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 58 of 295
Found at i:17021996 original size:57 final size:57
Alignment explanation
Indices: 17021876--17022026 Score: 259
Period size: 57 Copynumber: 2.6 Consensus size: 57
17021866 CGATTGAATG
17021876 TTAAATTTATTACTAAAATACATTACTTACTAAAAATAAATTACTTACTAAAATTTGT
1 TTAAATTTATTACTAAAATACATTACTTACT-AAAATAAATTACTTACTAAAATTTGT
*
17021934 TTAAATTTATTACTAAAATACATTACTTACTAAAATACATTACTTAC-ATAAATTTGT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTA-AAATTTGT
*
17021991 TTAAATTTATTTCTAAAATACATTACTTACTAAAAT
1 TTAAATTTATTACTAAAATACATTACTTACTAAAAT
17022027 TTGTTTAAAT
Statistics
Matches: 90, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
56 1 0.01
57 58 0.64
58 31 0.34
ACGTcount: A:0.45, C:0.11, G:0.01, T:0.42
Consensus pattern (57 bp):
TTAAATTTATTACTAAAATACATTACTTACTAAAATAAATTACTTACTAAAATTTGT
Found at i:17022025 original size:97 final size:100
Alignment explanation
Indices: 17021897--17022167 Score: 460
Period size: 97 Copynumber: 2.7 Consensus size: 100
17021887 ACTAAAATAC
*
17021897 ATTACTTACTAAAAATAAATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTT
1 ATTA-TTACT-AAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTT
17021962 ACTAAAATACATTACTTAC-ATAAATTTGTTTAAATTT
64 ACTAAAATACATTACTTACTA-AAATTTGTTTAAATTT
17021999 A-T-TT-CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTAC
1 ATTATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTAC
17022061 TAAAATACATTACTTACTAAAATTTGTTTAAATTT
66 TAAAATACATTACTTACTAAAATTTGTTTAAATTT
*
17022096 ATTAATTACTTAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTA
1 ATT-ATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTA
17022161 CTAAAAT
65 CTAAAAT
17022168 TTGTTTAAAT
Statistics
Matches: 162, Mismatches: 2, Indels: 11
0.93 0.01 0.06
Matches are distributed among these distances:
97 89 0.55
98 4 0.02
99 2 0.01
100 2 0.01
101 64 0.40
102 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.44
Consensus pattern (100 bp):
ATTATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTACTAAAATACATTACTTAC
TAAAATACATTACTTACTAAAATTTGTTTAAATTT
Found at i:17022064 original size:57 final size:60
Alignment explanation
Indices: 17022003--17022127 Score: 211
Period size: 57 Copynumber: 2.1 Consensus size: 60
17021993 AAATTTATTT
17022003 CTAAAATACATTACTTACTAAAATTTGTTTAAA-T-TT-ATTACTAAAATACATTACTTA
1 CTAAAATACATTACTTACTAAAATTTGTTTAAATTATTAATTACTAAAATACATTACTTA
*
17022060 CTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTAATTACTTAAATACATTACTTA
1 CTAAAATACATTACTTACTAAAATTTGTTTAAA-TTATTAATTACTAAAATACATTACTTA
17022121 CTAAAAT
1 CTAAAAT
17022128 TTGTTTAAAT
Statistics
Matches: 63, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
57 33 0.52
59 1 0.02
60 2 0.03
61 27 0.43
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (60 bp):
CTAAAATACATTACTTACTAAAATTTGTTTAAATTATTAATTACTAAAATACATTACTTA
Found at i:17022111 original size:44 final size:44
Alignment explanation
Indices: 17022052--17022183 Score: 218
Period size: 44 Copynumber: 3.1 Consensus size: 44
17022042 ACTAAAATAC
*
17022052 ATTACTTACTAAAATACATTACTTACTAAAATTTGTTTAAATTT
1 ATTAATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTT
*
17022096 ATTAATTACTTAAATACATTACTTACTAAAATTTGTTTAAA--T
1 ATTAATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTT
17022138 -TT-ATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTT
1 ATTAATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTT
17022180 ATTA
1 ATTA
17022184 CTTAAATATG
Statistics
Matches: 81, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
40 36 0.44
41 2 0.02
42 2 0.02
43 2 0.02
44 39 0.48
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (44 bp):
ATTAATTACTAAAATACATTACTTACTAAAATTTGTTTAAATTT
Found at i:17022144 original size:40 final size:40
Alignment explanation
Indices: 17022057--17022200 Score: 216
Period size: 40 Copynumber: 3.5 Consensus size: 40
17022047 AATACATTAC
17022057 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTATTAA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAA--T-TT-A
*
17022101 TTACTTAAATACATTACTTACTAAAATTTGTTTAAATTTA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
17022141 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
1 TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
* **
17022181 TTACTTAAATATGTTACTTA
1 TTACTAAAATACATTACTTA
17022201 AATTTATTAC
Statistics
Matches: 95, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
40 57 0.60
41 2 0.02
42 1 0.01
44 35 0.37
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.47
Consensus pattern (40 bp):
TTACTAAAATACATTACTTACTAAAATTTGTTTAAATTTA
Found at i:17022190 original size:13 final size:13
Alignment explanation
Indices: 17022172--17022242 Score: 106
Period size: 13 Copynumber: 5.5 Consensus size: 13
17022162 TAAAATTTGT
17022172 TTAAATTTATTAC
1 TTAAATTTATTAC
* *
17022185 TTAAATATGTTAC
1 TTAAATTTATTAC
17022198 TTAAATTTATTAC
1 TTAAATTTATTAC
* *
17022211 TTAAATATGTTAC
1 TTAAATTTATTAC
17022224 TTAAATTTATTAC
1 TTAAATTTATTAC
17022237 TTAAAT
1 TTAAAT
17022243 AATTATAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 50 1.00
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (13 bp):
TTAAATTTATTAC
Found at i:17022208 original size:26 final size:26
Alignment explanation
Indices: 17022172--17022243 Score: 144
Period size: 26 Copynumber: 2.8 Consensus size: 26
17022162 TAAAATTTGT
17022172 TTAAATTTATTACTTAAATATGTTAC
1 TTAAATTTATTACTTAAATATGTTAC
17022198 TTAAATTTATTACTTAAATATGTTAC
1 TTAAATTTATTACTTAAATATGTTAC
17022224 TTAAATTTATTACTTAAATA
1 TTAAATTTATTACTTAAATA
17022244 ATTATAAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (26 bp):
TTAAATTTATTACTTAAATATGTTAC
Found at i:17025805 original size:21 final size:21
Alignment explanation
Indices: 17025779--17025849 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
17025769 CTACAACTTA
* *
17025779 AAGCAGAGGCGGAAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
17025800 AAGCAGCGACTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* * *
17025821 AAGCGGAGGCTGCAGCAAGAG
1 AAGCAGAGGCTGCAGCGAGGG
17025842 AAGCAGAG
1 AAGCAGAG
17025850 CAGAGCAAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.34, C:0.18, G:0.45, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:17026326 original size:42 final size:41
Alignment explanation
Indices: 17026175--17026587 Score: 461
Period size: 42 Copynumber: 9.9 Consensus size: 41
17026165 TTTTGTATAA
* * * ***
17026175 AAGCGCCACTAAAGAACATGTTCTTTTGCGGCGTTTGTAAA
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTCTT
** * ******
17026216 AAATGCCACTAAAGAACATGTTCTTTAGCGGCGATTAGAAAAA
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCG-TT-TTTCTT
* *
17026259 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTCCTT
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT-CTT
*
17026301 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTTCCT
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTCTT
*
17026341 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTCCT
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTCTT
* * *
17026382 AAGCGCCGCTAAAGAACATGGTCTTTAGTGGCATTTTT-TT
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTCTT
* *
17026422 ACAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTCT
1 --AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTCT-T
* *
17026466 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTCT-T
* * *
17026508 AAGCGCCACTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTCT-T
* *
17026550 AAGCGCCGCTAAAGAACATGGTCTTTAACGGCGTTTTT
1 AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT
17026588 GTTTGTAAAC
Statistics
Matches: 332, Mismatches: 32, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
40 36 0.11
41 76 0.23
42 185 0.56
43 34 0.10
44 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (41 bp):
AAGCGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTCTT
Found at i:17027192 original size:14 final size:14
Alignment explanation
Indices: 17027150--17027193 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
17027140 TCCATCATTT
17027150 AAAATATTACTAAA
1 AAAATATTACTAAA
* *
17027164 AAGAT-TTGACAAAA
1 AAAATATT-ACTAAA
17027178 AAAATATTACTAAA
1 AAAATATTACTAAA
17027192 AA
1 AA
17027194 GAATTTTCAG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
13 2 0.08
14 20 0.83
15 2 0.08
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.25
Consensus pattern (14 bp):
AAAATATTACTAAA
Found at i:17027449 original size:16 final size:17
Alignment explanation
Indices: 17027430--17027462 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17027420 AAATAGATTT
17027430 TTAATT-AAATTTTTAA
1 TTAATTAAAATTTTTAA
17027446 TTAATTAAAATTTTTAA
1 TTAATTAAAATTTTTAA
17027463 ACCTAAACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTAATTAAAATTTTTAA
Found at i:17029083 original size:21 final size:19
Alignment explanation
Indices: 17029058--17029108 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
17029048 ATTTTAAAAT
17029058 ATTTATAAAAAAATCTTGAAA
1 ATTTATAAAAAAAT-TT-AAA
*
17029079 ATTTATCAAAAATATTTAAA
1 ATTTAT-AAAAAAATTTAAA
*
17029099 AATTATAAAA
1 ATTTATAAAA
17029109 CAAAACTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 4 0.15
20 8 0.30
21 8 0.30
22 7 0.26
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (19 bp):
ATTTATAAAAAAATTTAAA
Found at i:17029566 original size:23 final size:23
Alignment explanation
Indices: 17029519--17029566 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
17029509 ATTATTTACT
* **
17029519 TATTTATTCAATCAGTTTTTTAA
1 TATTTATTCAATAAGTTTTAAAA
*
17029542 TATTTATTTAATAAGTTTTAAAA
1 TATTTATTCAATAAGTTTTAAAA
17029565 TA
1 TA
17029567 ATTCAAGTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
TATTTATTCAATAAGTTTTAAAA
Found at i:17030326 original size:23 final size:23
Alignment explanation
Indices: 17030294--17030338 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
17030284 CTTAAACACT
*
17030294 AAAATGTTATGTTCTTGCTTTCC
1 AAAATATTATGTTCTTGCTTTCC
17030317 AAAATATTATGTTCTTGCTTTC
1 AAAATATTATGTTCTTGCTTTC
17030339 TTCGTAGGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.16, G:0.11, T:0.49
Consensus pattern (23 bp):
AAAATATTATGTTCTTGCTTTCC
Found at i:17036116 original size:48 final size:48
Alignment explanation
Indices: 17036051--17036155 Score: 156
Period size: 48 Copynumber: 2.2 Consensus size: 48
17036041 GGCTTCAGGC
* **
17036051 TATTAGCACTTCAGGTGCGAGTTACATTGATTTGGCTTTGGGCCATGA
1 TATTAGCACTTCAGGTGCGAGTTACATTGATTTGGCTTCGGGAAATGA
* *
17036099 TATTAGCATTTCGGGTGCGAGTTACATTGATTTGGCTTCGGGAAATGA
1 TATTAGCACTTCAGGTGCGAGTTACATTGATTTGGCTTCGGGAAATGA
*
17036147 TATTGGCAC
1 TATTAGCAC
17036156 CTAGGGTGCG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (48 bp):
TATTAGCACTTCAGGTGCGAGTTACATTGATTTGGCTTCGGGAAATGA
Found at i:17036163 original size:48 final size:48
Alignment explanation
Indices: 17036051--17036167 Score: 146
Period size: 48 Copynumber: 2.4 Consensus size: 48
17036041 GGCTTCAGGC
* * **
17036051 TATTAGCACTTCA-GGTGCGAGTTACATTGATTTGGCTTTGGGCCATGA
1 TATTAGCACCT-AGGGTGCGAGTTACATTGATTTGGCTTCGGGAAATGA
** *
17036099 TATTAGCATTTCGGGTGCGAGTTACATTGATTTGGCTTCGGGAAATGA
1 TATTAGCACCTAGGGTGCGAGTTACATTGATTTGGCTTCGGGAAATGA
*
17036147 TATTGGCACCTAGGGTGCGAG
1 TATTAGCACCTAGGGTGCGAG
17036168 ACTTCCGAGT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
48 59 1.00
ACGTcount: A:0.21, C:0.15, G:0.30, T:0.33
Consensus pattern (48 bp):
TATTAGCACCTAGGGTGCGAGTTACATTGATTTGGCTTCGGGAAATGA
Found at i:17041061 original size:21 final size:21
Alignment explanation
Indices: 17041036--17041105 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
17041026 TAAAACCTAG
17041036 AACTCTAAATTATTTTAAAAA
1 AACTCTAAATTATTTTAAAAA
* * *
17041057 AACTCTAAATCA-TATAAACTA
1 AACTCTAAATTATTTTAAA-AA
*
17041078 AAC-CTAAATTATTTTAACAA
1 AACTCTAAATTATTTTAAAAA
*
17041098 AACCCTAA
1 AACTCTAA
17041106 CCCTAAAAAC
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
20 16 0.41
21 23 0.59
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.31
Consensus pattern (21 bp):
AACTCTAAATTATTTTAAAAA
Found at i:17041100 original size:20 final size:20
Alignment explanation
Indices: 17041040--17041101 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
17041030 ACCTAGAACT
*
17041040 CTAAATTATTTTAAAAAAAC
1 CTAAATTATTTTAACAAAAC
* * * *
17041060 TCTAAATCATATAAACTAAAC
1 -CTAAATTATTTTAACAAAAC
17041081 CTAAATTATTTTAACAAAAC
1 CTAAATTATTTTAACAAAAC
17041101 C
1 C
17041102 CTAACCCTAA
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (20 bp):
CTAAATTATTTTAACAAAAC
Found at i:17041128 original size:15 final size:15
Alignment explanation
Indices: 17041096--17041129 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
17041086 TTATTTTAAC
* *
17041096 AAAACCCTAACCCTA
1 AAAACCCTAAACCAA
17041111 AAAACCCTAAACCAA
1 AAAACCCTAAACCAA
17041126 AAAA
1 AAAA
17041130 ATCTTAGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.32, G:0.00, T:0.09
Consensus pattern (15 bp):
AAAACCCTAAACCAA
Found at i:17041508 original size:30 final size:28
Alignment explanation
Indices: 17041456--17041527 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 28
17041446 AATTATTAAA
*
17041456 ATATTTTATATATTTAAAATAAATTATATTAC
1 ATATTTTA-ATAATTAAAATAAA--AT-TTAC
*
17041488 AT-TTTTAATAATTAATATAAAATTTAC
1 ATATTTTAATAATTAAAATAAAATTTAC
17041515 ATATTTTAA-AATT
1 ATATTTTAATAATT
17041528 TAAACTCATA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
27 10 0.27
28 8 0.22
30 12 0.32
31 5 0.14
32 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (28 bp):
ATATTTTAATAATTAAAATAAAATTTAC
Found at i:17042560 original size:27 final size:27
Alignment explanation
Indices: 17042522--17042575 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
17042512 ATTTTTGACA
17042522 ATCACATCCTGTATTTTCATCAAAAGT
1 ATCACATCCTGTATTTTCATCAAAAGT
17042549 ATCACATCCTGTATTTTCATCAAAAGT
1 ATCACATCCTGTATTTTCATCAAAAGT
17042576 TAGATAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (27 bp):
ATCACATCCTGTATTTTCATCAAAAGT
Found at i:17042684 original size:32 final size:32
Alignment explanation
Indices: 17042643--17042707 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
17042633 ATCTCGCTAG
17042643 TCTTCCAATTCGATTACGATCAATTGTGAATT
1 TCTTCCAATTCGATTACGATCAATTGTGAATT
*
17042675 TCTTTCAATTCGATTACGATCAATTGTGAATT
1 TCTTCCAATTCGATTACGATCAATTGTGAATT
17042707 T
1 T
17042708 TGTCAAAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (32 bp):
TCTTCCAATTCGATTACGATCAATTGTGAATT
Found at i:17042699 original size:15 final size:15
Alignment explanation
Indices: 17042648--17042699 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
17042638 GCTAGTCTTC
17042648 CAATTCGATTACGAT
1 CAATTCGATTACGAT
* * **
17042663 CAATTGTGAATTTCTTT
1 CAATT-CG-ATTACGAT
17042680 CAATTCGATTACGAT
1 CAATTCGATTACGAT
17042695 CAATT
1 CAATT
17042700 GTGAATTTTG
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
15 15 0.56
16 2 0.07
17 10 0.37
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (15 bp):
CAATTCGATTACGAT
Found at i:17043695 original size:20 final size:18
Alignment explanation
Indices: 17043648--17043738 Score: 58
Period size: 17 Copynumber: 5.3 Consensus size: 18
17043638 GTAGATAAAC
17043648 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
17043665 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
17043685 ATTAAATTAATA---AA-
1 ATTAAATTAATATTTAAT
*
17043699 A-TACAATTAAGA--TAAGT
1 ATTA-AATTAATATTTAA-T
17043716 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
17043733 ATTAAA
1 ATTAAA
17043739 CTATTAAAAT
Statistics
Matches: 61, Mismatches: 1, Indels: 24
0.71 0.01 0.28
Matches are distributed among these distances:
13 2 0.03
14 8 0.13
15 4 0.07
16 1 0.02
17 22 0.36
18 6 0.10
19 3 0.05
20 15 0.25
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:17045473 original size:28 final size:28
Alignment explanation
Indices: 17045427--17045593 Score: 108
Period size: 28 Copynumber: 6.0 Consensus size: 28
17045417 GGCTGTGTGT
*
17045427 CCCTTG-TTTTCAAATTTTATAGTTTTG
1 CCCTTGTTTTTCAGATTTTATAGTTTTG
* *
17045454 CCCTTGTTTTTTAGATTTTAAAGTTTTG
1 CCCTTGTTTTTCAGATTTTATAGTTTTG
* * * **
17045482 CCTCTT-TTTTTTAGATTTTACAAATTTAC
1 CC-CTTGTTTTTCAGATTTTA-TAGTTTTG
** * *
17045511 CCCTAATTTTT-AGATTTTGTAATTTTG
1 CCCTTGTTTTTCAGATTTTATAGTTTTG
* * * *
17045538 -CCTCTATTTTCCAAATTTTATAGTTTTA
1 CCCT-TGTTTTTCAGATTTTATAGTTTTG
* * *
17045566 CCCCTGTTATTCATATTTTATAGTTTTG
1 CCCTTGTTTTTCAGATTTTATAGTTTTG
17045594 ACCTAGAATT
Statistics
Matches: 110, Mismatches: 23, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
26 3 0.03
27 16 0.15
28 74 0.67
29 17 0.15
ACGTcount: A:0.21, C:0.15, G:0.09, T:0.55
Consensus pattern (28 bp):
CCCTTGTTTTTCAGATTTTATAGTTTTG
Found at i:17045566 original size:56 final size:55
Alignment explanation
Indices: 17045433--17045570 Score: 143
Period size: 56 Copynumber: 2.5 Consensus size: 55
17045423 GTGTCCCTTG
* * ** *
17045433 TTTTCAAATTTTATAGTTTTGCCCTTGTTTTTTAGATTTTAAAGTTTTGCCTCTTT
1 TTTTCAAATTTTATAGTTTTACCCCTAATTTTTAGATTTTAAAGTTTTGCCTC-TA
* * * ** *
17045489 TTTTTAGATTTTACAAATTTACCCCTAATTTTTAGATTTTGTAA-TTTTGCCTCTA
1 TTTTCAAATTTTATAGTTTTACCCCTAATTTTTAGATTTT-AAAGTTTTGCCTCTA
17045544 TTTTCCAAATTTTATAGTTTTACCCCT
1 TTTT-CAAATTTTATAGTTTTACCCCT
17045571 GTTATTCATA
Statistics
Matches: 64, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
55 5 0.08
56 57 0.89
57 2 0.03
ACGTcount: A:0.22, C:0.15, G:0.08, T:0.55
Consensus pattern (55 bp):
TTTTCAAATTTTATAGTTTTACCCCTAATTTTTAGATTTTAAAGTTTTGCCTCTA
Found at i:17046276 original size:85 final size:85
Alignment explanation
Indices: 17046116--17046278 Score: 236
Period size: 85 Copynumber: 1.9 Consensus size: 85
17046106 CTGCAAACAG
* * * *
17046116 TGTGGTTCGATTATGAACCAAGTGGCAATTTGTTTAATCTGCAAATATGTTGTGTACTCACAACA
1 TGTGGTTCAATCATGAACCAAGTGGCAATTTGTTTAATCTGCAAATATGTTGTGCACCCACAACA
** *
17046181 ACCGGTAGTAACTGAAAATA
66 AAAGGCAGTAACTGAAAATA
* * *
17046201 TGTGGTTCAATCATGAACCAAGTGGTAGTTTGTTTAATCTGTAAATATGTTGTGCACCCACAACA
1 TGTGGTTCAATCATGAACCAAGTGGCAATTTGTTTAATCTGCAAATATGTTGTGCACCCACAACA
17046266 AAAGGCAGTAACT
66 AAAGGCAGTAACT
17046279 ACAAATCAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
85 68 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (85 bp):
TGTGGTTCAATCATGAACCAAGTGGCAATTTGTTTAATCTGCAAATATGTTGTGCACCCACAACA
AAAGGCAGTAACTGAAAATA
Found at i:17046781 original size:24 final size:21
Alignment explanation
Indices: 17046752--17046802 Score: 57
Period size: 24 Copynumber: 2.3 Consensus size: 21
17046742 TATTTAGCAT
17046752 GCATGACATTTAACTTAATTTAA
1 GCATGACATTTAA-TTAA-TTAA
**
17046775 GACATGATTTTTAATTAATTAA
1 G-CATGACATTTAATTAATTAA
17046797 GCATGA
1 GCATGA
17046803 AATATAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 5 0.20
22 5 0.20
23 5 0.20
24 10 0.40
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
GCATGACATTTAATTAATTAA
Found at i:17046796 original size:22 final size:23
Alignment explanation
Indices: 17046760--17046802 Score: 63
Period size: 21 Copynumber: 1.9 Consensus size: 23
17046750 ATGCATGACA
17046760 TTTAACTTAATTTAAGACATGATT
1 TTTAACTTAATTTAAG-CATGATT
17046784 TTTAA-TTAA-TTAAGCATGA
1 TTTAACTTAATTTAAGCATGA
17046803 AATATAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 5 0.26
23 4 0.21
24 5 0.26
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (23 bp):
TTTAACTTAATTTAAGCATGATT
Found at i:17046854 original size:21 final size:19
Alignment explanation
Indices: 17046830--17046878 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 19
17046820 TTAACTCGCT
17046830 ATTTTTCTGAAAATAAACTAA
1 ATTTTTCT-AAAATAAA-TAA
17046851 ATTTTCTTCTAAAATAAATAA
1 A-TTT-TTCTAAAATAAATAA
17046872 ATATTTT
1 AT-TTTT
17046879 AAATTGATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
20 3 0.12
21 7 0.28
22 11 0.44
23 4 0.16
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (19 bp):
ATTTTTCTAAAATAAATAA
Found at i:17050611 original size:15 final size:15
Alignment explanation
Indices: 17050591--17050647 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
17050581 ATTCAATATT
17050591 AATATTTTAATAATA
1 AATATTTTAATAATA
*
17050606 AATATTTATTACAATCATA
1 AATA-TT-TT--AATAATA
**
17050625 AATATACTAATAATA
1 AATATTTTAATAATA
17050640 AATATTTT
1 AATATTTT
17050648 GTAATATAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 16 0.50
16 2 0.06
17 3 0.09
18 1 0.03
19 10 0.31
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:17056801 original size:3 final size:3
Alignment explanation
Indices: 17056787--17056837 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
17056777 ACACTAGTAC
* * * * *
17056787 ATA ATT ATA ATA ATA GTA ATA CTA ATA ATA CTA ATA AT- ATA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17056834 ATA A
1 ATA A
17056838 GGATATTTAA
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:17058547 original size:134 final size:134
Alignment explanation
Indices: 17058388--17059055 Score: 1112
Period size: 134 Copynumber: 5.0 Consensus size: 134
17058378 CCTCTACTGC
* * * ** * *
17058388 CAGGGAGATAGAATTACCGGCTTCAATATACTCCACTGTAATCAGGGAGGTAAAATCCGCCGTCT
1 CAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCT
** * * *
17058453 TCAACCTGCTTTGCTGCCAAATACAGGAAGGCAAGATCTACAATCTTCAATCTATTCCACTGCCA
66 TTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
17058518 AATA
131 AATA
17058522 CAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCT
1 CAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCT
*
17058587 TTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGTCA
66 TTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
17058652 AATA
131 AATA
* *
17058656 TAGGGAGATAGAGTTATCGGCTTAAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCT
1 CAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCT
17058721 TTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
66 TTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
17058786 AATA
131 AATA
*
17058790 CAGGGACA-AGAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCT
1 CAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCT
17058854 TTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
66 TTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
17058919 AATA
131 AATA
* *
17058923 CAGGGACA-AGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCT
1 CAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCT
* *
17058987 TCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCGATCTACTT-CAC-GCC
66 TTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTA-TTCCACTGCC
17059050 -AATA
130 AAATA
17059054 CA
1 CA
17059056 TGAAGATAAG
Statistics
Matches: 511, Mismatches: 22, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
131 6 0.01
132 3 0.01
133 242 0.47
134 260 0.51
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (134 bp):
CAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCT
TTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
AATA
Found at i:17059177 original size:132 final size:132
Alignment explanation
Indices: 17058976--17060082 Score: 1962
Period size: 132 Copynumber: 8.4 Consensus size: 132
17058966 GGGAGGTAAA
** * * ** * * *
17058976 ATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCGATCTA
1 ATCTG-CATCTTCGATCCACTTC-CTACC-AATATAGGAAGATAGGATCTGCTACCTTCGATCTA
* * *
17059041 CTTCACGCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAG
63 CTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAG
17059106 ACAAG
128 ACAAG
* * *
17059111 ATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGGATCTGCTACCTTCGATTTACTT
1 ATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTT
* *
17059176 CACGCCAATACATGCAGACAAGATCTGCTTTCTGCTATCTACTTCGCCACCAATATGGGAAGACA
66 CACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACA
17059241 AG
131 AG
*
17059243 ATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACATTCGATCTACTT
1 ATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTT
17059308 CACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACA
66 CACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACA
17059373 AG
131 AG
17059375 ATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTT
1 ATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTT
17059440 CACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACA
66 CACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACA
17059505 AG
131 AG
*
17059507 ATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATTTACTT
1 ATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTT
* *
17059572 CACGCCAATACATGCAGACAAGATCTGCTTTCTGCTATCTACTTCGCCACCAATATGGGAAGACA
66 CACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACA
17059637 AG
131 AG
17059639 ATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTT
1 ATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTT
* *
17059704 CACGCCAATACATGAAGACAAGATCTACTTTCTGCTATCTACTTCGCCACCAATATGGGAAGACA
66 CACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACA
17059769 AG
131 AG
17059771 ATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTT
1 ATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTT
17059836 CACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACA
66 CACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACA
17059901 AG
131 AG
17059903 ATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTT
1 ATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTT
*
17059968 CACGCCAATACATGAAGACAATATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACA
66 CACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACA
17060033 AG
131 AG
*
17060035 ATCTGCATCTTTGATCCACTTCCTACCAATATAGGAAGATAGGATCTG
1 ATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTG
17060083 TTCCTTTGAC
Statistics
Matches: 938, Mismatches: 34, Indels: 3
0.96 0.03 0.00
Matches are distributed among these distances:
132 916 0.98
133 3 0.00
134 14 0.01
135 5 0.01
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (132 bp):
ATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTT
CACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACA
AG
Found at i:17072072 original size:22 final size:23
Alignment explanation
Indices: 17072046--17072091 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
17072036 AGAAACGAAC
*
17072046 ATAAAATTAAT-AAAATATTAAA
1 ATAAAATGAATAAAAATATTAAA
*
17072068 ATAAAGTGAATGAAAAATATTAAA
1 ATAAAATGAAT-AAAAATATTAAA
17072092 TATGAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.45
24 11 0.55
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (23 bp):
ATAAAATGAATAAAAATATTAAA
Found at i:17072158 original size:3 final size:3
Alignment explanation
Indices: 17072145--17072194 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
17072135 ACACTAGTAC
* * * *
17072145 ATA AT- ATA ATA ATA GTA ATA CTA ATA ATA CTA ATA AT- ATA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17072191 ATA A
1 ATA A
17072195 GGATATTTAA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:17083370 original size:7 final size:7
Alignment explanation
Indices: 17083360--17083392 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
17083350 ACTAAACATA
17083360 AATAATT
1 AATAATT
17083367 AATAATT
1 AATAATT
17083374 AATAATT
1 AATAATT
17083381 AATAATT
1 AATAATT
17083388 AATAA
1 AATAA
17083393 CAAAAAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AATAATT
Found at i:17083477 original size:4 final size:4
Alignment explanation
Indices: 17083464--17083527 Score: 52
Period size: 4 Copynumber: 17.8 Consensus size: 4
17083454 TAATACATTA
17083464 CTTT -TTT CTTT CTTT CTTT CTTT C-TT C-TT C-TT C-TT C-TT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
* * *
17083506 TTTT CTCT -TTT CTTT CTCT CTT
1 CTTT CTTT CTTT CTTT CTTT CTT
17083528 CCGGTGGATG
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
3 20 0.39
4 31 0.61
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
CTTT
Found at i:17083505 original size:27 final size:29
Alignment explanation
Indices: 17083469--17083528 Score: 68
Period size: 31 Copynumber: 2.0 Consensus size: 29
17083459 CATTACTTTT
*
17083469 TTCTTTCTTTCTTTCTTTC-TTCTTCTTCTTC
1 TTCTTTCTTTCTCT-TTTCTTTC-TC-TCTTC
*
17083500 TTCTTTTTTTCTCTTTTCTTTCTCTCTTC
1 TTCTTTCTTTCTCTTTTCTTTCTCTCTTC
17083529 CGGTGGATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 5 0.19
30 6 0.23
31 15 0.58
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (29 bp):
TTCTTTCTTTCTCTTTTCTTTCTCTCTTC
Found at i:17083842 original size:18 final size:17
Alignment explanation
Indices: 17083819--17083889 Score: 63
Period size: 17 Copynumber: 4.0 Consensus size: 17
17083809 GTGCGACTCA
17083819 ATTTTTTATATTAAAAAT
1 ATTTTTTAT-TTAAAAAT
*
17083837 A-TTTTTATTAAAAAATT
1 ATTTTTTATTTAAAAA-T
*
17083854 AATATTTTATTTAAAAAAT
1 -ATTTTTTATTT-AAAAAT
* *
17083873 ATTTTTAATATAAAAAT
1 ATTTTTTATTTAAAAAT
17083890 TGAGTCGCAC
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
16 6 0.14
17 14 0.33
18 10 0.23
19 8 0.19
20 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTTTTATTTAAAAAT
Found at i:17083861 original size:19 final size:21
Alignment explanation
Indices: 17083834--17083872 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
17083824 TTATATTAAA
17083834 AATATTTTTA-TTAAAAAATT
1 AATATTTTTATTTAAAAAATT
17083854 AATA-TTTTATTTAAAAAAT
1 AATATTTTTATTTAAAAAAT
17083873 ATTTTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AATATTTTTATTTAAAAAATT
Found at i:17084019 original size:5 final size:5
Alignment explanation
Indices: 17084009--17084035 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
17083999 AAAACCCTAC
17084009 ACCCA ACCCA ACCCA ACCCA ACCCA AC
1 ACCCA ACCCA ACCCA ACCCA ACCCA AC
17084036 GGAACCGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.59, G:0.00, T:0.00
Consensus pattern (5 bp):
ACCCA
Found at i:17090544 original size:23 final size:23
Alignment explanation
Indices: 17090497--17090544 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
17090487 AAAATTTATT
**
17090497 TATTTATTCAATAAGTTTTTTAA
1 TATTTATTCAATAAGTTTTAAAA
*
17090520 TATTTATTTAATAAGTTTTAAAA
1 TATTTATTCAATAAGTTTTAAAA
17090543 TA
1 TA
17090545 ATTCAAGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (23 bp):
TATTTATTCAATAAGTTTTAAAA
Found at i:17094805 original size:19 final size:21
Alignment explanation
Indices: 17094781--17094824 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
17094771 CATCGTTTTT
*
17094781 AGAAGCCCG-AAG-GCTAAAC
1 AGAAGCACGTAAGCGCTAAAC
17094800 AGAAGCACGTAAGCGCTAAAC
1 AGAAGCACGTAAGCGCTAAAC
17094821 AGAA
1 AGAA
17094825 ACCCATAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.36
20 3 0.14
21 11 0.50
ACGTcount: A:0.45, C:0.23, G:0.25, T:0.07
Consensus pattern (21 bp):
AGAAGCACGTAAGCGCTAAAC
Found at i:17094833 original size:21 final size:21
Alignment explanation
Indices: 17094793--17094833 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
17094783 AAGCCCGAAG
* *
17094793 GCTAAACAGAAGCACGTAAGC
1 GCTAAACAGAAACACATAAGC
*
17094814 GCTAAACAGAAACCCATAAG
1 GCTAAACAGAAACACATAAG
17094834 GGTTGAACAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (21 bp):
GCTAAACAGAAACACATAAGC
Found at i:17094842 original size:21 final size:21
Alignment explanation
Indices: 17094818--17094936 Score: 73
Period size: 21 Copynumber: 5.7 Consensus size: 21
17094808 GTAAGCGCTA
17094818 AACAGAAACCCATAAGGGTTG
1 AACAGAAACCCATAAGGGTTG
* * * *
17094839 AACA-AAAGCTCATTAGAGCTG
1 AACAGAAA-CCCATAAGGGTTG
* *
17094860 AACAGAAACCTATAAGGGTTA
1 AACAGAAACCCATAAGGGTTG
* * *
17094881 AACA-AAAGCTCA-ATAGAGCTG
1 AACAGAAA-CCCATA-AGGGTTG
** *
17094902 AATGGAAACCCATTAGGGTTG
1 AACAGAAACCCATAAGGGTTG
*
17094923 AACAGAAACTCATA
1 AACAGAAACCCATA
17094937 TGAGTTAAAT
Statistics
Matches: 67, Mismatches: 25, Indels: 12
0.64 0.24 0.12
Matches are distributed among these distances:
20 7 0.10
21 54 0.81
22 6 0.09
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.18
Consensus pattern (21 bp):
AACAGAAACCCATAAGGGTTG
Found at i:17094877 original size:42 final size:42
Alignment explanation
Indices: 17094818--17094935 Score: 166
Period size: 42 Copynumber: 2.8 Consensus size: 42
17094808 GTAAGCGCTA
17094818 AACAGAAACCCATAAGGGTTGAACAAAAGCTCATTAGAGCTG
1 AACAGAAACCCATAAGGGTTGAACAAAAGCTCATTAGAGCTG
* * *
17094860 AACAGAAACCTATAAGGGTTAAACAAAAGCTCAATAGAGCTG
1 AACAGAAACCCATAAGGGTTGAACAAAAGCTCATTAGAGCTG
** *
17094902 AATGGAAACCCATTAGGGTTGAACAGAAA-CTCAT
1 AACAGAAACCCATAAGGGTTGAACA-AAAGCTCAT
17094936 ATGAGTTAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
42 63 0.95
43 3 0.05
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (42 bp):
AACAGAAACCCATAAGGGTTGAACAAAAGCTCATTAGAGCTG
Found at i:17102161 original size:18 final size:20
Alignment explanation
Indices: 17102124--17102162 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
17102114 TTTCCCTCTA
*
17102124 TTCTCTATATATTTTGCTTT
1 TTCTCTATATATTTTCCTTT
17102144 TTCTCT-TAT-TTTTCCTTT
1 TTCTCTATATATTTTCCTTT
17102162 T
1 T
17102163 CTTTTATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 3 0.17
20 6 0.33
ACGTcount: A:0.10, C:0.18, G:0.03, T:0.69
Consensus pattern (20 bp):
TTCTCTATATATTTTCCTTT
Found at i:17103092 original size:24 final size:25
Alignment explanation
Indices: 17103059--17103108 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
17103049 TGTAAATCAG
17103059 AAAAATATCTC-TAGA-AATTTTCT
1 AAAAATATCTCTTAGATAATTTTCT
17103082 AAAAATAATCTCTTTAGATAATTTTCT
1 AAAAAT-ATCTC-TTAGATAATTTTCT
17103109 CTCTACAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 6 0.26
24 5 0.22
26 4 0.17
27 8 0.35
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (25 bp):
AAAAATATCTCTTAGATAATTTTCT
Found at i:17105228 original size:28 final size:28
Alignment explanation
Indices: 17105189--17105347 Score: 124
Period size: 28 Copynumber: 5.7 Consensus size: 28
17105179 GTGTCCACTG
* *
17105189 TTTTCAAATTTTATAGTTTTGCCCTTAT
1 TTTTCAGATTTTACAGTTTTGCCCTTAT
* *
17105217 TTTTCAGATTTTATAGTTTT-ACCTCTAT
1 TTTTCAGATTTTACAGTTTTGCCCT-TAT
* * * * *
17105245 TTTTTAAATTTTACAATTTTACCCCTAAT
1 TTTTCAGATTTTACAGTTTT-GCCCTTAT
** *
17105274 TTTT-AGATTTTACAAATTTGCCTTTAT
1 TTTTCAGATTTTACAGTTTTGCCCTTAT
* * *
17105301 TTTCCAGATTTTACAGTTTTTCCCTTGT
1 TTTTCAGATTTTACAGTTTTGCCCTTAT
* * *
17105329 TATTCATATTTTATAGTTT
1 TTTTCAGATTTTACAGTTT
17105348 GGACCTAGAA
Statistics
Matches: 104, Mismatches: 23, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
27 11 0.11
28 84 0.81
29 6 0.06
30 3 0.03
ACGTcount: A:0.23, C:0.14, G:0.06, T:0.56
Consensus pattern (28 bp):
TTTTCAGATTTTACAGTTTTGCCCTTAT
Found at i:17116806 original size:23 final size:26
Alignment explanation
Indices: 17116748--17116809 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 26
17116738 TACAAGGACT
17116748 TATGACATATTTTAAACTAGTATAAAA
1 TATGA-ATATTTTAAACTAGTATAAAA
* *
17116775 AATGAATATTTT-AATTA-TAT-AAA
1 TATGAATATTTTAAACTAGTATAAAA
17116798 TATGAATATTTT
1 TATGAATATTTT
17116810 TTTAAATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 14 0.44
24 3 0.09
25 4 0.12
26 7 0.22
27 4 0.12
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (26 bp):
TATGAATATTTTAAACTAGTATAAAA
Found at i:17120615 original size:16 final size:16
Alignment explanation
Indices: 17120586--17120633 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
17120576 GTTAACTTGT
17120586 TTTATTTTTAAAATATTA
1 TTTA-TTTT-AAATATTA
17120604 TTTATTTTAAATATTA
1 TTTATTTTAAATATTA
*
17120620 TTTATATTAAATAT
1 TTTATTTTAAATAT
17120634 GTTATACATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 21 0.72
17 4 0.14
18 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTATTTTAAATATTA
Found at i:17123022 original size:25 final size:25
Alignment explanation
Indices: 17122976--17123064 Score: 90
Period size: 25 Copynumber: 3.6 Consensus size: 25
17122966 TTCAGCTCTT
* * * *
17122976 ATGAGCTTCTCGATAGACAGCTCGC
1 ATGAGCTTCCCGTTATATAGCTCGC
* * *
17123001 ATGAGCTTCCTGTTATTTAGCTCAC
1 ATGAGCTTCCCGTTATATAGCTCGC
17123026 ATGAGCTTCCCGTTATATAGCTCG-
1 ATGAGCTTCCCGTTATATAGCTCGC
*
17123050 GTAGAGCTTCCCGTT
1 AT-GAGCTTCCCGTT
17123065 TACATGCTCA
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
24 1 0.02
25 51 0.98
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.33
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATATAGCTCGC
Found at i:17123081 original size:25 final size:25
Alignment explanation
Indices: 17122969--17123081 Score: 77
Period size: 25 Copynumber: 4.5 Consensus size: 25
17122959 TTTCGATTTC
* * * * *
17122969 AGCTCTTATGAGCTTCTCGATAGAC
1 AGCTCATATGAGCTTCCCGTTACAT
** * **
17122994 AGCTCGCATGAGCTTCCTGTTATTT
1 AGCTCATATGAGCTTCCCGTTACAT
* *
17123019 AGCTCACATGAGCTTCCCGTTATAT
1 AGCTCATATGAGCTTCCCGTTACAT
*
17123044 AGCTCGGTA-GAGCTTCCCGTTTACAT
1 AGCTC-ATATGAGCTTCCCG-TTACAT
17123070 -GCTCATATGAGC
1 AGCTCATATGAGC
17123082 ATACATGTAC
Statistics
Matches: 70, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
24 2 0.03
25 62 0.89
26 6 0.09
ACGTcount: A:0.21, C:0.26, G:0.20, T:0.33
Consensus pattern (25 bp):
AGCTCATATGAGCTTCCCGTTACAT
Found at i:17123578 original size:33 final size:33
Alignment explanation
Indices: 17123536--17123602 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 33
17123526 AGCTGGTCGG
17123536 AGCTGAATCACACTATCCATC-GACTCCTTTGGT
1 AGCTGAATCACACTATCCATCTGA-TCCTTTGGT
17123569 AGCTGAATCACACTATCCATCTGATCCTTTGGT
1 AGCTGAATCACACTATCCATCTGATCCTTTGGT
17123602 A
1 A
17123603 TTTTCAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 31 0.94
34 2 0.06
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.31
Consensus pattern (33 bp):
AGCTGAATCACACTATCCATCTGATCCTTTGGT
Found at i:17129788 original size:26 final size:26
Alignment explanation
Indices: 17129757--17129864 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
17129747 TGAAATGCCC
*
17129757 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
17129783 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
17129809 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
17129835 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
17129861 ATCA
1 ATCA
17129865 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:17136262 original size:13 final size:13
Alignment explanation
Indices: 17136246--17136272 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17136236 ACATTATGCA
17136246 AACAAATGGTTTT
1 AACAAATGGTTTT
17136259 AACAAATGGTTTT
1 AACAAATGGTTTT
17136272 A
1 A
17136273 TTTAAACACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
AACAAATGGTTTT
Found at i:17136952 original size:16 final size:16
Alignment explanation
Indices: 17136923--17136970 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
17136913 GTTAACTTGT
17136923 TTTATTTTTAAAATATTA
1 TTTA-TTTT-AAATATTA
17136941 TTTATTTTAAATATTA
1 TTTATTTTAAATATTA
* *
17136957 CTTATATTAAATAT
1 TTTATTTTAAATAT
17136971 GTTATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 20 0.71
17 4 0.14
18 4 0.14
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTATTTTAAATATTA
Found at i:17137339 original size:12 final size:11
Alignment explanation
Indices: 17137321--17137368 Score: 71
Period size: 11 Copynumber: 4.4 Consensus size: 11
17137311 ATTTTTCTTC
17137321 ATATTTTTTAA
1 ATATTTTTTAA
17137332 ATATTTTTTAA
1 ATATTTTTTAA
*
17137343 ATAATTTTTAA
1 ATATTTTTTAA
17137354 A-ATTCTTTTAA
1 ATATT-TTTTAA
17137365 ATAT
1 ATAT
17137369 ATACTAACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
10 2 0.06
11 29 0.88
12 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
ATATTTTTTAA
Found at i:17142389 original size:20 final size:20
Alignment explanation
Indices: 17142353--17142413 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 20
17142343 AAAAGTTAGA
17142353 AAAAACTAAAAGT--TTAAAT
1 AAAAACTAAAA-TAATTAAAT
17142372 AAAAACTAAAATAATTAAA-
1 AAAAACTAAAATAATTAAAT
* * *
17142391 AAAAATTTAAATAACTAAAT
1 AAAAACTAAAATAATTAAAT
17142411 AAA
1 AAA
17142414 TTATTGTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 1 0.03
19 27 0.75
20 8 0.22
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAAACTAAAATAATTAAAT
Found at i:17142859 original size:24 final size:24
Alignment explanation
Indices: 17142830--17142881 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
17142820 TTAAACTATT
*
17142830 ATATTTAATAATTATTATGTTAAA
1 ATATTTAATAATAATTATGTTAAA
17142854 ATATTTAATAATAATTATGTTAAA
1 ATATTTAATAATAATTATGTTAAA
17142878 ATAT
1 ATAT
17142882 GGTTAAACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
ATATTTAATAATAATTATGTTAAA
Found at i:17145966 original size:3 final size:3
Alignment explanation
Indices: 17145958--17145985 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
17145948 AATGGTGATG
17145958 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
17145986 GCCATCTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:17151873 original size:3 final size:3
Alignment explanation
Indices: 17151865--17151904 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
17151855 GCTCTCTCTC
*
17151865 TCT TCT TCT TCT TCT TCT TCT TCT TCT T-T TTT TCT T-T TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
17151905 GAAATGGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TCT
Found at i:17152374 original size:26 final size:26
Alignment explanation
Indices: 17152320--17152390 Score: 83
Period size: 26 Copynumber: 2.7 Consensus size: 26
17152310 TTTTAATCCT
**
17152320 TTTTTATTT-TAAATATTTTTATATTA
1 TTTTTATTTATAAATATTAGT-TATTA
17152346 TTTATT-TTTATAAATATTAGTTATTA
1 TTT-TTATTTATAAATATTAGTTATTA
*
17152372 TTTTTATTTATATATATTA
1 TTTTTATTTATAAATATTA
17152391 TCCATTATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
25 2 0.05
26 26 0.67
27 11 0.28
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (26 bp):
TTTTTATTTATAAATATTAGTTATTA
Found at i:17152377 original size:28 final size:27
Alignment explanation
Indices: 17152329--17152385 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
17152319 TTTTTTATTT
* *
17152329 TAAATATTTTTATATTATTTATTTTTA
1 TAAATATTGTTATATTATTTATTTATA
17152356 TAAATATTAGTTATTATT-TTTATTTATA
1 TAAATATT-GTTA-TATTATTTATTTATA
17152384 TA
1 TA
17152386 TATTATCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 8 0.31
28 14 0.54
29 4 0.15
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (27 bp):
TAAATATTGTTATATTATTTATTTATA
Found at i:17152391 original size:22 final size:22
Alignment explanation
Indices: 17152339--17152391 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
17152329 TAAATATTTT
17152339 TATATTATTTATTTTTATAAATA
1 TATATTA-TTATTTTTATAAATA
**
17152362 T-TAGTTATTATTTTTATTTATA
1 TATA-TTATTATTTTTATAAATA
17152384 TATATTAT
1 TATATTAT
17152392 CCATTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
TATATTATTATTTTTATAAATA
Found at i:17152397 original size:26 final size:26
Alignment explanation
Indices: 17152342--17152421 Score: 65
Period size: 26 Copynumber: 3.0 Consensus size: 26
17152332 ATATTTTTAT
* *
17152342 ATTATTTATT-TTTATAAATATTAGT-T
1 ATTATTT-TTATTTATATATATTA-TCC
17152368 ATTATTTTTATTTATATATATTATCC
1 ATTATTTTTATTTATATATATTATCC
* *
17152394 ATTATATTATATTATTGTATATATTATC
1 ATTAT-TTTTA-T-TTATATATATTATC
17152422 TATAAATTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
25 3 0.07
26 24 0.53
27 4 0.09
28 1 0.02
29 13 0.29
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.60
Consensus pattern (26 bp):
ATTATTTTTATTTATATATATTATCC
Found at i:17152453 original size:33 final size:33
Alignment explanation
Indices: 17152394--17152458 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
17152384 TATATTATCC
* *
17152394 ATTATATTATATTATTGTATATATTATCTATAA
1 ATTATATTATATTATTATATATATTATATATAA
* *
17152427 ATTATATTTTATTA-TATATTTCATTATATATA
1 ATTATATTATATTATTATATAT-ATTATATATA
17152459 TATCTTATGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 5 0.19
33 22 0.81
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (33 bp):
ATTATATTATATTATTATATATATTATATATAA
Found at i:17154128 original size:136 final size:136
Alignment explanation
Indices: 17153877--17154172 Score: 376
Period size: 136 Copynumber: 2.2 Consensus size: 136
17153867 CCAGATTGAA
* * * * *
17153877 CTCATGTTTAATGTCTCGGGGGACTTTTTATGATGCCATAGTCAAGCTATGGTCTTACATAATTG
1 CTCATATTTAATGTCTCGGGGGACTCTTTATAATGCCATAGTCAAGCTATGATCTTACACAATTG
* ** * *
17153942 AATGCCCATGTTTACTGTCTTGACGGACAACCTATGTTGCCAAGGTCAAGCCAAGGCCTTACACC
66 AATGCCCATGTTTACTATCCCGACGAACAACCTATGTTGCCAAGGCCAAGCCAAGGCCTTACACC
17154007 TAAAAT
131 TAAAAT
* * *
17154013 CTCATATTTAATGTCTTGGTGGACTCTTTATAATGCCATAGTCGAGCTATGATCTTACACAATTG
1 CTCATATTTAATGTCTCGGGGGACTCTTTATAATGCCATAGTCAAGCTATGATCTTACACAATTG
* * * * * * * *
17154078 AATGCTCGTGTTTACTATCCCGATGAACTACCTATGTTGCCATGGCCAAGCCAGGGTCTTACACT
66 AATGCCCATGTTTACTATCCCGACGAACAACCTATGTTGCCAAGGCCAAGCCAAGGCCTTACACC
*
17154143 TGAAAT
131 TAAAAT
* *
17154149 CTCATATTTAATATCTCGGCGGAC
1 CTCATATTTAATGTCTCGGGGGAC
17154173 ATCCCCGTGT
Statistics
Matches: 135, Mismatches: 25, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
136 135 1.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (136 bp):
CTCATATTTAATGTCTCGGGGGACTCTTTATAATGCCATAGTCAAGCTATGATCTTACACAATTG
AATGCCCATGTTTACTATCCCGACGAACAACCTATGTTGCCAAGGCCAAGCCAAGGCCTTACACC
TAAAAT
Found at i:17155374 original size:14 final size:15
Alignment explanation
Indices: 17155352--17155392 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
17155342 GTTAAATATA
17155352 TTTATAATATATTAT
1 TTTATAATATATTAT
17155367 TTTA-AATATA-TAT
1 TTTATAATATATTAT
17155380 TTTATAATATATT
1 TTTATAATATATT
17155393 TTAAATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.29
14 12 0.50
15 5 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTATAATATATTAT
Found at i:17155374 original size:25 final size:25
Alignment explanation
Indices: 17155343--17155404 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 25
17155333 ATTAAGTTAG
17155343 TTAAATATATTTATAAT-ATATTATT
1 TTAAATATATTTATAATAATA-TATT
*
17155368 TTAAATATATATT-TTATAATATATT
1 TTAAATATAT-TTATAATAATATATT
17155393 TTAAATA-ATTTA
1 TTAAATATATTTA
17155405 GTTAATTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
23 2 0.06
24 2 0.06
25 24 0.73
26 5 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TTAAATATATTTATAATAATATATT
Found at i:17155400 original size:14 final size:14
Alignment explanation
Indices: 17155346--17155401 Score: 59
Period size: 14 Copynumber: 4.2 Consensus size: 14
17155336 AAGTTAGTTA
17155346 AATATA-TTTATAAT
1 AATATATTTTA-AAT
17155360 -ATATTATTTTAAAT
1 AATA-TATTTTAAAT
17155374 -ATATATTTT--AT
1 AATATATTTTAAAT
17155385 AATATATTTTAAAT
1 AATATATTTTAAAT
17155399 AAT
1 AAT
17155402 TTAGTTAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
11 2 0.05
12 9 0.24
13 9 0.24
14 13 0.35
15 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AATATATTTTAAAT
Found at i:17155403 original size:10 final size:12
Alignment explanation
Indices: 17155346--17155403 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
17155336 AAGTTAGTTA
17155346 AATATA-TTTAT
1 AATATATTTTAT
*
17155357 AATATATTATTTTAA
1 -A-ATA-TATTTTAT
17155372 ATATATATTTTAT
1 A-ATATATTTTAT
17155385 AATATATTTTA-
1 AATATATTTTAT
17155396 AATA-ATTT
1 AATATATTT
17155404 AGTTAATTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
10 4 0.10
11 4 0.10
12 11 0.27
13 11 0.27
14 7 0.17
15 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
AATATATTTTAT
Found at i:17165553 original size:13 final size:13
Alignment explanation
Indices: 17165537--17165562 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17165527 GTTTTGTGCT
17165537 GATATTTTTCTTA
1 GATATTTTTCTTA
17165550 GATATTTTTCTTA
1 GATATTTTTCTTA
17165563 TTTGAGTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (13 bp):
GATATTTTTCTTA
Found at i:17168556 original size:20 final size:20
Alignment explanation
Indices: 17168519--17168556 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
17168509 CAAAATAATA
*
17168519 CTAAATAAATAAATATTTAT
1 CTAAATAAATAAAGATTTAT
17168539 CTAAAT-AATATAAGATTT
1 CTAAATAAATA-AAGATTT
17168557 TTTTTTTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (20 bp):
CTAAATAAATAAAGATTTAT
Found at i:17169899 original size:18 final size:18
Alignment explanation
Indices: 17169876--17169928 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 18
17169866 CGTCTAACTT
17169876 CTTGTCACACGGGTTCAG
1 CTTGTCACACGGGTTCAG
17169894 CTTGTCACATCACACGGGTTCAG
1 CTTG-----TCACACGGGTTCAG
17169917 CTTGTCACACGG
1 CTTGTCACACGG
17169929 TCGTGTGACC
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
18 12 0.40
23 18 0.60
ACGTcount: A:0.19, C:0.30, G:0.25, T:0.26
Consensus pattern (18 bp):
CTTGTCACACGGGTTCAG
Found at i:17169906 original size:23 final size:23
Alignment explanation
Indices: 17169880--17169925 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
17169870 TAACTTCTTG
17169880 TCACACGGGTTCAGCTTGTCACA
1 TCACACGGGTTCAGCTTGTCACA
17169903 TCACACGGGTTCAGCTTGTCACA
1 TCACACGGGTTCAGCTTGTCACA
17169926 CGGTCGTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (23 bp):
TCACACGGGTTCAGCTTGTCACA
Found at i:17170991 original size:25 final size:25
Alignment explanation
Indices: 17170963--17171010 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
17170953 TTTATCTTGC
17170963 TATTAAATTTAAT-TTAATATTAAGA
1 TATTAAATTTAATATTAA-ATTAAGA
* *
17170988 TATTCACTTTAATATTAAATTAA
1 TATTAAATTTAATATTAAATTAA
17171011 TAAAATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (25 bp):
TATTAAATTTAATATTAAATTAAGA
Found at i:17171012 original size:11 final size:11
Alignment explanation
Indices: 17170996--17171047 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
17170986 GATATTCACT
17170996 TTAATATTAAA
1 TTAATATTAAA
17171007 TTAATA--AAA
1 TTAATATTAAA
17171016 -TAATATTAAGA
1 TTAATATTAA-A
*
17171027 TAAATATTAAA
1 TTAATATTAAA
*
17171038 TTAATTTTAA
1 TTAATATTAA
17171048 TACTAAACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
8 5 0.15
9 3 0.09
10 2 0.06
11 16 0.47
12 8 0.24
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:17173441 original size:51 final size:49
Alignment explanation
Indices: 17173313--17173456 Score: 198
Period size: 51 Copynumber: 2.9 Consensus size: 49
17173303 TATTGTGAGG
* * * *
17173313 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATTGG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATTGA
* * * *
17173362 TCGCATGTGTGGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAA-TT-GA
17173413 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
17173457 GCTTTGGCTA
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
49 38 0.47
50 2 0.02
51 41 0.51
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (49 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATTGA
Found at i:17175342 original size:20 final size:20
Alignment explanation
Indices: 17175319--17175382 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
17175309 GTTACTCGAA
17175319 ATGAATGACATGATTGAGAT
1 ATGAATGACATGATTGAGAT
* *
17175339 ATGATTG-CTATGA-TGA-AA
1 ATGAATGAC-ATGATTGAGAT
*
17175357 ACTGTGATGACATGATTGAGAT
1 A-TG-AATGACATGATTGAGAT
17175379 ATGA
1 ATGA
17175383 TTGTTATGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
18 2 0.06
19 6 0.19
20 16 0.50
21 6 0.19
22 2 0.06
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.31
Consensus pattern (20 bp):
ATGAATGACATGATTGAGAT
Found at i:17175367 original size:40 final size:40
Alignment explanation
Indices: 17175323--17175402 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
17175313 CTCGAAATGA
17175323 ATGACATGATTGAGATATGATTGCTATGATGAAAACTGTG
1 ATGACATGATTGAGATATGATTGCTATGATGAAAACTGTG
*
17175363 ATGACATGATTGAGATATGATTGTTATGATGAAAACTGTG
1 ATGACATGATTGAGATATGATTGCTATGATGAAAACTGTG
17175403 TTATATAAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.35, C:0.06, G:0.25, T:0.34
Consensus pattern (40 bp):
ATGACATGATTGAGATATGATTGCTATGATGAAAACTGTG
Found at i:17175391 original size:20 final size:20
Alignment explanation
Indices: 17175328--17175392 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
17175318 AATGAATGAC
*
17175328 ATGATTGAGATATGATTGCT
1 ATGATTGAGATATGATTGAT
* * *
17175348 ATGA-TGAAAACTGTGA-TGAC
1 ATGATTG-AGA-TATGATTGAT
*
17175368 ATGATTGAGATATGATTGTT
1 ATGATTGAGATATGATTGAT
17175388 ATGAT
1 ATGAT
17175393 GAAAACTGTG
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
19 6 0.18
20 21 0.64
21 6 0.18
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.37
Consensus pattern (20 bp):
ATGATTGAGATATGATTGAT
Found at i:17179341 original size:135 final size:135
Alignment explanation
Indices: 17179151--17179665 Score: 708
Period size: 135 Copynumber: 3.8 Consensus size: 135
17179141 TGTCGATCCA
* * * * * * * * ** * *
17179151 TGGAGATAAGATTCACCGAAATTTGGTCTGCTCCGCTCCTACTTAGCGAAAATAAGACCTGGTAT
1 TGGAGATAAGATTCTCCAAAATTCGATCTGCTTCACTCCTGCTCAATGAAGATAAGATCTGGTAT
* **
17179216 ATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAAGCTGATGATTGGAATCTGTTTAATCGCCG
66 ATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAAGCTGATGATTGGAATCTGCTCCATCGCCG
17179281 GTACG
131 GTACG
* * *
17179286 TGTAGATAAGATTATCCAAAATTCGATCTGCTTCACTCTTGCTCAATGAAGATAAGATCTGGTAT
1 TGGAGATAAGATTCTCCAAAATTCGATCTGCTTCACTCCTGCTCAATGAAGATAAGATCTGGTAT
* * *
17179351 ATTTAGCCTACTCCACTCCTGCTCAGTGAAGATAAGGTTGATGATTGGAATCTGCTCCATCGCCG
66 ATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAAGCTGATGATTGGAATCTGCTCCATCGCCG
17179416 GTACG
131 GTACG
* * *
17179421 TGGAGATAAGATTCTCCAAAATTCGATCTACTTCACTCCTACTCAATGAAGATAATATCTGGTAT
1 TGGAGATAAGATTCTCCAAAATTCGATCTGCTTCACTCCTGCTCAATGAAGATAAGATCTGGTAT
* *
17179486 ATTTAGCCTGCTCCACTCC-GACTCAGTGAAGATAAAGTTGATGATTGGAATCTGCTCCATCGCT
66 ATTTAGCCTGCTCCACTCCTG-CTCAGTGAAGATAAAGCTGATGATTGGAATCTGCTCCATCGCC
*
17179550 GGTACA
130 GGTACG
* * * *
17179556 TGGAGATAAGATTCTCCAAAACTCGATCTGTTTCACTCCTGCTCAGTGAAGATAAGATCGGGTAT
1 TGGAGATAAGATTCTCCAAAATTCGATCTGCTTCACTCCTGCTCAATGAAGATAAGATCTGGTAT
* * *
17179621 GTTTAACCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGAT
66 ATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAAGCTGATGAT
17179666 ATCTGTCTTT
Statistics
Matches: 336, Mismatches: 42, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
134 1 0.00
135 334 0.99
136 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (135 bp):
TGGAGATAAGATTCTCCAAAATTCGATCTGCTTCACTCCTGCTCAATGAAGATAAGATCTGGTAT
ATTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAAGCTGATGATTGGAATCTGCTCCATCGCCG
GTACG
Found at i:17179593 original size:270 final size:270
Alignment explanation
Indices: 17179091--17179665 Score: 747
Period size: 270 Copynumber: 2.1 Consensus size: 270
17179081 ATCTGATCTG
* * * * * ** * * *
17179091 CTCCGCTCCTGGTTAGTGAAGATAAGATTGGTGGCTGAAATCTGCTCCATTGTCGATCCATGGAG
1 CTCCACTCCTGCTCAGTGAAGATAAGGTTGATGATTGAAATCTGCTCCATCGCCGATACATGGAG
* * * * * * *
17179156 ATAAGATTCACCGAAATTTGGTCTGCTCCGCTCCTACTTAGCGAAAATAAGACCTGGTATATTTA
66 ATAAGATTCACCAAAATTCGATCTACTCCACTCCTACTCAACGAAAATAAGACCTGGTATATTTA
* * *
17179221 GCCTGCTCCACTCCTGCTCAGTGAAGATAAAGCTGATGATTGGAATCTGTTTAATCGCCGGTACG
131 GCCTGCTCCACTCCTGCTCAGTGAAGATAAAGCTGATGATTGGAATCTGCTCAATCGCCGGTACA
* * * *
17179286 TGTAGATAAGATTATCCAAAATTCGATCTGCTTCACTCTTGCTCAATGAAGATAAGATCTGGTAT
196 TGGAGATAAGATTATCCAAAACTCGATCTGCTTCACTCCTGCTCAATGAAGATAAGATCGGGTAT
*
17179351 ATTTAGCCTA
261 ATTTAACCTA
* * *
17179361 CTCCACTCCTGCTCAGTGAAGATAAGGTTGATGATTGGAATCTGCTCCATCGCCGGTACGTGGAG
1 CTCCACTCCTGCTCAGTGAAGATAAGGTTGATGATTGAAATCTGCTCCATCGCCGATACATGGAG
* * * * * *
17179426 ATAAGATTCTCCAAAATTCGATCTACTTCACTCCTACTCAATGAAGATAATATCTGGTATATTTA
66 ATAAGATTCACCAAAATTCGATCTACTCCACTCCTACTCAACGAAAATAAGACCTGGTATATTTA
* * *
17179491 GCCTGCTCCACTCC-GACTCAGTGAAGATAAAGTTGATGATTGGAATCTGCTCCATCGCTGGTAC
131 GCCTGCTCCACTCCTG-CTCAGTGAAGATAAAGCTGATGATTGGAATCTGCTCAATCGCCGGTAC
* * *
17179555 ATGGAGATAAGATTCTCCAAAACTCGATCTGTTTCACTCCTGCTCAGTGAAGATAAGATCGGGTA
195 ATGGAGATAAGATTATCCAAAACTCGATCTGCTTCACTCCTGCTCAATGAAGATAAGATCGGGTA
* *
17179620 TGTTTAACCTG
260 TATTTAACCTA
*
17179631 CTCCACTCCTGCTCAGTGAAGATAAGGCTGATGAT
1 CTCCACTCCTGCTCAGTGAAGATAAGGTTGATGAT
17179666 ATCTGTCTTT
Statistics
Matches: 261, Mismatches: 43, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
269 1 0.00
270 260 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (270 bp):
CTCCACTCCTGCTCAGTGAAGATAAGGTTGATGATTGAAATCTGCTCCATCGCCGATACATGGAG
ATAAGATTCACCAAAATTCGATCTACTCCACTCCTACTCAACGAAAATAAGACCTGGTATATTTA
GCCTGCTCCACTCCTGCTCAGTGAAGATAAAGCTGATGATTGGAATCTGCTCAATCGCCGGTACA
TGGAGATAAGATTATCCAAAACTCGATCTGCTTCACTCCTGCTCAATGAAGATAAGATCGGGTAT
ATTTAACCTA
Found at i:17202394 original size:21 final size:21
Alignment explanation
Indices: 17202370--17202414 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
17202360 GCTGGCTCAT
*
17202370 CATGTTGTTCTGTGACTCCAG
1 CATGTTGTTCTGGGACTCCAG
* *
17202391 CATGTTTTTCTGGGACTCTAG
1 CATGTTGTTCTGGGACTCCAG
17202412 CAT
1 CAT
17202415 TTGATCATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (21 bp):
CATGTTGTTCTGGGACTCCAG
Found at i:17208820 original size:22 final size:22
Alignment explanation
Indices: 17208792--17208839 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
17208782 AAAAAAATAT
17208792 ATTATAATTAATTTCAAGTAAC
1 ATTATAATTAATTTCAAGTAAC
17208814 ATTATAATTAATTTCAAGTAAC
1 ATTATAATTAATTTCAAGTAAC
17208836 ATTA
1 ATTA
17208840 CTATGAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (22 bp):
ATTATAATTAATTTCAAGTAAC
Found at i:17208848 original size:22 final size:22
Alignment explanation
Indices: 17208792--17208849 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
17208782 AAAAAAATAT
*
17208792 ATTATAATTAATTTCAAGTAAC
1 ATTATAATGAATTTCAAGTAAC
*
17208814 ATTATAATTAATTTCAAGTAAC
1 ATTATAATGAATTTCAAGTAAC
17208836 ATTACT-ATGAATTT
1 ATTA-TAATGAATTT
17208850 ATGTATTTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 33 0.97
23 1 0.03
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (22 bp):
ATTATAATGAATTTCAAGTAAC
Found at i:17212055 original size:17 final size:16
Alignment explanation
Indices: 17212033--17212066 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
17212023 ATCCAAGTCG
17212033 GCTACTTTATTCTCAGT
1 GCTACTTTATTC-CAGT
17212050 GCTACTTTATTCCAGT
1 GCTACTTTATTCCAGT
17212066 G
1 G
17212067 TACAAGCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.44
Consensus pattern (16 bp):
GCTACTTTATTCCAGT
Found at i:17212786 original size:57 final size:57
Alignment explanation
Indices: 17212715--17212830 Score: 232
Period size: 57 Copynumber: 2.0 Consensus size: 57
17212705 TTACATACTT
17212715 AATTTTTAATTATTGTTACTTATAGTGATAATTTCTCTTAATTTTTAAATAATATAC
1 AATTTTTAATTATTGTTACTTATAGTGATAATTTCTCTTAATTTTTAAATAATATAC
17212772 AATTTTTAATTATTGTTACTTATAGTGATAATTTCTCTTAATTTTTAAATAATATAC
1 AATTTTTAATTATTGTTACTTATAGTGATAATTTCTCTTAATTTTTAAATAATATAC
17212829 AA
1 AA
17212831 ATTTGAAACT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (57 bp):
AATTTTTAATTATTGTTACTTATAGTGATAATTTCTCTTAATTTTTAAATAATATAC
Found at i:17212833 original size:29 final size:28
Alignment explanation
Indices: 17212744--17212830 Score: 81
Period size: 27 Copynumber: 3.1 Consensus size: 28
17212734 TTATAGTGAT
17212744 AATTTCTCTTAATTTTTAAATAATATAC
1 AATTTCTCTTAATTTTTAAATAATATAC
* * * *
17212772 AA-TT-T-TTAATTATTGTTACTTATAGTGAT
1 AATTTCTCTTAATT-TT-TAAATAATA-T-AC
17212801 AATTTCTCTTAATTTTTAAATAATATAC
1 AATTTCTCTTAATTTTTAAATAATATAC
17212829 AA
1 AA
17212831 ATTTGAAACT
Statistics
Matches: 44, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 6 0.14
26 3 0.07
27 8 0.18
28 6 0.14
29 4 0.09
30 8 0.18
31 3 0.07
32 6 0.14
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTTCTCTTAATTTTTAAATAATATAC
Found at i:17213791 original size:24 final size:24
Alignment explanation
Indices: 17213744--17213791 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
17213734 TAATATATCA
* *
17213744 ATTTTTTTATATTTTAAGATTTTT
1 ATTTTTTTATATTATAAGAATTTT
17213768 ATTTTTTTA-ATTATAAGAAATTTT
1 ATTTTTTTATATTATAAG-AATTTT
17213792 GCATTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (24 bp):
ATTTTTTTATATTATAAGAATTTT
Found at i:17213812 original size:23 final size:23
Alignment explanation
Indices: 17213747--17213813 Score: 66
Period size: 25 Copynumber: 2.9 Consensus size: 23
17213737 TATATCAATT
* *
17213747 TTTTTATATTTTAAG-ATTTTTA
1 TTTTTATAATTTAAGAATTTTCA
*
17213769 TTTTTTTAATTATAAGAAATTTTGCA
1 TTTTTATAATT-TAAG-AATTTT-CA
17213795 -TTTTATAATTTAAGAATTT
1 TTTTTATAATTTAAGAATTT
17213814 AGATTTATTG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
22 9 0.24
23 9 0.24
24 4 0.11
25 14 0.38
26 1 0.03
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.60
Consensus pattern (23 bp):
TTTTTATAATTTAAGAATTTTCA
Found at i:17215091 original size:6 final size:6
Alignment explanation
Indices: 17215080--17215111 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
17215070 AAGAATTTTT
17215080 ATCCTA ATCCTA ATCCTA ATCCTA AT-CTA ATC
1 ATCCTA ATCCTA ATCCTA ATCCTA ATCCTA ATC
17215112 ACAATCTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (6 bp):
ATCCTA
Found at i:17219382 original size:50 final size:49
Alignment explanation
Indices: 17219267--17219393 Score: 164
Period size: 50 Copynumber: 2.6 Consensus size: 49
17219257 GTACGAATAG
* * ** * *
17219267 TAGCCTGCACATAGTACTACACATGCGACCAATTATCCGGTACACGTAG
1 TAGCCTGCACATAGTACTACACACGTGACCAACCATCCGATACACGTAA
*
17219316 TAGCCTGCACATAGTACTACACACGTGACCTAACCATCTGATACACGTAA
1 TAGCCTGCACATAGTACTACACACGTGACC-AACCATCCGATACACGTAA
**
17219366 TAGCCTGCATTTAGTACTACACACGTGA
1 TAGCCTGCACATAGTACTACACACGTGA
17219394 TCGAAGTTAT
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
49 28 0.41
50 40 0.59
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (49 bp):
TAGCCTGCACATAGTACTACACACGTGACCAACCATCCGATACACGTAA
Found at i:17219447 original size:101 final size:99
Alignment explanation
Indices: 17219267--17219447 Score: 236
Period size: 101 Copynumber: 1.8 Consensus size: 99
17219257 GTACGAATAG
* *
17219267 TAGCCTGCACATAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACATAGTA
1 TAGCCTGCACATAGTACTACACACGCGACCAATTATCCGGTACACATAGTAGCCTGCACATAGTA
*
17219332 CTACACACGTGACCTAACCATCTGATACACGTAA
66 CTACACACGCGACCTAACCATCTGATACACGTAA
** * * * * *
17219366 TAGCCTGCATTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCATAGTAGCCTGCACTTAG
1 TAGCCTGCACATAGTACTACACACGCGA-CCAA-TTATCCGGTACACATAGTAGCCTGCACATAG
* *
17219431 TATTACACATGCGACCT
64 TACTACACACGCGACCT
17219448 CACAATAGAT
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
99 24 0.35
100 3 0.04
101 41 0.60
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (99 bp):
TAGCCTGCACATAGTACTACACACGCGACCAATTATCCGGTACACATAGTAGCCTGCACATAGTA
CTACACACGCGACCTAACCATCTGATACACGTAA
Found at i:17221469 original size:20 final size:18
Alignment explanation
Indices: 17221428--17221471 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
17221418 TCATACAAAT
17221428 TAAGAA-AGAAAAAGAAA
1 TAAGAAGAGAAAAAGAAA
*
17221445 GAAGAAGAGAAATAAGAAAA
1 TAAGAAGAGAAA-AAG-AAA
17221465 TAAGAAG
1 TAAGAAG
17221472 TCACGCAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 5 0.23
18 5 0.23
19 3 0.14
20 9 0.41
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (18 bp):
TAAGAAGAGAAAAAGAAA
Found at i:17229886 original size:23 final size:22
Alignment explanation
Indices: 17229835--17229886 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
17229825 CCTCGTCTTT
*
17229835 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
17229857 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
17229880 TTCTTTT
1 TTCTTTT
17229887 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:17229901 original size:18 final size:18
Alignment explanation
Indices: 17229880--17229918 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
17229870 TTTCTTCAAC
* *
17229880 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
17229898 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
17229916 TTC
1 TTC
17229919 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:17233990 original size:2 final size:2
Alignment explanation
Indices: 17233983--17234047 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
17233973 CAAGAACTAT
17233983 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
17234025 GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA G
17234048 GGAGGGAGGG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17252053 original size:5 final size:5
Alignment explanation
Indices: 17252043--17252079 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
17252033 TATTTGCTTC
17252043 TGATA TGATA TGATA TGATA TGATA TGATA TGATA TG
1 TGATA TGATA TGATA TGATA TGATA TGATA TGATA TG
17252080 TGGTGATGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.22, T:0.41
Consensus pattern (5 bp):
TGATA
Found at i:17253791 original size:18 final size:18
Alignment explanation
Indices: 17253754--17253801 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
17253744 TGTAGTTTTT
*
17253754 AAATTATAAAAATTTTAAA
1 AAATTAT-AAAATTTAAAA
*
17253773 AAATTATAGAATTTAAAA
1 AAATTATAAAATTTAAAA
17253791 AAATTATAAAA
1 AAATTATAAAA
17253802 CATTATAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
AAATTATAAAATTTAAAA
Found at i:17253806 original size:10 final size:9
Alignment explanation
Indices: 17253754--17253808 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
17253744 TGTAGTTTTT
17253754 AAATTATAA
1 AAATTATAA
*
17253763 AAATTTTAAA
1 AAATTAT-AA
*
17253773 AAATTATAG
1 AAATTATAA
* *
17253782 AATTTAAAA
1 AAATTATAA
17253791 AAATTATAA
1 AAATTATAA
17253800 AACATTATA
1 AA-ATTATA
17253809 GAGAAATAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
9 22 0.61
10 14 0.39
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (9 bp):
AAATTATAA
Found at i:17253819 original size:28 final size:27
Alignment explanation
Indices: 17253761--17253827 Score: 66
Period size: 28 Copynumber: 2.5 Consensus size: 27
17253751 TTTAAATTAT
* **
17253761 AAAAATTTTAAAAAATTATAGAATTTAA
1 AAAAATTATAAAAAATTATAGAAAAT-A
*
17253789 AAAAATTATAAAACATTATAGAGAAAT-
1 AAAAATTATAAAAAATTATAGA-AAATA
17253816 AAAAATTA-AAAA
1 AAAAATTATAAAA
17253828 GAAAGTATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
26 4 0.12
27 8 0.24
28 20 0.59
29 2 0.06
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.28
Consensus pattern (27 bp):
AAAAATTATAAAAAATTATAGAAAATA
Found at i:17257174 original size:15 final size:15
Alignment explanation
Indices: 17257154--17257193 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
17257144 ACTCCATTCC
17257154 CTTTAGTCATGGTAA
1 CTTTAGTCATGGTAA
17257169 CTTTAGTCATGGTAA
1 CTTTAGTCATGGTAA
17257184 CTTTAGTCAT
1 CTTTAGTCAT
17257194 TGCTTGAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (15 bp):
CTTTAGTCATGGTAA
Found at i:17261238 original size:26 final size:26
Alignment explanation
Indices: 17261201--17261282 Score: 128
Period size: 26 Copynumber: 3.2 Consensus size: 26
17261191 TGAAATTCCC
*
17261201 ATCATGGAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
*
17261227 ATTATGAAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
* *
17261253 ATCATGGAACATTTACCTAACCTATT
1 ATCATGAAACATTTACCTAACCCATT
17261279 ATCA
1 ATCA
17261283 ATTTGTATCA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (26 bp):
ATCATGAAACATTTACCTAACCCATT
Found at i:17266451 original size:22 final size:22
Alignment explanation
Indices: 17266423--17266465 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
17266413 CTATCTCTAA
17266423 GGTTTAGTACTAACTACAGTAC
1 GGTTTAGTACTAACTACAGTAC
17266445 GGTTTAGTACTAACTACAGTA
1 GGTTTAGTACTAACTACAGTA
17266466 TAGTTCAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (22 bp):
GGTTTAGTACTAACTACAGTAC
Found at i:17266475 original size:22 final size:22
Alignment explanation
Indices: 17266428--17266475 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
17266418 TCTAAGGTTT
* *
17266428 AGTACTAACTACAGTACGGTTT
1 AGTACTAACTACAGTACAGTTC
*
17266450 AGTACTAACTACAGTATAGTTC
1 AGTACTAACTACAGTACAGTTC
17266472 AGTA
1 AGTA
17266476 TATAAAACAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (22 bp):
AGTACTAACTACAGTACAGTTC
Found at i:17269405 original size:26 final size:26
Alignment explanation
Indices: 17269375--17269456 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
17269365 TGAAATTCCC
17269375 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
17269401 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
17269427 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
17269453 ATCA
1 ATCA
17269457 ATTTGTATCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:17269995 original size:31 final size:31
Alignment explanation
Indices: 17269922--17270001 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 31
17269912 AAATTTTAGT
* *
17269922 TTGTTGGATTTTGAAATTATTATGCCTTGAAT
1 TTGTTGGATATTGAAATTATTATG-CTTGAAC
* * *
17269954 TTGTTAGATATTGAATTTATTATG-TTTAAGC
1 TTGTTGGATATTGAAATTATTATGCTTGAA-C
17269985 TTGTTGGATATTGAAAT
1 TTGTTGGATATTGAAAT
17270002 GATTGATAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
30 4 0.10
31 15 0.38
32 21 0.52
ACGTcount: A:0.28, C:0.04, G:0.19, T:0.50
Consensus pattern (31 bp):
TTGTTGGATATTGAAATTATTATGCTTGAAC
Found at i:17278195 original size:15 final size:17
Alignment explanation
Indices: 17278162--17278200 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
17278152 TTTAATTAAT
17278162 AAAAATATAAGAATATA
1 AAAAATATAAGAATATA
*
17278179 AAAAATATTA-AAT-TA
1 AAAAATATAAGAATATA
17278194 AAAAATA
1 AAAAATA
17278201 ATTATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
16 3 0.14
17 9 0.43
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAAATATAAGAATATA
Found at i:17282050 original size:41 final size:41
Alignment explanation
Indices: 17281995--17282191 Score: 292
Period size: 41 Copynumber: 4.8 Consensus size: 41
17281985 GAATGTAATA
* *
17281995 CAGACGTTACGTCTAGCAGGCTTAATGCCGGTGAAGTA-A-TT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG-A-TACATTT
17282036 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
17282077 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* *
17282118 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
* *
17282159 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG
1 CAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTG
17282192 TACTGAATCA
Statistics
Matches: 149, Mismatches: 4, Indels: 6
0.94 0.03 0.04
Matches are distributed among these distances:
39 2 0.01
40 5 0.03
41 142 0.95
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.29
Consensus pattern (41 bp):
CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
Found at i:17282100 original size:82 final size:80
Alignment explanation
Indices: 17281995--17282220 Score: 294
Period size: 82 Copynumber: 2.8 Consensus size: 80
17281985 GAATGTAATA
* *
17281995 CAGACGTTACGTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTAAGTCTAGCAGGCTTA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG-A-TAATTCAGACTTTAAGTCTAGCAGGCTTA
17282060 ATGCCGGTGATACATTT
64 ATGCCGGTGATACATTT
* *
17282077 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTA
1 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATA-A-TTCAGACTTTAAGTCTAGCAGGCTTA
17282142 ATGCCGGTGATACATTT
64 ATGCCGGTGATACATTT
* * * *
17282159 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTGTACTGAA-TCAGGCTTTAAGCCTAGCAGGC
1 CAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTG-A-T-AATTCAGACTTTAAGTCTAGCAGGC
17282221 AAAATGCAGG
Statistics
Matches: 128, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
80 2 0.02
81 5 0.04
82 117 0.91
83 1 0.01
84 2 0.02
85 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (80 bp):
CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATAATTCAGACTTTAAGTCTAGCAGGCTTAAT
GCCGGTGATACATTT
Found at i:17282227 original size:123 final size:123
Alignment explanation
Indices: 17282005--17282233 Score: 306
Period size: 123 Copynumber: 1.9 Consensus size: 123
17281995 CAGACGTTAC
*
17282005 GTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGA
1 GTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGA
* * ** *
17282070 TACATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATAT
66 TACATATCAGACTTTAAGCCTAGCAGGCAAAATGCAGGTGATACATTTCAGACTATAT
*
17282128 GTCTAGCAGGCTTAATGCCGGTG-A-TACATTTCAGACTATATGTCTAGCAGGC-TAAGTGCCGG
1 GTCTAGCAGGCTTAATGCCGGTGAAGTA-A-TTCAGACTATAAGTCTAGCAGGCTTAA-TGCCGG
*
17282190 TG-TAC-TGAATCAGGCTTTAAGCCTAGCAGGCAAAATGCAGGTGA
63 TGATACAT--ATCAGACTTTAAGCCTAGCAGGCAAAATGCAGGTGA
17282234 ATCTGTTTAA
Statistics
Matches: 93, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
121 3 0.03
122 8 0.09
123 82 0.88
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (123 bp):
GTCTAGCAGGCTTAATGCCGGTGAAGTAATTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGA
TACATATCAGACTTTAAGCCTAGCAGGCAAAATGCAGGTGATACATTTCAGACTATAT
Found at i:17285593 original size:8 final size:8
Alignment explanation
Indices: 17285582--17285606 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
17285572 CCACCTACCC
17285582 CCCACTTG
1 CCCACTTG
17285590 CCCACTTG
1 CCCACTTG
17285598 CCCACTTG
1 CCCACTTG
17285606 C
1 C
17285607 GCCGAACACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.52, G:0.12, T:0.24
Consensus pattern (8 bp):
CCCACTTG
Found at i:17286127 original size:13 final size:12
Alignment explanation
Indices: 17286091--17286128 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
17286081 CCTTCCCCCC
17286091 TCCCTTCTCTC-
1 TCCCTTCTCTCT
17286102 TCCCTTCTCTCT
1 TCCCTTCTCTCT
17286114 TCCCTCTCTCTCT
1 TCCCT-TCTCTCT
17286127 TC
1 TC
17286129 TTTTTTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.44
12 5 0.20
13 9 0.36
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (12 bp):
TCCCTTCTCTCT
Found at i:17287437 original size:30 final size:32
Alignment explanation
Indices: 17287377--17287440 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
17287367 CACTTATTTT
17287377 CACCTATGCGGAATGCATACACATAAATATATC
1 CACCTATGCGGAATGCA-ACACATAAATATATC
* * *
17287410 CACCTATGCTGAATGCAACATATATATATAT
1 CACCTATGCGGAATGCAACACATAAATATAT
17287441 ACATATCTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (32 bp):
CACCTATGCGGAATGCAACACATAAATATATC
Found at i:17287700 original size:41 final size:41
Alignment explanation
Indices: 17287655--17287851 Score: 317
Period size: 41 Copynumber: 4.8 Consensus size: 41
17287645 ACCGGCTCTT
*
17287655 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
17287696 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
17287737 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
17287778 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTG-A-AATGTGTCACCGGCATTA
* * * *
17287819 AGCCTGCTAGACGTAAAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
17287852 TAACGATAAA
Statistics
Matches: 148, Mismatches: 4, Indels: 8
0.93 0.03 0.05
Matches are distributed among these distances:
39 2 0.01
40 2 0.01
41 139 0.94
42 2 0.01
43 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:17289403 original size:13 final size:13
Alignment explanation
Indices: 17289385--17289409 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17289375 CCATCGAATG
17289385 CACACAAAATAAA
1 CACACAAAATAAA
17289398 CACACAAAATAA
1 CACACAAAATAA
17289410 TATTAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:17294525 original size:30 final size:32
Alignment explanation
Indices: 17294465--17294527 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
17294455 CACTTATTTT
*
17294465 CACCTATGCGGAATGCATACACATAAATATATC
1 CACCTATGCCGAATGCA-ACACATAAATATATC
* *
17294498 CACCTATGCCGAATGCAACATATATATATA
1 CACCTATGCCGAATGCAACACATAAATATA
17294528 CATATCTATC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.40, C:0.24, G:0.11, T:0.25
Consensus pattern (32 bp):
CACCTATGCCGAATGCAACACATAAATATATC
Done.