bp):
CTTATCTCTCTGAGGTAGCAAGGGAGCAGACTGAAGATTGTAGT
Found at i:41404097 original size:45 final size:45
Alignment explanation
Indices: 41403870--41404101 Score: 109
Period size: 44 Copynumber: 5.2 Consensus size: 45
41403860 AAATAGCAGT
* * *
41403870 GGAGCAGATCGAAGACGGCAAATCTTATCTTCCCGAGGTAGCAGG
1 GGAGCAGATCAAAGACCGCAAATCTTATCTTCCCGAGGTAGCAAG
*** * ** * * * *
41403915 GGAGCAGATTTTAG-CCACCGACCTTATC-TCTCTGAAGTAGAAAG
1 GGAGCAGATCAAAGACCGCAAATCTTATCTTC-CCGAGGTAGCAAG
* ** * * **
41403959 GGAGCAG-GCTAAAGATTG-TAGTCTTATCTTCTTGAGGTAGCAAG
1 GGAGCAGATC-AAAGACCGCAAATCTTATCTTCCCGAGGTAGCAAG
* ** * * * ** *
41404003 GGAGCAGAAT-GAAGATTGTAGATCTTGTC-TCCCTGAAATAG-TAG
1 GGAGCAG-ATCAAAGACCGCAAATCTTATCTTCCC-GAGGTAGCAAG
41404047 TGGAGCAGATCAAAGACCGCAAATCTTATCTTCCCGAGGTAGCAAG
1 -GGAGCAGATCAAAGACCGCAAATCTTATCTTCCCGAGGTAGCAAG
41404093 GGAGCAGAT
1 GGAGCAGAT
41404102 TTTAGCCACT
Statistics
Matches: 129, Mismatches: 46, Indels: 24
0.65 0.23 0.12
Matches are distributed among these distances:
43 2 0.02
44 63 0.49
45 58 0.45
46 6 0.05
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (45 bp):
GGAGCAGATCAAAGACCGCAAATCTTATCTTCCCGAGGTAGCAAG
Found at i:41404157 original size:178 final size:177
Alignment explanation
Indices: 41403843--41404305 Score: 676
Period size: 178 Copynumber: 2.6 Consensus size: 177
41403833 TCGGTGAATT
* *
41403843 TAGATTTTGTCTCCCTGAAATAGCAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCCGAGG
1 TAGATCTTGTCTCCCTGAAATAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCCGAGG
*
41403908 TAGCAGGGGAGCAGATTTTAGCCACCGACCTTATCTCTCTGAAGTAGAAAGGGAGCAGGCTAAAG
66 TAGCAGGGGAGCAGATTTTAGCCACAG-CCTTATCTCTCTGAAGTAGAAAGGGAGCAGGCTAAAG
* *
41403973 ATTGTAGTCTTATCTTCTTGAGGTAGCAAGGGAGCAGAATGAAGATTG
130 ATTGTAGTCTTATCTTCCTGAGGTAGCAAAGGAGCAGAATGAAGATTG
* *
41404021 TAGATCTTGTCTCCCTGAAATAGTAGTGGAGCAGATCAAAGACCGCAAATCTTATCTTCCCGAGG
1 TAGATCTTGTCTCCCTGAAATAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCCGAGG
* * * * *
41404086 TAGCAAGGGAGCAGATTTTAGCCACTAGCCTTATCTCTCTGAGGTAGCAAGGGAGCAGGCTGAAT
66 TAGCAGGGGAGCAGATTTTAGCCAC-AGCCTTATCTCTCTGAAGTAGAAAGGGAGCAGGCTAAAG
* *
41404151 ATTGTAGTCTTATCTTCCTGAGGTAGTAAAGGAGCAGACTGAAGATTG
130 ATTGTAGTCTTATCTTCCTGAGGTAGCAAAGGAGCAGAATGAAGATTG
* ** * * *
41404199 TAGATCTTATCTCCCT-AAGCAGTAGTGGAGCAGATCGAAGATGGCAAATCTTATCTTCCCAAGC
1 TAGATCTTGTCTCCCTGAAATAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCCGAGG
* * * *
41404263 TAGCAGGGGAGTAGAGTTTAGCCTCCAGCCTTATCTCCCTGAA
66 TAGCAGGGGAGCAGATTTTAGCC-ACAGCCTTATCTCTCTGAA
41404306 ATTGCAGTGG
Statistics
Matches: 255, Mismatches: 28, Indels: 5
0.89 0.10 0.02
Matches are distributed among these distances:
177 76 0.30
178 178 0.70
179 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (177 bp):
TAGATCTTGTCTCCCTGAAATAGTAGTGGAGCAGATCGAAGACGGCAAATCTTATCTTCCCGAGG
TAGCAGGGGAGCAGATTTTAGCCACAGCCTTATCTCTCTGAAGTAGAAAGGGAGCAGGCTAAAGA
TTGTAGTCTTATCTTCCTGAGGTAGCAAAGGAGCAGAATGAAGATTG
Found at i:41404229 original size:44 final size:44
Alignment explanation
Indices: 41404137--41404262 Score: 114
Period size: 44 Copynumber: 2.9 Consensus size: 44
41404127 AGGTAGCAAG
* * * * *
41404137 GGAGCAGGCTGAATATTGTAG-TCTTATCTTCCTGAGGTAGTAAA
1 GGAGCAGACTGAAGATTGTAGATCTTATCTCCCT-AAGCAGTAAA
**
41404181 GGAGCAGACTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGT
1 GGAGCAGACTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAAA
* * *
41404225 GGAGCAGA-TCGAAGATGGCAAATCTTATCTTCCC-AAGC
1 GGAGCAGACT-GAAGATTGTAGATCTTATC-TCCCTAAGC
41404263 TAGCAGGGGA
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
43 1 0.01
44 53 0.77
45 15 0.22
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (44 bp):
GGAGCAGACTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAAA
Found at i:41415265 original size:27 final size:26
Alignment explanation
Indices: 41415234--41415411 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 26
41415224 TAAATTGTAC
41415234 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
41415261 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
41415287 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
41415315 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA--TTGACTATGT
* *
41415343 GGCACTAAGTGTGCGATTTGATTATGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
41415370 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
41415397 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
41415412 GACTCGATAT
Statistics
Matches: 131, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.01
27 104 0.79
28 26 0.20
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:41415350 original size:82 final size:81
Alignment explanation
Indices: 41415235--41415390 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41415225 AAATTGTACA
*
41415235 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTCGACTATGTGGCACTAAGTGTGCGAAATGAATATGTA-GCACTAAGTG
41415299 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
41415316 GCACTAAGTGTGCGAGTTTGACTATGTGGCACTAAGTGTGCGATTTGATTATGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTCGACTATGTGGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTG
*
41415381 TGCGAGTTGA
65 TGCGAATTGA
41415391 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCGACTATGTGGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:41415402 original size:82 final size:81
Alignment explanation
Indices: 41415231--41415411 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
41415221 GATTAAATTG
*
41415231 TACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTCGACTATGTGGCACTAAGTGTGCGAAATGAATATGATGCACTAA
41415296 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
41415312 TGCGGCACTAAGTGTGCGAGTTTGACTATGTGGCACTAAGTGTGCGATTTGATTATG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTCGACTATGTGGCACTAAGTGTGCGAAATGAATATGAT-GCACT
* **
41415376 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
41415394 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
41415412 GACTCGATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTCGACTATGTGGCACTAAGTGTGCGAAATGAATATGATGCACTAA
GTGTGCGAATTGACCA
Done.