Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 18 of 167
Found at i:5348055 original size:22 final size:21
Alignment explanation
Indices: 5347929--5348057 Score: 84
Period size: 22 Copynumber: 6.0 Consensus size: 21
5347919 AAGGGTTAGT
5347929 GATTT-GAGTTTAA-GGTTTAA
1 GATTTAGA-TTTAAGGGTTTAA
* * * *
5347949 GGTTTAGAGTTTTAGGATTTAG
1 GATTTAGA-TTTAAGGGTTTAA
** *
5347971 GATTTTTATTTAAGGGTTTAGT
1 GATTTAGATTTAAGGGTTTA-A
*
5347993 GATTTAGGTTT-AGGGTTTAA
1 GATTTAGATTTAAGGGTTTAA
* * *
5348013 GGTTTAGAGTTTTAGGATTTAA
1 GATTTAGA-TTTAAGGGTTTAA
*
5348035 GATTTTGTATTTAAGGGTTTAA
1 GATTTAG-ATTTAAGGGTTTAA
5348057 G
1 G
5348058 GGAGTGTTTA
Statistics
Matches: 82, Mismatches: 21, Indels: 10
0.73 0.19 0.09
Matches are distributed among these distances:
20 10 0.12
21 28 0.34
22 43 0.52
23 1 0.01
ACGTcount: A:0.26, C:0.00, G:0.27, T:0.47
Consensus pattern (21 bp):
GATTTAGATTTAAGGGTTTAA
Found at i:5348073 original size:64 final size:63
Alignment explanation
Indices: 5347917--5348082 Score: 203
Period size: 64 Copynumber: 2.6 Consensus size: 63
5347907 ATTTAAGGGC
* * * *
5347917 TTAAGGG-TTAGTGATTTGAGTTTAAGGTTTAAGGTTTAGAGTTTTAGGATTTAGGATTTTTAT
1 TTAAGGGTTTAGGGATGT-AGTTTAGGGTTTAAGGTTTAGAGTTTTAGGATTTAAGATTTTTAT
* *
5347980 TTAAGGGTTTAGTGATTTAGGTTTAGGGTTTAAGGTTTAGAGTTTTAGGATTTAAGATTTTGTAT
1 TTAAGGGTTTAGGGATGTA-GTTTAGGGTTTAAGGTTTAGAGTTTTAGGATTTAAGATTTT-TAT
*
5348045 TTAAGGGTTTAAGGGA-GT-GTTTACGGGTTTAGGGTTTA
1 TTAAGGGTTT-AGGGATGTAGTTTA-GGGTTTAAGGTTTA
5348083 CAGATAATTA
Statistics
Matches: 93, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
63 13 0.14
64 62 0.67
65 14 0.15
66 4 0.04
ACGTcount: A:0.24, C:0.01, G:0.30, T:0.46
Consensus pattern (63 bp):
TTAAGGGTTTAGGGATGTAGTTTAGGGTTTAAGGTTTAGAGTTTTAGGATTTAAGATTTTTAT
Found at i:5348443 original size:40 final size:40
Alignment explanation
Indices: 5348385--5348477 Score: 132
Period size: 40 Copynumber: 2.3 Consensus size: 40
5348375 AATATTTTTT
* * *
5348385 GCGGCGTTTTTCAGAAAGCGTCGCTAATGCTCAATCTATA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCAATCTATA
* *
5348425 GCGGCATTTTTTAAAAAGCGCCGCTAATGCTCGATCTATA
1 GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCAATCTATA
*
5348465 GGGGCGTTTTTTA
1 GCGGCGTTTTTTA
5348478 TCCAAACGCC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (40 bp):
GCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCAATCTATA
Found at i:5353080 original size:16 final size:18
Alignment explanation
Indices: 5353044--5353081 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5353034 ATAACATATT
*
5353044 TAATCAAATTAGACCAAC
1 TAATCAAATTAGACAAAC
5353062 TAATCAAATTA-A-AAAC
1 TAATCAAATTAGACAAAC
5353078 TAAT
1 TAAT
5353082 GACTTGATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 1 0.05
18 11 0.58
ACGTcount: A:0.55, C:0.16, G:0.03, T:0.26
Consensus pattern (18 bp):
TAATCAAATTAGACAAAC
Found at i:5353675 original size:26 final size:27
Alignment explanation
Indices: 5353625--5353675 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
5353615 TGTGTTTTGT
5353625 TCGTGTTCATTAATTTTAAATTTATGC
1 TCGTGTTCATTAATTTTAAATTTATGC
* *
5353652 TCGTGTTTATTTA-TTTAAATTTAT
1 TCGTGTTCATTAATTTTAAATTTAT
5353676 AAATTTTGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.25, C:0.08, G:0.10, T:0.57
Consensus pattern (27 bp):
TCGTGTTCATTAATTTTAAATTTATGC
Found at i:5354702 original size:20 final size:20
Alignment explanation
Indices: 5354677--5354716 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5354667 CGTAAAATGA
* *
5354677 TTTCTGGAAAGTGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
5354697 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
5354717 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.10, G:0.15, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:5355957 original size:13 final size:11
Alignment explanation
Indices: 5355925--5355958 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
5355915 GCAGGAATTA
5355925 GTACAATATAT
1 GTACAATATAT
5355936 GTACAATATAT
1 GTACAATATAT
5355947 GTACAATATAT
1 GTACAATATAT
5355958 G
1 G
5355959 AGAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (11 bp):
GTACAATATAT
Found at i:5356848 original size:16 final size:16
Alignment explanation
Indices: 5356827--5356860 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5356817 GGACGAAGAG
*
5356827 GAAATGAGGAGGAAAT
1 GAAATGAGAAGGAAAT
5356843 GAAATGAGAAGGAAAT
1 GAAATGAGAAGGAAAT
5356859 GA
1 GA
5356861 GAGGTTGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.35, T:0.12
Consensus pattern (16 bp):
GAAATGAGAAGGAAAT
Found at i:5359210 original size:17 final size:16
Alignment explanation
Indices: 5359176--5359206 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5359166 TATATACCTC
5359176 TTTTTTAAAATATTTA
1 TTTTTTAAAATATTTA
5359192 TTTTTTAAAATATTT
1 TTTTTTAAAATATTT
5359207 TATTATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTTTAAAATATTTA
Found at i:5365832 original size:5 final size:5
Alignment explanation
Indices: 5365822--5365853 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
5365812 TTTGTGTGAA
5365822 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
5365854 GAACACTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:5365847 original size:9 final size:9
Alignment explanation
Indices: 5365823--5365853 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
5365813 TTGTGTGAAA
5365823 AAATAAAAT
1 AAATAAAAT
5365832 AAAATAAAAT
1 -AAATAAAAT
5365842 AAATAAAAT
1 AAATAAAAT
5365851 AAA
1 AAA
5365854 GAACACTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:5373812 original size:31 final size:31
Alignment explanation
Indices: 5373718--5373814 Score: 92
Period size: 31 Copynumber: 3.2 Consensus size: 31
5373708 CACATAATGT
* * * *
5373718 CTGATACAATATAAACACTAGTACAAAGTAC
1 CTGATATAATATAATCATTAGTACATAGTAC
* * *
5373749 CTG--ATAATATAGTCATTAATACGTACGT-C
1 CTGATATAATATAATCATTAGTACATA-GTAC
*
5373778 CTGATATAATATAATCATTGGTACATAGTAC
1 CTGATATAATATAATCATTAGTACATAGTAC
5373809 CTGATA
1 CTGATA
5373815 CTTTAAACCC
Statistics
Matches: 51, Mismatches: 11, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
29 19 0.37
30 4 0.08
31 28 0.55
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.31
Consensus pattern (31 bp):
CTGATATAATATAATCATTAGTACATAGTAC
Found at i:5378603 original size:25 final size:26
Alignment explanation
Indices: 5378565--5378618 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
5378555 TTTGTTTTTG
5378565 TTTTTCTTGGTGTT-TTTGTGCTATT
1 TTTTTCTTGGTGTTATTTGTGCTATT
* * * *
5378590 TTTTTGTTGTTGTTATTTTTGTTATT
1 TTTTTCTTGGTGTTATTTGTGCTATT
5378616 TTT
1 TTT
5378619 ACTATTATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.06, C:0.04, G:0.17, T:0.74
Consensus pattern (26 bp):
TTTTTCTTGGTGTTATTTGTGCTATT
Found at i:5380427 original size:6 final size:6
Alignment explanation
Indices: 5380411--5380456 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
5380401 TTTAAAAGCA
*
5380411 AGGAA- AGGAAT AGGAAT TGGAAT AGGAAT AGGAAT AGGAAT AGGAA
1 AGGAAT AGGAAT AGGAAT AGGAAT AGGAAT AGGAAT AGGAAT AGGAA
5380457 ATTTAAGTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (6 bp):
AGGAAT
Found at i:5385791 original size:31 final size:31
Alignment explanation
Indices: 5385753--5385848 Score: 192
Period size: 31 Copynumber: 3.1 Consensus size: 31
5385743 AGAAGCTAAC
5385753 TCAATGAAGCACATTCGTTTGATCTTATCTT
1 TCAATGAAGCACATTCGTTTGATCTTATCTT
5385784 TCAATGAAGCACATTCGTTTGATCTTATCTT
1 TCAATGAAGCACATTCGTTTGATCTTATCTT
5385815 TCAATGAAGCACATTCGTTTGATCTTATCTT
1 TCAATGAAGCACATTCGTTTGATCTTATCTT
5385846 TCA
1 TCA
5385849 TTCCTTTTTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 65 1.00
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (31 bp):
TCAATGAAGCACATTCGTTTGATCTTATCTT
Found at i:5389203 original size:11 final size:11
Alignment explanation
Indices: 5389187--5389211 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5389177 AATTTGGCAA
5389187 ATGGCAAATAC
1 ATGGCAAATAC
5389198 ATGGCAAATAC
1 ATGGCAAATAC
5389209 ATG
1 ATG
5389212 TCTACTGGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (11 bp):
ATGGCAAATAC
Found at i:5394771 original size:37 final size:37
Alignment explanation
Indices: 5394714--5394819 Score: 162
Period size: 37 Copynumber: 2.9 Consensus size: 37
5394704 TATGATCACT
*
5394714 TATCAC-TTGTC-CCTGATCAGATAAGTGTAGCCACC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
* *
5394749 TATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACT
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
*
5394786 TATCACTTTGTCTCTTGATCAGATAAGTATAGCC
1 TATCACTTTGTCTCTTGATCAGATAAGTGTAGCC
5394820 GAAGCTATCA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
35 6 0.09
36 4 0.06
37 54 0.84
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (37 bp):
TATCACTTTGTCTCTTGATCAGATAAGTGTAGCCACC
Found at i:5394861 original size:52 final size:52
Alignment explanation
Indices: 5394782--5394946 Score: 243
Period size: 46 Copynumber: 3.2 Consensus size: 52
5394772 TAAGTGTAGC
* *
5394782 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
*
5394835 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
5394887 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
5394933 CACTTTGTCACTTG
1 CACTTT-TCACTTG
5394947 ATCAGAAGTA
Statistics
Matches: 101, Mismatches: 4, Indels: 14
0.85 0.03 0.12
Matches are distributed among these distances:
46 44 0.44
49 1 0.01
50 1 0.01
52 43 0.43
53 12 0.12
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:5402691 original size:21 final size:21
Alignment explanation
Indices: 5402665--5402705 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5402655 ATCTGCTCAA
* *
5402665 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
5402686 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
5402706 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:5405954 original size:20 final size:20
Alignment explanation
Indices: 5405931--5405971 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
5405921 TCCATATTTG
5405931 TATATTAAT-TTTAATATTAT
1 TATA-TAATATTTAATATTAT
*
5405951 TATATATTATTTAATATTAT
1 TATATAATATTTAATATTAT
5405971 T
1 T
5405972 TTTTCTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TATATAATATTTAATATTAT
Found at i:5405959 original size:10 final size:10
Alignment explanation
Indices: 5405940--5405972 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
5405930 GTATATTAAT
5405940 TTTAATATTA
1 TTTAATATTA
5405950 -TTATATATTA
1 TTTA-ATATTA
5405960 TTTAATATTA
1 TTTAATATTA
5405970 TTT
1 TTT
5405973 TTTCTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 3 0.14
10 15 0.71
11 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTAATATTA
Found at i:5406568 original size:35 final size:35
Alignment explanation
Indices: 5406508--5406578 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
5406498 CATCTCCGGA
*
5406508 GCTTGGCAAATATGGAAAGTAATCTTCAAAGATAT
1 GCTTGGCAAATATGGAAAGGAATCTTCAAAGATAT
* * * *
5406543 GCTTGGCAAATATGGAAGGGGATCTTTAAATATAT
1 GCTTGGCAAATATGGAAAGGAATCTTCAAAGATAT
5406578 G
1 G
5406579 TGATCCTAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.30
Consensus pattern (35 bp):
GCTTGGCAAATATGGAAAGGAATCTTCAAAGATAT
Found at i:5413174 original size:3 final size:3
Alignment explanation
Indices: 5413168--5413437 Score: 180
Period size: 3 Copynumber: 91.3 Consensus size: 3
5413158 ATTAATTAAT
* * * * * *
5413168 TTA TTA TCA CTA TTA TTA TTA TTA CTA TTA TTA TTT TTA -CA TTA TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
5413215 TTA -CA TTA TTG TTG TTA TTA TTA TTA TTCC CTA TT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
* * *
5413259 TTA TT- GTA TTA TTA TTC TTCA TT- TTA TTA TTA TTA TT- TTA CTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
5413302 TTA TTA TTTA TTA TCA ATA TTTA TTA TCA TTG CTA TT- TTT TTA TTA
1 TTA TTA -TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * ** *
5413348 CTA TTA TTA TTA CTA TTA TTA TTA TT- TT- TTA CCA TTA TTA TTT TCTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* * *
5413395 TTA TTA TTA CTA TTA TTA GTA TTA TTA TCA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5413438 CATCATTTTT
Statistics
Matches: 201, Mismatches: 53, Indels: 26
0.72 0.19 0.09
Matches are distributed among these distances:
2 15 0.07
3 176 0.88
4 10 0.05
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:5413213 original size:11 final size:11
Alignment explanation
Indices: 5413197--5413224 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
5413187 TATTACTATT
5413197 ATTATTTTTAC
1 ATTATTTTTAC
5413208 ATTATTTTTAC
1 ATTATTTTTAC
5413219 ATTATT
1 ATTATT
5413225 GTTGTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTATTTTTAC
Found at i:5413274 original size:32 final size:32
Alignment explanation
Indices: 5413233--5413306 Score: 105
Period size: 32 Copynumber: 2.3 Consensus size: 32
5413223 TTGTTGTTAT
5413233 TATTATTATTCC-CTATTTTATTATTATTATTG
1 TATTATTATTCCTC-ATTTTATTATTATTATTG
* *
5413265 TATTATTATTCTTCATTTTATTATTATTATTT
1 TATTATTATTCCTCATTTTATTATTATTATTG
*
5413297 TACTATTATT
1 TATTATTATT
5413307 ATTTATTATC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 37 0.97
33 1 0.03
ACGTcount: A:0.26, C:0.08, G:0.01, T:0.65
Consensus pattern (32 bp):
TATTATTATTCCTCATTTTATTATTATTATTG
Found at i:5413322 original size:13 final size:13
Alignment explanation
Indices: 5413306--5413330 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5413296 TTACTATTAT
5413306 TATTTATTATCAA
1 TATTTATTATCAA
5413319 TATTTATTATCA
1 TATTTATTATCA
5413331 TTGCTATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTTATTATCAA
Found at i:5413397 original size:13 final size:13
Alignment explanation
Indices: 5413367--5413412 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
5413357 TTACTATTAT
5413367 TATTATT-TTTTAC
1 TATTATTATTTT-C
*
5413380 CATTATTATTTTC
1 TATTATTATTTTC
*
5413393 TATTATTA-TTAC
1 TATTATTATTTTC
5413405 TATTATTA
1 TATTATTA
5413413 GTATTATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 11 0.38
13 14 0.48
14 4 0.14
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (13 bp):
TATTATTATTTTC
Found at i:5413401 original size:32 final size:32
Alignment explanation
Indices: 5413252--5413403 Score: 105
Period size: 32 Copynumber: 4.7 Consensus size: 32
5413242 TCCCTATTTT
* * **
5413252 ATTATTATTATTGTATTATTATTCTTCATTTTATT
1 ATTATTATT-TTCTATTATTATTATT--TTTTACC
* * *
5413287 ATTATTA-TTT-TACTATTATTATTTATTATC
1 ATTATTATTTTCTATTATTATTATTTTTTACC
* * ** * *
5413317 AATATTTATTATC-ATTGCTATTTTTTTATTACT
1 ATTA-TTATTTTCTATTATTATTATTTT-TTACC
*
5413350 ATTATTA-TTACTATTATTATTATTTTTTACC
1 ATTATTATTTTCTATTATTATTATTTTTTACC
5413381 ATTATTATTTTCTATTATTATTA
1 ATTATTATTTTCTATTATTATTA
5413404 CTATTATTAG
Statistics
Matches: 90, Mismatches: 21, Indels: 15
0.71 0.17 0.12
Matches are distributed among these distances:
30 8 0.09
31 16 0.18
32 50 0.56
33 8 0.09
34 1 0.01
35 7 0.08
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.63
Consensus pattern (32 bp):
ATTATTATTTTCTATTATTATTATTTTTTACC
Found at i:5419280 original size:26 final size:26
Alignment explanation
Indices: 5419251--5419310 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
5419241 TCCCTTTGAA
* * *
5419251 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
5419277 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
*
5419305 CCATTC
1 TCATTC
5419311 TCAATATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.18
27 2 0.07
28 21 0.75
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:5419296 original size:28 final size:28
Alignment explanation
Indices: 5419265--5419336 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
5419255 TCGATATTTT
*
5419265 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
5419293 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
* * *
5419321 GTACACTGAGTACCAT
1 GCACACTAAGTGCCAT
5419337 ATTTGATTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:5423798 original size:141 final size:143
Alignment explanation
Indices: 5423624--5423905 Score: 453
Period size: 141 Copynumber: 2.0 Consensus size: 143
5423614 GTAGATCTAG
* *
5423624 TATGGCAGATCTTATCTTCCTGAAGTTGGAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCT
1 TATGGCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCT
*
5423689 GAAGTTGCAGC-AGAGCAGACTGAAAATAACGAATCTCATTTCCCT-AAATT-CAATTGAACAGA
66 GAAGTTGCAGCGA-AGCAGACTGAAAATAACGAATCTCATTTCCCTGAAATTGCAATAGAACAGA
5423751 TTGAAGCTACAAAT
130 TTGAAGCTACAAAT
*
5423765 TATGGCAAATCTTATCTTCCTGAAGTTGCAGTGGAGTAGATTGAAGCCACCAGCCTTATCTCCCT
1 TATGGCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCT
* * * * *
5423830 GAAGTTGCAGCGAAGCAGACTGAAGATAGCGAATCTCATTTCCCTGAAGTTGTAGTAGAACAGAT
66 GAAGTTGCAGCGAAGCAGACTGAAAATAACGAATCTCATTTCCCTGAAATTGCAATAGAACAGAT
5423895 TGAAGCTACAA
131 TGAAGCTACAA
5423906 GTCACAATCC
Statistics
Matches: 129, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
141 103 0.80
142 5 0.04
143 21 0.16
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (143 bp):
TATGGCAAATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCT
GAAGTTGCAGCGAAGCAGACTGAAAATAACGAATCTCATTTCCCTGAAATTGCAATAGAACAGAT
TGAAGCTACAAAT
Found at i:5425683 original size:3 final size:3
Alignment explanation
Indices: 5425677--5425984 Score: 205
Period size: 3 Copynumber: 101.3 Consensus size: 3
5425667 ATTAATTAAT
* * * *
5425677 TTA TTA TCA CTA TTA TTA TT- TTCA CTA TTA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
* * *
5425722 TTA TTA TTA CTA TTA TTA TT- TATA TTA TTG TTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
* *
5425767 TTCC TTA TT- TTA TTA TTAA TGTA TTA TTA TTA TTC TTCA TT- TTA TTA
1 TT-A TTA TTA TTA TTA TT-A T-TA TTA TTA TTA TTA TT-A TTA TTA TTA
* * * * *
5425814 TTA TTT TCTA TTA TTA CTA TT- TTT TTA CTA TTA TTA TTTA TTA TCA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
* * * * * * * *
5425860 ATA TTA TTA TTA TCA TTG CTG TT- TTT TTA TTT TTA TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* ** * * *
5425907 TTA CTTT TTA CCA TTA TTA TTT TCTA TTA TTA TTA CTA TTA TTA GTA
1 TTA -TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
* * *
5425954 TTA TTA TCA TTA TTA TTA TCA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5425985 AATCTTTTTA
Statistics
Matches: 234, Mismatches: 55, Indels: 32
0.73 0.17 0.10
Matches are distributed among these distances:
2 11 0.05
3 203 0.87
4 19 0.08
5 1 0.00
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:5426311 original size:3 final size:3
Alignment explanation
Indices: 5426305--5426614 Score: 184
Period size: 3 Copynumber: 102.3 Consensus size: 3
5426295 ATTAATCAAT
* * * *
5426305 TTA TTA TCA CTA TTA TTA TT- TTCA CTA TTA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
* * * *
5426350 TTA CTA TTA TTA TT- TATA TTA TTG TTG TTA TTA TTA TTA TAA CTTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
5426396 TT- TTA TTA TTAA TGTA TTA TTA TTA TTC TTCA TT- TTA TTA TTA TTA
1 TTA TTA TTA TT-A T-TA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
* * * * * *
5426442 TTT TCTA TTA TTA CTA TT- TTT TTA CTA TTA TTA TTTA TTA TCA ATA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
* * * * * * * * *
5426488 TTA TTA TTA TCA TTG CTG TTT TTA TTT TTA TTT TTA TTA CTA TTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** * *
5426536 TTA CTT- TT- TTA CCA TTA TTA TTT TCTA TTA TTA TTA CTA TTA TTA
1 TTA -TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
* * * * *
5426581 GTA TTC TTA TCA TTA TTA TTA TCA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5426615 AATCTTTTTA
Statistics
Matches: 231, Mismatches: 60, Indels: 32
0.72 0.19 0.10
Matches are distributed among these distances:
2 13 0.06
3 198 0.86
4 19 0.08
5 1 0.00
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:5426801 original size:630 final size:630
Alignment explanation
Indices: 5425421--5427326 Score: 3470
Period size: 630 Copynumber: 3.0 Consensus size: 630
5425411 CTTCCGCTTT
5425421 TTTATTGTTTTGAAATTAGTTTTTATTTTTTAAATTTTCGCCCATTAATTTATTTCGTTTCCAAT
1 TTTATT-TTTTGAAATTAGTTTTTATTTTTTAAATTTTCGCCCATTAATTTATTTCGTTTCCAAT
*
5425486 TTAGTCCTTCCTGCAACTGTGCGTTTTGGATGGGAGGAATAATTTCCTTTCTAGTCCCTCCTTGT
65 TTAGTCCTTCCTGCAACTGTGCGTTTTGGATGGGAGGAATAATTTCCTTTCTAGTCCCTCCTTAT
5425551 TATTCACGCATGCAAATTGGT-ACTTTTCTTTTATTTTTATTTCGAATTTGCCCCGAATTTCTAT
130 TATTCACGCATGCAAATTGGTCA-TTTTCTTTTATTTTTATTTCGAATTTGCCCCGAATTTCTAT
5425615 TTTGAATTCAATTTAGTCCTTTTTCTAGTTATTTTGCTATTTTATTATTAAAATTAATTAATTTA
194 TTTGAATTCAATTTAGTCCTTTTTCTAGTTATTTTGCTATTTTATTATTAAAATTAATTAATTTA
5425680 TTATCACTATTATTATTTTCACTATTACTATTATTATTATTATTATTATTACTATTATTATTTAT
259 TTATCACTATTATTATTTTCACTATTAC------TATTATTATTATTATTACTATTATTATTTAT
5425745 ATTATTGTTGTTATTATTATTATTCCTTATTTTATTATTAATGTATTATTATTATTCTTCA--TT
318 ATTATTGTTGTTATTATTATTATTCCTTATTTTATTATTAATGTATTATTATTATTCTTCATTTT
5425808 -TTATTATTATTTTCTATTATTACTATTTTTTTACTATTATTATTTATTATCAATATTATTATTA
383 ATTATTATTATTTTCTATTATTACTATTTTTTTACTATTATTATTTATTATCAATATTATTATTA
*
5425872 TCATTGCTG---TT-TTTTTATTTTTATTACTATTATTATTAC-TTTTTACCATTATTATTTTCT
448 TCATTGCTGTTTTTATTTTTATTTTTATTACTATTGTTATTACTTTTTTACCATTATTATTTTCT
*
5425932 ATTATTATTACTATTATTAGTATTATTATCATTATTATTATCATTATTTTTATAATCTTTTTACT
513 ATTATTATTACTATTATTAGTATTCTTATCATTATTATTATCATTATTTTTATAATCTTTTTACT
5425997 TAATATTTATTTATTCATTTATCATTCTTTTTTGGCTCGTTTTATCTTATTCG
578 TAATATTTATTTATTCATTTATCATTCTTTTTTGGCTCGTTTTATCTTATTCG
*
5426050 TTTATTTTTTGAAATTAGTTTTTATTTTTTAAATTTTCGCCCATTAATTTAGTTCGTTTCCAATT
1 TTTATTTTTTGAAATTAGTTTTTATTTTTTAAATTTTCGCCCATTAATTTATTTCGTTTCCAATT
*
5426115 TAGTCCTTCCTGCAACTGTGCGTTTTGGATGGGAGGAATAATTTCCTTTCTAGTCCCTCTTTATT
66 TAGTCCTTCCTGCAACTGTGCGTTTTGGATGGGAGGAATAATTTCCTTTCTAGTCCCTCCTTATT
*
5426180 ATTCACACATGCAAATTGGTCATTTTCTTTTATTTTTATTTCGAATTTGCCCCGAATTTCTATTT
131 ATTCACGCATGCAAATTGGTCATTTTCTTTTATTTTTATTTCGAATTTGCCCCGAATTTCTATTT
* *
5426245 TGAATTCAATTTTGTCCTTTTTCTAGTTATTTTGCTATTTTATTATTAAAATTAATCAATTTATT
196 TGAATTCAATTTAGTCCTTTTTCTAGTTATTTTGCTATTTTATTATTAAAATTAATTAATTTATT
5426310 ATCACTATTATTATTTTCACTATTACTATTATTATTATTATTACTATTATTATTTATATTATTGT
261 ATCACTATTATTATTTTCACTATTACTATTATTATTATTATTACTATTATTATTTATATTATTGT
**
5426375 TGTTATTATTATTATAACTTATTTTATTATTAATGTATTATTATTATTCTTCATTTTATTATTAT
326 TGTTATTATTATTATTCCTTATTTTATTATTAATGTATTATTATTATTCTTCATTTTATTATTAT
5426440 TATTTTCTATTATTACTATTTTTTTACTATTATTATTTATTATCAATATTATTATTATCATTGCT
391 TATTTTCTATTATTACTATTTTTTTACTATTATTATTTATTATCAATATTATTATTATCATTGCT
5426505 GTTTTTATTTTTATTTTTATTACTATTGTTATTACTTTTTTACCATTATTATTTTCTATTATTAT
456 GTTTTTATTTTTATTTTTATTACTATTGTTATTACTTTTTTACCATTATTATTTTCTATTATTAT
5426570 TACTATTATTAGTATTCTTATCATTATTATTATCATTATTTTTATAATCTTTTTACTTAATATTT
521 TACTATTATTAGTATTCTTATCATTATTATTATCATTATTTTTATAATCTTTTTACTTAATATTT
5426635 ATTTATTCATTTATCATTCTTTTTTGGCTCGTTTTATCTTATTCG
586 ATTTATTCATTTATCATTCTTTTTTGGCTCGTTTTATCTTATTCG
5426680 TTTATTTTTTGAAATTAGTTTTTATTTTTTAAATTTTCGCCCATTAATTTATTTCGTTTCCAATT
1 TTTATTTTTTGAAATTAGTTTTTATTTTTTAAATTTTCGCCCATTAATTTATTTCGTTTCCAATT
5426745 TAGTCCTTCCTGCAACTGTGCGTTTTGGATGGGAGGAATAATTTCCTTTCTAGTCCCTCCTTATT
66 TAGTCCTTCCTGCAACTGTGCGTTTTGGATGGGAGGAATAATTTCCTTTCTAGTCCCTCCTTATT
5426810 ATTCACGCATGCAAATTGGTCATTTTCTTTTATTTTTATTTCGAATTTGCCCCGAATTTCTATTT
131 ATTCACGCATGCAAATTGGTCATTTTCTTTTATTTTTATTTCGAATTTGCCCCGAATTTCTATTT
5426875 TGAATTCAATTTAGTCCTTTTTCTAGTTATTTTGCTATTTTATTATTAAAATTAATTAATTTATT
196 TGAATTCAATTTAGTCCTTTTTCTAGTTATTTTGCTATTTTATTATTAAAATTAATTAATTTATT
5426940 ATCACTATTATTATTTTCACTATTACTATTATTATTATTATTACTATTATTATTATTTATATTAT
261 ATCACTATTATTATTTTCACTATTACTATTATTATTATTATTAC---TATTATTATTTATATTAT
5427005 TGTTGTTATTATTATTATTCCTTATTTTATTATTAATGTATTATTATTATTCTTCATTTTATTAT
323 TGTTGTTATTATTATTATTCCTTATTTTATTATTAATGTATTATTATTATTCTTCATTTTATTAT
5427070 TATTATTTTCTATTATTACTATTTTTTTACTATTATTATTTATTATCAATATTATTATTATCATT
388 TATTATTTTCTATTATTACTATTTTTTTACTATTATTATTTATTATCAATATTATTATTATCATT
5427135 GCTGTTTTTATTTTTATTTTTATTACTATTGTTATTACTTTTTTACCATTATTATTTTCTATTAT
453 GCTGTTTTTATTTTTATTTTTATTACTATTGTTATTACTTTTTTACCATTATTATTTTCTATTAT
* * *
5427200 TATTACTATTATTATTATTATTATCATTATCATTATCATTATCATCATTTTTATAATCTTTTTAC
518 TATTAC---TATTATTAGTA-T-TC-TTATCATTATTATTATCATTATTTTTATAATCTTTTTAC
*
5427265 TTAATATTTATTTATTCATTTATCATTCTTTTTTGGCTAGTTTTATCTTATTCG
577 TTAATATTTATTTATTCATTTATCATTCTTTTTTGGCTCGTTTTATCTTATTCG
5427319 TTTATTTT
1 TTTATTTT
5427327 ATTCATATTT
Statistics
Matches: 1238, Mismatches: 21, Indels: 26
0.96 0.02 0.02
Matches are distributed among these distances:
622 90 0.07
624 2 0.00
625 73 0.06
628 274 0.22
629 34 0.03
630 437 0.35
633 217 0.18
636 10 0.01
637 1 0.00
638 2 0.00
639 98 0.08
ACGTcount: A:0.25, C:0.11, G:0.06, T:0.58
Consensus pattern (630 bp):
TTTATTTTTTGAAATTAGTTTTTATTTTTTAAATTTTCGCCCATTAATTTATTTCGTTTCCAATT
TAGTCCTTCCTGCAACTGTGCGTTTTGGATGGGAGGAATAATTTCCTTTCTAGTCCCTCCTTATT
ATTCACGCATGCAAATTGGTCATTTTCTTTTATTTTTATTTCGAATTTGCCCCGAATTTCTATTT
TGAATTCAATTTAGTCCTTTTTCTAGTTATTTTGCTATTTTATTATTAAAATTAATTAATTTATT
ATCACTATTATTATTTTCACTATTACTATTATTATTATTATTACTATTATTATTTATATTATTGT
TGTTATTATTATTATTCCTTATTTTATTATTAATGTATTATTATTATTCTTCATTTTATTATTAT
TATTTTCTATTATTACTATTTTTTTACTATTATTATTTATTATCAATATTATTATTATCATTGCT
GTTTTTATTTTTATTTTTATTACTATTGTTATTACTTTTTTACCATTATTATTTTCTATTATTAT
TACTATTATTAGTATTCTTATCATTATTATTATCATTATTTTTATAATCTTTTTACTTAATATTT
ATTTATTCATTTATCATTCTTTTTTGGCTCGTTTTATCTTATTCG
Found at i:5426941 original size:3 final size:3
Alignment explanation
Indices: 5426935--5427241 Score: 196
Period size: 3 Copynumber: 101.3 Consensus size: 3
5426925 ATTAATTAAT
* * * *
5426935 TTA TTA TCA CTA TTA TTA TT- TTCA CTA TTA CTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
* * * *
5426980 TTA CTA TTA TTA TTA TT- TATA TTA TTG TTG TTA TTA TTA TTA TTCC
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TT-A
*
5427026 TTA TT- TTA TTA TTAA TGTA TTA TTA TTA TTC TTCA TT- TTA TTA TTA
1 TTA TTA TTA TTA TT-A T-TA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
* * * * *
5427072 TTA TTT TCTA TTA TTA CTA TT- TTT TTA CTA TTA TTA TTTA TTA TCA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
* * * * * * * * * *
5427118 ATA TTA TTA TTA TCA TTG CTG TTT TTA TTT TTA TTT TTA TTA CTA TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** * *
5427166 TTA TTA CTT- TT- TTA CCA TTA TTA TTT TCTA TTA TTA TTA CTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
* * *
5427211 TTA TTA TTA TTA TCA TTA TCA TTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5427242 CATCATTTTT
Statistics
Matches: 232, Mismatches: 56, Indels: 32
0.73 0.17 0.10
Matches are distributed among these distances:
2 13 0.06
3 199 0.86
4 19 0.08
5 1 0.00
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:5427540 original size:116 final size:116
Alignment explanation
Indices: 5427398--5427627 Score: 442
Period size: 116 Copynumber: 2.0 Consensus size: 116
5427388 CGATTATGCA
*
5427398 TATCGTTACCGTAATCCATTTTCCATTTTACTACGAAATAGTGTTACATTTTACCCGACACACTA
1 TATCGGTACCGTAATCCATTTTCCATTTTACTACGAAATAGTGTTACATTTTACCCGACACACTA
*
5427463 AAATGTTGTTTTAAACAAGCAATATCTCGTCTTTTGAGATTCGAAAAGTAT
66 AAATGTTGTTTTAAACAAGCAATATCTCGTATTTTGAGATTCGAAAAGTAT
5427514 TATCGGTACCGTAATCCATTTTCCATTTTACTACGAAATAGTGTTACATTTTACCCGACACACTA
1 TATCGGTACCGTAATCCATTTTCCATTTTACTACGAAATAGTGTTACATTTTACCCGACACACTA
5427579 AAATGTTGTTTTAAACAAGCAATATCTCGTATTTTGAGATTCGAAAAGT
66 AAATGTTGTTTTAAACAAGCAATATCTCGTATTTTGAGATTCGAAAAGT
5427628 CGATCCTTAA
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
116 112 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (116 bp):
TATCGGTACCGTAATCCATTTTCCATTTTACTACGAAATAGTGTTACATTTTACCCGACACACTA
AAATGTTGTTTTAAACAAGCAATATCTCGTATTTTGAGATTCGAAAAGTAT
Found at i:5429906 original size:407 final size:407
Alignment explanation
Indices: 5429221--5430036 Score: 1632
Period size: 407 Copynumber: 2.0 Consensus size: 407
5429211 TTAAATTCAT
5429221 CACGACTTTATCGTACTAGAATTTATAAGTAAGTAAATTTAATTATCTTGTTCAACAAAATAGCA
1 CACGACTTTATCGTACTAGAATTTATAAGTAAGTAAATTTAATTATCTTGTTCAACAAAATAGCA
5429286 ATGACTAATTAATTTAATTTCAACTTCGAACTTCAATTATTTAATTACAATCAATTAAATAGTAG
66 ATGACTAATTAATTTAATTTCAACTTCGAACTTCAATTATTTAATTACAATCAATTAAATAGTAG
5429351 TTTGAAAAATTAATTTAATCTCTAAGCCATCTCTAACTTATTGCGAGAAAATGCATTCACTATGA
131 TTTGAAAAATTAATTTAATCTCTAAGCCATCTCTAACTTATTGCGAGAAAATGCATTCACTATGA
5429416 ATAATGATACACACGATCTATTTCTCTAATTCATCATTTTCATTATATTCATCTCGTCCATTCAA
196 ATAATGATACACACGATCTATTTCTCTAATTCATCATTTTCATTATATTCATCTCGTCCATTCAA
5429481 ATGCAAACCGTCAAGGTTGTATTAAACTAGTGGAGGGACCAATTGGACATATATATAATTAGGAC
261 ATGCAAACCGTCAAGGTTGTATTAAACTAGTGGAGGGACCAATTGGACATATATATAATTAGGAC
5429546 TCAAATAATTTGTAATTAAGTTTTGACTATTTGTCTATCAATTATAATGTTTATTTAGTCATGGA
326 TCAAATAATTTGTAATTAAGTTTTGACTATTTGTCTATCAATTATAATGTTTATTTAGTCATGGA
5429611 CTCATTTCACTAAAGTA
391 CTCATTTCACTAAAGTA
5429628 CACGACTTTATCGTACTAGAATTTATAAGTAAGTAAATTTAATTATCTTGTTCAACAAAATAGCA
1 CACGACTTTATCGTACTAGAATTTATAAGTAAGTAAATTTAATTATCTTGTTCAACAAAATAGCA
5429693 ATGACTAATTAATTTAATTTCAACTTCGAACTTCAATTATTTAATTACAATCAATTAAATAGTAG
66 ATGACTAATTAATTTAATTTCAACTTCGAACTTCAATTATTTAATTACAATCAATTAAATAGTAG
5429758 TTTGAAAAATTAATTTAATCTCTAAGCCATCTCTAACTTATTGCGAGAAAATGCATTCACTATGA
131 TTTGAAAAATTAATTTAATCTCTAAGCCATCTCTAACTTATTGCGAGAAAATGCATTCACTATGA
5429823 ATAATGATACACACGATCTATTTCTCTAATTCATCATTTTCATTATATTCATCTCGTCCATTCAA
196 ATAATGATACACACGATCTATTTCTCTAATTCATCATTTTCATTATATTCATCTCGTCCATTCAA
5429888 ATGCAAACCGTCAAGGTTGTATTAAACTAGTGGAGGGACCAATTGGACATATATATAATTAGGAC
261 ATGCAAACCGTCAAGGTTGTATTAAACTAGTGGAGGGACCAATTGGACATATATATAATTAGGAC
5429953 TCAAATAATTTGTAATTAAGTTTTGACTATTTGTCTATCAATTATAATGTTTATTTAGTCATGGA
326 TCAAATAATTTGTAATTAAGTTTTGACTATTTGTCTATCAATTATAATGTTTATTTAGTCATGGA
5430018 CTCATTTCACTAAAGTA
391 CTCATTTCACTAAAGTA
5430035 CA
1 CA
5430037 ATGACTGAGA
Statistics
Matches: 409, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
407 409 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (407 bp):
CACGACTTTATCGTACTAGAATTTATAAGTAAGTAAATTTAATTATCTTGTTCAACAAAATAGCA
ATGACTAATTAATTTAATTTCAACTTCGAACTTCAATTATTTAATTACAATCAATTAAATAGTAG
TTTGAAAAATTAATTTAATCTCTAAGCCATCTCTAACTTATTGCGAGAAAATGCATTCACTATGA
ATAATGATACACACGATCTATTTCTCTAATTCATCATTTTCATTATATTCATCTCGTCCATTCAA
ATGCAAACCGTCAAGGTTGTATTAAACTAGTGGAGGGACCAATTGGACATATATATAATTAGGAC
TCAAATAATTTGTAATTAAGTTTTGACTATTTGTCTATCAATTATAATGTTTATTTAGTCATGGA
CTCATTTCACTAAAGTA
Found at i:5432159 original size:30 final size:30
Alignment explanation
Indices: 5432125--5432186 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
5432115 ACTTATTTTG
*
5432125 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
* * *
5432155 TTGTTAATTTTATTTTTATTTTAGAGGCAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
5432185 TT
1 TT
5432187 ACTTGTTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.26, C:0.03, G:0.11, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:5438816 original size:7 final size:7
Alignment explanation
Indices: 5438801--5438840 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
5438791 TACACTTATC
*
5438801 TGATCAG
1 TGATAAG
5438808 TGATAAG
1 TGATAAG
*
5438815 TGACAAG
1 TGATAAG
*
5438822 TGACAAG
1 TGATAAG
5438829 TGATAAG
1 TGATAAG
5438836 TGATA
1 TGATA
5438841 GCTTTAGCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.40, C:0.07, G:0.28, T:0.25
Consensus pattern (7 bp):
TGATAAG
Found at i:5438852 original size:58 final size:58
Alignment explanation
Indices: 5438762--5438874 Score: 190
Period size: 58 Copynumber: 1.9 Consensus size: 58
5438752 ACTTCTGATC
* *
5438762 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATAAGTGACA
1 AGTGACAAGTGATAAGTGATAGCCTCAGCTACACTTATCTGATCAGTAATAAGTGACA
* *
5438820 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTAATAAGTG
1 AGTGACAAGTGATAAGTGATAGCCTCAGCTACACTTATCTGATCAGTAATAAGTG
5438875 GTAGCTTTAG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (58 bp):
AGTGACAAGTGATAAGTGATAGCCTCAGCTACACTTATCTGATCAGTAATAAGTGACA
Found at i:5438881 original size:37 final size:37
Alignment explanation
Indices: 5438831--5438914 Score: 132
Period size: 37 Copynumber: 2.3 Consensus size: 37
5438821 GTGACAAGTG
5438831 ATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTA
1 ATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTA
* * *
5438868 ATAAGTGGTAGCTTTAGCTACACTTATCTGCTCAGTG
1 ATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTA
*
5438905 ACAAGTGATA
1 ATAAGTGATA
5438915 AATGTGATCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (37 bp):
ATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTA
Found at i:5445086 original size:19 final size:19
Alignment explanation
Indices: 5445062--5445099 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5445052 TCGACGGAAA
5445062 GAGGCATGAAATCAGCAGG
1 GAGGCATGAAATCAGCAGG
*
5445081 GAGGCATGAAATTAGCAGG
1 GAGGCATGAAATCAGCAGG
5445100 AAAATTGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.13, G:0.37, T:0.13
Consensus pattern (19 bp):
GAGGCATGAAATCAGCAGG
Found at i:5446340 original size:44 final size:44
Alignment explanation
Indices: 5446274--5446434 Score: 214
Period size: 44 Copynumber: 3.5 Consensus size: 44
5446264 TTTGAGTACT
* * *
5446274 TCTGATCAGTGACAAGTAATAAGTGGTAGCCTCAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
5446318 TCTGATCAGTGACAAGTGATAAGTGGTAGATTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
5446362 TCTAATCAGTGACAAATGATAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGAC-------AAGTGATAAGTGGTAGCTTTAGCTACACTTA
5446413 TCTGATCAGTGACAAGTGATAA
1 TCTGATCAGTGACAAGTGATAA
5446435 ATGTGATCAG
Statistics
Matches: 103, Mismatches: 7, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
44 61 0.59
51 42 0.41
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.30
Consensus pattern (44 bp):
TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:5446407 original size:51 final size:51
Alignment explanation
Indices: 5446331--5446434 Score: 181
Period size: 51 Copynumber: 2.0 Consensus size: 51
5446321 GATCAGTGAC
5446331 AAGTGATAAGTGGTAGATTTAGCTACACTTATCTAATCAGTGACAAATGAT
1 AAGTGATAAGTGGTAGATTTAGCTACACTTATCTAATCAGTGACAAATGAT
* * *
5446382 AAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGAT
1 AAGTGATAAGTGGTAGATTTAGCTACACTTATCTAATCAGTGACAAATGAT
5446433 AA
1 AA
5446435 ATGTGATCAG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (51 bp):
AAGTGATAAGTGGTAGATTTAGCTACACTTATCTAATCAGTGACAAATGAT
Found at i:5449195 original size:19 final size:19
Alignment explanation
Indices: 5449171--5449225 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
5449161 TGAGTTAATT
5449171 TTATTTAGATAATTATGAG
1 TTATTTAGATAATTATGAG
5449190 TTATTT---TAA-T-T---
1 TTATTTAGATAATTATGAG
5449201 TTATTTAGATAATTATGAG
1 TTATTTAGATAATTATGAG
5449220 TTATTT
1 TTATTT
5449226 TTTAATCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 16
0.64 0.00 0.36
Matches are distributed among these distances:
11 6 0.21
14 4 0.14
15 2 0.07
16 4 0.14
19 12 0.43
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (19 bp):
TTATTTAGATAATTATGAG
Found at i:5449201 original size:30 final size:30
Alignment explanation
Indices: 5449165--5449226 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
5449155 TTCTACTGAG
5449165 TTAATTTTATTTAGATAATTATGAGTTATT
1 TTAATTTTATTTAGATAATTATGAGTTATT
5449195 TTAATTTTATTTAGATAATTATGAGTTATT
1 TTAATTTTATTTAGATAATTATGAGTTATT
5449225 TT
1 TT
5449227 TTAATCTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (30 bp):
TTAATTTTATTTAGATAATTATGAGTTATT
Found at i:5449415 original size:24 final size:25
Alignment explanation
Indices: 5449388--5449434 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
5449378 AATCTGTTAG
* *
5449388 AAAAAGTAGATTG-AAAAAAAGAAC
1 AAAAAATAGATGGCAAAAAAAGAAC
*
5449412 AAAAAATTGATGGCAAAAAAAGA
1 AAAAAATAGATGGCAAAAAAAGA
5449435 CTCAAAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.66, C:0.04, G:0.17, T:0.13
Consensus pattern (25 bp):
AAAAAATAGATGGCAAAAAAAGAAC
Found at i:5450664 original size:17 final size:20
Alignment explanation
Indices: 5450622--5450665 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 20
5450612 TTAATTTTAA
5450622 AATAATTGTAAAAATTAGAT
1 AATAATTGTAAAAATTAGAT
5450642 AA-AATT-TAAAAA-TAG-T
1 AATAATTGTAAAAATTAGAT
5450658 AATAATTG
1 AATAATTG
5450666 CTCATTTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 6 0.27
19 4 0.18
20 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (20 bp):
AATAATTGTAAAAATTAGAT
Found at i:5451730 original size:21 final size:20
Alignment explanation
Indices: 5451678--5451727 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
5451668 AATCTTTGAA
*
5451678 TAGAAATGTATATTCATAAT
1 TAGAAATTTATATTCATAAT
* *
5451698 TATAAAACTTATATTCATAAT
1 TA-GAAATTTATATTCATAAT
5451719 TAGAAATTT
1 TAGAAATTT
5451728 TATGTGAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (20 bp):
TAGAAATTTATATTCATAAT
Found at i:5452054 original size:7 final size:7
Alignment explanation
Indices: 5452042--5452076 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
5452032 AAACGTGAGT
5452042 AATAATA
1 AATAATA
5452049 AATAATA
1 AATAATA
5452056 AATAATA
1 AATAATA
5452063 AATAA-A
1 AATAATA
5452069 AAGTAATA
1 AA-TAATA
5452077 TGAAGCTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 3 0.12
7 22 0.85
8 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (7 bp):
AATAATA
Found at i:5454971 original size:28 final size:29
Alignment explanation
Indices: 5454923--5454985 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
5454913 AGACAATAGC
* *
5454923 TTTTTCCTTGCATTTAAATGTTTTAATGT
1 TTTTTCCATGCATTTAAATGTCTTAATGT
*
5454952 TTTTTCCATGCATTT-TATGTCTTAATGT
1 TTTTTCCATGCATTTAAATGTCTTAATGT
*
5454980 CTTTTC
1 TTTTTC
5454986 TTTACATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 16 0.53
29 14 0.47
ACGTcount: A:0.17, C:0.14, G:0.10, T:0.59
Consensus pattern (29 bp):
TTTTTCCATGCATTTAAATGTCTTAATGT
Found at i:5455072 original size:35 final size:35
Alignment explanation
Indices: 5455026--5455095 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
5455016 TTAGAGAATA
5455026 CCATCTTTATTCTCTTTCAAAGAATAATTGGGTGG
1 CCATCTTTATTCTCTTTCAAAGAATAATTGGGTGG
5455061 CCATCTTTATTCTCTTTCAAAGAATAATTGGGTGG
1 CCATCTTTATTCTCTTTCAAAGAATAATTGGGTGG
5455096 TGTGGGTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (35 bp):
CCATCTTTATTCTCTTTCAAAGAATAATTGGGTGG
Found at i:5457241 original size:48 final size:48
Alignment explanation
Indices: 5457116--5457434 Score: 284
Period size: 48 Copynumber: 6.7 Consensus size: 48
5457106 GAGTAAATTA
* * * * * * *
5457116 CCGATGCCATGCCCCACACATGGTCTTACACTAGCTCTCGTCTCAATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCGCTCATATCAACG
* * * * * ****
5457164 TCGATGTCATGTTCCA-AAATGGTCTTACACTGGCTCTCATATTGTGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCGCTCATATCAACG
* * * *
5457211 CTGACGCCATGTCCCAGACATGGTCTTACACTAGCGCACATATCAACG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCGCTCATATCAACG
*
5457259 CTGATGCCATGTCCCAGACATGGTCTTACACTGGCGCTCATATCAACG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCGCTCATATCAACG
* * * *
5457307 CCAATGCCATGTCCCAGACATGGTCTTACACTAGCGCACATATCAACA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCGCTCATATCAACG
* * * * ***
5457355 CCGATGCCATGTCCTCA-ACATGATCTTAAACTGTCTCTCATAAT-GTGG
1 CCGATGCCATGTCC-CAGACATGGTCTTACACTGGCGCTCAT-ATCAACG
* * *
5457403 CCGATGTCATGTTCCAAACATGGTCTTACACT
1 CCGATGCCATGTCCCAGACATGGTCTTACACT
5457435 AACACACATA
Statistics
Matches: 219, Mismatches: 48, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
47 36 0.16
48 179 0.82
49 4 0.02
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (48 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTGGCGCTCATATCAACG
Found at i:5457316 original size:96 final size:94
Alignment explanation
Indices: 5457116--5457447 Score: 360
Period size: 96 Copynumber: 3.5 Consensus size: 94
5457106 GAGTAAATTA
* * * * * * * * *
5457116 CCGATGCCATGCCCCACACATGGTCTTACACTAGCTCTCGTCTCAATG-TCGATGTCATGTTCCA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCGCACATATCAACGCT-GATGCCATGTCCCA
*
5457180 AAATGGTCTTACACTGGCTCTCATATTGTGG
65 ACATGGTCTTACACTGGCTCTCATA-TGTGG
* *
5457211 CTGACGCCATGTCCCAGACATGGTCTTACACTAGCGCACATATCAACGCTGATGCCATGTCCCAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCGCACATATCAACGCTGATGCCATGTCCCA-
* ***
5457276 ACATGGTCTTACACTGGCGCTCATATCAACG
65 ACATGGTCTTACACTGGCTCTCATAT-GTGG
* * *
5457307 CCAATGCCATGTCCCAGACATGGTCTTACACTAGCGCACATATCAACACCGATGCCATGTCCTCA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCGCACATATCAACGCTGATGCCATGTCC-CA
* * *
5457372 ACATGATCTTAAACTGTCTCTCATAATGTGG
65 ACATGGTCTTACACTGGCTCTCAT-ATGTGG
* * * * *
5457403 CCGATGTCATGTTCCAAACATGGTCTTACACTAACACACATATCA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCGCACATATCA
5457448 CTCAAATGTC
Statistics
Matches: 198, Mismatches: 34, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
95 52 0.26
96 142 0.72
97 4 0.02
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (94 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCGCACATATCAACGCTGATGCCATGTCCCAA
CATGGTCTTACACTGGCTCTCATATGTGG
Found at i:5466279 original size:48 final size:48
Alignment explanation
Indices: 5466224--5466498 Score: 259
Period size: 48 Copynumber: 5.7 Consensus size: 48
5466214 GAGTAAATTA
* * * * *
5466224 CCGATGCCATGTCTCAGACATGGTCTTACACTGGCT-TACATGTCGAGG
1 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCT-CATATCAAGG
* * * **
5466272 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCGTCTTAATA
1 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATCAAGG
* * * * * ***
5466320 TCGATGTCATGTTCCAAACATGGTCATACACTGGCTCTCATATTGTGG
1 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATCAAGG
* * * *
5466368 CCGACGCCATGTCCCAAACATGGTCTTACACTAGCGCACATATCAACG
1 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATCAAGG
* * *
5466416 CCGATGCCATGTCCCAGACATGGTCTTGCACTTGCTCTCATAAT-ATA-G
1 CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCAT-ATCA-AGG
* *
5466464 CCGATTCCATGTTCCAAACATGGTCTTACACTAGC
1 CCGATGCCATGTCCCAAACATGGTCTTACACTAGC
5466499 ATACATATCA
Statistics
Matches: 181, Mismatches: 43, Indels: 6
0.79 0.19 0.03
Matches are distributed among these distances:
48 177 0.98
49 4 0.02
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (48 bp):
CCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATATCAAGG
Found at i:5466389 original size:96 final size:96
Alignment explanation
Indices: 5466223--5466508 Score: 313
Period size: 96 Copynumber: 3.0 Consensus size: 96
5466213 AGAGTAAATT
* * * * *
5466223 ACCGATGCCATGTCTCAGACATGGTCTTACACTGGCT-TACATGTCGAGGCCGATGCCATGTCCC
1 ACCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCT-CATATTGTGGCCGATGCCATGTCCC
* * * * * *
5466287 AAACATGGTCTTACACTAGCTCTCGTCTTAAT
65 AAACATGGTCTTACACTAGCGCACATATCAAC
* * * * *
5466319 ATCGATGTCATGTTCCAAACATGGTCATACACTGGCTCTCATATTGTGGCCGACGCCATGTCCCA
1 ACCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATATTGTGGCCGATGCCATGTCCCA
5466384 AACATGGTCTTACACTAGCGCACATATCAAC
66 AACATGGTCTTACACTAGCGCACATATCAAC
* * * * * * * * *
5466415 GCCGATGCCATGTCCCAGACATGGTCTTGCACTTGCTCTCATAATATAGCCGATTCCATGTTCCA
1 ACCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATATTGTGGCCGATGCCATGTCCCA
**
5466480 AACATGGTCTTACACTAGCATACATATCA
66 AACATGGTCTTACACTAGCGCACATATCA
5466509 CTCAAATGTC
Statistics
Matches: 157, Mismatches: 32, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
96 156 0.99
97 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.28
Consensus pattern (96 bp):
ACCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATATTGTGGCCGATGCCATGTCCCA
AACATGGTCTTACACTAGCGCACATATCAAC
Found at i:5466494 original size:144 final size:144
Alignment explanation
Indices: 5466224--5466495 Score: 359
Period size: 144 Copynumber: 1.9 Consensus size: 144
5466214 GAGTAAATTA
* * * * ** * * *
5466224 CCGATGCCATGTCTCAGACATGGTCTTACACTGGCTTACATGTCGAGGCCGATGCCATGTCCCAA
1 CCGACGCCATGTCCCAAACATGGTCTTACACTAGCGCACATATCAACGCCGATGCCATGTCCCAA
* ** *
5466289 ACATGGTCTTACACTAGCTCTCGTCTTAATATCGATGTCATGTTCCAAACATGGTCATACACTGG
66 ACATGGTCTTACACTAGCTCTCATAATAATACCGATGTCATGTTCCAAACATGGTCATACACTGG
5466354 CTCTCATATTGTGG
131 CTCTCATATTGTGG
*
5466368 CCGACGCCATGTCCCAAACATGGTCTTACACTAGCGCACATATCAACGCCGATGCCATGTCCCAG
1 CCGACGCCATGTCCCAAACATGGTCTTACACTAGCGCACATATCAACGCCGATGCCATGTCCCAA
* * *
5466433 ACATGGTCTTGCACTTGCTCTCATAAT-ATAGCCGAT-TCCATGTTCCAAACATGGTCTTACACT
66 ACATGGTCTTACACTAGCTCTCATAATAATA-CCGATGT-CATGTTCCAAACATGGTCATACACT
5466496 AGCATACATA
Statistics
Matches: 109, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
143 4 0.04
144 105 0.96
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.28
Consensus pattern (144 bp):
CCGACGCCATGTCCCAAACATGGTCTTACACTAGCGCACATATCAACGCCGATGCCATGTCCCAA
ACATGGTCTTACACTAGCTCTCATAATAATACCGATGTCATGTTCCAAACATGGTCATACACTGG
CTCTCATATTGTGG
Found at i:5467690 original size:12 final size:12
Alignment explanation
Indices: 5467673--5467698 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5467663 ATTCCGATTA
5467673 GGCCCAAAATCG
1 GGCCCAAAATCG
5467685 GGCCCAAAATCG
1 GGCCCAAAATCG
5467697 GG
1 GG
5467699 TTGTTACAAT
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:0.31, C:0.31, G:0.31, T:0.08
Consensus pattern (12 bp):
GGCCCAAAATCG
Found at i:5469664 original size:18 final size:18
Alignment explanation
Indices: 5469629--5469666 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5469619 TTGCTTGGTA
*
5469629 ATTGGAAAAGAAATAAAT
1 ATTGGAAAAGAAAGAAAT
5469647 ATTGGAAAATG-AAGAAAT
1 ATTGGAAAA-GAAAGAAAT
5469665 AT
1 AT
5469667 ATGTGTAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.24
Consensus pattern (18 bp):
ATTGGAAAAGAAAGAAAT
Found at i:5470614 original size:18 final size:18
Alignment explanation
Indices: 5470591--5470626 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5470581 AAATCAGTGG
5470591 ATTGACAAAATAATGGGT
1 ATTGACAAAATAATGGGT
5470609 ATTGACAAAATAATGGGT
1 ATTGACAAAATAATGGGT
5470627 TGTGTTCGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (18 bp):
ATTGACAAAATAATGGGT
Found at i:5473149 original size:19 final size:19
Alignment explanation
Indices: 5473122--5473170 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
5473112 ATACACATTA
5473122 AAATATATAAAAATAAAAT
1 AAATATATAAAAATAAAAT
*
5473141 AAATGTATAAAAATAAAA-
1 AAATATATAAAAATAAAAT
*
5473159 ATATATATAAAA
1 AAATATATAAAA
5473171 TAATTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 10 0.37
19 17 0.63
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
AAATATATAAAAATAAAAT
Found at i:5473270 original size:20 final size:20
Alignment explanation
Indices: 5473247--5473293 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
5473237 TAAAACTAAC
5473247 AATATTATTAAAAAATATAA
1 AATATTATTAAAAAATATAA
* *
5473267 AATATTTTTAAAAATTATAA
1 AATATTATTAAAAAATATAA
*
5473287 AAAATTA
1 AATATTA
5473294 AATTTTTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATTATTAAAAAATATAA
Found at i:5473283 original size:27 final size:28
Alignment explanation
Indices: 5473253--5473316 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
5473243 TAACAATATT
5473253 ATTA-AAAAATATAAAATATTTT-TA-AAA
1 ATTATAAAAA-ATAAAAT-TTTTATATAAA
*
5473280 ATTATAAAAAATTAAATTTTTATATAAA
1 ATTATAAAAAATAAAATTTTTATATAAA
*
5473308 ATTCTAAAA
1 ATTATAAAA
5473317 TACATAATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 4 0.12
27 12 0.38
28 16 0.50
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (28 bp):
ATTATAAAAAATAAAATTTTTATATAAA
Found at i:5473425 original size:19 final size:19
Alignment explanation
Indices: 5473384--5473434 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
5473374 TTAATTACTT
*
5473384 TTTTATAATATTTTTTAAT
1 TTTTATAATATTTTTTAAC
*
5473403 TTTTAT-ATATTATTTTGAC
1 TTTTATAATATT-TTTTAAC
*
5473422 TTTT-TAAAATTTT
1 TTTTATAATATTTT
5473435 AAATTATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTATAATATTTTTTAAC
Found at i:5473426 original size:21 final size:20
Alignment explanation
Indices: 5473378--5473426 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
5473368 TTAAATTTAA
5473378 TTACTTTTTTATAATATTTT
1 TTACTTTTTTATAATATTTT
*
5473398 TTA-ATTTTTAT-ATATTATT
1 TTACTTTTTTATAATATT-TT
5473417 TTGACTTTTT
1 TT-ACTTTTT
5473427 AAAATTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 5 0.21
19 11 0.46
20 4 0.17
21 4 0.17
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (20 bp):
TTACTTTTTTATAATATTTT
Found at i:5473653 original size:19 final size:19
Alignment explanation
Indices: 5473631--5473675 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
5473621 ATTATAATTT
5473631 ATTTTTATA-A-TATTTTTG
1 ATTTTTATATATTA-TTTTG
5473649 AATTTTTATATATTATTTTG
1 -ATTTTTATATATTATTTTG
5473669 ATTTTTA
1 ATTTTTA
5473676 AAATTTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 16 0.67
20 6 0.25
21 2 0.08
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (19 bp):
ATTTTTATATATTATTTTG
Found at i:5473660 original size:21 final size:19
Alignment explanation
Indices: 5473632--5473675 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
5473622 TTATAATTTA
5473632 TTTT-TATAATATTTTTGAAT
1 TTTTATATAATA-TTTTG-AT
*
5473652 TTTTATATATTATTTTGAT
1 TTTTATATAATATTTTGAT
5473671 TTTTA
1 TTTTA
5473676 AAATTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 9 0.41
21 6 0.27
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTTATATAATATTTTGAT
Found at i:5473734 original size:27 final size:27
Alignment explanation
Indices: 5473675--5473726 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
5473665 TTTGATTTTT
*
5473675 AAAA-TTT-AAAATTATATATTTTTAA
1 AAAATTTTAAAAATTATATATTTATAA
5473700 AAAATTTTAAAAATTATATATTATATA
1 AAAATTTTAAAAATTATATATT-TATA
5473727 TAATTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 4 0.17
26 3 0.13
27 13 0.57
28 3 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
AAAATTTTAAAAATTATATATTTATAA
Found at i:5474034 original size:27 final size:27
Alignment explanation
Indices: 5474003--5474055 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
5473993 AAATTGATAC
* * *
5474003 TTTAGATATTAAAATGGGATAAAAAAG
1 TTTAGATATCAAAATGAGAAAAAAAAG
5474030 TTTAGATATCAAAATGAGAAAAAAAA
1 TTTAGATATCAAAATGAGAAAAAAAA
5474056 TATACTTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.57, C:0.02, G:0.15, T:0.26
Consensus pattern (27 bp):
TTTAGATATCAAAATGAGAAAAAAAAG
Found at i:5476493 original size:12 final size:12
Alignment explanation
Indices: 5476476--5476502 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5476466 ACTCGTGACA
5476476 AATAAGAATTTT
1 AATAAGAATTTT
5476488 AATAAGAATTTT
1 AATAAGAATTTT
5476500 AAT
1 AAT
5476503 GTATTCAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (12 bp):
AATAAGAATTTT
Found at i:5484214 original size:25 final size:26
Alignment explanation
Indices: 5484152--5484218 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 26
5484142 CAGACACACC
*
5484152 ACAGCTCGTATGAGCTTTCCGTTATT
1 ACAGCTCGTATGAGCTTTCCGATATT
* * *
5484178 A-AGATTGCATGAGCTTTCCGAT-TT
1 ACAGCTCGTATGAGCTTTCCGATATT
5484202 ACAGCTCGTATGAGCTT
1 ACAGCTCGTATGAGCTT
5484219 CCCATTATCC
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
24 3 0.09
25 29 0.88
26 1 0.03
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (26 bp):
ACAGCTCGTATGAGCTTTCCGATATT
Found at i:5484231 original size:25 final size:25
Alignment explanation
Indices: 5484152--5484233 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 25
5484142 CAGACACACC
* *
5484152 ACAGCTCGTATGAGCTTTCCGTTATT
1 ACAGCTCGTATGAGCTTCCCATTA-T
* * * *
5484178 A-AGATTGCATGAGCTTTCCGATT-T
1 ACAGCTCGTATGAGC-TTCCCATTAT
5484202 ACAGCTCGTATGAGCTTCCCATTAT
1 ACAGCTCGTATGAGCTTCCCATTAT
*
5484227 CCAGCTC
1 ACAGCTC
5484234 ACATGAGATT
Statistics
Matches: 42, Mismatches: 11, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
24 9 0.21
25 27 0.64
26 6 0.14
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (25 bp):
ACAGCTCGTATGAGCTTCCCATTAT
Found at i:5484239 original size:25 final size:25
Alignment explanation
Indices: 5484185--5484240 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
5484175 ATTAAGATTG
* *
5484185 CATGAGCTTTCCGATTTACAGCTCG
1 CATGAGCTTTCCCATTTACAGCTCA
* *
5484210 TATGAGC-TTCCCATTATCCAGCTCA
1 CATGAGCTTTCCCATT-TACAGCTCA
5484235 CATGAG
1 CATGAG
5484241 ATTGCCGTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.30
Consensus pattern (25 bp):
CATGAGCTTTCCCATTTACAGCTCA
Found at i:5484239 original size:50 final size:49
Alignment explanation
Indices: 5484152--5484265 Score: 120
Period size: 50 Copynumber: 2.3 Consensus size: 49
5484142 CAGACACACC
* * * ** * *
5484152 ACAGCTCGTATGAGCTTTCCGTTATTAAGATTGCATGAGCTTTCCGATTT
1 ACAGCTCGTATGAGCTTCCCATTATCAAGATCACATGAGATTGCCG-TTT
* *
5484202 ACAGCTCGTATGAGCTTCCCATTATCCAGCTCACATGAGATTGCCGTTT
1 ACAGCTCGTATGAGCTTCCCATTATCAAGATCACATGAGATTGCCGTTT
* *
5484251 ATAGCTCCTATGAGC
1 ACAGCTCGTATGAGC
5484266 ATACATGTAC
Statistics
Matches: 53, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
49 16 0.30
50 37 0.70
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (49 bp):
ACAGCTCGTATGAGCTTCCCATTATCAAGATCACATGAGATTGCCGTTT
Found at i:5489167 original size:5 final size:5
Alignment explanation
Indices: 5489157--5489190 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
5489147 AAAAATTATG
5489157 AATAT AATAT AATAT AATAT AATAT AATAT AATA
1 AATAT AATAT AATAT AATAT AATAT AATAT AATA
5489191 AATTTATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:5492947 original size:13 final size:13
Alignment explanation
Indices: 5492904--5492947 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
5492894 TTTAATTATA
5492904 TTTTTAAA-TTTT
1 TTTTTAAACTTTT
5492916 TTTATTATTAACTTTT
1 TTT-TTA--AACTTTT
5492932 TTTTTAAACTTTT
1 TTTTTAAACTTTT
5492945 TTT
1 TTT
5492948 AATAGATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
15 5 0.18
16 7 0.25
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTTAAACTTTT
Found at i:5493438 original size:16 final size:18
Alignment explanation
Indices: 5493417--5493453 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5493407 ACACACGTGT
5493417 ATATTA-TCA-AAATTTA
1 ATATTATTCATAAATTTA
*
5493433 ATATTATTCATTAATTTA
1 ATATTATTCATAAATTTA
5493451 ATA
1 ATA
5493454 ACATTACACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 3 0.17
18 9 0.50
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATTATTCATAAATTTA
Found at i:5493684 original size:22 final size:22
Alignment explanation
Indices: 5493658--5493699 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5493648 GTAGCTGCTG
*
5493658 TTTGCTGCCATTTTGATATTGT
1 TTTGCTACCATTTTGATATTGT
* *
5493680 TTTGCTATCATTTTGTTATT
1 TTTGCTACCATTTTGATATT
5493700 ATATTACTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.14, C:0.12, G:0.14, T:0.60
Consensus pattern (22 bp):
TTTGCTACCATTTTGATATTGT
Found at i:5493709 original size:22 final size:22
Alignment explanation
Indices: 5493666--5493723 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
5493656 TGTTTGCTGC
* * * *
5493666 CATTTTGATATTGTTTTGCTAT
1 CATTTTGTTATTATATTACTAT
5493688 CATTTTGTTATTATATTACTAT
1 CATTTTGTTATTATATTACTAT
* *
5493710 TATTTTGTTTTTAT
1 CATTTTGTTATTAT
5493724 TGTTTGAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.21, C:0.07, G:0.09, T:0.64
Consensus pattern (22 bp):
CATTTTGTTATTATATTACTAT
Found at i:5494450 original size:3 final size:3
Alignment explanation
Indices: 5494442--5494474 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5494432 ATATTACAAC
5494442 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5494475 GATGACTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5499239 original size:18 final size:18
Alignment explanation
Indices: 5499181--5499227 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
5499171 AGGAACACTG
5499181 CCTTGTTAATAAGCAACC
1 CCTTGTTAATAAGCAACC
5499199 CCTTGTTAATAAGCAACC
1 CCTTGTTAATAAGCAACC
5499217 CCTTGTTAATA
1 CCTTGTTAATA
5499228 TGCGAATCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (18 bp):
CCTTGTTAATAAGCAACC
Found at i:5499399 original size:22 final size:22
Alignment explanation
Indices: 5499285--5499392 Score: 137
Period size: 22 Copynumber: 4.8 Consensus size: 22
5499275 TACGAACATG
5499285 CTATGTTGAATGATATGTGAAC
1 CTATGTTGAATGATATGTGAAC
5499307 CTATGTTGAATGATATGTGAAC
1 CTATGTTGAATGATATGTGAAC
* **
5499329 TTATGTTGAATTG-TATACGAAC
1 CTATGTTGAA-TGATATGTGAAC
*
5499351 ATGCTATGTTGAATGATATATGAAC
1 ---CTATGTTGAATGATATGTGAAC
5499376 CTATGTTGAATGATATG
1 CTATGTTGAATGATATG
5499393 CAAACCTTGT
Statistics
Matches: 75, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
22 54 0.72
23 2 0.03
24 2 0.03
25 17 0.23
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.38
Consensus pattern (22 bp):
CTATGTTGAATGATATGTGAAC
Found at i:5499406 original size:47 final size:46
Alignment explanation
Indices: 5499285--5499407 Score: 144
Period size: 47 Copynumber: 2.7 Consensus size: 46
5499275 TACGAACATG
* *
5499285 CTATGTTGAATGATATGTGAACC--TATGTTGAATGATATGTGAAC
1 CTATGTTGAATGATATGCGAACCTGTATGTTGAATGATATATGAAC
* * *
5499329 TTATGTTGAATTG-TATACGAACATGCTATGTTGAATGATATATGAAC
1 CTATGTTGAA-TGATATGCGAACCTG-TATGTTGAATGATATATGAAC
*
5499376 CTATGTTGAATGATATGCAAACCTTGTATGTT
1 CTATGTTGAATGATATGCGAACC-TGTATGTT
5499408 AGCATGCGAG
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
44 16 0.25
45 2 0.03
46 2 0.03
47 42 0.66
48 2 0.03
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (46 bp):
CTATGTTGAATGATATGCGAACCTGTATGTTGAATGATATATGAAC
Found at i:5499700 original size:19 final size:18
Alignment explanation
Indices: 5499659--5499747 Score: 69
Period size: 18 Copynumber: 5.1 Consensus size: 18
5499649 TGTGCAAACT
*
5499659 CCTACCTAAAGTGCGAAC
1 CCTACCTATAGTGCGAAC
*
5499677 CCTACCTATAGTGCTAACC
1 CCTACCTATAGTGCGAA-C
*
5499696 CCTACC-ATAGTGTGAAC
1 CCTACCTATAGTGCGAAC
* * *
5499713 CTTACCGT-T-GTGCTAGC
1 CCTACC-TATAGTGCGAAC
*
5499730 CATACC-ATAGTGCGAAC
1 CCTACCTATAGTGCGAAC
5499747 C
1 C
5499748 TTACTAGTGT
Statistics
Matches: 55, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
16 1 0.02
17 23 0.42
18 24 0.44
19 7 0.13
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.24
Consensus pattern (18 bp):
CCTACCTATAGTGCGAAC
Found at i:5499759 original size:34 final size:34
Alignment explanation
Indices: 5499698--5499781 Score: 98
Period size: 34 Copynumber: 2.5 Consensus size: 34
5499688 TGCTAACCCC
* * *
5499698 TACCATAGTGTGAACCTTACCGTTGTGCTAGCCA
1 TACCATAGTGCGAACCTTACAGTTGTGCGAGCCA
*
5499732 TACCATAGTGCGAACCTTACTAG-TGTGCGAGTCA
1 TACCATAGTGCGAACCTTAC-AGTTGTGCGAGCCA
* *
5499766 TAACATTGTGCGAACC
1 TACCATAGTGCGAACC
5499782 GTACCATGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
34 42 0.98
35 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.27
Consensus pattern (34 bp):
TACCATAGTGCGAACCTTACAGTTGTGCGAGCCA
Found at i:5499794 original size:34 final size:34
Alignment explanation
Indices: 5499701--5499795 Score: 86
Period size: 34 Copynumber: 2.8 Consensus size: 34
5499691 TAACCCCTAC
* * * * *
5499701 CATAGTGTGAACCTTACC-GTTGTGCTAGCCATAC
1 CATAGTGCGAACCGTACCAG-TGTGCGAGTCATAA
* *
5499735 CATAGTGCGAACCTTACTAGTGTGCGAGTCATAA
1 CATAGTGCGAACCGTACCAGTGTGCGAGTCATAA
*
5499769 CATTGTGCGAACCGTACCA-TGGTGCGA
1 CATAGTGCGAACCGTACCAGT-GTGCGA
5499796 ACCCCTATTG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
33 1 0.02
34 49 0.96
35 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.26
Consensus pattern (34 bp):
CATAGTGCGAACCGTACCAGTGTGCGAGTCATAA
Found at i:5500149 original size:14 final size:14
Alignment explanation
Indices: 5500130--5500174 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
5500120 ATTGTGCTAA
5500130 TGTGAACTATGAAT
1 TGTGAACTATGAAT
*
5500144 TGTGAACTATGATGT
1 TGTGAACTATGA-AT
*
5500159 TGTGAATTATGAAT
1 TGTGAACTATGAAT
5500173 TG
1 TG
5500175 CAAATTATGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.31, C:0.04, G:0.24, T:0.40
Consensus pattern (14 bp):
TGTGAACTATGAAT
Found at i:5500602 original size:17 final size:16
Alignment explanation
Indices: 5500582--5500644 Score: 72
Period size: 17 Copynumber: 3.8 Consensus size: 16
5500572 TATGATATTG
*
5500582 TATGAAATGTTATGTTA
1 TATGAACTGTTAT-TTA
*
5500599 TATGAACTGTTATATTG
1 TATGAACTGTTAT-TTA
*
5500616 TATGAACTATTATTTCA
1 TATGAACTGTTATTT-A
5500633 TATGAACTGTTA
1 TATGAACTGTTA
5500645 CTCTCTGCGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
16 2 0.05
17 37 0.95
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.46
Consensus pattern (16 bp):
TATGAACTGTTATTTA
Found at i:5500614 original size:34 final size:34
Alignment explanation
Indices: 5500576--5500644 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 34
5500566 ATGAGTTATG
*
5500576 ATATTGTATGAAATGTTATGTT-ATATGAACTGTT
1 ATATTGTATGAAATATTAT-TTCATATGAACTGTT
*
5500610 ATATTGTATGAACTATTATTTCATATGAACTGTT
1 ATATTGTATGAAATATTATTTCATATGAACTGTT
5500644 A
1 A
5500645 CTCTCTGCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 2 0.06
34 30 0.94
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.46
Consensus pattern (34 bp):
ATATTGTATGAAATATTATTTCATATGAACTGTT
Found at i:5502108 original size:25 final size:24
Alignment explanation
Indices: 5502078--5502125 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
5502068 AATATTTATT
5502078 TTATATCA-TAAAAAATAAAAAATAA
1 TTATAT-ATTAAAAAA-AAAAAATAA
*
5502103 TTATATATTAAATAAAAAAAATA
1 TTATATATTAAAAAAAAAAAATA
5502126 GATTTCAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (24 bp):
TTATATATTAAAAAAAAAAAATAA
Found at i:5502611 original size:12 final size:12
Alignment explanation
Indices: 5502594--5502623 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5502584 AAATTTACTA
5502594 TATATTTGCTAT
1 TATATTTGCTAT
5502606 TATATTTGCTAT
1 TATATTTGCTAT
5502618 TA-ATTT
1 TATATTT
5502624 TTATTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.60
Consensus pattern (12 bp):
TATATTTGCTAT
Found at i:5517097 original size:17 final size:17
Alignment explanation
Indices: 5517069--5517109 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
5517059 ATCCTAATCA
*
5517069 AATCAG-TATGTCCAAC
1 AATCAGATATGTCAAAC
5517085 AATCAGATATGTCAAAC
1 AATCAGATATGTCAAAC
5517102 AATCAGAT
1 AATCAGAT
5517110 CATTCGGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (17 bp):
AATCAGATATGTCAAAC
Found at i:5518624 original size:77 final size:77
Alignment explanation
Indices: 5518531--5518684 Score: 308
Period size: 77 Copynumber: 2.0 Consensus size: 77
5518521 TTAAAAGTTA
5518531 AATAAGCATTTTAATAAATAATGTATTTGAGCTAATTAGTGACATTATAAAAAATTAATTAAAGT
1 AATAAGCATTTTAATAAATAATGTATTTGAGCTAATTAGTGACATTATAAAAAATTAATTAAAGT
5518596 ACCAAATCATGT
66 ACCAAATCATGT
5518608 AATAAGCATTTTAATAAATAATGTATTTGAGCTAATTAGTGACATTATAAAAAATTAATTAAAGT
1 AATAAGCATTTTAATAAATAATGTATTTGAGCTAATTAGTGACATTATAAAAAATTAATTAAAGT
5518673 ACCAAATCATGT
66 ACCAAATCATGT
5518685 CAAAAAGTTA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (77 bp):
AATAAGCATTTTAATAAATAATGTATTTGAGCTAATTAGTGACATTATAAAAAATTAATTAAAGT
ACCAAATCATGT
Found at i:5520584 original size:55 final size:55
Alignment explanation
Indices: 5520519--5520628 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
5520509 GTATCCATTG
*
5520519 GATGATAAATCATCACTTTTAATTTGAACAGTGCTTATGAATAATTAATTTGCAA
1 GATGATAAATCATCACTTTTAATTTGAACAGTGCTCATGAATAATTAATTTGCAA
*
5520574 GATGATAAATCATCACTTTTAATTTGAATAGTGCTCATGAATAATTAATTTGCAA
1 GATGATAAATCATCACTTTTAATTTGAACAGTGCTCATGAATAATTAATTTGCAA
5520629 TCTATAATTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (55 bp):
GATGATAAATCATCACTTTTAATTTGAACAGTGCTCATGAATAATTAATTTGCAA
Found at i:5520864 original size:20 final size:21
Alignment explanation
Indices: 5520839--5520878 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5520829 TCAAGCTGAC
5520839 AAGGGC-ACACGCCTGTGTGG
1 AAGGGCGACACGCCTGTGTGG
*
5520859 AAGGGCGACATGCCTGTGTG
1 AAGGGCGACACGCCTGTGTG
5520879 TCTTACTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.20, C:0.23, G:0.40, T:0.17
Consensus pattern (21 bp):
AAGGGCGACACGCCTGTGTGG
Found at i:5522218 original size:96 final size:96
Alignment explanation
Indices: 5522061--5522289 Score: 262
Period size: 96 Copynumber: 2.4 Consensus size: 96
5522051 AATTGCCAAA
* * * * *** * **
5522061 GCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTTGAGGTTGATGCCATGTCCCAGACATG
1 GCCATGTCCCAGACATGGTCTTACACTGGCACTCATAAGGTGGCCGATGCCATGTCCCAGACATG
* * * * *
5522126 GTCTTACACTAGCT-CTCGTCTCATTGCCGAT
66 GTCTTACACTAG-TGCACATATCAATACCGAT
* * * *
5522157 GTCATGTCCCAGACATGGTCTTACATTGGCTCTCATAAGGTGGCCGATGCCATGTCTCAGACATG
1 GCCATGTCCCAGACATGGTCTTACACTGGCACTCATAAGGTGGCCGATGCCATGTCCCAGACATG
*
5522222 GTCTTAGACTAGTGCACATATCAATACCGAT
66 GTCTTACACTAGTGCACATATCAATACCGAT
5522253 GCCATGTCCCAGACATGGTCTTACACTGGCACTCATA
1 GCCATGTCCCAGACATGGTCTTACACTGGCACTCATA
5522290 TCATCCAAAT
Statistics
Matches: 111, Mismatches: 21, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
95 1 0.01
96 110 0.99
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (96 bp):
GCCATGTCCCAGACATGGTCTTACACTGGCACTCATAAGGTGGCCGATGCCATGTCCCAGACATG
GTCTTACACTAGTGCACATATCAATACCGAT
Found at i:5522290 original size:48 final size:48
Alignment explanation
Indices: 5522061--5522292 Score: 202
Period size: 48 Copynumber: 4.8 Consensus size: 48
5522051 AATTGCCAAA
* * * * * ** * **
5522061 GCCATGTTCCAAACATGGTCTTACACTGGCTCACATGTTGAGGTTGAT
1 GCCATGTCCCAGACATGGTCTTACACTGGCACTCATATCAATGCCGAT
* * * * *
5522109 GCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTCTCATTGCCGAT
1 GCCATGTCCCAGACATGGTCTTACACTGGCACTCATATCAATGCCGAT
* * * *
5522157 GTCATGTCCCAGACATGGTCTTACATTGGCTCTCATA--AGGTGGCCGAT
1 GCCATGTCCCAGACATGGTCTTACACTGGCACTCATATCA-AT-GCCGAT
* * *
5522205 GCCATGTCTCAGACATGGTCTTAGACTAGTGCA--CATATCAATACCGAT
1 GCCATGTCCCAGACATGGTCTTACACT-G-GCACTCATATCAATGCCGAT
5522253 GCCATGTCCCAGACATGGTCTTACACTGGCACTCATATCA
1 GCCATGTCCCAGACATGGTCTTACACTGGCACTCATATCA
5522293 TCCAAATGTC
Statistics
Matches: 149, Mismatches: 27, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
46 4 0.03
47 2 0.01
48 138 0.93
49 2 0.01
50 3 0.02
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (48 bp):
GCCATGTCCCAGACATGGTCTTACACTGGCACTCATATCAATGCCGAT
Found at i:5526033 original size:17 final size:18
Alignment explanation
Indices: 5525999--5526033 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5525989 ACTGCACGAC
5525999 CTCATGCAAATTACCAAAG
1 CTCATGCAAA-TACCAAAG
5526018 CTCATGCAAA-ACCAAA
1 CTCATGCAAATACCAAA
5526034 ATGAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.46, C:0.29, G:0.09, T:0.17
Consensus pattern (18 bp):
CTCATGCAAATACCAAAG
Found at i:5537749 original size:22 final size:22
Alignment explanation
Indices: 5537721--5537765 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
5537711 GGTTTGATCA
5537721 TAAAGGAAAACTAAGTCCATGG
1 TAAAGGAAAACTAAGTCCATGG
5537743 TAAAGGAAAACTAAGTCCATGG
1 TAAAGGAAAACTAAGTCCATGG
5537765 T
1 T
5537766 TCATTGGGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.20
Consensus pattern (22 bp):
TAAAGGAAAACTAAGTCCATGG
Found at i:5542017 original size:26 final size:26
Alignment explanation
Indices: 5541988--5542110 Score: 73
Period size: 25 Copynumber: 5.0 Consensus size: 26
5541978 CCTCTCTCAA
5541988 CCATATAACAGGAAGCTCACAAAGAG
1 CCATATAACAGGAAGCTCACAAAGAG
* * *
5542014 CCAT-TAATCGGGTAGCTCACAAAAAG
1 CCATATAA-CAGGAAGCTCACAAAGAG
* * *
5542040 CC-TAT--CAGGAAGCTTATC--TGGG
1 CCATATAACAGGAAGCTCA-CAAAGAG
* * *
5542062 CTATATAATAGGAAGCTCA-TAAGAG
1 CCATATAACAGGAAGCTCACAAAGAG
* *
5542087 CCATA-ATCAGGAAGTTCACAAAGA
1 CCATATAACAGGAAGCTCACAAAGA
5542111 ACTTTTAACT
Statistics
Matches: 69, Mismatches: 19, Indels: 19
0.64 0.18 0.18
Matches are distributed among these distances:
22 2 0.03
23 11 0.16
24 11 0.16
25 23 0.33
26 22 0.32
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (26 bp):
CCATATAACAGGAAGCTCACAAAGAG
Found at i:5544121 original size:16 final size:16
Alignment explanation
Indices: 5544100--5544130 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5544090 TGGGTATGAT
5544100 CCTTATATTTTCTTCA
1 CCTTATATTTTCTTCA
5544116 CCTTATATTTTCTTC
1 CCTTATATTTTCTTC
5544131 TGTTGGGTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58
Consensus pattern (16 bp):
CCTTATATTTTCTTCA
Found at i:5550770 original size:79 final size:82
Alignment explanation
Indices: 5550659--5550843 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
5550649 GCTACTCGTT
* *
5550659 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
5550722 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
5550739 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
5550802 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
*
5550819 CCAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
5550844 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 33 0.36
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:5550843 original size:40 final size:40
Alignment explanation
Indices: 5550640--5550843 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
5550630 CGGAATTTAA
** *
5550640 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
5550680 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
5550720 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
5550759 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * * *
5550799 CCGGATATGGTCACTTAGCACCAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
5550839 CCGGA
1 CCGGA
5550844 CATCATTCAA
Statistics
Matches: 140, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 94 0.67
41 11 0.08
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:5555905 original size:31 final size:31
Alignment explanation
Indices: 5555862--5555920 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
5555852 TGCCGCACAA
*
5555862 CCGTGTCTAGCTTCGTTCACTTCTCCCATGC
1 CCGTATCTAGCTTCGTTCACTTCTCCCATGC
* *
5555893 CCGTATCTAGCTTCGTTCGCTTTTCCCA
1 CCGTATCTAGCTTCGTTCACTTCTCCCA
5555921 CGTCCATGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.10, C:0.37, G:0.15, T:0.37
Consensus pattern (31 bp):
CCGTATCTAGCTTCGTTCACTTCTCCCATGC
Found at i:5566030 original size:22 final size:21
Alignment explanation
Indices: 5565983--5566039 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
5565973 TTTACAGTCC
*
5565983 AAAACTGAATAATAATAATGA
1 AAAAATGAATAATAATAATGA
*
5566004 GAAAATGAACTAATAATAA-GA
1 AAAAATGAA-TAATAATAATGA
*
5566025 TAAAAAT-AAAAATAA
1 -AAAAATGAATAATAA
5566040 AGTAATATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 5 0.17
21 11 0.37
22 14 0.47
ACGTcount: A:0.67, C:0.04, G:0.09, T:0.21
Consensus pattern (21 bp):
AAAAATGAATAATAATAATGA
Found at i:5570993 original size:16 final size:16
Alignment explanation
Indices: 5570968--5571006 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
5570958 TAATAATTAA
5570968 TTTA-TTTTATTATAT
1 TTTATTTTTATTATAT
*
5570983 TTTATTTTTATTATTT
1 TTTATTTTTATTATAT
*
5570999 TTTCTTTT
1 TTTATTTT
5571007 CTTTTCCATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTATTTTTATTATAT
Found at i:5587263 original size:17 final size:18
Alignment explanation
Indices: 5587233--5587267 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5587223 TATTTTTCAC
*
5587233 TTTATTTCTATTTTGTTT
1 TTTATTTATATTTTGTTT
5587251 TTTATTTAT-TTTTGTTT
1 TTTATTTATATTTTGTTT
5587268 ACTTTCTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.11, C:0.03, G:0.06, T:0.80
Consensus pattern (18 bp):
TTTATTTATATTTTGTTT
Found at i:5588908 original size:17 final size:17
Alignment explanation
Indices: 5588888--5588928 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5588878 TATTTTACTA
*
5588888 TTATTTTTAT-TTTTAT
1 TTATTTTTATCTCTTAT
5588904 TT-TATTTTATCTCTTAT
1 TTAT-TTTTATCTCTTAT
5588921 TTATTTTT
1 TTATTTTT
5588929 GAAGACTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
15 1 0.05
16 8 0.38
17 11 0.52
18 1 0.05
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (17 bp):
TTATTTTTATCTCTTAT
Found at i:5589869 original size:4 final size:4
Alignment explanation
Indices: 5589860--5590159 Score: 564
Period size: 4 Copynumber: 75.0 Consensus size: 4
5589850 TAACTATGTT
5589860 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5589908 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5589956 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5590004 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5590052 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
5590100 CATT CATT CATT TATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5590148 CATA CATA CATA
1 CATA CATA CATA
5590160 TTGGTAGTAA
Statistics
Matches: 292, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 292 1.00
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:5591085 original size:19 final size:19
Alignment explanation
Indices: 5591048--5591085 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5591038 CAACTCAGAA
*
5591048 TTACACACGGTTTGAGCAC
1 TTACACACGGTGTGAGCAC
5591067 TTACACACGGATGTG-GCAC
1 TTACACACGG-TGTGAGCAC
5591086 ACAGTCGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (19 bp):
TTACACACGGTGTGAGCAC
Found at i:5592735 original size:27 final size:28
Alignment explanation
Indices: 5592676--5592737 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
5592666 ACGAAATGTT
5592676 TTGA-CTAGTCCAATACTTTATTTTTCC
1 TTGATCTAGTCCAATACTTTATTTTTCC
* *
5592703 TCGATCTAGATCCAA-ACTTTGTTTTT-C
1 TTGATCTAG-TCCAATACTTTATTTTTCC
5592730 TTGATCTA
1 TTGATCTA
5592738 TATAATATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 11 0.37
28 14 0.47
29 5 0.17
ACGTcount: A:0.23, C:0.21, G:0.10, T:0.47
Consensus pattern (28 bp):
TTGATCTAGTCCAATACTTTATTTTTCC
Found at i:5596437 original size:44 final size:44
Alignment explanation
Indices: 5596388--5596478 Score: 146
Period size: 44 Copynumber: 2.1 Consensus size: 44
5596378 GTAGGTCAAA
* *
5596388 TAATATTAAAATAACCTATACTAATTAGAGTTTAAATAGGAAAC
1 TAATATTAAAATAACCTACACGAATTAGAGTTTAAATAGGAAAC
* *
5596432 TAATATTAAAATAACCTACACGAATTAGAGTTTAAGTGGGAAAC
1 TAATATTAAAATAACCTACACGAATTAGAGTTTAAATAGGAAAC
5596476 TAA
1 TAA
5596479 AAACAGAGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.30
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACGAATTAGAGTTTAAATAGGAAAC
Found at i:5597772 original size:13 final size:13
Alignment explanation
Indices: 5597754--5597780 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5597744 CTTCTGAGAC
5597754 GGTGTATTTATAG
1 GGTGTATTTATAG
5597767 GGTGTATTTATAG
1 GGTGTATTTATAG
5597780 G
1 G
5597781 CTTTCGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.44
Consensus pattern (13 bp):
GGTGTATTTATAG
Found at i:5608330 original size:287 final size:287
Alignment explanation
Indices: 5607814--5608387 Score: 1148
Period size: 287 Copynumber: 2.0 Consensus size: 287
5607804 TATTACTAAT
5607814 TAACTTCTTTTTTCCTTCTCTTGGCAGGTTTTCATAGTTTATGACTAGAAGAAACCCGTCGGGAC
1 TAACTTCTTTTTTCCTTCTCTTGGCAGGTTTTCATAGTTTATGACTAGAAGAAACCCGTCGGGAC
5607879 CATTACTTTTTAACGAAGAAATCGATTGCACAGTTCGTAGAAACCAAAGAGAAATAAGGCGAAGC
66 CATTACTTTTTAACGAAGAAATCGATTGCACAGTTCGTAGAAACCAAAGAGAAATAAGGCGAAGC
5607944 TTAAGATACATGGAGAACGAGCAAGAAGACGATACTCAACCCTCAACCAAAAAGATGGCTAAAAA
131 TTAAGATACATGGAGAACGAGCAAGAAGACGATACTCAACCCTCAACCAAAAAGATGGCTAAAAA
5608009 CCAAGGCAATCAGCTACCTCCTGCAATTGCGGCTAATCAAAATCCTGCTCCACGTATTATGTATG
196 CCAAGGCAATCAGCTACCTCCTGCAATTGCGGCTAATCAAAATCCTGCTCCACGTATTATGTATG
5608074 ACTATGCTAAACCTTCTTTAACAAGAA
261 ACTATGCTAAACCTTCTTTAACAAGAA
5608101 TAACTTCTTTTTTCCTTCTCTTGGCAGGTTTTCATAGTTTATGACTAGAAGAAACCCGTCGGGAC
1 TAACTTCTTTTTTCCTTCTCTTGGCAGGTTTTCATAGTTTATGACTAGAAGAAACCCGTCGGGAC
5608166 CATTACTTTTTAACGAAGAAATCGATTGCACAGTTCGTAGAAACCAAAGAGAAATAAGGCGAAGC
66 CATTACTTTTTAACGAAGAAATCGATTGCACAGTTCGTAGAAACCAAAGAGAAATAAGGCGAAGC
5608231 TTAAGATACATGGAGAACGAGCAAGAAGACGATACTCAACCCTCAACCAAAAAGATGGCTAAAAA
131 TTAAGATACATGGAGAACGAGCAAGAAGACGATACTCAACCCTCAACCAAAAAGATGGCTAAAAA
5608296 CCAAGGCAATCAGCTACCTCCTGCAATTGCGGCTAATCAAAATCCTGCTCCACGTATTATGTATG
196 CCAAGGCAATCAGCTACCTCCTGCAATTGCGGCTAATCAAAATCCTGCTCCACGTATTATGTATG
5608361 ACTATGCTAAACCTTCTTTAACAAGAA
261 ACTATGCTAAACCTTCTTTAACAAGAA
5608388 CTGAGTCAAG
Statistics
Matches: 287, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
287 287 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.25
Consensus pattern (287 bp):
TAACTTCTTTTTTCCTTCTCTTGGCAGGTTTTCATAGTTTATGACTAGAAGAAACCCGTCGGGAC
CATTACTTTTTAACGAAGAAATCGATTGCACAGTTCGTAGAAACCAAAGAGAAATAAGGCGAAGC
TTAAGATACATGGAGAACGAGCAAGAAGACGATACTCAACCCTCAACCAAAAAGATGGCTAAAAA
CCAAGGCAATCAGCTACCTCCTGCAATTGCGGCTAATCAAAATCCTGCTCCACGTATTATGTATG
ACTATGCTAAACCTTCTTTAACAAGAA
Found at i:5611195 original size:55 final size:55
Alignment explanation
Indices: 5611075--5611196 Score: 131
Period size: 55 Copynumber: 2.2 Consensus size: 55
5611065 GAGCCTGCCA
* ** * * *
5611075 AAAC-AACACGGGCGTGCGACACGCCCGTGTGGAAGACCTGTGGTTGAAACTGAG
1 AAACTAACACGGGTGTATGACACGCCCGTGTCGAACACCTGTGGTCGAAACTGAG
* * * *
5611129 AAACTAGCACGGGTGTATGACACGCCCGTGTCTAACACCTGTGGTCGAACCTGTTG
1 AAACTAACACGGGTGTATGACACGCCCGTGTCGAACACCTGTGGTCGAAACTG-AG
5611185 AAA-TAACACGGG
1 AAACTAACACGGG
5611197 CGTGGGGATT
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
54 4 0.07
55 47 0.85
56 4 0.07
ACGTcount: A:0.28, C:0.25, G:0.30, T:0.18
Consensus pattern (55 bp):
AAACTAACACGGGTGTATGACACGCCCGTGTCGAACACCTGTGGTCGAAACTGAG
Found at i:5622549 original size:10 final size:10
Alignment explanation
Indices: 5622518--5622576 Score: 68
Period size: 10 Copynumber: 6.0 Consensus size: 10
5622508 TTAAATTCTA
5622518 AAAGATAAAT
1 AAAGATAAAT
5622528 ACAA-AT-AAT
1 A-AAGATAAAT
*
5622537 AAAGATAATT
1 AAAGATAAAT
*
5622547 AAAGATAATT
1 AAAGATAAAT
5622557 AAAGATAAAT
1 AAAGATAAAT
*
5622567 AAATATAAAT
1 AAAGATAAAT
5622577 CCTAAATTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
8 2 0.05
9 6 0.14
10 33 0.77
11 2 0.05
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:5627950 original size:10 final size:10
Alignment explanation
Indices: 5627931--5627970 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
5627921 TTAAATTCTA
5627931 AAAGATAAAT
1 AAAGATAAAT
5627941 ACAA-ATAAAT
1 A-AAGATAAAT
5627951 AAAGATAAAT
1 AAAGATAAAT
*
5627961 AAATATAAAT
1 AAAGATAAAT
5627971 CCTAAATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 2 0.07
10 23 0.85
11 2 0.07
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.23
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:5627954 original size:20 final size:20
Alignment explanation
Indices: 5627931--5627970 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5627921 TTAAATTCTA
5627931 AAAGATAAATACAA-ATAAAT
1 AAAGATAAATA-AATATAAAT
5627951 AAAGATAAATAAATATAAAT
1 AAAGATAAATAAATATAAAT
5627971 CCTAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.23
Consensus pattern (20 bp):
AAAGATAAATAAATATAAAT
Found at i:5630537 original size:23 final size:22
Alignment explanation
Indices: 5630507--5630555 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
5630497 GTTTCAGCAT
*
5630507 AATATAAGGCTAAAACTAAAA-A
1 AATATAAGAC-AAAACTAAAAGA
*
5630529 AATAGTAAGACAAACCTAAAAGA
1 AATA-TAAGACAAAACTAAAAGA
5630552 AATA
1 AATA
5630556 AAAAAGCTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.63, C:0.10, G:0.10, T:0.16
Consensus pattern (22 bp):
AATATAAGACAAAACTAAAAGA
Found at i:5631775 original size:18 final size:19
Alignment explanation
Indices: 5631742--5631777 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5631732 GATATAATAC
*
5631742 TAAAATTATTTAAAAAAAT
1 TAAAATTATATAAAAAAAT
5631761 TAAAA-TATATAAAAAAA
1 TAAAATTATATAAAAAAA
5631778 GAGGAAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAATTATATAAAAAAAT
Done.