Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, whole genome shotgun sequence
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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 20 of 126
Found at i:4622797 original size:126 final size:128
Alignment explanation
Indices: 4622542--4622847 Score: 320
Period size: 129 Copynumber: 2.5 Consensus size: 128
4622532 TGATCTTTTT
* *
4622542 AAAATAAAATTTTGAAAAATAAATATTTTTGAAAAAAAAGTTGAAAGTATTAATTTTCCTTGAAA
1 AAAATAAAATTTTGAAAAATAAATATTTTTGAAAAAAAAGTTAAAAGTATCAATTTTCCTTGAAA
* * * * *
4622607 ATAAAATTTCTAAAAACTATATTCGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATATA
66 ATAAAATTTCAAAAAAATATATTCGAGAAAAAGTTGAAAGTACCAATTTTCCTTGAAAATATA
* **
4622670 AAAATAAAAATTTT-TAAAA-AAATATTTTTG-AGGAAAAGTTAAAAGTATCAATTTTCCTTGAA
1 AAAAT-AAAATTTTGAAAAATAAATATTTTTGAAAAAAAAGTTAAAAGTATCAATTTTCCTTGAA
* * *
4622732 AATAAAATTTTCAAAAAAAAATATTTTTGAGAAAAAGTTGGAAGTACCAA-TTTCC-------T-
65 AATAAAA-TTTC--AAAAAAATATATTCGAGAAAAAGTTGAAAGTACCAATTTTCCTTGAAAATA
4622788 TA
127 TA
* * *
4622790 AAAATAAAATTTTCAAAAA-AAA-A-TTTT-AAGAAAAAGTTGAAAGTATCAATTTTCCTTG
1 AAAATAAAATTTTGAAAAATAAATATTTTTGAAAAAAAAGTTAAAAGTATCAATTTTCCTTG
4622848 TATAAAAGCA
Statistics
Matches: 156, Mismatches: 16, Indels: 22
0.80 0.08 0.11
Matches are distributed among these distances:
118 32 0.21
119 9 0.06
120 14 0.09
121 1 0.01
126 35 0.22
127 15 0.10
128 13 0.08
129 37 0.24
ACGTcount: A:0.50, C:0.06, G:0.10, T:0.34
Consensus pattern (128 bp):
AAAATAAAATTTTGAAAAATAAATATTTTTGAAAAAAAAGTTAAAAGTATCAATTTTCCTTGAAA
ATAAAATTTCAAAAAAATATATTCGAGAAAAAGTTGAAAGTACCAATTTTCCTTGAAAATATA
Found at i:4623410 original size:306 final size:305
Alignment explanation
Indices: 4622832--4623442 Score: 967
Period size: 306 Copynumber: 2.0 Consensus size: 305
4622822 AAAGTTGAAA
*
4622832 GTATCAATTTTCCTTGTATAAAAGCATGAGTTTTTTCTTATAAAACAAAAAAAGGATCTATATTG
1 GTATCAATTTTCCTTGTATAAAAGCATGAGTTTTTTCTTATAAAACAAAAAAAAGATCTATATTG
* *
4622897 AAAGTCGAATCATTATTCCTTTCTCATTTTCTCTTTTTTATTTTCTTGAAAAATTTTTAATATTA
66 AAAGTCGAATCATCATTCCTTTCTCATTTTCTCATTTTTATTTTCTTGAAAAATTTTTAATATTA
* * *
4622962 AATAATCCGACGATGGAGCTTCTGTAAAAGAAATAATAGTTTTCTTGTATACTCTTGAGGTGATA
131 AATAATCCGACGATGAAGCTTCTGTAAAAGAAATAATAGTTTTCTTGTATACTCTTAAGGTGAGA
* * *
4623027 GAATTTTCTTAATTTTTTGCCAAAAATATTGGAGTCAATTAAGAATTATATCCAATAATTAATCA
196 GAATTTTCTTAATTTTCTGCCAAAAATATTAGAGTCAATTAAAAATTATATCCAATAATTAATCA
4623092 TTTGGTAAATTTTTTAAAGCTTAATGGATAACACAAAATTGAGTTG
261 TTTGGTAAA-TTTTTAAAGCTTAATGGATAACACAAAATTGAGTTG
4623138 GTATC-ATCTTTCCTTGTATAAAAGCATGAGTTTTTTCTTATAAAACAAAAAAAAGATCTATATT
1 GTATCAAT-TTTCCTTGTATAAAAGCATGAGTTTTTTCTTATAAAACAAAAAAAAGATCTATATT
* *
4623202 GAAAGTCGAATCATCATTCCTTTCTCATTTTCTCATTTTTCTTTTCTTGAAAACTTTTTAATATT
65 GAAAGTCGAATCATCATTCCTTTCTCATTTTCTCATTTTTATTTTCTTGAAAAATTTTTAATATT
* * * * *
4623267 AAATAATCTGATGATGAAGCTTTTGTAAGAGAAA-CATAGTTTTCTTGTATACTCTTAAGGTGAG
130 AAATAATCCGACGATGAAGCTTCTGTAAAAGAAATAATAGTTTTCTTGTATACTCTTAAGGTGAG
* * * *
4623331 -GAAATTTTTTTAATTTTCTGCCAAAAGTATTAGAGTCAATTAAAAATTATTTTCAATAATTAAT
195 AG-AATTTTCTTAATTTTCTGCCAAAAATATTAGAGTCAATTAAAAATTATATCCAATAATTAAT
* *
4623395 CATTTGGTAAAATTTTTAAGGCTTAATGGATAATACAAAATTGAGTTG
259 CATTTGGT-AAATTTTTAAAGCTTAATGGATAACACAAAATTGAGTTG
4623443 ATACCATTTT
Statistics
Matches: 280, Mismatches: 22, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
304 1 0.00
305 126 0.45
306 153 0.55
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.41
Consensus pattern (305 bp):
GTATCAATTTTCCTTGTATAAAAGCATGAGTTTTTTCTTATAAAACAAAAAAAAGATCTATATTG
AAAGTCGAATCATCATTCCTTTCTCATTTTCTCATTTTTATTTTCTTGAAAAATTTTTAATATTA
AATAATCCGACGATGAAGCTTCTGTAAAAGAAATAATAGTTTTCTTGTATACTCTTAAGGTGAGA
GAATTTTCTTAATTTTCTGCCAAAAATATTAGAGTCAATTAAAAATTATATCCAATAATTAATCA
TTTGGTAAATTTTTAAAGCTTAATGGATAACACAAAATTGAGTTG
Found at i:4634749 original size:44 final size:44
Alignment explanation
Indices: 4634695--4634817 Score: 140
Period size: 44 Copynumber: 2.8 Consensus size: 44
4634685 ATTATCGATA
*
4634695 AGCCTTGTTTATTTTTTCAAAGTTGTTGAGCCTCTGATTGA-AGG
1 AGCCTTGTTTATTTTTTCAAAGTTGTTGAGCCTCTGATT-ATAAG
* * * * *
4634739 AGCTTTGTTTATCTTTTCAAAGTCGTTAAGTCTCTGATTATAAG
1 AGCCTTGTTTATTTTTTCAAAGTTGTTGAGCCTCTGATTATAAG
* * * *
4634783 AGCCTTGTTCATTTTTCCAAAGTTGTGGTGCCTCT
1 AGCCTTGTTTATTTTTTCAAAGTTGTTGAGCCTCT
4634818 ATTTAGAGGA
Statistics
Matches: 63, Mismatches: 15, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
43 1 0.02
44 62 0.98
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.44
Consensus pattern (44 bp):
AGCCTTGTTTATTTTTTCAAAGTTGTTGAGCCTCTGATTATAAG
Found at i:4634840 original size:42 final size:42
Alignment explanation
Indices: 4634793--4635118 Score: 354
Period size: 42 Copynumber: 7.8 Consensus size: 42
4634783 AGCCTTGTTC
* *
4634793 ATTTTTCCAAAGTTGTGGTGCCTCTATTTAGAGGAGCAATTT
1 ATTTTTCCAAAGTTATGGTGCCTCTGTTTAGAGGAGCAATTT
* * *
4634835 ATTTTT-CAAAGTTATGTTGCTTCTGTTTAGAGGAGTAATTT
1 ATTTTTCCAAAGTTATGGTGCCTCTGTTTAGAGGAGCAATTT
* * *
4634876 ATTTTTCCAAAGTTATGGTGCTTTTGTTTAGATGAGCAATTT
1 ATTTTTCCAAAGTTATGGTGCCTCTGTTTAGAGGAGCAATTT
*
4634918 ATTTTT-CAAAGTTGTGGT-CCTCTGTTTAGAGGAGCAATTT
1 ATTTTTCCAAAGTTATGGTGCCTCTGTTTAGAGGAGCAATTT
* * * *
4634958 ATTTTTTCAAAGTTATGGTGCCTCTATTTAAAGGAGCATTTT
1 ATTTTTCCAAAGTTATGGTGCCTCTGTTTAGAGGAGCAATTT
* * * * *
4635000 ATTTTTCAAAAGTTATGGTACCTTTGCTTAGAGTAGCAATTT
1 ATTTTTCCAAAGTTATGGTGCCTCTGTTTAGAGGAGCAATTT
** * * * * *
4635042 ATTTTTTAAAAGTTGTAGAGCCTCTATTTAAAGGAGC-ATTT
1 ATTTTTCCAAAGTTATGGTGCCTCTGTTTAGAGGAGCAATTT
** * *
4635083 ATTTTTCTCAAAGTCGTTGAGCCTCTGTTTAGAGGA
1 ATTTTTC-CAAAGTTATGGTGCCTCTGTTTAGAGGA
4635119 ACTTTGTTTA
Statistics
Matches: 238, Mismatches: 42, Indels: 8
0.83 0.15 0.03
Matches are distributed among these distances:
40 25 0.11
41 68 0.29
42 145 0.61
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (42 bp):
ATTTTTCCAAAGTTATGGTGCCTCTGTTTAGAGGAGCAATTT
Found at i:4634974 original size:124 final size:124
Alignment explanation
Indices: 4634793--4635096 Score: 400
Period size: 124 Copynumber: 2.4 Consensus size: 124
4634783 AGCCTTGTTC
* *
4634793 ATTTTTCCAAAGTTGTGGTGCCTCTATTTAGAGGAGCAATTTA-TTTTTCAAAGTTATGTTGCTT
1 ATTTTT-CAAAGTTGTGGT-CCTCTATTTAGAGGAGCAATTTATTTTTTCAAAGTTATGGTGCCT
* * * * * * *
4634857 CTGTTTAGAGGAGTAATTTATTTTTCCAAAGTTATGGTGCTTTTGTTTAGA-TGAGCAATTT
64 CTATTTAAAGGAGCAATTTATTTTTCAAAAGTTATGGTACCTTTGCTTAGAGT-AGCAATTT
*
4634918 ATTTTTCAAAGTTGTGGTCCTCTGTTTAGAGGAGCAATTTATTTTTTCAAAGTTATGGTGCCTCT
1 ATTTTTCAAAGTTGTGGTCCTCTATTTAGAGGAGCAATTTATTTTTTCAAAGTTATGGTGCCTCT
*
4634983 ATTTAAAGGAGCATTTTATTTTTCAAAAGTTATGGTACCTTTGCTTAGAGTAGCAATTT
66 ATTTAAAGGAGCAATTTATTTTTCAAAAGTTATGGTACCTTTGCTTAGAGTAGCAATTT
* *
4635042 ATTTTTTAAAAGTTGTAGAG-CCTCTATTTAAAGGAGC-ATTTATTTTTCTCAAAGT
1 A-TTTTTCAAAGTTGT-G-GTCCTCTATTTAGAGGAGCAATTTATTTTT-TCAAAGT
4635097 CGTTGAGCCT
Statistics
Matches: 159, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
123 22 0.14
124 83 0.52
125 30 0.19
126 23 0.14
127 1 0.01
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.44
Consensus pattern (124 bp):
ATTTTTCAAAGTTGTGGTCCTCTATTTAGAGGAGCAATTTATTTTTTCAAAGTTATGGTGCCTCT
ATTTAAAGGAGCAATTTATTTTTCAAAAGTTATGGTACCTTTGCTTAGAGTAGCAATTT
Found at i:4635563 original size:20 final size:20
Alignment explanation
Indices: 4635533--4635574 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
4635523 AGAAGTGGTC
4635533 TTAAGATTTTTAGGAATTTTT
1 TTAAGATTTTT-GGAATTTTT
*
4635554 TTAA-ATTTTTGGGATTTTT
1 TTAAGATTTTTGGAATTTTT
4635573 TT
1 TT
4635575 TCTTTTTCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.50
20 6 0.30
21 4 0.20
ACGTcount: A:0.24, C:0.00, G:0.14, T:0.62
Consensus pattern (20 bp):
TTAAGATTTTTGGAATTTTT
Found at i:4635575 original size:20 final size:21
Alignment explanation
Indices: 4635533--4635575 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
4635523 AGAAGTGGTC
4635533 TTAAGATTTTTAGGAATTTTT
1 TTAAGATTTTTAGGAATTTTT
* *
4635554 TTAA-ATTTTTGGGATTTTTT
1 TTAAGATTTTTAGGAATTTTT
4635574 TT
1 TT
4635576 CTTTTTCTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.23, C:0.00, G:0.14, T:0.63
Consensus pattern (21 bp):
TTAAGATTTTTAGGAATTTTT
Found at i:4636372 original size:119 final size:120
Alignment explanation
Indices: 4636146--4636379 Score: 328
Period size: 120 Copynumber: 2.0 Consensus size: 120
4636136 TGATCTCTTT
** * * * * *
4636146 AAAATAAAATTTTGAAAAAAAAATATTTTTGAATAAAAGTCGAAAGTATCAATTTTTCTGGAAAA
1 AAAATAAAATTTCCAAAAAAAAATATTTTTAAAGAAAAGTCGAAAGTACCAATTTTCCTGAAAAA
* *
4636211 TAAAATTTTAAAAAAATATTTTTGAAGGAAAAGTTGAAAGTATCAATTTTCCTTA
66 TAAAATTTAAAAAAAATATTTTTGAAGAAAAAGTTGAAAGTATCAATTTTCCTTA
* * * *
4636266 AAAATAAAGTTTCCAAAAAAAAATATTTTTAAAGAAAAGTTGGAAGTACCAA-TTTCCTTAAAAA
1 AAAATAAAATTTCCAAAAAAAAATATTTTTAAAGAAAAGTCGAAAGTACCAATTTTCCTGAAAAA
4636330 TAAAATTCTAAAAAAAATATTTTT-AAGAAAAAGTTGAAAGTATCAATTTT
66 TAAAATT-TAAAAAAAATATTTTTGAAGAAAAAGTTGAAAGTATCAATTTT
4636380 TTTTGTATAA
Statistics
Matches: 100, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
119 41 0.41
120 59 0.59
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.33
Consensus pattern (120 bp):
AAAATAAAATTTCCAAAAAAAAATATTTTTAAAGAAAAGTCGAAAGTACCAATTTTCCTGAAAAA
TAAAATTTAAAAAAAATATTTTTGAAGAAAAAGTTGAAAGTATCAATTTTCCTTA
Found at i:4638030 original size:59 final size:58
Alignment explanation
Indices: 4637909--4638043 Score: 150
Period size: 59 Copynumber: 2.3 Consensus size: 58
4637899 TGTTATAAAT
* * *
4637909 TTGTTGAAACTTATTTGAG-TTTGATTACTAATGTGTTGAGGTTTTGTTAGTTATTTAT
1 TTGTTGAAATTTATTTG-GTTTTGATAACTAATGTGTTGAGGTTTTGTTAGTTATTTAG
* * *
4637967 TTGTTGAAATTTATTTAGGTTTTGAATAAC-AATTTGTTGAGTTTTTGTTGGTT-TTATAG
1 TTGTTGAAATTTATTT-GGTTTTG-ATAACTAATGTGTTGAGGTTTTGTTAGTTATT-TAG
*
4638026 TTGTTGAAATTTGTTTGG
1 TTGTTGAAATTTATTTGG
4638044 GTTGCGGTTA
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
58 20 0.30
59 42 0.64
60 4 0.06
ACGTcount: A:0.22, C:0.02, G:0.21, T:0.54
Consensus pattern (58 bp):
TTGTTGAAATTTATTTGGTTTTGATAACTAATGTGTTGAGGTTTTGTTAGTTATTTAG
Found at i:4645649 original size:3 final size:3
Alignment explanation
Indices: 4645641--4645676 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
4645631 CTCCAACCCC
*
4645641 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCG TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
4645677 AAAAAACAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.31, C:0.33, G:0.03, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:4646734 original size:22 final size:22
Alignment explanation
Indices: 4646709--4646755 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
4646699 CATAACCTTT
*
4646709 AGCTTTTATATATTTATACAAG
1 AGCTTTTATATATTTAAACAAG
4646731 AGCTTTTATATATTTAAACAAG
1 AGCTTTTATATATTTAAACAAG
4646753 AGC
1 AGC
4646756 AACCTCTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (22 bp):
AGCTTTTATATATTTAAACAAG
Found at i:4648928 original size:4 final size:4
Alignment explanation
Indices: 4648919--4648943 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
4648909 GTTACTCTTG
4648919 TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC T
4648944 AGGGCACCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:4651710 original size:10 final size:10
Alignment explanation
Indices: 4651697--4651771 Score: 51
Period size: 10 Copynumber: 7.4 Consensus size: 10
4651687 CTTTTTTCAA
4651697 TTTTTAAAAT
1 TTTTTAAAAT
*
4651707 TTTTAAAAAT
1 TTTTTAAAAT
* * * *
4651717 ATTTCAGATT
1 TTTTTAAAAT
*
4651727 TTTTTAAACT
1 TTTTTAAAAT
* *
4651737 TGTTTTATAAC
1 T-TTTTAAAAT
4651748 TTTTTAAAAT
1 TTTTTAAAAT
* *
4651758 ATTTCAAAAT
1 TTTTTAAAAT
4651768 TTTT
1 TTTT
4651772 AAATTAAAAT
Statistics
Matches: 47, Mismatches: 17, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
10 40 0.85
11 7 0.15
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (10 bp):
TTTTTAAAAT
Found at i:4651772 original size:19 final size:19
Alignment explanation
Indices: 4651670--4651774 Score: 61
Period size: 19 Copynumber: 5.4 Consensus size: 19
4651660 ATTTTTTTAA
*
4651670 TTTTAAAATTTTCATAACT
1 TTTTAAAATTTTCATAAAT
** *
4651689 TTTTTCAATTTTTA-AAAT
1 TTTTAAAATTTTCATAAAT
* **
4651707 TTTTAAAAATATTTCAGATTT
1 TTTT-AAAAT-TTTCATAAAT
* * *
4651728 TTTTAAACTTGTTTTATAACT
1 TTTTAAA-AT-TTTCATAAAT
4651749 TTTTAAAATATTTCA-AAAT
1 TTTTAAAAT-TTTCATAAAT
4651768 TTTTAAA
1 TTTTAAA
4651775 TTAAAATTTT
Statistics
Matches: 63, Mismatches: 19, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
18 7 0.11
19 24 0.38
20 12 0.19
21 20 0.32
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (19 bp):
TTTTAAAATTTTCATAAAT
Found at i:4652214 original size:12 final size:12
Alignment explanation
Indices: 4652197--4652232 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
4652187 AAGTAAACAG
4652197 GGCGTTTGAACT
1 GGCGTTTGAACT
*
4652209 GGCGTTTGATCT
1 GGCGTTTGAACT
*
4652221 GGCGCTTGAACT
1 GGCGTTTGAACT
4652233 ATTTTTGTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.14, C:0.19, G:0.33, T:0.33
Consensus pattern (12 bp):
GGCGTTTGAACT
Found at i:4656281 original size:27 final size:27
Alignment explanation
Indices: 4656219--4656272 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
4656209 CATTTTATTA
* **
4656219 AAATCATATTTTATATTTTAATAGTTAG
1 AAATAATA-TTTATATTTTAATAAATAG
4656247 AAATAATATTTATATTTTAATAAATA
1 AAATAATATTTATATTTTAATAAATA
4656273 TAATAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (27 bp):
AAATAATATTTATATTTTAATAAATAG
Found at i:4656536 original size:14 final size:13
Alignment explanation
Indices: 4656488--4656540 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 13
4656478 TGAATGTAGA
4656488 TTTTTTTATT-AT
1 TTTTTTTATTAAT
*
4656500 TTTTTATATATACAT
1 TTTTTTTAT-TA-AT
4656515 TTTCTTTTATTAAT
1 TTT-TTTTATTAAT
4656529 TATTTTTTATTA
1 T-TTTTTTATTA
4656541 TAGTCAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
12 8 0.24
13 1 0.03
14 11 0.32
15 9 0.26
16 5 0.15
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTTATTAAT
Found at i:4657856 original size:11 final size:11
Alignment explanation
Indices: 4657792--4657858 Score: 59
Period size: 11 Copynumber: 6.0 Consensus size: 11
4657782 ATACATTATC
*
4657792 AAACATCCATC
1 AAACATCCATA
*
4657803 AAATATCCAT-
1 AAACATCCATA
4657813 -AACATCCATA
1 AAACATCCATA
4657823 AAACAT-CATAA
1 AAACATCCAT-A
4657834 AATATCCATCCATA
1 AA-A--CATCCATA
4657848 AAACATCCATA
1 AAACATCCATA
4657859 GCATCCATCC
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
9 8 0.17
10 3 0.06
11 25 0.53
12 1 0.02
13 1 0.02
14 6 0.13
15 3 0.06
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (11 bp):
AAACATCCATA
Found at i:4662647 original size:6 final size:6
Alignment explanation
Indices: 4662636--4662662 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4662626 TTGAGTTTTT
4662636 TAATTC TAATTC TAATTC TAATTC TAA
1 TAATTC TAATTC TAATTC TAATTC TAA
4662663 ATATTTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (6 bp):
TAATTC
Found at i:4674586 original size:262 final size:259
Alignment explanation
Indices: 4674010--4675069 Score: 1225
Period size: 265 Copynumber: 4.0 Consensus size: 259
4674000 ACAAAAAACT
* * * *
4674010 AAAAATTATCACGTATCTTCTAATATATTAATTACATTTATATTTTATTATTTATCTTAAATTAT
1 AAAAATTATCATGTATCTTCTAATAAATTAATTACATTTATATTTTATTATTTATCTTAAATCAC
* * *
4674075 TCTTAATCAAA-TCATATTAAAGATAATAAAATTTTAATTGCCATAATCATAAAATAATTGTCAC
66 TCTTAATCAAATTCATATTAAAGATAATAAAACTTTAATTGCCATTATCATAGAATAATTGTCAC
* * *
4674139 CTCCTTTTTCAATTAT-AATACTCAACTTTTAAATTACATCTTATCTTATGTAAATATACAAAAG
131 CTCCTTTTTCAATTATAAATATTCAACTCTTAAATTACATCTTA---TA--TAAATATATAAAAG
* * * * *
4674203 CCAAAACTTTTGATAAAAAAAGAAATTATCCAACTAGATAGCCTACATAATTGACATGTGGACAA
191 CCAAACCTTTT-ACAAAAAAAGAAATTGTCCAACTAGATAGCCTATATAATTGACATGTAGACAA
*
4674268 TTTAAAA
255 TTT--TA
* * *
4674275 AAAAATTGTCATGTATCTTATAATAAATTAATTACATTTATGTTTTATTATTTA-CTTTAAATCA
1 AAAAATTATCATGTATCTTCTAATAAATTAATTACATTTATATTTTATTATTTATC-TTAAATCA
* * * * *
4674339 CTCTTAA-CTAAATTCATATTAAAGGTAATACAATTTTAATTGTCATTATCATAGAATAGTTTTG
65 CTCTTAATC-AAATTCATATTAAAGATAATAAAACTTTAATTGCCATTATCATAGAATA--ATTG
* * * *
4674403 TCACCTTCTTTTTTAATTGTAAATATTTAACTCTTAAATTACATCTTATATAAATATATAAAAGC
127 TCACCTCCTTTTTCAATTATAAATATTCAACTCTTAAATTACATCTTATATAAATATATAAAAGC
* * * * *
4674468 CAAACCTTTTACAAAAAAAGAAATTGTCCAATATAGATAGCCTATTTAATTGCCATATTGACAAT
192 CAAACCTTTTACAAAAAAAGAAATTGTCCAA-CTAGATAGCCTATATAATTGACATGTAGACAAT
4674533 TTTA
256 TTTA
** *
4674537 AAAAATTATCATGTATCTTCTAATAAATTAATTACATACATATTTTATTATTTACCTTAAATCAC
1 AAAAATTATCATGTATCTTCTAATAAATTAATTACATTTATATTTTATTATTTATCTTAAATCAC
*
4674602 TCTTAATCAAATTCATATTAAAGATAATGAAACTTTAATTGCCATTATCATAGAATAATTGTCAC
66 TCTTAATCAAATTCATATTAAAGATAATAAAACTTTAATTGCCATTATCATAGAATAATTGTCAC
* * * * *
4674667 CTTCTTTTCCAATAATAAATATTCAACTCTTAAATTATATTTTATCTTATATAAATACATAAAAG
131 CTCCTTTTTCAATTATAAATATTCAACTCTTAAA-T-TA---CATCTTATATAAATATATAAAA-
* * ** * * * *
4674732 GCAAAACCTTTAACAAAAATGGAAATTGTCTAACTGGATAGCTTATATAATTGACATGTAGATAA
190 GCCAAACCTTTTACAAAAAAAGAAATTGTCCAACTAGATAGCCTATATAATTGACATGTAGACAA
4674797 TTTTA
255 TTTTA
* * * *
4674802 AAAAATTGTCATGTATCTTTTAATAAATTAATTACATTTATATTTTATTGTTTATCTTAAATTAC
1 AAAAATTATCATGTATCTTCTAATAAATTAATTACATTTATATTTTATTATTTATCTTAAATCAC
4674867 T-TTCAA-CTAAATTCATATTAAA-AGTAATAAAACTTTAATTGCCATTATCATAGAATAATTTT
66 TCTT-AATC-AAATTCATATTAAAGA-TAATAAAACTTTAATTGCCATTATCATAGAATAA--TT
* * *
4674929 ATCACCTCCTTTTTCAATTGTAAATATTCAACTCTTAAATTACATCTTATGTAAATATATAAAAG
126 GTCACCTCCTTTTTCAATTATAAATATTCAACTCTTAAATTACATCTTATATAAATATATAAAAG
* ** * * * ** * * *
4674994 CCAAAACCTTTGACAAAAAAAGAAATCATTCAATGTGGATAGTTTATATAATTGATATGTGGATA
191 CC-AAACCTTTTACAAAAAAAGAAATTGTCCAA-CTAGATAGCCTATATAATTGACATGTAGACA
4675059 ATTTTA
254 ATTTTA
4675065 AAAAA
1 AAAAA
4675070 ATGTCAGTCG
Statistics
Matches: 684, Mismatches: 89, Indels: 46
0.84 0.11 0.06
Matches are distributed among these distances:
260 36 0.05
261 3 0.00
262 153 0.22
263 59 0.09
264 58 0.08
265 224 0.33
266 71 0.10
267 36 0.05
268 20 0.03
269 24 0.04
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.40
Consensus pattern (259 bp):
AAAAATTATCATGTATCTTCTAATAAATTAATTACATTTATATTTTATTATTTATCTTAAATCAC
TCTTAATCAAATTCATATTAAAGATAATAAAACTTTAATTGCCATTATCATAGAATAATTGTCAC
CTCCTTTTTCAATTATAAATATTCAACTCTTAAATTACATCTTATATAAATATATAAAAGCCAAA
CCTTTTACAAAAAAAGAAATTGTCCAACTAGATAGCCTATATAATTGACATGTAGACAATTTTA
Found at i:4676367 original size:527 final size:528
Alignment explanation
Indices: 4675662--4676891 Score: 1748
Period size: 527 Copynumber: 2.3 Consensus size: 528
4675652 ACCTTCAACA
* *
4675662 AAAAATATTATCATGTATCTTCTAATATATTAATTACATTTGTATTTTATTATTTATCTTAAATC
1 AAAAA-ATTATCATGTATCTTCTAATAAATTAATTACATTTATATTTTATTATTTATCTTAAATC
* * * * *
4675727 ATTCTCAATCAAA-TCATATTAAAGATAATAAAATTTTAATTGCCATAATCATAAAATAATTGTC
65 ACTCTTAATCAAATTCATATTAAAGATAATAAAACTTTAATTGCCATTATCATAGAATAATTGTC
* * * * * * *
4675791 ACCTCCTTTTTCAATTATAAATACTCAACTTTTAAATTACATCTTATCTTATGTAAATATATAAA
130 ACCTCCTTTTCCAATTATAAATATTCAACTCTTAAATTATATTTTATCTTATATAAATACATAAA
* * * *
4675856 AGCCAAAACTTTTGACAAAAAAGAAAATTATCCAACTAGATAACCTATATAATTGACATGTGGAC
195 AGACAAAACCTTTAACAAAAAAGAAAATTATCCAACTAGATAACCTATATAATTGACATGTAGAC
* *
4675921 AATTTAAAAAAAATTGTCATGTATCTTATAATAAATTAATTACATTTATGTTTTATTATTTACTT
260 AATTT-AAAAAAATTGTCATGTATCTTATAATAAATTAATTACATTTATATTTTATTATTTACCT
* * * * *
4675986 TAAATCACTCTTAACTAAATTCATATTAAAGGTAATAAAATTTTAATTGTCATTATCATAGAATA
324 TAAATCACTATCAACTAAATTCATATTAAAAGTAATAAAACTTTAATTGCCATTATCATAGAATA
* *
4676051 ATTTTGTCACCTTCTTTTT-AATTGTAAATATTCAACTCTTAAATTACATCTTATATAAATATAT
389 ATTTTATCACCTCCTTTTTCAATTGTAAATATTCAACTCTTAAATTACATCTTATATAAATATAT
* * * *
4676115 AAAAGC-CAAACCTTTTACAAAAAAAGA-AATTGTCCAATATAGATAGCCTATTTAATTGACATA
454 AAAAGCTAAAACCTTTGACAAAAAAA-ACAATCGTCCAATATAGATAGCCTATATAATTGACATA
*
4676178 TTGACAATTTT
518 TGGACAATTTT
* ** *
4676189 AAAAAATTATCATGTTTCTTCTAATAAATTAATTACATACATATTTTATTATTTACCTTAAATCA
1 AAAAAATTATCATGTATCTTCTAATAAATTAATTACATTTATATTTTATTATTTATCTTAAATCA
* * *
4676254 CTCTTAATCAAATTCATATTAAAGATAATGAAACTTTAATTACCATTATCACAGAATAATTGTCA
66 CTCTTAATCAAATTCATATTAAAGATAATAAAACTTTAATTGCCATTATCATAGAATAATTGTCA
* *
4676319 CCTTCTTTTCCAATAATAAATATTCAACTCTTAAATTATATTTTATCTTATATAAATACATAAAA
131 CCTCCTTTTCCAATTATAAATATTCAACTCTTAAATTATATTTTATCTTATATAAATACATAAAA
* * * * * *
4676384 GACAAAACCTTTAACAAAAAAGGAAATTGTCCAACTGGATAGCTTATATAATTGACATGTAGATA
196 GACAAAACCTTTAACAAAAAAGAAAATTATCCAACTAGATAACCTATATAATTGACATGTAGACA
* * * *
4676449 ATTTTAAAAAATTGTCATGTATCTTTTAATAAATTAGTTATATTTATATTTTATTATTTACCTTA
261 ATTTAAAAAAATTGTCATGTATCTTATAATAAATTAATTACATTTATATTTTATTATTTACCTTA
*
4676514 AATTACTATCAACTAAATTCATATTAAAAGTAATAAAACTTTAATTGCCATTATCATAGAATAAT
326 AATCACTATCAACTAAATTCATATTAAAAGTAATAAAACTTTAATTGCCATTATCATAGAATAAT
* *
4676579 TTTATCACCTCCTTTTTCAATTGTAAATATTCAACTCTTATATTACATCTTATGTAAATATATAA
391 TTTATCACCTCCTTTTTCAATTGTAAATATTCAACTCTTAAATTACATCTTATATAAATATATAA
* * * * *
4676644 AAGCTAAAACCTTTGACAAAAAAAACAATCGTTCAATGTGGATAGTCTATATAATTGACATGTGG
456 AAGCTAAAACCTTTGACAAAAAAAACAATCGTCCAATATAGATAGCCTATATAATTGACATATGG
*
4676709 ATAATTTT
521 ACAATTTT
* * * *
4676717 AAAAAATTATCATGTATCTTCTAATAAATTAATCACATTTTTATTTTATTATTTATTTTAAATTA
1 AAAAAATTATCATGTATCTTCTAATAAATTAATTACATTTATATTTTATTATTTATCTTAAATCA
* * * * *
4676782 CTCTTAATTAAATTTATATTAAAGGTAATAAAACTCTAATTGCCATTATCATAGAATAATTTTAT
66 CTCTTAATCAAATTCATATTAAAGATAATAAAACTTTAATTGCCATTATCATAGAATAA--TTGT
* *
4676847 CACCTCCTTTTCCAATTGTAAATATTCAATTCTTAAATTATATTT
129 CACCTCCTTTTCCAATTATAAATATTCAACTCTTAAATTATATTT
4676892 GTGTAAAAAA
Statistics
Matches: 617, Mismatches: 80, Indels: 9
0.87 0.11 0.01
Matches are distributed among these distances:
526 193 0.31
527 216 0.35
528 164 0.27
530 44 0.07
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.41
Consensus pattern (528 bp):
AAAAAATTATCATGTATCTTCTAATAAATTAATTACATTTATATTTTATTATTTATCTTAAATCA
CTCTTAATCAAATTCATATTAAAGATAATAAAACTTTAATTGCCATTATCATAGAATAATTGTCA
CCTCCTTTTCCAATTATAAATATTCAACTCTTAAATTATATTTTATCTTATATAAATACATAAAA
GACAAAACCTTTAACAAAAAAGAAAATTATCCAACTAGATAACCTATATAATTGACATGTAGACA
ATTTAAAAAAATTGTCATGTATCTTATAATAAATTAATTACATTTATATTTTATTATTTACCTTA
AATCACTATCAACTAAATTCATATTAAAAGTAATAAAACTTTAATTGCCATTATCATAGAATAAT
TTTATCACCTCCTTTTTCAATTGTAAATATTCAACTCTTAAATTACATCTTATATAAATATATAA
AAGCTAAAACCTTTGACAAAAAAAACAATCGTCCAATATAGATAGCCTATATAATTGACATATGG
ACAATTTT
Found at i:4676764 original size:263 final size:260
Alignment explanation
Indices: 4675662--4676886 Score: 1480
Period size: 265 Copynumber: 4.7 Consensus size: 260
4675652 ACCTTCAACA
* * *
4675662 AAAAATATTATCATGTATCTTCTAATATATTAATTACATTTGTATTTTATTATTTATCTTAAATC
1 AAAAA-ATTATCATGTATCTTCTAATAAATTAATTACATTTATATTTTATTATTTACCTTAAATC
* * * * *
4675727 ATTCTCAATCAAA-TCATATT-AAAGATAATAAAATTTTAATTGCCATAATCATAAAATAA--TT
65 ACTCTTAAT-AAATTCATATTAAAAG-TAATAAAACTTTAATTGCCATTATCATAGAATAATTTT
* * *
4675788 GTCACCTCCTTTTTCAATTATAAATACTCAACTTTTAAATTACATCTTATCTTATGTAAATATAT
128 GTCACCTCCTTTTTCAATTGTAAATATTCAACTCTTAAATTACATCTTA---TA--TAAATATAT
* * *
4675853 AAAAGCCAAAACTTTTGACAAAAAAGAAAATTATCCAACTAGATAACCTATATAATTGACATGTG
188 AAAAG-CAAAACCTTTGACAAAAAAGAAAATTGTCCAACTAGATAGCCTATATAATTGACATGTG
*
4675918 GACAATTTAA
252 GACAATTT-T
* * * *
4675928 AAAAAATTGTCATGTATCTTATAATAAATTAATTACATTTATGTTTTATTATTTACTTTAAATCA
1 AAAAAATTATCATGTATCTTCTAATAAATTAATTACATTTATATTTTATTATTTACCTTAAATCA
* * *
4675993 CTCTTAACTAAATTCATATTAAAGGTAATAAAATTTTAATTGTCATTATCATAGAATAATTTTGT
66 CTCTTAA-TAAATTCATATTAAAAGTAATAAAACTTTAATTGCCATTATCATAGAATAATTTTGT
* *
4676058 CACCTTCTTTTT-AATTGTAAATATTCAACTCTTAAATTACATCTTATATAAATATATAAAAGCC
130 CACCTCCTTTTTCAATTGTAAATATTCAACTCTTAAATTACATCTTATATAAATATATAAAAGCA
* * * * *
4676122 AAACCTTTTACAAAAAA-AGAAATTGTCCAATATAGATAGCCTATTTAATTGACATATTGACAAT
195 AAACCTTTGACAAAAAAGA-AAATTGTCCAA-CTAGATAGCCTATATAATTGACATGTGGACAAT
4676186 TTT
258 TTT
* **
4676189 AAAAAATTATCATGTTTCTTCTAATAAATTAATTACATACATATTTTATTATTTACCTTAAATCA
1 AAAAAATTATCATGTATCTTCTAATAAATTAATTACATTTATATTTTATTATTTACCTTAAATCA
* * *
4676254 CTCTTAATCAAATTCATATT-AAAGATAATGAAACTTTAATTACCATTATCACAGAATAA--TTG
66 CTCTTAAT-AAATTCATATTAAAAG-TAATAAAACTTTAATTGCCATTATCATAGAATAATTTTG
* * ** * *
4676316 TCACCTTCTTTTCCAATAATAAATATTCAACTCTTAAATTATATTTTATCTTATATAAATACATA
129 TCACCTCCTTTTTCAATTGTAAATATTCAACTCTTAAA-T-TA---CATCTTATATAAATATATA
* * * * *
4676381 AAAGACAAAACCTTTAACAAAAAAGGAAATTGTCCAACTGGATAGCTTATATAATTGACATGTAG
189 AAAG-CAAAACCTTTGACAAAAAAGAAAATTGTCCAACTAGATAGCCTATATAATTGACATGTGG
*
4676446 ATAATTTT
253 ACAATTTT
* * * * *
4676454 AAAAAATTGTCATGTATCTTTTAATAAATTAGTTATATTTATATTTTATTATTTACCTTAAATTA
1 AAAAAATTATCATGTATCTTCTAATAAATTAATTACATTTATATTTTATTATTTACCTTAAATCA
* * *
4676519 CTATCAACTAAATTCATATTAAAAGTAATAAAACTTTAATTGCCATTATCATAGAATAATTTTAT
66 CTCTTAA-TAAATTCATATTAAAAGTAATAAAACTTTAATTGCCATTATCATAGAATAATTTTGT
* *
4676584 CACCTCCTTTTTCAATTGTAAATATTCAACTCTTATATTACATCTTATGTAAATATATAAAAGCT
130 CACCTCCTTTTTCAATTGTAAATATTCAACTCTTAAATTACATCTTATATAAATATATAAAAGC-
* * * * * *
4676649 AAAACCTTTGACAAAAAA-AACAATCGTTCAATGTGGATAGTCTATATAATTGACATGTGGATAA
194 AAAACCTTTGACAAAAAAGAA-AATTGTCCAA-CTAGATAGCCTATATAATTGACATGTGGACAA
4676713 TTTT
257 TTTT
* * ** *
4676717 AAAAAATTATCATGTATCTTCTAATAAATTAATCACATTTTTATTTTATTATTTATTTTAAATTA
1 AAAAAATTATCATGTATCTTCTAATAAATTAATTACATTTATATTTTATTATTTACCTTAAATCA
* * * *
4676782 CTCTTAATTAAATTTATATTAAAGGTAATAAAACTCTAATTGCCATTATCATAGAATAATTTTAT
66 CTCTTAA-TAAATTCATATTAAAAGTAATAAAACTTTAATTGCCATTATCATAGAATAATTTTGT
* *
4676847 CACCTCCTTTTCCAATTGTAAATATTCAATTCTTAAATTA
130 CACCTCCTTTTTCAATTGTAAATATTCAACTCTTAAATTA
4676887 TATTTGTGTA
Statistics
Matches: 833, Mismatches: 102, Indels: 51
0.84 0.10 0.05
Matches are distributed among these distances:
259 15 0.02
260 27 0.03
261 134 0.16
262 91 0.11
263 185 0.22
264 2 0.00
265 217 0.26
266 78 0.09
267 69 0.08
268 15 0.02
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.40
Consensus pattern (260 bp):
AAAAAATTATCATGTATCTTCTAATAAATTAATTACATTTATATTTTATTATTTACCTTAAATCA
CTCTTAATAAATTCATATTAAAAGTAATAAAACTTTAATTGCCATTATCATAGAATAATTTTGTC
ACCTCCTTTTTCAATTGTAAATATTCAACTCTTAAATTACATCTTATATAAATATATAAAAGCAA
AACCTTTGACAAAAAAGAAAATTGTCCAACTAGATAGCCTATATAATTGACATGTGGACAATTTT
Found at i:4682502 original size:29 final size:29
Alignment explanation
Indices: 4682446--4682524 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
4682436 GCAAATTCTA
*
4682446 TGAAA-CTTAAATCCTATGAAACCCCAAATT
1 TGAAACCTTAAACCCTA--AAACCCCAAATT
*
4682476 TGAAACCTTAAACCCTAAAACCTCAAATT
1 TGAAACCTTAAACCCTAAAACCCCAAATT
*
4682505 TGAAACCTTAAACCTTAAAA
1 TGAAACCTTAAACCCTAAAA
4682525 GCCTAAACCC
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 30 0.67
30 5 0.11
31 10 0.22
ACGTcount: A:0.46, C:0.24, G:0.05, T:0.25
Consensus pattern (29 bp):
TGAAACCTTAAACCCTAAAACCCCAAATT
Found at i:4682519 original size:7 final size:7
Alignment explanation
Indices: 4682478--4682672 Score: 102
Period size: 7 Copynumber: 27.7 Consensus size: 7
4682468 CCCAAATTTG
4682478 AAACCTT
1 AAACCTT
*
4682485 AAACCCTA
1 AAA-CCTT
*
4682493 AAACCTC
1 AAACCTT
*
4682500 AAA-TTT
1 AAACCTT
4682506 GAAACCTT
1 -AAACCTT
4682514 AAACCTT
1 AAACCTT
4682521 AAAAGCC-T
1 -AAA-CCTT
*
4682529 AAACCCT
1 AAACCTT
*
4682536 AAACCTG
1 AAACCTT
4682543 AAA-CTCT
1 AAACCT-T
4682550 AAACCTT
1 AAACCTT
*
4682557 AATCCTT
1 AAACCTT
4682564 AAAACCTT
1 -AAACCTT
4682572 AAA-CTT
1 AAACCTT
4682578 AAAACCTT
1 -AAACCTT
*
4682586 AAAACCCT
1 -AAACCTT
4682594 AAACC-T
1 AAACCTT
*
4682600 AAA-TTCT
1 AAACCT-T
*
4682607 AAATCTT
1 AAACCTT
*
4682614 AAACCCT
1 AAACCTT
*
4682621 AAACC-C
1 AAACCTT
4682627 AAACCTT
1 AAACCTT
4682634 AAA-CTT
1 AAACCTT
*
4682640 GAAACCCT
1 -AAACCTT
*
4682648 AAACC-C
1 AAACCTT
*
4682654 AAACCCT
1 AAACCTT
*
4682661 AAACCCT
1 AAACCTT
4682668 AAACC
1 AAACC
4682673 CAAACCCTAA
Statistics
Matches: 150, Mismatches: 20, Indels: 36
0.73 0.10 0.17
Matches are distributed among these distances:
6 25 0.17
7 90 0.60
8 33 0.22
9 2 0.01
ACGTcount: A:0.45, C:0.31, G:0.02, T:0.22
Consensus pattern (7 bp):
AAACCTT
Found at i:4682532 original size:22 final size:21
Alignment explanation
Indices: 4682507--4682599 Score: 100
Period size: 22 Copynumber: 4.3 Consensus size: 21
4682497 CTCAAATTTG
4682507 AAACCTTAAACCTTAAAAGCCT
1 AAACCTTAAACCTTAAAA-CCT
* *
4682529 AAACCCTAAACC-TGAAACTCT
1 AAACCTTAAACCTTAAAAC-CT
*
4682550 AAACCTTAATCCTTAAAACCTT
1 AAACCTTAAACCTTAAAACC-T
4682572 AAA-CTTAAAACCTTAAAACCCT
1 AAACCTT-AAACCTTAAAA-CCT
4682594 AAACCT
1 AAACCT
4682600 AAATTCTAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
20 1 0.02
21 20 0.34
22 34 0.58
23 4 0.07
ACGTcount: A:0.45, C:0.29, G:0.02, T:0.24
Consensus pattern (21 bp):
AAACCTTAAACCTTAAAACCT
Found at i:4682533 original size:36 final size:37
Alignment explanation
Indices: 4682478--4682575 Score: 89
Period size: 36 Copynumber: 2.7 Consensus size: 37
4682468 CCCAAATTTG
**
4682478 AAACCTT-AAACCCTAAAA-CCTCAAATTTGAAAC-CTT
1 AAACCTTAAAACCCTAAAACCCT-AAACCTGAAACTC-T
*
4682514 AAACCTTAAAAGCCT-AAACCCTAAACCTGAAACTCT
1 AAACCTTAAAACCCTAAAACCCTAAACCTGAAACTCT
* * *
4682550 AAACCTT-AATCCTTAAAACCTTAAAC
1 AAACCTTAAAACCCTAAAACCCTAAAC
4682576 TTAAAACCTT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
35 4 0.08
36 37 0.73
37 10 0.20
ACGTcount: A:0.45, C:0.29, G:0.03, T:0.23
Consensus pattern (37 bp):
AAACCTTAAAACCCTAAAACCCTAAACCTGAAACTCT
Found at i:4682551 original size:14 final size:14
Alignment explanation
Indices: 4682478--4682691 Score: 138
Period size: 14 Copynumber: 15.3 Consensus size: 14
4682468 CCCAAATTTG
4682478 AAACCTTAAACCCT
1 AAACCTTAAACCCT
* **
4682492 AAAACCTCAAA-TTT
1 -AAACCTTAAACCCT
*
4682506 GAAACCTTAAACCTT
1 -AAACCTTAAACCCT
4682521 AAAAGCC-TAAACCCT
1 -AAA-CCTTAAACCCT
* *
4682536 AAACCTGAAACTCT
1 AAACCTTAAACCCT
* *
4682550 AAACCTTAATCCTT
1 AAACCTTAAACCCT
*
4682564 AAAACCTTAAA-CTT
1 -AAACCTTAAACCCT
4682578 AAAACCTTAAAACCCT
1 -AAACCTT-AAACCCT
**
4682594 AAACC-TAAATTCT
1 AAACCTTAAACCCT
*
4682607 AAATCTTAAACCCT
1 AAACCTTAAACCCT
* *
4682621 AAACC-CAAACCTT
1 AAACCTTAAACCCT
4682634 AAA-CTTGAAACCCT
1 AAACCTT-AAACCCT
*
4682648 AAACC-CAAACCCT
1 AAACCTTAAACCCT
*
4682661 AAACCCTAAACCC-
1 AAACCTTAAACCCT
* *
4682674 AAACCCTAAATCCT
1 AAACCTTAAACCCT
4682688 AAAC
1 AAAC
4682692 TTATCTAAAC
Statistics
Matches: 158, Mismatches: 29, Indels: 25
0.75 0.14 0.12
Matches are distributed among these distances:
12 1 0.01
13 44 0.28
14 70 0.44
15 39 0.25
16 4 0.03
ACGTcount: A:0.45, C:0.31, G:0.02, T:0.21
Consensus pattern (14 bp):
AAACCTTAAACCCT
Found at i:4682623 original size:27 final size:27
Alignment explanation
Indices: 4682528--4682691 Score: 131
Period size: 27 Copynumber: 5.9 Consensus size: 27
4682518 CTTAAAAGCC
4682528 TAAACCCTAAACCTGAAA-CTCTAAACCT
1 TAAACCCTAAACCT-AAATC-CTAAACCT
* * *
4682556 TAATCCTTAAAACCTTAAA-CTTAAAACCT
1 TAAACCCT-AAACC-TAAATCCT-AAACCT
* *
4682585 TAAAACCCTAAACCTAAATTCTAAATCT
1 T-AAACCCTAAACCTAAATCCTAAACCT
*
4682613 TAAACCCTAAACCCAAA-CCTTAAA-CT
1 TAAACCCTAAACCTAAATCC-TAAACCT
* * *
4682639 TGAAACCCTAAACCCAAACCCTAAACCC
1 T-AAACCCTAAACCTAAATCCTAAACCT
4682667 TAAACCC-AAACCCTAAATCCTAAAC
1 TAAACCCTAAA-CCTAAATCCTAAAC
4682692 TTATCTAAAC
Statistics
Matches: 113, Mismatches: 13, Indels: 21
0.77 0.09 0.14
Matches are distributed among these distances:
26 7 0.06
27 57 0.50
28 21 0.19
29 22 0.19
30 6 0.05
ACGTcount: A:0.45, C:0.32, G:0.01, T:0.21
Consensus pattern (27 bp):
TAAACCCTAAACCTAAATCCTAAACCT
Found at i:4682634 original size:20 final size:20
Alignment explanation
Indices: 4682614--4682691 Score: 97
Period size: 20 Copynumber: 3.9 Consensus size: 20
4682604 TCTAAATCTT
*
4682614 AAACCCTAAACCC-AAACCTT
1 AAACCCTAAACCCTAAACC-C
*
4682634 AAA-CTTGAAACCCTAAACCC
1 AAACCCT-AAACCCTAAACCC
4682654 AAACCCTAAACCCTAAACCC
1 AAACCCTAAACCCTAAACCC
*
4682674 AAACCCTAAATCCTAAAC
1 AAACCCTAAACCCTAAAC
4682692 TTATCTAAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
19 2 0.04
20 42 0.82
21 7 0.14
ACGTcount: A:0.46, C:0.38, G:0.01, T:0.14
Consensus pattern (20 bp):
AAACCCTAAACCCTAAACCC
Found at i:4682708 original size:7 final size:7
Alignment explanation
Indices: 4682507--4682691 Score: 114
Period size: 7 Copynumber: 26.6 Consensus size: 7
4682497 CTCAAATTTG
*
4682507 AAACCTT
1 AAACCCT
*
4682514 AAACCTT
1 AAACCCT
*
4682521 AAAAGCCT
1 -AAACCCT
4682529 AAACCCT
1 AAACCCT
4682536 AAA-CCT
1 AAACCCT
*
4682542 GAAACTCT
1 -AAACCCT
*
4682550 AAACCTT
1 AAACCCT
* *
4682557 AATCCTT
1 AAACCCT
*
4682564 AAAACCTT
1 -AAACCCT
*
4682572 AAA-CTT
1 AAACCCT
*
4682578 AAAACCTT
1 -AAACCCT
4682586 AAAACCCT
1 -AAACCCT
4682594 AAA-CCT
1 AAACCCT
**
4682600 AAATTCT
1 AAACCCT
* *
4682607 AAATCTT
1 AAACCCT
4682614 AAACCCT
1 AAACCCT
4682621 AAACCC-
1 AAACCCT
*
4682627 AAACCTT
1 AAACCCT
*
4682634 AAA-CTT
1 AAACCCT
4682640 GAAACCCT
1 -AAACCCT
4682648 AAACCC-
1 AAACCCT
4682654 AAACCCT
1 AAACCCT
4682661 AAACCCT
1 AAACCCT
4682668 AAACCC-
1 AAACCCT
4682674 AAACCCT
1 AAACCCT
*
4682681 AAATCCT
1 AAACCCT
4682688 AAAC
1 AAAC
4682692 TTATCTAAAC
Statistics
Matches: 148, Mismatches: 18, Indels: 24
0.78 0.09 0.13
Matches are distributed among these distances:
6 32 0.22
7 91 0.61
8 25 0.17
ACGTcount: A:0.45, C:0.32, G:0.02, T:0.21
Consensus pattern (7 bp):
AAACCCT
Found at i:4684865 original size:18 final size:18
Alignment explanation
Indices: 4684844--4684915 Score: 58
Period size: 18 Copynumber: 4.0 Consensus size: 18
4684834 TAGGGCTTAG
4684844 GGGTTCGGTTTAGGGTTT
1 GGGTTCGGTTTAGGGTTT
*
4684862 GGGTT-GGTTT-GGAGTCT
1 GGGTTCGGTTTAGG-GTTT
* *
4684879 AGGTTAGGGTTTAGGGTTT
1 GGGTT-CGGTTTAGGGTTT
* * *
4684898 GGGGTCGATTTGGGGTTT
1 GGGTTCGGTTTAGGGTTT
4684916 AGGGCTTGTG
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
16 2 0.05
17 12 0.29
18 15 0.36
19 11 0.26
20 2 0.05
ACGTcount: A:0.08, C:0.04, G:0.46, T:0.42
Consensus pattern (18 bp):
GGGTTCGGTTTAGGGTTT
Found at i:4689711 original size:43 final size:42
Alignment explanation
Indices: 4689664--4689802 Score: 136
Period size: 43 Copynumber: 3.2 Consensus size: 42
4689654 ACATAAAAAT
* *
4689664 TCCTCTAAGCAAAAGCTCATAACTTTTGAAAAATATATAAGGC
1 TCCTCTAA-CAAAAGCTAATAACTTTTGAAAAATAAATAAGGC
* ** * * *
4689707 TCCTCTAAACAAAAGCTTACGACTTTTGATAAATAAACAAGGT
1 TCCTCT-AACAAAAGCTAATAACTTTTGAAAAATAAATAAGGC
*
4689750 TCCTTTAA-AATAGAGACTTAATAACTTTTGAAAAATAAATAAGGC
1 TCCTCTAACAA-A-AG-C-TAATAACTTTTGAAAAATAAATAAGGC
4689795 TCCTCTAA
1 TCCTCTAA
4689803 ATAGAGGCTC
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
41 2 0.03
42 3 0.04
43 40 0.53
44 3 0.04
45 28 0.37
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.29
Consensus pattern (42 bp):
TCCTCTAACAAAAGCTAATAACTTTTGAAAAATAAATAAGGC
Found at i:4689831 original size:43 final size:44
Alignment explanation
Indices: 4689685--4689871 Score: 189
Period size: 43 Copynumber: 4.3 Consensus size: 44
4689675 AAAGCTCATA
* * * * * *
4689685 ACTTTTGAAAAATATATAAGGCTCCTCTAAACAAAAGCT-TACG
1 ACTTTTGAAAAATAAATAAGGCTCCTCTAAATAGAGGCTCAATG
* * * * * * *
4689728 ACTTTTGATAAATAAACAAGGTTCCTTTAAAATAGAGACTTAATA
1 ACTTTTGAAAAATAAATAAGGCTCCTCT-AAATAGAGGCTCAATG
*
4689773 ACTTTTGAAAAATAAATAAGGCTCCTCTAAATAGAGGCTCGATG
1 ACTTTTGAAAAATAAATAAGGCTCCTCTAAATAGAGGCTCAATG
* * * *
4689817 AC-TTTGAAAAATAAATAAAGCTCTTTTAAATTGAGGCTCAATG
1 ACTTTTGAAAAATAAATAAGGCTCCTCTAAATAGAGGCTCAATG
4689860 ACTTTTGAAAAA
1 ACTTTTGAAAAA
4689872 AGAAAGGCTC
Statistics
Matches: 116, Mismatches: 25, Indels: 5
0.79 0.17 0.03
Matches are distributed among these distances:
43 61 0.53
44 30 0.26
45 25 0.22
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (44 bp):
ACTTTTGAAAAATAAATAAGGCTCCTCTAAATAGAGGCTCAATG
Found at i:4689872 original size:88 final size:88
Alignment explanation
Indices: 4689682--4689871 Score: 222
Period size: 88 Copynumber: 2.2 Consensus size: 88
4689672 GCAAAAGCTC
* * *
4689682 ATAACTTTTGAAAAATATATAAGGCTCCTCTAAACAAAAGCTTACGACTTTTGATAAATAAACAA
1 ATAACTTTTGAAAAATAAATAAGGCTCCTCTAAACAAAAGCTGACGACTTTTGAAAAATAAACAA
* * *
4689747 GGTTCCTTTAAAATAGAGACTTA
66 AGCTCCTTTAAAATAGAGACTCA
* * * * *
4689770 ATAACTTTTGAAAAATAAATAAGGCTCCTCTAAATAGAGGCTCGATGAC-TTTGAAAAATAAATA
1 ATAACTTTTGAAAAATAAATAAGGCTCCTCTAAACAAAAGCT-GACGACTTTTGAAAAATAAACA
* * *
4689834 AAGCT-CTTTTAAATTGAGGCTCA
65 AAGCTCCTTTAAAATAGAGACTCA
*
4689857 ATGACTTTTGAAAAA
1 ATAACTTTTGAAAAA
4689872 AGAAAGGCTC
Statistics
Matches: 86, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
87 28 0.33
88 54 0.63
89 4 0.05
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.31
Consensus pattern (88 bp):
ATAACTTTTGAAAAATAAATAAGGCTCCTCTAAACAAAAGCTGACGACTTTTGAAAAATAAACAA
AGCTCCTTTAAAATAGAGACTCA
Found at i:4700662 original size:17 final size:16
Alignment explanation
Indices: 4700624--4700663 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
4700614 TAAACATATT
4700624 TAAAATAAATAAATAA
1 TAAAATAAATAAATAA
4700640 TCAAAATAAATAAATAAA
1 T-AAAATAAATAAAT-AA
4700658 TAAAAT
1 TAAAAT
4700664 TAGAAAAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.05
17 18 0.82
18 3 0.14
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (16 bp):
TAAAATAAATAAATAA
Found at i:4700975 original size:22 final size:22
Alignment explanation
Indices: 4700931--4700978 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
4700921 TATTTTTAAT
* *
4700931 TATTTATTTATATTTATTGTTA
1 TATTTATTTAAATTTAATGTTA
4700953 TATTTATTTAAATTTAAAT-TTA
1 TATTTATTTAAATTT-AATGTTA
4700975 TATT
1 TATT
4700979 AAAAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TATTTATTTAAATTTAATGTTA
Found at i:4701326 original size:19 final size:18
Alignment explanation
Indices: 4701294--4701332 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
4701284 TATAAAAGGG
*
4701294 TCAAATTTTCCTTTTTTC
1 TCAAATTTTCCTTTTCTC
*
4701312 TCAAATTTTTTCTTTTCTC
1 TCAAA-TTTTCCTTTTCTC
4701331 TC
1 TC
4701333 TCTCTTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (18 bp):
TCAAATTTTCCTTTTCTC
Found at i:4701730 original size:18 final size:20
Alignment explanation
Indices: 4701700--4701742 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
4701690 ATTCTTCAAT
4701700 TCCAACTTCAAACTTTA-AA
1 TCCAACTTCAAACTTTACAA
4701719 TCCAAC-TCAAACTTTACAA
1 TCCAACTTCAAACTTTACAA
4701738 TCCAA
1 TCCAA
4701743 ACAAACAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (20 bp):
TCCAACTTCAAACTTTACAA
Found at i:4701747 original size:18 final size:18
Alignment explanation
Indices: 4701708--4701748 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
4701698 ATTCCAACTT
*
4701708 CAAACTTTAAATCCAACT
1 CAAACTTTAAATCCAACA
4701726 CAAACTTTACAATCCAA-A
1 CAAACTTTA-AATCCAACA
4701744 CAAAC
1 CAAAC
4701749 AATTTCATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (18 bp):
CAAACTTTAAATCCAACA
Found at i:4707164 original size:18 final size:18
Alignment explanation
Indices: 4707138--4707183 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
4707128 GGGTTTAGGT
*
4707138 TTTCA-TGAAATTTGGTG
1 TTTCATTGAAATTTGGGG
4707155 TTTCATTG-AATTTGGGG
1 TTTCATTGAAATTTGGGG
*
4707172 TTTCATGGAAAT
1 TTTCATTGAAAT
4707184 GGACATGTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 20 0.80
18 5 0.20
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.46
Consensus pattern (18 bp):
TTTCATTGAAATTTGGGG
Found at i:4708266 original size:16 final size:15
Alignment explanation
Indices: 4708245--4708279 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
4708235 CCAATGAAGA
4708245 TTTTTTTTCTTTTTTC
1 TTTTTTTTC-TTTTTC
4708261 TTTTTTTTCTTTTTC
1 TTTTTTTTCTTTTTC
4708276 TTTT
1 TTTT
4708280 CTGTCCTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTTTTCTTTTTC
Found at i:4710901 original size:16 final size:15
Alignment explanation
Indices: 4710852--4710902 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 15
4710842 TCATCCTTTT
*
4710852 AAAGAGAGAATGAGAG
1 AAAGAGGGAA-GAGAG
4710868 AAA-ATGGGAAGATGAG
1 AAAGA-GGGAAGA-GAG
4710884 AAAGAGGGAAGAGAAG
1 AAAGAGGGAAGAG-AG
4710900 AAA
1 AAA
4710903 TTTAAAGGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
15 4 0.13
16 25 0.83
17 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.37, T:0.06
Consensus pattern (15 bp):
AAAGAGGGAAGAGAG
Found at i:4711158 original size:12 final size:12
Alignment explanation
Indices: 4711141--4711165 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4711131 CGAACCAAGA
4711141 TTTATATTTATT
1 TTTATATTTATT
4711153 TTTATATTTATT
1 TTTATATTTATT
4711165 T
1 T
4711166 ATTTGTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTATATTTATT
Found at i:4711183 original size:22 final size:22
Alignment explanation
Indices: 4711158--4711213 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
4711148 TTATTTTTAT
* *
4711158 ATTTATTTATTTGTTATTACTC
1 ATTTATTTAATTGATATTACTC
* * *
4711180 ATTTGTTAAATTGATATTATTC
1 ATTTATTTAATTGATATTACTC
4711202 ATTTATTTAATT
1 ATTTATTTAATT
4711214 TTTGAATAGG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (22 bp):
ATTTATTTAATTGATATTACTC
Found at i:4711399 original size:50 final size:49
Alignment explanation
Indices: 4711344--4711447 Score: 154
Period size: 50 Copynumber: 2.1 Consensus size: 49
4711334 AAAATATTTG
* * *
4711344 AAAAAATATTTTTGAGGAAAAGTTGAAATATTAATTTTTCTTAAATAAA
1 AAAAAATATTTTTAAGGAAAAGTTGAAATATAAATTTTCCTTAAATAAA
* *
4711393 ATAAAAATATTTTTAAGGAAAAGTTGAACTATAAATTTTCCTTAACTAAA
1 A-AAAAATATTTTTAAGGAAAAGTTGAAATATAAATTTTCCTTAAATAAA
4711443 AAAAA
1 AAAAA
4711448 TTTCAAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
49 5 0.10
50 44 0.90
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.36
Consensus pattern (49 bp):
AAAAAATATTTTTAAGGAAAAGTTGAAATATAAATTTTCCTTAAATAAA
Found at i:4711477 original size:59 final size:57
Alignment explanation
Indices: 4711395--4711555 Score: 196
Period size: 59 Copynumber: 2.8 Consensus size: 57
4711385 TAAATAAAAT
* * * * * *
4711395 AAAAATATTTTTAAGGAAAAGTTGAACTATAAATTTTCCTTAACTAAAAAAAATTTCAAA
1 AAAAATA-TTTGAAGAAAAAGTTGAAGTATCAATTTTTCTTAAATAAAAAAAATTT--AA
* * *
4711455 AAAAATATTTGAAGAAAAAGTTGAAGTATCAATTTTTCTAAAATAAAAAATATTTTA
1 AAAAATATTTGAAGAAAAAGTTGAAGTATCAATTTTTCTTAAATAAAAAAAATTTAA
*
4711512 AAAAATATTTGAGGAAAAAGTTGAAAGTATCAATTTTTCTTAAA
1 AAAAATATTTGAAGAAAAAGTTG-AAGTATCAATTTTTCTTAAA
4711556 AAGAGCATCA
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
57 23 0.26
58 19 0.21
59 40 0.45
60 7 0.08
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (57 bp):
AAAAATATTTGAAGAAAAAGTTGAAGTATCAATTTTTCTTAAATAAAAAAAATTTAA
Found at i:4714631 original size:16 final size:16
Alignment explanation
Indices: 4714610--4714642 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
4714600 AATATAAATA
4714610 GATTAAGCATTTCTAT
1 GATTAAGCATTTCTAT
4714626 GATTAAGCATTTCTAT
1 GATTAAGCATTTCTAT
4714642 G
1 G
4714643 GATATAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (16 bp):
GATTAAGCATTTCTAT
Found at i:4715939 original size:17 final size:17
Alignment explanation
Indices: 4715892--4715940 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
4715882 ATGATATTTT
4715892 ATGAAGTTAGTTTTTGC
1 ATGAAGTTAGTTTTTGC
* *
4715909 ATGTTATTTA-TTTTTGC
1 ATG-AAGTTAGTTTTTGC
4715926 ATGAAGTTAGTTTTT
1 ATGAAGTTAGTTTTT
4715941 TTCATGTCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 4 0.15
17 18 0.69
18 4 0.15
ACGTcount: A:0.22, C:0.04, G:0.18, T:0.55
Consensus pattern (17 bp):
ATGAAGTTAGTTTTTGC
Found at i:4716007 original size:41 final size:40
Alignment explanation
Indices: 4715949--4716107 Score: 151
Period size: 41 Copynumber: 3.8 Consensus size: 40
4715939 TTTTCATGTC
* * *
4715949 ATTTATATATGTGCATTGGTT-TAGTTTAATTGCGATGATTTT
1 ATTTAT-TATTTGCATTGATTATAATTTAATT-CGATGA-TTT
**
4715991 ATTTATTATTTGCATTGATTATATATTTAATTATATGATTT
1 ATTTATTATTTGCATTGATTATA-ATTTAATTCGATGATTT
* *
4716032 GTTTATTATTTGTA-TGATTATATATTTTAATTCGCATGATTT
1 ATTTATTATTTGCATTGATTATA-A-TTTAATTCG-ATGATTT
4716074 ATTTATTATTTGCATTGCATTATATAATTTAATT
1 ATTTATTATTTGCATTG-A-T-TATAATTTAATT
4716108 GTGTAATTTA
Statistics
Matches: 98, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
40 10 0.10
41 34 0.35
42 31 0.32
43 9 0.09
44 8 0.08
45 2 0.02
46 4 0.04
ACGTcount: A:0.28, C:0.04, G:0.11, T:0.56
Consensus pattern (40 bp):
ATTTATTATTTGCATTGATTATAATTTAATTCGATGATTT
Found at i:4716029 original size:42 final size:42
Alignment explanation
Indices: 4715983--4716107 Score: 164
Period size: 42 Copynumber: 2.9 Consensus size: 42
4715973 TTTAATTGCG
*
4715983 ATGATTTTATTTATTATTTGCATTGATTATATATTTAATT-AT
1 ATGA-TTTATTTATTATTTGCATTGATTATATATTTAATTCAC
* * *
4716025 ATGATTTGTTTATTATTTGTA-TGATTATATATTTTAATTCGC
1 ATGATTTATTTATTATTTGCATTGATTATATA-TTTAATTCAC
4716067 ATGATTTATTTATTATTTGCATTGCATTATATAATTTAATT
1 ATGATTTATTTATTATTTGCATTG-ATTATAT-ATTTAATT
4716108 GTGTAATTTA
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
40 10 0.14
41 22 0.31
42 23 0.32
43 2 0.03
44 14 0.19
45 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.58
Consensus pattern (42 bp):
ATGATTTATTTATTATTTGCATTGATTATATATTTAATTCAC
Found at i:4716124 original size:83 final size:84
Alignment explanation
Indices: 4715973--4716141 Score: 222
Period size: 83 Copynumber: 2.0 Consensus size: 84
4715963 ATTGGTTTAG
* *
4715973 TTTAATTGCGATGATTTTATTTATTATTTGCATTGATTATATATTTAATTATATGATTTGTTTAT
1 TTTAATTGCGATGATTTTATTTATTATTTGCATTGATTATATATTTAATTATATAATTTGATTAT
*
4716038 TATTTGTATGA-TTATATAT
66 TATTTGCATGATTTAT-TAT
* *
4716057 TTTAATT-CGCATGA-TTTATTTATTATTTGCATTGCATTATATAATTTAATTGTGTAATTT-AT
1 TTTAATTGCG-ATGATTTTATTTATTATTTGCATTG-ATTATAT-ATTTAATTATATAATTTGAT
4716119 T-TTATTTGCATGATTTATTAT
63 TATTATTTGCATGATTTATTAT
4716140 TT
1 TT
4716142 GTATGATTTA
Statistics
Matches: 76, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
83 38 0.50
84 24 0.32
85 14 0.18
ACGTcount: A:0.28, C:0.04, G:0.10, T:0.58
Consensus pattern (84 bp):
TTTAATTGCGATGATTTTATTTATTATTTGCATTGATTATATATTTAATTATATAATTTGATTAT
TATTTGCATGATTTATTAT
Found at i:4716141 original size:16 final size:16
Alignment explanation
Indices: 4716120--4716163 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 16
4716110 GTAATTTATT
4716120 TTATTTGCATGATTTA
1 TTATTTGCATGATTTA
*
4716136 TTATTTGTATGATTTA
1 TTATTTGCATGATTTA
4716152 TAATATTTGCAT
1 T--TATTTGCAT
4716164 ATATATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.67
18 8 0.33
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (16 bp):
TTATTTGCATGATTTA
Found at i:4716651 original size:60 final size:60
Alignment explanation
Indices: 4716579--4716692 Score: 201
Period size: 60 Copynumber: 1.9 Consensus size: 60
4716569 AGACTGGACC
* *
4716579 CTTAGTTTAAACTAAGGATAATTTTAAAAGGGATAGATTCACATAGATGGCCAATCACAA
1 CTTAGTTTAAACTAAAGATAATCTTAAAAGGGATAGATTCACATAGATGGCCAATCACAA
*
4716639 CTTAGTTTAAACTAAAGATAATCTTAAAAGGGATATATTCACATAGATGGCCAA
1 CTTAGTTTAAACTAAAGATAATCTTAAAAGGGATAGATTCACATAGATGGCCAA
4716693 AAACTCCTAG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (60 bp):
CTTAGTTTAAACTAAAGATAATCTTAAAAGGGATAGATTCACATAGATGGCCAATCACAA
Found at i:4721290 original size:21 final size:22
Alignment explanation
Indices: 4721252--4721294 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
4721242 TAATTAGAGA
4721252 TTCATGACATTGATTTTTGCAT
1 TTCATGACATTGATTTTTGCAT
4721274 TTCATG-CATTGCA-TTTTGCAT
1 TTCATGACATTG-ATTTTTGCAT
4721295 GCATCATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.21, C:0.16, G:0.14, T:0.49
Consensus pattern (22 bp):
TTCATGACATTGATTTTTGCAT
Found at i:4721764 original size:44 final size:43
Alignment explanation
Indices: 4721716--4721843 Score: 116
Period size: 44 Copynumber: 2.9 Consensus size: 43
4721706 AGACTTCCAA
* *
4721716 GCATGATTTATAAGATCTTCAGGCATAATCTTCAAGACCTTTAG
1 GCATGATTTGTAAGA-CTTCAGGCATAATCTTCAAGACCTTAAG
* * *** * * *
4721760 GCATGATCTGTAAGACCTCAAAATATAATCTTTAAGACCATAAT
1 GCATGATTTGTAAGACTTC-AGGCATAATCTTCAAGACCTTAAG
4721804 GCATGATTTGTATA-ACTTCAGGCATAATC-TCTAAGACCTT
1 GCATGATTTGTA-AGACTTCAGGCATAATCTTC-AAGACCTT
4721844 CGAGCATAAT
Statistics
Matches: 64, Mismatches: 17, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
42 1 0.02
43 17 0.27
44 45 0.70
45 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (43 bp):
GCATGATTTGTAAGACTTCAGGCATAATCTTCAAGACCTTAAG
Found at i:4721844 original size:22 final size:22
Alignment explanation
Indices: 4721726--4721864 Score: 90
Period size: 22 Copynumber: 6.4 Consensus size: 22
4721716 GCATGATTTA
*
4721726 TAAGATCTTCAGGCATAATCT-
1 TAAGACCTTCAGGCATAATCTG
* *
4721747 TCAAGACCTTTAGGCATGATCTG
1 T-AAGACCTTCAGGCATAATCTG
*** *
4721770 TAAGACC-TCAAAATATAATCTT
1 TAAGACCTTC-AGGCATAATCTG
* * * * *
4721792 TAAGACCATAATGCATGATTTG
1 TAAGACCTTCAGGCATAATCTG
*
4721814 TATA-A-CTTCAGGCATAATCTC
1 TA-AGACCTTCAGGCATAATCTG
4721835 TAAGACCTTC-GAGCATAATCTG
1 TAAGACCTTCAG-GCATAATCTG
4721857 TAAGACCT
1 TAAGACCT
4721865 CAAAGCATAA
Statistics
Matches: 87, Mismatches: 23, Indels: 15
0.70 0.18 0.12
Matches are distributed among these distances:
20 1 0.01
21 16 0.18
22 67 0.77
23 3 0.03
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (22 bp):
TAAGACCTTCAGGCATAATCTG
Found at i:4722011 original size:39 final size:39
Alignment explanation
Indices: 4721931--4722024 Score: 109
Period size: 39 Copynumber: 2.4 Consensus size: 39
4721921 TTAGATTTTA
*
4721931 TTCAAAAGTT-AAAGCCTCGATGGATGAATACATTATTT
1 TTCAAAAGTTCAAAGCCTCGATGGATGAATACATTATGT
* * * * *
4721969 TTCAAAAGTTCAAAGCCTTGGTGGGTGAGTACTTTATGT
1 TTCAAAAGTTCAAAGCCTCGATGGATGAATACATTATGT
* *
4722008 TTCAAAAATTCACAGCC
1 TTCAAAAGTTCAAAGCC
4722025 CCAATTGTGG
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
38 10 0.21
39 37 0.79
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (39 bp):
TTCAAAAGTTCAAAGCCTCGATGGATGAATACATTATGT
Found at i:4722286 original size:16 final size:18
Alignment explanation
Indices: 4722249--4722288 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
4722239 CCCAAATAAA
*
4722249 AATTTTTGGTTTTGATTT
1 AATTTTTGGTTTTGAGTT
4722267 AATTTTT-GTTTT-AGTT
1 AATTTTTGGTTTTGAGTT
4722283 AATTTT
1 AATTTT
4722289 AATTTTAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.43
17 5 0.24
18 7 0.33
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
AATTTTTGGTTTTGAGTT
Found at i:4722296 original size:12 final size:13
Alignment explanation
Indices: 4722281--4722313 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
4722271 TTTGTTTTAG
4722281 TTAATTTTAA-TT
1 TTAATTTTAATTT
*
4722293 TTAACTTTAATTT
1 TTAATTTTAATTT
4722306 TTAATTTT
1 TTAATTTT
4722314 GTTTTTGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (13 bp):
TTAATTTTAATTT
Found at i:4723288 original size:21 final size:21
Alignment explanation
Indices: 4723264--4723327 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
4723254 AAAGCCCTAT
*
4723264 CTCACATGTAGATCTAGTTGA
1 CTCACGTGTAGATCTAGTTGA
* *
4723285 CTCACGTGTCA-ATCCAATTGA
1 CTCACGTGT-AGATCTAGTTGA
* *
4723306 CTTACGTGTAGATTTAGTTGA
1 CTCACGTGTAGATCTAGTTGA
4723327 C
1 C
4723328 CCGCGGGCTG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (21 bp):
CTCACGTGTAGATCTAGTTGA
Found at i:4723396 original size:12 final size:13
Alignment explanation
Indices: 4723381--4723433 Score: 51
Period size: 12 Copynumber: 4.4 Consensus size: 13
4723371 TTACTTTTCT
4723381 TTTTTC-ATTTTA
1 TTTTTCTATTTTA
*
4723393 -TTTTCTATTTTG
1 TTTTTCTATTTTA
*
4723405 TTTTT-TATATTA
1 TTTTTCTATTTTA
*
4723417 -TTTTCTATTTGA
1 TTTTTCTATTTTA
4723429 TTTTT
1 TTTTT
4723434 AAAATTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
11 9 0.28
12 15 0.47
13 8 0.25
ACGTcount: A:0.15, C:0.06, G:0.04, T:0.75
Consensus pattern (13 bp):
TTTTTCTATTTTA
Found at i:4723408 original size:24 final size:24
Alignment explanation
Indices: 4723381--4723458 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 24
4723371 TTACTTTTCT
*
4723381 TTTTTCATTTTATTTTCTATTTTG
1 TTTTTCATATTATTTTCTATTTTG
*
4723405 TTTTTTATATTATTTTCTA-TTTG
1 TTTTTCATATTATTTTCTATTTTG
* * *
4723428 ATTTTTAAAATTTTTTTCTATTCTT-
1 -TTTTTCATATTATTTTCTATT-TTG
4723453 TTTTTC
1 TTTTTC
4723459 CTTTTTTTAG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
23 4 0.09
24 38 0.84
25 1 0.02
26 2 0.04
ACGTcount: A:0.17, C:0.08, G:0.03, T:0.73
Consensus pattern (24 bp):
TTTTTCATATTATTTTCTATTTTG
Found at i:4723597 original size:35 final size:37
Alignment explanation
Indices: 4723558--4723634 Score: 122
Period size: 35 Copynumber: 2.1 Consensus size: 37
4723548 TAATGTTTTT
4723558 ATGAAGTTAGTTTCTTGCA-ATTTACTTATT-TTTGC
1 ATGAAGTTAGTTTCTTGCAGATTTACTTATTATTTGC
*
4723593 ATGAAGTTAGTTTCTTGCATGATTTATTTATTATTTGC
1 ATGAAGTTAGTTTCTTGCA-GATTTACTTATTATTTGC
4723631 ATGA
1 ATGA
4723635 TTATATATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
35 19 0.50
37 10 0.26
38 9 0.24
ACGTcount: A:0.25, C:0.09, G:0.16, T:0.51
Consensus pattern (37 bp):
ATGAAGTTAGTTTCTTGCAGATTTACTTATTATTTGC
Found at i:4723612 original size:18 final size:18
Alignment explanation
Indices: 4723558--4723614 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
4723548 TAATGTTTTT
4723558 ATGAAGTTAGTTTCTTGC
1 ATGAAGTTAGTTTCTTGC
** *
4723576 AATTTACTTA-TTT-TTGC
1 -ATGAAGTTAGTTTCTTGC
4723593 ATGAAGTTAGTTTCTTGC
1 ATGAAGTTAGTTTCTTGC
4723611 ATGA
1 ATGA
4723615 TTTATTTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
16 6 0.20
17 7 0.23
18 11 0.37
19 6 0.20
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.47
Consensus pattern (18 bp):
ATGAAGTTAGTTTCTTGC
Found at i:4723632 original size:20 final size:20
Alignment explanation
Indices: 4723607--4723700 Score: 77
Period size: 20 Copynumber: 4.7 Consensus size: 20
4723597 AGTTAGTTTC
4723607 TTGCATGATTTATTTATTAT
1 TTGCATGATTTATTTATTAT
*
4723627 TTGCATGATTATATATT-TAAT
1 TTGCATGATT-TAT-TTATTAT
* *
4723648 TT-TATGATCTATTTATTAT
1 TTGCATGATTTATTTATTAT
* * *
4723667 TTGCATG-CTTATATATTTAA
1 TTGCATGATTTATTTA-TTAT
*
4723687 TTGCGTGATTTATT
1 TTGCATGATTTATT
4723701 ATTTCTAAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
18 2 0.04
19 13 0.23
20 27 0.48
21 12 0.21
22 2 0.04
ACGTcount: A:0.27, C:0.06, G:0.11, T:0.56
Consensus pattern (20 bp):
TTGCATGATTTATTTATTAT
Found at i:4723655 original size:40 final size:40
Alignment explanation
Indices: 4723611--4723688 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
4723601 AGTTTCTTGC
*
4723611 ATGATTTATTTATTATTTGCATGATTATATATTTAATTTT
1 ATGATCTATTTATTATTTGCATGATTATATATTTAATTTT
*
4723651 ATGATCTATTTATTATTTGCATGCTTATATATTTAATT
1 ATGATCTATTTATTATTTGCATGATTATATATTTAATT
4723689 GCGTGATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.29, C:0.05, G:0.08, T:0.58
Consensus pattern (40 bp):
ATGATCTATTTATTATTTGCATGATTATATATTTAATTTT
Found at i:4723684 original size:23 final size:22
Alignment explanation
Indices: 4723617--4723685 Score: 67
Period size: 23 Copynumber: 3.3 Consensus size: 22
4723607 TTGCATGATT
4723617 TATTTATTATTTGCATGATTATA
1 TATTTATTATTTGCATG-TTATA
* *
4723640 TATTTA--ATTT-TATG--ATC
1 TATTTATTATTTGCATGTTATA
4723657 TATTTATTATTTGCATGCTTATA
1 TATTTATTATTTGCATG-TTATA
4723680 TATTTA
1 TATTTA
4723686 ATTGCGTGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
17 8 0.22
19 4 0.11
20 6 0.17
21 4 0.11
23 14 0.39
ACGTcount: A:0.29, C:0.06, G:0.07, T:0.58
Consensus pattern (22 bp):
TATTTATTATTTGCATGTTATA
Found at i:4725499 original size:18 final size:19
Alignment explanation
Indices: 4725460--4725503 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
4725450 AACATAAAGC
*
4725460 TTTTATAACAAAATTAATA
1 TTTTATAACAAAATTAAAA
4725479 TTTTGATAA-AAAA-TAAAA
1 TTTT-ATAACAAAATTAAAA
4725497 TTTTATA
1 TTTTATA
4725504 TTGAAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 3 0.13
18 8 0.35
19 8 0.35
20 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
TTTTATAACAAAATTAAAA
Found at i:4726651 original size:73 final size:73
Alignment explanation
Indices: 4726566--4726786 Score: 442
Period size: 73 Copynumber: 3.0 Consensus size: 73
4726556 TTGAGTATAT
4726566 ATGATATCTTGATAATTGAATGGGACATTCTTTAATAAAAGAATGCAAATTTGGACATGGTGGGG
1 ATGATATCTTGATAATTGAATGGGACATTCTTTAATAAAAGAATGCAAATTTGGACATGGTGGGG
4726631 TGATAAGA
66 TGATAAGA
4726639 ATGATATCTTGATAATTGAATGGGACATTCTTTAATAAAAGAATGCAAATTTGGACATGGTGGGG
1 ATGATATCTTGATAATTGAATGGGACATTCTTTAATAAAAGAATGCAAATTTGGACATGGTGGGG
4726704 TGATAAGA
66 TGATAAGA
4726712 ATGATATCTTGATAATTGAATGGGACATTCTTTAATAAAAGAATGCAAATTTGGACATGGTGGGG
1 ATGATATCTTGATAATTGAATGGGACATTCTTTAATAAAAGAATGCAAATTTGGACATGGTGGGG
4726777 TGATAAGA
66 TGATAAGA
4726785 AT
1 AT
4726787 CAAAAGAAAT
Statistics
Matches: 148, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 148 1.00
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (73 bp):
ATGATATCTTGATAATTGAATGGGACATTCTTTAATAAAAGAATGCAAATTTGGACATGGTGGGG
TGATAAGA
Found at i:4728687 original size:23 final size:22
Alignment explanation
Indices: 4728646--4728688 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
4728636 TTATAGATTT
**
4728646 GTTAAGATTTGTTGGGTTTTAC
1 GTTAAGATTTGTTAAGTTTTAC
4728668 GTTATAGATTTGTTAAGTTTT
1 GTTA-AGATTTGTTAAGTTTT
4728689 TTATTGGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.21, C:0.02, G:0.23, T:0.53
Consensus pattern (22 bp):
GTTAAGATTTGTTAAGTTTTAC
Found at i:4732651 original size:16 final size:17
Alignment explanation
Indices: 4732609--4732653 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
4732599 GTGAAAGAAT
4732609 AAGAAAAAA-AATGGGAA
1 AAGAAAAAAGAAT-GGAA
4732626 AA-AAATAAAGAAT-GAA
1 AAGAAA-AAAGAATGGAA
4732642 AAGAAAAAAGAA
1 AAGAAAAAAGAA
4732654 AAGATTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
16 14 0.56
17 8 0.32
18 3 0.12
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.07
Consensus pattern (17 bp):
AAGAAAAAAGAATGGAA
Found at i:4732656 original size:21 final size:20
Alignment explanation
Indices: 4732623--4732677 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
4732613 AAAAAAATGG
4732623 GAAAAAA-ATAAAGAATGAAAA
1 GAAAAAAGA-AAAG-ATGAAAA
*
4732644 GAAAAAAGAAAAGATTAAAA
1 GAAAAAAGAAAAGATGAAAA
*
4732664 AAAAAAGAGAAAAG
1 GAAAAA-AGAAAAG
4732678 GGGAATGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 11 0.37
21 18 0.60
22 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.07
Consensus pattern (20 bp):
GAAAAAAGAAAAGATGAAAA
Found at i:4735460 original size:57 final size:57
Alignment explanation
Indices: 4735366--4735500 Score: 148
Period size: 57 Copynumber: 2.4 Consensus size: 57
4735356 TTCTCATCAA
* * * *
4735366 TGGTGAAATCCAAAGTCGTTAGCATTTACTCAGTAGTGATATCTAAGTA-TCTTTCTG
1 TGGTGAAATCCGAAGTCATTTGCATTTACTCAGTAGTGATATCTAAGTACTCTTT-GG
* * * *
4735423 TGGTGATATCCGAAGTCATTTGCGTTTACTC-GATAGTGATATTTGAGTACTCTTTGG
1 TGGTGAAATCCGAAGTCATTTGCATTTACTCAG-TAGTGATATCTAAGTACTCTTTGG
**
4735480 TGGTGAAATATGAAGTCATTT
1 TGGTGAAATCCGAAGTCATTT
4735501 ACTCAATGGT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
56 1 0.02
57 59 0.91
58 5 0.08
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (57 bp):
TGGTGAAATCCGAAGTCATTTGCATTTACTCAGTAGTGATATCTAAGTACTCTTTGG
Found at i:4746453 original size:16 final size:17
Alignment explanation
Indices: 4746432--4746464 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4746422 TTCAAATAAG
*
4746432 ATAATAA-AATTAAAAA
1 ATAATAATAAATAAAAA
4746448 ATAATAATAAATAAAAA
1 ATAATAATAAATAAAAA
4746465 TAAAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
ATAATAATAAATAAAAA
Found at i:4746863 original size:31 final size:30
Alignment explanation
Indices: 4746823--4746881 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
4746813 AGGTTGAATT
4746823 TTTCAATG-AAAATTCAAGTTTTCTGGTGACC
1 TTTCAATGAAAAATT-AAGTTTT-TGGTGACC
* *
4746854 TTTCGATGAAAAATTGAGTTTTTGGTGA
1 TTTCAATGAAAAATTAAGTTTTTGGTGA
4746882 TAAAACCTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 6 0.24
31 13 0.52
32 6 0.24
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (30 bp):
TTTCAATGAAAAATTAAGTTTTTGGTGACC
Found at i:4747428 original size:43 final size:43
Alignment explanation
Indices: 4747348--4747432 Score: 109
Period size: 45 Copynumber: 2.0 Consensus size: 43
4747338 TAAAAATCTA
* *
4747348 AAAAAAAATTCTTTAAGGAAAAGTTAAAAGTAGATCAAATTTTTT
1 AAAAAAAATACTTTAAAGAAAAGTTAAAAGTA-ATC-AATTTTTT
* *
4747393 AAAAAATATACTTTAAAGAAAAGTTGAAAGT-ATCAATTTT
1 AAAAAAAATACTTTAAAGAAAAGTTAAAAGTAATCAATTTT
4747433 CCTTAAAGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 6 0.17
43 3 0.08
45 27 0.75
ACGTcount: A:0.52, C:0.05, G:0.11, T:0.33
Consensus pattern (43 bp):
AAAAAAAATACTTTAAAGAAAAGTTAAAAGTAATCAATTTTTT
Found at i:4747498 original size:58 final size:60
Alignment explanation
Indices: 4747410--4747557 Score: 237
Period size: 58 Copynumber: 2.5 Consensus size: 60
4747400 ATACTTTAAA
*
4747410 GAAAAGTTGAAAGTATCAATTTTCCTTAAAGATAAAATTTTCAAAAGATA-TTTTTTGAG
1 GAAAAGTTGAAAGTATTAATTTTCCTTAAAGATAAAATTTTCAAAAGATATTTTTTTGAG
* * *
4747469 GAAAAGTT-AAATTATTAATTTTTCTTAAAGATAAAATTTTTAAAAGATATTTTTTTGAG
1 GAAAAGTTGAAAGTATTAATTTTCCTTAAAGATAAAATTTTCAAAAGATATTTTTTTGAG
*
4747528 GAAAAATTGAAAGTATTAATTTTCCTTAAA
1 GAAAAGTTGAAAGTATTAATTTTCCTTAAA
4747558 TAAAGGCATT
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
58 37 0.46
59 24 0.30
60 19 0.24
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (60 bp):
GAAAAGTTGAAAGTATTAATTTTCCTTAAAGATAAAATTTTCAAAAGATATTTTTTTGAG
Found at i:4750875 original size:30 final size:30
Alignment explanation
Indices: 4750834--4750890 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
4750824 GATAGCTCAA
4750834 CCATCGATAAATTCAAGCCAACCTGCATAT
1 CCATCGATAAATTCAAGCCAACCTGCATAT
*
4750864 CCATTGATAAATTCAAGCCAACCTGCA
1 CCATCGATAAATTCAAGCCAACCTGCA
4750891 CATCATCCGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.37, C:0.30, G:0.11, T:0.23
Consensus pattern (30 bp):
CCATCGATAAATTCAAGCCAACCTGCATAT
Found at i:4758162 original size:52 final size:51
Alignment explanation
Indices: 4758106--4758288 Score: 167
Period size: 60 Copynumber: 3.5 Consensus size: 51
4758096 AACAAAAGAG
* * *
4758106 AAAAAAA-CTCAAATTGAAAACTCGCAAATGGTGGTTTGAGTTAAAAAAAACAAAA
1 AAAAAAAGCTCAAATTGAAAAC-CGCAAAGGGCGGTTTGAGTT-TAAAAAAC---A
* *
4758161 AAAAATAGATGGCTCAAATTGAAAACCTGTAAAGGGCGGTTTAAGTTTAAAAAACA
1 AAAAA-A-A--GCTCAAATTGAAAACC-GCAAAGGGCGGTTTGAGTTTAAAAAACA
* * *
4758217 AAAAAAAGCTCAAATT-AAAACCCACAAAGGGCGGTTTGAATTT-TAAAA-A
1 AAAAAAAGCTCAAATTGAAAA-CCGCAAAGGGCGGTTTGAGTTTAAAAAACA
4758266 AAAAAAAGCTCAAATTGAAAACC
1 AAAAAAAGCTCAAATTGAAAACC
4758289 CATAAAGGGC
Statistics
Matches: 110, Mismatches: 10, Indels: 22
0.77 0.07 0.15
Matches are distributed among these distances:
49 19 0.17
50 8 0.07
51 20 0.18
52 11 0.10
54 1 0.01
55 6 0.05
56 7 0.06
57 1 0.01
59 8 0.07
60 29 0.26
ACGTcount: A:0.52, C:0.13, G:0.15, T:0.20
Consensus pattern (51 bp):
AAAAAAAGCTCAAATTGAAAACCGCAAAGGGCGGTTTGAGTTTAAAAAACA
Found at i:4758213 original size:51 final size:50
Alignment explanation
Indices: 4758172--4758298 Score: 177
Period size: 50 Copynumber: 2.5 Consensus size: 50
4758162 AAAATAGATG
**
4758172 GCTCAAATTGAAAACCTGTAAAGGGCGGTTT-AAGTTTAAAAAACAAAAAAAA
1 GCTCAAATTGAAAACCCATAAAGGGCGGTTTGAAGTTT--AAAA-AAAAAAAA
* *
4758224 GCTCAAATT-AAAACCCACAAAGGGCGGTTTGAATTTTAAAAAAAAAAAA
1 GCTCAAATTGAAAACCCATAAAGGGCGGTTTGAAGTTTAAAAAAAAAAAA
4758273 GCTCAAATTGAAAACCCATAAAGGGC
1 GCTCAAATTGAAAACCCATAAAGGGC
4758299 AATCTGAGTC
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
49 17 0.25
50 19 0.28
51 18 0.26
52 14 0.21
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.20
Consensus pattern (50 bp):
GCTCAAATTGAAAACCCATAAAGGGCGGTTTGAAGTTTAAAAAAAAAAAA
Found at i:4758314 original size:49 final size:49
Alignment explanation
Indices: 4758210--4758314 Score: 122
Period size: 49 Copynumber: 2.1 Consensus size: 49
4758200 TTTAAGTTTA
** * * *
4758210 AAAAACAAAAAAAAGCTCAAATTAAAACCCACAAAGGGCGGTTTGAATTT
1 AAAAA-AAAAAAAAGCTCAAATTAAAACCCACAAAGGGCAATCTGAAGTC
* *
4758260 TAAAAAAAAAAAAGCTCAAATTGAAAACCCATAAAGGGCAATCTG-AGTC
1 AAAAAAAAAAAAAGCTCAAATT-AAAACCCACAAAGGGCAATCTGAAGTC
4758309 AAAAAA
1 AAAAAA
4758315 GGATATCTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
49 24 0.52
50 22 0.48
ACGTcount: A:0.55, C:0.15, G:0.13, T:0.16
Consensus pattern (49 bp):
AAAAAAAAAAAAAGCTCAAATTAAAACCCACAAAGGGCAATCTGAAGTC
Found at i:4759415 original size:85 final size:84
Alignment explanation
Indices: 4759268--4759547 Score: 275
Period size: 85 Copynumber: 3.3 Consensus size: 84
4759258 GGTTATTTGG
* * * * *
4759268 TTTAG-ATTTCGACCTATGCTAGATCCTTTTTTAGTTCAATCCAAGTTACTTATTTCATACTTTA
1 TTTAGAATTTCGTCCTATGCTAGAT-CTTTTTTAGTTTAGTCCAAGTTATTTATTTCAGACTTT-
*
4759332 GTTCCATCTAGGTCATTTTAT
64 GTTCCATCCAGGTCATTTTAT
4759353 TTTAGAATTT-GTCCTATGCTAGATCTTTTTTCAGTTTAGTCCAAGTTATTTATCTT-AGACTTT
1 TTTAGAATTTCGTCCTATGCTAGATCTTTTTT-AGTTTAGTCCAAGTTATTTAT-TTCAGACTTT
* *
4759416 GGTTCCATCCAAGTCATTTTGT
64 -GTTCCATCCAGGTCATTTTAT
* * * * * * *
4759438 TTTGGATTTTGGT-CTATG-TCAAATTTGTTTTTAGTTTGGTTCAAGTTATTTATTTCAGACTTT
1 TTTAGAATTTCGTCCTATGCT-AGATCT-TTTTTAGTTTAGTCCAAGTTATTTATTTCAGACTTT
* *
4759501 GATTTCAACCAGGTCATTTTAT
64 G-TTCCATCCAGGTCATTTTAT
**
4759523 TTTAG-ATTTCAACCTATGCTAGATC
1 TTTAGAATTTCGTCCTATGCTAGATC
4759548 CATCTTCGAA
Statistics
Matches: 159, Mismatches: 26, Indels: 20
0.78 0.13 0.10
Matches are distributed among these distances:
84 14 0.09
85 131 0.82
86 14 0.09
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.48
Consensus pattern (84 bp):
TTTAGAATTTCGTCCTATGCTAGATCTTTTTTAGTTTAGTCCAAGTTATTTATTTCAGACTTTGT
TCCATCCAGGTCATTTTAT
Found at i:4759753 original size:16 final size:17
Alignment explanation
Indices: 4759732--4759764 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4759722 TTTAGATAAG
*
4759732 ATAATAA-AATTAAAAA
1 ATAATAATAAATAAAAA
4759748 ATAATAATAAATAAAAA
1 ATAATAATAAATAAAAA
4759765 TAGAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
ATAATAATAAATAAAAA
Found at i:4760572 original size:22 final size:20
Alignment explanation
Indices: 4760546--4760591 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
4760536 ATATTTATTT
*
4760546 ATTTATTGATTAAATTGAAATC
1 ATTTATTCATTAAATT-AAA-C
*
4760568 ATTTATTCATTTAATTAAAC
1 ATTTATTCATTAAATTAAAC
4760588 ATTT
1 ATTT
4760592 TTTAAGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 3 0.14
22 14 0.64
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (20 bp):
ATTTATTCATTAAATTAAAC
Found at i:4760678 original size:59 final size:58
Alignment explanation
Indices: 4760606--4760819 Score: 238
Period size: 59 Copynumber: 3.7 Consensus size: 58
4760596 AGTTTTCAAT
* * *
4760606 AATTTT-CTT-AAAATAAAAATCTCAAAAAATATATTTTAAGAAGAAGTTGAAAGTATC
1 AATTTTCCTTGAAAATAAAAATTTCAAAAGATATTTTTTAAGAA-AAGTTGAAAGTATC
* * * *
4760663 AACTTTCTTTGAAAATAAAAATTTC-AAACATATTTTTTTGAGGAAAAGTTGAAAGTATC
1 AATTTTCCTTGAAAATAAAAATTTCAAAAGATA-TTTTTT-AAGAAAAGTTGAAAGTATC
* * * *
4760722 TATTTTCCTT-AAAGATAAAATTTTCAAAAGATATTTTTTAAGGAAAAGTCGAAAGCATC
1 AATTTTCCTTGAAA-ATAAAAATTTCAAAAGATATTTTTTAA-GAAAAGTTGAAAGTATC
* *
4760781 AATTTTCCTTGAAGATAAAATTTTCAAAAGATATTTTTT
1 AATTTTCCTTGAAAATAAAAATTTCAAAAGATATTTTTT
4760820 TTGAGAAAAA
Statistics
Matches: 133, Mismatches: 16, Indels: 14
0.82 0.10 0.09
Matches are distributed among these distances:
57 5 0.04
58 12 0.09
59 104 0.78
60 12 0.09
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.37
Consensus pattern (58 bp):
AATTTTCCTTGAAAATAAAAATTTCAAAAGATATTTTTTAAGAAAAGTTGAAAGTATC
Found at i:4760749 original size:118 final size:118
Alignment explanation
Indices: 4760607--4760852 Score: 300
Period size: 118 Copynumber: 2.1 Consensus size: 118
4760597 GTTTTCAATA
* * *
4760607 ATTTTCTTAAAATAAAAATCTCAAAAAATATATTTTAA-GAAGAAGTTGAAAGTATCAACTTTCT
1 ATTTTCTTAAAATAAAAATCTCAAAAAATATATTTTAAGGAA-AAGTCGAAAGCATCAACTTTCC
* * *
4760671 TTGAAAATAAAAATTTC-AAACATA-TTTTTTTGAGGAAAAGTTGAAAGTATCT
65 TTGAAAATAAAAATTTCAAAACATATTTTTTTTGAGAAAAAATTGAAAATATCT
* * * * *
4760723 ATTTTCCTTAAAGATAAAATTTTCAAAAGATATTTTTTAAGGAAAAGTCGAAAGCATCAATTTTC
1 ATTTT-CTTAAA-ATAAAAATCTCAAAAAATATATTTTAAGGAAAAGTCGAAAGCATCAACTTTC
* * * *
4760788 CTTGAAGATAAAATTTTCAAAAGATATTTTTTTTGAGAAAAAATTGAAAATATCAA
64 CTTGAAAATAAAAATTTCAAAACATATTTTTTTTGAGAAAAAATTGAAAATATC-T
4760844 ATTTTCTTA
1 ATTTTCTTA
4760853 CATAAAGGCA
Statistics
Matches: 109, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
116 5 0.05
117 6 0.06
118 56 0.51
119 9 0.08
120 28 0.26
121 5 0.05
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.37
Consensus pattern (118 bp):
ATTTTCTTAAAATAAAAATCTCAAAAAATATATTTTAAGGAAAAGTCGAAAGCATCAACTTTCCT
TGAAAATAAAAATTTCAAAACATATTTTTTTTGAGAAAAAATTGAAAATATCT
Found at i:4760858 original size:59 final size:59
Alignment explanation
Indices: 4760606--4760849 Score: 237
Period size: 59 Copynumber: 4.1 Consensus size: 59
4760596 AGTTTTCAAT
* * * * * *
4760606 AATTTT-CTTAAAATAAAAATCTCAAAAAATA-TATTTT-AAGAAGAAGTTGAAAGTATC
1 AATTTTCCTTAAGATAAAATTTTCAAAAGATATTTTTTTGAGGAA-AAGTTGAAAGTATC
* * * * *
4760663 AACTTTCTTTGAAAATAAAAATTTC-AAACATATTTTTTTGAGGAAAAGTTGAAAGTATC
1 AATTTTCCTT-AAGATAAAATTTTCAAAAGATATTTTTTTGAGGAAAAGTTGAAAGTATC
* * * *
4760722 TATTTTCCTTAAAGATAAAATTTTCAAAAGATA-TTTTTTAAGGAAAAGTCGAAAGCATC
1 AATTTTCCTT-AAGATAAAATTTTCAAAAGATATTTTTTTGAGGAAAAGTTGAAAGTATC
* * *
4760781 AATTTTCCTTGAAGATAAAATTTTCAAAAGATATTTTTTTTGAGAAAAAATTGAAAATATC
1 AATTTTCCTT-AAGATAAAATTTTCAAAAGATA-TTTTTTTGAGGAAAAGTTGAAAGTATC
4760842 AAATTTTC
1 -AATTTTC
4760850 TTACATAAAG
Statistics
Matches: 155, Mismatches: 24, Indels: 11
0.82 0.13 0.06
Matches are distributed among these distances:
57 5 0.03
58 8 0.05
59 105 0.68
60 10 0.06
61 20 0.13
62 7 0.05
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (59 bp):
AATTTTCCTTAAGATAAAATTTTCAAAAGATATTTTTTTGAGGAAAAGTTGAAAGTATC
Found at i:4765988 original size:29 final size:29
Alignment explanation
Indices: 4765956--4766016 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
4765946 AATAAAGAAT
* *
4765956 AAATTACT-CAATAAAAATAAATAATAAGA
1 AAATTACTAAAAT-AAAATAAATAATAAAA
*
4765985 AAATTAGTAAAATAAAATAAATAATAAAA
1 AAATTACTAAAATAAAATAAATAATAAAA
4766014 AAA
1 AAA
4766017 CTAAATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 25 0.89
30 3 0.11
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.23
Consensus pattern (29 bp):
AAATTACTAAAATAAAATAAATAATAAAA
Found at i:4766026 original size:15 final size:16
Alignment explanation
Indices: 4765968--4766029 Score: 53
Period size: 15 Copynumber: 4.1 Consensus size: 16
4765958 ATTACTCAAT
4765968 AAAAATAAATAAT-AA
1 AAAAATAAATAATAAA
* *
4765983 GAAAAT---TAGTAAA
1 AAAAATAAATAATAAA
4765996 ATAAAATAAATAATAAA
1 A-AAAATAAATAATAAA
*
4766013 AAAACTAAAT-ATAAA
1 AAAAATAAATAATAAA
4766028 AA
1 AA
4766030 TATAAAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
12 3 0.08
13 2 0.05
14 5 0.14
15 12 0.32
16 8 0.22
17 7 0.19
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.21
Consensus pattern (16 bp):
AAAAATAAATAATAAA
Found at i:4766036 original size:22 final size:19
Alignment explanation
Indices: 4765993--4766077 Score: 59
Period size: 21 Copynumber: 4.1 Consensus size: 19
4765983 GAAAATTAGT
4765993 AAAATAAA-ATAAATAATAAA
1 AAAATAAATATAAA-AAT-AA
4766013 AAAACTAAATATAAAAATATA
1 AAAA-TAAATATAAAAATA-A
4766034 AAAATTGAAATATAAAAGGA-AA
1 AAAA-T-AAATATAAAA--ATAA
4766056 TAAAATAAAT-TAGAAAATAA
1 -AAAATAAATATA-AAAATAA
4766076 AA
1 AA
4766078 TGAAAATGAA
Statistics
Matches: 55, Mismatches: 1, Indels: 19
0.73 0.01 0.25
Matches are distributed among these distances:
19 3 0.05
20 9 0.16
21 20 0.36
22 17 0.31
23 5 0.09
24 1 0.02
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.21
Consensus pattern (19 bp):
AAAATAAATATAAAAATAA
Found at i:4766075 original size:27 final size:26
Alignment explanation
Indices: 4766027--4766091 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
4766017 CTAAATATAA
*
4766027 AAATATAAAAATTGAAATATAAAAGG
1 AAATAAAAAAATTGAAATATAAAAGG
*
4766053 AAATAAAATAAATTAGAAA-ATAAAATGA
1 AAATAAAA-AAATT-GAAATATAAAA-GG
*
4766081 AAATGAAAAAA
1 AAATAAAAAAA
4766092 GAAAAATATG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 7 0.21
27 14 0.42
28 12 0.36
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (26 bp):
AAATAAAAAAATTGAAATATAAAAGG
Found at i:4766088 original size:17 final size:17
Alignment explanation
Indices: 4765992--4766089 Score: 50
Period size: 17 Copynumber: 6.0 Consensus size: 17
4765982 AGAAAATTAG
4765992 TAAAATAAAATA-AATAA
1 TAAAATAAAATAGAA-AA
* *
4766009 TAAAA-AAACTA-AATA
1 TAAAATAAAATAGAAAA
*
4766024 T-AAA-AATATA-AAAA
1 TAAAATAAAATAGAAAA
* *
4766038 TTGAAATATAAA-AGGAAA
1 -TAAAATA-AAATAGAAAA
*
4766056 TAAAATAAATTAGAAAA
1 TAAAATAAAATAGAAAA
4766073 TAAAATGAAAAT-GAAAA
1 TAAAAT-AAAATAGAAAA
4766090 AAGAAAAATA
Statistics
Matches: 63, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
14 10 0.16
15 3 0.05
16 12 0.19
17 29 0.46
18 9 0.14
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.21
Consensus pattern (17 bp):
TAAAATAAAATAGAAAA
Found at i:4766950 original size:3 final size:3
Alignment explanation
Indices: 4766942--4767110 Score: 167
Period size: 3 Copynumber: 58.3 Consensus size: 3
4766932 AATAAAGTTG
*
4766942 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA AT- GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
4766988 ATG ATA ATA ATA ACA ATA ATA AT- ATA AT- ATA AT- ATA AT- ATA CCATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA --ATA
* * * *
4767034 GTA AT- ATA ATA CTA GTA ACA ATA ATA ATA ATA ATA ATAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
* *
4767079 ATA ATA ATA CTA ATA ACA A-A A-A ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4767111 AAGTACTAAT
Statistics
Matches: 139, Mismatches: 16, Indels: 22
0.79 0.09 0.12
Matches are distributed among these distances:
2 17 0.12
3 116 0.83
4 3 0.02
5 3 0.02
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:4767102 original size:28 final size:28
Alignment explanation
Indices: 4767053--4767131 Score: 97
Period size: 28 Copynumber: 2.8 Consensus size: 28
4767043 TACTAGTAAC
* * *
4767053 AATAATAATAATAATAATAAATAATAAT
1 AATAATACTAATAACAAAAAATAATAAT
4767081 AATAATACTAATAACAAAAAATAATAAT
1 AATAATACTAATAACAAAAAATAATAAT
4767109 AA-AAGTACTAATACACATAAAAA
1 AATAA-TACTAATA-ACA-AAAAA
4767132 ATCAACATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
27 2 0.04
28 35 0.78
29 3 0.07
30 5 0.11
ACGTcount: A:0.67, C:0.06, G:0.01, T:0.25
Consensus pattern (28 bp):
AATAATACTAATAACAAAAAATAATAAT
Found at i:4770526 original size:10 final size:10
Alignment explanation
Indices: 4770513--4770540 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
4770503 TAGATATGCA
4770513 CTTTATTACC
1 CTTTATTACC
4770523 CTTTATTACC
1 CTTTATTACC
4770533 CTTTATTA
1 CTTTATTA
4770541 TATCTTATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.25, G:0.00, T:0.54
Consensus pattern (10 bp):
CTTTATTACC
Found at i:4774365 original size:29 final size:29
Alignment explanation
Indices: 4774323--4774380 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
4774313 GAGGAAGAAA
4774323 ATTCTATTCTTCATATAATTAATTTTTCT
1 ATTCTATTCTTCATATAATTAATTTTTCT
4774352 ATTCTATTCTTCATATAATTAATTTTTCT
1 ATTCTATTCTTCATATAATTAATTTTTCT
4774381 TACACCTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.14, G:0.00, T:0.59
Consensus pattern (29 bp):
ATTCTATTCTTCATATAATTAATTTTTCT
Found at i:4774759 original size:29 final size:28
Alignment explanation
Indices: 4774722--4774781 Score: 74
Period size: 25 Copynumber: 2.3 Consensus size: 28
4774712 AAAAATTTAG
4774722 TAAA-TTATTTATTA--TATACATAATA
1 TAAATTTATTTATTATTTATACATAATA
**
4774747 -AAATTTATTTATTATTTATTTATAATA
1 TAAATTTATTTATTATTTATACATAATA
4774774 TAAATTTA
1 TAAATTTA
4774782 AAATATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 3 0.10
25 10 0.34
27 9 0.31
28 7 0.24
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
TAAATTTATTTATTATTTATACATAATA
Found at i:4777491 original size:29 final size:27
Alignment explanation
Indices: 4777422--4777496 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 27
4777412 ACCGAAAAAT
*
4777422 GAAATGATTTCAAATATCACCATCGAA
1 GAAATGACTTCAAATATCACCATCGAA
** *
4777449 G-AA--ACTTCGGATATCACTATCGGGAA
1 GAAATGACTTCAAATATCACCATC--GAA
4777475 GAAATGACTTCAAATATCACCA
1 GAAATGACTTCAAATATCACCA
4777497 CTAAAGAGGA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
24 14 0.39
26 6 0.17
27 3 0.08
29 13 0.36
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (27 bp):
GAAATGACTTCAAATATCACCATCGAA
Found at i:4777806 original size:170 final size:172
Alignment explanation
Indices: 4777490--4777807 Score: 374
Period size: 170 Copynumber: 1.9 Consensus size: 172
4777480 GACTTCAAAT
* * *
4777490 ATCACCACTAAAGAGGAATGCAAATTCAAATTTGGATACACAGATATCACTACTTAGAAGAAATG
1 ATCACCACTAAAGAAGAATACAAATTCAAATTTGGATACACAGATATCACCACTTAGAAGAAATG
* * * *** * * *
4777555 ACTTCAGATTTCACCACTAAAGAGTTCTTGGATATCTCTATTGAGTAAACATAAATGACTTCGAA
66 ACTTCAGATTTCACCACCAAAAAGTACTCAAATATCACTATCGAGTAAACACAAATGACTTCGAA
** *
4777620 TATGGCCACCAAAAGATAGAAGAAATACAGATGAATTCAGAC
131 TATCACCACAAAAAGATAGAAGAAATACAGATGAATTCAGAC
* * ***
4777662 ATCACCACTGAAGAATAATACAAATTCAAATTTGGATACTTGGATATCACCA-TT-G-AGTAAAT
1 ATCACCACTAAAGAAGAATACAAATTCAAATTTGGATACACAGATATCACCACTTAGAAG-AAAT
* **
4777724 GACTTCATATTTCACCACCAAAAAGTACTCAAATATCACTATCGAGTAAATGCAAATGACTTC-A
65 GACTTCAGATTTCACCACCAAAAAGTACTCAAATATCACTATCGAGTAAACACAAATGACTTCGA
*
4777788 GATATCACTACAAAAAGATA
130 -ATATCACCACAAAAAGATA
4777808 CTTAGATATC
Statistics
Matches: 120, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
169 3 0.03
170 71 0.59
171 2 0.02
172 44 0.37
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (172 bp):
ATCACCACTAAAGAAGAATACAAATTCAAATTTGGATACACAGATATCACCACTTAGAAGAAATG
ACTTCAGATTTCACCACCAAAAAGTACTCAAATATCACTATCGAGTAAACACAAATGACTTCGAA
TATCACCACAAAAAGATAGAAGAAATACAGATGAATTCAGAC
Found at i:4777817 original size:57 final size:57
Alignment explanation
Indices: 4777720--4777854 Score: 184
Period size: 57 Copynumber: 2.4 Consensus size: 57
4777710 ACCATTGAGT
*
4777720 AAATGACTTCATATTTCACCACCAAAAAGTACTCAAATATCACTA-TCGAGTAAATGC
1 AAATGACTTCAGATTTCACCACCAAAAAGTACTCAAATATCACTACT-GAGTAAATGC
* * * *
4777777 AAATGACTTCAGATATCACTA-CAAAAAGATACTTAGATATCACTACTGAGTAAATGC
1 AAATGACTTCAGATTTCACCACCAAAAAG-TACTCAAATATCACTACTGAGTAAATGC
*
4777834 TAATGACTTCAGATTTCACCA
1 AAATGACTTCAGATTTCACCA
4777855 TCGACGAGGA
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
56 7 0.10
57 60 0.88
58 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.27
Consensus pattern (57 bp):
AAATGACTTCAGATTTCACCACCAAAAAGTACTCAAATATCACTACTGAGTAAATGC
Found at i:4778373 original size:43 final size:46
Alignment explanation
Indices: 4778326--4778424 Score: 123
Period size: 47 Copynumber: 2.2 Consensus size: 46
4778316 ACCACTAAAT
*
4778326 TATCACCATCAAGATTTGAAA-ACA-TAGA-TTTTGAATACTTGAA
1 TATCACCATCAAGATTTGAAAGAAACTAGAGTTTTGAATACTTGAA
** * *
4778369 TATCACCATTGAGATTTGAAAGAAATCTAGAGTTTTGAATGCTTGGA
1 TATCACCATCAAGATTTGAAAGAAA-CTAGAGTTTTGAATACTTGAA
4778416 TATCACCAT
1 TATCACCAT
4778425 AAAAAAGTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 19 0.40
44 2 0.04
46 4 0.09
47 22 0.47
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.33
Consensus pattern (46 bp):
TATCACCATCAAGATTTGAAAGAAACTAGAGTTTTGAATACTTGAA
Found at i:4778771 original size:25 final size:24
Alignment explanation
Indices: 4778724--4778775 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
4778714 TTTTTAACCT
4778724 TTTTCTTAAAAACTTCATTTTTTAC
1 TTTTCTTAAAAACTTCATTTTTT-C
* *
4778749 TTTTCTTAAAGAGTT-ATTGTTTTC
1 TTTTCTTAAAAACTTCATT-TTTTC
4778773 TTT
1 TTT
4778776 CTTTTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.23, C:0.12, G:0.06, T:0.60
Consensus pattern (24 bp):
TTTTCTTAAAAACTTCATTTTTTC
Found at i:4780602 original size:16 final size:18
Alignment explanation
Indices: 4780582--4780630 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
4780572 TTTTTAATCT
4780582 TTTCTTTTTTCTTTT-CA
1 TTTCTTTTTTCTTTTCCA
*
4780599 -TTCTTTATTTTTTTTCCCA
1 TTTCTTT-TTTCTTTT-CCA
4780618 TTTCTTTTTTCTT
1 TTTCTTTTTTCTT
4780631 ATTCTTTCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 6 0.23
17 7 0.27
19 7 0.27
20 6 0.23
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTCTTTTTTCTTTTCCA
Found at i:4781182 original size:16 final size:15
Alignment explanation
Indices: 4781163--4781205 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
4781153 ATTTCATTTC
4781163 ATTTTGTTATTTTGTT
1 ATTTT-TTATTTTGTT
*
4781179 ATTTATTTTTTTTGTT
1 ATTT-TTTATTTTGTT
4781195 ATTTTTT-TTTT
1 ATTTTTTATTTT
4781206 TCTTTGCGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 4 0.16
15 3 0.12
16 17 0.68
17 1 0.04
ACGTcount: A:0.12, C:0.00, G:0.07, T:0.81
Consensus pattern (15 bp):
ATTTTTTATTTTGTT
Found at i:4781196 original size:12 final size:12
Alignment explanation
Indices: 4781164--4781203 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
4781154 TTTCATTTCA
4781164 TTTTGTTATTTT
1 TTTTGTTATTTT
*
4781176 GTTAT-TTATTTT
1 -TTTTGTTATTTT
4781188 TTTTGTTATTTT
1 TTTTGTTATTTT
4781200 TTTT
1 TTTT
4781204 TTTCTTTGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 3 0.12
12 18 0.75
13 3 0.12
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.82
Consensus pattern (12 bp):
TTTTGTTATTTT
Found at i:4781206 original size:16 final size:16
Alignment explanation
Indices: 4781172--4781206 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
4781162 CATTTTGTTA
4781172 TTTTGTTATTTATTTT
1 TTTTGTTATTTATTTT
4781188 TTTTGTTATTT-TTTT
1 TTTTGTTATTTATTTT
4781203 TTTT
1 TTTT
4781207 CTTTGCGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.09, C:0.00, G:0.06, T:0.86
Consensus pattern (16 bp):
TTTTGTTATTTATTTT
Found at i:4784610 original size:22 final size:22
Alignment explanation
Indices: 4784578--4784619 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
4784568 AACCCAATAA
4784578 AAAACTCAACAAATCTATAACGT
1 AAAACTCAACAAATCT-TAACGT
4784601 AAAAC-CAACAAATCTTAAC
1 AAAACTCAACAAATCTTAAC
4784620 AAATCTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 10 0.53
23 5 0.26
ACGTcount: A:0.55, C:0.24, G:0.02, T:0.19
Consensus pattern (22 bp):
AAAACTCAACAAATCTTAACGT
Found at i:4787670 original size:18 final size:19
Alignment explanation
Indices: 4787646--4787689 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
4787636 CATATTTCAA
*
4787646 TATAAAAT-TTTATTTT-T
1 TATAAAATATTAATTTTAT
4787663 TATCAAAATATTAATTTTAT
1 TAT-AAAATATTAATTTTAT
4787683 TATAAAA
1 TATAAAA
4787690 GCCTTACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 3 0.13
18 5 0.22
19 11 0.48
20 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TATAAAATATTAATTTTAT
Found at i:4789493 original size:20 final size:20
Alignment explanation
Indices: 4789464--4789564 Score: 98
Period size: 20 Copynumber: 5.0 Consensus size: 20
4789454 ACAAATAATA
* *
4789464 AATCACGCAATTAAATATAT
1 AATCATGCAATTAAATAAAT
* *
4789484 AAGCATGCAAAT-AATAAAT
1 AATCATGCAATTAAATAAAT
* *
4789503 AGATCATACAATTAAATATAT
1 A-ATCATGCAATTAAATAAAT
*
4789524 AATCATGCAAAT-AATAAAT
1 AATCATGCAATTAAATAAAT
4789543 AAATCATGCAATTAAACTAAAT
1 -AATCATGCAATTAAA-TAAAT
4789565 CCATGCATAT
Statistics
Matches: 64, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
19 13 0.20
20 37 0.58
21 9 0.14
22 5 0.08
ACGTcount: A:0.54, C:0.12, G:0.06, T:0.28
Consensus pattern (20 bp):
AATCATGCAATTAAATAAAT
Found at i:4789522 original size:40 final size:40
Alignment explanation
Indices: 4789460--4789583 Score: 153
Period size: 40 Copynumber: 3.1 Consensus size: 40
4789450 TTTTACAAAT
**
4789460 AATAAATCACGCAATTAAATATATAAGCATGCAAATAATA
1 AATAAATCATACAATTAAATATATAAGCATGCAAATAATA
* *
4789500 AATAGATCATACAATTAAATATATAATCATGCAAATAATA
1 AATAAATCATACAATTAAATATATAAGCATGCAAATAATA
* ** *
4789540 AATAAATCATGCAATTAAACTA-A-ATCCATGCATATAATA
1 AATAAATCATACAATTAAA-TATATAAGCATGCAAATAATA
4789579 AATAA
1 AATAA
4789584 CATGCAAGAA
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
39 18 0.24
40 54 0.73
41 2 0.03
ACGTcount: A:0.55, C:0.12, G:0.06, T:0.27
Consensus pattern (40 bp):
AATAAATCATACAATTAAATATATAAGCATGCAAATAATA
Found at i:4789605 original size:18 final size:18
Alignment explanation
Indices: 4789584--4789639 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
4789574 TAATAAATAA
4789584 CATGCAAGAAACTAACTT
1 CATGCAAGAAACTAACTT
* *
4789602 CATGCAA-AAA-TAAGTA
1 CATGCAAGAAACTAACTT
*
4789618 AATTGCAAGAAACTAACTT
1 CA-TGCAAGAAACTAACTT
4789637 CAT
1 CAT
4789640 AAAAACATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
16 5 0.17
17 8 0.28
18 11 0.38
19 5 0.17
ACGTcount: A:0.48, C:0.18, G:0.11, T:0.23
Consensus pattern (18 bp):
CATGCAAGAAACTAACTT
Found at i:4789614 original size:35 final size:35
Alignment explanation
Indices: 4789526--4789639 Score: 122
Period size: 35 Copynumber: 3.1 Consensus size: 35
4789516 AAATATATAA
* *
4789526 TCATGCAAATAATAAATAAATCATGCAATTAAACTAAAT
1 TCATGCAAA-AATAAAT-AA-CATGCAA-GAAACTAACT
* *
4789565 CCATGCATATAATAAATAACATGCAAGAAACTAACT
1 TCATGCA-AAAATAAATAACATGCAAGAAACTAACT
*
4789601 TCATGCAAAAATAAGTAA-ATTGCAAGAAACTAACT
1 TCATGCAAAAATAAATAACA-TGCAAGAAACTAACT
4789636 TCAT
1 TCAT
4789640 AAAAACATTA
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
34 1 0.02
35 28 0.42
36 14 0.21
37 7 0.11
38 2 0.03
39 13 0.20
40 1 0.02
ACGTcount: A:0.51, C:0.16, G:0.08, T:0.25
Consensus pattern (35 bp):
TCATGCAAAAATAAATAACATGCAAGAAACTAACT
Found at i:4789780 original size:12 final size:12
Alignment explanation
Indices: 4789765--4789814 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
4789755 AAAAATTTTA
4789765 AAAATCAAATAG
1 AAAATCAAATAG
4789777 AAAAT-AATATA-
1 AAAATCAA-ATAG
4789788 AAAATCAAAATAG
1 AAAATC-AAATAG
*
4789801 AAAATAAAAT-G
1 AAAATCAAATAG
4789812 AAA
1 AAA
4789815 TAAGAAAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
11 11 0.33
12 15 0.45
13 7 0.21
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.18
Consensus pattern (12 bp):
AAAATCAAATAG
Found at i:4789805 original size:24 final size:24
Alignment explanation
Indices: 4789748--4789807 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
4789738 GAAAAAAAAG
* *
4789748 AATAGAAAAAAATTTTAAAAATCA
1 AATAGAAAATAATTATAAAAATCA
4789772 AATAGAAAATAA-TATAAAAATCAA
1 AATAGAAAATAATTATAAAAATC-A
4789796 AATAGAAAATAA
1 AATAGAAAATAA
4789808 AATGAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 9 0.27
24 24 0.73
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (24 bp):
AATAGAAAATAATTATAAAAATCA
Found at i:4789809 original size:18 final size:19
Alignment explanation
Indices: 4789788--4789828 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
4789778 AAATAATATA
4789788 AAAATCAAAAT-AGAAAA-T
1 AAAAT-AAAATAAGAAAAGT
*
4789806 AAAATGAAATAAGAAAAGT
1 AAAATAAAATAAGAAAAGT
4789825 AAAA
1 AAAA
4789829 ACCTGTGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 4 0.20
18 11 0.55
19 5 0.25
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (19 bp):
AAAATAAAATAAGAAAAGT
Found at i:4791342 original size:22 final size:22
Alignment explanation
Indices: 4791316--4791478 Score: 122
Period size: 22 Copynumber: 7.4 Consensus size: 22
4791306 ATCATACTAT
* * *
4791316 AAGGTTTTAGAAATTATGCTTTG
1 AAGGTCTTAGAGATTATGC-CTG
4791339 -AGGTCTTAGAGATTATGCCTG
1 AAGGTCTTAGAGATTATGCCTG
4791360 AAGGTCTTAGAGATTATGCCTG
1 AAGGTCTTAGAGATTATGCCTG
* * *
4791382 AAGGT-TATACAAATCATGCCTTG
1 AAGGTCT-TAGAGATTATGCC-TG
* * *
4791405 -TGGTCTTAAAGATTATACCTCG
1 AAGGTCTTAGAGATTATGCCT-G
* *
4791427 -AGGTCTTACG-GATCATGCCTA
1 AAGGTCTTA-GAGATTATGCCTG
4791448 AAGGTCTT-GAAGATTATGCCTG
1 AAGGTCTTAG-AGATTATGCCTG
*
4791470 AAGATCTTA
1 AAGGTCTTA
4791479 TAAATCATGC
Statistics
Matches: 111, Mismatches: 19, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
20 1 0.01
21 4 0.04
22 103 0.93
23 3 0.03
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.34
Consensus pattern (22 bp):
AAGGTCTTAGAGATTATGCCTG
Found at i:4791401 original size:44 final size:44
Alignment explanation
Indices: 4791316--4791488 Score: 140
Period size: 44 Copynumber: 3.9 Consensus size: 44
4791306 ATCATACTAT
* * * * * *
4791316 AAGGTTTTAGAAATTATGCTTTG-AGGTCTTAGAGATTATGCCTG
1 AAGGTCTTAGAGATTATGC-CTGAAGGTCTTACAAATCATGCCTG
4791360 AAGGTCTTAGAGATTATGCCTGAAGGT-TATACAAATCATGCCTTG
1 AAGGTCTTAGAGATTATGCCTGAAGGTCT-TACAAATCATGCC-TG
* * * ** *
4791405 -TGGTCTTAAAGATTATACCTCG-AGGTCTTACGGATCATGCCTA
1 AAGGTCTTAGAGATTATGCCT-GAAGGTCTTACAAATCATGCCTG
* *
4791448 AAGGTCTT-GAAGATTATGCCTGAAGATCTTATAAATCATGC
1 AAGGTCTTAG-AGATTATGCCTGAAGGTCTTACAAATCATGC
4791489 TTGGAAGTCT
Statistics
Matches: 102, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
43 5 0.05
44 93 0.91
45 4 0.04
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (44 bp):
AAGGTCTTAGAGATTATGCCTGAAGGTCTTACAAATCATGCCTG
Found at i:4791468 original size:66 final size:66
Alignment explanation
Indices: 4791300--4791452 Score: 168
Period size: 66 Copynumber: 2.3 Consensus size: 66
4791290 CTCAAAGATT
* * * * * *
4791300 TTAGAGATCAT-ACTATAAGGTTTTAGAAATTATGCTTTGAGGTCTTAGAGATTATGCCTGAAGG
1 TTAGAGATCATGCCTA-AAGGTTATACAAATTATGCCTTGAGGTCTTAAAGATTATACCTGAAGG
4791364 TC
65 TC
* * * *
4791366 TTAGAGATTATGCCTGAAGGTTATACAAATCATGCCTTGTGGTCTTAAAGATTATACCTCG-AGG
1 TTAGAGATCATGCCTAAAGGTTATACAAATTATGCCTTGAGGTCTTAAAGATTATACCT-GAAGG
4791430 TC
65 TC
4791432 TTACG-GATCATGCCTAAAGGT
1 TTA-GAGATCATGCCTAAAGGT
4791453 CTTGAAGATT
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
66 68 0.94
67 4 0.06
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.34
Consensus pattern (66 bp):
TTAGAGATCATGCCTAAAGGTTATACAAATTATGCCTTGAGGTCTTAAAGATTATACCTGAAGGT
C
Found at i:4794466 original size:19 final size:19
Alignment explanation
Indices: 4794442--4794489 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
4794432 TGGCAGCTGT
4794442 TTAGGGATAGGGACTTACA
1 TTAGGGATAGGGACTTACA
4794461 TTAGGGATAGGGACTTACA
1 TTAGGGATAGGGACTTACA
4794480 TTAGGGATAG
1 TTAGGGATAG
4794490 TTGCACAGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.31, C:0.08, G:0.33, T:0.27
Consensus pattern (19 bp):
TTAGGGATAGGGACTTACA
Found at i:4796674 original size:60 final size:60
Alignment explanation
Indices: 4796581--4796694 Score: 210
Period size: 60 Copynumber: 1.9 Consensus size: 60
4796571 CTAGGAGTTT
*
4796581 TTGGCCATCTATGTGAATATATCCCTTTTAAGATTATCTTTAGTTTAAACTAAGTTATGA
1 TTGGCCATCTATGTGAATATATCCCTTTTAAGATTATCCTTAGTTTAAACTAAGTTATGA
*
4796641 TTGGCCATCTATGTGAATCTATCCCTTTTAAGATTATCCTTAGTTTAAACTAAG
1 TTGGCCATCTATGTGAATATATCCCTTTTAAGATTATCCTTAGTTTAAACTAAG
4796695 GGTCCAGCCT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (60 bp):
TTGGCCATCTATGTGAATATATCCCTTTTAAGATTATCCTTAGTTTAAACTAAGTTATGA
Done.