Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 59 of 126
Found at i:17354481 original size:29 final size:29
Alignment explanation
Indices: 17354448--17354516 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
17354438 CATCACATGC
* *
17354448 CCTCTCACACGATTGTGTGGCACACACGG
1 CCTCTCACACAATCGTGTGGCACACACGG
17354477 CCTCTCACACAATCGTGTGGCACACACGG
1 CCTCTCACACAATCGTGTGGCACACACGG
*
17354506 CCT-GCACACAA
1 CCTCTCACACAA
17354517 GCCCTTGTGG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
28 7 0.19
29 30 0.81
ACGTcount: A:0.25, C:0.38, G:0.20, T:0.17
Consensus pattern (29 bp):
CCTCTCACACAATCGTGTGGCACACACGG
Found at i:17354901 original size:116 final size:115
Alignment explanation
Indices: 17354698--17354935 Score: 440
Period size: 116 Copynumber: 2.1 Consensus size: 115
17354688 CAAAACTCAT
*
17354698 CCAACAAATATGTCGTCACCGCGACACACTTCCCCCGAAATCAATGCTTACCCAAAGAACACTCG
1 CCAACAAATATGTCGTCACCGCGACACACTTCCCCCGAAATCAATGCTTACCCAAAGAACACTCA
*
17354763 CACGAAATAACCATGAGGCTTGCGGATTGCCAAACGTACTGTAACTTTCC
66 CACGAAATAACCATGAGGCTTGCGGATTGCCAAACGTACTGTAACTGTCC
17354813 CCAACAAATATGTCGTCACCCGCGACACACTTCCCCCGAAATCAATGCTTACCCAAAGAACACTC
1 CCAACAAATATGTCGTCA-CCGCGACACACTTCCCCCGAAATCAATGCTTACCCAAAGAACACTC
17354878 ACACGAAATAACCATGAGGCTTGCGGATTGCCAAACGTACTGTAACTGTCC
65 ACACGAAATAACCATGAGGCTTGCGGATTGCCAAACGTACTGTAACTGTCC
*
17354929 CCTACAA
1 CCAACAA
17354936 CGAATCAACA
Statistics
Matches: 119, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
115 18 0.15
116 101 0.85
ACGTcount: A:0.33, C:0.33, G:0.15, T:0.19
Consensus pattern (115 bp):
CCAACAAATATGTCGTCACCGCGACACACTTCCCCCGAAATCAATGCTTACCCAAAGAACACTCA
CACGAAATAACCATGAGGCTTGCGGATTGCCAAACGTACTGTAACTGTCC
Found at i:17356950 original size:30 final size:30
Alignment explanation
Indices: 17356914--17356973 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
17356904 CCAAGGAGTT
17356914 ACATTGGATGCTGAAAGGTTAGCTCAGATC
1 ACATTGGATGCTGAAAGGTTAGCTCAGATC
*
17356944 ACATTGGGTGCTGAAAGGTTAGCTCAGATC
1 ACATTGGATGCTGAAAGGTTAGCTCAGATC
17356974 CTGCTGCAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (30 bp):
ACATTGGATGCTGAAAGGTTAGCTCAGATC
Found at i:17361486 original size:6 final size:6
Alignment explanation
Indices: 17361468--17361545 Score: 83
Period size: 6 Copynumber: 13.0 Consensus size: 6
17361458 TTAAATTGAT
17361468 TTTAAA TTT--A TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTAATTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAA--A
*
17361515 TTTAAA TTTAAA TTTAAA TTAAAA TTATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA
17361546 ACAAATTTAA
Statistics
Matches: 62, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
4 6 0.10
5 2 0.03
6 43 0.69
7 5 0.08
8 6 0.10
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:17361486 original size:17 final size:17
Alignment explanation
Indices: 17361468--17361530 Score: 83
Period size: 17 Copynumber: 3.6 Consensus size: 17
17361458 TTAAATTGAT
17361468 TTTAAATTTAT-TTAAA
1 TTTAAATTTATCTTAAA
17361484 TTTAAATTTATCTTAAA
1 TTTAAATTTATCTTAAA
*
17361501 TTTAAATTTAATTATTTAAA
1 TTTAAATTT-A-T-CTTAAA
17361521 TTTAAATTTA
1 TTTAAATTTA
17361531 AATTAAAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
16 11 0.26
17 14 0.33
18 1 0.02
19 2 0.05
20 14 0.33
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATCTTAAA
Found at i:17361513 original size:11 final size:11
Alignment explanation
Indices: 17361458--17361537 Score: 60
Period size: 11 Copynumber: 7.5 Consensus size: 11
17361448 AATTTAGAGG
* *
17361458 TTAAATTGATT
1 TTAAATTTAAT
17361469 TTAAATTT-AT
1 TTAAATTTAAT
17361479 TTAAATTTAAAT
1 TTAAATTT-AAT
** *
17361491 TTATCTTAAAT
1 TTAAATTTAAT
17361502 TTAAATTTAA-
1 TTAAATTTAAT
17361512 TT--ATTTAAAT
1 TTAAATTT-AAT
*
17361522 TTAAATTTAAA
1 TTAAATTTAAT
17361533 TTAAA
1 TTAAA
17361538 ATTATAAAAC
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
8 4 0.07
9 2 0.04
10 13 0.24
11 24 0.44
12 11 0.20
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:17363480 original size:28 final size:30
Alignment explanation
Indices: 17363443--17363534 Score: 102
Period size: 28 Copynumber: 3.1 Consensus size: 30
17363433 CAAATAGTCC
*
17363443 AAAAATTACATTTTGACCCC-AAA-TTTCA
1 AAAAATTACATTTTGACCCCGAAACTTCCA
* *
17363471 AGAAATTACATTCTGACCCCGAAACTTCCA
1 AAAAATTACATTTTGACCCCGAAACTTCCA
17363501 AAAAATTACCATTTT-ACCCCCG-AACTTTCCA
1 AAAAATTA-CATTTTGA-CCCCGAAAC-TTCCA
17363532 AAA
1 AAA
17363535 TTCCATTTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
28 18 0.33
29 3 0.06
30 15 0.28
31 18 0.33
ACGTcount: A:0.40, C:0.27, G:0.05, T:0.27
Consensus pattern (30 bp):
AAAAATTACATTTTGACCCCGAAACTTCCA
Found at i:17363509 original size:30 final size:29
Alignment explanation
Indices: 17363443--17363534 Score: 91
Period size: 31 Copynumber: 3.1 Consensus size: 29
17363433 CAAATAGTCC
*
17363443 AAAAATTACATTTTGACCCC-AAA-TTTCA
1 AAAAATTACA-TTTGACCCCGAAACTTCCA
*
17363471 AGAAATTACATTCTGACCCCGAAACTTCCA
1 AAAAATTACATT-TGACCCCGAAACTTCCA
*
17363501 AAAAATTACCATTTTACCCCCG-AACTTTCCA
1 AAAAATTA-CATTTGA-CCCCGAAAC-TTCCA
17363532 AAA
1 AAA
17363535 TTCCATTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
27 2 0.04
28 16 0.30
29 3 0.06
30 16 0.30
31 17 0.31
ACGTcount: A:0.40, C:0.27, G:0.05, T:0.27
Consensus pattern (29 bp):
AAAAATTACATTTGACCCCGAAACTTCCA
Found at i:17363561 original size:29 final size:30
Alignment explanation
Indices: 17363528--17363618 Score: 84
Period size: 30 Copynumber: 3.1 Consensus size: 30
17363518 CCCCGAACTT
17363528 TCCAAAATTCCATTTTTAACCCCGATTTCA
1 TCCAAAATTCCATTTTTAACCCCGATTTCA
**
17363558 -CCAAAAATTACCA-TTTT-ACCCTCG-GGT-A
1 TCC-AAAATT-CCATTTTTAACCC-CGATTTCA
*
17363586 TCCAAAAGTCCCATTTTTAACCCCGATTTCA
1 TCCAAAA-TTCCATTTTTAACCCCGATTTCA
17363617 TC
1 TC
17363619 GTTTCTTCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 17
0.68 0.07 0.25
Matches are distributed among these distances:
28 8 0.17
29 16 0.34
30 17 0.36
31 6 0.13
ACGTcount: A:0.30, C:0.31, G:0.07, T:0.33
Consensus pattern (30 bp):
TCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:17363564 original size:59 final size:59
Alignment explanation
Indices: 17363501--17363616 Score: 171
Period size: 59 Copynumber: 2.0 Consensus size: 59
17363491 GAAACTTCCA
* *
17363501 AAAAATTACCATTTTACCCCCGAACTTTCCAAAA-TTCCATTTTTAACCCCGATTTCACC
1 AAAAATTACCATTTTACCCCCG-ACTATCCAAAAGTCCCATTTTTAACCCCGATTTCACC
* **
17363560 AAAAATTACCATTTTACCCTCGGGTATCCAAAAGTCCCATTTTTAACCCCGATTTCA
1 AAAAATTACCATTTTACCCCCGACTATCCAAAAGTCCCATTTTTAACCCCGATTTCA
17363617 TCGTTTCTTC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 8 0.16
59 43 0.84
ACGTcount: A:0.32, C:0.30, G:0.06, T:0.32
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCCGACTATCCAAAAGTCCCATTTTTAACCCCGATTTCACC
Found at i:17365141 original size:34 final size:34
Alignment explanation
Indices: 17365075--17365141 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
17365065 ACTAAATTCA
* *** *
17365075 AAATCCTAAACTCTAACCCAAAATTTAGAACCCC
1 AAATCCTAAACTCAAACCCAAAACCCAAAACCCC
17365109 AAATCCTAAACTCAAACCCAAAACCCAAAACCC
1 AAATCCTAAACTCAAACCCAAAACCCAAAACCC
17365142 TTGAACCCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.48, C:0.36, G:0.01, T:0.15
Consensus pattern (34 bp):
AAATCCTAAACTCAAACCCAAAACCCAAAACCCC
Found at i:17365232 original size:19 final size:21
Alignment explanation
Indices: 17365208--17365246 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
17365198 AACATAAAAT
17365208 CCTAAACC-TAAA-CTCGAAC
1 CCTAAACCTTAAATCTCGAAC
17365227 CCTAAACCTTAAATCTCGAA
1 CCTAAACCTTAAATCTCGAA
17365247 TCCAAACTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 4 0.22
21 6 0.33
ACGTcount: A:0.41, C:0.33, G:0.05, T:0.21
Consensus pattern (21 bp):
CCTAAACCTTAAATCTCGAAC
Found at i:17365424 original size:26 final size:23
Alignment explanation
Indices: 17365361--17365424 Score: 65
Period size: 26 Copynumber: 2.6 Consensus size: 23
17365351 GCACAAAAAT
*
17365361 AAAAAAAAATATTAACTTTTGAA
1 AAAAAAAAATATTAAATTTTGAA
*
17365384 AAAAAGAAAATTATTAAAATTTTTAA
1 AAAAA-AAAA-TATT-AAATTTTGAA
17365410 AAGAAAAAAGATATT
1 AA-AAAAAA-ATATT
17365425 TATTTATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
23 5 0.15
24 4 0.12
25 4 0.12
26 17 0.50
27 4 0.12
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (23 bp):
AAAAAAAAATATTAAATTTTGAA
Found at i:17366772 original size:30 final size:30
Alignment explanation
Indices: 17366738--17367091 Score: 378
Period size: 30 Copynumber: 11.9 Consensus size: 30
17366728 TTTAAGGTCG
* * *
17366738 AAAATGTGATTTTAGAGAAGTTTAGGGGTC
1 AAAATGTAATTTTAGAAAAGTTTAGGGGTT
* *
17366768 AAAATGCAATTTTAGAAAAGTTTAGGGGTAA
1 AAAATGTAATTTTAGAAAAGTTTAGGGGT-T
* *
17366799 AAAAT-TCAATTTTGGAAAAGTTTAAGGGTT
1 AAAATGT-AATTTTAGAAAAGTTTAGGGGTT
* ** *
17366829 AAAGTGTAATTTTAGGGAAGCTT-GGGG-T
1 AAAATGTAATTTTAGAAAAGTTTAGGGGTT
* * *
17366857 CAAATATAATTTTGGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTAGAAAAGTTTAGGGGTT
*
17366887 AAAATGTAATTTTAGAAAAATTTAGGGGTT
1 AAAATGTAATTTTAGAAAAGTTTAGGGGTT
* * *
17366917 AAAATGCAATTTTGGAAAAGTTTAGAGGTT
1 AAAATGTAATTTTAGAAAAGTTTAGGGGTT
*
17366947 AACATGTAATTTT-GAAAAAGTTTAGGGGTT
1 AAAATGTAATTTTAG-AAAAGTTTAGGGGTT
*
17366977 AAAATGTAATTTTGGAAAAGTTTA-GGGTT
1 AAAATGTAATTTTAGAAAAGTTTAGGGGTT
* * *
17367006 AAAATATAATTTTAGAAAAGTTTAGAGGTC
1 AAAATGTAATTTTAGAAAAGTTTAGGGGTT
* * *
17367036 AAAATATAATTTT-GAAAAATTTAAGGGTT
1 AAAATGTAATTTTAGAAAAGTTTAGGGGTT
* * *
17367065 AAAATGCAATTTTGGAGAAGTTTAGGG
1 AAAATGTAATTTTAGAAAAGTTTAGGG
17367092 TCAAAATATT
Statistics
Matches: 269, Mismatches: 46, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
28 17 0.06
29 58 0.22
30 167 0.62
31 27 0.10
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (30 bp):
AAAATGTAATTTTAGAAAAGTTTAGGGGTT
Found at i:17366800 original size:89 final size:85
Alignment explanation
Indices: 17366673--17367115 Score: 356
Period size: 89 Copynumber: 5.0 Consensus size: 85
17366663 GAGGAATTGG
* * * *
17366673 GGGGTCAAATTGAAATTTTTGGAAAA-TTT-GGGATTAAAATCAAACTTTTGGAAAATTTAAGGT
1 GGGGTCAAAATGTAA-TTTT-GAAAAGTTTAGGG-GTAAAATC-AA-TTTTGGAAAATTTAGGGT
* * *
17366736 CGAAAATGTGATTTTAGAGAAGTTTA
61 -TAAAATGTAATTTTAGAAAAGTTTA
*
17366762 GGGGTCAAAATGCAATTTTAGAAAAGTTTAGGGGTAAAAAATTCAATTTTGGAAAAGTTTAAGGG
1 GGGGTCAAAATGTAATTTT-GAAAAGTTTAGGGGT--AAAA-TCAATTTTGGAAAA-TTT-AGGG
* ** *
17366827 TTAAAGTGTAATTTTAGGGAAGCTT-
60 TTAAAATGTAATTTTAGAAAAGTTTA
* * *
17366852 GGGGTC-AAATATAATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTAGAAAAATTTAGGGGT
1 GGGGTCAAAATGTAATTTT-GAAAAGTTTAGGGG-TAAAAT-CAATTTT-GGAAAATTTA-GGGT
* *
17366916 TAAAATGCAATTTTGGAAAAGTTTA
61 TAAAATGTAATTTTAGAAAAGTTTA
* * * *
17366941 GAGGTTAACATGTAATTTTGAAAAAGTTTAGGGGTTAAAATGTAATTTTGGAAAAGTTTAGGGTT
1 GGGGTCAAAATGTAATTTTG-AAAAGTTTAGGGG-TAAAAT-CAATTTTGGAAAA-TTTAGGGTT
*
17367006 AAAATATAATTTTAGAAAAGTTTA
62 AAAATGTAATTTTAGAAAAGTTTA
* * * * * *
17367030 GAGGTCAAAATATAATTTTGAAAAATTTAAGGGTTAAAATGCAATTTTGGAGAAGTTTAGGGTCA
1 GGGGTCAAAATGTAATTTTGAAAAGTTT-AGGGGTAAAAT-CAATTTTGGA-AAATTTAGGGTTA
* *
17367095 AAATATTATTTCTA-AAAAGTT
63 AAATGTAATTT-TAGAAAAGTT
17367116 CAAGGACCTT
Statistics
Matches: 298, Mismatches: 38, Indels: 37
0.80 0.10 0.10
Matches are distributed among these distances:
87 2 0.01
88 93 0.31
89 107 0.36
90 62 0.21
91 28 0.09
92 6 0.02
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.35
Consensus pattern (85 bp):
GGGGTCAAAATGTAATTTTGAAAAGTTTAGGGGTAAAATCAATTTTGGAAAATTTAGGGTTAAAA
TGTAATTTTAGAAAAGTTTA
Found at i:17366869 original size:119 final size:116
Alignment explanation
Indices: 17366746--17367105 Score: 413
Period size: 119 Copynumber: 3.0 Consensus size: 116
17366736 CGAAAATGTG
* * * *
17366746 ATTTTAGAGAAGTTTAGGGGTCAAAATGCAATTTTAGAAAAGTTTAGGGGTAAAAAATTCAATTT
1 ATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGGT-AAAAATTCAATTT
*
17366811 TGGAAAAGTTTAAGGGTTAAAGTGTAATTTTAGGGAAGCTTGGGGTCAAATATA
65 TGGAAAAGTTTAAGGGTTAAA-TGTAATTTT-GGGAAGTTTGGGGTCAAATATA
* * *
17366865 ATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTAGAAAAATTTAGGGGTTAAAATGCAATTTT
1 ATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGGTAAAAATTCAATTTT
** * *
17366930 GGAAAAGTTT-AGAGGTTAACATGTAATTTTGAAAAAGTTTAGGGGTTAAAATGTA
66 GGAAAAGTTTAAG-GGTTAA-ATGTAATTTTG-GGAAGTTT-GGGG-TCAAATATA
* * *
17366985 ATTTTGGAAAAGTTTA-GGGTTAAAATATAATTTTAGAAAAGTTTAGAGGTCAAAATAT-AATTT
1 ATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGGTAAAAAT-TCAATTT
* * * *
17367048 T-GAAAAATTTAAGGGTTAAAATGCAATTTTGGAGAAGTTTAGGGTCAAAATATT
65 TGGAAAAGTTTAAGGGTT-AAATGTAATTTTGG-GAAGTTTGGGGTC-AAATATA
17367102 ATTT
1 ATTT
17367106 CTAAAAAGTT
Statistics
Matches: 206, Mismatches: 25, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
116 1 0.00
117 15 0.07
118 70 0.34
119 97 0.47
120 23 0.11
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (116 bp):
ATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGGTAAAAATTCAATTTT
GGAAAAGTTTAAGGGTTAAATGTAATTTTGGGAAGTTTGGGGTCAAATATA
Found at i:17379920 original size:28 final size:28
Alignment explanation
Indices: 17379889--17380214 Score: 141
Period size: 29 Copynumber: 11.2 Consensus size: 28
17379879 TGAAAATATG
*
17379889 ATTTTGGAAA-TTTGAGGGT-AAAATGGTA
1 ATTTTGGAAAGTTCG-GGGTCAAAAT-GTA
* * * * *
17379917 ATTTTTGATA-TTCGTGG-AAAAATGTG
1 ATTTTGGAAAGTTCGGGGTCAAAATGTA
* *
17379943 ATTTTGGAAAAGTTTGGGGTCAAAATATA
1 ATTTTGG-AAAGTTCGGGGTCAAAATGTA
*
17379972 ATTTTGGAAAGTTCGAGGGTCAAAATATGA
1 ATTTTGGAAAGTTCG-GGGTCAAAATGT-A
*
17380002 CTTTTGTG-AAG-TCGAGGGTCAAAATGTA
1 ATTTTG-GAAAGTTCG-GGGTCAAAATGTA
* * *
17380030 ATTTT-TATGAAGTTCGAGGATTAAAATGTA
1 ATTTTGGA--AAGTTCG-GGGTCAAAATGTA
* * ** *
17380060 TTTTTTGTAAAGTTTAAGGGTAAAAATGTGA
1 -ATTTTGGAAAG-TTCGGGGTCAAAATGT-A
* * *
17380091 TTTTTGG-GAGTTTGAGGGTCAAAATGTA
1 ATTTTGGAAAGTTCG-GGGTCAAAATGTA
* * *
17380119 ATTTTGGTGAAGTTTGGGGAGGT-AAAATGCA
1 ATTTTGG-AAAG-TT-CGG-GGTCAAAATGTA
* * *
17380150 AATTTGGAAAAGTT-TGGGACGAAAATGTA
1 ATTTTGG-AAAGTTCGGGGTC-AAAATGTA
17380179 ATTTTGGAAAAGTTCAGGGGTCAAAATGTA
1 ATTTTGG-AAAGTTC-GGGGTCAAAATGTA
17380209 ATTTTG
1 ATTTTG
17380215 AGAAGTTAGA
Statistics
Matches: 231, Mismatches: 42, Indels: 48
0.72 0.13 0.15
Matches are distributed among these distances:
26 8 0.03
27 11 0.05
28 38 0.16
29 76 0.33
30 61 0.26
31 31 0.13
32 6 0.03
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.36
Consensus pattern (28 bp):
ATTTTGGAAAGTTCGGGGTCAAAATGTA
Found at i:17380056 original size:30 final size:30
Alignment explanation
Indices: 17379959--17380132 Score: 167
Period size: 29 Copynumber: 5.9 Consensus size: 30
17379949 GAAAAGTTTG
*
17379959 GGGTCAAAATATAA-TTTTG-GAAAGTTCGA
1 GGGTCAAAATGTAATTTTTGTG-AAGTTCGA
* * *
17379988 GGGTCAAAATATGACTTTTGTGAAG-TCGA
1 GGGTCAAAATGTAATTTTTGTGAAGTTCGA
*
17380017 GGGTCAAAATGTAATTTTTATGAAGTTCGA
1 GGGTCAAAATGTAATTTTTGTGAAGTTCGA
* * * * **
17380047 GGATTAAAATGTATTTTTTGTAAAGTTTAA
1 GGGTCAAAATGTAATTTTTGTGAAGTTCGA
* * * *
17380077 GGGTAAAAATGTGATTTTTG-GGAGTTTGA
1 GGGTCAAAATGTAATTTTTGTGAAGTTCGA
*
17380106 GGGTCAAAATGTAATTTTGGTGAAGTT
1 GGGTCAAAATGTAATTTTTGTGAAGTT
17380133 TGGGGAGGTA
Statistics
Matches: 118, Mismatches: 23, Indels: 7
0.80 0.16 0.05
Matches are distributed among these distances:
29 61 0.52
30 56 0.47
31 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.37
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTTGTGAAGTTCGA
Found at i:17380066 original size:59 final size:58
Alignment explanation
Indices: 17379959--17380131 Score: 150
Period size: 59 Copynumber: 2.9 Consensus size: 58
17379949 GAAAAGTTTG
* * * * * * *
17379959 GGGTCAAAATATAA-TTTTGGAAAGTTCGAGGGTCAAAATATGACTTTTGTGAAGTCGA
1 GGGTAAAAATGTAATTTTTGG-AAGTTCGAGGATCAAAATGTAATTTTTGTGAAGTCAA
* * * * * *
17380017 GGGTCAAAATGTAATTTTTATGAAGTTCGAGGATTAAAATGTATTTTTTGTAAAGTTTAA
1 GGGTAAAAATGTAATTTTT-GGAAGTTCGAGGATCAAAATGTAATTTTTGTGAAG-TCAA
* * * * *
17380077 GGGTAAAAATGTGATTTTTGGGAGTTTGAGGGTCAAAATGTAATTTTGGTGAAGT
1 GGGTAAAAATGTAATTTTTGGAAGTTCGAGGATCAAAATGTAATTTTTGTGAAGT
17380132 TTGGGGAGGT
Statistics
Matches: 91, Mismatches: 21, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
58 14 0.15
59 57 0.63
60 20 0.22
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (58 bp):
GGGTAAAAATGTAATTTTTGGAAGTTCGAGGATCAAAATGTAATTTTTGTGAAGTCAA
Found at i:17380147 original size:31 final size:29
Alignment explanation
Indices: 17380111--17380214 Score: 102
Period size: 31 Copynumber: 3.5 Consensus size: 29
17380101 TTTGAGGGTC
** *
17380111 AAAATGTAATTTTGGTGAAGTTTGGGGAGG
1 AAAATGTAATTTTGGAAAAGTTT-GGGACG
* *
17380141 TAAAATGCAAATTTGGAAAAGTTTGGGACG
1 -AAAATGTAATTTTGGAAAAGTTTGGGACG
* *
17380171 AAAATGTAATTTTGGAAAAGTTCAGGGGTC-
1 AAAATGTAATTTTGGAAAAGTT--TGGGACG
17380201 AAAATGTAATTTTG
1 AAAATGTAATTTTG
17380215 AGAAGTTAGA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
29 20 0.32
30 19 0.31
31 23 0.37
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.32
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAAGTTTGGGACG
Found at i:17380207 original size:30 final size:29
Alignment explanation
Indices: 17379935--17380214 Score: 146
Period size: 29 Copynumber: 9.5 Consensus size: 29
17379925 TATTCGTGGA
* *
17379935 AAAATGTGATTTTGGAAAAGTTTGGGGTC
1 AAAATGTAATTTTGGAAAAGTTCGGGGTC
*
17379964 AAAATATAATTTTGG-AAAGTTCGAGGGTC
1 AAAATGTAATTTTGGAAAAGTTCG-GGGTC
* *
17379993 AAAATATGACTTTTGTG--AAG-TCGAGGGTC
1 AAAATGT-AATTTTG-GAAAAGTTCG-GGGTC
* * * *
17380022 AAAATGTAATTTT-TATGAAGTTCGAGGATT
1 AAAATGTAATTTTGGA-AAAGTTCG-GGGTC
* * * ** *
17380052 AAAATGTATTTTTTGTAAAGTTTAAGGGTA
1 AAAATGTAATTTTGGAAAAG-TTCGGGGTC
* * *
17380082 AAAATGTGATTTTTGG--GAGTTTGAGGGTC
1 AAAATGT-AATTTTGGAAAAGTTCG-GGGTC
** *
17380111 AAAATGTAATTTTGGTGAAGTTTGGGGAGGT-
1 AAAATGTAATTTTGGAAAAG-TT-CGG-GGTC
* * * *
17380142 AAAATGCAAATTTGGAAAAGTT-TGGGAC
1 AAAATGTAATTTTGGAAAAGTTCGGGGTC
17380170 GAAAATGTAATTTTGGAAAAGTTCAGGGGTC
1 -AAAATGTAATTTTGGAAAAGTTC-GGGGTC
17380201 AAAATGTAATTTTG
1 AAAATGTAATTTTG
17380215 AGAAGTTAGA
Statistics
Matches: 196, Mismatches: 35, Indels: 39
0.73 0.13 0.14
Matches are distributed among these distances:
27 2 0.01
28 22 0.11
29 76 0.39
30 59 0.30
31 33 0.17
32 4 0.02
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAAGTTCGGGGTC
Found at i:17380901 original size:3 final size:3
Alignment explanation
Indices: 17380895--17380935 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
17380885 TTTTAGATCG
17380895 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
17380936 AAAAATAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:17382444 original size:50 final size:50
Alignment explanation
Indices: 17382375--17382860 Score: 252
Period size: 50 Copynumber: 9.8 Consensus size: 50
17382365 TTGGATTCGT
* * *
17382375 CGTTGCGACCTCAATCTTTCCCATCACATCTTTTTAGGTACCGGGTTCTC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAGGTACCGGGTTCTC
* ** * *
17382425 CGTTGCGGCTTCAACCTTTCCC-TCTGTATC-TTCATGGTACCGGGTTCGT-
1 CGTTGCGGCCTCAACCTTTCCCATC-ACATCTTTTAAGGTACCGGGTTC-TC
* * * *
17382474 CGTTGCAGCCTTAACCTTTCCCATCACATCTTTTAAGATACCGGATT-TGC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAGGTACCGGGTTCT-C
** ** * * * **
17382524 CGTCACAACCTCAATCC-TTCCC-T-TCATCTCTTCATGGTACTAGGTTCGT-
1 CGTTGCGGCCTCAA-CCTTTCCCATCACATCT-TTTAAGGTACCGGGTTC-TC
* * * *
17382573 CGTTGCAGCCTCAATCTTTCCCATCACATCTTCTT-AGGTACTGGGTTCAC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTT-TTAAGGTACCGGGTTCTC
* * * * **
17382623 CGTTGCGGCCTCTACCTTTCCTATCACATCTTTTAAGGTATCGGATTAGC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAGGTACCGGGTTCTC
* * * * ** *
17382673 CGTCGCGGCCTCAATCC-TT-CC-T-TCATCTCTTCATGGTACTAGGTTCAC
1 CGTTGCGGCCTCAA-CCTTTCCCATCACATCT-TTTAAGGTACCGGGTTCTC
* * * * *
17382721 CGTTGCGGCCTCATCCTTTCCCATCACGTCTTCTAAGGTACCAGATT-TGC
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAGGTACCGGGTTCT-C
* ** * * * * *
17382771 CGTCGCGGCCTCAATCC-TTCCTTTCATCTTCATGGTTCAGGTA---GGTTTTT
1 CGTTGCGGCCTCAA-CCTTTCCCATCA-CATC-T-TTTAAGGTACCGGGTTCTC
*
17382821 CGTTGCGGCCTCAACCTTTCCCTTCACATCTTTTAAGGTA
1 CGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAGGTA
17382861 TGGATTCATT
Statistics
Matches: 324, Mismatches: 83, Indels: 61
0.69 0.18 0.13
Matches are distributed among these distances:
47 14 0.04
48 34 0.10
49 75 0.23
50 173 0.53
51 21 0.06
52 1 0.00
53 6 0.02
ACGTcount: A:0.16, C:0.32, G:0.17, T:0.35
Consensus pattern (50 bp):
CGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAGGTACCGGGTTCTC
Found at i:17382457 original size:99 final size:97
Alignment explanation
Indices: 17382325--17382643 Score: 347
Period size: 99 Copynumber: 3.2 Consensus size: 97
17382315 ATTAGGTTTG
* *
17382325 CCGTTGCAGCCTCAACCTTTCCCTTTATGTCTTCATGGTATTGGATTCGTCGTTGC-GACCTCAA
1 CCGTTGCAGCCTCAACCTTTCCC-TTATATCTTCATGGTATAGG-TTCGTCGTTGCAG-CCTCAA
17382389 TCTTTCCCATCACATCTTTTTAGGTACCGGGTTCT
63 TCTTTCCCATCACATCTTTTTAGGTACCGGGTTCT
* * * ** * *
17382424 CCGTTGCGGCTTCAACCTTTCCCTCTGTATCTTCATGGTACCGGGTTCGTCGTTGCAGCCTTAAC
1 CCGTTGCAGCCTCAACCTTTCCCT-TATATCTTCATGGTA-TAGGTTCGTCGTTGCAGCCTCAAT
* * *
17382489 CTTTCCCATCACATCTTTTAAGATACCGGATT-T
64 CTTTCCCATCACATCTTTTTAGGTACCGGGTTCT
** * *
17382522 GCCGTCACAACCTCAATCC-TTCCCTTCATCTCTTCATGGTACTAGGTTCGTCGTTGCAGCCTCA
1 -CCGTTGCAGCCTCAA-CCTTTCCCTT-ATATCTTCATGGTA-TAGGTTCGTCGTTGCAGCCTCA
* * *
17382586 ATCTTTCCCATCACATCTTCTTAGGTACTGGGTTCA
62 ATCTTTCCCATCACATCTTTTTAGGTACCGGGTTCT
* *
17382622 CCGTTGCGGCCTCTACCTTTCC
1 CCGTTGCAGCCTCAACCTTTCC
17382644 TATCACATCT
Statistics
Matches: 179, Mismatches: 33, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
98 5 0.03
99 169 0.94
100 5 0.03
ACGTcount: A:0.16, C:0.32, G:0.17, T:0.36
Consensus pattern (97 bp):
CCGTTGCAGCCTCAACCTTTCCCTTATATCTTCATGGTATAGGTTCGTCGTTGCAGCCTCAATCT
TTCCCATCACATCTTTTTAGGTACCGGGTTCT
Found at i:17382490 original size:49 final size:48
Alignment explanation
Indices: 17382326--17382643 Score: 162
Period size: 50 Copynumber: 6.4 Consensus size: 48
17382316 TTAGGTTTGC
* * ** *
17382326 CGTTGCAGCCTCAACCTTTCCCTTTATGTCTTCATGGTATTGGATTCGT
1 CGTTGC-GCCTCAACCTTTCCCTCTATATCTTCATGGTACCGGGTTCGT
* * **
17382375 CGTTGCGACCTCAATCTTTCCCATC-ACATCTTTTTAGGTACCGGGTTC-T
1 CGTTGCG-CCTCAACCTTTCCC-TCTATATCTTCAT-GGTACCGGGTTCGT
* *
17382424 CCGTTGCGGCTTCAACCTTTCCCTCTGTATCTTCATGGTACCGGGTTCGT
1 -CGTTGC-GCCTCAACCTTTCCCTCTATATCTTCATGGTACCGGGTTCGT
* * * * * * * *
17382474 CGTTGCAGCCTTAACCTTTCCCATC-ACATCTTTTAAGATACCGGATTTGC
1 CGTTGC-GCCTCAACCTTTCCC-TCTATATC-TTCATGGTACCGGGTTCGT
** * * **
17382524 CGTCACAACCTCAATCC-TTCCCT-TCATCTCTTCATGGTACTAGGTTCGT
1 CGTTGC-GCCTCAA-CCTTTCCCTCT-ATATCTTCATGGTACCGGGTTCGT
* * * * **
17382573 CGTTGCAGCCTCAATCTTTCCCATC-ACATCTTCTTAGGTACTGGGTTCAC
1 CGTTGC-GCCTCAACCTTTCCC-TCTATATCTTCAT-GGTACCGGGTTCGT
*
17382623 CGTTGCGGCCTCTACCTTTCC
1 CGTTGC-GCCTCAACCTTTCC
17382644 TATCACATCT
Statistics
Matches: 200, Mismatches: 53, Indels: 31
0.70 0.19 0.11
Matches are distributed among these distances:
48 2 0.01
49 97 0.49
50 98 0.49
51 3 0.01
ACGTcount: A:0.16, C:0.32, G:0.17, T:0.36
Consensus pattern (48 bp):
CGTTGCGCCTCAACCTTTCCCTCTATATCTTCATGGTACCGGGTTCGT
Found at i:17382594 original size:148 final size:148
Alignment explanation
Indices: 17382418--17382762 Score: 421
Period size: 148 Copynumber: 2.3 Consensus size: 148
17382408 TTAGGTACCG
* * * ** **
17382418 GGTTCTCCGTTGCGGCTTCAACCTTTCCC-TCTGTATCTTCAT-GGTACCGGGTTCGTCGTTGCA
1 GGTTCACCGTTGCGGCCTCAATCTTTCCCATC-ACATCTTCATAGGTACCGGGTTCACCGTTGCA
*
17382481 GCCT-TAACCTTTCCCATCACATCTTTTAAGATACCGGATTTGCCGTCACAACCTCAATCCTTCC
65 GCCTCT-ACCTTTCCCATCACATCTTTTAAGATACCGGATTAGCCGTCACAACCTCAATCCTT-C
17382545 CTTCATCTCTTCATGGTACTA
128 CTTCATCTCTTCATGGTACTA
** * * * *
17382566 GGTTCGTCGTTGCAGCCTCAATCTTTCCCATCACATCTTCTTAGGTACTGGGTTCACCGTTGCGG
1 GGTTCACCGTTGCGGCCTCAATCTTTCCCATCACATCTTCATAGGTACCGGGTTCACCGTTGCAG
* * * * **
17382631 CCTCTACCTTTCCTATCACATCTTTTAAGGTATCGGATTAGCCGTCGCGGCCTCAATCCTTCCTT
66 CCTCTACCTTTCCCATCACATCTTTTAAGATACCGGATTAGCCGTCACAACCTCAATCCTTCCTT
17382696 CATCTCTTCATGGTACTA
131 CATCTCTTCATGGTACTA
*
17382714 GGTTCACCGTTGCGGCCTC-ATCCTTTCCCATCACGTCTTC-TAAGGTACC
1 GGTTCACCGTTGCGGCCTCAAT-CTTTCCCATCACATCTTCAT-AGGTACC
17382763 AGATTTGCCG
Statistics
Matches: 168, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
147 3 0.02
148 92 0.55
149 72 0.43
150 1 0.01
ACGTcount: A:0.16, C:0.32, G:0.17, T:0.34
Consensus pattern (148 bp):
GGTTCACCGTTGCGGCCTCAATCTTTCCCATCACATCTTCATAGGTACCGGGTTCACCGTTGCAG
CCTCTACCTTTCCCATCACATCTTTTAAGATACCGGATTAGCCGTCACAACCTCAATCCTTCCTT
CATCTCTTCATGGTACTA
Found at i:17382720 original size:98 final size:96
Alignment explanation
Indices: 17382599--17382866 Score: 317
Period size: 98 Copynumber: 2.7 Consensus size: 96
17382589 TTTCCCATCA
* *
17382599 CATCTTCTTAGGTACTGGGTTCACCGTTGCGGCCTCTACCTTTCCTATCACATCTTTTAAGGTAT
1 CATCTTCAT-GGTACTAGGTTCACCGTTGCGGCCTC-ACCTTTCCTATCACATCTTTTAAGGTAT
17382664 CGGATTAGCCGTCGCGGCCTCAATCCTTCC-TT
64 CGGATTAGCCGTCGCGGCCTCAATCCTTCCTTT
* * *
17382696 CATCTCTTCATGGTACTAGGTTCACCGTTGCGGCCTCATCCTTTCCCATCACGTCTTCTAAGGTA
1 CA--TCTTCATGGTACTAGGTTCACCGTTGCGGCCTCA-CCTTTCCTATCACATCTTTTAAGGTA
* * *
17382761 CCAGATTTGCCGTCGCGGCCTCAATCCTTCCTTT
63 TCGGATTAGCCGTCGCGGCCTCAATCCTTCCTTT
* ***
17382795 CATCTTCATGGTTCAGGTAGGTTTTTCGTTGCGGCCTCAACCTTTCCCT-TCACATCTTTTAAGG
1 CATCTTCATGG-T-A-CTAGGTTCACCGTTGCGGCCTC-ACCTTT-CCTATCACATCTTTTAAGG
17382859 TAT-GGATT
61 TATCGGATT
17382867 CATTGTTGCC
Statistics
Matches: 145, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
97 12 0.08
98 77 0.53
99 15 0.10
100 38 0.26
101 3 0.02
ACGTcount: A:0.16, C:0.30, G:0.18, T:0.36
Consensus pattern (96 bp):
CATCTTCATGGTACTAGGTTCACCGTTGCGGCCTCACCTTTCCTATCACATCTTTTAAGGTATCG
GATTAGCCGTCGCGGCCTCAATCCTTCCTTT
Found at i:17390942 original size:209 final size:207
Alignment explanation
Indices: 17390576--17391023 Score: 689
Period size: 209 Copynumber: 2.1 Consensus size: 207
17390566 TTCAAACCCC
* *
17390576 ATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGG
1 ATCTTCCTGATGAGATA-AGAGAAATGGACCAAATCCGTCTTCCTGATGAGATACAAAGAAGTGG
* * * * * *
17390641 ATTAAAACAAGTGATGCGGTCATCTTCCTAATGAGGTACAGAGAAGTAGACTAATTCAATGAAGT
65 ATTAAAAAAAGTGATACAGTCATCTTCCTAATGAGGTACAGAGAAGTAGACCAATTCAAGGAAGA
**
17390706 GAAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCGTGATGAGATATTGAGAAGTGGGTCAAA
130 GAAGCTCAATGTGAGTGAAACTTCAAA-CCCATCTTCGTGATGAGATACAGAGAAGTGGGTCAAA
17390771 GCAATAAAGCGGTA
194 GCAATAAAGCGGTA
*
17390785 ATCTTCCTGATGAGATATAGAGAAATGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGTGG
1 ATCTTCCTGATGAGATA-AGAGAAATGGACCAAATCCGTCTTCCTGATGAGATACAAAGAAGTGG
* *
17390850 ATTAAAAAAAGTGATACAGTCATCTTCTTGATGAGGTACAGAGAAGTAGACCAATTCAAGGAAGA
65 ATTAAAAAAAGTGATACAGTCATCTTCCTAATGAGGTACAGAGAAGTAGACCAATTCAAGGAAGA
* ** *
17390915 GAAGCTCAATGTGAGTGAAATTTCAAACCCATCTTTTTGATGAGATACAGAGAAGTGGGTCGAAG
130 GAAGCTCAATGTGAGTGAAACTTCAAACCCATCTTCGTGATGAGATACAGAGAAGTGGGTCAAAG
*
17390980 CAATAAAGCGGTC
195 CAATAAAGCGGTA
*
17390993 ATCTTCCTGATGAGATAAGGAGAAATAGACC
1 ATCTTCCTGATGAGATAA-GAGAAATGGACC
17391024 GAGAGATGAA
Statistics
Matches: 218, Mismatches: 20, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
207 1 0.00
208 73 0.33
209 144 0.66
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (207 bp):
ATCTTCCTGATGAGATAAGAGAAATGGACCAAATCCGTCTTCCTGATGAGATACAAAGAAGTGGA
TTAAAAAAAGTGATACAGTCATCTTCCTAATGAGGTACAGAGAAGTAGACCAATTCAAGGAAGAG
AAGCTCAATGTGAGTGAAACTTCAAACCCATCTTCGTGATGAGATACAGAGAAGTGGGTCAAAGC
AATAAAGCGGTA
Found at i:17391413 original size:17 final size:17
Alignment explanation
Indices: 17391393--17391430 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
17391383 TAAACCAAAC
17391393 AAATAAATTTTAAATTT
1 AAATAAATTTTAAATTT
**
17391410 AAATTTATTTTAAATTT
1 AAATAAATTTTAAATTT
17391427 AAAT
1 AAAT
17391431 GTCCAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATAAATTTTAAATTT
Found at i:17392254 original size:22 final size:21
Alignment explanation
Indices: 17392226--17392268 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
17392216 AGATCTAGGG
17392226 TTTTTAAAAAATAAAAAAATGA
1 TTTTTAAAAAA-AAAAAAATGA
* *
17392248 TTTTTAAAGAAAAGAAAATGA
1 TTTTTAAAAAAAAAAAAATGA
17392269 AAAAAAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.30
Consensus pattern (21 bp):
TTTTTAAAAAAAAAAAAATGA
Found at i:17392357 original size:29 final size:29
Alignment explanation
Indices: 17392314--17392572 Score: 240
Period size: 30 Copynumber: 8.8 Consensus size: 29
17392304 AAACCTCTTT
* * * *
17392314 TTTTACCCCCAAACTTCTCTAAAATTATA
1 TTTTAACCCTAAACTTCTCTAAAATCACA
* * * *
17392343 TTTTGATCCTAAACTTTTCTAAAATTACA
1 TTTTAACCCTAAACTTCTCTAAAATCACA
*
17392372 TTTTAGCCCCTAAACTTCT-TCAAAATCACA
1 TTTTA-ACCCTAAACTTCTCT-AAAATCACA
*
17392402 TTTTAACCCTCAAACCTT-TCCAAAATCACA
1 TTTTAACCCT-AAA-CTTCTCTAAAATCACA
*
17392432 TTTTAACCCTAAACCTTCTC-AAAATCACT
1 TTTTAACCCTAAA-CTTCTCTAAAATCACA
* *
17392461 TTTTAACCCCCAAACTTCTCCAAAATCACA
1 TTTTAA-CCCTAAACTTCTCTAAAATCACA
* * *
17392491 TTTTGACCCCAAACTT-TCCTAAAATTACA
1 TTTTAACCCTAAACTTCT-CTAAAATCACA
* * *
17392520 TTTTTACCCCTAAACTTTTCTAAAATTACA
1 -TTTTAACCCTAAACTTCTCTAAAATCACA
17392550 TTTTAACCCTAAA-TTCTCTAAAA
1 TTTTAACCCTAAACTTCTCTAAAA
17392573 CTTCATTTTC
Statistics
Matches: 195, Mismatches: 24, Indels: 23
0.81 0.10 0.10
Matches are distributed among these distances:
28 10 0.05
29 90 0.46
30 91 0.47
31 4 0.02
ACGTcount: A:0.35, C:0.28, G:0.01, T:0.36
Consensus pattern (29 bp):
TTTTAACCCTAAACTTCTCTAAAATCACA
Found at i:17392397 original size:59 final size:60
Alignment explanation
Indices: 17392314--17392572 Score: 250
Period size: 59 Copynumber: 4.4 Consensus size: 60
17392304 AAACCTCTTT
* * * * * * *
17392314 TTTTACCCCCAAACTTC-TCTAAAATTATATTTTGA-TCCTAAACTTTTCTAAAATTACA
1 TTTTACCCCTAAACTTCTTCTAAAATCACATTTTAACCCCTAAACTTTTCCAAAATCACA
*
17392372 TTTTAGCCCCTAAACTTCTTC-AAAATCACATTTTAA-CCCTCAAACCTTTCCAAAATCACA
1 TTTTA-CCCCTAAACTTCTTCTAAAATCACATTTTAACCCCT-AAACTTTTCCAAAATCACA
* * * *
17392432 TTTTAACCCTAAAC--CTTCTCAAAATCACTTTTTAACCCCCAAACTTCTCCAAAATCACA
1 TTTTACCCCTAAACTTCTTCT-AAAATCACATTTTAACCCCTAAACTTTTCCAAAATCACA
* * * * *
17392491 TTTTGACCCC-AAACTT-TCCTAAAATTACATTTTTACCCCTAAACTTTTCTAAAATTACA
1 TTTT-ACCCCTAAACTTCTTCTAAAATCACATTTTAACCCCTAAACTTTTCCAAAATCACA
*
17392550 TTTTAACCCTAAA-TTC-TCTAAAA
1 TTTTACCCCTAAACTTCTTCTAAAA
17392573 CTTCATTTTC
Statistics
Matches: 166, Mismatches: 24, Indels: 22
0.78 0.11 0.10
Matches are distributed among these distances:
57 4 0.02
58 17 0.10
59 112 0.67
60 33 0.20
ACGTcount: A:0.35, C:0.28, G:0.01, T:0.36
Consensus pattern (60 bp):
TTTTACCCCTAAACTTCTTCTAAAATCACATTTTAACCCCTAAACTTTTCCAAAATCACA
Found at i:17392588 original size:29 final size:29
Alignment explanation
Indices: 17392314--17392581 Score: 242
Period size: 29 Copynumber: 9.1 Consensus size: 29
17392304 AAACCTCTTT
* * *
17392314 TTTTACCCCCAAACTTCTCTAAAATTATA
1 TTTTAACCCTAAACTTCTCTAAAATTACA
* * *
17392343 TTTTGATCCTAAACTTTTCTAAAATTACA
1 TTTTAACCCTAAACTTCTCTAAAATTACA
* *
17392372 TTTTAGCCCCTAAACTTCT-TCAAAATCACA
1 TTTTA-ACCCTAAACTTCTCT-AAAATTACA
* *
17392402 TTTTAACCCTCAAACCTT-TCCAAAATCACA
1 TTTTAACCCT-AAA-CTTCTCTAAAATTACA
* *
17392432 TTTTAACCCTAAACCTTCTC-AAAATCACT
1 TTTTAACCCTAAA-CTTCTCTAAAATTACA
* * *
17392461 TTTTAACCCCCAAACTTCTCCAAAATCACA
1 TTTTAA-CCCTAAACTTCTCTAAAATTACA
* *
17392491 TTTTGACCCCAAACTT-TCCTAAAATTACA
1 TTTTAACCCTAAACTTCT-CTAAAATTACA
* *
17392520 TTTTTACCCCTAAACTTTTCTAAAATTACA
1 -TTTTAACCCTAAACTTCTCTAAAATTACA
17392550 TTTTAACCCTAAA-TTCTCTAAAACTT-CA
1 TTTTAACCCTAAACTTCTCTAAAA-TTACA
17392578 TTTT
1 TTTT
17392582 CGACCCTTTT
Statistics
Matches: 203, Mismatches: 24, Indels: 25
0.81 0.10 0.10
Matches are distributed among these distances:
28 16 0.08
29 92 0.45
30 91 0.45
31 4 0.02
ACGTcount: A:0.34, C:0.28, G:0.01, T:0.37
Consensus pattern (29 bp):
TTTTAACCCTAAACTTCTCTAAAATTACA
Found at i:17393484 original size:30 final size:29
Alignment explanation
Indices: 17393442--17393582 Score: 192
Period size: 30 Copynumber: 4.7 Consensus size: 29
17393432 TCAAATTTAA
* *
17393442 AATTTTAGAAAGTTTAGGGGTTAAAATGT
1 AATTTTAGAAAGTTTAAGGGTTAAAATGC
*
17393471 AATTTTGAGAAAGTTTAAGGTTTAAAATGC
1 AATTTT-AGAAAGTTTAAGGGTTAAAATGC
* *
17393501 AATTAATAGAAAGTTTAAGGGTTAAAATGT
1 AATT-TTAGAAAGTTTAAGGGTTAAAATGC
*
17393531 AATTTTTAGAAAGTTTAAGGGCTAAAATGC
1 AA-TTTTAGAAAGTTTAAGGGTTAAAATGC
17393561 AATTTTTAGAAAGTTTAAGGGT
1 AA-TTTTAGAAAGTTTAAGGGT
17393583 CAAATTTGAA
Statistics
Matches: 99, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
29 6 0.06
30 90 0.91
31 3 0.03
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.36
Consensus pattern (29 bp):
AATTTTAGAAAGTTTAAGGGTTAAAATGC
Found at i:17393523 original size:60 final size:60
Alignment explanation
Indices: 17393447--17393582 Score: 218
Period size: 60 Copynumber: 2.3 Consensus size: 60
17393437 TTTAAAATTT
* **
17393447 TAGAAAGTTTAGGGGTTAAAATGTAATTTTGAGAAAGTTTAAGGTTTAAAATGCAATTAA
1 TAGAAAGTTTAAGGGTTAAAATGTAATTTTGAGAAAGTTTAAGGGCTAAAATGCAATTAA
* **
17393507 TAGAAAGTTTAAGGGTTAAAATGTAATTTTTAGAAAGTTTAAGGGCTAAAATGCAATTTT
1 TAGAAAGTTTAAGGGTTAAAATGTAATTTTGAGAAAGTTTAAGGGCTAAAATGCAATTAA
17393567 TAGAAAGTTTAAGGGT
1 TAGAAAGTTTAAGGGT
17393583 CAAATTTGAA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 70 1.00
ACGTcount: A:0.40, C:0.02, G:0.22, T:0.35
Consensus pattern (60 bp):
TAGAAAGTTTAAGGGTTAAAATGTAATTTTGAGAAAGTTTAAGGGCTAAAATGCAATTAA
Found at i:17393603 original size:60 final size:59
Alignment explanation
Indices: 17393444--17393612 Score: 203
Period size: 60 Copynumber: 2.8 Consensus size: 59
17393434 AAATTTAAAA
* * **
17393444 TTTTAGAAAGTTTAGGGGTTAAAATGTAATTTTGAGAAAGTTTAAGGTTTAAAATGCAAT
1 TTTTAGAAAGTTTAAGGGTTAAAATGAAATTTTG-GAAAGTTTAAGGGCTAAAATGCAAT
** * *
17393504 TAATAGAAAGTTTAAGGGTTAAAATGTAATTTTTAGAAAGTTTAAGGGCTAAAATGCAAT
1 TTTTAGAAAGTTTAAGGGTTAAAATG-AAATTTTGGAAAGTTTAAGGGCTAAAATGCAAT
* * * *
17393564 TTTTAGAAAGTTTAAGGGTCAAATTTGAAATATTGGAAAGTTTGAGGGC
1 TTTTAGAAAGTTTAAGGGTTAAA-ATGAAATTTTGGAAAGTTTAAGGGC
17393613 CGAAACATAA
Statistics
Matches: 91, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
60 84 0.92
61 7 0.08
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (59 bp):
TTTTAGAAAGTTTAAGGGTTAAAATGAAATTTTGGAAAGTTTAAGGGCTAAAATGCAAT
Found at i:17393624 original size:90 final size:90
Alignment explanation
Indices: 17393444--17393626 Score: 206
Period size: 90 Copynumber: 2.0 Consensus size: 90
17393434 AAATTTAAAA
* * * * * *
17393444 TTTTAGAAAGTTTAGGGGTTAAAATGTAATTTTGAGAAAGTTTAAGGTTTAAAATGCAATTAATA
1 TTTTAGAAAGTTTAAGGGCTAAAATGCAATTTTGAGAAAGTTTAAGGGTCAAAATGCAAATAATA
** **
17393509 GAAAGTTTAAGGGTTAAAATGTAAT
66 GAAAGTTTAAGGGCCAAAACATAAT
* * *
17393534 TTTTAGAAAGTTTAAGGGCTAAAATGCAATTTTTAGAAAGTTTAAGGGTCAAATTTG-AAATATT
1 TTTTAGAAAGTTTAAGGGCTAAAATGCAATTTTGAGAAAGTTTAAGGGTCAAA-ATGCAAATAAT
* * *
17393598 GGAAAGTTTGAGGGCCGAAACATAAT
65 AGAAAGTTTAAGGGCCAAAACATAAT
17393624 TTT
1 TTT
17393627 AAAATAAAAC
Statistics
Matches: 76, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
90 74 0.97
91 2 0.03
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.36
Consensus pattern (90 bp):
TTTTAGAAAGTTTAAGGGCTAAAATGCAATTTTGAGAAAGTTTAAGGGTCAAAATGCAAATAATA
GAAAGTTTAAGGGCCAAAACATAAT
Found at i:17394876 original size:11 final size:11
Alignment explanation
Indices: 17394857--17394893 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
17394847 GTCACGTGGT
*
17394857 TGACATGGCGC
1 TGACATGGCAC
*
17394868 TGACGTGGCAC
1 TGACATGGCAC
17394879 TGACATGGCAC
1 TGACATGGCAC
17394890 TGAC
1 TGAC
17394894 GTGGTCGGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.22, C:0.27, G:0.32, T:0.19
Consensus pattern (11 bp):
TGACATGGCAC
Found at i:17395761 original size:44 final size:44
Alignment explanation
Indices: 17395674--17395761 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
17395664 TTGCAGCTTC
* *
17395674 AACCTTTCCCTCCATATCTCCATGGTACAATATTCCCCGTTGCG
1 AACCTTTCCCTCCATATCTCCATGGTACAAGATTCCCCATTGCG
* *
17395718 AACCTTTCCCTCCATATCTCCATGGTATAAGATTCGCCATTGCG
1 AACCTTTCCCTCCATATCTCCATGGTACAAGATTCCCCATTGCG
17395762 GCTTCAATCT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.22, C:0.34, G:0.12, T:0.32
Consensus pattern (44 bp):
AACCTTTCCCTCCATATCTCCATGGTACAAGATTCCCCATTGCG
Found at i:17395857 original size:142 final size:144
Alignment explanation
Indices: 17395575--17395923 Score: 479
Period size: 142 Copynumber: 2.4 Consensus size: 144
17395565 GTTGCGACTT
* * *
17395575 CAACTTTTCCCTCCATATCTCTATGGTACAAGATTCGCCATTGCGGCCTCAATCTTTCCCATCAC
1 CAACCTTTCCCTCCATATCTCTATGGTATAAGATTCGCCATTGCGGCTTCAATCTTTCCCATCAC
* *
17395640 ATTTCTAAGGTATAAGGTTCACCGTTGCAGCTTCAACCTTTCCCTCCATATCTCCATGGTACAAT
66 ATCTCTAAGGTATAAGGTTCACCGTTGCAGCTTCAACCTTTCCCTCCATATCTCCATGGTACAAG
17395705 ATTCCCCGTTGC-G
131 ATTCCCCGTTGCAG
* *
17395718 -AACCTTTCCCTCCATATCTCCATGGTATAAGATTCGCCATTGCGGCTTCAATCTTTCCCATTAC
1 CAACCTTTCCCTCCATATCTCTATGGTATAAGATTCGCCATTGCGGCTTCAATCTTTCCCATCAC
* *
17395782 ATCTCTAAGGTATAAGGTTCGCCGTTGCGGCTTCAACCTTTCCCTCCATATCTCCATGGTACAAG
66 ATCTCTAAGGTATAAGGTTCACCGTTGCAGCTTCAACCTTTCCCTCCATATCTCCATGGTACAAG
***
17395847 ATTTGTCGTTGCAG
131 ATTCCCCGTTGCAG
* * * * * *
17395861 CTTCAATCTTTCCCAT-CACATCTCTAAGGTATAAGATTGGCCGTTGTGGCTTCAATCTTTCCC
1 ---CAACCTTTCCC-TCCATATCTCTATGGTATAAGATTCGCCATTGCGGCTTCAATCTTTCCC
17395924 TTTGTAATTT
Statistics
Matches: 181, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
142 129 0.71
143 1 0.01
147 50 0.28
148 1 0.01
ACGTcount: A:0.21, C:0.30, G:0.15, T:0.34
Consensus pattern (144 bp):
CAACCTTTCCCTCCATATCTCTATGGTATAAGATTCGCCATTGCGGCTTCAATCTTTCCCATCAC
ATCTCTAAGGTATAAGGTTCACCGTTGCAGCTTCAACCTTTCCCTCCATATCTCCATGGTACAAG
ATTCCCCGTTGCAG
Found at i:17395923 original size:49 final size:49
Alignment explanation
Indices: 17395501--17395924 Score: 382
Period size: 49 Copynumber: 8.8 Consensus size: 49
17395491 TTAACTTTAG
* * * *
17395501 GGTATAAGATTCACCGTTGTGACTTCAATCTTT-CCTATCACATCTCTAA
1 GGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCT-CCACATCTCTAA
* * * *
17395550 GGTATAAGGTTCGCCGTTGCGACTTCAA-CTTTTCCCTCCATATCTCTAT
1 GGTATAAGATTCGCCGTTGCGGCTTCAATC-TTTCCCTCCACATCTCTAA
* * * *
17395599 GGTACAAGATTCGCCATTGCGGCCTCAATCTTTCCCAT-CACATTTCTAA
1 GGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCC-TCCACATCTCTAA
* * * * * * *
17395648 GGTATAAGGTTCACCGTTGCAGCTTCAACCTTTCCCTCCATATCTCCAT
1 GGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTCCACATCTCTAA
* * * * * * *
17395697 GGTACAATATTCCCCGTTGC-G----AACCTTTCCCTCCATATCTCCAT
1 GGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTCCACATCTCTAA
* *
17395741 GGTATAAGATTCGCCATTGCGGCTTCAATCTTTCCCAT-TACATCTCTAA
1 GGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCC-TCCACATCTCTAA
* * * * *
17395790 GGTATAAGGTTCGCCGTTGCGGCTTCAACCTTTCCCTCCATATCTCCAT
1 GGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTCCACATCTCTAA
* * * *
17395839 GGTACAAGATTTGTCGTTGCAGCTTCAATCTTTCCCAT-CACATCTCTAA
1 GGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCC-TCCACATCTCTAA
* *
17395888 GGTATAAGATTGGCCGTTGTGGCTTCAATCTTTCCCT
1 GGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCT
17395925 TTGTAATTTG
Statistics
Matches: 303, Mismatches: 59, Indels: 27
0.78 0.15 0.07
Matches are distributed among these distances:
44 39 0.13
45 1 0.00
48 5 0.02
49 251 0.83
50 7 0.02
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.34
Consensus pattern (49 bp):
GGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTCCACATCTCTAA
Found at i:17396986 original size:29 final size:30
Alignment explanation
Indices: 17396949--17397025 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
17396939 AGAATTTTGG
*
17396949 GGGTCAAAATGTAA-TTTGGAAAAGTTCAA
1 GGGTCAAAATATAATTTTGGAAAAGTTCAA
* ** *
17396978 GGGTTAAAATATAATTTTGGTGAAGTTCAG
1 GGGTCAAAATATAATTTTGGAAAAGTTCAA
*
17397008 GGGTCAAAATATAGTTTT
1 GGGTCAAAATATAATTTT
17397026 TAAATAAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 12 0.30
30 28 0.70
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (30 bp):
GGGTCAAAATATAATTTTGGAAAAGTTCAA
Found at i:17399044 original size:208 final size:208
Alignment explanation
Indices: 17398679--17399508 Score: 1038
Period size: 208 Copynumber: 4.0 Consensus size: 208
17398669 GCTTCATTTC
* * ** * * ** *
17398679 TTGGTCTACTTCTCTGTATCTCATCATAAAGATGATCGCTTTAGTACTTCGACCCACTTCTTTGT
1 TTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCGCTTTATTGTTTTGACCCACTTCTTTGT
* * * * *
17398744 ATCTCATCAGGAAGATAGGGGTTTAAAGTCTCATTCGTATTGAGCTTCGCTTTATTTATTTAGTC
66 ATCTCATCAGGAAGAT-GGGGTTTGAAGTCTCATTCGTACTGAGCTTCGCTTCATTGATTTGGTC
** * * *
17398809 TACTTCTCTGTATCTCATTGGGAAGATGACCGCTTCTTTGATTTAATCCAATTCTCTGTATCTCA
130 TACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTATATCTCA
17398874 TCAGGAAGATGAAT
195 TCAGGAAGATGAAT
** * * *
17398888 TTGGTTTACTTCTCTATATTTTATCAGGAAGATGACCTCTTTATTGTTTTGACCCACTTCTTTGT
1 TTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCGCTTTATTGTTTTGACCCACTTCTTTGT
* *
17398953 AGCTCATCAGGAAGATGGGGTTCGAAGTCTCATTCGTACTGAGCTTCGCTTCATT-AGTTTGGTC
66 ATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTACTGAGCTTCGCTTCATTGA-TTTGGTC
* *
17399017 TACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTTAATCCACTTCTCTACATCTCA
130 TACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTATATCTCA
*
17399082 TCAGGAAGGT-AGAT
195 TCAGGAAGATGA-AT
* * * * * * * *
17399096 TTGGTCCACTTTTCTCTATCTCATTAGGTAGATGATCGCTTTAATGTTTTGATCGACTTCTCTT-
1 TTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCGCTTTATTGTTTTGACCCACTTCT-TTG
* *
17399160 TATCTCATCAGAAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTC
65 TATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTACTGAGCTTCGCTTCATTGATTTGGTC
* *
17399225 TACTTCTATGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTATATCTTA
130 TACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTATATCTCA
* ***
17399290 TCAAGAAGGCAAAT
195 TCAGGAAGATGAAT
* * * ** *
17399304 TTGGTCCACTTCTTTGTATCTCATCAGGAAGATGACAGCTTTATTACTTTGACCCACTTCTCTGT
1 TTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCGCTTTATTGTTTTGACCCACTTCTTTGT
* *
17399369 ATCTCATAAGGAAGATGGGGTTTGAAGTCTCATTCGTACTAAGCTTCGCTTCATTGATTTGGTCT
66 ATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTACTGAGCTTCGCTTCATTGATTTGGTCT
* * * * * * * *
17399434 ACTTCTCTGTATCTCATCAAGAAGATCACCTCTTTATTGCTTTCATCCACTTCAT-TGTATATCA
131 ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTC-TCTATATCTCA
17399498 TCAGGAAGATG
195 TCAGGAAGATG
17399509 GGTTTGAAGT
Statistics
Matches: 534, Mismatches: 80, Indels: 15
0.85 0.13 0.02
Matches are distributed among these distances:
207 3 0.01
208 458 0.86
209 73 0.14
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (208 bp):
TTGGTCCACTTCTCTATATCTCATCAGGAAGATGACCGCTTTATTGTTTTGACCCACTTCTTTGT
ATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTACTGAGCTTCGCTTCATTGATTTGGTCT
ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTATATCTCAT
CAGGAAGATGAAT
Found at i:17399155 original size:85 final size:85
Alignment explanation
Indices: 17399010--17399170 Score: 196
Period size: 85 Copynumber: 1.9 Consensus size: 85
17399000 GCTTCATTAG
* * *
17399010 TTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTTAATCCACTTCTCTA
1 TTTGGTCCACTTCTCTCTATCTCATCAGGAAGATGACCACTTCAATGATTTAATCCACTTCTCTA
17399075 CATCTCATCAGGAAGGTAGA
66 CATCTCATCAGGAAGGTAGA
* * * * * * * * * *
17399095 TTTGGTCCACTTTTCTCTATCTCATTAGGTAGATGATCGCTTTAATGTTTTGATCGACTTCTCTT
1 TTTGGTCCACTTCTCTCTATCTCATCAGGAAGATGACCACTTCAATGATTTAATCCACTTCTCTA
*
17399160 TATCTCATCAG
66 CATCTCATCAG
17399171 AAAGATGGGG
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
85 62 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.40
Consensus pattern (85 bp):
TTTGGTCCACTTCTCTCTATCTCATCAGGAAGATGACCACTTCAATGATTTAATCCACTTCTCTA
CATCTCATCAGGAAGGTAGA
Found at i:17399361 original size:85 final size:85
Alignment explanation
Indices: 17399217--17399372 Score: 233
Period size: 85 Copynumber: 1.8 Consensus size: 85
17399207 CGCTTCATTG
* * *
17399217 ATTTGGTCTACTTCTATGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCT
1 ATTTGGTCCACTTCTATGTATCTCATCAGGAAGATGACAGCTTCATTGATTTAACCCACTTCTCT
17399282 ATATCTTATCAAGAAGGCAA
66 ATATCTTATCAAGAAGGCAA
* * *
17399302 ATTTGGTCCACTTCTTTGTATCTCATCAGGAAGATGACAGCTTTATT-ACTTTGACCCACTTCTC
1 ATTTGGTCCACTTCTATGTATCTCATCAGGAAGATGACAGCTTCATTGA-TTTAACCCACTTCTC
*
17399366 TGTATCT
65 TATATCT
17399373 CATAAGGAAG
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
84 1 0.02
85 62 0.98
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.38
Consensus pattern (85 bp):
ATTTGGTCCACTTCTATGTATCTCATCAGGAAGATGACAGCTTCATTGATTTAACCCACTTCTCT
ATATCTTATCAAGAAGGCAA
Found at i:17399575 original size:121 final size:123
Alignment explanation
Indices: 17399302--17399626 Score: 440
Period size: 121 Copynumber: 2.7 Consensus size: 123
17399292 AAGAAGGCAA
* * * * * *
17399302 ATTTGGTCCACTTCTTTGTATCTCATCAGGAAGATGACAGCTTTATTACTTTGACCCACTTCTCT
1 ATTTGGTCTACTTCTTTGTATCTCATCAAGAAGATGACCGCTTTATTGCTTTAATCCACTTCTCT
* *
17399367 GTATCTCATAAGGAAGATGGGGTTTGAAGTCTCATTCGTACTAAGCTTCGCTTCATTG
66 GTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTACTAAGCGTCGCTTCATTG
* * * *
17399425 ATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATCACCTCTTTATTGCTTTCATCCACTTCAT-
1 ATTTGGTCTACTTCTTTGTATCTCATCAAGAAGATGACCGCTTTATTGCTTTAATCCACTTC-TC
* * **
17399489 TGTATATCATCAGGAAGAT-GGGTTTGAAGT-TCATTCGTATTGTGCGTCGCTTCATTG
65 TGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTACTAAGCGTCGCTTCATTG
* * *
17399546 ATTTGGTCTACTTCTTTTTATCTCATCAAGAAGATGACCGCTTCATTGATTTAATCCACTTCTCT
1 ATTTGGTCTACTTCTTTGTATCTCATCAAGAAGATGACCGCTTTATTGCTTTAATCCACTTCTCT
*
17399611 ATATCTCATCAGGAAG
66 GTATCTCATCAGGAAG
17399627 GCAGATTTGA
Statistics
Matches: 176, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
120 1 0.01
121 93 0.53
122 11 0.06
123 70 0.40
124 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (123 bp):
ATTTGGTCTACTTCTTTGTATCTCATCAAGAAGATGACCGCTTTATTGCTTTAATCCACTTCTCT
GTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTACTAAGCGTCGCTTCATTG
Found at i:17399643 original size:37 final size:37
Alignment explanation
Indices: 17399593--17399673 Score: 126
Period size: 37 Copynumber: 2.2 Consensus size: 37
17399583 CCGCTTCATT
* *
17399593 GATTTAATCCACTTCTCTATATCTCATCAGGAAGGCA
1 GATTTGATCCACTTCTCTATATCTCATCAAGAAGGCA
* *
17399630 GATTTGATCCACTTCTCTGTATCTCATCAAGAAGGCG
1 GATTTGATCCACTTCTCTATATCTCATCAAGAAGGCA
17399667 GATTTGA
1 GATTTGA
17399674 AGCCTCATTC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.33
Consensus pattern (37 bp):
GATTTGATCCACTTCTCTATATCTCATCAAGAAGGCA
Found at i:17399766 original size:159 final size:158
Alignment explanation
Indices: 17399478--17399823 Score: 487
Period size: 159 Copynumber: 2.2 Consensus size: 158
17399468 TATTGCTTTC
* * * * * *
17399478 ATCCACTTCAT-TGTATATCATCAGGAAGATGGGTTTGAAGTTCATTCGTATTGTGCGTCGCTTC
1 ATCCACTTC-TCTGTATCTCATCAAGAAGACGGATTTGAAGCTCATTCGTATTGAGCGTCGCTTC
* * *
17399542 ATTGATTTGGTCTACTTCTTTTTATCTCATCAAGAAGATGACCGCTTCATTGATTTAATCCACTT
65 ATTAATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAATCCACTT
*
17399607 CTCTATATCTCATCAGGAAGGCAGATTTG
130 CTCTATATCTCATCAAGAAGGCAGATTTG
* *
17399636 ATCCACTTCTCTGTATCTCATCAAGAAGGCGGATTTGAAGCCTCATTCGTATTGAGCTTCGCTTC
1 ATCCACTTCTCTGTATCTCATCAAGAAGACGGATTTGAAG-CTCATTCGTATTGAGCGTCGCTTC
* *
17399701 ATTAATTTGGTCTACTTCTCTGTATCTCATTAGGAAGATGACCGCTTCATTGATTTAATCCACTT
65 ATTAATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAATCCACTT
* * *
17399766 CTCTGTATCTCGTTAAGAAGGCAGATTTG
130 CTCTATATCTCATCAAGAAGGCAGATTTG
** *
17399795 GCCCACTTCTCTATATCTCATCAAGAAGA
1 ATCCACTTCTCTGTATCTCATCAAGAAGA
17399824 TGATCGTTTT
Statistics
Matches: 165, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
157 1 0.01
158 33 0.20
159 131 0.79
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (158 bp):
ATCCACTTCTCTGTATCTCATCAAGAAGACGGATTTGAAGCTCATTCGTATTGAGCGTCGCTTCA
TTAATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAATCCACTTC
TCTATATCTCATCAAGAAGGCAGATTTG
Found at i:17399849 original size:85 final size:85
Alignment explanation
Indices: 17399705--17399870 Score: 190
Period size: 85 Copynumber: 2.0 Consensus size: 85
17399695 CGCTTCATTA
* * * * * *
17399705 ATTTGGTCTACTTCTCTGTATCTCATTAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCT
1 ATTTGGCCCACTTCTCTATATCTCATCAAGAAGATGACCGCTTCATTGATTTAACCCACTTCTCT
* * *
17399770 GTATCTCGTTAAGAAGGCAG
66 ATATCTCATCAAGAAGGCAG
* * * * *
17399790 ATTTGGCCCACTTCTCTATATCTCATCAAGAAGATGATCGTTTTATT-ATTTTGACCCACTTCTT
1 ATTTGGCCCACTTCTCTATATCTCATCAAGAAGATGACCGCTTCATTGA-TTTAACCCACTTCTC
17399854 TATATCTCATCAAGAAG
65 TATATCTCATCAAGAAG
17399871 ATGGGGTTTG
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
84 1 0.02
85 65 0.98
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (85 bp):
ATTTGGCCCACTTCTCTATATCTCATCAAGAAGATGACCGCTTCATTGATTTAACCCACTTCTCT
ATATCTCATCAAGAAGGCAG
Found at i:17399922 original size:208 final size:207
Alignment explanation
Indices: 17399632--17400374 Score: 1103
Period size: 208 Copynumber: 3.6 Consensus size: 207
17399622 GGAAGGCAGA
* * *
17399632 TTTGATCCACTTCTCTGTATCTCATCAAGAAG--GCGGATTTGAAGCCTCATTCGTATTGAGCTT
1 TTTGACCCACTTCTCTGTATCTCATCAAGAAGATG-GGGTTTGAAGTCTCATTCGTATTGAGCTT
* * * *
17399695 CGCTTCATTAATTTGGTCTACTTCTCTGTATCTCATTAGGAAGATGACCGCTTCATTGATTTAAT
65 CGCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTCAAT
* * * *
17399760 CCACTTCTCTGTATCTCGTTAAGAAGGCAGATTTGGCCCACTTCTCTATATCTCATCAAGAAGAT
130 CCACTTCTCTGTATCTCATCAAGAAGGC-GATTTGGTCCACTTCTCTATATCTCATCAGGAAGAT
* * **
17399825 GATCGTTTTATTAT
194 GACCATTTTATTGC
* * *
17399839 TTTGACCCACTTCTTTATATCTCATCAAGAAGATGGGGTTTGAGGTCTCATTCGTATTGAGCTTC
1 TTTGACCCACTTCTCTGTATCTCATCAAGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTC
*
17399904 GCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTCAATC
66 GCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTCAATC
*
17399969 CACTTCTCTGTATCTCATCAAGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATG
131 CACTTCTCTGTATCTCATCAAGAAGGC-GATTTGGTCCACTTCTCTATATCTCATCAGGAAGATG
17400034 ACCATTTTATTGC
195 ACCATTTTATTGC
* * * * *
17400047 TTTGACCCACTTCTCTGTATCTCATCAGGAAGATGTGGTTTGAAGTGTCATCCATATTGAGCTTC
1 TTTGACCCACTTCTCTGTATCTCATCAAGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTC
* * * *
17400112 GCTTCATTGATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGATCACTTCACTGATTCAATC
66 GCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTCAATC
* * * *
17400177 CACTTCCCTGTATCTCATCAAGAAGGCGAATTTGGTTCACTTCTTTATTTCTCATCAGGAAGATG
131 CACTTCTCTGTATCTCATCAAGAAGGCG-ATTTGGTCCACTTCTCTATATCTCATCAGGAAGATG
17400242 ACCATTTTATTGC
195 ACCATTTTATTGC
* * *
17400255 TTTGACCCACTTCTCTGTATCTCATTAGGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGTTTC
1 TTTGACCCACTTCTCTGTATCTCATCAAGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTC
*
17400320 GCTTCATTGATTTTGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCAT
66 GCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCAT
17400375 CATTTTGATG
Statistics
Matches: 485, Mismatches: 48, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
207 30 0.06
208 454 0.94
209 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (207 bp):
TTTGACCCACTTCTCTGTATCTCATCAAGAAGATGGGGTTTGAAGTCTCATTCGTATTGAGCTTC
GCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTCAATC
CACTTCTCTGTATCTCATCAAGAAGGCGATTTGGTCCACTTCTCTATATCTCATCAGGAAGATGA
CCATTTTATTGC
Found at i:17400057 original size:85 final size:85
Alignment explanation
Indices: 17399912--17400078 Score: 253
Period size: 85 Copynumber: 2.0 Consensus size: 85
17399902 TCGCTTCATT
* * *
17399912 GATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTCAATCCACTTCTC
1 GATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTCAACCCACTTCTC
17399977 TGTATCTCATCAAGAAGGCG
66 TGTATCTCATCAAGAAGGCG
* * * **
17399997 GATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCATTTTATTGCTTTGACCCACTTCTC
1 GATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTCAACCCACTTCTC
*
17400062 TGTATCTCATCAGGAAG
66 TGTATCTCATCAAGAAG
17400079 ATGTGGTTTG
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
85 73 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (85 bp):
GATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTCAACCCACTTCTC
TGTATCTCATCAAGAAGGCG
Found at i:17408543 original size:30 final size:30
Alignment explanation
Indices: 17408504--17408575 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
17408494 TTTGGGGGCC
*
17408504 AAAATGTAATTTTAGGAA-AGTTTGAGGGTT
1 AAAATGTAATTTT-GGAAGAGTTTAAGGGTT
*
17408534 AAAAAGTAATTTTGGAAGAGTTTAAGGGTT
1 AAAATGTAATTTTGGAAGAGTTTAAGGGTT
17408564 AAAATGTAATTT
1 AAAATGTAATTT
17408576 ATGGTCAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 4 0.11
30 34 0.89
ACGTcount: A:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAGAGTTTAAGGGTT
Found at i:17408585 original size:78 final size:78
Alignment explanation
Indices: 17408503--17408646 Score: 202
Period size: 78 Copynumber: 1.8 Consensus size: 78
17408493 TTTTGGGGGC
** *
17408503 CAAAATGTAATTTTAGGAAAGTTTGAGGGTTAAAAAGTAA-TTTTG-GAAGAGTTTAAGGGTTAA
1 CAAAATGTAATTTTAGGAAAGTTCAAGGGTCAAAAAGTAATTTTTGTG-A-AGTTTAAGGGTTAA
17408566 AATGTAATTTATGGT
64 AATGTAATTTATGGT
* * *
17408581 CAAAATGTAATTTTTGGAAAGTTCAAGGGTCAAAATGTAATTTTTGTGAATTTTAAGGGTTAAAA
1 CAAAATGTAATTTTAGGAAAGTTCAAGGGTCAAAAAGTAATTTTTGTGAAGTTTAAGGGTTAAAA
17408646 T
66 T
17408647 ATAGTTTTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
78 51 0.88
79 6 0.10
80 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.37
Consensus pattern (78 bp):
CAAAATGTAATTTTAGGAAAGTTCAAGGGTCAAAAAGTAATTTTTGTGAAGTTTAAGGGTTAAAA
TGTAATTTATGGT
Found at i:17417952 original size:23 final size:23
Alignment explanation
Indices: 17417909--17417952 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
17417899 TTGTGTTAAA
*
17417909 ATGCAATGCAAATGAATGCATGT
1 ATGCAATGCAAATGAAGGCATGT
*
17417932 ATGCAATGTAAGA-GAAGGCAT
1 ATGCAATGCAA-ATGAAGGCAT
17417953 TGATTCTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 17 0.94
24 1 0.06
ACGTcount: A:0.41, C:0.11, G:0.25, T:0.23
Consensus pattern (23 bp):
ATGCAATGCAAATGAAGGCATGT
Found at i:17426990 original size:18 final size:20
Alignment explanation
Indices: 17426968--17427017 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 20
17426958 TGAATGCAAT
17426968 TAAATATTATTAT-ATTTGA
1 TAAATATTATTATAATTTGA
* *
17426987 -AAATATAAATATAATTTGA
1 TAAATATTATTATAATTTGA
*
17427006 TAAATGTTATTA
1 TAAATATTATTA
17427018 ATATGTGTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
18 10 0.42
19 6 0.25
20 8 0.33
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (20 bp):
TAAATATTATTATAATTTGA
Found at i:17432357 original size:17 final size:18
Alignment explanation
Indices: 17432329--17432363 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
17432319 CAAAAAAGTC
*
17432329 TCGAACAAAATTTTAAAA
1 TCGAACAAAATTATAAAA
17432347 TCGAA-AAAATTATAAAA
1 TCGAACAAAATTATAAAA
17432364 AAGGGAGTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.60, C:0.09, G:0.06, T:0.26
Consensus pattern (18 bp):
TCGAACAAAATTATAAAA
Found at i:17433508 original size:29 final size:28
Alignment explanation
Indices: 17433421--17433687 Score: 166
Period size: 29 Copynumber: 9.1 Consensus size: 28
17433411 CTTCGAGAAC
* *
17433421 AAAATGGTAATTTTCGAAAATTTTGAGGT
1 AAAATGGTAATTTTTG-AAATTTTGGGGT
* **
17433450 CAAAAATGG-AATTTTTGGATATTCGCGGGGT
1 --AAAATGGTAATTTTT-GAAATT-TTGGGGT
17433481 AAAATGGTAATTTTTGAAAGTTTTGGGGTT
1 AAAATGGTAATTTTTGAAA-TTTTGGGG-T
* * **
17433511 AAAATAG-AATTTTTAGACATTTAAGGGT
1 AAAATGGTAATTTTT-GAAATTTTGGGGT
*
17433539 AAAATGGTAAATTTT-AAATTTTGGGGT
1 AAAATGGTAATTTTTGAAATTTTGGGGT
* *
17433566 CAAAAATGG-AATTTTT-AGATATTCGAGGGT
1 --AAAATGGTAATTTTTGAAAT-TTTG-GGGT
**
17433596 AAAATGGTAATTTTCAAAAGTTTTGGGGTT
1 AAAATGGTAATTTTTGAAA-TTTTGGGG-T
** * * *
17433626 AAAAATGAAAATTTTAGACATTTGGGGGT
1 -AAAATGGTAATTTTTGAAATTTTGGGGT
**
17433655 AAAATGGTAATTTTTTGAAGGTTTGGGGT
1 AAAATGGTAA-TTTTTGAAATTTTGGGGT
17433684 AAAA
1 AAAA
17433688 AAATGTAATT
Statistics
Matches: 183, Mismatches: 36, Indels: 36
0.72 0.14 0.14
Matches are distributed among these distances:
27 9 0.05
28 31 0.17
29 70 0.38
30 46 0.25
31 27 0.15
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (28 bp):
AAAATGGTAATTTTTGAAATTTTGGGGT
Found at i:17433553 original size:59 final size:58
Alignment explanation
Indices: 17433421--17433688 Score: 283
Period size: 59 Copynumber: 4.6 Consensus size: 58
17433411 CTTCGAGAAC
* * * * * * * *
17433421 AAAATGGTAATTTTCGAAAATTTTGAGGTCAAAAATGGAATTTTTGGATATTCGCGGGGT
1 AAAATGGTAATTTTTGAAAGTTTTGGGGT-AAAAATAGAATTTTTAGACATTTG-AGGGT
* *
17433481 AAAATGGTAATTTTTGAAAGTTTTGGGGTTAAAATAGAATTTTTAGACATTTAAGGGT
1 AAAATGGTAATTTTTGAAAGTTTTGGGGTAAAAATAGAATTTTTAGACATTTGAGGGT
* * * *
17433539 AAAATGGTAAATTTT-AAA-TTTTGGGGTCAAAAATGGAATTTTTAGATATTCGAGGGT
1 AAAATGGTAATTTTTGAAAGTTTTGGGGT-AAAAATAGAATTTTTAGACATTTGAGGGT
** * *
17433596 AAAATGGTAATTTTCAAAAGTTTTGGGGTTAAAAAT-GAAAATTTTAGACATTTGGGGGT
1 AAAATGGTAATTTTTGAAAGTTTTGGGG-TAAAAATAG-AATTTTTAGACATTTGAGGGT
*
17433655 AAAATGGTAATTTTTTG-AAGGTTTGGGGTAAAAA
1 AAAATGGTAA-TTTTTGAAAGTTTTGGGGTAAAAA
17433689 AATGTAATTT
Statistics
Matches: 177, Mismatches: 25, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
56 9 0.05
57 40 0.23
58 28 0.16
59 69 0.39
60 31 0.18
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (58 bp):
AAAATGGTAATTTTTGAAAGTTTTGGGGTAAAAATAGAATTTTTAGACATTTGAGGGT
Found at i:17433571 original size:116 final size:117
Alignment explanation
Indices: 17433421--17433669 Score: 353
Period size: 116 Copynumber: 2.1 Consensus size: 117
17433411 CTTCGAGAAC
* *
17433421 AAAATGGT-AATTTTCGAAAATTTTGAGGTCAAAAATGGAATTTTTGGATATTCGCGGGGTAAAA
1 AAAATGGTAAATTTT--AAAATTTTGAGGTCAAAAATGGAATTTTTAGATATTCG-AGGGTAAAA
** *
17433485 TGGTAATTTTTGAAAGTTTTGGGGTT-AAAAT-AGAATTTTTAGACATTTAAGGGT
63 TGGTAATTTTCAAAAGTTTTGGGGTTAAAAATGA-AAATTTTAGACATTTAAGGGT
*
17433539 AAAATGGTAAATTTT-AAATTTTGGGGTCAAAAATGGAATTTTTAGATATTCGAGGGTAAAATGG
1 AAAATGGTAAATTTTAAAATTTTGAGGTCAAAAATGGAATTTTTAGATATTCGAGGGTAAAATGG
**
17433603 TAATTTTCAAAAGTTTTGGGGTTAAAAATGAAAATTTTAGACATTTGGGGGT
66 TAATTTTCAAAAGTTTTGGGGTTAAAAATGAAAATTTTAGACATTTAAGGGT
*
17433655 AAAATGGTAATTTTT
1 AAAATGGTAAATTTT
17433670 TGAAGGTTTG
Statistics
Matches: 119, Mismatches: 9, Indels: 8
0.88 0.07 0.06
Matches are distributed among these distances:
115 32 0.27
116 72 0.61
117 1 0.01
118 8 0.07
119 6 0.05
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.37
Consensus pattern (117 bp):
AAAATGGTAAATTTTAAAATTTTGAGGTCAAAAATGGAATTTTTAGATATTCGAGGGTAAAATGG
TAATTTTCAAAAGTTTTGGGGTTAAAAATGAAAATTTTAGACATTTAAGGGT
Found at i:17433717 original size:29 final size:29
Alignment explanation
Indices: 17433685--17433792 Score: 101
Period size: 30 Copynumber: 3.7 Consensus size: 29
17433675 GTTTGGGGTA
17433685 AAAAAATGTAATTTTGGAAAAGTCGGGGG
1 AAAAAATGTAATTTTGGAAAAGTCGGGGG
* * * *
17433714 AAAAACTATAATCTTTGGAAAAGTCAGGGT
1 AAAAAATGTAAT-TTTGGAAAAGTCGGGGG
* * * * *
17433744 CAAAAATG-GATTTTGAAAAATTCGAGGG
1 AAAAAATGTAATTTTGGAAAAGTCGGGGG
*
17433772 TAAAAATGTAATTTTTGGAAA
1 AAAAAATGTAA-TTTTGGAAA
17433793 GTTTAGGGTT
Statistics
Matches: 60, Mismatches: 16, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
28 19 0.32
29 13 0.22
30 28 0.47
ACGTcount: A:0.44, C:0.06, G:0.23, T:0.28
Consensus pattern (29 bp):
AAAAAATGTAATTTTGGAAAAGTCGGGGG
Found at i:17433806 original size:30 final size:29
Alignment explanation
Indices: 17433477--17433907 Score: 135
Period size: 29 Copynumber: 14.7 Consensus size: 29
17433467 GATATTCGCG
*
17433477 GGGT-AAAATGGTAATTTTT-GAAAGTTTTG
1 GGGTAAAAAT-GTAATTTTTGGAAAG-TTTA
* * *
17433506 GGGTTAAAATAG-AATTTTTAGACA-TTTAA
1 GGGTAAAAAT-GTAATTTTTGGAAAGTTT-A
* * *
17433535 GGGT-AAAATGGTAAATTTT--AAATTTTG
1 GGGTAAAAAT-GTAATTTTTGGAAAGTTTA
* * * *
17433562 GGGTCAAAAATGGAATTTTTAGATA-TTCGA
1 GGGT-AAAAATGTAATTTTTGGAAAGTT-TA
** *
17433592 GGGT-AAAATGGTAA-TTTTCAAAAGTTTTG
1 GGGTAAAAAT-GTAATTTTTGGAAAG-TTTA
* * * * *
17433621 GGGTTAAAAATGAAAATTTTAGACA-TTTGG
1 GGG-TAAAAATGTAATTTTTGGAAAGTTT-A
* * *
17433651 GGGT-AAAATGGTAATTTTTTGAAGGTTTG
1 GGGTAAAAAT-GTAATTTTTGGAAAGTTTA
**
17433680 GGGTAAAAAAATGTAA-TTTTGGAAAAG-TCG
1 GGGT--AAAAATGTAATTTTTGG-AAAGTTTA
* * * *
17433710 GGGGAAAAACTATAATCTTTGGAAAAG-TCA
1 GGGTAAAAA-TGTAATTTTTGG-AAAGTTTA
* * * *
17433740 GGGTCAAAAATG-GA-TTTTGAAAAATTCGA
1 GGGT-AAAAATGTAATTTTTGGAAAGTT-TA
17433769 GGGTAAAAATGTAATTTTTGGAAAGTTTA
1 GGGTAAAAATGTAATTTTTGGAAAGTTTA
* *
17433798 GGGTTAAAAATGGAA-TTTTAGAAAGTTTA
1 GGG-TAAAAATGTAATTTTTGGAAAGTTTA
* * * *
17433827 GGGGCAAAAATGTAATGTTTTAGAAAATTCGA
1 -GGGTAAAAATGTAAT-TTTTGGAAAGTT-TA
* * * *
17433859 TGTTAAAAATG-AAATTTTGGAAAGTTCAA
1 GGGTAAAAATGTAATTTTTGGAAAGTT-TA
17433888 GGGTAAAAATGTAATTTTTG
1 GGGTAAAAATGTAATTTTTG
17433908 AAGACTTCAG
Statistics
Matches: 305, Mismatches: 61, Indels: 71
0.70 0.14 0.16
Matches are distributed among these distances:
27 9 0.03
28 52 0.17
29 110 0.36
30 86 0.28
31 42 0.14
32 6 0.02
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGGAAAGTTTA
Found at i:17435110 original size:14 final size:14
Alignment explanation
Indices: 17435077--17435114 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
17435067 TTTTATTTAA
*
17435077 TAATAATATT-GAT
1 TAATATTATTAGAT
*
17435090 TATTATTATTAGAT
1 TAATATTATTAGAT
17435104 TAATATTATTA
1 TAATATTATTA
17435115 ATATTATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (14 bp):
TAATATTATTAGAT
Found at i:17435127 original size:20 final size:20
Alignment explanation
Indices: 17435076--17435140 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 20
17435066 CTTTTATTTA
*
17435076 ATAATAATATTGATTATTATT
1 ATAATAATATT-ATTAATATT
17435097 ATTAGATTAATATTATTAATATT
1 A-TA-A-TAATATTATTAATATT
17435120 ATAATAAT-TATATTAATATT
1 ATAATAATAT-TATTAATATT
17435140 A
1 A
17435141 ATGGTATTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
19 1 0.03
20 15 0.38
21 2 0.05
22 4 0.10
23 10 0.26
24 7 0.18
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
ATAATAATATTATTAATATT
Found at i:17435728 original size:16 final size:16
Alignment explanation
Indices: 17435707--17435737 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17435697 GGTTTGAGTC
17435707 ACTTGGGCTCATTTGT
1 ACTTGGGCTCATTTGT
*
17435723 ACTTGGGGTCATTTG
1 ACTTGGGCTCATTTG
17435738 GGATTGAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.16, G:0.29, T:0.42
Consensus pattern (16 bp):
ACTTGGGCTCATTTGT
Found at i:17435870 original size:11 final size:11
Alignment explanation
Indices: 17435854--17435931 Score: 77
Period size: 11 Copynumber: 7.0 Consensus size: 11
17435844 AAACCGTTTC
*
17435854 AAATTTAAACT
1 AAATTTAAATT
17435865 AAATTTAAATTT
1 AAATTTAAA-TT
**
17435877 AAA-ACAAATT
1 AAATTTAAATT
* *
17435887 TAATTTAAAAT
1 AAATTTAAATT
17435898 AAATTTAAATTT
1 AAATTTAAA-TT
*
17435910 AAATTTAAAGT
1 AAATTTAAATT
17435921 AAATTTAAATT
1 AAATTTAAATT
17435932 TAAAAATAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
10 4 0.08
11 35 0.66
12 14 0.26
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (11 bp):
AAATTTAAATT
Found at i:17435874 original size:17 final size:17
Alignment explanation
Indices: 17435854--17435963 Score: 93
Period size: 17 Copynumber: 6.5 Consensus size: 17
17435844 AAACCGTTTC
17435854 AAATTTAAACTAAATTT
1 AAATTTAAACTAAATTT
17435871 AAATTTAAAAC-AAATTT
1 AAATTT-AAACTAAATTT
*
17435888 -AATTTAAAATAAATTT
1 AAATTTAAACTAAATTT
* *
17435904 AAATTTAAATTTAAA-GT
1 AAATTTAAA-CTAAATTT
* **
17435921 AAATTTAAATTTAAAAAT
1 AAATTTAAA-CTAAATTT
17435939 AAATTTAAAAC-AAATTT
1 AAATTT-AAACTAAATTT
*
17435956 AAACTTAA
1 AAATTTAA
17435964 TATGAATTTA
Statistics
Matches: 79, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
15 3 0.04
16 13 0.16
17 45 0.57
18 15 0.19
19 3 0.04
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (17 bp):
AAATTTAAACTAAATTT
Found at i:17435893 original size:5 final size:6
Alignment explanation
Indices: 17435816--17435947 Score: 94
Period size: 6 Copynumber: 22.0 Consensus size: 6
17435806 GTATTTAGAC
* * * *
17435816 TTTAAA ATTAAA TTTAAA GTTAAG TTTAAAA CCGTTTCAAA TTTAAA -CTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA ---TTT-AAA TTTAAA TTTAAA
** *
17435868 TTTAAA TTTAAA -ACAAA TTT-AA TTTAAA -ATAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* **
17435913 TTTAAA -GTAAA TTTAAA TTTAAA AATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
17435948 ACAAATTTAA
Statistics
Matches: 96, Mismatches: 21, Indels: 18
0.71 0.16 0.13
Matches are distributed among these distances:
5 20 0.21
6 65 0.68
7 5 0.05
10 6 0.06
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (6 bp):
TTTAAA
Found at i:17435914 original size:23 final size:23
Alignment explanation
Indices: 17435882--17435935 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
17435872 AATTTAAAAC
17435882 AAATTT-AATTTAAAATAAATTT
1 AAATTTAAATTTAAAATAAATTT
*
17435904 AAATTTAAATTTAAAGTAAATTT
1 AAATTTAAATTTAAAATAAATTT
17435927 AAATTTAAA
1 AAATTTAAA
17435936 AATAAATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 6 0.20
23 24 0.80
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
AAATTTAAATTTAAAATAAATTT
Found at i:17435941 original size:23 final size:23
Alignment explanation
Indices: 17435892--17435941 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
17435882 AAATTTAATT
**
17435892 TAAAATAAATTTAAATTTAAATT
1 TAAAATAAATTTAAATTTAAAAA
*
17435915 TAAAGTAAATTTAAATTTAAAAA
1 TAAAATAAATTTAAATTTAAAAA
17435938 TAAA
1 TAAA
17435942 TTTAAAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
TAAAATAAATTTAAATTTAAAAA
Found at i:17435948 original size:11 final size:11
Alignment explanation
Indices: 17435888--17435958 Score: 69
Period size: 11 Copynumber: 6.7 Consensus size: 11
17435878 AAACAAATTT
17435888 AATTTAAAATA
1 AATTTAAAATA
*
17435899 AATTTAAATTTA
1 AATTTAAA-ATA
*
17435911 AATTTAAAGTA
1 AATTTAAAATA
17435922 AATTT-AAAT-
1 AATTTAAAATA
*
17435931 --TTAAAAATA
1 AATTTAAAATA
*
17435940 AATTTAAAACA
1 AATTTAAAATA
17435951 AATTTAAA
1 AATTTAAA
17435959 CTTAATATGA
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
7 2 0.04
8 4 0.08
10 3 0.06
11 30 0.61
12 10 0.20
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (11 bp):
AATTTAAAATA
Found at i:17435953 original size:23 final size:23
Alignment explanation
Indices: 17435870--17435958 Score: 64
Period size: 23 Copynumber: 3.9 Consensus size: 23
17435860 AAACTAAATT
17435870 TAAATTTAAAACAAATTTAATTTAAAA
1 TAAATTTAAAACAAATTT-A---AAAA
** *
17435897 TAAATTTAAATTTAAATTT-AAAG
1 TAAATTTAAA-ACAAATTTAAAAA
17435920 TAAATTT-----AAATTTAAAAA
1 TAAATTTAAAACAAATTTAAAAA
17435938 TAAATTTAAAACAAATTTAAA
1 TAAATTTAAAACAAATTTAAA
17435959 CTTAATATGA
Statistics
Matches: 51, Mismatches: 4, Indels: 18
0.70 0.05 0.25
Matches are distributed among these distances:
17 6 0.12
18 10 0.20
23 19 0.37
27 10 0.20
28 6 0.12
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.38
Consensus pattern (23 bp):
TAAATTTAAAACAAATTTAAAAA
Found at i:17439299 original size:18 final size:19
Alignment explanation
Indices: 17439266--17439304 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
17439256 GACTTAAATA
*
17439266 AAAACTTTTTGAATAGTTC
1 AAAACTTTTCGAATAGTTC
17439285 AAAAC-TTTCGAATAGTTC
1 AAAACTTTTCGAATAGTTC
17439303 AA
1 AA
17439305 GATCAAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (19 bp):
AAAACTTTTCGAATAGTTC
Found at i:17451998 original size:3 final size:3
Alignment explanation
Indices: 17451992--17452030 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
17451982 GGAAGAAGTG
17451992 GAA GAA GAA GAA GAA GAA GAA -AGA GAA GAA GAA -AA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GA-A GAA GAA GAA GAA GAA G
17452031 TCGAGGCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 3 0.09
3 29 0.88
4 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:17452506 original size:17 final size:17
Alignment explanation
Indices: 17452463--17452507 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
17452453 ATCTCCTTTG
*
17452463 TCATTGCATTTTAATTA
1 TCATTGCATTTGAATTA
* * *
17452480 TCACTACATTTGCATTA
1 TCATTGCATTTGAATTA
17452497 TCATTGCATTT
1 TCATTGCATTT
17452508 CCACTTTTCA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.49
Consensus pattern (17 bp):
TCATTGCATTTGAATTA
Found at i:17454833 original size:22 final size:22
Alignment explanation
Indices: 17454792--17454844 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
17454782 GTATTCTACC
*
17454792 TAAGGATGA-TAAAGACTTAAT
1 TAAGGATAATTAAAGACTTAAT
*
17454813 TAAGGATAATTAATGACTTAAT
1 TAAGGATAATTAAAGACTTAAT
17454835 T-A-GATAATTA
1 TAAGGATAATTA
17454845 GGGATTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 8 0.28
21 9 0.31
22 12 0.41
ACGTcount: A:0.47, C:0.04, G:0.15, T:0.34
Consensus pattern (22 bp):
TAAGGATAATTAAAGACTTAAT
Found at i:17456070 original size:20 final size:18
Alignment explanation
Indices: 17456023--17456101 Score: 74
Period size: 17 Copynumber: 4.3 Consensus size: 18
17456013 CAAGATAAAA
17456023 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
17456040 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
***
17456060 ATTAAATTAATAAAAAACT
1 ATTAAATTAATATTTAA-T
17456079 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
17456096 ATTAAA
1 ATTAAA
17456102 CTATTAAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
17 15 0.30
18 6 0.12
19 14 0.28
20 15 0.30
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:17456083 original size:25 final size:25
Alignment explanation
Indices: 17456055--17456109 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
17456045 GATAATCACT
17456055 TTAATATTAAA-TTAATAAAAAACTA
1 TTAA-ATTAAATTTAATAAAAAACTA
**
17456080 TTAAATTAAATTTAATATTAAACTA
1 TTAAATTAAATTTAATAAAAAACTA
17456105 TTAAA
1 TTAAA
17456110 ATAATTTCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 6 0.22
25 21 0.78
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (25 bp):
TTAAATTAAATTTAATAAAAAACTA
Found at i:17472981 original size:37 final size:37
Alignment explanation
Indices: 17472908--17473038 Score: 194
Period size: 37 Copynumber: 3.6 Consensus size: 37
17472898 AATCACATTA
*
17472908 CATGAAGAACATA-CCCACATATTTTCTATCACATGG
1 CATGAAGAACATACCCCACATATTTTCTGTCACATGG
* *
17472944 CATGAAGAACATACCCCATATATTTTCTGTCATATGG
1 CATGAAGAACATACCCCACATATTTTCTGTCACATGG
* **
17472981 CATGAAGAATATACTTCACATATTTTCTGTCACATGG
1 CATGAAGAACATACCCCACATATTTTCTGTCACATGG
17473018 CATGAAGAACATA-CCCACATA
1 CATGAAGAACATACCCCACATA
17473039 GTCACTTTCA
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
36 19 0.23
37 64 0.77
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (37 bp):
CATGAAGAACATACCCCACATATTTTCTGTCACATGG
Found at i:17473155 original size:23 final size:23
Alignment explanation
Indices: 17473120--17473895 Score: 885
Period size: 23 Copynumber: 33.9 Consensus size: 23
17473110 ATCTTAATTC
17473120 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
17473143 TTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
17473166 TTTAAGCACAAATCACAGTAATA
1 TTTAAGCACAAATCACATTAATA
17473189 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
17473212 TTTAAGTATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
17473235 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
17473258 TTTAAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* * * *
17473281 TTTGAGAATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
17473304 TTTAAGAACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
17473327 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * * *
17473350 TTAAAGCATAAATCAGATTATTA
1 TTTAAGCACAAATCACATTAATA
*
17473373 TTTAAGCACAAATTACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
17473396 TTTGAGCACAAACCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
17473419 CTTAAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
17473442 TTTTAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* **
17473465 TTTAAGCATAAATCATGTTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
17473488 CTTAAGCACAAGTCACATTACTA
1 TTTAAGCACAAATCACATTAATA
* ** *
17473511 TTTAATCGTAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
17473534 TTAAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
17473557 TTTAAGCA-TAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
17473579 TTTGAGCACAAACCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
17473602 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * * *
17473625 TTTAAGAATAAATCATATTAACA
1 TTTAAGCACAAATCACATTAATA
* * *
17473648 TTTAAGCATAAATCACAATATTA
1 TTTAAGCACAAATCACATTAATA
*
17473671 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
17473694 TTTAAGCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
**
17473717 TTGGAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * **
17473740 TTTAAGCATAAATCATATTAGCA
1 TTTAAGCACAAATCACATTAATA
* *
17473763 TTCAAGCATC-AATCACAATAATA
1 TTTAAGCA-CAAATCACATTAATA
*
17473786 TTTAAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
17473809 TTTAAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
17473832 TTTAAGCACAAGTCAAATTAACA
1 TTTAAGCACAAATCACATTAATA
* *
17473855 --TAAGCACAAATCACAATAATT
1 TTTAAGCACAAATCACATTAATA
*
17473876 TTTAAGCATAAATCACATTA
1 TTTAAGCACAAATCACATTA
17473896 TCGATGTATA
Statistics
Matches: 638, Mismatches: 110, Indels: 10
0.84 0.15 0.01
Matches are distributed among these distances:
21 16 0.03
22 21 0.03
23 601 0.94
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.34
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:17491301 original size:21 final size:21
Alignment explanation
Indices: 17491275--17491440 Score: 138
Period size: 21 Copynumber: 7.9 Consensus size: 21
17491265 AATAAAACCT
17491275 TGTATTGCACTTCGGTGCCCC
1 TGTATTGCACTTCGGTGCCCC
** *
17491296 TGTATTGCAC-TCTAATGCCTC
1 TGTATTGCACTTC-GGTGCCCC
*
17491317 TATATTGCACTTCGGTGCCCC
1 TGTATTGCACTTCGGTGCCCC
*
17491338 TGTATTGCAC-TCTGGTGCCCA
1 TGTATTGCACTTC-GGTGCCCC
* ** *
17491359 TGTATTGCACTCCAATGCCTC
1 TGTATTGCACTTCGGTGCCCC
* * **
17491380 TGTAATGCATTTTAGTGCCCC
1 TGTATTGCACTTCGGTGCCCC
* * *
17491401 TGTATAGCACTTCGATGCCTC
1 TGTATTGCACTTCGGTGCCCC
* *
17491422 TGTGTTGCACTTTGGTGCC
1 TGTATTGCACTTCGGTGCC
17491441 GTTACGTGTT
Statistics
Matches: 110, Mismatches: 31, Indels: 8
0.74 0.21 0.05
Matches are distributed among these distances:
20 4 0.04
21 103 0.94
22 3 0.03
ACGTcount: A:0.15, C:0.29, G:0.20, T:0.36
Consensus pattern (21 bp):
TGTATTGCACTTCGGTGCCCC
Found at i:17491376 original size:63 final size:63
Alignment explanation
Indices: 17491275--17491432 Score: 194
Period size: 63 Copynumber: 2.5 Consensus size: 63
17491265 AATAAAACCT
* * * *
17491275 TGTATTGCACTTCGGTGCCCCTGTATTGCACTCTAATGCCTCTATATTGCACTTCGGTGCCCC
1 TGTATTGCACTTCGGTGCCCATGTATTGCACTCCAATGCCTCTATAATGCACTTCAGTGCCCC
* * *
17491338 TGTATTGCAC-TCTGGTGCCCATGTATTGCACTCCAATGCCTCTGTAATGCATTTTAGTGCCCC
1 TGTATTGCACTTC-GGTGCCCATGTATTGCACTCCAATGCCTCTATAATGCACTTCAGTGCCCC
* * *
17491401 TGTATAGCACTTCGATGCCTC-TGTGTTGCACT
1 TGTATTGCACTTCGGTGCC-CATGTATTGCACT
17491433 TTGGTGCCGT
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
62 2 0.02
63 77 0.94
64 3 0.04
ACGTcount: A:0.16, C:0.29, G:0.20, T:0.35
Consensus pattern (63 bp):
TGTATTGCACTTCGGTGCCCATGTATTGCACTCCAATGCCTCTATAATGCACTTCAGTGCCCC
Found at i:17491440 original size:42 final size:42
Alignment explanation
Indices: 17491275--17491432 Score: 172
Period size: 42 Copynumber: 3.8 Consensus size: 42
17491265 AATAAAACCT
* * *
17491275 TGTATTGCACTTCGGTGCCCCTGTATTGCACTCTAATGCCTC
1 TGTATTGCACTTCGATGCCCCTGTATTGCACTCTAGTGCCCC
* * * *
17491317 TATATTGCACTTCGGTGCCCCTGTATTGCACTCTGGTGCCCA
1 TGTATTGCACTTCGATGCCCCTGTATTGCACTCTAGTGCCCC
* * * * * *
17491359 TGTATTGCACTCCAATGCCTCTGTAATGCATTTTAGTGCCCC
1 TGTATTGCACTTCGATGCCCCTGTATTGCACTCTAGTGCCCC
* * *
17491401 TGTATAGCACTTCGATGCCTCTGTGTTGCACT
1 TGTATTGCACTTCGATGCCCCTGTATTGCACT
17491433 TTGGTGCCGT
Statistics
Matches: 95, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 95 1.00
ACGTcount: A:0.16, C:0.29, G:0.20, T:0.35
Consensus pattern (42 bp):
TGTATTGCACTTCGATGCCCCTGTATTGCACTCTAGTGCCCC
Found at i:17498932 original size:12 final size:13
Alignment explanation
Indices: 17498915--17498943 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17498905 CAGTAATTTA
17498915 TTCTTTC-TCTTT
1 TTCTTTCTTCTTT
17498927 TTCTTTCTTCTTT
1 TTCTTTCTTCTTT
17498940 TTCT
1 TTCT
17498944 CTTTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTCTTTCTTCTTT
Found at i:17526153 original size:47 final size:47
Alignment explanation
Indices: 17526102--17526231 Score: 172
Period size: 47 Copynumber: 2.8 Consensus size: 47
17526092 ATAGAGGCAT
*
17526102 CATACAGAA-TACGCCACAAAGGCCAGATTAAAATACCACAGAGGTAA
1 CATACA-AATTACGCCACAAAGGCCAGATCAAAATACCACAGAGGTAA
* * *
17526149 CATACAAATTACGCCACAAAGGCCAGATCAGAGTACCACATAGGTAA
1 CATACAAATTACGCCACAAAGGCCAGATCAAAATACCACAGAGGTAA
** * *
17526196 CATACAAATTACATCACAAAGTCCAGATCATAATAC
1 CATACAAATTACGCCACAAAGGCCAGATCAAAATAC
17526232 ACAATAAAGG
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
46 2 0.03
47 71 0.97
ACGTcount: A:0.45, C:0.25, G:0.14, T:0.16
Consensus pattern (47 bp):
CATACAAATTACGCCACAAAGGCCAGATCAAAATACCACAGAGGTAA
Found at i:17531519 original size:17 final size:17
Alignment explanation
Indices: 17531499--17531539 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
17531489 ACATTTCTTC
17531499 TGTCATTGCATTTTTAT
1 TGTCATTGCATTTTTAT
*
17531516 TGTCACTGCATTTTTAT
1 TGTCATTGCATTTTTAT
17531533 TGTCATT
1 TGTCATT
17531540 ACATCTACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.56
Consensus pattern (17 bp):
TGTCATTGCATTTTTAT
Found at i:17533812 original size:23 final size:24
Alignment explanation
Indices: 17533786--17533832 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
17533776 AACTATTTAT
17533786 TTTATTTTA-ATTTG-CTCTGACAA
1 TTTATTTTATATTTGCCTC-GACAA
17533809 TTTATTTTATATTTGCCTCGACAA
1 TTTATTTTATATTTGCCTCGACAA
17533833 CTTAACTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.41
24 10 0.45
25 3 0.14
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.51
Consensus pattern (24 bp):
TTTATTTTATATTTGCCTCGACAA
Found at i:17545276 original size:61 final size:61
Alignment explanation
Indices: 17545211--17545327 Score: 207
Period size: 61 Copynumber: 1.9 Consensus size: 61
17545201 AATCCACTAT
*
17545211 GTTAACAACGACCACACTGTTACGCGAAATTATGGGCATCTCAAAACAAATTGGGCAGTAC
1 GTTAACAACAACCACACTGTTACGCGAAATTATGGGCATCTCAAAACAAATTGGGCAGTAC
* *
17545272 GTTAACAACAATCACACTGTTACGCGAAATTATGGGCATCTCGAAACAAATTGGGC
1 GTTAACAACAACCACACTGTTACGCGAAATTATGGGCATCTCAAAACAAATTGGGC
17545328 TAATAGAATC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (61 bp):
GTTAACAACAACCACACTGTTACGCGAAATTATGGGCATCTCAAAACAAATTGGGCAGTAC
Found at i:17558581 original size:466 final size:466
Alignment explanation
Indices: 17557710--17558641 Score: 1641
Period size: 466 Copynumber: 2.0 Consensus size: 466
17557700 CTATCCCAAC
17557710 AAGGACATGGTGAAGAAGATGTTGAATAGTCTCTCAAAGTCTTGGGAAGCTAAAGTGACGACAAT
1 AAGGACATGGTGAAGAAGATGTTGAATAGTCTCTCAAAGTCTTGGGAAGCTAAAGTGACGACAAT
* *
17557775 AGAAGAATCAAAGGATCTCAACTTACTCTCCCTTGATGAGCTCATCGGTTCCTTGTTGACATATG
66 AGAAGAATCAAAGGATCTCAACTTACTCTCCCTTGATGAGCTCATCGGTTCCTTGTTAACATAAG
*
17557840 AAATAATTATCAACCACAATGCGTTAGAAATCAAAGAAGCTCCAAAAAAAGTGGGAGTTGCCTTG
131 AAATAATTATCAACCACAATGCATTAGAAATCAAAGAAGCTCCAAAAAAAGTGGGAGTTGCCTTG
* * *
17557905 AAATCAACAACTTGTGAGCAGGGTGAAGGATCTAGTAATGATGATGATGAGGAAGAGATGGCTAT
196 AAATAAACAACTAGTGAGCAGGATGAAGGATCTAGTAATGATGATGATGAGGAAGAGATGGCTAT
* *
17557970 GCTTGCAAATAAATTTAAAAAATTCACGAAGTTCAACAAATCCAAAAGATTCTCGAGAAGAGACA
261 GCTTGCAAATAAATTCAAAAAATTCACGAAGTTCAACAAATCCAAAAGATTCCCGAGAAGAGACA
* * **
17558035 TCATCAAGGGTGAACCAAGCAAGAAGGAAAATGACTTAATCATTTGCTATGAGTGCAAAAAGTTT
326 TCATCAAGGGTGAACCAAGCAAGAAGGAAAATGACTCAATCATTTCCTATGAGTGCAAAAAGTCG
*
17558100 GGTCACATTAAATTTGATTGCCCATAATTGAAGAAGAAATAGGCATTAAAACAAAAGAAGAAAGC
391 GGTCACATTAAATTTGATTGCCCACAATTGAAGAAGAAATAGGCATTAAAACAAAAGAAGAAAGC
17558165 CATGATGGCAA
456 CATGATGGCAA
*
17558176 AAGGACATGGTGAAGAAGATGTTGAATAGTCTC-CTAAAGTCTTGGGAAGCTAAAGTGACGGCAA
1 AAGGACATGGTGAAGAAGATGTTGAATAGTCTCTC-AAAGTCTTGGGAAGCTAAAGTGACGACAA
*
17558240 TAGAAGAATCAAAGGATCTTAACTTACTCTCCCTTGATGAGCTCATCGGTTCCTTGTTAACATAA
65 TAGAAGAATCAAAGGATCTCAACTTACTCTCCCTTGATGAGCTCATCGGTTCCTTGTTAACATAA
*
17558305 GAAATAATTATCAACCACAATGCATTAGAAATCAAAGAAGCTCCAAAGAAAGTGGGAGTTGCCTT
130 GAAATAATTATCAACCACAATGCATTAGAAATCAAAGAAGCTCCAAAAAAAGTGGGAGTTGCCTT
* * *
17558370 GAAATAAACAACTAGTGAGCAGGATTAAGGATCTAGTAATTATGATGATGAGGAGGAGATGGCTA
195 GAAATAAACAACTAGTGAGCAGGATGAAGGATCTAGTAATGATGATGATGAGGAAGAGATGGCTA
* **
17558435 TGCTTGCAAATAAATTCAAAAAATTTATTAAGTTCAACAAATCCAAAAGATTCCCGAGAAGAGAC
260 TGCTTGCAAATAAATTCAAAAAATTCACGAAGTTCAACAAATCCAAAAGATTCCCGAGAAGAGAC
17558500 ATCATCAAGGGTGAACCAAGCAAGAAGGAAAATGACTCAATCATTTCCTATGAGTGCAAAAAGTC
325 ATCATCAAGGGTGAACCAAGCAAGAAGGAAAATGACTCAATCATTTCCTATGAGTGCAAAAAGTC
*
17558565 GGGTCATATTAAATTTGATTGCCCACAATTGAAGAAGAAATAGGCATTAAAACAAAAGAAGAAAG
390 GGGTCACATTAAATTTGATTGCCCACAATTGAAGAAGAAATAGGCATTAAAACAAAAGAAGAAAG
17558630 CCATGATGGCAA
455 CCATGATGGCAA
17558642 CTTGGAGCGA
Statistics
Matches: 442, Mismatches: 23, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
465 1 0.00
466 441 1.00
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.23
Consensus pattern (466 bp):
AAGGACATGGTGAAGAAGATGTTGAATAGTCTCTCAAAGTCTTGGGAAGCTAAAGTGACGACAAT
AGAAGAATCAAAGGATCTCAACTTACTCTCCCTTGATGAGCTCATCGGTTCCTTGTTAACATAAG
AAATAATTATCAACCACAATGCATTAGAAATCAAAGAAGCTCCAAAAAAAGTGGGAGTTGCCTTG
AAATAAACAACTAGTGAGCAGGATGAAGGATCTAGTAATGATGATGATGAGGAAGAGATGGCTAT
GCTTGCAAATAAATTCAAAAAATTCACGAAGTTCAACAAATCCAAAAGATTCCCGAGAAGAGACA
TCATCAAGGGTGAACCAAGCAAGAAGGAAAATGACTCAATCATTTCCTATGAGTGCAAAAAGTCG
GGTCACATTAAATTTGATTGCCCACAATTGAAGAAGAAATAGGCATTAAAACAAAAGAAGAAAGC
CATGATGGCAA
Found at i:17573574 original size:21 final size:20
Alignment explanation
Indices: 17573544--17573582 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
17573534 GTTATTTTCG
17573544 TTCTTACTCTCACAAGTTTAT
1 TTCTTACTCT-ACAAGTTTAT
* *
17573565 TTCTTTCTCTGCAAGTTT
1 TTCTTACTCTACAAGTTT
17573583 CTTTTAACCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.18, C:0.23, G:0.08, T:0.51
Consensus pattern (20 bp):
TTCTTACTCTACAAGTTTAT
Found at i:17576182 original size:6 final size:6
Alignment explanation
Indices: 17576171--17576213 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
17576161 ATGTTAAATG
* *
17576171 AGAAAA AGAAAA GAAAAAA AGAGAAA AGAGAA AGAAAA AGAAA
1 AGAAAA AGAAAA -AGAAAA AGA-AAA AGAAAA AGAAAA AGAAA
17576214 TATTGCTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
6 20 0.65
7 11 0.35
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:17583299 original size:13 final size:15
Alignment explanation
Indices: 17583276--17583307 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
17583266 TTGTCTTTTA
17583276 GTTTACTTTAA-TTT
1 GTTTACTTTAAGTTT
17583290 GTTT-CTTTAAGTTT
1 GTTTACTTTAAGTTT
17583304 GTTT
1 GTTT
17583308 TGCAAGAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.16, C:0.06, G:0.12, T:0.66
Consensus pattern (15 bp):
GTTTACTTTAAGTTT
Found at i:17585085 original size:3 final size:3
Alignment explanation
Indices: 17585062--17585112 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
17585052 AAGAAAATAA
* *
17585062 AAG AA- AAG AAG ATG AAA AAG AAG -AG AAG AAAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG
17585106 AAG AAG A
1 AAG AAG A
17585113 TGTTGCCCGA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:17590387 original size:20 final size:20
Alignment explanation
Indices: 17590374--17590427 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
17590364 ATACTTGCAT
17590374 AAAAATATTGATACTCGAGG
1 AAAAATATTGATACTCGAGG
17590394 AAAAATATTGATACTCGAGG
1 AAAAATATTGATACTCGAGG
17590414 AAAAATATTGATAC
1 AAAAATATTGATAC
17590428 CACGGGCTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.26
Consensus pattern (20 bp):
AAAAATATTGATACTCGAGG
Found at i:17592515 original size:22 final size:23
Alignment explanation
Indices: 17592468--17592517 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
17592458 CTTTATTTGA
17592468 TAAAATATTTTGATATAACAAAT
1 TAAAATATTTTGATATAACAAAT
*
17592491 TAAAATATTTTTGA-AT-ACAAGT
1 TAAAATA-TTTTGATATAACAAAT
17592513 TAAAA
1 TAAAA
17592518 CTGACAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 10 0.40
23 9 0.36
24 6 0.24
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (23 bp):
TAAAATATTTTGATATAACAAAT
Found at i:17594128 original size:14 final size:16
Alignment explanation
Indices: 17594099--17594130 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
17594089 CAGCCGATGC
17594099 ACACCTCAACCTTATA
1 ACACCTCAACCTTATA
17594115 ACACCTC-A-CTTATA
1 ACACCTCAACCTTATA
17594129 AC
1 AC
17594131 TAATTAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 1 0.06
16 7 0.44
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
ACACCTCAACCTTATA
Found at i:17594614 original size:20 final size:21
Alignment explanation
Indices: 17594581--17594619 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
17594571 CGCAAAAACC
*
17594581 CACACGCCCATGTG-AAACGA
1 CACACACCCATGTGCAAACGA
*
17594601 CACACACCCGTGTGCAAAC
1 CACACACCCATGTGCAAAC
17594620 CACTGCACCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.33, C:0.38, G:0.18, T:0.10
Consensus pattern (21 bp):
CACACACCCATGTGCAAACGA
Found at i:17596924 original size:19 final size:19
Alignment explanation
Indices: 17596884--17596931 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
17596874 AAATTATTTT
*
17596884 AAAATTA-TAATTTAACCC
1 AAAATTATTTATTTAACCC
*
17596902 AAAA-TATTTATTTTACCC
1 AAAATTATTTATTTAACCC
17596920 AAAAATTATTTA
1 -AAAATTATTTA
17596932 AAACCATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 2 0.08
18 13 0.52
19 4 0.16
20 6 0.24
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATTATTTATTTAACCC
Found at i:17598091 original size:21 final size:21
Alignment explanation
Indices: 17598050--17598091 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 21
17598040 AGCCTTTAGA
* *
17598050 TAAGGAGAGATTTTGGATAAT
1 TAAGGAGAGAGTTAGGATAAT
17598071 TAAGG-GAGAGTTAGGACTAAT
1 TAAGGAGAGAGTTAGGA-TAAT
17598092 GAACATGCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.38, C:0.02, G:0.31, T:0.29
Consensus pattern (21 bp):
TAAGGAGAGAGTTAGGATAAT
Found at i:17603611 original size:12 final size:12
Alignment explanation
Indices: 17603594--17603619 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17603584 TGTTATCATG
17603594 ATGAATGCTATT
1 ATGAATGCTATT
17603606 ATGAATGCTATT
1 ATGAATGCTATT
17603618 AT
1 AT
17603620 TTCTTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:17606630 original size:22 final size:21
Alignment explanation
Indices: 17606602--17606646 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
17606592 ATATAAACAT
17606602 TCAATTATATTGGCACAATCAA
1 TCAATTATATTGGCACAAT-AA
*
17606624 TCAATTATATTGGCATAATAA
1 TCAATTATATTGGCACAATAA
17606645 TC
1 TC
17606647 CATGGCACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.36
Consensus pattern (21 bp):
TCAATTATATTGGCACAATAA
Found at i:17612621 original size:21 final size:21
Alignment explanation
Indices: 17612597--17612650 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
17612587 CTGATGATAG
*
17612597 TTCTACCGATACAAGTGTAAC
1 TTCTACCGATACAAGTCTAAC
* * *
17612618 TTCTATCGAAACAAGTCTTAC
1 TTCTACCGATACAAGTCTAAC
*
17612639 TTCTACGGATAC
1 TTCTACCGATAC
17612651 TAAAAACTCT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.31
Consensus pattern (21 bp):
TTCTACCGATACAAGTCTAAC
Found at i:17615157 original size:14 final size:14
Alignment explanation
Indices: 17615138--17615169 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
17615128 ACTAACTTCT
17615138 AATTCACTAATTAA
1 AATTCACTAATTAA
*
17615152 AATTCACTAATTCA
1 AATTCACTAATTAA
17615166 AATT
1 AATT
17615170 TTTCATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.38
Consensus pattern (14 bp):
AATTCACTAATTAA
Found at i:17615208 original size:14 final size:14
Alignment explanation
Indices: 17615189--17615219 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
17615179 AAAATTCACT
17615189 AATTCACTAATTAA
1 AATTCACTAATTAA
*
17615203 AATTCACTAATTCA
1 AATTCACTAATTAA
17615217 AAT
1 AAT
17615220 CTTTAACAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.35
Consensus pattern (14 bp):
AATTCACTAATTAA
Found at i:17618155 original size:24 final size:25
Alignment explanation
Indices: 17618106--17618266 Score: 139
Period size: 25 Copynumber: 6.4 Consensus size: 25
17618096 AGTTTAGCTT
* *
17618106 TTACGAGCGCAGATAGAATA-CTGCTC
1 TTACGAGC-CAGACAAAATATC-GCTC
*
17618132 TTAC-AGCCAGTCAAAACT-TCGCTC
1 TTACGAGCCAGACAAAA-TATCGCTC
* *
17618156 TTACGAGCCAAACGAAATATCGCTC
1 TTACGAGCCAGACAAAATATCGCTC
**
17618181 TTACGAGCCAGACGGAATATCGCTC
1 TTACGAGCCAGACAAAATATCGCTC
* *** *
17618206 TTACGAGCCAAATGGAATATCACTC
1 TTACGAGCCAGACAAAATATCGCTC
* * *
17618231 TTACGAGCTAGACGAAATATCACTC
1 TTACGAGCCAGACAAAATATCGCTC
17618256 TTACGAGCCAG
1 TTACGAGCCAG
17618267 TCTTTAGTAA
Statistics
Matches: 115, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
24 15 0.13
25 96 0.83
26 4 0.03
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (25 bp):
TTACGAGCCAGACAAAATATCGCTC
Found at i:17618178 original size:25 final size:25
Alignment explanation
Indices: 17618150--17618265 Score: 160
Period size: 25 Copynumber: 4.6 Consensus size: 25
17618140 AGTCAAAACT
17618150 TCGCTCTTACGAGCCAAACGAAATA
1 TCGCTCTTACGAGCCAAACGAAATA
* *
17618175 TCGCTCTTACGAGCCAGACGGAATA
1 TCGCTCTTACGAGCCAAACGAAATA
* *
17618200 TCGCTCTTACGAGCCAAATGGAATA
1 TCGCTCTTACGAGCCAAACGAAATA
* * *
17618225 TCACTCTTACGAGCTAGACGAAATA
1 TCGCTCTTACGAGCCAAACGAAATA
*
17618250 TCACTCTTACGAGCCA
1 TCGCTCTTACGAGCCA
17618266 GTCTTTAGTA
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 81 1.00
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (25 bp):
TCGCTCTTACGAGCCAAACGAAATA
Found at i:17618185 original size:75 final size:75
Alignment explanation
Indices: 17618106--17618266 Score: 177
Period size: 75 Copynumber: 2.1 Consensus size: 75
17618096 AGTTTAGCTT
* * *
17618106 TTACGAGCGCAGATAGAATA-CTGCTCTTAC-AGCC-AGTCAAAACT-TCGCTCTTACGAGCCAA
1 TTACGAGC-CAGACAGAATATC-GCTCTTACGAGCCAAAT-AAAA-TATCACTCTTACGAGCCAA
*
17618167 ACGAAATATCGCTC
62 ACGAAATATCACTC
* ** * *
17618181 TTACGAGCCAGACGGAATATCGCTCTTACGAGCCAAATGGAATATCACTCTTACGAGCTAGACGA
1 TTACGAGCCAGACAGAATATCGCTCTTACGAGCCAAATAAAATATCACTCTTACGAGCCAAACGA
17618246 AATATCACTC
66 AATATCACTC
17618256 TTACGAGCCAG
1 TTACGAGCCAG
17618267 TCTTTAGTAA
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
74 18 0.25
75 53 0.73
76 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (75 bp):
TTACGAGCCAGACAGAATATCGCTCTTACGAGCCAAATAAAATATCACTCTTACGAGCCAAACGA
AATATCACTC
Found at i:17618190 original size:50 final size:50
Alignment explanation
Indices: 17618128--17618265 Score: 181
Period size: 50 Copynumber: 2.8 Consensus size: 50
17618118 ATAGAATACT
* *
17618128 GCTCTTAC-AGCCAGTCAAAACT-TCGCTCTTACGAGCCAAACGAAATATC
1 GCTCTTACGAGCCAGACGAAA-TATCGCTCTTACGAGCCAAACGAAATATC
* * *
17618177 GCTCTTACGAGCCAGACGGAATATCGCTCTTACGAGCCAAATGGAATATC
1 GCTCTTACGAGCCAGACGAAATATCGCTCTTACGAGCCAAACGAAATATC
* * *
17618227 ACTCTTACGAGCTAGACGAAATATCACTCTTACGAGCCA
1 GCTCTTACGAGCCAGACGAAATATCGCTCTTACGAGCCA
17618266 GTCTTTAGTA
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
49 9 0.12
50 69 0.88
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.22
Consensus pattern (50 bp):
GCTCTTACGAGCCAGACGAAATATCGCTCTTACGAGCCAAACGAAATATC
Found at i:17620425 original size:19 final size:19
Alignment explanation
Indices: 17620398--17620436 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
17620388 ATTATCCAGG
*
17620398 TAAGTTTGAACAATCTAAT
1 TAAGGTTGAACAATCTAAT
*
17620417 TAAGGTTGAATAATCTAAT
1 TAAGGTTGAACAATCTAAT
17620436 T
1 T
17620437 CATCATATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (19 bp):
TAAGGTTGAACAATCTAAT
Found at i:17621056 original size:19 final size:20
Alignment explanation
Indices: 17621034--17621075 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
17621024 ATGCAAACAC
*
17621034 AATAAGAA-ATATCAAAAAG
1 AATAAGAACATACCAAAAAG
*
17621053 AAT-AGAACATACCAAAAAT
1 AATAAGAACATACCAAAAAG
17621072 AATA
1 AATA
17621076 TTAGACACTG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.67, C:0.10, G:0.07, T:0.17
Consensus pattern (20 bp):
AATAAGAACATACCAAAAAG
Found at i:17621715 original size:25 final size:23
Alignment explanation
Indices: 17621674--17621719 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
17621664 CCAATTAGGG
17621674 AATTATTGTTTAGATTTAATTCT
1 AATTATTGTTTAGATTTAATTCT
*
17621697 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTAG-ATTTAATT
17621720 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTCT
Found at i:17625666 original size:12 final size:12
Alignment explanation
Indices: 17625628--17625655 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
17625618 TCATGTTTTT
17625628 AAAAAAAATTGA
1 AAAAAAAATTGA
17625640 AAAAAAAATTGA
1 AAAAAAAATTGA
17625652 AAAA
1 AAAA
17625656 TTCAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAAAAATTGA
Found at i:17625701 original size:6 final size:6
Alignment explanation
Indices: 17625675--17625735 Score: 70
Period size: 6 Copynumber: 10.3 Consensus size: 6
17625665 AATTAGAATA
* * * *
17625675 TTTATT TTCATT TTCATT TTTATT TTTAGT TTTAGT TTTA-T TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
17625722 TTTAAT TTTATT TT
1 TTTATT TTTATT TT
17625736 AATTATGCAC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
5 5 0.10
6 44 0.90
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.75
Consensus pattern (6 bp):
TTTATT
Found at i:17625724 original size:17 final size:17
Alignment explanation
Indices: 17625675--17625736 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
17625665 AATTAGAATA
* *
17625675 TTTATTTTCATTTTCATT
1 TTTATTTT-ATTTTTAAT
* *
17625693 TTTATTTTTAGTTTTAGT
1 TTTA-TTTTATTTTTAAT
17625711 TTTATTTTATTTTTAAT
1 TTTATTTTATTTTTAAT
17625728 TTTATTTTA
1 TTTATTTTA
17625737 ATTATGCACT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
17 20 0.53
18 14 0.37
19 4 0.11
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTATTTTATTTTTAAT
Found at i:17626657 original size:12 final size:12
Alignment explanation
Indices: 17626640--17626725 Score: 67
Period size: 11 Copynumber: 7.4 Consensus size: 12
17626630 TTAGAAAAAG
17626640 AAAAAAAAGAG-
1 AAAAAAAAGAGA
*
17626651 -AAAAAAAGTTGA
1 AAAAAAAAG-AGA
*
17626663 AAAGAAAAATTA-A
1 AAA-AAAAA-GAGA
17626676 AAAAAAAAGAG-
1 AAAAAAAAGAGA
**
17626687 AAAAATGAG-GA
1 AAAAAAAAGAGA
17626698 AAAAAAAAGAGA
1 AAAAAAAAGAGA
17626710 AAAAAAAAGA-A
1 AAAAAAAAGAGA
17626721 AAAAA
1 AAAAA
17626726 TATGTCTGAG
Statistics
Matches: 59, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
10 9 0.15
11 22 0.37
12 17 0.29
13 6 0.10
14 5 0.08
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (12 bp):
AAAAAAAAGAGA
Found at i:17626691 original size:34 final size:34
Alignment explanation
Indices: 17626632--17626726 Score: 113
Period size: 34 Copynumber: 2.8 Consensus size: 34
17626622 TTTATTGTTT
* **
17626632 AGAAAAAGAAAAAAAAGAGAAAAAAA-GTTGAAA
1 AGAAAAAGAAAAAAAAAAGAAAAAAATGAGGAAA
* *
17626665 AGAAAAATTAAAAAAAAAAGAGAAAAATGAGGAAA
1 AGAAAAA-GAAAAAAAAAAGAAAAAAATGAGGAAA
17626700 A-AAAAAGAGAAAAAAAAAGAAAAAAAT
1 AGAAAAAGA-AAAAAAAAAGAAAAAAAT
17626727 ATGTCTGAGC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
33 8 0.15
34 38 0.73
35 6 0.12
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (34 bp):
AGAAAAAGAAAAAAAAAAGAAAAAAATGAGGAAA
Found at i:17627789 original size:23 final size:24
Alignment explanation
Indices: 17627762--17627806 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
17627752 CCAATTAGGG
*
17627762 AATTATTGTTTAG-ATTTAATTAT
1 AATTATCGTTTAGAATTTAATTAT
17627785 AATTATCGTTTAGAATTTAATT
1 AATTATCGTTTAGAATTTAATT
17627807 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (24 bp):
AATTATCGTTTAGAATTTAATTAT
Found at i:17630362 original size:24 final size:26
Alignment explanation
Indices: 17630320--17630374 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
17630310 AGGGTTTAGT
*
17630320 TCTTACAAGCCTAGATAGAATACCGC
1 TCTTACAAGCCTAGATAGAACACCGC
* *
17630346 TCTTAC-AG-CTAGTTAGAACATCGC
1 TCTTACAAGCCTAGATAGAACACCGC
17630370 TCTTA
1 TCTTA
17630375 TGAGCCAGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 18 0.69
25 2 0.08
26 6 0.23
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (26 bp):
TCTTACAAGCCTAGATAGAACACCGC
Found at i:17630393 original size:25 final size:25
Alignment explanation
Indices: 17630320--17630557 Score: 232
Period size: 25 Copynumber: 9.5 Consensus size: 25
17630310 AGGGTTTAGT
* * *
17630320 TCTTACAAGCCTAGATAGAATACCGC
1 TCTTACGAGCC-AGACAGAATATCGC
* ** *
17630346 TCTTAC-AGCTAGTTAGAACATCGC
1 TCTTACGAGCCAGACAGAATATCGC
*
17630370 TCTTATGAGCCAGACAGAATATCGC
1 TCTTACGAGCCAGACAGAATATCGC
* *
17630395 TATTACGAGCCAAAC-GAAATATCGC
1 TCTTACGAGCCAGACAG-AATATCGC
*
17630420 TCTTACGAGCCAGACAAAATATCGC
1 TCTTACGAGCCAGACAGAATATCGC
*
17630445 T-TTCACGAGCCAGA-TGAAATATCGC
1 TCTT-ACGAGCCAGACAG-AATATCGC
* *
17630470 TCTTATGAGCCAGACAGAATATCAC
1 TCTTACGAGCCAGACAGAATATCGC
* * *
17630495 TCTTATGAACCAGATAGAATATCGC
1 TCTTACGAGCCAGACAGAATATCGC
* *
17630520 TCTTACGAGCCAGACAAAATATTGC
1 TCTTACGAGCCAGACAGAATATCGC
*
17630545 TCTTACAAGCCAG
1 TCTTACGAGCCAG
17630558 CCTTTAGTAA
Statistics
Matches: 176, Mismatches: 29, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
24 19 0.11
25 148 0.84
26 9 0.05
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (25 bp):
TCTTACGAGCCAGACAGAATATCGC
Found at i:17642529 original size:17 final size:18
Alignment explanation
Indices: 17642507--17642544 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
17642497 ATTAAATCTA
*
17642507 TATAAAATATTAT-TTAT
1 TATAAAACATTATCTTAT
17642524 TATAAAACATTATCTTAT
1 TATAAAACATTATCTTAT
17642542 TAT
1 TAT
17642545 TATAGAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (18 bp):
TATAAAACATTATCTTAT
Found at i:17650959 original size:29 final size:29
Alignment explanation
Indices: 17650800--17650941 Score: 214
Period size: 29 Copynumber: 4.9 Consensus size: 29
17650790 AATTACCACT
*
17650800 ATTTTATAGTTTTGCCACTGGTTTTCCGA
1 ATTTTATAGTTTTGCCACTGGTTTTCCAA
*
17650829 ATTTTATAGTTTTGTCACT-GTTTTCCAA
1 ATTTTATAGTTTTGCCACTGGTTTTCCAA
* *
17650857 ATTTTACAGTTTTGTCACTGGTTTTTCCAA
1 ATTTTATAGTTTTGCCACTGG-TTTTCCAA
* *
17650887 ATTTTATAGTTTTGCCACTAGTTTTTCAA
1 ATTTTATAGTTTTGCCACTGGTTTTCCAA
17650916 ATTTTATAGTTTTGCCACTGGTTTTC
1 ATTTTATAGTTTTGCCACTGGTTTTC
17650942 TAGCTTTTAC
Statistics
Matches: 102, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
28 26 0.25
29 50 0.49
30 26 0.25
ACGTcount: A:0.20, C:0.15, G:0.13, T:0.51
Consensus pattern (29 bp):
ATTTTATAGTTTTGCCACTGGTTTTCCAA
Done.